ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

update parser for bonded topology data

Browse Source
This commit is contained in:
Axel Kohlmeyer
2022-09-04 22:13:23 -04:00
parent fc738ea239
commit e0b6ae77d3
1 changed files with 131 additions and 91 deletions
Download Patch File Download Diff File Expand all files Collapse all files

222
src/molecule.cpp
View File

@ -774,13 +774,11 @@ void Molecule::types(char *line)
typestr = utils::utf8_subst(values[1]);
switch (utils::is_type(typestr)) {
case 0: { // numeric
type[iatom] = utils::inumeric(FLERR, typestr, false, lmp);
type[iatom] += toffset;
break;
}
case 1: { // type label
if (!atom->labelmapflag)
error->all(FLERR, "Invalid atom type {} in {}: {}", typestr, location, utils::trim(line));
@ -789,7 +787,6 @@ void Molecule::types(char *line)
error->all(FLERR, "Unknown atom type {} in {}: {}", typestr, location, utils::trim(line));
break;
}
default: // invalid
error->one(FLERR, "Invalid format in {}: {}", location, utils::trim(line));
break;
@ -971,15 +968,9 @@ void Molecule::masses(char *line)
for (int i = 0; i < natoms; i++) {
if (count[i] == 0)
error->all(FLERR,
"Atom {} missing in Masses "
"section of molecule file",
i + 1);
error->all(FLERR, "Atom {} missing in Masses section of molecule file", i + 1);
if (rmass[i] <= 0.0)
error->all(FLERR,
"Invalid atom mass {} for atom {} "
"in molecule file",
radius[i], i + 1);
error->all(FLERR, "Invalid atom mass {} for atom {} in molecule file", radius[i], i + 1);
}
}
@ -993,6 +984,7 @@ void Molecule::masses(char *line)
void Molecule::bonds(int flag, char *line)
{
const std::string location = "Bonds section of molecule file";
int itype;
tagint m, atom1, atom2;
std::string typestr;
@ -1005,31 +997,43 @@ void Molecule::bonds(int flag, char *line)
for (int i = 0; i < nbonds; i++) {
readline(line);
auto values = Tokenizer(utils::trim(line)).as_vector();
int nwords = values.size();
for (std::size_t i = 0; i < values.size(); ++i) {
if (utils::strmatch(values[i], "^#")) {
nwords = i;
break;
}
}
if (nwords != 4) error->all(FLERR, "Invalid format in {}: {}", location, utils::trim(line));
try {
ValueTokenizer values(utils::trim_comment(line));
if (values.count() != 4)
error->all(FLERR, "Invalid line in Bonds section of molecule file: {}", line);
values.next_int();
typestr = values.next_string();
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR, "Invalid Bonds section in molecule file");
itype = atom->lmap->find(typestr, Atom::BOND);
if (itype == -1) error->one(FLERR, "Invalid Bonds section in molecule file");
} else
typestr = utils::utf8_subst(values[1]);
switch (utils::is_type(typestr)) {
case 0: { // numeric
itype = utils::inumeric(FLERR, typestr, false, lmp);
atom1 = values.next_tagint();
atom2 = values.next_tagint();
} catch (TokenizerException &e) {
error->all(FLERR, "Invalid line in Bonds section of molecule file: {}\n{}", e.what(), line);
itype += boffset;
break;
}
case 1: { // type label
if (!atom->labelmapflag)
error->all(FLERR, "Invalid bond type {} in {}: {}", typestr, location, utils::trim(line));
itype = atom->lmap->find(typestr, Atom::BOND);
if (itype == -1)
error->all(FLERR, "Unknown bond type {} in {}: {}", typestr, location, utils::trim(line));
break;
}
default: // invalid
error->one(FLERR, "Invalid format in {}: {}", location, utils::trim(line));
break;
}
itype += boffset;
atom1 = utils::tnumeric(FLERR, values[2], false, lmp);
atom2 = utils::tnumeric(FLERR, values[3], false, lmp);
if ((atom1 <= 0) || (atom1 > natoms) || (atom2 <= 0) || (atom2 > natoms) || (atom1 == atom2))
error->all(FLERR, "Invalid atom ID in Bonds section of molecule file");
error->all(FLERR, "Invalid atom ID in {}: {}", location, utils::trim(line));
if ((itype <= 0) || (domain->box_exist && (itype > atom->nbondtypes)))
error->all(FLERR, "Invalid bond type in Bonds section of molecule file");
error->all(FLERR, "Invalid bond type in {}: {}", location, utils::trim(line));
if (flag) {
m = atom1 - 1;
@ -1066,6 +1070,7 @@ void Molecule::bonds(int flag, char *line)
void Molecule::angles(int flag, char *line)
{
const std::string location = "Angles section of molecule file";
int itype;
tagint m, atom1, atom2, atom3;
std::string typestr;
@ -1078,33 +1083,45 @@ void Molecule::angles(int flag, char *line)
for (int i = 0; i < nangles; i++) {
readline(line);
auto values = Tokenizer(utils::trim(line)).as_vector();
int nwords = values.size();
for (std::size_t i = 0; i < values.size(); ++i) {
if (utils::strmatch(values[i], "^#")) {
nwords = i;
break;
}
}
if (nwords != 5) error->all(FLERR, "Invalid format in {}: {}", location, utils::trim(line));
try {
ValueTokenizer values(utils::trim_comment(line));
if (values.count() != 5)
error->all(FLERR, "Invalid line in Angles section of molecule file: {}", line);
values.next_int();
typestr = values.next_string();
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR, "Invalid Angles section in molecule file");
itype = atom->lmap->find(typestr, Atom::ANGLE);
if (itype == -1) error->one(FLERR, "Invalid Angles section in molecule file");
} else
typestr = utils::utf8_subst(values[1]);
switch (utils::is_type(typestr)) {
case 0: { // numeric
itype = utils::inumeric(FLERR, typestr, false, lmp);
atom1 = values.next_tagint();
atom2 = values.next_tagint();
atom3 = values.next_tagint();
} catch (TokenizerException &e) {
error->all(FLERR, "Invalid line in Angles section of molecule file: {}\n{}", e.what(), line);
itype += aoffset;
break;
}
case 1: { // type label
if (!atom->labelmapflag)
error->all(FLERR, "Invalid angle type {} in {}: {}", typestr, location, utils::trim(line));
itype = atom->lmap->find(typestr, Atom::ANGLE);
if (itype == -1)
error->all(FLERR, "Unknown angle type {} in {}: {}", typestr, location, utils::trim(line));
break;
}
default: // invalid
error->one(FLERR, "Invalid format in {}: {}", location, utils::trim(line));
break;
}
itype += aoffset;
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 ((atom1 <= 0) || (atom1 > natoms) || (atom2 <= 0) || (atom2 > natoms) || (atom3 <= 0) ||
(atom3 > natoms) || (atom1 == atom2) || (atom1 == atom3) || (atom2 == atom3))
error->all(FLERR, "Invalid atom ID in Angles section of molecule file");
error->all(FLERR, "Invalid atom ID in {}: {}", location, utils::trim(line));
if ((itype <= 0) || (domain->box_exist && (itype > atom->nangletypes)))
error->all(FLERR, "Invalid angle type in Angles section of molecule file");
error->all(FLERR, "Invalid angle type in {}: {}", location, utils::trim(line));
if (flag) {
m = atom2 - 1;
@ -1154,6 +1171,7 @@ void Molecule::angles(int flag, char *line)
void Molecule::dihedrals(int flag, char *line)
{
const std::string location = "Dihedrals section of molecule file";
int itype;
tagint m, atom1, atom2, atom3, atom4;
std::string typestr;
@ -1166,38 +1184,48 @@ void Molecule::dihedrals(int flag, char *line)
for (int i = 0; i < ndihedrals; i++) {
readline(line);
auto values = Tokenizer(utils::trim(line)).as_vector();
int nwords = values.size();
for (std::size_t i = 0; i < values.size(); ++i) {
if (utils::strmatch(values[i], "^#")) {
nwords = i;
break;
}
}
if (nwords != 6) error->all(FLERR, "Invalid format in {}: {}", location, utils::trim(line));
try {
ValueTokenizer values(utils::trim_comment(line));
if (values.count() != 6)
error->all(FLERR, "Invalid line in Dihedrals section of molecule file: {}", line);
values.next_int();
typestr = values.next_string();
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR, "Invalid Dihedrals section in molecule file");
itype = atom->lmap->find(typestr, Atom::DIHEDRAL);
if (itype == -1) error->one(FLERR, "Invalid Dihedrals section in molecule file");
} else
typestr = utils::utf8_subst(values[1]);
switch (utils::is_type(typestr)) {
case 0: { // numeric
itype = utils::inumeric(FLERR, typestr, false, lmp);
atom1 = values.next_tagint();
atom2 = values.next_tagint();
atom3 = values.next_tagint();
atom4 = values.next_tagint();
} catch (TokenizerException &e) {
error->all(FLERR, "Invalid line in Dihedrals section of molecule file: {}\n{}", e.what(),
line);
itype += doffset;
break;
}
case 1: { // type label
if (!atom->labelmapflag)
error->all(FLERR, "Invalid dihedral type {} in {}: {}", typestr, location, utils::trim(line));
itype = atom->lmap->find(typestr, Atom::DIHEDRAL);
if (itype == -1)
error->all(FLERR, "Unknown dihedral type {} in {}: {}", typestr, location, utils::trim(line));
break;
}
default: // invalid
error->one(FLERR, "Invalid format in {}: {}", location, utils::trim(line));
break;
}
itype += doffset;
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 ((atom1 <= 0) || (atom1 > natoms) || (atom2 <= 0) || (atom2 > natoms) || (atom3 <= 0) ||
(atom3 > natoms) || (atom4 <= 0) || (atom4 > natoms) || (atom1 == atom2) ||
(atom1 == atom3) || (atom1 == atom4) || (atom2 == atom3) || (atom2 == atom4) ||
(atom3 == atom4))
error->all(FLERR, "Invalid atom ID in Dihedrals section of molecule file");
error->all(FLERR, "Invalid atom ID in {}: {}", location, utils::trim(line));
if ((itype <= 0) || (domain->box_exist && (itype > atom->ndihedraltypes)))
error->all(FLERR, "Invalid dihedral type in Dihedrals section of molecule file");
error->all(FLERR, "Invalid dihedral type in {}: {}", location, utils::trim(line));
if (flag) {
m = atom2 - 1;
@ -1258,6 +1286,7 @@ void Molecule::dihedrals(int flag, char *line)
void Molecule::impropers(int flag, char *line)
{
const std::string location = "Impropers section of molecule file";
int itype;
tagint m, atom1, atom2, atom3, atom4;
std::string typestr;
@ -1270,37 +1299,48 @@ void Molecule::impropers(int flag, char *line)
for (int i = 0; i < nimpropers; i++) {
readline(line);
auto values = Tokenizer(utils::trim(line)).as_vector();
int nwords = values.size();
for (std::size_t i = 0; i < values.size(); ++i) {
if (utils::strmatch(values[i], "^#")) {
nwords = i;
break;
}
}
if (nwords != 6) error->all(FLERR, "Invalid format in {}: {}", location, utils::trim(line));
try {
ValueTokenizer values(utils::trim_comment(line));
if (values.count() != 6)
error->all(FLERR, "Invalid line in Impropers section of molecule file: {}", line);
values.next_int();
typestr = values.next_string();
if (!isdigit(typestr[0])) {
if (!atom->labelmapflag) error->one(FLERR, "Invalid Impropers section in molecule file");
itype = atom->lmap->find(typestr, Atom::IMPROPER);
if (itype == -1) error->one(FLERR, "Invalid Impropers section in molecule file");
} else
typestr = utils::utf8_subst(values[1]);
switch (utils::is_type(typestr)) {
case 0: { // numeric
itype = utils::inumeric(FLERR, typestr, false, lmp);
atom1 = values.next_tagint();
atom2 = values.next_tagint();
atom3 = values.next_tagint();
atom4 = values.next_tagint();
} catch (TokenizerException &e) {
error->all(FLERR, "Invalid line in Impropers section of molecule file: {}\n{}", e.what(),
line);
itype += ioffset;
break;
}
case 1: { // type label
if (!atom->labelmapflag)
error->all(FLERR, "Invalid improper type {} in {}: {}", typestr, location, utils::trim(line));
itype = atom->lmap->find(typestr, Atom::IMPROPER);
if (itype == -1)
error->all(FLERR, "Unknown improper type {} in {}: {}", typestr, location, utils::trim(line));
break;
}
default: // invalid
error->one(FLERR, "Invalid format in {}: {}", location, utils::trim(line));
break;
}
itype += ioffset;
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 ((atom1 <= 0) || (atom1 > natoms) || (atom2 <= 0) || (atom2 > natoms) || (atom3 <= 0) ||
(atom3 > natoms) || (atom4 <= 0) || (atom4 > natoms) || (atom1 == atom2) ||
(atom1 == atom3) || (atom1 == atom4) || (atom2 == atom3) || (atom2 == atom4) ||
(atom3 == atom4))
error->all(FLERR, "Invalid atom ID in impropers section of molecule file");
error->all(FLERR, "Invalid atom ID in {}: {}", location, utils::trim(line));
if ((itype <= 0) || (domain->box_exist && (itype > atom->nimpropertypes)))
error->all(FLERR, "Invalid improper type in Impropers section of molecule file");
error->all(FLERR, "Invalid improper type in {}: {}", location, utils::trim(line));
if (flag) {
m = atom2 - 1;