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revise/refacor Type Label section parsing and Atoms section parsing

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- do not ignore numeric type in Type Label sections
- refuse invalid numeric types that will overflow arrays
- check for duplicate numeric type entries or non-unique labels
- better error messages
- use Tokenizer class instead of sscanf()
This commit is contained in:
Axel Kohlmeyer
2022-09-04 01:01:36 -04:00
parent 389c87ab7e
commit ad8a931fe4
5 changed files with 77 additions and 73 deletions
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37
src/atom.cpp
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@ -87,7 +87,7 @@ are updated by the AtomVec class as needed.
* instances of classes derived from the AtomVec base
* class, which correspond to the selected atom style.
*
* \param lmp pointer to the base LAMMPS class */
* \param _lmp pointer to the base LAMMPS class */
Atom::Atom(LAMMPS *_lmp) : Pointers(_lmp)
{
@ -1186,17 +1186,36 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
avec->data_atom(xdata,imagedata,values,typestr);
if (id_offset) tag[nlocal-1] += id_offset;
if (mol_offset) molecule[nlocal-1] += mol_offset;
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Atoms section in data file");
type[nlocal-1] = lmap->find(typestr,Atom::ATOM);
if (type[nlocal-1] == -1) error->one(FLERR,"Invalid Atoms section in data file");
} else {
type[nlocal-1] = utils::inumeric(FLERR,typestr.c_str(),true,lmp);
if (labelflag) type[nlocal-1] = ilabel[type[nlocal-1]-1];
// clang-format on
switch (utils::is_type(typestr)) {
case 0: { // numeric
int itype = utils::inumeric(FLERR, typestr.c_str(), true, lmp);
if ((itype < 1) || (itype > ntypes))
error->one(FLERR, "Invalid atom type {} in Atoms section of data file: {}", itype,
buf);
type[nlocal - 1] = itype;
if (labelflag) type[nlocal - 1] = ilabel[itype - 1];
break;
}
case 1: { // type label
if (!atom->labelmapflag)
error->one(FLERR, "Invalid Atoms section line in data file: {}", buf);
type[nlocal - 1] = lmap->find(typestr, Atom::ATOM);
if (type[nlocal - 1] == -1)
error->one(FLERR, "Invalid Atoms section line in data file: {}", buf);
break;
}
default: // invalid
error->one(FLERR, "Invalid Atoms section line in data file: {}", buf);
break;
}
// clang-format off
if (type_offset) type[nlocal-1] += type_offset;
if (type[nlocal-1] <= 0 || type[nlocal-1] > ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
error->one(FLERR,"Invalid atom type {} in Atoms section of data file", typestr);
}
}
buf = next + 1;