Merge branch 'master' into prepare-clang-format
# Conflicts: # src/KOKKOS/nbin_kokkos.h # src/KOKKOS/nbin_ssa_kokkos.h # src/MOLECULE/bond_fene_expand.h # src/USER-DPD/nbin_ssa.h # src/USER-DPD/nstencil_half_bin_2d_ssa.h # src/USER-DPD/nstencil_half_bin_3d_ssa.h # src/USER-INTEL/nbin_intel.h # src/USER-MISC/fix_propel_self.cpp # src/USER-OMP/npair_full_multi_old_omp.h # src/USER-OMP/npair_half_multi_old_newton_omp.h # src/USER-OMP/npair_half_size_multi_newtoff_omp.h # src/USER-OMP/npair_halffull_newtoff_omp.h # src/USER-OMP/npair_halffull_newton_omp.h # src/USER-OMP/npair_skip_omp.h # src/main.cpp # src/nbin_standard.h # src/npair_full_multi_old.h # src/npair_halffull_newtoff.h # src/npair_halffull_newton.h # src/npair_skip.h # src/npair_skip_respa.h # src/npair_skip_size.h # src/npair_skip_size_off2on.h # src/npair_skip_size_off2on_oneside.h # src/nstencil_full_bin_2d.h # src/nstencil_full_bin_3d.h # src/nstencil_full_ghost_bin_2d.h # src/nstencil_full_ghost_bin_3d.h # src/nstencil_full_multi_2d.h # src/nstencil_full_multi_3d.h # src/nstencil_full_multi_old_2d.h # src/nstencil_full_multi_old_3d.h # src/nstencil_half_bin_2d_newtoff.cpp # src/nstencil_half_bin_3d_newtoff.cpp # src/nstencil_half_bin_3d_newton_tri.h # src/nstencil_half_ghost_bin_2d_newtoff.cpp # src/nstencil_half_ghost_bin_2d_newtoff.h # src/nstencil_half_ghost_bin_3d_newtoff.cpp # src/nstencil_half_ghost_bin_3d_newtoff.h # src/nstencil_half_multi_2d.h # src/nstencil_half_multi_2d_newtoff.h # src/nstencil_half_multi_2d_newton_tri.h # src/nstencil_half_multi_2d_tri.h # src/nstencil_half_multi_3d_newtoff.h # src/nstencil_half_multi_3d_newton_tri.h
This commit is contained in:
Axel Kohlmeyer
@ -13,13 +13,15 @@
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------------------------------------------------------------------------- */
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#include "npair_half_multi_newton.h"
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#include "neigh_list.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "molecule.h"
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#include "domain.h"
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#include "my_page.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 "neighbor.h"
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#include "neigh_list.h"
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using namespace LAMMPS_NS;
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@ -29,19 +31,20 @@ NPairHalfMultiNewton::NPairHalfMultiNewton(LAMMPS *lmp) : NPair(lmp) {}
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/* ----------------------------------------------------------------------
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binned neighbor list construction with full Newton's 3rd law
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multi stencil is icollection-jcollection dependent
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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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void NPairHalfMultiNewton::build(NeighList *list)
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{
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int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate;
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int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,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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int *neighptr,*s;
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double *cutsq,*distsq;
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int js;
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int *collection = neighbor->collection;
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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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@ -55,7 +58,7 @@ void NPairHalfMultiNewton::build(NeighList *list)
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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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if (molecular == 2) moltemplate = 1;
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else moltemplate = 0;
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int *ilist = list->ilist;
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@ -69,8 +72,8 @@ void NPairHalfMultiNewton::build(NeighList *list)
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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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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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@ -80,80 +83,103 @@ void NPairHalfMultiNewton::build(NeighList *list)
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tagprev = tag[i] - iatom - 1;
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}
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// loop over rest of atoms in i's bin, ghosts are at end of linked list
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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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for (j = bins[i]; j >= 0; j = bins[j]) {
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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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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],
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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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// loop over all atoms in other bins in stencil, store every pair
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// skip if i,j neighbor cutoff is less than bin distance
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ibin = atom2bin[i];
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s = stencil_multi[itype];
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distsq = distsq_multi[itype];
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cutsq = cutneighsq[itype];
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ns = nstencil_multi[itype];
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for (k = 0; k < ns; k++) {
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for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
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jtype = type[j];
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if (cutsq[jtype] < distsq[k]) continue;
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if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
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// loop through stencils for all collections
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for (jcollection = 0; jcollection < ncollections; jcollection++) {
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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 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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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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// if same size: uses half stencil so check central bin
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if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){
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if (icollection == jcollection) js = bins[i];
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else js = binhead_multi[jcollection][jbin];
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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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for (j = js; j >= 0; j = bins[j]) {
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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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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) {
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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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// for all collections, loop over all atoms in other bins in stencil, store every pair
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// stencil is empty if i larger than j
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// stencil is half if i same size as j
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// stencil is full if i smaller than j
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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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for (j = js; j >= 0; j = bins[j]) {
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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],
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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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