tx258/lammps-gran-kokkos
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

consistently quote JSON fields with double quotes

Browse Source
This commit is contained in:
Axel Kohlmeyer
2025-06-21 12:26:30 -04:00
parent c08ee92801
commit 9d38652033
1 changed files with 54 additions and 43 deletions
Download Patch File Download Diff File Expand all files Collapse all files

97
src/molecule.cpp
View File

@ -243,7 +243,7 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
std::string(moldata["application"]));
} else {
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON data does not contain required 'application' field", id);
"Molecule template {}: JSON data does not contain required \"application\" field", id);
}
if (moldata.contains("format")) {
if (moldata["format"] != "molecule")
@ -252,7 +252,7 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
std::string(moldata["format"]));
} else {
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON data does not contain required 'format' field", id);
"Molecule template {}: JSON data does not contain required \"format\" field", id);
}
if (moldata.contains("revision")) {
int rev = moldata["revision"];
@ -261,13 +261,13 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
"Molecule template {}: JSON molecule data with unsupported revision {}", id, rev);
} else {
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON data does not contain required 'revision' field", id);
"Molecule template {}: JSON data does not contain required \"revision\" field", id);
}
// length of types data list determines the number of atoms in the template and is thus required
if (!moldata.contains("types"))
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON data does not contain required 'types' field", id);
"Molecule template {}: JSON data does not contain required \"types\" field", id);
// optional fields
@ -301,7 +301,7 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
if (moldata.contains(#field)) { \
if (!moldata[#field].contains("format")) \
error->all(FLERR, Error::NOLASTLINE, \
"Molecule template {}: JSON molecule data does not contain required 'format' " \
"Molecule template {}: JSON molecule data does not contain required \"format\" " \
"field for '{}'", \
id, #field); \
if (moldata[#field].contains("data")) { \
@ -309,7 +309,7 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
sizevar = moldata[#field]["data"].size(); \
} else { \
error->all(FLERR, Error::NOLASTLINE, \
"Molecule template {}: JSON molecule data does not contain required 'data' " \
"Molecule template {}: JSON molecule data does not contain required \"data\" " \
"field for '{}'", \
id, #field); \
} \
@ -351,7 +351,7 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
const auto &specialcounts = moldata["special"]["counts"];
if (!specialcounts.contains("format"))
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON molecule data does not contain required 'format' "
"Molecule template {}: JSON molecule data does not contain required \"format\" "
"field for 'special:counts'",
id);
if (specialcounts.contains("data")) {
@ -373,14 +373,14 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
}
} else {
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON molecule data does not contain required 'data' "
"Molecule template {}: JSON molecule data does not contain required \"data\" "
"field for 'special:counts'",
id);
}
} else {
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON molecule data does not contain required 'counts' "
"field for 'special'",
"field for \"special\"",
id);
}
@ -389,25 +389,36 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
const auto &specialbonds = moldata["special"]["bonds"];
if (!specialbonds.contains("format"))
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON molecule data does not contain required 'format' "
"field for 'special:bonds'",
"Molecule template {}: JSON molecule data does not contain required \"format\" "
"field for \"special:bonds\"",
id);
if (specialbonds.contains("data")) {
if (specialbonds["data"].size() != natoms)
error->all(
FLERR, Error::NOLASTLINE,
"Molecule template {}: Found {} instead of {} data entries for 'special:bonds'", id,
"Molecule template {}: Found {} instead of {} data entries for \"special:bonds\"", id,
specialbonds["data"].size(), natoms);
if (specialbonds["data"][0] != 2)
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: \"special:bonds\" is incorrectly formatted: {}", id,
to_string(specialbonds["data"][0]));
for (int i = 0; i < natoms; ++i) {
if (specialbonds["data"][i][1].size() > maxspecial)
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: Number of data entries in \"special:bonds\" for atom "
"{} exceeds limit: {} vs {}",
id, specialbonds["data"][i][1].size(), maxspecial);
}
} else {
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON molecule data does not contain required 'data' "
"field for 'special:bonds'",
"Molecule template {}: JSON molecule data does not contain required \"data\" "
"field for \"special:bonds\"",
id);
}
} else {
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON molecule data does not contain required 'bonds' "
"field for 'special'",
"Molecule template {}: JSON molecule data does not contain required \"bonds\" "
"field for \"special\"",
id);
}
}
@ -421,77 +432,77 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
if (shakedata.contains("flags")) {
if (!shakedata["flags"].contains("format"))
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON molecule data does not contain required 'format' "
"field for 'shake:flags'",
"Molecule template {}: JSON molecule data does not contain required \"format\" "
"field for \"shake:flags\"",
id);
if (shakedata["flags"].contains("data")) {
shakeflagflag = 1;
if (shakedata["flags"]["data"].size() != natoms)
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: Found {} instead of {} data entries for 'shake:flags'",
"Molecule template {}: Found {} instead of {} data entries for \"shake:flags\"",
id, shakedata["flags"]["data"].size(), natoms);
} else {
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON molecule data does not contain required 'data' "
"field for 'shake:flags'",
"Molecule template {}: JSON molecule data does not contain required \"data\" "
"field for \"shake:flags\"",
id);
}
} else {
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON molecule data does not contain required 'flags' "
"field for 'shake'",
"field for \"shake\"",
id);
}
if (shakedata.contains("atoms")) {
if (!shakedata["atoms"].contains("format"))
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON molecule data does not contain required 'format' "
"field for 'shake:atoms'",
"Molecule template {}: JSON molecule data does not contain required \"format\" "
"field for \"shake:atoms\"",
id);
if (shakedata["atoms"].contains("data")) {
shakeatomflag = 1;
tag_require = 1;
if (shakedata["atoms"]["data"].size() != natoms)
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: Found {} instead of {} data entries for 'shake:atoms'",
"Molecule template {}: Found {} instead of {} data entries for \"shake:atoms\"",
id, shakedata["atoms"]["data"].size(), natoms);
} else {
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON molecule data does not contain required 'data' "
"field for 'shake:atoms'",
"Molecule template {}: JSON molecule data does not contain required \"data\" "
"field for \"shake:atoms\"",
id);
}
} else {
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON molecule data does not contain required 'atoms' "
"field for 'shake'",
"Molecule template {}: JSON molecule data does not contain required \"atoms\" "
"field for \"shake\"",
id);
}
if (shakedata.contains("types")) {
if (!shakedata["types"].contains("format"))
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON molecule data does not contain required 'format' "
"field for 'shake:types'",
"Molecule template {}: JSON molecule data does not contain required \"format\" "
"field for \"shake:types\"",
id);
if (shakedata["types"].contains("data")) {
shaketypeflag = 1;
tag_require = 1;
if (shakedata["types"]["data"].size() != natoms)
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: Found {} instead of {} data entries for 'shake:types'",
"Molecule template {}: Found {} instead of {} data entries for \"shake:types\"",
id, shakedata["types"]["data"].size(), natoms);
} else {
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON molecule data does not contain required 'data' "
"field for 'shake:types'",
"Molecule template {}: JSON molecule data does not contain required \"data\" "
"field for \"shake:types\"",
id);
}
} else {
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON molecule data does not contain required 'types' "
"field for 'shake'",
"Molecule template {}: JSON molecule data does not contain required \"types\" "
"field for \"shake\"",
id);
}
if (shakeflagflag && shakeatomflag && shaketypeflag) shakeflag = 1;
@ -1489,25 +1500,25 @@ void Molecule::from_json(const std::string &molid, const json &moldata)
const auto &specialbonds = moldata["special"]["bonds"];
if (!specialbonds.contains("format"))
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON molecule data does not contain required 'format' "
"field for 'special:bonds'",
"Molecule template {}: JSON molecule data does not contain required \"format\" "
"field for \"special:bonds\"",
id);
if (specialbonds.contains("data")) {
if (specialbonds["data"].size() != natoms)
error->all(
FLERR, Error::NOLASTLINE,
"Molecule template {}: Found {} instead of {} data entries for 'special:bonds'", id,
"Molecule template {}: Found {} instead of {} data entries for \"special:bonds\"", id,
specialbonds["data"].size(), natoms);
} else {
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON molecule data does not contain required 'data' "
"field for 'special:bonds'",
"Molecule template {}: JSON molecule data does not contain required \"data\" "
"field for \"special:bonds\"",
id);
}
} else {
error->all(FLERR, Error::NOLASTLINE,
"Molecule template {}: JSON molecule data does not contain required 'bonds' "
"field for 'special'",
"Molecule template {}: JSON molecule data does not contain required \"bonds\" "
"field for \"special\"",
id);
}
#endif