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support processing "bodies" sections from JSON data

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This commit is contained in:
Axel Kohlmeyer
2025-06-20 07:30:43 -04:00
parent 500373d72b
commit 9615cb466c
2 changed files with 47 additions and 19 deletions
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43
src/molecule.cpp
View File

@ -439,14 +439,22 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
itensor[5] = double(moldata["inertia"][5]) * scale5;
}
if (moldata.contains("body") && (moldata["body"].size() == 2)) {
bodyflag = 1;
if (moldata.contains("body")) {
avec_body = dynamic_cast<AtomVecBody *>(atom->style_match("body"));
if (!avec_body)
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON molecule data requires atom style body", id);
nibody = moldata["body"][0];
ndbody = moldata["body"][1];
if (moldata["body"].contains("integers") && moldata["body"].contains("doubles")) {
bodyflag = radiusflag = dbodyflag = ibodyflag = 1;
nibody = moldata["body"]["integers"].size();
ndbody = moldata["body"]["doubles"].size();
} else {
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON molecule \"body\" data requires \"integers\" and "
"\"doubles\" sections",
id);
}
}
// checks. No checks for < 0 needed since size() is at least 0
@ -726,7 +734,7 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
// diameters
if (radiusflag) {
if (radiusflag && !bodyflag) {
maxradius = 0.0;
secfmt.clear();
for (int i = 0; i < 2; ++i) secfmt.push_back(moldata["diameters"]["format"][i]);
@ -1576,8 +1584,11 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
}
#undef SET_SHAKE_TYPE
// body_integers
// body_doubles
// body integers and doubles
if (bodyflag) {
for (int i = 0; i < nibody; ++i) ibodyparams[i] = moldata["body"]["integers"][i];
for (int i = 0; i < ndbody; ++i) dbodyparams[i] = moldata["body"]["doubles"][i];
}
// error checks
@ -1587,6 +1598,9 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
error->all(FLERR, fileiarg, "Molecule file has special flags but no bonds");
if ((shakeflagflag || shakeatomflag || shaketypeflag) && !shakeflag)
error->all(FLERR, fileiarg, "Molecule file shake info is incomplete");
if (bodyflag && !rmassflag)
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: \"body\" JSON section requires \"masses\" section", id);
if (bodyflag && nibody && ibodyflag == 0)
error->all(FLERR, fileiarg, "Molecule file has no Body Integers section");
if (bodyflag && ndbody && dbodyflag == 0)
@ -2148,6 +2162,8 @@ void Molecule::read(int flag)
error->all(FLERR, fileiarg, "Molecule file has special flags but no bonds");
if ((shakeflagflag || shakeatomflag || shaketypeflag) && !shakeflag)
error->all(FLERR, fileiarg, "Molecule file shake info is incomplete");
if (bodyflag && !rmassflag)
error->all(FLERR, fileiarg, "Molecule file must have Masses section for body particle");
if (bodyflag && nibody && ibodyflag == 0)
error->all(FLERR, fileiarg, "Molecule file has no Body Integers section");
if (bodyflag && ndbody && dbodyflag == 0)
@ -3329,7 +3345,6 @@ void Molecule::body(int flag, int pflag, char *line)
if (pflag) nparam = ndbody;
int nword = 0;
try {
while (nword < nparam) {
readline(line);
@ -3337,15 +3352,16 @@ void Molecule::body(int flag, int pflag, char *line)
ValueTokenizer values(utils::trim_comment(line));
int ncount = values.count();
if (ncount == 0) error->all(FLERR, fileiarg, "Too few values in body section of molecule file");
if (ncount == 0)
error->all(FLERR, fileiarg, "Too few values in body section of molecule file");
if (nword + ncount > nparam)
error->all(FLERR, fileiarg, "Too many values in body section of molecule file");
if (flag) {
if (pflag == 0) {
while (values.has_next()) { ibodyparams[nword++] = values.next_int(); }
while (values.has_next()) ibodyparams[nword++] = values.next_int();
} else {
while (values.has_next()) { dbodyparams[nword++] = values.next_double(); }
while (values.has_next()) dbodyparams[nword++] = values.next_double();
}
} else
nword += ncount;
@ -3707,13 +3723,14 @@ void Molecule::stats()
"Read molecule template {}:\n{}\n"
" {} molecules\n"
" {} fragments\n"
" {} bodies\n"
" {} atoms with max type {}\n"
" {} bonds with max type {}\n"
" {} angles with max type {}\n"
" {} dihedrals with max type {}\n"
" {} impropers with max type {}\n",
id, title, nmolecules, nfragments, natoms, ntypes, nbonds, nbondtypes, nangles,
nangletypes, ndihedrals, ndihedraltypes, nimpropers, nimpropertypes);
id, title, nmolecules, nfragments, bodyflag, natoms, ntypes, nbonds, nbondtypes,
nangles, nangletypes, ndihedrals, ndihedraltypes, nimpropers, nimpropertypes);
}
/* ----------------------------------------------------------------------

23
tools/json/molecule-schema.json
View File

@ -27,13 +27,8 @@
"items": { "type": "number"},
"minItems": 3,
"maxItems": 3
},
},
"masstotal": {"type": "number"},
"body": {"type": "array",
"items": { "type": "integer"},
"minItems": 2,
"maxItems": 2
},
"inertia": {"type": "array",
"items": { "type": "number"},
"minItems": 6,
@ -361,6 +356,22 @@
}
},
"required": ["flags", "atoms", "types"]
},
"body": {
"type": "object",
"properties": {
"integers": {
"type": "array",
"items": {"type": "integer"},
"minItems" : 1
},
"doubles": {
"type": "array",
"items": {"type": "number"},
"minItems" : 1
}
},
"required": ["integers", "doubles"]
}
},
"required": ["application", "format", "revision", "types"]