816 lines
24 KiB
C++
816 lines
24 KiB
C++
// clang-format off
|
|
/* ----------------------------------------------------------------------
|
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
https://www.lammps.org/, 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: Aidan Thompson (SNL) - original Tersoff implementation
|
|
Wengen Ouyang (TAU) - Shift addition
|
|
------------------------------------------------------------------------- */
|
|
|
|
#include "pair_tersoff.h"
|
|
|
|
#include "atom.h"
|
|
#include "comm.h"
|
|
#include "error.h"
|
|
#include "force.h"
|
|
#include "math_const.h"
|
|
#include "math_extra.h"
|
|
#include "math_special.h"
|
|
#include "memory.h"
|
|
#include "neigh_list.h"
|
|
#include "neigh_request.h"
|
|
#include "neighbor.h"
|
|
#include "potential_file_reader.h"
|
|
#include "suffix.h"
|
|
#include "tokenizer.h"
|
|
|
|
#include <cmath>
|
|
#include <cstring>
|
|
|
|
using namespace LAMMPS_NS;
|
|
using namespace MathConst;
|
|
using namespace MathSpecial;
|
|
using namespace MathExtra;
|
|
|
|
#define DELTA 4
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
PairTersoff::PairTersoff(LAMMPS *lmp) : Pair(lmp)
|
|
{
|
|
single_enable = 0;
|
|
restartinfo = 0;
|
|
one_coeff = 1;
|
|
manybody_flag = 1;
|
|
centroidstressflag = CENTROID_NOTAVAIL;
|
|
unit_convert_flag = utils::get_supported_conversions(utils::ENERGY);
|
|
|
|
params = nullptr;
|
|
|
|
maxshort = 10;
|
|
neighshort = nullptr;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
check if allocated, since class can be destructed when incomplete
|
|
------------------------------------------------------------------------- */
|
|
|
|
PairTersoff::~PairTersoff()
|
|
{
|
|
if (copymode) return;
|
|
|
|
memory->destroy(params);
|
|
memory->destroy(elem3param);
|
|
|
|
if (allocated) {
|
|
memory->destroy(setflag);
|
|
memory->destroy(cutsq);
|
|
memory->destroy(neighshort);
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void PairTersoff::compute(int eflag, int vflag)
|
|
{
|
|
ev_init(eflag,vflag);
|
|
|
|
if (shift_flag) {
|
|
if (evflag) {
|
|
if (eflag) {
|
|
if (vflag_either) eval<1,1,1,1>();
|
|
else eval<1,1,1,0>();
|
|
} else {
|
|
if (vflag_either) eval<1,1,0,1>();
|
|
else eval<1,1,0,0>();
|
|
}
|
|
} else eval<1,0,0,0>();
|
|
|
|
} else {
|
|
|
|
if (evflag) {
|
|
if (eflag) {
|
|
if (vflag_either) eval<0,1,1,1>();
|
|
else eval<0,1,1,0>();
|
|
} else {
|
|
if (vflag_either) eval<0,1,0,1>();
|
|
else eval<0,1,0,0>();
|
|
}
|
|
} else eval<0,0,0,0>();
|
|
}
|
|
}
|
|
|
|
template <int SHIFT_FLAG, int EVFLAG, int EFLAG, int VFLAG_EITHER>
|
|
void PairTersoff::eval()
|
|
{
|
|
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 fforce;
|
|
double rsq,rsq1,rsq2;
|
|
double delr1[3],delr2[3],fi[3],fj[3],fk[3];
|
|
double r1_hat[3],r2_hat[3];
|
|
double zeta_ij,prefactor;
|
|
double forceshiftfac;
|
|
int *ilist,*jlist,*numneigh,**firstneigh;
|
|
|
|
evdwl = 0.0;
|
|
|
|
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;
|
|
const double cutshortsq = cutmax*cutmax;
|
|
|
|
inum = list->inum;
|
|
ilist = list->ilist;
|
|
numneigh = list->numneigh;
|
|
firstneigh = list->firstneigh;
|
|
|
|
double fxtmp,fytmp,fztmp;
|
|
|
|
// 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];
|
|
fxtmp = fytmp = fztmp = 0.0;
|
|
|
|
// two-body interactions, skip half of them
|
|
|
|
jlist = firstneigh[i];
|
|
jnum = numneigh[i];
|
|
int numshort = 0;
|
|
|
|
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;
|
|
|
|
// shift rsq and store correction for force
|
|
|
|
if (SHIFT_FLAG) {
|
|
double rsqtmp = rsq + shift*shift + 2*sqrt(rsq)*shift;
|
|
forceshiftfac = sqrt(rsqtmp/rsq);
|
|
rsq = rsqtmp;
|
|
}
|
|
|
|
if (rsq < cutshortsq) {
|
|
neighshort[numshort++] = j;
|
|
if (numshort >= maxshort) {
|
|
maxshort += maxshort/2;
|
|
memory->grow(neighshort,maxshort,"pair:neighshort");
|
|
}
|
|
}
|
|
|
|
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]];
|
|
iparam_ij = elem3param[itype][jtype][jtype];
|
|
if (rsq >= params[iparam_ij].cutsq) continue;
|
|
|
|
repulsive(¶ms[iparam_ij],rsq,fpair,EFLAG,evdwl);
|
|
|
|
// correct force for shift in rsq
|
|
|
|
if (SHIFT_FLAG) fpair *= forceshiftfac;
|
|
|
|
fxtmp += delx*fpair;
|
|
fytmp += dely*fpair;
|
|
fztmp += 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
|
|
// skip immediately if I-J is not within cutoff
|
|
double fjxtmp,fjytmp,fjztmp;
|
|
|
|
for (jj = 0; jj < numshort; jj++) {
|
|
j = neighshort[jj];
|
|
jtype = map[type[j]];
|
|
iparam_ij = elem3param[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 (SHIFT_FLAG)
|
|
rsq1 += shift*shift + 2*sqrt(rsq1)*shift;
|
|
|
|
if (rsq1 >= params[iparam_ij].cutsq) continue;
|
|
|
|
const double r1inv = 1.0/sqrt(dot3(delr1, delr1));
|
|
scale3(r1inv, delr1, r1_hat);
|
|
|
|
// accumulate bondorder zeta for each i-j interaction via loop over k
|
|
|
|
fjxtmp = fjytmp = fjztmp = 0.0;
|
|
zeta_ij = 0.0;
|
|
|
|
for (kk = 0; kk < numshort; kk++) {
|
|
if (jj == kk) continue;
|
|
k = neighshort[kk];
|
|
ktype = map[type[k]];
|
|
iparam_ijk = elem3param[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 (SHIFT_FLAG)
|
|
rsq2 += shift*shift + 2*sqrt(rsq2)*shift;
|
|
|
|
if (rsq2 >= params[iparam_ijk].cutsq) continue;
|
|
|
|
double r2inv = 1.0/sqrt(dot3(delr2, delr2));
|
|
scale3(r2inv, delr2, r2_hat);
|
|
|
|
zeta_ij += zeta(¶ms[iparam_ijk],rsq1,rsq2,r1_hat,r2_hat);
|
|
}
|
|
|
|
// pairwise force due to zeta
|
|
|
|
force_zeta(¶ms[iparam_ij],rsq1,zeta_ij,fforce,prefactor,EFLAG,evdwl);
|
|
|
|
fpair = fforce*r1inv;
|
|
|
|
fxtmp += delr1[0]*fpair;
|
|
fytmp += delr1[1]*fpair;
|
|
fztmp += delr1[2]*fpair;
|
|
fjxtmp -= delr1[0]*fpair;
|
|
fjytmp -= delr1[1]*fpair;
|
|
fjztmp -= 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 < numshort; kk++) {
|
|
if (jj == kk) continue;
|
|
k = neighshort[kk];
|
|
ktype = map[type[k]];
|
|
iparam_ijk = elem3param[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 (SHIFT_FLAG)
|
|
rsq2 += shift*shift + 2*sqrt(rsq2)*shift;
|
|
|
|
if (rsq2 >= params[iparam_ijk].cutsq) continue;
|
|
|
|
double r2inv = 1.0/sqrt(dot3(delr2, delr2));
|
|
scale3(r2inv, delr2, r2_hat);
|
|
|
|
attractive(¶ms[iparam_ijk],prefactor,
|
|
rsq1,rsq2,r1_hat,r2_hat,fi,fj,fk);
|
|
|
|
fxtmp += fi[0];
|
|
fytmp += fi[1];
|
|
fztmp += fi[2];
|
|
fjxtmp += fj[0];
|
|
fjytmp += fj[1];
|
|
fjztmp += fj[2];
|
|
f[k][0] += fk[0];
|
|
f[k][1] += fk[1];
|
|
f[k][2] += fk[2];
|
|
|
|
if (VFLAG_EITHER) v_tally3(i,j,k,fj,fk,delr1,delr2);
|
|
}
|
|
f[j][0] += fjxtmp;
|
|
f[j][1] += fjytmp;
|
|
f[j][2] += fjztmp;
|
|
}
|
|
f[i][0] += fxtmp;
|
|
f[i][1] += fytmp;
|
|
f[i][2] += fztmp;
|
|
}
|
|
|
|
if (vflag_fdotr) virial_fdotr_compute();
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void PairTersoff::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(neighshort,maxshort,"pair:neighshort");
|
|
map = new int[n+1];
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
global settings
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairTersoff::settings(int narg, char **arg)
|
|
{
|
|
|
|
// default values
|
|
|
|
shift_flag = 0;
|
|
|
|
// process optional keywords
|
|
|
|
int iarg = 0;
|
|
|
|
while (iarg < narg) {
|
|
if (strcmp(arg[iarg],"shift") == 0) {
|
|
if (suffix_flag & (Suffix::INTEL|Suffix::GPU|Suffix::KOKKOS))
|
|
error->all(FLERR,"Keyword 'shift' not supported for this style");
|
|
if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style command");
|
|
shift = utils::numeric(FLERR,arg[iarg+1],false,lmp);
|
|
shift_flag = 1;
|
|
iarg += 2;
|
|
} else error->all(FLERR,"Illegal pair_style command");
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
set coeffs for one or more type pairs
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairTersoff::coeff(int narg, char **arg)
|
|
{
|
|
if (!allocated) allocate();
|
|
|
|
map_element2type(narg-3,arg+3);
|
|
|
|
// read potential file and initialize potential parameters
|
|
|
|
read_file(arg[2]);
|
|
setup_params();
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
init specific to this pair style
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairTersoff::init_style()
|
|
{
|
|
if (atom->tag_enable == 0)
|
|
error->all(FLERR,"Pair style Tersoff requires atom IDs");
|
|
if (force->newton_pair == 0)
|
|
error->all(FLERR,"Pair style Tersoff 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 PairTersoff::init_one(int i, int j)
|
|
{
|
|
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
|
|
|
|
return cutmax;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void PairTersoff::read_file(char *file)
|
|
{
|
|
memory->sfree(params);
|
|
params = nullptr;
|
|
nparams = maxparam = 0;
|
|
|
|
// open file on proc 0
|
|
|
|
if (comm->me == 0) {
|
|
PotentialFileReader reader(lmp, file, "tersoff", unit_convert_flag);
|
|
char *line;
|
|
|
|
// transparently convert units for supported conversions
|
|
|
|
int unit_convert = reader.get_unit_convert();
|
|
double conversion_factor = utils::get_conversion_factor(utils::ENERGY,
|
|
unit_convert);
|
|
while ((line = reader.next_line(NPARAMS_PER_LINE))) {
|
|
try {
|
|
ValueTokenizer values(line);
|
|
|
|
std::string iname = values.next_string();
|
|
std::string jname = values.next_string();
|
|
std::string kname = values.next_string();
|
|
|
|
// ielement,jelement,kelement = 1st args
|
|
// if all 3 args are in element list, then parse this line
|
|
// else skip to next entry in file
|
|
int ielement, jelement, kelement;
|
|
|
|
for (ielement = 0; ielement < nelements; ielement++)
|
|
if (iname == elements[ielement]) break;
|
|
if (ielement == nelements) continue;
|
|
for (jelement = 0; jelement < nelements; jelement++)
|
|
if (jname == elements[jelement]) break;
|
|
if (jelement == nelements) continue;
|
|
for (kelement = 0; kelement < nelements; kelement++)
|
|
if (kname == elements[kelement]) 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");
|
|
|
|
// make certain all addional allocated storage is initialized
|
|
// to avoid false positives when checking with valgrind
|
|
|
|
memset(params + nparams, 0, DELTA*sizeof(Param));
|
|
}
|
|
|
|
params[nparams].ielement = ielement;
|
|
params[nparams].jelement = jelement;
|
|
params[nparams].kelement = kelement;
|
|
params[nparams].powerm = values.next_double();
|
|
params[nparams].gamma = values.next_double();
|
|
params[nparams].lam3 = values.next_double();
|
|
params[nparams].c = values.next_double();
|
|
params[nparams].d = values.next_double();
|
|
params[nparams].h = values.next_double();
|
|
params[nparams].powern = values.next_double();
|
|
params[nparams].beta = values.next_double();
|
|
params[nparams].lam2 = values.next_double();
|
|
params[nparams].bigb = values.next_double();
|
|
params[nparams].bigr = values.next_double();
|
|
params[nparams].bigd = values.next_double();
|
|
params[nparams].lam1 = values.next_double();
|
|
params[nparams].biga = values.next_double();
|
|
params[nparams].powermint = int(params[nparams].powerm);
|
|
|
|
if (unit_convert) {
|
|
params[nparams].biga *= conversion_factor;
|
|
params[nparams].bigb *= conversion_factor;
|
|
}
|
|
} catch (TokenizerException &e) {
|
|
error->one(FLERR, e.what());
|
|
}
|
|
|
|
// currently only allow m exponent of 1 or 3
|
|
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->one(FLERR,"Illegal Tersoff parameter");
|
|
|
|
nparams++;
|
|
}
|
|
}
|
|
|
|
MPI_Bcast(&nparams, 1, MPI_INT, 0, world);
|
|
MPI_Bcast(&maxparam, 1, MPI_INT, 0, world);
|
|
|
|
if (comm->me != 0) {
|
|
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), "pair:params");
|
|
}
|
|
|
|
MPI_Bcast(params, maxparam*sizeof(Param), MPI_BYTE, 0, world);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void PairTersoff::setup_params()
|
|
{
|
|
int i,j,k,m,n;
|
|
|
|
// set elem3param 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(elem3param);
|
|
memory->create(elem3param,nelements,nelements,nelements,"pair:elem3param");
|
|
|
|
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");
|
|
elem3param[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;
|
|
|
|
if (params[m].powern > 0.0) {
|
|
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;
|
|
} else {
|
|
params[m].c1 = params[m].c2 = params[m].c3 = params[m].c4 = 0.0;
|
|
}
|
|
}
|
|
|
|
// 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 PairTersoff::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 PairTersoff::zeta(Param *param, double rsqij, double rsqik,
|
|
double *rij_hat, double *rik_hat)
|
|
{
|
|
double rij,rik,costheta,arg,ex_delr;
|
|
|
|
rij = sqrt(rsqij);
|
|
rik = sqrt(rsqik);
|
|
costheta = dot3(rij_hat,rik_hat);
|
|
|
|
if (param->powermint == 3) arg = cube(param->lam3 * (rij-rik));
|
|
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 PairTersoff::force_zeta(Param *param, double rsq, double zeta_ij,
|
|
double &fforce, double &prefactor,
|
|
int eflag, double &eng)
|
|
{
|
|
double r,fa,fa_d,bij;
|
|
|
|
r = sqrt(rsq);
|
|
fa = ters_fa(r,param);
|
|
fa_d = ters_fa_d(r,param);
|
|
bij = ters_bij(zeta_ij,param);
|
|
fforce = 0.5*bij*fa_d;
|
|
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 PairTersoff::attractive(Param *param, double prefactor,
|
|
double rsqij, double rsqik,
|
|
double *rij_hat, double *rik_hat,
|
|
double *fi, double *fj, double *fk)
|
|
{
|
|
double rij,rijinv,rik,rikinv;
|
|
|
|
rij = sqrt(rsqij);
|
|
rik = sqrt(rsqik);
|
|
|
|
// correct 1/r for shift in rsq
|
|
|
|
if (shift_flag == 1) {
|
|
rijinv = 1.0/(rij - shift);
|
|
rikinv = 1.0/(rik - shift);
|
|
} else {
|
|
rijinv = 1.0/rij;
|
|
rikinv = 1.0/rik;
|
|
}
|
|
|
|
ters_zetaterm_d(prefactor,rij_hat,rij,rijinv,rik_hat,rik,rikinv,fi,fj,fk,param);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
double PairTersoff::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 PairTersoff::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 PairTersoff::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 PairTersoff::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 PairTersoff::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 PairTersoff::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) *
|
|
// error in negligible 2nd term fixed 9/30/2015
|
|
// (1.0 - 0.5*(1.0 + 1.0/(2.0*param->powern)) *
|
|
(1.0 - (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 PairTersoff::ters_zetaterm_d(double prefactor,
|
|
double *rij_hat, double rij, double rijinv,
|
|
double *rik_hat, double rik, double rikinv,
|
|
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 = cube(param->lam3 * (rij-rik));
|
|
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*cube(param->lam3) * square(rij-rik)*ex_delr;
|
|
else ex_delr_d = param->lam3 * ex_delr;
|
|
|
|
cos_theta = dot3(rij_hat,rik_hat);
|
|
gijk = ters_gijk(cos_theta,param);
|
|
gijk_d = ters_gijk_d(cos_theta,param);
|
|
costheta_d(rij_hat,rijinv,rik_hat,rikinv,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);
|
|
|
|
scale3(-dfc*gijk*ex_delr,rik_hat,dri);
|
|
scaleadd3(fc*gijk_d*ex_delr,dcosdri,dri,dri);
|
|
scaleadd3(fc*gijk*ex_delr_d,rik_hat,dri,dri);
|
|
scaleadd3(-fc*gijk*ex_delr_d,rij_hat,dri,dri);
|
|
scale3(prefactor,dri);
|
|
|
|
// compute the derivative wrt Rj
|
|
// drj = fc*gijk_d*ex_delr*dcosdrj;
|
|
// drj += fc*gijk*ex_delr_d*rij_hat;
|
|
|
|
scale3(fc*gijk_d*ex_delr,dcosdrj,drj);
|
|
scaleadd3(fc*gijk*ex_delr_d,rij_hat,drj,drj);
|
|
scale3(prefactor,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;
|
|
|
|
scale3(dfc*gijk*ex_delr,rik_hat,drk);
|
|
scaleadd3(fc*gijk_d*ex_delr,dcosdrk,drk,drk);
|
|
scaleadd3(-fc*gijk*ex_delr_d,rik_hat,drk,drk);
|
|
scale3(prefactor,drk);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void PairTersoff::costheta_d(double *rij_hat, double rijinv,
|
|
double *rik_hat, double rikinv,
|
|
double *dri, double *drj, double *drk)
|
|
{
|
|
// first element is devative wrt Ri, second wrt Rj, third wrt Rk
|
|
|
|
double cos_theta = dot3(rij_hat,rik_hat);
|
|
|
|
scaleadd3(-cos_theta,rij_hat,rik_hat,drj);
|
|
scale3(rijinv,drj);
|
|
scaleadd3(-cos_theta,rik_hat,rij_hat,drk);
|
|
scale3(rikinv,drk,drk);
|
|
add3(drj,drk,dri);
|
|
scale3(-1.0,dri);
|
|
}
|