git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10367 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
386
src/MISC/fix_evaporate.cpp
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386
src/MISC/fix_evaporate.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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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 "math.h"
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#include "stdlib.h"
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#include "string.h"
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#include "fix_evaporate.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "update.h"
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#include "domain.h"
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#include "region.h"
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#include "comm.h"
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#include "force.h"
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#include "group.h"
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#include "random_park.h"
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#include "random_mars.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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/* ---------------------------------------------------------------------- */
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FixEvaporate::FixEvaporate(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg < 7) error->all(FLERR,"Illegal fix evaporate command");
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scalar_flag = 1;
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global_freq = 1;
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extscalar = 0;
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nevery = force->inumeric(FLERR,arg[3]);
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nflux = force->inumeric(FLERR,arg[4]);
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iregion = domain->find_region(arg[5]);
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int n = strlen(arg[5]) + 1;
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idregion = new char[n];
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strcpy(idregion,arg[5]);
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int seed = force->inumeric(FLERR,arg[6]);
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if (nevery <= 0 || nflux <= 0)
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error->all(FLERR,"Illegal fix evaporate command");
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if (iregion == -1)
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error->all(FLERR,"Region ID for fix evaporate does not exist");
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if (seed <= 0) error->all(FLERR,"Illegal fix evaporate command");
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// random number generator, same for all procs
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random = new RanPark(lmp,seed);
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// optional args
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molflag = 0;
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int iarg = 7;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"molecule") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal fix evaporate command");
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if (strcmp(arg[iarg+1],"no") == 0) molflag = 0;
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else if (strcmp(arg[iarg+1],"yes") == 0) molflag = 1;
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else error->all(FLERR,"Illegal fix evaporate command");
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iarg += 2;
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} else error->all(FLERR,"Illegal fix evaporate command");
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}
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// set up reneighboring
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force_reneighbor = 1;
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next_reneighbor = (update->ntimestep/nevery)*nevery + nevery;
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ndeleted = 0;
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nmax = 0;
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list = NULL;
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mark = NULL;
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}
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/* ---------------------------------------------------------------------- */
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FixEvaporate::~FixEvaporate()
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{
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delete [] idregion;
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delete random;
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memory->destroy(list);
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memory->destroy(mark);
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}
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/* ---------------------------------------------------------------------- */
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int FixEvaporate::setmask()
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{
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int mask = 0;
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mask |= PRE_EXCHANGE;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixEvaporate::init()
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{
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// set index and check validity of region
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iregion = domain->find_region(idregion);
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if (iregion == -1)
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error->all(FLERR,"Region ID for fix evaporate does not exist");
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// check that no deletable atoms are in atom->firstgroup
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// deleting such an atom would not leave firstgroup atoms first
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if (atom->firstgroup >= 0) {
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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int firstgroupbit = group->bitmask[atom->firstgroup];
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int flag = 0;
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for (int i = 0; i < nlocal; i++)
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if ((mask[i] & groupbit) && (mask[i] && firstgroupbit)) flag = 1;
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int flagall;
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MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
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if (flagall)
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error->all(FLERR,"Cannot evaporate atoms in atom_modify first group");
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}
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// if molflag not set, warn if any deletable atom has a mol ID
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if (molflag == 0 && atom->molecule_flag) {
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int *molecule = atom->molecule;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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int flag = 0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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if (molecule[i]) flag = 1;
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int flagall;
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MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
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if (flagall && comm->me == 0)
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error->warning(FLERR,
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"Fix evaporate may delete atom with non-zero molecule ID");
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}
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if (molflag && atom->molecule_flag == 0)
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error->all(FLERR,
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"Fix evaporate molecule requires atom attribute molecule");
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}
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/* ----------------------------------------------------------------------
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perform particle deletion
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done before exchange, borders, reneighbor
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so that ghost atoms and neighbor lists will be correct
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------------------------------------------------------------------------- */
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void FixEvaporate::pre_exchange()
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{
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int i,j,m,iwhichglobal,iwhichlocal;
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int ndel,ndeltopo[4];
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if (update->ntimestep != next_reneighbor) return;
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// grow list and mark arrays if necessary
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if (atom->nlocal > nmax) {
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memory->destroy(list);
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memory->destroy(mark);
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nmax = atom->nmax;
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memory->create(list,nmax,"evaporate:list");
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memory->create(mark,nmax,"evaporate:mark");
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}
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// ncount = # of deletable atoms in region that I own
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// nall = # on all procs
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// nbefore = # on procs before me
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// list[ncount] = list of local indices of atoms I can delete
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double **x = atom->x;
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int *mask = atom->mask;
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int *tag = atom->tag;
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int nlocal = atom->nlocal;
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int ncount = 0;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
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list[ncount++] = i;
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int nall,nbefore;
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MPI_Allreduce(&ncount,&nall,1,MPI_INT,MPI_SUM,world);
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MPI_Scan(&ncount,&nbefore,1,MPI_INT,MPI_SUM,world);
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nbefore -= ncount;
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// ndel = total # of atom deletions, in or out of region
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// ndeltopo[1,2,3,4] = ditto for bonds, angles, dihedrals, impropers
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// mark[] = 1 if deleted
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ndel = 0;
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for (i = 0; i < nlocal; i++) mark[i] = 0;
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// atomic deletions
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// choose atoms randomly across all procs and mark them for deletion
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// shrink eligible list as my atoms get marked
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// keep ndel,ncount,nall,nbefore current after each atom deletion
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if (molflag == 0) {
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while (nall && ndel < nflux) {
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iwhichglobal = static_cast<int> (nall*random->uniform());
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if (iwhichglobal < nbefore) nbefore--;
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else if (iwhichglobal < nbefore + ncount) {
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iwhichlocal = iwhichglobal - nbefore;
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mark[list[iwhichlocal]] = 1;
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list[iwhichlocal] = list[ncount-1];
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ncount--;
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}
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ndel++;
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nall--;
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}
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// molecule deletions
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// choose one atom in one molecule randomly across all procs
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// bcast mol ID and delete all atoms in that molecule on any proc
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// update deletion count by total # of atoms in molecule
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// shrink list of eligible candidates as any of my atoms get marked
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// keep ndel,ndeltopo,ncount,nall,nbefore current after each mol deletion
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} else {
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int me,proc,iatom,imolecule,ndelone,ndelall;
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int *molecule = atom->molecule;
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ndeltopo[0] = ndeltopo[1] = ndeltopo[2] = ndeltopo[3] = 0;
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while (nall && ndel < nflux) {
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// pick an iatom,imolecule on proc me to delete
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iwhichglobal = static_cast<int> (nall*random->uniform());
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if (iwhichglobal >= nbefore && iwhichglobal < nbefore + ncount) {
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iwhichlocal = iwhichglobal - nbefore;
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iatom = list[iwhichlocal];
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imolecule = molecule[iatom];
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me = comm->me;
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} else me = -1;
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// bcast mol ID to delete all atoms from
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// if mol ID > 0, delete any atom in molecule and decrement counters
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// if mol ID == 0, delete single iatom
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// be careful to delete correct # of bond,angle,etc for newton on or off
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MPI_Allreduce(&me,&proc,1,MPI_INT,MPI_MAX,world);
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MPI_Bcast(&imolecule,1,MPI_INT,proc,world);
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ndelone = 0;
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for (i = 0; i < nlocal; i++) {
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if (imolecule && molecule[i] == imolecule) {
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mark[i] = 1;
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ndelone++;
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if (atom->avec->bonds_allow) {
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if (force->newton_bond) ndeltopo[0] += atom->num_bond[i];
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else {
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for (j = 0; j < atom->num_bond[i]; j++) {
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if (tag[i] < atom->bond_atom[i][j]) ndeltopo[0]++;
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}
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}
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}
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if (atom->avec->angles_allow) {
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if (force->newton_bond) ndeltopo[1] += atom->num_angle[i];
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else {
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for (j = 0; j < atom->num_angle[i]; j++) {
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m = atom->map(atom->angle_atom2[i][j]);
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if (m >= 0 && m < nlocal) ndeltopo[1]++;
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}
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}
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}
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if (atom->avec->dihedrals_allow) {
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if (force->newton_bond) ndeltopo[2] += atom->num_dihedral[i];
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else {
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for (j = 0; j < atom->num_dihedral[i]; j++) {
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m = atom->map(atom->dihedral_atom2[i][j]);
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if (m >= 0 && m < nlocal) ndeltopo[2]++;
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}
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}
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}
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if (atom->avec->impropers_allow) {
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if (force->newton_bond) ndeltopo[3] += atom->num_improper[i];
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else {
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for (j = 0; j < atom->num_improper[i]; j++) {
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m = atom->map(atom->improper_atom2[i][j]);
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if (m >= 0 && m < nlocal) ndeltopo[3]++;
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}
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}
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}
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} else if (me == proc && i == iatom) {
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mark[i] = 1;
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ndelone++;
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}
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}
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// remove any atoms marked for deletion from my eligible list
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i = 0;
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while (i < ncount) {
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if (mark[list[i]]) {
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list[i] = list[ncount-1];
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ncount--;
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} else i++;
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}
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// update ndel,ncount,nall,nbefore
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// ndelall is total atoms deleted on this iteration
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// ncount is already correct, so resum to get nall and nbefore
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MPI_Allreduce(&ndelone,&ndelall,1,MPI_INT,MPI_SUM,world);
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ndel += ndelall;
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MPI_Allreduce(&ncount,&nall,1,MPI_INT,MPI_SUM,world);
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MPI_Scan(&ncount,&nbefore,1,MPI_INT,MPI_SUM,world);
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nbefore -= ncount;
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}
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}
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// delete my marked atoms
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// loop in reverse order to avoid copying marked atoms
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AtomVec *avec = atom->avec;
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for (i = nlocal-1; i >= 0; i--) {
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if (mark[i]) {
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avec->copy(atom->nlocal-1,i,1);
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atom->nlocal--;
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}
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}
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// reset global natoms and bonds, angles, etc
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// if global map exists, reset it now instead of waiting for comm
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// since deleting atoms messes up ghosts
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atom->natoms -= ndel;
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if (molflag) {
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int all[4];
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MPI_Allreduce(ndeltopo,all,4,MPI_INT,MPI_SUM,world);
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atom->nbonds -= all[0];
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atom->nangles -= all[1];
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atom->ndihedrals -= all[2];
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atom->nimpropers -= all[3];
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}
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if (ndel && 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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// statistics
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ndeleted += ndel;
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next_reneighbor = update->ntimestep + nevery;
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}
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/* ----------------------------------------------------------------------
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return number of deleted particles
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------------------------------------------------------------------------- */
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double FixEvaporate::compute_scalar()
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{
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return 1.0*ndeleted;
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}
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/* ----------------------------------------------------------------------
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memory usage of local atom-based arrays
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------------------------------------------------------------------------- */
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double FixEvaporate::memory_usage()
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{
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double bytes = 2*nmax * sizeof(int);
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return bytes;
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}
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