264 lines
8.5 KiB
C++
264 lines
8.5 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_bin.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 "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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NPairRespaBin<NEWTON, TRI>::NPairRespaBin(LAMMPS *lmp) : NPair(lmp) {}
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/* ----------------------------------------------------------------------
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multiple respa lists
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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 surrounding bins in non-Newton stencil
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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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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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every pair stored exactly once by some processor
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------------------------------------------------------------------------- */
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template<int NEWTON, int TRI>
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void NPairRespaBin<NEWTON, TRI>::build(NeighList *list)
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{
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int i, j, k, n, itype, jtype, ibin, bin_start, n_inner, n_middle, imol, iatom, moltemplate;
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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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const double delta = 0.01 * force->angstrom;
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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 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)
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moltemplate = 1;
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else
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moltemplate = 0;
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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 *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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MyPage<int> *ipage_inner = list->ipage_inner;
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int *ilist_middle, *numneigh_middle, **firstneigh_middle;
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MyPage<int> *ipage_middle;
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int respamiddle = list->respamiddle;
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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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ipage_middle = list->ipage_middle;
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}
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int inum = 0;
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int which = 0;
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int minchange = 0;
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ipage->reset();
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ipage_inner->reset();
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if (respamiddle) ipage_middle->reset();
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for (i = 0; i < nlocal; 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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itag = tag[i];
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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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for (k = 0; k < nstencil; k++) {
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bin_start = binhead[ibin+stencil[k]];
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if (NEWTON && (!TRI)) {
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if (k == 0) {
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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 (!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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// for triclinic, bin stencil is full in all 3 dims
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// must use itag/jtag to eliminate half the I/J interactions
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// cannot use I/J exact coord comparision
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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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if (j <= i) continue;
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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 {
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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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}
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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 (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 (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)
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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 &&
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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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}
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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()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
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ilist_inner[inum] = i;
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firstneigh_inner[i] = neighptr_inner;
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numneigh_inner[i] = n_inner;
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ipage_inner->vgot(n_inner);
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if (ipage_inner->status()) error->one(FLERR, "Neighbor list overflow, boost neigh_modify one");
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if (respamiddle) {
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ilist_middle[inum] = 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, "Neighbor list overflow, boost neigh_modify one");
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}
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inum++;
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}
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list->inum = inum;
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list->inum_inner = inum;
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if (respamiddle) list->inum_middle = inum;
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}
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namespace LAMMPS_NS {
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template class NPairRespaBin<0,0>;
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template class NPairRespaBin<1,0>;
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template class NPairRespaBin<1,1>;
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}
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