diff --git a/sPuReMD/src/allocate.c b/sPuReMD/src/allocate.c
index 92c1d80dba39f85a214db63c377b210d741f2843..4f980bc8c07a26672966c18420cfbfd2eb3f77cd 100644
--- a/sPuReMD/src/allocate.c
+++ b/sPuReMD/src/allocate.c
@@ -36,24 +36,19 @@ void PreAllocate_Space( reax_system * const system,
{
system->prealloc_allocated = TRUE;
- system->atoms = scalloc( n, sizeof(reax_atom),
- "PreAllocate_Space::system->atoms" );
- workspace->orig_id = scalloc( n, sizeof(int),
- "PreAllocate_Space::workspace->orid_id" );
+ system->atoms = scalloc( n, sizeof(reax_atom), __FILE__, __LINE__ );
+ workspace->orig_id = scalloc( n, sizeof(int), __FILE__, __LINE__ );
/* bond restriction info */
if ( control->restrict_bonds )
{
- workspace->restricted = scalloc( n, sizeof(int),
- "PreAllocate_Space::workspace->restricted_atoms" );
-
- workspace->restricted_list = scalloc( n, sizeof(int*),
- "PreAllocate_Space::workspace->restricted_list" );
+ workspace->restricted = scalloc( n, sizeof(int), __FILE__, __LINE__ );
+ workspace->restricted_list = scalloc( n, sizeof(int*), __FILE__, __LINE__ );
for ( i = 0; i < n; ++i )
{
workspace->restricted_list[i] = scalloc( MAX_RESTRICT, sizeof(int),
- "PreAllocate_Space::workspace->restricted_list[i]" );
+ __FILE__, __LINE__ );
}
}
@@ -62,48 +57,40 @@ void PreAllocate_Space( reax_system * const system,
|| control->geo_format == BINARY_RESTART )
{
workspace->map_serials = scalloc( MAX_ATOM_ID, sizeof(int),
- "Read_BGF::workspace->map_serials" );
+ __FILE__, __LINE__ );
}
}
else
{
- sfree( system->atoms, "PreAllocate_Space::system->atoms" );
- sfree( workspace->orig_id, "PreAllocate_Space::workspace->orid_id" );
+ sfree( system->atoms, __FILE__, __LINE__ );
+ sfree( workspace->orig_id, __FILE__, __LINE__ );
/* bond restriction info */
if ( control->restrict_bonds )
{
- sfree( workspace->restricted,
- "PreAllocate_Space::workspace->restricted_atoms" );
+ sfree( workspace->restricted, __FILE__, __LINE__ );
for ( i = 0; i < n; ++i )
{
- sfree( workspace->restricted_list[i],
- "PreAllocate_Space::workspace->restricted_list[i]" );
+ sfree( workspace->restricted_list[i], __FILE__, __LINE__ );
}
- sfree( workspace->restricted_list,
- "PreAllocate_Space::workspace->restricted_list" );
+ sfree( workspace->restricted_list, __FILE__, __LINE__ );
}
- system->atoms = scalloc( n, sizeof(reax_atom),
- "PreAllocate_Space::system->atoms" );
- workspace->orig_id = scalloc( n, sizeof(int),
- "PreAllocate_Space::workspace->orid_id" );
+ system->atoms = scalloc( n, sizeof(reax_atom), __FILE__, __LINE__ );
+ workspace->orig_id = scalloc( n, sizeof(int), __FILE__, __LINE__ );
/* bond restriction info */
if ( control->restrict_bonds )
{
- workspace->restricted = scalloc( n, sizeof(int),
- "PreAllocate_Space::workspace->restricted_atoms" );
-
- workspace->restricted_list = scalloc( n, sizeof(int*),
- "PreAllocate_Space::workspace->restricted_list" );
+ workspace->restricted = scalloc( n, sizeof(int), __FILE__, __LINE__ );
+ workspace->restricted_list = scalloc( n, sizeof(int*), __FILE__, __LINE__ );
for ( i = 0; i < n; ++i )
{
workspace->restricted_list[i] = scalloc( MAX_RESTRICT, sizeof(int),
- "PreAllocate_Space::workspace->restricted_list[i]" );
+ __FILE__, __LINE__ );
}
}
}
@@ -136,9 +123,9 @@ void Allocate_Matrix( sparse_matrix * const H, int n, int n_max, int m )
H->n_max = n_max;
H->m = m;
- H->start = smalloc( sizeof(unsigned int) * (n_max + 1), "Allocate_Matrix::H->start" );
- H->j = smalloc( sizeof(unsigned int) * m, "Allocate_Matrix::H->j" );
- H->val = smalloc( sizeof(real) * m, "Allocate_Matrix::H->val" );
+ H->start = smalloc( sizeof(unsigned int) * (n_max + 1), __FILE__, __LINE__ );
+ H->j = smalloc( sizeof(unsigned int) * m, __FILE__, __LINE__ );
+ H->val = smalloc( sizeof(real) * m, __FILE__, __LINE__ );
}
@@ -150,9 +137,9 @@ void Deallocate_Matrix( sparse_matrix * const H )
{
H->allocated = FALSE;
- sfree( H->start, "Deallocate_Matrix::H->start" );
- sfree( H->j, "Deallocate_Matrix::H->j" );
- sfree( H->val, "Deallocate_Matrix::H->val" );
+ sfree( H->start, __FILE__, __LINE__ );
+ sfree( H->j, __FILE__, __LINE__ );
+ sfree( H->val, __FILE__, __LINE__ );
}
@@ -196,8 +183,7 @@ static void Reallocate_Initialize_HBond_List( int n, int num_h, int num_h_max,
{
int i, num_hbonds, *hb_top;
- hb_top = scalloc( n, sizeof(int),
- "Reallocate_Initialize_HBond_List::hb_top" );
+ hb_top = scalloc( n, sizeof(int), __FILE__, __LINE__ );
num_hbonds = 0;
for ( i = 0; i < n; ++i )
@@ -218,7 +204,7 @@ static void Reallocate_Initialize_HBond_List( int n, int num_h, int num_h_max,
Initialize_HBond_List( n, h_index, hb_top, hbond_list );
- sfree( hb_top, "Reallocate_Initialize_HBond_List::hb_top" );
+ sfree( hb_top, __FILE__, __LINE__ );
}
@@ -249,8 +235,7 @@ static void Reallocate_Initialize_Bond_List( int n, int n_max,
int i;
int *bond_top;
- bond_top = (int *) scalloc( n, sizeof(int),
- "Reallocate_Initialize_Bond_List::hb_top" );
+ bond_top = scalloc( n, sizeof(int), __FILE__, __LINE__ );
*num_bonds = 0;
*est_3body = 0;
@@ -270,7 +255,7 @@ static void Reallocate_Initialize_Bond_List( int n, int n_max,
Initialize_Bond_List( bond_top, bond_list );
- sfree( bond_top, "Reallocate_Initialize_Bond_List::bond_top" );
+ sfree( bond_top, __FILE__, __LINE__ );
}
@@ -357,9 +342,9 @@ void Reallocate( reax_system * const system, control_params const * const contro
{
for ( k = 0; k < g->ncell_max[2]; k++ )
{
- sfree( g->atoms[i][j][k], "Reallocate::g->atoms[i][j][k]" );
+ sfree( g->atoms[i][j][k], __FILE__, __LINE__ );
g->atoms[i][j][k] = scalloc( workspace->realloc.gcell_atoms, sizeof(int),
- "Reallocate::g->atoms[i][j][k]" );
+ __FILE__, __LINE__ );
}
}
}
diff --git a/sPuReMD/src/analyze.c b/sPuReMD/src/analyze.c
index 33e5e1cdf0644add0906051fd8de36fa5002b7bd..e75da430ac5a29e48ccab8d85e3fd5341660e009 100644
--- a/sPuReMD/src/analyze.c
+++ b/sPuReMD/src/analyze.c
@@ -1069,28 +1069,28 @@ void Analysis( reax_system *system, control_params *control,
steps = data->step - data->prev_steps;
- if ( steps == 1 )
+ /****** Molecular Analysis ******/
+ if ( control->molec_anal
+ && steps % control->freq_molec_anal == 0 )
{
- if ( lists[OLD_BONDS]->allocated == FALSE )
+ if ( steps == 1 )
{
- Make_List( lists[BONDS]->n, lists[BONDS]->n_max, lists[BONDS]->total_intrs,
- TYP_BOND, lists[OLD_BONDS] );
- }
+ if ( lists[OLD_BONDS]->allocated == FALSE )
+ {
+ Make_List( lists[BONDS]->n, lists[BONDS]->n_max, lists[BONDS]->total_intrs,
+ TYP_BOND, lists[OLD_BONDS] );
+ }
- if ( control->molec_anal == REACTIONS )
- {
- Copy_Bond_List( system, control, lists );
- }
- if ( control->diffusion_coef )
- {
- Copy_Positions( system, workspace );
+ if ( control->molec_anal == REACTIONS )
+ {
+ Copy_Bond_List( system, control, lists );
+ }
+ if ( control->diffusion_coef )
+ {
+ Copy_Positions( system, workspace );
+ }
}
- }
- /****** Molecular Analysis ******/
- if ( control->molec_anal
- && steps % control->freq_molec_anal == 0 )
- {
if ( control->molec_anal == FRAGMENTS )
{
/* discover molecules */
diff --git a/sPuReMD/src/charges.c b/sPuReMD/src/charges.c
index 998357a81743362acc038fceddef5dcfb7f33b11..3b760d682c96a22f223f316f305041bea0f80ad7 100644
--- a/sPuReMD/src/charges.c
+++ b/sPuReMD/src/charges.c
@@ -107,13 +107,13 @@ int is_refactoring_step( control_params * const control,
#if defined(HAVE_TENSORFLOW)
static void TF_Tensor_Deallocator( void* data, size_t length, void* arg )
{
-// sfree( data, "TF_Tensor_Deallocator::data" );
+// sfree( data, __FILE__, __LINE__ );
}
static void TF_free( void* data, size_t length )
{
- sfree( data, "TF_free::data" );
+ sfree( data, __FILE__, __LINE__ );
}
@@ -226,8 +226,8 @@ static void Predict_Charges_TF_LSTM( const reax_system * const system,
// batch_size = 3;
win_size = control->cm_init_guess_win_size;
batch_size = system->N_cm;
- obs_flat = smalloc( sizeof(float) * batch_size * win_size, "Predict_Charges_TF_LSTM:obs_flat" );
- obs_norm = smalloc( sizeof(float) * batch_size, "Predict_Charges_TF_LSTM:obs_norm" );
+ obs_flat = smalloc( sizeof(float) * batch_size * win_size, __FILE__, __LINE__ );
+ obs_norm = smalloc( sizeof(float) * batch_size, __FILE__, __LINE__ );
/* load the frozen model from file in GraphDef format
*
@@ -327,8 +327,8 @@ static void Predict_Charges_TF_LSTM( const reax_system * const system,
workspace->s[0][i] = predictions[i] + obs_norm[i];
}
- sfree( obs_norm, "Predict_Charges_TF_LSTM:obs_norm" );
- sfree( obs_flat, "Predict_Charges_TF_LSTM:obs_flat" );
+ sfree( obs_norm, __FILE__, __LINE__ );
+ sfree( obs_flat, __FILE__, __LINE__ );
TF_DeleteTensor( input_tensor[0] );
TF_DeleteTensor( output_tensor[0] );
TF_DeleteSession( s.session, status );
@@ -930,13 +930,12 @@ static void Setup_Preconditioner_QEq( const reax_system * const system,
if ( workspace->Hdia_inv == NULL )
{
workspace->Hdia_inv = scalloc( Hptr->n_max, sizeof( real ),
- "Setup_Preconditioner_QEq::workspace->Hdia_inv" );
+ __FILE__, __LINE__ );
}
else if ( realloc == TRUE )
{
workspace->Hdia_inv = srealloc( workspace->Hdia_inv,
- sizeof( real ) * Hptr->n_max,
- "Setup_Preconditioner_QEq::workspace->Hdia_inv" );
+ sizeof( real ) * Hptr->n_max, __FILE__, __LINE__ );
}
break;
@@ -1056,13 +1055,12 @@ static void Setup_Preconditioner_EE( const reax_system * const system,
if ( workspace->Hdia_inv == NULL )
{
workspace->Hdia_inv = scalloc( Hptr->n_max, sizeof( real ),
- "Setup_Preconditioner_EE::workspace->Hdiv_inv" );
+ __FILE__, __LINE__ );
}
else if ( realloc == TRUE )
{
workspace->Hdia_inv = srealloc( workspace->Hdia_inv,
- sizeof( real ) * Hptr->n_max,
- "Setup_Preconditioner_EE::workspace->Hdiv_inv" );
+ sizeof( real ) * Hptr->n_max, __FILE__, __LINE__ );
}
break;
@@ -1179,13 +1177,12 @@ static void Setup_Preconditioner_ACKS2( const reax_system * const system,
if ( workspace->Hdia_inv == NULL )
{
workspace->Hdia_inv = scalloc( Hptr->n_max, sizeof( real ),
- "Setup_Preconditioner_ACKS2::workspace->Hdiv_inv" );
+ __FILE__, __LINE__ );
}
else if ( realloc == TRUE )
{
workspace->Hdia_inv = srealloc( workspace->Hdia_inv,
- sizeof( real ) * Hptr->n_max,
- "Setup_Preconditioner_ACKS2::workspace->Hdiv_inv" );
+ sizeof( real ) * Hptr->n_max, __FILE__, __LINE__ );
}
break;
@@ -1627,9 +1624,9 @@ static void ACKS2( reax_system * const system, control_params * const control,
if ( data->step % 10 == 0 )
{
snprintf( fname, SIZE, "s_%d_%s.out", data->step, control->sim_name );
- fp = sfopen( fname, "w" );
+ fp = sfopen( fname, "w", __FILE__, __LINE__ );
Vector_Print( fp, NULL, workspace->s[0], system->N_cm );
- sfclose( fp, "ACKS2::fp" );
+ sfclose( fp, __FILE__, __LINE__ );
}
#undef SIZE
#endif
@@ -1712,14 +1709,14 @@ void Compute_Charges( reax_system * const system, control_params * const control
// Print_Sparse_Matrix_Binary( workspace->H, fname );
snprintf( fname, SIZE, "b_s_%d_%s.out", data->step, control->sim_name );
- fp = sfopen( fname, "w" );
+ fp = sfopen( fname, "w", __FILE__, __LINE__ );
Vector_Print( fp, NULL, workspace->b_s, system->N_cm );
- sfclose( fp, "Compute_Charges::fp" );
+ sfclose( fp, __FILE__, __LINE__ );
// snprintf( fname, SIZE, "b_t_%d_%s.out", data->step, control->sim_name );
-// fp = sfopen( fname, "w" );
+// fp = sfopen( fname, "w", __FILE__, __LINE__ );
// Vector_Print( fp, NULL, workspace->b_t, system->N_cm );
-// sfclose( fp, "Compute_Charges::fp" );
+// sfclose( fp, __FILE__, __LINE__ );
}
#undef SIZE
#endif
diff --git a/sPuReMD/src/control.c b/sPuReMD/src/control.c
index c46775a4261b8739a62a0a49c8139db44371b125..8803e10bac2f2604f23103512814c4bc90426d09 100644
--- a/sPuReMD/src/control.c
+++ b/sPuReMD/src/control.c
@@ -562,17 +562,17 @@ void Read_Control_File( const char * const control_file, reax_system * const sys
int c, i, ret;
FILE *fp;
- fp = sfopen( control_file, "r" );
+ fp = sfopen( control_file, "r", __FILE__, __LINE__ );
assert( fp != NULL );
if ( fp != NULL )
{
- s = smalloc( sizeof(char) * MAX_LINE, "Read_Control_File::s" );
- tmp = smalloc( sizeof(char*) * MAX_TOKENS, "Read_Control_File::tmp" );
+ s = smalloc( sizeof(char) * MAX_LINE, __FILE__, __LINE__ );
+ tmp = smalloc( sizeof(char*) * MAX_TOKENS, __FILE__, __LINE__ );
for ( i = 0; i < MAX_TOKENS; i++ )
{
- tmp[i] = smalloc( sizeof(char) * MAX_LINE, "Read_Control_File::tmp[i]" );
+ tmp[i] = smalloc( sizeof(char) * MAX_LINE, __FILE__, __LINE__ );
}
/* read control parameters file */
@@ -601,13 +601,13 @@ void Read_Control_File( const char * const control_file, reax_system * const sys
for ( i = 0; i < MAX_TOKENS; i++ )
{
- sfree( tmp[i], "Read_Control_File::tmp[i]" );
+ sfree( tmp[i], __FILE__, __LINE__ );
}
- sfree( tmp, "Read_Control_File::tmp" );
- sfree( s, "Read_Control_File::s" );
+ sfree( tmp, __FILE__, __LINE__ );
+ sfree( s, __FILE__, __LINE__ );
}
- sfclose( fp, "Read_Control_File::fp" );
+ sfclose( fp, __FILE__, __LINE__ );
}
diff --git a/sPuReMD/src/ffield.c b/sPuReMD/src/ffield.c
index 39d78b2026a56c217ca3ab32dc55e8bd93f09f89..b611538d4bc9e366da75d35d2e139f0fbae32151 100644
--- a/sPuReMD/src/ffield.c
+++ b/sPuReMD/src/ffield.c
@@ -36,17 +36,17 @@ void Read_Force_Field( const char * const ffield_file,
real val;
FILE *fp;
- fp = sfopen( ffield_file, "r" );
+ fp = sfopen( ffield_file, "r", __FILE__, __LINE__ );
assert( fp != NULL );
if ( fp != NULL )
{
- s = smalloc( sizeof(char) * MAX_LINE, "Read_Force_Field::s" );
- tmp = smalloc( sizeof(char*) * MAX_TOKENS, "Read_Force_Field::tmp" );
+ s = smalloc( sizeof(char) * MAX_LINE, __FILE__, __LINE__ );
+ tmp = smalloc( sizeof(char*) * MAX_TOKENS, __FILE__, __LINE__ );
for ( i = 0; i < MAX_TOKENS; i++ )
{
- tmp[i] = smalloc( sizeof(char) * MAX_TOKEN_LEN, "Read_Force_Field::tmp[i]" );
+ tmp[i] = smalloc( sizeof(char) * MAX_TOKEN_LEN, __FILE__, __LINE__ );
}
/* reading first header comment */
@@ -66,15 +66,13 @@ void Read_Force_Field( const char * const ffield_file,
if ( system->ffield_params_allocated == FALSE )
{
- reax->gp.l = (real*) smalloc( sizeof(real) * n,
- "Read_Force_Field::reax->gp-l" );
+ reax->gp.l = (real*) smalloc( sizeof(real) * n, __FILE__, __LINE__ );
reax->gp.max_n_global = n;
}
else if ( reax->gp.max_n_global < n )
{
- reax->gp.l = (real*) srealloc( reax->gp.l, sizeof(real) * n,
- "Read_Force_Field::reax->gp-l" );
+ reax->gp.l = srealloc( reax->gp.l, sizeof(real) * n, __FILE__, __LINE__ );
reax->gp.max_n_global = n;
}
@@ -106,41 +104,28 @@ void Read_Force_Field( const char * const ffield_file,
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" );
- reax->tbp = (two_body_parameters**) scalloc( n, sizeof(two_body_parameters*),
- "Read_Force_Field::reax->tbp" );
- reax->thbp = (three_body_header***) scalloc( n, sizeof(three_body_header**),
- "Read_Force_Field::reax->thbp" );
- reax->hbp = (hbond_parameters***) scalloc( n, sizeof(hbond_parameters**),
- "Read_Force_Field::reax->hbp" );
- reax->fbp = (four_body_header****) scalloc( n, sizeof(four_body_header***),
- "Read_Force_Field::reax->fbp" );
+ reax->sbp = scalloc( n, sizeof(single_body_parameters), __FILE__, __LINE__ );
+ reax->tbp = scalloc( n, sizeof(two_body_parameters*), __FILE__, __LINE__ );
+ reax->thbp = scalloc( n, sizeof(three_body_header**), __FILE__, __LINE__ );
+ reax->hbp = scalloc( n, sizeof(hbond_parameters**), __FILE__, __LINE__ );
+ reax->fbp = scalloc( n, sizeof(four_body_header***), __FILE__, __LINE__ );
for ( i = 0; i < n; i++ )
{
- reax->tbp[i] = (two_body_parameters*) scalloc( n, sizeof(two_body_parameters),
- "Read_Force_Field::reax->tbp[i]" );
- reax->thbp[i] = (three_body_header**) scalloc( n, sizeof(three_body_header*),
- "Read_Force_Field::reax->thbp[i]" );
- reax->hbp[i] = (hbond_parameters**) scalloc( n, sizeof(hbond_parameters*),
- "Read_Force_Field::reax->hbp[i]" );
- reax->fbp[i] = (four_body_header***) scalloc( n, sizeof(four_body_header**),
- "Read_Force_Field::reax->fbp[i]" );
+ reax->tbp[i] = scalloc( n, sizeof(two_body_parameters), __FILE__, __LINE__ );
+ reax->thbp[i] = scalloc( n, sizeof(three_body_header*), __FILE__, __LINE__ );
+ reax->hbp[i] = scalloc( n, sizeof(hbond_parameters*), __FILE__, __LINE__ );
+ reax->fbp[i] = scalloc( n, sizeof(four_body_header**), __FILE__, __LINE__ );
for ( j = 0; j < n; j++ )
{
- reax->thbp[i][j] = (three_body_header*) scalloc( n, sizeof(three_body_header),
- "Read_Force_Field::reax->thbp[i][j]" );
- reax->hbp[i][j] = (hbond_parameters*) scalloc( n, sizeof(hbond_parameters),
- "Read_Force_Field::reax->hbp[i][j]" );
- reax->fbp[i][j] = (four_body_header**) scalloc( n, sizeof(four_body_header*),
- "Read_Force_Field::reax->fbp[i][j]" );
+ reax->thbp[i][j] = scalloc( n, sizeof(three_body_header), __FILE__, __LINE__ );
+ reax->hbp[i][j] = scalloc( n, sizeof(hbond_parameters), __FILE__, __LINE__ );
+ reax->fbp[i][j] = scalloc( n, sizeof(four_body_header*), __FILE__, __LINE__ );
for ( k = 0; k < n; k++ )
{
- reax->fbp[i][j][k] = (four_body_header*) scalloc( n, sizeof(four_body_header),
- "Read_Force_Field::reax->fbp[i][j][k]" );
+ reax->fbp[i][j][k] = scalloc( n, sizeof(four_body_header), __FILE__, __LINE__ );
}
}
}
@@ -152,66 +137,53 @@ void Read_Force_Field( const char * const ffield_file,
for ( i = 0; i < reax->max_num_atom_types; i++ )
for ( j = 0; j < reax->max_num_atom_types; j++ )
for ( k = 0; k < reax->max_num_atom_types; k++ )
- sfree( reax->fbp[i][j][k], "Finalize_System::reax->fbp[i][j][k]" );
+ sfree( reax->fbp[i][j][k], __FILE__, __LINE__ );
for ( i = 0; i < reax->max_num_atom_types; i++ )
for ( j = 0; j < reax->max_num_atom_types; j++ )
{
- sfree( reax->thbp[i][j], "Finalize_System::reax->thbp[i][j]" );
- sfree( reax->hbp[i][j], "Finalize_System::reax->hbp[i][j]" );
- sfree( reax->fbp[i][j], "Finalize_System::reax->fbp[i][j]" );
+ sfree( reax->thbp[i][j], __FILE__, __LINE__ );
+ sfree( reax->hbp[i][j], __FILE__, __LINE__ );
+ sfree( reax->fbp[i][j], __FILE__, __LINE__ );
}
for ( i = 0; i < reax->max_num_atom_types; i++ )
{
- sfree( reax->tbp[i], "Finalize_System::reax->tbp[i]" );
- sfree( reax->thbp[i], "Finalize_System::reax->thbp[i]" );
- sfree( reax->hbp[i], "Finalize_System::reax->hbp[i]" );
- sfree( reax->fbp[i], "Finalize_System::reax->fbp[i]" );
+ sfree( reax->tbp[i], __FILE__, __LINE__ );
+ sfree( reax->thbp[i], __FILE__, __LINE__ );
+ sfree( reax->hbp[i], __FILE__, __LINE__ );
+ sfree( reax->fbp[i], __FILE__, __LINE__ );
}
- sfree( reax->sbp, "Finalize_System::reax->sbp" );
- sfree( reax->tbp, "Finalize_System::reax->tbp" );
- sfree( reax->thbp, "Finalize_System::reax->thbp" );
- sfree( reax->hbp, "Finalize_System::reax->hbp" );
- sfree( reax->fbp, "Finalize_System::reax->fbp" );
+ sfree( reax->sbp, __FILE__, __LINE__ );
+ sfree( reax->tbp, __FILE__, __LINE__ );
+ sfree( reax->thbp, __FILE__, __LINE__ );
+ sfree( reax->hbp, __FILE__, __LINE__ );
+ sfree( reax->fbp, __FILE__, __LINE__ );
/* Allocating structures in reax_interaction */
- reax->sbp = (single_body_parameters*) scalloc( n, sizeof(single_body_parameters),
- "Read_Force_Field::reax->sbp" );
- reax->tbp = (two_body_parameters**) scalloc( n, sizeof(two_body_parameters*),
- "Read_Force_Field::reax->tbp" );
- reax->thbp = (three_body_header***) scalloc( n, sizeof(three_body_header**),
- "Read_Force_Field::reax->thbp" );
- reax->hbp = (hbond_parameters***) scalloc( n, sizeof(hbond_parameters**),
- "Read_Force_Field::reax->hbp" );
- reax->fbp = (four_body_header****) scalloc( n, sizeof(four_body_header***),
- "Read_Force_Field::reax->fbp" );
+ reax->sbp = scalloc( n, sizeof(single_body_parameters), __FILE__, __LINE__ );
+ reax->tbp = scalloc( n, sizeof(two_body_parameters*), __FILE__, __LINE__ );
+ reax->thbp = scalloc( n, sizeof(three_body_header**), __FILE__, __LINE__ );
+ reax->hbp = scalloc( n, sizeof(hbond_parameters**), __FILE__, __LINE__ );
+ reax->fbp = scalloc( n, sizeof(four_body_header***), __FILE__, __LINE__ );
for ( i = 0; i < n; i++ )
{
- reax->tbp[i] = (two_body_parameters*) scalloc( n, sizeof(two_body_parameters),
- "Read_Force_Field::reax->tbp[i]" );
- reax->thbp[i] = (three_body_header**) scalloc( n, sizeof(three_body_header*),
- "Read_Force_Field::reax->thbp[i]" );
- reax->hbp[i] = (hbond_parameters**) scalloc( n, sizeof(hbond_parameters*),
- "Read_Force_Field::reax->hbp[i]" );
- reax->fbp[i] = (four_body_header***) scalloc( n, sizeof(four_body_header**),
- "Read_Force_Field::reax->fbp[i]" );
+ reax->tbp[i] = scalloc( n, sizeof(two_body_parameters), __FILE__, __LINE__ );
+ reax->thbp[i] = scalloc( n, sizeof(three_body_header*), __FILE__, __LINE__ );
+ reax->hbp[i] = scalloc( n, sizeof(hbond_parameters*), __FILE__, __LINE__ );
+ reax->fbp[i] = scalloc( n, sizeof(four_body_header**), __FILE__, __LINE__ );
for ( j = 0; j < n; j++ )
{
- reax->thbp[i][j] = (three_body_header*) scalloc( n, sizeof(three_body_header),
- "Read_Force_Field::reax->thbp[i][j]" );
- reax->hbp[i][j] = (hbond_parameters*) scalloc( n, sizeof(hbond_parameters),
- "Read_Force_Field::reax->hbp[i][j]" );
- reax->fbp[i][j] = (four_body_header**) scalloc( n, sizeof(four_body_header*),
- "Read_Force_Field::reax->fbp[i][j]" );
+ reax->thbp[i][j] = scalloc( n, sizeof(three_body_header), __FILE__, __LINE__ );
+ reax->hbp[i][j] = scalloc( n, sizeof(hbond_parameters), __FILE__, __LINE__ );
+ reax->fbp[i][j] = scalloc( n, sizeof(four_body_header*), __FILE__, __LINE__ );
for ( k = 0; k < n; k++ )
{
- reax->fbp[i][j][k] = (four_body_header*) scalloc( n, sizeof(four_body_header),
- "Read_Force_Field::reax->fbp[i][j][k]" );
+ reax->fbp[i][j][k] = scalloc( n, sizeof(four_body_header), __FILE__, __LINE__ );
}
}
}
@@ -219,23 +191,19 @@ void Read_Force_Field( const char * const ffield_file,
reax->max_num_atom_types = n;
}
- tor_flag = (char****) smalloc( n * sizeof(char***),
- "Read_Force_Field::tor_flag" );
+ tor_flag = smalloc( n * sizeof(char***), __FILE__, __LINE__ );
for ( i = 0; i < n; i++ )
{
- tor_flag[i] = (char***) smalloc( n * sizeof(char**),
- "Read_Force_Field::tor_flag[i]" );
+ tor_flag[i] = smalloc( n * sizeof(char**), __FILE__, __LINE__ );
for ( j = 0; j < n; j++ )
{
- tor_flag[i][j] = (char**) smalloc( n * sizeof(char*),
- "Read_Force_Field::tor_flag[i][j]" );
+ tor_flag[i][j] = smalloc( n * sizeof(char*), __FILE__, __LINE__ );
for ( k = 0; k < n; k++ )
{
- tor_flag[i][j][k] = (char*) smalloc( n * sizeof(char),
- "Read_Force_Field::tor_flag[i][j][k]" );
+ tor_flag[i][j][k] = smalloc( n * sizeof(char), __FILE__, __LINE__ );
}
}
}
@@ -847,10 +815,10 @@ void Read_Force_Field( const char * const ffield_file,
/* deallocate helper storage */
for ( i = 0; i < MAX_TOKENS; i++ )
{
- sfree( tmp[i], "Read_Force_Field::tmp[i]" );
+ sfree( tmp[i], __FILE__, __LINE__ );
}
- sfree( tmp, "Read_Force_Field::tmp" );
- sfree( s, "Read_Force_Field::s" );
+ sfree( tmp, __FILE__, __LINE__ );
+ sfree( s, __FILE__, __LINE__ );
/* deallocate tor_flag */
for ( i = 0; i < reax->num_atom_types; i++ )
@@ -859,17 +827,17 @@ void Read_Force_Field( const char * const ffield_file,
{
for ( k = 0; k < reax->num_atom_types; k++ )
{
- sfree( tor_flag[i][j][k], "Read_Force_Field::tor_flag[i][j][k]" );
+ sfree( tor_flag[i][j][k], __FILE__, __LINE__ );
}
- sfree( tor_flag[i][j], "Read_Force_Field::tor_flag[i][j]" );
+ sfree( tor_flag[i][j], __FILE__, __LINE__ );
}
- sfree( tor_flag[i], "Read_Force_Field::tor_flag[i]" );
+ sfree( tor_flag[i], __FILE__, __LINE__ );
}
- sfree( tor_flag, "Read_Force_Field::tor_flag" );
+ sfree( tor_flag, __FILE__, __LINE__ );
}
- sfclose( fp, "Read_Force_Field::fp" );
+ sfclose( fp, __FILE__, __LINE__ );
}
diff --git a/sPuReMD/src/forces.c b/sPuReMD/src/forces.c
index 42f7f9fef1ef03f9a1be5e4de40834e2a80ba6c5..8857fd343dbb91bcbb69c3e9120d99ee8004fbeb 100644
--- a/sPuReMD/src/forces.c
+++ b/sPuReMD/src/forces.c
@@ -567,8 +567,7 @@ static void Init_Charge_Matrix_Remaining_Entries( reax_system *system,
break;
case ACKS2_CM:
- X_diag = smalloc( sizeof(real) * system->N,
- "Init_Charge_Matrix_Remaining_Entries::X_diag" );
+ X_diag = smalloc( sizeof(real) * system->N, __FILE__, __LINE__ );
for ( i = 0; i < system->N; ++i )
{
@@ -736,7 +735,7 @@ static void Init_Charge_Matrix_Remaining_Entries( reax_system *system,
H_sp->val[*H_sp_top] = 0.0;
*H_sp_top = *H_sp_top + 1;
- sfree( X_diag, "Init_Charge_Matrix_Remaining_Entries::X_diag" );
+ sfree( X_diag, __FILE__, __LINE__ );
break;
default:
@@ -1272,8 +1271,10 @@ static void Init_Forces_Tab( reax_system *system, control_params *control,
++H_sp_top;
}
}
+
/* Only non-dummy atoms can form bonds */
- if (system->atoms[i].dummy == FALSE && system->atoms[j].dummy == FALSE)
+ if ( system->atoms[i].is_dummy == FALSE
+ && system->atoms[j].is_dummy == FALSE )
{
/* hydrogen bond lists */
if ( control->hbond_cut > 0.0
diff --git a/sPuReMD/src/geo_tools.c b/sPuReMD/src/geo_tools.c
index e1429630952a9816f84f9f4a472b1ee2048e1fad..dfd2c5b4ed85310298e76589af090d429fd0e7a9 100644
--- a/sPuReMD/src/geo_tools.c
+++ b/sPuReMD/src/geo_tools.c
@@ -284,6 +284,14 @@ static int Count_Atoms( reax_system *system, FILE *fp, int geo_format )
}
+/* Parser for geometry file in free-form custom PuReMD format
+ *
+ * geo_file: filename for custom geometry file to parse
+ * system: struct containing atom-related information
+ * control: struct containing simulation parameters
+ * data: struct containing information on active simulations
+ * workspace: struct containing intermediate structures used for calculations
+ */
void Read_Geo( const char * const geo_file, reax_system* system, control_params *control,
simulation_data *data, static_storage *workspace )
{
@@ -293,7 +301,7 @@ void Read_Geo( const char * const geo_file, reax_system* system, control_params
char element[3], name[9];
reax_atom *atom;
- geo = sfopen( geo_file, "r" );
+ geo = sfopen( geo_file, "r", __FILE__, __LINE__ );
if ( Read_Box_Info( system, geo, CUSTOM ) == FAILURE )
{
@@ -339,14 +347,32 @@ void Read_Geo( const char * const geo_file, reax_system* system, control_params
rvec_MakeZero( atom->v );
rvec_MakeZero( atom->f );
atom->q = 0.0;
+
+ /* check for dummy atom */
+ if ( strncmp( element, "X\0", 2 ) == 0 )
+ {
+ atom->is_dummy = TRUE;
+ }
+ else
+ {
+ atom->is_dummy = FALSE;
+ }
top++;
}
- sfclose( geo, "Read_Geo::geo" );
+ sfclose( geo, __FILE__, __LINE__ );
}
+/* Parser for geometry file in fixed-form PDB format
+ *
+ * pdb_file: filename for PDB geometry file to parse
+ * system: struct containing atom-related information
+ * control: struct containing simulation parameters
+ * data: struct containing information on active simulations
+ * workspace: struct containing intermediate structures used for calculations
+ */
void Read_PDB( const char * const pdb_file, reax_system* system, control_params *control,
simulation_data *data, static_storage *workspace )
{
@@ -363,7 +389,7 @@ void Read_PDB( const char * const pdb_file, reax_system* system, control_params
rvec x;
reax_atom *atom;
- pdb = sfopen( pdb_file, "r" );
+ pdb = sfopen( pdb_file, "r", __FILE__, __LINE__ );
Allocate_Tokenizer_Space( &s, MAX_LINE, &s1, MAX_LINE,
&tmp, MAX_TOKENS, MAX_TOKEN_LEN );
@@ -478,28 +504,38 @@ void Read_PDB( const char * const pdb_file, reax_system* system, control_params
pdb_serial = (int) sstrtod( serial, __FILE__, __LINE__ );
workspace->orig_id[top] = pdb_serial;
+ strncpy( atom->name, atom_name, sizeof(atom->name) - 1 );
+ atom->name[sizeof(atom->name) - 1] = '\0';
Trim_Spaces( element, sizeof(element) );
for ( i = 0; i < sizeof(element) - 1; ++i )
{
element[i] = toupper( element[i] );
}
atom->type = Get_Atom_Type( &system->reax_param, element, sizeof(element) );
- strncpy( atom->name, atom_name, sizeof(atom->name) - 1 );
- atom->name[sizeof(atom->name) - 1] = '\0';
+
+ /* check for dummy atom */
+ if ( strncmp( element, "X\0", 2 ) == 0 )
+ {
+ system->atoms[top].is_dummy = TRUE;
+ }
+ else
+ {
+ system->atoms[top].is_dummy = FALSE;
+ }
rvec_Copy( atom->x, x );
rvec_MakeZero( atom->v );
rvec_MakeZero( atom->f );
atom->q = 0;
- top++;
-
#if defined(DEBUG_FOCUS)
fprintf( stderr, "[INFO] atom: id = %d, name = %s, serial = %d, type = %d, ",
top, atom->name, pdb_serial, atom->type );
fprintf( stderr, "x = (%7.3f, %7.3f, %7.3f)\n",
atom->x[0], atom->x[1], atom->x[2] );
#endif
+
+ top++;
}
c++;
@@ -515,8 +551,7 @@ void Read_PDB( const char * const pdb_file, reax_system* system, control_params
if ( control->restrict_bonds )
{
/* error check */
-// Check_Input_Range( c1 - 2, 0, MAX_RESTRICT,
-// "CONECT line exceeds max num restrictions allowed.\n" );
+// Check_Input_Range( c1 - 2, 0, MAX_RESTRICT, __FILE__, __LINE__ );
/* read bond restrictions */
// pdb_serial = sstrtol( tmp[1], __FILE__, __LINE__ );
@@ -553,7 +588,7 @@ void Read_PDB( const char * const pdb_file, reax_system* system, control_params
exit( INVALID_INPUT );
}
- sfclose( pdb, "Read_PDB::pdb" );
+ sfclose( pdb, __FILE__, __LINE__ );
Deallocate_Tokenizer_Space( &s, &s1, &tmp, MAX_TOKENS );
}
@@ -595,7 +630,7 @@ void Write_PDB( reax_system* system, reax_list* bonds, simulation_data *data,
sizeof(control->sim_name) ),
control->sim_name, snprintf(NULL, 0, "%d", data->step), data->step );
fname[sizeof(fname) - 1] = '\0';
- pdb = sfopen( fname, "w" );
+ pdb = sfopen( fname, "w", __FILE__, __LINE__ );
fprintf( pdb, PDB_CRYST1_FORMAT_O,
"CRYST1",
system->box.box_norms[0], system->box.box_norms[1],
@@ -626,12 +661,13 @@ void Write_PDB( reax_system* system, reax_list* bonds, simulation_data *data,
exit( INVALID_INPUT );
}
- sfclose( pdb, "Write_PDB::pdb" );
+ sfclose( pdb, __FILE__, __LINE__ );
}
/* Parser for geometry files in BGF format
*
+ * bgf_file: filename for BGF file to parse
* system: struct containing atom-related information
* control: struct containing simulation parameters
* data: struct containing information on active simulations
@@ -656,7 +692,7 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
ratom = 0;
crystx_found = FALSE;
- bgf = sfopen( bgf_file, "r" );
+ bgf = sfopen( bgf_file, "r", __FILE__, __LINE__ );
Allocate_Tokenizer_Space( &line, MAX_LINE, &backup, MAX_LINE,
&tokens, MAX_TOKENS, MAX_TOKEN_LEN );
@@ -696,9 +732,9 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
if ( system->prealloc_allocated == FALSE && num_mcc > 0 )
{
system->molec_charge_constraints = smalloc(
- sizeof(real) * num_mcc, "Read_BGF::molec_charge_constraints" );
+ sizeof(real) * num_mcc, __FILE__, __LINE__ );
system->molec_charge_constraint_ranges = smalloc(
- sizeof(int) * 2 * num_mcc, "Read_BGF::molec_charge_constraint_ranges" );
+ sizeof(int) * 2 * num_mcc, __FILE__, __LINE__ );
system->max_num_molec_charge_constraints = num_mcc;
}
@@ -706,14 +742,14 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
{
if ( system->max_num_molec_charge_constraints > 0 )
{
- sfree( system->molec_charge_constraints, "Read_BGF::molec_charge_constraints" );
- sfree( system->molec_charge_constraint_ranges, "Read_BGF::molec_charge_constraint_ranges" );
+ sfree( system->molec_charge_constraints, __FILE__, __LINE__ );
+ sfree( system->molec_charge_constraint_ranges, __FILE__, __LINE__ );
}
system->molec_charge_constraints = smalloc(
- sizeof(real) * num_mcc, "Read_BGF::molec_charge_constraints" );
+ sizeof(real) * num_mcc, __FILE__, __LINE__ );
system->molec_charge_constraint_ranges = smalloc(
- sizeof(int) * 2 * num_mcc, "Read_BGF::molec_charge_constraint_ranges" );
+ sizeof(int) * 2 * num_mcc, __FILE__, __LINE__ );
system->max_num_molec_charge_constraints = num_mcc;
}
@@ -819,7 +855,7 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
/* add to mapping */
bgf_serial = sstrtod( serial, __FILE__, __LINE__ );
- Check_Input_Range( bgf_serial, 0, MAX_ATOM_ID, "Invalid bgf serial" );
+ Check_Input_Range( bgf_serial, 0, MAX_ATOM_ID, __FILE__, __LINE__ );
workspace->map_serials[ bgf_serial ] = atom_cnt;
workspace->orig_id[ atom_cnt ] = bgf_serial;
@@ -846,15 +882,16 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
system->atoms[atom_cnt].type =
Get_Atom_Type( &system->reax_param, element, sizeof(element) );
- // TODO: finalize dummy atom name (Amber uses "Du")
- if ( strncmp( element, "X\0", 2) == 0 )
+ /* check for dummy atom */
+ if ( strncmp( element, "X\0", 2 ) == 0 )
{
- system->atoms[atom_cnt].dummy = TRUE;
+ system->atoms[atom_cnt].is_dummy = TRUE;
}
else
{
- system->atoms[atom_cnt].dummy = FALSE;
+ system->atoms[atom_cnt].is_dummy = FALSE;
}
+
#if defined(DEBUG_FOCUS)
fprintf( stderr,
"[INFO] atom_cnt = %5d, atom_type = %3d, x = (%10.5f,%10.5f,%10.5f), q = %10.5f, occ = %s, temp = %s, res_name = %4s, element = %s\n",
@@ -872,8 +909,7 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
if ( control->restrict_bonds )
{
/* check number of restrictions */
- Check_Input_Range( token_cnt - 2, 0, MAX_RESTRICT,
- "CONECT line exceeds max restrictions allowed.\n" );
+ Check_Input_Range( token_cnt - 2, 0, MAX_RESTRICT, __FILE__, __LINE__ );
/* read bond restrictions */
bgf_serial = sstrtol( tokens[1], __FILE__, __LINE__ );
@@ -929,5 +965,5 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
Deallocate_Tokenizer_Space( &line, &backup, &tokens, MAX_TOKENS );
- sfclose( bgf, "Read_BGF::bgf" );
+ sfclose( bgf, __FILE__, __LINE__ );
}
diff --git a/sPuReMD/src/grid.c b/sPuReMD/src/grid.c
index f5bfde6686432c6d760dea90b34893b6fbe913b6..3c6eb47bdfe8348e4d821364254125e8d82df2d1 100644
--- a/sPuReMD/src/grid.c
+++ b/sPuReMD/src/grid.c
@@ -89,101 +89,101 @@ static void Allocate_Space_for_Grid( reax_system * const system, int alloc )
if ( alloc == TRUE )
{
/* allocate space for the new grid */
- g->atoms = (int****) scalloc( g->ncell_max[0], sizeof( int*** ),
- "Allocate_Space_for_Grid::g->atoms" );
+ g->atoms = scalloc( g->ncell_max[0], sizeof( int*** ),
+ __FILE__, __LINE__ );
for ( i = 0; i < g->ncell_max[0]; i++ )
- g->atoms[i] = (int***) scalloc( g->ncell_max[1], sizeof( int** ),
- "Allocate_Space_for_Grid::g->atoms[i]" );
+ g->atoms[i] = scalloc( g->ncell_max[1], sizeof( int** ),
+ __FILE__, __LINE__ );
for ( i = 0; i < g->ncell_max[0]; i++ )
for ( j = 0; j < g->ncell_max[1]; j++ )
- g->atoms[i][j] = (int**) scalloc( g->ncell_max[2], sizeof( int* ),
- "Allocate_Space_for_Grid::g->atoms[i][j]" );
+ g->atoms[i][j] = scalloc( g->ncell_max[2], sizeof( int* ),
+ __FILE__, __LINE__ );
- g->top = (int***) scalloc( g->ncell_max[0], sizeof( int** ),
- "Allocate_Space_for_Grid::g->top" );
+ g->top = scalloc( g->ncell_max[0], sizeof( int** ),
+ __FILE__, __LINE__ );
for ( i = 0; i < g->ncell_max[0]; i++ )
- g->top[i] = (int**) scalloc( g->ncell_max[1], sizeof( int* ),
- "Allocate_Space_for_Grid::g->top[i]" );
+ g->top[i] = scalloc( g->ncell_max[1], sizeof( int* ),
+ __FILE__, __LINE__ );
for ( i = 0; i < g->ncell_max[0]; i++ )
for ( j = 0; j < g->ncell_max[1]; j++ )
- g->top[i][j] = (int*) scalloc( g->ncell_max[2], sizeof( int ),
- "Allocate_Space_for_Grid::g->top[i][j]" );
+ g->top[i][j] = scalloc( g->ncell_max[2], sizeof( int ),
+ __FILE__, __LINE__ );
- g->mark = (int***) scalloc( g->ncell_max[0], sizeof( int** ),
- "Allocate_Space_for_Grid::g->mark" );
+ g->mark = scalloc( g->ncell_max[0], sizeof( int** ),
+ __FILE__, __LINE__ );
for ( i = 0; i < g->ncell_max[0]; i++ )
- g->mark[i] = (int**) scalloc( g->ncell_max[1], sizeof( int* ),
- "Allocate_Space_for_Grid::g->mark[i]" );
+ g->mark[i] = scalloc( g->ncell_max[1], sizeof( int* ),
+ __FILE__, __LINE__ );
for ( i = 0; i < g->ncell_max[0]; i++ )
for ( j = 0; j < g->ncell_max[1]; j++ )
- g->mark[i][j] = (int*) scalloc( g->ncell_max[2], sizeof( int ),
- "Allocate_Space_for_Grid::g->mark[i][j]" );
+ g->mark[i][j] = scalloc( g->ncell_max[2], sizeof( int ),
+ __FILE__, __LINE__ );
- g->start = (int***) scalloc( g->ncell_max[0], sizeof( int** ),
- "Allocate_Space_for_Grid::g->start" );
+ g->start = scalloc( g->ncell_max[0], sizeof( int** ),
+ __FILE__, __LINE__ );
for ( i = 0; i < g->ncell_max[0]; i++ )
- g->start[i] = (int**) scalloc( g->ncell_max[1], sizeof( int* ),
- "Allocate_Space_for_Grid::g->start[i]" );
+ g->start[i] = scalloc( g->ncell_max[1], sizeof( int* ),
+ __FILE__, __LINE__ );
for ( i = 0; i < g->ncell_max[0]; i++ )
for ( j = 0; j < g->ncell_max[1]; j++ )
- g->start[i][j] = (int*) scalloc( g->ncell_max[2], sizeof( int ),
- "Allocate_Space_for_Grid::g->start[i][j]" );
+ g->start[i][j] = scalloc( g->ncell_max[2], sizeof( int ),
+ __FILE__, __LINE__ );
- g->end = (int***) scalloc( g->ncell_max[0], sizeof( int** ),
- "Allocate_Space_for_Grid::g->end" );
+ g->end = scalloc( g->ncell_max[0], sizeof( int** ),
+ __FILE__, __LINE__ );
for ( i = 0; i < g->ncell_max[0]; i++ )
- g->end[i] = (int**) scalloc( g->ncell_max[1], sizeof( int* ),
- "Allocate_Space_for_Grid::g->end[i]" );
+ g->end[i] = scalloc( g->ncell_max[1], sizeof( int* ),
+ __FILE__, __LINE__ );
for ( i = 0; i < g->ncell_max[0]; i++ )
for ( j = 0; j < g->ncell_max[1]; j++ )
- g->end[i][j] = (int*) scalloc( g->ncell_max[2], sizeof( int ),
- "Allocate_Space_for_Grid::g->end[i][j]" );
+ g->end[i][j] = scalloc( g->ncell_max[2], sizeof( int ),
+ __FILE__, __LINE__ );
- g->nbrs = (ivec****) scalloc( g->ncell_max[0], sizeof( ivec*** ),
- "Allocate_Space_for_Grid::g->nbrs" );
+ g->nbrs = scalloc( g->ncell_max[0], sizeof( ivec*** ),
+ __FILE__, __LINE__ );
for ( i = 0; i < g->ncell_max[0]; i++ )
- g->nbrs[i] = (ivec***) scalloc( g->ncell_max[1], sizeof( ivec** ),
- "Allocate_Space_for_Grid::g->nbrs[i]" );
+ g->nbrs[i] = scalloc( g->ncell_max[1], sizeof( ivec** ),
+ __FILE__, __LINE__ );
for ( i = 0; i < g->ncell_max[0]; i++ )
for ( j = 0; j < g->ncell_max[1]; j++ )
- g->nbrs[i][j] = (ivec**) scalloc( g->ncell_max[2], sizeof( ivec* ),
- "Allocate_Space_for_Grid::g->nbrs[i][j]" );
+ g->nbrs[i][j] = scalloc( g->ncell_max[2], sizeof( ivec* ),
+ __FILE__, __LINE__ );
for ( i = 0; i < g->ncell_max[0]; i++ )
for ( j = 0; j < g->ncell_max[1]; j++ )
for ( k = 0; k < g->ncell_max[2]; k++ )
- g->nbrs[i][j][k] = (ivec*) smalloc( g->max_nbrs * sizeof( ivec ),
- "Allocate_Space_for_Grid::g->nbrs[i][j][k]" );
+ g->nbrs[i][j][k] = smalloc( g->max_nbrs * sizeof( ivec ),
+ __FILE__, __LINE__ );
- g->nbrs_cp = (rvec****) scalloc( g->ncell_max[0], sizeof( rvec*** ),
- "Allocate_Space_for_Grid::g->nbrs_cp" );
+ g->nbrs_cp = scalloc( g->ncell_max[0], sizeof( rvec*** ),
+ __FILE__, __LINE__ );
for ( i = 0; i < g->ncell_max[0]; i++ )
- g->nbrs_cp[i] = (rvec***) scalloc( g->ncell_max[1], sizeof( rvec** ),
- "Allocate_Space_for_Grid::g->nbrs_cp[i]" );
+ g->nbrs_cp[i] = scalloc( g->ncell_max[1], sizeof( rvec** ),
+ __FILE__, __LINE__ );
for ( i = 0; i < g->ncell_max[0]; i++ )
for ( j = 0; j < g->ncell_max[1]; j++ )
- g->nbrs_cp[i][j] = (rvec**) scalloc( g->ncell_max[2], sizeof( rvec* ),
- "Allocate_Space_for_Grid::g->nbrs_cp[i][j]" );
+ g->nbrs_cp[i][j] = scalloc( g->ncell_max[2], sizeof( rvec* ),
+ __FILE__, __LINE__ );
for ( i = 0; i < g->ncell_max[0]; i++ )
for ( j = 0; j < g->ncell_max[1]; j++ )
for ( k = 0; k < g->ncell_max[2]; k++ )
- g->nbrs_cp[i][j][k] = (rvec*) smalloc( g->max_nbrs * sizeof( rvec ),
- "Allocate_Space_for_Grid::g->nbrs_cp[i][j][k]" );
+ g->nbrs_cp[i][j][k] = smalloc( g->max_nbrs * sizeof( rvec ),
+ __FILE__, __LINE__ );
}
for ( i = 0; i < g->ncell[0]; i++ )
@@ -235,8 +235,8 @@ static void Allocate_Space_for_Grid( reax_system * const system, int alloc )
for ( i = 0; i < g->ncell_max[0]; i++ )
for ( j = 0; j < g->ncell_max[1]; j++ )
for ( k = 0; k < g->ncell_max[2]; k++ )
- g->atoms[i][j][k] = (int*) smalloc( g->max_atoms * sizeof( int ),
- "Allocate_Space_for_Grid::g->atoms[i][j][k]" );
+ g->atoms[i][j][k] = smalloc( g->max_atoms * sizeof( int ),
+ __FILE__, __LINE__ );
}
/* case: grid large enough but max. atoms per grid cells insufficient */
else if ( g->max_atoms > 0 && g->max_atoms < max_atoms )
@@ -246,13 +246,13 @@ static void Allocate_Space_for_Grid( reax_system * const system, int alloc )
for ( i = 0; i < g->ncell_max[0]; i++ )
for ( j = 0; j < g->ncell_max[1]; j++ )
for ( k = 0; k < g->ncell_max[2]; k++ )
- sfree( g->atoms[i][j][k], "Allocate_Space_for_Grid::g->atoms[i][j][k]" );
+ sfree( g->atoms[i][j][k], __FILE__, __LINE__ );
for ( i = 0; i < g->ncell_max[0]; i++ )
for ( j = 0; j < g->ncell_max[1]; j++ )
for ( k = 0; k < g->ncell_max[2]; k++ )
- g->atoms[i][j][k] = (int*) smalloc( g->max_atoms * sizeof( int ),
- "Allocate_Space_for_Grid::g->atoms[i][j][k]" );
+ g->atoms[i][j][k] = smalloc( g->max_atoms * sizeof( int ),
+ __FILE__, __LINE__ );
}
for ( i = 0; i < g->ncell[0]; i++ )
@@ -274,41 +274,41 @@ static void Deallocate_Grid_Space( grid * const g )
for ( j = 0; j < g->ncell_max[1]; j++ )
for ( k = 0; k < g->ncell_max[2]; k++ )
{
- sfree( g->atoms[i][j][k], "Deallocate_Grid_Space::g->atoms[i][j][k]" );
- sfree( g->nbrs[i][j][k], "Deallocate_Grid_Space::g->nbrs[i][j][k]" );
- sfree( g->nbrs_cp[i][j][k], "Deallocate_Grid_Space::g->nbrs_cp[i][j][k]" );
+ sfree( g->atoms[i][j][k], __FILE__, __LINE__ );
+ sfree( g->nbrs[i][j][k], __FILE__, __LINE__ );
+ sfree( g->nbrs_cp[i][j][k], __FILE__, __LINE__ );
}
for ( i = 0; i < g->ncell_max[0]; i++ )
for ( j = 0; j < g->ncell_max[1]; j++ )
{
- sfree( g->atoms[i][j], "Deallocate_Grid_Space::g->atoms[i][j]" );
- sfree( g->top[i][j], "Deallocate_Grid_Space::g->top[i][j]" );
- sfree( g->mark[i][j], "Deallocate_Grid_Space::g->mark[i][j]" );
- sfree( g->start[i][j], "Deallocate_Grid_Space::g->start[i][j]" );
- sfree( g->end[i][j], "Deallocate_Grid_Space::g->end[i][j]" );
- sfree( g->nbrs[i][j], "Deallocate_Grid_Space::g->nbrs[i][j]" );
- sfree( g->nbrs_cp[i][j], "Deallocate_Grid_Space::g->nbrs_cp[i][j]" );
+ sfree( g->atoms[i][j], __FILE__, __LINE__ );
+ sfree( g->top[i][j], __FILE__, __LINE__ );
+ sfree( g->mark[i][j], __FILE__, __LINE__ );
+ sfree( g->start[i][j], __FILE__, __LINE__ );
+ sfree( g->end[i][j], __FILE__, __LINE__ );
+ sfree( g->nbrs[i][j], __FILE__, __LINE__ );
+ sfree( g->nbrs_cp[i][j], __FILE__, __LINE__ );
}
for ( i = 0; i < g->ncell_max[0]; i++ )
{
- sfree( g->atoms[i], "Deallocate_Grid_Space::g->atoms[i]" );
- sfree( g->top[i], "Deallocate_Grid_Space::g->top[i]" );
- sfree( g->mark[i], "Deallocate_Grid_Space::g->mark[i]" );
- sfree( g->start[i], "Deallocate_Grid_Space::g->start[i]" );
- sfree( g->end[i], "Deallocate_Grid_Space::g->end[i]" );
- sfree( g->nbrs[i], "Deallocate_Grid_Space::g->nbrs[i]" );
- sfree( g->nbrs_cp[i], "Deallocate_Grid_Space::g->nbrs_cp[i]" );
+ sfree( g->atoms[i], __FILE__, __LINE__ );
+ sfree( g->top[i], __FILE__, __LINE__ );
+ sfree( g->mark[i], __FILE__, __LINE__ );
+ sfree( g->start[i], __FILE__, __LINE__ );
+ sfree( g->end[i], __FILE__, __LINE__ );
+ sfree( g->nbrs[i], __FILE__, __LINE__ );
+ sfree( g->nbrs_cp[i], __FILE__, __LINE__ );
}
- sfree( g->atoms, "Deallocate_Grid_Space::g->atoms" );
- sfree( g->top, "Deallocate_Grid_Space::g->top" );
- sfree( g->mark, "Deallocate_Grid_Space::g->mark" );
- sfree( g->start, "Deallocate_Grid_Space::g->start" );
- sfree( g->end, "Deallocate_Grid_Space::g->end" );
- sfree( g->nbrs, "Deallocate_Grid_Space::g->nbrs" );
- sfree( g->nbrs_cp, "Deallocate_Grid_Space::g->nbrs_cp" );
+ sfree( g->atoms, __FILE__, __LINE__ );
+ sfree( g->top, __FILE__, __LINE__ );
+ sfree( g->mark, __FILE__, __LINE__ );
+ sfree( g->start, __FILE__, __LINE__ );
+ sfree( g->end, __FILE__, __LINE__ );
+ sfree( g->nbrs, __FILE__, __LINE__ );
+ sfree( g->nbrs_cp, __FILE__, __LINE__ );
}
@@ -750,19 +750,19 @@ static void Free_Storage( static_storage * const workspace,
for ( i = 0; i < control->cm_solver_restart + 1; ++i )
{
- sfree( workspace->v[i], "Free_Storage::workspace->v[i]" );
+ sfree( workspace->v[i], __FILE__, __LINE__ );
}
- sfree( workspace->v, "Free_Storage::workspace->v" );
+ sfree( workspace->v, __FILE__, __LINE__ );
for ( i = 0; i < 3; ++i )
{
- sfree( workspace->s[i], "Free_Storage::workspace->s[i]" );
- sfree( workspace->t[i], "Free_Storage::workspace->t[i]" );
+ sfree( workspace->s[i], __FILE__, __LINE__ );
+ sfree( workspace->t[i], __FILE__, __LINE__ );
}
- sfree( workspace->s, "Free_Storage::workspace->s" );
- sfree( workspace->t, "Free_Storage::workspace->t" );
+ sfree( workspace->s, __FILE__, __LINE__ );
+ sfree( workspace->t, __FILE__, __LINE__ );
- sfree( workspace->orig_id, "Free_Storage::workspace->orig_id" );
+ sfree( workspace->orig_id, __FILE__, __LINE__ );
}
@@ -793,23 +793,23 @@ void Reorder_Atoms( reax_system * const system, static_storage * const workspace
top = 0;
g = &system->g;
- new_atoms = scalloc( system->N, sizeof(reax_atom), "Reorder_Atoms::new_atoms" );
- orig_id = scalloc( system->N, sizeof(int), "Reorder_Atoms::orig_id" );
- f_old = scalloc( system->N, sizeof(rvec), "Reorder_Atoms::f_old" );
+ new_atoms = scalloc( system->N, sizeof(reax_atom), __FILE__, __LINE__ );
+ orig_id = scalloc( system->N, sizeof(int), __FILE__, __LINE__ );
+ f_old = scalloc( system->N, sizeof(rvec), __FILE__, __LINE__ );
- s = scalloc( 5, sizeof(real *), "Reorder_Atoms::s" );
- t = scalloc( 5, sizeof(real *), "Reorder_Atoms::t" );
+ s = scalloc( 5, sizeof(real *), __FILE__, __LINE__ );
+ t = scalloc( 5, sizeof(real *), __FILE__, __LINE__ );
for ( i = 0; i < 5; ++i )
{
- s[i] = scalloc( system->N_cm, sizeof(real), "Reorder_Atoms::s[i]" );
- t[i] = scalloc( system->N_cm, sizeof(real), "Reorder_Atoms::t[i]" );
+ s[i] = scalloc( system->N_cm, sizeof(real), __FILE__, __LINE__ );
+ t[i] = scalloc( system->N_cm, sizeof(real), __FILE__, __LINE__ );
}
v = scalloc( control->cm_solver_restart + 1, sizeof(real *),
- "Reorder_Atoms::v" );
+ __FILE__, __LINE__ );
for ( i = 0; i < control->cm_solver_restart + 1; ++i )
{
- v[i] = scalloc( system->N_cm, sizeof(real), "Reorder_Atoms::v[i]" );
+ v[i] = scalloc( system->N_cm, sizeof(real), __FILE__, __LINE__ );
}
for ( i = 0; i < g->ncell[0]; i++ )
@@ -837,7 +837,7 @@ void Reorder_Atoms( reax_system * const system, static_storage * const workspace
}
}
- sfree( system->atoms, "Reorder_Atoms::system->atoms" );
+ sfree( system->atoms, __FILE__, __LINE__ );
Free_Storage( workspace, control );
system->atoms = new_atoms;
diff --git a/sPuReMD/src/init_md.c b/sPuReMD/src/init_md.c
index c97368cb6e67a068bbf09184ce6ab26d0f444be0..f57684d7381bcf835b6e8badd5d4408bb0ff7f96 100644
--- a/sPuReMD/src/init_md.c
+++ b/sPuReMD/src/init_md.c
@@ -167,7 +167,7 @@ static void Init_Simulation_Data( reax_system *system, control_params *control,
|| control->ensemble == aNPT || control->compute_pressure == TRUE) )
{
data->press_local = smalloc( sizeof( rtensor ) * control->num_threads,
- "Init_Simulation_Data::data->press_local" );
+ __FILE__, __LINE__ );
}
#endif
@@ -331,42 +331,42 @@ static void Init_Workspace( reax_system *system, control_params *control,
{
/* hydrogen bond list */
workspace->hbond_index = smalloc( system->N_max * sizeof( int ),
- "Init_Workspace::workspace->hbond_index" );
+ __FILE__, __LINE__ );
/* bond order related storage */
workspace->total_bond_order = smalloc( system->N_max * sizeof( real ),
- "Init_Workspace::workspace->bond_order" );
+ __FILE__, __LINE__ );
workspace->Deltap = smalloc( system->N_max * sizeof( real ),
- "Init_Workspace::workspace->Deltap" );
+ __FILE__, __LINE__ );
workspace->Deltap_boc = smalloc( system->N_max * sizeof( real ),
- "Init_Workspace::workspace->Deltap_boc" );
+ __FILE__, __LINE__ );
workspace->dDeltap_self = smalloc( system->N_max * sizeof( rvec ),
- "Init_Workspace::workspace->dDeltap_self" );
+ __FILE__, __LINE__ );
workspace->Delta = smalloc( system->N_max * sizeof( real ),
- "Init_Workspace::workspace->Delta" );
+ __FILE__, __LINE__ );
workspace->Delta_lp = smalloc( system->N_max * sizeof( real ),
- "Init_Workspace::workspace->Delta_lp" );
+ __FILE__, __LINE__ );
workspace->Delta_lp_temp = smalloc( system->N_max * sizeof( real ),
- "Init_Workspace::workspace->Delta_lp_temp" );
+ __FILE__, __LINE__ );
workspace->dDelta_lp = smalloc( system->N_max * sizeof( real ),
- "Init_Workspace::workspace->dDelta_lp" );
+ __FILE__, __LINE__ );
workspace->dDelta_lp_temp = smalloc( system->N_max * sizeof( real ),
- "Init_Workspace::workspace->dDelta_lp_temp" );
+ __FILE__, __LINE__ );
workspace->Delta_e = smalloc( system->N_max * sizeof( real ),
- "Init_Workspace::workspace->Delta_e" );
+ __FILE__, __LINE__ );
workspace->Delta_boc = smalloc( system->N_max * sizeof( real ),
- "Init_Workspace::workspace->Delta_boc" );
+ __FILE__, __LINE__ );
workspace->nlp = smalloc( system->N_max * sizeof( real ),
- "Init_Workspace::workspace->nlp" );
+ __FILE__, __LINE__ );
workspace->nlp_temp = smalloc( system->N_max * sizeof( real ),
- "Init_Workspace::workspace->nlp_temp" );
+ __FILE__, __LINE__ );
workspace->Clp = smalloc( system->N_max * sizeof( real ),
- "Init_Workspace::workspace->Clp" );
+ __FILE__, __LINE__ );
workspace->CdDelta = smalloc( system->N_max * sizeof( real ),
- "Init_Workspace::workspace->CdDelta" );
+ __FILE__, __LINE__ );
workspace->vlpex = smalloc( system->N_max * sizeof( real ),
- "Init_Workspace::workspace->vlpex" );
+ __FILE__, __LINE__ );
}
/* charge method storage */
@@ -408,27 +408,27 @@ static void Init_Workspace( reax_system *system, control_params *control,
|| control->cm_solver_pre_comp_type == FG_ILUT_PC )
{
workspace->droptol = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->droptol" );
+ __FILE__, __LINE__ );
}
workspace->b_s = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->b_s" );
+ __FILE__, __LINE__ );
workspace->b_t = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->b_t" );
+ __FILE__, __LINE__ );
workspace->b_prc = scalloc( system->N_cm_max * 2, sizeof( real ),
- "Init_Workspace::workspace->b_prc" );
+ __FILE__, __LINE__ );
workspace->b_prm = scalloc( system->N_cm_max * 2, sizeof( real ),
- "Init_Workspace::workspace->b_prm" );
+ __FILE__, __LINE__ );
workspace->s = scalloc( 5, sizeof( real* ),
- "Init_Workspace::workspace->s" );
+ __FILE__, __LINE__ );
workspace->t = scalloc( 5, sizeof( real* ),
- "Init_Workspace::workspace->t" );
+ __FILE__, __LINE__ );
for ( i = 0; i < 5; ++i )
{
workspace->s[i] = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->s[i]" );
+ __FILE__, __LINE__ );
workspace->t[i] = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->t[i]" );
+ __FILE__, __LINE__ );
}
}
@@ -494,81 +494,81 @@ static void Init_Workspace( reax_system *system, control_params *control,
case GMRES_S:
case GMRES_H_S:
workspace->y = scalloc( control->cm_solver_restart + 1, sizeof( real ),
- "Init_Workspace::workspace->y" );
+ __FILE__, __LINE__ );
workspace->z = scalloc( control->cm_solver_restart + 1, sizeof( real ),
- "Init_Workspace::workspace->z" );
+ __FILE__, __LINE__ );
workspace->g = scalloc( control->cm_solver_restart + 1, sizeof( real ),
- "Init_Workspace::workspace->g" );
+ __FILE__, __LINE__ );
workspace->h = scalloc( control->cm_solver_restart + 1, sizeof( real*),
- "Init_Workspace::workspace->h" );
+ __FILE__, __LINE__ );
workspace->hs = scalloc( control->cm_solver_restart + 1, sizeof( real ),
- "Init_Workspace::workspace->hs" );
+ __FILE__, __LINE__ );
workspace->hc = scalloc( control->cm_solver_restart + 1, sizeof( real ),
- "Init_Workspace::workspace->hc" );
+ __FILE__, __LINE__ );
workspace->rn = scalloc( control->cm_solver_restart + 1, sizeof( real*),
- "Init_Workspace::workspace->rn" );
+ __FILE__, __LINE__ );
workspace->v = scalloc( control->cm_solver_restart + 1, sizeof( real*),
- "Init_Workspace::workspace->v" );
+ __FILE__, __LINE__ );
for ( i = 0; i < control->cm_solver_restart + 1; ++i )
{
workspace->h[i] = scalloc( control->cm_solver_restart + 1, sizeof( real ),
- "Init_Workspace::workspace->h[i]" );
+ __FILE__, __LINE__ );
workspace->rn[i] = scalloc( system->N_cm_max * 2, sizeof( real ),
- "Init_Workspace::workspace->rn[i]" );
+ __FILE__, __LINE__ );
workspace->v[i] = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->v[i]" );
+ __FILE__, __LINE__ );
}
workspace->r = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->r" );
+ __FILE__, __LINE__ );
workspace->d = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->d" );
+ __FILE__, __LINE__ );
workspace->q = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->q" );
+ __FILE__, __LINE__ );
workspace->p = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->p" );
+ __FILE__, __LINE__ );
break;
case CG_S:
workspace->r = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->r" );
+ __FILE__, __LINE__ );
workspace->d = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->d" );
+ __FILE__, __LINE__ );
workspace->q = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->q" );
+ __FILE__, __LINE__ );
workspace->p = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->p" );
+ __FILE__, __LINE__ );
break;
case SDM_S:
workspace->r = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->r" );
+ __FILE__, __LINE__ );
workspace->d = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->d" );
+ __FILE__, __LINE__ );
workspace->q = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->q" );
+ __FILE__, __LINE__ );
break;
case BiCGStab_S:
workspace->r = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->r" );
+ __FILE__, __LINE__ );
workspace->r_hat = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->r_hat" );
+ __FILE__, __LINE__ );
workspace->d = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->d" );
+ __FILE__, __LINE__ );
workspace->q = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->q" );
+ __FILE__, __LINE__ );
workspace->q_hat = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->q_hat" );
+ __FILE__, __LINE__ );
workspace->p = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->p" );
+ __FILE__, __LINE__ );
workspace->y = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->y" );
+ __FILE__, __LINE__ );
workspace->z = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->z" );
+ __FILE__, __LINE__ );
workspace->g = scalloc( system->N_cm_max, sizeof( real ),
- "Init_Workspace::workspace->g" );
+ __FILE__, __LINE__ );
break;
default:
@@ -580,7 +580,7 @@ static void Init_Workspace( reax_system *system, control_params *control,
#if defined(_OPENMP)
/* SpMV related */
workspace->b_local = smalloc( control->num_threads * system->N_cm_max * sizeof(real),
- "Init_Workspace::b_local" );
+ __FILE__, __LINE__ );
#endif
}
@@ -593,19 +593,19 @@ static void Init_Workspace( reax_system *system, control_params *control,
control->cm_solver_pre_app_type == TRI_SOLVE_GC_PA )
{
workspace->row_levels_L = smalloc( system->N_cm_max * sizeof(unsigned int),
- "Init_Workspace::row_levels_L" );
+ __FILE__, __LINE__ );
workspace->level_rows_L = smalloc( system->N_cm_max * sizeof(unsigned int),
- "Init_Workspace::level_rows_L" );
+ __FILE__, __LINE__ );
workspace->level_rows_cnt_L = smalloc( (system->N_cm_max + 1) * sizeof(unsigned int),
- "Init_Workspace::level_rows_cnt_L" );
+ __FILE__, __LINE__ );
workspace->row_levels_U = smalloc( system->N_cm_max * sizeof(unsigned int),
- "Init_Workspace::row_levels_U" );
+ __FILE__, __LINE__ );
workspace->level_rows_U = smalloc( system->N_cm_max * sizeof(unsigned int),
- "Init_Workspace::level_rows_U" );
+ __FILE__, __LINE__ );
workspace->level_rows_cnt_U = smalloc( (system->N_cm_max + 1) * sizeof(unsigned int),
- "Init_Workspace::level_rows_cnt_U" );
+ __FILE__, __LINE__ );
workspace->top = smalloc( (system->N_cm_max + 1) * sizeof(unsigned int),
- "Init_Workspace::top" );
+ __FILE__, __LINE__ );
}
else
{
@@ -626,21 +626,21 @@ static void Init_Workspace( reax_system *system, control_params *control,
if ( control->cm_solver_pre_app_type == TRI_SOLVE_GC_PA )
{
workspace->color = smalloc( sizeof(unsigned int) * system->N_cm_max,
- "Init_Workspace::color" );
+ __FILE__, __LINE__ );
workspace->to_color = smalloc( sizeof(unsigned int) * system->N_cm_max,
- "Init_Workspace::to_color" );
+ __FILE__, __LINE__ );
workspace->conflict = smalloc( sizeof(unsigned int) * system->N_cm_max,
- "setup_graph_coloring::conflict" );
+ __FILE__, __LINE__ );
workspace->conflict_cnt = smalloc( sizeof(unsigned int) * (control->num_threads + 1),
- "Init_Workspace::conflict_cnt" );
+ __FILE__, __LINE__ );
workspace->recolor = smalloc( sizeof(unsigned int) * system->N_cm_max,
- "Init_Workspace::recolor" );
+ __FILE__, __LINE__ );
workspace->color_top = smalloc( sizeof(unsigned int) * (system->N_cm_max + 1),
- "Init_Workspace::color_top" );
+ __FILE__, __LINE__ );
workspace->permuted_row_col = smalloc( sizeof(unsigned int) * system->N_cm_max,
- "Init_Workspace::premuted_row_col" );
+ __FILE__, __LINE__ );
workspace->permuted_row_col_inv = smalloc( sizeof(unsigned int) * system->N_cm_max,
- "Init_Workspace::premuted_row_col_inv" );
+ __FILE__, __LINE__ );
}
else
{
@@ -658,8 +658,8 @@ static void Init_Workspace( reax_system *system, control_params *control,
if ( control->cm_solver_pre_app_type == TRI_SOLVE_GC_PA
|| control->cm_solver_pre_comp_type == ILUTP_PC )
{
- workspace->y_p = smalloc( sizeof(real) * system->N_cm_max, "Init_Workspace::y_p" );
- workspace->x_p = smalloc( sizeof(real) * system->N_cm_max, "Init_Workspace::x_p" );
+ workspace->y_p = smalloc( sizeof(real) * system->N_cm_max, __FILE__, __LINE__ );
+ workspace->x_p = smalloc( sizeof(real) * system->N_cm_max, __FILE__, __LINE__ );
}
else
{
@@ -671,15 +671,15 @@ static void Init_Workspace( reax_system *system, control_params *control,
if ( control->cm_solver_pre_app_type == JACOBI_ITER_PA )
{
workspace->Dinv_L = smalloc( sizeof(real) * system->N_cm_max,
- "Init_Workspace::Dinv_L" );
+ __FILE__, __LINE__ );
workspace->Dinv_U = smalloc( sizeof(real) * system->N_cm_max,
- "Init_Workspace::Dinv_U" );
+ __FILE__, __LINE__ );
workspace->Dinv_b = smalloc( sizeof(real) * system->N_cm_max,
- "Init_Workspace::Dinv_b" );
+ __FILE__, __LINE__ );
workspace->rp = smalloc( sizeof(real) * system->N_cm_max,
- "Init_Workspace::rp" );
+ __FILE__, __LINE__ );
workspace->rp2 = smalloc( sizeof(real) * system->N_cm_max,
- "Init_Workspace::rp2" );
+ __FILE__, __LINE__ );
}
else
{
@@ -694,7 +694,7 @@ static void Init_Workspace( reax_system *system, control_params *control,
if ( control->cm_solver_pre_comp_type == ILUTP_PC )
{
workspace->perm_ilutp = smalloc( sizeof( int ) * system->N_cm_max,
- "Init_Workspace::workspace->perm_ilutp" );
+ __FILE__, __LINE__ );
}
else
{
@@ -703,29 +703,29 @@ static void Init_Workspace( reax_system *system, control_params *control,
#if defined(QMMM)
workspace->mask_qmmm = smalloc( system->N_cm_max * sizeof( int ),
- "Init_Workspace::workspace->mask_qmmm" );
+ __FILE__, __LINE__ );
#endif
/* integrator storage */
workspace->a = smalloc( system->N_max * sizeof( rvec ),
- "Init_Workspace::workspace->a" );
+ __FILE__, __LINE__ );
workspace->f_old = smalloc( system->N_max * sizeof( rvec ),
- "Init_Workspace::workspace->f_old" );
+ __FILE__, __LINE__ );
workspace->v_const = smalloc( system->N_max * sizeof( rvec ),
- "Init_Workspace::workspace->v_const" );
+ __FILE__, __LINE__ );
#if defined(_OPENMP)
workspace->f_local = smalloc( control->num_threads * system->N_max * sizeof( rvec ),
- "Init_Workspace::workspace->f_local" );
+ __FILE__, __LINE__ );
#endif
/* storage for analysis */
if ( control->molec_anal || control->diffusion_coef )
{
workspace->mark = scalloc( system->N_max, sizeof(int),
- "Init_Workspace::workspace->mark" );
+ __FILE__, __LINE__ );
workspace->old_mark = scalloc( system->N_max, sizeof(int),
- "Init_Workspace::workspace->old_mark" );
+ __FILE__, __LINE__ );
}
else
{
@@ -735,7 +735,7 @@ static void Init_Workspace( reax_system *system, control_params *control,
if ( control->diffusion_coef )
{
workspace->x_old = scalloc( system->N_max, sizeof( rvec ),
- "Init_Workspace::workspace->x_old" );
+ __FILE__, __LINE__ );
}
else
{
@@ -745,31 +745,31 @@ static void Init_Workspace( reax_system *system, control_params *control,
#if defined(TEST_FORCES)
workspace->dDelta = smalloc( system->N_max * sizeof( rvec ),
- "Init_Workspace::workspace->dDelta" );
+ __FILE__, __LINE__ );
workspace->f_ele = smalloc( system->N_max * sizeof( rvec ),
- "Init_Workspace::workspace->f_ele" );
+ __FILE__, __LINE__ );
workspace->f_vdw = smalloc( system->N_max * sizeof( rvec ),
- "Init_Workspace::workspace->f_vdw" );
+ __FILE__, __LINE__ );
workspace->f_be = smalloc( system->N_max * sizeof( rvec ),
- "Init_Workspace::workspace->f_be" );
+ __FILE__, __LINE__ );
workspace->f_lp = smalloc( system->N_max * sizeof( rvec ),
- "Init_Workspace::workspace->f_lp" );
+ __FILE__, __LINE__ );
workspace->f_ov = smalloc( system->N_max * sizeof( rvec ),
- "Init_Workspace::workspace->f_ov" );
+ __FILE__, __LINE__ );
workspace->f_un = smalloc( system->N_max * sizeof( rvec ),
- "Init_Workspace::workspace->f_un" );
+ __FILE__, __LINE__ );
workspace->f_ang = smalloc( system->N_max * sizeof( rvec ),
- "Init_Workspace::workspace->f_ang" );
+ __FILE__, __LINE__ );
workspace->f_coa = smalloc( system->N_max * sizeof( rvec ),
- "Init_Workspace::workspace->f_coa" );
+ __FILE__, __LINE__ );
workspace->f_pen = smalloc( system->N_max * sizeof( rvec ),
- "Init_Workspace::workspace->f_pen" );
+ __FILE__, __LINE__ );
workspace->f_hb = smalloc( system->N_max * sizeof( rvec ),
- "Init_Workspace::workspace->f_hb" );
+ __FILE__, __LINE__ );
workspace->f_tor = smalloc( system->N_max * sizeof( rvec ),
- "Init_Workspace::workspace->f_tor" );
+ __FILE__, __LINE__ );
workspace->f_con = smalloc( system->N_max * sizeof( rvec ),
- "Init_Workspace::workspace->f_con" );
+ __FILE__, __LINE__ );
#endif
workspace->realloc.num_far = -1;
@@ -817,8 +817,8 @@ static void Init_Lists( reax_system *system, control_params *control,
Generate_Neighbor_Lists( system, control, data, workspace, lists );
Htop = 0;
- hb_top = scalloc( system->N, sizeof(int), "Init_Lists::hb_top" );
- bond_top = scalloc( system->N, sizeof(int), "Init_Lists::bond_top" );
+ hb_top = scalloc( system->N, sizeof(int), __FILE__, __LINE__ );
+ bond_top = scalloc( system->N, sizeof(int), __FILE__, __LINE__ );
num_3body = 0;
Estimate_Storage_Sizes( system, control, lists, &Htop,
@@ -1032,8 +1032,8 @@ static void Init_Lists( reax_system *system, control_params *control,
}
#endif
- sfree( hb_top, "Init_Lists::hb_top" );
- sfree( bond_top, "Init_Lists::bond_top" );
+ sfree( hb_top, __FILE__, __LINE__ );
+ sfree( bond_top, __FILE__, __LINE__ );
}
@@ -1048,7 +1048,7 @@ static void Init_Out_Controls( reax_system *system, control_params *control,
strncpy( temp, control->sim_name, TEMP_SIZE - 5 );
temp[TEMP_SIZE - 5] = '\0';
strcat( temp, ".trj" );
- out_control->trj = sfopen( temp, "w" );
+ out_control->trj = sfopen( temp, "w", __FILE__, __LINE__ );
out_control->write_header( system, control, workspace, out_control );
}
else
@@ -1061,7 +1061,7 @@ static void Init_Out_Controls( reax_system *system, control_params *control,
strncpy( temp, control->sim_name, TEMP_SIZE - 5 );
temp[TEMP_SIZE - 5] = '\0';
strcat( temp, ".out" );
- out_control->out = sfopen( temp, "w" );
+ out_control->out = sfopen( temp, "w", __FILE__, __LINE__ );
fprintf( out_control->out, "%-6s%16s%16s%16s%11s%11s%13s%13s%13s\n",
"step", "total_energy", "poten_energy", "kin_energy",
"temp", "target", "volume", "press", "target" );
@@ -1070,7 +1070,7 @@ static void Init_Out_Controls( reax_system *system, control_params *control,
strncpy( temp, control->sim_name, TEMP_SIZE - 5 );
temp[TEMP_SIZE - 5] = '\0';
strcat( temp, ".pot" );
- out_control->pot = sfopen( temp, "w" );
+ out_control->pot = sfopen( temp, "w", __FILE__, __LINE__ );
fprintf( out_control->pot,
"%-6s%13s%13s%13s%13s%13s%13s%13s%13s%13s%13s%13s\n",
"step", "ebond", "eatom", "elp", "eang", "ecoa", "ehb",
@@ -1080,7 +1080,7 @@ static void Init_Out_Controls( reax_system *system, control_params *control,
strncpy( temp, control->sim_name, TEMP_SIZE - 5 );
temp[TEMP_SIZE - 5] = '\0';
strcat( temp, ".log" );
- out_control->log = sfopen( temp, "w" );
+ out_control->log = sfopen( temp, "w", __FILE__, __LINE__ );
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", "cm", "cm_sort", "s_iters", "pre_comp", "pre_app",
@@ -1099,7 +1099,7 @@ static void Init_Out_Controls( reax_system *system, control_params *control,
strncpy( temp, control->sim_name, TEMP_SIZE - 5 );
temp[TEMP_SIZE - 5] = '\0';
strcat( temp, ".prs" );
- out_control->prs = sfopen( temp, "w" );
+ out_control->prs = sfopen( temp, "w", __FILE__, __LINE__ );
#if defined(DEBUG) || defined(DEBUG_FOCUS)
fprintf( out_control->prs, "%-8s %13s %13s %13s %13s %13s %13s\n",
"step", "KExx", "KEyy", "KEzz",
@@ -1120,11 +1120,11 @@ static void Init_Out_Controls( reax_system *system, control_params *control,
if ( output_enabled == TRUE && control->molec_anal )
{
snprintf( temp, TEMP_SIZE, "%.*s.mol", TEMP_SIZE - 5, control->sim_name );
- out_control->mol = sfopen( temp, "w" );
+ out_control->mol = sfopen( temp, "w", __FILE__, __LINE__ );
if ( control->num_ignored )
{
snprintf( temp, TEMP_SIZE, "%.*s.ign", TEMP_SIZE - 5, control->sim_name );
- out_control->ign = sfopen( temp, "w" );
+ out_control->ign = sfopen( temp, "w", __FILE__, __LINE__ );
}
}
else
@@ -1138,7 +1138,7 @@ static void Init_Out_Controls( reax_system *system, control_params *control,
strncpy( temp, control->sim_name, TEMP_SIZE - 5 );
temp[TEMP_SIZE - 5] = '\0';
strcat( temp, ".dpl" );
- out_control->dpl = sfopen( temp, "w" );
+ out_control->dpl = sfopen( temp, "w", __FILE__, __LINE__ );
fprintf( out_control->dpl,
"Step Molecule Count Avg. Dipole Moment Norm\n" );
fflush( out_control->dpl );
@@ -1153,7 +1153,7 @@ static void Init_Out_Controls( reax_system *system, control_params *control,
strncpy( temp, control->sim_name, TEMP_SIZE - 6 );
temp[TEMP_SIZE - 6] = '\0';
strcat( temp, ".drft" );
- out_control->drft = sfopen( temp, "w" );
+ out_control->drft = sfopen( temp, "w", __FILE__, __LINE__ );
fprintf( out_control->drft, "Step Type Count Avg Squared Disp\n" );
fflush( out_control->drft );
}
@@ -1167,62 +1167,62 @@ static void Init_Out_Controls( reax_system *system, control_params *control,
strncpy( temp, control->sim_name, TEMP_SIZE - 6 );
temp[TEMP_SIZE - 6] = '\0';
strcat( temp, ".ebond" );
- out_control->ebond = sfopen( temp, "w" );
+ out_control->ebond = sfopen( temp, "w", __FILE__, __LINE__ );
strncpy( temp, control->sim_name, TEMP_SIZE - 5 );
temp[TEMP_SIZE - 5] = '\0';
strcat( temp, ".elp" );
- out_control->elp = sfopen( temp, "w" );
+ out_control->elp = sfopen( temp, "w", __FILE__, __LINE__ );
strncpy( temp, control->sim_name, TEMP_SIZE - 5 );
temp[TEMP_SIZE - 5] = '\0';
strcat( temp, ".eov" );
- out_control->eov = sfopen( temp, "w" );
+ out_control->eov = sfopen( temp, "w", __FILE__, __LINE__ );
strncpy( temp, control->sim_name, TEMP_SIZE - 5 );
temp[TEMP_SIZE - 5] = '\0';
strcat( temp, ".eun" );
- out_control->eun = sfopen( temp, "w" );
+ out_control->eun = sfopen( temp, "w", __FILE__, __LINE__ );
strncpy( temp, control->sim_name, TEMP_SIZE - 6 );
temp[TEMP_SIZE - 6] = '\0';
strcat( temp, ".eval" );
- out_control->eval = sfopen( temp, "w" );
+ out_control->eval = sfopen( temp, "w", __FILE__, __LINE__ );
strncpy( temp, control->sim_name, TEMP_SIZE - 6 );
temp[TEMP_SIZE - 6] = '\0';
strcat( temp, ".epen" );
- out_control->epen = sfopen( temp, "w" );
+ out_control->epen = sfopen( temp, "w", __FILE__, __LINE__ );
strncpy( temp, control->sim_name, TEMP_SIZE - 6 );
temp[TEMP_SIZE - 6] = '\0';
strcat( temp, ".ecoa" );
- out_control->ecoa = sfopen( temp, "w" );
+ out_control->ecoa = sfopen( temp, "w", __FILE__, __LINE__ );
strncpy( temp, control->sim_name, TEMP_SIZE - 5 );
temp[TEMP_SIZE - 5] = '\0';
strcat( temp, ".ehb" );
- out_control->ehb = sfopen( temp, "w" );
+ out_control->ehb = sfopen( temp, "w", __FILE__, __LINE__ );
strncpy( temp, control->sim_name, TEMP_SIZE - 6 );
temp[TEMP_SIZE - 6] = '\0';
strcat( temp, ".etor" );
- out_control->etor = sfopen( temp, "w" );
+ out_control->etor = sfopen( temp, "w", __FILE__, __LINE__ );
strncpy( temp, control->sim_name, TEMP_SIZE - 6 );
temp[TEMP_SIZE - 6] = '\0';
strcat( temp, ".econ" );
- out_control->econ = sfopen( temp, "w" );
+ out_control->econ = sfopen( temp, "w", __FILE__, __LINE__ );
strncpy( temp, control->sim_name, TEMP_SIZE - 6 );
temp[TEMP_SIZE - 6] = '\0';
strcat( temp, ".evdw" );
- out_control->evdw = sfopen( temp, "w" );
+ out_control->evdw = sfopen( temp, "w", __FILE__, __LINE__ );
strncpy( temp, control->sim_name, TEMP_SIZE - 6 );
temp[TEMP_SIZE - 6] = '\0';
strcat( temp, ".ecou" );
- out_control->ecou = sfopen( temp, "w" );
+ out_control->ecou = sfopen( temp, "w", __FILE__, __LINE__ );
#endif
@@ -1231,67 +1231,67 @@ static void Init_Out_Controls( reax_system *system, control_params *control,
strncpy( temp, control->sim_name, TEMP_SIZE - 5 );
temp[TEMP_SIZE - 5] = '\0';
strcat( temp, ".fbo" );
- out_control->fbo = sfopen( temp, "w" );
+ out_control->fbo = sfopen( temp, "w", __FILE__, __LINE__ );
/* open bond orders derivatives file */
strncpy( temp, control->sim_name, TEMP_SIZE - 6 );
temp[TEMP_SIZE - 6] = '\0';
strcat( temp, ".fdbo" );
- out_control->fdbo = sfopen( temp, "w" );
+ out_control->fdbo = sfopen( temp, "w", __FILE__, __LINE__ );
/* open bond forces file */
strncpy( temp, control->sim_name, TEMP_SIZE - 7 );
temp[TEMP_SIZE - 7] = '\0';
strcat( temp, ".fbond" );
- out_control->fbond = sfopen( temp, "w" );
+ out_control->fbond = sfopen( temp, "w", __FILE__, __LINE__ );
/* open lone-pair forces file */
strncpy( temp, control->sim_name, TEMP_SIZE - 6 );
temp[TEMP_SIZE - 6] = '\0';
strcat( temp, ".flp" );
- out_control->flp = sfopen( temp, "w" );
+ out_control->flp = sfopen( temp, "w", __FILE__, __LINE__ );
/* open overcoordination forces file */
strncpy( temp, control->sim_name, TEMP_SIZE - 7 );
temp[TEMP_SIZE - 7] = '\0';
strcat( temp, ".fatom" );
- out_control->fatom = sfopen( temp, "w" );
+ out_control->fatom = sfopen( temp, "w", __FILE__, __LINE__ );
/* open angle forces file */
strncpy( temp, control->sim_name, TEMP_SIZE - 8 );
temp[TEMP_SIZE - 8] = '\0';
strcat( temp, ".f3body" );
- out_control->f3body = sfopen( temp, "w" );
+ out_control->f3body = sfopen( temp, "w", __FILE__, __LINE__ );
/* open hydrogen bond forces file */
strncpy( temp, control->sim_name, TEMP_SIZE - 5 );
temp[TEMP_SIZE - 5] = '\0';
strcat( temp, ".fhb" );
- out_control->fhb = sfopen( temp, "w" );
+ out_control->fhb = sfopen( temp, "w", __FILE__, __LINE__ );
/* open torsion forces file */
strncpy( temp, control->sim_name, TEMP_SIZE - 8 );
temp[TEMP_SIZE - 8] = '\0';
strcat( temp, ".f4body" );
- out_control->f4body = sfopen( temp, "w" );
+ out_control->f4body = sfopen( temp, "w", __FILE__, __LINE__ );
/* open nonbonded forces file */
strncpy( temp, control->sim_name, TEMP_SIZE - 7 );
temp[TEMP_SIZE - 7] = '\0';
strcat( temp, ".fnonb" );
- out_control->fnonb = sfopen( temp, "w" );
+ out_control->fnonb = sfopen( temp, "w", __FILE__, __LINE__ );
/* open total force file */
strncpy( temp, control->sim_name, TEMP_SIZE - 6 );
temp[TEMP_SIZE - 6] = '\0';
strcat( temp, ".ftot" );
- out_control->ftot = sfopen( temp, "w" );
+ out_control->ftot = sfopen( temp, "w", __FILE__, __LINE__ );
/* open coulomb forces file */
strncpy( temp, control->sim_name, TEMP_SIZE - 7 );
temp[TEMP_SIZE - 7] = '\0';
strcat( temp, ".ftot2" );
- out_control->ftot2 = sfopen( temp, "w" );
+ out_control->ftot2 = sfopen( temp, "w", __FILE__, __LINE__ );
#endif
#undef TEMP_SIZE
@@ -1359,8 +1359,8 @@ static void Finalize_System( reax_system *system, control_params *control,
if ( system->max_num_molec_charge_constraints > 0 )
{
- sfree( system->molec_charge_constraints, "Read_BGF::molec_charge_constraints" );
- sfree( system->molec_charge_constraint_ranges, "Read_BGF::molec_charge_constraint_ranges" );
+ sfree( system->molec_charge_constraints, __FILE__, __LINE__ );
+ sfree( system->molec_charge_constraint_ranges, __FILE__, __LINE__ );
}
system->max_num_molec_charge_constraints = 0;
@@ -1372,7 +1372,7 @@ static void Finalize_System( reax_system *system, control_params *control,
if ( reset == FALSE )
{
- sfree( reax->gp.l, "Finalize_System::reax->gp.l" );
+ sfree( reax->gp.l, __FILE__, __LINE__ );
for ( i = 0; i < reax->max_num_atom_types; i++ )
{
@@ -1380,27 +1380,27 @@ static void Finalize_System( reax_system *system, control_params *control,
{
for ( k = 0; k < reax->max_num_atom_types; k++ )
{
- sfree( reax->fbp[i][j][k], "Finalize_System::reax->fbp[i][j][k]" );
+ sfree( reax->fbp[i][j][k], __FILE__, __LINE__ );
}
- sfree( reax->thbp[i][j], "Finalize_System::reax->thbp[i][j]" );
- sfree( reax->hbp[i][j], "Finalize_System::reax->hbp[i][j]" );
- sfree( reax->fbp[i][j], "Finalize_System::reax->fbp[i][j]" );
+ sfree( reax->thbp[i][j], __FILE__, __LINE__ );
+ sfree( reax->hbp[i][j], __FILE__, __LINE__ );
+ sfree( reax->fbp[i][j], __FILE__, __LINE__ );
}
- sfree( reax->tbp[i], "Finalize_System::reax->tbp[i]" );
- sfree( reax->thbp[i], "Finalize_System::reax->thbp[i]" );
- sfree( reax->hbp[i], "Finalize_System::reax->hbp[i]" );
- sfree( reax->fbp[i], "Finalize_System::reax->fbp[i]" );
+ sfree( reax->tbp[i], __FILE__, __LINE__ );
+ sfree( reax->thbp[i], __FILE__, __LINE__ );
+ sfree( reax->hbp[i], __FILE__, __LINE__ );
+ sfree( reax->fbp[i], __FILE__, __LINE__ );
}
- sfree( reax->sbp, "Finalize_System::reax->sbp" );
- sfree( reax->tbp, "Finalize_System::reax->tbp" );
- sfree( reax->thbp, "Finalize_System::reax->thbp" );
- sfree( reax->hbp, "Finalize_System::reax->hbp" );
- sfree( reax->fbp, "Finalize_System::reax->fbp" );
+ sfree( reax->sbp, __FILE__, __LINE__ );
+ sfree( reax->tbp, __FILE__, __LINE__ );
+ sfree( reax->thbp, __FILE__, __LINE__ );
+ sfree( reax->hbp, __FILE__, __LINE__ );
+ sfree( reax->fbp, __FILE__, __LINE__ );
- sfree( system->atoms, "Finalize_System::system->atoms" );
+ sfree( system->atoms, __FILE__, __LINE__ );
}
}
@@ -1412,7 +1412,7 @@ static void Finalize_Simulation_Data( reax_system *system, control_params *contr
if ( control->ensemble == sNPT || control->ensemble == iNPT
|| control->ensemble == aNPT || control->compute_pressure == TRUE )
{
- sfree( data->press_local, "Finalize_Simulation_Data::data->press_local" );
+ sfree( data->press_local, __FILE__, __LINE__ );
}
#endif
}
@@ -1423,29 +1423,29 @@ static void Finalize_Workspace( reax_system *system, control_params *control,
{
int i;
- sfree( workspace->hbond_index, "Finalize_Workspace::workspace->hbond_index" );
- sfree( workspace->total_bond_order, "Finalize_Workspace::workspace->total_bond_order" );
- sfree( workspace->Deltap, "Finalize_Workspace::workspace->Deltap" );
- sfree( workspace->Deltap_boc, "Finalize_Workspace::workspace->Deltap_boc" );
- sfree( workspace->dDeltap_self, "Finalize_Workspace::workspace->dDeltap_self" );
- sfree( workspace->Delta, "Finalize_Workspace::workspace->Delta" );
- sfree( workspace->Delta_lp, "Finalize_Workspace::workspace->Delta_lp" );
- sfree( workspace->Delta_lp_temp, "Finalize_Workspace::workspace->Delta_lp_temp" );
- sfree( workspace->dDelta_lp, "Finalize_Workspace::workspace->dDelta_lp" );
- sfree( workspace->dDelta_lp_temp, "Finalize_Workspace::workspace->dDelta_lp_temp" );
- sfree( workspace->Delta_e, "Finalize_Workspace::workspace->Delta_e" );
- sfree( workspace->Delta_boc, "Finalize_Workspace::workspace->Delta_boc" );
- sfree( workspace->nlp, "Finalize_Workspace::workspace->nlp" );
- sfree( workspace->nlp_temp, "Finalize_Workspace::workspace->nlp_temp" );
- sfree( workspace->Clp, "Finalize_Workspace::workspace->Clp" );
- sfree( workspace->CdDelta, "Finalize_Workspace::workspace->CdDelta" );
- sfree( workspace->vlpex, "Finalize_Workspace::workspace->vlpex" );
+ sfree( workspace->hbond_index, __FILE__, __LINE__ );
+ 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, "Finalize_Workspace::workspace->map_serials" );
+ sfree( workspace->map_serials, __FILE__, __LINE__ );
}
if ( workspace->H.allocated == TRUE )
@@ -1487,27 +1487,27 @@ static void Finalize_Workspace( reax_system *system, control_params *control,
for ( i = 0; i < 5; ++i )
{
- sfree( workspace->s[i], "Finalize_Workspace::workspace->s[i]" );
- sfree( workspace->t[i], "Finalize_Workspace::workspace->t[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, "Finalize_Workspace::workspace->Hdia_inv" );
+ 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, "Finalize_Workspace::workspace->droptol" );
+ sfree( workspace->droptol, __FILE__, __LINE__ );
}
- sfree( workspace->b_s, "Finalize_Workspace::workspace->b_s" );
- sfree( workspace->b_t, "Finalize_Workspace::workspace->b_t" );
- sfree( workspace->b_prc, "Finalize_Workspace::workspace->b_prc" );
- sfree( workspace->b_prm, "Finalize_Workspace::workspace->b_prm" );
- sfree( workspace->s, "Finalize_Workspace::workspace->s" );
- sfree( workspace->t, "Finalize_Workspace::workspace->t" );
+ 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 )
{
@@ -1515,49 +1515,49 @@ static void Finalize_Workspace( reax_system *system, control_params *control,
case GMRES_H_S:
for ( i = 0; i < control->cm_solver_restart + 1; ++i )
{
- sfree( workspace->h[i], "Finalize_Workspace::workspace->h[i]" );
- sfree( workspace->rn[i], "Finalize_Workspace::workspace->rn[i]" );
- sfree( workspace->v[i], "Finalize_Workspace::workspace->v[i]" );
+ sfree( workspace->h[i], __FILE__, __LINE__ );
+ sfree( workspace->rn[i], __FILE__, __LINE__ );
+ sfree( workspace->v[i], __FILE__, __LINE__ );
}
- sfree( workspace->y, "Finalize_Workspace::workspace->y" );
- sfree( workspace->z, "Finalize_Workspace::workspace->z" );
- sfree( workspace->g, "Finalize_Workspace::workspace->g" );
- sfree( workspace->h, "Finalize_Workspace::workspace->h" );
- sfree( workspace->hs, "Finalize_Workspace::workspace->hs" );
- sfree( workspace->hc, "Finalize_Workspace::workspace->hc" );
- sfree( workspace->rn, "Finalize_Workspace::workspace->rn" );
- sfree( workspace->v, "Finalize_Workspace::workspace->v" );
-
- sfree( workspace->r, "Finalize_Workspace::workspace->r" );
- sfree( workspace->d, "Finalize_Workspace::workspace->d" );
- sfree( workspace->q, "Finalize_Workspace::workspace->q" );
- sfree( workspace->p, "Finalize_Workspace::workspace->p" );
+ 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, "Finalize_Workspace::workspace->r" );
- sfree( workspace->d, "Finalize_Workspace::workspace->d" );
- sfree( workspace->q, "Finalize_Workspace::workspace->q" );
- sfree( workspace->p, "Finalize_Workspace::workspace->p" );
+ 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, "Finalize_Workspace::workspace->r" );
- sfree( workspace->d, "Finalize_Workspace::workspace->d" );
- sfree( workspace->q, "Finalize_Workspace::workspace->q" );
+ sfree( workspace->r, __FILE__, __LINE__ );
+ sfree( workspace->d, __FILE__, __LINE__ );
+ sfree( workspace->q, __FILE__, __LINE__ );
break;
case BiCGStab_S:
- sfree( workspace->r, "Finalize_Workspace::workspace->r" );
- sfree( workspace->r_hat, "Finalize_Workspace::workspace->r_hat" );
- sfree( workspace->d, "Finalize_Workspace::workspace->d" );
- sfree( workspace->q, "Finalize_Workspace::workspace->q" );
- sfree( workspace->q_hat, "Finalize_Workspace::workspace->q_hat" );
- sfree( workspace->p, "Finalize_Workspace::workspace->p" );
- sfree( workspace->y, "Finalize_Workspace::workspace->y" );
- sfree( workspace->z, "Finalize_Workspace::workspace->z" );
- sfree( workspace->g, "Finalize_Workspace::workspace->g" );
+ 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:
@@ -1568,87 +1568,87 @@ static void Finalize_Workspace( reax_system *system, control_params *control,
/* SpMV related */
#if defined(_OPENMP)
- sfree( workspace->b_local, "Finalize_Workspace::b_local" );
+ 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, "Finalize_Workspace::row_levels_L" );
- sfree( workspace->level_rows_L, "Finalize_Workspace::level_rows_L" );
- sfree( workspace->level_rows_cnt_L, "Finalize_Workspace::level_rows_cnt_L" );
- sfree( workspace->row_levels_U, "Finalize_Workspace::row_levels_U" );
- sfree( workspace->level_rows_U, "Finalize_Workspace::level_rows_U" );
- sfree( workspace->level_rows_cnt_U, "Finalize_Workspace::level_rows_cnt_U" );
- sfree( workspace->top, "Finalize_Workspace::top" );
+ 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, "Finalize_Workspace::workspace->color" );
- sfree( workspace->to_color, "Finalize_Workspace::workspace->to_color" );
- sfree( workspace->conflict, "Finalize_Workspace::workspace->conflict" );
- sfree( workspace->conflict_cnt, "Finalize_Workspace::workspace->conflict_cnt" );
- sfree( workspace->recolor, "Finalize_Workspace::workspace->recolor" );
- sfree( workspace->color_top, "Finalize_Workspace::workspace->color_top" );
- sfree( workspace->permuted_row_col, "Finalize_Workspace::workspace->permuted_row_col" );
- sfree( workspace->permuted_row_col_inv, "Finalize_Workspace::workspace->permuted_row_col_inv" );
+ 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, "Finalize_Workspace::workspace->y_p" );
- sfree( workspace->x_p, "Finalize_Workspace::workspace->x_p" );
+ 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, "Finalize_Workspace::Dinv_L" );
- sfree( workspace->Dinv_U, "Finalize_Workspace::Dinv_U" );
- sfree( workspace->Dinv_b, "Finalize_Workspace::Dinv_b" );
- sfree( workspace->rp, "Finalize_Workspace::rp" );
- sfree( workspace->rp2, "Finalize_Workspace::rp2" );
+ 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, "Finalize_Workspace::workspace->perm_ilutp" );
+ sfree( workspace->perm_ilutp, __FILE__, __LINE__ );
}
#if defined(QMMM)
- sfree( workspace->mask_qmmm, "Init_Workspace::workspace->mask_qmmm" );
+ sfree( workspace->mask_qmmm, __FILE__, __LINE__ );
#endif
/* integrator storage */
- sfree( workspace->a, "Finalize_Workspace::workspace->a" );
- sfree( workspace->f_old, "Finalize_Workspace::workspace->f_old" );
- sfree( workspace->v_const, "Finalize_Workspace::workspace->v_const" );
+ sfree( workspace->a, __FILE__, __LINE__ );
+ sfree( workspace->f_old, __FILE__, __LINE__ );
+ sfree( workspace->v_const, __FILE__, __LINE__ );
#if defined(_OPENMP)
- sfree( workspace->f_local, "Finalize_Workspace::workspace->f_local" );
+ sfree( workspace->f_local, __FILE__, __LINE__ );
#endif
/* storage for analysis */
if ( control->molec_anal || control->diffusion_coef )
{
- sfree( workspace->mark, "Finalize_Workspace::workspace->mark" );
- sfree( workspace->old_mark, "Finalize_Workspace::workspace->old_mark" );
+ sfree( workspace->mark, __FILE__, __LINE__ );
+ sfree( workspace->old_mark, __FILE__, __LINE__ );
}
if ( control->diffusion_coef )
{
- sfree( workspace->x_old, "Finalize_Workspace::workspace->x_old" );
+ sfree( workspace->x_old, __FILE__, __LINE__ );
}
if ( reset == FALSE )
{
- sfree( workspace->orig_id, "Finalize_Workspace::workspace->orig_id" );
+ sfree( workspace->orig_id, __FILE__, __LINE__ );
/* space for keeping restriction info, if any */
if ( control->restrict_bonds )
@@ -1656,28 +1656,28 @@ static void Finalize_Workspace( reax_system *system, control_params *control,
for ( i = 0; i < system->N; ++i )
{
sfree( workspace->restricted_list[i],
- "Finalize_Workspace::workspace->restricted_list[i]" );
+ __FILE__, __LINE__ );
}
- sfree( workspace->restricted, "Finalize_Workspace::workspace->restricted" );
- sfree( workspace->restricted_list, "Finalize_Workspace::workspace->restricted_list" );
+ sfree( workspace->restricted, __FILE__, __LINE__ );
+ sfree( workspace->restricted_list, __FILE__, __LINE__ );
}
}
#if defined(TEST_FORCES)
- sfree( workspace->dDelta, "Finalize_Workspace::workspace->dDelta" );
- sfree( workspace->f_ele, "Finalize_Workspace::workspace->f_ele" );
- sfree( workspace->f_vdw, "Finalize_Workspace::workspace->f_vdw" );
- sfree( workspace->f_be, "Finalize_Workspace::workspace->f_be" );
- sfree( workspace->f_lp, "Finalize_Workspace::workspace->f_lp" );
- sfree( workspace->f_ov, "Finalize_Workspace::workspace->f_ov" );
- sfree( workspace->f_un, "Finalize_Workspace::workspace->f_un" );
- sfree( workspace->f_ang, "Finalize_Workspace::workspace->f_ang" );
- sfree( workspace->f_coa, "Finalize_Workspace::workspace->f_coa" );
- sfree( workspace->f_pen, "Finalize_Workspace::workspace->f_pen" );
- sfree( workspace->f_hb, "Finalize_Workspace::workspace->f_hb" );
- sfree( workspace->f_tor, "Finalize_Workspace::workspace->f_tor" );
- sfree( workspace->f_con, "Finalize_Workspace::workspace->f_con" );
+ sfree( workspace->dDelta, __FILE__, __LINE__ );
+ sfree( workspace->f_ele, __FILE__, __LINE__ );
+ sfree( workspace->f_vdw, __FILE__, __LINE__ );
+ sfree( workspace->f_be, __FILE__, __LINE__ );
+ sfree( workspace->f_lp, __FILE__, __LINE__ );
+ sfree( workspace->f_ov, __FILE__, __LINE__ );
+ sfree( workspace->f_un, __FILE__, __LINE__ );
+ sfree( workspace->f_ang, __FILE__, __LINE__ );
+ sfree( workspace->f_coa, __FILE__, __LINE__ );
+ sfree( workspace->f_pen, __FILE__, __LINE__ );
+ sfree( workspace->f_hb, __FILE__, __LINE__ );
+ sfree( workspace->f_tor, __FILE__, __LINE__ );
+ sfree( workspace->f_con, __FILE__, __LINE__ );
#endif
}
@@ -1696,6 +1696,10 @@ static void Finalize_Lists( reax_list **lists )
{
Delete_List( TYP_BOND, lists[BONDS] );
}
+ if ( lists[OLD_BONDS]->allocated == TRUE )
+ {
+ Delete_List( TYP_BOND, lists[OLD_BONDS] );
+ }
if ( lists[THREE_BODIES]->allocated == TRUE )
{
Delete_List( TYP_THREE_BODY, lists[THREE_BODIES] );
@@ -1719,70 +1723,70 @@ void Finalize_Out_Controls( reax_system *system, control_params *control,
{
if ( out_control->write_steps > 0 )
{
- sfclose( out_control->trj, "Finalize_Out_Controls::out_control->trj" );
+ sfclose( out_control->trj, __FILE__, __LINE__ );
}
if ( out_control->log_update_freq > 0 )
{
- sfclose( out_control->out, "Finalize_Out_Controls::out_control->out" );
- sfclose( out_control->pot, "Finalize_Out_Controls::out_control->pot" );
- sfclose( out_control->log, "Finalize_Out_Controls::out_control->log" );
+ 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, "Finalize_Out_Controls::out_control->prs" );
+ sfclose( out_control->prs, __FILE__, __LINE__ );
}
if ( control->molec_anal )
{
- sfclose( out_control->mol, "Finalize_Out_Controls::out_control->mol" );
+ sfclose( out_control->mol, __FILE__, __LINE__ );
if ( control->num_ignored )
{
- sfclose( out_control->ign, "Finalize_Out_Controls::out_control->ign" );
+ sfclose( out_control->ign, __FILE__, __LINE__ );
}
}
if ( control->dipole_anal )
{
- sfclose( out_control->dpl, "Finalize_Out_Controls::out_control->dpl" );
+ sfclose( out_control->dpl, __FILE__, __LINE__ );
}
if ( control->diffusion_coef )
{
- sfclose( out_control->drft, "Finalize_Out_Controls::out_control->drft" );
+ sfclose( out_control->drft, __FILE__, __LINE__ );
}
#if defined(TEST_ENERGY)
- sfclose( out_control->ebond, "Finalize_Out_Controls::out_control->ebond" );
- sfclose( out_control->elp, "Finalize_Out_Controls::out_control->elp" );
- sfclose( out_control->eov, "Finalize_Out_Controls::out_control->eov" );
- sfclose( out_control->eun, "Finalize_Out_Controls::out_control->eun" );
- sfclose( out_control->eval, "Finalize_Out_Controls::out_control->eval" );
- sfclose( out_control->epen, "Finalize_Out_Controls::out_control->epen" );
- sfclose( out_control->ecoa, "Finalize_Out_Controls::out_control->ecoa" );
- sfclose( out_control->ehb, "Finalize_Out_Controls::out_control->ehb" );
- sfclose( out_control->etor, "Finalize_Out_Controls::out_control->etor" );
- sfclose( out_control->econ, "Finalize_Out_Controls::out_control->econ" );
- sfclose( out_control->evdw, "Finalize_Out_Controls::out_control->evdw" );
- sfclose( out_control->ecou, "Finalize_Out_Controls::out_control->ecou" );
+ 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, "Finalize_Out_Controls::out_control->fbo" );
- sfclose( out_control->fdbo, "Finalize_Out_Controls::out_control->fdbo" );
- sfclose( out_control->fbond, "Finalize_Out_Controls::out_control->fbond" );
- sfclose( out_control->flp, "Finalize_Out_Controls::out_control->flp" );
- sfclose( out_control->fatom, "Finalize_Out_Controls::out_control->fatom" );
- sfclose( out_control->f3body, "Finalize_Out_Controls::out_control->f3body" );
- sfclose( out_control->fhb, "Finalize_Out_Controls::out_control->fhb" );
- sfclose( out_control->f4body, "Finalize_Out_Controls::out_control->f4body" );
- sfclose( out_control->fnonb, "Finalize_Out_Controls::out_control->fnonb" );
- sfclose( out_control->ftot, "Finalize_Out_Controls::out_control->ftot" );
- sfclose( out_control->ftot2, "Finalize_Out_Controls::out_control->ftot2" );
+ 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
}
diff --git a/sPuReMD/src/io_tools.c b/sPuReMD/src/io_tools.c
index 24fda64895773228647cffb54e4b562eeeb2420b..c0332ccd7e00c61a66a9b08c1b0170b828fe97e0 100644
--- a/sPuReMD/src/io_tools.c
+++ b/sPuReMD/src/io_tools.c
@@ -400,7 +400,7 @@ void Print_Near_Neighbors( reax_system *system, control_params *control,
reax_list *near_nbrs = lists[NEAR_NBRS];
snprintf( fname, MAX_STR, "%.*s.near_nbrs", MAX_STR - 11, control->sim_name );
- fout = sfopen( fname, "w" );
+ fout = sfopen( fname, "w", __FILE__, __LINE__ );
for ( i = 0; i < system->N; ++i )
{
@@ -420,7 +420,7 @@ void Print_Near_Neighbors( reax_system *system, control_params *control,
}
}
- sfclose( fout, "Print_Near_Neighbors::fout" );
+ sfclose( fout, __FILE__, __LINE__ );
}
@@ -434,7 +434,7 @@ void Print_Near_Neighbors2( reax_system *system, control_params *control,
reax_list *near_nbrs = lists[NEAR_NBRS];
snprintf( fname, MAX_STR, "%.*s.near_nbrs_lgj", MAX_STR - 15, control->sim_name );
- fout = sfopen( fname, "w" );
+ fout = sfopen( fname, "w", __FILE__, __LINE__ );
for ( i = 0; i < system->N; ++i )
{
@@ -455,7 +455,7 @@ void Print_Near_Neighbors2( reax_system *system, control_params *control,
fprintf( fout, "\n");
}
- sfclose( fout, "Print_Near_Neighbors2::fout" );
+ sfclose( fout, __FILE__, __LINE__ );
}
@@ -473,7 +473,7 @@ void Print_Far_Neighbors( reax_system const * const system,
far_nbrs = lists[FAR_NBRS];
snprintf( fname, MAX_STR, "%.*s.%010d.far_nbrs", MAX_STR - 21, control->sim_name, data->step );
- fout = sfopen( fname, "w" );
+ fout = sfopen( fname, "w", __FILE__, __LINE__ );
for ( i = 0; i < system->N; ++i )
{
@@ -506,7 +506,7 @@ void Print_Far_Neighbors( reax_system const * const system,
}
}
- sfclose( fout, "Print_Far_Neighbors::fout" );
+ sfclose( fout, __FILE__, __LINE__ );
}
@@ -525,7 +525,7 @@ void Print_Far_Neighbors2( reax_system *system, control_params *control,
reax_list *far_nbrs = lists[FAR_NBRS];
snprintf( fname, MAX_STR, "%.*s.far_nbrs_lgj", MAX_STR - 14, control->sim_name );
- fout = sfopen( fname, "w" );
+ fout = sfopen( fname, "w", __FILE__, __LINE__ );
int num = 0;
int temp[500];
@@ -546,7 +546,7 @@ void Print_Far_Neighbors2( reax_system *system, control_params *control,
fprintf( fout, "\n");
}
- sfclose( fout, "Print_Far_Neighbors2::fout" );
+ sfclose( fout, __FILE__, __LINE__ );
}
@@ -559,7 +559,7 @@ void Print_Total_Force( reax_system *system, control_params *control,
FILE *fout;
snprintf( fname, MAX_STR, "%.*s.%d.forces", MAX_STR - 10, control->sim_name, data->step );
- fout = sfopen( fname, "w" );
+ fout = sfopen( fname, "w", __FILE__, __LINE__ );
for ( i = 0; i < system->N; ++i )
{
@@ -577,7 +577,7 @@ void Print_Total_Force( reax_system *system, control_params *control,
// fflush( out_control->ftot );
fflush( fout );
- sfclose( fout, "Print_Total_Force::fout" );
+ sfclose( fout, __FILE__, __LINE__ );
}
@@ -711,7 +711,7 @@ void Print_Linear_System( reax_system *system, control_params *control,
FILE *out;
snprintf( fname, 100, "%.*s.state%10d.out", 79, control->sim_name, step );
- out = sfopen( fname, "w" );
+ out = sfopen( fname, "w", __FILE__, __LINE__ );
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",
@@ -720,16 +720,16 @@ void Print_Linear_System( reax_system *system, control_params *control,
system->atoms[i].x[2],
workspace->s[0][i], workspace->b_s[i],
workspace->t[0][i], workspace->b_t[i] );
- sfclose( out, "Print_Linear_System::out" );
+ sfclose( out, __FILE__, __LINE__ );
// snprintf( fname, 100, "x2_%d", step );
- // out = sfopen( fname, "w" );
+ // out = sfopen( fname, "w", __FILE__, __LINE__ );
// for( i = 0; i < system->N; i++ )
// fprintf( out, "%g\n", workspace->s_t[i+system->N] );
- // sfclose( out, "Print_Linear_System::out" );
+ // sfclose( out, __FILE__, __LINE__ );
snprintf( fname, 100, "%.*s.H%10d.out", 83, control->sim_name, step );
- out = sfopen( fname, "w" );
+ out = sfopen( fname, "w", __FILE__, __LINE__ );
H = &workspace->H;
for ( i = 0; i < system->N_cm; ++i )
@@ -749,10 +749,10 @@ void Print_Linear_System( reax_system *system, control_params *control,
workspace->orig_id[i], workspace->orig_id[i], H->val[j] );
}
- sfclose( out, "Print_Linear_System::out" );
+ sfclose( out, __FILE__, __LINE__ );
snprintf( fname, 100, "%.*s.H_sp%10d.out", 80, control->sim_name, step );
- out = sfopen( fname, "w" );
+ out = sfopen( fname, "w", __FILE__, __LINE__ );
H = &workspace->H_sp;
for ( i = 0; i < system->N_cm; ++i )
@@ -772,19 +772,19 @@ void Print_Linear_System( reax_system *system, control_params *control,
workspace->orig_id[i], workspace->orig_id[i], H->val[j] );
}
- sfclose( out, "Print_Linear_System::out" );
+ sfclose( out, __FILE__, __LINE__ );
/*snprintf( fname, 100, "%.*s.b_s%10d", 84, control->sim_name, step );
- out = sfopen( fname, "w" );
+ out = sfopen( fname, "w", __FILE__, __LINE__ );
for( i = 0; i < system->N; i++ )
fprintf( out, "%12.7f\n", workspace->b_s[i] );
- sfclose( out, "Print_Linear_System::out" );
+ sfclose( out, __FILE__, __LINE__ );
snprintf( fname, 100, "%.*s.b_t%10d", 84, control->sim_name, step );
- out = sfopen( fname, "w" );
+ out = sfopen( fname, "w", __FILE__, __LINE__ );
for( i = 0; i < system->N; i++ )
fprintf( out, "%12.7f\n", workspace->b_t[i] );
- sfclose( out, "Print_Linear_System::out" );*/
+ sfclose( out, __FILE__, __LINE__ );*/
}
@@ -796,7 +796,7 @@ void Print_Charges( reax_system *system, control_params *control,
FILE *fout;
snprintf( fname, 100, "%.*s.q%010d", 87, control->sim_name, step );
- fout = sfopen( fname, "w" );
+ fout = sfopen( fname, "w", __FILE__, __LINE__ );
for ( i = 0; i < system->N; ++i )
{
@@ -805,7 +805,7 @@ void Print_Charges( reax_system *system, control_params *control,
workspace->s[0][i], workspace->t[0][i], system->atoms[i].q );
}
- sfclose( fout, "Print_Charges::fout" );
+ sfclose( fout, __FILE__, __LINE__ );
}
@@ -849,11 +849,11 @@ void Print_Sparse_Matrix2( sparse_matrix *A, char *fname, char *mode )
if ( mode == NULL )
{
- f = sfopen( fname, "w" );
+ f = sfopen( fname, "w", __FILE__, __LINE__ );
}
else
{
- f = sfopen( fname, mode );
+ f = sfopen( fname, mode, __FILE__, __LINE__ );
}
for ( i = 0; i < A->n; ++i )
@@ -871,7 +871,7 @@ void Print_Sparse_Matrix2( sparse_matrix *A, char *fname, char *mode )
fprintf( f, "%6d %6d %24.15f\n", i + 1, A->j[A->start[i + 1] - 1] + 1, A->val[A->start[i + 1] - 1] );
}
- sfclose( f, "Print_Sparse_Matrix2::f" );
+ sfclose( f, __FILE__, __LINE__ );
}
@@ -886,7 +886,7 @@ void Read_Sparse_Matrix2( sparse_matrix *A, char *fname )
real val;
FILE *f;
- f = sfopen( fname, "r" );
+ f = sfopen( fname, "r", __FILE__, __LINE__ );
top = 0;
cur_row = 0;
@@ -908,7 +908,7 @@ void Read_Sparse_Matrix2( sparse_matrix *A, char *fname )
A->start[A->n] = top;
- sfclose( f, "Read_Sparse_Matrix2::f" );
+ sfclose( f, __FILE__, __LINE__ );
}
@@ -923,14 +923,14 @@ void Read_Permutation_Matrix( unsigned int *v, char *fname )
double val;
FILE *f;
- f = sfopen( fname, "r" );
+ f = sfopen( fname, "r", __FILE__, __LINE__ );
while ( fscanf( f, "%6u %6u %24lf", &row, &col, &val ) == 3 )
{
v[row - 1] = col - 1;
}
- sfclose( f, "Read_Permuation_Matrix::f" );
+ sfclose( f, __FILE__, __LINE__ );
}
@@ -941,7 +941,7 @@ void Print_Sparse_Matrix_Binary( sparse_matrix *A, char *fname )
int i, j, temp;
FILE *f;
- f = sfopen( fname, "wb" );
+ f = sfopen( fname, "wb", __FILE__, __LINE__ );
/* header: # rows, # nonzeros */
fwrite( &A->n, sizeof(unsigned int), 1, f );
@@ -967,7 +967,7 @@ void Print_Sparse_Matrix_Binary( sparse_matrix *A, char *fname )
}
}
- sfclose( f, "Print_Sparse_Matrix_Binary::f" );
+ sfclose( f, __FILE__, __LINE__ );
}
@@ -976,7 +976,7 @@ void Print_Bonds( reax_system *system, reax_list *bonds, char *fname )
int i, pj;
bond_data *pbond;
bond_order_data *bo_ij;
- FILE *f = sfopen( fname, "w" );
+ FILE *f = sfopen( fname, "w", __FILE__, __LINE__ );
for ( i = 0; i < system->N; ++i )
{
@@ -992,14 +992,14 @@ void Print_Bonds( reax_system *system, reax_list *bonds, char *fname )
}
}
- sfclose( f, "Print_Bonds::f" );
+ sfclose( f, __FILE__, __LINE__ );
}
void Print_Bond_List2( reax_system *system, reax_list *bonds, char *fname )
{
int i, j, id_i, id_j, nbr, pj;
- FILE *f = sfopen( fname, "w" );
+ FILE *f = sfopen( fname, "w", __FILE__, __LINE__ );
int temp[500];
int num = 0;
diff --git a/sPuReMD/src/lin_alg.c b/sPuReMD/src/lin_alg.c
index 5f630a41a296d0f53991d50f6f95ea3feaa978a1..c6abc8347b38295c43c3f086c2de94310764ec18 100644
--- a/sPuReMD/src/lin_alg.c
+++ b/sPuReMD/src/lin_alg.c
@@ -119,7 +119,7 @@ void Sort_Matrix_Rows( sparse_matrix * const A )
// #pragma omp parallel default(none) private(i, j, si, ei, temp) shared(stderr)
#endif
{
- temp = smalloc( sizeof(sparse_matrix_entry) * (A->n + 1), "Sort_Matrix_Rows::temp" );
+ temp = smalloc( sizeof(sparse_matrix_entry) * (A->n + 1), __FILE__, __LINE__ );
/* sort each row of A using column indices */
#if defined(_OPENMP)
@@ -146,7 +146,7 @@ void Sort_Matrix_Rows( sparse_matrix * const A )
}
}
- sfree( temp, "Sort_Matrix_Rows::temp" );
+ sfree( temp, __FILE__, __LINE__ );
}
}
@@ -242,8 +242,7 @@ void setup_sparse_approx_inverse( const sparse_matrix * const A,
Allocate_Matrix( A_spar_patt, A->n, A->n_max, A->m );
}
- list = smalloc( sizeof(real) * A->start[A->n],
- "setup_sparse_approx_inverse::list" );
+ list = smalloc( sizeof(real) * A->start[A->n], __FILE__, __LINE__ );
/* quick-select algorithm for finding the k-th greatest element in the matrix, where
* list: values from the matrix
@@ -366,7 +365,7 @@ void setup_sparse_approx_inverse( const sparse_matrix * const A,
A_spar_patt_full->n_max, A_spar_patt_full->m );
}
- sfree( list, "setup_sparse_approx_inverse::list" );
+ sfree( list, __FILE__, __LINE__ );
}
@@ -399,7 +398,7 @@ void Calculate_Droptol( const sparse_matrix * const A,
if ( droptol_local == NULL )
{
droptol_local = smalloc( omp_get_num_threads() * A->n * sizeof(real),
- "Calculate_Droptol::droptol_local" );
+ __FILE__, __LINE__ );
}
}
@@ -476,7 +475,7 @@ void Calculate_Droptol( const sparse_matrix * const A,
#if defined(_OPENMP)
#pragma omp master
{
- sfree( droptol_local, "Calculate_Droptol::droptol_local" );
+ sfree( droptol_local, __FILE__, __LINE__ );
}
#endif
}
@@ -552,9 +551,9 @@ real ICHOLT( const sparse_matrix * const A, const real * const droptol,
start = Get_Time( );
- Utop = smalloc( (A->n + 1) * sizeof(unsigned int), "ICHOLT::Utop" );
- tmp_j = smalloc( A->n * sizeof(int), "ICHOLT::Utop" );
- tmp_val = smalloc( A->n * sizeof(real), "ICHOLT::Utop" );
+ Utop = smalloc( (A->n + 1) * sizeof(unsigned int), __FILE__, __LINE__ );
+ tmp_j = smalloc( A->n * sizeof(int), __FILE__, __LINE__ );
+ tmp_val = smalloc( A->n * sizeof(real), __FILE__, __LINE__ );
Ltop = 0;
tmptop = 0;
@@ -683,9 +682,9 @@ real ICHOLT( const sparse_matrix * const A, const real * const droptol,
// fprintf( stderr, "nnz(U): %d, max: %d\n", Utop[U->n], U->n * 50 );
- sfree( tmp_val, "ICHOLT::tmp_val" );
- sfree( tmp_j, "ICHOLT::tmp_j" );
- sfree( Utop, "ICHOLT::Utop" );
+ sfree( tmp_val, __FILE__, __LINE__ );
+ sfree( tmp_j, __FILE__, __LINE__ );
+ sfree( Utop, __FILE__, __LINE__ );
return Get_Timing_Info( start );
}
@@ -824,8 +823,8 @@ real ILUT( const sparse_matrix * const A, const real * const droptol,
start = Get_Time( );
/* use a dense vector with masking for the intermediate row w */
- w = smalloc( sizeof(real) * A->n, "ILUT::w" );
- nz_mask = smalloc( sizeof(unsigned int) * A->n, "ILUT::nz_mask" );
+ w = smalloc( sizeof(real) * A->n, __FILE__, __LINE__ );
+ nz_mask = smalloc( sizeof(unsigned int) * A->n, __FILE__, __LINE__ );
compute_full_sparse_matrix( A, A_full, FALSE );
@@ -900,8 +899,8 @@ real ILUT( const sparse_matrix * const A, const real * const droptol,
if ( Ltop + nz_cnt > L->m )
{
L->m = MAX( (5 * nz_cnt) + L->m, (unsigned int) (L->m * SAFE_ZONE) );
- L->j = srealloc( L->j, sizeof(unsigned int) * L->m, "ILUT::L->j" );
- L->val = srealloc( L->val, sizeof(real) * L->m, "ILUT::L->val" );
+ L->j = srealloc( L->j, sizeof(unsigned int) * L->m, __FILE__, __LINE__ );
+ L->val = srealloc( L->val, sizeof(real) * L->m, __FILE__, __LINE__ );
}
/* copy w[0:i-1] to row i of L */
@@ -928,8 +927,8 @@ real ILUT( const sparse_matrix * const A, const real * const droptol,
if ( Utop + nz_cnt > U->m )
{
U->m = MAX( (5 * nz_cnt) + U->m, (unsigned int) (U->m * SAFE_ZONE) );
- U->j = srealloc( U->j, sizeof(unsigned int) * U->m, "ILUT::L->j" );
- U->val = srealloc( U->val, sizeof(real) * U->m, "ILUT::L->val" );
+ U->j = srealloc( U->j, sizeof(unsigned int) * U->m, __FILE__, __LINE__ );
+ U->val = srealloc( U->val, sizeof(real) * U->m, __FILE__, __LINE__ );
}
/* diagonal for U */
@@ -954,8 +953,8 @@ real ILUT( const sparse_matrix * const A, const real * const droptol,
U->start[U->n] = Utop;
Deallocate_Matrix( A_full );
- sfree( nz_mask, "ILUT::nz_mask" );
- sfree( w, "ILUT::w" );
+ sfree( nz_mask, __FILE__, __LINE__ );
+ sfree( w, __FILE__, __LINE__ );
return Get_Timing_Info( start );
}
@@ -980,10 +979,10 @@ real ILUTP( const sparse_matrix * const A, const real * const droptol,
start = Get_Time( );
/* use a dense vector with masking for the intermediate row w */
- w = smalloc( sizeof(real) * A->n, "ILUTP::w" );
- nz_mask = smalloc( sizeof(int) * A->n, "ILUTP::nz_mask" );
- perm = smalloc( sizeof(int) * A->n, "ILUTP::perm" );
- perm_inv = smalloc( sizeof(int) * A->n, "ILUTP::perm_inv" );
+ w = smalloc( sizeof(real) * A->n, __FILE__, __LINE__ );
+ nz_mask = smalloc( sizeof(int) * A->n, __FILE__, __LINE__ );
+ perm = smalloc( sizeof(int) * A->n, __FILE__, __LINE__ );
+ perm_inv = smalloc( sizeof(int) * A->n, __FILE__, __LINE__ );
compute_full_sparse_matrix( A, A_full, FALSE );
@@ -1112,10 +1111,10 @@ real ILUTP( const sparse_matrix * const A, const real * const droptol,
U->start[U->n] = Utop;
Deallocate_Matrix( A_full );
- sfree( perm_inv, "ILUTP::perm_inv" );
- sfree( perm, "ILUTP::perm" );
- sfree( nz_mask, "ILUTP::nz_mask" );
- sfree( w, "ILUTP::w" );
+ sfree( perm_inv, __FILE__, __LINE__ );
+ sfree( perm, __FILE__, __LINE__ );
+ sfree( nz_mask, __FILE__, __LINE__ );
+ sfree( w, __FILE__, __LINE__ );
return Get_Timing_Info( start );
}
@@ -1144,9 +1143,9 @@ real FG_ICHOLT( const sparse_matrix * const A, const real * droptol,
Allocate_Matrix( &DAD, A->n, A->n_max, A->m );
Allocate_Matrix( &U_T_temp, A->n, A->n_max, A->m );
- D = smalloc( sizeof(real) * A->n, "FG_ICHOLT::D" );
- D_inv = smalloc( sizeof(real) * A->n, "FG_ICHOLT::D_inv" );
- gamma = smalloc( sizeof(real) * A->n, "FG_ICHOLT::gamma" );
+ D = smalloc( sizeof(real) * A->n, __FILE__, __LINE__ );
+ D_inv = smalloc( sizeof(real) * A->n, __FILE__, __LINE__ );
+ gamma = smalloc( sizeof(real) * A->n, __FILE__, __LINE__ );
#if defined(_OPENMP)
#pragma omp parallel for schedule(dynamic,512) \
@@ -1321,9 +1320,9 @@ real FG_ICHOLT( const sparse_matrix * const A, const real * droptol,
Deallocate_Matrix( &U_T_temp );
Deallocate_Matrix( &DAD );
- sfree( gamma, "FG_ICHOLT::gamma" );
- sfree( D_inv, "FG_ICHOLT::D_inv" );
- sfree( D, "FG_ICHOLT::D" );
+ sfree( gamma, __FILE__, __LINE__ );
+ sfree( D_inv, __FILE__, __LINE__ );
+ sfree( D, __FILE__, __LINE__ );
return Get_Timing_Info( start );
}
@@ -1353,9 +1352,9 @@ real FG_ILUT( const sparse_matrix * const A, const real * droptol,
Allocate_Matrix( &L_temp, A->n, A->n_max, A->m );
Allocate_Matrix( &U_T_temp, A->n, A->n_max, A->m );
- D = smalloc( sizeof(real) * A->n, "FG_ILUT::D" );
- D_inv = smalloc( sizeof(real) * A->n, "FG_ILUT::D_inv" );
- gamma = smalloc( sizeof(real) * A->n, "FG_ILUT::gamma" );
+ D = smalloc( sizeof(real) * A->n, __FILE__, __LINE__ );
+ D_inv = smalloc( sizeof(real) * A->n, __FILE__, __LINE__ );
+ gamma = smalloc( sizeof(real) * A->n, __FILE__, __LINE__ );
#if defined(_OPENMP)
#pragma omp parallel for schedule(dynamic,512) \
@@ -1617,9 +1616,9 @@ real FG_ILUT( const sparse_matrix * const A, const real * droptol,
Deallocate_Matrix( &U_T_temp );
Deallocate_Matrix( &L_temp );
Deallocate_Matrix( &DAD );
- sfree( gamma, "FG_ILUT::gamma" );
- sfree( D_inv, "FG_ILUT::D_inv" );
- sfree( D, "FG_ILUT::D_inv" );
+ sfree( gamma, __FILE__, __LINE__ );
+ sfree( D_inv, __FILE__, __LINE__ );
+ sfree( D, __FILE__, __LINE__ );
return Get_Timing_Info( start );
}
@@ -1677,10 +1676,10 @@ real sparse_approx_inverse( const sparse_matrix * const A,
shared(stderr)
#endif
{
- X = smalloc( sizeof(char) * A->n, "sparse_approx_inverse::X" );
- Y = smalloc( sizeof(char) * A->n, "sparse_approx_inverse::Y" );
- pos_x = smalloc( sizeof(int) * A->n, "sparse_approx_inverse::pos_x" );
- pos_y = smalloc( sizeof(int) * A->n, "sparse_approx_inverse::pos_y" );
+ X = smalloc( sizeof(char) * A->n, __FILE__, __LINE__ );
+ Y = smalloc( sizeof(char) * A->n, __FILE__, __LINE__ );
+ pos_x = smalloc( sizeof(int) * A->n, __FILE__, __LINE__ );
+ pos_y = smalloc( sizeof(int) * A->n, __FILE__, __LINE__ );
e_j = NULL;
dense_matrix = NULL;
@@ -1750,15 +1749,13 @@ real sparse_approx_inverse( const sparse_matrix * const A,
/* N x M dense matrix */
if ( dense_matrix == NULL )
{
- dense_matrix = smalloc( sizeof(real) * N * M,
- "sparse_approx_inverse::dense_matrix" );
+ dense_matrix = smalloc( sizeof(real) * N * M, __FILE__, __LINE__ );
dense_matrix_size = sizeof(real) * N * M;
}
else if ( dense_matrix_size < sizeof(real) * N * M )
{
- sfree( dense_matrix, "sparse_approx_inverse::dense_matrix" );
- dense_matrix = smalloc( sizeof(real) * N * M,
- "sparse_approx_inverse::dense_matrix" );
+ sfree( dense_matrix, __FILE__, __LINE__ );
+ dense_matrix = smalloc( sizeof(real) * N * M, __FILE__, __LINE__ );
dense_matrix_size = sizeof(real) * N * M;
}
@@ -1786,13 +1783,13 @@ real sparse_approx_inverse( const sparse_matrix * const A,
* that is the full column of the identity matrix */
if ( e_j == NULL )
{
- e_j = smalloc( sizeof(real) * M, "sparse_approx_inverse::e_j" );
+ e_j = smalloc( sizeof(real) * M, __FILE__, __LINE__ );
e_j_size = sizeof(real) * M;
}
else if ( e_j_size < sizeof(real) * M )
{
- sfree( e_j, "sparse_approx_inverse::e_j" );
- e_j = smalloc( sizeof(real) * M, "sparse_approx_inverse::e_j" );
+ sfree( e_j, __FILE__, __LINE__ );
+ e_j = smalloc( sizeof(real) * M, __FILE__, __LINE__ );
e_j_size = sizeof(real) * M;
}
@@ -1833,12 +1830,12 @@ real sparse_approx_inverse( const sparse_matrix * const A,
}
}
- sfree( dense_matrix, "sparse_approx_inverse::dense_matrix" );
- sfree( e_j, "sparse_approx_inverse::e_j" );
- sfree( pos_y, "sparse_approx_inverse::pos_y" );
- sfree( pos_x, "sparse_approx_inverse::pos_x" );
- sfree( Y, "sparse_approx_inverse::Y" );
- sfree( X, "sparse_approx_inverse::X" );
+ sfree( dense_matrix, __FILE__, __LINE__ );
+ sfree( e_j, __FILE__, __LINE__ );
+ sfree( pos_y, __FILE__, __LINE__ );
+ sfree( pos_x, __FILE__, __LINE__ );
+ sfree( Y, __FILE__, __LINE__ );
+ sfree( X, __FILE__, __LINE__ );
}
return Get_Timing_Info( start );
@@ -1945,7 +1942,7 @@ void Transpose( const sparse_matrix * const A, sparse_matrix * const A_t )
{
unsigned int i, j, pj, *A_t_top;
- A_t_top = scalloc( A->n + 1, sizeof(unsigned int), "Transpose::A_t_top" );
+ A_t_top = scalloc( A->n + 1, sizeof(unsigned int), __FILE__, __LINE__ );
for ( i = 0; i < A->n + 1; ++i )
{
@@ -1980,7 +1977,7 @@ void Transpose( const sparse_matrix * const A, sparse_matrix * const A_t )
}
}
- sfree( A_t_top, "Transpose::A_t_top" );
+ sfree( A_t_top, __FILE__, __LINE__ );
}
@@ -2317,8 +2314,8 @@ void graph_coloring( const control_params * const control,
}
}
- fb_color = smalloc( sizeof(int) * A->n, "graph_coloring::fb_color" );
- conflict_local = smalloc( sizeof(unsigned int) * A->n, "graph_coloring::fb_color" );
+ fb_color = smalloc( sizeof(int) * A->n, __FILE__, __LINE__ );
+ conflict_local = smalloc( sizeof(unsigned int) * A->n, __FILE__, __LINE__ );
while ( workspace->recolor_cnt > 0 )
{
@@ -2415,8 +2412,8 @@ void graph_coloring( const control_params * const control,
p_conflict = p_temp;
}
- sfree( conflict_local, "graph_coloring::conflict_local" );
- sfree( fb_color, "graph_coloring::fb_color" );
+ sfree( conflict_local, __FILE__, __LINE__ );
+ sfree( fb_color, __FILE__, __LINE__ );
}
}
@@ -3925,7 +3922,7 @@ real condest( const sparse_matrix * const L, const sparse_matrix * const U )
N = L->n;
- e = smalloc( sizeof(real) * N, "condest::e" );
+ e = smalloc( sizeof(real) * N, __FILE__, __LINE__ );
for ( i = 0; i < N; ++i )
e[i] = 1.0;
@@ -3944,7 +3941,7 @@ real condest( const sparse_matrix * const L, const sparse_matrix * const U )
}
- sfree( e, "condest::e" );
+ sfree( e, __FILE__, __LINE__ );
return c;
}
diff --git a/sPuReMD/src/list.c b/sPuReMD/src/list.c
index 21dd6a69e64ad0e742f939e8d31440c684b1ccd0..fd9087e4f23de79b6a1b1a06ec58d0941fdf2c8b 100644
--- a/sPuReMD/src/list.c
+++ b/sPuReMD/src/list.c
@@ -44,8 +44,8 @@ void Make_List( int n, int n_max, int total_intrs, int type, reax_list* l )
l->n_max = n_max;
l->total_intrs = total_intrs;
- l->index = smalloc( n_max * sizeof(int), "Make_List::l->index" );
- l->end_index = smalloc( n_max * sizeof(int), "Make_List::l->end_index" );
+ l->index = smalloc( n_max * sizeof(int), __FILE__, __LINE__ );
+ l->end_index = smalloc( n_max * sizeof(int), __FILE__, __LINE__ );
switch ( type )
{
@@ -53,7 +53,7 @@ void Make_List( int n, int n_max, int total_intrs, int type, reax_list* l )
if ( l->total_intrs > 0 )
{
l->three_body_list = smalloc( l->total_intrs * sizeof(three_body_interaction_data),
- "Make_List::l->three_body_list" );
+ __FILE__, __LINE__ );
}
else
{
@@ -65,7 +65,7 @@ void Make_List( int n, int n_max, int total_intrs, int type, reax_list* l )
if ( l->total_intrs > 0 )
{
l->bond_list = smalloc( l->total_intrs * sizeof(bond_data),
- "Make_List::l->bond_list" );
+ __FILE__, __LINE__ );
}
else
{
@@ -77,7 +77,7 @@ void Make_List( int n, int n_max, int total_intrs, int type, reax_list* l )
if ( l->total_intrs > 0 )
{
l->dbo_list = smalloc( l->total_intrs * sizeof(dbond_data),
- "Make_List::l->dbo_list" );
+ __FILE__, __LINE__ );
}
else
{
@@ -89,7 +89,7 @@ void Make_List( int n, int n_max, int total_intrs, int type, reax_list* l )
if ( l->total_intrs > 0 )
{
l->dDelta_list = smalloc( l->total_intrs * sizeof(dDelta_data),
- "Make_List::l->dDelta_list" );
+ __FILE__, __LINE__ );
}
else
{
@@ -101,7 +101,7 @@ void Make_List( int n, int n_max, int total_intrs, int type, reax_list* l )
if ( l->total_intrs > 0 )
{
l->far_nbr_list = smalloc( l->total_intrs * sizeof(far_neighbor_data),
- "Make_List::l->far_nbr_list" );
+ __FILE__, __LINE__ );
}
else
{
@@ -113,7 +113,7 @@ void Make_List( int n, int n_max, int total_intrs, int type, reax_list* l )
if ( l->total_intrs > 0 )
{
l->near_nbr_list = smalloc( l->total_intrs * sizeof(near_neighbor_data),
- "Make_List::l->near_nbr_list" );
+ __FILE__, __LINE__ );
}
else
{
@@ -125,7 +125,7 @@ void Make_List( int n, int n_max, int total_intrs, int type, reax_list* l )
if ( l->total_intrs > 0 )
{
l->hbond_list = smalloc( l->total_intrs * sizeof(hbond_data),
- "Make_List::l->hbond_list" );
+ __FILE__, __LINE__ );
}
else
{
@@ -157,57 +157,57 @@ void Delete_List( int type, reax_list* l )
l->n_max = 0;
l->total_intrs = 0;
- sfree( l->index, "Delete_List::l->index" );
- sfree( l->end_index, "Delete_List::l->end_index" );
+ sfree( l->index, __FILE__, __LINE__ );
+ sfree( l->end_index, __FILE__, __LINE__ );
switch ( type )
{
case TYP_THREE_BODY:
if ( l->three_body_list != NULL )
{
- sfree( l->three_body_list, "Delete_List::l->three_body_list" );
+ sfree( l->three_body_list, __FILE__, __LINE__ );
}
break;
case TYP_BOND:
if ( l->bond_list != NULL )
{
- sfree( l->bond_list, "Delete_List::l->bond_list" );
+ sfree( l->bond_list, __FILE__, __LINE__ );
}
break;
case TYP_DBO:
if ( l->dbo_list != NULL )
{
- sfree( l->dbo_list, "Delete_List::l->dbo_list" );
+ sfree( l->dbo_list, __FILE__, __LINE__ );
}
break;
case TYP_DDELTA:
if ( l->dDelta_list != NULL )
{
- sfree( l->dDelta_list, "Delete_List::l->dDelta_list" );
+ sfree( l->dDelta_list, __FILE__, __LINE__ );
}
break;
case TYP_FAR_NEIGHBOR:
if ( l->far_nbr_list != NULL )
{
- sfree( l->far_nbr_list, "Delete_List::l->far_nbr_list" );
+ sfree( l->far_nbr_list, __FILE__, __LINE__ );
}
break;
case TYP_NEAR_NEIGHBOR:
if ( l->near_nbr_list != NULL )
{
- sfree( l->near_nbr_list, "Delete_List::l->near_nbr_list" );
+ sfree( l->near_nbr_list, __FILE__, __LINE__ );
}
break;
case TYP_HBOND:
if ( l->hbond_list != NULL )
{
- sfree( l->hbond_list, "Delete_List::l->hbond_list" );
+ sfree( l->hbond_list, __FILE__, __LINE__ );
}
break;
diff --git a/sPuReMD/src/lookup.c b/sPuReMD/src/lookup.c
index a7b0b99c139e65034ea1591796649becb4a029bf..ec2b4b5441719f5c40563ffb9b3a73a0c67c948a 100644
--- a/sPuReMD/src/lookup.c
+++ b/sPuReMD/src/lookup.c
@@ -58,11 +58,11 @@ static void Natural_Cubic_Spline( const real *h, const real *f,
real *a, *b, *c, *d, *v;
/* allocate space for linear system */
- a = smalloc( sizeof(real) * n, "Natural_Cubic_Spline::a" );
- b = smalloc( sizeof(real) * n, "Natural_Cubic_Spline::b" );
- c = smalloc( sizeof(real) * n, "Natural_Cubic_Spline::c" );
- d = smalloc( sizeof(real) * n, "Natural_Cubic_Spline::d" );
- v = smalloc( sizeof(real) * n, "Natural_Cubic_Spline::v" );
+ a = smalloc( sizeof(real) * n, __FILE__, __LINE__ );
+ b = smalloc( sizeof(real) * n, __FILE__, __LINE__ );
+ c = smalloc( sizeof(real) * n, __FILE__, __LINE__ );
+ d = smalloc( sizeof(real) * n, __FILE__, __LINE__ );
+ v = smalloc( sizeof(real) * n, __FILE__, __LINE__ );
/* build linear system */
a[0] = 0.0;
@@ -113,11 +113,11 @@ static void Natural_Cubic_Spline( const real *h, const real *f,
coef[i - 1].a = f[i];
}
- sfree( a, "Natural_Cubic_Spline::a" );
- sfree( b, "Natural_Cubic_Spline::b" );
- sfree( c, "Natural_Cubic_Spline::c" );
- sfree( d, "Natural_Cubic_Spline::d" );
- sfree( v, "Natural_Cubic_Spline::v" );
+ sfree( a, __FILE__, __LINE__ );
+ sfree( b, __FILE__, __LINE__ );
+ sfree( c, __FILE__, __LINE__ );
+ sfree( d, __FILE__, __LINE__ );
+ sfree( v, __FILE__, __LINE__ );
}
@@ -128,11 +128,11 @@ static void Complete_Cubic_Spline( const real *h, const real *f, real v0, real v
real *a, *b, *c, *d, *v;
/* allocate space for the linear system */
- a = smalloc( sizeof(real) * n, "Complete_Cubic_Spline::a" );
- b = smalloc( sizeof(real) * n, "Complete_Cubic_Spline::b" );
- c = smalloc( sizeof(real) * n, "Complete_Cubic_Spline::c" );
- d = smalloc( sizeof(real) * n, "Complete_Cubic_Spline::d" );
- v = smalloc( sizeof(real) * n, "Complete_Cubic_Spline::v" );
+ a = smalloc( sizeof(real) * n, __FILE__, __LINE__ );
+ b = smalloc( sizeof(real) * n, __FILE__, __LINE__ );
+ c = smalloc( sizeof(real) * n, __FILE__, __LINE__ );
+ d = smalloc( sizeof(real) * n, __FILE__, __LINE__ );
+ v = smalloc( sizeof(real) * n, __FILE__, __LINE__ );
/* build the linear system */
a[0] = 0.0;
@@ -176,11 +176,11 @@ static void Complete_Cubic_Spline( const real *h, const real *f, real v0, real v
coef[i - 1].a = f[i];
}
- sfree( a, "Complete_Cubic_Spline::a" );
- sfree( b, "Complete_Cubic_Spline::b" );
- sfree( c, "Complete_Cubic_Spline::c" );
- sfree( d, "Complete_Cubic_Spline::d" );
- sfree( v, "Complete_Cubic_Spline::v" );
+ sfree( a, __FILE__, __LINE__ );
+ sfree( b, __FILE__, __LINE__ );
+ sfree( c, __FILE__, __LINE__ );
+ sfree( d, __FILE__, __LINE__ );
+ sfree( v, __FILE__, __LINE__ );
}
@@ -239,27 +239,21 @@ void Make_LR_Lookup_Table( reax_system *system, control_params *control,
num_atom_types = system->reax_param.num_atom_types;
dr = control->nonb_cut / control->tabulate;
- h = scalloc( control->tabulate + 2, sizeof(real),
- "Make_LR_Lookup_Table::h" );
- fh = scalloc( control->tabulate + 2, sizeof(real),
- "Make_LR_Lookup_Table::fh" );
- fvdw = scalloc( control->tabulate + 2, sizeof(real),
- "Make_LR_Lookup_Table::fvdw" );
- fCEvd = scalloc( control->tabulate + 2, sizeof(real),
- "Make_LR_Lookup_Table::fCEvd" );
- fele = scalloc( control->tabulate + 2, sizeof(real),
- "Make_LR_Lookup_Table::fele" );
- fCEclmb = scalloc( control->tabulate + 2, sizeof(real),
- "Make_LR_Lookup_Table::fCEclmb" );
+ h = scalloc( control->tabulate + 2, sizeof(real), __FILE__, __LINE__ );
+ fh = scalloc( control->tabulate + 2, sizeof(real), __FILE__, __LINE__ );
+ fvdw = scalloc( control->tabulate + 2, sizeof(real), __FILE__, __LINE__ );
+ fCEvd = scalloc( control->tabulate + 2, sizeof(real), __FILE__, __LINE__ );
+ fele = scalloc( control->tabulate + 2, sizeof(real), __FILE__, __LINE__ );
+ fCEclmb = scalloc( control->tabulate + 2, sizeof(real), __FILE__, __LINE__ );
/* allocate Long-Range LookUp Table space based on
number of atom types in the ffield file */
- workspace->LR = (LR_lookup_table**) smalloc( num_atom_types * sizeof(LR_lookup_table*),
- "Make_LR_Lookup_Table::LR" );
+ workspace->LR = smalloc( num_atom_types * sizeof(LR_lookup_table*),
+ __FILE__, __LINE__ );
for ( i = 0; i < num_atom_types; ++i )
{
- workspace->LR[i] = (LR_lookup_table*) smalloc( num_atom_types * sizeof(LR_lookup_table),
- "Make_LR_Lookup_Table::LR[i]");
+ workspace->LR[i] = smalloc( num_atom_types * sizeof(LR_lookup_table),
+ __FILE__, __LINE__ );
}
/* most atom types in ffield file will not exist in the current
@@ -291,22 +285,22 @@ void Make_LR_Lookup_Table( reax_system *system, control_params *control,
workspace->LR[i][j].inv_dx = control->tabulate / control->nonb_cut;
workspace->LR[i][j].y =
smalloc( workspace->LR[i][j].n * sizeof(LR_data),
- "Make_LR_Lookup_Table::LR[i][j].y" );
+ __FILE__, __LINE__ );
workspace->LR[i][j].H =
smalloc( workspace->LR[i][j].n * sizeof(cubic_spline_coef),
- "Make_LR_Lookup_Table::LR[i][j].H" );
+ __FILE__, __LINE__ );
workspace->LR[i][j].vdW =
smalloc( workspace->LR[i][j].n * sizeof(cubic_spline_coef),
- "Make_LR_Lookup_Table::LR[i][j].vdW" );
+ __FILE__, __LINE__ );
workspace->LR[i][j].CEvd =
smalloc( workspace->LR[i][j].n * sizeof(cubic_spline_coef),
- "Make_LR_Lookup_Table::LR[i][j].CEvd" );
+ __FILE__, __LINE__ );
workspace->LR[i][j].ele =
smalloc( workspace->LR[i][j].n * sizeof(cubic_spline_coef),
- "Make_LR_Lookup_Table::LR[i][j].ele" );
+ __FILE__, __LINE__ );
workspace->LR[i][j].CEclmb =
smalloc( workspace->LR[i][j].n * sizeof(cubic_spline_coef),
- "Make_LR_Lookup_Table::LR[i][j].CEclmb" );
+ __FILE__, __LINE__ );
for ( r = 1; r <= control->tabulate; ++r )
{
@@ -417,12 +411,12 @@ void Make_LR_Lookup_Table( reax_system *system, control_params *control,
fprintf( stderr, "eele_maxerr: %24.15e\n", eele_maxerr );
*******/
- sfree( h, "Make_LR_Lookup_Table::h" );
- sfree( fh, "Make_LR_Lookup_Table::fh" );
- sfree( fvdw, "Make_LR_Lookup_Table::fvdw" );
- sfree( fCEvd, "Make_LR_Lookup_Table::fCEvd" );
- sfree( fele, "Make_LR_Lookup_Table::fele" );
- sfree( fCEclmb, "Make_LR_Lookup_Table::fCEclmb" );
+ sfree( h, __FILE__, __LINE__ );
+ sfree( fh, __FILE__, __LINE__ );
+ sfree( fvdw, __FILE__, __LINE__ );
+ sfree( fCEvd, __FILE__, __LINE__ );
+ sfree( fele, __FILE__, __LINE__ );
+ sfree( fCEclmb, __FILE__, __LINE__ );
}
@@ -452,18 +446,18 @@ void Finalize_LR_Lookup_Table( reax_system *system, control_params *control,
{
if ( existing_types[j] )
{
- sfree( workspace->LR[i][j].y, "Finalize_LR_Lookup_Table::LR[i][j].y" );
- sfree( workspace->LR[i][j].H, "Finalize_LR_Lookup_Table::LR[i][j].H" );
- sfree( workspace->LR[i][j].vdW, "Finalize_LR_Lookup_Table::LR[i][j].vdW" );
- sfree( workspace->LR[i][j].CEvd, "Finalize_LR_Lookup_Table::LR[i][j].CEvd" );
- sfree( workspace->LR[i][j].ele, "Finalize_LR_Lookup_Table::LR[i][j].ele" );
- sfree( workspace->LR[i][j].CEclmb, "Finalize_LR_Lookup_Table::LR[i][j].CEclmb" );
+ sfree( workspace->LR[i][j].y, __FILE__, __LINE__ );
+ sfree( workspace->LR[i][j].H, __FILE__, __LINE__ );
+ sfree( workspace->LR[i][j].vdW, __FILE__, __LINE__ );
+ sfree( workspace->LR[i][j].CEvd, __FILE__, __LINE__ );
+ sfree( workspace->LR[i][j].ele, __FILE__, __LINE__ );
+ sfree( workspace->LR[i][j].CEclmb, __FILE__, __LINE__ );
}
}
}
- sfree( workspace->LR[i], "Finalize_LR_Lookup_Table::LR[i]" );
+ sfree( workspace->LR[i], __FILE__, __LINE__ );
}
- sfree( workspace->LR, "Finalize_LR_Lookup_Table::LR" );
+ sfree( workspace->LR, __FILE__, __LINE__ );
}
diff --git a/sPuReMD/src/reax_types.h b/sPuReMD/src/reax_types.h
index be9c48fe94c5739625d1d3fcda28ac2ec81b5fea..2179e26a4cc5fb4a93d522d52e9a7347fdec8ab5 100644
--- a/sPuReMD/src/reax_types.h
+++ b/sPuReMD/src/reax_types.h
@@ -759,8 +759,10 @@ struct reax_atom
{
/* integer representation of element type of this atom */
int type;
- /* TRUE if the atom is a dummy atom, FALSE otherwise */
- int dummy;
+ /* TRUE if the atom is a dummy atom, FALSE otherwise
+ * Note: dummy atoms do not form bonds but participate
+ * in other (non-bonded) interactions */
+ int is_dummy;
/* relative coordinates in terms of periodic images of the
* simulation box which are used to track if this atom moves
* between images between simulation steps which regenerate
diff --git a/sPuReMD/src/restart.c b/sPuReMD/src/restart.c
index 43ef92027138ace8de2199b232732c068fdd23a8..037d2870598d01a7a2ebfe19904f4077eae6d5c6 100644
--- a/sPuReMD/src/restart.c
+++ b/sPuReMD/src/restart.c
@@ -38,7 +38,7 @@ void Write_Binary_Restart( reax_system *system, control_params *control,
restart_atom res_data;
snprintf( fname, MAX_STR, "%.*s.res%d", MAX_STR - 12, control->sim_name, data->step );
- fres = sfopen( fname, "wb" );
+ fres = sfopen( fname, "wb", __FILE__, __LINE__ );
res_header.step = data->step;
res_header.N = system->N;
@@ -63,7 +63,7 @@ void Write_Binary_Restart( reax_system *system, control_params *control,
fwrite( &res_data, sizeof(restart_atom), 1, fres );
}
- sfclose( fres, "Write_Binary_Restart::fres" );
+ sfclose( fres, __FILE__, __LINE__ );
#if defined(DEBUG_FOCUS)
fprintf( stderr, "write restart - " );
@@ -81,7 +81,7 @@ void Read_Binary_Restart( const char * const fname, reax_system *system,
restart_header res_header;
restart_atom res_data;
- fres = sfopen( fname, "rb" );
+ fres = sfopen( fname, "rb", __FILE__, __LINE__ );
/* parse header of restart file */
fread( &res_header, sizeof(restart_header), 1, fres );
@@ -139,7 +139,7 @@ void Read_Binary_Restart( const char * const fname, reax_system *system,
fprintf( stderr, "system->N: %d, i: %d\n", system->N, i );
#endif
- sfclose( fres, "Read_Binary_Restart::fres" );
+ sfclose( fres, __FILE__, __LINE__ );
data->step = data->prev_steps;
/* target num. of MD sim. steps (nsteps)
@@ -157,7 +157,7 @@ void Write_ASCII_Restart( reax_system *system, control_params *control,
reax_atom *p_atom;
snprintf( fname, MAX_STR + 8, "%s.res%d", control->sim_name, data->step );
- fres = sfopen( fname, "w" );
+ fres = sfopen( fname, "w", __FILE__, __LINE__ );
fprintf( fres, RESTART_HEADER,
data->step, system->N, data->therm.T, data->therm.xi,
@@ -176,7 +176,7 @@ void Write_ASCII_Restart( reax_system *system, control_params *control,
p_atom->v[0], p_atom->v[1], p_atom->v[2] );
}
- sfclose( fres, "Write_ASCII_Restart::fres" );
+ sfclose( fres, __FILE__, __LINE__ );
#if defined(DEBUG_FOCUS)
fprintf( stderr, "write restart - " );
@@ -192,7 +192,7 @@ void Read_ASCII_Restart( const char * const fname, reax_system *system,
FILE *fres;
reax_atom *p_atom;
- fres = sfopen( fname, "r" );
+ fres = sfopen( fname, "r", __FILE__, __LINE__ );
/* parse header of restart file */
fscanf( fres, READ_RESTART_HEADER,
@@ -238,7 +238,7 @@ void Read_ASCII_Restart( const char * const fname, reax_system *system,
workspace->map_serials[workspace->orig_id[i]] = i;
}
- sfclose( fres, "Read_ASCII_Restart::fres" );
+ sfclose( fres, __FILE__, __LINE__ );
data->step = data->prev_steps;
/* target num. of MD sim. steps (nsteps)
diff --git a/sPuReMD/src/spuremd.c b/sPuReMD/src/spuremd.c
index b3f5ebd83cdd329829800735679f779801b80562..564f3312c860d1376b205bb86761e415b1a20b58 100644
--- a/sPuReMD/src/spuremd.c
+++ b/sPuReMD/src/spuremd.c
@@ -158,30 +158,19 @@ static void Allocate_Top_Level_Structs( spuremd_handle ** handle )
int i;
/* top-level allocation */
- *handle = smalloc( sizeof(spuremd_handle), "Allocate_Top_Level_Structs::handle" );
+ *handle = smalloc( sizeof(spuremd_handle), __FILE__, __LINE__ );
/* second-level allocations */
- (*handle)->system = smalloc( sizeof(reax_system),
- "Allocate_Top_Level_Structs::handle->system" );
-
- (*handle)->control = smalloc( sizeof(control_params),
- "Allocate_Top_Level_Structs::handle->control" );
-
- (*handle)->data = smalloc( sizeof(simulation_data),
- "Allocate_Top_Level_Structs::handle->data" );
-
- (*handle)->workspace = smalloc( sizeof(static_storage),
- "Allocate_Top_Level_Structs::handle->workspace" );
-
- (*handle)->lists = smalloc( sizeof(reax_list *) * LIST_N,
- "Allocate_Top_Level_Structs::handle->lists" );
+ (*handle)->system = smalloc( sizeof(reax_system), __FILE__, __LINE__ );
+ (*handle)->control = smalloc( sizeof(control_params), __FILE__, __LINE__ );
+ (*handle)->data = smalloc( sizeof(simulation_data), __FILE__, __LINE__ );
+ (*handle)->workspace = smalloc( sizeof(static_storage), __FILE__, __LINE__ );
+ (*handle)->lists = smalloc( sizeof(reax_list *) * LIST_N, __FILE__, __LINE__ );
for ( i = 0; i < LIST_N; ++i )
{
- (*handle)->lists[i] = smalloc( sizeof(reax_list),
- "Allocate_Top_Level_Structs::handle->lists[i]" );
+ (*handle)->lists[i] = smalloc( sizeof(reax_list), __FILE__, __LINE__ );
}
- (*handle)->out_control = smalloc( sizeof(output_controls),
- "Allocate_Top_Level_Structs::handle->out_control" );
+ (*handle)->out_control = smalloc( sizeof(output_controls), __FILE__, __LINE__ );
}
@@ -503,18 +492,18 @@ int cleanup( const void * const handle )
spmd_handle->workspace, spmd_handle->lists, spmd_handle->out_control,
spmd_handle->output_enabled, FALSE );
- sfree( spmd_handle->out_control, "cleanup::spmd_handle->out_control" );
+ sfree( spmd_handle->out_control, __FILE__, __LINE__ );
for ( i = 0; i < LIST_N; ++i )
{
- sfree( spmd_handle->lists[i], "cleanup::spmd_handle->lists[i]" );
+ sfree( spmd_handle->lists[i], __FILE__, __LINE__ );
}
- sfree( spmd_handle->lists, "cleanup::spmd_handle->lists" );
- sfree( spmd_handle->workspace, "cleanup::spmd_handle->workspace" );
- sfree( spmd_handle->data, "cleanup::spmd_handle->data" );
- sfree( spmd_handle->control, "cleanup::spmd_handle->control" );
- sfree( spmd_handle->system, "cleanup::spmd_handle->system" );
+ sfree( spmd_handle->lists, __FILE__, __LINE__ );
+ sfree( spmd_handle->workspace, __FILE__, __LINE__ );
+ sfree( spmd_handle->data, __FILE__, __LINE__ );
+ sfree( spmd_handle->control, __FILE__, __LINE__ );
+ sfree( spmd_handle->system, __FILE__, __LINE__ );
- sfree( spmd_handle, "cleanup::spmd_handle" );
+ sfree( spmd_handle, __FILE__, __LINE__ );
ret = SPUREMD_SUCCESS;
}
@@ -997,10 +986,10 @@ void * setup_qmmm( int qm_num_atoms, const char * const qm_symbols,
{
spmd_handle->system->molec_charge_constraints = smalloc(
sizeof(real) * spmd_handle->system->num_molec_charge_constraints,
- "setup_qmmm::molec_charge_constraints" );
+ __FILE__, __LINE__ );
spmd_handle->system->molec_charge_constraint_ranges = smalloc(
sizeof(int) * 2 * spmd_handle->system->num_molec_charge_constraints,
- "setup_qmmm::molec_charge_constraint_ranges" );
+ __FILE__, __LINE__ );
for ( i = 0; i < spmd_handle->system->num_molec_charge_constraints; ++i )
{
@@ -1148,17 +1137,17 @@ int reset_qmmm( const void * const handle, int qm_num_atoms,
if ( spmd_handle->system->max_num_molec_charge_constraints > 0 )
{
sfree( spmd_handle->system->molec_charge_constraints,
- "reset_qmmm::molec_charge_constraints" );
+ __FILE__, __LINE__ );
sfree( spmd_handle->system->molec_charge_constraint_ranges,
- "reset_qmmm::molec_charge_constraint_ranges" );
+ __FILE__, __LINE__ );
}
spmd_handle->system->molec_charge_constraints = smalloc(
sizeof(real) * spmd_handle->system->num_molec_charge_constraints,
- "reset_qmmm::molec_charge_constraints" );
+ __FILE__, __LINE__ );
spmd_handle->system->molec_charge_constraint_ranges = smalloc(
sizeof(int) * 2 * spmd_handle->system->num_molec_charge_constraints,
- "reset_qmmm::molec_charge_constraint_ranges" );
+ __FILE__, __LINE__ );
spmd_handle->system->max_num_molec_charge_constraints
= spmd_handle->system->num_molec_charge_constraints;
diff --git a/sPuReMD/src/tool_box.c b/sPuReMD/src/tool_box.c
index 0483e048cec24801e1bf05a1e0f4851818ce11dc..dab56c3393c01ec740274dac33eba96b0b8cd59f 100644
--- a/sPuReMD/src/tool_box.c
+++ b/sPuReMD/src/tool_box.c
@@ -170,12 +170,24 @@ int is_Valid_Serial( int serial )
}
-int Check_Input_Range( int val, int lo, int hi, char *message )
+/* Validate atom serial numbers in BGF geometry file
+ *
+ * val: atom serial to validate
+ * lo: lower limit of valid serial range
+ * hi: upper limit of valid serial range
+ * filename: source filename of caller
+ * line: source line of caller
+ */
+int Check_Input_Range( int val, int lo, int hi, const char * const filename,
+ int line )
{
if ( val < lo || val > hi )
{
- fprintf( stderr, "[ERROR] %s\nInput %d - Out of range %d-%d. Terminating...\n",
- message, val, lo, hi );
+ fprintf( stderr, "[ERROR] Invalid BGF serial\n" );
+ fprintf( stderr, " [INFO] At line %d in file %.*s\n",
+ line, (int) strlen(filename), filename );
+ fprintf( stderr, " [INFO] Input %d - Out of range %d-%d. Terminating...\n",
+ val, lo, hi );
exit( INVALID_INPUT );
}
@@ -290,14 +302,14 @@ void Allocate_Tokenizer_Space( char **line, size_t line_size,
{
int i;
- *line = smalloc( sizeof(char) * line_size, "Allocate_Tokenizer_Space::*line" );
- *backup = smalloc( sizeof(char) * backup_size, "Allocate_Tokenizer_Space::*backup" );
- *tokens = smalloc( sizeof(char*) * num_tokens, "Allocate_Tokenizer_Space::*tokens" );
+ *line = smalloc( sizeof(char) * line_size, __FILE__, __LINE__ );
+ *backup = smalloc( sizeof(char) * backup_size, __FILE__, __LINE__ );
+ *tokens = smalloc( sizeof(char*) * num_tokens, __FILE__, __LINE__ );
for ( i = 0; i < num_tokens; i++ )
{
(*tokens)[i] = smalloc( sizeof(char) * token_size,
- "Allocate_Tokenizer_Space::(*tokens)[i]" );
+ __FILE__, __LINE__ );
}
}
@@ -309,12 +321,12 @@ void Deallocate_Tokenizer_Space( char **line, char **backup,
for ( i = 0; i < num_tokens; i++ )
{
- sfree( (*tokens)[i], "Deallocate_Tokenizer_Space::tokens[i]" );
+ sfree( (*tokens)[i], __FILE__, __LINE__ );
}
- sfree( *line, "Deallocate_Tokenizer_Space::line" );
- sfree( *backup, "Deallocate_Tokenizer_Space::backup" );
- sfree( *tokens, "Deallocate_Tokenizer_Space::tokens" );
+ sfree( *line, __FILE__, __LINE__ );
+ sfree( *backup, __FILE__, __LINE__ );
+ sfree( *tokens, __FILE__, __LINE__ );
}
@@ -343,27 +355,30 @@ int Tokenize( char* s, char*** tok, size_t token_len )
}
-/***************** taken from lammps ************************/
/* Safe wrapper around libc malloc
*
* n: num. of bytes to allocated
- * name: message with details about pointer, used for warnings/errors
+ * filename: source filename of caller
+ * line: source line of caller
*
* returns: ptr to allocated memory
* */
-void * smalloc( size_t n, const char *name )
+void * smalloc( size_t n, const char * const filename, int line )
{
void *ptr;
if ( n == 0 )
{
- fprintf( stderr, "[ERROR] failed to allocate %zu bytes for array %s.\n",
- n, name );
+ fprintf( stderr, "[ERROR] failed to allocate %zu bytes for array\n",
+ n );
+ fprintf( stderr, " [INFO] At line %d in file %.*s\n",
+ line, (int) strlen(filename), filename );
exit( INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "[INFO] requesting memory for %s\n", name );
+ fprintf( stderr, "[INFO] requesting allocation of %zu bytes of memory at line %d in file %.*s\n",
+ n, line, (int) strlen(filename), filename );
fflush( stderr );
#endif
@@ -371,8 +386,10 @@ void * smalloc( size_t n, const char *name )
if ( ptr == NULL )
{
- fprintf( stderr, "[ERROR] failed to allocate %zu bytes for array %s.\n",
- n, name );
+ fprintf( stderr, "[ERROR] failed to allocate %zu bytes for array\n",
+ n );
+ fprintf( stderr, " [INFO] At line %d in file %.*s\n",
+ line, (int) strlen(filename), filename );
exit( INSUFFICIENT_MEMORY );
}
@@ -388,29 +405,27 @@ void * smalloc( size_t n, const char *name )
/* Safe wrapper around libc realloc
*
* n: num. of bytes to reallocated
- * name: message with details about pointer, used for warnings/errors
+ * filename: source filename of caller
+ * line: source line of caller
*
* returns: ptr to reallocated memory
* */
-void * srealloc( void *ptr, size_t n, const char *name )
+void * srealloc( void *ptr, size_t n, const char * const filename, int line )
{
void *new_ptr;
if ( n == 0 )
{
- fprintf( stderr, "[ERROR] failed to reallocate %zu bytes for array %s.\n",
- n, name );
+ fprintf( stderr, "[ERROR] failed to reallocate %zu bytes for array\n",
+ n );
+ fprintf( stderr, " [INFO] At line %d in file %.*s\n",
+ line, (int) strlen(filename), filename );
exit( INSUFFICIENT_MEMORY );
}
- if ( ptr == NULL )
- {
- fprintf( stderr, "[INFO] trying to allocate %zu NEW bytes for array %s.\n",
- n, name );
- }
-
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "[INFO] requesting memory for %s\n", name );
+ fprintf( stderr, "[INFO] requesting reallocation of %zu bytes of memory at line %d in file %.*s\n",
+ n, line, (int) strlen(filename), filename );
fflush( stderr );
#endif
@@ -420,8 +435,10 @@ void * srealloc( void *ptr, size_t n, const char *name )
* but we needed more memory, so abort */
if ( new_ptr == NULL )
{
- fprintf( stderr, "[ERROR] failed to reallocate %zu bytes for array %s.\n",
- n, name );
+ fprintf( stderr, "[ERROR] failed to reallocate %zu bytes for array\n",
+ n );
+ fprintf( stderr, " [INFO] At line %d in file %.*s\n",
+ line, (int) strlen(filename), filename );
exit( INSUFFICIENT_MEMORY );
}
@@ -438,23 +455,27 @@ void * srealloc( void *ptr, size_t n, const char *name )
*
* n: num. of elements to allocated (each of size bytes)
* size: num. of bytes per element
- * name: message with details about pointer, used for warnings/errors
+ * filename: source filename of caller
+ * line: source line of caller
*
* returns: ptr to allocated memory, all bits initialized to zeros
* */
-void * scalloc( size_t n, size_t size, const char *name )
+void * scalloc( size_t n, size_t size, const char * const filename, int line )
{
void *ptr;
if ( n == 0 )
{
- fprintf( stderr, "[ERROR] failed to allocate %zu bytes for array %s.\n",
- n * size, name );
+ fprintf( stderr, "[ERROR] failed to allocate %zu bytes for array\n",
+ n * size );
+ fprintf( stderr, " [INFO] At line %d in file %.*s\n",
+ line, (int) strlen(filename), filename );
exit( INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "[INFO] requesting memory for %s\n", name );
+ fprintf( stderr, "[INFO] requesting allocation of %zu bytes of zeroed memory at line %d in file %.*s\n",
+ n * size, line, (int) strlen(filename), filename );
fflush( stderr );
#endif
@@ -462,8 +483,10 @@ void * scalloc( size_t n, size_t size, const char *name )
if ( ptr == NULL )
{
- fprintf( stderr, "[ERROR] failed to allocate %zu bytes for array %s.\n",
- n * size, name );
+ fprintf( stderr, "[ERROR] failed to allocate %zu bytes for array\n",
+ n * size );
+ fprintf( stderr, " [INFO] At line %d in file %.*s\n",
+ line, (int) strlen(filename), filename );
exit( INSUFFICIENT_MEMORY );
}
@@ -479,19 +502,22 @@ void * scalloc( size_t n, size_t size, const char *name )
/* Safe wrapper around libc free
*
* ptr: pointer to dynamically allocated memory which will be deallocated
- * name: message with details about pointer, used for warnings/errors
+ * filename: source filename of caller
+ * line: source line of caller
* */
-void sfree( void *ptr, const char *name )
+void sfree( void *ptr, const char * const filename, int line )
{
if ( ptr == NULL )
{
- fprintf( stderr, "[WARNING] trying to free the already NULL pointer %s!\n",
- name );
+ fprintf( stderr, "[WARNING] trying to free the already NULL pointer\n" );
+ fprintf( stderr, " [INFO] At line %d in file %.*s\n",
+ line, (int) strlen(filename), filename );
return;
}
#if defined(DEBUG_FOCUS)
- fprintf( stderr, "[INFO] trying to free pointer %s\n", name );
+ fprintf( stderr, "[INFO] trying to free pointer at line %d in file %.*s\n",
+ line, (int) strlen(filename), filename );
fflush( stderr );
fprintf( stderr, "[INFO] address: %p [SFREE]\n", (void *) ptr );
fflush( stderr );
@@ -505,20 +531,27 @@ void sfree( void *ptr, const char *name )
*
* fname: name of file to be opened
* mode: mode in which to open file
+ * filename: source filename of caller
+ * line: source line of caller
* */
-FILE * sfopen( const char * fname, const char * mode )
+FILE * sfopen( const char * fname, const char * mode,
+ const char * const filename, int line )
{
FILE * ptr;
if ( fname == NULL )
{
fprintf( stderr, "[ERROR] trying to open file\n" );
+ fprintf( stderr, " [INFO] At line %d in file %.*s\n",
+ line, (int) strlen(filename), filename );
fprintf( stderr, " [INFO] NULL file name\n" );
exit( INVALID_INPUT );
}
if ( mode == NULL )
{
fprintf( stderr, "[ERROR] trying to open file\n" );
+ fprintf( stderr, " [INFO] At line %d in file %.*s\n",
+ line, (int) strlen(filename), filename );
fprintf( stderr, " [INFO] NULL mode\n" );
exit( INVALID_INPUT );
}
@@ -529,6 +562,8 @@ FILE * sfopen( const char * fname, const char * mode )
{
fprintf( stderr, "[ERROR] failed to open file %s with mode %s\n",
fname, mode );
+ fprintf( stderr, " [INFO] At line %d in file %.*s\n",
+ line, (int) strlen(filename), filename );
exit( INVALID_INPUT );
}
@@ -538,18 +573,19 @@ FILE * sfopen( const char * fname, const char * mode )
/* Safe wrapper around libc fclose
*
- * fname: name of file to be opened
- * mode: mode in which to open file
- * msg: message to be printed in case of error
+ * fp: pointer to file to close
+ * filename: source filename of caller
+ * line: source line of caller
* */
-void sfclose( FILE * fp, const char * msg )
+void sfclose( FILE * fp, const char * const filename, int line )
{
int ret;
if ( fp == NULL )
{
fprintf( stderr, "[WARNING] trying to close NULL file pointer. Returning...\n" );
- fprintf( stderr, " [INFO] %s\n", msg );
+ fprintf( stderr, " [INFO] At line %d in file %.*s\n",
+ line, (int) strlen(filename), filename );
return;
}
@@ -558,7 +594,8 @@ void sfclose( FILE * fp, const char * msg )
if ( ret != 0 )
{
fprintf( stderr, "[ERROR] error detected when closing file\n" );
- fprintf( stderr, " [INFO] %s\n", msg );
+ fprintf( stderr, " [INFO] At line %d in file %.*s\n",
+ line, (int) strlen(filename), filename );
exit( INVALID_INPUT );
}
}
diff --git a/sPuReMD/src/tool_box.h b/sPuReMD/src/tool_box.h
index 88e333c9a9a6b8d0a0a7a69240e0523177883c67..dbc8028e0b55ebfdce33bed6b6559aeb94912474 100644
--- a/sPuReMD/src/tool_box.h
+++ b/sPuReMD/src/tool_box.h
@@ -39,7 +39,7 @@ void Make_Point( real, real, real, rvec * );
int is_Valid_Serial( int );
-int Check_Input_Range( int, int, int, char * );
+int Check_Input_Range( int, int, int, const char * const, int );
void Trim_Spaces( char * const, const size_t );
@@ -63,23 +63,20 @@ void Deallocate_Tokenizer_Space( char **, char **, char ***,
int Tokenize( char *, char ***, size_t );
-/* from lammps */
-void * smalloc( size_t, const char * );
+void * smalloc( size_t, const char * const, int );
-void * srealloc( void *, size_t, const char * );
+void * srealloc( void *, size_t, const char * const, int );
-void * scalloc( size_t, size_t, const char * );
+void * scalloc( size_t, size_t, const char * const, int );
-void sfree( void *, const char * );
+void sfree( void *, const char * const, int );
-FILE * sfopen( const char *, const char * );
+FILE * sfopen( const char *, const char *, const char * const, int );
-void sfclose( FILE *, const char * );
+void sfclose( FILE *, const char * const, int );
-int sstrtol( const char * const,
- const char * const, int );
+int sstrtol( const char * const, const char * const, int );
-double sstrtod( const char * const,
- const char * const, int );
+double sstrtod( const char * const, const char * const, int );
#endif