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correctly honor atom-id in Special Bond Counts section

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This commit is contained in:
Axel Kohlmeyer
2025-06-20 23:05:58 -04:00
parent 95fb6c75d2
commit c08ee92801
1 changed files with 28 additions and 11 deletions
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39
src/molecule.cpp
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@ -965,7 +965,9 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
const int iatom = int(c[0]) - 1;
if ((iatom < 0) || (iatom >= natoms))
error->all(FLERR, Error::NOLASTLINE,
"Invalid atom-id {} in \"masses\" section of molecule JSON data", iatom + 1);
"Molecule template {}: invalid atom-id {} in \"masses\" section of molecule "
"JSON data",
iatom + 1);
if (!c[1].is_number())
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: invalid mass in \"masses\" section of "
@ -3105,33 +3107,48 @@ void Molecule::nspecial_read(int flag, char *line)
{
if (flag == 0) maxspecial = 0;
for (int i = 0; i < natoms; i++) {
for (int i = 0; i < natoms; ++i) count[i] = 0;
for (int i = 0; i < natoms; ++i) {
readline(line);
int c1, c2, c3;
int c0, c1, c2, c3;
try {
ValueTokenizer values(utils::trim_comment(line));
if (values.count() != 4)
error->all(FLERR, fileiarg, "Invalid line in Special Bond Counts section of molecule file: {}", line);
values.next_int();
c1 = values.next_tagint();
c2 = values.next_tagint();
c3 = values.next_tagint();
c0 = values.next_int();
c1 = values.next_int();
c2 = values.next_int();
c3 = values.next_int();
} catch (TokenizerException &e) {
error->all(FLERR, fileiarg, "Invalid line in Special Bond Counts section of molecule file: {}\n{}",
e.what(), line);
}
if (flag) {
nspecial[i][0] = c1;
nspecial[i][1] = c1 + c2;
nspecial[i][2] = c1 + c2 + c3;
} else
int iatom = c0 - 1;
if (iatom < 0 || iatom >= natoms)
error->all(FLERR, fileiarg, "Invalid atom index in Special Bond Counts section of molecule file");
count[iatom]++;
nspecial[iatom][0] = c1;
nspecial[iatom][1] = c1 + c2;
nspecial[iatom][2] = c1 + c2 + c3;
} else {
maxspecial = MAX(maxspecial, c1 + c2 + c3);
}
}
// check
if (flag) {
for (int i = 0; i < natoms; i++) {
if (count[i] == 0)
error->all(FLERR, fileiarg, "Atom {} missing in Special Bond Counts section of molecule file", i + 1);
}
}
}
/* ----------------------------------------------------------------------
read special bond indices from file
------------------------------------------------------------------------- */