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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1502 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2008-02-14 23:05:04 +00:00
parent c751561455
commit f89945e8e5
15 changed files with 166 additions and 100 deletions
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13
src/COLLOID/pair_colloid.cpp
View File

@ -53,6 +53,7 @@ PairColloid::~PairColloid()
memory->destroy_2d_double_array(d2);
memory->destroy_2d_double_array(a1);
memory->destroy_2d_double_array(a2);
memory->destroy_2d_double_array(diameter);
memory->destroy_2d_double_array(cut);
memory->destroy_2d_double_array(offset);
memory->destroy_2d_double_array(sigma3);
@ -229,6 +230,7 @@ void PairColloid::allocate()
d2 = memory->create_2d_double_array(n+1,n+1,"pair:d2");
a1 = memory->create_2d_double_array(n+1,n+1,"pair:a1");
a2 = memory->create_2d_double_array(n+1,n+1,"pair:a2");
diameter = memory->create_2d_double_array(n+1,n+1,"pair:diameter");
cut = memory->create_2d_double_array(n+1,n+1,"pair:cut");
offset = memory->create_2d_double_array(n+1,n+1,"pair:offset");
sigma3 = memory->create_2d_double_array(n+1,n+1,"pair:sigma3");
@ -292,6 +294,7 @@ void PairColloid::coeff(int narg, char **arg)
error->all("Invalid d1 or d2 value for pair colloid coeff");
d1[i][j] = d1_one;
d2[i][j] = d2_one;
diameter[i][j] = 0.5*(d1_one+d2_one);
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
@ -312,6 +315,7 @@ double PairColloid::init_one(int i, int j)
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
d1[i][j] = mix_distance(d1[i][i],d1[j][j]);
d2[i][j] = mix_distance(d2[i][i],d2[j][j]);
diameter[i][j] = 0.5 * (d1[i][j] + d2[i][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
@ -340,6 +344,7 @@ double PairColloid::init_one(int i, int j)
sigma[j][i] = sigma[i][j];
sigma3[j][i] = sigma3[i][j];
sigma6[j][i] = sigma6[i][j];
diameter[j][i] = diameter[i][j];
cut[j][i] = cut[i][j];
cutsq[j][i] = cutsq[i][j] = cut[i][j] * cut[i][j];
@ -516,3 +521,11 @@ double PairColloid::single(int i, int j, int itype, int jtype, double rsq,
return factor_lj*phi;
}
/* ---------------------------------------------------------------------- */
void *PairColloid::extract(char *str)
{
if (strcmp(str,"diameter") == 0) return (void *) diameter;
return NULL;
}

3
src/COLLOID/pair_colloid.h
View File

@ -31,11 +31,12 @@ class PairColloid : public Pair {
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
double single(int, int, int, int, double, double, double, double &);
void *extract(char *);
private:
double cut_global;
double **cut;
double **a12,**d1,**d2,**a1,**a2,**offset;
double **a12,**d1,**d2,**diameter,**a1,**a2,**offset;
double **sigma,**sigma3,**sigma6;
double **lj1,**lj2,**lj3,**lj4;
int **form;

2
src/COLLOID/pair_lubricate.cpp
View File

@ -352,8 +352,6 @@ void PairLubricate::init_style()
{
if (!atom->torque_flag || atom->shape == NULL)
error->all("Pair lubricate requires atom attributes torque, shape");
if (domain->dimension != 3)
error->all("Pair lubricate only available for 3d");
// insure all particle shapes are spherical

43
src/comm.cpp
View File

@ -29,6 +29,7 @@
#include "neighbor.h"
#include "modify.h"
#include "fix.h"
#include "group.h"
#include "compute.h"
#include "error.h"
#include "memory.h"
@ -57,6 +58,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp)
user_procgrid[0] = user_procgrid[1] = user_procgrid[2] = 0;
grid2proc = NULL;
igroup = 0;
style = SINGLE;
multilo = multihi = NULL;
cutghostmulti = NULL;
@ -170,6 +172,7 @@ 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
@ -605,7 +608,7 @@ void Comm::borders()
{
int i,n,itype,iswap,dim,ineed,maxneed,nsend,nrecv,nfirst,nlast,smax,rmax;
double lo,hi;
int *type;
int *type,*mask;
double **x;
double *buf,*mlo,*mhi;
MPI_Request request;
@ -648,6 +651,30 @@ void Comm::borders()
}
nsend = 0;
// SINGLE vs MULTI, all atoms versus only atoms in group
if (igroup) {
mask = atom->mask;
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;
}
}
} 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;
}
}
}
} else {
if (style == SINGLE) {
for (i = nfirst; i < nlast; i++)
if (x[i][dim] >= lo && x[i][dim] <= hi) {
@ -663,6 +690,7 @@ void Comm::borders()
}
}
}
}
// pack up list of border atoms
@ -1466,11 +1494,22 @@ void Comm::free_multi()
void Comm::set(int narg, char **arg)
{
if (narg != 1) error->all("Illegal communicate command");
if (narg < 1) error->all("Illegal communicate command");
if (strcmp(arg[0],"single") == 0) style = SINGLE;
else if (strcmp(arg[0],"multi") == 0) style = MULTI;
else error->all("Illegal communicate command");
int iarg = 1;
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)
error->all("Invalid group ID in communicate command");
iarg += 2;
} else error->all("Illegal communicate command");
}
}
/* ----------------------------------------------------------------------

1
src/comm.h
View File

@ -71,6 +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 *firstrecv; // where to put 1st recv atom in each swap
int **sendlist; // list of atoms to send in each swap

15
src/neigh_derive.cpp
View File

@ -67,10 +67,9 @@ void Neighbor::half_from_full_no_newton(NeighList *list)
if (j > i) neighptr[n++] = j;
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@ -145,10 +144,9 @@ void Neighbor::half_from_full_newton(NeighList *list)
neighptr[n++] = joriginal;
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@ -217,10 +215,9 @@ void Neighbor::skip_from(NeighList *list)
neighptr[n++] = joriginal;
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@ -311,12 +308,11 @@ void Neighbor::skip_from_granular(NeighList *list)
shearptr[nn++] = shearptr_skip[3*jj+2];
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
firsttouch[i] = touchptr;
firstshear[i] = shearptr;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@ -454,10 +450,9 @@ void Neighbor::skip_from_respa(NeighList *list)
}
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");

12
src/neigh_full.cpp
View File

@ -47,6 +47,7 @@ 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;
@ -83,10 +84,9 @@ void Neighbor::full_nsq(NeighList *list)
}
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@ -132,6 +132,7 @@ 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;
@ -173,10 +174,9 @@ void Neighbor::full_bin(NeighList *list)
}
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@ -225,6 +225,7 @@ 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;
@ -271,10 +272,9 @@ void Neighbor::full_multi(NeighList *list)
}
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");

22
src/neigh_gran.cpp
View File

@ -74,6 +74,7 @@ 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;
@ -142,15 +143,13 @@ void Neighbor::granular_nsq_no_newton(NeighList *list)
}
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
if (fix_history) {
firsttouch[i] = touchptr;
firstshear[i] = shearptr;
}
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@ -194,6 +193,7 @@ 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;
@ -239,10 +239,9 @@ void Neighbor::granular_nsq_newton(NeighList *list)
if (rsq <= cutsq) neighptr[n++] = j;
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@ -314,6 +313,7 @@ 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;
@ -389,15 +389,13 @@ void Neighbor::granular_bin_no_newton(NeighList *list)
}
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
if (fix_history) {
firsttouch[i] = touchptr;
firstshear[i] = shearptr;
}
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@ -446,6 +444,7 @@ 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;
@ -501,10 +500,9 @@ void Neighbor::granular_bin_newton(NeighList *list)
}
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@ -553,6 +551,7 @@ 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;
@ -592,10 +591,9 @@ void Neighbor::granular_bin_newton_tri(NeighList *list)
}
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");

12
src/neigh_half_bin.cpp
View File

@ -57,6 +57,7 @@ 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;
@ -100,10 +101,9 @@ void Neighbor::half_bin_no_newton(NeighList *list)
}
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@ -150,6 +150,7 @@ 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;
@ -214,10 +215,9 @@ void Neighbor::half_bin_newton(NeighList *list)
}
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@ -264,6 +264,7 @@ 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;
@ -308,10 +309,9 @@ void Neighbor::half_bin_newton_tri(NeighList *list)
}
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");

12
src/neigh_half_multi.cpp
View File

@ -60,6 +60,7 @@ 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;
@ -108,10 +109,9 @@ void Neighbor::half_multi_no_newton(NeighList *list)
}
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@ -161,6 +161,7 @@ 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;
@ -232,10 +233,9 @@ void Neighbor::half_multi_newton(NeighList *list)
}
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@ -285,6 +285,7 @@ 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;
@ -334,10 +335,9 @@ void Neighbor::half_multi_newton_tri(NeighList *list)
}
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");

8
src/neigh_half_nsq.cpp
View File

@ -48,6 +48,7 @@ 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;
@ -82,10 +83,9 @@ void Neighbor::half_nsq_no_newton(NeighList *list)
}
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@ -125,6 +125,7 @@ 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;
@ -175,10 +176,9 @@ void Neighbor::half_nsq_newton(NeighList *list)
}
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");

20
src/neigh_respa.cpp
View File

@ -68,6 +68,7 @@ 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;
@ -131,10 +132,9 @@ void Neighbor::respa_nsq_no_newton(NeighList *list)
}
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@ -209,6 +209,7 @@ 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;
@ -288,10 +289,9 @@ void Neighbor::respa_nsq_newton(NeighList *list)
}
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@ -373,6 +373,7 @@ 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;
@ -445,10 +446,9 @@ void Neighbor::respa_bin_no_newton(NeighList *list)
}
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@ -529,6 +529,7 @@ 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;
@ -634,10 +635,9 @@ void Neighbor::respa_bin_newton(NeighList *list)
}
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@ -718,6 +718,7 @@ 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;
@ -792,10 +793,9 @@ void Neighbor::respa_bin_newton_tri(NeighList *list)
}
}
ilist[inum] = i;
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");

54
src/neighbor.cpp
View File

@ -90,6 +90,8 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
// pair exclusion list info
include_group = 0;
nex_type = maxex_type = 0;
ex1_type = ex2_type = NULL;
ex_type = NULL;
@ -338,6 +340,8 @@ 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;
@ -920,9 +924,21 @@ int Neighbor::check_distance()
{
double delx,dely,delz,rsq;
int nlocal = atom->nlocal;
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int flag = 0;
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];
@ -930,6 +946,7 @@ int Neighbor::check_distance()
rsq = delx*delx + dely*dely + delz*delz;
if (rsq > triggersq) flag = 1;
}
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_MAX,world);
@ -1288,6 +1305,12 @@ void Neighbor::modify_params(int narg, char **arg)
if (binsize_user <= 0.0) binsizeflag = 0;
else binsizeflag = 1;
iarg += 2;
} 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)
error->all("Invalid group ID in neigh_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"exclude") == 0) {
if (iarg+2 > narg) error->all("Illegal neigh_modify command");
@ -1395,35 +1418,30 @@ int Neighbor::find_special(int i, int j)
void Neighbor::bin_atoms()
{
int i,ibin,nall;
double **x;
nall = atom->nlocal + atom->nghost;
x = atom->x;
for (i = 0; i < mbins; i++) binhead[i] = -1;
// bin in reverse order so linked list will be in forward order
// also puts ghost atoms at end of list, which is necessary
double **x = atom->x;
int *mask = atom->mask;
nall = atom->nlocal + atom->nghost;
if (include_group) {
for (i = nall-1; i >= 0; i--)
if (mask[i] & include_groupbit) {
ibin = coord2bin(x[i]);
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
} else {
for (i = nall-1; i >= 0; i--) {
ibin = coord2bin(x[i]);
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
/*
for (i = nlocal; i < nall; i++) {
ibin = coord2bin(x[i]);
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
for (i = 0; i < nlocal; i++) {
ibin = coord2bin(x[i]);
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
*/
}
/* ----------------------------------------------------------------------

3
src/neighbor.h
View File

@ -123,6 +123,9 @@ 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 exclude; // 0 if no type/group exclusions, 1 if yes
int nex_type; // # of entries in type exclusion list

2
src/pair_lj_cut.cpp
View File

@ -717,6 +717,6 @@ double PairLJCut::single(int i, int j, int itype, int jtype, double rsq,
void *PairLJCut::extract(char *str)
{
if (strcmp(str,"sigma") == 0) return (void *) sigma;
if (strcmp(str,"diameter") == 0) return (void *) sigma;
return NULL;
}