307 lines
11 KiB
C++
307 lines
11 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_multi_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 "molecule.h"
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#include "my_page.h"
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#include "neigh_list.h"
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#include "neighbor.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, int ATOMONLY>
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NPairMultiOmp<HALF, NEWTON, TRI, SIZE, ATOMONLY>::NPairMultiOmp(LAMMPS *lmp) : NPair(lmp) {}
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/* ----------------------------------------------------------------------
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multi stencil is icollection-jcollection dependent
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Full:
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binned neighbor list construction for all neighbors
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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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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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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, int ATOMONLY>
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void NPairMultiOmp<HALF, NEWTON, TRI, SIZE, ATOMONLY>::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 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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#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, jh, js, k, n, itype, jtype, ibin, jbin, icollection, jcollection, which, ns, imol, iatom;
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tagint itag, jtag, tagprev;
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double xtmp, ytmp, ztmp, delx, dely, delz, rsq, radsum, cut, cutsq;
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int *neighptr, *s;
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int *collection = neighbor->collection;
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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 *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 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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// each thread has its own page allocator
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MyPage<int> &ipage = list->ipage[tid];
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ipage.reset();
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for (i = ifrom; i < ito; i++) {
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n = 0;
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neighptr = ipage.vget();
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itag = tag[i];
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itype = type[i];
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icollection = collection[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 (!ATOMONLY) {
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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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}
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ibin = atom2bin[i];
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// loop through stencils for all collections
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for (jcollection = 0; jcollection < ncollections; jcollection++) {
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// if same collection use own bin
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if (icollection == jcollection) jbin = ibin;
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else jbin = coord2bin(x[i], jcollection);
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s = stencil_multi[icollection][jcollection];
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ns = nstencil_multi[icollection][jcollection];
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for (k = 0; k < ns; k++) {
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js = binhead_multi[jcollection][jbin + s[k]];
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// own-bin for half stencil
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if (HALF && !TRI)
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if (flag_half_multi[icollection][jcollection] && s[k] == 0) js = bins[i];
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for (j = js; 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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// if same size (same collection), use half stencil
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// Always have full stencil
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// if same size (same collection), exclude half of interactions
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// stencil is empty if i larger than j
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// stencil is full if i smaller than j
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// stencil is full if i same size as j
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// for i smaller than j:
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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 (flag_same_multi[icollection][jcollection]) {
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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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}
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} else {
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// Half neighbor list, newton on, orthonormal
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// if same size: uses half stencil so includes a check of the central bin
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if (flag_half_multi[icollection][jcollection]){
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if (s[k] == 0) {
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// if same collection,
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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 different collections,
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// if j is owned atom, store it if j > i
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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 ((icollection != jcollection) && (j < i)) continue;
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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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}
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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 (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 (ATOMONLY) {
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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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neighptr[n++] = jh;
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}
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} else {
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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], 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++] = 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)
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neighptr[n++] = jh ^ (which << SBBITS);
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} else
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neighptr[n++] = jh;
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}
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}
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} else {
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if (ATOMONLY) {
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if (rsq <= cutneighsq[itype][jtype]) neighptr[n++] = j;
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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], 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 (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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}
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}
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}
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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,"Neighbor list overflow, boost neigh_modify one");
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}
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NPAIR_OMP_CLOSE;
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list->inum = nlocal;
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list->gnum = 0;
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}
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namespace LAMMPS_NS {
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template class NPairMultiOmp<0,1,0,0,0>;
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template class NPairMultiOmp<1,0,0,0,0>;
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template class NPairMultiOmp<1,1,0,0,0>;
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template class NPairMultiOmp<1,1,1,0,0>;
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template class NPairMultiOmp<0,1,0,1,0>;
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template class NPairMultiOmp<1,0,0,1,0>;
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template class NPairMultiOmp<1,1,0,1,0>;
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template class NPairMultiOmp<1,1,1,1,0>;
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template class NPairMultiOmp<0,1,0,0,1>;
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template class NPairMultiOmp<1,0,0,0,1>;
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template class NPairMultiOmp<1,1,0,0,1>;
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template class NPairMultiOmp<1,1,1,0,1>;
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template class NPairMultiOmp<0,1,0,1,1>;
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template class NPairMultiOmp<1,0,0,1,1>;
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template class NPairMultiOmp<1,1,0,1,1>;
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template class NPairMultiOmp<1,1,1,1,1>;
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}
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