diff --git a/puremd_rc_1003/sPuReMD/GMRES.c b/puremd_rc_1003/sPuReMD/GMRES.c
index 8488ac69ff5a0180314ab28eb3513347824a9f53..2d8e1ab7bb1f425ac7e990995f267b140ea55419 100644
--- a/puremd_rc_1003/sPuReMD/GMRES.c
+++ b/puremd_rc_1003/sPuReMD/GMRES.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -31,33 +31,33 @@
* x: vector
* b: vector (result) */
static void Sparse_MatVec( const sparse_matrix * const A,
- const real * const x, real * const b )
+ const real * const x, real * const b )
{
- int i, j, k, n, si, ei;
- real H;
-
- n = A->n;
- for( i = 0; i < n; ++i )
- {
- b[i] = 0;
- }
-
- for( i = 0; i < n; ++i )
- {
- si = A->start[i];
- ei = A->start[i+1]-1;
-
- for( k = si; k < ei; ++k )
+ int i, j, k, n, si, ei;
+ real H;
+
+ n = A->n;
+ for ( i = 0; i < n; ++i )
{
- j = A->entries[k].j;
- H = A->entries[k].val;
- b[j] += H * x[i];
- b[i] += H * x[j];
+ b[i] = 0;
}
- // the diagonal entry is the last one in
- b[i] += A->entries[A->start[i+1]-1].val * x[i];
- }
+ for ( i = 0; i < n; ++i )
+ {
+ si = A->start[i];
+ ei = A->start[i + 1] - 1;
+
+ for ( k = si; k < ei; ++k )
+ {
+ j = A->entries[k].j;
+ H = A->entries[k].val;
+ b[j] += H * x[i];
+ b[i] += H * x[j];
+ }
+
+ // the diagonal entry is the last one in
+ b[i] += A->entries[A->start[i + 1] - 1].val * x[i];
+ }
}
@@ -68,82 +68,82 @@ static void Sparse_MatVec( const sparse_matrix * const A,
* b: vector (result)
* tri: triangularity of A (lower/upper) */
static void Sparse_MatVec2( const sparse_matrix * const A,
- const TRIANGULARITY tri, const real * const x, real * const b)
+ const TRIANGULARITY tri, const real * const x, real * const b)
{
- int i, k, n, si = 0, ei = 0;
+ int i, k, n, si = 0, ei = 0;
- n = A->n;
- for( i = 0; i < n; ++i )
- {
- b[i] = 0;
- }
-
- for( i = 0; i < n; ++i )
- {
- if(tri == LOWER)
+ n = A->n;
+ for ( i = 0; i < n; ++i )
{
- si = A->start[i];
- ei = A->start[i+1]-1;
+ b[i] = 0;
}
- else if(tri == UPPER)
- {
- si = A->start[i]+1;
- ei = A->start[i+1];
- }
-
- for( k = si; k < ei; ++k )
+ for ( i = 0; i < n; ++i )
{
- b[A->entries[k].j] += A->entries[k].j * x[i];
- b[i] += A->entries[k].j * x[A->entries[k].j];
+ if (tri == LOWER)
+ {
+ si = A->start[i];
+ ei = A->start[i + 1] - 1;
+ }
+ else if (tri == UPPER)
+ {
+
+ si = A->start[i] + 1;
+ ei = A->start[i + 1];
+ }
+
+ for ( k = si; k < ei; ++k )
+ {
+ b[A->entries[k].j] += A->entries[k].j * x[i];
+ b[i] += A->entries[k].j * x[A->entries[k].j];
+ }
}
- }
}
/* solve sparse lower triangular linear system using forward substitution */
void Forward_Subs( sparse_matrix *L, real *b, real *y )
{
- int i, pj, j, si, ei;
- real val;
-
- for( i = 0; i < L->n; ++i )
- {
- y[i] = b[i];
- si = L->start[i];
- ei = L->start[i+1];
- for( pj = si; pj < ei-1; ++pj )
+ int i, pj, j, si, ei;
+ real val;
+
+ for ( i = 0; i < L->n; ++i )
{
- // TODO: remove assignments? compiler optimizes away?
- j = L->entries[pj].j;
- val = L->entries[pj].val;
- y[i] -= val * y[j];
+ y[i] = b[i];
+ si = L->start[i];
+ ei = L->start[i + 1];
+ for ( pj = si; pj < ei - 1; ++pj )
+ {
+ // TODO: remove assignments? compiler optimizes away?
+ j = L->entries[pj].j;
+ val = L->entries[pj].val;
+ y[i] -= val * y[j];
+ }
+ y[i] /= L->entries[pj].val;
}
- y[i] /= L->entries[pj].val;
- }
}
/* solve sparse upper triangular linear system using backward substitution */
void Backward_Subs( sparse_matrix *U, real *y, real *x )
{
- int i, pj, j, si, ei;
- real val;
-
- for( i = U->n-1; i >= 0; --i )
- {
- x[i] = y[i];
- si = U->start[i];
- ei = U->start[i+1];
- for( pj = si+1; pj < ei; ++pj )
+ int i, pj, j, si, ei;
+ real val;
+
+ for ( i = U->n - 1; i >= 0; --i )
{
- // TODO: remove assignments? compiler optimizes away?
- j = U->entries[pj].j;
- val = U->entries[pj].val;
- x[i] -= val * x[j];
+ x[i] = y[i];
+ si = U->start[i];
+ ei = U->start[i + 1];
+ for ( pj = si + 1; pj < ei; ++pj )
+ {
+ // TODO: remove assignments? compiler optimizes away?
+ j = U->entries[pj].j;
+ val = U->entries[pj].val;
+ x[i] -= val * x[j];
+ }
+ x[i] /= U->entries[si].val;
}
- x[i] /= U->entries[si].val;
- }
}
@@ -159,767 +159,800 @@ void Backward_Subs( sparse_matrix *U, real *y, real *x )
* Note: Newmann series arises from series expansion of the inverse of
* the coefficient matrix in the triangular system. */
static void Jacobi_Iter( const sparse_matrix * const G, const TRIANGULARITY tri,
- const sparse_matrix * const Dinv, const real * const b,
- real * const x, const unsigned int maxiter )
+ const sparse_matrix * const Dinv, const real * const b,
+ real * const x, const unsigned int maxiter )
{
- unsigned int iter = 0;
- real *Dinv_b;
-
- if( (Dinv_b = (real*) malloc(sizeof(real)*(Dinv->n))) == NULL )
- {
- fprintf( stderr, "not enough memory for Jacobi iteration matrices. terminating.\n" );
- exit(INSUFFICIENT_SPACE);
- }
-
- /* precompute and cache, as invariant in loop below */
- Sparse_MatVec( (sparse_matrix*)Dinv, (real*)b, Dinv_b );
-
- do
- {
- // x_{k+1} = G*x_{k} + Dinv*b;
- Sparse_MatVec2( (sparse_matrix*)G, tri, x, x );
- Vector_Add2( x, Dinv_b, Dinv->n );
- ++iter;
- } while( iter < maxiter );
-
- free(Dinv_b);
+ unsigned int iter = 0;
+ real *Dinv_b;
+
+ if ( (Dinv_b = (real*) malloc(sizeof(real) * (Dinv->n))) == NULL )
+ {
+ fprintf( stderr, "not enough memory for Jacobi iteration matrices. terminating.\n" );
+ exit(INSUFFICIENT_SPACE);
+ }
+
+ /* precompute and cache, as invariant in loop below */
+ Sparse_MatVec( (sparse_matrix*)Dinv, (real*)b, Dinv_b );
+
+ do
+ {
+ // x_{k+1} = G*x_{k} + Dinv*b;
+ Sparse_MatVec2( (sparse_matrix*)G, tri, x, x );
+ Vector_Add2( x, Dinv_b, Dinv->n );
+ ++iter;
+ }
+ while ( iter < maxiter );
+
+ free(Dinv_b);
}
/* generalized minimual residual iterative solver for sparse linear systems,
* no preconditioner */
-int GMRES( static_storage *workspace, sparse_matrix *H,
- real *b, real tol, real *x, FILE *fout )
+int GMRES( static_storage *workspace, sparse_matrix *H,
+ real *b, real tol, real *x, FILE *fout )
{
- int i, j, k, itr, N;
- real cc, tmp1, tmp2, temp, bnorm;
-
- N = H->n;
- bnorm = Norm( b, N );
- /* apply the diagonal pre-conditioner to rhs */
- for( i = 0; i < N; ++i )
- workspace->b_prc[i] = b[i] * workspace->Hdia_inv[i];
-
- /* GMRES outer-loop */
- for( itr = 0; itr < MAX_ITR; ++itr ) {
- /* calculate r0 */
- Sparse_MatVec( H, x, workspace->b_prm );
- for( i = 0; i < N; ++i )
- workspace->b_prm[i] *= workspace->Hdia_inv[i]; /* pre-conditioner */
-
- Vector_Sum(workspace->v[0], 1.,workspace->b_prc, -1., workspace->b_prm, N);
- workspace->g[0] = Norm( workspace->v[0], N );
- Vector_Scale( workspace->v[0], 1. / workspace->g[0], workspace->v[0], N );
- //fprintf( stderr, "res: %.15e\n", workspace->g[0] );
-
- /* GMRES inner-loop */
- for( j = 0; j < RESTART && fabs(workspace->g[j]) / bnorm > tol; j++ ) {
- /* matvec */
- Sparse_MatVec( H, workspace->v[j], workspace->v[j+1] );
- for( k = 0; k < N; ++k )
- workspace->v[j+1][k] *= workspace->Hdia_inv[k]; /*pre-conditioner*/
- //fprintf( stderr, "%d-%d: matvec done.\n", itr, j );
-
- /* apply modified Gram-Schmidt to orthogonalize the new residual */
- for( i = 0; i <= j; i++ ) {
- workspace->h[i][j] = Dot( workspace->v[i], workspace->v[j+1], N );
- Vector_Add( workspace->v[j+1],
- -workspace->h[i][j], workspace->v[i], N );
- }
-
- workspace->h[j+1][j] = Norm( workspace->v[j+1], N );
- Vector_Scale( workspace->v[j+1],
- 1. / workspace->h[j+1][j], workspace->v[j+1], N );
- // fprintf( stderr, "%d-%d: orthogonalization completed.\n", itr, j );
-
-
- /* Givens rotations on the upper-Hessenberg matrix to make it U */
- for( i = 0; i <= j; i++ ) {
- if( i == j ) {
- cc = SQRT( SQR(workspace->h[j][j])+SQR(workspace->h[j+1][j]) );
- workspace->hc[j] = workspace->h[j][j] / cc;
- workspace->hs[j] = workspace->h[j+1][j] / cc;
- }
-
- tmp1 = workspace->hc[i] * workspace->h[i][j] +
- workspace->hs[i] * workspace->h[i+1][j];
- tmp2 = -workspace->hs[i] * workspace->h[i][j] +
- workspace->hc[i] * workspace->h[i+1][j];
-
- workspace->h[i][j] = tmp1;
- workspace->h[i+1][j] = tmp2;
- }
-
- /* apply Givens rotations to the rhs as well */
- tmp1 = workspace->hc[j] * workspace->g[j];
- tmp2 = -workspace->hs[j] * workspace->g[j];
- workspace->g[j] = tmp1;
- workspace->g[j+1] = tmp2;
-
- // fprintf( stderr, "h: " );
- // for( i = 0; i <= j+1; ++i )
- // fprintf( stderr, "%.6f ", workspace->h[i][j] );
- // fprintf( stderr, "\n" );
- //fprintf( stderr, "res: %.15e\n", workspace->g[j+1] );
+ int i, j, k, itr, N;
+ real cc, tmp1, tmp2, temp, bnorm;
+
+ N = H->n;
+ bnorm = Norm( b, N );
+ /* apply the diagonal pre-conditioner to rhs */
+ for ( i = 0; i < N; ++i )
+ workspace->b_prc[i] = b[i] * workspace->Hdia_inv[i];
+
+ /* GMRES outer-loop */
+ for ( itr = 0; itr < MAX_ITR; ++itr )
+ {
+ /* calculate r0 */
+ Sparse_MatVec( H, x, workspace->b_prm );
+ for ( i = 0; i < N; ++i )
+ workspace->b_prm[i] *= workspace->Hdia_inv[i]; /* pre-conditioner */
+
+ Vector_Sum(workspace->v[0], 1., workspace->b_prc, -1., workspace->b_prm, N);
+ workspace->g[0] = Norm( workspace->v[0], N );
+ Vector_Scale( workspace->v[0], 1. / workspace->g[0], workspace->v[0], N );
+ //fprintf( stderr, "res: %.15e\n", workspace->g[0] );
+
+ /* GMRES inner-loop */
+ for ( j = 0; j < RESTART && fabs(workspace->g[j]) / bnorm > tol; j++ )
+ {
+ /* matvec */
+ Sparse_MatVec( H, workspace->v[j], workspace->v[j + 1] );
+ for ( k = 0; k < N; ++k )
+ workspace->v[j + 1][k] *= workspace->Hdia_inv[k]; /*pre-conditioner*/
+ //fprintf( stderr, "%d-%d: matvec done.\n", itr, j );
+
+ /* apply modified Gram-Schmidt to orthogonalize the new residual */
+ for ( i = 0; i <= j; i++ )
+ {
+ workspace->h[i][j] = Dot( workspace->v[i], workspace->v[j + 1], N );
+ Vector_Add( workspace->v[j + 1],
+ -workspace->h[i][j], workspace->v[i], N );
+ }
+
+ workspace->h[j + 1][j] = Norm( workspace->v[j + 1], N );
+ Vector_Scale( workspace->v[j + 1],
+ 1. / workspace->h[j + 1][j], workspace->v[j + 1], N );
+ // fprintf( stderr, "%d-%d: orthogonalization completed.\n", itr, j );
+
+
+ /* Givens rotations on the upper-Hessenberg matrix to make it U */
+ for ( i = 0; i <= j; i++ )
+ {
+ if ( i == j )
+ {
+ cc = SQRT( SQR(workspace->h[j][j]) + SQR(workspace->h[j + 1][j]) );
+ workspace->hc[j] = workspace->h[j][j] / cc;
+ workspace->hs[j] = workspace->h[j + 1][j] / cc;
+ }
+
+ tmp1 = workspace->hc[i] * workspace->h[i][j] +
+ workspace->hs[i] * workspace->h[i + 1][j];
+ tmp2 = -workspace->hs[i] * workspace->h[i][j] +
+ workspace->hc[i] * workspace->h[i + 1][j];
+
+ workspace->h[i][j] = tmp1;
+ workspace->h[i + 1][j] = tmp2;
+ }
+
+ /* apply Givens rotations to the rhs as well */
+ tmp1 = workspace->hc[j] * workspace->g[j];
+ tmp2 = -workspace->hs[j] * workspace->g[j];
+ workspace->g[j] = tmp1;
+ workspace->g[j + 1] = tmp2;
+
+ // fprintf( stderr, "h: " );
+ // for( i = 0; i <= j+1; ++i )
+ // fprintf( stderr, "%.6f ", workspace->h[i][j] );
+ // fprintf( stderr, "\n" );
+ //fprintf( stderr, "res: %.15e\n", workspace->g[j+1] );
+ }
+
+
+ /* solve Hy = g.
+ H is now upper-triangular, do back-substitution */
+ for ( i = j - 1; i >= 0; i-- )
+ {
+ temp = workspace->g[i];
+ for ( k = j - 1; k > i; k-- )
+ temp -= workspace->h[i][k] * workspace->y[k];
+
+ workspace->y[i] = temp / workspace->h[i][i];
+ }
+
+ /* update x = x_0 + Vy */
+ for ( i = 0; i < j; i++ )
+ Vector_Add( x, workspace->y[i], workspace->v[i], N );
+
+ /* stopping condition */
+ if ( fabs(workspace->g[j]) / bnorm <= tol )
+ break;
}
-
-
- /* solve Hy = g.
- H is now upper-triangular, do back-substitution */
- for( i = j-1; i >= 0; i-- ) {
- temp = workspace->g[i];
- for( k = j-1; k > i; k-- )
- temp -= workspace->h[i][k] * workspace->y[k];
-
- workspace->y[i] = temp / workspace->h[i][i];
+
+ // Sparse_MatVec( H, x, workspace->b_prm );
+ // for( i = 0; i < N; ++i )
+ // workspace->b_prm[i] *= workspace->Hdia_inv[i];
+ // fprintf( fout, "\n%10s%15s%15s\n", "b_prc", "b_prm", "x" );
+ // for( i = 0; i < N; ++i )
+ // fprintf( fout, "%10.5f%15.12f%15.12f\n",
+ // workspace->b_prc[i], workspace->b_prm[i], x[i] );*/
+
+ // fprintf(fout,"GMRES outer:%d, inner:%d iters - residual norm: %25.20f\n",
+ // itr, j, fabs( workspace->g[j] ) / bnorm );
+ // data->timing.matvec += itr * RESTART + j;
+
+ if ( itr >= MAX_ITR )
+ {
+ fprintf( stderr, "GMRES convergence failed\n" );
+ // return -1;
+ return itr * (RESTART + 1) + j + 1;
}
-
- /* update x = x_0 + Vy */
- for( i = 0; i < j; i++ )
- Vector_Add( x, workspace->y[i], workspace->v[i], N );
-
- /* stopping condition */
- if( fabs(workspace->g[j]) / bnorm <= tol )
- break;
- }
-
- // Sparse_MatVec( H, x, workspace->b_prm );
- // for( i = 0; i < N; ++i )
- // workspace->b_prm[i] *= workspace->Hdia_inv[i];
- // fprintf( fout, "\n%10s%15s%15s\n", "b_prc", "b_prm", "x" );
- // for( i = 0; i < N; ++i )
- // fprintf( fout, "%10.5f%15.12f%15.12f\n",
- // workspace->b_prc[i], workspace->b_prm[i], x[i] );*/
-
- // fprintf(fout,"GMRES outer:%d, inner:%d iters - residual norm: %25.20f\n",
- // itr, j, fabs( workspace->g[j] ) / bnorm );
- // data->timing.matvec += itr * RESTART + j;
-
- if( itr >= MAX_ITR ) {
- fprintf( stderr, "GMRES convergence failed\n" );
- // return -1;
- return itr * (RESTART+1) + j + 1;
- }
-
- return itr * (RESTART+1) + j + 1;
+
+ return itr * (RESTART + 1) + j + 1;
}
-int GMRES_HouseHolder( static_storage *workspace, sparse_matrix *H,
- real *b, real tol, real *x, FILE *fout)
+int GMRES_HouseHolder( static_storage *workspace, sparse_matrix *H,
+ real *b, real tol, real *x, FILE *fout)
{
- int i, j, k, itr, N;
- real cc, tmp1, tmp2, temp, bnorm;
- real v[10000], z[RESTART+2][10000], w[RESTART+2];
- real u[RESTART+2][10000];
-
- N = H->n;
- bnorm = Norm( b, N );
-
- /* apply the diagonal pre-conditioner to rhs */
- for( i = 0; i < N; ++i )
- workspace->b_prc[i] = b[i] * workspace->Hdia_inv[i];
-
- // memset( x, 0, sizeof(real) * N );
-
- /* GMRES outer-loop */
- for( itr = 0; itr < MAX_ITR; ++itr ) {
- /* compute z = r0 */
- Sparse_MatVec( H, x, workspace->b_prm );
- for( i = 0; i < N; ++i )
- workspace->b_prm[i] *= workspace->Hdia_inv[i]; /* pre-conditioner */
- Vector_Sum( z[0], 1., workspace->b_prc, -1., workspace->b_prm, N );
-
- Vector_MakeZero( w, RESTART+1 );
- w[0] = Norm( z[0], N );
-
- Vector_Copy( u[0], z[0], N );
- u[0][0] += ( u[0][0] < 0.0 ? -1 : 1 ) * w[0];
- Vector_Scale( u[0], 1 / Norm( u[0], N ), u[0], N );
-
- w[0] *= ( u[0][0] < 0.0 ? 1 :-1 );
- // fprintf( stderr, "\n\n%12.6f\n", w[0] );
-
- /* GMRES inner-loop */
- for( j = 0; j < RESTART && fabs( w[j] ) / bnorm > tol; j++ ) {
- /* compute v_j */
- Vector_Scale( z[j], -2 * u[j][j], u[j], N );
- z[j][j] += 1.; /* due to e_j */
-
- for( i = j-1; i >= 0; --i )
- Vector_Add( z[j]+i, -2 * Dot( u[i]+i, z[j]+i, N-i ), u[i]+i, N-i );
-
-
- /* matvec */
- Sparse_MatVec( H, z[j], v );
-
- for( k = 0; k < N; ++k )
- v[k] *= workspace->Hdia_inv[k]; /* pre-conditioner */
-
- for( i = 0; i <= j; ++i )
- Vector_Add( v+i, -2 * Dot( u[i]+i, v+i, N-i ), u[i]+i, N-i );
-
-
- if( !Vector_isZero( v + (j+1), N - (j+1) ) ) {
- /* compute the HouseHolder unit vector u_j+1 */
- for( i = 0; i <= j; ++i )
- u[j+1][i] = 0;
-
- Vector_Copy( u[j+1] + (j+1), v + (j+1), N - (j+1) );
-
- u[j+1][j+1] += ( v[j+1]<0.0 ? -1:1 ) * Norm( v+(j+1), N-(j+1) );
-
- Vector_Scale( u[j+1], 1 / Norm( u[j+1], N ), u[j+1], N );
-
- /* overwrite v with P_m+1 * v */
- v[j+1] -= 2 * Dot( u[j+1]+(j+1), v+(j+1), N-(j+1) ) * u[j+1][j+1];
- Vector_MakeZero( v + (j+2), N - (j+2) );
- // Vector_Add( v, -2 * Dot( u[j+1], v, N ), u[j+1], N );
- }
-
-
- /* prev Givens rots on the upper-Hessenberg matrix to make it U */
- for( i = 0; i < j; i++ ) {
- tmp1 = workspace->hc[i] * v[i] + workspace->hs[i] * v[i+1];
- tmp2 = -workspace->hs[i] * v[i] + workspace->hc[i] * v[i+1];
-
- v[i] = tmp1;
- v[i+1] = tmp2;
- }
-
- /* apply the new Givens rotation to H and right-hand side */
- if( fabs(v[j+1]) >= ALMOST_ZERO ) {
- cc = SQRT( SQR( v[j] ) + SQR( v[j+1] ) );
- workspace->hc[j] = v[j] / cc;
- workspace->hs[j] = v[j+1] / cc;
-
- tmp1 = workspace->hc[j] * v[j] + workspace->hs[j] * v[j+1];
- tmp2 = -workspace->hs[j] * v[j] + workspace->hc[j] * v[j+1];
-
- v[j] = tmp1;
- v[j+1] = tmp2;
-
- /* Givens rotations to rhs */
- tmp1 = workspace->hc[j] * w[j];
- tmp2 = -workspace->hs[j] * w[j];
- w[j] = tmp1;
- w[j+1] = tmp2;
- }
-
- /* extend R */
- for( i = 0; i <= j; ++i )
- workspace->h[i][j] = v[i];
-
-
- // fprintf( stderr, "h:" );
- // for( i = 0; i <= j+1 ; ++i )
- // fprintf( stderr, "%.6f ", h[i][j] );
- // fprintf( stderr, "\n" );
- // fprintf( stderr, "%12.6f\n", w[j+1] );
- }
-
-
- /* solve Hy = w.
- H is now upper-triangular, do back-substitution */
- for( i = j-1; i >= 0; i-- ) {
- temp = w[i];
- for( k = j-1; k > i; k-- )
- temp -= workspace->h[i][k] * workspace->y[k];
-
- workspace->y[i] = temp / workspace->h[i][i];
+ int i, j, k, itr, N;
+ real cc, tmp1, tmp2, temp, bnorm;
+ real v[10000], z[RESTART + 2][10000], w[RESTART + 2];
+ real u[RESTART + 2][10000];
+
+ N = H->n;
+ bnorm = Norm( b, N );
+
+ /* apply the diagonal pre-conditioner to rhs */
+ for ( i = 0; i < N; ++i )
+ workspace->b_prc[i] = b[i] * workspace->Hdia_inv[i];
+
+ // memset( x, 0, sizeof(real) * N );
+
+ /* GMRES outer-loop */
+ for ( itr = 0; itr < MAX_ITR; ++itr )
+ {
+ /* compute z = r0 */
+ Sparse_MatVec( H, x, workspace->b_prm );
+ for ( i = 0; i < N; ++i )
+ workspace->b_prm[i] *= workspace->Hdia_inv[i]; /* pre-conditioner */
+ Vector_Sum( z[0], 1., workspace->b_prc, -1., workspace->b_prm, N );
+
+ Vector_MakeZero( w, RESTART + 1 );
+ w[0] = Norm( z[0], N );
+
+ Vector_Copy( u[0], z[0], N );
+ u[0][0] += ( u[0][0] < 0.0 ? -1 : 1 ) * w[0];
+ Vector_Scale( u[0], 1 / Norm( u[0], N ), u[0], N );
+
+ w[0] *= ( u[0][0] < 0.0 ? 1 : -1 );
+ // fprintf( stderr, "\n\n%12.6f\n", w[0] );
+
+ /* GMRES inner-loop */
+ for ( j = 0; j < RESTART && fabs( w[j] ) / bnorm > tol; j++ )
+ {
+ /* compute v_j */
+ Vector_Scale( z[j], -2 * u[j][j], u[j], N );
+ z[j][j] += 1.; /* due to e_j */
+
+ for ( i = j - 1; i >= 0; --i )
+ Vector_Add( z[j] + i, -2 * Dot( u[i] + i, z[j] + i, N - i ), u[i] + i, N - i );
+
+
+ /* matvec */
+ Sparse_MatVec( H, z[j], v );
+
+ for ( k = 0; k < N; ++k )
+ v[k] *= workspace->Hdia_inv[k]; /* pre-conditioner */
+
+ for ( i = 0; i <= j; ++i )
+ Vector_Add( v + i, -2 * Dot( u[i] + i, v + i, N - i ), u[i] + i, N - i );
+
+
+ if ( !Vector_isZero( v + (j + 1), N - (j + 1) ) )
+ {
+ /* compute the HouseHolder unit vector u_j+1 */
+ for ( i = 0; i <= j; ++i )
+ u[j + 1][i] = 0;
+
+ Vector_Copy( u[j + 1] + (j + 1), v + (j + 1), N - (j + 1) );
+
+ u[j + 1][j + 1] += ( v[j + 1] < 0.0 ? -1 : 1 ) * Norm( v + (j + 1), N - (j + 1) );
+
+ Vector_Scale( u[j + 1], 1 / Norm( u[j + 1], N ), u[j + 1], N );
+
+ /* overwrite v with P_m+1 * v */
+ v[j + 1] -= 2 * Dot( u[j + 1] + (j + 1), v + (j + 1), N - (j + 1) ) * u[j + 1][j + 1];
+ Vector_MakeZero( v + (j + 2), N - (j + 2) );
+ // Vector_Add( v, -2 * Dot( u[j+1], v, N ), u[j+1], N );
+ }
+
+
+ /* prev Givens rots on the upper-Hessenberg matrix to make it U */
+ for ( i = 0; i < j; i++ )
+ {
+ tmp1 = workspace->hc[i] * v[i] + workspace->hs[i] * v[i + 1];
+ tmp2 = -workspace->hs[i] * v[i] + workspace->hc[i] * v[i + 1];
+
+ v[i] = tmp1;
+ v[i + 1] = tmp2;
+ }
+
+ /* apply the new Givens rotation to H and right-hand side */
+ if ( fabs(v[j + 1]) >= ALMOST_ZERO )
+ {
+ cc = SQRT( SQR( v[j] ) + SQR( v[j + 1] ) );
+ workspace->hc[j] = v[j] / cc;
+ workspace->hs[j] = v[j + 1] / cc;
+
+ tmp1 = workspace->hc[j] * v[j] + workspace->hs[j] * v[j + 1];
+ tmp2 = -workspace->hs[j] * v[j] + workspace->hc[j] * v[j + 1];
+
+ v[j] = tmp1;
+ v[j + 1] = tmp2;
+
+ /* Givens rotations to rhs */
+ tmp1 = workspace->hc[j] * w[j];
+ tmp2 = -workspace->hs[j] * w[j];
+ w[j] = tmp1;
+ w[j + 1] = tmp2;
+ }
+
+ /* extend R */
+ for ( i = 0; i <= j; ++i )
+ workspace->h[i][j] = v[i];
+
+
+ // fprintf( stderr, "h:" );
+ // for( i = 0; i <= j+1 ; ++i )
+ // fprintf( stderr, "%.6f ", h[i][j] );
+ // fprintf( stderr, "\n" );
+ // fprintf( stderr, "%12.6f\n", w[j+1] );
+ }
+
+
+ /* solve Hy = w.
+ H is now upper-triangular, do back-substitution */
+ for ( i = j - 1; i >= 0; i-- )
+ {
+ temp = w[i];
+ for ( k = j - 1; k > i; k-- )
+ temp -= workspace->h[i][k] * workspace->y[k];
+
+ workspace->y[i] = temp / workspace->h[i][i];
+ }
+
+ // fprintf( stderr, "y: " );
+ // for( i = 0; i < RESTART+1; ++i )
+ // fprintf( stderr, "%8.3f ", workspace->y[i] );
+
+
+ /* update x = x_0 + Vy */
+ // memset( z, 0, sizeof(real) * N );
+ // for( i = j-1; i >= 0; i-- )
+ // {
+ // Vector_Copy( v, z, N );
+ // v[i] += workspace->y[i];
+ //
+ // Vector_Sum( z, 1., v, -2 * Dot( u[i], v, N ), u[i], N );
+ // }
+ //
+ // fprintf( stderr, "\nz: " );
+ // for( k = 0; k < N; ++k )
+ // fprintf( stderr, "%6.2f ", z[k] );
+
+ // fprintf( stderr, "\nx_bef: " );
+ // for( i = 0; i < N; ++i )
+ // fprintf( stderr, "%6.2f ", x[i] );
+
+ // Vector_Add( x, 1, z, N );
+ for ( i = j - 1; i >= 0; i-- )
+ Vector_Add( x, workspace->y[i], z[i], N );
+
+ // fprintf( stderr, "\nx_aft: " );
+ // for( i = 0; i < N; ++i )
+ // fprintf( stderr, "%6.2f ", x[i] );
+
+ /* stopping condition */
+ if ( fabs( w[j] ) / bnorm <= tol )
+ break;
}
-
- // fprintf( stderr, "y: " );
- // for( i = 0; i < RESTART+1; ++i )
- // fprintf( stderr, "%8.3f ", workspace->y[i] );
-
-
- /* update x = x_0 + Vy */
- // memset( z, 0, sizeof(real) * N );
- // for( i = j-1; i >= 0; i-- )
- // {
- // Vector_Copy( v, z, N );
- // v[i] += workspace->y[i];
- //
- // Vector_Sum( z, 1., v, -2 * Dot( u[i], v, N ), u[i], N );
- // }
- //
- // fprintf( stderr, "\nz: " );
- // for( k = 0; k < N; ++k )
- // fprintf( stderr, "%6.2f ", z[k] );
-
- // fprintf( stderr, "\nx_bef: " );
+
+ // Sparse_MatVec( H, x, workspace->b_prm );
// for( i = 0; i < N; ++i )
- // fprintf( stderr, "%6.2f ", x[i] );
-
- // Vector_Add( x, 1, z, N );
- for( i = j-1; i >= 0; i-- )
- Vector_Add( x, workspace->y[i], z[i], N );
-
- // fprintf( stderr, "\nx_aft: " );
+ // workspace->b_prm[i] *= workspace->Hdia_inv[i];
+
+ // fprintf( fout, "\n%10s%15s%15s\n", "b_prc", "b_prm", "x" );
// for( i = 0; i < N; ++i )
- // fprintf( stderr, "%6.2f ", x[i] );
-
- /* stopping condition */
- if( fabs( w[j] ) / bnorm <= tol )
- break;
- }
-
- // Sparse_MatVec( H, x, workspace->b_prm );
- // for( i = 0; i < N; ++i )
- // workspace->b_prm[i] *= workspace->Hdia_inv[i];
-
- // fprintf( fout, "\n%10s%15s%15s\n", "b_prc", "b_prm", "x" );
- // for( i = 0; i < N; ++i )
- // fprintf( fout, "%10.5f%15.12f%15.12f\n",
- // workspace->b_prc[i], workspace->b_prm[i], x[i] );
-
- //fprintf( fout,"GMRES outer:%d, inner:%d iters - residual norm: %15.10f\n",
- // itr, j, fabs( workspace->g[j] ) / bnorm );
-
- if( itr >= MAX_ITR ) {
- fprintf( stderr, "GMRES convergence failed\n" );
- // return -1;
- return itr * (RESTART+1) + j + 1;
- }
-
- return itr * (RESTART+1) + j + 1;
+ // fprintf( fout, "%10.5f%15.12f%15.12f\n",
+ // workspace->b_prc[i], workspace->b_prm[i], x[i] );
+
+ //fprintf( fout,"GMRES outer:%d, inner:%d iters - residual norm: %15.10f\n",
+ // itr, j, fabs( workspace->g[j] ) / bnorm );
+
+ if ( itr >= MAX_ITR )
+ {
+ fprintf( stderr, "GMRES convergence failed\n" );
+ // return -1;
+ return itr * (RESTART + 1) + j + 1;
+ }
+
+ return itr * (RESTART + 1) + j + 1;
}
/* generalized minimual residual iterative solver for sparse linear systems,
* with preconditioner using factors LU \approx H
* and forward / backward substitution */
-int PGMRES( static_storage *workspace, sparse_matrix *H, real *b, real tol,
- sparse_matrix *L, sparse_matrix *U, real *x, FILE *fout )
+int PGMRES( static_storage *workspace, sparse_matrix *H, real *b, real tol,
+ sparse_matrix *L, sparse_matrix *U, real *x, FILE *fout )
{
- int i, j, k, itr, N;
- real cc, tmp1, tmp2, temp, bnorm;
-
- N = H->n;
- bnorm = Norm( b, N );
-
- /* GMRES outer-loop */
- for( itr = 0; itr < MAX_ITR; ++itr ) {
- /* calculate r0 */
- Sparse_MatVec( H, x, workspace->b_prm );
- Vector_Sum( workspace->v[0], 1., b, -1., workspace->b_prm, N );
- Forward_Subs( L, workspace->v[0], workspace->v[0] );
- Backward_Subs( U, workspace->v[0], workspace->v[0] );
- workspace->g[0] = Norm( workspace->v[0], N );
- Vector_Scale( workspace->v[0], 1. / workspace->g[0], workspace->v[0], N );
- //fprintf( stderr, "res: %.15e\n", workspace->g[0] );
-
- /* GMRES inner-loop */
- for( j = 0; j < RESTART && fabs(workspace->g[j]) / bnorm > tol; j++ ) {
- /* matvec */
- Sparse_MatVec( H, workspace->v[j], workspace->v[j+1] );
- Forward_Subs( L, workspace->v[j+1], workspace->v[j+1] );
- Backward_Subs( U, workspace->v[j+1], workspace->v[j+1] );
-
- /* apply modified Gram-Schmidt to orthogonalize the new residual */
- for( i = 0; i < j-1; i++ ) workspace->h[i][j] = 0;
-
- //for( i = 0; i <= j; i++ ) {
- for( i = MAX(j-1,0); i <= j; i++ ) {
- workspace->h[i][j] = Dot( workspace->v[i], workspace->v[j+1], N );
- Vector_Add( workspace->v[j+1],-workspace->h[i][j], workspace->v[i], N );
- }
-
- workspace->h[j+1][j] = Norm( workspace->v[j+1], N );
- Vector_Scale( workspace->v[j+1],
- 1. / workspace->h[j+1][j], workspace->v[j+1], N );
- // fprintf( stderr, "%d-%d: orthogonalization completed.\n", itr, j );
-
- /* Givens rotations on the upper-Hessenberg matrix to make it U */
- for( i = MAX(j-1,0); i <= j; i++ ) {
- if( i == j ) {
- cc = SQRT( SQR(workspace->h[j][j])+SQR(workspace->h[j+1][j]) );
- workspace->hc[j] = workspace->h[j][j] / cc;
- workspace->hs[j] = workspace->h[j+1][j] / cc;
- }
-
- tmp1 = workspace->hc[i] * workspace->h[i][j] +
- workspace->hs[i] * workspace->h[i+1][j];
- tmp2 = -workspace->hs[i] * workspace->h[i][j] +
- workspace->hc[i] * workspace->h[i+1][j];
-
- workspace->h[i][j] = tmp1;
- workspace->h[i+1][j] = tmp2;
- }
-
- /* apply Givens rotations to the rhs as well */
- tmp1 = workspace->hc[j] * workspace->g[j];
- tmp2 = -workspace->hs[j] * workspace->g[j];
- workspace->g[j] = tmp1;
- workspace->g[j+1] = tmp2;
-
- //fprintf( stderr, "h: " );
- //for( i = 0; i <= j+1; ++i )
- //fprintf( stderr, "%.6f ", workspace->h[i][j] );
- //fprintf( stderr, "\n" );
- //fprintf( stderr, "res: %.15e\n", workspace->g[j+1] );
+ int i, j, k, itr, N;
+ real cc, tmp1, tmp2, temp, bnorm;
+
+ N = H->n;
+ bnorm = Norm( b, N );
+
+ /* GMRES outer-loop */
+ for ( itr = 0; itr < MAX_ITR; ++itr )
+ {
+ /* calculate r0 */
+ Sparse_MatVec( H, x, workspace->b_prm );
+ Vector_Sum( workspace->v[0], 1., b, -1., workspace->b_prm, N );
+ Forward_Subs( L, workspace->v[0], workspace->v[0] );
+ Backward_Subs( U, workspace->v[0], workspace->v[0] );
+ workspace->g[0] = Norm( workspace->v[0], N );
+ Vector_Scale( workspace->v[0], 1. / workspace->g[0], workspace->v[0], N );
+ //fprintf( stderr, "res: %.15e\n", workspace->g[0] );
+
+ /* GMRES inner-loop */
+ for ( j = 0; j < RESTART && fabs(workspace->g[j]) / bnorm > tol; j++ )
+ {
+ /* matvec */
+ Sparse_MatVec( H, workspace->v[j], workspace->v[j + 1] );
+ Forward_Subs( L, workspace->v[j + 1], workspace->v[j + 1] );
+ Backward_Subs( U, workspace->v[j + 1], workspace->v[j + 1] );
+
+ /* apply modified Gram-Schmidt to orthogonalize the new residual */
+ for ( i = 0; i < j - 1; i++ ) workspace->h[i][j] = 0;
+
+ //for( i = 0; i <= j; i++ ) {
+ for ( i = MAX(j - 1, 0); i <= j; i++ )
+ {
+ workspace->h[i][j] = Dot( workspace->v[i], workspace->v[j + 1], N );
+ Vector_Add( workspace->v[j + 1], -workspace->h[i][j], workspace->v[i], N );
+ }
+
+ workspace->h[j + 1][j] = Norm( workspace->v[j + 1], N );
+ Vector_Scale( workspace->v[j + 1],
+ 1. / workspace->h[j + 1][j], workspace->v[j + 1], N );
+ // fprintf( stderr, "%d-%d: orthogonalization completed.\n", itr, j );
+
+ /* Givens rotations on the upper-Hessenberg matrix to make it U */
+ for ( i = MAX(j - 1, 0); i <= j; i++ )
+ {
+ if ( i == j )
+ {
+ cc = SQRT( SQR(workspace->h[j][j]) + SQR(workspace->h[j + 1][j]) );
+ workspace->hc[j] = workspace->h[j][j] / cc;
+ workspace->hs[j] = workspace->h[j + 1][j] / cc;
+ }
+
+ tmp1 = workspace->hc[i] * workspace->h[i][j] +
+ workspace->hs[i] * workspace->h[i + 1][j];
+ tmp2 = -workspace->hs[i] * workspace->h[i][j] +
+ workspace->hc[i] * workspace->h[i + 1][j];
+
+ workspace->h[i][j] = tmp1;
+ workspace->h[i + 1][j] = tmp2;
+ }
+
+ /* apply Givens rotations to the rhs as well */
+ tmp1 = workspace->hc[j] * workspace->g[j];
+ tmp2 = -workspace->hs[j] * workspace->g[j];
+ workspace->g[j] = tmp1;
+ workspace->g[j + 1] = tmp2;
+
+ //fprintf( stderr, "h: " );
+ //for( i = 0; i <= j+1; ++i )
+ //fprintf( stderr, "%.6f ", workspace->h[i][j] );
+ //fprintf( stderr, "\n" );
+ //fprintf( stderr, "res: %.15e\n", workspace->g[j+1] );
+ }
+
+
+ /* solve Hy = g: H is now upper-triangular, do back-substitution */
+ for ( i = j - 1; i >= 0; i-- )
+ {
+ temp = workspace->g[i];
+ for ( k = j - 1; k > i; k-- )
+ temp -= workspace->h[i][k] * workspace->y[k];
+
+ workspace->y[i] = temp / workspace->h[i][i];
+ }
+
+ /* update x = x_0 + Vy */
+ Vector_MakeZero( workspace->p, N );
+ for ( i = 0; i < j; i++ )
+ Vector_Add( workspace->p, workspace->y[i], workspace->v[i], N );
+ //Backward_Subs( U, workspace->p, workspace->p );
+ //Forward_Subs( L, workspace->p, workspace->p );
+ Vector_Add( x, 1., workspace->p, N );
+
+ /* stopping condition */
+ if ( fabs(workspace->g[j]) / bnorm <= tol )
+ break;
}
-
-
- /* solve Hy = g: H is now upper-triangular, do back-substitution */
- for( i = j-1; i >= 0; i-- ) {
- temp = workspace->g[i];
- for( k = j-1; k > i; k-- )
- temp -= workspace->h[i][k] * workspace->y[k];
-
- workspace->y[i] = temp / workspace->h[i][i];
+
+ // Sparse_MatVec( H, x, workspace->b_prm );
+ // for( i = 0; i < N; ++i )
+ // workspace->b_prm[i] *= workspace->Hdia_inv[i];
+ // fprintf( fout, "\n%10s%15s%15s\n", "b_prc", "b_prm", "x" );
+ // for( i = 0; i < N; ++i )
+ // fprintf( fout, "%10.5f%15.12f%15.12f\n",
+ // workspace->b_prc[i], workspace->b_prm[i], x[i] );*/
+
+ // fprintf(fout,"GMRES outer:%d, inner:%d iters - residual norm: %25.20f\n",
+ // itr, j, fabs( workspace->g[j] ) / bnorm );
+ // data->timing.matvec += itr * RESTART + j;
+
+ if ( itr >= MAX_ITR )
+ {
+ fprintf( stderr, "GMRES convergence failed\n" );
+ // return -1;
+ return itr * (RESTART + 1) + j + 1;
}
-
- /* update x = x_0 + Vy */
- Vector_MakeZero( workspace->p, N );
- for( i = 0; i < j; i++ )
- Vector_Add( workspace->p, workspace->y[i], workspace->v[i], N );
- //Backward_Subs( U, workspace->p, workspace->p );
- //Forward_Subs( L, workspace->p, workspace->p );
- Vector_Add( x, 1., workspace->p, N );
-
- /* stopping condition */
- if( fabs(workspace->g[j]) / bnorm <= tol )
- break;
- }
-
- // Sparse_MatVec( H, x, workspace->b_prm );
- // for( i = 0; i < N; ++i )
- // workspace->b_prm[i] *= workspace->Hdia_inv[i];
- // fprintf( fout, "\n%10s%15s%15s\n", "b_prc", "b_prm", "x" );
- // for( i = 0; i < N; ++i )
- // fprintf( fout, "%10.5f%15.12f%15.12f\n",
- // workspace->b_prc[i], workspace->b_prm[i], x[i] );*/
-
- // fprintf(fout,"GMRES outer:%d, inner:%d iters - residual norm: %25.20f\n",
- // itr, j, fabs( workspace->g[j] ) / bnorm );
- // data->timing.matvec += itr * RESTART + j;
-
- if( itr >= MAX_ITR ) {
- fprintf( stderr, "GMRES convergence failed\n" );
- // return -1;
- return itr * (RESTART+1) + j + 1;
- }
-
- return itr * (RESTART+1) + j + 1;
+
+ return itr * (RESTART + 1) + j + 1;
}
/* generalized minimual residual iterative solver for sparse linear systems,
* with preconditioner using factors LU \approx H
* and Jacobi iteration for approximate factor application */
-int PGMRES_Jacobi( static_storage *workspace, sparse_matrix *H, real *b, real tol,
- sparse_matrix *L, sparse_matrix *U, real *x, FILE *fout )
+int PGMRES_Jacobi( static_storage *workspace, sparse_matrix *H, real *b, real tol,
+ sparse_matrix *L, sparse_matrix *U, real *x, FILE *fout )
{
- int i, j, k, itr, N, pj, si, ei;
- real cc, tmp1, tmp2, temp, bnorm;
- sparse_matrix *Dinv_L, *Dinv_U;
-
- N = H->n;
- bnorm = Norm( b, N );
-
- /* Compute Jacobi iteration matrices from
- * truncated Newmann series: x_{k+1} = Gx_k + D^{-1}b
- * where:
- * G = I - D^{-1}R
- * R = triangular matrix
- * D = diagonal matrix, diagonals from R */
- if( Allocate_Matrix( &Dinv_L, L->n, L->n ) == 0 ||
- Allocate_Matrix( &Dinv_U, U->n, U->n ) == 0 )
- {
- fprintf( stderr, "not enough memory for Jacobi iteration matrices. terminating.\n" );
- exit(INSUFFICIENT_SPACE);
- }
-
- /* construct D^{-1}_L and D^{-1}_U */
- for( i = 0; i < N; ++i )
- {
- si = L->start[i+1]-1;
- Dinv_L->start[i] = i;
- Dinv_L->entries[i].j = i;
- Dinv_L->entries[i].val = 1. / L->entries[si].val;
-
- si = U->start[i];
- Dinv_U->start[i] = i;
- Dinv_U->entries[i].j = i;
- Dinv_U->entries[i].val = 1. / U->entries[si].val;
- }
- Dinv_L->start[N] = N;
- Dinv_U->start[N] = N;
-
- /* GMRES outer-loop */
- for( itr = 0; itr < MAX_ITR; ++itr ) {
- /* calculate r0 */
- Sparse_MatVec( H, x, workspace->b_prm );
- Vector_Sum( workspace->v[0], 1., b, -1., workspace->b_prm, N );
- // TODO: add parameters to config file
- // TODO: cache results and use for inital guess?
- Jacobi_Iter( (const sparse_matrix*)L, LOWER, (const sparse_matrix*)Dinv_L,
- (const real*)workspace->v[0], workspace->v[0], 100 );
- Jacobi_Iter( (const sparse_matrix*)U, UPPER, (const sparse_matrix*)Dinv_U,
- (const real*)workspace->v[0], workspace->v[0], 100 );
- workspace->g[0] = Norm( workspace->v[0], N );
- Vector_Scale( workspace->v[0], 1. / workspace->g[0], workspace->v[0], N );
- //fprintf( stderr, "res: %.15e\n", workspace->g[0] );
-
- /* GMRES inner-loop */
- for( j = 0; j < RESTART && fabs(workspace->g[j]) / bnorm > tol; j++ ) {
- /* matvec */
- Sparse_MatVec( H, workspace->v[j], workspace->v[j+1] );
- // TODO: add parameters to config file
- // TODO: cache results and use for inital guess?
- Jacobi_Iter( (const sparse_matrix*)L, LOWER, (const sparse_matrix*)Dinv_L,
- (const real*)workspace->v[j+1], workspace->v[j+1], 100 );
- Jacobi_Iter( (const sparse_matrix*)U, UPPER, (const sparse_matrix*)Dinv_U,
- (const real*)workspace->v[j+1], workspace->v[j+1], 100 );
-
- /* apply modified Gram-Schmidt to orthogonalize the new residual */
- for( i = 0; i < j-1; i++ ) workspace->h[i][j] = 0;
-
- //for( i = 0; i <= j; i++ ) {
- for( i = MAX(j-1,0); i <= j; i++ ) {
- workspace->h[i][j] = Dot( workspace->v[i], workspace->v[j+1], N );
- Vector_Add( workspace->v[j+1],-workspace->h[i][j], workspace->v[i], N );
- }
-
- workspace->h[j+1][j] = Norm( workspace->v[j+1], N );
- Vector_Scale( workspace->v[j+1],
- 1. / workspace->h[j+1][j], workspace->v[j+1], N );
- // fprintf( stderr, "%d-%d: orthogonalization completed.\n", itr, j );
-
- /* Givens rotations on the upper-Hessenberg matrix to make it U */
- for( i = MAX(j-1,0); i <= j; i++ ) {
- if( i == j ) {
- cc = SQRT( SQR(workspace->h[j][j])+SQR(workspace->h[j+1][j]) );
- workspace->hc[j] = workspace->h[j][j] / cc;
- workspace->hs[j] = workspace->h[j+1][j] / cc;
- }
-
- tmp1 = workspace->hc[i] * workspace->h[i][j] +
- workspace->hs[i] * workspace->h[i+1][j];
- tmp2 = -workspace->hs[i] * workspace->h[i][j] +
- workspace->hc[i] * workspace->h[i+1][j];
-
- workspace->h[i][j] = tmp1;
- workspace->h[i+1][j] = tmp2;
- }
-
- /* apply Givens rotations to the rhs as well */
- tmp1 = workspace->hc[j] * workspace->g[j];
- tmp2 = -workspace->hs[j] * workspace->g[j];
- workspace->g[j] = tmp1;
- workspace->g[j+1] = tmp2;
-
- //fprintf( stderr, "h: " );
- //for( i = 0; i <= j+1; ++i )
- //fprintf( stderr, "%.6f ", workspace->h[i][j] );
- //fprintf( stderr, "\n" );
- //fprintf( stderr, "res: %.15e\n", workspace->g[j+1] );
+ int i, j, k, itr, N, pj, si, ei;
+ real cc, tmp1, tmp2, temp, bnorm;
+ sparse_matrix *Dinv_L, *Dinv_U;
+
+ N = H->n;
+ bnorm = Norm( b, N );
+
+ /* Compute Jacobi iteration matrices from
+ * truncated Newmann series: x_{k+1} = Gx_k + D^{-1}b
+ * where:
+ * G = I - D^{-1}R
+ * R = triangular matrix
+ * D = diagonal matrix, diagonals from R */
+ if ( Allocate_Matrix( &Dinv_L, L->n, L->n ) == 0 ||
+ Allocate_Matrix( &Dinv_U, U->n, U->n ) == 0 )
+ {
+ fprintf( stderr, "not enough memory for Jacobi iteration matrices. terminating.\n" );
+ exit(INSUFFICIENT_SPACE);
+ }
+
+ /* construct D^{-1}_L and D^{-1}_U */
+ for ( i = 0; i < N; ++i )
+ {
+ si = L->start[i + 1] - 1;
+ Dinv_L->start[i] = i;
+ Dinv_L->entries[i].j = i;
+ Dinv_L->entries[i].val = 1. / L->entries[si].val;
+
+ si = U->start[i];
+ Dinv_U->start[i] = i;
+ Dinv_U->entries[i].j = i;
+ Dinv_U->entries[i].val = 1. / U->entries[si].val;
}
-
-
- /* solve Hy = g: H is now upper-triangular, do back-substitution */
- for( i = j-1; i >= 0; i-- ) {
- temp = workspace->g[i];
- for( k = j-1; k > i; k-- )
- temp -= workspace->h[i][k] * workspace->y[k];
-
- workspace->y[i] = temp / workspace->h[i][i];
+ Dinv_L->start[N] = N;
+ Dinv_U->start[N] = N;
+
+ /* GMRES outer-loop */
+ for ( itr = 0; itr < MAX_ITR; ++itr )
+ {
+ /* calculate r0 */
+ Sparse_MatVec( H, x, workspace->b_prm );
+ Vector_Sum( workspace->v[0], 1., b, -1., workspace->b_prm, N );
+ // TODO: add parameters to config file
+ // TODO: cache results and use for inital guess?
+ Jacobi_Iter( (const sparse_matrix*)L, LOWER, (const sparse_matrix*)Dinv_L,
+ (const real*)workspace->v[0], workspace->v[0], 100 );
+ Jacobi_Iter( (const sparse_matrix*)U, UPPER, (const sparse_matrix*)Dinv_U,
+ (const real*)workspace->v[0], workspace->v[0], 100 );
+ workspace->g[0] = Norm( workspace->v[0], N );
+ Vector_Scale( workspace->v[0], 1. / workspace->g[0], workspace->v[0], N );
+ //fprintf( stderr, "res: %.15e\n", workspace->g[0] );
+
+ /* GMRES inner-loop */
+ for ( j = 0; j < RESTART && fabs(workspace->g[j]) / bnorm > tol; j++ )
+ {
+ /* matvec */
+ Sparse_MatVec( H, workspace->v[j], workspace->v[j + 1] );
+ // TODO: add parameters to config file
+ // TODO: cache results and use for inital guess?
+ Jacobi_Iter( (const sparse_matrix*)L, LOWER, (const sparse_matrix*)Dinv_L,
+ (const real*)workspace->v[j + 1], workspace->v[j + 1], 100 );
+ Jacobi_Iter( (const sparse_matrix*)U, UPPER, (const sparse_matrix*)Dinv_U,
+ (const real*)workspace->v[j + 1], workspace->v[j + 1], 100 );
+
+ /* apply modified Gram-Schmidt to orthogonalize the new residual */
+ for ( i = 0; i < j - 1; i++ ) workspace->h[i][j] = 0;
+
+ //for( i = 0; i <= j; i++ ) {
+ for ( i = MAX(j - 1, 0); i <= j; i++ )
+ {
+ workspace->h[i][j] = Dot( workspace->v[i], workspace->v[j + 1], N );
+ Vector_Add( workspace->v[j + 1], -workspace->h[i][j], workspace->v[i], N );
+ }
+
+ workspace->h[j + 1][j] = Norm( workspace->v[j + 1], N );
+ Vector_Scale( workspace->v[j + 1],
+ 1. / workspace->h[j + 1][j], workspace->v[j + 1], N );
+ // fprintf( stderr, "%d-%d: orthogonalization completed.\n", itr, j );
+
+ /* Givens rotations on the upper-Hessenberg matrix to make it U */
+ for ( i = MAX(j - 1, 0); i <= j; i++ )
+ {
+ if ( i == j )
+ {
+ cc = SQRT( SQR(workspace->h[j][j]) + SQR(workspace->h[j + 1][j]) );
+ workspace->hc[j] = workspace->h[j][j] / cc;
+ workspace->hs[j] = workspace->h[j + 1][j] / cc;
+ }
+
+ tmp1 = workspace->hc[i] * workspace->h[i][j] +
+ workspace->hs[i] * workspace->h[i + 1][j];
+ tmp2 = -workspace->hs[i] * workspace->h[i][j] +
+ workspace->hc[i] * workspace->h[i + 1][j];
+
+ workspace->h[i][j] = tmp1;
+ workspace->h[i + 1][j] = tmp2;
+ }
+
+ /* apply Givens rotations to the rhs as well */
+ tmp1 = workspace->hc[j] * workspace->g[j];
+ tmp2 = -workspace->hs[j] * workspace->g[j];
+ workspace->g[j] = tmp1;
+ workspace->g[j + 1] = tmp2;
+
+ //fprintf( stderr, "h: " );
+ //for( i = 0; i <= j+1; ++i )
+ //fprintf( stderr, "%.6f ", workspace->h[i][j] );
+ //fprintf( stderr, "\n" );
+ //fprintf( stderr, "res: %.15e\n", workspace->g[j+1] );
+ }
+
+
+ /* solve Hy = g: H is now upper-triangular, do back-substitution */
+ for ( i = j - 1; i >= 0; i-- )
+ {
+ temp = workspace->g[i];
+ for ( k = j - 1; k > i; k-- )
+ temp -= workspace->h[i][k] * workspace->y[k];
+
+ workspace->y[i] = temp / workspace->h[i][i];
+ }
+
+ /* update x = x_0 + Vy */
+ Vector_MakeZero( workspace->p, N );
+ for ( i = 0; i < j; i++ )
+ Vector_Add( workspace->p, workspace->y[i], workspace->v[i], N );
+ //Backward_Subs( U, workspace->p, workspace->p );
+ //Forward_Subs( L, workspace->p, workspace->p );
+ Vector_Add( x, 1., workspace->p, N );
+
+ /* stopping condition */
+ if ( fabs(workspace->g[j]) / bnorm <= tol )
+ break;
}
-
- /* update x = x_0 + Vy */
- Vector_MakeZero( workspace->p, N );
- for( i = 0; i < j; i++ )
- Vector_Add( workspace->p, workspace->y[i], workspace->v[i], N );
- //Backward_Subs( U, workspace->p, workspace->p );
- //Forward_Subs( L, workspace->p, workspace->p );
- Vector_Add( x, 1., workspace->p, N );
-
- /* stopping condition */
- if( fabs(workspace->g[j]) / bnorm <= tol )
- break;
- }
-
- // Sparse_MatVec( H, x, workspace->b_prm );
- // for( i = 0; i < N; ++i )
- // workspace->b_prm[i] *= workspace->Hdia_inv[i];
- // fprintf( fout, "\n%10s%15s%15s\n", "b_prc", "b_prm", "x" );
- // for( i = 0; i < N; ++i )
- // fprintf( fout, "%10.5f%15.12f%15.12f\n",
- // workspace->b_prc[i], workspace->b_prm[i], x[i] );*/
-
- // fprintf(fout,"GMRES outer:%d, inner:%d iters - residual norm: %25.20f\n",
- // itr, j, fabs( workspace->g[j] ) / bnorm );
- // data->timing.matvec += itr * RESTART + j;
-
- Deallocate_Matrix( Dinv_U );
- Deallocate_Matrix( Dinv_L );
-
- if( itr >= MAX_ITR )
- {
- fprintf( stderr, "GMRES convergence failed\n" );
- // return -1;
- return itr * (RESTART+1) + j + 1;
- }
-
- return itr * (RESTART+1) + j + 1;
+
+ // Sparse_MatVec( H, x, workspace->b_prm );
+ // for( i = 0; i < N; ++i )
+ // workspace->b_prm[i] *= workspace->Hdia_inv[i];
+ // fprintf( fout, "\n%10s%15s%15s\n", "b_prc", "b_prm", "x" );
+ // for( i = 0; i < N; ++i )
+ // fprintf( fout, "%10.5f%15.12f%15.12f\n",
+ // workspace->b_prc[i], workspace->b_prm[i], x[i] );*/
+
+ // fprintf(fout,"GMRES outer:%d, inner:%d iters - residual norm: %25.20f\n",
+ // itr, j, fabs( workspace->g[j] ) / bnorm );
+ // data->timing.matvec += itr * RESTART + j;
+
+ Deallocate_Matrix( Dinv_U );
+ Deallocate_Matrix( Dinv_L );
+
+ if ( itr >= MAX_ITR )
+ {
+ fprintf( stderr, "GMRES convergence failed\n" );
+ // return -1;
+ return itr * (RESTART + 1) + j + 1;
+ }
+
+ return itr * (RESTART + 1) + j + 1;
}
-int PCG( static_storage *workspace, sparse_matrix *A, real *b, real tol,
- sparse_matrix *L, sparse_matrix *U, real *x, FILE *fout )
+int PCG( static_storage *workspace, sparse_matrix *A, real *b, real tol,
+ sparse_matrix *L, sparse_matrix *U, real *x, FILE *fout )
{
- int i, N;
- real tmp, alpha, beta, b_norm, r_norm;
- real sig0, sig_old, sig_new;
-
- N = A->n;
- b_norm = Norm( b, N );
- //fprintf( stderr, "b_norm: %.15e\n", b_norm );
-
- Sparse_MatVec( A, x, workspace->q );
- Vector_Sum( workspace->r , 1., b, -1., workspace->q, N );
- r_norm = Norm(workspace->r, N);
- //Print_Soln( workspace, x, q, b, N );
- //fprintf( stderr, "res: %.15e\n", r_norm );
-
- Forward_Subs( L, workspace->r, workspace->d );
- Backward_Subs( U, workspace->d, workspace->p );
- sig_new = Dot( workspace->r, workspace->p, N );
- sig0 = sig_new;
-
- for( i = 0; i < 200 && r_norm/b_norm > tol; ++i ) {
- //for( i = 0; i < 200 && sig_new > SQR(tol) * sig0; ++i ) {
- Sparse_MatVec( A, workspace->p, workspace->q );
- tmp = Dot( workspace->q, workspace->p, N );
- alpha = sig_new / tmp;
- Vector_Add( x, alpha, workspace->p, N );
- //fprintf( stderr, "iter%d: |p|=%.15e |q|=%.15e tmp=%.15e\n",
- // i+1, Norm(workspace->p,N), Norm(workspace->q,N), tmp );
-
- Vector_Add( workspace->r, -alpha, workspace->q, N );
+ int i, N;
+ real tmp, alpha, beta, b_norm, r_norm;
+ real sig0, sig_old, sig_new;
+
+ N = A->n;
+ b_norm = Norm( b, N );
+ //fprintf( stderr, "b_norm: %.15e\n", b_norm );
+
+ Sparse_MatVec( A, x, workspace->q );
+ Vector_Sum( workspace->r , 1., b, -1., workspace->q, N );
r_norm = Norm(workspace->r, N);
+ //Print_Soln( workspace, x, q, b, N );
//fprintf( stderr, "res: %.15e\n", r_norm );
-
+
Forward_Subs( L, workspace->r, workspace->d );
- Backward_Subs( U, workspace->d, workspace->d );
- sig_old = sig_new;
- sig_new = Dot( workspace->r, workspace->d, N );
- beta = sig_new / sig_old;
- Vector_Sum( workspace->p, 1., workspace->d, beta, workspace->p, N );
- }
-
- //fprintf( fout, "CG took %d iterations\n", i );
- if( i >= 200 ) {
- fprintf( stderr, "CG convergence failed!\n" );
+ Backward_Subs( U, workspace->d, workspace->p );
+ sig_new = Dot( workspace->r, workspace->p, N );
+ sig0 = sig_new;
+
+ for ( i = 0; i < 200 && r_norm / b_norm > tol; ++i )
+ {
+ //for( i = 0; i < 200 && sig_new > SQR(tol) * sig0; ++i ) {
+ Sparse_MatVec( A, workspace->p, workspace->q );
+ tmp = Dot( workspace->q, workspace->p, N );
+ alpha = sig_new / tmp;
+ Vector_Add( x, alpha, workspace->p, N );
+ //fprintf( stderr, "iter%d: |p|=%.15e |q|=%.15e tmp=%.15e\n",
+ // i+1, Norm(workspace->p,N), Norm(workspace->q,N), tmp );
+
+ Vector_Add( workspace->r, -alpha, workspace->q, N );
+ r_norm = Norm(workspace->r, N);
+ //fprintf( stderr, "res: %.15e\n", r_norm );
+
+ Forward_Subs( L, workspace->r, workspace->d );
+ Backward_Subs( U, workspace->d, workspace->d );
+ sig_old = sig_new;
+ sig_new = Dot( workspace->r, workspace->d, N );
+ beta = sig_new / sig_old;
+ Vector_Sum( workspace->p, 1., workspace->d, beta, workspace->p, N );
+ }
+
+ //fprintf( fout, "CG took %d iterations\n", i );
+ if ( i >= 200 )
+ {
+ fprintf( stderr, "CG convergence failed!\n" );
+ return i;
+ }
+
return i;
- }
-
- return i;
}
-int CG( static_storage *workspace, sparse_matrix *H,
- real *b, real tol, real *x, FILE *fout )
+int CG( static_storage *workspace, sparse_matrix *H,
+ real *b, real tol, real *x, FILE *fout )
{
- int i, j, N;
- real tmp, alpha, beta, b_norm;
- real sig_old, sig_new, sig0;
-
- N = H->n;
- b_norm = Norm( b, N );
- //fprintf( stderr, "b_norm: %10.6f\n", b_norm );
-
- Sparse_MatVec( H, x, workspace->q );
- Vector_Sum( workspace->r , 1., b, -1., workspace->q, N );
- for( j = 0; j < N; ++j )
- workspace->d[j] = workspace->r[j] * workspace->Hdia_inv[j];
-
- sig_new = Dot( workspace->r, workspace->d, N );
- sig0 = sig_new;
- //Print_Soln( workspace, x, q, b, N );
- //fprintf( stderr, "sig_new: %24.15e, d_norm:%24.15e, q_norm:%24.15e\n",
- // sqrt(sig_new), Norm(workspace->d,N), Norm(workspace->q,N) );
- //fprintf( stderr, "sig_new: %f\n", sig_new );
-
- for( i = 0; i < 300 && SQRT(sig_new) / b_norm > tol; ++i ) {
- //for( i = 0; i < 300 && sig_new > SQR(tol)*sig0; ++i ) {
- Sparse_MatVec( H, workspace->d, workspace->q );
- tmp = Dot( workspace->d, workspace->q, N );
- //fprintf( stderr, "tmp: %f\n", tmp );
- alpha = sig_new / tmp;
- Vector_Add( x, alpha, workspace->d, N );
- //fprintf( stderr, "d_norm:%24.15e, q_norm:%24.15e, tmp:%24.15e\n",
- // Norm(workspace->d,N), Norm(workspace->q,N), tmp );
-
- Vector_Add( workspace->r, -alpha, workspace->q, N );
- for( j = 0; j < N; ++j )
- workspace->p[j] = workspace->r[j] * workspace->Hdia_inv[j];
-
- sig_old = sig_new;
- sig_new = Dot( workspace->r, workspace->p, N );
- beta = sig_new / sig_old;
- Vector_Sum( workspace->d, 1., workspace->p, beta, workspace->d, N );
+ int i, j, N;
+ real tmp, alpha, beta, b_norm;
+ real sig_old, sig_new, sig0;
+
+ N = H->n;
+ b_norm = Norm( b, N );
+ //fprintf( stderr, "b_norm: %10.6f\n", b_norm );
+
+ Sparse_MatVec( H, x, workspace->q );
+ Vector_Sum( workspace->r , 1., b, -1., workspace->q, N );
+ for ( j = 0; j < N; ++j )
+ workspace->d[j] = workspace->r[j] * workspace->Hdia_inv[j];
+
+ sig_new = Dot( workspace->r, workspace->d, N );
+ sig0 = sig_new;
+ //Print_Soln( workspace, x, q, b, N );
+ //fprintf( stderr, "sig_new: %24.15e, d_norm:%24.15e, q_norm:%24.15e\n",
+ // sqrt(sig_new), Norm(workspace->d,N), Norm(workspace->q,N) );
//fprintf( stderr, "sig_new: %f\n", sig_new );
- }
-
- fprintf( stderr, "CG took %d iterations\n", i );
-
- if( i >= 300 ) {
- fprintf( stderr, "CG convergence failed!\n" );
- return i;
- }
- return i;
+ for ( i = 0; i < 300 && SQRT(sig_new) / b_norm > tol; ++i )
+ {
+ //for( i = 0; i < 300 && sig_new > SQR(tol)*sig0; ++i ) {
+ Sparse_MatVec( H, workspace->d, workspace->q );
+ tmp = Dot( workspace->d, workspace->q, N );
+ //fprintf( stderr, "tmp: %f\n", tmp );
+ alpha = sig_new / tmp;
+ Vector_Add( x, alpha, workspace->d, N );
+ //fprintf( stderr, "d_norm:%24.15e, q_norm:%24.15e, tmp:%24.15e\n",
+ // Norm(workspace->d,N), Norm(workspace->q,N), tmp );
+
+ Vector_Add( workspace->r, -alpha, workspace->q, N );
+ for ( j = 0; j < N; ++j )
+ workspace->p[j] = workspace->r[j] * workspace->Hdia_inv[j];
+
+ sig_old = sig_new;
+ sig_new = Dot( workspace->r, workspace->p, N );
+ beta = sig_new / sig_old;
+ Vector_Sum( workspace->d, 1., workspace->p, beta, workspace->d, N );
+ //fprintf( stderr, "sig_new: %f\n", sig_new );
+ }
+
+ fprintf( stderr, "CG took %d iterations\n", i );
+
+ if ( i >= 300 )
+ {
+ fprintf( stderr, "CG convergence failed!\n" );
+ return i;
+ }
+
+ return i;
}
/* Steepest Descent */
-int SDM( static_storage *workspace, sparse_matrix *H,
- real *b, real tol, real *x, FILE *fout )
+int SDM( static_storage *workspace, sparse_matrix *H,
+ real *b, real tol, real *x, FILE *fout )
{
- int i, j, N;
- real tmp, alpha, beta, b_norm;
- real sig0, sig;
-
- N = H->n;
- b_norm = Norm( b, N );
- //fprintf( stderr, "b_norm: %10.6f\n", b_norm );
-
- Sparse_MatVec( H, x, workspace->q );
- Vector_Sum( workspace->r , 1., b, -1., workspace->q, N );
- for( j = 0; j < N; ++j )
- workspace->d[j] = workspace->r[j] * workspace->Hdia_inv[j];
-
- sig = Dot( workspace->r, workspace->d, N );
- sig0 = sig;
-
- for( i = 0; i < 300 && SQRT(sig) / b_norm > tol; ++i ) {
- Sparse_MatVec( H, workspace->d, workspace->q );
-
- sig = Dot( workspace->r, workspace->d, N );
- tmp = Dot( workspace->d, workspace->q, N );
- alpha = sig / tmp;
-
- Vector_Add( x, alpha, workspace->d, N );
- Vector_Add( workspace->r, -alpha, workspace->q, N );
- for( j = 0; j < N; ++j )
- workspace->d[j] = workspace->r[j] * workspace->Hdia_inv[j];
-
- //fprintf( stderr, "d_norm:%24.15e, q_norm:%24.15e, tmp:%24.15e\n",
- // Norm(workspace->d,N), Norm(workspace->q,N), tmp );
- }
-
- fprintf( stderr, "SDM took %d iterations\n", i );
-
- if( i >= 300 ) {
- fprintf( stderr, "SDM convergence failed!\n" );
- return i;
- }
-
- return i;
-}
+ int i, j, N;
+ real tmp, alpha, beta, b_norm;
+ real sig0, sig;
+ N = H->n;
+ b_norm = Norm( b, N );
+ //fprintf( stderr, "b_norm: %10.6f\n", b_norm );
+
+ Sparse_MatVec( H, x, workspace->q );
+ Vector_Sum( workspace->r , 1., b, -1., workspace->q, N );
+ for ( j = 0; j < N; ++j )
+ workspace->d[j] = workspace->r[j] * workspace->Hdia_inv[j];
+
+ sig = Dot( workspace->r, workspace->d, N );
+ sig0 = sig;
+
+ for ( i = 0; i < 300 && SQRT(sig) / b_norm > tol; ++i )
+ {
+ Sparse_MatVec( H, workspace->d, workspace->q );
+
+ sig = Dot( workspace->r, workspace->d, N );
+ tmp = Dot( workspace->d, workspace->q, N );
+ alpha = sig / tmp;
+
+ Vector_Add( x, alpha, workspace->d, N );
+ Vector_Add( workspace->r, -alpha, workspace->q, N );
+ for ( j = 0; j < N; ++j )
+ workspace->d[j] = workspace->r[j] * workspace->Hdia_inv[j];
+
+ //fprintf( stderr, "d_norm:%24.15e, q_norm:%24.15e, tmp:%24.15e\n",
+ // Norm(workspace->d,N), Norm(workspace->q,N), tmp );
+ }
+
+ fprintf( stderr, "SDM took %d iterations\n", i );
+
+ if ( i >= 300 )
+ {
+ fprintf( stderr, "SDM convergence failed!\n" );
+ return i;
+ }
+
+ return i;
+}
diff --git a/puremd_rc_1003/sPuReMD/GMRES.h b/puremd_rc_1003/sPuReMD/GMRES.h
index c5db381f95387c99140f6b9a402390dd52c3131b..37aa994baa2a8cda08b9b37960f24b643cecca50 100644
--- a/puremd_rc_1003/sPuReMD/GMRES.h
+++ b/puremd_rc_1003/sPuReMD/GMRES.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -28,29 +28,29 @@
typedef enum
{
- LOWER = 0,
- UPPER = 1,
+ LOWER = 0,
+ UPPER = 1,
} TRIANGULARITY;
-int GMRES( static_storage*, sparse_matrix*,
- real*, real, real*, FILE* );
+int GMRES( static_storage*, sparse_matrix*,
+ real*, real, real*, FILE* );
-int GMRES_HouseHolder( static_storage*, sparse_matrix*,
- real*, real, real*, FILE* );
+int GMRES_HouseHolder( static_storage*, sparse_matrix*,
+ real*, real, real*, FILE* );
-int PGMRES( static_storage*, sparse_matrix*, real*, real,
- sparse_matrix*, sparse_matrix*, real*, FILE* );
+int PGMRES( static_storage*, sparse_matrix*, real*, real,
+ sparse_matrix*, sparse_matrix*, real*, FILE* );
-int PGMRES_Jacobi( static_storage*, sparse_matrix*, real*, real,
- sparse_matrix*, sparse_matrix*, real*, FILE* );
+int PGMRES_Jacobi( static_storage*, sparse_matrix*, real*, real,
+ sparse_matrix*, sparse_matrix*, real*, FILE* );
-int PCG( static_storage*, sparse_matrix*, real*, real,
- sparse_matrix*, sparse_matrix*, real*, FILE* );
+int PCG( static_storage*, sparse_matrix*, real*, real,
+ sparse_matrix*, sparse_matrix*, real*, FILE* );
-int CG( static_storage*, sparse_matrix*,
- real*, real, real*, FILE* );
+int CG( static_storage*, sparse_matrix*,
+ real*, real, real*, FILE* );
-int uyduruk_GMRES( static_storage*, sparse_matrix*,
- real*, real, real*, int, FILE* );
+int uyduruk_GMRES( static_storage*, sparse_matrix*,
+ real*, real, real*, int, FILE* );
#endif
diff --git a/puremd_rc_1003/sPuReMD/QEq.c b/puremd_rc_1003/sPuReMD/QEq.c
index ad1c0cbc91e001bb8a46ef0f0eea49017806dc39..6a445347bdd4527a107c173a08025c1c096d8eb6 100644
--- a/puremd_rc_1003/sPuReMD/QEq.c
+++ b/puremd_rc_1003/sPuReMD/QEq.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -27,357 +27,373 @@
int compare_matrix_entry(const void *v1, const void *v2)
{
- /* larger element has larger column index */
- return ((sparse_matrix_entry *)v1)->j - ((sparse_matrix_entry *)v2)->j;
+ /* larger element has larger column index */
+ return ((sparse_matrix_entry *)v1)->j - ((sparse_matrix_entry *)v2)->j;
}
void Sort_Matrix_Rows( sparse_matrix *A )
{
- int i, si, ei;
-
- /* sort each row of A using column indices */
- for( i = 0; i < A->n; ++i ) {
- si = A->start[i];
- ei = A->start[i+1];
- /* polymorphic sort in standard C library */
- qsort( &(A->entries[si]), ei - si,
- sizeof(sparse_matrix_entry), compare_matrix_entry );
- }
+ int i, si, ei;
+
+ /* sort each row of A using column indices */
+ for ( i = 0; i < A->n; ++i )
+ {
+ si = A->start[i];
+ ei = A->start[i + 1];
+ /* polymorphic sort in standard C library */
+ qsort( &(A->entries[si]), ei - si,
+ sizeof(sparse_matrix_entry), compare_matrix_entry );
+ }
}
void Calculate_Droptol( sparse_matrix *A, real *droptol, real dtol )
{
- int i, j, k;
- real val;
-
- /* init droptol to 0 */
- for( i = 0; i < A->n; ++i )
- droptol[i] = 0;
-
- /* calculate sqaure of the norm of each row */
- for( i = 0; i < A->n; ++i ) {
- for( k = A->start[i]; k < A->start[i+1]-1; ++k ) {
- j = A->entries[k].j;
- val = A->entries[k].val;
-
- droptol[i] += val*val;
- droptol[j] += val*val;
+ int i, j, k;
+ real val;
+
+ /* init droptol to 0 */
+ for ( i = 0; i < A->n; ++i )
+ droptol[i] = 0;
+
+ /* calculate sqaure of the norm of each row */
+ for ( i = 0; i < A->n; ++i )
+ {
+ for ( k = A->start[i]; k < A->start[i + 1] - 1; ++k )
+ {
+ j = A->entries[k].j;
+ val = A->entries[k].val;
+
+ droptol[i] += val * val;
+ droptol[j] += val * val;
+ }
+
+ val = A->entries[k].val; // diagonal entry
+ droptol[i] += val * val;
}
-
- val = A->entries[k].val; // diagonal entry
- droptol[i] += val*val;
- }
-
- /* calculate local droptol for each row */
- //fprintf( stderr, "droptol: " );
- for( i = 0; i < A->n; ++i ) {
- //fprintf( stderr, "%f-->", droptol[i] );
- droptol[i] = SQRT( droptol[i] ) * dtol;
- //fprintf( stderr, "%f ", droptol[i] );
- }
- //fprintf( stderr, "\n" );
+
+ /* calculate local droptol for each row */
+ //fprintf( stderr, "droptol: " );
+ for ( i = 0; i < A->n; ++i )
+ {
+ //fprintf( stderr, "%f-->", droptol[i] );
+ droptol[i] = SQRT( droptol[i] ) * dtol;
+ //fprintf( stderr, "%f ", droptol[i] );
+ }
+ //fprintf( stderr, "\n" );
}
int Estimate_LU_Fill( sparse_matrix *A, real *droptol )
{
- int i, j, pj;
- int fillin;
- real val;
-
- fillin = 0;
-
- //fprintf( stderr, "n: %d\n", A->n );
- for( i = 0; i < A->n; ++i )
- for( pj = A->start[i]; pj < A->start[i+1]-1; ++pj ){
- j = A->entries[pj].j;
- val = A->entries[pj].val;
- //fprintf( stderr, "i: %d, j: %d", i, j );
-
- if( fabs(val) > droptol[i] )
- ++fillin;
- }
+ int i, j, pj;
+ int fillin;
+ real val;
+
+ fillin = 0;
+
+ //fprintf( stderr, "n: %d\n", A->n );
+ for ( i = 0; i < A->n; ++i )
+ for ( pj = A->start[i]; pj < A->start[i + 1] - 1; ++pj )
+ {
+ j = A->entries[pj].j;
+ val = A->entries[pj].val;
+ //fprintf( stderr, "i: %d, j: %d", i, j );
- return fillin + A->n;
+ if ( fabs(val) > droptol[i] )
+ ++fillin;
+ }
+
+ return fillin + A->n;
}
/* Incomplete Cholesky factorization with thresholding */
-void ICHOLT( sparse_matrix *A, real *droptol,
- sparse_matrix *L, sparse_matrix *U )
+void ICHOLT( sparse_matrix *A, real *droptol,
+ sparse_matrix *L, sparse_matrix *U )
{
- sparse_matrix_entry tmp[1000];
- int i, j, pj, k1, k2, tmptop, Ltop;
- real val;
- int *Utop;
-
- Utop = (int*) malloc((A->n+1) * sizeof(int));
-
- // clear variables
- Ltop = 0;
- tmptop = 0;
- for( i = 0; i <= A->n; ++i )
- L->start[i] = U->start[i] = 0;
-
- for( i = 0; i < A->n; ++i )
- Utop[i] = 0;
-
- //fprintf( stderr, "n: %d\n", A->n );
- for( i = 0; i < A->n; ++i ){
- L->start[i] = Ltop;
+ sparse_matrix_entry tmp[1000];
+ int i, j, pj, k1, k2, tmptop, Ltop;
+ real val;
+ int *Utop;
+
+ Utop = (int*) malloc((A->n + 1) * sizeof(int));
+
+ // clear variables
+ Ltop = 0;
tmptop = 0;
+ for ( i = 0; i <= A->n; ++i )
+ L->start[i] = U->start[i] = 0;
+
+ for ( i = 0; i < A->n; ++i )
+ Utop[i] = 0;
- for( pj = A->start[i]; pj < A->start[i+1]-1; ++pj ){
- j = A->entries[pj].j;
- val = A->entries[pj].val;
- //fprintf( stderr, "i: %d, j: %d", i, j );
-
- if( fabs(val) > droptol[i] ){
- k1 = 0;
- k2 = L->start[j];
- while( k1 < tmptop && k2 < L->start[j+1] ){
- if( tmp[k1].j < L->entries[k2].j )
- ++k1;
- else if( tmp[k1].j > L->entries[k2].j )
- ++k2;
- else
- val -= (tmp[k1++].val * L->entries[k2++].val);
- }
-
- // L matrix is lower triangular,
- // so right before the start of next row comes jth diagonal
- val /= L->entries[L->start[j+1]-1].val;
-
- tmp[tmptop].j = j;
- tmp[tmptop].val = val;
- ++tmptop;
- }
- //fprintf( stderr, " -- done\n" );
+ //fprintf( stderr, "n: %d\n", A->n );
+ for ( i = 0; i < A->n; ++i )
+ {
+ L->start[i] = Ltop;
+ tmptop = 0;
+
+ for ( pj = A->start[i]; pj < A->start[i + 1] - 1; ++pj )
+ {
+ j = A->entries[pj].j;
+ val = A->entries[pj].val;
+ //fprintf( stderr, "i: %d, j: %d", i, j );
+
+ if ( fabs(val) > droptol[i] )
+ {
+ k1 = 0;
+ k2 = L->start[j];
+ while ( k1 < tmptop && k2 < L->start[j + 1] )
+ {
+ if ( tmp[k1].j < L->entries[k2].j )
+ ++k1;
+ else if ( tmp[k1].j > L->entries[k2].j )
+ ++k2;
+ else
+ val -= (tmp[k1++].val * L->entries[k2++].val);
+ }
+
+ // L matrix is lower triangular,
+ // so right before the start of next row comes jth diagonal
+ val /= L->entries[L->start[j + 1] - 1].val;
+
+ tmp[tmptop].j = j;
+ tmp[tmptop].val = val;
+ ++tmptop;
+ }
+ //fprintf( stderr, " -- done\n" );
+ }
+
+ // compute the ith diagonal in L
+ // sanity check
+ if ( A->entries[pj].j != i )
+ {
+ fprintf( stderr, "i=%d, badly built A matrix!\n", i );
+ exit(999);
+ }
+
+ val = A->entries[pj].val;
+ for ( k1 = 0; k1 < tmptop; ++k1 )
+ val -= (tmp[k1].val * tmp[k1].val);
+
+ tmp[tmptop].j = i;
+ tmp[tmptop].val = SQRT(val);
+
+ // apply the dropping rule once again
+ //fprintf( stderr, "row%d: tmptop: %d\n", i, tmptop );
+ //for( k1 = 0; k1<= tmptop; ++k1 )
+ // fprintf( stderr, "%d(%f) ", tmp[k1].j, tmp[k1].val );
+ //fprintf( stderr, "\n" );
+ //fprintf( stderr, "row(%d): droptol=%.4f\n", i+1, droptol[i] );
+ for ( k1 = 0; k1 < tmptop; ++k1 )
+ if ( fabs(tmp[k1].val) > droptol[i] / tmp[tmptop].val )
+ {
+ L->entries[Ltop].j = tmp[k1].j;
+ L->entries[Ltop].val = tmp[k1].val;
+ U->start[tmp[k1].j + 1]++;
+ ++Ltop;
+ //fprintf( stderr, "%d(%.4f) ", tmp[k1].j+1, tmp[k1].val );
+ }
+ // keep the diagonal in any case
+ L->entries[Ltop].j = tmp[k1].j;
+ L->entries[Ltop].val = tmp[k1].val;
+ ++Ltop;
+ //fprintf( stderr, "%d(%.4f)\n", tmp[k1].j+1, tmp[k1].val );
}
-
- // compute the ith diagonal in L
- // sanity check
- if( A->entries[pj].j != i ) {
- fprintf( stderr, "i=%d, badly built A matrix!\n", i );
- exit(999);
+
+ L->start[i] = Ltop;
+ //fprintf( stderr, "nnz(L): %d, max: %d\n", Ltop, L->n * 50 );
+
+ /* U = L^T (Cholesky factorization) */
+ for ( i = 1; i <= U->n; ++i )
+ {
+ Utop[i] = U->start[i] = U->start[i] + U->start[i - 1] + 1;
}
-
- val = A->entries[pj].val;
- for( k1 = 0; k1 < tmptop; ++k1 )
- val -= (tmp[k1].val * tmp[k1].val);
-
- tmp[tmptop].j = i;
- tmp[tmptop].val = SQRT(val);
-
- // apply the dropping rule once again
- //fprintf( stderr, "row%d: tmptop: %d\n", i, tmptop );
- //for( k1 = 0; k1<= tmptop; ++k1 )
- // fprintf( stderr, "%d(%f) ", tmp[k1].j, tmp[k1].val );
- //fprintf( stderr, "\n" );
- //fprintf( stderr, "row(%d): droptol=%.4f\n", i+1, droptol[i] );
- for( k1 = 0; k1 < tmptop; ++k1 )
- if( fabs(tmp[k1].val) > droptol[i] / tmp[tmptop].val ){
- L->entries[Ltop].j = tmp[k1].j;
- L->entries[Ltop].val = tmp[k1].val;
- U->start[tmp[k1].j+1]++;
- ++Ltop;
- //fprintf( stderr, "%d(%.4f) ", tmp[k1].j+1, tmp[k1].val );
- }
- // keep the diagonal in any case
- L->entries[Ltop].j = tmp[k1].j;
- L->entries[Ltop].val = tmp[k1].val;
- ++Ltop;
- //fprintf( stderr, "%d(%.4f)\n", tmp[k1].j+1, tmp[k1].val );
- }
-
- L->start[i] = Ltop;
- //fprintf( stderr, "nnz(L): %d, max: %d\n", Ltop, L->n * 50 );
-
- /* U = L^T (Cholesky factorization) */
- for( i = 1; i <= U->n; ++i )
- {
- Utop[i] = U->start[i] = U->start[i] + U->start[i-1] + 1;
- }
- for( i = 0; i < L->n; ++i )
- {
- for( pj = L->start[i]; pj < L->start[i+1]; ++pj )
+ for ( i = 0; i < L->n; ++i )
{
- j = L->entries[pj].j;
- U->entries[Utop[j]].j = i;
- U->entries[Utop[j]].val = L->entries[pj].val;
- Utop[j]++;
+ for ( pj = L->start[i]; pj < L->start[i + 1]; ++pj )
+ {
+ j = L->entries[pj].j;
+ U->entries[Utop[j]].j = i;
+ U->entries[Utop[j]].val = L->entries[pj].val;
+ Utop[j]++;
+ }
}
- }
- //fprintf( stderr, "nnz(U): %d, max: %d\n", Utop[U->n], U->n * 50 );
+ //fprintf( stderr, "nnz(U): %d, max: %d\n", Utop[U->n], U->n * 50 );
- free(Utop);
+ free(Utop);
}
-void Init_MatVec( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list *far_nbrs )
+void Init_MatVec( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list *far_nbrs )
{
- int i, fillin;
- real s_tmp, t_tmp;
- //char fname[100];
-
- if(control->refactor > 0 &&
- ((data->step-data->prev_steps)%control->refactor==0 || workspace->L==NULL)){
- //Print_Linear_System( system, control, workspace, data->step );
- Sort_Matrix_Rows( workspace->H );
- //fprintf( stderr, "H matrix sorted\n" );
- // TODO: comment out
- Calculate_Droptol( workspace->H, workspace->droptol, control->droptol );
- //fprintf( stderr, "drop tolerances calculated\n" );
- if( workspace->L == NULL ) {
- // TODO: ilu_par & ichol_par contain same sparsity pattern as H,
- // so allocate with same NNZ (workspace->H->m)
- fillin = Estimate_LU_Fill( workspace->H, workspace->droptol );
- if( Allocate_Matrix( &(workspace->L), far_nbrs->n, fillin ) == 0 ||
- Allocate_Matrix( &(workspace->U), far_nbrs->n, fillin ) == 0 ){
- fprintf( stderr, "not enough memory for LU matrices. terminating.\n" );
- exit(INSUFFICIENT_SPACE);
- }
+ int i, fillin;
+ real s_tmp, t_tmp;
+ //char fname[100];
+
+ if (control->refactor > 0 &&
+ ((data->step - data->prev_steps) % control->refactor == 0 || workspace->L == NULL))
+ {
+ //Print_Linear_System( system, control, workspace, data->step );
+ Sort_Matrix_Rows( workspace->H );
+ //fprintf( stderr, "H matrix sorted\n" );
+ // TODO: comment out
+ Calculate_Droptol( workspace->H, workspace->droptol, control->droptol );
+ //fprintf( stderr, "drop tolerances calculated\n" );
+ if ( workspace->L == NULL )
+ {
+ // TODO: ilu_par & ichol_par contain same sparsity pattern as H,
+ // so allocate with same NNZ (workspace->H->m)
+ fillin = Estimate_LU_Fill( workspace->H, workspace->droptol );
+ if ( Allocate_Matrix( &(workspace->L), far_nbrs->n, fillin ) == 0 ||
+ Allocate_Matrix( &(workspace->U), far_nbrs->n, fillin ) == 0 )
+ {
+ fprintf( stderr, "not enough memory for LU matrices. terminating.\n" );
+ exit(INSUFFICIENT_SPACE);
+ }
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "fillin = %d\n", fillin );
- fprintf( stderr, "allocated memory: L = U = %ldMB\n",
- fillin * sizeof(sparse_matrix_entry) / (1024*1024) );
+ fprintf( stderr, "fillin = %d\n", fillin );
+ fprintf( stderr, "allocated memory: L = U = %ldMB\n",
+ fillin * sizeof(sparse_matrix_entry) / (1024 * 1024) );
#endif
- }
+ }
- // TODO: replace with ilu_par or ichol_par
- // TODO: add parameters for sweeps to control file
- //ICHOL_PAR( workspace->H, 3, workspace->L, workspace->U );
- ICHOLT( workspace->H, workspace->droptol, workspace->L, workspace->U );
+ // TODO: replace with ilu_par or ichol_par
+ // TODO: add parameters for sweeps to control file
+ //ICHOL_PAR( workspace->H, 3, workspace->L, workspace->U );
+ ICHOLT( workspace->H, workspace->droptol, workspace->L, workspace->U );
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "icholt-" );
- //sprintf( fname, "%s.L%d.out", control->sim_name, data->step );
- //Print_Sparse_Matrix2( workspace->L, fname );
- //Print_Sparse_Matrix( U );
+ fprintf( stderr, "icholt-" );
+ //sprintf( fname, "%s.L%d.out", control->sim_name, data->step );
+ //Print_Sparse_Matrix2( workspace->L, fname );
+ //Print_Sparse_Matrix( U );
#endif
- }
-
- /* extrapolation for s & t */
- for( i = 0; i < system->N; ++i ) {
- // no extrapolation
- //s_tmp = workspace->s[0][i];
- //t_tmp = workspace->t[0][i];
-
- // linear
- //s_tmp = 2 * workspace->s[0][i] - workspace->s[1][i];
- //t_tmp = 2 * workspace->t[0][i] - workspace->t[1][i];
-
- // quadratic
- //s_tmp = workspace->s[2][i] + 3 * (workspace->s[0][i]-workspace->s[1][i]);
- t_tmp = workspace->t[2][i] + 3*(workspace->t[0][i]-workspace->t[1][i]);
-
- // cubic
- s_tmp = 4 * (workspace->s[0][i] + workspace->s[2][i]) -
- (6 * workspace->s[1][i] + workspace->s[3][i] );
- //t_tmp = 4 * (workspace->t[0][i] + workspace->t[2][i]) -
- // (6 * workspace->t[1][i] + workspace->t[3][i] );
-
- // 4th order
- //s_tmp = 5 * (workspace->s[0][i] - workspace->s[3][i]) +
- // 10 * (-workspace->s[1][i] + workspace->s[2][i] ) + workspace->s[4][i];
- //t_tmp = 5 * (workspace->t[0][i] - workspace->t[3][i]) +
- // 10 * (-workspace->t[1][i] + workspace->t[2][i] ) + workspace->t[4][i];
-
- workspace->s[4][i] = workspace->s[3][i];
- workspace->s[3][i] = workspace->s[2][i];
- workspace->s[2][i] = workspace->s[1][i];
- workspace->s[1][i] = workspace->s[0][i];
- workspace->s[0][i] = s_tmp;
-
- workspace->t[4][i] = workspace->t[3][i];
- workspace->t[3][i] = workspace->t[2][i];
- workspace->t[2][i] = workspace->t[1][i];
- workspace->t[1][i] = workspace->t[0][i];
- workspace->t[0][i] = t_tmp;
- }
+ }
+
+ /* extrapolation for s & t */
+ for ( i = 0; i < system->N; ++i )
+ {
+ // no extrapolation
+ //s_tmp = workspace->s[0][i];
+ //t_tmp = workspace->t[0][i];
+
+ // linear
+ //s_tmp = 2 * workspace->s[0][i] - workspace->s[1][i];
+ //t_tmp = 2 * workspace->t[0][i] - workspace->t[1][i];
+
+ // quadratic
+ //s_tmp = workspace->s[2][i] + 3 * (workspace->s[0][i]-workspace->s[1][i]);
+ t_tmp = workspace->t[2][i] + 3 * (workspace->t[0][i] - workspace->t[1][i]);
+
+ // cubic
+ s_tmp = 4 * (workspace->s[0][i] + workspace->s[2][i]) -
+ (6 * workspace->s[1][i] + workspace->s[3][i] );
+ //t_tmp = 4 * (workspace->t[0][i] + workspace->t[2][i]) -
+ // (6 * workspace->t[1][i] + workspace->t[3][i] );
+
+ // 4th order
+ //s_tmp = 5 * (workspace->s[0][i] - workspace->s[3][i]) +
+ // 10 * (-workspace->s[1][i] + workspace->s[2][i] ) + workspace->s[4][i];
+ //t_tmp = 5 * (workspace->t[0][i] - workspace->t[3][i]) +
+ // 10 * (-workspace->t[1][i] + workspace->t[2][i] ) + workspace->t[4][i];
+
+ workspace->s[4][i] = workspace->s[3][i];
+ workspace->s[3][i] = workspace->s[2][i];
+ workspace->s[2][i] = workspace->s[1][i];
+ workspace->s[1][i] = workspace->s[0][i];
+ workspace->s[0][i] = s_tmp;
+
+ workspace->t[4][i] = workspace->t[3][i];
+ workspace->t[3][i] = workspace->t[2][i];
+ workspace->t[2][i] = workspace->t[1][i];
+ workspace->t[1][i] = workspace->t[0][i];
+ workspace->t[0][i] = t_tmp;
+ }
}
void Calculate_Charges( reax_system *system, static_storage *workspace )
{
- int i;
- real u, s_sum, t_sum;
-
- s_sum = t_sum = 0.;
- for( i = 0; i < system->N; ++i ) {
- s_sum += workspace->s[0][i];
- t_sum += workspace->t[0][i];
- }
-
- u = s_sum / t_sum;
- for( i = 0; i < system->N; ++i )
- system->atoms[i].q = workspace->s[0][i] - u * workspace->t[0][i];
+ int i;
+ real u, s_sum, t_sum;
+
+ s_sum = t_sum = 0.;
+ for ( i = 0; i < system->N; ++i )
+ {
+ s_sum += workspace->s[0][i];
+ t_sum += workspace->t[0][i];
+ }
+
+ u = s_sum / t_sum;
+ for ( i = 0; i < system->N; ++i )
+ system->atoms[i].q = workspace->s[0][i] - u * workspace->t[0][i];
}
-void QEq( reax_system *system, control_params *control, simulation_data *data,
- static_storage *workspace, list *far_nbrs,
- output_controls *out_control )
+void QEq( reax_system *system, control_params *control, simulation_data *data,
+ static_storage *workspace, list *far_nbrs,
+ output_controls *out_control )
{
- int matvecs;
+ int matvecs;
- Init_MatVec( system, control, data, workspace, far_nbrs );
+ Init_MatVec( system, control, data, workspace, far_nbrs );
- //if( data->step % 10 == 0 )
- // Print_Linear_System( system, control, workspace, far_nbrs, data->step );
+ //if( data->step % 10 == 0 )
+ // Print_Linear_System( system, control, workspace, far_nbrs, data->step );
- //TODO: add parameters in control file for solver choice and options
-// matvecs = GMRES( workspace, workspace->H,
+ //TODO: add parameters in control file for solver choice and options
+// matvecs = GMRES( workspace, workspace->H,
// workspace->b_s, control->q_err, workspace->s[0], out_control->log );
-// matvecs += GMRES( workspace, workspace->H,
+// matvecs += GMRES( workspace, workspace->H,
// workspace->b_t, control->q_err, workspace->t[0], out_control->log );
- //matvecs = GMRES_HouseHolder( workspace, workspace->H,
- // workspace->b_s, control->q_err, workspace->s[0], out_control->log );
- //matvecs += GMRES_HouseHolder( workspace, workspace->H,
- // workspace->b_t, control->q_err, workspace->t[0], out_control->log );
-
- //matvecs = PGMRES( workspace, workspace->H, workspace->b_s, control->q_err,
- // workspace->L, workspace->U, workspace->s[0], out_control->log );
- //matvecs += PGMRES( workspace, workspace->H, workspace->b_t, control->q_err,
- // workspace->L, workspace->U, workspace->t[0], out_control->log );
-
- matvecs = PGMRES_Jacobi( workspace, workspace->H, workspace->b_s, control->q_err,
- workspace->L, workspace->U, workspace->s[0], out_control->log );
- matvecs += PGMRES_Jacobi( workspace, workspace->H, workspace->b_t, control->q_err,
- workspace->L, workspace->U, workspace->t[0], out_control->log );
-
- //matvecs=PCG( workspace, workspace->H, workspace->b_s, control->q_err,
- // workspace->L, workspace->U, workspace->s[0], out_control->log ) + 1;
- ///matvecs+=PCG( workspace, workspace->H, workspace->b_t, control->q_err,
- // workspace->L, workspace->U, workspace->t[0], out_control->log ) + 1;
-
- //matvecs = CG( workspace, workspace->H,
- // workspace->b_s, control->q_err, workspace->s[0], out_control->log ) + 1;
- //matvecs += CG( workspace, workspace->H,
- // workspace->b_t, control->q_err, workspace->t[0], out_control->log ) + 1;
-
- //matvecs = SDM( workspace, workspace->H,
- // workspace->b_s, control->q_err, workspace->s[0], out_control->log ) + 1;
- //matvecs += SDM( workspace, workspace->H,
- // workspace->b_t, control->q_err, workspace->t[0], out_control->log ) + 1;
-
- data->timing.matvecs += matvecs;
+ //matvecs = GMRES_HouseHolder( workspace, workspace->H,
+ // workspace->b_s, control->q_err, workspace->s[0], out_control->log );
+ //matvecs += GMRES_HouseHolder( workspace, workspace->H,
+ // workspace->b_t, control->q_err, workspace->t[0], out_control->log );
+
+ //matvecs = PGMRES( workspace, workspace->H, workspace->b_s, control->q_err,
+ // workspace->L, workspace->U, workspace->s[0], out_control->log );
+ //matvecs += PGMRES( workspace, workspace->H, workspace->b_t, control->q_err,
+ // workspace->L, workspace->U, workspace->t[0], out_control->log );
+
+ matvecs = PGMRES_Jacobi( workspace, workspace->H, workspace->b_s, control->q_err,
+ workspace->L, workspace->U, workspace->s[0], out_control->log );
+ matvecs += PGMRES_Jacobi( workspace, workspace->H, workspace->b_t, control->q_err,
+ workspace->L, workspace->U, workspace->t[0], out_control->log );
+
+ //matvecs=PCG( workspace, workspace->H, workspace->b_s, control->q_err,
+ // workspace->L, workspace->U, workspace->s[0], out_control->log ) + 1;
+ ///matvecs+=PCG( workspace, workspace->H, workspace->b_t, control->q_err,
+ // workspace->L, workspace->U, workspace->t[0], out_control->log ) + 1;
+
+ //matvecs = CG( workspace, workspace->H,
+ // workspace->b_s, control->q_err, workspace->s[0], out_control->log ) + 1;
+ //matvecs += CG( workspace, workspace->H,
+ // workspace->b_t, control->q_err, workspace->t[0], out_control->log ) + 1;
+
+ //matvecs = SDM( workspace, workspace->H,
+ // workspace->b_s, control->q_err, workspace->s[0], out_control->log ) + 1;
+ //matvecs += SDM( workspace, workspace->H,
+ // workspace->b_t, control->q_err, workspace->t[0], out_control->log ) + 1;
+
+ data->timing.matvecs += matvecs;
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "linsolve-" );
+ fprintf( stderr, "linsolve-" );
#endif
- Calculate_Charges( system, workspace );
- //fprintf( stderr, "%d %.9f %.9f %.9f %.9f %.9f %.9f\n",
- // data->step,
- // workspace->s[0][0], workspace->t[0][0],
- // workspace->s[0][1], workspace->t[0][1],
- // workspace->s[0][2], workspace->t[0][2] );
- // if( data->step == control->nsteps )
- //Print_Charges( system, control, workspace, data->step );
+ Calculate_Charges( system, workspace );
+ //fprintf( stderr, "%d %.9f %.9f %.9f %.9f %.9f %.9f\n",
+ // data->step,
+ // workspace->s[0][0], workspace->t[0][0],
+ // workspace->s[0][1], workspace->t[0][1],
+ // workspace->s[0][2], workspace->t[0][2] );
+ // if( data->step == control->nsteps )
+ //Print_Charges( system, control, workspace, data->step );
}
diff --git a/puremd_rc_1003/sPuReMD/QEq.h b/puremd_rc_1003/sPuReMD/QEq.h
index f594d1ed954345ab9874e37ebe8289a35e9dcf6d..f598061be2c530e58ad90f04f779adafeba2f44d 100644
--- a/puremd_rc_1003/sPuReMD/QEq.h
+++ b/puremd_rc_1003/sPuReMD/QEq.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -24,7 +24,7 @@
#include "mytypes.h"
-void QEq( reax_system*, control_params*, simulation_data*, static_storage*,
- list*, output_controls* );
+void QEq( reax_system*, control_params*, simulation_data*, static_storage*,
+ list*, output_controls* );
#endif
diff --git a/puremd_rc_1003/sPuReMD/allocate.c b/puremd_rc_1003/sPuReMD/allocate.c
index c9e8e1d9fb7bec3672b328455d9054a0e39b781d..56bacd6d70db16bdf0d5701c589aa11a782eb5d3 100644
--- a/puremd_rc_1003/sPuReMD/allocate.c
+++ b/puremd_rc_1003/sPuReMD/allocate.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -24,267 +24,283 @@
void Reallocate_Neighbor_List( list *far_nbrs, int n, int num_intrs )
{
- Delete_List( far_nbrs );
- if(!Make_List( n, num_intrs, TYP_FAR_NEIGHBOR, far_nbrs )){
- fprintf(stderr, "Problem in initializing far nbrs list. Terminating!\n");
- exit( INIT_ERR );
- }
+ Delete_List( far_nbrs );
+ if (!Make_List( n, num_intrs, TYP_FAR_NEIGHBOR, far_nbrs ))
+ {
+ fprintf(stderr, "Problem in initializing far nbrs list. Terminating!\n");
+ exit( INIT_ERR );
+ }
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "num_far = %d, far_nbrs = %d -> reallocating!\n",
- num_intrs, far_nbrs->num_intrs );
- fprintf( stderr, "memory allocated: far_nbrs = %ldMB\n",
- num_intrs * sizeof(far_neighbor_data) / (1024*1024) );
+ fprintf( stderr, "num_far = %d, far_nbrs = %d -> reallocating!\n",
+ num_intrs, far_nbrs->num_intrs );
+ fprintf( stderr, "memory allocated: far_nbrs = %ldMB\n",
+ num_intrs * sizeof(far_neighbor_data) / (1024 * 1024) );
#endif
}
int Allocate_Matrix( sparse_matrix **pH, int n, int m )
{
- sparse_matrix *H;
-
- if( (*pH = (sparse_matrix*) malloc(sizeof(sparse_matrix))) == NULL )
- {
- return 0;
- }
-
- H = *pH;
- H->n = n;
- H->m = m;
- if( (H->start = (int*) malloc(sizeof(int) * (n+1))) == NULL )
- {
- return 0;
- }
- if( (H->entries =
- (sparse_matrix_entry*) malloc(sizeof(sparse_matrix_entry)*m)) == NULL )
- {
- return 0;
- }
+ sparse_matrix *H;
+
+ if ( (*pH = (sparse_matrix*) malloc(sizeof(sparse_matrix))) == NULL )
+ {
+ return 0;
+ }
+
+ H = *pH;
+ H->n = n;
+ H->m = m;
+ if ( (H->start = (int*) malloc(sizeof(int) * (n + 1))) == NULL )
+ {
+ return 0;
+ }
+ if ( (H->entries =
+ (sparse_matrix_entry*) malloc(sizeof(sparse_matrix_entry) * m)) == NULL )
+ {
+ return 0;
+ }
// if( ((H->j = (int*) malloc(sizeof(int)*m)) == NULL) ||
// ((H->val = (real*) malloc(sizeof(real)*m)) == NULL) )
// {
// return 0;
// }
- return 1;
+ return 1;
}
void Deallocate_Matrix( sparse_matrix *H )
{
- free(H->start);
- free(H->entries);
- free(H);
+ free(H->start);
+ free(H->entries);
+ free(H);
}
int Reallocate_Matrix( sparse_matrix **H, int n, int m, char *name )
{
- Deallocate_Matrix( *H );
- if( !Allocate_Matrix( H, n, m ) ) {
- fprintf(stderr, "not enough space for %s matrix. terminating!\n", name);
- exit( 1 );
- }
+ Deallocate_Matrix( *H );
+ if ( !Allocate_Matrix( H, n, m ) )
+ {
+ fprintf(stderr, "not enough space for %s matrix. terminating!\n", name);
+ exit( 1 );
+ }
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "reallocating %s matrix, n = %d, m = %d\n",
- name, n, m );
- fprintf( stderr, "memory allocated: %s = %ldMB\n",
- name, m * sizeof(sparse_matrix_entry) / (1024*1024) );
+ fprintf( stderr, "reallocating %s matrix, n = %d, m = %d\n",
+ name, n, m );
+ fprintf( stderr, "memory allocated: %s = %ldMB\n",
+ name, m * sizeof(sparse_matrix_entry) / (1024 * 1024) );
#endif
- return 1;
+ return 1;
}
-int Allocate_HBond_List( int n, int num_h, int *h_index, int *hb_top,
- list *hbonds )
+int Allocate_HBond_List( int n, int num_h, int *h_index, int *hb_top,
+ list *hbonds )
{
- int i, num_hbonds;
-
- num_hbonds = 0;
- /* find starting indexes for each H and the total number of hbonds */
- for( i = 1; i < n; ++i )
- hb_top[i] += hb_top[i-1];
- num_hbonds = hb_top[n-1];
-
- if( !Make_List(num_h, num_hbonds, TYP_HBOND, hbonds ) ) {
- fprintf( stderr, "not enough space for hbonds list. terminating!\n" );
- exit( INIT_ERR );
- }
-
- for( i = 0; i < n; ++i )
- if( h_index[i] == 0 ){
- Set_Start_Index( 0, 0, hbonds );
- Set_End_Index( 0, 0, hbonds );
+ int i, num_hbonds;
+
+ num_hbonds = 0;
+ /* find starting indexes for each H and the total number of hbonds */
+ for ( i = 1; i < n; ++i )
+ hb_top[i] += hb_top[i - 1];
+ num_hbonds = hb_top[n - 1];
+
+ if ( !Make_List(num_h, num_hbonds, TYP_HBOND, hbonds ) )
+ {
+ fprintf( stderr, "not enough space for hbonds list. terminating!\n" );
+ exit( INIT_ERR );
}
- else if( h_index[i] > 0 ){
- Set_Start_Index( h_index[i], hb_top[i-1], hbonds );
- Set_End_Index( h_index[i], hb_top[i-1], hbonds );
- }
-
+
+ for ( i = 0; i < n; ++i )
+ if ( h_index[i] == 0 )
+ {
+ Set_Start_Index( 0, 0, hbonds );
+ Set_End_Index( 0, 0, hbonds );
+ }
+ else if ( h_index[i] > 0 )
+ {
+ Set_Start_Index( h_index[i], hb_top[i - 1], hbonds );
+ Set_End_Index( h_index[i], hb_top[i - 1], hbonds );
+ }
+
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "allocating hbonds - num_hbonds: %d\n", num_hbonds );
- fprintf( stderr, "memory allocated: hbonds = %ldMB\n",
- num_hbonds * sizeof(hbond_data) / (1024*1024) );
+ fprintf( stderr, "allocating hbonds - num_hbonds: %d\n", num_hbonds );
+ fprintf( stderr, "memory allocated: hbonds = %ldMB\n",
+ num_hbonds * sizeof(hbond_data) / (1024 * 1024) );
#endif
- return 1;
+ return 1;
}
int Reallocate_HBonds_List( int n, int num_h, int *h_index, list *hbonds )
{
- int i;
- int *hb_top;
+ int i;
+ int *hb_top;
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "reallocating hbonds\n" );
+ fprintf( stderr, "reallocating hbonds\n" );
#endif
- hb_top = calloc( n, sizeof(int) );
- for( i = 0; i < n; ++i )
- if( h_index[i] >= 0 )
- hb_top[i] = MAX(Num_Entries(h_index[i],hbonds)*SAFE_HBONDS, MIN_HBONDS);
-
- Delete_List( hbonds );
-
- Allocate_HBond_List( n, num_h, h_index, hb_top, hbonds );
-
- free( hb_top );
-
- return 1;
+ hb_top = calloc( n, sizeof(int) );
+ for ( i = 0; i < n; ++i )
+ if ( h_index[i] >= 0 )
+ hb_top[i] = MAX(Num_Entries(h_index[i], hbonds) * SAFE_HBONDS, MIN_HBONDS);
+
+ Delete_List( hbonds );
+
+ Allocate_HBond_List( n, num_h, h_index, hb_top, hbonds );
+
+ free( hb_top );
+
+ return 1;
}
int Allocate_Bond_List( int n, int *bond_top, list *bonds )
{
- int i, num_bonds;
-
- num_bonds = 0;
- /* find starting indexes for each atom and the total number of bonds */
- for( i = 1; i < n; ++i )
- bond_top[i] += bond_top[i-1];
- num_bonds = bond_top[n-1];
-
- if( !Make_List(n, num_bonds, TYP_BOND, bonds ) ) {
- fprintf( stderr, "not enough space for bonds list. terminating!\n" );
- exit( INIT_ERR );
- }
-
- Set_Start_Index( 0, 0, bonds );
- Set_End_Index( 0, 0, bonds );
- for( i = 1; i < n; ++i ) {
- Set_Start_Index( i, bond_top[i-1], bonds );
- Set_End_Index( i, bond_top[i-1], bonds );
- }
+ int i, num_bonds;
+
+ num_bonds = 0;
+ /* find starting indexes for each atom and the total number of bonds */
+ for ( i = 1; i < n; ++i )
+ bond_top[i] += bond_top[i - 1];
+ num_bonds = bond_top[n - 1];
+
+ if ( !Make_List(n, num_bonds, TYP_BOND, bonds ) )
+ {
+ fprintf( stderr, "not enough space for bonds list. terminating!\n" );
+ exit( INIT_ERR );
+ }
+
+ Set_Start_Index( 0, 0, bonds );
+ Set_End_Index( 0, 0, bonds );
+ for ( i = 1; i < n; ++i )
+ {
+ Set_Start_Index( i, bond_top[i - 1], bonds );
+ Set_End_Index( i, bond_top[i - 1], bonds );
+ }
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "allocating bonds - num_bonds: %d\n", num_bonds );
- fprintf( stderr, "memory allocated: bonds = %ldMB\n",
- num_bonds * sizeof(bond_data) / (1024*1024) );
+ fprintf( stderr, "allocating bonds - num_bonds: %d\n", num_bonds );
+ fprintf( stderr, "memory allocated: bonds = %ldMB\n",
+ num_bonds * sizeof(bond_data) / (1024 * 1024) );
#endif
- return 1;
+ return 1;
}
int Reallocate_Bonds_List( int n, list *bonds, int *num_bonds, int *est_3body )
{
- int i;
- int *bond_top;
+ int i;
+ int *bond_top;
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "reallocating bonds\n" );
+ fprintf( stderr, "reallocating bonds\n" );
#endif
- bond_top = calloc( n, sizeof(int) );
- *est_3body = 0;
- for( i = 0; i < n; ++i ){
- *est_3body += SQR( Num_Entries( i, bonds ) );
- bond_top[i] = MAX( Num_Entries( i, bonds ) * 2, MIN_BONDS );
- }
+ bond_top = calloc( n, sizeof(int) );
+ *est_3body = 0;
+ for ( i = 0; i < n; ++i )
+ {
+ *est_3body += SQR( Num_Entries( i, bonds ) );
+ bond_top[i] = MAX( Num_Entries( i, bonds ) * 2, MIN_BONDS );
+ }
+
+ Delete_List( bonds );
- Delete_List( bonds );
+ Allocate_Bond_List( n, bond_top, bonds );
+ *num_bonds = bond_top[n - 1];
- Allocate_Bond_List( n, bond_top, bonds );
- *num_bonds = bond_top[n-1];
-
- free( bond_top );
+ free( bond_top );
- return 1;
+ return 1;
}
-void Reallocate( reax_system *system, static_storage *workspace, list **lists,
- int nbr_flag )
+void Reallocate( reax_system *system, static_storage *workspace, list **lists,
+ int nbr_flag )
{
- int i, j, k;
- int num_bonds, est_3body;
- reallocate_data *realloc;
- grid *g;
-
- realloc = &(workspace->realloc);
- g = &(system->g);
-
- if( realloc->num_far > 0 && nbr_flag ) {
- Reallocate_Neighbor_List( (*lists)+FAR_NBRS,
- system->N, realloc->num_far * SAFE_ZONE );
- realloc->num_far = -1;
- }
-
- if( realloc->Htop > 0 ){
- Reallocate_Matrix(&(workspace->H), system->N, realloc->Htop*SAFE_ZONE,"H");
- realloc->Htop = -1;
-
- Deallocate_Matrix( workspace->L );
- Deallocate_Matrix( workspace->U );
- workspace->L = NULL;
- workspace->U = NULL;
- }
-
- if( realloc->hbonds > 0 ){
- Reallocate_HBonds_List(system->N, workspace->num_H, workspace->hbond_index,
- (*lists)+HBONDS );
- realloc->hbonds = -1;
- }
-
- num_bonds = est_3body = -1;
- if( realloc->bonds > 0 ){
- Reallocate_Bonds_List( system->N, (*lists)+BONDS, &num_bonds, &est_3body );
- realloc->bonds = -1;
- realloc->num_3body = MAX( realloc->num_3body, est_3body );
- }
-
- if( realloc->num_3body > 0 ) {
- Delete_List( (*lists)+THREE_BODIES );
-
- if( num_bonds == -1 )
- num_bonds = ((*lists)+BONDS)->num_intrs;
- realloc->num_3body *= SAFE_ZONE;
-
- if( !Make_List( num_bonds, realloc->num_3body,
- TYP_THREE_BODY, (*lists)+THREE_BODIES ) ) {
- fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
- exit( INIT_ERR );
+ int i, j, k;
+ int num_bonds, est_3body;
+ reallocate_data *realloc;
+ grid *g;
+
+ realloc = &(workspace->realloc);
+ g = &(system->g);
+
+ if ( realloc->num_far > 0 && nbr_flag )
+ {
+ Reallocate_Neighbor_List( (*lists) + FAR_NBRS,
+ system->N, realloc->num_far * SAFE_ZONE );
+ realloc->num_far = -1;
+ }
+
+ if ( realloc->Htop > 0 )
+ {
+ Reallocate_Matrix(&(workspace->H), system->N, realloc->Htop * SAFE_ZONE, "H");
+ realloc->Htop = -1;
+
+ Deallocate_Matrix( workspace->L );
+ Deallocate_Matrix( workspace->U );
+ workspace->L = NULL;
+ workspace->U = NULL;
+ }
+
+ if ( realloc->hbonds > 0 )
+ {
+ Reallocate_HBonds_List(system->N, workspace->num_H, workspace->hbond_index,
+ (*lists) + HBONDS );
+ realloc->hbonds = -1;
+ }
+
+ num_bonds = est_3body = -1;
+ if ( realloc->bonds > 0 )
+ {
+ Reallocate_Bonds_List( system->N, (*lists) + BONDS, &num_bonds, &est_3body );
+ realloc->bonds = -1;
+ realloc->num_3body = MAX( realloc->num_3body, est_3body );
}
- realloc->num_3body = -1;
+
+ if ( realloc->num_3body > 0 )
+ {
+ Delete_List( (*lists) + THREE_BODIES );
+
+ if ( num_bonds == -1 )
+ num_bonds = ((*lists) + BONDS)->num_intrs;
+ realloc->num_3body *= SAFE_ZONE;
+
+ if ( !Make_List( num_bonds, realloc->num_3body,
+ TYP_THREE_BODY, (*lists) + THREE_BODIES ) )
+ {
+ fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
+ exit( INIT_ERR );
+ }
+ realloc->num_3body = -1;
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "reallocating 3 bodies\n" );
- fprintf( stderr, "reallocated - num_bonds: %d\n", num_bonds );
- fprintf( stderr, "reallocated - num_3body: %d\n", realloc->num_3body );
- fprintf( stderr, "reallocated 3body memory: %ldMB\n",
- realloc->num_3body*sizeof(three_body_interaction_data)/
- (1024*1024) );
+ fprintf( stderr, "reallocating 3 bodies\n" );
+ fprintf( stderr, "reallocated - num_bonds: %d\n", num_bonds );
+ fprintf( stderr, "reallocated - num_3body: %d\n", realloc->num_3body );
+ fprintf( stderr, "reallocated 3body memory: %ldMB\n",
+ realloc->num_3body * sizeof(three_body_interaction_data) /
+ (1024 * 1024) );
#endif
- }
+ }
- if( realloc->gcell_atoms > -1 ){
+ if ( realloc->gcell_atoms > -1 )
+ {
#if defined(DEBUG_FOCUS)
- fprintf(stderr, "reallocating gcell: g->max_atoms: %d\n", g->max_atoms);
+ fprintf(stderr, "reallocating gcell: g->max_atoms: %d\n", g->max_atoms);
#endif
- for( i = 0; i < g->ncell[0]; i++ )
- for( j = 0; j < g->ncell[1]; j++ )
- for( k = 0; k < g->ncell[2]; k++ ) {
- // reallocate g->atoms
- free( g->atoms[i][j][k] );
- g->atoms[i][j][k] = (int*)
- calloc(workspace->realloc.gcell_atoms, sizeof(int));
- }
- realloc->gcell_atoms = -1;
- }
+ for ( i = 0; i < g->ncell[0]; i++ )
+ for ( j = 0; j < g->ncell[1]; j++ )
+ for ( k = 0; k < g->ncell[2]; k++ )
+ {
+ // reallocate g->atoms
+ free( g->atoms[i][j][k] );
+ g->atoms[i][j][k] = (int*)
+ calloc(workspace->realloc.gcell_atoms, sizeof(int));
+ }
+ realloc->gcell_atoms = -1;
+ }
}
diff --git a/puremd_rc_1003/sPuReMD/allocate.h b/puremd_rc_1003/sPuReMD/allocate.h
index c7f9bf15dd432fe931025b8fd39815bea577f9f3..2581b3bab0976fe65e2ea14b80cee1a8267ee2a9 100644
--- a/puremd_rc_1003/sPuReMD/allocate.h
+++ b/puremd_rc_1003/sPuReMD/allocate.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
diff --git a/puremd_rc_1003/sPuReMD/analyze.c b/puremd_rc_1003/sPuReMD/analyze.c
index ac5cfe3054aa500a9a0dc80354626cdd84cad8a9..45af4c6b36caaf3403abe9f90a2c113e51d87b98 100644
--- a/puremd_rc_1003/sPuReMD/analyze.c
+++ b/puremd_rc_1003/sPuReMD/analyze.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -27,865 +27,924 @@
#define MAX_FRAGMENT_TYPES 100
// copy bond list into old bond list
-void Copy_Bond_List( reax_system *system, control_params *control,
- list **lists )
+void Copy_Bond_List( reax_system *system, control_params *control,
+ list **lists )
{
- int i, j, top_old;
- list *new_bonds = (*lists) + BONDS;
- list *old_bonds = (*lists) + OLD_BONDS;
-
- for( top_old = 0, i = 0; i < system->N; ++i ) {
- Set_Start_Index( i, top_old, old_bonds );
-
- // fprintf( stdout, "%d: ", i );
- for( j = Start_Index( i, new_bonds ); j < End_Index( i, new_bonds ); ++j )
- if( new_bonds->select.bond_list[j].bo_data.BO >= control->bg_cut ) {
- // fprintf( stderr, "%d ", new_bonds->select.bond_list[j].nbr );
- old_bonds->select.bond_list[ top_old ].nbr =
- new_bonds->select.bond_list[j].nbr;
- old_bonds->select.bond_list[ top_old ].bo_data.BO =
- new_bonds->select.bond_list[j].bo_data.BO;
- top_old++;
- }
-
- Set_End_Index( i, top_old, old_bonds);
- // fprintf( stderr, "--- s: %d, e: %d\n",
- // Start_Index( i, old_bonds ), End_Index( i, old_bonds ) );
- }
+ int i, j, top_old;
+ list *new_bonds = (*lists) + BONDS;
+ list *old_bonds = (*lists) + OLD_BONDS;
+
+ for ( top_old = 0, i = 0; i < system->N; ++i )
+ {
+ Set_Start_Index( i, top_old, old_bonds );
+
+ // fprintf( stdout, "%d: ", i );
+ for ( j = Start_Index( i, new_bonds ); j < End_Index( i, new_bonds ); ++j )
+ if ( new_bonds->select.bond_list[j].bo_data.BO >= control->bg_cut )
+ {
+ // fprintf( stderr, "%d ", new_bonds->select.bond_list[j].nbr );
+ old_bonds->select.bond_list[ top_old ].nbr =
+ new_bonds->select.bond_list[j].nbr;
+ old_bonds->select.bond_list[ top_old ].bo_data.BO =
+ new_bonds->select.bond_list[j].bo_data.BO;
+ top_old++;
+ }
+
+ Set_End_Index( i, top_old, old_bonds);
+ // fprintf( stderr, "--- s: %d, e: %d\n",
+ // Start_Index( i, old_bonds ), End_Index( i, old_bonds ) );
+ }
}
// ASSUMPTION: Bond lists are sorted
int Compare_Bond_Lists( int atom, control_params *control, list **lists )
{
- int oldp, newp;
- list *new_bonds = (*lists) + BONDS;
- list *old_bonds = (*lists) + OLD_BONDS;
-
- /*fprintf( stdout, "\n%d\nold_bonds:", atom );
- for( oldp = Start_Index( atom, old_bonds );
- oldp < End_Index( atom, old_bonds ); ++oldp )
- if( old_bonds->select.bond_list[oldp].bo_data.BO >= control->bg_cut )
- fprintf( stdout, "%5d", old_bonds->select.bond_list[oldp].nbr );
-
- fprintf( stdout, "\nnew_bonds:" );
- for( newp = Start_Index( atom, new_bonds );
- newp < End_Index( atom, new_bonds ); ++newp )
- if( new_bonds->select.bond_list[newp].bo_data.BO >= control->bg_cut )
- fprintf( stdout, "%5d", new_bonds->select.bond_list[newp].nbr );*/
-
-
- for( oldp = Start_Index( atom, old_bonds ),
- newp = Start_Index( atom, new_bonds );
- oldp < End_Index(atom, old_bonds) || newp < End_Index(atom, new_bonds);
- oldp = MIN( oldp + 1, End_Index( atom, old_bonds ) ),
- newp = MIN( newp + 1, End_Index( atom, new_bonds ) ) ) {
- while( oldp < End_Index( atom, old_bonds ) &&
- old_bonds->select.bond_list[oldp].bo_data.BO < control->bg_cut )
- ++oldp;
-
- while( newp < End_Index( atom, new_bonds ) &&
- new_bonds->select.bond_list[newp].bo_data.BO < control->bg_cut )
- ++newp;
-
- /*fprintf( fout, "%d, oldp: %d - %d, newp: %d - %d",
- atom, oldp, old_bonds->select.bond_list[oldp].nbr,
- newp, new_bonds->select.bond_list[newp].nbr );*/
-
- if( oldp < End_Index( atom, old_bonds ) ) {
- /* there are some other bonds in the old list */
- if( newp < End_Index( atom, new_bonds ) ) {
- if( old_bonds->select.bond_list[oldp].nbr !=
- new_bonds->select.bond_list[newp].nbr ) {
- //fprintf( fout, " --> case1, return 1\n" );
- return 1;
- }
- }
- else {
- /* there is no other bond in the new list */
- //fprintf( fout, " --> case2, return 1\n" );
- return 1;
- }
- }
- else {
- /* there are no more bonds in old_bond list */
- if( newp < End_Index( atom, new_bonds ) ) {
- /* there is at least one other bond in the new list */
- //fprintf( fout, " --> case 3, return 1\n" );
- return 1;
- }
- else {
- /* there is no other bond in the new list, either */
- //fprintf( fout, " --> case 4, return 0\n" );
- return 0;
- }
+ int oldp, newp;
+ list *new_bonds = (*lists) + BONDS;
+ list *old_bonds = (*lists) + OLD_BONDS;
+
+ /*fprintf( stdout, "\n%d\nold_bonds:", atom );
+ for( oldp = Start_Index( atom, old_bonds );
+ oldp < End_Index( atom, old_bonds ); ++oldp )
+ if( old_bonds->select.bond_list[oldp].bo_data.BO >= control->bg_cut )
+ fprintf( stdout, "%5d", old_bonds->select.bond_list[oldp].nbr );
+
+ fprintf( stdout, "\nnew_bonds:" );
+ for( newp = Start_Index( atom, new_bonds );
+ newp < End_Index( atom, new_bonds ); ++newp )
+ if( new_bonds->select.bond_list[newp].bo_data.BO >= control->bg_cut )
+ fprintf( stdout, "%5d", new_bonds->select.bond_list[newp].nbr );*/
+
+
+ for ( oldp = Start_Index( atom, old_bonds ),
+ newp = Start_Index( atom, new_bonds );
+ oldp < End_Index(atom, old_bonds) || newp < End_Index(atom, new_bonds);
+ oldp = MIN( oldp + 1, End_Index( atom, old_bonds ) ),
+ newp = MIN( newp + 1, End_Index( atom, new_bonds ) ) )
+ {
+ while ( oldp < End_Index( atom, old_bonds ) &&
+ old_bonds->select.bond_list[oldp].bo_data.BO < control->bg_cut )
+ ++oldp;
+
+ while ( newp < End_Index( atom, new_bonds ) &&
+ new_bonds->select.bond_list[newp].bo_data.BO < control->bg_cut )
+ ++newp;
+
+ /*fprintf( fout, "%d, oldp: %d - %d, newp: %d - %d",
+ atom, oldp, old_bonds->select.bond_list[oldp].nbr,
+ newp, new_bonds->select.bond_list[newp].nbr );*/
+
+ if ( oldp < End_Index( atom, old_bonds ) )
+ {
+ /* there are some other bonds in the old list */
+ if ( newp < End_Index( atom, new_bonds ) )
+ {
+ if ( old_bonds->select.bond_list[oldp].nbr !=
+ new_bonds->select.bond_list[newp].nbr )
+ {
+ //fprintf( fout, " --> case1, return 1\n" );
+ return 1;
+ }
+ }
+ else
+ {
+ /* there is no other bond in the new list */
+ //fprintf( fout, " --> case2, return 1\n" );
+ return 1;
+ }
+ }
+ else
+ {
+ /* there are no more bonds in old_bond list */
+ if ( newp < End_Index( atom, new_bonds ) )
+ {
+ /* there is at least one other bond in the new list */
+ //fprintf( fout, " --> case 3, return 1\n" );
+ return 1;
+ }
+ else
+ {
+ /* there is no other bond in the new list, either */
+ //fprintf( fout, " --> case 4, return 0\n" );
+ return 0;
+ }
+ }
}
- }
-
- return 0;
+
+ return 0;
}
-void Get_Molecule( int atom, molecule *m, int *mark, reax_system *system,
- control_params *control, list *bonds, int print,
- FILE *fout )
+void Get_Molecule( int atom, molecule *m, int *mark, reax_system *system,
+ control_params *control, list *bonds, int print,
+ FILE *fout )
{
- int i, start, end;
-
- start = Start_Index( atom, bonds );
- end = End_Index( atom, bonds );
-
- if( print )
- fprintf( fout, "%5d(%2s)",
- atom+1, system->reaxprm.sbp[ system->atoms[atom].type ].name );
- mark[atom] = 1;
- m->atom_list[ m->atom_count++ ] = atom;
- m->mtypes[ system->atoms[ atom ].type ]++;
-
- for( i = start; i < end; ++i )
- if( bonds->select.bond_list[i].bo_data.BO >= control->bg_cut &&
- !mark[bonds->select.bond_list[i].nbr] )
- Get_Molecule( bonds->select.bond_list[i].nbr, m, mark,
- system, control, bonds, print, fout );
+ int i, start, end;
+
+ start = Start_Index( atom, bonds );
+ end = End_Index( atom, bonds );
+
+ if ( print )
+ fprintf( fout, "%5d(%2s)",
+ atom + 1, system->reaxprm.sbp[ system->atoms[atom].type ].name );
+ mark[atom] = 1;
+ m->atom_list[ m->atom_count++ ] = atom;
+ m->mtypes[ system->atoms[ atom ].type ]++;
+
+ for ( i = start; i < end; ++i )
+ if ( bonds->select.bond_list[i].bo_data.BO >= control->bg_cut &&
+ !mark[bonds->select.bond_list[i].nbr] )
+ Get_Molecule( bonds->select.bond_list[i].nbr, m, mark,
+ system, control, bonds, print, fout );
}
void Print_Molecule( reax_system *system, molecule *m, int mode, char *s )
{
- int j, atom;
+ int j, atom;
- s[0] = 0;
+ s[0] = 0;
- if( mode == 1 ) {
- /* print molecule summary */
- for( j = 0; j < MAX_ATOM_TYPES; ++j )
- if( m->mtypes[j] )
- sprintf( s, "%s%s%d", s, system->reaxprm.sbp[j].name, m->mtypes[j] );
+ if ( mode == 1 )
+ {
+ /* print molecule summary */
+ for ( j = 0; j < MAX_ATOM_TYPES; ++j )
+ if ( m->mtypes[j] )
+ sprintf( s, "%s%s%d", s, system->reaxprm.sbp[j].name, m->mtypes[j] );
}
- else if( mode == 2 ) {
- /* print molecule details */
- for( j = 0; j < m->atom_count; ++j ) {
- atom = m->atom_list[j];
- sprintf( s, "%s%s(%d)",
- s, system->reaxprm.sbp[ system->atoms[atom].type ].name, atom );
+ else if ( mode == 2 )
+ {
+ /* print molecule details */
+ for ( j = 0; j < m->atom_count; ++j )
+ {
+ atom = m->atom_list[j];
+ sprintf( s, "%s%s(%d)",
+ s, system->reaxprm.sbp[ system->atoms[atom].type ].name, atom );
+ }
}
- }
}
-void Analyze_Molecules( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, FILE *fout )
+void Analyze_Molecules( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, FILE *fout )
{
- int atom, i, j, k, l, flag;
- int *mark = workspace->mark;
- int *old_mark = workspace->old_mark;
- int num_old, num_new;
- char s[MAX_MOLECULE_SIZE * 10];
- list *new_bonds = (*lists) + BONDS;
- list *old_bonds = (*lists) + OLD_BONDS;
- molecule old_molecules[20], new_molecules[20];
-
- fprintf( fout, "molecular analysis @ %d\n", data->step );
- memset( mark, 0, system->N * sizeof(int) );
- memset( old_mark, 0, system->N * sizeof(int) );
-
- /* compare new molecules to old molecules */
- for( atom = 0; atom < system->N; ++atom )
- if( !mark[atom] ) {
- //fprintf( fout, "atom %d is being compared\n", atom );
- if( Compare_Bond_Lists( atom, control, lists ) ) {
- /* old & new lists are different, print the old and new molecules */
- num_old = num_new = 0;
- flag = 0;
- i = k = 0;
- memset( &old_molecules[0], 0, sizeof(molecule) *20 );
- memset( &new_molecules[0], 0, sizeof(molecule) *20 );
-
- fprintf( fout, "get_old_mol: " );
- Get_Molecule( atom, &old_molecules[num_old++], old_mark,
- system, control, old_bonds, 1, fout );
- fprintf( fout, "\nget_new_mol: " );
- Get_Molecule( atom, &new_molecules[num_new++], mark,
- system, control, new_bonds, 1, fout );
- fprintf( fout, "\n" );
-
- while( !flag ) {
- flag = 1;
-
- for( ; i < num_old; ++i )
- for( j = 0; j < old_molecules[i].atom_count; ++j )
- if( !mark[old_molecules[i].atom_list[j]] ) {
- fprintf( fout, "get_new_mol: " );
- Get_Molecule( old_molecules[i].atom_list[j],
- &new_molecules[num_new++],
- mark, system, control, new_bonds, 1, fout );
- fprintf( fout, "\n" );
- flag = 0;
- }
-
- for( ; k < num_new; ++k )
- for( l = 0; l < new_molecules[k].atom_count; ++l )
- if( !old_mark[new_molecules[k].atom_list[l]] ) {
- fprintf( fout, "get_old_mol: " );
- Get_Molecule( new_molecules[k].atom_list[l],
- &old_molecules[num_old++],
- old_mark, system, control, old_bonds, 1, fout );
- fprintf( fout, "\n" );
- flag = 0;
- }
- }
-
- fprintf( fout, "old molecules: " );
- for( i = 0; i < num_old; ++i ) {
- Print_Molecule( system, &old_molecules[i], 1, &s[0] );
- fprintf( fout, "%s\t", s );
- }
- fprintf( fout, "\n" );
-
- fprintf( fout, "new molecules: " );
- for( i = 0; i < num_new; ++i ) {
- Print_Molecule( system, &new_molecules[i], 1, &s[0] );
- fprintf( fout, "%s\t", s );
- }
- fprintf( fout, "\n" );
- }
- }
-
- Copy_Bond_List( system, control, lists );
-
- //free( mark );
- //free( old_mark );
-
- fprintf( fout, "\n" );
- fflush( fout );
+ int atom, i, j, k, l, flag;
+ int *mark = workspace->mark;
+ int *old_mark = workspace->old_mark;
+ int num_old, num_new;
+ char s[MAX_MOLECULE_SIZE * 10];
+ list *new_bonds = (*lists) + BONDS;
+ list *old_bonds = (*lists) + OLD_BONDS;
+ molecule old_molecules[20], new_molecules[20];
+
+ fprintf( fout, "molecular analysis @ %d\n", data->step );
+ memset( mark, 0, system->N * sizeof(int) );
+ memset( old_mark, 0, system->N * sizeof(int) );
+
+ /* compare new molecules to old molecules */
+ for ( atom = 0; atom < system->N; ++atom )
+ if ( !mark[atom] )
+ {
+ //fprintf( fout, "atom %d is being compared\n", atom );
+ if ( Compare_Bond_Lists( atom, control, lists ) )
+ {
+ /* old & new lists are different, print the old and new molecules */
+ num_old = num_new = 0;
+ flag = 0;
+ i = k = 0;
+ memset( &old_molecules[0], 0, sizeof(molecule) * 20 );
+ memset( &new_molecules[0], 0, sizeof(molecule) * 20 );
+
+ fprintf( fout, "get_old_mol: " );
+ Get_Molecule( atom, &old_molecules[num_old++], old_mark,
+ system, control, old_bonds, 1, fout );
+ fprintf( fout, "\nget_new_mol: " );
+ Get_Molecule( atom, &new_molecules[num_new++], mark,
+ system, control, new_bonds, 1, fout );
+ fprintf( fout, "\n" );
+
+ while ( !flag )
+ {
+ flag = 1;
+
+ for ( ; i < num_old; ++i )
+ for ( j = 0; j < old_molecules[i].atom_count; ++j )
+ if ( !mark[old_molecules[i].atom_list[j]] )
+ {
+ fprintf( fout, "get_new_mol: " );
+ Get_Molecule( old_molecules[i].atom_list[j],
+ &new_molecules[num_new++],
+ mark, system, control, new_bonds, 1, fout );
+ fprintf( fout, "\n" );
+ flag = 0;
+ }
+
+ for ( ; k < num_new; ++k )
+ for ( l = 0; l < new_molecules[k].atom_count; ++l )
+ if ( !old_mark[new_molecules[k].atom_list[l]] )
+ {
+ fprintf( fout, "get_old_mol: " );
+ Get_Molecule( new_molecules[k].atom_list[l],
+ &old_molecules[num_old++],
+ old_mark, system, control, old_bonds, 1, fout );
+ fprintf( fout, "\n" );
+ flag = 0;
+ }
+ }
+
+ fprintf( fout, "old molecules: " );
+ for ( i = 0; i < num_old; ++i )
+ {
+ Print_Molecule( system, &old_molecules[i], 1, &s[0] );
+ fprintf( fout, "%s\t", s );
+ }
+ fprintf( fout, "\n" );
+
+ fprintf( fout, "new molecules: " );
+ for ( i = 0; i < num_new; ++i )
+ {
+ Print_Molecule( system, &new_molecules[i], 1, &s[0] );
+ fprintf( fout, "%s\t", s );
+ }
+ fprintf( fout, "\n" );
+ }
+ }
+
+ Copy_Bond_List( system, control, lists );
+
+ //free( mark );
+ //free( old_mark );
+
+ fprintf( fout, "\n" );
+ fflush( fout );
}
-void Report_Bond_Change( reax_system *system, control_params *control,
- static_storage *workspace, list *old_bonds,
- list *new_bonds, int a1, int a2, int flag,
- FILE *fout )
+void Report_Bond_Change( reax_system *system, control_params *control,
+ static_storage *workspace, list *old_bonds,
+ list *new_bonds, int a1, int a2, int flag,
+ FILE *fout )
{
- int i;
- int rev1, rev2;
- int mol1 = -1, mol2 = -1;
- // which molecule the atom belongs to, 0: Silica, 1: Water
-
- rev1 = workspace->orig_id[a1];
- rev2 = workspace->orig_id[a2];
-
- if( !strcmp( system->atoms[a1].name, " Si" ) ||
- !strcmp( system->atoms[a1].name, " O" ) )
- mol1 = 0;
- else mol1 = 1;
-
- if( !strcmp( system->atoms[a2].name, " Si" ) ||
- !strcmp( system->atoms[a2].name, " O" ) )
- mol2 = 0;
- else mol2 = 1;
-
-
- if( mol1 == 0 && mol2 == 0 ) { // silica-silica
- if( flag )
- fprintf( fout, "silica bond formation:" );
- else fprintf( fout, "silica bond breakage :" );
-
- fprintf( fout, "%5d(%s)-%5d(%s)\n",
- rev1, system->atoms[a1].name, rev2, system->atoms[a2].name );
- }
- else if( mol1 == 1 && mol2 == 1 ) { // water-water
- if( flag )
- fprintf( fout, "water bond formation:" );
- else fprintf( fout, "water bond breakage :" );
-
- fprintf( fout, "%5d(%s)-%5d(%s)\n",
- rev1, system->atoms[a1].name, rev2, system->atoms[a2].name );
- }
- else { // water-silica!
- if( flag )
- fprintf( fout, "SILICA-WATER bond formation:" );
- else fprintf( fout, "SILICA-WATER bond breakage :" );
-
- fprintf( fout, "%5d(%s)-%5d(%s)\n",
- rev1, system->atoms[a1].name, rev2, system->atoms[a2].name );
-
- fprintf( fout, "%5d(%s) was connected to:", rev1, system->atoms[a1].name );
- for( i = Start_Index(a1, old_bonds); i < End_Index(a1, old_bonds); ++i )
- if( old_bonds->select.bond_list[i].bo_data.BO >= control->bg_cut )
- fprintf( fout, " %5d(%s)",
- workspace->orig_id[ old_bonds->select.bond_list[i].nbr ],
- system->atoms[ old_bonds->select.bond_list[i].nbr ].name );
- fprintf( fout, "\n" );
-
- fprintf( fout, "%5d(%s) was connected to:", rev2, system->atoms[a2].name );
- for( i = Start_Index(a2, old_bonds); i < End_Index(a2, old_bonds); ++i )
- if( old_bonds->select.bond_list[i].bo_data.BO >= control->bg_cut )
- fprintf( fout, " %5d(%s)",
- workspace->orig_id[ old_bonds->select.bond_list[i].nbr ],
- system->atoms[ old_bonds->select.bond_list[i].nbr ].name );
- fprintf( fout, "\n" );
- }
+ int i;
+ int rev1, rev2;
+ int mol1 = -1, mol2 = -1;
+ // which molecule the atom belongs to, 0: Silica, 1: Water
+
+ rev1 = workspace->orig_id[a1];
+ rev2 = workspace->orig_id[a2];
+
+ if ( !strcmp( system->atoms[a1].name, " Si" ) ||
+ !strcmp( system->atoms[a1].name, " O" ) )
+ mol1 = 0;
+ else mol1 = 1;
+
+ if ( !strcmp( system->atoms[a2].name, " Si" ) ||
+ !strcmp( system->atoms[a2].name, " O" ) )
+ mol2 = 0;
+ else mol2 = 1;
+
+
+ if ( mol1 == 0 && mol2 == 0 ) // silica-silica
+ {
+ if ( flag )
+ fprintf( fout, "silica bond formation:" );
+ else fprintf( fout, "silica bond breakage :" );
+
+ fprintf( fout, "%5d(%s)-%5d(%s)\n",
+ rev1, system->atoms[a1].name, rev2, system->atoms[a2].name );
+ }
+ else if ( mol1 == 1 && mol2 == 1 ) // water-water
+ {
+ if ( flag )
+ fprintf( fout, "water bond formation:" );
+ else fprintf( fout, "water bond breakage :" );
+
+ fprintf( fout, "%5d(%s)-%5d(%s)\n",
+ rev1, system->atoms[a1].name, rev2, system->atoms[a2].name );
+ }
+ else // water-silica!
+ {
+ if ( flag )
+ fprintf( fout, "SILICA-WATER bond formation:" );
+ else fprintf( fout, "SILICA-WATER bond breakage :" );
+
+ fprintf( fout, "%5d(%s)-%5d(%s)\n",
+ rev1, system->atoms[a1].name, rev2, system->atoms[a2].name );
+
+ fprintf( fout, "%5d(%s) was connected to:", rev1, system->atoms[a1].name );
+ for ( i = Start_Index(a1, old_bonds); i < End_Index(a1, old_bonds); ++i )
+ if ( old_bonds->select.bond_list[i].bo_data.BO >= control->bg_cut )
+ fprintf( fout, " %5d(%s)",
+ workspace->orig_id[ old_bonds->select.bond_list[i].nbr ],
+ system->atoms[ old_bonds->select.bond_list[i].nbr ].name );
+ fprintf( fout, "\n" );
+
+ fprintf( fout, "%5d(%s) was connected to:", rev2, system->atoms[a2].name );
+ for ( i = Start_Index(a2, old_bonds); i < End_Index(a2, old_bonds); ++i )
+ if ( old_bonds->select.bond_list[i].bo_data.BO >= control->bg_cut )
+ fprintf( fout, " %5d(%s)",
+ workspace->orig_id[ old_bonds->select.bond_list[i].nbr ],
+ system->atoms[ old_bonds->select.bond_list[i].nbr ].name );
+ fprintf( fout, "\n" );
+ }
}
/* ASSUMPTION: Bond lists are sorted */
-void Compare_Bonding( int atom, reax_system *system, control_params *control,
- static_storage *workspace, list *old_bonds,
- list *new_bonds, FILE *fout )
+void Compare_Bonding( int atom, reax_system *system, control_params *control,
+ static_storage *workspace, list *old_bonds,
+ list *new_bonds, FILE *fout )
{
- int oldp, newp;
-
- /* fprintf( fout, "\n%d\nold_bonds:", atom );
- for( oldp = Start_Index( atom, old_bonds );
- oldp < End_Index( atom, old_bonds ); ++oldp )
- if( old_bonds->select.bond_list[oldp].bo_data.BO >= control->bg_cut )
- fprintf( fout, "%5d", old_bonds->select.bond_list[oldp].nbr );
-
- fprintf( fout, "\nnew_bonds:" );
- for( newp = Start_Index( atom, new_bonds );
- newp < End_Index( atom, new_bonds ); ++newp )
- if( new_bonds->select.bond_list[newp].bo_data.BO >= control->bg_cut )
- fprintf( fout, "%6d", new_bonds->select.bond_list[newp].nbr );
- fprintf( fout, "\n" ); */
-
- for( oldp = Start_Index( atom, old_bonds );
- oldp < End_Index( atom, old_bonds ) &&
- old_bonds->select.bond_list[oldp].nbr < atom;
- ++oldp );
-
- for( newp = Start_Index( atom, new_bonds );
- newp < End_Index( atom, new_bonds ) &&
- new_bonds->select.bond_list[newp].nbr < atom;
- ++newp );
-
- while( oldp < End_Index( atom, old_bonds ) ||
- newp < End_Index( atom, new_bonds ) ) {
- while( oldp < End_Index( atom, old_bonds ) &&
- old_bonds->select.bond_list[oldp].bo_data.BO < control->bg_cut )
- ++oldp;
-
- while( newp < End_Index( atom, new_bonds ) &&
- new_bonds->select.bond_list[newp].bo_data.BO < control->bg_cut )
- ++newp;
-
- /*fprintf( fout, "%d, oldp: %d - %d: %f newp: %d - %d: %f",
- atom, oldp, old_bonds->select.bond_list[oldp].nbr,
- old_bonds->select.bond_list[oldp].bo_data.BO,
- newp, new_bonds->select.bond_list[newp].nbr,
- new_bonds->select.bond_list[newp].bo_data.BO ); */
-
- if( oldp < End_Index( atom, old_bonds ) ) {
- /* there are some more bonds in the old list */
- if( newp < End_Index( atom, new_bonds ) ) {
- if( old_bonds->select.bond_list[oldp].nbr <
- new_bonds->select.bond_list[newp].nbr ) {
- // fprintf( fout, "%5d-%5d bond broken\n",
- // atom, old_bonds->select.bond_list[oldp].nbr );
- Report_Bond_Change( system, control, workspace, old_bonds, new_bonds,
- atom, old_bonds->select.bond_list[oldp].nbr, 0,
- fout );
- ++oldp;
- }
- else if( old_bonds->select.bond_list[oldp].nbr >
- new_bonds->select.bond_list[newp].nbr ) {
- // fprintf( fout, "%5d-%5d bond formed\n",
- // atom, new_bonds->select.bond_list[newp].nbr );
- Report_Bond_Change( system, control, workspace, old_bonds, new_bonds,
- atom, new_bonds->select.bond_list[newp].nbr, 1,
- fout );
- ++newp;
- }
- else
- ++newp, ++oldp;
- }
- else
- /* there is no other bond in the new list */
- while( oldp < End_Index( atom, old_bonds ) ) {
- if( old_bonds->select.bond_list[oldp].bo_data.BO>=control->bg_cut ) {
- // fprintf( fout, "%5d-%5d bond broken\n",
- // atom, old_bonds->select.bond_list[oldp].nbr );
- Report_Bond_Change( system, control, workspace,
- old_bonds, new_bonds, atom,
- old_bonds->select.bond_list[oldp].nbr, 0,
- fout );
- }
- ++oldp;
- }
- }
- else {
- /* there are no more bonds in old_bond list */
- if( newp < End_Index( atom, new_bonds ) )
- /* there is at least one other bond in the new list */
- while( newp < End_Index( atom, new_bonds ) ) {
- if( new_bonds->select.bond_list[newp].bo_data.BO>=control->bg_cut ){
- // fprintf( fout, "%5d-%5d bond formed\n",
- // atom, new_bonds->select.bond_list[newp].nbr );
- Report_Bond_Change( system, control, workspace,
- old_bonds, new_bonds, atom,
- new_bonds->select.bond_list[newp].nbr, 1,
- fout );
- }
- ++newp;
- }
- else {
- /* there is no other bond in the new list, either --
- no need to do anything */
- }
+ int oldp, newp;
+
+ /* fprintf( fout, "\n%d\nold_bonds:", atom );
+ for( oldp = Start_Index( atom, old_bonds );
+ oldp < End_Index( atom, old_bonds ); ++oldp )
+ if( old_bonds->select.bond_list[oldp].bo_data.BO >= control->bg_cut )
+ fprintf( fout, "%5d", old_bonds->select.bond_list[oldp].nbr );
+
+ fprintf( fout, "\nnew_bonds:" );
+ for( newp = Start_Index( atom, new_bonds );
+ newp < End_Index( atom, new_bonds ); ++newp )
+ if( new_bonds->select.bond_list[newp].bo_data.BO >= control->bg_cut )
+ fprintf( fout, "%6d", new_bonds->select.bond_list[newp].nbr );
+ fprintf( fout, "\n" ); */
+
+ for ( oldp = Start_Index( atom, old_bonds );
+ oldp < End_Index( atom, old_bonds ) &&
+ old_bonds->select.bond_list[oldp].nbr < atom;
+ ++oldp );
+
+ for ( newp = Start_Index( atom, new_bonds );
+ newp < End_Index( atom, new_bonds ) &&
+ new_bonds->select.bond_list[newp].nbr < atom;
+ ++newp );
+
+ while ( oldp < End_Index( atom, old_bonds ) ||
+ newp < End_Index( atom, new_bonds ) )
+ {
+ while ( oldp < End_Index( atom, old_bonds ) &&
+ old_bonds->select.bond_list[oldp].bo_data.BO < control->bg_cut )
+ ++oldp;
+
+ while ( newp < End_Index( atom, new_bonds ) &&
+ new_bonds->select.bond_list[newp].bo_data.BO < control->bg_cut )
+ ++newp;
+
+ /*fprintf( fout, "%d, oldp: %d - %d: %f newp: %d - %d: %f",
+ atom, oldp, old_bonds->select.bond_list[oldp].nbr,
+ old_bonds->select.bond_list[oldp].bo_data.BO,
+ newp, new_bonds->select.bond_list[newp].nbr,
+ new_bonds->select.bond_list[newp].bo_data.BO ); */
+
+ if ( oldp < End_Index( atom, old_bonds ) )
+ {
+ /* there are some more bonds in the old list */
+ if ( newp < End_Index( atom, new_bonds ) )
+ {
+ if ( old_bonds->select.bond_list[oldp].nbr <
+ new_bonds->select.bond_list[newp].nbr )
+ {
+ // fprintf( fout, "%5d-%5d bond broken\n",
+ // atom, old_bonds->select.bond_list[oldp].nbr );
+ Report_Bond_Change( system, control, workspace, old_bonds, new_bonds,
+ atom, old_bonds->select.bond_list[oldp].nbr, 0,
+ fout );
+ ++oldp;
+ }
+ else if ( old_bonds->select.bond_list[oldp].nbr >
+ new_bonds->select.bond_list[newp].nbr )
+ {
+ // fprintf( fout, "%5d-%5d bond formed\n",
+ // atom, new_bonds->select.bond_list[newp].nbr );
+ Report_Bond_Change( system, control, workspace, old_bonds, new_bonds,
+ atom, new_bonds->select.bond_list[newp].nbr, 1,
+ fout );
+ ++newp;
+ }
+ else
+ ++newp, ++oldp;
+ }
+ else
+ /* there is no other bond in the new list */
+ while ( oldp < End_Index( atom, old_bonds ) )
+ {
+ if ( old_bonds->select.bond_list[oldp].bo_data.BO >= control->bg_cut )
+ {
+ // fprintf( fout, "%5d-%5d bond broken\n",
+ // atom, old_bonds->select.bond_list[oldp].nbr );
+ Report_Bond_Change( system, control, workspace,
+ old_bonds, new_bonds, atom,
+ old_bonds->select.bond_list[oldp].nbr, 0,
+ fout );
+ }
+ ++oldp;
+ }
+ }
+ else
+ {
+ /* there are no more bonds in old_bond list */
+ if ( newp < End_Index( atom, new_bonds ) )
+ /* there is at least one other bond in the new list */
+ while ( newp < End_Index( atom, new_bonds ) )
+ {
+ if ( new_bonds->select.bond_list[newp].bo_data.BO >= control->bg_cut )
+ {
+ // fprintf( fout, "%5d-%5d bond formed\n",
+ // atom, new_bonds->select.bond_list[newp].nbr );
+ Report_Bond_Change( system, control, workspace,
+ old_bonds, new_bonds, atom,
+ new_bonds->select.bond_list[newp].nbr, 1,
+ fout );
+ }
+ ++newp;
+ }
+ else
+ {
+ /* there is no other bond in the new list, either --
+ no need to do anything */
+ }
+ }
}
- }
}
-void Visit_Bonds( int atom, int *mark, int *type, reax_system *system,
- control_params *control, list *bonds, int ignore )
+void Visit_Bonds( int atom, int *mark, int *type, reax_system *system,
+ control_params *control, list *bonds, int ignore )
{
- int i, t, start, end, nbr;
- real bo;
-
- mark[atom] = 1;
- t = system->atoms[atom].type;
- if( ignore && control->ignore[t] )
- return;
- type[t]++;
-
- start = Start_Index( atom, bonds );
- end = End_Index( atom, bonds );
- for( i = start; i < end; ++i ) {
- nbr = bonds->select.bond_list[i].nbr;
- bo = bonds->select.bond_list[i].bo_data.BO;
- if( bo >= control->bg_cut && !mark[nbr] )
- Visit_Bonds( nbr, mark, type, system, control, bonds, ignore );
- }
+ int i, t, start, end, nbr;
+ real bo;
+
+ mark[atom] = 1;
+ t = system->atoms[atom].type;
+ if ( ignore && control->ignore[t] )
+ return;
+ type[t]++;
+
+ start = Start_Index( atom, bonds );
+ end = End_Index( atom, bonds );
+ for ( i = start; i < end; ++i )
+ {
+ nbr = bonds->select.bond_list[i].nbr;
+ bo = bonds->select.bond_list[i].bo_data.BO;
+ if ( bo >= control->bg_cut && !mark[nbr] )
+ Visit_Bonds( nbr, mark, type, system, control, bonds, ignore );
+ }
}
-void Analyze_Fragments( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, FILE *fout, int ignore )
+void Analyze_Fragments( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, FILE *fout, int ignore )
{
- int atom, i, flag;
- int *mark = workspace->mark;
- int num_fragments, num_fragment_types;
- char fragment[MAX_ATOM_TYPES];
- char fragments[MAX_FRAGMENT_TYPES][MAX_ATOM_TYPES];
- int fragment_count[MAX_FRAGMENT_TYPES];
- molecule m;
- list *new_bonds = (*lists) + BONDS;
- //list *old_bonds = (*lists) + OLD_BONDS;
-
- /* fragment analysis */
- fprintf( fout, "step%d fragments\n", data->step );
- num_fragments = 0;
- num_fragment_types = 0;
- memset( mark, 0, system->N * sizeof(int) );
-
- for( atom = 0; atom < system->N; ++atom )
- if( !mark[atom] ) {
- /* discover a new fragment */
- memset( m.mtypes, 0, MAX_ATOM_TYPES * sizeof(int) );
- Visit_Bonds( atom, mark, m.mtypes, system, control, new_bonds, ignore );
- ++num_fragments;
- Print_Molecule( system, &m, 1, fragment );
-
- /* check if a similar fragment already exists */
- flag = 0;
- for( i = 0; i < num_fragment_types; ++i )
- if( !strcmp( fragments[i], fragment ) ) {
- ++fragment_count[i];
- flag = 1;
- break;
- }
-
- if( flag == 0 ) {
- /* it is a new one, add to the fragments list */
- strcpy( fragments[num_fragment_types], fragment );
- fragment_count[num_fragment_types] = 1;
- ++num_fragment_types;
- }
- }
-
- /* output the results of fragment analysis */
- for( i = 0; i < num_fragment_types; ++i )
- if( strlen(fragments[i]) )
- fprintf( fout, "%d of %s\n", fragment_count[i], fragments[i] );
- fprintf( fout, "\n" );
- fflush( fout );
-
- /* compare new bonds to old bonds */
- //for( atom = 0; atom < system->N; ++atom ) {
- // fprintf( fout, "atom: %d\n", atom ); fflush( fout );
- // Compare_Bonding( atom, system, control, workspace,
- // old_bonds, new_bonds, fout );
- //}
- //Copy_Bond_List( system, control, lists );
+ int atom, i, flag;
+ int *mark = workspace->mark;
+ int num_fragments, num_fragment_types;
+ char fragment[MAX_ATOM_TYPES];
+ char fragments[MAX_FRAGMENT_TYPES][MAX_ATOM_TYPES];
+ int fragment_count[MAX_FRAGMENT_TYPES];
+ molecule m;
+ list *new_bonds = (*lists) + BONDS;
+ //list *old_bonds = (*lists) + OLD_BONDS;
+
+ /* fragment analysis */
+ fprintf( fout, "step%d fragments\n", data->step );
+ num_fragments = 0;
+ num_fragment_types = 0;
+ memset( mark, 0, system->N * sizeof(int) );
+
+ for ( atom = 0; atom < system->N; ++atom )
+ if ( !mark[atom] )
+ {
+ /* discover a new fragment */
+ memset( m.mtypes, 0, MAX_ATOM_TYPES * sizeof(int) );
+ Visit_Bonds( atom, mark, m.mtypes, system, control, new_bonds, ignore );
+ ++num_fragments;
+ Print_Molecule( system, &m, 1, fragment );
+
+ /* check if a similar fragment already exists */
+ flag = 0;
+ for ( i = 0; i < num_fragment_types; ++i )
+ if ( !strcmp( fragments[i], fragment ) )
+ {
+ ++fragment_count[i];
+ flag = 1;
+ break;
+ }
+
+ if ( flag == 0 )
+ {
+ /* it is a new one, add to the fragments list */
+ strcpy( fragments[num_fragment_types], fragment );
+ fragment_count[num_fragment_types] = 1;
+ ++num_fragment_types;
+ }
+ }
+
+ /* output the results of fragment analysis */
+ for ( i = 0; i < num_fragment_types; ++i )
+ if ( strlen(fragments[i]) )
+ fprintf( fout, "%d of %s\n", fragment_count[i], fragments[i] );
+ fprintf( fout, "\n" );
+ fflush( fout );
+
+ /* compare new bonds to old bonds */
+ //for( atom = 0; atom < system->N; ++atom ) {
+ // fprintf( fout, "atom: %d\n", atom ); fflush( fout );
+ // Compare_Bonding( atom, system, control, workspace,
+ // old_bonds, new_bonds, fout );
+ //}
+ //Copy_Bond_List( system, control, lists );
}
-void Analyze_Silica( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, FILE *fout )
+void Analyze_Silica( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, FILE *fout )
{
- int atom, i, j, k, pi, pk, pk_j, newp, coord;
- int O_SI_O_count, SI_O_SI_count;
- int si_coord[10], ox_coord[10];
- real O_SI_O, SI_O_SI;
- list *new_bonds = (*lists) + BONDS;
- list *thb_intrs = (*lists) + THREE_BODIES;
-
- Analyze_Fragments( system, control, data, workspace, lists, fout, 0 );
-
- /* analyze atom coordinations */
- for( i = 0; i < 10; ++i )
- si_coord[i] = ox_coord[i] = 0;
-
- for( atom = 0; atom < system->N; ++atom ) {
- coord = 0;
-
- for( newp = Start_Index( atom, new_bonds );
- newp < End_Index( atom, new_bonds ); ++newp )
- if( new_bonds->select.bond_list[newp].bo_data.BO >= control->bg_cut )
- ++coord;
-
- if( system->atoms[ atom ].type == SI_ATOM ) {
- /*if( coord == 4 )
- full_coord_SI++;
- else less_coord_SI++;*/
- ++si_coord[coord];
- }
- else if( system->atoms[ atom ].type == O_ATOM ) {
- /*if( coord == 2 )
- full_coord_O++;
- else less_coord_O++;*/
- ++ox_coord[coord];
+ int atom, i, j, k, pi, pk, pk_j, newp, coord;
+ int O_SI_O_count, SI_O_SI_count;
+ int si_coord[10], ox_coord[10];
+ real O_SI_O, SI_O_SI;
+ list *new_bonds = (*lists) + BONDS;
+ list *thb_intrs = (*lists) + THREE_BODIES;
+
+ Analyze_Fragments( system, control, data, workspace, lists, fout, 0 );
+
+ /* analyze atom coordinations */
+ for ( i = 0; i < 10; ++i )
+ si_coord[i] = ox_coord[i] = 0;
+
+ for ( atom = 0; atom < system->N; ++atom )
+ {
+ coord = 0;
+
+ for ( newp = Start_Index( atom, new_bonds );
+ newp < End_Index( atom, new_bonds ); ++newp )
+ if ( new_bonds->select.bond_list[newp].bo_data.BO >= control->bg_cut )
+ ++coord;
+
+ if ( system->atoms[ atom ].type == SI_ATOM )
+ {
+ /*if( coord == 4 )
+ full_coord_SI++;
+ else less_coord_SI++;*/
+ ++si_coord[coord];
+ }
+ else if ( system->atoms[ atom ].type == O_ATOM )
+ {
+ /*if( coord == 2 )
+ full_coord_O++;
+ else less_coord_O++;*/
+ ++ox_coord[coord];
+ }
}
- }
-
- /* fprintf( fout, "\nFour Coordinated SI: %.2f%\n",
- (double)full_coord_SI / (full_coord_SI + less_coord_SI) * 100. );
- fprintf( fout, "Four Coordinated O : %.2f%\n",
- (double)full_coord_O / (full_coord_O + less_coord_O ) * 100. ); */
-
- fprintf( fout, "Silicon coordinations:\n" );
- for( i = 1; i < 10; ++i )
- if( si_coord[i] )
- fprintf( fout, "\t%d-coord: %d\n", i, si_coord[i] );
-
- fprintf( fout, "\nOxygen coordinations:\n" );
- for( i = 1; i < 10; ++i )
- if( ox_coord[i] )
- fprintf( fout, "\t%d-coord: %d\n", i, ox_coord[i] );
-
-
- /* analyze bond angles */
- O_SI_O = 0;
- O_SI_O_count = 0;
-
- SI_O_SI = 0;
- SI_O_SI_count = 0;
-
- for( j = 0; j < system->N; ++j )
- if( system->atoms[j].type == O_ATOM || system->atoms[j].type == SI_ATOM )
- for( pi = Start_Index(j, new_bonds); pi < End_Index(j, new_bonds); ++pi )
- if( new_bonds->select.bond_list[pi].bo_data.BO >= control->bg_cut ) {
- i = new_bonds->select.bond_list[pi].nbr;
-
- if(system->atoms[i].type==O_ATOM || system->atoms[i].type==SI_ATOM) {
- for( pk = Start_Index( pi, thb_intrs );
- pk < End_Index( pi, thb_intrs ); ++pk ) {
- k = thb_intrs->select.three_body_list[pk].thb;
- pk_j = thb_intrs->select.three_body_list[pk].pthb;
- // get k's pointer on j's bond list
-
- if( new_bonds->select.bond_list[pk_j].bo_data.BO >=
- control->bg_cut ) { // physical j&k bond
- /*fprintf( fout, "%5d(%d) %5d(%d) %5d(%d) %8.3f\n",
- i, system->atoms[i].type, j, system->atoms[j].type,
- k, system->atoms[k].type,
- thb_intrs->select.three_body_list[pk].theta );*/
-
- if( system->atoms[i].type == O_ATOM &&
- system->atoms[j].type == SI_ATOM &&
- system->atoms[k].type == O_ATOM ){
- O_SI_O_count++;
- O_SI_O += thb_intrs->select.three_body_list[pk].theta;
- }
- else if ( system->atoms[i].type == SI_ATOM &&
- system->atoms[j].type == O_ATOM &&
- system->atoms[k].type == SI_ATOM ){
- SI_O_SI_count++;
- SI_O_SI += thb_intrs->select.three_body_list[pk].theta;
- }
- }
- }
- }
- }
-
- fprintf( fout, "\nAverage O-Si-O angle: %8.2f\n",
- RAD2DEG(O_SI_O / O_SI_O_count) );
- fprintf( fout, "Average Si-O-Si angle: %8.2f\n\n\n",
- RAD2DEG(SI_O_SI / SI_O_SI_count) );
-
- fflush( fout );
+
+ /* fprintf( fout, "\nFour Coordinated SI: %.2f%\n",
+ (double)full_coord_SI / (full_coord_SI + less_coord_SI) * 100. );
+ fprintf( fout, "Four Coordinated O : %.2f%\n",
+ (double)full_coord_O / (full_coord_O + less_coord_O ) * 100. ); */
+
+ fprintf( fout, "Silicon coordinations:\n" );
+ for ( i = 1; i < 10; ++i )
+ if ( si_coord[i] )
+ fprintf( fout, "\t%d-coord: %d\n", i, si_coord[i] );
+
+ fprintf( fout, "\nOxygen coordinations:\n" );
+ for ( i = 1; i < 10; ++i )
+ if ( ox_coord[i] )
+ fprintf( fout, "\t%d-coord: %d\n", i, ox_coord[i] );
+
+
+ /* analyze bond angles */
+ O_SI_O = 0;
+ O_SI_O_count = 0;
+
+ SI_O_SI = 0;
+ SI_O_SI_count = 0;
+
+ for ( j = 0; j < system->N; ++j )
+ if ( system->atoms[j].type == O_ATOM || system->atoms[j].type == SI_ATOM )
+ for ( pi = Start_Index(j, new_bonds); pi < End_Index(j, new_bonds); ++pi )
+ if ( new_bonds->select.bond_list[pi].bo_data.BO >= control->bg_cut )
+ {
+ i = new_bonds->select.bond_list[pi].nbr;
+
+ if (system->atoms[i].type == O_ATOM || system->atoms[i].type == SI_ATOM)
+ {
+ for ( pk = Start_Index( pi, thb_intrs );
+ pk < End_Index( pi, thb_intrs ); ++pk )
+ {
+ k = thb_intrs->select.three_body_list[pk].thb;
+ pk_j = thb_intrs->select.three_body_list[pk].pthb;
+ // get k's pointer on j's bond list
+
+ if ( new_bonds->select.bond_list[pk_j].bo_data.BO >=
+ control->bg_cut ) // physical j&k bond
+ {
+ /*fprintf( fout, "%5d(%d) %5d(%d) %5d(%d) %8.3f\n",
+ i, system->atoms[i].type, j, system->atoms[j].type,
+ k, system->atoms[k].type,
+ thb_intrs->select.three_body_list[pk].theta );*/
+
+ if ( system->atoms[i].type == O_ATOM &&
+ system->atoms[j].type == SI_ATOM &&
+ system->atoms[k].type == O_ATOM )
+ {
+ O_SI_O_count++;
+ O_SI_O += thb_intrs->select.three_body_list[pk].theta;
+ }
+ else if ( system->atoms[i].type == SI_ATOM &&
+ system->atoms[j].type == O_ATOM &&
+ system->atoms[k].type == SI_ATOM )
+ {
+ SI_O_SI_count++;
+ SI_O_SI += thb_intrs->select.three_body_list[pk].theta;
+ }
+ }
+ }
+ }
+ }
+
+ fprintf( fout, "\nAverage O-Si-O angle: %8.2f\n",
+ RAD2DEG(O_SI_O / O_SI_O_count) );
+ fprintf( fout, "Average Si-O-Si angle: %8.2f\n\n\n",
+ RAD2DEG(SI_O_SI / SI_O_SI_count) );
+
+ fflush( fout );
}
int Get_Type_of_Molecule( molecule *m )
{
- if( m->atom_count == 3 && m->mtypes[1] == 2 && m->mtypes[2] == 1 )
- return WATER;
+ if ( m->atom_count == 3 && m->mtypes[1] == 2 && m->mtypes[2] == 1 )
+ return WATER;
- return UNKNOWN;
+ return UNKNOWN;
}
-void Calculate_Dipole_Moment( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list *bonds, FILE *fout )
+void Calculate_Dipole_Moment( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list *bonds, FILE *fout )
{
- int i, atom, count;
- molecule m;
- real mu_sum;
- rvec tmpvec, mu;
- int *mark = workspace->mark;
-
- //fprintf( fout, "starting dipole moment calculations...\n" );
-
- mu_sum = 0;
- count = 0;
-
- for( atom = 0; atom < system->N; ++atom )
- /* start discovering water molecules from the central O atom */
- if( !mark[atom] && system->atoms[atom].type == 2 ) {
- rvec_MakeZero( mu );
-
- memset( &m, 0, sizeof(molecule) );
- Get_Molecule( atom, &m, mark, system, control, bonds, 0, fout );
-
- if( Get_Type_of_Molecule( &m ) == WATER ) {
- ++count;
-
- for( i = 1; i < 2; ++i ) {
- Distance_on_T3_Gen( system->atoms[ m.atom_list[0] ].x,
- system->atoms[ m.atom_list[i] ].x,
- &(system->box), tmpvec );
- rvec_ScaledAdd( mu, -system->atoms[m.atom_list[0]].q / 2.0, tmpvec );
- }
-
- mu_sum += rvec_Norm( mu );
- }
- }
-
- fprintf( fout, "%7d %10d %10.5f\n",
- data->step, count, mu_sum / count * ECxA_to_DEBYE );
- fflush( fout );
+ int i, atom, count;
+ molecule m;
+ real mu_sum;
+ rvec tmpvec, mu;
+ int *mark = workspace->mark;
+
+ //fprintf( fout, "starting dipole moment calculations...\n" );
+
+ mu_sum = 0;
+ count = 0;
+
+ for ( atom = 0; atom < system->N; ++atom )
+ /* start discovering water molecules from the central O atom */
+ if ( !mark[atom] && system->atoms[atom].type == 2 )
+ {
+ rvec_MakeZero( mu );
+
+ memset( &m, 0, sizeof(molecule) );
+ Get_Molecule( atom, &m, mark, system, control, bonds, 0, fout );
+
+ if ( Get_Type_of_Molecule( &m ) == WATER )
+ {
+ ++count;
+
+ for ( i = 1; i < 2; ++i )
+ {
+ Distance_on_T3_Gen( system->atoms[ m.atom_list[0] ].x,
+ system->atoms[ m.atom_list[i] ].x,
+ &(system->box), tmpvec );
+ rvec_ScaledAdd( mu, -system->atoms[m.atom_list[0]].q / 2.0, tmpvec );
+ }
+
+ mu_sum += rvec_Norm( mu );
+ }
+ }
+
+ fprintf( fout, "%7d %10d %10.5f\n",
+ data->step, count, mu_sum / count * ECxA_to_DEBYE );
+ fflush( fout );
}
void Copy_Positions( reax_system *system, static_storage *workspace )
{
- int i;
-
- for( i = 0; i < system->N; ++i )
- rvec_Copy( workspace->x_old[i], system->atoms[i].x );
+ int i;
+
+ for ( i = 0; i < system->N; ++i )
+ rvec_Copy( workspace->x_old[i], system->atoms[i].x );
}
-void Calculate_Drift( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- FILE *fout )
+void Calculate_Drift( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ FILE *fout )
{
- int i, type;
- int count[MAX_ATOM_TYPES];
- real drift;
- rvec driftvec;
- real sum_sqr_drift[MAX_ATOM_TYPES], sum_drift[MAX_ATOM_TYPES];
+ int i, type;
+ int count[MAX_ATOM_TYPES];
+ real drift;
+ rvec driftvec;
+ real sum_sqr_drift[MAX_ATOM_TYPES], sum_drift[MAX_ATOM_TYPES];
- for( i = 0; i < MAX_ATOM_TYPES; ++i )
+ for ( i = 0; i < MAX_ATOM_TYPES; ++i )
{
- count[i] = 0;
- sum_sqr_drift[i] = sum_drift[i] = 0.0;
+ count[i] = 0;
+ sum_sqr_drift[i] = sum_drift[i] = 0.0;
}
- for( i = 0; i < system->N; ++i )
- //if( control->restrict_type == -1 ||
- // system->atoms[i].type == control->restrict_type )
- if( workspace->x_old[i][0] > -system->box.box_norms[0] &&
- workspace->x_old[i][1] > -system->box.box_norms[1] &&
- workspace->x_old[i][2] > -system->box.box_norms[2] )
- {
- type = system->atoms[i].type;
- ++count[type];
-
- Distance_on_T3_Gen( workspace->x_old[i], system->atoms[i].x,
- &(system->box), driftvec );
-
- if( fabs( driftvec[0] ) >= system->box.box_norms[0] / 2.0 - 2.0 ||
- fabs( driftvec[0] ) >= system->box.box_norms[0] / 2.0 - 2.0 ||
- fabs( driftvec[0] ) >= system->box.box_norms[0] / 2.0 - 2.0 ) {
- /* the atom has moved almost half the box size.
- exclude it from further drift computations as it might have an
- improper contribution due to periodic boudnaries. */
- workspace->x_old[i][0] = -999999999999.0;
- workspace->x_old[i][2] = -999999999999.0;
- workspace->x_old[i][2] = -999999999999.0;
- continue;
- }
-
- drift = rvec_Norm_Sqr( driftvec );
- sum_sqr_drift[type] += drift;
- sum_drift[type] += SQRT( drift );
- }
-
- fprintf( fout, "%7d oxy %6d %10.6f\n",
- data->step, count[2], sum_sqr_drift[2] / count[2] );
- fprintf( fout, "%7d hyd %6d %10.6f\n",
- data->step, count[1], sum_sqr_drift[1] / count[1] );
-
- fflush( fout );
+ for ( i = 0; i < system->N; ++i )
+ //if( control->restrict_type == -1 ||
+ // system->atoms[i].type == control->restrict_type )
+ if ( workspace->x_old[i][0] > -system->box.box_norms[0] &&
+ workspace->x_old[i][1] > -system->box.box_norms[1] &&
+ workspace->x_old[i][2] > -system->box.box_norms[2] )
+ {
+ type = system->atoms[i].type;
+ ++count[type];
+
+ Distance_on_T3_Gen( workspace->x_old[i], system->atoms[i].x,
+ &(system->box), driftvec );
+
+ if ( fabs( driftvec[0] ) >= system->box.box_norms[0] / 2.0 - 2.0 ||
+ fabs( driftvec[0] ) >= system->box.box_norms[0] / 2.0 - 2.0 ||
+ fabs( driftvec[0] ) >= system->box.box_norms[0] / 2.0 - 2.0 )
+ {
+ /* the atom has moved almost half the box size.
+ exclude it from further drift computations as it might have an
+ improper contribution due to periodic boudnaries. */
+ workspace->x_old[i][0] = -999999999999.0;
+ workspace->x_old[i][2] = -999999999999.0;
+ workspace->x_old[i][2] = -999999999999.0;
+ continue;
+ }
+
+ drift = rvec_Norm_Sqr( driftvec );
+ sum_sqr_drift[type] += drift;
+ sum_drift[type] += SQRT( drift );
+ }
+
+ fprintf( fout, "%7d oxy %6d %10.6f\n",
+ data->step, count[2], sum_sqr_drift[2] / count[2] );
+ fprintf( fout, "%7d hyd %6d %10.6f\n",
+ data->step, count[1], sum_sqr_drift[1] / count[1] );
+
+ fflush( fout );
}
-void Calculate_Density_3DMesh( reax_system *system, simulation_data *data,
- FILE *fout )
+void Calculate_Density_3DMesh( reax_system *system, simulation_data *data,
+ FILE *fout )
{
- int i, j, k;
- int occupied_cells;
- int ***cell_counter;
- ivec my_cell;
- rvec mesh_cell_lens = { 1, 1, 1 };
- ivec mesh_dims;
- real occupied_vol, density;
-
- /* determine the mesh dimensions based on the current box size */
- for( i = 0; i < 3; ++i )
- mesh_dims[i] = system->box.box_norms[i] / mesh_cell_lens[i] + 0.99;
-
- fprintf( stderr, "mesh_dims: %3d %3d %3d\n",
- mesh_dims[0], mesh_dims[1], mesh_dims[2] );
-
- /* allocate counter for each mesh cell */
- cell_counter = (int ***) calloc( mesh_dims[0], sizeof(int) );
-
- for( i = 0; i < mesh_dims[0]; ++i ) {
- cell_counter[i] = (int **) calloc( mesh_dims[1], sizeof(int) );
-
- for( j = 0; j < mesh_dims[1]; ++j )
- cell_counter[i][j] = (int *) calloc( mesh_dims[2], sizeof(int) );
- }
-
-
- /* go over the atoms and assign each into their corresponding mesh cell */
- for( i = 0; i < system->N; ++i ) {
- my_cell[0] = system->atoms[i].x[0] / mesh_cell_lens[0];
- my_cell[1] = system->atoms[i].x[1] / mesh_cell_lens[1];
- my_cell[2] = system->atoms[i].x[2] / mesh_cell_lens[2];
-
- cell_counter[ my_cell[0] ][ my_cell[1] ][ my_cell[2] ]++;
- }
-
-
- /* calculate volume occupied */
- occupied_cells = 0;
- for( i = 0; i < mesh_dims[0]; ++i )
- for( j = 0; j < mesh_dims[1]; ++j )
- for( k = 0; k < mesh_dims[2]; ++k )
- if( cell_counter[i][j][k] )
- ++occupied_cells;
-
- occupied_vol =
- occupied_cells * mesh_cell_lens[0] * mesh_cell_lens[1] * mesh_cell_lens[2];
-
- fprintf( stderr, "occupied cells: %8d\n", occupied_cells );
- fprintf( stderr, "occupied vol : %8.2f\n", occupied_vol );
- fprintf( stderr, "system volume : %8.2f\n", system->box.volume );
- fprintf( stderr, "system mass : %8.2f\n", data->M );
-
- density = data->M * AMU_to_GRAM / (occupied_vol * POW( ANG_to_CM, 3 ));
- fprintf( stderr, "density : %g\n", density );
- fprintf( stderr, "AMU_to_GRAM : %g\n", AMU_to_GRAM );
- fprintf( stderr, "ANG_to_CM : %g\n", ANG_to_CM );
+ int i, j, k;
+ int occupied_cells;
+ int ***cell_counter;
+ ivec my_cell;
+ rvec mesh_cell_lens = { 1, 1, 1 };
+ ivec mesh_dims;
+ real occupied_vol, density;
+
+ /* determine the mesh dimensions based on the current box size */
+ for ( i = 0; i < 3; ++i )
+ mesh_dims[i] = system->box.box_norms[i] / mesh_cell_lens[i] + 0.99;
+
+ fprintf( stderr, "mesh_dims: %3d %3d %3d\n",
+ mesh_dims[0], mesh_dims[1], mesh_dims[2] );
+
+ /* allocate counter for each mesh cell */
+ cell_counter = (int ***) calloc( mesh_dims[0], sizeof(int) );
+
+ for ( i = 0; i < mesh_dims[0]; ++i )
+ {
+ cell_counter[i] = (int **) calloc( mesh_dims[1], sizeof(int) );
+
+ for ( j = 0; j < mesh_dims[1]; ++j )
+ cell_counter[i][j] = (int *) calloc( mesh_dims[2], sizeof(int) );
+ }
+
+
+ /* go over the atoms and assign each into their corresponding mesh cell */
+ for ( i = 0; i < system->N; ++i )
+ {
+ my_cell[0] = system->atoms[i].x[0] / mesh_cell_lens[0];
+ my_cell[1] = system->atoms[i].x[1] / mesh_cell_lens[1];
+ my_cell[2] = system->atoms[i].x[2] / mesh_cell_lens[2];
+
+ cell_counter[ my_cell[0] ][ my_cell[1] ][ my_cell[2] ]++;
+ }
+
+
+ /* calculate volume occupied */
+ occupied_cells = 0;
+ for ( i = 0; i < mesh_dims[0]; ++i )
+ for ( j = 0; j < mesh_dims[1]; ++j )
+ for ( k = 0; k < mesh_dims[2]; ++k )
+ if ( cell_counter[i][j][k] )
+ ++occupied_cells;
+
+ occupied_vol =
+ occupied_cells * mesh_cell_lens[0] * mesh_cell_lens[1] * mesh_cell_lens[2];
+
+ fprintf( stderr, "occupied cells: %8d\n", occupied_cells );
+ fprintf( stderr, "occupied vol : %8.2f\n", occupied_vol );
+ fprintf( stderr, "system volume : %8.2f\n", system->box.volume );
+ fprintf( stderr, "system mass : %8.2f\n", data->M );
+
+ density = data->M * AMU_to_GRAM / (occupied_vol * POW( ANG_to_CM, 3 ));
+ fprintf( stderr, "density : %g\n", density );
+ fprintf( stderr, "AMU_to_GRAM : %g\n", AMU_to_GRAM );
+ fprintf( stderr, "ANG_to_CM : %g\n", ANG_to_CM );
}
-void Calculate_Density_Slice( reax_system *system, simulation_data *data,
- FILE *fout )
+void Calculate_Density_Slice( reax_system *system, simulation_data *data,
+ FILE *fout )
{
- real slice_thickness = 0.5;
- int *slice_occ;
- int i, num_slices, my_slice, max_occ = 0;
-
- /* allocate counter */
- num_slices = system->box.box_norms[2] / slice_thickness + 1.;
- slice_occ = (int*) calloc( num_slices, sizeof(int) );
-
- /* distribute atoms to slices */
- for( i = 0; i < system->N; ++i ) {
- my_slice = system->atoms[i].x[2] / slice_thickness;
- slice_occ[ my_slice ]++;
- }
-
- /* determine maximum occupancy */
- for( i = 0; i < num_slices; ++i ) {
- fprintf( stderr, "occ[%d]: %d\n", i, slice_occ[i] );
- if( slice_occ[i] > max_occ )
- max_occ = slice_occ[i];
- }
-
- /* find luzzatti-interface slice */
- for( i = 0; i < num_slices; ++i )
- if( (real)slice_occ[i] / max_occ > 0.5 ) {
- fprintf( stderr, "%d - %d is the luzzatti interface\n", i-1, i );
- break;
+ real slice_thickness = 0.5;
+ int *slice_occ;
+ int i, num_slices, my_slice, max_occ = 0;
+
+ /* allocate counter */
+ num_slices = system->box.box_norms[2] / slice_thickness + 1.;
+ slice_occ = (int*) calloc( num_slices, sizeof(int) );
+
+ /* distribute atoms to slices */
+ for ( i = 0; i < system->N; ++i )
+ {
+ my_slice = system->atoms[i].x[2] / slice_thickness;
+ slice_occ[ my_slice ]++;
+ }
+
+ /* determine maximum occupancy */
+ for ( i = 0; i < num_slices; ++i )
+ {
+ fprintf( stderr, "occ[%d]: %d\n", i, slice_occ[i] );
+ if ( slice_occ[i] > max_occ )
+ max_occ = slice_occ[i];
}
+
+ /* find luzzatti-interface slice */
+ for ( i = 0; i < num_slices; ++i )
+ if ( (real)slice_occ[i] / max_occ > 0.5 )
+ {
+ fprintf( stderr, "%d - %d is the luzzatti interface\n", i - 1, i );
+ break;
+ }
}
-void Analysis( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+void Analysis( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int steps;
-
- steps = data->step - data->prev_steps;
- // fprintf( stderr, "prev_steps: %d\n", data->prev_steps );
-
- if( steps == 1 ) {
- if( control->molec_anal == REACTIONS )
- Copy_Bond_List( system, control, lists );
- if( control->diffusion_coef )
- Copy_Positions( system, workspace );
- }
-
- /****** Molecular Analysis ******/
- if( control->molec_anal && steps%control->freq_molec_anal == 0 ) {
- if( control->molec_anal == FRAGMENTS ) {
- /* discover molecules */
- Analyze_Fragments( system, control, data, workspace, lists,
- out_control->mol, 0 );
- /* discover fragments without the ignored atoms */
- if( control->num_ignored )
- Analyze_Fragments( system, control, data, workspace, lists,
- out_control->ign, 1 );
+ int steps;
+
+ steps = data->step - data->prev_steps;
+ // fprintf( stderr, "prev_steps: %d\n", data->prev_steps );
+
+ if ( steps == 1 )
+ {
+ if ( control->molec_anal == REACTIONS )
+ Copy_Bond_List( system, control, lists );
+ if ( control->diffusion_coef )
+ Copy_Positions( system, workspace );
}
- else if( control->molec_anal == REACTIONS )
- /* discover molecular changes - reactions */
- Analyze_Molecules( system, control, data, workspace,
- lists, out_control->mol );
- }
-
- /****** Electric Dipole Moment ******/
- if( control->dipole_anal && steps%control->freq_dipole_anal == 0 )
- Calculate_Dipole_Moment( system, control, data, workspace,
- (*lists) + BONDS, out_control->dpl );
-
- /****** Drift ******/
- if( control->diffusion_coef && steps%control->freq_diffusion_coef == 0 )
- Calculate_Drift( system, control, data, workspace, out_control->drft );
+
+ /****** Molecular Analysis ******/
+ if ( control->molec_anal && steps % control->freq_molec_anal == 0 )
+ {
+ if ( control->molec_anal == FRAGMENTS )
+ {
+ /* discover molecules */
+ Analyze_Fragments( system, control, data, workspace, lists,
+ out_control->mol, 0 );
+ /* discover fragments without the ignored atoms */
+ if ( control->num_ignored )
+ Analyze_Fragments( system, control, data, workspace, lists,
+ out_control->ign, 1 );
+ }
+ else if ( control->molec_anal == REACTIONS )
+ /* discover molecular changes - reactions */
+ Analyze_Molecules( system, control, data, workspace,
+ lists, out_control->mol );
+ }
+
+ /****** Electric Dipole Moment ******/
+ if ( control->dipole_anal && steps % control->freq_dipole_anal == 0 )
+ Calculate_Dipole_Moment( system, control, data, workspace,
+ (*lists) + BONDS, out_control->dpl );
+
+ /****** Drift ******/
+ if ( control->diffusion_coef && steps % control->freq_diffusion_coef == 0 )
+ Calculate_Drift( system, control, data, workspace, out_control->drft );
#if defined(DEBUG)
- fprintf( stderr, "analysis... done\n" );
+ fprintf( stderr, "analysis... done\n" );
#endif
}
diff --git a/puremd_rc_1003/sPuReMD/analyze.h b/puremd_rc_1003/sPuReMD/analyze.h
index 01c193ad69ee9d469fe47c9015b136e5351966e3..e296e57a5871f0bca3c379a281673cd5e1f10cc3 100644
--- a/puremd_rc_1003/sPuReMD/analyze.h
+++ b/puremd_rc_1003/sPuReMD/analyze.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -24,18 +24,18 @@
#include "mytypes.h"
-void Analysis( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+void Analysis( reax_system*, control_params*, simulation_data*,
+ static_storage*, list**, output_controls* );
//void Copy_Bond_List( reax_system*, control_params*, list** );
-//void Analyze_Molecules( reax_system*, control_params*, simulation_data*,
+//void Analyze_Molecules( reax_system*, control_params*, simulation_data*,
// static_storage*, list**, FILE* );
-//void Analyze_Bonding( reax_system*, control_params*, simulation_data*,
+//void Analyze_Bonding( reax_system*, control_params*, simulation_data*,
// static_storage*, list**, FILE* );
-//void Analyze_Silica( reax_system*, control_params*, simulation_data*,
+//void Analyze_Silica( reax_system*, control_params*, simulation_data*,
// static_storage*, list**, FILE* );
//void Calculate_Dipole_Moment( reax_system*, control_params*, simulation_data*,
@@ -43,7 +43,7 @@ void Analysis( reax_system*, control_params*, simulation_data*,
//void Copy_Positions( reax_system*, static_storage* );
-//void Calculate_Drift( reax_system*, control_params*,
+//void Calculate_Drift( reax_system*, control_params*,
// simulation_data*, static_storage*, FILE* );
//void Calculate_Density_3DMesh( reax_system*, simulation_data*, FILE* );
diff --git a/puremd_rc_1003/sPuReMD/bond_orders.c b/puremd_rc_1003/sPuReMD/bond_orders.c
index 718659dab7082ea391f5be37e0c44724a2aa2c07..348184680ac82d13a2531753c1c4d1c26049f393 100644
--- a/puremd_rc_1003/sPuReMD/bond_orders.c
+++ b/puremd_rc_1003/sPuReMD/bond_orders.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -28,606 +28,619 @@
inline real Cf45( real p1, real p2 )
{
- return -EXP(-p2 / 2) /
- ( SQR( EXP(-p1 / 2) + EXP(p1 / 2) ) * (EXP(-p2 / 2) + EXP(p2 / 2)) );
+ return -EXP(-p2 / 2) /
+ ( SQR( EXP(-p1 / 2) + EXP(p1 / 2) ) * (EXP(-p2 / 2) + EXP(p2 / 2)) );
}
#ifdef TEST_FORCES
-void Get_dBO( reax_system *system, list **lists,
- int i, int pj, real C, rvec *v )
+void Get_dBO( reax_system *system, list **lists,
+ int i, int pj, real C, rvec *v )
{
- list *bonds = (*lists) + BONDS;
- list *dBOs = (*lists) + DBO;
- int start_pj, end_pj, k;
-
- pj = bonds->select.bond_list[pj].dbond_index;
- start_pj = Start_Index(pj, dBOs);
- end_pj = End_Index(pj, dBOs);
-
- for( k = start_pj; k < end_pj; ++k )
- rvec_Scale( v[dBOs->select.dbo_list[k].wrt],
- C, dBOs->select.dbo_list[k].dBO );
+ list *bonds = (*lists) + BONDS;
+ list *dBOs = (*lists) + DBO;
+ int start_pj, end_pj, k;
+
+ pj = bonds->select.bond_list[pj].dbond_index;
+ start_pj = Start_Index(pj, dBOs);
+ end_pj = End_Index(pj, dBOs);
+
+ for ( k = start_pj; k < end_pj; ++k )
+ rvec_Scale( v[dBOs->select.dbo_list[k].wrt],
+ C, dBOs->select.dbo_list[k].dBO );
}
-void Get_dBOpinpi2( reax_system *system, list **lists,
- int i, int pj, real Cpi, real Cpi2, rvec *vpi, rvec *vpi2 )
+void Get_dBOpinpi2( reax_system *system, list **lists,
+ int i, int pj, real Cpi, real Cpi2, rvec *vpi, rvec *vpi2 )
{
- list *bonds = (*lists) + BONDS;
- list *dBOs = (*lists) + DBO;
- dbond_data *dbo_k;
- int start_pj, end_pj, k;
-
- pj = bonds->select.bond_list[pj].dbond_index;
- start_pj = Start_Index(pj, dBOs);
- end_pj = End_Index(pj, dBOs);
-
- for( k = start_pj; k < end_pj; ++k ) {
- dbo_k = &(dBOs->select.dbo_list[k]);
- rvec_Scale( vpi[dbo_k->wrt], Cpi, dbo_k->dBOpi );
- rvec_Scale( vpi2[dbo_k->wrt], Cpi2, dbo_k->dBOpi2 );
- }
+ list *bonds = (*lists) + BONDS;
+ list *dBOs = (*lists) + DBO;
+ dbond_data *dbo_k;
+ int start_pj, end_pj, k;
+
+ pj = bonds->select.bond_list[pj].dbond_index;
+ start_pj = Start_Index(pj, dBOs);
+ end_pj = End_Index(pj, dBOs);
+
+ for ( k = start_pj; k < end_pj; ++k )
+ {
+ dbo_k = &(dBOs->select.dbo_list[k]);
+ rvec_Scale( vpi[dbo_k->wrt], Cpi, dbo_k->dBOpi );
+ rvec_Scale( vpi2[dbo_k->wrt], Cpi2, dbo_k->dBOpi2 );
+ }
}
-void Add_dBO( reax_system *system, list **lists,
- int i, int pj, real C, rvec *v )
+void Add_dBO( reax_system *system, list **lists,
+ int i, int pj, real C, rvec *v )
{
- list *bonds = (*lists) + BONDS;
- list *dBOs = (*lists) + DBO;
- int start_pj, end_pj, k;
+ list *bonds = (*lists) + BONDS;
+ list *dBOs = (*lists) + DBO;
+ int start_pj, end_pj, k;
- pj = bonds->select.bond_list[pj].dbond_index;
- start_pj = Start_Index(pj, dBOs);
- end_pj = End_Index(pj, dBOs);
-
- //fprintf( stderr, "i=%d j=%d start=%d end=%d\n", i, pj, start_pj, end_pj );
+ pj = bonds->select.bond_list[pj].dbond_index;
+ start_pj = Start_Index(pj, dBOs);
+ end_pj = End_Index(pj, dBOs);
- for( k = start_pj; k < end_pj; ++k )
- rvec_ScaledAdd( v[dBOs->select.dbo_list[k].wrt],
- C, dBOs->select.dbo_list[k].dBO );
+ //fprintf( stderr, "i=%d j=%d start=%d end=%d\n", i, pj, start_pj, end_pj );
+
+ for ( k = start_pj; k < end_pj; ++k )
+ rvec_ScaledAdd( v[dBOs->select.dbo_list[k].wrt],
+ C, dBOs->select.dbo_list[k].dBO );
}
-void Add_dBOpinpi2( reax_system *system, list **lists,
- int i, int pj, real Cpi, real Cpi2, rvec *vpi, rvec *vpi2 )
+void Add_dBOpinpi2( reax_system *system, list **lists,
+ int i, int pj, real Cpi, real Cpi2, rvec *vpi, rvec *vpi2 )
{
- list *bonds = (*lists) + BONDS;
- list *dBOs = (*lists) + DBO;
- dbond_data *dbo_k;
- int start_pj, end_pj, k;
+ list *bonds = (*lists) + BONDS;
+ list *dBOs = (*lists) + DBO;
+ dbond_data *dbo_k;
+ int start_pj, end_pj, k;
- pj = bonds->select.bond_list[pj].dbond_index;
- start_pj = Start_Index(pj, dBOs);
- end_pj = End_Index(pj, dBOs);
+ pj = bonds->select.bond_list[pj].dbond_index;
+ start_pj = Start_Index(pj, dBOs);
+ end_pj = End_Index(pj, dBOs);
- for( k = start_pj; k < end_pj; ++k )
+ for ( k = start_pj; k < end_pj; ++k )
{
- dbo_k = &(dBOs->select.dbo_list[k]);
- rvec_ScaledAdd( vpi[dbo_k->wrt], Cpi, dbo_k->dBOpi );
- rvec_ScaledAdd( vpi2[dbo_k->wrt], Cpi2, dbo_k->dBOpi2 );
+ dbo_k = &(dBOs->select.dbo_list[k]);
+ rvec_ScaledAdd( vpi[dbo_k->wrt], Cpi, dbo_k->dBOpi );
+ rvec_ScaledAdd( vpi2[dbo_k->wrt], Cpi2, dbo_k->dBOpi2 );
}
}
-void Add_dBO_to_Forces( reax_system *system, list **lists,
- int i, int pj, real C )
+void Add_dBO_to_Forces( reax_system *system, list **lists,
+ int i, int pj, real C )
{
- list *bonds = (*lists) + BONDS;
- list *dBOs = (*lists) + DBO;
- int start_pj, end_pj, k;
+ list *bonds = (*lists) + BONDS;
+ list *dBOs = (*lists) + DBO;
+ int start_pj, end_pj, k;
- pj = bonds->select.bond_list[pj].dbond_index;
- start_pj = Start_Index(pj, dBOs);
- end_pj = End_Index(pj, dBOs);
+ pj = bonds->select.bond_list[pj].dbond_index;
+ start_pj = Start_Index(pj, dBOs);
+ end_pj = End_Index(pj, dBOs);
- for( k = start_pj; k < end_pj; ++k )
- rvec_ScaledAdd( system->atoms[dBOs->select.dbo_list[k].wrt].f,
- C, dBOs->select.dbo_list[k].dBO );
+ for ( k = start_pj; k < end_pj; ++k )
+ rvec_ScaledAdd( system->atoms[dBOs->select.dbo_list[k].wrt].f,
+ C, dBOs->select.dbo_list[k].dBO );
}
-void Add_dBOpinpi2_to_Forces( reax_system *system, list **lists,
- int i, int pj, real Cpi, real Cpi2 )
+void Add_dBOpinpi2_to_Forces( reax_system *system, list **lists,
+ int i, int pj, real Cpi, real Cpi2 )
{
- list *bonds = (*lists) + BONDS;
- list *dBOs = (*lists) + DBO;
- dbond_data *dbo_k;
- int start_pj, end_pj, k;
+ list *bonds = (*lists) + BONDS;
+ list *dBOs = (*lists) + DBO;
+ dbond_data *dbo_k;
+ int start_pj, end_pj, k;
- pj = bonds->select.bond_list[pj].dbond_index;
- start_pj = Start_Index(pj, dBOs);
- end_pj = End_Index(pj, dBOs);
+ pj = bonds->select.bond_list[pj].dbond_index;
+ start_pj = Start_Index(pj, dBOs);
+ end_pj = End_Index(pj, dBOs);
- for( k = start_pj; k < end_pj; ++k )
+ for ( k = start_pj; k < end_pj; ++k )
{
- dbo_k = &(dBOs->select.dbo_list[k]);
- rvec_ScaledAdd( system->atoms[dbo_k->wrt].f, Cpi, dbo_k->dBOpi );
- rvec_ScaledAdd( system->atoms[dbo_k->wrt].f, Cpi2, dbo_k->dBOpi2 );
+ dbo_k = &(dBOs->select.dbo_list[k]);
+ rvec_ScaledAdd( system->atoms[dbo_k->wrt].f, Cpi, dbo_k->dBOpi );
+ rvec_ScaledAdd( system->atoms[dbo_k->wrt].f, Cpi2, dbo_k->dBOpi2 );
}
}
void Add_dDelta( reax_system *system, list **lists, int i, real C, rvec *v )
{
- list *dDeltas = &((*lists)[DDELTA]);
- int start = Start_Index(i, dDeltas);
- int end = End_Index(i, dDeltas);
- int k;
-
- for( k = start; k < end; ++k )
- rvec_ScaledAdd( v[dDeltas->select.dDelta_list[k].wrt],
- C, dDeltas->select.dDelta_list[k].dVal );
+ list *dDeltas = &((*lists)[DDELTA]);
+ int start = Start_Index(i, dDeltas);
+ int end = End_Index(i, dDeltas);
+ int k;
+
+ for ( k = start; k < end; ++k )
+ rvec_ScaledAdd( v[dDeltas->select.dDelta_list[k].wrt],
+ C, dDeltas->select.dDelta_list[k].dVal );
}
void Add_dDelta_to_Forces( reax_system *system, list **lists, int i, real C )
{
- list *dDeltas = &((*lists)[DDELTA]);
- int start = Start_Index(i, dDeltas);
- int end = End_Index(i, dDeltas);
- int k;
-
- for( k = start; k < end; ++k )
- rvec_ScaledAdd( system->atoms[dDeltas->select.dDelta_list[k].wrt].f,
- C, dDeltas->select.dDelta_list[k].dVal );
+ list *dDeltas = &((*lists)[DDELTA]);
+ int start = Start_Index(i, dDeltas);
+ int end = End_Index(i, dDeltas);
+ int k;
+
+ for ( k = start; k < end; ++k )
+ rvec_ScaledAdd( system->atoms[dDeltas->select.dDelta_list[k].wrt].f,
+ C, dDeltas->select.dDelta_list[k].dVal );
}
-void Calculate_dBO( int i, int pj, static_storage *workspace, list **lists,
- int *top )
+void Calculate_dBO( int i, int pj, static_storage *workspace, list **lists,
+ int *top )
{
- /* Initializations */
- int j, k, l, start_i, end_i, end_j;
- rvec dDeltap_self, dBOp;
- list *bonds, *dBOs;
- bond_data *nbr_l, *nbr_k;
- bond_order_data *bo_ij;
- dbond_data *top_dbo;
-
- bonds = (*lists)+BONDS;
- dBOs = (*lists)+DBO;
-
- j = bonds->select.bond_list[pj].nbr;
- bo_ij = &(bonds->select.bond_list[pj].bo_data);
-
- /*rvec due_j[1000], due_i[1000];
- rvec due_j_pi[1000], due_i_pi[1000];
-
- memset(due_j, 0, sizeof(rvec)*1000 );
- memset(due_i, 0, sizeof(rvec)*1000 );
- memset(due_j_pi, 0, sizeof(rvec)*1000 );
- memset(due_i_pi, 0, sizeof(rvec)*1000 );*/
-
- //fprintf( stderr,"dbo %d-%d\n",workspace->orig_id[i],workspace->orig_id[j] );
-
- start_i = Start_Index(i, bonds);
- end_i = End_Index(i, bonds);
-
- l = Start_Index(j, bonds);
- end_j = End_Index(j, bonds);
-
- top_dbo = &(dBOs->select.dbo_list[ (*top) ]);
-
- for( k = start_i; k < end_i; ++k ) {
- nbr_k = &(bonds->select.bond_list[k]);
- //fprintf( stderr, "\tnbr_k = %d\n", workspace->orig_id[nbr_k->nbr] );
-
- for( ; l < end_j && bonds->select.bond_list[l].nbr < nbr_k->nbr; ++l ) {
- /* These are the neighbors of j which aren't in the neighbor_list of i
- Note that they might also include i! */
- nbr_l = &(bonds->select.bond_list[l]);
- top_dbo->wrt = nbr_l->nbr;
- rvec_Copy( dBOp, nbr_l->bo_data.dBOp );
- //fprintf( stderr,"\t\tnbr_l = %d\n",workspace->orig_id[nbr_l->nbr] );
-
- rvec_Scale( top_dbo->dBO, -bo_ij->C3dbo, dBOp ); // dBO, 3rd
- rvec_Scale( top_dbo->dBOpi, -bo_ij->C4dbopi, dBOp ); // dBOpi, 4th
- rvec_Scale( top_dbo->dBOpi2, -bo_ij->C4dbopi2, dBOp );// dBOpipi, 4th
- //rvec_ScaledAdd(due_j[top_dbo->wrt],-bo_ij->BO*bo_ij->A2_ji, dBOp);
-
- if( nbr_l->nbr == i ) {
- rvec_Copy( dDeltap_self, workspace->dDeltap_self[i] );
-
- /* dBO */
- rvec_ScaledAdd( top_dbo->dBO, bo_ij->C1dbo, bo_ij->dBOp ); //1st
- rvec_ScaledAdd( top_dbo->dBO, bo_ij->C2dbo, dDeltap_self ); //2nd
-
- /* dBOpi */
- rvec_ScaledAdd(top_dbo->dBOpi,bo_ij->C1dbopi,bo_ij->dln_BOp_pi);//1
- rvec_ScaledAdd(top_dbo->dBOpi,bo_ij->C2dbopi,bo_ij->dBOp); //2nd
- rvec_ScaledAdd(top_dbo->dBOpi,bo_ij->C3dbopi,dDeltap_self); //3rd
-
- /* dBOpp, 1st */
- rvec_ScaledAdd(top_dbo->dBOpi2,bo_ij->C1dbopi2,bo_ij->dln_BOp_pi2);
- rvec_ScaledAdd(top_dbo->dBOpi2,bo_ij->C2dbopi2,bo_ij->dBOp); //2nd
- rvec_ScaledAdd(top_dbo->dBOpi2,bo_ij->C3dbopi2,dDeltap_self);//3rd
-
- /* do the adjustments on i */
- //rvec_ScaledAdd( due_i[i],
- //bo_ij->A0_ij + bo_ij->BO * bo_ij->A1_ij, bo_ij->dBOp );//1st,dBO
- //rvec_ScaledAdd( due_i[i], bo_ij->BO * bo_ij->A2_ij,
- //dDeltap_self ); //2nd, dBO
- }
-
- //rvec_Add( workspace->dDelta[nbr_l->nbr], top_dbo->dBO );
- ++(*top), ++top_dbo;
- }
-
- /* Now we are processing neighbor k of i. */
- top_dbo->wrt = nbr_k->nbr;
- rvec_Copy( dBOp, nbr_k->bo_data.dBOp );
-
- rvec_Scale( top_dbo->dBO, -bo_ij->C2dbo, dBOp ); //dBO-2
- rvec_Scale( top_dbo->dBOpi, -bo_ij->C3dbopi, dBOp ); //dBOpi-3
- rvec_Scale( top_dbo->dBOpi2, -bo_ij->C3dbopi2, dBOp );//dBOpp-3
- //rvec_ScaledAdd(due_i[top_dbo->wrt],-bo_ij->BO*bo_ij->A2_ij,dBOp);//dBO-2
-
- // fprintf( stderr, "\tnbr_k = %d, nbr_l = %d, l = %d, end_j = %d\n",
- // workspace->orig_id[nbr_k->nbr],
- // workspace->orig_id[bonds->select.bond_list[l].nbr], l, end_j );
-
- if( l < end_j && bonds->select.bond_list[l].nbr == nbr_k->nbr ) {
- /* This is a common neighbor of i and j. */
- nbr_l = &(bonds->select.bond_list[l]);
- rvec_Copy( dBOp, nbr_l->bo_data.dBOp );
-
- rvec_ScaledAdd( top_dbo->dBO, -bo_ij->C3dbo, dBOp ); //dBO,3rd
- rvec_ScaledAdd( top_dbo->dBOpi, -bo_ij->C4dbopi, dBOp ); //dBOpi,4th
- rvec_ScaledAdd( top_dbo->dBOpi2, -bo_ij->C4dbopi2, dBOp );//dBOpp.4th
- ++l;
-
- //rvec_ScaledAdd( due_j[top_dbo->wrt], -bo_ij->BO * bo_ij->A2_ji,
- //nbr_l->bo_data.dBOp ); //3rd, dBO
- }
- else if( k == pj ) {
- /* This negihbor is j. */
- rvec_Copy( dDeltap_self, workspace->dDeltap_self[j] );
-
- rvec_ScaledAdd( top_dbo->dBO, -bo_ij->C1dbo, bo_ij->dBOp );// 1st, dBO
- rvec_ScaledAdd( top_dbo->dBO, bo_ij->C3dbo, dDeltap_self );// 3rd, dBO
-
- /* dBOpi, 1st */
- rvec_ScaledAdd(top_dbo->dBOpi,-bo_ij->C1dbopi,bo_ij->dln_BOp_pi);
- rvec_ScaledAdd(top_dbo->dBOpi,-bo_ij->C2dbopi,bo_ij->dBOp); //2nd
- rvec_ScaledAdd( top_dbo->dBOpi, bo_ij->C4dbopi, dDeltap_self ); //4th
-
- /* dBOpi2, 1st */
- rvec_ScaledAdd(top_dbo->dBOpi2,-bo_ij->C1dbopi2,bo_ij->dln_BOp_pi2 );
- rvec_ScaledAdd(top_dbo->dBOpi2,-bo_ij->C2dbopi2,bo_ij->dBOp ); //2nd
- rvec_ScaledAdd(top_dbo->dBOpi2,bo_ij->C4dbopi2,dDeltap_self ); //4th
-
- //rvec_ScaledAdd( due_j[j], -(bo_ij->A0_ij + bo_ij->BO*bo_ij->A1_ij),
- //bo_ij->dBOp ); //1st, dBO
- //rvec_ScaledAdd( due_j[j], bo_ij->BO * bo_ij->A2_ji,
- //workspace->dDeltap_self[j] ); //3rd, dBO
+ /* Initializations */
+ int j, k, l, start_i, end_i, end_j;
+ rvec dDeltap_self, dBOp;
+ list *bonds, *dBOs;
+ bond_data *nbr_l, *nbr_k;
+ bond_order_data *bo_ij;
+ dbond_data *top_dbo;
+
+ bonds = (*lists) + BONDS;
+ dBOs = (*lists) + DBO;
+
+ j = bonds->select.bond_list[pj].nbr;
+ bo_ij = &(bonds->select.bond_list[pj].bo_data);
+
+ /*rvec due_j[1000], due_i[1000];
+ rvec due_j_pi[1000], due_i_pi[1000];
+
+ memset(due_j, 0, sizeof(rvec)*1000 );
+ memset(due_i, 0, sizeof(rvec)*1000 );
+ memset(due_j_pi, 0, sizeof(rvec)*1000 );
+ memset(due_i_pi, 0, sizeof(rvec)*1000 );*/
+
+ //fprintf( stderr,"dbo %d-%d\n",workspace->orig_id[i],workspace->orig_id[j] );
+
+ start_i = Start_Index(i, bonds);
+ end_i = End_Index(i, bonds);
+
+ l = Start_Index(j, bonds);
+ end_j = End_Index(j, bonds);
+
+ top_dbo = &(dBOs->select.dbo_list[ (*top) ]);
+
+ for ( k = start_i; k < end_i; ++k )
+ {
+ nbr_k = &(bonds->select.bond_list[k]);
+ //fprintf( stderr, "\tnbr_k = %d\n", workspace->orig_id[nbr_k->nbr] );
+
+ for ( ; l < end_j && bonds->select.bond_list[l].nbr < nbr_k->nbr; ++l )
+ {
+ /* These are the neighbors of j which aren't in the neighbor_list of i
+ Note that they might also include i! */
+ nbr_l = &(bonds->select.bond_list[l]);
+ top_dbo->wrt = nbr_l->nbr;
+ rvec_Copy( dBOp, nbr_l->bo_data.dBOp );
+ //fprintf( stderr,"\t\tnbr_l = %d\n",workspace->orig_id[nbr_l->nbr] );
+
+ rvec_Scale( top_dbo->dBO, -bo_ij->C3dbo, dBOp ); // dBO, 3rd
+ rvec_Scale( top_dbo->dBOpi, -bo_ij->C4dbopi, dBOp ); // dBOpi, 4th
+ rvec_Scale( top_dbo->dBOpi2, -bo_ij->C4dbopi2, dBOp );// dBOpipi, 4th
+ //rvec_ScaledAdd(due_j[top_dbo->wrt],-bo_ij->BO*bo_ij->A2_ji, dBOp);
+
+ if ( nbr_l->nbr == i )
+ {
+ rvec_Copy( dDeltap_self, workspace->dDeltap_self[i] );
+
+ /* dBO */
+ rvec_ScaledAdd( top_dbo->dBO, bo_ij->C1dbo, bo_ij->dBOp ); //1st
+ rvec_ScaledAdd( top_dbo->dBO, bo_ij->C2dbo, dDeltap_self ); //2nd
+
+ /* dBOpi */
+ rvec_ScaledAdd(top_dbo->dBOpi, bo_ij->C1dbopi, bo_ij->dln_BOp_pi); //1
+ rvec_ScaledAdd(top_dbo->dBOpi, bo_ij->C2dbopi, bo_ij->dBOp); //2nd
+ rvec_ScaledAdd(top_dbo->dBOpi, bo_ij->C3dbopi, dDeltap_self); //3rd
+
+ /* dBOpp, 1st */
+ rvec_ScaledAdd(top_dbo->dBOpi2, bo_ij->C1dbopi2, bo_ij->dln_BOp_pi2);
+ rvec_ScaledAdd(top_dbo->dBOpi2, bo_ij->C2dbopi2, bo_ij->dBOp); //2nd
+ rvec_ScaledAdd(top_dbo->dBOpi2, bo_ij->C3dbopi2, dDeltap_self); //3rd
+
+ /* do the adjustments on i */
+ //rvec_ScaledAdd( due_i[i],
+ //bo_ij->A0_ij + bo_ij->BO * bo_ij->A1_ij, bo_ij->dBOp );//1st,dBO
+ //rvec_ScaledAdd( due_i[i], bo_ij->BO * bo_ij->A2_ij,
+ //dDeltap_self ); //2nd, dBO
+ }
+
+ //rvec_Add( workspace->dDelta[nbr_l->nbr], top_dbo->dBO );
+ ++(*top), ++top_dbo;
+ }
+
+ /* Now we are processing neighbor k of i. */
+ top_dbo->wrt = nbr_k->nbr;
+ rvec_Copy( dBOp, nbr_k->bo_data.dBOp );
+
+ rvec_Scale( top_dbo->dBO, -bo_ij->C2dbo, dBOp ); //dBO-2
+ rvec_Scale( top_dbo->dBOpi, -bo_ij->C3dbopi, dBOp ); //dBOpi-3
+ rvec_Scale( top_dbo->dBOpi2, -bo_ij->C3dbopi2, dBOp );//dBOpp-3
+ //rvec_ScaledAdd(due_i[top_dbo->wrt],-bo_ij->BO*bo_ij->A2_ij,dBOp);//dBO-2
+
+ // fprintf( stderr, "\tnbr_k = %d, nbr_l = %d, l = %d, end_j = %d\n",
+ // workspace->orig_id[nbr_k->nbr],
+ // workspace->orig_id[bonds->select.bond_list[l].nbr], l, end_j );
+
+ if ( l < end_j && bonds->select.bond_list[l].nbr == nbr_k->nbr )
+ {
+ /* This is a common neighbor of i and j. */
+ nbr_l = &(bonds->select.bond_list[l]);
+ rvec_Copy( dBOp, nbr_l->bo_data.dBOp );
+
+ rvec_ScaledAdd( top_dbo->dBO, -bo_ij->C3dbo, dBOp ); //dBO,3rd
+ rvec_ScaledAdd( top_dbo->dBOpi, -bo_ij->C4dbopi, dBOp ); //dBOpi,4th
+ rvec_ScaledAdd( top_dbo->dBOpi2, -bo_ij->C4dbopi2, dBOp );//dBOpp.4th
+ ++l;
+
+ //rvec_ScaledAdd( due_j[top_dbo->wrt], -bo_ij->BO * bo_ij->A2_ji,
+ //nbr_l->bo_data.dBOp ); //3rd, dBO
+ }
+ else if ( k == pj )
+ {
+ /* This negihbor is j. */
+ rvec_Copy( dDeltap_self, workspace->dDeltap_self[j] );
+
+ rvec_ScaledAdd( top_dbo->dBO, -bo_ij->C1dbo, bo_ij->dBOp );// 1st, dBO
+ rvec_ScaledAdd( top_dbo->dBO, bo_ij->C3dbo, dDeltap_self );// 3rd, dBO
+
+ /* dBOpi, 1st */
+ rvec_ScaledAdd(top_dbo->dBOpi, -bo_ij->C1dbopi, bo_ij->dln_BOp_pi);
+ rvec_ScaledAdd(top_dbo->dBOpi, -bo_ij->C2dbopi, bo_ij->dBOp); //2nd
+ rvec_ScaledAdd( top_dbo->dBOpi, bo_ij->C4dbopi, dDeltap_self ); //4th
+
+ /* dBOpi2, 1st */
+ rvec_ScaledAdd(top_dbo->dBOpi2, -bo_ij->C1dbopi2, bo_ij->dln_BOp_pi2 );
+ rvec_ScaledAdd(top_dbo->dBOpi2, -bo_ij->C2dbopi2, bo_ij->dBOp ); //2nd
+ rvec_ScaledAdd(top_dbo->dBOpi2, bo_ij->C4dbopi2, dDeltap_self ); //4th
+
+ //rvec_ScaledAdd( due_j[j], -(bo_ij->A0_ij + bo_ij->BO*bo_ij->A1_ij),
+ //bo_ij->dBOp ); //1st, dBO
+ //rvec_ScaledAdd( due_j[j], bo_ij->BO * bo_ij->A2_ji,
+ //workspace->dDeltap_self[j] ); //3rd, dBO
+ }
+
+ // rvec_Add( workspace->dDelta[nbr_k->nbr], top_dbo->dBO );
+ ++(*top), ++top_dbo;
}
-
- // rvec_Add( workspace->dDelta[nbr_k->nbr], top_dbo->dBO );
- ++(*top), ++top_dbo;
- }
-
- for( ; l < end_j; ++l ) {
- /* These are the remaining neighbors of j which are not in the
- neighbor_list of i. Note that they might also include i!*/
- nbr_l = &(bonds->select.bond_list[l]);
- top_dbo->wrt = nbr_l->nbr;
- rvec_Copy( dBOp, nbr_l->bo_data.dBOp );
- //fprintf( stderr,"\tl=%d, nbr_l=%d\n",l,workspace->orig_id[nbr_l->nbr] );
-
- rvec_Scale( top_dbo->dBO, -bo_ij->C3dbo, dBOp ); //3rd, dBO
- rvec_Scale( top_dbo->dBOpi, -bo_ij->C4dbopi, dBOp ); //4th, dBOpi
- rvec_Scale( top_dbo->dBOpi2, -bo_ij->C4dbopi2, dBOp );//4th, dBOpp
-
- // rvec_ScaledAdd( due_j[top_dbo->wrt], -bo_ij->BO * bo_ij->A2_ji,
- // nbr_l->bo_data.dBOp );
-
- if( nbr_l->nbr == i ) {
- /* do the adjustments on i */
- rvec_Copy( dDeltap_self, workspace->dDeltap_self[i] );
-
- /* dBO, 1st */
- rvec_ScaledAdd( top_dbo->dBO, bo_ij->C1dbo, bo_ij->dBOp );
- rvec_ScaledAdd( top_dbo->dBO, bo_ij->C2dbo, dDeltap_self ); //2nd, dBO
-
- /* dBOpi, 1st */
- rvec_ScaledAdd( top_dbo->dBOpi, bo_ij->C1dbopi, bo_ij->dln_BOp_pi );
- rvec_ScaledAdd( top_dbo->dBOpi, bo_ij->C2dbopi, bo_ij->dBOp ); //2nd
- rvec_ScaledAdd( top_dbo->dBOpi, bo_ij->C3dbopi, dDeltap_self ); //3rd
-
- /* dBOpipi, 1st */
- rvec_ScaledAdd(top_dbo->dBOpi2, bo_ij->C1dbopi2, bo_ij->dln_BOp_pi2);
- rvec_ScaledAdd( top_dbo->dBOpi2, bo_ij->C2dbopi2, bo_ij->dBOp ); //2nd
- rvec_ScaledAdd( top_dbo->dBOpi2, bo_ij->C3dbopi2, dDeltap_self );//3rd
-
- //rvec_ScaledAdd( due_i[i], bo_ij->A0_ij + bo_ij->BO * bo_ij->A1_ij,
- //bo_ij->dBOp ); /*1st, dBO*/
- //rvec_ScaledAdd( due_i[i], bo_ij->BO * bo_ij->A2_ij,
- //dDeltap_self ); /*2nd, dBO*/
+
+ for ( ; l < end_j; ++l )
+ {
+ /* These are the remaining neighbors of j which are not in the
+ neighbor_list of i. Note that they might also include i!*/
+ nbr_l = &(bonds->select.bond_list[l]);
+ top_dbo->wrt = nbr_l->nbr;
+ rvec_Copy( dBOp, nbr_l->bo_data.dBOp );
+ //fprintf( stderr,"\tl=%d, nbr_l=%d\n",l,workspace->orig_id[nbr_l->nbr] );
+
+ rvec_Scale( top_dbo->dBO, -bo_ij->C3dbo, dBOp ); //3rd, dBO
+ rvec_Scale( top_dbo->dBOpi, -bo_ij->C4dbopi, dBOp ); //4th, dBOpi
+ rvec_Scale( top_dbo->dBOpi2, -bo_ij->C4dbopi2, dBOp );//4th, dBOpp
+
+ // rvec_ScaledAdd( due_j[top_dbo->wrt], -bo_ij->BO * bo_ij->A2_ji,
+ // nbr_l->bo_data.dBOp );
+
+ if ( nbr_l->nbr == i )
+ {
+ /* do the adjustments on i */
+ rvec_Copy( dDeltap_self, workspace->dDeltap_self[i] );
+
+ /* dBO, 1st */
+ rvec_ScaledAdd( top_dbo->dBO, bo_ij->C1dbo, bo_ij->dBOp );
+ rvec_ScaledAdd( top_dbo->dBO, bo_ij->C2dbo, dDeltap_self ); //2nd, dBO
+
+ /* dBOpi, 1st */
+ rvec_ScaledAdd( top_dbo->dBOpi, bo_ij->C1dbopi, bo_ij->dln_BOp_pi );
+ rvec_ScaledAdd( top_dbo->dBOpi, bo_ij->C2dbopi, bo_ij->dBOp ); //2nd
+ rvec_ScaledAdd( top_dbo->dBOpi, bo_ij->C3dbopi, dDeltap_self ); //3rd
+
+ /* dBOpipi, 1st */
+ rvec_ScaledAdd(top_dbo->dBOpi2, bo_ij->C1dbopi2, bo_ij->dln_BOp_pi2);
+ rvec_ScaledAdd( top_dbo->dBOpi2, bo_ij->C2dbopi2, bo_ij->dBOp ); //2nd
+ rvec_ScaledAdd( top_dbo->dBOpi2, bo_ij->C3dbopi2, dDeltap_self );//3rd
+
+ //rvec_ScaledAdd( due_i[i], bo_ij->A0_ij + bo_ij->BO * bo_ij->A1_ij,
+ //bo_ij->dBOp ); /*1st, dBO*/
+ //rvec_ScaledAdd( due_i[i], bo_ij->BO * bo_ij->A2_ij,
+ //dDeltap_self ); /*2nd, dBO*/
+ }
+
+ // rvec_Add( workspace->dDelta[nbr_l->nbr], top_dbo->dBO );
+ ++(*top), ++top_dbo;
}
- // rvec_Add( workspace->dDelta[nbr_l->nbr], top_dbo->dBO );
- ++(*top), ++top_dbo;
- }
-
- /*for( k = 0; k < 21; ++k ){
- fprintf( stderr, "%d %d %d, due_i:[%g %g %g]\n",
- i+1, j+1, k+1, due_i[k][0], due_i[k][1], due_i[k][2] );
- fprintf( stderr, "%d %d %d, due_j:[%g %g %g]\n",
- i+1, j+1, k+1, due_j[k][0], due_j[k][1], due_j[k][2] );
- }*/
+ /*for( k = 0; k < 21; ++k ){
+ fprintf( stderr, "%d %d %d, due_i:[%g %g %g]\n",
+ i+1, j+1, k+1, due_i[k][0], due_i[k][1], due_i[k][2] );
+ fprintf( stderr, "%d %d %d, due_j:[%g %g %g]\n",
+ i+1, j+1, k+1, due_j[k][0], due_j[k][1], due_j[k][2] );
+ }*/
}
#endif
-void Add_dBond_to_Forces_NPT( int i, int pj, reax_system *system,
- simulation_data *data, static_storage *workspace,
- list **lists )
+void Add_dBond_to_Forces_NPT( int i, int pj, reax_system *system,
+ simulation_data *data, static_storage *workspace,
+ list **lists )
{
- list *bonds = (*lists) + BONDS;
- bond_data *nbr_j, *nbr_k;
- bond_order_data *bo_ij, *bo_ji;
- dbond_coefficients coef;
- rvec temp, ext_press;
- ivec rel_box;
- int pk, k, j;
-
- /* Initializations */
- nbr_j = &(bonds->select.bond_list[pj]);
- j = nbr_j->nbr;
- bo_ij = &(nbr_j->bo_data);
- bo_ji = &(bonds->select.bond_list[ nbr_j->sym_index ].bo_data);
-
- coef.C1dbo = bo_ij->C1dbo * (bo_ij->Cdbo + bo_ji->Cdbo);
- coef.C2dbo = bo_ij->C2dbo * (bo_ij->Cdbo + bo_ji->Cdbo);
- coef.C3dbo = bo_ij->C3dbo * (bo_ij->Cdbo + bo_ji->Cdbo);
-
- coef.C1dbopi = bo_ij->C1dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
- coef.C2dbopi = bo_ij->C2dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
- coef.C3dbopi = bo_ij->C3dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
- coef.C4dbopi = bo_ij->C4dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
-
- coef.C1dbopi2 = bo_ij->C1dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
- coef.C2dbopi2 = bo_ij->C2dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
- coef.C3dbopi2 = bo_ij->C3dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
- coef.C4dbopi2 = bo_ij->C4dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
-
- coef.C1dDelta = bo_ij->C1dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]);
- coef.C2dDelta = bo_ij->C2dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]);
- coef.C3dDelta = bo_ij->C3dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]);
-
-
- /************************************
- * forces related to atom i *
- * first neighbors of atom i *
- ************************************/
- for( pk = Start_Index(i, bonds); pk < End_Index(i, bonds); ++pk ) {
- nbr_k = &(bonds->select.bond_list[pk]);
- k = nbr_k->nbr;
-
- rvec_Scale( temp, -coef.C2dbo, nbr_k->bo_data.dBOp ); /*2nd,dBO*/
- rvec_ScaledAdd( temp, -coef.C2dDelta, nbr_k->bo_data.dBOp );/*dDelta*/
- rvec_ScaledAdd( temp, -coef.C3dbopi, nbr_k->bo_data.dBOp ); /*3rd,dBOpi*/
- rvec_ScaledAdd( temp, -coef.C3dbopi2, nbr_k->bo_data.dBOp );/*3rd,dBOpi2*/
-
+ list *bonds = (*lists) + BONDS;
+ bond_data *nbr_j, *nbr_k;
+ bond_order_data *bo_ij, *bo_ji;
+ dbond_coefficients coef;
+ rvec temp, ext_press;
+ ivec rel_box;
+ int pk, k, j;
+
+ /* Initializations */
+ nbr_j = &(bonds->select.bond_list[pj]);
+ j = nbr_j->nbr;
+ bo_ij = &(nbr_j->bo_data);
+ bo_ji = &(bonds->select.bond_list[ nbr_j->sym_index ].bo_data);
+
+ coef.C1dbo = bo_ij->C1dbo * (bo_ij->Cdbo + bo_ji->Cdbo);
+ coef.C2dbo = bo_ij->C2dbo * (bo_ij->Cdbo + bo_ji->Cdbo);
+ coef.C3dbo = bo_ij->C3dbo * (bo_ij->Cdbo + bo_ji->Cdbo);
+
+ coef.C1dbopi = bo_ij->C1dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
+ coef.C2dbopi = bo_ij->C2dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
+ coef.C3dbopi = bo_ij->C3dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
+ coef.C4dbopi = bo_ij->C4dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
+
+ coef.C1dbopi2 = bo_ij->C1dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
+ coef.C2dbopi2 = bo_ij->C2dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
+ coef.C3dbopi2 = bo_ij->C3dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
+ coef.C4dbopi2 = bo_ij->C4dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
+
+ coef.C1dDelta = bo_ij->C1dbo * (workspace->CdDelta[i] + workspace->CdDelta[j]);
+ coef.C2dDelta = bo_ij->C2dbo * (workspace->CdDelta[i] + workspace->CdDelta[j]);
+ coef.C3dDelta = bo_ij->C3dbo * (workspace->CdDelta[i] + workspace->CdDelta[j]);
+
+
+ /************************************
+ * forces related to atom i *
+ * first neighbors of atom i *
+ ************************************/
+ for ( pk = Start_Index(i, bonds); pk < End_Index(i, bonds); ++pk )
+ {
+ nbr_k = &(bonds->select.bond_list[pk]);
+ k = nbr_k->nbr;
+
+ rvec_Scale( temp, -coef.C2dbo, nbr_k->bo_data.dBOp ); /*2nd,dBO*/
+ rvec_ScaledAdd( temp, -coef.C2dDelta, nbr_k->bo_data.dBOp );/*dDelta*/
+ rvec_ScaledAdd( temp, -coef.C3dbopi, nbr_k->bo_data.dBOp ); /*3rd,dBOpi*/
+ rvec_ScaledAdd( temp, -coef.C3dbopi2, nbr_k->bo_data.dBOp );/*3rd,dBOpi2*/
+
+ /* force */
+ rvec_Add( system->atoms[k].f, temp );
+ /* pressure */
+ rvec_iMultiply( ext_press, nbr_k->rel_box, temp );
+ rvec_Add( data->ext_press, ext_press );
+
+ /* if( !ivec_isZero( nbr_k->rel_box ) )
+ fprintf( stderr, "%3d %3d %3d: dvec[%10.6f %10.6f %10.6f]
+ ext[%3d %3d %3d] f[%10.6f %10.6f %10.6f]\n",
+ i+1,
+ system->atoms[i].x[0],system->atoms[i].x[1],system->atoms[i].x[2],
+ j+1, k+1,
+ system->atoms[k].x[0], system->atoms[k].x[1], system->atoms[k].x[2],
+ nbr_k->dvec[0], nbr_k->dvec[1], nbr_k->dvec[2],
+ nbr_k->rel_box[0], nbr_k->rel_box[1], nbr_k->rel_box[2],
+ temp[0], temp[1], temp[2] ); */
+ }
+
+ /* then atom i itself */
+ rvec_Scale( temp, coef.C1dbo, bo_ij->dBOp ); /*1st, dBO*/
+ rvec_ScaledAdd( temp, coef.C2dbo, workspace->dDeltap_self[i] ); /*2nd, dBO*/
+
+ rvec_ScaledAdd( temp, coef.C1dDelta, bo_ij->dBOp ); /*1st, dBO*/
+ rvec_ScaledAdd( temp, coef.C2dDelta, workspace->dDeltap_self[i] );/*2nd, dBO*/
+
+ rvec_ScaledAdd( temp, coef.C1dbopi, bo_ij->dln_BOp_pi ); /*1st,dBOpi*/
+ rvec_ScaledAdd( temp, coef.C2dbopi, bo_ij->dBOp ); /*2nd,dBOpi*/
+ rvec_ScaledAdd( temp, coef.C3dbopi, workspace->dDeltap_self[i] );/*3rd,dBOpi*/
+
+ rvec_ScaledAdd(temp, coef.C1dbopi2, bo_ij->dln_BOp_pi2) ; /*1st,dBO_pi2*/
+ rvec_ScaledAdd(temp, coef.C2dbopi2, bo_ij->dBOp); /*2nd,dBO_pi2*/
+ rvec_ScaledAdd(temp, coef.C3dbopi2, workspace->dDeltap_self[i]);/*3rd,dBO_pi2*/
+
/* force */
- rvec_Add( system->atoms[k].f, temp );
+ rvec_Add( system->atoms[i].f, temp );
+ /* ext pressure due to i dropped, counting force on j only will be enough */
+
+
+ /****************************************************************************
+ * forces and pressure related to atom j *
+ * first neighbors of atom j *
+ ***************************************************************************/
+ for ( pk = Start_Index(j, bonds); pk < End_Index(j, bonds); ++pk )
+ {
+ nbr_k = &(bonds->select.bond_list[pk]);
+ k = nbr_k->nbr;
+
+ rvec_Scale( temp, -coef.C3dbo, nbr_k->bo_data.dBOp ); /*3rd,dBO*/
+ rvec_ScaledAdd( temp, -coef.C3dDelta, nbr_k->bo_data.dBOp );/*dDelta*/
+ rvec_ScaledAdd( temp, -coef.C4dbopi, nbr_k->bo_data.dBOp ); /*4th,dBOpi*/
+ rvec_ScaledAdd( temp, -coef.C4dbopi2, nbr_k->bo_data.dBOp );/*4th,dBOpi2*/
+
+ /* force */
+ rvec_Add( system->atoms[k].f, temp );
+ /* pressure */
+ if ( k != i )
+ {
+ ivec_Sum(rel_box, nbr_k->rel_box, nbr_j->rel_box);//k's rel_box wrt i
+ rvec_iMultiply( ext_press, rel_box, temp );
+ rvec_Add( data->ext_press, ext_press );
+
+ /* if( !ivec_isZero( rel_box ) )
+ fprintf( stderr, "%3d %3d %3d: dvec[%10.6f %10.6f %10.6f]
+ ext[%3d %3d %3d] f[%10.6f %10.6f %10.6f]\n",
+ i+1, j+1,
+ system->atoms[j].x[0],system->atoms[j].x[1],system->atoms[j].x[2],
+ k+1,
+ system->atoms[k].x[0], system->atoms[k].x[1], system->atoms[k].x[2],
+ nbr_k->dvec[0], nbr_k->dvec[1], nbr_k->dvec[2],
+ rel_box[0], rel_box[1], rel_box[2],
+ temp[0], temp[1], temp[2] ); */
+ }
+ }
+
+ /* then atom j itself */
+ rvec_Scale( temp, -coef.C1dbo, bo_ij->dBOp ); /*1st, dBO*/
+ rvec_ScaledAdd( temp, coef.C3dbo, workspace->dDeltap_self[j] ); /*2nd, dBO*/
+
+ rvec_ScaledAdd( temp, -coef.C1dDelta, bo_ij->dBOp ); /*1st, dBO*/
+ rvec_ScaledAdd( temp, coef.C3dDelta, workspace->dDeltap_self[j] );/*2nd, dBO*/
+
+ rvec_ScaledAdd( temp, -coef.C1dbopi, bo_ij->dln_BOp_pi ); /*1st,dBOpi*/
+ rvec_ScaledAdd( temp, -coef.C2dbopi, bo_ij->dBOp ); /*2nd,dBOpi*/
+ rvec_ScaledAdd( temp, coef.C4dbopi, workspace->dDeltap_self[j] );/*3rd,dBOpi*/
+
+ rvec_ScaledAdd(temp, -coef.C1dbopi2, bo_ij->dln_BOp_pi2); /*1st,dBOpi2*/
+ rvec_ScaledAdd(temp, -coef.C2dbopi2, bo_ij->dBOp); /*2nd,dBOpi2*/
+ rvec_ScaledAdd(temp, coef.C4dbopi2, workspace->dDeltap_self[j]);/*3rd,dBOpi2*/
+
+ /* force */
+ rvec_Add( system->atoms[j].f, temp );
/* pressure */
- rvec_iMultiply( ext_press, nbr_k->rel_box, temp );
+ rvec_iMultiply( ext_press, nbr_j->rel_box, temp );
rvec_Add( data->ext_press, ext_press );
-
- /* if( !ivec_isZero( nbr_k->rel_box ) )
- fprintf( stderr, "%3d %3d %3d: dvec[%10.6f %10.6f %10.6f]
+
+ /* if( !ivec_isZero( nbr_j->rel_box ) )
+ fprintf( stderr, "%3d %3d %3d: dvec[%10.6f %10.6f %10.6f]
ext[%3d %3d %3d] f[%10.6f %10.6f %10.6f]\n",
- i+1,
- system->atoms[i].x[0],system->atoms[i].x[1],system->atoms[i].x[2],
- j+1, k+1,
- system->atoms[k].x[0], system->atoms[k].x[1], system->atoms[k].x[2],
- nbr_k->dvec[0], nbr_k->dvec[1], nbr_k->dvec[2],
- nbr_k->rel_box[0], nbr_k->rel_box[1], nbr_k->rel_box[2],
+ i+1, system->atoms[i].x[0], system->atoms[i].x[1], system->atoms[i].x[2],
+ j+1, system->atoms[j].x[0], system->atoms[j].x[1], system->atoms[j].x[2],
+ j+1, nbr_j->dvec[0], nbr_j->dvec[1], nbr_j->dvec[2],
+ nbr_j->rel_box[0], nbr_j->rel_box[1], nbr_j->rel_box[2],
temp[0], temp[1], temp[2] ); */
- }
-
- /* then atom i itself */
- rvec_Scale( temp, coef.C1dbo, bo_ij->dBOp ); /*1st, dBO*/
- rvec_ScaledAdd( temp, coef.C2dbo, workspace->dDeltap_self[i] ); /*2nd, dBO*/
-
- rvec_ScaledAdd( temp, coef.C1dDelta, bo_ij->dBOp ); /*1st, dBO*/
- rvec_ScaledAdd( temp, coef.C2dDelta, workspace->dDeltap_self[i] );/*2nd, dBO*/
-
- rvec_ScaledAdd( temp, coef.C1dbopi, bo_ij->dln_BOp_pi ); /*1st,dBOpi*/
- rvec_ScaledAdd( temp, coef.C2dbopi, bo_ij->dBOp ); /*2nd,dBOpi*/
- rvec_ScaledAdd( temp, coef.C3dbopi, workspace->dDeltap_self[i] );/*3rd,dBOpi*/
-
- rvec_ScaledAdd(temp, coef.C1dbopi2, bo_ij->dln_BOp_pi2) ; /*1st,dBO_pi2*/
- rvec_ScaledAdd(temp, coef.C2dbopi2, bo_ij->dBOp); /*2nd,dBO_pi2*/
- rvec_ScaledAdd(temp, coef.C3dbopi2, workspace->dDeltap_self[i]);/*3rd,dBO_pi2*/
-
- /* force */
- rvec_Add( system->atoms[i].f, temp );
- /* ext pressure due to i dropped, counting force on j only will be enough */
-
-
- /****************************************************************************
- * forces and pressure related to atom j *
- * first neighbors of atom j *
- ***************************************************************************/
- for( pk = Start_Index(j, bonds); pk < End_Index(j, bonds); ++pk ) {
- nbr_k = &(bonds->select.bond_list[pk]);
- k = nbr_k->nbr;
-
- rvec_Scale( temp, -coef.C3dbo, nbr_k->bo_data.dBOp ); /*3rd,dBO*/
- rvec_ScaledAdd( temp, -coef.C3dDelta, nbr_k->bo_data.dBOp );/*dDelta*/
- rvec_ScaledAdd( temp, -coef.C4dbopi, nbr_k->bo_data.dBOp ); /*4th,dBOpi*/
- rvec_ScaledAdd( temp, -coef.C4dbopi2, nbr_k->bo_data.dBOp );/*4th,dBOpi2*/
-
- /* force */
- rvec_Add( system->atoms[k].f, temp );
- /* pressure */
- if( k != i ) {
- ivec_Sum(rel_box, nbr_k->rel_box, nbr_j->rel_box);//k's rel_box wrt i
- rvec_iMultiply( ext_press, rel_box, temp );
- rvec_Add( data->ext_press, ext_press );
-
- /* if( !ivec_isZero( rel_box ) )
- fprintf( stderr, "%3d %3d %3d: dvec[%10.6f %10.6f %10.6f]
- ext[%3d %3d %3d] f[%10.6f %10.6f %10.6f]\n",
- i+1, j+1,
- system->atoms[j].x[0],system->atoms[j].x[1],system->atoms[j].x[2],
- k+1,
- system->atoms[k].x[0], system->atoms[k].x[1], system->atoms[k].x[2],
- nbr_k->dvec[0], nbr_k->dvec[1], nbr_k->dvec[2],
- rel_box[0], rel_box[1], rel_box[2],
- temp[0], temp[1], temp[2] ); */
- }
- }
-
- /* then atom j itself */
- rvec_Scale( temp, -coef.C1dbo, bo_ij->dBOp ); /*1st, dBO*/
- rvec_ScaledAdd( temp, coef.C3dbo, workspace->dDeltap_self[j] ); /*2nd, dBO*/
-
- rvec_ScaledAdd( temp, -coef.C1dDelta, bo_ij->dBOp ); /*1st, dBO*/
- rvec_ScaledAdd( temp, coef.C3dDelta, workspace->dDeltap_self[j] );/*2nd, dBO*/
-
- rvec_ScaledAdd( temp, -coef.C1dbopi, bo_ij->dln_BOp_pi ); /*1st,dBOpi*/
- rvec_ScaledAdd( temp, -coef.C2dbopi, bo_ij->dBOp ); /*2nd,dBOpi*/
- rvec_ScaledAdd( temp, coef.C4dbopi, workspace->dDeltap_self[j] );/*3rd,dBOpi*/
-
- rvec_ScaledAdd(temp, -coef.C1dbopi2, bo_ij->dln_BOp_pi2); /*1st,dBOpi2*/
- rvec_ScaledAdd(temp, -coef.C2dbopi2, bo_ij->dBOp); /*2nd,dBOpi2*/
- rvec_ScaledAdd(temp, coef.C4dbopi2, workspace->dDeltap_self[j]);/*3rd,dBOpi2*/
-
- /* force */
- rvec_Add( system->atoms[j].f, temp );
- /* pressure */
- rvec_iMultiply( ext_press, nbr_j->rel_box, temp );
- rvec_Add( data->ext_press, ext_press );
-
- /* if( !ivec_isZero( nbr_j->rel_box ) )
- fprintf( stderr, "%3d %3d %3d: dvec[%10.6f %10.6f %10.6f]
- ext[%3d %3d %3d] f[%10.6f %10.6f %10.6f]\n",
- i+1, system->atoms[i].x[0], system->atoms[i].x[1], system->atoms[i].x[2],
- j+1, system->atoms[j].x[0], system->atoms[j].x[1], system->atoms[j].x[2],
- j+1, nbr_j->dvec[0], nbr_j->dvec[1], nbr_j->dvec[2],
- nbr_j->rel_box[0], nbr_j->rel_box[1], nbr_j->rel_box[2],
- temp[0], temp[1], temp[2] ); */
}
-void Add_dBond_to_Forces( int i, int pj, reax_system *system,
- simulation_data *data, static_storage *workspace,
- list **lists )
+void Add_dBond_to_Forces( int i, int pj, reax_system *system,
+ simulation_data *data, static_storage *workspace,
+ list **lists )
{
- list *bonds = (*lists) + BONDS;
- bond_data *nbr_j, *nbr_k;
- bond_order_data *bo_ij, *bo_ji;
- dbond_coefficients coef;
- int pk, k, j;
-
- /* Initializations */
- nbr_j = &(bonds->select.bond_list[pj]);
- j = nbr_j->nbr;
- bo_ij = &(nbr_j->bo_data);
- bo_ji = &(bonds->select.bond_list[ nbr_j->sym_index ].bo_data);
-
- coef.C1dbo = bo_ij->C1dbo * (bo_ij->Cdbo + bo_ji->Cdbo);
- coef.C2dbo = bo_ij->C2dbo * (bo_ij->Cdbo + bo_ji->Cdbo);
- coef.C3dbo = bo_ij->C3dbo * (bo_ij->Cdbo + bo_ji->Cdbo);
-
- coef.C1dbopi = bo_ij->C1dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
- coef.C2dbopi = bo_ij->C2dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
- coef.C3dbopi = bo_ij->C3dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
- coef.C4dbopi = bo_ij->C4dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
-
- coef.C1dbopi2 = bo_ij->C1dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
- coef.C2dbopi2 = bo_ij->C2dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
- coef.C3dbopi2 = bo_ij->C3dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
- coef.C4dbopi2 = bo_ij->C4dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
-
- coef.C1dDelta = bo_ij->C1dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]);
- coef.C2dDelta = bo_ij->C2dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]);
- coef.C3dDelta = bo_ij->C3dbo * (workspace->CdDelta[i]+workspace->CdDelta[j]);
-
- for( pk = Start_Index(i, bonds); pk < End_Index(i, bonds); ++pk ) {
- nbr_k = &(bonds->select.bond_list[pk]);
- k = nbr_k->nbr;
-
- rvec_ScaledAdd( system->atoms[k].f, -coef.C2dbo, nbr_k->bo_data.dBOp );
+ list *bonds = (*lists) + BONDS;
+ bond_data *nbr_j, *nbr_k;
+ bond_order_data *bo_ij, *bo_ji;
+ dbond_coefficients coef;
+ int pk, k, j;
+
+ /* Initializations */
+ nbr_j = &(bonds->select.bond_list[pj]);
+ j = nbr_j->nbr;
+ bo_ij = &(nbr_j->bo_data);
+ bo_ji = &(bonds->select.bond_list[ nbr_j->sym_index ].bo_data);
+
+ coef.C1dbo = bo_ij->C1dbo * (bo_ij->Cdbo + bo_ji->Cdbo);
+ coef.C2dbo = bo_ij->C2dbo * (bo_ij->Cdbo + bo_ji->Cdbo);
+ coef.C3dbo = bo_ij->C3dbo * (bo_ij->Cdbo + bo_ji->Cdbo);
+
+ coef.C1dbopi = bo_ij->C1dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
+ coef.C2dbopi = bo_ij->C2dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
+ coef.C3dbopi = bo_ij->C3dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
+ coef.C4dbopi = bo_ij->C4dbopi * (bo_ij->Cdbopi + bo_ji->Cdbopi);
+
+ coef.C1dbopi2 = bo_ij->C1dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
+ coef.C2dbopi2 = bo_ij->C2dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
+ coef.C3dbopi2 = bo_ij->C3dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
+ coef.C4dbopi2 = bo_ij->C4dbopi2 * (bo_ij->Cdbopi2 + bo_ji->Cdbopi2);
+
+ coef.C1dDelta = bo_ij->C1dbo * (workspace->CdDelta[i] + workspace->CdDelta[j]);
+ coef.C2dDelta = bo_ij->C2dbo * (workspace->CdDelta[i] + workspace->CdDelta[j]);
+ coef.C3dDelta = bo_ij->C3dbo * (workspace->CdDelta[i] + workspace->CdDelta[j]);
+
+ for ( pk = Start_Index(i, bonds); pk < End_Index(i, bonds); ++pk )
+ {
+ nbr_k = &(bonds->select.bond_list[pk]);
+ k = nbr_k->nbr;
+
+ rvec_ScaledAdd( system->atoms[k].f, -coef.C2dbo, nbr_k->bo_data.dBOp );
+ /*2nd, dBO*/
+ rvec_ScaledAdd( system->atoms[k].f, -coef.C2dDelta, nbr_k->bo_data.dBOp );
+ /*dDelta*/
+ rvec_ScaledAdd( system->atoms[k].f, -coef.C3dbopi, nbr_k->bo_data.dBOp );
+ /*3rd, dBOpi*/
+ rvec_ScaledAdd( system->atoms[k].f, -coef.C3dbopi2, nbr_k->bo_data.dBOp );
+ /*3rd, dBOpi2*/
+ }
+
+ rvec_ScaledAdd( system->atoms[i].f, coef.C1dbo, bo_ij->dBOp );
+ /*1st, dBO*/
+ rvec_ScaledAdd( system->atoms[i].f, coef.C2dbo, workspace->dDeltap_self[i] );
+ /*2nd, dBO*/
+
+ rvec_ScaledAdd(system->atoms[i].f, coef.C1dDelta, bo_ij->dBOp);
+ /*1st, dBO*/
+ rvec_ScaledAdd(system->atoms[i].f, coef.C2dDelta, workspace->dDeltap_self[i]);
+ /*2nd, dBO*/
+
+ rvec_ScaledAdd( system->atoms[i].f, coef.C1dbopi, bo_ij->dln_BOp_pi );
+ /*1st, dBOpi*/
+ rvec_ScaledAdd( system->atoms[i].f, coef.C2dbopi, bo_ij->dBOp );
+ /*2nd, dBOpi*/
+ rvec_ScaledAdd(system->atoms[i].f, coef.C3dbopi, workspace->dDeltap_self[i]);
+ /*3rd, dBOpi*/
+
+ rvec_ScaledAdd( system->atoms[i].f, coef.C1dbopi2, bo_ij->dln_BOp_pi2 );
+ /*1st, dBO_pi2*/
+ rvec_ScaledAdd( system->atoms[i].f, coef.C2dbopi2, bo_ij->dBOp );
+ /*2nd, dBO_pi2*/
+ rvec_ScaledAdd(system->atoms[i].f, coef.C3dbopi2, workspace->dDeltap_self[i]);
+ /*3rd, dBO_pi2*/
+
+
+ for ( pk = Start_Index(j, bonds); pk < End_Index(j, bonds); ++pk )
+ {
+ nbr_k = &(bonds->select.bond_list[pk]);
+ k = nbr_k->nbr;
+
+ rvec_ScaledAdd( system->atoms[k].f, -coef.C3dbo, nbr_k->bo_data.dBOp );
+ /*3rd, dBO*/
+ rvec_ScaledAdd( system->atoms[k].f, -coef.C3dDelta, nbr_k->bo_data.dBOp );
+ /*dDelta*/
+ rvec_ScaledAdd( system->atoms[k].f, -coef.C4dbopi, nbr_k->bo_data.dBOp );
+ /*4th, dBOpi*/
+ rvec_ScaledAdd( system->atoms[k].f, -coef.C4dbopi2, nbr_k->bo_data.dBOp );
+ /*4th, dBOpi2*/
+ }
+
+ rvec_ScaledAdd( system->atoms[j].f, -coef.C1dbo, bo_ij->dBOp );
+ /*1st, dBO*/
+ rvec_ScaledAdd( system->atoms[j].f, coef.C3dbo, workspace->dDeltap_self[j] );
/*2nd, dBO*/
- rvec_ScaledAdd( system->atoms[k].f, -coef.C2dDelta, nbr_k->bo_data.dBOp );
- /*dDelta*/
- rvec_ScaledAdd( system->atoms[k].f, -coef.C3dbopi, nbr_k->bo_data.dBOp );
+
+ rvec_ScaledAdd( system->atoms[j].f, -coef.C1dDelta, bo_ij->dBOp );
+ /*1st, dBO*/
+ rvec_ScaledAdd(system->atoms[j].f, coef.C3dDelta, workspace->dDeltap_self[j]);
+ /*2nd, dBO*/
+
+ rvec_ScaledAdd( system->atoms[j].f, -coef.C1dbopi, bo_ij->dln_BOp_pi );
+ /*1st, dBOpi*/
+ rvec_ScaledAdd( system->atoms[j].f, -coef.C2dbopi, bo_ij->dBOp );
+ /*2nd, dBOpi*/
+ rvec_ScaledAdd(system->atoms[j].f, coef.C4dbopi, workspace->dDeltap_self[j]);
/*3rd, dBOpi*/
- rvec_ScaledAdd( system->atoms[k].f, -coef.C3dbopi2, nbr_k->bo_data.dBOp );
+
+ rvec_ScaledAdd( system->atoms[j].f, -coef.C1dbopi2, bo_ij->dln_BOp_pi2 );
+ /*1st, dBOpi2*/
+ rvec_ScaledAdd( system->atoms[j].f, -coef.C2dbopi2, bo_ij->dBOp );
+ /*2nd, dBOpi2*/
+ rvec_ScaledAdd(system->atoms[j].f, coef.C4dbopi2, workspace->dDeltap_self[j]);
/*3rd, dBOpi2*/
- }
-
- rvec_ScaledAdd( system->atoms[i].f, coef.C1dbo, bo_ij->dBOp );
- /*1st, dBO*/
- rvec_ScaledAdd( system->atoms[i].f, coef.C2dbo, workspace->dDeltap_self[i] );
- /*2nd, dBO*/
-
- rvec_ScaledAdd(system->atoms[i].f, coef.C1dDelta, bo_ij->dBOp);
- /*1st, dBO*/
- rvec_ScaledAdd(system->atoms[i].f, coef.C2dDelta, workspace->dDeltap_self[i]);
- /*2nd, dBO*/
-
- rvec_ScaledAdd( system->atoms[i].f, coef.C1dbopi, bo_ij->dln_BOp_pi );
- /*1st, dBOpi*/
- rvec_ScaledAdd( system->atoms[i].f, coef.C2dbopi, bo_ij->dBOp );
- /*2nd, dBOpi*/
- rvec_ScaledAdd(system->atoms[i].f, coef.C3dbopi, workspace->dDeltap_self[i]);
- /*3rd, dBOpi*/
-
- rvec_ScaledAdd( system->atoms[i].f, coef.C1dbopi2, bo_ij->dln_BOp_pi2 );
- /*1st, dBO_pi2*/
- rvec_ScaledAdd( system->atoms[i].f, coef.C2dbopi2, bo_ij->dBOp );
- /*2nd, dBO_pi2*/
- rvec_ScaledAdd(system->atoms[i].f, coef.C3dbopi2, workspace->dDeltap_self[i]);
- /*3rd, dBO_pi2*/
-
-
- for( pk = Start_Index(j, bonds); pk < End_Index(j, bonds); ++pk ) {
- nbr_k = &(bonds->select.bond_list[pk]);
- k = nbr_k->nbr;
-
- rvec_ScaledAdd( system->atoms[k].f, -coef.C3dbo, nbr_k->bo_data.dBOp );
- /*3rd, dBO*/
- rvec_ScaledAdd( system->atoms[k].f, -coef.C3dDelta, nbr_k->bo_data.dBOp );
- /*dDelta*/
- rvec_ScaledAdd( system->atoms[k].f, -coef.C4dbopi, nbr_k->bo_data.dBOp );
- /*4th, dBOpi*/
- rvec_ScaledAdd( system->atoms[k].f, -coef.C4dbopi2, nbr_k->bo_data.dBOp );
- /*4th, dBOpi2*/
- }
-
- rvec_ScaledAdd( system->atoms[j].f, -coef.C1dbo, bo_ij->dBOp );
- /*1st, dBO*/
- rvec_ScaledAdd( system->atoms[j].f, coef.C3dbo, workspace->dDeltap_self[j] );
- /*2nd, dBO*/
-
- rvec_ScaledAdd( system->atoms[j].f, -coef.C1dDelta, bo_ij->dBOp );
- /*1st, dBO*/
- rvec_ScaledAdd(system->atoms[j].f, coef.C3dDelta, workspace->dDeltap_self[j]);
- /*2nd, dBO*/
-
- rvec_ScaledAdd( system->atoms[j].f, -coef.C1dbopi, bo_ij->dln_BOp_pi );
- /*1st, dBOpi*/
- rvec_ScaledAdd( system->atoms[j].f, -coef.C2dbopi, bo_ij->dBOp );
- /*2nd, dBOpi*/
- rvec_ScaledAdd(system->atoms[j].f, coef.C4dbopi, workspace->dDeltap_self[j]);
- /*3rd, dBOpi*/
-
- rvec_ScaledAdd( system->atoms[j].f, -coef.C1dbopi2, bo_ij->dln_BOp_pi2 );
- /*1st, dBOpi2*/
- rvec_ScaledAdd( system->atoms[j].f, -coef.C2dbopi2, bo_ij->dBOp );
- /*2nd, dBOpi2*/
- rvec_ScaledAdd(system->atoms[j].f, coef.C4dbopi2, workspace->dDeltap_self[j]);
- /*3rd, dBOpi2*/
}
@@ -636,436 +649,455 @@ void Add_dBond_to_Forces( int i, int pj, reax_system *system,
And this is the case given our method of neighbor generation*/
int Locate_Symmetric_Bond( list *bonds, int i, int j )
{
- int start = Start_Index(i, bonds);
- int end = End_Index(i, bonds);
- int mid = (start + end) / 2;
- int mid_nbr;
-
- while( (mid_nbr = bonds->select.bond_list[mid].nbr) != j ) {
- /*fprintf( stderr, "\tstart: %d end: %d mid: %d\n",
- start, end, mid );*/
- if( mid_nbr < j )
- start = mid+1;
- else end = mid - 1;
-
- mid = (start + end) / 2;
+ int start = Start_Index(i, bonds);
+ int end = End_Index(i, bonds);
+ int mid = (start + end) / 2;
+ int mid_nbr;
+
+ while ( (mid_nbr = bonds->select.bond_list[mid].nbr) != j )
+ {
+ /*fprintf( stderr, "\tstart: %d end: %d mid: %d\n",
+ start, end, mid );*/
+ if ( mid_nbr < j )
+ start = mid + 1;
+ else end = mid - 1;
+
+ mid = (start + end) / 2;
}
-
- return mid;
+
+ return mid;
}
inline void Copy_Neighbor_Data( bond_data *dest, near_neighbor_data *src )
{
- dest->nbr = src->nbr;
- dest->d = src->d;
- rvec_Copy( dest->dvec, src->dvec );
- ivec_Copy( dest->rel_box, src->rel_box );
- /* rvec_Copy( dest->ext_factor, src->ext_factor );*/
+ dest->nbr = src->nbr;
+ dest->d = src->d;
+ rvec_Copy( dest->dvec, src->dvec );
+ ivec_Copy( dest->rel_box, src->rel_box );
+ /* rvec_Copy( dest->ext_factor, src->ext_factor );*/
}
inline void Copy_Bond_Order_Data( bond_order_data *dest, bond_order_data *src )
{
- dest->BO = src->BO;
- dest->BO_s = src->BO_s;
- dest->BO_pi = src->BO_pi;
- dest->BO_pi2 = src->BO_pi2;
-
- rvec_Scale( dest->dBOp, -1.0, src->dBOp );
- rvec_Scale( dest->dln_BOp_s, -1.0, src->dln_BOp_s );
- rvec_Scale( dest->dln_BOp_pi, -1.0, src->dln_BOp_pi );
- rvec_Scale( dest->dln_BOp_pi2, -1.0, src->dln_BOp_pi2 );
+ dest->BO = src->BO;
+ dest->BO_s = src->BO_s;
+ dest->BO_pi = src->BO_pi;
+ dest->BO_pi2 = src->BO_pi2;
+
+ rvec_Scale( dest->dBOp, -1.0, src->dBOp );
+ rvec_Scale( dest->dln_BOp_s, -1.0, src->dln_BOp_s );
+ rvec_Scale( dest->dln_BOp_pi, -1.0, src->dln_BOp_pi );
+ rvec_Scale( dest->dln_BOp_pi2, -1.0, src->dln_BOp_pi2 );
}
int compare_bonds( const void *p1, const void *p2 )
{
- return ((bond_data *)p1)->nbr - ((bond_data *)p2)->nbr;
+ return ((bond_data *)p1)->nbr - ((bond_data *)p2)->nbr;
}
/* A very important and crucial assumption here is that each segment
belonging to a different atom in nbrhoods->nbr_list is sorted in its own.
This can either be done in the general coordinator function or here */
-void Calculate_Bond_Orders( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+void Calculate_Bond_Orders( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int i, j, pj, type_i, type_j;
- int start_i, end_i;
- int num_bonds, sym_index;
- real p_boc1, p_boc2;
- real val_i, Deltap_i, Deltap_boc_i;
- real val_j, Deltap_j, Deltap_boc_j;
- real temp, f1, f2, f3, f4, f5, f4f5, exp_f4, exp_f5;
- real exp_p1i, exp_p2i, exp_p1j, exp_p2j;
- real u1_ij, u1_ji, Cf1A_ij, Cf1B_ij, Cf1_ij, Cf1_ji;
- real Cf45_ij, Cf45_ji, p_lp1;
- real A0_ij, A1_ij, A2_ij, A2_ji, A3_ij, A3_ji;
- real explp1;
- two_body_parameters *twbp;
- bond_order_data *bo_ij, *bo_ji;
- single_body_parameters *sbp_i, *sbp_j;
- list *bonds = (*lists) + BONDS;
+ int i, j, pj, type_i, type_j;
+ int start_i, end_i;
+ int num_bonds, sym_index;
+ real p_boc1, p_boc2;
+ real val_i, Deltap_i, Deltap_boc_i;
+ real val_j, Deltap_j, Deltap_boc_j;
+ real temp, f1, f2, f3, f4, f5, f4f5, exp_f4, exp_f5;
+ real exp_p1i, exp_p2i, exp_p1j, exp_p2j;
+ real u1_ij, u1_ji, Cf1A_ij, Cf1B_ij, Cf1_ij, Cf1_ji;
+ real Cf45_ij, Cf45_ji, p_lp1;
+ real A0_ij, A1_ij, A2_ij, A2_ji, A3_ij, A3_ji;
+ real explp1;
+ two_body_parameters *twbp;
+ bond_order_data *bo_ij, *bo_ji;
+ single_body_parameters *sbp_i, *sbp_j;
+ list *bonds = (*lists) + BONDS;
#if defined(TEST_FORCES)
- int k, pk, start_j, end_j;
- int top_dbo=0, top_dDelta=0;
- dbond_data *pdbo;
- dDelta_data *ptop_dDelta;
- list *dDeltas = (*lists) + DDELTA;
- list *dBOs = (*lists) + DBO;
+ int k, pk, start_j, end_j;
+ int top_dbo = 0, top_dDelta = 0;
+ dbond_data *pdbo;
+ dDelta_data *ptop_dDelta;
+ list *dDeltas = (*lists) + DDELTA;
+ list *dBOs = (*lists) + DBO;
#endif
- num_bonds = 0;
- p_boc1 = system->reaxprm.gp.l[0];
- p_boc2 = system->reaxprm.gp.l[1];
-
- /* Calculate Deltaprime, Deltaprime_boc values */
- for( i = 0; i < system->N; ++i ) {
- type_i = system->atoms[i].type;
- sbp_i = &(system->reaxprm.sbp[type_i]);
- workspace->Deltap[i] = workspace->total_bond_order[i] - sbp_i->valency;
- workspace->Deltap_boc[i] =
- workspace->total_bond_order[i] - sbp_i->valency_val;
- workspace->total_bond_order[i] = 0;
- }
- // fprintf( stderr, "done with uncorrected bond orders\n" );
-
-
- /* Corrected Bond Order calculations */
- for( i = 0; i < system->N; ++i ) {
- type_i = system->atoms[i].type;
- sbp_i = &(system->reaxprm.sbp[type_i]);
- val_i = sbp_i->valency;
- Deltap_i = workspace->Deltap[i];
- Deltap_boc_i = workspace->Deltap_boc[i];
- start_i = Start_Index(i, bonds);
- end_i = End_Index(i, bonds);
- //fprintf( stderr, "i:%d Dp:%g Dbocp:%g s:%d e:%d\n",
- // i+1, Deltap_i, Deltap_boc_i, start_i, end_i );
-
- for( pj = start_i; pj < end_i; ++pj ) {
- j = bonds->select.bond_list[pj].nbr;
- type_j = system->atoms[j].type;
- bo_ij = &( bonds->select.bond_list[pj].bo_data );
- //fprintf( stderr, "\tj:%d - ubo: %8.3f\n", j+1, bo_ij->BO );
-
- if( i < j ) {
- twbp = &( system->reaxprm.tbp[type_i][type_j] );
+ num_bonds = 0;
+ p_boc1 = system->reaxprm.gp.l[0];
+ p_boc2 = system->reaxprm.gp.l[1];
+
+ /* Calculate Deltaprime, Deltaprime_boc values */
+ for ( i = 0; i < system->N; ++i )
+ {
+ type_i = system->atoms[i].type;
+ sbp_i = &(system->reaxprm.sbp[type_i]);
+ workspace->Deltap[i] = workspace->total_bond_order[i] - sbp_i->valency;
+ workspace->Deltap_boc[i] =
+ workspace->total_bond_order[i] - sbp_i->valency_val;
+ workspace->total_bond_order[i] = 0;
+ }
+ // fprintf( stderr, "done with uncorrected bond orders\n" );
+
+
+ /* Corrected Bond Order calculations */
+ for ( i = 0; i < system->N; ++i )
+ {
+ type_i = system->atoms[i].type;
+ sbp_i = &(system->reaxprm.sbp[type_i]);
+ val_i = sbp_i->valency;
+ Deltap_i = workspace->Deltap[i];
+ Deltap_boc_i = workspace->Deltap_boc[i];
+ start_i = Start_Index(i, bonds);
+ end_i = End_Index(i, bonds);
+ //fprintf( stderr, "i:%d Dp:%g Dbocp:%g s:%d e:%d\n",
+ // i+1, Deltap_i, Deltap_boc_i, start_i, end_i );
+
+ for ( pj = start_i; pj < end_i; ++pj )
+ {
+ j = bonds->select.bond_list[pj].nbr;
+ type_j = system->atoms[j].type;
+ bo_ij = &( bonds->select.bond_list[pj].bo_data );
+ //fprintf( stderr, "\tj:%d - ubo: %8.3f\n", j+1, bo_ij->BO );
+
+ if ( i < j )
+ {
+ twbp = &( system->reaxprm.tbp[type_i][type_j] );
#ifdef TEST_FORCES
- Set_Start_Index( pj, top_dbo, dBOs );
- /* fprintf( stderr, "%6d%6d%23.15e%23.15e%23.15e\n",
- workspace->reverse_map[i], workspace->reverse_map[j],
- twbp->ovc, twbp->v13cor, bo_ij->BO ); */
+ Set_Start_Index( pj, top_dbo, dBOs );
+ /* fprintf( stderr, "%6d%6d%23.15e%23.15e%23.15e\n",
+ workspace->reverse_map[i], workspace->reverse_map[j],
+ twbp->ovc, twbp->v13cor, bo_ij->BO ); */
#endif
- if( twbp->ovc < 0.001 && twbp->v13cor < 0.001 ) {
- /* There is no correction to bond orders nor to derivatives of
- bond order prime! So we leave bond orders unchanged and
- set derivative of bond order coefficients s.t.
- dBO = dBOp & dBOxx = dBOxxp in Add_dBO_to_Forces */
- bo_ij->C1dbo = 1.000000;
- bo_ij->C2dbo = 0.000000;
- bo_ij->C3dbo = 0.000000;
-
- bo_ij->C1dbopi = bo_ij->BO_pi;
- bo_ij->C2dbopi = 0.000000;
- bo_ij->C3dbopi = 0.000000;
- bo_ij->C4dbopi = 0.000000;
-
- bo_ij->C1dbopi2 = bo_ij->BO_pi2;
- bo_ij->C2dbopi2 = 0.000000;
- bo_ij->C3dbopi2 = 0.000000;
- bo_ij->C4dbopi2 = 0.000000;
-
+ if ( twbp->ovc < 0.001 && twbp->v13cor < 0.001 )
+ {
+ /* There is no correction to bond orders nor to derivatives of
+ bond order prime! So we leave bond orders unchanged and
+ set derivative of bond order coefficients s.t.
+ dBO = dBOp & dBOxx = dBOxxp in Add_dBO_to_Forces */
+ bo_ij->C1dbo = 1.000000;
+ bo_ij->C2dbo = 0.000000;
+ bo_ij->C3dbo = 0.000000;
+
+ bo_ij->C1dbopi = bo_ij->BO_pi;
+ bo_ij->C2dbopi = 0.000000;
+ bo_ij->C3dbopi = 0.000000;
+ bo_ij->C4dbopi = 0.000000;
+
+ bo_ij->C1dbopi2 = bo_ij->BO_pi2;
+ bo_ij->C2dbopi2 = 0.000000;
+ bo_ij->C3dbopi2 = 0.000000;
+ bo_ij->C4dbopi2 = 0.000000;
+
#ifdef TEST_FORCES
- pdbo = &(dBOs->select.dbo_list[ top_dbo ]);
-
- // compute dBO_ij/dr_i
- pdbo->wrt = i;
- rvec_Copy( pdbo->dBO, bo_ij->dBOp );
- rvec_Scale( pdbo->dBOpi, bo_ij->BO_pi, bo_ij->dln_BOp_pi );
- rvec_Scale( pdbo->dBOpi2, bo_ij->BO_pi2, bo_ij->dln_BOp_pi2 );
-
- // compute dBO_ij/dr_j
- pdbo++;
- pdbo->wrt = j;
- rvec_Scale( pdbo->dBO,-1.0,bo_ij->dBOp );
- rvec_Scale( pdbo->dBOpi,-bo_ij->BO_pi,bo_ij->dln_BOp_pi );
- rvec_Scale( pdbo->dBOpi2,-bo_ij->BO_pi2,bo_ij->dln_BOp_pi2 );
-
- top_dbo += 2;
+ pdbo = &(dBOs->select.dbo_list[ top_dbo ]);
+
+ // compute dBO_ij/dr_i
+ pdbo->wrt = i;
+ rvec_Copy( pdbo->dBO, bo_ij->dBOp );
+ rvec_Scale( pdbo->dBOpi, bo_ij->BO_pi, bo_ij->dln_BOp_pi );
+ rvec_Scale( pdbo->dBOpi2, bo_ij->BO_pi2, bo_ij->dln_BOp_pi2 );
+
+ // compute dBO_ij/dr_j
+ pdbo++;
+ pdbo->wrt = j;
+ rvec_Scale( pdbo->dBO, -1.0, bo_ij->dBOp );
+ rvec_Scale( pdbo->dBOpi, -bo_ij->BO_pi, bo_ij->dln_BOp_pi );
+ rvec_Scale( pdbo->dBOpi2, -bo_ij->BO_pi2, bo_ij->dln_BOp_pi2 );
+
+ top_dbo += 2;
#endif
- }
- else {
- val_j = system->reaxprm.sbp[type_j].valency;
- Deltap_j = workspace->Deltap[j];
- Deltap_boc_j = workspace->Deltap_boc[j];
-
- /* on page 1 */
- if( twbp->ovc >= 0.001 ) {
- /* Correction for overcoordination */
- exp_p1i = EXP( -p_boc1 * Deltap_i );
- exp_p2i = EXP( -p_boc2 * Deltap_i );
- exp_p1j = EXP( -p_boc1 * Deltap_j );
- exp_p2j = EXP( -p_boc2 * Deltap_j );
-
- f2 = exp_p1i + exp_p1j;
- f3 = -1.0 / p_boc2 * log( 0.5 * ( exp_p2i + exp_p2j ) );
- f1 = 0.5 * ( ( val_i + f2 )/( val_i + f2 + f3 ) +
- ( val_j + f2 )/( val_j + f2 + f3 ) );
-
- /*fprintf( stderr,"%6d%6d\t%g %g j:%g %g p_boc:%g %g\n",
- i+1, j+1, val_i, Deltap_i, val_j, Deltap_j, p_boc1, p_boc2 );
- fprintf( stderr,"\tf:%g %g %g, exp:%g %g %g %g\n",
- f1, f2, f3, exp_p1i, exp_p2i, exp_p1j, exp_p2j );*/
-
- /* Now come the derivates */
- /* Bond Order pages 5-7, derivative of f1 */
- temp = f2 + f3;
- u1_ij = val_i + temp;
- u1_ji = val_j + temp;
- Cf1A_ij = 0.5 * f3 * (1.0 / SQR( u1_ij ) + 1.0 / SQR( u1_ji ));
- Cf1B_ij = -0.5 * (( u1_ij - f3 ) / SQR( u1_ij ) +
- ( u1_ji - f3 ) / SQR( u1_ji ));
-
- //Cf1_ij = -Cf1A_ij * p_boc1 * exp_p1i +
- // Cf1B_ij * exp_p2i / ( exp_p2i + exp_p2j );
- Cf1_ij = 0.50 * ( -p_boc1 * exp_p1i / u1_ij -
- ((val_i+f2) / SQR(u1_ij)) *
- ( -p_boc1 * exp_p1i +
- exp_p2i / ( exp_p2i + exp_p2j ) ) +
- -p_boc1 * exp_p1i / u1_ji -
- ((val_j+f2)/SQR(u1_ji)) * ( -p_boc1*exp_p1i +
- exp_p2i / ( exp_p2i + exp_p2j ) ));
-
- Cf1_ji = -Cf1A_ij * p_boc1 * exp_p1j +
- Cf1B_ij * exp_p2j / ( exp_p2i + exp_p2j );
- //fprintf( stderr, "\tCf1:%g %g\n", Cf1_ij, Cf1_ji );
- }
- else {
- /* No overcoordination correction! */
- f1 = 1.0;
- Cf1_ij = Cf1_ji = 0.0;
- }
-
- if( twbp->v13cor >= 0.001 ) {
- /* Correction for 1-3 bond orders */
- exp_f4 =EXP(-(twbp->p_boc4 * SQR( bo_ij->BO ) -
- Deltap_boc_i) * twbp->p_boc3 + twbp->p_boc5);
- exp_f5 =EXP(-(twbp->p_boc4 * SQR( bo_ij->BO ) -
- Deltap_boc_j) * twbp->p_boc3 + twbp->p_boc5);
-
- f4 = 1. / (1. + exp_f4);
- f5 = 1. / (1. + exp_f5);
- f4f5 = f4 * f5;
-
- /* Bond Order pages 8-9, derivative of f4 and f5 */
- /*temp = twbp->p_boc5 -
- twbp->p_boc3 * twbp->p_boc4 * SQR( bo_ij->BO );
- u_ij = temp + twbp->p_boc3 * Deltap_boc_i;
- u_ji = temp + twbp->p_boc3 * Deltap_boc_j;
- Cf45_ij = Cf45( u_ij, u_ji ) / f4f5;
- Cf45_ji = Cf45( u_ji, u_ij ) / f4f5;*/
- Cf45_ij = -f4 * exp_f4;
- Cf45_ji = -f5 * exp_f5;
- }
- else {
- f4 = f5 = f4f5 = 1.0;
- Cf45_ij = Cf45_ji = 0.0;
- }
-
- /* Bond Order page 10, derivative of total bond order */
- A0_ij = f1 * f4f5;
- A1_ij = -2 * twbp->p_boc3 * twbp->p_boc4 * bo_ij->BO *
- (Cf45_ij + Cf45_ji);
- A2_ij = Cf1_ij / f1 + twbp->p_boc3 * Cf45_ij;
- A2_ji = Cf1_ji / f1 + twbp->p_boc3 * Cf45_ji;
- A3_ij = A2_ij + Cf1_ij / f1;
- A3_ji = A2_ji + Cf1_ji / f1;
-
- /*fprintf( stderr, "\tBO: %f, A0: %f, A1: %f, A2_ij: %f
- A2_ji: %f, A3_ij: %f, A3_ji: %f\n",
- bo_ij->BO, A0_ij, A1_ij, A2_ij, A2_ji, A3_ij, A3_ji );*/
-
-
- /* find corrected bond order values and their deriv coefs */
- bo_ij->BO = bo_ij->BO * A0_ij;
- bo_ij->BO_pi = bo_ij->BO_pi * A0_ij *f1;
- bo_ij->BO_pi2= bo_ij->BO_pi2* A0_ij *f1;
- bo_ij->BO_s = bo_ij->BO - ( bo_ij->BO_pi + bo_ij->BO_pi2 );
-
- bo_ij->C1dbo = A0_ij + bo_ij->BO * A1_ij;
- bo_ij->C2dbo = bo_ij->BO * A2_ij;
- bo_ij->C3dbo = bo_ij->BO * A2_ji;
-
- bo_ij->C1dbopi = f1*f1*f4*f5;
- bo_ij->C2dbopi = bo_ij->BO_pi * A1_ij;
- bo_ij->C3dbopi = bo_ij->BO_pi * A3_ij;
- bo_ij->C4dbopi = bo_ij->BO_pi * A3_ji;
-
- bo_ij->C1dbopi2 = f1*f1*f4*f5;
- bo_ij->C2dbopi2 = bo_ij->BO_pi2 * A1_ij;
- bo_ij->C3dbopi2 = bo_ij->BO_pi2 * A3_ij;
- bo_ij->C4dbopi2 = bo_ij->BO_pi2 * A3_ji;
-
+ }
+ else
+ {
+ val_j = system->reaxprm.sbp[type_j].valency;
+ Deltap_j = workspace->Deltap[j];
+ Deltap_boc_j = workspace->Deltap_boc[j];
+
+ /* on page 1 */
+ if ( twbp->ovc >= 0.001 )
+ {
+ /* Correction for overcoordination */
+ exp_p1i = EXP( -p_boc1 * Deltap_i );
+ exp_p2i = EXP( -p_boc2 * Deltap_i );
+ exp_p1j = EXP( -p_boc1 * Deltap_j );
+ exp_p2j = EXP( -p_boc2 * Deltap_j );
+
+ f2 = exp_p1i + exp_p1j;
+ f3 = -1.0 / p_boc2 * log( 0.5 * ( exp_p2i + exp_p2j ) );
+ f1 = 0.5 * ( ( val_i + f2 ) / ( val_i + f2 + f3 ) +
+ ( val_j + f2 ) / ( val_j + f2 + f3 ) );
+
+ /*fprintf( stderr,"%6d%6d\t%g %g j:%g %g p_boc:%g %g\n",
+ i+1, j+1, val_i, Deltap_i, val_j, Deltap_j, p_boc1, p_boc2 );
+ fprintf( stderr,"\tf:%g %g %g, exp:%g %g %g %g\n",
+ f1, f2, f3, exp_p1i, exp_p2i, exp_p1j, exp_p2j );*/
+
+ /* Now come the derivates */
+ /* Bond Order pages 5-7, derivative of f1 */
+ temp = f2 + f3;
+ u1_ij = val_i + temp;
+ u1_ji = val_j + temp;
+ Cf1A_ij = 0.5 * f3 * (1.0 / SQR( u1_ij ) + 1.0 / SQR( u1_ji ));
+ Cf1B_ij = -0.5 * (( u1_ij - f3 ) / SQR( u1_ij ) +
+ ( u1_ji - f3 ) / SQR( u1_ji ));
+
+ //Cf1_ij = -Cf1A_ij * p_boc1 * exp_p1i +
+ // Cf1B_ij * exp_p2i / ( exp_p2i + exp_p2j );
+ Cf1_ij = 0.50 * ( -p_boc1 * exp_p1i / u1_ij -
+ ((val_i + f2) / SQR(u1_ij)) *
+ ( -p_boc1 * exp_p1i +
+ exp_p2i / ( exp_p2i + exp_p2j ) ) +
+ -p_boc1 * exp_p1i / u1_ji -
+ ((val_j + f2) / SQR(u1_ji)) * ( -p_boc1 * exp_p1i +
+ exp_p2i / ( exp_p2i + exp_p2j ) ));
+
+ Cf1_ji = -Cf1A_ij * p_boc1 * exp_p1j +
+ Cf1B_ij * exp_p2j / ( exp_p2i + exp_p2j );
+ //fprintf( stderr, "\tCf1:%g %g\n", Cf1_ij, Cf1_ji );
+ }
+ else
+ {
+ /* No overcoordination correction! */
+ f1 = 1.0;
+ Cf1_ij = Cf1_ji = 0.0;
+ }
+
+ if ( twbp->v13cor >= 0.001 )
+ {
+ /* Correction for 1-3 bond orders */
+ exp_f4 = EXP(-(twbp->p_boc4 * SQR( bo_ij->BO ) -
+ Deltap_boc_i) * twbp->p_boc3 + twbp->p_boc5);
+ exp_f5 = EXP(-(twbp->p_boc4 * SQR( bo_ij->BO ) -
+ Deltap_boc_j) * twbp->p_boc3 + twbp->p_boc5);
+
+ f4 = 1. / (1. + exp_f4);
+ f5 = 1. / (1. + exp_f5);
+ f4f5 = f4 * f5;
+
+ /* Bond Order pages 8-9, derivative of f4 and f5 */
+ /*temp = twbp->p_boc5 -
+ twbp->p_boc3 * twbp->p_boc4 * SQR( bo_ij->BO );
+ u_ij = temp + twbp->p_boc3 * Deltap_boc_i;
+ u_ji = temp + twbp->p_boc3 * Deltap_boc_j;
+ Cf45_ij = Cf45( u_ij, u_ji ) / f4f5;
+ Cf45_ji = Cf45( u_ji, u_ij ) / f4f5;*/
+ Cf45_ij = -f4 * exp_f4;
+ Cf45_ji = -f5 * exp_f5;
+ }
+ else
+ {
+ f4 = f5 = f4f5 = 1.0;
+ Cf45_ij = Cf45_ji = 0.0;
+ }
+
+ /* Bond Order page 10, derivative of total bond order */
+ A0_ij = f1 * f4f5;
+ A1_ij = -2 * twbp->p_boc3 * twbp->p_boc4 * bo_ij->BO *
+ (Cf45_ij + Cf45_ji);
+ A2_ij = Cf1_ij / f1 + twbp->p_boc3 * Cf45_ij;
+ A2_ji = Cf1_ji / f1 + twbp->p_boc3 * Cf45_ji;
+ A3_ij = A2_ij + Cf1_ij / f1;
+ A3_ji = A2_ji + Cf1_ji / f1;
+
+ /*fprintf( stderr, "\tBO: %f, A0: %f, A1: %f, A2_ij: %f
+ A2_ji: %f, A3_ij: %f, A3_ji: %f\n",
+ bo_ij->BO, A0_ij, A1_ij, A2_ij, A2_ji, A3_ij, A3_ji );*/
+
+
+ /* find corrected bond order values and their deriv coefs */
+ bo_ij->BO = bo_ij->BO * A0_ij;
+ bo_ij->BO_pi = bo_ij->BO_pi * A0_ij * f1;
+ bo_ij->BO_pi2 = bo_ij->BO_pi2 * A0_ij * f1;
+ bo_ij->BO_s = bo_ij->BO - ( bo_ij->BO_pi + bo_ij->BO_pi2 );
+
+ bo_ij->C1dbo = A0_ij + bo_ij->BO * A1_ij;
+ bo_ij->C2dbo = bo_ij->BO * A2_ij;
+ bo_ij->C3dbo = bo_ij->BO * A2_ji;
+
+ bo_ij->C1dbopi = f1 * f1 * f4 * f5;
+ bo_ij->C2dbopi = bo_ij->BO_pi * A1_ij;
+ bo_ij->C3dbopi = bo_ij->BO_pi * A3_ij;
+ bo_ij->C4dbopi = bo_ij->BO_pi * A3_ji;
+
+ bo_ij->C1dbopi2 = f1 * f1 * f4 * f5;
+ bo_ij->C2dbopi2 = bo_ij->BO_pi2 * A1_ij;
+ bo_ij->C3dbopi2 = bo_ij->BO_pi2 * A3_ij;
+ bo_ij->C4dbopi2 = bo_ij->BO_pi2 * A3_ji;
+
#ifdef TEST_FORCES
- /*fprintf( stderr, "%6d%6d%13.6f%13.6f%13.6f%13.6f\n",
- i+1, j+1, bo_ij->BO, bo_ij->C1dbo, Cf45_ij, Cf45_ji );*/
-
- /* fprintf( stderr, "%6d%6d%13.6f%13.6f%13.6f%13.6f\n",
- //"%6d%6d%10.6f%10.6f%10.6f%10.6f\n%10.6f%10.6f%10.6f\n%10.6f%10.6f%10.6f%10.6f\n%10.6f%10.6f%10.6f%10.6f\n\n",
- workspace->orig_id[i], workspace->orig_id[j]
- A0_ij, A1_ij, A2_ij, A2_ji, A3_ij, A3_ji
- bo_ij->BO, bo_ij->BO_pi, bo_ij->BO_pi2, bo_ij->BO_s,
- bo_ij->C1dbo, bo_ij->C2dbo, bo_ij->C3dbo,
- bo_ij->C1dbopi,bo_ij->C2dbopi,bo_ij->C3dbopi,bo_ij->C4dbopi,
- bo_ij->C1dbopi2,bo_ij->C2dbopi2,bo_ij->C3dbopi2,bo_ij->C4dbopi2
- ); */
-
- Calculate_dBO( i, pj, workspace, lists, &top_dbo );
+ /*fprintf( stderr, "%6d%6d%13.6f%13.6f%13.6f%13.6f\n",
+ i+1, j+1, bo_ij->BO, bo_ij->C1dbo, Cf45_ij, Cf45_ji );*/
+
+ /* fprintf( stderr, "%6d%6d%13.6f%13.6f%13.6f%13.6f\n",
+ //"%6d%6d%10.6f%10.6f%10.6f%10.6f\n%10.6f%10.6f%10.6f\n%10.6f%10.6f%10.6f%10.6f\n%10.6f%10.6f%10.6f%10.6f\n\n",
+ workspace->orig_id[i], workspace->orig_id[j]
+ A0_ij, A1_ij, A2_ij, A2_ji, A3_ij, A3_ji
+ bo_ij->BO, bo_ij->BO_pi, bo_ij->BO_pi2, bo_ij->BO_s,
+ bo_ij->C1dbo, bo_ij->C2dbo, bo_ij->C3dbo,
+ bo_ij->C1dbopi,bo_ij->C2dbopi,bo_ij->C3dbopi,bo_ij->C4dbopi,
+ bo_ij->C1dbopi2,bo_ij->C2dbopi2,bo_ij->C3dbopi2,bo_ij->C4dbopi2
+ ); */
+
+ Calculate_dBO( i, pj, workspace, lists, &top_dbo );
#endif
- }
-
- /* neglect bonds that are < 1e-10 */
- if( bo_ij->BO < 1e-10 )
- bo_ij->BO = 0.0;
- if( bo_ij->BO_s < 1e-10 )
- bo_ij->BO_s = 0.0;
- if( bo_ij->BO_pi < 1e-10 )
- bo_ij->BO_pi = 0.0;
- if( bo_ij->BO_pi2 < 1e-10 )
- bo_ij->BO_pi2 = 0.0;
-
- workspace->total_bond_order[i] += bo_ij->BO; // now keeps total_BO
-
-
- /* fprintf( stderr, "%d %d\t%g %g %g %g\n
- Cdbo:\t%g %g %g\n
- Cdbopi:\t%g %g %g %g\n
- Cdbopi2:%g %g %g %g\n\n",
- i+1, j+1, bonds->select.bond_list[ pj ].d,
- bo_ij->BO,bo_ij->BO_pi, bo_ij->BO_pi2,
- bo_ij->C1dbo, bo_ij->C2dbo, bo_ij->C3dbo,
- bo_ij->C1dbopi, bo_ij->C2dbopi, bo_ij->C3dbopi, bo_ij->C4dbopi,
- bo_ij->C1dbopi2, bo_ij->C2dbopi2,
- bo_ij->C3dbopi2, bo_ij->C4dbopi2 ); */
-
- /* fprintf( stderr, "%d %d, BO:%f BO_s:%f BO_pi:%f BO_pi2:%f\n",
- i+1,j+1,bo_ij->BO,bo_ij->BO_s,bo_ij->BO_pi,bo_ij->BO_pi2 ); */
-
+ }
+
+ /* neglect bonds that are < 1e-10 */
+ if ( bo_ij->BO < 1e-10 )
+ bo_ij->BO = 0.0;
+ if ( bo_ij->BO_s < 1e-10 )
+ bo_ij->BO_s = 0.0;
+ if ( bo_ij->BO_pi < 1e-10 )
+ bo_ij->BO_pi = 0.0;
+ if ( bo_ij->BO_pi2 < 1e-10 )
+ bo_ij->BO_pi2 = 0.0;
+
+ workspace->total_bond_order[i] += bo_ij->BO; // now keeps total_BO
+
+
+ /* fprintf( stderr, "%d %d\t%g %g %g %g\n
+ Cdbo:\t%g %g %g\n
+ Cdbopi:\t%g %g %g %g\n
+ Cdbopi2:%g %g %g %g\n\n",
+ i+1, j+1, bonds->select.bond_list[ pj ].d,
+ bo_ij->BO,bo_ij->BO_pi, bo_ij->BO_pi2,
+ bo_ij->C1dbo, bo_ij->C2dbo, bo_ij->C3dbo,
+ bo_ij->C1dbopi, bo_ij->C2dbopi, bo_ij->C3dbopi, bo_ij->C4dbopi,
+ bo_ij->C1dbopi2, bo_ij->C2dbopi2,
+ bo_ij->C3dbopi2, bo_ij->C4dbopi2 ); */
+
+ /* fprintf( stderr, "%d %d, BO:%f BO_s:%f BO_pi:%f BO_pi2:%f\n",
+ i+1,j+1,bo_ij->BO,bo_ij->BO_s,bo_ij->BO_pi,bo_ij->BO_pi2 ); */
+
#ifdef TEST_FORCES
- Set_End_Index( pj, top_dbo, dBOs );
- Add_dBO( system, lists, i, pj, 1.0, workspace->dDelta );
+ Set_End_Index( pj, top_dbo, dBOs );
+ Add_dBO( system, lists, i, pj, 1.0, workspace->dDelta );
#endif
- }
- else {
- /* We only need to update bond orders from bo_ji
- everything else is set in uncorrected_bo calculations */
- sym_index = bonds->select.bond_list[pj].sym_index;
- bo_ji = &(bonds->select.bond_list[ sym_index ].bo_data);
- bo_ij->BO = bo_ji->BO;
- bo_ij->BO_s = bo_ji->BO_s;
- bo_ij->BO_pi = bo_ji->BO_pi;
- bo_ij->BO_pi2 = bo_ji->BO_pi2;
-
- workspace->total_bond_order[i] += bo_ij->BO; // now keeps total_BO
+ }
+ else
+ {
+ /* We only need to update bond orders from bo_ji
+ everything else is set in uncorrected_bo calculations */
+ sym_index = bonds->select.bond_list[pj].sym_index;
+ bo_ji = &(bonds->select.bond_list[ sym_index ].bo_data);
+ bo_ij->BO = bo_ji->BO;
+ bo_ij->BO_s = bo_ji->BO_s;
+ bo_ij->BO_pi = bo_ji->BO_pi;
+ bo_ij->BO_pi2 = bo_ji->BO_pi2;
+
+ workspace->total_bond_order[i] += bo_ij->BO; // now keeps total_BO
#ifdef TEST_FORCES
- Add_dBO( system, lists, j, sym_index, 1.0, workspace->dDelta );
+ Add_dBO( system, lists, j, sym_index, 1.0, workspace->dDelta );
#endif
- }
- }
-
-#ifdef TEST_FORCES
- // fprintf( stderr, "dDelta computations\nj:" );
- Set_Start_Index( i, top_dDelta, dDeltas );
- ptop_dDelta = &( dDeltas->select.dDelta_list[top_dDelta] );
-
- for( pj = start_i; pj < end_i; ++pj ) {
- j = bonds->select.bond_list[pj].nbr;
- // fprintf( stderr, "%d ", j );
-
- if( !rvec_isZero( workspace->dDelta[j] ) ) {
- ptop_dDelta->wrt = j;
- rvec_Copy( ptop_dDelta->dVal, workspace->dDelta[j] );
- rvec_MakeZero( workspace->dDelta[j] );
- ++top_dDelta, ++ptop_dDelta;
- }
-
- start_j = Start_Index(j, bonds);
- end_j = End_Index(j, bonds);
- for( pk = start_j; pk < end_j; ++pk ) {
- k = bonds->select.bond_list[pk].nbr;
- if( !rvec_isZero( workspace->dDelta[k] ) ) {
- ptop_dDelta->wrt = k;
- rvec_Copy( ptop_dDelta->dVal, workspace->dDelta[k] );
- rvec_MakeZero( workspace->dDelta[k] );
- ++top_dDelta, ++ptop_dDelta;
- }
- }
- }
-
- Set_End_Index( i, top_dDelta, dDeltas );
-
- /*for( pj=Start_Index(i,dDeltas); pj<End_Index(i,dDeltas); ++pj )
- fprintf( stdout, "dDel: %d %d [%g %g %g]\n",
- i+1, dDeltas->select.dDelta_list[pj].wrt+1,
- dDeltas->select.dDelta_list[pj].dVal[0],
- dDeltas->select.dDelta_list[pj].dVal[1],
- dDeltas->select.dDelta_list[pj].dVal[2] );*/
+ }
+ }
+
+#ifdef TEST_FORCES
+ // fprintf( stderr, "dDelta computations\nj:" );
+ Set_Start_Index( i, top_dDelta, dDeltas );
+ ptop_dDelta = &( dDeltas->select.dDelta_list[top_dDelta] );
+
+ for ( pj = start_i; pj < end_i; ++pj )
+ {
+ j = bonds->select.bond_list[pj].nbr;
+ // fprintf( stderr, "%d ", j );
+
+ if ( !rvec_isZero( workspace->dDelta[j] ) )
+ {
+ ptop_dDelta->wrt = j;
+ rvec_Copy( ptop_dDelta->dVal, workspace->dDelta[j] );
+ rvec_MakeZero( workspace->dDelta[j] );
+ ++top_dDelta, ++ptop_dDelta;
+ }
+
+ start_j = Start_Index(j, bonds);
+ end_j = End_Index(j, bonds);
+ for ( pk = start_j; pk < end_j; ++pk )
+ {
+ k = bonds->select.bond_list[pk].nbr;
+ if ( !rvec_isZero( workspace->dDelta[k] ) )
+ {
+ ptop_dDelta->wrt = k;
+ rvec_Copy( ptop_dDelta->dVal, workspace->dDelta[k] );
+ rvec_MakeZero( workspace->dDelta[k] );
+ ++top_dDelta, ++ptop_dDelta;
+ }
+ }
+ }
+
+ Set_End_Index( i, top_dDelta, dDeltas );
+
+ /*for( pj=Start_Index(i,dDeltas); pj<End_Index(i,dDeltas); ++pj )
+ fprintf( stdout, "dDel: %d %d [%g %g %g]\n",
+ i+1, dDeltas->select.dDelta_list[pj].wrt+1,
+ dDeltas->select.dDelta_list[pj].dVal[0],
+ dDeltas->select.dDelta_list[pj].dVal[1],
+ dDeltas->select.dDelta_list[pj].dVal[2] );*/
#endif
- }
-
- /*fprintf(stderr,"\tCalculated actual bond orders ...\n" );
- fprintf(stderr,"%6s%8s%8s%8s%8s%8s%8s%8s\n",
- "atom", "Delta", "Delta_e", "Delta_boc", "nlp",
- "Delta_lp", "Clp", "dDelta_lp" );*/
-
- p_lp1 = system->reaxprm.gp.l[15];
- /* Calculate some helper variables that are used at many places
- throughout force calculations */
- for( j = 0; j < system->N; ++j ) {
- type_j = system->atoms[j].type;
- sbp_j = &(system->reaxprm.sbp[ type_j ]);
-
- workspace->Delta[j] = workspace->total_bond_order[j] - sbp_j->valency;
- workspace->Delta_e[j] = workspace->total_bond_order[j] - sbp_j->valency_e;
- workspace->Delta_boc[j] = workspace->total_bond_order[j] -
- sbp_j->valency_boc;
-
- workspace->vlpex[j] = workspace->Delta_e[j] -
- 2.0 * (int)(workspace->Delta_e[j]/2.0);
- explp1 = EXP(-p_lp1 * SQR(2.0 + workspace->vlpex[j]));
- workspace->nlp[j] = explp1 - (int)(workspace->Delta_e[j] / 2.0);
- workspace->Delta_lp[j] = sbp_j->nlp_opt - workspace->nlp[j];
- workspace->Clp[j] = 2.0 * p_lp1 * explp1 * (2.0 + workspace->vlpex[j]);
- /* Adri uses different dDelta_lp values than the ones in notes... */
- workspace->dDelta_lp[j] = workspace->Clp[j];
- //workspace->dDelta_lp[j] = workspace->Clp[j] + (0.5-workspace->Clp[j]) *
- //((fabs(workspace->Delta_e[j]/2.0 -
- // (int)(workspace->Delta_e[j]/2.0)) < 0.1) ? 1 : 0 );
-
- if( sbp_j->mass > 21.0 ) {
- workspace->nlp_temp[j] = 0.5 * (sbp_j->valency_e - sbp_j->valency);
- workspace->Delta_lp_temp[j] = sbp_j->nlp_opt - workspace->nlp_temp[j];
- workspace->dDelta_lp_temp[j] = 0.;
- }
- else {
- workspace->nlp_temp[j] = workspace->nlp[j];
- workspace->Delta_lp_temp[j] = sbp_j->nlp_opt - workspace->nlp_temp[j];
- workspace->dDelta_lp_temp[j] = workspace->Clp[j];
}
- //fprintf( stderr, "%d\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
- //j, workspace->Delta[j], workspace->Delta_e[j], workspace->Delta_boc[j],
- //workspace->nlp[j], system->reaxprm.sbp[type_j].nlp_opt,
- //workspace->Delta_lp[j], workspace->Clp[j], workspace->dDelta_lp[j] );
- }
+ /*fprintf(stderr,"\tCalculated actual bond orders ...\n" );
+ fprintf(stderr,"%6s%8s%8s%8s%8s%8s%8s%8s\n",
+ "atom", "Delta", "Delta_e", "Delta_boc", "nlp",
+ "Delta_lp", "Clp", "dDelta_lp" );*/
+
+ p_lp1 = system->reaxprm.gp.l[15];
+ /* Calculate some helper variables that are used at many places
+ throughout force calculations */
+ for ( j = 0; j < system->N; ++j )
+ {
+ type_j = system->atoms[j].type;
+ sbp_j = &(system->reaxprm.sbp[ type_j ]);
+
+ workspace->Delta[j] = workspace->total_bond_order[j] - sbp_j->valency;
+ workspace->Delta_e[j] = workspace->total_bond_order[j] - sbp_j->valency_e;
+ workspace->Delta_boc[j] = workspace->total_bond_order[j] -
+ sbp_j->valency_boc;
+
+ workspace->vlpex[j] = workspace->Delta_e[j] -
+ 2.0 * (int)(workspace->Delta_e[j] / 2.0);
+ explp1 = EXP(-p_lp1 * SQR(2.0 + workspace->vlpex[j]));
+ workspace->nlp[j] = explp1 - (int)(workspace->Delta_e[j] / 2.0);
+ workspace->Delta_lp[j] = sbp_j->nlp_opt - workspace->nlp[j];
+ workspace->Clp[j] = 2.0 * p_lp1 * explp1 * (2.0 + workspace->vlpex[j]);
+ /* Adri uses different dDelta_lp values than the ones in notes... */
+ workspace->dDelta_lp[j] = workspace->Clp[j];
+ //workspace->dDelta_lp[j] = workspace->Clp[j] + (0.5-workspace->Clp[j]) *
+ //((fabs(workspace->Delta_e[j]/2.0 -
+ // (int)(workspace->Delta_e[j]/2.0)) < 0.1) ? 1 : 0 );
+
+ if ( sbp_j->mass > 21.0 )
+ {
+ workspace->nlp_temp[j] = 0.5 * (sbp_j->valency_e - sbp_j->valency);
+ workspace->Delta_lp_temp[j] = sbp_j->nlp_opt - workspace->nlp_temp[j];
+ workspace->dDelta_lp_temp[j] = 0.;
+ }
+ else
+ {
+ workspace->nlp_temp[j] = workspace->nlp[j];
+ workspace->Delta_lp_temp[j] = sbp_j->nlp_opt - workspace->nlp_temp[j];
+ workspace->dDelta_lp_temp[j] = workspace->Clp[j];
+ }
+
+ //fprintf( stderr, "%d\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
+ //j, workspace->Delta[j], workspace->Delta_e[j], workspace->Delta_boc[j],
+ //workspace->nlp[j], system->reaxprm.sbp[type_j].nlp_opt,
+ //workspace->Delta_lp[j], workspace->Clp[j], workspace->dDelta_lp[j] );
+ }
- //Print_Bonds( system, bonds, "sbonds.out" );
+ //Print_Bonds( system, bonds, "sbonds.out" );
#if defined(DEBUG)
- fprintf( stderr, "Number of bonds: %d\n", num_bonds );
- Print_Bond_Orders( system, control, data, workspace, lists, out_control );
+ fprintf( stderr, "Number of bonds: %d\n", num_bonds );
+ Print_Bond_Orders( system, control, data, workspace, lists, out_control );
#endif
}
diff --git a/puremd_rc_1003/sPuReMD/bond_orders.h b/puremd_rc_1003/sPuReMD/bond_orders.h
index 8ac3492c80f7092e7cd4e768c2d119633c70e8e7..b6ca199ed923b74a126b993cdeafbe98eb414756 100644
--- a/puremd_rc_1003/sPuReMD/bond_orders.h
+++ b/puremd_rc_1003/sPuReMD/bond_orders.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -24,12 +24,13 @@
#include "mytypes.h"
-typedef struct{
- real C1dbo, C2dbo, C3dbo;
- real C1dbopi, C2dbopi, C3dbopi, C4dbopi;
- real C1dbopi2, C2dbopi2, C3dbopi2, C4dbopi2;
- real C1dDelta, C2dDelta, C3dDelta;
-}dbond_coefficients;
+typedef struct
+{
+ real C1dbo, C2dbo, C3dbo;
+ real C1dbopi, C2dbopi, C3dbopi, C4dbopi;
+ real C1dbopi2, C2dbopi2, C3dbopi2, C4dbopi2;
+ real C1dDelta, C2dDelta, C3dDelta;
+} dbond_coefficients;
#ifdef TEST_FORCES
void Get_dBO( reax_system*, list**, int, int, real, rvec* );
@@ -45,10 +46,10 @@ void Add_dDelta( reax_system*, list**, int, real, rvec* );
void Add_dDelta_to_Forces( reax_system *, list**, int, real );
#endif
-void Add_dBond_to_Forces( int, int, reax_system*, simulation_data*,
- static_storage*, list** );
-void Add_dBond_to_Forces_NPT( int, int, reax_system*, simulation_data*,
- static_storage*, list** );
+void Add_dBond_to_Forces( int, int, reax_system*, simulation_data*,
+ static_storage*, list** );
+void Add_dBond_to_Forces_NPT( int, int, reax_system*, simulation_data*,
+ static_storage*, list** );
void Calculate_Bond_Orders( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, list**, output_controls* );
#endif
diff --git a/puremd_rc_1003/sPuReMD/box.c b/puremd_rc_1003/sPuReMD/box.c
index d0daa6a5e1e58b4f9c6245790d5a328607b89065..c9bd50c4a14392759f0eb8935748b0b64a46ee63 100644
--- a/puremd_rc_1003/sPuReMD/box.c
+++ b/puremd_rc_1003/sPuReMD/box.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -23,540 +23,565 @@
#include "vector.h"
-void Init_Box_From_CRYST(real a, real b, real c,
- real alpha, real beta, real gamma,
- simulation_box* box )
+void Init_Box_From_CRYST(real a, real b, real c,
+ real alpha, real beta, real gamma,
+ simulation_box* box )
{
- double c_alpha, c_beta, c_gamma, s_gamma, zi;
+ double c_alpha, c_beta, c_gamma, s_gamma, zi;
- c_alpha = cos(DEG2RAD(alpha));
- c_beta = cos(DEG2RAD(beta));
- c_gamma = cos(DEG2RAD(gamma));
- s_gamma = sin(DEG2RAD(gamma));
+ c_alpha = cos(DEG2RAD(alpha));
+ c_beta = cos(DEG2RAD(beta));
+ c_gamma = cos(DEG2RAD(gamma));
+ s_gamma = sin(DEG2RAD(gamma));
- zi = (c_alpha - c_beta * c_gamma)/s_gamma;
+ zi = (c_alpha - c_beta * c_gamma) / s_gamma;
- box->box[0][0] = a;
- box->box[0][1] = 0.0;
- box->box[0][2] = 0.0;
-
- box->box[1][0] = b * c_gamma;
- box->box[1][1] = b * s_gamma;
- box->box[1][2] = 0.0;
+ box->box[0][0] = a;
+ box->box[0][1] = 0.0;
+ box->box[0][2] = 0.0;
- box->box[2][0] = c * c_beta;
- box->box[2][1] = c * zi;
- box->box[2][2] = c * SQRT(1.0 - SQR(c_beta) - SQR(zi));
+ box->box[1][0] = b * c_gamma;
+ box->box[1][1] = b * s_gamma;
+ box->box[1][2] = 0.0;
- Make_Consistent( box );
+ box->box[2][0] = c * c_beta;
+ box->box[2][1] = c * zi;
+ box->box[2][2] = c * SQRT(1.0 - SQR(c_beta) - SQR(zi));
+
+ Make_Consistent( box );
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "box is %8.2f x %8.2f x %8.2f\n",
- box->box[0][0], box->box[1][1], box->box[2][2] );
+ fprintf( stderr, "box is %8.2f x %8.2f x %8.2f\n",
+ box->box[0][0], box->box[1][1], box->box[2][2] );
#endif
}
void Update_Box( rtensor box_tensor, simulation_box* box )
{
- int i, j;
+ int i, j;
- for (i=0; i < 3; i++)
- for (j=0; j < 3; j++)
- box->box[i][j] = box_tensor[i][j];
+ for (i = 0; i < 3; i++)
+ for (j = 0; j < 3; j++)
+ box->box[i][j] = box_tensor[i][j];
- Make_Consistent( box );
+ Make_Consistent( box );
}
void Update_Box_Isotropic( simulation_box *box, real mu )
{
- /*box->box[0][0] =
- POW( V_new / ( box->side_prop[1] * box->side_prop[2] ), 1.0/3.0 );
- box->box[1][1] = box->box[0][0] * box->side_prop[1];
- box->box[2][2] = box->box[0][0] * box->side_prop[2];
- */
- rtensor_Copy( box->old_box, box->box );
- box->box[0][0] *= mu;
- box->box[1][1] *= mu;
- box->box[2][2] *= mu;
-
- box->volume = box->box[0][0]*box->box[1][1]*box->box[2][2];
- Make_Consistent(box/*, periodic*/);
+ /*box->box[0][0] =
+ POW( V_new / ( box->side_prop[1] * box->side_prop[2] ), 1.0/3.0 );
+ box->box[1][1] = box->box[0][0] * box->side_prop[1];
+ box->box[2][2] = box->box[0][0] * box->side_prop[2];
+ */
+ rtensor_Copy( box->old_box, box->box );
+ box->box[0][0] *= mu;
+ box->box[1][1] *= mu;
+ box->box[2][2] *= mu;
+
+ box->volume = box->box[0][0] * box->box[1][1] * box->box[2][2];
+ Make_Consistent(box/*, periodic*/);
}
void Update_Box_SemiIsotropic( simulation_box *box, rvec mu )
{
- /*box->box[0][0] =
- POW( V_new / ( box->side_prop[1] * box->side_prop[2] ), 1.0/3.0 );
- box->box[1][1] = box->box[0][0] * box->side_prop[1];
- box->box[2][2] = box->box[0][0] * box->side_prop[2]; */
- rtensor_Copy( box->old_box, box->box );
- box->box[0][0] *= mu[0];
- box->box[1][1] *= mu[1];
- box->box[2][2] *= mu[2];
-
- box->volume = box->box[0][0]*box->box[1][1]*box->box[2][2];
- Make_Consistent(box);
+ /*box->box[0][0] =
+ POW( V_new / ( box->side_prop[1] * box->side_prop[2] ), 1.0/3.0 );
+ box->box[1][1] = box->box[0][0] * box->side_prop[1];
+ box->box[2][2] = box->box[0][0] * box->side_prop[2]; */
+ rtensor_Copy( box->old_box, box->box );
+ box->box[0][0] *= mu[0];
+ box->box[1][1] *= mu[1];
+ box->box[2][2] *= mu[2];
+
+ box->volume = box->box[0][0] * box->box[1][1] * box->box[2][2];
+ Make_Consistent(box);
}
void Make_Consistent(simulation_box* box)
{
- real one_vol;
-
- box->volume =
- box->box[0][0] * (box->box[1][1]*box->box[2][2] -
- box->box[2][1]*box->box[2][1]) +
- box->box[0][1] * (box->box[2][0]*box->box[1][2] -
- box->box[1][0]*box->box[2][2]) +
- box->box[0][2] * (box->box[1][0]*box->box[2][1] -
- box->box[2][0]*box->box[1][1]);
-
- one_vol = 1.0/box->volume;
-
- box->box_inv[0][0] = (box->box[1][1]*box->box[2][2] -
- box->box[1][2]*box->box[2][1]) * one_vol;
- box->box_inv[0][1] = (box->box[0][2]*box->box[2][1] -
- box->box[0][1]*box->box[2][2]) * one_vol;
- box->box_inv[0][2] = (box->box[0][1]*box->box[1][2] -
- box->box[0][2]*box->box[1][1]) * one_vol;
-
- box->box_inv[1][0] = (box->box[1][2]*box->box[2][0] -
- box->box[1][0]*box->box[2][2]) * one_vol;
- box->box_inv[1][1] = (box->box[0][0]*box->box[2][2] -
- box->box[0][2]*box->box[2][0]) * one_vol;
- box->box_inv[1][2] = (box->box[0][2]*box->box[1][0] -
- box->box[0][0]*box->box[1][2]) * one_vol;
-
- box->box_inv[2][0] = (box->box[1][0]*box->box[2][1] -
- box->box[1][1]*box->box[2][0]) * one_vol;
- box->box_inv[2][1] = (box->box[0][1]*box->box[2][0] -
- box->box[0][0]*box->box[2][1]) * one_vol;
- box->box_inv[2][2] = (box->box[0][0]*box->box[1][1] -
- box->box[0][1]*box->box[1][0]) * one_vol;
-
- box->box_norms[0] = SQRT( SQR(box->box[0][0]) +
- SQR(box->box[0][1]) +
- SQR(box->box[0][2]) );
- box->box_norms[1] = SQRT( SQR(box->box[1][0]) +
- SQR(box->box[1][1]) +
- SQR(box->box[1][2]) );
- box->box_norms[2] = SQRT( SQR(box->box[2][0]) +
- SQR(box->box[2][1]) +
- SQR(box->box[2][2]) );
-
- box->trans[0][0] = box->box[0][0]/box->box_norms[0];
- box->trans[0][1] = box->box[1][0]/box->box_norms[0];
- box->trans[0][2] = box->box[2][0]/box->box_norms[0];
-
- box->trans[1][0] = box->box[0][1]/box->box_norms[1];
- box->trans[1][1] = box->box[1][1]/box->box_norms[1];
- box->trans[1][2] = box->box[2][1]/box->box_norms[1];
-
- box->trans[2][0] = box->box[0][2]/box->box_norms[2];
- box->trans[2][1] = box->box[1][2]/box->box_norms[2];
- box->trans[2][2] = box->box[2][2]/box->box_norms[2];
-
- one_vol = box->box_norms[0]*box->box_norms[1]*box->box_norms[2]*one_vol;
-
- box->trans_inv[0][0] = (box->trans[1][1]*box->trans[2][2] -
- box->trans[1][2]*box->trans[2][1]) * one_vol;
- box->trans_inv[0][1] = (box->trans[0][2]*box->trans[2][1] -
- box->trans[0][1]*box->trans[2][2]) * one_vol;
- box->trans_inv[0][2] = (box->trans[0][1]*box->trans[1][2] -
- box->trans[0][2]*box->trans[1][1]) * one_vol;
-
- box->trans_inv[1][0] = (box->trans[1][2]*box->trans[2][0] -
- box->trans[1][0]*box->trans[2][2]) * one_vol;
- box->trans_inv[1][1] = (box->trans[0][0]*box->trans[2][2] -
- box->trans[0][2]*box->trans[2][0]) * one_vol;
- box->trans_inv[1][2] = (box->trans[0][2]*box->trans[1][0] -
- box->trans[0][0]*box->trans[1][2]) * one_vol;
-
- box->trans_inv[2][0] = (box->trans[1][0]*box->trans[2][1] -
- box->trans[1][1]*box->trans[2][0]) * one_vol;
- box->trans_inv[2][1] = (box->trans[0][1]*box->trans[2][0] -
- box->trans[0][0]*box->trans[2][1]) * one_vol;
- box->trans_inv[2][2] = (box->trans[0][0]*box->trans[1][1] -
- box->trans[0][1]*box->trans[1][0]) * one_vol;
+ real one_vol;
+
+ box->volume =
+ box->box[0][0] * (box->box[1][1] * box->box[2][2] -
+ box->box[2][1] * box->box[2][1]) +
+ box->box[0][1] * (box->box[2][0] * box->box[1][2] -
+ box->box[1][0] * box->box[2][2]) +
+ box->box[0][2] * (box->box[1][0] * box->box[2][1] -
+ box->box[2][0] * box->box[1][1]);
+
+ one_vol = 1.0 / box->volume;
+
+ box->box_inv[0][0] = (box->box[1][1] * box->box[2][2] -
+ box->box[1][2] * box->box[2][1]) * one_vol;
+ box->box_inv[0][1] = (box->box[0][2] * box->box[2][1] -
+ box->box[0][1] * box->box[2][2]) * one_vol;
+ box->box_inv[0][2] = (box->box[0][1] * box->box[1][2] -
+ box->box[0][2] * box->box[1][1]) * one_vol;
+
+ box->box_inv[1][0] = (box->box[1][2] * box->box[2][0] -
+ box->box[1][0] * box->box[2][2]) * one_vol;
+ box->box_inv[1][1] = (box->box[0][0] * box->box[2][2] -
+ box->box[0][2] * box->box[2][0]) * one_vol;
+ box->box_inv[1][2] = (box->box[0][2] * box->box[1][0] -
+ box->box[0][0] * box->box[1][2]) * one_vol;
+
+ box->box_inv[2][0] = (box->box[1][0] * box->box[2][1] -
+ box->box[1][1] * box->box[2][0]) * one_vol;
+ box->box_inv[2][1] = (box->box[0][1] * box->box[2][0] -
+ box->box[0][0] * box->box[2][1]) * one_vol;
+ box->box_inv[2][2] = (box->box[0][0] * box->box[1][1] -
+ box->box[0][1] * box->box[1][0]) * one_vol;
+
+ box->box_norms[0] = SQRT( SQR(box->box[0][0]) +
+ SQR(box->box[0][1]) +
+ SQR(box->box[0][2]) );
+ box->box_norms[1] = SQRT( SQR(box->box[1][0]) +
+ SQR(box->box[1][1]) +
+ SQR(box->box[1][2]) );
+ box->box_norms[2] = SQRT( SQR(box->box[2][0]) +
+ SQR(box->box[2][1]) +
+ SQR(box->box[2][2]) );
+
+ box->trans[0][0] = box->box[0][0] / box->box_norms[0];
+ box->trans[0][1] = box->box[1][0] / box->box_norms[0];
+ box->trans[0][2] = box->box[2][0] / box->box_norms[0];
+
+ box->trans[1][0] = box->box[0][1] / box->box_norms[1];
+ box->trans[1][1] = box->box[1][1] / box->box_norms[1];
+ box->trans[1][2] = box->box[2][1] / box->box_norms[1];
+
+ box->trans[2][0] = box->box[0][2] / box->box_norms[2];
+ box->trans[2][1] = box->box[1][2] / box->box_norms[2];
+ box->trans[2][2] = box->box[2][2] / box->box_norms[2];
+
+ one_vol = box->box_norms[0] * box->box_norms[1] * box->box_norms[2] * one_vol;
+
+ box->trans_inv[0][0] = (box->trans[1][1] * box->trans[2][2] -
+ box->trans[1][2] * box->trans[2][1]) * one_vol;
+ box->trans_inv[0][1] = (box->trans[0][2] * box->trans[2][1] -
+ box->trans[0][1] * box->trans[2][2]) * one_vol;
+ box->trans_inv[0][2] = (box->trans[0][1] * box->trans[1][2] -
+ box->trans[0][2] * box->trans[1][1]) * one_vol;
+
+ box->trans_inv[1][0] = (box->trans[1][2] * box->trans[2][0] -
+ box->trans[1][0] * box->trans[2][2]) * one_vol;
+ box->trans_inv[1][1] = (box->trans[0][0] * box->trans[2][2] -
+ box->trans[0][2] * box->trans[2][0]) * one_vol;
+ box->trans_inv[1][2] = (box->trans[0][2] * box->trans[1][0] -
+ box->trans[0][0] * box->trans[1][2]) * one_vol;
+
+ box->trans_inv[2][0] = (box->trans[1][0] * box->trans[2][1] -
+ box->trans[1][1] * box->trans[2][0]) * one_vol;
+ box->trans_inv[2][1] = (box->trans[0][1] * box->trans[2][0] -
+ box->trans[0][0] * box->trans[2][1]) * one_vol;
+ box->trans_inv[2][2] = (box->trans[0][0] * box->trans[1][1] -
+ box->trans[0][1] * box->trans[1][0]) * one_vol;
// for (i=0; i < 3; i++)
// {
// for (j=0; j < 3; j++)
-// fprintf(stderr,"%lf\t",box->trans[i][j]);
+// fprintf(stderr,"%lf\t",box->trans[i][j]);
// fprintf(stderr,"\n");
// }
// fprintf(stderr,"\n");
// for (i=0; i < 3; i++)
// {
// for (j=0; j < 3; j++)
-// fprintf(stderr,"%lf\t",box->trans_inv[i][j]);
+// fprintf(stderr,"%lf\t",box->trans_inv[i][j]);
// fprintf(stderr,"\n");
// }
- box->g[0][0] = box->box[0][0] * box->box[0][0] +
- box->box[0][1] * box->box[0][1] +
- box->box[0][2] * box->box[0][2];
- box->g[1][0] =
- box->g[0][1] = box->box[0][0] * box->box[1][0] +
- box->box[0][1] * box->box[1][1] +
- box->box[0][2] * box->box[1][2];
- box->g[2][0] =
- box->g[0][2] = box->box[0][0] * box->box[2][0] +
- box->box[0][1] * box->box[2][1] +
- box->box[0][2] * box->box[2][2];
-
- box->g[1][1] = box->box[1][0] * box->box[1][0] +
- box->box[1][1] * box->box[1][1] +
- box->box[1][2] * box->box[1][2];
- box->g[1][2] =
- box->g[2][1] = box->box[1][0] * box->box[2][0] +
- box->box[1][1] * box->box[2][1] +
- box->box[1][2] * box->box[2][2];
-
- box->g[2][2] = box->box[2][0] * box->box[2][0] +
- box->box[2][1] * box->box[2][1] +
- box->box[2][2] * box->box[2][2];
-
- // These proportions are only used for isotropic_NPT!
- box->side_prop[0] = box->box[0][0] / box->box[0][0];
- box->side_prop[1] = box->box[1][1] / box->box[0][0];
- box->side_prop[2] = box->box[2][2] / box->box[0][0];
+ box->g[0][0] = box->box[0][0] * box->box[0][0] +
+ box->box[0][1] * box->box[0][1] +
+ box->box[0][2] * box->box[0][2];
+ box->g[1][0] =
+ box->g[0][1] = box->box[0][0] * box->box[1][0] +
+ box->box[0][1] * box->box[1][1] +
+ box->box[0][2] * box->box[1][2];
+ box->g[2][0] =
+ box->g[0][2] = box->box[0][0] * box->box[2][0] +
+ box->box[0][1] * box->box[2][1] +
+ box->box[0][2] * box->box[2][2];
+
+ box->g[1][1] = box->box[1][0] * box->box[1][0] +
+ box->box[1][1] * box->box[1][1] +
+ box->box[1][2] * box->box[1][2];
+ box->g[1][2] =
+ box->g[2][1] = box->box[1][0] * box->box[2][0] +
+ box->box[1][1] * box->box[2][1] +
+ box->box[1][2] * box->box[2][2];
+
+ box->g[2][2] = box->box[2][0] * box->box[2][0] +
+ box->box[2][1] * box->box[2][1] +
+ box->box[2][2] * box->box[2][2];
+
+ // These proportions are only used for isotropic_NPT!
+ box->side_prop[0] = box->box[0][0] / box->box[0][0];
+ box->side_prop[1] = box->box[1][1] / box->box[0][0];
+ box->side_prop[2] = box->box[2][2] / box->box[0][0];
}
void Transform( rvec x1, simulation_box *box, char flag, rvec x2 )
{
- int i, j;
- real tmp;
-
- // printf(">x1: (%lf, %lf, %lf)\n",x1[0],x1[1],x1[2]);
-
- if (flag > 0) {
- for (i=0; i < 3; i++) {
- tmp = 0.0;
- for (j=0; j < 3; j++)
- tmp += box->trans[i][j]*x1[j];
- x2[i] = tmp;
+ int i, j;
+ real tmp;
+
+ // printf(">x1: (%lf, %lf, %lf)\n",x1[0],x1[1],x1[2]);
+
+ if (flag > 0)
+ {
+ for (i = 0; i < 3; i++)
+ {
+ tmp = 0.0;
+ for (j = 0; j < 3; j++)
+ tmp += box->trans[i][j] * x1[j];
+ x2[i] = tmp;
+ }
}
- }
- else {
- for (i=0; i < 3; i++) {
- tmp = 0.0;
- for (j=0; j < 3; j++)
- tmp += box->trans_inv[i][j]*x1[j];
- x2[i] = tmp;
+ else
+ {
+ for (i = 0; i < 3; i++)
+ {
+ tmp = 0.0;
+ for (j = 0; j < 3; j++)
+ tmp += box->trans_inv[i][j] * x1[j];
+ x2[i] = tmp;
+ }
}
- }
- // printf(">x2: (%lf, %lf, %lf)\n", x2[0], x2[1], x2[2]);
+ // printf(">x2: (%lf, %lf, %lf)\n", x2[0], x2[1], x2[2]);
}
void Transform_to_UnitBox( rvec x1, simulation_box *box, char flag, rvec x2 )
{
- Transform( x1, box, flag, x2 );
-
- x2[0] /= box->box_norms[0];
- x2[1] /= box->box_norms[1];
- x2[2] /= box->box_norms[2];
+ Transform( x1, box, flag, x2 );
+
+ x2[0] /= box->box_norms[0];
+ x2[1] /= box->box_norms[1];
+ x2[2] /= box->box_norms[2];
}
void Inc_on_T3( rvec x, rvec dx, simulation_box *box )
{
- int i;
- real tmp;
+ int i;
+ real tmp;
- for (i=0; i < 3; i++) {
- tmp = x[i] + dx[i];
- if( tmp <= -box->box_norms[i] || tmp >= box->box_norms[i] )
- tmp = fmod( tmp, box->box_norms[i] );
+ for (i = 0; i < 3; i++)
+ {
+ tmp = x[i] + dx[i];
+ if ( tmp <= -box->box_norms[i] || tmp >= box->box_norms[i] )
+ tmp = fmod( tmp, box->box_norms[i] );
- if( tmp < 0 ) tmp += box->box_norms[i];
- x[i] = tmp;
- }
+ if ( tmp < 0 ) tmp += box->box_norms[i];
+ x[i] = tmp;
+ }
}
real Sq_Distance_on_T3(rvec x1, rvec x2, simulation_box* box, rvec r)
{
- real norm=0.0;
- real d, tmp;
- int i;
-
- for (i=0; i < 3; i++) {
- d = x2[i] - x1[i];
- tmp = SQR(d);
-
- if( tmp >= SQR( box->box_norms[i] / 2.0 ) ) {
- if (x2[i] > x1[i])
- d -= box->box_norms[i];
- else
- d += box->box_norms[i];
-
- r[i] = d;
- norm += SQR(d);
+ real norm = 0.0;
+ real d, tmp;
+ int i;
+
+ for (i = 0; i < 3; i++)
+ {
+ d = x2[i] - x1[i];
+ tmp = SQR(d);
+
+ if ( tmp >= SQR( box->box_norms[i] / 2.0 ) )
+ {
+ if (x2[i] > x1[i])
+ d -= box->box_norms[i];
+ else
+ d += box->box_norms[i];
+
+ r[i] = d;
+ norm += SQR(d);
+ }
+ else
+ {
+ r[i] = d;
+ norm += tmp;
+ }
}
- else {
- r[i] = d;
- norm += tmp;
- }
- }
-
- return norm;
+
+ return norm;
}
void Distance_on_T3_Gen( rvec x1, rvec x2, simulation_box* box, rvec r )
{
- rvec xa, xb, ra;
+ rvec xa, xb, ra;
+
+ Transform( x1, box, -1, xa );
+ Transform( x2, box, -1, xb );
- Transform( x1, box, -1, xa );
- Transform( x2, box, -1, xb );
+ //printf(">xa: (%lf, %lf, %lf)\n",xa[0],xa[1],xa[2]);
+ //printf(">xb: (%lf, %lf, %lf)\n",xb[0],xb[1],xb[2]);
- //printf(">xa: (%lf, %lf, %lf)\n",xa[0],xa[1],xa[2]);
- //printf(">xb: (%lf, %lf, %lf)\n",xb[0],xb[1],xb[2]);
-
- Sq_Distance_on_T3( xa, xb, box, ra );
+ Sq_Distance_on_T3( xa, xb, box, ra );
- Transform( ra, box, 1, r );
+ Transform( ra, box, 1, r );
}
void Inc_on_T3_Gen( rvec x, rvec dx, simulation_box* box )
{
- rvec xa, dxa;
+ rvec xa, dxa;
- Transform( x, box, -1, xa );
- Transform( dx, box, -1, dxa );
+ Transform( x, box, -1, xa );
+ Transform( dx, box, -1, dxa );
- //printf(">xa: (%lf, %lf, %lf)\n",xa[0],xa[1],xa[2]);
- //printf(">dxa: (%lf, %lf, %lf)\n",dxa[0],dxa[1],dxa[2]);
-
- Inc_on_T3( xa, dxa, box );
+ //printf(">xa: (%lf, %lf, %lf)\n",xa[0],xa[1],xa[2]);
+ //printf(">dxa: (%lf, %lf, %lf)\n",dxa[0],dxa[1],dxa[2]);
- //printf(">new_xa: (%lf, %lf, %lf)\n",xa[0],xa[1],xa[2]);
+ Inc_on_T3( xa, dxa, box );
- Transform( xa, box, 1, x );
+ //printf(">new_xa: (%lf, %lf, %lf)\n",xa[0],xa[1],xa[2]);
+
+ Transform( xa, box, 1, x );
}
real Metric_Product( rvec x1, rvec x2, simulation_box* box )
{
- int i, j;
- real dist=0.0, tmp;
+ int i, j;
+ real dist = 0.0, tmp;
- for( i = 0; i < 3; i++ )
+ for ( i = 0; i < 3; i++ )
{
- tmp = 0.0;
- for( j = 0; j < 3; j++ )
- tmp += box->g[i][j] * x2[j];
- dist += x1[i] * tmp;
+ tmp = 0.0;
+ for ( j = 0; j < 3; j++ )
+ tmp += box->g[i][j] * x2[j];
+ dist += x1[i] * tmp;
}
- return dist;
+ return dist;
}
-int Are_Far_Neighbors( rvec x1, rvec x2, simulation_box *box,
- real cutoff, far_neighbor_data *data )
+int Are_Far_Neighbors( rvec x1, rvec x2, simulation_box *box,
+ real cutoff, far_neighbor_data *data )
{
- real norm_sqr, d, tmp;
- int i;
-
- norm_sqr = 0;
-
- for( i = 0; i < 3; i++ ) {
- d = x2[i] - x1[i];
- tmp = SQR(d);
-
- if( tmp >= SQR( box->box_norms[i] / 2.0 ) ) {
- if( x2[i] > x1[i] ) {
- d -= box->box_norms[i];
- data->rel_box[i] = -1;
- }
- else {
- d += box->box_norms[i];
- data->rel_box[i] = +1;
- }
-
- data->dvec[i] = d;
- norm_sqr += SQR(d);
+ real norm_sqr, d, tmp;
+ int i;
+
+ norm_sqr = 0;
+
+ for ( i = 0; i < 3; i++ )
+ {
+ d = x2[i] - x1[i];
+ tmp = SQR(d);
+
+ if ( tmp >= SQR( box->box_norms[i] / 2.0 ) )
+ {
+ if ( x2[i] > x1[i] )
+ {
+ d -= box->box_norms[i];
+ data->rel_box[i] = -1;
+ }
+ else
+ {
+ d += box->box_norms[i];
+ data->rel_box[i] = +1;
+ }
+
+ data->dvec[i] = d;
+ norm_sqr += SQR(d);
+ }
+ else
+ {
+ data->dvec[i] = d;
+ norm_sqr += tmp;
+ data->rel_box[i] = 0;
+ }
}
- else {
- data->dvec[i] = d;
- norm_sqr += tmp;
- data->rel_box[i] = 0;
- }
- }
-
- if( norm_sqr <= SQR(cutoff) ){
- data->d = sqrt(norm_sqr);
- return 1;
- }
-
- return 0;
+
+ if ( norm_sqr <= SQR(cutoff) )
+ {
+ data->d = sqrt(norm_sqr);
+ return 1;
+ }
+
+ return 0;
}
-/* Determines if the distance between x1 and x2 is < vlist_cut.
+/* Determines if the distance between x1 and x2 is < vlist_cut.
If so, this neighborhood is added to the list of far neighbors.
Periodic boundary conditions do not apply. */
-void Get_NonPeriodic_Far_Neighbors( rvec x1, rvec x2, simulation_box *box,
- control_params *control,
- far_neighbor_data *new_nbrs, int *count )
+void Get_NonPeriodic_Far_Neighbors( rvec x1, rvec x2, simulation_box *box,
+ control_params *control,
+ far_neighbor_data *new_nbrs, int *count )
{
- real norm_sqr;
-
- rvec_ScaledSum( new_nbrs[0].dvec, 1.0, x2, -1.0, x1 );
-
- norm_sqr = rvec_Norm_Sqr( new_nbrs[0].dvec );
-
- if( norm_sqr <= SQR( control->vlist_cut ) ) {
- *count = 1;
- new_nbrs[0].d = SQRT( norm_sqr );
-
- ivec_MakeZero( new_nbrs[0].rel_box );
- // rvec_MakeZero( new_nbrs[0].ext_factor );
- }
- else *count = 0;
+ real norm_sqr;
+
+ rvec_ScaledSum( new_nbrs[0].dvec, 1.0, x2, -1.0, x1 );
+
+ norm_sqr = rvec_Norm_Sqr( new_nbrs[0].dvec );
+
+ if ( norm_sqr <= SQR( control->vlist_cut ) )
+ {
+ *count = 1;
+ new_nbrs[0].d = SQRT( norm_sqr );
+
+ ivec_MakeZero( new_nbrs[0].rel_box );
+ // rvec_MakeZero( new_nbrs[0].ext_factor );
+ }
+ else *count = 0;
}
/* Finds periodic neighbors in a 'big_box'. Here 'big_box' means:
the current simulation box has all dimensions > 2 *vlist_cut.
- If the periodic distance between x1 and x2 is than vlist_cut, this
+ If the periodic distance between x1 and x2 is than vlist_cut, this
neighborhood is added to the list of far neighbors. */
-void Get_Periodic_Far_Neighbors_Big_Box( rvec x1, rvec x2, simulation_box *box,
- control_params *control,
- far_neighbor_data *periodic_nbrs,
- int *count )
+void Get_Periodic_Far_Neighbors_Big_Box( rvec x1, rvec x2, simulation_box *box,
+ control_params *control,
+ far_neighbor_data *periodic_nbrs,
+ int *count )
{
- real norm_sqr, d, tmp;
- int i;
-
- norm_sqr = 0;
-
- for( i = 0; i < 3; i++ ) {
- d = x2[i] - x1[i];
- tmp = SQR(d);
- // fprintf(out,"Inside Sq_Distance_on_T3, %d, %lf, %lf\n",
- // i,tmp,SQR(box->box_norms[i]/2.0));
-
- if( tmp >= SQR( box->box_norms[i] / 2.0 ) ) {
- if( x2[i] > x1[i] ) {
- d -= box->box_norms[i];
- periodic_nbrs[0].rel_box[i] = -1;
- // periodic_nbrs[0].ext_factor[i] = +1;
- }
- else {
- d += box->box_norms[i];
- periodic_nbrs[0].rel_box[i] = +1;
- // periodic_nbrs[0].ext_factor[i] = -1;
- }
-
- periodic_nbrs[0].dvec[i] = d;
- norm_sqr += SQR(d);
+ real norm_sqr, d, tmp;
+ int i;
+
+ norm_sqr = 0;
+
+ for ( i = 0; i < 3; i++ )
+ {
+ d = x2[i] - x1[i];
+ tmp = SQR(d);
+ // fprintf(out,"Inside Sq_Distance_on_T3, %d, %lf, %lf\n",
+ // i,tmp,SQR(box->box_norms[i]/2.0));
+
+ if ( tmp >= SQR( box->box_norms[i] / 2.0 ) )
+ {
+ if ( x2[i] > x1[i] )
+ {
+ d -= box->box_norms[i];
+ periodic_nbrs[0].rel_box[i] = -1;
+ // periodic_nbrs[0].ext_factor[i] = +1;
+ }
+ else
+ {
+ d += box->box_norms[i];
+ periodic_nbrs[0].rel_box[i] = +1;
+ // periodic_nbrs[0].ext_factor[i] = -1;
+ }
+
+ periodic_nbrs[0].dvec[i] = d;
+ norm_sqr += SQR(d);
+ }
+ else
+ {
+ periodic_nbrs[0].dvec[i] = d;
+ norm_sqr += tmp;
+ periodic_nbrs[0].rel_box[i] = 0;
+ // periodic_nbrs[0].ext_factor[i] = 0;
+ }
+ }
+
+ if ( norm_sqr <= SQR( control->vlist_cut ) )
+ {
+ *count = 1;
+ periodic_nbrs[0].d = SQRT( norm_sqr );
}
- else {
- periodic_nbrs[0].dvec[i] = d;
- norm_sqr += tmp;
- periodic_nbrs[0].rel_box[i] = 0;
- // periodic_nbrs[0].ext_factor[i] = 0;
- }
- }
-
- if( norm_sqr <= SQR( control->vlist_cut ) ) {
- *count = 1;
- periodic_nbrs[0].d = SQRT( norm_sqr );
- }
- else *count = 0;
+ else *count = 0;
}
-/* Finds all periodic far neighborhoods between x1 and x2
+/* Finds all periodic far neighborhoods between x1 and x2
((dist(x1, x2') < vlist_cut, periodic images of x2 are also considered).
Here the box is 'small' meaning that at least one dimension is < 2*vlist_cut.
- IMPORTANT: This part might need some improvement. In NPT, the simulation box
- might get too small (such as <5 A!). In this case we have to consider the
+ IMPORTANT: This part might need some improvement. In NPT, the simulation box
+ might get too small (such as <5 A!). In this case we have to consider the
periodic images of x2 that are two boxs away!!!
*/
void Get_Periodic_Far_Neighbors_Small_Box( rvec x1, rvec x2, simulation_box *box,
- control_params *control,
- far_neighbor_data *periodic_nbrs,
- int *count )
+ control_params *control,
+ far_neighbor_data *periodic_nbrs,
+ int *count )
{
- int i, j, k;
- int imax, jmax, kmax;
- real sqr_norm, d_i, d_j, d_k;
-
- *count = 0;
- /* determine the max stretch of imaginary boxs in each direction
- to handle periodic boundary conditions correctly. */
- imax = (int)(control->vlist_cut / box->box_norms[0] + 1);
- jmax = (int)(control->vlist_cut / box->box_norms[1] + 1);
- kmax = (int)(control->vlist_cut / box->box_norms[2] + 1);
- /*if( imax > 1 || jmax > 1 || kmax > 1 )
- fprintf( stderr, "box %8.3f x %8.3f x %8.3f --> %2d %2d %2d\n",
- box->box_norms[0], box->box_norms[1], box->box_norms[2],
- imax, jmax, kmax ); */
-
-
- for( i = -imax; i <= imax; ++i )
- if(fabs(d_i=((x2[0]+i*box->box_norms[0])-x1[0]))<=control->vlist_cut) {
- for( j = -jmax; j <= jmax; ++j )
- if(fabs(d_j=((x2[1]+j*box->box_norms[1])-x1[1]))<=control->vlist_cut) {
- for( k = -kmax; k <= kmax; ++k )
- if(fabs(d_k=((x2[2]+k*box->box_norms[2])-x1[2]))<=control->vlist_cut) {
- sqr_norm = SQR(d_i) + SQR(d_j) + SQR(d_k);
- if( sqr_norm <= SQR(control->vlist_cut) ) {
- periodic_nbrs[ *count ].d = SQRT( sqr_norm );
-
- periodic_nbrs[ *count ].dvec[0] = d_i;
- periodic_nbrs[ *count ].dvec[1] = d_j;
- periodic_nbrs[ *count ].dvec[2] = d_k;
-
- periodic_nbrs[ *count ].rel_box[0] = i;
- periodic_nbrs[ *count ].rel_box[1] = j;
- periodic_nbrs[ *count ].rel_box[2] = k;
-
- /* if( i || j || k ) {
- fprintf(stderr, "x1: %.2f %.2f %.2f\n", x1[0], x1[1], x1[2]);
- fprintf(stderr, "x2: %.2f %.2f %.2f\n", x2[0], x2[1], x2[2]);
- fprintf( stderr, "d : %8.2f%8.2f%8.2f\n\n", d_i, d_j, d_k );
- } */
-
- /* if(i) periodic_nbrs[*count].ext_factor[0] = (real)i/-abs(i);
- else periodic_nbrs[*count].ext_factor[0] = 0;
-
- if(j) periodic_nbrs[*count].ext_factor[1] = (real)j/-abs(j);
- else periodic_nbrs[*count].ext_factor[1] = 0;
-
- if(k) periodic_nbrs[*count].ext_factor[2] = (real)k/-abs(k);
- else periodic_nbrs[*count].ext_factor[2] = 0; */
-
-
- /* if( i == 0 && j == 0 && k == 0 )
- * periodic_nbrs[ *count ].imaginary = 0;
- * else periodic_nbrs[ *count ].imaginary = 1;
- */
- ++(*count);
- }
- }
- }
- }
+ int i, j, k;
+ int imax, jmax, kmax;
+ real sqr_norm, d_i, d_j, d_k;
+
+ *count = 0;
+ /* determine the max stretch of imaginary boxs in each direction
+ to handle periodic boundary conditions correctly. */
+ imax = (int)(control->vlist_cut / box->box_norms[0] + 1);
+ jmax = (int)(control->vlist_cut / box->box_norms[1] + 1);
+ kmax = (int)(control->vlist_cut / box->box_norms[2] + 1);
+ /*if( imax > 1 || jmax > 1 || kmax > 1 )
+ fprintf( stderr, "box %8.3f x %8.3f x %8.3f --> %2d %2d %2d\n",
+ box->box_norms[0], box->box_norms[1], box->box_norms[2],
+ imax, jmax, kmax ); */
+
+
+ for ( i = -imax; i <= imax; ++i )
+ if (fabs(d_i = ((x2[0] + i * box->box_norms[0]) - x1[0])) <= control->vlist_cut)
+ {
+ for ( j = -jmax; j <= jmax; ++j )
+ if (fabs(d_j = ((x2[1] + j * box->box_norms[1]) - x1[1])) <= control->vlist_cut)
+ {
+ for ( k = -kmax; k <= kmax; ++k )
+ if (fabs(d_k = ((x2[2] + k * box->box_norms[2]) - x1[2])) <= control->vlist_cut)
+ {
+ sqr_norm = SQR(d_i) + SQR(d_j) + SQR(d_k);
+ if ( sqr_norm <= SQR(control->vlist_cut) )
+ {
+ periodic_nbrs[ *count ].d = SQRT( sqr_norm );
+
+ periodic_nbrs[ *count ].dvec[0] = d_i;
+ periodic_nbrs[ *count ].dvec[1] = d_j;
+ periodic_nbrs[ *count ].dvec[2] = d_k;
+
+ periodic_nbrs[ *count ].rel_box[0] = i;
+ periodic_nbrs[ *count ].rel_box[1] = j;
+ periodic_nbrs[ *count ].rel_box[2] = k;
+
+ /* if( i || j || k ) {
+ fprintf(stderr, "x1: %.2f %.2f %.2f\n", x1[0], x1[1], x1[2]);
+ fprintf(stderr, "x2: %.2f %.2f %.2f\n", x2[0], x2[1], x2[2]);
+ fprintf( stderr, "d : %8.2f%8.2f%8.2f\n\n", d_i, d_j, d_k );
+ } */
+
+ /* if(i) periodic_nbrs[*count].ext_factor[0] = (real)i/-abs(i);
+ else periodic_nbrs[*count].ext_factor[0] = 0;
+
+ if(j) periodic_nbrs[*count].ext_factor[1] = (real)j/-abs(j);
+ else periodic_nbrs[*count].ext_factor[1] = 0;
+
+ if(k) periodic_nbrs[*count].ext_factor[2] = (real)k/-abs(k);
+ else periodic_nbrs[*count].ext_factor[2] = 0; */
+
+
+ /* if( i == 0 && j == 0 && k == 0 )
+ * periodic_nbrs[ *count ].imaginary = 0;
+ * else periodic_nbrs[ *count ].imaginary = 1;
+ */
+ ++(*count);
+ }
+ }
+ }
+ }
}
-
+
/* Returns the mapping for the neighbor box pointed by (ix,iy,iz) */
/*int Get_Nbr_Box( simulation_box *box, int ix, int iy, int iz )
{
- return (9 * ix + 3 * iy + iz + 13);
+ return (9 * ix + 3 * iy + iz + 13);
// 13 is to handle negative indexes properly
}*/
@@ -566,7 +591,7 @@ void Get_Periodic_Far_Neighbors_Small_Box( rvec x1, rvec x2, simulation_box *box
{
int map;
- map = 9 * ix + 3 * iy + iz + 13;
+ map = 9 * ix + 3 * iy + iz + 13;
// 13 is to adjust -1,-1,-1 correspond to index 0
return box->nbr_box_press[map];
@@ -577,10 +602,10 @@ void Get_Periodic_Far_Neighbors_Small_Box( rvec x1, rvec x2, simulation_box *box
/*void Inc_Nbr_Box_Press( simulation_box *box, int ix, int iy, int iz, rvec v )
{
int map;
-
- map = 9 * ix + 3 * iy + iz + 13;
+
+ map = 9 * ix + 3 * iy + iz + 13;
// 13 is to adjust -1,-1,-1 correspond to index 0
-
+
rvec_Add( box->nbr_box_press[map], v );
}*/
@@ -594,39 +619,39 @@ void Get_Periodic_Far_Neighbors_Small_Box( rvec x1, rvec x2, simulation_box *box
void Print_Box_Information( simulation_box* box, FILE *out )
{
- int i, j;
+ int i, j;
- fprintf( out, "box: {" );
- for( i = 0; i < 3; ++i )
+ fprintf( out, "box: {" );
+ for ( i = 0; i < 3; ++i )
{
- fprintf( out, "{" );
- for( j = 0; j < 3; ++j )
- fprintf( out, "%8.3f ", box->box[i][j] );
- fprintf( out, "}" );
+ fprintf( out, "{" );
+ for ( j = 0; j < 3; ++j )
+ fprintf( out, "%8.3f ", box->box[i][j] );
+ fprintf( out, "}" );
}
- fprintf( out, "}\n" );
+ fprintf( out, "}\n" );
- fprintf( out, "V: %8.3f\tdims: {%8.3f, %8.3f, %8.3f}\n",
- box->volume,
- box->box_norms[0], box->box_norms[1], box->box_norms[2] );
+ fprintf( out, "V: %8.3f\tdims: {%8.3f, %8.3f, %8.3f}\n",
+ box->volume,
+ box->box_norms[0], box->box_norms[1], box->box_norms[2] );
- fprintf( out, "box_trans: {" );
- for( i = 0; i < 3; ++i )
+ fprintf( out, "box_trans: {" );
+ for ( i = 0; i < 3; ++i )
{
- fprintf( out, "{" );
- for( j = 0; j < 3; ++j )
- fprintf( out, "%8.3f ", box->trans[i][j] );
- fprintf( out, "}" );
+ fprintf( out, "{" );
+ for ( j = 0; j < 3; ++j )
+ fprintf( out, "%8.3f ", box->trans[i][j] );
+ fprintf( out, "}" );
}
- fprintf( out, "}\n" );
+ fprintf( out, "}\n" );
- fprintf( out, "box_trinv: {" );
- for( i = 0; i < 3; ++i )
+ fprintf( out, "box_trinv: {" );
+ for ( i = 0; i < 3; ++i )
{
- fprintf( out, "{" );
- for( j = 0; j < 3; ++j )
- fprintf( out, "%8.3f ", box->trans_inv[i][j] );
- fprintf( out, "}" );
+ fprintf( out, "{" );
+ for ( j = 0; j < 3; ++j )
+ fprintf( out, "%8.3f ", box->trans_inv[i][j] );
+ fprintf( out, "}" );
}
- fprintf( out, "}\n" );
+ fprintf( out, "}\n" );
}
diff --git a/puremd_rc_1003/sPuReMD/box.h b/puremd_rc_1003/sPuReMD/box.h
index 88a2147ace5214a32df95a57666624ff208b599c..de3e33debea62d57bd15731e97eadfdf623d96de 100644
--- a/puremd_rc_1003/sPuReMD/box.h
+++ b/puremd_rc_1003/sPuReMD/box.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -25,33 +25,33 @@
#include "mytypes.h"
/* Initializes box from CRYST1 line of PDB */
-void Init_Box_From_CRYST(real, real, real, real, real, real,
- simulation_box*/*, int*/);
+void Init_Box_From_CRYST(real, real, real, real, real, real,
+ simulation_box*/*, int*/);
/* Initializes box from box rtensor */
void Update_Box(rtensor, simulation_box* /*, int*/);
void Update_Box_Isotropic(simulation_box*, real /*, int*/);
void Update_Box_SemiIsotropic( simulation_box*, rvec /*, int*/ );
-/* Computes all the transformations,
+/* Computes all the transformations,
metric and other quantities from box rtensor */
void Make_Consistent(simulation_box*/*, int*/ );
-/* Applies transformation to and from
+/* Applies transformation to and from
Cartesian to Triclinic coordinates based on flag */
/* Use -1 flag for Cartesian -> Triclinic and +1 for otherway */
void Transform( rvec, simulation_box*, char, rvec );
void Transform_to_UnitBox( rvec, simulation_box*, char, rvec );
int Are_Far_Neighbors( rvec, rvec, simulation_box*, real, far_neighbor_data* );
-void Get_NonPeriodic_Far_Neighbors( rvec, rvec, simulation_box*,
- control_params*, far_neighbor_data*, int* );
-void Get_Periodic_Far_Neighbors_Big_Box( rvec, rvec, simulation_box*,
- control_params*, far_neighbor_data*,
- int* );
-void Get_Periodic_Far_Neighbors_Small_Box( rvec, rvec, simulation_box*,
- control_params*, far_neighbor_data*,
- int* );
+void Get_NonPeriodic_Far_Neighbors( rvec, rvec, simulation_box*,
+ control_params*, far_neighbor_data*, int* );
+void Get_Periodic_Far_Neighbors_Big_Box( rvec, rvec, simulation_box*,
+ control_params*, far_neighbor_data*,
+ int* );
+void Get_Periodic_Far_Neighbors_Small_Box( rvec, rvec, simulation_box*,
+ control_params*, far_neighbor_data*,
+ int* );
void Distance_on_T3_Gen( rvec, rvec, simulation_box*, rvec );
void Inc_on_T3_Gen( rvec, rvec, simulation_box* );
diff --git a/puremd_rc_1003/sPuReMD/forces.c b/puremd_rc_1003/sPuReMD/forces.c
index 195008af9188c28acb286c176916f0865ee81ffb..ae6128c6e2b222d47b43c3eea60c7c40af8e991f 100644
--- a/puremd_rc_1003/sPuReMD/forces.c
+++ b/puremd_rc_1003/sPuReMD/forces.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -33,854 +33,906 @@
#include "vector.h"
-void Dummy_Interaction( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+void Dummy_Interaction( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
}
void Init_Bonded_Force_Functions( control_params *control )
-{
- Interaction_Functions[0] = Calculate_Bond_Orders;
- Interaction_Functions[1] = Bond_Energy; //*/Dummy_Interaction;
- Interaction_Functions[2] = LonePair_OverUnder_Coordination_Energy;
- //*/Dummy_Interaction;
- Interaction_Functions[3] = Three_Body_Interactions; //*/Dummy_Interaction;
- Interaction_Functions[4] = Four_Body_Interactions; //*/Dummy_Interaction;
- if( control->hb_cut > 0 )
- Interaction_Functions[5] = Hydrogen_Bonds; //*/Dummy_Interaction;
- else Interaction_Functions[5] = Dummy_Interaction;
- Interaction_Functions[6] = Dummy_Interaction; //empty
- Interaction_Functions[7] = Dummy_Interaction; //empty
- Interaction_Functions[8] = Dummy_Interaction; //empty
- Interaction_Functions[9] = Dummy_Interaction; //empty
+{
+ Interaction_Functions[0] = Calculate_Bond_Orders;
+ Interaction_Functions[1] = Bond_Energy; //*/Dummy_Interaction;
+ Interaction_Functions[2] = LonePair_OverUnder_Coordination_Energy;
+ //*/Dummy_Interaction;
+ Interaction_Functions[3] = Three_Body_Interactions; //*/Dummy_Interaction;
+ Interaction_Functions[4] = Four_Body_Interactions; //*/Dummy_Interaction;
+ if ( control->hb_cut > 0 )
+ Interaction_Functions[5] = Hydrogen_Bonds; //*/Dummy_Interaction;
+ else Interaction_Functions[5] = Dummy_Interaction;
+ Interaction_Functions[6] = Dummy_Interaction; //empty
+ Interaction_Functions[7] = Dummy_Interaction; //empty
+ Interaction_Functions[8] = Dummy_Interaction; //empty
+ Interaction_Functions[9] = Dummy_Interaction; //empty
}
-void Compute_Bonded_Forces( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+void Compute_Bonded_Forces( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int i;
- // real t_start, t_end, t_elapsed;
+ int i;
+ // real t_start, t_end, t_elapsed;
#ifdef TEST_ENERGY
- /* Mark beginning of a new timestep in each energy file */
- fprintf( out_control->ebond, "step: %d\n%6s%6s%12s%12s%12s\n",
- data->step, "atom1", "atom2", "bo", "ebond", "total" );
- fprintf( out_control->elp, "step: %d\n%6s%12s%12s%12s\n",
- data->step, "atom", "nlp", "elp", "total" );
- fprintf( out_control->eov, "step: %d\n%6s%12s%12s\n",
- data->step, "atom", "eov", "total" );
- fprintf( out_control->eun, "step: %d\n%6s%12s%12s\n",
- data->step, "atom", "eun", "total" );
- fprintf( out_control->eval, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s%12s\n",
- data->step, "atom1", "atom2", "atom3",
- "angle", "bo(12)", "bo(23)", "eval", "epen", "total" );
- fprintf( out_control->epen, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s\n",
- data->step, "atom1", "atom2", "atom3",
- "angle", "bo(12)", "bo(23)", "epen", "total" );
- fprintf( out_control->ecoa, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s\n",
- data->step, "atom1", "atom2", "atom3",
- "angle", "bo(12)", "bo(23)", "ecoa", "total" );
- fprintf( out_control->ehb, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s\n",
- data->step, "atom1", "atom2", "atom3",
- "r(23)", "angle", "bo(12)", "ehb", "total" );
- fprintf( out_control->etor, "step: %d\n%6s%6s%6s%6s%12s%12s%12s%12s\n",
- data->step, "atom1", "atom2", "atom3", "atom4",
- "phi", "bo(23)", "etor", "total" );
- fprintf( out_control->econ, "step:%d\n%6s%6s%6s%6s%12s%12s%12s%12s%12s%12s\n",
- data->step, "atom1", "atom2", "atom3", "atom4",
- "phi", "bo(12)", "bo(23)", "bo(34)", "econ", "total" );
-#endif
-
- /* Implement all the function calls as function pointers */
- for( i = 0; i < NO_OF_INTERACTIONS; i++ ) {
- (Interaction_Functions[i])(system, control, data, workspace,
- lists, out_control);
+ /* Mark beginning of a new timestep in each energy file */
+ fprintf( out_control->ebond, "step: %d\n%6s%6s%12s%12s%12s\n",
+ data->step, "atom1", "atom2", "bo", "ebond", "total" );
+ fprintf( out_control->elp, "step: %d\n%6s%12s%12s%12s\n",
+ data->step, "atom", "nlp", "elp", "total" );
+ fprintf( out_control->eov, "step: %d\n%6s%12s%12s\n",
+ data->step, "atom", "eov", "total" );
+ fprintf( out_control->eun, "step: %d\n%6s%12s%12s\n",
+ data->step, "atom", "eun", "total" );
+ fprintf( out_control->eval, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s%12s\n",
+ data->step, "atom1", "atom2", "atom3",
+ "angle", "bo(12)", "bo(23)", "eval", "epen", "total" );
+ fprintf( out_control->epen, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s\n",
+ data->step, "atom1", "atom2", "atom3",
+ "angle", "bo(12)", "bo(23)", "epen", "total" );
+ fprintf( out_control->ecoa, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s\n",
+ data->step, "atom1", "atom2", "atom3",
+ "angle", "bo(12)", "bo(23)", "ecoa", "total" );
+ fprintf( out_control->ehb, "step: %d\n%6s%6s%6s%12s%12s%12s%12s%12s\n",
+ data->step, "atom1", "atom2", "atom3",
+ "r(23)", "angle", "bo(12)", "ehb", "total" );
+ fprintf( out_control->etor, "step: %d\n%6s%6s%6s%6s%12s%12s%12s%12s\n",
+ data->step, "atom1", "atom2", "atom3", "atom4",
+ "phi", "bo(23)", "etor", "total" );
+ fprintf( out_control->econ, "step:%d\n%6s%6s%6s%6s%12s%12s%12s%12s%12s%12s\n",
+ data->step, "atom1", "atom2", "atom3", "atom4",
+ "phi", "bo(12)", "bo(23)", "bo(34)", "econ", "total" );
+#endif
+
+ /* Implement all the function calls as function pointers */
+ for ( i = 0; i < NO_OF_INTERACTIONS; i++ )
+ {
+ (Interaction_Functions[i])(system, control, data, workspace,
+ lists, out_control);
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "f%d-", i );
+ fprintf( stderr, "f%d-", i );
#endif
#ifdef TEST_FORCES
- (Print_Interactions[i])(system, control, data, workspace,
- lists, out_control);
+ (Print_Interactions[i])(system, control, data, workspace,
+ lists, out_control);
#endif
- }
+ }
}
-void Compute_NonBonded_Forces( reax_system *system, control_params *control,
- simulation_data *data,static_storage *workspace,
- list** lists, output_controls *out_control )
+void Compute_NonBonded_Forces( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list** lists, output_controls *out_control )
{
- real t_start, t_elapsed;
+ real t_start, t_elapsed;
#ifdef TEST_ENERGY
- fprintf( out_control->evdw, "step: %d\n%6s%6s%12s%12s%12s\n",
- data->step, "atom1", "atom2", "r12", "evdw", "total" );
- fprintf( out_control->ecou, "step: %d\n%6s%6s%12s%12s%12s%12s%12s\n",
- data->step, "atom1", "atom2", "r12", "q1", "q2", "ecou", "total" );
+ fprintf( out_control->evdw, "step: %d\n%6s%6s%12s%12s%12s\n",
+ data->step, "atom1", "atom2", "r12", "evdw", "total" );
+ fprintf( out_control->ecou, "step: %d\n%6s%6s%12s%12s%12s%12s%12s\n",
+ data->step, "atom1", "atom2", "r12", "q1", "q2", "ecou", "total" );
#endif
- t_start = Get_Time( );
- QEq( system, control, data, workspace, lists[FAR_NBRS], out_control );
- t_elapsed = Get_Timing_Info( t_start );
- data->timing.QEq += t_elapsed;
+ t_start = Get_Time( );
+ QEq( system, control, data, workspace, lists[FAR_NBRS], out_control );
+ t_elapsed = Get_Timing_Info( t_start );
+ data->timing.QEq += t_elapsed;
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "qeq - " );
+ fprintf( stderr, "qeq - " );
#endif
- if ( control->tabulate == 0)
- vdW_Coulomb_Energy( system, control, data, workspace, lists, out_control );
- else
- Tabulated_vdW_Coulomb_Energy( system, control, data, workspace,
- lists, out_control );
+ if ( control->tabulate == 0)
+ vdW_Coulomb_Energy( system, control, data, workspace, lists, out_control );
+ else
+ Tabulated_vdW_Coulomb_Energy( system, control, data, workspace,
+ lists, out_control );
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "nonb forces - " );
+ fprintf( stderr, "nonb forces - " );
#endif
#ifdef TEST_FORCES
- Print_vdW_Coulomb_Forces( system, control, data, workspace,
- lists, out_control );
+ Print_vdW_Coulomb_Forces( system, control, data, workspace,
+ lists, out_control );
#endif
}
-/* This version of Compute_Total_Force computes forces from coefficients
+/* This version of Compute_Total_Force computes forces from coefficients
accumulated by all interaction functions. Saves enormous time & space! */
-void Compute_Total_Force( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists )
+void Compute_Total_Force( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists )
{
- int i, pj;
- list *bonds = (*lists) + BONDS;
-
- for( i = 0; i < system->N; ++i )
- for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
- if( i < bonds->select.bond_list[pj].nbr ) {
- if( control->ensemble == NVE || control->ensemble == NVT || control->ensemble == bNVT)
- Add_dBond_to_Forces( i, pj, system, data, workspace, lists );
- else
- Add_dBond_to_Forces_NPT( i, pj, system, data, workspace, lists );
- }
+ int i, pj;
+ list *bonds = (*lists) + BONDS;
+
+ for ( i = 0; i < system->N; ++i )
+ for ( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
+ if ( i < bonds->select.bond_list[pj].nbr )
+ {
+ if ( control->ensemble == NVE || control->ensemble == NVT || control->ensemble == bNVT)
+ Add_dBond_to_Forces( i, pj, system, data, workspace, lists );
+ else
+ Add_dBond_to_Forces_NPT( i, pj, system, data, workspace, lists );
+ }
}
void Validate_Lists( static_storage *workspace, list **lists, int step, int n,
- int Hmax, int Htop, int num_bonds, int num_hbonds )
+ int Hmax, int Htop, int num_bonds, int num_hbonds )
{
- int i, flag;
- list *bonds, *hbonds;
-
- bonds = *lists + BONDS;
- hbonds = *lists + HBONDS;
-
- /* far neighbors */
- if( Htop > Hmax * DANGER_ZONE ) {
- workspace->realloc.Htop = Htop;
- if( Htop > Hmax ) {
- fprintf( stderr,
- "step%d - ran out of space on H matrix: Htop=%d, max = %d",
- step, Htop, Hmax );
- exit(INSUFFICIENT_SPACE);
+ int i, flag;
+ list *bonds, *hbonds;
+
+ bonds = *lists + BONDS;
+ hbonds = *lists + HBONDS;
+
+ /* far neighbors */
+ if ( Htop > Hmax * DANGER_ZONE )
+ {
+ workspace->realloc.Htop = Htop;
+ if ( Htop > Hmax )
+ {
+ fprintf( stderr,
+ "step%d - ran out of space on H matrix: Htop=%d, max = %d",
+ step, Htop, Hmax );
+ exit(INSUFFICIENT_SPACE);
+ }
}
- }
-
- /* bond list */
- flag = -1;
- workspace->realloc.num_bonds = num_bonds;
- for( i = 0; i < n-1; ++i )
- if( End_Index(i, bonds) >= Start_Index(i+1, bonds)-2 ) {
- workspace->realloc.bonds = 1;
- if( End_Index(i, bonds) > Start_Index(i+1, bonds) )
- flag = i;
- }
-
- if( flag > -1 ) {
- fprintf( stderr, "step%d-bondchk failed: i=%d end(i)=%d str(i+1)=%d\n",
- step, flag, End_Index(flag,bonds), Start_Index(flag+1,bonds) );
- exit(INSUFFICIENT_SPACE);
- }
-
- if( End_Index(i, bonds) >= bonds->num_intrs-2 ) {
- workspace->realloc.bonds = 1;
-
- if( End_Index(i, bonds) > bonds->num_intrs ) {
- fprintf( stderr, "step%d-bondchk failed: i=%d end(i)=%d bond_end=%d\n",
- step, flag, End_Index(i,bonds), bonds->num_intrs );
- exit(INSUFFICIENT_SPACE);
- }
- }
-
-
- /* hbonds list */
- if( workspace->num_H > 0 ) {
+
+ /* bond list */
flag = -1;
- workspace->realloc.num_hbonds = num_hbonds;
- for( i = 0; i < workspace->num_H-1; ++i )
- if( Num_Entries(i, hbonds) >=
- (Start_Index(i+1, hbonds) - Start_Index(i, hbonds)) * DANGER_ZONE ) {
- workspace->realloc.hbonds = 1;
- if( End_Index(i, hbonds) > Start_Index(i+1, hbonds) )
- flag = i;
- }
-
- if( flag > -1 ) {
- fprintf( stderr, "step%d-hbondchk failed: i=%d end(i)=%d str(i+1)=%d\n",
- step, flag, End_Index(flag,hbonds), Start_Index(flag+1,hbonds) );
- exit(INSUFFICIENT_SPACE);
+ workspace->realloc.num_bonds = num_bonds;
+ for ( i = 0; i < n - 1; ++i )
+ if ( End_Index(i, bonds) >= Start_Index(i + 1, bonds) - 2 )
+ {
+ workspace->realloc.bonds = 1;
+ if ( End_Index(i, bonds) > Start_Index(i + 1, bonds) )
+ flag = i;
+ }
+
+ if ( flag > -1 )
+ {
+ fprintf( stderr, "step%d-bondchk failed: i=%d end(i)=%d str(i+1)=%d\n",
+ step, flag, End_Index(flag, bonds), Start_Index(flag + 1, bonds) );
+ exit(INSUFFICIENT_SPACE);
+ }
+
+ if ( End_Index(i, bonds) >= bonds->num_intrs - 2 )
+ {
+ workspace->realloc.bonds = 1;
+
+ if ( End_Index(i, bonds) > bonds->num_intrs )
+ {
+ fprintf( stderr, "step%d-bondchk failed: i=%d end(i)=%d bond_end=%d\n",
+ step, flag, End_Index(i, bonds), bonds->num_intrs );
+ exit(INSUFFICIENT_SPACE);
+ }
}
- if( Num_Entries(i,hbonds) >=
- (hbonds->num_intrs - Start_Index(i,hbonds)) * DANGER_ZONE ) {
- workspace->realloc.hbonds = 1;
- if( End_Index(i, hbonds) > hbonds->num_intrs ) {
- fprintf( stderr, "step%d-hbondchk failed: i=%d end(i)=%d hbondend=%d\n",
- step, flag, End_Index(i,hbonds), hbonds->num_intrs );
- exit(INSUFFICIENT_SPACE);
- }
+ /* hbonds list */
+ if ( workspace->num_H > 0 )
+ {
+ flag = -1;
+ workspace->realloc.num_hbonds = num_hbonds;
+ for ( i = 0; i < workspace->num_H - 1; ++i )
+ if ( Num_Entries(i, hbonds) >=
+ (Start_Index(i + 1, hbonds) - Start_Index(i, hbonds)) * DANGER_ZONE )
+ {
+ workspace->realloc.hbonds = 1;
+ if ( End_Index(i, hbonds) > Start_Index(i + 1, hbonds) )
+ flag = i;
+ }
+
+ if ( flag > -1 )
+ {
+ fprintf( stderr, "step%d-hbondchk failed: i=%d end(i)=%d str(i+1)=%d\n",
+ step, flag, End_Index(flag, hbonds), Start_Index(flag + 1, hbonds) );
+ exit(INSUFFICIENT_SPACE);
+ }
+
+ if ( Num_Entries(i, hbonds) >=
+ (hbonds->num_intrs - Start_Index(i, hbonds)) * DANGER_ZONE )
+ {
+ workspace->realloc.hbonds = 1;
+
+ if ( End_Index(i, hbonds) > hbonds->num_intrs )
+ {
+ fprintf( stderr, "step%d-hbondchk failed: i=%d end(i)=%d hbondend=%d\n",
+ step, flag, End_Index(i, hbonds), hbonds->num_intrs );
+ exit(INSUFFICIENT_SPACE);
+ }
+ }
}
- }
}
-void Init_Forces( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control ) {
- int i, j, pj;
- int start_i, end_i;
- int type_i, type_j;
- int Htop, btop_i, btop_j, num_bonds, num_hbonds;
- int ihb, jhb, ihb_top, jhb_top;
- int flag;
- real r_ij, r2, self_coef;
- real dr3gamij_1, dr3gamij_3, Tap;
- //real val, dif, base;
- real C12, C34, C56;
- real Cln_BOp_s, Cln_BOp_pi, Cln_BOp_pi2;
- real BO, BO_s, BO_pi, BO_pi2;
- real p_boc1, p_boc2;
- sparse_matrix *H;
- list *far_nbrs, *bonds, *hbonds;
- single_body_parameters *sbp_i, *sbp_j;
- two_body_parameters *twbp;
- far_neighbor_data *nbr_pj;
- //LR_lookup_table *t;
- reax_atom *atom_i, *atom_j;
- bond_data *ibond, *jbond;
- bond_order_data *bo_ij, *bo_ji;
-
- far_nbrs = *lists + FAR_NBRS;
- bonds = *lists + BONDS;
- hbonds = *lists + HBONDS;
-
- H = workspace->H;
- Htop = 0;
- num_bonds = 0;
- num_hbonds = 0;
- btop_i = btop_j = 0;
- p_boc1 = system->reaxprm.gp.l[0];
- p_boc2 = system->reaxprm.gp.l[1];
-
- for( i = 0; i < system->N; ++i ) {
- atom_i = &(system->atoms[i]);
- type_i = atom_i->type;
- start_i = Start_Index(i, far_nbrs);
- end_i = End_Index(i, far_nbrs);
- H->start[i] = Htop;
- btop_i = End_Index( i, bonds );
- sbp_i = &(system->reaxprm.sbp[type_i]);
- ihb = ihb_top = -1;
- if( control->hb_cut > 0 && (ihb=sbp_i->p_hbond) == 1 )
- ihb_top = End_Index( workspace->hbond_index[i], hbonds );
-
- for( pj = start_i; pj < end_i; ++pj ) {
- nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
- j = nbr_pj->nbr;
- atom_j = &(system->atoms[j]);
-
- flag = 0;
- if((data->step-data->prev_steps) % control->reneighbor == 0) {
- if( nbr_pj->d <= control->r_cut)
- flag = 1;
- else flag = 0;
- }
- else if((nbr_pj->d=Sq_Distance_on_T3(atom_i->x,atom_j->x,&(system->box),
- nbr_pj->dvec))<=SQR(control->r_cut)){
- nbr_pj->d = sqrt(nbr_pj->d);
- flag = 1;
- }
-
- if( flag ){
- type_j = system->atoms[j].type;
- r_ij = nbr_pj->d;
- sbp_j = &(system->reaxprm.sbp[type_j]);
- twbp = &(system->reaxprm.tbp[type_i][type_j]);
- self_coef = (i == j) ? 0.5 : 1.0;
-
- /* H matrix entry */
- Tap = control->Tap7 * r_ij + control->Tap6;
- Tap = Tap * r_ij + control->Tap5;
- Tap = Tap * r_ij + control->Tap4;
- Tap = Tap * r_ij + control->Tap3;
- Tap = Tap * r_ij + control->Tap2;
- Tap = Tap * r_ij + control->Tap1;
- Tap = Tap * r_ij + control->Tap0;
-
- dr3gamij_1 = ( r_ij * r_ij * r_ij + twbp->gamma );
- dr3gamij_3 = POW( dr3gamij_1 , 0.33333333333333 );
-
- H->entries[Htop].j = j;
- H->entries[Htop].val = self_coef * Tap * EV_to_KCALpMOL / dr3gamij_3;
- ++Htop;
-
- /* hydrogen bond lists */
- if( control->hb_cut > 0 && (ihb==1 || ihb==2) &&
- nbr_pj->d <= control->hb_cut ) {
- // fprintf( stderr, "%d %d\n", atom1, atom2 );
- jhb = sbp_j->p_hbond;
- if( ihb == 1 && jhb == 2 ) {
- hbonds->select.hbond_list[ihb_top].nbr = j;
- hbonds->select.hbond_list[ihb_top].scl = 1;
- hbonds->select.hbond_list[ihb_top].ptr = nbr_pj;
- ++ihb_top;
- ++num_hbonds;
- }
- else if( ihb == 2 && jhb == 1 ) {
- jhb_top = End_Index( workspace->hbond_index[j], hbonds );
- hbonds->select.hbond_list[jhb_top].nbr = i;
- hbonds->select.hbond_list[jhb_top].scl = -1;
- hbonds->select.hbond_list[jhb_top].ptr = nbr_pj;
- Set_End_Index( workspace->hbond_index[j], jhb_top+1, hbonds );
- ++num_hbonds;
- }
- }
-
- /* uncorrected bond orders */
- if( far_nbrs->select.far_nbr_list[pj].d <= control->nbr_cut ) {
- r2 = SQR(r_ij);
-
- if( sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0) {
- C12 = twbp->p_bo1 * POW( r_ij / twbp->r_s, twbp->p_bo2 );
- BO_s = (1.0 + control->bo_cut) * EXP( C12 );
- }
- else BO_s = C12 = 0.0;
-
- if( sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0) {
- C34 = twbp->p_bo3 * POW( r_ij / twbp->r_p, twbp->p_bo4 );
- BO_pi = EXP( C34 );
- }
- else BO_pi = C34 = 0.0;
-
- if( sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0) {
- C56 = twbp->p_bo5 * POW( r_ij / twbp->r_pp, twbp->p_bo6 );
- BO_pi2= EXP( C56 );
- }
- else BO_pi2 = C56 = 0.0;
-
- /* Initially BO values are the uncorrected ones, page 1 */
- BO = BO_s + BO_pi + BO_pi2;
-
- if( BO >= control->bo_cut ) {
- num_bonds += 2;
- /****** bonds i-j and j-i ******/
- ibond = &( bonds->select.bond_list[btop_i] );
- btop_j = End_Index( j, bonds );
- jbond = &(bonds->select.bond_list[btop_j]);
-
- ibond->nbr = j;
- jbond->nbr = i;
- ibond->d = r_ij;
- jbond->d = r_ij;
- rvec_Copy( ibond->dvec, nbr_pj->dvec );
- rvec_Scale( jbond->dvec, -1, nbr_pj->dvec );
- ivec_Copy( ibond->rel_box, nbr_pj->rel_box );
- ivec_Scale( jbond->rel_box, -1, nbr_pj->rel_box );
- ibond->dbond_index = btop_i;
- jbond->dbond_index = btop_i;
- ibond->sym_index = btop_j;
- jbond->sym_index = btop_i;
- ++btop_i;
- Set_End_Index( j, btop_j+1, bonds );
-
- bo_ij = &( ibond->bo_data );
- bo_ji = &( jbond->bo_data );
- bo_ji->BO = bo_ij->BO = BO;
- bo_ji->BO_s = bo_ij->BO_s = BO_s;
- bo_ji->BO_pi = bo_ij->BO_pi = BO_pi;
- bo_ji->BO_pi2 = bo_ij->BO_pi2 = BO_pi2;
-
- /* Bond Order page2-3, derivative of total bond order prime */
- Cln_BOp_s = twbp->p_bo2 * C12 / r2;
- Cln_BOp_pi = twbp->p_bo4 * C34 / r2;
- Cln_BOp_pi2 = twbp->p_bo6 * C56 / r2;
-
- /* Only dln_BOp_xx wrt. dr_i is stored here, note that
- dln_BOp_xx/dr_i = -dln_BOp_xx/dr_j and all others are 0 */
- rvec_Scale(bo_ij->dln_BOp_s,-bo_ij->BO_s*Cln_BOp_s,ibond->dvec);
- rvec_Scale(bo_ij->dln_BOp_pi,-bo_ij->BO_pi*Cln_BOp_pi,ibond->dvec);
- rvec_Scale(bo_ij->dln_BOp_pi2,
- -bo_ij->BO_pi2*Cln_BOp_pi2,ibond->dvec);
- rvec_Scale(bo_ji->dln_BOp_s, -1., bo_ij->dln_BOp_s);
- rvec_Scale(bo_ji->dln_BOp_pi, -1., bo_ij->dln_BOp_pi );
- rvec_Scale(bo_ji->dln_BOp_pi2, -1., bo_ij->dln_BOp_pi2 );
-
- /* Only dBOp wrt. dr_i is stored here, note that
- dBOp/dr_i = -dBOp/dr_j and all others are 0 */
- rvec_Scale( bo_ij->dBOp,
- -(bo_ij->BO_s * Cln_BOp_s +
- bo_ij->BO_pi * Cln_BOp_pi +
- bo_ij->BO_pi2 * Cln_BOp_pi2), ibond->dvec );
- rvec_Scale( bo_ji->dBOp, -1., bo_ij->dBOp );
-
- rvec_Add( workspace->dDeltap_self[i], bo_ij->dBOp );
- rvec_Add( workspace->dDeltap_self[j], bo_ji->dBOp );
-
- bo_ij->BO_s -= control->bo_cut;
- bo_ij->BO -= control->bo_cut;
- bo_ji->BO_s -= control->bo_cut;
- bo_ji->BO -= control->bo_cut;
- workspace->total_bond_order[i] += bo_ij->BO; //currently total_BOp
- workspace->total_bond_order[j] += bo_ji->BO; //currently total_BOp
- bo_ij->Cdbo = bo_ij->Cdbopi = bo_ij->Cdbopi2 = 0.0;
- bo_ji->Cdbo = bo_ji->Cdbopi = bo_ji->Cdbopi2 = 0.0;
-
- /*fprintf( stderr, "%d %d %g %g %g\n",
- i+1, j+1, bo_ij->BO, bo_ij->BO_pi, bo_ij->BO_pi2 );*/
-
- /*fprintf( stderr, "Cln_BOp_s: %f, pbo2: %f, C12:%f\n",
- Cln_BOp_s, twbp->p_bo2, C12 );
- fprintf( stderr, "Cln_BOp_pi: %f, pbo4: %f, C34:%f\n",
- Cln_BOp_pi, twbp->p_bo4, C34 );
- fprintf( stderr, "Cln_BOp_pi2: %f, pbo6: %f, C56:%f\n",
- Cln_BOp_pi2, twbp->p_bo6, C56 );*/
- /*fprintf(stderr, "pbo1: %f, pbo2:%f\n", twbp->p_bo1, twbp->p_bo2);
- fprintf(stderr, "pbo3: %f, pbo4:%f\n", twbp->p_bo3, twbp->p_bo4);
- fprintf(stderr, "pbo5: %f, pbo6:%f\n", twbp->p_bo5, twbp->p_bo6);
- fprintf( stderr, "r_s: %f, r_p: %f, r_pp: %f\n",
- twbp->r_s, twbp->r_p, twbp->r_pp );
- fprintf( stderr, "C12: %g, C34:%g, C56:%g\n", C12, C34, C56 );*/
-
- /*fprintf( stderr, "\tfactors: %g %g %g\n",
- -(bo_ij->BO_s * Cln_BOp_s + bo_ij->BO_pi * Cln_BOp_pi +
- bo_ij->BO_pi2 * Cln_BOp_pp),
- -bo_ij->BO_pi * Cln_BOp_pi, -bo_ij->BO_pi2 * Cln_BOp_pi2 );*/
- /*fprintf( stderr, "dBOpi:\t[%g, %g, %g]\n",
- bo_ij->dBOp[0], bo_ij->dBOp[1], bo_ij->dBOp[2] );
- fprintf( stderr, "dBOpi:\t[%g, %g, %g]\n",
- bo_ij->dln_BOp_pi[0], bo_ij->dln_BOp_pi[1],
- bo_ij->dln_BOp_pi[2] );
- fprintf( stderr, "dBOpi2:\t[%g, %g, %g]\n\n",
- bo_ij->dln_BOp_pi2[0], bo_ij->dln_BOp_pi2[1],
- bo_ij->dln_BOp_pi2[2] );*/
-
- Set_End_Index( j, btop_j+1, bonds );
- }
- }
- }
+void Init_Forces( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
+{
+ int i, j, pj;
+ int start_i, end_i;
+ int type_i, type_j;
+ int Htop, btop_i, btop_j, num_bonds, num_hbonds;
+ int ihb, jhb, ihb_top, jhb_top;
+ int flag;
+ real r_ij, r2, self_coef;
+ real dr3gamij_1, dr3gamij_3, Tap;
+ //real val, dif, base;
+ real C12, C34, C56;
+ real Cln_BOp_s, Cln_BOp_pi, Cln_BOp_pi2;
+ real BO, BO_s, BO_pi, BO_pi2;
+ real p_boc1, p_boc2;
+ sparse_matrix *H;
+ list *far_nbrs, *bonds, *hbonds;
+ single_body_parameters *sbp_i, *sbp_j;
+ two_body_parameters *twbp;
+ far_neighbor_data *nbr_pj;
+ //LR_lookup_table *t;
+ reax_atom *atom_i, *atom_j;
+ bond_data *ibond, *jbond;
+ bond_order_data *bo_ij, *bo_ji;
+
+ far_nbrs = *lists + FAR_NBRS;
+ bonds = *lists + BONDS;
+ hbonds = *lists + HBONDS;
+
+ H = workspace->H;
+ Htop = 0;
+ num_bonds = 0;
+ num_hbonds = 0;
+ btop_i = btop_j = 0;
+ p_boc1 = system->reaxprm.gp.l[0];
+ p_boc2 = system->reaxprm.gp.l[1];
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ atom_i = &(system->atoms[i]);
+ type_i = atom_i->type;
+ start_i = Start_Index(i, far_nbrs);
+ end_i = End_Index(i, far_nbrs);
+ H->start[i] = Htop;
+ btop_i = End_Index( i, bonds );
+ sbp_i = &(system->reaxprm.sbp[type_i]);
+ ihb = ihb_top = -1;
+ if ( control->hb_cut > 0 && (ihb = sbp_i->p_hbond) == 1 )
+ ihb_top = End_Index( workspace->hbond_index[i], hbonds );
+
+ for ( pj = start_i; pj < end_i; ++pj )
+ {
+ nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
+ j = nbr_pj->nbr;
+ atom_j = &(system->atoms[j]);
+
+ flag = 0;
+ if ((data->step - data->prev_steps) % control->reneighbor == 0)
+ {
+ if ( nbr_pj->d <= control->r_cut)
+ flag = 1;
+ else flag = 0;
+ }
+ else if ((nbr_pj->d = Sq_Distance_on_T3(atom_i->x, atom_j->x, &(system->box),
+ nbr_pj->dvec)) <= SQR(control->r_cut))
+ {
+ nbr_pj->d = sqrt(nbr_pj->d);
+ flag = 1;
+ }
+
+ if ( flag )
+ {
+ type_j = system->atoms[j].type;
+ r_ij = nbr_pj->d;
+ sbp_j = &(system->reaxprm.sbp[type_j]);
+ twbp = &(system->reaxprm.tbp[type_i][type_j]);
+ self_coef = (i == j) ? 0.5 : 1.0;
+
+ /* H matrix entry */
+ Tap = control->Tap7 * r_ij + control->Tap6;
+ Tap = Tap * r_ij + control->Tap5;
+ Tap = Tap * r_ij + control->Tap4;
+ Tap = Tap * r_ij + control->Tap3;
+ Tap = Tap * r_ij + control->Tap2;
+ Tap = Tap * r_ij + control->Tap1;
+ Tap = Tap * r_ij + control->Tap0;
+
+ dr3gamij_1 = ( r_ij * r_ij * r_ij + twbp->gamma );
+ dr3gamij_3 = POW( dr3gamij_1 , 0.33333333333333 );
+
+ H->entries[Htop].j = j;
+ H->entries[Htop].val = self_coef * Tap * EV_to_KCALpMOL / dr3gamij_3;
+ ++Htop;
+
+ /* hydrogen bond lists */
+ if ( control->hb_cut > 0 && (ihb == 1 || ihb == 2) &&
+ nbr_pj->d <= control->hb_cut )
+ {
+ // fprintf( stderr, "%d %d\n", atom1, atom2 );
+ jhb = sbp_j->p_hbond;
+ if ( ihb == 1 && jhb == 2 )
+ {
+ hbonds->select.hbond_list[ihb_top].nbr = j;
+ hbonds->select.hbond_list[ihb_top].scl = 1;
+ hbonds->select.hbond_list[ihb_top].ptr = nbr_pj;
+ ++ihb_top;
+ ++num_hbonds;
+ }
+ else if ( ihb == 2 && jhb == 1 )
+ {
+ jhb_top = End_Index( workspace->hbond_index[j], hbonds );
+ hbonds->select.hbond_list[jhb_top].nbr = i;
+ hbonds->select.hbond_list[jhb_top].scl = -1;
+ hbonds->select.hbond_list[jhb_top].ptr = nbr_pj;
+ Set_End_Index( workspace->hbond_index[j], jhb_top + 1, hbonds );
+ ++num_hbonds;
+ }
+ }
+
+ /* uncorrected bond orders */
+ if ( far_nbrs->select.far_nbr_list[pj].d <= control->nbr_cut )
+ {
+ r2 = SQR(r_ij);
+
+ if ( sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0)
+ {
+ C12 = twbp->p_bo1 * POW( r_ij / twbp->r_s, twbp->p_bo2 );
+ BO_s = (1.0 + control->bo_cut) * EXP( C12 );
+ }
+ else BO_s = C12 = 0.0;
+
+ if ( sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0)
+ {
+ C34 = twbp->p_bo3 * POW( r_ij / twbp->r_p, twbp->p_bo4 );
+ BO_pi = EXP( C34 );
+ }
+ else BO_pi = C34 = 0.0;
+
+ if ( sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0)
+ {
+ C56 = twbp->p_bo5 * POW( r_ij / twbp->r_pp, twbp->p_bo6 );
+ BO_pi2 = EXP( C56 );
+ }
+ else BO_pi2 = C56 = 0.0;
+
+ /* Initially BO values are the uncorrected ones, page 1 */
+ BO = BO_s + BO_pi + BO_pi2;
+
+ if ( BO >= control->bo_cut )
+ {
+ num_bonds += 2;
+ /****** bonds i-j and j-i ******/
+ ibond = &( bonds->select.bond_list[btop_i] );
+ btop_j = End_Index( j, bonds );
+ jbond = &(bonds->select.bond_list[btop_j]);
+
+ ibond->nbr = j;
+ jbond->nbr = i;
+ ibond->d = r_ij;
+ jbond->d = r_ij;
+ rvec_Copy( ibond->dvec, nbr_pj->dvec );
+ rvec_Scale( jbond->dvec, -1, nbr_pj->dvec );
+ ivec_Copy( ibond->rel_box, nbr_pj->rel_box );
+ ivec_Scale( jbond->rel_box, -1, nbr_pj->rel_box );
+ ibond->dbond_index = btop_i;
+ jbond->dbond_index = btop_i;
+ ibond->sym_index = btop_j;
+ jbond->sym_index = btop_i;
+ ++btop_i;
+ Set_End_Index( j, btop_j + 1, bonds );
+
+ bo_ij = &( ibond->bo_data );
+ bo_ji = &( jbond->bo_data );
+ bo_ji->BO = bo_ij->BO = BO;
+ bo_ji->BO_s = bo_ij->BO_s = BO_s;
+ bo_ji->BO_pi = bo_ij->BO_pi = BO_pi;
+ bo_ji->BO_pi2 = bo_ij->BO_pi2 = BO_pi2;
+
+ /* Bond Order page2-3, derivative of total bond order prime */
+ Cln_BOp_s = twbp->p_bo2 * C12 / r2;
+ Cln_BOp_pi = twbp->p_bo4 * C34 / r2;
+ Cln_BOp_pi2 = twbp->p_bo6 * C56 / r2;
+
+ /* Only dln_BOp_xx wrt. dr_i is stored here, note that
+ dln_BOp_xx/dr_i = -dln_BOp_xx/dr_j and all others are 0 */
+ rvec_Scale(bo_ij->dln_BOp_s, -bo_ij->BO_s * Cln_BOp_s, ibond->dvec);
+ rvec_Scale(bo_ij->dln_BOp_pi, -bo_ij->BO_pi * Cln_BOp_pi, ibond->dvec);
+ rvec_Scale(bo_ij->dln_BOp_pi2,
+ -bo_ij->BO_pi2 * Cln_BOp_pi2, ibond->dvec);
+ rvec_Scale(bo_ji->dln_BOp_s, -1., bo_ij->dln_BOp_s);
+ rvec_Scale(bo_ji->dln_BOp_pi, -1., bo_ij->dln_BOp_pi );
+ rvec_Scale(bo_ji->dln_BOp_pi2, -1., bo_ij->dln_BOp_pi2 );
+
+ /* Only dBOp wrt. dr_i is stored here, note that
+ dBOp/dr_i = -dBOp/dr_j and all others are 0 */
+ rvec_Scale( bo_ij->dBOp,
+ -(bo_ij->BO_s * Cln_BOp_s +
+ bo_ij->BO_pi * Cln_BOp_pi +
+ bo_ij->BO_pi2 * Cln_BOp_pi2), ibond->dvec );
+ rvec_Scale( bo_ji->dBOp, -1., bo_ij->dBOp );
+
+ rvec_Add( workspace->dDeltap_self[i], bo_ij->dBOp );
+ rvec_Add( workspace->dDeltap_self[j], bo_ji->dBOp );
+
+ bo_ij->BO_s -= control->bo_cut;
+ bo_ij->BO -= control->bo_cut;
+ bo_ji->BO_s -= control->bo_cut;
+ bo_ji->BO -= control->bo_cut;
+ workspace->total_bond_order[i] += bo_ij->BO; //currently total_BOp
+ workspace->total_bond_order[j] += bo_ji->BO; //currently total_BOp
+ bo_ij->Cdbo = bo_ij->Cdbopi = bo_ij->Cdbopi2 = 0.0;
+ bo_ji->Cdbo = bo_ji->Cdbopi = bo_ji->Cdbopi2 = 0.0;
+
+ /*fprintf( stderr, "%d %d %g %g %g\n",
+ i+1, j+1, bo_ij->BO, bo_ij->BO_pi, bo_ij->BO_pi2 );*/
+
+ /*fprintf( stderr, "Cln_BOp_s: %f, pbo2: %f, C12:%f\n",
+ Cln_BOp_s, twbp->p_bo2, C12 );
+ fprintf( stderr, "Cln_BOp_pi: %f, pbo4: %f, C34:%f\n",
+ Cln_BOp_pi, twbp->p_bo4, C34 );
+ fprintf( stderr, "Cln_BOp_pi2: %f, pbo6: %f, C56:%f\n",
+ Cln_BOp_pi2, twbp->p_bo6, C56 );*/
+ /*fprintf(stderr, "pbo1: %f, pbo2:%f\n", twbp->p_bo1, twbp->p_bo2);
+ fprintf(stderr, "pbo3: %f, pbo4:%f\n", twbp->p_bo3, twbp->p_bo4);
+ fprintf(stderr, "pbo5: %f, pbo6:%f\n", twbp->p_bo5, twbp->p_bo6);
+ fprintf( stderr, "r_s: %f, r_p: %f, r_pp: %f\n",
+ twbp->r_s, twbp->r_p, twbp->r_pp );
+ fprintf( stderr, "C12: %g, C34:%g, C56:%g\n", C12, C34, C56 );*/
+
+ /*fprintf( stderr, "\tfactors: %g %g %g\n",
+ -(bo_ij->BO_s * Cln_BOp_s + bo_ij->BO_pi * Cln_BOp_pi +
+ bo_ij->BO_pi2 * Cln_BOp_pp),
+ -bo_ij->BO_pi * Cln_BOp_pi, -bo_ij->BO_pi2 * Cln_BOp_pi2 );*/
+ /*fprintf( stderr, "dBOpi:\t[%g, %g, %g]\n",
+ bo_ij->dBOp[0], bo_ij->dBOp[1], bo_ij->dBOp[2] );
+ fprintf( stderr, "dBOpi:\t[%g, %g, %g]\n",
+ bo_ij->dln_BOp_pi[0], bo_ij->dln_BOp_pi[1],
+ bo_ij->dln_BOp_pi[2] );
+ fprintf( stderr, "dBOpi2:\t[%g, %g, %g]\n\n",
+ bo_ij->dln_BOp_pi2[0], bo_ij->dln_BOp_pi2[1],
+ bo_ij->dln_BOp_pi2[2] );*/
+
+ Set_End_Index( j, btop_j + 1, bonds );
+ }
+ }
+ }
+ }
+
+ H->entries[Htop].j = i;
+ H->entries[Htop].val = system->reaxprm.sbp[type_i].eta;
+ ++Htop;
+
+ Set_End_Index( i, btop_i, bonds );
+ if ( ihb == 1 )
+ Set_End_Index( workspace->hbond_index[i], ihb_top, hbonds );
+ //fprintf( stderr, "%d bonds start: %d, end: %d\n",
+ // i, Start_Index( i, bonds ), End_Index( i, bonds ) );
}
- H->entries[Htop].j = i;
- H->entries[Htop].val = system->reaxprm.sbp[type_i].eta;
- ++Htop;
-
- Set_End_Index( i, btop_i, bonds );
- if( ihb == 1 )
- Set_End_Index( workspace->hbond_index[i], ihb_top, hbonds );
- //fprintf( stderr, "%d bonds start: %d, end: %d\n",
- // i, Start_Index( i, bonds ), End_Index( i, bonds ) );
- }
-
- // mark the end of j list
- H->start[i] = Htop;
- /* validate lists - decide if reallocation is required! */
- Validate_Lists( workspace, lists,
- data->step, system->N, H->m, Htop, num_bonds, num_hbonds );
+ // mark the end of j list
+ H->start[i] = Htop;
+ /* validate lists - decide if reallocation is required! */
+ Validate_Lists( workspace, lists,
+ data->step, system->N, H->m, Htop, num_bonds, num_hbonds );
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "step%d: Htop = %d, num_bonds = %d, num_hbonds = %d\n",
- data->step, Htop, num_bonds, num_hbonds );
-
+ fprintf( stderr, "step%d: Htop = %d, num_bonds = %d, num_hbonds = %d\n",
+ data->step, Htop, num_bonds, num_hbonds );
+
#endif
}
-void Init_Forces_Tab( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control ) {
- int i, j, pj;
- int start_i, end_i;
- int type_i, type_j;
- int Htop, btop_i, btop_j, num_bonds, num_hbonds;
- int tmin, tmax, r;
- int ihb, jhb, ihb_top, jhb_top;
- int flag;
- real r_ij, r2, self_coef;
- real val, dif, base;
- real C12, C34, C56;
- real Cln_BOp_s, Cln_BOp_pi, Cln_BOp_pi2;
- real BO, BO_s, BO_pi, BO_pi2;
- real p_boc1, p_boc2;
- sparse_matrix *H;
- list *far_nbrs, *bonds, *hbonds;
- single_body_parameters *sbp_i, *sbp_j;
- two_body_parameters *twbp;
- far_neighbor_data *nbr_pj;
- LR_lookup_table *t;
- reax_atom *atom_i, *atom_j;
- bond_data *ibond, *jbond;
- bond_order_data *bo_ij, *bo_ji;
-
- far_nbrs = *lists + FAR_NBRS;
- bonds = *lists + BONDS;
- hbonds = *lists + HBONDS;
-
- H = workspace->H;
- Htop = 0;
- num_bonds = 0;
- num_hbonds = 0;
- btop_i = btop_j = 0;
- p_boc1 = system->reaxprm.gp.l[0];
- p_boc2 = system->reaxprm.gp.l[1];
-
- for( i = 0; i < system->N; ++i ) {
- atom_i = &(system->atoms[i]);
- type_i = atom_i->type;
- start_i = Start_Index(i, far_nbrs);
- end_i = End_Index(i, far_nbrs);
- H->start[i] = Htop;
- btop_i = End_Index( i, bonds );
- sbp_i = &(system->reaxprm.sbp[type_i]);
- ihb = ihb_top = -1;
- if( control->hb_cut > 0 && (ihb=sbp_i->p_hbond) == 1 )
- ihb_top = End_Index( workspace->hbond_index[i], hbonds );
-
- for( pj = start_i; pj < end_i; ++pj ) {
- nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
- j = nbr_pj->nbr;
- atom_j = &(system->atoms[j]);
-
- flag = 0;
- if((data->step-data->prev_steps) % control->reneighbor == 0) {
- if(nbr_pj->d <= control->r_cut)
- flag = 1;
- else flag = 0;
- }
- else if((nbr_pj->d=Sq_Distance_on_T3(atom_i->x,atom_j->x,&(system->box),
- nbr_pj->dvec))<=SQR(control->r_cut)){
- nbr_pj->d = sqrt(nbr_pj->d);
- flag = 1;
- }
-
- if( flag ){
- type_j = system->atoms[j].type;
- r_ij = nbr_pj->d;
- sbp_j = &(system->reaxprm.sbp[type_j]);
- twbp = &(system->reaxprm.tbp[type_i][type_j]);
- self_coef = (i == j) ? 0.5 : 1.0;
- tmin = MIN( type_i, type_j );
- tmax = MAX( type_i, type_j );
- t = &( LR[tmin][tmax] );
-
- /* cubic spline interpolation */
- r = (int)(r_ij * t->inv_dx);
- if( r == 0 ) ++r;
- base = (real)(r+1) * t->dx;
- dif = r_ij - base;
- val = ((t->ele[r].d*dif + t->ele[r].c)*dif + t->ele[r].b)*dif +
- t->ele[r].a;
- val *= EV_to_KCALpMOL / C_ele;
-
- H->entries[Htop].j = j;
- H->entries[Htop].val = self_coef * val;
- ++Htop;
-
- /* hydrogen bond lists */
- if( control->hb_cut > 0 && (ihb==1 || ihb==2) &&
- nbr_pj->d <= control->hb_cut ) {
- // fprintf( stderr, "%d %d\n", atom1, atom2 );
- jhb = sbp_j->p_hbond;
- if( ihb == 1 && jhb == 2 ) {
- hbonds->select.hbond_list[ihb_top].nbr = j;
- hbonds->select.hbond_list[ihb_top].scl = 1;
- hbonds->select.hbond_list[ihb_top].ptr = nbr_pj;
- ++ihb_top;
- ++num_hbonds;
- }
- else if( ihb == 2 && jhb == 1 ) {
- jhb_top = End_Index( workspace->hbond_index[j], hbonds );
- hbonds->select.hbond_list[jhb_top].nbr = i;
- hbonds->select.hbond_list[jhb_top].scl = -1;
- hbonds->select.hbond_list[jhb_top].ptr = nbr_pj;
- Set_End_Index( workspace->hbond_index[j], jhb_top+1, hbonds );
- ++num_hbonds;
- }
- }
-
- /* uncorrected bond orders */
- if( far_nbrs->select.far_nbr_list[pj].d <= control->nbr_cut ) {
- r2 = SQR(r_ij);
-
- if( sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0) {
- C12 = twbp->p_bo1 * POW( r_ij / twbp->r_s, twbp->p_bo2 );
- BO_s = (1.0 + control->bo_cut) * EXP( C12 );
- }
- else BO_s = C12 = 0.0;
-
- if( sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0) {
- C34 = twbp->p_bo3 * POW( r_ij / twbp->r_p, twbp->p_bo4 );
- BO_pi = EXP( C34 );
- }
- else BO_pi = C34 = 0.0;
-
- if( sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0) {
- C56 = twbp->p_bo5 * POW( r_ij / twbp->r_pp, twbp->p_bo6 );
- BO_pi2= EXP( C56 );
- }
- else BO_pi2 = C56 = 0.0;
-
- /* Initially BO values are the uncorrected ones, page 1 */
- BO = BO_s + BO_pi + BO_pi2;
-
- if( BO >= control->bo_cut ) {
- num_bonds += 2;
- /****** bonds i-j and j-i ******/
- ibond = &( bonds->select.bond_list[btop_i] );
- btop_j = End_Index( j, bonds );
- jbond = &(bonds->select.bond_list[btop_j]);
-
- ibond->nbr = j;
- jbond->nbr = i;
- ibond->d = r_ij;
- jbond->d = r_ij;
- rvec_Copy( ibond->dvec, nbr_pj->dvec );
- //fprintf (stderr, " %f - %f - %f \n", nbr_pj->dvec[0], nbr_pj->dvec[1], nbr_pj->dvec[2]);
- rvec_Scale( jbond->dvec, -1, nbr_pj->dvec );
- ivec_Copy( ibond->rel_box, nbr_pj->rel_box );
- ivec_Scale( jbond->rel_box, -1, nbr_pj->rel_box );
- ibond->dbond_index = btop_i;
- jbond->dbond_index = btop_i;
- ibond->sym_index = btop_j;
- jbond->sym_index = btop_i;
- ++btop_i;
- Set_End_Index( j, btop_j+1, bonds );
-
- bo_ij = &( ibond->bo_data );
- bo_ji = &( jbond->bo_data );
- bo_ji->BO = bo_ij->BO = BO;
- bo_ji->BO_s = bo_ij->BO_s = BO_s;
- bo_ji->BO_pi = bo_ij->BO_pi = BO_pi;
- bo_ji->BO_pi2 = bo_ij->BO_pi2 = BO_pi2;
-
- /* Bond Order page2-3, derivative of total bond order prime */
- Cln_BOp_s = twbp->p_bo2 * C12 / r2;
- Cln_BOp_pi = twbp->p_bo4 * C34 / r2;
- Cln_BOp_pi2 = twbp->p_bo6 * C56 / r2;
-
- /* Only dln_BOp_xx wrt. dr_i is stored here, note that
- dln_BOp_xx/dr_i = -dln_BOp_xx/dr_j and all others are 0 */
- rvec_Scale(bo_ij->dln_BOp_s,-bo_ij->BO_s*Cln_BOp_s,ibond->dvec);
- rvec_Scale(bo_ij->dln_BOp_pi,-bo_ij->BO_pi*Cln_BOp_pi,ibond->dvec);
- rvec_Scale(bo_ij->dln_BOp_pi2,
- -bo_ij->BO_pi2*Cln_BOp_pi2,ibond->dvec);
- rvec_Scale(bo_ji->dln_BOp_s, -1., bo_ij->dln_BOp_s);
- rvec_Scale(bo_ji->dln_BOp_pi, -1., bo_ij->dln_BOp_pi );
- rvec_Scale(bo_ji->dln_BOp_pi2, -1., bo_ij->dln_BOp_pi2 );
-
- /* Only dBOp wrt. dr_i is stored here, note that
- dBOp/dr_i = -dBOp/dr_j and all others are 0 */
- rvec_Scale( bo_ij->dBOp,
- -(bo_ij->BO_s * Cln_BOp_s +
- bo_ij->BO_pi * Cln_BOp_pi +
- bo_ij->BO_pi2 * Cln_BOp_pi2), ibond->dvec );
- rvec_Scale( bo_ji->dBOp, -1., bo_ij->dBOp );
-
- rvec_Add( workspace->dDeltap_self[i], bo_ij->dBOp );
- rvec_Add( workspace->dDeltap_self[j], bo_ji->dBOp );
-
- bo_ij->BO_s -= control->bo_cut;
- bo_ij->BO -= control->bo_cut;
- bo_ji->BO_s -= control->bo_cut;
- bo_ji->BO -= control->bo_cut;
- workspace->total_bond_order[i] += bo_ij->BO; //currently total_BOp
- workspace->total_bond_order[j] += bo_ji->BO; //currently total_BOp
- bo_ij->Cdbo = bo_ij->Cdbopi = bo_ij->Cdbopi2 = 0.0;
- bo_ji->Cdbo = bo_ji->Cdbopi = bo_ji->Cdbopi2 = 0.0;
-
- Set_End_Index( j, btop_j+1, bonds );
- }
- }
- }
+void Init_Forces_Tab( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
+{
+ int i, j, pj;
+ int start_i, end_i;
+ int type_i, type_j;
+ int Htop, btop_i, btop_j, num_bonds, num_hbonds;
+ int tmin, tmax, r;
+ int ihb, jhb, ihb_top, jhb_top;
+ int flag;
+ real r_ij, r2, self_coef;
+ real val, dif, base;
+ real C12, C34, C56;
+ real Cln_BOp_s, Cln_BOp_pi, Cln_BOp_pi2;
+ real BO, BO_s, BO_pi, BO_pi2;
+ real p_boc1, p_boc2;
+ sparse_matrix *H;
+ list *far_nbrs, *bonds, *hbonds;
+ single_body_parameters *sbp_i, *sbp_j;
+ two_body_parameters *twbp;
+ far_neighbor_data *nbr_pj;
+ LR_lookup_table *t;
+ reax_atom *atom_i, *atom_j;
+ bond_data *ibond, *jbond;
+ bond_order_data *bo_ij, *bo_ji;
+
+ far_nbrs = *lists + FAR_NBRS;
+ bonds = *lists + BONDS;
+ hbonds = *lists + HBONDS;
+
+ H = workspace->H;
+ Htop = 0;
+ num_bonds = 0;
+ num_hbonds = 0;
+ btop_i = btop_j = 0;
+ p_boc1 = system->reaxprm.gp.l[0];
+ p_boc2 = system->reaxprm.gp.l[1];
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ atom_i = &(system->atoms[i]);
+ type_i = atom_i->type;
+ start_i = Start_Index(i, far_nbrs);
+ end_i = End_Index(i, far_nbrs);
+ H->start[i] = Htop;
+ btop_i = End_Index( i, bonds );
+ sbp_i = &(system->reaxprm.sbp[type_i]);
+ ihb = ihb_top = -1;
+ if ( control->hb_cut > 0 && (ihb = sbp_i->p_hbond) == 1 )
+ ihb_top = End_Index( workspace->hbond_index[i], hbonds );
+
+ for ( pj = start_i; pj < end_i; ++pj )
+ {
+ nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
+ j = nbr_pj->nbr;
+ atom_j = &(system->atoms[j]);
+
+ flag = 0;
+ if ((data->step - data->prev_steps) % control->reneighbor == 0)
+ {
+ if (nbr_pj->d <= control->r_cut)
+ flag = 1;
+ else flag = 0;
+ }
+ else if ((nbr_pj->d = Sq_Distance_on_T3(atom_i->x, atom_j->x, &(system->box),
+ nbr_pj->dvec)) <= SQR(control->r_cut))
+ {
+ nbr_pj->d = sqrt(nbr_pj->d);
+ flag = 1;
+ }
+
+ if ( flag )
+ {
+ type_j = system->atoms[j].type;
+ r_ij = nbr_pj->d;
+ sbp_j = &(system->reaxprm.sbp[type_j]);
+ twbp = &(system->reaxprm.tbp[type_i][type_j]);
+ self_coef = (i == j) ? 0.5 : 1.0;
+ tmin = MIN( type_i, type_j );
+ tmax = MAX( type_i, type_j );
+ t = &( LR[tmin][tmax] );
+
+ /* cubic spline interpolation */
+ r = (int)(r_ij * t->inv_dx);
+ if ( r == 0 ) ++r;
+ base = (real)(r + 1) * t->dx;
+ dif = r_ij - base;
+ val = ((t->ele[r].d * dif + t->ele[r].c) * dif + t->ele[r].b) * dif +
+ t->ele[r].a;
+ val *= EV_to_KCALpMOL / C_ele;
+
+ H->entries[Htop].j = j;
+ H->entries[Htop].val = self_coef * val;
+ ++Htop;
+
+ /* hydrogen bond lists */
+ if ( control->hb_cut > 0 && (ihb == 1 || ihb == 2) &&
+ nbr_pj->d <= control->hb_cut )
+ {
+ // fprintf( stderr, "%d %d\n", atom1, atom2 );
+ jhb = sbp_j->p_hbond;
+ if ( ihb == 1 && jhb == 2 )
+ {
+ hbonds->select.hbond_list[ihb_top].nbr = j;
+ hbonds->select.hbond_list[ihb_top].scl = 1;
+ hbonds->select.hbond_list[ihb_top].ptr = nbr_pj;
+ ++ihb_top;
+ ++num_hbonds;
+ }
+ else if ( ihb == 2 && jhb == 1 )
+ {
+ jhb_top = End_Index( workspace->hbond_index[j], hbonds );
+ hbonds->select.hbond_list[jhb_top].nbr = i;
+ hbonds->select.hbond_list[jhb_top].scl = -1;
+ hbonds->select.hbond_list[jhb_top].ptr = nbr_pj;
+ Set_End_Index( workspace->hbond_index[j], jhb_top + 1, hbonds );
+ ++num_hbonds;
+ }
+ }
+
+ /* uncorrected bond orders */
+ if ( far_nbrs->select.far_nbr_list[pj].d <= control->nbr_cut )
+ {
+ r2 = SQR(r_ij);
+
+ if ( sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0)
+ {
+ C12 = twbp->p_bo1 * POW( r_ij / twbp->r_s, twbp->p_bo2 );
+ BO_s = (1.0 + control->bo_cut) * EXP( C12 );
+ }
+ else BO_s = C12 = 0.0;
+
+ if ( sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0)
+ {
+ C34 = twbp->p_bo3 * POW( r_ij / twbp->r_p, twbp->p_bo4 );
+ BO_pi = EXP( C34 );
+ }
+ else BO_pi = C34 = 0.0;
+
+ if ( sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0)
+ {
+ C56 = twbp->p_bo5 * POW( r_ij / twbp->r_pp, twbp->p_bo6 );
+ BO_pi2 = EXP( C56 );
+ }
+ else BO_pi2 = C56 = 0.0;
+
+ /* Initially BO values are the uncorrected ones, page 1 */
+ BO = BO_s + BO_pi + BO_pi2;
+
+ if ( BO >= control->bo_cut )
+ {
+ num_bonds += 2;
+ /****** bonds i-j and j-i ******/
+ ibond = &( bonds->select.bond_list[btop_i] );
+ btop_j = End_Index( j, bonds );
+ jbond = &(bonds->select.bond_list[btop_j]);
+
+ ibond->nbr = j;
+ jbond->nbr = i;
+ ibond->d = r_ij;
+ jbond->d = r_ij;
+ rvec_Copy( ibond->dvec, nbr_pj->dvec );
+ //fprintf (stderr, " %f - %f - %f \n", nbr_pj->dvec[0], nbr_pj->dvec[1], nbr_pj->dvec[2]);
+ rvec_Scale( jbond->dvec, -1, nbr_pj->dvec );
+ ivec_Copy( ibond->rel_box, nbr_pj->rel_box );
+ ivec_Scale( jbond->rel_box, -1, nbr_pj->rel_box );
+ ibond->dbond_index = btop_i;
+ jbond->dbond_index = btop_i;
+ ibond->sym_index = btop_j;
+ jbond->sym_index = btop_i;
+ ++btop_i;
+ Set_End_Index( j, btop_j + 1, bonds );
+
+ bo_ij = &( ibond->bo_data );
+ bo_ji = &( jbond->bo_data );
+ bo_ji->BO = bo_ij->BO = BO;
+ bo_ji->BO_s = bo_ij->BO_s = BO_s;
+ bo_ji->BO_pi = bo_ij->BO_pi = BO_pi;
+ bo_ji->BO_pi2 = bo_ij->BO_pi2 = BO_pi2;
+
+ /* Bond Order page2-3, derivative of total bond order prime */
+ Cln_BOp_s = twbp->p_bo2 * C12 / r2;
+ Cln_BOp_pi = twbp->p_bo4 * C34 / r2;
+ Cln_BOp_pi2 = twbp->p_bo6 * C56 / r2;
+
+ /* Only dln_BOp_xx wrt. dr_i is stored here, note that
+ dln_BOp_xx/dr_i = -dln_BOp_xx/dr_j and all others are 0 */
+ rvec_Scale(bo_ij->dln_BOp_s, -bo_ij->BO_s * Cln_BOp_s, ibond->dvec);
+ rvec_Scale(bo_ij->dln_BOp_pi, -bo_ij->BO_pi * Cln_BOp_pi, ibond->dvec);
+ rvec_Scale(bo_ij->dln_BOp_pi2,
+ -bo_ij->BO_pi2 * Cln_BOp_pi2, ibond->dvec);
+ rvec_Scale(bo_ji->dln_BOp_s, -1., bo_ij->dln_BOp_s);
+ rvec_Scale(bo_ji->dln_BOp_pi, -1., bo_ij->dln_BOp_pi );
+ rvec_Scale(bo_ji->dln_BOp_pi2, -1., bo_ij->dln_BOp_pi2 );
+
+ /* Only dBOp wrt. dr_i is stored here, note that
+ dBOp/dr_i = -dBOp/dr_j and all others are 0 */
+ rvec_Scale( bo_ij->dBOp,
+ -(bo_ij->BO_s * Cln_BOp_s +
+ bo_ij->BO_pi * Cln_BOp_pi +
+ bo_ij->BO_pi2 * Cln_BOp_pi2), ibond->dvec );
+ rvec_Scale( bo_ji->dBOp, -1., bo_ij->dBOp );
+
+ rvec_Add( workspace->dDeltap_self[i], bo_ij->dBOp );
+ rvec_Add( workspace->dDeltap_self[j], bo_ji->dBOp );
+
+ bo_ij->BO_s -= control->bo_cut;
+ bo_ij->BO -= control->bo_cut;
+ bo_ji->BO_s -= control->bo_cut;
+ bo_ji->BO -= control->bo_cut;
+ workspace->total_bond_order[i] += bo_ij->BO; //currently total_BOp
+ workspace->total_bond_order[j] += bo_ji->BO; //currently total_BOp
+ bo_ij->Cdbo = bo_ij->Cdbopi = bo_ij->Cdbopi2 = 0.0;
+ bo_ji->Cdbo = bo_ji->Cdbopi = bo_ji->Cdbopi2 = 0.0;
+
+ Set_End_Index( j, btop_j + 1, bonds );
+ }
+ }
+ }
+ }
+
+ H->entries[Htop].j = i;
+ H->entries[Htop].val = system->reaxprm.sbp[type_i].eta;
+ ++Htop;
+
+ Set_End_Index( i, btop_i, bonds );
+ if ( ihb == 1 )
+ Set_End_Index( workspace->hbond_index[i], ihb_top, hbonds );
}
- H->entries[Htop].j = i;
- H->entries[Htop].val = system->reaxprm.sbp[type_i].eta;
- ++Htop;
-
- Set_End_Index( i, btop_i, bonds );
- if( ihb == 1 )
- Set_End_Index( workspace->hbond_index[i], ihb_top, hbonds );
- }
-
- // mark the end of j list
- H->start[i] = Htop;
- /* validate lists - decide if reallocation is required! */
- Validate_Lists( workspace, lists,
- data->step, system->N, H->m, Htop, num_bonds, num_hbonds );
+ // mark the end of j list
+ H->start[i] = Htop;
+ /* validate lists - decide if reallocation is required! */
+ Validate_Lists( workspace, lists,
+ data->step, system->N, H->m, Htop, num_bonds, num_hbonds );
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "step%d: Htop = %d, num_bonds = %d, num_hbonds = %d\n",
- data->step, Htop, num_bonds, num_hbonds );
- //Print_Bonds( system, bonds, "sbonds.out" );
- //Print_Bond_List2( system, bonds, "sbonds.out" );
- //Print_Sparse_Matrix2( H, "H.out" );
+ fprintf( stderr, "step%d: Htop = %d, num_bonds = %d, num_hbonds = %d\n",
+ data->step, Htop, num_bonds, num_hbonds );
+ //Print_Bonds( system, bonds, "sbonds.out" );
+ //Print_Bond_List2( system, bonds, "sbonds.out" );
+ //Print_Sparse_Matrix2( H, "H.out" );
#endif
}
-void Estimate_Storage_Sizes( reax_system *system, control_params *control,
- list **lists, int *Htop, int *hb_top,
- int *bond_top, int *num_3body ) {
- int i, j, pj;
- int start_i, end_i;
- int type_i, type_j;
- int ihb, jhb;
- real r_ij, r2;
- real C12, C34, C56;
- real BO, BO_s, BO_pi, BO_pi2;
- real p_boc1, p_boc2;
- list *far_nbrs;
- single_body_parameters *sbp_i, *sbp_j;
- two_body_parameters *twbp;
- far_neighbor_data *nbr_pj;
- reax_atom *atom_i, *atom_j;
-
- far_nbrs = *lists + FAR_NBRS;
- p_boc1 = system->reaxprm.gp.l[0];
- p_boc2 = system->reaxprm.gp.l[1];
-
- for( i = 0; i < system->N; ++i ) {
- atom_i = &(system->atoms[i]);
- type_i = atom_i->type;
- start_i = Start_Index(i, far_nbrs);
- end_i = End_Index(i, far_nbrs);
- sbp_i = &(system->reaxprm.sbp[type_i]);
- ihb = sbp_i->p_hbond;
-
- for( pj = start_i; pj < end_i; ++pj ) {
- nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
- j = nbr_pj->nbr;
- atom_j = &(system->atoms[j]);
- type_j = atom_j->type;
- sbp_j = &(system->reaxprm.sbp[type_j]);
- twbp = &(system->reaxprm.tbp[type_i][type_j]);
-
- if( nbr_pj->d <= control->r_cut ) {
- ++(*Htop);
-
- /* hydrogen bond lists */
- if( control->hb_cut > 0.1 && (ihb==1 || ihb==2) &&
- nbr_pj->d <= control->hb_cut ) {
- jhb = sbp_j->p_hbond;
- if( ihb == 1 && jhb == 2 )
- ++hb_top[i];
- else if( ihb == 2 && jhb == 1 )
- ++hb_top[j];
- }
-
- /* uncorrected bond orders */
- if( nbr_pj->d <= control->nbr_cut ) {
- r_ij = nbr_pj->d;
- r2 = SQR(r_ij);
-
- if( sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0) {
- C12 = twbp->p_bo1 * POW( r_ij / twbp->r_s, twbp->p_bo2 );
- BO_s = (1.0 + control->bo_cut) * EXP( C12 );
- }
- else BO_s = C12 = 0.0;
-
- if( sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0) {
- C34 = twbp->p_bo3 * POW( r_ij / twbp->r_p, twbp->p_bo4 );
- BO_pi = EXP( C34 );
- }
- else BO_pi = C34 = 0.0;
-
- if( sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0) {
- C56 = twbp->p_bo5 * POW( r_ij / twbp->r_pp, twbp->p_bo6 );
- BO_pi2= EXP( C56 );
- }
- else BO_pi2 = C56 = 0.0;
-
- /* Initially BO values are the uncorrected ones, page 1 */
- BO = BO_s + BO_pi + BO_pi2;
-
- if( BO >= control->bo_cut ) {
- ++bond_top[i];
- ++bond_top[j];
- }
- }
- }
+void Estimate_Storage_Sizes( reax_system *system, control_params *control,
+ list **lists, int *Htop, int *hb_top,
+ int *bond_top, int *num_3body )
+{
+ int i, j, pj;
+ int start_i, end_i;
+ int type_i, type_j;
+ int ihb, jhb;
+ real r_ij, r2;
+ real C12, C34, C56;
+ real BO, BO_s, BO_pi, BO_pi2;
+ real p_boc1, p_boc2;
+ list *far_nbrs;
+ single_body_parameters *sbp_i, *sbp_j;
+ two_body_parameters *twbp;
+ far_neighbor_data *nbr_pj;
+ reax_atom *atom_i, *atom_j;
+
+ far_nbrs = *lists + FAR_NBRS;
+ p_boc1 = system->reaxprm.gp.l[0];
+ p_boc2 = system->reaxprm.gp.l[1];
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ atom_i = &(system->atoms[i]);
+ type_i = atom_i->type;
+ start_i = Start_Index(i, far_nbrs);
+ end_i = End_Index(i, far_nbrs);
+ sbp_i = &(system->reaxprm.sbp[type_i]);
+ ihb = sbp_i->p_hbond;
+
+ for ( pj = start_i; pj < end_i; ++pj )
+ {
+ nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
+ j = nbr_pj->nbr;
+ atom_j = &(system->atoms[j]);
+ type_j = atom_j->type;
+ sbp_j = &(system->reaxprm.sbp[type_j]);
+ twbp = &(system->reaxprm.tbp[type_i][type_j]);
+
+ if ( nbr_pj->d <= control->r_cut )
+ {
+ ++(*Htop);
+
+ /* hydrogen bond lists */
+ if ( control->hb_cut > 0.1 && (ihb == 1 || ihb == 2) &&
+ nbr_pj->d <= control->hb_cut )
+ {
+ jhb = sbp_j->p_hbond;
+ if ( ihb == 1 && jhb == 2 )
+ ++hb_top[i];
+ else if ( ihb == 2 && jhb == 1 )
+ ++hb_top[j];
+ }
+
+ /* uncorrected bond orders */
+ if ( nbr_pj->d <= control->nbr_cut )
+ {
+ r_ij = nbr_pj->d;
+ r2 = SQR(r_ij);
+
+ if ( sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0)
+ {
+ C12 = twbp->p_bo1 * POW( r_ij / twbp->r_s, twbp->p_bo2 );
+ BO_s = (1.0 + control->bo_cut) * EXP( C12 );
+ }
+ else BO_s = C12 = 0.0;
+
+ if ( sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0)
+ {
+ C34 = twbp->p_bo3 * POW( r_ij / twbp->r_p, twbp->p_bo4 );
+ BO_pi = EXP( C34 );
+ }
+ else BO_pi = C34 = 0.0;
+
+ if ( sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0)
+ {
+ C56 = twbp->p_bo5 * POW( r_ij / twbp->r_pp, twbp->p_bo6 );
+ BO_pi2 = EXP( C56 );
+ }
+ else BO_pi2 = C56 = 0.0;
+
+ /* Initially BO values are the uncorrected ones, page 1 */
+ BO = BO_s + BO_pi + BO_pi2;
+
+ if ( BO >= control->bo_cut )
+ {
+ ++bond_top[i];
+ ++bond_top[j];
+ }
+ }
+ }
+ }
+ }
+
+ *Htop += system->N;
+ *Htop *= SAFE_ZONE;
+ for ( i = 0; i < system->N; ++i )
+ {
+ hb_top[i] = MAX( hb_top[i] * SAFE_HBONDS, MIN_HBONDS );
+ *num_3body += SQR(bond_top[i]);
+ bond_top[i] = MAX( bond_top[i] * 2, MIN_BONDS );
}
- }
-
- *Htop += system->N;
- *Htop *= SAFE_ZONE;
- for( i = 0; i < system->N; ++i ) {
- hb_top[i] = MAX( hb_top[i] * SAFE_HBONDS, MIN_HBONDS );
- *num_3body += SQR(bond_top[i]);
- bond_top[i] = MAX( bond_top[i] * 2, MIN_BONDS );
- }
- *num_3body *= SAFE_ZONE;
+ *num_3body *= SAFE_ZONE;
}
-void Compute_Forces( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list** lists, output_controls *out_control )
+void Compute_Forces( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list** lists, output_controls *out_control )
{
- real t_start, t_elapsed;
-
- t_start = Get_Time( );
- if( !control->tabulate )
- Init_Forces( system, control, data, workspace, lists, out_control );
- else Init_Forces_Tab( system, control, data, workspace, lists, out_control );
- t_elapsed = Get_Timing_Info( t_start );
- data->timing.init_forces += t_elapsed;
+ real t_start, t_elapsed;
+
+ t_start = Get_Time( );
+ if ( !control->tabulate )
+ Init_Forces( system, control, data, workspace, lists, out_control );
+ else Init_Forces_Tab( system, control, data, workspace, lists, out_control );
+ t_elapsed = Get_Timing_Info( t_start );
+ data->timing.init_forces += t_elapsed;
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "init_forces - ");
+ fprintf( stderr, "init_forces - ");
#endif
- t_start = Get_Time( );
- Compute_Bonded_Forces( system, control, data, workspace, lists, out_control );
- t_elapsed = Get_Timing_Info( t_start );
- data->timing.bonded += t_elapsed;
-#if defined(DEBUG_FOCUS)
- fprintf( stderr, "bonded_forces - ");
+ t_start = Get_Time( );
+ Compute_Bonded_Forces( system, control, data, workspace, lists, out_control );
+ t_elapsed = Get_Timing_Info( t_start );
+ data->timing.bonded += t_elapsed;
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "bonded_forces - ");
#endif
- t_start = Get_Time( );
- Compute_NonBonded_Forces( system, control, data, workspace,
- lists, out_control );
- t_elapsed = Get_Timing_Info( t_start );
- data->timing.nonb += t_elapsed;
+ t_start = Get_Time( );
+ Compute_NonBonded_Forces( system, control, data, workspace,
+ lists, out_control );
+ t_elapsed = Get_Timing_Info( t_start );
+ data->timing.nonb += t_elapsed;
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "nonbondeds - ");
+ fprintf( stderr, "nonbondeds - ");
#endif
- Compute_Total_Force( system, control, data, workspace, lists );
- //Print_Total_Force( system, control, data, workspace, lists, out_control );
+ Compute_Total_Force( system, control, data, workspace, lists );
+ //Print_Total_Force( system, control, data, workspace, lists, out_control );
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "totalforces - ");
- //Print_Total_Force( system, control, data, workspace, lists, out_control );
+ fprintf( stderr, "totalforces - ");
+ //Print_Total_Force( system, control, data, workspace, lists, out_control );
#endif
#ifdef TEST_FORCES
- Print_Total_Force( system, control, data, workspace, lists, out_control );
- Compare_Total_Forces( system, control, data, workspace, lists, out_control );
+ Print_Total_Force( system, control, data, workspace, lists, out_control );
+ Compare_Total_Forces( system, control, data, workspace, lists, out_control );
#endif
-#if defined(DEBUG_FOCUS)
- fprintf( stderr, "forces - ");
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "forces - ");
#endif
}
diff --git a/puremd_rc_1003/sPuReMD/forces.h b/puremd_rc_1003/sPuReMD/forces.h
index b34dac5f4ff65818815ad700265b7500a1ab2fae..c57aa1596a85674f47737183b63b57c6a0bd46a9 100644
--- a/puremd_rc_1003/sPuReMD/forces.h
+++ b/puremd_rc_1003/sPuReMD/forces.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -26,9 +26,9 @@
void Init_Bonded_Force_Functions( control_params* );
-void Compute_Forces( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+void Compute_Forces( reax_system*, control_params*, simulation_data*,
+ static_storage*, list**, output_controls* );
-void Estimate_Storage_Sizes( reax_system*, control_params*, list**,
- int*, int*, int*, int* );
+void Estimate_Storage_Sizes( reax_system*, control_params*, list**,
+ int*, int*, int*, int* );
#endif
diff --git a/puremd_rc_1003/sPuReMD/four_body_interactions.c b/puremd_rc_1003/sPuReMD/four_body_interactions.c
index 09a0c6c00743fb6c2616951139b79215d4d3187a..1fc7e99c5e0b7d3738ac04cd23bccbbfba397b52 100644
--- a/puremd_rc_1003/sPuReMD/four_body_interactions.c
+++ b/puremd_rc_1003/sPuReMD/four_body_interactions.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -30,635 +30,645 @@
#define MIN_SINE 1e-10
real Calculate_Omega( rvec dvec_ij, real r_ij, rvec dvec_jk, real r_jk,
- rvec dvec_kl, real r_kl, rvec dvec_li, real r_li,
- three_body_interaction_data *p_ijk,
- three_body_interaction_data *p_jkl,
- rvec dcos_omega_di, rvec dcos_omega_dj,
- rvec dcos_omega_dk, rvec dcos_omega_dl,
- output_controls *out_control )
+ rvec dvec_kl, real r_kl, rvec dvec_li, real r_li,
+ three_body_interaction_data *p_ijk,
+ three_body_interaction_data *p_jkl,
+ rvec dcos_omega_di, rvec dcos_omega_dj,
+ rvec dcos_omega_dk, rvec dcos_omega_dl,
+ output_controls *out_control )
{
- real unnorm_cos_omega, unnorm_sin_omega, omega;
- real sin_ijk, cos_ijk, sin_jkl, cos_jkl;
- real htra, htrb, htrc, hthd, hthe, hnra, hnrc, hnhd, hnhe;
- real arg, poem, tel;
- rvec cross_jk_kl;
-
- sin_ijk = SIN( p_ijk->theta );
- cos_ijk = COS( p_ijk->theta );
- sin_jkl = SIN( p_jkl->theta );
- cos_jkl = COS( p_jkl->theta );
-
- /* omega */
- unnorm_cos_omega = -rvec_Dot( dvec_ij,dvec_jk )*rvec_Dot( dvec_jk,dvec_kl ) +
- SQR( r_jk ) * rvec_Dot( dvec_ij,dvec_kl );
- rvec_Cross( cross_jk_kl, dvec_jk, dvec_kl );
- unnorm_sin_omega = -r_jk * rvec_Dot( dvec_ij, cross_jk_kl );
- omega = atan2( unnorm_sin_omega, unnorm_cos_omega );
-
- /* derivatives */
- /* coef for adjusments to cos_theta's */
- /* rla = r_ij, rlb = r_jk, rlc = r_kl, r4 = r_li;
- coshd = cos_ijk, coshe = cos_jkl;
- sinhd = sin_ijk, sinhe = sin_jkl; */
- htra = r_ij + cos_ijk * ( r_kl * cos_jkl - r_jk );
- htrb = r_jk - r_ij * cos_ijk - r_kl * cos_jkl;
- htrc = r_kl + cos_jkl * ( r_ij * cos_ijk - r_jk );
- hthd = r_ij * sin_ijk * ( r_jk - r_kl * cos_jkl );
- hthe = r_kl * sin_jkl * ( r_jk - r_ij * cos_ijk );
- hnra = r_kl * sin_ijk * sin_jkl;
- hnrc = r_ij * sin_ijk * sin_jkl;
- hnhd = r_ij * r_kl * cos_ijk * sin_jkl;
- hnhe = r_ij * r_kl * sin_ijk * cos_jkl;
-
-
- poem = 2.0 * r_ij * r_kl * sin_ijk * sin_jkl;
- if( poem < 1e-20 ) poem = 1e-20;
-
- tel = (SQR(r_ij) + SQR(r_jk) + SQR(r_kl) - SQR(r_li)) -
- 2.0 * ( r_ij * r_jk * cos_ijk - r_ij * r_kl * cos_ijk * cos_jkl +
- r_jk * r_kl * cos_jkl );
-
- arg = tel / poem;
- if( arg > 1.0 ) arg = 1.0;
- if( arg < -1.0 ) arg = -1.0;
-
-
- /*fprintf( out_control->etor,
- "%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e\n",
- htra, htrb, htrc, hthd, hthe, hnra, hnrc, hnhd, hnhe );
- fprintf( out_control->etor, "%23.15e%23.15e%23.15e\n",
- dvec_ij[0]/r_ij, dvec_ij[1]/r_ij, dvec_ij[2]/r_ij );
- fprintf( out_control->etor, "%23.15e%23.15e%23.15e\n",
- -dvec_jk[0]/r_jk, -dvec_jk[1]/r_jk, -dvec_jk[2]/r_jk );
- fprintf( out_control->etor, "%23.15e%23.15e%23.15e\n",
- -dvec_kl[0]/r_kl, -dvec_kl[1]/r_kl, -dvec_kl[2]/r_kl );
- fprintf( out_control->etor, "%23.15e%23.15e%23.15e%23.15e\n",
- r_li, dvec_li[0], dvec_li[1], dvec_li[2] );
- fprintf( out_control->etor, "%23.15e%23.15e%23.15e%23.15e\n",
- r_ij, r_jk, r_kl, r_li );
- fprintf( out_control->etor, "%23.15e%23.15e%23.15e%23.15e\n",
- cos_ijk, cos_jkl, sin_ijk, sin_jkl );
- fprintf( out_control->etor, "%23.15e%23.15e%23.15e\n",
- poem, tel, arg );*/
- /* fprintf( out_control->etor, "%23.15e%23.15e%23.15e\n",
- -p_ijk->dcos_dk[0]/sin_ijk,
- -p_ijk->dcos_dk[1]/sin_ijk,
- -p_ijk->dcos_dk[2]/sin_ijk );
- fprintf( out_control->etor, "%23.15e%23.15e%23.15e\n",
- -p_jkl->dcos_dk[0]/sin_jkl,
- -p_jkl->dcos_dk[1]/sin_jkl,
- -p_jkl->dcos_dk[2]/sin_jkl );*/
-
- if( sin_ijk >= 0 && sin_ijk <= MIN_SINE ) sin_ijk = MIN_SINE;
- else if( sin_ijk <= 0 && sin_ijk >= -MIN_SINE ) sin_ijk = -MIN_SINE;
- if( sin_jkl >= 0 && sin_jkl <= MIN_SINE ) sin_jkl = MIN_SINE;
- else if( sin_jkl <= 0 && sin_jkl >= -MIN_SINE ) sin_jkl = -MIN_SINE;
-
- // dcos_omega_di
- rvec_ScaledSum( dcos_omega_di, (htra-arg*hnra)/r_ij, dvec_ij, -1., dvec_li );
- rvec_ScaledAdd( dcos_omega_di,-(hthd - arg*hnhd)/sin_ijk, p_ijk->dcos_dk );
- rvec_Scale( dcos_omega_di, 2.0 / poem, dcos_omega_di );
-
- // dcos_omega_dj
- rvec_ScaledSum( dcos_omega_dj,-(htra-arg*hnra)/r_ij, dvec_ij,
- -htrb / r_jk, dvec_jk );
- rvec_ScaledAdd( dcos_omega_dj,-(hthd-arg*hnhd) / sin_ijk, p_ijk->dcos_dj );
- rvec_ScaledAdd( dcos_omega_dj,-(hthe-arg*hnhe) / sin_jkl, p_jkl->dcos_di );
- rvec_Scale( dcos_omega_dj, 2.0 / poem, dcos_omega_dj );
-
- // dcos_omega_dk
- rvec_ScaledSum( dcos_omega_dk,-(htrc-arg*hnrc) / r_kl, dvec_kl,
- htrb / r_jk, dvec_jk );
- rvec_ScaledAdd( dcos_omega_dk,-(hthd-arg*hnhd) / sin_ijk, p_ijk->dcos_di );
- rvec_ScaledAdd( dcos_omega_dk,-(hthe-arg*hnhe) / sin_jkl, p_jkl->dcos_dj );
- rvec_Scale( dcos_omega_dk, 2.0 / poem, dcos_omega_dk );
-
- // dcos_omega_dl
- rvec_ScaledSum( dcos_omega_dl, (htrc-arg*hnrc) / r_kl, dvec_kl, 1., dvec_li );
- rvec_ScaledAdd( dcos_omega_dl,-(hthe-arg*hnhe) / sin_jkl, p_jkl->dcos_dk );
- rvec_Scale( dcos_omega_dl, 2.0 / poem, dcos_omega_dl );
-
- return omega;
- //return arg;
+ real unnorm_cos_omega, unnorm_sin_omega, omega;
+ real sin_ijk, cos_ijk, sin_jkl, cos_jkl;
+ real htra, htrb, htrc, hthd, hthe, hnra, hnrc, hnhd, hnhe;
+ real arg, poem, tel;
+ rvec cross_jk_kl;
+
+ sin_ijk = SIN( p_ijk->theta );
+ cos_ijk = COS( p_ijk->theta );
+ sin_jkl = SIN( p_jkl->theta );
+ cos_jkl = COS( p_jkl->theta );
+
+ /* omega */
+ unnorm_cos_omega = -rvec_Dot( dvec_ij, dvec_jk ) * rvec_Dot( dvec_jk, dvec_kl ) +
+ SQR( r_jk ) * rvec_Dot( dvec_ij, dvec_kl );
+ rvec_Cross( cross_jk_kl, dvec_jk, dvec_kl );
+ unnorm_sin_omega = -r_jk * rvec_Dot( dvec_ij, cross_jk_kl );
+ omega = atan2( unnorm_sin_omega, unnorm_cos_omega );
+
+ /* derivatives */
+ /* coef for adjusments to cos_theta's */
+ /* rla = r_ij, rlb = r_jk, rlc = r_kl, r4 = r_li;
+ coshd = cos_ijk, coshe = cos_jkl;
+ sinhd = sin_ijk, sinhe = sin_jkl; */
+ htra = r_ij + cos_ijk * ( r_kl * cos_jkl - r_jk );
+ htrb = r_jk - r_ij * cos_ijk - r_kl * cos_jkl;
+ htrc = r_kl + cos_jkl * ( r_ij * cos_ijk - r_jk );
+ hthd = r_ij * sin_ijk * ( r_jk - r_kl * cos_jkl );
+ hthe = r_kl * sin_jkl * ( r_jk - r_ij * cos_ijk );
+ hnra = r_kl * sin_ijk * sin_jkl;
+ hnrc = r_ij * sin_ijk * sin_jkl;
+ hnhd = r_ij * r_kl * cos_ijk * sin_jkl;
+ hnhe = r_ij * r_kl * sin_ijk * cos_jkl;
+
+
+ poem = 2.0 * r_ij * r_kl * sin_ijk * sin_jkl;
+ if ( poem < 1e-20 ) poem = 1e-20;
+
+ tel = (SQR(r_ij) + SQR(r_jk) + SQR(r_kl) - SQR(r_li)) -
+ 2.0 * ( r_ij * r_jk * cos_ijk - r_ij * r_kl * cos_ijk * cos_jkl +
+ r_jk * r_kl * cos_jkl );
+
+ arg = tel / poem;
+ if ( arg > 1.0 ) arg = 1.0;
+ if ( arg < -1.0 ) arg = -1.0;
+
+
+ /*fprintf( out_control->etor,
+ "%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e\n",
+ htra, htrb, htrc, hthd, hthe, hnra, hnrc, hnhd, hnhe );
+ fprintf( out_control->etor, "%23.15e%23.15e%23.15e\n",
+ dvec_ij[0]/r_ij, dvec_ij[1]/r_ij, dvec_ij[2]/r_ij );
+ fprintf( out_control->etor, "%23.15e%23.15e%23.15e\n",
+ -dvec_jk[0]/r_jk, -dvec_jk[1]/r_jk, -dvec_jk[2]/r_jk );
+ fprintf( out_control->etor, "%23.15e%23.15e%23.15e\n",
+ -dvec_kl[0]/r_kl, -dvec_kl[1]/r_kl, -dvec_kl[2]/r_kl );
+ fprintf( out_control->etor, "%23.15e%23.15e%23.15e%23.15e\n",
+ r_li, dvec_li[0], dvec_li[1], dvec_li[2] );
+ fprintf( out_control->etor, "%23.15e%23.15e%23.15e%23.15e\n",
+ r_ij, r_jk, r_kl, r_li );
+ fprintf( out_control->etor, "%23.15e%23.15e%23.15e%23.15e\n",
+ cos_ijk, cos_jkl, sin_ijk, sin_jkl );
+ fprintf( out_control->etor, "%23.15e%23.15e%23.15e\n",
+ poem, tel, arg );*/
+ /* fprintf( out_control->etor, "%23.15e%23.15e%23.15e\n",
+ -p_ijk->dcos_dk[0]/sin_ijk,
+ -p_ijk->dcos_dk[1]/sin_ijk,
+ -p_ijk->dcos_dk[2]/sin_ijk );
+ fprintf( out_control->etor, "%23.15e%23.15e%23.15e\n",
+ -p_jkl->dcos_dk[0]/sin_jkl,
+ -p_jkl->dcos_dk[1]/sin_jkl,
+ -p_jkl->dcos_dk[2]/sin_jkl );*/
+
+ if ( sin_ijk >= 0 && sin_ijk <= MIN_SINE ) sin_ijk = MIN_SINE;
+ else if ( sin_ijk <= 0 && sin_ijk >= -MIN_SINE ) sin_ijk = -MIN_SINE;
+ if ( sin_jkl >= 0 && sin_jkl <= MIN_SINE ) sin_jkl = MIN_SINE;
+ else if ( sin_jkl <= 0 && sin_jkl >= -MIN_SINE ) sin_jkl = -MIN_SINE;
+
+ // dcos_omega_di
+ rvec_ScaledSum( dcos_omega_di, (htra - arg * hnra) / r_ij, dvec_ij, -1., dvec_li );
+ rvec_ScaledAdd( dcos_omega_di, -(hthd - arg * hnhd) / sin_ijk, p_ijk->dcos_dk );
+ rvec_Scale( dcos_omega_di, 2.0 / poem, dcos_omega_di );
+
+ // dcos_omega_dj
+ rvec_ScaledSum( dcos_omega_dj, -(htra - arg * hnra) / r_ij, dvec_ij,
+ -htrb / r_jk, dvec_jk );
+ rvec_ScaledAdd( dcos_omega_dj, -(hthd - arg * hnhd) / sin_ijk, p_ijk->dcos_dj );
+ rvec_ScaledAdd( dcos_omega_dj, -(hthe - arg * hnhe) / sin_jkl, p_jkl->dcos_di );
+ rvec_Scale( dcos_omega_dj, 2.0 / poem, dcos_omega_dj );
+
+ // dcos_omega_dk
+ rvec_ScaledSum( dcos_omega_dk, -(htrc - arg * hnrc) / r_kl, dvec_kl,
+ htrb / r_jk, dvec_jk );
+ rvec_ScaledAdd( dcos_omega_dk, -(hthd - arg * hnhd) / sin_ijk, p_ijk->dcos_di );
+ rvec_ScaledAdd( dcos_omega_dk, -(hthe - arg * hnhe) / sin_jkl, p_jkl->dcos_dj );
+ rvec_Scale( dcos_omega_dk, 2.0 / poem, dcos_omega_dk );
+
+ // dcos_omega_dl
+ rvec_ScaledSum( dcos_omega_dl, (htrc - arg * hnrc) / r_kl, dvec_kl, 1., dvec_li );
+ rvec_ScaledAdd( dcos_omega_dl, -(hthe - arg * hnhe) / sin_jkl, p_jkl->dcos_dk );
+ rvec_Scale( dcos_omega_dl, 2.0 / poem, dcos_omega_dl );
+
+ return omega;
+ //return arg;
}
-void Four_Body_Interactions( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+void Four_Body_Interactions( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int i, j, k, l, pi, pj, pk, pl, pij, plk;
- int type_i, type_j, type_k, type_l;
- int start_j, end_j, start_k, end_k;
- int start_pj, end_pj, start_pk, end_pk;
- int num_frb_intrs = 0;
-
- real Delta_j, Delta_k;
- real r_ij, r_jk, r_kl, r_li;
- real BOA_ij, BOA_jk, BOA_kl;
-
- real exp_tor2_ij, exp_tor2_jk, exp_tor2_kl;
- real exp_tor1, exp_tor3_DjDk, exp_tor4_DjDk, exp_tor34_inv;
- real exp_cot2_jk, exp_cot2_ij, exp_cot2_kl;
- real fn10, f11_DjDk, dfn11, fn12;
-
- real theta_ijk, theta_jkl;
- real sin_ijk, sin_jkl;
- real cos_ijk, cos_jkl;
- real tan_ijk_i, tan_jkl_i;
-
- real omega, cos_omega, cos2omega, cos3omega;
- rvec dcos_omega_di, dcos_omega_dj, dcos_omega_dk, dcos_omega_dl;
-
- real CV, cmn, CEtors1, CEtors2, CEtors3, CEtors4;
- real CEtors5, CEtors6, CEtors7, CEtors8, CEtors9;
- real Cconj, CEconj1, CEconj2, CEconj3;
- real CEconj4, CEconj5, CEconj6;
-
- real e_tor, e_con;
- rvec dvec_li;
- rvec force, ext_press;
- ivec rel_box_jl;
- // rtensor total_rtensor, temp_rtensor;
-
- four_body_header *fbh;
- four_body_parameters *fbp;
- bond_data *pbond_ij, *pbond_jk, *pbond_kl;
- bond_order_data *bo_ij, *bo_jk, *bo_kl;
- three_body_interaction_data *p_ijk, *p_jkl;
-
- real p_tor2 = system->reaxprm.gp.l[23];
- real p_tor3 = system->reaxprm.gp.l[24];
- real p_tor4 = system->reaxprm.gp.l[25];
- real p_cot2 = system->reaxprm.gp.l[27];
-
- list *bonds = (*lists) + BONDS;
- list *thb_intrs = (*lists) + THREE_BODIES;
-
-
- for( j = 0; j < system->N; ++j ) {
- type_j = system->atoms[j].type;
- Delta_j = workspace->Delta_boc[j];
- start_j = Start_Index(j, bonds);
- end_j = End_Index(j, bonds);
-
-
- for( pk = start_j; pk < end_j; ++pk ) {
- pbond_jk = &( bonds->select.bond_list[pk] );
- k = pbond_jk->nbr;
- bo_jk = &( pbond_jk->bo_data );
- BOA_jk = bo_jk->BO - control->thb_cut;
-
- /* see if there are any 3-body interactions involving j&k
- where j is the central atom. Otherwise there is no point in
- trying to form a 4-body interaction out of this neighborhood */
- if( j < k && bo_jk->BO > control->thb_cut/*0*/ &&
- Num_Entries(pk, thb_intrs) ) {
- start_k = Start_Index(k, bonds);
- end_k = End_Index(k, bonds);
- pj = pbond_jk->sym_index; // pj points to j on k's list
-
- /* do the same check as above: are there any 3-body interactions
- involving k&j where k is the central atom */
- if( Num_Entries(pj, thb_intrs) ) {
- type_k = system->atoms[k].type;
- Delta_k = workspace->Delta_boc[k];
- r_jk = pbond_jk->d;
-
- start_pk = Start_Index(pk, thb_intrs );
- end_pk = End_Index(pk, thb_intrs );
- start_pj = Start_Index(pj, thb_intrs );
- end_pj = End_Index(pj, thb_intrs );
-
- exp_tor2_jk = EXP( -p_tor2 * BOA_jk );
- exp_cot2_jk = EXP( -p_cot2 * SQR(BOA_jk - 1.5) );
- exp_tor3_DjDk = EXP( -p_tor3 * (Delta_j + Delta_k) );
- exp_tor4_DjDk = EXP( p_tor4 * (Delta_j + Delta_k) );
- exp_tor34_inv = 1.0 / (1.0 + exp_tor3_DjDk + exp_tor4_DjDk);
- f11_DjDk = (2.0 + exp_tor3_DjDk) * exp_tor34_inv;
-
-
- /* pick i up from j-k interaction where j is the centre atom */
- for( pi = start_pk; pi < end_pk; ++pi ) {
- p_ijk = &( thb_intrs->select.three_body_list[pi] );
- pij = p_ijk->pthb; // pij is pointer to i on j's bond_list
- pbond_ij = &( bonds->select.bond_list[pij] );
- bo_ij = &( pbond_ij->bo_data );
-
-
- if( bo_ij->BO > control->thb_cut/*0*/ ) {
- i = p_ijk->thb;
- type_i = system->atoms[i].type;
- r_ij = pbond_ij->d;
- BOA_ij = bo_ij->BO - control->thb_cut;
-
- theta_ijk = p_ijk->theta;
- sin_ijk = SIN( theta_ijk );
- cos_ijk = COS( theta_ijk );
- //tan_ijk_i = 1. / TAN( theta_ijk );
- if( sin_ijk >= 0 && sin_ijk <= MIN_SINE )
- tan_ijk_i = cos_ijk / MIN_SINE;
- else if( sin_ijk <= 0 && sin_ijk >= -MIN_SINE )
- tan_ijk_i = cos_ijk / -MIN_SINE;
- else tan_ijk_i = cos_ijk / sin_ijk;
-
- exp_tor2_ij = EXP( -p_tor2 * BOA_ij );
- exp_cot2_ij = EXP( -p_cot2 * SQR(BOA_ij -1.5) );
-
- /* pick l up from j-k intr. where k is the centre */
- for( pl = start_pj; pl < end_pj; ++pl ) {
- p_jkl = &( thb_intrs->select.three_body_list[pl] );
- l = p_jkl->thb;
- plk = p_jkl->pthb; //pointer to l on k's bond_list!
- pbond_kl = &( bonds->select.bond_list[plk] );
- bo_kl = &( pbond_kl->bo_data );
- type_l = system->atoms[l].type;
- fbh = &(system->reaxprm.fbp[type_i][type_j][type_k][type_l]);
- fbp = &(system->reaxprm.fbp[type_i][type_j]
- [type_k][type_l].prm[0]);
-
- if( i != l && fbh->cnt && bo_kl->BO > control->thb_cut/*0*/ &&
- bo_ij->BO * bo_jk->BO * bo_kl->BO > control->thb_cut/*0*/ ){
- ++num_frb_intrs;
- r_kl = pbond_kl->d;
- BOA_kl = bo_kl->BO - control->thb_cut;
-
- theta_jkl = p_jkl->theta;
- sin_jkl = SIN( theta_jkl );
- cos_jkl = COS( theta_jkl );
- //tan_jkl_i = 1. / TAN( theta_jkl );
- if( sin_jkl >= 0 && sin_jkl <= MIN_SINE )
- tan_jkl_i = cos_jkl / MIN_SINE;
- else if( sin_jkl <= 0 && sin_jkl >= -MIN_SINE )
- tan_jkl_i = cos_jkl / -MIN_SINE;
- else tan_jkl_i = cos_jkl /sin_jkl;
-
- Sq_Distance_on_T3( system->atoms[l].x, system->atoms[i].x,
- &(system->box), dvec_li );
- r_li = rvec_Norm( dvec_li );
-
-
- /* omega and its derivative */
- //cos_omega=Calculate_Omega(pbond_ij->dvec,r_ij,pbond_jk->dvec,
- omega = Calculate_Omega(pbond_ij->dvec, r_ij, pbond_jk->dvec,
- r_jk, pbond_kl->dvec, r_kl,
- dvec_li, r_li, p_ijk, p_jkl,
- dcos_omega_di, dcos_omega_dj,
- dcos_omega_dk, dcos_omega_dl,
- out_control);
- cos_omega = COS( omega );
- cos2omega = COS( 2. * omega );
- cos3omega = COS( 3. * omega );
- /* end omega calculations */
-
- /* torsion energy */
- exp_tor1 = EXP(fbp->p_tor1 * SQR(2.-bo_jk->BO_pi-f11_DjDk));
- exp_tor2_kl = EXP( -p_tor2 * BOA_kl );
- exp_cot2_kl = EXP( -p_cot2 * SQR(BOA_kl-1.5) );
- fn10 = (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jk) *
- (1.0 - exp_tor2_kl);
-
- CV = 0.5 * ( fbp->V1 * (1.0 + cos_omega) +
- fbp->V2 * exp_tor1 * (1.0 - cos2omega) +
- fbp->V3 * (1.0 + cos3omega) );
- //CV = 0.5 * fbp->V1 * (1.0 + cos_omega) +
- // fbp->V2 * exp_tor1 * (1.0 - SQR(cos_omega)) +
- // fbp->V3 * (0.5 + 2.0*CUBE(cos_omega) - 1.5 * cos_omega);
-
- data->E_Tor += e_tor = fn10 * sin_ijk * sin_jkl * CV;
-
- dfn11 = (-p_tor3 * exp_tor3_DjDk +
- (p_tor3 * exp_tor3_DjDk - p_tor4 * exp_tor4_DjDk) *
- (2.+exp_tor3_DjDk) * exp_tor34_inv) * exp_tor34_inv;
-
- CEtors1 = sin_ijk * sin_jkl * CV;
-
- CEtors2 = -fn10 * 2.0 * fbp->p_tor1 * fbp->V2 * exp_tor1 *
- (2.0 - bo_jk->BO_pi - f11_DjDk) * (1.0 - SQR(cos_omega)) *
- sin_ijk * sin_jkl;
-
- CEtors3 = CEtors2 * dfn11;
-
- CEtors4 = CEtors1 * p_tor2 * exp_tor2_ij *
- (1.0 - exp_tor2_jk) * (1.0 - exp_tor2_kl);
-
- CEtors5 = CEtors1 * p_tor2 * exp_tor2_jk *
- (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_kl);
-
- CEtors6 = CEtors1 * p_tor2 * exp_tor2_kl *
- (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jk);
-
- cmn = -fn10 * CV;
- CEtors7 = cmn * sin_jkl * tan_ijk_i;
- CEtors8 = cmn * sin_ijk * tan_jkl_i;
- CEtors9 = fn10 * sin_ijk * sin_jkl *
- (0.5 * fbp->V1 - 2.0 * fbp->V2 * exp_tor1 * cos_omega +
- 1.5 * fbp->V3 * (cos2omega + 2. * SQR(cos_omega)));
- //cmn = -fn10 * CV;
- //CEtors7 = cmn * sin_jkl * cos_ijk;
- //CEtors8 = cmn * sin_ijk * cos_jkl;
- //CEtors9 = fn10 * sin_ijk * sin_jkl *
- // (0.5 * fbp->V1 - 2.0 * fbp->V2 * exp_tor1 * cos_omega +
- // fbp->V3 * (6*SQR(cos_omega) - 1.50));
- /* end of torsion energy */
-
-
- /* 4-body conjugation energy */
- fn12 = exp_cot2_ij * exp_cot2_jk * exp_cot2_kl;
- data->E_Con += e_con = fbp->p_cot1 * fn12 *
- (1. + (SQR(cos_omega)-1.) * sin_ijk*sin_jkl);
-
- Cconj = -2.0 * fn12 * fbp->p_cot1 * p_cot2 *
- (1. + (SQR(cos_omega)-1.) * sin_ijk*sin_jkl);
-
- CEconj1 = Cconj * (BOA_ij - 1.5e0);
- CEconj2 = Cconj * (BOA_jk - 1.5e0);
- CEconj3 = Cconj * (BOA_kl - 1.5e0);
-
- CEconj4 = -fbp->p_cot1 * fn12 *
- (SQR(cos_omega) - 1.0) * sin_jkl * tan_ijk_i;
- CEconj5 = -fbp->p_cot1 * fn12 *
- (SQR(cos_omega) - 1.0) * sin_ijk * tan_jkl_i;
- //CEconj4 = -fbp->p_cot1 * fn12 *
- // (SQR(cos_omega) - 1.0) * sin_jkl * cos_ijk;
- //CEconj5 = -fbp->p_cot1 * fn12 *
- // (SQR(cos_omega) - 1.0) * sin_ijk * cos_jkl;
- CEconj6 = 2.0 * fbp->p_cot1 * fn12 *
- cos_omega * sin_ijk * sin_jkl;
- /* end 4-body conjugation energy */
-
- //fprintf(stdout, "%6d %6d %6d %6d %7.3f %7.3f %7.3f %7.3f ",
- // workspace->orig_id[i], workspace->orig_id[j],
- // workspace->orig_id[k], workspace->orig_id[l],
- // omega, cos_omega, cos2omega, cos3omega );
- //fprintf(stdout,
- // "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
- // CEtors2, CEtors3, CEtors4, CEtors5,
- // CEtors6, CEtors7, CEtors8, CEtors9 );
- //fprintf(stdout, "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
- // theta_ijk, theta_jkl, sin_ijk,
- // sin_jkl, cos_jkl, tan_jkl_i );
-
- /* forces */
- bo_jk->Cdbopi += CEtors2;
- workspace->CdDelta[j] += CEtors3;
- workspace->CdDelta[k] += CEtors3;
- bo_ij->Cdbo += (CEtors4 + CEconj1);
- bo_jk->Cdbo += (CEtors5 + CEconj2);
- bo_kl->Cdbo += (CEtors6 + CEconj3);
-
- if( control->ensemble == NVE || control->ensemble == NVT || control->ensemble == bNVT ) {
- /* dcos_theta_ijk */
- rvec_ScaledAdd( system->atoms[i].f,
- CEtors7 + CEconj4, p_ijk->dcos_dk );
- rvec_ScaledAdd( system->atoms[j].f,
- CEtors7 + CEconj4, p_ijk->dcos_dj );
- rvec_ScaledAdd( system->atoms[k].f,
- CEtors7 + CEconj4, p_ijk->dcos_di );
-
- /* dcos_theta_jkl */
- rvec_ScaledAdd( system->atoms[j].f,
- CEtors8 + CEconj5, p_jkl->dcos_di );
- rvec_ScaledAdd( system->atoms[k].f,
- CEtors8 + CEconj5, p_jkl->dcos_dj );
- rvec_ScaledAdd( system->atoms[l].f,
- CEtors8 + CEconj5, p_jkl->dcos_dk );
-
- /* dcos_omega */
- rvec_ScaledAdd( system->atoms[i].f,
- CEtors9 + CEconj6, dcos_omega_di );
- rvec_ScaledAdd( system->atoms[j].f,
- CEtors9 + CEconj6, dcos_omega_dj );
- rvec_ScaledAdd( system->atoms[k].f,
- CEtors9 + CEconj6, dcos_omega_dk );
- rvec_ScaledAdd( system->atoms[l].f,
- CEtors9 + CEconj6, dcos_omega_dl );
- }
- else {
- ivec_Sum(rel_box_jl, pbond_jk->rel_box, pbond_kl->rel_box);
-
- /* dcos_theta_ijk */
- rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_dk );
- rvec_Add( system->atoms[i].f, force );
- rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
- rvec_Add( data->ext_press, ext_press );
-
- rvec_ScaledAdd( system->atoms[j].f,
- CEtors7 + CEconj4, p_ijk->dcos_dj );
-
- rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_di );
- rvec_Add( system->atoms[k].f, force );
- rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
- rvec_Add( data->ext_press, ext_press );
-
-
- /* dcos_theta_jkl */
- rvec_ScaledAdd( system->atoms[j].f,
- CEtors8 + CEconj5, p_jkl->dcos_di );
-
- rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dj );
- rvec_Add( system->atoms[k].f, force );
- rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
- rvec_Add( data->ext_press, ext_press );
-
- rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dk );
- rvec_Add( system->atoms[l].f, force );
- rvec_iMultiply( ext_press, rel_box_jl, force );
- rvec_Add( data->ext_press, ext_press );
-
-
- /* dcos_omega */
- rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_di );
- rvec_Add( system->atoms[i].f, force );
- rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
- rvec_Add( data->ext_press, ext_press );
-
- rvec_ScaledAdd( system->atoms[j].f,
- CEtors9 + CEconj6, dcos_omega_dj );
-
- rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dk );
- rvec_Add( system->atoms[k].f, force );
- rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
- rvec_Add( data->ext_press, ext_press );
-
- rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dl );
- rvec_Add( system->atoms[l].f, force );
- rvec_iMultiply( ext_press, rel_box_jl, force );
- rvec_Add( data->ext_press, ext_press );
-
-
- /* This part is intended for a fully-flexible box */
- /* rvec_ScaledSum( temp_rvec,
- CEtors7 + CEconj4, p_ijk->dcos_dk, // i
- CEtors9 + CEconj6, dcos_omega_di );
- rvec_OuterProduct( temp_rtensor,
- temp_rvec, system->atoms[i].x );
- rtensor_Copy( total_rtensor, temp_rtensor );
-
- rvec_ScaledSum( temp_rvec,
- CEtors7 + CEconj4, p_ijk->dcos_dj, // j
- CEtors8 + CEconj5, p_jkl->dcos_di );
- rvec_ScaledAdd( temp_rvec,
- CEtors9 + CEconj6, dcos_omega_dj );
- rvec_OuterProduct( temp_rtensor,
- temp_rvec, system->atoms[j].x );
- rtensor_Add( total_rtensor, temp_rtensor );
-
- rvec_ScaledSum( temp_rvec,
- CEtors7 + CEconj4, p_ijk->dcos_di, // k
- CEtors8 + CEconj5, p_jkl->dcos_dj );
- rvec_ScaledAdd( temp_rvec,
- CEtors9 + CEconj6, dcos_omega_dk );
- rvec_OuterProduct( temp_rtensor,
- temp_rvec, system->atoms[k].x );
- rtensor_Add( total_rtensor, temp_rtensor );
-
- rvec_ScaledSum( temp_rvec,
- CEtors8 + CEconj5, p_jkl->dcos_dk, // l
- CEtors9 + CEconj6, dcos_omega_dl );
- rvec_OuterProduct( temp_rtensor,
- temp_rvec, system->atoms[l].x );
- rtensor_Copy( total_rtensor, temp_rtensor );
-
- if( pbond_ij->imaginary || pbond_jk->imaginary ||
- pbond_kl->imaginary )
- rtensor_ScaledAdd( data->flex_bar.P, -1., total_rtensor );
- else
- rtensor_Add( data->flex_bar.P, total_rtensor ); */
- }
-
+ int i, j, k, l, pi, pj, pk, pl, pij, plk;
+ int type_i, type_j, type_k, type_l;
+ int start_j, end_j, start_k, end_k;
+ int start_pj, end_pj, start_pk, end_pk;
+ int num_frb_intrs = 0;
+
+ real Delta_j, Delta_k;
+ real r_ij, r_jk, r_kl, r_li;
+ real BOA_ij, BOA_jk, BOA_kl;
+
+ real exp_tor2_ij, exp_tor2_jk, exp_tor2_kl;
+ real exp_tor1, exp_tor3_DjDk, exp_tor4_DjDk, exp_tor34_inv;
+ real exp_cot2_jk, exp_cot2_ij, exp_cot2_kl;
+ real fn10, f11_DjDk, dfn11, fn12;
+
+ real theta_ijk, theta_jkl;
+ real sin_ijk, sin_jkl;
+ real cos_ijk, cos_jkl;
+ real tan_ijk_i, tan_jkl_i;
+
+ real omega, cos_omega, cos2omega, cos3omega;
+ rvec dcos_omega_di, dcos_omega_dj, dcos_omega_dk, dcos_omega_dl;
+
+ real CV, cmn, CEtors1, CEtors2, CEtors3, CEtors4;
+ real CEtors5, CEtors6, CEtors7, CEtors8, CEtors9;
+ real Cconj, CEconj1, CEconj2, CEconj3;
+ real CEconj4, CEconj5, CEconj6;
+
+ real e_tor, e_con;
+ rvec dvec_li;
+ rvec force, ext_press;
+ ivec rel_box_jl;
+ // rtensor total_rtensor, temp_rtensor;
+
+ four_body_header *fbh;
+ four_body_parameters *fbp;
+ bond_data *pbond_ij, *pbond_jk, *pbond_kl;
+ bond_order_data *bo_ij, *bo_jk, *bo_kl;
+ three_body_interaction_data *p_ijk, *p_jkl;
+
+ real p_tor2 = system->reaxprm.gp.l[23];
+ real p_tor3 = system->reaxprm.gp.l[24];
+ real p_tor4 = system->reaxprm.gp.l[25];
+ real p_cot2 = system->reaxprm.gp.l[27];
+
+ list *bonds = (*lists) + BONDS;
+ list *thb_intrs = (*lists) + THREE_BODIES;
+
+
+ for ( j = 0; j < system->N; ++j )
+ {
+ type_j = system->atoms[j].type;
+ Delta_j = workspace->Delta_boc[j];
+ start_j = Start_Index(j, bonds);
+ end_j = End_Index(j, bonds);
+
+
+ for ( pk = start_j; pk < end_j; ++pk )
+ {
+ pbond_jk = &( bonds->select.bond_list[pk] );
+ k = pbond_jk->nbr;
+ bo_jk = &( pbond_jk->bo_data );
+ BOA_jk = bo_jk->BO - control->thb_cut;
+
+ /* see if there are any 3-body interactions involving j&k
+ where j is the central atom. Otherwise there is no point in
+ trying to form a 4-body interaction out of this neighborhood */
+ if ( j < k && bo_jk->BO > control->thb_cut/*0*/ &&
+ Num_Entries(pk, thb_intrs) )
+ {
+ start_k = Start_Index(k, bonds);
+ end_k = End_Index(k, bonds);
+ pj = pbond_jk->sym_index; // pj points to j on k's list
+
+ /* do the same check as above: are there any 3-body interactions
+ involving k&j where k is the central atom */
+ if ( Num_Entries(pj, thb_intrs) )
+ {
+ type_k = system->atoms[k].type;
+ Delta_k = workspace->Delta_boc[k];
+ r_jk = pbond_jk->d;
+
+ start_pk = Start_Index(pk, thb_intrs );
+ end_pk = End_Index(pk, thb_intrs );
+ start_pj = Start_Index(pj, thb_intrs );
+ end_pj = End_Index(pj, thb_intrs );
+
+ exp_tor2_jk = EXP( -p_tor2 * BOA_jk );
+ exp_cot2_jk = EXP( -p_cot2 * SQR(BOA_jk - 1.5) );
+ exp_tor3_DjDk = EXP( -p_tor3 * (Delta_j + Delta_k) );
+ exp_tor4_DjDk = EXP( p_tor4 * (Delta_j + Delta_k) );
+ exp_tor34_inv = 1.0 / (1.0 + exp_tor3_DjDk + exp_tor4_DjDk);
+ f11_DjDk = (2.0 + exp_tor3_DjDk) * exp_tor34_inv;
+
+
+ /* pick i up from j-k interaction where j is the centre atom */
+ for ( pi = start_pk; pi < end_pk; ++pi )
+ {
+ p_ijk = &( thb_intrs->select.three_body_list[pi] );
+ pij = p_ijk->pthb; // pij is pointer to i on j's bond_list
+ pbond_ij = &( bonds->select.bond_list[pij] );
+ bo_ij = &( pbond_ij->bo_data );
+
+
+ if ( bo_ij->BO > control->thb_cut/*0*/ )
+ {
+ i = p_ijk->thb;
+ type_i = system->atoms[i].type;
+ r_ij = pbond_ij->d;
+ BOA_ij = bo_ij->BO - control->thb_cut;
+
+ theta_ijk = p_ijk->theta;
+ sin_ijk = SIN( theta_ijk );
+ cos_ijk = COS( theta_ijk );
+ //tan_ijk_i = 1. / TAN( theta_ijk );
+ if ( sin_ijk >= 0 && sin_ijk <= MIN_SINE )
+ tan_ijk_i = cos_ijk / MIN_SINE;
+ else if ( sin_ijk <= 0 && sin_ijk >= -MIN_SINE )
+ tan_ijk_i = cos_ijk / -MIN_SINE;
+ else tan_ijk_i = cos_ijk / sin_ijk;
+
+ exp_tor2_ij = EXP( -p_tor2 * BOA_ij );
+ exp_cot2_ij = EXP( -p_cot2 * SQR(BOA_ij - 1.5) );
+
+ /* pick l up from j-k intr. where k is the centre */
+ for ( pl = start_pj; pl < end_pj; ++pl )
+ {
+ p_jkl = &( thb_intrs->select.three_body_list[pl] );
+ l = p_jkl->thb;
+ plk = p_jkl->pthb; //pointer to l on k's bond_list!
+ pbond_kl = &( bonds->select.bond_list[plk] );
+ bo_kl = &( pbond_kl->bo_data );
+ type_l = system->atoms[l].type;
+ fbh = &(system->reaxprm.fbp[type_i][type_j][type_k][type_l]);
+ fbp = &(system->reaxprm.fbp[type_i][type_j]
+ [type_k][type_l].prm[0]);
+
+ if ( i != l && fbh->cnt && bo_kl->BO > control->thb_cut/*0*/ &&
+ bo_ij->BO * bo_jk->BO * bo_kl->BO > control->thb_cut/*0*/ )
+ {
+ ++num_frb_intrs;
+ r_kl = pbond_kl->d;
+ BOA_kl = bo_kl->BO - control->thb_cut;
+
+ theta_jkl = p_jkl->theta;
+ sin_jkl = SIN( theta_jkl );
+ cos_jkl = COS( theta_jkl );
+ //tan_jkl_i = 1. / TAN( theta_jkl );
+ if ( sin_jkl >= 0 && sin_jkl <= MIN_SINE )
+ tan_jkl_i = cos_jkl / MIN_SINE;
+ else if ( sin_jkl <= 0 && sin_jkl >= -MIN_SINE )
+ tan_jkl_i = cos_jkl / -MIN_SINE;
+ else tan_jkl_i = cos_jkl / sin_jkl;
+
+ Sq_Distance_on_T3( system->atoms[l].x, system->atoms[i].x,
+ &(system->box), dvec_li );
+ r_li = rvec_Norm( dvec_li );
+
+
+ /* omega and its derivative */
+ //cos_omega=Calculate_Omega(pbond_ij->dvec,r_ij,pbond_jk->dvec,
+ omega = Calculate_Omega(pbond_ij->dvec, r_ij, pbond_jk->dvec,
+ r_jk, pbond_kl->dvec, r_kl,
+ dvec_li, r_li, p_ijk, p_jkl,
+ dcos_omega_di, dcos_omega_dj,
+ dcos_omega_dk, dcos_omega_dl,
+ out_control);
+ cos_omega = COS( omega );
+ cos2omega = COS( 2. * omega );
+ cos3omega = COS( 3. * omega );
+ /* end omega calculations */
+
+ /* torsion energy */
+ exp_tor1 = EXP(fbp->p_tor1 * SQR(2. - bo_jk->BO_pi - f11_DjDk));
+ exp_tor2_kl = EXP( -p_tor2 * BOA_kl );
+ exp_cot2_kl = EXP( -p_cot2 * SQR(BOA_kl - 1.5) );
+ fn10 = (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jk) *
+ (1.0 - exp_tor2_kl);
+
+ CV = 0.5 * ( fbp->V1 * (1.0 + cos_omega) +
+ fbp->V2 * exp_tor1 * (1.0 - cos2omega) +
+ fbp->V3 * (1.0 + cos3omega) );
+ //CV = 0.5 * fbp->V1 * (1.0 + cos_omega) +
+ // fbp->V2 * exp_tor1 * (1.0 - SQR(cos_omega)) +
+ // fbp->V3 * (0.5 + 2.0*CUBE(cos_omega) - 1.5 * cos_omega);
+
+ data->E_Tor += e_tor = fn10 * sin_ijk * sin_jkl * CV;
+
+ dfn11 = (-p_tor3 * exp_tor3_DjDk +
+ (p_tor3 * exp_tor3_DjDk - p_tor4 * exp_tor4_DjDk) *
+ (2. + exp_tor3_DjDk) * exp_tor34_inv) * exp_tor34_inv;
+
+ CEtors1 = sin_ijk * sin_jkl * CV;
+
+ CEtors2 = -fn10 * 2.0 * fbp->p_tor1 * fbp->V2 * exp_tor1 *
+ (2.0 - bo_jk->BO_pi - f11_DjDk) * (1.0 - SQR(cos_omega)) *
+ sin_ijk * sin_jkl;
+
+ CEtors3 = CEtors2 * dfn11;
+
+ CEtors4 = CEtors1 * p_tor2 * exp_tor2_ij *
+ (1.0 - exp_tor2_jk) * (1.0 - exp_tor2_kl);
+
+ CEtors5 = CEtors1 * p_tor2 * exp_tor2_jk *
+ (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_kl);
+
+ CEtors6 = CEtors1 * p_tor2 * exp_tor2_kl *
+ (1.0 - exp_tor2_ij) * (1.0 - exp_tor2_jk);
+
+ cmn = -fn10 * CV;
+ CEtors7 = cmn * sin_jkl * tan_ijk_i;
+ CEtors8 = cmn * sin_ijk * tan_jkl_i;
+ CEtors9 = fn10 * sin_ijk * sin_jkl *
+ (0.5 * fbp->V1 - 2.0 * fbp->V2 * exp_tor1 * cos_omega +
+ 1.5 * fbp->V3 * (cos2omega + 2. * SQR(cos_omega)));
+ //cmn = -fn10 * CV;
+ //CEtors7 = cmn * sin_jkl * cos_ijk;
+ //CEtors8 = cmn * sin_ijk * cos_jkl;
+ //CEtors9 = fn10 * sin_ijk * sin_jkl *
+ // (0.5 * fbp->V1 - 2.0 * fbp->V2 * exp_tor1 * cos_omega +
+ // fbp->V3 * (6*SQR(cos_omega) - 1.50));
+ /* end of torsion energy */
+
+
+ /* 4-body conjugation energy */
+ fn12 = exp_cot2_ij * exp_cot2_jk * exp_cot2_kl;
+ data->E_Con += e_con = fbp->p_cot1 * fn12 *
+ (1. + (SQR(cos_omega) - 1.) * sin_ijk * sin_jkl);
+
+ Cconj = -2.0 * fn12 * fbp->p_cot1 * p_cot2 *
+ (1. + (SQR(cos_omega) - 1.) * sin_ijk * sin_jkl);
+
+ CEconj1 = Cconj * (BOA_ij - 1.5e0);
+ CEconj2 = Cconj * (BOA_jk - 1.5e0);
+ CEconj3 = Cconj * (BOA_kl - 1.5e0);
+
+ CEconj4 = -fbp->p_cot1 * fn12 *
+ (SQR(cos_omega) - 1.0) * sin_jkl * tan_ijk_i;
+ CEconj5 = -fbp->p_cot1 * fn12 *
+ (SQR(cos_omega) - 1.0) * sin_ijk * tan_jkl_i;
+ //CEconj4 = -fbp->p_cot1 * fn12 *
+ // (SQR(cos_omega) - 1.0) * sin_jkl * cos_ijk;
+ //CEconj5 = -fbp->p_cot1 * fn12 *
+ // (SQR(cos_omega) - 1.0) * sin_ijk * cos_jkl;
+ CEconj6 = 2.0 * fbp->p_cot1 * fn12 *
+ cos_omega * sin_ijk * sin_jkl;
+ /* end 4-body conjugation energy */
+
+ //fprintf(stdout, "%6d %6d %6d %6d %7.3f %7.3f %7.3f %7.3f ",
+ // workspace->orig_id[i], workspace->orig_id[j],
+ // workspace->orig_id[k], workspace->orig_id[l],
+ // omega, cos_omega, cos2omega, cos3omega );
+ //fprintf(stdout,
+ // "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
+ // CEtors2, CEtors3, CEtors4, CEtors5,
+ // CEtors6, CEtors7, CEtors8, CEtors9 );
+ //fprintf(stdout, "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
+ // theta_ijk, theta_jkl, sin_ijk,
+ // sin_jkl, cos_jkl, tan_jkl_i );
+
+ /* forces */
+ bo_jk->Cdbopi += CEtors2;
+ workspace->CdDelta[j] += CEtors3;
+ workspace->CdDelta[k] += CEtors3;
+ bo_ij->Cdbo += (CEtors4 + CEconj1);
+ bo_jk->Cdbo += (CEtors5 + CEconj2);
+ bo_kl->Cdbo += (CEtors6 + CEconj3);
+
+ if ( control->ensemble == NVE || control->ensemble == NVT || control->ensemble == bNVT )
+ {
+ /* dcos_theta_ijk */
+ rvec_ScaledAdd( system->atoms[i].f,
+ CEtors7 + CEconj4, p_ijk->dcos_dk );
+ rvec_ScaledAdd( system->atoms[j].f,
+ CEtors7 + CEconj4, p_ijk->dcos_dj );
+ rvec_ScaledAdd( system->atoms[k].f,
+ CEtors7 + CEconj4, p_ijk->dcos_di );
+
+ /* dcos_theta_jkl */
+ rvec_ScaledAdd( system->atoms[j].f,
+ CEtors8 + CEconj5, p_jkl->dcos_di );
+ rvec_ScaledAdd( system->atoms[k].f,
+ CEtors8 + CEconj5, p_jkl->dcos_dj );
+ rvec_ScaledAdd( system->atoms[l].f,
+ CEtors8 + CEconj5, p_jkl->dcos_dk );
+
+ /* dcos_omega */
+ rvec_ScaledAdd( system->atoms[i].f,
+ CEtors9 + CEconj6, dcos_omega_di );
+ rvec_ScaledAdd( system->atoms[j].f,
+ CEtors9 + CEconj6, dcos_omega_dj );
+ rvec_ScaledAdd( system->atoms[k].f,
+ CEtors9 + CEconj6, dcos_omega_dk );
+ rvec_ScaledAdd( system->atoms[l].f,
+ CEtors9 + CEconj6, dcos_omega_dl );
+ }
+ else
+ {
+ ivec_Sum(rel_box_jl, pbond_jk->rel_box, pbond_kl->rel_box);
+
+ /* dcos_theta_ijk */
+ rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_dk );
+ rvec_Add( system->atoms[i].f, force );
+ rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
+ rvec_Add( data->ext_press, ext_press );
+
+ rvec_ScaledAdd( system->atoms[j].f,
+ CEtors7 + CEconj4, p_ijk->dcos_dj );
+
+ rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_di );
+ rvec_Add( system->atoms[k].f, force );
+ rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
+ rvec_Add( data->ext_press, ext_press );
+
+
+ /* dcos_theta_jkl */
+ rvec_ScaledAdd( system->atoms[j].f,
+ CEtors8 + CEconj5, p_jkl->dcos_di );
+
+ rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dj );
+ rvec_Add( system->atoms[k].f, force );
+ rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
+ rvec_Add( data->ext_press, ext_press );
+
+ rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dk );
+ rvec_Add( system->atoms[l].f, force );
+ rvec_iMultiply( ext_press, rel_box_jl, force );
+ rvec_Add( data->ext_press, ext_press );
+
+
+ /* dcos_omega */
+ rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_di );
+ rvec_Add( system->atoms[i].f, force );
+ rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
+ rvec_Add( data->ext_press, ext_press );
+
+ rvec_ScaledAdd( system->atoms[j].f,
+ CEtors9 + CEconj6, dcos_omega_dj );
+
+ rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dk );
+ rvec_Add( system->atoms[k].f, force );
+ rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
+ rvec_Add( data->ext_press, ext_press );
+
+ rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dl );
+ rvec_Add( system->atoms[l].f, force );
+ rvec_iMultiply( ext_press, rel_box_jl, force );
+ rvec_Add( data->ext_press, ext_press );
+
+
+ /* This part is intended for a fully-flexible box */
+ /* rvec_ScaledSum( temp_rvec,
+ CEtors7 + CEconj4, p_ijk->dcos_dk, // i
+ CEtors9 + CEconj6, dcos_omega_di );
+ rvec_OuterProduct( temp_rtensor,
+ temp_rvec, system->atoms[i].x );
+ rtensor_Copy( total_rtensor, temp_rtensor );
+
+ rvec_ScaledSum( temp_rvec,
+ CEtors7 + CEconj4, p_ijk->dcos_dj, // j
+ CEtors8 + CEconj5, p_jkl->dcos_di );
+ rvec_ScaledAdd( temp_rvec,
+ CEtors9 + CEconj6, dcos_omega_dj );
+ rvec_OuterProduct( temp_rtensor,
+ temp_rvec, system->atoms[j].x );
+ rtensor_Add( total_rtensor, temp_rtensor );
+
+ rvec_ScaledSum( temp_rvec,
+ CEtors7 + CEconj4, p_ijk->dcos_di, // k
+ CEtors8 + CEconj5, p_jkl->dcos_dj );
+ rvec_ScaledAdd( temp_rvec,
+ CEtors9 + CEconj6, dcos_omega_dk );
+ rvec_OuterProduct( temp_rtensor,
+ temp_rvec, system->atoms[k].x );
+ rtensor_Add( total_rtensor, temp_rtensor );
+
+ rvec_ScaledSum( temp_rvec,
+ CEtors8 + CEconj5, p_jkl->dcos_dk, // l
+ CEtors9 + CEconj6, dcos_omega_dl );
+ rvec_OuterProduct( temp_rtensor,
+ temp_rvec, system->atoms[l].x );
+ rtensor_Copy( total_rtensor, temp_rtensor );
+
+ if( pbond_ij->imaginary || pbond_jk->imaginary ||
+ pbond_kl->imaginary )
+ rtensor_ScaledAdd( data->flex_bar.P, -1., total_rtensor );
+ else
+ rtensor_Add( data->flex_bar.P, total_rtensor ); */
+ }
+
#ifdef TEST_ENERGY
- /*fprintf( out_control->etor,
- //"%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
- //r_ij, r_jk, r_kl,
- "%12.8f%12.8f%12.8f%12.8f\n",
- cos_ijk, cos_jkl, sin_ijk, sin_jkl );*/
- // fprintf( out_control->etor, "%12.8f\n", dfn11 );
- fprintf( out_control->etor, "%12.8f%12.8f%12.8f\n",
- fn10, cos_omega, CV );
-
- fprintf( out_control->etor,
- "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
- CEtors2, CEtors3, CEtors4, CEtors5,
- CEtors6, CEtors7, CEtors8, CEtors9 );
-
- /* fprintf( out_control->etor,
- "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
- htra, htrb, htrc, hthd, hthe, hnra, hnrc, hnhd, hnhe ); */
-
- fprintf( out_control->etor,
- "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
- CEconj1, CEconj2, CEconj3, CEconj4, CEconj5, CEconj6 );
- /* fprintf(out_control->etor,"%23.15e%23.15e%23.15e%23.15e\n",
- fbp->V1, fbp->V2, fbp->V3, fbp->p_tor1 );*/
-
- fprintf( out_control->etor,
- //"%6d%6d%6d%6d%23.15e%23.15e%23.15e%23.15e\n",
- "%6d%6d%6d%6d%12.8f%12.8f\n",
- workspace->orig_id[i], workspace->orig_id[j],
- workspace->orig_id[k], workspace->orig_id[l],
- e_tor, e_con );
- //RAD2DEG(omega), BOA_jk, e_tor, data->E_Tor );
-
- fprintf( out_control->econ,
- "%6d%6d%6d%6d%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e\n",
- workspace->orig_id[i], workspace->orig_id[j],
- workspace->orig_id[k], workspace->orig_id[l],
- RAD2DEG(omega), BOA_ij, BOA_jk, BOA_kl,
- e_con,data->E_Con );
-
- /* fprintf( out_control->etor,
- "%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n",
- (CEtors7 + CEconj4)*p_ijk->dcos_dk[0],
- (CEtors7 + CEconj4)*p_ijk->dcos_dk[1],
- (CEtors7 + CEconj4)*p_ijk->dcos_dk[2],
- (CEtors7 + CEconj4)*p_ijk->dcos_dj[0],
- (CEtors7 + CEconj4)*p_ijk->dcos_dj[1],
- (CEtors7 + CEconj4)*p_ijk->dcos_dj[2],
- (CEtors7 + CEconj4)*p_ijk->dcos_di[0],
- (CEtors7 + CEconj4)*p_ijk->dcos_di[1],
- (CEtors7 + CEconj4)*p_ijk->dcos_di[2] ); */
-
-
- /* fprintf( out_control->etor,
- "%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n",
- (CEtors8 + CEconj5)*p_jkl->dcos_di[0],
- (CEtors8 + CEconj5)*p_jkl->dcos_di[1],
- (CEtors8 + CEconj5)*p_jkl->dcos_di[2],
- (CEtors8 + CEconj5)*p_jkl->dcos_dj[0],
- (CEtors8 + CEconj5)*p_jkl->dcos_dj[1],
- (CEtors8 + CEconj5)*p_jkl->dcos_dj[2],
- (CEtors8 + CEconj5)*p_jkl->dcos_dk[0],
- (CEtors8 + CEconj5)*p_jkl->dcos_dk[1],
- (CEtors8 + CEconj5)*p_jkl->dcos_dk[2] ); */
-
- fprintf( out_control->etor,
- "%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n",
- dcos_omega_di[0], dcos_omega_di[1], dcos_omega_di[2],
- dcos_omega_dj[0], dcos_omega_dj[1], dcos_omega_dj[2],
- dcos_omega_dk[0], dcos_omega_dk[1], dcos_omega_dk[2],
- dcos_omega_dl[0], dcos_omega_dl[1], dcos_omega_dl[2] );
+ /*fprintf( out_control->etor,
+ //"%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
+ //r_ij, r_jk, r_kl,
+ "%12.8f%12.8f%12.8f%12.8f\n",
+ cos_ijk, cos_jkl, sin_ijk, sin_jkl );*/
+ // fprintf( out_control->etor, "%12.8f\n", dfn11 );
+ fprintf( out_control->etor, "%12.8f%12.8f%12.8f\n",
+ fn10, cos_omega, CV );
+
+ fprintf( out_control->etor,
+ "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
+ CEtors2, CEtors3, CEtors4, CEtors5,
+ CEtors6, CEtors7, CEtors8, CEtors9 );
+
+ /* fprintf( out_control->etor,
+ "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
+ htra, htrb, htrc, hthd, hthe, hnra, hnrc, hnhd, hnhe ); */
+
+ fprintf( out_control->etor,
+ "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
+ CEconj1, CEconj2, CEconj3, CEconj4, CEconj5, CEconj6 );
+ /* fprintf(out_control->etor,"%23.15e%23.15e%23.15e%23.15e\n",
+ fbp->V1, fbp->V2, fbp->V3, fbp->p_tor1 );*/
+
+ fprintf( out_control->etor,
+ //"%6d%6d%6d%6d%23.15e%23.15e%23.15e%23.15e\n",
+ "%6d%6d%6d%6d%12.8f%12.8f\n",
+ workspace->orig_id[i], workspace->orig_id[j],
+ workspace->orig_id[k], workspace->orig_id[l],
+ e_tor, e_con );
+ //RAD2DEG(omega), BOA_jk, e_tor, data->E_Tor );
+
+ fprintf( out_control->econ,
+ "%6d%6d%6d%6d%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e\n",
+ workspace->orig_id[i], workspace->orig_id[j],
+ workspace->orig_id[k], workspace->orig_id[l],
+ RAD2DEG(omega), BOA_ij, BOA_jk, BOA_kl,
+ e_con, data->E_Con );
+
+ /* fprintf( out_control->etor,
+ "%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n",
+ (CEtors7 + CEconj4)*p_ijk->dcos_dk[0],
+ (CEtors7 + CEconj4)*p_ijk->dcos_dk[1],
+ (CEtors7 + CEconj4)*p_ijk->dcos_dk[2],
+ (CEtors7 + CEconj4)*p_ijk->dcos_dj[0],
+ (CEtors7 + CEconj4)*p_ijk->dcos_dj[1],
+ (CEtors7 + CEconj4)*p_ijk->dcos_dj[2],
+ (CEtors7 + CEconj4)*p_ijk->dcos_di[0],
+ (CEtors7 + CEconj4)*p_ijk->dcos_di[1],
+ (CEtors7 + CEconj4)*p_ijk->dcos_di[2] ); */
+
+
+ /* fprintf( out_control->etor,
+ "%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n",
+ (CEtors8 + CEconj5)*p_jkl->dcos_di[0],
+ (CEtors8 + CEconj5)*p_jkl->dcos_di[1],
+ (CEtors8 + CEconj5)*p_jkl->dcos_di[2],
+ (CEtors8 + CEconj5)*p_jkl->dcos_dj[0],
+ (CEtors8 + CEconj5)*p_jkl->dcos_dj[1],
+ (CEtors8 + CEconj5)*p_jkl->dcos_dj[2],
+ (CEtors8 + CEconj5)*p_jkl->dcos_dk[0],
+ (CEtors8 + CEconj5)*p_jkl->dcos_dk[1],
+ (CEtors8 + CEconj5)*p_jkl->dcos_dk[2] ); */
+
+ fprintf( out_control->etor,
+ "%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n",
+ dcos_omega_di[0], dcos_omega_di[1], dcos_omega_di[2],
+ dcos_omega_dj[0], dcos_omega_dj[1], dcos_omega_dj[2],
+ dcos_omega_dk[0], dcos_omega_dk[1], dcos_omega_dk[2],
+ dcos_omega_dl[0], dcos_omega_dl[1], dcos_omega_dl[2] );
#endif
#ifdef TEST_FORCES
- /* Torsion Forces */
- Add_dBOpinpi2(system, lists, j, pk, CEtors2, 0.,
- workspace->f_tor, workspace->f_tor);
- Add_dDelta( system, lists, j, CEtors3, workspace->f_tor );
- Add_dDelta( system, lists, k, CEtors3, workspace->f_tor );
- Add_dBO( system, lists, j, pij, CEtors4, workspace->f_tor );
- Add_dBO( system, lists, j, pk, CEtors5, workspace->f_tor );
- Add_dBO( system, lists, k, plk, CEtors6, workspace->f_tor );
-
- rvec_ScaledAdd(workspace->f_tor[i], CEtors7, p_ijk->dcos_dk);
- rvec_ScaledAdd(workspace->f_tor[j], CEtors7, p_ijk->dcos_dj);
- rvec_ScaledAdd(workspace->f_tor[k], CEtors7, p_ijk->dcos_di);
-
- rvec_ScaledAdd(workspace->f_tor[j], CEtors8, p_jkl->dcos_di);
- rvec_ScaledAdd(workspace->f_tor[k], CEtors8, p_jkl->dcos_dj);
- rvec_ScaledAdd(workspace->f_tor[l], CEtors8, p_jkl->dcos_dk);
-
- rvec_ScaledAdd( workspace->f_tor[i], CEtors9, dcos_omega_di );
- rvec_ScaledAdd( workspace->f_tor[j], CEtors9, dcos_omega_dj );
- rvec_ScaledAdd( workspace->f_tor[k], CEtors9, dcos_omega_dk );
- rvec_ScaledAdd( workspace->f_tor[l], CEtors9, dcos_omega_dl );
-
- /* Conjugation Forces */
- Add_dBO( system, lists, j, pij, CEconj1, workspace->f_con );
- Add_dBO( system, lists, j, pk, CEconj2, workspace->f_con );
- Add_dBO( system, lists, k, plk, CEconj3, workspace->f_con );
-
- rvec_ScaledAdd(workspace->f_con[i], CEconj4, p_ijk->dcos_dk);
- rvec_ScaledAdd(workspace->f_con[j], CEconj4, p_ijk->dcos_dj);
- rvec_ScaledAdd(workspace->f_con[k], CEconj4, p_ijk->dcos_di);
-
- rvec_ScaledAdd(workspace->f_con[j], CEconj5, p_jkl->dcos_di);
- rvec_ScaledAdd(workspace->f_con[k], CEconj5, p_jkl->dcos_dj);
- rvec_ScaledAdd(workspace->f_con[l], CEconj5, p_jkl->dcos_dk);
-
- rvec_ScaledAdd( workspace->f_con[i], CEconj6, dcos_omega_di );
- rvec_ScaledAdd( workspace->f_con[j], CEconj6, dcos_omega_dj );
- rvec_ScaledAdd( workspace->f_con[k], CEconj6, dcos_omega_dk );
- rvec_ScaledAdd( workspace->f_con[l], CEconj6, dcos_omega_dl );
+ /* Torsion Forces */
+ Add_dBOpinpi2(system, lists, j, pk, CEtors2, 0.,
+ workspace->f_tor, workspace->f_tor);
+ Add_dDelta( system, lists, j, CEtors3, workspace->f_tor );
+ Add_dDelta( system, lists, k, CEtors3, workspace->f_tor );
+ Add_dBO( system, lists, j, pij, CEtors4, workspace->f_tor );
+ Add_dBO( system, lists, j, pk, CEtors5, workspace->f_tor );
+ Add_dBO( system, lists, k, plk, CEtors6, workspace->f_tor );
+
+ rvec_ScaledAdd(workspace->f_tor[i], CEtors7, p_ijk->dcos_dk);
+ rvec_ScaledAdd(workspace->f_tor[j], CEtors7, p_ijk->dcos_dj);
+ rvec_ScaledAdd(workspace->f_tor[k], CEtors7, p_ijk->dcos_di);
+
+ rvec_ScaledAdd(workspace->f_tor[j], CEtors8, p_jkl->dcos_di);
+ rvec_ScaledAdd(workspace->f_tor[k], CEtors8, p_jkl->dcos_dj);
+ rvec_ScaledAdd(workspace->f_tor[l], CEtors8, p_jkl->dcos_dk);
+
+ rvec_ScaledAdd( workspace->f_tor[i], CEtors9, dcos_omega_di );
+ rvec_ScaledAdd( workspace->f_tor[j], CEtors9, dcos_omega_dj );
+ rvec_ScaledAdd( workspace->f_tor[k], CEtors9, dcos_omega_dk );
+ rvec_ScaledAdd( workspace->f_tor[l], CEtors9, dcos_omega_dl );
+
+ /* Conjugation Forces */
+ Add_dBO( system, lists, j, pij, CEconj1, workspace->f_con );
+ Add_dBO( system, lists, j, pk, CEconj2, workspace->f_con );
+ Add_dBO( system, lists, k, plk, CEconj3, workspace->f_con );
+
+ rvec_ScaledAdd(workspace->f_con[i], CEconj4, p_ijk->dcos_dk);
+ rvec_ScaledAdd(workspace->f_con[j], CEconj4, p_ijk->dcos_dj);
+ rvec_ScaledAdd(workspace->f_con[k], CEconj4, p_ijk->dcos_di);
+
+ rvec_ScaledAdd(workspace->f_con[j], CEconj5, p_jkl->dcos_di);
+ rvec_ScaledAdd(workspace->f_con[k], CEconj5, p_jkl->dcos_dj);
+ rvec_ScaledAdd(workspace->f_con[l], CEconj5, p_jkl->dcos_dk);
+
+ rvec_ScaledAdd( workspace->f_con[i], CEconj6, dcos_omega_di );
+ rvec_ScaledAdd( workspace->f_con[j], CEconj6, dcos_omega_dj );
+ rvec_ScaledAdd( workspace->f_con[k], CEconj6, dcos_omega_dk );
+ rvec_ScaledAdd( workspace->f_con[l], CEconj6, dcos_omega_dl );
#endif
- } // pl check ends
- } // pl loop ends
- } // pi check ends
- } // pi loop ends
- } // k-j neighbor check ends
- } // j<k && j-k neighbor check ends
- } // pk loop ends
- } // j loop
-
- /* fprintf( stderr, "4body: ext_press (%23.15e %23.15e %23.15e)\n",
- data->ext_press[0], data->ext_press[1], data->ext_press[2] );*/
-
+ } // pl check ends
+ } // pl loop ends
+ } // pi check ends
+ } // pi loop ends
+ } // k-j neighbor check ends
+ } // j<k && j-k neighbor check ends
+ } // pk loop ends
+ } // j loop
+
+ /* fprintf( stderr, "4body: ext_press (%23.15e %23.15e %23.15e)\n",
+ data->ext_press[0], data->ext_press[1], data->ext_press[2] );*/
+
#ifdef TEST_FORCES
- fprintf( stderr, "Number of torsion angles: %d\n", num_frb_intrs );
- fprintf( stderr, "Torsion Energy: %g\t Conjugation Energy: %g\n",
- data->E_Tor, data->E_Con );
+ fprintf( stderr, "Number of torsion angles: %d\n", num_frb_intrs );
+ fprintf( stderr, "Torsion Energy: %g\t Conjugation Energy: %g\n",
+ data->E_Tor, data->E_Con );
#endif
}
diff --git a/puremd_rc_1003/sPuReMD/four_body_interactions.h b/puremd_rc_1003/sPuReMD/four_body_interactions.h
index d633396b5e12368060916ed3bc3c2bfd8f202b5c..37136cd2ef5b536bb97e3776d8743c108eed71a2 100644
--- a/puremd_rc_1003/sPuReMD/four_body_interactions.h
+++ b/puremd_rc_1003/sPuReMD/four_body_interactions.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -25,6 +25,6 @@
#include "mytypes.h"
void Four_Body_Interactions( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, list**, output_controls* );
#endif
diff --git a/puremd_rc_1003/sPuReMD/grid.c b/puremd_rc_1003/sPuReMD/grid.c
index 407b8b9662c204353407be404ab16a6bca8ef82b..20c87c12514caa6673c6212978bb8aaa45f987ef 100644
--- a/puremd_rc_1003/sPuReMD/grid.c
+++ b/puremd_rc_1003/sPuReMD/grid.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -26,501 +26,532 @@
int Estimate_GCell_Population( reax_system* system )
{
- int i, j, k, l;
- int max_atoms;
- grid *g;
-
- g = &( system->g );
- Reset_Grid( g );
-
- for( l = 0; l < system->N; l++ ) {
- i = (int)(system->atoms[l].x[0] * g->inv_len[0]);
- j = (int)(system->atoms[l].x[1] * g->inv_len[1]);
- k = (int)(system->atoms[l].x[2] * g->inv_len[2]);
- g->top[i][j][k]++;
- // fprintf( stderr, "\tatom%-6d (%8.3f%8.3f%8.3f) --> (%3d%3d%3d)\n",
- // l, system->atoms[l].x[0], system->atoms[l].x[1], system->atoms[l].x[2],
- // i, j, k );
- }
-
- max_atoms = 0;
- for( i = 0; i < g->ncell[0]; i++ )
- for( j = 0; j < g->ncell[1]; j++ )
- for( k = 0; k < g->ncell[2]; k++ )
- if( max_atoms < g->top[i][j][k] )
- max_atoms = g->top[i][j][k];
-
- return MAX(max_atoms*SAFE_ZONE, MIN_GCELL_POPL);
+ int i, j, k, l;
+ int max_atoms;
+ grid *g;
+
+ g = &( system->g );
+ Reset_Grid( g );
+
+ for ( l = 0; l < system->N; l++ )
+ {
+ i = (int)(system->atoms[l].x[0] * g->inv_len[0]);
+ j = (int)(system->atoms[l].x[1] * g->inv_len[1]);
+ k = (int)(system->atoms[l].x[2] * g->inv_len[2]);
+ g->top[i][j][k]++;
+ // fprintf( stderr, "\tatom%-6d (%8.3f%8.3f%8.3f) --> (%3d%3d%3d)\n",
+ // l, system->atoms[l].x[0], system->atoms[l].x[1], system->atoms[l].x[2],
+ // i, j, k );
+ }
+
+ max_atoms = 0;
+ for ( i = 0; i < g->ncell[0]; i++ )
+ for ( j = 0; j < g->ncell[1]; j++ )
+ for ( k = 0; k < g->ncell[2]; k++ )
+ if ( max_atoms < g->top[i][j][k] )
+ max_atoms = g->top[i][j][k];
+
+ return MAX(max_atoms * SAFE_ZONE, MIN_GCELL_POPL);
}
void Allocate_Space_for_Grid( reax_system *system )
{
- int i, j, k, l;
- grid *g;
-
- g = &(system->g);
- g->max_nbrs = (2*g->spread[0]+1) * (2*g->spread[1]+1) * (2*g->spread[2]+1)+3;
-
- /* allocate space for the new grid */
- g->atoms = (int****) calloc( g->ncell[0], sizeof( int*** ));
- g->top = (int***) calloc( g->ncell[0], sizeof( int** ));
- g->mark = (int***) calloc( g->ncell[0], sizeof( int** ));
- g->start = (int***) calloc( g->ncell[0], sizeof( int** ));
- g->end = (int***) calloc( g->ncell[0], sizeof( int** ));
- g->nbrs = (ivec****) calloc( g->ncell[0], sizeof( ivec*** ));
- g->nbrs_cp = (rvec****) calloc( g->ncell[0], sizeof( rvec*** ));
-
- for( i = 0; i < g->ncell[0]; i++ ) {
- g->atoms[i] = (int***) calloc( g->ncell[1], sizeof( int** ));
- g->top [i] = (int**) calloc( g->ncell[1], sizeof( int* ));
- g->mark[i] = (int**) calloc( g->ncell[1], sizeof( int* ));
- g->start[i] = (int**) calloc( g->ncell[1], sizeof( int* ));
- g->end[i] = (int**) calloc( g->ncell[1], sizeof( int* ));
- g->nbrs[i] = (ivec***) calloc( g->ncell[1], sizeof( ivec** ));
- g->nbrs_cp[i] = (rvec***) calloc( g->ncell[1], sizeof( rvec** ));
-
- for( j = 0; j < g->ncell[1]; j++ ) {
- g->atoms[i][j] = (int**) calloc( g->ncell[2], sizeof( int* ));
- g->top[i][j] = (int*) calloc( g->ncell[2], sizeof( int ));
- g->mark[i][j] = (int*) calloc( g->ncell[2], sizeof( int ));
- g->start[i][j] = (int*) calloc( g->ncell[2], sizeof( int ));
- g->end[i][j] = (int*) calloc( g->ncell[2], sizeof( int ));
- g->nbrs[i][j] = (ivec**) calloc( g->ncell[2], sizeof( ivec* ));
- g->nbrs_cp[i][j] = (rvec**) calloc( g->ncell[2], sizeof( rvec* ));
-
- for( k = 0; k < g->ncell[2]; k++ ) {
- g->top[i][j][k] = 0;
- g->mark[i][j][k] = 0;
- g->start[i][j][k] = 0;
- g->end[i][j][k] = 0;
- g->nbrs[i][j][k] = (ivec*) calloc( g->max_nbrs, sizeof( ivec ) );
- g->nbrs_cp[i][j][k] = (rvec*) calloc( g->max_nbrs, sizeof( rvec ) );
-
- for( l = 0; l < g->max_nbrs; ++l ){
- g->nbrs[i][j][k][l][0] = -1;
- g->nbrs[i][j][k][l][1] = -1;
- g->nbrs[i][j][k][l][2] = -1;
-
- g->nbrs_cp[i][j][k][l][0] = -1;
- g->nbrs_cp[i][j][k][l][1] = -1;
- g->nbrs_cp[i][j][k][l][2] = -1;
- }
- }
+ int i, j, k, l;
+ grid *g;
+
+ g = &(system->g);
+ g->max_nbrs = (2 * g->spread[0] + 1) * (2 * g->spread[1] + 1) * (2 * g->spread[2] + 1) + 3;
+
+ /* allocate space for the new grid */
+ g->atoms = (int****) calloc( g->ncell[0], sizeof( int*** ));
+ g->top = (int***) calloc( g->ncell[0], sizeof( int** ));
+ g->mark = (int***) calloc( g->ncell[0], sizeof( int** ));
+ g->start = (int***) calloc( g->ncell[0], sizeof( int** ));
+ g->end = (int***) calloc( g->ncell[0], sizeof( int** ));
+ g->nbrs = (ivec****) calloc( g->ncell[0], sizeof( ivec*** ));
+ g->nbrs_cp = (rvec****) calloc( g->ncell[0], sizeof( rvec*** ));
+
+ for ( i = 0; i < g->ncell[0]; i++ )
+ {
+ g->atoms[i] = (int***) calloc( g->ncell[1], sizeof( int** ));
+ g->top [i] = (int**) calloc( g->ncell[1], sizeof( int* ));
+ g->mark[i] = (int**) calloc( g->ncell[1], sizeof( int* ));
+ g->start[i] = (int**) calloc( g->ncell[1], sizeof( int* ));
+ g->end[i] = (int**) calloc( g->ncell[1], sizeof( int* ));
+ g->nbrs[i] = (ivec***) calloc( g->ncell[1], sizeof( ivec** ));
+ g->nbrs_cp[i] = (rvec***) calloc( g->ncell[1], sizeof( rvec** ));
+
+ for ( j = 0; j < g->ncell[1]; j++ )
+ {
+ g->atoms[i][j] = (int**) calloc( g->ncell[2], sizeof( int* ));
+ g->top[i][j] = (int*) calloc( g->ncell[2], sizeof( int ));
+ g->mark[i][j] = (int*) calloc( g->ncell[2], sizeof( int ));
+ g->start[i][j] = (int*) calloc( g->ncell[2], sizeof( int ));
+ g->end[i][j] = (int*) calloc( g->ncell[2], sizeof( int ));
+ g->nbrs[i][j] = (ivec**) calloc( g->ncell[2], sizeof( ivec* ));
+ g->nbrs_cp[i][j] = (rvec**) calloc( g->ncell[2], sizeof( rvec* ));
+
+ for ( k = 0; k < g->ncell[2]; k++ )
+ {
+ g->top[i][j][k] = 0;
+ g->mark[i][j][k] = 0;
+ g->start[i][j][k] = 0;
+ g->end[i][j][k] = 0;
+ g->nbrs[i][j][k] = (ivec*) calloc( g->max_nbrs, sizeof( ivec ) );
+ g->nbrs_cp[i][j][k] = (rvec*) calloc( g->max_nbrs, sizeof( rvec ) );
+
+ for ( l = 0; l < g->max_nbrs; ++l )
+ {
+ g->nbrs[i][j][k][l][0] = -1;
+ g->nbrs[i][j][k][l][1] = -1;
+ g->nbrs[i][j][k][l][2] = -1;
+
+ g->nbrs_cp[i][j][k][l][0] = -1;
+ g->nbrs_cp[i][j][k][l][1] = -1;
+ g->nbrs_cp[i][j][k][l][2] = -1;
+ }
+ }
+ }
}
- }
- g->max_atoms = Estimate_GCell_Population( system );
- for( i = 0; i < g->ncell[0]; i++ )
- for( j = 0; j < g->ncell[1]; j++ )
- for( k = 0; k < g->ncell[2]; k++ )
- g->atoms[i][j][k] = (int*) calloc( g->max_atoms, sizeof(int) );
+ g->max_atoms = Estimate_GCell_Population( system );
+ for ( i = 0; i < g->ncell[0]; i++ )
+ for ( j = 0; j < g->ncell[1]; j++ )
+ for ( k = 0; k < g->ncell[2]; k++ )
+ g->atoms[i][j][k] = (int*) calloc( g->max_atoms, sizeof(int) );
}
void Deallocate_Grid_Space( grid *g )
{
- int i, j, k;
-
- /* deallocate the old grid */
- for( i = 0; i < g->ncell[0]; i++ ) {
- for( j = 0; j < g->ncell[1]; j++ ) {
- for( k = 0; k < g->ncell[2]; k++ ){
- free( g->atoms[i][j][k] );
- free( g->nbrs[i][j][k] );
- free( g->nbrs_cp[i][j][k] );
- }
-
- free( g->atoms[i][j] );
- free( g->top[i][j] );
- free( g->mark[i][j] );
- free( g->nbrs[i][j] );
- free( g->nbrs_cp[i][j] );
+ int i, j, k;
+
+ /* deallocate the old grid */
+ for ( i = 0; i < g->ncell[0]; i++ )
+ {
+ for ( j = 0; j < g->ncell[1]; j++ )
+ {
+ for ( k = 0; k < g->ncell[2]; k++ )
+ {
+ free( g->atoms[i][j][k] );
+ free( g->nbrs[i][j][k] );
+ free( g->nbrs_cp[i][j][k] );
+ }
+
+ free( g->atoms[i][j] );
+ free( g->top[i][j] );
+ free( g->mark[i][j] );
+ free( g->nbrs[i][j] );
+ free( g->nbrs_cp[i][j] );
+ }
+
+ free( g->atoms[i] );
+ free( g->top[i] );
+ free( g->mark[i] );
+ free( g->nbrs[i] );
+ free( g->nbrs_cp[i] );
}
-
- free( g->atoms[i] );
- free( g->top[i] );
- free( g->mark[i] );
- free( g->nbrs[i] );
- free( g->nbrs_cp[i] );
- }
-
- free( g->atoms );
- free( g->top );
- free( g->mark );
- free( g->nbrs );
- free( g->nbrs_cp );
+
+ free( g->atoms );
+ free( g->top );
+ free( g->mark );
+ free( g->nbrs );
+ free( g->nbrs_cp );
}
int Shift(int p, int dp, int dim, grid *g )
{
- int dim_len = 0;
- int newp = p + dp;
-
- switch( dim ) {
- case 0: dim_len = g->ncell[0];
- break;
- case 1: dim_len = g->ncell[1];
- break;
- case 2: dim_len = g->ncell[2];
- }
-
- while( newp < 0 ) newp = newp + dim_len;
- while( newp >= dim_len ) newp = newp - dim_len;
- return newp;
+ int dim_len = 0;
+ int newp = p + dp;
+
+ switch ( dim )
+ {
+ case 0:
+ dim_len = g->ncell[0];
+ break;
+ case 1:
+ dim_len = g->ncell[1];
+ break;
+ case 2:
+ dim_len = g->ncell[2];
+ }
+
+ while ( newp < 0 ) newp = newp + dim_len;
+ while ( newp >= dim_len ) newp = newp - dim_len;
+ return newp;
}
/* finds the closest point between two grid cells denoted by c1 and c2.
periodic boundary conditions are taken into consideration as well. */
-void Find_Closest_Point( grid *g, int c1x, int c1y, int c1z,
- int c2x, int c2y, int c2z, rvec closest_point )
+void Find_Closest_Point( grid *g, int c1x, int c1y, int c1z,
+ int c2x, int c2y, int c2z, rvec closest_point )
{
- int i, d;
- ivec c1 = { c1x, c1y, c1z };
- ivec c2 = { c2x, c2y, c2z };
-
- for( i = 0; i < 3; i++ ) {
- if( g->ncell[i] < 5 ) {
- closest_point[i] = NEG_INF - 1.;
- continue;
- }
-
- d = c2[i] - c1[i];
- if( abs(d) <= g->ncell[i] / 2 ) {
- if( d > 0 )
- closest_point[i] = c2[i] * g->len[i];
- else if ( d == 0 )
- closest_point[i] = NEG_INF - 1.;
- else
- closest_point[i] = ( c2[i] + 1 ) * g->len[i];
+ int i, d;
+ ivec c1 = { c1x, c1y, c1z };
+ ivec c2 = { c2x, c2y, c2z };
+
+ for ( i = 0; i < 3; i++ )
+ {
+ if ( g->ncell[i] < 5 )
+ {
+ closest_point[i] = NEG_INF - 1.;
+ continue;
+ }
+
+ d = c2[i] - c1[i];
+ if ( abs(d) <= g->ncell[i] / 2 )
+ {
+ if ( d > 0 )
+ closest_point[i] = c2[i] * g->len[i];
+ else if ( d == 0 )
+ closest_point[i] = NEG_INF - 1.;
+ else
+ closest_point[i] = ( c2[i] + 1 ) * g->len[i];
+ }
+ else
+ {
+ if ( d > 0 )
+ closest_point[i] = ( c2[i] - g->ncell[i] + 1 ) * g->len[i];
+ else
+ closest_point[i] = ( c2[i] + g->ncell[i] ) * g->len[i];
+ }
}
- else {
- if( d > 0 )
- closest_point[i] = ( c2[i] - g->ncell[i] + 1 ) * g->len[i];
- else
- closest_point[i] = ( c2[i] + g->ncell[i] ) * g->len[i];
- }
- }
}
void Find_Neighbor_GridCells( grid *g )
{
- int i, j, k;
- int di, dj, dk;
- int x, y, z;
- int stack_top;
- ivec *nbrs_stack;
- rvec *cp_stack;
-
- /* pick up a cell in the grid */
- for( i = 0; i < g->ncell[0]; i++ )
- for( j = 0; j < g->ncell[1]; j++ )
- for( k = 0; k < g->ncell[2]; k++ ) {
- nbrs_stack = g->nbrs[i][j][k];
- cp_stack = g->nbrs_cp[i][j][k];
- stack_top = 0;
- //fprintf( stderr, "grid1: %d %d %d\n", i, j, k );
-
- /* choose an unmarked neighbor cell*/
- for( di = -g->spread[0]; di <= g->spread[0]; di++ ) {
- x = Shift( i, di, 0, g );
-
- for( dj = -g->spread[1]; dj <= g->spread[1]; dj++ ) {
- y = Shift( j, dj, 1, g );
-
- for( dk = -g->spread[2]; dk <= g->spread[2]; dk++ ) {
- z = Shift( k, dk, 2, g );
- //fprintf( stderr, "\tgrid2: %d %d %d\n", x, y, z );
-
- if( !g->mark[x][y][z] ) {
- /*(di < 0 || // 9 combinations
- (di == 0 && dj < 0) || // 3 combinations
- (di == 0 && dj == 0 && dk < 0) ) )*/
- /* put the neighbor cell into the stack and mark it */
- nbrs_stack[stack_top][0] = x;
- nbrs_stack[stack_top][1] = y;
- nbrs_stack[stack_top][2] = z;
- g->mark[x][y][z] = 1;
-
- Find_Closest_Point( g, i, j, k, x, y, z, cp_stack[stack_top] );
- //fprintf( stderr, "\tcp: %lf %lf %lf\n",
- // cp_stack[stack_top][0], cp_stack[stack_top][1],
- // cp_stack[stack_top][2]);
- stack_top++;
- }
- }
- }
- }
-
- /*nbrs_stack[stack_top][0] = i;
- nbrs_stack[stack_top][1] = j;
- nbrs_stack[stack_top][2] = k;
- Find_Closest_Point( g, i, j, k, i, j, k, cp_stack[stack_top] );
- nbrs_stack[stack_top+1][0] = -1;
- nbrs_stack[stack_top+1][1] = -1;
- nbrs_stack[stack_top+1][2] = -1;
- Reset_Marks( g, nbrs_stack, stack_top+1 );*/
- nbrs_stack[stack_top][0] = -1;
- nbrs_stack[stack_top][1] = -1;
- nbrs_stack[stack_top][2] = -1;
- Reset_Marks( g, nbrs_stack, stack_top );
- }
+ int i, j, k;
+ int di, dj, dk;
+ int x, y, z;
+ int stack_top;
+ ivec *nbrs_stack;
+ rvec *cp_stack;
+
+ /* pick up a cell in the grid */
+ for ( i = 0; i < g->ncell[0]; i++ )
+ for ( j = 0; j < g->ncell[1]; j++ )
+ for ( k = 0; k < g->ncell[2]; k++ )
+ {
+ nbrs_stack = g->nbrs[i][j][k];
+ cp_stack = g->nbrs_cp[i][j][k];
+ stack_top = 0;
+ //fprintf( stderr, "grid1: %d %d %d\n", i, j, k );
+
+ /* choose an unmarked neighbor cell*/
+ for ( di = -g->spread[0]; di <= g->spread[0]; di++ )
+ {
+ x = Shift( i, di, 0, g );
+
+ for ( dj = -g->spread[1]; dj <= g->spread[1]; dj++ )
+ {
+ y = Shift( j, dj, 1, g );
+
+ for ( dk = -g->spread[2]; dk <= g->spread[2]; dk++ )
+ {
+ z = Shift( k, dk, 2, g );
+ //fprintf( stderr, "\tgrid2: %d %d %d\n", x, y, z );
+
+ if ( !g->mark[x][y][z] )
+ {
+ /*(di < 0 || // 9 combinations
+ (di == 0 && dj < 0) || // 3 combinations
+ (di == 0 && dj == 0 && dk < 0) ) )*/
+ /* put the neighbor cell into the stack and mark it */
+ nbrs_stack[stack_top][0] = x;
+ nbrs_stack[stack_top][1] = y;
+ nbrs_stack[stack_top][2] = z;
+ g->mark[x][y][z] = 1;
+
+ Find_Closest_Point( g, i, j, k, x, y, z, cp_stack[stack_top] );
+ //fprintf( stderr, "\tcp: %lf %lf %lf\n",
+ // cp_stack[stack_top][0], cp_stack[stack_top][1],
+ // cp_stack[stack_top][2]);
+ stack_top++;
+ }
+ }
+ }
+ }
+
+ /*nbrs_stack[stack_top][0] = i;
+ nbrs_stack[stack_top][1] = j;
+ nbrs_stack[stack_top][2] = k;
+ Find_Closest_Point( g, i, j, k, i, j, k, cp_stack[stack_top] );
+ nbrs_stack[stack_top+1][0] = -1;
+ nbrs_stack[stack_top+1][1] = -1;
+ nbrs_stack[stack_top+1][2] = -1;
+ Reset_Marks( g, nbrs_stack, stack_top+1 );*/
+ nbrs_stack[stack_top][0] = -1;
+ nbrs_stack[stack_top][1] = -1;
+ nbrs_stack[stack_top][2] = -1;
+ Reset_Marks( g, nbrs_stack, stack_top );
+ }
}
void Setup_Grid( reax_system* system )
{
- int d;
- ivec ncell;
- grid *g = &( system->g );
- simulation_box *my_box = &( system->box );
+ int d;
+ ivec ncell;
+ grid *g = &( system->g );
+ simulation_box *my_box = &( system->box );
+
+ /* determine number of grid cells in each direction */
+ ivec_rScale( ncell, 1. / g->cell_size, my_box->box_norms );
- /* determine number of grid cells in each direction */
- ivec_rScale( ncell, 1. / g->cell_size, my_box->box_norms );
+ for ( d = 0; d < 3; ++d )
+ if ( ncell[d] <= 0 )
+ ncell[d] = 1;
- for( d = 0; d < 3; ++d )
- if( ncell[d] <= 0 )
- ncell[d] = 1;
-
- /* find the number of grid cells */
- g->total = ncell[0] * ncell[1] * ncell[2];
- ivec_Copy( g->ncell, ncell );
+ /* find the number of grid cells */
+ g->total = ncell[0] * ncell[1] * ncell[2];
+ ivec_Copy( g->ncell, ncell );
- /* compute cell lengths */
- rvec_iDivide( g->len, my_box->box_norms, g->ncell );
- rvec_Invert( g->inv_len, g->len );
+ /* compute cell lengths */
+ rvec_iDivide( g->len, my_box->box_norms, g->ncell );
+ rvec_Invert( g->inv_len, g->len );
- Allocate_Space_for_Grid( system );
- Find_Neighbor_GridCells( g );
+ Allocate_Space_for_Grid( system );
+ Find_Neighbor_GridCells( g );
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "setting up the grid: " );
- fprintf( stderr, "ncell[%d %d %d] ", g->ncell[0], g->ncell[1], g->ncell[2] );
- fprintf( stderr, "len[%5.2f %5.2f %5.2f] ", g->len[0], g->len[1], g->len[2] );
- fprintf( stderr, "g->max_atoms = %d\n", g->max_atoms );
+ fprintf( stderr, "setting up the grid: " );
+ fprintf( stderr, "ncell[%d %d %d] ", g->ncell[0], g->ncell[1], g->ncell[2] );
+ fprintf( stderr, "len[%5.2f %5.2f %5.2f] ", g->len[0], g->len[1], g->len[2] );
+ fprintf( stderr, "g->max_atoms = %d\n", g->max_atoms );
#endif
}
void Update_Grid( reax_system* system )
{
- int d, i, j, k, x, y, z, itr;
- ivec ncell;
- ivec *nbrs;
- rvec *nbrs_cp;
- grid *g = &( system->g );
- simulation_box *my_box = &( system->box );
-
- /* determine number of grid cells in each direction */
- ivec_rScale( ncell, 1. / g->cell_size, my_box->box_norms );
-
- for( d = 0; d < 3; ++d )
- if( ncell[d] == 0 )
- ncell[d] = 1;
-
- if( ivec_isEqual( ncell, g->ncell ) ) {/* ncell are unchanged */
- /* update cell lengths */
- rvec_iDivide( g->len, my_box->box_norms, g->ncell );
- rvec_Invert( g->inv_len, g->len );
-
- /* update closest point distances between gcells */
- for( i = 0; i < g->ncell[0]; i++ )
- for( j = 0; j < g->ncell[1]; j++ )
- for( k = 0; k < g->ncell[2]; k++ ) {
- nbrs = g->nbrs[i][j][k];
- nbrs_cp = g->nbrs_cp[i][j][k];
- //fprintf( stderr, "gridcell %d %d %d\n", i, j, k );
-
- itr = 0;
- while( nbrs[itr][0] >= 0 ){
- x = nbrs[itr][0];
- y = nbrs[itr][1];
- z = nbrs[itr][2];
-
- Find_Closest_Point( g, i, j, k, x, y, z, nbrs_cp[itr] );
- ++itr;
- }
- }
- }
- else{ /* at least one of ncell has changed */
- Deallocate_Grid_Space( g );
- /* update number of grid cells */
- g->total = ncell[0] * ncell[1] * ncell[2];
- ivec_Copy( g->ncell, ncell );
- /* update cell lengths */
- rvec_iDivide( g->len, my_box->box_norms, g->ncell );
- rvec_Invert( g->inv_len, g->len );
-
- Allocate_Space_for_Grid( system );
- Find_Neighbor_GridCells( g );
+ int d, i, j, k, x, y, z, itr;
+ ivec ncell;
+ ivec *nbrs;
+ rvec *nbrs_cp;
+ grid *g = &( system->g );
+ simulation_box *my_box = &( system->box );
+
+ /* determine number of grid cells in each direction */
+ ivec_rScale( ncell, 1. / g->cell_size, my_box->box_norms );
+
+ for ( d = 0; d < 3; ++d )
+ if ( ncell[d] == 0 )
+ ncell[d] = 1;
+
+ if ( ivec_isEqual( ncell, g->ncell ) ) /* ncell are unchanged */
+ {
+ /* update cell lengths */
+ rvec_iDivide( g->len, my_box->box_norms, g->ncell );
+ rvec_Invert( g->inv_len, g->len );
+
+ /* update closest point distances between gcells */
+ for ( i = 0; i < g->ncell[0]; i++ )
+ for ( j = 0; j < g->ncell[1]; j++ )
+ for ( k = 0; k < g->ncell[2]; k++ )
+ {
+ nbrs = g->nbrs[i][j][k];
+ nbrs_cp = g->nbrs_cp[i][j][k];
+ //fprintf( stderr, "gridcell %d %d %d\n", i, j, k );
+
+ itr = 0;
+ while ( nbrs[itr][0] >= 0 )
+ {
+ x = nbrs[itr][0];
+ y = nbrs[itr][1];
+ z = nbrs[itr][2];
+
+ Find_Closest_Point( g, i, j, k, x, y, z, nbrs_cp[itr] );
+ ++itr;
+ }
+ }
+ }
+ else /* at least one of ncell has changed */
+ {
+ Deallocate_Grid_Space( g );
+ /* update number of grid cells */
+ g->total = ncell[0] * ncell[1] * ncell[2];
+ ivec_Copy( g->ncell, ncell );
+ /* update cell lengths */
+ rvec_iDivide( g->len, my_box->box_norms, g->ncell );
+ rvec_Invert( g->inv_len, g->len );
+
+ Allocate_Space_for_Grid( system );
+ Find_Neighbor_GridCells( g );
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "updated grid: " );
- fprintf( stderr, "ncell[%d %d %d] ",
- g->ncell[0], g->ncell[1], g->ncell[2] );
- fprintf( stderr, "len[%5.2f %5.2f %5.2f] ",
- g->len[0], g->len[1], g->len[2] );
- fprintf( stderr, "g->max_atoms = %d\n", g->max_atoms );
+ fprintf( stderr, "updated grid: " );
+ fprintf( stderr, "ncell[%d %d %d] ",
+ g->ncell[0], g->ncell[1], g->ncell[2] );
+ fprintf( stderr, "len[%5.2f %5.2f %5.2f] ",
+ g->len[0], g->len[1], g->len[2] );
+ fprintf( stderr, "g->max_atoms = %d\n", g->max_atoms );
#endif
- }
+ }
}
void Bin_Atoms( reax_system* system, static_storage *workspace )
{
- int i, j, k, l;
- int max_atoms;
- grid *g = &( system->g );
-
- Reset_Grid( g );
- for( l = 0; l < system->N; l++ ) {
- i = (int)(system->atoms[l].x[0] * g->inv_len[0]);
- j = (int)(system->atoms[l].x[1] * g->inv_len[1]);
- k = (int)(system->atoms[l].x[2] * g->inv_len[2]);
- g->atoms[i][j][k][g->top[i][j][k]] = l;
- g->top[i][j][k]++;
- // fprintf( stderr, "\tatom%-6d (%8.3f%8.3f%8.3f) --> (%3d%3d%3d)\n",
- // l, system->atoms[l].x[0], system->atoms[l].x[1], system->atoms[l].x[2],
- // i, j, k );
- }
-
- max_atoms = 0;
- for( i = 0; i < g->ncell[0]; i++ )
- for( j = 0; j < g->ncell[1]; j++ )
- for( k = 0; k < g->ncell[2]; k++ )
- if( max_atoms < g->top[i][j][k] )
- max_atoms = g->top[i][j][k];
-
- /* check if current gcell->max_atoms is safe */
- if( max_atoms >= g->max_atoms * SAFE_ZONE )
- workspace->realloc.gcell_atoms = MAX(max_atoms*SAFE_ZONE,MIN_GCELL_POPL);
+ int i, j, k, l;
+ int max_atoms;
+ grid *g = &( system->g );
+
+ Reset_Grid( g );
+ for ( l = 0; l < system->N; l++ )
+ {
+ i = (int)(system->atoms[l].x[0] * g->inv_len[0]);
+ j = (int)(system->atoms[l].x[1] * g->inv_len[1]);
+ k = (int)(system->atoms[l].x[2] * g->inv_len[2]);
+ g->atoms[i][j][k][g->top[i][j][k]] = l;
+ g->top[i][j][k]++;
+ // fprintf( stderr, "\tatom%-6d (%8.3f%8.3f%8.3f) --> (%3d%3d%3d)\n",
+ // l, system->atoms[l].x[0], system->atoms[l].x[1], system->atoms[l].x[2],
+ // i, j, k );
+ }
+
+ max_atoms = 0;
+ for ( i = 0; i < g->ncell[0]; i++ )
+ for ( j = 0; j < g->ncell[1]; j++ )
+ for ( k = 0; k < g->ncell[2]; k++ )
+ if ( max_atoms < g->top[i][j][k] )
+ max_atoms = g->top[i][j][k];
+
+ /* check if current gcell->max_atoms is safe */
+ if ( max_atoms >= g->max_atoms * SAFE_ZONE )
+ workspace->realloc.gcell_atoms = MAX(max_atoms * SAFE_ZONE, MIN_GCELL_POPL);
}
inline void reax_atom_Copy( reax_atom *dest, reax_atom *src )
{
- dest->type = src->type;
- rvec_Copy( dest->x, src->x );
- rvec_Copy( dest->v, src->v );
- strcpy( dest->name, src->name );
+ dest->type = src->type;
+ rvec_Copy( dest->x, src->x );
+ rvec_Copy( dest->v, src->v );
+ strcpy( dest->name, src->name );
}
-void Copy_Storage( reax_system *system, static_storage *workspace,
- int top, int old_id, int old_type,
- int *num_H, real **v, real **s, real **t,
- int *orig_id, rvec *f_old )
+void Copy_Storage( reax_system *system, static_storage *workspace,
+ int top, int old_id, int old_type,
+ int *num_H, real **v, real **s, real **t,
+ int *orig_id, rvec *f_old )
{
- int i;
-
- for( i = 0; i < RESTART+1; ++i )
- v[i][top] = workspace->v[i][old_id];
-
- for( i = 0; i < 3; ++i ) {
- s[i][top] = workspace->s[i][old_id];
- t[i][top] = workspace->t[i][old_id];
- }
-
- orig_id[top] = workspace->orig_id[old_id];
-
- workspace->Hdia_inv[top] = 1. / system->reaxprm.sbp[ old_type ].eta;
- workspace->b_s[top] = -system->reaxprm.sbp[ old_type ].chi;
- workspace->b_t[top] = -1.0;
-
- if( system->reaxprm.sbp[ old_type ].p_hbond == 1 ) // H atom
- workspace->hbond_index[top] = (*num_H)++;
- else workspace->hbond_index[top] = -1;
-
- rvec_Copy( f_old[top], workspace->f_old[old_id] );
+ int i;
+
+ for ( i = 0; i < RESTART + 1; ++i )
+ v[i][top] = workspace->v[i][old_id];
+
+ for ( i = 0; i < 3; ++i )
+ {
+ s[i][top] = workspace->s[i][old_id];
+ t[i][top] = workspace->t[i][old_id];
+ }
+
+ orig_id[top] = workspace->orig_id[old_id];
+
+ workspace->Hdia_inv[top] = 1. / system->reaxprm.sbp[ old_type ].eta;
+ workspace->b_s[top] = -system->reaxprm.sbp[ old_type ].chi;
+ workspace->b_t[top] = -1.0;
+
+ if ( system->reaxprm.sbp[ old_type ].p_hbond == 1 ) // H atom
+ workspace->hbond_index[top] = (*num_H)++;
+ else workspace->hbond_index[top] = -1;
+
+ rvec_Copy( f_old[top], workspace->f_old[old_id] );
}
void Free_Storage( static_storage *workspace )
{
- int i;
+ int i;
- for( i = 0; i < RESTART+1; ++i )
- free( workspace->v[i] );
- free( workspace->v );
+ for ( i = 0; i < RESTART + 1; ++i )
+ free( workspace->v[i] );
+ free( workspace->v );
- for( i = 0; i < 3; ++i ) {
- free( workspace->s[i] );
- free( workspace->t[i] );
- }
- free( workspace->s );
- free( workspace->t );
+ for ( i = 0; i < 3; ++i )
+ {
+ free( workspace->s[i] );
+ free( workspace->t[i] );
+ }
+ free( workspace->s );
+ free( workspace->t );
- free( workspace->orig_id );
+ free( workspace->orig_id );
}
-void Assign_New_Storage( static_storage *workspace,
- real **v, real **s, real **t,
- int *orig_id, rvec *f_old )
+void Assign_New_Storage( static_storage *workspace,
+ real **v, real **s, real **t,
+ int *orig_id, rvec *f_old )
{
- workspace->v = v;
+ workspace->v = v;
+
+ workspace->s = s;
+ workspace->t = t;
- workspace->s = s;
- workspace->t = t;
-
- workspace->orig_id = orig_id;
+ workspace->orig_id = orig_id;
- workspace->f_old = f_old;
+ workspace->f_old = f_old;
}
void Cluster_Atoms( reax_system *system, static_storage *workspace )
{
- int i, j, k, l, top, old_id, num_H = 0;
- reax_atom *old_atom;
- grid *g = &( system->g );
- reax_atom *new_atoms = (reax_atom*) calloc( system->N, sizeof(reax_atom) );
- int *orig_id = (int *) calloc( system->N, sizeof( int ) );
- real **v;
- real **s, **t;
- rvec *f_old = (rvec*) calloc( system->N, sizeof(rvec) );
-
- s = (real**) calloc( 3, sizeof( real* ) );
- t = (real**) calloc( 3, sizeof( real* ) );
- for( i = 0; i < 3; ++i ) {
- s[i] = (real *) calloc( system->N, sizeof( real ) );
- t[i] = (real *) calloc( system->N, sizeof( real ) );
- }
-
- v = (real**) calloc( RESTART+1, sizeof( real* ) );
- for( i = 0; i < RESTART+1; ++i )
- v[i] = (real *) calloc( system->N, sizeof( real ) );
-
-
- top = 0;
-
- for( i = 0; i < g->ncell[0]; i++ )
- for( j = 0; j < g->ncell[1]; j++ )
- for( k = 0; k < g->ncell[2]; k++ ) {
- g->start[i][j][k] = top;
-
- for( l = 0; l < g->top[i][j][k]; ++l ) {
- old_id = g->atoms[i][j][k][l];
- old_atom = &( system->atoms[old_id] );
- // fprintf( stderr, "%d <-- %d\n", top, old_id );
-
- reax_atom_Copy( &(new_atoms[top]), old_atom );
- Copy_Storage( system, workspace, top, old_id, old_atom->type,
- &num_H, v, s, t, orig_id, f_old );
- ++top;
- }
-
- g->end[i][j][k] = top;
- }
-
-
- free( system->atoms );
- Free_Storage( workspace );
-
- system->atoms = new_atoms;
- Assign_New_Storage( workspace, v, s, t, orig_id, f_old );
+ int i, j, k, l, top, old_id, num_H = 0;
+ reax_atom *old_atom;
+ grid *g = &( system->g );
+ reax_atom *new_atoms = (reax_atom*) calloc( system->N, sizeof(reax_atom) );
+ int *orig_id = (int *) calloc( system->N, sizeof( int ) );
+ real **v;
+ real **s, **t;
+ rvec *f_old = (rvec*) calloc( system->N, sizeof(rvec) );
+
+ s = (real**) calloc( 3, sizeof( real* ) );
+ t = (real**) calloc( 3, sizeof( real* ) );
+ for ( i = 0; i < 3; ++i )
+ {
+ s[i] = (real *) calloc( system->N, sizeof( real ) );
+ t[i] = (real *) calloc( system->N, sizeof( real ) );
+ }
+
+ v = (real**) calloc( RESTART + 1, sizeof( real* ) );
+ for ( i = 0; i < RESTART + 1; ++i )
+ v[i] = (real *) calloc( system->N, sizeof( real ) );
+
+
+ top = 0;
+
+ for ( i = 0; i < g->ncell[0]; i++ )
+ for ( j = 0; j < g->ncell[1]; j++ )
+ for ( k = 0; k < g->ncell[2]; k++ )
+ {
+ g->start[i][j][k] = top;
+
+ for ( l = 0; l < g->top[i][j][k]; ++l )
+ {
+ old_id = g->atoms[i][j][k][l];
+ old_atom = &( system->atoms[old_id] );
+ // fprintf( stderr, "%d <-- %d\n", top, old_id );
+
+ reax_atom_Copy( &(new_atoms[top]), old_atom );
+ Copy_Storage( system, workspace, top, old_id, old_atom->type,
+ &num_H, v, s, t, orig_id, f_old );
+ ++top;
+ }
+
+ g->end[i][j][k] = top;
+ }
+
+
+ free( system->atoms );
+ Free_Storage( workspace );
+
+ system->atoms = new_atoms;
+ Assign_New_Storage( workspace, v, s, t, orig_id, f_old );
}
diff --git a/puremd_rc_1003/sPuReMD/grid.h b/puremd_rc_1003/sPuReMD/grid.h
index af755efda20b763cce878805adb889ea92de136c..41d7b57edb2ba271bd41f71c6a77d5f179370910 100644
--- a/puremd_rc_1003/sPuReMD/grid.h
+++ b/puremd_rc_1003/sPuReMD/grid.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
diff --git a/puremd_rc_1003/sPuReMD/init_md.c b/puremd_rc_1003/sPuReMD/init_md.c
index def855fce2a3ee84015ef4664bf305afb7f61b69..d6f15a1e167b7907b903d0ff1bb5f9a916ee679a 100644
--- a/puremd_rc_1003/sPuReMD/init_md.c
+++ b/puremd_rc_1003/sPuReMD/init_md.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -38,643 +38,669 @@
void Generate_Initial_Velocities( reax_system *system, real T )
{
- int i;
- real scale, norm;
-
-
- if( T <= 0.1 ) {
- for (i=0; i < system->N; i++)
- rvec_MakeZero( system->atoms[i].v );
+ int i;
+ real scale, norm;
+
+
+ if ( T <= 0.1 )
+ {
+ for (i = 0; i < system->N; i++)
+ rvec_MakeZero( system->atoms[i].v );
#if defined(DEBUG)
- fprintf( stderr, "no random velocities...\n" );
+ fprintf( stderr, "no random velocities...\n" );
#endif
- }
- else {
- for( i = 0; i < system->N; i++ ) {
- rvec_Random( system->atoms[i].v );
-
- norm = rvec_Norm_Sqr( system->atoms[i].v );
- scale = SQRT( system->reaxprm.sbp[ system->atoms[i].type ].mass *
- norm / (3.0 * K_B * T) );
-
- rvec_Scale( system->atoms[i].v, 1.0/scale, system->atoms[i].v );
-
- /*fprintf( stderr, "v = %f %f %f\n",
- system->atoms[i].v[0],system->atoms[i].v[1],system->atoms[i].v[2]);
- fprintf( stderr, "scale = %f\n", scale );
- fprintf( stderr, "v = %f %f %f\n",
- system->atoms[i].v[0],system->atoms[i].v[1],system->atoms[i].v[2]);*/
}
- }
+ else
+ {
+ for ( i = 0; i < system->N; i++ )
+ {
+ rvec_Random( system->atoms[i].v );
+
+ norm = rvec_Norm_Sqr( system->atoms[i].v );
+ scale = SQRT( system->reaxprm.sbp[ system->atoms[i].type ].mass *
+ norm / (3.0 * K_B * T) );
+
+ rvec_Scale( system->atoms[i].v, 1.0 / scale, system->atoms[i].v );
+
+ /*fprintf( stderr, "v = %f %f %f\n",
+ system->atoms[i].v[0],system->atoms[i].v[1],system->atoms[i].v[2]);
+ fprintf( stderr, "scale = %f\n", scale );
+ fprintf( stderr, "v = %f %f %f\n",
+ system->atoms[i].v[0],system->atoms[i].v[1],system->atoms[i].v[2]);*/
+ }
+ }
}
-void Init_System( reax_system *system, control_params *control,
- simulation_data *data )
+void Init_System( reax_system *system, control_params *control,
+ simulation_data *data )
{
- int i;
- rvec dx;
-
- if( !control->restart )
- Reset_Atoms( system );
-
- Compute_Total_Mass( system, data );
- Compute_Center_of_Mass( system, data, stderr );
-
- /* reposition atoms */
- // just fit the atoms to the periodic box
- if( control->reposition_atoms == 0 ) {
- rvec_MakeZero( dx );
- }
- // put the center of mass to the center of the box
- else if( control->reposition_atoms == 1 ) {
- rvec_Scale( dx, 0.5, system->box.box_norms );
- rvec_ScaledAdd( dx, -1., data->xcm );
- }
- // put the center of mass to the origin
- else if( control->reposition_atoms == 2 ) {
- rvec_Scale( dx, -1., data->xcm );
- }
- else {
- fprintf( stderr, "UNKNOWN OPTION: reposition_atoms. Terminating...\n" );
- exit( UNKNOWN_OPTION );
- }
-
- for( i = 0; i < system->N; ++i ) {
- Inc_on_T3( system->atoms[i].x, dx, &(system->box) );
- /*fprintf( stderr, "%6d%2d%8.3f%8.3f%8.3f\n",
- i, system->atoms[i].type,
- system->atoms[i].x[0], system->atoms[i].x[1], system->atoms[i].x[2] );*/
- }
-
- /* Initialize velocities so that desired init T can be attained */
- if( !control->restart || (control->restart && control->random_vel) )
- Generate_Initial_Velocities( system, control->T_init );
-
- Setup_Grid( system );
+ int i;
+ rvec dx;
+
+ if ( !control->restart )
+ Reset_Atoms( system );
+
+ Compute_Total_Mass( system, data );
+ Compute_Center_of_Mass( system, data, stderr );
+
+ /* reposition atoms */
+ // just fit the atoms to the periodic box
+ if ( control->reposition_atoms == 0 )
+ {
+ rvec_MakeZero( dx );
+ }
+ // put the center of mass to the center of the box
+ else if ( control->reposition_atoms == 1 )
+ {
+ rvec_Scale( dx, 0.5, system->box.box_norms );
+ rvec_ScaledAdd( dx, -1., data->xcm );
+ }
+ // put the center of mass to the origin
+ else if ( control->reposition_atoms == 2 )
+ {
+ rvec_Scale( dx, -1., data->xcm );
+ }
+ else
+ {
+ fprintf( stderr, "UNKNOWN OPTION: reposition_atoms. Terminating...\n" );
+ exit( UNKNOWN_OPTION );
+ }
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ Inc_on_T3( system->atoms[i].x, dx, &(system->box) );
+ /*fprintf( stderr, "%6d%2d%8.3f%8.3f%8.3f\n",
+ i, system->atoms[i].type,
+ system->atoms[i].x[0], system->atoms[i].x[1], system->atoms[i].x[2] );*/
+ }
+
+ /* Initialize velocities so that desired init T can be attained */
+ if ( !control->restart || (control->restart && control->random_vel) )
+ Generate_Initial_Velocities( system, control->T_init );
+
+ Setup_Grid( system );
}
-void Init_Simulation_Data( reax_system *system, control_params *control,
- simulation_data *data, output_controls *out_control,
- evolve_function *Evolve )
+void Init_Simulation_Data( reax_system *system, control_params *control,
+ simulation_data *data, output_controls *out_control,
+ evolve_function *Evolve )
{
-
- Reset_Simulation_Data( data );
-
- if( !control->restart )
- data->step = data->prev_steps = 0;
-
- switch( control->ensemble ) {
- case NVE:
- data->N_f = 3 * system->N;
- *Evolve = Velocity_Verlet_NVE;
- break;
-
-
- case NVT:
- data->N_f = 3 * system->N + 1;
- //control->Tau_T = 100 * data->N_f * K_B * control->T_final;
- if( !control->restart || (control->restart && control->random_vel) ) {
- data->therm.G_xi = control->Tau_T * (2.0 * data->E_Kin -
- data->N_f * K_B * control->T );
- data->therm.v_xi = data->therm.G_xi * control->dt;
- data->therm.v_xi_old = 0;
- data->therm.xi = 0;
+
+ Reset_Simulation_Data( data );
+
+ if ( !control->restart )
+ data->step = data->prev_steps = 0;
+
+ switch ( control->ensemble )
+ {
+ case NVE:
+ data->N_f = 3 * system->N;
+ *Evolve = Velocity_Verlet_NVE;
+ break;
+
+
+ case NVT:
+ data->N_f = 3 * system->N + 1;
+ //control->Tau_T = 100 * data->N_f * K_B * control->T_final;
+ if ( !control->restart || (control->restart && control->random_vel) )
+ {
+ data->therm.G_xi = control->Tau_T * (2.0 * data->E_Kin -
+ data->N_f * K_B * control->T );
+ data->therm.v_xi = data->therm.G_xi * control->dt;
+ data->therm.v_xi_old = 0;
+ data->therm.xi = 0;
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "init_md: G_xi=%f Tau_T=%f E_kin=%f N_f=%f v_xi=%f\n",
- data->therm.G_xi, control->Tau_T, data->E_Kin,
- data->N_f, data->therm.v_xi );
+ fprintf( stderr, "init_md: G_xi=%f Tau_T=%f E_kin=%f N_f=%f v_xi=%f\n",
+ data->therm.G_xi, control->Tau_T, data->E_Kin,
+ data->N_f, data->therm.v_xi );
#endif
+ }
+
+ *Evolve = Velocity_Verlet_Nose_Hoover_NVT_Klein;
+ break;
+
+
+ case NPT: // Anisotropic NPT
+ fprintf( stderr, "THIS OPTION IS NOT YET IMPLEMENTED! TERMINATING...\n" );
+ exit( UNKNOWN_OPTION );
+ data->N_f = 3 * system->N + 9;
+ if ( !control->restart )
+ {
+ data->therm.G_xi = control->Tau_T * (2.0 * data->E_Kin -
+ data->N_f * K_B * control->T );
+ data->therm.v_xi = data->therm.G_xi * control->dt;
+ data->iso_bar.eps = 0.33333 * log(system->box.volume);
+ //data->inv_W = 1. / (data->N_f*K_B*control->T*SQR(control->Tau_P));
+ //Compute_Pressure( system, data, workspace );
+ }
+ *Evolve = Velocity_Verlet_Berendsen_Isotropic_NPT;
+ break;
+
+
+ case sNPT: // Semi-Isotropic NPT
+ data->N_f = 3 * system->N + 4;
+ *Evolve = Velocity_Verlet_Berendsen_SemiIsotropic_NPT;
+ break;
+
+
+ case iNPT: // Isotropic NPT
+ data->N_f = 3 * system->N + 2;
+ *Evolve = Velocity_Verlet_Berendsen_Isotropic_NPT;
+ break;
+
+ case bNVT:
+ data->N_f = 3 * system->N + 1;
+ *Evolve = Velocity_Verlet_Berendsen_NVT;
+ fprintf (stderr, " Initializing Velocity_Verlet_Berendsen_NVT .... \n");
+ break;
+
+ default:
+ break;
}
-
- *Evolve = Velocity_Verlet_Nose_Hoover_NVT_Klein;
- break;
-
-
- case NPT: // Anisotropic NPT
- fprintf( stderr, "THIS OPTION IS NOT YET IMPLEMENTED! TERMINATING...\n" );
- exit( UNKNOWN_OPTION );
- data->N_f = 3 * system->N + 9;
- if( !control->restart ) {
- data->therm.G_xi = control->Tau_T * (2.0 * data->E_Kin -
- data->N_f * K_B * control->T );
- data->therm.v_xi = data->therm.G_xi * control->dt;
- data->iso_bar.eps = 0.33333 * log(system->box.volume);
- //data->inv_W = 1. / (data->N_f*K_B*control->T*SQR(control->Tau_P));
- //Compute_Pressure( system, data, workspace );
- }
- *Evolve = Velocity_Verlet_Berendsen_Isotropic_NPT;
- break;
-
-
- case sNPT: // Semi-Isotropic NPT
- data->N_f = 3 * system->N + 4;
- *Evolve = Velocity_Verlet_Berendsen_SemiIsotropic_NPT;
- break;
-
-
- case iNPT: // Isotropic NPT
- data->N_f = 3 * system->N + 2;
- *Evolve = Velocity_Verlet_Berendsen_Isotropic_NPT;
- break;
-
- case bNVT:
- data->N_f = 3 * system->N + 1;
- *Evolve = Velocity_Verlet_Berendsen_NVT;
- fprintf (stderr, " Initializing Velocity_Verlet_Berendsen_NVT .... \n");
- break;
-
- default:
- break;
- }
-
- Compute_Kinetic_Energy( system, data );
-
- /* init timing info */
- data->timing.start = Get_Time( );
- data->timing.total = data->timing.start;
- data->timing.nbrs = 0;
- data->timing.init_forces = 0;
- data->timing.bonded = 0;
- data->timing.nonb = 0;
- data->timing.QEq = 0;
- data->timing.matvecs = 0;
+
+ Compute_Kinetic_Energy( system, data );
+
+ /* init timing info */
+ data->timing.start = Get_Time( );
+ data->timing.total = data->timing.start;
+ data->timing.nbrs = 0;
+ data->timing.init_forces = 0;
+ data->timing.bonded = 0;
+ data->timing.nonb = 0;
+ data->timing.QEq = 0;
+ data->timing.matvecs = 0;
}
-void Init_Workspace( reax_system *system, control_params *control,
- static_storage *workspace )
-{
- int i;
-
- /* Allocate space for hydrogen bond list */
- workspace->hbond_index = (int *) malloc( system->N * sizeof( int ) );
-
- /* bond order related storage */
- workspace->total_bond_order = (real *) malloc( system->N * sizeof( real ) );
- workspace->Deltap = (real *) malloc( system->N * sizeof( real ) );
- workspace->Deltap_boc = (real *) malloc( system->N * sizeof( real ) );
- workspace->dDeltap_self = (rvec *) malloc( system->N * sizeof( rvec ) );
-
- workspace->Delta = (real *) malloc( system->N * sizeof( real ) );
- workspace->Delta_lp = (real *) malloc( system->N * sizeof( real ) );
- workspace->Delta_lp_temp = (real *) malloc( system->N * sizeof( real ) );
- workspace->dDelta_lp = (real *) malloc( system->N * sizeof( real ) );
- workspace->dDelta_lp_temp = (real *) malloc( system->N * sizeof( real ) );
- workspace->Delta_e = (real *) malloc( system->N * sizeof( real ) );
- workspace->Delta_boc = (real *) malloc( system->N * sizeof( real ) );
- workspace->nlp = (real *) malloc( system->N * sizeof( real ) );
- workspace->nlp_temp = (real *) malloc( system->N * sizeof( real ) );
- workspace->Clp = (real *) malloc( system->N * sizeof( real ) );
- workspace->CdDelta = (real *) malloc( system->N * sizeof( real ) );
- workspace->vlpex = (real *) malloc( system->N * sizeof( real ) );
-
- /* QEq storage */
- workspace->H = NULL;
- workspace->L = NULL;
- workspace->U = NULL;
- workspace->droptol = (real *) calloc( system->N, sizeof( real ) );
- workspace->w = (real *) calloc( system->N, sizeof( real ) );
- workspace->Hdia_inv = (real *) calloc( system->N, sizeof( real ) );
- workspace->b = (real *) calloc( system->N * 2, sizeof( real ) );
- workspace->b_s = (real *) calloc( system->N, sizeof( real ) );
- workspace->b_t = (real *) calloc( system->N, sizeof( real ) );
- workspace->b_prc = (real *) calloc( system->N * 2, sizeof( real ) );
- workspace->b_prm = (real *) calloc( system->N * 2, sizeof( real ) );
- workspace->s_t = (real *) calloc( system->N * 2, sizeof( real ) );
- workspace->s = (real**) calloc( 5, sizeof( real* ) );
- workspace->t = (real**) calloc( 5, sizeof( real* ) );
- for( i = 0; i < 5; ++i ) {
- workspace->s[i] = (real *) calloc( system->N, sizeof( real ) );
- workspace->t[i] = (real *) calloc( system->N, sizeof( real ) );
- }
- // workspace->s_old = (real *) calloc( system->N, sizeof( real ) );
- // workspace->t_old = (real *) calloc( system->N, sizeof( real ) );
- // workspace->s_oldest = (real *) calloc( system->N, sizeof( real ) );
- // workspace->t_oldest = (real *) calloc( system->N, sizeof( real ) );
-
- for( i = 0; i < system->N; ++i ) {
- workspace->Hdia_inv[i] = 1./system->reaxprm.sbp[system->atoms[i].type].eta;
- workspace->b_s[i] = -system->reaxprm.sbp[ system->atoms[i].type ].chi;
- workspace->b_t[i] = -1.0;
-
- workspace->b[i] = -system->reaxprm.sbp[ system->atoms[i].type ].chi;
- workspace->b[i+system->N] = -1.0;
- }
-
- /* GMRES storage */
- workspace->y = (real *) calloc( RESTART+1, sizeof( real ) );
- workspace->z = (real *) calloc( RESTART+1, sizeof( real ) );
- workspace->g = (real *) calloc( RESTART+1, sizeof( real ) );
- workspace->h = (real **) calloc( RESTART+1, sizeof( real*) );
- workspace->hs = (real *) calloc( RESTART+1, sizeof( real ) );
- workspace->hc = (real *) calloc( RESTART+1, sizeof( real ) );
- workspace->rn = (real **) calloc( RESTART+1, sizeof( real*) );
- workspace->v = (real **) calloc( RESTART+1, sizeof( real*) );
-
- for( i = 0; i < RESTART+1; ++i )
+void Init_Workspace( reax_system *system, control_params *control,
+ static_storage *workspace )
+{
+ int i;
+
+ /* Allocate space for hydrogen bond list */
+ workspace->hbond_index = (int *) malloc( system->N * sizeof( int ) );
+
+ /* bond order related storage */
+ workspace->total_bond_order = (real *) malloc( system->N * sizeof( real ) );
+ workspace->Deltap = (real *) malloc( system->N * sizeof( real ) );
+ workspace->Deltap_boc = (real *) malloc( system->N * sizeof( real ) );
+ workspace->dDeltap_self = (rvec *) malloc( system->N * sizeof( rvec ) );
+
+ workspace->Delta = (real *) malloc( system->N * sizeof( real ) );
+ workspace->Delta_lp = (real *) malloc( system->N * sizeof( real ) );
+ workspace->Delta_lp_temp = (real *) malloc( system->N * sizeof( real ) );
+ workspace->dDelta_lp = (real *) malloc( system->N * sizeof( real ) );
+ workspace->dDelta_lp_temp = (real *) malloc( system->N * sizeof( real ) );
+ workspace->Delta_e = (real *) malloc( system->N * sizeof( real ) );
+ workspace->Delta_boc = (real *) malloc( system->N * sizeof( real ) );
+ workspace->nlp = (real *) malloc( system->N * sizeof( real ) );
+ workspace->nlp_temp = (real *) malloc( system->N * sizeof( real ) );
+ workspace->Clp = (real *) malloc( system->N * sizeof( real ) );
+ workspace->CdDelta = (real *) malloc( system->N * sizeof( real ) );
+ workspace->vlpex = (real *) malloc( system->N * sizeof( real ) );
+
+ /* QEq storage */
+ workspace->H = NULL;
+ workspace->L = NULL;
+ workspace->U = NULL;
+ workspace->droptol = (real *) calloc( system->N, sizeof( real ) );
+ workspace->w = (real *) calloc( system->N, sizeof( real ) );
+ workspace->Hdia_inv = (real *) calloc( system->N, sizeof( real ) );
+ workspace->b = (real *) calloc( system->N * 2, sizeof( real ) );
+ workspace->b_s = (real *) calloc( system->N, sizeof( real ) );
+ workspace->b_t = (real *) calloc( system->N, sizeof( real ) );
+ workspace->b_prc = (real *) calloc( system->N * 2, sizeof( real ) );
+ workspace->b_prm = (real *) calloc( system->N * 2, sizeof( real ) );
+ workspace->s_t = (real *) calloc( system->N * 2, sizeof( real ) );
+ workspace->s = (real**) calloc( 5, sizeof( real* ) );
+ workspace->t = (real**) calloc( 5, sizeof( real* ) );
+ for ( i = 0; i < 5; ++i )
+ {
+ workspace->s[i] = (real *) calloc( system->N, sizeof( real ) );
+ workspace->t[i] = (real *) calloc( system->N, sizeof( real ) );
+ }
+ // workspace->s_old = (real *) calloc( system->N, sizeof( real ) );
+ // workspace->t_old = (real *) calloc( system->N, sizeof( real ) );
+ // workspace->s_oldest = (real *) calloc( system->N, sizeof( real ) );
+ // workspace->t_oldest = (real *) calloc( system->N, sizeof( real ) );
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ workspace->Hdia_inv[i] = 1. / system->reaxprm.sbp[system->atoms[i].type].eta;
+ workspace->b_s[i] = -system->reaxprm.sbp[ system->atoms[i].type ].chi;
+ workspace->b_t[i] = -1.0;
+
+ workspace->b[i] = -system->reaxprm.sbp[ system->atoms[i].type ].chi;
+ workspace->b[i + system->N] = -1.0;
+ }
+
+ /* GMRES storage */
+ workspace->y = (real *) calloc( RESTART + 1, sizeof( real ) );
+ workspace->z = (real *) calloc( RESTART + 1, sizeof( real ) );
+ workspace->g = (real *) calloc( RESTART + 1, sizeof( real ) );
+ workspace->h = (real **) calloc( RESTART + 1, sizeof( real*) );
+ workspace->hs = (real *) calloc( RESTART + 1, sizeof( real ) );
+ workspace->hc = (real *) calloc( RESTART + 1, sizeof( real ) );
+ workspace->rn = (real **) calloc( RESTART + 1, sizeof( real*) );
+ workspace->v = (real **) calloc( RESTART + 1, sizeof( real*) );
+
+ for ( i = 0; i < RESTART + 1; ++i )
{
- workspace->h[i] = (real *) calloc( RESTART+1, sizeof( real ) );
- workspace->rn[i] = (real *) calloc( system->N * 2, sizeof( real ) );
- workspace->v[i] = (real *) calloc( system->N, sizeof( real ) );
+ workspace->h[i] = (real *) calloc( RESTART + 1, sizeof( real ) );
+ workspace->rn[i] = (real *) calloc( system->N * 2, sizeof( real ) );
+ workspace->v[i] = (real *) calloc( system->N, sizeof( real ) );
}
- /* CG storage */
- workspace->r = (real *) calloc( system->N, sizeof( real ) );
- workspace->d = (real *) calloc( system->N, sizeof( real ) );
- workspace->q = (real *) calloc( system->N, sizeof( real ) );
- workspace->p = (real *) calloc( system->N, sizeof( real ) );
+ /* CG storage */
+ workspace->r = (real *) calloc( system->N, sizeof( real ) );
+ workspace->d = (real *) calloc( system->N, sizeof( real ) );
+ workspace->q = (real *) calloc( system->N, sizeof( real ) );
+ workspace->p = (real *) calloc( system->N, sizeof( real ) );
- /* integrator storage */
- workspace->a = (rvec *) malloc( system->N * sizeof( rvec ) );
- workspace->f_old = (rvec *) malloc( system->N * sizeof( rvec ) );
- workspace->v_const = (rvec *) malloc( system->N * sizeof( rvec ) );
+ /* integrator storage */
+ workspace->a = (rvec *) malloc( system->N * sizeof( rvec ) );
+ workspace->f_old = (rvec *) malloc( system->N * sizeof( rvec ) );
+ workspace->v_const = (rvec *) malloc( system->N * sizeof( rvec ) );
- /* storage for analysis */
- if( control->molec_anal || control->diffusion_coef )
+ /* storage for analysis */
+ if ( control->molec_anal || control->diffusion_coef )
{
- workspace->mark = (int *) calloc( system->N, sizeof(int) );
- workspace->old_mark = (int *) calloc( system->N, sizeof(int) );
+ workspace->mark = (int *) calloc( system->N, sizeof(int) );
+ workspace->old_mark = (int *) calloc( system->N, sizeof(int) );
}
- else
- workspace->mark = workspace->old_mark = NULL;
-
- if( control->diffusion_coef )
- workspace->x_old = (rvec *) calloc( system->N, sizeof( rvec ) );
- else workspace->x_old = NULL;
-
-
+ else
+ workspace->mark = workspace->old_mark = NULL;
+
+ if ( control->diffusion_coef )
+ workspace->x_old = (rvec *) calloc( system->N, sizeof( rvec ) );
+ else workspace->x_old = NULL;
+
+
#ifdef TEST_FORCES
- workspace->dDelta = (rvec *) malloc( system->N * sizeof( rvec ) );
- workspace->f_ele = (rvec *) malloc( system->N * sizeof( rvec ) );
- workspace->f_vdw = (rvec *) malloc( system->N * sizeof( rvec ) );
- workspace->f_bo = (rvec *) malloc( system->N * sizeof( rvec ) );
- workspace->f_be = (rvec *) malloc( system->N * sizeof( rvec ) );
- workspace->f_lp = (rvec *) malloc( system->N * sizeof( rvec ) );
- workspace->f_ov = (rvec *) malloc( system->N * sizeof( rvec ) );
- workspace->f_un = (rvec *) malloc( system->N * sizeof( rvec ) );
- workspace->f_ang = (rvec *) malloc( system->N * sizeof( rvec ) );
- workspace->f_coa = (rvec *) malloc( system->N * sizeof( rvec ) );
- workspace->f_pen = (rvec *) malloc( system->N * sizeof( rvec ) );
- workspace->f_hb = (rvec *) malloc( system->N * sizeof( rvec ) );
- workspace->f_tor = (rvec *) malloc( system->N * sizeof( rvec ) );
- workspace->f_con = (rvec *) malloc( system->N * sizeof( rvec ) );
+ workspace->dDelta = (rvec *) malloc( system->N * sizeof( rvec ) );
+ workspace->f_ele = (rvec *) malloc( system->N * sizeof( rvec ) );
+ workspace->f_vdw = (rvec *) malloc( system->N * sizeof( rvec ) );
+ workspace->f_bo = (rvec *) malloc( system->N * sizeof( rvec ) );
+ workspace->f_be = (rvec *) malloc( system->N * sizeof( rvec ) );
+ workspace->f_lp = (rvec *) malloc( system->N * sizeof( rvec ) );
+ workspace->f_ov = (rvec *) malloc( system->N * sizeof( rvec ) );
+ workspace->f_un = (rvec *) malloc( system->N * sizeof( rvec ) );
+ workspace->f_ang = (rvec *) malloc( system->N * sizeof( rvec ) );
+ workspace->f_coa = (rvec *) malloc( system->N * sizeof( rvec ) );
+ workspace->f_pen = (rvec *) malloc( system->N * sizeof( rvec ) );
+ workspace->f_hb = (rvec *) malloc( system->N * sizeof( rvec ) );
+ workspace->f_tor = (rvec *) malloc( system->N * sizeof( rvec ) );
+ workspace->f_con = (rvec *) malloc( system->N * sizeof( rvec ) );
#endif
- workspace->realloc.num_far = -1;
- workspace->realloc.Htop = -1;
- workspace->realloc.hbonds = -1;
- workspace->realloc.bonds = -1;
- workspace->realloc.num_3body = -1;
- workspace->realloc.gcell_atoms = -1;
+ workspace->realloc.num_far = -1;
+ workspace->realloc.Htop = -1;
+ workspace->realloc.hbonds = -1;
+ workspace->realloc.bonds = -1;
+ workspace->realloc.num_3body = -1;
+ workspace->realloc.gcell_atoms = -1;
- Reset_Workspace( system, workspace );
+ Reset_Workspace( system, workspace );
}
-void Init_Lists( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+void Init_Lists( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int i, num_nbrs, num_hbonds, num_bonds, num_3body, Htop;
- int *hb_top, *bond_top;
-
- num_nbrs = Estimate_NumNeighbors( system, control, workspace, lists );
- if( !Make_List(system->N, num_nbrs, TYP_FAR_NEIGHBOR, (*lists)+FAR_NBRS) ) {
- fprintf(stderr, "Problem in initializing far nbrs list. Terminating!\n");
- exit( INIT_ERR );
- }
+ int i, num_nbrs, num_hbonds, num_bonds, num_3body, Htop;
+ int *hb_top, *bond_top;
+
+ num_nbrs = Estimate_NumNeighbors( system, control, workspace, lists );
+ if ( !Make_List(system->N, num_nbrs, TYP_FAR_NEIGHBOR, (*lists) + FAR_NBRS) )
+ {
+ fprintf(stderr, "Problem in initializing far nbrs list. Terminating!\n");
+ exit( INIT_ERR );
+ }
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "memory allocated: far_nbrs = %ldMB\n",
- num_nbrs * sizeof(far_neighbor_data) / (1024*1024) );
+ fprintf( stderr, "memory allocated: far_nbrs = %ldMB\n",
+ num_nbrs * sizeof(far_neighbor_data) / (1024 * 1024) );
#endif
- Generate_Neighbor_Lists(system,control,data,workspace,lists,out_control);
- Htop = 0;
- hb_top = (int*) calloc( system->N, sizeof(int) );
- bond_top = (int*) calloc( system->N, sizeof(int) );
- num_3body = 0;
- Estimate_Storage_Sizes( system, control, lists,
- &Htop, hb_top, bond_top, &num_3body );
-
- Allocate_Matrix( &(workspace->H), system->N, Htop );
+ Generate_Neighbor_Lists(system, control, data, workspace, lists, out_control);
+ Htop = 0;
+ hb_top = (int*) calloc( system->N, sizeof(int) );
+ bond_top = (int*) calloc( system->N, sizeof(int) );
+ num_3body = 0;
+ Estimate_Storage_Sizes( system, control, lists,
+ &Htop, hb_top, bond_top, &num_3body );
+
+ Allocate_Matrix( &(workspace->H), system->N, Htop );
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "estimated storage - Htop: %d\n", Htop );
- fprintf( stderr, "memory allocated: H = %ldMB\n",
- Htop * sizeof(sparse_matrix_entry) / (1024*1024) );
+ fprintf( stderr, "estimated storage - Htop: %d\n", Htop );
+ fprintf( stderr, "memory allocated: H = %ldMB\n",
+ Htop * sizeof(sparse_matrix_entry) / (1024 * 1024) );
#endif
- workspace->num_H = 0;
- if( control->hb_cut > 0 ) {
- /* init H indexes */
- for( i = 0; i < system->N; ++i )
- if( system->reaxprm.sbp[ system->atoms[i].type ].p_hbond == 1 ) // H atom
- workspace->hbond_index[i] = workspace->num_H++;
- else workspace->hbond_index[i] = -1;
-
- Allocate_HBond_List( system->N, workspace->num_H, workspace->hbond_index,
- hb_top, (*lists)+HBONDS );
- num_hbonds = hb_top[system->N-1];
+ workspace->num_H = 0;
+ if ( control->hb_cut > 0 )
+ {
+ /* init H indexes */
+ for ( i = 0; i < system->N; ++i )
+ if ( system->reaxprm.sbp[ system->atoms[i].type ].p_hbond == 1 ) // H atom
+ workspace->hbond_index[i] = workspace->num_H++;
+ else workspace->hbond_index[i] = -1;
+
+ Allocate_HBond_List( system->N, workspace->num_H, workspace->hbond_index,
+ hb_top, (*lists) + HBONDS );
+ num_hbonds = hb_top[system->N - 1];
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "estimated storage - num_hbonds: %d\n", num_hbonds );
- fprintf( stderr, "memory allocated: hbonds = %ldMB\n",
- num_hbonds * sizeof(hbond_data) / (1024*1024) );
+ fprintf( stderr, "estimated storage - num_hbonds: %d\n", num_hbonds );
+ fprintf( stderr, "memory allocated: hbonds = %ldMB\n",
+ num_hbonds * sizeof(hbond_data) / (1024 * 1024) );
#endif
- }
-
- /* bonds list */
- Allocate_Bond_List( system->N, bond_top, (*lists)+BONDS );
- num_bonds = bond_top[system->N-1];
+ }
+
+ /* bonds list */
+ Allocate_Bond_List( system->N, bond_top, (*lists) + BONDS );
+ num_bonds = bond_top[system->N - 1];
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "estimated storage - num_bonds: %d\n", num_bonds );
- fprintf( stderr, "memory allocated: bonds = %ldMB\n",
- num_bonds * sizeof(bond_data) / (1024*1024) );
+ fprintf( stderr, "estimated storage - num_bonds: %d\n", num_bonds );
+ fprintf( stderr, "memory allocated: bonds = %ldMB\n",
+ num_bonds * sizeof(bond_data) / (1024 * 1024) );
#endif
//fprintf (stderr, " **** sizeof 3 body : %d \n", sizeof (three_body_interaction_data));
//fprintf (stderr, " **** num_3body : %d \n", num_3body);
//fprintf (stderr, " **** num_bonds : %d \n", num_bonds);
- /* 3bodies list */
- if(!Make_List(num_bonds, num_3body, TYP_THREE_BODY, (*lists)+THREE_BODIES)) {
- fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
- exit( INIT_ERR );
- }
+ /* 3bodies list */
+ if (!Make_List(num_bonds, num_3body, TYP_THREE_BODY, (*lists) + THREE_BODIES))
+ {
+ fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
+ exit( INIT_ERR );
+ }
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "estimated storage - num_3body: %d\n", num_3body );
- fprintf( stderr, "memory allocated: 3-body = %ldMB\n",
- num_3body * sizeof(three_body_interaction_data) / (1024*1024) );
+ fprintf( stderr, "estimated storage - num_3body: %d\n", num_3body );
+ fprintf( stderr, "memory allocated: 3-body = %ldMB\n",
+ num_3body * sizeof(three_body_interaction_data) / (1024 * 1024) );
#endif
#ifdef TEST_FORCES
- if(!Make_List( system->N, num_bonds * 8, TYP_DDELTA, (*lists) + DDELTA )) {
- fprintf( stderr, "Problem in initializing dDelta list. Terminating!\n" );
- exit( INIT_ERR );
- }
-
- if( !Make_List( num_bonds, num_bonds*MAX_BONDS*3, TYP_DBO, (*lists)+DBO ) ) {
- fprintf( stderr, "Problem in initializing dBO list. Terminating!\n" );
- exit( INIT_ERR );
- }
+ if (!Make_List( system->N, num_bonds * 8, TYP_DDELTA, (*lists) + DDELTA ))
+ {
+ fprintf( stderr, "Problem in initializing dDelta list. Terminating!\n" );
+ exit( INIT_ERR );
+ }
+
+ if ( !Make_List( num_bonds, num_bonds * MAX_BONDS * 3, TYP_DBO, (*lists) + DBO ) )
+ {
+ fprintf( stderr, "Problem in initializing dBO list. Terminating!\n" );
+ exit( INIT_ERR );
+ }
#endif
- free( hb_top );
- free( bond_top );
+ free( hb_top );
+ free( bond_top );
}
-void Init_Out_Controls(reax_system *system, control_params *control,
- static_storage *workspace, output_controls *out_control)
+void Init_Out_Controls(reax_system *system, control_params *control,
+ static_storage *workspace, output_controls *out_control)
{
- char temp[1000];
+ char temp[1000];
- /* Init trajectory file */
- if( out_control->write_steps > 0 ) {
+ /* Init trajectory file */
+ if ( out_control->write_steps > 0 )
+ {
+ strcpy( temp, control->sim_name );
+ strcat( temp, ".trj" );
+ out_control->trj = fopen( temp, "w" );
+ out_control->write_header( system, control, workspace, out_control );
+ }
+
+ if ( out_control->energy_update_freq > 0 )
+ {
+ /* Init out file */
+ strcpy( temp, control->sim_name );
+ strcat( temp, ".out" );
+ out_control->out = fopen( temp, "w" );
+ fprintf( out_control->out, "%-6s%16s%16s%16s%11s%11s%13s%13s%13s\n",
+ "step", "total energy", "poten. energy", "kin. energy",
+ "temp.", "target", "volume", "press.", "target" );
+ fflush( out_control->out );
+
+ /* Init potentials file */
+ strcpy( temp, control->sim_name );
+ strcat( temp, ".pot" );
+ out_control->pot = fopen( temp, "w" );
+ fprintf( out_control->pot,
+ "%-6s%13s%13s%13s%13s%13s%13s%13s%13s%13s%13s%13s\n",
+ "step", "ebond", "eatom", "elp", "eang", "ecoa", "ehb",
+ "etor", "econj", "evdw", "ecoul", "epol" );
+ fflush( out_control->pot );
+
+ /* Init log file */
+ strcpy( temp, control->sim_name );
+ strcat( temp, ".log" );
+ out_control->log = fopen( temp, "w" );
+ fprintf( out_control->log, "%-6s%10s%10s%10s%10s%10s%10s%10s\n",
+ "step", "total", "neighbors", "init", "bonded",
+ "nonbonded", "QEq", "matvec" );
+ }
+
+ /* Init pressure file */
+ if ( control->ensemble == NPT ||
+ control->ensemble == iNPT ||
+ control->ensemble == sNPT )
+ {
+ strcpy( temp, control->sim_name );
+ strcat( temp, ".prs" );
+ out_control->prs = fopen( temp, "w" );
+ fprintf( out_control->prs, "%-6s%13s%13s%13s%13s%13s%13s%13s%13s\n",
+ "step", "norm_x", "norm_y", "norm_z",
+ "press_x", "press_y", "press_z", "target_p", "volume" );
+ fflush( out_control->prs );
+ }
+
+ /* Init molecular analysis file */
+ if ( control->molec_anal )
+ {
+ sprintf( temp, "%s.mol", control->sim_name );
+ out_control->mol = fopen( temp, "w" );
+ if ( control->num_ignored )
+ {
+ sprintf( temp, "%s.ign", control->sim_name );
+ out_control->ign = fopen( temp, "w" );
+ }
+ }
+
+ /* Init electric dipole moment analysis file */
+ if ( control->dipole_anal )
+ {
+ strcpy( temp, control->sim_name );
+ strcat( temp, ".dpl" );
+ out_control->dpl = fopen( temp, "w" );
+ fprintf( out_control->dpl,
+ "Step Molecule Count Avg. Dipole Moment Norm\n" );
+ fflush( out_control->dpl );
+ }
+
+ /* Init diffusion coef analysis file */
+ if ( control->diffusion_coef )
+ {
+ strcpy( temp, control->sim_name );
+ strcat( temp, ".drft" );
+ out_control->drft = fopen( temp, "w" );
+ fprintf( out_control->drft, "Step Type Count Avg Squared Disp\n" );
+ fflush( out_control->drft );
+ }
+
+
+#ifdef TEST_ENERGY
+ /* open bond energy file */
strcpy( temp, control->sim_name );
- strcat( temp, ".trj" );
- out_control->trj = fopen( temp, "w" );
- out_control->write_header( system, control, workspace, out_control );
- }
+ strcat( temp, ".ebond" );
+ out_control->ebond = fopen( temp, "w" );
- if( out_control->energy_update_freq > 0 ) {
- /* Init out file */
+ /* open lone-pair energy file */
strcpy( temp, control->sim_name );
- strcat( temp, ".out" );
- out_control->out = fopen( temp, "w" );
- fprintf( out_control->out, "%-6s%16s%16s%16s%11s%11s%13s%13s%13s\n",
- "step", "total energy", "poten. energy", "kin. energy",
- "temp.", "target", "volume", "press.", "target" );
- fflush( out_control->out );
-
- /* Init potentials file */
+ strcat( temp, ".elp" );
+ out_control->elp = fopen( temp, "w" );
+
+ /* open overcoordination energy file */
+ strcpy( temp, control->sim_name );
+ strcat( temp, ".eov" );
+ out_control->eov = fopen( temp, "w" );
+
+ /* open undercoordination energy file */
strcpy( temp, control->sim_name );
- strcat( temp, ".pot" );
- out_control->pot = fopen( temp, "w" );
- fprintf( out_control->pot,
- "%-6s%13s%13s%13s%13s%13s%13s%13s%13s%13s%13s%13s\n",
- "step", "ebond", "eatom", "elp", "eang", "ecoa", "ehb",
- "etor", "econj", "evdw","ecoul", "epol" );
- fflush( out_control->pot );
-
- /* Init log file */
+ strcat( temp, ".eun" );
+ out_control->eun = fopen( temp, "w" );
+
+ /* open angle energy file */
strcpy( temp, control->sim_name );
- strcat( temp, ".log" );
- out_control->log = fopen( temp, "w" );
- fprintf( out_control->log, "%-6s%10s%10s%10s%10s%10s%10s%10s\n",
- "step", "total", "neighbors", "init", "bonded",
- "nonbonded", "QEq", "matvec" );
- }
-
- /* Init pressure file */
- if( control->ensemble == NPT ||
- control->ensemble == iNPT ||
- control->ensemble == sNPT ) {
+ strcat( temp, ".eval" );
+ out_control->eval = fopen( temp, "w" );
+
+ /* open penalty energy file */
strcpy( temp, control->sim_name );
- strcat( temp, ".prs" );
- out_control->prs = fopen( temp, "w" );
- fprintf( out_control->prs, "%-6s%13s%13s%13s%13s%13s%13s%13s%13s\n",
- "step", "norm_x", "norm_y", "norm_z",
- "press_x", "press_y", "press_z", "target_p", "volume" );
- fflush( out_control->prs );
- }
-
- /* Init molecular analysis file */
- if( control->molec_anal ) {
- sprintf( temp, "%s.mol", control->sim_name );
- out_control->mol = fopen( temp, "w" );
- if( control->num_ignored ) {
- sprintf( temp, "%s.ign", control->sim_name );
- out_control->ign = fopen( temp, "w" );
- }
- }
-
- /* Init electric dipole moment analysis file */
- if( control->dipole_anal ) {
+ strcat( temp, ".epen" );
+ out_control->epen = fopen( temp, "w" );
+
+ /* open coalition energy file */
strcpy( temp, control->sim_name );
- strcat( temp, ".dpl" );
- out_control->dpl = fopen( temp, "w" );
- fprintf( out_control->dpl,
- "Step Molecule Count Avg. Dipole Moment Norm\n" );
- fflush( out_control->dpl );
- }
-
- /* Init diffusion coef analysis file */
- if( control->diffusion_coef ) {
+ strcat( temp, ".ecoa" );
+ out_control->ecoa = fopen( temp, "w" );
+
+ /* open hydrogen bond energy file */
strcpy( temp, control->sim_name );
- strcat( temp, ".drft" );
- out_control->drft = fopen( temp, "w" );
- fprintf( out_control->drft, "Step Type Count Avg Squared Disp\n" );
- fflush( out_control->drft );
- }
+ strcat( temp, ".ehb" );
+ out_control->ehb = fopen( temp, "w" );
+ /* open torsion energy file */
+ strcpy( temp, control->sim_name );
+ strcat( temp, ".etor" );
+ out_control->etor = fopen( temp, "w" );
-#ifdef TEST_ENERGY
- /* open bond energy file */
- strcpy( temp, control->sim_name );
- strcat( temp, ".ebond" );
- out_control->ebond = fopen( temp, "w" );
-
- /* open lone-pair energy file */
- strcpy( temp, control->sim_name );
- strcat( temp, ".elp" );
- out_control->elp = fopen( temp, "w" );
-
- /* open overcoordination energy file */
- strcpy( temp, control->sim_name );
- strcat( temp, ".eov" );
- out_control->eov = fopen( temp, "w" );
-
- /* open undercoordination energy file */
- strcpy( temp, control->sim_name );
- strcat( temp, ".eun" );
- out_control->eun = fopen( temp, "w" );
-
- /* open angle energy file */
- strcpy( temp, control->sim_name );
- strcat( temp, ".eval" );
- out_control->eval = fopen( temp, "w" );
-
- /* open penalty energy file */
- strcpy( temp, control->sim_name );
- strcat( temp, ".epen" );
- out_control->epen = fopen( temp, "w" );
-
- /* open coalition energy file */
- strcpy( temp, control->sim_name );
- strcat( temp, ".ecoa" );
- out_control->ecoa = fopen( temp, "w" );
-
- /* open hydrogen bond energy file */
- strcpy( temp, control->sim_name );
- strcat( temp, ".ehb" );
- out_control->ehb = fopen( temp, "w" );
-
- /* open torsion energy file */
- strcpy( temp, control->sim_name );
- strcat( temp, ".etor" );
- out_control->etor = fopen( temp, "w" );
-
- /* open conjugation energy file */
- strcpy( temp, control->sim_name );
- strcat( temp, ".econ" );
- out_control->econ = fopen( temp, "w" );
-
- /* open vdWaals energy file */
- strcpy( temp, control->sim_name );
- strcat( temp, ".evdw" );
- out_control->evdw = fopen( temp, "w" );
-
- /* open coulomb energy file */
- strcpy( temp, control->sim_name );
- strcat( temp, ".ecou" );
- out_control->ecou = fopen( temp, "w" );
+ /* open conjugation energy file */
+ strcpy( temp, control->sim_name );
+ strcat( temp, ".econ" );
+ out_control->econ = fopen( temp, "w" );
+
+ /* open vdWaals energy file */
+ strcpy( temp, control->sim_name );
+ strcat( temp, ".evdw" );
+ out_control->evdw = fopen( temp, "w" );
+
+ /* open coulomb energy file */
+ strcpy( temp, control->sim_name );
+ strcat( temp, ".ecou" );
+ out_control->ecou = fopen( temp, "w" );
#endif
#ifdef TEST_FORCES
- /* open bond orders file */
- strcpy( temp, control->sim_name );
- strcat( temp, ".fbo" );
- out_control->fbo = fopen( temp, "w" );
-
- /* open bond orders derivatives file */
- strcpy( temp, control->sim_name );
- strcat( temp, ".fdbo" );
- out_control->fdbo = fopen( temp, "w" );
-
- /* open bond forces file */
- strcpy( temp, control->sim_name );
- strcat( temp, ".fbond" );
- out_control->fbond = fopen( temp, "w" );
-
- /* open lone-pair forces file */
- strcpy( temp, control->sim_name );
- strcat( temp, ".flp" );
- out_control->flp = fopen( temp, "w" );
-
- /* open overcoordination forces file */
- strcpy( temp, control->sim_name );
- strcat( temp, ".fatom" );
- out_control->fatom = fopen( temp, "w" );
-
- /* open angle forces file */
- strcpy( temp, control->sim_name );
- strcat( temp, ".f3body" );
- out_control->f3body = fopen( temp, "w" );
-
- /* open hydrogen bond forces file */
- strcpy( temp, control->sim_name );
- strcat( temp, ".fhb" );
- out_control->fhb = fopen( temp, "w" );
-
- /* open torsion forces file */
- strcpy( temp, control->sim_name );
- strcat( temp, ".f4body" );
- out_control->f4body = fopen( temp, "w" );
-
- /* open nonbonded forces file */
- strcpy( temp, control->sim_name );
- strcat( temp, ".fnonb" );
- out_control->fnonb = fopen( temp, "w" );
-
- /* open total force file */
- strcpy( temp, control->sim_name );
- strcat( temp, ".ftot" );
- out_control->ftot = fopen( temp, "w" );
-
- /* open coulomb forces file */
- strcpy( temp, control->sim_name );
- strcat( temp, ".ftot2" );
- out_control->ftot2 = fopen( temp, "w" );
+ /* open bond orders file */
+ strcpy( temp, control->sim_name );
+ strcat( temp, ".fbo" );
+ out_control->fbo = fopen( temp, "w" );
+
+ /* open bond orders derivatives file */
+ strcpy( temp, control->sim_name );
+ strcat( temp, ".fdbo" );
+ out_control->fdbo = fopen( temp, "w" );
+
+ /* open bond forces file */
+ strcpy( temp, control->sim_name );
+ strcat( temp, ".fbond" );
+ out_control->fbond = fopen( temp, "w" );
+
+ /* open lone-pair forces file */
+ strcpy( temp, control->sim_name );
+ strcat( temp, ".flp" );
+ out_control->flp = fopen( temp, "w" );
+
+ /* open overcoordination forces file */
+ strcpy( temp, control->sim_name );
+ strcat( temp, ".fatom" );
+ out_control->fatom = fopen( temp, "w" );
+
+ /* open angle forces file */
+ strcpy( temp, control->sim_name );
+ strcat( temp, ".f3body" );
+ out_control->f3body = fopen( temp, "w" );
+
+ /* open hydrogen bond forces file */
+ strcpy( temp, control->sim_name );
+ strcat( temp, ".fhb" );
+ out_control->fhb = fopen( temp, "w" );
+
+ /* open torsion forces file */
+ strcpy( temp, control->sim_name );
+ strcat( temp, ".f4body" );
+ out_control->f4body = fopen( temp, "w" );
+
+ /* open nonbonded forces file */
+ strcpy( temp, control->sim_name );
+ strcat( temp, ".fnonb" );
+ out_control->fnonb = fopen( temp, "w" );
+
+ /* open total force file */
+ strcpy( temp, control->sim_name );
+ strcat( temp, ".ftot" );
+ out_control->ftot = fopen( temp, "w" );
+
+ /* open coulomb forces file */
+ strcpy( temp, control->sim_name );
+ strcat( temp, ".ftot2" );
+ out_control->ftot2 = fopen( temp, "w" );
#endif
-/* Error handling */
- /* if ( out_control->out == NULL || out_control->pot == NULL ||
- out_control->log == NULL || out_control->mol == NULL ||
- out_control->dpl == NULL || out_control->drft == NULL ||
- out_control->pdb == NULL )
- {
- fprintf( stderr, "FILE OPEN ERROR. TERMINATING..." );
- exit( CANNOT_OPEN_OUTFILE );
- }*/
+ /* Error handling */
+ /* if ( out_control->out == NULL || out_control->pot == NULL ||
+ out_control->log == NULL || out_control->mol == NULL ||
+ out_control->dpl == NULL || out_control->drft == NULL ||
+ out_control->pdb == NULL )
+ {
+ fprintf( stderr, "FILE OPEN ERROR. TERMINATING..." );
+ exit( CANNOT_OPEN_OUTFILE );
+ }*/
}
-void Initialize(reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace, list **lists,
- output_controls *out_control, evolve_function *Evolve)
+void Initialize(reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace, list **lists,
+ output_controls *out_control, evolve_function *Evolve)
{
- real start, end;
- Randomize();
+ real start, end;
+ Randomize();
- Init_System( system, control, data );
+ Init_System( system, control, data );
- Init_Simulation_Data( system, control, data, out_control, Evolve );
+ Init_Simulation_Data( system, control, data, out_control, Evolve );
- Init_Workspace( system, control, workspace );
-
- Init_Lists( system, control, data, workspace, lists, out_control );
+ Init_Workspace( system, control, workspace );
- Init_Out_Controls( system, control, workspace, out_control );
+ Init_Lists( system, control, data, workspace, lists, out_control );
- /* These are done in forces.c, only forces.c can see all those functions */
- Init_Bonded_Force_Functions( control );
+ Init_Out_Controls( system, control, workspace, out_control );
+
+ /* These are done in forces.c, only forces.c can see all those functions */
+ Init_Bonded_Force_Functions( control );
#ifdef TEST_FORCES
- Init_Force_Test_Functions( );
+ Init_Force_Test_Functions( );
#endif
- if( control->tabulate ) {
- start = Get_Time ();
- Make_LR_Lookup_Table( system, control );
- end = Get_Timing_Info (start);
+ if ( control->tabulate )
+ {
+ start = Get_Time ();
+ Make_LR_Lookup_Table( system, control );
+ end = Get_Timing_Info (start);
- //fprintf (stderr, "Time for LR Lookup Table calculation is %f \n", end );
- }
+ //fprintf (stderr, "Time for LR Lookup Table calculation is %f \n", end );
+ }
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "data structures have been initialized...\n" );
+ fprintf( stderr, "data structures have been initialized...\n" );
#endif
}
diff --git a/puremd_rc_1003/sPuReMD/init_md.h b/puremd_rc_1003/sPuReMD/init_md.h
index 52b78a82cbcacadf50f4f145c47fa36eddb1c358..3fc59053a9d569623d0004e7b5b9a86a6cbf3cb0 100644
--- a/puremd_rc_1003/sPuReMD/init_md.h
+++ b/puremd_rc_1003/sPuReMD/init_md.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -25,6 +25,6 @@
#include "mytypes.h"
void Initialize( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls*, evolve_function* );
+ static_storage*, list**, output_controls*, evolve_function* );
#endif
diff --git a/puremd_rc_1003/sPuReMD/integrate.c b/puremd_rc_1003/sPuReMD/integrate.c
index 6316ad868ca7281f768b259bc96382b6455dd457..142863cad18291a04f4f56fc364c73cf8fdabd3b 100644
--- a/puremd_rc_1003/sPuReMD/integrate.c
+++ b/puremd_rc_1003/sPuReMD/integrate.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -35,382 +35,397 @@
-void Velocity_Verlet_NVE(reax_system* system, control_params* control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+void Velocity_Verlet_NVE(reax_system* system, control_params* control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int i, steps, renbr;
- real inv_m, dt, dt_sqr;
- rvec dx;
-
- dt = control->dt;
- dt_sqr = SQR(dt);
- steps = data->step - data->prev_steps;
- renbr = (steps % control->reneighbor == 0);
-#if defined(DEBUG_FOCUS)
- fprintf( stderr, "step%d: ", data->step );
+ int i, steps, renbr;
+ real inv_m, dt, dt_sqr;
+ rvec dx;
+
+ dt = control->dt;
+ dt_sqr = SQR(dt);
+ steps = data->step - data->prev_steps;
+ renbr = (steps % control->reneighbor == 0);
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "step%d: ", data->step );
#endif
- for( i = 0; i < system->N; i++ ) {
- inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
-
- rvec_ScaledSum( dx, dt, system->atoms[i].v,
- 0.5 * dt_sqr * -F_CONV * inv_m, system->atoms[i].f );
- Inc_on_T3( system->atoms[i].x, dx, &( system->box ) );
-
- rvec_ScaledAdd( system->atoms[i].v,
- 0.5 * dt * -F_CONV * inv_m, system->atoms[i].f );
- }
-#if defined(DEBUG_FOCUS)
- fprintf( stderr, "verlet1 - ");
+ for ( i = 0; i < system->N; i++ )
+ {
+ inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
+
+ rvec_ScaledSum( dx, dt, system->atoms[i].v,
+ 0.5 * dt_sqr * -F_CONV * inv_m, system->atoms[i].f );
+ Inc_on_T3( system->atoms[i].x, dx, &( system->box ) );
+
+ rvec_ScaledAdd( system->atoms[i].v,
+ 0.5 * dt * -F_CONV * inv_m, system->atoms[i].f );
+ }
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "verlet1 - ");
#endif
- Reallocate( system, workspace, lists, renbr );
- Reset( system, control, data, workspace, lists );
- if( renbr )
- Generate_Neighbor_Lists( system, control, data, workspace,
- lists, out_control );
- Compute_Forces( system, control, data, workspace, lists, out_control );
-
- for( i = 0; i < system->N; i++ ) {
- inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
- rvec_ScaledAdd( system->atoms[i].v,
- 0.5 * dt * -F_CONV * inv_m, system->atoms[i].f );
- }
-#if defined(DEBUG_FOCUS)
- fprintf( stderr, "verlet2\n");
+ Reallocate( system, workspace, lists, renbr );
+ Reset( system, control, data, workspace, lists );
+ if ( renbr )
+ Generate_Neighbor_Lists( system, control, data, workspace,
+ lists, out_control );
+ Compute_Forces( system, control, data, workspace, lists, out_control );
+
+ for ( i = 0; i < system->N; i++ )
+ {
+ inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
+ rvec_ScaledAdd( system->atoms[i].v,
+ 0.5 * dt * -F_CONV * inv_m, system->atoms[i].f );
+ }
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "verlet2\n");
#endif
}
-void Velocity_Verlet_Nose_Hoover_NVT_Klein(reax_system* system,
- control_params* control,
- simulation_data *data,
- static_storage *workspace,
- list **lists,
- output_controls *out_control )
+void Velocity_Verlet_Nose_Hoover_NVT_Klein(reax_system* system,
+ control_params* control,
+ simulation_data *data,
+ static_storage *workspace,
+ list **lists,
+ output_controls *out_control )
{
- int i, itr, steps, renbr;
- real inv_m, coef_v, dt, dt_sqr;
- real E_kin_new, G_xi_new, v_xi_new, v_xi_old;
- rvec dx;
- thermostat *therm;
-
- dt = control->dt;
- dt_sqr = SQR( dt );
- therm = &( data->therm );
- steps = data->step - data->prev_steps;
- renbr = (steps % control->reneighbor == 0);
+ int i, itr, steps, renbr;
+ real inv_m, coef_v, dt, dt_sqr;
+ real E_kin_new, G_xi_new, v_xi_new, v_xi_old;
+ rvec dx;
+ thermostat *therm;
+
+ dt = control->dt;
+ dt_sqr = SQR( dt );
+ therm = &( data->therm );
+ steps = data->step - data->prev_steps;
+ renbr = (steps % control->reneighbor == 0);
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "step%d: ", data->step );
+ fprintf( stderr, "step%d: ", data->step );
#endif
-
- /* Compute x(t + dt) and copy old forces */
- for (i=0; i < system->N; i++) {
- inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
-
- rvec_ScaledSum( dx, dt - 0.5 * dt_sqr * therm->v_xi, system->atoms[i].v,
- 0.5 * dt_sqr * inv_m * -F_CONV, system->atoms[i].f );
-
- Inc_on_T3( system->atoms[i].x, dx, &(system->box) );
-
- rvec_Copy( workspace->f_old[i], system->atoms[i].f );
- }
- /* Compute xi(t + dt) */
- therm->xi += ( therm->v_xi * dt + 0.5 * dt_sqr * therm->G_xi );
+
+ /* Compute x(t + dt) and copy old forces */
+ for (i = 0; i < system->N; i++)
+ {
+ inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
+
+ rvec_ScaledSum( dx, dt - 0.5 * dt_sqr * therm->v_xi, system->atoms[i].v,
+ 0.5 * dt_sqr * inv_m * -F_CONV, system->atoms[i].f );
+
+ Inc_on_T3( system->atoms[i].x, dx, &(system->box) );
+
+ rvec_Copy( workspace->f_old[i], system->atoms[i].f );
+ }
+ /* Compute xi(t + dt) */
+ therm->xi += ( therm->v_xi * dt + 0.5 * dt_sqr * therm->G_xi );
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "verlet1 - " );
+ fprintf( stderr, "verlet1 - " );
#endif
-
- Reallocate( system, workspace, lists, renbr );
- Reset( system, control, data, workspace, lists );
- if( renbr )
- Generate_Neighbor_Lists( system, control, data, workspace,
- lists, out_control );
- /* Calculate Forces at time (t + dt) */
- Compute_Forces( system,control,data, workspace, lists, out_control );
-
- /* Compute iteration constants for each atom's velocity */
- for( i = 0; i < system->N; ++i ) {
- inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
-
- rvec_Scale( workspace->v_const[i],
- 1.0 - 0.5 * dt * therm->v_xi, system->atoms[i].v );
- rvec_ScaledAdd( workspace->v_const[i],
- 0.5 * dt * inv_m * -F_CONV, workspace->f_old[i] );
- rvec_ScaledAdd( workspace->v_const[i],
- 0.5 * dt * inv_m * -F_CONV, system->atoms[i].f );
+
+ Reallocate( system, workspace, lists, renbr );
+ Reset( system, control, data, workspace, lists );
+ if ( renbr )
+ Generate_Neighbor_Lists( system, control, data, workspace,
+ lists, out_control );
+ /* Calculate Forces at time (t + dt) */
+ Compute_Forces( system, control, data, workspace, lists, out_control );
+
+ /* Compute iteration constants for each atom's velocity */
+ for ( i = 0; i < system->N; ++i )
+ {
+ inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
+
+ rvec_Scale( workspace->v_const[i],
+ 1.0 - 0.5 * dt * therm->v_xi, system->atoms[i].v );
+ rvec_ScaledAdd( workspace->v_const[i],
+ 0.5 * dt * inv_m * -F_CONV, workspace->f_old[i] );
+ rvec_ScaledAdd( workspace->v_const[i],
+ 0.5 * dt * inv_m * -F_CONV, system->atoms[i].f );
#if defined(DEBUG)
- fprintf( stderr, "atom%d: inv_m=%f, C1=%f, C2=%f, v_const=%f %f %f\n",
- i, inv_m, 1.0 - 0.5 * dt * therm->v_xi,
- 0.5 * dt * inv_m * -F_CONV, workspace->v_const[i][0],
- workspace->v_const[i][1], workspace->v_const[i][2] );
+ fprintf( stderr, "atom%d: inv_m=%f, C1=%f, C2=%f, v_const=%f %f %f\n",
+ i, inv_m, 1.0 - 0.5 * dt * therm->v_xi,
+ 0.5 * dt * inv_m * -F_CONV, workspace->v_const[i][0],
+ workspace->v_const[i][1], workspace->v_const[i][2] );
#endif
- }
-
- v_xi_new = therm->v_xi_old + 2.0 * dt * therm->G_xi;
- E_kin_new = G_xi_new = v_xi_old = 0;
- itr = 0;
- do {
- itr++;
-
- /* new values become old in this iteration */
- v_xi_old = v_xi_new;
- coef_v = 1.0 / (1.0 + 0.5 * dt * v_xi_old);
- E_kin_new = 0;
- for( i = 0; i < system->N; ++i ) {
- rvec_Scale( system->atoms[i].v, coef_v, workspace->v_const[i] );
-
- E_kin_new += ( 0.5*system->reaxprm.sbp[system->atoms[i].type].mass *
- rvec_Dot( system->atoms[i].v, system->atoms[i].v ) );
+ }
+
+ v_xi_new = therm->v_xi_old + 2.0 * dt * therm->G_xi;
+ E_kin_new = G_xi_new = v_xi_old = 0;
+ itr = 0;
+ do
+ {
+ itr++;
+
+ /* new values become old in this iteration */
+ v_xi_old = v_xi_new;
+ coef_v = 1.0 / (1.0 + 0.5 * dt * v_xi_old);
+ E_kin_new = 0;
+ for ( i = 0; i < system->N; ++i )
+ {
+ rvec_Scale( system->atoms[i].v, coef_v, workspace->v_const[i] );
+
+ E_kin_new += ( 0.5 * system->reaxprm.sbp[system->atoms[i].type].mass *
+ rvec_Dot( system->atoms[i].v, system->atoms[i].v ) );
#if defined(DEBUG)
- fprintf( stderr, "itr%d-atom%d: coef_v = %f, v_xi_old = %f\n",
- itr, i, coef_v, v_xi_old );
+ fprintf( stderr, "itr%d-atom%d: coef_v = %f, v_xi_old = %f\n",
+ itr, i, coef_v, v_xi_old );
#endif
- }
-
- G_xi_new = control->Tau_T * ( 2.0 * E_kin_new -
- data->N_f * K_B * control->T );
- v_xi_new = therm->v_xi + 0.5 * dt * ( therm->G_xi + G_xi_new );
+ }
+
+ G_xi_new = control->Tau_T * ( 2.0 * E_kin_new -
+ data->N_f * K_B * control->T );
+ v_xi_new = therm->v_xi + 0.5 * dt * ( therm->G_xi + G_xi_new );
#if defined(DEBUG)
- fprintf( stderr, "itr%d: G_xi_new = %f, v_xi_new = %f, v_xi_old = %f\n",
- itr, G_xi_new, v_xi_new, v_xi_old );
+ fprintf( stderr, "itr%d: G_xi_new = %f, v_xi_new = %f, v_xi_old = %f\n",
+ itr, G_xi_new, v_xi_new, v_xi_old );
+#endif
+ }
+ while ( fabs(v_xi_new - v_xi_old ) > 1e-5 );
+
+ therm->v_xi_old = therm->v_xi;
+ therm->v_xi = v_xi_new;
+ therm->G_xi = G_xi_new;
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "vel scale\n" );
#endif
- }
- while( fabs(v_xi_new - v_xi_old ) > 1e-5 );
-
- therm->v_xi_old = therm->v_xi;
- therm->v_xi = v_xi_new;
- therm->G_xi = G_xi_new;
-#if defined(DEBUG_FOCUS)
- fprintf( stderr,"vel scale\n" );
-#endif
}
-/* uses Berendsen-type coupling for both T and P.
- All box dimensions are scaled by the same amount,
+/* uses Berendsen-type coupling for both T and P.
+ All box dimensions are scaled by the same amount,
there is no change in the angles between axes. */
-void Velocity_Verlet_Berendsen_Isotropic_NPT( reax_system* system,
- control_params* control,
- simulation_data *data,
- static_storage *workspace,
- list **lists,
- output_controls *out_control )
+void Velocity_Verlet_Berendsen_Isotropic_NPT( reax_system* system,
+ control_params* control,
+ simulation_data *data,
+ static_storage *workspace,
+ list **lists,
+ output_controls *out_control )
{
- int i, steps, renbr;
- real inv_m, dt, lambda, mu;
- rvec dx;
+ int i, steps, renbr;
+ real inv_m, dt, lambda, mu;
+ rvec dx;
- dt = control->dt;
- steps = data->step - data->prev_steps;
- renbr = (steps % control->reneighbor == 0);
+ dt = control->dt;
+ steps = data->step - data->prev_steps;
+ renbr = (steps % control->reneighbor == 0);
#if defined(DEBUG_FOCUS)
- //fprintf( out_control->prs,
- // "tau_t: %g tau_p: %g dt/tau_t: %g dt/tau_p: %g\n",
- //control->Tau_T, control->Tau_P, dt / control->Tau_T, dt / control->Tau_P );
- fprintf( stderr, "step %d: ", data->step );
+ //fprintf( out_control->prs,
+ // "tau_t: %g tau_p: %g dt/tau_t: %g dt/tau_p: %g\n",
+ //control->Tau_T, control->Tau_P, dt / control->Tau_T, dt / control->Tau_P );
+ fprintf( stderr, "step %d: ", data->step );
#endif
- /* velocity verlet, 1st part */
- for( i = 0; i < system->N; i++ ) {
- inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
- /* Compute x(t + dt) */
- rvec_ScaledSum( dx, dt, system->atoms[i].v,
- 0.5 * -F_CONV * inv_m * SQR(dt), system->atoms[i].f );
- Inc_on_T3( system->atoms[i].x, dx, &(system->box) );
- /* Compute v(t + dt/2) */
- rvec_ScaledAdd( system->atoms[i].v,
- 0.5 * -F_CONV * inv_m * dt, system->atoms[i].f );
- /*fprintf( stderr, "%6d %15.8f %15.8f %15.8f %15.8f %15.8f %15.8f\n",
- workspace->orig_id[i],
- system->atoms[i].x[0], system->atoms[i].x[1], system->atoms[i].x[2],
- 0.5 * SQR(dt) * -F_CONV * inv_m * system->atoms[i].f[0],
- 0.5 * SQR(dt) * -F_CONV * inv_m * system->atoms[i].f[1],
- 0.5 * SQR(dt) * -F_CONV * inv_m * system->atoms[i].f[2] ); */
- }
-#if defined(DEBUG_FOCUS)
- fprintf( stderr, "verlet1 - " );
+ /* velocity verlet, 1st part */
+ for ( i = 0; i < system->N; i++ )
+ {
+ inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
+ /* Compute x(t + dt) */
+ rvec_ScaledSum( dx, dt, system->atoms[i].v,
+ 0.5 * -F_CONV * inv_m * SQR(dt), system->atoms[i].f );
+ Inc_on_T3( system->atoms[i].x, dx, &(system->box) );
+ /* Compute v(t + dt/2) */
+ rvec_ScaledAdd( system->atoms[i].v,
+ 0.5 * -F_CONV * inv_m * dt, system->atoms[i].f );
+ /*fprintf( stderr, "%6d %15.8f %15.8f %15.8f %15.8f %15.8f %15.8f\n",
+ workspace->orig_id[i],
+ system->atoms[i].x[0], system->atoms[i].x[1], system->atoms[i].x[2],
+ 0.5 * SQR(dt) * -F_CONV * inv_m * system->atoms[i].f[0],
+ 0.5 * SQR(dt) * -F_CONV * inv_m * system->atoms[i].f[1],
+ 0.5 * SQR(dt) * -F_CONV * inv_m * system->atoms[i].f[2] ); */
+ }
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "verlet1 - " );
#endif
- Reallocate( system, workspace, lists, renbr );
- Reset( system, control, data, workspace, lists );
- if( renbr ) {
- Update_Grid( system );
- Generate_Neighbor_Lists( system, control, data, workspace,
- lists, out_control );
- }
- Compute_Forces( system, control, data, workspace, lists, out_control );
-
- /* velocity verlet, 2nd part */
- for( i = 0; i < system->N; i++ ) {
- inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
- /* Compute v(t + dt) */
- rvec_ScaledAdd( system->atoms[i].v,
- 0.5 * dt * -F_CONV * inv_m, system->atoms[i].f );
- /* fprintf( stderr, "%6d %15f %15f %15f %15.8f %15.8f %15.8f\n",
- workspace->orig_id[i],
- system->atoms[i].v[0], system->atoms[i].v[1], system->atoms[i].v[2],
- 0.5 * dt * -F_CONV * inv_m * system->atoms[i].f[0],
- 0.5 * dt * -F_CONV * inv_m * system->atoms[i].f[1],
- 0.5 * dt * -F_CONV * inv_m * system->atoms[i].f[2] );*/
- }
- Compute_Kinetic_Energy( system, data );
- Compute_Pressure_Isotropic( system, control, data, out_control );
-#if defined(DEBUG_FOCUS)
- fprintf( stderr, "verlet2 - " );
+ Reallocate( system, workspace, lists, renbr );
+ Reset( system, control, data, workspace, lists );
+ if ( renbr )
+ {
+ Update_Grid( system );
+ Generate_Neighbor_Lists( system, control, data, workspace,
+ lists, out_control );
+ }
+ Compute_Forces( system, control, data, workspace, lists, out_control );
+
+ /* velocity verlet, 2nd part */
+ for ( i = 0; i < system->N; i++ )
+ {
+ inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
+ /* Compute v(t + dt) */
+ rvec_ScaledAdd( system->atoms[i].v,
+ 0.5 * dt * -F_CONV * inv_m, system->atoms[i].f );
+ /* fprintf( stderr, "%6d %15f %15f %15f %15.8f %15.8f %15.8f\n",
+ workspace->orig_id[i],
+ system->atoms[i].v[0], system->atoms[i].v[1], system->atoms[i].v[2],
+ 0.5 * dt * -F_CONV * inv_m * system->atoms[i].f[0],
+ 0.5 * dt * -F_CONV * inv_m * system->atoms[i].f[1],
+ 0.5 * dt * -F_CONV * inv_m * system->atoms[i].f[2] );*/
+ }
+ Compute_Kinetic_Energy( system, data );
+ Compute_Pressure_Isotropic( system, control, data, out_control );
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "verlet2 - " );
#endif
- /* pressure scaler */
- mu = POW( 1.0 + (dt / control->Tau_P[0]) * (data->iso_bar.P - control->P[0]),
- 1.0 / 3 );
- if( mu < MIN_dV )
- mu = MIN_dV;
- else if( mu > MAX_dV )
- mu = MAX_dV;
-
- /* temperature scaler */
- lambda = 1.0 + (dt / control->Tau_T) * (control->T / data->therm.T - 1.0);
- if( lambda < MIN_dT )
- lambda = MIN_dT;
- else if (lambda > MAX_dT )
- lambda = MAX_dT;
- lambda = SQRT( lambda );
-
- /* Scale velocities and positions at t+dt */
- for( i = 0; i < system->N; ++i ) {
- rvec_Scale( system->atoms[i].v, lambda, system->atoms[i].v );
- /* IMPORTANT: What Adri does with scaling positions first to
- unit coordinates and then back to cartesian coordinates essentially
- is scaling the coordinates with mu^2. However, this causes unphysical
- modifications on the system because box dimensions
- are being scaled with mu! We need to discuss this with Adri! */
- rvec_Scale( system->atoms[i].x, mu, system->atoms[i].x );
- }
- Compute_Kinetic_Energy( system, data );
-#if defined(DEBUG_FOCUS)
- fprintf( stderr, "scaling - " );
+ /* pressure scaler */
+ mu = POW( 1.0 + (dt / control->Tau_P[0]) * (data->iso_bar.P - control->P[0]),
+ 1.0 / 3 );
+ if ( mu < MIN_dV )
+ mu = MIN_dV;
+ else if ( mu > MAX_dV )
+ mu = MAX_dV;
+
+ /* temperature scaler */
+ lambda = 1.0 + (dt / control->Tau_T) * (control->T / data->therm.T - 1.0);
+ if ( lambda < MIN_dT )
+ lambda = MIN_dT;
+ else if (lambda > MAX_dT )
+ lambda = MAX_dT;
+ lambda = SQRT( lambda );
+
+ /* Scale velocities and positions at t+dt */
+ for ( i = 0; i < system->N; ++i )
+ {
+ rvec_Scale( system->atoms[i].v, lambda, system->atoms[i].v );
+ /* IMPORTANT: What Adri does with scaling positions first to
+ unit coordinates and then back to cartesian coordinates essentially
+ is scaling the coordinates with mu^2. However, this causes unphysical
+ modifications on the system because box dimensions
+ are being scaled with mu! We need to discuss this with Adri! */
+ rvec_Scale( system->atoms[i].x, mu, system->atoms[i].x );
+ }
+ Compute_Kinetic_Energy( system, data );
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "scaling - " );
#endif
- Update_Box_Isotropic( &(system->box), mu );
+ Update_Box_Isotropic( &(system->box), mu );
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "updated box\n" );
+ fprintf( stderr, "updated box\n" );
#endif
}
-/* uses Berendsen-type coupling for both T and P.
- All box dimensions are scaled by the same amount,
+/* uses Berendsen-type coupling for both T and P.
+ All box dimensions are scaled by the same amount,
there is no change in the angles between axes. */
-void Velocity_Verlet_Berendsen_SemiIsotropic_NPT( reax_system* system,
- control_params* control,
- simulation_data *data,
- static_storage *workspace,
- list **lists,
- output_controls *out_control )
+void Velocity_Verlet_Berendsen_SemiIsotropic_NPT( reax_system* system,
+ control_params* control,
+ simulation_data *data,
+ static_storage *workspace,
+ list **lists,
+ output_controls *out_control )
{
- int i, d, steps, renbr;
- real dt, inv_m, lambda;
- rvec dx, mu;
+ int i, d, steps, renbr;
+ real dt, inv_m, lambda;
+ rvec dx, mu;
- dt = control->dt;
- steps = data->step - data->prev_steps;
- renbr = (steps % control->reneighbor == 0);
+ dt = control->dt;
+ steps = data->step - data->prev_steps;
+ renbr = (steps % control->reneighbor == 0);
#if defined(DEBUG_FOCUS)
- //fprintf( out_control->prs,
- // "tau_t: %g tau_p: %g dt/tau_t: %g dt/tau_p: %g\n",
- //control->Tau_T, control->Tau_P, dt / control->Tau_T, dt / control->Tau_P );
- fprintf( stderr, "step %d: ", data->step );
+ //fprintf( out_control->prs,
+ // "tau_t: %g tau_p: %g dt/tau_t: %g dt/tau_p: %g\n",
+ //control->Tau_T, control->Tau_P, dt / control->Tau_T, dt / control->Tau_P );
+ fprintf( stderr, "step %d: ", data->step );
#endif
- /* velocity verlet, 1st part */
- for( i = 0; i < system->N; i++ ) {
- inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
- /* Compute x(t + dt) */
- rvec_ScaledSum( dx, dt, system->atoms[i].v,
- 0.5 * -F_CONV * inv_m * SQR(dt), system->atoms[i].f );
- Inc_on_T3( system->atoms[i].x, dx, &(system->box) );
- /* Compute v(t + dt/2) */
- rvec_ScaledAdd( system->atoms[i].v,
- 0.5 * -F_CONV * inv_m * dt, system->atoms[i].f );
- /*fprintf( stderr, "%6d %15.8f %15.8f %15.8f %15.8f %15.8f %15.8f\n",
- workspace->orig_id[i],
- system->atoms[i].x[0], system->atoms[i].x[1], system->atoms[i].x[2],
- 0.5 * SQR(dt) * -F_CONV * inv_m * system->atoms[i].f[0],
- 0.5 * SQR(dt) * -F_CONV * inv_m * system->atoms[i].f[1],
- 0.5 * SQR(dt) * -F_CONV * inv_m * system->atoms[i].f[2] ); */
- }
+ /* velocity verlet, 1st part */
+ for ( i = 0; i < system->N; i++ )
+ {
+ inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
+ /* Compute x(t + dt) */
+ rvec_ScaledSum( dx, dt, system->atoms[i].v,
+ 0.5 * -F_CONV * inv_m * SQR(dt), system->atoms[i].f );
+ Inc_on_T3( system->atoms[i].x, dx, &(system->box) );
+ /* Compute v(t + dt/2) */
+ rvec_ScaledAdd( system->atoms[i].v,
+ 0.5 * -F_CONV * inv_m * dt, system->atoms[i].f );
+ /*fprintf( stderr, "%6d %15.8f %15.8f %15.8f %15.8f %15.8f %15.8f\n",
+ workspace->orig_id[i],
+ system->atoms[i].x[0], system->atoms[i].x[1], system->atoms[i].x[2],
+ 0.5 * SQR(dt) * -F_CONV * inv_m * system->atoms[i].f[0],
+ 0.5 * SQR(dt) * -F_CONV * inv_m * system->atoms[i].f[1],
+ 0.5 * SQR(dt) * -F_CONV * inv_m * system->atoms[i].f[2] ); */
+ }
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "verlet1 - " );
+ fprintf( stderr, "verlet1 - " );
#endif
- Reallocate( system, workspace, lists, renbr );
- Reset( system, control, data, workspace, lists );
- if( renbr ) {
- Update_Grid( system );
- Generate_Neighbor_Lists( system, control, data, workspace,
- lists, out_control );
- }
- Compute_Forces( system, control, data, workspace, lists, out_control );
-
- /* velocity verlet, 2nd part */
- for( i = 0; i < system->N; i++ ) {
- inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
- /* Compute v(t + dt) */
- rvec_ScaledAdd( system->atoms[i].v,
- 0.5 * dt * -F_CONV * inv_m, system->atoms[i].f );
- /* fprintf( stderr, "%6d %15f %15f %15f %15.8f %15.8f %15.8f\n",
- workspace->orig_id[i],
- system->atoms[i].v[0], system->atoms[i].v[1], system->atoms[i].v[2],
- 0.5 * dt * -F_CONV * inv_m * system->atoms[i].f[0],
- 0.5 * dt * -F_CONV * inv_m * system->atoms[i].f[1],
- 0.5 * dt * -F_CONV * inv_m * system->atoms[i].f[2] );*/
- }
- Compute_Kinetic_Energy( system, data );
- Compute_Pressure_Isotropic( system, control, data, out_control );
-#if defined(DEBUG_FOCUS)
- fprintf( stderr, "verlet2 - " );
+ Reallocate( system, workspace, lists, renbr );
+ Reset( system, control, data, workspace, lists );
+ if ( renbr )
+ {
+ Update_Grid( system );
+ Generate_Neighbor_Lists( system, control, data, workspace,
+ lists, out_control );
+ }
+ Compute_Forces( system, control, data, workspace, lists, out_control );
+
+ /* velocity verlet, 2nd part */
+ for ( i = 0; i < system->N; i++ )
+ {
+ inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
+ /* Compute v(t + dt) */
+ rvec_ScaledAdd( system->atoms[i].v,
+ 0.5 * dt * -F_CONV * inv_m, system->atoms[i].f );
+ /* fprintf( stderr, "%6d %15f %15f %15f %15.8f %15.8f %15.8f\n",
+ workspace->orig_id[i],
+ system->atoms[i].v[0], system->atoms[i].v[1], system->atoms[i].v[2],
+ 0.5 * dt * -F_CONV * inv_m * system->atoms[i].f[0],
+ 0.5 * dt * -F_CONV * inv_m * system->atoms[i].f[1],
+ 0.5 * dt * -F_CONV * inv_m * system->atoms[i].f[2] );*/
+ }
+ Compute_Kinetic_Energy( system, data );
+ Compute_Pressure_Isotropic( system, control, data, out_control );
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "verlet2 - " );
#endif
- /* pressure scaler */
- for( d = 0; d < 3; ++d ){
- mu[d] = POW( 1.0+(dt/control->Tau_P[d])*(data->tot_press[d]-control->P[d]),
- 1.0 / 3 );
- if( mu[d] < MIN_dV )
- mu[d] = MIN_dV;
- else if( mu[d] > MAX_dV )
- mu[d] = MAX_dV;
- }
-
- /* temperature scaler */
- lambda = 1.0 + (dt / control->Tau_T) * (control->T / data->therm.T - 1.0);
- if( lambda < MIN_dT )
- lambda = MIN_dT;
- else if (lambda > MAX_dT )
- lambda = MAX_dT;
- lambda = SQRT( lambda );
-
- /* Scale velocities and positions at t+dt */
- for( i = 0; i < system->N; ++i ) {
- rvec_Scale( system->atoms[i].v, lambda, system->atoms[i].v );
- /* IMPORTANT: What Adri does with scaling positions first to
- unit coordinates and then back to cartesian coordinates essentially
- is scaling the coordinates with mu^2. However, this causes unphysical
- modifications on the system because box dimensions
- are being scaled with mu! We need to discuss this with Adri! */
- for( d = 0; d < 3; ++d )
- system->atoms[i].x[d] = system->atoms[i].x[d] * mu[d];
- }
- Compute_Kinetic_Energy( system, data );
-#if defined(DEBUG_FOCUS)
- fprintf( stderr, "scaling - " );
+ /* pressure scaler */
+ for ( d = 0; d < 3; ++d )
+ {
+ mu[d] = POW( 1.0 + (dt / control->Tau_P[d]) * (data->tot_press[d] - control->P[d]),
+ 1.0 / 3 );
+ if ( mu[d] < MIN_dV )
+ mu[d] = MIN_dV;
+ else if ( mu[d] > MAX_dV )
+ mu[d] = MAX_dV;
+ }
+
+ /* temperature scaler */
+ lambda = 1.0 + (dt / control->Tau_T) * (control->T / data->therm.T - 1.0);
+ if ( lambda < MIN_dT )
+ lambda = MIN_dT;
+ else if (lambda > MAX_dT )
+ lambda = MAX_dT;
+ lambda = SQRT( lambda );
+
+ /* Scale velocities and positions at t+dt */
+ for ( i = 0; i < system->N; ++i )
+ {
+ rvec_Scale( system->atoms[i].v, lambda, system->atoms[i].v );
+ /* IMPORTANT: What Adri does with scaling positions first to
+ unit coordinates and then back to cartesian coordinates essentially
+ is scaling the coordinates with mu^2. However, this causes unphysical
+ modifications on the system because box dimensions
+ are being scaled with mu! We need to discuss this with Adri! */
+ for ( d = 0; d < 3; ++d )
+ system->atoms[i].x[d] = system->atoms[i].x[d] * mu[d];
+ }
+ Compute_Kinetic_Energy( system, data );
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "scaling - " );
#endif
- Update_Box_SemiIsotropic( &(system->box), mu );
-#if defined(DEBUG_FOCUS)
- fprintf( stderr, "updated box & grid\n" );
+ Update_Box_SemiIsotropic( &(system->box), mu );
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "updated box & grid\n" );
#endif
}
@@ -425,333 +440,341 @@ void Velocity_Verlet_Berendsen_SemiIsotropic_NPT( reax_system* system,
#ifdef ANISOTROPIC
-void Velocity_Verlet_Nose_Hoover_NVT(reax_system* system,
- control_params* control,
- simulation_data *data,
- static_storage *workspace,
- list **lists,
- output_controls *out_control )
+void Velocity_Verlet_Nose_Hoover_NVT(reax_system* system,
+ control_params* control,
+ simulation_data *data,
+ static_storage *workspace,
+ list **lists,
+ output_controls *out_control )
{
- int i;
- real inv_m;
- real dt = control->dt;
- real dt_sqr = SQR(dt);
- rvec dx;
+ int i;
+ real inv_m;
+ real dt = control->dt;
+ real dt_sqr = SQR(dt);
+ rvec dx;
- for (i=0; i < system->N; i++)
+ for (i = 0; i < system->N; i++)
{
- inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
-
- // Compute x(t + dt)
- rvec_ScaledSum( dx, dt, system->atoms[i].v,
- 0.5 * dt_sqr * -F_CONV * inv_m, system->atoms[i].f );
- Inc_on_T3_Gen( system->atoms[i].x, dx, &(system->box) );
-
- // Compute v(t + dt/2)
- rvec_ScaledAdd( system->atoms[i].v,
- -0.5 * dt * data->therm.xi, system->atoms[i].v );
- rvec_ScaledAdd( system->atoms[i].v,
- 0.5 * dt * -F_CONV * inv_m, system->atoms[i].f );
+ inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
+
+ // Compute x(t + dt)
+ rvec_ScaledSum( dx, dt, system->atoms[i].v,
+ 0.5 * dt_sqr * -F_CONV * inv_m, system->atoms[i].f );
+ Inc_on_T3_Gen( system->atoms[i].x, dx, &(system->box) );
+
+ // Compute v(t + dt/2)
+ rvec_ScaledAdd( system->atoms[i].v,
+ -0.5 * dt * data->therm.xi, system->atoms[i].v );
+ rvec_ScaledAdd( system->atoms[i].v,
+ 0.5 * dt * -F_CONV * inv_m, system->atoms[i].f );
}
- // Compute zeta(t + dt/2), E_Kininetic(t + dt/2)
- // IMPORTANT: What will be the initial value of zeta? and what is g?
- data->therm.xi += 0.5 * dt * control->Tau_T *
- ( 2.0 * data->E_Kin - data->N_f * K_B * control->T );
+ // Compute zeta(t + dt/2), E_Kininetic(t + dt/2)
+ // IMPORTANT: What will be the initial value of zeta? and what is g?
+ data->therm.xi += 0.5 * dt * control->Tau_T *
+ ( 2.0 * data->E_Kin - data->N_f * K_B * control->T );
- Reset( system, control, data, workspace );
- fprintf(out_control->log,"reset-"); fflush( out_control->log );
+ Reset( system, control, data, workspace );
+ fprintf(out_control->log, "reset-");
+ fflush( out_control->log );
- Generate_Neighbor_Lists( system, control, data, workspace,
- lists, out_control );
- fprintf(out_control->log,"nbrs-"); fflush( out_control->log );
+ Generate_Neighbor_Lists( system, control, data, workspace,
+ lists, out_control );
+ fprintf(out_control->log, "nbrs-");
+ fflush( out_control->log );
- /* QEq( system, control, workspace, lists[FAR_NBRS], out_control );
- fprintf(out_control->log,"qeq-"); fflush( out_control->log ); */
+ /* QEq( system, control, workspace, lists[FAR_NBRS], out_control );
+ fprintf(out_control->log,"qeq-"); fflush( out_control->log ); */
- Compute_Forces( system, control, data, workspace, lists, out_control );
- fprintf(out_control->log,"forces\n"); fflush( out_control->log );
+ Compute_Forces( system, control, data, workspace, lists, out_control );
+ fprintf(out_control->log, "forces\n");
+ fflush( out_control->log );
- Compute_Kinetic_Energy( system, data );
+ Compute_Kinetic_Energy( system, data );
- for( i = 0; i < system->N; i++ )
+ for ( i = 0; i < system->N; i++ )
{
- inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
+ inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
- // compute v(t + dt)
- rvec_ScaledAdd( system->atoms[i].v,
- -0.5 * dt * data->therm.xi, system->atoms[i].v );
- rvec_ScaledAdd( system->atoms[i].v,
- 0.5 * dt * -F_CONV * inv_m, system->atoms[i].f );
+ // compute v(t + dt)
+ rvec_ScaledAdd( system->atoms[i].v,
+ -0.5 * dt * data->therm.xi, system->atoms[i].v );
+ rvec_ScaledAdd( system->atoms[i].v,
+ 0.5 * dt * -F_CONV * inv_m, system->atoms[i].f );
}
-
- // Compute zeta(t + dt)
- data->therm.xi += 0.5*dt * control->Tau_T * ( 2.0 * data->E_Kin -
- data->N_f * K_B * control->T );
-
- fprintf( out_control->log,"Xi: %8.3f %8.3f %8.3f\n",
- data->therm.xi, data->E_Kin, data->N_f * K_B * control->T );
- fflush( out_control->log );
+
+ // Compute zeta(t + dt)
+ data->therm.xi += 0.5 * dt * control->Tau_T * ( 2.0 * data->E_Kin -
+ data->N_f * K_B * control->T );
+
+ fprintf( out_control->log, "Xi: %8.3f %8.3f %8.3f\n",
+ data->therm.xi, data->E_Kin, data->N_f * K_B * control->T );
+ fflush( out_control->log );
}
-void Velocity_Verlet_Isotropic_NPT( reax_system* system,
- control_params* control,
- simulation_data *data,
- static_storage *workspace,
- list **lists,
- output_controls *out_control )
+void Velocity_Verlet_Isotropic_NPT( reax_system* system,
+ control_params* control,
+ simulation_data *data,
+ static_storage *workspace,
+ list **lists,
+ output_controls *out_control )
{
- int i, itr;
- real deps, v_eps_new=0, v_eps_old=0, G_xi_new;
- real dxi, v_xi_new=0, v_xi_old=0, a_eps_new;
- real inv_m, exp_deps, inv_3V;
- real E_kin, P_int, P_int_const;
- real coef_v, coef_v_eps;
- real dt = control->dt;
- real dt_sqr = SQR( dt );
- thermostat *therm = &( data->therm );
- isotropic_barostat *iso_bar = &( data->iso_bar );
- simulation_box *box = &( system->box );
- rvec dx, dv;
-
- // Here we just calculate how much to increment eps, xi, v_eps, v_xi.
- // Commits are done after positions and velocities of atoms are updated
- // because position, velocity updates uses v_eps, v_xi terms;
- // yet we need EXP( deps ) to be able to calculate
- // positions and velocities accurately.
- iso_bar->a_eps = control->Tau_P *
- ( 3.0 * box->volume * (iso_bar->P - control->P) +
- 6.0 * data->E_Kin / data->N_f ) - iso_bar->v_eps * therm->v_xi;
- deps = dt * iso_bar->v_eps + 0.5 * dt_sqr * iso_bar->a_eps;
- exp_deps = EXP( deps );
-
- therm->G_xi = control->Tau_T * ( 2.0 * data->E_Kin +
- SQR( iso_bar->v_eps ) / control->Tau_P -
- (data->N_f +1) * K_B * control->T );
- dxi = therm->v_xi * dt + 0.5 * therm->G_xi * dt_sqr;
-
- fprintf(out_control->log, "a: %12.6f eps: %12.6f deps: %12.6f\n",
- iso_bar->a_eps, iso_bar->v_eps, iso_bar->eps);
- fprintf(out_control->log, "G: %12.6f xi : %12.6f dxi : %12.6f\n",
- therm->G_xi, therm->v_xi, therm->xi );
-
- // Update positions and velocities
- // NOTE: v_old, v_xi_old, v_eps_old are meant to be the old values
- // in the iteration not the old values at time t or before!
- for (i=0; i < system->N; i++)
+ int i, itr;
+ real deps, v_eps_new = 0, v_eps_old = 0, G_xi_new;
+ real dxi, v_xi_new = 0, v_xi_old = 0, a_eps_new;
+ real inv_m, exp_deps, inv_3V;
+ real E_kin, P_int, P_int_const;
+ real coef_v, coef_v_eps;
+ real dt = control->dt;
+ real dt_sqr = SQR( dt );
+ thermostat *therm = &( data->therm );
+ isotropic_barostat *iso_bar = &( data->iso_bar );
+ simulation_box *box = &( system->box );
+ rvec dx, dv;
+
+ // Here we just calculate how much to increment eps, xi, v_eps, v_xi.
+ // Commits are done after positions and velocities of atoms are updated
+ // because position, velocity updates uses v_eps, v_xi terms;
+ // yet we need EXP( deps ) to be able to calculate
+ // positions and velocities accurately.
+ iso_bar->a_eps = control->Tau_P *
+ ( 3.0 * box->volume * (iso_bar->P - control->P) +
+ 6.0 * data->E_Kin / data->N_f ) - iso_bar->v_eps * therm->v_xi;
+ deps = dt * iso_bar->v_eps + 0.5 * dt_sqr * iso_bar->a_eps;
+ exp_deps = EXP( deps );
+
+ therm->G_xi = control->Tau_T * ( 2.0 * data->E_Kin +
+ SQR( iso_bar->v_eps ) / control->Tau_P -
+ (data->N_f + 1) * K_B * control->T );
+ dxi = therm->v_xi * dt + 0.5 * therm->G_xi * dt_sqr;
+
+ fprintf(out_control->log, "a: %12.6f eps: %12.6f deps: %12.6f\n",
+ iso_bar->a_eps, iso_bar->v_eps, iso_bar->eps);
+ fprintf(out_control->log, "G: %12.6f xi : %12.6f dxi : %12.6f\n",
+ therm->G_xi, therm->v_xi, therm->xi );
+
+ // Update positions and velocities
+ // NOTE: v_old, v_xi_old, v_eps_old are meant to be the old values
+ // in the iteration not the old values at time t or before!
+ for (i = 0; i < system->N; i++)
{
- inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
-
- // Compute x(t + dt)
- rvec_ScaledSum( workspace->a[i], -F_CONV * inv_m, system->atoms[i].f,
- -( (2.0 + 3.0/data->N_f) * iso_bar->v_eps + therm->v_xi ),
- system->atoms[i].v );
- rvec_ScaledSum( dx, dt, system->atoms[i].v,
- 0.5 * dt_sqr, workspace->a[i] );
- Inc_on_T3( system->atoms[i].x, dx, &(system->box) );
- rvec_Scale( system->atoms[i].x, exp_deps, system->atoms[i].x );
+ inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
+
+ // Compute x(t + dt)
+ rvec_ScaledSum( workspace->a[i], -F_CONV * inv_m, system->atoms[i].f,
+ -( (2.0 + 3.0 / data->N_f) * iso_bar->v_eps + therm->v_xi ),
+ system->atoms[i].v );
+ rvec_ScaledSum( dx, dt, system->atoms[i].v,
+ 0.5 * dt_sqr, workspace->a[i] );
+ Inc_on_T3( system->atoms[i].x, dx, &(system->box) );
+ rvec_Scale( system->atoms[i].x, exp_deps, system->atoms[i].x );
}
- // Commit updates
- therm->xi += dxi;
- iso_bar->eps += deps;
- //Update_Box_Isotropic( EXP( 3.0 * iso_bar->eps ), &(system->box) );
- Update_Box_Isotropic( &(system->box), EXP( 3.0 * iso_bar->eps ) );
+ // Commit updates
+ therm->xi += dxi;
+ iso_bar->eps += deps;
+ //Update_Box_Isotropic( EXP( 3.0 * iso_bar->eps ), &(system->box) );
+ Update_Box_Isotropic( &(system->box), EXP( 3.0 * iso_bar->eps ) );
- // Calculate new forces, f(t + dt)
- Reset( system, control, data, workspace );
- fprintf(out_control->log,"reset-"); fflush( out_control->log );
+ // Calculate new forces, f(t + dt)
+ Reset( system, control, data, workspace );
+ fprintf(out_control->log, "reset-");
+ fflush( out_control->log );
- Generate_Neighbor_Lists( system, control, data, workspace,
- lists, out_control );
- fprintf(out_control->log,"nbrs-"); fflush( out_control->log );
+ Generate_Neighbor_Lists( system, control, data, workspace,
+ lists, out_control );
+ fprintf(out_control->log, "nbrs-");
+ fflush( out_control->log );
- /* QEq( system, control, workspace, lists[FAR_NBRS], out_control );
- fprintf(out_control->log,"qeq-"); fflush( out_control->log ); */
+ /* QEq( system, control, workspace, lists[FAR_NBRS], out_control );
+ fprintf(out_control->log,"qeq-"); fflush( out_control->log ); */
- Compute_Forces( system, control, data, workspace, lists, out_control );
- fprintf(out_control->log,"forces\n"); fflush( out_control->log );
+ Compute_Forces( system, control, data, workspace, lists, out_control );
+ fprintf(out_control->log, "forces\n");
+ fflush( out_control->log );
- // Compute iteration constants for each atom's velocity and for P_internal
- // Compute kinetic energy for initial velocities of the iteration
- P_int_const = E_kin = 0;
- for( i = 0; i < system->N; ++i )
+ // Compute iteration constants for each atom's velocity and for P_internal
+ // Compute kinetic energy for initial velocities of the iteration
+ P_int_const = E_kin = 0;
+ for ( i = 0; i < system->N; ++i )
{
- inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
+ inv_m = 1.0 / system->reaxprm.sbp[system->atoms[i].type].mass;
- rvec_ScaledSum( dv, 0.5 * dt, workspace->a[i],
- 0.5 * dt * -F_CONV * inv_m, system->atoms[i].f );
- rvec_Add( dv, system->atoms[i].v );
- rvec_Scale( workspace->v_const[i], exp_deps, dv );
+ rvec_ScaledSum( dv, 0.5 * dt, workspace->a[i],
+ 0.5 * dt * -F_CONV * inv_m, system->atoms[i].f );
+ rvec_Add( dv, system->atoms[i].v );
+ rvec_Scale( workspace->v_const[i], exp_deps, dv );
- P_int_const += ( -F_CONV *
- rvec_Dot( system->atoms[i].f, system->atoms[i].x ) );
+ P_int_const += ( -F_CONV *
+ rvec_Dot( system->atoms[i].f, system->atoms[i].x ) );
- E_kin += (0.5 * system->reaxprm.sbp[system->atoms[i].type].mass *
- rvec_Dot( system->atoms[i].v, system->atoms[i].v ) );
+ E_kin += (0.5 * system->reaxprm.sbp[system->atoms[i].type].mass *
+ rvec_Dot( system->atoms[i].v, system->atoms[i].v ) );
}
-
- // Compute initial p_int
- inv_3V = 1.0 / (3.0 * system->box.volume);
- P_int = inv_3V * ( 2.0 * E_kin + P_int_const );
- v_xi_new = therm->v_xi_old + 2.0 * dt * therm->G_xi;
- v_eps_new = iso_bar->v_eps_old + 2.0 * dt * iso_bar->a_eps;
+ // Compute initial p_int
+ inv_3V = 1.0 / (3.0 * system->box.volume);
+ P_int = inv_3V * ( 2.0 * E_kin + P_int_const );
+
+ v_xi_new = therm->v_xi_old + 2.0 * dt * therm->G_xi;
+ v_eps_new = iso_bar->v_eps_old + 2.0 * dt * iso_bar->a_eps;
- itr = 0;
- do
+ itr = 0;
+ do
{
- itr++;
- // new values become old in this iteration
- v_xi_old = v_xi_new;
- v_eps_old = v_eps_new;
+ itr++;
+ // new values become old in this iteration
+ v_xi_old = v_xi_new;
+ v_eps_old = v_eps_new;
- for( i = 0; i < system->N; ++i )
- {
- coef_v = 1.0 / (1.0 + 0.5 * dt * exp_deps *
- ( (2.0 + 3.0/data->N_f) * v_eps_old + v_xi_old ) );
- rvec_Scale( system->atoms[i].v, coef_v, workspace->v_const[i] );
- }
-
+ for ( i = 0; i < system->N; ++i )
+ {
+ coef_v = 1.0 / (1.0 + 0.5 * dt * exp_deps *
+ ( (2.0 + 3.0 / data->N_f) * v_eps_old + v_xi_old ) );
+ rvec_Scale( system->atoms[i].v, coef_v, workspace->v_const[i] );
+ }
- coef_v_eps = 1.0 / (1.0 + 0.5 * dt * v_xi_old);
- a_eps_new = 3.0 * control->Tau_P *
- ( system->box.volume * (P_int - control->P) + 2.0 * E_kin / data->N_f );
- v_eps_new = coef_v_eps * ( iso_bar->v_eps +
- 0.5 * dt * ( iso_bar->a_eps + a_eps_new ) );
+ coef_v_eps = 1.0 / (1.0 + 0.5 * dt * v_xi_old);
+ a_eps_new = 3.0 * control->Tau_P *
+ ( system->box.volume * (P_int - control->P) + 2.0 * E_kin / data->N_f );
+ v_eps_new = coef_v_eps * ( iso_bar->v_eps +
+ 0.5 * dt * ( iso_bar->a_eps + a_eps_new ) );
- G_xi_new = control->Tau_T * ( 2.0 * E_kin +
- SQR( v_eps_old ) / control->Tau_P -
- (data->N_f + 1) * K_B * control->T );
- v_xi_new = therm->v_xi + 0.5 * dt * ( therm->G_xi + G_xi_new );
-
- E_kin = 0;
- for( i = 0; i < system->N; ++i )
- E_kin += (0.5 * system->reaxprm.sbp[system->atoms[i].type].mass *
- rvec_Dot( system->atoms[i].v, system->atoms[i].v ) );
+ G_xi_new = control->Tau_T * ( 2.0 * E_kin +
+ SQR( v_eps_old ) / control->Tau_P -
+ (data->N_f + 1) * K_B * control->T );
+ v_xi_new = therm->v_xi + 0.5 * dt * ( therm->G_xi + G_xi_new );
- P_int = inv_3V * ( 2.0*E_kin + P_int_const );
+ E_kin = 0;
+ for ( i = 0; i < system->N; ++i )
+ E_kin += (0.5 * system->reaxprm.sbp[system->atoms[i].type].mass *
+ rvec_Dot( system->atoms[i].v, system->atoms[i].v ) );
- fprintf( out_control->log,
- "itr %d E_kin: %8.3f veps_n:%8.3f veps_o:%8.3f vxi_n:%8.3f vxi_o: %8.3f\n",
- itr, E_kin, v_eps_new, v_eps_old, v_xi_new, v_xi_old );
+ P_int = inv_3V * ( 2.0 * E_kin + P_int_const );
+
+
+ fprintf( out_control->log,
+ "itr %d E_kin: %8.3f veps_n:%8.3f veps_o:%8.3f vxi_n:%8.3f vxi_o: %8.3f\n",
+ itr, E_kin, v_eps_new, v_eps_old, v_xi_new, v_xi_old );
}
- while( fabs(v_eps_new - v_eps_old) + fabs(v_xi_new - v_xi_old) > 2e-3 );
+ while ( fabs(v_eps_new - v_eps_old) + fabs(v_xi_new - v_xi_old) > 2e-3 );
- therm->v_xi_old = therm->v_xi;
- therm->v_xi = v_xi_new;
- therm->G_xi = G_xi_new;
+ therm->v_xi_old = therm->v_xi;
+ therm->v_xi = v_xi_new;
+ therm->G_xi = G_xi_new;
- iso_bar->v_eps_old = iso_bar->v_eps;
- iso_bar->v_eps = v_eps_new;
- iso_bar->a_eps = a_eps_new;
+ iso_bar->v_eps_old = iso_bar->v_eps;
+ iso_bar->v_eps = v_eps_new;
+ iso_bar->a_eps = a_eps_new;
- fprintf( out_control->log, "V: %8.3ff\tsides{%8.3f, %8.3f, %8.3f}\n",
- system->box.volume,
- system->box.box[0][0],system->box.box[1][1],system->box.box[2][2] );
- fprintf(out_control->log,"eps:\ta- %8.3f v- %8.3f eps- %8.3f\n",
- iso_bar->a_eps, iso_bar->v_eps, iso_bar->eps);
- fprintf(out_control->log,"xi: \tG- %8.3f v- %8.3f xi - %8.3f\n",
- therm->G_xi, therm->v_xi, therm->xi);
+ fprintf( out_control->log, "V: %8.3ff\tsides{%8.3f, %8.3f, %8.3f}\n",
+ system->box.volume,
+ system->box.box[0][0], system->box.box[1][1], system->box.box[2][2] );
+ fprintf(out_control->log, "eps:\ta- %8.3f v- %8.3f eps- %8.3f\n",
+ iso_bar->a_eps, iso_bar->v_eps, iso_bar->eps);
+ fprintf(out_control->log, "xi: \tG- %8.3f v- %8.3f xi - %8.3f\n",
+ therm->G_xi, therm->v_xi, therm->xi);
}
#endif
-/* uses Berendsen-type coupling for both T and P.
- All box dimensions are scaled by the same amount,
+/* uses Berendsen-type coupling for both T and P.
+ All box dimensions are scaled by the same amount,
there is no change in the angles between axes. */
-void Velocity_Verlet_Berendsen_NVT( reax_system* system,
- control_params* control,
- simulation_data *data,
- static_storage *workspace,
- list **lists,
- output_controls *out_control
- )
+void Velocity_Verlet_Berendsen_NVT( reax_system* system,
+ control_params* control,
+ simulation_data *data,
+ static_storage *workspace,
+ list **lists,
+ output_controls *out_control
+ )
{
- int i, steps, renbr;
- real inv_m, dt, lambda;
- rvec dx;
- reax_atom *atom;
+ int i, steps, renbr;
+ real inv_m, dt, lambda;
+ rvec dx;
+ reax_atom *atom;
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "step%d\n", data->step );
-#endif
- dt = control->dt;
- steps = data->step - data->prev_steps;
- renbr = (steps % control->reneighbor == 0);
-
- /* velocity verlet, 1st part */
- for( i = 0; i < system->N; i++ ) {
- atom = &(system->atoms[i]);
- inv_m = 1.0 / system->reaxprm.sbp[atom->type].mass;
- /* Compute x(t + dt) */
- rvec_ScaledSum( dx, dt, atom->v, 0.5 * -F_CONV * inv_m * SQR(dt), atom->f );
-
- /* bNVT fix - Metin's suggestion */
- /* ORIGINAL CHANGE -- CHECK THE branch serial-bnvt for the fix */
- //rvec_Add( atom->x, dx );
- Inc_on_T3( atom->x, dx, &( system->box ) );
-
- /* Compute v(t + dt/2) */
- rvec_ScaledAdd( atom->v, 0.5 * -F_CONV * inv_m * dt, atom->f );
- }
+ fprintf( stderr, "step%d\n", data->step );
+#endif
+ dt = control->dt;
+ steps = data->step - data->prev_steps;
+ renbr = (steps % control->reneighbor == 0);
+
+ /* velocity verlet, 1st part */
+ for ( i = 0; i < system->N; i++ )
+ {
+ atom = &(system->atoms[i]);
+ inv_m = 1.0 / system->reaxprm.sbp[atom->type].mass;
+ /* Compute x(t + dt) */
+ rvec_ScaledSum( dx, dt, atom->v, 0.5 * -F_CONV * inv_m * SQR(dt), atom->f );
+
+ /* bNVT fix - Metin's suggestion */
+ /* ORIGINAL CHANGE -- CHECK THE branch serial-bnvt for the fix */
+ //rvec_Add( atom->x, dx );
+ Inc_on_T3( atom->x, dx, &( system->box ) );
+
+ /* Compute v(t + dt/2) */
+ rvec_ScaledAdd( atom->v, 0.5 * -F_CONV * inv_m * dt, atom->f );
+ }
#if defined(DEBUG_FOCUS)
- fprintf(stderr, "step%d: verlet1 done\n", data->step);
-#endif
-
- Reallocate( system, workspace, lists, renbr );
- Reset( system, control, data, workspace, lists );
-
- if( renbr )
- Generate_Neighbor_Lists( system, control, data, workspace, lists, out_control );
-
- Compute_Forces( system, control, data, workspace,
- lists, out_control );
-
- /* velocity verlet, 2nd part */
- for( i = 0; i < system->N; i++ ) {
- atom = &(system->atoms[i]);
- inv_m = 1.0 / system->reaxprm.sbp[atom->type].mass;
- /* Compute v(t + dt) */
- rvec_ScaledAdd( atom->v, 0.5 * dt * -F_CONV * inv_m, atom->f );
- }
-#if defined(DEBUG_FOCUS)
- fprintf(stderr, "step%d: verlet2 done\n", data->step);
+ fprintf(stderr, "step%d: verlet1 done\n", data->step);
#endif
- /* temperature scaler */
- Compute_Kinetic_Energy( system, data );
- lambda = 1.0 + (dt / control->Tau_T) * (control->T / data->therm.T - 1.0);
- if( lambda < MIN_dT )
- lambda = MIN_dT;
- else if (lambda > MAX_dT )
- lambda = MAX_dT;
- lambda = SQRT( lambda );
-
- fprintf (stderr, "step:%d lambda -> %f \n", data->step, lambda);
-
- /* Scale velocities and positions at t+dt */
- for( i = 0; i < system->N; ++i ) {
- atom = &(system->atoms[i]);
- rvec_Scale( atom->v, lambda, atom->v );
- }
- Compute_Kinetic_Energy( system, data );
-
-#if defined(DEBUG_FOCUS)
- fprintf( stderr, "step%d: scaled velocities\n",
- data->step );
+ Reallocate( system, workspace, lists, renbr );
+ Reset( system, control, data, workspace, lists );
+
+ if ( renbr )
+ Generate_Neighbor_Lists( system, control, data, workspace, lists, out_control );
+
+ Compute_Forces( system, control, data, workspace,
+ lists, out_control );
+
+ /* velocity verlet, 2nd part */
+ for ( i = 0; i < system->N; i++ )
+ {
+ atom = &(system->atoms[i]);
+ inv_m = 1.0 / system->reaxprm.sbp[atom->type].mass;
+ /* Compute v(t + dt) */
+ rvec_ScaledAdd( atom->v, 0.5 * dt * -F_CONV * inv_m, atom->f );
+ }
+#if defined(DEBUG_FOCUS)
+ fprintf(stderr, "step%d: verlet2 done\n", data->step);
#endif
-}
+ /* temperature scaler */
+ Compute_Kinetic_Energy( system, data );
+ lambda = 1.0 + (dt / control->Tau_T) * (control->T / data->therm.T - 1.0);
+ if ( lambda < MIN_dT )
+ lambda = MIN_dT;
+ else if (lambda > MAX_dT )
+ lambda = MAX_dT;
+ lambda = SQRT( lambda );
+
+ fprintf (stderr, "step:%d lambda -> %f \n", data->step, lambda);
+
+ /* Scale velocities and positions at t+dt */
+ for ( i = 0; i < system->N; ++i )
+ {
+ atom = &(system->atoms[i]);
+ rvec_Scale( atom->v, lambda, atom->v );
+ }
+ Compute_Kinetic_Energy( system, data );
+
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "step%d: scaled velocities\n",
+ data->step );
+#endif
+}
diff --git a/puremd_rc_1003/sPuReMD/integrate.h b/puremd_rc_1003/sPuReMD/integrate.h
index 8baee8ba68fd75f8ac9c139b97ff5b705ef7f378..55d9878619a6128d856b9c8476e054eb1c092981 100644
--- a/puremd_rc_1003/sPuReMD/integrate.h
+++ b/puremd_rc_1003/sPuReMD/integrate.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -25,33 +25,33 @@
#include "mytypes.h"
void Velocity_Verlet_NVE( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
-void Velocity_Verlet_Nose_Hoover_NVT( reax_system*, control_params*,
- simulation_data*, static_storage*,
- list**, output_controls* );
-void Velocity_Verlet_Nose_Hoover_NVT_Klein( reax_system*, control_params*,
- simulation_data*, static_storage*,
- list**, output_controls* );
-void Velocity_Verlet_Flexible_NPT( reax_system*, control_params*,
- simulation_data*,static_storage*,
- list**, output_controls* );
-void Velocity_Verlet_Isotropic_NPT( reax_system*, control_params*,
- simulation_data*, static_storage*,
- list**, output_controls* );
-void Velocity_Verlet_Berendsen_Isotropic_NPT( reax_system*, control_params*,
- simulation_data*, static_storage*,
- list**, output_controls* );
+ static_storage*, list**, output_controls* );
+void Velocity_Verlet_Nose_Hoover_NVT( reax_system*, control_params*,
+ simulation_data*, static_storage*,
+ list**, output_controls* );
+void Velocity_Verlet_Nose_Hoover_NVT_Klein( reax_system*, control_params*,
+ simulation_data*, static_storage*,
+ list**, output_controls* );
+void Velocity_Verlet_Flexible_NPT( reax_system*, control_params*,
+ simulation_data*, static_storage*,
+ list**, output_controls* );
+void Velocity_Verlet_Isotropic_NPT( reax_system*, control_params*,
+ simulation_data*, static_storage*,
+ list**, output_controls* );
+void Velocity_Verlet_Berendsen_Isotropic_NPT( reax_system*, control_params*,
+ simulation_data*, static_storage*,
+ list**, output_controls* );
void Velocity_Verlet_Berendsen_SemiIsotropic_NPT( reax_system*, control_params*,
- simulation_data*,
- static_storage*, list**,
- output_controls* );
+ simulation_data*,
+ static_storage*, list**,
+ output_controls* );
//upon Adri's request moved from parallel code to serial code
-void Velocity_Verlet_Berendsen_NVT( reax_system* ,
- control_params* ,
- simulation_data *,
- static_storage *,
- list **,
- output_controls *
- );
+void Velocity_Verlet_Berendsen_NVT( reax_system* ,
+ control_params* ,
+ simulation_data *,
+ static_storage *,
+ list **,
+ output_controls *
+ );
#endif
diff --git a/puremd_rc_1003/sPuReMD/list.c b/puremd_rc_1003/sPuReMD/list.c
index 01d4fb80caac264ebec3090278a469ec118b88cf..f9044a6cc9e5ea7b625794c14c079582a4bc742b 100644
--- a/puremd_rc_1003/sPuReMD/list.c
+++ b/puremd_rc_1003/sPuReMD/list.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -23,147 +23,147 @@
char Make_List(int n, int num_intrs, int type, list* l)
{
- char success=1;
-
- l->n = n;
- l->num_intrs = num_intrs;
-
- l->index = (int*) malloc( n * sizeof(int) );
- l->end_index = (int*) malloc( n * sizeof(int) );
-
- if (l->index == NULL) success = 0;
- if (l->end_index == NULL) success = 0;
-
- switch(type)
+ char success = 1;
+
+ l->n = n;
+ l->num_intrs = num_intrs;
+
+ l->index = (int*) malloc( n * sizeof(int) );
+ l->end_index = (int*) malloc( n * sizeof(int) );
+
+ if (l->index == NULL) success = 0;
+ if (l->end_index == NULL) success = 0;
+
+ switch (type)
{
case TYP_VOID:
- l->select.v = (void *) malloc(l->num_intrs*sizeof(void));
- if (l->select.v == NULL) success = 0;
- break;
+ l->select.v = (void *) malloc(l->num_intrs * sizeof(void));
+ if (l->select.v == NULL) success = 0;
+ break;
case TYP_THREE_BODY:
- l->select.three_body_list = (three_body_interaction_data*)
- malloc(l->num_intrs*sizeof(three_body_interaction_data));
- if (l->select.three_body_list == NULL) success = 0;
- break;
+ l->select.three_body_list = (three_body_interaction_data*)
+ malloc(l->num_intrs * sizeof(three_body_interaction_data));
+ if (l->select.three_body_list == NULL) success = 0;
+ break;
case TYP_BOND:
- l->select.bond_list = (bond_data*)
- malloc(l->num_intrs * sizeof(bond_data));
- if (l->select.bond_list == NULL) success = 0;
- break;
+ l->select.bond_list = (bond_data*)
+ malloc(l->num_intrs * sizeof(bond_data));
+ if (l->select.bond_list == NULL) success = 0;
+ break;
case TYP_DBO:
- l->select.dbo_list = (dbond_data*)
- malloc(l->num_intrs * sizeof(dbond_data));
- if (l->select.dbo_list == NULL) success = 0;
- break;
+ l->select.dbo_list = (dbond_data*)
+ malloc(l->num_intrs * sizeof(dbond_data));
+ if (l->select.dbo_list == NULL) success = 0;
+ break;
case TYP_DDELTA:
- l->select.dDelta_list = (dDelta_data*)
- malloc(l->num_intrs*sizeof(dDelta_data));
- if (l->select.dDelta_list == NULL) success = 0;
- break;
+ l->select.dDelta_list = (dDelta_data*)
+ malloc(l->num_intrs * sizeof(dDelta_data));
+ if (l->select.dDelta_list == NULL) success = 0;
+ break;
case TYP_FAR_NEIGHBOR:
- l->select.far_nbr_list = (far_neighbor_data*)
- malloc(l->num_intrs*sizeof(far_neighbor_data));
- if (l->select.far_nbr_list == NULL) success = 0;
- break;
+ l->select.far_nbr_list = (far_neighbor_data*)
+ malloc(l->num_intrs * sizeof(far_neighbor_data));
+ if (l->select.far_nbr_list == NULL) success = 0;
+ break;
case TYP_NEAR_NEIGHBOR:
- l->select.near_nbr_list = (near_neighbor_data*)
- malloc(l->num_intrs*sizeof(near_neighbor_data));
- if (l->select.near_nbr_list == NULL) success = 0;
- break;
+ l->select.near_nbr_list = (near_neighbor_data*)
+ malloc(l->num_intrs * sizeof(near_neighbor_data));
+ if (l->select.near_nbr_list == NULL) success = 0;
+ break;
case TYP_HBOND:
- l->select.hbond_list = (hbond_data*)
- malloc( l->num_intrs * sizeof(hbond_data) );
- if (l->select.hbond_list == NULL) success = 0;
- break;
-
+ l->select.hbond_list = (hbond_data*)
+ malloc( l->num_intrs * sizeof(hbond_data) );
+ if (l->select.hbond_list == NULL) success = 0;
+ break;
+
default:
- l->select.v = (void *) malloc(l->num_intrs*sizeof(void));
- if (l->select.v == NULL) success = 0;
- l->type = TYP_VOID;
- break;
+ l->select.v = (void *) malloc(l->num_intrs * sizeof(void));
+ if (l->select.v == NULL) success = 0;
+ l->type = TYP_VOID;
+ break;
}
- return success;
+ return success;
}
void Delete_List(list* l)
{
- if( l->index != NULL )
- free(l->index);
- if( l->end_index != NULL )
- free(l->end_index);
+ if ( l->index != NULL )
+ free(l->index);
+ if ( l->end_index != NULL )
+ free(l->end_index);
- switch(l->type)
+ switch (l->type)
{
case TYP_VOID:
- if( l->select.v != NULL )
- free(l->select.v);
- break;
+ if ( l->select.v != NULL )
+ free(l->select.v);
+ break;
case TYP_THREE_BODY:
- if( l->select.three_body_list != NULL )
- free(l->select.three_body_list);
- break;
+ if ( l->select.three_body_list != NULL )
+ free(l->select.three_body_list);
+ break;
case TYP_BOND:
- if( l->select.bond_list != NULL )
- free(l->select.bond_list);
- break;
+ if ( l->select.bond_list != NULL )
+ free(l->select.bond_list);
+ break;
case TYP_DBO:
- if( l->select.dbo_list != NULL )
- free(l->select.dbo_list);
- break;
+ if ( l->select.dbo_list != NULL )
+ free(l->select.dbo_list);
+ break;
case TYP_DDELTA:
- if( l->select.dDelta_list != NULL )
- free(l->select.dDelta_list);
- break;
+ if ( l->select.dDelta_list != NULL )
+ free(l->select.dDelta_list);
+ break;
case TYP_FAR_NEIGHBOR:
- if( l->select.far_nbr_list != NULL )
- free(l->select.far_nbr_list);
- break;
+ if ( l->select.far_nbr_list != NULL )
+ free(l->select.far_nbr_list);
+ break;
case TYP_NEAR_NEIGHBOR:
- if( l->select.near_nbr_list != NULL )
- free(l->select.near_nbr_list);
- break;
+ if ( l->select.near_nbr_list != NULL )
+ free(l->select.near_nbr_list);
+ break;
case TYP_HBOND:
- if( l->select.hbond_list != NULL )
- free(l->select.hbond_list);
- break;
-
+ if ( l->select.hbond_list != NULL )
+ free(l->select.hbond_list);
+ break;
+
default:
- // Report fatal error
- break;
+ // Report fatal error
+ break;
}
-
+
}
inline int Num_Entries(int i, list* l)
{
- return l->end_index[i] - l->index[i];
+ return l->end_index[i] - l->index[i];
}
inline int Start_Index(int i, list *l )
{
- return l->index[i];
+ return l->index[i];
}
inline int End_Index( int i, list *l )
{
- return l->end_index[i];
+ return l->end_index[i];
}
inline void Set_Start_Index(int i, int val, list *l)
{
- l->index[i] = val;
+ l->index[i] = val;
}
inline void Set_End_Index(int i, int val, list *l)
{
- l->end_index[i] = val;
+ l->end_index[i] = val;
}
diff --git a/puremd_rc_1003/sPuReMD/list.h b/puremd_rc_1003/sPuReMD/list.h
index 4b8a726bbe3546c21678f42a73bad4ef97a48132..e3ecc584e865c419747886c590e15dc0709feccc 100644
--- a/puremd_rc_1003/sPuReMD/list.h
+++ b/puremd_rc_1003/sPuReMD/list.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SeriallReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -27,11 +27,11 @@
char Make_List( int, int, int, list* );
void Delete_List( list* );
-int Num_Entries(int,list*);
+int Num_Entries(int, list*);
int Start_Index( int, list* );
int End_Index( int, list* );
-void Set_Start_Index(int,int,list*);
-void Set_End_Index(int,int,list*);
+void Set_Start_Index(int, int, list*);
+void Set_End_Index(int, int, list*);
#endif
diff --git a/puremd_rc_1003/sPuReMD/lookup.c b/puremd_rc_1003/sPuReMD/lookup.c
index f4634a21bfbcd3c8d112184232b6953e08efd83c..62ca75ec32576d28fd7b48de4d5cf7736e8713b0 100644
--- a/puremd_rc_1003/sPuReMD/lookup.c
+++ b/puremd_rc_1003/sPuReMD/lookup.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -23,384 +23,391 @@
#include "two_body_interactions.h"
void Make_Lookup_Table(real xmin, real xmax, int n,
- lookup_function f, lookup_table* t)
+ lookup_function f, lookup_table* t)
{
- int i;
-
- t->xmin = xmin;
- t->xmax = xmax;
- t->n = n;
- t->dx = (xmax - xmin)/(n-1);
- t->inv_dx = 1.0 / t->dx;
- t->a = (n-1)/(xmax-xmin);
- t->y = (real*) malloc(n*sizeof(real));
-
- for(i=0; i < n; i++)
- t->y[i] = f(i*t->dx + t->xmin);
-
- // fprintf(stdout,"dx = %lf\n",t->dx);
- // for(i=0; i < n; i++)
- // fprintf( stdout,"%d %lf %lf %lf\n",
- // i, i/t->a+t->xmin, t->y[i], exp(i/t->a+t->xmin) );
+ int i;
+
+ t->xmin = xmin;
+ t->xmax = xmax;
+ t->n = n;
+ t->dx = (xmax - xmin) / (n - 1);
+ t->inv_dx = 1.0 / t->dx;
+ t->a = (n - 1) / (xmax - xmin);
+ t->y = (real*) malloc(n * sizeof(real));
+
+ for (i = 0; i < n; i++)
+ t->y[i] = f(i * t->dx + t->xmin);
+
+ // fprintf(stdout,"dx = %lf\n",t->dx);
+ // for(i=0; i < n; i++)
+ // fprintf( stdout,"%d %lf %lf %lf\n",
+ // i, i/t->a+t->xmin, t->y[i], exp(i/t->a+t->xmin) );
}
/* Fills solution into x. Warning: will modify c and d! */
-void Tridiagonal_Solve( const real *a, const real *b,
- real *c, real *d, real *x, unsigned int n){
- int i;
- real id;
-
- /* Modify the coefficients. */
- c[0] /= b[0]; /* Division by zero risk. */
- d[0] /= b[0]; /* Division by zero would imply a singular matrix. */
- for(i = 1; i < n; i++){
- id = (b[i] - c[i-1] * a[i]); /* Division by zero risk. */
- c[i] /= id; /* Last value calculated is redundant. */
- d[i] = (d[i] - d[i-1] * a[i])/id;
- }
-
- /* Now back substitute. */
- x[n - 1] = d[n - 1];
- for(i = n - 2; i >= 0; i--)
- x[i] = d[i] - c[i] * x[i + 1];
+void Tridiagonal_Solve( const real *a, const real *b,
+ real *c, real *d, real *x, unsigned int n)
+{
+ int i;
+ real id;
+
+ /* Modify the coefficients. */
+ c[0] /= b[0]; /* Division by zero risk. */
+ d[0] /= b[0]; /* Division by zero would imply a singular matrix. */
+ for (i = 1; i < n; i++)
+ {
+ id = (b[i] - c[i - 1] * a[i]); /* Division by zero risk. */
+ c[i] /= id; /* Last value calculated is redundant. */
+ d[i] = (d[i] - d[i - 1] * a[i]) / id;
+ }
+
+ /* Now back substitute. */
+ x[n - 1] = d[n - 1];
+ for (i = n - 2; i >= 0; i--)
+ x[i] = d[i] - c[i] * x[i + 1];
}
-void Natural_Cubic_Spline( const real *h, const real *f,
- cubic_spline_coef *coef, unsigned int n )
+void Natural_Cubic_Spline( const real *h, const real *f,
+ cubic_spline_coef *coef, unsigned int n )
{
- int i;
- real *a, *b, *c, *d, *v;
-
- /* allocate space for the linear system */
- a = (real*) malloc( n * sizeof(real) );
- b = (real*) malloc( n * sizeof(real) );
- c = (real*) malloc( n * sizeof(real) );
- d = (real*) malloc( n * sizeof(real) );
- v = (real*) malloc( n * sizeof(real) );
-
- /* build the linear system */
- a[0] = a[1] = a[n-1] = 0;
- for( i = 2; i < n-1; ++i )
- a[i] = h[i-1];
-
- b[0] = b[n-1] = 0;
- for( i = 1; i < n-1; ++i )
- b[i] = 2 * (h[i-1] + h[i]);
-
- c[0] = c[n-2] = c[n-1] = 0;
- for( i = 1; i < n-2; ++i )
- c[i] = h[i];
-
- d[0] = d[n-1] = 0;
- for( i = 1; i < n-1; ++i )
- d[i] = 6 * ((f[i+1]-f[i])/h[i] - (f[i]-f[i-1])/h[i-1]);
-
- /*fprintf( stderr, "i a b c d\n" );
- for( i = 0; i < n; ++i )
- fprintf( stderr, "%d %f %f %f %f\n", i, a[i], b[i], c[i], d[i] );*/
- v[0] = 0;
- v[n-1] = 0;
- Tridiagonal_Solve( &(a[1]), &(b[1]), &(c[1]), &(d[1]), &(v[1]), n-2 );
-
- for( i = 1; i < n; ++i ){
- coef[i-1].d = (v[i] - v[i-1]) / (6*h[i-1]);
- coef[i-1].c = v[i]/2;
- coef[i-1].b = (f[i]-f[i-1])/h[i-1] + h[i-1]*(2*v[i] + v[i-1])/6;
- coef[i-1].a = f[i];
- }
-
- /*fprintf( stderr, "i v coef\n" );
- for( i = 0; i < n; ++i )
- fprintf( stderr, "%d %f %f %f %f %f\n",
- i, v[i], coef[i].a, coef[i].b, coef[i].c, coef[i].d ); */
+ int i;
+ real *a, *b, *c, *d, *v;
+
+ /* allocate space for the linear system */
+ a = (real*) malloc( n * sizeof(real) );
+ b = (real*) malloc( n * sizeof(real) );
+ c = (real*) malloc( n * sizeof(real) );
+ d = (real*) malloc( n * sizeof(real) );
+ v = (real*) malloc( n * sizeof(real) );
+
+ /* build the linear system */
+ a[0] = a[1] = a[n - 1] = 0;
+ for ( i = 2; i < n - 1; ++i )
+ a[i] = h[i - 1];
+
+ b[0] = b[n - 1] = 0;
+ for ( i = 1; i < n - 1; ++i )
+ b[i] = 2 * (h[i - 1] + h[i]);
+
+ c[0] = c[n - 2] = c[n - 1] = 0;
+ for ( i = 1; i < n - 2; ++i )
+ c[i] = h[i];
+
+ d[0] = d[n - 1] = 0;
+ for ( i = 1; i < n - 1; ++i )
+ d[i] = 6 * ((f[i + 1] - f[i]) / h[i] - (f[i] - f[i - 1]) / h[i - 1]);
+
+ /*fprintf( stderr, "i a b c d\n" );
+ for( i = 0; i < n; ++i )
+ fprintf( stderr, "%d %f %f %f %f\n", i, a[i], b[i], c[i], d[i] );*/
+ v[0] = 0;
+ v[n - 1] = 0;
+ Tridiagonal_Solve( &(a[1]), &(b[1]), &(c[1]), &(d[1]), &(v[1]), n - 2 );
+
+ for ( i = 1; i < n; ++i )
+ {
+ coef[i - 1].d = (v[i] - v[i - 1]) / (6 * h[i - 1]);
+ coef[i - 1].c = v[i] / 2;
+ coef[i - 1].b = (f[i] - f[i - 1]) / h[i - 1] + h[i - 1] * (2 * v[i] + v[i - 1]) / 6;
+ coef[i - 1].a = f[i];
+ }
+
+ /*fprintf( stderr, "i v coef\n" );
+ for( i = 0; i < n; ++i )
+ fprintf( stderr, "%d %f %f %f %f %f\n",
+ i, v[i], coef[i].a, coef[i].b, coef[i].c, coef[i].d ); */
}
void Complete_Cubic_Spline( const real *h, const real *f, real v0, real vlast,
- cubic_spline_coef *coef, unsigned int n )
+ cubic_spline_coef *coef, unsigned int n )
{
- int i;
- real *a, *b, *c, *d, *v;
-
- /* allocate space for the linear system */
- a = (real*) malloc( n * sizeof(real) );
- b = (real*) malloc( n * sizeof(real) );
- c = (real*) malloc( n * sizeof(real) );
- d = (real*) malloc( n * sizeof(real) );
- v = (real*) malloc( n * sizeof(real) );
-
- /* build the linear system */
- a[0] = 0;
- for( i = 1; i < n; ++i )
- a[i] = h[i-1];
-
- b[0] = 2*h[0];
- for( i = 1; i < n; ++i )
- b[i] = 2 * (h[i-1] + h[i]);
-
- c[n-1] = 0;
- for( i = 0; i < n-1; ++i )
- c[i] = h[i];
-
- d[0] = 6 * (f[1]-f[0])/h[0] - 6 * v0;
- d[n-1] = 6 * vlast - 6 * (f[n-1]-f[n-2]/h[n-2]);
- for( i = 1; i < n-1; ++i )
- d[i] = 6 * ((f[i+1]-f[i])/h[i] - (f[i]-f[i-1])/h[i-1]);
-
- /*fprintf( stderr, "i a b c d\n" );
- for( i = 0; i < n; ++i )
- fprintf( stderr, "%d %f %f %f %f\n", i, a[i], b[i], c[i], d[i] );*/
- Tridiagonal_Solve( &(a[0]), &(b[0]), &(c[0]), &(d[0]), &(v[0]), n );
- // Tridiagonal_Solve( &(a[1]), &(b[1]), &(c[1]), &(d[1]), &(v[1]), n-2 );
-
- for( i = 1; i < n; ++i ){
- coef[i-1].d = (v[i] - v[i-1]) / (6*h[i-1]);
- coef[i-1].c = v[i]/2;
- coef[i-1].b = (f[i]-f[i-1])/h[i-1] + h[i-1]*(2*v[i] + v[i-1])/6;
- coef[i-1].a = f[i];
- }
-
- /*fprintf( stderr, "i v coef\n" );
- for( i = 0; i < n; ++i )
- fprintf( stderr, "%d %f %f %f %f %f\n",
- i, v[i], coef[i].a, coef[i].b, coef[i].c, coef[i].d ); */
+ int i;
+ real *a, *b, *c, *d, *v;
+
+ /* allocate space for the linear system */
+ a = (real*) malloc( n * sizeof(real) );
+ b = (real*) malloc( n * sizeof(real) );
+ c = (real*) malloc( n * sizeof(real) );
+ d = (real*) malloc( n * sizeof(real) );
+ v = (real*) malloc( n * sizeof(real) );
+
+ /* build the linear system */
+ a[0] = 0;
+ for ( i = 1; i < n; ++i )
+ a[i] = h[i - 1];
+
+ b[0] = 2 * h[0];
+ for ( i = 1; i < n; ++i )
+ b[i] = 2 * (h[i - 1] + h[i]);
+
+ c[n - 1] = 0;
+ for ( i = 0; i < n - 1; ++i )
+ c[i] = h[i];
+
+ d[0] = 6 * (f[1] - f[0]) / h[0] - 6 * v0;
+ d[n - 1] = 6 * vlast - 6 * (f[n - 1] - f[n - 2] / h[n - 2]);
+ for ( i = 1; i < n - 1; ++i )
+ d[i] = 6 * ((f[i + 1] - f[i]) / h[i] - (f[i] - f[i - 1]) / h[i - 1]);
+
+ /*fprintf( stderr, "i a b c d\n" );
+ for( i = 0; i < n; ++i )
+ fprintf( stderr, "%d %f %f %f %f\n", i, a[i], b[i], c[i], d[i] );*/
+ Tridiagonal_Solve( &(a[0]), &(b[0]), &(c[0]), &(d[0]), &(v[0]), n );
+ // Tridiagonal_Solve( &(a[1]), &(b[1]), &(c[1]), &(d[1]), &(v[1]), n-2 );
+
+ for ( i = 1; i < n; ++i )
+ {
+ coef[i - 1].d = (v[i] - v[i - 1]) / (6 * h[i - 1]);
+ coef[i - 1].c = v[i] / 2;
+ coef[i - 1].b = (f[i] - f[i - 1]) / h[i - 1] + h[i - 1] * (2 * v[i] + v[i - 1]) / 6;
+ coef[i - 1].a = f[i];
+ }
+
+ /*fprintf( stderr, "i v coef\n" );
+ for( i = 0; i < n; ++i )
+ fprintf( stderr, "%d %f %f %f %f %f\n",
+ i, v[i], coef[i].a, coef[i].b, coef[i].c, coef[i].d ); */
}
void LR_Lookup( LR_lookup_table *t, real r, LR_data *y )
{
- int i;
- real base, dif;
-
- i = (int)(r * t->inv_dx);
- if( i == 0 ) ++i;
- base = (real)(i+1) * t->dx;
- dif = r - base;
- //fprintf( stderr, "r: %f, i: %d, base: %f, dif: %f\n", r, i, base, dif );
-
- y->e_vdW = ((t->vdW[i].d*dif + t->vdW[i].c)*dif + t->vdW[i].b)*dif +
- t->vdW[i].a;
- y->CEvd = ((t->CEvd[i].d*dif + t->CEvd[i].c)*dif +
- t->CEvd[i].b)*dif + t->CEvd[i].a;
- //y->CEvd = (3*t->vdW[i].d*dif + 2*t->vdW[i].c)*dif + t->vdW[i].b;
-
- y->e_ele = ((t->ele[i].d*dif + t->ele[i].c)*dif + t->ele[i].b)*dif +
- t->ele[i].a;
- y->CEclmb = ((t->CEclmb[i].d*dif + t->CEclmb[i].c)*dif + t->CEclmb[i].b)*dif +
- t->CEclmb[i].a;
-
- y->H = y->e_ele * EV_to_KCALpMOL / C_ele;
- //y->H = ((t->H[i].d*dif + t->H[i].c)*dif + t->H[i].b)*dif + t->H[i].a;
+ int i;
+ real base, dif;
+
+ i = (int)(r * t->inv_dx);
+ if ( i == 0 ) ++i;
+ base = (real)(i + 1) * t->dx;
+ dif = r - base;
+ //fprintf( stderr, "r: %f, i: %d, base: %f, dif: %f\n", r, i, base, dif );
+
+ y->e_vdW = ((t->vdW[i].d * dif + t->vdW[i].c) * dif + t->vdW[i].b) * dif +
+ t->vdW[i].a;
+ y->CEvd = ((t->CEvd[i].d * dif + t->CEvd[i].c) * dif +
+ t->CEvd[i].b) * dif + t->CEvd[i].a;
+ //y->CEvd = (3*t->vdW[i].d*dif + 2*t->vdW[i].c)*dif + t->vdW[i].b;
+
+ y->e_ele = ((t->ele[i].d * dif + t->ele[i].c) * dif + t->ele[i].b) * dif +
+ t->ele[i].a;
+ y->CEclmb = ((t->CEclmb[i].d * dif + t->CEclmb[i].c) * dif + t->CEclmb[i].b) * dif +
+ t->CEclmb[i].a;
+
+ y->H = y->e_ele * EV_to_KCALpMOL / C_ele;
+ //y->H = ((t->H[i].d*dif + t->H[i].c)*dif + t->H[i].b)*dif + t->H[i].a;
}
void Make_LR_Lookup_Table( reax_system *system, control_params *control )
{
- int i, j, r;
- int num_atom_types;
- int existing_types[MAX_ATOM_TYPES];
- real dr;
- real *h, *fh, *fvdw, *fele, *fCEvd, *fCEclmb;
- real v0_vdw, v0_ele, vlast_vdw, vlast_ele;
- /* real rand_dist;
- real evdw_abserr, evdw_relerr, fvdw_abserr, fvdw_relerr;
- real eele_abserr, eele_relerr, fele_abserr, fele_relerr;
- real evdw_maxerr, eele_maxerr;
- LR_data y, y_spline; */
-
- /* initializations */
- vlast_ele = 0;
- vlast_vdw = 0;
- v0_ele = 0;
- v0_vdw = 0;
-
- num_atom_types = system->reaxprm.num_atom_types;
- dr = control->r_cut / control->tabulate;
- h = (real*) malloc( (control->tabulate+1) * sizeof(real) );
- fh = (real*) malloc( (control->tabulate+1) * sizeof(real) );
- fvdw = (real*) malloc( (control->tabulate+1) * sizeof(real) );
- fCEvd = (real*) malloc( (control->tabulate+1) * sizeof(real) );
- fele = (real*) malloc( (control->tabulate+1) * sizeof(real) );
- fCEclmb = (real*) malloc( (control->tabulate+1) * sizeof(real) );
-
- /* allocate Long-Range LookUp Table space based on
- number of atom types in the ffield file */
- LR = (LR_lookup_table**) malloc( num_atom_types * sizeof(LR_lookup_table*) );
- for( i = 0; i < num_atom_types; ++i )
- LR[i] = (LR_lookup_table*) malloc(num_atom_types * sizeof(LR_lookup_table));
-
- /* most atom types in ffield file will not exist in the current
- simulation. to avoid unnecessary lookup table space, determine
- the atom types that exist in the current simulation */
- for( i = 0; i < MAX_ATOM_TYPES; ++i )
- existing_types[i] = 0;
- for( i = 0; i < system->N; ++i )
- existing_types[ system->atoms[i].type ] = 1;
-
- /* fill in the lookup table entries for existing atom types.
- only lower half should be enough. */
- for( i = 0; i < num_atom_types; ++i )
- if( existing_types[i] )
- for( j = i; j < num_atom_types; ++j )
- if( existing_types[j] ) {
- LR[i][j].xmin = 0;
- LR[i][j].xmax = control->r_cut;
- LR[i][j].n = control->tabulate + 1;
- LR[i][j].dx = dr;
- LR[i][j].inv_dx = control->tabulate / control->r_cut;
- LR[i][j].y = (LR_data*)
- malloc(LR[i][j].n * sizeof(LR_data));
- LR[i][j].H = (cubic_spline_coef*)
- malloc(LR[i][j].n * sizeof(cubic_spline_coef));
- LR[i][j].vdW = (cubic_spline_coef*)
- malloc(LR[i][j].n * sizeof(cubic_spline_coef));
- LR[i][j].CEvd = (cubic_spline_coef*)
- malloc(LR[i][j].n * sizeof(cubic_spline_coef));
- LR[i][j].ele = (cubic_spline_coef*)
- malloc(LR[i][j].n * sizeof(cubic_spline_coef));
- LR[i][j].CEclmb = (cubic_spline_coef*)
- malloc(LR[i][j].n * sizeof(cubic_spline_coef));
-
- for( r = 1; r <= control->tabulate; ++r ) {
- LR_vdW_Coulomb( system, control, i, j, r * dr, &(LR[i][j].y[r]) );
- h[r] = LR[i][j].dx;
- fh[r] = LR[i][j].y[r].H;
- fvdw[r] = LR[i][j].y[r].e_vdW;
- fCEvd[r] = LR[i][j].y[r].CEvd;
- fele[r] = LR[i][j].y[r].e_ele;
- fCEclmb[r] = LR[i][j].y[r].CEclmb;
-
- if( r == 1 ){
- v0_vdw = LR[i][j].y[r].CEvd;
- v0_ele = LR[i][j].y[r].CEclmb;
- }
- else if( r == control->tabulate ){
- vlast_vdw = LR[i][j].y[r].CEvd;
- vlast_ele = LR[i][j].y[r].CEclmb;
- }
- }
-
- /*fprintf( stderr, "%-6s %-6s %-6s\n", "r", "h", "fh" );
- for( r = 1; r <= control->tabulate; ++r )
- fprintf( stderr, "%f %f %f\n", r * dr, h[r], fh[r] ); */
- Natural_Cubic_Spline( &h[1], &fh[1],
- &(LR[i][j].H[1]), control->tabulate+1 );
-
- /*fprintf( stderr, "%-6s %-6s %-6s\n", "r", "h", "fvdw" );
- for( r = 1; r <= control->tabulate; ++r )
- fprintf( stderr, "%f %f %f\n", r * dr, h[r], fvdw[r] );
- fprintf( stderr, "v0_vdw: %f, vlast_vdw: %f\n", v0_vdw, vlast_vdw );
- */
- Complete_Cubic_Spline( &h[1], &fvdw[1], v0_vdw, vlast_vdw,
- &(LR[i][j].vdW[1]), control->tabulate+1 );
- Natural_Cubic_Spline( &h[1], &fCEvd[1],
- &(LR[i][j].CEvd[1]), control->tabulate+1 );
-
- /*fprintf( stderr, "%-6s %-6s %-6s\n", "r", "h", "fele" );
- for( r = 1; r <= control->tabulate; ++r )
- fprintf( stderr, "%f %f %f\n", r * dr, h[r], fele[r] );
- fprintf( stderr, "v0_ele: %f, vlast_ele: %f\n", v0_ele, vlast_ele );
- */
- Complete_Cubic_Spline( &h[1], &fele[1], v0_ele, vlast_ele,
- &(LR[i][j].ele[1]), control->tabulate+1 );
- Natural_Cubic_Spline( &h[1], &fCEclmb[1],
- &(LR[i][j].CEclmb[1]), control->tabulate+1 );
- }
-
- /***** //test LR-Lookup table
- evdw_maxerr = 0;
- eele_maxerr = 0;
- for( i = 0; i < num_atom_types; ++i )
- if( existing_types[i] )
- for( j = i; j < num_atom_types; ++j )
- if( existing_types[j] ) {
- for( r = 1; r <= 100; ++r ) {
- rand_dist = (real)rand()/RAND_MAX * control->r_cut;
- LR_vdW_Coulomb( system, control, i, j, rand_dist, &y );
- LR_Lookup( &(LR[i][j]), rand_dist, &y_spline );
-
- evdw_abserr = fabs(y.e_vdW - y_spline.e_vdW);
- evdw_relerr = fabs(evdw_abserr / y.e_vdW);
- fvdw_abserr = fabs(y.CEvd - y_spline.CEvd);
- fvdw_relerr = fabs(fvdw_abserr / y.CEvd);
- eele_abserr = fabs(y.e_ele - y_spline.e_ele);
- eele_relerr = fabs(eele_abserr / y.e_ele);
- fele_abserr = fabs(y.CEclmb - y_spline.CEclmb);
- fele_relerr = fabs(fele_abserr / y.CEclmb);
-
- if( evdw_relerr > 1e-10 || eele_relerr > 1e-10 ){
- fprintf( stderr, "rand_dist = %24.15e\n", rand_dist );
- fprintf( stderr, "%24.15e %24.15e %24.15e %24.15e\n",
- y.H, y_spline.H,
- fabs(y.H-y_spline.H), fabs((y.H-y_spline.H)/y.H) );
-
- fprintf( stderr, "%24.15e %24.15e %24.15e %24.15e\n",
- y.e_vdW, y_spline.e_vdW, evdw_abserr, evdw_relerr );
- fprintf( stderr, "%24.15e %24.15e %24.15e %24.15e\n",
- y.CEvd, y_spline.CEvd, fvdw_abserr, fvdw_relerr );
-
- fprintf( stderr, "%24.15e %24.15e %24.15e %24.15e\n",
- y.e_ele, y_spline.e_ele, eele_abserr, eele_relerr );
- fprintf( stderr, "%24.15e %24.15e %24.15e %24.15e\n",
- y.CEclmb, y_spline.CEclmb, fele_abserr, fele_relerr );
- }
-
- if( evdw_relerr > evdw_maxerr )
- evdw_maxerr = evdw_relerr;
- if( eele_relerr > eele_maxerr )
- eele_maxerr = eele_relerr;
- }
- }
- fprintf( stderr, "evdw_maxerr: %24.15e\n", evdw_maxerr );
- fprintf( stderr, "eele_maxerr: %24.15e\n", eele_maxerr );
- *******/
-
- free(h);
- free(fh);
- free(fvdw);
- free(fCEvd);
- free(fele);
- free(fCEclmb);
+ int i, j, r;
+ int num_atom_types;
+ int existing_types[MAX_ATOM_TYPES];
+ real dr;
+ real *h, *fh, *fvdw, *fele, *fCEvd, *fCEclmb;
+ real v0_vdw, v0_ele, vlast_vdw, vlast_ele;
+ /* real rand_dist;
+ real evdw_abserr, evdw_relerr, fvdw_abserr, fvdw_relerr;
+ real eele_abserr, eele_relerr, fele_abserr, fele_relerr;
+ real evdw_maxerr, eele_maxerr;
+ LR_data y, y_spline; */
+
+ /* initializations */
+ vlast_ele = 0;
+ vlast_vdw = 0;
+ v0_ele = 0;
+ v0_vdw = 0;
+
+ num_atom_types = system->reaxprm.num_atom_types;
+ dr = control->r_cut / control->tabulate;
+ h = (real*) malloc( (control->tabulate + 1) * sizeof(real) );
+ fh = (real*) malloc( (control->tabulate + 1) * sizeof(real) );
+ fvdw = (real*) malloc( (control->tabulate + 1) * sizeof(real) );
+ fCEvd = (real*) malloc( (control->tabulate + 1) * sizeof(real) );
+ fele = (real*) malloc( (control->tabulate + 1) * sizeof(real) );
+ fCEclmb = (real*) malloc( (control->tabulate + 1) * sizeof(real) );
+
+ /* allocate Long-Range LookUp Table space based on
+ number of atom types in the ffield file */
+ LR = (LR_lookup_table**) malloc( num_atom_types * sizeof(LR_lookup_table*) );
+ for ( i = 0; i < num_atom_types; ++i )
+ LR[i] = (LR_lookup_table*) malloc(num_atom_types * sizeof(LR_lookup_table));
+
+ /* most atom types in ffield file will not exist in the current
+ simulation. to avoid unnecessary lookup table space, determine
+ the atom types that exist in the current simulation */
+ for ( i = 0; i < MAX_ATOM_TYPES; ++i )
+ existing_types[i] = 0;
+ for ( i = 0; i < system->N; ++i )
+ existing_types[ system->atoms[i].type ] = 1;
+
+ /* fill in the lookup table entries for existing atom types.
+ only lower half should be enough. */
+ for ( i = 0; i < num_atom_types; ++i )
+ if ( existing_types[i] )
+ for ( j = i; j < num_atom_types; ++j )
+ if ( existing_types[j] )
+ {
+ LR[i][j].xmin = 0;
+ LR[i][j].xmax = control->r_cut;
+ LR[i][j].n = control->tabulate + 1;
+ LR[i][j].dx = dr;
+ LR[i][j].inv_dx = control->tabulate / control->r_cut;
+ LR[i][j].y = (LR_data*)
+ malloc(LR[i][j].n * sizeof(LR_data));
+ LR[i][j].H = (cubic_spline_coef*)
+ malloc(LR[i][j].n * sizeof(cubic_spline_coef));
+ LR[i][j].vdW = (cubic_spline_coef*)
+ malloc(LR[i][j].n * sizeof(cubic_spline_coef));
+ LR[i][j].CEvd = (cubic_spline_coef*)
+ malloc(LR[i][j].n * sizeof(cubic_spline_coef));
+ LR[i][j].ele = (cubic_spline_coef*)
+ malloc(LR[i][j].n * sizeof(cubic_spline_coef));
+ LR[i][j].CEclmb = (cubic_spline_coef*)
+ malloc(LR[i][j].n * sizeof(cubic_spline_coef));
+
+ for ( r = 1; r <= control->tabulate; ++r )
+ {
+ LR_vdW_Coulomb( system, control, i, j, r * dr, &(LR[i][j].y[r]) );
+ h[r] = LR[i][j].dx;
+ fh[r] = LR[i][j].y[r].H;
+ fvdw[r] = LR[i][j].y[r].e_vdW;
+ fCEvd[r] = LR[i][j].y[r].CEvd;
+ fele[r] = LR[i][j].y[r].e_ele;
+ fCEclmb[r] = LR[i][j].y[r].CEclmb;
+
+ if ( r == 1 )
+ {
+ v0_vdw = LR[i][j].y[r].CEvd;
+ v0_ele = LR[i][j].y[r].CEclmb;
+ }
+ else if ( r == control->tabulate )
+ {
+ vlast_vdw = LR[i][j].y[r].CEvd;
+ vlast_ele = LR[i][j].y[r].CEclmb;
+ }
+ }
+
+ /*fprintf( stderr, "%-6s %-6s %-6s\n", "r", "h", "fh" );
+ for( r = 1; r <= control->tabulate; ++r )
+ fprintf( stderr, "%f %f %f\n", r * dr, h[r], fh[r] ); */
+ Natural_Cubic_Spline( &h[1], &fh[1],
+ &(LR[i][j].H[1]), control->tabulate + 1 );
+
+ /*fprintf( stderr, "%-6s %-6s %-6s\n", "r", "h", "fvdw" );
+ for( r = 1; r <= control->tabulate; ++r )
+ fprintf( stderr, "%f %f %f\n", r * dr, h[r], fvdw[r] );
+ fprintf( stderr, "v0_vdw: %f, vlast_vdw: %f\n", v0_vdw, vlast_vdw );
+ */
+ Complete_Cubic_Spline( &h[1], &fvdw[1], v0_vdw, vlast_vdw,
+ &(LR[i][j].vdW[1]), control->tabulate + 1 );
+ Natural_Cubic_Spline( &h[1], &fCEvd[1],
+ &(LR[i][j].CEvd[1]), control->tabulate + 1 );
+
+ /*fprintf( stderr, "%-6s %-6s %-6s\n", "r", "h", "fele" );
+ for( r = 1; r <= control->tabulate; ++r )
+ fprintf( stderr, "%f %f %f\n", r * dr, h[r], fele[r] );
+ fprintf( stderr, "v0_ele: %f, vlast_ele: %f\n", v0_ele, vlast_ele );
+ */
+ Complete_Cubic_Spline( &h[1], &fele[1], v0_ele, vlast_ele,
+ &(LR[i][j].ele[1]), control->tabulate + 1 );
+ Natural_Cubic_Spline( &h[1], &fCEclmb[1],
+ &(LR[i][j].CEclmb[1]), control->tabulate + 1 );
+ }
+
+ /***** //test LR-Lookup table
+ evdw_maxerr = 0;
+ eele_maxerr = 0;
+ for( i = 0; i < num_atom_types; ++i )
+ if( existing_types[i] )
+ for( j = i; j < num_atom_types; ++j )
+ if( existing_types[j] ) {
+ for( r = 1; r <= 100; ++r ) {
+ rand_dist = (real)rand()/RAND_MAX * control->r_cut;
+ LR_vdW_Coulomb( system, control, i, j, rand_dist, &y );
+ LR_Lookup( &(LR[i][j]), rand_dist, &y_spline );
+
+ evdw_abserr = fabs(y.e_vdW - y_spline.e_vdW);
+ evdw_relerr = fabs(evdw_abserr / y.e_vdW);
+ fvdw_abserr = fabs(y.CEvd - y_spline.CEvd);
+ fvdw_relerr = fabs(fvdw_abserr / y.CEvd);
+ eele_abserr = fabs(y.e_ele - y_spline.e_ele);
+ eele_relerr = fabs(eele_abserr / y.e_ele);
+ fele_abserr = fabs(y.CEclmb - y_spline.CEclmb);
+ fele_relerr = fabs(fele_abserr / y.CEclmb);
+
+ if( evdw_relerr > 1e-10 || eele_relerr > 1e-10 ){
+ fprintf( stderr, "rand_dist = %24.15e\n", rand_dist );
+ fprintf( stderr, "%24.15e %24.15e %24.15e %24.15e\n",
+ y.H, y_spline.H,
+ fabs(y.H-y_spline.H), fabs((y.H-y_spline.H)/y.H) );
+
+ fprintf( stderr, "%24.15e %24.15e %24.15e %24.15e\n",
+ y.e_vdW, y_spline.e_vdW, evdw_abserr, evdw_relerr );
+ fprintf( stderr, "%24.15e %24.15e %24.15e %24.15e\n",
+ y.CEvd, y_spline.CEvd, fvdw_abserr, fvdw_relerr );
+
+ fprintf( stderr, "%24.15e %24.15e %24.15e %24.15e\n",
+ y.e_ele, y_spline.e_ele, eele_abserr, eele_relerr );
+ fprintf( stderr, "%24.15e %24.15e %24.15e %24.15e\n",
+ y.CEclmb, y_spline.CEclmb, fele_abserr, fele_relerr );
+ }
+
+ if( evdw_relerr > evdw_maxerr )
+ evdw_maxerr = evdw_relerr;
+ if( eele_relerr > eele_maxerr )
+ eele_maxerr = eele_relerr;
+ }
+ }
+ fprintf( stderr, "evdw_maxerr: %24.15e\n", evdw_maxerr );
+ fprintf( stderr, "eele_maxerr: %24.15e\n", eele_maxerr );
+ *******/
+
+ free(h);
+ free(fh);
+ free(fvdw);
+ free(fCEvd);
+ free(fele);
+ free(fCEclmb);
}
int Lookup_Index_Of( real x, lookup_table* t )
{
- return (int)( t->a * ( x - t->xmin ) );
+ return (int)( t->a * ( x - t->xmin ) );
}
real Lookup( real x, lookup_table* t )
{
- real x1, x2;
- real b;
- int i;
-
- /* if ( x < t->xmin)
- {
- fprintf(stderr,"Domain check %lf > %lf\n",t->xmin,x);
- exit(0);
- }
- if ( x > t->xmax)
- {
- fprintf(stderr,"Domain check %lf < %lf\n",t->xmax,x);
- exit(0);
- } */
-
- i = Lookup_Index_Of( x, t );
- x1 = i * t->dx + t->xmin;
- x2 = (i+1) * t->dx + t->xmin;
-
- b = ( x2 * t->y[i] - x1 * t->y[i+1] ) * t->inv_dx;
- // fprintf( stdout,"SLookup_Entry: %d, %lf, %lf, %lf, %lf: %lf, %lf\n",
- // i,x1,x2,x,b,t->one_over_dx*(t->y[i+1]-t->y[i])*x+b,exp(x));
-
- return t->inv_dx * ( t->y[i+1] - t->y[i] ) * x + b;
+ real x1, x2;
+ real b;
+ int i;
+
+ /* if ( x < t->xmin)
+ {
+ fprintf(stderr,"Domain check %lf > %lf\n",t->xmin,x);
+ exit(0);
+ }
+ if ( x > t->xmax)
+ {
+ fprintf(stderr,"Domain check %lf < %lf\n",t->xmax,x);
+ exit(0);
+ } */
+
+ i = Lookup_Index_Of( x, t );
+ x1 = i * t->dx + t->xmin;
+ x2 = (i + 1) * t->dx + t->xmin;
+
+ b = ( x2 * t->y[i] - x1 * t->y[i + 1] ) * t->inv_dx;
+ // fprintf( stdout,"SLookup_Entry: %d, %lf, %lf, %lf, %lf: %lf, %lf\n",
+ // i,x1,x2,x,b,t->one_over_dx*(t->y[i+1]-t->y[i])*x+b,exp(x));
+
+ return t->inv_dx * ( t->y[i + 1] - t->y[i] ) * x + b;
}
-
diff --git a/puremd_rc_1003/sPuReMD/lookup.h b/puremd_rc_1003/sPuReMD/lookup.h
index 13ffc5536a37aca46726f205130df0cf5a89c959..a0b9e51620716aeae13ca7743f554f3704c01110 100644
--- a/puremd_rc_1003/sPuReMD/lookup.h
+++ b/puremd_rc_1003/sPuReMD/lookup.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
diff --git a/puremd_rc_1003/sPuReMD/mytypes.h b/puremd_rc_1003/sPuReMD/mytypes.h
index 8d346bd449374b6d75736a67416a1e740848b20b..26617a5d3dab24203503b6a10189b0e57d32f8ce 100644
--- a/puremd_rc_1003/sPuReMD/mytypes.h
+++ b/puremd_rc_1003/sPuReMD/mytypes.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -64,7 +64,7 @@
#define CAL_to_JOULES 4.184000 // CALories --> JOULES
#define JOULES_to_CAL 1/4.184000 // JOULES --> CALories
#define AMU_to_GRAM 1.6605e-24
-#define ANG_to_CM 1.0e-8
+#define ANG_to_CM 1.0e-8
#define AVOGNR 6.0221367e23
#define P_CONV 1.0e-24 * AVOGNR * JOULES_to_CAL
@@ -103,8 +103,8 @@
#define GE_ATOM 6
#define X_ATOM 7
-#define ZERO 0.000000000000000e+00
-#define ALMOST_ZERO 1e-10
+#define ZERO 0.000000000000000e+00
+#define ALMOST_ZERO 1e-10
#define NEG_INF -1e10
#define NO_BOND 1e-3
#define HB_THRESHOLD 1e-2
@@ -124,10 +124,12 @@ typedef int ivec[3];
typedef real rtensor[3][3];
enum {NVE, NVT, NPT, sNPT, iNPT, ensNR, bNVT};
-enum {FAR_NBRS, NEAR_NBRS, THREE_BODIES, BONDS, OLD_BONDS,
- HBONDS, DBO, DDELTA, LIST_N};
-enum {TYP_VOID, TYP_THREE_BODY, TYP_BOND, TYP_HBOND, TYP_DBO,
- TYP_DDELTA, TYP_FAR_NEIGHBOR, TYP_NEAR_NEIGHBOR, TYP_N};
+enum {FAR_NBRS, NEAR_NBRS, THREE_BODIES, BONDS, OLD_BONDS,
+ HBONDS, DBO, DDELTA, LIST_N
+ };
+enum {TYP_VOID, TYP_THREE_BODY, TYP_BOND, TYP_HBOND, TYP_DBO,
+ TYP_DDELTA, TYP_FAR_NEIGHBOR, TYP_NEAR_NEIGHBOR, TYP_N
+ };
enum {UNKNOWN, WATER};
enum {NO_ANALYSIS, FRAGMENTS, REACTIONS, NUM_ANALYSIS};
enum {WRITE_ASCII, WRITE_BINARY, RF_N};
@@ -136,7 +138,7 @@ enum {XYZ, PDB, BGF, ASCII_RESTART, BINARY_RESTART, GF_N};
/* Global params mapping */
-/*
+/*
l[0] = p_boc1
l[1] = p_boc2
l[2] = p_coa2
@@ -179,440 +181,455 @@ l[38] = p_coa3
*/
typedef struct
-{
- int n_global;
- real* l;
- int vdw_type;
+{
+ int n_global;
+ real* l;
+ int vdw_type;
} global_parameters;
typedef struct
{
- /* Line one in field file */
- char name[15]; /* Two character atom name */
-
- real r_s;
- real valency; /* Valency of the atom */
- real mass; /* Mass of atom */
- real r_vdw;
- real epsilon;
- real gamma;
- real r_pi;
- real valency_e;
- real nlp_opt;
-
- /* Line two in field file */
- real alpha;
- real gamma_w;
- real valency_boc;
- real p_ovun5;
- real chi;
- real eta;
- int p_hbond; /* Determines whether this type of atom participates in H_bonds.
- It is 1 for donor H, 2 for acceptors (O,S,N), 0 for others*/
-
- /* Line three in field file */
- real r_pi_pi;
- real p_lp2;
- real b_o_131;
- real b_o_132;
- real b_o_133;
-
- /* Line four in the field file */
- real p_ovun2;
- real p_val3;
- real valency_val;
- real p_val5;
- real rcore2;
- real ecore2;
- real acore2;
+ /* Line one in field file */
+ char name[15]; /* Two character atom name */
+
+ real r_s;
+ real valency; /* Valency of the atom */
+ real mass; /* Mass of atom */
+ real r_vdw;
+ real epsilon;
+ real gamma;
+ real r_pi;
+ real valency_e;
+ real nlp_opt;
+
+ /* Line two in field file */
+ real alpha;
+ real gamma_w;
+ real valency_boc;
+ real p_ovun5;
+ real chi;
+ real eta;
+ int p_hbond; /* Determines whether this type of atom participates in H_bonds.
+ It is 1 for donor H, 2 for acceptors (O,S,N), 0 for others*/
+
+ /* Line three in field file */
+ real r_pi_pi;
+ real p_lp2;
+ real b_o_131;
+ real b_o_132;
+ real b_o_133;
+
+ /* Line four in the field file */
+ real p_ovun2;
+ real p_val3;
+ real valency_val;
+ real p_val5;
+ real rcore2;
+ real ecore2;
+ real acore2;
} single_body_parameters;
/* Two Body Parameters */
-typedef struct {
- /* Bond Order parameters */
- real p_bo1,p_bo2,p_bo3,p_bo4,p_bo5,p_bo6;
- real r_s, r_p, r_pp; /* r_o distances in BO formula */
- real p_boc3, p_boc4, p_boc5;
-
- /* Bond Energy parameters */
- real p_be1, p_be2;
- real De_s, De_p, De_pp;
-
- /* Over/Under coordination parameters */
- real p_ovun1;
-
- /* Van der Waal interaction parameters */
- real D;
- real alpha;
- real r_vdW;
- real gamma_w;
- real rcore, ecore, acore;
-
- /* electrostatic parameters */
- real gamma; // note: this parameter is gamma^-3 and not gamma.
-
- real v13cor, ovc;
+typedef struct
+{
+ /* Bond Order parameters */
+ real p_bo1, p_bo2, p_bo3, p_bo4, p_bo5, p_bo6;
+ real r_s, r_p, r_pp; /* r_o distances in BO formula */
+ real p_boc3, p_boc4, p_boc5;
+
+ /* Bond Energy parameters */
+ real p_be1, p_be2;
+ real De_s, De_p, De_pp;
+
+ /* Over/Under coordination parameters */
+ real p_ovun1;
+
+ /* Van der Waal interaction parameters */
+ real D;
+ real alpha;
+ real r_vdW;
+ real gamma_w;
+ real rcore, ecore, acore;
+
+ /* electrostatic parameters */
+ real gamma; // note: this parameter is gamma^-3 and not gamma.
+
+ real v13cor, ovc;
} two_body_parameters;
/* 3-body parameters */
-typedef struct {
- /* valence angle */
- real theta_00;
- real p_val1, p_val2, p_val4, p_val7;
+typedef struct
+{
+ /* valence angle */
+ real theta_00;
+ real p_val1, p_val2, p_val4, p_val7;
- /* penalty */
- real p_pen1;
+ /* penalty */
+ real p_pen1;
- /* 3-body conjugation */
- real p_coa1;
+ /* 3-body conjugation */
+ real p_coa1;
} three_body_parameters;
-typedef struct{
- int cnt;
- three_body_parameters prm[MAX_3BODY_PARAM];
+typedef struct
+{
+ int cnt;
+ three_body_parameters prm[MAX_3BODY_PARAM];
} three_body_header;
/* hydrogen-bond parameters */
-typedef struct{
- real r0_hb, p_hb1, p_hb2, p_hb3;
+typedef struct
+{
+ real r0_hb, p_hb1, p_hb2, p_hb3;
} hbond_parameters;
/* 4-body parameters */
-typedef struct {
- real V1, V2, V3;
+typedef struct
+{
+ real V1, V2, V3;
- /* torsion angle */
- real p_tor1;
+ /* torsion angle */
+ real p_tor1;
- /* 4-body conjugation */
- real p_cot1;
+ /* 4-body conjugation */
+ real p_cot1;
} four_body_parameters;
-typedef struct{
- int cnt;
- four_body_parameters prm[MAX_4BODY_PARAM];
+typedef struct
+{
+ int cnt;
+ four_body_parameters prm[MAX_4BODY_PARAM];
} four_body_header;
-typedef struct{
- int num_atom_types;
- global_parameters gp;
- single_body_parameters *sbp;
- two_body_parameters **tbp;
- three_body_header ***thbp;
- hbond_parameters ***hbp;
- four_body_header ****fbp;
+typedef struct
+{
+ int num_atom_types;
+ global_parameters gp;
+ single_body_parameters *sbp;
+ two_body_parameters **tbp;
+ three_body_header ***thbp;
+ hbond_parameters ***hbp;
+ four_body_header ****fbp;
} reax_interaction;
typedef struct
{
- rvec x, v, f; /* Position, velocity, force on atom */
- real q; /* Charge on the atom */
- int type; /* Type of this atom */
- char name[5];
+ rvec x, v, f; /* Position, velocity, force on atom */
+ real q; /* Charge on the atom */
+ int type; /* Type of this atom */
+ char name[5];
} reax_atom;
typedef struct
{
- real volume;
+ real volume;
- rvec box_norms;
- rvec side_prop;
- rvec nbr_box_press[27];
- // rvec lower_end;
+ rvec box_norms;
+ rvec side_prop;
+ rvec nbr_box_press[27];
+ // rvec lower_end;
- rtensor box, box_inv, old_box;
- rtensor trans, trans_inv;
- rtensor g;
+ rtensor box, box_inv, old_box;
+ rtensor trans, trans_inv;
+ rtensor g;
} simulation_box;
typedef struct
{
- int max_atoms;
- int max_nbrs;
- int total;
- real cell_size;
- ivec spread;
-
- ivec ncell;
- rvec len;
- rvec inv_len;
-
- int**** atoms;
- int*** top;
- int*** mark;
- int*** start;
- int*** end;
- ivec**** nbrs;
- rvec**** nbrs_cp;
+ int max_atoms;
+ int max_nbrs;
+ int total;
+ real cell_size;
+ ivec spread;
+
+ ivec ncell;
+ rvec len;
+ rvec inv_len;
+
+ int**** atoms;
+ int*** top;
+ int*** mark;
+ int*** start;
+ int*** end;
+ ivec**** nbrs;
+ rvec**** nbrs_cp;
} grid;
typedef struct
{
- int N;
- reax_atom *atoms;
- reax_interaction reaxprm;
- simulation_box box;
- grid g;
+ int N;
+ reax_atom *atoms;
+ reax_interaction reaxprm;
+ simulation_box box;
+ grid g;
} reax_system;
/* Simulation control parameters not related to the system */
typedef struct
{
- char sim_name[MAX_STR];
- char restart_from[MAX_STR];
- int restart;
- int random_vel;
-
- int reposition_atoms;
-
- /* ensemble values:
- 0 : NVE
- 1 : NVT (Nose-Hoover)
- 2 : NPT (Parrinello-Rehman-Nose-Hoover) Anisotropic
- 3 : sNPT (Parrinello-Rehman-Nose-Hoover) semiisotropic
- 4 : iNPT (Parrinello-Rehman-Nose-Hoover) isotropic */
- int ensemble;
- int nsteps;
- int periodic_boundaries;
- int restrict_bonds;
- int tabulate;
- ivec periodic_images;
- real dt;
-
- int reneighbor;
- real vlist_cut;
- real nbr_cut;
- real r_cut, r_low; // upper and lower taper
- real bo_cut;
- real thb_cut;
- real hb_cut;
- real Tap7, Tap6, Tap5, Tap4, Tap3, Tap2, Tap1, Tap0;
- real q_err;
- int max_far_nbrs;
-
- real T_init, T_final, T;
- real Tau_T;
- int T_mode;
- real T_rate, T_freq;
-
- real Tau_PT;
- rvec P, Tau_P;
- int press_mode;
- real compressibility;
-
- int remove_CoM_vel;
-
- int geo_format;
-
- int dipole_anal;
- int freq_dipole_anal;
-
- int diffusion_coef;
- int freq_diffusion_coef;
- int restrict_type;
-
- int refactor;
- real droptol;
-
- int molec_anal;
- int freq_molec_anal;
- real bg_cut;
- int num_ignored;
- int ignore[MAX_ATOM_TYPES];
+ char sim_name[MAX_STR];
+ char restart_from[MAX_STR];
+ int restart;
+ int random_vel;
+
+ int reposition_atoms;
+
+ /* ensemble values:
+ 0 : NVE
+ 1 : NVT (Nose-Hoover)
+ 2 : NPT (Parrinello-Rehman-Nose-Hoover) Anisotropic
+ 3 : sNPT (Parrinello-Rehman-Nose-Hoover) semiisotropic
+ 4 : iNPT (Parrinello-Rehman-Nose-Hoover) isotropic */
+ int ensemble;
+ int nsteps;
+ int periodic_boundaries;
+ int restrict_bonds;
+ int tabulate;
+ ivec periodic_images;
+ real dt;
+
+ int reneighbor;
+ real vlist_cut;
+ real nbr_cut;
+ real r_cut, r_low; // upper and lower taper
+ real bo_cut;
+ real thb_cut;
+ real hb_cut;
+ real Tap7, Tap6, Tap5, Tap4, Tap3, Tap2, Tap1, Tap0;
+ real q_err;
+ int max_far_nbrs;
+
+ real T_init, T_final, T;
+ real Tau_T;
+ int T_mode;
+ real T_rate, T_freq;
+
+ real Tau_PT;
+ rvec P, Tau_P;
+ int press_mode;
+ real compressibility;
+
+ int remove_CoM_vel;
+
+ int geo_format;
+
+ int dipole_anal;
+ int freq_dipole_anal;
+
+ int diffusion_coef;
+ int freq_diffusion_coef;
+ int restrict_type;
+
+ int refactor;
+ real droptol;
+
+ int molec_anal;
+ int freq_molec_anal;
+ real bg_cut;
+ int num_ignored;
+ int ignore[MAX_ATOM_TYPES];
} control_params;
typedef struct
{
- real T;
- real xi;
- real v_xi;
- real v_xi_old;
- real G_xi;
+ real T;
+ real xi;
+ real v_xi;
+ real v_xi_old;
+ real G_xi;
} thermostat;
typedef struct
{
- real P;
- real eps;
- real v_eps;
- real v_eps_old;
- real a_eps;
+ real P;
+ real eps;
+ real v_eps;
+ real v_eps_old;
+ real a_eps;
} isotropic_barostat;
typedef struct
{
- rtensor P;
- real P_scalar;
-
- real eps;
- real v_eps;
- real v_eps_old;
- real a_eps;
+ rtensor P;
+ real P_scalar;
- rtensor h0;
- rtensor v_g0;
- rtensor v_g0_old;
- rtensor a_g0;
+ real eps;
+ real v_eps;
+ real v_eps_old;
+ real a_eps;
+
+ rtensor h0;
+ rtensor v_g0;
+ rtensor v_g0_old;
+ rtensor a_g0;
} flexible_barostat;
typedef struct
{
- real start;
- real end;
- real elapsed;
-
- real total;
- real nbrs;
- real init_forces;
- real bonded;
- real nonb;
- real QEq;
- int matvecs;
+ real start;
+ real end;
+ real elapsed;
+
+ real total;
+ real nbrs;
+ real init_forces;
+ real bonded;
+ real nonb;
+ real QEq;
+ int matvecs;
} reax_timing;
typedef struct
{
- int step;
- int prev_steps;
- real time;
-
- real M; /* Total Mass */
- real inv_M; /* 1 / Total Mass */
-
- rvec xcm; /* Center of mass */
- rvec vcm; /* Center of mass velocity */
- rvec fcm; /* Center of mass force */
- rvec amcm; /* Angular momentum of CoM */
- rvec avcm; /* Angular velocity of CoM */
- real etran_cm; /* Translational kinetic energy of CoM */
- real erot_cm; /* Rotational kinetic energy of CoM */
-
- rtensor kinetic; /* Kinetic energy tensor */
- rtensor virial; /* Hydrodynamic virial */
-
- real E_Tot;
- real E_Kin; /* Total kinetic energy */
- real E_Pot;
-
- real E_BE; /* Total bond energy */
- real E_Ov; /* Total over coordination */
- real E_Un; /* Total under coordination energy */
- real E_Lp; /* Total under coordination energy */
- real E_Ang; /* Total valance angle energy */
- real E_Pen; /* Total penalty energy */
- real E_Coa; /* Total three body conjgation energy */
- real E_HB; /* Total Hydrogen bond energy */
- real E_Tor; /* Total torsional energy */
- real E_Con; /* Total four body conjugation energy */
- real E_vdW; /* Total van der Waals energy */
- real E_Ele; /* Total electrostatics energy */
- real E_Pol; /* Polarization energy */
-
- real N_f; /*Number of degrees of freedom */
- rvec t_scale;
- rtensor p_scale;
- thermostat therm; /* Used in Nose_Hoover method */
- isotropic_barostat iso_bar;
- flexible_barostat flex_bar;
- real inv_W;
-
- rvec int_press;
- rvec ext_press;
- real kin_press;
- rvec tot_press;
-
- reax_timing timing;
+ int step;
+ int prev_steps;
+ real time;
+
+ real M; /* Total Mass */
+ real inv_M; /* 1 / Total Mass */
+
+ rvec xcm; /* Center of mass */
+ rvec vcm; /* Center of mass velocity */
+ rvec fcm; /* Center of mass force */
+ rvec amcm; /* Angular momentum of CoM */
+ rvec avcm; /* Angular velocity of CoM */
+ real etran_cm; /* Translational kinetic energy of CoM */
+ real erot_cm; /* Rotational kinetic energy of CoM */
+
+ rtensor kinetic; /* Kinetic energy tensor */
+ rtensor virial; /* Hydrodynamic virial */
+
+ real E_Tot;
+ real E_Kin; /* Total kinetic energy */
+ real E_Pot;
+
+ real E_BE; /* Total bond energy */
+ real E_Ov; /* Total over coordination */
+ real E_Un; /* Total under coordination energy */
+ real E_Lp; /* Total under coordination energy */
+ real E_Ang; /* Total valance angle energy */
+ real E_Pen; /* Total penalty energy */
+ real E_Coa; /* Total three body conjgation energy */
+ real E_HB; /* Total Hydrogen bond energy */
+ real E_Tor; /* Total torsional energy */
+ real E_Con; /* Total four body conjugation energy */
+ real E_vdW; /* Total van der Waals energy */
+ real E_Ele; /* Total electrostatics energy */
+ real E_Pol; /* Polarization energy */
+
+ real N_f; /*Number of degrees of freedom */
+ rvec t_scale;
+ rtensor p_scale;
+ thermostat therm; /* Used in Nose_Hoover method */
+ isotropic_barostat iso_bar;
+ flexible_barostat flex_bar;
+ real inv_W;
+
+ rvec int_press;
+ rvec ext_press;
+ real kin_press;
+ rvec tot_press;
+
+ reax_timing timing;
} simulation_data;
-typedef struct {
- int thb;
- int pthb; /* pointer to the third body on the central atom's nbrlist */
- real theta, cos_theta;
- rvec dcos_di, dcos_dj, dcos_dk;
+typedef struct
+{
+ int thb;
+ int pthb; /* pointer to the third body on the central atom's nbrlist */
+ real theta, cos_theta;
+ rvec dcos_di, dcos_dj, dcos_dk;
} three_body_interaction_data;
-typedef struct {
- int nbr;
- ivec rel_box;
- // rvec ext_factor;
- real d;
- rvec dvec;
+typedef struct
+{
+ int nbr;
+ ivec rel_box;
+ // rvec ext_factor;
+ real d;
+ rvec dvec;
} near_neighbor_data;
-typedef struct {
- int nbr;
- ivec rel_box;
- // rvec ext_factor;
- real d;
- rvec dvec;
- // real H; //, Tap, inv_dr3gamij_1, inv_dr3gamij_3;
+typedef struct
+{
+ int nbr;
+ ivec rel_box;
+ // rvec ext_factor;
+ real d;
+ rvec dvec;
+ // real H; //, Tap, inv_dr3gamij_1, inv_dr3gamij_3;
} far_neighbor_data;
-typedef struct {
- int nbr;
- int scl;
- far_neighbor_data *ptr;
+typedef struct
+{
+ int nbr;
+ int scl;
+ far_neighbor_data *ptr;
} hbond_data;
-typedef struct {
- int wrt;
- rvec dVal;
+typedef struct
+{
+ int wrt;
+ rvec dVal;
} dDelta_data;
-typedef struct {
- int wrt;
- rvec dBO, dBOpi, dBOpi2;
+typedef struct
+{
+ int wrt;
+ rvec dBO, dBOpi, dBOpi2;
} dbond_data;
-typedef struct {
- real BO, BO_s, BO_pi, BO_pi2;
- real Cdbo, Cdbopi, Cdbopi2;
- real C1dbo, C2dbo, C3dbo;
- real C1dbopi, C2dbopi, C3dbopi, C4dbopi;
- real C1dbopi2, C2dbopi2, C3dbopi2, C4dbopi2;
- rvec dBOp, dln_BOp_s, dln_BOp_pi, dln_BOp_pi2;
+typedef struct
+{
+ real BO, BO_s, BO_pi, BO_pi2;
+ real Cdbo, Cdbopi, Cdbopi2;
+ real C1dbo, C2dbo, C3dbo;
+ real C1dbopi, C2dbopi, C3dbopi, C4dbopi;
+ real C1dbopi2, C2dbopi2, C3dbopi2, C4dbopi2;
+ rvec dBOp, dln_BOp_s, dln_BOp_pi, dln_BOp_pi2;
} bond_order_data;
-typedef struct {
- int nbr;
- int sym_index;
- int dbond_index;
- ivec rel_box;
- // rvec ext_factor;
- real d;
- rvec dvec;
- bond_order_data bo_data;
+typedef struct
+{
+ int nbr;
+ int sym_index;
+ int dbond_index;
+ ivec rel_box;
+ // rvec ext_factor;
+ real d;
+ rvec dvec;
+ bond_order_data bo_data;
} bond_data;
@@ -625,9 +642,10 @@ typedef struct {
// to avoid having the compiler add padding bytes (manual alignment along word boundary)
// Warning: padding is implementation (compiler) dependent, so not portable,
// and also potentially dangerous
-typedef struct {
- int j;
- real val;
+typedef struct
+{
+ int j;
+ real val;
} sparse_matrix_entry;
/* compressed row storage (crs) format
@@ -639,231 +657,234 @@ typedef struct {
* start: row pointer (last element contains NNZ + 1)
* entries: (column index, val) pairs
* */
-typedef struct {
- int n, m;
- int *start;
- sparse_matrix_entry *entries;
+typedef struct
+{
+ int n, m;
+ int *start;
+ sparse_matrix_entry *entries;
// int *j;
// real *val;
} sparse_matrix;
-typedef struct {
- int num_far;
- int Htop;
- int hbonds;
- int num_hbonds;
- int bonds;
- int num_bonds;
- int num_3body;
- int gcell_atoms;
+typedef struct
+{
+ int num_far;
+ int Htop;
+ int hbonds;
+ int num_hbonds;
+ int bonds;
+ int num_bonds;
+ int num_3body;
+ int gcell_atoms;
} reallocate_data;
-typedef struct {
- /* bond order related storage */
- real *total_bond_order;
- real *Deltap, *Deltap_boc;
- real *Delta, *Delta_lp, *Delta_lp_temp, *Delta_e, *Delta_boc;
- real *dDelta_lp, *dDelta_lp_temp;
- real *nlp, *nlp_temp, *Clp, *vlpex;
- rvec *dDeltap_self;
-
- /* QEq storage */
- sparse_matrix *H, *L, *U;
- real *droptol;
- real *w;
- real *Hdia_inv;
- real *b, *b_s, *b_t, *b_prc, *b_prm;
- real **s, **t;
- real *s_t; //, *s_old, *t_old, *s_oldest, *t_oldest;
-
- /* GMRES related storage */
- real *y, *z, *g;
- real *hc, *hs;
- real **h, **rn, **v;
- /* CG related storage */
- real *r, *d, *q, *p;
- int s_dims, t_dims;
-
- int num_H;
- int *hbond_index; // for hydrogen bonds
-
- rvec *v_const, *f_old, *a; // used in integrators
-
- real *CdDelta; // coefficient of dDelta for force calculations
-
- int *mark, *old_mark; // storage for analysis
- rvec *x_old;
-
- /* storage space for bond restrictions */
- int *map_serials;
- int *orig_id;
- int *restricted;
- int **restricted_list;
-
- reallocate_data realloc;
-
+typedef struct
+{
+ /* bond order related storage */
+ real *total_bond_order;
+ real *Deltap, *Deltap_boc;
+ real *Delta, *Delta_lp, *Delta_lp_temp, *Delta_e, *Delta_boc;
+ real *dDelta_lp, *dDelta_lp_temp;
+ real *nlp, *nlp_temp, *Clp, *vlpex;
+ rvec *dDeltap_self;
+
+ /* QEq storage */
+ sparse_matrix *H, *L, *U;
+ real *droptol;
+ real *w;
+ real *Hdia_inv;
+ real *b, *b_s, *b_t, *b_prc, *b_prm;
+ real **s, **t;
+ real *s_t; //, *s_old, *t_old, *s_oldest, *t_oldest;
+
+ /* GMRES related storage */
+ real *y, *z, *g;
+ real *hc, *hs;
+ real **h, **rn, **v;
+ /* CG related storage */
+ real *r, *d, *q, *p;
+ int s_dims, t_dims;
+
+ int num_H;
+ int *hbond_index; // for hydrogen bonds
+
+ rvec *v_const, *f_old, *a; // used in integrators
+
+ real *CdDelta; // coefficient of dDelta for force calculations
+
+ int *mark, *old_mark; // storage for analysis
+ rvec *x_old;
+
+ /* storage space for bond restrictions */
+ int *map_serials;
+ int *orig_id;
+ int *restricted;
+ int **restricted_list;
+
+ reallocate_data realloc;
+
#ifdef TEST_FORCES
- rvec *f_ele;
- rvec *f_vdw;
- rvec *f_bo;
- rvec *f_be;
- rvec *f_lp;
- rvec *f_ov;
- rvec *f_un;
- rvec *f_ang;
- rvec *f_coa;
- rvec *f_pen;
- rvec *f_hb;
- rvec *f_tor;
- rvec *f_con;
- rvec *dDelta; /* Calculated on the fly in bond_orders.c */
+ rvec *f_ele;
+ rvec *f_vdw;
+ rvec *f_bo;
+ rvec *f_be;
+ rvec *f_lp;
+ rvec *f_ov;
+ rvec *f_un;
+ rvec *f_ang;
+ rvec *f_coa;
+ rvec *f_pen;
+ rvec *f_hb;
+ rvec *f_tor;
+ rvec *f_con;
+ rvec *dDelta; /* Calculated on the fly in bond_orders.c */
#endif
} static_storage;
typedef struct
{
- int n;
- int num_intrs;
- int *index;
- int *end_index;
- int type;
- union
- {
- void *v;
- three_body_interaction_data *three_body_list;
- bond_data *bond_list;
- dbond_data *dbo_list;
- dDelta_data *dDelta_list;
- far_neighbor_data *far_nbr_list;
- near_neighbor_data *near_nbr_list;
- hbond_data *hbond_list;
- }select;
+ int n;
+ int num_intrs;
+ int *index;
+ int *end_index;
+ int type;
+ union
+ {
+ void *v;
+ three_body_interaction_data *three_body_list;
+ bond_data *bond_list;
+ dbond_data *dbo_list;
+ dDelta_data *dDelta_list;
+ far_neighbor_data *far_nbr_list;
+ near_neighbor_data *near_nbr_list;
+ hbond_data *hbond_list;
+ } select;
} list;
typedef struct
{
- FILE *trj;
- FILE *out;
- FILE *pot;
- FILE *log;
- FILE *mol, *ign;
- FILE *dpl;
- FILE *drft;
- FILE *pdb;
- FILE *prs;
-
- int write_steps;
- int traj_compress;
- int traj_format;
- char traj_title[81];
- int atom_format;
- int bond_info;
- int angle_info;
-
- int restart_format;
- int restart_freq;
- int debug_level;
- int energy_update_freq;
-
- // trajectory output functions
- int (* write_header)( reax_system*, control_params*, static_storage*, void* );
- int (* append_traj_frame)(reax_system*, control_params*,
- simulation_data*, static_storage*, list **, void* );
- int (* write)( FILE *, const char *, ... );
+ FILE *trj;
+ FILE *out;
+ FILE *pot;
+ FILE *log;
+ FILE *mol, *ign;
+ FILE *dpl;
+ FILE *drft;
+ FILE *pdb;
+ FILE *prs;
+
+ int write_steps;
+ int traj_compress;
+ int traj_format;
+ char traj_title[81];
+ int atom_format;
+ int bond_info;
+ int angle_info;
+
+ int restart_format;
+ int restart_freq;
+ int debug_level;
+ int energy_update_freq;
+
+ // trajectory output functions
+ int (* write_header)( reax_system*, control_params*, static_storage*, void* );
+ int (* append_traj_frame)(reax_system*, control_params*,
+ simulation_data*, static_storage*, list **, void* );
+ int (* write)( FILE *, const char *, ... );
#ifdef TEST_ENERGY
- FILE *ebond;
- FILE *elp, *eov, *eun;
- FILE *eval, *epen, *ecoa;
- FILE *ehb;
- FILE *etor, *econ;
- FILE *evdw, *ecou;
+ FILE *ebond;
+ FILE *elp, *eov, *eun;
+ FILE *eval, *epen, *ecoa;
+ FILE *ehb;
+ FILE *etor, *econ;
+ FILE *evdw, *ecou;
#endif
- FILE *ftot;
+ FILE *ftot;
#ifdef TEST_FORCES
- FILE *fbo, *fdbo;
- FILE *fbond;
- FILE *flp, *fatom;
- FILE *f3body;
- FILE *fhb;
- FILE *f4body;
- FILE *fnonb;
- FILE *ftot2;
+ FILE *fbo, *fdbo;
+ FILE *fbond;
+ FILE *flp, *fatom;
+ FILE *f3body;
+ FILE *fhb;
+ FILE *f4body;
+ FILE *fnonb;
+ FILE *ftot2;
#endif
} output_controls;
typedef struct
{
- int atom_count;
- int atom_list[MAX_MOLECULE_SIZE];
- int mtypes[MAX_ATOM_TYPES];
-} molecule;
+ int atom_count;
+ int atom_list[MAX_MOLECULE_SIZE];
+ int mtypes[MAX_ATOM_TYPES];
+} molecule;
typedef struct
{
- real H;
- real e_vdW, CEvd;
- real e_ele, CEclmb;
+ real H;
+ real e_vdW, CEvd;
+ real e_ele, CEclmb;
} LR_data;
typedef struct
{
- real a, b, c, d;
+ real a, b, c, d;
} cubic_spline_coef;
typedef struct
{
- real xmin, xmax;
- int n;
- real dx, inv_dx;
- real a;
+ real xmin, xmax;
+ int n;
+ real dx, inv_dx;
+ real a;
- real m;
- real c;
+ real m;
+ real c;
- real *y;
+ real *y;
} lookup_table;
typedef struct
{
- real xmin, xmax;
- int n;
- real dx, inv_dx;
- real a;
- real m;
- real c;
-
- LR_data *y;
- cubic_spline_coef *H;
- cubic_spline_coef *vdW, *CEvd;
- cubic_spline_coef *ele, *CEclmb;
+ real xmin, xmax;
+ int n;
+ real dx, inv_dx;
+ real a;
+ real m;
+ real c;
+
+ LR_data *y;
+ cubic_spline_coef *H;
+ cubic_spline_coef *vdW, *CEvd;
+ cubic_spline_coef *ele, *CEclmb;
} LR_lookup_table;
-typedef void (*interaction_function)(reax_system*, control_params*,
- simulation_data*, static_storage*,
- list**, output_controls*);
+typedef void (*interaction_function)(reax_system*, control_params*,
+ simulation_data*, static_storage*,
+ list**, output_controls*);
interaction_function Interaction_Functions[NO_OF_INTERACTIONS];
-typedef void (*evolve_function)(reax_system*, control_params*,
- simulation_data*, static_storage*,
- list**, output_controls*);
+typedef void (*evolve_function)(reax_system*, control_params*,
+ simulation_data*, static_storage*,
+ list**, output_controls*);
typedef real (*lookup_function)(real);
lookup_table Exp, Sqrt, Cube_Root, Four_Third_Root, Cos, Sin, ACos;
LR_lookup_table **LR;
-typedef void (*get_far_neighbors_function)(rvec, rvec, simulation_box*,
- control_params*, far_neighbor_data*,
- int*);
+typedef void (*get_far_neighbors_function)(rvec, rvec, simulation_box*,
+ control_params*, far_neighbor_data*,
+ int*);
#endif
diff --git a/puremd_rc_1003/sPuReMD/neighbors.c b/puremd_rc_1003/sPuReMD/neighbors.c
index 9d3821e7774a4dee87f1b631e63d6e3c07bc0917..9b04cfa8c4e6f1d1886adc09a4fe68d73a060a45 100644
--- a/puremd_rc_1003/sPuReMD/neighbors.c
+++ b/puremd_rc_1003/sPuReMD/neighbors.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -31,115 +31,125 @@
inline real DistSqr_to_CP( rvec cp, rvec x )
{
- int i;
- real d_sqr = 0;
+ int i;
+ real d_sqr = 0;
- for( i = 0; i < 3; ++i )
- if( cp[i] > NEG_INF )
- d_sqr += SQR( cp[i] - x[i] );
+ for ( i = 0; i < 3; ++i )
+ if ( cp[i] > NEG_INF )
+ d_sqr += SQR( cp[i] - x[i] );
- return d_sqr;
+ return d_sqr;
}
-void Generate_Neighbor_Lists( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+void Generate_Neighbor_Lists( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int i, j, k, l, m, itr;
- int x, y, z;
- int atom1, atom2, max;
- int num_far;
- int *nbr_atoms;
- ivec *nbrs;
- rvec *nbrs_cp;
- grid *g;
- list *far_nbrs;
- far_neighbor_data *nbr_data;
- real t_start, t_elapsed;
-
- t_start = Get_Time( );
- // fprintf( stderr, "\n\tentered nbrs - " );
- g = &( system->g );
- far_nbrs = (*lists) + FAR_NBRS;
- Bin_Atoms( system, workspace );
- // fprintf( stderr, "atoms sorted - " );
- num_far = 0;
-
- /* first pick up a cell in the grid */
- for( i = 0; i < g->ncell[0]; i++ )
- for( j = 0; j < g->ncell[1]; j++ )
- for( k = 0; k < g->ncell[2]; k++ ) {
- nbrs = g->nbrs[i][j][k];
- nbrs_cp = g->nbrs_cp[i][j][k];
- //fprintf( stderr, "gridcell %d %d %d\n", i, j, k );
-
- /* pick up an atom from the current cell */
- for(l = 0; l < g->top[i][j][k]; ++l ){
- atom1 = g->atoms[i][j][k][l];
- Set_Start_Index( atom1, num_far, far_nbrs );
- //fprintf( stderr, "\tatom %d\n", atom1 );
-
- itr = 0;
- while( nbrs[itr][0] >= 0 ){
- x = nbrs[itr][0];
- y = nbrs[itr][1];
- z = nbrs[itr][2];
- //fprintf( stderr, "\t\tgridcell %d %d %d\n", x, y, z );
-
- if( DistSqr_to_CP(nbrs_cp[itr], system->atoms[atom1].x ) <=
- SQR(control->vlist_cut) ) {
- nbr_atoms = g->atoms[x][y][z];
- max = g->top[x][y][z];
- //fprintf( stderr, "\t\tmax: %d\n", max );
-
- /* pick up another atom from the neighbor cell */
- for( m = 0; m < max; ++m ) {
- atom2 = nbr_atoms[m];
- if( atom1 > atom2 ) {
- nbr_data = &(far_nbrs->select.far_nbr_list[num_far]);
- //fprintf (stderr, " %f %f %f \n", nbr_data->dvec[0], nbr_data->dvec[1], nbr_data->dvec[2]);
- if(Are_Far_Neighbors(system->atoms[atom1].x,
- system->atoms[atom2].x,
- &(system->box), control->vlist_cut,
- nbr_data)) {
- nbr_data->nbr = atom2;
- ++num_far;
- }
- }
- }
- }
-
- ++itr;
- }
-
- Set_End_Index( atom1, num_far, far_nbrs );
- //fprintf(stderr, "i:%d, start: %d, end: %d - itr: %d\n",
- // atom1,Start_Index(atom1,far_nbrs),End_Index(atom1,far_nbrs),
- // itr);
- }
- }
-
- if( num_far > far_nbrs->num_intrs * DANGER_ZONE ) {
- workspace->realloc.num_far = num_far;
- if( num_far > far_nbrs->num_intrs ){
- fprintf( stderr, "step%d-ran out of space on far_nbrs: top=%d, max=%d",
- data->step, num_far, far_nbrs->num_intrs );
- exit( INSUFFICIENT_SPACE );
+ int i, j, k, l, m, itr;
+ int x, y, z;
+ int atom1, atom2, max;
+ int num_far;
+ int *nbr_atoms;
+ ivec *nbrs;
+ rvec *nbrs_cp;
+ grid *g;
+ list *far_nbrs;
+ far_neighbor_data *nbr_data;
+ real t_start, t_elapsed;
+
+ t_start = Get_Time( );
+ // fprintf( stderr, "\n\tentered nbrs - " );
+ g = &( system->g );
+ far_nbrs = (*lists) + FAR_NBRS;
+ Bin_Atoms( system, workspace );
+ // fprintf( stderr, "atoms sorted - " );
+ num_far = 0;
+
+ /* first pick up a cell in the grid */
+ for ( i = 0; i < g->ncell[0]; i++ )
+ for ( j = 0; j < g->ncell[1]; j++ )
+ for ( k = 0; k < g->ncell[2]; k++ )
+ {
+ nbrs = g->nbrs[i][j][k];
+ nbrs_cp = g->nbrs_cp[i][j][k];
+ //fprintf( stderr, "gridcell %d %d %d\n", i, j, k );
+
+ /* pick up an atom from the current cell */
+ for (l = 0; l < g->top[i][j][k]; ++l )
+ {
+ atom1 = g->atoms[i][j][k][l];
+ Set_Start_Index( atom1, num_far, far_nbrs );
+ //fprintf( stderr, "\tatom %d\n", atom1 );
+
+ itr = 0;
+ while ( nbrs[itr][0] >= 0 )
+ {
+ x = nbrs[itr][0];
+ y = nbrs[itr][1];
+ z = nbrs[itr][2];
+ //fprintf( stderr, "\t\tgridcell %d %d %d\n", x, y, z );
+
+ if ( DistSqr_to_CP(nbrs_cp[itr], system->atoms[atom1].x ) <=
+ SQR(control->vlist_cut) )
+ {
+ nbr_atoms = g->atoms[x][y][z];
+ max = g->top[x][y][z];
+ //fprintf( stderr, "\t\tmax: %d\n", max );
+
+ /* pick up another atom from the neighbor cell */
+ for ( m = 0; m < max; ++m )
+ {
+ atom2 = nbr_atoms[m];
+ if ( atom1 > atom2 )
+ {
+ nbr_data = &(far_nbrs->select.far_nbr_list[num_far]);
+ //fprintf (stderr, " %f %f %f \n", nbr_data->dvec[0], nbr_data->dvec[1], nbr_data->dvec[2]);
+ if (Are_Far_Neighbors(system->atoms[atom1].x,
+ system->atoms[atom2].x,
+ &(system->box), control->vlist_cut,
+ nbr_data))
+ {
+ nbr_data->nbr = atom2;
+ ++num_far;
+ }
+ }
+ }
+ }
+
+ ++itr;
+ }
+
+ Set_End_Index( atom1, num_far, far_nbrs );
+ //fprintf(stderr, "i:%d, start: %d, end: %d - itr: %d\n",
+ // atom1,Start_Index(atom1,far_nbrs),End_Index(atom1,far_nbrs),
+ // itr);
+ }
+ }
+
+ if ( num_far > far_nbrs->num_intrs * DANGER_ZONE )
+ {
+ workspace->realloc.num_far = num_far;
+ if ( num_far > far_nbrs->num_intrs )
+ {
+ fprintf( stderr, "step%d-ran out of space on far_nbrs: top=%d, max=%d",
+ data->step, num_far, far_nbrs->num_intrs );
+ exit( INSUFFICIENT_SPACE );
+ }
}
- }
- t_elapsed = Get_Timing_Info( t_start );
- data->timing.nbrs += t_elapsed;
+ t_elapsed = Get_Timing_Info( t_start );
+ data->timing.nbrs += t_elapsed;
#if defined(DEBUG)
- for( i = 0; i < system->N; ++i ) {
- qsort( &(far_nbrs->select.far_nbr_list[ Start_Index(i, far_nbrs) ]),
- Num_Entries(i, far_nbrs), sizeof(far_neighbor_data),
- compare_far_nbrs );
- }
+ for ( i = 0; i < system->N; ++i )
+ {
+ qsort( &(far_nbrs->select.far_nbr_list[ Start_Index(i, far_nbrs) ]),
+ Num_Entries(i, far_nbrs), sizeof(far_neighbor_data),
+ compare_far_nbrs );
+ }
#endif
-#if defined(DEBUG_FOCUS)
+#if defined(DEBUG_FOCUS)
fprintf( stderr, "nbrs - ");
fprintf( stderr, "nbrs done, num_far: %d\n", num_far );
#endif
@@ -149,128 +159,134 @@ void Generate_Neighbor_Lists( reax_system *system, control_params *control,
}
-int Estimate_NumNeighbors( reax_system *system, control_params *control,
- static_storage *workspace, list **lists )
+int Estimate_NumNeighbors( reax_system *system, control_params *control,
+ static_storage *workspace, list **lists )
{
- int i, j, k, l, m, itr;
- int x, y, z;
- int atom1, atom2, max;
- int num_far;
- int *nbr_atoms;
- ivec *nbrs;
- rvec *nbrs_cp;
- grid *g;
- far_neighbor_data nbr_data;
-
- // fprintf( stderr, "\n\tentered nbrs - " );
- g = &( system->g );
- Bin_Atoms( system, workspace );
- // fprintf( stderr, "atoms sorted - " );
- num_far = 0;
-
- /* first pick up a cell in the grid */
- for( i = 0; i < g->ncell[0]; i++ )
- for( j = 0; j < g->ncell[1]; j++ )
- for( k = 0; k < g->ncell[2]; k++ ) {
- nbrs = g->nbrs[i][j][k];
- nbrs_cp = g->nbrs_cp[i][j][k];
- //fprintf( stderr, "gridcell %d %d %d\n", i, j, k );
-
- /* pick up an atom from the current cell */
- for(l = 0; l < g->top[i][j][k]; ++l ){
- atom1 = g->atoms[i][j][k][l];
-
- itr = 0;
- while( nbrs[itr][0] >= 0 ){
- x = nbrs[itr][0];
- y = nbrs[itr][1];
- z = nbrs[itr][2];
- //fprintf( stderr, "\t\tgridcell %d %d %d\n", x, y, z );
-
- if( DistSqr_to_CP(nbrs_cp[itr], system->atoms[atom1].x ) <=
- SQR(control->vlist_cut) ) {
- nbr_atoms = g->atoms[x][y][z];
- max = g->top[x][y][z];
- //fprintf( stderr, "\t\tmax: %d\n", max );
-
- /* pick up another atom from the neighbor cell -
- we have to compare atom1 with its own periodic images as well,
- that's why there is also equality in the if stmt below */
- for( m = 0; m < max; ++m ) {
- atom2 = nbr_atoms[m];
- //if( nbrs[itr+1][0] >= 0 || atom1 > atom2 ) {
- if( atom1 > atom2 ) {
- if(Are_Far_Neighbors(system->atoms[atom1].x,
- system->atoms[atom2].x,
- &(system->box), control->vlist_cut,
- &nbr_data))
- ++num_far;
- }
- }
- }
-
- ++itr;
- }
- }
- }
-
-#if defined(DEBUG_FOCUS)
- fprintf( stderr, "estimate nbrs done, num_far: %d\n", num_far );
+ int i, j, k, l, m, itr;
+ int x, y, z;
+ int atom1, atom2, max;
+ int num_far;
+ int *nbr_atoms;
+ ivec *nbrs;
+ rvec *nbrs_cp;
+ grid *g;
+ far_neighbor_data nbr_data;
+
+ // fprintf( stderr, "\n\tentered nbrs - " );
+ g = &( system->g );
+ Bin_Atoms( system, workspace );
+ // fprintf( stderr, "atoms sorted - " );
+ num_far = 0;
+
+ /* first pick up a cell in the grid */
+ for ( i = 0; i < g->ncell[0]; i++ )
+ for ( j = 0; j < g->ncell[1]; j++ )
+ for ( k = 0; k < g->ncell[2]; k++ )
+ {
+ nbrs = g->nbrs[i][j][k];
+ nbrs_cp = g->nbrs_cp[i][j][k];
+ //fprintf( stderr, "gridcell %d %d %d\n", i, j, k );
+
+ /* pick up an atom from the current cell */
+ for (l = 0; l < g->top[i][j][k]; ++l )
+ {
+ atom1 = g->atoms[i][j][k][l];
+
+ itr = 0;
+ while ( nbrs[itr][0] >= 0 )
+ {
+ x = nbrs[itr][0];
+ y = nbrs[itr][1];
+ z = nbrs[itr][2];
+ //fprintf( stderr, "\t\tgridcell %d %d %d\n", x, y, z );
+
+ if ( DistSqr_to_CP(nbrs_cp[itr], system->atoms[atom1].x ) <=
+ SQR(control->vlist_cut) )
+ {
+ nbr_atoms = g->atoms[x][y][z];
+ max = g->top[x][y][z];
+ //fprintf( stderr, "\t\tmax: %d\n", max );
+
+ /* pick up another atom from the neighbor cell -
+ we have to compare atom1 with its own periodic images as well,
+ that's why there is also equality in the if stmt below */
+ for ( m = 0; m < max; ++m )
+ {
+ atom2 = nbr_atoms[m];
+ //if( nbrs[itr+1][0] >= 0 || atom1 > atom2 ) {
+ if ( atom1 > atom2 )
+ {
+ if (Are_Far_Neighbors(system->atoms[atom1].x,
+ system->atoms[atom2].x,
+ &(system->box), control->vlist_cut,
+ &nbr_data))
+ ++num_far;
+ }
+ }
+ }
+
+ ++itr;
+ }
+ }
+ }
+
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "estimate nbrs done, num_far: %d\n", num_far );
#endif
- return num_far * SAFE_ZONE;
+ return num_far * SAFE_ZONE;
}
#if defined DONE
-void Choose_Neighbor_Finder( reax_system *system, control_params *control,
- get_far_neighbors_function *Get_Far_Neighbors )
+void Choose_Neighbor_Finder( reax_system *system, control_params *control,
+ get_far_neighbors_function *Get_Far_Neighbors )
{
- if( control->periodic_boundaries )
+ if ( control->periodic_boundaries )
{
- if( system->box.box_norms[0] > 2.0 * control->vlist_cut &&
- system->box.box_norms[1] > 2.0 * control->vlist_cut &&
- system->box.box_norms[2] > 2.0 * control->vlist_cut )
- (*Get_Far_Neighbors) = Get_Periodic_Far_Neighbors_Big_Box;
- else (*Get_Far_Neighbors) = Get_Periodic_Far_Neighbors_Small_Box;
+ if ( system->box.box_norms[0] > 2.0 * control->vlist_cut &&
+ system->box.box_norms[1] > 2.0 * control->vlist_cut &&
+ system->box.box_norms[2] > 2.0 * control->vlist_cut )
+ (*Get_Far_Neighbors) = Get_Periodic_Far_Neighbors_Big_Box;
+ else (*Get_Far_Neighbors) = Get_Periodic_Far_Neighbors_Small_Box;
}
- else
- (*Get_Far_Neighbors) = Get_NonPeriodic_Far_Neighbors;
+ else
+ (*Get_Far_Neighbors) = Get_NonPeriodic_Far_Neighbors;
}
int compare_near_nbrs(const void *v1, const void *v2)
{
- return ((*(near_neighbor_data *)v1).nbr - (*(near_neighbor_data *)v2).nbr);
+ return ((*(near_neighbor_data *)v1).nbr - (*(near_neighbor_data *)v2).nbr);
}
int compare_far_nbrs(const void *v1, const void *v2)
{
- return ((*(far_neighbor_data *)v1).nbr - (*(far_neighbor_data *)v2).nbr);
+ return ((*(far_neighbor_data *)v1).nbr - (*(far_neighbor_data *)v2).nbr);
}
inline void Set_Far_Neighbor( far_neighbor_data *dest, int nbr, real d, real C,
- rvec dvec, ivec rel_box/*, rvec ext_factor*/ )
+ rvec dvec, ivec rel_box/*, rvec ext_factor*/ )
{
- dest->nbr = nbr;
- dest->d = d;
- rvec_Scale( dest->dvec, C, dvec );
- ivec_Copy( dest->rel_box, rel_box );
- // rvec_Scale( dest->ext_factor, C, ext_factor );
+ dest->nbr = nbr;
+ dest->d = d;
+ rvec_Scale( dest->dvec, C, dvec );
+ ivec_Copy( dest->rel_box, rel_box );
+ // rvec_Scale( dest->ext_factor, C, ext_factor );
}
inline void Set_Near_Neighbor(near_neighbor_data *dest, int nbr, real d, real C,
- rvec dvec, ivec rel_box/*, rvec ext_factor*/)
+ rvec dvec, ivec rel_box/*, rvec ext_factor*/)
{
- dest->nbr = nbr;
- dest->d = d;
- rvec_Scale( dest->dvec, C, dvec );
- ivec_Scale( dest->rel_box, C, rel_box );
- // rvec_Scale( dest->ext_factor, C, ext_factor );
+ dest->nbr = nbr;
+ dest->d = d;
+ rvec_Scale( dest->dvec, C, dvec );
+ ivec_Scale( dest->rel_box, C, rel_box );
+ // rvec_Scale( dest->ext_factor, C, ext_factor );
}
@@ -278,381 +294,399 @@ inline void Set_Near_Neighbor(near_neighbor_data *dest, int nbr, real d, real C,
atom1 and atom2 are allowed to bond with each other */
inline int can_Bond( static_storage *workspace, int atom1, int atom2 )
{
- int i;
+ int i;
- // fprintf( stderr, "can bond %6d %6d?\n", atom1, atom2 );
+ // fprintf( stderr, "can bond %6d %6d?\n", atom1, atom2 );
- if( !workspace->restricted[ atom1 ] && !workspace->restricted[ atom2 ] )
- return 1;
+ if ( !workspace->restricted[ atom1 ] && !workspace->restricted[ atom2 ] )
+ return 1;
- for( i = 0; i < workspace->restricted[ atom1 ]; ++i )
- if( workspace->restricted_list[ atom1 ][i] == atom2 )
- return 1;
+ for ( i = 0; i < workspace->restricted[ atom1 ]; ++i )
+ if ( workspace->restricted_list[ atom1 ][i] == atom2 )
+ return 1;
- for( i = 0; i < workspace->restricted[ atom2 ]; ++i )
- if( workspace->restricted_list[ atom2 ][i] == atom1 )
- return 1;
+ for ( i = 0; i < workspace->restricted[ atom2 ]; ++i )
+ if ( workspace->restricted_list[ atom2 ][i] == atom1 )
+ return 1;
- return 0;
+ return 0;
}
/* check if atom2 is on atom1's near neighbor list */
inline int is_Near_Neighbor( list *near_nbrs, int atom1, int atom2 )
{
- int i;
+ int i;
- for( i=Start_Index(atom1,near_nbrs); i<End_Index(atom1,near_nbrs); ++i )
- if( near_nbrs->select.near_nbr_list[i].nbr == atom2 )
- {
- // fprintf( stderr, "near neighbors %6d %6d\n", atom1, atom2 );
- return 1;
- }
+ for ( i = Start_Index(atom1, near_nbrs); i < End_Index(atom1, near_nbrs); ++i )
+ if ( near_nbrs->select.near_nbr_list[i].nbr == atom2 )
+ {
+ // fprintf( stderr, "near neighbors %6d %6d\n", atom1, atom2 );
+ return 1;
+ }
- return 0;
+ return 0;
}
-void Generate_Neighbor_Lists( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+void Generate_Neighbor_Lists( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int i, j, k;
- int x, y, z;
- int *nbr_atoms;
- int atom1, atom2, max;
- int num_far;
- int c, count;
- int grid_top;
- grid *g = &( system->g );
- list *far_nbrs = (*lists) + FAR_NBRS;
- //int hb_type1, hb_type2;
- //list *hbonds = (*lists) + HBOND;
- //int top_hbond1, top_hbond2;
- get_far_neighbors_function Get_Far_Neighbors;
- far_neighbor_data new_nbrs[125];
+ int i, j, k;
+ int x, y, z;
+ int *nbr_atoms;
+ int atom1, atom2, max;
+ int num_far;
+ int c, count;
+ int grid_top;
+ grid *g = &( system->g );
+ list *far_nbrs = (*lists) + FAR_NBRS;
+ //int hb_type1, hb_type2;
+ //list *hbonds = (*lists) + HBOND;
+ //int top_hbond1, top_hbond2;
+ get_far_neighbors_function Get_Far_Neighbors;
+ far_neighbor_data new_nbrs[125];
#ifndef REORDER_ATOMS
- int l, m;
+ int l, m;
#endif
- // fprintf( stderr, "\n\tentered nbrs - " );
- if( control->ensemble == iNPT || control->ensemble == sNPT ||
- control->ensemble == NPT )
- Update_Grid( system );
- // fprintf( stderr, "grid updated - " );
+ // fprintf( stderr, "\n\tentered nbrs - " );
+ if ( control->ensemble == iNPT || control->ensemble == sNPT ||
+ control->ensemble == NPT )
+ Update_Grid( system );
+ // fprintf( stderr, "grid updated - " );
- Bin_Atoms( system, out_control );
- // fprintf( stderr, "atoms sorted - " );
+ Bin_Atoms( system, out_control );
+ // fprintf( stderr, "atoms sorted - " );
#ifdef REORDER_ATOMS
- Cluster_Atoms( system, workspace );
- // fprintf( stderr, "atoms clustered - " );
+ Cluster_Atoms( system, workspace );
+ // fprintf( stderr, "atoms clustered - " );
#endif
- Choose_Neighbor_Finder( system, control, &Get_Far_Neighbors );
- // fprintf( stderr, "function chosen - " );
-
- Reset_Neighbor_Lists( system, workspace, lists );
- // fprintf( stderr, "lists cleared - " );
-
- num_far = 0;
- num_near = 0;
- c = 0;
-
- /* first pick up a cell in the grid */
- for( i = 0; i < g->ncell[0]; i++ )
- for( j = 0; j < g->ncell[1]; j++ )
- for( k = 0; k < g->ncell[2]; k++ ) {
- nbrs = g->nbrs[i][j][k];
- nbrs_cp = g->nbrs_cp[i][j][k];
-
- /* pick up an atom from the current cell */
- //#ifdef REORDER_ATOMS
- // for(atom1 = g->start[i][j][k]; atom1 < g->end[i][j][k]; atom1++)
- //#else
- for(l = 0; l < g->top[i][j][k]; ++l ){
- atom1 = g->atoms[i][j][k][l];
- Set_End_Index( atom1, num_far, far_nbrs );
- // fprintf( stderr, "atom %d:\n", atom1 );
-
- itr = 0;
- while( nbrs[itr][0] > 0 ){
- x = nbrs[itr][0];
- y = nbrs[itr][1];
- z = nbrs[itr][2];
-
- // if( DistSqr_to_CP(nbrs_cp[itr], system->atoms[atom1].x ) <=
- // SQR(control->r_cut))
- nbr_atoms = g->atoms[x][y][z];
- max_atoms = g->top[x][y][z];
-
- /* pick up another atom from the neighbor cell -
- we have to compare atom1 with its own periodic images as well,
- that's why there is also equality in the if stmt below */
- //#ifdef REORDER_ATOMS
- //for(atom2=g->start[x][y][z]; atom2<g->end[x][y][z]; atom2++)
- //#else
- for( m = 0, atom2=nbr_atoms[m]; m < max; ++m, atom2=nbr_atoms[m] )
- if( atom1 >= atom2 ) {
- //fprintf( stderr, "\tatom2 %d", atom2 );
- //top_near1 = End_Index( atom1, near_nbrs );
- //Set_Start_Index( atom1, num_far, far_nbrs );
- //hb_type1=system->reaxprm.sbp[system->atoms[atom1].type].p_hbond;
- Get_Far_Neighbors( system->atoms[atom1].x,
- system->atoms[atom2].x,
- &(system->box), control, new_nbrs, &count );
- fprintf( stderr, "\t%d count:%d\n", atom2, count );
-
- for( c = 0; c < count; ++c )
- if(atom1 != atom2 || (atom1 == atom2 && new_nbrs[c].d>=0.1)){
- Set_Far_Neighbor(&(far_nbrs->select.far_nbr_list[num_far]),
- atom2, new_nbrs[c].d, 1.0,
- new_nbrs[c].dvec, new_nbrs[c].rel_box );
- ++num_far;
-
- /*fprintf(stderr,"FARNBR:%6d%6d%8.3f[%8.3f%8.3f%8.3f]\n",
- atom1, atom2, new_nbrs[c].d,
- new_nbrs[c].dvec[0], new_nbrs[c].dvec[1],
- new_nbrs[c].dvec[2] ); */
-
-
- /* hydrogen bond lists */
- /*if( control->hb_cut > 0.1 &&
- new_nbrs[c].d <= control->hb_cut ) {
- // fprintf( stderr, "%d %d\n", atom1, atom2 );
- hb_type2=system->reaxprm.sbp[system->atoms[atom2].type].p_hbond;
- if( hb_type1 == 1 && hb_type2 == 2 ) {
- top_hbond1=End_Index(workspace->hbond_index[atom1],hbonds);
- Set_Near_Neighbor(&(hbonds->select.hbond_list[top_hbond1]),
- atom2, new_nbrs[c].d, 1.0, new_nbrs[c].dvec,
- new_nbrs[c].rel_box );
- Set_End_Index( workspace->hbond_index[atom1],
- top_hbond1 + 1, hbonds );
- }
- else if( hb_type1 == 2 && hb_type2 == 1 ) {
- top_hbond2 = End_Index( workspace->hbond_index[atom2], hbonds );
- Set_Near_Neighbor(&(hbonds->select.hbond_list[top_hbond2]),
- atom1, new_nbrs[c].d, -1.0, new_nbrs[c].dvec,
- new_nbrs[c].rel_box );
- Set_End_Index( workspace->hbond_index[atom2],
- top_hbond2 + 1, hbonds );
- }*/
- }
- }
- }
-
- Set_End_Index( atom1, top_far1, far_nbrs );
- }
- }
-
-
- fprintf( stderr, "nbrs done-" );
-
-
- /* apply restrictions on near neighbors only */
- if( (data->step - data->prev_steps) < control->restrict_bonds ) {
- for( atom1 = 0; atom1 < system->N; ++atom1 )
- if( workspace->restricted[ atom1 ] ) {
- // fprintf( stderr, "atom1: %d\n", atom1 );
-
- top_near1 = End_Index( atom1, near_nbrs );
-
- for( j = 0; j < workspace->restricted[ atom1 ]; ++j )
- if(!is_Near_Neighbor(near_nbrs, atom1,
- atom2 = workspace->restricted_list[atom1][j])) {
- fprintf( stderr, "%3d-%3d: added bond by applying restrictions!\n",
- atom1, atom2 );
-
- top_near2 = End_Index( atom2, near_nbrs );
-
- /* we just would like to get the nearest image, so a call to
- Get_Periodic_Far_Neighbors_Big_Box is good enough. */
- Get_Periodic_Far_Neighbors_Big_Box( system->atoms[ atom1 ].x,
- system->atoms[ atom2 ].x,
- &(system->box), control,
- new_nbrs, &count );
-
- Set_Near_Neighbor( &(near_nbrs->select.near_nbr_list[ top_near1 ]),
- atom2, new_nbrs[c].d, 1.0,
- new_nbrs[c].dvec, new_nbrs[c].rel_box );
- ++top_near1;
-
- Set_Near_Neighbor( &(near_nbrs->select.near_nbr_list[ top_near2 ]),
- atom1, new_nbrs[c].d, -1.0,
- new_nbrs[c].dvec, new_nbrs[c].rel_box );
- Set_End_Index( atom2, top_near2+1, near_nbrs );
- }
-
- Set_End_Index( atom1, top_near1, near_nbrs );
- }
- }
- // fprintf( stderr, "restrictions applied-" );
-
-
- /* verify nbrlists, count num_intrs, sort nearnbrs */
- near_nbrs->num_intrs = 0;
- far_nbrs->num_intrs = 0;
- for( i = 0; i < system->N-1; ++i ) {
- if( End_Index(i, near_nbrs) > Start_Index(i+1, near_nbrs) ) {
- fprintf( stderr,
- "step%3d: nearnbr list of atom%d is overwritten by atom%d\n",
- data->step, i+1, i );
- exit( 1 );
+ Choose_Neighbor_Finder( system, control, &Get_Far_Neighbors );
+ // fprintf( stderr, "function chosen - " );
+
+ Reset_Neighbor_Lists( system, workspace, lists );
+ // fprintf( stderr, "lists cleared - " );
+
+ num_far = 0;
+ num_near = 0;
+ c = 0;
+
+ /* first pick up a cell in the grid */
+ for ( i = 0; i < g->ncell[0]; i++ )
+ for ( j = 0; j < g->ncell[1]; j++ )
+ for ( k = 0; k < g->ncell[2]; k++ )
+ {
+ nbrs = g->nbrs[i][j][k];
+ nbrs_cp = g->nbrs_cp[i][j][k];
+
+ /* pick up an atom from the current cell */
+ //#ifdef REORDER_ATOMS
+ // for(atom1 = g->start[i][j][k]; atom1 < g->end[i][j][k]; atom1++)
+ //#else
+ for (l = 0; l < g->top[i][j][k]; ++l )
+ {
+ atom1 = g->atoms[i][j][k][l];
+ Set_End_Index( atom1, num_far, far_nbrs );
+ // fprintf( stderr, "atom %d:\n", atom1 );
+
+ itr = 0;
+ while ( nbrs[itr][0] > 0 )
+ {
+ x = nbrs[itr][0];
+ y = nbrs[itr][1];
+ z = nbrs[itr][2];
+
+ // if( DistSqr_to_CP(nbrs_cp[itr], system->atoms[atom1].x ) <=
+ // SQR(control->r_cut))
+ nbr_atoms = g->atoms[x][y][z];
+ max_atoms = g->top[x][y][z];
+
+ /* pick up another atom from the neighbor cell -
+ we have to compare atom1 with its own periodic images as well,
+ that's why there is also equality in the if stmt below */
+ //#ifdef REORDER_ATOMS
+ //for(atom2=g->start[x][y][z]; atom2<g->end[x][y][z]; atom2++)
+ //#else
+ for ( m = 0, atom2 = nbr_atoms[m]; m < max; ++m, atom2 = nbr_atoms[m] )
+ if ( atom1 >= atom2 )
+ {
+ //fprintf( stderr, "\tatom2 %d", atom2 );
+ //top_near1 = End_Index( atom1, near_nbrs );
+ //Set_Start_Index( atom1, num_far, far_nbrs );
+ //hb_type1=system->reaxprm.sbp[system->atoms[atom1].type].p_hbond;
+ Get_Far_Neighbors( system->atoms[atom1].x,
+ system->atoms[atom2].x,
+ &(system->box), control, new_nbrs, &count );
+ fprintf( stderr, "\t%d count:%d\n", atom2, count );
+
+ for ( c = 0; c < count; ++c )
+ if (atom1 != atom2 || (atom1 == atom2 && new_nbrs[c].d >= 0.1))
+ {
+ Set_Far_Neighbor(&(far_nbrs->select.far_nbr_list[num_far]),
+ atom2, new_nbrs[c].d, 1.0,
+ new_nbrs[c].dvec, new_nbrs[c].rel_box );
+ ++num_far;
+
+ /*fprintf(stderr,"FARNBR:%6d%6d%8.3f[%8.3f%8.3f%8.3f]\n",
+ atom1, atom2, new_nbrs[c].d,
+ new_nbrs[c].dvec[0], new_nbrs[c].dvec[1],
+ new_nbrs[c].dvec[2] ); */
+
+
+ /* hydrogen bond lists */
+ /*if( control->hb_cut > 0.1 &&
+ new_nbrs[c].d <= control->hb_cut ) {
+ // fprintf( stderr, "%d %d\n", atom1, atom2 );
+ hb_type2=system->reaxprm.sbp[system->atoms[atom2].type].p_hbond;
+ if( hb_type1 == 1 && hb_type2 == 2 ) {
+ top_hbond1=End_Index(workspace->hbond_index[atom1],hbonds);
+ Set_Near_Neighbor(&(hbonds->select.hbond_list[top_hbond1]),
+ atom2, new_nbrs[c].d, 1.0, new_nbrs[c].dvec,
+ new_nbrs[c].rel_box );
+ Set_End_Index( workspace->hbond_index[atom1],
+ top_hbond1 + 1, hbonds );
+ }
+ else if( hb_type1 == 2 && hb_type2 == 1 ) {
+ top_hbond2 = End_Index( workspace->hbond_index[atom2], hbonds );
+ Set_Near_Neighbor(&(hbonds->select.hbond_list[top_hbond2]),
+ atom1, new_nbrs[c].d, -1.0, new_nbrs[c].dvec,
+ new_nbrs[c].rel_box );
+ Set_End_Index( workspace->hbond_index[atom2],
+ top_hbond2 + 1, hbonds );
+ }*/
+ }
+ }
+ }
+
+ Set_End_Index( atom1, top_far1, far_nbrs );
+ }
+ }
+
+
+ fprintf( stderr, "nbrs done-" );
+
+
+ /* apply restrictions on near neighbors only */
+ if ( (data->step - data->prev_steps) < control->restrict_bonds )
+ {
+ for ( atom1 = 0; atom1 < system->N; ++atom1 )
+ if ( workspace->restricted[ atom1 ] )
+ {
+ // fprintf( stderr, "atom1: %d\n", atom1 );
+
+ top_near1 = End_Index( atom1, near_nbrs );
+
+ for ( j = 0; j < workspace->restricted[ atom1 ]; ++j )
+ if (!is_Near_Neighbor(near_nbrs, atom1,
+ atom2 = workspace->restricted_list[atom1][j]))
+ {
+ fprintf( stderr, "%3d-%3d: added bond by applying restrictions!\n",
+ atom1, atom2 );
+
+ top_near2 = End_Index( atom2, near_nbrs );
+
+ /* we just would like to get the nearest image, so a call to
+ Get_Periodic_Far_Neighbors_Big_Box is good enough. */
+ Get_Periodic_Far_Neighbors_Big_Box( system->atoms[ atom1 ].x,
+ system->atoms[ atom2 ].x,
+ &(system->box), control,
+ new_nbrs, &count );
+
+ Set_Near_Neighbor( &(near_nbrs->select.near_nbr_list[ top_near1 ]),
+ atom2, new_nbrs[c].d, 1.0,
+ new_nbrs[c].dvec, new_nbrs[c].rel_box );
+ ++top_near1;
+
+ Set_Near_Neighbor( &(near_nbrs->select.near_nbr_list[ top_near2 ]),
+ atom1, new_nbrs[c].d, -1.0,
+ new_nbrs[c].dvec, new_nbrs[c].rel_box );
+ Set_End_Index( atom2, top_near2 + 1, near_nbrs );
+ }
+
+ Set_End_Index( atom1, top_near1, near_nbrs );
+ }
+ }
+ // fprintf( stderr, "restrictions applied-" );
+
+
+ /* verify nbrlists, count num_intrs, sort nearnbrs */
+ near_nbrs->num_intrs = 0;
+ far_nbrs->num_intrs = 0;
+ for ( i = 0; i < system->N - 1; ++i )
+ {
+ if ( End_Index(i, near_nbrs) > Start_Index(i + 1, near_nbrs) )
+ {
+ fprintf( stderr,
+ "step%3d: nearnbr list of atom%d is overwritten by atom%d\n",
+ data->step, i + 1, i );
+ exit( 1 );
+ }
+
+ near_nbrs->num_intrs += Num_Entries(i, near_nbrs);
+
+ if ( End_Index(i, far_nbrs) > Start_Index(i + 1, far_nbrs) )
+ {
+ fprintf( stderr,
+ "step%3d: farnbr list of atom%d is overwritten by atom%d\n",
+ data->step, i + 1, i );
+ exit( 1 );
+ }
+
+ far_nbrs->num_intrs += Num_Entries(i, far_nbrs);
}
-
- near_nbrs->num_intrs += Num_Entries(i, near_nbrs);
-
- if( End_Index(i, far_nbrs) > Start_Index(i+1, far_nbrs) ) {
- fprintf( stderr,
- "step%3d: farnbr list of atom%d is overwritten by atom%d\n",
- data->step, i+1, i );
- exit( 1 );
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ qsort( &(near_nbrs->select.near_nbr_list[ Start_Index(i, near_nbrs) ]),
+ Num_Entries(i, near_nbrs), sizeof(near_neighbor_data),
+ compare_near_nbrs );
}
-
- far_nbrs->num_intrs += Num_Entries(i, far_nbrs);
- }
-
- for( i = 0; i < system->N; ++i ) {
- qsort( &(near_nbrs->select.near_nbr_list[ Start_Index(i, near_nbrs) ]),
- Num_Entries(i, near_nbrs), sizeof(near_neighbor_data),
- compare_near_nbrs );
- }
- // fprintf( stderr, "near nbrs sorted\n" );
-
+ // fprintf( stderr, "near nbrs sorted\n" );
+
#ifdef TEST_ENERGY
- /* for( i = 0; i < system->N; ++i ) {
- qsort( &(far_nbrs->select.far_nbr_list[ Start_Index(i, far_nbrs) ]),
- Num_Entries(i, far_nbrs), sizeof(far_neighbor_data),
- compare_far_nbrs );
- } */
-
- fprintf( stderr, "Near neighbors/atom: %d (compare to 150)\n",
- num_near / system->N );
- fprintf( stderr, "Far neighbors per atom: %d (compare to %d)\n",
- num_far / system->N, control->max_far_nbrs );
+ /* for( i = 0; i < system->N; ++i ) {
+ qsort( &(far_nbrs->select.far_nbr_list[ Start_Index(i, far_nbrs) ]),
+ Num_Entries(i, far_nbrs), sizeof(far_neighbor_data),
+ compare_far_nbrs );
+ } */
+
+ fprintf( stderr, "Near neighbors/atom: %d (compare to 150)\n",
+ num_near / system->N );
+ fprintf( stderr, "Far neighbors per atom: %d (compare to %d)\n",
+ num_far / system->N, control->max_far_nbrs );
#endif
-
- //fprintf( stderr, "step%d: num of nearnbrs = %6d num of farnbrs: %6d\n",
- // data->step, num_near, num_far );
- //fprintf( stderr, "\talloc nearnbrs = %6d alloc farnbrs: %6d\n",
- // system->N * near_nbrs->intrs_per_unit,
- // system->N * far_nbrs->intrs_per_unit );
+ //fprintf( stderr, "step%d: num of nearnbrs = %6d num of farnbrs: %6d\n",
+ // data->step, num_near, num_far );
+
+ //fprintf( stderr, "\talloc nearnbrs = %6d alloc farnbrs: %6d\n",
+ // system->N * near_nbrs->intrs_per_unit,
+ // system->N * far_nbrs->intrs_per_unit );
}
-void Generate_Neighbor_Lists( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+void Generate_Neighbor_Lists( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int i, j, k, l, m, itr;
- int x, y, z;
- int atom1, atom2, max;
- int num_far, c, count;
- int *nbr_atoms;
- ivec *nbrs;
- rvec *nbrs_cp;
- grid *g;
- list *far_nbrs;
- get_far_neighbors_function Get_Far_Neighbors;
- far_neighbor_data new_nbrs[125];
-
- g = &( system->g );
- far_nbrs = (*lists) + FAR_NBRS;
-
- // fprintf( stderr, "\n\tentered nbrs - " );
- if( control->ensemble == iNPT ||
- control->ensemble == sNPT ||
- control->ensemble == NPT )
- Update_Grid( system );
- // fprintf( stderr, "grid updated - " );
-
- Bin_Atoms( system, out_control );
- // fprintf( stderr, "atoms sorted - " );
- Choose_Neighbor_Finder( system, control, &Get_Far_Neighbors );
- // fprintf( stderr, "function chosen - " );
- Reset_Neighbor_Lists( system, workspace, lists );
- // fprintf( stderr, "lists cleared - " );
-
- num_far = 0;
- c = 0;
-
- /* first pick up a cell in the grid */
- for( i = 0; i < g->ncell[0]; i++ )
- for( j = 0; j < g->ncell[1]; j++ )
- for( k = 0; k < g->ncell[2]; k++ ) {
- nbrs = g->nbrs[i][j][k];
- nbrs_cp = g->nbrs_cp[i][j][k];
- fprintf( stderr, "gridcell %d %d %d\n", i, j, k );
-
- /* pick up an atom from the current cell */
- for(l = 0; l < g->top[i][j][k]; ++l ){
- atom1 = g->atoms[i][j][k][l];
- Set_Start_Index( atom1, num_far, far_nbrs );
- fprintf( stderr, "\tatom %d\n", atom1 );
-
- itr = 0;
- while( nbrs[itr][0] > 0 ){
- x = nbrs[itr][0];
- y = nbrs[itr][1];
- z = nbrs[itr][2];
- fprintf( stderr, "\t\tgridcell %d %d %d\n", x, y, z );
-
- // if( DistSqr_to_CP(nbrs_cp[itr], system->atoms[atom1].x ) <=
- // SQR(control->r_cut))
- nbr_atoms = g->atoms[x][y][z];
- max = g->top[x][y][z];
- fprintf( stderr, "\t\tmax: %d\n", max );
-
-
- /* pick up another atom from the neighbor cell -
- we have to compare atom1 with its own periodic images as well,
- that's why there is also equality in the if stmt below */
- for( m = 0, atom2=nbr_atoms[m]; m < max; ++m, atom2=nbr_atoms[m] )
- if( atom1 >= atom2 ) {
- Get_Far_Neighbors( system->atoms[atom1].x,
- system->atoms[atom2].x,
- &(system->box), control, new_nbrs, &count );
- fprintf( stderr, "\t\t\t%d count:%d\n", atom2, count );
-
- for( c = 0; c < count; ++c )
- if(atom1 != atom2 || (atom1 == atom2 && new_nbrs[c].d>=0.1)){
- Set_Far_Neighbor(&(far_nbrs->select.far_nbr_list[num_far]),
- atom2, new_nbrs[c].d, 1.0,
- new_nbrs[c].dvec, new_nbrs[c].rel_box );
- ++num_far;
-
- /*fprintf(stderr,"FARNBR:%6d%6d%8.3f[%8.3f%8.3f%8.3f]\n",
- atom1, atom2, new_nbrs[c].d,
- new_nbrs[c].dvec[0], new_nbrs[c].dvec[1],
- new_nbrs[c].dvec[2] ); */
- }
- }
-
- ++itr;
- }
-
- Set_End_Index( atom1, num_far, far_nbrs );
- }
- }
-
- far_nbrs->num_intrs = num_far;
- fprintf( stderr, "nbrs done, num_far: %d\n", num_far );
+ int i, j, k, l, m, itr;
+ int x, y, z;
+ int atom1, atom2, max;
+ int num_far, c, count;
+ int *nbr_atoms;
+ ivec *nbrs;
+ rvec *nbrs_cp;
+ grid *g;
+ list *far_nbrs;
+ get_far_neighbors_function Get_Far_Neighbors;
+ far_neighbor_data new_nbrs[125];
+
+ g = &( system->g );
+ far_nbrs = (*lists) + FAR_NBRS;
+
+ // fprintf( stderr, "\n\tentered nbrs - " );
+ if ( control->ensemble == iNPT ||
+ control->ensemble == sNPT ||
+ control->ensemble == NPT )
+ Update_Grid( system );
+ // fprintf( stderr, "grid updated - " );
+
+ Bin_Atoms( system, out_control );
+ // fprintf( stderr, "atoms sorted - " );
+ Choose_Neighbor_Finder( system, control, &Get_Far_Neighbors );
+ // fprintf( stderr, "function chosen - " );
+ Reset_Neighbor_Lists( system, workspace, lists );
+ // fprintf( stderr, "lists cleared - " );
+
+ num_far = 0;
+ c = 0;
+
+ /* first pick up a cell in the grid */
+ for ( i = 0; i < g->ncell[0]; i++ )
+ for ( j = 0; j < g->ncell[1]; j++ )
+ for ( k = 0; k < g->ncell[2]; k++ )
+ {
+ nbrs = g->nbrs[i][j][k];
+ nbrs_cp = g->nbrs_cp[i][j][k];
+ fprintf( stderr, "gridcell %d %d %d\n", i, j, k );
+
+ /* pick up an atom from the current cell */
+ for (l = 0; l < g->top[i][j][k]; ++l )
+ {
+ atom1 = g->atoms[i][j][k][l];
+ Set_Start_Index( atom1, num_far, far_nbrs );
+ fprintf( stderr, "\tatom %d\n", atom1 );
+
+ itr = 0;
+ while ( nbrs[itr][0] > 0 )
+ {
+ x = nbrs[itr][0];
+ y = nbrs[itr][1];
+ z = nbrs[itr][2];
+ fprintf( stderr, "\t\tgridcell %d %d %d\n", x, y, z );
+
+ // if( DistSqr_to_CP(nbrs_cp[itr], system->atoms[atom1].x ) <=
+ // SQR(control->r_cut))
+ nbr_atoms = g->atoms[x][y][z];
+ max = g->top[x][y][z];
+ fprintf( stderr, "\t\tmax: %d\n", max );
+
+
+ /* pick up another atom from the neighbor cell -
+ we have to compare atom1 with its own periodic images as well,
+ that's why there is also equality in the if stmt below */
+ for ( m = 0, atom2 = nbr_atoms[m]; m < max; ++m, atom2 = nbr_atoms[m] )
+ if ( atom1 >= atom2 )
+ {
+ Get_Far_Neighbors( system->atoms[atom1].x,
+ system->atoms[atom2].x,
+ &(system->box), control, new_nbrs, &count );
+ fprintf( stderr, "\t\t\t%d count:%d\n", atom2, count );
+
+ for ( c = 0; c < count; ++c )
+ if (atom1 != atom2 || (atom1 == atom2 && new_nbrs[c].d >= 0.1))
+ {
+ Set_Far_Neighbor(&(far_nbrs->select.far_nbr_list[num_far]),
+ atom2, new_nbrs[c].d, 1.0,
+ new_nbrs[c].dvec, new_nbrs[c].rel_box );
+ ++num_far;
+
+ /*fprintf(stderr,"FARNBR:%6d%6d%8.3f[%8.3f%8.3f%8.3f]\n",
+ atom1, atom2, new_nbrs[c].d,
+ new_nbrs[c].dvec[0], new_nbrs[c].dvec[1],
+ new_nbrs[c].dvec[2] ); */
+ }
+ }
+
+ ++itr;
+ }
+
+ Set_End_Index( atom1, num_far, far_nbrs );
+ }
+ }
+
+ far_nbrs->num_intrs = num_far;
+ fprintf( stderr, "nbrs done, num_far: %d\n", num_far );
#if defined(DEBUG)
- for( i = 0; i < system->N; ++i ) {
- qsort( &(far_nbrs->select.far_nbr_list[ Start_Index(i, far_nbrs) ]),
- Num_Entries(i, far_nbrs), sizeof(far_neighbor_data),
- compare_far_nbrs );
- }
-
- fprintf( stderr, "step%d: num of farnbrs=%6d\n", data->step, num_far );
- fprintf( stderr, "\tallocated farnbrs: %6d\n",
- system->N * far_nbrs->intrs_per_unit );
+ for ( i = 0; i < system->N; ++i )
+ {
+ qsort( &(far_nbrs->select.far_nbr_list[ Start_Index(i, far_nbrs) ]),
+ Num_Entries(i, far_nbrs), sizeof(far_neighbor_data),
+ compare_far_nbrs );
+ }
+
+ fprintf( stderr, "step%d: num of farnbrs=%6d\n", data->step, num_far );
+ fprintf( stderr, "\tallocated farnbrs: %6d\n",
+ system->N * far_nbrs->intrs_per_unit );
#endif
}
-
+
#endif
diff --git a/puremd_rc_1003/sPuReMD/neighbors.h b/puremd_rc_1003/sPuReMD/neighbors.h
index bca35b82a9b8156671203cb9d31cb6089daa218a..e849b1e4542e5f6f9c8c5b75d34d847a4467a528 100644
--- a/puremd_rc_1003/sPuReMD/neighbors.h
+++ b/puremd_rc_1003/sPuReMD/neighbors.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -25,8 +25,8 @@
#include "mytypes.h"
void Generate_Neighbor_Lists( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, list**, output_controls* );
-int Estimate_NumNeighbors( reax_system*, control_params*,
- static_storage*, list** );
+int Estimate_NumNeighbors( reax_system*, control_params*,
+ static_storage*, list** );
#endif
diff --git a/puremd_rc_1003/sPuReMD/param.c b/puremd_rc_1003/sPuReMD/param.c
index 045e97bc7e5f020d86eb311ef8a0184ea9f14122..9694527459063e606c658ae03f458005026e2205 100644
--- a/puremd_rc_1003/sPuReMD/param.c
+++ b/puremd_rc_1003/sPuReMD/param.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -26,1184 +26,1296 @@
int Get_Atom_Type( reax_interaction *reaxprm, char *s )
{
- int i;
+ int i;
- for( i = 0; i < reaxprm->num_atom_types; ++i )
- if( !strcmp( reaxprm->sbp[i].name, s ) )
- return i;
+ for ( i = 0; i < reaxprm->num_atom_types; ++i )
+ if ( !strcmp( reaxprm->sbp[i].name, s ) )
+ return i;
- fprintf( stderr, "Unknown atom type %s. Terminating...\n", s );
- exit( UNKNOWN_ATOM_TYPE_ERR );
+ fprintf( stderr, "Unknown atom type %s. Terminating...\n", s );
+ exit( UNKNOWN_ATOM_TYPE_ERR );
}
int Tokenize(char* s, char*** tok)
{
- char test[MAX_LINE];
- char *sep = "\t \n!=";
- char *word;
- int count=0;
+ char test[MAX_LINE];
+ char *sep = "\t \n!=";
+ char *word;
+ int count = 0;
+
+ strncpy( test, s, MAX_LINE );
- strncpy( test, s, MAX_LINE );
+ // fprintf( stderr, "|%s|\n", test );
- // fprintf( stderr, "|%s|\n", test );
-
- for( word = strtok(test, sep); word; word = strtok(NULL, sep) )
+ for ( word = strtok(test, sep); word; word = strtok(NULL, sep) )
{
- strncpy( (*tok)[count], word, MAX_LINE );
- count++;
+ strncpy( (*tok)[count], word, MAX_LINE );
+ count++;
}
- return count;
+ return count;
}
/* Initialize Taper params */
void Init_Taper( control_params *control )
{
- real d1, d7;
- real swa, swa2, swa3;
- real swb, swb2, swb3;
+ real d1, d7;
+ real swa, swa2, swa3;
+ real swb, swb2, swb3;
- swa = control->r_low;
- swb = control->r_cut;
+ swa = control->r_low;
+ swb = control->r_cut;
- if( fabs( swa ) > 0.01 )
- fprintf( stderr,"Warning: non-zero value for lower Taper-radius cutoff\n" );
-
- if( swb < 0 )
+ if ( fabs( swa ) > 0.01 )
+ fprintf( stderr, "Warning: non-zero value for lower Taper-radius cutoff\n" );
+
+ if ( swb < 0 )
{
- fprintf( stderr, "Negative value for upper Taper-radius cutoff\n" );
- exit( INVALID_INPUT );
- }
- else if( swb < 5 )
- fprintf( stderr,"Warning: low value for upper Taper-radius cutoff:%f\n",
- swb );
-
- d1 = swb - swa;
- d7 = POW( d1, 7.0 );
- swa2 = SQR( swa );
- swa3 = CUBE( swa );
- swb2 = SQR( swb );
- swb3 = CUBE( swb );
-
- control->Tap7 = 20.0 / d7;
- control->Tap6 = -70.0 * (swa + swb) / d7;
- control->Tap5 = 84.0 * (swa2 + 3.0*swa*swb + swb2) / d7;
- control->Tap4 = -35.0 * (swa3 + 9.0*swa2*swb + 9.0*swa*swb2 + swb3 ) / d7;
- control->Tap3 = 140.0 * (swa3*swb + 3.0*swa2*swb2 + swa*swb3 ) / d7;
- control->Tap2 =-210.0 * (swa3*swb2 + swa2*swb3) / d7;
- control->Tap1 = 140.0 * swa3 * swb3 / d7;
- control->Tap0 = (-35.0*swa3*swb2*swb2 + 21.0*swa2*swb3*swb2 +
- 7.0*swa*swb3*swb3 + swb3*swb3*swb ) / d7;
+ fprintf( stderr, "Negative value for upper Taper-radius cutoff\n" );
+ exit( INVALID_INPUT );
+ }
+ else if ( swb < 5 )
+ fprintf( stderr, "Warning: low value for upper Taper-radius cutoff:%f\n",
+ swb );
+
+ d1 = swb - swa;
+ d7 = POW( d1, 7.0 );
+ swa2 = SQR( swa );
+ swa3 = CUBE( swa );
+ swb2 = SQR( swb );
+ swb3 = CUBE( swb );
+
+ control->Tap7 = 20.0 / d7;
+ control->Tap6 = -70.0 * (swa + swb) / d7;
+ control->Tap5 = 84.0 * (swa2 + 3.0 * swa * swb + swb2) / d7;
+ control->Tap4 = -35.0 * (swa3 + 9.0 * swa2 * swb + 9.0 * swa * swb2 + swb3 ) / d7;
+ control->Tap3 = 140.0 * (swa3 * swb + 3.0 * swa2 * swb2 + swa * swb3 ) / d7;
+ control->Tap2 = -210.0 * (swa3 * swb2 + swa2 * swb3) / d7;
+ control->Tap1 = 140.0 * swa3 * swb3 / d7;
+ control->Tap0 = (-35.0 * swa3 * swb2 * swb2 + 21.0 * swa2 * swb3 * swb2 +
+ 7.0 * swa * swb3 * swb3 + swb3 * swb3 * swb ) / d7;
}
char Read_Force_Field( FILE* fp, reax_interaction* reax )
{
- char *s;
- char **tmp;
- char ****tor_flag;
- int c, i, j, k, l, m, n, o, p, cnt;
- real val;
-
- s = (char*) malloc(sizeof(char)*MAX_LINE);
- tmp = (char**) malloc(sizeof(char*)*MAX_TOKENS);
- for (i=0; i < MAX_TOKENS; i++)
- tmp[i] = (char*) malloc(sizeof(char)*MAX_TOKEN_LEN);
-
-
- /* reading first header comment */
- fgets( s, MAX_LINE, fp );
-
-
- /* line 2 is number of global parameters */
- fgets( s, MAX_LINE, fp );
- c = Tokenize( s, &tmp );
-
- /* reading the number of global parameters */
- n = atoi(tmp[0]);
- if (n < 1)
- {
- fprintf( stderr, "WARNING: number of globals in ffield file is 0!\n" );
- return 1;
- }
+ char *s;
+ char **tmp;
+ char ****tor_flag;
+ int c, i, j, k, l, m, n, o, p, cnt;
+ real val;
- reax->gp.n_global = n;
- reax->gp.l = (real*) malloc(sizeof(real)*n);
+ s = (char*) malloc(sizeof(char) * MAX_LINE);
+ tmp = (char**) malloc(sizeof(char*)*MAX_TOKENS);
+ for (i = 0; i < MAX_TOKENS; i++)
+ tmp[i] = (char*) malloc(sizeof(char) * MAX_TOKEN_LEN);
- /* see mytypes.h for mapping between l[i] and the lambdas used in ff */
- for (i=0; i < n; i++)
- {
- fgets(s,MAX_LINE,fp);
- c=Tokenize(s,&tmp);
-
- val = (real) atof(tmp[0]);
- reax->gp.l[i] = val;
+ /* reading first header comment */
+ fgets( s, MAX_LINE, fp );
+
+
+ /* line 2 is number of global parameters */
+ fgets( s, MAX_LINE, fp );
+ c = Tokenize( s, &tmp );
+
+ /* reading the number of global parameters */
+ n = atoi(tmp[0]);
+ if (n < 1)
+ {
+ fprintf( stderr, "WARNING: number of globals in ffield file is 0!\n" );
+ return 1;
}
+ reax->gp.n_global = n;
+ reax->gp.l = (real*) malloc(sizeof(real) * n);
- /* next line is number of atom types and some comments */
- fgets( s, MAX_LINE, fp );
- c = Tokenize( s, &tmp );
- reax->num_atom_types = atoi(tmp[0]);
-
-
- /* 3 lines of comments */
- fgets(s,MAX_LINE,fp);
- fgets(s,MAX_LINE,fp);
- fgets(s,MAX_LINE,fp);
-
-
- /* Allocating structures in reax_interaction */
- reax->sbp = (single_body_parameters*)
- calloc( reax->num_atom_types, sizeof(single_body_parameters) );
- reax->tbp = (two_body_parameters**)
- calloc( reax->num_atom_types, sizeof(two_body_parameters*) );
- reax->thbp= (three_body_header***)
- calloc( reax->num_atom_types, sizeof(three_body_header**) );
- reax->hbp = (hbond_parameters***)
- calloc( reax->num_atom_types, sizeof(hbond_parameters**) );
- reax->fbp = (four_body_header****)
- calloc( reax->num_atom_types, sizeof(four_body_header***) );
- tor_flag = (char****)
- calloc( reax->num_atom_types, sizeof(char***) );
-
- for( i = 0; i < reax->num_atom_types; i++ )
+ /* see mytypes.h for mapping between l[i] and the lambdas used in ff */
+ for (i = 0; i < n; i++)
{
- reax->tbp[i] = (two_body_parameters*)
- calloc( reax->num_atom_types, sizeof(two_body_parameters) );
- reax->thbp[i]= (three_body_header**)
- calloc( reax->num_atom_types, sizeof(three_body_header*) );
- reax->hbp[i] = (hbond_parameters**)
- calloc( reax->num_atom_types, sizeof(hbond_parameters*) );
- reax->fbp[i] = (four_body_header***)
- calloc( reax->num_atom_types, sizeof(four_body_header**) );
- tor_flag[i] = (char***)
- calloc( reax->num_atom_types, sizeof(char**) );
-
- for( j = 0; j < reax->num_atom_types; j++ )
- {
- reax->thbp[i][j]= (three_body_header*)
- calloc( reax->num_atom_types, sizeof(three_body_header) );
- reax->hbp[i][j] = (hbond_parameters*)
- calloc( reax->num_atom_types, sizeof(hbond_parameters) );
- reax->fbp[i][j] = (four_body_header**)
- calloc( reax->num_atom_types, sizeof(four_body_header*) );
- tor_flag[i][j] = (char**)
- calloc( reax->num_atom_types, sizeof(char*) );
-
- for (k=0; k < reax->num_atom_types; k++)
- {
- reax->fbp[i][j][k] = (four_body_header*)
- calloc( reax->num_atom_types, sizeof(four_body_header) );
- tor_flag[i][j][k] = (char*)
- calloc( reax->num_atom_types, sizeof(char) );
- }
- }
+ fgets(s, MAX_LINE, fp);
+ c = Tokenize(s, &tmp);
+
+ val = (real) atof(tmp[0]);
+
+ reax->gp.l[i] = val;
}
- // vdWaals type: 1: Shielded Morse, no inner-wall
- // 2: inner wall, no shielding
- // 3: inner wall+shielding
- reax->gp.vdw_type = 0;
-
- /* reading single atom parameters */
- /* there are 4 lines of each single atom parameters in ff files. these
- parameters later determine some of the pair and triplet parameters using
- combination rules. */
- for( i = 0; i < reax->num_atom_types; i++ ) {
- /* line one */
- fgets( s, MAX_LINE, fp );
- c = Tokenize( s, &tmp );
-
- for( j = 0; j < strlen( tmp[0] ); ++j )
- reax->sbp[i].name[j] = toupper( tmp[0][j] );
-
- val = atof(tmp[1]); reax->sbp[i].r_s = val;
- val = atof(tmp[2]); reax->sbp[i].valency = val;
- val = atof(tmp[3]); reax->sbp[i].mass = val;
- val = atof(tmp[4]); reax->sbp[i].r_vdw = val;
- val = atof(tmp[5]); reax->sbp[i].epsilon = val;
- val = atof(tmp[6]); reax->sbp[i].gamma = val;
- val = atof(tmp[7]); reax->sbp[i].r_pi = val;
- val = atof(tmp[8]); reax->sbp[i].valency_e = val;
- reax->sbp[i].nlp_opt = 0.5*(reax->sbp[i].valency_e-reax->sbp[i].valency);
-
- /* line two */
- fgets( s, MAX_LINE, fp );
- c = Tokenize( s, &tmp );
-
- val = atof(tmp[0]); reax->sbp[i].alpha = val;
- val = atof(tmp[1]); reax->sbp[i].gamma_w = val;
- val = atof(tmp[2]); reax->sbp[i].valency_boc= val;
- val = atof(tmp[3]); reax->sbp[i].p_ovun5 = val;
- val = atof(tmp[4]);
- val = atof(tmp[5]); reax->sbp[i].chi = val;
- val = atof(tmp[6]); reax->sbp[i].eta = 2.0 * val;
- /* this is the parameter that is used to determine
- which type of atoms participate in h-bonds.
- 1 is for H - 2 for O, N, S - 0 for all others.*/
- val = atof(tmp[7]); reax->sbp[i].p_hbond = (int)(val+0.1);
- //0.1 is to avoid from truncating down!
-
- /* line 3 */
- fgets( s, MAX_LINE, fp );
- c = Tokenize( s, &tmp );
-
- val = atof(tmp[0]); reax->sbp[i].r_pi_pi = val;
- val = atof(tmp[1]); reax->sbp[i].p_lp2 = val;
- val = atof(tmp[2]);
- val = atof(tmp[3]); reax->sbp[i].b_o_131 = val;
- val = atof(tmp[4]); reax->sbp[i].b_o_132 = val;
- val = atof(tmp[5]); reax->sbp[i].b_o_133 = val;
- val = atof(tmp[6]);
- val = atof(tmp[7]);
-
- /* line 4 */
+
+ /* next line is number of atom types and some comments */
fgets( s, MAX_LINE, fp );
c = Tokenize( s, &tmp );
-
- val = atof(tmp[0]); reax->sbp[i].p_ovun2 = val;
- val = atof(tmp[1]); reax->sbp[i].p_val3 = val;
- val = atof(tmp[2]);
- val = atof(tmp[3]); reax->sbp[i].valency_val= val;
- val = atof(tmp[4]); reax->sbp[i].p_val5 = val;
- val = atof(tmp[5]); reax->sbp[i].rcore2 = val;
- val = atof(tmp[6]); reax->sbp[i].ecore2 = val;
- val = atof(tmp[7]); reax->sbp[i].acore2 = val;
-
- if( reax->sbp[i].rcore2>0.01 && reax->sbp[i].acore2>0.01 ){ // Inner-wall
- if( reax->sbp[i].gamma_w>0.5 ){ // Shielding vdWaals
- if( reax->gp.vdw_type != 0 && reax->gp.vdw_type != 3 )
- fprintf( stderr, "Warning: inconsistent vdWaals-parameters\n" \
- "Force field parameters for element %s\n" \
- "indicate inner wall+shielding, but earlier\n" \
- "atoms indicate different vdWaals-method.\n" \
- "This may cause division-by-zero errors.\n" \
- "Keeping vdWaals-setting for earlier atoms.\n",
- reax->sbp[i].name );
- else{
- reax->gp.vdw_type = 3;
+ reax->num_atom_types = atoi(tmp[0]);
+
+
+ /* 3 lines of comments */
+ fgets(s, MAX_LINE, fp);
+ fgets(s, MAX_LINE, fp);
+ fgets(s, MAX_LINE, fp);
+
+
+ /* Allocating structures in reax_interaction */
+ reax->sbp = (single_body_parameters*)
+ calloc( reax->num_atom_types, sizeof(single_body_parameters) );
+ reax->tbp = (two_body_parameters**)
+ calloc( reax->num_atom_types, sizeof(two_body_parameters*) );
+ reax->thbp = (three_body_header***)
+ calloc( reax->num_atom_types, sizeof(three_body_header**) );
+ reax->hbp = (hbond_parameters***)
+ calloc( reax->num_atom_types, sizeof(hbond_parameters**) );
+ reax->fbp = (four_body_header****)
+ calloc( reax->num_atom_types, sizeof(four_body_header***) );
+ tor_flag = (char****)
+ calloc( reax->num_atom_types, sizeof(char***) );
+
+ for ( i = 0; i < reax->num_atom_types; i++ )
+ {
+ reax->tbp[i] = (two_body_parameters*)
+ calloc( reax->num_atom_types, sizeof(two_body_parameters) );
+ reax->thbp[i] = (three_body_header**)
+ calloc( reax->num_atom_types, sizeof(three_body_header*) );
+ reax->hbp[i] = (hbond_parameters**)
+ calloc( reax->num_atom_types, sizeof(hbond_parameters*) );
+ reax->fbp[i] = (four_body_header***)
+ calloc( reax->num_atom_types, sizeof(four_body_header**) );
+ tor_flag[i] = (char***)
+ calloc( reax->num_atom_types, sizeof(char**) );
+
+ for ( j = 0; j < reax->num_atom_types; j++ )
+ {
+ reax->thbp[i][j] = (three_body_header*)
+ calloc( reax->num_atom_types, sizeof(three_body_header) );
+ reax->hbp[i][j] = (hbond_parameters*)
+ calloc( reax->num_atom_types, sizeof(hbond_parameters) );
+ reax->fbp[i][j] = (four_body_header**)
+ calloc( reax->num_atom_types, sizeof(four_body_header*) );
+ tor_flag[i][j] = (char**)
+ calloc( reax->num_atom_types, sizeof(char*) );
+
+ for (k = 0; k < reax->num_atom_types; k++)
+ {
+ reax->fbp[i][j][k] = (four_body_header*)
+ calloc( reax->num_atom_types, sizeof(four_body_header) );
+ tor_flag[i][j][k] = (char*)
+ calloc( reax->num_atom_types, sizeof(char) );
+ }
+ }
+ }
+
+ // vdWaals type: 1: Shielded Morse, no inner-wall
+ // 2: inner wall, no shielding
+ // 3: inner wall+shielding
+ reax->gp.vdw_type = 0;
+
+ /* reading single atom parameters */
+ /* there are 4 lines of each single atom parameters in ff files. these
+ parameters later determine some of the pair and triplet parameters using
+ combination rules. */
+ for ( i = 0; i < reax->num_atom_types; i++ )
+ {
+ /* line one */
+ fgets( s, MAX_LINE, fp );
+ c = Tokenize( s, &tmp );
+
+ for ( j = 0; j < strlen( tmp[0] ); ++j )
+ reax->sbp[i].name[j] = toupper( tmp[0][j] );
+
+ val = atof(tmp[1]);
+ reax->sbp[i].r_s = val;
+ val = atof(tmp[2]);
+ reax->sbp[i].valency = val;
+ val = atof(tmp[3]);
+ reax->sbp[i].mass = val;
+ val = atof(tmp[4]);
+ reax->sbp[i].r_vdw = val;
+ val = atof(tmp[5]);
+ reax->sbp[i].epsilon = val;
+ val = atof(tmp[6]);
+ reax->sbp[i].gamma = val;
+ val = atof(tmp[7]);
+ reax->sbp[i].r_pi = val;
+ val = atof(tmp[8]);
+ reax->sbp[i].valency_e = val;
+ reax->sbp[i].nlp_opt = 0.5 * (reax->sbp[i].valency_e - reax->sbp[i].valency);
+
+ /* line two */
+ fgets( s, MAX_LINE, fp );
+ c = Tokenize( s, &tmp );
+
+ val = atof(tmp[0]);
+ reax->sbp[i].alpha = val;
+ val = atof(tmp[1]);
+ reax->sbp[i].gamma_w = val;
+ val = atof(tmp[2]);
+ reax->sbp[i].valency_boc = val;
+ val = atof(tmp[3]);
+ reax->sbp[i].p_ovun5 = val;
+ val = atof(tmp[4]);
+ val = atof(tmp[5]);
+ reax->sbp[i].chi = val;
+ val = atof(tmp[6]);
+ reax->sbp[i].eta = 2.0 * val;
+ /* this is the parameter that is used to determine
+ which type of atoms participate in h-bonds.
+ 1 is for H - 2 for O, N, S - 0 for all others.*/
+ val = atof(tmp[7]);
+ reax->sbp[i].p_hbond = (int)(val + 0.1);
+ //0.1 is to avoid from truncating down!
+
+ /* line 3 */
+ fgets( s, MAX_LINE, fp );
+ c = Tokenize( s, &tmp );
+
+ val = atof(tmp[0]);
+ reax->sbp[i].r_pi_pi = val;
+ val = atof(tmp[1]);
+ reax->sbp[i].p_lp2 = val;
+ val = atof(tmp[2]);
+ val = atof(tmp[3]);
+ reax->sbp[i].b_o_131 = val;
+ val = atof(tmp[4]);
+ reax->sbp[i].b_o_132 = val;
+ val = atof(tmp[5]);
+ reax->sbp[i].b_o_133 = val;
+ val = atof(tmp[6]);
+ val = atof(tmp[7]);
+
+ /* line 4 */
+ fgets( s, MAX_LINE, fp );
+ c = Tokenize( s, &tmp );
+
+ val = atof(tmp[0]);
+ reax->sbp[i].p_ovun2 = val;
+ val = atof(tmp[1]);
+ reax->sbp[i].p_val3 = val;
+ val = atof(tmp[2]);
+ val = atof(tmp[3]);
+ reax->sbp[i].valency_val = val;
+ val = atof(tmp[4]);
+ reax->sbp[i].p_val5 = val;
+ val = atof(tmp[5]);
+ reax->sbp[i].rcore2 = val;
+ val = atof(tmp[6]);
+ reax->sbp[i].ecore2 = val;
+ val = atof(tmp[7]);
+ reax->sbp[i].acore2 = val;
+
+ if ( reax->sbp[i].rcore2 > 0.01 && reax->sbp[i].acore2 > 0.01 ) // Inner-wall
+ {
+ if ( reax->sbp[i].gamma_w > 0.5 ) // Shielding vdWaals
+ {
+ if ( reax->gp.vdw_type != 0 && reax->gp.vdw_type != 3 )
+ fprintf( stderr, "Warning: inconsistent vdWaals-parameters\n" \
+ "Force field parameters for element %s\n" \
+ "indicate inner wall+shielding, but earlier\n" \
+ "atoms indicate different vdWaals-method.\n" \
+ "This may cause division-by-zero errors.\n" \
+ "Keeping vdWaals-setting for earlier atoms.\n",
+ reax->sbp[i].name );
+ else
+ {
+ reax->gp.vdw_type = 3;
#if defined(DEBUG)
- fprintf( stderr, "vdWaals type for element %s: Shielding+inner-wall",
- reax->sbp[i].name );
+ fprintf( stderr, "vdWaals type for element %s: Shielding+inner-wall",
+ reax->sbp[i].name );
#endif
- }
- }
- else { // No shielding vdWaals parameters present
- if( reax->gp.vdw_type != 0 && reax->gp.vdw_type != 2 )
- fprintf( stderr, "Warning: inconsistent vdWaals-parameters\n" \
- "Force field parameters for element %s\n" \
- "indicate inner wall without shielding, but earlier\n" \
- "atoms indicate different vdWaals-method.\n" \
- "This may cause division-by-zero errors.\n" \
- "Keeping vdWaals-setting for earlier atoms.\n",
- reax->sbp[i].name );
- else{
- reax->gp.vdw_type = 2;
+ }
+ }
+ else // No shielding vdWaals parameters present
+ {
+ if ( reax->gp.vdw_type != 0 && reax->gp.vdw_type != 2 )
+ fprintf( stderr, "Warning: inconsistent vdWaals-parameters\n" \
+ "Force field parameters for element %s\n" \
+ "indicate inner wall without shielding, but earlier\n" \
+ "atoms indicate different vdWaals-method.\n" \
+ "This may cause division-by-zero errors.\n" \
+ "Keeping vdWaals-setting for earlier atoms.\n",
+ reax->sbp[i].name );
+ else
+ {
+ reax->gp.vdw_type = 2;
#if defined(DEBUG)
- fprintf( stderr,"vdWaals type for element%s: No Shielding,inner-wall",
- reax->sbp[i].name );
+ fprintf( stderr, "vdWaals type for element%s: No Shielding,inner-wall",
+ reax->sbp[i].name );
#endif
- }
- }
- }
- else{ // No Inner wall parameters present
- if( reax->sbp[i].gamma_w>0.5 ){ // Shielding vdWaals
- if( reax->gp.vdw_type != 0 && reax->gp.vdw_type != 1 )
- fprintf( stderr, "Warning: inconsistent vdWaals-parameters\n" \
- "Force field parameters for element %s\n" \
- "indicate shielding without inner wall, but earlier\n" \
- "atoms indicate different vdWaals-method.\n" \
- "This may cause division-by-zero errors.\n" \
- "Keeping vdWaals-setting for earlier atoms.\n",
- reax->sbp[i].name );
- else{
- reax->gp.vdw_type = 1;
+ }
+ }
+ }
+ else // No Inner wall parameters present
+ {
+ if ( reax->sbp[i].gamma_w > 0.5 ) // Shielding vdWaals
+ {
+ if ( reax->gp.vdw_type != 0 && reax->gp.vdw_type != 1 )
+ fprintf( stderr, "Warning: inconsistent vdWaals-parameters\n" \
+ "Force field parameters for element %s\n" \
+ "indicate shielding without inner wall, but earlier\n" \
+ "atoms indicate different vdWaals-method.\n" \
+ "This may cause division-by-zero errors.\n" \
+ "Keeping vdWaals-setting for earlier atoms.\n",
+ reax->sbp[i].name );
+ else
+ {
+ reax->gp.vdw_type = 1;
#if defined(DEBUG)
- fprintf( stderr,"vdWaals type for element%s: Shielding,no inner-wall",
- reax->sbp[i].name );
+ fprintf( stderr, "vdWaals type for element%s: Shielding,no inner-wall",
+ reax->sbp[i].name );
#endif
- }
- }
- else{
- fprintf( stderr, "Error: inconsistent vdWaals-parameters\n"\
- "No shielding or inner-wall set for element %s\n",
- reax->sbp[i].name );
- exit( INVALID_INPUT );
- }
- }
- }
-
-
- /* next line is number of two body combination and some comments */
- fgets(s,MAX_LINE,fp);
- c=Tokenize(s,&tmp);
- l = atoi(tmp[0]);
-
- /* a line of comments */
- fgets(s,MAX_LINE,fp);
-
- for (i=0; i < l; i++)
- {
- /* line 1 */
- fgets(s,MAX_LINE,fp);
- c=Tokenize(s,&tmp);
-
- j = atoi(tmp[0]) - 1;
- k = atoi(tmp[1]) - 1;
-
- if (j < reax->num_atom_types && k < reax->num_atom_types)
- {
-
- val = atof(tmp[2]); reax->tbp[j][k].De_s = val;
- reax->tbp[k][j].De_s = val;
- val = atof(tmp[3]); reax->tbp[j][k].De_p = val;
- reax->tbp[k][j].De_p = val;
- val = atof(tmp[4]); reax->tbp[j][k].De_pp = val;
- reax->tbp[k][j].De_pp = val;
- val = atof(tmp[5]); reax->tbp[j][k].p_be1 = val;
- reax->tbp[k][j].p_be1 = val;
- val = atof(tmp[6]); reax->tbp[j][k].p_bo5 = val;
- reax->tbp[k][j].p_bo5 = val;
- val = atof(tmp[7]); reax->tbp[j][k].v13cor = val;
- reax->tbp[k][j].v13cor = val;
-
- val = atof(tmp[8]); reax->tbp[j][k].p_bo6 = val;
- reax->tbp[k][j].p_bo6 = val;
- val = atof(tmp[9]); reax->tbp[j][k].p_ovun1 = val;
- reax->tbp[k][j].p_ovun1 = val;
-
- /* line 2 */
- fgets(s,MAX_LINE,fp);
- c=Tokenize(s,&tmp);
-
- val = atof(tmp[0]); reax->tbp[j][k].p_be2 = val;
- reax->tbp[k][j].p_be2 = val;
- val = atof(tmp[1]); reax->tbp[j][k].p_bo3 = val;
- reax->tbp[k][j].p_bo3 = val;
- val = atof(tmp[2]); reax->tbp[j][k].p_bo4 = val;
- reax->tbp[k][j].p_bo4 = val;
- val = atof(tmp[3]);
-
- val = atof(tmp[4]); reax->tbp[j][k].p_bo1 = val;
- reax->tbp[k][j].p_bo1 = val;
- val = atof(tmp[5]); reax->tbp[j][k].p_bo2 = val;
- reax->tbp[k][j].p_bo2 = val;
- val = atof(tmp[6]); reax->tbp[j][k].ovc = val;
- reax->tbp[k][j].ovc = val;
-
- val = atof(tmp[7]);
- }
+ }
+ }
+ else
+ {
+ fprintf( stderr, "Error: inconsistent vdWaals-parameters\n"\
+ "No shielding or inner-wall set for element %s\n",
+ reax->sbp[i].name );
+ exit( INVALID_INPUT );
+ }
+ }
}
- /* calculating combination rules and filling up remaining fields. */
-
- for (i=0; i < reax->num_atom_types; i++)
- for (j=i; j < reax->num_atom_types; j++)
- {
- reax->tbp[i][j].r_s = 0.5 *
- (reax->sbp[i].r_s + reax->sbp[j].r_s);
- reax->tbp[j][i].r_s = 0.5 *
- (reax->sbp[j].r_s + reax->sbp[i].r_s);
-
- reax->tbp[i][j].r_p = 0.5 *
- (reax->sbp[i].r_pi + reax->sbp[j].r_pi);
- reax->tbp[j][i].r_p = 0.5 *
- (reax->sbp[j].r_pi + reax->sbp[i].r_pi);
-
- reax->tbp[i][j].r_pp = 0.5 *
- (reax->sbp[i].r_pi_pi + reax->sbp[j].r_pi_pi);
- reax->tbp[j][i].r_pp = 0.5 *
- (reax->sbp[j].r_pi_pi + reax->sbp[i].r_pi_pi);
-
-
- reax->tbp[i][j].p_boc3 =
- sqrt(reax->sbp[i].b_o_132 *
- reax->sbp[j].b_o_132);
- reax->tbp[j][i].p_boc3 =
- sqrt(reax->sbp[j].b_o_132 *
- reax->sbp[i].b_o_132);
-
- reax->tbp[i][j].p_boc4 =
- sqrt(reax->sbp[i].b_o_131 *
- reax->sbp[j].b_o_131);
- reax->tbp[j][i].p_boc4 =
- sqrt(reax->sbp[j].b_o_131 *
- reax->sbp[i].b_o_131);
-
- reax->tbp[i][j].p_boc5 =
- sqrt(reax->sbp[i].b_o_133 *
- reax->sbp[j].b_o_133);
- reax->tbp[j][i].p_boc5 =
- sqrt(reax->sbp[j].b_o_133 *
- reax->sbp[i].b_o_133);
-
-
- reax->tbp[i][j].D =
- sqrt(reax->sbp[i].epsilon *
- reax->sbp[j].epsilon);
-
- reax->tbp[j][i].D =
- sqrt(reax->sbp[j].epsilon *
- reax->sbp[i].epsilon);
-
- reax->tbp[i][j].alpha =
- sqrt(reax->sbp[i].alpha *
- reax->sbp[j].alpha);
-
- reax->tbp[j][i].alpha =
- sqrt(reax->sbp[j].alpha *
- reax->sbp[i].alpha);
-
- reax->tbp[i][j].r_vdW =
- 2.0 * sqrt(reax->sbp[i].r_vdw * reax->sbp[j].r_vdw);
-
- reax->tbp[j][i].r_vdW =
- 2.0 * sqrt(reax->sbp[j].r_vdw * reax->sbp[i].r_vdw);
-
- reax->tbp[i][j].gamma_w =
- sqrt(reax->sbp[i].gamma_w *
- reax->sbp[j].gamma_w);
-
- reax->tbp[j][i].gamma_w =
- sqrt(reax->sbp[j].gamma_w *
- reax->sbp[i].gamma_w);
-
- reax->tbp[i][j].gamma =
- POW(reax->sbp[i].gamma *
- reax->sbp[j].gamma,-1.5);
-
- reax->tbp[j][i].gamma =
- POW(reax->sbp[j].gamma *
- reax->sbp[i].gamma,-1.5);
-
- }
-
-
- /* next line is number of 2-body offdiagonal combinations and some comments */
- /* these are two body offdiagonal terms that are different from the
- combination rules defined above */
- fgets(s,MAX_LINE,fp);
- c=Tokenize(s,&tmp);
- l = atoi(tmp[0]);
-
- for (i=0; i < l; i++)
- {
- fgets(s,MAX_LINE,fp);
- c=Tokenize(s,&tmp);
-
- j = atoi(tmp[0]) - 1;
- k = atoi(tmp[1]) - 1;
-
- if (j < reax->num_atom_types && k < reax->num_atom_types)
- {
- val = atof(tmp[2]);
- if (val > 0.0)
- {
- reax->tbp[j][k].D = val;
- reax->tbp[k][j].D = val;
- }
-
- val = atof(tmp[3]);
- if (val > 0.0)
- {
- reax->tbp[j][k].r_vdW = 2 * val;
- reax->tbp[k][j].r_vdW = 2 * val;
- }
-
- val = atof(tmp[4]);
- if (val > 0.0)
- {
- reax->tbp[j][k].alpha = val;
- reax->tbp[k][j].alpha = val;
- }
-
- val = atof(tmp[5]);
- if (val > 0.0)
- {
- reax->tbp[j][k].r_s = val;
- reax->tbp[k][j].r_s = val;
- }
-
- val = atof(tmp[6]);
- if (val > 0.0)
- {
- reax->tbp[j][k].r_p = val;
- reax->tbp[k][j].r_p = val;
- }
-
- val = atof(tmp[7]);
- if (val > 0.0)
- {
- reax->tbp[j][k].r_pp = val;
- reax->tbp[k][j].r_pp = val;
- }
- }
- }
-
-
- /* 3-body parameters -
- supports multi-well potentials (upto MAX_3BODY_PARAM in mytypes.h) */
- /* clear entries first */
- for( i = 0; i < reax->num_atom_types; ++i )
- for( j = 0; j < reax->num_atom_types; ++j )
- for( k = 0; k < reax->num_atom_types; ++k )
- reax->thbp[i][j][k].cnt = 0;
-
- /* next line is number of 3-body params and some comments */
- fgets( s, MAX_LINE, fp );
- c = Tokenize( s, &tmp );
- l = atoi( tmp[0] );
-
- for( i = 0; i < l; i++ )
- {
- fgets(s,MAX_LINE,fp);
- c=Tokenize(s,&tmp);
-
- j = atoi(tmp[0]) - 1;
- k = atoi(tmp[1]) - 1;
- m = atoi(tmp[2]) - 1;
-
- if (j < reax->num_atom_types &&
- k < reax->num_atom_types &&
- m < reax->num_atom_types)
- {
- cnt = reax->thbp[j][k][m].cnt;
- reax->thbp[j][k][m].cnt++;
- reax->thbp[m][k][j].cnt++;
-
- val = atof(tmp[3]);
- reax->thbp[j][k][m].prm[cnt].theta_00 = val;
- reax->thbp[m][k][j].prm[cnt].theta_00 = val;
-
- val = atof(tmp[4]);
- reax->thbp[j][k][m].prm[cnt].p_val1 = val;
- reax->thbp[m][k][j].prm[cnt].p_val1 = val;
-
- val = atof(tmp[5]);
- reax->thbp[j][k][m].prm[cnt].p_val2 = val;
- reax->thbp[m][k][j].prm[cnt].p_val2 = val;
-
- val = atof(tmp[6]);
- reax->thbp[j][k][m].prm[cnt].p_coa1 = val;
- reax->thbp[m][k][j].prm[cnt].p_coa1 = val;
-
- val = atof(tmp[7]);
- reax->thbp[j][k][m].prm[cnt].p_val7 = val;
- reax->thbp[m][k][j].prm[cnt].p_val7 = val;
-
- val = atof(tmp[8]);
- reax->thbp[j][k][m].prm[cnt].p_pen1 = val;
- reax->thbp[m][k][j].prm[cnt].p_pen1 = val;
-
- val = atof(tmp[9]);
- reax->thbp[j][k][m].prm[cnt].p_val4 = val;
- reax->thbp[m][k][j].prm[cnt].p_val4 = val;
- }
- }
+ /* next line is number of two body combination and some comments */
+ fgets(s, MAX_LINE, fp);
+ c = Tokenize(s, &tmp);
+ l = atoi(tmp[0]);
- /* 4-body parameters are entered in compact form. i.e. 0-X-Y-0
- correspond to any type of pair of atoms in 1 and 4
- position. However, explicit X-Y-Z-W takes precedence over the
- default description.
- supports multi-well potentials (upto MAX_4BODY_PARAM in mytypes.h)
- IMPORTANT: for now, directions on how to read multi-entries from ffield
- is not clear */
-
- /* clear all entries first */
- for( i = 0; i < reax->num_atom_types; ++i )
- for( j = 0; j < reax->num_atom_types; ++j )
- for( k = 0; k < reax->num_atom_types; ++k )
- for( m = 0; m < reax->num_atom_types; ++m )
- {
- reax->fbp[i][j][k][m].cnt = 0;
- tor_flag[i][j][k][m] = 0;
- }
-
- /* next line is number of 4-body params and some comments */
- fgets( s, MAX_LINE, fp );
- c = Tokenize( s, &tmp );
- l = atoi( tmp[0] );
-
- for( i = 0; i < l; i++ )
+ /* a line of comments */
+ fgets(s, MAX_LINE, fp);
+
+ for (i = 0; i < l; i++)
{
- fgets( s, MAX_LINE, fp );
- c = Tokenize( s, &tmp );
-
- j = atoi(tmp[0]) - 1;
- k = atoi(tmp[1]) - 1;
- m = atoi(tmp[2]) - 1;
- n = atoi(tmp[3]) - 1;
-
- if (j >= 0 && n >= 0) // this means the entry is not in compact form
- {
- if (j < reax->num_atom_types &&
- k < reax->num_atom_types &&
- m < reax->num_atom_types &&
- n < reax->num_atom_types)
- {
- /* these flags ensure that this entry take precedence
- over the compact form entries */
- tor_flag[j][k][m][n] = 1;
- tor_flag[n][m][k][j] = 1;
-
- reax->fbp[j][k][m][n].cnt = 1;
- reax->fbp[n][m][k][j].cnt = 1;
- /* cnt = reax->fbp[j][k][m][n].cnt;
- reax->fbp[j][k][m][n].cnt++;
- reax->fbp[n][m][k][j].cnt++; */
-
- val = atof(tmp[4]);
- reax->fbp[j][k][m][n].prm[0].V1 = val;
- reax->fbp[n][m][k][j].prm[0].V1 = val;
-
- val = atof(tmp[5]);
- reax->fbp[j][k][m][n].prm[0].V2 = val;
- reax->fbp[n][m][k][j].prm[0].V2 = val;
-
- val = atof(tmp[6]);
- reax->fbp[j][k][m][n].prm[0].V3 = val;
- reax->fbp[n][m][k][j].prm[0].V3 = val;
-
- val = atof(tmp[7]);
- reax->fbp[j][k][m][n].prm[0].p_tor1 = val;
- reax->fbp[n][m][k][j].prm[0].p_tor1 = val;
-
- val = atof(tmp[8]);
- reax->fbp[j][k][m][n].prm[0].p_cot1 = val;
- reax->fbp[n][m][k][j].prm[0].p_cot1 = val;
- }
- }
- else /* This means the entry is of the form 0-X-Y-0 */
- {
- if( k < reax->num_atom_types && m < reax->num_atom_types )
- for( p = 0; p < reax->num_atom_types; p++ )
- for( o = 0; o < reax->num_atom_types; o++ )
- {
- reax->fbp[p][k][m][o].cnt = 1;
- reax->fbp[o][m][k][p].cnt = 1;
- /* cnt = reax->fbp[p][k][m][o].cnt;
- reax->fbp[p][k][m][o].cnt++;
- reax->fbp[o][m][k][p].cnt++; */
-
- if (tor_flag[p][k][m][o] == 0)
- {
- reax->fbp[p][k][m][o].prm[0].V1 = atof(tmp[4]);
- reax->fbp[p][k][m][o].prm[0].V2 = atof(tmp[5]);
- reax->fbp[p][k][m][o].prm[0].V3 = atof(tmp[6]);
- reax->fbp[p][k][m][o].prm[0].p_tor1 = atof(tmp[7]);
- reax->fbp[p][k][m][o].prm[0].p_cot1 = atof(tmp[8]);
- }
-
- if (tor_flag[o][m][k][p] == 0)
- {
- reax->fbp[o][m][k][p].prm[0].V1 = atof(tmp[4]);
- reax->fbp[o][m][k][p].prm[0].V2 = atof(tmp[5]);
- reax->fbp[o][m][k][p].prm[0].V3 = atof(tmp[6]);
- reax->fbp[o][m][k][p].prm[0].p_tor1 = atof(tmp[7]);
- reax->fbp[o][m][k][p].prm[0].p_cot1 = atof(tmp[8]);
- }
- }
- }
- }
+ /* line 1 */
+ fgets(s, MAX_LINE, fp);
+ c = Tokenize(s, &tmp);
+
+ j = atoi(tmp[0]) - 1;
+ k = atoi(tmp[1]) - 1;
+
+ if (j < reax->num_atom_types && k < reax->num_atom_types)
+ {
+
+ val = atof(tmp[2]);
+ reax->tbp[j][k].De_s = val;
+ reax->tbp[k][j].De_s = val;
+ val = atof(tmp[3]);
+ reax->tbp[j][k].De_p = val;
+ reax->tbp[k][j].De_p = val;
+ val = atof(tmp[4]);
+ reax->tbp[j][k].De_pp = val;
+ reax->tbp[k][j].De_pp = val;
+ val = atof(tmp[5]);
+ reax->tbp[j][k].p_be1 = val;
+ reax->tbp[k][j].p_be1 = val;
+ val = atof(tmp[6]);
+ reax->tbp[j][k].p_bo5 = val;
+ reax->tbp[k][j].p_bo5 = val;
+ val = atof(tmp[7]);
+ reax->tbp[j][k].v13cor = val;
+ reax->tbp[k][j].v13cor = val;
+
+ val = atof(tmp[8]);
+ reax->tbp[j][k].p_bo6 = val;
+ reax->tbp[k][j].p_bo6 = val;
+ val = atof(tmp[9]);
+ reax->tbp[j][k].p_ovun1 = val;
+ reax->tbp[k][j].p_ovun1 = val;
+
+ /* line 2 */
+ fgets(s, MAX_LINE, fp);
+ c = Tokenize(s, &tmp);
+
+ val = atof(tmp[0]);
+ reax->tbp[j][k].p_be2 = val;
+ reax->tbp[k][j].p_be2 = val;
+ val = atof(tmp[1]);
+ reax->tbp[j][k].p_bo3 = val;
+ reax->tbp[k][j].p_bo3 = val;
+ val = atof(tmp[2]);
+ reax->tbp[j][k].p_bo4 = val;
+ reax->tbp[k][j].p_bo4 = val;
+ val = atof(tmp[3]);
+
+ val = atof(tmp[4]);
+ reax->tbp[j][k].p_bo1 = val;
+ reax->tbp[k][j].p_bo1 = val;
+ val = atof(tmp[5]);
+ reax->tbp[j][k].p_bo2 = val;
+ reax->tbp[k][j].p_bo2 = val;
+ val = atof(tmp[6]);
+ reax->tbp[j][k].ovc = val;
+ reax->tbp[k][j].ovc = val;
+
+ val = atof(tmp[7]);
+ }
+ }
+
+ /* calculating combination rules and filling up remaining fields. */
+
+ for (i = 0; i < reax->num_atom_types; i++)
+ for (j = i; j < reax->num_atom_types; j++)
+ {
+ reax->tbp[i][j].r_s = 0.5 *
+ (reax->sbp[i].r_s + reax->sbp[j].r_s);
+ reax->tbp[j][i].r_s = 0.5 *
+ (reax->sbp[j].r_s + reax->sbp[i].r_s);
+
+ reax->tbp[i][j].r_p = 0.5 *
+ (reax->sbp[i].r_pi + reax->sbp[j].r_pi);
+ reax->tbp[j][i].r_p = 0.5 *
+ (reax->sbp[j].r_pi + reax->sbp[i].r_pi);
+
+ reax->tbp[i][j].r_pp = 0.5 *
+ (reax->sbp[i].r_pi_pi + reax->sbp[j].r_pi_pi);
+ reax->tbp[j][i].r_pp = 0.5 *
+ (reax->sbp[j].r_pi_pi + reax->sbp[i].r_pi_pi);
+
+
+ reax->tbp[i][j].p_boc3 =
+ sqrt(reax->sbp[i].b_o_132 *
+ reax->sbp[j].b_o_132);
+ reax->tbp[j][i].p_boc3 =
+ sqrt(reax->sbp[j].b_o_132 *
+ reax->sbp[i].b_o_132);
+
+ reax->tbp[i][j].p_boc4 =
+ sqrt(reax->sbp[i].b_o_131 *
+ reax->sbp[j].b_o_131);
+ reax->tbp[j][i].p_boc4 =
+ sqrt(reax->sbp[j].b_o_131 *
+ reax->sbp[i].b_o_131);
+
+ reax->tbp[i][j].p_boc5 =
+ sqrt(reax->sbp[i].b_o_133 *
+ reax->sbp[j].b_o_133);
+ reax->tbp[j][i].p_boc5 =
+ sqrt(reax->sbp[j].b_o_133 *
+ reax->sbp[i].b_o_133);
+
+
+ reax->tbp[i][j].D =
+ sqrt(reax->sbp[i].epsilon *
+ reax->sbp[j].epsilon);
+
+ reax->tbp[j][i].D =
+ sqrt(reax->sbp[j].epsilon *
+ reax->sbp[i].epsilon);
+
+ reax->tbp[i][j].alpha =
+ sqrt(reax->sbp[i].alpha *
+ reax->sbp[j].alpha);
+
+ reax->tbp[j][i].alpha =
+ sqrt(reax->sbp[j].alpha *
+ reax->sbp[i].alpha);
+
+ reax->tbp[i][j].r_vdW =
+ 2.0 * sqrt(reax->sbp[i].r_vdw * reax->sbp[j].r_vdw);
+
+ reax->tbp[j][i].r_vdW =
+ 2.0 * sqrt(reax->sbp[j].r_vdw * reax->sbp[i].r_vdw);
+
+ reax->tbp[i][j].gamma_w =
+ sqrt(reax->sbp[i].gamma_w *
+ reax->sbp[j].gamma_w);
+
+ reax->tbp[j][i].gamma_w =
+ sqrt(reax->sbp[j].gamma_w *
+ reax->sbp[i].gamma_w);
+
+ reax->tbp[i][j].gamma =
+ POW(reax->sbp[i].gamma *
+ reax->sbp[j].gamma, -1.5);
+
+ reax->tbp[j][i].gamma =
+ POW(reax->sbp[j].gamma *
+ reax->sbp[i].gamma, -1.5);
+
+ }
+
+
+ /* next line is number of 2-body offdiagonal combinations and some comments */
+ /* these are two body offdiagonal terms that are different from the
+ combination rules defined above */
+ fgets(s, MAX_LINE, fp);
+ c = Tokenize(s, &tmp);
+ l = atoi(tmp[0]);
+ for (i = 0; i < l; i++)
+ {
+ fgets(s, MAX_LINE, fp);
+ c = Tokenize(s, &tmp);
+
+ j = atoi(tmp[0]) - 1;
+ k = atoi(tmp[1]) - 1;
+
+ if (j < reax->num_atom_types && k < reax->num_atom_types)
+ {
+ val = atof(tmp[2]);
+ if (val > 0.0)
+ {
+ reax->tbp[j][k].D = val;
+ reax->tbp[k][j].D = val;
+ }
+
+ val = atof(tmp[3]);
+ if (val > 0.0)
+ {
+ reax->tbp[j][k].r_vdW = 2 * val;
+ reax->tbp[k][j].r_vdW = 2 * val;
+ }
+
+ val = atof(tmp[4]);
+ if (val > 0.0)
+ {
+ reax->tbp[j][k].alpha = val;
+ reax->tbp[k][j].alpha = val;
+ }
+
+ val = atof(tmp[5]);
+ if (val > 0.0)
+ {
+ reax->tbp[j][k].r_s = val;
+ reax->tbp[k][j].r_s = val;
+ }
+
+ val = atof(tmp[6]);
+ if (val > 0.0)
+ {
+ reax->tbp[j][k].r_p = val;
+ reax->tbp[k][j].r_p = val;
+ }
+
+ val = atof(tmp[7]);
+ if (val > 0.0)
+ {
+ reax->tbp[j][k].r_pp = val;
+ reax->tbp[k][j].r_pp = val;
+ }
+ }
+ }
+
+
+ /* 3-body parameters -
+ supports multi-well potentials (upto MAX_3BODY_PARAM in mytypes.h) */
+ /* clear entries first */
+ for ( i = 0; i < reax->num_atom_types; ++i )
+ for ( j = 0; j < reax->num_atom_types; ++j )
+ for ( k = 0; k < reax->num_atom_types; ++k )
+ reax->thbp[i][j][k].cnt = 0;
+
+ /* next line is number of 3-body params and some comments */
+ fgets( s, MAX_LINE, fp );
+ c = Tokenize( s, &tmp );
+ l = atoi( tmp[0] );
+ for ( i = 0; i < l; i++ )
+ {
+ fgets(s, MAX_LINE, fp);
+ c = Tokenize(s, &tmp);
+
+ j = atoi(tmp[0]) - 1;
+ k = atoi(tmp[1]) - 1;
+ m = atoi(tmp[2]) - 1;
+
+ if (j < reax->num_atom_types &&
+ k < reax->num_atom_types &&
+ m < reax->num_atom_types)
+ {
+ cnt = reax->thbp[j][k][m].cnt;
+ reax->thbp[j][k][m].cnt++;
+ reax->thbp[m][k][j].cnt++;
+
+ val = atof(tmp[3]);
+ reax->thbp[j][k][m].prm[cnt].theta_00 = val;
+ reax->thbp[m][k][j].prm[cnt].theta_00 = val;
+
+ val = atof(tmp[4]);
+ reax->thbp[j][k][m].prm[cnt].p_val1 = val;
+ reax->thbp[m][k][j].prm[cnt].p_val1 = val;
+
+ val = atof(tmp[5]);
+ reax->thbp[j][k][m].prm[cnt].p_val2 = val;
+ reax->thbp[m][k][j].prm[cnt].p_val2 = val;
+
+ val = atof(tmp[6]);
+ reax->thbp[j][k][m].prm[cnt].p_coa1 = val;
+ reax->thbp[m][k][j].prm[cnt].p_coa1 = val;
+
+ val = atof(tmp[7]);
+ reax->thbp[j][k][m].prm[cnt].p_val7 = val;
+ reax->thbp[m][k][j].prm[cnt].p_val7 = val;
+
+ val = atof(tmp[8]);
+ reax->thbp[j][k][m].prm[cnt].p_pen1 = val;
+ reax->thbp[m][k][j].prm[cnt].p_pen1 = val;
+
+ val = atof(tmp[9]);
+ reax->thbp[j][k][m].prm[cnt].p_val4 = val;
+ reax->thbp[m][k][j].prm[cnt].p_val4 = val;
+ }
+ }
+
+
+ /* 4-body parameters are entered in compact form. i.e. 0-X-Y-0
+ correspond to any type of pair of atoms in 1 and 4
+ position. However, explicit X-Y-Z-W takes precedence over the
+ default description.
+ supports multi-well potentials (upto MAX_4BODY_PARAM in mytypes.h)
+ IMPORTANT: for now, directions on how to read multi-entries from ffield
+ is not clear */
+
+ /* clear all entries first */
+ for ( i = 0; i < reax->num_atom_types; ++i )
+ for ( j = 0; j < reax->num_atom_types; ++j )
+ for ( k = 0; k < reax->num_atom_types; ++k )
+ for ( m = 0; m < reax->num_atom_types; ++m )
+ {
+ reax->fbp[i][j][k][m].cnt = 0;
+ tor_flag[i][j][k][m] = 0;
+ }
+
+ /* next line is number of 4-body params and some comments */
+ fgets( s, MAX_LINE, fp );
+ c = Tokenize( s, &tmp );
+ l = atoi( tmp[0] );
- /* next line is number of hydrogen bond params and some comments */
- fgets( s, MAX_LINE, fp );
- c = Tokenize( s, &tmp );
- l = atoi( tmp[0] );
+ for ( i = 0; i < l; i++ )
+ {
+ fgets( s, MAX_LINE, fp );
+ c = Tokenize( s, &tmp );
+
+ j = atoi(tmp[0]) - 1;
+ k = atoi(tmp[1]) - 1;
+ m = atoi(tmp[2]) - 1;
+ n = atoi(tmp[3]) - 1;
+
+ if (j >= 0 && n >= 0) // this means the entry is not in compact form
+ {
+ if (j < reax->num_atom_types &&
+ k < reax->num_atom_types &&
+ m < reax->num_atom_types &&
+ n < reax->num_atom_types)
+ {
+ /* these flags ensure that this entry take precedence
+ over the compact form entries */
+ tor_flag[j][k][m][n] = 1;
+ tor_flag[n][m][k][j] = 1;
+
+ reax->fbp[j][k][m][n].cnt = 1;
+ reax->fbp[n][m][k][j].cnt = 1;
+ /* cnt = reax->fbp[j][k][m][n].cnt;
+ reax->fbp[j][k][m][n].cnt++;
+ reax->fbp[n][m][k][j].cnt++; */
+
+ val = atof(tmp[4]);
+ reax->fbp[j][k][m][n].prm[0].V1 = val;
+ reax->fbp[n][m][k][j].prm[0].V1 = val;
+
+ val = atof(tmp[5]);
+ reax->fbp[j][k][m][n].prm[0].V2 = val;
+ reax->fbp[n][m][k][j].prm[0].V2 = val;
+
+ val = atof(tmp[6]);
+ reax->fbp[j][k][m][n].prm[0].V3 = val;
+ reax->fbp[n][m][k][j].prm[0].V3 = val;
+
+ val = atof(tmp[7]);
+ reax->fbp[j][k][m][n].prm[0].p_tor1 = val;
+ reax->fbp[n][m][k][j].prm[0].p_tor1 = val;
+
+ val = atof(tmp[8]);
+ reax->fbp[j][k][m][n].prm[0].p_cot1 = val;
+ reax->fbp[n][m][k][j].prm[0].p_cot1 = val;
+ }
+ }
+ else /* This means the entry is of the form 0-X-Y-0 */
+ {
+ if ( k < reax->num_atom_types && m < reax->num_atom_types )
+ for ( p = 0; p < reax->num_atom_types; p++ )
+ for ( o = 0; o < reax->num_atom_types; o++ )
+ {
+ reax->fbp[p][k][m][o].cnt = 1;
+ reax->fbp[o][m][k][p].cnt = 1;
+ /* cnt = reax->fbp[p][k][m][o].cnt;
+ reax->fbp[p][k][m][o].cnt++;
+ reax->fbp[o][m][k][p].cnt++; */
+
+ if (tor_flag[p][k][m][o] == 0)
+ {
+ reax->fbp[p][k][m][o].prm[0].V1 = atof(tmp[4]);
+ reax->fbp[p][k][m][o].prm[0].V2 = atof(tmp[5]);
+ reax->fbp[p][k][m][o].prm[0].V3 = atof(tmp[6]);
+ reax->fbp[p][k][m][o].prm[0].p_tor1 = atof(tmp[7]);
+ reax->fbp[p][k][m][o].prm[0].p_cot1 = atof(tmp[8]);
+ }
+
+ if (tor_flag[o][m][k][p] == 0)
+ {
+ reax->fbp[o][m][k][p].prm[0].V1 = atof(tmp[4]);
+ reax->fbp[o][m][k][p].prm[0].V2 = atof(tmp[5]);
+ reax->fbp[o][m][k][p].prm[0].V3 = atof(tmp[6]);
+ reax->fbp[o][m][k][p].prm[0].p_tor1 = atof(tmp[7]);
+ reax->fbp[o][m][k][p].prm[0].p_cot1 = atof(tmp[8]);
+ }
+ }
+ }
+ }
+
+
+
+ /* next line is number of hydrogen bond params and some comments */
+ fgets( s, MAX_LINE, fp );
+ c = Tokenize( s, &tmp );
+ l = atoi( tmp[0] );
- for( i = 0; i < l; i++ )
+ for ( i = 0; i < l; i++ )
{
- fgets( s, MAX_LINE, fp );
- c = Tokenize( s, &tmp );
-
- j = atoi(tmp[0]) - 1;
- k = atoi(tmp[1]) - 1;
- m = atoi(tmp[2]) - 1;
+ fgets( s, MAX_LINE, fp );
+ c = Tokenize( s, &tmp );
+
+ j = atoi(tmp[0]) - 1;
+ k = atoi(tmp[1]) - 1;
+ m = atoi(tmp[2]) - 1;
- if (j < reax->num_atom_types && m < reax->num_atom_types)
- {
- val = atof(tmp[3]);
- reax->hbp[j][k][m].r0_hb = val;
+ if (j < reax->num_atom_types && m < reax->num_atom_types)
+ {
+ val = atof(tmp[3]);
+ reax->hbp[j][k][m].r0_hb = val;
- val = atof(tmp[4]);
- reax->hbp[j][k][m].p_hb1 = val;
+ val = atof(tmp[4]);
+ reax->hbp[j][k][m].p_hb1 = val;
- val = atof(tmp[5]);
- reax->hbp[j][k][m].p_hb2 = val;
+ val = atof(tmp[5]);
+ reax->hbp[j][k][m].p_hb2 = val;
- val = atof(tmp[6]);
- reax->hbp[j][k][m].p_hb3 = val;
+ val = atof(tmp[6]);
+ reax->hbp[j][k][m].p_hb3 = val;
- }
+ }
}
-
- /* deallocate helper storage */
- for( i = 0; i < MAX_TOKENS; i++ )
- free( tmp[i] );
- free( tmp );
- free( s );
+
+ /* deallocate helper storage */
+ for ( i = 0; i < MAX_TOKENS; i++ )
+ free( tmp[i] );
+ free( tmp );
+ free( s );
- /* deallocate tor_flag */
- for( i = 0; i < reax->num_atom_types; i++ )
+ /* deallocate tor_flag */
+ for ( i = 0; i < reax->num_atom_types; i++ )
{
- for( j = 0; j < reax->num_atom_types; j++ )
- {
- for( k = 0; k < reax->num_atom_types; k++ )
- free( tor_flag[i][j][k] );
-
- free( tor_flag[i][j] );
- }
-
- free( tor_flag[i] );
+ for ( j = 0; j < reax->num_atom_types; j++ )
+ {
+ for ( k = 0; k < reax->num_atom_types; k++ )
+ free( tor_flag[i][j][k] );
+
+ free( tor_flag[i][j] );
+ }
+
+ free( tor_flag[i] );
}
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "force field read\n" );
+ fprintf( stderr, "force field read\n" );
#endif
- return 0;
+ return 0;
}
char Read_Control_File( FILE* fp, reax_system *system, control_params* control,
- output_controls *out_control )
+ output_controls *out_control )
{
- char *s, **tmp;
- int c,i;
- real val;
- int ival;
-
- /* assign default values */
- strcpy( control->sim_name, "default.sim" );
-
- control->restart = 0;
- out_control->restart_format = 1;
- out_control->restart_freq = 0;
- strcpy( control->restart_from, "default.res" );
- out_control->restart_freq = 0;
- control->random_vel = 0;
-
- control->reposition_atoms = 0;
-
- control->ensemble = 0;
- control->nsteps = 0;
- control->dt = 0.25;
-
- control->geo_format = 1;
- control->restrict_bonds = 0;
-
- control->periodic_boundaries = 1;
- control->periodic_images[0] = 0;
- control->periodic_images[1] = 0;
- control->periodic_images[2] = 0;
-
- control->reneighbor = 1;
- control->vlist_cut = 0;
- control->nbr_cut = 4.;
- control->r_cut = 10;
- control->max_far_nbrs = 1000;
- control->bo_cut = 0.01;
- control->thb_cut = 0.001;
- control->hb_cut = 7.50;
-
- control->q_err = 0.000001;
- control->tabulate = 0;
- control->refactor = 100;
- control->droptol = 0.01;
-
- control->T_init = 0.;
- control->T_final = 300.;
- control->Tau_T = 1.0;
- control->T_mode = 0.;
- control->T_rate = 1.;
- control->T_freq = 1.;
-
- control->P[0] = 0.000101325;
- control->P[1] = 0.000101325;
- control->P[2] = 0.000101325;
- control->Tau_P[0] = 500.0;
- control->Tau_P[1] = 500.0;
- control->Tau_P[2] = 500.0;
- control->Tau_PT = 500.0;
- control->compressibility = 1.0;
- control->press_mode = 0;
-
- control->remove_CoM_vel = 25;
-
- out_control->debug_level = 0;
- out_control->energy_update_freq = 10;
-
- out_control->write_steps = 100;
- out_control->traj_compress = 0;
- out_control->write = fprintf;
- out_control->traj_format = 0;
- out_control->write_header =
- (int (*)( reax_system*, control_params*,
- static_storage*, void* )) Write_Custom_Header;
- out_control->append_traj_frame =
- (int (*)( reax_system*, control_params*, simulation_data*,
- static_storage*, list **, void* )) Append_Custom_Frame;
-
- strcpy( out_control->traj_title, "default_title" );
- out_control->atom_format = 0;
- out_control->bond_info = 0;
- out_control->angle_info = 0;
-
- control->molec_anal = 0;
- control->freq_molec_anal = 0;
- control->bg_cut = 0.3;
- control->num_ignored = 0;
- memset( control->ignore, 0, sizeof(int)*MAX_ATOM_TYPES );
-
- control->dipole_anal = 0;
- control->freq_dipole_anal = 0;
-
- control->diffusion_coef = 0;
- control->freq_diffusion_coef = 0;
- control->restrict_type = 0;
-
- /* memory allocations */
- s = (char*) malloc(sizeof(char)*MAX_LINE);
- tmp = (char**) malloc(sizeof(char*)*MAX_TOKENS);
- for (i=0; i < MAX_TOKENS; i++)
- tmp[i] = (char*) malloc(sizeof(char)*MAX_LINE);
-
- /* read control parameters file */
+ char *s, **tmp;
+ int c, i;
+ real val;
+ int ival;
+
+ /* assign default values */
+ strcpy( control->sim_name, "default.sim" );
+
+ control->restart = 0;
+ out_control->restart_format = 1;
+ out_control->restart_freq = 0;
+ strcpy( control->restart_from, "default.res" );
+ out_control->restart_freq = 0;
+ control->random_vel = 0;
+
+ control->reposition_atoms = 0;
+
+ control->ensemble = 0;
+ control->nsteps = 0;
+ control->dt = 0.25;
+
+ control->geo_format = 1;
+ control->restrict_bonds = 0;
+
+ control->periodic_boundaries = 1;
+ control->periodic_images[0] = 0;
+ control->periodic_images[1] = 0;
+ control->periodic_images[2] = 0;
+
+ control->reneighbor = 1;
+ control->vlist_cut = 0;
+ control->nbr_cut = 4.;
+ control->r_cut = 10;
+ control->max_far_nbrs = 1000;
+ control->bo_cut = 0.01;
+ control->thb_cut = 0.001;
+ control->hb_cut = 7.50;
+
+ control->q_err = 0.000001;
+ control->tabulate = 0;
+ control->refactor = 100;
+ control->droptol = 0.01;
+
+ control->T_init = 0.;
+ control->T_final = 300.;
+ control->Tau_T = 1.0;
+ control->T_mode = 0.;
+ control->T_rate = 1.;
+ control->T_freq = 1.;
+
+ control->P[0] = 0.000101325;
+ control->P[1] = 0.000101325;
+ control->P[2] = 0.000101325;
+ control->Tau_P[0] = 500.0;
+ control->Tau_P[1] = 500.0;
+ control->Tau_P[2] = 500.0;
+ control->Tau_PT = 500.0;
+ control->compressibility = 1.0;
+ control->press_mode = 0;
+
+ control->remove_CoM_vel = 25;
+
+ out_control->debug_level = 0;
+ out_control->energy_update_freq = 10;
+
+ out_control->write_steps = 100;
+ out_control->traj_compress = 0;
+ out_control->write = fprintf;
+ out_control->traj_format = 0;
+ out_control->write_header =
+ (int (*)( reax_system*, control_params*,
+ static_storage*, void* )) Write_Custom_Header;
+ out_control->append_traj_frame =
+ (int (*)( reax_system*, control_params*, simulation_data*,
+ static_storage*, list **, void* )) Append_Custom_Frame;
+
+ strcpy( out_control->traj_title, "default_title" );
+ out_control->atom_format = 0;
+ out_control->bond_info = 0;
+ out_control->angle_info = 0;
+
+ control->molec_anal = 0;
+ control->freq_molec_anal = 0;
+ control->bg_cut = 0.3;
+ control->num_ignored = 0;
+ memset( control->ignore, 0, sizeof(int)*MAX_ATOM_TYPES );
+
+ control->dipole_anal = 0;
+ control->freq_dipole_anal = 0;
+
+ control->diffusion_coef = 0;
+ control->freq_diffusion_coef = 0;
+ control->restrict_type = 0;
+
+ /* memory allocations */
+ s = (char*) malloc(sizeof(char) * MAX_LINE);
+ tmp = (char**) malloc(sizeof(char*)*MAX_TOKENS);
+ for (i = 0; i < MAX_TOKENS; i++)
+ tmp[i] = (char*) malloc(sizeof(char) * MAX_LINE);
+
+ /* read control parameters file */
// while (!feof(fp)) {
- while(fgets(s,MAX_LINE,fp))
- {
- c=Tokenize(s,&tmp);
-
- if( strcmp(tmp[0], "simulation_name") == 0 ) {
- strcpy( control->sim_name, tmp[1] );
- }
- //else if( strcmp(tmp[0], "restart") == 0 ) {
- // ival = atoi(tmp[1]);
- // control->restart = ival;
- //}
- else if( strcmp(tmp[0], "restart_format") == 0 ) {
- ival = atoi(tmp[1]);
- out_control->restart_format = ival;
- }
- else if( strcmp(tmp[0], "restart_freq") == 0 ) {
- ival = atoi(tmp[1]);
- out_control->restart_freq = ival;
- }
- else if( strcmp(tmp[0], "random_vel") == 0 ) {
- ival = atoi(tmp[1]);
- control->random_vel = ival;
- }
- else if( strcmp(tmp[0], "reposition_atoms") == 0 ) {
- ival = atoi(tmp[1]);
- control->reposition_atoms = ival;
- }
- else if( strcmp(tmp[0], "ensemble_type") == 0 ) {
- ival = atoi(tmp[1]);
- control->ensemble = ival;
- }
- else if( strcmp(tmp[0], "nsteps") == 0 ) {
- ival = atoi(tmp[1]);
- control->nsteps = ival;
- }
- else if( strcmp(tmp[0], "dt") == 0 ) {
- val = atof(tmp[1]);
- control->dt = val * 1.e-3; // convert dt from fs to ps!
- }
- else if( strcmp(tmp[0], "periodic_boundaries") == 0 ) {
- ival = atoi( tmp[1] );
- control->periodic_boundaries = ival;
- }
- else if( strcmp(tmp[0], "periodic_images") == 0 ) {
- ival = atoi(tmp[1]);
- control->periodic_images[0] = ival;
- ival = atoi(tmp[2]);
- control->periodic_images[1] = ival;
- ival = atoi(tmp[3]);
- control->periodic_images[2] = ival;
- }
- else if( strcmp(tmp[0], "geo_format") == 0 ) {
- ival = atoi( tmp[1] );
- control->geo_format = ival;
- }
- else if( strcmp(tmp[0], "restrict_bonds") == 0 ) {
- ival = atoi( tmp[1] );
- control->restrict_bonds = ival;
- }
- else if( strcmp(tmp[0], "tabulate_long_range") == 0 ) {
- ival = atoi( tmp[1] );
- control->tabulate = ival;
- }
- else if( strcmp(tmp[0], "reneighbor") == 0 ) {
- ival = atoi( tmp[1] );
- control->reneighbor = ival;
- }
- else if( strcmp(tmp[0], "vlist_buffer") == 0 ) {
- val = atof(tmp[1]);
- control->vlist_cut= val;
- }
- else if( strcmp(tmp[0], "nbrhood_cutoff") == 0 ) {
- val = atof(tmp[1]);
- control->nbr_cut = val;
- }
- else if( strcmp(tmp[0], "thb_cutoff") == 0 ) {
- val = atof(tmp[1]);
- control->thb_cut = val;
- }
- else if( strcmp(tmp[0], "hbond_cutoff") == 0 ) {
- val = atof( tmp[1] );
- control->hb_cut = val;
- }
- else if( strcmp(tmp[0], "q_err") == 0 ) {
- val = atof( tmp[1] );
- control->q_err = val;
- }
- else if( strcmp(tmp[0], "ilu_refactor") == 0 ) {
- ival = atoi( tmp[1] );
- control->refactor = ival;
- }
- else if( strcmp(tmp[0], "ilu_droptol") == 0 ) {
- val = atof( tmp[1] );
- control->droptol = val;
- }
- else if( strcmp(tmp[0], "temp_init") == 0 ) {
- val = atof(tmp[1]);
- control->T_init = val;
-
- if( control->T_init < 0.001 )
- control->T_init = 0.001;
- }
- else if( strcmp(tmp[0], "temp_final") == 0 ) {
- val = atof(tmp[1]);
- control->T_final = val;
-
- if( control->T_final < 0.1 )
- control->T_final = 0.1;
- }
- else if( strcmp(tmp[0], "t_mass") == 0 ) {
- val = atof(tmp[1]);
- control->Tau_T = val * 1.e-3; // convert t_mass from fs to ps
- }
- else if( strcmp(tmp[0], "t_mode") == 0 ) {
- ival = atoi(tmp[1]);
- control->T_mode = ival;
- }
- else if( strcmp(tmp[0], "t_rate") == 0 ) {
- val = atof(tmp[1]);
- control->T_rate = val;
- }
- else if( strcmp(tmp[0], "t_freq") == 0 ) {
- val = atof(tmp[1]);
- control->T_freq = val;
- }
- else if( strcmp(tmp[0], "pressure") == 0 ) {
- if( control->ensemble == iNPT ) {
- val = atof(tmp[1]);
- control->P[0] = control->P[1] = control->P[2] = val;
- }
- else if( control->ensemble == sNPT ) {
- val = atof(tmp[1]);
- control->P[0] = val;
-
- val = atof(tmp[2]);
- control->P[1] = val;
-
- val = atof(tmp[3]);
- control->P[2] = val;
- }
- }
- else if( strcmp(tmp[0], "p_mass") == 0 ) {
- if( control->ensemble == iNPT ) {
- val = atof(tmp[1]);
- control->Tau_P[0] = val * 1.e-3; // convert p_mass from fs to ps
- }
- else if( control->ensemble == sNPT ) {
- val = atof(tmp[1]);
- control->Tau_P[0] = val * 1.e-3; // convert p_mass from fs to ps
-
- val = atof(tmp[2]);
- control->Tau_P[1] = val * 1.e-3; // convert p_mass from fs to ps
-
- val = atof(tmp[3]);
- control->Tau_P[2] = val * 1.e-3; // convert p_mass from fs to ps
- }
- }
- else if( strcmp(tmp[0], "pt_mass") == 0 ) {
- val = atof(tmp[1]);
- control->Tau_PT = val * 1.e-3; // convert pt_mass from fs to ps
- }
- else if( strcmp(tmp[0], "compress") == 0 ) {
- val = atof(tmp[1]);
- control->compressibility = val;
- }
- else if( strcmp(tmp[0], "press_mode") == 0 ) {
- val = atoi(tmp[1]);
- control->press_mode = val;
- }
- else if( strcmp(tmp[0], "remove_CoM_vel") == 0 ) {
- val = atoi(tmp[1]);
- control->remove_CoM_vel = val;
- }
- else if( strcmp(tmp[0], "debug_level") == 0 ) {
- ival = atoi(tmp[1]);
- out_control->debug_level = ival;
- }
- else if( strcmp(tmp[0], "energy_update_freq") == 0 ) {
- ival = atoi(tmp[1]);
- out_control->energy_update_freq = ival;
- }
- else if( strcmp(tmp[0], "write_freq") == 0 ) {
- ival = atoi(tmp[1]);
- out_control->write_steps = ival;
- }
- else if( strcmp(tmp[0], "traj_compress") == 0 ) {
- ival = atoi(tmp[1]);
- out_control->traj_compress = ival;
-
- if( out_control->traj_compress )
- out_control->write = (int (*)(FILE *, const char *, ...)) gzprintf;
- else out_control->write = fprintf;
- }
- else if( strcmp(tmp[0], "traj_format") == 0 ) {
- ival = atoi(tmp[1]);
- out_control->traj_format = ival;
-
- if( out_control->traj_format == 0 ) {
- out_control->write_header =
- (int (*)( reax_system*, control_params*,
- static_storage*, void* )) Write_Custom_Header;
- out_control->append_traj_frame =
- (int (*)(reax_system*, control_params*, simulation_data*,
- static_storage*, list **, void*)) Append_Custom_Frame;
- }
- else if( out_control->traj_format == 1 ) {
- out_control->write_header =
- (int (*)( reax_system*, control_params*,
- static_storage*, void* )) Write_xyz_Header;
- out_control->append_traj_frame =
- (int (*)( reax_system*, control_params*, simulation_data*,
- static_storage*, list **, void* )) Append_xyz_Frame;
- }
- }
- else if( strcmp(tmp[0], "traj_title") == 0 ) {
- strcpy( out_control->traj_title, tmp[1] );
- }
- else if( strcmp(tmp[0], "atom_info") == 0 ) {
- ival = atoi(tmp[1]);
- out_control->atom_format += ival * 4;
- }
- else if( strcmp(tmp[0], "atom_velocities") == 0 ) {
- ival = atoi(tmp[1]);
- out_control->atom_format += ival * 2;
- }
- else if( strcmp(tmp[0], "atom_forces") == 0 ) {
- ival = atoi(tmp[1]);
- out_control->atom_format += ival * 1;
- }
- else if( strcmp(tmp[0], "bond_info") == 0 ) {
- ival = atoi(tmp[1]);
- out_control->bond_info = ival;
- }
- else if( strcmp(tmp[0], "angle_info") == 0 ) {
- ival = atoi(tmp[1]);
- out_control->angle_info = ival;
- }
- else if( strcmp(tmp[0], "test_forces") == 0 ) {
- ival = atoi(tmp[1]);
- }
- else if( strcmp(tmp[0], "molec_anal") == 0 ) {
- ival = atoi(tmp[1]);
- control->molec_anal = ival;
- }
- else if( strcmp(tmp[0], "freq_molec_anal") == 0 ) {
- ival = atoi(tmp[1]);
- control->freq_molec_anal = ival;
- }
- else if( strcmp(tmp[0], "bond_graph_cutoff") == 0 ) {
- val = atof(tmp[1]);
- control->bg_cut = val;
- }
- else if( strcmp(tmp[0], "ignore") == 0 ) {
- control->num_ignored = atoi(tmp[1]);
- for( i = 0; i < control->num_ignored; ++i )
- control->ignore[atoi(tmp[i+2])] = 1;
- }
- else if( strcmp(tmp[0], "dipole_anal") == 0 ) {
- ival = atoi(tmp[1]);
- control->dipole_anal = ival;
- }
- else if( strcmp(tmp[0], "freq_dipole_anal") == 0 ) {
- ival = atoi(tmp[1]);
- control->freq_dipole_anal = ival;
- }
- else if( strcmp(tmp[0], "diffusion_coef") == 0 ) {
- ival = atoi(tmp[1]);
- control->diffusion_coef = ival;
- }
- else if( strcmp(tmp[0], "freq_diffusion_coef") == 0 ) {
- ival = atoi(tmp[1]);
- control->freq_diffusion_coef = ival;
- }
- else if( strcmp(tmp[0], "restrict_type") == 0 ) {
- ival = atoi(tmp[1]);
- control->restrict_type = ival;
- }
- else {
- fprintf( stderr, "WARNING: unknown parameter %s\n", tmp[0] );
- exit( 15 );
+ while (fgets(s, MAX_LINE, fp))
+ {
+ c = Tokenize(s, &tmp);
+
+ if ( strcmp(tmp[0], "simulation_name") == 0 )
+ {
+ strcpy( control->sim_name, tmp[1] );
+ }
+ //else if( strcmp(tmp[0], "restart") == 0 ) {
+ // ival = atoi(tmp[1]);
+ // control->restart = ival;
+ //}
+ else if ( strcmp(tmp[0], "restart_format") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ out_control->restart_format = ival;
+ }
+ else if ( strcmp(tmp[0], "restart_freq") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ out_control->restart_freq = ival;
+ }
+ else if ( strcmp(tmp[0], "random_vel") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ control->random_vel = ival;
+ }
+ else if ( strcmp(tmp[0], "reposition_atoms") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ control->reposition_atoms = ival;
+ }
+ else if ( strcmp(tmp[0], "ensemble_type") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ control->ensemble = ival;
+ }
+ else if ( strcmp(tmp[0], "nsteps") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ control->nsteps = ival;
+ }
+ else if ( strcmp(tmp[0], "dt") == 0 )
+ {
+ val = atof(tmp[1]);
+ control->dt = val * 1.e-3; // convert dt from fs to ps!
+ }
+ else if ( strcmp(tmp[0], "periodic_boundaries") == 0 )
+ {
+ ival = atoi( tmp[1] );
+ control->periodic_boundaries = ival;
+ }
+ else if ( strcmp(tmp[0], "periodic_images") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ control->periodic_images[0] = ival;
+ ival = atoi(tmp[2]);
+ control->periodic_images[1] = ival;
+ ival = atoi(tmp[3]);
+ control->periodic_images[2] = ival;
+ }
+ else if ( strcmp(tmp[0], "geo_format") == 0 )
+ {
+ ival = atoi( tmp[1] );
+ control->geo_format = ival;
+ }
+ else if ( strcmp(tmp[0], "restrict_bonds") == 0 )
+ {
+ ival = atoi( tmp[1] );
+ control->restrict_bonds = ival;
+ }
+ else if ( strcmp(tmp[0], "tabulate_long_range") == 0 )
+ {
+ ival = atoi( tmp[1] );
+ control->tabulate = ival;
+ }
+ else if ( strcmp(tmp[0], "reneighbor") == 0 )
+ {
+ ival = atoi( tmp[1] );
+ control->reneighbor = ival;
+ }
+ else if ( strcmp(tmp[0], "vlist_buffer") == 0 )
+ {
+ val = atof(tmp[1]);
+ control->vlist_cut = val;
+ }
+ else if ( strcmp(tmp[0], "nbrhood_cutoff") == 0 )
+ {
+ val = atof(tmp[1]);
+ control->nbr_cut = val;
+ }
+ else if ( strcmp(tmp[0], "thb_cutoff") == 0 )
+ {
+ val = atof(tmp[1]);
+ control->thb_cut = val;
+ }
+ else if ( strcmp(tmp[0], "hbond_cutoff") == 0 )
+ {
+ val = atof( tmp[1] );
+ control->hb_cut = val;
+ }
+ else if ( strcmp(tmp[0], "q_err") == 0 )
+ {
+ val = atof( tmp[1] );
+ control->q_err = val;
+ }
+ else if ( strcmp(tmp[0], "ilu_refactor") == 0 )
+ {
+ ival = atoi( tmp[1] );
+ control->refactor = ival;
+ }
+ else if ( strcmp(tmp[0], "ilu_droptol") == 0 )
+ {
+ val = atof( tmp[1] );
+ control->droptol = val;
+ }
+ else if ( strcmp(tmp[0], "temp_init") == 0 )
+ {
+ val = atof(tmp[1]);
+ control->T_init = val;
+
+ if ( control->T_init < 0.001 )
+ control->T_init = 0.001;
+ }
+ else if ( strcmp(tmp[0], "temp_final") == 0 )
+ {
+ val = atof(tmp[1]);
+ control->T_final = val;
+
+ if ( control->T_final < 0.1 )
+ control->T_final = 0.1;
+ }
+ else if ( strcmp(tmp[0], "t_mass") == 0 )
+ {
+ val = atof(tmp[1]);
+ control->Tau_T = val * 1.e-3; // convert t_mass from fs to ps
+ }
+ else if ( strcmp(tmp[0], "t_mode") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ control->T_mode = ival;
+ }
+ else if ( strcmp(tmp[0], "t_rate") == 0 )
+ {
+ val = atof(tmp[1]);
+ control->T_rate = val;
+ }
+ else if ( strcmp(tmp[0], "t_freq") == 0 )
+ {
+ val = atof(tmp[1]);
+ control->T_freq = val;
+ }
+ else if ( strcmp(tmp[0], "pressure") == 0 )
+ {
+ if ( control->ensemble == iNPT )
+ {
+ val = atof(tmp[1]);
+ control->P[0] = control->P[1] = control->P[2] = val;
+ }
+ else if ( control->ensemble == sNPT )
+ {
+ val = atof(tmp[1]);
+ control->P[0] = val;
+
+ val = atof(tmp[2]);
+ control->P[1] = val;
+
+ val = atof(tmp[3]);
+ control->P[2] = val;
+ }
+ }
+ else if ( strcmp(tmp[0], "p_mass") == 0 )
+ {
+ if ( control->ensemble == iNPT )
+ {
+ val = atof(tmp[1]);
+ control->Tau_P[0] = val * 1.e-3; // convert p_mass from fs to ps
+ }
+ else if ( control->ensemble == sNPT )
+ {
+ val = atof(tmp[1]);
+ control->Tau_P[0] = val * 1.e-3; // convert p_mass from fs to ps
+
+ val = atof(tmp[2]);
+ control->Tau_P[1] = val * 1.e-3; // convert p_mass from fs to ps
+
+ val = atof(tmp[3]);
+ control->Tau_P[2] = val * 1.e-3; // convert p_mass from fs to ps
+ }
+ }
+ else if ( strcmp(tmp[0], "pt_mass") == 0 )
+ {
+ val = atof(tmp[1]);
+ control->Tau_PT = val * 1.e-3; // convert pt_mass from fs to ps
+ }
+ else if ( strcmp(tmp[0], "compress") == 0 )
+ {
+ val = atof(tmp[1]);
+ control->compressibility = val;
+ }
+ else if ( strcmp(tmp[0], "press_mode") == 0 )
+ {
+ val = atoi(tmp[1]);
+ control->press_mode = val;
+ }
+ else if ( strcmp(tmp[0], "remove_CoM_vel") == 0 )
+ {
+ val = atoi(tmp[1]);
+ control->remove_CoM_vel = val;
+ }
+ else if ( strcmp(tmp[0], "debug_level") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ out_control->debug_level = ival;
+ }
+ else if ( strcmp(tmp[0], "energy_update_freq") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ out_control->energy_update_freq = ival;
+ }
+ else if ( strcmp(tmp[0], "write_freq") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ out_control->write_steps = ival;
+ }
+ else if ( strcmp(tmp[0], "traj_compress") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ out_control->traj_compress = ival;
+
+ if ( out_control->traj_compress )
+ out_control->write = (int (*)(FILE *, const char *, ...)) gzprintf;
+ else out_control->write = fprintf;
+ }
+ else if ( strcmp(tmp[0], "traj_format") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ out_control->traj_format = ival;
+
+ if ( out_control->traj_format == 0 )
+ {
+ out_control->write_header =
+ (int (*)( reax_system*, control_params*,
+ static_storage*, void* )) Write_Custom_Header;
+ out_control->append_traj_frame =
+ (int (*)(reax_system*, control_params*, simulation_data*,
+ static_storage*, list **, void*)) Append_Custom_Frame;
+ }
+ else if ( out_control->traj_format == 1 )
+ {
+ out_control->write_header =
+ (int (*)( reax_system*, control_params*,
+ static_storage*, void* )) Write_xyz_Header;
+ out_control->append_traj_frame =
+ (int (*)( reax_system*, control_params*, simulation_data*,
+ static_storage*, list **, void* )) Append_xyz_Frame;
+ }
+ }
+ else if ( strcmp(tmp[0], "traj_title") == 0 )
+ {
+ strcpy( out_control->traj_title, tmp[1] );
+ }
+ else if ( strcmp(tmp[0], "atom_info") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ out_control->atom_format += ival * 4;
+ }
+ else if ( strcmp(tmp[0], "atom_velocities") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ out_control->atom_format += ival * 2;
+ }
+ else if ( strcmp(tmp[0], "atom_forces") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ out_control->atom_format += ival * 1;
+ }
+ else if ( strcmp(tmp[0], "bond_info") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ out_control->bond_info = ival;
+ }
+ else if ( strcmp(tmp[0], "angle_info") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ out_control->angle_info = ival;
+ }
+ else if ( strcmp(tmp[0], "test_forces") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ }
+ else if ( strcmp(tmp[0], "molec_anal") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ control->molec_anal = ival;
+ }
+ else if ( strcmp(tmp[0], "freq_molec_anal") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ control->freq_molec_anal = ival;
+ }
+ else if ( strcmp(tmp[0], "bond_graph_cutoff") == 0 )
+ {
+ val = atof(tmp[1]);
+ control->bg_cut = val;
+ }
+ else if ( strcmp(tmp[0], "ignore") == 0 )
+ {
+ control->num_ignored = atoi(tmp[1]);
+ for ( i = 0; i < control->num_ignored; ++i )
+ control->ignore[atoi(tmp[i + 2])] = 1;
+ }
+ else if ( strcmp(tmp[0], "dipole_anal") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ control->dipole_anal = ival;
+ }
+ else if ( strcmp(tmp[0], "freq_dipole_anal") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ control->freq_dipole_anal = ival;
+ }
+ else if ( strcmp(tmp[0], "diffusion_coef") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ control->diffusion_coef = ival;
+ }
+ else if ( strcmp(tmp[0], "freq_diffusion_coef") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ control->freq_diffusion_coef = ival;
+ }
+ else if ( strcmp(tmp[0], "restrict_type") == 0 )
+ {
+ ival = atoi(tmp[1]);
+ control->restrict_type = ival;
+ }
+ else
+ {
+ fprintf( stderr, "WARNING: unknown parameter %s\n", tmp[0] );
+ exit( 15 );
+ }
+ }
+
+ if (ferror(fp))
+ {
+ fprintf(stderr, "Error reading control file. Terminating.\n");
+ exit( INVALID_INPUT );
}
- }
-
- if(ferror(fp))
- {
- fprintf(stderr, "Error reading control file. Terminating.\n");
- exit( INVALID_INPUT );
- }
-
- /* determine target T */
- if( control->T_mode == 0 )
- control->T = control->T_final;
- else control->T = control->T_init;
+
+ /* determine target T */
+ if ( control->T_mode == 0 )
+ control->T = control->T_final;
+ else control->T = control->T_init;
- /* near neighbor and far neighbor cutoffs */
- control->bo_cut = 0.01 * system->reaxprm.gp.l[29];
- control->r_low = system->reaxprm.gp.l[11];
- control->r_cut = system->reaxprm.gp.l[12];
- control->vlist_cut += control->r_cut;
+ /* near neighbor and far neighbor cutoffs */
+ control->bo_cut = 0.01 * system->reaxprm.gp.l[29];
+ control->r_low = system->reaxprm.gp.l[11];
+ control->r_cut = system->reaxprm.gp.l[12];
+ control->vlist_cut += control->r_cut;
- system->g.cell_size = control->vlist_cut / 2.;
- for( i = 0; i < 3; ++i )
- system->g.spread[i] = 2;
+ system->g.cell_size = control->vlist_cut / 2.;
+ for ( i = 0; i < 3; ++i )
+ system->g.spread[i] = 2;
- /* Initialize Taper function */
- Init_Taper( control );
+ /* Initialize Taper function */
+ Init_Taper( control );
- /* free memory allocations at the top */
- for( i = 0; i < MAX_TOKENS; i++ )
- free( tmp[i] );
- free( tmp );
- free( s );
+ /* free memory allocations at the top */
+ for ( i = 0; i < MAX_TOKENS; i++ )
+ free( tmp[i] );
+ free( tmp );
+ free( s );
#if defined(DEBUG_FOCUS)
- fprintf( stderr,
- "en=%d steps=%d dt=%.5f opt=%d T=%.5f P=%.5f %.5f %.5f\n",
- control->ensemble, control->nsteps, control->dt, control->tabulate,
- control->T, control->P[0], control->P[1], control->P[2] );
+ fprintf( stderr,
+ "en=%d steps=%d dt=%.5f opt=%d T=%.5f P=%.5f %.5f %.5f\n",
+ control->ensemble, control->nsteps, control->dt, control->tabulate,
+ control->T, control->P[0], control->P[1], control->P[2] );
- fprintf(stderr, "control file read\n" );
+ fprintf(stderr, "control file read\n" );
#endif
- return 0;
+ return 0;
}
diff --git a/puremd_rc_1003/sPuReMD/param.h b/puremd_rc_1003/sPuReMD/param.h
index bd8661fe293363d4bcdb9eeed6f8b9d60d2350fd..838bb1a0d004672978a35f94547d511104aba9ea 100644
--- a/puremd_rc_1003/sPuReMD/param.h
+++ b/puremd_rc_1003/sPuReMD/param.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -34,7 +34,7 @@ int Tokenize( char*, char*** );
char Read_Force_Field( FILE*, reax_interaction* );
-char Read_Control_File( FILE*, reax_system*, control_params*,
- output_controls* );
+char Read_Control_File( FILE*, reax_system*, control_params*,
+ output_controls* );
#endif
diff --git a/puremd_rc_1003/sPuReMD/pdb_tools.c b/puremd_rc_1003/sPuReMD/pdb_tools.c
index 0cd0331bed28c7d4f31c9b7af2c3f026befcf3fb..e7b1b57d07b91d5bf1c5f96eaf2b314ee55c6f02 100644
--- a/puremd_rc_1003/sPuReMD/pdb_tools.c
+++ b/puremd_rc_1003/sPuReMD/pdb_tools.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -29,546 +29,614 @@
int is_Valid_Serial( static_storage *workspace, int serial )
{
- if( workspace->map_serials[ serial ] < 0 )
+ if ( workspace->map_serials[ serial ] < 0 )
{
- fprintf( stderr, "CONECT line includes invalid pdb serial number %d.\n",
- serial );
- fprintf( stderr, "Please correct the input file.Terminating...\n" );
- exit( INVALID_INPUT );
+ fprintf( stderr, "CONECT line includes invalid pdb serial number %d.\n",
+ serial );
+ fprintf( stderr, "Please correct the input file.Terminating...\n" );
+ exit( INVALID_INPUT );
}
-
- return 1;
+
+ return 1;
}
int Check_Input_Range( int val, int lo, int hi, char *message )
{
- if( val < lo || val > hi )
+ if ( val < lo || val > hi )
{
- fprintf( stderr, "%s\nInput %d - Out of range %d-%d. Terminating...\n",
- message, val, lo, hi );
- exit( INVALID_INPUT );
+ fprintf( stderr, "%s\nInput %d - Out of range %d-%d. Terminating...\n",
+ message, val, lo, hi );
+ exit( INVALID_INPUT );
}
- return 1;
+ return 1;
}
void Trim_Spaces( char *element )
{
- int i, j;
+ int i, j;
- for( i = 0; element[i] == ' '; ++i ); // skip initial space chars
-
- for( j = i; j < strlen(element) && element[j] != ' '; ++j )
- element[j-i] = toupper( element[j] ); // make uppercase, move to beginning
- element[j-i] = 0; // finalize the string
+ for ( i = 0; element[i] == ' '; ++i ); // skip initial space chars
+
+ for ( j = i; j < strlen(element) && element[j] != ' '; ++j )
+ element[j - i] = toupper( element[j] ); // make uppercase, move to beginning
+ element[j - i] = 0; // finalize the string
}
-char Read_PDB( char* pdb_file, reax_system* system, control_params *control,
- simulation_data *data, static_storage *workspace )
+char Read_PDB( char* pdb_file, reax_system* system, control_params *control,
+ simulation_data *data, static_storage *workspace )
{
- FILE *pdb;
- char **tmp;
- char *s, *s1;
- char descriptor[9], serial[9];
- char atom_name[9], res_name[9], res_seq[9];
- char s_x[9], s_y[9], s_z[9];
- char occupancy[9], temp_factor[9];
- char seg_id[9], element[9], charge[9];
- char alt_loc, chain_id, icode;
- char s_a[10], s_b[10], s_c[10], s_alpha[9], s_beta[9], s_gamma[9];
- char s_group[12], s_zValue[9];
- char *endptr = NULL;
- int i, c, c1, pdb_serial, ratom = 0;
- /* open pdb file */
- if ( (pdb = fopen(pdb_file, "r")) == NULL ) {
- fprintf( stderr, "Error opening the pdb file!\n" );
- exit( FILE_NOT_FOUND_ERR );
- }
-
-
- /* allocate memory for tokenizing pdb lines */
- s = (char*) malloc( sizeof(char) * MAX_LINE );
- s1 = (char*) malloc( sizeof(char) * MAX_LINE );
- tmp = (char**) malloc( sizeof(char*) * MAX_TOKENS );
- for( i = 0; i < MAX_TOKENS; i++ )
- tmp[i] = (char*) malloc( sizeof(char) * MAX_TOKEN_LEN );
-
-
- /* count number of atoms in the pdb file */
- system->N = 0;
- s[0] = 0;
- while (fgets( s, MAX_LINE, pdb ))
- {
-
- tmp[0][0] = 0;
- c = Tokenize( s, &tmp );
-
- if( strncmp( tmp[0], "ATOM", 4 ) == 0 ||
- strncmp( tmp[0], "HETATM", 6 ) == 0 )
- (system->N)++;
+ FILE *pdb;
+ char **tmp;
+ char *s, *s1;
+ char descriptor[9], serial[9];
+ char atom_name[9], res_name[9], res_seq[9];
+ char s_x[9], s_y[9], s_z[9];
+ char occupancy[9], temp_factor[9];
+ char seg_id[9], element[9], charge[9];
+ char alt_loc, chain_id, icode;
+ char s_a[10], s_b[10], s_c[10], s_alpha[9], s_beta[9], s_gamma[9];
+ char s_group[12], s_zValue[9];
+ char *endptr = NULL;
+ int i, c, c1, pdb_serial, ratom = 0;
+ /* open pdb file */
+ if ( (pdb = fopen(pdb_file, "r")) == NULL )
+ {
+ fprintf( stderr, "Error opening the pdb file!\n" );
+ exit( FILE_NOT_FOUND_ERR );
+ }
+
+
+ /* allocate memory for tokenizing pdb lines */
+ s = (char*) malloc( sizeof(char) * MAX_LINE );
+ s1 = (char*) malloc( sizeof(char) * MAX_LINE );
+ tmp = (char**) malloc( sizeof(char*) * MAX_TOKENS );
+ for ( i = 0; i < MAX_TOKENS; i++ )
+ tmp[i] = (char*) malloc( sizeof(char) * MAX_TOKEN_LEN );
+
+
+ /* count number of atoms in the pdb file */
+ system->N = 0;
s[0] = 0;
- }
- if(ferror(pdb))
- {
- fprintf(stderr, "Error reading PDB file. Terminating.\n");
- exit( INVALID_INPUT );
- }
-
- fclose(pdb);
+ while (fgets( s, MAX_LINE, pdb ))
+ {
+
+ tmp[0][0] = 0;
+ c = Tokenize( s, &tmp );
+
+ if ( strncmp( tmp[0], "ATOM", 4 ) == 0 ||
+ strncmp( tmp[0], "HETATM", 6 ) == 0 )
+ (system->N)++;
+ s[0] = 0;
+ }
+ if (ferror(pdb))
+ {
+ fprintf(stderr, "Error reading PDB file. Terminating.\n");
+ exit( INVALID_INPUT );
+ }
+
+ fclose(pdb);
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "system->N: %d\n", system->N );
+ fprintf( stderr, "system->N: %d\n", system->N );
#endif
- /* memory allocations for atoms, atom maps, bond restrictions */
- system->atoms = (reax_atom*) calloc( system->N, sizeof(reax_atom) );
-
- workspace->map_serials = (int*) calloc( MAX_ATOM_ID, sizeof(int) );
- for( i = 0; i < MAX_ATOM_ID; ++i )
- workspace->map_serials[i] = -1;
-
- workspace->orig_id = (int*) calloc( system->N, sizeof(int) );
- workspace->restricted = (int*) calloc( system->N, sizeof(int) );
- workspace->restricted_list = (int**) calloc( system->N, sizeof(int*) );
- for( i = 0; i < system->N; ++i )
- workspace->restricted_list[i] = (int*) calloc( MAX_RESTRICT, sizeof(int) );
-
-
- /* start reading and processing pdb file */
- if ( (pdb = fopen(pdb_file,"r")) == NULL )
- {
- fprintf( stderr, "Error opening the pdb file!\n" );
- exit( FILE_NOT_FOUND_ERR );
- }
- c = 0;
- c1 = 0;
-
- while (!feof(pdb)) {
- /* clear previous input line */
- s[0] = 0;
- for( i = 0; i < c1; ++i )
- tmp[i][0] = 0;
-
- /* read new line and tokenize it */
- fgets( s, MAX_LINE, pdb );
- strncpy( s1, s, MAX_LINE-1 );
- c1 = Tokenize( s, &tmp );
-
- /* process new line */
- if( strncmp(tmp[0],"ATOM",4) == 0 || strncmp(tmp[0],"HETATM", 6) == 0 ) {
- if( strncmp(tmp[0],"ATOM",4) == 0 ) {
- strncpy( &descriptor[0], s1, 6 ); descriptor[6] = 0;
- strncpy( &serial[0], s1+6, 5 ); serial[5] = 0;
- strncpy( &atom_name[0], s1+12, 4 ); atom_name[4] = 0;
- alt_loc = s1[16];
- strncpy( &res_name[0], s1+17, 3 ); res_name[3] = 0;
- chain_id = s1[21];
- strncpy( &res_seq[0], s1+22, 4 ); res_seq[4] = 0;
- icode = s1[26];
- strncpy( &s_x[0], s1+30, 8 ); s_x[8] = 0;
- strncpy( &s_y[0], s1+38, 8 ); s_y[8] = 0;
- strncpy( &s_z[0], s1+46, 8 ); s_z[8] = 0;
- strncpy( &occupancy[0], s1+54, 6 ); occupancy[6] = 0;
- strncpy( &temp_factor[0], s1+60, 6 ); temp_factor[6] = 0;
- strncpy( &seg_id[0], s1+72, 4 ); seg_id[4] = 0;
- strncpy( &element[0], s1+76, 2 ); element[2] = 0;
- strncpy( &charge[0], s1+78, 2 ); charge[2] = 0;
- }
- else if (strncmp(tmp[0],"HETATM", 6) == 0) {
- strncpy( &descriptor[0], s1, 6 ); descriptor[6] = 0;
- strncpy( &serial[0], s1+6, 5 ); serial[5] = 0;
- strncpy( &atom_name[0], s1+12, 4 ); atom_name[4] = 0;
- alt_loc = s1[16];
- strncpy( &res_name[0], s1+17, 3 ); res_name[3] = 0;
- chain_id = s1[21];
- strncpy( &res_seq[0], s1+22, 4 ); res_seq[4] = 0;
- icode = s1[26];
- strncpy( &s_x[0], s1+30, 8 ); s_x[8] = 0;
- strncpy( &s_y[0], s1+38, 8 ); s_y[8] = 0;
- strncpy( &s_z[0], s1+46, 8 ); s_z[8] = 0;
- strncpy( &occupancy[0], s1+54, 6 ); occupancy[6] = 0;
- strncpy( &temp_factor[0], s1+60, 6 ); temp_factor[6] = 0;
- //strncpy( &seg_id[0], s1+72, 4 ); seg_id[4] = 0;
- strncpy( &element[0], s1+76, 2 ); element[2] = 0;
- strncpy( &charge[0], s1+78, 2 ); charge[2] = 0;
- }
-
-
- /* add to mapping */
- pdb_serial = strtod( &serial[0], &endptr );
- Check_Input_Range( pdb_serial, 0, MAX_ATOM_ID, "Invalid pdb_serial" );
- workspace->map_serials[ pdb_serial ] = c;
- workspace->orig_id[ c ] = pdb_serial;
- // fprintf( stderr, "map %d --> %d\n", pdb_serial, c );
-
-
- /* copy atomic positions */
- system->atoms[c].x[0] = strtod( &s_x[0], &endptr );
- system->atoms[c].x[1] = strtod( &s_y[0], &endptr );
- system->atoms[c].x[2] = strtod( &s_z[0], &endptr );
-
- /* atom name and type */
- strcpy( system->atoms[c].name, atom_name );
- Trim_Spaces( element );
- system->atoms[c].type = Get_Atom_Type( &(system->reaxprm), element );
-
- /* fprintf( stderr,
- "%d%8.3f%8.3f%8.3fq:%8.3f occ:%s temp:%s seg_id:%s element:%s\n",
- system->atoms[c].type,
- system->atoms[c].x[0], system->atoms[c].x[1], system->atoms[c].x[2],
- system->atoms[c].q, occupancy, temp_factor, seg_id, element ); */
- c++;
+ /* memory allocations for atoms, atom maps, bond restrictions */
+ system->atoms = (reax_atom*) calloc( system->N, sizeof(reax_atom) );
+
+ workspace->map_serials = (int*) calloc( MAX_ATOM_ID, sizeof(int) );
+ for ( i = 0; i < MAX_ATOM_ID; ++i )
+ workspace->map_serials[i] = -1;
+
+ workspace->orig_id = (int*) calloc( system->N, sizeof(int) );
+ workspace->restricted = (int*) calloc( system->N, sizeof(int) );
+ workspace->restricted_list = (int**) calloc( system->N, sizeof(int*) );
+ for ( i = 0; i < system->N; ++i )
+ workspace->restricted_list[i] = (int*) calloc( MAX_RESTRICT, sizeof(int) );
+
+
+ /* start reading and processing pdb file */
+ if ( (pdb = fopen(pdb_file, "r")) == NULL )
+ {
+ fprintf( stderr, "Error opening the pdb file!\n" );
+ exit( FILE_NOT_FOUND_ERR );
}
- else if(!strncmp( tmp[0], "CRYST1", 6 )) {
- sscanf( s1, PDB_CRYST1_FORMAT,
- &descriptor[0],
- &s_a[0],
- &s_b[0],
- &s_c[0],
- &s_alpha[0],
- &s_beta[0],
- &s_gamma[0],
- &s_group[0],
- &s_zValue[0] );
-
- /* Compute full volume tensor from the angles */
- Init_Box_From_CRYST( atof(s_a), atof(s_b), atof(s_c),
- atof(s_alpha), atof(s_beta), atof(s_gamma),
- &(system->box) );
+ c = 0;
+ c1 = 0;
+
+ while (!feof(pdb))
+ {
+ /* clear previous input line */
+ s[0] = 0;
+ for ( i = 0; i < c1; ++i )
+ tmp[i][0] = 0;
+
+ /* read new line and tokenize it */
+ fgets( s, MAX_LINE, pdb );
+ strncpy( s1, s, MAX_LINE - 1 );
+ c1 = Tokenize( s, &tmp );
+
+ /* process new line */
+ if ( strncmp(tmp[0], "ATOM", 4) == 0 || strncmp(tmp[0], "HETATM", 6) == 0 )
+ {
+ if ( strncmp(tmp[0], "ATOM", 4) == 0 )
+ {
+ strncpy( &descriptor[0], s1, 6 );
+ descriptor[6] = 0;
+ strncpy( &serial[0], s1 + 6, 5 );
+ serial[5] = 0;
+ strncpy( &atom_name[0], s1 + 12, 4 );
+ atom_name[4] = 0;
+ alt_loc = s1[16];
+ strncpy( &res_name[0], s1 + 17, 3 );
+ res_name[3] = 0;
+ chain_id = s1[21];
+ strncpy( &res_seq[0], s1 + 22, 4 );
+ res_seq[4] = 0;
+ icode = s1[26];
+ strncpy( &s_x[0], s1 + 30, 8 );
+ s_x[8] = 0;
+ strncpy( &s_y[0], s1 + 38, 8 );
+ s_y[8] = 0;
+ strncpy( &s_z[0], s1 + 46, 8 );
+ s_z[8] = 0;
+ strncpy( &occupancy[0], s1 + 54, 6 );
+ occupancy[6] = 0;
+ strncpy( &temp_factor[0], s1 + 60, 6 );
+ temp_factor[6] = 0;
+ strncpy( &seg_id[0], s1 + 72, 4 );
+ seg_id[4] = 0;
+ strncpy( &element[0], s1 + 76, 2 );
+ element[2] = 0;
+ strncpy( &charge[0], s1 + 78, 2 );
+ charge[2] = 0;
+ }
+ else if (strncmp(tmp[0], "HETATM", 6) == 0)
+ {
+ strncpy( &descriptor[0], s1, 6 );
+ descriptor[6] = 0;
+ strncpy( &serial[0], s1 + 6, 5 );
+ serial[5] = 0;
+ strncpy( &atom_name[0], s1 + 12, 4 );
+ atom_name[4] = 0;
+ alt_loc = s1[16];
+ strncpy( &res_name[0], s1 + 17, 3 );
+ res_name[3] = 0;
+ chain_id = s1[21];
+ strncpy( &res_seq[0], s1 + 22, 4 );
+ res_seq[4] = 0;
+ icode = s1[26];
+ strncpy( &s_x[0], s1 + 30, 8 );
+ s_x[8] = 0;
+ strncpy( &s_y[0], s1 + 38, 8 );
+ s_y[8] = 0;
+ strncpy( &s_z[0], s1 + 46, 8 );
+ s_z[8] = 0;
+ strncpy( &occupancy[0], s1 + 54, 6 );
+ occupancy[6] = 0;
+ strncpy( &temp_factor[0], s1 + 60, 6 );
+ temp_factor[6] = 0;
+ //strncpy( &seg_id[0], s1+72, 4 ); seg_id[4] = 0;
+ strncpy( &element[0], s1 + 76, 2 );
+ element[2] = 0;
+ strncpy( &charge[0], s1 + 78, 2 );
+ charge[2] = 0;
+ }
+
+
+ /* add to mapping */
+ pdb_serial = strtod( &serial[0], &endptr );
+ Check_Input_Range( pdb_serial, 0, MAX_ATOM_ID, "Invalid pdb_serial" );
+ workspace->map_serials[ pdb_serial ] = c;
+ workspace->orig_id[ c ] = pdb_serial;
+ // fprintf( stderr, "map %d --> %d\n", pdb_serial, c );
+
+
+ /* copy atomic positions */
+ system->atoms[c].x[0] = strtod( &s_x[0], &endptr );
+ system->atoms[c].x[1] = strtod( &s_y[0], &endptr );
+ system->atoms[c].x[2] = strtod( &s_z[0], &endptr );
+
+ /* atom name and type */
+ strcpy( system->atoms[c].name, atom_name );
+ Trim_Spaces( element );
+ system->atoms[c].type = Get_Atom_Type( &(system->reaxprm), element );
+
+ /* fprintf( stderr,
+ "%d%8.3f%8.3f%8.3fq:%8.3f occ:%s temp:%s seg_id:%s element:%s\n",
+ system->atoms[c].type,
+ system->atoms[c].x[0], system->atoms[c].x[1], system->atoms[c].x[2],
+ system->atoms[c].q, occupancy, temp_factor, seg_id, element ); */
+ c++;
+ }
+ else if (!strncmp( tmp[0], "CRYST1", 6 ))
+ {
+ sscanf( s1, PDB_CRYST1_FORMAT,
+ &descriptor[0],
+ &s_a[0],
+ &s_b[0],
+ &s_c[0],
+ &s_alpha[0],
+ &s_beta[0],
+ &s_gamma[0],
+ &s_group[0],
+ &s_zValue[0] );
+
+ /* Compute full volume tensor from the angles */
+ Init_Box_From_CRYST( atof(s_a), atof(s_b), atof(s_c),
+ atof(s_alpha), atof(s_beta), atof(s_gamma),
+ &(system->box) );
+ }
+
+ /* IMPORTANT: We do not check for the soundness of restrictions here.
+ When atom2 is on atom1's restricted list, and there is a restriction on
+ atom2, then atom1 has to be on atom2's restricted list, too. However,
+ we do not check if this is the case in the input file,
+ this is upto the user. */
+ else if (!strncmp( tmp[0], "CONECT", 6 ))
+ {
+ /* error check */
+ //fprintf(stderr, "CONECT: %d\n", c1 );
+ Check_Input_Range( c1 - 2, 0, MAX_RESTRICT,
+ "CONECT line exceeds max restrictions allowed.\n" );
+
+ /* read bond restrictions */
+ if ( is_Valid_Serial( workspace, pdb_serial = atoi(tmp[1]) ) )
+ ratom = workspace->map_serials[ pdb_serial ];
+
+ workspace->restricted[ ratom ] = c1 - 2;
+ for ( i = 2; i < c1; ++i )
+ {
+ if ( is_Valid_Serial( workspace, pdb_serial = atoi(tmp[i]) ) )
+ workspace->restricted_list[ ratom ][ i - 2 ] =
+ workspace->map_serials[ pdb_serial ];
+ }
+
+ /* fprintf( stderr, "restriction on %d:", ratom );
+ for( i = 0; i < workspace->restricted[ ratom ]; ++i )
+ fprintf( stderr, " %d", workspace->restricted_list[ratom][i] );
+ fprintf( stderr, "\n" ); */
+ }
}
- /* IMPORTANT: We do not check for the soundness of restrictions here.
- When atom2 is on atom1's restricted list, and there is a restriction on
- atom2, then atom1 has to be on atom2's restricted list, too. However,
- we do not check if this is the case in the input file,
- this is upto the user. */
- else if(!strncmp( tmp[0], "CONECT", 6 )) {
- /* error check */
- //fprintf(stderr, "CONECT: %d\n", c1 );
- Check_Input_Range( c1 - 2, 0, MAX_RESTRICT,
- "CONECT line exceeds max restrictions allowed.\n" );
-
- /* read bond restrictions */
- if( is_Valid_Serial( workspace, pdb_serial = atoi(tmp[1]) ) )
- ratom = workspace->map_serials[ pdb_serial ];
-
- workspace->restricted[ ratom ] = c1 - 2;
- for( i = 2; i < c1; ++i )
- {
- if( is_Valid_Serial( workspace, pdb_serial = atoi(tmp[i]) ) )
- workspace->restricted_list[ ratom ][ i-2 ] =
- workspace->map_serials[ pdb_serial ];
- }
-
- /* fprintf( stderr, "restriction on %d:", ratom );
- for( i = 0; i < workspace->restricted[ ratom ]; ++i )
- fprintf( stderr, " %d", workspace->restricted_list[ratom][i] );
- fprintf( stderr, "\n" ); */
- }
- }
-
- fclose(pdb);
+ fclose(pdb);
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "pdb file read\n" );
+ fprintf( stderr, "pdb file read\n" );
#endif
- return 1;
+ return 1;
}
-char Write_PDB( reax_system* system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list* bonds, output_controls *out_control )
+char Write_PDB( reax_system* system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list* bonds, output_controls *out_control )
{
- int i, j, k, count;
- int connect[4];
- char temp[MAX_STR], name[10];
- real bo;
- real alpha, beta, gamma;
-
-
- /* open output pdb file */
- sprintf( temp, "%s%d.pdb", control->sim_name, data->step );
- if ( (out_control->pdb = fopen( temp, "w" )) == NULL )
- {
- fprintf( stderr, "Error opening the pdb output file!\n" );
- exit( FILE_NOT_FOUND_ERR );
- }
-
-
- /* Writing Box information */
- /* Write full volume tensor from the angles (as soon as possible) TODO_SOON */
- gamma = acos( (system->box.box[0][0] * system->box.box[1][0] +
- system->box.box[0][1] * system->box.box[1][1] +
- system->box.box[0][2] * system->box.box[1][2]) /
- (system->box.box_norms[0]*system->box.box_norms[1]));
- beta = acos( (system->box.box[0][0] * system->box.box[2][0] +
- system->box.box[0][1] * system->box.box[2][1] +
- system->box.box[0][2] * system->box.box[2][2]) /
- (system->box.box_norms[0]*system->box.box_norms[2]));
- alpha = acos( (system->box.box[2][0] * system->box.box[1][0] +
- system->box.box[2][1] * system->box.box[1][1] +
- system->box.box[2][2] * system->box.box[1][2]) /
- (system->box.box_norms[2]*system->box.box_norms[1]));
-
- fprintf(out_control->pdb,PDB_CRYST1_FORMAT_O,
- "CRYST1",
- system->box.box_norms[0],
- system->box.box_norms[1],
- system->box.box_norms[2],
- RAD2DEG(alpha),
- RAD2DEG(beta),
- RAD2DEG(gamma),
- " ",
- 0);
- fprintf( out_control->log, "Box written\n" ); fflush( out_control->log );
-
- /* Writing atom information */
- for (i=0; i < system->N; i++) {
- strncpy( name, system->reaxprm.sbp[system->atoms[i].type].name, 2 );
- name[2] = '\0';
- fprintf( out_control->pdb,PDB_ATOM_FORMAT_O,
- "ATOM ",
- workspace->orig_id[i],
- name,
- ' ',
- "REX",
- ' ',
- 1,
- ' ',
- system->atoms[i].x[0],
- system->atoms[i].x[1],
- system->atoms[i].x[2],
- 1.0,
- 0.0,
- "0",
- name,
- " " );
- }
-
- fprintf( out_control->log, "ATOM written\n" ); fflush( out_control->log );
-
- /* Writing connect information */
- for(i=0; i < system->N; i++) {
- count = 0;
-
- for(j = Start_Index(i, bonds); j < End_Index(i, bonds); ++j) {
- bo = bonds->select.bond_list[j].bo_data.BO;
- if (bo > 0.3)
- {
- connect[count]=workspace->orig_id[bonds->select.bond_list[j].nbr];
- count++;
- }
+ int i, j, k, count;
+ int connect[4];
+ char temp[MAX_STR], name[10];
+ real bo;
+ real alpha, beta, gamma;
+
+
+ /* open output pdb file */
+ sprintf( temp, "%s%d.pdb", control->sim_name, data->step );
+ if ( (out_control->pdb = fopen( temp, "w" )) == NULL )
+ {
+ fprintf( stderr, "Error opening the pdb output file!\n" );
+ exit( FILE_NOT_FOUND_ERR );
}
- fprintf( out_control->pdb, "%6s%6d", "CONECT", workspace->orig_id[i] );
- for( k=0; k < count; k++ )
- fprintf( out_control->pdb, "%6d", connect[k] );
- fprintf( out_control->pdb, "\n" );
- }
- fprintf( out_control->pdb, "END\n" );
+ /* Writing Box information */
+ /* Write full volume tensor from the angles (as soon as possible) TODO_SOON */
+ gamma = acos( (system->box.box[0][0] * system->box.box[1][0] +
+ system->box.box[0][1] * system->box.box[1][1] +
+ system->box.box[0][2] * system->box.box[1][2]) /
+ (system->box.box_norms[0] * system->box.box_norms[1]));
+ beta = acos( (system->box.box[0][0] * system->box.box[2][0] +
+ system->box.box[0][1] * system->box.box[2][1] +
+ system->box.box[0][2] * system->box.box[2][2]) /
+ (system->box.box_norms[0] * system->box.box_norms[2]));
+ alpha = acos( (system->box.box[2][0] * system->box.box[1][0] +
+ system->box.box[2][1] * system->box.box[1][1] +
+ system->box.box[2][2] * system->box.box[1][2]) /
+ (system->box.box_norms[2] * system->box.box_norms[1]));
+
+ fprintf(out_control->pdb, PDB_CRYST1_FORMAT_O,
+ "CRYST1",
+ system->box.box_norms[0],
+ system->box.box_norms[1],
+ system->box.box_norms[2],
+ RAD2DEG(alpha),
+ RAD2DEG(beta),
+ RAD2DEG(gamma),
+ " ",
+ 0);
+ fprintf( out_control->log, "Box written\n" );
+ fflush( out_control->log );
+
+ /* Writing atom information */
+ for (i = 0; i < system->N; i++)
+ {
+ strncpy( name, system->reaxprm.sbp[system->atoms[i].type].name, 2 );
+ name[2] = '\0';
+ fprintf( out_control->pdb, PDB_ATOM_FORMAT_O,
+ "ATOM ",
+ workspace->orig_id[i],
+ name,
+ ' ',
+ "REX",
+ ' ',
+ 1,
+ ' ',
+ system->atoms[i].x[0],
+ system->atoms[i].x[1],
+ system->atoms[i].x[2],
+ 1.0,
+ 0.0,
+ "0",
+ name,
+ " " );
+ }
- fclose( out_control->pdb );
+ fprintf( out_control->log, "ATOM written\n" );
+ fflush( out_control->log );
+
+ /* Writing connect information */
+ for (i = 0; i < system->N; i++)
+ {
+ count = 0;
+
+ for (j = Start_Index(i, bonds); j < End_Index(i, bonds); ++j)
+ {
+ bo = bonds->select.bond_list[j].bo_data.BO;
+ if (bo > 0.3)
+ {
+ connect[count] = workspace->orig_id[bonds->select.bond_list[j].nbr];
+ count++;
+ }
+ }
+
+ fprintf( out_control->pdb, "%6s%6d", "CONECT", workspace->orig_id[i] );
+ for ( k = 0; k < count; k++ )
+ fprintf( out_control->pdb, "%6d", connect[k] );
+ fprintf( out_control->pdb, "\n" );
+ }
- return 1;
+ fprintf( out_control->pdb, "END\n" );
+
+ fclose( out_control->pdb );
+
+ return 1;
}
-char Read_BGF( char* bgf_file, reax_system* system, control_params *control,
- simulation_data *data, static_storage *workspace )
+char Read_BGF( char* bgf_file, reax_system* system, control_params *control,
+ simulation_data *data, static_storage *workspace )
{
- FILE *bgf;
- char **tokens;
- char *line, *backup;
- char descriptor[10], serial[10];
- char atom_name[10], res_name[10], res_seq[10];
- char s_x[12], s_y[12], s_z[12];
- char occupancy[10], temp_factor[10];
- char element[10], charge[10];
- char chain_id;
- char s_a[12], s_b[12], s_c[12], s_alpha[12], s_beta[12], s_gamma[12];
- char *endptr = NULL;
- int i, atom_cnt, token_cnt, bgf_serial, ratom = 0;
-
- /* open biograf file */
- if ( (bgf = fopen( bgf_file, "r" )) == NULL )
+ FILE *bgf;
+ char **tokens;
+ char *line, *backup;
+ char descriptor[10], serial[10];
+ char atom_name[10], res_name[10], res_seq[10];
+ char s_x[12], s_y[12], s_z[12];
+ char occupancy[10], temp_factor[10];
+ char element[10], charge[10];
+ char chain_id;
+ char s_a[12], s_b[12], s_c[12], s_alpha[12], s_beta[12], s_gamma[12];
+ char *endptr = NULL;
+ int i, atom_cnt, token_cnt, bgf_serial, ratom = 0;
+
+ /* open biograf file */
+ if ( (bgf = fopen( bgf_file, "r" )) == NULL )
+ {
+ fprintf( stderr, "Error opening the bgf file!\n" );
+ exit( FILE_NOT_FOUND_ERR );
+ }
+
+
+ /* allocate memory for tokenizing biograf file lines */
+ line = (char*) malloc( sizeof(char) * MAX_LINE );
+ backup = (char*) malloc( sizeof(char) * MAX_LINE );
+ tokens = (char**) malloc( sizeof(char*) * MAX_TOKENS );
+ for ( i = 0; i < MAX_TOKENS; i++ )
+ tokens[i] = (char*) malloc( sizeof(char) * MAX_TOKEN_LEN );
+
+
+ /* count number of atoms in the pdb file */
+ system->N = 0;
+ while ( !feof( bgf ) )
{
- fprintf( stderr, "Error opening the bgf file!\n" );
- exit( FILE_NOT_FOUND_ERR );
+ line[0] = 0;
+ fgets( line, MAX_LINE, bgf );
+
+ tokens[0][0] = 0;
+ token_cnt = Tokenize( line, &tokens );
+
+ if ( !strcmp( tokens[0], "ATOM" ) || !strcmp( tokens[0], "HETATM" ) )
+ (system->N)++;
}
+ //fprintf( stderr, "system->N: %d\n", system->N );
+ fclose( bgf );
+
+
+ /* memory allocations for atoms, atom maps, bond restrictions */
+ system->atoms = (reax_atom*) calloc( system->N, sizeof(reax_atom) );
+
+ workspace->map_serials = (int*) calloc( MAX_ATOM_ID, sizeof(int) );
+ for ( i = 0; i < MAX_ATOM_ID; ++i )
+ workspace->map_serials[i] = -1;
+ workspace->orig_id = (int*) calloc( system->N, sizeof(int) );
+ workspace->restricted = (int*) calloc( system->N, sizeof(int) );
+ workspace->restricted_list = (int**) calloc( system->N, sizeof(int*) );
+ for ( i = 0; i < system->N; ++i )
+ workspace->restricted_list[i] = (int*) calloc( MAX_RESTRICT, sizeof(int) );
- /* allocate memory for tokenizing biograf file lines */
- line = (char*) malloc( sizeof(char) * MAX_LINE );
- backup = (char*) malloc( sizeof(char) * MAX_LINE );
- tokens = (char**) malloc( sizeof(char*) * MAX_TOKENS );
- for( i = 0; i < MAX_TOKENS; i++ )
- tokens[i] = (char*) malloc( sizeof(char) * MAX_TOKEN_LEN );
-
-
- /* count number of atoms in the pdb file */
- system->N = 0;
- while( !feof( bgf ) ) {
- line[0] = 0;
- fgets( line, MAX_LINE, bgf );
-
- tokens[0][0] = 0;
- token_cnt = Tokenize( line, &tokens );
-
- if( !strcmp( tokens[0], "ATOM" ) || !strcmp( tokens[0], "HETATM" ) )
- (system->N)++;
- }
- //fprintf( stderr, "system->N: %d\n", system->N );
- fclose( bgf );
-
-
- /* memory allocations for atoms, atom maps, bond restrictions */
- system->atoms = (reax_atom*) calloc( system->N, sizeof(reax_atom) );
-
- workspace->map_serials = (int*) calloc( MAX_ATOM_ID, sizeof(int) );
- for( i = 0; i < MAX_ATOM_ID; ++i )
- workspace->map_serials[i] = -1;
-
- workspace->orig_id = (int*) calloc( system->N, sizeof(int) );
- workspace->restricted = (int*) calloc( system->N, sizeof(int) );
- workspace->restricted_list = (int**) calloc( system->N, sizeof(int*) );
- for( i = 0; i < system->N; ++i )
- workspace->restricted_list[i] = (int*) calloc( MAX_RESTRICT, sizeof(int) );
-
-
- /* start reading and processing bgf file */
- if ( (bgf = fopen( bgf_file, "r" )) == NULL )
- {
- fprintf( stderr, "Error opening the bgf file!\n" );
- exit( FILE_NOT_FOUND_ERR );
- }
- atom_cnt = 0;
- token_cnt = 0;
-
- while( !feof( bgf ) ) {
- /* clear previous input line */
- line[0] = 0;
- for( i = 0; i < token_cnt; ++i )
- tokens[i][0] = 0;
-
- /* read new line and tokenize it */
- fgets( line, MAX_LINE, bgf );
- strncpy( backup, line, MAX_LINE-1 );
- token_cnt = Tokenize( line, &tokens );
-
- /* process new line */
- if( !strncmp(tokens[0], "ATOM", 4) || !strncmp(tokens[0], "HETATM", 6) ) {
- if( !strncmp(tokens[0], "ATOM", 4) ) {
- strncpy( &descriptor[0], backup, 6 ); descriptor[6] = 0;
- strncpy( &serial[0], backup+7, 5 ); serial[5] = 0;
- strncpy( &atom_name[0], backup+13, 5 ); atom_name[5] = 0;
- strncpy( &res_name[0], backup+19, 3 ); res_name[3] = 0;
- chain_id = backup[23];
- strncpy( &res_seq[0], backup+25, 5 ); res_seq[5] = 0;
- strncpy( &s_x[0], backup+30, 10 ); s_x[10] = 0;
- strncpy( &s_y[0], backup+40, 10 ); s_y[10] = 0;
- strncpy( &s_z[0], backup+50, 10 ); s_z[10] = 0;
- strncpy( &element[0], backup+61, 5 ); element[5] = 0;
- strncpy( &occupancy[0], backup+66, 3 ); occupancy[3] = 0;
- strncpy( &temp_factor[0], backup+69, 2 ); temp_factor[2] = 0;
- strncpy( &charge[0], backup+72, 8 ); charge[8] = 0;
- }
- else if( !strncmp(tokens[0],"HETATM", 6) ) {
- /* bgf hetatm:
- (7x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x,a5,i3,i2,1x,f8.5) */
- strncpy( &descriptor[0], backup, 6 ); descriptor[6] = 0;
- strncpy( &serial[0], backup+7, 5 ); serial[5] = 0;
- strncpy( &atom_name[0], backup+13, 5 ); atom_name[5] = 0;
- strncpy( &res_name[0], backup+19, 3 ); res_name[3] = 0;
- chain_id = backup[23];
- strncpy( &res_seq[0], backup+25, 5 ); res_seq[5] = 0;
- strncpy( &s_x[0], backup+30, 10 ); s_x[10] = 0;
- strncpy( &s_y[0], backup+40, 10 ); s_y[10] = 0;
- strncpy( &s_z[0], backup+50, 10 ); s_z[10] = 0;
- strncpy( &element[0], backup+61, 5 ); element[5] = 0;
- strncpy( &occupancy[0], backup+66, 3 ); occupancy[3] = 0;
- strncpy( &temp_factor[0], backup+69, 2 ); temp_factor[2] = 0;
- strncpy( &charge[0], backup+72, 8 ); charge[8] = 0;
- }
-
-
- /* add to mapping */
- bgf_serial = strtod( &serial[0], &endptr );
- Check_Input_Range( bgf_serial, 0, MAX_ATOM_ID, "Invalid bgf serial" );
- workspace->map_serials[ bgf_serial ] = atom_cnt;
- workspace->orig_id[ atom_cnt ] = bgf_serial;
- // fprintf( stderr, "map %d --> %d\n", bgf_serial, atom_cnt );
-
-
- /* copy atomic positions */
- system->atoms[atom_cnt].x[0] = strtod( &s_x[0], &endptr );
- system->atoms[atom_cnt].x[1] = strtod( &s_y[0], &endptr );
- system->atoms[atom_cnt].x[2] = strtod( &s_z[0], &endptr );
-
-
- /* atom name and type */
- strcpy( system->atoms[atom_cnt].name, atom_name );
- Trim_Spaces( element );
- system->atoms[atom_cnt].type =
- Get_Atom_Type( &(system->reaxprm), element );
-
- /* fprintf( stderr,
- "a:%3d(%1d) c:%10.5f%10.5f%10.5f q:%10.5f occ:%s temp:%s seg_id:%s element:%s\n",
- atom_cnt, system->atoms[ atom_cnt ].type,
- system->atoms[ atom_cnt ].x[0],
- system->atoms[ atom_cnt ].x[1], system->atoms[ atom_cnt ].x[2],
- system->atoms[ atom_cnt ].q, occupancy, temp_factor,
- seg_id, element ); */
-
- atom_cnt++;
+
+ /* start reading and processing bgf file */
+ if ( (bgf = fopen( bgf_file, "r" )) == NULL )
+ {
+ fprintf( stderr, "Error opening the bgf file!\n" );
+ exit( FILE_NOT_FOUND_ERR );
}
- else if(!strncmp( tokens[0], "CRYSTX", 6 )) {
- sscanf( backup, BGF_CRYSTX_FORMAT,
- &descriptor[0],
- &s_a[0],
- &s_b[0],
- &s_c[0],
- &s_alpha[0],
- &s_beta[0],
- &s_gamma[0] );
-
- /* Compute full volume tensor from the angles */
- Init_Box_From_CRYST( atof(s_a), atof(s_b), atof(s_c),
- atof(s_alpha), atof(s_beta), atof(s_gamma),
- &(system->box) );
+ atom_cnt = 0;
+ token_cnt = 0;
+
+ while ( !feof( bgf ) )
+ {
+ /* clear previous input line */
+ line[0] = 0;
+ for ( i = 0; i < token_cnt; ++i )
+ tokens[i][0] = 0;
+
+ /* read new line and tokenize it */
+ fgets( line, MAX_LINE, bgf );
+ strncpy( backup, line, MAX_LINE - 1 );
+ token_cnt = Tokenize( line, &tokens );
+
+ /* process new line */
+ if ( !strncmp(tokens[0], "ATOM", 4) || !strncmp(tokens[0], "HETATM", 6) )
+ {
+ if ( !strncmp(tokens[0], "ATOM", 4) )
+ {
+ strncpy( &descriptor[0], backup, 6 );
+ descriptor[6] = 0;
+ strncpy( &serial[0], backup + 7, 5 );
+ serial[5] = 0;
+ strncpy( &atom_name[0], backup + 13, 5 );
+ atom_name[5] = 0;
+ strncpy( &res_name[0], backup + 19, 3 );
+ res_name[3] = 0;
+ chain_id = backup[23];
+ strncpy( &res_seq[0], backup + 25, 5 );
+ res_seq[5] = 0;
+ strncpy( &s_x[0], backup + 30, 10 );
+ s_x[10] = 0;
+ strncpy( &s_y[0], backup + 40, 10 );
+ s_y[10] = 0;
+ strncpy( &s_z[0], backup + 50, 10 );
+ s_z[10] = 0;
+ strncpy( &element[0], backup + 61, 5 );
+ element[5] = 0;
+ strncpy( &occupancy[0], backup + 66, 3 );
+ occupancy[3] = 0;
+ strncpy( &temp_factor[0], backup + 69, 2 );
+ temp_factor[2] = 0;
+ strncpy( &charge[0], backup + 72, 8 );
+ charge[8] = 0;
+ }
+ else if ( !strncmp(tokens[0], "HETATM", 6) )
+ {
+ /* bgf hetatm:
+ (7x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x,a5,i3,i2,1x,f8.5) */
+ strncpy( &descriptor[0], backup, 6 );
+ descriptor[6] = 0;
+ strncpy( &serial[0], backup + 7, 5 );
+ serial[5] = 0;
+ strncpy( &atom_name[0], backup + 13, 5 );
+ atom_name[5] = 0;
+ strncpy( &res_name[0], backup + 19, 3 );
+ res_name[3] = 0;
+ chain_id = backup[23];
+ strncpy( &res_seq[0], backup + 25, 5 );
+ res_seq[5] = 0;
+ strncpy( &s_x[0], backup + 30, 10 );
+ s_x[10] = 0;
+ strncpy( &s_y[0], backup + 40, 10 );
+ s_y[10] = 0;
+ strncpy( &s_z[0], backup + 50, 10 );
+ s_z[10] = 0;
+ strncpy( &element[0], backup + 61, 5 );
+ element[5] = 0;
+ strncpy( &occupancy[0], backup + 66, 3 );
+ occupancy[3] = 0;
+ strncpy( &temp_factor[0], backup + 69, 2 );
+ temp_factor[2] = 0;
+ strncpy( &charge[0], backup + 72, 8 );
+ charge[8] = 0;
+ }
+
+
+ /* add to mapping */
+ bgf_serial = strtod( &serial[0], &endptr );
+ Check_Input_Range( bgf_serial, 0, MAX_ATOM_ID, "Invalid bgf serial" );
+ workspace->map_serials[ bgf_serial ] = atom_cnt;
+ workspace->orig_id[ atom_cnt ] = bgf_serial;
+ // fprintf( stderr, "map %d --> %d\n", bgf_serial, atom_cnt );
+
+
+ /* copy atomic positions */
+ system->atoms[atom_cnt].x[0] = strtod( &s_x[0], &endptr );
+ system->atoms[atom_cnt].x[1] = strtod( &s_y[0], &endptr );
+ system->atoms[atom_cnt].x[2] = strtod( &s_z[0], &endptr );
+
+
+ /* atom name and type */
+ strcpy( system->atoms[atom_cnt].name, atom_name );
+ Trim_Spaces( element );
+ system->atoms[atom_cnt].type =
+ Get_Atom_Type( &(system->reaxprm), element );
+
+ /* fprintf( stderr,
+ "a:%3d(%1d) c:%10.5f%10.5f%10.5f q:%10.5f occ:%s temp:%s seg_id:%s element:%s\n",
+ atom_cnt, system->atoms[ atom_cnt ].type,
+ system->atoms[ atom_cnt ].x[0],
+ system->atoms[ atom_cnt ].x[1], system->atoms[ atom_cnt ].x[2],
+ system->atoms[ atom_cnt ].q, occupancy, temp_factor,
+ seg_id, element ); */
+
+ atom_cnt++;
+ }
+ else if (!strncmp( tokens[0], "CRYSTX", 6 ))
+ {
+ sscanf( backup, BGF_CRYSTX_FORMAT,
+ &descriptor[0],
+ &s_a[0],
+ &s_b[0],
+ &s_c[0],
+ &s_alpha[0],
+ &s_beta[0],
+ &s_gamma[0] );
+
+ /* Compute full volume tensor from the angles */
+ Init_Box_From_CRYST( atof(s_a), atof(s_b), atof(s_c),
+ atof(s_alpha), atof(s_beta), atof(s_gamma),
+ &(system->box) );
+ }
+ else if (!strncmp( tokens[0], "CONECT", 6 ))
+ {
+ /* check number of restrictions */
+ Check_Input_Range( token_cnt - 2, 0, MAX_RESTRICT,
+ "CONECT line exceeds max restrictions allowed.\n" );
+
+ /* read bond restrictions */
+ if ( is_Valid_Serial( workspace, bgf_serial = atoi(tokens[1]) ) )
+ ratom = workspace->map_serials[ bgf_serial ];
+
+ workspace->restricted[ ratom ] = token_cnt - 2;
+ for ( i = 2; i < token_cnt; ++i )
+ if ( is_Valid_Serial( workspace, bgf_serial = atoi(tokens[i]) ) )
+ workspace->restricted_list[ ratom ][ i - 2 ] =
+ workspace->map_serials[ bgf_serial ];
+
+ /* fprintf( stderr, "restriction on %d:", ratom );
+ for( i = 0; i < workspace->restricted[ ratom ]; ++i )
+ fprintf( stderr, " %d", workspace->restricted_list[ratom][i] );
+ fprintf( stderr, "\n" ); */
+ }
}
- else if(!strncmp( tokens[0], "CONECT", 6 )) {
- /* check number of restrictions */
- Check_Input_Range( token_cnt - 2, 0, MAX_RESTRICT,
- "CONECT line exceeds max restrictions allowed.\n" );
-
- /* read bond restrictions */
- if( is_Valid_Serial( workspace, bgf_serial = atoi(tokens[1]) ) )
- ratom = workspace->map_serials[ bgf_serial ];
-
- workspace->restricted[ ratom ] = token_cnt - 2;
- for( i = 2; i < token_cnt; ++i )
- if( is_Valid_Serial( workspace, bgf_serial = atoi(tokens[i]) ) )
- workspace->restricted_list[ ratom ][ i-2 ] =
- workspace->map_serials[ bgf_serial ];
-
- /* fprintf( stderr, "restriction on %d:", ratom );
- for( i = 0; i < workspace->restricted[ ratom ]; ++i )
- fprintf( stderr, " %d", workspace->restricted_list[ratom][i] );
- fprintf( stderr, "\n" ); */
- }
- }
-
- fclose( bgf );
+
+ fclose( bgf );
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "bgf file read\n" );
+ fprintf( stderr, "bgf file read\n" );
#endif
- return 1;
-}
+ return 1;
+}
diff --git a/puremd_rc_1003/sPuReMD/pdb_tools.h b/puremd_rc_1003/sPuReMD/pdb_tools.h
index 212cf6a57cf3b5ea2da3ed2ee148ce875f0a4b4f..c3afab9f601a666f54b00c99c80502bbecb64c41 100644
--- a/puremd_rc_1003/sPuReMD/pdb_tools.h
+++ b/puremd_rc_1003/sPuReMD/pdb_tools.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -25,14 +25,14 @@
#include "mytypes.h"
/*
-PDB format :
+PDB format :
http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/guide2.2_frame.html
#define PDB_ATOM_FORMAT "%6s%5d%4s%c%4s%c%4d%c%8s%8s%8s%6s%6s%4s%2s%2s\n"
COLUMNS DATA TYPE FIELD DEFINITION
--------------------------------------------------------------------------------
-1 - 6 Record name "ATOM "
+1 - 6 Record name "ATOM "
7 - 11 Integer serial Atom serial number.
13 - 16 Atom name Atom name.
17 Character altLoc Alternate location indicator.
@@ -43,7 +43,7 @@ COLUMNS DATA TYPE FIELD DEFINITION
31 - 38 Real(8.3) x Orthogonal coord for X in Angstroms
39 - 46 Real(8.3) y Orthogonal coord for Y in Angstroms
47 - 54 Real(8.3) z Orthogonal coord for Z in Angstroms
-55 - 60 Real(6.2) occupancy Occupancy.
+55 - 60 Real(6.2) occupancy Occupancy.
61 - 66 Real(6.2) tempFactor Temperature factor.
73 - 76 LString(4) segID Segment identifier, left-justified.
77 - 78 LString(2) element Element symbol, right-justified.
@@ -82,9 +82,9 @@ COLUMNS DATA TYPE FIELD DEFINITION
*/
/*
-COLUMNS DATA TYPE FIELD DEFINITION
-----------------------------------------------------------
-1 - 6 Record name "CRYST1"
+COLUMNS DATA TYPE FIELD DEFINITION
+----------------------------------------------------------
+1 - 6 Record name "CRYST1"
7 - 15 Real(9.3) a a (Angstroms)
16 - 24 Real(9.3) b b (Angstroms)
25 - 33 Real(9.3) c c (Angstroms)
@@ -107,12 +107,12 @@ COLUMNS DATA TYPE FIELD DEFINITION
#define BGF_CRYSTX_FORMAT "%8s%11s%11s%11s%11s%11s%11s"
-char Read_PDB( char*, reax_system*, control_params*,
- simulation_data*, static_storage* );
-char Read_BGF( char*, reax_system*, control_params*,
- simulation_data*, static_storage* );
+char Read_PDB( char*, reax_system*, control_params*,
+ simulation_data*, static_storage* );
+char Read_BGF( char*, reax_system*, control_params*,
+ simulation_data*, static_storage* );
-char Write_PDB( reax_system*, control_params*, simulation_data*,
- static_storage*, list*, output_controls* );
+char Write_PDB( reax_system*, control_params*, simulation_data*,
+ static_storage*, list*, output_controls* );
#endif
diff --git a/puremd_rc_1003/sPuReMD/print_utils.c b/puremd_rc_1003/sPuReMD/print_utils.c
index 46127cd5f10b4dca5bc79c162ad5417c3160963b..20d58e7576b185ca65c84f78ac3548ce7621b57d 100644
--- a/puremd_rc_1003/sPuReMD/print_utils.c
+++ b/puremd_rc_1003/sPuReMD/print_utils.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -27,843 +27,868 @@
#ifdef TEST_FORCES
-void Dummy_Printer( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+void Dummy_Printer( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
}
-void Print_Bond_Orders( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+void Print_Bond_Orders( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int i, pj, pk;
- bond_order_data *bo_ij;
- list *bonds = (*lists) + BONDS;
- list *dBOs = (*lists) + DBO;
- dbond_data *dbo_k;
-
-
- /* bond orders */
- fprintf( out_control->fbo, "%6s%6s%12s%12s%12s%12s%12s\n",
- "atom1", "atom2", "r_ij", "total_bo", "bo_s", "bo_p", "bo_pp" );
-
- for( i = 0; i < system->N; ++i )
- for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
- bo_ij = &(bonds->select.bond_list[pj].bo_data);
- fprintf( out_control->fbo, "%6d%6d%23.15e%23.15e%23.15e%23.15e%23.15e\n",
- //workspace->orig_id[i],
- //workspace->orig_id[bonds->select.bond_list[pj].nbr],
- i+1,
- bonds->select.bond_list[pj].nbr+1,
- bonds->select.bond_list[pj].d,
- bo_ij->BO, bo_ij->BO_s, bo_ij->BO_pi, bo_ij->BO_pi2 );
- }
-
- /* derivatives of bond orders */
- /* fprintf( out_control->fbo, "%6s%6s%10s%10s%10s%10s\n",
- "atom1", "atom2", "total_bo", "bo_s", "bo_p", "bo_pp"\n ); */
-
- for( i = 0; i < system->N; ++i )
- for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
- /*fprintf( out_control->fdbo, "%6d %6d\tstart: %6d\tend: %6d\n",
- workspace->orig_id[i],
- workspace->orig_id[bonds->select.bond_list[pj].nbr],
- Start_Index( pj, dBOs ), End_Index( pj, dBOs ) );*/
-
- for( pk = Start_Index(pj,dBOs); pk < End_Index(pj,dBOs); ++pk ) {
- dbo_k = &(dBOs->select.dbo_list[pk]);
-
- //if( !rvec_isZero( dbo_k->dBO ) )
- fprintf( out_control->fdbo, "%6d%6d%6d%23.15e%23.15e%23.15e\n",
- workspace->orig_id[i],
- workspace->orig_id[bonds->select.bond_list[pj].nbr],
- workspace->orig_id[dbo_k->wrt],
- dbo_k->dBO[0], dbo_k->dBO[1], dbo_k->dBO[2] );
-
- fprintf( out_control->fdbo, "%6d%6d%6d%23.15e%23.15e%23.15e\n",
- workspace->orig_id[i],
- workspace->orig_id[bonds->select.bond_list[pj].nbr],
- workspace->orig_id[dbo_k->wrt],
- dbo_k->dBOpi[0], dbo_k->dBOpi[1], dbo_k->dBOpi[2] );
-
- fprintf( out_control->fdbo, "%6d%6d%6d%23.15e%23.15e%23.15e\n",
- workspace->orig_id[i],
- workspace->orig_id[bonds->select.bond_list[pj].nbr],
- workspace->orig_id[dbo_k->wrt],
- dbo_k->dBOpi2[0], dbo_k->dBOpi2[1], dbo_k->dBOpi2[2] );
- }
- }
-
- fflush(out_control->fdbo);
+ int i, pj, pk;
+ bond_order_data *bo_ij;
+ list *bonds = (*lists) + BONDS;
+ list *dBOs = (*lists) + DBO;
+ dbond_data *dbo_k;
+
+
+ /* bond orders */
+ fprintf( out_control->fbo, "%6s%6s%12s%12s%12s%12s%12s\n",
+ "atom1", "atom2", "r_ij", "total_bo", "bo_s", "bo_p", "bo_pp" );
+
+ for ( i = 0; i < system->N; ++i )
+ for ( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
+ {
+ bo_ij = &(bonds->select.bond_list[pj].bo_data);
+ fprintf( out_control->fbo, "%6d%6d%23.15e%23.15e%23.15e%23.15e%23.15e\n",
+ //workspace->orig_id[i],
+ //workspace->orig_id[bonds->select.bond_list[pj].nbr],
+ i + 1,
+ bonds->select.bond_list[pj].nbr + 1,
+ bonds->select.bond_list[pj].d,
+ bo_ij->BO, bo_ij->BO_s, bo_ij->BO_pi, bo_ij->BO_pi2 );
+ }
+
+ /* derivatives of bond orders */
+ /* fprintf( out_control->fbo, "%6s%6s%10s%10s%10s%10s\n",
+ "atom1", "atom2", "total_bo", "bo_s", "bo_p", "bo_pp"\n ); */
+
+ for ( i = 0; i < system->N; ++i )
+ for ( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
+ {
+ /*fprintf( out_control->fdbo, "%6d %6d\tstart: %6d\tend: %6d\n",
+ workspace->orig_id[i],
+ workspace->orig_id[bonds->select.bond_list[pj].nbr],
+ Start_Index( pj, dBOs ), End_Index( pj, dBOs ) );*/
+
+ for ( pk = Start_Index(pj, dBOs); pk < End_Index(pj, dBOs); ++pk )
+ {
+ dbo_k = &(dBOs->select.dbo_list[pk]);
+
+ //if( !rvec_isZero( dbo_k->dBO ) )
+ fprintf( out_control->fdbo, "%6d%6d%6d%23.15e%23.15e%23.15e\n",
+ workspace->orig_id[i],
+ workspace->orig_id[bonds->select.bond_list[pj].nbr],
+ workspace->orig_id[dbo_k->wrt],
+ dbo_k->dBO[0], dbo_k->dBO[1], dbo_k->dBO[2] );
+
+ fprintf( out_control->fdbo, "%6d%6d%6d%23.15e%23.15e%23.15e\n",
+ workspace->orig_id[i],
+ workspace->orig_id[bonds->select.bond_list[pj].nbr],
+ workspace->orig_id[dbo_k->wrt],
+ dbo_k->dBOpi[0], dbo_k->dBOpi[1], dbo_k->dBOpi[2] );
+
+ fprintf( out_control->fdbo, "%6d%6d%6d%23.15e%23.15e%23.15e\n",
+ workspace->orig_id[i],
+ workspace->orig_id[bonds->select.bond_list[pj].nbr],
+ workspace->orig_id[dbo_k->wrt],
+ dbo_k->dBOpi2[0], dbo_k->dBOpi2[1], dbo_k->dBOpi2[2] );
+ }
+ }
+
+ fflush(out_control->fdbo);
}
-void Print_Bond_Forces( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+void Print_Bond_Forces( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int i;
+ int i;
- fprintf( out_control->fbond, "%d\n", data->step );
- fprintf( out_control->fbond, "%6s\t%s\n", "atom", "fbond" );
+ fprintf( out_control->fbond, "%d\n", data->step );
+ fprintf( out_control->fbond, "%6s\t%s\n", "atom", "fbond" );
- for( i = 0; i < system->N; ++i )
- fprintf(out_control->fbond, "%6d %23.15e%23.15e%23.15e\n",
- workspace->orig_id[i],
- workspace->f_be[i][0],workspace->f_be[i][1],workspace->f_be[i][2]);
+ for ( i = 0; i < system->N; ++i )
+ fprintf(out_control->fbond, "%6d %23.15e%23.15e%23.15e\n",
+ workspace->orig_id[i],
+ workspace->f_be[i][0], workspace->f_be[i][1], workspace->f_be[i][2]);
}
-void Print_LonePair_Forces( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+void Print_LonePair_Forces( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int i;
+ int i;
- fprintf( out_control->flp, "%d\n", data->step );
- fprintf( out_control->flp, "%6s\t%s\n", "atom","f_lonepair" );
+ fprintf( out_control->flp, "%d\n", data->step );
+ fprintf( out_control->flp, "%6s\t%s\n", "atom", "f_lonepair" );
- for( i = 0; i < system->N; ++i )
- fprintf(out_control->flp, "%6d %23.15e%23.15e%23.15e\n",
- workspace->orig_id[i],
- workspace->f_lp[i][0],workspace->f_lp[i][1],workspace->f_lp[i][2]);
+ for ( i = 0; i < system->N; ++i )
+ fprintf(out_control->flp, "%6d %23.15e%23.15e%23.15e\n",
+ workspace->orig_id[i],
+ workspace->f_lp[i][0], workspace->f_lp[i][1], workspace->f_lp[i][2]);
- fflush(out_control->flp);
+ fflush(out_control->flp);
}
-void Print_OverUnderCoor_Forces( reax_system *system, control_params *control,
- simulation_data *data,
- static_storage *workspace, list **lists,
- output_controls *out_control )
+void Print_OverUnderCoor_Forces( reax_system *system, control_params *control,
+ simulation_data *data,
+ static_storage *workspace, list **lists,
+ output_controls *out_control )
{
- int i;
-
- fprintf( out_control->fatom, "%d\n", data->step );
- fprintf( out_control->fatom, "%6s\t%-38s%-38s%-38s\n",
- "atom","f_atom", "f_over", "f_under" );
-
- for( i = 0; i < system->N; ++i ){
- if( rvec_isZero( workspace->f_un[i] ) )
- fprintf( out_control->fatom,
- "%6d %23.15e%23.15e%23.15e 0 0 0\n",
- workspace->orig_id[i], workspace->f_ov[i][0],
- workspace->f_ov[i][1], workspace->f_ov[i][2] );
- else
- fprintf( out_control->fatom,
- "%6d %23.15e%23.15e%23.15e %23.15e%23.15e%23.15e"\
- "%23.15e%23.15e%23.15e\n",
- workspace->orig_id[i],
- workspace->f_un[i][0] + workspace->f_ov[i][0],
- workspace->f_un[i][1] + workspace->f_ov[i][1],
- workspace->f_un[i][2] + workspace->f_ov[i][2],
- workspace->f_ov[i][0], workspace->f_ov[i][1],
- workspace->f_ov[i][2],
- workspace->f_un[i][0], workspace->f_un[i][1],
- workspace->f_un[i][2] );
- }
-
- fflush(out_control->fatom);
+ int i;
+
+ fprintf( out_control->fatom, "%d\n", data->step );
+ fprintf( out_control->fatom, "%6s\t%-38s%-38s%-38s\n",
+ "atom", "f_atom", "f_over", "f_under" );
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ if ( rvec_isZero( workspace->f_un[i] ) )
+ fprintf( out_control->fatom,
+ "%6d %23.15e%23.15e%23.15e 0 0 0\n",
+ workspace->orig_id[i], workspace->f_ov[i][0],
+ workspace->f_ov[i][1], workspace->f_ov[i][2] );
+ else
+ fprintf( out_control->fatom,
+ "%6d %23.15e%23.15e%23.15e %23.15e%23.15e%23.15e"\
+ "%23.15e%23.15e%23.15e\n",
+ workspace->orig_id[i],
+ workspace->f_un[i][0] + workspace->f_ov[i][0],
+ workspace->f_un[i][1] + workspace->f_ov[i][1],
+ workspace->f_un[i][2] + workspace->f_ov[i][2],
+ workspace->f_ov[i][0], workspace->f_ov[i][1],
+ workspace->f_ov[i][2],
+ workspace->f_un[i][0], workspace->f_un[i][1],
+ workspace->f_un[i][2] );
+ }
+
+ fflush(out_control->fatom);
}
-void Print_Three_Body_Forces( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+void Print_Three_Body_Forces( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int j;
-
- fprintf( out_control->f3body, "%d\n", data->step );
- fprintf( out_control->f3body, "%6s%-37s%-37s%-37s%-38s\n",
- "atom", "3-body total", "f_ang", "f_pen", "f_coa" );
-
- for( j = 0; j < system->N; ++j ){
- if( rvec_isZero(workspace->f_pen[j]) && rvec_isZero(workspace->f_coa[j]) )
- fprintf( out_control->f3body, "%6d %23.15e%23.15e%23.15e 0 0 0 0 0 0\n",
- workspace->orig_id[j], workspace->f_ang[j][0],
- workspace->f_ang[j][1], workspace->f_ang[j][2] );
- else if( rvec_isZero(workspace->f_coa[j]) )
- fprintf( out_control->f3body,
- "%6d %23.15e%23.15e%23.15e %23.15e%23.15e%23.15e "\
- "%23.15e%23.15e%23.15e\n",
- workspace->orig_id[j],
- workspace->f_ang[j][0] + workspace->f_pen[j][0],
- workspace->f_ang[j][1] + workspace->f_pen[j][1],
- workspace->f_ang[j][2] + workspace->f_pen[j][2],
- workspace->f_ang[j][0], workspace->f_ang[j][1],
- workspace->f_ang[j][2],
- workspace->f_pen[j][0], workspace->f_pen[j][1],
- workspace->f_pen[j][2] );
- else{
- fprintf( out_control->f3body, "%6d %23.15e%23.15e%23.15e ",
- workspace->orig_id[j],
- workspace->f_ang[j][0] + workspace->f_pen[j][0] +
- workspace->f_coa[j][0],
- workspace->f_ang[j][1] + workspace->f_pen[j][1] +
- workspace->f_coa[j][1],
- workspace->f_ang[j][2] + workspace->f_pen[j][2] +
- workspace->f_coa[j][2] );
-
- fprintf( out_control->f3body,
- "%23.15e%23.15e%23.15e %23.15e%23.15e%23.15e "\
- "%23.15e%23.15e%23.15e\n",
- workspace->f_ang[j][0], workspace->f_ang[j][1],
- workspace->f_ang[j][2],
- workspace->f_pen[j][0], workspace->f_pen[j][1],
- workspace->f_pen[j][2],
- workspace->f_coa[j][0], workspace->f_coa[j][1],
- workspace->f_coa[j][2] );
+ int j;
+
+ fprintf( out_control->f3body, "%d\n", data->step );
+ fprintf( out_control->f3body, "%6s%-37s%-37s%-37s%-38s\n",
+ "atom", "3-body total", "f_ang", "f_pen", "f_coa" );
+
+ for ( j = 0; j < system->N; ++j )
+ {
+ if ( rvec_isZero(workspace->f_pen[j]) && rvec_isZero(workspace->f_coa[j]) )
+ fprintf( out_control->f3body, "%6d %23.15e%23.15e%23.15e 0 0 0 0 0 0\n",
+ workspace->orig_id[j], workspace->f_ang[j][0],
+ workspace->f_ang[j][1], workspace->f_ang[j][2] );
+ else if ( rvec_isZero(workspace->f_coa[j]) )
+ fprintf( out_control->f3body,
+ "%6d %23.15e%23.15e%23.15e %23.15e%23.15e%23.15e "\
+ "%23.15e%23.15e%23.15e\n",
+ workspace->orig_id[j],
+ workspace->f_ang[j][0] + workspace->f_pen[j][0],
+ workspace->f_ang[j][1] + workspace->f_pen[j][1],
+ workspace->f_ang[j][2] + workspace->f_pen[j][2],
+ workspace->f_ang[j][0], workspace->f_ang[j][1],
+ workspace->f_ang[j][2],
+ workspace->f_pen[j][0], workspace->f_pen[j][1],
+ workspace->f_pen[j][2] );
+ else
+ {
+ fprintf( out_control->f3body, "%6d %23.15e%23.15e%23.15e ",
+ workspace->orig_id[j],
+ workspace->f_ang[j][0] + workspace->f_pen[j][0] +
+ workspace->f_coa[j][0],
+ workspace->f_ang[j][1] + workspace->f_pen[j][1] +
+ workspace->f_coa[j][1],
+ workspace->f_ang[j][2] + workspace->f_pen[j][2] +
+ workspace->f_coa[j][2] );
+
+ fprintf( out_control->f3body,
+ "%23.15e%23.15e%23.15e %23.15e%23.15e%23.15e "\
+ "%23.15e%23.15e%23.15e\n",
+ workspace->f_ang[j][0], workspace->f_ang[j][1],
+ workspace->f_ang[j][2],
+ workspace->f_pen[j][0], workspace->f_pen[j][1],
+ workspace->f_pen[j][2],
+ workspace->f_coa[j][0], workspace->f_coa[j][1],
+ workspace->f_coa[j][2] );
+ }
}
- }
- fflush(out_control->f3body);
+ fflush(out_control->f3body);
}
-void Print_Hydrogen_Bond_Forces( reax_system *system, control_params *control,
- simulation_data *data,
- static_storage *workspace, list **lists,
- output_controls *out_control )
+void Print_Hydrogen_Bond_Forces( reax_system *system, control_params *control,
+ simulation_data *data,
+ static_storage *workspace, list **lists,
+ output_controls *out_control )
{
- int j;
-
- fprintf( out_control->fhb, "%d\n", data->step );
- fprintf( out_control->fhb, "%6s\t%-38s\n", "atom", "f_hb" );
-
- for( j = 0; j < system->N; ++j )
- fprintf(out_control->fhb, "%6d\t[%23.15e%23.15e%23.15e]\n",
- workspace->orig_id[j],
- workspace->f_hb[j][0],workspace->f_hb[j][1],workspace->f_hb[j][2]);
-
- fflush(out_control->fhb);
+ int j;
+
+ fprintf( out_control->fhb, "%d\n", data->step );
+ fprintf( out_control->fhb, "%6s\t%-38s\n", "atom", "f_hb" );
+
+ for ( j = 0; j < system->N; ++j )
+ fprintf(out_control->fhb, "%6d\t[%23.15e%23.15e%23.15e]\n",
+ workspace->orig_id[j],
+ workspace->f_hb[j][0], workspace->f_hb[j][1], workspace->f_hb[j][2]);
+
+ fflush(out_control->fhb);
}
-
-void Print_Four_Body_Forces( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+
+void Print_Four_Body_Forces( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int j;
-
- fprintf( out_control->f4body, "%6s\t%-38s%-38s%-38s\n",
- "atom", "4-body total", "f_tor", "f_con" );
-
- for( j = 0; j < system->N; ++j ){
- if( !rvec_isZero( workspace->f_con[j] ) )
- fprintf( out_control->f4body,
- "%6d %23.15e%23.15e%23.15e %23.15e%23.15e%23.15e "\
- "%23.15e%23.15e%23.15e\n",
- workspace->orig_id[j],
- workspace->f_tor[j][0] + workspace->f_con[j][0],
- workspace->f_tor[j][1] + workspace->f_con[j][1],
- workspace->f_tor[j][2] + workspace->f_con[j][2],
- workspace->f_tor[j][0], workspace->f_tor[j][1],
- workspace->f_tor[j][2],
- workspace->f_con[j][0], workspace->f_con[j][1],
- workspace->f_con[j][2] );
- else
- fprintf( out_control->f4body,
- "%6d %23.15e%23.15e%23.15e 0 0 0\n",
- workspace->orig_id[j], workspace->f_tor[j][0],
- workspace->f_tor[j][1], workspace->f_tor[j][2] );
- }
-
- fflush(out_control->f4body);
+ int j;
+
+ fprintf( out_control->f4body, "%6s\t%-38s%-38s%-38s\n",
+ "atom", "4-body total", "f_tor", "f_con" );
+
+ for ( j = 0; j < system->N; ++j )
+ {
+ if ( !rvec_isZero( workspace->f_con[j] ) )
+ fprintf( out_control->f4body,
+ "%6d %23.15e%23.15e%23.15e %23.15e%23.15e%23.15e "\
+ "%23.15e%23.15e%23.15e\n",
+ workspace->orig_id[j],
+ workspace->f_tor[j][0] + workspace->f_con[j][0],
+ workspace->f_tor[j][1] + workspace->f_con[j][1],
+ workspace->f_tor[j][2] + workspace->f_con[j][2],
+ workspace->f_tor[j][0], workspace->f_tor[j][1],
+ workspace->f_tor[j][2],
+ workspace->f_con[j][0], workspace->f_con[j][1],
+ workspace->f_con[j][2] );
+ else
+ fprintf( out_control->f4body,
+ "%6d %23.15e%23.15e%23.15e 0 0 0\n",
+ workspace->orig_id[j], workspace->f_tor[j][0],
+ workspace->f_tor[j][1], workspace->f_tor[j][2] );
+ }
+
+ fflush(out_control->f4body);
}
-void Print_vdW_Coulomb_Forces( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+void Print_vdW_Coulomb_Forces( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int i;
-
- fprintf( out_control->fnonb, "%d\n", data->step );
- fprintf( out_control->fnonb, "%6s\t%-38s%-38s%-38s\n",
- "atom", "nonbonded total", "f_vdw", "f_ele" );
-
- for( i = 0; i < system->N; ++i )
- if( !rvec_isZero(workspace->f_ele[i]) )
- fprintf(out_control->fnonb,
- "%6d %23.15e%23.15e%23.15e %23.15e%23.15e%23.15e "\
- "%23.15e%23.15e%23.15e\n",
- workspace->orig_id[i],
- workspace->f_vdw[i][0] + workspace->f_ele[i][0],
- workspace->f_vdw[i][1] + workspace->f_ele[i][1],
- workspace->f_vdw[i][2] + workspace->f_ele[i][2],
- workspace->f_vdw[i][0], workspace->f_vdw[i][1],
- workspace->f_vdw[i][2],
- workspace->f_ele[i][0], workspace->f_ele[i][1],
- workspace->f_ele[i][2] );
- else
- fprintf(out_control->fnonb,
- "%6d %23.15e%23.15e%23.15e 0 0 0\n",
- workspace->orig_id[i], workspace->f_vdw[i][0],
- workspace->f_vdw[i][1], workspace->f_vdw[i][2] );
-
- fflush(out_control->fnonb);
+ int i;
+
+ fprintf( out_control->fnonb, "%d\n", data->step );
+ fprintf( out_control->fnonb, "%6s\t%-38s%-38s%-38s\n",
+ "atom", "nonbonded total", "f_vdw", "f_ele" );
+
+ for ( i = 0; i < system->N; ++i )
+ if ( !rvec_isZero(workspace->f_ele[i]) )
+ fprintf(out_control->fnonb,
+ "%6d %23.15e%23.15e%23.15e %23.15e%23.15e%23.15e "\
+ "%23.15e%23.15e%23.15e\n",
+ workspace->orig_id[i],
+ workspace->f_vdw[i][0] + workspace->f_ele[i][0],
+ workspace->f_vdw[i][1] + workspace->f_ele[i][1],
+ workspace->f_vdw[i][2] + workspace->f_ele[i][2],
+ workspace->f_vdw[i][0], workspace->f_vdw[i][1],
+ workspace->f_vdw[i][2],
+ workspace->f_ele[i][0], workspace->f_ele[i][1],
+ workspace->f_ele[i][2] );
+ else
+ fprintf(out_control->fnonb,
+ "%6d %23.15e%23.15e%23.15e 0 0 0\n",
+ workspace->orig_id[i], workspace->f_vdw[i][0],
+ workspace->f_vdw[i][1], workspace->f_vdw[i][2] );
+
+ fflush(out_control->fnonb);
}
-void Compare_Total_Forces( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+void Compare_Total_Forces( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int i;
-
- fprintf( out_control->ftot2, "%d\n", data->step );
- fprintf( out_control->ftot2, "%6s\t%-38s%-38s\n",
- "atom", "f_total", "test_force total" );
-
- for( i = 0; i < system->N; ++i )
- fprintf( out_control->ftot2,
- "%6d %23.15e%23.15e%23.15e vs %23.15e%23.15e%23.15e\n",
- workspace->orig_id[i],
- system->atoms[i].f[0],system->atoms[i].f[1],system->atoms[i].f[2],
- workspace->f_be[i][0]+
- workspace->f_lp[i][0]+workspace->f_ov[i][0]+workspace->f_un[i][0]+
- workspace->f_ang[i][0]+workspace->f_pen[i][0]+
- workspace->f_coa[i][0]+workspace->f_hb[i][0]+
- workspace->f_tor[i][0]+workspace->f_con[i][0]+
- workspace->f_vdw[i][0]+workspace->f_ele[i][0],
- workspace->f_be[i][1]+
- workspace->f_lp[i][1]+workspace->f_ov[i][1]+workspace->f_un[i][1]+
- workspace->f_ang[i][1]+workspace->f_pen[i][1]+
- workspace->f_coa[i][1]+workspace->f_hb[i][1]+
- workspace->f_tor[i][1]+workspace->f_con[i][1]+
- workspace->f_vdw[i][1]+workspace->f_ele[i][1],
- workspace->f_be[i][2]+
- workspace->f_lp[i][2]+workspace->f_ov[i][2]+workspace->f_un[i][2]+
- workspace->f_ang[i][2]+workspace->f_pen[i][2]+
- workspace->f_coa[i][2]+workspace->f_hb[i][2]+
- workspace->f_tor[i][2]+workspace->f_con[i][2]+
- workspace->f_vdw[i][2]+workspace->f_ele[i][2] );
-
- fflush(out_control->ftot2);
+ int i;
+
+ fprintf( out_control->ftot2, "%d\n", data->step );
+ fprintf( out_control->ftot2, "%6s\t%-38s%-38s\n",
+ "atom", "f_total", "test_force total" );
+
+ for ( i = 0; i < system->N; ++i )
+ fprintf( out_control->ftot2,
+ "%6d %23.15e%23.15e%23.15e vs %23.15e%23.15e%23.15e\n",
+ workspace->orig_id[i],
+ system->atoms[i].f[0], system->atoms[i].f[1], system->atoms[i].f[2],
+ workspace->f_be[i][0] +
+ workspace->f_lp[i][0] + workspace->f_ov[i][0] + workspace->f_un[i][0] +
+ workspace->f_ang[i][0] + workspace->f_pen[i][0] +
+ workspace->f_coa[i][0] + workspace->f_hb[i][0] +
+ workspace->f_tor[i][0] + workspace->f_con[i][0] +
+ workspace->f_vdw[i][0] + workspace->f_ele[i][0],
+ workspace->f_be[i][1] +
+ workspace->f_lp[i][1] + workspace->f_ov[i][1] + workspace->f_un[i][1] +
+ workspace->f_ang[i][1] + workspace->f_pen[i][1] +
+ workspace->f_coa[i][1] + workspace->f_hb[i][1] +
+ workspace->f_tor[i][1] + workspace->f_con[i][1] +
+ workspace->f_vdw[i][1] + workspace->f_ele[i][1],
+ workspace->f_be[i][2] +
+ workspace->f_lp[i][2] + workspace->f_ov[i][2] + workspace->f_un[i][2] +
+ workspace->f_ang[i][2] + workspace->f_pen[i][2] +
+ workspace->f_coa[i][2] + workspace->f_hb[i][2] +
+ workspace->f_tor[i][2] + workspace->f_con[i][2] +
+ workspace->f_vdw[i][2] + workspace->f_ele[i][2] );
+
+ fflush(out_control->ftot2);
}
void Init_Force_Test_Functions( )
{
- Print_Interactions[0] = Print_Bond_Orders;
- Print_Interactions[1] = Print_Bond_Forces;
- Print_Interactions[2] = Print_LonePair_Forces;
- Print_Interactions[3] = Print_OverUnderCoor_Forces;
- Print_Interactions[4] = Print_Three_Body_Forces;
- Print_Interactions[5] = Print_Four_Body_Forces;
- Print_Interactions[6] = Print_Hydrogen_Bond_Forces;
- Print_Interactions[7] = Dummy_Printer;
- Print_Interactions[8] = Dummy_Printer;
- Print_Interactions[9] = Dummy_Printer;
+ Print_Interactions[0] = Print_Bond_Orders;
+ Print_Interactions[1] = Print_Bond_Forces;
+ Print_Interactions[2] = Print_LonePair_Forces;
+ Print_Interactions[3] = Print_OverUnderCoor_Forces;
+ Print_Interactions[4] = Print_Three_Body_Forces;
+ Print_Interactions[5] = Print_Four_Body_Forces;
+ Print_Interactions[6] = Print_Hydrogen_Bond_Forces;
+ Print_Interactions[7] = Dummy_Printer;
+ Print_Interactions[8] = Dummy_Printer;
+ Print_Interactions[9] = Dummy_Printer;
}
#endif
char *Get_Element( reax_system *system, int i )
{
- return &( system->reaxprm.sbp[system->atoms[i].type].name[0] );
+ return &( system->reaxprm.sbp[system->atoms[i].type].name[0] );
}
char *Get_Atom_Name( reax_system *system, int i )
{
- return &(system->atoms[i].name[0]);
+ return &(system->atoms[i].name[0]);
}
/* near nbrs contain both i-j, j-i nbrhood info */
-void Print_Near_Neighbors( reax_system *system, control_params *control,
- static_storage *workspace, list **lists )
+void Print_Near_Neighbors( reax_system *system, control_params *control,
+ static_storage *workspace, list **lists )
{
- int i, j, id_i, id_j;
- char fname[MAX_STR];
- FILE *fout;
- list *near_nbrs = &((*lists)[NEAR_NBRS]);
-
- sprintf( fname, "%s.near_nbrs", control->sim_name );
- fout = fopen( fname, "w" );
-
- fprintf( fout, "hello:!\n" );
-
- for( i = 0; i < system->N; ++i ) {
- id_i = workspace->orig_id[i];
-
- for( j = Start_Index(i,near_nbrs); j < End_Index(i,near_nbrs); ++j ) {
- id_j = workspace->orig_id[near_nbrs->select.near_nbr_list[j].nbr];
-
- // if( id_i < id_j )
- fprintf( fout, "%6d%6d%23.15e%23.15e%23.15e%23.15e\n",
- id_i, id_j,
- near_nbrs->select.near_nbr_list[j].d,
- near_nbrs->select.near_nbr_list[j].dvec[0],
- near_nbrs->select.near_nbr_list[j].dvec[1],
- near_nbrs->select.near_nbr_list[j].dvec[2] );
+ int i, j, id_i, id_j;
+ char fname[MAX_STR];
+ FILE *fout;
+ list *near_nbrs = &((*lists)[NEAR_NBRS]);
+
+ sprintf( fname, "%s.near_nbrs", control->sim_name );
+ fout = fopen( fname, "w" );
+
+ fprintf( fout, "hello:!\n" );
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ id_i = workspace->orig_id[i];
+
+ for ( j = Start_Index(i, near_nbrs); j < End_Index(i, near_nbrs); ++j )
+ {
+ id_j = workspace->orig_id[near_nbrs->select.near_nbr_list[j].nbr];
+
+ // if( id_i < id_j )
+ fprintf( fout, "%6d%6d%23.15e%23.15e%23.15e%23.15e\n",
+ id_i, id_j,
+ near_nbrs->select.near_nbr_list[j].d,
+ near_nbrs->select.near_nbr_list[j].dvec[0],
+ near_nbrs->select.near_nbr_list[j].dvec[1],
+ near_nbrs->select.near_nbr_list[j].dvec[2] );
+ }
}
- }
-
- fclose( fout );
+
+ fclose( fout );
}
/* near nbrs contain both i-j, j-i nbrhood info */
-void Print_Near_Neighbors2( reax_system *system, control_params *control,
- static_storage *workspace, list **lists )
+void Print_Near_Neighbors2( reax_system *system, control_params *control,
+ static_storage *workspace, list **lists )
{
- int i, j, id_i, id_j;
- char fname[MAX_STR];
- FILE *fout;
- list *near_nbrs = &((*lists)[NEAR_NBRS]);
-
- sprintf( fname, "%s.near_nbrs_lgj", control->sim_name );
- fout = fopen( fname, "w" );
-
- for( i = 0; i < system->N; ++i ) {
- id_i = workspace->orig_id[i];
- fprintf( fout, "%6d:",id_i);
- for( j = Start_Index(i,near_nbrs); j < End_Index(i,near_nbrs); ++j ) {
- id_j = workspace->orig_id[near_nbrs->select.near_nbr_list[j].nbr];
- fprintf( fout, "%6d", id_j);
-
- /* fprintf( fout, "%6d%6d%23.15e%23.15e%23.15e%23.15e\n",
- id_i, id_j,
- near_nbrs->select.near_nbr_list[j].d,
- near_nbrs->select.near_nbr_list[j].dvec[0],
- near_nbrs->select.near_nbr_list[j].dvec[1],
- near_nbrs->select.near_nbr_list[j].dvec[2] ); */
+ int i, j, id_i, id_j;
+ char fname[MAX_STR];
+ FILE *fout;
+ list *near_nbrs = &((*lists)[NEAR_NBRS]);
+
+ sprintf( fname, "%s.near_nbrs_lgj", control->sim_name );
+ fout = fopen( fname, "w" );
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ id_i = workspace->orig_id[i];
+ fprintf( fout, "%6d:", id_i);
+ for ( j = Start_Index(i, near_nbrs); j < End_Index(i, near_nbrs); ++j )
+ {
+ id_j = workspace->orig_id[near_nbrs->select.near_nbr_list[j].nbr];
+ fprintf( fout, "%6d", id_j);
+
+ /* fprintf( fout, "%6d%6d%23.15e%23.15e%23.15e%23.15e\n",
+ id_i, id_j,
+ near_nbrs->select.near_nbr_list[j].d,
+ near_nbrs->select.near_nbr_list[j].dvec[0],
+ near_nbrs->select.near_nbr_list[j].dvec[1],
+ near_nbrs->select.near_nbr_list[j].dvec[2] ); */
+ }
+ fprintf( fout, "\n");
}
- fprintf( fout, "\n");
- }
-
- fclose( fout );
+
+ fclose( fout );
}
/* far nbrs contain only i-j nbrhood info, no j-i. */
-void Print_Far_Neighbors( reax_system *system, control_params *control,
- static_storage *workspace, list **lists )
+void Print_Far_Neighbors( reax_system *system, control_params *control,
+ static_storage *workspace, list **lists )
{
- int i, j, id_i, id_j;
- char fname[MAX_STR];
- FILE *fout;
- list *far_nbrs = &((*lists)[FAR_NBRS]);
-
- sprintf( fname, "%s.far_nbrs", control->sim_name );
- fout = fopen( fname, "w" );
-
- for( i = 0; i < system->N; ++i ) {
- id_i = workspace->orig_id[i];
-
- for( j = Start_Index(i, far_nbrs); j < End_Index(i, far_nbrs); ++j ) {
- id_j = workspace->orig_id[far_nbrs->select.far_nbr_list[j].nbr];
-
- fprintf( fout, "%6d%6d%23.15e%23.15e%23.15e%23.15e\n",
- id_i, id_j,
- far_nbrs->select.far_nbr_list[j].d,
- far_nbrs->select.far_nbr_list[j].dvec[0],
- far_nbrs->select.far_nbr_list[j].dvec[1],
- far_nbrs->select.far_nbr_list[j].dvec[2] );
-
- fprintf( fout, "%6d%6d%23.15e%23.15e%23.15e%23.15e\n",
- id_j, id_i,
- far_nbrs->select.far_nbr_list[j].d,
- -far_nbrs->select.far_nbr_list[j].dvec[0],
- -far_nbrs->select.far_nbr_list[j].dvec[1],
- -far_nbrs->select.far_nbr_list[j].dvec[2] );
+ int i, j, id_i, id_j;
+ char fname[MAX_STR];
+ FILE *fout;
+ list *far_nbrs = &((*lists)[FAR_NBRS]);
+
+ sprintf( fname, "%s.far_nbrs", control->sim_name );
+ fout = fopen( fname, "w" );
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ id_i = workspace->orig_id[i];
+
+ for ( j = Start_Index(i, far_nbrs); j < End_Index(i, far_nbrs); ++j )
+ {
+ id_j = workspace->orig_id[far_nbrs->select.far_nbr_list[j].nbr];
+
+ fprintf( fout, "%6d%6d%23.15e%23.15e%23.15e%23.15e\n",
+ id_i, id_j,
+ far_nbrs->select.far_nbr_list[j].d,
+ far_nbrs->select.far_nbr_list[j].dvec[0],
+ far_nbrs->select.far_nbr_list[j].dvec[1],
+ far_nbrs->select.far_nbr_list[j].dvec[2] );
+
+ fprintf( fout, "%6d%6d%23.15e%23.15e%23.15e%23.15e\n",
+ id_j, id_i,
+ far_nbrs->select.far_nbr_list[j].d,
+ -far_nbrs->select.far_nbr_list[j].dvec[0],
+ -far_nbrs->select.far_nbr_list[j].dvec[1],
+ -far_nbrs->select.far_nbr_list[j].dvec[2] );
+ }
}
- }
-
- fclose( fout );
+
+ fclose( fout );
}
-int fn_qsort_intcmp( const void *a, const void *b )
-{
- return( *(int *)a - *(int *)b);
-}
+int fn_qsort_intcmp( const void *a, const void *b )
+{
+ return ( *(int *)a - * (int *)b);
+}
-void Print_Far_Neighbors2( reax_system *system, control_params *control,
- static_storage *workspace, list **lists )
+void Print_Far_Neighbors2( reax_system *system, control_params *control,
+ static_storage *workspace, list **lists )
{
- int i, j, id_i, id_j;
- char fname[MAX_STR];
- FILE *fout;
- list *far_nbrs = &((*lists)[FAR_NBRS]);
-
- sprintf( fname, "%s.far_nbrs_lgj", control->sim_name );
- fout = fopen( fname, "w" );
- int num=0;
- int temp[500];
-
- for( i = 0; i < system->N; ++i ) {
- id_i = workspace->orig_id[i];
- num=0;
- fprintf( fout, "%6d:",id_i);
-
- for( j = Start_Index(i, far_nbrs); j < End_Index(i, far_nbrs); ++j ) {
- id_j = workspace->orig_id[far_nbrs->select.far_nbr_list[j].nbr];
- temp[num++] = id_j;
+ int i, j, id_i, id_j;
+ char fname[MAX_STR];
+ FILE *fout;
+ list *far_nbrs = &((*lists)[FAR_NBRS]);
+
+ sprintf( fname, "%s.far_nbrs_lgj", control->sim_name );
+ fout = fopen( fname, "w" );
+ int num = 0;
+ int temp[500];
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ id_i = workspace->orig_id[i];
+ num = 0;
+ fprintf( fout, "%6d:", id_i);
+
+ for ( j = Start_Index(i, far_nbrs); j < End_Index(i, far_nbrs); ++j )
+ {
+ id_j = workspace->orig_id[far_nbrs->select.far_nbr_list[j].nbr];
+ temp[num++] = id_j;
+ }
+ qsort(&temp, num, sizeof(int), fn_qsort_intcmp);
+ for (j = 0; j < num; j++)
+ fprintf(fout, "%6d", temp[j]);
+ fprintf( fout, "\n");
}
- qsort(&temp, num, sizeof(int), fn_qsort_intcmp);
- for(j=0; j < num; j++)
- fprintf(fout, "%6d",temp[j]);
- fprintf( fout, "\n");
- }
- fclose( fout );
+ fclose( fout );
}
-void Print_Total_Force( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+void Print_Total_Force( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int i;
+ int i;
#if !defined(TEST_FORCES)
- char temp[1000];
- sprintf( temp, "%s.ftot", control->sim_name );
- out_control->ftot = fopen( temp, "w" );
+ char temp[1000];
+ sprintf( temp, "%s.ftot", control->sim_name );
+ out_control->ftot = fopen( temp, "w" );
#endif
- for( i = 0; i < system->N; ++i )
- fprintf(out_control->ftot, "%6d %23.15e %23.15e %23.15e\n",
- //fprintf(out_control->ftot, "%6d %19.9e %19.9e %19.9e\n",
- //fprintf(out_control->ftot, "%3d %12.6f %12.6f %12.6f\n",
- workspace->orig_id[i],
- system->atoms[i].f[0],system->atoms[i].f[1],system->atoms[i].f[2]);
+ for ( i = 0; i < system->N; ++i )
+ fprintf(out_control->ftot, "%6d %23.15e %23.15e %23.15e\n",
+ //fprintf(out_control->ftot, "%6d %19.9e %19.9e %19.9e\n",
+ //fprintf(out_control->ftot, "%3d %12.6f %12.6f %12.6f\n",
+ workspace->orig_id[i],
+ system->atoms[i].f[0], system->atoms[i].f[1], system->atoms[i].f[2]);
- fflush(out_control->ftot);
+ fflush(out_control->ftot);
#if !defined(TEST_FORCES)
- fclose(out_control->ftot);
+ fclose(out_control->ftot);
#endif
}
-void Output_Results( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+void Output_Results( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int i, type_i, f_update;
- real q;
- real t_elapsed = 0;;
-
-
- /* Compute Polarization Energy */
- data->E_Pol = 0.0;
- for( i = 0; i < system->N; i++ ) {
- q = system->atoms[i].q;
- type_i = system->atoms[i].type;
-
- data->E_Pol += ( system->reaxprm.sbp[ type_i ].chi * q +
- (system->reaxprm.sbp[ type_i ].eta / 2.0) * SQR(q) ) *
- KCALpMOL_to_EV;
- /* fprintf( stderr, "%6d%23.15e%23.15e%23.15e%23.15e\n",
- i, q, system->reaxprm.sbp[ type_i ].chi,
- system->reaxprm.sbp[ type_i ].eta, data->E_Pol ); */
- }
-
- data->E_Pot = data->E_BE + data->E_Ov + data->E_Un + data->E_Lp +
- data->E_Ang + data->E_Pen + data->E_Coa + data->E_HB +
- data->E_Tor + data->E_Con +
- data->E_vdW + data->E_Ele + data->E_Pol;
-
- data->E_Tot = data->E_Pot + E_CONV*data->E_Kin;
-
-
- /* output energies if it is the time */
- if( out_control->energy_update_freq > 0 &&
- data->step % out_control->energy_update_freq == 0 ) {
+ int i, type_i, f_update;
+ real q;
+ real t_elapsed = 0;;
+
+
+ /* Compute Polarization Energy */
+ data->E_Pol = 0.0;
+ for ( i = 0; i < system->N; i++ )
+ {
+ q = system->atoms[i].q;
+ type_i = system->atoms[i].type;
+
+ data->E_Pol += ( system->reaxprm.sbp[ type_i ].chi * q +
+ (system->reaxprm.sbp[ type_i ].eta / 2.0) * SQR(q) ) *
+ KCALpMOL_to_EV;
+ /* fprintf( stderr, "%6d%23.15e%23.15e%23.15e%23.15e\n",
+ i, q, system->reaxprm.sbp[ type_i ].chi,
+ system->reaxprm.sbp[ type_i ].eta, data->E_Pol ); */
+ }
+
+ data->E_Pot = data->E_BE + data->E_Ov + data->E_Un + data->E_Lp +
+ data->E_Ang + data->E_Pen + data->E_Coa + data->E_HB +
+ data->E_Tor + data->E_Con +
+ data->E_vdW + data->E_Ele + data->E_Pol;
+
+ data->E_Tot = data->E_Pot + E_CONV * data->E_Kin;
+
+
+ /* output energies if it is the time */
+ if ( out_control->energy_update_freq > 0 &&
+ data->step % out_control->energy_update_freq == 0 )
+ {
#if defined(TEST_ENERGY) || defined(DEBUG) || defined(DEBUG_FOCUS)
- fprintf( out_control->out,
- "%-6d%24.15e%24.15e%24.15e%13.5f%13.5f%16.5f%13.5f%13.5f\n",
- data->step, data->E_Tot, data->E_Pot, E_CONV*data->E_Kin,
- data->therm.T, control->T, system->box.volume, data->iso_bar.P,
- (control->P[0] + control->P[1] + control->P[2])/3 );
-
- fprintf( out_control->pot,
- "%-6d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
- data->step,
- data->E_BE,
- data->E_Ov + data->E_Un, data->E_Lp,
- data->E_Ang+data->E_Pen, data->E_Coa, data->E_HB,
- data->E_Tor, data->E_Con,
- data->E_vdW, data->E_Ele, data->E_Pol );
+ fprintf( out_control->out,
+ "%-6d%24.15e%24.15e%24.15e%13.5f%13.5f%16.5f%13.5f%13.5f\n",
+ data->step, data->E_Tot, data->E_Pot, E_CONV * data->E_Kin,
+ data->therm.T, control->T, system->box.volume, data->iso_bar.P,
+ (control->P[0] + control->P[1] + control->P[2]) / 3 );
+
+ fprintf( out_control->pot,
+ "%-6d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
+ data->step,
+ data->E_BE,
+ data->E_Ov + data->E_Un, data->E_Lp,
+ data->E_Ang + data->E_Pen, data->E_Coa, data->E_HB,
+ data->E_Tor, data->E_Con,
+ data->E_vdW, data->E_Ele, data->E_Pol );
#else
- fprintf( out_control->out,
- "%-6d%16.2f%16.2f%16.2f%11.2f%11.2f%13.2f%13.5f%13.5f\n",
- data->step, data->E_Tot, data->E_Pot, E_CONV*data->E_Kin,
- data->therm.T, control->T, system->box.volume, data->iso_bar.P,
- (control->P[0] + control->P[1] + control->P[2])/3 );
-
- fprintf( out_control->pot,
- "%-6d%13.2f%13.2f%13.2f%13.2f%13.2f%13.2f%13.2f%13.2f%13.2f%13.2f%13.2f\n",
- data->step,
- data->E_BE,
- data->E_Ov + data->E_Un, data->E_Lp,
- data->E_Ang + data->E_Pen, data->E_Coa, data->E_HB,
- data->E_Tor, data->E_Con,
- data->E_vdW, data->E_Ele, data->E_Pol );
+ fprintf( out_control->out,
+ "%-6d%16.2f%16.2f%16.2f%11.2f%11.2f%13.2f%13.5f%13.5f\n",
+ data->step, data->E_Tot, data->E_Pot, E_CONV * data->E_Kin,
+ data->therm.T, control->T, system->box.volume, data->iso_bar.P,
+ (control->P[0] + control->P[1] + control->P[2]) / 3 );
+
+ fprintf( out_control->pot,
+ "%-6d%13.2f%13.2f%13.2f%13.2f%13.2f%13.2f%13.2f%13.2f%13.2f%13.2f%13.2f\n",
+ data->step,
+ data->E_BE,
+ data->E_Ov + data->E_Un, data->E_Lp,
+ data->E_Ang + data->E_Pen, data->E_Coa, data->E_HB,
+ data->E_Tor, data->E_Con,
+ data->E_vdW, data->E_Ele, data->E_Pol );
#endif
-
- t_elapsed = Get_Timing_Info( data->timing.total );
- if( data->step == data->prev_steps )
- f_update = 1;
- else f_update = out_control->energy_update_freq;
-
- fprintf( out_control->log,"%6d%10.2f%10.2f%10.2f%10.2f%10.2f%10.2f%10.2f\n",
- data->step, t_elapsed/f_update,
- data->timing.nbrs/f_update,
- data->timing.init_forces/f_update,
- data->timing.bonded/f_update,
- data->timing.nonb/f_update,
- data->timing.QEq/f_update,
- (double)data->timing.matvecs/f_update );
-
- data->timing.total = Get_Time( );
- data->timing.nbrs = 0;
- data->timing.init_forces = 0;
- data->timing.bonded = 0;
- data->timing.nonb = 0;
- data->timing.QEq = 0;
- data->timing.matvecs = 0;
-
- fflush( out_control->out );
- fflush( out_control->pot );
- fflush( out_control->log );
-
- /* output pressure */
- if( control->ensemble == NPT || control->ensemble == iNPT ||
- control->ensemble == sNPT ) {
- fprintf( out_control->prs, "%-8d%13.6f%13.6f%13.6f",
- data->step,
- data->int_press[0], data->int_press[1], data->int_press[2] );
-
- /* external pressure is calculated together with forces */
- fprintf( out_control->prs, "%13.6f%13.6f%13.6f",
- data->ext_press[0], data->ext_press[1], data->ext_press[2] );
-
- fprintf( out_control->prs, "%13.6f\n", data->kin_press );
-
- fprintf( out_control->prs,
- "%-8d%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f\n",
- data->step,
- system->box.box_norms[0], system->box.box_norms[1],
- system->box.box_norms[2],
- data->tot_press[0], data->tot_press[1], data->tot_press[2],
- control->P[0],control->P[1],control->P[2],system->box.volume );
- fflush( out_control->prs);
+
+ t_elapsed = Get_Timing_Info( data->timing.total );
+ if ( data->step == data->prev_steps )
+ f_update = 1;
+ else f_update = out_control->energy_update_freq;
+
+ fprintf( out_control->log, "%6d%10.2f%10.2f%10.2f%10.2f%10.2f%10.2f%10.2f\n",
+ data->step, t_elapsed / f_update,
+ data->timing.nbrs / f_update,
+ data->timing.init_forces / f_update,
+ data->timing.bonded / f_update,
+ data->timing.nonb / f_update,
+ data->timing.QEq / f_update,
+ (double)data->timing.matvecs / f_update );
+
+ data->timing.total = Get_Time( );
+ data->timing.nbrs = 0;
+ data->timing.init_forces = 0;
+ data->timing.bonded = 0;
+ data->timing.nonb = 0;
+ data->timing.QEq = 0;
+ data->timing.matvecs = 0;
+
+ fflush( out_control->out );
+ fflush( out_control->pot );
+ fflush( out_control->log );
+
+ /* output pressure */
+ if ( control->ensemble == NPT || control->ensemble == iNPT ||
+ control->ensemble == sNPT )
+ {
+ fprintf( out_control->prs, "%-8d%13.6f%13.6f%13.6f",
+ data->step,
+ data->int_press[0], data->int_press[1], data->int_press[2] );
+
+ /* external pressure is calculated together with forces */
+ fprintf( out_control->prs, "%13.6f%13.6f%13.6f",
+ data->ext_press[0], data->ext_press[1], data->ext_press[2] );
+
+ fprintf( out_control->prs, "%13.6f\n", data->kin_press );
+
+ fprintf( out_control->prs,
+ "%-8d%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f\n",
+ data->step,
+ system->box.box_norms[0], system->box.box_norms[1],
+ system->box.box_norms[2],
+ data->tot_press[0], data->tot_press[1], data->tot_press[2],
+ control->P[0], control->P[1], control->P[2], system->box.volume );
+ fflush( out_control->prs);
+ }
+ }
+
+ if ( out_control->write_steps > 0 &&
+ data->step % out_control->write_steps == 0 )
+ {
+ // t_start = Get_Time( );
+ out_control->append_traj_frame( system, control, data,
+ workspace, lists, out_control );
+
+ //Write_PDB( system, control, data, workspace, *lists+BONDS, out_control );
+ // t_elapsed = Get_Timing_Info( t_start );
+ // fprintf(stdout, "append_frame took %.6f seconds\n", t_elapsed );
}
- }
-
- if( out_control->write_steps > 0 &&
- data->step % out_control->write_steps == 0 ){
- // t_start = Get_Time( );
- out_control->append_traj_frame( system, control, data,
- workspace, lists, out_control );
-
- //Write_PDB( system, control, data, workspace, *lists+BONDS, out_control );
- // t_elapsed = Get_Timing_Info( t_start );
- // fprintf(stdout, "append_frame took %.6f seconds\n", t_elapsed );
- }
-
- // fprintf( stderr, "output_results... done\n" );
+
+ // fprintf( stderr, "output_results... done\n" );
}
-void Print_Linear_System( reax_system *system, control_params *control,
- static_storage *workspace, int step )
+void Print_Linear_System( reax_system *system, control_params *control,
+ static_storage *workspace, int step )
{
- int i, j;
- char fname[100];
- sparse_matrix *H;
- FILE *out;
-
- sprintf( fname, "%s.state%d.out", control->sim_name, step );
- out = fopen( fname, "w" );
-
- for( i = 0; i < system->N; i++ )
- fprintf( out, "%6d%2d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
- workspace->orig_id[i],system->atoms[i].type,
- system->atoms[i].x[0], system->atoms[i].x[1],
- system->atoms[i].x[2],
- workspace->s[0][i], workspace->b_s[i],
- workspace->t[0][i], workspace->b_t[i] );
- fclose( out );
-
- // sprintf( fname, "x2_%d", step );
- // out = fopen( fname, "w" );
- // for( i = 0; i < system->N; i++ )
- // fprintf( out, "%g\n", workspace->s_t[i+system->N] );
- // fclose( out );
-
-
- sprintf( fname, "%s.H%d.out", control->sim_name, step );
- out = fopen( fname, "w" );
- H = workspace->H;
-
- for( i = 0; i < system->N; ++i ) {
- for( j = H->start[i]; j < H->start[i+1]-1; ++j ) {
- fprintf( out, "%6d%6d %24.15e\n",
- workspace->orig_id[i], workspace->orig_id[H->entries[j].j],
- H->entries[j].val );
-
- fprintf( out, "%6d%6d %24.15e\n",
- workspace->orig_id[H->entries[j].j], workspace->orig_id[i],
- H->entries[j].val );
- }
- // the diagonal entry
- fprintf( out, "%6d%6d %24.15e\n",
- workspace->orig_id[i], workspace->orig_id[i], H->entries[j].val );
- }
-
- fclose( out );
-
- /*sprintf( fname, "%s.b_s%d", control->sim_name, step );
+ int i, j;
+ char fname[100];
+ sparse_matrix *H;
+ FILE *out;
+
+ sprintf( fname, "%s.state%d.out", control->sim_name, step );
out = fopen( fname, "w" );
- for( i = 0; i < system->N; i++ )
- fprintf( out, "%12.7f\n", workspace->b_s[i] );
+
+ for ( i = 0; i < system->N; i++ )
+ fprintf( out, "%6d%2d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
+ workspace->orig_id[i], system->atoms[i].type,
+ system->atoms[i].x[0], system->atoms[i].x[1],
+ system->atoms[i].x[2],
+ workspace->s[0][i], workspace->b_s[i],
+ workspace->t[0][i], workspace->b_t[i] );
fclose( out );
-
- sprintf( fname, "%s.b_t%d", control->sim_name, step );
+
+ // sprintf( fname, "x2_%d", step );
+ // out = fopen( fname, "w" );
+ // for( i = 0; i < system->N; i++ )
+ // fprintf( out, "%g\n", workspace->s_t[i+system->N] );
+ // fclose( out );
+
+
+ sprintf( fname, "%s.H%d.out", control->sim_name, step );
out = fopen( fname, "w" );
- for( i = 0; i < system->N; i++ )
- fprintf( out, "%12.7f\n", workspace->b_t[i] );
- fclose( out );*/
+ H = workspace->H;
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ for ( j = H->start[i]; j < H->start[i + 1] - 1; ++j )
+ {
+ fprintf( out, "%6d%6d %24.15e\n",
+ workspace->orig_id[i], workspace->orig_id[H->entries[j].j],
+ H->entries[j].val );
+
+ fprintf( out, "%6d%6d %24.15e\n",
+ workspace->orig_id[H->entries[j].j], workspace->orig_id[i],
+ H->entries[j].val );
+ }
+ // the diagonal entry
+ fprintf( out, "%6d%6d %24.15e\n",
+ workspace->orig_id[i], workspace->orig_id[i], H->entries[j].val );
+ }
+
+ fclose( out );
+
+ /*sprintf( fname, "%s.b_s%d", control->sim_name, step );
+ out = fopen( fname, "w" );
+ for( i = 0; i < system->N; i++ )
+ fprintf( out, "%12.7f\n", workspace->b_s[i] );
+ fclose( out );
+
+ sprintf( fname, "%s.b_t%d", control->sim_name, step );
+ out = fopen( fname, "w" );
+ for( i = 0; i < system->N; i++ )
+ fprintf( out, "%12.7f\n", workspace->b_t[i] );
+ fclose( out );*/
}
-void Print_Charges( reax_system *system, control_params *control,
- static_storage *workspace, int step )
+void Print_Charges( reax_system *system, control_params *control,
+ static_storage *workspace, int step )
{
- int i;
- char fname[100];
- FILE *fout;
+ int i;
+ char fname[100];
+ FILE *fout;
- sprintf( fname, "%s.q%d", control->sim_name, step );
- fout = fopen( fname, "w" );
+ sprintf( fname, "%s.q%d", control->sim_name, step );
+ fout = fopen( fname, "w" );
- for( i = 0; i < system->N; ++i )
- fprintf( fout, "%6d%12.7f%12.7f%12.7f\n",
- workspace->orig_id[i],
- workspace->s[0][i], workspace->t[0][i], system->atoms[i].q );
+ for ( i = 0; i < system->N; ++i )
+ fprintf( fout, "%6d%12.7f%12.7f%12.7f\n",
+ workspace->orig_id[i],
+ workspace->s[0][i], workspace->t[0][i], system->atoms[i].q );
- fclose( fout );
+ fclose( fout );
}
-void Print_Soln( static_storage *workspace,
- real *x, real *b_prm, real *b, int N )
+void Print_Soln( static_storage *workspace,
+ real *x, real *b_prm, real *b, int N )
{
- int i;
+ int i;
- fprintf( stdout, "%6s%10s%10s%10s\n", "id", "x", "b_prm", "b" );
+ fprintf( stdout, "%6s%10s%10s%10s\n", "id", "x", "b_prm", "b" );
- for( i = 0; i < N; ++i )
- fprintf( stdout, "%6d%10.4f%10.4f%10.4f\n",
- workspace->orig_id[i], x[i], b_prm[i], b[i] );
+ for ( i = 0; i < N; ++i )
+ fprintf( stdout, "%6d%10.4f%10.4f%10.4f\n",
+ workspace->orig_id[i], x[i], b_prm[i], b[i] );
- fflush( stdout );
+ fflush( stdout );
}
void Print_Sparse_Matrix( sparse_matrix *A )
{
- int i, j;
-
- for( i = 0; i < A->n; ++i ) {
- fprintf( stderr, "i:%d j(val):", i );
- for( j = A->start[i]; j < A->start[i+1]; ++j )
- fprintf( stderr, "%d(%.4f) ", A->entries[j].j, A->entries[j].val );
- fprintf( stderr, "\n" );
- }
+ int i, j;
+
+ for ( i = 0; i < A->n; ++i )
+ {
+ fprintf( stderr, "i:%d j(val):", i );
+ for ( j = A->start[i]; j < A->start[i + 1]; ++j )
+ fprintf( stderr, "%d(%.4f) ", A->entries[j].j, A->entries[j].val );
+ fprintf( stderr, "\n" );
+ }
}
void Print_Sparse_Matrix2( sparse_matrix *A, char *fname )
{
- int i, j;
- FILE *f = fopen( fname, "w" );
+ int i, j;
+ FILE *f = fopen( fname, "w" );
- for( i = 0; i < A->n; ++i )
- for( j = A->start[i]; j < A->start[i+1]; ++j )
- fprintf( f, "%d%d %.15e\n", A->entries[j].j, i, A->entries[j].val );
+ for ( i = 0; i < A->n; ++i )
+ for ( j = A->start[i]; j < A->start[i + 1]; ++j )
+ fprintf( f, "%d%d %.15e\n", A->entries[j].j, i, A->entries[j].val );
- fclose(f);
+ fclose(f);
}
void Print_Bonds( reax_system *system, list *bonds, char *fname )
{
- int i, pj;
- bond_data *pbond;
- bond_order_data *bo_ij;
- FILE *f = fopen( fname, "w" );
-
- for( i = 0; i < system->N; ++i )
- for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
- pbond = &(bonds->select.bond_list[pj]);
- bo_ij = &(pbond->bo_data);
- //fprintf( f, "%6d%6d%23.15e%23.15e%23.15e%23.15e%23.15e\n",
- // i+1, pbond->nbr+1, pbond->d,
- // bo_ij->BO, bo_ij->BO_s, bo_ij->BO_pi, bo_ij->BO_pi2 );
- fprintf( f, "%6d%6d %9.5f %9.5f\n",
- i+1, pbond->nbr+1, pbond->d, bo_ij->BO );
- }
- fclose(f);
+ int i, pj;
+ bond_data *pbond;
+ bond_order_data *bo_ij;
+ FILE *f = fopen( fname, "w" );
+
+ for ( i = 0; i < system->N; ++i )
+ for ( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
+ {
+ pbond = &(bonds->select.bond_list[pj]);
+ bo_ij = &(pbond->bo_data);
+ //fprintf( f, "%6d%6d%23.15e%23.15e%23.15e%23.15e%23.15e\n",
+ // i+1, pbond->nbr+1, pbond->d,
+ // bo_ij->BO, bo_ij->BO_s, bo_ij->BO_pi, bo_ij->BO_pi2 );
+ fprintf( f, "%6d%6d %9.5f %9.5f\n",
+ i + 1, pbond->nbr + 1, pbond->d, bo_ij->BO );
+ }
+ fclose(f);
}
void Print_Bond_List2( reax_system *system, list *bonds, char *fname )
{
- int i,j, id_i, id_j, nbr, pj;
- FILE *f = fopen( fname, "w" );
- int temp[500];
- int num=0;
-
- for( i = 0; i < system->N; ++i ) {
- num=0;
- id_i = i+1; //system->atoms[i].orig_id;
- fprintf( f, "%6d:", id_i);
- for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
- nbr = bonds->select.bond_list[pj].nbr;
- id_j = nbr+1; //system->my_atoms[nbr].orig_id;
- if( id_i < id_j )
- temp[num++] = id_j;
+ int i, j, id_i, id_j, nbr, pj;
+ FILE *f = fopen( fname, "w" );
+ int temp[500];
+ int num = 0;
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ num = 0;
+ id_i = i + 1; //system->atoms[i].orig_id;
+ fprintf( f, "%6d:", id_i);
+ for ( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
+ {
+ nbr = bonds->select.bond_list[pj].nbr;
+ id_j = nbr + 1; //system->my_atoms[nbr].orig_id;
+ if ( id_i < id_j )
+ temp[num++] = id_j;
+ }
+
+ qsort(&temp, num, sizeof(int), fn_qsort_intcmp);
+ for (j = 0; j < num; j++)
+ fprintf(f, "%6d", temp[j] );
+ fprintf(f, "\n");
}
-
- qsort(&temp, num, sizeof(int), fn_qsort_intcmp);
- for(j=0; j < num; j++)
- fprintf(f, "%6d", temp[j] );
- fprintf(f, "\n");
- }
}
#ifdef LGJ
Print_XYZ_Serial(reax_system* system, static_storage *workspace)
{
- rvec p;
-
- char fname[100];
- FILE *fout;
- sprintf( fname, "READ_PDB.0" );
- fout = fopen( fname, "w" );
-int i;
-for(i=0; i < system->N; i++)
- fprintf( fout, "%6d%24.15e%24.15e%24.15e\n",
- workspace->orig_id[i],
- p[0] = system->atoms[i].x[0],
- p[1] = system->atoms[i].x[1],
- p[2] = system->atoms[i].x[2]);
-
-
- fclose(fout);
+ rvec p;
+
+ char fname[100];
+ FILE *fout;
+ sprintf( fname, "READ_PDB.0" );
+ fout = fopen( fname, "w" );
+ int i;
+ for (i = 0; i < system->N; i++)
+ fprintf( fout, "%6d%24.15e%24.15e%24.15e\n",
+ workspace->orig_id[i],
+ p[0] = system->atoms[i].x[0],
+ p[1] = system->atoms[i].x[1],
+ p[2] = system->atoms[i].x[2]);
+
+
+ fclose(fout);
}
#endif
diff --git a/puremd_rc_1003/sPuReMD/print_utils.h b/puremd_rc_1003/sPuReMD/print_utils.h
index c13cc87b2b6e03a90cfbbcb0183b05663c25596c..8b3b363571ca5b7c50195b4c91bca8951c1caa7b 100644
--- a/puremd_rc_1003/sPuReMD/print_utils.h
+++ b/puremd_rc_1003/sPuReMD/print_utils.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -24,28 +24,28 @@
#include "mytypes.h"
-typedef void (*print_interaction)(reax_system*,control_params*,simulation_data*,
- static_storage*,list**,output_controls*);
+typedef void (*print_interaction)(reax_system*, control_params*, simulation_data*,
+ static_storage*, list**, output_controls*);
print_interaction Print_Interactions[NO_OF_INTERACTIONS];
char *Get_Element( reax_system*, int );
char *Get_Atom_Name( reax_system*, int );
-void Print_Near_Neighbors( reax_system*, control_params*, static_storage*,
- list** );
+void Print_Near_Neighbors( reax_system*, control_params*, static_storage*,
+ list** );
-void Print_Far_Neighbors( reax_system*, control_params*, static_storage*,
- list** );
+void Print_Far_Neighbors( reax_system*, control_params*, static_storage*,
+ list** );
-void Print_Total_Force( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+void Print_Total_Force( reax_system*, control_params*, simulation_data*,
+ static_storage*, list**, output_controls* );
-void Output_Results( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+void Output_Results( reax_system*, control_params*, simulation_data*,
+ static_storage*, list**, output_controls* );
-void Print_Bond_Orders( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+void Print_Bond_Orders( reax_system*, control_params*, simulation_data*,
+ static_storage*, list**, output_controls* );
void Print_Linear_System( reax_system*, control_params*, static_storage*, int );
@@ -61,24 +61,24 @@ void Print_Bonds( reax_system*, list*, char* );
void Print_Bond_List2( reax_system*, list*, char* );
#ifdef TEST_FORCES
-void Dummy_Printer( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
-void Print_Bond_Forces( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
-void Print_LonePair_Forces( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+void Dummy_Printer( reax_system*, control_params*, simulation_data*,
+ static_storage*, list**, output_controls* );
+void Print_Bond_Forces( reax_system*, control_params*, simulation_data*,
+ static_storage*, list**, output_controls* );
+void Print_LonePair_Forces( reax_system*, control_params*, simulation_data*,
+ static_storage*, list**, output_controls* );
void Print_OverUnderCoor_Forces(reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls*);
-void Print_Three_Body_Forces( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, list**, output_controls*);
+void Print_Three_Body_Forces( reax_system*, control_params*, simulation_data*,
+ static_storage*, list**, output_controls* );
void Print_Hydrogen_Bond_Forces(reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls*);
-void Print_Four_Body_Forces( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
-void Print_vdW_Coulomb_Forces( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
-void Compare_Total_Forces( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, list**, output_controls*);
+void Print_Four_Body_Forces( reax_system*, control_params*, simulation_data*,
+ static_storage*, list**, output_controls* );
+void Print_vdW_Coulomb_Forces( reax_system*, control_params*, simulation_data*,
+ static_storage*, list**, output_controls* );
+void Compare_Total_Forces( reax_system*, control_params*, simulation_data*,
+ static_storage*, list**, output_controls* );
void Init_Force_Test_Functions( );
#endif
diff --git a/puremd_rc_1003/sPuReMD/random.c b/puremd_rc_1003/sPuReMD/random.c
index 0771d63561a2df632a495bd75859e904683b2cb6..f3a5096c65485111fb5cba7321976518a2e42972 100644
--- a/puremd_rc_1003/sPuReMD/random.c
+++ b/puremd_rc_1003/sPuReMD/random.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -27,7 +27,7 @@
0 <= Random(range) < range */
double Random(double range)
{
- return (random()*range)/2147483647L;
+ return (random() * range) / 2147483647L;
}
/* This function seeds the system pseudo random number generator with
@@ -35,23 +35,23 @@ double Random(double range)
the system */
void Randomize()
{
- srandom(time(NULL));
+ srandom(time(NULL));
}
/* GRandom return random number with gaussian distribution with mean
and standard deviation "sigma" */
double GRandom(double mean, double sigma)
{
- double v1 = Random(2.0) - 1.0;
- double v2 = Random(2.0) - 1.0;
- double rsq = v1*v1 + v2*v2;
+ double v1 = Random(2.0) - 1.0;
+ double v2 = Random(2.0) - 1.0;
+ double rsq = v1 * v1 + v2 * v2;
- while (rsq >= 1.0 || rsq == 0.0)
+ while (rsq >= 1.0 || rsq == 0.0)
{
- v1 = Random(2.0) - 1.0;
- v2 = Random(2.0) - 1.0;
- rsq = v1*v1 + v2*v2;
+ v1 = Random(2.0) - 1.0;
+ v2 = Random(2.0) - 1.0;
+ rsq = v1 * v1 + v2 * v2;
}
- return mean+v1*sigma*sqrt(-2.0*log(rsq)/rsq);
+ return mean + v1 * sigma * sqrt(-2.0 * log(rsq) / rsq);
}
diff --git a/puremd_rc_1003/sPuReMD/random.h b/puremd_rc_1003/sPuReMD/random.h
index 78d9a3951dde54bf5667a2619b883af1ca242e9e..a90b181dc78a9491944ffc4b666ba4201ae32e26 100644
--- a/puremd_rc_1003/sPuReMD/random.h
+++ b/puremd_rc_1003/sPuReMD/random.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
diff --git a/puremd_rc_1003/sPuReMD/reset_utils.c b/puremd_rc_1003/sPuReMD/reset_utils.c
index 7c0e73530afd3ba710493de8b594bd26885ecbe4..36d6b414063c4c37a7399c07b039cdc0b80d8a85 100644
--- a/puremd_rc_1003/sPuReMD/reset_utils.c
+++ b/puremd_rc_1003/sPuReMD/reset_utils.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -26,138 +26,140 @@
void Reset_Atoms( reax_system* system )
{
- int i;
+ int i;
- for( i = 0; i < system->N; ++i )
- memset( system->atoms[i].f, 0.0, sizeof(rvec) );
+ for ( i = 0; i < system->N; ++i )
+ memset( system->atoms[i].f, 0.0, sizeof(rvec) );
}
void Reset_Pressures( simulation_data *data )
{
- rtensor_MakeZero( data->flex_bar.P );
- data->iso_bar.P = 0;
- rvec_MakeZero( data->int_press );
- rvec_MakeZero( data->ext_press );
- /* fprintf( stderr, "reset: ext_press (%12.6f %12.6f %12.6f)\n",
- data->ext_press[0], data->ext_press[1], data->ext_press[2] ); */
+ rtensor_MakeZero( data->flex_bar.P );
+ data->iso_bar.P = 0;
+ rvec_MakeZero( data->int_press );
+ rvec_MakeZero( data->ext_press );
+ /* fprintf( stderr, "reset: ext_press (%12.6f %12.6f %12.6f)\n",
+ data->ext_press[0], data->ext_press[1], data->ext_press[2] ); */
}
void Reset_Simulation_Data( simulation_data* data )
{
- data->E_BE = 0;
- data->E_Ov = 0;
- data->E_Un = 0;
- data->E_Lp = 0;
- data->E_Ang = 0;
- data->E_Pen = 0;
- data->E_Coa = 0;
- data->E_HB = 0;
- data->E_Tor = 0;
- data->E_Con = 0;
- data->E_vdW = 0;
- data->E_Ele = 0;
- data->E_Kin = 0;
+ data->E_BE = 0;
+ data->E_Ov = 0;
+ data->E_Un = 0;
+ data->E_Lp = 0;
+ data->E_Ang = 0;
+ data->E_Pen = 0;
+ data->E_Coa = 0;
+ data->E_HB = 0;
+ data->E_Tor = 0;
+ data->E_Con = 0;
+ data->E_vdW = 0;
+ data->E_Ele = 0;
+ data->E_Kin = 0;
}
#ifdef TEST_FORCES
void Reset_Test_Forces( reax_system *system, static_storage *workspace )
{
- memset( workspace->f_ele, 0, system->N * sizeof(rvec) );
- memset( workspace->f_vdw, 0, system->N * sizeof(rvec) );
- memset( workspace->f_bo, 0, system->N * sizeof(rvec) );
- memset( workspace->f_be, 0, system->N * sizeof(rvec) );
- memset( workspace->f_lp, 0, system->N * sizeof(rvec) );
- memset( workspace->f_ov, 0, system->N * sizeof(rvec) );
- memset( workspace->f_un, 0, system->N * sizeof(rvec) );
- memset( workspace->f_ang, 0, system->N * sizeof(rvec) );
- memset( workspace->f_coa, 0, system->N * sizeof(rvec) );
- memset( workspace->f_pen, 0, system->N * sizeof(rvec) );
- memset( workspace->f_hb, 0, system->N * sizeof(rvec) );
- memset( workspace->f_tor, 0, system->N * sizeof(rvec) );
- memset( workspace->f_con, 0, system->N * sizeof(rvec) );
+ memset( workspace->f_ele, 0, system->N * sizeof(rvec) );
+ memset( workspace->f_vdw, 0, system->N * sizeof(rvec) );
+ memset( workspace->f_bo, 0, system->N * sizeof(rvec) );
+ memset( workspace->f_be, 0, system->N * sizeof(rvec) );
+ memset( workspace->f_lp, 0, system->N * sizeof(rvec) );
+ memset( workspace->f_ov, 0, system->N * sizeof(rvec) );
+ memset( workspace->f_un, 0, system->N * sizeof(rvec) );
+ memset( workspace->f_ang, 0, system->N * sizeof(rvec) );
+ memset( workspace->f_coa, 0, system->N * sizeof(rvec) );
+ memset( workspace->f_pen, 0, system->N * sizeof(rvec) );
+ memset( workspace->f_hb, 0, system->N * sizeof(rvec) );
+ memset( workspace->f_tor, 0, system->N * sizeof(rvec) );
+ memset( workspace->f_con, 0, system->N * sizeof(rvec) );
}
#endif
void Reset_Workspace( reax_system *system, static_storage *workspace )
{
- memset( workspace->total_bond_order, 0, system->N * sizeof( real ) );
- memset( workspace->dDeltap_self, 0, system->N * sizeof( rvec ) );
+ memset( workspace->total_bond_order, 0, system->N * sizeof( real ) );
+ memset( workspace->dDeltap_self, 0, system->N * sizeof( rvec ) );
- memset( workspace->CdDelta, 0, system->N * sizeof( real ) );
- //memset( workspace->virial_forces, 0, system->N * sizeof( rvec ) );
+ memset( workspace->CdDelta, 0, system->N * sizeof( real ) );
+ //memset( workspace->virial_forces, 0, system->N * sizeof( rvec ) );
#ifdef TEST_FORCES
- memset( workspace->dDelta, 0, sizeof(rvec) * system->N );
- Reset_Test_Forces( system, workspace );
+ memset( workspace->dDelta, 0, sizeof(rvec) * system->N );
+ Reset_Test_Forces( system, workspace );
#endif
}
-void Reset_Neighbor_Lists( reax_system *system, control_params *control,
- static_storage *workspace, list **lists )
+void Reset_Neighbor_Lists( reax_system *system, control_params *control,
+ static_storage *workspace, list **lists )
{
- int i, tmp;
- list *bonds = (*lists) + BONDS;
- list *hbonds = (*lists) + HBONDS;
-
- for( i = 0; i < system->N; ++i ) {
- tmp = Start_Index( i, bonds );
- Set_End_Index( i, tmp, bonds );
- }
-
- if( control->hb_cut > 0 )
- for( i = 0; i < system->N; ++i )
- if( system->reaxprm.sbp[system->atoms[i].type].p_hbond == 1) {
- tmp = Start_Index( workspace->hbond_index[i], hbonds );
- Set_End_Index( workspace->hbond_index[i], tmp, hbonds );
- /* fprintf( stderr, "i:%d, hbond: %d-%d\n",
- i, Start_Index( workspace->hbond_index[i], hbonds ),
- End_Index( workspace->hbond_index[i], hbonds ) );*/
- }
+ int i, tmp;
+ list *bonds = (*lists) + BONDS;
+ list *hbonds = (*lists) + HBONDS;
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ tmp = Start_Index( i, bonds );
+ Set_End_Index( i, tmp, bonds );
+ }
+
+ if ( control->hb_cut > 0 )
+ for ( i = 0; i < system->N; ++i )
+ if ( system->reaxprm.sbp[system->atoms[i].type].p_hbond == 1)
+ {
+ tmp = Start_Index( workspace->hbond_index[i], hbonds );
+ Set_End_Index( workspace->hbond_index[i], tmp, hbonds );
+ /* fprintf( stderr, "i:%d, hbond: %d-%d\n",
+ i, Start_Index( workspace->hbond_index[i], hbonds ),
+ End_Index( workspace->hbond_index[i], hbonds ) );*/
+ }
}
-void Reset( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace, list **lists )
+void Reset( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace, list **lists )
{
- Reset_Atoms( system );
-
- Reset_Simulation_Data( data );
+ Reset_Atoms( system );
- if( control->ensemble == NPT || control->ensemble == sNPT ||
- control->ensemble == iNPT )
- Reset_Pressures( data );
+ Reset_Simulation_Data( data );
- Reset_Workspace( system, workspace );
+ if ( control->ensemble == NPT || control->ensemble == sNPT ||
+ control->ensemble == iNPT )
+ Reset_Pressures( data );
- Reset_Neighbor_Lists( system, control, workspace, lists );
+ Reset_Workspace( system, workspace );
-#if defined(DEBUG_FOCUS)
- fprintf( stderr, "reset - ");
+ Reset_Neighbor_Lists( system, control, workspace, lists );
+
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "reset - ");
#endif
}
void Reset_Grid( grid *g )
{
- int i, j, k;
+ int i, j, k;
- for( i = 0; i < g->ncell[0]; i++ )
- for( j = 0; j < g->ncell[1]; j++ )
- for( k = 0; k < g->ncell[2]; k++ )
- g->top[i][j][k] = 0;
+ for ( i = 0; i < g->ncell[0]; i++ )
+ for ( j = 0; j < g->ncell[1]; j++ )
+ for ( k = 0; k < g->ncell[2]; k++ )
+ g->top[i][j][k] = 0;
}
void Reset_Marks( grid *g, ivec *grid_stack, int grid_top )
{
- int i;
-
- for( i = 0; i < grid_top; ++i )
- g->mark[grid_stack[i][0]][grid_stack[i][1]][grid_stack[i][2]] = 0;
+ int i;
+
+ for ( i = 0; i < grid_top; ++i )
+ g->mark[grid_stack[i][0]][grid_stack[i][1]][grid_stack[i][2]] = 0;
}
diff --git a/puremd_rc_1003/sPuReMD/reset_utils.h b/puremd_rc_1003/sPuReMD/reset_utils.h
index bda3b39072616bf31991767c3bfdbb7077b7291e..aadfe736a0d5a49883dfe6253304ce38c9fcff92 100644
--- a/puremd_rc_1003/sPuReMD/reset_utils.h
+++ b/puremd_rc_1003/sPuReMD/reset_utils.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -36,11 +36,11 @@ void Reset_Test_Forces( reax_system*, static_storage* );
void Reset_Workspace( reax_system*, static_storage* );
-void Reset_Neighbor_Lists( reax_system*, control_params*,
- static_storage*, list** );
+void Reset_Neighbor_Lists( reax_system*, control_params*,
+ static_storage*, list** );
-void Reset( reax_system*, control_params*, simulation_data*,
- static_storage*, list** );
+void Reset( reax_system*, control_params*, simulation_data*,
+ static_storage*, list** );
//void Reset_Neighbor_Lists( reax_system*, static_storage*, list** );
diff --git a/puremd_rc_1003/sPuReMD/restart.c b/puremd_rc_1003/sPuReMD/restart.c
index c594de14aeda86455adbdf1f92b639bc3b09a296..c15d51c502f5960984c38f5485384c122878b720 100644
--- a/puremd_rc_1003/sPuReMD/restart.c
+++ b/puremd_rc_1003/sPuReMD/restart.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -23,221 +23,225 @@
#include "box.h"
#include "vector.h"
-void Write_Binary_Restart( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace )
+void Write_Binary_Restart( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace )
{
- int i;
- char fname[MAX_STR];
- FILE *fres;
- reax_atom *p_atom;
- restart_header res_header;
- restart_atom res_data;
-
- sprintf( fname, "%s.res%d", control->sim_name, data->step );
- fres = fopen( fname, "wb" );
-
- res_header.step = data->step;
- res_header.N = system->N;
- res_header.T = data->therm.T;
- res_header.xi = data->therm.xi;
- res_header.v_xi = data->therm.v_xi;
- res_header.v_xi_old = data->therm.v_xi_old;
- res_header.G_xi = data->therm.G_xi;
- rtensor_Copy( res_header.box, system->box.box );
- fwrite(&res_header, sizeof(restart_header), 1, fres);
-
- for( i = 0; i < system->N; ++i ) {
- p_atom = &( system->atoms[i] );
- res_data.orig_id = workspace->orig_id[i];
- res_data.type = p_atom->type;
- strncpy( res_data.name, p_atom->name, 8 );
- rvec_Copy( res_data.x, p_atom->x );
- rvec_Copy( res_data.v, p_atom->v );
- fwrite( &res_data, sizeof(restart_atom), 1, fres );
- }
-
- fclose( fres );
-
-#if defined(DEBUG_FOCUS)
+ int i;
+ char fname[MAX_STR];
+ FILE *fres;
+ reax_atom *p_atom;
+ restart_header res_header;
+ restart_atom res_data;
+
+ sprintf( fname, "%s.res%d", control->sim_name, data->step );
+ fres = fopen( fname, "wb" );
+
+ res_header.step = data->step;
+ res_header.N = system->N;
+ res_header.T = data->therm.T;
+ res_header.xi = data->therm.xi;
+ res_header.v_xi = data->therm.v_xi;
+ res_header.v_xi_old = data->therm.v_xi_old;
+ res_header.G_xi = data->therm.G_xi;
+ rtensor_Copy( res_header.box, system->box.box );
+ fwrite(&res_header, sizeof(restart_header), 1, fres);
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ p_atom = &( system->atoms[i] );
+ res_data.orig_id = workspace->orig_id[i];
+ res_data.type = p_atom->type;
+ strncpy( res_data.name, p_atom->name, 8 );
+ rvec_Copy( res_data.x, p_atom->x );
+ rvec_Copy( res_data.v, p_atom->v );
+ fwrite( &res_data, sizeof(restart_atom), 1, fres );
+ }
+
+ fclose( fres );
+
+#if defined(DEBUG_FOCUS)
fprintf( stderr, "write restart - " );
#endif
}
-void Read_Binary_Restart( char *fname, reax_system *system,
- control_params *control, simulation_data *data,
- static_storage *workspace )
+void Read_Binary_Restart( char *fname, reax_system *system,
+ control_params *control, simulation_data *data,
+ static_storage *workspace )
{
- int i;
- FILE *fres;
- reax_atom *p_atom;
- restart_header res_header;
- restart_atom res_data;
-
- fres = fopen( fname, "rb" );
-
- fread(&res_header, sizeof(restart_header), 1, fres);
- data->prev_steps = res_header.step;
- system->N = res_header.N;
- data->therm.T = res_header.T;
- data->therm.xi = res_header.xi;
- data->therm.v_xi = res_header.v_xi;
- data->therm.v_xi_old = res_header.v_xi_old;
- data->therm.G_xi = res_header.G_xi;
- Update_Box( res_header.box, &(system->box) );
+ int i;
+ FILE *fres;
+ reax_atom *p_atom;
+ restart_header res_header;
+ restart_atom res_data;
+
+ fres = fopen( fname, "rb" );
+
+ fread(&res_header, sizeof(restart_header), 1, fres);
+ data->prev_steps = res_header.step;
+ system->N = res_header.N;
+ data->therm.T = res_header.T;
+ data->therm.xi = res_header.xi;
+ data->therm.v_xi = res_header.v_xi;
+ data->therm.v_xi_old = res_header.v_xi_old;
+ data->therm.G_xi = res_header.G_xi;
+ Update_Box( res_header.box, &(system->box) );
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "restart step: %d\n", data->prev_steps );
- fprintf( stderr, "restart thermostat: %10.6f %10.6f %10.6f %10.6f %10.6f\n",
- data->therm.T, data->therm.xi,
- data->therm.v_xi, data->therm.v_xi_old, data->therm.G_xi );
- fprintf( stderr, "restart box:\n" );
- fprintf( stderr, "%9.5f %9.5f %9.5f\n%9.5f %9.5f %9.5f\n%9.5f %9.5f %9.5f\n",
- system->box.box[0][0],system->box.box[0][1],system->box.box[0][2],
- system->box.box[1][0],system->box.box[1][1],system->box.box[1][2],
- system->box.box[2][0],system->box.box[2][1],system->box.box[2][2] );
+ fprintf( stderr, "restart step: %d\n", data->prev_steps );
+ fprintf( stderr, "restart thermostat: %10.6f %10.6f %10.6f %10.6f %10.6f\n",
+ data->therm.T, data->therm.xi,
+ data->therm.v_xi, data->therm.v_xi_old, data->therm.G_xi );
+ fprintf( stderr, "restart box:\n" );
+ fprintf( stderr, "%9.5f %9.5f %9.5f\n%9.5f %9.5f %9.5f\n%9.5f %9.5f %9.5f\n",
+ system->box.box[0][0], system->box.box[0][1], system->box.box[0][2],
+ system->box.box[1][0], system->box.box[1][1], system->box.box[1][2],
+ system->box.box[2][0], system->box.box[2][1], system->box.box[2][2] );
#endif
- /* memory allocations for atoms, atom maps, bond restrictions */
- system->atoms = (reax_atom*) calloc( system->N, sizeof(reax_atom) );
+ /* memory allocations for atoms, atom maps, bond restrictions */
+ system->atoms = (reax_atom*) calloc( system->N, sizeof(reax_atom) );
- workspace->map_serials = (int*) calloc( MAX_ATOM_ID, sizeof(int) );
- for( i = 0; i < MAX_ATOM_ID; ++i )
- workspace->map_serials[i] = -1;
+ workspace->map_serials = (int*) calloc( MAX_ATOM_ID, sizeof(int) );
+ for ( i = 0; i < MAX_ATOM_ID; ++i )
+ workspace->map_serials[i] = -1;
- workspace->orig_id = (int*) calloc( system->N, sizeof(int) );
- workspace->restricted = (int*) calloc( system->N, sizeof(int) );
- workspace->restricted_list = (int**) calloc( system->N, sizeof(int*) );
- for( i = 0; i < system->N; ++i )
- workspace->restricted_list[i] = (int*) calloc( MAX_RESTRICT, sizeof(int) );
+ workspace->orig_id = (int*) calloc( system->N, sizeof(int) );
+ workspace->restricted = (int*) calloc( system->N, sizeof(int) );
+ workspace->restricted_list = (int**) calloc( system->N, sizeof(int*) );
+ for ( i = 0; i < system->N; ++i )
+ workspace->restricted_list[i] = (int*) calloc( MAX_RESTRICT, sizeof(int) );
- for( i = 0; i < system->N; ++i ) {
- fread( &res_data, sizeof(restart_atom), 1, fres);
+ for ( i = 0; i < system->N; ++i )
+ {
+ fread( &res_data, sizeof(restart_atom), 1, fres);
- workspace->orig_id[i] = res_data.orig_id;
- workspace->map_serials[res_data.orig_id] = i;
+ workspace->orig_id[i] = res_data.orig_id;
+ workspace->map_serials[res_data.orig_id] = i;
- p_atom = &( system->atoms[i] );
- p_atom->type = res_data.type;
- strcpy( p_atom->name, res_data.name );
- rvec_Copy( p_atom->x, res_data.x );
- rvec_Copy( p_atom->v, res_data.v );
- }
+ p_atom = &( system->atoms[i] );
+ p_atom->type = res_data.type;
+ strcpy( p_atom->name, res_data.name );
+ rvec_Copy( p_atom->x, res_data.x );
+ rvec_Copy( p_atom->v, res_data.v );
+ }
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "system->N: %d, i: %d\n", system->N, i );
+ fprintf( stderr, "system->N: %d, i: %d\n", system->N, i );
#endif
-
- fclose( fres );
-
- data->step = data->prev_steps;
- // nsteps is updated based on the number of steps in the previous run
- control->nsteps += data->prev_steps;
+
+ fclose( fres );
+
+ data->step = data->prev_steps;
+ // nsteps is updated based on the number of steps in the previous run
+ control->nsteps += data->prev_steps;
}
-void Write_ASCII_Restart( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace )
+void Write_ASCII_Restart( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace )
{
- int i;
- char fname[MAX_STR];
- FILE *fres;
- reax_atom *p_atom;
-
- sprintf( fname, "%s.res%d", control->sim_name, data->step );
- fres = fopen( fname, "w" );
-
- fprintf( fres, RESTART_HEADER,
- data->step, system->N, data->therm.T, data->therm.xi,
- data->therm.v_xi, data->therm.v_xi_old, data->therm.G_xi,
- system->box.box[0][0], system->box.box[0][1], system->box.box[0][2],
- system->box.box[1][0], system->box.box[1][1], system->box.box[1][2],
- system->box.box[2][0], system->box.box[2][1], system->box.box[2][2]);
- fflush(fres);
-
- for( i = 0; i < system->N; ++i ) {
- p_atom = &( system->atoms[i] );
- fprintf( fres, RESTART_LINE,
- workspace->orig_id[i], p_atom->type, p_atom->name,
- p_atom->x[0], p_atom->x[1], p_atom->x[2],
- p_atom->v[0], p_atom->v[1], p_atom->v[2] );
- }
-
- fclose( fres );
-
-#if defined(DEBUG_FOCUS)
+ int i;
+ char fname[MAX_STR];
+ FILE *fres;
+ reax_atom *p_atom;
+
+ sprintf( fname, "%s.res%d", control->sim_name, data->step );
+ fres = fopen( fname, "w" );
+
+ fprintf( fres, RESTART_HEADER,
+ data->step, system->N, data->therm.T, data->therm.xi,
+ data->therm.v_xi, data->therm.v_xi_old, data->therm.G_xi,
+ system->box.box[0][0], system->box.box[0][1], system->box.box[0][2],
+ system->box.box[1][0], system->box.box[1][1], system->box.box[1][2],
+ system->box.box[2][0], system->box.box[2][1], system->box.box[2][2]);
+ fflush(fres);
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ p_atom = &( system->atoms[i] );
+ fprintf( fres, RESTART_LINE,
+ workspace->orig_id[i], p_atom->type, p_atom->name,
+ p_atom->x[0], p_atom->x[1], p_atom->x[2],
+ p_atom->v[0], p_atom->v[1], p_atom->v[2] );
+ }
+
+ fclose( fres );
+
+#if defined(DEBUG_FOCUS)
fprintf( stderr, "write restart - " );
#endif
}
-void Read_ASCII_Restart( char *fname, reax_system *system,
- control_params *control, simulation_data *data,
- static_storage *workspace )
+void Read_ASCII_Restart( char *fname, reax_system *system,
+ control_params *control, simulation_data *data,
+ static_storage *workspace )
{
- int i;
- FILE *fres;
- reax_atom *p_atom;
+ int i;
+ FILE *fres;
+ reax_atom *p_atom;
- fres = fopen( fname, "r" );
+ fres = fopen( fname, "r" );
- /* header */
- fscanf( fres, READ_RESTART_HEADER,
- &data->prev_steps, &system->N, &data->therm.T, &data->therm.xi,
- &data->therm.v_xi, &data->therm.v_xi_old, &data->therm.G_xi,
- &system->box.box[0][0],&system->box.box[0][1],&system->box.box[0][2],
- &system->box.box[1][0],&system->box.box[1][1],&system->box.box[1][2],
- &system->box.box[2][0],&system->box.box[2][1],&system->box.box[2][2]);
- Make_Consistent( &(system->box) );
+ /* header */
+ fscanf( fres, READ_RESTART_HEADER,
+ &data->prev_steps, &system->N, &data->therm.T, &data->therm.xi,
+ &data->therm.v_xi, &data->therm.v_xi_old, &data->therm.G_xi,
+ &system->box.box[0][0], &system->box.box[0][1], &system->box.box[0][2],
+ &system->box.box[1][0], &system->box.box[1][1], &system->box.box[1][2],
+ &system->box.box[2][0], &system->box.box[2][1], &system->box.box[2][2]);
+ Make_Consistent( &(system->box) );
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "restart step: %d\n", data->prev_steps );
- fprintf( stderr, "restart thermostat: %10.6f %10.6f %10.6f %10.6f %10.6f\n",
- data->therm.T, data->therm.xi,
- data->therm.v_xi, data->therm.v_xi_old, data->therm.G_xi );
- fprintf( stderr, "restart box:\n" );
- fprintf( stderr, "%9.5f %9.5f %9.5f\n%9.5f %9.5f %9.5f\n%9.5f %9.5f %9.5f\n",
- system->box.box[0][0],system->box.box[0][1],system->box.box[0][2],
- system->box.box[1][0],system->box.box[1][1],system->box.box[1][2],
- system->box.box[2][0],system->box.box[2][1],system->box.box[2][2] );
+ fprintf( stderr, "restart step: %d\n", data->prev_steps );
+ fprintf( stderr, "restart thermostat: %10.6f %10.6f %10.6f %10.6f %10.6f\n",
+ data->therm.T, data->therm.xi,
+ data->therm.v_xi, data->therm.v_xi_old, data->therm.G_xi );
+ fprintf( stderr, "restart box:\n" );
+ fprintf( stderr, "%9.5f %9.5f %9.5f\n%9.5f %9.5f %9.5f\n%9.5f %9.5f %9.5f\n",
+ system->box.box[0][0], system->box.box[0][1], system->box.box[0][2],
+ system->box.box[1][0], system->box.box[1][1], system->box.box[1][2],
+ system->box.box[2][0], system->box.box[2][1], system->box.box[2][2] );
#endif
- /* memory allocations for atoms, atom maps, bond restrictions */
- system->atoms = (reax_atom*) calloc( system->N, sizeof(reax_atom) );
-
- workspace->map_serials = (int*) calloc( MAX_ATOM_ID, sizeof(int) );
- for( i = 0; i < MAX_ATOM_ID; ++i )
- workspace->map_serials[i] = -1;
-
- workspace->orig_id = (int*) calloc( system->N, sizeof(int) );
- workspace->restricted = (int*) calloc( system->N, sizeof(int) );
- workspace->restricted_list = (int**) calloc( system->N, sizeof(int*) );
- for( i = 0; i < system->N; ++i )
- workspace->restricted_list[i] = (int*) calloc( MAX_RESTRICT, sizeof(int) );
-
- for( i = 0; i < system->N; ++i ) {
- p_atom = &( system->atoms[i] );
- fscanf( fres, READ_RESTART_LINE,
- &workspace->orig_id[i], &p_atom->type, p_atom->name,
- &p_atom->x[0], &p_atom->x[1], &p_atom->x[2],
- &p_atom->v[0], &p_atom->v[1], &p_atom->v[2] );
- workspace->map_serials[workspace->orig_id[i]] = i;
- }
-
- fclose( fres );
-
- data->step = data->prev_steps;
- // nsteps is updated based on the number of steps in the previous run
- control->nsteps += data->prev_steps;
+ /* memory allocations for atoms, atom maps, bond restrictions */
+ system->atoms = (reax_atom*) calloc( system->N, sizeof(reax_atom) );
+
+ workspace->map_serials = (int*) calloc( MAX_ATOM_ID, sizeof(int) );
+ for ( i = 0; i < MAX_ATOM_ID; ++i )
+ workspace->map_serials[i] = -1;
+
+ workspace->orig_id = (int*) calloc( system->N, sizeof(int) );
+ workspace->restricted = (int*) calloc( system->N, sizeof(int) );
+ workspace->restricted_list = (int**) calloc( system->N, sizeof(int*) );
+ for ( i = 0; i < system->N; ++i )
+ workspace->restricted_list[i] = (int*) calloc( MAX_RESTRICT, sizeof(int) );
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ p_atom = &( system->atoms[i] );
+ fscanf( fres, READ_RESTART_LINE,
+ &workspace->orig_id[i], &p_atom->type, p_atom->name,
+ &p_atom->x[0], &p_atom->x[1], &p_atom->x[2],
+ &p_atom->v[0], &p_atom->v[1], &p_atom->v[2] );
+ workspace->map_serials[workspace->orig_id[i]] = i;
+ }
+
+ fclose( fres );
+
+ data->step = data->prev_steps;
+ // nsteps is updated based on the number of steps in the previous run
+ control->nsteps += data->prev_steps;
}
-void Write_Restart( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- output_controls *out_control )
+void Write_Restart( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ output_controls *out_control )
{
- if( out_control->restart_format == WRITE_ASCII )
- Write_ASCII_Restart( system, control, data, workspace );
- else if( out_control->restart_format == WRITE_BINARY )
- Write_Binary_Restart( system, control, data, workspace );
+ if ( out_control->restart_format == WRITE_ASCII )
+ Write_ASCII_Restart( system, control, data, workspace );
+ else if ( out_control->restart_format == WRITE_BINARY )
+ Write_Binary_Restart( system, control, data, workspace );
}
diff --git a/puremd_rc_1003/sPuReMD/restart.h b/puremd_rc_1003/sPuReMD/restart.h
index 7249aa63a155780a290a39effd641e046788f648..d0ea4ca8191dd307d0ea7287b9a65d5d010e885a 100644
--- a/puremd_rc_1003/sPuReMD/restart.h
+++ b/puremd_rc_1003/sPuReMD/restart.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -24,39 +24,41 @@
#include "mytypes.h"
-typedef struct {
- int step, N;
- real T, xi, v_xi, v_xi_old, G_xi;
- rtensor box;
+typedef struct
+{
+ int step, N;
+ real T, xi, v_xi, v_xi_old, G_xi;
+ rtensor box;
} restart_header;
-typedef struct {
- int orig_id, type;
- char name[8];
- rvec x, v;
+typedef struct
+{
+ int orig_id, type;
+ char name[8];
+ rvec x, v;
} restart_atom;
#define RESTART_HEADER "%8d%12d%8.3f%8.3f%8.3f%8.3f%8.3f\n%15.5f%15.5f%15.5f\n%15.5f%15.5f%15.5f\n%15.5f%15.5f%15.5f\n"
#define RESTART_HEADER_LINE_LEN 200
-/* step, system->bigN, data->therm.T, data->therm.xi,
+/* step, system->bigN, data->therm.T, data->therm.xi,
data->therm.v_xi data->therm.v_xi_old data->therm.G_xi
system->big_box.box[0][0], [0][1], [0][2]
system->big_box.box[1][0], [1][1], [1][2]
system->big_box.box[2][0], [2][1], [2][2] */
#define RESTART_LINE "%6d%4d%8s%15.5f%15.5f%15.5f%15.5f%15.5f%15.5f\n"
-#define RESTART_LINE_LEN 109
+#define RESTART_LINE_LEN 109
/* id type name x y z vx vy vz */
#define READ_RESTART_HEADER " %d %d %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf"
#define READ_RESTART_LINE " %d %d %s %lf %lf %lf %lf %lf %lf"
-void Write_Restart( reax_system*, control_params*,
- simulation_data*, static_storage*, output_controls* );
+void Write_Restart( reax_system*, control_params*,
+ simulation_data*, static_storage*, output_controls* );
-void Read_Binary_Restart( char*, reax_system*, control_params*,
- simulation_data*, static_storage* );
-void Read_ASCII_Restart( char*, reax_system*, control_params*,
- simulation_data*, static_storage* );
+void Read_Binary_Restart( char*, reax_system*, control_params*,
+ simulation_data*, static_storage* );
+void Read_ASCII_Restart( char*, reax_system*, control_params*,
+ simulation_data*, static_storage* );
#endif
diff --git a/puremd_rc_1003/sPuReMD/single_body_interactions.c b/puremd_rc_1003/sPuReMD/single_body_interactions.c
index acfd4ef41ec359878c64c8d5401534f7a25e2020..484104a8d8dff533ab12c7033e35969d69f0a60d 100644
--- a/puremd_rc_1003/sPuReMD/single_body_interactions.c
+++ b/puremd_rc_1003/sPuReMD/single_body_interactions.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -26,288 +26,295 @@
#include "vector.h"
-void LonePair_OverUnder_Coordination_Energy( reax_system *system,
- control_params *control,
- simulation_data *data,
- static_storage *workspace,
- list **lists,
- output_controls *out_control )
+void LonePair_OverUnder_Coordination_Energy( reax_system *system,
+ control_params *control,
+ simulation_data *data,
+ static_storage *workspace,
+ list **lists,
+ output_controls *out_control )
{
- int i, j, pj, type_i, type_j;
- real Delta_lpcorr, dfvl;
- real e_lp, expvd2, inv_expvd2, dElp, CElp, DlpVi;
- real e_lph, Di, vov3, deahu2dbo, deahu2dsbo;
- real e_ov, CEover1, CEover2, CEover3, CEover4;
- real exp_ovun1, exp_ovun2, sum_ovun1, sum_ovun2;
- real exp_ovun2n, exp_ovun6, exp_ovun8;
- real inv_exp_ovun1, inv_exp_ovun2, inv_exp_ovun2n, inv_exp_ovun8;
- real e_un, CEunder1, CEunder2, CEunder3, CEunder4;
- real p_lp1, p_lp2, p_lp3;
- real p_ovun2, p_ovun3, p_ovun4, p_ovun5, p_ovun6, p_ovun7, p_ovun8;
-
- single_body_parameters *sbp_i, *sbp_j;
- two_body_parameters *twbp;
- bond_data *pbond;
- bond_order_data *bo_ij;
- list *bonds = (*lists) + BONDS;
-
- /* Initialize parameters */
- p_lp1 = system->reaxprm.gp.l[15];
- p_lp3 = system->reaxprm.gp.l[5];
- p_ovun3 = system->reaxprm.gp.l[32];
- p_ovun4 = system->reaxprm.gp.l[31];
- p_ovun6 = system->reaxprm.gp.l[6];
- p_ovun7 = system->reaxprm.gp.l[8];
- p_ovun8 = system->reaxprm.gp.l[9];
-
- for( i = 0; i < system->N; ++i ) {
- /* set the parameter pointer */
- type_i = system->atoms[i].type;
- sbp_i = &(system->reaxprm.sbp[ type_i ]);
-
- /* lone-pair Energy */
- p_lp2 = sbp_i->p_lp2;
- expvd2 = EXP( -75 * workspace->Delta_lp[i] );
- inv_expvd2 = 1. / (1. + expvd2 );
-
- /* calculate the energy */
- data->E_Lp += e_lp =
- p_lp2 * workspace->Delta_lp[i] * inv_expvd2;
-
- dElp = p_lp2 * inv_expvd2 +
- 75 * p_lp2 * workspace->Delta_lp[i] * expvd2 * SQR(inv_expvd2);
- CElp = dElp * workspace->dDelta_lp[i];
-
- workspace->CdDelta[i] += CElp; // lp - 1st term
+ int i, j, pj, type_i, type_j;
+ real Delta_lpcorr, dfvl;
+ real e_lp, expvd2, inv_expvd2, dElp, CElp, DlpVi;
+ real e_lph, Di, vov3, deahu2dbo, deahu2dsbo;
+ real e_ov, CEover1, CEover2, CEover3, CEover4;
+ real exp_ovun1, exp_ovun2, sum_ovun1, sum_ovun2;
+ real exp_ovun2n, exp_ovun6, exp_ovun8;
+ real inv_exp_ovun1, inv_exp_ovun2, inv_exp_ovun2n, inv_exp_ovun8;
+ real e_un, CEunder1, CEunder2, CEunder3, CEunder4;
+ real p_lp1, p_lp2, p_lp3;
+ real p_ovun2, p_ovun3, p_ovun4, p_ovun5, p_ovun6, p_ovun7, p_ovun8;
+
+ single_body_parameters *sbp_i, *sbp_j;
+ two_body_parameters *twbp;
+ bond_data *pbond;
+ bond_order_data *bo_ij;
+ list *bonds = (*lists) + BONDS;
+
+ /* Initialize parameters */
+ p_lp1 = system->reaxprm.gp.l[15];
+ p_lp3 = system->reaxprm.gp.l[5];
+ p_ovun3 = system->reaxprm.gp.l[32];
+ p_ovun4 = system->reaxprm.gp.l[31];
+ p_ovun6 = system->reaxprm.gp.l[6];
+ p_ovun7 = system->reaxprm.gp.l[8];
+ p_ovun8 = system->reaxprm.gp.l[9];
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ /* set the parameter pointer */
+ type_i = system->atoms[i].type;
+ sbp_i = &(system->reaxprm.sbp[ type_i ]);
+
+ /* lone-pair Energy */
+ p_lp2 = sbp_i->p_lp2;
+ expvd2 = EXP( -75 * workspace->Delta_lp[i] );
+ inv_expvd2 = 1. / (1. + expvd2 );
+
+ /* calculate the energy */
+ data->E_Lp += e_lp =
+ p_lp2 * workspace->Delta_lp[i] * inv_expvd2;
+
+ dElp = p_lp2 * inv_expvd2 +
+ 75 * p_lp2 * workspace->Delta_lp[i] * expvd2 * SQR(inv_expvd2);
+ CElp = dElp * workspace->dDelta_lp[i];
+
+ workspace->CdDelta[i] += CElp; // lp - 1st term
#ifdef TEST_ENERGY
- fprintf( out_control->elp, "%23.15e%23.15e%23.15e%23.15e\n",
- p_lp2, workspace->Delta_lp_temp[i], expvd2, dElp );
- fprintf( out_control->elp, "%6d%23.15e%23.15e%23.15e\n",
- workspace->orig_id[i]+1, workspace->nlp[i], e_lp, data->E_Lp );
+ fprintf( out_control->elp, "%23.15e%23.15e%23.15e%23.15e\n",
+ p_lp2, workspace->Delta_lp_temp[i], expvd2, dElp );
+ fprintf( out_control->elp, "%6d%23.15e%23.15e%23.15e\n",
+ workspace->orig_id[i] + 1, workspace->nlp[i], e_lp, data->E_Lp );
#endif
#ifdef TEST_FORCES
- Add_dDelta( system, lists, i, CElp, workspace->f_lp ); // lp - 1st term
+ Add_dDelta( system, lists, i, CElp, workspace->f_lp ); // lp - 1st term
#endif
- /* correction for C2 */
- if( system->reaxprm.gp.l[5] > 0.001 &&
- !strcmp( system->reaxprm.sbp[type_i].name, "C" ) )
- for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
- if( i < bonds->select.bond_list[pj].nbr ) {
- j = bonds->select.bond_list[pj].nbr;
- type_j = system->atoms[j].type;
-
- if( !strcmp( system->reaxprm.sbp[type_j].name, "C" ) ) {
- twbp = &( system->reaxprm.tbp[type_i][type_j]);
- bo_ij = &( bonds->select.bond_list[pj].bo_data );
- Di = workspace->Delta[i];
- vov3 = bo_ij->BO - Di - 0.040*POW(Di, 4.);
-
- if( vov3 > 3. ) {
- data->E_Lp += e_lph = p_lp3 * SQR(vov3-3.0);
- //estrain(i) += e_lph;
-
- deahu2dbo = 2.*p_lp3*(vov3 - 3.);
- deahu2dsbo = 2.*p_lp3*(vov3 - 3.)*(-1. - 0.16*POW(Di, 3.));
-
- bo_ij->Cdbo += deahu2dbo;
- workspace->CdDelta[i] += deahu2dsbo;
+ /* correction for C2 */
+ if ( system->reaxprm.gp.l[5] > 0.001 &&
+ !strcmp( system->reaxprm.sbp[type_i].name, "C" ) )
+ for ( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
+ if ( i < bonds->select.bond_list[pj].nbr )
+ {
+ j = bonds->select.bond_list[pj].nbr;
+ type_j = system->atoms[j].type;
+
+ if ( !strcmp( system->reaxprm.sbp[type_j].name, "C" ) )
+ {
+ twbp = &( system->reaxprm.tbp[type_i][type_j]);
+ bo_ij = &( bonds->select.bond_list[pj].bo_data );
+ Di = workspace->Delta[i];
+ vov3 = bo_ij->BO - Di - 0.040 * POW(Di, 4.);
+
+ if ( vov3 > 3. )
+ {
+ data->E_Lp += e_lph = p_lp3 * SQR(vov3 - 3.0);
+ //estrain(i) += e_lph;
+
+ deahu2dbo = 2.*p_lp3 * (vov3 - 3.);
+ deahu2dsbo = 2.*p_lp3 * (vov3 - 3.) * (-1. - 0.16 * POW(Di, 3.));
+
+ bo_ij->Cdbo += deahu2dbo;
+ workspace->CdDelta[i] += deahu2dsbo;
#ifdef TEST_ENERGY
- fprintf(out_control->elp,"C2cor%6d%6d%23.15e%23.15e%23.15e\n",
- // workspace->orig_id[i], workspace->orig_id[j],
- i+1, j+1, e_lph, deahu2dbo, deahu2dsbo );
+ fprintf(out_control->elp, "C2cor%6d%6d%23.15e%23.15e%23.15e\n",
+ // workspace->orig_id[i], workspace->orig_id[j],
+ i + 1, j + 1, e_lph, deahu2dbo, deahu2dsbo );
#endif
#ifdef TEST_FORCES
- Add_dBO(system, lists, i, pj, deahu2dbo, workspace->f_lp);
- Add_dDelta(system, lists, i, deahu2dsbo, workspace->f_lp);
+ Add_dBO(system, lists, i, pj, deahu2dbo, workspace->f_lp);
+ Add_dDelta(system, lists, i, deahu2dsbo, workspace->f_lp);
#endif
- }
- }
-
- }
- }
-
-
- for( i = 0; i < system->N; ++i ) {
- type_i = system->atoms[i].type;
- sbp_i = &(system->reaxprm.sbp[ type_i ]);
-
- /* over-coordination energy */
- if( sbp_i->mass > 21.0 )
- dfvl = 0.0;
- else dfvl = 1.0; // only for 1st-row elements
-
- p_ovun2 = sbp_i->p_ovun2;
- sum_ovun1 = 0;
- sum_ovun2 = 0;
-
- for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
- j = bonds->select.bond_list[pj].nbr;
- type_j = system->atoms[j].type;
- bo_ij = &(bonds->select.bond_list[pj].bo_data);
- sbp_j = &(system->reaxprm.sbp[ type_j ]);
- twbp = &(system->reaxprm.tbp[ type_i ][ type_j ]);
-
- sum_ovun1 += twbp->p_ovun1 * twbp->De_s * bo_ij->BO;
- sum_ovun2 += (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j])*
- ( bo_ij->BO_pi + bo_ij->BO_pi2 );
-
- /*fprintf( stdout, "%4d%4d%23.15e%23.15e%23.15e\n",
- i+1, j+1,
- dfvl * workspace->Delta_lp_temp[j],
- sbp_j->nlp_opt,
- workspace->nlp_temp[j] );*/
+ }
+ }
+
+ }
}
-
- exp_ovun1 = p_ovun3 * EXP( p_ovun4 * sum_ovun2 );
- inv_exp_ovun1 = 1.0 / (1 + exp_ovun1);
- Delta_lpcorr = workspace->Delta[i] -
- (dfvl*workspace->Delta_lp_temp[i]) * inv_exp_ovun1;
-
- exp_ovun2 = EXP( p_ovun2 * Delta_lpcorr );
- inv_exp_ovun2 = 1.0 / (1.0 + exp_ovun2);
-
- DlpVi = 1.0 / (Delta_lpcorr + sbp_i->valency + 1e-8 );
- CEover1 = Delta_lpcorr * DlpVi * inv_exp_ovun2;
-
- data->E_Ov += e_ov = sum_ovun1 * CEover1;
-
- CEover2 = sum_ovun1 * DlpVi * inv_exp_ovun2 *
- ( 1.0 - Delta_lpcorr*( DlpVi + p_ovun2 * exp_ovun2 * inv_exp_ovun2 ) );
-
- CEover3 = CEover2 * (1.0 - dfvl*workspace->dDelta_lp[i]*inv_exp_ovun1 );
-
- CEover4 = CEover2 * (dfvl*workspace->Delta_lp_temp[i]) *
- p_ovun4 * exp_ovun1 * SQR(inv_exp_ovun1);
-
-
- /* under-coordination potential */
- p_ovun2 = sbp_i->p_ovun2;
- p_ovun5 = sbp_i->p_ovun5;
-
- exp_ovun2n = 1.0 / exp_ovun2;
- exp_ovun6 = EXP( p_ovun6 * Delta_lpcorr );
- exp_ovun8 = p_ovun7 * EXP(p_ovun8 * sum_ovun2);
- inv_exp_ovun2n = 1.0 / (1.0 + exp_ovun2n);
- inv_exp_ovun8 = 1.0 / (1.0 + exp_ovun8);
-
- data->E_Un += e_un =
- -p_ovun5 * (1.0 - exp_ovun6) * inv_exp_ovun2n * inv_exp_ovun8;
-
- CEunder1 = inv_exp_ovun2n * ( p_ovun5*p_ovun6*exp_ovun6*inv_exp_ovun8 +
- p_ovun2 * e_un * exp_ovun2n);
- CEunder2 = -e_un * p_ovun8 * exp_ovun8 * inv_exp_ovun8;
- CEunder3 = CEunder1 * (1.0 - dfvl*workspace->dDelta_lp[i]*inv_exp_ovun1);
- CEunder4 = CEunder1 * (dfvl*workspace->Delta_lp_temp[i]) *
- p_ovun4 * exp_ovun1 * SQR(inv_exp_ovun1) + CEunder2;
-
- //fprintf( stdout, "%6d%23.15e%23.15e%23.15e\n",
- // i+1, sum_ovun2, e_ov, e_un );
-
- /* forces */
- workspace->CdDelta[i] += CEover3; // OvCoor - 2nd term
- workspace->CdDelta[i] += CEunder3; // UnCoor - 1st term
+
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ type_i = system->atoms[i].type;
+ sbp_i = &(system->reaxprm.sbp[ type_i ]);
+
+ /* over-coordination energy */
+ if ( sbp_i->mass > 21.0 )
+ dfvl = 0.0;
+ else dfvl = 1.0; // only for 1st-row elements
+
+ p_ovun2 = sbp_i->p_ovun2;
+ sum_ovun1 = 0;
+ sum_ovun2 = 0;
+
+ for ( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
+ {
+ j = bonds->select.bond_list[pj].nbr;
+ type_j = system->atoms[j].type;
+ bo_ij = &(bonds->select.bond_list[pj].bo_data);
+ sbp_j = &(system->reaxprm.sbp[ type_j ]);
+ twbp = &(system->reaxprm.tbp[ type_i ][ type_j ]);
+
+ sum_ovun1 += twbp->p_ovun1 * twbp->De_s * bo_ij->BO;
+ sum_ovun2 += (workspace->Delta[j] - dfvl * workspace->Delta_lp_temp[j]) *
+ ( bo_ij->BO_pi + bo_ij->BO_pi2 );
+
+ /*fprintf( stdout, "%4d%4d%23.15e%23.15e%23.15e\n",
+ i+1, j+1,
+ dfvl * workspace->Delta_lp_temp[j],
+ sbp_j->nlp_opt,
+ workspace->nlp_temp[j] );*/
+ }
+
+ exp_ovun1 = p_ovun3 * EXP( p_ovun4 * sum_ovun2 );
+ inv_exp_ovun1 = 1.0 / (1 + exp_ovun1);
+ Delta_lpcorr = workspace->Delta[i] -
+ (dfvl * workspace->Delta_lp_temp[i]) * inv_exp_ovun1;
+
+ exp_ovun2 = EXP( p_ovun2 * Delta_lpcorr );
+ inv_exp_ovun2 = 1.0 / (1.0 + exp_ovun2);
+
+ DlpVi = 1.0 / (Delta_lpcorr + sbp_i->valency + 1e-8 );
+ CEover1 = Delta_lpcorr * DlpVi * inv_exp_ovun2;
+
+ data->E_Ov += e_ov = sum_ovun1 * CEover1;
+
+ CEover2 = sum_ovun1 * DlpVi * inv_exp_ovun2 *
+ ( 1.0 - Delta_lpcorr * ( DlpVi + p_ovun2 * exp_ovun2 * inv_exp_ovun2 ) );
+
+ CEover3 = CEover2 * (1.0 - dfvl * workspace->dDelta_lp[i] * inv_exp_ovun1 );
+
+ CEover4 = CEover2 * (dfvl * workspace->Delta_lp_temp[i]) *
+ p_ovun4 * exp_ovun1 * SQR(inv_exp_ovun1);
+
+
+ /* under-coordination potential */
+ p_ovun2 = sbp_i->p_ovun2;
+ p_ovun5 = sbp_i->p_ovun5;
+
+ exp_ovun2n = 1.0 / exp_ovun2;
+ exp_ovun6 = EXP( p_ovun6 * Delta_lpcorr );
+ exp_ovun8 = p_ovun7 * EXP(p_ovun8 * sum_ovun2);
+ inv_exp_ovun2n = 1.0 / (1.0 + exp_ovun2n);
+ inv_exp_ovun8 = 1.0 / (1.0 + exp_ovun8);
+
+ data->E_Un += e_un =
+ -p_ovun5 * (1.0 - exp_ovun6) * inv_exp_ovun2n * inv_exp_ovun8;
+
+ CEunder1 = inv_exp_ovun2n * ( p_ovun5 * p_ovun6 * exp_ovun6 * inv_exp_ovun8 +
+ p_ovun2 * e_un * exp_ovun2n);
+ CEunder2 = -e_un * p_ovun8 * exp_ovun8 * inv_exp_ovun8;
+ CEunder3 = CEunder1 * (1.0 - dfvl * workspace->dDelta_lp[i] * inv_exp_ovun1);
+ CEunder4 = CEunder1 * (dfvl * workspace->Delta_lp_temp[i]) *
+ p_ovun4 * exp_ovun1 * SQR(inv_exp_ovun1) + CEunder2;
+
+ //fprintf( stdout, "%6d%23.15e%23.15e%23.15e\n",
+ // i+1, sum_ovun2, e_ov, e_un );
+
+ /* forces */
+ workspace->CdDelta[i] += CEover3; // OvCoor - 2nd term
+ workspace->CdDelta[i] += CEunder3; // UnCoor - 1st term
#ifdef TEST_FORCES
- Add_dDelta( system, lists, i, CEover3, workspace->f_ov ); // OvCoor - 2nd
- Add_dDelta( system, lists, i, CEunder3, workspace->f_un ); // UnCoor - 1st
+ Add_dDelta( system, lists, i, CEover3, workspace->f_ov ); // OvCoor - 2nd
+ Add_dDelta( system, lists, i, CEunder3, workspace->f_un ); // UnCoor - 1st
#endif
-
- for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ){
- pbond = &(bonds->select.bond_list[pj]);
- j = pbond->nbr;
- type_j = system->atoms[j].type;
- bo_ij = &(pbond->bo_data);
- twbp = &(system->reaxprm.tbp[ type_i ][ type_j ]);
+
+ for ( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
+ {
+ pbond = &(bonds->select.bond_list[pj]);
+ j = pbond->nbr;
+ type_j = system->atoms[j].type;
+ bo_ij = &(pbond->bo_data);
+ twbp = &(system->reaxprm.tbp[ type_i ][ type_j ]);
- bo_ij->Cdbo += CEover1 * twbp->p_ovun1 * twbp->De_s; // OvCoor - 1st
- workspace->CdDelta[j] += CEover4*(1.0 - dfvl*workspace->dDelta_lp[j])*
- (bo_ij->BO_pi + bo_ij->BO_pi2); // OvCoor - 3a
- bo_ij->Cdbopi += CEover4 *
- (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]);//OvCoor-3b
- bo_ij->Cdbopi2 += CEover4 *
- (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]);//OvCoor-3b
+ bo_ij->Cdbo += CEover1 * twbp->p_ovun1 * twbp->De_s; // OvCoor - 1st
+ workspace->CdDelta[j] += CEover4 * (1.0 - dfvl * workspace->dDelta_lp[j]) *
+ (bo_ij->BO_pi + bo_ij->BO_pi2); // OvCoor - 3a
+ bo_ij->Cdbopi += CEover4 *
+ (workspace->Delta[j] - dfvl * workspace->Delta_lp_temp[j]); //OvCoor-3b
+ bo_ij->Cdbopi2 += CEover4 *
+ (workspace->Delta[j] - dfvl * workspace->Delta_lp_temp[j]); //OvCoor-3b
- workspace->CdDelta[j] += CEunder4*(1.0-dfvl*workspace->dDelta_lp[j]) *
- (bo_ij->BO_pi + bo_ij->BO_pi2); // UnCoor - 2a
- bo_ij->Cdbopi += CEunder4 *
- (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]);//UnCoor-2b
- bo_ij->Cdbopi2 += CEunder4 *
- (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]);//UnCoor-2b
+ workspace->CdDelta[j] += CEunder4 * (1.0 - dfvl * workspace->dDelta_lp[j]) *
+ (bo_ij->BO_pi + bo_ij->BO_pi2); // UnCoor - 2a
+ bo_ij->Cdbopi += CEunder4 *
+ (workspace->Delta[j] - dfvl * workspace->Delta_lp_temp[j]); //UnCoor-2b
+ bo_ij->Cdbopi2 += CEunder4 *
+ (workspace->Delta[j] - dfvl * workspace->Delta_lp_temp[j]); //UnCoor-2b
#ifdef TEST_ENERGY
- /* fprintf( out_control->eov, "%6d%23.15e%23.15e"
- workspace->orig_id[j]+1,
- //twbp->p_ovun1,twbp->De_s,Delta_lpcorr*DlpVi*inv_exp_ovun2,
- CEover1*twbp->p_ovun1*twbp->De_s, CEover3 ); */
-
- /*fprintf( out_control->eov, "%6d%23.15e%23.15e%23.15e%23.15e%23.15e\n",
- workspace->orig_id[j]+1,
- CEover4,
- CEover4*
- (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]),
- CEover4 * (bo_ij->BO_pi + bo_ij->BO_pi2),
- (1.0 - dfvl*workspace->dDelta_lp[j]),
- CEover4 * (1.0 - dfvl*workspace->dDelta_lp[j]) *
- (bo_ij->BO_pi + bo_ij->BO_pi2) );*/
-
- /* fprintf( out_control->eun, "%6d%23.15e\n",
- workspace->orig_id[j]+1, CEunder3 ); */
-
- /*fprintf( out_control->eun, "%6d%23.15e%23.15e%23.15e%23.15e\n",
- workspace->orig_id[j]+1,
- CEunder4,
- (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]),
- CEunder4*
- (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]),
- CEunder4*(1.0 - dfvl*workspace->dDelta_lp[j])*
- (bo_ij->BO_pi + bo_ij->BO_pi2) );*/
+ /* fprintf( out_control->eov, "%6d%23.15e%23.15e"
+ workspace->orig_id[j]+1,
+ //twbp->p_ovun1,twbp->De_s,Delta_lpcorr*DlpVi*inv_exp_ovun2,
+ CEover1*twbp->p_ovun1*twbp->De_s, CEover3 ); */
+
+ /*fprintf( out_control->eov, "%6d%23.15e%23.15e%23.15e%23.15e%23.15e\n",
+ workspace->orig_id[j]+1,
+ CEover4,
+ CEover4*
+ (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]),
+ CEover4 * (bo_ij->BO_pi + bo_ij->BO_pi2),
+ (1.0 - dfvl*workspace->dDelta_lp[j]),
+ CEover4 * (1.0 - dfvl*workspace->dDelta_lp[j]) *
+ (bo_ij->BO_pi + bo_ij->BO_pi2) );*/
+
+ /* fprintf( out_control->eun, "%6d%23.15e\n",
+ workspace->orig_id[j]+1, CEunder3 ); */
+
+ /*fprintf( out_control->eun, "%6d%23.15e%23.15e%23.15e%23.15e\n",
+ workspace->orig_id[j]+1,
+ CEunder4,
+ (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]),
+ CEunder4*
+ (workspace->Delta[j] - dfvl*workspace->Delta_lp_temp[j]),
+ CEunder4*(1.0 - dfvl*workspace->dDelta_lp[j])*
+ (bo_ij->BO_pi + bo_ij->BO_pi2) );*/
#endif
#ifdef TEST_FORCES
- Add_dBO( system, lists, i, pj, CEover1 * twbp->p_ovun1 * twbp->De_s,
- workspace->f_ov ); // OvCoor - 1st term
-
- Add_dDelta( system, lists, j,
- CEover4 * (1.0 - dfvl*workspace->dDelta_lp[j]) *
- (bo_ij->BO_pi+bo_ij->BO_pi2), workspace->f_ov );//OvCoor3a
-
- Add_dBOpinpi2( system, lists, i, pj,
- CEover4 * (workspace->Delta[j] -
- dfvl * workspace->Delta_lp_temp[j]),
- CEover4 * (workspace->Delta[j] -
- dfvl * workspace->Delta_lp_temp[j]),
- workspace->f_ov, workspace->f_ov ); // OvCoor - 3b
-
- Add_dDelta( system, lists, j,
- CEunder4 * (1.0 - dfvl*workspace->dDelta_lp[j]) *
- (bo_ij->BO_pi + bo_ij->BO_pi2),
- workspace->f_un ); // UnCoor - 2a
-
- Add_dBOpinpi2( system, lists, i, pj,
- CEunder4 * (workspace->Delta[j] -
- dfvl * workspace->Delta_lp_temp[j]),
- CEunder4 * (workspace->Delta[j] -
- dfvl * workspace->Delta_lp_temp[j]),
- workspace->f_un, workspace->f_un ); // UnCoor - 2b
+ Add_dBO( system, lists, i, pj, CEover1 * twbp->p_ovun1 * twbp->De_s,
+ workspace->f_ov ); // OvCoor - 1st term
+
+ Add_dDelta( system, lists, j,
+ CEover4 * (1.0 - dfvl * workspace->dDelta_lp[j]) *
+ (bo_ij->BO_pi + bo_ij->BO_pi2), workspace->f_ov ); //OvCoor3a
+
+ Add_dBOpinpi2( system, lists, i, pj,
+ CEover4 * (workspace->Delta[j] -
+ dfvl * workspace->Delta_lp_temp[j]),
+ CEover4 * (workspace->Delta[j] -
+ dfvl * workspace->Delta_lp_temp[j]),
+ workspace->f_ov, workspace->f_ov ); // OvCoor - 3b
+
+ Add_dDelta( system, lists, j,
+ CEunder4 * (1.0 - dfvl * workspace->dDelta_lp[j]) *
+ (bo_ij->BO_pi + bo_ij->BO_pi2),
+ workspace->f_un ); // UnCoor - 2a
+
+ Add_dBOpinpi2( system, lists, i, pj,
+ CEunder4 * (workspace->Delta[j] -
+ dfvl * workspace->Delta_lp_temp[j]),
+ CEunder4 * (workspace->Delta[j] -
+ dfvl * workspace->Delta_lp_temp[j]),
+ workspace->f_un, workspace->f_un ); // UnCoor - 2b
#endif
- }
+ }
-#ifdef TEST_ENERGY
+#ifdef TEST_ENERGY
- fprintf( out_control->eov, "%6d%15.8f%15.8f%15.8f\n",
- i+1, DlpVi, Delta_lpcorr, sbp_i->valency );
+ fprintf( out_control->eov, "%6d%15.8f%15.8f%15.8f\n",
+ i + 1, DlpVi, Delta_lpcorr, sbp_i->valency );
- fprintf( out_control->eov, "%6d%15.8f%15.8f\n",
- i+1/*workspace->orig_id[i]+1*/, e_ov, data->E_Ov + data->E_Un );
+ fprintf( out_control->eov, "%6d%15.8f%15.8f\n",
+ i + 1/*workspace->orig_id[i]+1*/, e_ov, data->E_Ov + data->E_Un );
- fprintf( out_control->eov, "%6d%15.8f%15.8f\n",
- i+1/*workspace->orig_id[i]+1*/, e_un, data->E_Ov + data->E_Un );
+ fprintf( out_control->eov, "%6d%15.8f%15.8f\n",
+ i + 1/*workspace->orig_id[i]+1*/, e_un, data->E_Ov + data->E_Un );
#endif
- }
+ }
}
diff --git a/puremd_rc_1003/sPuReMD/single_body_interactions.h b/puremd_rc_1003/sPuReMD/single_body_interactions.h
index a7502b83b824a17616c78d38857c2aa1aade2f6c..41cc6493af410a25b6807bd9779e6ceb9483c57f 100644
--- a/puremd_rc_1003/sPuReMD/single_body_interactions.h
+++ b/puremd_rc_1003/sPuReMD/single_body_interactions.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -24,8 +24,7 @@
#include <mytypes.h>
-void LonePair_OverUnder_Coordination_Energy( reax_system*, control_params*,
- simulation_data*, static_storage*,
- list**, output_controls* );
+void LonePair_OverUnder_Coordination_Energy( reax_system*, control_params*,
+ simulation_data*, static_storage*,
+ list**, output_controls* );
#endif
-
diff --git a/puremd_rc_1003/sPuReMD/system_props.c b/puremd_rc_1003/sPuReMD/system_props.c
index 60c4f0e9586ad154e9370582b9ed91ef3f0c5168..52c1d2713ea0b84f8ea729306ba856645d191d2f 100644
--- a/puremd_rc_1003/sPuReMD/system_props.c
+++ b/puremd_rc_1003/sPuReMD/system_props.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -26,310 +26,320 @@
real Get_Time( )
{
- struct timeval tim;
-
- gettimeofday(&tim, NULL );
- return( tim.tv_sec + (tim.tv_usec / 1000000.0) );
+ struct timeval tim;
+
+ gettimeofday(&tim, NULL );
+ return ( tim.tv_sec + (tim.tv_usec / 1000000.0) );
}
real Get_Timing_Info( real t_start )
{
- struct timeval tim;
- real t_end;
-
- gettimeofday(&tim, NULL );
- t_end = tim.tv_sec + (tim.tv_usec / 1000000.0);
- return (t_end - t_start);
+ struct timeval tim;
+ real t_end;
+
+ gettimeofday(&tim, NULL );
+ t_end = tim.tv_sec + (tim.tv_usec / 1000000.0);
+ return (t_end - t_start);
}
-void Temperature_Control( control_params *control, simulation_data *data,
- output_controls *out_control )
+void Temperature_Control( control_params *control, simulation_data *data,
+ output_controls *out_control )
{
- real tmp;
-
- if( control->T_mode == 1 ) { // step-wise temperature control
- if( (data->step - data->prev_steps) %
- ((int)(control->T_freq / control->dt)) == 0 ) {
- if( fabs( control->T - control->T_final ) >= fabs( control->T_rate ) )
- control->T += control->T_rate;
- else control->T = control->T_final;
+ real tmp;
+
+ if ( control->T_mode == 1 ) // step-wise temperature control
+ {
+ if ( (data->step - data->prev_steps) %
+ ((int)(control->T_freq / control->dt)) == 0 )
+ {
+ if ( fabs( control->T - control->T_final ) >= fabs( control->T_rate ) )
+ control->T += control->T_rate;
+ else control->T = control->T_final;
+ }
+ }
+ else if ( control->T_mode == 2 ) // constant slope control
+ {
+ tmp = control->T_rate * control->dt / control->T_freq;
+
+ if ( fabs( control->T - control->T_final ) >= fabs( tmp ) )
+ control->T += tmp;
}
- }
- else if( control->T_mode == 2 ) { // constant slope control
- tmp = control->T_rate * control->dt / control->T_freq;
-
- if( fabs( control->T - control->T_final ) >= fabs( tmp ) )
- control->T += tmp;
- }
}
void Compute_Total_Mass( reax_system *system, simulation_data *data )
{
- int i;
-
- data->M = 0;
+ int i;
+
+ data->M = 0;
- for( i = 0; i < system->N; i++ )
- data->M += system->reaxprm.sbp[ system->atoms[i].type ].mass;
+ for ( i = 0; i < system->N; i++ )
+ data->M += system->reaxprm.sbp[ system->atoms[i].type ].mass;
- //fprintf ( stderr, "Compute_total_Mass -->%f<-- \n", data->M );
- data->inv_M = 1. / data->M;
+ //fprintf ( stderr, "Compute_total_Mass -->%f<-- \n", data->M );
+ data->inv_M = 1. / data->M;
}
-void Compute_Center_of_Mass( reax_system *system, simulation_data *data,
- FILE *fout )
+void Compute_Center_of_Mass( reax_system *system, simulation_data *data,
+ FILE *fout )
{
- int i;
- real m, xx, xy, xz, yy, yz, zz, det;
- rvec tvec, diff;
- rtensor mat, inv;
-
- rvec_MakeZero( data->xcm ); // position of CoM
- rvec_MakeZero( data->vcm ); // velocity of CoM
- rvec_MakeZero( data->amcm ); // angular momentum of CoM
- rvec_MakeZero( data->avcm ); // angular velocity of CoM
-
-
- /* Compute the position, velocity and angular momentum about the CoM */
- for( i = 0; i < system->N; ++i ) {
- m = system->reaxprm.sbp[ system->atoms[i].type ].mass;
-
- rvec_ScaledAdd( data->xcm, m, system->atoms[i].x );
- rvec_ScaledAdd( data->vcm, m, system->atoms[i].v );
-
- rvec_Cross( tvec, system->atoms[i].x, system->atoms[i].v );
- rvec_ScaledAdd( data->amcm, m, tvec );
-
- /*fprintf( fout,"%3d %g %g %g\n",
- i+1,
- system->atoms[i].v[0], system->atoms[i].v[1], system->atoms[i].v[2] );
- fprintf( fout, "vcm: %g %g %g\n",
- data->vcm[0], data->vcm[1], data->vcm[2] );
- */
- /* fprintf( stderr, "amcm: %12.6f %12.6f %12.6f\n",
- data->amcm[0], data->amcm[1], data->amcm[2] ); */
- }
-
- rvec_Scale( data->xcm, data->inv_M, data->xcm );
- rvec_Scale( data->vcm, data->inv_M, data->vcm );
-
- rvec_Cross( tvec, data->xcm, data->vcm );
- rvec_ScaledAdd( data->amcm, -data->M, tvec );
-
- data->etran_cm = 0.5 * data->M * rvec_Norm_Sqr( data->vcm );
-
- /* Calculate and then invert the inertial tensor */
- xx = xy = xz = yy = yz = zz = 0;
-
- for( i = 0; i < system->N; ++i ) {
- m = system->reaxprm.sbp[ system->atoms[i].type ].mass;
-
- rvec_ScaledSum( diff, 1., system->atoms[i].x, -1., data->xcm );
- xx += diff[0] * diff[0] * m;
- xy += diff[0] * diff[1] * m;
- xz += diff[0] * diff[2] * m;
- yy += diff[1] * diff[1] * m;
- yz += diff[1] * diff[2] * m;
- zz += diff[2] * diff[2] * m;
- }
-
- mat[0][0] = yy + zz;
- mat[0][1] = mat[1][0] = -xy;
- mat[0][2] = mat[2][0] = -xz;
- mat[1][1] = xx + zz;
- mat[2][1] = mat[1][2] = -yz;
- mat[2][2] = xx + yy;
-
- /* invert the inertial tensor */
- det = ( mat[0][0] * mat[1][1] * mat[2][2] +
- mat[0][1] * mat[1][2] * mat[2][0] +
- mat[0][2] * mat[1][0] * mat[2][1] ) -
- ( mat[0][0] * mat[1][2] * mat[2][1] +
- mat[0][1] * mat[1][0] * mat[2][2] +
- mat[0][2] * mat[1][1] * mat[2][0] );
-
- inv[0][0] = mat[1][1] * mat[2][2] - mat[1][2] * mat[2][1];
- inv[0][1] = mat[0][2] * mat[2][1] - mat[0][1] * mat[2][2];
- inv[0][2] = mat[0][1] * mat[1][2] - mat[0][2] * mat[1][1];
- inv[1][0] = mat[1][2] * mat[2][0] - mat[1][0] * mat[2][2];
- inv[1][1] = mat[0][0] * mat[2][2] - mat[0][2] * mat[2][0];
- inv[1][2] = mat[0][2] * mat[1][0] - mat[0][0] * mat[1][2];
- inv[2][0] = mat[1][0] * mat[2][1] - mat[2][0] * mat[1][1];
- inv[2][1] = mat[2][0] * mat[0][1] - mat[0][0] * mat[2][1];
- inv[2][2] = mat[0][0] * mat[1][1] - mat[1][0] * mat[0][1];
-
- if( fabs(det) > ALMOST_ZERO )
- rtensor_Scale( inv, 1./det, inv );
- else
- rtensor_MakeZero( inv );
-
- /* Compute the angular velocity about the centre of mass */
- rtensor_MatVec( data->avcm, inv, data->amcm );
- data->erot_cm = 0.5 * E_CONV * rvec_Dot( data->avcm, data->amcm );
+ int i;
+ real m, xx, xy, xz, yy, yz, zz, det;
+ rvec tvec, diff;
+ rtensor mat, inv;
+
+ rvec_MakeZero( data->xcm ); // position of CoM
+ rvec_MakeZero( data->vcm ); // velocity of CoM
+ rvec_MakeZero( data->amcm ); // angular momentum of CoM
+ rvec_MakeZero( data->avcm ); // angular velocity of CoM
+
+
+ /* Compute the position, velocity and angular momentum about the CoM */
+ for ( i = 0; i < system->N; ++i )
+ {
+ m = system->reaxprm.sbp[ system->atoms[i].type ].mass;
+
+ rvec_ScaledAdd( data->xcm, m, system->atoms[i].x );
+ rvec_ScaledAdd( data->vcm, m, system->atoms[i].v );
+
+ rvec_Cross( tvec, system->atoms[i].x, system->atoms[i].v );
+ rvec_ScaledAdd( data->amcm, m, tvec );
+
+ /*fprintf( fout,"%3d %g %g %g\n",
+ i+1,
+ system->atoms[i].v[0], system->atoms[i].v[1], system->atoms[i].v[2] );
+ fprintf( fout, "vcm: %g %g %g\n",
+ data->vcm[0], data->vcm[1], data->vcm[2] );
+ */
+ /* fprintf( stderr, "amcm: %12.6f %12.6f %12.6f\n",
+ data->amcm[0], data->amcm[1], data->amcm[2] ); */
+ }
+
+ rvec_Scale( data->xcm, data->inv_M, data->xcm );
+ rvec_Scale( data->vcm, data->inv_M, data->vcm );
+
+ rvec_Cross( tvec, data->xcm, data->vcm );
+ rvec_ScaledAdd( data->amcm, -data->M, tvec );
+
+ data->etran_cm = 0.5 * data->M * rvec_Norm_Sqr( data->vcm );
+
+ /* Calculate and then invert the inertial tensor */
+ xx = xy = xz = yy = yz = zz = 0;
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ m = system->reaxprm.sbp[ system->atoms[i].type ].mass;
+
+ rvec_ScaledSum( diff, 1., system->atoms[i].x, -1., data->xcm );
+ xx += diff[0] * diff[0] * m;
+ xy += diff[0] * diff[1] * m;
+ xz += diff[0] * diff[2] * m;
+ yy += diff[1] * diff[1] * m;
+ yz += diff[1] * diff[2] * m;
+ zz += diff[2] * diff[2] * m;
+ }
+
+ mat[0][0] = yy + zz;
+ mat[0][1] = mat[1][0] = -xy;
+ mat[0][2] = mat[2][0] = -xz;
+ mat[1][1] = xx + zz;
+ mat[2][1] = mat[1][2] = -yz;
+ mat[2][2] = xx + yy;
+
+ /* invert the inertial tensor */
+ det = ( mat[0][0] * mat[1][1] * mat[2][2] +
+ mat[0][1] * mat[1][2] * mat[2][0] +
+ mat[0][2] * mat[1][0] * mat[2][1] ) -
+ ( mat[0][0] * mat[1][2] * mat[2][1] +
+ mat[0][1] * mat[1][0] * mat[2][2] +
+ mat[0][2] * mat[1][1] * mat[2][0] );
+
+ inv[0][0] = mat[1][1] * mat[2][2] - mat[1][2] * mat[2][1];
+ inv[0][1] = mat[0][2] * mat[2][1] - mat[0][1] * mat[2][2];
+ inv[0][2] = mat[0][1] * mat[1][2] - mat[0][2] * mat[1][1];
+ inv[1][0] = mat[1][2] * mat[2][0] - mat[1][0] * mat[2][2];
+ inv[1][1] = mat[0][0] * mat[2][2] - mat[0][2] * mat[2][0];
+ inv[1][2] = mat[0][2] * mat[1][0] - mat[0][0] * mat[1][2];
+ inv[2][0] = mat[1][0] * mat[2][1] - mat[2][0] * mat[1][1];
+ inv[2][1] = mat[2][0] * mat[0][1] - mat[0][0] * mat[2][1];
+ inv[2][2] = mat[0][0] * mat[1][1] - mat[1][0] * mat[0][1];
+
+ if ( fabs(det) > ALMOST_ZERO )
+ rtensor_Scale( inv, 1. / det, inv );
+ else
+ rtensor_MakeZero( inv );
+
+ /* Compute the angular velocity about the centre of mass */
+ rtensor_MatVec( data->avcm, inv, data->amcm );
+ data->erot_cm = 0.5 * E_CONV * rvec_Dot( data->avcm, data->amcm );
#if defined(DEBUG)
- fprintf( stderr, "xcm: %24.15e %24.15e %24.15e\n",
- data->xcm[0], data->xcm[1], data->xcm[2] );
- fprintf( stderr, "vcm: %24.15e %24.15e %24.15e\n",
- data->vcm[0], data->vcm[1], data->vcm[2] );
- fprintf( stderr, "amcm: %24.15e %24.15e %24.15e\n",
- data->amcm[0], data->amcm[1], data->amcm[2] );
- /* fprintf( fout, "mat: %f %f %f\n %f %f %f\n %f %f %f\n",
- mat[0][0], mat[0][1], mat[0][2],
- mat[1][0], mat[1][1], mat[1][2],
- mat[2][0], mat[2][1], mat[2][2] );
- fprintf( fout, "inv: %g %g %g\n %g %g %g\n %g %g %g\n",
- inv[0][0], inv[0][1], inv[0][2],
- inv[1][0], inv[1][1], inv[1][2],
- inv[2][0], inv[2][1], inv[2][2] );
- fflush( fout ); */
- fprintf( stderr, "avcm: %24.15e %24.15e %24.15e\n",
- data->avcm[0], data->avcm[1], data->avcm[2] );
+ fprintf( stderr, "xcm: %24.15e %24.15e %24.15e\n",
+ data->xcm[0], data->xcm[1], data->xcm[2] );
+ fprintf( stderr, "vcm: %24.15e %24.15e %24.15e\n",
+ data->vcm[0], data->vcm[1], data->vcm[2] );
+ fprintf( stderr, "amcm: %24.15e %24.15e %24.15e\n",
+ data->amcm[0], data->amcm[1], data->amcm[2] );
+ /* fprintf( fout, "mat: %f %f %f\n %f %f %f\n %f %f %f\n",
+ mat[0][0], mat[0][1], mat[0][2],
+ mat[1][0], mat[1][1], mat[1][2],
+ mat[2][0], mat[2][1], mat[2][2] );
+ fprintf( fout, "inv: %g %g %g\n %g %g %g\n %g %g %g\n",
+ inv[0][0], inv[0][1], inv[0][2],
+ inv[1][0], inv[1][1], inv[1][2],
+ inv[2][0], inv[2][1], inv[2][2] );
+ fflush( fout ); */
+ fprintf( stderr, "avcm: %24.15e %24.15e %24.15e\n",
+ data->avcm[0], data->avcm[1], data->avcm[2] );
#endif
}
void Compute_Kinetic_Energy( reax_system* system, simulation_data* data )
{
- int i;
- rvec p;
- real m;
-
- data->E_Kin = 0.0;
-
- for (i=0; i < system->N; i++) {
- m = system->reaxprm.sbp[system->atoms[i].type].mass;
-
- rvec_Scale( p, m, system->atoms[i].v );
- data->E_Kin += 0.5 * rvec_Dot( p, system->atoms[i].v );
-
- /* fprintf(stderr,"%d, %lf, %lf, %lf %lf\n",
- i,system->atoms[i].v[0], system->atoms[i].v[1], system->atoms[i].v[2],
- system->reaxprm.sbp[system->atoms[i].type].mass); */
- }
-
- data->therm.T = (2. * data->E_Kin) / (data->N_f * K_B);
-
- if ( fabs(data->therm.T) < ALMOST_ZERO ) /* avoid T being an absolute zero! */
- data->therm.T = ALMOST_ZERO;
+ int i;
+ rvec p;
+ real m;
+
+ data->E_Kin = 0.0;
+
+ for (i = 0; i < system->N; i++)
+ {
+ m = system->reaxprm.sbp[system->atoms[i].type].mass;
+
+ rvec_Scale( p, m, system->atoms[i].v );
+ data->E_Kin += 0.5 * rvec_Dot( p, system->atoms[i].v );
+
+ /* fprintf(stderr,"%d, %lf, %lf, %lf %lf\n",
+ i,system->atoms[i].v[0], system->atoms[i].v[1], system->atoms[i].v[2],
+ system->reaxprm.sbp[system->atoms[i].type].mass); */
+ }
+
+ data->therm.T = (2. * data->E_Kin) / (data->N_f * K_B);
+
+ if ( fabs(data->therm.T) < ALMOST_ZERO ) /* avoid T being an absolute zero! */
+ data->therm.T = ALMOST_ZERO;
}
-/* IMPORTANT: This function assumes that current kinetic energy and
- * the center of mass of the system is already computed before.
+/* IMPORTANT: This function assumes that current kinetic energy and
+ * the center of mass of the system is already computed before.
*
- * IMPORTANT: In Klein's paper, it is stated that a dU/dV term needs
- * to be added when there are long-range interactions or long-range
+ * IMPORTANT: In Klein's paper, it is stated that a dU/dV term needs
+ * to be added when there are long-range interactions or long-range
* corrections to short-range interactions present.
- * We may want to add that for more accuracy.
+ * We may want to add that for more accuracy.
*/
-void Compute_Pressure_Isotropic( reax_system* system, control_params *control,
- simulation_data* data,
- output_controls *out_control )
+void Compute_Pressure_Isotropic( reax_system* system, control_params *control,
+ simulation_data* data,
+ output_controls *out_control )
{
- int i;
- reax_atom *p_atom;
- rvec tx;
- rvec tmp;
- simulation_box *box = &(system->box);
-
- /* Calculate internal pressure */
- rvec_MakeZero( data->int_press );
-
- // 0: both int and ext, 1: ext only, 2: int only
- if( control->press_mode == 0 || control->press_mode == 2 ) {
- for( i = 0; i < system->N; ++i ) {
- p_atom = &( system->atoms[i] );
-
- /* transform x into unitbox coordinates */
- Transform_to_UnitBox( p_atom->x, box, 1, tx );
-
- /* this atom's contribution to internal pressure */
- rvec_Multiply( tmp, p_atom->f, tx );
- rvec_Add( data->int_press, tmp );
-
- if( out_control->debug_level > 0 ) {
- fprintf( out_control->prs, "%-8d%8.2f%8.2f%8.2f",
- i+1, p_atom->x[0], p_atom->x[1], p_atom->x[2] );
- fprintf( out_control->prs, "%8.2f%8.2f%8.2f",
- p_atom->f[0], p_atom->f[1], p_atom->f[2] );
- fprintf( out_control->prs, "%8.2f%8.2f%8.2f\n",
- data->int_press[0],data->int_press[1],data->int_press[2]);
- }
+ int i;
+ reax_atom *p_atom;
+ rvec tx;
+ rvec tmp;
+ simulation_box *box = &(system->box);
+
+ /* Calculate internal pressure */
+ rvec_MakeZero( data->int_press );
+
+ // 0: both int and ext, 1: ext only, 2: int only
+ if ( control->press_mode == 0 || control->press_mode == 2 )
+ {
+ for ( i = 0; i < system->N; ++i )
+ {
+ p_atom = &( system->atoms[i] );
+
+ /* transform x into unitbox coordinates */
+ Transform_to_UnitBox( p_atom->x, box, 1, tx );
+
+ /* this atom's contribution to internal pressure */
+ rvec_Multiply( tmp, p_atom->f, tx );
+ rvec_Add( data->int_press, tmp );
+
+ if ( out_control->debug_level > 0 )
+ {
+ fprintf( out_control->prs, "%-8d%8.2f%8.2f%8.2f",
+ i + 1, p_atom->x[0], p_atom->x[1], p_atom->x[2] );
+ fprintf( out_control->prs, "%8.2f%8.2f%8.2f",
+ p_atom->f[0], p_atom->f[1], p_atom->f[2] );
+ fprintf( out_control->prs, "%8.2f%8.2f%8.2f\n",
+ data->int_press[0], data->int_press[1], data->int_press[2]);
+ }
+ }
}
- }
-
- /* kinetic contribution */
- data->kin_press = 2. * (E_CONV * data->E_Kin) / ( 3. * box->volume * P_CONV );
-
- /* Calculate total pressure in each direction */
- data->tot_press[0] = data->kin_press -
- ((data->int_press[0] + data->ext_press[0]) /
- (box->box_norms[1] * box->box_norms[2] * P_CONV));
-
- data->tot_press[1] = data->kin_press -
- ((data->int_press[1] + data->ext_press[1])/
- (box->box_norms[0] * box->box_norms[2] * P_CONV));
-
- data->tot_press[2] = data->kin_press -
- ((data->int_press[2] + data->ext_press[2])/
- (box->box_norms[0] * box->box_norms[1] * P_CONV));
-
- /* Average pressure for the whole box */
- data->iso_bar.P=(data->tot_press[0]+data->tot_press[1]+data->tot_press[2])/3;
+
+ /* kinetic contribution */
+ data->kin_press = 2. * (E_CONV * data->E_Kin) / ( 3. * box->volume * P_CONV );
+
+ /* Calculate total pressure in each direction */
+ data->tot_press[0] = data->kin_press -
+ ((data->int_press[0] + data->ext_press[0]) /
+ (box->box_norms[1] * box->box_norms[2] * P_CONV));
+
+ data->tot_press[1] = data->kin_press -
+ ((data->int_press[1] + data->ext_press[1]) /
+ (box->box_norms[0] * box->box_norms[2] * P_CONV));
+
+ data->tot_press[2] = data->kin_press -
+ ((data->int_press[2] + data->ext_press[2]) /
+ (box->box_norms[0] * box->box_norms[1] * P_CONV));
+
+ /* Average pressure for the whole box */
+ data->iso_bar.P = (data->tot_press[0] + data->tot_press[1] + data->tot_press[2]) / 3;
}
-void Compute_Pressure_Isotropic_Klein( reax_system* system,
- simulation_data* data )
+void Compute_Pressure_Isotropic_Klein( reax_system* system,
+ simulation_data* data )
{
- int i;
- reax_atom *p_atom;
- rvec dx;
+ int i;
+ reax_atom *p_atom;
+ rvec dx;
- // IMPORTANT: This function assumes that current kinetic energy and
- // the center of mass of the system is already computed before.
- data->iso_bar.P = 2.0 * data->E_Kin;
+ // IMPORTANT: This function assumes that current kinetic energy and
+ // the center of mass of the system is already computed before.
+ data->iso_bar.P = 2.0 * data->E_Kin;
- for( i = 0; i < system->N; ++i )
+ for ( i = 0; i < system->N; ++i )
{
- p_atom = &( system->atoms[i] );
- rvec_ScaledSum(dx,1.0,p_atom->x,-1.0,data->xcm);
- data->iso_bar.P += ( -F_CONV * rvec_Dot(p_atom->f, dx) );
+ p_atom = &( system->atoms[i] );
+ rvec_ScaledSum(dx, 1.0, p_atom->x, -1.0, data->xcm);
+ data->iso_bar.P += ( -F_CONV * rvec_Dot(p_atom->f, dx) );
}
- data->iso_bar.P /= (3.0 * system->box.volume);
+ data->iso_bar.P /= (3.0 * system->box.volume);
- // IMPORTANT: In Klein's paper, it is stated that a dU/dV term needs
- // to be added when there are long-range interactions or long-range
- // corrections to short-range interactions present.
- // We may want to add that for more accuracy.
+ // IMPORTANT: In Klein's paper, it is stated that a dU/dV term needs
+ // to be added when there are long-range interactions or long-range
+ // corrections to short-range interactions present.
+ // We may want to add that for more accuracy.
}
-void Compute_Pressure( reax_system* system, simulation_data* data,
- static_storage *workspace )
+void Compute_Pressure( reax_system* system, simulation_data* data,
+ static_storage *workspace )
{
- int i;
- reax_atom *p_atom;
- rtensor temp;
-
- rtensor_MakeZero( data->flex_bar.P );
-
- for( i = 0; i < system->N; ++i ) {
- p_atom = &( system->atoms[i] );
- // Distance_on_T3_Gen( data->rcm, p_atom->x, &(system->box), &dx );
- rvec_OuterProduct( temp, p_atom->v, p_atom->v );
- rtensor_ScaledAdd( data->flex_bar.P,
- system->reaxprm.sbp[ p_atom->type ].mass, temp );
- // rvec_OuterProduct(temp, workspace->virial_forces[i], p_atom->x );
- rtensor_ScaledAdd( data->flex_bar.P, -F_CONV, temp );
- }
-
- rtensor_Scale( data->flex_bar.P, 1.0 / system->box.volume, data->flex_bar.P );
- data->iso_bar.P = rtensor_Trace( data->flex_bar.P ) / 3.0;
+ int i;
+ reax_atom *p_atom;
+ rtensor temp;
+
+ rtensor_MakeZero( data->flex_bar.P );
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ p_atom = &( system->atoms[i] );
+ // Distance_on_T3_Gen( data->rcm, p_atom->x, &(system->box), &dx );
+ rvec_OuterProduct( temp, p_atom->v, p_atom->v );
+ rtensor_ScaledAdd( data->flex_bar.P,
+ system->reaxprm.sbp[ p_atom->type ].mass, temp );
+ // rvec_OuterProduct(temp, workspace->virial_forces[i], p_atom->x );
+ rtensor_ScaledAdd( data->flex_bar.P, -F_CONV, temp );
+ }
+
+ rtensor_Scale( data->flex_bar.P, 1.0 / system->box.volume, data->flex_bar.P );
+ data->iso_bar.P = rtensor_Trace( data->flex_bar.P ) / 3.0;
}
diff --git a/puremd_rc_1003/sPuReMD/system_props.h b/puremd_rc_1003/sPuReMD/system_props.h
index 0300707e7f8af7c580a0aae58396b8fc77fda62e..6a5ed1d9b4235d406ee56b8c6536175e32c189ab 100644
--- a/puremd_rc_1003/sPuReMD/system_props.h
+++ b/puremd_rc_1003/sPuReMD/system_props.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
diff --git a/puremd_rc_1003/sPuReMD/testmd.c b/puremd_rc_1003/sPuReMD/testmd.c
index 527adca07f3fde49e0a9d5129e75372a4da3e572..f6e9003c3e81cfec46f2292d35a08b398d549bb4 100644
--- a/puremd_rc_1003/sPuReMD/testmd.c
+++ b/puremd_rc_1003/sPuReMD/testmd.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -36,94 +36,100 @@
#include "vector.h"
-void Post_Evolve( reax_system* system, control_params* control,
- simulation_data* data, static_storage* workspace,
- list** lists, output_controls *out_control )
+void Post_Evolve( reax_system* system, control_params* control,
+ simulation_data* data, static_storage* workspace,
+ list** lists, output_controls *out_control )
{
- int i;
- rvec diff, cross;
-
- /* if velocity dependent force then
- {
- Generate_Neighbor_Lists( &system, &control, &lists );
- QEq(system, control, workspace, lists[FAR_NBRS]);
- Introduce compute_force here if we are using velocity dependent forces
- Compute_Forces(system,control,data,workspace,lists);
- } */
-
- /* compute kinetic energy of the system */
- Compute_Kinetic_Energy( system, data );
-
- /* remove rotational and translational velocity of the center of mass */
- if( control->ensemble != NVE &&
- control->remove_CoM_vel &&
- data->step && data->step % control->remove_CoM_vel == 0 ) {
-
- /* compute velocity of the center of mass */
- Compute_Center_of_Mass( system, data, out_control->prs );
-
- for( i = 0; i < system->N; i++ ) {
- // remove translational
- rvec_ScaledAdd( system->atoms[i].v, -1., data->vcm );
-
- // remove rotational
- rvec_ScaledSum( diff, 1., system->atoms[i].x, -1., data->xcm );
- rvec_Cross( cross, data->avcm, diff );
- rvec_ScaledAdd( system->atoms[i].v, -1., cross );
+ int i;
+ rvec diff, cross;
+
+ /* if velocity dependent force then
+ {
+ Generate_Neighbor_Lists( &system, &control, &lists );
+ QEq(system, control, workspace, lists[FAR_NBRS]);
+ Introduce compute_force here if we are using velocity dependent forces
+ Compute_Forces(system,control,data,workspace,lists);
+ } */
+
+ /* compute kinetic energy of the system */
+ Compute_Kinetic_Energy( system, data );
+
+ /* remove rotational and translational velocity of the center of mass */
+ if ( control->ensemble != NVE &&
+ control->remove_CoM_vel &&
+ data->step && data->step % control->remove_CoM_vel == 0 )
+ {
+
+ /* compute velocity of the center of mass */
+ Compute_Center_of_Mass( system, data, out_control->prs );
+
+ for ( i = 0; i < system->N; i++ )
+ {
+ // remove translational
+ rvec_ScaledAdd( system->atoms[i].v, -1., data->vcm );
+
+ // remove rotational
+ rvec_ScaledSum( diff, 1., system->atoms[i].x, -1., data->xcm );
+ rvec_Cross( cross, data->avcm, diff );
+ rvec_ScaledAdd( system->atoms[i].v, -1., cross );
+ }
}
- }
}
-void Read_System( char *geof, char *ff, char *ctrlf,
- reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- output_controls *out_control )
+void Read_System( char *geof, char *ff, char *ctrlf,
+ reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ output_controls *out_control )
{
- FILE *ffield, *ctrl;
-
- if ( (ffield = fopen( ff, "r" )) == NULL )
- {
- fprintf( stderr, "Error opening the ffield file!\n" );
- exit( FILE_NOT_FOUND_ERR );
- }
- if ( (ctrl = fopen( ctrlf, "r" )) == NULL )
- {
- fprintf( stderr, "Error opening the ffield file!\n" );
- exit( FILE_NOT_FOUND_ERR );
- }
-
- /* ffield file */
- Read_Force_Field( ffield, &(system->reaxprm) );
-
- /* control file */
- Read_Control_File( ctrl, system, control, out_control );
-
- /* geo file */
- if( control->geo_format == XYZ ) {
- fprintf( stderr, "xyz input is not implemented yet\n" );
- exit(1);
- }
- else if( control->geo_format == PDB )
- Read_PDB( geof, system, control, data, workspace );
- else if( control->geo_format == BGF )
- Read_BGF( geof, system, control, data, workspace );
- else if( control->geo_format == ASCII_RESTART ) {
- Read_ASCII_Restart( geof, system, control, data, workspace );
- control->restart = 1;
- }
- else if( control->geo_format == BINARY_RESTART ) {
- Read_Binary_Restart( geof, system, control, data, workspace );
- control->restart = 1;
- }
- else {
- fprintf( stderr, "unknown geo file format. terminating!\n" );
- exit(1);
- }
+ FILE *ffield, *ctrl;
+
+ if ( (ffield = fopen( ff, "r" )) == NULL )
+ {
+ fprintf( stderr, "Error opening the ffield file!\n" );
+ exit( FILE_NOT_FOUND_ERR );
+ }
+ if ( (ctrl = fopen( ctrlf, "r" )) == NULL )
+ {
+ fprintf( stderr, "Error opening the ffield file!\n" );
+ exit( FILE_NOT_FOUND_ERR );
+ }
+
+ /* ffield file */
+ Read_Force_Field( ffield, &(system->reaxprm) );
+
+ /* control file */
+ Read_Control_File( ctrl, system, control, out_control );
+
+ /* geo file */
+ if ( control->geo_format == XYZ )
+ {
+ fprintf( stderr, "xyz input is not implemented yet\n" );
+ exit(1);
+ }
+ else if ( control->geo_format == PDB )
+ Read_PDB( geof, system, control, data, workspace );
+ else if ( control->geo_format == BGF )
+ Read_BGF( geof, system, control, data, workspace );
+ else if ( control->geo_format == ASCII_RESTART )
+ {
+ Read_ASCII_Restart( geof, system, control, data, workspace );
+ control->restart = 1;
+ }
+ else if ( control->geo_format == BINARY_RESTART )
+ {
+ Read_Binary_Restart( geof, system, control, data, workspace );
+ control->restart = 1;
+ }
+ else
+ {
+ fprintf( stderr, "unknown geo file format. terminating!\n" );
+ exit(1);
+ }
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "input files have been read...\n" );
- Print_Box_Information( &(system->box), stderr );
+ fprintf( stderr, "input files have been read...\n" );
+ Print_Box_Information( &(system->box), stderr );
#endif
}
@@ -136,67 +142,69 @@ static void usage(char* argv[])
int main(int argc, char* argv[])
{
- reax_system system;
- control_params control;
- simulation_data data;
- static_storage workspace;
- list *lists;
- output_controls out_control;
- evolve_function Evolve;
- int steps;
-
- if( argc != 4 )
- {
- usage(argv);
- exit( INVALID_INPUT );
- }
-
- lists = (list*) malloc( sizeof(list) * LIST_N );
-
- Read_System( argv[1], argv[2], argv[3], &system, &control,
- &data, &workspace, &out_control );
-
- Initialize( &system, &control, &data, &workspace, &lists,
- &out_control, &Evolve );
-
- /* compute f_0 */
- //if( control.restart == 0 ) {
- Reset( &system, &control, &data, &workspace, &lists );
- Generate_Neighbor_Lists( &system, &control, &data, &workspace,
- &lists, &out_control );
-
- //fprintf( stderr, "total: %.2f secs\n", data.timing.nbrs);
- Compute_Forces(&system, &control, &data, &workspace, &lists, &out_control);
- Compute_Kinetic_Energy( &system, &data );
- Output_Results(&system, &control, &data, &workspace, &lists, &out_control);
- ++data.step;
- //}
- //
-
-
- for( ; data.step <= control.nsteps; data.step++ ) {
- if( control.T_mode )
- Temperature_Control( &control, &data, &out_control );
- Evolve( &system, &control, &data, &workspace, &lists, &out_control );
- Post_Evolve( &system, &control, &data, &workspace, &lists, &out_control );
+ reax_system system;
+ control_params control;
+ simulation_data data;
+ static_storage workspace;
+ list *lists;
+ output_controls out_control;
+ evolve_function Evolve;
+ int steps;
+
+ if ( argc != 4 )
+ {
+ usage(argv);
+ exit( INVALID_INPUT );
+ }
+
+ lists = (list*) malloc( sizeof(list) * LIST_N );
+
+ Read_System( argv[1], argv[2], argv[3], &system, &control,
+ &data, &workspace, &out_control );
+
+ Initialize( &system, &control, &data, &workspace, &lists,
+ &out_control, &Evolve );
+
+ /* compute f_0 */
+ //if( control.restart == 0 ) {
+ Reset( &system, &control, &data, &workspace, &lists );
+ Generate_Neighbor_Lists( &system, &control, &data, &workspace,
+ &lists, &out_control );
+
+ //fprintf( stderr, "total: %.2f secs\n", data.timing.nbrs);
+ Compute_Forces(&system, &control, &data, &workspace, &lists, &out_control);
+ Compute_Kinetic_Energy( &system, &data );
Output_Results(&system, &control, &data, &workspace, &lists, &out_control);
- Analysis( &system, &control, &data, &workspace, &lists, &out_control );
-
- steps = data.step - data.prev_steps;
- if( steps && out_control.restart_freq &&
- steps % out_control.restart_freq == 0 )
- Write_Restart( &system, &control, &data, &workspace, &out_control );
- }
-
- if( out_control.write_steps > 0 ) {
- fclose( out_control.trj );
- Write_PDB( &system, &control, &data, &workspace,
- &(lists[BONDS]), &out_control );
- }
-
- data.timing.end = Get_Time( );
- data.timing.elapsed = Get_Timing_Info( data.timing.start );
- fprintf( out_control.log, "total: %.2f secs\n", data.timing.elapsed );
-
- return 0;
+ ++data.step;
+ //}
+ //
+
+
+ for ( ; data.step <= control.nsteps; data.step++ )
+ {
+ if ( control.T_mode )
+ Temperature_Control( &control, &data, &out_control );
+ Evolve( &system, &control, &data, &workspace, &lists, &out_control );
+ Post_Evolve( &system, &control, &data, &workspace, &lists, &out_control );
+ Output_Results(&system, &control, &data, &workspace, &lists, &out_control);
+ Analysis( &system, &control, &data, &workspace, &lists, &out_control );
+
+ steps = data.step - data.prev_steps;
+ if ( steps && out_control.restart_freq &&
+ steps % out_control.restart_freq == 0 )
+ Write_Restart( &system, &control, &data, &workspace, &out_control );
+ }
+
+ if ( out_control.write_steps > 0 )
+ {
+ fclose( out_control.trj );
+ Write_PDB( &system, &control, &data, &workspace,
+ &(lists[BONDS]), &out_control );
+ }
+
+ data.timing.end = Get_Time( );
+ data.timing.elapsed = Get_Timing_Info( data.timing.start );
+ fprintf( out_control.log, "total: %.2f secs\n", data.timing.elapsed );
+
+ return 0;
}
diff --git a/puremd_rc_1003/sPuReMD/three_body_interactions.c b/puremd_rc_1003/sPuReMD/three_body_interactions.c
index 317571bfa0437fabc6049b7439225f98eaa5dd55..9aef73d4692e50b6a75de4897108b43bcd0e9a5b 100644
--- a/puremd_rc_1003/sPuReMD/three_body_interactions.c
+++ b/puremd_rc_1003/sPuReMD/three_body_interactions.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -27,750 +27,777 @@
/* calculates the theta angle between i-j-k */
-void Calculate_Theta( rvec dvec_ji, real d_ji, rvec dvec_jk, real d_jk,
- real *theta, real *cos_theta )
+void Calculate_Theta( rvec dvec_ji, real d_ji, rvec dvec_jk, real d_jk,
+ real *theta, real *cos_theta )
{
- (*cos_theta) = Dot( dvec_ji, dvec_jk, 3 ) / ( d_ji * d_jk );
- if( *cos_theta > 1. ) *cos_theta = 1.0;
- if( *cos_theta < -1. ) *cos_theta = -1.0;
+ (*cos_theta) = Dot( dvec_ji, dvec_jk, 3 ) / ( d_ji * d_jk );
+ if ( *cos_theta > 1. ) *cos_theta = 1.0;
+ if ( *cos_theta < -1. ) *cos_theta = -1.0;
- (*theta) = ACOS( *cos_theta );
+ (*theta) = ACOS( *cos_theta );
}
/* calculates the derivative of the cosine of the angle between i-j-k */
-void Calculate_dCos_Theta( rvec dvec_ji, real d_ji, rvec dvec_jk, real d_jk,
- rvec* dcos_theta_di, rvec* dcos_theta_dj,
- rvec* dcos_theta_dk )
+void Calculate_dCos_Theta( rvec dvec_ji, real d_ji, rvec dvec_jk, real d_jk,
+ rvec* dcos_theta_di, rvec* dcos_theta_dj,
+ rvec* dcos_theta_dk )
{
- int t;
- real sqr_d_ji = SQR(d_ji);
- real sqr_d_jk = SQR(d_jk);
- real inv_dists = 1.0 / (d_ji * d_jk);
- real inv_dists3 = POW( inv_dists, 3 );
- real dot_dvecs = Dot( dvec_ji, dvec_jk, 3 );
- real Cdot_inv3 = dot_dvecs * inv_dists3;
-
- for( t = 0; t < 3; ++t ) {
- (*dcos_theta_di)[t] = dvec_jk[t] * inv_dists -
- Cdot_inv3 * sqr_d_jk * dvec_ji[t];
-
- (*dcos_theta_dj)[t] = -(dvec_jk[t] + dvec_ji[t]) * inv_dists +
- Cdot_inv3 * ( sqr_d_jk * dvec_ji[t] + sqr_d_ji * dvec_jk[t] );
-
- (*dcos_theta_dk)[t] = dvec_ji[t] * inv_dists -
- Cdot_inv3 * sqr_d_ji * dvec_jk[t];
- }
-
- /*fprintf( stderr,
- "%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e\n",
- dvec_jk[t] * inv_dists*/
+ int t;
+ real sqr_d_ji = SQR(d_ji);
+ real sqr_d_jk = SQR(d_jk);
+ real inv_dists = 1.0 / (d_ji * d_jk);
+ real inv_dists3 = POW( inv_dists, 3 );
+ real dot_dvecs = Dot( dvec_ji, dvec_jk, 3 );
+ real Cdot_inv3 = dot_dvecs * inv_dists3;
+
+ for ( t = 0; t < 3; ++t )
+ {
+ (*dcos_theta_di)[t] = dvec_jk[t] * inv_dists -
+ Cdot_inv3 * sqr_d_jk * dvec_ji[t];
+
+ (*dcos_theta_dj)[t] = -(dvec_jk[t] + dvec_ji[t]) * inv_dists +
+ Cdot_inv3 * ( sqr_d_jk * dvec_ji[t] + sqr_d_ji * dvec_jk[t] );
+
+ (*dcos_theta_dk)[t] = dvec_ji[t] * inv_dists -
+ Cdot_inv3 * sqr_d_ji * dvec_jk[t];
+ }
+
+ /*fprintf( stderr,
+ "%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e\n",
+ dvec_jk[t] * inv_dists*/
}
-/* this is a 3-body interaction in which the main role is
+/* this is a 3-body interaction in which the main role is
played by j which sits in the middle of the other two. */
-void Three_Body_Interactions( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+void Three_Body_Interactions( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int i, j, pi, k, pk, t;
- int type_i, type_j, type_k;
- int start_j, end_j, start_pk, end_pk;
- int flag, cnt, num_thb_intrs;
-
- real temp, temp_bo_jt, pBOjt7;
- real p_val1, p_val2, p_val3, p_val4, p_val5;
- real p_val6, p_val7, p_val8, p_val9, p_val10;
- real p_pen1, p_pen2, p_pen3, p_pen4;
- real p_coa1, p_coa2, p_coa3, p_coa4;
- real trm8, expval6, expval7, expval2theta, expval12theta, exp3ij, exp3jk;
- real exp_pen2ij, exp_pen2jk, exp_pen3, exp_pen4, trm_pen34, exp_coa2;
- real dSBO1, dSBO2, SBO, SBO2, CSBO2, SBOp, prod_SBO;
- real CEval1, CEval2, CEval3, CEval4, CEval5, CEval6, CEval7, CEval8;
- real CEpen1, CEpen2, CEpen3;
- real e_ang, e_coa, e_pen;
- real CEcoa1, CEcoa2, CEcoa3, CEcoa4, CEcoa5;
- real Cf7ij, Cf7jk, Cf8j, Cf9j;
- real f7_ij, f7_jk, f8_Dj, f9_Dj;
- real Ctheta_0, theta_0, theta_00, theta, cos_theta, sin_theta;
- real r_ij, r_jk;
- real BOA_ij, BOA_jk;
- real vlpadj;
- rvec force, ext_press;
- // rtensor temp_rtensor, total_rtensor;
- real *total_bo;
- three_body_header *thbh;
- three_body_parameters *thbp;
- three_body_interaction_data *p_ijk, *p_kji;
- bond_data *pbond_ij, *pbond_jk, *pbond_jt;
- bond_order_data *bo_ij, *bo_jk, *bo_jt;
- list *bonds, *thb_intrs;
- bond_data *bond_list;
- three_body_interaction_data *thb_list;
-
- total_bo = workspace->total_bond_order;
- bonds = (*lists) + BONDS;
- bond_list = bonds->select.bond_list;
- thb_intrs = (*lists) + THREE_BODIES;
- thb_list = thb_intrs->select.three_body_list;
-
- /* global parameters used in these calculations */
- p_val6 = system->reaxprm.gp.l[14];
- p_val8 = system->reaxprm.gp.l[33];
- p_val9 = system->reaxprm.gp.l[16];
- p_val10 = system->reaxprm.gp.l[17];
- num_thb_intrs = 0;
-
- for( j = 0; j < system->N; ++j ) {
- // fprintf( out_control->eval, "j: %d\n", j );
- type_j = system->atoms[j].type;
- start_j = Start_Index(j, bonds);
- end_j = End_Index(j, bonds);
-
- p_val3 = system->reaxprm.sbp[ type_j ].p_val3;
- p_val5 = system->reaxprm.sbp[ type_j ].p_val5;
-
- SBOp = 0, prod_SBO = 1;
- for( t = start_j; t < end_j; ++t ) {
- bo_jt = &(bond_list[t].bo_data);
- SBOp += (bo_jt->BO_pi + bo_jt->BO_pi2);
- temp = SQR( bo_jt->BO );
- temp *= temp;
- temp *= temp;
- prod_SBO *= EXP( -temp );
- }
-
- /* modifications to match Adri's code - 09/01/09 */
- if( workspace->vlpex[j] >= 0 ){
- vlpadj = 0;
- dSBO2 = prod_SBO - 1;
- }
- else{
- vlpadj = workspace->nlp[j];
- dSBO2 = (prod_SBO - 1) * (1 - p_val8 * workspace->dDelta_lp[j]);
- }
+ int i, j, pi, k, pk, t;
+ int type_i, type_j, type_k;
+ int start_j, end_j, start_pk, end_pk;
+ int flag, cnt, num_thb_intrs;
- SBO = SBOp + (1 - prod_SBO) * (-workspace->Delta_boc[j] - p_val8 * vlpadj);
- dSBO1 = -8 * prod_SBO * ( workspace->Delta_boc[j] + p_val8 * vlpadj );
+ real temp, temp_bo_jt, pBOjt7;
+ real p_val1, p_val2, p_val3, p_val4, p_val5;
+ real p_val6, p_val7, p_val8, p_val9, p_val10;
+ real p_pen1, p_pen2, p_pen3, p_pen4;
+ real p_coa1, p_coa2, p_coa3, p_coa4;
+ real trm8, expval6, expval7, expval2theta, expval12theta, exp3ij, exp3jk;
+ real exp_pen2ij, exp_pen2jk, exp_pen3, exp_pen4, trm_pen34, exp_coa2;
+ real dSBO1, dSBO2, SBO, SBO2, CSBO2, SBOp, prod_SBO;
+ real CEval1, CEval2, CEval3, CEval4, CEval5, CEval6, CEval7, CEval8;
+ real CEpen1, CEpen2, CEpen3;
+ real e_ang, e_coa, e_pen;
+ real CEcoa1, CEcoa2, CEcoa3, CEcoa4, CEcoa5;
+ real Cf7ij, Cf7jk, Cf8j, Cf9j;
+ real f7_ij, f7_jk, f8_Dj, f9_Dj;
+ real Ctheta_0, theta_0, theta_00, theta, cos_theta, sin_theta;
+ real r_ij, r_jk;
+ real BOA_ij, BOA_jk;
+ real vlpadj;
+ rvec force, ext_press;
+ // rtensor temp_rtensor, total_rtensor;
+ real *total_bo;
+ three_body_header *thbh;
+ three_body_parameters *thbp;
+ three_body_interaction_data *p_ijk, *p_kji;
+ bond_data *pbond_ij, *pbond_jk, *pbond_jt;
+ bond_order_data *bo_ij, *bo_jk, *bo_jt;
+ list *bonds, *thb_intrs;
+ bond_data *bond_list;
+ three_body_interaction_data *thb_list;
+
+ total_bo = workspace->total_bond_order;
+ bonds = (*lists) + BONDS;
+ bond_list = bonds->select.bond_list;
+ thb_intrs = (*lists) + THREE_BODIES;
+ thb_list = thb_intrs->select.three_body_list;
+
+ /* global parameters used in these calculations */
+ p_val6 = system->reaxprm.gp.l[14];
+ p_val8 = system->reaxprm.gp.l[33];
+ p_val9 = system->reaxprm.gp.l[16];
+ p_val10 = system->reaxprm.gp.l[17];
+ num_thb_intrs = 0;
+
+ for ( j = 0; j < system->N; ++j )
+ {
+ // fprintf( out_control->eval, "j: %d\n", j );
+ type_j = system->atoms[j].type;
+ start_j = Start_Index(j, bonds);
+ end_j = End_Index(j, bonds);
+
+ p_val3 = system->reaxprm.sbp[ type_j ].p_val3;
+ p_val5 = system->reaxprm.sbp[ type_j ].p_val5;
+
+ SBOp = 0, prod_SBO = 1;
+ for ( t = start_j; t < end_j; ++t )
+ {
+ bo_jt = &(bond_list[t].bo_data);
+ SBOp += (bo_jt->BO_pi + bo_jt->BO_pi2);
+ temp = SQR( bo_jt->BO );
+ temp *= temp;
+ temp *= temp;
+ prod_SBO *= EXP( -temp );
+ }
+
+ /* modifications to match Adri's code - 09/01/09 */
+ if ( workspace->vlpex[j] >= 0 )
+ {
+ vlpadj = 0;
+ dSBO2 = prod_SBO - 1;
+ }
+ else
+ {
+ vlpadj = workspace->nlp[j];
+ dSBO2 = (prod_SBO - 1) * (1 - p_val8 * workspace->dDelta_lp[j]);
+ }
+
+ SBO = SBOp + (1 - prod_SBO) * (-workspace->Delta_boc[j] - p_val8 * vlpadj);
+ dSBO1 = -8 * prod_SBO * ( workspace->Delta_boc[j] + p_val8 * vlpadj );
+
+ if ( SBO <= 0 )
+ SBO2 = 0, CSBO2 = 0;
+ else if ( SBO > 0 && SBO <= 1 )
+ {
+ SBO2 = POW( SBO, p_val9 );
+ CSBO2 = p_val9 * POW( SBO, p_val9 - 1 );
+ }
+ else if ( SBO > 1 && SBO < 2 )
+ {
+ SBO2 = 2 - POW( 2 - SBO, p_val9 );
+ CSBO2 = p_val9 * POW( 2 - SBO, p_val9 - 1 );
+ }
+ else
+ SBO2 = 2, CSBO2 = 0;
+
+ expval6 = EXP( p_val6 * workspace->Delta_boc[j] );
+
+ /* unlike 2-body intrs where we enforce i<j, we cannot put any such
+ restrictions here. such a restriction would prevent us from producing
+ all 4-body intrs correctly */
+ for ( pi = start_j; pi < end_j; ++pi )
+ {
+ Set_Start_Index( pi, num_thb_intrs, thb_intrs );
+ pbond_ij = &(bond_list[pi]);
+ bo_ij = &(pbond_ij->bo_data);
+ BOA_ij = bo_ij->BO - control->thb_cut;
+
+
+ if ( BOA_ij/*bo_ij->BO*/ > 0.0 )
+ {
+ i = pbond_ij->nbr;
+ r_ij = pbond_ij->d;
+ type_i = system->atoms[i].type;
+ // fprintf( out_control->eval, "i: %d\n", i );
+
+
+ /* first copy 3-body intrs from previously computed ones where i>k.
+ IMPORTANT: if it is less costly to compute theta and its
+ derivative, we should definitely re-compute them,
+ instead of copying!
+ in the second for-loop below, we compute only new 3-body intrs
+ where i < k */
+ for ( pk = start_j; pk < pi; ++pk )
+ {
+ // fprintf( out_control->eval, "pk: %d\n", pk );
+ start_pk = Start_Index( pk, thb_intrs );
+ end_pk = End_Index( pk, thb_intrs );
+
+ for ( t = start_pk; t < end_pk; ++t )
+ if ( thb_list[t].thb == i )
+ {
+ p_ijk = &(thb_list[num_thb_intrs]);
+ p_kji = &(thb_list[t]);
+
+ p_ijk->thb = bond_list[pk].nbr;
+ p_ijk->pthb = pk;
+ p_ijk->theta = p_kji->theta;
+ rvec_Copy( p_ijk->dcos_di, p_kji->dcos_dk );
+ rvec_Copy( p_ijk->dcos_dj, p_kji->dcos_dj );
+ rvec_Copy( p_ijk->dcos_dk, p_kji->dcos_di );
+
+ ++num_thb_intrs;
+ break;
+ }
+ }
+
+
+ /* and this is the second for loop mentioned above */
+ for ( pk = pi + 1; pk < end_j; ++pk )
+ {
+ pbond_jk = &(bond_list[pk]);
+ bo_jk = &(pbond_jk->bo_data);
+ BOA_jk = bo_jk->BO - control->thb_cut;
+ k = pbond_jk->nbr;
+ type_k = system->atoms[k].type;
+ p_ijk = &( thb_list[num_thb_intrs] );
+
+ //CHANGE ORIGINAL
+ if (BOA_jk <= 0) continue;
+ //CHANGE ORIGINAL
+
+
+ Calculate_Theta( pbond_ij->dvec, pbond_ij->d,
+ pbond_jk->dvec, pbond_jk->d,
+ &theta, &cos_theta );
+
+ Calculate_dCos_Theta( pbond_ij->dvec, pbond_ij->d,
+ pbond_jk->dvec, pbond_jk->d,
+ &(p_ijk->dcos_di), &(p_ijk->dcos_dj),
+ &(p_ijk->dcos_dk) );
+
+ p_ijk->thb = k;
+ p_ijk->pthb = pk;
+ p_ijk->theta = theta;
+
+ sin_theta = SIN( theta );
+ if ( sin_theta < 1.0e-5 )
+ sin_theta = 1.0e-5;
+
+ ++num_thb_intrs;
+
+
+ if ( BOA_jk > 0.0 &&
+ (bo_ij->BO * bo_jk->BO) > SQR(control->thb_cut)/*0*/)
+ {
+ r_jk = pbond_jk->d;
+ thbh = &( system->reaxprm.thbp[type_i][type_j][type_k] );
+ flag = 0;
+
+ /* if( workspace->orig_id[i] < workspace->orig_id[k] )
+ fprintf( stdout, "%6d %6d %6d %7.3f %7.3f %7.3f\n",
+ workspace->orig_id[i], workspace->orig_id[j],
+ workspace->orig_id[k], bo_ij->BO, bo_jk->BO, p_ijk->theta );
+ else
+ fprintf( stdout, "%6d %6d %6d %7.3f %7.3f %7.3f\n",
+ workspace->orig_id[k], workspace->orig_id[j],
+ workspace->orig_id[i], bo_jk->BO, bo_ij->BO, p_ijk->theta ); */
+
+
+ for ( cnt = 0; cnt < thbh->cnt; ++cnt )
+ {
+ // fprintf( out_control->eval,
+ // "%6d%6d%6d -- exists in thbp\n", i+1, j+1, k+1 );
+
+ if ( fabs(thbh->prm[cnt].p_val1) > 0.001 )
+ {
+ thbp = &( thbh->prm[cnt] );
+
+ /* ANGLE ENERGY */
+ p_val1 = thbp->p_val1;
+ p_val2 = thbp->p_val2;
+ p_val4 = thbp->p_val4;
+ p_val7 = thbp->p_val7;
+ theta_00 = thbp->theta_00;
+
+ exp3ij = EXP( -p_val3 * POW( BOA_ij, p_val4 ) );
+ f7_ij = 1.0 - exp3ij;
+ Cf7ij = p_val3 * p_val4 *
+ POW( BOA_ij, p_val4 - 1.0 ) * exp3ij;
+
+ exp3jk = EXP( -p_val3 * POW( BOA_jk, p_val4 ) );
+ f7_jk = 1.0 - exp3jk;
+ Cf7jk = p_val3 * p_val4 *
+ POW( BOA_jk, p_val4 - 1.0 ) * exp3jk;
+
+ expval7 = EXP( -p_val7 * workspace->Delta_boc[j] );
+ trm8 = 1.0 + expval6 + expval7;
+ f8_Dj = p_val5 - ( (p_val5 - 1.0) * (2.0 + expval6) / trm8 );
+ Cf8j = ( (1.0 - p_val5) / SQR(trm8) ) *
+ (p_val6 * expval6 * trm8 -
+ (2.0 + expval6) * ( p_val6 * expval6 - p_val7 * expval7 ));
+
+ theta_0 = 180.0 -
+ theta_00 * (1.0 - EXP(-p_val10 * (2.0 - SBO2)));
+ theta_0 = DEG2RAD( theta_0 );
+
+ expval2theta = EXP(-p_val2 * SQR(theta_0 - theta));
+ if ( p_val1 >= 0 )
+ expval12theta = p_val1 * (1.0 - expval2theta);
+ else // To avoid linear Me-H-Me angles (6/6/06)
+ expval12theta = p_val1 * -expval2theta;
+
+ CEval1 = Cf7ij * f7_jk * f8_Dj * expval12theta;
+ CEval2 = Cf7jk * f7_ij * f8_Dj * expval12theta;
+ CEval3 = Cf8j * f7_ij * f7_jk * expval12theta;
+ CEval4 = -2.0 * p_val1 * p_val2 * f7_ij * f7_jk * f8_Dj *
+ expval2theta * (theta_0 - theta);
+
+ Ctheta_0 = p_val10 * DEG2RAD(theta_00) *
+ exp( -p_val10 * (2.0 - SBO2) );
+
+ CEval5 = -CEval4 * Ctheta_0 * CSBO2;
+ CEval6 = CEval5 * dSBO1;
+ CEval7 = CEval5 * dSBO2;
+ CEval8 = -CEval4 / sin_theta;
+
+ data->E_Ang += e_ang = f7_ij * f7_jk * f8_Dj * expval12theta;
+ /* END ANGLE ENERGY*/
+
+
+ /* PENALTY ENERGY */
+ p_pen1 = thbp->p_pen1;
+ p_pen2 = system->reaxprm.gp.l[19];
+ p_pen3 = system->reaxprm.gp.l[20];
+ p_pen4 = system->reaxprm.gp.l[21];
+
+ exp_pen2ij = EXP( -p_pen2 * SQR( BOA_ij - 2.0 ) );
+ exp_pen2jk = EXP( -p_pen2 * SQR( BOA_jk - 2.0 ) );
+ exp_pen3 = EXP( -p_pen3 * workspace->Delta[j] );
+ exp_pen4 = EXP( p_pen4 * workspace->Delta[j] );
+ trm_pen34 = 1.0 + exp_pen3 + exp_pen4;
+ f9_Dj = ( 2.0 + exp_pen3 ) / trm_pen34;
+ Cf9j = (-p_pen3 * exp_pen3 * trm_pen34 -
+ (2.0 + exp_pen3) * ( -p_pen3 * exp_pen3 +
+ p_pen4 * exp_pen4 )) /
+ SQR( trm_pen34 );
+
+ data->E_Pen += e_pen =
+ p_pen1 * f9_Dj * exp_pen2ij * exp_pen2jk;
+
+ CEpen1 = e_pen * Cf9j / f9_Dj;
+ temp = -2.0 * p_pen2 * e_pen;
+ CEpen2 = temp * (BOA_ij - 2.0);
+ CEpen3 = temp * (BOA_jk - 2.0);
+ /* END PENALTY ENERGY */
+
+
+ /* COALITION ENERGY */
+ p_coa1 = thbp->p_coa1;
+ p_coa2 = system->reaxprm.gp.l[2];
+ p_coa3 = system->reaxprm.gp.l[38];
+ p_coa4 = system->reaxprm.gp.l[30];
+
+ exp_coa2 = EXP( p_coa2 * workspace->Delta_boc[j] );
+ data->E_Coa += e_coa =
+ p_coa1 / (1. + exp_coa2) *
+ EXP( -p_coa3 * SQR(total_bo[i] - BOA_ij) ) *
+ EXP( -p_coa3 * SQR(total_bo[k] - BOA_jk) ) *
+ EXP( -p_coa4 * SQR(BOA_ij - 1.5) ) *
+ EXP( -p_coa4 * SQR(BOA_jk - 1.5) );
+
+ CEcoa1 = -2 * p_coa4 * (BOA_ij - 1.5) * e_coa;
+ CEcoa2 = -2 * p_coa4 * (BOA_jk - 1.5) * e_coa;
+ CEcoa3 = -p_coa2 * exp_coa2 * e_coa / (1 + exp_coa2);
+ CEcoa4 = -2 * p_coa3 * (total_bo[i] - BOA_ij) * e_coa;
+ CEcoa5 = -2 * p_coa3 * (total_bo[k] - BOA_jk) * e_coa;
+ /* END COALITION ENERGY */
+
+ /* FORCES */
+ bo_ij->Cdbo += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4));
+ bo_jk->Cdbo += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5));
+ workspace->CdDelta[j] += ((CEval3 + CEval7) +
+ CEpen1 + CEcoa3);
+ workspace->CdDelta[i] += CEcoa4;
+ workspace->CdDelta[k] += CEcoa5;
+
+ for ( t = start_j; t < end_j; ++t )
+ {
+ pbond_jt = &( bond_list[t] );
+ bo_jt = &(pbond_jt->bo_data);
+ temp_bo_jt = bo_jt->BO;
+ temp = CUBE( temp_bo_jt );
+ pBOjt7 = temp * temp * temp_bo_jt;
+
+ // fprintf( out_control->eval, "%6d%12.8f\n",
+ // workspace->orig_id[ bond_list[t].nbr ],
+ // (CEval6 * pBOjt7) );
+
+ bo_jt->Cdbo += (CEval6 * pBOjt7);
+ bo_jt->Cdbopi += CEval5;
+ bo_jt->Cdbopi2 += CEval5;
+ }
+
+
+ if ( control->ensemble == NVE || control->ensemble == NVT || control->ensemble == bNVT)
+ {
+ rvec_ScaledAdd( system->atoms[i].f, CEval8, p_ijk->dcos_di );
+ rvec_ScaledAdd( system->atoms[j].f, CEval8, p_ijk->dcos_dj );
+ rvec_ScaledAdd( system->atoms[k].f, CEval8, p_ijk->dcos_dk );
+ }
+ else
+ {
+ /* terms not related to bond order derivatives
+ are added directly into
+ forces and pressure vector/tensor */
+ rvec_Scale( force, CEval8, p_ijk->dcos_di );
+ rvec_Add( system->atoms[i].f, force );
+ rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
+ rvec_Add( data->ext_press, ext_press );
+
+ rvec_ScaledAdd( system->atoms[j].f,
+ CEval8, p_ijk->dcos_dj );
+
+ rvec_Scale( force, CEval8, p_ijk->dcos_dk );
+ rvec_Add( system->atoms[k].f, force );
+ rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
+ rvec_Add( data->ext_press, ext_press );
+
+
+ /* This part is for a fully-flexible box */
+ /* rvec_OuterProduct( temp_rtensor,
+ p_ijk->dcos_di, system->atoms[i].x );
+ rtensor_Scale( total_rtensor, +CEval8, temp_rtensor );
+
+ rvec_OuterProduct( temp_rtensor,
+ p_ijk->dcos_dj, system->atoms[j].x );
+ rtensor_ScaledAdd(total_rtensor, CEval8, temp_rtensor);
+
+ rvec_OuterProduct( temp_rtensor,
+ p_ijk->dcos_dk, system->atoms[k].x );
+ rtensor_ScaledAdd(total_rtensor, CEval8, temp_rtensor);
+
+ if( pbond_ij->imaginary || pbond_jk->imaginary )
+ rtensor_ScaledAdd( data->flex_bar.P,
+ -1.0, total_rtensor );
+ else
+ rtensor_Add( data->flex_bar.P, total_rtensor ); */
+ }
- if( SBO <= 0 )
- SBO2 = 0, CSBO2 = 0;
- else if( SBO > 0 && SBO <= 1 ) {
- SBO2 = POW( SBO, p_val9 );
- CSBO2 = p_val9 * POW( SBO, p_val9 - 1 );
- }
- else if( SBO > 1 && SBO < 2 ) {
- SBO2 = 2 - POW( 2-SBO, p_val9 );
- CSBO2 = p_val9 * POW( 2 - SBO, p_val9 - 1 );
- }
- else
- SBO2 = 2, CSBO2 = 0;
-
- expval6 = EXP( p_val6 * workspace->Delta_boc[j] );
-
- /* unlike 2-body intrs where we enforce i<j, we cannot put any such
- restrictions here. such a restriction would prevent us from producing
- all 4-body intrs correctly */
- for( pi = start_j; pi < end_j; ++pi ) {
- Set_Start_Index( pi, num_thb_intrs, thb_intrs );
- pbond_ij = &(bond_list[pi]);
- bo_ij = &(pbond_ij->bo_data);
- BOA_ij = bo_ij->BO - control->thb_cut;
-
-
- if( BOA_ij/*bo_ij->BO*/ > 0.0 ) {
- i = pbond_ij->nbr;
- r_ij = pbond_ij->d;
- type_i = system->atoms[i].type;
- // fprintf( out_control->eval, "i: %d\n", i );
-
-
- /* first copy 3-body intrs from previously computed ones where i>k.
- IMPORTANT: if it is less costly to compute theta and its
- derivative, we should definitely re-compute them,
- instead of copying!
- in the second for-loop below, we compute only new 3-body intrs
- where i < k */
- for( pk = start_j; pk < pi; ++pk ) {
- // fprintf( out_control->eval, "pk: %d\n", pk );
- start_pk = Start_Index( pk, thb_intrs );
- end_pk = End_Index( pk, thb_intrs );
-
- for( t = start_pk; t < end_pk; ++t )
- if( thb_list[t].thb == i ) {
- p_ijk = &(thb_list[num_thb_intrs]);
- p_kji = &(thb_list[t]);
-
- p_ijk->thb = bond_list[pk].nbr;
- p_ijk->pthb = pk;
- p_ijk->theta = p_kji->theta;
- rvec_Copy( p_ijk->dcos_di, p_kji->dcos_dk );
- rvec_Copy( p_ijk->dcos_dj, p_kji->dcos_dj );
- rvec_Copy( p_ijk->dcos_dk, p_kji->dcos_di );
-
- ++num_thb_intrs;
- break;
- }
- }
-
-
- /* and this is the second for loop mentioned above */
- for( pk = pi+1; pk < end_j; ++pk ) {
- pbond_jk = &(bond_list[pk]);
- bo_jk = &(pbond_jk->bo_data);
- BOA_jk = bo_jk->BO - control->thb_cut;
- k = pbond_jk->nbr;
- type_k = system->atoms[k].type;
- p_ijk = &( thb_list[num_thb_intrs] );
-
- //CHANGE ORIGINAL
- if (BOA_jk <= 0) continue;
- //CHANGE ORIGINAL
-
-
- Calculate_Theta( pbond_ij->dvec, pbond_ij->d,
- pbond_jk->dvec, pbond_jk->d,
- &theta, &cos_theta );
-
- Calculate_dCos_Theta( pbond_ij->dvec, pbond_ij->d,
- pbond_jk->dvec, pbond_jk->d,
- &(p_ijk->dcos_di), &(p_ijk->dcos_dj),
- &(p_ijk->dcos_dk) );
-
- p_ijk->thb = k;
- p_ijk->pthb = pk;
- p_ijk->theta = theta;
-
- sin_theta = SIN( theta );
- if( sin_theta < 1.0e-5 )
- sin_theta = 1.0e-5;
-
- ++num_thb_intrs;
-
-
- if( BOA_jk > 0.0 &&
- (bo_ij->BO * bo_jk->BO) > SQR(control->thb_cut)/*0*/) {
- r_jk = pbond_jk->d;
- thbh = &( system->reaxprm.thbp[type_i][type_j][type_k] );
- flag = 0;
-
- /* if( workspace->orig_id[i] < workspace->orig_id[k] )
- fprintf( stdout, "%6d %6d %6d %7.3f %7.3f %7.3f\n",
- workspace->orig_id[i], workspace->orig_id[j],
- workspace->orig_id[k], bo_ij->BO, bo_jk->BO, p_ijk->theta );
- else
- fprintf( stdout, "%6d %6d %6d %7.3f %7.3f %7.3f\n",
- workspace->orig_id[k], workspace->orig_id[j],
- workspace->orig_id[i], bo_jk->BO, bo_ij->BO, p_ijk->theta ); */
-
-
- for( cnt = 0; cnt < thbh->cnt; ++cnt ) {
- // fprintf( out_control->eval,
- // "%6d%6d%6d -- exists in thbp\n", i+1, j+1, k+1 );
-
- if( fabs(thbh->prm[cnt].p_val1) > 0.001 ) {
- thbp = &( thbh->prm[cnt] );
-
- /* ANGLE ENERGY */
- p_val1 = thbp->p_val1;
- p_val2 = thbp->p_val2;
- p_val4 = thbp->p_val4;
- p_val7 = thbp->p_val7;
- theta_00 = thbp->theta_00;
-
- exp3ij = EXP( -p_val3 * POW( BOA_ij, p_val4 ) );
- f7_ij = 1.0 - exp3ij;
- Cf7ij = p_val3 * p_val4 *
- POW( BOA_ij, p_val4 - 1.0 ) * exp3ij;
-
- exp3jk = EXP( -p_val3 * POW( BOA_jk, p_val4 ) );
- f7_jk = 1.0 - exp3jk;
- Cf7jk = p_val3 * p_val4 *
- POW( BOA_jk, p_val4 - 1.0 ) * exp3jk;
-
- expval7 = EXP( -p_val7 * workspace->Delta_boc[j] );
- trm8 = 1.0 + expval6 + expval7;
- f8_Dj = p_val5 - ( (p_val5 - 1.0) * (2.0 + expval6) / trm8 );
- Cf8j = ( (1.0 - p_val5) / SQR(trm8) ) *
- (p_val6 * expval6 * trm8 -
- (2.0 + expval6) * ( p_val6 * expval6 - p_val7 * expval7 ));
-
- theta_0 = 180.0 -
- theta_00 * (1.0 - EXP(-p_val10 * (2.0 - SBO2)));
- theta_0 = DEG2RAD( theta_0 );
-
- expval2theta = EXP(-p_val2 * SQR(theta_0-theta));
- if( p_val1 >= 0 )
- expval12theta = p_val1 * (1.0 - expval2theta);
- else // To avoid linear Me-H-Me angles (6/6/06)
- expval12theta = p_val1 * -expval2theta;
-
- CEval1 = Cf7ij * f7_jk * f8_Dj * expval12theta;
- CEval2 = Cf7jk * f7_ij * f8_Dj * expval12theta;
- CEval3 = Cf8j * f7_ij * f7_jk * expval12theta;
- CEval4 = -2.0 * p_val1 * p_val2 * f7_ij * f7_jk * f8_Dj *
- expval2theta * (theta_0 - theta);
-
- Ctheta_0 = p_val10 * DEG2RAD(theta_00) *
- exp( -p_val10 * (2.0 - SBO2) );
-
- CEval5 = -CEval4 * Ctheta_0 * CSBO2;
- CEval6 = CEval5 * dSBO1;
- CEval7 = CEval5 * dSBO2;
- CEval8 = -CEval4 / sin_theta;
-
- data->E_Ang += e_ang = f7_ij * f7_jk * f8_Dj * expval12theta;
- /* END ANGLE ENERGY*/
-
-
- /* PENALTY ENERGY */
- p_pen1 = thbp->p_pen1;
- p_pen2 = system->reaxprm.gp.l[19];
- p_pen3 = system->reaxprm.gp.l[20];
- p_pen4 = system->reaxprm.gp.l[21];
-
- exp_pen2ij = EXP( -p_pen2 * SQR( BOA_ij - 2.0 ) );
- exp_pen2jk = EXP( -p_pen2 * SQR( BOA_jk - 2.0 ) );
- exp_pen3 = EXP( -p_pen3 * workspace->Delta[j] );
- exp_pen4 = EXP( p_pen4 * workspace->Delta[j] );
- trm_pen34 = 1.0 + exp_pen3 + exp_pen4;
- f9_Dj = ( 2.0 + exp_pen3 ) / trm_pen34;
- Cf9j = (-p_pen3 * exp_pen3 * trm_pen34 -
- (2.0 + exp_pen3) * ( -p_pen3 * exp_pen3 +
- p_pen4 * exp_pen4 )) /
- SQR( trm_pen34 );
-
- data->E_Pen += e_pen =
- p_pen1 * f9_Dj * exp_pen2ij * exp_pen2jk;
-
- CEpen1 = e_pen * Cf9j / f9_Dj;
- temp = -2.0 * p_pen2 * e_pen;
- CEpen2 = temp * (BOA_ij - 2.0);
- CEpen3 = temp * (BOA_jk - 2.0);
- /* END PENALTY ENERGY */
-
-
- /* COALITION ENERGY */
- p_coa1 = thbp->p_coa1;
- p_coa2 = system->reaxprm.gp.l[2];
- p_coa3 = system->reaxprm.gp.l[38];
- p_coa4 = system->reaxprm.gp.l[30];
-
- exp_coa2 = EXP( p_coa2 * workspace->Delta_boc[j] );
- data->E_Coa += e_coa =
- p_coa1 / (1. + exp_coa2) *
- EXP( -p_coa3 * SQR(total_bo[i] - BOA_ij) ) *
- EXP( -p_coa3 * SQR(total_bo[k] - BOA_jk) ) *
- EXP( -p_coa4 * SQR(BOA_ij - 1.5) ) *
- EXP( -p_coa4 * SQR(BOA_jk - 1.5) );
-
- CEcoa1 = -2 * p_coa4 * (BOA_ij - 1.5) * e_coa;
- CEcoa2 = -2 * p_coa4 * (BOA_jk - 1.5) * e_coa;
- CEcoa3 = -p_coa2 * exp_coa2 * e_coa / (1+exp_coa2);
- CEcoa4 = -2*p_coa3 * (total_bo[i]-BOA_ij) * e_coa;
- CEcoa5 = -2*p_coa3 * (total_bo[k]-BOA_jk) * e_coa;
- /* END COALITION ENERGY */
-
- /* FORCES */
- bo_ij->Cdbo += (CEval1 + CEpen2 + (CEcoa1-CEcoa4));
- bo_jk->Cdbo += (CEval2 + CEpen3 + (CEcoa2-CEcoa5));
- workspace->CdDelta[j] += ((CEval3 + CEval7) +
- CEpen1 + CEcoa3);
- workspace->CdDelta[i] += CEcoa4;
- workspace->CdDelta[k] += CEcoa5;
-
- for( t = start_j; t < end_j; ++t ) {
- pbond_jt = &( bond_list[t] );
- bo_jt = &(pbond_jt->bo_data);
- temp_bo_jt = bo_jt->BO;
- temp = CUBE( temp_bo_jt );
- pBOjt7 = temp * temp * temp_bo_jt;
-
- // fprintf( out_control->eval, "%6d%12.8f\n",
- // workspace->orig_id[ bond_list[t].nbr ],
- // (CEval6 * pBOjt7) );
-
- bo_jt->Cdbo += (CEval6 * pBOjt7);
- bo_jt->Cdbopi += CEval5;
- bo_jt->Cdbopi2 += CEval5;
- }
-
-
- if( control->ensemble == NVE || control->ensemble == NVT || control->ensemble == bNVT) {
- rvec_ScaledAdd( system->atoms[i].f, CEval8, p_ijk->dcos_di );
- rvec_ScaledAdd( system->atoms[j].f, CEval8, p_ijk->dcos_dj );
- rvec_ScaledAdd( system->atoms[k].f, CEval8, p_ijk->dcos_dk );
- }
- else {
- /* terms not related to bond order derivatives
- are added directly into
- forces and pressure vector/tensor */
- rvec_Scale( force, CEval8, p_ijk->dcos_di );
- rvec_Add( system->atoms[i].f, force );
- rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
- rvec_Add( data->ext_press, ext_press );
-
- rvec_ScaledAdd( system->atoms[j].f,
- CEval8, p_ijk->dcos_dj );
-
- rvec_Scale( force, CEval8, p_ijk->dcos_dk );
- rvec_Add( system->atoms[k].f, force );
- rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
- rvec_Add( data->ext_press, ext_press );
-
-
- /* This part is for a fully-flexible box */
- /* rvec_OuterProduct( temp_rtensor,
- p_ijk->dcos_di, system->atoms[i].x );
- rtensor_Scale( total_rtensor, +CEval8, temp_rtensor );
-
- rvec_OuterProduct( temp_rtensor,
- p_ijk->dcos_dj, system->atoms[j].x );
- rtensor_ScaledAdd(total_rtensor, CEval8, temp_rtensor);
-
- rvec_OuterProduct( temp_rtensor,
- p_ijk->dcos_dk, system->atoms[k].x );
- rtensor_ScaledAdd(total_rtensor, CEval8, temp_rtensor);
-
- if( pbond_ij->imaginary || pbond_jk->imaginary )
- rtensor_ScaledAdd( data->flex_bar.P,
- -1.0, total_rtensor );
- else
- rtensor_Add( data->flex_bar.P, total_rtensor ); */
- }
-
#ifdef TEST_ENERGY
- fprintf( out_control->eval,
- //"%6d%6d%6d%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e",
- "%6d%6d%6d%23.15e%23.15e%23.15e\n",
- i+1, j+1, k+1,
- //workspace->orig_id[i]+1,
- //workspace->orig_id[j]+1,
- //workspace->orig_id[k]+1,
- //workspace->Delta_boc[j],
- RAD2DEG(theta), /*BOA_ij, BOA_jk, */
- e_ang, data->E_Ang );
-
- /*fprintf( out_control->eval,
- "%23.15e%23.15e%23.15e%23.15e",
- p_val3, p_val4, BOA_ij, BOA_jk );
- fprintf( out_control->eval,
- "%23.15e%23.15e%23.15e%23.15e",
- f7_ij, f7_jk, f8_Dj, expval12theta );
- fprintf( out_control->eval,
- "%23.15e%23.15e%23.15e%23.15e%23.15e\n",
- CEval1, CEval2, CEval3, CEval4, CEval5
- //CEval6, CEval7, CEval8 );*/
-
- /*fprintf( out_control->eval,
- "%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e\n",
- -p_ijk->dcos_di[0]/sin_theta,
- -p_ijk->dcos_di[1]/sin_theta,
- -p_ijk->dcos_di[2]/sin_theta,
- -p_ijk->dcos_dj[0]/sin_theta,
- -p_ijk->dcos_dj[1]/sin_theta,
- -p_ijk->dcos_dj[2]/sin_theta,
- -p_ijk->dcos_dk[0]/sin_theta,
- -p_ijk->dcos_dk[1]/sin_theta,
- -p_ijk->dcos_dk[2]/sin_theta );*/
-
- /* fprintf( out_control->epen,
- "%23.15e%23.15e%23.15e\n",
- CEpen1, CEpen2, CEpen3 );
- fprintf( out_control->epen,
- "%6d%6d%6d%23.15e%23.15e%23.15e%23.15e%23.15e\n",
- workspace->orig_id[i], workspace->orig_id[j],
- workspace->orig_id[k], RAD2DEG(theta),
- BOA_ij, BOA_jk, e_pen, data->E_Pen ); */
-
- fprintf( out_control->ecoa,
- "%6d%6d%6d%23.15e%23.15e%23.15e%23.15e%23.15e\n",
- workspace->orig_id[i],
- workspace->orig_id[j],
- workspace->orig_id[k],
- RAD2DEG(theta), BOA_ij, BOA_jk,
- e_coa, data->E_Coa );
+ fprintf( out_control->eval,
+ //"%6d%6d%6d%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e",
+ "%6d%6d%6d%23.15e%23.15e%23.15e\n",
+ i + 1, j + 1, k + 1,
+ //workspace->orig_id[i]+1,
+ //workspace->orig_id[j]+1,
+ //workspace->orig_id[k]+1,
+ //workspace->Delta_boc[j],
+ RAD2DEG(theta), /*BOA_ij, BOA_jk, */
+ e_ang, data->E_Ang );
+
+ /*fprintf( out_control->eval,
+ "%23.15e%23.15e%23.15e%23.15e",
+ p_val3, p_val4, BOA_ij, BOA_jk );
+ fprintf( out_control->eval,
+ "%23.15e%23.15e%23.15e%23.15e",
+ f7_ij, f7_jk, f8_Dj, expval12theta );
+ fprintf( out_control->eval,
+ "%23.15e%23.15e%23.15e%23.15e%23.15e\n",
+ CEval1, CEval2, CEval3, CEval4, CEval5
+ //CEval6, CEval7, CEval8 );*/
+
+ /*fprintf( out_control->eval,
+ "%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e%23.15e\n",
+ -p_ijk->dcos_di[0]/sin_theta,
+ -p_ijk->dcos_di[1]/sin_theta,
+ -p_ijk->dcos_di[2]/sin_theta,
+ -p_ijk->dcos_dj[0]/sin_theta,
+ -p_ijk->dcos_dj[1]/sin_theta,
+ -p_ijk->dcos_dj[2]/sin_theta,
+ -p_ijk->dcos_dk[0]/sin_theta,
+ -p_ijk->dcos_dk[1]/sin_theta,
+ -p_ijk->dcos_dk[2]/sin_theta );*/
+
+ /* fprintf( out_control->epen,
+ "%23.15e%23.15e%23.15e\n",
+ CEpen1, CEpen2, CEpen3 );
+ fprintf( out_control->epen,
+ "%6d%6d%6d%23.15e%23.15e%23.15e%23.15e%23.15e\n",
+ workspace->orig_id[i], workspace->orig_id[j],
+ workspace->orig_id[k], RAD2DEG(theta),
+ BOA_ij, BOA_jk, e_pen, data->E_Pen ); */
+
+ fprintf( out_control->ecoa,
+ "%6d%6d%6d%23.15e%23.15e%23.15e%23.15e%23.15e\n",
+ workspace->orig_id[i],
+ workspace->orig_id[j],
+ workspace->orig_id[k],
+ RAD2DEG(theta), BOA_ij, BOA_jk,
+ e_coa, data->E_Coa );
#endif
-
+
#ifdef TEST_FORCES /* angle forces */
- Add_dBO( system, lists, j, pi, CEval1, workspace->f_ang );
- Add_dBO( system, lists, j, pk, CEval2, workspace->f_ang );
- Add_dDelta( system, lists,
- j, CEval3 + CEval7, workspace->f_ang );
-
- for( t = start_j; t < end_j; ++t ) {
- pbond_jt = &( bond_list[t] );
- bo_jt = &(pbond_jt->bo_data);
- temp_bo_jt = bo_jt->BO;
- temp = CUBE( temp_bo_jt );
- pBOjt7 = temp * temp * temp_bo_jt;
-
- Add_dBO( system, lists, j, t, pBOjt7 * CEval6,
- workspace->f_ang );
- Add_dBOpinpi2( system, lists, j, t,
- CEval5, CEval5,
- workspace->f_ang, workspace->f_ang );
- }
-
- rvec_ScaledAdd( workspace->f_ang[i], CEval8, p_ijk->dcos_di );
- rvec_ScaledAdd( workspace->f_ang[j], CEval8, p_ijk->dcos_dj );
- rvec_ScaledAdd( workspace->f_ang[k], CEval8, p_ijk->dcos_dk );
- /* end angle forces */
-
- /* penalty forces */
- Add_dDelta( system, lists, j, CEpen1, workspace->f_pen );
- Add_dBO( system, lists, j, pi, CEpen2, workspace->f_pen );
- Add_dBO( system, lists, j, pk, CEpen3, workspace->f_pen );
- /* end penalty forces */
-
- /* coalition forces */
- Add_dBO( system, lists,
- j, pi, CEcoa1-CEcoa4, workspace->f_coa );
- Add_dBO( system, lists,
- j, pk, CEcoa2-CEcoa5, workspace->f_coa );
- Add_dDelta( system, lists, j, CEcoa3, workspace->f_coa );
- Add_dDelta( system, lists, i, CEcoa4, workspace->f_coa );
- Add_dDelta( system, lists, k, CEcoa5, workspace->f_coa );
- /* end coalition forces */
+ Add_dBO( system, lists, j, pi, CEval1, workspace->f_ang );
+ Add_dBO( system, lists, j, pk, CEval2, workspace->f_ang );
+ Add_dDelta( system, lists,
+ j, CEval3 + CEval7, workspace->f_ang );
+
+ for ( t = start_j; t < end_j; ++t )
+ {
+ pbond_jt = &( bond_list[t] );
+ bo_jt = &(pbond_jt->bo_data);
+ temp_bo_jt = bo_jt->BO;
+ temp = CUBE( temp_bo_jt );
+ pBOjt7 = temp * temp * temp_bo_jt;
+
+ Add_dBO( system, lists, j, t, pBOjt7 * CEval6,
+ workspace->f_ang );
+ Add_dBOpinpi2( system, lists, j, t,
+ CEval5, CEval5,
+ workspace->f_ang, workspace->f_ang );
+ }
+
+ rvec_ScaledAdd( workspace->f_ang[i], CEval8, p_ijk->dcos_di );
+ rvec_ScaledAdd( workspace->f_ang[j], CEval8, p_ijk->dcos_dj );
+ rvec_ScaledAdd( workspace->f_ang[k], CEval8, p_ijk->dcos_dk );
+ /* end angle forces */
+
+ /* penalty forces */
+ Add_dDelta( system, lists, j, CEpen1, workspace->f_pen );
+ Add_dBO( system, lists, j, pi, CEpen2, workspace->f_pen );
+ Add_dBO( system, lists, j, pk, CEpen3, workspace->f_pen );
+ /* end penalty forces */
+
+ /* coalition forces */
+ Add_dBO( system, lists,
+ j, pi, CEcoa1 - CEcoa4, workspace->f_coa );
+ Add_dBO( system, lists,
+ j, pk, CEcoa2 - CEcoa5, workspace->f_coa );
+ Add_dDelta( system, lists, j, CEcoa3, workspace->f_coa );
+ Add_dDelta( system, lists, i, CEcoa4, workspace->f_coa );
+ Add_dDelta( system, lists, k, CEcoa5, workspace->f_coa );
+ /* end coalition forces */
#endif
- }
- }
- }
- }
- }
-
- Set_End_Index(pi, num_thb_intrs, thb_intrs );
+ }
+ }
+ }
+ }
+ }
+
+ Set_End_Index(pi, num_thb_intrs, thb_intrs );
+ }
}
- }
-
-
- if( num_thb_intrs >= thb_intrs->num_intrs * DANGER_ZONE ) {
- workspace->realloc.num_3body = num_thb_intrs;
- if( num_thb_intrs > thb_intrs->num_intrs ) {
- fprintf( stderr, "step%d-ran out of space on angle_list: top=%d, max=%d",
- data->step, num_thb_intrs, thb_intrs->num_intrs );
- exit( INSUFFICIENT_SPACE );
+
+
+ if ( num_thb_intrs >= thb_intrs->num_intrs * DANGER_ZONE )
+ {
+ workspace->realloc.num_3body = num_thb_intrs;
+ if ( num_thb_intrs > thb_intrs->num_intrs )
+ {
+ fprintf( stderr, "step%d-ran out of space on angle_list: top=%d, max=%d",
+ data->step, num_thb_intrs, thb_intrs->num_intrs );
+ exit( INSUFFICIENT_SPACE );
+ }
}
- }
-
- //fprintf( stderr,"%d: Number of angle interactions: %d\n",
- // data->step, num_thb_intrs );
+
+ //fprintf( stderr,"%d: Number of angle interactions: %d\n",
+ // data->step, num_thb_intrs );
#ifdef TEST_ENERGY
- fprintf( stderr,"Number of angle interactions: %d\n", num_thb_intrs );
-
- fprintf( stderr,"Angle Energy:%g\t Penalty Energy:%g\t Coalition Energy:%g\n",
- data->E_Ang, data->E_Pen, data->E_Coa );
-
- fprintf( stderr,"3body: ext_press (%23.15e %23.15e %23.15e)\n",
- data->ext_press[0], data->ext_press[1], data->ext_press[2] );
+ fprintf( stderr, "Number of angle interactions: %d\n", num_thb_intrs );
+
+ fprintf( stderr, "Angle Energy:%g\t Penalty Energy:%g\t Coalition Energy:%g\n",
+ data->E_Ang, data->E_Pen, data->E_Coa );
+
+ fprintf( stderr, "3body: ext_press (%23.15e %23.15e %23.15e)\n",
+ data->ext_press[0], data->ext_press[1], data->ext_press[2] );
#endif
}
-void Hydrogen_Bonds( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+void Hydrogen_Bonds( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int i, j, k, pi, pk, itr, top;
- int type_i, type_j, type_k;
- int start_j, end_j, hb_start_j, hb_end_j;
- int hblist[MAX_BONDS];
- int num_hb_intrs = 0;
- real r_ij, r_jk, theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2;
- real e_hb, exp_hb2, exp_hb3, CEhb1, CEhb2, CEhb3;
- rvec dcos_theta_di, dcos_theta_dj, dcos_theta_dk;
- rvec dvec_jk, force, ext_press;
- ivec rel_jk;
- // rtensor temp_rtensor, total_rtensor;
- hbond_parameters *hbp;
- bond_order_data *bo_ij;
- bond_data *pbond_ij;
- far_neighbor_data *nbr_jk;
- list *bonds, *hbonds;
- bond_data *bond_list;
- hbond_data *hbond_list;
-
- bonds = (*lists) + BONDS;
- bond_list = bonds->select.bond_list;
-
- hbonds = (*lists) + HBONDS;
- hbond_list = hbonds->select.hbond_list;
-
- /* loops below discover the Hydrogen bonds between i-j-k triplets.
- here j is H atom and there has to be some bond between i and j.
- Hydrogen bond is between j and k.
- so in this function i->X, j->H, k->Z when we map
- variables onto the ones in the handout.*/
- for( j = 0; j < system->N; ++j )
- if( system->reaxprm.sbp[system->atoms[j].type].p_hbond==1 ) {// j must be H
- /*set j's variables */
- type_j = system->atoms[j].type;
- start_j = Start_Index(j, bonds);
- end_j = End_Index(j, bonds);
- hb_start_j = Start_Index( workspace->hbond_index[j], hbonds );
- hb_end_j = End_Index ( workspace->hbond_index[j], hbonds );
-
- top = 0;
- for( pi = start_j; pi < end_j; ++pi ) {
- pbond_ij = &( bond_list[pi] );
- i = pbond_ij->nbr;
- bo_ij = &(pbond_ij->bo_data);
- type_i = system->atoms[i].type;
-
- if( system->reaxprm.sbp[type_i].p_hbond == 2 &&
- bo_ij->BO >= HB_THRESHOLD )
- hblist[top++] = pi;
- }
-
- // fprintf( stderr, "j: %d, top: %d, hb_start_j: %d, hb_end_j:%d\n",
- // j, top, hb_start_j, hb_end_j );
-
- for( pk = hb_start_j; pk < hb_end_j; ++pk ) {
- /* set k's varibles */
- k = hbond_list[pk].nbr;
- type_k = system->atoms[k].type;
- nbr_jk = hbond_list[pk].ptr;
- r_jk = nbr_jk->d;
- rvec_Scale( dvec_jk, hbond_list[pk].scl, nbr_jk->dvec );
-
- for( itr=0; itr < top; ++itr ) {
- pi = hblist[itr];
- pbond_ij = &( bond_list[pi] );
- i = pbond_ij->nbr;
-
- if( i != k ) {
- bo_ij = &(pbond_ij->bo_data);
- type_i = system->atoms[i].type;
- r_ij = pbond_ij->d;
- hbp = &(system->reaxprm.hbp[ type_i ][ type_j ][ type_k ]);
- ++num_hb_intrs;
-
- Calculate_Theta( pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk,
- &theta, &cos_theta );
- /* the derivative of cos(theta) */
- Calculate_dCos_Theta( pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk,
- &dcos_theta_di, &dcos_theta_dj,
- &dcos_theta_dk );
-
- /* hydrogen bond energy*/
- sin_theta2 = SIN( theta/2.0 );
- sin_xhz4 = SQR(sin_theta2);
- sin_xhz4 *= sin_xhz4;
- cos_xhz1 = ( 1.0 - cos_theta );
- exp_hb2 = EXP( -hbp->p_hb2 * bo_ij->BO );
- exp_hb3 = EXP( -hbp->p_hb3 * ( hbp->r0_hb / r_jk +
- r_jk / hbp->r0_hb - 2.0 ) );
-
- data->E_HB += e_hb =
- hbp->p_hb1 * (1.0 - exp_hb2) * exp_hb3 * sin_xhz4;
-
- CEhb1 = hbp->p_hb1*hbp->p_hb2 * exp_hb2*exp_hb3 * sin_xhz4;
- CEhb2 = -hbp->p_hb1/2.0*(1.0 - exp_hb2) * exp_hb3 * cos_xhz1;
- CEhb3 = -hbp->p_hb3 * e_hb * (-hbp->r0_hb / SQR(r_jk) +
- 1.0 / hbp->r0_hb);
-
- /* hydrogen bond forces */
- bo_ij->Cdbo += CEhb1; // dbo term
-
- if( control->ensemble == NVE || control->ensemble == NVT || control->ensemble == bNVT) {
- rvec_ScaledAdd( system->atoms[i].f,
- +CEhb2, dcos_theta_di ); //dcos terms
- rvec_ScaledAdd( system->atoms[j].f,
- +CEhb2, dcos_theta_dj );
- rvec_ScaledAdd( system->atoms[k].f,
- +CEhb2, dcos_theta_dk );
- //dr terms
- rvec_ScaledAdd( system->atoms[j].f, -CEhb3/r_jk, dvec_jk );
- rvec_ScaledAdd( system->atoms[k].f, +CEhb3/r_jk, dvec_jk );
- }
- else
- {
- /* for pressure coupling, terms that are not related
- to bond order derivatives are added directly into
- pressure vector/tensor */
- rvec_Scale( force, +CEhb2, dcos_theta_di ); // dcos terms
- rvec_Add( system->atoms[i].f, force );
- rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
- rvec_ScaledAdd( data->ext_press, 1.0, ext_press );
-
- rvec_ScaledAdd( system->atoms[j].f, +CEhb2, dcos_theta_dj );
-
- ivec_Scale( rel_jk, hbond_list[pk].scl, nbr_jk->rel_box );
- rvec_Scale( force, +CEhb2, dcos_theta_dk );
- rvec_Add( system->atoms[k].f, force );
- rvec_iMultiply( ext_press, rel_jk, force );
- rvec_ScaledAdd( data->ext_press, 1.0, ext_press );
-
- //dr terms
- rvec_ScaledAdd( system->atoms[j].f, -CEhb3/r_jk, dvec_jk );
-
- rvec_Scale( force, CEhb3/r_jk, dvec_jk );
- rvec_Add( system->atoms[k].f, force );
- rvec_iMultiply( ext_press, rel_jk, force );
- rvec_ScaledAdd( data->ext_press, 1.0, ext_press );
-
- /* This part is intended for a fully-flexible box */
- /* rvec_OuterProduct( temp_rtensor,
- dcos_theta_di, system->atoms[i].x );
- rtensor_Scale( total_rtensor, -CEhb2, temp_rtensor );
-
- rvec_ScaledSum( temp_rvec, -CEhb2, dcos_theta_dj,
- -CEhb3/r_jk, pbond_jk->dvec );
- rvec_OuterProduct( temp_rtensor,
- temp_rvec, system->atoms[j].x );
- rtensor_Add( total_rtensor, temp_rtensor );
-
- rvec_ScaledSum( temp_rvec, -CEhb2, dcos_theta_dk,
- +CEhb3/r_jk, pbond_jk->dvec );
- rvec_OuterProduct( temp_rtensor,
- temp_rvec, system->atoms[k].x );
- rtensor_Add( total_rtensor, temp_rtensor );
-
- if( pbond_ij->imaginary || pbond_jk->imaginary )
- rtensor_ScaledAdd( data->flex_bar.P, -1.0, total_rtensor );
- else
- rtensor_Add( data->flex_bar.P, total_rtensor ); */
- }
-
+ int i, j, k, pi, pk, itr, top;
+ int type_i, type_j, type_k;
+ int start_j, end_j, hb_start_j, hb_end_j;
+ int hblist[MAX_BONDS];
+ int num_hb_intrs = 0;
+ real r_ij, r_jk, theta, cos_theta, sin_xhz4, cos_xhz1, sin_theta2;
+ real e_hb, exp_hb2, exp_hb3, CEhb1, CEhb2, CEhb3;
+ rvec dcos_theta_di, dcos_theta_dj, dcos_theta_dk;
+ rvec dvec_jk, force, ext_press;
+ ivec rel_jk;
+ // rtensor temp_rtensor, total_rtensor;
+ hbond_parameters *hbp;
+ bond_order_data *bo_ij;
+ bond_data *pbond_ij;
+ far_neighbor_data *nbr_jk;
+ list *bonds, *hbonds;
+ bond_data *bond_list;
+ hbond_data *hbond_list;
+
+ bonds = (*lists) + BONDS;
+ bond_list = bonds->select.bond_list;
+
+ hbonds = (*lists) + HBONDS;
+ hbond_list = hbonds->select.hbond_list;
+
+ /* loops below discover the Hydrogen bonds between i-j-k triplets.
+ here j is H atom and there has to be some bond between i and j.
+ Hydrogen bond is between j and k.
+ so in this function i->X, j->H, k->Z when we map
+ variables onto the ones in the handout.*/
+ for ( j = 0; j < system->N; ++j )
+ if ( system->reaxprm.sbp[system->atoms[j].type].p_hbond == 1 ) // j must be H
+ {
+ /*set j's variables */
+ type_j = system->atoms[j].type;
+ start_j = Start_Index(j, bonds);
+ end_j = End_Index(j, bonds);
+ hb_start_j = Start_Index( workspace->hbond_index[j], hbonds );
+ hb_end_j = End_Index ( workspace->hbond_index[j], hbonds );
+
+ top = 0;
+ for ( pi = start_j; pi < end_j; ++pi )
+ {
+ pbond_ij = &( bond_list[pi] );
+ i = pbond_ij->nbr;
+ bo_ij = &(pbond_ij->bo_data);
+ type_i = system->atoms[i].type;
+
+ if ( system->reaxprm.sbp[type_i].p_hbond == 2 &&
+ bo_ij->BO >= HB_THRESHOLD )
+ hblist[top++] = pi;
+ }
+
+ // fprintf( stderr, "j: %d, top: %d, hb_start_j: %d, hb_end_j:%d\n",
+ // j, top, hb_start_j, hb_end_j );
+
+ for ( pk = hb_start_j; pk < hb_end_j; ++pk )
+ {
+ /* set k's varibles */
+ k = hbond_list[pk].nbr;
+ type_k = system->atoms[k].type;
+ nbr_jk = hbond_list[pk].ptr;
+ r_jk = nbr_jk->d;
+ rvec_Scale( dvec_jk, hbond_list[pk].scl, nbr_jk->dvec );
+
+ for ( itr = 0; itr < top; ++itr )
+ {
+ pi = hblist[itr];
+ pbond_ij = &( bond_list[pi] );
+ i = pbond_ij->nbr;
+
+ if ( i != k )
+ {
+ bo_ij = &(pbond_ij->bo_data);
+ type_i = system->atoms[i].type;
+ r_ij = pbond_ij->d;
+ hbp = &(system->reaxprm.hbp[ type_i ][ type_j ][ type_k ]);
+ ++num_hb_intrs;
+
+ Calculate_Theta( pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk,
+ &theta, &cos_theta );
+ /* the derivative of cos(theta) */
+ Calculate_dCos_Theta( pbond_ij->dvec, pbond_ij->d, dvec_jk, r_jk,
+ &dcos_theta_di, &dcos_theta_dj,
+ &dcos_theta_dk );
+
+ /* hydrogen bond energy*/
+ sin_theta2 = SIN( theta / 2.0 );
+ sin_xhz4 = SQR(sin_theta2);
+ sin_xhz4 *= sin_xhz4;
+ cos_xhz1 = ( 1.0 - cos_theta );
+ exp_hb2 = EXP( -hbp->p_hb2 * bo_ij->BO );
+ exp_hb3 = EXP( -hbp->p_hb3 * ( hbp->r0_hb / r_jk +
+ r_jk / hbp->r0_hb - 2.0 ) );
+
+ data->E_HB += e_hb =
+ hbp->p_hb1 * (1.0 - exp_hb2) * exp_hb3 * sin_xhz4;
+
+ CEhb1 = hbp->p_hb1 * hbp->p_hb2 * exp_hb2 * exp_hb3 * sin_xhz4;
+ CEhb2 = -hbp->p_hb1 / 2.0 * (1.0 - exp_hb2) * exp_hb3 * cos_xhz1;
+ CEhb3 = -hbp->p_hb3 * e_hb * (-hbp->r0_hb / SQR(r_jk) +
+ 1.0 / hbp->r0_hb);
+
+ /* hydrogen bond forces */
+ bo_ij->Cdbo += CEhb1; // dbo term
+
+ if ( control->ensemble == NVE || control->ensemble == NVT || control->ensemble == bNVT)
+ {
+ rvec_ScaledAdd( system->atoms[i].f,
+ +CEhb2, dcos_theta_di ); //dcos terms
+ rvec_ScaledAdd( system->atoms[j].f,
+ +CEhb2, dcos_theta_dj );
+ rvec_ScaledAdd( system->atoms[k].f,
+ +CEhb2, dcos_theta_dk );
+ //dr terms
+ rvec_ScaledAdd( system->atoms[j].f, -CEhb3 / r_jk, dvec_jk );
+ rvec_ScaledAdd( system->atoms[k].f, +CEhb3 / r_jk, dvec_jk );
+ }
+ else
+ {
+ /* for pressure coupling, terms that are not related
+ to bond order derivatives are added directly into
+ pressure vector/tensor */
+ rvec_Scale( force, +CEhb2, dcos_theta_di ); // dcos terms
+ rvec_Add( system->atoms[i].f, force );
+ rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
+ rvec_ScaledAdd( data->ext_press, 1.0, ext_press );
+
+ rvec_ScaledAdd( system->atoms[j].f, +CEhb2, dcos_theta_dj );
+
+ ivec_Scale( rel_jk, hbond_list[pk].scl, nbr_jk->rel_box );
+ rvec_Scale( force, +CEhb2, dcos_theta_dk );
+ rvec_Add( system->atoms[k].f, force );
+ rvec_iMultiply( ext_press, rel_jk, force );
+ rvec_ScaledAdd( data->ext_press, 1.0, ext_press );
+
+ //dr terms
+ rvec_ScaledAdd( system->atoms[j].f, -CEhb3 / r_jk, dvec_jk );
+
+ rvec_Scale( force, CEhb3 / r_jk, dvec_jk );
+ rvec_Add( system->atoms[k].f, force );
+ rvec_iMultiply( ext_press, rel_jk, force );
+ rvec_ScaledAdd( data->ext_press, 1.0, ext_press );
+
+ /* This part is intended for a fully-flexible box */
+ /* rvec_OuterProduct( temp_rtensor,
+ dcos_theta_di, system->atoms[i].x );
+ rtensor_Scale( total_rtensor, -CEhb2, temp_rtensor );
+
+ rvec_ScaledSum( temp_rvec, -CEhb2, dcos_theta_dj,
+ -CEhb3/r_jk, pbond_jk->dvec );
+ rvec_OuterProduct( temp_rtensor,
+ temp_rvec, system->atoms[j].x );
+ rtensor_Add( total_rtensor, temp_rtensor );
+
+ rvec_ScaledSum( temp_rvec, -CEhb2, dcos_theta_dk,
+ +CEhb3/r_jk, pbond_jk->dvec );
+ rvec_OuterProduct( temp_rtensor,
+ temp_rvec, system->atoms[k].x );
+ rtensor_Add( total_rtensor, temp_rtensor );
+
+ if( pbond_ij->imaginary || pbond_jk->imaginary )
+ rtensor_ScaledAdd( data->flex_bar.P, -1.0, total_rtensor );
+ else
+ rtensor_Add( data->flex_bar.P, total_rtensor ); */
+ }
+
#ifdef TEST_ENERGY
- /*fprintf( out_control->ehb,
- "%23.15e%23.15e%23.15e\n%23.15e%23.15e%23.15e\n%23.15e%23.15e%23.15e\n",
- dcos_theta_di[0], dcos_theta_di[1], dcos_theta_di[2],
- dcos_theta_dj[0], dcos_theta_dj[1], dcos_theta_dj[2],
- dcos_theta_dk[0], dcos_theta_dk[1], dcos_theta_dk[2]);
- fprintf( out_control->ehb, "%23.15e%23.15e%23.15e\n",
- CEhb1, CEhb2, CEhb3 ); */
- fprintf( stderr, //out_control->ehb,
- "%6d%6d%6d%23.15e%23.15e%23.15e%23.15e%23.15e\n",
- workspace->orig_id[i],
- workspace->orig_id[j],
- workspace->orig_id[k],
- r_jk, theta, bo_ij->BO, e_hb, data->E_HB );
-
+ /*fprintf( out_control->ehb,
+ "%23.15e%23.15e%23.15e\n%23.15e%23.15e%23.15e\n%23.15e%23.15e%23.15e\n",
+ dcos_theta_di[0], dcos_theta_di[1], dcos_theta_di[2],
+ dcos_theta_dj[0], dcos_theta_dj[1], dcos_theta_dj[2],
+ dcos_theta_dk[0], dcos_theta_dk[1], dcos_theta_dk[2]);
+ fprintf( out_control->ehb, "%23.15e%23.15e%23.15e\n",
+ CEhb1, CEhb2, CEhb3 ); */
+ fprintf( stderr, //out_control->ehb,
+ "%6d%6d%6d%23.15e%23.15e%23.15e%23.15e%23.15e\n",
+ workspace->orig_id[i],
+ workspace->orig_id[j],
+ workspace->orig_id[k],
+ r_jk, theta, bo_ij->BO, e_hb, data->E_HB );
+
#endif
#ifdef TEST_FORCES
- // dbo term
- Add_dBO( system, lists, j, pi, +CEhb1, workspace->f_hb );
- // dcos terms
- rvec_ScaledAdd( workspace->f_hb[i], +CEhb2, dcos_theta_di );
- rvec_ScaledAdd( workspace->f_hb[j], +CEhb2, dcos_theta_dj );
- rvec_ScaledAdd( workspace->f_hb[k], +CEhb2, dcos_theta_dk );
- // dr terms
- rvec_ScaledAdd( workspace->f_hb[j], -CEhb3/r_jk, dvec_jk );
- rvec_ScaledAdd( workspace->f_hb[k], +CEhb3/r_jk, dvec_jk );
+ // dbo term
+ Add_dBO( system, lists, j, pi, +CEhb1, workspace->f_hb );
+ // dcos terms
+ rvec_ScaledAdd( workspace->f_hb[i], +CEhb2, dcos_theta_di );
+ rvec_ScaledAdd( workspace->f_hb[j], +CEhb2, dcos_theta_dj );
+ rvec_ScaledAdd( workspace->f_hb[k], +CEhb2, dcos_theta_dk );
+ // dr terms
+ rvec_ScaledAdd( workspace->f_hb[j], -CEhb3 / r_jk, dvec_jk );
+ rvec_ScaledAdd( workspace->f_hb[k], +CEhb3 / r_jk, dvec_jk );
#endif
- }
- }
- }
- }
-
- /* fprintf( stderr, "hydbonds: ext_press (%23.15e %23.15e %23.15e)\n",
- data->ext_press[0], data->ext_press[1], data->ext_press[2] ); */
-
+ }
+ }
+ }
+ }
+
+ /* fprintf( stderr, "hydbonds: ext_press (%23.15e %23.15e %23.15e)\n",
+ data->ext_press[0], data->ext_press[1], data->ext_press[2] ); */
+
#ifdef TEST_FORCES
- fprintf( stderr, "Number of hydrogen bonds: %d\n", num_hb_intrs );
- fprintf( stderr, "Hydrogen Bond Energy: %g\n", data->E_HB );
+ fprintf( stderr, "Number of hydrogen bonds: %d\n", num_hb_intrs );
+ fprintf( stderr, "Hydrogen Bond Energy: %g\n", data->E_HB );
#endif
}
diff --git a/puremd_rc_1003/sPuReMD/three_body_interactions.h b/puremd_rc_1003/sPuReMD/three_body_interactions.h
index 7a1d67e395e8b990525ceeab7da178fbeaebdd2a..55a1188b44e230f59512e6c2789eee0802b542d4 100644
--- a/puremd_rc_1003/sPuReMD/three_body_interactions.h
+++ b/puremd_rc_1003/sPuReMD/three_body_interactions.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -25,13 +25,13 @@
#include "mytypes.h"
void Three_Body_Interactions( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, list**, output_controls* );
void Hydrogen_Bonds( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, list**, output_controls* );
void Calculate_Theta( rvec, real, rvec, real, real*, real* );
-
+
void Calculate_dCos_Theta( rvec, real, rvec, real, rvec*, rvec*, rvec* );
-
+
#endif
diff --git a/puremd_rc_1003/sPuReMD/traj.c b/puremd_rc_1003/sPuReMD/traj.c
index bbff8f15b5b0654555bc15d565309090b5b0908d..49a1595adce827cc0926af740e9aae59d127bf1f 100644
--- a/puremd_rc_1003/sPuReMD/traj.c
+++ b/puremd_rc_1003/sPuReMD/traj.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -26,426 +26,438 @@
/* CUSTOM FORMAT ROUTINES */
/************************************************/
-int Write_Custom_Header(reax_system *system, control_params *control,
- static_storage *workspace, output_controls *out_control)
+int Write_Custom_Header(reax_system *system, control_params *control,
+ static_storage *workspace, output_controls *out_control)
{
- int i, header_len, control_block_len, frame_format_len;
- // char buffer[2048];
- char control_block[2048];
- char frame_format[2048];
- char atom_format[100], bond_format[100], angle_format[100];
-
- sprintf( control_block, CONTROL_BLOCK,
- system->N,
- control->restart,
- control->restart_from,
- control->random_vel,
- out_control->restart_freq,
- control->ensemble,
- control->nsteps,
- control->dt,
- control->reposition_atoms,
- control->restrict_bonds,
- control->tabulate,
- control->nbr_cut,
- control->r_cut,
- control->bg_cut,
- control->bo_cut,
- control->thb_cut,
- control->hb_cut,
- control->q_err,
- control->T_init,
- control->T_final,
- control->Tau_T,
- control->T_mode,
- control->T_rate,
- control->T_freq,
- control->P[0], control->P[1], control->P[2],
- control->Tau_P[0], control->Tau_P[1], control->Tau_P[2],
- control->compressibility,
- control->press_mode,
- control->remove_CoM_vel,
- out_control->write_steps,
- out_control->traj_compress,
- out_control->traj_format,
- out_control->atom_format,
- out_control->bond_info,
- out_control->angle_info,
- out_control->energy_update_freq,
- control->molec_anal,
- control->freq_molec_anal );
-
- control_block_len = strlen( control_block );
-
-
- sprintf( frame_format, "Frame Format: %d\n%s\n%s\n",
- NUM_FRAME_GLOBALS, FRAME_GLOBALS_FORMAT, FRAME_GLOBAL_NAMES );
-
- atom_format[0] = OPT_NOATOM;
- switch( out_control->atom_format )
+ int i, header_len, control_block_len, frame_format_len;
+ // char buffer[2048];
+ char control_block[2048];
+ char frame_format[2048];
+ char atom_format[100], bond_format[100], angle_format[100];
+
+ sprintf( control_block, CONTROL_BLOCK,
+ system->N,
+ control->restart,
+ control->restart_from,
+ control->random_vel,
+ out_control->restart_freq,
+ control->ensemble,
+ control->nsteps,
+ control->dt,
+ control->reposition_atoms,
+ control->restrict_bonds,
+ control->tabulate,
+ control->nbr_cut,
+ control->r_cut,
+ control->bg_cut,
+ control->bo_cut,
+ control->thb_cut,
+ control->hb_cut,
+ control->q_err,
+ control->T_init,
+ control->T_final,
+ control->Tau_T,
+ control->T_mode,
+ control->T_rate,
+ control->T_freq,
+ control->P[0], control->P[1], control->P[2],
+ control->Tau_P[0], control->Tau_P[1], control->Tau_P[2],
+ control->compressibility,
+ control->press_mode,
+ control->remove_CoM_vel,
+ out_control->write_steps,
+ out_control->traj_compress,
+ out_control->traj_format,
+ out_control->atom_format,
+ out_control->bond_info,
+ out_control->angle_info,
+ out_control->energy_update_freq,
+ control->molec_anal,
+ control->freq_molec_anal );
+
+ control_block_len = strlen( control_block );
+
+
+ sprintf( frame_format, "Frame Format: %d\n%s\n%s\n",
+ NUM_FRAME_GLOBALS, FRAME_GLOBALS_FORMAT, FRAME_GLOBAL_NAMES );
+
+ atom_format[0] = OPT_NOATOM;
+ switch ( out_control->atom_format )
{
- case OPT_ATOM_BASIC: sprintf( atom_format, "Atom_Basic: %s", ATOM_BASIC );
- break;
- case OPT_ATOM_wF: sprintf( atom_format, "Atom_wF: %s", ATOM_wF );
- break;
- case OPT_ATOM_wV: sprintf( atom_format, "Atom_wV: %s", ATOM_wV );
- break;
- case OPT_ATOM_FULL: sprintf( atom_format, "Atom_Full: %s", ATOM_FULL );
- break;
- }
- strcat( frame_format, atom_format );
-
- bond_format[0] = OPT_NOBOND;
- if( out_control->bond_info == OPT_BOND_BASIC )
- sprintf( bond_format, "Bond_Line: %s", BOND_BASIC );
- else if( out_control->bond_info == OPT_BOND_FULL )
- sprintf( bond_format, "Bond_Line_Full: %s", BOND_FULL );
- strcat( frame_format, bond_format );
-
- angle_format[0] = OPT_NOANGLE;
- if( out_control->angle_info == OPT_ANGLE_BASIC )
- sprintf( angle_format, "Angle_Line: %s", ANGLE_BASIC );
- strcat( frame_format, angle_format );
-
- frame_format_len = strlen( frame_format );
-
-
- header_len = HEADER_INIT_LEN + (control_block_len + SIZE_INFO_LEN2)+
- (frame_format_len + SIZE_INFO_LEN2) +
- (ATOM_MAPPING_LEN * system->N + SIZE_INFO_LEN2);
-
- out_control->write( out_control->trj, HEADER_INIT,
- header_len, HEADER_INIT_LEN, out_control->traj_title );
-
- out_control->write( out_control->trj, SIZE_INFO_LINE2,
- control_block_len + (frame_format_len + SIZE_INFO_LEN2) +
- (ATOM_MAPPING_LEN * system->N + SIZE_INFO_LEN2),
- control_block_len );
- out_control->write( out_control->trj, "%s", control_block );
-
- out_control->write( out_control->trj, SIZE_INFO_LINE2,
- frame_format_len +
- (ATOM_MAPPING_LEN * system->N + SIZE_INFO_LEN2),
- frame_format_len );
- out_control->write( out_control->trj, "%s", frame_format );
-
- out_control->write( out_control->trj, SIZE_INFO_LINE2,
- ATOM_MAPPING_LEN * system->N,
- ATOM_MAPPING_LEN * system->N );
-
- for( i = 0; i < system->N; ++i )
- out_control->write( out_control->trj, ATOM_MAPPING,
- workspace->orig_id[i],
- system->atoms[i].type,
- system->atoms[i].name,
- system->reaxprm.sbp[ system->atoms[i].type ].mass );
-
- fflush( out_control->trj );
-
- return 0;
+ case OPT_ATOM_BASIC:
+ sprintf( atom_format, "Atom_Basic: %s", ATOM_BASIC );
+ break;
+ case OPT_ATOM_wF:
+ sprintf( atom_format, "Atom_wF: %s", ATOM_wF );
+ break;
+ case OPT_ATOM_wV:
+ sprintf( atom_format, "Atom_wV: %s", ATOM_wV );
+ break;
+ case OPT_ATOM_FULL:
+ sprintf( atom_format, "Atom_Full: %s", ATOM_FULL );
+ break;
+ }
+ strcat( frame_format, atom_format );
+
+ bond_format[0] = OPT_NOBOND;
+ if ( out_control->bond_info == OPT_BOND_BASIC )
+ sprintf( bond_format, "Bond_Line: %s", BOND_BASIC );
+ else if ( out_control->bond_info == OPT_BOND_FULL )
+ sprintf( bond_format, "Bond_Line_Full: %s", BOND_FULL );
+ strcat( frame_format, bond_format );
+
+ angle_format[0] = OPT_NOANGLE;
+ if ( out_control->angle_info == OPT_ANGLE_BASIC )
+ sprintf( angle_format, "Angle_Line: %s", ANGLE_BASIC );
+ strcat( frame_format, angle_format );
+
+ frame_format_len = strlen( frame_format );
+
+
+ header_len = HEADER_INIT_LEN + (control_block_len + SIZE_INFO_LEN2) +
+ (frame_format_len + SIZE_INFO_LEN2) +
+ (ATOM_MAPPING_LEN * system->N + SIZE_INFO_LEN2);
+
+ out_control->write( out_control->trj, HEADER_INIT,
+ header_len, HEADER_INIT_LEN, out_control->traj_title );
+
+ out_control->write( out_control->trj, SIZE_INFO_LINE2,
+ control_block_len + (frame_format_len + SIZE_INFO_LEN2) +
+ (ATOM_MAPPING_LEN * system->N + SIZE_INFO_LEN2),
+ control_block_len );
+ out_control->write( out_control->trj, "%s", control_block );
+
+ out_control->write( out_control->trj, SIZE_INFO_LINE2,
+ frame_format_len +
+ (ATOM_MAPPING_LEN * system->N + SIZE_INFO_LEN2),
+ frame_format_len );
+ out_control->write( out_control->trj, "%s", frame_format );
+
+ out_control->write( out_control->trj, SIZE_INFO_LINE2,
+ ATOM_MAPPING_LEN * system->N,
+ ATOM_MAPPING_LEN * system->N );
+
+ for ( i = 0; i < system->N; ++i )
+ out_control->write( out_control->trj, ATOM_MAPPING,
+ workspace->orig_id[i],
+ system->atoms[i].type,
+ system->atoms[i].name,
+ system->reaxprm.sbp[ system->atoms[i].type ].mass );
+
+ fflush( out_control->trj );
+
+ return 0;
}
-int Append_Custom_Frame( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+int Append_Custom_Frame( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int i, j, pi, pk, pk_j;
- int write_atoms, write_bonds, write_angles;
- int frame_len, atom_line_len, bond_line_len, angle_line_len, rest_of_frame_len;
- int frame_globals_len, num_bonds, num_thb_intrs;
- real P;
- char buffer[2048];
- list *bonds = (*lists) + BONDS;
- list *thb_intrs = (*lists) + THREE_BODIES;
- bond_data *bo_ij;
-
-
- /* IMPORTANT: This whole part will go to init_trj after finalized! */
- switch( out_control->atom_format )
+ int i, j, pi, pk, pk_j;
+ int write_atoms, write_bonds, write_angles;
+ int frame_len, atom_line_len, bond_line_len, angle_line_len, rest_of_frame_len;
+ int frame_globals_len, num_bonds, num_thb_intrs;
+ real P;
+ char buffer[2048];
+ list *bonds = (*lists) + BONDS;
+ list *thb_intrs = (*lists) + THREE_BODIES;
+ bond_data *bo_ij;
+
+
+ /* IMPORTANT: This whole part will go to init_trj after finalized! */
+ switch ( out_control->atom_format )
{
- case OPT_ATOM_BASIC:
- atom_line_len = ATOM_BASIC_LEN;
- write_atoms = 1;
- break;
- case OPT_ATOM_wF:
- atom_line_len = ATOM_wF_LEN;
- write_atoms = 1;
- break;
- case OPT_ATOM_wV:
- atom_line_len = ATOM_wV_LEN;
- write_atoms = 1;
- break;
- case OPT_ATOM_FULL:
- atom_line_len = ATOM_FULL_LEN;
- write_atoms = 1;
- break;
- default:
- atom_line_len = 0;
- write_atoms = 0;
- }
-
-
- /* bond preparations */
- bond_line_len = write_bonds = 0;
- if( out_control->bond_info == OPT_BOND_BASIC )
+ case OPT_ATOM_BASIC:
+ atom_line_len = ATOM_BASIC_LEN;
+ write_atoms = 1;
+ break;
+ case OPT_ATOM_wF:
+ atom_line_len = ATOM_wF_LEN;
+ write_atoms = 1;
+ break;
+ case OPT_ATOM_wV:
+ atom_line_len = ATOM_wV_LEN;
+ write_atoms = 1;
+ break;
+ case OPT_ATOM_FULL:
+ atom_line_len = ATOM_FULL_LEN;
+ write_atoms = 1;
+ break;
+ default:
+ atom_line_len = 0;
+ write_atoms = 0;
+ }
+
+
+ /* bond preparations */
+ bond_line_len = write_bonds = 0;
+ if ( out_control->bond_info == OPT_BOND_BASIC )
{
- bond_line_len = BOND_BASIC_LEN;
- write_bonds = 1;
+ bond_line_len = BOND_BASIC_LEN;
+ write_bonds = 1;
}
- else if( out_control->bond_info == OPT_BOND_FULL )
+ else if ( out_control->bond_info == OPT_BOND_FULL )
{
- bond_line_len = BOND_FULL_LEN;
- write_bonds = 1;
+ bond_line_len = BOND_FULL_LEN;
+ write_bonds = 1;
}
- num_bonds = 0;
- if( write_bonds )
+ num_bonds = 0;
+ if ( write_bonds )
{
- for( i = 0; i < system->N; ++i )
- for( j = Start_Index( i, bonds ); j < End_Index( i, bonds ); ++j )
- if( i < bonds->select.bond_list[j].nbr &&
- bonds->select.bond_list[j].bo_data.BO >= control->bg_cut )
- ++num_bonds;
+ for ( i = 0; i < system->N; ++i )
+ for ( j = Start_Index( i, bonds ); j < End_Index( i, bonds ); ++j )
+ if ( i < bonds->select.bond_list[j].nbr &&
+ bonds->select.bond_list[j].bo_data.BO >= control->bg_cut )
+ ++num_bonds;
}
- /* angle preparations */
- if( out_control->angle_info == OPT_ANGLE_BASIC )
+ /* angle preparations */
+ if ( out_control->angle_info == OPT_ANGLE_BASIC )
{
- angle_line_len = ANGLE_BASIC_LEN;
- write_angles = 1;
+ angle_line_len = ANGLE_BASIC_LEN;
+ write_angles = 1;
}
- else
+ else
{
- angle_line_len = 0;
- write_angles = 0;
+ angle_line_len = 0;
+ write_angles = 0;
}
- num_thb_intrs = 0;
- if( write_angles ) {
- for( j = 0; j < system->N; ++j )
- for( pi = Start_Index(j, bonds); pi < End_Index(j, bonds); ++pi )
- if( bonds->select.bond_list[pi].bo_data.BO >= control->bg_cut )
- // physical j&i bond
- for( pk = Start_Index( pi, thb_intrs );
- pk < End_Index( pi, thb_intrs ); ++pk )
- if( bonds->select.bond_list[pi].nbr <
- thb_intrs->select.three_body_list[pk].thb ) {
- // get k's pointer on j's bond list
- pk_j = thb_intrs->select.three_body_list[pk].pthb;
-
- if( bonds->select.bond_list[pk_j].bo_data.BO >= control->bg_cut )
- // physical j&k bond
- ++num_thb_intrs;
- }
- }
-
-
-
- /* get correct pressure */
- if( control->ensemble == NPT || control->ensemble == sNPT )
- P = data->flex_bar.P_scalar;
- else if( control->ensemble == iNPT )
- P = data->iso_bar.P;
- else P = 0;
-
-
- /* calculate total frame length*/
- sprintf( buffer, FRAME_GLOBALS,
- data->step, data->time,
- data->E_Tot, data->E_Pot, E_CONV * data->E_Kin, data->therm.T,
- P, system->box.volume,
- system->box.box_norms[0],
- system->box.box_norms[1],
- system->box.box_norms[2],
- 90.0, 90.0, 90.0, // IMPORTANT: need to rewrite for flexible boxes!
- data->E_BE,
- data->E_Ov, data->E_Un, data->E_Lp,
- data->E_Ang, data->E_Pen, data->E_Coa, data->E_HB,
- data->E_Tor, data->E_Con,
- data->E_vdW, data->E_Ele, data->E_Pol );
- frame_globals_len = strlen( buffer );
-
- frame_len = frame_globals_len +
- write_atoms * SIZE_INFO_LEN3 + system->N * atom_line_len +
- write_bonds * SIZE_INFO_LEN3 + num_bonds * bond_line_len +
- write_angles * SIZE_INFO_LEN3 + num_thb_intrs * angle_line_len;
-
-
- /* write size info & frame globals */
- out_control->write( out_control->trj, SIZE_INFO_LINE2,
- frame_len, frame_globals_len );
- out_control->write( out_control->trj, "%s", buffer );
-
-
- /* write size info & atom lines */
- if( write_atoms )
+ num_thb_intrs = 0;
+ if ( write_angles )
{
- rest_of_frame_len = system->N * atom_line_len +
- write_bonds * SIZE_INFO_LEN3 + num_bonds * bond_line_len +
- write_angles * SIZE_INFO_LEN3 + num_thb_intrs * angle_line_len;
-
- out_control->write( out_control->trj, SIZE_INFO_LINE3,
- rest_of_frame_len, system->N * atom_line_len,
- system->N );
+ for ( j = 0; j < system->N; ++j )
+ for ( pi = Start_Index(j, bonds); pi < End_Index(j, bonds); ++pi )
+ if ( bonds->select.bond_list[pi].bo_data.BO >= control->bg_cut )
+ // physical j&i bond
+ for ( pk = Start_Index( pi, thb_intrs );
+ pk < End_Index( pi, thb_intrs ); ++pk )
+ if ( bonds->select.bond_list[pi].nbr <
+ thb_intrs->select.three_body_list[pk].thb )
+ {
+ // get k's pointer on j's bond list
+ pk_j = thb_intrs->select.three_body_list[pk].pthb;
+
+ if ( bonds->select.bond_list[pk_j].bo_data.BO >= control->bg_cut )
+ // physical j&k bond
+ ++num_thb_intrs;
+ }
}
- switch( out_control->atom_format )
+
+
+ /* get correct pressure */
+ if ( control->ensemble == NPT || control->ensemble == sNPT )
+ P = data->flex_bar.P_scalar;
+ else if ( control->ensemble == iNPT )
+ P = data->iso_bar.P;
+ else P = 0;
+
+
+ /* calculate total frame length*/
+ sprintf( buffer, FRAME_GLOBALS,
+ data->step, data->time,
+ data->E_Tot, data->E_Pot, E_CONV * data->E_Kin, data->therm.T,
+ P, system->box.volume,
+ system->box.box_norms[0],
+ system->box.box_norms[1],
+ system->box.box_norms[2],
+ 90.0, 90.0, 90.0, // IMPORTANT: need to rewrite for flexible boxes!
+ data->E_BE,
+ data->E_Ov, data->E_Un, data->E_Lp,
+ data->E_Ang, data->E_Pen, data->E_Coa, data->E_HB,
+ data->E_Tor, data->E_Con,
+ data->E_vdW, data->E_Ele, data->E_Pol );
+ frame_globals_len = strlen( buffer );
+
+ frame_len = frame_globals_len +
+ write_atoms * SIZE_INFO_LEN3 + system->N * atom_line_len +
+ write_bonds * SIZE_INFO_LEN3 + num_bonds * bond_line_len +
+ write_angles * SIZE_INFO_LEN3 + num_thb_intrs * angle_line_len;
+
+
+ /* write size info & frame globals */
+ out_control->write( out_control->trj, SIZE_INFO_LINE2,
+ frame_len, frame_globals_len );
+ out_control->write( out_control->trj, "%s", buffer );
+
+
+ /* write size info & atom lines */
+ if ( write_atoms )
{
- case 4:
- for( i = 0; i < system->N; ++i )
- out_control->write( out_control->trj, ATOM_BASIC,
- workspace->orig_id[i],
- system->atoms[i].x[0],
- system->atoms[i].x[1],
- system->atoms[i].x[2],
- system->atoms[i].q );
- break;
+ rest_of_frame_len = system->N * atom_line_len +
+ write_bonds * SIZE_INFO_LEN3 + num_bonds * bond_line_len +
+ write_angles * SIZE_INFO_LEN3 + num_thb_intrs * angle_line_len;
+
+ out_control->write( out_control->trj, SIZE_INFO_LINE3,
+ rest_of_frame_len, system->N * atom_line_len,
+ system->N );
+ }
+
+ switch ( out_control->atom_format )
+ {
+ case 4:
+ for ( i = 0; i < system->N; ++i )
+ out_control->write( out_control->trj, ATOM_BASIC,
+ workspace->orig_id[i],
+ system->atoms[i].x[0],
+ system->atoms[i].x[1],
+ system->atoms[i].x[2],
+ system->atoms[i].q );
+ break;
case 5:
- for( i = 0; i < system->N; ++i )
- out_control->write( out_control->trj, ATOM_wF,
- workspace->orig_id[i],
- system->atoms[i].x[0],
- system->atoms[i].x[1],
- system->atoms[i].x[2],
- system->atoms[i].f[0],
- system->atoms[i].f[1],
- system->atoms[i].f[2],
- system->atoms[i].q );
- break;
- case 6:
- for( i = 0; i < system->N; ++i )
- out_control->write( out_control->trj, ATOM_wV,
- workspace->orig_id[i],
- system->atoms[i].x[0],
- system->atoms[i].x[1],
- system->atoms[i].x[2],
- system->atoms[i].v[0],
- system->atoms[i].v[1],
- system->atoms[i].v[2],
- system->atoms[i].q );
- break;
- case 7:
- for( i = 0; i < system->N; ++i )
- out_control->write( out_control->trj, ATOM_FULL,
- workspace->orig_id[i],
- system->atoms[i].x[0],
- system->atoms[i].x[1],
- system->atoms[i].x[2],
- system->atoms[i].v[0],
- system->atoms[i].v[1],
- system->atoms[i].v[2],
- system->atoms[i].f[0],
- system->atoms[i].f[1],
- system->atoms[i].f[2],
- system->atoms[i].q );
- break;
- }
- fflush( out_control->trj );
-
-
- /* write size info & bond lines */
- if( write_bonds )
+ for ( i = 0; i < system->N; ++i )
+ out_control->write( out_control->trj, ATOM_wF,
+ workspace->orig_id[i],
+ system->atoms[i].x[0],
+ system->atoms[i].x[1],
+ system->atoms[i].x[2],
+ system->atoms[i].f[0],
+ system->atoms[i].f[1],
+ system->atoms[i].f[2],
+ system->atoms[i].q );
+ break;
+ case 6:
+ for ( i = 0; i < system->N; ++i )
+ out_control->write( out_control->trj, ATOM_wV,
+ workspace->orig_id[i],
+ system->atoms[i].x[0],
+ system->atoms[i].x[1],
+ system->atoms[i].x[2],
+ system->atoms[i].v[0],
+ system->atoms[i].v[1],
+ system->atoms[i].v[2],
+ system->atoms[i].q );
+ break;
+ case 7:
+ for ( i = 0; i < system->N; ++i )
+ out_control->write( out_control->trj, ATOM_FULL,
+ workspace->orig_id[i],
+ system->atoms[i].x[0],
+ system->atoms[i].x[1],
+ system->atoms[i].x[2],
+ system->atoms[i].v[0],
+ system->atoms[i].v[1],
+ system->atoms[i].v[2],
+ system->atoms[i].f[0],
+ system->atoms[i].f[1],
+ system->atoms[i].f[2],
+ system->atoms[i].q );
+ break;
+ }
+ fflush( out_control->trj );
+
+
+ /* write size info & bond lines */
+ if ( write_bonds )
{
- rest_of_frame_len = num_bonds * bond_line_len +
- write_angles * SIZE_INFO_LEN3 + num_thb_intrs * angle_line_len;
+ rest_of_frame_len = num_bonds * bond_line_len +
+ write_angles * SIZE_INFO_LEN3 + num_thb_intrs * angle_line_len;
+
+ out_control->write( out_control->trj, SIZE_INFO_LINE3,
+ rest_of_frame_len, num_bonds * bond_line_len,
+ num_bonds );
+ }
+
+ if ( out_control->bond_info == 1 )
+ {
+ for ( i = 0; i < system->N; ++i )
+ for ( j = Start_Index( i, bonds ); j < End_Index( i, bonds ); ++j )
+ if ( i < bonds->select.bond_list[j].nbr &&
+ bonds->select.bond_list[j].bo_data.BO >= control->bg_cut )
+ {
+ bo_ij = &( bonds->select.bond_list[j] );
+ out_control->write( out_control->trj, BOND_BASIC,
+ workspace->orig_id[i],
+ workspace->orig_id[bo_ij->nbr],
+ bo_ij->d, bo_ij->bo_data.BO );
+ }
+ }
+ else if ( out_control->bond_info == 2 )
+ {
+ for ( i = 0; i < system->N; ++i )
+ for ( j = Start_Index( i, bonds ); j < End_Index( i, bonds ); ++j )
+ if ( i < bonds->select.bond_list[j].nbr &&
+ bonds->select.bond_list[j].bo_data.BO >= control->bg_cut )
+ {
+ bo_ij = &( bonds->select.bond_list[j] );
+ out_control->write( out_control->trj, BOND_FULL,
+ workspace->orig_id[i],
+ workspace->orig_id[bo_ij->nbr],
+ bo_ij->d, bo_ij->bo_data.BO, bo_ij->bo_data.BO_s,
+ bo_ij->bo_data.BO_pi, bo_ij->bo_data.BO_pi2 );
+ }
+ }
- out_control->write( out_control->trj, SIZE_INFO_LINE3,
- rest_of_frame_len, num_bonds * bond_line_len,
- num_bonds );
+ fflush( out_control->trj );
+
+
+ /* write size info & angle lines */
+ if ( out_control->angle_info )
+ {
+ out_control->write( out_control->trj, SIZE_INFO_LINE3,
+ num_thb_intrs * angle_line_len,
+ num_thb_intrs * angle_line_len, num_thb_intrs );
+
+ for ( j = 0; j < system->N; ++j )
+ for ( pi = Start_Index(j, bonds); pi < End_Index(j, bonds); ++pi )
+ if ( bonds->select.bond_list[pi].bo_data.BO >= control->bg_cut )
+ // physical j&i bond
+ for ( pk = Start_Index( pi, thb_intrs );
+ pk < End_Index( pi, thb_intrs ); ++pk )
+ if ( bonds->select.bond_list[pi].nbr <
+ thb_intrs->select.three_body_list[pk].thb )
+ {
+ pk_j = thb_intrs->select.three_body_list[pk].pthb;
+ // get k's pointer on j's bond list
+
+ if ( bonds->select.bond_list[pk_j].bo_data.BO >= control->bg_cut )
+ // physical j&k bond
+ out_control->write( out_control->trj, ANGLE_BASIC,
+ workspace->orig_id[bonds->select.bond_list[pi].nbr],
+ workspace->orig_id[j],
+ workspace->orig_id[thb_intrs->select.three_body_list[pk].thb],
+ RAD2DEG(thb_intrs->select.three_body_list[pk].theta) );
+ }
}
- if( out_control->bond_info == 1 ) {
- for( i = 0; i < system->N; ++i )
- for( j = Start_Index( i, bonds ); j < End_Index( i, bonds ); ++j )
- if( i < bonds->select.bond_list[j].nbr &&
- bonds->select.bond_list[j].bo_data.BO >= control->bg_cut ) {
- bo_ij = &( bonds->select.bond_list[j] );
- out_control->write( out_control->trj, BOND_BASIC,
- workspace->orig_id[i],
- workspace->orig_id[bo_ij->nbr],
- bo_ij->d, bo_ij->bo_data.BO );
- }
- }
- else if( out_control->bond_info == 2 ) {
- for( i = 0; i < system->N; ++i )
- for( j = Start_Index( i, bonds ); j < End_Index( i, bonds ); ++j )
- if( i < bonds->select.bond_list[j].nbr &&
- bonds->select.bond_list[j].bo_data.BO >= control->bg_cut ) {
- bo_ij = &( bonds->select.bond_list[j] );
- out_control->write( out_control->trj, BOND_FULL,
- workspace->orig_id[i],
- workspace->orig_id[bo_ij->nbr],
- bo_ij->d, bo_ij->bo_data.BO, bo_ij->bo_data.BO_s,
- bo_ij->bo_data.BO_pi, bo_ij->bo_data.BO_pi2 );
- }
- }
-
- fflush( out_control->trj );
-
-
- /* write size info & angle lines */
- if( out_control->angle_info ) {
- out_control->write( out_control->trj, SIZE_INFO_LINE3,
- num_thb_intrs * angle_line_len,
- num_thb_intrs * angle_line_len, num_thb_intrs );
-
- for( j = 0; j < system->N; ++j )
- for( pi = Start_Index(j, bonds); pi < End_Index(j, bonds); ++pi )
- if( bonds->select.bond_list[pi].bo_data.BO >= control->bg_cut )
- // physical j&i bond
- for( pk = Start_Index( pi, thb_intrs );
- pk < End_Index( pi, thb_intrs ); ++pk )
- if( bonds->select.bond_list[pi].nbr <
- thb_intrs->select.three_body_list[pk].thb ) {
- pk_j = thb_intrs->select.three_body_list[pk].pthb;
- // get k's pointer on j's bond list
-
- if( bonds->select.bond_list[pk_j].bo_data.BO >= control->bg_cut )
- // physical j&k bond
- out_control->write( out_control->trj, ANGLE_BASIC,
- workspace->orig_id[bonds->select.bond_list[pi].nbr],
- workspace->orig_id[j],
- workspace->orig_id[thb_intrs->select.three_body_list[pk].thb],
- RAD2DEG(thb_intrs->select.three_body_list[pk].theta) );
- }
- }
-
- fflush( out_control->trj );
-
- return 0;
+ fflush( out_control->trj );
+
+ return 0;
}
void Read_Traj( output_controls *out_control, char *traj_name )
{
- int skip_all, skip_part, n;
- char size_buffer[50];
- // char read_buffer[2048];
-
- out_control->trj = gzopen( traj_name, "r" );
-
- fprintf( stderr, "file opened!\n" );
-
- while( !gzeof( out_control->trj ) )
- {
- if( gzgets( out_control->trj, size_buffer, 50 ) == Z_NULL )
- break;
-
- fprintf( stderr, "read line\n" );
-
- if( strlen( size_buffer ) >= SIZE_INFO_LEN3 )
- sscanf( size_buffer, "%d %d %d", &skip_all, &skip_part, &n );
- else
- sscanf( size_buffer, "%d %d", &skip_all, &skip_part );
+ int skip_all, skip_part, n;
+ char size_buffer[50];
+ // char read_buffer[2048];
+
+ out_control->trj = gzopen( traj_name, "r" );
+
+ fprintf( stderr, "file opened!\n" );
- fprintf( stderr, "%d %d\n", skip_all, skip_part );
+ while ( !gzeof( out_control->trj ) )
+ {
+ if ( gzgets( out_control->trj, size_buffer, 50 ) == Z_NULL )
+ break;
+
+ fprintf( stderr, "read line\n" );
- gzseek( out_control->trj, skip_part, SEEK_CUR );
- }
+ if ( strlen( size_buffer ) >= SIZE_INFO_LEN3 )
+ sscanf( size_buffer, "%d %d %d", &skip_all, &skip_part, &n );
+ else
+ sscanf( size_buffer, "%d %d", &skip_all, &skip_part );
- gzclose( out_control->trj );
+ fprintf( stderr, "%d %d\n", skip_all, skip_part );
+
+ gzseek( out_control->trj, skip_part, SEEK_CUR );
+ }
+
+ gzclose( out_control->trj );
}
@@ -455,36 +467,36 @@ void Read_Traj( output_controls *out_control, char *traj_name )
/************ XYZ FORMAT ROUTINES ***************/
/********************************************************/
-int Write_xyz_Header( reax_system *system, control_params *control,
- static_storage* workspace, output_controls *out_control )
+int Write_xyz_Header( reax_system *system, control_params *control,
+ static_storage* workspace, output_controls *out_control )
{
- fflush( out_control->trj );
-
- return 1;
+ fflush( out_control->trj );
+
+ return 1;
}
-int Append_xyz_Frame( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+int Append_xyz_Frame( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int i;
+ int i;
+
+ out_control->write( out_control->trj, "%d\n", system->N );
- out_control->write( out_control->trj, "%d\n", system->N );
+ out_control->write( out_control->trj, "%d\t%8.3f\t%8.3f\t%8.3f\t%8.3f\n",
+ data->step,
+ data->E_Tot, data->E_Pot,
+ E_CONV * data->E_Kin, data->therm.T );
- out_control->write( out_control->trj, "%d\t%8.3f\t%8.3f\t%8.3f\t%8.3f\n",
- data->step,
- data->E_Tot, data->E_Pot,
- E_CONV*data->E_Kin, data->therm.T );
-
- for( i = 0; i < system->N; ++i )
- out_control->write( out_control->trj, "%3s %10.5f %10.5f %10.5f\n",
- system->reaxprm.sbp[ system->atoms[i].type ].name,
- system->atoms[i].x[0],
- system->atoms[i].x[1],
- system->atoms[i].x[2] );
+ for ( i = 0; i < system->N; ++i )
+ out_control->write( out_control->trj, "%3s %10.5f %10.5f %10.5f\n",
+ system->reaxprm.sbp[ system->atoms[i].type ].name,
+ system->atoms[i].x[0],
+ system->atoms[i].x[1],
+ system->atoms[i].x[2] );
- fflush( out_control->trj );
+ fflush( out_control->trj );
- return 1;
+ return 1;
}
diff --git a/puremd_rc_1003/sPuReMD/traj.h b/puremd_rc_1003/sPuReMD/traj.h
index 092f7100ca87607509bd17580ed9a4ca7220df47..0e759059e3293eb56ec16756f6d94b430fb2fd03 100644
--- a/puremd_rc_1003/sPuReMD/traj.h
+++ b/puremd_rc_1003/sPuReMD/traj.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -74,17 +74,18 @@
#define SIZE_INFO_LINE3 "%-10d %-10d %-10d\n"
#define SIZE_INFO_LEN3 33
-enum ATOM_LINE_OPTS {OPT_NOATOM = 0, OPT_ATOM_BASIC = 4, OPT_ATOM_wF = 5,
- OPT_ATOM_wV = 6, OPT_ATOM_FULL = 7};
+enum ATOM_LINE_OPTS {OPT_NOATOM = 0, OPT_ATOM_BASIC = 4, OPT_ATOM_wF = 5,
+ OPT_ATOM_wV = 6, OPT_ATOM_FULL = 7
+ };
enum BOND_LINE_OPTS {OPT_NOBOND, OPT_BOND_BASIC, OPT_BOND_FULL};
enum ANGLE_LINE_OPTS {OPT_NOANGLE, OPT_ANGLE_BASIC};
typedef struct
{
- int no_of_sub_blocks;
- int size;
- char* buffer;
- struct block** sub_blocks;
+ int no_of_sub_blocks;
+ int size;
+ char* buffer;
+ struct block** sub_blocks;
} block;
@@ -98,19 +99,19 @@ int Skip_Next_Block( gzFile, int*);
{HEADER}
size flag char (1)
- size of header to skip (int)
+ size of header to skip (int)
Title (char[80])
size flag char (2)
size of control param block (int)
- Entire control param structure
+ Entire control param structure
size of frame descriptor (int)
- Frame descriptor Block
+ Frame descriptor Block
[ Frame descriptor block
No. of global quantities lines (say m) (int)
- Format for each global quantity line [m].
- Comma separated names for each global quantity line [m].
+ Format for each global quantity line [m].
+ Comma separated names for each global quantity line [m].
]
-
+
{FRAMES}
size flag char (1)
size of the entire frame to skip it (int)
@@ -142,17 +143,17 @@ int Skip_Next_Block( gzFile, int*);
*/
-int Write_Custom_Header( reax_system*, control_params*,
- static_storage*, output_controls* );
-int Write_xyz_Header ( reax_system*, control_params*,
- static_storage*, output_controls* );
+int Write_Custom_Header( reax_system*, control_params*,
+ static_storage*, output_controls* );
+int Write_xyz_Header ( reax_system*, control_params*,
+ static_storage*, output_controls* );
/*
Write_Traj_Header( gzfile file,
- int No. of lines of global qunatities,
- char** format for global quantities,
- char** names for global quantities,
- control_params* control);
+ int No. of lines of global qunatities,
+ char** format for global quantities,
+ char** names for global quantities,
+ control_params* control);
*/
char Write_Traj_Header( FILE*, int, char**, char**, control_params* );
@@ -160,28 +161,28 @@ char Write_Traj_Header( FILE*, int, char**, char**, control_params* );
/*
Push_Traj_Frame(gzfile file,
reax_system* system,
- control_params* control,
- simulation_data* data,
- static_storage* workspace,
- list** lists,
- char** various flags);
+ control_params* control,
+ simulation_data* data,
+ static_storage* workspace,
+ list** lists,
+ char** various flags);
*/
-int Push_Traj_Frame( /*gzfile*/ FILE*, reax_system*, control_params*,
- simulation_data*, static_storage*, list**, char** );
+int Push_Traj_Frame( /*gzfile*/ FILE*, reax_system*, control_params*,
+ simulation_data*, static_storage*, list**, char** );
/*
Append_Traj_Frame( gzfile file,
reax_system* system,
control_params* control,
- simulation_data* data,
- static_storage* workspace,
- list** lists,
- char** various flags);
+ simulation_data* data,
+ static_storage* workspace,
+ list** lists,
+ char** various flags);
*/
-int Append_Custom_Frame( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
-int Append_xyz_Frame ( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+int Append_Custom_Frame( reax_system*, control_params*, simulation_data*,
+ static_storage*, list**, output_controls* );
+int Append_xyz_Frame ( reax_system*, control_params*, simulation_data*,
+ static_storage*, list**, output_controls* );
void Read_Traj( output_controls*, char * );
diff --git a/puremd_rc_1003/sPuReMD/two_body_interactions.c b/puremd_rc_1003/sPuReMD/two_body_interactions.c
index 9d6acd209555521aba304b1950c27848afb0ee06..cd005cfe4b0ec9dfe7b75edb2a20e756d7147f51 100644
--- a/puremd_rc_1003/sPuReMD/two_body_interactions.c
+++ b/puremd_rc_1003/sPuReMD/two_body_interactions.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -26,526 +26,545 @@
#include "vector.h"
-void Bond_Energy( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+void Bond_Energy( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int i, j, pj;
- int start_i, end_i;
- int type_i, type_j;
- real ebond, pow_BOs_be2, exp_be12, CEbo;
- real gp3, gp4, gp7, gp10, gp37;
- real exphu, exphua1, exphub1, exphuov, hulpov, estriph;
- real decobdbo, decobdboua, decobdboub;
- single_body_parameters *sbp_i, *sbp_j;
- two_body_parameters *twbp;
- bond_order_data *bo_ij;
- list *bonds;
-
- bonds = (*lists) + BONDS;
- gp3 = system->reaxprm.gp.l[3];
- gp4 = system->reaxprm.gp.l[4];
- gp7 = system->reaxprm.gp.l[7];
- gp10 = system->reaxprm.gp.l[10];
- gp37 = (int) system->reaxprm.gp.l[37];
-
- for( i=0; i < system->N; ++i ) {
- start_i = Start_Index(i, bonds);
- end_i = End_Index(i, bonds);
- //fprintf( stderr, "i=%d start=%d end=%d\n", i, start_i, end_i );
- for( pj = start_i; pj < end_i; ++pj )
- if( i < bonds->select.bond_list[pj].nbr ) {
- /* set the pointers */
- j = bonds->select.bond_list[pj].nbr;
- type_i = system->atoms[i].type;
- type_j = system->atoms[j].type;
- sbp_i = &( system->reaxprm.sbp[type_i] );
- sbp_j = &( system->reaxprm.sbp[type_j] );
- twbp = &( system->reaxprm.tbp[type_i][type_j] );
- bo_ij = &( bonds->select.bond_list[pj].bo_data );
-
- /* calculate the constants */
- pow_BOs_be2 = POW( bo_ij->BO_s, twbp->p_be2 );
- exp_be12 = EXP( twbp->p_be1 * ( 1.0 - pow_BOs_be2 ) );
- CEbo = -twbp->De_s * exp_be12 *
- ( 1.0 - twbp->p_be1 * twbp->p_be2 * pow_BOs_be2 );
-
- /* calculate the Bond Energy */
- data->E_BE += ebond =
- -twbp->De_s * bo_ij->BO_s * exp_be12
- -twbp->De_p * bo_ij->BO_pi
- -twbp->De_pp * bo_ij->BO_pi2;
-
- /* calculate derivatives of Bond Orders */
- bo_ij->Cdbo += CEbo;
- bo_ij->Cdbopi -= (CEbo + twbp->De_p);
- bo_ij->Cdbopi2 -= (CEbo + twbp->De_pp);
+ int i, j, pj;
+ int start_i, end_i;
+ int type_i, type_j;
+ real ebond, pow_BOs_be2, exp_be12, CEbo;
+ real gp3, gp4, gp7, gp10, gp37;
+ real exphu, exphua1, exphub1, exphuov, hulpov, estriph;
+ real decobdbo, decobdboua, decobdboub;
+ single_body_parameters *sbp_i, *sbp_j;
+ two_body_parameters *twbp;
+ bond_order_data *bo_ij;
+ list *bonds;
+
+ bonds = (*lists) + BONDS;
+ gp3 = system->reaxprm.gp.l[3];
+ gp4 = system->reaxprm.gp.l[4];
+ gp7 = system->reaxprm.gp.l[7];
+ gp10 = system->reaxprm.gp.l[10];
+ gp37 = (int) system->reaxprm.gp.l[37];
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ start_i = Start_Index(i, bonds);
+ end_i = End_Index(i, bonds);
+ //fprintf( stderr, "i=%d start=%d end=%d\n", i, start_i, end_i );
+ for ( pj = start_i; pj < end_i; ++pj )
+ if ( i < bonds->select.bond_list[pj].nbr )
+ {
+ /* set the pointers */
+ j = bonds->select.bond_list[pj].nbr;
+ type_i = system->atoms[i].type;
+ type_j = system->atoms[j].type;
+ sbp_i = &( system->reaxprm.sbp[type_i] );
+ sbp_j = &( system->reaxprm.sbp[type_j] );
+ twbp = &( system->reaxprm.tbp[type_i][type_j] );
+ bo_ij = &( bonds->select.bond_list[pj].bo_data );
+
+ /* calculate the constants */
+ pow_BOs_be2 = POW( bo_ij->BO_s, twbp->p_be2 );
+ exp_be12 = EXP( twbp->p_be1 * ( 1.0 - pow_BOs_be2 ) );
+ CEbo = -twbp->De_s * exp_be12 *
+ ( 1.0 - twbp->p_be1 * twbp->p_be2 * pow_BOs_be2 );
+
+ /* calculate the Bond Energy */
+ data->E_BE += ebond =
+ -twbp->De_s * bo_ij->BO_s * exp_be12
+ - twbp->De_p * bo_ij->BO_pi
+ - twbp->De_pp * bo_ij->BO_pi2;
+
+ /* calculate derivatives of Bond Orders */
+ bo_ij->Cdbo += CEbo;
+ bo_ij->Cdbopi -= (CEbo + twbp->De_p);
+ bo_ij->Cdbopi2 -= (CEbo + twbp->De_pp);
#ifdef TEST_ENERGY
- fprintf( out_control->ebond, "%6d%6d%24.15e%24.15e\n",
- workspace->orig_id[i], workspace->orig_id[j],
- // i+1, j+1,
- bo_ij->BO, ebond/*, data->E_BE*/ );
- /* fprintf( out_control->ebond, "%6d%6d%12.6f%12.6f%12.6f\n",
- workspace->orig_id[i], workspace->orig_id[j],
- CEbo, -twbp->De_p, -twbp->De_pp );*/
+ fprintf( out_control->ebond, "%6d%6d%24.15e%24.15e\n",
+ workspace->orig_id[i], workspace->orig_id[j],
+ // i+1, j+1,
+ bo_ij->BO, ebond/*, data->E_BE*/ );
+ /* fprintf( out_control->ebond, "%6d%6d%12.6f%12.6f%12.6f\n",
+ workspace->orig_id[i], workspace->orig_id[j],
+ CEbo, -twbp->De_p, -twbp->De_pp );*/
#endif
#ifdef TEST_FORCES
- Add_dBO( system, lists, i, pj, CEbo, workspace->f_be );
- Add_dBOpinpi2( system, lists, i, pj,
- -(CEbo + twbp->De_p), -(CEbo + twbp->De_pp),
- workspace->f_be, workspace->f_be );
+ Add_dBO( system, lists, i, pj, CEbo, workspace->f_be );
+ Add_dBOpinpi2( system, lists, i, pj,
+ -(CEbo + twbp->De_p), -(CEbo + twbp->De_pp),
+ workspace->f_be, workspace->f_be );
#endif
- /* Stabilisation terminal triple bond */
- if( bo_ij->BO >= 1.00 ) {
- if( gp37 == 2 ||
- (sbp_i->mass == 12.0000 && sbp_j->mass == 15.9990) ||
- (sbp_j->mass == 12.0000 && sbp_i->mass == 15.9990) ) {
- // ba = SQR(bo_ij->BO - 2.50);
- exphu = EXP( -gp7 * SQR(bo_ij->BO - 2.50) );
- //oboa=abo(j1)-boa;
- //obob=abo(j2)-boa;
- exphua1 = EXP(-gp3*(workspace->total_bond_order[i]-bo_ij->BO));
- exphub1 = EXP(-gp3*(workspace->total_bond_order[j]-bo_ij->BO));
- //ovoab=abo(j1)-aval(it1)+abo(j2)-aval(it2);
- exphuov = EXP(gp4*(workspace->Delta[i] + workspace->Delta[j]));
- hulpov = 1.0 / (1.0 + 25.0 * exphuov);
-
- estriph = gp10 * exphu * hulpov * (exphua1 + exphub1);
- //estrain(j1) = estrain(j1) + 0.50*estriph;
- //estrain(j2) = estrain(j2) + 0.50*estriph;
- data->E_BE += estriph;
-
- decobdbo = gp10 * exphu * hulpov * (exphua1 + exphub1) *
- ( gp3 - 2.0 * gp7 * (bo_ij->BO-2.50) );
- decobdboua = -gp10 * exphu * hulpov *
- (gp3*exphua1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1));
- decobdboub = -gp10 * exphu * hulpov *
- (gp3*exphub1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1));
-
- bo_ij->Cdbo += decobdbo;
- workspace->CdDelta[i] += decobdboua;
- workspace->CdDelta[j] += decobdboub;
+ /* Stabilisation terminal triple bond */
+ if ( bo_ij->BO >= 1.00 )
+ {
+ if ( gp37 == 2 ||
+ (sbp_i->mass == 12.0000 && sbp_j->mass == 15.9990) ||
+ (sbp_j->mass == 12.0000 && sbp_i->mass == 15.9990) )
+ {
+ // ba = SQR(bo_ij->BO - 2.50);
+ exphu = EXP( -gp7 * SQR(bo_ij->BO - 2.50) );
+ //oboa=abo(j1)-boa;
+ //obob=abo(j2)-boa;
+ exphua1 = EXP(-gp3 * (workspace->total_bond_order[i] - bo_ij->BO));
+ exphub1 = EXP(-gp3 * (workspace->total_bond_order[j] - bo_ij->BO));
+ //ovoab=abo(j1)-aval(it1)+abo(j2)-aval(it2);
+ exphuov = EXP(gp4 * (workspace->Delta[i] + workspace->Delta[j]));
+ hulpov = 1.0 / (1.0 + 25.0 * exphuov);
+
+ estriph = gp10 * exphu * hulpov * (exphua1 + exphub1);
+ //estrain(j1) = estrain(j1) + 0.50*estriph;
+ //estrain(j2) = estrain(j2) + 0.50*estriph;
+ data->E_BE += estriph;
+
+ decobdbo = gp10 * exphu * hulpov * (exphua1 + exphub1) *
+ ( gp3 - 2.0 * gp7 * (bo_ij->BO - 2.50) );
+ decobdboua = -gp10 * exphu * hulpov *
+ (gp3 * exphua1 + 25.0 * gp4 * exphuov * hulpov * (exphua1 + exphub1));
+ decobdboub = -gp10 * exphu * hulpov *
+ (gp3 * exphub1 + 25.0 * gp4 * exphuov * hulpov * (exphua1 + exphub1));
+
+ bo_ij->Cdbo += decobdbo;
+ workspace->CdDelta[i] += decobdboua;
+ workspace->CdDelta[j] += decobdboub;
#ifdef TEST_ENERGY
- fprintf( out_control->ebond,
- "%6d%6d%24.15e%24.15e%24.15e%24.15e\n",
- workspace->orig_id[i], workspace->orig_id[j],
- //i+1, j+1,
- estriph, decobdbo, decobdboua, decobdboub );
+ fprintf( out_control->ebond,
+ "%6d%6d%24.15e%24.15e%24.15e%24.15e\n",
+ workspace->orig_id[i], workspace->orig_id[j],
+ //i+1, j+1,
+ estriph, decobdbo, decobdboua, decobdboub );
#endif
#ifdef TEST_FORCES
- Add_dBO( system, lists, i, pj, decobdbo, workspace->f_be );
- Add_dDelta( system, lists, i, decobdboua, workspace->f_be );
- Add_dDelta( system, lists, j, decobdboub, workspace->f_be );
+ Add_dBO( system, lists, i, pj, decobdbo, workspace->f_be );
+ Add_dDelta( system, lists, i, decobdboua, workspace->f_be );
+ Add_dDelta( system, lists, j, decobdboub, workspace->f_be );
#endif
- }
- }
- }
- }
+ }
+ }
+ }
+ }
}
-void vdW_Coulomb_Energy( reax_system *system, control_params *control,
- simulation_data *data, static_storage *workspace,
- list **lists, output_controls *out_control )
+void vdW_Coulomb_Energy( reax_system *system, control_params *control,
+ simulation_data *data, static_storage *workspace,
+ list **lists, output_controls *out_control )
{
- int i, j, pj;
- int start_i, end_i;
- real self_coef;
- real p_vdW1, p_vdW1i;
- real powr_vdW1, powgi_vdW1;
- real tmp, r_ij, fn13, exp1, exp2;
- real Tap, dTap, dfn13, CEvd, CEclmb;
- real dr3gamij_1, dr3gamij_3;
- real e_ele, e_vdW, e_core, de_core;
- rvec temp, ext_press;
- // rtensor temp_rtensor, total_rtensor;
- two_body_parameters *twbp;
- far_neighbor_data *nbr_pj;
- list *far_nbrs;
-
- p_vdW1 = system->reaxprm.gp.l[28];
- p_vdW1i = 1.0 / p_vdW1;
- far_nbrs = (*lists) + FAR_NBRS;
- e_ele = 0;
- e_vdW = 0;
- e_core = 0;
- de_core = 0;
-
- for( i = 0; i < system->N; ++i ) {
- start_i = Start_Index(i, far_nbrs);
- end_i = End_Index(i, far_nbrs);
- // fprintf( stderr, "i: %d, start: %d, end: %d\n",
- // i, start_i, end_i );
-
- for( pj = start_i; pj < end_i; ++pj )
- if( far_nbrs->select.far_nbr_list[pj].d <= control->r_cut ) {
- nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
- j = nbr_pj->nbr;
- r_ij = nbr_pj->d;
- twbp = &(system->reaxprm.tbp[ system->atoms[i].type ]
- [ system->atoms[j].type ]);
- self_coef = (i == j) ? 0.5 : 1.0; // for supporting small boxes!
-
- /* Calculate Taper and its derivative */
- // Tap = nbr_pj->Tap; -- precomputed during compte_H
- Tap = control->Tap7 * r_ij + control->Tap6;
- Tap = Tap * r_ij + control->Tap5;
- Tap = Tap * r_ij + control->Tap4;
- Tap = Tap * r_ij + control->Tap3;
- Tap = Tap * r_ij + control->Tap2;
- Tap = Tap * r_ij + control->Tap1;
- Tap = Tap * r_ij + control->Tap0;
-
- dTap = 7*control->Tap7 * r_ij + 6*control->Tap6;
- dTap = dTap * r_ij + 5*control->Tap5;
- dTap = dTap * r_ij + 4*control->Tap4;
- dTap = dTap * r_ij + 3*control->Tap3;
- dTap = dTap * r_ij + 2*control->Tap2;
- dTap += control->Tap1/r_ij;
-
- /*vdWaals Calculations*/
- if(system->reaxprm.gp.vdw_type==1 || system->reaxprm.gp.vdw_type==3) {
- // shielding
- powr_vdW1 = POW(r_ij, p_vdW1);
- powgi_vdW1 = POW( 1.0 / twbp->gamma_w, p_vdW1);
-
- fn13 = POW( powr_vdW1 + powgi_vdW1, p_vdW1i );
- exp1 = EXP( twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
- exp2 = EXP( 0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
-
- data->E_vdW += e_vdW =
- self_coef * Tap * twbp->D * (exp1 - 2.0 * exp2);
-
- dfn13 = POW( powr_vdW1 + powgi_vdW1, p_vdW1i - 1.0) *
- POW(r_ij, p_vdW1 - 2.0);
-
- CEvd = self_coef * ( dTap * twbp->D * (exp1 - 2 * exp2) -
- Tap * twbp->D * (twbp->alpha / twbp->r_vdW) *
- (exp1 - exp2) * dfn13 );
- }
- else{ // no shielding
- exp1 = EXP( twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
- exp2 = EXP( 0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
-
- data->E_vdW += e_vdW =
- self_coef * Tap * twbp->D * (exp1 - 2.0 * exp2);
-
- CEvd = self_coef * ( dTap * twbp->D * (exp1 - 2.0 * exp2) -
- Tap * twbp->D * (twbp->alpha / twbp->r_vdW) *
- (exp1 - exp2) );
- }
-
- if(system->reaxprm.gp.vdw_type==2 || system->reaxprm.gp.vdw_type==3) {
- // innner wall
- e_core = twbp->ecore * EXP(twbp->acore * (1.0-(r_ij/twbp->rcore)));
- e_vdW += self_coef * Tap * e_core;
- data->E_vdW += self_coef * Tap * e_core;
-
- de_core = -(twbp->acore/twbp->rcore) * e_core;
- CEvd += self_coef * ( dTap * e_core + Tap * de_core );
- }
-
- /*Coulomb Calculations*/
- dr3gamij_1 = ( r_ij * r_ij * r_ij + twbp->gamma );
- dr3gamij_3 = POW( dr3gamij_1 , 0.33333333333333 );
-
- tmp = Tap / dr3gamij_3;
- //tmp = Tap * nbr_pj->inv_dr3gamij_3; -- precomputed during compte_H
- data->E_Ele += e_ele =
- self_coef * C_ele * system->atoms[i].q * system->atoms[j].q * tmp;
-
-
- CEclmb = self_coef * C_ele * system->atoms[i].q * system->atoms[j].q *
- ( dTap - Tap * r_ij / dr3gamij_1 ) / dr3gamij_3;
- /*CEclmb = self_coef*C_ele*system->atoms[i].q*system->atoms[j].q*
- ( dTap- Tap*r_ij*nbr_pj->inv_dr3gamij_1 )*nbr_pj->inv_dr3gamij_3;*/
-
-
- if( control->ensemble == NVE || control->ensemble == NVT || control->ensemble == bNVT ) {
- rvec_ScaledAdd( system->atoms[i].f,
- -(CEvd+CEclmb), nbr_pj->dvec );
- rvec_ScaledAdd( system->atoms[j].f,
- +(CEvd+CEclmb), nbr_pj->dvec );
- }
- else { // NPT, iNPT or sNPT
- /* for pressure coupling, terms not related to bond order
- derivatives are added directly into pressure vector/tensor */
- rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec );
-
- rvec_ScaledAdd( system->atoms[i].f, -1., temp );
- rvec_Add( system->atoms[j].f, temp );
-
- rvec_iMultiply( ext_press, nbr_pj->rel_box, temp );
- rvec_Add( data->ext_press, ext_press );
-
- /*fprintf( stderr, "nonbonded(%d,%d): rel_box (%f %f %f)",
- i,j,nbr_pj->rel_box[0],nbr_pj->rel_box[1],nbr_pj->rel_box[2] );
-
- fprintf( stderr, "force(%f %f %f)", temp[0], temp[1], temp[2] );
-
- fprintf( stderr, "ext_press (%12.6f %12.6f %12.6f)\n",
- data->ext_press[0], data->ext_press[1], data->ext_press[2] );*/
-
- /* This part is intended for a fully-flexible box */
- /* rvec_OuterProduct( temp_rtensor, nbr_pj->dvec,
- system->atoms[i].x );
- rtensor_Scale( total_rtensor,
- F_C * -(CEvd + CEclmb), temp_rtensor );
- rvec_OuterProduct( temp_rtensor,
- nbr_pj->dvec, system->atoms[j].x );
- rtensor_ScaledAdd( total_rtensor,
- F_C * +(CEvd + CEclmb), temp_rtensor );
-
- if( nbr_pj->imaginary )
- // This is an external force due to an imaginary nbr
- rtensor_ScaledAdd( data->flex_bar.P, -1.0, total_rtensor );
- else
- // This interaction is completely internal
- rtensor_Add( data->flex_bar.P, total_rtensor ); */
- }
-
+ int i, j, pj;
+ int start_i, end_i;
+ real self_coef;
+ real p_vdW1, p_vdW1i;
+ real powr_vdW1, powgi_vdW1;
+ real tmp, r_ij, fn13, exp1, exp2;
+ real Tap, dTap, dfn13, CEvd, CEclmb;
+ real dr3gamij_1, dr3gamij_3;
+ real e_ele, e_vdW, e_core, de_core;
+ rvec temp, ext_press;
+ // rtensor temp_rtensor, total_rtensor;
+ two_body_parameters *twbp;
+ far_neighbor_data *nbr_pj;
+ list *far_nbrs;
+
+ p_vdW1 = system->reaxprm.gp.l[28];
+ p_vdW1i = 1.0 / p_vdW1;
+ far_nbrs = (*lists) + FAR_NBRS;
+ e_ele = 0;
+ e_vdW = 0;
+ e_core = 0;
+ de_core = 0;
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ start_i = Start_Index(i, far_nbrs);
+ end_i = End_Index(i, far_nbrs);
+ // fprintf( stderr, "i: %d, start: %d, end: %d\n",
+ // i, start_i, end_i );
+
+ for ( pj = start_i; pj < end_i; ++pj )
+ if ( far_nbrs->select.far_nbr_list[pj].d <= control->r_cut )
+ {
+ nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
+ j = nbr_pj->nbr;
+ r_ij = nbr_pj->d;
+ twbp = &(system->reaxprm.tbp[ system->atoms[i].type ]
+ [ system->atoms[j].type ]);
+ self_coef = (i == j) ? 0.5 : 1.0; // for supporting small boxes!
+
+ /* Calculate Taper and its derivative */
+ // Tap = nbr_pj->Tap; -- precomputed during compte_H
+ Tap = control->Tap7 * r_ij + control->Tap6;
+ Tap = Tap * r_ij + control->Tap5;
+ Tap = Tap * r_ij + control->Tap4;
+ Tap = Tap * r_ij + control->Tap3;
+ Tap = Tap * r_ij + control->Tap2;
+ Tap = Tap * r_ij + control->Tap1;
+ Tap = Tap * r_ij + control->Tap0;
+
+ dTap = 7 * control->Tap7 * r_ij + 6 * control->Tap6;
+ dTap = dTap * r_ij + 5 * control->Tap5;
+ dTap = dTap * r_ij + 4 * control->Tap4;
+ dTap = dTap * r_ij + 3 * control->Tap3;
+ dTap = dTap * r_ij + 2 * control->Tap2;
+ dTap += control->Tap1 / r_ij;
+
+ /*vdWaals Calculations*/
+ if (system->reaxprm.gp.vdw_type == 1 || system->reaxprm.gp.vdw_type == 3)
+ {
+ // shielding
+ powr_vdW1 = POW(r_ij, p_vdW1);
+ powgi_vdW1 = POW( 1.0 / twbp->gamma_w, p_vdW1);
+
+ fn13 = POW( powr_vdW1 + powgi_vdW1, p_vdW1i );
+ exp1 = EXP( twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
+ exp2 = EXP( 0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
+
+ data->E_vdW += e_vdW =
+ self_coef * Tap * twbp->D * (exp1 - 2.0 * exp2);
+
+ dfn13 = POW( powr_vdW1 + powgi_vdW1, p_vdW1i - 1.0) *
+ POW(r_ij, p_vdW1 - 2.0);
+
+ CEvd = self_coef * ( dTap * twbp->D * (exp1 - 2 * exp2) -
+ Tap * twbp->D * (twbp->alpha / twbp->r_vdW) *
+ (exp1 - exp2) * dfn13 );
+ }
+ else // no shielding
+ {
+ exp1 = EXP( twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
+ exp2 = EXP( 0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
+
+ data->E_vdW += e_vdW =
+ self_coef * Tap * twbp->D * (exp1 - 2.0 * exp2);
+
+ CEvd = self_coef * ( dTap * twbp->D * (exp1 - 2.0 * exp2) -
+ Tap * twbp->D * (twbp->alpha / twbp->r_vdW) *
+ (exp1 - exp2) );
+ }
+
+ if (system->reaxprm.gp.vdw_type == 2 || system->reaxprm.gp.vdw_type == 3)
+ {
+ // innner wall
+ e_core = twbp->ecore * EXP(twbp->acore * (1.0 - (r_ij / twbp->rcore)));
+ e_vdW += self_coef * Tap * e_core;
+ data->E_vdW += self_coef * Tap * e_core;
+
+ de_core = -(twbp->acore / twbp->rcore) * e_core;
+ CEvd += self_coef * ( dTap * e_core + Tap * de_core );
+ }
+
+ /*Coulomb Calculations*/
+ dr3gamij_1 = ( r_ij * r_ij * r_ij + twbp->gamma );
+ dr3gamij_3 = POW( dr3gamij_1 , 0.33333333333333 );
+
+ tmp = Tap / dr3gamij_3;
+ //tmp = Tap * nbr_pj->inv_dr3gamij_3; -- precomputed during compte_H
+ data->E_Ele += e_ele =
+ self_coef * C_ele * system->atoms[i].q * system->atoms[j].q * tmp;
+
+
+ CEclmb = self_coef * C_ele * system->atoms[i].q * system->atoms[j].q *
+ ( dTap - Tap * r_ij / dr3gamij_1 ) / dr3gamij_3;
+ /*CEclmb = self_coef*C_ele*system->atoms[i].q*system->atoms[j].q*
+ ( dTap- Tap*r_ij*nbr_pj->inv_dr3gamij_1 )*nbr_pj->inv_dr3gamij_3;*/
+
+
+ if ( control->ensemble == NVE || control->ensemble == NVT || control->ensemble == bNVT )
+ {
+ rvec_ScaledAdd( system->atoms[i].f,
+ -(CEvd + CEclmb), nbr_pj->dvec );
+ rvec_ScaledAdd( system->atoms[j].f,
+ +(CEvd + CEclmb), nbr_pj->dvec );
+ }
+ else // NPT, iNPT or sNPT
+ {
+ /* for pressure coupling, terms not related to bond order
+ derivatives are added directly into pressure vector/tensor */
+ rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec );
+
+ rvec_ScaledAdd( system->atoms[i].f, -1., temp );
+ rvec_Add( system->atoms[j].f, temp );
+
+ rvec_iMultiply( ext_press, nbr_pj->rel_box, temp );
+ rvec_Add( data->ext_press, ext_press );
+
+ /*fprintf( stderr, "nonbonded(%d,%d): rel_box (%f %f %f)",
+ i,j,nbr_pj->rel_box[0],nbr_pj->rel_box[1],nbr_pj->rel_box[2] );
+
+ fprintf( stderr, "force(%f %f %f)", temp[0], temp[1], temp[2] );
+
+ fprintf( stderr, "ext_press (%12.6f %12.6f %12.6f)\n",
+ data->ext_press[0], data->ext_press[1], data->ext_press[2] );*/
+
+ /* This part is intended for a fully-flexible box */
+ /* rvec_OuterProduct( temp_rtensor, nbr_pj->dvec,
+ system->atoms[i].x );
+ rtensor_Scale( total_rtensor,
+ F_C * -(CEvd + CEclmb), temp_rtensor );
+ rvec_OuterProduct( temp_rtensor,
+ nbr_pj->dvec, system->atoms[j].x );
+ rtensor_ScaledAdd( total_rtensor,
+ F_C * +(CEvd + CEclmb), temp_rtensor );
+
+ if( nbr_pj->imaginary )
+ // This is an external force due to an imaginary nbr
+ rtensor_ScaledAdd( data->flex_bar.P, -1.0, total_rtensor );
+ else
+ // This interaction is completely internal
+ rtensor_Add( data->flex_bar.P, total_rtensor ); */
+ }
+
#ifdef TEST_ENERGY
- rvec_MakeZero( temp );
- rvec_ScaledAdd( temp, +CEvd, nbr_pj->dvec );
- fprintf( out_control->evdw,
- "%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
- //i+1, j+1,
- MIN( workspace->orig_id[i], workspace->orig_id[j] ),
- MAX( workspace->orig_id[i], workspace->orig_id[j] ),
- r_ij, e_vdW, temp[0], temp[1], temp[2]/*, data->E_vdW*/ );
-
- fprintf( out_control->ecou, "%6d%6d%24.15e%24.15e%24.15e%24.15e\n",
- MIN( workspace->orig_id[i], workspace->orig_id[j] ),
- MAX( workspace->orig_id[i], workspace->orig_id[j] ),
- r_ij, system->atoms[i].q, system->atoms[j].q,
- e_ele/*, data->E_Ele*/ );
+ rvec_MakeZero( temp );
+ rvec_ScaledAdd( temp, +CEvd, nbr_pj->dvec );
+ fprintf( out_control->evdw,
+ "%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
+ //i+1, j+1,
+ MIN( workspace->orig_id[i], workspace->orig_id[j] ),
+ MAX( workspace->orig_id[i], workspace->orig_id[j] ),
+ r_ij, e_vdW, temp[0], temp[1], temp[2]/*, data->E_vdW*/ );
+
+ fprintf( out_control->ecou, "%6d%6d%24.15e%24.15e%24.15e%24.15e\n",
+ MIN( workspace->orig_id[i], workspace->orig_id[j] ),
+ MAX( workspace->orig_id[i], workspace->orig_id[j] ),
+ r_ij, system->atoms[i].q, system->atoms[j].q,
+ e_ele/*, data->E_Ele*/ );
#endif
#ifdef TEST_FORCES
- rvec_ScaledAdd( workspace->f_vdw[i], -CEvd, nbr_pj->dvec );
- rvec_ScaledAdd( workspace->f_vdw[j], +CEvd, nbr_pj->dvec );
- rvec_ScaledAdd( workspace->f_ele[i], -CEclmb, nbr_pj->dvec );
- rvec_ScaledAdd( workspace->f_ele[j], +CEclmb, nbr_pj->dvec );
+ rvec_ScaledAdd( workspace->f_vdw[i], -CEvd, nbr_pj->dvec );
+ rvec_ScaledAdd( workspace->f_vdw[j], +CEvd, nbr_pj->dvec );
+ rvec_ScaledAdd( workspace->f_ele[i], -CEclmb, nbr_pj->dvec );
+ rvec_ScaledAdd( workspace->f_ele[j], +CEclmb, nbr_pj->dvec );
#endif
- }
- }
-
- // fclose( fout );
-
- // fprintf( stderr, "nonbonded: ext_press (%24.15e %24.15e %24.15e)\n",
- // data->ext_press[0], data->ext_press[1], data->ext_press[2] );
+ }
+ }
+
+ // fclose( fout );
+
+ // fprintf( stderr, "nonbonded: ext_press (%24.15e %24.15e %24.15e)\n",
+ // data->ext_press[0], data->ext_press[1], data->ext_press[2] );
}
-void LR_vdW_Coulomb( reax_system *system, control_params *control,
- int i, int j, real r_ij, LR_data *lr )
+void LR_vdW_Coulomb( reax_system *system, control_params *control,
+ int i, int j, real r_ij, LR_data *lr )
{
- real p_vdW1 = system->reaxprm.gp.l[28];
- real p_vdW1i = 1.0 / p_vdW1;
- real powr_vdW1, powgi_vdW1;
- real tmp, fn13, exp1, exp2;
- real Tap, dTap, dfn13;
- real dr3gamij_1, dr3gamij_3;
- real e_core, de_core;
- two_body_parameters *twbp;
-
- twbp = &(system->reaxprm.tbp[i][j]);
- e_core = 0;
- de_core = 0;
-
- /* calculate taper and its derivative */
- Tap = control->Tap7 * r_ij + control->Tap6;
- Tap = Tap * r_ij + control->Tap5;
- Tap = Tap * r_ij + control->Tap4;
- Tap = Tap * r_ij + control->Tap3;
- Tap = Tap * r_ij + control->Tap2;
- Tap = Tap * r_ij + control->Tap1;
- Tap = Tap * r_ij + control->Tap0;
-
- dTap = 7*control->Tap7 * r_ij + 6*control->Tap6;
- dTap = dTap * r_ij + 5*control->Tap5;
- dTap = dTap * r_ij + 4*control->Tap4;
- dTap = dTap * r_ij + 3*control->Tap3;
- dTap = dTap * r_ij + 2*control->Tap2;
- dTap += control->Tap1/r_ij;
-
-
- /* vdWaals calculations */
- powr_vdW1 = POW(r_ij, p_vdW1);
- powgi_vdW1 = POW( 1.0 / twbp->gamma_w, p_vdW1);
-
- fn13 = POW( powr_vdW1 + powgi_vdW1, p_vdW1i );
- exp1 = EXP( twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
- exp2 = EXP( 0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
-
- lr->e_vdW = Tap * twbp->D * (exp1 - 2.0 * exp2);
- /* fprintf(stderr,"vdW: Tap:%f, r: %f, f13:%f, D:%f, Energy:%f,\
- Gamma_w:%f, p_vdw: %f, alpha: %f, r_vdw: %f, %lf %lf\n",
- Tap, r_ij, fn13, twbp->D, Tap * twbp->D * (exp1 - 2.0 * exp2),
- powgi_vdW1, p_vdW1, twbp->alpha, twbp->r_vdW, exp1, exp2); */
-
- dfn13 = POW( powr_vdW1 + powgi_vdW1, p_vdW1i - 1.0) * POW(r_ij, p_vdW1 - 2.0);
-
- lr->CEvd = dTap * twbp->D * (exp1 - 2 * exp2) -
- Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13;
-
- /*vdWaals Calculations*/
- if(system->reaxprm.gp.vdw_type==1 || system->reaxprm.gp.vdw_type==3)
- { // shielding
- powr_vdW1 = POW(r_ij, p_vdW1);
- powgi_vdW1 = POW( 1.0 / twbp->gamma_w, p_vdW1);
-
- fn13 = POW( powr_vdW1 + powgi_vdW1, p_vdW1i );
- exp1 = EXP( twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
- exp2 = EXP( 0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
-
- lr->e_vdW = Tap * twbp->D * (exp1 - 2.0 * exp2);
-
- dfn13 = POW( powr_vdW1 + powgi_vdW1, p_vdW1i - 1.0) *
- POW(r_ij, p_vdW1 - 2.0);
-
- lr->CEvd = dTap * twbp->D * (exp1 - 2.0 * exp2) -
- Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13;
- }
- else{ // no shielding
- exp1 = EXP( twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
- exp2 = EXP( 0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
-
+ real p_vdW1 = system->reaxprm.gp.l[28];
+ real p_vdW1i = 1.0 / p_vdW1;
+ real powr_vdW1, powgi_vdW1;
+ real tmp, fn13, exp1, exp2;
+ real Tap, dTap, dfn13;
+ real dr3gamij_1, dr3gamij_3;
+ real e_core, de_core;
+ two_body_parameters *twbp;
+
+ twbp = &(system->reaxprm.tbp[i][j]);
+ e_core = 0;
+ de_core = 0;
+
+ /* calculate taper and its derivative */
+ Tap = control->Tap7 * r_ij + control->Tap6;
+ Tap = Tap * r_ij + control->Tap5;
+ Tap = Tap * r_ij + control->Tap4;
+ Tap = Tap * r_ij + control->Tap3;
+ Tap = Tap * r_ij + control->Tap2;
+ Tap = Tap * r_ij + control->Tap1;
+ Tap = Tap * r_ij + control->Tap0;
+
+ dTap = 7 * control->Tap7 * r_ij + 6 * control->Tap6;
+ dTap = dTap * r_ij + 5 * control->Tap5;
+ dTap = dTap * r_ij + 4 * control->Tap4;
+ dTap = dTap * r_ij + 3 * control->Tap3;
+ dTap = dTap * r_ij + 2 * control->Tap2;
+ dTap += control->Tap1 / r_ij;
+
+
+ /* vdWaals calculations */
+ powr_vdW1 = POW(r_ij, p_vdW1);
+ powgi_vdW1 = POW( 1.0 / twbp->gamma_w, p_vdW1);
+
+ fn13 = POW( powr_vdW1 + powgi_vdW1, p_vdW1i );
+ exp1 = EXP( twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
+ exp2 = EXP( 0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
+
lr->e_vdW = Tap * twbp->D * (exp1 - 2.0 * exp2);
-
- lr->CEvd = dTap * twbp->D * (exp1 - 2.0 * exp2) -
- Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2);
- }
-
- if(system->reaxprm.gp.vdw_type==2 || system->reaxprm.gp.vdw_type==3)
- { // innner wall
- e_core = twbp->ecore * EXP(twbp->acore * (1.0-(r_ij/twbp->rcore)));
- lr->e_vdW += Tap * e_core;
-
- de_core = -(twbp->acore/twbp->rcore) * e_core;
- lr->CEvd += dTap * e_core + Tap * de_core;
+ /* fprintf(stderr,"vdW: Tap:%f, r: %f, f13:%f, D:%f, Energy:%f,\
+ Gamma_w:%f, p_vdw: %f, alpha: %f, r_vdw: %f, %lf %lf\n",
+ Tap, r_ij, fn13, twbp->D, Tap * twbp->D * (exp1 - 2.0 * exp2),
+ powgi_vdW1, p_vdW1, twbp->alpha, twbp->r_vdW, exp1, exp2); */
+
+ dfn13 = POW( powr_vdW1 + powgi_vdW1, p_vdW1i - 1.0) * POW(r_ij, p_vdW1 - 2.0);
+
+ lr->CEvd = dTap * twbp->D * (exp1 - 2 * exp2) -
+ Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13;
+
+ /*vdWaals Calculations*/
+ if (system->reaxprm.gp.vdw_type == 1 || system->reaxprm.gp.vdw_type == 3)
+ {
+ // shielding
+ powr_vdW1 = POW(r_ij, p_vdW1);
+ powgi_vdW1 = POW( 1.0 / twbp->gamma_w, p_vdW1);
+
+ fn13 = POW( powr_vdW1 + powgi_vdW1, p_vdW1i );
+ exp1 = EXP( twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
+ exp2 = EXP( 0.5 * twbp->alpha * (1.0 - fn13 / twbp->r_vdW) );
+
+ lr->e_vdW = Tap * twbp->D * (exp1 - 2.0 * exp2);
+
+ dfn13 = POW( powr_vdW1 + powgi_vdW1, p_vdW1i - 1.0) *
+ POW(r_ij, p_vdW1 - 2.0);
+
+ lr->CEvd = dTap * twbp->D * (exp1 - 2.0 * exp2) -
+ Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13;
+ }
+ else // no shielding
+ {
+ exp1 = EXP( twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
+ exp2 = EXP( 0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW) );
+
+ lr->e_vdW = Tap * twbp->D * (exp1 - 2.0 * exp2);
+
+ lr->CEvd = dTap * twbp->D * (exp1 - 2.0 * exp2) -
+ Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2);
+ }
+
+ if (system->reaxprm.gp.vdw_type == 2 || system->reaxprm.gp.vdw_type == 3)
+ {
+ // innner wall
+ e_core = twbp->ecore * EXP(twbp->acore * (1.0 - (r_ij / twbp->rcore)));
+ lr->e_vdW += Tap * e_core;
+
+ de_core = -(twbp->acore / twbp->rcore) * e_core;
+ lr->CEvd += dTap * e_core + Tap * de_core;
}
-
- /* Coulomb calculations */
- dr3gamij_1 = ( r_ij * r_ij * r_ij + twbp->gamma );
- dr3gamij_3 = POW( dr3gamij_1 , 0.33333333333333 );
-
- tmp = Tap / dr3gamij_3;
- lr->H = EV_to_KCALpMOL * tmp;
- lr->e_ele = C_ele * tmp;
- /* fprintf( stderr,"i:%d(%d), j:%d(%d), gamma:%f,\
- Tap:%f, dr3gamij_3:%f, qi: %f, qj: %f\n",
- i, system->atoms[i].type, j, system->atoms[j].type,
- twbp->gamma, Tap, dr3gamij_3,
- system->atoms[i].q, system->atoms[j].q ); */
-
- lr->CEclmb = C_ele * ( dTap - Tap * r_ij / dr3gamij_1 ) / dr3gamij_3;
- /* fprintf( stdout, "%d %d\t%g\t%g %g\t%g %g\t%g %g\n",
- i+1, j+1, r_ij, e_vdW, CEvd * r_ij,
- system->atoms[i].q, system->atoms[j].q, e_ele, CEclmb * r_ij ); */
-
- /* fprintf( stderr,"LR_Lookup:%3d%3d%5.3f-%8.5f,%8.5f%8.5f,%8.5f%8.5f\n",
- i, j, r_ij, lr->H, lr->e_vdW, lr->CEvd, lr->e_ele, lr->CEclmb ); */
+
+ /* Coulomb calculations */
+ dr3gamij_1 = ( r_ij * r_ij * r_ij + twbp->gamma );
+ dr3gamij_3 = POW( dr3gamij_1 , 0.33333333333333 );
+
+ tmp = Tap / dr3gamij_3;
+ lr->H = EV_to_KCALpMOL * tmp;
+ lr->e_ele = C_ele * tmp;
+ /* fprintf( stderr,"i:%d(%d), j:%d(%d), gamma:%f,\
+ Tap:%f, dr3gamij_3:%f, qi: %f, qj: %f\n",
+ i, system->atoms[i].type, j, system->atoms[j].type,
+ twbp->gamma, Tap, dr3gamij_3,
+ system->atoms[i].q, system->atoms[j].q ); */
+
+ lr->CEclmb = C_ele * ( dTap - Tap * r_ij / dr3gamij_1 ) / dr3gamij_3;
+ /* fprintf( stdout, "%d %d\t%g\t%g %g\t%g %g\t%g %g\n",
+ i+1, j+1, r_ij, e_vdW, CEvd * r_ij,
+ system->atoms[i].q, system->atoms[j].q, e_ele, CEclmb * r_ij ); */
+
+ /* fprintf( stderr,"LR_Lookup:%3d%3d%5.3f-%8.5f,%8.5f%8.5f,%8.5f%8.5f\n",
+ i, j, r_ij, lr->H, lr->e_vdW, lr->CEvd, lr->e_ele, lr->CEclmb ); */
}
void Tabulated_vdW_Coulomb_Energy( reax_system *system, control_params *control,
- simulation_data *data,
- static_storage *workspace, list **lists,
- output_controls *out_control )
+ simulation_data *data,
+ static_storage *workspace, list **lists,
+ output_controls *out_control )
{
- int i, j, pj, r, steps, update_freq, update_energies;
- int type_i, type_j, tmin, tmax;
- int start_i, end_i;
- real r_ij, self_coef, base, dif;
- real e_vdW, e_ele;
- real CEvd, CEclmb;
- rvec temp, ext_press;
- far_neighbor_data *nbr_pj;
- list *far_nbrs = (*lists) + FAR_NBRS;
- LR_lookup_table *t;
-
- steps = data->step - data->prev_steps;
- update_freq = out_control->energy_update_freq;
- update_energies = update_freq > 0 && steps % update_freq == 0;
-
- for( i = 0; i < system->N; ++i ) {
- type_i = system->atoms[i].type;
- start_i = Start_Index(i,far_nbrs);
- end_i = End_Index(i,far_nbrs);
-
- for( pj = start_i; pj < end_i; ++pj )
- if( far_nbrs->select.far_nbr_list[pj].d <= control->r_cut ) {
- nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
- j = nbr_pj->nbr;
- type_j = system->atoms[j].type;
- r_ij = nbr_pj->d;
- self_coef = (i == j) ? 0.5 : 1.0;
- tmin = MIN( type_i, type_j );
- tmax = MAX( type_i, type_j );
- t = &( LR[tmin][tmax] );
-
- /* Cubic Spline Interpolation */
- r = (int)(r_ij * t->inv_dx);
- if( r == 0 ) ++r;
- base = (real)(r+1) * t->dx;
- dif = r_ij - base;
- //fprintf(stderr, "r: %f, i: %d, base: %f, dif: %f\n", r, i, base, dif);
-
- if( update_energies ) {
- e_vdW = ((t->vdW[r].d*dif + t->vdW[r].c)*dif + t->vdW[r].b)*dif +
- t->vdW[r].a;
- e_vdW *= self_coef;
-
- e_ele = ((t->ele[r].d*dif + t->ele[r].c)*dif + t->ele[r].b)*dif +
- t->ele[r].a;
- e_ele *= self_coef * system->atoms[i].q * system->atoms[j].q;
-
- data->E_vdW += e_vdW;
- data->E_Ele += e_ele;
- }
-
- CEvd = ((t->CEvd[r].d*dif + t->CEvd[r].c)*dif + t->CEvd[r].b)*dif +
- t->CEvd[r].a;
- CEvd *= self_coef;
- //CEvd = (3*t->vdW[r].d*dif + 2*t->vdW[r].c)*dif + t->vdW[r].b;
-
- CEclmb = ((t->CEclmb[r].d*dif+t->CEclmb[r].c)*dif+t->CEclmb[r].b)*dif +
- t->CEclmb[r].a;
- CEclmb *= self_coef * system->atoms[i].q * system->atoms[j].q;
-
- if( control->ensemble == NVE || control->ensemble == NVT || control->ensemble == bNVT) {
- rvec_ScaledAdd( system->atoms[i].f, -(CEvd + CEclmb), nbr_pj->dvec );
- rvec_ScaledAdd( system->atoms[j].f, +(CEvd + CEclmb), nbr_pj->dvec );
- }
- else { // NPT, iNPT or sNPT
- /* for pressure coupling, terms not related to bond order
- derivatives are added directly into pressure vector/tensor */
- rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec );
- rvec_ScaledAdd( system->atoms[i].f, -1., temp );
- rvec_Add( system->atoms[j].f, temp );
- rvec_iMultiply( ext_press, nbr_pj->rel_box, temp );
- rvec_Add( data->ext_press, ext_press );
- }
-
+ int i, j, pj, r, steps, update_freq, update_energies;
+ int type_i, type_j, tmin, tmax;
+ int start_i, end_i;
+ real r_ij, self_coef, base, dif;
+ real e_vdW, e_ele;
+ real CEvd, CEclmb;
+ rvec temp, ext_press;
+ far_neighbor_data *nbr_pj;
+ list *far_nbrs = (*lists) + FAR_NBRS;
+ LR_lookup_table *t;
+
+ steps = data->step - data->prev_steps;
+ update_freq = out_control->energy_update_freq;
+ update_energies = update_freq > 0 && steps % update_freq == 0;
+
+ for ( i = 0; i < system->N; ++i )
+ {
+ type_i = system->atoms[i].type;
+ start_i = Start_Index(i, far_nbrs);
+ end_i = End_Index(i, far_nbrs);
+
+ for ( pj = start_i; pj < end_i; ++pj )
+ if ( far_nbrs->select.far_nbr_list[pj].d <= control->r_cut )
+ {
+ nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
+ j = nbr_pj->nbr;
+ type_j = system->atoms[j].type;
+ r_ij = nbr_pj->d;
+ self_coef = (i == j) ? 0.5 : 1.0;
+ tmin = MIN( type_i, type_j );
+ tmax = MAX( type_i, type_j );
+ t = &( LR[tmin][tmax] );
+
+ /* Cubic Spline Interpolation */
+ r = (int)(r_ij * t->inv_dx);
+ if ( r == 0 ) ++r;
+ base = (real)(r + 1) * t->dx;
+ dif = r_ij - base;
+ //fprintf(stderr, "r: %f, i: %d, base: %f, dif: %f\n", r, i, base, dif);
+
+ if ( update_energies )
+ {
+ e_vdW = ((t->vdW[r].d * dif + t->vdW[r].c) * dif + t->vdW[r].b) * dif +
+ t->vdW[r].a;
+ e_vdW *= self_coef;
+
+ e_ele = ((t->ele[r].d * dif + t->ele[r].c) * dif + t->ele[r].b) * dif +
+ t->ele[r].a;
+ e_ele *= self_coef * system->atoms[i].q * system->atoms[j].q;
+
+ data->E_vdW += e_vdW;
+ data->E_Ele += e_ele;
+ }
+
+ CEvd = ((t->CEvd[r].d * dif + t->CEvd[r].c) * dif + t->CEvd[r].b) * dif +
+ t->CEvd[r].a;
+ CEvd *= self_coef;
+ //CEvd = (3*t->vdW[r].d*dif + 2*t->vdW[r].c)*dif + t->vdW[r].b;
+
+ CEclmb = ((t->CEclmb[r].d * dif + t->CEclmb[r].c) * dif + t->CEclmb[r].b) * dif +
+ t->CEclmb[r].a;
+ CEclmb *= self_coef * system->atoms[i].q * system->atoms[j].q;
+
+ if ( control->ensemble == NVE || control->ensemble == NVT || control->ensemble == bNVT)
+ {
+ rvec_ScaledAdd( system->atoms[i].f, -(CEvd + CEclmb), nbr_pj->dvec );
+ rvec_ScaledAdd( system->atoms[j].f, +(CEvd + CEclmb), nbr_pj->dvec );
+ }
+ else // NPT, iNPT or sNPT
+ {
+ /* for pressure coupling, terms not related to bond order
+ derivatives are added directly into pressure vector/tensor */
+ rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec );
+ rvec_ScaledAdd( system->atoms[i].f, -1., temp );
+ rvec_Add( system->atoms[j].f, temp );
+ rvec_iMultiply( ext_press, nbr_pj->rel_box, temp );
+ rvec_Add( data->ext_press, ext_press );
+ }
+
#ifdef TEST_ENERGY
- fprintf(out_control->evdw, "%6d%6d%24.15e%24.15e%24.15e\n",
- workspace->orig_id[i], workspace->orig_id[j],
- r_ij, e_vdW, data->E_vdW );
- fprintf(out_control->ecou,"%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
- workspace->orig_id[i], workspace->orig_id[j],
- r_ij, system->atoms[i].q, system->atoms[j].q,
- e_ele, data->E_Ele );
+ fprintf(out_control->evdw, "%6d%6d%24.15e%24.15e%24.15e\n",
+ workspace->orig_id[i], workspace->orig_id[j],
+ r_ij, e_vdW, data->E_vdW );
+ fprintf(out_control->ecou, "%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
+ workspace->orig_id[i], workspace->orig_id[j],
+ r_ij, system->atoms[i].q, system->atoms[j].q,
+ e_ele, data->E_Ele );
#endif
#ifdef TEST_FORCES
- rvec_ScaledAdd( workspace->f_vdw[i], -CEvd, nbr_pj->dvec );
- rvec_ScaledAdd( workspace->f_vdw[j], +CEvd, nbr_pj->dvec );
- rvec_ScaledAdd( workspace->f_ele[i], -CEclmb, nbr_pj->dvec );
- rvec_ScaledAdd( workspace->f_ele[j], +CEclmb, nbr_pj->dvec );
+ rvec_ScaledAdd( workspace->f_vdw[i], -CEvd, nbr_pj->dvec );
+ rvec_ScaledAdd( workspace->f_vdw[j], +CEvd, nbr_pj->dvec );
+ rvec_ScaledAdd( workspace->f_ele[i], -CEclmb, nbr_pj->dvec );
+ rvec_ScaledAdd( workspace->f_ele[j], +CEclmb, nbr_pj->dvec );
#endif
- }
- }
+ }
+ }
}
@@ -555,11 +574,11 @@ void Tabulated_vdW_Coulomb_Energy( reax_system *system, control_params *control,
r = (int) p;
prev = &( t->y[r] );
next = &( t->y[r+1] );
-
+
tmp = p - r;
e_vdW = self_coef * (prev->e_vdW + tmp*(next->e_vdW - prev->e_vdW ));
CEvd = self_coef * (prev->CEvd + tmp*(next->CEvd - prev->CEvd ));
-
+
e_ele = self_coef * (prev->e_ele + tmp*(next->e_ele - prev->e_ele ));
e_ele = e_ele * system->atoms[i].q * system->atoms[j].q;
CEclmb = self_coef * (prev->CEclmb+tmp*(next->CEclmb - prev->CEclmb));
diff --git a/puremd_rc_1003/sPuReMD/two_body_interactions.h b/puremd_rc_1003/sPuReMD/two_body_interactions.h
index 484383428aafc9772da8559c82ea935f4fcf62fb..bee9779bbccb4fe932ad545b8b091e2b7a0fa266 100644
--- a/puremd_rc_1003/sPuReMD/two_body_interactions.h
+++ b/puremd_rc_1003/sPuReMD/two_body_interactions.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -24,11 +24,11 @@
#include <mytypes.h>
-void Bond_Energy( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+void Bond_Energy( reax_system*, control_params*, simulation_data*,
+ static_storage*, list**, output_controls* );
void vdW_Coulomb_Energy( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, list**, output_controls* );
void LR_vdW_Coulomb( reax_system*, control_params*, int, int, real, LR_data* );
void Tabulated_vdW_Coulomb_Energy( reax_system*, control_params*, simulation_data*,
- static_storage*, list**, output_controls* );
+ static_storage*, list**, output_controls* );
#endif
diff --git a/puremd_rc_1003/sPuReMD/vector.c b/puremd_rc_1003/sPuReMD/vector.c
index d6bed7ae87081656283b860184b00e2c9e8e37c4..b5eef5c6cecde54a95da0170caa99f394d734037 100644
--- a/puremd_rc_1003/sPuReMD/vector.c
+++ b/puremd_rc_1003/sPuReMD/vector.c
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
@@ -24,535 +24,535 @@
inline int Vector_isZero( const real * const v, const unsigned int k )
{
- unsigned int i;
+ unsigned int i;
- for( i=0; i<k; ++i )
- {
- if( fabs( v[i] ) > ALMOST_ZERO )
+ for ( i = 0; i < k; ++i )
{
- return 0;
+ if ( fabs( v[i] ) > ALMOST_ZERO )
+ {
+ return 0;
+ }
}
- }
-
- return 1;
+
+ return 1;
}
inline void Vector_MakeZero( real * const v, const unsigned int k )
{
- unsigned int i;
+ unsigned int i;
- for( i=0; i<k; ++i )
- {
- v[i] = ZERO;
- }
+ for ( i = 0; i < k; ++i )
+ {
+ v[i] = ZERO;
+ }
}
inline void Vector_Copy( real * const dest, const real * const v, const unsigned int k )
{
- unsigned int i;
+ unsigned int i;
- for( i=0; i<k; ++i )
- {
- dest[i] = v[i];
- }
+ for ( i = 0; i < k; ++i )
+ {
+ dest[i] = v[i];
+ }
}
inline void Vector_Scale( real * const dest, const real c, const real * const v, const unsigned int k )
{
- unsigned int i;
+ unsigned int i;
- for( i=0; i<k; ++i )
- {
- dest[i] = c * v[i];
- }
+ for ( i = 0; i < k; ++i )
+ {
+ dest[i] = c * v[i];
+ }
}
inline void Vector_Sum( real * const dest, const real c, const real * const v, const real d,
- const real * const y, const unsigned int k )
+ const real * const y, const unsigned int k )
{
- unsigned int i;
+ unsigned int i;
- for( i=0; i<k; ++i )
- {
- dest[i] = c * v[i] + d * y[i];
- }
+ for ( i = 0; i < k; ++i )
+ {
+ dest[i] = c * v[i] + d * y[i];
+ }
}
inline void Vector_Add( real * const dest, const real c, const real * const v, const unsigned int k )
{
- unsigned int i;
+ unsigned int i;
- for( i=0; i<k; ++i )
- {
- dest[i] += c * v[i];
- }
+ for ( i = 0; i < k; ++i )
+ {
+ dest[i] += c * v[i];
+ }
}
inline void Vector_Add2( real * const dest, const real * const v, const unsigned int k )
{
- unsigned int i;
+ unsigned int i;
- for( i=0; i<k; ++i )
- {
- dest[i] += v[i];
- }
+ for ( i = 0; i < k; ++i )
+ {
+ dest[i] += v[i];
+ }
}
void Vector_Print( FILE * const fout, const char * const vname, const real * const v,
- const unsigned int k )
+ const unsigned int k )
{
- unsigned int i;
+ unsigned int i;
- fprintf( fout, "%s:\n", vname );
- for( i = 0; i < k; ++i )
- {
- fprintf( fout, "%24.15e\n", v[i] );
- }
- fprintf( fout, "\n" );
+ fprintf( fout, "%s:\n", vname );
+ for ( i = 0; i < k; ++i )
+ {
+ fprintf( fout, "%24.15e\n", v[i] );
+ }
+ fprintf( fout, "\n" );
}
inline real Dot( const real * const v1, const real * const v2, const unsigned int k )
{
- real ret = ZERO;
- unsigned int i;
+ real ret = ZERO;
+ unsigned int i;
- for( i=0; i<k; ++i )
- {
- ret += v1[i] * v2[i];
- }
+ for ( i = 0; i < k; ++i )
+ {
+ ret += v1[i] * v2[i];
+ }
- return ret;
+ return ret;
}
inline real Norm( const real * const v1, const unsigned int k )
{
- real ret = ZERO;
- unsigned int i;
+ real ret = ZERO;
+ unsigned int i;
- for( i=0; i<k; ++i )
- {
- ret += SQR( v1[i] );
- }
+ for ( i = 0; i < k; ++i )
+ {
+ ret += SQR( v1[i] );
+ }
- return SQRT( ret );
+ return SQRT( ret );
}
inline void rvec_Copy( rvec dest, const rvec src )
{
- dest[0] = src[0], dest[1] = src[1], dest[2] = src[2];
+ dest[0] = src[0], dest[1] = src[1], dest[2] = src[2];
}
inline void rvec_Scale( rvec ret, const real c, const rvec v )
{
- ret[0] = c * v[0], ret[1] = c * v[1], ret[2] = c * v[2];
+ ret[0] = c * v[0], ret[1] = c * v[1], ret[2] = c * v[2];
}
inline void rvec_Add( rvec ret, const rvec v )
{
- ret[0] += v[0], ret[1] += v[1], ret[2] += v[2];
+ ret[0] += v[0], ret[1] += v[1], ret[2] += v[2];
}
inline void rvec_ScaledAdd( rvec ret, const real c, const rvec v )
{
- ret[0] += c * v[0], ret[1] += c * v[1], ret[2] += c * v[2];
+ ret[0] += c * v[0], ret[1] += c * v[1], ret[2] += c * v[2];
}
inline void rvec_Sum( rvec ret, const rvec v1 , const rvec v2 )
{
- ret[0] = v1[0] + v2[0];
- ret[1] = v1[1] + v2[1];
- ret[2] = v1[2] + v2[2];
+ ret[0] = v1[0] + v2[0];
+ ret[1] = v1[1] + v2[1];
+ ret[2] = v1[2] + v2[2];
}
inline void rvec_ScaledSum( rvec ret, const real c1, const rvec v1,
- const real c2, const rvec v2 )
+ const real c2, const rvec v2 )
{
- ret[0] = c1 * v1[0] + c2 * v2[0];
- ret[1] = c1 * v1[1] + c2 * v2[1];
- ret[2] = c1 * v1[2] + c2 * v2[2];
+ ret[0] = c1 * v1[0] + c2 * v2[0];
+ ret[1] = c1 * v1[1] + c2 * v2[1];
+ ret[2] = c1 * v1[2] + c2 * v2[2];
}
inline real rvec_Dot( const rvec v1, const rvec v2 )
{
- return v1[0]*v2[0] + v1[1]*v2[1] + v1[2]*v2[2];
+ return v1[0] * v2[0] + v1[1] * v2[1] + v1[2] * v2[2];
}
inline real rvec_ScaledDot( const real c1, const rvec v1,
- const real c2, const rvec v2 )
+ const real c2, const rvec v2 )
{
- return (c1*c2) * (v1[0]*v2[0] + v1[1]*v2[1] + v1[2]*v2[2]);
+ return (c1 * c2) * (v1[0] * v2[0] + v1[1] * v2[1] + v1[2] * v2[2]);
}
inline void rvec_Multiply( rvec r, const rvec v1, const rvec v2 )
{
- r[0] = v1[0] * v2[0];
- r[1] = v1[1] * v2[1];
- r[2] = v1[2] * v2[2];
+ r[0] = v1[0] * v2[0];
+ r[1] = v1[1] * v2[1];
+ r[2] = v1[2] * v2[2];
}
inline void rvec_iMultiply( rvec r, const ivec v1, const rvec v2 )
{
- r[0] = v1[0] * v2[0];
- r[1] = v1[1] * v2[1];
- r[2] = v1[2] * v2[2];
+ r[0] = v1[0] * v2[0];
+ r[1] = v1[1] * v2[1];
+ r[2] = v1[2] * v2[2];
}
inline void rvec_Divide( rvec r, const rvec v1, const rvec v2 )
{
- r[0] = v1[0] / v2[0];
- r[1] = v1[1] / v2[1];
- r[2] = v1[2] / v2[2];
+ r[0] = v1[0] / v2[0];
+ r[1] = v1[1] / v2[1];
+ r[2] = v1[2] / v2[2];
}
inline void rvec_iDivide( rvec r, const rvec v1, const ivec v2 )
{
- r[0] = v1[0] / v2[0];
- r[1] = v1[1] / v2[1];
- r[2] = v1[2] / v2[2];
+ r[0] = v1[0] / v2[0];
+ r[1] = v1[1] / v2[1];
+ r[2] = v1[2] / v2[2];
}
inline void rvec_Invert( rvec r, const rvec v )
{
- r[0] = 1. / v[0];
- r[1] = 1. / v[1];
- r[2] = 1. / v[2];
+ r[0] = 1. / v[0];
+ r[1] = 1. / v[1];
+ r[2] = 1. / v[2];
}
inline void rvec_Cross( rvec ret, const rvec v1, const rvec v2 )
{
- ret[0] = v1[1] * v2[2] - v1[2] * v2[1];
- ret[1] = v1[2] * v2[0] - v1[0] * v2[2];
- ret[2] = v1[0] * v2[1] - v1[1] * v2[0];
+ ret[0] = v1[1] * v2[2] - v1[2] * v2[1];
+ ret[1] = v1[2] * v2[0] - v1[0] * v2[2];
+ ret[2] = v1[0] * v2[1] - v1[1] * v2[0];
}
inline void rvec_OuterProduct( rtensor r, const rvec v1, const rvec v2 )
{
- unsigned int i, j;
+ unsigned int i, j;
- for( i = 0; i < 3; ++i )
- {
- for( j = 0; j < 3; ++j )
+ for ( i = 0; i < 3; ++i )
{
- r[i][j] = v1[i] * v2[j];
+ for ( j = 0; j < 3; ++j )
+ {
+ r[i][j] = v1[i] * v2[j];
+ }
}
- }
}
inline real rvec_Norm_Sqr( const rvec v )
{
- return SQR(v[0]) + SQR(v[1]) + SQR(v[2]);
+ return SQR(v[0]) + SQR(v[1]) + SQR(v[2]);
}
inline real rvec_Norm( const rvec v )
{
- return SQRT( SQR(v[0]) + SQR(v[1]) + SQR(v[2]) );
+ return SQRT( SQR(v[0]) + SQR(v[1]) + SQR(v[2]) );
}
inline int rvec_isZero( const rvec v )
{
- if( fabs(v[0]) > ALMOST_ZERO ||
- fabs(v[1]) > ALMOST_ZERO ||
- fabs(v[2]) > ALMOST_ZERO )
- {
- return 0;
- }
- return 1;
+ if ( fabs(v[0]) > ALMOST_ZERO ||
+ fabs(v[1]) > ALMOST_ZERO ||
+ fabs(v[2]) > ALMOST_ZERO )
+ {
+ return 0;
+ }
+ return 1;
}
inline void rvec_MakeZero( rvec v )
{
- v[0] = v[1] = v[2] = ZERO;
+ v[0] = v[1] = v[2] = ZERO;
}
inline void rvec_Random( rvec v )
{
- v[0] = Random(2.0)-1.0;
- v[1] = Random(2.0)-1.0;
- v[2] = Random(2.0)-1.0;
+ v[0] = Random(2.0) - 1.0;
+ v[1] = Random(2.0) - 1.0;
+ v[2] = Random(2.0) - 1.0;
}
inline void rtensor_Multiply( rtensor ret, rtensor m1, rtensor m2 )
{
- unsigned int i, j, k;
- rtensor temp;
+ unsigned int i, j, k;
+ rtensor temp;
- // check if the result matrix is the same as one of m1, m2.
- // if so, we cannot modify the contents of m1 or m2, so
- // we have to use a temp matrix.
- if( ret == m1 || ret == m2 )
+ // check if the result matrix is the same as one of m1, m2.
+ // if so, we cannot modify the contents of m1 or m2, so
+ // we have to use a temp matrix.
+ if ( ret == m1 || ret == m2 )
{
- for( i = 0; i < 3; ++i )
- for( j = 0; j < 3; ++j )
- {
- temp[i][j] = 0;
- for( k = 0; k < 3; ++k )
- temp[i][j] += m1[i][k] * m2[k][j];
- }
-
- for( i = 0; i < 3; ++i )
- for( j = 0; j < 3; ++j )
- ret[i][j] = temp[i][j];
+ for ( i = 0; i < 3; ++i )
+ for ( j = 0; j < 3; ++j )
+ {
+ temp[i][j] = 0;
+ for ( k = 0; k < 3; ++k )
+ temp[i][j] += m1[i][k] * m2[k][j];
+ }
+
+ for ( i = 0; i < 3; ++i )
+ for ( j = 0; j < 3; ++j )
+ ret[i][j] = temp[i][j];
}
- else
+ else
{
- for( i = 0; i < 3; ++i )
- for( j = 0; j < 3; ++j )
- {
- ret[i][j] = 0;
- for( k = 0; k < 3; ++k )
- ret[i][j] += m1[i][k] * m2[k][j];
- }
+ for ( i = 0; i < 3; ++i )
+ for ( j = 0; j < 3; ++j )
+ {
+ ret[i][j] = 0;
+ for ( k = 0; k < 3; ++k )
+ ret[i][j] += m1[i][k] * m2[k][j];
+ }
}
}
inline void rtensor_MatVec( rvec ret, rtensor m, const rvec v )
{
- unsigned int i;
- rvec temp;
+ unsigned int i;
+ rvec temp;
- // if ret is the same vector as v, we cannot modify the
- // contents of v until all computation is finished.
- if( ret == v )
- {
- for( i = 0; i < 3; ++i )
+ // if ret is the same vector as v, we cannot modify the
+ // contents of v until all computation is finished.
+ if ( ret == v )
{
- temp[i] = m[i][0] * v[0] + m[i][1] * v[1] + m[i][2] * v[2];
+ for ( i = 0; i < 3; ++i )
+ {
+ temp[i] = m[i][0] * v[0] + m[i][1] * v[1] + m[i][2] * v[2];
+ }
+
+ for ( i = 0; i < 3; ++i )
+ {
+ ret[i] = temp[i];
+ }
}
-
- for( i = 0; i < 3; ++i )
+ else
{
- ret[i] = temp[i];
+ for ( i = 0; i < 3; ++i )
+ {
+ ret[i] = m[i][0] * v[0] + m[i][1] * v[1] + m[i][2] * v[2];
+ }
}
- }
- else
- {
- for( i = 0; i < 3; ++i )
- {
- ret[i] = m[i][0] * v[0] + m[i][1] * v[1] + m[i][2] * v[2];
- }
- }
}
inline void rtensor_Scale( rtensor ret, const real c, rtensor m )
{
- unsigned int i, j;
+ unsigned int i, j;
- for( i = 0; i < 3; ++i )
- {
- for( j = 0; j < 3; ++j )
+ for ( i = 0; i < 3; ++i )
{
- ret[i][j] = c * m[i][j];
+ for ( j = 0; j < 3; ++j )
+ {
+ ret[i][j] = c * m[i][j];
+ }
}
- }
}
inline void rtensor_Add( rtensor ret, rtensor t )
{
- int i, j;
+ int i, j;
- for( i = 0; i < 3; ++i )
- {
- for( j = 0; j < 3; ++j )
+ for ( i = 0; i < 3; ++i )
{
- ret[i][j] += t[i][j];
+ for ( j = 0; j < 3; ++j )
+ {
+ ret[i][j] += t[i][j];
+ }
}
- }
}
inline void rtensor_ScaledAdd( rtensor ret, const real c, rtensor t )
{
- unsigned int i, j;
+ unsigned int i, j;
- for( i = 0; i < 3; ++i )
- {
- for( j = 0; j < 3; ++j )
+ for ( i = 0; i < 3; ++i )
{
- ret[i][j] += c * t[i][j];
+ for ( j = 0; j < 3; ++j )
+ {
+ ret[i][j] += c * t[i][j];
+ }
}
- }
}
inline void rtensor_Sum( rtensor ret, rtensor t1, rtensor t2 )
{
- unsigned int i, j;
+ unsigned int i, j;
- for( i = 0; i < 3; ++i )
- {
- for( j = 0; j < 3; ++j )
+ for ( i = 0; i < 3; ++i )
{
- ret[i][j] = t1[i][j] + t2[i][j];
+ for ( j = 0; j < 3; ++j )
+ {
+ ret[i][j] = t1[i][j] + t2[i][j];
+ }
}
- }
}
-inline void rtensor_ScaledSum( rtensor ret, const real c1, rtensor t1,
- const real c2, rtensor t2 )
+inline void rtensor_ScaledSum( rtensor ret, const real c1, rtensor t1,
+ const real c2, rtensor t2 )
{
- unsigned int i, j;
+ unsigned int i, j;
- for( i = 0; i < 3; ++i )
- {
- for( j = 0; j < 3; ++j )
+ for ( i = 0; i < 3; ++i )
{
- ret[i][j] = c1 * t1[i][j] + c2 * t2[i][j];
+ for ( j = 0; j < 3; ++j )
+ {
+ ret[i][j] = c1 * t1[i][j] + c2 * t2[i][j];
+ }
}
- }
}
inline void rtensor_Copy( rtensor ret, rtensor t )
{
- unsigned int i, j;
+ unsigned int i, j;
- for( i = 0; i < 3; ++i )
- {
- for( j = 0; j < 3; ++j )
+ for ( i = 0; i < 3; ++i )
{
- ret[i][j] = t[i][j];
+ for ( j = 0; j < 3; ++j )
+ {
+ ret[i][j] = t[i][j];
+ }
}
- }
}
inline void rtensor_Identity( rtensor t )
{
- t[0][0] = t[1][1] = t[2][2] = 1;
- t[0][1] = t[0][2] = t[1][0] = t[1][2] = t[2][0] = t[2][1] = ZERO;
+ t[0][0] = t[1][1] = t[2][2] = 1;
+ t[0][1] = t[0][2] = t[1][0] = t[1][2] = t[2][0] = t[2][1] = ZERO;
}
inline void rtensor_MakeZero( rtensor t )
{
- t[0][0] = t[0][1] = t[0][2] = ZERO;
- t[1][0] = t[1][1] = t[1][2] = ZERO;
- t[2][0] = t[2][1] = t[2][2] = ZERO;
+ t[0][0] = t[0][1] = t[0][2] = ZERO;
+ t[1][0] = t[1][1] = t[1][2] = ZERO;
+ t[2][0] = t[2][1] = t[2][2] = ZERO;
}
inline void rtensor_Transpose( rtensor ret, rtensor t )
{
- ret[0][0] = t[0][0], ret[1][1] = t[1][1], ret[2][2] = t[2][2];
- ret[0][1] = t[1][0], ret[0][2] = t[2][0];
- ret[1][0] = t[0][1], ret[1][2] = t[2][1];
- ret[2][0] = t[0][2], ret[2][1] = t[1][2];
+ ret[0][0] = t[0][0], ret[1][1] = t[1][1], ret[2][2] = t[2][2];
+ ret[0][1] = t[1][0], ret[0][2] = t[2][0];
+ ret[1][0] = t[0][1], ret[1][2] = t[2][1];
+ ret[2][0] = t[0][2], ret[2][1] = t[1][2];
}
inline real rtensor_Det( rtensor t )
{
- return ( t[0][0] * (t[1][1] * t[2][2] - t[1][2] * t[2][1] ) +
- t[0][1] * (t[1][2] * t[2][0] - t[1][0] * t[2][2] ) +
- t[0][2] * (t[1][0] * t[2][1] - t[1][1] * t[2][0] ) );
+ return ( t[0][0] * (t[1][1] * t[2][2] - t[1][2] * t[2][1] ) +
+ t[0][1] * (t[1][2] * t[2][0] - t[1][0] * t[2][2] ) +
+ t[0][2] * (t[1][0] * t[2][1] - t[1][1] * t[2][0] ) );
}
inline real rtensor_Trace( rtensor t )
{
- return (t[0][0] + t[1][1] + t[2][2]);
+ return (t[0][0] + t[1][1] + t[2][2]);
}
void Print_rTensor(FILE * const fp, rtensor t)
{
- unsigned int i, j;
+ unsigned int i, j;
- for (i=0; i < 3; i++)
+ for (i = 0; i < 3; i++)
{
- fprintf(fp,"[");
- for (j=0; j < 3; j++)
- fprintf(fp,"%8.3f,\t",t[i][j]);
- fprintf(fp,"]\n");
+ fprintf(fp, "[");
+ for (j = 0; j < 3; j++)
+ fprintf(fp, "%8.3f,\t", t[i][j]);
+ fprintf(fp, "]\n");
}
}
inline void ivec_MakeZero( ivec v )
{
- v[0] = v[1] = v[2] = 0;
+ v[0] = v[1] = v[2] = 0;
}
inline void ivec_Copy( ivec dest, const ivec src )
{
- dest[0] = src[0], dest[1] = src[1], dest[2] = src[2];
+ dest[0] = src[0], dest[1] = src[1], dest[2] = src[2];
}
inline void ivec_Scale( ivec dest, const real C, const ivec src )
{
- dest[0] = C * src[0];
- dest[1] = C * src[1];
- dest[2] = C * src[2];
+ dest[0] = C * src[0];
+ dest[1] = C * src[1];
+ dest[2] = C * src[2];
}
inline void ivec_rScale( ivec dest, const real C, const rvec src )
{
- dest[0] = (int)(C * src[0]);
- dest[1] = (int)(C * src[1]);
- dest[2] = (int)(C * src[2]);
+ dest[0] = (int)(C * src[0]);
+ dest[1] = (int)(C * src[1]);
+ dest[2] = (int)(C * src[2]);
}
inline int ivec_isZero( const ivec v )
{
- if( v[0]==0 && v[1]==0 && v[2]==0 )
- {
- return 1;
- }
- return 0;
+ if ( v[0] == 0 && v[1] == 0 && v[2] == 0 )
+ {
+ return 1;
+ }
+ return 0;
}
inline int ivec_isEqual( const ivec v1, const ivec v2 )
{
- if( v1[0]==v2[0] && v1[1]==v2[1] && v1[2]==v2[2] )
- {
- return 1;
- }
+ if ( v1[0] == v2[0] && v1[1] == v2[1] && v1[2] == v2[2] )
+ {
+ return 1;
+ }
- return 0;
+ return 0;
}
inline void ivec_Sum( ivec dest, const ivec v1, const ivec v2 )
{
- dest[0] = v1[0] + v2[0];
- dest[1] = v1[1] + v2[1];
- dest[2] = v1[2] + v2[2];
+ dest[0] = v1[0] + v2[0];
+ dest[1] = v1[1] + v2[1];
+ dest[2] = v1[2] + v2[2];
}
diff --git a/puremd_rc_1003/sPuReMD/vector.h b/puremd_rc_1003/sPuReMD/vector.h
index 58b94180ec55fc380e24aa95af1c25de6f5cbbd0..68fd4892357018d645c82caff3bd0d475bd3a7d6 100644
--- a/puremd_rc_1003/sPuReMD/vector.h
+++ b/puremd_rc_1003/sPuReMD/vector.h
@@ -1,20 +1,20 @@
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
-
+
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
-
+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
- published by the Free Software Foundation; either version 2 of
+ published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/