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pair_eam.cpp
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Tue, Feb 18, 23:08

pair_eam.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_eam.h"
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
#define MAXLINE 1024
/* ---------------------------------------------------------------------- */
PairEAM::PairEAM(LAMMPS *lmp) : Pair(lmp)
{
nmax = 0;
rho = NULL;
fp = NULL;
nfuncfl = 0;
funcfl = NULL;
setfl = NULL;
fs = NULL;
frho = NULL;
rhor = NULL;
z2r = NULL;
frho_spline = NULL;
rhor_spline = NULL;
z2r_spline = NULL;
// set comm size needed by this Pair
comm_forward = 1;
comm_reverse = 1;
}
/* ----------------------------------------------------------------------
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
PairEAM::~PairEAM()
{
memory->sfree(rho);
memory->sfree(fp);
if (allocated) {
memory->destroy_2d_int_array(setflag);
memory->destroy_2d_double_array(cutsq);
delete [] map;
delete [] type2frho;
memory->destroy_2d_int_array(type2rhor);
memory->destroy_2d_int_array(type2z2r);
}
if (funcfl) {
for (int i = 0; i < nfuncfl; i++) {
delete [] funcfl[i].file;
memory->sfree(funcfl[i].frho);
memory->sfree(funcfl[i].rhor);
memory->sfree(funcfl[i].zr);
}
memory->sfree(funcfl);
}
if (setfl) {
for (int i = 0; i < setfl->nelements; i++) delete [] setfl->elements[i];
delete [] setfl->elements;
delete [] setfl->mass;
memory->destroy_2d_double_array(setfl->frho);
memory->destroy_2d_double_array(setfl->rhor);
memory->destroy_3d_double_array(setfl->z2r);
delete setfl;
}
if (fs) {
for (int i = 0; i < fs->nelements; i++) delete [] fs->elements[i];
delete [] fs->elements;
delete [] fs->mass;
memory->destroy_2d_double_array(fs->frho);
memory->destroy_3d_double_array(fs->rhor);
memory->destroy_3d_double_array(fs->z2r);
delete fs;
}
memory->destroy_2d_double_array(frho);
memory->destroy_2d_double_array(rhor);
memory->destroy_2d_double_array(z2r);
memory->destroy_3d_double_array(frho_spline);
memory->destroy_3d_double_array(rhor_spline);
memory->destroy_3d_double_array(z2r_spline);
}
/* ---------------------------------------------------------------------- */
void PairEAM::compute(int eflag, int vflag)
{
int i,j,ii,jj,m,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r,p,fforce,rhoip,rhojp,z2,z2p,recip,phi,phip,psip;
double *coeff;
int *ilist,*jlist,*numneigh,**firstneigh;
// grow energy array if necessary
if (atom->nmax > nmax) {
memory->sfree(rho);
memory->sfree(fp);
nmax = atom->nmax;
rho = (double *) memory->smalloc(nmax*sizeof(double),"pair:rho");
fp = (double *) memory->smalloc(nmax*sizeof(double),"pair:fp");
}
eng_vdwl = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// zero out density
if (newton_pair) {
m = nlocal + atom->nghost;
for (i = 0; i < m; i++) rho[i] = 0.0;
} else for (i = 0; i < nlocal; i++) rho[i] = 0.0;
// rho = density at each atom
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq) {
jtype = type[j];
p = sqrt(rsq)*rdr + 1.0;
m = static_cast<int> (p);
m = MIN(m,nr-1);
p -= m;
p = MIN(p,1.0);
coeff = rhor_spline[type2rhor[jtype][itype]][m];
rho[i] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
if (newton_pair || j < nlocal) {
coeff = rhor_spline[type2rhor[itype][jtype]][m];
rho[j] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
}
}
}
}
// communicate and sum densities
if (newton_pair) comm->reverse_comm_pair(this);
// fp = derivative of embedding energy at each atom
// phi = embedding energy at each atom
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
p = rho[i]*rdrho + 1.0;
m = static_cast<int> (p);
m = MAX(1,MIN(m,nrho-1));
p -= m;
p = MIN(p,1.0);
coeff = frho_spline[type2frho[type[i]]][m];
fp[i] = (coeff[0]*p + coeff[1])*p + coeff[2];
if (eflag) eng_vdwl += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
}
// communicate derivative of embedding function
comm->comm_pair(this);
// compute forces on each atom
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutforcesq) {
jtype = type[j];
r = sqrt(rsq);
p = r*rdr + 1.0;
m = static_cast<int> (p);
m = MIN(m,nr-1);
p -= m;
p = MIN(p,1.0);
// rhoip = derivative of (density at atom j due to atom i)
// rhojp = derivative of (density at atom i due to atom j)
// phi = pair potential energy
// phip = phi'
// z2 = phi * r
// z2p = (phi * r)' = (phi' r) + phi
// psip needs both fp[i] and fp[j] terms since r_ij appears in two
// terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
// hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
coeff = rhor_spline[type2rhor[itype][jtype]][m];
rhoip = (coeff[0]*p + coeff[1])*p + coeff[2];
coeff = rhor_spline[type2rhor[jtype][itype]][m];
rhojp = (coeff[0]*p + coeff[1])*p + coeff[2];
coeff = z2r_spline[type2z2r[itype][jtype]][m];
z2p = (coeff[0]*p + coeff[1])*p + coeff[2];
z2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
recip = 1.0/r;
phi = z2*recip;
phip = z2p*recip - phi*recip;
psip = fp[i]*rhojp + fp[j]*rhoip + phip;
fforce = -psip*recip;
f[i][0] += delx*fforce;
f[i][1] += dely*fforce;
f[i][2] += delz*fforce;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fforce;
f[j][1] -= dely*fforce;
f[j][2] -= delz*fforce;
}
if (eflag) {
if (newton_pair || j < nlocal) eng_vdwl += phi;
else eng_vdwl += 0.5*phi;
}
if (vflag == 1) {
if (newton_pair == 0 && j >= nlocal) fforce *= 0.5;
virial[0] += delx*delx*fforce;
virial[1] += dely*dely*fforce;
virial[2] += delz*delz*fforce;
virial[3] += delx*dely*fforce;
virial[4] += delx*delz*fforce;
virial[5] += dely*delz*fforce;
}
}
}
}
if (vflag == 2) virial_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairEAM::allocate()
{
allocated = 1;
int n = atom->ntypes;
setflag = memory->create_2d_int_array(n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq");
map = new int[n+1];
for (int i = 1; i <= n; i++) map[i] = -1;
type2frho = new int[n+1];
type2rhor = memory->create_2d_int_array(n+1,n+1,"pair:type2rhor");
type2z2r = memory->create_2d_int_array(n+1,n+1,"pair:type2z2r");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairEAM::settings(int narg, char **arg)
{
if (narg > 0) error->all("Illegal pair_style command");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
read DYNAMO funcfl file
------------------------------------------------------------------------- */
void PairEAM::coeff(int narg, char **arg)
{
if (!allocated) allocate();
if (narg != 3) error->all("Incorrect args for pair coefficients");
// parse pair of atom types
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
// read funcfl file if hasn't already been read
// store filename in Funcfl data struct
int ifuncfl;
for (ifuncfl = 0; ifuncfl < nfuncfl; ifuncfl++)
if (strcmp(arg[2],funcfl[ifuncfl].file) == 0) break;
if (ifuncfl == nfuncfl) {
nfuncfl++;
funcfl = (Funcfl *)
memory->srealloc(funcfl,nfuncfl*sizeof(Funcfl),"pair:funcfl");
read_file(arg[2]);
int n = strlen(arg[2]) + 1;
funcfl[ifuncfl].file = new char[n];
strcpy(funcfl[ifuncfl].file,arg[2]);
}
// set setflag and map only for i,i type pairs
// set mass of atom type if i = j
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
if (i == j) {
setflag[i][i] = 1;
map[i] = ifuncfl;
atom->set_mass(i,funcfl[ifuncfl].mass);
count++;
}
}
}
if (count == 0) error->all("Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairEAM::init_style()
{
// convert read-in file(s) to arrays and spline them
file2array();
array2spline();
int irequest = neighbor->request(this);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairEAM::init_one(int i, int j)
{
// single global cutoff = max of cut from all files read in
// for funcfl could be multiple files
// for setfl or fs, just one file
if (funcfl) {
cutmax = 0.0;
for (int m = 0; m < nfuncfl; m++)
cutmax = MAX(cutmax,funcfl[m].cut);
} else if (setfl) cutmax = setfl->cut;
else if (fs) cutmax = fs->cut;
cutforcesq = cutmax*cutmax;
return cutmax;
}
/* ----------------------------------------------------------------------
read potential values from a DYNAMO single element funcfl file
------------------------------------------------------------------------- */
void PairEAM::read_file(char *filename)
{
Funcfl *file = &funcfl[nfuncfl-1];
int me = comm->me;
FILE *fp;
char line[MAXLINE];
if (me == 0) {
fp = fopen(filename,"r");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open EAM potential file %s",filename);
error->one(str);
}
}
int tmp;
if (me == 0) {
fgets(line,MAXLINE,fp);
fgets(line,MAXLINE,fp);
sscanf(line,"%d %lg",&tmp,&file->mass);
fgets(line,MAXLINE,fp);
sscanf(line,"%d %lg %d %lg %lg",
&file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
}
MPI_Bcast(&file->mass,1,MPI_DOUBLE,0,world);
MPI_Bcast(&file->nrho,1,MPI_INT,0,world);
MPI_Bcast(&file->drho,1,MPI_DOUBLE,0,world);
MPI_Bcast(&file->nr,1,MPI_INT,0,world);
MPI_Bcast(&file->dr,1,MPI_DOUBLE,0,world);
MPI_Bcast(&file->cut,1,MPI_DOUBLE,0,world);
file->frho = (double *) memory->smalloc((file->nrho+1)*sizeof(double),
"pair:frho");
file->rhor = (double *) memory->smalloc((file->nr+1)*sizeof(double),
"pair:rhor");
file->zr = (double *) memory->smalloc((file->nr+1)*sizeof(double),
"pair:zr");
if (me == 0) grab(fp,file->nrho,&file->frho[1]);
MPI_Bcast(&file->frho[1],file->nrho,MPI_DOUBLE,0,world);
if (me == 0) grab(fp,file->nr,&file->zr[1]);
MPI_Bcast(&file->zr[1],file->nr,MPI_DOUBLE,0,world);
if (me == 0) grab(fp,file->nr,&file->rhor[1]);
MPI_Bcast(&file->rhor[1],file->nr,MPI_DOUBLE,0,world);
if (me == 0) fclose(fp);
}
/* ----------------------------------------------------------------------
convert read-in funcfl potential(s) to standard array format
interpolate all file values to a single grid and cutoff
------------------------------------------------------------------------- */
void PairEAM::file2array()
{
int i,j,k,m,n;
int ntypes = atom->ntypes;
// determine max function params from all active funcfl files
// active means some element is pointing at it via map
int active;
double rmax,rhomax;
dr = drho = rmax = rhomax = 0.0;
for (int i = 0; i < nfuncfl; i++) {
active = 0;
for (j = 1; j <= ntypes; j++)
if (map[j] == i) active = 1;
if (active == 0) continue;
Funcfl *file = &funcfl[i];
dr = MAX(dr,file->dr);
drho = MAX(drho,file->drho);
rmax = MAX(rmax,(file->nr-1) * file->dr);
rhomax = MAX(rhomax,(file->nrho-1) * file->drho);
}
// set nr,nrho from cutoff and spacings
// 0.5 is for round-off in divide
nr = static_cast<int> (rmax/dr + 0.5);
nrho = static_cast<int> (rhomax/drho + 0.5);
// ------------------------------------------------------------------
// setup frho arrays
// ------------------------------------------------------------------
// allocate frho arrays
// nfrho = # of funcfl files + 1 for zero array
nfrho = nfuncfl + 1;
memory->destroy_2d_double_array(frho);
frho = (double **) memory->create_2d_double_array(nfrho,nrho+1,"pair:frho");
// interpolate each file's frho to a single grid and cutoff
double r,p,cof1,cof2,cof3,cof4;
n = 0;
for (i = 0; i < nfuncfl; i++) {
Funcfl *file = &funcfl[i];
for (m = 1; m <= nrho; m++) {
r = (m-1)*drho;
p = r/file->drho + 1.0;
k = static_cast<int> (p);
k = MIN(k,file->nrho-2);
k = MAX(k,2);
p -= k;
p = MIN(p,2.0);
cof1 = -0.166666667*p*(p-1.0)*(p-2.0);
cof2 = 0.5*(p*p-1.0)*(p-2.0);
cof3 = -0.5*p*(p+1.0)*(p-2.0);
cof4 = 0.166666667*p*(p*p-1.0);
frho[n][m] = cof1*file->frho[k-1] + cof2*file->frho[k] +
cof3*file->frho[k+1] + cof4*file->frho[k+2];
}
n++;
}
// add extra frho of zeroes for non-EAM types to point to (pair hybrid)
// this is necessary b/c fp is still computed for non-EAM atoms
for (m = 1; m <= nrho; m++) frho[nfrho-1][m] = 0.0;
// type2frho[i] = which frho array (0 to nfrho-1) each atom type maps to
// if atom type doesn't point to file (non-EAM atom in pair hybrid)
// then map it to last frho array of zeroes
for (i = 1; i <= ntypes; i++)
if (map[i] >= 0) type2frho[i] = map[i];
else type2frho[i] = nfrho-1;
// ------------------------------------------------------------------
// setup rhor arrays
// ------------------------------------------------------------------
// allocate rhor arrays
// nrhor = # of funcfl files
nrhor = nfuncfl;
memory->destroy_2d_double_array(rhor);
rhor = (double **) memory->create_2d_double_array(nrhor,nr+1,"pair:rhor");
// interpolate each file's rhor to a single grid and cutoff
n = 0;
for (i = 0; i < nfuncfl; i++) {
Funcfl *file = &funcfl[i];
for (m = 1; m <= nr; m++) {
r = (m-1)*dr;
p = r/file->dr + 1.0;
k = static_cast<int> (p);
k = MIN(k,file->nr-2);
k = MAX(k,2);
p -= k;
p = MIN(p,2.0);
cof1 = -0.166666667*p*(p-1.0)*(p-2.0);
cof2 = 0.5*(p*p-1.0)*(p-2.0);
cof3 = -0.5*p*(p+1.0)*(p-2.0);
cof4 = 0.166666667*p*(p*p-1.0);
rhor[n][m] = cof1*file->rhor[k-1] + cof2*file->rhor[k] +
cof3*file->rhor[k+1] + cof4*file->rhor[k+2];
}
n++;
}
// type2rhor[i][j] = which rhor array (0 to nrhor-1) each type pair maps to
// for funcfl files, I,J mapping only depends on I
// OK if map = -1 (non-EAM atom in pair hybrid) b/c type2rhor not used
for (i = 1; i <= ntypes; i++)
for (j = 1; j <= ntypes; j++)
type2rhor[i][j] = map[i];
// ------------------------------------------------------------------
// setup z2r arrays
// ------------------------------------------------------------------
// allocate z2r arrays
// nz2r = N*(N+1)/2 where N = # of funcfl files
nz2r = nfuncfl*(nfuncfl+1)/2;
memory->destroy_2d_double_array(z2r);
z2r = (double **) memory->create_2d_double_array(nz2r,nr+1,"pair:z2r");
// create a z2r array for each file against other files, only for I >= J
// interpolate zri and zrj to a single grid and cutoff
double zri,zrj;
n = 0;
for (i = 0; i < nfuncfl; i++) {
Funcfl *ifile = &funcfl[i];
for (j = 0; j <= i; j++) {
Funcfl *jfile = &funcfl[j];
for (m = 1; m <= nr; m++) {
r = (m-1)*dr;
p = r/ifile->dr + 1.0;
k = static_cast<int> (p);
k = MIN(k,ifile->nr-2);
k = MAX(k,2);
p -= k;
p = MIN(p,2.0);
cof1 = -0.166666667*p*(p-1.0)*(p-2.0);
cof2 = 0.5*(p*p-1.0)*(p-2.0);
cof3 = -0.5*p*(p+1.0)*(p-2.0);
cof4 = 0.166666667*p*(p*p-1.0);
zri = cof1*ifile->zr[k-1] + cof2*ifile->zr[k] +
cof3*ifile->zr[k+1] + cof4*ifile->zr[k+2];
p = r/jfile->dr + 1.0;
k = static_cast<int> (p);
k = MIN(k,jfile->nr-2);
k = MAX(k,2);
p -= k;
p = MIN(p,2.0);
cof1 = -0.166666667*p*(p-1.0)*(p-2.0);
cof2 = 0.5*(p*p-1.0)*(p-2.0);
cof3 = -0.5*p*(p+1.0)*(p-2.0);
cof4 = 0.166666667*p*(p*p-1.0);
zrj = cof1*jfile->zr[k-1] + cof2*jfile->zr[k] +
cof3*jfile->zr[k+1] + cof4*jfile->zr[k+2];
z2r[n][m] = 27.2*0.529 * zri*zrj;
}
n++;
}
}
// type2z2r[i][j] = which z2r array (0 to nz2r-1) each type pair maps to
// set of z2r arrays only fill lower triangular Nelement matrix
// value = n = sum over rows of lower-triangular matrix until reach irow,icol
// swap indices when irow < icol to stay lower triangular
// OK if map = -1 (non-EAM atom in pair hybrid) b/c type2z2r not used
int irow,icol;
for (i = 1; i <= ntypes; i++) {
for (j = 1; j <= ntypes; j++) {
irow = map[i];
icol = map[j];
if (irow == -1 || icol == -1) continue;
if (irow < icol) {
irow = map[j];
icol = map[i];
}
n = 0;
for (m = 0; m < irow; m++) n += m + 1;
n += icol;
type2z2r[i][j] = n;
}
}
}
/* ---------------------------------------------------------------------- */
void PairEAM::array2spline()
{
rdr = 1.0/dr;
rdrho = 1.0/drho;
memory->destroy_3d_double_array(frho_spline);
memory->destroy_3d_double_array(rhor_spline);
memory->destroy_3d_double_array(z2r_spline);
frho_spline = memory->create_3d_double_array(nfrho,nrho+1,7,"pair:frho");
rhor_spline = memory->create_3d_double_array(nrhor,nr+1,7,"pair:rhor");
z2r_spline = memory->create_3d_double_array(nz2r,nr+1,7,"pair:z2r");
for (int i = 0; i < nfrho; i++)
interpolate(nrho,drho,frho[i],frho_spline[i]);
for (int i = 0; i < nrhor; i++)
interpolate(nr,dr,rhor[i],rhor_spline[i]);
for (int i = 0; i < nz2r; i++)
interpolate(nr,dr,z2r[i],z2r_spline[i]);
}
/* ---------------------------------------------------------------------- */
void PairEAM::interpolate(int n, double delta, double *f, double **spline)
{
for (int m = 1; m <= n; m++) spline[m][6] = f[m];
spline[1][5] = spline[2][6] - spline[1][6];
spline[2][5] = 0.5 * (spline[3][6]-spline[1][6]);
spline[n-1][5] = 0.5 * (spline[n][6]-spline[n-2][6]);
spline[n][5] = spline[n][6] - spline[n-1][6];
for (int m = 3; m <= n-2; m++)
spline[m][5] = ((spline[m-2][6]-spline[m+2][6]) +
8.0*(spline[m+1][6]-spline[m-1][6])) / 12.0;
for (int m = 1; m <= n-1; m++) {
spline[m][4] = 3.0*(spline[m+1][6]-spline[m][6]) -
2.0*spline[m][5] - spline[m+1][5];
spline[m][3] = spline[m][5] + spline[m+1][5] -
2.0*(spline[m+1][6]-spline[m][6]);
}
spline[n][4] = 0.0;
spline[n][3] = 0.0;
for (int m = 1; m <= n; m++) {
spline[m][2] = spline[m][5]/delta;
spline[m][1] = 2.0*spline[m][4]/delta;
spline[m][0] = 3.0*spline[m][3]/delta;
}
}
/* ----------------------------------------------------------------------
grab n values from file fp and put them in list
values can be several to a line
only called by proc 0
------------------------------------------------------------------------- */
void PairEAM::grab(FILE *fp, int n, double *list)
{
char *ptr;
char line[MAXLINE];
int i = 0;
while (i < n) {
fgets(line,MAXLINE,fp);
ptr = strtok(line," \t\n\r\f");
list[i++] = atof(ptr);
while (ptr = strtok(NULL," \t\n\r\f")) list[i++] = atof(ptr);
}
}
/* ---------------------------------------------------------------------- */
void PairEAM::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj,
int eflag, One &one)
{
int m;
double r,p,rhoip,rhojp,z2,z2p,recip,phi,phip,psip;
double *coeff;
r = sqrt(rsq);
p = r*rdr + 1.0;
m = static_cast<int> (p);
m = MIN(m,nr-1);
p -= m;
p = MIN(p,1.0);
coeff = rhor_spline[type2rhor[itype][jtype]][m];
rhoip = (coeff[0]*p + coeff[1])*p + coeff[2];
coeff = rhor_spline[type2rhor[jtype][itype]][m];
rhojp = (coeff[0]*p + coeff[1])*p + coeff[2];
coeff = z2r_spline[type2z2r[itype][jtype]][m];
z2p = (coeff[0]*p + coeff[1])*p + coeff[2];
z2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
recip = 1.0/r;
phi = z2*recip;
phip = z2p*recip - phi*recip;
psip = fp[i]*rhojp + fp[j]*rhoip + phip;
one.fforce = -psip*recip;
if (eflag) {
one.eng_vdwl = phi;
one.eng_coul = 0.0;
}
}
/* ---------------------------------------------------------------------- */
void PairEAM::single_embed(int i, int itype, double &phi)
{
double p = rho[i]*rdrho + 1.0;
int m = static_cast<int> (p);
m = MAX(1,MIN(m,nrho-1));
p -= m;
double *coeff = frho_spline[type2frho[itype]][m];
phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
}
/* ---------------------------------------------------------------------- */
int PairEAM::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = fp[j];
}
return 1;
}
/* ---------------------------------------------------------------------- */
void PairEAM::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) fp[i] = buf[m++];
}
/* ---------------------------------------------------------------------- */
int PairEAM::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) buf[m++] = rho[i];
return 1;
}
/* ---------------------------------------------------------------------- */
void PairEAM::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
rho[j] += buf[m++];
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairEAM::memory_usage()
{
double bytes = 2 * nmax * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
swap fp array with one passed in by caller
------------------------------------------------------------------------- */
void PairEAM::swap_eam(double *fp_caller, double **fp_caller_hold)
{
double *tmp = fp;
fp = fp_caller;
*fp_caller_hold = tmp;
}

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