lammps-sys 0.6.0

/* ----------------------------------------------------------------------
   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 "delete_atoms.h"
#include <mpi.h>
#include <cstring>
#include <utility>
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_ellipsoid.h"
#include "atom_vec_line.h"
#include "atom_vec_tri.h"
#include "atom_vec_body.h"
#include "molecule.h"
#include "comm.h"
#include "domain.h"
#include "force.h"
#include "group.h"
#include "region.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h"

#include <map>

using namespace LAMMPS_NS;

/* ---------------------------------------------------------------------- */

DeleteAtoms::DeleteAtoms(LAMMPS *lmp) : Pointers(lmp) {}

/* ---------------------------------------------------------------------- */

void DeleteAtoms::command(int narg, char **arg)
{
  if (domain->box_exist == 0)
    error->all(FLERR,"Delete_atoms command before simulation box is defined");
  if (narg < 1) error->all(FLERR,"Illegal delete_atoms command");
  if (atom->tag_enable == 0)
    error->all(FLERR,"Cannot use delete_atoms unless atoms have IDs");

  // store state before delete

  bigint natoms_previous = atom->natoms;
  bigint nbonds_previous = atom->nbonds;
  bigint nangles_previous = atom->nangles;
  bigint ndihedrals_previous = atom->ndihedrals;
  bigint nimpropers_previous = atom->nimpropers;

  // flag atoms for deletion

  allflag = 0;

  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(FLERR,"Illegal delete_atoms command");

  if (allflag) {
    int igroup = group->find("all");
    if ((igroup >= 0) &&
        modify->check_rigid_group_overlap(group->bitmask[igroup]))
      error->warning(FLERR,"Attempting to delete atoms in rigid bodies");
  } else {
    if (modify->check_rigid_list_overlap(dlist))
      error->warning(FLERR,"Attempting to delete atoms in rigid bodies");
  }

  // if allflag = 1, just reset atom->nlocal
  // else delete atoms one by one

  if (allflag) atom->nlocal = 0;
  else {

    // optionally delete additional bonds or atoms in molecules

    if (bond_flag) delete_bond();
    if (mol_flag) delete_molecule();

    // 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,1);
        dlist[i] = dlist[nlocal-1];
        nlocal--;
      } else i++;
    }

    atom->nlocal = nlocal;
    memory->destroy(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 (compress_flag) {
    if (atom->molecular == 0) {
      tagint *tag = atom->tag;
      int nlocal = atom->nlocal;
      for (int i = 0; i < nlocal; i++) tag[i] = 0;
      atom->tag_extend();
    } else if (comm->me == 0)
        error->warning(FLERR,"Ignoring 'compress yes' for molecular system");
  }

  // reset atom->natoms and also topology counts

  bigint nblocal = atom->nlocal;
  MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);

  // reset bonus data counts

  AtomVecEllipsoid *avec_ellipsoid =
    (AtomVecEllipsoid *) atom->style_match("ellipsoid");
  AtomVecLine *avec_line = (AtomVecLine *) atom->style_match("line");
  AtomVecTri *avec_tri = (AtomVecTri *) atom->style_match("tri");
  AtomVecBody *avec_body = (AtomVecBody *) atom->style_match("body");
  bigint nlocal_bonus;

  if (atom->nellipsoids > 0) {
    nlocal_bonus = avec_ellipsoid->nlocal_bonus;
    MPI_Allreduce(&nlocal_bonus,&atom->nellipsoids,1,MPI_LMP_BIGINT,MPI_SUM,world);
  }
  if (atom->nlines > 0) {
    nlocal_bonus = avec_line->nlocal_bonus;
    MPI_Allreduce(&nlocal_bonus,&atom->nlines,1,MPI_LMP_BIGINT,MPI_SUM,world);
  }
  if (atom->ntris > 0) {
    nlocal_bonus = avec_tri->nlocal_bonus;
    MPI_Allreduce(&nlocal_bonus,&atom->ntris,1,MPI_LMP_BIGINT,MPI_SUM,world);
  }
  if (atom->nbodies > 0) {
    nlocal_bonus = avec_body->nlocal_bonus;
    MPI_Allreduce(&nlocal_bonus,&atom->nbodies,1,MPI_LMP_BIGINT,MPI_SUM,world);
  }

  // reset atom->map if it exists
  // set nghost to 0 so old ghosts of deleted atoms won't be mapped

  if (atom->map_style) {
    atom->nghost = 0;
    atom->map_init();
    atom->map_set();
  }

  recount_topology();

  // print before and after atom and topology counts

  bigint ndelete = natoms_previous - atom->natoms;
  bigint ndelete_bonds = nbonds_previous - atom->nbonds;
  bigint ndelete_angles = nangles_previous - atom->nangles;
  bigint ndelete_dihedrals = ndihedrals_previous - atom->ndihedrals;
  bigint ndelete_impropers = nimpropers_previous - atom->nimpropers;

  if (comm->me == 0) {
    if (screen) {
      fprintf(screen,"Deleted " BIGINT_FORMAT
              " atoms, new total = " BIGINT_FORMAT "\n",
              ndelete,atom->natoms);
      if (bond_flag || mol_flag) {
        if (nbonds_previous)
          fprintf(screen,"Deleted " BIGINT_FORMAT
                  " bonds, new total = " BIGINT_FORMAT "\n",
                  ndelete_bonds,atom->nbonds);
        if (nangles_previous)
          fprintf(screen,"Deleted " BIGINT_FORMAT
                  " angles, new total = " BIGINT_FORMAT "\n",
                  ndelete_angles,atom->nangles);
        if (ndihedrals_previous)
          fprintf(screen,"Deleted " BIGINT_FORMAT
                  " dihedrals, new total = " BIGINT_FORMAT "\n",
                  ndelete_dihedrals,atom->ndihedrals);
        if (nimpropers_previous)
          fprintf(screen,"Deleted " BIGINT_FORMAT
                  " impropers, new total = " BIGINT_FORMAT "\n",
                  ndelete_impropers,atom->nimpropers);
      }
    }

    if (logfile) {
      fprintf(logfile,"Deleted " BIGINT_FORMAT
              " atoms, new total = " BIGINT_FORMAT "\n",
              ndelete,atom->natoms);
      if (bond_flag || mol_flag) {
        if (nbonds_previous)
          fprintf(logfile,"Deleted " BIGINT_FORMAT
                  " bonds, new total = " BIGINT_FORMAT "\n",
                  ndelete_bonds,atom->nbonds);
        if (nangles_previous)
          fprintf(logfile,"Deleted " BIGINT_FORMAT
                  " angles, new total = " BIGINT_FORMAT "\n",
                  ndelete_angles,atom->nangles);
        if (ndihedrals_previous)
          fprintf(logfile,"Deleted " BIGINT_FORMAT
                  " dihedrals, new total = " BIGINT_FORMAT "\n",
                  ndelete_dihedrals,atom->ndihedrals);
        if (nimpropers_previous)
          fprintf(logfile,"Deleted " BIGINT_FORMAT
                  " impropers, new total = " BIGINT_FORMAT "\n",
                  ndelete_impropers,atom->nimpropers);
      }
    }
  }
}

/* ----------------------------------------------------------------------
   delete all atoms in group, group will still exist
------------------------------------------------------------------------- */

void DeleteAtoms::delete_group(int narg, char **arg)
{
  if (narg < 2) error->all(FLERR,"Illegal delete_atoms command");

  int igroup = group->find(arg[1]);
  if (igroup == -1) error->all(FLERR,"Could not find delete_atoms group ID");
  options(narg-2,&arg[2]);

  // check for special case of group = all

  if (strcmp(arg[1],"all") == 0) {
    allflag = 1;
    return;
  }

  // allocate and initialize deletion list

  int nlocal = atom->nlocal;
  memory->create(dlist,nlocal,"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(FLERR,"Illegal delete_atoms command");

  int iregion = domain->find_region(arg[1]);
  if (iregion == -1) error->all(FLERR,"Could not find delete_atoms region ID");
  domain->regions[iregion]->prematch();

  options(narg-2,&arg[2]);

  // allocate and initialize deletion list

  int nlocal = atom->nlocal;
  memory->create(dlist,nlocal,"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(FLERR,"Illegal delete_atoms command");

  // read args

  double cut = force->numeric(FLERR,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(FLERR,"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(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;
  neighbor->requests[irequest]->command_style = "delete_atoms";

  // 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(FLERR,"Delete_atoms requires a pair style be defined");
  if (cut > neighbor->cutneighmax)
    error->all(FLERR,"Delete_atoms cutoff > max neighbor cutoff");
  if (cut > neighbor->cutneighmin && comm->me == 0)
    error->warning(FLERR,"Delete_atoms cutoff > minimum neighbor cutoff");

  // setup domain, communication and neighboring
  // acquire ghosts and build standard neighbor lists

  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);
  neighbor->build(1);

  // build neighbor list this command needs based on earlier request

  NeighList *list = neighbor->lists[irequest];
  neighbor->build_one(list);

  // allocate and initialize deletion list
  // must be after exchange potentially changes nlocal

  int nlocal = atom->nlocal;
  memory->create(dlist,nlocal,"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 in I loop iteration, never J even if owned

  tagint *tag = atom->tag;
  int *mask = atom->mask;
  double **x = atom->x;
  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;
  double factor_lj,factor_coul;

  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];
      factor_lj = special_lj[sbmask(j)];
      factor_coul = special_coul[sbmask(j)];
      j &= NEIGHMASK;

      // if both 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 (factor_lj == 0.0 && factor_coul == 0.0) continue;

      // only consider deletion if I,J distance < cutoff
      // compute rsq identically on both I,J loop iterations
      // ignoring possibility that I,J tags are equal

      if (tag[i] < tag[j]) {
        delx = xtmp - x[j][0];
        dely = ytmp - x[j][1];
        delz = ztmp - x[j][2];
      } else {
        delx = x[j][0] - xtmp;
        dely = x[j][1] - ytmp;
        delz = x[j][2] - ztmp;
      }
      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(FLERR,"Illegal delete_atoms command");

  int iregion = domain->find_region(arg[1]);
  if (iregion == -1) error->all(FLERR,"Could not find delete_atoms region ID");
  domain->regions[iregion]->prematch();

  double porosity_fraction = force->numeric(FLERR,arg[2]);
  int seed = force->inumeric(FLERR,arg[3]);
  options(narg-4,&arg[4]);

  RanMars *random = new RanMars(lmp,seed + comm->me);

  // allocate and initialize deletion list

  int nlocal = atom->nlocal;
  memory->create(dlist,nlocal,"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;

  delete random;
}

/* ----------------------------------------------------------------------
   delete all topology interactions that include deleted atoms
------------------------------------------------------------------------- */

void DeleteAtoms::delete_bond()
{
  // hash = for atom IDs being deleted by one processor
  // list of these IDs is sent around ring
  // at each stage of ring pass, hash is re-populated with received IDs

  hash = new std::map<tagint,int>();

  // list = set of unique molecule IDs from which I deleted atoms
  // pass list to all other procs via comm->ring()

  tagint *tag = atom->tag;
  int nlocal = atom->nlocal;

  int n = 0;
  for (int i = 0; i < nlocal; i++)
    if (dlist[i]) n++;
  tagint *list;
  memory->create(list,n,"delete_atoms:list");

  n = 0;
  for (int i = 0; i < nlocal; i++)
    if (dlist[i]) list[n++] = tag[i];

  comm->ring(n,sizeof(tagint),list,1,bondring,NULL,(void *)this);

  delete hash;
  memory->destroy(list);
}

/* ----------------------------------------------------------------------
   delete atoms in molecules with any deletions
   use dlist marked with atom deletions, and mark additional atoms
   do not include molID = 0
------------------------------------------------------------------------- */

void DeleteAtoms::delete_molecule()
{
  // hash = unique molecule IDs from which I deleted atoms

  hash = new std::map<tagint,int>();

  tagint *molecule = atom->molecule;
  int nlocal = atom->nlocal;

  for (int i = 0; i < nlocal; i++) {
    if (molecule[i] == 0) continue;
    if (dlist[i] && hash->find(molecule[i]) == hash->end())
      (*hash)[molecule[i]] = 1;
  }

  // list = set of unique molecule IDs from which I deleted atoms
  // pass list to all other procs via comm->ring()

  int n = hash->size();
  tagint *list;
  memory->create(list,n,"delete_atoms:list");

  n = 0;
  std::map<tagint,int>::iterator pos;
  for (pos = hash->begin(); pos != hash->end(); ++pos) list[n++] = pos->first;

  comm->ring(n,sizeof(tagint),list,1,molring,NULL,(void *)this);

  delete hash;
  memory->destroy(list);
}

/* ----------------------------------------------------------------------
   update bond,angle,etc counts
   different for atom->molecular = 1 or 2
------------------------------------------------------------------------- */

void DeleteAtoms::recount_topology()
{
  bigint nbonds = 0;
  bigint nangles = 0;
  bigint ndihedrals = 0;
  bigint nimpropers = 0;

  if (atom->molecular == 1) {
    int *num_bond = atom->num_bond;
    int *num_angle = atom->num_angle;
    int *num_dihedral = atom->num_dihedral;
    int *num_improper = atom->num_improper;
    int nlocal = atom->nlocal;

    for (int i = 0; i < nlocal; i++) {
      if (num_bond) nbonds += num_bond[i];
      if (num_angle) nangles += num_angle[i];
      if (num_dihedral) ndihedrals += num_dihedral[i];
      if (num_improper) nimpropers += num_improper[i];
    }

  } else if (atom->molecular == 2) {
    Molecule **onemols = atom->avec->onemols;
    int *molindex = atom->molindex;
    int *molatom = atom->molatom;
    int nlocal = atom->nlocal;

    int imol,iatom;

    for (int i = 0; i < nlocal; i++) {
      imol = molindex[i];
      iatom = molatom[i];
      nbonds += onemols[imol]->num_bond[iatom];
      nangles += onemols[imol]->num_angle[iatom];
      ndihedrals += onemols[imol]->num_dihedral[iatom];
      nimpropers += onemols[imol]->num_improper[iatom];
    }
  }

  if (atom->avec->bonds_allow) {
    MPI_Allreduce(&nbonds,&atom->nbonds,1,MPI_LMP_BIGINT,MPI_SUM,world);
    if (!force->newton_bond) atom->nbonds /= 2;
  }
  if (atom->avec->angles_allow) {
    MPI_Allreduce(&nangles,&atom->nangles,1,MPI_LMP_BIGINT,MPI_SUM,world);
    if (!force->newton_bond) atom->nangles /= 3;
  }
  if (atom->avec->dihedrals_allow) {
    MPI_Allreduce(&ndihedrals,&atom->ndihedrals,1,MPI_LMP_BIGINT,MPI_SUM,world);
    if (!force->newton_bond) atom->ndihedrals /= 4;
  }
  if (atom->avec->impropers_allow) {
    MPI_Allreduce(&nimpropers,&atom->nimpropers,1,MPI_LMP_BIGINT,MPI_SUM,world);
    if (!force->newton_bond) atom->nimpropers /= 4;
  }
}

/* ----------------------------------------------------------------------
   callback from comm->ring() in delete_bond()
------------------------------------------------------------------------- */

void DeleteAtoms::bondring(int nbuf, char *cbuf, void *ptr)
{
  DeleteAtoms *daptr = (DeleteAtoms *) ptr;
  tagint *list = (tagint *) cbuf;
  std::map<tagint,int> *hash = daptr->hash;

  int *num_bond = daptr->atom->num_bond;
  int *num_angle = daptr->atom->num_angle;
  int *num_dihedral = daptr->atom->num_dihedral;
  int *num_improper = daptr->atom->num_improper;

  int **bond_type = daptr->atom->bond_type;
  tagint **bond_atom = daptr->atom->bond_atom;

  int **angle_type = daptr->atom->angle_type;
  tagint **angle_atom1 = daptr->atom->angle_atom1;
  tagint **angle_atom2 = daptr->atom->angle_atom2;
  tagint **angle_atom3 = daptr->atom->angle_atom3;

  int **dihedral_type = daptr->atom->dihedral_type;
  tagint **dihedral_atom1 = daptr->atom->dihedral_atom1;
  tagint **dihedral_atom2 = daptr->atom->dihedral_atom2;
  tagint **dihedral_atom3 = daptr->atom->dihedral_atom3;
  tagint **dihedral_atom4 = daptr->atom->dihedral_atom4;

  int **improper_type = daptr->atom->improper_type;
  tagint **improper_atom1 = daptr->atom->improper_atom1;
  tagint **improper_atom2 = daptr->atom->improper_atom2;
  tagint **improper_atom3 = daptr->atom->improper_atom3;
  tagint **improper_atom4 = daptr->atom->improper_atom4;

  int nlocal = daptr->atom->nlocal;

  // cbuf = list of N deleted atom IDs from other proc, put them in hash

  hash->clear();
  for (int i = 0; i < nbuf; i++) (*hash)[list[i]] = 1;

  // loop over my atoms and their bond topology lists
  // if any atom in an interaction matches atom ID in hash, delete interaction

  int m,n;
  for (int i = 0; i < nlocal; i++) {
    if (num_bond) {
      m = 0;
      n = num_bond[i];
      while (m < n) {
        if (hash->find(bond_atom[i][m]) != hash->end()) {
          bond_type[i][m] = bond_type[i][n-1];
          bond_atom[i][m] = bond_atom[i][n-1];
          n--;
        } else m++;
      }
      num_bond[i] = n;
    }

    if (num_angle) {
      m = 0;
      n = num_angle[i];
      while (m < n) {
        if (hash->find(angle_atom1[i][m]) != hash->end() ||
            hash->find(angle_atom2[i][m]) != hash->end() ||
            hash->find(angle_atom3[i][m]) != hash->end()) {
          angle_type[i][m] = angle_type[i][n-1];
          angle_atom1[i][m] = angle_atom1[i][n-1];
          angle_atom2[i][m] = angle_atom2[i][n-1];
          angle_atom3[i][m] = angle_atom3[i][n-1];
          n--;
        } else m++;
      }
      num_angle[i] = n;
    }

    if (num_dihedral) {
      m = 0;
      n = num_dihedral[i];
      while (m < n) {
        if (hash->find(dihedral_atom1[i][m]) != hash->end() ||
            hash->find(dihedral_atom2[i][m]) != hash->end() ||
            hash->find(dihedral_atom3[i][m]) != hash->end() ||
            hash->find(dihedral_atom4[i][m]) != hash->end()) {
          dihedral_type[i][m] = dihedral_type[i][n-1];
          dihedral_atom1[i][m] = dihedral_atom1[i][n-1];
          dihedral_atom2[i][m] = dihedral_atom2[i][n-1];
          dihedral_atom3[i][m] = dihedral_atom3[i][n-1];
          dihedral_atom4[i][m] = dihedral_atom4[i][n-1];
          n--;
        } else m++;
      }
      num_dihedral[i] = n;
    }

    if (num_improper) {
      m = 0;
      n = num_improper[i];
      while (m < n) {
        if (hash->find(improper_atom1[i][m]) != hash->end() ||
            hash->find(improper_atom2[i][m]) != hash->end() ||
            hash->find(improper_atom3[i][m]) != hash->end() ||
            hash->find(improper_atom4[i][m]) != hash->end()) {
          improper_type[i][m] = improper_type[i][n-1];
          improper_atom1[i][m] = improper_atom1[i][n-1];
          improper_atom2[i][m] = improper_atom2[i][n-1];
          improper_atom3[i][m] = improper_atom3[i][n-1];
          improper_atom4[i][m] = improper_atom4[i][n-1];
          n--;
        } else m++;
      }
      num_improper[i] = n;
    }
  }
}

/* ----------------------------------------------------------------------
   callback from comm->ring() in delete_molecule()
------------------------------------------------------------------------- */

void DeleteAtoms::molring(int n, char *cbuf, void *ptr)
{
  DeleteAtoms *daptr = (DeleteAtoms *)ptr;
  tagint *list = (tagint *) cbuf;
  int *dlist = daptr->dlist;
  std::map<tagint,int> *hash = daptr->hash;
  int nlocal = daptr->atom->nlocal;
  tagint *molecule = daptr->atom->molecule;

  // cbuf = list of N molecule IDs from other proc, put them in hash

  hash->clear();
  for (int i = 0; i < n; i++) (*hash)[list[i]] = 1;

  // loop over my atoms, if matches molecule ID in hash, delete that atom

  for (int i = 0; i < nlocal; i++)
    if (hash->find(molecule[i]) != hash->end()) dlist[i] = 1;
}

/* ----------------------------------------------------------------------
   process command options
------------------------------------------------------------------------- */

void DeleteAtoms::options(int narg, char **arg)
{
  compress_flag = 1;
  bond_flag = mol_flag = 0;

  int iarg = 0;
  while (iarg < narg) {
    if (strcmp(arg[iarg],"compress") == 0) {
      if (iarg+2 > narg) error->all(FLERR,"Illegal delete_atoms 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(FLERR,"Illegal delete_atoms command");
      iarg += 2;
    } else if (strcmp(arg[iarg],"bond") == 0) {
      if (iarg+2 > narg) error->all(FLERR,"Illegal delete_atoms command");
      if (atom->molecular == 0)
        error->all(FLERR,"Cannot delete_atoms bond yes for "
                   "non-molecular systems");
      if (atom->molecular == 2)
        error->all(FLERR,"Cannot use delete_atoms bond yes with "
                   "atom_style template");
      if (strcmp(arg[iarg+1],"yes") == 0) bond_flag = 1;
      else if (strcmp(arg[iarg+1],"no") == 0) bond_flag = 0;
      else error->all(FLERR,"Illegal delete_atoms command");
      iarg += 2;
    } else if (strcmp(arg[iarg],"mol") == 0) {
      if (iarg+2 > narg) error->all(FLERR,"Illegal delete_atoms command");
      if (atom->molecule_flag == 0)
        error->all(FLERR,"Delete_atoms mol yes requires "
                   "atom attribute molecule");
      if (strcmp(arg[iarg+1],"yes") == 0) mol_flag = 1;
      else if (strcmp(arg[iarg+1],"no") == 0) mol_flag = 0;
      else error->all(FLERR,"Illegal delete_atoms command");
      iarg += 2;
    } else error->all(FLERR,"Illegal delete_atoms command");
  }
}