diff --git a/sPuReMD/src/allocate.c b/sPuReMD/src/allocate.c
index 70946afa7cbcba94a88d56c1df839a7e487c22ac..2531612a65ccfe2019e97bb20b743dc84cabc384 100644
--- a/sPuReMD/src/allocate.c
+++ b/sPuReMD/src/allocate.c
@@ -28,12 +28,14 @@
/* allocate space for atoms */
void PreAllocate_Space( reax_system * const system,
control_params const * const control,
- static_storage * const workspace, int n, int first_run )
+ static_storage * const workspace, int n )
{
int i;
- if ( first_run == TRUE )
+ if ( system->prealloc_allocated == FALSE )
{
+ system->prealloc_allocated = TRUE;
+
system->atoms = scalloc( n, sizeof(reax_atom),
"PreAllocate_Space::system->atoms" );
workspace->orig_id = scalloc( n, sizeof(int),
diff --git a/sPuReMD/src/allocate.h b/sPuReMD/src/allocate.h
index ed8664665c7484f44cd2296c13200057c65b47c5..1716bf42ecb307686a1f6b935f09c7298b1e605e 100644
--- a/sPuReMD/src/allocate.h
+++ b/sPuReMD/src/allocate.h
@@ -26,7 +26,7 @@
void PreAllocate_Space( reax_system * const, control_params const * const,
- static_storage * const, int, int );
+ static_storage * const, int );
void Reallocate( reax_system * const, control_params const * const,
static_storage * const, reax_list ** const, int );
diff --git a/sPuReMD/src/ffield.c b/sPuReMD/src/ffield.c
index 716fcfb67a6a2868eb6dd35c998e502b1df53136..84028b332bee5b0113f46d10fe1eff23024e9e4f 100644
--- a/sPuReMD/src/ffield.c
+++ b/sPuReMD/src/ffield.c
@@ -26,7 +26,8 @@
#include "tool_box.h"
-void Read_Force_Field( FILE *fp, reax_interaction *reax, int first_run )
+void Read_Force_Field( FILE *fp, reax_system * const system,
+ reax_interaction * const reax )
{
char *s;
char **tmp;
@@ -60,7 +61,7 @@ void Read_Force_Field( FILE *fp, reax_interaction *reax, int first_run )
return;
}
- if ( first_run == TRUE )
+ if ( system->ffield_params_allocated == FALSE )
{
reax->gp.l = (real*) smalloc( sizeof(real) * n,
"Read_Force_Field::reax->gp-l" );
@@ -97,8 +98,10 @@ void Read_Force_Field( FILE *fp, reax_interaction *reax, int first_run )
fgets( s, MAX_LINE, fp );
fgets( s, MAX_LINE, fp );
- if ( first_run == TRUE )
+ if ( system->ffield_params_allocated == FALSE )
{
+ system->ffield_params_allocated = TRUE;
+
/* Allocating structures in reax_interaction */
reax->sbp = (single_body_parameters*) scalloc( n, sizeof(single_body_parameters),
"Read_Force_Field::reax->sbp" );
diff --git a/sPuReMD/src/ffield.h b/sPuReMD/src/ffield.h
index 47b0eb6b4d9fcec9e7fc792f1bd15b97cd022c5d..692e772c18e776bea1c1b508409b41bde90347ff 100644
--- a/sPuReMD/src/ffield.h
+++ b/sPuReMD/src/ffield.h
@@ -25,7 +25,7 @@
#include "reax_types.h"
-void Read_Force_Field( FILE *, reax_interaction *, int );
+void Read_Force_Field( FILE *, reax_system * const, reax_interaction * const );
#endif
diff --git a/sPuReMD/src/geo_tools.c b/sPuReMD/src/geo_tools.c
index 94472a6d7bd4e76b392b0f234a6c6402b021cb56..068f14088a07f85a14378e06e16e0cfd49ddafff 100644
--- a/sPuReMD/src/geo_tools.c
+++ b/sPuReMD/src/geo_tools.c
@@ -283,7 +283,7 @@ static int Count_Atoms( reax_system *system, FILE *fp, int geo_format )
void Read_Geo( const char * const geo_file, reax_system* system, control_params *control,
- simulation_data *data, static_storage *workspace, int first_run )
+ simulation_data *data, static_storage *workspace )
{
FILE *geo;
int i, n, serial, top;
@@ -302,9 +302,9 @@ void Read_Geo( const char * const geo_file, reax_system* system, control_params
/* count atoms and allocate storage */
n = Count_Atoms( system, geo, CUSTOM );
- if ( first_run == TRUE || n > system->N )
+ if ( system->prealloc_allocated == FALSE || n > system->N )
{
- PreAllocate_Space( system, control, workspace, n, first_run );
+ PreAllocate_Space( system, control, workspace, n );
}
system->N = n;
@@ -339,7 +339,7 @@ void Read_Geo( const char * const geo_file, reax_system* system, control_params
void Read_PDB( const char * const pdb_file, reax_system* system, control_params *control,
- simulation_data *data, static_storage *workspace, int first_run )
+ simulation_data *data, static_storage *workspace )
{
int i, n, c, c1, pdb_serial, top;
FILE *pdb;
@@ -370,9 +370,9 @@ void Read_PDB( const char * const pdb_file, reax_system* system, control_params
}
n = Count_Atoms( system, pdb, PDB );
- if ( first_run == TRUE || n > system->N )
+ if ( system->prealloc_allocated == FALSE || n > system->N )
{
- PreAllocate_Space( system, control, workspace, n, first_run );
+ PreAllocate_Space( system, control, workspace, n );
}
system->N = n;
@@ -613,7 +613,7 @@ void Write_PDB( reax_system* system, reax_list* bonds, simulation_data *data,
void Read_BGF( const char * const bgf_file, reax_system* system, control_params *control,
- simulation_data *data, static_storage *workspace, int first_run )
+ simulation_data *data, static_storage *workspace )
{
FILE *bgf;
char **tokens;
@@ -662,9 +662,9 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
sfclose( bgf, "Read_BGF::bgf" );
- if ( first_run == TRUE || n > system->N )
+ if ( system->prealloc_allocated == FALSE || n > system->N )
{
- PreAllocate_Space( system, control, workspace, n, first_run );
+ PreAllocate_Space( system, control, workspace, n );
}
system->N = n;
diff --git a/sPuReMD/src/geo_tools.h b/sPuReMD/src/geo_tools.h
index af91cb3c349e50c6c30b2191d8db2a943a8cf856..26028db94ea798e8c8e542b3692b20119c3a4a1d 100644
--- a/sPuReMD/src/geo_tools.h
+++ b/sPuReMD/src/geo_tools.h
@@ -26,16 +26,16 @@
void Read_Geo( const char * const, reax_system *, control_params *,
- simulation_data *, static_storage *, int );
+ simulation_data *, static_storage * );
void Read_PDB( const char * const, reax_system *, control_params *,
- simulation_data *, static_storage *, int );
-
-void Read_BGF( const char * const, reax_system *, control_params *,
- simulation_data *, static_storage *, int );
+ simulation_data *, static_storage * );
void Write_PDB( reax_system *, reax_list *, simulation_data *,
control_params *, static_storage *, output_controls * );
+void Read_BGF( const char * const, reax_system *, control_params *,
+ simulation_data *, static_storage * );
+
#endif
diff --git a/sPuReMD/src/init_md.c b/sPuReMD/src/init_md.c
index 6b8929150277dd33757c3702f0ecbd22d68375f5..caf475ee05180bbca263509e7c9ad781995e8307 100644
--- a/sPuReMD/src/init_md.c
+++ b/sPuReMD/src/init_md.c
@@ -1318,6 +1318,9 @@ static void Finalize_System( reax_system *system, control_params *control,
int i, j, k;
reax_interaction *reax;
+ system->prealloc_allocated = FALSE;
+ system->ffield_params_allocated = FALSE;
+
reax = &system->reax_param;
Finalize_Grid( system );
diff --git a/sPuReMD/src/reax_types.h b/sPuReMD/src/reax_types.h
index 6b5defeecf16afd2e64d0001d1c9f39f1ef53e89..fa5401d1a3df3d672a7103d0c562c584001a3b10 100644
--- a/sPuReMD/src/reax_types.h
+++ b/sPuReMD/src/reax_types.h
@@ -854,6 +854,10 @@ struct grid
struct reax_system
{
+ /* 0 if struct members are NOT allocated, 1 otherwise */
+ int prealloc_allocated;
+ /* 0 if struct members are NOT allocated, 1 otherwise */
+ int ffield_params_allocated;
/* number of local (non-periodic image) atoms for the current simulation */
int N;
/* max. number of local (non-periodic image) atoms across all simulations */
@@ -1765,8 +1769,6 @@ struct spuremd_handle
reax_list **lists;
/* Output controls */
output_controls *out_control;
- /* TRUE for first simulation, FALSE otherwise */
- int first_run;
/* TRUE if file I/O for simulation output enabled, FALSE otherwise */
int output_enabled;
/* TRUE if reallocation is required due to num. atoms increasing, FALSE otherwise */
diff --git a/sPuReMD/src/restart.c b/sPuReMD/src/restart.c
index 4afaa3676065c25c6f3364d8386cc019ade01b54..34ad174c5fa00b503ce9f012facac8e6692f738e 100644
--- a/sPuReMD/src/restart.c
+++ b/sPuReMD/src/restart.c
@@ -73,7 +73,7 @@ void Write_Binary_Restart( reax_system *system, control_params *control,
void Read_Binary_Restart( const char * const fname, reax_system *system,
control_params *control, simulation_data *data,
- static_storage *workspace, int first_run )
+ static_storage *workspace )
{
int i;
FILE *fres;
@@ -108,13 +108,13 @@ void Read_Binary_Restart( const char * const fname, reax_system *system,
system->box.box[2][0], system->box.box[2][1], system->box.box[2][2] );
#endif
- if ( first_run == TRUE || res_header.N > system->N )
+ if ( system->prealloc_allocated == FALSE || res_header.N > system->N )
{
- PreAllocate_Space( system, control, workspace, res_header.N, first_run );
+ PreAllocate_Space( system, control, workspace, res_header.N );
}
system->N = res_header.N;
- if ( first_run == TRUE )
+ if ( system->prealloc_allocated == FALSE )
{
workspace->map_serials = scalloc( MAX_ATOM_ID, sizeof(int),
"Read_Binary_Restart::workspace->map_serials" );
@@ -191,7 +191,7 @@ void Write_ASCII_Restart( reax_system *system, control_params *control,
void Read_ASCII_Restart( const char * const fname, reax_system *system,
control_params *control, simulation_data *data,
- static_storage *workspace, int first_run )
+ static_storage *workspace )
{
int i, n;
FILE *fres;
@@ -222,13 +222,13 @@ void Read_ASCII_Restart( const char * const fname, reax_system *system,
system->box.box[2][0], system->box.box[2][1], system->box.box[2][2] );
#endif
- if ( first_run == TRUE || n > system->N )
+ if ( system->prealloc_allocated == FALSE || n > system->N )
{
- PreAllocate_Space( system, control, workspace, n, first_run );
+ PreAllocate_Space( system, control, workspace, n );
}
system->N = n;
- if ( first_run == TRUE )
+ if ( system->prealloc_allocated == FALSE )
{
workspace->map_serials = scalloc( MAX_ATOM_ID, sizeof(int),
"Read_ASCII_Restart::workspace->map_serials" );
diff --git a/sPuReMD/src/restart.h b/sPuReMD/src/restart.h
index 41e221eaafc0c99b558b0116344cb83b45cecef8..0bc101cfa561bb9d3234d7ab97efad08d8d0f6fe 100644
--- a/sPuReMD/src/restart.h
+++ b/sPuReMD/src/restart.h
@@ -54,11 +54,12 @@ typedef struct
#define READ_RESTART_LINE " %d %d %s %lf %lf %lf %lf %lf %lf"
void Write_Restart( reax_system *, control_params *,
- simulation_data *, static_storage *, output_controls * );
+ simulation_data *, static_storage *, output_controls * );
void Read_Binary_Restart( const char * const, reax_system *, control_params *,
- simulation_data *, static_storage *, int );
+ simulation_data *, static_storage * );
+
void Read_ASCII_Restart( const char * const, reax_system *, control_params *,
- simulation_data *, static_storage *, int );
+ simulation_data *, static_storage * );
#endif
diff --git a/sPuReMD/src/spuremd.c b/sPuReMD/src/spuremd.c
index a63cf59a2bb45a58228c7a14fef0fa36e16e077a..41fa92f7759836aac66621834b68d3a1c180fe10 100644
--- a/sPuReMD/src/spuremd.c
+++ b/sPuReMD/src/spuremd.c
@@ -99,37 +99,37 @@ static void Read_Input_Files( const char * const geo_file,
const char * const ffield_file, const char * const control_file,
reax_system * const system, control_params * const control,
simulation_data * const data, static_storage * const workspace,
- output_controls * const out_control, int first_run )
+ output_controls * const out_control )
{
FILE *ffield, *ctrl;
ffield = sfopen( ffield_file, "r" );
ctrl = sfopen( control_file, "r" );
- Read_Force_Field( ffield, &system->reax_param, first_run );
+ Read_Force_Field( ffield, system, &system->reax_param );
Read_Control_File( ctrl, system, control, out_control );
if ( control->geo_format == CUSTOM )
{
- Read_Geo( geo_file, system, control, data, workspace, first_run );
+ Read_Geo( geo_file, system, control, data, workspace );
}
else if ( control->geo_format == PDB )
{
- Read_PDB( geo_file, system, control, data, workspace, first_run );
+ Read_PDB( geo_file, system, control, data, workspace );
}
else if ( control->geo_format == BGF )
{
- Read_BGF( geo_file, system, control, data, workspace, first_run );
+ Read_BGF( geo_file, system, control, data, workspace );
}
else if ( control->geo_format == ASCII_RESTART )
{
- Read_ASCII_Restart( geo_file, system, control, data, workspace, first_run );
+ Read_ASCII_Restart( geo_file, system, control, data, workspace );
control->restart = TRUE;
}
else if ( control->geo_format == BINARY_RESTART )
{
- Read_Binary_Restart( geo_file, system, control, data, workspace, first_run );
+ Read_Binary_Restart( geo_file, system, control, data, workspace );
control->restart = TRUE;
}
else
@@ -167,6 +167,8 @@ void* setup( const char * const geo_file, const char * const ffield_file,
/* second-level allocations */
spmd_handle->system = smalloc( sizeof(reax_system),
"Setup::spmd_handle->system" );
+ spmd_handle->system->prealloc_allocated = FALSE;
+ spmd_handle->system->ffield_params_allocated = FALSE;
spmd_handle->system->g.allocated = FALSE;
spmd_handle->control = smalloc( sizeof(control_params),
@@ -198,7 +200,6 @@ void* setup( const char * const geo_file, const char * const ffield_file,
spmd_handle->out_control = smalloc( sizeof(output_controls),
"Setup::spmd_handle->out_control" );
- spmd_handle->first_run = TRUE;
spmd_handle->output_enabled = TRUE;
spmd_handle->realloc = TRUE;
spmd_handle->callback = NULL;
@@ -207,7 +208,7 @@ void* setup( const char * const geo_file, const char * const ffield_file,
Read_Input_Files( geo_file, ffield_file, control_file,
spmd_handle->system, spmd_handle->control,
spmd_handle->data, spmd_handle->workspace,
- spmd_handle->out_control, spmd_handle->first_run );
+ spmd_handle->out_control );
spmd_handle->system->N_max = (int) CEIL( SAFE_ZONE * spmd_handle->system->N );
@@ -453,14 +454,13 @@ int reset( const void * const handle, const char * const geo_file,
spmd_handle->workspace, spmd_handle->out_control );
}
- spmd_handle->first_run = FALSE;
spmd_handle->realloc = FALSE;
spmd_handle->data->sim_id++;
Read_Input_Files( geo_file, ffield_file, control_file,
spmd_handle->system, spmd_handle->control,
spmd_handle->data, spmd_handle->workspace,
- spmd_handle->out_control, spmd_handle->first_run );
+ spmd_handle->out_control );
if ( spmd_handle->system->N > spmd_handle->system->N_max )
{