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add missing type check and setting of ntypes for json data molecules

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This commit is contained in:
Axel Kohlmeyer
2025-06-14 11:48:11 -04:00
parent ea23af48d3
commit faa1dbc19d
1 changed files with 7 additions and 0 deletions
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7
src/molecule.cpp
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@ -483,11 +483,18 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
count[iatom]++; count[iatom]++;
} }
// checks // checks
ntypes = 0;
for (int i = 0; i < natoms; i++) { for (int i = 0; i < natoms; i++) {
if (count[i] == 0) { if (count[i] == 0) {
error->all(FLERR, Error::NOLASTLINE, error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: atom {} missing in \"types\" JSON section", id, i + 1); "Molecule template {}: atom {} missing in \"types\" JSON section", id, i + 1);
} }
for (int i = 0; i < natoms; i++) {
if ((type[i] <= 0) || (domain->box_exist && (type[i] > atom->ntypes)))
error->all(FLERR, fileiarg, "Invalid atom type {} for atom {} in molecule file", type[i],
i + 1);
ntypes = MAX(ntypes, type[i]);
}
} }
} else { } else {
error->all(FLERR, Error::NOLASTLINE, error->all(FLERR, Error::NOLASTLINE,