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make code more consistent by always using "item" for topology data entry

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This commit is contained in:
Axel Kohlmeyer
2025-06-11 23:31:21 -04:00
parent 5e948b1450
commit d4be195d81
1 changed files with 22 additions and 21 deletions
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43
src/molecule.cpp
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@ -790,16 +790,16 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
}
for (int i = 0; i < nbonds; ++i) {
const auto &b = moldata["bonds"]["data"][i];
if (b.size() < 3)
const auto &item = moldata["bonds"]["data"][i];
if (item.size() < 3)
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: invalid format of JSON data for bond {}: {}", id,
i + 1, to_string(b));
i + 1, to_string(item));
if (b[0].is_number_integer()) { // numeric type
itype = int(b[0]) + boffset;
if (item[0].is_number_integer()) { // numeric type
itype = int(item[0]) + boffset;
} else {
const auto &typestr = std::string(b[0]);
const auto &typestr = std::string(item[0]);
if (!atom->labelmapflag)
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: invalid bond type in \"bonds\" JSON section", id,
@ -811,17 +811,17 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
typestr);
}
atom1 = tagint(b[1]);
atom2 = tagint(b[2]);
atom1 = tagint(item[1]);
atom2 = tagint(item[2]);
if ((atom1 <= 0) || (atom1 > natoms) || (atom2 <= 0) || (atom2 > natoms) ||
(atom1 == atom2))
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: invalid atom ID in bond {}: {}", id, i + 1,
to_string(b));
to_string(item));
if ((itype <= 0) || (domain->box_exist && (itype > atom->nbondtypes)))
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: invalid bond type in bond {}: {}", id, i + 1,
to_string(b));
to_string(item));
if (flag == 0) {
count[atom1 - 1]++;
if (newton_bond == 0) count[atom2 - 1]++;
@ -881,16 +881,16 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
}
for (int i = 0; i < nangles; ++i) {
const auto &a = moldata["angles"]["data"][i];
if (a.size() < 4)
const auto &item = moldata["angles"]["data"][i];
if (item.size() < 4)
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: invalid format of JSON data for angle {}: {}", id,
i + 1, to_string(a));
i + 1, to_string(item));
if (a[0].is_number_integer()) { // numeric type
itype = int(a[0]) + aoffset;
if (item[0].is_number_integer()) { // numeric type
itype = int(item[0]) + aoffset;
} else {
const auto &typestr = std::string(a[0]);
const auto &typestr = std::string(item[0]);
if (!atom->labelmapflag)
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: invalid angle type in \"angles\" JSON section", id,
@ -902,20 +902,20 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
id, typestr);
}
atom1 = tagint(a[1]);
atom2 = tagint(a[2]);
atom3 = tagint(a[3]);
atom1 = tagint(item[1]);
atom2 = tagint(item[2]);
atom3 = tagint(item[3]);
if ((atom1 <= 0) || (atom1 > natoms) || (atom2 <= 0) || (atom2 > natoms) ||
(atom3 <= 0) || (atom3 > natoms) || (atom1 == atom2) || (atom1 == atom3) ||
(atom2 == atom3))
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: invalid atom ID in angle {}: {}", id, i + 1,
to_string(a));
to_string(item));
if ((itype <= 0) || (domain->box_exist && (itype > atom->nangletypes)))
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: invalid angle type in angle {}: {}", id, i + 1,
to_string(a));
to_string(item));
if (flag == 0) {
count[atom1 - 1]++;
if (newton_bond == 0) {
@ -936,6 +936,7 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
angle_atom1[m][num_angle[m]] = atom1;
angle_atom2[m][num_angle[m]] = atom2;
angle_atom3[m][num_angle[m]] = atom3;
num_angle[m]++;
m = atom3 - 1;
angle_type[m][num_angle[m]] = itype;
angle_atom1[m][num_angle[m]] = atom1;