void CreateAtoms::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all(FLERR,"Create_atoms command before simulation box is defined");
if (modify->nfix_restart_peratom)
error->all(FLERR,"Cannot create_atoms after "
"reading restart file with per-atom info");
// parse arguments
if (narg < 2) error->all(FLERR,"Illegal create_atoms command");
itype = force->inumeric(FLERR,arg[0]);
if (itype <= 0 || itype > atom->ntypes)
error->all(FLERR,"Invalid atom type in create_atoms command");
int iarg = 0;
if (strcmp(arg[1],"box") == 0) {
style = BOX;
iarg = 2;
} else if (strcmp(arg[1],"region") == 0) {
style = REGION;
if (narg < 3) error->all(FLERR,"Illegal create_atoms command");
nregion = domain->find_region(arg[2]);
if (nregion == -1) error->all(FLERR,
"Create_atoms region ID does not exist");
domain->regions[nregion]->init();
iarg = 3;;
} else if (strcmp(arg[1],"single") == 0) {
style = SINGLE;
if (narg < 5) error->all(FLERR,"Illegal create_atoms command");
xone[0] = force->numeric(FLERR,arg[2]);
xone[1] = force->numeric(FLERR,arg[3]);
xone[2] = force->numeric(FLERR,arg[4]);
iarg = 5;
} else if (strcmp(arg[1],"random") == 0) {
style = RANDOM;
if (narg < 5) error->all(FLERR,"Illegal create_atoms command");
nrandom = force->inumeric(FLERR,arg[2]);
seed = force->inumeric(FLERR,arg[3]);
if (strcmp(arg[4],"NULL") == 0) nregion = -1;
else {
nregion = domain->find_region(arg[4]);
if (nregion == -1) error->all(FLERR,
"Create_atoms region ID does not exist");
domain->regions[nregion]->init();
}
iarg = 5;
} else error->all(FLERR,"Illegal create_atoms command");
// process optional keywords
int scaleflag = 1;
remapflag = 0;
nbasis = domain->lattice->nbasis;
basistype = new int[nbasis];
for (int i = 0; i < nbasis; i++) basistype[i] = itype;
while (iarg < narg) {
if (strcmp(arg[iarg],"basis") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal create_atoms command");
int ibasis = force->inumeric(FLERR,arg[iarg+1]);
itype = force->inumeric(FLERR,arg[iarg+2]);
if (ibasis <= 0 || ibasis > nbasis ||
itype <= 0 || itype > atom->ntypes)
error->all(FLERR,"Invalid basis setting in create_atoms command");
basistype[ibasis-1] = itype;
iarg += 3;
} else if (strcmp(arg[iarg],"remap") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_atoms command");
if (strcmp(arg[iarg+1],"yes") == 0) remapflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) remapflag = 0;
else error->all(FLERR,"Illegal create_atoms command");
iarg += 2;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_atoms command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
else error->all(FLERR,"Illegal create_atoms command");
iarg += 2;
} else error->all(FLERR,"Illegal create_atoms command");
}
// error checks
if (style == RANDOM) {
if (nrandom < 0) error->all(FLERR,"Illegal create_atoms command");
if (seed <= 0) error->all(FLERR,"Illegal create_atoms command");
}
// demand non-none lattice be defined for BOX and REGION
// else setup scaling for SINGLE and RANDOM
// could use domain->lattice->lattice2box() to do conversion of
// lattice to box, but not consistent with other uses of units=lattice
// triclinic remapping occurs in add_single()
if (style == BOX || style == REGION) {
if (nbasis == 0)
error->all(FLERR,"Cannot create atoms with undefined lattice");
} else if (scaleflag == 1) {
xone[0] *= domain->lattice->xlattice;
xone[1] *= domain->lattice->ylattice;
xone[2] *= domain->lattice->zlattice;
}
// set bounds for my proc in sublo[3] & subhi[3]
// if periodic and style = BOX or REGION, i.e. using lattice:
// should create exactly 1 atom when 2 images are both "on" the boundary
// either image may be slightly inside/outside true box due to round-off
// if I am lo proc, decrement lower bound by EPSILON
// this will insure lo image is created
// if I am hi proc, decrement upper bound by 2.0*EPSILON
// this will insure hi image is not created
// thus insertion box is EPSILON smaller than true box
// and is shifted away from true boundary
// which is where atoms are likely to be generated
triclinic = domain->triclinic;
double epsilon[3];
if (triclinic) epsilon[0] = epsilon[1] = epsilon[2] = EPSILON;
else {
epsilon[0] = domain->prd[0] * EPSILON;
epsilon[1] = domain->prd[1] * EPSILON;
epsilon[2] = domain->prd[2] * EPSILON;
}
if (triclinic == 0) {
sublo[0] = domain->sublo[0]; subhi[0] = domain->subhi[0];
sublo[1] = domain->sublo[1]; subhi[1] = domain->subhi[1];
sublo[2] = domain->sublo[2]; subhi[2] = domain->subhi[2];
} else {
sublo[0] = domain->sublo_lamda[0]; subhi[0] = domain->subhi_lamda[0];
sublo[1] = domain->sublo_lamda[1]; subhi[1] = domain->subhi_lamda[1];
sublo[2] = domain->sublo_lamda[2]; subhi[2] = domain->subhi_lamda[2];
}
if (style == BOX || style == REGION) {
if (domain->xperiodic) {
if (comm->myloc[0] == 0) sublo[0] -= epsilon[0];
if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] -= 2.0*epsilon[0];
}
if (domain->yperiodic) {
if (comm->myloc[1] == 0) sublo[1] -= epsilon[1];
if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] -= 2.0*epsilon[1];
}
if (domain->zperiodic) {
if (comm->myloc[2] == 0) sublo[2] -= epsilon[2];
if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] -= 2.0*epsilon[2];
}
}
// add atoms in one of 3 ways
bigint natoms_previous = atom->natoms;
int nlocal_previous = atom->nlocal;
if (style == SINGLE) add_single();
else if (style == RANDOM) add_random();
else add_lattice();
// invoke set_arrays() for fixes that need initialization of new atoms
int nlocal = atom->nlocal;
for (int m = 0; m < modify->nfix; m++) {
Fix *fix = modify->fix[m];
if (fix->create_attribute)
{
fix->pre_set_arrays();
for (int i = nlocal_previous; i < nlocal; i++)
fix->set_arrays(i);
}
}
// clean up
if (domain->lattice) delete [] basistype;
// new total # of atoms
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
error->all(FLERR,"Too many total atoms");
// print status
if (comm->me == 0) {
if (screen)
fprintf(screen,"Created " BIGINT_FORMAT " atoms\n",
atom->natoms-natoms_previous);
if (logfile)
fprintf(logfile,"Created " BIGINT_FORMAT " atoms\n",
atom->natoms-natoms_previous);
}
// reset simulation now that more atoms are defined
// add tags for newly created atoms if possible
// if global map exists, reset it
// change these to MAXTAGINT when allow tagint = bigint
if (atom->natoms > MAXSMALLINT) {
if (comm->me == 0)
error->warning(FLERR,"Total atom count exceeds ID limit, "
"atoms will not have individual IDs");
atom->tag_enable = 0;
}
if (atom->natoms <= MAXSMALLINT) atom->tag_extend();
if (atom->map_style) {
atom->nghost = 0;
atom->map_init();
atom->map_set();
}
// if a molecular system, set nspecial to 0 for new atoms
// NOTE: 31May12, don't think this is needed, avec->create_atom() does it
//if (atom->molecular) {
// int **nspecial = atom->nspecial;
// for (int i = nlocal_previous; i < atom->nlocal; i++) {
// nspecial[i][0] = 0;
// nspecial[i][1] = 0;
// nspecial[i][2] = 0;
// }
//}
// error checks on coarsegraining
if(force->cg_active())
error->cg(FLERR,"create_atoms");
}
