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add optional create_atoms group keyword to add new atoms to a custom group

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This commit is contained in:
Axel Kohlmeyer
2025-04-10 05:36:26 -04:00
parent 980bf70310
commit f2bf0d0a8b
3 changed files with 41 additions and 17 deletions
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46
src/create_atoms.cpp
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@ -23,6 +23,7 @@
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "group.h"
#include "input.h"
#include "irregular.h"
#include "lattice.h"
@ -64,6 +65,16 @@ enum { NONE, RATIO, SUBSET };
enum { BISECTION, QUASIRANDOM };
static constexpr const char *mesh_name[] = {"recursive bisection", "quasi-random"};
/* ---------------------------------------------------------------------- */
CreateAtoms::CreateAtoms(LAMMPS *lmp) :
Command(lmp), basistype(nullptr), xmol(nullptr), vstr(nullptr), xstr(nullptr), ystr(nullptr),
zstr(nullptr), groupname(nullptr), region(nullptr), onemol(nullptr), ranmol(nullptr),
ranlatt(nullptr)
{
}
/* ---------------------------------------------------------------------- */
CreateAtoms::~CreateAtoms()
@ -80,7 +91,6 @@ CreateAtoms::~CreateAtoms()
delete ranmol;
delete ranlatt;
}
CreateAtoms::CreateAtoms(LAMMPS *lmp) : Command(lmp), basistype(nullptr) {}
/* ---------------------------------------------------------------------- */
@ -179,8 +189,10 @@ void CreateAtoms::command(int narg, char **arg)
mesh_density = 1.0;
nbasis = domain->lattice->nbasis;
basistype = new int[nbasis];
for (int i = 0; i < nbasis; i++) basistype[i] = ntype;
if (nbasis > 0) {
basistype = new int[nbasis];
for (int i = 0; i < nbasis; i++) basistype[i] = ntype;
}
while (iarg < narg) {
if (strcmp(arg[iarg], "basis") == 0) {
@ -273,6 +285,15 @@ void CreateAtoms::command(int narg, char **arg)
if ((nsubset <= 0) || (subsetseed <= 0))
error->all(FLERR, Error::NOPOINTER, "Illegal create_atoms subset settings");
iarg += 3;
} else if (strcmp(arg[iarg], "group") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_atoms group", error);
if (strcmp(arg[iarg + 1], "none") == 0) {
delete[] groupname;
groupname = nullptr;
} else {
groupname = utils::strdup(arg[iarg + 1]);
}
iarg += 2;
} else if (strcmp(arg[iarg], "overlap") == 0) {
if (style != RANDOM)
error->all(FLERR, iarg, "Create_atoms overlap can only be used with random style");
@ -675,18 +696,6 @@ void CreateAtoms::command(int narg, char **arg)
if (domain->triclinic) domain->lamda2x(atom->nlocal);
}
// clean up
delete ranmol;
delete ranlatt;
delete[] basistype;
delete[] vstr;
delete[] xstr;
delete[] ystr;
delete[] zstr;
if (mode == MOLECULE) memory->destroy(xmol);
// for MOLECULE mode:
// create special bond lists for molecular systems,
// but not for atom style template
@ -699,6 +708,13 @@ void CreateAtoms::command(int narg, char **arg)
}
}
// add atoms to group
if (groupname) {
int groupbit = group->bitmask[group->find_or_create(groupname)];
for (int i = nlocal_previous; i < atom->nlocal; ++i) atom->mask[i] |= groupbit;
}
// print status
MPI_Barrier(world);