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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5797 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2011-03-18 15:09:03 +00:00
parent b4fc6e0421
commit 159d131e37
21 changed files with 493 additions and 167 deletions
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4
src/COLLOID/pair_colloid.cpp
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@ -348,7 +348,6 @@ double PairColloid::init_one(int i, int 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];
double epsilon = a12[i][j]/144.0;
lj1[j][i] = lj1[i][j] = 48.0 * epsilon * sigma6[i][j] * sigma6[i][j];
@ -359,7 +358,8 @@ double PairColloid::init_one(int i, int j)
offset[j][i] = offset[i][j] = 0.0;
if (offset_flag) {
double tmp;
offset[j][i] = offset[i][j] = single(0,0,i,j,cutsq[i][j],0.0,1.0,tmp);
offset[j][i] = offset[i][j] =
single(0,0,i,j,cut[i][j]*cut[i][j],0.0,1.0,tmp);
}
return cut[i][j];

119
src/MANYBODY/pair_airebo.cpp
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@ -48,14 +48,17 @@ PairAIREBO::PairAIREBO(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
one_coeff = 1;
ghostneigh = 1;
maxlocal = 0;
REBO_numneigh = NULL;
REBO_firstneigh = NULL;
closestdistsq = NULL;
maxpage = 0;
pages = NULL;
nC = nH = NULL;
time1 = 0.0;
time2 = 0.0;
}
/* ----------------------------------------------------------------------
@ -68,13 +71,13 @@ PairAIREBO::~PairAIREBO()
memory->sfree(REBO_firstneigh);
for (int i = 0; i < maxpage; i++) memory->sfree(pages[i]);
memory->sfree(pages);
memory->sfree(closestdistsq);
memory->sfree(nC);
memory->sfree(nH);
if (allocated) {
memory->destroy_2d_int_array(setflag);
memory->destroy_2d_double_array(cutsq);
memory->destroy_2d_double_array(cutghost);
memory->destroy_2d_double_array(cutljsq);
memory->destroy_2d_double_array(lj1);
@ -92,12 +95,18 @@ void PairAIREBO::compute(int eflag, int vflag)
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = vflag_atom = 0;
double tstart = MPI_Wtime();
REBO_neigh();
double tmid = MPI_Wtime();
FREBO(eflag,vflag);
if (ljflag) FLJ(eflag,vflag);
if (torflag) TORSION(eflag,vflag);
if (vflag_fdotr) virial_compute();
double tstop = MPI_Wtime();
time1 += tmid-tstart;
time2 += tstop-tmid;
}
/* ----------------------------------------------------------------------
@ -115,6 +124,7 @@ void PairAIREBO::allocate()
setflag[i][j] = 0;
cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq");
cutghost = memory->create_2d_double_array(n+1,n+1,"pair:cutghost");
// only sized by C,H = 2 types
@ -210,11 +220,12 @@ void PairAIREBO::init_style()
if (force->newton_pair == 0)
error->all("Pair style AIREBO requires newton pair on");
// need a full neighbor list
// need a full neighbor list, including neighbors of ghosts
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->ghost = 1;
// local REBO neighbor list memory
@ -261,6 +272,7 @@ double PairAIREBO::init_one(int i, int j)
// rcLJmax + 2*rcmax, since I-J < rcLJmax and J-L,L-N = REBO distances
// long interaction = I-J with I = owned and J = ghost
// cutlj*sigma, since I-J < LJ cutoff
// cutghost = REBO cutoff used in REBO_neigh() for neighbors of ghosts
double cutmax = cut3rebo;
if (ljflag) {
@ -268,14 +280,14 @@ double PairAIREBO::init_one(int i, int j)
cutmax = MAX(cutmax,cutlj*sigma[0][0]);
}
cutsq[i][j] = cutmax * cutmax;
cutghost[i][j] = rcmax[ii][jj];
cutljsq[ii][jj] = cutlj*sigma[ii][jj] * cutlj*sigma[ii][jj];
lj1[ii][jj] = 48.0 * epsilon[ii][jj] * pow(sigma[ii][jj],12.0);
lj2[ii][jj] = 24.0 * epsilon[ii][jj] * pow(sigma[ii][jj],6.0);
lj3[ii][jj] = 4.0 * epsilon[ii][jj] * pow(sigma[ii][jj],12.0);
lj4[ii][jj] = 4.0 * epsilon[ii][jj] * pow(sigma[ii][jj],6.0);
cutsq[j][i] = cutsq[i][j];
cutghost[j][i] = cutghost[i][j];
cutljsq[jj][ii] = cutljsq[ii][jj];
lj1[jj][ii] = lj1[ii][jj];
lj2[jj][ii] = lj2[ii][jj];
@ -292,7 +304,7 @@ double PairAIREBO::init_one(int i, int j)
void PairAIREBO::REBO_neigh()
{
int i,j,ii,jj,m,n,inum,jnum,itype,jtype;
int i,j,ii,jj,m,n,allnum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq,dS;
int *ilist,*jlist,*numneigh,**firstneigh;
int *neighptr;
@ -306,41 +318,28 @@ void PairAIREBO::REBO_neigh()
maxlocal = atom->nmax;
memory->sfree(REBO_numneigh);
memory->sfree(REBO_firstneigh);
memory->sfree(closestdistsq);
memory->sfree(nC);
memory->sfree(nH);
REBO_numneigh = (int *)
memory->smalloc(maxlocal*sizeof(int),"AIREBO:numneigh");
REBO_firstneigh = (int **)
memory->smalloc(maxlocal*sizeof(int *),"AIREBO:firstneigh");
closestdistsq = (double *)
memory->smalloc(maxlocal*sizeof(double),"AIREBO:closestdistsq");
nC = (double *) memory->smalloc(maxlocal*sizeof(double),"AIREBO:nC");
nH = (double *) memory->smalloc(maxlocal*sizeof(double),"AIREBO:nH");
}
inum = list->inum;
allnum = list->inum + list->gnum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// initialize ghost atom references to -1 and closest distance = cutljrebosq
for (i = nlocal; i < nall; i++) {
REBO_numneigh[i] = -1;
closestdistsq[i] = cutljrebosq;
}
// store all REBO neighs of owned atoms
// store all REBO neighs of owned and ghost atoms
// scan full neighbor list of I
// if J is ghost and within LJ cutoff:
// flag it via REBO_numneigh so its REBO neighbors will be stored below
// REBO requires neighbors of neighbors of i,j in each i,j LJ interaction
npage = 0;
int npnt = 0;
for (ii = 0; ii < inum; ii++) {
for (ii = 0; ii < allnum; ii++) {
i = ilist[ii];
if (pgsize - npnt < oneatom) {
@ -367,82 +366,6 @@ void PairAIREBO::REBO_neigh()
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < rcmaxsq[itype][jtype]) {
neighptr[n++] = j;
if (jtype == 0)
nC[i] += Sp(sqrt(rsq),rcmin[itype][jtype],rcmax[itype][jtype],dS);
else
nH[i] += Sp(sqrt(rsq),rcmin[itype][jtype],rcmax[itype][jtype],dS);
}
if (j >= nlocal && rsq < closestdistsq[j]) {
REBO_numneigh[j] = i;
closestdistsq[j] = rsq;
}
}
REBO_firstneigh[i] = neighptr;
REBO_numneigh[i] = n;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
// store REBO neighs of ghost atoms I that have been flagged in REBO_numneigh
// find by scanning full neighbor list of owned atom M = closest neigh of I
for (i = nlocal; i < nall; i++) {
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
if (npage == maxpage) add_pages(npage);
}
neighptr = &pages[npage][npnt];
n = 0;
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = map[type[i]];
nC[i] = nH[i] = 0.0;
m = REBO_numneigh[i];
if (m < 0) {
REBO_firstneigh[i] = neighptr;
REBO_numneigh[i] = 0;
continue;
}
jtype = map[type[m]];
delx = xtmp - x[m][0];
dely = ytmp - x[m][1];
delz = ztmp - x[m][2];
rsq = delx*delx + dely*dely + delz*delz;
// add M as neigh of I if close enough
if (rsq < rcmaxsq[itype][jtype]) {
neighptr[n++] = m;
if (jtype == 0)
nC[i] += Sp(sqrt(rsq),rcmin[itype][jtype],rcmax[itype][jtype],dS);
else
nH[i] += Sp(sqrt(rsq),rcmin[itype][jtype],rcmax[itype][jtype],dS);
}
jlist = firstneigh[m];
jnum = numneigh[m];
// add M's neighbors as neighs of I if close enough
// skip I itself
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j == i) continue;
jtype = map[type[j]];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < rcmaxsq[itype][jtype]) {
neighptr[n++] = j;
if (jtype == 0)

2
src/MANYBODY/pair_airebo.h
View File

@ -36,6 +36,8 @@ class PairAIREBO : public Pair {
double memory_usage();
private:
double time1,time2;
int me;
int ljflag,torflag; // 0/1 if LJ,torsion terms included
int maxlocal; // size of numneigh, firstneigh arrays

5
src/PERI/pair_peri_lps.cpp
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@ -409,11 +409,6 @@ double PairPeriLPS::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all("All pair coeffs are not set");
cutsq[i][j] = cut[i][j] * cut[i][j];
cutsq[j][i] = cutsq[i][j];
// set other j,i parameters
bulkmodulus[j][i] = bulkmodulus[i][j];
shearmodulus[j][i] = shearmodulus[i][j];
s00[j][i] = s00[i][j];

5
src/PERI/pair_peri_pmb.cpp
View File

@ -346,11 +346,6 @@ double PairPeriPMB::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all("All pair coeffs are not set");
cutsq[i][j] = cut[i][j] * cut[i][j];
cutsq[j][i] = cutsq[i][j];
// set other j,i parameters
kspring[j][i] = kspring[i][j];
alpha[j][i] = alpha[i][j];
s00[j][i] = s00[i][j];

2
src/USER-REAXC/fix_reax_c.cpp
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@ -152,5 +152,5 @@ void FixReaxC::unpack_comm(int n, int first, double *buf)
m = 0;
last = first + n;
for (i = first; i < last; i++)
num_bonds[i] = buf[m++];
num_bonds[i] = static_cast<int> (buf[m++]);
}

1
src/USER-REAXC/reaxc_types.h
View File

@ -30,7 +30,6 @@
#include "string.h"
#include "sys/time.h"
#include "time.h"
#include "zlib.h"
/************* SOME DEFS - crucial for reax_types.h *********/

9
src/atom.cpp
View File

@ -55,6 +55,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
firstgroupname = NULL;
sortfreq = 1000;
nextsort = 0;
userbinsize = 0.0;
maxbin = maxnext = 0;
binhead = NULL;
@ -1357,6 +1358,10 @@ void Atom::sort()
{
int i,m,n,ix,iy,iz,ibin,empty;
// set next timestep for sorting to take place
nextsort = (update->ntimestep/sortfreq)*sortfreq + sortfreq;
// re-setup sort bins if needed
if (domain->box_change) setup_sort_bins();
@ -1440,10 +1445,6 @@ void Atom::sort()
//int flagall;
//MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
//if (flagall) error->all("Atom sort did not operate correctly");
// set next timestep for sorting to take place
nextsort = (update->ntimestep/sortfreq)*sortfreq + sortfreq;
}
/* ----------------------------------------------------------------------

6
src/comm.cpp
View File

@ -77,7 +77,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp)
allocate_swap(maxswap);
sendlist = (int **) memory->smalloc(maxswap*sizeof(int *),"comm:sendlist");
maxsendlist = new int[maxswap];
memory->create(maxsendlist,maxswap,"comm:maxsendlist");
for (int i = 0; i < maxswap; i++) {
maxsendlist[i] = BUFMIN;
memory->create(sendlist[i],BUFMIN,"comm:sendlist[i]");
@ -101,7 +101,7 @@ Comm::~Comm()
if (sendlist) for (int i = 0; i < maxswap; i++) memory->destroy(sendlist[i]);
memory->sfree(sendlist);
delete [] maxsendlist;
memory->destroy(maxsendlist);
memory->destroy(buf_send);
memory->destroy(buf_recv);
@ -1225,7 +1225,7 @@ void Comm::free_swap()
memory->destroy(slabhi);
memory->destroy(firstrecv);
memory->destroy(pbc_flag);
memory->destroy_2d_int_array(pbc);
memory->destroy(pbc);
}
/* ----------------------------------------------------------------------

16
src/neigh_derive.cpp
View File

@ -161,6 +161,7 @@ void Neighbor::half_from_full_newton(NeighList *list)
build skip list for subset of types from parent list
iskip and ijskip flag which atom types and type pairs to skip
this is for half and full lists
if ghostflag, also store neighbors of ghost atoms & set inum,gnum correctly
------------------------------------------------------------------------- */
void Neighbor::skip_from(NeighList *list)
@ -169,6 +170,7 @@ void Neighbor::skip_from(NeighList *list)
int *neighptr,*jlist;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
int *ilist = list->ilist;
@ -178,7 +180,8 @@ void Neighbor::skip_from(NeighList *list)
int *ilist_skip = list->listskip->ilist;
int *numneigh_skip = list->listskip->numneigh;
int **firstneigh_skip = list->listskip->firstneigh;
int inum_skip = list->listskip->inum;
int num_skip = list->listskip->inum;
if (list->ghostflag) num_skip += list->listskip->gnum;
int *iskip = list->iskip;
int **ijskip = list->ijskip;
@ -191,7 +194,7 @@ void Neighbor::skip_from(NeighList *list)
// skip I atom entirely if iskip is set for type[I]
// skip I,J pair if ijskip is set for type[I],type[J]
for (ii = 0; ii < inum_skip; ii++) {
for (ii = 0; ii < num_skip; ii++) {
i = ilist_skip[ii];
itype = type[i];
if (iskip[itype]) continue;
@ -226,6 +229,14 @@ void Neighbor::skip_from(NeighList *list)
}
list->inum = inum;
if (list->ghostflag) {
int num = 0;
for (i = 0; i < inum; i++)
if (ilist[i] < nlocal) num++;
else break;
list->inum = num;
list->gnum = inum - num;
}
}
/* ----------------------------------------------------------------------
@ -486,6 +497,7 @@ void Neighbor::copy_from(NeighList *list)
NeighList *listcopy = list->listcopy;
list->inum = listcopy->inum;
list->gnum = listcopy->gnum;
list->ilist = listcopy->ilist;
list->numneigh = listcopy->numneigh;
list->firstneigh = listcopy->firstneigh;

241
src/neigh_full.cpp
View File

@ -55,6 +55,8 @@ void Neighbor::full_nsq(NeighList *list)
int npage = 0;
int npnt = 0;
// loop over owned atoms, storing neighbors
for (i = 0; i < nlocal; i++) {
if (pgsize - npnt < oneatom) {
@ -101,6 +103,109 @@ void Neighbor::full_nsq(NeighList *list)
}
list->inum = inum;
list->gnum = 0;
}
/* ----------------------------------------------------------------------
N^2 search for all neighbors
include neighbors of ghost atoms
every neighbor pair appears in list of both atoms i and j
------------------------------------------------------------------------- */
void Neighbor::full_nsq_ghost(NeighList *list)
{
int i,j,n,itype,jtype,which;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
int **special = atom->special;
int **nspecial = atom->nspecial;
int *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int **pages = list->pages;
int inum = 0;
int npage = 0;
int npnt = 0;
// loop over owned & ghost atoms, storing neighbors
for (i = 0; i < nall; i++) {
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
if (npage == list->maxpage) pages = list->add_pages();
}
neighptr = &pages[npage][npnt];
n = 0;
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// loop over all atoms, owned and ghost
// skip i = j
if (i < nlocal) {
for (j = 0; j < nall; j++) {
if (i == j) continue;
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
}
}
} else {
for (j = 0; j < nall; j++) {
if (i == j) continue;
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighghostsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
}
}
}
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (n > oneatom || npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
list->inum = atom->nlocal;
list->gnum = inum - atom->nlocal;
}
/* ----------------------------------------------------------------------
@ -114,12 +219,10 @@ void Neighbor::full_bin(NeighList *list)
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
// bin local & ghost atoms
// bin owned & ghost atoms
bin_atoms();
// loop over each atom, storing neighbors
int **special = atom->special;
int **nspecial = atom->nspecial;
int *tag = atom->tag;
@ -144,6 +247,8 @@ void Neighbor::full_bin(NeighList *list)
int npage = 0;
int npnt = 0;
// loop over owned atoms, storing neighbors
for (i = 0; i < nlocal; i++) {
if (pgsize - npnt < oneatom) {
@ -195,6 +300,135 @@ void Neighbor::full_bin(NeighList *list)
}
list->inum = inum;
list->gnum = 0;
}
/* ----------------------------------------------------------------------
binned neighbor list construction for all neighbors
include neighbors of ghost atoms
every neighbor pair appears in list of both atoms i and j
------------------------------------------------------------------------- */
void Neighbor::full_bin_ghost(NeighList *list)
{
int i,j,k,n,itype,jtype,ibin,which;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int xbin,ybin,zbin,xbin2,ybin2,zbin2;
int *neighptr;
// bin owned & ghost atoms
bin_atoms();
int **special = atom->special;
int **nspecial = atom->nspecial;
int *tag = atom->tag;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int molecular = atom->molecular;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
int **pages = list->pages;
int nstencil = list->nstencil;
int *stencil = list->stencil;
int **stencilxyz = list->stencilxyz;
int inum = 0;
int npage = 0;
int npnt = 0;
// loop over owned & ghost atoms, storing neighbors
for (i = 0; i < nall; i++) {
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
if (npage == list->maxpage) pages = list->add_pages();
}
neighptr = &pages[npage][npnt];
n = 0;
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// loop over all atoms in surrounding bins in stencil including self
// when i is a ghost atom, must check if stencil bin is out of bounds
// skip i = j
if (i < nlocal) {
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (i == j) continue;
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
}
}
}
} else {
ibin = coord2bin(x[i],xbin,ybin,zbin);
for (k = 0; k < nstencil; k++) {
xbin2 = xbin + stencilxyz[k][0];
ybin2 = ybin + stencilxyz[k][1];
zbin2 = zbin + stencilxyz[k][2];
if (xbin2 < 0 || xbin2 >= mbinx ||
ybin2 < 0 || ybin2 >= mbiny ||
zbin2 < 0 || zbin2 >= mbinz) continue;
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (i == j) continue;
jtype = type[j];
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighghostsq[itype][jtype]) {
if (molecular) which = find_special(special[i],nspecial[i],tag[j]);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (which > 0) neighptr[n++] = which*nall + j;
}
}
}
}
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
npnt += n;
if (n > oneatom || npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
list->inum = atom->nlocal;
list->gnum = inum - atom->nlocal;
}
/* ----------------------------------------------------------------------
@ -297,4 +531,5 @@ void Neighbor::full_multi(NeighList *list)
}
list->inum = inum;
list->gnum = 0;
}

44
src/neigh_list.cpp
View File

@ -30,10 +30,10 @@ enum{NSQ,BIN,MULTI}; // also in neighbor.cpp
NeighList::NeighList(LAMMPS *lmp, int size) : Pointers(lmp)
{
maxlocal = 0;
maxatoms = 0;
pgsize = size;
inum = 0;
inum = gnum = 0;
ilist = NULL;
numneigh = NULL;
firstneigh = NULL;
@ -59,6 +59,7 @@ NeighList::NeighList(LAMMPS *lmp, int size) : Pointers(lmp)
maxstencil = 0;
stencil = NULL;
stencilxyz = NULL;
maxstencil_multi = 0;
nstencil_multi = NULL;
@ -88,6 +89,8 @@ NeighList::~NeighList()
memory->destroy(ijskip);
if (maxstencil) memory->destroy(stencil);
if (ghostflag) memory->destroy(stencilxyz);
if (maxstencil_multi) {
for (int i = 1; i <= atom->ntypes; i++) {
memory->destroy(stencil_multi[i]);
@ -106,22 +109,27 @@ NeighList::~NeighList()
void NeighList::grow(int nmax)
{
// skip if grow not needed
// skip if grow not needed by this list
// each list stores own maxatoms, b/c list->grow() called at different times
// if list does not store neighbors of ghosts, compare nmax to maxatoms
// else compare nlocal+nghost to maxatoms
// if reset list size, set it to nmax
if (nmax <= maxlocal) return;
maxlocal = nmax;
if (!ghostflag && atom->nlocal <= maxatoms) return;
if (ghostflag && atom->nlocal+atom->nghost <= maxatoms) return;
maxatoms = nmax;
memory->destroy(ilist);
memory->destroy(numneigh);
memory->sfree(firstneigh);
memory->create(ilist,maxlocal,"neighlist:ilist");
memory->create(numneigh,maxlocal,"neighlist:numneigh");
memory->create(ilist,maxatoms,"neighlist:ilist");
memory->create(numneigh,maxatoms,"neighlist:numneigh");
firstneigh = (int **)
memory->smalloc(maxlocal*sizeof(int *),"neighlist:firstneigh");
memory->smalloc(maxatoms*sizeof(int *),"neighlist:firstneigh");
if (dnum)
firstdouble = (double **)
memory->smalloc(maxlocal*sizeof(double *),"neighlist:firstdouble");
memory->smalloc(maxatoms*sizeof(double *),"neighlist:firstdouble");
}
/* ----------------------------------------------------------------------
@ -138,6 +146,10 @@ void NeighList::stencil_allocate(int smax, int style)
maxstencil = smax;
memory->destroy(stencil);
memory->create(stencil,maxstencil,"neighlist:stencil");
if (ghostflag) {
memory->destroy(stencilxyz);
memory->create(stencilxyz,maxstencil,3,"neighlist:stencilxyz");
}
}
} else {
@ -220,6 +232,7 @@ void NeighList::print_attributes()
printf(" %d = build flag\n",buildflag);
printf(" %d = grow flag\n",growflag);
printf(" %d = stencil flag\n",stencilflag);
printf(" %d = ghost flag\n",ghostflag);
printf("\n");
printf(" %d = pair\n",rq->pair);
printf(" %d = fix\n",rq->fix);
@ -237,6 +250,7 @@ void NeighList::print_attributes()
printf("\n");
printf(" %d = occasional\n",rq->occasional);
printf(" %d = dnum\n",rq->dnum);
printf(" %d = ghost\n",rq->ghost);
printf(" %d = copy\n",rq->copy);
printf(" %d = skip\n",rq->skip);
printf(" %d = otherlist\n",rq->otherlist);
@ -246,24 +260,26 @@ void NeighList::print_attributes()
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
if growflag = 0, maxlocal & maxpage will also be 0
if growflag = 0, maxatoms & maxpage will also be 0
if stencilflag = 0, maxstencil * maxstencil_multi will also be 0
------------------------------------------------------------------------- */
bigint NeighList::memory_usage()
{
bigint bytes = 0;
bytes += memory->usage(ilist,maxlocal);
bytes += memory->usage(numneigh,maxlocal);
bytes += maxlocal * sizeof(int *);
bytes += memory->usage(ilist,maxatoms);
bytes += memory->usage(numneigh,maxatoms);
bytes += maxatoms * sizeof(int *);
bytes += memory->usage(pages,maxpage,pgsize);
if (dnum) {
bytes += maxlocal * sizeof(double *);
bytes += maxatoms * sizeof(double *);
bytes += memory->usage(dpages,maxpage,dnum*pgsize);
}
if (maxstencil) bytes += memory->usage(stencil,maxstencil);
if (ghostflag) bytes += memory->usage(stencilxyz,maxstencil,3);
if (maxstencil_multi) {
bytes += memory->usage(stencil_multi,atom->ntypes,maxstencil_multi);
bytes += memory->usage(distsq_multi,atom->ntypes,maxstencil_multi);

7
src/neigh_list.h
View File

@ -26,10 +26,12 @@ class NeighList : protected Pointers {
int buildflag; // 1 if pair_build invoked every reneigh
int growflag; // 1 if stores atom-based arrays & pages
int stencilflag; // 1 if stores stencil arrays
int ghostflag; // 1 if it stores neighbors of ghosts
// data structs to store neighbor pairs I,J and associated values
int inum; // # of I atoms neighbors are stored for
int gnum; // # of ghost atoms neighbors are stored for
int *ilist; // local indices of I atoms
int *numneigh; // # of J neighbors for each I atom
int **firstneigh; // ptr to 1st J int value of each I atom
@ -45,7 +47,7 @@ class NeighList : protected Pointers {
// iskip,ijskip are just ptrs to corresponding request
int *iskip; // iskip[i] = 1 if atoms of type I are not in list
int **ijskip; // ijskip[i][j] =1 if pairs of type I,J are not in list
int **ijskip; // ijskip[i][j] = 1 if pairs of type I,J are not in list
// settings and pointers for related neighbor lists and fixes
@ -64,6 +66,7 @@ class NeighList : protected Pointers {
int maxstencil; // max size of stencil
int nstencil; // # of bins in stencil
int *stencil; // list of bin offsets
int **stencilxyz; // bin offsets in xyz dims
int maxstencil_multi; // max sizes of stencils
int *nstencil_multi; // # bins in each type-based multi stencil
@ -80,7 +83,7 @@ class NeighList : protected Pointers {
bigint memory_usage();
private:
int maxlocal; // size of allocated atom arrays
int maxatoms; // size of allocated atom arrays
};
}

8
src/neigh_request.cpp
View File

@ -37,6 +37,7 @@ NeighRequest::NeighRequest(LAMMPS *lmp) : Pointers(lmp)
gran = granhistory = 0;
respainner = respamiddle = respaouter = 0;
half_from_full = 0;
ghost = 0;
// default is use newton_pair setting in force
@ -50,6 +51,10 @@ NeighRequest::NeighRequest(LAMMPS *lmp) : Pointers(lmp)
dnum = 0;
// default is no neighbors of ghosts
ghost = 0;
// default is no copy or skip
copy = 0;
@ -96,6 +101,7 @@ int NeighRequest::identical(NeighRequest *other)
if (newton != other->newton) same = 0;
if (occasional != other->occasional) same = 0;
if (dnum != other->dnum) same = 0;
if (ghost != other->ghost) same = 0;
if (copy != other->copy) same = 0;
if (same_skip(other) == 0) same = 0;
@ -122,6 +128,7 @@ int NeighRequest::same_kind(NeighRequest *other)
if (respaouter != other->respaouter) same = 0;
if (half_from_full != other->half_from_full) same = 0;
if (newton != other->newton) same = 0;
if (ghost != other->ghost) same = 0;
return same;
}
@ -169,4 +176,5 @@ void NeighRequest::copy_request(NeighRequest *other)
newton = other->newton;
dnum = other->dnum;
ghost = other->ghost;
}

6
src/neigh_request.h
View File

@ -31,7 +31,7 @@ class NeighRequest : protected Pointers {
int compute;
int command;
// kind of list requested, one flag is 1, others are 0
// kind of list requested
// set by requesting class
int half; // 1 if half neigh list
@ -63,6 +63,10 @@ class NeighRequest : protected Pointers {
int dnum;
// 1 if also need neighbors of ghosts
int ghost;
// set by neighbor and pair_hybrid after all requests are made
// these settings do not change kind value

44
src/neigh_stencil.cpp
View File

@ -366,6 +366,28 @@ void Neighbor::stencil_full_bin_2d(NeighList *list,
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_full_ghost_bin_2d(NeighList *list,
int sx, int sy, int sz)
{
int i,j;
int *stencil = list->stencil;
int **stencilxyz = list->stencilxyz;
int nstencil = 0;
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
if (bin_distance(i,j,0) < cutneighmaxsq) {
stencilxyz[nstencil][0] = i;
stencilxyz[nstencil][1] = j;
stencilxyz[nstencil][2] = 0;
stencil[nstencil++] = j*mbinx + i;
}
list->nstencil = nstencil;
}
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_full_bin_3d(NeighList *list,
int sx, int sy, int sz)
{
@ -382,6 +404,28 @@ void Neighbor::stencil_full_bin_3d(NeighList *list,
list->nstencil = nstencil;
}
/* ---------------------------------------------------------------------- */
void Neighbor::stencil_full_ghost_bin_3d(NeighList *list,
int sx, int sy, int sz)
{
int i,j,k;
int *stencil = list->stencil;
int **stencilxyz = list->stencilxyz;
int nstencil = 0;
for (k = -sz; k <= sz; k++)
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
if (bin_distance(i,j,k) < cutneighmaxsq) {
stencilxyz[nstencil][0] = i;
stencilxyz[nstencil][1] = j;
stencilxyz[nstencil][2] = k;
stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
}
list->nstencil = nstencil;
}
/* ---------------------------------------------------------------------- */

111
src/neighbor.cpp
View File

@ -73,6 +73,7 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
build_once = 0;
cutneighsq = NULL;
cutneighghostsq = NULL;
cuttype = NULL;
cuttypesq = NULL;
fixchecklist = NULL;
@ -139,6 +140,7 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
Neighbor::~Neighbor()
{
memory->destroy(cutneighsq);
memory->destroy(cutneighghostsq);
delete [] cuttype;
delete [] cuttypesq;
delete [] fixchecklist;
@ -226,6 +228,7 @@ void Neighbor::init()
n = atom->ntypes;
if (cutneighsq == NULL) {
memory->create(cutneighsq,n+1,n+1,"neigh:cutneighsq");
memory->create(cutneighghostsq,n+1,n+1,"neigh:cutneighghostsq");
cuttype = new double[n+1];
cuttypesq = new double[n+1];
}
@ -248,6 +251,11 @@ void Neighbor::init()
cuttypesq[i] = MAX(cuttypesq[i],cut*cut);
cutneighmin = MIN(cutneighmin,cut);
cutneighmax = MAX(cutneighmax,cut);
if (force->pair && force->pair->ghostneigh) {
cut = force->pair->cutghost[i][j] + skin;
cutneighghostsq[i][j] = cut*cut;
}
}
}
cutneighmaxsq = cutneighmax * cutneighmax;
@ -463,7 +471,7 @@ void Neighbor::init()
// skip: point this list at request->otherlist, copy skip info from request
// half_from_full: point this list at preceeding full list
// granhistory: set preceeding list's listgranhistory to this list
// also set precedding list's ptr to FixShearHistory
// also set preceeding list's ptr to FixShearHistory
// respaouter: point this list at preceeding 1/2 inner/middle lists
// pair and half: if there is a full non-occasional non-skip list
// change this list to half_from_full and point at the full list
@ -551,11 +559,14 @@ void Neighbor::init()
else stencil_create[i] = NULL;
}
// set each list's build/grow/stencil flags based on neigh request
// set each list's build/grow/stencil/ghost flags based on neigh request
// buildflag = 1 if its pair_build() invoked every reneighbor
// growflag = 1 if it stores atom-based arrays and pages
// stencilflag = 1 if it stores stencil arrays
// ghostflag = 1 if it stores neighbors of ghosts
// anyghostlist = 1 if any non-occasional list stores neighbors of ghosts
anyghostlist = 0;
for (i = 0; i < nlist; i++) {
lists[i]->buildflag = 1;
if (pair_build[i] == NULL) lists[i]->buildflag = 0;
@ -567,6 +578,10 @@ void Neighbor::init()
lists[i]->stencilflag = 1;
if (style == NSQ) lists[i]->stencilflag = 0;
if (stencil_create[i] == NULL) lists[i]->stencilflag = 0;
lists[i]->ghostflag = 0;
if (requests[i]->ghost) lists[i]->ghostflag = 1;
if (requests[i]->ghost && !requests[i]->occasional) anyghostlist = 1;
}
#ifdef NEIGH_LIST_DEBUG
@ -773,8 +788,8 @@ int Neighbor::request(void *requestor)
determine which pair_build function each neigh list needs
based on settings of neigh request
copy -> copy_from function
skip -> granular function if gran with granhistory
respa function if respaouter
skip -> granular function if gran with granhistory,
respa function if respaouter,
skip_from function for everything else
half_from_full, half, full, gran, respaouter ->
choose by newton and rq->newton and tri settings
@ -804,10 +819,8 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
} else if (rq->half) {
if (style == NSQ) {
if (rq->newton == 0) {
if (newton_pair == 0)
pb = &Neighbor::half_nsq_no_newton;
else if (newton_pair == 1)
pb = &Neighbor::half_nsq_newton;
if (newton_pair == 0) pb = &Neighbor::half_nsq_no_newton;
else if (newton_pair == 1) pb = &Neighbor::half_nsq_newton;
} else if (rq->newton == 1) {
pb = &Neighbor::half_nsq_newton;
} else if (rq->newton == 2) {
@ -821,9 +834,7 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
} else if (rq->newton == 1) {
if (triclinic == 0) pb = &Neighbor::half_bin_newton;
else if (triclinic == 1) pb = &Neighbor::half_bin_newton_tri;
} else if (rq->newton == 2) {
pb = &Neighbor::half_bin_no_newton;
}
} else if (rq->newton == 2) pb = &Neighbor::half_bin_no_newton;
} else if (style == MULTI) {
if (rq->newton == 0) {
if (newton_pair == 0) pb = &Neighbor::half_multi_no_newton;
@ -832,15 +843,20 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
} else if (rq->newton == 1) {
if (triclinic == 0) pb = &Neighbor::half_multi_newton;
else if (triclinic == 1) pb = &Neighbor::half_multi_newton_tri;
} else if (rq->newton == 2) {
pb = &Neighbor::half_multi_no_newton;
}
} else if (rq->newton == 2) pb = &Neighbor::half_multi_no_newton;
}
} else if (rq->full) {
if (style == NSQ) pb = &Neighbor::full_nsq;
else if (style == BIN) pb = &Neighbor::full_bin;
else if (style == MULTI) pb = &Neighbor::full_multi;
if (style == NSQ) {
if (rq->ghost == 0) pb = &Neighbor::full_nsq;
else if (rq->ghost == 1) pb = &Neighbor::full_nsq_ghost;
} else if (style == BIN) {
if (rq->ghost == 0) pb = &Neighbor::full_bin;
else if (rq->ghost == 1) pb = &Neighbor::full_bin_ghost;
} else if (style == MULTI) {
if (rq->ghost == 0) pb = &Neighbor::full_multi;
else error->all("Neighbor multi not yet enabled for ghost neighbors");
}
} else if (rq->gran) {
if (style == NSQ) {
@ -865,6 +881,11 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
error->all("Neighbor multi not yet enabled for rRESPA");
}
// general error check
if (rq->ghost && !rq->full)
error->all("Neighbors of ghost atoms only allowed for full neighbor lists");
pair_build[index] = pb;
}
@ -961,8 +982,14 @@ void Neighbor::choose_stencil(int index, NeighRequest *rq)
} else if (rq->full) {
if (style == BIN) {
if (dimension == 2) sc = &Neighbor::stencil_full_bin_2d;
else if (dimension == 3) sc = &Neighbor::stencil_full_bin_3d;
if (dimension == 2) {
if (rq->ghost) sc = &Neighbor::stencil_full_ghost_bin_2d;
else sc = &Neighbor::stencil_full_bin_2d;
}
else if (dimension == 3) {
if (rq->ghost) sc = &Neighbor::stencil_full_ghost_bin_3d;
else sc = &Neighbor::stencil_full_bin_3d;
}
} else if (style == MULTI) {
if (dimension == 2) sc = &Neighbor::stencil_full_multi_2d;
else if (dimension == 3) sc = &Neighbor::stencil_full_multi_3d;
@ -1119,14 +1146,16 @@ void Neighbor::build()
}
}
// if necessary, extend atom arrays in pairwise lists
// only for lists with growflag set and which are used every reneighbor
// if any lists store neighbors of ghosts:
// invoke grow() on all in case nlocal+nghost is now too big
// else only invoke grow() if nlocal has exceeded previous list size
// only for lists with growflag set and which are perpetual
if (atom->nlocal > maxlocal) {
if (anyghostlist || atom->nlocal > maxlocal) {
maxlocal = atom->nmax;
for (i = 0; i < nglist; i++) lists[glist[i]]->grow(maxlocal);
}
// extend atom bin list if necessary
if (style != NSQ && atom->nmax > maxbin) {
@ -1612,6 +1641,42 @@ int Neighbor::coord2bin(double *x)
return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo);
}
/* ----------------------------------------------------------------------
same as coord2bin, but also return ix,iy,iz offsets in each dim
------------------------------------------------------------------------- */
int Neighbor::coord2bin(double *x, int &ix, int &iy, int &iz)
{
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;
ix -= mbinxlo;
iy -= mbinylo;
iz -= mbinzlo;
return iz*mbiny*mbinx + iy*mbinx + ix;
}
/* ----------------------------------------------------------------------
test if atom pair i,j is excluded from neighbor list
due to type, group, molecule settings from neigh_modify command

9
src/neighbor.h
View File

@ -86,6 +86,7 @@ class Neighbor : protected Pointers {
int *fixchecklist; // which fixes to check
double **cutneighsq; // neighbor cutneigh sq for each type pair
double **cutneighghostsq; // neighbor cutnsq for each ghost type pair
double cutneighmaxsq; // cutneighmax squared
double *cuttypesq; // cuttype squared
@ -130,6 +131,9 @@ class Neighbor : protected Pointers {
int special_flag[4]; // flags for 1-2, 1-3, 1-4 neighbors
int anyghostlist; // 1 if any non-occasional list
// stores neighbors of ghosts
int exclude; // 0 if no type/group exclusions, 1 if yes
int nex_type; // # of entries in type exclusion list
@ -155,6 +159,7 @@ class Neighbor : protected Pointers {
void bin_atoms(); // bin all atoms
double bin_distance(int, int, int); // distance between binx
int coord2bin(double *); // mapping atom coord to a bin
int coord2bin(double *, int &, int &, int&); // ditto
int exclusion(int, int, int, int, int *, int *); // test for pair exclusion
void choose_build(int, class NeighRequest *);
@ -210,7 +215,9 @@ class Neighbor : protected Pointers {
void half_multi_newton_tri(class NeighList *);
void full_nsq(class NeighList *);
void full_nsq_ghost(class NeighList *);
void full_bin(class NeighList *);
void full_bin_ghost(class NeighList *);
void full_multi(class NeighList *);
void half_from_full_no_newton(class NeighList *);
@ -252,7 +259,9 @@ class Neighbor : protected Pointers {
void stencil_half_multi_3d_newton_tri(class NeighList *, int, int, int);
void stencil_full_bin_2d(class NeighList *, int, int, int);
void stencil_full_ghost_bin_2d(class NeighList *, int, int, int);
void stencil_full_bin_3d(class NeighList *, int, int, int);
void stencil_full_ghost_bin_3d(class NeighList *, int, int, int);
void stencil_full_multi_2d(class NeighList *, int, int, int);
void stencil_full_multi_3d(class NeighList *, int, int, int);

2
src/pair.cpp
View File

@ -55,6 +55,8 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp)
respa_enable = 0;
one_coeff = 0;
no_virial_compute = 0;
ghostneigh = 0;
nextra = 0;
pvector = NULL;

4
src/pair.h
View File

@ -29,7 +29,7 @@ class Pair : protected Pointers {
double *eatom,**vatom; // accumulated per-atom energy/virial
double cutforce; // max cutoff for all atom pairs
double **cutsq; // max cutoff sq for each atom pair
double **cutsq; // cutoff sq for each atom pair
int **setflag; // 0/1 = whether each i,j has been set
int comm_forward; // size of forward communication (0 if none)
@ -39,6 +39,8 @@ class Pair : protected Pointers {
int respa_enable; // 1 if inner/middle/outer rRESPA routines
int one_coeff; // 1 if allows only one coeff * * call
int no_virial_compute; // 1 if does not invoke virial_compute()
int ghostneigh; // 1 if pair style needs neighbors of ghosts
double **cutghost; // cutoff for each ghost pair
int tail_flag; // pair_modify flag for LJ tail correction
double etail,ptail; // energy/pressure tail corrections

15
src/pair_hybrid.cpp
View File

@ -51,6 +51,7 @@ PairHybrid::~PairHybrid()
if (allocated) {
memory->destroy_2d_int_array(setflag);
memory->destroy_2d_double_array(cutsq);
memory->destroy_2d_double_array(cutghost);
memory->destroy_2d_int_array(nmap);
memory->destroy_3d_int_array(map);
}
@ -157,6 +158,7 @@ void PairHybrid::allocate()
setflag[i][j] = 0;
cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq");
cutghost = memory->create_2d_double_array(n+1,n+1,"pair:cutghost");
nmap = memory->create_2d_int_array(n+1,n+1,"pair:nmap");
map = memory->create_3d_int_array(n+1,n+1,nstyles,"pair:map");
@ -187,6 +189,7 @@ void PairHybrid::settings(int narg, char **arg)
if (allocated) {
memory->destroy_2d_int_array(setflag);
memory->destroy_2d_double_array(cutsq);
memory->destroy_2d_double_array(cutghost);
memory->destroy_2d_int_array(nmap);
memory->destroy_3d_int_array(map);
}
@ -262,6 +265,7 @@ void PairHybrid::settings(int narg, char **arg)
// single_enable = 0 if any sub-style = 0
// respa_enable = 1 if any sub-style is set
// no_virial_compute = 1 if any sub-style is set
// ghostneigh = 1 if any sub-style is set
for (m = 0; m < nstyles; m++)
if (styles[m]->single_enable == 0) single_enable = 0;
@ -269,6 +273,8 @@ void PairHybrid::settings(int narg, char **arg)
if (styles[m]->respa_enable) respa_enable = 1;
for (m = 0; m < nstyles; m++)
if (styles[m]->no_virial_compute) no_virial_compute = 1;
for (m = 0; m < nstyles; m++)
if (styles[m]->ghostneigh) ghostneigh = 1;
}
/* ----------------------------------------------------------------------
@ -455,12 +461,14 @@ double PairHybrid::init_one(int i, int j)
}
// call init/mixing for all sub-styles of I,J
// set cutsq in sub-style just as pair::init_one() does
// set cutsq in sub-style just as Pair::init() does via call to init_one()
// set cutghost for I,J and J,I just as sub-style does
// sum tail corrections for I,J
// return max cutoff of all sub-styles assigned to I,J
// if no sub-styles assigned to I,J (pair_coeff none), cutmax = 0.0 returned
double cutmax = 0.0;
cutghost[i][j] = cutghost[j][i] = 0.0;
if (tail_flag) etail_ij = ptail_ij = 0.0;
nmap[j][i] = nmap[i][j];
@ -470,6 +478,9 @@ double PairHybrid::init_one(int i, int j)
double cut = styles[map[i][j][k]]->init_one(i,j);
styles[map[i][j][k]]->cutsq[i][j] =
styles[map[i][j][k]]->cutsq[j][i] = cut*cut;
if (styles[map[i][j][k]]->ghostneigh)
cutghost[i][j] = cutghost[j][i] =
MAX(cutghost[i][j],styles[map[i][j][k]]->cutghost[i][j]);
if (tail_flag) {
etail_ij += styles[map[i][j][k]]->etail_ij;
ptail_ij += styles[map[i][j][k]]->ptail_ij;
@ -491,7 +502,7 @@ void PairHybrid::modify_requests()
// loop over pair requests only
// if list is skip list and not copy, look for non-skip list of same kind
// if one exists, point at that one
// if one exists, point at that one via otherlist
// else make new non-skip request of same kind and point at that one
// don't bother to set ID for new request, since pair hybrid ignores list
// only exception is half_from_full: