add support for neighbor list history refactoring in USER-OMP part 1 (7e35042c) · Commits · 郑智淋 / lammps

src/Purge.list

+3 −0

Original line number	Diff line number	Diff line
		@@ -16,6 +16,9 @@ style_region.h
		style_neigh_bin.h
		style_neigh_pair.h
		style_neigh_stencil.h
		# deleted on 11 October 2017
		fix_shear_history_omp.cpp
		fix_shear_history_omp.h
		# deleted on 5 September 2017
		npair_halffull_newton_ssa.cpp
		npair_halffull_newton_ssa.h

src/USER-OMP/fix_shear_history_omp.cpp

+50 −29

Original line number	Diff line number	Diff line
		@@ -13,7 +13,7 @@

		#include <string.h>
		#include <stdio.h>
		#include "fix_shear_history_omp.h"
		#include "fix_neigh_history_omp.h"
		#include "atom.h"
		#include "comm.h"
		#include "neighbor.h"
		@@ -31,15 +31,38 @@
		using namespace LAMMPS_NS;
		using namespace FixConst;


		FixNeighHistoryOMP::FixNeighHistoryOMP(class LAMMPS lmp,int narg,char *argv)
		: FixNeighHistory(lmp,narg,argv) {

		if (onesided)
		error->all(FLERR,"tri/lj and line/lj are not supported by USER-OMP");
		if (!newton_pair)
		error->all(FLERR,"Newton off for granular is not supported by USER-OMP");
		}


		/* ----------------------------------------------------------------------
		copy shear partner info from neighbor lists to per-atom arrays
		so it can be exchanged with those atoms
		copy partner info from neighbor data structs (NDS) to atom arrays
		should be called whenever NDS store current history info
		and need to transfer the info to owned atoms
		e.g. when atoms migrate to new procs, new neigh list built, or between runs
		when atoms may be added or deleted (NDS becomes out-of-date)
		the next post_neighbor() will put this info back into new NDS
		called during run before atom exchanges, including for restart files
		called at end of run via post_run()
		do not call during setup of run (setup_pre_exchange)
		b/c there is no guarantee of a current NDS (even on continued run)
		if run command does a 2nd run with pre = no, then no neigh list
		will be built, but old neigh list will still have the info

		the USER-OMP version only supports newton on
		------------------------------------------------------------------------- */

		void FixShearHistoryOMP::pre_exchange()
		void FixNeighHistoryOMP::pre_exchange()
		{
		const int nthreads = comm->nthreads;
		maxtouch = 0;
		maxpartner = 0;

		#if defined(_OPENMP)
		#pragma omp parallel default(none)
		@@ -54,16 +77,16 @@ void FixShearHistoryOMP::pre_exchange()

		int i,j,ii,jj,m,n,inum,jnum;
		int ilist,jlist,numneigh,*firstneigh;
		int touch,*firsttouch;
		double shear,shearj,allshear,*firstshear;
		int allflags,*firstflag;
		double allvalues,onevalues,*jvalues;

		MyPage <tagint> &ipg = ipage[tid];
		MyPage <double> &dpg = dpage[tid];
		MyPage <tagint> &ipg = ipage_atom[tid];
		MyPage <double> &dpg = dpage_atom[tid];
		ipg.reset();
		dpg.reset();

		// 1st loop over neighbor list
		// calculate nparter for each owned atom
		// calculate npartner for each owned atom

		tagint *tag = atom->tag;

		@@ -72,8 +95,6 @@ void FixShearHistoryOMP::pre_exchange()
		ilist = list->ilist;
		numneigh = list->numneigh;
		firstneigh = list->firstneigh;
		firsttouch = list->listhistory->firstneigh;
		firstshear = list->listhistory->firstdouble;

		int nlocal_neigh = 0;
		if (inum) nlocal_neigh = ilist[inum-1] + 1;
		@@ -94,10 +115,10 @@ void FixShearHistoryOMP::pre_exchange()
		i = ilist[ii];
		jlist = firstneigh[i];
		jnum = numneigh[i];
		touch = firsttouch[i];
		allflags = firstflag[i];

		for (jj = 0; jj < jnum; jj++) {
		if (touch[jj]) {
		if (allflags[jj]) {
		if ((i >= lfrom) && (i < lto))
		npartner[i]++;

		@@ -116,55 +137,55 @@ void FixShearHistoryOMP::pre_exchange()
		if ((i >= lfrom) && (i < lto)) {
		n = npartner[i];
		partner[i] = ipg.get(n);
		shearpartner[i] = dpg.get(dnum*n);
		if (partner[i] == NULL \|\| shearpartner[i] == NULL)
		error->one(FLERR,"Shear history overflow, boost neigh_modify one");
		valuepartner[i] = dpg.get(dnum*n);
		if (partner[i] == NULL \|\| valuepartner[i] == NULL)
		error->one(FLERR,"Neighbor history overflow, boost neigh_modify one");
		}
		}

		// 2nd loop over neighbor list
		// store atom IDs and shear history for my atoms
		// re-zero npartner to use as counter for all my atoms
		// store partner IDs and values for owned+ghost atoms
		// re-zero npartner to use as counter

		for (i = lfrom; i < lto; i++) npartner[i] = 0;

		for (ii = 0; ii < inum; ii++) {
		i = ilist[ii];
		jlist = firstneigh[i];
		allshear = firstshear[i];
		jnum = numneigh[i];
		touch = firsttouch[i];
		allflags = firstflag[i];
		allvalues = firstvalue[i];

		for (jj = 0; jj < jnum; jj++) {
		if (touch[jj]) {
		shear = &allshear[3*jj];
		if (allflags[jj]) {
		onevalues = &allvalues[3*jj];
		j = jlist[jj];
		j &= NEIGHMASK;

		if ((i >= lfrom) && (i < lto)) {
		m = npartner[i]++;
		partner[i][m] = tag[j];
		memcpy(&shearpartner[i][dnum*m],shear,dnumbytes);
		memcpy(&valuepartner[i][dnum*m],onevalues,dnumbytes);
		}

		if ((j >= lfrom) && (j < lto)) {
		m = npartner[j]++;
		partner[j][m] = tag[i];
		shearj = &shearpartner[j][dnum*m];
		for (n = 0; n < dnum; n++) shearj[n] = -shear[n];
		jvalues = &valuepartner[j][dnum*m];
		for (n = 0; n < dnum; n++) jvalues[n] = -onevalues[n];
		}
		}
		}
		}

		// set maxtouch = max # of partners of any owned atom
		maxtouch = m = 0;
		// set maxpartner = max # of partners of any owned atom
		maxpartner = m = 0;
		for (i = lfrom; i < lto; i++)
		m = MAX(m,npartner[i]);

		#if defined(_OPENMP)
		#pragma omp critical
		#endif
		maxtouch = MAX(m,maxtouch);
		maxpartner = MAX(m,maxpartner);
		}
		}

src/USER-OMP/fix_shear_history_omp.h

+6 −7

Original line number	Diff line number	Diff line
		@@ -13,22 +13,21 @@

		#ifdef FIX_CLASS

		FixStyle(SHEAR_HISTORY/omp,FixShearHistoryOMP)
		FixStyle(NEIGH_HISTORY/omp,FixNeighHistoryOMP)

		#else

		#ifndef LMP_FIX_SHEAR_HISTORY_OMP_H
		#define LMP_FIX_SHEAR_HISTORY_OMP_H
		#ifndef LMP_FIX_NEIGH_HISTORY_OMP_H
		#define LMP_FIX_NEIGH_HISTORY_OMP_H

		#include "fix_shear_history.h"
		#include "fix_neigh_history.h"

		namespace LAMMPS_NS {

		class FixShearHistoryOMP : public FixShearHistory {
		class FixNeighHistoryOMP : public FixNeighHistory {

		public:
		FixShearHistoryOMP(class LAMMPS lmp, int narg, char *argv)
		: FixShearHistory(lmp,narg,argv) {};
		FixNeighHistoryOMP(class LAMMPS lmp, int narg, char *argv);
		virtual void pre_exchange();
		};

src/USER-OMP/pair_gran_hertz_history_omp.cpp

+2 −2

Original line number	Diff line number	Diff line
		@@ -134,8 +134,8 @@ void PairGranHertzHistoryOMP::eval(int iifrom, int iito, ThrData * const thr)
		ilist = list->ilist;
		numneigh = list->numneigh;
		firstneigh = list->firstneigh;
		firsttouch = list->listhistory->firstneigh;
		firstshear = list->listhistory->firstdouble;
		firsttouch = fix_history->firstflag;
		firstshear = fix_history->firstvalue;

		// loop over neighbors of my atoms

src/USER-OMP/pair_gran_hooke_history_omp.cpp

+2 −2

Original line number	Diff line number	Diff line
		@@ -137,8 +137,8 @@ void PairGranHookeHistoryOMP::eval(int iifrom, int iito, ThrData * const thr)
		ilist = list->ilist;
		numneigh = list->numneigh;
		firstneigh = list->firstneigh;
		firsttouch = listhistory->firstneigh;
		firstshear = listhistory->firstdouble;
		firsttouch = fix_history->firstflag;
		firstshear = fix_history->firstvalue;

		// loop over neighbors of my atoms

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