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new neigh_modify exclude option, other SNAP changes

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This commit is contained in:
Steve Plimpton
2017-03-07 09:31:12 -07:00
parent 49e83b4348
commit efaa4c6710
32 changed files with 108 additions and 44 deletions
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16
src/neighbor.cpp
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@ -166,7 +166,7 @@ pairclass(NULL), pairnames(NULL), pairmasks(NULL)
ex1_group = ex2_group = ex1_bit = ex2_bit = NULL;
nex_mol = maxex_mol = 0;
ex_mol_group = ex_mol_bit = NULL;
ex_mol_group = ex_mol_bit = ex_mol_intra = NULL;
// Kokkos setting
@ -234,6 +234,7 @@ Neighbor::~Neighbor()
memory->destroy(ex_mol_group);
delete [] ex_mol_bit;
memory->destroy(ex_mol_intra);
}
/* ---------------------------------------------------------------------- */
@ -2323,7 +2324,8 @@ void Neighbor::modify_params(int narg, char **arg)
nex_group++;
iarg += 4;
} else if (strcmp(arg[iarg+1],"molecule") == 0) {
} else if (strcmp(arg[iarg+1],"molecule/inter") == 0 ||
strcmp(arg[iarg+1],"molecule/intra") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal neigh_modify command");
if (atom->molecule_flag == 0)
error->all(FLERR,"Neigh_modify exclude molecule "
@ -2331,13 +2333,21 @@ void Neighbor::modify_params(int narg, char **arg)
if (nex_mol == maxex_mol) {
maxex_mol += EXDELTA;
memory->grow(ex_mol_group,maxex_mol,"neigh:ex_mol_group");
if (lmp->kokkos)
grow_ex_mol_intra_kokkos();
else
memory->grow(ex_mol_intra,maxex_mol,"neigh:ex_mol_intra");
}
ex_mol_group[nex_mol] = group->find(arg[iarg+2]);
if (ex_mol_group[nex_mol] == -1)
error->all(FLERR,"Invalid group ID in neigh_modify command");
if (strcmp(arg[iarg+1],"molecule/intra") == 0)
ex_mol_intra[nex_mol] = 1;
else
ex_mol_intra[nex_mol] = 0;
nex_mol++;
iarg += 3;
} else if (strcmp(arg[iarg+1],"none") == 0) {
nex_type = nex_group = nex_mol = 0;
iarg += 2;