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Commit 2f02d984 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
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remove USER-DPD files that should not be where they are

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src/USER-DPD/#npair_half_bin_newton_ssa.cpp# deleted 100644 → 0
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View file @ 4553881f
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
James Larentzos and Timothy I. Mattox (Engility Corporation)
------------------------------------------------------------------------- */
#include "npair_half_bin_newton_ssa.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "domain.h"
#include "group.h"
#include "memory.h"
#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
// allocate space for static class variable
// prototype for non-class function
static int *ssaAIRptr;
static int cmp_ssaAIR(const void *, const void *);
/* ---------------------------------------------------------------------- */
NPairHalfBinNewtonSSA::NPairHalfBinNewtonSSA(LAMMPS *lmp) : NPair(lmp) {}
/* ----------------------------------------------------------------------
binned neighbor list construction with full Newton's 3rd law
for use by Shardlow Spliting Algorithm
each owned atom i checks its own bin and other bins in Newton stencil
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
void NPairHalfBinNewtonSSA::build(NeighList *list)
{
int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
if (includegroup) nlocal = atom->nfirst;
int *ssaAIR = atom->ssaAIR;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int molecular = atom->molecular;
if (molecular == 2) moltemplate = 1;
else moltemplate = 0;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
MyPage<int> *ipage = list->ipage;
int inum = 0;
// bin owned and ghost atoms for use by Shardlow Splitting Algorithm
// exclude ghost atoms that are not in the Active Interaction Regions (AIR)
// NOTE to Tim: this binatomflag no longer exists
// the logic up higher assures that binning has been done
// before this build() method is called
// maybe this code below needs to be in a new NBinShardlow class?
// this class also inherits NPair::nb from its parent
// which points to the NBin class that did the binning
// there are last_step variables stored there which indicate
// the last time binning was done
// the basic question is what data is created/stored by SSA binning
// and in what class should it live?
// if it is created by the binning operation, then I think
// it should be in a new NBinShardlow class
if (true /* binatomflag */) { // only false in Neighbor::build_one
if (mbins > list->maxhead_ssa) {
list->maxhead_ssa = mbins;
memory->destroy(list->gbinhead_ssa);
memory->destroy(list->binhead_ssa);
memory->create(list->binhead_ssa,list->maxhead_ssa,"binhead_ssa");
memory->create(list->gbinhead_ssa,list->maxhead_ssa,"gbinhead_ssa");
}
for (i = 0; i < mbins; i++) {
list->gbinhead_ssa[i] = -1;
list->binhead_ssa[i] = -1;
}
if (nall > list->maxbin_ssa) {
list->maxbin_ssa = nall;
memory->destroy(list->bins_ssa);
memory->create(list->bins_ssa,list->maxbin_ssa,"bins_ssa");
}
// bin in reverse order so linked list will be in forward order
if (includegroup) {
int bitmask = group->bitmask[includegroup];
int nowned = atom->nlocal; // NOTE: nlocal was set to atom->nfirst above
for (i = nall-1; i >= nowned; i--) {
if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR
if (mask[i] & bitmask) {
ibin = coord2bin(x[i]);
list->bins_ssa[i] = list->gbinhead_ssa[ibin];
list->gbinhead_ssa[ibin] = i;
}
}
} else {
for (i = nall-1; i >= nlocal; i--) {
if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR
ibin = coord2bin(x[i]);
list->bins_ssa[i] = list->gbinhead_ssa[ibin];
list->gbinhead_ssa[ibin] = i;
}
}
for (i = nlocal-1; i >= 0; i--) {
ibin = coord2bin(x[i]);
list->bins_ssa[i] = list->binhead_ssa[ibin];
list->binhead_ssa[ibin] = i;
}
} // else reuse previous binning. See Neighbor::build_one comment
ipage->reset();
// loop over owned atoms, storing half of the neighbors
for (i = 0; i < nlocal; i++) {
int AIRct[8] = { 0 };
n = 0;
neighptr = ipage->vget();
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
// loop over rest of local atoms in i's bin
// just store them, since j is beyond i in linked list
for (j = list->bins_ssa[i]; j >= 0; j = list->bins_ssa[j]) {
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) {
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >= 0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
ibin = coord2bin(x[i]);
// loop over all local atoms in other bins in "half" stencil
for (k = 0; k < nstencil; k++) {
for (j = list->binhead_ssa[ibin+stencil[k]]; j >= 0;
j = list->bins_ssa[j]) {
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) {
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >= 0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
}
AIRct[0] = n;
// loop over AIR ghost atoms in all bins in "full" stencil
// Note: the non-AIR ghost atoms have already been filtered out
// That is a significant time savings because of the "full" stencil
// Note2: only non-pure locals can have ghosts as neighbors
if (ssaAIR[i] == 1) for (k = 0; k < nstencil_ssa; k++) {
for (j = list->gbinhead_ssa[ibin+stencil[k]]; j >= 0;
j = list->bins_ssa[j]) {
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) {
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >= 0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) {
neighptr[n++] = j;
++(AIRct[ssaAIR[j] - 1]);
} else if (domain->minimum_image_check(delx,dely,delz)) {
neighptr[n++] = j;
++(AIRct[ssaAIR[j] - 1]);
} else if (which > 0) {
neighptr[n++] = j ^ (which << SBBITS);
++(AIRct[ssaAIR[j] - 1]);
}
} else {
neighptr[n++] = j;
++(AIRct[ssaAIR[j] - 1]);
}
}
}
}
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
// sort the ghosts in the neighbor list by their ssaAIR number
ssaAIRptr = atom->ssaAIR;
qsort(&(neighptr[AIRct[0]]), n - AIRct[0], sizeof(int), cmp_ssaAIR);
// do a prefix sum on the counts to turn them into indexes
list->ndxAIR_ssa[i][0] = AIRct[0];
for (int ndx = 1; ndx < 8; ++ndx) {
list->ndxAIR_ssa[i][ndx] = AIRct[ndx] + list->ndxAIR_ssa[i][ndx - 1];
}
}
list->inum = inum;
}
/* ----------------------------------------------------------------------
comparison function invoked by qsort()
accesses static class member ssaAIRptr, set before call to qsort()
------------------------------------------------------------------------- */
static int cmp_ssaAIR(const void *iptr, const void *jptr)
{
int i = *((int *) iptr);
int j = *((int *) jptr);
if (ssaAIRptr[i] < ssaAIRptr[j]) return -1;
if (ssaAIRptr[i] > ssaAIRptr[j]) return 1;
return 0;
}
src/npair_half_bin_newton_ssa.cpp deleted 100644 → 0
+ 0
− 311
View file @ 4553881f
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
James Larentzos and Timothy I. Mattox (Engility Corporation)
------------------------------------------------------------------------- */
#include "npair_half_bin_newton_ssa.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "domain.h"
#include "group.h"
#include "memory.h"
#include "my_page.h"
#include "error.h"
using namespace LAMMPS_NS;
// allocate space for static class variable
// prototype for non-class function
static int *ssaAIRptr;
static int cmp_ssaAIR(const void *, const void *);
/* ---------------------------------------------------------------------- */
NPairHalfBinNewtonSSA::NPairHalfBinNewtonSSA(LAMMPS *lmp) : NPair(lmp) {}
/* ----------------------------------------------------------------------
binned neighbor list construction with full Newton's 3rd law
for use by Shardlow Spliting Algorithm
each owned atom i checks its own bin and other bins in Newton stencil
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
void NPairHalfBinNewtonSSA::build(NeighList *list)
{
int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;
tagint tagprev;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *neighptr;
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
tagint *tag = atom->tag;
tagint *molecule = atom->molecule;
tagint **special = atom->special;
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
if (includegroup) nlocal = atom->nfirst;
int *ssaAIR = atom->ssaAIR;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int molecular = atom->molecular;
if (molecular == 2) moltemplate = 1;
else moltemplate = 0;
int *ilist = list->ilist;
int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
MyPage<int> *ipage = list->ipage;
int inum = 0;
// bin owned and ghost atoms for use by Shardlow Splitting Algorithm
// exclude ghost atoms that are not in the Active Interaction Regions (AIR)
// NOTE to Tim: this binatomflag no longer exists
// the logic up higher assures that binning has been done
// before this build() method is called
// maybe this code below needs to be in a new NBinShardlow class?
// this class also inherits NPair::nb from its parent
// which points to the NBin class that did the binning
// there are last_step variables stored there which indicate
// the last time binning was done
// the basic question is what data is created/stored by SSA binning
// and in what class should it live?
// if it is created by the binning operation, then I think
// it should be in a new NBinShardlow class
if (true /* binatomflag */) { // only false in Neighbor::build_one
if (mbins > list->maxhead_ssa) {
list->maxhead_ssa = mbins;
memory->destroy(list->gbinhead_ssa);
memory->destroy(list->binhead_ssa);
memory->create(list->binhead_ssa,list->maxhead_ssa,"binhead_ssa");
memory->create(list->gbinhead_ssa,list->maxhead_ssa,"gbinhead_ssa");
}
for (i = 0; i < mbins; i++) {
list->gbinhead_ssa[i] = -1;
list->binhead_ssa[i] = -1;
}
if (nall > list->maxbin_ssa) {
list->maxbin_ssa = nall;
memory->destroy(list->bins_ssa);
memory->create(list->bins_ssa,list->maxbin_ssa,"bins_ssa");
}
// bin in reverse order so linked list will be in forward order
if (includegroup) {
int bitmask = group->bitmask[includegroup];
int nowned = atom->nlocal; // NOTE: nlocal was set to atom->nfirst above
for (i = nall-1; i >= nowned; i--) {
if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR
if (mask[i] & bitmask) {
ibin = coord2bin(x[i]);
list->bins_ssa[i] = list->gbinhead_ssa[ibin];
list->gbinhead_ssa[ibin] = i;
}
}
} else {
for (i = nall-1; i >= nlocal; i--) {
if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR
ibin = coord2bin(x[i]);
list->bins_ssa[i] = list->gbinhead_ssa[ibin];
list->gbinhead_ssa[ibin] = i;
}
}
for (i = nlocal-1; i >= 0; i--) {
ibin = coord2bin(x[i]);
list->bins_ssa[i] = list->binhead_ssa[ibin];
list->binhead_ssa[ibin] = i;
}
} // else reuse previous binning. See Neighbor::build_one comment
ipage->reset();
// loop over owned atoms, storing half of the neighbors
for (i = 0; i < nlocal; i++) {
int AIRct[8] = { 0 };
n = 0;
neighptr = ipage->vget();
itype = type[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
if (moltemplate) {
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
}
// loop over rest of local atoms in i's bin
// just store them, since j is beyond i in linked list
for (j = list->bins_ssa[i]; j >= 0; j = list->bins_ssa[j]) {
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) {
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >= 0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
ibin = coord2bin(x[i]);
// loop over all local atoms in other bins in "half" stencil
for (k = 0; k < nstencil; k++) {
for (j = list->binhead_ssa[ibin+stencil[k]]; j >= 0;
j = list->bins_ssa[j]) {
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) {
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >= 0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) neighptr[n++] = j;
else if (domain->minimum_image_check(delx,dely,delz))
neighptr[n++] = j;
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
} else neighptr[n++] = j;
}
}
}
AIRct[0] = n;
// loop over AIR ghost atoms in all bins in "full" stencil
// Note: the non-AIR ghost atoms have already been filtered out
// That is a significant time savings because of the "full" stencil
// Note2: only non-pure locals can have ghosts as neighbors
if (ssaAIR[i] == 1) for (k = 0; k < nstencil_ssa; k++) {
for (j = list->gbinhead_ssa[ibin+stencil[k]]; j >= 0;
j = list->bins_ssa[j]) {
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) {
if (!moltemplate)
which = find_special(special[i],nspecial[i],tag[j]);
else if (imol >= 0)
which = find_special(onemols[imol]->special[iatom],
onemols[imol]->nspecial[iatom],
tag[j]-tagprev);
else which = 0;
if (which == 0) {
neighptr[n++] = j;
++(AIRct[ssaAIR[j] - 1]);
} else if (domain->minimum_image_check(delx,dely,delz)) {
neighptr[n++] = j;
++(AIRct[ssaAIR[j] - 1]);
} else if (which > 0) {
neighptr[n++] = j ^ (which << SBBITS);
++(AIRct[ssaAIR[j] - 1]);
}
} else {
neighptr[n++] = j;
++(AIRct[ssaAIR[j] - 1]);
}
}
}
}
ilist[inum++] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
// sort the ghosts in the neighbor list by their ssaAIR number
ssaAIRptr = atom->ssaAIR;
qsort(&(neighptr[AIRct[0]]), n - AIRct[0], sizeof(int), cmp_ssaAIR);
// do a prefix sum on the counts to turn them into indexes
list->ndxAIR_ssa[i][0] = AIRct[0];
for (int ndx = 1; ndx < 8; ++ndx) {
list->ndxAIR_ssa[i][ndx] = AIRct[ndx] + list->ndxAIR_ssa[i][ndx - 1];
}
}
list->inum = inum;
}
/* ----------------------------------------------------------------------
comparison function invoked by qsort()
accesses static class member ssaAIRptr, set before call to qsort()
------------------------------------------------------------------------- */
static int cmp_ssaAIR(const void *iptr, const void *jptr)
{
int i = *((int *) iptr);
int j = *((int *) jptr);
if (ssaAIRptr[i] < ssaAIRptr[j]) return -1;
if (ssaAIRptr[i] > ssaAIRptr[j]) return 1;
return 0;
}
src/npair_half_bin_newton_ssa.h deleted 100644 → 0
+ 0
− 43
View file @ 4553881f
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef NPAIR_CLASS
NPairStyle(half/bin/newton/ssa,
NPairHalfBinNewtonSSA,
NP_BIN | NP_NEWTON | NP_ORTHO | NP_SSA)
#else
#ifndef LMP_NPAIR_HALF_BIN_NEWTON_SSA_H
#define LMP_NPAIR_HALF_BIN_NEWTON_SSA_H
#include "npair.h"
namespace LAMMPS_NS {
class NPairHalfBinNewtonSSA : public NPair {
public:
NPairHalfBinNewtonSSA(class LAMMPS *);
~NPairHalfBinNewtonSSA() {}
void build(class NeighList *);
};
}
#endif
#endif
/* ERROR/WARNING messages:
*/
src/nstencil_half_bin_2d_newton_ssa.cpp deleted 100644 → 0
+ 0
− 64
View file @ 4553881f
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
James Larentzos and Timothy I. Mattox (Engility Corporation)
------------------------------------------------------------------------- */
#include "nstencil_half_bin_2d_newton_ssa.h"
#include "neighbor.h"
#include "neigh_list.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NStencilHalfBin2dNewtonSSA::NStencilHalfBin2dNewtonSSA(LAMMPS *lmp) :
NStencil(lmp) {}
/* ----------------------------------------------------------------------
create stencil based on bin geometry and cutoff
stencil = bins whose closest corner to central bin is within cutoff
sx,sy,sz = bin bounds = furthest the stencil could possibly extend
3d creates xyz stencil, 2d creates xy stencil
for half list with newton on:
stencil is bins to the "upper right" of central bin
stencil does not include self
additionally, includes the bins beyond nstencil that are needed
to locate all the Active Interaction Region (AIR) ghosts for SSA
------------------------------------------------------------------------- */
void NStencilHalfBin2dNewtonSSA::create()
{
int i,j,pos = 0;
for (j = 0; j <= sy; j++)
for (i = -sx; i <= sx; i++)
if (j > 0 || (j == 0 && i > 0))
if (bin_distance(i,j,0) < cutneighmaxsq)
stencil[pos++] = j*mbinx + i;
nstencil = pos; // record where normal half stencil ends
// include additional bins for AIR ghosts only
for (j = -sy; j <= 0; j++)
for (i = -sx; i <= sx; i++) {
if (j == 0 && i > 0) continue;
if (bin_distance(i,j,0) < cutneighmaxsq)
stencil[pos++] = j*mbinx + i;
}
nstencil_ssa = pos; // record where full stencil ends
}
src/nstencil_half_bin_2d_newton_ssa.h deleted 100644 → 0
+ 0
− 43
View file @ 4553881f
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef NSTENCIL_CLASS
NStencilStyle(half/bin/2d/newton/ssa,
NStencilHalfBin2dNewtonSSA,
NS_HALF | NS_BIN | NS_2D | NS_NEWTON | NS_SSA | NS_ORTHO)
#else
#ifndef LMP_NSTENCIL_HALF_BIN_2D_NEWTON_SSA_H
#define LMP_NSTENCIL_HALF_BIN_2D_NEWTON_SSA_H
#include "nstencil.h"
namespace LAMMPS_NS {
class NStencilHalfBin2dNewtonSSA : public NStencil {
public:
NStencilHalfBin2dNewtonSSA(class LAMMPS *);
~NStencilHalfBin2dNewtonSSA() {}
void create();
};
}
#endif
#endif
/* ERROR/WARNING messages:
*/
src/nstencil_half_bin_3d_newton_ssa.cpp deleted 100644 → 0
+ 0
− 74
View file @ 4553881f
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors:
James Larentzos and Timothy I. Mattox (Engility Corporation)
------------------------------------------------------------------------- */
#include "nstencil_half_bin_3d_newton_ssa.h"
#include "neighbor.h"
#include "neigh_list.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
NStencilHalfBin3dNewtonSSA::NStencilHalfBin3dNewtonSSA(LAMMPS *lmp) :
NStencil(lmp) {}
/* ----------------------------------------------------------------------
create stencil based on bin geometry and cutoff
stencil = bins whose closest corner to central bin is within cutoff
sx,sy,sz = bin bounds = furthest the stencil could possibly extend
3d creates xyz stencil, 2d creates xy stencil
for half list with newton on:
stencil is bins to the "upper right" of central bin
stencil does not include self
additionally, includes the bins beyond nstencil that are needed
to locate all the Active Interaction Region (AIR) ghosts for SSA
------------------------------------------------------------------------- */
void NStencilHalfBin3dNewtonSSA::create()
{
int i,j,k,pos = 0;
for (k = 0; k <= sz; k++)
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
if (k > 0 || j > 0 || (j == 0 && i > 0))
if (bin_distance(i,j,k) < cutneighmaxsq)
stencil[pos++] = k*mbiny*mbinx + j*mbinx + i;
nstencil = pos; // record where normal half stencil ends
// include additional bins for AIR ghosts only
for (k = -sz; k < 0; k++)
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
if (bin_distance(i,j,k) < cutneighmaxsq)
stencil[pos++] = k*mbiny*mbinx + j*mbinx + i;
// For k==0, make sure to skip already included bins
k = 0;
for (j = -sy; j <= 0; j++)
for (i = -sx; i <= sx; i++) {
if (j == 0 && i > 0) continue;
if (bin_distance(i,j,k) < cutneighmaxsq)
stencil[pos++] = k*mbiny*mbinx + j*mbinx + i;
}
nstencil_ssa = pos; // record where full stencil ends
}
src/nstencil_half_bin_3d_newton_ssa.h deleted 100644 → 0
+ 0
− 43
View file @ 4553881f
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef NSTENCIL_CLASS
NStencilStyle(half/bin/3d/newton/ssa,
NStencilHalfBin3dNewtonSSA,
NS_HALF | NS_BIN | NS_3D | NS_NEWTON | NS_SSA | NS_ORTHO)
#else
#ifndef LMP_NSTENCIL_HALF_BIN_3D_NEWTON_SSA_H
#define LMP_NSTENCIL_HALF_BIN_3D_NEWTON_SSA_H
#include "nstencil.h"
namespace LAMMPS_NS {
class NStencilHalfBin3dNewtonSSA : public NStencil {
public:
NStencilHalfBin3dNewtonSSA(class LAMMPS *);
~NStencilHalfBin3dNewtonSSA() {}
void create();
};
}
#endif
#endif
/* ERROR/WARNING messages:
*/
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