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need to transfer molecule templates when using "replicate"

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This commit is contained in:
Axel Kohlmeyer
2020-10-29 05:58:39 -04:00
parent 584943fc92
commit c7b39283b1
1 changed files with 20 additions and 7 deletions
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27
src/replicate.cpp
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@ -43,9 +43,6 @@ void Replicate::command(int narg, char **arg)
error->all(FLERR,"Replicate command before simulation box is defined");
if (narg < 3 || narg > 4) error->all(FLERR,"Illegal replicate command");
if (atom->molecular == Atom::TEMPLATE)
error->all(FLERR,"Cannot use replicate command with atom style template");
int me = comm->me;
int nprocs = comm->nprocs;
@ -162,6 +159,20 @@ void Replicate::command(int narg, char **arg)
else atom = new Atom(lmp);
atom->settings(old);
// transfer molecule templates. needs to be done early for atom style template
if (old->nmolecule) {
atom->molecules = (Molecule **) memory->smalloc((old->nmolecule)*sizeof(Molecule *),
"atom::molecules");
atom->nmolecule = old->nmolecule;
for (int i = 0; i < old->nmolecule; ++i)
atom->molecules[i] = old->molecules[i];
memory->sfree(old->molecules);
old->molecules = nullptr;
old->nmolecule = 0;
}
atom->create_avec(old->atom_style,old->avec->nargcopy,old->avec->argcopy,0);
// check that new system will not be too large
@ -749,17 +760,19 @@ void Replicate::command(int narg, char **arg)
error->all(FLERR,"Replicate did not assign all atoms correctly");
if (me == 0) {
const char *molstyle = "";
if (atom->molecular == Atom::TEMPLATE) molstyle = "template ";
if (atom->nbonds) {
utils::logmesg(lmp,fmt::format(" {} bonds\n",atom->nbonds));
utils::logmesg(lmp,fmt::format(" {} {}bonds\n",atom->nbonds,molstyle));
}
if (atom->nangles) {
utils::logmesg(lmp,fmt::format(" {} angles\n",atom->nangles));
utils::logmesg(lmp,fmt::format(" {} {}angles\n",atom->nangles,molstyle));
}
if (atom->ndihedrals) {
utils::logmesg(lmp,fmt::format(" {} dihedrals\n",atom->ndihedrals));
utils::logmesg(lmp,fmt::format(" {} {}dihedrals\n",atom->ndihedrals,molstyle));
}
if (atom->nimpropers) {
utils::logmesg(lmp,fmt::format(" {} impropers\n",atom->nimpropers));
utils::logmesg(lmp,fmt::format(" {} {}impropers\n",atom->nimpropers,molstyle));
}
}