254 lines
8.0 KiB
C++
254 lines
8.0 KiB
C++
// 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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LAMMPS development team: developers@lammps.org
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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_respa_nsq_omp.h"
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#include "npair_omp.h"
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#include "omp_compat.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 "force.h"
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#include "group.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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#include <cmath>
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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template<int NEWTON, int TRI>
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NPairRespaNsqOmp<NEWTON, TRI>::NPairRespaNsqOmp(LAMMPS *lmp) :
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NPair(lmp) {}
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/* ----------------------------------------------------------------------
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multiple respa lists
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Newtoff
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N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
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pair added to list if atoms i and j are both owned and i < j
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pair added if j is ghost (also stored by proc owning j)
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Newton
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N^2 / 2 search for neighbor pairs with full Newton's 3rd law
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pair added to list if atoms i and j are both owned and i < j
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if j is ghost only me or other proc adds pair
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decision based on itag,jtag tests
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use itag/jtag comparision to eliminate half the interactions
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itag = jtag is possible for long cutoffs that include images of self
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Newton + Triclinic:
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for triclinic, must use delta to eliminate half the I/J interactions
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cannot use I/J exact coord comparision as for orthog
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b/c transforming orthog -> lambda -> orthog for ghost atoms
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with an added PBC offset can shift all 3 coords by epsilon
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------------------------------------------------------------------------- */
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template<int NEWTON, int TRI>
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void NPairRespaNsqOmp<NEWTON, TRI>::build(NeighList *list)
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{
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const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
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const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0;
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const int molecular = atom->molecular;
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const int moltemplate = (molecular == Atom::TEMPLATE) ? 1 : 0;
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const double delta = 0.01 * force->angstrom;
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NPAIR_OMP_INIT;
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const int respamiddle = list->respamiddle;
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#if defined(_OPENMP)
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#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list)
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#endif
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NPAIR_OMP_SETUP(nlocal);
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int i, j, n, itype, jtype, n_inner, n_middle, imol, iatom;
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tagint itag, jtag, tagprev;
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double xtmp, ytmp, ztmp, delx, dely, delz, rsq;
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int *neighptr, *neighptr_inner, *neighptr_middle;
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double **x = atom->x;
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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 *molindex = atom->molindex;
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int *molatom = atom->molatom;
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Molecule **onemols = atom->avec->onemols;
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int nall = atom->nlocal + atom->nghost;
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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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int *ilist_inner = list->ilist_inner;
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int *numneigh_inner = list->numneigh_inner;
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int **firstneigh_inner = list->firstneigh_inner;
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int *ilist_middle, *numneigh_middle, **firstneigh_middle;
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if (respamiddle) {
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ilist_middle = list->ilist_middle;
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numneigh_middle = list->numneigh_middle;
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firstneigh_middle = list->firstneigh_middle;
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}
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// each thread has its own page allocator
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MyPage<int> &ipage = list->ipage[tid];
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MyPage<int> &ipage_inner = list->ipage_inner[tid];
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ipage.reset();
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ipage_inner.reset();
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MyPage<int> *ipage_middle;
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if (respamiddle) {
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ipage_middle = list->ipage_middle + tid;
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ipage_middle->reset();
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}
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int which = 0;
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int minchange = 0;
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for (i = ifrom; i < ito; i++) {
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n = n_inner = 0;
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neighptr = ipage.vget();
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neighptr_inner = ipage_inner.vget();
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if (respamiddle) {
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n_middle = 0;
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neighptr_middle = ipage_middle->vget();
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}
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itype = type[i];
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itag = tag[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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// loop over remaining atoms, owned and ghost
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for (j = i + 1; j < nall; j++) {
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if (includegroup && !(mask[j] & bitmask)) continue;
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if (NEWTON) {
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if (j >= nlocal) {
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jtag = tag[j];
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if (itag > jtag) {
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if ((itag + jtag) % 2 == 0) continue;
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} else if (itag < jtag) {
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if ((itag + jtag) % 2 == 1) continue;
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} else if (TRI) {
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if (fabs(x[j][2] - ztmp) > delta) {
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if (x[j][2] < ztmp) continue;
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} else if (fabs(x[j][1] - ytmp) > delta) {
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if (x[j][1] < ytmp) continue;
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} else {
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if (x[j][0] < xtmp) continue;
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}
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} else {
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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 (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 (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) && onemols[imol]->special)
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which = find_special(onemols[imol]->special[iatom], onemols[imol]->nspecial[iatom],
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tag[j] - tagprev);
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else
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which = 0;
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if (which == 0)
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neighptr[n++] = j;
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else if ((minchange = domain->minimum_image_check(delx, dely, delz)))
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neighptr[n++] = j;
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else if (which > 0)
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neighptr[n++] = j ^ (which << SBBITS);
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} else
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neighptr[n++] = j;
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if (rsq < cut_inner_sq) {
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if (which == 0)
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neighptr_inner[n_inner++] = j;
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else if (minchange)
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neighptr_inner[n_inner++] = j;
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else if (which > 0)
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neighptr_inner[n_inner++] = j ^ (which << SBBITS);
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}
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if (respamiddle && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
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if (which == 0)
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neighptr_middle[n_middle++] = j;
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else if (minchange)
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neighptr_middle[n_middle++] = j;
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else if (which > 0)
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neighptr_middle[n_middle++] = j ^ (which << SBBITS);
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}
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}
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}
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ilist[i] = 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()) error->one(FLERR, Error::NOLASTLINE, "Neighbor list overflow, boost neigh_modify one" + utils::errorurl(36));
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ilist_inner[i] = i;
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firstneigh_inner[i] = neighptr_inner;
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numneigh_inner[i] = n_inner;
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ipage.vgot(n_inner);
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if (ipage_inner.status()) error->one(FLERR, Error::NOLASTLINE, "Neighbor list overflow, boost neigh_modify one" + utils::errorurl(36));
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if (respamiddle) {
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ilist_middle[i] = i;
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firstneigh_middle[i] = neighptr_middle;
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numneigh_middle[i] = n_middle;
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ipage_middle->vgot(n_middle);
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if (ipage_middle->status()) error->one(FLERR, Error::NOLASTLINE, "Neighbor list overflow, boost neigh_modify one" + utils::errorurl(36));
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}
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}
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NPAIR_OMP_CLOSE;
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list->inum = nlocal;
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list->inum_inner = nlocal;
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if (respamiddle) list->inum_middle = nlocal;
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}
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namespace LAMMPS_NS {
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template class NPairRespaNsqOmp<0,0>;
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template class NPairRespaNsqOmp<1,0>;
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template class NPairRespaNsqOmp<1,1>;
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}
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