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consistently skip over computing interactions with atoms set to NULL in hybrid styles

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This commit is contained in:
Axel Kohlmeyer
2023-01-27 22:12:33 -05:00
parent 66e3d8c564
commit 2e52afbd86
7 changed files with 19 additions and 12 deletions
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1
src/OPENMP/reaxff_bonds_omp.cpp
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@ -99,6 +99,7 @@ namespace ReaxFF {
/* set the pointers */
type_i = system->my_atoms[i].type;
type_j = system->my_atoms[j].type;
if ((type_i < 0) || (type_j < 0)) continue;
sbp_i = &(system->reax_param.sbp[type_i]);
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);

3
src/OPENMP/reaxff_forces_omp.cpp
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@ -265,6 +265,7 @@ namespace ReaxFF {
for (int i = 0; i < system->N; ++i) {
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
if (type_i < 0) continue;
sbp_i = &(system->reax_param.sbp[type_i]);
start_i = Start_Index(i, far_nbrs);
@ -276,6 +277,7 @@ namespace ReaxFF {
int j = nbr_pj->nbr;
atom_j = &(system->my_atoms[j]);
type_j = atom_j->type;
if (type_j < 0) continue;
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);
@ -376,6 +378,7 @@ namespace ReaxFF {
for (int i = 0; i < system->n; ++i) {
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
if (type_i < 0) continue;
sbp_i = &(system->reax_param.sbp[type_i]);
ihb = sbp_i->p_hbond;

6
src/OPENMP/reaxff_hydrogen_bonds_omp.cpp
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@ -98,14 +98,14 @@ namespace ReaxFF {
// for (j = 0; j < system->n; ++j)
for (j = ifrom; j < ito; ++j) {
/* j has to be of type H */
if (system->reax_param.sbp[system->my_atoms[j].type].p_hbond == 1) {
type_j = system->my_atoms[j].type;
if (type_j < 0) continue;
if (system->reax_param.sbp[type_j].p_hbond == 1) {
/*set j's variables */
type_j = system->my_atoms[j].type;
start_j = Start_Index(j, bonds);
end_j = End_Index(j, bonds);
hb_start_j = Start_Index(system->my_atoms[j].Hindex, hbonds);
hb_end_j = End_Index(system->my_atoms[j].Hindex, hbonds);
if (type_j < 0) continue;
top = 0;
for (pi = start_j; pi < end_j; ++pi) {

1
src/REAXFF/reaxff_bonds.cpp
View File

@ -75,6 +75,7 @@ namespace ReaxFF {
/* set the pointers */
type_i = system->my_atoms[i].type;
type_j = system->my_atoms[j].type;
if ((type_i < 0) || (type_j < 0)) continue;
sbp_i = &(system->reax_param.sbp[type_i]);
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);

9
src/REAXFF/reaxff_hydrogen_bonds.cpp
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@ -59,14 +59,14 @@ namespace ReaxFF {
hbonds = (*lists) + HBONDS;
hbond_list = hbonds->select.hbond_list;
for (j = 0; j < system->n; ++j)
if ((system->my_atoms[j].type >= 0) && (system->reax_param.sbp[system->my_atoms[j].type].p_hbond == 1)) {
type_j = system->my_atoms[j].type;
for (j = 0; j < system->n; ++j) {
type_j = system->my_atoms[j].type;
if (type_j < 0) continue;
if (system->reax_param.sbp[type_j].p_hbond == 1) {
start_j = Start_Index(j, bonds);
end_j = End_Index(j, bonds);
hb_start_j = Start_Index(system->my_atoms[j].Hindex, hbonds);
hb_end_j = End_Index(system->my_atoms[j].Hindex, hbonds);
if (type_j < 0) continue;
top = 0;
for (pi = start_j; pi < end_j; ++pi) {
@ -154,5 +154,6 @@ namespace ReaxFF {
}
}
}
}
}
}

3
src/REAXFF/reaxff_init_md.cpp
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@ -56,7 +56,8 @@ namespace ReaxFF {
if (control->hbond_cut > 0)
for (i = 0; i < system->n; ++i) {
atom = &(system->my_atoms[i]);
if ((atom->type >= 0) && (system->reax_param.sbp[atom->type].p_hbond == 1 && atom->type >= 0))
if ((atom->type >= 0)
&& (system->reax_param.sbp[atom->type].p_hbond == 1 && atom->type >= 0))
atom->Hindex = system->numH++;
else atom->Hindex = -1;
}

8
src/REAXFF/reaxff_nonbonded.cpp
View File

@ -233,8 +233,8 @@ namespace ReaxFF {
flag = 0;
/* kinetic energy terms */
double xcut = 0.5 * ( system->reax_param.sbp[ system->my_atoms[i].type ].bcut_acks2
+ system->reax_param.sbp[ system->my_atoms[j].type ].bcut_acks2 );
double xcut = 0.5 * (system->reax_param.sbp[system->my_atoms[i].type].bcut_acks2
+ system->reax_param.sbp[system->my_atoms[j].type].bcut_acks2);
if(nbr_pj->d <= xcut) {
if (j < natoms) flag = 1;
@ -409,8 +409,8 @@ namespace ReaxFF {
flag = 0;
/* kinetic energy terms */
double xcut = 0.5 * ( system->reax_param.sbp[ system->my_atoms[i].type ].bcut_acks2
+ system->reax_param.sbp[ system->my_atoms[j].type ].bcut_acks2 );
double xcut = 0.5 * (system->reax_param.sbp[ system->my_atoms[i].type ].bcut_acks2
+ system->reax_param.sbp[ system->my_atoms[j].type ].bcut_acks2);
if(nbr_pj->d <= xcut) {
if (j < natoms) flag = 1;