git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@26 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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src/delete_atoms.cpp
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303
src/delete_atoms.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "stdlib.h"
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#include "string.h"
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#include "delete_atoms.h"
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#include "system.h"
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#include "atom.h"
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#include "comm.h"
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#include "domain.h"
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#include "force.h"
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#include "group.h"
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#include "region.h"
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#include "neighbor.h"
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#include "comm.h"
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#include "force.h"
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#include "error.h"
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#define MIN(a,b) ((a) < (b) ? (a) : (b))
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#define MAX(a,b) ((a) > (b) ? (a) : (b))
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/* ---------------------------------------------------------------------- */
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void DeleteAtoms::command(int narg, char **arg)
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{
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if (domain->box_exist == 0)
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error->all("Delete_atoms command before simulation box is defined");
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if (narg < 1) error->all("Illegal delete_atoms command");
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// store state before delete
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if (atom->tag_enable == 0)
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error->all("Cannot use delete_atoms unless atoms have IDs");
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int natoms_previous = static_cast<int> (atom->natoms);
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int tag_lowest = natoms_previous + 1;
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// allocate and initialize deletion list
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int nlocal = atom->nlocal;
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int *list = new int[nlocal];
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for (int i = 0; i < nlocal; i++) list[i] = 0;
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// delete the atoms
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// return tag_lowest = min tag of each proc's deleted atoms
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if (strcmp(arg[0],"group") == 0) delete_group(narg,arg,list);
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else if (strcmp(arg[0],"region") == 0) delete_region(narg,arg,list);
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else if (strcmp(arg[0],"overlap") == 0) delete_overlap(narg,arg,list);
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else error->all("Illegal delete_atoms command");
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// delete local atoms in list
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// reset nlocal
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// tag_lowest_all = smallest deleted atom tag on any proc
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int *tag = atom->tag;
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int i = 0;
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while (i < nlocal) {
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if (list[i]) {
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tag_lowest = MIN(tag_lowest,tag[i]);
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atom->copy(nlocal-1,i);
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list[i] = list[nlocal-1];
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nlocal--;
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} else i++;
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}
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atom->nlocal = nlocal;
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delete [] list;
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int tag_lowest_all;
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MPI_Allreduce(&tag_lowest,&tag_lowest_all,1,MPI_INT,MPI_MIN,world);
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// if non-molecular system, reset atom tags to be contiguous
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// set all atom IDs >= tag_lowest_all to 0
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// tag_extend() will reset tags for those atoms
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if (atom->molecular == 0) {
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int *tag = atom->tag;
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int nlocal = atom->nlocal;
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for (i = 0; i < nlocal; i++)
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if (tag[i] >= tag_lowest_all) tag[i] = 0;
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atom->tag_extend();
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}
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// reset atom->natoms
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// reset atom->map if it exists
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// set nghost to 0 so old ghosts of deleted atoms won't be mapped
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double rlocal = atom->nlocal;
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MPI_Allreduce(&rlocal,&atom->natoms,1,MPI_DOUBLE,MPI_SUM,world);
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if (atom->map_style) {
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atom->nghost = 0;
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atom->map_init();
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atom->map_set();
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}
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// print before and after atom count
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int ndelete = static_cast<int> (natoms_previous - atom->natoms);
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if (comm->me == 0) {
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if (screen) fprintf(screen,"Deleted %d atoms, new total = %.15g\n",
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ndelete,atom->natoms);
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if (logfile) fprintf(logfile,"Deleted %d atoms, new total = %.15g\n",
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ndelete,atom->natoms);
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}
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}
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/* ----------------------------------------------------------------------
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delete all atoms in group
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group will still exist
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------------------------------------------------------------------------- */
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void DeleteAtoms::delete_group(int narg, char **arg, int *list)
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{
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if (narg != 2) error->all("Illegal delete_atoms command");
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int igroup = group->find(arg[1]);
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if (igroup == -1) error->all("Could not find delete_atoms group ID");
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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int groupbit = group->bitmask[igroup];
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) list[i] = 1;
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}
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/* ----------------------------------------------------------------------
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delete all atoms in region
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------------------------------------------------------------------------- */
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void DeleteAtoms::delete_region(int narg, char **arg, int *list)
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{
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if (narg != 2) error->all("Illegal delete_atoms command");
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int iregion;
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for (iregion = 0; iregion < domain->nregion; iregion++)
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if (strcmp(arg[1],domain->regions[iregion]->id) == 0) break;
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if (iregion == domain->nregion)
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error->all("Could not find delete_atoms region ID");
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double **x = atom->x;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2])) list[i] = 1;
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}
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/* ----------------------------------------------------------------------
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delete atoms so there are no pairs within cutoff
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which atoms are deleted depends on ordering of atoms within proc
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deletions can vary with processor count
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no guarantee that minimium number of atoms will be deleted
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------------------------------------------------------------------------- */
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void DeleteAtoms::delete_overlap(int narg, char **arg, int *list)
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{
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if (narg < 2) error->all("Illegal delete_atoms command");
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// read args including optional type info
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double cut = atof(arg[1]);
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double cutsq = cut*cut;
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int typeflag,type1,type2;
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if (narg == 2) typeflag = 0;
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else if (narg == 3) {
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typeflag = 1;
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type1 = atoi(arg[2]);
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} else if (narg == 4) {
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typeflag = 2;
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type1 = atoi(arg[2]);
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type2 = atoi(arg[3]);
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} else error->all("Illegal delete_atoms command");
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// init entire system since comm->borders and neighbor->build is done
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// comm::init needs neighbor::init needs pair::init needs kspace::init, etc
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if (comm->me == 0 && screen)
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fprintf(screen,"System init for delete_atoms ...\n");
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sys->init();
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// setup domain, communication and neighboring
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// acquire ghosts
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// build half neighbor list via explicit call
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domain->pbc();
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domain->reset_box();
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comm->setup();
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if (neighbor->style) neighbor->setup_bins();
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comm->exchange();
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comm->borders();
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if (!neighbor->half) neighbor->build_half_setup();
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neighbor->build_half();
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// error check on cutoff
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if (cut > neighbor->cutneigh)
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error->all("Delete_atoms cutoff > neighbor cutoff");
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// create an atom map if one doesn't exist already
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int mapflag = 0;
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if (atom->map_style == 0) {
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mapflag = 1;
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atom->map_style = 1;
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atom->map_init();
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atom->map_set();
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}
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// double loop over owned atoms and their neighbors
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// at end of loop, there are no more overlaps
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// criteria for i,j to undergo a deletion event:
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// weighting factor != 0.0 for this pair
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// could be 0 and still be in neigh list for long-range Coulombics
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// local copy of j (map[tag[j]]) has not already been deleted
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// distance between i,j is less than cutoff
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// i,j are of valid types
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// if all criteria met, delete i and skip to next i in outer loop
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// unless j is ghost and newton_pair off and tag[j] < tag[i]
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// then rely on other proc to delete
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int *tag = atom->tag;
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int *type = atom->type;
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double **x = atom->x;
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int nlocal = atom->nlocal;
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int nall = atom->nlocal + atom->nghost;
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double *special_coul = force->special_coul;
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double *special_lj = force->special_lj;
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int newton_pair = force->newton_pair;
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int i,j,k,m,itype,jtype,numneigh;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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int *neighs;
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for (i = 0; i < nlocal; i++) {
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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itype = type[i];
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neighs = neighbor->firstneigh[i];
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numneigh = neighbor->numneigh[i];
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for (k = 0; k < numneigh; k++) {
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j = neighs[k];
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list[i] = 1;
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if (j >= nall) {
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if (special_coul[j/nall] == 0.0 && special_lj[j/nall] == 0.0) continue;
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j %= nall;
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}
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if (j < nlocal) {
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if (list[j]) continue;
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} else {
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m = atom->map(tag[j]);
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if (m < nlocal && list[m]) continue;
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}
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq >= cutsq) continue;
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if (typeflag) {
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jtype = type[j];
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if (typeflag == 1 && itype != type1 && jtype != type1) continue;
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if (typeflag == 2 && !(itype == type1 && jtype == type2) &&
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!(itype == type2 && jtype == type1)) continue;
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}
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if (j >= nlocal && newton_pair == 0 && tag[j] < tag[i]) continue;
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list[i] = 1;
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break;
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}
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}
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// cleanup after neighbor list
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if (!neighbor->half) neighbor->build_half_cleanup();
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// delete temporary atom map
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if (mapflag) {
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atom->map_delete();
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atom->map_style = 0;
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}
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}
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