diff --git a/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp index 45add8709..f094691b7 100644 --- a/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp @@ -1,204 +1,202 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #include "npair_half_respa_bin_newtoff_omp.h" #include "npair_omp.h" #include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" #include "domain.h" #include "my_page.h" #include "error.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ NPairHalfRespaBinNewtoffOmp::NPairHalfRespaBinNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- multiple respa lists binned neighbor list construction with partial Newton's 3rd law each owned atom i checks own bin and surrounding bins in non-Newton stencil pair stored once if i,j are both owned and i < j pair stored by me if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ void NPairHalfRespaBinNewtoffOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; const int moltemplate = (molecular == 2) ? 1 : 0; NPAIR_OMP_INIT; - NeighList *listinner = list->listinner; - NeighList *listmiddle = list->listmiddle; const int respamiddle = list->respamiddle; #if defined(_OPENMP) -#pragma omp parallel default(none) shared(list,listinner,listmiddle) +#pragma omp parallel default(none) shared(list) #endif NPAIR_OMP_SETUP(nlocal); int i,j,k,n,itype,jtype,ibin,n_inner,n_middle,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*neighptr_inner,*neighptr_middle; // loop over each atom, storing neighbors double **x = atom->x; int *type = atom->type; int *mask = atom->mask; tagint *tag = atom->tag; tagint *molecule = atom->molecule; tagint **special = atom->special; int **nspecial = atom->nspecial; int *molindex = atom->molindex; int *molatom = atom->molatom; Molecule **onemols = atom->avec->onemols; int *ilist = list->ilist; int *numneigh = list->numneigh; int **firstneigh = list->firstneigh; - int *ilist_inner = listinner->ilist; - int *numneigh_inner = listinner->numneigh; - int **firstneigh_inner = listinner->firstneigh; + int *ilist_inner = list->ilist_inner; + int *numneigh_inner = list->numneigh_inner; + int **firstneigh_inner = list->firstneigh_inner; int *ilist_middle,*numneigh_middle,**firstneigh_middle; if (respamiddle) { - ilist_middle = listmiddle->ilist; - numneigh_middle = listmiddle->numneigh; - firstneigh_middle = listmiddle->firstneigh; + ilist_middle = list->ilist_middle; + numneigh_middle = list->numneigh_middle; + firstneigh_middle = list->firstneigh_middle; } // each thread has its own page allocator MyPage &ipage = list->ipage[tid]; - MyPage &ipage_inner = listinner->ipage[tid]; + MyPage &ipage_inner = list->ipage_inner[tid]; ipage.reset(); ipage_inner.reset(); MyPage *ipage_middle; if (respamiddle) { - ipage_middle = listmiddle->ipage + tid; + ipage_middle = list->ipage_middle + tid; ipage_middle->reset(); } int which = 0; int minchange = 0; for (i = ifrom; i < ito; i++) { n = n_inner = 0; neighptr = ipage.vget(); neighptr_inner = ipage_inner.vget(); if (respamiddle) { n_middle = 0; neighptr_middle = ipage_middle->vget(); } itype = type[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; ibin = atom2bin[i]; if (moltemplate) { imol = molindex[i]; iatom = molatom[i]; tagprev = tag[i] - iatom - 1; } // loop over all atoms in surrounding bins in stencil including self // only store pair if i < j // stores own/own pairs only once // stores own/ghost pairs on both procs for (k = 0; k < nstencil; k++) { for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) { if (j <= i) continue; jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; if (rsq <= cutneighsq[itype][jtype]) { if (molecular) { if (!moltemplate) which = find_special(special[i],nspecial[i],tag[j]); else if (imol >=0) which = find_special(onemols[imol]->special[iatom], onemols[imol]->nspecial[iatom], tag[j]-tagprev); else which = 0; if (which == 0) neighptr[n++] = j; else if ((minchange = domain->minimum_image_check(delx,dely,delz))) neighptr[n++] = j; else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); } else neighptr[n++] = j; if (rsq < cut_inner_sq) { if (which == 0) neighptr_inner[n_inner++] = j; else if (minchange) neighptr_inner[n_inner++] = j; else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS); } if (respamiddle && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) { if (which == 0) neighptr_middle[n_middle++] = j; else if (minchange) neighptr_middle[n_middle++] = j; else if (which > 0) neighptr_middle[n_middle++] = j ^ (which << SBBITS); } } } } ilist[i] = i; firstneigh[i] = neighptr; numneigh[i] = n; ipage.vgot(n); if (ipage.status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); ilist_inner[i] = i; firstneigh_inner[i] = neighptr_inner; numneigh_inner[i] = n_inner; ipage.vgot(n_inner); if (ipage_inner.status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (respamiddle) { ilist_middle[i] = i; firstneigh_middle[i] = neighptr_middle; numneigh_middle[i] = n_middle; ipage_middle->vgot(n_middle); if (ipage_middle->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); } } NPAIR_OMP_CLOSE; list->inum = nlocal; - listinner->inum = nlocal; - if (respamiddle) listmiddle->inum = nlocal; + list->inum_inner = nlocal; + if (respamiddle) list->inum_middle = nlocal; } diff --git a/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp b/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp index ee6b9b750..de7ef5f7d 100644 --- a/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp +++ b/src/USER-OMP/npair_half_respa_bin_newton_omp.cpp @@ -1,250 +1,248 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #include "npair_half_respa_bin_newton_omp.h" #include "neighbor.h" #include "npair_omp.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" #include "domain.h" #include "my_page.h" #include "error.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ NPairHalfRespaBinNewtonOmp::NPairHalfRespaBinNewtonOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- multiple respa lists binned neighbor list construction with full Newton's 3rd law each owned atom i checks its own bin and other bins in Newton stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ void NPairHalfRespaBinNewtonOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; const int moltemplate = (molecular == 2) ? 1 : 0; NPAIR_OMP_INIT; - NeighList *listinner = list->listinner; - NeighList *listmiddle = list->listmiddle; const int respamiddle = list->respamiddle; #if defined(_OPENMP) -#pragma omp parallel default(none) shared(list,listinner,listmiddle) +#pragma omp parallel default(none) shared(list) #endif NPAIR_OMP_SETUP(nlocal); int i,j,k,n,itype,jtype,ibin,n_inner,n_middle,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*neighptr_inner,*neighptr_middle; // loop over each atom, storing neighbors double **x = atom->x; int *type = atom->type; int *mask = atom->mask; tagint *tag = atom->tag; tagint *molecule = atom->molecule; tagint **special = atom->special; int **nspecial = atom->nspecial; int *molindex = atom->molindex; int *molatom = atom->molatom; Molecule **onemols = atom->avec->onemols; int *ilist = list->ilist; int *numneigh = list->numneigh; int **firstneigh = list->firstneigh; - int *ilist_inner = listinner->ilist; - int *numneigh_inner = listinner->numneigh; - int **firstneigh_inner = listinner->firstneigh; + int *ilist_inner = list->ilist_inner; + int *numneigh_inner = list->numneigh_inner; + int **firstneigh_inner = list->firstneigh_inner; int *ilist_middle,*numneigh_middle,**firstneigh_middle; if (respamiddle) { - ilist_middle = listmiddle->ilist; - numneigh_middle = listmiddle->numneigh; - firstneigh_middle = listmiddle->firstneigh; + ilist_middle = list->ilist_middle; + numneigh_middle = list->numneigh_middle; + firstneigh_middle = list->firstneigh_middle; } // each thread has its own page allocator MyPage &ipage = list->ipage[tid]; - MyPage &ipage_inner = listinner->ipage[tid]; + MyPage &ipage_inner = list->ipage_inner[tid]; ipage.reset(); ipage_inner.reset(); MyPage *ipage_middle; if (respamiddle) { - ipage_middle = listmiddle->ipage + tid; + ipage_middle = list->ipage_middle + tid; ipage_middle->reset(); } int which = 0; int minchange = 0; for (i = ifrom; i < ito; i++) { n = n_inner = 0; neighptr = ipage.vget(); neighptr_inner = ipage_inner.vget(); if (respamiddle) { n_middle = 0; neighptr_middle = ipage_middle->vget(); } itype = type[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; if (moltemplate) { imol = molindex[i]; iatom = molatom[i]; tagprev = tag[i] - iatom - 1; } // loop over rest of atoms in i's bin, ghosts are at end of linked list // if j is owned atom, store it, since j is beyond i in linked list // if j is ghost, only store if j coords are "above and to the right" of i for (j = bins[i]; j >= 0; j = bins[j]) { if (j >= nlocal) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; if (x[j][1] == ytmp && x[j][0] < xtmp) continue; } } jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; if (rsq <= cutneighsq[itype][jtype]) { if (molecular) { if (!moltemplate) which = find_special(special[i],nspecial[i],tag[j]); else if (imol >=0) which = find_special(onemols[imol]->special[iatom], onemols[imol]->nspecial[iatom], tag[j]-tagprev); else which = 0; if (which == 0) neighptr[n++] = j; else if ((minchange = domain->minimum_image_check(delx,dely,delz))) neighptr[n++] = j; else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); } else neighptr[n++] = j; if (rsq < cut_inner_sq) { if (which == 0) neighptr_inner[n_inner++] = j; else if (minchange) neighptr_inner[n_inner++] = j; else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS); } if (respamiddle && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) { if (which == 0) neighptr_middle[n_middle++] = j; else if (minchange) neighptr_middle[n_middle++] = j; else if (which > 0) neighptr_middle[n_middle++] = j ^ (which << SBBITS); } } } // loop over all atoms in other bins in stencil, store every pair ibin = atom2bin[i]; for (k = 0; k < nstencil; k++) { for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) { jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; if (rsq <= cutneighsq[itype][jtype]) { if (molecular) { if (!moltemplate) which = find_special(special[i],nspecial[i],tag[j]); else if (imol >=0) which = find_special(onemols[imol]->special[iatom], onemols[imol]->nspecial[iatom], tag[j]-tagprev); else which = 0; if (which == 0) neighptr[n++] = j; else if ((minchange = domain->minimum_image_check(delx,dely,delz))) neighptr[n++] = j; else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); } else neighptr[n++] = j; if (rsq < cut_inner_sq) { if (which == 0) neighptr_inner[n_inner++] = j; else if (minchange) neighptr_inner[n_inner++] = j; else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS); } if (respamiddle && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) { if (which == 0) neighptr_middle[n_middle++] = j; else if (minchange) neighptr_middle[n_middle++] = j; else if (which > 0) neighptr_middle[n_middle++] = j ^ (which << SBBITS); } } } } ilist[i] = i; firstneigh[i] = neighptr; numneigh[i] = n; ipage.vgot(n); if (ipage.status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); ilist_inner[i] = i; firstneigh_inner[i] = neighptr_inner; numneigh_inner[i] = n_inner; ipage.vgot(n_inner); if (ipage_inner.status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (respamiddle) { ilist_middle[i] = i; firstneigh_middle[i] = neighptr_middle; numneigh_middle[i] = n_middle; ipage_middle->vgot(n_middle); if (ipage_middle->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); } } NPAIR_OMP_CLOSE; list->inum = nlocal; - listinner->inum = nlocal; - if (respamiddle) listmiddle->inum = nlocal; + list->inum_inner = nlocal; + if (respamiddle) list->inum_middle = nlocal; } diff --git a/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp b/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp index fbb512ba6..f20d101bc 100644 --- a/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp +++ b/src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp @@ -1,211 +1,209 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #include "npair_half_respa_bin_newton_tri_omp.h" #include "npair_omp.h" #include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" #include "molecule.h" #include "domain.h" #include "my_page.h" #include "error.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ NPairHalfRespaBinNewtonTriOmp::NPairHalfRespaBinNewtonTriOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- multiple respa lists binned neighbor list construction with Newton's 3rd law for triclinic each owned atom i checks its own bin and other bins in triclinic stencil every pair stored exactly once by some processor ------------------------------------------------------------------------- */ void NPairHalfRespaBinNewtonTriOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int molecular = atom->molecular; const int moltemplate = (molecular == 2) ? 1 : 0; NPAIR_OMP_INIT; - NeighList *listinner = list->listinner; - NeighList *listmiddle = list->listmiddle; const int respamiddle = list->respamiddle; #if defined(_OPENMP) -#pragma omp parallel default(none) shared(list,listinner,listmiddle) +#pragma omp parallel default(none) shared(list) #endif NPAIR_OMP_SETUP(nlocal); int i,j,k,n,itype,jtype,ibin,n_inner,n_middle,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*neighptr_inner,*neighptr_middle; // loop over each atom, storing neighbors double **x = atom->x; int *type = atom->type; int *mask = atom->mask; tagint *tag = atom->tag; tagint *molecule = atom->molecule; tagint **special = atom->special; int **nspecial = atom->nspecial; int *molindex = atom->molindex; int *molatom = atom->molatom; Molecule **onemols = atom->avec->onemols; int *ilist = list->ilist; int *numneigh = list->numneigh; int **firstneigh = list->firstneigh; - int *ilist_inner = listinner->ilist; - int *numneigh_inner = listinner->numneigh; - int **firstneigh_inner = listinner->firstneigh; + int *ilist_inner = list->ilist_inner; + int *numneigh_inner = list->numneigh_inner; + int **firstneigh_inner = list->firstneigh_inner; int *ilist_middle,*numneigh_middle,**firstneigh_middle; if (respamiddle) { - ilist_middle = listmiddle->ilist; - numneigh_middle = listmiddle->numneigh; - firstneigh_middle = listmiddle->firstneigh; + ilist_middle = list->ilist_middle; + numneigh_middle = list->numneigh_middle; + firstneigh_middle = list->firstneigh_middle; } // each thread has its own page allocator MyPage &ipage = list->ipage[tid]; - MyPage &ipage_inner = listinner->ipage[tid]; + MyPage &ipage_inner = list->ipage_inner[tid]; ipage.reset(); ipage_inner.reset(); MyPage *ipage_middle; if (respamiddle) { - ipage_middle = listmiddle->ipage + tid; + ipage_middle = list->ipage_middle + tid; ipage_middle->reset(); } int which = 0; int minchange = 0; for (i = ifrom; i < ito; i++) { n = n_inner = 0; neighptr = ipage.vget(); neighptr_inner = ipage_inner.vget(); if (respamiddle) { n_middle = 0; neighptr_middle = ipage_middle->vget(); } itype = type[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; if (moltemplate) { imol = molindex[i]; iatom = molatom[i]; tagprev = tag[i] - iatom - 1; } // loop over all atoms in bins in stencil // pairs for atoms j "below" i are excluded // below = lower z or (equal z and lower y) or (equal zy and lower x) // (equal zyx and j <= i) // latter excludes self-self interaction but allows superposed atoms ibin = atom2bin[i]; for (k = 0; k < nstencil; k++) { for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; if (x[j][1] == ytmp) { if (x[j][0] < xtmp) continue; if (x[j][0] == xtmp && j <= i) continue; } } jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; if (rsq <= cutneighsq[itype][jtype]) { if (molecular) { if (!moltemplate) which = find_special(special[i],nspecial[i],tag[j]); else if (imol >=0) which = find_special(onemols[imol]->special[iatom], onemols[imol]->nspecial[iatom], tag[j]-tagprev); else which = 0; if (which == 0) neighptr[n++] = j; else if ((minchange = domain->minimum_image_check(delx,dely,delz))) neighptr[n++] = j; else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); } else neighptr[n++] = j; if (rsq < cut_inner_sq) { if (which == 0) neighptr_inner[n_inner++] = j; else if (minchange) neighptr_inner[n_inner++] = j; else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS); } if (respamiddle && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) { if (which == 0) neighptr_middle[n_middle++] = j; else if (minchange) neighptr_middle[n_middle++] = j; else if (which > 0) neighptr_middle[n_middle++] = j ^ (which << SBBITS); } } } } ilist[i] = i; firstneigh[i] = neighptr; numneigh[i] = n; ipage.vgot(n); if (ipage.status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); ilist_inner[i] = i; firstneigh_inner[i] = neighptr_inner; numneigh_inner[i] = n_inner; ipage_inner.vgot(n_inner); if (ipage_inner.status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (respamiddle) { ilist_middle[i] = i; firstneigh_middle[i] = neighptr_middle; numneigh_middle[i] = n_middle; ipage_middle->vgot(n_middle); if (ipage_middle->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); } } NPAIR_OMP_CLOSE; list->inum = nlocal; - listinner->inum = nlocal; - if (respamiddle) listmiddle->inum = nlocal; + list->inum_inner = nlocal; + if (respamiddle) list->inum_middle = nlocal; } diff --git a/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp b/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp index 5ee71beba..0f726cdd7 100644 --- a/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp +++ b/src/USER-OMP/npair_half_respa_nsq_newtoff_omp.cpp @@ -1,198 +1,196 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #include "npair_half_respa_nsq_newtoff_omp.h" #include "npair_omp.h" #include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" #include "group.h" #include "molecule.h" #include "domain.h" #include "my_page.h" #include "error.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ NPairHalfRespaNsqNewtoffOmp::NPairHalfRespaNsqNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- multiple respa lists N^2 / 2 search for neighbor pairs with partial Newton's 3rd law pair added to list if atoms i and j are both owned and i < j pair added if j is ghost (also stored by proc owning j) ------------------------------------------------------------------------- */ void NPairHalfRespaNsqNewtoffOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0; const int molecular = atom->molecular; const int moltemplate = (molecular == 2) ? 1 : 0; NPAIR_OMP_INIT; - NeighList *listinner = list->listinner; - NeighList *listmiddle = list->listmiddle; const int respamiddle = list->respamiddle; #if defined(_OPENMP) -#pragma omp parallel default(none) shared(list,listinner,listmiddle) +#pragma omp parallel default(none) shared(list) #endif NPAIR_OMP_SETUP(nlocal); int i,j,n,itype,jtype,n_inner,n_middle,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*neighptr_inner,*neighptr_middle; // loop over each atom, storing neighbors double **x = atom->x; int *type = atom->type; int *mask = atom->mask; tagint *tag = atom->tag; tagint *molecule = atom->molecule; tagint **special = atom->special; int **nspecial = atom->nspecial; int *molindex = atom->molindex; int *molatom = atom->molatom; Molecule **onemols = atom->avec->onemols; int nall = atom->nlocal + atom->nghost; int *ilist = list->ilist; int *numneigh = list->numneigh; int **firstneigh = list->firstneigh; - int *ilist_inner = listinner->ilist; - int *numneigh_inner = listinner->numneigh; - int **firstneigh_inner = listinner->firstneigh; + int *ilist_inner = list->ilist_inner; + int *numneigh_inner = list->numneigh_inner; + int **firstneigh_inner = list->firstneigh_inner; int *ilist_middle,*numneigh_middle,**firstneigh_middle; if (respamiddle) { - ilist_middle = listmiddle->ilist; - numneigh_middle = listmiddle->numneigh; - firstneigh_middle = listmiddle->firstneigh; + ilist_middle = list->ilist_middle; + numneigh_middle = list->numneigh_middle; + firstneigh_middle = list->firstneigh_middle; } // each thread has its own page allocator MyPage &ipage = list->ipage[tid]; - MyPage &ipage_inner = listinner->ipage[tid]; + MyPage &ipage_inner = list->ipage_inner[tid]; ipage.reset(); ipage_inner.reset(); MyPage *ipage_middle; if (respamiddle) { - ipage_middle = listmiddle->ipage + tid; + ipage_middle = list->ipage_middle + tid; ipage_middle->reset(); } int which = 0; int minchange = 0; for (i = ifrom; i < ito; i++) { n = n_inner = 0; neighptr = ipage.vget(); neighptr_inner = ipage_inner.vget(); if (respamiddle) { n_middle = 0; neighptr_middle = ipage_middle->vget(); } itype = type[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; if (moltemplate) { imol = molindex[i]; iatom = molatom[i]; tagprev = tag[i] - iatom - 1; } // loop over remaining atoms, owned and ghost for (j = i+1; j < nall; j++) { if (includegroup && !(mask[j] & bitmask)) continue; jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; if (rsq <= cutneighsq[itype][jtype]) { if (molecular) { if (!moltemplate) which = find_special(special[i],nspecial[i],tag[j]); else if (imol >=0) which = find_special(onemols[imol]->special[iatom], onemols[imol]->nspecial[iatom], tag[j]-tagprev); else which = 0; if (which == 0) neighptr[n++] = j; else if ((minchange = domain->minimum_image_check(delx,dely,delz))) neighptr[n++] = j; else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); } else neighptr[n++] = j; if (rsq < cut_inner_sq) { if (which == 0) neighptr_inner[n_inner++] = j; else if (minchange) neighptr_inner[n_inner++] = j; else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS); } if (respamiddle && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) { if (which == 0) neighptr_middle[n_middle++] = j; else if (minchange) neighptr_middle[n_middle++] = j; else if (which > 0) neighptr_middle[n_middle++] = j ^ (which << SBBITS); } } } ilist[i] = i; firstneigh[i] = neighptr; numneigh[i] = n; ipage.vgot(n); if (ipage.status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); ilist_inner[i] = i; firstneigh_inner[i] = neighptr_inner; numneigh_inner[i] = n_inner; ipage.vgot(n_inner); if (ipage_inner.status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (respamiddle) { ilist_middle[i] = i; firstneigh_middle[i] = neighptr_middle; numneigh_middle[i] = n_middle; ipage_middle->vgot(n_middle); if (ipage_middle->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); } } NPAIR_OMP_CLOSE; list->inum = nlocal; - listinner->inum = nlocal; - if (respamiddle) listmiddle->inum = nlocal; + list->inum_inner = nlocal; + if (respamiddle) list->inum_middle = nlocal; } diff --git a/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp b/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp index 89cff732c..2783e1255 100644 --- a/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp +++ b/src/USER-OMP/npair_half_respa_nsq_newton_omp.cpp @@ -1,217 +1,215 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #include "npair_half_respa_nsq_newton_omp.h" #include "npair_omp.h" #include "neighbor.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" #include "group.h" #include "molecule.h" #include "domain.h" #include "my_page.h" #include "error.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ NPairHalfRespaNsqNewtonOmp::NPairHalfRespaNsqNewtonOmp(LAMMPS *lmp) : NPair(lmp) {} /* ---------------------------------------------------------------------- multiple respa lists N^2 / 2 search for neighbor pairs with full Newton's 3rd law pair added to list if atoms i and j are both owned and i < j if j is ghost only me or other proc adds pair decision based on itag,jtag tests ------------------------------------------------------------------------- */ void NPairHalfRespaNsqNewtonOmp::build(NeighList *list) { const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal; const int bitmask = (includegroup) ? group->bitmask[includegroup] : 0; const int molecular = atom->molecular; const int moltemplate = (molecular == 2) ? 1 : 0; NPAIR_OMP_INIT; - NeighList *listinner = list->listinner; - NeighList *listmiddle = list->listmiddle; const int respamiddle = list->respamiddle; #if defined(_OPENMP) -#pragma omp parallel default(none) shared(list,listinner,listmiddle) +#pragma omp parallel default(none) shared(list) #endif NPAIR_OMP_SETUP(nlocal); int i,j,n,itype,jtype,itag,jtag,n_inner,n_middle,imol,iatom; tagint tagprev; double xtmp,ytmp,ztmp,delx,dely,delz,rsq; int *neighptr,*neighptr_inner,*neighptr_middle; // loop over each atom, storing neighbors double **x = atom->x; int *type = atom->type; int *mask = atom->mask; tagint *tag = atom->tag; tagint *molecule = atom->molecule; tagint **special = atom->special; int **nspecial = atom->nspecial; int *molindex = atom->molindex; int *molatom = atom->molatom; Molecule **onemols = atom->avec->onemols; int nall = atom->nlocal + atom->nghost; int *ilist = list->ilist; int *numneigh = list->numneigh; int **firstneigh = list->firstneigh; - int *ilist_inner = listinner->ilist; - int *numneigh_inner = listinner->numneigh; - int **firstneigh_inner = listinner->firstneigh; + int *ilist_inner = list->ilist_inner; + int *numneigh_inner = list->numneigh_inner; + int **firstneigh_inner = list->firstneigh_inner; int *ilist_middle,*numneigh_middle,**firstneigh_middle; if (respamiddle) { - ilist_middle = listmiddle->ilist; - numneigh_middle = listmiddle->numneigh; - firstneigh_middle = listmiddle->firstneigh; + ilist_middle = list->ilist_middle; + numneigh_middle = list->numneigh_middle; + firstneigh_middle = list->firstneigh_middle; } // each thread has its own page allocator MyPage &ipage = list->ipage[tid]; - MyPage &ipage_inner = listinner->ipage[tid]; + MyPage &ipage_inner = list->ipage_inner[tid]; ipage.reset(); ipage_inner.reset(); MyPage *ipage_middle; if (respamiddle) { - ipage_middle = listmiddle->ipage + tid; + ipage_middle = list->ipage_middle + tid; ipage_middle->reset(); } int which = 0; int minchange = 0; for (i = ifrom; i < ito; i++) { n = n_inner = 0; neighptr = ipage.vget(); neighptr_inner = ipage_inner.vget(); if (respamiddle) { n_middle = 0; neighptr_middle = ipage_middle->vget(); } itag = tag[i]; itype = type[i]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; if (moltemplate) { imol = molindex[i]; iatom = molatom[i]; tagprev = tag[i] - iatom - 1; } // loop over remaining atoms, owned and ghost for (j = i+1; j < nall; j++) { if (includegroup && !(mask[j] & bitmask)) continue; if (j >= nlocal) { jtag = tag[j]; if (itag > jtag) { if ((itag+jtag) % 2 == 0) continue; } else if (itag < jtag) { if ((itag+jtag) % 2 == 1) continue; } else { if (x[j][2] < ztmp) continue; if (x[j][2] == ztmp) { if (x[j][1] < ytmp) continue; if (x[j][1] == ytmp && x[j][0] < xtmp) continue; } } } jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; if (rsq <= cutneighsq[itype][jtype]) { if (molecular) { if (!moltemplate) which = find_special(special[i],nspecial[i],tag[j]); else if (imol >=0) which = find_special(onemols[imol]->special[iatom], onemols[imol]->nspecial[iatom], tag[j]-tagprev); else which = 0; if (which == 0) neighptr[n++] = j; else if ((minchange = domain->minimum_image_check(delx,dely,delz))) neighptr[n++] = j; else if (which > 0) neighptr[n++] = j ^ (which << SBBITS); } else neighptr[n++] = j; if (rsq < cut_inner_sq) { if (which == 0) neighptr_inner[n_inner++] = j; else if (minchange) neighptr_inner[n_inner++] = j; else if (which > 0) neighptr_inner[n_inner++] = j ^ (which << SBBITS); } if (respamiddle && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) { if (which == 0) neighptr_middle[n_middle++] = j; else if (minchange) neighptr_middle[n_middle++] = j; else if (which > 0) neighptr_middle[n_middle++] = j ^ (which << SBBITS); } } } ilist[i] = i; firstneigh[i] = neighptr; numneigh[i] = n; ipage.vgot(n); if (ipage.status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); ilist_inner[i] = i; firstneigh_inner[i] = neighptr_inner; numneigh_inner[i] = n_inner; ipage.vgot(n_inner); if (ipage_inner.status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); if (respamiddle) { ilist_middle[i] = i; firstneigh_middle[i] = neighptr_middle; numneigh_middle[i] = n_middle; ipage_middle->vgot(n_middle); if (ipage_middle->status()) error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); } } NPAIR_OMP_CLOSE; list->inum = nlocal; - listinner->inum = nlocal; - if (respamiddle) listmiddle->inum = nlocal; + list->inum_inner = nlocal; + if (respamiddle) list->inum_middle = nlocal; }