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add support for dipoles section

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This commit is contained in:
Axel Kohlmeyer
2025-06-11 18:09:40 -04:00
parent 3d7f7af8c7
commit b0694e4e73
2 changed files with 79 additions and 3 deletions
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59
src/molecule.cpp
View File

@ -651,8 +651,61 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
id, secfmt[0], secfmt[1]);
}
}
// dipoles
if (muflag) {
for (int i = 0; i < 4; ++i) secfmt[i] = moldata["dipoles"]["format"][i];
if ((secfmt[0] == "atom-id") && (secfmt[1] == "mux") && (secfmt[2] == "muy") &&
(secfmt[3] == "muz")) {
memset(count, 0, natoms * sizeof(count));
for (const auto &c : moldata["dipoles"]["data"]) {
if (c.size() < 4)
error->all(
FLERR, Error::NOLASTLINE,
"Molecule template {}: missing data in \"dipoles\" section of molecule JSON data: {}",
id, to_string(c));
if (!c[0].is_number_integer())
error->all(
FLERR, Error::NOLASTLINE,
"Molecule template {}: invalid atom-id in \"dipoles\" section of molecule JSON "
"data: {}",
id, to_string(c[0]));
const int iatom = int(c[0]) - 1;
if ((iatom < 0) || (iatom >= natoms))
error->all(
FLERR, Error::NOLASTLINE,
"Molecule template {}: invalid atom-id {} in dipoles section of molecule JSON data",
id, iatom + 1);
count[iatom]++;
mu[iatom][0] = c[1];
mu[iatom][1] = c[2];
mu[iatom][2] = c[3];
mu[iatom][0] *= sizescale;
mu[iatom][1] *= sizescale;
mu[iatom][2] *= sizescale;
}
// checks
for (int i = 0; i < natoms; i++) {
if (count[i] == 0) {
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: atom {} missing in \"dipoles\" JSON section", id,
i + 1);
}
}
} else {
error->all(
FLERR, Error::NOLASTLINE,
"Molecule template {}: Expected \"dipoles\" format [\"atom-id\",\"mux\",\"muy\",\"muz\"] "
"but found [\"{}\",\"{}\",\"{}\",\"{}\"]",
id, secfmt[0], secfmt[1], secfmt[2], secfmt[3]);
}
}
// masses
if (rmassflag) {
@ -1590,9 +1643,9 @@ void Molecule::dipoles(char *line)
error->all(FLERR, fileiarg, "Invalid atom index in Dipoles section of molecule file");
count[iatom]++;
mu[iatom][0] = values.next_double();
mu[iatom][1] = values.next_double();
mu[iatom][2] = values.next_double();
mu[iatom][0] = values.next_double() * sizescale;
mu[iatom][1] = values.next_double() * sizescale;
mu[iatom][2] = values.next_double() * sizescale;
}
} catch (TokenizerException &e) {
error->all(FLERR, fileiarg, "Invalid line in Dipoles section of molecule file: {}\n{}", e.what(), line);

23
tools/json/molecule-schema.json
View File

@ -143,6 +143,29 @@
},
"required": ["format", "data"]
},
"dipoles": {
"type": "object",
"properties": {
"format": {
"type": "array",
"const": ["atom-id", "mux", "muy", "muz"]
},
"data": {
"type": "array",
"items": {
"type": "array",
"prefixItems": [
{"type": "integer"},
{"type": "number"},
{"type": "number"},
{"type": "number"}
],
"items": false
}
}
},
"required": ["format", "data"]
},
"diameters": {
"type": "object",
"properties": {