new neighbor list changes (c9c2ae6c) · Commits · 郑智淋 / lammps

src/Make.sh

+8 −9

Original line number	Diff line number	Diff line
		@@ -5,12 +5,6 @@
		# sh Make.sh Makefile.shlib
		# sh Make.sh Makefile.list

		# turn off enforced customizations
		GREP_OPTIONS=
		# enforce using portable C locale
		LC_ALL=C
		export LC_ALL GREP_OPTIONS

		# function to create one style_*.h file
		# must whack .d files that depend on style_.h file,
		# else Make will not recreate them
		@@ -59,8 +53,9 @@ style () {
		# called by "make machine"
		# col 1 = string to search for
		# col 2 = search in *.h files starting with this name
		# col 3 = prefix of style file
		# col 4
		# col 3 = name of style file
		# col 4 = file that includes the style file
		# col 5 = optional 2nd file that includes the style file

		if (test $1 = "style") then

		@@ -69,7 +64,7 @@ if (test $1 = "style") then
		style BODY_CLASS body_ body atom_vec_body
		style BOND_CLASS bond_ bond force
		style COMMAND_CLASS "" command input
		style COMPUTE_CLASS compute_ compute modify modify_cuda
		style COMPUTE_CLASS compute_ compute modify
		style DIHEDRAL_CLASS dihedral_ dihedral force
		style DUMP_CLASS dump_ dump output write_dump
		style FIX_CLASS fix_ fix modify
		@@ -77,6 +72,10 @@ if (test $1 = "style") then
		style INTEGRATE_CLASS "" integrate update
		style KSPACE_CLASS "" kspace force
		style MINIMIZE_CLASS min_ minimize update
		style NBIN_CLASS nbin_ nbin neighbor
		style NPAIR_CLASS npair_ npair neighbor
		style NSTENCIL_CLASS nstencil_ nstencil neighbor
		style NTOPO_CLASS ntopo_ ntopo neighbor
		style PAIR_CLASS pair_ pair force
		style READER_CLASS reader_ reader read_dump
		style REGION_CLASS region_ region domain

src/Purge.list

+33 −0

Original line number	Diff line number	Diff line
		@@ -13,6 +13,39 @@ style_kspace.h
		style_minimize.h
		style_pair.h
		style_region.h
		style_neigh_bin.h
		style_neigh_pair.h
		style_neigh_stencil.h
		# deleted on 30 Aug 2016
		accelerator_intel.h
		neigh_bond.cpp
		neigh_bond.h
		neigh_derive.cpp
		neigh_derive.h
		neigh_full.cpp
		neigh_full.h
		neigh_gran.cpp
		neigh_gran.h
		neigh_half_bin.cpp
		neigh_half_bin.h
		neigh_half_multi.cpp
		neigh_half_multi.h
		neigh_half_nsq.cpp
		neigh_half_nsq.h
		neigh_respa.cpp
		neigh_respa.h
		neigh_shardlow.cpp
		neigh_shardlow.h
		neigh_stencil.cpp
		neigh_half_bin_intel.cpp
		neighbor_omp.h
		neigh_derive_omp.cpp
		neigh_full_omp.cpp
		neigh_gran_omp.cpp
		neigh_half_bin_omp.cpp
		neigh_half_multi_omp.cpp
		neigh_half_nsq_omp.cpp
		neigh_respa_omp.cpp
		# deleted on 31 May 2016
		fix_ave_spatial_sphere.cpp
		fix_ave_spatial_sphere.h

src/neigh_shardlow.cpp→src/USER-DPD/#npair_half_bin_newton_ssa.cpp#

+57 −184

Original line number	Diff line number	Diff line
		@@ -16,195 +16,38 @@
		James Larentzos and Timothy I. Mattox (Engility Corporation)
		------------------------------------------------------------------------- */

		#include "npair_half_bin_newton_ssa.h"
		#include "neighbor.h"
		#include "neigh_list.h"
		#include "neigh_request.h"
		#include "atom.h"
		#include "atom_vec.h"
		#include "molecule.h"
		#include "domain.h"
		#include "group.h"
		#include "memory.h"
		#include "my_page.h"
		#include "error.h"
		#include "update.h"

		using namespace LAMMPS_NS;

		/* ----------------------------------------------------------------------
		routines to create a stencil = list of bin offsets
		stencil = bins whose closest corner to central bin is within cutoff
		sx,sy,sz = bin bounds = furthest the stencil could possibly extend
		3d creates xyz stencil, 2d creates xy stencil
		for half list with newton on:
		stencil is bins to the "upper right" of central bin
		stencil does not include self
		------------------------------------------------------------------------- */

		/* ---------------------------------------------------------------------- */

		void Neighbor::stencil_half_bin_2d_ssa(NeighList *list,
		int sx, int sy, int sz)
		{
		int i,j;
		int *stencil = list->stencil;
		int nstencil = 0;

		for (j = 0; j <= sy; j++)
		for (i = -sx; i <= sx; i++)
		if (j > 0 \|\| (j == 0 && i > 0))
		if (bin_distance(i,j,0) < cutneighmaxsq)
		stencil[nstencil++] = j*mbinx + i;

		list->nstencil = nstencil;

		// Now include additional bins for AIR ghosts only
		for (j = -sy; j <= 0; j++)
		for (i = -sx; i <= sx; i++) {
		if (j == 0 && i > 0) continue;
		if (bin_distance(i,j,0) < cutneighmaxsq)
		stencil[nstencil++] = j*mbinx + i;
		}
		// allocate space for static class variable
		// prototype for non-class function

		while (nstencil < list->maxstencil) {
		stencil[nstencil++] = INT_MAX;
		}
		}

		/* ---------------------------------------------------------------------- */

		void Neighbor::stencil_half_bin_3d_ssa(NeighList *list,
		int sx, int sy, int sz)
		{
		int i,j,k;
		int *stencil = list->stencil;
		int nstencil = 0;

		for (k = 0; k <= sz; k++)
		for (j = -sy; j <= sy; j++)
		for (i = -sx; i <= sx; i++)
		if (k > 0 \|\| j > 0 \|\| (j == 0 && i > 0))
		if (bin_distance(i,j,k) < cutneighmaxsq)
		stencil[nstencil++] = kmbinymbinx + j*mbinx + i;

		list->nstencil = nstencil;

		// Now include additional bins for AIR ghosts only
		for (k = -sz; k < 0; k++)
		for (j = -sy; j <= sy; j++)
		for (i = -sx; i <= sx; i++)
		if (bin_distance(i,j,k) < cutneighmaxsq)
		stencil[nstencil++] = kmbinymbinx + j*mbinx + i;
		k = 0; // skip already included bins at k == 0
		for (j = -sy; j <= 0; j++)
		for (i = -sx; i <= sx; i++) {
		if (j == 0 && i > 0) continue;
		if (bin_distance(i,j,k) < cutneighmaxsq)
		stencil[nstencil++] = kmbinymbinx + j*mbinx + i;
		}

		while (nstencil < list->maxstencil) {
		stencil[nstencil++] = INT_MAX;
		}
		}

		// space for static variable ssaAIRptr so it
		// can be used in qsort's compair function "cmp_ssaAIR()"
		static int *ssaAIRptr;
		static int cmp_ssaAIR(const void , const void );

		static int cmp_ssaAIR(const void iptr, const void jptr)
		{
		int i = ((int ) iptr);
		int j = ((int ) jptr);
		if (ssaAIRptr[i] < ssaAIRptr[j]) return -1;
		if (ssaAIRptr[i] > ssaAIRptr[j]) return 1;
		return 0;
		}


		/* ----------------------------------------------------------------------
		build half list from full list for use by Shardlow Spliting Algorithm
		pair stored once if i,j are both owned and i < j
		if j is ghost, only store if j coords are "above and to the right" of i
		works if full list is a skip list
		------------------------------------------------------------------------- */

		void Neighbor::half_from_full_newton_ssa(NeighList *list)
		{
		int i,j,ii,jj,n,jnum,joriginal;
		int neighptr,jlist;

		int nlocal = atom->nlocal;
		int *ssaAIR = atom->ssaAIR;

		int *ilist = list->ilist;
		int *numneigh = list->numneigh;
		int **firstneigh = list->firstneigh;
		MyPage<int> *ipage = list->ipage;

		int *ilist_full = list->listfull->ilist;
		int *numneigh_full = list->listfull->numneigh;
		int **firstneigh_full = list->listfull->firstneigh;
		int inum_full = list->listfull->inum;

		int inum = 0;
		ipage->reset();

		// loop over parent full list

		for (ii = 0; ii < inum_full; ii++) {
		int AIRct[8] = { 0 };
		n = 0;
		neighptr = ipage->vget();

		i = ilist_full[ii];

		// loop over full neighbor list

		jlist = firstneigh_full[i];
		jnum = numneigh_full[i];

		for (jj = 0; jj < jnum; jj++) {
		joriginal = jlist[jj];
		j = joriginal & NEIGHMASK;
		if (j < nlocal) {
		if (i > j) continue;
		++(AIRct[0]);
		} else {
		if (ssaAIR[j] < 2) continue; // skip ghost atoms not in AIR
		++(AIRct[ssaAIR[j] - 1]);
		}
		neighptr[n++] = joriginal;
		}

		ilist[inum++] = i;
		firstneigh[i] = neighptr;
		numneigh[i] = n;
		ipage->vgot(n);
		if (ipage->status())
		error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");

		// sort the locals+ghosts in the neighbor list by their ssaAIR number
		ssaAIRptr = atom->ssaAIR;
		qsort(&(neighptr[0]), n, sizeof(int), cmp_ssaAIR);

		// Do a prefix sum on the counts to turn them into indexes.
		list->ndxAIR_ssa[i][0] = AIRct[0];
		for (int ndx = 1; ndx < 8; ++ndx) {
		list->ndxAIR_ssa[i][ndx] = AIRct[ndx] + list->ndxAIR_ssa[i][ndx - 1];
		}
		}
		/* ---------------------------------------------------------------------- */

		list->inum = inum;
		}
		NPairHalfBinNewtonSSA::NPairHalfBinNewtonSSA(LAMMPS *lmp) : NPair(lmp) {}

		/* ----------------------------------------------------------------------
		for Shardlow Spliting Algorithm:
		binned neighbor list construction with full Newton's 3rd law
		for use by Shardlow Spliting Algorithm
		each owned atom i checks its own bin and other bins in Newton stencil
		every pair stored exactly once by some processor
		------------------------------------------------------------------------- */

		void Neighbor::half_bin_newton_ssa(NeighList *list)
		void NPairHalfBinNewtonSSA::build(NeighList *list)
		{
		int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;
		tagint tagprev;
		@@ -220,6 +63,7 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
		int **nspecial = atom->nspecial;
		int nlocal = atom->nlocal;
		int nall = nlocal + atom->nghost;
		if (includegroup) nlocal = atom->nfirst;
		int *ssaAIR = atom->ssaAIR;

		int *molindex = atom->molindex;
		@@ -232,18 +76,27 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
		int *ilist = list->ilist;
		int *numneigh = list->numneigh;
		int **firstneigh = list->firstneigh;
		int nstencil = list->nstencil;
		int maxstencil = list->maxstencil;
		int *stencil = list->stencil;
		MyPage<int> *ipage = list->ipage;

		int inum = 0;

		if (binatomflag) { /* only false in Neighbor::build_one */
		/* ----------------------------------------------------------------------
		bin owned and ghost atoms for use by Shardlow Splitting Algorithm
		exclude ghost atoms that are not in the Active Interaction Regions (AIR)
		------------------------------------------------------------------------- */
		// bin owned and ghost atoms for use by Shardlow Splitting Algorithm
		// exclude ghost atoms that are not in the Active Interaction Regions (AIR)

		// NOTE to Tim: this binatomflag no longer exists
		// the logic up higher assures that binning has been done
		// before this build() method is called
		// maybe this code below needs to be in a new NBinShardlow class?
		// this class also inherits NPair::nb from its parent
		// which points to the NBin class that did the binning
		// there are last_step variables stored there which indicate
		// the last time binning was done
		// the basic question is what data is created/stored by SSA binning
		// and in what class should it live?
		// if it is created by the binning operation, then I think
		// it should be in a new NBinShardlow class

		if (true /* binatomflag */) { // only false in Neighbor::build_one

		if (mbins > list->maxhead_ssa) {
		list->maxhead_ssa = mbins;
		@@ -257,8 +110,8 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
		list->binhead_ssa[i] = -1;
		}

		if (maxbin > list->maxbin_ssa) {
		list->maxbin_ssa = maxbin;
		if (nall > list->maxbin_ssa) {
		list->maxbin_ssa = nall;
		memory->destroy(list->bins_ssa);
		memory->create(list->bins_ssa,list->maxbin_ssa,"bins_ssa");
		}
		@@ -267,7 +120,8 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)

		if (includegroup) {
		int bitmask = group->bitmask[includegroup];
		for (i = nall-1; i >= nlocal; i--) {
		int nowned = atom->nlocal; // NOTE: nlocal was set to atom->nfirst above
		for (i = nall-1; i >= nowned; i--) {
		if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR
		if (mask[i] & bitmask) {
		ibin = coord2bin(x[i]);
		@@ -275,7 +129,6 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
		list->gbinhead_ssa[ibin] = i;
		}
		}
		nlocal = atom->nfirst; // This is important for the code that follows!
		} else {
		for (i = nall-1; i >= nlocal; i--) {
		if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR
		@@ -289,7 +142,7 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
		list->bins_ssa[i] = list->binhead_ssa[ibin];
		list->binhead_ssa[ibin] = i;
		}
		} /* else reuse previous binning. See Neighbor::build_one comment. */
		} // else reuse previous binning. See Neighbor::build_one comment

		ipage->reset();

		@@ -343,8 +196,10 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
		ibin = coord2bin(x[i]);

		// loop over all local atoms in other bins in "half" stencil

		for (k = 0; k < nstencil; k++) {
		for (j = list->binhead_ssa[ibin+stencil[k]]; j >= 0; j = list->bins_ssa[j]) {
		for (j = list->binhead_ssa[ibin+stencil[k]]; j >= 0;
		j = list->bins_ssa[j]) {

		jtype = type[j];
		if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
		@@ -377,9 +232,10 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
		// Note: the non-AIR ghost atoms have already been filtered out
		// That is a significant time savings because of the "full" stencil
		// Note2: only non-pure locals can have ghosts as neighbors
		if (ssaAIR[i] == 1) for (k = 0; k < maxstencil; k++) {
		if (stencil[k] > mbins) break; /* Check if ghost stencil bins are exhausted */
		for (j = list->gbinhead_ssa[ibin+stencil[k]]; j >= 0; j = list->bins_ssa[j]) {

		if (ssaAIR[i] == 1) for (k = 0; k < nstencil_ssa; k++) {
		for (j = list->gbinhead_ssa[ibin+stencil[k]]; j >= 0;
		j = list->bins_ssa[j]) {

		jtype = type[j];
		if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
		@@ -424,10 +280,12 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)
		error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");

		// sort the ghosts in the neighbor list by their ssaAIR number

		ssaAIRptr = atom->ssaAIR;
		qsort(&(neighptr[AIRct[0]]), n - AIRct[0], sizeof(int), cmp_ssaAIR);

		// Do a prefix sum on the counts to turn them into indexes.
		// do a prefix sum on the counts to turn them into indexes

		list->ndxAIR_ssa[i][0] = AIRct[0];
		for (int ndx = 1; ndx < 8; ++ndx) {
		list->ndxAIR_ssa[i][ndx] = AIRct[ndx] + list->ndxAIR_ssa[i][ndx - 1];
		@@ -436,3 +294,18 @@ void Neighbor::half_bin_newton_ssa(NeighList *list)

		list->inum = inum;
		}

		/* ----------------------------------------------------------------------
		comparison function invoked by qsort()
		accesses static class member ssaAIRptr, set before call to qsort()
		------------------------------------------------------------------------- */

		static int cmp_ssaAIR(const void iptr, const void jptr)
		{
		int i = ((int ) iptr);
		int j = ((int ) jptr);
		if (ssaAIRptr[i] < ssaAIRptr[j]) return -1;
		if (ssaAIRptr[i] > ssaAIRptr[j]) return 1;
		return 0;
		}

src/USER-DPD/fix_shardlow.cpp

+0 −1

Original line number	Diff line number	Diff line
		@@ -226,7 +226,6 @@ void FixShardlow::ssa_update(
		int newton_pair = force->newton_pair;
		double randPair;

		int *ssaAIR = atom->ssaAIR;
		double *uCond = atom->uCond;
		double *uMech = atom->uMech;
		double *dpdTheta = atom->dpdTheta;

src/neigh_half_nsq.cpp→src/USER-DPD/npair_half_bin_newton_ssa.cpp

+311 −0

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