diff --git a/src/KOKKOS/fix_reaxc_species_kokkos.cpp b/src/KOKKOS/fix_reaxc_species_kokkos.cpp
index ce84de30cb2eaf83cf8230e916f82ef19754de33..8b778ecf650e582b53dd757e460e0e937e115f34 100644
--- a/src/KOKKOS/fix_reaxc_species_kokkos.cpp
+++ b/src/KOKKOS/fix_reaxc_species_kokkos.cpp
@@ -48,7 +48,7 @@ FixReaxCSpeciesKokkos::FixReaxCSpeciesKokkos(LAMMPS *lmp, int narg, char **arg)
{
kokkosable = 1;
atomKK = (AtomKokkos *) atom;
-
+
// NOTE: Could improve performance if a Kokkos version of ComputeSpecAtom is added
datamask_read = X_MASK | V_MASK | Q_MASK | MASK_MASK;
@@ -116,35 +116,30 @@ void FixReaxCSpeciesKokkos::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]
+ && 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;
- }
- }
+ done = 0;
+ }
+ }
}
if (!done) change = 1;
if (done) break;
diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp
index 23a37455e82ae5587ad6da4f43476a84aaf14b84..df28a34fe884bbe28a02f5c6058cccf53e521fbf 100644
--- a/src/USER-REAXC/fix_reaxc_species.cpp
+++ b/src/USER-REAXC/fix_reaxc_species.cpp
@@ -68,7 +68,7 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) :
nrepeat = atoi(arg[4]);
global_freq = nfreq = atoi(arg[5]);
- comm_forward = 5;
+ comm_forward = 4;
if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0)
error->all(FLERR,"Illegal fix reax/c/species command");
@@ -133,12 +133,10 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) :
}
x0 = NULL;
- PBCconnected = NULL;
clusterID = NULL;
int ntmp = 1;
memory->create(x0,ntmp,"reax/c/species:x0");
- memory->create(PBCconnected,ntmp,"reax/c/species:PBCconnected");
memory->create(clusterID,ntmp,"reax/c/species:clusterID");
vector_atom = clusterID;
@@ -251,7 +249,6 @@ FixReaxCSpecies::~FixReaxCSpecies()
memory->destroy(ele);
memory->destroy(BOCut);
memory->destroy(clusterID);
- memory->destroy(PBCconnected);
memory->destroy(x0);
memory->destroy(nd);
@@ -458,16 +455,13 @@ void FixReaxCSpecies::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
if (atom->nmax > nmax) {
nmax = atom->nmax;
memory->destroy(x0);
- memory->destroy(PBCconnected);
memory->destroy(clusterID);
memory->create(x0,nmax,"reax/c/species:x0");
- memory->create(PBCconnected,nmax,"reax/c/species:PBCconnected");
memory->create(clusterID,nmax,"reax/c/species:clusterID");
vector_atom = clusterID;
}
for (int i = 0; i < nmax; i++) {
- PBCconnected[i] = 0;
x0[i].x = x0[i].y = x0[i].z = 0.0;
}
@@ -559,7 +553,6 @@ void FixReaxCSpecies::FindMolecule ()
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;
@@ -570,21 +563,7 @@ void FixReaxCSpecies::FindMolecule ()
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]);
- // 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;
}
}
@@ -878,20 +857,18 @@ void FixReaxCSpecies::WritePos(int Nmole, int Nspec)
Name[itype] ++;
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];
- if ((x0[i].y - spec_atom[i][2]) > halfbox[1])
- spec_atom[i][2] += box[1];
- if ((spec_atom[i][2] - x0[i].y) > halfbox[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];
- }
+ 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];
+ if ((x0[i].y - spec_atom[i][2]) > halfbox[1])
+ spec_atom[i][2] += box[1];
+ if ((spec_atom[i][2] - x0[i].y) > halfbox[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];
for (n = 0; n < 3; n++)
avx[n] += spec_atom[i][n+1];
}
@@ -977,11 +954,10 @@ int FixReaxCSpecies::pack_forward_comm(int n, int *list, double *buf,
for (i = 0; i < n; i++) {
j = list[i];
buf[m] = clusterID[j];
- buf[m+1] = (double)PBCconnected[j];
- buf[m+2] = x0[j].x;
- buf[m+3] = x0[j].y;
- buf[m+4] = x0[j].z;
- m += 5;
+ buf[m+1] = x0[j].x;
+ buf[m+2] = x0[j].y;
+ buf[m+3] = x0[j].z;
+ m += 4;
}
return m;
}
@@ -996,11 +972,10 @@ void FixReaxCSpecies::unpack_forward_comm(int n, int first, double *buf)
last = first + n;
for (i = first; i < last; i++) {
clusterID[i] = buf[m];
- PBCconnected[i] = (int)buf[m+1];
- x0[i].x = buf[m+2];
- x0[i].y = buf[m+3];
- x0[i].z = buf[m+4];
- m += 5;
+ x0[i].x = buf[m+1];
+ x0[i].y = buf[m+2];
+ x0[i].z = buf[m+3];
+ m += 4;
}
}
@@ -1010,7 +985,7 @@ double FixReaxCSpecies::memory_usage()
{
double bytes;
- bytes = 5*nmax*sizeof(double); // clusterID + PBCconnected + x0
+ bytes = 4*nmax*sizeof(double); // clusterID + x0
return bytes;
}
diff --git a/src/USER-REAXC/fix_reaxc_species.h b/src/USER-REAXC/fix_reaxc_species.h
index 563a10f39db3913a49abbf97cb28b63975b64d51..23a470fd0ac63a37862bd032d51e953c261db3f9 100644
--- a/src/USER-REAXC/fix_reaxc_species.h
+++ b/src/USER-REAXC/fix_reaxc_species.h
@@ -52,7 +52,6 @@ class FixReaxCSpecies : public Fix {
int Nmoltype, vector_nmole, vector_nspec;
int *Name, *MolName, *NMol, *nd, *MolType, *molmap;
double *clusterID;
- int *PBCconnected;
AtomCoord *x0;
double bg_cut;