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delete_atoms.cpp
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Fri, Jul 5, 12:17

delete_atoms.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "stdlib.h"
#include "string.h"
#include "delete_atoms.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "domain.h"
#include "force.h"
#include "group.h"
#include "region.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
DeleteAtoms::DeleteAtoms(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void DeleteAtoms::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all("Delete_atoms command before simulation box is defined");
if (narg < 1) error->all("Illegal delete_atoms command");
if (atom->tag_enable == 0)
error->all("Cannot use delete_atoms unless atoms have IDs");
// store state before delete
bigint natoms_previous = atom->natoms;
// delete the atoms
if (strcmp(arg[0],"group") == 0) delete_group(narg,arg);
else if (strcmp(arg[0],"region") == 0) delete_region(narg,arg);
else if (strcmp(arg[0],"overlap") == 0) delete_overlap(narg,arg);
else if (strcmp(arg[0],"porosity") == 0) delete_porosity(narg,arg);
else error->all("Illegal delete_atoms command");
// delete local atoms flagged in dlist
// reset nlocal
AtomVec *avec = atom->avec;
int nlocal = atom->nlocal;
int i = 0;
while (i < nlocal) {
if (dlist[i]) {
avec->copy(nlocal-1,i);
dlist[i] = dlist[nlocal-1];
nlocal--;
} else i++;
}
atom->nlocal = nlocal;
memory->sfree(dlist);
// if non-molecular system and compress flag set,
// reset atom tags to be contiguous
// set all atom IDs to 0, call tag_extend()
if (atom->molecular == 0 && compress_flag) {
int *tag = atom->tag;
for (i = 0; i < nlocal; i++) tag[i] = 0;
atom->tag_extend();
}
// reset atom->natoms
// reset atom->map if it exists
// set nghost to 0 so old ghosts of deleted atoms won't be mapped
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (atom->map_style) {
atom->nghost = 0;
atom->map_init();
atom->map_set();
}
// print before and after atom count
bigint ndelete = natoms_previous - atom->natoms;
if (comm->me == 0) {
if (screen) fprintf(screen,"Deleted " BIGINT_FORMAT
" atoms, new total = " BIGINT_FORMAT "\n",
ndelete,atom->natoms);
if (logfile) fprintf(logfile,"Deleted " BIGINT_FORMAT
" atoms, new total = " BIGINT_FORMAT "\n",
ndelete,atom->natoms);
}
}
/* ----------------------------------------------------------------------
delete all atoms in group
group will still exist
------------------------------------------------------------------------- */
void DeleteAtoms::delete_group(int narg, char **arg)
{
if (narg < 2) error->all("Illegal delete_atoms command");
int igroup = group->find(arg[1]);
if (igroup == -1) error->all("Could not find delete_atoms group ID");
options(narg-2,&arg[2]);
// allocate and initialize deletion list
int nlocal = atom->nlocal;
dlist = (int *) memory->smalloc(nlocal*sizeof(int),"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
int *mask = atom->mask;
int groupbit = group->bitmask[igroup];
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) dlist[i] = 1;
}
/* ----------------------------------------------------------------------
delete all atoms in region
------------------------------------------------------------------------- */
void DeleteAtoms::delete_region(int narg, char **arg)
{
if (narg < 2) error->all("Illegal delete_atoms command");
int iregion = domain->find_region(arg[1]);
if (iregion == -1) error->all("Could not find delete_atoms region ID");
options(narg-2,&arg[2]);
// allocate and initialize deletion list
int nlocal = atom->nlocal;
dlist = (int *) memory->smalloc(nlocal*sizeof(int),"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
double **x = atom->x;
for (int i = 0; i < nlocal; i++)
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2])) dlist[i] = 1;
}
/* ----------------------------------------------------------------------
delete atoms so there are no pairs within cutoff
which atoms are deleted depends on ordering of atoms within proc
deletions can vary with processor count
no guarantee that minimium number of atoms will be deleted
------------------------------------------------------------------------- */
void DeleteAtoms::delete_overlap(int narg, char **arg)
{
if (narg < 4) error->all("Illegal delete_atoms command");
// read args
double cut = atof(arg[1]);
double cutsq = cut*cut;
int igroup1 = group->find(arg[2]);
int igroup2 = group->find(arg[3]);
if (igroup1 < 0 || igroup2 < 0)
error->all("Could not find delete_atoms group ID");
options(narg-4,&arg[4]);
int group1bit = group->bitmask[igroup1];
int group2bit = group->bitmask[igroup2];
if (comm->me == 0 && screen)
fprintf(screen,"System init for delete_atoms ...\n");
// request a full neighbor list for use by this command
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->command = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->occasional = 1;
// init entire system since comm->borders and neighbor->build is done
// comm::init needs neighbor::init needs pair::init needs kspace::init, etc
lmp->init();
// error check on cutoff
// if no pair style, neighbor list will be empty
if (force->pair == NULL)
error->all("Delete_atoms requires a pair style be defined");
if (cut > neighbor->cutneighmax)
error->all("Delete_atoms cutoff > neighbor cutoff");
// setup domain, communication and neighboring
// acquire ghosts
// build neighbor list based on earlier request
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
comm->exchange();
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
NeighList *list = neighbor->lists[irequest];
neighbor->build_one(irequest);
// allocate and initialize deletion list
// must be after exchange potentially changes nlocal
int nlocal = atom->nlocal;
dlist = (int *) memory->smalloc(nlocal*sizeof(int),"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
// double loop over owned atoms and their full neighbor list
// at end of loop, there are no more overlaps
// only ever delete owned atom I, never J even if owned
int *tag = atom->tag;
int *mask = atom->mask;
double **x = atom->x;
int nall = atom->nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int i,j,ii,jj,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
// if weighting factors are 0, skip this pair
// could be 0 and still be in neigh list for long-range Coulombics
// want consistency with non-charged pairs which wouldn't be in list
if (j >= nall) {
if (special_coul[j/nall] == 0.0 && special_lj[j/nall] == 0.0) continue;
j %= nall;
}
// only consider deletion if I,J distance < cutoff
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq >= cutsq) continue;
// only consider deletion if I,J are in groups 1,2 respectively
// true whether J is owned or ghost atom
if (!(mask[i] & group1bit)) continue;
if (!(mask[j] & group2bit)) continue;
// J is owned atom:
// delete atom I if atom J has not already been deleted
// J is ghost atom:
// delete atom I if J,I is not a candidate deletion pair
// due to being in groups 1,2 respectively
// if they are candidate pair, then either:
// another proc owns J and could delete J
// J is a ghost of another of my owned atoms, and I could delete J
// test on tags of I,J insures that only I or J is deleted
if (j < nlocal) {
if (dlist[j]) continue;
} else if ((mask[i] & group2bit) && (mask[j] & group1bit)) {
if (tag[i] > tag[j]) continue;
}
dlist[i] = 1;
break;
}
}
}
/* ----------------------------------------------------------------------
create porosity by deleting atoms in a specified region
------------------------------------------------------------------------- */
void DeleteAtoms::delete_porosity(int narg, char **arg)
{
if (narg < 4) error->all("Illegal delete_atoms command");
int iregion = domain->find_region(arg[1]);
if (iregion == -1) error->all("Could not find delete_atoms region ID");
double porosity_fraction = atof(arg[2]);
int seed = atoi(arg[3]);
options(narg-4,&arg[4]);
RanMars *random = new RanMars(lmp,seed + comm->me);
// allocate and initialize deletion list
int nlocal = atom->nlocal;
dlist = (int *) memory->smalloc(nlocal*sizeof(int),"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
double **x = atom->x;
for (int i = 0; i < nlocal; i++)
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
if (random->uniform() <= porosity_fraction) dlist[i] = 1;
}
/* ----------------------------------------------------------------------
process command options
------------------------------------------------------------------------- */
void DeleteAtoms::options(int narg, char **arg)
{
compress_flag = 1;
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"compress") == 0) {
if (iarg+2 > narg) error->all("Illegal delete_bonds command");
if (strcmp(arg[iarg+1],"yes") == 0) compress_flag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) compress_flag = 0;
else error->all("Illegal delete_bonds command");
iarg += 2;
} else error->all("Illegal delete_bonds command");
}
}

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