Adding other npair classes
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jtclemm
236
src/npair_multi_old.cpp
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236
src/npair_multi_old.cpp
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// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "npair_multi_old.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "domain.h"
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#include "error.h"
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#include "molecule.h"
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#include "my_page.h"
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#include "neigh_list.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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template<int HALF, int NEWTON, int TRI, int SIZE>
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NPairMultiOld<HALF, NEWTON, TRI, SIZE>::NPairMultiOld(LAMMPS *lmp) : NPair(lmp) {}
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/* ----------------------------------------------------------------------
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multi/old-type stencil is itype dependent and is distance checked
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Full:
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binned neighbor list construction for all neighbors
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multi-type stencil is itype dependent and is distance checked
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every neighbor pair appears in list of both atoms i and j
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Half + newtoff:
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binned neighbor list construction with partial Newton's 3rd law
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each owned atom i checks own bin and other bins in stencil
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multi-type stencil is itype dependent and is distance checked
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pair stored once if i,j are both owned and i < j
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pair stored by me if j is ghost (also stored by proc owning j)
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Half + newton:
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binned neighbor list construction with full Newton's 3rd law
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each owned atom i checks its own bin and other bins in Newton stencil
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multi-type stencil is itype dependent and is distance checked
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every pair stored exactly once by some processor
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------------------------------------------------------------------------- */
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template<int HALF, int NEWTON, int TRI, int SIZE>
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void NPairMultiOld<HALF, NEWTON, TRI, SIZE>::build(NeighList *list)
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{
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int i,j,jh,k,n,itype,jtype,ibin,bin_start,which,ns,imol,iatom,moltemplate;
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tagint tagprev;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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double radsum,cut,cutsq;
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int *neighptr,*s;
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double *cutsq,*distsq;
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double **x = atom->x;
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double *radius = atom->radius;
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int *type = atom->type;
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int *mask = atom->mask;
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tagint *tag = atom->tag;
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tagint *molecule = atom->molecule;
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tagint **special = atom->special;
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int **nspecial = atom->nspecial;
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int nlocal = atom->nlocal;
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if (includegroup) nlocal = atom->nfirst;
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int *molindex = atom->molindex;
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int *molatom = atom->molatom;
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Molecule **onemols = atom->avec->onemols;
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if (molecular == Atom::TEMPLATE) moltemplate = 1;
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else moltemplate = 0;
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int history = list->history;
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int mask_history = 1 << HISTBITS;
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int *ilist = list->ilist;
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int *numneigh = list->numneigh;
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int **firstneigh = list->firstneigh;
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MyPage<int> *ipage = list->ipage;
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int inum = 0;
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ipage->reset();
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for (i = 0; i < nlocal; i++) {
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n = 0;
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neighptr = ipage->vget();
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itype = type[i];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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if (moltemplate) {
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imol = molindex[i];
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iatom = molatom[i];
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tagprev = tag[i] - iatom - 1;
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}
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ibin = atom2bin[i];
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s = stencil_multi_old[itype];
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distsq = distsq_multi_old[itype];
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cutsq = cutneighsq[itype];
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ns = nstencil_multi_old[itype];
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for (k = 0; k < ns; k++) {
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bin_start = binhead[ibin+stencil[k]];
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if (stencil[k] == 0) {
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if (HALF && NEWTON && (!TRI)) {
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// Half neighbor list, newton on, orthonormal
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// loop over rest of atoms in i's bin, ghosts are at end of linked list
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bin_start = bins[i];
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}
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}
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for (j = bin_start; j >= 0; j = bins[j]) {
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if (!HALF) {
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// Full neighbor list
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// only skip i = j
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if (i == j) continue;
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} else if (!NEWTON) {
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// Half neighbor list, newton off
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// only store pair if i < j
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// stores own/own pairs only once
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// stores own/ghost pairs on both procs
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if (j <= i) continue;
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} else if (TRI) {
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// Half neighbor list, newton on, triclinic
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// pairs for atoms j "below" i are excluded
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// below = lower z or (equal z and lower y) or (equal zy and lower x)
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// (equal zyx and j <= i)
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// latter excludes self-self interaction but allows superposed atoms
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if (x[j][2] < ztmp) continue;
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if (x[j][2] == ztmp) {
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if (x[j][1] < ytmp) continue;
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if (x[j][1] == ytmp) {
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if (x[j][0] < xtmp) continue;
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if (x[j][0] == xtmp && j <= i) continue;
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}
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}
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} else {
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// Half neighbor list, newton on, orthonormal
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// store every pair for every bin in stencil,except for i's bin
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if (stencil[k] == 0) {
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// if j is owned atom, store it, since j is beyond i in linked list
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// if j is ghost, only store if j coords are "above and to the "right" of i
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if (j >= nlocal) {
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if (x[j][2] < ztmp) continue;
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if (x[j][2] == ztmp) {
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if (x[j][1] < ytmp) continue;
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if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
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}
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}
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}
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}
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jtype = type[j];
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if (cutsq[jtype] < distsq[k]) continue;
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if (i == j) continue;
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if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (SIZE) {
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radsum = radius[i] + radius[j];
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cut = radsum + skin;
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cutsq = cut * cut;
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if (rsq <= cutsq) {
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jh = j;
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if (history && rsq < radsum * radsum)
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jh = jh ^ mask_history;
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if (molecular != Atom::ATOMIC) {
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if (!moltemplate)
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which = find_special(special[i],nspecial[i],tag[j]);
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else if (imol >= 0)
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which = find_special(onemols[imol]->special[iatom],
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onemols[imol]->nspecial[iatom],
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tag[j]-tagprev);
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else which = 0;
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if (which == 0) neighptr[n++] = jh;
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else if (domain->minimum_image_check(delx,dely,delz))
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neighptr[n++] = jh;
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else if (which > 0) neighptr[n++] = jh ^ (which << SBBITS);
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} else neighptr[n++] = jh;
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}
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} else {
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if (rsq <= cutneighsq[itype][jtype]) {
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if (molecular != Atom::ATOMIC) {
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if (!moltemplate)
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which = find_special(special[i],nspecial[i],tag[j]);
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else if (imol >= 0)
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which = find_special(onemols[imol]->special[iatom],
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onemols[imol]->nspecial[iatom],
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tag[j]-tagprev);
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else which = 0;
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if (which == 0) neighptr[n++] = j;
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else if (domain->minimum_image_check(delx,dely,delz))
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neighptr[n++] = j;
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else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
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} else neighptr[n++] = j;
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}
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}
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}
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}
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ilist[inum++] = i;
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firstneigh[i] = neighptr;
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numneigh[i] = n;
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ipage->vgot(n);
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if (ipage->status())
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error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
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}
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list->inum = inum;
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list->gnum = 0;
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}
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namespace LAMMPS_NS {
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template class NPairMultiOld<0,1,0,0>;
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template class NPairMultiOld<1,0,0,0>;
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template class NPairMultiOld<1,1,0,0>;
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template class NPairMultiOld<1,1,1,0>;
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template class NPairMultiOld<0,1,0,1>;
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template class NPairMultiOld<1,0,0,1>;
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template class NPairMultiOld<1,1,0,1>;
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template class NPairMultiOld<1,1,1,1>;
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}
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