diff --git a/PG-PuReMD/src/control.c b/PG-PuReMD/src/control.c
index a35e4b8733bfd2c355568a3607eb30f84b8c2d7c..eea11eea839a2e6ebc7390e997b29875eee796e0 100644
--- a/PG-PuReMD/src/control.c
+++ b/PG-PuReMD/src/control.c
@@ -111,12 +111,13 @@ char Read_Control_File( char *control_file, control_params* control,
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 ) )
{
- fgets( s, MAX_LINE, fp );
c = Tokenize( s, &tmp );
//fprintf( stderr, "%s\n", s );
@@ -269,7 +270,9 @@ char Read_Control_File( char *control_file, control_params* control,
control->T_init = val;
if ( control->T_init < 0.1 )
+ {
control->T_init = 0.1;
+ }
}
else if ( strcmp(tmp[0], "temp_final") == 0 )
{
@@ -277,7 +280,9 @@ char Read_Control_File( char *control_file, control_params* control,
control->T_final = val;
if ( control->T_final < 0.1 )
+ {
control->T_final = 0.1;
+ }
}
else if ( strcmp(tmp[0], "t_mass") == 0 )
{
@@ -401,7 +406,9 @@ char Read_Control_File( char *control_file, control_params* control,
{
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 )
{
@@ -431,18 +438,31 @@ char Read_Control_File( char *control_file, control_params* control,
else
{
fprintf( stderr, "WARNING: unknown parameter %s\n", tmp[0] );
- MPI_Abort( MPI_COMM_WORLD, 15 );
+ MPI_Abort( MPI_COMM_WORLD, INVALID_INPUT );
}
}
+ if ( ferror( fp ) )
+ {
+ fprintf( stderr, "ERROR: parsing control file failed (I/O error). TERMINATING...\n" );
+ MPI_Abort( MPI_COMM_WORLD, INVALID_INPUT );
+ }
+
/* determine target T */
if ( control->T_mode == 0 )
+ {
control->T = control->T_final;
- else control->T = control->T_init;
+ }
+ else
+ {
+ control->T = control->T_init;
+ }
/* free memory allocations at the top */
for ( i = 0; i < MAX_TOKENS; i++ )
+ {
free( tmp[i] );
+ }
free( tmp );
free( s );
diff --git a/PG-PuReMD/src/cuda_forces.cu b/PG-PuReMD/src/cuda_forces.cu
index 8d9dd4c293f8f2ad55532df7e460fac0c9b96736..ea32d7edbb4579b841f06c58f313a6c8cb7d3210 100644
--- a/PG-PuReMD/src/cuda_forces.cu
+++ b/PG-PuReMD/src/cuda_forces.cu
@@ -902,6 +902,7 @@ int Cuda_Validate_Lists (reax_system *system, storage *workspace, reax_list **li
int max_sp_entries, num_hbonds, num_bonds;
int total_sp_entries;
+ int max_bonds;
blocks = system->n / DEF_BLOCK_SIZE +
((system->n % DEF_BLOCK_SIZE == 0) ? 0 : 1);
@@ -1018,18 +1019,21 @@ int Cuda_Validate_Lists (reax_system *system, storage *workspace, reax_list **li
realloc->num_bonds = num_bonds;
*/
- int max_bonds = 0;
- for (i = 0; i < N; i++) {
- if (end_index[i] - index[i] >= system->max_bonds) {
+ max_bonds = 0;
+ for (i = 0; i < N; i++)
+ {
+ if (end_index[i] - index[i] >= system->max_bonds)
+ {
fprintf( stderr, "step%d-bondchk failed: i=%d start(i)=%d end(i)=%d max_bonds=%d\n",
step, i, index[i], end_index[i], system->max_bonds);
return FAILURE;
}
if (end_index[i] - index[i] >= max_bonds)
+ {
max_bonds = end_index[i] - index[i];
+ }
}
realloc->num_bonds = max_bonds;
-
}
//validate Hbonds list
diff --git a/PG-PuReMD/src/grid.c b/PG-PuReMD/src/grid.c
index 2a423be3b5187b893b6fd99152181dd05da93c11..405636dbc70a4bb70d425b7541aa21875198a0d6 100644
--- a/PG-PuReMD/src/grid.c
+++ b/PG-PuReMD/src/grid.c
@@ -40,15 +40,23 @@ void Mark_GCells( reax_system* system, grid *g, ivec procs, MPI_Comm comm )
/* clear all gcell type info */
for ( x = 0; x < g->ncells[0]; x++ )
+ {
for ( y = 0; y < g->ncells[1]; y++ )
+ {
for ( z = 0; z < g->ncells[2]; z++ )
+ {
//SUDHIR
//g->cells[x][y][z].type = 0;
g->cells[ index_grid_3d (x, y, z, g) ].type = 0;
+ }
+ }
+ }
/* mark native cells */
for ( x = g->native_str[0]; x < g->native_end[0]; x++ )
+ {
for ( y = g->native_str[1]; y < g->native_end[1]; y++ )
+ {
for ( z = g->native_str[2]; z < g->native_end[2]; z++ )
{
//SUDHIR
@@ -58,10 +66,14 @@ void Mark_GCells( reax_system* system, grid *g, ivec procs, MPI_Comm comm )
//ivec_MakeZero( g->cells[ index_grid_3d(x, y, z, g) ].rel_box );
ivec_MakeZero( g->rel_box[ index_grid_3d(x, y, z, g) ]);
}
+ }
+ }
/* loop over neighbors */
for ( r[0] = -1; r[0] <= 1; ++r[0])
+ {
for ( r[1] = -1; r[1] <= 1; ++r[1] )
+ {
for ( r[2] = -1; r[2] <= 1; ++r[2] )
{
/* determine the width of exchange with nbr_pr */
@@ -73,9 +85,18 @@ void Mark_GCells( reax_system* system, grid *g, ivec procs, MPI_Comm comm )
for ( d = 0; d < 3; ++d )
{
/* determine the periodicity of this neighbor */
- if ( nbr_coord[d] < 0 ) prdc[d] = -1;
- else if ( nbr_coord[d] >= procs[d] ) prdc[d] = +1;
- else prdc[d] = 0;
+ if ( nbr_coord[d] < 0 )
+ {
+ prdc[d] = -1;
+ }
+ else if ( nbr_coord[d] >= procs[d] )
+ {
+ prdc[d] = +1;
+ }
+ else
+ {
+ prdc[d] = 0;
+ }
/* determine gcells to be sent & recv'd */
if ( r[d] == -1 )
@@ -102,13 +123,21 @@ void Mark_GCells( reax_system* system, grid *g, ivec procs, MPI_Comm comm )
}
for ( x = str_recv[0]; x < end_recv[0]; ++x )
+ {
for ( y = str_recv[1]; y < end_recv[1]; ++y )
+ {
for ( z = str_recv[2]; z < end_recv[2]; ++z )
+ {
//SUDHIR
//ivec_Copy( g->cells[x][y][z].rel_box, prdc );
//ivec_Copy( g->cells[ index_grid_3d(x, y, z, g) ].rel_box, prdc );
ivec_Copy( g->rel_box[ index_grid_3d(x, y, z, g) ], prdc );
+ }
+ }
+ }
}
+ }
+ }
}
@@ -123,15 +152,21 @@ void Find_Closest_Point( grid *g, ivec c1, ivec c2, rvec closest_point )
d = c2[i] - c1[i];
if ( d > 0 )
+ {
//SUDHIR
//closest_point[i] = g->cells[c2[0]][c2[1]][c2[2]].min[i];
closest_point[i] = g->cells[ index_grid_3d(c2[0], c2[1], c2[2], g) ].min[i];
+ }
else if ( d == 0 )
+ {
closest_point[i] = NEG_INF - 1.;
+ }
else
+ {
//SUDHIR
//closest_point[i] = g->cells[c2[0]][c2[1]][c2[2]].max[i];
closest_point[i] = g->cells[ index_grid_3d(c2[0], c2[1], c2[2], g) ].max[i];
+ }
}
}
@@ -160,7 +195,9 @@ void Find_Neighbor_GridCells( grid *g, control_params *control )
/* pick up a cell in the grid */
for ( ci[0] = 0; ci[0] < g->ncells[0]; ci[0]++ )
+ {
for ( ci[1] = 0; ci[1] < g->ncells[1]; ci[1]++ )
+ {
for ( ci[2] = 0; ci[2] < g->ncells[2]; ci[2]++ )
{
//SUDHIR
@@ -176,9 +213,13 @@ void Find_Neighbor_GridCells( grid *g, control_params *control )
//else gc->cutoff = control->bond_cut;
//gc->cutoff = control->vlist_cut;
if (gc->type == NATIVE)
+ {
g->cutoff [index_grid_3d (ci[0], ci[1], ci[2], g)] = control->vlist_cut;
+ }
else
+ {
g->cutoff [index_grid_3d (ci[0], ci[1], ci[2], g)] = control->bond_cut;
+ }
/////////////////////////////////////////////////////////////////
//TODO
@@ -194,7 +235,9 @@ void Find_Neighbor_GridCells( grid *g, control_params *control )
/* loop over neighboring gcells */
for ( cj[0] = cmin[0]; cj[0] < cmax[0]; ++cj[0] )
+ {
for ( cj[1] = cmin[1]; cj[1] < cmax[1]; ++cj[1] )
+ {
for ( cj[2] = cmin[2]; cj[2] < cmax[2]; ++cj[2] )
{
//fprintf( stderr, "\tgrid2: %d %d %d (%d - %d) - ", cj[0], cj[1], cj[2], top, g->max_nbrs );
@@ -209,9 +252,13 @@ void Find_Neighbor_GridCells( grid *g, control_params *control )
// gc->nbrs_cp[top][2] );
++top;
}
+ }
+ }
//gc->nbrs[top] = NULL;
//fprintf( stderr, "top=%d\n", top );
}
+ }
+ }
}
@@ -229,10 +276,15 @@ void Reorder_GridCells( grid *g )
top = 0;
for ( i = 0; i < nblocks[0]; ++i )
+ {
for ( j = 0; j < nblocks[1]; ++j )
+ {
for ( k = 0; k < nblocks[2]; ++k )
+ {
for ( x = i * dblock[0]; x < MIN((i + 1)*dblock[0], g->ncells[0]); ++x )
+ {
for ( y = j * dblock[1]; y < MIN((j + 1)*dblock[1], g->ncells[1]); ++y )
+ {
for ( z = k * dblock[2]; z < MIN((k + 1)*dblock[2], g->ncells[2]); ++z )
{
g->order[top][0] = x;
@@ -240,6 +292,11 @@ void Reorder_GridCells( grid *g )
g->order[top][2] = z;
++top;
}
+ }
+ }
+ }
+ }
+ }
#if defined(DEBUG)
fprintf( stderr, "reorder_gcells: total_gcells=%d top=%d\n", g->total, top );
@@ -247,8 +304,10 @@ void Reorder_GridCells( grid *g )
fprintf( stderr, "nblocks: %d %d %d\n", nblocks[0], nblocks[1], nblocks[2] );
fprintf( stderr, "reordered gcells:\n" );
for ( i = 0; i < top; ++i )
+ {
fprintf( stderr, "order%d: %d %d %d\n",
i, g->order[i][0], g->order[i][1], g->order[i][2] );
+ }
#endif
}
@@ -264,6 +323,7 @@ void Setup_New_Grid( reax_system* system, control_params* control,
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: setup new grid\n", system->my_rank );
#endif
+
g = &( system->my_grid );
my_box = &( system->my_box );
my_ext_box = &( system->my_ext_box );
@@ -274,7 +334,10 @@ void Setup_New_Grid( reax_system* system, control_params* control,
{
/* estimate the number of native cells */
g->native_cells[d] = (int)(my_box->box_norms[d] / (control->vlist_cut / 2));
- if ( g->native_cells[d] == 0 ) g->native_cells[d] = 1;
+ if ( g->native_cells[d] == 0 )
+ {
+ g->native_cells[d] = 1;
+ }
}
/* cell lengths */
@@ -318,7 +381,9 @@ void Setup_New_Grid( reax_system* system, control_params* control,
/* compute min and max coords for each grid cell */
for ( i = 0; i < g->ncells[0]; i++ )
+ {
for ( j = 0; j < g->ncells[1]; j++ )
+ {
for ( k = 0; k < g->ncells[2]; k++ )
{
/*
@@ -338,6 +403,8 @@ void Setup_New_Grid( reax_system* system, control_params* control,
g->cells[ index_grid_3d(i, j, k, g) ].max[1] = my_ext_box->min[1] + (j + 1) * g->cell_len[1];
g->cells[ index_grid_3d(i, j, k, g) ].max[2] = my_ext_box->min[2] + (k + 1) * g->cell_len[2];
}
+ }
+ }
/* determine the exchange boundaries with nbrs in terms of gcells */
Mark_GCells( system, g, control->procs_by_dim, comm );
@@ -372,7 +439,10 @@ void Update_Grid( reax_system* system, control_params* control, MPI_Comm comm )
{
/* estimate the number of native cells */
native_cells[d] = (int)(my_box->box_norms[d] / (control->vlist_cut / 2));
- if ( native_cells[d] == 0 ) native_cells[d] = 1;
+ if ( native_cells[d] == 0 )
+ {
+ native_cells[d] = 1;
+ }
}
/* cell lengths */
@@ -403,7 +473,9 @@ void Update_Grid( reax_system* system, control_params* control, MPI_Comm comm )
/* compute min and max coords for each grid cell */
for ( i = 0; i < g->ncells[0]; i++ )
+ {
for ( j = 0; j < g->ncells[1]; j++ )
+ {
for ( k = 0; k < g->ncells[2]; k++ )
{
/*
@@ -423,10 +495,14 @@ void Update_Grid( reax_system* system, control_params* control, MPI_Comm comm )
g->cells[ index_grid_3d(i, j, k, g) ].max[1] = my_ext_box->min[1] + (j + 1) * g->cell_len[1];
g->cells[ index_grid_3d(i, j, k, g) ].max[2] = my_ext_box->min[2] + (k + 1) * g->cell_len[2];
}
+ }
+ }
/* pick up a cell in the grid */
for ( ci[0] = 0; ci[0] < g->ncells[0]; ci[0]++ )
+ {
for ( ci[1] = 0; ci[1] < g->ncells[1]; ci[1]++ )
+ {
for ( ci[2] = 0; ci[2] < g->ncells[2]; ci[2]++ )
{
//SUDHIR
@@ -443,12 +519,15 @@ void Update_Grid( reax_system* system, control_params* control, MPI_Comm comm )
++itr;
}
}
+ }
+ }
}
else // the grid has changed!
{
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: whole grid is being updated\n", system->my_rank );
#endif
+
Deallocate_Grid( g );
Setup_New_Grid( system, control, comm );
}
@@ -474,9 +553,11 @@ void Bin_My_Atoms( reax_system *system, reallocate_data *realloc )
#if defined(DEBUG)
fprintf( stderr, "p%d bin_my_atoms: entered\n", system->my_rank );
#endif
+
Reset_Grid( g );
for ( l = 0; l < system->n; l++ )
+ {
// outgoing atoms are marked with orig_id = -1
if ( atoms[l].orig_id >= 0 )
{
@@ -500,10 +581,15 @@ void Bin_My_Atoms( reax_system *system, reallocate_data *realloc )
c[d] = (int)((atoms[l].x[d] - my_ext_box->min[d]) * g->inv_len[d]);
if ( c[d] >= g->native_end[d] )
+ {
c[d] = g->native_end[d] - 1;
+ }
else if ( c[d] < g->native_str[d] )
+ {
c[d] = g->native_str[d];
+ }
}
+
#if defined(DEBUG)
fprintf( stderr, "p%d bin_my_atoms: l:%d - atom%d @ %.5f %.5f %.5f"\
"--> cell: %d %d %d\n",
@@ -511,11 +597,13 @@ void Bin_My_Atoms( reax_system *system, reallocate_data *realloc )
atoms[l].x[0], atoms[l].x[1], atoms[l].x[2],
c[0], c[1], c[2] );
#endif
+
//SUDHIR
//gc = &( g->cells[c[0]][c[1]][c[2]] );
gc = &( g->cells[ index_grid_3d(c[0], c[1], c[2], g) ] );
gc->atoms[ gc->top++ ] = l;
}
+ }
#if defined(DEBUG)
fprintf( stderr, "p%d bin_my_atoms: sorted atoms\n", system->my_rank );
@@ -523,19 +611,26 @@ void Bin_My_Atoms( reax_system *system, reallocate_data *realloc )
max_atoms = 0;
for ( i = g->native_str[0]; i < g->native_end[0]; i++ )
+ {
for ( j = g->native_str[1]; j < g->native_end[1]; j++ )
+ {
for ( k = g->native_str[2]; k < g->native_end[2]; k++ )
{
//SUDHIR
//gc = &(g->cells[i][j][k]);
gc = &(g->cells[ index_grid_3d(i, j, k, g) ]);
if ( max_atoms < gc->top )
+ {
max_atoms = gc->top;
+ }
+
#if defined(DEBUG)
fprintf( stderr, "p%d gc[%d,%d,%d]->top=%d\n",
system->my_rank, i, j, k, gc->top );
#endif
}
+ }
+ }
#if defined(DEBUG)
fprintf( stderr, "p%d max_atoms=%d, g->max_atoms=%d\n",
@@ -560,7 +655,6 @@ void Bin_My_Atoms( reax_system *system, reallocate_data *realloc )
}
-
/* reorder atoms falling into the same gcell together in the atom list */
void Reorder_My_Atoms( reax_system *system, storage *workspace )
{
@@ -620,11 +714,18 @@ void Get_Boundary_GCell( grid *g, rvec base, rvec x, grid_cell **gc,
for ( d = 0; d < 3; ++d )
{
c[d] = (int)((x[d] - base[d]) * g->inv_len[d]);
- if ( c[d] < 0 ) c[d] = 0;
+ if ( c[d] < 0 )
+ {
+ c[d] = 0;
+ }
//else if( c[d] == g->native_str[d] ) --c[d];
//else if( c[d] == g->native_end[d] - 1 ) ++c[d];
- else if ( c[d] >= g->ncells[d] ) c[d] = g->ncells[d] - 1;
+ else if ( c[d] >= g->ncells[d] )
+ {
+ c[d] = g->ncells[d] - 1;
+ }
}
+
#if defined(DEBUG)
fprintf( stderr, "get_bndry_gc: base=[%f %f %f] x=[%f %f %f] c=[%d %d %d]\n",
base[0], base[1], base[2], x[0], x[1], x[2], c[0], c[1], c[2] );
@@ -637,6 +738,7 @@ void Get_Boundary_GCell( grid *g, rvec base, rvec x, grid_cell **gc,
*gc = &( g->cells[ index_grid_3d(c[0], c[1], c[2], g) ] );
rvec_ScaledSum( *cur_min, 1, (*gc)->min, -1, loosen );
rvec_Sum( *cur_max, (*gc)->max, loosen );
+
#if defined(DEBUG)
fprintf( stderr, "get_bndry_gc: gcmin=[%f %f %f] gcmax=[%f %f %f]\n",
(*gc)->min[0], (*gc)->min[1], (*gc)->min[2],
@@ -653,10 +755,14 @@ int is_Within_GCell( rvec x, rvec cur_min, rvec cur_max )
int d;
for ( d = 0; d < 3; ++d )
+ {
if ( x[d] < cur_min[d] || x[d] > cur_max[d] )
- return 0;
+ {
+ return FALSE;
+ }
+ }
- return 1;
+ return TRUE;
}
@@ -674,12 +780,15 @@ void Bin_Boundary_Atoms( reax_system *system )
#if defined(DEBUG)
fprintf( stderr, "p%d bin_boundary_atoms: entered with start: %d, end: %d\n", system->my_rank, system->n, system->N );
#endif
+
g = &(system->my_grid);
atoms = system->my_atoms;
start = system->n;
end = system->N;
if ( start == end )
+ {
return;
+ }
ext_box = &(system->my_ext_box);
memcpy( base, ext_box->min, sizeof(rvec) );
@@ -688,7 +797,7 @@ void Bin_Boundary_Atoms( reax_system *system )
g->str[index_grid_3d (gcell_cood[0], gcell_cood[1], gcell_cood[2], g)] = start;
gc->top = 1;
/* error check */
- if ( !is_Within_GCell( atoms[start].x, ext_box->min, ext_box->max ) )
+ if ( is_Within_GCell( atoms[start].x, ext_box->min, ext_box->max ) == FALSE )
{
fprintf( stderr, "p%d: (start):ghost atom%d [%f %f %f] is out of my box!\n",
system->my_rank, start,
@@ -702,7 +811,7 @@ void Bin_Boundary_Atoms( reax_system *system )
//if(atoms[i].x[0]<ext_box->min[0] || atoms[i].x[0]>ext_box->max[0] ||
// atoms[i].x[1]<ext_box->min[1] || atoms[i].x[1]>ext_box->max[1] ||
// atoms[i].x[2]<ext_box->min[2] || atoms[i].x[2]>ext_box->max[2] ){
- if ( !is_Within_GCell( atoms[i].x, ext_box->min, ext_box->max ) )
+ if ( is_Within_GCell( atoms[i].x, ext_box->min, ext_box->max ) == FALSE )
{
fprintf( stderr, "p%d: (middle )ghost atom%d [%f %f %f] is out of my box!\n",
system->my_rank, i,
@@ -710,8 +819,10 @@ void Bin_Boundary_Atoms( reax_system *system )
//MPI_Abort( MPI_COMM_WORLD, -1 );
}
- if ( is_Within_GCell( atoms[i].x, cur_min, cur_max ) )
+ if ( is_Within_GCell( atoms[i].x, cur_min, cur_max ) == TRUE )
+ {
++gc->top;
+ }
else
{
g->end[index_grid_3d (gcell_cood[0], gcell_cood[1], gcell_cood[2], g)] = i;
diff --git a/PG-PuReMD/src/init_md.c b/PG-PuReMD/src/init_md.c
index 1a8b0dbe7efcc243555ebbba2b67acd9e55ff5ac..8a85ca0359751aec1de1953b9a84688e09ae2ad2 100644
--- a/PG-PuReMD/src/init_md.c
+++ b/PG-PuReMD/src/init_md.c
@@ -897,21 +897,21 @@ int Cuda_Init_Lists( reax_system *system, control_params *control,
int *nbr_indices = (int *) host_scratch;
//num_nbrs = Estimate_NumNeighbors( system, lists );
- Cuda_Estimate_Neighbors (system, nbr_indices);
+ Cuda_Estimate_Neighbors( system, nbr_indices );
num_nbrs = 0;
//for (i = 0; i < 20; i++)
//fprintf (stderr, "atom: %d -- %d \n", i, nbr_indices[i]);
for (i = 0; i < system->N; i++)
{
- num_nbrs += nbr_indices [i];
+ num_nbrs += nbr_indices[i];
}
//fprintf (stderr, "DEVICE Total Neighbors: %d (%d)\n", num_nbrs, (int)(num_nbrs*SAFE_ZONE));
for (i = 0; i < system->N; i++)
{
- nbr_indices[i] = MAX (nbr_indices [i] * SAFER_ZONE, MIN_NBRS);
+ nbr_indices[i] = MAX( nbr_indices[i] * SAFER_ZONE, MIN_NBRS );
}
num_nbrs = 0;
diff --git a/PG-PuReMD/src/neighbors.c b/PG-PuReMD/src/neighbors.c
index ada23dc07963eb820c33fcf21666a7fd130dab4a..989577b57a1f219d1b17fd9a614e2d5c314aa7df 100644
--- a/PG-PuReMD/src/neighbors.c
+++ b/PG-PuReMD/src/neighbors.c
@@ -201,19 +201,21 @@ int Estimate_NumNeighbors( reax_system *system, reax_list **lists )
/* first pick up a cell in the grid */
for ( i = 0; i < g->ncells[0]; i++ )
+ {
for ( j = 0; j < g->ncells[1]; j++ )
+ {
for ( k = 0; k < g->ncells[2]; k++ )
{
//SUDHIR
//gci = &(g->cells[i][j][k]);
- gci = &(g->cells[ index_grid_3d (i, j, k, g) ]);
+ gci = &(g->cells[ index_grid_3d(i, j, k, g) ]);
//cutoff = SQR(gci->cutoff);
- cutoff = SQR(g->cutoff [index_grid_3d (i, j, k, g)]);
+ cutoff = SQR(g->cutoff[ index_grid_3d(i, j, k, g) ]);
//fprintf( stderr, "gridcell %d %d %d\n", i, j, k );
/* pick up an atom from the current cell */
- for ( l = g->str[index_grid_3d (i, j, k, g)]; l < g->end[index_grid_3d (i, j, k, g)]; ++l )
+ for ( l = g->str[ index_grid_3d(i, j, k, g) ]; l < g->end[ index_grid_3d( i, j, k, g) ]; ++l )
{
atom1 = &(system->my_atoms[l]);
@@ -228,18 +230,18 @@ int Estimate_NumNeighbors( reax_system *system, reax_list **lists )
//fprintf( stderr, "\tatom %d: ", l );
//tmp = num_far; tested = 0;
itr = 0;
- while ( (g->nbrs_x[index_grid_nbrs (i, j, k, itr, g)][0]) >= 0)
+ while ( (g->nbrs_x[index_grid_nbrs(i, j, k, itr, g)][0]) >= 0 )
{
- ivec_Copy (nbrs_x, g->nbrs_x[index_grid_nbrs (i, j, k, itr, g)]);
+ ivec_Copy( nbrs_x, g->nbrs_x[index_grid_nbrs(i, j, k, itr, g)] );
- if (g->str[index_grid_3d (i, j, k, g)] <= g->str[index_grid_3d (nbrs_x[0], nbrs_x[1], nbrs_x[2], g)] &&
- (DistSqr_to_Special_Point(g->nbrs_cp[index_grid_nbrs (i, j, k, itr, g)], atom1->x) <= cutoff))
+ if ( g->str[index_grid_3d(i, j, k, g)] <= g->str[index_grid_3d(nbrs_x[0], nbrs_x[1], nbrs_x[2], g)] &&
+ (DistSqr_to_Special_Point(g->nbrs_cp[index_grid_nbrs(i, j, k, itr, g)], atom1->x) <= cutoff) )
//fprintf( stderr, "\t\tgcell2: %d\n", itr );
/* pick up another atom from the neighbor cell */
//for( m = gcj->str; m < gcj->end; ++m )
- for ( m = g->str[index_grid_3d (nbrs_x[0], nbrs_x[1], nbrs_x[2], g)];
- m < g->end[index_grid_3d (nbrs_x[0], nbrs_x[1], nbrs_x[2], g)]; ++m )
+ for ( m = g->str[index_grid_3d(nbrs_x[0], nbrs_x[1], nbrs_x[2], g)];
+ m < g->end[index_grid_3d(nbrs_x[0], nbrs_x[1], nbrs_x[2], g)]; ++m )
{
if ( l < m )
{
@@ -250,15 +252,21 @@ int Estimate_NumNeighbors( reax_system *system, reax_list **lists )
dvec[2] = atom2->x[2] - atom1->x[2];
d = rvec_Norm_Sqr( dvec );
if ( d <= cutoff )
+ {
++num_far;
+ }
}
}
+
++itr;
+
//fprintf( stderr, "itr: %d, tested: %d, num_nbrs: %d\n",
// itr, tested, num_far-tmp );
}
}
}
+ }
+ }
#if defined(DEBUG)
fprintf (stderr, "Total number of host neighbors: %d \n", num_far);
@@ -272,6 +280,7 @@ int Estimate_NumNeighbors( reax_system *system, reax_list **lists )
return MAX( num_far * SAFE_ZONE, MIN_CAP * MIN_NBRS );
}
+
/*
int Estimate_NumNeighbors1( reax_system *system, reax_list **lists )
{
diff --git a/environ/parallel_control b/environ/parallel_control
index d69d3eae3610ae57df68a0a26fafaf4f71bbec2e..195ab1bad87ba813efb2f2a392a6d2ac82052d9b 100644
--- a/environ/parallel_control
+++ b/environ/parallel_control
@@ -3,6 +3,7 @@ ensemble_type 1 ! 0: NVE, 1: Berendsen NVT, 2: N
nsteps 100 ! number of simulation steps
dt 0.25 ! time step in fs
proc_by_dim 1 1 1 ! distribution of processors by dimensions
+gpus_per_node 1 ! GPUs per node
reposition_atoms 1 ! 0: just fit to periodic boundaries, 1: CoM to the center of box, 3: CoM to the origin
tabulate_long_range 0 ! number of sampling points for cubic spline interpolation, 0 no interpolation