Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F81316049
pair_eam.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Thu, Sep 5, 07:53
Size
24 KB
Mime Type
text/x-c
Expires
Sat, Sep 7, 07:53 (1 d, 23 h)
Engine
blob
Format
Raw Data
Handle
20450067
Attached To
rLAMMPS lammps
pair_eam.cpp
View Options
/* ----------------------------------------------------------------------
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 MAXLINE 1024
/* ---------------------------------------------------------------------- */
PairEAM::PairEAM(LAMMPS *lmp) : Pair(lmp)
{
restartinfo = 0;
manybody_flag = 1;
nmax = 0;
rho = NULL;
fp = NULL;
map = NULL;
type2frho = 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()
{
if (copymode) return;
memory->destroy(rho);
memory->destroy(fp);
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
delete [] map;
delete [] type2frho;
map = NULL;
type2frho = NULL;
memory->destroy(type2rhor);
memory->destroy(type2z2r);
memory->destroy(scale);
}
if (funcfl) {
for (int i = 0; i < nfuncfl; i++) {
delete [] funcfl[i].file;
memory->destroy(funcfl[i].frho);
memory->destroy(funcfl[i].rhor);
memory->destroy(funcfl[i].zr);
}
memory->sfree(funcfl);
funcfl = NULL;
}
if (setfl) {
for (int i = 0; i < setfl->nelements; i++) delete [] setfl->elements[i];
delete [] setfl->elements;
delete [] setfl->mass;
memory->destroy(setfl->frho);
memory->destroy(setfl->rhor);
memory->destroy(setfl->z2r);
delete setfl;
setfl = NULL;
}
if (fs) {
for (int i = 0; i < fs->nelements; i++) delete [] fs->elements[i];
delete [] fs->elements;
delete [] fs->mass;
memory->destroy(fs->frho);
memory->destroy(fs->rhor);
memory->destroy(fs->z2r);
delete fs;
fs = NULL;
}
memory->destroy(frho);
memory->destroy(rhor);
memory->destroy(z2r);
memory->destroy(frho_spline);
memory->destroy(rhor_spline);
memory->destroy(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,evdwl,fpair;
double rsq,r,p,rhoip,rhojp,z2,z2p,recip,phip,psip,phi;
double *coeff;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
// grow energy and fp arrays if necessary
// need to be atom->nmax in length
if (atom->nmax > nmax) {
memory->destroy(rho);
memory->destroy(fp);
nmax = atom->nmax;
memory->create(rho,nmax,"pair:rho");
memory->create(fp,nmax,"pair:fp");
}
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// zero out density
if (newton_pair) {
for (i = 0; i < nall; 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];
j &= NEIGHMASK;
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
// if rho > rhomax (e.g. due to close approach of two atoms),
// will exceed table, so add linear term to conserve energy
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) {
phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax);
if (eflag_global) eng_vdwl += phi;
if (eflag_atom) eatom[i] += phi;
}
}
// communicate derivative of embedding function
comm->forward_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];
j &= NEIGHMASK;
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
// scale factor can be applied by thermodynamic integration
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;
fpair = -scale[itype][jtype]*psip*recip;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) evdwl = phi;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairEAM::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,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];
memory->create(type2rhor,n+1,n+1,"pair:type2rhor");
memory->create(type2z2r,n+1,n+1,"pair:type2z2r");
memory->create(scale,n+1,n+1,"pair:scale");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairEAM::settings(int narg, char **arg)
{
if (narg > 0) error->all(FLERR,"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(FLERR,"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++;
}
scale[i][j] = 1.0;
}
}
if (count == 0) error->all(FLERR,"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();
neighbor->request(this,instance_me);
}
/* ----------------------------------------------------------------------
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
scale[j][i] = scale[i][j];
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 *fptr;
char line[MAXLINE];
if (me == 0) {
fptr = force->open_potential(filename);
if (fptr == NULL) {
char str[128];
sprintf(str,"Cannot open EAM potential file %s",filename);
error->one(FLERR,str);
}
}
int tmp;
if (me == 0) {
fgets(line,MAXLINE,fptr);
fgets(line,MAXLINE,fptr);
sscanf(line,"%d %lg",&tmp,&file->mass);
fgets(line,MAXLINE,fptr);
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);
memory->create(file->frho,(file->nrho+1),"pair:frho");
memory->create(file->rhor,(file->nr+1),"pair:rhor");
memory->create(file->zr,(file->nr+1),"pair:zr");
if (me == 0) grab(fptr,file->nrho,&file->frho[1]);
MPI_Bcast(&file->frho[1],file->nrho,MPI_DOUBLE,0,world);
if (me == 0) grab(fptr,file->nr,&file->zr[1]);
MPI_Bcast(&file->zr[1],file->nr,MPI_DOUBLE,0,world);
if (me == 0) grab(fptr,file->nr,&file->rhor[1]);
MPI_Bcast(&file->rhor[1],file->nr,MPI_DOUBLE,0,world);
if (me == 0) fclose(fptr);
}
/* ----------------------------------------------------------------------
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;
double sixth = 1.0/6.0;
// determine max function params from all active funcfl files
// active means some element is pointing at it via map
int active;
double rmax;
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(frho);
memory->create(frho,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 = -sixth*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 = sixth*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(rhor);
memory->create(rhor,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 = -sixth*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 = sixth*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(z2r);
memory->create(z2r,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 = -sixth*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 = sixth*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 = -sixth*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 = sixth*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
// if map = -1 (non-EAM atom in pair hybrid):
// type2z2r is not used by non-opt
// but set type2z2r to 0 since accessed by opt
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) {
type2z2r[i][j] = 0;
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(frho_spline);
memory->destroy(rhor_spline);
memory->destroy(z2r_spline);
memory->create(frho_spline,nfrho,nrho+1,7,"pair:frho");
memory->create(rhor_spline,nrhor,nr+1,7,"pair:rhor");
memory->create(z2r_spline,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 *fptr, int n, double *list)
{
char *ptr;
char line[MAXLINE];
int i = 0;
while (i < n) {
fgets(line,MAXLINE,fptr);
ptr = strtok(line," \t\n\r\f");
list[i++] = atof(ptr);
while ((ptr = strtok(NULL," \t\n\r\f"))) list[i++] = atof(ptr);
}
}
/* ---------------------------------------------------------------------- */
double PairEAM::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj,
double &fforce)
{
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;
fforce = -psip*recip;
return phi;
}
/* ---------------------------------------------------------------------- */
int PairEAM::pack_forward_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 m;
}
/* ---------------------------------------------------------------------- */
void PairEAM::unpack_forward_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 m;
}
/* ---------------------------------------------------------------------- */
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 = maxeatom * sizeof(double);
bytes += maxvatom*6 * sizeof(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;
}
/* ---------------------------------------------------------------------- */
void *PairEAM::extract(const char *str, int &dim)
{
dim = 2;
if (strcmp(str,"scale") == 0) return (void *) scale;
return NULL;
}
Event Timeline
Log In to Comment