336 lines
11 KiB
C++
336 lines
11 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Aidan Thompson (SNL) - original Tersoff implementation
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Vitaly Dozhdikov (JIHT of RAS) - MOD addition
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------------------------------------------------------------------------- */
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#include "pair_tersoff_mod.h"
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#include "comm.h"
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#include "error.h"
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#include "math_const.h"
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#include "math_special.h"
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#include "memory.h"
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#include "potential_file_reader.h"
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#include "tokenizer.h"
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#include <cmath>
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#include <cstring>
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using namespace LAMMPS_NS;
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using namespace MathConst;
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using namespace MathSpecial;
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#define DELTA 4
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/* ---------------------------------------------------------------------- */
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PairTersoffMOD::PairTersoffMOD(LAMMPS *lmp) : PairTersoff(lmp) {}
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/* ---------------------------------------------------------------------- */
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void PairTersoffMOD::read_file(char *file)
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{
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memory->sfree(params);
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params = nullptr;
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nparams = maxparam = 0;
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// open file on proc 0
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if (comm->me == 0) {
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PotentialFileReader reader(lmp, file, "tersoff/mod", unit_convert_flag);
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char * line;
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// transparently convert units for supported conversions
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int unit_convert = reader.get_unit_convert();
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double conversion_factor = utils::get_conversion_factor(utils::ENERGY,
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unit_convert);
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while((line = reader.next_line(NPARAMS_PER_LINE))) {
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try {
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ValueTokenizer values(line);
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std::string iname = values.next_string();
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std::string jname = values.next_string();
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std::string kname = values.next_string();
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// ielement,jelement,kelement = 1st args
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// if all 3 args are in element list, then parse this line
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// else skip to next entry in file
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int ielement, jelement, kelement;
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for (ielement = 0; ielement < nelements; ielement++)
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if (iname == elements[ielement]) break;
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if (ielement == nelements) continue;
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for (jelement = 0; jelement < nelements; jelement++)
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if (jname == elements[jelement]) break;
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if (jelement == nelements) continue;
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for (kelement = 0; kelement < nelements; kelement++)
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if (kname == elements[kelement]) break;
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if (kelement == nelements) continue;
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// load up parameter settings and error check their values
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if (nparams == maxparam) {
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maxparam += DELTA;
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params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
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"pair:params");
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// make certain all addional allocated storage is initialized
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// to avoid false positives when checking with valgrind
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memset(params + nparams, 0, DELTA*sizeof(Param));
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}
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params[nparams].ielement = ielement;
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params[nparams].jelement = jelement;
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params[nparams].kelement = kelement;
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params[nparams].powerm = values.next_double();
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params[nparams].lam3 = values.next_double();
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params[nparams].h = values.next_double();
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params[nparams].powern = values.next_double();
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params[nparams].beta = values.next_double();
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params[nparams].lam2 = values.next_double();
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params[nparams].bigb = values.next_double();
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params[nparams].bigr = values.next_double();
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params[nparams].bigd = values.next_double();
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params[nparams].lam1 = values.next_double();
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params[nparams].biga = values.next_double();
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params[nparams].powern_del = values.next_double();
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params[nparams].c1 = values.next_double();
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params[nparams].c2 = values.next_double();
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params[nparams].c3 = values.next_double();
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params[nparams].c4 = values.next_double();
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params[nparams].c5 = values.next_double();
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params[nparams].powermint = int(params[nparams].powerm);
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if (unit_convert) {
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params[nparams].biga *= conversion_factor;
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params[nparams].bigb *= conversion_factor;
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}
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} catch (TokenizerException & e) {
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error->one(FLERR, e.what());
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}
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// currently only allow m exponent of 1 or 3
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if (params[nparams].powern < 0.0 ||
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params[nparams].beta < 0.0 ||
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params[nparams].lam2 < 0.0 ||
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params[nparams].bigb < 0.0 ||
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params[nparams].bigr < 0.0 ||
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params[nparams].bigd < 0.0 ||
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params[nparams].bigd > params[nparams].bigr ||
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params[nparams].lam1 < 0.0 ||
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params[nparams].biga < 0.0 ||
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params[nparams].powerm - params[nparams].powermint != 0.0 ||
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(params[nparams].powermint != 3 &&
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params[nparams].powermint != 1)
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)
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error->one(FLERR,"Illegal Tersoff parameter");
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nparams++;
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}
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}
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MPI_Bcast(&nparams, 1, MPI_INT, 0, world);
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MPI_Bcast(&maxparam, 1, MPI_INT, 0, world);
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if(comm->me != 0) {
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params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), "pair:params");
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}
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MPI_Bcast(params, maxparam*sizeof(Param), MPI_BYTE, 0, world);
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}
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/* ---------------------------------------------------------------------- */
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void PairTersoffMOD::setup_params()
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{
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int i,j,k,m,n;
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// set elem2param for all element triplet combinations
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// must be a single exact match to lines read from file
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// do not allow for ACB in place of ABC
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memory->destroy(elem2param);
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memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param");
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for (i = 0; i < nelements; i++)
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for (j = 0; j < nelements; j++)
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for (k = 0; k < nelements; k++) {
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n = -1;
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for (m = 0; m < nparams; m++) {
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if (i == params[m].ielement && j == params[m].jelement &&
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k == params[m].kelement) {
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if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
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n = m;
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}
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}
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if (n < 0) error->all(FLERR,"Potential file is missing an entry");
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elem2param[i][j][k] = n;
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}
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// compute parameter values derived from inputs
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for (m = 0; m < nparams; m++) {
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params[m].cut = params[m].bigr + params[m].bigd;
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params[m].cutsq = params[m].cut*params[m].cut;
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if (params[m].powern > 0.0) {
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params[m].ca1 = pow(2.0*params[m].powern_del*1.0e-16,-1.0/params[m].powern);
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params[m].ca4 = 1.0/params[m].ca1;
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} else params[m].ca1 = params[m].ca4 = 0.0;
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}
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// set cutmax to max of all params
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cutmax = 0.0;
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for (m = 0; m < nparams; m++)
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if (params[m].cut > cutmax) cutmax = params[m].cut;
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}
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/* ---------------------------------------------------------------------- */
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double PairTersoffMOD::zeta(Param *param, double rsqij, double rsqik,
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double *delrij, double *delrik)
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{
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double rij,rik,costheta,arg,ex_delr;
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rij = sqrt(rsqij);
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rik = sqrt(rsqik);
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costheta = (delrij[0]*delrik[0] + delrij[1]*delrik[1] +
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delrij[2]*delrik[2]) / (rij*rik);
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if (param->powermint == 3) arg = cube(param->lam3 * (rij-rik));
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else arg = param->lam3 * (rij-rik);
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if (arg > 69.0776) ex_delr = 1.e30;
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else if (arg < -69.0776) ex_delr = 0.0;
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else ex_delr = exp(arg);
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return ters_fc(rik,param) * ters_gijk_mod(costheta,param) * ex_delr;
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}
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/* ---------------------------------------------------------------------- */
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double PairTersoffMOD::ters_fc(double r, Param *param)
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{
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double ters_R = param->bigr;
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double ters_D = param->bigd;
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if (r < ters_R-ters_D) return 1.0;
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if (r > ters_R+ters_D) return 0.0;
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return 0.5*(1.0 - 1.125*sin(MY_PI2*(r - ters_R)/ters_D) -
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0.125*sin(3*MY_PI2*(r - ters_R)/ters_D));
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}
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/* ---------------------------------------------------------------------- */
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double PairTersoffMOD::ters_fc_d(double r, Param *param)
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{
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double ters_R = param->bigr;
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double ters_D = param->bigd;
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if (r < ters_R-ters_D) return 0.0;
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if (r > ters_R+ters_D) return 0.0;
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return -(0.375*MY_PI4/ters_D) * (3*cos(MY_PI2*(r - ters_R)/ters_D) +
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cos(3*MY_PI2*(r - ters_R)/ters_D));
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}
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/* ---------------------------------------------------------------------- */
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double PairTersoffMOD::ters_bij(double zeta, Param *param)
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{
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double tmp = param->beta * zeta;
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if (tmp > param->ca1) return pow(tmp, -param->powern/(2.0*param->powern_del));
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if (tmp < param->ca4) return 1.0;
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return pow(1.0 + pow(tmp,param->powern), -1.0/(2.0*param->powern_del));
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}
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/* ---------------------------------------------------------------------- */
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double PairTersoffMOD::ters_bij_d(double zeta, Param *param)
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{
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double tmp = param->beta * zeta;
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if (tmp > param->ca1) return -0.5*(param->powern/param->powern_del)*
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pow(tmp,-0.5*(param->powern/param->powern_del)) / zeta;
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if (tmp < param->ca4) return 0.0;
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double tmp_n = pow(tmp,param->powern);
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return -0.5 *(param->powern/param->powern_del)*
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pow(1.0+tmp_n, -1.0-(1.0/(2.0*param->powern_del)))*tmp_n / zeta;
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}
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/* ---------------------------------------------------------------------- */
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void PairTersoffMOD::ters_zetaterm_d(double prefactor,
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double *rij_hat, double rij,
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double *rik_hat, double rik,
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double *dri, double *drj, double *drk,
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Param *param)
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{
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double gijk,gijk_d,ex_delr,ex_delr_d,fc,dfc,cos_theta,tmp;
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double dcosdri[3],dcosdrj[3],dcosdrk[3];
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fc = ters_fc(rik,param);
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dfc = ters_fc_d(rik,param);
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if (param->powermint == 3) tmp = cube(param->lam3 * (rij-rik));
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else tmp = param->lam3 * (rij-rik);
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if (tmp > 69.0776) ex_delr = 1.e30;
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else if (tmp < -69.0776) ex_delr = 0.0;
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else ex_delr = exp(tmp);
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if (param->powermint == 3)
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ex_delr_d = 3.0*cube(param->lam3) * square(rij-rik)*ex_delr;
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else ex_delr_d = param->lam3 * ex_delr;
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cos_theta = vec3_dot(rij_hat,rik_hat);
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gijk = ters_gijk_mod(cos_theta,param);
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gijk_d = ters_gijk_d_mod(cos_theta,param);
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costheta_d(rij_hat,rij,rik_hat,rik,dcosdri,dcosdrj,dcosdrk);
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// compute the derivative wrt Ri
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// dri = -dfc*gijk*ex_delr*rik_hat;
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// dri += fc*gijk_d*ex_delr*dcosdri;
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// dri += fc*gijk*ex_delr_d*(rik_hat - rij_hat);
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vec3_scale(-dfc*gijk*ex_delr,rik_hat,dri);
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vec3_scaleadd(fc*gijk_d*ex_delr,dcosdri,dri,dri);
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vec3_scaleadd(fc*gijk*ex_delr_d,rik_hat,dri,dri);
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vec3_scaleadd(-fc*gijk*ex_delr_d,rij_hat,dri,dri);
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vec3_scale(prefactor,dri,dri);
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// compute the derivative wrt Rj
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// drj = fc*gijk_d*ex_delr*dcosdrj;
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// drj += fc*gijk*ex_delr_d*rij_hat;
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vec3_scale(fc*gijk_d*ex_delr,dcosdrj,drj);
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vec3_scaleadd(fc*gijk*ex_delr_d,rij_hat,drj,drj);
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vec3_scale(prefactor,drj,drj);
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// compute the derivative wrt Rk
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// drk = dfc*gijk*ex_delr*rik_hat;
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// drk += fc*gijk_d*ex_delr*dcosdrk;
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// drk += -fc*gijk*ex_delr_d*rik_hat;
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vec3_scale(dfc*gijk*ex_delr,rik_hat,drk);
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vec3_scaleadd(fc*gijk_d*ex_delr,dcosdrk,drk,drk);
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vec3_scaleadd(-fc*gijk*ex_delr_d,rik_hat,drk,drk);
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vec3_scale(prefactor,drk,drk);
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}
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