From e8553618eb2bb6125b100083b4bbbd20ec223292 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnku@msu.edu>
Date: Mon, 25 Oct 2021 13:09:58 -0400
Subject: [PATCH] Fix memory allocation issues related to API usage (setup =>
cleanup but no simulate) as detailed in Issue #9.
---
sPuReMD/src/init_md.c | 512 ++++++++++++++++++++-------------------
sPuReMD/src/reax_types.h | 20 +-
sPuReMD/src/spuremd.c | 4 +
tools/driver.py | 19 +-
4 files changed, 295 insertions(+), 260 deletions(-)
diff --git a/sPuReMD/src/init_md.c b/sPuReMD/src/init_md.c
index 81377aea..8563ff82 100644
--- a/sPuReMD/src/init_md.c
+++ b/sPuReMD/src/init_md.c
@@ -104,6 +104,8 @@ static void Init_System( reax_system * const system, control_params * const cont
int i;
rvec dx;
+ system->allocated = TRUE;
+
if ( control->restart == FALSE )
{
Reset_Atomic_Forces( system );
@@ -343,6 +345,8 @@ static void Init_Workspace( reax_system * const system,
{
int i;
+ workspace->allocated = TRUE;
+
if ( realloc == TRUE )
{
/* bond order related storage */
@@ -1001,6 +1005,8 @@ static void Init_Out_Controls( reax_system *system, control_params *control,
#define TEMP_SIZE (1000)
char temp[TEMP_SIZE];
+ out_control->allocated = TRUE;
+
if ( output_enabled == TRUE && out_control->write_steps > 0 )
{
strncpy( temp, control->sim_name, TEMP_SIZE - 5 );
@@ -1361,8 +1367,13 @@ static void Finalize_System( reax_system *system, control_params *control,
sfree( system->atoms, __FILE__, __LINE__ );
}
- sfree( system->bonds, __FILE__, __LINE__ );
- sfree( system->hbonds, __FILE__, __LINE__ );
+ if ( system->allocated == TRUE )
+ {
+ sfree( system->bonds, __FILE__, __LINE__ );
+ sfree( system->hbonds, __FILE__, __LINE__ );
+ }
+
+ system->allocated = FALSE;
}
@@ -1384,222 +1395,225 @@ static void Finalize_Workspace( reax_system *system, control_params *control,
{
int i;
- sfree( workspace->total_bond_order, __FILE__, __LINE__ );
- sfree( workspace->Deltap, __FILE__, __LINE__ );
- sfree( workspace->Deltap_boc, __FILE__, __LINE__ );
- sfree( workspace->dDeltap_self, __FILE__, __LINE__ );
- sfree( workspace->Delta, __FILE__, __LINE__ );
- sfree( workspace->Delta_lp, __FILE__, __LINE__ );
- sfree( workspace->Delta_lp_temp, __FILE__, __LINE__ );
- sfree( workspace->dDelta_lp, __FILE__, __LINE__ );
- sfree( workspace->dDelta_lp_temp, __FILE__, __LINE__ );
- sfree( workspace->Delta_e, __FILE__, __LINE__ );
- sfree( workspace->Delta_boc, __FILE__, __LINE__ );
- sfree( workspace->nlp, __FILE__, __LINE__ );
- sfree( workspace->nlp_temp, __FILE__, __LINE__ );
- sfree( workspace->Clp, __FILE__, __LINE__ );
- sfree( workspace->CdDelta, __FILE__, __LINE__ );
- sfree( workspace->vlpex, __FILE__, __LINE__ );
+ if ( workspace->allocated == TRUE )
+ {
+ sfree( workspace->total_bond_order, __FILE__, __LINE__ );
+ sfree( workspace->Deltap, __FILE__, __LINE__ );
+ sfree( workspace->Deltap_boc, __FILE__, __LINE__ );
+ sfree( workspace->dDeltap_self, __FILE__, __LINE__ );
+ sfree( workspace->Delta, __FILE__, __LINE__ );
+ sfree( workspace->Delta_lp, __FILE__, __LINE__ );
+ sfree( workspace->Delta_lp_temp, __FILE__, __LINE__ );
+ sfree( workspace->dDelta_lp, __FILE__, __LINE__ );
+ sfree( workspace->dDelta_lp_temp, __FILE__, __LINE__ );
+ sfree( workspace->Delta_e, __FILE__, __LINE__ );
+ sfree( workspace->Delta_boc, __FILE__, __LINE__ );
+ sfree( workspace->nlp, __FILE__, __LINE__ );
+ sfree( workspace->nlp_temp, __FILE__, __LINE__ );
+ sfree( workspace->Clp, __FILE__, __LINE__ );
+ sfree( workspace->CdDelta, __FILE__, __LINE__ );
+ sfree( workspace->vlpex, __FILE__, __LINE__ );
- if ( reset == FALSE && (control->geo_format == BGF
- || control->geo_format == ASCII_RESTART
- || control->geo_format == BINARY_RESTART) )
- {
- sfree( workspace->map_serials, __FILE__, __LINE__ );
- }
-
- if ( workspace->H.allocated == TRUE )
- {
- Deallocate_Matrix( &workspace->H );
- }
- if ( workspace->H_full.allocated == TRUE )
- {
- Deallocate_Matrix( &workspace->H_full );
- }
- if ( workspace->H_sp.allocated == TRUE )
- {
- Deallocate_Matrix( &workspace->H_sp );
- }
- if ( workspace->H_p.allocated == TRUE )
- {
- Deallocate_Matrix( &workspace->H_p );
- }
- if ( workspace->H_spar_patt.allocated == TRUE )
- {
- Deallocate_Matrix( &workspace->H_spar_patt );
- }
- if ( workspace->H_spar_patt_full.allocated == TRUE )
- {
- Deallocate_Matrix( &workspace->H_spar_patt_full );
- }
- if ( workspace->H_app_inv.allocated == TRUE )
- {
- Deallocate_Matrix( &workspace->H_app_inv );
- }
- if ( workspace->L.allocated == TRUE )
- {
- Deallocate_Matrix( &workspace->L );
- }
- if ( workspace->U.allocated == TRUE )
- {
- Deallocate_Matrix( &workspace->U );
- }
+ if ( workspace->H.allocated == TRUE )
+ {
+ Deallocate_Matrix( &workspace->H );
+ }
+ if ( workspace->H_full.allocated == TRUE )
+ {
+ Deallocate_Matrix( &workspace->H_full );
+ }
+ if ( workspace->H_sp.allocated == TRUE )
+ {
+ Deallocate_Matrix( &workspace->H_sp );
+ }
+ if ( workspace->H_p.allocated == TRUE )
+ {
+ Deallocate_Matrix( &workspace->H_p );
+ }
+ if ( workspace->H_spar_patt.allocated == TRUE )
+ {
+ Deallocate_Matrix( &workspace->H_spar_patt );
+ }
+ if ( workspace->H_spar_patt_full.allocated == TRUE )
+ {
+ Deallocate_Matrix( &workspace->H_spar_patt_full );
+ }
+ if ( workspace->H_app_inv.allocated == TRUE )
+ {
+ Deallocate_Matrix( &workspace->H_app_inv );
+ }
+ if ( workspace->L.allocated == TRUE )
+ {
+ Deallocate_Matrix( &workspace->L );
+ }
+ if ( workspace->U.allocated == TRUE )
+ {
+ Deallocate_Matrix( &workspace->U );
+ }
- for ( i = 0; i < 5; ++i )
- {
- sfree( workspace->s[i], __FILE__, __LINE__ );
- sfree( workspace->t[i], __FILE__, __LINE__ );
- }
+ for ( i = 0; i < 5; ++i )
+ {
+ sfree( workspace->s[i], __FILE__, __LINE__ );
+ sfree( workspace->t[i], __FILE__, __LINE__ );
+ }
- if ( control->cm_solver_pre_comp_type == JACOBI_PC )
- {
- sfree( workspace->Hdia_inv, __FILE__, __LINE__ );
- }
- if ( control->cm_solver_pre_comp_type == ICHOLT_PC
- || (control->cm_solver_pre_comp_type == ILUT_PC && control->cm_solver_pre_comp_droptol > 0.0 )
- || control->cm_solver_pre_comp_type == ILUTP_PC
- || control->cm_solver_pre_comp_type == FG_ILUT_PC )
- {
- sfree( workspace->droptol, __FILE__, __LINE__ );
- }
- sfree( workspace->b_s, __FILE__, __LINE__ );
- sfree( workspace->b_t, __FILE__, __LINE__ );
- sfree( workspace->b_prc, __FILE__, __LINE__ );
- sfree( workspace->b_prm, __FILE__, __LINE__ );
- sfree( workspace->s, __FILE__, __LINE__ );
- sfree( workspace->t, __FILE__, __LINE__ );
+ if ( control->cm_solver_pre_comp_type == JACOBI_PC )
+ {
+ sfree( workspace->Hdia_inv, __FILE__, __LINE__ );
+ }
+ if ( control->cm_solver_pre_comp_type == ICHOLT_PC
+ || (control->cm_solver_pre_comp_type == ILUT_PC && control->cm_solver_pre_comp_droptol > 0.0 )
+ || control->cm_solver_pre_comp_type == ILUTP_PC
+ || control->cm_solver_pre_comp_type == FG_ILUT_PC )
+ {
+ sfree( workspace->droptol, __FILE__, __LINE__ );
+ }
+ sfree( workspace->b_s, __FILE__, __LINE__ );
+ sfree( workspace->b_t, __FILE__, __LINE__ );
+ sfree( workspace->b_prc, __FILE__, __LINE__ );
+ sfree( workspace->b_prm, __FILE__, __LINE__ );
+ sfree( workspace->s, __FILE__, __LINE__ );
+ sfree( workspace->t, __FILE__, __LINE__ );
- switch ( control->cm_solver_type )
- {
- case GMRES_S:
- case GMRES_H_S:
- for ( i = 0; i < control->cm_solver_restart + 1; ++i )
- {
- sfree( workspace->h[i], __FILE__, __LINE__ );
- sfree( workspace->rn[i], __FILE__, __LINE__ );
- sfree( workspace->v[i], __FILE__, __LINE__ );
- }
+ switch ( control->cm_solver_type )
+ {
+ case GMRES_S:
+ case GMRES_H_S:
+ for ( i = 0; i < control->cm_solver_restart + 1; ++i )
+ {
+ sfree( workspace->h[i], __FILE__, __LINE__ );
+ sfree( workspace->rn[i], __FILE__, __LINE__ );
+ sfree( workspace->v[i], __FILE__, __LINE__ );
+ }
- sfree( workspace->y, __FILE__, __LINE__ );
- sfree( workspace->z, __FILE__, __LINE__ );
- sfree( workspace->g, __FILE__, __LINE__ );
- sfree( workspace->h, __FILE__, __LINE__ );
- sfree( workspace->hs, __FILE__, __LINE__ );
- sfree( workspace->hc, __FILE__, __LINE__ );
- sfree( workspace->rn, __FILE__, __LINE__ );
- sfree( workspace->v, __FILE__, __LINE__ );
-
- sfree( workspace->r, __FILE__, __LINE__ );
- sfree( workspace->d, __FILE__, __LINE__ );
- sfree( workspace->q, __FILE__, __LINE__ );
- sfree( workspace->p, __FILE__, __LINE__ );
- break;
+ sfree( workspace->y, __FILE__, __LINE__ );
+ sfree( workspace->z, __FILE__, __LINE__ );
+ sfree( workspace->g, __FILE__, __LINE__ );
+ sfree( workspace->h, __FILE__, __LINE__ );
+ sfree( workspace->hs, __FILE__, __LINE__ );
+ sfree( workspace->hc, __FILE__, __LINE__ );
+ sfree( workspace->rn, __FILE__, __LINE__ );
+ sfree( workspace->v, __FILE__, __LINE__ );
+
+ sfree( workspace->r, __FILE__, __LINE__ );
+ sfree( workspace->d, __FILE__, __LINE__ );
+ sfree( workspace->q, __FILE__, __LINE__ );
+ sfree( workspace->p, __FILE__, __LINE__ );
+ break;
- case CG_S:
- sfree( workspace->r, __FILE__, __LINE__ );
- sfree( workspace->d, __FILE__, __LINE__ );
- sfree( workspace->q, __FILE__, __LINE__ );
- sfree( workspace->p, __FILE__, __LINE__ );
- break;
+ case CG_S:
+ sfree( workspace->r, __FILE__, __LINE__ );
+ sfree( workspace->d, __FILE__, __LINE__ );
+ sfree( workspace->q, __FILE__, __LINE__ );
+ sfree( workspace->p, __FILE__, __LINE__ );
+ break;
- case SDM_S:
- sfree( workspace->r, __FILE__, __LINE__ );
- sfree( workspace->d, __FILE__, __LINE__ );
- sfree( workspace->q, __FILE__, __LINE__ );
- break;
+ case SDM_S:
+ sfree( workspace->r, __FILE__, __LINE__ );
+ sfree( workspace->d, __FILE__, __LINE__ );
+ sfree( workspace->q, __FILE__, __LINE__ );
+ break;
- case BiCGStab_S:
- sfree( workspace->r, __FILE__, __LINE__ );
- sfree( workspace->r_hat, __FILE__, __LINE__ );
- sfree( workspace->d, __FILE__, __LINE__ );
- sfree( workspace->q, __FILE__, __LINE__ );
- sfree( workspace->q_hat, __FILE__, __LINE__ );
- sfree( workspace->p, __FILE__, __LINE__ );
- sfree( workspace->y, __FILE__, __LINE__ );
- sfree( workspace->z, __FILE__, __LINE__ );
- sfree( workspace->g, __FILE__, __LINE__ );
- break;
+ case BiCGStab_S:
+ sfree( workspace->r, __FILE__, __LINE__ );
+ sfree( workspace->r_hat, __FILE__, __LINE__ );
+ sfree( workspace->d, __FILE__, __LINE__ );
+ sfree( workspace->q, __FILE__, __LINE__ );
+ sfree( workspace->q_hat, __FILE__, __LINE__ );
+ sfree( workspace->p, __FILE__, __LINE__ );
+ sfree( workspace->y, __FILE__, __LINE__ );
+ sfree( workspace->z, __FILE__, __LINE__ );
+ sfree( workspace->g, __FILE__, __LINE__ );
+ break;
- default:
- fprintf( stderr, "[ERROR] Unknown charge method linear solver type. Terminating...\n" );
- exit( INVALID_INPUT );
- break;
- }
+ default:
+ fprintf( stderr, "[ERROR] Unknown charge method linear solver type. Terminating...\n" );
+ exit( INVALID_INPUT );
+ break;
+ }
- /* SpMV related */
+ /* SpMV related */
#if defined(_OPENMP)
- sfree( workspace->b_local, __FILE__, __LINE__ );
+ sfree( workspace->b_local, __FILE__, __LINE__ );
#endif
- /* level scheduling related */
- if ( control->cm_solver_pre_app_type == TRI_SOLVE_LEVEL_SCHED_PA ||
- control->cm_solver_pre_app_type == TRI_SOLVE_GC_PA )
- {
- sfree( workspace->row_levels_L, __FILE__, __LINE__ );
- sfree( workspace->level_rows_L, __FILE__, __LINE__ );
- sfree( workspace->level_rows_cnt_L, __FILE__, __LINE__ );
- sfree( workspace->row_levels_U, __FILE__, __LINE__ );
- sfree( workspace->level_rows_U, __FILE__, __LINE__ );
- sfree( workspace->level_rows_cnt_U, __FILE__, __LINE__ );
- sfree( workspace->top, __FILE__, __LINE__ );
- }
+ /* level scheduling related */
+ if ( control->cm_solver_pre_app_type == TRI_SOLVE_LEVEL_SCHED_PA ||
+ control->cm_solver_pre_app_type == TRI_SOLVE_GC_PA )
+ {
+ sfree( workspace->row_levels_L, __FILE__, __LINE__ );
+ sfree( workspace->level_rows_L, __FILE__, __LINE__ );
+ sfree( workspace->level_rows_cnt_L, __FILE__, __LINE__ );
+ sfree( workspace->row_levels_U, __FILE__, __LINE__ );
+ sfree( workspace->level_rows_U, __FILE__, __LINE__ );
+ sfree( workspace->level_rows_cnt_U, __FILE__, __LINE__ );
+ sfree( workspace->top, __FILE__, __LINE__ );
+ }
- /* graph coloring related */
- if ( control->cm_solver_pre_app_type == TRI_SOLVE_GC_PA )
- {
- sfree( workspace->color, __FILE__, __LINE__ );
- sfree( workspace->to_color, __FILE__, __LINE__ );
- sfree( workspace->conflict, __FILE__, __LINE__ );
- sfree( workspace->conflict_cnt, __FILE__, __LINE__ );
- sfree( workspace->recolor, __FILE__, __LINE__ );
- sfree( workspace->color_top, __FILE__, __LINE__ );
- sfree( workspace->permuted_row_col, __FILE__, __LINE__ );
- sfree( workspace->permuted_row_col_inv, __FILE__, __LINE__ );
- }
+ /* graph coloring related */
+ if ( control->cm_solver_pre_app_type == TRI_SOLVE_GC_PA )
+ {
+ sfree( workspace->color, __FILE__, __LINE__ );
+ sfree( workspace->to_color, __FILE__, __LINE__ );
+ sfree( workspace->conflict, __FILE__, __LINE__ );
+ sfree( workspace->conflict_cnt, __FILE__, __LINE__ );
+ sfree( workspace->recolor, __FILE__, __LINE__ );
+ sfree( workspace->color_top, __FILE__, __LINE__ );
+ sfree( workspace->permuted_row_col, __FILE__, __LINE__ );
+ sfree( workspace->permuted_row_col_inv, __FILE__, __LINE__ );
+ }
- /* graph coloring related OR ILUTP preconditioner */
- if ( control->cm_solver_pre_app_type == TRI_SOLVE_GC_PA
- || control->cm_solver_pre_comp_type == ILUTP_PC )
- {
- sfree( workspace->y_p, __FILE__, __LINE__ );
- sfree( workspace->x_p, __FILE__, __LINE__ );
- }
+ /* graph coloring related OR ILUTP preconditioner */
+ if ( control->cm_solver_pre_app_type == TRI_SOLVE_GC_PA
+ || control->cm_solver_pre_comp_type == ILUTP_PC )
+ {
+ sfree( workspace->y_p, __FILE__, __LINE__ );
+ sfree( workspace->x_p, __FILE__, __LINE__ );
+ }
- /* Jacobi iteration related */
- if ( control->cm_solver_pre_app_type == JACOBI_ITER_PA )
- {
- sfree( workspace->Dinv_L, __FILE__, __LINE__ );
- sfree( workspace->Dinv_U, __FILE__, __LINE__ );
- sfree( workspace->Dinv_b, __FILE__, __LINE__ );
- sfree( workspace->rp, __FILE__, __LINE__ );
- sfree( workspace->rp2, __FILE__, __LINE__ );
- }
+ /* Jacobi iteration related */
+ if ( control->cm_solver_pre_app_type == JACOBI_ITER_PA )
+ {
+ sfree( workspace->Dinv_L, __FILE__, __LINE__ );
+ sfree( workspace->Dinv_U, __FILE__, __LINE__ );
+ sfree( workspace->Dinv_b, __FILE__, __LINE__ );
+ sfree( workspace->rp, __FILE__, __LINE__ );
+ sfree( workspace->rp2, __FILE__, __LINE__ );
+ }
- /* ILUTP preconditioner related */
- if ( control->cm_solver_pre_comp_type == ILUTP_PC )
- {
- sfree( workspace->perm_ilutp, __FILE__, __LINE__ );
- }
+ /* ILUTP preconditioner related */
+ if ( control->cm_solver_pre_comp_type == ILUTP_PC )
+ {
+ sfree( workspace->perm_ilutp, __FILE__, __LINE__ );
+ }
- /* integrator storage */
- sfree( workspace->a, __FILE__, __LINE__ );
- sfree( workspace->f_old, __FILE__, __LINE__ );
- sfree( workspace->v_const, __FILE__, __LINE__ );
+ /* integrator storage */
+ sfree( workspace->a, __FILE__, __LINE__ );
+ sfree( workspace->f_old, __FILE__, __LINE__ );
+ sfree( workspace->v_const, __FILE__, __LINE__ );
#if defined(_OPENMP)
- sfree( workspace->f_local, __FILE__, __LINE__ );
+ sfree( workspace->f_local, __FILE__, __LINE__ );
#endif
- /* storage for analysis */
- if ( control->molec_anal || control->diffusion_coef )
- {
- sfree( workspace->mark, __FILE__, __LINE__ );
- sfree( workspace->old_mark, __FILE__, __LINE__ );
+ /* storage for analysis */
+ if ( control->molec_anal || control->diffusion_coef )
+ {
+ sfree( workspace->mark, __FILE__, __LINE__ );
+ sfree( workspace->old_mark, __FILE__, __LINE__ );
+ }
+
+ if ( control->diffusion_coef )
+ {
+ sfree( workspace->x_old, __FILE__, __LINE__ );
+ }
}
- if ( control->diffusion_coef )
+ if ( reset == FALSE && (control->geo_format == BGF
+ || control->geo_format == ASCII_RESTART
+ || control->geo_format == BINARY_RESTART) )
{
- sfree( workspace->x_old, __FILE__, __LINE__ );
+ sfree( workspace->map_serials, __FILE__, __LINE__ );
}
if ( reset == FALSE )
@@ -1635,6 +1649,8 @@ static void Finalize_Workspace( reax_system *system, control_params *control,
sfree( workspace->f_tor, __FILE__, __LINE__ );
sfree( workspace->f_con, __FILE__, __LINE__ );
#endif
+
+ workspace->allocated = FALSE;
}
@@ -1677,73 +1693,77 @@ static void Finalize_Lists( reax_list **lists )
void Finalize_Out_Controls( reax_system *system, control_params *control,
static_storage *workspace, output_controls *out_control )
{
- if ( out_control->write_steps > 0 )
- {
- sfclose( out_control->trj, __FILE__, __LINE__ );
- }
-
- if ( out_control->log_update_freq > 0 )
+ if ( out_control->allocated == TRUE )
{
- sfclose( out_control->out, __FILE__, __LINE__ );
- sfclose( out_control->pot, __FILE__, __LINE__ );
- sfclose( out_control->log, __FILE__, __LINE__ );
- }
-
- if ( control->ensemble == sNPT || control->ensemble == iNPT
- || control->ensemble == aNPT || control->compute_pressure == TRUE )
- {
- sfclose( out_control->prs, __FILE__, __LINE__ );
- }
+ if ( out_control->write_steps > 0 )
+ {
+ sfclose( out_control->trj, __FILE__, __LINE__ );
+ }
- if ( control->molec_anal )
- {
- sfclose( out_control->mol, __FILE__, __LINE__ );
+ if ( out_control->log_update_freq > 0 )
+ {
+ sfclose( out_control->out, __FILE__, __LINE__ );
+ sfclose( out_control->pot, __FILE__, __LINE__ );
+ sfclose( out_control->log, __FILE__, __LINE__ );
+ }
- if ( control->num_ignored )
+ if ( control->ensemble == sNPT || control->ensemble == iNPT
+ || control->ensemble == aNPT || control->compute_pressure == TRUE )
{
- sfclose( out_control->ign, __FILE__, __LINE__ );
+ sfclose( out_control->prs, __FILE__, __LINE__ );
}
- }
- if ( control->dipole_anal )
- {
- sfclose( out_control->dpl, __FILE__, __LINE__ );
- }
+ if ( control->molec_anal )
+ {
+ sfclose( out_control->mol, __FILE__, __LINE__ );
- if ( control->diffusion_coef )
- {
- sfclose( out_control->drft, __FILE__, __LINE__ );
- }
+ if ( control->num_ignored )
+ {
+ sfclose( out_control->ign, __FILE__, __LINE__ );
+ }
+ }
+ if ( control->dipole_anal )
+ {
+ sfclose( out_control->dpl, __FILE__, __LINE__ );
+ }
+
+ if ( control->diffusion_coef )
+ {
+ sfclose( out_control->drft, __FILE__, __LINE__ );
+ }
#if defined(TEST_ENERGY)
- sfclose( out_control->ebond, __FILE__, __LINE__ );
- sfclose( out_control->elp, __FILE__, __LINE__ );
- sfclose( out_control->eov, __FILE__, __LINE__ );
- sfclose( out_control->eun, __FILE__, __LINE__ );
- sfclose( out_control->eval, __FILE__, __LINE__ );
- sfclose( out_control->epen, __FILE__, __LINE__ );
- sfclose( out_control->ecoa, __FILE__, __LINE__ );
- sfclose( out_control->ehb, __FILE__, __LINE__ );
- sfclose( out_control->etor, __FILE__, __LINE__ );
- sfclose( out_control->econ, __FILE__, __LINE__ );
- sfclose( out_control->evdw, __FILE__, __LINE__ );
- sfclose( out_control->ecou, __FILE__, __LINE__ );
+ sfclose( out_control->ebond, __FILE__, __LINE__ );
+ sfclose( out_control->elp, __FILE__, __LINE__ );
+ sfclose( out_control->eov, __FILE__, __LINE__ );
+ sfclose( out_control->eun, __FILE__, __LINE__ );
+ sfclose( out_control->eval, __FILE__, __LINE__ );
+ sfclose( out_control->epen, __FILE__, __LINE__ );
+ sfclose( out_control->ecoa, __FILE__, __LINE__ );
+ sfclose( out_control->ehb, __FILE__, __LINE__ );
+ sfclose( out_control->etor, __FILE__, __LINE__ );
+ sfclose( out_control->econ, __FILE__, __LINE__ );
+ sfclose( out_control->evdw, __FILE__, __LINE__ );
+ sfclose( out_control->ecou, __FILE__, __LINE__ );
#endif
#if defined(TEST_FORCES)
- sfclose( out_control->fbo, __FILE__, __LINE__ );
- sfclose( out_control->fdbo, __FILE__, __LINE__ );
- sfclose( out_control->fbond, __FILE__, __LINE__ );
- sfclose( out_control->flp, __FILE__, __LINE__ );
- sfclose( out_control->fatom, __FILE__, __LINE__ );
- sfclose( out_control->f3body, __FILE__, __LINE__ );
- sfclose( out_control->fhb, __FILE__, __LINE__ );
- sfclose( out_control->f4body, __FILE__, __LINE__ );
- sfclose( out_control->fnonb, __FILE__, __LINE__ );
- sfclose( out_control->ftot, __FILE__, __LINE__ );
- sfclose( out_control->ftot2, __FILE__, __LINE__ );
+ sfclose( out_control->fbo, __FILE__, __LINE__ );
+ sfclose( out_control->fdbo, __FILE__, __LINE__ );
+ sfclose( out_control->fbond, __FILE__, __LINE__ );
+ sfclose( out_control->flp, __FILE__, __LINE__ );
+ sfclose( out_control->fatom, __FILE__, __LINE__ );
+ sfclose( out_control->f3body, __FILE__, __LINE__ );
+ sfclose( out_control->fhb, __FILE__, __LINE__ );
+ sfclose( out_control->f4body, __FILE__, __LINE__ );
+ sfclose( out_control->fnonb, __FILE__, __LINE__ );
+ sfclose( out_control->ftot, __FILE__, __LINE__ );
+ sfclose( out_control->ftot2, __FILE__, __LINE__ );
#endif
+ }
+
+ out_control->allocated = FALSE;
}
diff --git a/sPuReMD/src/reax_types.h b/sPuReMD/src/reax_types.h
index 4bf2c52a..49975296 100644
--- a/sPuReMD/src/reax_types.h
+++ b/sPuReMD/src/reax_types.h
@@ -868,10 +868,12 @@ struct grid
struct reax_system
{
- /* 0 if struct members are NOT allocated, 1 otherwise */
+ /* 0 if struct members for first phase (file I/O) are NOT allocated, 1 otherwise */
int prealloc_allocated;
/* 0 if struct members are NOT allocated, 1 otherwise */
int ffield_params_allocated;
+ /* FALSE if struct members are NOT allocated, TRUE otherwise */
+ int allocated;
/* number of local (non-periodic image) atoms for the current simulation */
int N;
#if defined(QMMM)
@@ -1525,6 +1527,8 @@ struct LR_lookup_table
struct static_storage
{
+ /* FALSE if struct members are NOT allocated, TRUE otherwise */
+ int allocated;
/* bond order related storage */
real *total_bond_order;
real *Deltap;
@@ -1748,15 +1752,27 @@ struct reax_list
struct output_controls
{
+ /* FALSE if struct members are NOT allocated, TRUE otherwise */
+ int allocated;
+ /* trajectory file */
FILE *trj;
+ /* system-wide info file */
FILE *out;
+ /* potential file */
FILE *pot;
+ /* log file */
FILE *log;
+ /**/
FILE *mol;
+ /**/
FILE *ign;
+ /**/
FILE *dpl;
+ /**/
FILE *drft;
+ /**/
FILE *pdb;
+ /**/
FILE *prs;
int write_steps;
@@ -1773,7 +1789,7 @@ struct output_controls
* (excluding trajectory and restart files) */
int log_update_freq;
- /* trajectory file pointer pointers */
+ /* trajectory-related function pointers */
write_header_function write_header;
append_traj_frame_function append_traj_frame;
write_function write;
diff --git a/sPuReMD/src/spuremd.c b/sPuReMD/src/spuremd.c
index f8cb8ec6..81feaa42 100644
--- a/sPuReMD/src/spuremd.c
+++ b/sPuReMD/src/spuremd.c
@@ -186,9 +186,11 @@ static void Initialize_Top_Level_Structs( spuremd_handle * handle )
/* second-level initializations */
handle->system->prealloc_allocated = FALSE;
+ handle->system->allocated = FALSE;
handle->system->ffield_params_allocated = FALSE;
handle->system->g.allocated = FALSE;
+ handle->workspace->allocated = FALSE;
handle->workspace->H.allocated = FALSE;
handle->workspace->H_full.allocated = FALSE;
handle->workspace->H_sp.allocated = FALSE;
@@ -203,6 +205,8 @@ static void Initialize_Top_Level_Structs( spuremd_handle * handle )
{
handle->lists[i]->allocated = FALSE;
}
+
+ handle->out_control->allocated = FALSE;
}
diff --git a/tools/driver.py b/tools/driver.py
index fd0f1000..f1baa28e 100644
--- a/tools/driver.py
+++ b/tools/driver.py
@@ -375,8 +375,7 @@ if __name__ == '__main__':
reset.restype = c_int
get_atom_positions = lib.get_atom_positions
- get_atom_positions.argtypes = [c_void_p, POINTER(c_double),
- POINTER(c_double), POINTER(c_double)]
+ get_atom_positions.argtypes = [c_void_p, POINTER(c_double)]
get_atom_positions.restype = c_int
get_atom_charges = lib.get_atom_charges
@@ -456,10 +455,8 @@ if __name__ == '__main__':
print("{0:24}|{1:24}|{2:24}".format("Total Energy", "Kinetic Energy", "Potential Energy"))
ret = simulate(handle)
- x = (c_double * 6540)()
- y = (c_double * 6540)()
- z = (c_double * 6540)()
- atoms = get_atom_positions(handle, x, y, z)
+ x = (c_double * (3 * 6540))()
+ atoms = get_atom_positions(handle, x)
q = (c_double * 6540)()
atoms = get_atom_charges(handle, q)
@@ -468,7 +465,7 @@ if __name__ == '__main__':
print("{0:9}|{1:24}|{2:24}|{3:24}|{4:24}".format("Atom Num", "x-Position", "y-Position", "z-Position", "Charge"))
for i in range(10):
print("{0:9d} {1:24.15f} {2:24.15f} {3:24.15f} {4:24.15f}".format(
- i + 1, x[i], y[i], z[i], q[i]))
+ i + 1, x[3*i], x[3*i+1], x[3*i+2], q[i]))
ret = reset(handle, b"data/benchmarks/silica/silica_6000.pdb",
b"data/benchmarks/silica/ffield-bio",
@@ -478,10 +475,8 @@ if __name__ == '__main__':
print("{0:24}|{1:24}|{2:24}".format("Total Energy", "Kinetic Energy", "Potential Energy"))
ret = simulate(handle)
- x = (c_double * 6000)()
- y = (c_double * 6000)()
- z = (c_double * 6000)()
- atoms = get_atom_positions(handle, x, y, z)
+ x = (c_double * (3 * 6000))()
+ atoms = get_atom_positions(handle, x)
q = (c_double * 6000)()
atoms = get_atom_charges(handle, q)
@@ -490,7 +485,7 @@ if __name__ == '__main__':
print("{0:9}|{1:24}|{2:24}|{3:24}|{4:24}".format("Atom Num", "x-Position", "y-Position", "z-Position", "Charge"))
for i in range(10):
print("{0:9d} {1:24.15f} {2:24.15f} {3:24.15f} {4:24.15f}".format(
- i + 1, x[i], y[i], z[i], q[i]))
+ i + 1, x[3*i], x[3*i+1], x[3*i+2], q[i]))
conn.close()
cleanup(handle)
--
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