From f9dedbf23b555b5bd904b08feee8978c9367b4c2 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnku@cse.msu.edu>
Date: Thu, 16 Feb 2017 11:04:40 -0500
Subject: [PATCH] Complete code refactoring for EEM. Implement EEM charge
matrix construction.
---
sPuReMD/Makefile.am | 4 +-
sPuReMD/src/{QEq.c => charges.c} | 356 ++++++++++++++++++++++---------
sPuReMD/src/{QEq.h => charges.h} | 6 +-
sPuReMD/src/control.c | 6 +
sPuReMD/src/forces.c | 82 ++++++-
sPuReMD/src/init_md.c | 230 ++++++++++++++------
sPuReMD/src/integrate.c | 6 +-
sPuReMD/src/lin_alg.c | 32 +--
sPuReMD/src/mytypes.h | 28 ++-
sPuReMD/src/print_utils.c | 49 +++--
sPuReMD/src/testmd.c | 2 +-
11 files changed, 570 insertions(+), 231 deletions(-)
rename sPuReMD/src/{QEq.c => charges.c} (85%)
rename sPuReMD/src/{QEq.h => charges.h} (88%)
diff --git a/sPuReMD/Makefile.am b/sPuReMD/Makefile.am
index 7c986471..4102573d 100644
--- a/sPuReMD/Makefile.am
+++ b/sPuReMD/Makefile.am
@@ -4,7 +4,7 @@ bin_PROGRAMS = bin/spuremd
bin_spuremd_SOURCES = src/ffield.c src/grid.c src/list.c src/lookup.c src/print_utils.c \
src/reset_utils.c src/restart.c src/random.c src/tool_box.c src/traj.c \
src/vector.c src/allocate.c src/analyze.c src/box.c src/system_props.c src/control.c \
- src/geo_tools.c src/neighbors.c src/lin_alg.c src/QEq.c src/bond_orders.c \
+ src/geo_tools.c src/neighbors.c src/lin_alg.c src/charges.c src/bond_orders.c \
src/single_body_interactions.c src/two_body_interactions.c \
src/three_body_interactions.c src/four_body_interactions.c src/forces.c \
src/integrate.c src/init_md.c src/testmd.c
@@ -12,7 +12,7 @@ bin_spuremd_SOURCES = src/ffield.c src/grid.c src/list.c src/lookup.c src/print_
include_HEADERS = src/mytypes.h src/ffield.h src/grid.h src/list.h src/lookup.h src/print_utils.h \
src/reset_utils.h src/restart.h src/random.h src/tool_box.h src/traj.h \
src/vector.h src/allocate.h src/analyze.h src/box.h src/system_props.h src/control.h \
- src/geo_tools.h src/neighbors.h src/lin_alg.h src/QEq.h src/bond_orders.h \
+ src/geo_tools.h src/neighbors.h src/lin_alg.h src/charges.h src/bond_orders.h \
src/single_body_interactions.h src/two_body_interactions.h \
src/three_body_interactions.h src/four_body_interactions.h src/forces.h \
src/integrate.h src/init_md.h
diff --git a/sPuReMD/src/QEq.c b/sPuReMD/src/charges.c
similarity index 85%
rename from sPuReMD/src/QEq.c
rename to sPuReMD/src/charges.c
index 972886fd..8ac55b47 100644
--- a/sPuReMD/src/QEq.c
+++ b/sPuReMD/src/charges.c
@@ -19,7 +19,7 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#include "QEq.h"
+#include "charges.h"
#include "allocate.h"
#include "list.h"
@@ -145,8 +145,8 @@ static void Sort_Matrix_Rows( sparse_matrix * const A )
}
-static void Calculate_Droptol( const sparse_matrix * const A, real * const droptol,
- const real dtol )
+static void Calculate_Droptol( const sparse_matrix * const A,
+ real * const droptol, const real dtol )
{
int i, j, k;
real val;
@@ -275,7 +275,7 @@ static int Estimate_LU_Fill( const sparse_matrix * const A, const real * const d
#if defined(HAVE_SUPERLU_MT)
static real SuperLU_Factorize( const sparse_matrix * const A,
- sparse_matrix * const L, sparse_matrix * const U )
+ sparse_matrix * const L, sparse_matrix * const U )
{
unsigned int i, pj, count, *Ltop, *Utop, r;
sparse_matrix *A_t;
@@ -581,7 +581,7 @@ static real diag_pre_comp( const reax_system * const system, real * const Hdia_i
#pragma omp parallel for schedule(static) \
default(none) private(i)
- for ( i = 0; i < system->N; ++i )
+ for ( i = 0; i < system->N_cm; ++i )
{
Hdia_inv[i] = 1.0 / system->reaxprm.sbp[system->atoms[i].type].eta;
}
@@ -592,7 +592,7 @@ static real diag_pre_comp( const reax_system * const system, real * const Hdia_i
/* Incomplete Cholesky factorization with dual thresholding */
static real ICHOLT( const sparse_matrix * const A, const real * const droptol,
- sparse_matrix * const L, sparse_matrix * const U )
+ sparse_matrix * const L, sparse_matrix * const U )
{
int *tmp_j;
real *tmp_val;
@@ -738,7 +738,7 @@ static real ICHOLT( const sparse_matrix * const A, const real * const droptol,
* Fine-Grained Parallel Incomplete LU Factorization
* SIAM J. Sci. Comp. */
static real ICHOL_PAR( const sparse_matrix * const A, const unsigned int sweeps,
- sparse_matrix * const U_t, sparse_matrix * const U )
+ sparse_matrix * const U_t, sparse_matrix * const U )
{
unsigned int i, j, k, pj, x = 0, y = 0, ei_x, ei_y;
real *D, *D_inv, sum, start;
@@ -757,7 +757,7 @@ static real ICHOL_PAR( const sparse_matrix * const A, const unsigned int sweeps,
}
#pragma omp parallel for schedule(static) \
- default(none) shared(D_inv, D) private(i)
+ default(none) shared(D_inv, D) private(i)
for ( i = 0; i < A->n; ++i )
{
D_inv[i] = SQRT( A->val[A->start[i + 1] - 1] );
@@ -771,7 +771,7 @@ static real ICHOL_PAR( const sparse_matrix * const A, const unsigned int sweeps,
* transformation DAD, where D = D(1./sqrt(D(A))) */
memcpy( DAD->start, A->start, sizeof(int) * (A->n + 1) );
#pragma omp parallel for schedule(guided) \
- default(none) shared(DAD, D_inv, D) private(i, pj)
+ default(none) shared(DAD, D_inv, D) private(i, pj)
for ( i = 0; i < A->n; ++i )
{
/* non-diagonals */
@@ -795,7 +795,7 @@ static real ICHOL_PAR( const sparse_matrix * const A, const unsigned int sweeps,
{
/* for each nonzero */
#pragma omp parallel for schedule(static) \
- default(none) shared(DAD, stderr) private(sum, ei_x, ei_y, k) firstprivate(x, y)
+ default(none) shared(DAD, stderr) private(sum, ei_x, ei_y, k) firstprivate(x, y)
for ( j = 0; j < A->start[A->n]; ++j )
{
sum = ZERO;
@@ -868,7 +868,7 @@ static real ICHOL_PAR( const sparse_matrix * const A, const unsigned int sweeps,
* since DAD \approx U^{T}U, so
* D^{-1}DADD^{-1} = A \approx D^{-1}U^{T}UD^{-1} */
#pragma omp parallel for schedule(guided) \
- default(none) shared(D_inv) private(i, pj)
+ default(none) shared(D_inv) private(i, pj)
for ( i = 0; i < A->n; ++i )
{
for ( pj = A->start[i]; pj < A->start[i + 1]; ++pj )
@@ -925,7 +925,7 @@ static real ILU_PAR( const sparse_matrix * const A, const unsigned int sweeps,
}
#pragma omp parallel for schedule(static) \
- default(none) shared(D, D_inv) private(i)
+ default(none) shared(D, D_inv) private(i)
for ( i = 0; i < A->n; ++i )
{
D_inv[i] = SQRT( A->val[A->start[i + 1] - 1] );
@@ -936,7 +936,7 @@ static real ILU_PAR( const sparse_matrix * const A, const unsigned int sweeps,
* transformation DAD, where D = D(1./sqrt(D(A))) */
memcpy( DAD->start, A->start, sizeof(int) * (A->n + 1) );
#pragma omp parallel for schedule(static) \
- default(none) shared(DAD, D) private(i, pj)
+ default(none) shared(DAD, D) private(i, pj)
for ( i = 0; i < A->n; ++i )
{
/* non-diagonals */
@@ -971,7 +971,7 @@ static real ILU_PAR( const sparse_matrix * const A, const unsigned int sweeps,
{
/* for each nonzero in L */
#pragma omp parallel for schedule(static) \
- default(none) shared(DAD) private(j, k, x, y, ei_x, ei_y, sum)
+ default(none) shared(DAD) private(j, k, x, y, ei_x, ei_y, sum)
for ( j = 0; j < DAD->start[DAD->n]; ++j )
{
sum = ZERO;
@@ -1021,7 +1021,7 @@ static real ILU_PAR( const sparse_matrix * const A, const unsigned int sweeps,
}
#pragma omp parallel for schedule(static) \
- default(none) shared(DAD) private(j, k, x, y, ei_x, ei_y, sum)
+ default(none) shared(DAD) private(j, k, x, y, ei_x, ei_y, sum)
for ( j = 0; j < DAD->start[DAD->n]; ++j )
{
sum = ZERO;
@@ -1072,7 +1072,7 @@ static real ILU_PAR( const sparse_matrix * const A, const unsigned int sweeps,
* since DAD \approx LU, then
* D^{-1}DADD^{-1} = A \approx D^{-1}LUD^{-1} */
#pragma omp parallel for schedule(static) \
- default(none) shared(DAD, D_inv) private(i, pj)
+ default(none) shared(DAD, D_inv) private(i, pj)
for ( i = 0; i < DAD->n; ++i )
{
for ( pj = DAD->start[i]; pj < DAD->start[i + 1]; ++pj )
@@ -1110,7 +1110,7 @@ static real ILU_PAR( const sparse_matrix * const A, const unsigned int sweeps,
* sweeps: number of loops over non-zeros for computation
* L / U: factorized triangular matrices (A \approx LU), CSR format */
static real ILUT_PAR( const sparse_matrix * const A, const real * droptol,
- const unsigned int sweeps, sparse_matrix * const L, sparse_matrix * const U )
+ const unsigned int sweeps, sparse_matrix * const L, sparse_matrix * const U )
{
unsigned int i, j, k, pj, x, y, ei_x, ei_y, Ltop, Utop;
real *D, *D_inv, sum, start;
@@ -1134,7 +1134,7 @@ static real ILUT_PAR( const sparse_matrix * const A, const real * droptol,
}
#pragma omp parallel for schedule(static) \
- default(none) shared(D, D_inv) private(i)
+ default(none) shared(D, D_inv) private(i)
for ( i = 0; i < A->n; ++i )
{
D_inv[i] = SQRT( A->val[A->start[i + 1] - 1] );
@@ -1145,7 +1145,7 @@ static real ILUT_PAR( const sparse_matrix * const A, const real * droptol,
* transformation DAD, where D = D(1./sqrt(D(A))) */
memcpy( DAD->start, A->start, sizeof(int) * (A->n + 1) );
#pragma omp parallel for schedule(static) \
- default(none) shared(DAD, D) private(i, pj)
+ default(none) shared(DAD, D) private(i, pj)
for ( i = 0; i < A->n; ++i )
{
/* non-diagonals */
@@ -1171,7 +1171,7 @@ static real ILUT_PAR( const sparse_matrix * const A, const real * droptol,
/* L has unit diagonal, by convention */
#pragma omp parallel for schedule(static) \
- default(none) private(i) shared(L_temp)
+ default(none) private(i) shared(L_temp)
for ( i = 0; i < A->n; ++i )
{
L_temp->val[L_temp->start[i + 1] - 1] = 1.0;
@@ -1231,7 +1231,7 @@ static real ILUT_PAR( const sparse_matrix * const A, const real * droptol,
}
#pragma omp parallel for schedule(static) \
- default(none) shared(DAD, L_temp, U_temp) private(j, k, x, y, ei_x, ei_y, sum)
+ default(none) shared(DAD, L_temp, U_temp) private(j, k, x, y, ei_x, ei_y, sum)
for ( j = 0; j < DAD->start[DAD->n]; ++j )
{
sum = ZERO;
@@ -1352,13 +1352,106 @@ static real ILUT_PAR( const sparse_matrix * const A, const real * droptol,
}
+static void Extrapolate_Charges_QEq( const reax_system * const system,
+ const control_params * const control,
+ simulation_data * const data, static_storage * const workspace )
+{
+ int i;
+ real s_tmp, t_tmp;
+
+ /* extrapolation for s & t */
+ //TODO: good candidate for vectorization, avoid moving data with head pointer and circular buffer
+ #pragma omp parallel for schedule(static) \
+ default(none) private(i, s_tmp, t_tmp)
+ for ( i = 0; i < system->N_cm; ++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;
+ }
+}
+
+
+static void Extrapolate_Charges_EEM( const reax_system * const system,
+ const control_params * const control,
+ simulation_data * const data, static_storage * const workspace )
+{
+ int i;
+ real s_tmp;
+
+ /* extrapolation for s */
+ //TODO: good candidate for vectorization, avoid moving data with head pointer and circular buffer
+ #pragma omp parallel for schedule(static) \
+ default(none) private(i, s_tmp)
+ for ( i = 0; i < system->N_cm; ++i )
+ {
+ // no extrapolation
+ //s_tmp = workspace->s[0][i];
+
+ // linear
+ //s_tmp = 2 * workspace->s[0][i] - workspace->s[1][i];
+
+ // quadratic
+ //s_tmp = workspace->s[2][i] + 3 * (workspace->s[0][i]-workspace->s[1][i]);
+
+ // cubic
+ s_tmp = 4 * (workspace->s[0][i] + workspace->s[2][i]) -
+ (6 * workspace->s[1][i] + workspace->s[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];
+
+ 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;
+ }
+}
+
+
/* Setup routine which performs the following:
* 1) init storage for QEq matrices and other dependent routines
* 2) compute preconditioner (if sim. step matches refactor step)
* 3) extrapolate ficticious charges s and t
*/
-static void Init_MatVec( const reax_system * const system, const control_params * const control,
- simulation_data * const data, static_storage * const workspace, const list * const far_nbrs )
+static void Init_Charges( const reax_system * const system,
+ const control_params * const control,
+ simulation_data * const data, static_storage * const workspace,
+ const list * const far_nbrs )
{
int i, fillin;
real s_tmp, t_tmp, time;
@@ -1379,9 +1472,12 @@ static void Init_MatVec( const reax_system * const system, const control_params
#endif
if (control->cm_solver_pre_comp_refactor > 0 &&
- ((data->step - data->prev_steps) % control->cm_solver_pre_comp_refactor == 0 || workspace->L == NULL))
+ ((data->step - data->prev_steps) % control->cm_solver_pre_comp_refactor == 0
+ || workspace->L == NULL))
{
- //Print_Linear_System( system, control, workspace, data->step );
+// Print_Linear_System( system, control, workspace, data->step );
+ Print_Sparse_Matrix2( workspace->H, "H_0.out" );
+ exit(0);
time = Get_Time( );
if ( control->cm_solver_pre_comp_type != DIAG_PC )
@@ -1406,7 +1502,7 @@ static void Init_MatVec( const reax_system * const system, const control_params
Sort_Matrix_Rows( Hptr );
}
}
- data->timing.QEq_sort_mat_rows += Get_Timing_Info( time );
+ data->timing.cm_sort_mat_rows += Get_Timing_Info( time );
#if defined(DEBUG)
fprintf( stderr, "H matrix sorted\n" );
@@ -1417,13 +1513,14 @@ static void Init_MatVec( const reax_system * const system, const control_params
case DIAG_PC:
if ( workspace->Hdia_inv == NULL )
{
- if ( ( workspace->Hdia_inv = (real *) calloc( system->N, sizeof( real ) ) ) == NULL )
+ if ( ( workspace->Hdia_inv = (real *) calloc( system->N_cm, sizeof( real ) ) ) == NULL )
{
fprintf( stderr, "not enough memory for preconditioning matrices. terminating.\n" );
exit( INSUFFICIENT_MEMORY );
}
}
- data->timing.pre_comp += diag_pre_comp( system, workspace->Hdia_inv );
+
+ data->timing.cm_solver_pre_comp += diag_pre_comp( system, workspace->Hdia_inv );
break;
case ICHOLT_PC:
@@ -1450,7 +1547,8 @@ static void Init_MatVec( const reax_system * const system, const control_params
#endif
}
- data->timing.pre_comp += ICHOLT( Hptr, workspace->droptol, workspace->L, workspace->U );
+ data->timing.cm_solver_pre_comp +=
+ ICHOLT( Hptr, workspace->droptol, workspace->L, workspace->U );
break;
case ILU_PAR_PC:
@@ -1465,11 +1563,13 @@ static void Init_MatVec( const reax_system * const system, const control_params
}
}
- data->timing.pre_comp += ILU_PAR( Hptr, control->cm_solver_pre_comp_sweeps, workspace->L, workspace->U );
+ data->timing.cm_solver_pre_comp +=
+ ILU_PAR( Hptr, control->cm_solver_pre_comp_sweeps, workspace->L, workspace->U );
break;
case ILUT_PAR_PC:
Calculate_Droptol( Hptr, workspace->droptol, control->cm_solver_pre_comp_droptol );
+
#if defined(DEBUG_FOCUS)
fprintf( stderr, "drop tolerances calculated\n" );
#endif
@@ -1485,8 +1585,9 @@ static void Init_MatVec( const reax_system * const system, const control_params
}
}
- data->timing.pre_comp += ILUT_PAR( Hptr, workspace->droptol, control->cm_solver_pre_comp_sweeps,
- workspace->L, workspace->U );
+ data->timing.cm_solver_pre_comp +=
+ ILUT_PAR( Hptr, workspace->droptol, control->cm_solver_pre_comp_sweeps,
+ workspace->L, workspace->U );
break;
case ILU_SUPERLU_MT_PC:
@@ -1502,7 +1603,7 @@ static void Init_MatVec( const reax_system * const system, const control_params
}
#if defined(HAVE_SUPERLU_MT)
- data->timing.pre_comp += SuperLU_Factorize( Hptr, workspace->L, workspace->U );
+ data->timing.cm_solver_pre_comp += SuperLU_Factorize( Hptr, workspace->L, workspace->U );
#else
fprintf( stderr, "SuperLU MT support disabled. Re-compile before enabling. Terminating...\n" );
exit( INVALID_INPUT );
@@ -1531,68 +1632,26 @@ static void Init_MatVec( const reax_system * const system, const control_params
//Print_Sparse_Matrix( U );
#endif
}
-
- /* extrapolation for s & t */
- //TODO: good candidate for vectorization, avoid moving data with head pointer and circular buffer
- #pragma omp parallel for schedule(static) \
- default(none) private(i, s_tmp, t_tmp)
- 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;
- }
}
-/* Combine ficticious charges s and t to get atomic charge q
+/* Combine ficticious charges s and t to get atomic charge q for QEq method
*/
-static void Calculate_Charges( const reax_system * const system, static_storage * const workspace )
+static void Calculate_Charges_QEq( const reax_system * const system,
+ static_storage * const workspace )
{
int i;
real u, s_sum, t_sum;
s_sum = t_sum = 0.;
- for ( i = 0; i < system->N; ++i )
+ for ( i = 0; i < system->N_cm; ++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 )
+ for ( i = 0; i < system->N_cm; ++i )
{
system->atoms[i].q = workspace->s[0][i] - u * workspace->t[0][i];
}
@@ -1606,13 +1665,15 @@ static void Calculate_Charges( const reax_system * const system, static_storage
* 2) perform 2 linear solves
* 3) compute atomic charges based on output of 2)
*/
-void QEq( reax_system * const system, control_params * const control, simulation_data * const data,
- static_storage * const workspace, const list * const far_nbrs,
- const output_controls * const out_control )
+static void QEq( reax_system * const system, control_params * const control,
+ simulation_data * const data, static_storage * const workspace,
+ const list * const far_nbrs, const output_controls * const out_control )
{
int iters;
- Init_MatVec( system, control, data, workspace, far_nbrs );
+ Init_Charges( system, control, data, workspace, far_nbrs );
+
+ Extrapolate_Charges_QEq( system, control, data, workspace );
// if( data->step == 0 || data->step == 100 )
// {
@@ -1622,17 +1683,21 @@ void QEq( reax_system * const system, control_params * const control, simulation
switch ( control->cm_solver_type )
{
case GMRES_S:
- iters = GMRES( workspace, control, data, workspace->H, workspace->b_s, control->cm_solver_q_err,
- workspace->s[0], out_control->log,
- ((data->step - data->prev_steps) % control->cm_solver_pre_comp_refactor == 0) ? TRUE : FALSE );
- iters += GMRES( workspace, control, data, workspace->H, workspace->b_t, control->cm_solver_q_err,
- workspace->t[0], out_control->log, FALSE );
+ iters = GMRES( workspace, control, data, workspace->H,
+ workspace->b_s, control->cm_solver_q_err, workspace->s[0],
+ out_control->log,
+ ((data->step - data->prev_steps) % control->cm_solver_pre_comp_refactor == 0) ? TRUE : FALSE );
+ iters += GMRES( workspace, control, data, workspace->H,
+ workspace->b_t, control->cm_solver_q_err, workspace->t[0],
+ out_control->log, FALSE );
break;
case GMRES_H_S:
- iters = GMRES_HouseHolder( workspace, control, data, workspace->H, workspace->b_s, control->cm_solver_q_err,
- workspace->s[0], out_control->log, (data->step - data->prev_steps) % control->cm_solver_pre_comp_refactor == 0 );
- iters += GMRES_HouseHolder( workspace, control, data, workspace->H, workspace->b_t, control->cm_solver_q_err,
- workspace->t[0], out_control->log, 0 );
+ iters = GMRES_HouseHolder( workspace, control, data, workspace->H,
+ workspace->b_s, control->cm_solver_q_err, workspace->s[0],
+ out_control->log, (data->step - data->prev_steps) % control->cm_solver_pre_comp_refactor == 0 );
+ iters += GMRES_HouseHolder( workspace, control, data, workspace->H,
+ workspace->b_t, control->cm_solver_q_err, workspace->t[0],
+ out_control->log, 0 );
break;
case CG_S:
iters = CG( workspace, workspace->H, workspace->b_s, control->cm_solver_q_err,
@@ -1664,13 +1729,13 @@ void QEq( reax_system * const system, control_params * const control, simulation
break;
}
- data->timing.solver_iters += iters;
+ data->timing.cm_solver_iters += iters;
#if defined(DEBUG_FOCUS)
fprintf( stderr, "linsolve-" );
#endif
- Calculate_Charges( system, workspace );
+ Calculate_Charges_QEq( system, workspace );
//fprintf( stderr, "%d %.9f %.9f %.9f %.9f %.9f %.9f\n",
// data->step,
@@ -1680,3 +1745,104 @@ void QEq( reax_system * const system, control_params * const control, simulation
// if( data->step == control->nsteps )
//Print_Charges( system, control, workspace, data->step );
}
+
+
+/* Get atomic charge q for EEM method
+ */
+static void Calculate_Charges_EEM( const reax_system * const system,
+ static_storage * const workspace )
+{
+ int i;
+// real s_sum;
+
+// s_sum = 0.0;
+// for ( i = 0; i < system->N_cm; ++i )
+// {
+// s_sum += workspace->s[0][i];
+// }
+
+ for ( i = 0; i < system->N_cm; ++i )
+ {
+ system->atoms[i].q = workspace->s[0][i];
+ }
+}
+
+
+/* Main driver method for EEM kernel
+ *
+ * Rough outline:
+ * 1) init / setup routines
+ * 2) perform 1 linear solve
+ */
+static void EEM( reax_system * const system, control_params * const control,
+ simulation_data * const data, static_storage * const workspace,
+ const list * const far_nbrs, const output_controls * const out_control )
+{
+ int iters;
+
+ Init_Charges( system, control, data, workspace, far_nbrs );
+
+ Extrapolate_Charges_EEM( system, control, data, workspace );
+
+ switch ( control->cm_solver_type )
+ {
+ case GMRES_S:
+ iters = GMRES( workspace, control, data, workspace->H,
+ workspace->b_s, control->cm_solver_q_err, workspace->s[0],
+ out_control->log,
+ ((data->step - data->prev_steps) % control->cm_solver_pre_comp_refactor == 0) ? TRUE : FALSE );
+ break;
+ case GMRES_H_S:
+ iters = GMRES_HouseHolder( workspace, control, data,workspace->H,
+ workspace->b_s, control->cm_solver_q_err, workspace->s[0],
+ out_control->log,
+ (data->step - data->prev_steps) % control->cm_solver_pre_comp_refactor == 0 );
+ break;
+ case CG_S:
+ iters = CG( workspace, workspace->H, workspace->b_s, control->cm_solver_q_err,
+ workspace->s[0], out_control->log ) + 1;
+ break;
+ case SDM_S:
+ iters = SDM( workspace, workspace->H, workspace->b_s, control->cm_solver_q_err,
+ workspace->s[0], out_control->log ) + 1;
+ break;
+ default:
+ fprintf( stderr, "Unrecognized QEq solver selection. Terminating...\n" );
+ exit( INVALID_INPUT );
+ break;
+ }
+
+ data->timing.cm_solver_iters += iters;
+
+#if defined(DEBUG_FOCUS)
+ fprintf( stderr, "linsolve-" );
+#endif
+
+ Calculate_Charges_EEM( system, workspace );
+
+ // if( data->step == control->nsteps )
+ //Print_Charges( system, control, workspace, data->step );
+}
+
+
+void Compute_Charges( reax_system * const system, control_params * const control,
+ simulation_data * const data, static_storage * const workspace,
+ const list * const far_nbrs, const output_controls * const out_control )
+{
+ switch ( control->charge_method )
+ {
+ case QEQ_CM:
+ QEq( system, control, data, workspace, far_nbrs, out_control );
+ break;
+ case EEM_CM:
+ EEM( system, control, data, workspace, far_nbrs, out_control );
+ break;
+ case ACKS2_CM:
+ //TODO
+ break;
+ default:
+ fprintf( stderr, "Invalid charge method. Terminating...\n" );
+ exit( INVALID_INPUT );
+ break;
+ }
+}
diff --git a/sPuReMD/src/QEq.h b/sPuReMD/src/charges.h
similarity index 88%
rename from sPuReMD/src/QEq.h
rename to sPuReMD/src/charges.h
index c7186aae..50f563c3 100644
--- a/sPuReMD/src/QEq.h
+++ b/sPuReMD/src/charges.h
@@ -19,12 +19,12 @@
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
-#ifndef __QEq_H_
-#define __QEq_H_
+#ifndef __CHARGES_H_
+#define __CHARGES_H_
#include "mytypes.h"
-void QEq( reax_system* const, control_params* const, simulation_data* const,
+void Compute_Charges( reax_system* const, control_params* const, simulation_data* const,
static_storage* const, const list* const,
const output_controls* const );
diff --git a/sPuReMD/src/control.c b/sPuReMD/src/control.c
index a10ee4f2..e9470449 100644
--- a/sPuReMD/src/control.c
+++ b/sPuReMD/src/control.c
@@ -71,6 +71,7 @@ char Read_Control_File( FILE* fp, reax_system *system, control_params* control,
control->tabulate = 0;
control->charge_method = QEQ_CM;
+ control->cm_q_net = 0.0;
control->cm_solver_type = GMRES_S;
control->cm_solver_q_err = 0.000001;
control->cm_domain_sparsify_enabled = FALSE;
@@ -246,6 +247,11 @@ char Read_Control_File( FILE* fp, reax_system *system, control_params* control,
ival = atoi( tmp[1] );
control->charge_method = ival;
}
+ else if ( strcmp(tmp[0], "cm_q_net") == 0 )
+ {
+ val = atof( tmp[1] );
+ control->cm_q_net = val;
+ }
else if ( strcmp(tmp[0], "cm_solver_type") == 0 )
{
ival = atoi( tmp[1] );
diff --git a/sPuReMD/src/forces.c b/sPuReMD/src/forces.c
index 8c21776a..91e3430f 100644
--- a/sPuReMD/src/forces.c
+++ b/sPuReMD/src/forces.c
@@ -29,7 +29,7 @@
#include "list.h"
#include "print_utils.h"
#include "system_props.h"
-#include "QEq.h"
+#include "charges.h"
#include "vector.h"
@@ -132,9 +132,10 @@ void Compute_NonBonded_Forces( reax_system *system, control_params *control,
#endif
t_start = Get_Time( );
- QEq( system, control, data, workspace, lists[FAR_NBRS], out_control );
+ Compute_Charges( system, control, data, workspace, lists[FAR_NBRS], out_control );
t_elapsed = Get_Timing_Info( t_start );
- data->timing.QEq += t_elapsed;
+ data->timing.cm += t_elapsed;
+
#if defined(DEBUG_FOCUS)
fprintf( stderr, "qeq - " );
#endif
@@ -352,7 +353,7 @@ static inline real Init_Charge_Matrix_Entry( reax_system *system,
control_params *control, int i, int j,
real r_ij, MATRIX_ENTRY_POSITION pos )
{
- real Tap, dr3gamij_1, dr3gamij_3, ret = 0.0;
+ real Tap, gamij, dr3gamij_1, dr3gamij_3, ret = 0.0;
switch ( control->charge_method )
{
@@ -368,15 +369,18 @@ static inline real Init_Charge_Matrix_Entry( reax_system *system,
Tap = Tap * r_ij + control->Tap1;
Tap = Tap * r_ij + control->Tap0;
+ /* shielding */
dr3gamij_1 = ( r_ij * r_ij * r_ij +
system->reaxprm.tbp[system->atoms[i].type][system->atoms[j].type].gamma );
dr3gamij_3 = POW( dr3gamij_1 , 0.33333333333333 );
ret = ((i == j) ? 0.5 : 1.0) * Tap * EV_to_KCALpMOL / dr3gamij_3;
break;
+
case DIAGONAL:
ret = system->reaxprm.sbp[system->atoms[i].type].eta;
break;
+
default:
fprintf( stderr, "[Init_forces] Invalid matrix position. Terminating...\n" );
exit( INVALID_INPUT );
@@ -388,9 +392,35 @@ static inline real Init_Charge_Matrix_Entry( reax_system *system,
switch ( pos )
{
case OFF_DIAGONAL:
+ 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;
+
+// gamij = system->reaxprm.sbp[system->atoms[i].type].gamma
+// + system->reaxprm.sbp[system->atoms[j].type].gamma;
+// gamij = SQRT( gamij );
+// dr3gamij_1 = ( r_ij * r_ij * r_ij +
+// 1.0 / ( gamij * gamij * gamij ) );
+// dr3gamij_3 = POW( dr3gamij_1 , 0.33333333333333 );
+//
+// ret = Tap * EV_to_KCALpMOL / dr3gamij_3;
+
+ /* shielding */
+ dr3gamij_1 = ( r_ij * r_ij * r_ij +
+ system->reaxprm.tbp[system->atoms[i].type][system->atoms[j].type].gamma );
+ dr3gamij_3 = POW( dr3gamij_1 , 0.33333333333333 );
+
+ ret = ((i == j) ? 0.5 : 1.0) * Tap * EV_to_KCALpMOL / dr3gamij_3;
break;
+
case DIAGONAL:
+ ret = 2.0 * system->reaxprm.sbp[system->atoms[i].type].eta;
break;
+
default:
fprintf( stderr, "[Init_forces] Invalid matrix position. Terminating...\n" );
exit( INVALID_INPUT );
@@ -423,6 +453,42 @@ static inline real Init_Charge_Matrix_Entry( reax_system *system,
}
+static void Init_Charge_Matrix_Remaining_Entries( reax_system *system,
+ control_params *control, sparse_matrix * H, sparse_matrix * H_sp,
+ int * Htop, int * H_sp_top )
+{
+ int i;
+
+ switch ( control->charge_method )
+ {
+ case QEQ_CM:
+ break;
+
+ case EEM_CM:
+ H->start[system->N] = *Htop;
+ H_sp->start[system->N] = *H_sp_top;
+
+ for ( i = 0; i < system->N_cm; ++i )
+ {
+ H->j[*Htop] = i;
+ H->val[*Htop] = 1.0;
+ ++(*Htop);
+
+ H_sp->j[*H_sp_top] = i;
+ H_sp->val[*H_sp_top] = 1.0;
+ ++(*H_sp_top);
+ }
+ break;
+
+ case ACKS2_CM:
+ break;
+
+ default:
+ break;
+ }
+}
+
+
void Init_Forces( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
list **lists, output_controls *out_control )
@@ -696,7 +762,9 @@ void Init_Forces( reax_system *system, control_params *control,
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 ) );
}
@@ -705,8 +773,10 @@ void Init_Forces( reax_system *system, control_params *control,
// printf("H_sp_top = %d\n", H_sp_top);
// mark the end of j list
- H->start[i] = Htop;
- H_sp->start[i] = H_sp_top;
+ Init_Charge_Matrix_Remaining_Entries( system, control, H, H_sp, &Htop, &H_sp_top );
+ H->start[system->N_cm] = Htop;
+ H_sp->start[system->N_cm] = H_sp_top;
+
/* validate lists - decide if reallocation is required! */
Validate_Lists( workspace, lists,
data->step, system->N, H->m, Htop, num_bonds, num_hbonds );
diff --git a/sPuReMD/src/init_md.c b/sPuReMD/src/init_md.c
index af3e234b..aed06740 100644
--- a/sPuReMD/src/init_md.c
+++ b/sPuReMD/src/init_md.c
@@ -209,15 +209,15 @@ void Init_Simulation_Data( reax_system *system, control_params *control,
data->timing.init_forces = 0;
data->timing.bonded = 0;
data->timing.nonb = 0;
- data->timing.QEq = ZERO;
- data->timing.QEq_sort_mat_rows = ZERO;
- data->timing.pre_comp = ZERO;
- data->timing.pre_app = ZERO;
- data->timing.solver_iters = 0;
- data->timing.solver_spmv = ZERO;
- data->timing.solver_vector_ops = ZERO;
- data->timing.solver_orthog = ZERO;
- data->timing.solver_tri_solve = ZERO;
+ data->timing.cm = ZERO;
+ data->timing.cm_sort_mat_rows = ZERO;
+ data->timing.cm_solver_pre_comp = ZERO;
+ data->timing.cm_solver_pre_app = ZERO;
+ data->timing.cm_solver_iters = 0;
+ data->timing.cm_solver_spmv = ZERO;
+ data->timing.cm_solver_vector_ops = ZERO;
+ data->timing.cm_solver_orthog = ZERO;
+ data->timing.cm_solver_tri_solve = ZERO;
}
@@ -231,8 +231,10 @@ void Init_Taper( control_params *control )
swa = control->r_low;
swb = control->r_cut;
- if ( fabs( swa ) > 0.01 )
+ if ( FABS( swa ) > 0.01 )
+ {
fprintf( stderr, "Warning: non-zero value for lower Taper-radius cutoff\n" );
+ }
if ( swb < 0 )
{
@@ -240,8 +242,10 @@ void Init_Taper( control_params *control )
exit( INVALID_INPUT );
}
else if ( swb < 5 )
+ {
fprintf( stderr, "Warning: low value for upper Taper-radius cutoff:%f\n",
- swb );
+ swb );
+ }
d1 = swb - swa;
d7 = POW( d1, 7.0 );
@@ -258,7 +262,7 @@ void Init_Taper( control_params *control )
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;
+ 7.0 * swa * swb3 * swb3 + swb3 * swb3 * swb ) / d7;
}
@@ -289,71 +293,136 @@ void Init_Workspace( reax_system *system, control_params *control,
workspace->CdDelta = (real *) malloc( system->N * sizeof( real ) );
workspace->vlpex = (real *) malloc( system->N * sizeof( real ) );
- /* QEq storage */
- workspace->H = NULL;
- workspace->H_sp = NULL;
- workspace->L = NULL;
- workspace->U = NULL;
+ /* charge method storage */
+ switch ( control->charge_method )
+ {
+ case QEQ_CM:
+ system->N_cm = system->N;
+ break;
+ case EEM_CM:
+ system->N_cm = system->N + 1;
+ break;
+ case ACKS2_CM:
+ system->N_cm = 2 * system->N + 2;
+ break;
+ default:
+ fprintf( stderr, "Unknown charge method type. Terminating...\n" );
+ exit( INVALID_INPUT );
+ break;
+ }
+
+ workspace->H = NULL;
+ workspace->H_sp = NULL;
+ workspace->L = NULL;
+ workspace->U = NULL;
workspace->Hdia_inv = NULL;
- workspace->droptol = (real *) calloc( system->N, sizeof( real ) );
- workspace->w = (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 ) );
+ if ( control->cm_solver_pre_comp_type == ICHOLT_PC ||
+ control->cm_solver_pre_comp_type == ILUT_PAR_PC )
+ {
+ workspace->droptol = (real *) calloc( system->N_cm, sizeof( real ) );
+ }
+ //TODO: check if unused
+ //workspace->w = (real *) calloc( cm_lin_sys_size, sizeof( real ) );
+ //TODO: check if unused
+ workspace->b = (real *) calloc( system->N_cm * 2, sizeof( real ) );
+ workspace->b_s = (real *) calloc( system->N_cm, sizeof( real ) );
+ workspace->b_t = (real *) calloc( system->N_cm, sizeof( real ) );
+ workspace->b_prc = (real *) calloc( system->N_cm * 2, sizeof( real ) );
+ workspace->b_prm = (real *) calloc( system->N_cm * 2, sizeof( real ) );
+ //TODO: check if unused
+ //workspace->s_t = (real *) calloc( cm_lin_sys_size * 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[i] = (real *) calloc( system->N_cm, sizeof( real ) );
+ workspace->t[i] = (real *) calloc( system->N_cm, 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 )
+ switch ( control->charge_method )
{
- 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;
+ case QEQ_CM:
+ for ( i = 0; i < system->N; ++i )
+ {
+ workspace->b_s[i] = -system->reaxprm.sbp[ system->atoms[i].type ].chi;
+ workspace->b_t[i] = -1.0;
+
+ //TODO: check if unused (redundant)
+ workspace->b[i] = -system->reaxprm.sbp[ system->atoms[i].type ].chi;
+ workspace->b[i + system->N] = -1.0;
+ }
+ break;
+ case EEM_CM:
+ for ( i = 0; i < system->N; ++i )
+ {
+ workspace->b_s[i] = -system->reaxprm.sbp[ system->atoms[i].type ].chi;
+
+ //TODO: check if unused (redundant)
+ workspace->b[i] = -system->reaxprm.sbp[ system->atoms[i].type ].chi;
+ }
+
+ workspace->b_s[system->N] = control->cm_q_net;
+ workspace->b[system->N] = control->cm_q_net;
+ break;
+ case ACKS2_CM:
+ //TODO
+ break;
+ default:
+ fprintf( stderr, "Unknown charge method type. Terminating...\n" );
+ exit( INVALID_INPUT );
+ break;
}
- /* 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 )
+ switch ( control->cm_solver_type )
{
- 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 ) );
+ /* GMRES storage */
+ case GMRES_S:
+ case GMRES_H_S:
+ 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_cm * 2, sizeof( real ) );
+ workspace->v[i] = (real *) calloc( system->N_cm, sizeof( real ) );
+ }
+
+ workspace->r = (real *) calloc( system->N_cm, sizeof( real ) );
+ workspace->d = (real *) calloc( system->N_cm, sizeof( real ) );
+ workspace->q = (real *) calloc( system->N_cm, sizeof( real ) );
+ workspace->p = (real *) calloc( system->N_cm, sizeof( real ) );
+ break;
+
+ /* CG storage */
+ case CG_S:
+ workspace->r = (real *) calloc( system->N_cm, sizeof( real ) );
+ workspace->d = (real *) calloc( system->N_cm, sizeof( real ) );
+ workspace->q = (real *) calloc( system->N_cm, sizeof( real ) );
+ workspace->p = (real *) calloc( system->N_cm, sizeof( real ) );
+ break;
+
+ case SDM_S:
+ //TODO
+ break;
+
+ default:
+ fprintf( stderr, "Unknown charge method linear solver type. Terminating...\n" );
+ exit( INVALID_INPUT );
+ break;
}
- /* 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 ) );
-
/* storage for analysis */
if ( control->molec_anal || control->diffusion_coef )
{
@@ -361,12 +430,18 @@ void Init_Workspace( reax_system *system, control_params *control,
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->x_old = NULL;
+ }
#ifdef TEST_FORCES
workspace->dDelta = (rvec *) malloc( system->N * sizeof( rvec ) );
@@ -407,11 +482,13 @@ void Init_Lists( reax_system *system, control_params *control,
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( CANNOT_INITIALIZE );
}
+
#if defined(DEBUG_FOCUS)
fprintf( stderr, "memory allocated: far_nbrs = %ldMB\n",
num_nbrs * sizeof(far_neighbor_data) / (1024 * 1024) );
@@ -422,10 +499,10 @@ void Init_Lists( reax_system *system, control_params *control,
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 );
+ Estimate_Storage_Sizes( system, control, lists, &Htop,
+ hb_top, bond_top, &num_3body );
- if ( Allocate_Matrix( &(workspace->H), system->N, Htop ) == FAILURE )
+ if ( Allocate_Matrix( &(workspace->H), system->N_cm, Htop ) == FAILURE )
{
fprintf( stderr, "Not enough space for init matrices. Terminating...\n" );
exit( INSUFFICIENT_MEMORY );
@@ -434,15 +511,16 @@ void Init_Lists( reax_system *system, control_params *control,
* If so, need to refactor Estimate_Storage_Sizes
* to use various cut-off distances as parameters
* (non-bonded, hydrogen, 3body, etc.) */
- if ( Allocate_Matrix( &(workspace->H_sp), system->N, Htop ) == FAILURE )
+ if ( Allocate_Matrix( &(workspace->H_sp), system->N_cm, Htop ) == FAILURE )
{
fprintf( stderr, "Not enough space for init matrices. Terminating...\n" );
exit( INSUFFICIENT_MEMORY );
}
+
#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) );
+ Htop * sizeof(sparse_matrix_entry) / (1024 * 1024) );
#endif
workspace->num_H = 0;
@@ -450,13 +528,22 @@ void Init_Lists( reax_system *system, control_params *control,
{
/* init H indexes */
for ( i = 0; i < system->N; ++i )
- if ( system->reaxprm.sbp[ system->atoms[i].type ].p_hbond == 1 ) // H atom
+ {
+ // H atom
+ if ( system->reaxprm.sbp[ system->atoms[i].type ].p_hbond == 1 )
+ {
workspace->hbond_index[i] = workspace->num_H++;
- else workspace->hbond_index[i] = -1;
+ }
+ else
+ {
+ workspace->hbond_index[i] = -1;
+ }
+ }
Allocate_HBond_List( system->N, workspace->num_H, workspace->hbond_index,
- hb_top, (*lists) + HBONDS );
+ 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",
@@ -467,6 +554,7 @@ void Init_Lists( reax_system *system, control_params *control,
/* 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",
@@ -483,11 +571,13 @@ void Init_Lists( reax_system *system, control_params *control,
fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
exit( CANNOT_INITIALIZE );
}
+
#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) );
#endif
+
#ifdef TEST_FORCES
if (!Make_List( system->N, num_bonds * 8, TYP_DDELTA, (*lists) + DDELTA ))
{
@@ -548,7 +638,7 @@ void Init_Out_Controls(reax_system *system, control_params *control,
out_control->log = fopen( temp, "w" );
fprintf( out_control->log, "%-6s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s %10s\n",
"step", "total", "neighbors", "init", "bonded",
- "nonbonded", "QEq", "QEq Sort", "S iters", "Pre Comp", "Pre App",
+ "nonbonded", "CM", "CM Sort", "S iters", "Pre Comp", "Pre App",
"S spmv", "S vec ops", "S orthog", "S tsolve" );
}
diff --git a/sPuReMD/src/integrate.c b/sPuReMD/src/integrate.c
index 142863ca..681ec92e 100644
--- a/sPuReMD/src/integrate.c
+++ b/sPuReMD/src/integrate.c
@@ -26,7 +26,7 @@
#include "grid.h"
#include "neighbors.h"
#include "print_utils.h"
-#include "QEq.h"
+#include "charges.h"
#include "reset_utils.h"
#include "restart.h"
#include "system_props.h"
@@ -483,7 +483,7 @@ void Velocity_Verlet_Nose_Hoover_NVT(reax_system* system,
fprintf(out_control->log, "nbrs-");
fflush( out_control->log );
- /* QEq( system, control, workspace, lists[FAR_NBRS], out_control );
+ /* Compute_Charges( 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 );
@@ -589,7 +589,7 @@ void Velocity_Verlet_Isotropic_NPT( reax_system* system,
fprintf(out_control->log, "nbrs-");
fflush( out_control->log );
- /* QEq( system, control, workspace, lists[FAR_NBRS], out_control );
+ /* Compute_Charges( 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 );
diff --git a/sPuReMD/src/lin_alg.c b/sPuReMD/src/lin_alg.c
index 4d37ae6f..727de37e 100644
--- a/sPuReMD/src/lin_alg.c
+++ b/sPuReMD/src/lin_alg.c
@@ -1200,7 +1200,7 @@ int GMRES( const static_storage * const workspace, const control_params * const
bnorm = Norm( b, N );
#pragma omp master
{
- data->timing.solver_vector_ops += Get_Timing_Info( time_start );
+ data->timing.cm_solver_vector_ops += Get_Timing_Info( time_start );
}
if ( control->cm_solver_pre_comp_type == DIAG_PC )
@@ -1213,7 +1213,7 @@ int GMRES( const static_storage * const workspace, const control_params * const
apply_preconditioner( workspace, control, b, workspace->b_prc, fresh_pre );
#pragma omp master
{
- data->timing.pre_app += Get_Timing_Info( time_start );
+ data->timing.cm_solver_pre_app += Get_Timing_Info( time_start );
}
}
@@ -1228,7 +1228,7 @@ int GMRES( const static_storage * const workspace, const control_params * const
Sparse_MatVec( H, x, workspace->b_prm );
#pragma omp master
{
- data->timing.solver_spmv += Get_Timing_Info( time_start );
+ data->timing.cm_solver_spmv += Get_Timing_Info( time_start );
}
if ( control->cm_solver_pre_comp_type == DIAG_PC )
@@ -1240,7 +1240,7 @@ int GMRES( const static_storage * const workspace, const control_params * const
apply_preconditioner( workspace, control, workspace->b_prm, workspace->b_prm, FALSE );
#pragma omp master
{
- data->timing.pre_app += Get_Timing_Info( time_start );
+ data->timing.cm_solver_pre_app += Get_Timing_Info( time_start );
}
}
@@ -1253,7 +1253,7 @@ int GMRES( const static_storage * const workspace, const control_params * const
Vector_Sum( workspace->v[0], 1., workspace->b_prc, -1., workspace->b_prm, N );
#pragma omp master
{
- data->timing.solver_vector_ops += Get_Timing_Info( time_start );
+ data->timing.cm_solver_vector_ops += Get_Timing_Info( time_start );
}
}
else
@@ -1265,7 +1265,7 @@ int GMRES( const static_storage * const workspace, const control_params * const
Vector_Sum( workspace->v[0], 1., b, -1., workspace->b_prm, N );
#pragma omp master
{
- data->timing.solver_vector_ops += Get_Timing_Info( time_start );
+ data->timing.cm_solver_vector_ops += Get_Timing_Info( time_start );
}
}
@@ -1279,7 +1279,7 @@ int GMRES( const static_storage * const workspace, const control_params * const
itr == 0 ? fresh_pre : FALSE );
#pragma omp master
{
- data->timing.pre_app += Get_Timing_Info( time_start );
+ data->timing.cm_solver_pre_app += Get_Timing_Info( time_start );
}
}
@@ -1295,7 +1295,7 @@ int GMRES( const static_storage * const workspace, const control_params * const
Vector_Scale( workspace->v[0], 1. / workspace->g[0], workspace->v[0], N );
#pragma omp master
{
- data->timing.solver_vector_ops += Get_Timing_Info( time_start );
+ data->timing.cm_solver_vector_ops += Get_Timing_Info( time_start );
}
/* GMRES inner-loop */
@@ -1309,7 +1309,7 @@ int GMRES( const static_storage * const workspace, const control_params * const
Sparse_MatVec( H, workspace->v[j], workspace->v[j + 1] );
#pragma omp master
{
- data->timing.solver_spmv += Get_Timing_Info( time_start );
+ data->timing.cm_solver_spmv += Get_Timing_Info( time_start );
}
#pragma omp master
@@ -1319,7 +1319,7 @@ int GMRES( const static_storage * const workspace, const control_params * const
apply_preconditioner( workspace, control, workspace->v[j + 1], workspace->v[j + 1], FALSE );
#pragma omp master
{
- data->timing.pre_app += Get_Timing_Info( time_start );
+ data->timing.cm_solver_pre_app += Get_Timing_Info( time_start );
}
if ( control->cm_solver_pre_comp_type == DIAG_PC )
@@ -1336,7 +1336,7 @@ int GMRES( const static_storage * const workspace, const control_params * const
}
#pragma omp master
{
- data->timing.solver_vector_ops += Get_Timing_Info( time_start );
+ data->timing.cm_solver_vector_ops += Get_Timing_Info( time_start );
}
}
else
@@ -1363,7 +1363,7 @@ int GMRES( const static_storage * const workspace, const control_params * const
}
#pragma omp master
{
- data->timing.solver_vector_ops += Get_Timing_Info( time_start );
+ data->timing.cm_solver_vector_ops += Get_Timing_Info( time_start );
}
}
@@ -1380,7 +1380,7 @@ int GMRES( const static_storage * const workspace, const control_params * const
1. / workspace->h[j + 1][j], workspace->v[j + 1], N );
#pragma omp master
{
- data->timing.solver_vector_ops += Get_Timing_Info( time_start );
+ data->timing.cm_solver_vector_ops += Get_Timing_Info( time_start );
}
#if defined(DEBUG)
fprintf( stderr, "%d-%d: orthogonalization completed.\n", itr, j );
@@ -1438,7 +1438,7 @@ int GMRES( const static_storage * const workspace, const control_params * const
tmp2 = -workspace->hs[j] * workspace->g[j];
workspace->g[j] = tmp1;
workspace->g[j + 1] = tmp2;
- data->timing.solver_orthog += Get_Timing_Info( time_start );
+ data->timing.cm_solver_orthog += Get_Timing_Info( time_start );
}
#pragma omp barrier
@@ -1464,7 +1464,7 @@ int GMRES( const static_storage * const workspace, const control_params * const
workspace->y[i] = temp / workspace->h[i][i];
}
- data->timing.solver_tri_solve += Get_Timing_Info( time_start );
+ data->timing.cm_solver_tri_solve += Get_Timing_Info( time_start );
/* update x = x_0 + Vy */
time_start = Get_Time( );
@@ -1478,7 +1478,7 @@ int GMRES( const static_storage * const workspace, const control_params * const
Vector_Add( x, 1., workspace->p, N );
#pragma omp master
{
- data->timing.solver_vector_ops += Get_Timing_Info( time_start );
+ data->timing.cm_solver_vector_ops += Get_Timing_Info( time_start );
}
/* stopping condition */
diff --git a/sPuReMD/src/mytypes.h b/sPuReMD/src/mytypes.h
index 23653bb3..a6e5a166 100644
--- a/sPuReMD/src/mytypes.h
+++ b/sPuReMD/src/mytypes.h
@@ -215,7 +215,7 @@ enum pre_app
};
-/* Global params mapping */
+/* Force field global params mapping */
/*
l[0] = p_boc1
l[1] = p_boc2
@@ -456,10 +456,17 @@ typedef struct
typedef struct
{
+ /* number of atoms */
int N;
+ /* dimension of the N x N sparse charge method matrix H */
+ int N_cm;
+ /* atom info */
reax_atom *atoms;
+ /* atomic interaction parameters */
reax_interaction reaxprm;
+ /* simulation space (a.k.a. box) parameters */
simulation_box box;
+ /* grid structure used for binning atoms and tracking neighboring bins */
grid g;
} reax_system;
@@ -521,6 +528,7 @@ typedef struct
unsigned int charge_method;
unsigned int cm_solver_type;
+ real cm_q_net;
real cm_solver_q_err;
real cm_domain_sparsity;
unsigned int cm_domain_sparsify_enabled;
@@ -589,15 +597,15 @@ typedef struct
real init_forces;
real bonded;
real nonb;
- real QEq;
- real QEq_sort_mat_rows;
- real pre_comp;
- real pre_app;
- int solver_iters;
- real solver_spmv;
- real solver_vector_ops;
- real solver_orthog;
- real solver_tri_solve;
+ real cm;
+ real cm_sort_mat_rows;
+ real cm_solver_pre_comp;
+ real cm_solver_pre_app;
+ int cm_solver_iters;
+ real cm_solver_spmv;
+ real cm_solver_vector_ops;
+ real cm_solver_orthog;
+ real cm_solver_tri_solve;
} reax_timing;
diff --git a/sPuReMD/src/print_utils.c b/sPuReMD/src/print_utils.c
index 579ba629..015e2573 100644
--- a/sPuReMD/src/print_utils.c
+++ b/sPuReMD/src/print_utils.c
@@ -622,30 +622,30 @@ void Output_Results( reax_system *system, control_params *control,
data->timing.init_forces / f_update,
data->timing.bonded / f_update,
data->timing.nonb / f_update,
- data->timing.QEq / f_update,
- data->timing.QEq_sort_mat_rows / f_update,
- (double)data->timing.solver_iters / f_update,
- data->timing.pre_comp / f_update,
- data->timing.pre_app / f_update,
- data->timing.solver_spmv / f_update,
- data->timing.solver_vector_ops / f_update,
- data->timing.solver_orthog / f_update,
- data->timing.solver_tri_solve / f_update );
+ data->timing.cm / f_update,
+ data->timing.cm_sort_mat_rows / f_update,
+ (double)data->timing.cm_solver_iters / f_update,
+ data->timing.cm_solver_pre_comp / f_update,
+ data->timing.cm_solver_pre_app / f_update,
+ data->timing.cm_solver_spmv / f_update,
+ data->timing.cm_solver_vector_ops / f_update,
+ data->timing.cm_solver_orthog / f_update,
+ data->timing.cm_solver_tri_solve / 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 = ZERO;
- data->timing.QEq_sort_mat_rows = ZERO;
- data->timing.pre_comp = ZERO;
- data->timing.pre_app = ZERO;
- data->timing.solver_iters = 0;
- data->timing.solver_spmv = ZERO;
- data->timing.solver_vector_ops = ZERO;
- data->timing.solver_orthog = ZERO;
- data->timing.solver_tri_solve = ZERO;
+ data->timing.cm = ZERO;
+ data->timing.cm_sort_mat_rows = ZERO;
+ data->timing.cm_solver_pre_comp = ZERO;
+ data->timing.cm_solver_pre_app = ZERO;
+ data->timing.cm_solver_iters = 0;
+ data->timing.cm_solver_spmv = ZERO;
+ data->timing.cm_solver_vector_ops = ZERO;
+ data->timing.cm_solver_orthog = ZERO;
+ data->timing.cm_solver_tri_solve = ZERO;
fflush( out_control->out );
fflush( out_control->pot );
@@ -694,17 +694,17 @@ void Output_Results( reax_system *system, control_params *control,
void Print_Linear_System( reax_system *system, control_params *control,
- static_storage *workspace, int step )
+ static_storage *workspace, int step )
{
- int i, j;
- char fname[100];
+ 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++ )
+ for ( i = 0; i < system->N_cm; 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],
@@ -719,12 +719,11 @@ void Print_Linear_System( reax_system *system, control_params *control,
// 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 ( i = 0; i < system->N_cm; ++i )
{
for ( j = H->start[i]; j < H->start[i + 1] - 1; ++j )
{
@@ -747,7 +746,7 @@ void Print_Linear_System( reax_system *system, control_params *control,
out = fopen( fname, "w" );
H = workspace->H_sp;
- for ( i = 0; i < system->N; ++i )
+ for ( i = 0; i < system->N_cm; ++i )
{
for ( j = H->start[i]; j < H->start[i + 1] - 1; ++j )
{
diff --git a/sPuReMD/src/testmd.c b/sPuReMD/src/testmd.c
index c4c66453..075a49b1 100644
--- a/sPuReMD/src/testmd.c
+++ b/sPuReMD/src/testmd.c
@@ -47,7 +47,7 @@ static void Post_Evolve( reax_system * const system,
/* if velocity dependent force then
{
Generate_Neighbor_Lists( &system, &control, &lists );
- QEq(system, control, workspace, lists[FAR_NBRS]);
+ Compute_Charges(system, control, workspace, lists[FAR_NBRS]);
Introduce compute_force here if we are using velocity dependent forces
Compute_Forces(system,control,data,workspace,lists);
} */
--
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