From 2fe37befd416f1ed0d8a05084d882651429e33b7 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnku@msu.edu>
Date: Thu, 24 Jun 2021 19:04:06 -0400
Subject: [PATCH] sPuReMD: correctly detect dummy atoms for non-standalone
simulations.
---
sPuReMD/src/spuremd.c | 88 ++++++++++++++++++++++++++++++++++++-------
1 file changed, 75 insertions(+), 13 deletions(-)
diff --git a/sPuReMD/src/spuremd.c b/sPuReMD/src/spuremd.c
index 564f331..22b93fd 100644
--- a/sPuReMD/src/spuremd.c
+++ b/sPuReMD/src/spuremd.c
@@ -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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