forked from lijiext/lammps
when identifying molecules/clusters fall back to unfiltered coordinates for ghost atoms
This commit is contained in:
Axel Kohlmeyer
parent
64e8000720
commit
d3a863e7af
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@ -13,7 +13,7 @@
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/* ----------------------------------------------------------------------
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Contributing authors: Ray Shan (Sandia, tnshan@sandia.gov)
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Oleg Sergeev (VNIIA, sergeev@vniia.ru)
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Oleg Sergeev (VNIIA, sergeev@vniia.ru)
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------------------------------------------------------------------------- */
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#include <stdlib.h>
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@ -182,35 +182,35 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) :
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jtype = atoi(arg[iarg+2]);
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bo_cut = atof(arg[iarg+3]);
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if (itype > ntypes || jtype > ntypes)
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error->all(FLERR,"Illegal fix reax/c/species command");
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error->all(FLERR,"Illegal fix reax/c/species command");
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if (itype <= 0 || jtype <= 0)
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error->all(FLERR,"Illegal fix reax/c/species command");
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error->all(FLERR,"Illegal fix reax/c/species command");
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if (bo_cut > 1.0 || bo_cut < 0.0)
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error->all(FLERR,"Illegal fix reax/c/species command");
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error->all(FLERR,"Illegal fix reax/c/species command");
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BOCut[itype][jtype] = bo_cut;
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BOCut[jtype][itype] = bo_cut;
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iarg += 4;
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// modify element type names
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// modify element type names
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} else if (strcmp(arg[iarg],"element") == 0) {
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if (iarg+ntypes+1 > narg) error->all(FLERR,"Illegal fix reax/c/species command");
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eletype = (char**) malloc(ntypes*sizeof(char*));
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for (int i = 0; i < ntypes; i ++) {
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eletype[i] = (char*) malloc(2*sizeof(char));
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strcpy(eletype[i],arg[iarg+1+i]);
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strcpy(eletype[i],arg[iarg+1+i]);
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}
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eleflag = 1;
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iarg += ntypes + 1;
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// position of molecules
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// position of molecules
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} else if (strcmp(arg[iarg],"position") == 0) {
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if (iarg+3 > narg) error->all(FLERR,"Illegal fix reax/c/species command");
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posflag = 1;
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posfreq = atoi(arg[iarg+1]);
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if (posfreq < nfreq || (posfreq%nfreq != 0))
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error->all(FLERR,"Illegal fix reax/c/species command");
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error->all(FLERR,"Illegal fix reax/c/species command");
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filepos = new char[255];
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strcpy(filepos,arg[iarg+2]);
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@ -221,8 +221,8 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) :
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pos = fopen(filepos, "w");
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if (pos == NULL) error->one(FLERR,"Cannot open fix reax/c/species position file");
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}
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singlepos_opened = 1;
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multipos = 0;
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singlepos_opened = 1;
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multipos = 0;
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}
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iarg += 3;
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} else error->all(FLERR,"Illegal fix reax/c/species command");
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@ -300,7 +300,7 @@ void FixReaxCSpecies::init()
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reaxc = (PairReaxC *) force->pair_match("reax/c",0);
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if (reaxc == NULL) error->all(FLERR,"Cannot use fix reax/c/species without "
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"pair_style reax/c, reax/c/kk, or reax/c/omp");
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"pair_style reax/c, reax/c/kk, or reax/c/omp");
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reaxc->fixspecies_flag = 1;
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@ -389,14 +389,14 @@ void FixReaxCSpecies::create_fix()
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args[3] = tmparg[0];
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args[4] = tmparg[1];
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args[5] = tmparg[2];
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args[6] = (char *) "c_SPECATOM[1]"; // q, array_atoms[i][0]
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args[7] = (char *) "c_SPECATOM[2]"; // x, 1
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args[8] = (char *) "c_SPECATOM[3]"; // y, 2
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args[9] = (char *) "c_SPECATOM[4]"; // z, 3
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args[10] = (char *) "c_SPECATOM[5]"; // vx, 4
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args[11] = (char *) "c_SPECATOM[6]"; // vy, 5
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args[12] = (char *) "c_SPECATOM[7]"; // vz, 6
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args[13] = (char *) "c_SPECATOM[8]"; // abo01, 7
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args[6] = (char *) "c_SPECATOM[1]"; // q, array_atoms[i][0]
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args[7] = (char *) "c_SPECATOM[2]"; // x, 1
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args[8] = (char *) "c_SPECATOM[3]"; // y, 2
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args[9] = (char *) "c_SPECATOM[4]"; // z, 3
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args[10] = (char *) "c_SPECATOM[5]"; // vx, 4
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args[11] = (char *) "c_SPECATOM[6]"; // vy, 5
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args[12] = (char *) "c_SPECATOM[7]"; // vz, 6
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args[13] = (char *) "c_SPECATOM[8]"; // abo01, 7
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args[14] = (char *) "c_SPECATOM[9]";
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args[15] = (char *) "c_SPECATOM[10]";
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args[16] = (char *) "c_SPECATOM[11]";
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@ -520,6 +520,8 @@ void FixReaxCSpecies::FindMolecule ()
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int *ilist;
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double bo_tmp,bo_cut;
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double **spec_atom = f_SPECBOND->array_atom;
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const double * const * const x = atom->x;
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const int nlocal = atom->nlocal;
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inum = reaxc->list->inum;
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ilist = reaxc->list->ilist;
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@ -545,35 +547,47 @@ void FixReaxCSpecies::FindMolecule ()
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done = 1;
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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if (!(mask[i] & groupbit)) continue;
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i = ilist[ii];
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if (!(mask[i] & groupbit)) continue;
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itype = atom->type[i];
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itype = atom->type[i];
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for (jj = 0; jj < MAXSPECBOND; jj++) {
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j = reaxc->tmpid[i][jj];
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j = reaxc->tmpid[i][jj];
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if (j < i) continue;
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if (!(mask[j] & groupbit)) continue;
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if ((j == 0) || (j < i)) continue;
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if (!(mask[j] & groupbit)) continue;
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if (clusterID[i] == clusterID[j] && PBCconnected[i] == PBCconnected[j]
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&& x0[i].x == x0[j].x && x0[i].y == x0[j].y && x0[i].z == x0[j].z) continue;
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if (clusterID[i] == clusterID[j]
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&& PBCconnected[i] == PBCconnected[j]
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&& x0[i].x == x0[j].x
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&& x0[i].y == x0[j].y
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&& x0[i].z == x0[j].z) continue;
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jtype = atom->type[j];
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bo_cut = BOCut[itype][jtype];
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bo_tmp = spec_atom[i][jj+7];
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bo_cut = BOCut[itype][jtype];
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bo_tmp = spec_atom[i][jj+7];
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if (bo_tmp > bo_cut) {
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if (bo_tmp > bo_cut) {
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clusterID[i] = clusterID[j] = MIN(clusterID[i], clusterID[j]);
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PBCconnected[i] = PBCconnected[j] = MAX(PBCconnected[i], PBCconnected[j]);
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x0[i] = x0[j] = chAnchor(x0[i], x0[j]);
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if ((fabs(spec_atom[i][1] - spec_atom[j][1]) > reaxc->control->bond_cut)
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|| (fabs(spec_atom[i][2] - spec_atom[j][2]) > reaxc->control->bond_cut)
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|| (fabs(spec_atom[i][3] - spec_atom[j][3]) > reaxc->control->bond_cut))
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PBCconnected[i] = PBCconnected[j] = 1;
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done = 0;
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}
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}
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// spec_atom[][] contains filtered coordinates only for local atoms,
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// so we have to use unfiltered ones for ghost atoms.
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if (j < nlocal) {
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if ((fabs(spec_atom[i][1] - spec_atom[j][1]) > reaxc->control->bond_cut)
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|| (fabs(spec_atom[i][2] - spec_atom[j][2]) > reaxc->control->bond_cut)
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|| (fabs(spec_atom[i][3] - spec_atom[j][3]) > reaxc->control->bond_cut))
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PBCconnected[i] = PBCconnected[j] = 1;
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} else {
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if ((fabs(spec_atom[i][1] - x[j][1]) > reaxc->control->bond_cut)
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|| (fabs(spec_atom[i][2] - x[j][2]) > reaxc->control->bond_cut)
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|| (fabs(spec_atom[i][3] - x[j][3]) > reaxc->control->bond_cut))
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PBCconnected[i] = PBCconnected[j] = 1;
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}
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done = 0;
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}
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}
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}
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if (!done) change = 1;
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if (done) break;
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@ -609,13 +623,13 @@ void FixReaxCSpecies::SortMolecule(int &Nmole)
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MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
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if (flagall && me == 0)
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error->warning(FLERR,"Atom with cluster ID = 0 included in "
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"fix reax/c/species group");
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"fix reax/c/species group");
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MPI_Allreduce(&lo,&idlo,1,MPI_INT,MPI_MIN,world);
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MPI_Allreduce(&hi,&idhi,1,MPI_INT,MPI_MAX,world);
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if (idlo == ntotal)
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if (me == 0)
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error->warning(FLERR,"Atom with cluster ID = maxmol "
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"included in fix reax/c/species group");
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"included in fix reax/c/species group");
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int nlen = idhi - idlo + 1;
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memory->create(molmap,nlen,"reax/c/species:molmap");
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@ -795,7 +809,7 @@ void FixReaxCSpecies::OpenPos()
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*ptr = '\0';
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if (padflag == 0)
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sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
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filepos,ntimestep,ptr+1);
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filepos,ntimestep,ptr+1);
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else {
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char bif[8],pad[16];
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strcpy(bif,BIGINT_FORMAT);
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@ -835,11 +849,11 @@ void FixReaxCSpecies::WritePos(int Nmole, int Nspec)
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if (me == 0) {
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fprintf(pos,"Timestep " BIGINT_FORMAT " NMole %d NSpec %d xlo %f "
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"xhi %f ylo %f yhi %f zlo %f zhi %f\n",
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update->ntimestep,Nmole, Nspec,
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domain->boxlo[0],domain->boxhi[0],
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domain->boxlo[1],domain->boxhi[1],
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domain->boxlo[2],domain->boxhi[2]);
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"xhi %f ylo %f yhi %f zlo %f zhi %f\n",
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update->ntimestep,Nmole, Nspec,
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domain->boxlo[0],domain->boxhi[0],
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domain->boxlo[1],domain->boxhi[1],
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domain->boxlo[2],domain->boxhi[2]);
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fprintf(pos,"ID\tAtom_Count\tType\tAve_q\t\tCoM_x\t\tCoM_y\t\tCoM_z\n");
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}
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@ -862,21 +876,21 @@ void FixReaxCSpecies::WritePos(int Nmole, int Nspec)
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if (cid == m) {
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itype = atom->type[i]-1;
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Name[itype] ++;
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count ++;
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avq += spec_atom[i][0];
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count ++;
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avq += spec_atom[i][0];
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if (PBCconnected[i]) {
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if ((x0[i].x - spec_atom[i][1]) > halfbox[0])
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spec_atom[i][1] += box[0];
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if ((spec_atom[i][1] - x0[i].x) > halfbox[0])
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spec_atom[i][1] -= box[0];
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spec_atom[i][1] -= box[0];
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if ((x0[i].y - spec_atom[i][2]) > halfbox[1])
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spec_atom[i][2] += box[1];
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spec_atom[i][2] += box[1];
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if ((spec_atom[i][2] - x0[i].y) > halfbox[1])
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spec_atom[i][2] -= box[1];
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spec_atom[i][2] -= box[1];
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if ((x0[i].z - spec_atom[i][3]) > halfbox[2])
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spec_atom[i][3] += box[2];
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if ((spec_atom[i][3] - x0[i].z) > halfbox[2])
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spec_atom[i][3] -= box[2];
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spec_atom[i][3] -= box[2];
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}
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for (n = 0; n < 3; n++)
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avx[n] += spec_atom[i][n+1];
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@ -911,17 +925,17 @@ void FixReaxCSpecies::WritePos(int Nmole, int Nspec)
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if (count > 0) {
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avq /= count;
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for (k = 0; k < 3; k++) {
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avx[k] /= count;
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avx[k] /= count;
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if (avx[k] >= domain->boxhi[k])
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avx[k] -= box[k];
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if (avx[k] < domain->boxlo[k])
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avx[k] += box[k];
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avx[k] -= domain->boxlo[k];
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avx[k] /= box[k];
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avx[k] -= domain->boxlo[k];
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avx[k] /= box[k];
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}
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fprintf(pos,"\t%.8f \t%.8f \t%.8f \t%.8f",
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avq,avx[0],avx[1],avx[2]);
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avq,avx[0],avx[1],avx[2]);
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}
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fprintf(pos,"\n");
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}
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