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Commit 2fe37bef authored by Kurt A. O'Hearn's avatar Kurt A. O'Hearn
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sPuReMD: correctly detect dummy atoms for non-standalone simulations.

parent dddd2882
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with 75 additions and 13 deletions
sPuReMD/src/spuremd.c
+ 75
− 13
View file @ 2fe37bef
......@@ -282,6 +282,9 @@ void * setup2( int num_atoms, const int * const atom_type,
for ( i = 0; i < spmd_handle->system->N; ++i )
{
assert( atom_type[i] >= 0
&& atom_type[i] < spmd_handle->system->reax_param->num_atom_types );
x[0] = pos[3 * i];
x[1] = pos[3 * i + 1];
x[2] = pos[3 * i + 2];
......@@ -289,16 +292,25 @@ void * setup2( int num_atoms, const int * const atom_type,
Fit_to_Periodic_Box( &spmd_handle->system->box, x );
spmd_handle->workspace->orig_id[i] = i + 1;
// spmd_handle->system->atoms[i].type = Get_Atom_Type( &system->reax_param,
// element, sizeof(element) );
spmd_handle->system->atoms[i].type = atom_type[i];
// strncpy( spmd_handle->system->atoms[i].name, atom_name,
// sizeof(spmd_handle->system->atoms[i].name) - 1 );
// spmd_handle->system->atoms[i].name[sizeof(spmd_handle->system->atoms[i].name) - 1] = '\0';
strncpy( spmd_handle->system->atoms[i].name,
spmd_handle->system->reax_param.sbp[atom_type[i]].name,
sizeof(spmd_handle->system->atoms[i].name) - 1 );
spmd_handle->system->atoms[i].name[sizeof(spmd_handle->system->atoms[i].name) - 1] = '\0';
rvec_Copy( spmd_handle->system->atoms[i].x, x );
rvec_MakeZero( spmd_handle->system->atoms[i].v );
rvec_MakeZero( spmd_handle->system->atoms[i].f );
spmd_handle->system->atoms[i].q = 0.0;
/* check for dummy atom */
if ( strncmp( spmd_handle->system->atoms[i].name, "X\0", 2 ) == 0 )
{
spmd_handle->system->atoms[i].is_dummy = TRUE;
}
else
{
spmd_handle->system->atoms[i].is_dummy = FALSE;
}
}
spmd_handle->system->N_max = (int) CEIL( SAFE_ZONE * spmd_handle->system->N );
......@@ -628,6 +640,9 @@ int reset2( const void * const handle, int num_atoms,
for ( i = 0; i < spmd_handle->system->N; ++i )
{
assert( atom_type[i] >= 0
&& atom_type[i] < spmd_handle->system->reax_param->num_atom_types );
x[0] = pos[3 * i];
x[1] = pos[3 * i + 1];
x[2] = pos[3 * i + 2];
......@@ -635,16 +650,25 @@ int reset2( const void * const handle, int num_atoms,
Fit_to_Periodic_Box( &spmd_handle->system->box, x );
spmd_handle->workspace->orig_id[i] = i + 1;
// spmd_handle->system->atoms[i].type = Get_Atom_Type( &system->reax_param,
// element, sizeof(element) );
spmd_handle->system->atoms[i].type = atom_type[i];
// strncpy( spmd_handle->system->atoms[i].name, atom_name,
// sizeof(spmd_handle->system->atoms[i].name) - 1 );
// spmd_handle->system->atoms[i].name[sizeof(spmd_handle->system->atoms[i].name) - 1] = '\0';
strncpy( spmd_handle->system->atoms[i].name,
spmd_handle->system->reax_param.sbp[atom_type[i]].name,
sizeof(spmd_handle->system->atoms[i].name) - 1 );
spmd_handle->system->atoms[i].name[sizeof(spmd_handle->system->atoms[i].name) - 1] = '\0';
rvec_Copy( spmd_handle->system->atoms[i].x, x );
rvec_MakeZero( spmd_handle->system->atoms[i].v );
rvec_MakeZero( spmd_handle->system->atoms[i].f );
spmd_handle->system->atoms[i].q = 0.0;
/* check for dummy atom */
if ( strncmp( spmd_handle->system->atoms[i].name, "X\0", 2 ) == 0 )
{
spmd_handle->system->atoms[i].is_dummy = TRUE;
}
else
{
spmd_handle->system->atoms[i].is_dummy = FALSE;
}
}
if ( spmd_handle->system->N > spmd_handle->system->N_max )
......@@ -1037,8 +1061,17 @@ void * setup_qmmm( int qm_num_atoms, const char * const qm_symbols,
rvec_MakeZero( spmd_handle->system->atoms[i].f );
spmd_handle->system->atoms[i].q = 0.0;
spmd_handle->system->atoms[i].q_init = 0.0;
spmd_handle->system->atoms[i].qmmm_mask = TRUE;
/* check for dummy atom */
if ( strncmp( element, "X\0", 2 ) == 0 )
{
spmd_handle->system->atoms[i].is_dummy = TRUE;
}
else
{
spmd_handle->system->atoms[i].is_dummy = FALSE;
}
}
for ( i = spmd_handle->system->N_qm; i < spmd_handle->system->N; ++i )
......@@ -1063,8 +1096,17 @@ void * setup_qmmm( int qm_num_atoms, const char * const qm_symbols,
rvec_MakeZero( spmd_handle->system->atoms[i].f );
spmd_handle->system->atoms[i].q = mm_pos_q[4 * (i - spmd_handle->system->N_qm) + 3];
spmd_handle->system->atoms[i].q_init = mm_pos_q[4 * (i - spmd_handle->system->N_qm) + 3];
spmd_handle->system->atoms[i].qmmm_mask = FALSE;
/* check for dummy atom */
if ( strncmp( element, "X\0", 2 ) == 0 )
{
spmd_handle->system->atoms[i].is_dummy = TRUE;
}
else
{
spmd_handle->system->atoms[i].is_dummy = FALSE;
}
}
spmd_handle->system->N_max = (int) CEIL( SAFE_ZONE * spmd_handle->system->N );
......@@ -1201,8 +1243,18 @@ int reset_qmmm( const void * const handle, int qm_num_atoms,
rvec_MakeZero( spmd_handle->system->atoms[i].v );
rvec_MakeZero( spmd_handle->system->atoms[i].f );
spmd_handle->system->atoms[i].q = 0.0;
spmd_handle->system->atoms[i].q_init = 0.0;
spmd_handle->system->atoms[i].qmmm_mask = TRUE;
/* check for dummy atom */
if ( strncmp( element, "X\0", 2 ) == 0 )
{
spmd_handle->system->atoms[i].is_dummy = TRUE;
}
else
{
spmd_handle->system->atoms[i].is_dummy = FALSE;
}
}
for ( i = spmd_handle->system->N_qm; i < spmd_handle->system->N; ++i )
......@@ -1228,6 +1280,16 @@ int reset_qmmm( const void * const handle, int qm_num_atoms,
spmd_handle->system->atoms[i].q = mm_pos_q[4 * (i - spmd_handle->system->N_qm) + 3];
spmd_handle->system->atoms[i].q_init = mm_pos_q[4 * (i - spmd_handle->system->N_qm) + 3];
spmd_handle->system->atoms[i].qmmm_mask = FALSE;
/* check for dummy atom */
if ( strncmp( element, "X\0", 2 ) == 0 )
{
spmd_handle->system->atoms[i].is_dummy = TRUE;
}
else
{
spmd_handle->system->atoms[i].is_dummy = FALSE;
}
}
if ( spmd_handle->system->N > spmd_handle->system->N_max )
......
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