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update parsers for bond topology data in data files

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This commit is contained in:
Axel Kohlmeyer
2022-09-04 05:27:29 -04:00
parent ad8a931fe4
commit 3dc7b7e0b3
2 changed files with 181 additions and 98 deletions
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277
src/atom.cpp
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@ -1052,10 +1052,11 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
double *coord;
char *next;
std::string typestr;
auto location = "Atoms section of data file";
// use the first line to detect and validate the number of words/tokens per line
next = strchr(buf,'\n');
if (!next) error->all(FLERR, "Missing data in Atoms section of data file");
if (!next) error->all(FLERR, "Missing data in {}", location);
*next = '\0';
auto values = Tokenizer(buf).as_vector();
int nwords = values.size();
@ -1068,7 +1069,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
*next = '\n';
if ((nwords != avec->size_data_atom) && (nwords != avec->size_data_atom + 3))
error->all(FLERR,"Incorrect atom format in data file: {}", utils::trim(buf));
error->all(FLERR,"Incorrect atom format in {}: {}", location, utils::trim(buf));
// set bounds for my proc
// if periodic and I am lo/hi proc, adjust bounds by EPSILON
@ -1140,7 +1141,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
if (!next) error->all(FLERR, "Missing data in Atoms section of data file");
if (!next) error->all(FLERR, "Missing data in {}", location);
*next = '\0';
auto values = Tokenizer(buf).as_vector();
int nvalues = values.size();
@ -1148,7 +1149,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
// skip over empty or comment lines
} else if ((nvalues < nwords) ||
((nvalues > nwords) && (!utils::strmatch(values[nwords],"^#")))) {
error->all(FLERR, "Incorrect atom format in data file: {}", utils::trim(buf));
error->all(FLERR, "Incorrect atom format in {}: {}", location, utils::trim(buf));
} else {
int imx = 0, imy = 0, imz = 0;
if (imageflag) {
@ -1192,8 +1193,8 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
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);
error->one(FLERR, "Invalid atom type {} in {}: {}", itype, location,
utils::trim(buf));
type[nlocal - 1] = itype;
if (labelflag) type[nlocal - 1] = ilabel[itype - 1];
break;
@ -1201,21 +1202,21 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
case 1: { // type label
if (!atom->labelmapflag)
error->one(FLERR, "Invalid Atoms section line in data file: {}", buf);
error->one(FLERR, "Invalid line in {}: {}", location, utils::trim(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);
error->one(FLERR, "Invalid line in {}: {}", location, utils::trim(buf));
break;
}
default: // invalid
error->one(FLERR, "Invalid Atoms section line in data file: {}", buf);
error->one(FLERR, "Invalid line in {}: {}", location, utils::trim(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", typestr);
error->one(FLERR,"Invalid atom type {} in {}", location, typestr);
}
}
buf = next + 1;
@ -1275,39 +1276,59 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
if (!next) error->all(FLERR, "Missing data in Bonds section of data file");
if (!next) error->all(FLERR, "Missing data in {}", location);
*next = '\0';
ValueTokenizer values(utils::trim_comment(buf));
// skip over empty or comment lines
if (values.has_next()) {
try {
values.next_int();
typestr = values.next_string();
atom1 = values.next_tagint();
atom2 = values.next_tagint();
if (values.has_next()) throw TokenizerException("Too many tokens","");
} catch (TokenizerException &e) {
error->one(FLERR,"{} in {}: {}", e.what(), location, utils::trim(buf));
auto values = Tokenizer(buf).as_vector();
int nwords = values.size();
for (std::size_t i = 0; i < values.size(); ++i) {
if (utils::strmatch(values[i], "^#")) {
nwords = i;
break;
}
}
// skip over empty or comment lines
// 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];
atom1 = utils::tnumeric(FLERR, values[2], false, lmp);
atom2 = utils::tnumeric(FLERR, values[3], false, lmp);
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
}
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Bonds section in data file");
itype = lmap->find(typestr,Atom::BOND);
if (itype == -1) error->one(FLERR,"Invalid Bonds section in data file");
} else {
itype = utils::inumeric(FLERR,typestr,true,lmp);
if (labelflag) itype = ilabel[itype-1];
// clang-format on
switch (utils::is_type(typestr)) {
case 0: { // numeric
itype = utils::inumeric(FLERR, typestr.c_str(), false, lmp);
if ((itype < 1) || (itype > nbondtypes))
error->all(FLERR, "Invalid bond type {} in {}: {}", itype, location, utils::trim(buf));
if (labelflag) itype = ilabel[itype - 1];
break;
}
case 1: { // type label
if (!atom->labelmapflag) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
itype = lmap->find(typestr, Atom::BOND);
if (itype == -1) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
default: // invalid
error->one(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
itype += type_offset;
// clang-format off
if ((atom1 <= 0) || (atom1 > map_tag_max) ||
(atom2 <= 0) || (atom2 > map_tag_max) || (atom1 == atom2))
error->one(FLERR,"Invalid atom ID in {}: {}", location, utils::trim(buf));
if (itype <= 0 || itype > nbondtypes)
error->one(FLERR,"Invalid bond type in {}: {}", location, utils::trim(buf));
error->all(FLERR,"Invalid atom ID in {}: {}", location, utils::trim(buf));
if ((itype <= 0) || (itype > nbondtypes))
error->all(FLERR,"Invalid bond type {} in {}: {}", itype, location, utils::trim(buf));
if ((m = map(atom1)) >= 0) {
if (count) count[m]++;
else {
@ -1352,35 +1373,55 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
if (!next) error->all(FLERR, "Missing data in Angles section of data file");
if (!next) error->all(FLERR, "Missing data in {}", location);
*next = '\0';
ValueTokenizer values(utils::trim_comment(buf));
// skip over empty or comment lines
if (values.has_next()) {
try {
values.next_int();
typestr = values.next_string();
atom1 = values.next_tagint();
atom2 = values.next_tagint();
atom3 = values.next_tagint();
if (values.has_next()) throw TokenizerException("Too many tokens","");
} catch (TokenizerException &e) {
error->one(FLERR,"{} in {}: {}", e.what(), location, utils::trim(buf));
auto values = Tokenizer(buf).as_vector();
int nwords = values.size();
for (std::size_t i = 0; i < values.size(); ++i) {
if (utils::strmatch(values[i], "^#")) {
nwords = i;
break;
}
}
// skip over empty or comment lines
// 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];
atom1 = utils::tnumeric(FLERR, values[2], false, lmp);
atom2 = utils::tnumeric(FLERR, values[3], false, lmp);
atom3 = utils::tnumeric(FLERR, values[4], false, lmp);
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
atom3 += id_offset;
}
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Angles section in data file");
itype = lmap->find(typestr,Atom::ANGLE);
if (itype == -1) error->one(FLERR,"Invalid Angles section in data file");
} else {
itype = utils::inumeric(FLERR,typestr,true,lmp);
if (labelflag) itype = ilabel[itype-1];
// clang-format on
switch (utils::is_type(typestr)) {
case 0: { // numeric
itype = utils::inumeric(FLERR, typestr.c_str(), false, lmp);
if ((itype < 1) || (itype > nangletypes))
error->all(FLERR, "Invalid angle type {} in {}: {}", itype, location, utils::trim(buf));
if (labelflag) itype = ilabel[itype - 1];
break;
}
case 1: { // type label
if (!atom->labelmapflag) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
itype = lmap->find(typestr, Atom::ANGLE);
if (itype == -1) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
default: // invalid
error->one(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
itype += type_offset;
// clang-format off
if ((atom1 <= 0) || (atom1 > map_tag_max) ||
(atom2 <= 0) || (atom2 > map_tag_max) ||
@ -1388,7 +1429,7 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
(atom1 == atom2) || (atom1 == atom3) || (atom2 == atom3))
error->one(FLERR,"Invalid atom ID in {}: {}", location, utils::trim(buf));
if (itype <= 0 || itype > nangletypes)
error->one(FLERR,"Invalid angle type in {}: {}", location, utils::trim(buf));
error->one(FLERR,"Invalid angle type {} in {}: {}", itype, location, utils::trim(buf));
if ((m = map(atom2)) >= 0) {
if (count) count[m]++;
else {
@ -1445,37 +1486,58 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
if (!next) error->all(FLERR, "Missing data in Dihedrals section of data file");
if (!next) error->all(FLERR, "Missing data in {}", location);
*next = '\0';
ValueTokenizer values(utils::trim_comment(buf));
// skip over empty or comment lines
if (values.has_next()) {
try {
values.next_int();
typestr = values.next_string();
atom1 = values.next_tagint();
atom2 = values.next_tagint();
atom3 = values.next_tagint();
atom4 = values.next_tagint();
if (values.has_next()) throw TokenizerException("Too many tokens","");
} catch (TokenizerException &e) {
error->one(FLERR,"{} in {}: {}", e.what(), location, utils::trim(buf));
auto values = Tokenizer(buf).as_vector();
int nwords = values.size();
for (std::size_t i = 0; i < values.size(); ++i) {
if (utils::strmatch(values[i], "^#")) {
nwords = i;
break;
}
}
// skip over empty or comment lines
// 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];
atom1 = utils::tnumeric(FLERR, values[2], false, lmp);
atom2 = utils::tnumeric(FLERR, values[3], false, lmp);
atom3 = utils::tnumeric(FLERR, values[4], false, lmp);
atom4 = utils::tnumeric(FLERR, values[5], false, lmp);
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
atom3 += id_offset;
atom4 += id_offset;
}
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Dihedrals section in data file");
itype = lmap->find(typestr,Atom::DIHEDRAL);
if (itype == -1) error->one(FLERR,"Invalid Dihedrals section in data file");
} else {
itype = utils::inumeric(FLERR,typestr,true,lmp);
if (labelflag) itype = ilabel[itype-1];
// clang-format on
switch (utils::is_type(typestr)) {
case 0: { // numeric
itype = utils::inumeric(FLERR, typestr.c_str(), false, lmp);
if ((itype < 1) || (itype > ndihedraltypes))
error->all(FLERR, "Invalid dihedral type {} in {}: {}", itype, location,
utils::trim(buf));
if (labelflag) itype = ilabel[itype - 1];
break;
}
case 1: { // type label
if (!atom->labelmapflag) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
itype = lmap->find(typestr, Atom::DIHEDRAL);
if (itype == -1) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
default: // invalid
error->one(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
itype += type_offset;
// clang-format off
if ((atom1 <= 0) || (atom1 > map_tag_max) ||
(atom2 <= 0) || (atom2 > map_tag_max) ||
@ -1485,7 +1547,7 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
(atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4))
error->one(FLERR, "Invalid atom ID in {}: {}", location, utils::trim(buf));
if (itype <= 0 || itype > ndihedraltypes)
error->one(FLERR, "Invalid dihedral type in {}: {}", location, utils::trim(buf));
error->one(FLERR, "Invalid dihedral type {} in {}: {}", itype, location, utils::trim(buf));
if ((m = map(atom2)) >= 0) {
if (count) count[m]++;
else {
@ -1556,37 +1618,58 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
if (!next) error->all(FLERR, "Missing data in Impropers section of data file");
if (!next) error->all(FLERR, "Missing data in {}", location);
*next = '\0';
ValueTokenizer values(utils::trim_comment(buf));
// skip over empty or comment lines
if (values.has_next()) {
try {
values.next_int();
typestr = values.next_string();
atom1 = values.next_tagint();
atom2 = values.next_tagint();
atom3 = values.next_tagint();
atom4 = values.next_tagint();
if (values.has_next()) throw TokenizerException("Too many tokens","");
} catch (TokenizerException &e) {
error->one(FLERR,"{} in {}: {}", e.what(), location, utils::trim(buf));
auto values = Tokenizer(buf).as_vector();
int nwords = values.size();
for (std::size_t i = 0; i < values.size(); ++i) {
if (utils::strmatch(values[i], "^#")) {
nwords = i;
break;
}
}
// skip over empty or comment lines
// 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];
atom1 = utils::tnumeric(FLERR, values[2], false, lmp);
atom2 = utils::tnumeric(FLERR, values[3], false, lmp);
atom3 = utils::tnumeric(FLERR, values[4], false, lmp);
atom4 = utils::tnumeric(FLERR, values[5], false, lmp);
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
atom3 += id_offset;
atom4 += id_offset;
}
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR,"Invalid Impropers section in data file");
itype = lmap->find(typestr,Atom::IMPROPER);
if (itype == -1) error->one(FLERR,"Invalid Impropers section in data file");
} else {
itype = utils::inumeric(FLERR,typestr,true,lmp);
if (labelflag) itype = ilabel[itype-1];
// clang-format on
switch (utils::is_type(typestr)) {
case 0: { // numeric
itype = utils::inumeric(FLERR, typestr.c_str(), false, lmp);
if ((itype < 1) || (itype > nimpropertypes))
error->all(FLERR, "Invalid improper type {} in {}: {}", itype, location,
utils::trim(buf));
if (labelflag) itype = ilabel[itype - 1];
break;
}
case 1: { // type label
if (!atom->labelmapflag) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
itype = lmap->find(typestr, Atom::IMPROPER);
if (itype == -1) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
default: // invalid
error->one(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
itype += type_offset;
// clang-format off
if ((atom1 <= 0) || (atom1 > map_tag_max) ||
(atom2 <= 0) || (atom2 > map_tag_max) ||
@ -1596,7 +1679,7 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
(atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4))
error->one(FLERR, "Invalid atom ID in {}: {}", location, utils::trim(buf));
if (itype <= 0 || itype > nimpropertypes)
error->one(FLERR, "Invalid improper type in {}: {}", location, utils::trim(buf));
error->one(FLERR, "Invalid improper type {} in {}: {}", itype, location, utils::trim(buf));
if ((m = map(atom2)) >= 0) {
if (count) count[m]++;
else {