From 9864ead23145217a2228883ca6b207ee2fb5f1c0 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Fri, 15 Feb 2008 19:06:53 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1515
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/ASPHERE/compute_temp_asphere.cpp | 1 +
src/ASPHERE/fix_npt_asphere.cpp | 2 +
src/ASPHERE/fix_nve_asphere.cpp | 4 +-
src/ASPHERE/fix_nvt_asphere.cpp | 2 +
src/DIPOLE/fix_nve_dipole.cpp | 2 +
src/GRANULAR/fix_freeze.cpp | 1 +
src/GRANULAR/fix_nve_gran.cpp | 2 +
src/atom.cpp | 50 ++++++++++++++++++++
src/atom.h | 6 +++
src/comm.cpp | 71 +++++++++++++++++-----------
src/comm.h | 2 +-
src/fix_enforce2d.cpp | 1 +
src/fix_npt.cpp | 4 ++
src/fix_nve.cpp | 2 +
src/fix_nve_limit.cpp | 2 +
src/fix_nve_noforce.cpp | 1 +
src/fix_nvt.cpp | 4 ++
src/fix_nvt_sllod.cpp | 3 ++
src/neigh_derive.cpp | 2 +-
src/neigh_full.cpp | 20 ++++----
src/neigh_gran.cpp | 28 +++++++----
src/neigh_half_bin.cpp | 12 ++---
src/neigh_half_multi.cpp | 12 ++---
src/neigh_half_nsq.cpp | 22 ++++++---
src/neigh_respa.cpp | 34 ++++++++-----
src/neighbor.cpp | 50 ++++++++++----------
src/neighbor.h | 3 +-
27 files changed, 238 insertions(+), 105 deletions(-)
diff --git a/src/ASPHERE/compute_temp_asphere.cpp b/src/ASPHERE/compute_temp_asphere.cpp
index 7ce242e15a..29cfaa5528 100755
--- a/src/ASPHERE/compute_temp_asphere.cpp
+++ b/src/ASPHERE/compute_temp_asphere.cpp
@@ -88,6 +88,7 @@ void ComputeTempAsphere::recount()
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
int itype;
int rot_dof = 0;
diff --git a/src/ASPHERE/fix_npt_asphere.cpp b/src/ASPHERE/fix_npt_asphere.cpp
index 16cc8b7071..f8d66e21ff 100755
--- a/src/ASPHERE/fix_npt_asphere.cpp
+++ b/src/ASPHERE/fix_npt_asphere.cpp
@@ -91,6 +91,7 @@ void FixNPTASphere::initial_integrate(int vflag)
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double dtfm;
for (i = 0; i < nlocal; i++) {
@@ -156,6 +157,7 @@ void FixNPTASphere::final_integrate()
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double dtfm;
for (i = 0; i < nlocal; i++) {
diff --git a/src/ASPHERE/fix_nve_asphere.cpp b/src/ASPHERE/fix_nve_asphere.cpp
index 19c1b6f681..5286913229 100755
--- a/src/ASPHERE/fix_nve_asphere.cpp
+++ b/src/ASPHERE/fix_nve_asphere.cpp
@@ -76,6 +76,7 @@ void FixNVEASphere::initial_integrate(int vflag)
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
@@ -113,7 +114,8 @@ void FixNVEASphere::final_integrate()
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
-
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
diff --git a/src/ASPHERE/fix_nvt_asphere.cpp b/src/ASPHERE/fix_nvt_asphere.cpp
index f4a9bb2b8f..440dcadf28 100755
--- a/src/ASPHERE/fix_nvt_asphere.cpp
+++ b/src/ASPHERE/fix_nvt_asphere.cpp
@@ -73,6 +73,7 @@ void FixNVTASphere::initial_integrate(int vflag)
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
@@ -115,6 +116,7 @@ void FixNVTASphere::final_integrate()
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
diff --git a/src/DIPOLE/fix_nve_dipole.cpp b/src/DIPOLE/fix_nve_dipole.cpp
index f9b847aaed..7015dce4c9 100644
--- a/src/DIPOLE/fix_nve_dipole.cpp
+++ b/src/DIPOLE/fix_nve_dipole.cpp
@@ -95,6 +95,7 @@ void FixNVEDipole::initial_integrate(int vflag)
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double g[3];
@@ -148,6 +149,7 @@ void FixNVEDipole::final_integrate()
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
// update v for all particles
// update omega for all dipoles
diff --git a/src/GRANULAR/fix_freeze.cpp b/src/GRANULAR/fix_freeze.cpp
index 67e3d1dbd8..d839d975b2 100644
--- a/src/GRANULAR/fix_freeze.cpp
+++ b/src/GRANULAR/fix_freeze.cpp
@@ -68,6 +68,7 @@ void FixFreeze::post_force(int vflag)
double **torque = atom->torque;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
diff --git a/src/GRANULAR/fix_nve_gran.cpp b/src/GRANULAR/fix_nve_gran.cpp
index 7b52b633e6..c196c0befb 100644
--- a/src/GRANULAR/fix_nve_gran.cpp
+++ b/src/GRANULAR/fix_nve_gran.cpp
@@ -75,6 +75,7 @@ void FixNVEGran::initial_integrate(int vflag)
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
@@ -111,6 +112,7 @@ void FixNVEGran::final_integrate()
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
diff --git a/src/atom.cpp b/src/atom.cpp
index 14d1d1e740..d706e958a8 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -52,6 +52,8 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
nbonds = nangles = ndihedrals = nimpropers = 0;
bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
+ firstgroupname = NULL;
+
// initialize atom arrays
// customize by adding new array
@@ -136,6 +138,7 @@ Atom::~Atom()
{
delete [] atom_style;
delete avec;
+ delete [] firstgroupname;
// delete atom arrays
// customize by adding new array
@@ -273,6 +276,14 @@ void Atom::init()
check_shape();
check_dipole();
+ // setup of firstgroup
+
+ if (firstgroupname) {
+ firstgroup = group->find(firstgroupname);
+ if (firstgroup < 0)
+ error->all("Could not find atom_modify first group ID");
+ } else firstgroup = -1;
+
// init sub-style
avec->init();
@@ -310,6 +321,15 @@ void Atom::modify_params(int narg, char **arg)
else if (strcmp(arg[iarg+1],"hash") == 0) map_style = 2;
else error->all("Illegal atom_modify command");
iarg += 2;
+ } else if (strcmp(arg[iarg],"first") == 0) {
+ if (iarg+2 > narg) error->all("Illegal atom_modify command");
+ if (strcmp(arg[iarg+1],"all") == 0) delete [] firstgroupname;
+ else {
+ int n = strlen(arg[iarg+1]) + 1;
+ firstgroupname = new char[n];
+ strcpy(firstgroupname,arg[iarg+1]);
+ }
+ iarg += 2;
} else error->all("Illegal atom_modify command");
}
}
@@ -1205,6 +1225,36 @@ void Atom::check_dipole()
error->all("All dipole moments are not set");
}
+/* ----------------------------------------------------------------------
+ reorder owned atoms so those in firstgroup appear first
+ called by comm->exchange() if atom_modify first group is set
+ only owned atoms exist at this point, no ghost atoms
+------------------------------------------------------------------------- */
+
+void Atom::first_reorder()
+{
+ // insure there is one extra atom location at end of arrays for swaps
+
+ if (nlocal == nmax) avec->grow(0);
+
+ // loop over owned atoms
+ // nfirst = index of first atom not in firstgroup
+ // when find firstgroup atom out of place, swap it with atom nfirst
+
+ int bitmask = group->bitmask[firstgroup];
+ nfirst = 0;
+ while (nfirst < nlocal && mask[nfirst] & bitmask) nfirst++;
+
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & bitmask && i > nfirst) {
+ avec->copy(i,nlocal);
+ avec->copy(nfirst,i);
+ avec->copy(nlocal,nfirst);
+ while (nfirst < nlocal && mask[nfirst] & bitmask) nfirst++;
+ }
+ }
+}
+
/* ----------------------------------------------------------------------
register a callback to a fix so it can manage atom-based arrays
happens when fix is created
diff --git a/src/atom.h b/src/atom.h
index fd9bd0f84f..b9404bae7f 100644
--- a/src/atom.h
+++ b/src/atom.h
@@ -35,6 +35,10 @@ class Atom : protected Pointers {
int nbonds,nangles,ndihedrals,nimpropers;
int bond_per_atom,angle_per_atom,dihedral_per_atom,improper_per_atom;
+ int firstgroup; // store atoms in this group first, -1 if unset
+ int nfirst; // # of atoms in first group on this proc
+ char *firstgroupname; // group-ID to store first, NULL if unset
+
// per-atom arrays
// customize by adding new array
@@ -132,6 +136,8 @@ class Atom : protected Pointers {
void set_dipole(double *);
void check_dipole();
+ void first_reorder();
+
void add_callback(int);
void delete_callback(const char *, int);
void update_callback(int);
diff --git a/src/comm.cpp b/src/comm.cpp
index 51f74e9b0f..7698e9c8c3 100644
--- a/src/comm.cpp
+++ b/src/comm.cpp
@@ -58,7 +58,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp)
user_procgrid[0] = user_procgrid[1] = user_procgrid[2] = 0;
grid2proc = NULL;
- igroup = 0;
+ bordergroup = 0;
style = SINGLE;
multilo = multihi = NULL;
cutghostmulti = NULL;
@@ -172,7 +172,6 @@ void Comm::init()
{
triclinic = domain->triclinic;
map_style = atom->map_style;
- groupbit = group->bitmask[igroup];
// comm_only = 1 if only x,f are exchanged in forward/reverse comm
@@ -488,8 +487,7 @@ void Comm::reverse_communicate()
}
/* ----------------------------------------------------------------------
- exchange:
- move atoms to correct processors
+ exchange: move atoms to correct processors
atoms exchanged with all 6 stencil neighbors
send out atoms that have left my box, receive ones entering my box
atoms will be lost if not inside some proc's box
@@ -591,11 +589,12 @@ void Comm::exchange()
else m += static_cast<int> (buf[m]);
}
}
+
+ if (atom->firstgroupname) atom->first_reorder();
}
/* ----------------------------------------------------------------------
- borders:
- make lists of nearby atoms to send to neighboring procs at every timestep
+ borders: list nearby atoms to send to neighboring procs at every timestep
one list is created for every swap that will be made
as list is made, actually do swaps
this does equivalent of a communicate (so don't need to explicitly
@@ -606,9 +605,10 @@ void Comm::exchange()
void Comm::borders()
{
- int i,n,itype,iswap,dim,ineed,maxneed,nsend,nrecv,nfirst,nlast,smax,rmax;
+ int i,n,itype,iswap,dim,ineed,maxneed,smax,rmax;
+ int nsend,nrecv,nfirst,nlast,ngroup;
double lo,hi;
- int *type,*mask;
+ int *type;
double **x;
double *buf,*mlo,*mhi;
MPI_Request request;
@@ -652,37 +652,51 @@ void Comm::borders()
nsend = 0;
- // SINGLE vs MULTI, all atoms versus only atoms in group
+ // find send atoms according to SINGLE vs MULTI
+ // all atoms eligible versus atoms in bordergroup
+ // only need to limit loop to bordergroup for first sends (ineed < 2)
+ // on these sends, break loop in two: owned (in group) and ghost
- if (igroup) {
- mask = atom->mask;
+ if (!bordergroup || ineed >= 2) {
if (style == SINGLE) {
for (i = nfirst; i < nlast; i++)
- if (mask[i] & groupbit) {
- if (x[i][dim] >= lo && x[i][dim] <= hi) {
- if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
- sendlist[iswap][nsend++] = i;
- }
+ if (x[i][dim] >= lo && x[i][dim] <= hi) {
+ if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
+ sendlist[iswap][nsend++] = i;
}
} else {
- for (i = nfirst; i < nlast; i++)
- if (mask[i] & groupbit) {
- itype = type[i];
- if (x[i][dim] >= mlo[itype] && x[i][dim] <= mhi[itype]) {
- if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
- sendlist[iswap][nsend++] = i;
- }
+ for (i = nfirst; i < nlast; i++) {
+ itype = type[i];
+ if (x[i][dim] >= mlo[itype] && x[i][dim] <= mhi[itype]) {
+ if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
+ sendlist[iswap][nsend++] = i;
}
+ }
}
+
} else {
if (style == SINGLE) {
- for (i = nfirst; i < nlast; i++)
+ ngroup = atom->nfirst;
+ for (i = 0; i < ngroup; i++)
+ if (x[i][dim] >= lo && x[i][dim] <= hi) {
+ if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
+ sendlist[iswap][nsend++] = i;
+ }
+ for (i = atom->nlocal; i < nlast; i++)
if (x[i][dim] >= lo && x[i][dim] <= hi) {
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
sendlist[iswap][nsend++] = i;
}
} else {
- for (i = nfirst; i < nlast; i++) {
+ ngroup = atom->nfirst;
+ for (i = 0; i < ngroup; i++) {
+ itype = type[i];
+ if (x[i][dim] >= mlo[itype] && x[i][dim] <= mhi[itype]) {
+ if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
+ sendlist[iswap][nsend++] = i;
+ }
+ }
+ for (i = atom->nlocal; i < nlast; i++) {
itype = type[i];
if (x[i][dim] >= mlo[itype] && x[i][dim] <= mhi[itype]) {
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
@@ -1504,9 +1518,12 @@ void Comm::set(int narg, char **arg)
while (iarg < narg) {
if (strcmp(arg[iarg],"group") == 0) {
if (iarg+2 > narg) error->all("Illegal communicate command");
- igroup = group->find(arg[iarg+1]);
- if (igroup < 0)
+ bordergroup = group->find(arg[iarg+1]);
+ if (bordergroup < 0)
error->all("Invalid group ID in communicate command");
+ if (bordergroup && (atom->firstgroupname == NULL ||
+ strcmp(arg[iarg+1],atom->firstgroupname) != 0))
+ error->all("Communicate group != atom_modify first group");
iarg += 2;
} else error->all("Illegal communicate command");
}
diff --git a/src/comm.h b/src/comm.h
index b6b8ef0576..54078ad950 100644
--- a/src/comm.h
+++ b/src/comm.h
@@ -71,7 +71,7 @@ class Comm : protected Pointers {
int comm_x_only,comm_f_only; // 1 if only exchange x,f in for/rev comm
int map_style; // non-0 if global->local mapping is done
int ***grid2proc; // which proc owns i,j,k loc in 3d grid
- int igroup,groupbit; // only communicate this group
+ int bordergroup; // only communicate this group in borders
int *firstrecv; // where to put 1st recv atom in each swap
int **sendlist; // list of atoms to send in each swap
diff --git a/src/fix_enforce2d.cpp b/src/fix_enforce2d.cpp
index 31a3e0d31a..8d0f1a123d 100644
--- a/src/fix_enforce2d.cpp
+++ b/src/fix_enforce2d.cpp
@@ -79,6 +79,7 @@ void FixEnforce2D::post_force(int vflag)
double **f = atom->f;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
diff --git a/src/fix_npt.cpp b/src/fix_npt.cpp
index 7b51897139..7636739f6c 100644
--- a/src/fix_npt.cpp
+++ b/src/fix_npt.cpp
@@ -374,6 +374,7 @@ void FixNPT::initial_integrate(int vflag)
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double dtfm;
for (i = 0; i < nlocal; i++) {
@@ -422,6 +423,7 @@ void FixNPT::final_integrate()
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double dtfm;
for (i = 0; i < nlocal; i++) {
@@ -499,6 +501,7 @@ void FixNPT::initial_integrate_respa(int vflag, int ilevel, int flag)
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
// outermost level - update eta_dot and omega_dot, apply to v, remap box
// all other levels - NVE update of v
@@ -604,6 +607,7 @@ void FixNPT::final_integrate_respa(int ilevel)
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
diff --git a/src/fix_nve.cpp b/src/fix_nve.cpp
index a471c7217e..8035cf25f5 100644
--- a/src/fix_nve.cpp
+++ b/src/fix_nve.cpp
@@ -70,6 +70,7 @@ void FixNVE::initial_integrate(int vflag)
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
if (mass) {
for (int i = 0; i < nlocal; i++) {
@@ -112,6 +113,7 @@ void FixNVE::final_integrate()
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
if (mass) {
for (int i = 0; i < nlocal; i++) {
diff --git a/src/fix_nve_limit.cpp b/src/fix_nve_limit.cpp
index d43684c708..f246ed6f5b 100644
--- a/src/fix_nve_limit.cpp
+++ b/src/fix_nve_limit.cpp
@@ -79,6 +79,7 @@ void FixNVELimit::initial_integrate(int vflag)
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
if (mass) {
for (int i = 0; i < nlocal; i++) {
@@ -141,6 +142,7 @@ void FixNVELimit::final_integrate()
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
if (mass) {
for (int i = 0; i < nlocal; i++) {
diff --git a/src/fix_nve_noforce.cpp b/src/fix_nve_noforce.cpp
index 2d8d91ec77..618daadb8a 100644
--- a/src/fix_nve_noforce.cpp
+++ b/src/fix_nve_noforce.cpp
@@ -57,6 +57,7 @@ void FixNVENoforce::initial_integrate(int vflag)
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
diff --git a/src/fix_nvt.cpp b/src/fix_nvt.cpp
index f6807c127c..76b4bc1caa 100644
--- a/src/fix_nvt.cpp
+++ b/src/fix_nvt.cpp
@@ -167,6 +167,7 @@ void FixNVT::initial_integrate(int vflag)
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
@@ -195,6 +196,7 @@ void FixNVT::final_integrate()
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
@@ -238,6 +240,7 @@ void FixNVT::initial_integrate_respa(int vflag, int ilevel, int flag)
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
// outermost level - update eta_dot and apply to v
// all other levels - NVE update of v
@@ -305,6 +308,7 @@ void FixNVT::final_integrate_respa(int ilevel)
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
diff --git a/src/fix_nvt_sllod.cpp b/src/fix_nvt_sllod.cpp
index 57db99d812..d0fcbdbb37 100644
--- a/src/fix_nvt_sllod.cpp
+++ b/src/fix_nvt_sllod.cpp
@@ -91,6 +91,7 @@ void FixNVTSlodd::initial_integrate(int vflag)
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double *h_rate = domain->h_rate;
double *h_ratelo = domain->h_ratelo;
@@ -146,6 +147,7 @@ void FixNVTSlodd::final_integrate()
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double *h_rate = domain->h_rate;
double *h_ratelo = domain->h_ratelo;
@@ -211,6 +213,7 @@ void FixNVTSlodd::initial_integrate_respa(int vflag, int ilevel, int flag)
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
// outermost level - update eta_dot and apply to v
// all other levels - NVE update of v
diff --git a/src/neigh_derive.cpp b/src/neigh_derive.cpp
index cb1a2a6709..3e7428f609 100644
--- a/src/neigh_derive.cpp
+++ b/src/neigh_derive.cpp
@@ -93,7 +93,7 @@ void Neighbor::half_from_full_newton(NeighList *list)
double **x = atom->x;
int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
+ int nall = nlocal + atom->nghost;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
diff --git a/src/neigh_full.cpp b/src/neigh_full.cpp
index 81c6c9586a..913760ee01 100644
--- a/src/neigh_full.cpp
+++ b/src/neigh_full.cpp
@@ -14,6 +14,7 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
+#include "group.h"
#include "error.h"
using namespace LAMMPS_NS;
@@ -25,7 +26,7 @@ using namespace LAMMPS_NS;
void Neighbor::full_nsq(NeighList *list)
{
- int i,j,n,itype,jtype,which;
+ int i,j,n,itype,jtype,which,bitmask;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
@@ -34,8 +35,12 @@ void Neighbor::full_nsq(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
+ int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
+ if (include_group) {
+ nlocal = atom->nfirst;
+ bitmask = group->bitmask[include_group];
+ }
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@@ -47,7 +52,6 @@ void Neighbor::full_nsq(NeighList *list)
int npnt = 0;
for (i = 0; i < nlocal; i++) {
- if (include_group && !(mask[i] & include_groupbit)) continue;
if (pgsize - npnt < oneatom) {
npnt = 0;
@@ -67,8 +71,8 @@ void Neighbor::full_nsq(NeighList *list)
// skip i = j
for (j = 0; j < nall; j++) {
+ if (include_group && !(mask[j] & bitmask)) continue;
if (i == j) continue;
-
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
@@ -117,8 +121,9 @@ void Neighbor::full_bin(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
+ int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
+ if (include_group) nlocal = atom->nfirst;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@@ -132,7 +137,6 @@ void Neighbor::full_bin(NeighList *list)
int npnt = 0;
for (i = 0; i < nlocal; i++) {
- if (include_group && !(mask[i] & include_groupbit)) continue;
if (pgsize - npnt < oneatom) {
npnt = 0;
@@ -209,8 +213,9 @@ void Neighbor::full_multi(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
+ int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
+ if (include_group) nlocal = atom->nfirst;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@@ -225,7 +230,6 @@ void Neighbor::full_multi(NeighList *list)
int npnt = 0;
for (i = 0; i < nlocal; i++) {
- if (include_group && !(mask[i] & include_groupbit)) continue;
if (pgsize - npnt < oneatom) {
npnt = 0;
diff --git a/src/neigh_gran.cpp b/src/neigh_gran.cpp
index 8adbc4501c..2fe5fd5f70 100644
--- a/src/neigh_gran.cpp
+++ b/src/neigh_gran.cpp
@@ -14,6 +14,7 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
+#include "group.h"
#include "fix_shear_history.h"
#include "error.h"
@@ -29,7 +30,7 @@ using namespace LAMMPS_NS;
void Neighbor::granular_nsq_no_newton(NeighList *list)
{
- int i,j,m,n,nn;
+ int i,j,m,n,nn,bitmask;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr,*touchptr;
@@ -50,7 +51,11 @@ void Neighbor::granular_nsq_no_newton(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
+ int nall = nlocal + atom->nghost;
+ if (include_group) {
+ nlocal = atom->nfirst;
+ bitmask = group->bitmask[include_group];
+ }
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@@ -74,7 +79,6 @@ void Neighbor::granular_nsq_no_newton(NeighList *list)
int npnt = 0;
for (i = 0; i < nlocal; i++) {
- if (include_group && !(mask[i] & include_groupbit)) continue;
if (pgsize - npnt < oneatom) {
npnt = 0;
@@ -104,6 +108,7 @@ void Neighbor::granular_nsq_no_newton(NeighList *list)
// loop over remaining atoms, owned and ghost
for (j = i+1; j < nall; j++) {
+ if (include_group && !(mask[j] & bitmask)) continue;
if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
delx = xtmp - x[j][0];
@@ -169,7 +174,7 @@ void Neighbor::granular_nsq_no_newton(NeighList *list)
void Neighbor::granular_nsq_newton(NeighList *list)
{
- int i,j,n,itag,jtag;
+ int i,j,n,itag,jtag,bitmask;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr;
@@ -181,7 +186,11 @@ void Neighbor::granular_nsq_newton(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
+ int nall = nlocal + atom->nghost;
+ if (include_group) {
+ nlocal = atom->nfirst;
+ bitmask = group->bitmask[include_group];
+ }
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@@ -193,7 +202,6 @@ void Neighbor::granular_nsq_newton(NeighList *list)
int npnt = 0;
for (i = 0; i < nlocal; i++) {
- if (include_group && !(mask[i] & include_groupbit)) continue;
if (pgsize - npnt < oneatom) {
npnt = 0;
@@ -213,6 +221,8 @@ void Neighbor::granular_nsq_newton(NeighList *list)
// loop over remaining atoms, owned and ghost
for (j = i+1; j < nall; j++) {
+ if (include_group && !(mask[j] & bitmask)) continue;
+
if (j >= nlocal) {
jtag = tag[j];
if (itag > jtag) {
@@ -288,6 +298,7 @@ void Neighbor::granular_bin_no_newton(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
+ if (include_group) nlocal = atom->nfirst;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@@ -313,7 +324,6 @@ void Neighbor::granular_bin_no_newton(NeighList *list)
int npnt = 0;
for (i = 0; i < nlocal; i++) {
- if (include_group && !(mask[i] & include_groupbit)) continue;
if (pgsize - npnt < oneatom) {
npnt = 0;
@@ -431,6 +441,7 @@ void Neighbor::granular_bin_newton(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
+ if (include_group) nlocal = atom->nfirst;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@@ -444,7 +455,6 @@ void Neighbor::granular_bin_newton(NeighList *list)
int npnt = 0;
for (i = 0; i < nlocal; i++) {
- if (include_group && !(mask[i] & include_groupbit)) continue;
if (pgsize - npnt < oneatom) {
npnt = 0;
@@ -538,6 +548,7 @@ void Neighbor::granular_bin_newton_tri(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
+ if (include_group) nlocal = atom->nfirst;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@@ -551,7 +562,6 @@ void Neighbor::granular_bin_newton_tri(NeighList *list)
int npnt = 0;
for (i = 0; i < nlocal; i++) {
- if (include_group && !(mask[i] & include_groupbit)) continue;
if (pgsize - npnt < oneatom) {
npnt = 0;
diff --git a/src/neigh_half_bin.cpp b/src/neigh_half_bin.cpp
index 3f19e4cd6e..628b37c369 100644
--- a/src/neigh_half_bin.cpp
+++ b/src/neigh_half_bin.cpp
@@ -42,7 +42,8 @@ void Neighbor::half_bin_no_newton(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
+ int nall = nlocal + atom->nghost;
+ if (include_group) nlocal = atom->nfirst;
int molecular = atom->molecular;
int *ilist = list->ilist;
@@ -57,7 +58,6 @@ void Neighbor::half_bin_no_newton(NeighList *list)
int npnt = 0;
for (i = 0; i < nlocal; i++) {
- if (include_group && !(mask[i] & include_groupbit)) continue;
if (pgsize - npnt < oneatom) {
npnt = 0;
@@ -135,8 +135,9 @@ void Neighbor::half_bin_newton(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
+ int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
+ if (include_group) nlocal = atom->nfirst;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@@ -150,7 +151,6 @@ void Neighbor::half_bin_newton(NeighList *list)
int npnt = 0;
for (i = 0; i < nlocal; i++) {
- if (include_group && !(mask[i] & include_groupbit)) continue;
if (pgsize - npnt < oneatom) {
npnt = 0;
@@ -249,8 +249,9 @@ void Neighbor::half_bin_newton_tri(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
+ int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
+ if (include_group) nlocal = atom->nfirst;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@@ -264,7 +265,6 @@ void Neighbor::half_bin_newton_tri(NeighList *list)
int npnt = 0;
for (i = 0; i < nlocal; i++) {
- if (include_group && !(mask[i] & include_groupbit)) continue;
if (pgsize - npnt < oneatom) {
npnt = 0;
diff --git a/src/neigh_half_multi.cpp b/src/neigh_half_multi.cpp
index cda4965ebc..d955b2e1fd 100644
--- a/src/neigh_half_multi.cpp
+++ b/src/neigh_half_multi.cpp
@@ -44,8 +44,9 @@ void Neighbor::half_multi_no_newton(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
+ int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
+ if (include_group) nlocal = atom->nfirst;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@@ -60,7 +61,6 @@ void Neighbor::half_multi_no_newton(NeighList *list)
int npnt = 0;
for (i = 0; i < nlocal; i++) {
- if (include_group && !(mask[i] & include_groupbit)) continue;
if (pgsize - npnt < oneatom) {
npnt = 0;
@@ -145,8 +145,9 @@ void Neighbor::half_multi_newton(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
+ int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
+ if (include_group) nlocal = atom->nfirst;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@@ -161,7 +162,6 @@ void Neighbor::half_multi_newton(NeighList *list)
int npnt = 0;
for (i = 0; i < nlocal; i++) {
- if (include_group && !(mask[i] & include_groupbit)) continue;
if (pgsize - npnt < oneatom) {
npnt = 0;
@@ -269,8 +269,9 @@ void Neighbor::half_multi_newton_tri(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
+ int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
+ if (include_group) nlocal = atom->nfirst;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@@ -285,7 +286,6 @@ void Neighbor::half_multi_newton_tri(NeighList *list)
int npnt = 0;
for (i = 0; i < nlocal; i++) {
- if (include_group && !(mask[i] & include_groupbit)) continue;
if (pgsize - npnt < oneatom) {
npnt = 0;
diff --git a/src/neigh_half_nsq.cpp b/src/neigh_half_nsq.cpp
index aaee116dcf..bffc77dfcf 100644
--- a/src/neigh_half_nsq.cpp
+++ b/src/neigh_half_nsq.cpp
@@ -14,6 +14,7 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
+#include "group.h"
#include "error.h"
using namespace LAMMPS_NS;
@@ -26,7 +27,7 @@ using namespace LAMMPS_NS;
void Neighbor::half_nsq_no_newton(NeighList *list)
{
- int i,j,n,itype,jtype,which;
+ int i,j,n,itype,jtype,which,bitmask;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
@@ -35,8 +36,12 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
+ int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
+ if (include_group) {
+ nlocal = atom->nfirst;
+ bitmask = group->bitmask[include_group];
+ }
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@@ -48,7 +53,6 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
int npnt = 0;
for (i = 0; i < nlocal; i++) {
- if (include_group && !(mask[i] & include_groupbit)) continue;
if (pgsize - npnt < oneatom) {
npnt = 0;
@@ -67,6 +71,7 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
// loop over remaining atoms, owned and ghost
for (j = i+1; j < nall; j++) {
+ if (include_group && !(mask[j] & bitmask)) continue;
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
@@ -102,7 +107,7 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
void Neighbor::half_nsq_newton(NeighList *list)
{
- int i,j,n,itype,jtype,itag,jtag,which;
+ int i,j,n,itype,jtype,itag,jtag,which,bitmask;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
@@ -112,8 +117,12 @@ void Neighbor::half_nsq_newton(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
+ int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
+ if (include_group) {
+ nlocal = atom->nfirst;
+ bitmask = group->bitmask[include_group];
+ }
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@@ -125,7 +134,6 @@ void Neighbor::half_nsq_newton(NeighList *list)
int npnt = 0;
for (i = 0; i < nlocal; i++) {
- if (include_group && !(mask[i] & include_groupbit)) continue;
if (pgsize - npnt < oneatom) {
npnt = 0;
@@ -146,6 +154,8 @@ void Neighbor::half_nsq_newton(NeighList *list)
// itag = jtag is possible for long cutoffs that include images of self
for (j = i+1; j < nall; j++) {
+ if (include_group && !(mask[j] & bitmask)) continue;
+
if (j >= nlocal) {
jtag = tag[j];
if (itag > jtag) {
diff --git a/src/neigh_respa.cpp b/src/neigh_respa.cpp
index 125bfecc99..50221dcf47 100644
--- a/src/neigh_respa.cpp
+++ b/src/neigh_respa.cpp
@@ -14,6 +14,7 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
+#include "group.h"
#include "error.h"
using namespace LAMMPS_NS;
@@ -27,7 +28,7 @@ using namespace LAMMPS_NS;
void Neighbor::respa_nsq_no_newton(NeighList *list)
{
- int i,j,n,itype,jtype,which,n_inner,n_middle;
+ int i,j,n,itype,jtype,which,n_inner,n_middle,bitmask;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*neighptr_inner,*neighptr_middle;
@@ -36,8 +37,12 @@ void Neighbor::respa_nsq_no_newton(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
+ int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
+ if (include_group) {
+ nlocal = atom->nfirst;
+ bitmask = group->bitmask[include_group];
+ }
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@@ -68,7 +73,6 @@ void Neighbor::respa_nsq_no_newton(NeighList *list)
int npnt_middle = 0;
for (i = 0; i < nlocal; i++) {
- if (include_group && !(mask[i] & include_groupbit)) continue;
if (pgsize - npnt < oneatom) {
npnt = 0;
@@ -106,6 +110,7 @@ void Neighbor::respa_nsq_no_newton(NeighList *list)
// loop over remaining atoms, owned and ghost
for (j = i+1; j < nall; j++) {
+ if (include_group && !(mask[j] & bitmask)) continue;
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
@@ -167,7 +172,7 @@ void Neighbor::respa_nsq_no_newton(NeighList *list)
void Neighbor::respa_nsq_newton(NeighList *list)
{
- int i,j,n,itype,jtype,itag,jtag,which,n_inner,n_middle;
+ int i,j,n,itype,jtype,itag,jtag,which,n_inner,n_middle,bitmask;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr,*neighptr_inner,*neighptr_middle;
@@ -177,8 +182,12 @@ void Neighbor::respa_nsq_newton(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
+ int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
+ if (include_group) {
+ nlocal = atom->nfirst;
+ bitmask = group->bitmask[include_group];
+ }
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@@ -209,7 +218,6 @@ void Neighbor::respa_nsq_newton(NeighList *list)
int npnt_middle = 0;
for (i = 0; i < nlocal; i++) {
- if (include_group && !(mask[i] & include_groupbit)) continue;
if (pgsize - npnt < oneatom) {
npnt = 0;
@@ -248,6 +256,8 @@ void Neighbor::respa_nsq_newton(NeighList *list)
// loop over remaining atoms, owned and ghost
for (j = i+1; j < nall; j++) {
+ if (include_group && !(mask[j] & bitmask)) continue;
+
if (j >= nlocal) {
jtag = tag[j];
if (itag > jtag) {
@@ -339,8 +349,9 @@ void Neighbor::respa_bin_no_newton(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
+ int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
+ if (include_group) nlocal = atom->nfirst;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@@ -373,7 +384,6 @@ void Neighbor::respa_bin_no_newton(NeighList *list)
int npnt_middle = 0;
for (i = 0; i < nlocal; i++) {
- if (include_group && !(mask[i] & include_groupbit)) continue;
if (pgsize - npnt < oneatom) {
npnt = 0;
@@ -495,8 +505,9 @@ void Neighbor::respa_bin_newton(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
+ int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
+ if (include_group) nlocal = atom->nfirst;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@@ -529,7 +540,6 @@ void Neighbor::respa_bin_newton(NeighList *list)
int npnt_middle = 0;
for (i = 0; i < nlocal; i++) {
- if (include_group && !(mask[i] & include_groupbit)) continue;
if (pgsize - npnt < oneatom) {
npnt = 0;
@@ -684,8 +694,9 @@ void Neighbor::respa_bin_newton_tri(NeighList *list)
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
+ int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
+ if (include_group) nlocal = atom->nfirst;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
@@ -718,7 +729,6 @@ void Neighbor::respa_bin_newton_tri(NeighList *list)
int npnt_middle = 0;
for (i = 0; i < nlocal; i++) {
- if (include_group && !(mask[i] & include_groupbit)) continue;
if (pgsize - npnt < oneatom) {
npnt = 0;
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index 0c0b6b2b84..06859a4fa5 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -340,8 +340,6 @@ void Neighbor::init()
n = atom->ntypes;
- include_groupbit = group->bitmask[include_group];
-
if (nex_type == 0 && nex_group == 0 && nex_mol == 0) exclude = 0;
else exclude = 1;
@@ -925,27 +923,16 @@ int Neighbor::check_distance()
double delx,dely,delz,rsq;
double **x = atom->x;
- int *mask = atom->mask;
int nlocal = atom->nlocal;
- int flag = 0;
+ if (include_group) nlocal = atom->nfirst;
- if (include_group) {
- for (int i = 0; i < nlocal; i++)
- if (mask[i] & include_groupbit) {
- delx = x[i][0] - xhold[i][0];
- dely = x[i][1] - xhold[i][1];
- delz = x[i][2] - xhold[i][2];
- rsq = delx*delx + dely*dely + delz*delz;
- if (rsq > triggersq) flag = 1;
- }
- } else {
- for (int i = 0; i < nlocal; i++) {
- delx = x[i][0] - xhold[i][0];
- dely = x[i][1] - xhold[i][1];
- delz = x[i][2] - xhold[i][2];
- rsq = delx*delx + dely*dely + delz*delz;
- if (rsq > triggersq) flag = 1;
- }
+ int flag = 0;
+ for (int i = 0; i < nlocal; i++) {
+ delx = x[i][0] - xhold[i][0];
+ dely = x[i][1] - xhold[i][1];
+ delz = x[i][2] - xhold[i][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ if (rsq > triggersq) flag = 1;
}
int flagall;
@@ -1308,8 +1295,11 @@ void Neighbor::modify_params(int narg, char **arg)
} else if (strcmp(arg[iarg],"include") == 0) {
if (iarg+2 > narg) error->all("Illegal neigh_modify command");
include_group = group->find(arg[iarg+1]);
- if (include_group == -1)
+ if (include_group < 0)
error->all("Invalid group ID in neigh_modify command");
+ if (include_group && (atom->firstgroupname == NULL ||
+ strcmp(arg[iarg+1],atom->firstgroupname) != 0))
+ error->all("Neigh_modify include group != atom_modify first group");
iarg += 2;
} else if (strcmp(arg[iarg],"exclude") == 0) {
if (iarg+2 > narg) error->all("Illegal neigh_modify command");
@@ -1417,7 +1407,7 @@ int Neighbor::find_special(int i, int j)
void Neighbor::bin_atoms()
{
- int i,ibin,nall;
+ int i,ibin;
for (i = 0; i < mbins; i++) binhead[i] = -1;
@@ -1426,15 +1416,23 @@ void Neighbor::bin_atoms()
double **x = atom->x;
int *mask = atom->mask;
- nall = atom->nlocal + atom->nghost;
+ int nlocal = atom->nlocal;
+ int nall = nlocal + atom->nghost;
if (include_group) {
- for (i = nall-1; i >= 0; i--)
- if (mask[i] & include_groupbit) {
+ int bitmask = group->bitmask[include_group];
+ for (i = nall-1; i >= nlocal; i--) {
+ if (mask[i] & bitmask) {
ibin = coord2bin(x[i]);
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
+ }
+ for (i = atom->nfirst; i >= 0; i--) {
+ ibin = coord2bin(x[i]);
+ bins[i] = binhead[ibin];
+ binhead[ibin] = i;
+ }
} else {
for (i = nall-1; i >= 0; i--) {
ibin = coord2bin(x[i]);
diff --git a/src/neighbor.h b/src/neighbor.h
index 3fc62c4421..233eb3c8bb 100644
--- a/src/neighbor.h
+++ b/src/neighbor.h
@@ -123,8 +123,7 @@ class Neighbor : protected Pointers {
int special_flag[4]; // flags for 1-2, 1-3, 1-4 neighbors
- int include_group; // only form neighbor lists on this group
- int include_groupbit;
+ int include_group; // only build pairwise lists for this group
int exclude; // 0 if no type/group exclusions, 1 if yes
--
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