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add UTF-8 substitution and detection

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This commit is contained in:
Axel Kohlmeyer
2022-09-04 06:45:11 -04:00
parent 34104bbbe9
commit 26e1b7c44d
7 changed files with 57 additions and 26 deletions
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59
src/atom.cpp
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@ -1185,6 +1185,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2]) {
avec->data_atom(xdata,imagedata,values,typestr);
typestr = utils::utf8_subst(typestr);
if (id_offset) tag[nlocal-1] += id_offset;
if (mol_offset) molecule[nlocal-1] += mol_offset;
// clang-format on
@ -1291,7 +1292,7 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
// Bonds line is: number(ignored), bond type, atomID 1, atomID 2
if (nwords > 0) {
if (nwords != 4) error->all(FLERR, "Incorrect format in {}: {}", location, utils::trim(buf));
typestr = values[1];
typestr = utils::utf8_subst(values[1]);
atom1 = utils::tnumeric(FLERR, values[2], false, lmp);
atom2 = utils::tnumeric(FLERR, values[3], false, lmp);
if (id_offset) {
@ -1388,7 +1389,7 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
// Angles line is: number(ignored), angle type, atomID 1, atomID 2, atomID 3
if (nwords > 0) {
if (nwords != 5) error->all(FLERR, "Incorrect format in {}: {}", location, utils::trim(buf));
typestr = values[1];
typestr = utils::utf8_subst(values[1]);
atom1 = utils::tnumeric(FLERR, values[2], false, lmp);
atom2 = utils::tnumeric(FLERR, values[3], false, lmp);
atom3 = utils::tnumeric(FLERR, values[4], false, lmp);
@ -1501,7 +1502,7 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
// Dihedrals line is: number(ignored), bond type, atomID 1, atomID 2, atomID 3, atomID 4
if (nwords > 0) {
if (nwords != 6) error->all(FLERR, "Incorrect format in {}: {}", location, utils::trim(buf));
typestr = values[1];
typestr = utils::utf8_subst(values[1]);
atom1 = utils::tnumeric(FLERR, values[2], false, lmp);
atom2 = utils::tnumeric(FLERR, values[3], false, lmp);
atom3 = utils::tnumeric(FLERR, values[4], false, lmp);
@ -1633,7 +1634,7 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
// Impropers line is: number(ignored), bond type, atomID 1, atomID 2, atomID 3, atomID 4
if (nwords > 0) {
if (nwords != 6) error->all(FLERR, "Incorrect format in {}: {}", location, utils::trim(buf));
typestr = values[1];
typestr = utils::utf8_subst(values[1]);
atom1 = utils::tnumeric(FLERR, values[2], false, lmp);
atom2 = utils::tnumeric(FLERR, values[3], false, lmp);
atom3 = utils::tnumeric(FLERR, values[4], false, lmp);
@ -1934,30 +1935,44 @@ void Atom::set_mass(const char *file, int line, int itype, double value)
void Atom::set_mass(const char *file, int line, int /*narg*/, char **arg)
{
if (mass == nullptr) error->all(file,line, "Cannot set atom mass for atom style {}", atom_style);
if (mass == nullptr)
error->all(file,line, "Cannot set per-type atom mass for atom style {}", atom_style);
std::string typestr = utils::trim(arg[0]);
if (!isdigit(typestr[0]) && typestr[0] != '*') {
int itype = lmap->find(typestr,Atom::ATOM);
if (itype == -1) error->all(file,line,"Invalid type for mass set");
mass[itype] = utils::numeric(FLERR,arg[1],false,lmp);
mass_setflag[itype] = 1;
// clang-format on
std::string typestr = utils::utf8_subst(utils::trim(arg[0]));
switch (utils::is_type(typestr)) {
if (mass[itype] <= 0.0) error->all(file,line,"Invalid mass value");
} else {
int lo,hi;
utils::bounds(file,line,arg[0],1,ntypes,lo,hi,error);
if ((lo < 1) || (hi > ntypes))
error->all(file,line,"Invalid type {} for atom mass {}", arg[1]);
case 0: { // numeric
int lo, hi;
utils::bounds(file, line, typestr.c_str(), 1, ntypes, lo, hi, error);
if ((lo < 1) || (hi > ntypes))
error->all(file, line, "Invalid atom type {} for atom mass", typestr);
const double value = utils::numeric(FLERR,arg[1],false,lmp);
if (value <= 0.0) error->all(file,line,"Invalid atom mass value {}", value);
const double value = utils::numeric(FLERR, arg[1], false, lmp);
if (value <= 0.0)
error->all(file, line, "Invalid atom mass value {} for type {}", value, typestr);
for (int itype = lo; itype <= hi; itype++) {
mass[itype] = value;
mass_setflag[itype] = 1;
for (int itype = lo; itype <= hi; itype++) {
mass[itype] = value;
mass_setflag[itype] = 1;
}
break;
}
case 1: { // type label
if (!atom->labelmapflag) error->all(FLERR, "Invalid atom type {} for setting mass", typestr);
int itype = lmap->find(typestr, Atom::ATOM);
if (itype == -1) error->all(file, line, "Invalid type {} for setting mass", typestr);
mass[itype] = utils::numeric(FLERR, arg[1], false, lmp);
mass_setflag[itype] = 1;
break;
}
default: // invalid
error->one(FLERR, "Invalid mass setting");
break;
}
// clang-format off
}
/* ----------------------------------------------------------------------