(9fe0fc37) · Commits · 郑智淋 / lammps

src/MEAM/pair_meam.cpp

+84 −42

Original line number	Diff line number	Diff line
		@@ -23,9 +23,10 @@
		#include "atom.h"
		#include "force.h"
		#include "comm.h"
		#include "update.h"
		#include "memory.h"
		#include "neighbor.h"
		#include "neigh_list.h"
		#include "neigh_request.h"
		#include "memory.h"
		#include "error.h"

		@@ -46,7 +47,6 @@ char *keywords[] = {"Ec","alpha","rho0","delta","lattce",

		PairMEAM::PairMEAM(LAMMPS *lmp) : Pair(lmp)
		{
		neigh_half_every = neigh_full_every = 1;
		single_enable = 0;
		one_coeff = 1;

		@@ -118,8 +118,9 @@ PairMEAM::~PairMEAM()

		void PairMEAM::compute(int eflag, int vflag)
		{
		int i,j,n,errorflag;
		double **f;
		int i,j,ii,n,inum_half,itype,jtype,errorflag;
		int ilist_half,jlist_half,numneigh_half,*firstneigh_half;
		int numneigh_full,firstneigh_full;

		// grow local arrays if necessary

		@@ -163,17 +164,23 @@ void PairMEAM::compute(int eflag, int vflag)
		strssa = memory->create_3d_double_array(nmax,3,3,"pair:strssa");
		}

		// neighbor list info

		inum_half = listhalf->inum;
		ilist_half = listhalf->ilist;
		numneigh_half = listhalf->numneigh;
		firstneigh_half = listhalf->firstneigh;
		numneigh_full = listfull->numneigh;
		firstneigh_full = listfull->firstneigh;

		// check size of scrfcn based on half neighbor list

		int **firstneigh = neighbor->firstneigh;
		int *numneigh = neighbor->numneigh;
		int **firstneigh_full = neighbor->firstneigh_full;
		int *numneigh_full = neighbor->numneigh_full;
		int nlocal = atom->nlocal;
		int nall = atom->nlocal + atom->nghost;

		n = 0;
		for (i = 0; i < nlocal; i++) n += numneigh[i];
		for (ii = 0; ii < inum_half; ii++) n += numneigh_half[ilist_half[ii]];

		if (n > maxneigh) {
		memory->sfree(scrfcn);
		memory->sfree(dscrfcn);
		@@ -202,26 +209,28 @@ void PairMEAM::compute(int eflag, int vflag)
		t_ave[i][0] = t_ave[i][1] = t_ave[i][2] = 0.0;
		}

		if (vflag == 2) f = update->f_pair;
		else f = atom->f;
		double **x = atom->x;
		double **f = atom->f;
		int *type = atom->type;
		int ntype = atom->ntypes;

		// change neighbor list indices to Fortran indexing

		neigh_c2f(numneigh,firstneigh);
		neigh_c2f(numneigh_full,firstneigh_full);
		neigh_c2f(inum_half,ilist_half,numneigh_half,firstneigh_half);
		neigh_c2f(inum_half,ilist_half,numneigh_full,firstneigh_full);

		// 3 stages of MEAM calculation
		// loop over my atoms followed by communication

		errorflag = 0;
		int ifort;
		int offset = 0;
		for (i = 0; i < nlocal; i++) {
		int ifort = i+1;
		errorflag = 0;

		for (ii = 0; ii < inum_half; ii++) {
		i = ilist[ii];
		ifort = i+1;
		meam_dens_init_(&ifort,&nmax,&eflag,&eng_vdwl,&ntype,type,fmap,&x[0][0],
		&numneigh[i],firstneigh[i],
		&numneigh_half[i],firstneigh_half[i],
		&numneigh_full[i],firstneigh_full[i],
		&scrfcn[offset],&dscrfcn[offset],&fcpair[offset],
		rho0,&arho1[0][0],&arho2[0][0],arho2b,
		@@ -250,10 +259,12 @@ void PairMEAM::compute(int eflag, int vflag)
		comm->comm_pair(this);

		offset = 0;
		for (i = 0; i < nlocal; i++) {
		int ifort = i+1;

		for (ii = 0; ii < inum_half; ii++) {
		i = ilist[ii];
		ifort = i+1;
		meam_force_(&ifort,&nmax,&eflag,&eng_vdwl,&ntype,type,fmap,&x[0][0],
		&numneigh[i],firstneigh[i],
		&numneigh_half[i],firstneigh_half[i],
		&numneigh_full[i],firstneigh_full[i],
		&scrfcn[offset],&dscrfcn[offset],&fcpair[offset],
		dgamma1,dgamma2,dgamma3,rho0,rho1,rho2,rho3,frhop,
		@@ -272,8 +283,8 @@ void PairMEAM::compute(int eflag, int vflag)

		// change neighbor list indices back to C indexing

		neigh_f2c(numneigh,firstneigh);
		neigh_f2c(numneigh_full,firstneigh_full);
		neigh_f2c(inum_half,ilist_half,numneigh_half,firstneigh_half);
		neigh_f2c(inum_half,ilist_half,numneigh_full,firstneigh_full);

		if (vflag == 2) virial_compute();
		}
		@@ -380,21 +391,26 @@ void PairMEAM::coeff(int narg, char **arg)
		}

		/* ----------------------------------------------------------------------
		init for one type pair i,j and corresponding j,i
		init specific to this pair style
		------------------------------------------------------------------------- */

		double PairMEAM::init_one(int i, int j)
		{
		return cutmax;
		}

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

		void PairMEAM::init_style()
		{
		if (force->newton_pair == 0)
		error->all("Pair style MEAM requires newton pair on");

		// need full and half neighbor list

		int irequest_full = neighbor->request(this);
		neighbor->requests[irequest_full]->id = 1;
		neighbor->requests[irequest_full]->half = 0;
		neighbor->requests[irequest_full]->full = 1;
		int irequest_half = neighbor->request(this);
		neighbor->requests[irequest_half]->id = 2;
		neighbor->requests[irequest_half]->half = 0;
		neighbor->requests[irequest_half]->half_from_full = 1;
		neighbor->requests[irequest_half]->otherlist = irequest_full;

		// setup Fortran-style mapping array needed by MEAM package
		// fmap is indexed from 1:ntypes by Fortran and stores a Fortran index
		// if type I is not a MEAM atom, fmap stores a 0
		@@ -402,6 +418,26 @@ void PairMEAM::init_style()
		for (int i = 1; i <= atom->ntypes; i++) fmap[i-1] = map[i] + 1;
		}

		/* ----------------------------------------------------------------------
		neighbor callback to inform pair style of neighbor list to use
		half or full
		------------------------------------------------------------------------- */

		void PairMEAM::init_list(int id, NeighList *ptr)
		{
		if (id == 1) listfull = ptr;
		else if (id == 2) listhalf = ptr;
		}

		/* ----------------------------------------------------------------------
		init for one type pair i,j and corresponding j,i
		------------------------------------------------------------------------- */

		double PairMEAM::init_one(int i, int j)
		{
		return cutmax;
		}

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

		void PairMEAM::read_files(char globalfile, char userfile)
		@@ -868,22 +904,28 @@ int PairMEAM::memory_usage()
		needed for access by MEAM Fortran library
		------------------------------------------------------------------------- */

		void PairMEAM::neigh_f2c(int numn, int *firstn)
		void PairMEAM::neigh_f2c(int inum, int nlist, int numneigh, int **firstneigh)
		{
		int nlocal = atom->nlocal;
		for (int i = 0; i < nlocal; i++) {
		int *neigh = firstn[i];
		int nsize = numn[i];
		for (int j = 0; j < nsize; j++) neigh[j] -= 1;
		int i,j,ii,jnum;
		int *jlist;

		for (ii = 0; ii < inum; ii++) {
		i = list[ii];
		jlist = firstneigh[i];
		jnum = numneigh[i];
		for (j = 0; j < jnum; j++) jlist[j]--;
		}
		}

		void PairMEAM::neigh_c2f(int numn, int *firstn)
		void PairMEAM::neigh_c2f(int inum, int nlist, int numneigh, int **firstneigh)
		{
		int nlocal = atom->nlocal;
		for (int i = 0; i < nlocal; i++) {
		int *neigh = firstn[i];
		int nsize = numn[i];
		for (int j = 0; j < nsize; j++) neigh[j] += 1;
		int i,j,ii,jnum;
		int *jlist;

		for (ii = 0; ii < inum; ii++) {
		i = list[ii];
		jlist = firstneigh[i];
		jnum = numneigh[i];
		for (j = 0; j < jnum; j++) jlist[j]++;
		}
		}

src/MEAM/pair_meam.h

+2 −1

Original line number	Diff line number	Diff line
		@@ -56,8 +56,9 @@ class PairMEAM : public Pair {
		void compute(int, int);
		void settings(int, char **);
		void coeff(int, char **);
		double init_one(int, int);
		void init_style();
		void init_list(int, class NeighList *);
		double init_one(int, int);

		int pack_comm(int, int , double , int, int *);
		void unpack_comm(int, int, double *);

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