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process "shake:atoms" and "shake:types" sections in JSON data

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This commit is contained in:
Axel Kohlmeyer
2025-06-17 23:15:14 -04:00
parent e01640c4f5
commit 210fdb8b98
2 changed files with 161 additions and 31 deletions
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190
src/molecule.cpp
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@ -1407,62 +1407,177 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
// shake_atoms // shake_atoms
#define APPLY_SHAKE_ATOMS(ncols) \
if (c[1].size() != ncols) \
error->all(FLERR, Error::NOLASTLINE, \
"Molecule template {}: invalid number of items for atom-id {} in \"shake:" \
"atoms\" section of molecue JSON data ({} vs {})", \
id, iatom + 1, c[1].size(), ncols); \
for (int i = 0; i < ncols; ++i) { \
if (!c[1][i].is_number_integer()) \
error->all(FLERR, Error::NOLASTLINE, \
"Molecule template {}: invalid atom-id {} in atom-id-list for atom {} " \
"in \"shake:atoms\" section of molecule JSON data", \
id, to_string(c[1][i]), iatom + 1); \
shake_atom[iatom][i] = int(c[1][i]); \
}
if (shakeatomflag) { if (shakeatomflag) {
const auto &shakedata = moldata["shake"]["atoms"]; const auto &shakedata = moldata["shake"]["atoms"];
secfmt.clear(); secfmt.clear();
for (int i = 0; i < 2; ++i) secfmt.push_back(shakedata["format"][i]); for (int i = 0; i < 2; ++i) secfmt.push_back(shakedata["format"][i]);
if ((secfmt[0] == "atom-id") && (secfmt[1] == "atom-id-list")) { if ((secfmt[0] == "atom-id") && (secfmt[1] == "atom-id-list")) {
for (int i = 0; i < natoms; i++) shake_flag[i] = -1;
memset(count, 0, natoms * sizeof(int)); memset(count, 0, natoms * sizeof(int));
for (const auto &c : shakedata["data"]) { for (const auto &c : shakedata["data"]) {
if (c.size() < 2) if (c.size() < 2)
error->all(FLERR, Error::NOLASTLINE, error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: missing data in \"shake:flags\" section of molecule " "Molecule template {}: missing data in \"shake:atoms\" section of molecule "
"JSON data: {}", "JSON data: {}",
id, to_string(c)); id, to_string(c));
if (!c[0].is_number_integer()) if (!c[0].is_number_integer())
error->all(FLERR, Error::NOLASTLINE, error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: invalid atom-id in \"shake:flags\" section of molecule " "Molecule template {}: invalid atom-id in \"shake:atoms\" section of molecule "
"JSON data: {}", "JSON data: {}",
id, to_string(c[0])); id, to_string(c[0]));
const int iatom = int(c[0]) - 1; const int iatom = int(c[0]) - 1;
if ((iatom < 0) || (iatom >= natoms)) if ((iatom < 0) || (iatom >= natoms))
error->all(FLERR, Error::NOLASTLINE, error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: invalid atom-id {} in \"shake:flags\" section of " "Molecule template {}: invalid atom-id {} in \"shake:atoms\" section of "
"molecule JSON data", "molecule JSON data",
id, iatom + 1); id, iatom + 1);
if (!c[1].is_number_integer())
error->all(FLERR, Error::NOLASTLINE, switch (shake_flag[iatom]) {
"Molecule template {}: invalid flag in \"shake:flags\" section of " case 1:
"molecule JSON data: {}", APPLY_SHAKE_ATOMS(3);
id, to_string(c[1])); break;
shake_flag[iatom] = int(c[1]); case 2:
APPLY_SHAKE_ATOMS(2);
break;
case 3:
APPLY_SHAKE_ATOMS(3);
break;
case 4:
APPLY_SHAKE_ATOMS(4);
break;
case 0:
APPLY_SHAKE_ATOMS(0);
break;
default:
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: Unsupported Shake flag {} for "
" atom {} in \"shake:atoms\" section of molecule JSON data",
id, shake_flag[iatom], iatom + 1);
}
count[iatom]++; count[iatom]++;
} }
// checks // checks
for (int i = 0; i < natoms; i++) { for (int i = 0; i < natoms; i++) {
if (count[i] == 0) { if (count[i] == 0)
error->all(FLERR, Error::NOLASTLINE, error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: atom {} missing in \"shake:flags\" JSON section", id, "Molecule template {}: atom {} missing in \"shake:atoms\" JSON section", id,
i + 1); i + 1);
}
if ((shake_flag[i] < 0) || (shake_flag[i] > 4))
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: invalid flag value {} in \"shake:flags\" section of "
"molecule JSON data",
id, shake_flag[i]);
} }
} else { } else {
error->all(FLERR, Error::NOLASTLINE, error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: Expected \"shake:flags\" format [\"atom-id\",\"mass\"] but " "Molecule template {}: Expected \"shake:atoms\" format "
"found [\"{}\",\"{}\"]", "[\"atom-id\",\"atom-id-list\"] but found [\"{}\",\"{}\"]",
id, secfmt[0], secfmt[1]); id, secfmt[0], secfmt[1]);
} }
} }
#undef APPLY_SHAKE_ATOMS
// shake_bond_types // shake_bond_types
if (shaketypeflag) {}
#define SET_SHAKE_TYPE(type, idx, ncols, offset) \
if (c[1].size() < ncols) \
error->all(FLERR, Error::NOLASTLINE, \
"Molecule template {}: invalid number of items for atom-id {} in \"shake:" \
"types\" section of molecue JSON data ({} vs {})", \
id, iatom + 1, c[1].size(), ncols); \
if (c[1][idx].is_number_integer()) { \
shake_type[iatom][idx] = int(c[1][idx]) + offset; \
} else { \
char *subst = utils::expand_type(FLERR, c[1][idx], type, lmp); \
if (subst) { \
shake_type[iatom][idx] = utils::inumeric(FLERR, subst, false, lmp); \
delete[] subst; \
} \
}
if (shaketypeflag) {
const auto &shakedata = moldata["shake"]["types"];
secfmt.clear();
for (int i = 0; i < 2; ++i) secfmt.push_back(shakedata["format"][i]);
if ((secfmt[0] == "atom-id") && (secfmt[1] == "type-list")) {
memset(count, 0, natoms * sizeof(int));
for (const auto &c : shakedata["data"]) {
if (c.size() < 2)
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: missing data in \"shake:types\" section of molecule "
"JSON data: {}",
id, to_string(c));
if (!c[0].is_number_integer())
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: invalid atom-id in \"shake:types\" section of molecule "
"JSON data: {}",
id, to_string(c[0]));
const int iatom = int(c[0]) - 1;
if ((iatom < 0) || (iatom >= natoms))
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: invalid atom-id {} in \"shake:types\" section of "
"molecule JSON data",
id, iatom + 1);
switch (shake_flag[iatom]) {
case 1:
SET_SHAKE_TYPE(Atom::BOND, 0, 3, boffset);
SET_SHAKE_TYPE(Atom::BOND, 1, 3, boffset);
SET_SHAKE_TYPE(Atom::ANGLE, 2, 3, aoffset);
break;
case 2:
SET_SHAKE_TYPE(Atom::BOND, 0, 2, boffset);
SET_SHAKE_TYPE(Atom::BOND, 1, 2, boffset);
break;
case 3:
SET_SHAKE_TYPE(Atom::BOND, 0, 3, boffset);
SET_SHAKE_TYPE(Atom::BOND, 1, 3, boffset);
SET_SHAKE_TYPE(Atom::BOND, 2, 3, boffset);
break;
case 4:
SET_SHAKE_TYPE(Atom::BOND, 0, 4, boffset);
SET_SHAKE_TYPE(Atom::BOND, 1, 4, boffset);
SET_SHAKE_TYPE(Atom::BOND, 2, 4, boffset);
SET_SHAKE_TYPE(Atom::BOND, 3, 4, boffset);
break;
case 0:
break;
default:
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: Unsupported Shake flag {} for "
" atom {} in \"shake:atoms\" section of molecule JSON data",
id, shake_flag[iatom], iatom + 1);
}
count[iatom]++;
}
// checks
for (int i = 0; i < natoms; i++) {
if (count[i] == 0)
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: atom {} missing in \"shake:atoms\" JSON section", id,
i + 1);
}
} else {
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: Expected \"shake:atoms\" format "
"[\"atom-id\",\"atom-id-list\"] but found [\"{}\",\"{}\"]",
id, secfmt[0], secfmt[1]);
}
}
#undef SET_SHAKE_TYPE
// body_integers // body_integers
// body_doubles // body_doubles
@ -3147,7 +3262,12 @@ void Molecule::shaketype_read(char *line)
shake_type[iatom][0] = utils::inumeric(FLERR, values[1], false, lmp) + ((subst) ? 0 : boffset); shake_type[iatom][0] = utils::inumeric(FLERR, values[1], false, lmp) + ((subst) ? 0 : boffset);
delete[] subst; delete[] subst;
nwant = 2; subst = utils::expand_type(FLERR, values[2], Atom::BOND, lmp);
if (subst) values[2] = subst;
shake_type[iatom][1] = utils::inumeric(FLERR, values[2], false, lmp) + ((subst) ? 0 : boffset);
delete[] subst;
nwant = 3;
break; break;
case 3: case 3:
@ -3156,12 +3276,17 @@ void Molecule::shaketype_read(char *line)
shake_type[iatom][0] = utils::inumeric(FLERR, values[1], false, lmp) + ((subst) ? 0 : boffset); shake_type[iatom][0] = utils::inumeric(FLERR, values[1], false, lmp) + ((subst) ? 0 : boffset);
delete[] subst; delete[] subst;
subst = utils::expand_type(FLERR, values[1], Atom::BOND, lmp); subst = utils::expand_type(FLERR, values[2], Atom::BOND, lmp);
if (subst) values[1] = subst; if (subst) values[2] = subst;
shake_type[iatom][1] = utils::inumeric(FLERR, values[2], false, lmp) + ((subst) ? 0 : boffset); shake_type[iatom][1] = utils::inumeric(FLERR, values[2], false, lmp) + ((subst) ? 0 : boffset);
delete[] subst; delete[] subst;
nwant = 3; subst = utils::expand_type(FLERR, values[1], Atom::BOND, lmp);
if (subst) values[3] = subst;
shake_type[iatom][2] = utils::inumeric(FLERR, values[3], false, lmp) + ((subst) ? 0 : boffset);
delete[] subst;
nwant = 4;
break; break;
case 4: case 4:
@ -3170,17 +3295,22 @@ void Molecule::shaketype_read(char *line)
shake_type[iatom][0] = utils::inumeric(FLERR, values[1], false, lmp) + ((subst) ? 0 : boffset); shake_type[iatom][0] = utils::inumeric(FLERR, values[1], false, lmp) + ((subst) ? 0 : boffset);
delete[] subst; delete[] subst;
subst = utils::expand_type(FLERR, values[1], Atom::BOND, lmp); subst = utils::expand_type(FLERR, values[2], Atom::BOND, lmp);
if (subst) values[1] = subst; if (subst) values[2] = subst;
shake_type[iatom][1] = utils::inumeric(FLERR, values[2], false, lmp) + ((subst) ? 0 : boffset); shake_type[iatom][1] = utils::inumeric(FLERR, values[2], false, lmp) + ((subst) ? 0 : boffset);
delete[] subst; delete[] subst;
subst = utils::expand_type(FLERR, values[1], Atom::BOND, lmp); subst = utils::expand_type(FLERR, values[3], Atom::BOND, lmp);
if (subst) values[1] = subst; if (subst) values[3] = subst;
shake_type[iatom][2] = utils::inumeric(FLERR, values[3], false, lmp) + ((subst) ? 0 : boffset); shake_type[iatom][2] = utils::inumeric(FLERR, values[3], false, lmp) + ((subst) ? 0 : boffset);
delete[] subst; delete[] subst;
nwant = 4; subst = utils::expand_type(FLERR, values[4], Atom::BOND, lmp);
if (subst) values[4] = subst;
shake_type[iatom][3] = utils::inumeric(FLERR, values[4], false, lmp) + ((subst) ? 0 : boffset);
delete[] subst;
nwant = 5;
break; break;
case 0: case 0:

2
tools/json/molecule-schema.json
View File

@ -347,7 +347,7 @@
"properties": { "properties": {
"format": { "format": {
"type": "array", "type": "array",
"const": ["atom-id", "bond-type-list"] "const": ["atom-id", "type-list"]
}, },
"data": { "data": {
"type": "array", "type": "array",