674 lines
20 KiB
C++
674 lines
20 KiB
C++
// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, 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: German Samolyuk (ORNL)
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based on PairTersoff by Aidan Thompson (SNL)
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------------------------------------------------------------------------- */
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#include "pair_gw.h"
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#include "atom.h"
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#include "comm.h"
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#include "error.h"
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#include "force.h"
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#include "math_const.h"
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#include "math_extra.h"
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#include "memory.h"
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#include "neigh_list.h"
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#include "neigh_request.h"
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#include "neighbor.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 MathExtra;
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#define DELTA 4
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/* ---------------------------------------------------------------------- */
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PairGW::PairGW(LAMMPS *lmp) : Pair(lmp)
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{
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single_enable = 0;
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restartinfo = 0;
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one_coeff = 1;
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manybody_flag = 1;
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centroidstressflag = CENTROID_NOTAVAIL;
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unit_convert_flag = utils::get_supported_conversions(utils::ENERGY);
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params = nullptr;
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}
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/* ----------------------------------------------------------------------
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check if allocated, since class can be destructed when incomplete
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------------------------------------------------------------------------- */
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PairGW::~PairGW()
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{
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memory->destroy(params);
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memory->destroy(elem3param);
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(cutsq);
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairGW::compute(int eflag, int vflag)
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{
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int i,j,k,ii,jj,kk,inum,jnum;
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int itag,jtag,itype,jtype,ktype,iparam_ij,iparam_ijk;
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double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
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double rsq,rsq1,rsq2;
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double delr1[3],delr2[3],fi[3],fj[3],fk[3];
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double zeta_ij, prefactor;
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int *ilist,*jlist,*numneigh,**firstneigh;
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evdwl = 0.0;
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ev_init(eflag,vflag);
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double **x = atom->x;
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double **f = atom->f;
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tagint *tag = atom->tag;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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int newton_pair = force->newton_pair;
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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// loop over full neighbor list of my atoms
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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itag = tag[i];
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itype = map[type[i]];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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// two-body interactions, skip half of them
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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jtag = tag[j];
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if (itag > jtag) {
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if ((itag+jtag) % 2 == 0) continue;
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} else if (itag < jtag) {
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if ((itag+jtag) % 2 == 1) continue;
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} else {
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if (x[j][2] < x[i][2]) continue;
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if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
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if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
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}
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jtype = map[type[j]];
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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iparam_ij = elem3param[itype][jtype][jtype];
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if (rsq > params[iparam_ij].cutsq) continue;
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repulsive(¶ms[iparam_ij],rsq,fpair,eflag,evdwl);
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f[i][0] += delx*fpair;
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f[i][1] += dely*fpair;
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f[i][2] += delz*fpair;
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f[j][0] -= delx*fpair;
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f[j][1] -= dely*fpair;
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f[j][2] -= delz*fpair;
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if (evflag) ev_tally(i,j,nlocal,newton_pair,
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evdwl,0.0,fpair,delx,dely,delz);
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}
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// three-body interactions
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// skip immediately if I-J is not within cutoff
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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jtype = map[type[j]];
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iparam_ij = elem3param[itype][jtype][jtype];
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delr1[0] = x[j][0] - xtmp;
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delr1[1] = x[j][1] - ytmp;
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delr1[2] = x[j][2] - ztmp;
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rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
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if (rsq1 > params[iparam_ij].cutsq) continue;
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// accumulate bondorder zeta for each i-j interaction via loop over k
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zeta_ij = 1.0;
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for (kk = 0; kk < jnum; kk++) {
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if (jj == kk) continue;
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k = jlist[kk];
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k &= NEIGHMASK;
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ktype = map[type[k]];
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iparam_ijk = elem3param[itype][jtype][ktype];
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delr2[0] = x[k][0] - xtmp;
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delr2[1] = x[k][1] - ytmp;
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delr2[2] = x[k][2] - ztmp;
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rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
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if (rsq2 > params[iparam_ijk].cutsq) continue;
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zeta_ij += zeta(¶ms[iparam_ijk],rsq1,rsq2,delr1,delr2);
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}
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// pairwise force due to zeta
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force_zeta(¶ms[iparam_ij],rsq1,zeta_ij,fpair,prefactor,eflag,evdwl);
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f[i][0] += delr1[0]*fpair;
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f[i][1] += delr1[1]*fpair;
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f[i][2] += delr1[2]*fpair;
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f[j][0] -= delr1[0]*fpair;
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f[j][1] -= delr1[1]*fpair;
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f[j][2] -= delr1[2]*fpair;
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if (evflag) ev_tally(i,j,nlocal,newton_pair,
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evdwl,0.0,-fpair,-delr1[0],-delr1[1],-delr1[2]);
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// attractive term via loop over k
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for (kk = 0; kk < jnum; kk++) {
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if (jj == kk) continue;
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k = jlist[kk];
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k &= NEIGHMASK;
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ktype = map[type[k]];
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iparam_ijk = elem3param[itype][jtype][ktype];
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delr2[0] = x[k][0] - xtmp;
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delr2[1] = x[k][1] - ytmp;
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delr2[2] = x[k][2] - ztmp;
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rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
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if (rsq2 > params[iparam_ijk].cutsq) continue;
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attractive(¶ms[iparam_ijk],prefactor,
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rsq1,rsq2,delr1,delr2,fi,fj,fk);
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f[i][0] += fi[0];
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f[i][1] += fi[1];
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f[i][2] += fi[2];
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f[j][0] += fj[0];
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f[j][1] += fj[1];
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f[j][2] += fj[2];
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f[k][0] += fk[0];
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f[k][1] += fk[1];
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f[k][2] += fk[2];
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if (vflag_either) v_tally3(i,j,k,fj,fk,delr1,delr2);
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} // kk
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} // jj
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} // ii
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if (vflag_fdotr) virial_fdotr_compute();
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}
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/* ---------------------------------------------------------------------- */
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void PairGW::allocate()
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{
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allocated = 1;
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int n = atom->ntypes;
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memory->create(setflag,n+1,n+1,"pair:setflag");
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memory->create(cutsq,n+1,n+1,"pair:cutsq");
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map = new int[n+1];
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}
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/* ----------------------------------------------------------------------
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global settings
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------------------------------------------------------------------------- */
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void PairGW::settings(int narg, char **/*arg*/)
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{
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if (narg != 0) error->all(FLERR,"Illegal pair_style command");
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}
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/* ----------------------------------------------------------------------
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set coeffs for one or more type pairs
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------------------------------------------------------------------------- */
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void PairGW::coeff(int narg, char **arg)
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{
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if (!allocated) allocate();
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map_element2type(narg-3,arg+3);
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// read potential file and initialize potential parameters
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read_file(arg[2]);
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setup_params();
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}
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/* ----------------------------------------------------------------------
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init specific to this pair style
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------------------------------------------------------------------------- */
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void PairGW::init_style()
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{
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if (atom->tag_enable == 0)
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error->all(FLERR,"Pair style GW requires atom IDs");
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if (force->newton_pair == 0)
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error->all(FLERR,"Pair style GW requires newton pair on");
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// need a full neighbor list
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int irequest = neighbor->request(this,instance_me);
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neighbor->requests[irequest]->half = 0;
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neighbor->requests[irequest]->full = 1;
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}
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/* ----------------------------------------------------------------------
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init for one type pair i,j and corresponding j,i
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------------------------------------------------------------------------- */
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double PairGW::init_one(int i, int j)
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{
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if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
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return cutmax;
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}
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/* ---------------------------------------------------------------------- */
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void PairGW::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, "gw", 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].gamma = values.next_double();
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params[nparams].lam3 = values.next_double();
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params[nparams].c = values.next_double();
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params[nparams].d = 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].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].c < 0.0 || params[nparams].d < 0.0 ||
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params[nparams].powern < 0.0 || params[nparams].beta < 0.0 ||
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params[nparams].lam2 < 0.0 || params[nparams].bigb < 0.0 ||
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params[nparams].bigr < 0.0 ||params[nparams].bigd < 0.0 ||
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params[nparams].bigd > params[nparams].bigr ||
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params[nparams].lam1 < 0.0 || 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 && params[nparams].powermint != 1) ||
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params[nparams].gamma < 0.0)
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error->one(FLERR,"Illegal GW 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 PairGW::setup_params()
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{
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int i,j,k,m,n;
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// set elem3param 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(elem3param);
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memory->create(elem3param,nelements,nelements,nelements,"pair:elem3param");
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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)
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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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elem3param[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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params[m].c1 = pow(2.0*params[m].powern*1.0e-16,-1.0/params[m].powern);
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params[m].c2 = pow(2.0*params[m].powern*1.0e-8,-1.0/params[m].powern);
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params[m].c3 = 1.0/params[m].c2;
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params[m].c4 = 1.0/params[m].c1;
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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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void PairGW::repulsive(Param *param, double rsq, double &fforce,
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int eflag, double &eng)
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{
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double r,tmp_fc,tmp_fc_d,tmp_exp;
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r = sqrt(rsq);
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tmp_fc = gw_fc(r,param);
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tmp_fc_d = gw_fc_d(r,param);
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tmp_exp = exp(-param->lam1 * r);
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fforce = -param->biga * tmp_exp * (tmp_fc_d - tmp_fc*param->lam1) / r;
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if (eflag) eng = tmp_fc * param->biga * tmp_exp;
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}
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/* ---------------------------------------------------------------------- */
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double PairGW::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 = pow(param->lam3 * (rij-rik),3.0);
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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;
|
|
else ex_delr = exp(arg);
|
|
|
|
return gw_fc(rik,param) * gw_gijk(costheta,param) * ex_delr;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void PairGW::force_zeta(Param *param_i, double rsq, double zeta_ij,
|
|
double &fforce, double &prefactor,
|
|
int eflag, double &eng)
|
|
{
|
|
double r,fa,fa_d,bij;
|
|
|
|
r = sqrt(rsq);
|
|
fa = gw_fa(r,param_i);
|
|
fa_d = gw_fa_d(r,param_i);
|
|
bij = gw_bij(zeta_ij,param_i);
|
|
fforce = 0.5*bij*fa_d / r;
|
|
prefactor = -0.5*fa * gw_bij_d(zeta_ij,param_i);
|
|
if (eflag) eng = 0.5*bij*fa;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
attractive term
|
|
use param_ij cutoff for rij test
|
|
use param_ijk cutoff for rik test
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairGW::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;
|
|
scale3(rijinv,delrij,rij_hat);
|
|
|
|
rik = sqrt(rsqik);
|
|
rikinv = 1.0/rik;
|
|
scale3(rikinv,delrik,rik_hat);
|
|
|
|
gw_zetaterm_d(prefactor,rij_hat,rij,rik_hat,rik,fi,fj,fk,param);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
double PairGW::gw_fc(double r, Param *param)
|
|
{
|
|
double gw_R = param->bigr;
|
|
double gw_D = param->bigd;
|
|
|
|
if (r < gw_R-gw_D) return 1.0;
|
|
if (r > gw_R+gw_D) return 0.0;
|
|
return 0.5*(1.0 - sin(MY_PI2*(r - gw_R)/gw_D));
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
double PairGW::gw_fc_d(double r, Param *param)
|
|
{
|
|
double gw_R = param->bigr;
|
|
double gw_D = param->bigd;
|
|
|
|
if (r < gw_R-gw_D) return 0.0;
|
|
if (r > gw_R+gw_D) return 0.0;
|
|
return -(MY_PI4/gw_D) * cos(MY_PI2*(r - gw_R)/gw_D);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
double PairGW::gw_fa(double r, Param *param)
|
|
{
|
|
if (r > param->bigr + param->bigd) return 0.0;
|
|
return -param->bigb * exp(-param->lam2 * r) * gw_fc(r,param);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
double PairGW::gw_fa_d(double r, Param *param)
|
|
{
|
|
if (r > param->bigr + param->bigd) return 0.0;
|
|
return param->bigb * exp(-param->lam2 * r) *
|
|
(param->lam2 * gw_fc(r,param) - gw_fc_d(r,param));
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
double PairGW::gw_bij(double zeta_ij, Param *param_i)
|
|
{
|
|
double tmp = param_i->beta * zeta_ij;
|
|
return pow(tmp,-param_i->powern);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
double PairGW::gw_bij_d(double zeta_ij, Param *param_i)
|
|
{
|
|
double tmp = param_i->beta * zeta_ij;
|
|
return - param_i->powern * pow(tmp,-param_i->powern-1)*tmp / zeta_ij;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void PairGW::gw_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 = gw_fc(rik,param);
|
|
dfc = gw_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 = dot3(rij_hat,rik_hat);
|
|
gijk = gw_gijk(cos_theta,param);
|
|
gijk_d = gw_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);
|
|
|
|
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 PairGW::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 = dot3(rij_hat,rik_hat);
|
|
|
|
scaleadd3(-cos_theta,rij_hat,rik_hat,drj);
|
|
scale3(1.0/rij,drj);
|
|
scaleadd3(-cos_theta,rik_hat,rij_hat,drk);
|
|
scale3(1.0/rik,drk);
|
|
add3(drj,drk,dri);
|
|
scale3(-1.0,dri);
|
|
}
|