mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@933 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
parent
d31eb1a080
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9fe0fc3757
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@ -23,9 +23,10 @@
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#include "atom.h"
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#include "force.h"
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#include "comm.h"
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#include "update.h"
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#include "memory.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "neigh_request.h"
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#include "memory.h"
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#include "error.h"
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@ -46,7 +47,6 @@ char *keywords[] = {"Ec","alpha","rho0","delta","lattce",
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PairMEAM::PairMEAM(LAMMPS *lmp) : Pair(lmp)
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{
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neigh_half_every = neigh_full_every = 1;
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single_enable = 0;
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one_coeff = 1;
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@ -118,8 +118,9 @@ PairMEAM::~PairMEAM()
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void PairMEAM::compute(int eflag, int vflag)
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{
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int i,j,n,errorflag;
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double **f;
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int i,j,ii,n,inum_half,itype,jtype,errorflag;
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int *ilist_half,*jlist_half,*numneigh_half,**firstneigh_half;
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int *numneigh_full,*firstneigh_full;
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// grow local arrays if necessary
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@ -163,17 +164,23 @@ void PairMEAM::compute(int eflag, int vflag)
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strssa = memory->create_3d_double_array(nmax,3,3,"pair:strssa");
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}
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// neighbor list info
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inum_half = listhalf->inum;
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ilist_half = listhalf->ilist;
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numneigh_half = listhalf->numneigh;
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firstneigh_half = listhalf->firstneigh;
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numneigh_full = listfull->numneigh;
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firstneigh_full = listfull->firstneigh;
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// check size of scrfcn based on half neighbor list
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int **firstneigh = neighbor->firstneigh;
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int *numneigh = neighbor->numneigh;
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int **firstneigh_full = neighbor->firstneigh_full;
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int *numneigh_full = neighbor->numneigh_full;
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int nlocal = atom->nlocal;
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int nall = atom->nlocal + atom->nghost;
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n = 0;
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for (i = 0; i < nlocal; i++) n += numneigh[i];
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for (ii = 0; ii < inum_half; ii++) n += numneigh_half[ilist_half[ii]];
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if (n > maxneigh) {
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memory->sfree(scrfcn);
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memory->sfree(dscrfcn);
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@ -202,26 +209,28 @@ void PairMEAM::compute(int eflag, int vflag)
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t_ave[i][0] = t_ave[i][1] = t_ave[i][2] = 0.0;
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}
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if (vflag == 2) f = update->f_pair;
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else f = atom->f;
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double **x = atom->x;
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double **f = atom->f;
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int *type = atom->type;
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int ntype = atom->ntypes;
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// change neighbor list indices to Fortran indexing
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neigh_c2f(numneigh,firstneigh);
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neigh_c2f(numneigh_full,firstneigh_full);
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neigh_c2f(inum_half,ilist_half,numneigh_half,firstneigh_half);
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neigh_c2f(inum_half,ilist_half,numneigh_full,firstneigh_full);
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// 3 stages of MEAM calculation
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// loop over my atoms followed by communication
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errorflag = 0;
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int ifort;
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int offset = 0;
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for (i = 0; i < nlocal; i++) {
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int ifort = i+1;
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errorflag = 0;
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for (ii = 0; ii < inum_half; ii++) {
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i = ilist[ii];
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ifort = i+1;
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meam_dens_init_(&ifort,&nmax,&eflag,&eng_vdwl,&ntype,type,fmap,&x[0][0],
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&numneigh[i],firstneigh[i],
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&numneigh_half[i],firstneigh_half[i],
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&numneigh_full[i],firstneigh_full[i],
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&scrfcn[offset],&dscrfcn[offset],&fcpair[offset],
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rho0,&arho1[0][0],&arho2[0][0],arho2b,
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@ -250,10 +259,12 @@ void PairMEAM::compute(int eflag, int vflag)
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comm->comm_pair(this);
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offset = 0;
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for (i = 0; i < nlocal; i++) {
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int ifort = i+1;
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for (ii = 0; ii < inum_half; ii++) {
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i = ilist[ii];
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ifort = i+1;
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meam_force_(&ifort,&nmax,&eflag,&eng_vdwl,&ntype,type,fmap,&x[0][0],
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&numneigh[i],firstneigh[i],
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&numneigh_half[i],firstneigh_half[i],
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&numneigh_full[i],firstneigh_full[i],
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&scrfcn[offset],&dscrfcn[offset],&fcpair[offset],
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dgamma1,dgamma2,dgamma3,rho0,rho1,rho2,rho3,frhop,
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@ -272,8 +283,8 @@ void PairMEAM::compute(int eflag, int vflag)
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// change neighbor list indices back to C indexing
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neigh_f2c(numneigh,firstneigh);
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neigh_f2c(numneigh_full,firstneigh_full);
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neigh_f2c(inum_half,ilist_half,numneigh_half,firstneigh_half);
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neigh_f2c(inum_half,ilist_half,numneigh_full,firstneigh_full);
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if (vflag == 2) virial_compute();
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}
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@ -380,21 +391,26 @@ void PairMEAM::coeff(int narg, char **arg)
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}
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/* ----------------------------------------------------------------------
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init for one type pair i,j and corresponding j,i
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init specific to this pair style
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------------------------------------------------------------------------- */
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double PairMEAM::init_one(int i, int j)
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{
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return cutmax;
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}
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/* ---------------------------------------------------------------------- */
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void PairMEAM::init_style()
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{
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if (force->newton_pair == 0)
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error->all("Pair style MEAM requires newton pair on");
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// need full and half neighbor list
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int irequest_full = neighbor->request(this);
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neighbor->requests[irequest_full]->id = 1;
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neighbor->requests[irequest_full]->half = 0;
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neighbor->requests[irequest_full]->full = 1;
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int irequest_half = neighbor->request(this);
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neighbor->requests[irequest_half]->id = 2;
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neighbor->requests[irequest_half]->half = 0;
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neighbor->requests[irequest_half]->half_from_full = 1;
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neighbor->requests[irequest_half]->otherlist = irequest_full;
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// setup Fortran-style mapping array needed by MEAM package
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// fmap is indexed from 1:ntypes by Fortran and stores a Fortran index
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// if type I is not a MEAM atom, fmap stores a 0
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@ -402,6 +418,26 @@ void PairMEAM::init_style()
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for (int i = 1; i <= atom->ntypes; i++) fmap[i-1] = map[i] + 1;
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}
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/* ----------------------------------------------------------------------
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neighbor callback to inform pair style of neighbor list to use
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half or full
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------------------------------------------------------------------------- */
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void PairMEAM::init_list(int id, NeighList *ptr)
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{
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if (id == 1) listfull = ptr;
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else if (id == 2) listhalf = ptr;
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}
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/* ----------------------------------------------------------------------
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init for one type pair i,j and corresponding j,i
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------------------------------------------------------------------------- */
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double PairMEAM::init_one(int i, int j)
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{
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return cutmax;
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}
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/* ---------------------------------------------------------------------- */
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void PairMEAM::read_files(char *globalfile, char *userfile)
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@ -868,22 +904,28 @@ int PairMEAM::memory_usage()
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needed for access by MEAM Fortran library
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------------------------------------------------------------------------- */
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void PairMEAM::neigh_f2c(int *numn, int **firstn)
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void PairMEAM::neigh_f2c(int inum, int *nlist, int *numneigh, int **firstneigh)
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{
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++) {
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int *neigh = firstn[i];
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int nsize = numn[i];
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for (int j = 0; j < nsize; j++) neigh[j] -= 1;
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int i,j,ii,jnum;
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int *jlist;
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for (ii = 0; ii < inum; ii++) {
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i = list[ii];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (j = 0; j < jnum; j++) jlist[j]--;
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}
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}
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void PairMEAM::neigh_c2f(int *numn, int **firstn)
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void PairMEAM::neigh_c2f(int inum, int *nlist, int *numneigh, int **firstneigh)
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{
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++) {
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int *neigh = firstn[i];
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int nsize = numn[i];
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for (int j = 0; j < nsize; j++) neigh[j] += 1;
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int i,j,ii,jnum;
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int *jlist;
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for (ii = 0; ii < inum; ii++) {
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i = list[ii];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (j = 0; j < jnum; j++) jlist[j]++;
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}
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}
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@ -56,8 +56,9 @@ class PairMEAM : public Pair {
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void compute(int, int);
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void settings(int, char **);
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void coeff(int, char **);
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double init_one(int, int);
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void init_style();
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void init_list(int, class NeighList *);
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double init_one(int, int);
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int pack_comm(int, int *, double *, int, int *);
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void unpack_comm(int, int, double *);
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