initial exact logic for delete_atoms partial
This commit is contained in:
Steve Plimpton
@ -40,6 +40,8 @@
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using namespace LAMMPS_NS;
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enum{FRACTION,COUNT};
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/* ---------------------------------------------------------------------- */
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DeleteAtoms::DeleteAtoms(LAMMPS *lmp) : Command(lmp) {}
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@ -71,8 +73,8 @@ void DeleteAtoms::command(int narg, char **arg)
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delete_region(narg, arg);
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else if (strcmp(arg[0], "overlap") == 0)
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delete_overlap(narg, arg);
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else if (strcmp(arg[0], "porosity") == 0)
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delete_porosity(narg, arg);
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else if (strcmp(arg[0], "partial") == 0)
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delete_partial(narg, arg);
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else if (strcmp(arg[0], "variable") == 0)
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delete_variable(narg, arg);
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else
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@ -412,25 +414,42 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
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}
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/* ----------------------------------------------------------------------
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create porosity by deleting atoms in a specified region
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delete specified portion of atoms within group and/or region
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------------------------------------------------------------------------- */
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void DeleteAtoms::delete_porosity(int narg, char **arg)
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void DeleteAtoms::delete_partial(int narg, char **arg)
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{
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if (narg < 5) utils::missing_cmd_args(FLERR, "delete_atoms porosity", error);
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if (narg < 5) utils::missing_cmd_args(FLERR, "delete_atoms portion", error);
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int igroup = group->find(arg[1]);
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if (igroup == -1) error->all(FLERR, "Could not find delete_atoms porosity group ID {}", arg[1]);
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int partial_style, exactflag;
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bigint ncount;
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double fraction;
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auto iregion = domain->get_region_by_id(arg[2]);
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if (!iregion && (strcmp(arg[2], "NULL") != 0))
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error->all(FLERR, "Could not find delete_atoms porosity region ID {}", arg[2]);
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if (strcmp(arg[1],"fraction") == 0) {
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partial_style = FRACTION;
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fraction = utils::numeric(FLERR, arg[2], false, lmp);
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exactflag = 0;
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} else if (strcmp(arg[1],"fraction/exact") == 0) {
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partial_style = FRACTION;
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fraction = utils::numeric(FLERR, arg[2], false, lmp);
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exactflag = 1;
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} else if (strcmp(arg[1],"count") == 0) {
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partial_style = COUNT;
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ncount = utils::bnumeric(FLERR, arg[2], false, lmp);
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exactflag = 1;
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}
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double porosity_fraction = utils::numeric(FLERR, arg[3], false, lmp);
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int seed = utils::inumeric(FLERR, arg[4], false, lmp);
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int igroup = group->find(arg[3]);
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if (igroup == -1) error->all(FLERR, "Could not find delete_atoms porosity group ID {}", arg[3]);
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auto region = domain->get_region_by_id(arg[4]);
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if (!region && (strcmp(arg[4], "NULL") != 0))
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error->all(FLERR, "Could not find delete_atoms porosity region ID {}", arg[4]);
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int seed = utils::inumeric(FLERR, arg[5], false, lmp);
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options(narg - 5, &arg[5]);
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auto random = new RanMars(lmp, seed + comm->me);
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auto ranmars = new RanMars(lmp, seed + comm->me);
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// allocate and initialize deletion list
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@ -438,21 +457,76 @@ void DeleteAtoms::delete_porosity(int narg, char **arg)
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memory->create(dlist, nlocal, "delete_atoms:dlist");
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for (int i = 0; i < nlocal; i++) dlist[i] = 0;
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// delete fraction of atoms which are in both group and region
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// setup
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double **x = atom->x;
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int *mask = atom->mask;
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int groupbit = group->bitmask[igroup];
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if (iregion) iregion->prematch();
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if (region) region->prematch();
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for (int i = 0; i < nlocal; i++) {
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if (!(mask[i] & groupbit)) continue;
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if (iregion && !iregion->match(x[i][0], x[i][1], x[i][2])) continue;
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if (random->uniform() <= porosity_fraction) dlist[i] = 1;
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// delete approximate fraction of atoms in both group and region
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if (partial_style == FRACTION && !exactflag) {
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for (int i = 0; i < nlocal; i++) {
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if (!(mask[i] & groupbit)) continue;
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if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
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if (ranmars->uniform() <= fraction) dlist[i] = 1;
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}
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// delete exact fraction or count of atoms in both group and region
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} else {
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double **x = atom->x;
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int *mask = atom->mask;
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// count = number of atoms I own in both group and region
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int count = 0;
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for (int i = 0; i < nlocal; i++) {
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if (!(mask[i] & groupbit)) continue;
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if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
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count++;
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}
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// convert specified fraction to ncount
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bigint bcount = count;
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bigint allcount;
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MPI_Allreduce(&bcount,&allcount,1,MPI_LMP_BIGINT,MPI_SUM,world);
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if (partial_style == FRACTION) {
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ncount = static_cast<bigint> (fraction * allcount);
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} else if (partial_style == COUNT) {
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if (ncount > allcount)
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error->all(FLERR,"Delete_atoms count exceeds eligible atoms");
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}
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// make selection
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int *flag = memory->create(flag,count,"delete_atoms:flag");
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int *work = memory->create(work,count,"delete_atoms:work");
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ranmars->select_subset(ncount,count,flag,work);
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// set dlist for atom indices in flag
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// flag vector from select_subset() is only for eligible atoms
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int j = 0;
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for (int i = 0; i < nlocal; i++) {
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if (!(mask[i] & groupbit)) continue;
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if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
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if (flag[j]) dlist[i] = 1;
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j++;
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}
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memory->destroy(flag);
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memory->destroy(work);
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}
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delete random;
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// delete RN generator
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delete ranmars;
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}
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/* ----------------------------------------------------------------------
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