diff --git a/sPuReMD/src/geo_tools.c b/sPuReMD/src/geo_tools.c
index 88f8799c27e783718ccb45f1fc93adea1a5070bb..4f929e9abf6762830697e166a1f265ec71837baf 100644
--- a/sPuReMD/src/geo_tools.c
+++ b/sPuReMD/src/geo_tools.c
@@ -624,6 +624,7 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
char chain_id;
char s_a[12], s_b[12], s_c[12], s_alpha[12], s_beta[12], s_gamma[12];
int i, n, atom_cnt, token_cnt, bgf_serial, ratom, crystx_found;
+ rvec x;
ratom = 0;
crystx_found = FALSE;
@@ -729,9 +730,15 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
workspace->orig_id[ atom_cnt ] = bgf_serial;
/* copy atomic positions */
- system->atoms[atom_cnt].x[0] = sstrtod( s_x, __FILE__, __LINE__ );
- system->atoms[atom_cnt].x[1] = sstrtod( s_y, __FILE__, __LINE__ );
- system->atoms[atom_cnt].x[2] = sstrtod( s_z, __FILE__, __LINE__ );
+ x[0] = sstrtod( s_x, __FILE__, __LINE__ );
+ x[1] = sstrtod( s_y, __FILE__, __LINE__ );
+ x[2] = sstrtod( s_z, __FILE__, __LINE__ );
+
+ Fit_to_Periodic_Box( &system->box, x );
+
+ system->atoms[atom_cnt].x[0] = x[0];
+ system->atoms[atom_cnt].x[1] = x[1];
+ system->atoms[atom_cnt].x[2] = x[2];
/* atom name and type */
strncpy( system->atoms[atom_cnt].name, atom_name,
diff --git a/sPuReMD/src/list.c b/sPuReMD/src/list.c
index 8f69ca35a0f8a75173a3a4273b6171dc2b21f282..4dd71e25922e02897ae59aba097684cfe93748f2 100644
--- a/sPuReMD/src/list.c
+++ b/sPuReMD/src/list.c
@@ -29,7 +29,7 @@ void Make_List( int n, int n_max, int total_intrs, int type, reax_list* l )
assert( n > 0 );
assert( n_max > 0 );
assert( n_max >= n );
- assert( total_intrs > 0 );
+ assert( total_intrs >= 0 );
assert( l != NULL );
if ( l->allocated == TRUE )
@@ -50,48 +50,104 @@ void Make_List( int n, int n_max, int total_intrs, int type, reax_list* l )
switch ( type )
{
case TYP_VOID:
- l->v = smalloc( l->total_intrs * sizeof(void),
- "Make_List::l->v" );
+ if ( l->total_intrs > 0 )
+ {
+ l->v = smalloc( l->total_intrs * sizeof(void),
+ "Make_List::l->v" );
+ }
+ else
+ {
+ l->v = NULL;
+ }
break;
case TYP_THREE_BODY:
- l->three_body_list = smalloc( l->total_intrs * sizeof(three_body_interaction_data),
- "Make_List::l->three_body_list" );
+ if ( l->total_intrs > 0 )
+ {
+ l->three_body_list = smalloc( l->total_intrs * sizeof(three_body_interaction_data),
+ "Make_List::l->three_body_list" );
+ }
+ else
+ {
+ l->three_body_list = NULL;
+ }
break;
case TYP_BOND:
- l->bond_list = smalloc( l->total_intrs * sizeof(bond_data),
- "Make_List::l->bond_list" );
+ if ( l->total_intrs > 0 )
+ {
+ l->bond_list = smalloc( l->total_intrs * sizeof(bond_data),
+ "Make_List::l->bond_list" );
+ }
+ else
+ {
+ l->bond_list = NULL;
+ }
break;
case TYP_DBO:
- l->dbo_list = smalloc( l->total_intrs * sizeof(dbond_data),
- "Make_List::l->dbo_list" );
+ if ( l->total_intrs > 0 )
+ {
+ l->dbo_list = smalloc( l->total_intrs * sizeof(dbond_data),
+ "Make_List::l->dbo_list" );
+ }
+ else
+ {
+ l->dbo_list = NULL;
+ }
break;
case TYP_DDELTA:
- l->dDelta_list = smalloc( l->total_intrs * sizeof(dDelta_data),
- "Make_List::l->dDelta_list" );
+ if ( l->total_intrs > 0 )
+ {
+ l->dDelta_list = smalloc( l->total_intrs * sizeof(dDelta_data),
+ "Make_List::l->dDelta_list" );
+ }
+ else
+ {
+ l->dDelta_list = NULL;
+ }
break;
case TYP_FAR_NEIGHBOR:
- l->far_nbr_list = smalloc( l->total_intrs * sizeof(far_neighbor_data),
- "Make_List::l->far_nbr_list" );
+ if ( l->total_intrs > 0 )
+ {
+ l->far_nbr_list = smalloc( l->total_intrs * sizeof(far_neighbor_data),
+ "Make_List::l->far_nbr_list" );
+ }
+ else
+ {
+ l->far_nbr_list = NULL;
+ }
break;
case TYP_NEAR_NEIGHBOR:
- l->near_nbr_list = smalloc( l->total_intrs * sizeof(near_neighbor_data),
- "Make_List::l->near_nbr_list" );
+ if ( l->total_intrs > 0 )
+ {
+ l->near_nbr_list = smalloc( l->total_intrs * sizeof(near_neighbor_data),
+ "Make_List::l->near_nbr_list" );
+ }
+ else
+ {
+ l->near_nbr_list = NULL;
+ }
break;
case TYP_HBOND:
- l->hbond_list = smalloc( l->total_intrs * sizeof(hbond_data),
- "Make_List::l->hbond_list" );
+ if ( l->total_intrs > 0 )
+ {
+ l->hbond_list = smalloc( l->total_intrs * sizeof(hbond_data),
+ "Make_List::l->hbond_list" );
+ }
+ else
+ {
+ l->hbond_list = NULL;
+ }
break;
default:
- l->v = smalloc( l->total_intrs * sizeof(void),
- "Make_List::l->v" );
+ fprintf( stderr, "[ERROR] unknown list type. Terminating...\n" );
+ exit( INVALID_INPUT );
break;
}
}
@@ -119,35 +175,59 @@ void Delete_List( int type, reax_list* l )
switch ( type )
{
case TYP_VOID:
- sfree( l->v, "Delete_List::l->v" );
+ if ( l->v != NULL )
+ {
+ sfree( l->v, "Delete_List::l->v" );
+ }
break;
case TYP_THREE_BODY:
- sfree( l->three_body_list, "Delete_List::l->three_body_list" );
+ if ( l->three_body_list != NULL )
+ {
+ sfree( l->three_body_list, "Delete_List::l->three_body_list" );
+ }
break;
case TYP_BOND:
- sfree( l->bond_list, "Delete_List::l->bond_list" );
+ if ( l->bond_list != NULL )
+ {
+ sfree( l->bond_list, "Delete_List::l->bond_list" );
+ }
break;
case TYP_DBO:
- sfree( l->dbo_list, "Delete_List::l->dbo_list" );
+ if ( l->dbo_list != NULL )
+ {
+ sfree( l->dbo_list, "Delete_List::l->dbo_list" );
+ }
break;
case TYP_DDELTA:
- sfree( l->dDelta_list, "Delete_List::l->dDelta_list" );
+ if ( l->dDelta_list != NULL )
+ {
+ sfree( l->dDelta_list, "Delete_List::l->dDelta_list" );
+ }
break;
case TYP_FAR_NEIGHBOR:
- sfree( l->far_nbr_list, "Delete_List::l->far_nbr_list" );
+ if ( l->far_nbr_list != NULL )
+ {
+ sfree( l->far_nbr_list, "Delete_List::l->far_nbr_list" );
+ }
break;
case TYP_NEAR_NEIGHBOR:
- sfree( l->near_nbr_list, "Delete_List::l->near_nbr_list" );
+ if ( l->near_nbr_list != NULL )
+ {
+ sfree( l->near_nbr_list, "Delete_List::l->near_nbr_list" );
+ }
break;
case TYP_HBOND:
- sfree( l->hbond_list, "Delete_List::l->hbond_list" );
+ if ( l->hbond_list != NULL )
+ {
+ sfree( l->hbond_list, "Delete_List::l->hbond_list" );
+ }
break;
default:
@@ -155,5 +235,4 @@ void Delete_List( int type, reax_list* l )
exit( INVALID_INPUT );
break;
}
-
}