Added 3-body neighbor list building for faster short range 3 body forces. (82d9f5f5) · Commits · 郑智淋 / lammps

src/MANYBODY/pair_vashishta.cpp

+35 −12

Original line number	Diff line number	Diff line
		@@ -54,6 +54,10 @@ PairVashishta::PairVashishta(LAMMPS *lmp) : Pair(lmp)
		elem2param = NULL;
		map = NULL;

		neigh3BodyMax = 0;
		neigh3BodyCount = NULL;
		neigh3Body = NULL;

		useTable = true;
		tableSize = 65536;
		forceTable = NULL;
		@@ -78,8 +82,7 @@ PairVashishta::~PairVashishta()
		delete [] map;
		}
		}
		#include <iostream>
		using namespace std;

		void PairVashishta::modify_params(int narg, char **arg)
		{
		if(narg < 2 \|\| narg > 3) // We accept table yes/no [tableSize]
		@@ -102,6 +105,16 @@ void PairVashishta::modify_params(int narg, char **arg)
		}
		}

		void PairVashishta::validateNeigh3Body() {
		if (atom->nlocal > neigh3BodyMax) {
		neigh3BodyMax = atom->nmax;
		memory->destroy(neigh3BodyCount);
		memory->destroy(neigh3Body);
		memory->create(neigh3BodyCount,neigh3BodyMax, "pair:vashishta:neigh3BodyCount");
		memory->create(neigh3Body,neigh3BodyMax, 1000, "pair:vashishta:neigh3Body"); // TODO: pick this number more wisely?
		}
		}

		void PairVashishta::createTable()
		{
		int ntypes = atom->ntypes+1;
		@@ -140,6 +153,7 @@ void PairVashishta::createTable()

		void PairVashishta::compute(int eflag, int vflag)
		{
		validateNeigh3Body();
		int i,j,k,ii,jj,kk,inum,jnum,jnumm1;
		int itype,jtype,ktype,ijparam,ikparam,ijkparam;
		tagint itag,jtag;
		@@ -174,6 +188,8 @@ void PairVashishta::compute(int eflag, int vflag)
		ytmp = x[i][1];
		ztmp = x[i][2];

		neigh3BodyCount[i] = 0; // Reset the 3-body neighbor list

		// two-body interactions, skip half of them

		jlist = firstneigh[i];
		@@ -184,6 +200,21 @@ void PairVashishta::compute(int eflag, int vflag)
		j &= NEIGHMASK;
		jtag = tag[j];

		jtype = map[type[j]];

		delx = xtmp - x[j][0];
		dely = ytmp - x[j][1];
		delz = ztmp - x[j][2];
		rsq = delxdelx + delydely + delz*delz;
		ijparam = elem2param[itype][jtype][jtype];

		if (rsq <= params[ijparam].cutsq2) {
		neigh3Body[i][neigh3BodyCount[i]] = j;
		neigh3BodyCount[i]++;
		}

		if (rsq > params[ijparam].cutsq) continue;

		if (itag > jtag) {
		if ((itag+jtag) % 2 == 0) continue;
		} else if (itag < jtag) {
		@@ -194,16 +225,6 @@ void PairVashishta::compute(int eflag, int vflag)
		if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
		}

		jtype = map[type[j]];

		delx = xtmp - x[j][0];
		dely = ytmp - x[j][1];
		delz = ztmp - x[j][2];
		rsq = delxdelx + delydely + delz*delz;

		ijparam = elem2param[itype][jtype][jtype];
		if (rsq > params[ijparam].cutsq) continue;

		twobody(&params[ijparam],rsq,fpair,eflag,evdwl, useTable);

		f[i][0] += delx*fpair;
		@@ -217,6 +238,8 @@ void PairVashishta::compute(int eflag, int vflag)
		evdwl,0.0,fpair,delx,dely,delz);
		}

		jlist = neigh3Body[i];
		jnum = neigh3BodyCount[i];
		jnumm1 = jnum - 1;

		for (jj = 0; jj < jnumm1; jj++) {

src/MANYBODY/pair_vashishta.h

+5 −0

Original line number	Diff line number	Diff line
		@@ -53,6 +53,10 @@ class PairVashishta : public Pair {
		double ***forceTable; // Table containing the forces
		double ***potentialTable; // Table containing the potential energies

		int neigh3BodyMax; // Max size of short neighborlist
		int *neigh3BodyCount; // Number of neighbors in short range 3 particle forces neighbor list
		int **neigh3Body; // Neighborlist for short range 3 particle forces

		double cutmax; // max cutoff for all elements
		int nelements; // # of unique elements
		char **elements; // names of unique elements
		@@ -66,6 +70,7 @@ class PairVashishta : public Pair {
		void read_file(char *);
		void setup_params();
		void createTable();
		void validateNeigh3Body();
		void twobody(Param *, double, double &, int, double &, bool);
		void threebody(Param , Param , Param , double, double, double , double *,
		double , double , int, double &);

src/USER-OMP/pair_vashishta_omp.cpp

+21 −10

Original line number	Diff line number	Diff line
		@@ -36,6 +36,8 @@ PairVashishtaOMP::PairVashishtaOMP(LAMMPS *lmp) :

		void PairVashishtaOMP::compute(int eflag, int vflag)
		{
		validateNeigh3Body();

		if (eflag \|\| vflag) {
		ev_setup(eflag,vflag);
		} else evflag = vflag_fdotr = 0;
		@@ -105,6 +107,8 @@ void PairVashishtaOMP::eval(int iifrom, int iito, ThrData * const thr)
		ztmp = x[i].z;
		fxtmp = fytmp = fztmp = 0.0;

		neigh3BodyCount[i] = 0;

		// two-body interactions, skip half of them

		jlist = firstneigh[i];
		@@ -114,6 +118,21 @@ void PairVashishtaOMP::eval(int iifrom, int iito, ThrData * const thr)
		j = jlist[jj];
		j &= NEIGHMASK;
		jtag = tag[j];
		jtype = map[type[j]];

		delx = xtmp - x[j].x;
		dely = ytmp - x[j].y;
		delz = ztmp - x[j].z;
		rsq = delxdelx + delydely + delz*delz;

		ijparam = elem2param[itype][jtype][jtype];

		if (rsq <= params[ijparam].cutsq2) {
		neigh3Body[i][neigh3BodyCount[i]] = j;
		neigh3BodyCount[i]++;
		}

		if (rsq >= params[ijparam].cutsq) continue;

		if (itag > jtag) {
		if ((itag+jtag) % 2 == 0) continue;
		@@ -125,16 +144,6 @@ void PairVashishtaOMP::eval(int iifrom, int iito, ThrData * const thr)
		if (x[j].z == ztmp && x[j].y == ytmp && x[j].x < xtmp) continue;
		}

		jtype = map[type[j]];

		delx = xtmp - x[j].x;
		dely = ytmp - x[j].y;
		delz = ztmp - x[j].z;
		rsq = delxdelx + delydely + delz*delz;

		ijparam = elem2param[itype][jtype][jtype];
		if (rsq >= params[ijparam].cutsq) continue;

		twobody(&params[ijparam],rsq,fpair,EFLAG,evdwl, useTable);

		fxtmp += delx*fpair;
		@@ -148,6 +157,8 @@ void PairVashishtaOMP::eval(int iifrom, int iito, ThrData * const thr)
		evdwl,0.0,fpair,delx,dely,delz,thr);
		}

		jlist = neigh3Body[i];
		jnum = neigh3BodyCount[i];
		jnumm1 = jnum - 1;

		for (jj = 0; jj < jnumm1; jj++) {

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