1002 lines
34 KiB
C++
1002 lines
34 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: Luca Ferraro (CASPUR)
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email: luca.ferraro@caspur.it
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Tersoff Potential
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References: (referenced as tersoff_2 functional form in LAMMPS manual)
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1) Tersoff, Phys. Rev. B 39, 5566 (1988)
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------------------------------------------------------------------------- */
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#include "pair_tersoff_table.h"
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#include <cmath>
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#include <cstring>
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#include "atom.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "neigh_request.h"
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#include "force.h"
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#include "comm.h"
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#include "memory.h"
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#include "tokenizer.h"
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#include "potential_file_reader.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define MAXLINE 1024
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#define DELTA 4
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#define GRIDSTART 0.1
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#define GRIDDENSITY_FCUTOFF 5000
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#define GRIDDENSITY_EXP 12000
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#define GRIDDENSITY_GTETA 12000
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#define GRIDDENSITY_BIJ 7500
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// max number of interaction per atom for environment potential
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#define leadingDimensionInteractionList 64
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/* ---------------------------------------------------------------------- */
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PairTersoffTable::PairTersoffTable(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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unit_convert_flag = utils::get_supported_conversions(utils::ENERGY);
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nelements = 0;
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elements = nullptr;
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nparams = maxparam = 0;
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params = nullptr;
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elem2param = nullptr;
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allocated = 0;
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preGtetaFunction = preGtetaFunctionDerived = nullptr;
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preCutoffFunction = preCutoffFunctionDerived = nullptr;
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exponential = nullptr;
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gtetaFunction = nullptr;
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gtetaFunctionDerived = nullptr;
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cutoffFunction = nullptr;
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cutoffFunctionDerived = nullptr;
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betaZetaPower = nullptr;
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betaZetaPowerDerived = 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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PairTersoffTable::~PairTersoffTable()
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{
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if (elements)
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for (int i = 0; i < nelements; i++) delete [] elements[i];
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delete [] elements;
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memory->destroy(params);
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memory->destroy(elem2param);
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(cutsq);
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delete [] map;
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}
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deallocateGrids();
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deallocatePreLoops();
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}
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/* ---------------------------------------------------------------------- */
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void PairTersoffTable::compute(int eflag, int vflag)
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{
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int i,j,k,ii,inum,jnum;
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int itype,jtype,ktype,ijparam,ikparam,ijkparam;
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double xtmp,ytmp,ztmp;
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double fxtmp,fytmp,fztmp;
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int *ilist,*jlist,*numneigh,**firstneigh;
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int interpolIDX;
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double directorCos_ij_x, directorCos_ij_y, directorCos_ij_z, directorCos_ik_x, directorCos_ik_y, directorCos_ik_z;
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double invR_ij, invR_ik, cosTeta;
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double repulsivePotential, attractivePotential;
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double exponentRepulsivePotential, exponentAttractivePotential,interpolTMP,interpolDeltaX,interpolY1;
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double interpolY2, cutoffFunctionIJ, attractiveExponential, repulsiveExponential, cutoffFunctionDerivedIJ,zeta;
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double gtetaFunctionIJK,gtetaFunctionDerivedIJK,cutoffFunctionIK;
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double cutoffFunctionDerivedIK,factor_force3_ij,factor_1_force3_ik;
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double factor_2_force3_ik,betaZetaPowerIJK,betaZetaPowerDerivedIJK,factor_force_tot;
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double factor_force_ij;
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double gtetaFunctionDerived_temp,gtetaFunction_temp;
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double 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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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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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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fxtmp = fytmp = fztmp = 0.0;
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jlist = firstneigh[i];
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jnum = numneigh[i];
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if (jnum > leadingDimensionInteractionList) {
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char errmsg[256];
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sprintf(errmsg,"Too many neighbors for interaction list: %d vs %d.\n"
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"Check your system or increase 'leadingDimensionInteractionList'",
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jnum, leadingDimensionInteractionList);
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error->one(FLERR,errmsg);
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}
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// Pre-calculate gteta and cutoff function
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for (int neighbor_j = 0; neighbor_j < jnum; neighbor_j++) {
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double dr_ij[3], r_ij;
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j = jlist[neighbor_j];
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j &= NEIGHMASK;
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dr_ij[0] = xtmp - x[j][0];
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dr_ij[1] = ytmp - x[j][1];
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dr_ij[2] = ztmp - x[j][2];
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r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[2];
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jtype = map[type[j]];
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ijparam = elem2param[itype][jtype][jtype];
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if (r_ij > params[ijparam].cutsq) continue;
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r_ij = sqrt(r_ij);
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invR_ij = 1.0 / r_ij;
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directorCos_ij_x = invR_ij * dr_ij[0];
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directorCos_ij_y = invR_ij * dr_ij[1];
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directorCos_ij_z = invR_ij * dr_ij[2];
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// preCutoffFunction
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interpolDeltaX = r_ij - GRIDSTART;
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interpolTMP = (interpolDeltaX * GRIDDENSITY_FCUTOFF);
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interpolIDX = (int) interpolTMP;
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interpolY1 = cutoffFunction[itype][jtype][interpolIDX];
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interpolY2 = cutoffFunction[itype][jtype][interpolIDX+1];
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preCutoffFunction[neighbor_j] = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
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// preCutoffFunctionDerived
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interpolY1 = cutoffFunctionDerived[itype][jtype][interpolIDX];
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interpolY2 = cutoffFunctionDerived[itype][jtype][interpolIDX+1];
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preCutoffFunctionDerived[neighbor_j] = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
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for (int neighbor_k = neighbor_j + 1; neighbor_k < jnum; neighbor_k++) {
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double dr_ik[3], r_ik;
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k = jlist[neighbor_k];
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k &= NEIGHMASK;
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ktype = map[type[k]];
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ikparam = elem2param[itype][ktype][ktype];
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ijkparam = elem2param[itype][jtype][ktype];
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dr_ik[0] = xtmp -x[k][0];
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dr_ik[1] = ytmp -x[k][1];
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dr_ik[2] = ztmp -x[k][2];
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r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
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if (r_ik > params[ikparam].cutsq) continue;
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r_ik = sqrt(r_ik);
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invR_ik = 1.0 / r_ik;
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directorCos_ik_x = invR_ik * dr_ik[0];
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directorCos_ik_y = invR_ik * dr_ik[1];
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directorCos_ik_z = invR_ik * dr_ik[2];
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cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y + directorCos_ij_z * directorCos_ik_z;
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// preGtetaFunction
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interpolDeltaX=cosTeta+1.0;
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interpolTMP = (interpolDeltaX * GRIDDENSITY_GTETA);
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interpolIDX = (int) interpolTMP;
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interpolY1 = gtetaFunction[itype][interpolIDX];
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interpolY2 = gtetaFunction[itype][interpolIDX+1];
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gtetaFunction_temp = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
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// preGtetaFunctionDerived
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interpolY1 = gtetaFunctionDerived[itype][interpolIDX];
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interpolY2 = gtetaFunctionDerived[itype][interpolIDX+1];
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gtetaFunctionDerived_temp = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
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preGtetaFunction[neighbor_j][neighbor_k]=params[ijkparam].gamma*gtetaFunction_temp;
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preGtetaFunctionDerived[neighbor_j][neighbor_k]=params[ijkparam].gamma*gtetaFunctionDerived_temp;
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preGtetaFunction[neighbor_k][neighbor_j]=params[ijkparam].gamma*gtetaFunction_temp;
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preGtetaFunctionDerived[neighbor_k][neighbor_j]=params[ijkparam].gamma*gtetaFunctionDerived_temp;
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} // loop on K
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} // loop on J
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// loop over neighbors of atom i
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for (int neighbor_j = 0; neighbor_j < jnum; neighbor_j++) {
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double dr_ij[3], r_ij, f_ij[3];
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j = jlist[neighbor_j];
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j &= NEIGHMASK;
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dr_ij[0] = xtmp - x[j][0];
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dr_ij[1] = ytmp - x[j][1];
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dr_ij[2] = ztmp - x[j][2];
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r_ij = dr_ij[0]*dr_ij[0] + dr_ij[1]*dr_ij[1] + dr_ij[2]*dr_ij[2];
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jtype = map[type[j]];
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ijparam = elem2param[itype][jtype][jtype];
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if (r_ij > params[ijparam].cutsq) continue;
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r_ij = sqrt(r_ij);
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invR_ij = 1.0 / r_ij;
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directorCos_ij_x = invR_ij * dr_ij[0];
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directorCos_ij_y = invR_ij * dr_ij[1];
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directorCos_ij_z = invR_ij * dr_ij[2];
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exponentRepulsivePotential = params[ijparam].lam1 * r_ij;
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exponentAttractivePotential = params[ijparam].lam2 * r_ij;
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// repulsiveExponential
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interpolDeltaX = exponentRepulsivePotential - minArgumentExponential;
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interpolTMP = (interpolDeltaX * GRIDDENSITY_EXP);
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interpolIDX = (int) interpolTMP;
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interpolY1 = exponential[interpolIDX];
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interpolY2 = exponential[interpolIDX+1];
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repulsiveExponential = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
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// attractiveExponential
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interpolDeltaX = exponentAttractivePotential - minArgumentExponential;
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interpolTMP = (interpolDeltaX * GRIDDENSITY_EXP);
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interpolIDX = (int) interpolTMP;
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interpolY1 = exponential[interpolIDX];
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interpolY2 = exponential[interpolIDX+1];
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attractiveExponential = interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX);
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repulsivePotential = params[ijparam].biga * repulsiveExponential;
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attractivePotential = -params[ijparam].bigb * attractiveExponential;
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cutoffFunctionIJ = preCutoffFunction[neighbor_j];
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cutoffFunctionDerivedIJ = preCutoffFunctionDerived[neighbor_j];
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zeta = 0.0;
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// first loop over neighbors of atom i except j - part 1/2
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for (int neighbor_k = 0; neighbor_k < neighbor_j; neighbor_k++) {
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double dr_ik[3], r_ik;
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k = jlist[neighbor_k];
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k &= NEIGHMASK;
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ktype = map[type[k]];
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ikparam = elem2param[itype][ktype][ktype];
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ijkparam = elem2param[itype][jtype][ktype];
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dr_ik[0] = xtmp -x[k][0];
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dr_ik[1] = ytmp -x[k][1];
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dr_ik[2] = ztmp -x[k][2];
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r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
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if (r_ik > params[ikparam].cutsq) continue;
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gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
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cutoffFunctionIK = preCutoffFunction[neighbor_k];
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zeta += cutoffFunctionIK * gtetaFunctionIJK;
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}
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// first loop over neighbors of atom i except j - part 2/2
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for (int neighbor_k = neighbor_j+1; neighbor_k < jnum; neighbor_k++) {
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double dr_ik[3], r_ik;
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k = jlist[neighbor_k];
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k &= NEIGHMASK;
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ktype = map[type[k]];
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ikparam = elem2param[itype][ktype][ktype];
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ijkparam = elem2param[itype][jtype][ktype];
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dr_ik[0] = xtmp -x[k][0];
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dr_ik[1] = ytmp -x[k][1];
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dr_ik[2] = ztmp -x[k][2];
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r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
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if (r_ik > params[ikparam].cutsq) continue;
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gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
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cutoffFunctionIK = preCutoffFunction[neighbor_k];
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zeta += cutoffFunctionIK * gtetaFunctionIJK;
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}
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// betaZetaPowerIJK
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interpolDeltaX= params[ijparam].beta * zeta;
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interpolTMP = (interpolDeltaX * GRIDDENSITY_BIJ);
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interpolIDX = (int) interpolTMP;
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interpolY1 = betaZetaPower[itype][interpolIDX];
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interpolY2 = betaZetaPower[itype][interpolIDX+1];
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betaZetaPowerIJK = (interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX));
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// betaZetaPowerDerivedIJK
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interpolY1 = betaZetaPowerDerived[itype][interpolIDX];
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interpolY2 = betaZetaPowerDerived[itype][interpolIDX+1];
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betaZetaPowerDerivedIJK = params[ijparam].beta*(interpolY1 + (interpolY2 - interpolY1) * (interpolTMP - interpolIDX));
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// Forces and virial
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factor_force_ij = 0.5*cutoffFunctionDerivedIJ*(repulsivePotential + attractivePotential * betaZetaPowerIJK)+0.5*cutoffFunctionIJ*(-repulsivePotential*params[ijparam].lam1-betaZetaPowerIJK*attractivePotential*params[ijparam].lam2);
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f_ij[0] = factor_force_ij * directorCos_ij_x;
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f_ij[1] = factor_force_ij * directorCos_ij_y;
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f_ij[2] = factor_force_ij * directorCos_ij_z;
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f[j][0] += f_ij[0];
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f[j][1] += f_ij[1];
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f[j][2] += f_ij[2];
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fxtmp -= f_ij[0];
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fytmp -= f_ij[1];
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fztmp -= f_ij[2];
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// potential energy
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evdwl = cutoffFunctionIJ * repulsivePotential + cutoffFunctionIJ * attractivePotential * betaZetaPowerIJK;
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if (evflag) ev_tally(i, j, nlocal, newton_pair, 0.5 * evdwl, 0.0,
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-factor_force_ij*invR_ij, dr_ij[0], dr_ij[1], dr_ij[2]);
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factor_force_tot= 0.5*cutoffFunctionIJ*attractivePotential*betaZetaPowerDerivedIJK;
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// second loop over neighbors of atom i except j, forces and virial only - part 1/2
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for (int neighbor_k = 0; neighbor_k < neighbor_j; neighbor_k++) {
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double dr_ik[3], r_ik, f_ik[3];
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k = jlist[neighbor_k];
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k &= NEIGHMASK;
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ktype = map[type[k]];
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ikparam = elem2param[itype][ktype][ktype];
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ijkparam = elem2param[itype][jtype][ktype];
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dr_ik[0] = xtmp -x[k][0];
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dr_ik[1] = ytmp -x[k][1];
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dr_ik[2] = ztmp -x[k][2];
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r_ik = dr_ik[0]*dr_ik[0] + dr_ik[1]*dr_ik[1] + dr_ik[2]*dr_ik[2];
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if (r_ik > params[ikparam].cutsq) continue;
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r_ik = sqrt(r_ik);
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invR_ik = 1.0 / r_ik;
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directorCos_ik_x = invR_ik * dr_ik[0];
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directorCos_ik_y = invR_ik * dr_ik[1];
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directorCos_ik_z = invR_ik * dr_ik[2];
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cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y + directorCos_ij_z * directorCos_ik_z;
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gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
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gtetaFunctionDerivedIJK = preGtetaFunctionDerived[neighbor_j][neighbor_k];
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cutoffFunctionIK = preCutoffFunction[neighbor_k];
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cutoffFunctionDerivedIK = preCutoffFunctionDerived[neighbor_k];
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factor_force3_ij= cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ij *factor_force_tot;
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f_ij[0] = factor_force3_ij * (directorCos_ij_x*cosTeta - directorCos_ik_x);
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f_ij[1] = factor_force3_ij * (directorCos_ij_y*cosTeta - directorCos_ik_y);
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f_ij[2] = factor_force3_ij * (directorCos_ij_z*cosTeta - directorCos_ik_z);
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factor_1_force3_ik = (cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ik)*factor_force_tot;
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factor_2_force3_ik = -(cutoffFunctionDerivedIK * gtetaFunctionIJK)*factor_force_tot;
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f_ik[0] = factor_1_force3_ik * (directorCos_ik_x*cosTeta - directorCos_ij_x) + factor_2_force3_ik * directorCos_ik_x;
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f_ik[1] = factor_1_force3_ik * (directorCos_ik_y*cosTeta - directorCos_ij_y) + factor_2_force3_ik * directorCos_ik_y;
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f_ik[2] = factor_1_force3_ik * (directorCos_ik_z*cosTeta - directorCos_ij_z) + factor_2_force3_ik * directorCos_ik_z;
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f[j][0] -= f_ij[0];
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f[j][1] -= f_ij[1];
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f[j][2] -= f_ij[2];
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|
|
f[k][0] -= f_ik[0];
|
|
f[k][1] -= f_ik[1];
|
|
f[k][2] -= f_ik[2];
|
|
|
|
fxtmp += f_ij[0] + f_ik[0];
|
|
fytmp += f_ij[1] + f_ik[1];
|
|
fztmp += f_ij[2] + f_ik[2];
|
|
|
|
// potential energy
|
|
evdwl = 0.0;
|
|
|
|
if (evflag) ev_tally3(i,j,k,evdwl,0.0,f_ij,f_ik,dr_ij,dr_ik);
|
|
}
|
|
|
|
// second loop over neighbors of atom i except j, forces and virial only - part 2/2
|
|
for (int neighbor_k = neighbor_j+1; neighbor_k < jnum; neighbor_k++) {
|
|
double dr_ik[3], r_ik, f_ik[3];
|
|
|
|
k = jlist[neighbor_k];
|
|
k &= NEIGHMASK;
|
|
ktype = map[type[k]];
|
|
ikparam = elem2param[itype][ktype][ktype];
|
|
ijkparam = elem2param[itype][jtype][ktype];
|
|
|
|
dr_ik[0] = xtmp -x[k][0];
|
|
dr_ik[1] = ytmp -x[k][1];
|
|
dr_ik[2] = ztmp -x[k][2];
|
|
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);
|
|
invR_ik = 1.0 / r_ik;
|
|
|
|
directorCos_ik_x = invR_ik * dr_ik[0];
|
|
directorCos_ik_y = invR_ik * dr_ik[1];
|
|
directorCos_ik_z = invR_ik * dr_ik[2];
|
|
|
|
cosTeta = directorCos_ij_x * directorCos_ik_x + directorCos_ij_y * directorCos_ik_y + directorCos_ij_z * directorCos_ik_z;
|
|
|
|
gtetaFunctionIJK = preGtetaFunction[neighbor_j][neighbor_k];
|
|
|
|
gtetaFunctionDerivedIJK = preGtetaFunctionDerived[neighbor_j][neighbor_k];
|
|
|
|
cutoffFunctionIK = preCutoffFunction[neighbor_k];
|
|
|
|
cutoffFunctionDerivedIK = preCutoffFunctionDerived[neighbor_k];
|
|
|
|
factor_force3_ij= cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ij *factor_force_tot;
|
|
|
|
f_ij[0] = factor_force3_ij * (directorCos_ij_x*cosTeta - directorCos_ik_x);
|
|
f_ij[1] = factor_force3_ij * (directorCos_ij_y*cosTeta - directorCos_ik_y);
|
|
f_ij[2] = factor_force3_ij * (directorCos_ij_z*cosTeta - directorCos_ik_z);
|
|
|
|
factor_1_force3_ik = (cutoffFunctionIK * gtetaFunctionDerivedIJK * invR_ik)*factor_force_tot;
|
|
factor_2_force3_ik = -(cutoffFunctionDerivedIK * gtetaFunctionIJK)*factor_force_tot;
|
|
|
|
f_ik[0] = factor_1_force3_ik * (directorCos_ik_x*cosTeta - directorCos_ij_x) + factor_2_force3_ik * directorCos_ik_x;
|
|
f_ik[1] = factor_1_force3_ik * (directorCos_ik_y*cosTeta - directorCos_ij_y) + factor_2_force3_ik * directorCos_ik_y;
|
|
f_ik[2] = factor_1_force3_ik * (directorCos_ik_z*cosTeta - directorCos_ij_z) + factor_2_force3_ik * directorCos_ik_z;
|
|
|
|
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];
|
|
|
|
fxtmp += f_ij[0] + f_ik[0];
|
|
fytmp += f_ij[1] + f_ik[1];
|
|
fztmp += f_ij[2] + f_ik[2];
|
|
|
|
// potential energy
|
|
evdwl = 0.0;
|
|
|
|
if (evflag) ev_tally3(i,j,k,evdwl,0.0,f_ij,f_ik,dr_ij,dr_ik);
|
|
|
|
}
|
|
} // loop on J
|
|
f[i][0] += fxtmp;
|
|
f[i][1] += fytmp;
|
|
f[i][2] += fztmp;
|
|
} // loop on I
|
|
|
|
if (vflag_fdotr) virial_fdotr_compute();
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void PairTersoffTable::deallocatePreLoops(void)
|
|
{
|
|
memory->destroy(preGtetaFunction);
|
|
memory->destroy(preGtetaFunctionDerived);
|
|
memory->destroy(preCutoffFunction);
|
|
memory->destroy(preCutoffFunctionDerived);
|
|
}
|
|
|
|
void PairTersoffTable::allocatePreLoops(void)
|
|
{
|
|
deallocatePreLoops();
|
|
memory->create(preGtetaFunction,leadingDimensionInteractionList,
|
|
leadingDimensionInteractionList,"tersofftable:preGtetaFunction");
|
|
memory->create(preGtetaFunctionDerived,leadingDimensionInteractionList,
|
|
leadingDimensionInteractionList,"tersofftable:preGtetaFunctionDerived");
|
|
memory->create(preCutoffFunction,leadingDimensionInteractionList,
|
|
"tersofftable:preCutoffFunction");
|
|
memory->create(preCutoffFunctionDerived,leadingDimensionInteractionList,
|
|
"tersofftable:preCutoffFunctionDerived");
|
|
}
|
|
|
|
void PairTersoffTable::deallocateGrids()
|
|
{
|
|
memory->destroy(exponential);
|
|
memory->destroy(gtetaFunction);
|
|
memory->destroy(gtetaFunctionDerived);
|
|
memory->destroy(cutoffFunction);
|
|
memory->destroy(cutoffFunctionDerived);
|
|
memory->destroy(betaZetaPower);
|
|
memory->destroy(betaZetaPowerDerived);
|
|
}
|
|
|
|
void PairTersoffTable::allocateGrids(void)
|
|
{
|
|
int i, j, k, l;
|
|
|
|
int numGridPointsExponential, numGridPointsGtetaFunction, numGridPointsOneCutoffFunction;
|
|
int numGridPointsNotOneCutoffFunction, numGridPointsCutoffFunction, numGridPointsBetaZetaPower;
|
|
// double minArgumentExponential;
|
|
double deltaArgumentCutoffFunction, deltaArgumentExponential, deltaArgumentBetaZetaPower;
|
|
double deltaArgumentGtetaFunction;
|
|
double r, minMu, maxLambda, maxCutoff;
|
|
double const PI=acos(-1.0);
|
|
|
|
deallocateGrids();
|
|
|
|
// exponential
|
|
|
|
// find min and max argument
|
|
minMu=params[0].lam2;
|
|
maxLambda=params[0].lam1;
|
|
for (i=1; i<nparams; i++) {
|
|
if (params[i].lam2 < minMu) minMu = params[i].lam2;
|
|
if (params[i].lam1 > maxLambda) maxLambda = params[i].lam1;
|
|
}
|
|
maxCutoff=cutmax;
|
|
|
|
minArgumentExponential=minMu*GRIDSTART;
|
|
numGridPointsExponential=(int)((maxLambda*maxCutoff-minArgumentExponential)*GRIDDENSITY_EXP)+2;
|
|
memory->create(exponential,numGridPointsExponential,"tersofftable:exponential");
|
|
|
|
r = minArgumentExponential;
|
|
deltaArgumentExponential = 1.0 / GRIDDENSITY_EXP;
|
|
for (i = 0; i < numGridPointsExponential; i++)
|
|
{
|
|
exponential[i] = exp(-r);
|
|
r += deltaArgumentExponential;
|
|
}
|
|
|
|
|
|
// gtetaFunction
|
|
|
|
numGridPointsGtetaFunction=(int)(2.0*GRIDDENSITY_GTETA)+2;
|
|
|
|
memory->create(gtetaFunction,nelements,numGridPointsGtetaFunction,"tersofftable:gtetaFunction");
|
|
memory->create(gtetaFunctionDerived,nelements,numGridPointsGtetaFunction,"tersofftable:gtetaFunctionDerived");
|
|
|
|
r = minArgumentExponential;
|
|
for (i=0; i<nelements; i++) {
|
|
r = -1.0;
|
|
deltaArgumentGtetaFunction = 1.0 / GRIDDENSITY_GTETA;
|
|
|
|
int iparam = elem2param[i][i][i];
|
|
double c = params[iparam].c;
|
|
double d = params[iparam].d;
|
|
double h = params[iparam].h;
|
|
|
|
for (j = 0; j < numGridPointsGtetaFunction; j++) {
|
|
gtetaFunction[i][j]=1.0+(c*c)/(d*d)-(c*c)/(d*d+(h-r)*(h-r));
|
|
gtetaFunctionDerived[i][j]= -2.0 * c * c * (h-r) / ((d*d+(h-r)*(h-r))*(d*d+(h-r)*(h-r)));
|
|
r += deltaArgumentGtetaFunction;
|
|
}
|
|
}
|
|
|
|
|
|
// cutoffFunction, zetaFunction, find grids.
|
|
|
|
int ngrid_max = -1;
|
|
int zeta_max = -1;
|
|
|
|
for (i=0; i<nelements; i++) {
|
|
|
|
int iparam = elem2param[i][i][i];
|
|
double c = params[iparam].c;
|
|
double d = params[iparam].d;
|
|
double beta = params[iparam].beta;
|
|
|
|
numGridPointsBetaZetaPower=(int)(((1.0+(c*c)/(d*d)-(c*c)/(d*d+4))*beta*leadingDimensionInteractionList*GRIDDENSITY_BIJ))+2;
|
|
zeta_max = MAX(zeta_max,numGridPointsBetaZetaPower);
|
|
|
|
for (j=0; j<nelements; j++) {
|
|
for (k=0; k<nelements; k++) {
|
|
|
|
int ijparam = elem2param[i][j][k];
|
|
double cutoffR = params[ijparam].cutoffR;
|
|
double cutoffS = params[ijparam].cutoffS;
|
|
|
|
numGridPointsOneCutoffFunction=(int) ((cutoffR-GRIDSTART)*GRIDDENSITY_FCUTOFF)+1;
|
|
numGridPointsNotOneCutoffFunction=(int) ((cutoffS-cutoffR)*GRIDDENSITY_FCUTOFF)+2;
|
|
numGridPointsCutoffFunction=numGridPointsOneCutoffFunction+numGridPointsNotOneCutoffFunction;
|
|
|
|
ngrid_max = MAX(ngrid_max,numGridPointsCutoffFunction);
|
|
}
|
|
}
|
|
}
|
|
|
|
memory->create(cutoffFunction,nelements,nelements,ngrid_max,"tersoff:cutfunc");
|
|
memory->create(cutoffFunctionDerived,nelements,nelements,ngrid_max,"tersoff:cutfuncD");
|
|
|
|
// cutoffFunction, compute.
|
|
|
|
for (i=0; i<nelements; i++) {
|
|
for (j=0; j<nelements; j++) {
|
|
for (j=0; j<nelements; j++) {
|
|
int ijparam = elem2param[i][j][j];
|
|
double cutoffR = params[ijparam].cutoffR;
|
|
double cutoffS = params[ijparam].cutoffS;
|
|
|
|
numGridPointsOneCutoffFunction=(int) ((cutoffR-GRIDSTART)*GRIDDENSITY_FCUTOFF)+1;
|
|
numGridPointsNotOneCutoffFunction=(int) ((cutoffS-cutoffR)*GRIDDENSITY_FCUTOFF)+2;
|
|
numGridPointsCutoffFunction=numGridPointsOneCutoffFunction+numGridPointsNotOneCutoffFunction;
|
|
|
|
r = GRIDSTART;
|
|
deltaArgumentCutoffFunction = 1.0 / GRIDDENSITY_FCUTOFF;
|
|
|
|
for (l = 0; l < numGridPointsOneCutoffFunction; l++) {
|
|
cutoffFunction[i][j][l] = 1.0;
|
|
cutoffFunctionDerived[i][j][l]=0.0;
|
|
r += deltaArgumentCutoffFunction;
|
|
}
|
|
|
|
for (l = numGridPointsOneCutoffFunction; l < numGridPointsCutoffFunction; l++) {
|
|
cutoffFunction[i][j][l] = 0.5 + 0.5 * cos (PI * (r - cutoffR)/(cutoffS-cutoffR)) ;
|
|
cutoffFunctionDerived[i][j][l] = -0.5 * PI * sin (PI * (r - cutoffR)/(cutoffS-cutoffR)) / (cutoffS-cutoffR) ;
|
|
r += deltaArgumentCutoffFunction;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
// betaZetaPower, compute
|
|
|
|
memory->create(betaZetaPower,nelements,zeta_max,"tersoff:zetafunc");
|
|
memory->create(betaZetaPowerDerived,nelements,zeta_max,"tersoff:zetafuncD");
|
|
|
|
for (i=0; i<nelements; i++) {
|
|
|
|
int iparam = elem2param[i][i][i];
|
|
double c = params[iparam].c;
|
|
double d = params[iparam].d;
|
|
double beta = params[iparam].beta;
|
|
|
|
numGridPointsBetaZetaPower=(int)(((1.0+(c*c)/(d*d)-(c*c)/(d*d+4))*beta*leadingDimensionInteractionList*GRIDDENSITY_BIJ))+2;
|
|
|
|
r=0.0;
|
|
deltaArgumentBetaZetaPower = 1.0 / GRIDDENSITY_BIJ;
|
|
|
|
betaZetaPower[i][0]=1.0;
|
|
|
|
r += deltaArgumentBetaZetaPower;
|
|
|
|
for (j = 1; j < numGridPointsBetaZetaPower; j++) {
|
|
double powern=params[iparam].powern;
|
|
betaZetaPower[i][j]=pow((1+pow(r,powern)),-1/(2*powern));
|
|
betaZetaPowerDerived[i][j]=-0.5*pow(r,powern-1.0)*pow((1+pow(r,powern)),-1/(2*powern)-1) ;
|
|
r += deltaArgumentBetaZetaPower;
|
|
}
|
|
betaZetaPowerDerived[i][0]=(betaZetaPower[i][1]-1.0)*GRIDDENSITY_BIJ;
|
|
}
|
|
}
|
|
|
|
void PairTersoffTable::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 PairTersoffTable::settings(int narg, char **/*arg*/)
|
|
{
|
|
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
set coeffs for one or more type pairs
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairTersoffTable::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] = nullptr;
|
|
|
|
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_params();
|
|
|
|
// 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();
|
|
allocateGrids();
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
init specific to this pair style
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairTersoffTable::init_style()
|
|
{
|
|
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 PairTersoffTable::init_one(int i, int j)
|
|
{
|
|
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
|
|
|
|
return cutmax;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void PairTersoffTable::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/table", 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));
|
|
}
|
|
|
|
// some parameters are not used since only Tersoff_2 is implemented
|
|
|
|
params[nparams].ielement = ielement;
|
|
params[nparams].jelement = jelement;
|
|
params[nparams].kelement = kelement;
|
|
params[nparams].powerm = values.next_double(); // not used
|
|
params[nparams].gamma = values.next_double(); // not used
|
|
params[nparams].lam3 = values.next_double(); // not used
|
|
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();
|
|
double bigr = values.next_double();
|
|
double bigd = values.next_double();
|
|
params[nparams].cutoffR = bigr - bigd;
|
|
params[nparams].cutoffS = bigr + bigd;
|
|
params[nparams].lam1 = values.next_double();
|
|
params[nparams].biga = values.next_double();
|
|
|
|
if (unit_convert) {
|
|
params[nparams].biga *= conversion_factor;
|
|
params[nparams].bigb *= conversion_factor;
|
|
}
|
|
} catch (TokenizerException &e) {
|
|
error->one(FLERR, e.what());
|
|
}
|
|
|
|
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].cutoffR < 0.0 ||
|
|
params[nparams].cutoffS < 0.0 ||
|
|
params[nparams].cutoffR > params[nparams].cutoffS ||
|
|
params[nparams].lam1 < 0.0 ||
|
|
params[nparams].biga < 0.0
|
|
) error->one(FLERR,"Illegal Tersoff parameter");
|
|
|
|
// only tersoff_2 parametrization is implemented
|
|
|
|
if (params[nparams].gamma != 1.0 || params[nparams].lam3 != 0.0)
|
|
error->one(FLERR,"Currently the tersoff/table pair_style only "
|
|
"implements the Tersoff_2 parametrization");
|
|
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 PairTersoffTable::setup_params()
|
|
{
|
|
int i,j,k,m,n;
|
|
|
|
// 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].cut = params[m].cutoffS;
|
|
params[m].cutsq = params[m].cut*params[m].cut;
|
|
}
|
|
|
|
// 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;
|
|
}
|
|
}
|