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stricter matching of header items and skip comments right away

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This commit is contained in:
Axel Kohlmeyer
2025-06-20 14:12:25 -04:00
parent fb088cdc57
commit 6f72a56b4c
1 changed files with 15 additions and 14 deletions
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29
src/molecule.cpp
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@ -1927,10 +1927,11 @@ void Molecule::read(int flag)
readline(line); readline(line);
// trim comments. if line is blank, continue // trim comments. if line is blank or comment, continue
auto text = utils::trim(utils::trim_comment(line)); auto text = utils::trim(utils::trim_comment(line));
if (text.empty()) continue; if (text.empty()) continue;
if (utils::strmatch(text, "^\\s*#")) continue;
// search line for header keywords and set corresponding variable // search line for header keywords and set corresponding variable
try { try {
@ -1938,31 +1939,31 @@ void Molecule::read(int flag)
int nmatch = values.count(); int nmatch = values.count();
int nwant = 0; int nwant = 0;
if (values.matches("^\\s*\\d+\\s+atoms")) { if (values.matches("^\\s*\\d+\\s+atoms\\s*$")) {
natoms = values.next_int(); natoms = values.next_int();
nwant = 2; nwant = 2;
has_atoms = true; has_atoms = true;
} else if (values.matches("^\\s*\\d+\\s+bonds")) { } else if (values.matches("^\\s*\\d+\\s+bonds\\s*$")) {
nbonds = values.next_int(); nbonds = values.next_int();
nwant = 2; nwant = 2;
} else if (values.matches("^\\s*\\d+\\s+angles")) { } else if (values.matches("^\\s*\\d+\\s+angles\\s*$")) {
nangles = values.next_int(); nangles = values.next_int();
nwant = 2; nwant = 2;
} else if (values.matches("^\\s*\\d+\\s+dihedrals")) { } else if (values.matches("^\\s*\\d+\\s+dihedrals\\s*$")) {
ndihedrals = values.next_int(); ndihedrals = values.next_int();
nwant = 2; nwant = 2;
} else if (values.matches("^\\s*\\d+\\s+impropers")) { } else if (values.matches("^\\s*\\d+\\s+impropers\\s*$")) {
nimpropers = values.next_int(); nimpropers = values.next_int();
nwant = 2; nwant = 2;
} else if (values.matches("^\\s*\\d+\\s+fragments")) { } else if (values.matches("^\\s*\\d+\\s+fragments\\s*$")) {
nfragments = values.next_int(); nfragments = values.next_int();
nwant = 2; nwant = 2;
} else if (values.matches("^\\s*\\f+\\s+mass")) { } else if (values.matches("^\\s*\\f+\\s+mass\\s*$")) {
massflag = 1; massflag = 1;
masstotal = values.next_double(); masstotal = values.next_double();
nwant = 2; nwant = 2;
masstotal *= sizescale * sizescale * sizescale; masstotal *= sizescale * sizescale * sizescale;
} else if (values.matches("^\\s*\\f+\\s+\\f+\\s+\\f+\\s+com")) { } else if (values.matches("^\\s*\\f+\\s+\\f+\\s+\\f+\\s+com\\s*$")) {
comflag = 1; comflag = 1;
com[0] = values.next_double(); com[0] = values.next_double();
com[1] = values.next_double(); com[1] = values.next_double();
@ -1973,7 +1974,7 @@ void Molecule::read(int flag)
com[2] *= sizescale; com[2] *= sizescale;
if ((domain->dimension == 2) && (com[2] != 0.0)) if ((domain->dimension == 2) && (com[2] != 0.0))
error->all(FLERR, fileiarg, "Molecule file z center-of-mass must be 0.0 for 2d systems"); error->all(FLERR, fileiarg, "Molecule file z center-of-mass must be 0.0 for 2d systems");
} else if (values.matches("^\\s*\\f+\\s+\\f+\\s+\\f+\\s+\\f+\\s+\\f+\\s+\\f+\\s+inertia")) { } else if (values.matches("^\\s*\\f+\\s+\\f+\\s+\\f+\\s+\\f+\\s+\\f+\\s+\\f+\\s+inertia\\s*$")) {
inertiaflag = 1; inertiaflag = 1;
itensor[0] = values.next_double(); itensor[0] = values.next_double();
itensor[1] = values.next_double(); itensor[1] = values.next_double();
@ -1989,7 +1990,7 @@ void Molecule::read(int flag)
itensor[3] *= scale5; itensor[3] *= scale5;
itensor[4] *= scale5; itensor[4] *= scale5;
itensor[5] *= scale5; itensor[5] *= scale5;
} else if (values.matches("^\\s*\\d+\\s+\\d+\\s+body")) { } else if (values.matches("^\\s*\\d+\\s+\\d+\\s+body\\s*$")) {
bodyflag = 1; bodyflag = 1;
avec_body = dynamic_cast<AtomVecBody *>(atom->style_match("body")); avec_body = dynamic_cast<AtomVecBody *>(atom->style_match("body"));
if (!avec_body) error->all(FLERR, fileiarg, "Molecule file requires atom style body"); if (!avec_body) error->all(FLERR, fileiarg, "Molecule file requires atom style body");
@ -1999,15 +2000,15 @@ void Molecule::read(int flag)
} else { } else {
// unknown header keyword // unknown header keyword
if (values.matches("^\\s*\\f+\\s+\\S+")) { if (values.matches("^\\s*\\f+\\s+\\S+")) {
error->one(FLERR, fileiarg, "Unknown keyword or incorrectly formatted header line: {}", error->all(FLERR, fileiarg, "Unknown keyword or incorrectly formatted header line: {}",
line); line);
} else } else
break; break;
} }
if (nmatch != nwant) if (nmatch != nwant)
error->one(FLERR, fileiarg, "Invalid header line format in molecule file"); error->all(FLERR, fileiarg, "Invalid header line format in molecule file: {}", line);
} catch (TokenizerException &e) { } catch (TokenizerException &e) {
error->one(FLERR, fileiarg, "Invalid header in molecule file: {}", e.what()); error->all(FLERR, fileiarg, "Invalid header in molecule file: {}", e.what());
} }
} }