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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@103 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2006-11-01 23:00:53 +00:00
parent ed0d30f88d
commit 290625c0cf
5 changed files with 749 additions and 1430 deletions
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777
src/MANYBODY/pair_eam.cpp
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@ -24,8 +24,8 @@
#include "force.h"
#include "update.h"
#include "comm.h"
#include "memory.h"
#include "neighbor.h"
#include "memory.h"
#include "error.h"
#define MIN(a,b) ((a) < (b) ? (a) : (b))
@ -40,16 +40,20 @@ PairEAM::PairEAM()
nmax = 0;
rho = NULL;
fp = NULL;
ntables = 0;
tables = NULL;
nfuncfl = 0;
funcfl = NULL;
setfl = NULL;
fs = NULL;
frho = NULL;
frho_0 = NULL;
// set rhor to NULL so memory deallocation will work
// even from derived classes that don't use rhor
rhor = NULL;
z2r = NULL;
frho_spline = NULL;
rhor_spline = NULL;
z2r_spline = NULL;
}
/* ----------------------------------------------------------------------
@ -65,26 +69,49 @@ PairEAM::~PairEAM()
if (allocated) {
memory->destroy_2d_int_array(setflag);
memory->destroy_2d_double_array(cutsq);
memory->destroy_2d_int_array(tabindex);
delete [] map;
delete [] type2frho;
memory->destroy_2d_int_array(type2rhor);
memory->destroy_2d_int_array(type2z2r);
}
for (int m = 0; m < ntables; m++) {
delete [] tables[m].filename;
delete [] tables[m].frho;
delete [] tables[m].rhor;
delete [] tables[m].zr;
delete [] tables[m].z2r;
}
memory->sfree(tables);
if (frho) {
memory->destroy_2d_double_array(frho);
memory->destroy_2d_double_array(rhor);
memory->destroy_2d_double_array(zrtmp);
memory->destroy_3d_double_array(z2r);
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 (frho_0) interpolate_deallocate();
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);
}
/* ---------------------------------------------------------------------- */
@ -94,6 +121,7 @@ void PairEAM::compute(int eflag, int vflag)
int i,j,k,m,numneigh,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 *neighs;
double **f;
@ -103,8 +131,8 @@ void PairEAM::compute(int eflag, int vflag)
memory->sfree(rho);
memory->sfree(fp);
nmax = atom->nmax;
rho = (double *) memory->smalloc(nmax*sizeof(double),"eam:rho");
fp = (double *) memory->smalloc(nmax*sizeof(double),"eam:fp");
rho = (double *) memory->smalloc(nmax*sizeof(double),"pair:rho");
fp = (double *) memory->smalloc(nmax*sizeof(double),"pair:fp");
}
eng_vdwl = 0.0;
@ -150,11 +178,12 @@ void PairEAM::compute(int eflag, int vflag)
m = MIN(m,nr-1);
p -= m;
p = MIN(p,1.0);
rho[i] += ((rhor_3[jtype][m]*p + rhor_2[jtype][m])*p +
rhor_1[jtype][m])*p + rhor_0[jtype][m];
if (newton_pair || j < nlocal)
rho[j] += ((rhor_3[itype][m]*p + rhor_2[itype][m])*p +
rhor_1[itype][m])*p + rhor_0[itype][m];
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];
}
}
}
}
@ -167,18 +196,14 @@ void PairEAM::compute(int eflag, int vflag)
// phi = embedding energy at each atom
for (i = 0; i < nlocal; i++) {
itype = type[i];
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);
fp[i] = (frho_6[itype][m]*p + frho_5[itype][m])*p + frho_4[itype][m];
if (eflag) {
phi = ((frho_3[itype][m]*p + frho_2[itype][m])*p +
frho_1[itype][m])*p + frho_0[itype][m];
eng_vdwl += phi;
}
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
@ -223,20 +248,20 @@ void PairEAM::compute(int eflag, int vflag)
// 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
rhoip = (rhor_6[itype][m]*p + rhor_5[itype][m])*p +
rhor_4[itype][m];
rhojp = (rhor_6[jtype][m]*p + rhor_5[jtype][m])*p +
rhor_4[jtype][m];
z2 = ((z2r_3[itype][jtype][m]*p + z2r_2[itype][jtype][m])*p +
z2r_1[itype][jtype][m])*p + z2r_0[itype][jtype][m];
z2p = (z2r_6[itype][jtype][m]*p + z2r_5[itype][jtype][m])*p +
z2r_4[itype][jtype][m];
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;
@ -289,7 +314,13 @@ void PairEAM::allocate()
setflag[i][j] = 0;
cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq");
tabindex = memory->create_2d_int_array(n+1,n+1,"pair:tabindex");
map = new int[n+1];
for (int i = 1; i <= n; i++) map[n] = -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");
}
/* ----------------------------------------------------------------------
@ -303,7 +334,7 @@ void PairEAM::settings(int narg, char **arg)
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
reading multiple funcfl files defines a funcfl alloy simulation
read DYNAMO funcfl file
------------------------------------------------------------------------- */
void PairEAM::coeff(int narg, char **arg)
@ -318,20 +349,33 @@ void PairEAM::coeff(int narg, char **arg)
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
// read funcfl file only for i,i pairs
// only setflag i,i will be set
// set mass of each atom type
// read funcfl file if hasn't already been read
// store filename in Funcfl data struct
int itable;
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) {
itable = read_funcfl(arg[2]);
atom->set_mass(i,tables[itable].mass);
tabindex[i][i] = itable;
setflag[i][i] = 1;
map[i] = ifuncfl;
atom->set_mass(i,funcfl[ifuncfl].mass);
count++;
}
}
@ -346,23 +390,16 @@ void PairEAM::coeff(int narg, char **arg)
double PairEAM::init_one(int i, int j)
{
// only setflag I,I was set by coeff
// mixing will occur in init_style if both I,I and J,J were set
// 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 (setflag[i][i] == 0 || setflag[j][j] == 0)
error->all("All EAM pair coeffs are not set");
// EAM has only one cutoff = max of all pairwise cutoffs
// determine max by checking table assigned to all type pairs
// only setflag[i][j] = 1 is relevant (if hybrid, some may not be set)
cutmax = 0.0;
for (int ii = 1; ii <= atom->ntypes; ii++) {
for (int jj = ii; jj <= atom->ntypes; jj++) {
if (setflag[ii][jj] == 0) continue;
cutmax = MAX(cutmax,tables[tabindex[ii][jj]].cut);
}
}
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;
return cutmax;
}
@ -378,120 +415,98 @@ void PairEAM::init_style()
comm->maxforward_pair = MAX(comm->maxforward_pair,1);
comm->maxreverse_pair = MAX(comm->maxreverse_pair,1);
// convert read-in funcfl tables to multi-type setfl format and mix I,J
// interpolate final spline coeffs
convert_funcfl();
interpolate();
// convert read-in file(s) to arrays and spline them
file2array();
array2spline();
cutforcesq = cutmax*cutmax;
}
/* ----------------------------------------------------------------------
read potential values from a single element EAM file
read values into table and bcast values
read potential values from a DYNAMO single element funcfl file
------------------------------------------------------------------------- */
int PairEAM::read_funcfl(char *file)
void PairEAM::read_file(char *filename)
{
// check if same file has already been read
// if yes, return index of table entry
// if no, extend table list
for (int i = 0; i < ntables; i++)
if (strcmp(file,tables->filename) == 0) return i;
tables = (Table *)
memory->srealloc(tables,(ntables+1)*sizeof(Table),"pair:tables");
Table *tb = &tables[ntables];
int n = strlen(file) + 1;
tb->filename = new char[n];
strcpy(tb->filename,file);
tb->ith = tb->jth = 0;
// open potential file
Funcfl *file = &funcfl[nfuncfl-1];
int me = comm->me;
FILE *fp;
char line[MAXLINE];
if (me == 0) {
fp = fopen(file,"r");
fp = fopen(filename,"r");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open EAM potential file %s",file);
sprintf(str,"Cannot open EAM potential file %s",filename);
error->one(str);
}
}
// read and broadcast header
int tmp;
if (me == 0) {
fgets(line,MAXLINE,fp);
fgets(line,MAXLINE,fp);
sscanf(line,"%d %lg",&tmp,&tb->mass);
sscanf(line,"%d %lg",&tmp,&file->mass);
fgets(line,MAXLINE,fp);
sscanf(line,"%d %lg %d %lg %lg",
&tb->nrho,&tb->drho,&tb->nr,&tb->dr,&tb->cut);
&file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
}
MPI_Bcast(&tb->mass,1,MPI_DOUBLE,0,world);
MPI_Bcast(&tb->nrho,1,MPI_INT,0,world);
MPI_Bcast(&tb->drho,1,MPI_DOUBLE,0,world);
MPI_Bcast(&tb->nr,1,MPI_INT,0,world);
MPI_Bcast(&tb->dr,1,MPI_DOUBLE,0,world);
MPI_Bcast(&tb->cut,1,MPI_DOUBLE,0,world);
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);
// allocate potential arrays and read/bcast them
// set z2r to NULL (setfl array) so it can be deallocated
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");
tb->frho = new double[tb->nrho+1];
tb->zr = new double[tb->nr+1];
tb->rhor = new double[tb->nr+1];
tb->z2r = NULL;
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,tb->nrho,&tb->frho[1]);
MPI_Bcast(&tb->frho[1],tb->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,tb->nr,&tb->zr[1]);
MPI_Bcast(&tb->zr[1],tb->nr,MPI_DOUBLE,0,world);
if (me == 0) grab(fp,tb->nr,&tb->rhor[1]);
MPI_Bcast(&tb->rhor[1],tb->nr,MPI_DOUBLE,0,world);
// close the potential file
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);
ntables++;
return ntables-1;
}
/* ----------------------------------------------------------------------
convert read-in funcfl potentials to multi-type setfl format
convert read-in funcfl potential(s) to standard array format
interpolate all file values to a single grid and cutoff
------------------------------------------------------------------------- */
void PairEAM::convert_funcfl()
void PairEAM::file2array()
{
int i,j,k,m;
int i,j,k,m,n;
int ntypes = atom->ntypes;
// determine max values for all i,i type pairs
// skip if setflag = 0 (if hybrid, some may not be set)
// 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 = 1; i <= ntypes; i++) {
if (setflag[i][i] == 0) continue;
Table *tb = &tables[tabindex[i][i]];
dr = MAX(dr,tb->dr);
drho = MAX(drho,tb->drho);
rmax = MAX(rmax,(tb->nr-1) * tb->dr);
rhomax = MAX(rhomax,(tb->nrho-1) * tb->drho);
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
@ -500,38 +515,29 @@ void PairEAM::convert_funcfl()
nr = static_cast<int> (rmax/dr + 0.5);
nrho = static_cast<int> (rhomax/drho + 0.5);
// allocate multi-type setfl arrays
// ------------------------------------------------------------------
// setup frho arrays
// ------------------------------------------------------------------
if (frho) {
memory->destroy_2d_double_array(frho);
memory->destroy_2d_double_array(rhor);
memory->destroy_2d_double_array(zrtmp);
memory->destroy_3d_double_array(z2r);
}
// 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");
frho = (double **)
memory->create_2d_double_array(ntypes+1,nrho+1,"eam:frho");
rhor = (double **)
memory->create_2d_double_array(ntypes+1,nr+1,"eam:rhor");
zrtmp = (double **)
memory->create_2d_double_array(ntypes+1,nr+1,"eam:zrtmp");
z2r = (double ***)
memory->create_3d_double_array(ntypes+1,ntypes+1,nr+1,"eam:frho");
// interpolate all potentials to a single grid and cutoff for all atom types
// frho,rhor are 1:ntypes, z2r is 1:ntypes,1:ntypes
// skip if setflag i,i or j,j = 0 (if hybrid, some may not be set)
// interpolate each file's frho to a single grid and cutoff
double r,p,cof1,cof2,cof3,cof4;
for (i = 1; i <= ntypes; i++) {
if (setflag[i][i] == 0) continue;
Table *tb = &tables[tabindex[i][i]];
n = 0;
for (i = 0; i < nfuncfl; i++) {
Funcfl *file = &funcfl[i];
for (m = 1; m <= nrho; m++) {
r = (m-1)*drho;
p = r/tb->drho + 1.0;
p = r/file->drho + 1.0;
k = static_cast<int> (p);
k = MIN(k,tb->nrho-2);
k = MIN(k,file->nrho-2);
k = MAX(k,2);
p -= k;
p = MIN(p,2.0);
@ -539,207 +545,203 @@ void PairEAM::convert_funcfl()
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[i][m] = cof1*tb->frho[k-1] + cof2*tb->frho[k] +
cof3*tb->frho[k+1] + cof4*tb->frho[k+2];
frho[n][m] = cof1*file->frho[k-1] + cof2*file->frho[k] +
cof3*file->frho[k+1] + cof4*file->frho[k+2];
}
n++;
}
for (i = 1; i <= ntypes; i++) {
if (setflag[i][i] == 0) continue;
Table *tb = &tables[tabindex[i][i]];
for (m = 1; m <= nr; m++) {
r = (m-1)*dr;
p = r/tb->dr + 1.0;
k = static_cast<int> (p);
k = MIN(k,tb->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[i][m] = cof1*tb->rhor[k-1] + cof2*tb->rhor[k] +
cof3*tb->rhor[k+1] + cof4*tb->rhor[k+2];
zrtmp[i][m] = cof1*tb->zr[k-1] + cof2*tb->zr[k] +
cof3*tb->zr[k+1] + cof4*tb->zr[k+2];
}
}
// 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++)
for (j = i; j <= ntypes; j++) {
if (setflag[i][i] == 0 || setflag[j][j] == 0) continue;
for (m = 1; m <= nr; m++)
z2r[i][j][m] = 27.2*0.529 * zrtmp[i][m]*zrtmp[j][m];
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++) {
irow = map[i];
if (irow == -1) continue;
for (j = 1; j <= ntypes; j++) {
icol = map[j];
if (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;
}
}
}
/* ----------------------------------------------------------------------
interpolate EAM potentials
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
void PairEAM::interpolate()
void PairEAM::array2spline()
{
// free memory from previous interpolation
if (frho_0) interpolate_deallocate();
// interpolation spacings
rdr = 1.0/dr;
rdrho = 1.0/drho;
// allocate coeff arrays
memory->destroy_3d_double_array(frho_spline);
memory->destroy_3d_double_array(rhor_spline);
memory->destroy_3d_double_array(z2r_spline);
int n = atom->ntypes;
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");
frho_0 = memory->create_2d_double_array(n+1,nrho+1,"eam:frho_0");
frho_1 = memory->create_2d_double_array(n+1,nrho+1,"eam:frho_1");
frho_2 = memory->create_2d_double_array(n+1,nrho+1,"eam:frho_2");
frho_3 = memory->create_2d_double_array(n+1,nrho+1,"eam:frho_3");
frho_4 = memory->create_2d_double_array(n+1,nrho+1,"eam:frho_4");
frho_5 = memory->create_2d_double_array(n+1,nrho+1,"eam:frho_5");
frho_6 = memory->create_2d_double_array(n+1,nrho+1,"eam:frho_6");
for (int i = 0; i < nfrho; i++)
interpolate(nrho,drho,frho[i],frho_spline[i]);
rhor_0 = memory->create_2d_double_array(n+1,nr+1,"eam:rhor_0");
rhor_1 = memory->create_2d_double_array(n+1,nr+1,"eam:rhor_1");
rhor_2 = memory->create_2d_double_array(n+1,nr+1,"eam:rhor_2");
rhor_3 = memory->create_2d_double_array(n+1,nr+1,"eam:rhor_3");
rhor_4 = memory->create_2d_double_array(n+1,nr+1,"eam:rhor_4");
rhor_5 = memory->create_2d_double_array(n+1,nr+1,"eam:rhor_5");
rhor_6 = memory->create_2d_double_array(n+1,nr+1,"eam:rhor_6");
for (int i = 0; i < nrhor; i++)
interpolate(nr,dr,rhor[i],rhor_spline[i]);
z2r_0 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam:z2r_0");
z2r_1 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam:z2r_1");
z2r_2 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam:z2r_2");
z2r_3 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam:z2r_3");
z2r_4 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam:z2r_4");
z2r_5 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam:z2r_5");
z2r_6 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam:z2r_6");
for (int i = 0; i < nz2r; i++)
interpolate(nr,dr,z2r[i],z2r_spline[i]);
}
// frho interpolation for 1:ntypes
// skip if setflag = 0 (if hybrid, some may not be set)
// if skip, set frho arrays to 0.0, since they will still be accessed
// for non-EAM atoms when compute() calculates embedding function
/* ---------------------------------------------------------------------- */
int i,j,m;
void PairEAM::interpolate(int n, double delta, double *f, double **spline)
{
for (int m = 1; m <= n; m++) spline[m][6] = f[m];
for (i = 1; i <= atom->ntypes; i++) {
if (setflag[i][i] == 0) {
for (j = 1; j <= n; j++)
for (m = 1; m <= nrho; m++)
frho_0[j][m] = frho_1[j][m] = frho_2[j][m] = frho_3[j][m] =
frho_4[j][m] = frho_5[j][m] = frho_6[j][m] = 0.0;
continue;
}
for (m = 1; m <= nrho; m++) frho_0[i][m] = frho[i][m];
frho_1[i][1] = frho_0[i][2]-frho_0[i][1];
frho_1[i][2] = 0.5*(frho_0[i][3]-frho_0[i][1]);
frho_1[i][nrho-1] = 0.5*(frho_0[i][nrho]-frho_0[i][nrho-2]);
frho_1[i][nrho] = frho_0[i][nrho]-frho_0[i][nrho-1];
for (m = 3; m <= nrho-2; m++)
frho_1[i][m] = ((frho_0[i][m-2]-frho_0[i][m+2]) +
8.0*(frho_0[i][m+1]-frho_0[i][m-1]))/12.0;
for (m = 1; m <= nrho-1; m++) {
frho_2[i][m] = 3.*(frho_0[i][m+1]-frho_0[i][m]) -
2.0*frho_1[i][m] - frho_1[i][m+1];
frho_3[i][m] = frho_1[i][m] + frho_1[i][m+1] -
2.0*(frho_0[i][m+1]-frho_0[i][m]);
}
frho_2[i][nrho] = 0.0;
frho_3[i][nrho] = 0.0;
for (m = 1; m <= nrho; m++) {
frho_4[i][m] = frho_1[i][m]/drho;
frho_5[i][m] = 2.0*frho_2[i][m]/drho;
frho_6[i][m] = 3.0*frho_3[i][m]/drho;
}
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]);
}
// rhor interpolation for 1:ntypes
// skip if setflag = 0 (if hybrid, some may not be set)
for (i = 1; i <= atom->ntypes; i++) {
if (setflag[i][i] == 0) continue;
for (m = 1; m <= nr; m++) rhor_0[i][m] = rhor[i][m];
rhor_1[i][1] = rhor_0[i][2]-rhor_0[i][1];
rhor_1[i][2] = 0.5*(rhor_0[i][3]-rhor_0[i][1]);
rhor_1[i][nr-1] = 0.5*(rhor_0[i][nr]-rhor_0[i][nr-2]);
rhor_1[i][nr] = 0.0;
for (m = 3; m <= nr-2; m++)
rhor_1[i][m] = ((rhor_0[i][m-2]-rhor_0[i][m+2]) +
8.0*(rhor_0[i][m+1]-rhor_0[i][m-1]))/12.;
for (m = 1; m <= nr-1; m++) {
rhor_2[i][m] = 3.0*(rhor_0[i][m+1]-rhor_0[i][m]) -
2.0*rhor_1[i][m] - rhor_1[i][m+1];
rhor_3[i][m] = rhor_1[i][m] + rhor_1[i][m+1] -
2.0*(rhor_0[i][m+1]-rhor_0[i][m]);
}
rhor_2[i][nr] = 0.0;
rhor_3[i][nr] = 0.0;
for (m = 1; m <= nr; m++) {
rhor_4[i][m] = rhor_1[i][m]/dr;
rhor_5[i][m] = 2.0*rhor_2[i][m]/dr;
rhor_6[i][m] = 3.0*rhor_3[i][m]/dr;
}
}
// z2r interpolation for 1:ntypes,1:ntypes
// skip if setflag i,i or j,j = 0 (if hybrid, some may not be set)
// set j,i coeffs = i,j coeffs
for (i = 1; i <= atom->ntypes; i++) {
for (j = i; j <= atom->ntypes; j++) {
if (setflag[i][i] == 0 || setflag[j][j] == 0) continue;
for (m = 1; m <= nr; m++) z2r_0[i][j][m] = z2r[i][j][m];
z2r_1[i][j][1] = z2r_0[i][j][2]-z2r_0[i][j][1];
z2r_1[i][j][2] = 0.5*(z2r_0[i][j][3]-z2r_0[i][j][1]);
z2r_1[i][j][nr-1] = 0.5*(z2r_0[i][j][nr]-z2r_0[i][j][nr-2]);
z2r_1[i][j][nr] = 0.0;
for (m = 3; m <= nr-2; m++)
z2r_1[i][j][m] = ((z2r_0[i][j][m-2]-z2r_0[i][j][m+2]) +
8.0*(z2r_0[i][j][m+1]-z2r_0[i][j][m-1]))/12.;
for (m = 1; m <= nr-1; m++) {
z2r_2[i][j][m] = 3.0*(z2r_0[i][j][m+1]-z2r_0[i][j][m]) -
2.0*z2r_1[i][j][m] - z2r_1[i][j][m+1];
z2r_3[i][j][m] = z2r_1[i][j][m] + z2r_1[i][j][m+1] -
2.0*(z2r_0[i][j][m+1]-z2r_0[i][j][m]);
}
z2r_2[i][j][nr] = 0.0;
z2r_3[i][j][nr] = 0.0;
for (m = 1; m <= nr; m++) {
z2r_4[i][j][m] = z2r_1[i][j][m]/dr;
z2r_5[i][j][m] = 2.0*z2r_2[i][j][m]/dr;
z2r_6[i][j][m] = 3.0*z2r_3[i][j][m]/dr;
}
for (m = 1; m <= nr; m++) {
z2r_0[j][i][m] = z2r_0[i][j][m];
z2r_1[j][i][m] = z2r_1[i][j][m];
z2r_2[j][i][m] = z2r_2[i][j][m];
z2r_3[j][i][m] = z2r_3[i][j][m];
z2r_4[j][i][m] = z2r_4[i][j][m];
z2r_5[j][i][m] = z2r_5[i][j][m];
z2r_6[j][i][m] = z2r_6[i][j][m];
}
}
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;
}
}
@ -763,64 +765,15 @@ void PairEAM::grab(FILE *fp, int n, double *list)
}
}
/* ----------------------------------------------------------------------
skip n values from file fp
values can be several to a line
only called by proc 0
------------------------------------------------------------------------- */
void PairEAM::skip(FILE *fp, int n)
{
char line[MAXLINE];
int i = 0;
while (i < n) {
fgets(line,MAXLINE,fp);
strtok(line," \t\n\r\f");
i++;
while (strtok(NULL," \t\n\r\f")) i++;
}
}
/* ----------------------------------------------------------------------
deallocate spline interpolation arrays
------------------------------------------------------------------------- */
void PairEAM::interpolate_deallocate()
{
memory->destroy_2d_double_array(frho_0);
memory->destroy_2d_double_array(frho_1);
memory->destroy_2d_double_array(frho_2);
memory->destroy_2d_double_array(frho_3);
memory->destroy_2d_double_array(frho_4);
memory->destroy_2d_double_array(frho_5);
memory->destroy_2d_double_array(frho_6);
memory->destroy_2d_double_array(rhor_0);
memory->destroy_2d_double_array(rhor_1);
memory->destroy_2d_double_array(rhor_2);
memory->destroy_2d_double_array(rhor_3);
memory->destroy_2d_double_array(rhor_4);
memory->destroy_2d_double_array(rhor_5);
memory->destroy_2d_double_array(rhor_6);
memory->destroy_3d_double_array(z2r_0);
memory->destroy_3d_double_array(z2r_1);
memory->destroy_3d_double_array(z2r_2);
memory->destroy_3d_double_array(z2r_3);
memory->destroy_3d_double_array(z2r_4);
memory->destroy_3d_double_array(z2r_5);
memory->destroy_3d_double_array(z2r_6);
}
/* ---------------------------------------------------------------------- */
void PairEAM::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj,
int eflag, One &one)
double rsq, double factor_coul, double factor_lj,
int eflag, One &one)
{
double r,p,rhoip,rhojp,z2,z2p,recip,phi,phip,psip;
int m;
double r,p,rhoip,rhojp,z2,z2p,recip,phi,phip,psip;
double *coeff;
r = sqrt(rsq);
p = r*rdr + 1.0;
@ -828,15 +781,14 @@ void PairEAM::single(int i, int j, int itype, int jtype,
m = MIN(m,nr-1);
p -= m;
p = MIN(p,1.0);
rhoip = (rhor_6[itype][m]*p + rhor_5[itype][m])*p +
rhor_4[itype][m];
rhojp = (rhor_6[jtype][m]*p + rhor_5[jtype][m])*p +
rhor_4[jtype][m];
z2 = ((z2r_3[itype][jtype][m]*p + z2r_2[itype][jtype][m])*p +
z2r_1[itype][jtype][m])*p + z2r_0[itype][jtype][m];
z2p = (z2r_6[itype][jtype][m]*p + z2r_5[itype][jtype][m])*p +
z2r_4[itype][jtype][m];
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;
@ -859,11 +811,10 @@ void PairEAM::single_embed(int i, int itype, double &fpi,
int m = static_cast<int> (p);
m = MAX(1,MIN(m,nrho-1));
p -= m;
fpi = (frho_6[itype][m]*p + frho_5[itype][m])*p + frho_4[itype][m];
if (eflag)
phi = ((frho_3[itype][m]*p + frho_2[itype][m])*p +
frho_1[itype][m])*p + frho_0[itype][m];
double *coeff = frho_spline[type2frho[itype]][m];
fpi = (coeff[0]*p + coeff[1])*p + coeff[2];
if (eflag) phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
}
/* ---------------------------------------------------------------------- */

538
src/MANYBODY/pair_eam_alloy.cpp
View File

@ -15,36 +15,26 @@
Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_eam_alloy.h"
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "neighbor.h"
#include "error.h"
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
#define MAXLINE 1024
/* ---------------------------------------------------------------------- */
PairEAMAlloy::PairEAMAlloy()
{
one_coeff = 1;
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
read DYNAMO setfl file
------------------------------------------------------------------------- */
void PairEAMAlloy::coeff(int narg, char **arg)
{
int i,j;
if (!allocated) allocate();
if (narg != 3 + atom->ntypes)
@ -55,32 +45,50 @@ void PairEAMAlloy::coeff(int narg, char **arg)
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
error->all("Incorrect args for pair coefficients");
// read EAM setfl file, possibly multiple times
// first clear setflag since are doing this once for I,J = *,*
// read for all i,j pairs where ith,jth mapping is non-zero
// set setflag i,j for non-zero pairs
// set mass of atom type if i = j
// read EAM setfl file
if (setfl) {
for (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);
memory->sfree(setfl);
}
setfl = new Setfl();
read_file(arg[2]);
// read args that map atom types to elements in potential file
// map[i] = which element the Ith atom type is, -1 if NULL
for (i = 3; i < narg; i++) {
if (strcmp(arg[i],"NULL") == 0) {
map[i-2] = -1;
continue;
}
for (j = 0; j < setfl->nelements; j++)
if (strcmp(arg[i],setfl->elements[j]) == 0) break;
if (j < setfl->nelements) map[i-2] = j;
else error->all("No matching element in EAM potential file");
}
// clear setflag since coeff() called once with I,J = * *
int n = atom->ntypes;
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
for (i = 1; i <= n; i++)
for (j = i; j <= n; j++)
setflag[i][j] = 0;
int itable,ith,jth;
int ilo,ihi,jlo,jhi;
ilo = jlo = 1;
ihi = jhi = n;
// set setflag i,j for type pairs where both are mapped to elements
// 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++) {
ith = atoi(arg[2+i]);
jth = atoi(arg[2+j]);
if (ith > 0 && jth > 0) {
itable = read_setfl(arg[2],ith,jth);
if (i == j) atom->set_mass(i,tables[itable].mass);
tabindex[i][j] = itable;
for (i = 1; i <= n; i++) {
for (j = i; j <= n; j++) {
if (map[i] >= 0 && map[j] >= 0) {
setflag[i][j] = 1;
if (i == j) atom->set_mass(i,setfl->mass[map[i]]);
count++;
}
}
@ -90,72 +98,12 @@ void PairEAMAlloy::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
read a multi-element DYNAMO setfl file
------------------------------------------------------------------------- */
double PairEAMAlloy::init_one(int i, int j)
void PairEAMAlloy::read_file(char *filename)
{
if (setflag[i][j] == 0)
error->all("All EAM pair coeffs are not set");
// EAM has only one cutoff = max of all pairwise cutoffs
// determine max by checking table assigned to all type pairs
// only setflag[i][j] = 1 is relevant (if hybrid, some may not be set)
cutmax = 0.0;
for (int ii = 1; ii <= atom->ntypes; ii++) {
for (int jj = ii; jj <= atom->ntypes; jj++) {
if (setflag[ii][jj] == 0) continue;
cutmax = MAX(cutmax,tables[tabindex[ii][jj]].cut);
}
}
return cutmax;
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairEAMAlloy::init_style()
{
// set communication sizes in comm class
comm->maxforward_pair = MAX(comm->maxforward_pair,1);
comm->maxreverse_pair = MAX(comm->maxreverse_pair,1);
// copy read-in-tables to multi-type setfl format
// interpolate final spline coeffs
store_setfl();
interpolate();
cutforcesq = cutmax*cutmax;
}
/* ----------------------------------------------------------------------
read ith,jth potential values from a multi-element alloy EAM file
read values into table and bcast values
------------------------------------------------------------------------- */
int PairEAMAlloy::read_setfl(char *file, int ith, int jth)
{
// check if ith,jth portion of same file has already been read
// if yes, return index of table entry
// if no, extend table list
for (int i = 0; i < ntables; i++)
if (ith == tables[i].ith && jth == tables[i].jth) return i;
tables = (Table *)
memory->srealloc(tables,(ntables+1)*sizeof(Table),"pair:tables");
Table *tb = &tables[ntables];
int n = strlen(file) + 1;
tb->filename = new char[n];
strcpy(tb->filename,file);
tb->ith = ith;
tb->jth = jth;
Setfl *file = setfl;
// open potential file
@ -164,309 +112,199 @@ int PairEAMAlloy::read_setfl(char *file, int ith, int jth)
char line[MAXLINE];
if (me == 0) {
fp = fopen(file,"r");
fp = fopen(filename,"r");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open EAM potential file %s",file);
sprintf(str,"Cannot open EAM potential file %s",filename);
error->one(str);
}
}
// read and broadcast header
// extract element names from nelements line
int ntypes;
int n;
if (me == 0) {
fgets(line,MAXLINE,fp);
fgets(line,MAXLINE,fp);
fgets(line,MAXLINE,fp);
fgets(line,MAXLINE,fp);
sscanf(line,"%d",&ntypes);
n = strlen(line) + 1;
}
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
sscanf(line,"%d",&file->nelements);
int nwords = atom->count_words(line);
if (nwords != file->nelements + 1)
error->all("Incorrect element names in EAM potential file");
char *words[file->nelements];
nwords = 0;
char *first = strtok(line," \t\n\r\f");
while (words[nwords++] = strtok(NULL," \t\n\r\f")) continue;
file->elements = new char*[file->nelements];
for (int i = 0; i < file->nelements; i++) {
n = strlen(words[i]) + 1;
file->elements[i] = new char[n];
strcpy(file->elements[i],words[i]);
}
if (me == 0) {
fgets(line,MAXLINE,fp);
sscanf(line,"%d %lg %d %lg %lg",
&tb->nrho,&tb->drho,&tb->nr,&tb->dr,&tb->cut);
&file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
}
MPI_Bcast(&ntypes,1,MPI_INT,0,world);
MPI_Bcast(&tb->nrho,1,MPI_INT,0,world);
MPI_Bcast(&tb->drho,1,MPI_DOUBLE,0,world);
MPI_Bcast(&tb->nr,1,MPI_INT,0,world);
MPI_Bcast(&tb->dr,1,MPI_DOUBLE,0,world);
MPI_Bcast(&tb->cut,1,MPI_DOUBLE,0,world);
// check if ith,jth are consistent with ntypes
if (ith > ntypes || jth > ntypes)
error->all("Requested atom types in EAM setfl file do not exist");
// allocate potential arrays and read/bcast them
// skip sections of file that don't correspond to ith,jth
// extract mass, frho, rhor for i,i from ith element section
// extract z2r for i,j from ith,jth array of z2r section
// note that ith can be < or > than jth
// set zr to NULL (funcl array) so it can be deallocated
tb->frho = new double[tb->nrho+1];
tb->rhor = new double[tb->nr+1];
tb->z2r = new double[tb->nr+1];
tb->zr = NULL;
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->mass = new double[file->nelements];
file->frho = memory->create_2d_double_array(file->nelements,file->nrho+1,
"pair:frho");
file->rhor = memory->create_2d_double_array(file->nelements,file->nr+1,
"pair:rhor");
file->z2r = memory->create_3d_double_array(file->nelements,file->nelements,
file->nr+1,"pair:z2r");
int i,j,tmp;
double mass;
for (i = 1; i <= ntypes; i++) {
for (i = 0; i < file->nelements; i++) {
if (me == 0) {
fgets(line,MAXLINE,fp);
sscanf(line,"%d %lg",&tmp,&mass);
sscanf(line,"%d %lg",&tmp,&file->mass[i]);
}
MPI_Bcast(&mass,1,MPI_DOUBLE,0,world);
MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world);
if (i == ith && ith == jth) {
tb->mass = mass;
if (me == 0) grab(fp,tb->nrho,&tb->frho[1]);
MPI_Bcast(&tb->frho[1],tb->nrho,MPI_DOUBLE,0,world);
if (me == 0) grab(fp,tb->nr,&tb->rhor[1]);
MPI_Bcast(&tb->rhor[1],tb->nr,MPI_DOUBLE,0,world);
} else {
if (me == 0) skip(fp,tb->nrho);
if (me == 0) skip(fp,tb->nr);
}
if (me == 0) grab(fp,file->nrho,&file->frho[i][1]);
MPI_Bcast(&file->frho[i][1],file->nrho,MPI_DOUBLE,0,world);
if (me == 0) grab(fp,file->nr,&file->rhor[i][1]);
MPI_Bcast(&file->rhor[i][1],file->nr,MPI_DOUBLE,0,world);
}
for (i = 1; i <= ntypes; i++) {
for (j = 1; j <= i; j++) {
if ((i == ith && j == jth) || (j == ith && i == jth)) {
if (me == 0) grab(fp,tb->nr,&tb->z2r[1]);
MPI_Bcast(&tb->z2r[1],tb->nr,MPI_DOUBLE,0,world);
} else if (me == 0) skip(fp,tb->nr);
for (i = 0; i < file->nelements; i++)
for (j = 0; j <= i; j++) {
if (me == 0) grab(fp,file->nr,&file->z2r[i][j][1]);
MPI_Bcast(&file->z2r[i][j][1],file->nr,MPI_DOUBLE,0,world);
}
}
// close the potential file
if (me == 0) fclose(fp);
ntables++;
return ntables-1;
}
/* ----------------------------------------------------------------------
store read-in setfl values in multi-type setfl format
copy read-in setfl potential to standard array format
------------------------------------------------------------------------- */
void PairEAMAlloy::store_setfl()
void PairEAMAlloy::file2array()
{
int i,j,m;
int i,j,m,n;
int ntypes = atom->ntypes;
// set function params directly from setfl file
nrho = setfl->nrho;
nr = setfl->nr;
drho = setfl->drho;
dr = setfl->dr;
// ------------------------------------------------------------------
// setup frho arrays
// ------------------------------------------------------------------
// allocate frho arrays
// nfrho = # of setfl elements + 1 for zero array
// set nrho,nr,drho,dr from any i,i table entry since all the same
nfrho = setfl->nelements + 1;
memory->destroy_2d_double_array(frho);
frho = (double **) memory->create_2d_double_array(nfrho,nrho+1,"pair:frho");
// copy each element's frho to global frho
for (i = 0; i < setfl->nelements; i++)
for (m = 1; m <= nrho; m++) frho[i][m] = setfl->frho[i][m];
// 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 element (non-EAM atom in pair hybrid)
// then map it to last frho array of zeroes
for (i = 1; i <= ntypes; i++)
if (setflag[i][i]) break;
if (map[i] >= 0) type2frho[i] = map[i];
else type2frho[i] = nfrho-1;
nrho = tables[tabindex[i][i]].nrho;
nr = tables[tabindex[i][i]].nr;
drho = tables[tabindex[i][i]].drho;
dr = tables[tabindex[i][i]].dr;
// ------------------------------------------------------------------
// setup rhor arrays
// ------------------------------------------------------------------
// allocate multi-type setfl arrays
// allocate rhor arrays
// nrhor = # of setfl elements
if (frho) {
memory->destroy_2d_double_array(frho);
memory->destroy_2d_double_array(rhor);
memory->destroy_2d_double_array(zrtmp);
memory->destroy_3d_double_array(z2r);
}
nrhor = setfl->nelements;
memory->destroy_2d_double_array(rhor);
rhor = (double **) memory->create_2d_double_array(nrhor,nr+1,"pair:rhor");
frho = (double **)
memory->create_2d_double_array(ntypes+1,nrho+1,"eam:frho");
rhor = (double **)
memory->create_2d_double_array(ntypes+1,nr+1,"eam:rhor");
zrtmp = (double **)
memory->create_2d_double_array(ntypes+1,nr+1,"eam:zrtmp");
z2r = (double ***)
memory->create_3d_double_array(ntypes+1,ntypes+1,nr+1,"eam:frho");
// copy each element's rhor to global rhor
// copy from read-in tables to multi-type setfl arrays
// frho,rhor are 1:ntypes, z2r is 1:ntypes,1:ntypes
// skip if setflag i,j = 0 (if hybrid, some may not be set)
for (i = 0; i < setfl->nelements; i++)
for (m = 1; m <= nr; m++) rhor[i][m] = setfl->rhor[i][m];
// type2rhor[i][j] = which rhor array (0 to nrhor-1) each type pair maps to
// for setfl 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 = i; j <= ntypes; j++) {
if (setflag[i][j] == 0) continue;
Table *tb = &tables[tabindex[i][j]];
if (i == j) {
for (m = 1; m <= nrho; m++) frho[i][m] = tb->frho[m];
for (m = 1; m <= nr; m++) rhor[i][m] = tb->rhor[m];
}
for (m = 1; m <= nr; m++) z2r[i][j][m] = tb->z2r[m];
}
}
/* ----------------------------------------------------------------------
interpolate EAM potentials
------------------------------------------------------------------------- */
void PairEAMAlloy::interpolate()
{
// free memory from previous interpolation
if (frho_0) interpolate_deallocate();
// interpolation spacings
rdr = 1.0/dr;
rdrho = 1.0/drho;
// allocate coeff arrays
int n = atom->ntypes;
frho_0 = memory->create_2d_double_array(n+1,nrho+1,"eam:frho_0");
frho_1 = memory->create_2d_double_array(n+1,nrho+1,"eam:frho_1");
frho_2 = memory->create_2d_double_array(n+1,nrho+1,"eam:frho_2");
frho_3 = memory->create_2d_double_array(n+1,nrho+1,"eam:frho_3");
frho_4 = memory->create_2d_double_array(n+1,nrho+1,"eam:frho_4");
frho_5 = memory->create_2d_double_array(n+1,nrho+1,"eam:frho_5");
frho_6 = memory->create_2d_double_array(n+1,nrho+1,"eam:frho_6");
rhor_0 = memory->create_2d_double_array(n+1,nr+1,"eam:rhor_0");
rhor_1 = memory->create_2d_double_array(n+1,nr+1,"eam:rhor_1");
rhor_2 = memory->create_2d_double_array(n+1,nr+1,"eam:rhor_2");
rhor_3 = memory->create_2d_double_array(n+1,nr+1,"eam:rhor_3");
rhor_4 = memory->create_2d_double_array(n+1,nr+1,"eam:rhor_4");
rhor_5 = memory->create_2d_double_array(n+1,nr+1,"eam:rhor_5");
rhor_6 = memory->create_2d_double_array(n+1,nr+1,"eam:rhor_6");
z2r_0 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam:z2r_0");
z2r_1 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam:z2r_1");
z2r_2 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam:z2r_2");
z2r_3 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam:z2r_3");
z2r_4 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam:z2r_4");
z2r_5 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam:z2r_5");
z2r_6 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam:z2r_6");
// frho interpolation for 1:ntypes
// skip if setflag = 0 (if hybrid, some may not be set)
// if skip, set frho arrays to 0.0, since they will still be accessed
// for non-EAM atoms when compute() calculates embedding function
int i,j,m;
for (i = 1; i <= atom->ntypes; i++) {
if (setflag[i][i] == 0) {
for (m = 1; m <= nrho; m++)
frho_0[i][m] = frho_1[i][m] = frho_2[i][m] = frho_3[i][m] =
frho_4[i][m] = frho_5[i][m] = frho_6[i][m] = 0.0;
continue;
}
for (m = 1; m <= nrho; m++) frho_0[i][m] = frho[i][m];
frho_1[i][1] = frho_0[i][2]-frho_0[i][1];
frho_1[i][2] = 0.5*(frho_0[i][3]-frho_0[i][1]);
frho_1[i][nrho-1] = 0.5*(frho_0[i][nrho]-frho_0[i][nrho-2]);
frho_1[i][nrho] = frho_0[i][nrho]-frho_0[i][nrho-1];
for (m = 3; m <= nrho-2; m++)
frho_1[i][m] = ((frho_0[i][m-2]-frho_0[i][m+2]) +
8.0*(frho_0[i][m+1]-frho_0[i][m-1]))/12.0;
for (m = 1; m <= nrho-1; m++) {
frho_2[i][m] = 3.*(frho_0[i][m+1]-frho_0[i][m]) -
2.0*frho_1[i][m] - frho_1[i][m+1];
frho_3[i][m] = frho_1[i][m] + frho_1[i][m+1] -
2.0*(frho_0[i][m+1]-frho_0[i][m]);
}
frho_2[i][nrho] = 0.0;
frho_3[i][nrho] = 0.0;
for (m = 1; m <= nrho; m++) {
frho_4[i][m] = frho_1[i][m]/drho;
frho_5[i][m] = 2.0*frho_2[i][m]/drho;
frho_6[i][m] = 3.0*frho_3[i][m]/drho;
}
}
// rhor interpolation for 1:ntypes
// skip if setflag = 0 (if hybrid, some may not be set)
for (i = 1; i <= atom->ntypes; i++) {
if (setflag[i][i] == 0) continue;
for (m = 1; m <= nr; m++) rhor_0[i][m] = rhor[i][m];
rhor_1[i][1] = rhor_0[i][2]-rhor_0[i][1];
rhor_1[i][2] = 0.5*(rhor_0[i][3]-rhor_0[i][1]);
rhor_1[i][nr-1] = 0.5*(rhor_0[i][nr]-rhor_0[i][nr-2]);
rhor_1[i][nr] = 0.0;
for (m = 3; m <= nr-2; m++)
rhor_1[i][m] = ((rhor_0[i][m-2]-rhor_0[i][m+2]) +
8.0*(rhor_0[i][m+1]-rhor_0[i][m-1]))/12.;
for (m = 1; m <= nr-1; m++) {
rhor_2[i][m] = 3.0*(rhor_0[i][m+1]-rhor_0[i][m]) -
2.0*rhor_1[i][m] - rhor_1[i][m+1];
rhor_3[i][m] = rhor_1[i][m] + rhor_1[i][m+1] -
2.0*(rhor_0[i][m+1]-rhor_0[i][m]);
}
rhor_2[i][nr] = 0.0;
rhor_3[i][nr] = 0.0;
for (m = 1; m <= nr; m++) {
rhor_4[i][m] = rhor_1[i][m]/dr;
rhor_5[i][m] = 2.0*rhor_2[i][m]/dr;
rhor_6[i][m] = 3.0*rhor_3[i][m]/dr;
}
}
// z2r interpolation for 1:ntypes,1:ntypes
// skip if setflag i,j = 0 (if hybrid, some may not be set)
// set j,i coeffs = i,j coeffs
for (i = 1; i <= atom->ntypes; i++) {
for (j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] == 0) continue;
for (m = 1; m <= nr; m++) z2r_0[i][j][m] = z2r[i][j][m];
z2r_1[i][j][1] = z2r_0[i][j][2]-z2r_0[i][j][1];
z2r_1[i][j][2] = 0.5*(z2r_0[i][j][3]-z2r_0[i][j][1]);
z2r_1[i][j][nr-1] = 0.5*(z2r_0[i][j][nr]-z2r_0[i][j][nr-2]);
z2r_1[i][j][nr] = 0.0;
for (m = 3; m <= nr-2; m++)
z2r_1[i][j][m] = ((z2r_0[i][j][m-2]-z2r_0[i][j][m+2]) +
8.0*(z2r_0[i][j][m+1]-z2r_0[i][j][m-1]))/12.;
for (m = 1; m <= nr-1; m++) {
z2r_2[i][j][m] = 3.0*(z2r_0[i][j][m+1]-z2r_0[i][j][m]) -
2.0*z2r_1[i][j][m] - z2r_1[i][j][m+1];
z2r_3[i][j][m] = z2r_1[i][j][m] + z2r_1[i][j][m+1] -
2.0*(z2r_0[i][j][m+1]-z2r_0[i][j][m]);
}
z2r_2[i][j][nr] = 0.0;
z2r_3[i][j][nr] = 0.0;
for (m = 1; m <= nr; m++) {
z2r_4[i][j][m] = z2r_1[i][j][m]/dr;
z2r_5[i][j][m] = 2.0*z2r_2[i][j][m]/dr;
z2r_6[i][j][m] = 3.0*z2r_3[i][j][m]/dr;
}
for (m = 1; m <= nr; m++) {
z2r_0[j][i][m] = z2r_0[i][j][m];
z2r_1[j][i][m] = z2r_1[i][j][m];
z2r_2[j][i][m] = z2r_2[i][j][m];
z2r_3[j][i][m] = z2r_3[i][j][m];
z2r_4[j][i][m] = z2r_4[i][j][m];
z2r_5[j][i][m] = z2r_5[i][j][m];
z2r_6[j][i][m] = z2r_6[i][j][m];
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 setfl elements
nz2r = setfl->nelements * (setfl->nelements+1) / 2;
memory->destroy_2d_double_array(z2r);
z2r = (double **) memory->create_2d_double_array(nz2r,nr+1,"pair:z2r");
// copy each element pair z2r to global z2r, only for I >= J
n = 0;
for (i = 0; i < setfl->nelements; i++)
for (j = 0; j <= i; j++) {
for (m = 1; m <= nr; m++) z2r[n][m] = setfl->z2r[i][j][m];
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++) {
irow = map[i];
if (irow == -1) continue;
for (j = 1; j <= ntypes; j++) {
icol = map[j];
if (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;
}
}
}

8
src/MANYBODY/pair_eam_alloy.h
View File

@ -18,15 +18,11 @@
class PairEAMAlloy : public PairEAM {
public:
PairEAMAlloy();
void coeff(int, char **);
double init_one(int, int);
void init_style();
private:
int read_setfl(char *, int, int);
void store_setfl();
void interpolate();
void read_file(char *);
void file2array();
};
#endif

840
src/MANYBODY/pair_eam_fs.cpp
View File

@ -12,286 +12,83 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Tim Lau (MIT)
Contributing authors: Tim Lau (MIT)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_eam_fs.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "comm.h"
#include "memory.h"
#include "neighbor.h"
#include "error.h"
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
#define MAXLINE 1024
/* ---------------------------------------------------------------------- */
PairEAMFS::PairEAMFS()
{
one_coeff = 1;
}
/* ---------------------------------------------------------------------- */
PairEAMFS::~PairEAMFS() {
// deallocate array unique to derived class, parent will deallocate the rest
if (frho) memory->destroy_3d_double_array(rhor_fs);
// insure derived-class's deallocate is called
// set ptr to NULL to prevent parent class from calling it's deallocate
if (frho_0) interpolate_deallocate();
frho_0 = NULL;
}
/* ---------------------------------------------------------------------- */
void PairEAMFS::compute(int eflag, int vflag)
{
int i,j,k,m,numneigh,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r,p,fforce,rhoip,rhojp,z2,z2p,recip,phi,phip,psip;
int *neighs;
double **f;
// 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),"eam:rho");
fp = (double *) memory->smalloc(nmax*sizeof(double),"eam:fp");
}
eng_vdwl = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
if (vflag == 2) f = update->f_pair;
else f = atom->f;
double **x = atom->x;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
// 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
// FS has type-specific rho functional
for (i = 0; i < nlocal; i++) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
neighs = neighbor->firstneigh[i];
numneigh = neighbor->numneigh[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
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);
rho[i] +=
((rhor_fs_3[jtype][itype][m]*p + rhor_fs_2[jtype][itype][m])*p +
rhor_fs_1[jtype][itype][m])*p + rhor_fs_0[jtype][itype][m];
if (newton_pair || j < nlocal)
rho[j] +=
((rhor_fs_3[itype][jtype][m]*p + rhor_fs_2[itype][jtype][m])*p +
rhor_fs_1[itype][jtype][m])*p + rhor_fs_0[itype][jtype][m];
}
}
}
// 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
// FS is same as standard EAM
for (i = 0; i < nlocal; i++) {
itype = type[i];
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);
fp[i] = (frho_6[itype][m]*p + frho_5[itype][m])*p + frho_4[itype][m];
if (eflag) {
phi = ((frho_3[itype][m]*p + frho_2[itype][m])*p +
frho_1[itype][m])*p + frho_0[itype][m];
eng_vdwl += phi;
}
}
// communicate derivative of embedding function
comm->comm_pair(this);
// compute forces on each atom
// loop over neighbors of my atoms
// FS has type-specific rhoip and rhojp
for (i = 0; i < nlocal; i++) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
neighs = neighbor->firstneigh[i];
numneigh = neighbor->numneigh[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
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
rhoip =
(rhor_fs_6[itype][jtype][m]*p + rhor_fs_5[itype][jtype][m])*p +
rhor_fs_4[itype][jtype][m];
rhojp =
(rhor_fs_6[jtype][itype][m]*p + rhor_fs_5[jtype][itype][m])*p +
rhor_fs_4[jtype][itype][m];
z2 = ((z2r_3[itype][jtype][m]*p + z2r_2[itype][jtype][m])*p +
z2r_1[itype][jtype][m])*p + z2r_0[itype][jtype][m];
z2p = (z2r_6[itype][jtype][m]*p + z2r_5[itype][jtype][m])*p +
z2r_4[itype][jtype][m];
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 || j < nlocal) {
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;
} else {
virial[0] -= 0.5*delx*delx*fforce;
virial[1] -= 0.5*dely*dely*fforce;
virial[2] -= 0.5*delz*delz*fforce;
virial[3] -= 0.5*delx*dely*fforce;
virial[4] -= 0.5*delx*delz*fforce;
virial[5] -= 0.5*dely*delz*fforce;
}
}
}
}
}
if (vflag == 2) virial_compute();
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
read EAM Finnis-Sinclair file
------------------------------------------------------------------------- */
void PairEAMFS::coeff(int narg, char **arg)
{
int i,j;
if (!allocated) allocate();
if (narg != 3 + atom->ntypes)
error->all("Incorrect args for pair coefficients");
// insure I,J args are * *
// can only have one file, so clear all setflag settings
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
error->all("Incorrect args for pair coefficients");
// read Finnis/Sinclair modified setfl file
// first clear setflag since are doing this once for I,J = *,*
// read for all i,j pairs where ith,jth mapping is non-zero
// set setflag i,j for non-zero pairs
// set mass of atom type if i = j
// read EAM Finnis-Sinclair file
if (fs) {
for (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);
memory->sfree(fs);
}
fs = new Fs();
read_file(arg[2]);
// read args that map atom types to elements in potential file
// map[i] = which element the Ith atom type is, -1 if NULL
for (i = 3; i < narg; i++) {
if (strcmp(arg[i],"NULL") == 0) {
map[i-2] = -1;
continue;
}
for (j = 0; j < fs->nelements; j++)
if (strcmp(arg[i],fs->elements[j]) == 0) break;
if (j < fs->nelements) map[i-2] = j;
else error->all("No matching element in EAM potential file");
}
// clear setflag since coeff() called once with I,J = * *
int n = atom->ntypes;
for (int i = 1; i <= n; i++)
for (int j = 1; j <= n; j++)
for (i = 1; i <= n; i++)
for (j = i; j <= n; j++)
setflag[i][j] = 0;
int itable,ith,jth;
int ilo,ihi,jlo,jhi;
ilo = jlo = 1;
ihi = jhi = n;
// set setflag i,j for type pairs where both are mapped to elements
// set mass of atom type if i = j
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = jlo; j <= jhi; j++) {
ith = atoi(arg[2+i]);
jth = atoi(arg[2+j]);
if (ith > 0 && jth > 0) {
itable = read_setfl(arg[2],ith,jth);
if (i == j) atom->set_mass(i,tables[itable].mass);
tabindex[i][j] = itable;
for (i = 1; i <= n; i++) {
for (j = i; j <= n; j++) {
if (map[i] >= 0 && map[j] >= 0) {
setflag[i][j] = 1;
if (i == j) atom->set_mass(i,fs->mass[map[i]]);
count++;
}
}
@ -301,73 +98,12 @@ void PairEAMFS::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
read a multi-element DYNAMO setfl file
------------------------------------------------------------------------- */
double PairEAMFS::init_one(int i, int j)
void PairEAMFS::read_file(char *filename)
{
if (setflag[i][j] == 0)
error->all("All EAM pair coeffs are not set");
// EAM has only one cutoff = max of all pairwise cutoffs
// determine max by checking table assigned to all type pairs
// only setflag[i][j] = 1 is relevant (if hybrid, some may not be set)
cutmax = 0.0;
for (int ii = 1; ii <= atom->ntypes; ii++) {
for (int jj = ii; jj <= atom->ntypes; jj++) {
if (setflag[ii][jj] == 0) continue;
cutmax = MAX(cutmax,tables[tabindex[ii][jj]].cut);
}
}
return cutmax;
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairEAMFS::init_style()
{
// set communication sizes in comm class
comm->maxforward_pair = MAX(comm->maxforward_pair,1);
comm->maxreverse_pair = MAX(comm->maxreverse_pair,1);
// copy read-in-tables to multi-type setfl format
// interpolate final spline coeffs
store_setfl();
interpolate();
cutforcesq = cutmax*cutmax;
}
/* ----------------------------------------------------------------------
read ith,jth potential values from a multi-element alloy EAM/FS file
read values into table and bcast values
this file has different format than standard EAM setfl file
------------------------------------------------------------------------- */
int PairEAMFS::read_setfl(char *file, int ith, int jth)
{
// check if ith,jth portion of same file has already been read
// if yes, return index of table entry
// if no, extend table list
for (int i = 0; i < ntables; i++)
if (ith == tables[i].ith && jth == tables[i].jth) return i;
tables = (Table *)
memory->srealloc(tables,(ntables+1)*sizeof(Table),"pair:tables");
Table *tb = &tables[ntables];
int n = strlen(file) + 1;
tb->filename = new char[n];
strcpy(tb->filename,file);
tb->ith = ith;
tb->jth = jth;
Fs *file = fs;
// open potential file
@ -376,396 +112,206 @@ int PairEAMFS::read_setfl(char *file, int ith, int jth)
char line[MAXLINE];
if (me == 0) {
fp = fopen(file,"r");
fp = fopen(filename,"r");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open EAM potential file %s",file);
sprintf(str,"Cannot open EAM potential file %s",filename);
error->one(str);
}
}
// read and broadcast header
// extract element names from nelements line
int ntypes;
int n;
if (me == 0) {
fgets(line,MAXLINE,fp);
fgets(line,MAXLINE,fp);
fgets(line,MAXLINE,fp);
fgets(line,MAXLINE,fp);
sscanf(line,"%d",&ntypes);
n = strlen(line) + 1;
}
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
sscanf(line,"%d",&file->nelements);
int nwords = atom->count_words(line);
if (nwords != file->nelements + 1)
error->all("Incorrect element names in EAM potential file");
char *words[file->nelements];
nwords = 0;
char *first = strtok(line," \t\n\r\f");
while (words[nwords++] = strtok(NULL," \t\n\r\f")) continue;
file->elements = new char*[file->nelements];
for (int i = 0; i < file->nelements; i++) {
n = strlen(words[i]) + 1;
file->elements[i] = new char[n];
strcpy(file->elements[i],words[i]);
}
if (me == 0) {
fgets(line,MAXLINE,fp);
sscanf(line,"%d %lg %d %lg %lg",
&tb->nrho,&tb->drho,&tb->nr,&tb->dr,&tb->cut);
&file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
}
MPI_Bcast(&ntypes,1,MPI_INT,0,world);
MPI_Bcast(&tb->nrho,1,MPI_INT,0,world);
MPI_Bcast(&tb->drho,1,MPI_DOUBLE,0,world);
MPI_Bcast(&tb->nr,1,MPI_INT,0,world);
MPI_Bcast(&tb->dr,1,MPI_DOUBLE,0,world);
MPI_Bcast(&tb->cut,1,MPI_DOUBLE,0,world);
// check if ith,jth are consistent with ntypes
if (ith > ntypes || jth > ntypes)
error->all("Requested atom types in EAM setfl file do not exist");
// allocate potential arrays and read/bcast them
// skip sections of file that don't correspond to ith,jth
// extract mass, frho for i,i from ith element section
// extract rhor for i,j from jth array of ith element section
// extract z2r for i,j from ith,jth array of z2r section
// note that ith can be < or > than jth
// set zr to NULL (funcl array) so it can be deallocated
tb->frho = new double[tb->nrho+1];
tb->rhor = new double[tb->nr+1];
tb->z2r = new double[tb->nr+1];
tb->zr = NULL;
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->mass = new double[file->nelements];
file->frho = memory->create_2d_double_array(file->nelements,file->nrho+1,
"pair:frho");
file->rhor = memory->create_3d_double_array(file->nelements,file->nelements,
file->nr+1,"pair:rhor");
file->z2r = memory->create_3d_double_array(file->nelements,file->nelements,
file->nr+1,"pair:z2r");
int i,j,tmp;
double mass;
for (i = 1; i <= ntypes; i++) {
for (i = 0; i < file->nelements; i++) {
if (me == 0) {
fgets(line,MAXLINE,fp);
sscanf(line,"%d %lg",&tmp,&mass);
sscanf(line,"%d %lg",&tmp,&file->mass[i]);
}
MPI_Bcast(&mass,1,MPI_DOUBLE,0,world);
MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world);
if (i == ith && ith == jth) {
tb->mass = mass;
if (me == 0) grab(fp,tb->nrho,&tb->frho[1]);
MPI_Bcast(&tb->frho[1],tb->nrho,MPI_DOUBLE,0,world);
if (me == 0) grab(fp,file->nrho,&file->frho[i][1]);
MPI_Bcast(&file->frho[i][1],file->nrho,MPI_DOUBLE,0,world);
for (j = 1; j <= ntypes; j++) {
if (j == jth) {
if (me == 0) grab(fp,tb->nr,&tb->rhor[1]);
MPI_Bcast(&tb->rhor[1],tb->nr,MPI_DOUBLE,0,world);
} else if (me == 0) skip(fp,tb->nr);
}
} else if (i == ith && ith != jth) {
if (me == 0) skip(fp,tb->nrho);
for (j = 1; j <= ntypes; j++) {
if (j == jth) {
if (me == 0) grab(fp,tb->nr,&tb->rhor[1]);
MPI_Bcast(&tb->rhor[1],tb->nr,MPI_DOUBLE,0,world);
} else if (me == 0) skip(fp,tb->nr);
}
} else {
if (me == 0) skip(fp,tb->nrho);
if (me == 0) for (j = 1; j <= ntypes; j = j + 1) skip(fp,tb->nr);
for (j = 0; j < file->nelements; j++) {
if (me == 0) grab(fp,file->nr,&file->rhor[i][j][1]);
MPI_Bcast(&file->rhor[i][j][1],file->nr,MPI_DOUBLE,0,world);
}
}
for (i = 1; i <= ntypes; i++) {
for (j = 1; j <= i; j++) {
if ((i == ith && j == jth) || (j == ith && i == jth)) {
if (me == 0) grab(fp,tb->nr,&tb->z2r[1]);
MPI_Bcast(&tb->z2r[1],tb->nr,MPI_DOUBLE,0,world);
} else if (me == 0) skip(fp,tb->nr);
for (i = 0; i < file->nelements; i++)
for (j = 0; j <= i; j++) {
if (me == 0) grab(fp,file->nr,&file->z2r[i][j][1]);
MPI_Bcast(&file->z2r[i][j][1],file->nr,MPI_DOUBLE,0,world);
}
}
// close the potential file
if (me == 0) fclose(fp);
ntables++;
return ntables-1;
}
/* ----------------------------------------------------------------------
store read-in setfl values in multi-type setfl format
copy read-in setfl potential to standard array format
------------------------------------------------------------------------- */
void PairEAMFS::store_setfl()
void PairEAMFS::file2array()
{
int i,j,m;
int i,j,m,n;
int ntypes = atom->ntypes;
// set function params directly from fs file
nrho = fs->nrho;
nr = fs->nr;
drho = fs->drho;
dr = fs->dr;
// ------------------------------------------------------------------
// setup frho arrays
// ------------------------------------------------------------------
// allocate frho arrays
// nfrho = # of fs elements + 1 for zero array
// set nrho,nr,drho,dr from any i,i table entry since all the same
nfrho = fs->nelements + 1;
memory->destroy_2d_double_array(frho);
frho = (double **) memory->create_2d_double_array(nfrho,nrho+1,"pair:frho");
// copy each element's frho to global frho
for (i = 0; i < fs->nelements; i++)
for (m = 1; m <= nrho; m++) frho[i][m] = fs->frho[i][m];
// 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 element (non-EAM atom in pair hybrid)
// then map it to last frho array of zeroes
for (i = 1; i <= ntypes; i++)
if (setflag[i][i]) break;
if (map[i] >= 0) type2frho[i] = map[i];
else type2frho[i] = nfrho-1;
nrho = tables[tabindex[i][i]].nrho;
nr = tables[tabindex[i][i]].nr;
drho = tables[tabindex[i][i]].drho;
dr = tables[tabindex[i][i]].dr;
// ------------------------------------------------------------------
// setup rhor arrays
// ------------------------------------------------------------------
// allocate multi-type setfl arrays
// allocate rhor arrays
// nrhor = square of # of fs elements
if (frho) {
memory->destroy_2d_double_array(frho);
memory->destroy_3d_double_array(rhor_fs);
memory->destroy_2d_double_array(zrtmp);
memory->destroy_3d_double_array(z2r);
}
nrhor = fs->nelements * fs->nelements;
memory->destroy_2d_double_array(rhor);
rhor = (double **) memory->create_2d_double_array(nrhor,nr+1,"pair:rhor");
frho = (double **)
memory->create_2d_double_array(ntypes+1,nrho+1,"eam/fs:frho");
rhor_fs = (double ***)
memory->create_3d_double_array(ntypes+1,ntypes+1,nr+1,"eam/fs:rhor_fs");
zrtmp = (double **)
memory->create_2d_double_array(ntypes+1,nr+1,"eam/fs:zrtmp");
z2r = (double ***)
memory->create_3d_double_array(ntypes+1,ntypes+1,nr+1,"eam/fs:frho");
// copy each element pair rhor to global rhor
// copy from read-in tables to multi-type setfl arrays
// frho,rhor are 1:ntypes, z2r is 1:ntypes,1:ntypes
// skip if setflag i,j = 0 (if hybrid, some may not be set)
n = 0;
for (i = 0; i < fs->nelements; i++)
for (j = 0; j < fs->nelements; j++) {
for (m = 1; m <= nr; m++) rhor[n][m] = fs->rhor[i][j][m];
n++;
}
// type2rhor[i][j] = which rhor array (0 to nrhor-1) each type pair maps to
// for fs files, there is a full NxN set of rhor arrays
// 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] * fs->nelements + map[j];
// ------------------------------------------------------------------
// setup z2r arrays
// ------------------------------------------------------------------
// allocate z2r arrays
// nz2r = N*(N+1)/2 where N = # of fs elements
nz2r = fs->nelements * (fs->nelements+1) / 2;
memory->destroy_2d_double_array(z2r);
z2r = (double **) memory->create_2d_double_array(nz2r,nr+1,"pair:z2r");
// copy each element pair z2r to global z2r, only for I >= J
n = 0;
for (i = 0; i < fs->nelements; i++)
for (j = 0; j <= i; j++) {
for (m = 1; m <= nr; m++) z2r[n][m] = fs->z2r[i][j][m];
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++) {
irow = map[i];
if (irow == -1) continue;
for (j = 1; j <= ntypes; j++) {
if (setflag[i][j] == 0) continue;
Table *tb = &tables[tabindex[i][j]];
if (i == j) for (m = 1; m <= nrho; m++) frho[i][m] = tb->frho[m];
for (m = 1; m <= nr; m++) {
rhor_fs[i][j][m] = tb->rhor[m];
z2r[i][j][m] = tb->z2r[m];
}
}
}
/* ----------------------------------------------------------------------
interpolate EAM potentials
------------------------------------------------------------------------- */
void PairEAMFS::interpolate()
{
// free memory from previous interpolation
if (frho_0) interpolate_deallocate();
// interpolation spacings
rdr = 1.0/dr;
rdrho = 1.0/drho;
// allocate coeff arrays
int n = atom->ntypes;
frho_0 = memory->create_2d_double_array(n+1,nrho+1,"eam/fs:frho_0");
frho_1 = memory->create_2d_double_array(n+1,nrho+1,"eam/fs:frho_1");
frho_2 = memory->create_2d_double_array(n+1,nrho+1,"eam/fs:frho_2");
frho_3 = memory->create_2d_double_array(n+1,nrho+1,"eam/fs:frho_3");
frho_4 = memory->create_2d_double_array(n+1,nrho+1,"eam/fs:frho_4");
frho_5 = memory->create_2d_double_array(n+1,nrho+1,"eam/fs:frho_5");
frho_6 = memory->create_2d_double_array(n+1,nrho+1,"eam/fs:frho_6");
rhor_fs_0 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam/fs:rhor_fs_0");
rhor_fs_1 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam/fs:rhor_fs_1");
rhor_fs_2 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam/fs:rhor_fs_2");
rhor_fs_3 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam/fs:rhor_fs_3");
rhor_fs_4 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam/fs:rhor_fs_4");
rhor_fs_5 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam/fs:rhor_fs_5");
rhor_fs_6 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam/fs:rhor_fs_6");
z2r_0 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam/fs:z2r_0");
z2r_1 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam/fs:z2r_1");
z2r_2 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam/fs:z2r_2");
z2r_3 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam/fs:z2r_3");
z2r_4 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam/fs:z2r_4");
z2r_5 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam/fs:z2r_5");
z2r_6 = memory->create_3d_double_array(n+1,n+1,nr+1,"eam/fs:z2r_6");
// frho interpolation for 1:ntypes
// skip if setflag = 0 (if hybrid, some may not be set)
// if skip, set frho arrays to 0.0, since they will still be accessed
// for non-EAM atoms when compute() calculates embedding function
int i,j,m;
for (i = 1; i <= atom->ntypes; i++) {
if (setflag[i][i] == 0) {
for (j = 1; j <= n; j++)
for (m = 1; m <= nrho; m++)
frho_0[j][m] = frho_1[j][m] = frho_2[j][m] = frho_3[j][m] =
frho_4[j][m] = frho_5[j][m] = frho_6[j][m] = 0.0;
continue;
}
for (m = 1; m <= nrho; m++) frho_0[i][m] = frho[i][m];
frho_1[i][1] = frho_0[i][2]-frho_0[i][1];
frho_1[i][2] = 0.5*(frho_0[i][3]-frho_0[i][1]);
frho_1[i][nrho-1] = 0.5*(frho_0[i][nrho]-frho_0[i][nrho-2]);
frho_1[i][nrho] = frho_0[i][nrho]-frho_0[i][nrho-1];
for (m = 3; m <= nrho-2; m++)
frho_1[i][m] = ((frho_0[i][m-2]-frho_0[i][m+2]) +
8.0*(frho_0[i][m+1]-frho_0[i][m-1]))/12.0;
for (m = 1; m <= nrho-1; m++) {
frho_2[i][m] = 3.*(frho_0[i][m+1]-frho_0[i][m]) -
2.0*frho_1[i][m] - frho_1[i][m+1];
frho_3[i][m] = frho_1[i][m] + frho_1[i][m+1] -
2.0*(frho_0[i][m+1]-frho_0[i][m]);
}
frho_2[i][nrho] = 0.0;
frho_3[i][nrho] = 0.0;
for (m = 1; m <= nrho; m++) {
frho_4[i][m] = frho_1[i][m]/drho;
frho_5[i][m] = 2.0*frho_2[i][m]/drho;
frho_6[i][m] = 3.0*frho_3[i][m]/drho;
}
}
// rhor interpolation for 1:ntypes
// skip if setflag = 0 (if hybrid, some may not be set)
for (i = 1; i <= atom->ntypes; i++) {
for (j = 1; j <= atom->ntypes; j++) {
if (setflag[i][j] == 0) continue;
for (m = 1; m <= nr; m++) rhor_fs_0[i][j][m] = rhor_fs[i][j][m];
rhor_fs_1[i][j][1] = rhor_fs_0[i][j][2]-rhor_fs_0[i][j][1];
rhor_fs_1[i][j][2] = 0.5*(rhor_fs_0[i][j][3]-rhor_fs_0[i][j][1]);
rhor_fs_1[i][j][nr-1] = 0.5*(rhor_fs_0[i][j][nr]-rhor_fs_0[i][j][nr-2]);
rhor_fs_1[i][j][nr] = 0.0;
for (m = 3; m <= nr-2; m++)
rhor_fs_1[i][j][m] = ((rhor_fs_0[i][j][m-2]-rhor_fs_0[i][j][m+2]) +
8.0*(rhor_fs_0[i][j][m+1]-rhor_fs_0[i][j][m-1]))/12.;
for (m = 1; m <= nr-1; m++) {
rhor_fs_2[i][j][m] = 3.0*(rhor_fs_0[i][j][m+1]-rhor_fs_0[i][j][m]) -
2.0*rhor_fs_1[i][j][m] - rhor_fs_1[i][j][m+1];
rhor_fs_3[i][j][m] = rhor_fs_1[i][j][m] + rhor_fs_1[i][j][m+1] -
2.0*(rhor_fs_0[i][j][m+1]-rhor_fs_0[i][j][m]);
}
rhor_fs_2[i][j][nr] = 0.0;
rhor_fs_3[i][j][nr] = 0.0;
for (m = 1; m <= nr; m++) {
rhor_fs_4[i][j][m] = rhor_fs_1[i][j][m]/dr;
rhor_fs_5[i][j][m] = 2.0*rhor_fs_2[i][j][m]/dr;
rhor_fs_6[i][j][m] = 3.0*rhor_fs_3[i][j][m]/dr;
}
}
}
// z2r interpolation for 1:ntypes,1:ntypes
// skip if setflag i,j = 0 (if hybrid, some may not be set)
// set j,i coeffs = i,j coeffs
for (i = 1; i <= atom->ntypes; i++) {
for (j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] == 0) continue;
for (m = 1; m <= nr; m++) z2r_0[i][j][m] = z2r[i][j][m];
z2r_1[i][j][1] = z2r_0[i][j][2]-z2r_0[i][j][1];
z2r_1[i][j][2] = 0.5*(z2r_0[i][j][3]-z2r_0[i][j][1]);
z2r_1[i][j][nr-1] = 0.5*(z2r_0[i][j][nr]-z2r_0[i][j][nr-2]);
z2r_1[i][j][nr] = 0.0;
for (m = 3; m <= nr-2; m++)
z2r_1[i][j][m] = ((z2r_0[i][j][m-2]-z2r_0[i][j][m+2]) +
8.0*(z2r_0[i][j][m+1]-z2r_0[i][j][m-1]))/12.;
for (m = 1; m <= nr-1; m++) {
z2r_2[i][j][m] = 3.0*(z2r_0[i][j][m+1]-z2r_0[i][j][m]) -
2.0*z2r_1[i][j][m] - z2r_1[i][j][m+1];
z2r_3[i][j][m] = z2r_1[i][j][m] + z2r_1[i][j][m+1] -
2.0*(z2r_0[i][j][m+1]-z2r_0[i][j][m]);
}
z2r_2[i][j][nr] = 0.0;
z2r_3[i][j][nr] = 0.0;
for (m = 1; m <= nr; m++) {
z2r_4[i][j][m] = z2r_1[i][j][m]/dr;
z2r_5[i][j][m] = 2.0*z2r_2[i][j][m]/dr;
z2r_6[i][j][m] = 3.0*z2r_3[i][j][m]/dr;
}
for (m = 1; m <= nr; m++) {
z2r_0[j][i][m] = z2r_0[i][j][m];
z2r_1[j][i][m] = z2r_1[i][j][m];
z2r_2[j][i][m] = z2r_2[i][j][m];
z2r_3[j][i][m] = z2r_3[i][j][m];
z2r_4[j][i][m] = z2r_4[i][j][m];
z2r_5[j][i][m] = z2r_5[i][j][m];
z2r_6[j][i][m] = z2r_6[i][j][m];
icol = map[j];
if (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;
}
}
}
/* ----------------------------------------------------------------------
deallocate spline interpolation arrays
------------------------------------------------------------------------- */
void PairEAMFS::interpolate_deallocate()
{
memory->destroy_2d_double_array(frho_0);
memory->destroy_2d_double_array(frho_1);
memory->destroy_2d_double_array(frho_2);
memory->destroy_2d_double_array(frho_3);
memory->destroy_2d_double_array(frho_4);
memory->destroy_2d_double_array(frho_5);
memory->destroy_2d_double_array(frho_6);
memory->destroy_3d_double_array(rhor_fs_0);
memory->destroy_3d_double_array(rhor_fs_1);
memory->destroy_3d_double_array(rhor_fs_2);
memory->destroy_3d_double_array(rhor_fs_3);
memory->destroy_3d_double_array(rhor_fs_4);
memory->destroy_3d_double_array(rhor_fs_5);
memory->destroy_3d_double_array(rhor_fs_6);
memory->destroy_3d_double_array(z2r_0);
memory->destroy_3d_double_array(z2r_1);
memory->destroy_3d_double_array(z2r_2);
memory->destroy_3d_double_array(z2r_3);
memory->destroy_3d_double_array(z2r_4);
memory->destroy_3d_double_array(z2r_5);
memory->destroy_3d_double_array(z2r_6);
}
/* ---------------------------------------------------------------------- */
void PairEAMFS::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj,
int eflag, One &one)
{
double r,p,rhoip,rhojp,z2,z2p,recip,phi,phip,psip;
int m;
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 = (rhor_fs_6[itype][jtype][m]*p + rhor_fs_5[itype][jtype][m])*p +
rhor_fs_4[itype][jtype][m];
rhojp = (rhor_fs_6[jtype][itype][m]*p + rhor_fs_5[jtype][itype][m])*p +
rhor_fs_4[jtype][itype][m];
z2 = ((z2r_3[itype][jtype][m]*p + z2r_2[itype][jtype][m])*p +
z2r_1[itype][jtype][m])*p + z2r_0[itype][jtype][m];
z2p = (z2r_6[itype][jtype][m]*p + z2r_5[itype][jtype][m])*p +
z2r_4[itype][jtype][m];
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;
}
}

16
src/MANYBODY/pair_eam_fs.h
View File

@ -18,23 +18,11 @@
class PairEAMFS : public PairEAM {
public:
PairEAMFS();
~PairEAMFS();
void compute(int, int);
void coeff(int, char **);
double init_one(int, int);
void init_style();
void single(int, int, int, int, double, double, double, int, One &);
private:
double ***rhor_fs;
double ***rhor_fs_0,***rhor_fs_1,***rhor_fs_2,***rhor_fs_3;
double ***rhor_fs_4,***rhor_fs_5,***rhor_fs_6;
int read_setfl(char *, int, int);
void store_setfl();
void interpolate();
void interpolate_deallocate();
void read_file(char *);
void file2array();
};
#endif