diff --git a/doc/src/pair_yukawa_colloid.txt b/doc/src/pair_yukawa_colloid.txt
index 3d5294bbdb524b668b4040e6d42e854ebc740ccd..ecdc1496ab734dcc8f59009de35a8990a6f09905 100644
--- a/doc/src/pair_yukawa_colloid.txt
+++ b/doc/src/pair_yukawa_colloid.txt
@@ -35,7 +35,7 @@ cutoff.
In contrast to "pair_style yukawa"_pair_yukawa.html, this functional
form arises from the Coulombic interaction between two colloid
particles, screened due to the presence of an electrolyte, see the
-book by "Safran"_#Safran for a derivation in the context of DVLO
+book by "Safran"_#Safran for a derivation in the context of DLVO
theory. "Pair_style yukawa"_pair_yukawa.html is a screened Coulombic
potential between two point-charges and uses no such approximation.
diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp
index 7e8db7632ccdc7f48448734b3170ec4cb9784fdd..c5b566eef785699559280eabe7bd0a681bef31a0 100644
--- a/src/QEQ/fix_qeq.cpp
+++ b/src/QEQ/fix_qeq.cpp
@@ -286,9 +286,6 @@ void FixQEq::setup_pre_force(int vflag)
if (force->newton_pair == 0)
error->all(FLERR,"QEQ with 'newton pair off' not supported");
- // should not be needed
- // neighbor->build_one(list);
-
deallocate_storage();
allocate_storage();
diff --git a/src/USER-DPD/nbin_ssa.cpp b/src/USER-DPD/nbin_ssa.cpp
index 73da5e0df3570945cb7a098500243da54f69fca6..f65a397e88d02e29fc81016733073dd8b0940db3 100644
--- a/src/USER-DPD/nbin_ssa.cpp
+++ b/src/USER-DPD/nbin_ssa.cpp
@@ -76,6 +76,7 @@ void NBinSSA::bin_atoms()
if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR
if (mask[i] & bitmask) {
ibin = coord2bin(x[i]);
+ atom2bin[i] = ibin;
bins_ssa[i] = gbinhead_ssa[ibin];
gbinhead_ssa[ibin] = i;
}
@@ -84,12 +85,14 @@ void NBinSSA::bin_atoms()
for (i = nall-1; i >= nlocal; i--) {
if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR
ibin = coord2bin(x[i]);
+ atom2bin[i] = ibin;
bins_ssa[i] = gbinhead_ssa[ibin];
gbinhead_ssa[ibin] = i;
}
}
for (i = nlocal-1; i >= 0; i--) {
ibin = coord2bin(x[i]);
+ atom2bin[i] = ibin;
bins_ssa[i] = binhead_ssa[ibin];
binhead_ssa[ibin] = i;
}
diff --git a/src/USER-DPD/npair_half_bin_newton_ssa.cpp b/src/USER-DPD/npair_half_bin_newton_ssa.cpp
index 59acbda301403c5e36e513b03a2df7e4608e90c2..e8e4b20a0ab64a5063de016f1cbeb1644c04e522 100644
--- a/src/USER-DPD/npair_half_bin_newton_ssa.cpp
+++ b/src/USER-DPD/npair_half_bin_newton_ssa.cpp
@@ -141,7 +141,7 @@ void NPairHalfBinNewtonSSA::build(NeighList *list)
}
}
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
// loop over all local atoms in other bins in "half" stencil
diff --git a/src/USER-OMP/npair_full_bin_ghost_omp.cpp b/src/USER-OMP/npair_full_bin_ghost_omp.cpp
index 7f7239fe63c9adbc76214e44f5c8f67d251d1b73..b915aca002a68ee7893aa18269a8128349b97a89 100644
--- a/src/USER-OMP/npair_full_bin_ghost_omp.cpp
+++ b/src/USER-OMP/npair_full_bin_ghost_omp.cpp
@@ -97,7 +97,7 @@ void NPairFullBinGhostOmp::build(NeighList *list)
// no molecular test when i = ghost atom
if (i < nlocal) {
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (i == j) continue;
diff --git a/src/USER-OMP/npair_full_bin_omp.cpp b/src/USER-OMP/npair_full_bin_omp.cpp
index ad9e48784ed2a8cbf1d7198676d3fd9c45750e34..e1f75c06e2a8f36d245cfa7b6589b2628eb6a159 100644
--- a/src/USER-OMP/npair_full_bin_omp.cpp
+++ b/src/USER-OMP/npair_full_bin_omp.cpp
@@ -90,7 +90,7 @@ void NPairFullBinOmp::build(NeighList *list)
// loop over all atoms in surrounding bins in stencil including self
// skip i = j
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
diff --git a/src/USER-OMP/npair_full_multi_omp.cpp b/src/USER-OMP/npair_full_multi_omp.cpp
index eb0153d63f7e7577df1530e48c61dde05f18a280..9bc196e17a1a39cda046bd1fe6b7327c64dd345c 100644
--- a/src/USER-OMP/npair_full_multi_omp.cpp
+++ b/src/USER-OMP/npair_full_multi_omp.cpp
@@ -94,7 +94,7 @@ void NPairFullMultiOmp::build(NeighList *list)
// skip if i,j neighbor cutoff is less than bin distance
// skip i = j
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
cutsq = cutneighsq[itype];
diff --git a/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp b/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp
index e46afebb0d8f6fe285bfc104a44933e8b639b53c..05763c3d689bd37f947c7556d5ef3d53ba69945a 100644
--- a/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp
+++ b/src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp
@@ -103,7 +103,7 @@ void NPairHalfBinNewtoffGhostOmp::build(NeighList *list)
// no molecular test when i = ghost atom
if (i < nlocal) {
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
diff --git a/src/USER-OMP/npair_half_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_bin_newtoff_omp.cpp
index 99698b1d30c7380b511cb973e2a4dff2d1f1eee8..ff74b54d7d68dd258fc6be84b9b3e4c35852ad53 100644
--- a/src/USER-OMP/npair_half_bin_newtoff_omp.cpp
+++ b/src/USER-OMP/npair_half_bin_newtoff_omp.cpp
@@ -94,7 +94,7 @@ void NPairHalfBinNewtoffOmp::build(NeighList *list)
// stores own/own pairs only once
// stores own/ghost pairs on both procs
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
diff --git a/src/USER-OMP/npair_half_bin_newton_omp.cpp b/src/USER-OMP/npair_half_bin_newton_omp.cpp
index 33d78fe55a61bbc96960fba41aa363ff19688dde..f7d969ba271a110edf8b83a631a48394ddb0ea63 100644
--- a/src/USER-OMP/npair_half_bin_newton_omp.cpp
+++ b/src/USER-OMP/npair_half_bin_newton_omp.cpp
@@ -130,7 +130,7 @@ void NPairHalfBinNewtonOmp::build(NeighList *list)
// loop over all atoms in other bins in stencil, store every pair
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
jtype = type[j];
diff --git a/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp b/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp
index 9eb96122351ec234a026c03d5d79403862662791..c843d623cd44960b8f8ebaaf68142f8896e10acb 100644
--- a/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp
+++ b/src/USER-OMP/npair_half_bin_newton_tri_omp.cpp
@@ -94,7 +94,7 @@ void NPairHalfBinNewtonTriOmp::build(NeighList *list)
// (equal zyx and j <= i)
// latter excludes self-self interaction but allows superposed atoms
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (x[j][2] < ztmp) continue;
diff --git a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp
index 37dc8058573947777affac3003dde019ea5f5f92..705d1b8d9ff1ec53e44c240f6a9ab02b647f2f25 100644
--- a/src/USER-OMP/npair_half_multi_newtoff_omp.cpp
+++ b/src/USER-OMP/npair_half_multi_newtoff_omp.cpp
@@ -97,7 +97,7 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list)
// stores own/own pairs only once
// stores own/ghost pairs on both procs
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
cutsq = cutneighsq[itype];
diff --git a/src/USER-OMP/npair_half_multi_newton_omp.cpp b/src/USER-OMP/npair_half_multi_newton_omp.cpp
index 9719911afa6b575056b3159cef517408b0ed5953..f16dd027a0c26552494726af0b8e53730beffeb9 100644
--- a/src/USER-OMP/npair_half_multi_newton_omp.cpp
+++ b/src/USER-OMP/npair_half_multi_newton_omp.cpp
@@ -131,7 +131,7 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list)
// loop over all atoms in other bins in stencil, store every pair
// skip if i,j neighbor cutoff is less than bin distance
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
cutsq = cutneighsq[itype];
diff --git a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp
index 717a709386e800b2fbb653975f4137ffdcd735e7..f66cf194e75342add192bcbd984930f0f301efb7 100644
--- a/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp
+++ b/src/USER-OMP/npair_half_multi_newton_tri_omp.cpp
@@ -99,7 +99,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list)
// (equal zyx and j <= i)
// latter excludes self-self interaction but allows superposed atoms
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
cutsq = cutneighsq[itype];
diff --git a/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp
index 287f11efa71107572a07cace735c0efe0d582f5d..12780fa4a371171810a4d548da341087fd5574a7 100644
--- a/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp
+++ b/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp
@@ -117,7 +117,7 @@ void NPairHalfRespaBinNewtoffOmp::build(NeighList *list)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
diff --git a/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp b/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp
index 30256bd20da24336006c689604c27a2315029d34..b9a636424262a52df2f61149e0e26b8f3dcb7298 100644
--- a/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp
+++ b/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp
@@ -176,7 +176,7 @@ void NPairHalfRespaBinNewtonOmp::build(NeighList *list)
// loop over all atoms in other bins in stencil, store every pair
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
jtype = type[j];
diff --git a/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp b/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp
index 27d02000c5b242ab2f84e3590c55c4ae7cc06115..bc03972d859a4101f1cbcb33ec8a8de7491ea541 100644
--- a/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp
+++ b/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp
@@ -128,7 +128,7 @@ void NPairHalfRespaBinNewtonTriOmp::build(NeighList *list)
// (equal zyx and j <= i)
// latter excludes self-self interaction but allows superposed atoms
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (x[j][2] < ztmp) continue;
diff --git a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
index 699d347db5cbae91b1fa45c4bbde6b33e08d7d73..dbb62e96efc9a2f3d800fe0585fd845cd473401b 100644
--- a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
+++ b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
@@ -113,7 +113,7 @@ void NPairHalfSizeBinNewtoffOmp::build(NeighList *list)
ytmp = x[i][1];
ztmp = x[i][2];
radi = radius[i];
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
// loop over all atoms in surrounding bins in stencil including self
// only store pair if i < j
diff --git a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp
index 0d7e4e68da6ed863eca0f4a41005de8399b478e8..2c26c7952cda571d4133281246bb781891f9b7f4 100644
--- a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp
+++ b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp
@@ -168,7 +168,7 @@ void NPairHalfSizeBinNewtonOmp::build(NeighList *list)
// loop over all atoms in other bins in stencil, store every pair
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
diff --git a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp b/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp
index 7463a6aba6085753b9ba23b30b60cc9c12bbf5fa..bf273f545f425b7b7bd6d660daf8f2c484c74222 100644
--- a/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp
+++ b/src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp
@@ -84,7 +84,7 @@ void NPairHalfSizeBinNewtonTriOmp::build(NeighList *list)
// (equal zyx and j <= i)
// latter excludes self-self interaction but allows superposed atoms
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (x[j][2] < ztmp) continue;
diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp
index 01ecd9d3994fce173ac4dbf9ca6b619314c62b3a..96df03c668a260ce63b87221bd63bac42b88a12c 100644
--- a/src/USER-REAXC/fix_qeq_reax.cpp
+++ b/src/USER-REAXC/fix_qeq_reax.cpp
@@ -416,9 +416,6 @@ void FixQEqReax::init_taper()
void FixQEqReax::setup_pre_force(int vflag)
{
- // should not be needed
- // neighbor->build_one(list);
-
deallocate_storage();
allocate_storage();
diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp
index 672b1e6a568c799218dcbfa705e2bf0d859b3f98..fe74337128088654e3b4e9aa0e265d63504b4c90 100644
--- a/src/USER-REAXC/fix_reaxc_species.cpp
+++ b/src/USER-REAXC/fix_reaxc_species.cpp
@@ -500,7 +500,7 @@ void FixReaxCSpecies::Output_ReaxC_Bonds(bigint ntimestep, FILE *fp)
AtomCoord FixReaxCSpecies::chAnchor(AtomCoord in1, AtomCoord in2)
{
- if (in1.x < in2.x)
+ if (in1.x <= in2.x)
return in1;
return in2;
}
diff --git a/src/nbin.cpp b/src/nbin.cpp
index 6aa37a4c43c6a5382cb398d3a80e18d1b090699d..6bd1ce322f6f93d93a80c50058d598f8abccfcc9 100644
--- a/src/nbin.cpp
+++ b/src/nbin.cpp
@@ -29,6 +29,7 @@ NBin::NBin(LAMMPS *lmp) : Pointers(lmp)
maxbin = maxatom = 0;
binhead = NULL;
bins = NULL;
+ atom2bin = NULL;
// geometry settings
@@ -42,6 +43,7 @@ NBin::~NBin()
{
memory->destroy(binhead);
memory->destroy(bins);
+ memory->destroy(atom2bin);
}
/* ---------------------------------------------------------------------- */
@@ -87,12 +89,15 @@ void NBin::bin_atoms_setup(int nall)
memory->create(binhead,maxbin,"neigh:binhead");
}
- // bins = per-atom vector
+ // bins and atom2bin = per-atom vectors
+ // for both local and ghost atoms
if (nall > maxatom) {
maxatom = nall;
memory->destroy(bins);
memory->create(bins,maxatom,"neigh:bins");
+ memory->destroy(atom2bin);
+ memory->create(atom2bin,maxatom,"neigh:atom2bin");
}
}
@@ -148,6 +153,6 @@ bigint NBin::memory_usage()
{
bigint bytes = 0;
bytes += maxbin*sizeof(int);
- bytes += maxatom*sizeof(int);
+ bytes += 2*maxatom*sizeof(int);
return bytes;
}
diff --git a/src/nbin.h b/src/nbin.h
index 9871a229d8542aef87caa8718e64ee758f7ff560..30c74ff29558e0d8dca424b52ece331211d126fb 100644
--- a/src/nbin.h
+++ b/src/nbin.h
@@ -31,10 +31,11 @@ class NBin : protected Pointers {
double binsizex,binsizey,binsizez; // bin sizes and inverse sizes
double bininvx,bininvy,bininvz;
- int *binhead; // index of first atom in each bin
- int *bins; // index of next atom in same bin
+ int *binhead; // index of first atom in each bin
+ int *bins; // index of next atom in same bin
+ int *atom2bin; // bin assignment for each atom (local+ghost)
- double cutoff_custom; // cutoff set by requestor
+ double cutoff_custom; // cutoff set by requestor
NBin(class LAMMPS *);
~NBin();
diff --git a/src/nbin_standard.cpp b/src/nbin_standard.cpp
index 2a72d996a51128082e27f1ac280d84a6853f2321..e6941014f9f60e441bc99831656465f2bb2d7a0e 100644
--- a/src/nbin_standard.cpp
+++ b/src/nbin_standard.cpp
@@ -211,12 +211,14 @@ void NBinStandard::bin_atoms()
for (i = nall-1; i >= nlocal; i--) {
if (mask[i] & bitmask) {
ibin = coord2bin(x[i]);
+ atom2bin[i] = ibin;
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
}
for (i = atom->nfirst-1; i >= 0; i--) {
ibin = coord2bin(x[i]);
+ atom2bin[i] = ibin;
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
@@ -224,6 +226,7 @@ void NBinStandard::bin_atoms()
} else {
for (i = nall-1; i >= 0; i--) {
ibin = coord2bin(x[i]);
+ atom2bin[i] = ibin;
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
diff --git a/src/neigh_request.cpp b/src/neigh_request.cpp
index 5e77c230773ab13b1b2ecc5c03055e3781dc795e..bb691d00baa8072d97f3d3bbcdbd92ec682864cc 100644
--- a/src/neigh_request.cpp
+++ b/src/neigh_request.cpp
@@ -50,6 +50,7 @@ NeighRequest::NeighRequest(LAMMPS *lmp) : Pointers(lmp)
// default is no Intel-specific neighbor list build
// default is no Kokkos neighbor list build
// default is no Shardlow Splitting Algorithm (SSA) neighbor list build
+ // default is no list-specific cutoff
// default is no storage of auxiliary floating point values
occasional = 0;
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index 545c8cf027c7a09d42feab261f9271db2cb7e246..62a9143226333455a55d1c61928a53d44d03dd8a 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -640,6 +640,24 @@ int Neighbor::init_pair()
delete [] neigh_stencil;
delete [] neigh_pair;
+ // error check on requests
+ // do not allow occasional, ghost, bin list
+ // b/c it still uses variant of coord2bin() in NPair() method
+ // instead of atom2bin, this could cause error b/c stoms have
+ // moved out of proc domain by time occasional list is built
+ // solution would be to use a different NBin variant
+ // that used Npair::coord2bin(x,ix,iy,iz) (then delete it from NPair)
+ // and stored the ix,iy,iz values for all atoms (including ghosts)
+ // at time of binning when neighbor lists are rebuilt,
+ // similar to what vanilla Nbin::coord2atom() does now in atom2bin
+
+ if (style == BIN) {
+ for (i = 0; i < nrequest; i++)
+ if (requests[i]->occasional && requests[i]->ghost)
+ error->all(FLERR,"Cannot request an occasional binned neighbor list "
+ "with ghost info");
+ }
+
// morph requests in various ways
// purpose is to avoid duplicate or inefficient builds
// may add new requests if a needed request to derive from does not exist
@@ -1669,7 +1687,6 @@ int Neighbor::choose_stencil(NeighRequest *rq)
else if (rq->newton == 1) newtflag = 1;
else if (rq->newton == 2) newtflag = 0;
-
//printf("STENCIL RQ FLAGS: hff %d %d n %d g %d s %d newtflag %d\n",
// rq->half,rq->full,rq->newton,rq->ghost,rq->ssa,
// newtflag);
@@ -2087,7 +2104,7 @@ void Neighbor::build(int topoflag)
}
// bin atoms for all NBin instances
- // not just NBin associated with perpetual lists
+ // not just NBin associated with perpetual lists, also occasional lists
// b/c cannot wait to bin occasional lists in build_one() call
// if bin then, atoms may have moved outside of proc domain & bin extent,
// leading to errors or even a crash
@@ -2193,6 +2210,7 @@ void Neighbor::build_one(class NeighList *mylist, int preflag)
// build the list
+ if (!mylist->copy) mylist->grow(atom->nlocal,atom->nlocal+atom->nghost);
np->build_setup();
np->build(mylist);
}
diff --git a/src/npair.cpp b/src/npair.cpp
index 6c3f8ac05e3545ca61b6087c64fa0dbb9a86b1ee..3451cd6eae4dcbdc5fcd442eeadad919f287d550 100644
--- a/src/npair.cpp
+++ b/src/npair.cpp
@@ -128,6 +128,7 @@ void NPair::copy_bin_info()
bininvy = nb->bininvy;
bininvz = nb->bininvz;
+ atom2bin = nb->atom2bin;
bins = nb->bins;
binhead = nb->binhead;
}
@@ -198,53 +199,8 @@ int NPair::exclusion(int i, int j, int itype, int jtype,
}
/* ----------------------------------------------------------------------
- convert atom coords into local bin #
- for orthogonal, only ghost atoms will have coord >= bboxhi or coord < bboxlo
- take special care to insure ghosts are in correct bins even w/ roundoff
- hi ghost atoms = nbin,nbin+1,etc
- owned atoms = 0 to nbin-1
- lo ghost atoms = -1,-2,etc
- this is necessary so that both procs on either side of PBC
- treat a pair of atoms straddling the PBC in a consistent way
- for triclinic, doesn't matter since stencil & neigh list built differently
-------------------------------------------------------------------------- */
-
-int NPair::coord2bin(double *x)
-{
- int ix,iy,iz;
-
- if (!ISFINITE(x[0]) || !ISFINITE(x[1]) || !ISFINITE(x[2]))
- error->one(FLERR,"Non-numeric positions - simulation unstable");
-
- if (x[0] >= bboxhi[0])
- ix = static_cast<int> ((x[0]-bboxhi[0])*bininvx) + nbinx;
- else if (x[0] >= bboxlo[0]) {
- ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx);
- ix = MIN(ix,nbinx-1);
- } else
- ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx) - 1;
-
- if (x[1] >= bboxhi[1])
- iy = static_cast<int> ((x[1]-bboxhi[1])*bininvy) + nbiny;
- else if (x[1] >= bboxlo[1]) {
- iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy);
- iy = MIN(iy,nbiny-1);
- } else
- iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy) - 1;
-
- if (x[2] >= bboxhi[2])
- iz = static_cast<int> ((x[2]-bboxhi[2])*bininvz) + nbinz;
- else if (x[2] >= bboxlo[2]) {
- iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz);
- iz = MIN(iz,nbinz-1);
- } else
- iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz) - 1;
-
- return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo);
-}
-
-/* ----------------------------------------------------------------------
- same as coord2bin, but also return ix,iy,iz offsets in each dim
+ same as coord2bin in Nbin, but also return ix,iy,iz offsets in each dim
+ used by some of the ghost neighbor lists
------------------------------------------------------------------------- */
int NPair::coord2bin(double *x, int &ix, int &iy, int &iz)
diff --git a/src/npair.h b/src/npair.h
index 8f2bcb13bc8d26f7fbb15f317b4bee7ec78e648f..4e5e3f5dfd38619db6a76c3f84e230019dfb9d12 100644
--- a/src/npair.h
+++ b/src/npair.h
@@ -77,7 +77,7 @@ class NPair : protected Pointers {
int mbinx,mbiny,mbinz;
int mbinxlo,mbinylo,mbinzlo;
double bininvx,bininvy,bininvz;
- int *bins;
+ int *atom2bin,*bins;
int *binhead;
// data from NStencil class
diff --git a/src/npair_full_bin.cpp b/src/npair_full_bin.cpp
index a29acb67abeb1382860744b8c759e11aa113cc6f..94a6af129cbed7b448d0bab554f6fd433a9483bc 100644
--- a/src/npair_full_bin.cpp
+++ b/src/npair_full_bin.cpp
@@ -80,7 +80,7 @@ void NPairFullBin::build(NeighList *list)
// loop over all atoms in surrounding bins in stencil including self
// skip i = j
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
diff --git a/src/npair_full_bin_atomonly.cpp b/src/npair_full_bin_atomonly.cpp
index 8d4fc254b525410171dd0ab05660832fdbdad747..db84733f1c584201d8d15c6e0bb01cd0bb8111ee 100644
--- a/src/npair_full_bin_atomonly.cpp
+++ b/src/npair_full_bin_atomonly.cpp
@@ -64,7 +64,7 @@ void NPairFullBinAtomonly::build(NeighList *list)
// loop over all atoms in surrounding bins in stencil including self
// skip i = j
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
diff --git a/src/npair_full_bin_ghost.cpp b/src/npair_full_bin_ghost.cpp
index 1e258cf5181a49c5c4588d10197fb725377527b1..2edd03cc9e5a48fa91c985613213d1e5f05f8674 100644
--- a/src/npair_full_bin_ghost.cpp
+++ b/src/npair_full_bin_ghost.cpp
@@ -87,7 +87,7 @@ void NPairFullBinGhost::build(NeighList *list)
// no molecular test when i = ghost atom
if (i < nlocal) {
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (i == j) continue;
diff --git a/src/npair_full_multi.cpp b/src/npair_full_multi.cpp
index 628a706e7aa16a3fbd890044248fd5b4bfe426b2..9a2490ac5d18acb07375675da9b4b1e795053abd 100644
--- a/src/npair_full_multi.cpp
+++ b/src/npair_full_multi.cpp
@@ -83,7 +83,7 @@ void NPairFullMulti::build(NeighList *list)
// skip if i,j neighbor cutoff is less than bin distance
// skip i = j
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
cutsq = cutneighsq[itype];
diff --git a/src/npair_half_bin_atomonly_newton.cpp b/src/npair_half_bin_atomonly_newton.cpp
index bc425cd22ee5459d2464bf105744e9293dd819b2..6bbef0700a36e681d444217d447c2fc421133952 100644
--- a/src/npair_half_bin_atomonly_newton.cpp
+++ b/src/npair_half_bin_atomonly_newton.cpp
@@ -90,7 +90,8 @@ void NPairHalfBinAtomonlyNewton::build(NeighList *list)
// loop over all atoms in other bins in stencil, store every pair
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
+
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
jtype = type[j];
diff --git a/src/npair_half_bin_newtoff.cpp b/src/npair_half_bin_newtoff.cpp
index dd072508a9483b93c66833e78afe545f4b8d898b..4c44741ffed9a19ab258223b7f2d2ea6c5b652b3 100644
--- a/src/npair_half_bin_newtoff.cpp
+++ b/src/npair_half_bin_newtoff.cpp
@@ -84,7 +84,7 @@ void NPairHalfBinNewtoff::build(NeighList *list)
// stores own/own pairs only once
// stores own/ghost pairs on both procs
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
diff --git a/src/npair_half_bin_newtoff_ghost.cpp b/src/npair_half_bin_newtoff_ghost.cpp
index f486df105a7a12fdf55ef9686c58369ba668751c..72ec15e66a733424d918250f8e52553f5f257be1 100644
--- a/src/npair_half_bin_newtoff_ghost.cpp
+++ b/src/npair_half_bin_newtoff_ghost.cpp
@@ -92,7 +92,7 @@ void NPairHalfBinNewtoffGhost::build(NeighList *list)
// no molecular test when i = ghost atom
if (i < nlocal) {
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
diff --git a/src/npair_half_bin_newton.cpp b/src/npair_half_bin_newton.cpp
index f1fc203403380147a6237299cc933a186a1a48e7..3a387870e3c48c8104813a5eae8576744c58ff2c 100644
--- a/src/npair_half_bin_newton.cpp
+++ b/src/npair_half_bin_newton.cpp
@@ -119,7 +119,7 @@ void NPairHalfBinNewton::build(NeighList *list)
// loop over all atoms in other bins in stencil, store every pair
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
jtype = type[j];
diff --git a/src/npair_half_bin_newton_tri.cpp b/src/npair_half_bin_newton_tri.cpp
index 3ef8c3260e154dab0fe6d06fab1cc2f6772350c0..169e710e0e5e18779d88aa4e039619c620351e1c 100644
--- a/src/npair_half_bin_newton_tri.cpp
+++ b/src/npair_half_bin_newton_tri.cpp
@@ -84,7 +84,7 @@ void NPairHalfBinNewtonTri::build(NeighList *list)
// (equal zyx and j <= i)
// latter excludes self-self interaction but allows superposed atoms
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (x[j][2] < ztmp) continue;
diff --git a/src/npair_half_multi_newtoff.cpp b/src/npair_half_multi_newtoff.cpp
index 11e45d91ffc093f85200eb9579f48f3decbc7d09..07b5c87a6cfb85b6c399597fdac9da27e3ff800b 100644
--- a/src/npair_half_multi_newtoff.cpp
+++ b/src/npair_half_multi_newtoff.cpp
@@ -87,7 +87,7 @@ void NPairHalfMultiNewtoff::build(NeighList *list)
// stores own/own pairs only once
// stores own/ghost pairs on both procs
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
cutsq = cutneighsq[itype];
diff --git a/src/npair_half_multi_newton.cpp b/src/npair_half_multi_newton.cpp
index cd3a37821f366c0b58f3567ed0b9826a55b0eba9..3d909793291cae7fedab4eed4420fa09a0c11242 100644
--- a/src/npair_half_multi_newton.cpp
+++ b/src/npair_half_multi_newton.cpp
@@ -121,7 +121,7 @@ void NPairHalfMultiNewton::build(NeighList *list)
// loop over all atoms in other bins in stencil, store every pair
// skip if i,j neighbor cutoff is less than bin distance
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
cutsq = cutneighsq[itype];
diff --git a/src/npair_half_multi_newton_tri.cpp b/src/npair_half_multi_newton_tri.cpp
index f9aaeb0414ec7d3ddd07dcced0ecfd49c34a83fa..909c69246b7e9c481ce97576400cbd7481d9f6aa 100644
--- a/src/npair_half_multi_newton_tri.cpp
+++ b/src/npair_half_multi_newton_tri.cpp
@@ -88,7 +88,7 @@ void NPairHalfMultiNewtonTri::build(NeighList *list)
// (equal zyx and j <= i)
// latter excludes self-self interaction but allows superposed atoms
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
cutsq = cutneighsq[itype];
diff --git a/src/npair_half_respa_bin_newtoff.cpp b/src/npair_half_respa_bin_newtoff.cpp
index 39f68a289dd49eb577465835de06d2dc73b6e7cc..11246b4af8746f7b008e8872cebcd64cc71a66bd 100644
--- a/src/npair_half_respa_bin_newtoff.cpp
+++ b/src/npair_half_respa_bin_newtoff.cpp
@@ -101,7 +101,7 @@ void NPairHalfRespaBinNewtoff::build(NeighList *list)
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
diff --git a/src/npair_half_respa_bin_newton.cpp b/src/npair_half_respa_bin_newton.cpp
index 537a72d0c1a2dcef8265414ab61a4eb4c57a933f..db766780360b2fc382eec5a87e9a1c8d5722da9d 100644
--- a/src/npair_half_respa_bin_newton.cpp
+++ b/src/npair_half_respa_bin_newton.cpp
@@ -160,7 +160,7 @@ void NPairHalfRespaBinNewton::build(NeighList *list)
// loop over all atoms in other bins in stencil, store every pair
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
jtype = type[j];
diff --git a/src/npair_half_respa_bin_newton_tri.cpp b/src/npair_half_respa_bin_newton_tri.cpp
index 9c5fd39fbe85e4aa07cb8fd50374374e88dcadaf..38621224c49df568fb7ed6b44a8c69ab7e2a6e1b 100644
--- a/src/npair_half_respa_bin_newton_tri.cpp
+++ b/src/npair_half_respa_bin_newton_tri.cpp
@@ -113,7 +113,7 @@ void NPairHalfRespaBinNewtonTri::build(NeighList *list)
// (equal zyx and j <= i)
// latter excludes self-self interaction but allows superposed atoms
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (x[j][2] < ztmp) continue;
diff --git a/src/npair_half_size_bin_newtoff.cpp b/src/npair_half_size_bin_newtoff.cpp
index e98923cd1160e1fe5619cd2ae90aaf7b29cb5afa..571b2484ea425aee53439974d08eb974d0cf2604 100644
--- a/src/npair_half_size_bin_newtoff.cpp
+++ b/src/npair_half_size_bin_newtoff.cpp
@@ -105,7 +105,7 @@ void NPairHalfSizeBinNewtoff::build(NeighList *list)
ytmp = x[i][1];
ztmp = x[i][2];
radi = radius[i];
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
// loop over all atoms in surrounding bins in stencil including self
// only store pair if i < j
diff --git a/src/npair_half_size_bin_newton.cpp b/src/npair_half_size_bin_newton.cpp
index 2cd0943ac2c287f47ca3018c78ed5798466d501e..a8be3ce691092d7843e03a1147afc9a8ccc79836 100644
--- a/src/npair_half_size_bin_newton.cpp
+++ b/src/npair_half_size_bin_newton.cpp
@@ -156,7 +156,7 @@ void NPairHalfSizeBinNewton::build(NeighList *list)
// loop over all atoms in other bins in stencil, store every pair
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
diff --git a/src/npair_half_size_bin_newton_tri.cpp b/src/npair_half_size_bin_newton_tri.cpp
index 054487d31f271ed1532beee2bbdaccf01633a3f8..1107f73026240fb75ac1bd1b1d79e239b3ee279d 100644
--- a/src/npair_half_size_bin_newton_tri.cpp
+++ b/src/npair_half_size_bin_newton_tri.cpp
@@ -112,7 +112,7 @@ void NPairHalfSizeBinNewtonTri::build(NeighList *list)
// (equal zyx and j <= i)
// latter excludes self-self interaction but allows superposed atoms
- ibin = coord2bin(x[i]);
+ ibin = atom2bin[i];
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (x[j][2] < ztmp) continue;