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e4071d7f46d9c6c8e47ffb38dd905d8e45fc5d13
lammps/src/USER-MISC/pair_extep.cpp
Axel Kohlmeyer e4071d7f46 replace C-style include files with their C++ equivalents
2018-04-27 18:00:24 -04:00

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Jan Los
------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_extep.h"
#include "atom.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "my_page.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "math_const.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define MAXLINE 1024
#define DELTA 4
#define PGDELTA 1
/* ---------------------------------------------------------------------- */
PairExTeP::PairExTeP(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
restartinfo = 0;
one_coeff = 1;
manybody_flag = 1;
ghostneigh = 1;
nelements = 0;
elements = NULL;
nparams = maxparam = 0;
params = NULL;
elem2param = NULL;
maxlocal = 0;
SR_numneigh = NULL;
SR_firstneigh = NULL;
ipage = NULL;
pgsize = oneatom = 0;
map = NULL;
Nt = NULL;
Nd = NULL;
}
/* ----------------------------------------------------------------------
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
PairExTeP::~PairExTeP()
{
if (elements)
for (int i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
memory->destroy(params);
memory->destroy(elem2param);
memory->destroy(SR_numneigh);
memory->sfree(SR_firstneigh);
delete [] ipage;
memory->destroy(Nt);
memory->destroy(Nd);
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cutghost);
delete [] map;
}
}
/* ----------------------------------------------------------------------
create SR neighbor list from main neighbor list
SR neighbor list stores neighbors of ghost atoms
------------------------------------------------------------------------- */
void PairExTeP::SR_neigh()
{
int i,j,ii,jj,n,allnum,jnum,itype,jtype,iparam_ij;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
int *neighptr;
double **x = atom->x;
int *type = atom->type;
if (atom->nmax > maxlocal) { // ensure there is enough space
maxlocal = atom->nmax; // for atoms and ghosts allocated
memory->destroy(SR_numneigh);
memory->sfree(SR_firstneigh);
memory->destroy(Nt);
memory->destroy(Nd);
memory->create(SR_numneigh,maxlocal,"ExTeP:numneigh");
SR_firstneigh = (int **) memory->smalloc(maxlocal*sizeof(int *),
"ExTeP:firstneigh");
memory->create(Nt,maxlocal,"ExTeP:Nt");
memory->create(Nd,maxlocal,"ExTeP:Nd");
}
allnum = list->inum + list->gnum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// store all SR neighs of owned and ghost atoms
// scan full neighbor list of I
ipage->reset();
for (ii = 0; ii < allnum; ii++) {
i = ilist[ii];
itype=map[type[i]];
n = 0;
neighptr = ipage->vget();
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
Nt[i] = 0.0;
Nd[i] = 0.0;
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;
jtype=map[type[j]];
iparam_ij = elem2param[itype][jtype][jtype];
if (rsq < params[iparam_ij].cutsq) {
neighptr[n++] = j;
double tmp_fc = ters_fc(sqrt(rsq),&params[iparam_ij]);
Nt[i] += tmp_fc;
if (itype!=jtype) {
Nd[i] += tmp_fc;
}
}
}
//printf("SR_neigh : N[%d] = %f\n",i,N[i]);
ipage->vgot(n);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
}
/* ---------------------------------------------------------------------- */
void PairExTeP::compute(int eflag, int vflag)
{
int i,j,k,ii,jj,kk,inum,jnum;
int itype,jtype,ktype,iparam_ij,iparam_ijk;
tagint itag,jtag;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,rsq1,rsq2,r2;
double delr1[3],delr2[3],fi[3],fj[3],fk[3];
double zeta_ij,prefactor;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = vflag_atom = 0;
SR_neigh();
double **x = atom->x;
double **f = atom->f;
tagint *tag = atom->tag;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over full neighbor list of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
itag = tag[i];
itype = map[type[i]];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// two-body interactions, skip half of them
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtag = tag[j];
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) continue;
} else {
if (x[j][2] < x[i][2]) continue;
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
jtype = map[type[j]];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
iparam_ij = elem2param[itype][jtype][jtype];
if (rsq > params[iparam_ij].cutsq) continue;
repulsive(&params[iparam_ij],rsq,fpair,eflag,evdwl);
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
// three-body interactions -(bij + Fcorrection) * fA
// skip immediately if I-J is not within cutoff
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtag = tag[j];
jtype = map[type[j]];
iparam_ij = elem2param[itype][jtype][jtype];
delr1[0] = x[j][0] - xtmp;
delr1[1] = x[j][1] - ytmp;
delr1[2] = x[j][2] - ztmp;
rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
if (rsq1 > params[iparam_ij].cutsq) continue;
// accumulate bondorder zeta for each i-j interaction via loop over k
zeta_ij = 0.0;
/* F_IJ (1) */
// compute correction to energy and forces
// dE/dr = -Fij(Zi,Zj) dV/dr
// - dFij/dZi dZi/dr V
// (conjugate term is computed when j is a central atom)
double FXY, dFXY_dNdij, dFXY_dNdji, fa, fa_d, deng, fpair;
double Ntij = Nt[i];
double Ndij = Nd[i];
double Ntji = Nt[j];
double Ndji = Nd[j];
double r = sqrt(rsq1);
double fc_ij = ters_fc(r,&params[iparam_ij]);
Ntij -= fc_ij;
Ntji -= fc_ij;
if (jtype!=itype) {
Ndij -= fc_ij;
Ndji -= fc_ij;
}
if (Ntij<0) { Ntij=0.; }
if (Ndij<0) { Ndij=0.; }
if (Ntji<0) { Ntji=0.; }
if (Ndji<0) { Ndji=0.; }
FXY = F_corr(itype, jtype, Ndij, Ndji, &dFXY_dNdij, &dFXY_dNdji);
// envelop functions
double fenv, dfenv_ij;
fenv = envelop_function(Ntij, Ntji, &dfenv_ij);
//
double Fc = fenv * FXY;
double dFc_dNtij = dfenv_ij * FXY;
double dFc_dNdij = fenv * dFXY_dNdij;
fa = ters_fa(r,&params[iparam_ij]);
fa_d = ters_fa_d(r,&params[iparam_ij]);
deng = 0.5 * fa * Fc;
fpair = 0.5 * fa_d * Fc / r;
f[i][0] += delr1[0]*fpair;
f[i][1] += delr1[1]*fpair;
f[i][2] += delr1[2]*fpair;
f[j][0] -= delr1[0]*fpair;
f[j][1] -= delr1[1]*fpair;
f[j][2] -= delr1[2]*fpair;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
deng,0.0,-fpair,-delr1[0],-delr1[1],-delr1[2]);
/* END F_IJ (1) */
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = jlist[kk];
k &= NEIGHMASK;
ktype = map[type[k]];
iparam_ijk = elem2param[itype][jtype][ktype];
delr2[0] = x[k][0] - xtmp;
delr2[1] = x[k][1] - ytmp;
delr2[2] = x[k][2] - ztmp;
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
if (rsq2 > params[iparam_ijk].cutsq) continue;
r2 = sqrt(rsq2);
zeta_ij += zeta(&params[iparam_ijk],r,r2,delr1,delr2);
/* F_IJ (2) */
// compute force components due to spline derivatives
// uses only the part with FXY_x (FXY_y is done when i and j are inversed)
int iparam_ik = elem2param[itype][ktype][0];
double fc_ik_d = ters_fc_d(r2,&params[iparam_ik]);
double fc_prefac_ik_0 = 1.0 * fc_ik_d * fa / r2;
double fc_prefac_ik = dFc_dNtij * fc_prefac_ik_0;
f[i][0] += fc_prefac_ik * delr2[0];
f[i][1] += fc_prefac_ik * delr2[1];
f[i][2] += fc_prefac_ik * delr2[2];
f[k][0] -= fc_prefac_ik * delr2[0];
f[k][1] -= fc_prefac_ik * delr2[1];
f[k][2] -= fc_prefac_ik * delr2[2];
if ( itype != ktype ) {
fc_prefac_ik = dFc_dNdij * fc_prefac_ik_0;
f[i][0] += fc_prefac_ik * delr2[0];
f[i][1] += fc_prefac_ik * delr2[1];
f[i][2] += fc_prefac_ik * delr2[2];
f[k][0] -= fc_prefac_ik * delr2[0];
f[k][1] -= fc_prefac_ik * delr2[1];
f[k][2] -= fc_prefac_ik * delr2[2];
}
/* END F_IJ (2) */
}
// pairwise force due to zeta
force_zeta(&params[iparam_ij],r,zeta_ij,fpair,prefactor,eflag,evdwl);
f[i][0] += delr1[0]*fpair;
f[i][1] += delr1[1]*fpair;
f[i][2] += delr1[2]*fpair;
f[j][0] -= delr1[0]*fpair;
f[j][1] -= delr1[1]*fpair;
f[j][2] -= delr1[2]*fpair;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,-fpair,-delr1[0],-delr1[1],-delr1[2]);
// attractive term via loop over k
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = jlist[kk];
k &= NEIGHMASK;
ktype = map[type[k]];
iparam_ijk = elem2param[itype][jtype][ktype];
delr2[0] = x[k][0] - xtmp;
delr2[1] = x[k][1] - ytmp;
delr2[2] = x[k][2] - ztmp;
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
if (rsq2 > params[iparam_ijk].cutsq) continue;
attractive(&params[iparam_ijk],prefactor,
rsq1,rsq2,delr1,delr2,fi,fj,fk);
f[i][0] += fi[0];
f[i][1] += fi[1];
f[i][2] += fi[2];
f[j][0] += fj[0];
f[j][1] += fj[1];
f[j][2] += fj[2];
f[k][0] += fk[0];
f[k][1] += fk[1];
f[k][2] += fk[2];
if (vflag_atom) v_tally3(i,j,k,fj,fk,delr1,delr2);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ---------------------------------------------------------------------- */
void PairExTeP::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cutghost,n+1,n+1,"pair:cutghost");
map = new int[n+1];
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairExTeP::settings(int narg, char **arg)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairExTeP::coeff(int narg, char **arg)
{
int i,j,n;
if (!allocated) allocate();
if (narg != 3 + atom->ntypes)
error->all(FLERR,"Incorrect args for pair coefficients");
// insure I,J args are * *
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
error->all(FLERR,"Incorrect args for pair coefficients");
// read args that map atom types to elements in potential file
// map[i] = which element the Ith atom type is, -1 if NULL
// nelements = # of unique elements
// elements = list of element names
if (elements) {
for (i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
}
elements = new char*[atom->ntypes];
for (i = 0; i < atom->ntypes; i++) elements[i] = NULL;
nelements = 0;
for (i = 3; i < narg; i++) {
if (strcmp(arg[i],"NULL") == 0) {
map[i-2] = -1;
continue;
}
for (j = 0; j < nelements; j++)
if (strcmp(arg[i],elements[j]) == 0) break;
map[i-2] = j;
if (j == nelements) {
n = strlen(arg[i]) + 1;
elements[j] = new char[n];
strcpy(elements[j],arg[i]);
nelements++;
}
}
// read potential file and initialize potential parameters
read_file(arg[2]);
spline_init();
setup();
// clear setflag since coeff() called once with I,J = * *
n = atom->ntypes;
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
// set setflag i,j for type pairs where both are mapped to elements
int count = 0;
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (map[i] >= 0 && map[j] >= 0) {
setflag[i][j] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairExTeP::init_style()
{
if (atom->tag_enable == 0)
error->all(FLERR,"Pair style ExTeP requires atom IDs");
if (force->newton_pair == 0)
error->all(FLERR,"Pair style ExTeP requires newton pair on");
// need a full neighbor list
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
// including neighbors of ghosts
neighbor->requests[irequest]->ghost = 1;
// create pages if first time or if neighbor pgsize/oneatom has changed
int create = 0;
if (ipage == NULL) create = 1;
if (pgsize != neighbor->pgsize) create = 1;
if (oneatom != neighbor->oneatom) create = 1;
if (create) {
delete [] ipage;
pgsize = neighbor->pgsize;
oneatom = neighbor->oneatom;
int nmypage= comm->nthreads;
ipage = new MyPage<int>[nmypage];
for (int i = 0; i < nmypage; i++)
ipage[i].init(oneatom,pgsize,PGDELTA);
}
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairExTeP::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
cutghost[i][j] = cutmax ;
cutghost[j][i] = cutghost[i][j];
return cutmax;
}
/* ---------------------------------------------------------------------- */
void PairExTeP::read_file(char *file)
{
int params_per_line = 17;
char **words = new char*[params_per_line+1];
memory->sfree(params);
params = NULL;
nparams = maxparam = 0;
// open file on proc 0
FILE *fp;
if (comm->me == 0) {
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open ExTeP potential file %s",file);
error->one(FLERR,str);
}
}
// read each line out of file, skipping blank lines or leading '#'
// store line of params if all 3 element tags are in element list
int n,nwords,ielement,jelement,kelement;
char line[MAXLINE],*ptr;
int eof = 0;
while (1) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
// strip comment, skip line if blank
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = atom->count_words(line);
if (nwords == 0) continue;
// concatenate additional lines until have params_per_line words
while (nwords < params_per_line) {
n = strlen(line);
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = atom->count_words(line);
}
if (nwords != params_per_line)
error->all(FLERR,"Insufficient spline parameters in potential file");
// words = ptrs to all words in line
nwords = 0;
words[nwords++] = strtok(line," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
// ielement,jelement,kelement = 1st args
// if all 3 args are in element list, then parse this line
// else skip to next line
for (ielement = 0; ielement < nelements; ielement++)
if (strcmp(words[0],elements[ielement]) == 0) break;
if (ielement == nelements) continue;
for (jelement = 0; jelement < nelements; jelement++)
if (strcmp(words[1],elements[jelement]) == 0) break;
if (jelement == nelements) continue;
for (kelement = 0; kelement < nelements; kelement++)
if (strcmp(words[2],elements[kelement]) == 0) break;
if (kelement == nelements) continue;
// load up parameter settings and error check their values
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
"pair:params");
}
params[nparams].ielement = ielement;
params[nparams].jelement = jelement;
params[nparams].kelement = kelement;
params[nparams].powerm = atof(words[3]);
params[nparams].gamma = atof(words[4]);
params[nparams].lam3 = atof(words[5]);
params[nparams].c = atof(words[6]);
params[nparams].d = atof(words[7]);
params[nparams].h = atof(words[8]);
params[nparams].powern = atof(words[9]);
params[nparams].beta = atof(words[10]);
params[nparams].lam2 = atof(words[11]);
params[nparams].bigb = atof(words[12]);
params[nparams].bigr = atof(words[13]);
params[nparams].bigd = atof(words[14]);
params[nparams].lam1 = atof(words[15]);
params[nparams].biga = atof(words[16]);
// currently only allow m exponent of 1 or 3
params[nparams].powermint = int(params[nparams].powerm);
if (params[nparams].c < 0.0 || params[nparams].d < 0.0 ||
params[nparams].powern < 0.0 || params[nparams].beta < 0.0 ||
params[nparams].lam2 < 0.0 || params[nparams].bigb < 0.0 ||
params[nparams].bigr < 0.0 ||params[nparams].bigd < 0.0 ||
params[nparams].bigd > params[nparams].bigr ||
params[nparams].lam1 < 0.0 || params[nparams].biga < 0.0 ||
params[nparams].powerm - params[nparams].powermint != 0.0 ||
(params[nparams].powermint != 3 && params[nparams].powermint != 1) ||
params[nparams].gamma < 0.0)
error->all(FLERR,"Illegal ExTeP parameter");
nparams++;
if (nparams >= pow(atom->ntypes,3)) break;
}
// deallocate words array
delete [] words;
/* F_IJ (3) */
// read the spline coefficients
params_per_line = 8;
// reallocate with new size
words = new char*[params_per_line+1];
// intialize F_corr_data to all zeros
for (int iel=0;iel<atom->ntypes;iel++)
for (int jel=0;jel<atom->ntypes;jel++)
for (int in=0;in<4;in++)
for (int jn=0;jn<4;jn++)
for (int ivar=0;ivar<3;ivar++)
F_corr_data[iel][jel][in][jn][ivar]=0;
// loop until EOF
while (1) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
//fputs(line,stdout);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
// strip comment, skip line if blank
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = atom->count_words(line);
if (nwords == 0) continue;
if (nwords != params_per_line)
error->all(FLERR,"Incorrect format in ExTeP potential file");
// words = ptrs to all words in line
nwords = 0;
words[nwords++] = strtok(line," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
// ielement,jelement = 1st args
// if all 3 args are in element list, then parse this line
// else skip to next line
// these lines set ielement and jelement to the
// integers matching the strings from the input
for (ielement = 0; ielement < nelements; ielement++)
if (strcmp(words[0],elements[ielement]) == 0) break;
if (ielement == nelements) continue;
for (jelement = 0; jelement < nelements; jelement++)
if (strcmp(words[1],elements[jelement]) == 0) break;
if (jelement == nelements) continue;
int Ni = atoi(words[2]);
int Nj = atoi(words[3]);
double spline_val = atof(words[4]);
double spline_derx = atof(words[5]);
double spline_dery = atof(words[6]);
// Set value for all pairs of ielement,jelement (any kelement)
for (int iparam = 0; iparam < nparams; iparam++) {
if ( ielement == params[iparam].ielement
&& jelement == params[iparam].jelement) {
F_corr_data[ielement][jelement][Ni][Nj][0] = spline_val;
F_corr_data[ielement][jelement][Ni][Nj][1] = spline_derx;
F_corr_data[ielement][jelement][Ni][Nj][2] = spline_dery;
F_corr_data[jelement][ielement][Nj][Ni][0] = spline_val;
F_corr_data[jelement][ielement][Nj][Ni][1] = spline_dery;
F_corr_data[jelement][ielement][Nj][Ni][2] = spline_derx;
}
}
}
delete [] words;
/* END F_IJ (3) */
}
/* ---------------------------------------------------------------------- */
void PairExTeP::setup()
{
int i,j,k,m,n;
// set elem2param for all element triplet combinations
// must be a single exact match to lines read from file
// do not allow for ACB in place of ABC
memory->destroy(elem2param);
memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param");
for (i = 0; i < nelements; i++)
for (j = 0; j < nelements; j++)
for (k = 0; k < nelements; k++) {
n = -1;
for (m = 0; m < nparams; m++) {
if (i == params[m].ielement && j == params[m].jelement &&
k == params[m].kelement) {
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
n = m;
}
}
if (n < 0) error->all(FLERR,"Potential file is missing an entry");
elem2param[i][j][k] = n;
}
// compute parameter values derived from inputs
for (m = 0; m < nparams; m++) {
params[m].cut = params[m].bigr + params[m].bigd;
params[m].cutsq = params[m].cut*params[m].cut;
params[m].c1 = pow(2.0*params[m].powern*1.0e-16,-1.0/params[m].powern);
params[m].c2 = pow(2.0*params[m].powern*1.0e-8,-1.0/params[m].powern);
params[m].c3 = 1.0/params[m].c2;
params[m].c4 = 1.0/params[m].c1;
}
// set cutmax to max of all params
cutmax = 0.0;
for (m = 0; m < nparams; m++)
if (params[m].cut > cutmax) cutmax = params[m].cut;
}
/* ---------------------------------------------------------------------- */
void PairExTeP::repulsive(Param *param, double rsq, double &fforce,
int eflag, double &eng)
{
double r,tmp_fc,tmp_fc_d,tmp_exp;
r = sqrt(rsq);
tmp_fc = ters_fc(r,param);
tmp_fc_d = ters_fc_d(r,param);
tmp_exp = exp(-param->lam1 * r);
fforce = -param->biga * tmp_exp * (tmp_fc_d - tmp_fc*param->lam1) / r;
if (eflag) eng = tmp_fc * param->biga * tmp_exp;
}
/* ---------------------------------------------------------------------- */
double PairExTeP::zeta(Param *param, double rij, double rik,
double *delrij, double *delrik)
{
double costheta,arg,ex_delr;
costheta = (delrij[0]*delrik[0] + delrij[1]*delrik[1] +
delrij[2]*delrik[2]) / (rij*rik);
if (param->powermint == 3) arg = pow(param->lam3 * (rij-rik),3.0);
else arg = param->lam3 * (rij-rik);
if (arg > 69.0776) ex_delr = 1.e30;
else if (arg < -69.0776) ex_delr = 0.0;
else ex_delr = exp(arg);
return ters_fc(rik,param) * ters_gijk(costheta,param) * ex_delr;
}
/* ---------------------------------------------------------------------- */
void PairExTeP::force_zeta(Param *param, double r, double zeta_ij,
double &fforce, double &prefactor,
int eflag, double &eng)
{
double fa,fa_d,bij;
fa = ters_fa(r,param);
fa_d = ters_fa_d(r,param);
bij = ters_bij(zeta_ij,param);
fforce = 0.5*bij*fa_d / r;
prefactor = -0.5*fa * ( ters_bij_d(zeta_ij,param) );
if (eflag) eng = 0.5*bij*fa;
}
/* ----------------------------------------------------------------------
attractive term
use param_ij cutoff for rij test
use param_ijk cutoff for rik test
------------------------------------------------------------------------- */
void PairExTeP::attractive(Param *param, double prefactor,
double rsqij, double rsqik,
double *delrij, double *delrik,
double *fi, double *fj, double *fk)
{
double rij_hat[3],rik_hat[3];
double rij,rijinv,rik,rikinv;
rij = sqrt(rsqij);
rijinv = 1.0/rij;
vec3_scale(rijinv,delrij,rij_hat);
rik = sqrt(rsqik);
rikinv = 1.0/rik;
vec3_scale(rikinv,delrik,rik_hat);
ters_zetaterm_d(prefactor,rij_hat,rij,rik_hat,rik,fi,fj,fk,param);
}
/* ---------------------------------------------------------------------- */
double PairExTeP::ters_fc(double r, Param *param)
{
double ters_R = param->bigr;
double ters_D = param->bigd;
if (r < ters_R-ters_D) return 1.0;
if (r > ters_R+ters_D) return 0.0;
return 0.5*(1.0 - sin(MY_PI2*(r - ters_R)/ters_D));
}
/* ---------------------------------------------------------------------- */
double PairExTeP::ters_fc_d(double r, Param *param)
{
double ters_R = param->bigr;
double ters_D = param->bigd;
if (r < ters_R-ters_D) return 0.0;
if (r > ters_R+ters_D) return 0.0;
return -(MY_PI4/ters_D) * cos(MY_PI2*(r - ters_R)/ters_D);
}
/* ---------------------------------------------------------------------- */
double PairExTeP::ters_fa(double r, Param *param)
{
if (r > param->bigr + param->bigd) return 0.0;
return -param->bigb * exp(-param->lam2 * r) * ters_fc(r,param);
}
/* ---------------------------------------------------------------------- */
double PairExTeP::ters_fa_d(double r, Param *param)
{
if (r > param->bigr + param->bigd) return 0.0;
return param->bigb * exp(-param->lam2 * r) *
(param->lam2 * ters_fc(r,param) - ters_fc_d(r,param));
}
/* ---------------------------------------------------------------------- */
double PairExTeP::ters_bij(double zeta, Param *param)
{
double tmp = param->beta * zeta;
if (tmp > param->c1) return 1.0/sqrt(tmp);
if (tmp > param->c2)
return (1.0 - pow(tmp,-param->powern) / (2.0*param->powern))/sqrt(tmp);
if (tmp < param->c4) return 1.0;
if (tmp < param->c3)
return 1.0 - pow(tmp,param->powern)/(2.0*param->powern);
return pow(1.0 + pow(tmp,param->powern), -1.0/(2.0*param->powern));
}
/* ---------------------------------------------------------------------- */
double PairExTeP::ters_bij_d(double zeta, Param *param)
{
double tmp = param->beta * zeta;
if (tmp > param->c1) return param->beta * -0.5*pow(tmp,-1.5);
if (tmp > param->c2)
return param->beta * (-0.5*pow(tmp,-1.5) *
(1.0 - 0.5*(1.0 + 1.0/(2.0*param->powern)) *
pow(tmp,-param->powern)));
if (tmp < param->c4) return 0.0;
if (tmp < param->c3)
return -0.5*param->beta * pow(tmp,param->powern-1.0);
double tmp_n = pow(tmp,param->powern);
return -0.5 * pow(1.0+tmp_n, -1.0-(1.0/(2.0*param->powern)))*tmp_n / zeta;
}
/* ---------------------------------------------------------------------- */
void PairExTeP::ters_zetaterm_d(double prefactor,
double *rij_hat, double rij,
double *rik_hat, double rik,
double *dri, double *drj, double *drk,
Param *param)
{
double gijk,gijk_d,ex_delr,ex_delr_d,fc,dfc,cos_theta,tmp;
double dcosdri[3],dcosdrj[3],dcosdrk[3];
fc = ters_fc(rik,param);
dfc = ters_fc_d(rik,param);
if (param->powermint == 3) tmp = pow(param->lam3 * (rij-rik),3.0);
else tmp = param->lam3 * (rij-rik);
if (tmp > 69.0776) ex_delr = 1.e30;
else if (tmp < -69.0776) ex_delr = 0.0;
else ex_delr = exp(tmp);
if (param->powermint == 3)
ex_delr_d = 3.0*pow(param->lam3,3.0) * pow(rij-rik,2.0)*ex_delr;
else ex_delr_d = param->lam3 * ex_delr;
cos_theta = vec3_dot(rij_hat,rik_hat);
gijk = ters_gijk(cos_theta,param);
gijk_d = ters_gijk_d(cos_theta,param);
costheta_d(rij_hat,rij,rik_hat,rik,dcosdri,dcosdrj,dcosdrk);
// compute the derivative wrt Ri
// dri = -dfc*gijk*ex_delr*rik_hat;
// dri += fc*gijk_d*ex_delr*dcosdri;
// dri += fc*gijk*ex_delr_d*(rik_hat - rij_hat);
vec3_scale(-dfc*gijk*ex_delr,rik_hat,dri);
vec3_scaleadd(fc*gijk_d*ex_delr,dcosdri,dri,dri);
vec3_scaleadd(fc*gijk*ex_delr_d,rik_hat,dri,dri);
vec3_scaleadd(-fc*gijk*ex_delr_d,rij_hat,dri,dri);
vec3_scale(prefactor,dri,dri);
// compute the derivative wrt Rj
// drj = fc*gijk_d*ex_delr*dcosdrj;
// drj += fc*gijk*ex_delr_d*rij_hat;
vec3_scale(fc*gijk_d*ex_delr,dcosdrj,drj);
vec3_scaleadd(fc*gijk*ex_delr_d,rij_hat,drj,drj);
vec3_scale(prefactor,drj,drj);
// compute the derivative wrt Rk
// drk = dfc*gijk*ex_delr*rik_hat;
// drk += fc*gijk_d*ex_delr*dcosdrk;
// drk += -fc*gijk*ex_delr_d*rik_hat;
vec3_scale(dfc*gijk*ex_delr,rik_hat,drk);
vec3_scaleadd(fc*gijk_d*ex_delr,dcosdrk,drk,drk);
vec3_scaleadd(-fc*gijk*ex_delr_d,rik_hat,drk,drk);
vec3_scale(prefactor,drk,drk);
}
/* ---------------------------------------------------------------------- */
void PairExTeP::costheta_d(double *rij_hat, double rij,
double *rik_hat, double rik,
double *dri, double *drj, double *drk)
{
// first element is devative wrt Ri, second wrt Rj, third wrt Rk
double cos_theta = vec3_dot(rij_hat,rik_hat);
vec3_scaleadd(-cos_theta,rij_hat,rik_hat,drj);
vec3_scale(1.0/rij,drj,drj);
vec3_scaleadd(-cos_theta,rik_hat,rij_hat,drk);
vec3_scale(1.0/rik,drk,drk);
vec3_add(drj,drk,dri);
vec3_scale(-1.0,dri,dri);
}
/* ---------------------------------------------------------------------- */
/* F_IJ (4) */
// initialize spline for F_corr (based on PairLCBOP::F_conj)
void PairExTeP::spline_init() {
for ( size_t iel=0; iel<atom->ntypes; iel++) {
for ( size_t jel=0; jel<atom->ntypes; jel++) {
for ( size_t N_ij=0; N_ij<4; N_ij++ ) {
for ( size_t N_ji=0; N_ji<4; N_ji++ ) {
TF_corr_param &f = F_corr_param[iel][jel][N_ij][N_ji];
// corner points for each spline function
f.f_00 = F_corr_data[iel][jel][N_ij ][N_ji ][0];
f.f_01 = F_corr_data[iel][jel][N_ij ][N_ji+1][0];
f.f_10 = F_corr_data[iel][jel][N_ij+1][N_ji ][0];
f.f_11 = F_corr_data[iel][jel][N_ij+1][N_ji+1][0];
// compute f tilde according to [Los & Fasolino, PRB 68, 024107 2003]
f.f_x_00 = F_corr_data[iel][jel][N_ij ][N_ji ][1] - f.f_10 + f.f_00;
f.f_x_01 = F_corr_data[iel][jel][N_ij ][N_ji+1][1] - f.f_11 + f.f_01;
f.f_x_10 = -(F_corr_data[iel][jel][N_ij+1][N_ji ][1] - f.f_10 + f.f_00);
f.f_x_11 = -(F_corr_data[iel][jel][N_ij+1][N_ji+1][1] - f.f_11 + f.f_01);
f.f_y_00 = F_corr_data[iel][jel][N_ij ][N_ji ][2] - f.f_01 + f.f_00;
f.f_y_01 = -(F_corr_data[iel][jel][N_ij ][N_ji+1][2] - f.f_01 + f.f_00);
f.f_y_10 = F_corr_data[iel][jel][N_ij+1][N_ji ][2] - f.f_11 + f.f_10;
f.f_y_11 = -(F_corr_data[iel][jel][N_ij+1][N_ji+1][2] - f.f_11 + f.f_10);
}
}
}
}
}
double PairExTeP::envelop_function(double x, double y, double *func_der) {
double fx,fy,fxy,dfx,dfxydx;
double del, delsq;
fxy = 1.0;
dfxydx = 0.0;
if (x <= 3.0) {
fx = 1.0;
dfx = 0.0;
if (x < 1.0 && y < 1.0) {
double gx=(1.0-x);
double gy=(1.0-y);
double gxsq=gx*gx;
double gysq=gy*gy;
fxy = 1.0 - gxsq*gysq;
dfxydx = 2.0*gx*gysq;
}
} else if (x < 4.0) {
del = 4.0-x;
delsq = del*del;
fx = (3.0-2.0*del)*delsq;
dfx = - 6.0*del*(1.0-del);
} else {
fx = 0.0;
dfx = 0.0;
}
if (y <= 3.0) {
fy = 1.0;
} else if (y < 4.0) {
del = 4.0-y;
delsq = del*del;
fy = (3.0-2.0*del)*delsq;
} else {
fy = 0.0;
}
double func_val = fxy*fx*fy;
*func_der = dfxydx*fx*fy+fxy*dfx*fy;
return func_val;
}
double PairExTeP::F_corr(int iel, int jel, double Ndij, double Ndji, double *dFN_x, double *dFN_y ) {
// compute F_XY
size_t Ndij_int = static_cast<size_t>( floor( Ndij ) );
size_t Ndji_int = static_cast<size_t>( floor( Ndji ) );
double x = Ndij - Ndij_int;
double y = Ndji - Ndji_int;
TF_corr_param &f = F_corr_param[iel][jel][Ndij_int][Ndji_int];
double F = 0;
double dF_dx = 0, dF_dy = 0;
double l, r;
if (Ndij_int < 4 && Ndji_int < 4) {
l = (1-y)* (1-x);
r = ( f.f_00 + x*x* f.f_x_10 + y*y* f.f_y_01 );
F += l*r;
dF_dx += -(1-y)*r +l*2*x* f.f_x_10;
dF_dy += -(1-x)*r +l*2*y* f.f_y_01;
l = (1-y)*x;
r = ( f.f_10 + (1-x)*(1-x)*f.f_x_00 + y* y* f.f_y_11 );
F += l*r;
dF_dx += (1-y)*r -l*2*(1-x)*f.f_x_00;
dF_dy += -x*r +l*2*y* f.f_y_11;
l = y* (1-x);
r = ( f.f_01 + x*x* f.f_x_11 + (1-y)*(1-y)*f.f_y_00 );
F += l*r;
dF_dx += -y*r +l*2*x* f.f_x_11;
dF_dy += (1-x)*r -l*2*(1-y)*f.f_y_00;
l = y* x;
r = ( f.f_11 + (1-x)*(1-x)*f.f_x_01 + (1-y)*(1-y)*f.f_y_10 );
F += l*r;
dF_dx += y*r -l*2*(1-x)*f.f_x_01;
dF_dy += x*r -l*2*(1-y)*f.f_y_10;
}
double result = F;
*dFN_x = dF_dx;
*dFN_y = dF_dy;
return result;
}
/* F_IJ (4) */
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