diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp
index 86454066b0261d05bb2fba9510ea57fad7ffaf65..23a37455e82ae5587ad6da4f43476a84aaf14b84 100644
--- a/src/USER-REAXC/fix_reaxc_species.cpp
+++ b/src/USER-REAXC/fix_reaxc_species.cpp
@@ -13,7 +13,7 @@
/* ----------------------------------------------------------------------
Contributing authors: Ray Shan (Sandia, tnshan@sandia.gov)
- Oleg Sergeev (VNIIA, sergeev@vniia.ru)
+ Oleg Sergeev (VNIIA, sergeev@vniia.ru)
------------------------------------------------------------------------- */
#include <stdlib.h>
@@ -182,35 +182,35 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) :
jtype = atoi(arg[iarg+2]);
bo_cut = atof(arg[iarg+3]);
if (itype > ntypes || jtype > ntypes)
- error->all(FLERR,"Illegal fix reax/c/species command");
+ error->all(FLERR,"Illegal fix reax/c/species command");
if (itype <= 0 || jtype <= 0)
- error->all(FLERR,"Illegal fix reax/c/species command");
+ error->all(FLERR,"Illegal fix reax/c/species command");
if (bo_cut > 1.0 || bo_cut < 0.0)
- error->all(FLERR,"Illegal fix reax/c/species command");
+ error->all(FLERR,"Illegal fix reax/c/species command");
BOCut[itype][jtype] = bo_cut;
BOCut[jtype][itype] = bo_cut;
iarg += 4;
- // modify element type names
+ // modify element type names
} else if (strcmp(arg[iarg],"element") == 0) {
if (iarg+ntypes+1 > narg) error->all(FLERR,"Illegal fix reax/c/species command");
eletype = (char**) malloc(ntypes*sizeof(char*));
for (int i = 0; i < ntypes; i ++) {
eletype[i] = (char*) malloc(2*sizeof(char));
- strcpy(eletype[i],arg[iarg+1+i]);
+ strcpy(eletype[i],arg[iarg+1+i]);
}
eleflag = 1;
iarg += ntypes + 1;
- // position of molecules
+ // position of molecules
} else if (strcmp(arg[iarg],"position") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix reax/c/species command");
posflag = 1;
posfreq = atoi(arg[iarg+1]);
if (posfreq < nfreq || (posfreq%nfreq != 0))
- error->all(FLERR,"Illegal fix reax/c/species command");
+ error->all(FLERR,"Illegal fix reax/c/species command");
filepos = new char[255];
strcpy(filepos,arg[iarg+2]);
@@ -221,8 +221,8 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) :
pos = fopen(filepos, "w");
if (pos == NULL) error->one(FLERR,"Cannot open fix reax/c/species position file");
}
- singlepos_opened = 1;
- multipos = 0;
+ singlepos_opened = 1;
+ multipos = 0;
}
iarg += 3;
} else error->all(FLERR,"Illegal fix reax/c/species command");
@@ -300,7 +300,7 @@ void FixReaxCSpecies::init()
reaxc = (PairReaxC *) force->pair_match("reax/c",0);
if (reaxc == NULL) error->all(FLERR,"Cannot use fix reax/c/species without "
- "pair_style reax/c, reax/c/kk, or reax/c/omp");
+ "pair_style reax/c, reax/c/kk, or reax/c/omp");
reaxc->fixspecies_flag = 1;
@@ -389,14 +389,14 @@ void FixReaxCSpecies::create_fix()
args[3] = tmparg[0];
args[4] = tmparg[1];
args[5] = tmparg[2];
- args[6] = (char *) "c_SPECATOM[1]"; // q, array_atoms[i][0]
- args[7] = (char *) "c_SPECATOM[2]"; // x, 1
- args[8] = (char *) "c_SPECATOM[3]"; // y, 2
- args[9] = (char *) "c_SPECATOM[4]"; // z, 3
- args[10] = (char *) "c_SPECATOM[5]"; // vx, 4
- args[11] = (char *) "c_SPECATOM[6]"; // vy, 5
- args[12] = (char *) "c_SPECATOM[7]"; // vz, 6
- args[13] = (char *) "c_SPECATOM[8]"; // abo01, 7
+ args[6] = (char *) "c_SPECATOM[1]"; // q, array_atoms[i][0]
+ args[7] = (char *) "c_SPECATOM[2]"; // x, 1
+ args[8] = (char *) "c_SPECATOM[3]"; // y, 2
+ args[9] = (char *) "c_SPECATOM[4]"; // z, 3
+ args[10] = (char *) "c_SPECATOM[5]"; // vx, 4
+ args[11] = (char *) "c_SPECATOM[6]"; // vy, 5
+ args[12] = (char *) "c_SPECATOM[7]"; // vz, 6
+ args[13] = (char *) "c_SPECATOM[8]"; // abo01, 7
args[14] = (char *) "c_SPECATOM[9]";
args[15] = (char *) "c_SPECATOM[10]";
args[16] = (char *) "c_SPECATOM[11]";
@@ -520,6 +520,8 @@ void FixReaxCSpecies::FindMolecule ()
int *ilist;
double bo_tmp,bo_cut;
double **spec_atom = f_SPECBOND->array_atom;
+ const double * const * const x = atom->x;
+ const int nlocal = atom->nlocal;
inum = reaxc->list->inum;
ilist = reaxc->list->ilist;
@@ -545,35 +547,47 @@ void FixReaxCSpecies::FindMolecule ()
done = 1;
for (ii = 0; ii < inum; ii++) {
- i = ilist[ii];
- if (!(mask[i] & groupbit)) continue;
+ i = ilist[ii];
+ if (!(mask[i] & groupbit)) continue;
- itype = atom->type[i];
+ itype = atom->type[i];
for (jj = 0; jj < MAXSPECBOND; jj++) {
- j = reaxc->tmpid[i][jj];
+ j = reaxc->tmpid[i][jj];
- if (j < i) continue;
- if (!(mask[j] & groupbit)) continue;
+ if ((j == 0) || (j < i)) continue;
+ if (!(mask[j] & groupbit)) continue;
- if (clusterID[i] == clusterID[j] && PBCconnected[i] == PBCconnected[j]
- && x0[i].x == x0[j].x && x0[i].y == x0[j].y && x0[i].z == x0[j].z) continue;
+ if (clusterID[i] == clusterID[j]
+ && PBCconnected[i] == PBCconnected[j]
+ && x0[i].x == x0[j].x
+ && x0[i].y == x0[j].y
+ && x0[i].z == x0[j].z) continue;
jtype = atom->type[j];
- bo_cut = BOCut[itype][jtype];
- bo_tmp = spec_atom[i][jj+7];
+ bo_cut = BOCut[itype][jtype];
+ bo_tmp = spec_atom[i][jj+7];
- if (bo_tmp > bo_cut) {
+ if (bo_tmp > bo_cut) {
clusterID[i] = clusterID[j] = MIN(clusterID[i], clusterID[j]);
PBCconnected[i] = PBCconnected[j] = MAX(PBCconnected[i], PBCconnected[j]);
x0[i] = x0[j] = chAnchor(x0[i], x0[j]);
- if ((fabs(spec_atom[i][1] - spec_atom[j][1]) > reaxc->control->bond_cut)
- || (fabs(spec_atom[i][2] - spec_atom[j][2]) > reaxc->control->bond_cut)
- || (fabs(spec_atom[i][3] - spec_atom[j][3]) > reaxc->control->bond_cut))
- PBCconnected[i] = PBCconnected[j] = 1;
- done = 0;
- }
- }
+ // spec_atom[][] contains filtered coordinates only for local atoms,
+ // so we have to use unfiltered ones for ghost atoms.
+ if (j < nlocal) {
+ if ((fabs(spec_atom[i][1] - spec_atom[j][1]) > reaxc->control->bond_cut)
+ || (fabs(spec_atom[i][2] - spec_atom[j][2]) > reaxc->control->bond_cut)
+ || (fabs(spec_atom[i][3] - spec_atom[j][3]) > reaxc->control->bond_cut))
+ PBCconnected[i] = PBCconnected[j] = 1;
+ } else {
+ if ((fabs(spec_atom[i][1] - x[j][1]) > reaxc->control->bond_cut)
+ || (fabs(spec_atom[i][2] - x[j][2]) > reaxc->control->bond_cut)
+ || (fabs(spec_atom[i][3] - x[j][3]) > reaxc->control->bond_cut))
+ PBCconnected[i] = PBCconnected[j] = 1;
+ }
+ done = 0;
+ }
+ }
}
if (!done) change = 1;
if (done) break;
@@ -609,13 +623,13 @@ void FixReaxCSpecies::SortMolecule(int &Nmole)
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall && me == 0)
error->warning(FLERR,"Atom with cluster ID = 0 included in "
- "fix reax/c/species group");
+ "fix reax/c/species group");
MPI_Allreduce(&lo,&idlo,1,MPI_INT,MPI_MIN,world);
MPI_Allreduce(&hi,&idhi,1,MPI_INT,MPI_MAX,world);
if (idlo == ntotal)
if (me == 0)
error->warning(FLERR,"Atom with cluster ID = maxmol "
- "included in fix reax/c/species group");
+ "included in fix reax/c/species group");
int nlen = idhi - idlo + 1;
memory->create(molmap,nlen,"reax/c/species:molmap");
@@ -795,7 +809,7 @@ void FixReaxCSpecies::OpenPos()
*ptr = '\0';
if (padflag == 0)
sprintf(filecurrent,"%s" BIGINT_FORMAT "%s",
- filepos,ntimestep,ptr+1);
+ filepos,ntimestep,ptr+1);
else {
char bif[8],pad[16];
strcpy(bif,BIGINT_FORMAT);
@@ -835,11 +849,11 @@ void FixReaxCSpecies::WritePos(int Nmole, int Nspec)
if (me == 0) {
fprintf(pos,"Timestep " BIGINT_FORMAT " NMole %d NSpec %d xlo %f "
- "xhi %f ylo %f yhi %f zlo %f zhi %f\n",
- update->ntimestep,Nmole, Nspec,
- domain->boxlo[0],domain->boxhi[0],
- domain->boxlo[1],domain->boxhi[1],
- domain->boxlo[2],domain->boxhi[2]);
+ "xhi %f ylo %f yhi %f zlo %f zhi %f\n",
+ update->ntimestep,Nmole, Nspec,
+ domain->boxlo[0],domain->boxhi[0],
+ domain->boxlo[1],domain->boxhi[1],
+ domain->boxlo[2],domain->boxhi[2]);
fprintf(pos,"ID\tAtom_Count\tType\tAve_q\t\tCoM_x\t\tCoM_y\t\tCoM_z\n");
}
@@ -862,21 +876,21 @@ void FixReaxCSpecies::WritePos(int Nmole, int Nspec)
if (cid == m) {
itype = atom->type[i]-1;
Name[itype] ++;
- count ++;
- avq += spec_atom[i][0];
+ count ++;
+ avq += spec_atom[i][0];
if (PBCconnected[i]) {
if ((x0[i].x - spec_atom[i][1]) > halfbox[0])
spec_atom[i][1] += box[0];
if ((spec_atom[i][1] - x0[i].x) > halfbox[0])
- spec_atom[i][1] -= box[0];
+ spec_atom[i][1] -= box[0];
if ((x0[i].y - spec_atom[i][2]) > halfbox[1])
- spec_atom[i][2] += box[1];
+ spec_atom[i][2] += box[1];
if ((spec_atom[i][2] - x0[i].y) > halfbox[1])
- spec_atom[i][2] -= box[1];
+ spec_atom[i][2] -= box[1];
if ((x0[i].z - spec_atom[i][3]) > halfbox[2])
spec_atom[i][3] += box[2];
if ((spec_atom[i][3] - x0[i].z) > halfbox[2])
- spec_atom[i][3] -= box[2];
+ spec_atom[i][3] -= box[2];
}
for (n = 0; n < 3; n++)
avx[n] += spec_atom[i][n+1];
@@ -911,17 +925,17 @@ void FixReaxCSpecies::WritePos(int Nmole, int Nspec)
if (count > 0) {
avq /= count;
for (k = 0; k < 3; k++) {
- avx[k] /= count;
+ avx[k] /= count;
if (avx[k] >= domain->boxhi[k])
avx[k] -= box[k];
if (avx[k] < domain->boxlo[k])
avx[k] += box[k];
- avx[k] -= domain->boxlo[k];
- avx[k] /= box[k];
+ avx[k] -= domain->boxlo[k];
+ avx[k] /= box[k];
}
fprintf(pos,"\t%.8f \t%.8f \t%.8f \t%.8f",
- avq,avx[0],avx[1],avx[2]);
+ avq,avx[0],avx[1],avx[2]);
}
fprintf(pos,"\n");
}