Homec4science
Diffusion lammps (master) Browse

lammps/src/USER-MISC/pair_edip_multi.cpp
4b1914aa1f29master

Last Change
Raw File

pair_edip_multi.cpp
View Options

/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Environment Dependent Interatomic Potential
Contributing author: Chao Jiang
------------------------------------------------------------------------- */
#include <math.h>
#include <float.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_edip_multi.h"
#include "atom.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "citeme.h"
using namespace LAMMPS_NS;
#define MAXLINE 1024
#define DELTA 4
static const char cite_pair_edip[] =
"@article{cjiang2012\n"
" author = {Jian, Chao and Morgan, Dane, and Szlufarska, Izabella},\n"
" title = {Carbon tri-interstitial defect: A model for DII center},\n"
" journal = {Physical Review B},\n"
" volume = {86},\n"
" pages = {144118},\n"
" year = {2012},\n"
"}\n\n"
"@article{lpizzagalli2010,\n"
" author = {G. Lucas, M. Bertolus, and L. Pizzagalli},\n"
" journal = {J. Phys. : Condens. Matter 22},\n"
" volume = {22},\n"
" pages = {035802},\n"
" year = {2010},\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
PairEDIPMulti::PairEDIPMulti(LAMMPS *lmp) : Pair(lmp)
{
if (lmp->citeme) lmp->citeme->add(cite_pair_edip);
single_enable = 0;
restartinfo = 0;
one_coeff = 1;
manybody_flag = 1;
nelements = 0;
elements = NULL;
nparams = maxparam = 0;
params = NULL;
elem2param = NULL;
}
/* ----------------------------------------------------------------------
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
PairEDIPMulti::~PairEDIPMulti()
{
if (elements)
for (int i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
memory->destroy(params);
memory->destroy(elem2param);
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
delete [] map;
//XXX deallocateGrids();
deallocatePreLoops();
}
}
/* ---------------------------------------------------------------------- */
void PairEDIPMulti::compute(int eflag, int vflag)
{
int i,j,k,ii,jj,kk,inum,jnum;
int itype,jtype,ktype,ijparam,ikparam,ijkparam;
double xtmp,ytmp,ztmp,evdwl;
int *ilist,*jlist,*numneigh,**firstneigh;
register int preForceCoord_counter;
double zeta_i;
double dzetair;
double fpair;
double costheta;
double dpairZ,dtripleZ;
// eflag != 0 means compute energy contributions in this step
// vflag != 0 means compute virial contributions in this step
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
inum = list->inum;//total number of atoms in the cell
ilist = list->ilist;//list of atoms
numneigh = list->numneigh;//number of near neighbors
firstneigh = list->firstneigh;//list of neighbors
// loop over full neighbor list of my atoms
for (ii = 0; ii < inum; ii++) {
zeta_i = 0.0;
int numForceCoordPairs = 0;
i = ilist[ii];
itype = map[type[i]];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
// all the neighbors of atom i
jlist = firstneigh[i];
jnum = numneigh[i];
// pre-loop to compute environment coordination f(Z)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
double delx, dely, delz, r_ij;
delx = x[j][0] - xtmp;
dely = x[j][1] - ytmp;
delz = x[j][2] - ztmp;
r_ij = delx * delx + dely * dely + delz * delz;
jtype = map[type[j]];
ijparam = elem2param[itype][jtype][jtype];
if (r_ij > params[ijparam].cutsq) continue;
r_ij = sqrt(r_ij);
// zeta and its derivative dZ/dr
if (r_ij < params[ijparam].cutoffC) zeta_i += 1.0;
else {
double f, fdr;
edip_fc(r_ij, &params[ijparam], f, fdr);
zeta_i += f;
dzetair = -fdr / r_ij;
preForceCoord_counter=numForceCoordPairs*5;
preForceCoord[preForceCoord_counter+0]=dzetair;
preForceCoord[preForceCoord_counter+1]=delx;
preForceCoord[preForceCoord_counter+2]=dely;
preForceCoord[preForceCoord_counter+3]=delz;
preForceCoord[preForceCoord_counter+4]=j;
numForceCoordPairs++;
}
}
// two-body interactions
dpairZ=0;
dtripleZ=0;
for (jj = 0; jj < jnum; jj++) {
double dr_ij[3], r_ij, f_ij[3];
j = jlist[jj];
j &= NEIGHMASK;
dr_ij[0] = x[j][0] - xtmp;
dr_ij[1] = x[j][1] - ytmp;
dr_ij[2] = x[j][2] - ztmp;
r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[2];
jtype = map[type[j]];
ijparam = elem2param[itype][jtype][jtype];
if (r_ij > params[ijparam].cutsq) continue;
r_ij = sqrt(r_ij);
// potential energy and force
// since pair i-j is different from pair j-i, double counting is
// already considered in constructing the potential
double fdr, fdZ;
edip_pair(r_ij, zeta_i, &params[ijparam], evdwl, fdr, fdZ);
fpair = -fdr / r_ij;
dpairZ += fdZ;
f[i][0] -= fpair * dr_ij[0];
f[i][1] -= fpair * dr_ij[1];
f[i][2] -= fpair * dr_ij[2];
f[j][0] += fpair * dr_ij[0];
f[j][1] += fpair * dr_ij[1];
f[j][2] += fpair * dr_ij[2];
if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, -dr_ij[0], -dr_ij[1], -dr_ij[2]);
// three-body Forces
for (kk = jj + 1; kk < jnum; kk++) {
double dr_ik[3], r_ik, f_ik[3];
k = jlist[kk];
k &= NEIGHMASK;
ktype = map[type[k]];
ikparam = elem2param[itype][ktype][ktype];
ijkparam = elem2param[itype][jtype][ktype];
dr_ik[0] = x[k][0] - xtmp;
dr_ik[1] = x[k][1] - ytmp;
dr_ik[2] = x[k][2] - ztmp;
r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
if (r_ik > params[ikparam].cutsq) continue;
r_ik = sqrt(r_ik);
costheta=vec3_dot(dr_ij, dr_ik) / r_ij / r_ik;
double v1, v2, v3, v4, v5, v6, v7;
edip_fcut3(r_ij, &params[ijparam], v1, v2);
edip_fcut3(r_ik, &params[ikparam], v3, v4);
edip_h(costheta, zeta_i, &params[ijkparam], v5, v6, v7);
// potential energy and forces
evdwl = v1 * v3 * v5;
dtripleZ += v1 * v3 * v7;
double dri[3], drj[3], drk[3];
double dhl, dfr;
dhl = v1 * v3 * v6;
costheta_d(dr_ij, r_ij, dr_ik, r_ik, dri, drj, drk);
f_ij[0] = -dhl * drj[0];
f_ij[1] = -dhl * drj[1];
f_ij[2] = -dhl * drj[2];
f_ik[0] = -dhl * drk[0];
f_ik[1] = -dhl * drk[1];
f_ik[2] = -dhl * drk[2];
dfr = v2 * v3 * v5;
fpair = -dfr / r_ij;
f_ij[0] += fpair * dr_ij[0];
f_ij[1] += fpair * dr_ij[1];
f_ij[2] += fpair * dr_ij[2];
dfr = v1 * v4 * v5;
fpair = -dfr / r_ik;
f_ik[0] += fpair * dr_ik[0];
f_ik[1] += fpair * dr_ik[1];
f_ik[2] += fpair * dr_ik[2];
f[j][0] += f_ij[0];
f[j][1] += f_ij[1];
f[j][2] += f_ij[2];
f[k][0] += f_ik[0];
f[k][1] += f_ik[1];
f[k][2] += f_ik[2];
f[i][0] -= f_ij[0] + f_ik[0];
f[i][1] -= f_ij[1] + f_ik[1];
f[i][2] -= f_ij[2] + f_ik[2];
if (evflag) ev_tally3(i,j,k,evdwl,0.0,f_ij,f_ik,dr_ij,dr_ik);
}
}
// forces due to environment coordination f(Z)
for (int idx = 0; idx < numForceCoordPairs; idx++) {
double delx, dely, delz;
preForceCoord_counter = idx * 5;
dzetair = preForceCoord[preForceCoord_counter+0];
delx = preForceCoord[preForceCoord_counter+1];
dely = preForceCoord[preForceCoord_counter+2];
delz = preForceCoord[preForceCoord_counter+3];
j = static_cast<int> (preForceCoord[preForceCoord_counter+4]);
dzetair *= (dpairZ + dtripleZ);
f[j][0] += dzetair * delx;
f[j][1] += dzetair * dely;
f[j][2] += dzetair * delz;
f[i][0] -= dzetair * delx;
f[i][1] -= dzetair * dely;
f[i][2] -= dzetair * delz;
evdwl = 0.0;
if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, dzetair, -delx, -dely, -delz);
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
double sqr(double x)
{
return x * x;
}
//pair Vij, partial derivatives dVij(r,Z)/dr and dVij(r,Z)/dZ
void PairEDIPMulti::edip_pair(double r, double z, Param *param, double &eng,
double &fdr, double &fZ)
{
double A = param->A;
double B = param->B;
double rho = param->rho;
double beta = param->beta;
double v1,v2,v3,v4;
v1 = pow(B / r, rho);
v2 = exp(-beta * z * z);
edip_fcut2(r, param, v3, v4);
eng = A * (v1 - v2) * v3;
fdr = A * (v1 - v2) * v4 + A * (-rho * v1 / r) * v3;
fZ = A * (2 * beta * z * v2) * v3;
}
//function fc(r) in calculating coordination Z and derivative fc'(r)
void PairEDIPMulti::edip_fc(double r, Param *param, double &f, double &fdr)
{
double a = param->cutoffA;
double c = param->cutoffC;
double alpha = param->alpha;
double x;
double v1, v2, v3;
if(r < c + 1E-6)
{
f=1.0;
fdr=0.0;
return;
}
if(r > a - 1E-6)
{
f=0.0;
fdr=0.0;
return;
}
x = (a - c) / (r - c);
v1 = x * x * x;
v2 = 1.0 / (1.0 - v1);
f = exp(alpha * v2);
fdr = (3.0 * x * v1 / (a - c)) * (-alpha * v2 * v2) * f;
}
//cut-off function for Vij and its derivative fcut2'(r)
void PairEDIPMulti::edip_fcut2(double r, Param *param, double &f, double &fdr)
{
double sigma = param->sigma;
double a = param->cutoffA;
double v1;
if(r > a - 1E-6)
{
f=0.0;
fdr=0.0;
return;
}
v1 = 1.0 / (r - a);
f = exp(sigma * v1);
fdr = (-sigma * v1 * v1) * f;
}
//function tau(Z) and its derivative tau'(Z)
void PairEDIPMulti::edip_tau(double z, Param *param, double &f, double &fdZ)
{
double u1 = param->u1;
double u2 = param->u2;
double u3 = param->u3;
double u4 = param->u4;
double v1, v2;
v1 = exp(-u4 * z);
v2 = exp(-2.0 * u4 * z);
f = u1 + u2 * u3 * v1 - u2 * v2;
fdZ = -u2 * u3 * u4 * v1 + 2.0 * u2 * u4 * v2;
}
//function h(l,Z) and its partial derivatives dh(l,Z)/dl and dh(l,Z)/dZ
void PairEDIPMulti::edip_h(double l, double z, Param *param, double &f,
double &fdl, double &fdZ)
{
double lambda = param->lambda;
double eta = param->eta;
double Q0 = param->Q0;
double mu = param->mu;
double Q, QdZ, Tau, TaudZ;
double u2, du2l, du2Z;
double v1, v2, v3;
//function Q(Z)
Q = Q0 * exp(-mu * z);
//derivative Q'(Z)
QdZ= -mu * Q;
edip_tau(z, param, Tau, TaudZ);
v1 = sqr(l + Tau);
u2 = Q * v1;
v2 = exp(-u2);
f = lambda * (1 - v2 + eta * u2);
//df/du2
v3 = lambda * (v2 + eta);
//du2/dl
du2l = Q * 2 * (l + Tau);
fdl = v3 * du2l;
//du2/dZ
du2Z = QdZ * v1 + Q * 2 * (l + Tau) * TaudZ;
fdZ = v3 * du2Z;
}
//cut-off function for Vijk and its derivative fcut3'(r)
void PairEDIPMulti::edip_fcut3(double r, Param *param, double &f, double &fdr)
{
double gamma = param->gamma;
double a = param->cutoffA;
double v1;
if(r > a - 1E-6)
{
f=0.0;
fdr=0.0;
return;
}
v1 = 1.0 / (r - a);
f = exp(gamma * v1);
fdr = (-gamma * v1 * v1) * f;
}
/* ----------------------------------------------------------------------
pre-calculated structures
------------------------------------------------------------------------- */
void PairEDIPMulti::allocatePreLoops(void)
{
int nthreads = comm->nthreads;
memory->create(preForceCoord,5*nthreads*leadDimInteractionList,"edip:preForceCoord");
}
/* ----------------------------------------------------------------------
deallocate preLoops
------------------------------------------------------------------------- */
void PairEDIPMulti::deallocatePreLoops(void)
{
memory->destroy(preForceCoord);
}
/* ---------------------------------------------------------------------- */
void PairEDIPMulti::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");
map = new int[n+1];
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairEDIPMulti::settings(int narg, char **arg)
{
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairEDIPMulti::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]);
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");
// allocate tables and internal structures
allocatePreLoops();
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairEDIPMulti::init_style()
{
if (atom->tag_enable == 0)
error->all(FLERR,"Pair style edip/multi requires atom IDs");
if (force->newton_pair == 0)
error->all(FLERR,"Pair style edip/multi requires newton pair on");
// need a full neighbor list
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairEDIPMulti::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
return cutmax;
}
/* ---------------------------------------------------------------------- */
void PairEDIPMulti::read_file(char *file)
{
int params_per_line = 20;
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 EDIP potential file %s",file);
error->one(FLERR,str);
}
}
// read each set of params from potential file
// one set of params can span multiple lines
// store 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,"Incorrect format in EDIP 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 entry in file
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].A = atof(words[3]);
params[nparams].B = atof(words[4]);
params[nparams].cutoffA = atof(words[5]);
params[nparams].cutoffC = atof(words[6]);
params[nparams].alpha = atof(words[7]);
params[nparams].beta = atof(words[8]);
params[nparams].eta = atof(words[9]);
params[nparams].gamma = atof(words[10]);
params[nparams].lambda = atof(words[11]);
params[nparams].mu = atof(words[12]);
params[nparams].rho = atof(words[13]);
params[nparams].sigma = atof(words[14]);
params[nparams].Q0 = atof(words[15]);
params[nparams].u1 = atof(words[16]);
params[nparams].u2 = atof(words[17]);
params[nparams].u3 = atof(words[18]);
params[nparams].u4 = atof(words[19]);
if (params[nparams].A < 0.0 || params[nparams].B < 0.0 ||
params[nparams].cutoffA < 0.0 || params[nparams].cutoffC < 0.0 ||
params[nparams].alpha < 0.0 || params[nparams].beta < 0.0 ||
params[nparams].eta < 0.0 || params[nparams].gamma < 0.0 ||
params[nparams].lambda < 0.0 || params[nparams].mu < 0.0 ||
params[nparams].rho < 0.0 || params[nparams].sigma < 0.0)
error->all(FLERR,"Illegal EDIP parameter");
nparams++;
}
delete [] words;
}
/* ---------------------------------------------------------------------- */
void PairEDIPMulti::setup()
{
int i,j,k,m,n;
double rtmp;
// set elem2param for all 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;
}
// set cutoff square
for (m = 0; m < nparams; m++) {
params[m].cutsq = params[m].cutoffA*params[m].cutoffA;
}
// set cutmax to max of all params
cutmax = 0.0;
for (m = 0; m < nparams; m++) {
rtmp = sqrt(params[m].cutsq);
if (rtmp > cutmax) cutmax = rtmp;
}
}
c4science · Help