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continued refactoring of Molecule class to include support for JSON

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This commit is contained in:
Axel Kohlmeyer
2025-05-21 16:24:41 -04:00
parent a46d32e4d4
commit 7b5b6f19b7
2 changed files with 98 additions and 9 deletions
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105
src/molecule.cpp
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@ -24,6 +24,7 @@
#include "label_map.h"
#include "math_eigen.h"
#include "math_extra.h"
#include "math_special.h"
#include "memory.h"
#include "tokenizer.h"
@ -31,6 +32,7 @@
#include <cstring>
using namespace LAMMPS_NS;
using MathSpecial::powint;
static constexpr int MAXLINE = 1024;
static constexpr double EPSILON = 1.0e-7;
@ -64,6 +66,7 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
toffset = 0;
boffset = aoffset = doffset = ioffset = 0;
json_format = 0;
sizescale = 1.0;
fileiarg = index;
@ -117,7 +120,7 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
} else
break;
}
// clang-format on
index = iarg;
if (atom->labelmapflag &&
@ -140,7 +143,7 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
Molecule::initialize();
json moldata;
int json_format = 0;
json_format = 0;
if (comm->me == 0) {
fp = fopen(arg[fileiarg], "r");
if (fp == nullptr)
@ -181,11 +184,96 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
}
MPI_Bcast(&json_format, 1, MPI_INT, 0, world);
if (json_format) {
// process JSON format molecule file
if (json_format) { // process JSON format molecule file
} else {
// process native molecule file
// determine sizes and broadcast
#define JSON_EXTRACT_SIZE(field, value) \
if ((comm->me == 0) && moldata.contains(#field) && moldata[#field].contains("data")) { \
value = moldata[#field]["data"].size(); \
} \
MPI_Bcast(&value, 1, MPI_INT, 0, world)
JSON_EXTRACT_SIZE(coords, natoms);
JSON_EXTRACT_SIZE(bonds, nbonds);
JSON_EXTRACT_SIZE(angles, nangles);
JSON_EXTRACT_SIZE(dihedrals, ndihedrals);
JSON_EXTRACT_SIZE(impropers, nimpropers);
JSON_EXTRACT_SIZE(fragments, nfragments);
#undef JSON_EXTRACT_SIZE
// extract global properties
if (comm->me == 0) {
if (moldata.contains("masstotal")) {
massflag = 1;
masstotal = double(moldata["masstotal"]) * sizescale * sizescale * sizescale;
}
if (moldata.contains("com") && (moldata["com"].size() == 3)) {
comflag = 1;
com[0] = double(moldata["com"][0]) * sizescale;
com[1] = double(moldata["com"][1]) * sizescale;
com[2] = double(moldata["com"][2]) * sizescale;
}
if (moldata.contains("inertia") && (moldata["inertia"].size() == 6)) {
inertiaflag = 1;
const double scale5 = powint(sizescale, 5);
itensor[0] = double(moldata["inertia"][0]) * scale5;
itensor[1] = double(moldata["inertia"][1]) * scale5;
itensor[2] = double(moldata["inertia"][2]) * scale5;
itensor[3] = double(moldata["inertia"][3]) * scale5;
itensor[4] = double(moldata["inertia"][4]) * scale5;
itensor[5] = double(moldata["inertia"][5]) * scale5;
}
if (moldata.contains("body") && (moldata["body"].size() == 2)) {
bodyflag = 1;
const double scale5 = powint(sizescale, 5);
avec_body = dynamic_cast<AtomVecBody *>(atom->style_match("body"));
if (!avec_body) error->all(FLERR, fileiarg, "Molecule file requires atom style body");
nibody = moldata["body"][0];
ndbody = moldata["body"][1];
}
if (moldata.contains("coords")) xflag = 1;
if (moldata.contains("types")) typeflag = 1;
if (moldata.contains("molecules")) moleculeflag = 1;
if (moldata.contains("fragments")) fragmentflag = 1;
if (moldata.contains("charges")) qflag = 1;
if (moldata.contains("diameters")) radiusflag = 1;
if (moldata.contains("dipoles")) muflag = 1;
if (moldata.contains("masses")) rmassflag = 1;
}
// broadcast data
MPI_Bcast(&massflag, 1, MPI_INT, 0, world);
MPI_Bcast(&masstotal, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&comflag, 1, MPI_INT, 0, world);
MPI_Bcast(&com, 3, MPI_DOUBLE, 0, world);
MPI_Bcast(&inertiaflag, 1, MPI_INT, 0, world);
MPI_Bcast(&inertia, 6, MPI_DOUBLE, 0, world);
MPI_Bcast(&bodyflag, 1, MPI_INT, 0, world);
MPI_Bcast(&nibody, 1, MPI_INT, 0, world);
MPI_Bcast(&ndbody, 1, MPI_INT, 0, world);
MPI_Bcast(&xflag, 1, MPI_INT, 0, world);
MPI_Bcast(&typeflag, 1, MPI_INT, 0, world);
MPI_Bcast(&moleculeflag, 1, MPI_INT, 0, world);
MPI_Bcast(&fragmentflag, 1, MPI_INT, 0, world);
MPI_Bcast(&qflag, 1, MPI_INT, 0, world);
MPI_Bcast(&radiusflag, 1, MPI_INT, 0, world);
MPI_Bcast(&muflag, 1, MPI_INT, 0, world);
MPI_Bcast(&rmassflag, 1, MPI_INT, 0, world);
if (nbonds > 0) bondflag = tag_require = 1;
if (nangles > 0) angleflag = tag_require = 1;
if (ndihedrals > 0) dihedralflag = tag_require = 1;
if (nimpropers > 0) improperflag = tag_require = 1;
// checks. No checks for < 0 needed since size() is at least 0
if (natoms < 1) error->all(FLERR, fileiarg, "No atoms in molecule file");
if ((domain->dimension == 2) && (com[2] != 0.0))
error->all(FLERR, fileiarg, "Molecule file z center-of-mass must be 0.0 for 2d systems");
// allocate required storage
Molecule::allocate();
} else { // process native molecule file
// scan file for sizes of all fields and allocate storage for them
@ -216,6 +304,7 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
nangletypes, ndihedrals, ndihedraltypes, nimpropers, nimpropertypes);
}
// clang-format off
/* ---------------------------------------------------------------------- */
Molecule::~Molecule()
@ -526,7 +615,7 @@ void Molecule::read(int flag)
com[0] *= sizescale;
com[1] *= sizescale;
com[2] *= sizescale;
if (domain->dimension == 2 && com[2] != 0.0)
if ((domain->dimension == 2) && (com[2] != 0.0))
error->all(FLERR, fileiarg, "Molecule file z center-of-mass must be 0.0 for 2d systems");
} else if (values.matches("^\\s*\\f+\\s+\\f+\\s+\\f+\\s+\\f+\\s+\\f+\\s+\\f+\\s+inertia")) {
inertiaflag = 1;
@ -537,7 +626,7 @@ void Molecule::read(int flag)
itensor[4] = values.next_double();
itensor[5] = values.next_double();
nwant = 7;
const double scale5 = sizescale * sizescale * sizescale * sizescale * sizescale;
const double scale5 = powint(sizescale, 5);
itensor[0] *= scale5;
itensor[1] *= scale5;
itensor[2] *= scale5;

2
src/molecule.h
View File

@ -135,7 +135,7 @@ class Molecule : protected Pointers {
FILE *fp;
int *count;
int toffset, boffset, aoffset, doffset, ioffset;
int autospecial;
int json_format;
double sizescale;
void read(int);