ICODE-ADC/lammps
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support creating body particles from molecule templates in create_atoms

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This commit is contained in:
Axel Kohlmeyer
2025-06-20 07:31:58 -04:00
parent 765b3ad487
commit c6057f3780
2 changed files with 26 additions and 9 deletions
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3
src/atom_vec_body.h
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@ -25,6 +25,7 @@ AtomStyle(body,AtomVecBody);
namespace LAMMPS_NS {
class AtomVecBody : public AtomVec {
friend class CreateAtoms;
public:
class Body *bptr;
@ -77,7 +78,7 @@ class AtomVecBody : public AtomVec {
int nlocal_bonus;
private:
protected:
int *body;
double *rmass, *radius;
double **angmom;

32
src/create_atoms.cpp
View File

@ -20,6 +20,7 @@
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_body.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
@ -390,14 +391,13 @@ void CreateAtoms::command(int narg, char **arg)
if (!input->variable->equalstyle(vvar))
error->all(FLERR, Error::NOLASTLINE, "Variable {} for create_atoms is invalid style", vstr);
#define SETUP_XYZ_VAR(str, var) \
if (str) { \
var = input->variable->find(str); \
if (var < 0) var = input->variable->internal_create(str, 0.0); \
if (!input->variable->internalstyle(var)) \
error->all(FLERR, Error::NOLASTLINE, \
"Variable {} for create_atoms is invalid style", str); \
}
#define SETUP_XYZ_VAR(str, var) \
if (str) { \
var = input->variable->find(str); \
if (var < 0) var = input->variable->internal_create(str, 0.0); \
if (!input->variable->internalstyle(var)) \
error->all(FLERR, Error::NOLASTLINE, "Variable {} for create_atoms is invalid style", str); \
}
SETUP_XYZ_VAR(xstr, xvar);
SETUP_XYZ_VAR(ystr, yvar);
@ -580,6 +580,10 @@ void CreateAtoms::command(int narg, char **arg)
atom->ndihedrals += nmoltotal * onemol->ndihedrals;
atom->nimpropers += nmoltotal * onemol->nimpropers;
// molecule files for bodies may only contain a single body
if (onemol->bodyflag) atom->nbodies += 1;
// if atom style template
// maxmol = max molecule ID across all procs, for previous atoms
// moloffset = max molecule ID for all molecules owned by previous procs
@ -662,6 +666,18 @@ void CreateAtoms::command(int narg, char **arg)
if (onemol->specialflag)
for (int j = 0; j < nspecial[ilocal][2]; j++) special[ilocal][j] += offset;
}
// create body particle
if (onemol->bodyflag) {
auto *avec_body = dynamic_cast<AtomVecBody *>(atom->avec);
if (avec_body)
avec_body->data_body(ilocal, onemol->nibody, onemol->ndbody, onemol->ibodyparams,
onemol->dbodyparams);
else
error->all(FLERR, Error::NOLASTLINE, "Molecule template {} requires a body atom style",
onemol->id);
}
ilocal++;
}
if (molecule_flag) {