1074 lines
32 KiB
C++
1074 lines
32 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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Environment Dependent Interatomic Potential
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References:
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1) J. F. Justo, M. Z. Bazant, E. Kaxiras, V. V. Bulatov, S. Yip
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Phys. Rev. B 58, 2539 (1998)
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------------------------------------------------------------------------- */
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#include "pair_edip.h"
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#include <mpi.h>
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#include <cmath>
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#include <cfloat>
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#include <cstdlib>
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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 "error.h"
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#include "utils.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 GRIDDENSITY 8000
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#define GRIDSTART 0.1
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// max number of interaction per atom for f(Z) environment potential
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#define leadDimInteractionList 64
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/* ---------------------------------------------------------------------- */
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PairEDIP::PairEDIP(LAMMPS *lmp) :
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Pair(lmp), preInvR_ij(NULL), preExp3B_ij(NULL), preExp3BDerived_ij(NULL),
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preExp2B_ij(NULL), preExp2BDerived_ij(NULL), prePow2B_ij(NULL),
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preForceCoord(NULL), cutoffFunction(NULL), cutoffFunctionDerived(NULL),
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pow2B(NULL), exp2B(NULL), exp3B(NULL), qFunctionGrid(NULL),
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expMinusBetaZeta_iZeta_iGrid(NULL), tauFunctionGrid(NULL),
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tauFunctionDerivedGrid(NULL)
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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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nelements = 0;
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elements = NULL;
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nparams = maxparam = 0;
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params = NULL;
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elem2param = NULL;
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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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PairEDIP::~PairEDIP()
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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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deallocateGrids();
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deallocatePreLoops();
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairEDIP::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;
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double xtmp,ytmp,ztmp,evdwl;
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int *ilist,*jlist,*numneigh,**firstneigh;
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int preForceCoord_counter;
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double invR_ij;
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double invR_ik;
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double directorCos_ij_x;
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double directorCos_ij_y;
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double directorCos_ij_z;
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double directorCos_ik_x;
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double directorCos_ik_y;
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double directorCos_ik_z;
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double cosTeta;
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int interpolIDX;
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double interpolTMP;
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double interpolDeltaX;
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double interpolY1;
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double interpolY2;
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double invRMinusCutoffA;
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double sigmaInvRMinusCutoffA;
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double gammInvRMinusCutoffA;
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double cosTetaDiff;
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double cosTetaDiffCosTetaDiff;
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double cutoffFunction_ij;
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double exp2B_ij;
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double exp2BDerived_ij;
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double pow2B_ij;
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double pow2BDerived_ij;
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double exp3B_ij;
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double exp3BDerived_ij;
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double exp3B_ik;
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double exp3BDerived_ik;
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double qFunction;
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double tauFunction;
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double tauFunctionDerived;
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double expMinusBetaZeta_iZeta_i;
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double qFunctionCosTetaDiffCosTetaDiff;
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double expMinusQFunctionCosTetaDiffCosTetaDiff;
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double zeta_i;
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double zeta_iDerived;
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double zeta_iDerivedInvR_ij;
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double forceModCoord_factor;
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double forceModCoord;
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double forceModCoord_ij;
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double forceMod2B;
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double forceMod3B_factor1_ij;
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double forceMod3B_factor2_ij;
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double forceMod3B_factor2;
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double forceMod3B_factor1_ik;
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double forceMod3B_factor2_ik;
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double potentia3B_factor;
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double potential2B_factor;
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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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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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zeta_i = 0.0;
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int numForceCoordPairs = 0;
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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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jlist = firstneigh[i];
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jnum = numneigh[i];
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// pre-loop to compute environment coordination f(Z)
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for (int neighbor_j = 0; neighbor_j < jnum; neighbor_j++) {
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j = jlist[neighbor_j];
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j &= NEIGHMASK;
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double dr_ij[3], r_ij;
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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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preInvR_ij[neighbor_j] = invR_ij;
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invRMinusCutoffA = 1.0 / (r_ij - cutoffA);
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sigmaInvRMinusCutoffA = sigma * invRMinusCutoffA;
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gammInvRMinusCutoffA = gamm * invRMinusCutoffA;
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interpolDeltaX = r_ij - GRIDSTART;
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interpolTMP = (interpolDeltaX * GRIDDENSITY);
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interpolIDX = (int) interpolTMP;
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interpolY1 = exp3B[interpolIDX];
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interpolY2 = exp3B[interpolIDX+1];
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exp3B_ij = interpolY1 + (interpolY2 - interpolY1) *
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(interpolTMP-interpolIDX);
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exp3BDerived_ij = - exp3B_ij * gammInvRMinusCutoffA * invRMinusCutoffA;
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preExp3B_ij[neighbor_j] = exp3B_ij;
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preExp3BDerived_ij[neighbor_j] = exp3BDerived_ij;
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interpolY1 = exp2B[interpolIDX];
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interpolY2 = exp2B[interpolIDX+1];
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exp2B_ij = interpolY1 + (interpolY2 - interpolY1) *
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(interpolTMP-interpolIDX);
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exp2BDerived_ij = - exp2B_ij * sigmaInvRMinusCutoffA * invRMinusCutoffA;
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preExp2B_ij[neighbor_j] = exp2B_ij;
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preExp2BDerived_ij[neighbor_j] = exp2BDerived_ij;
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interpolY1 = pow2B[interpolIDX];
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interpolY2 = pow2B[interpolIDX+1];
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pow2B_ij = interpolY1 + (interpolY2 - interpolY1) *
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(interpolTMP-interpolIDX);
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prePow2B_ij[neighbor_j] = pow2B_ij;
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// zeta and its derivative
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if (r_ij < cutoffC) zeta_i += 1.0;
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else {
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interpolY1 = cutoffFunction[interpolIDX];
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interpolY2 = cutoffFunction[interpolIDX+1];
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cutoffFunction_ij = interpolY1 + (interpolY2 - interpolY1) *
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(interpolTMP-interpolIDX);
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zeta_i += cutoffFunction_ij;
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interpolY1 = cutoffFunctionDerived[interpolIDX];
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interpolY2 = cutoffFunctionDerived[interpolIDX+1];
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zeta_iDerived = interpolY1 + (interpolY2 - interpolY1) *
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(interpolTMP-interpolIDX);
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zeta_iDerivedInvR_ij = zeta_iDerived * invR_ij;
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preForceCoord_counter=numForceCoordPairs*5;
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preForceCoord[preForceCoord_counter+0]=zeta_iDerivedInvR_ij;
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preForceCoord[preForceCoord_counter+1]=dr_ij[0];
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preForceCoord[preForceCoord_counter+2]=dr_ij[1];
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preForceCoord[preForceCoord_counter+3]=dr_ij[2];
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preForceCoord[preForceCoord_counter+4]=j;
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numForceCoordPairs++;
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}
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}
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// quantities depending on zeta_i
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interpolDeltaX = zeta_i;
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interpolTMP = (interpolDeltaX * GRIDDENSITY);
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interpolIDX = (int) interpolTMP;
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interpolY1 = expMinusBetaZeta_iZeta_iGrid[interpolIDX];
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interpolY2 = expMinusBetaZeta_iZeta_iGrid[interpolIDX+1];
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expMinusBetaZeta_iZeta_i = interpolY1 + (interpolY2 - interpolY1) *
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(interpolTMP-interpolIDX);
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interpolY1 = qFunctionGrid[interpolIDX];
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interpolY2 = qFunctionGrid[interpolIDX+1];
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qFunction = interpolY1 + (interpolY2 - interpolY1) *
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(interpolTMP-interpolIDX);
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interpolY1 = tauFunctionGrid[interpolIDX];
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interpolY2 = tauFunctionGrid[interpolIDX+1];
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tauFunction = interpolY1 + (interpolY2 - interpolY1) *
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(interpolTMP-interpolIDX);
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interpolY1 = tauFunctionDerivedGrid[interpolIDX];
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interpolY2 = tauFunctionDerivedGrid[interpolIDX+1];
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tauFunctionDerived = interpolY1 + (interpolY2 - interpolY1) *
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(interpolTMP-interpolIDX);
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forceModCoord_factor = 2.0 * beta * zeta_i * expMinusBetaZeta_iZeta_i;
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forceModCoord = 0.0;
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// two-body interactions, skip half of them
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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] = x[j][0] - xtmp;
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dr_ij[1] = x[j][1] - ytmp;
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dr_ij[2] = x[j][2] - ztmp;
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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 = preInvR_ij[neighbor_j];
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pow2B_ij = prePow2B_ij[neighbor_j];
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potential2B_factor = pow2B_ij - expMinusBetaZeta_iZeta_i;
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exp2B_ij = preExp2B_ij[neighbor_j];
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pow2BDerived_ij = - rho * invR_ij * pow2B_ij;
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forceModCoord += (forceModCoord_factor*exp2B_ij);
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exp2BDerived_ij = preExp2BDerived_ij[neighbor_j];
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forceMod2B = exp2BDerived_ij * potential2B_factor +
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exp2B_ij * pow2BDerived_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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exp3B_ij = preExp3B_ij[neighbor_j];
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exp3BDerived_ij = preExp3BDerived_ij[neighbor_j];
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f_ij[0] = forceMod2B * directorCos_ij_x;
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f_ij[1] = forceMod2B * directorCos_ij_y;
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f_ij[2] = forceMod2B * directorCos_ij_z;
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f[i][0] += f_ij[0];
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f[i][1] += f_ij[1];
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f[i][2] += f_ij[2];
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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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// potential energy
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evdwl = (exp2B_ij * potential2B_factor);
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if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0,
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-forceMod2B*invR_ij, dr_ij[0], dr_ij[1], dr_ij[2]);
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// three-body Forces
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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, 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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dr_ik[0] = x[k][0] - xtmp;
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dr_ik[1] = x[k][1] - ytmp;
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dr_ik[2] = x[k][2] - ztmp;
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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 = preInvR_ij[neighbor_k];
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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 +
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directorCos_ij_y * directorCos_ik_y +
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directorCos_ij_z * directorCos_ik_z;
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cosTetaDiff = cosTeta + tauFunction;
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cosTetaDiffCosTetaDiff = cosTetaDiff * cosTetaDiff;
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qFunctionCosTetaDiffCosTetaDiff = cosTetaDiffCosTetaDiff * qFunction;
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expMinusQFunctionCosTetaDiffCosTetaDiff =
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exp(-qFunctionCosTetaDiffCosTetaDiff);
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potentia3B_factor = lambda *
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((1.0 - expMinusQFunctionCosTetaDiffCosTetaDiff) +
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eta * qFunctionCosTetaDiffCosTetaDiff);
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exp3B_ik = preExp3B_ij[neighbor_k];
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exp3BDerived_ik = preExp3BDerived_ij[neighbor_k];
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forceMod3B_factor1_ij = - exp3BDerived_ij * exp3B_ik *
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potentia3B_factor;
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forceMod3B_factor2 = 2.0 * lambda * exp3B_ij * exp3B_ik *
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qFunction * cosTetaDiff *
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(eta + expMinusQFunctionCosTetaDiffCosTetaDiff);
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forceMod3B_factor2_ij = forceMod3B_factor2 * invR_ij;
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f_ij[0] = forceMod3B_factor1_ij * directorCos_ij_x +
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forceMod3B_factor2_ij *
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(cosTeta * directorCos_ij_x - directorCos_ik_x);
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f_ij[1] = forceMod3B_factor1_ij * directorCos_ij_y +
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forceMod3B_factor2_ij *
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(cosTeta * directorCos_ij_y - directorCos_ik_y);
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f_ij[2] = forceMod3B_factor1_ij * directorCos_ij_z +
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forceMod3B_factor2_ij *
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(cosTeta * directorCos_ij_z - directorCos_ik_z);
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forceMod3B_factor1_ik = - exp3BDerived_ik * exp3B_ij *
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potentia3B_factor;
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forceMod3B_factor2_ik = forceMod3B_factor2 * invR_ik;
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f_ik[0] = forceMod3B_factor1_ik * directorCos_ik_x +
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forceMod3B_factor2_ik *
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(cosTeta * directorCos_ik_x - directorCos_ij_x);
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f_ik[1] = forceMod3B_factor1_ik * directorCos_ik_y +
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forceMod3B_factor2_ik *
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(cosTeta * directorCos_ik_y - directorCos_ij_y);
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f_ik[2] = forceMod3B_factor1_ik * directorCos_ik_z +
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forceMod3B_factor2_ik *
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(cosTeta * directorCos_ik_z - directorCos_ij_z);
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forceModCoord += (forceMod3B_factor2 *
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(tauFunctionDerived - 0.5 * mu * cosTetaDiff));
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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];
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f[k][1] += f_ik[1];
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f[k][2] += f_ik[2];
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f[i][0] -= f_ij[0] + f_ik[0];
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f[i][1] -= f_ij[1] + f_ik[1];
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f[i][2] -= f_ij[2] + f_ik[2];
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// potential energy
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evdwl = (exp3B_ij * exp3B_ik * potentia3B_factor);
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if (evflag) ev_tally3(i,j,k,evdwl,0.0,f_ij,f_ik,dr_ij,dr_ik);
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}
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}
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// forces due to environment coordination f(Z)
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for (int idx = 0; idx < numForceCoordPairs; idx++) {
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double dr_ij[3],f_ij[3];
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preForceCoord_counter = idx * 5;
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zeta_iDerivedInvR_ij=preForceCoord[preForceCoord_counter+0];
|
|
dr_ij[0]=preForceCoord[preForceCoord_counter+1];
|
|
dr_ij[1]=preForceCoord[preForceCoord_counter+2];
|
|
dr_ij[2]=preForceCoord[preForceCoord_counter+3];
|
|
j = static_cast<int> (preForceCoord[preForceCoord_counter+4]);
|
|
|
|
forceModCoord_ij = forceModCoord * zeta_iDerivedInvR_ij;
|
|
|
|
f_ij[0] = forceModCoord_ij * dr_ij[0];
|
|
f_ij[1] = forceModCoord_ij * dr_ij[1];
|
|
f_ij[2] = forceModCoord_ij * dr_ij[2];
|
|
|
|
f[i][0] -= f_ij[0];
|
|
f[i][1] -= f_ij[1];
|
|
f[i][2] -= f_ij[2];
|
|
|
|
f[j][0] += f_ij[0];
|
|
f[j][1] += f_ij[1];
|
|
f[j][2] += f_ij[2];
|
|
|
|
// potential energy
|
|
|
|
evdwl = 0.0;
|
|
if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0,
|
|
-forceModCoord_ij, dr_ij[0], dr_ij[1], dr_ij[2]);
|
|
}
|
|
}
|
|
|
|
if (vflag_fdotr) virial_fdotr_compute();
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void PairEDIP::allocateGrids(void)
|
|
{
|
|
int numGridPointsOneCutoffFunction;
|
|
int numGridPointsNotOneCutoffFunction;
|
|
int numGridPointsCutoffFunction;
|
|
int numGridPointsR;
|
|
int numGridPointsRTotal;
|
|
int numGridPointsQFunctionGrid;
|
|
int numGridPointsExpMinusBetaZeta_iZeta_i;
|
|
int numGridPointsTauFunctionGrid;
|
|
double maxArgumentTauFunctionGrid;
|
|
double maxArgumentQFunctionGrid;
|
|
double maxArgumentExpMinusBetaZeta_iZeta_i;
|
|
double const leftLimitToZero = -DBL_MIN * 1000.0;
|
|
|
|
deallocateGrids();
|
|
|
|
// tauFunctionGrid
|
|
|
|
maxArgumentTauFunctionGrid = leadDimInteractionList;
|
|
numGridPointsTauFunctionGrid = (int)
|
|
((maxArgumentTauFunctionGrid) * GRIDDENSITY) + 2;
|
|
|
|
memory->create(tauFunctionGrid,numGridPointsTauFunctionGrid,
|
|
"edip:tauFunctionGrid");
|
|
memory->create(tauFunctionDerivedGrid,numGridPointsTauFunctionGrid,
|
|
"edip:tauFunctionDerivedGrid");
|
|
|
|
// expMinusBetaZeta_iZeta_iGrid
|
|
|
|
maxArgumentExpMinusBetaZeta_iZeta_i = leadDimInteractionList;
|
|
numGridPointsExpMinusBetaZeta_iZeta_i = (int)
|
|
((maxArgumentExpMinusBetaZeta_iZeta_i) * GRIDDENSITY) + 2;
|
|
memory->create(expMinusBetaZeta_iZeta_iGrid,
|
|
numGridPointsExpMinusBetaZeta_iZeta_i,
|
|
"edip:expMinusBetaZeta_iZeta_iGrid");
|
|
|
|
// qFunctionGrid
|
|
|
|
maxArgumentQFunctionGrid = leadDimInteractionList;
|
|
numGridPointsQFunctionGrid = (int)
|
|
((maxArgumentQFunctionGrid) * GRIDDENSITY) + 2;
|
|
memory->create(qFunctionGrid,numGridPointsQFunctionGrid,"edip:qFunctionGrid");
|
|
|
|
// cutoffFunction
|
|
|
|
numGridPointsOneCutoffFunction = (int) ((cutoffC - GRIDSTART) * GRIDDENSITY);
|
|
numGridPointsNotOneCutoffFunction = (int) ((cutoffA-cutoffC) * GRIDDENSITY);
|
|
numGridPointsCutoffFunction = numGridPointsOneCutoffFunction +
|
|
numGridPointsNotOneCutoffFunction+2;
|
|
|
|
memory->create(cutoffFunction,numGridPointsCutoffFunction,
|
|
"edip:cutoffFunction");
|
|
memory->create(cutoffFunctionDerived,numGridPointsCutoffFunction,
|
|
"edip:cutoffFunctionDerived");
|
|
|
|
// pow2B
|
|
|
|
numGridPointsR = (int)
|
|
((cutoffA + leftLimitToZero - GRIDSTART) * GRIDDENSITY);
|
|
numGridPointsRTotal = numGridPointsR + 2;
|
|
|
|
memory->create(pow2B,numGridPointsRTotal,"edip:pow2B");
|
|
memory->create(exp2B,numGridPointsRTotal,"edip:exp2B");
|
|
memory->create(exp3B,numGridPointsRTotal,"edip:exp3B");
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
pre-calculated structures
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairEDIP::allocatePreLoops(void)
|
|
{
|
|
int nthreads = comm->nthreads;
|
|
|
|
deallocatePreLoops();
|
|
memory->create(preInvR_ij,nthreads*leadDimInteractionList,"edip:preInvR_ij");
|
|
memory->create(preExp3B_ij,nthreads*leadDimInteractionList,"edip:preExp3B_ij");
|
|
memory->create(preExp3BDerived_ij,nthreads*leadDimInteractionList,
|
|
"edip:preExp3BDerived_ij");
|
|
memory->create(preExp2B_ij,nthreads*leadDimInteractionList,"edip:preExp2B_ij");
|
|
memory->create(preExp2BDerived_ij,nthreads*leadDimInteractionList,
|
|
"edip:preExp2BDerived_ij");
|
|
memory->create(prePow2B_ij,nthreads*leadDimInteractionList,"edip:prePow2B_ij");
|
|
memory->create(preForceCoord,5*nthreads*leadDimInteractionList,"edip:preForceCoord");
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
deallocate grids
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairEDIP::deallocateGrids(void)
|
|
{
|
|
memory->destroy(cutoffFunction);
|
|
memory->destroy(cutoffFunctionDerived);
|
|
memory->destroy(pow2B);
|
|
memory->destroy(exp2B);
|
|
memory->destroy(exp3B);
|
|
memory->destroy(qFunctionGrid);
|
|
memory->destroy(expMinusBetaZeta_iZeta_iGrid);
|
|
memory->destroy(tauFunctionGrid);
|
|
memory->destroy(tauFunctionDerivedGrid);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
deallocate preLoops
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairEDIP::deallocatePreLoops(void)
|
|
{
|
|
memory->destroy(preInvR_ij);
|
|
memory->destroy(preExp3B_ij);
|
|
memory->destroy(preExp3BDerived_ij);
|
|
memory->destroy(preExp2B_ij);
|
|
memory->destroy(preExp2BDerived_ij);
|
|
memory->destroy(prePow2B_ij);
|
|
memory->destroy(preForceCoord);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void PairEDIP::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 PairEDIP::settings(int narg, char **/*arg*/)
|
|
{
|
|
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void PairEDIP::initGrids(void)
|
|
{
|
|
int l;
|
|
int numGridPointsOneCutoffFunction;
|
|
int numGridPointsNotOneCutoffFunction;
|
|
int numGridPointsCutoffFunction;
|
|
int numGridPointsR;
|
|
int numGridPointsQFunctionGrid;
|
|
int numGridPointsExpMinusBetaZeta_iZeta_i;
|
|
int numGridPointsTauFunctionGrid;
|
|
double maxArgumentTauFunctionGrid;
|
|
double maxArgumentQFunctionGrid;
|
|
double maxArgumentExpMinusBetaZeta_iZeta_i;
|
|
double r;
|
|
double temp;
|
|
double temp3;
|
|
double temp4;
|
|
double deltaArgumentR;
|
|
double deltaArgumentCutoffFunction;
|
|
double deltaArgumentQFunctionGrid;
|
|
double deltaArgumentTauFunctionGrid;
|
|
double deltaArgumentExpMinusBetaZeta_iZeta_i;
|
|
double const leftLimitToZero = -DBL_MIN * 1000.0;
|
|
|
|
// tauFunctionGrid
|
|
|
|
maxArgumentTauFunctionGrid = leadDimInteractionList;
|
|
|
|
numGridPointsTauFunctionGrid = (int)
|
|
((maxArgumentTauFunctionGrid) * GRIDDENSITY) + 2;
|
|
|
|
r = 0.0;
|
|
deltaArgumentTauFunctionGrid = 1.0 / GRIDDENSITY;
|
|
|
|
for (l = 0; l < numGridPointsTauFunctionGrid; l++) {
|
|
tauFunctionGrid[l] = u1 + u2 * u3 * exp(-u4 * r) -
|
|
u2 * exp(-2.0 * u4 * r);
|
|
tauFunctionDerivedGrid[l] = - u2 * u3 * u4 * exp(-u4 * r) +
|
|
2.0 * u2 * u4 * exp(-2.0 * u4 * r);
|
|
r += deltaArgumentTauFunctionGrid;
|
|
}
|
|
|
|
// expMinusBetaZeta_iZeta_iGrid
|
|
|
|
maxArgumentExpMinusBetaZeta_iZeta_i = leadDimInteractionList;
|
|
|
|
numGridPointsExpMinusBetaZeta_iZeta_i = (int)
|
|
((maxArgumentExpMinusBetaZeta_iZeta_i) * GRIDDENSITY) + 2;
|
|
|
|
r = 0.0;
|
|
deltaArgumentExpMinusBetaZeta_iZeta_i = 1.0 / GRIDDENSITY;
|
|
|
|
for (l = 0; l < numGridPointsExpMinusBetaZeta_iZeta_i; l++) {
|
|
expMinusBetaZeta_iZeta_iGrid[l] = exp(-beta * r * r);
|
|
r += deltaArgumentExpMinusBetaZeta_iZeta_i;
|
|
}
|
|
|
|
// qFunctionGrid
|
|
|
|
maxArgumentQFunctionGrid = leadDimInteractionList;
|
|
numGridPointsQFunctionGrid =
|
|
(int) ((maxArgumentQFunctionGrid) * GRIDDENSITY) + 2;
|
|
|
|
r = 0.0;
|
|
deltaArgumentQFunctionGrid = 1.0 / GRIDDENSITY;
|
|
|
|
for (l = 0; l < numGridPointsQFunctionGrid; l++) {
|
|
qFunctionGrid[l] = Q0 * exp(-mu * r);
|
|
r += deltaArgumentQFunctionGrid;
|
|
}
|
|
|
|
// cutoffFunction
|
|
|
|
numGridPointsOneCutoffFunction =
|
|
(int) ((cutoffC - GRIDSTART) * GRIDDENSITY);
|
|
numGridPointsNotOneCutoffFunction =
|
|
(int) ((cutoffA-cutoffC) * GRIDDENSITY);
|
|
numGridPointsCutoffFunction =
|
|
numGridPointsOneCutoffFunction+numGridPointsNotOneCutoffFunction+2;
|
|
|
|
r = GRIDSTART;
|
|
deltaArgumentCutoffFunction = 1.0 / GRIDDENSITY;
|
|
|
|
for (l = 0; l < numGridPointsOneCutoffFunction; l++) {
|
|
cutoffFunction[l] = 1.0;
|
|
cutoffFunctionDerived[l] = 0.0;
|
|
r += deltaArgumentCutoffFunction;
|
|
}
|
|
|
|
for (l = numGridPointsOneCutoffFunction;
|
|
l < numGridPointsCutoffFunction; l++) {
|
|
temp = (cutoffA - cutoffC)/(r - cutoffC);
|
|
temp3 = temp * temp * temp;
|
|
temp4 = temp3 * temp;
|
|
cutoffFunction[l] = exp(alpha/(1.0-temp3));
|
|
cutoffFunctionDerived[l] = (-3*alpha/(cutoffA-cutoffC)) *
|
|
(temp4/((1-temp3)*(1-temp3)))*exp(alpha/(1.0-temp3));
|
|
r += deltaArgumentCutoffFunction;
|
|
}
|
|
|
|
// pow2B
|
|
|
|
numGridPointsR = (int)
|
|
((cutoffA + leftLimitToZero - GRIDSTART) * GRIDDENSITY);
|
|
|
|
r = GRIDSTART;
|
|
deltaArgumentR = 1.0 / GRIDDENSITY;
|
|
for (l = 0; l < numGridPointsR; l++) {
|
|
pow2B[l] = pow((B/r),rho);
|
|
exp2B[l] = A * exp(sigma/(r-cutoffA));
|
|
exp3B[l] = exp(gamm/(r-cutoffA));
|
|
r += deltaArgumentR;
|
|
}
|
|
|
|
pow2B[numGridPointsR] = pow((B/r),rho);
|
|
exp2B[numGridPointsR]=0;
|
|
exp3B[numGridPointsR]=0;
|
|
r += deltaArgumentR;
|
|
pow2B[numGridPointsR+1] = pow((B/r),rho);
|
|
exp2B[numGridPointsR+1]=0;
|
|
exp3B[numGridPointsR+1]=0;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
set coeffs for one or more type pairs
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairEDIP::coeff(int narg, char **arg)
|
|
{
|
|
int i,j,n;
|
|
|
|
if (!allocated) allocate();
|
|
|
|
if (narg != 3 + atom->ntypes)
|
|
error->all(FLERR,"Incorrect args for pair coefficients");
|
|
|
|
// insure I,J args are * *
|
|
|
|
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
|
|
error->all(FLERR,"Incorrect args for pair coefficients");
|
|
|
|
// read args that map atom types to elements in potential file
|
|
// map[i] = which element the Ith atom type is, -1 if NULL
|
|
// nelements = # of unique elements
|
|
// elements = list of element names
|
|
|
|
if (elements) {
|
|
for (i = 0; i < nelements; i++) delete [] elements[i];
|
|
delete [] elements;
|
|
}
|
|
elements = new char*[atom->ntypes];
|
|
for (i = 0; i < atom->ntypes; i++) elements[i] = NULL;
|
|
|
|
nelements = 0;
|
|
for (i = 3; i < narg; i++) {
|
|
if (strcmp(arg[i],"NULL") == 0) {
|
|
map[i-2] = -1;
|
|
continue;
|
|
}
|
|
for (j = 0; j < nelements; j++)
|
|
if (strcmp(arg[i],elements[j]) == 0) break;
|
|
map[i-2] = j;
|
|
if (j == nelements) {
|
|
n = strlen(arg[i]) + 1;
|
|
elements[j] = new char[n];
|
|
strcpy(elements[j],arg[i]);
|
|
nelements++;
|
|
}
|
|
}
|
|
|
|
if (nelements != 1)
|
|
error->all(FLERR,"Pair style edip only supports single element potentials");
|
|
|
|
// 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();
|
|
initGrids();
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
init specific to this pair style
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairEDIP::init_style()
|
|
{
|
|
if (force->newton_pair == 0)
|
|
error->all(FLERR,"Pair style edip 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 PairEDIP::init_one(int i, int j)
|
|
{
|
|
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
|
|
|
|
return cutmax;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void PairEDIP::read_file(char *file)
|
|
{
|
|
int params_per_line = 20;
|
|
char **words = new char*[params_per_line+1];
|
|
|
|
memory->sfree(params);
|
|
params = NULL;
|
|
nparams = maxparam = 0;
|
|
|
|
// open file on proc 0
|
|
|
|
FILE *fp;
|
|
if (comm->me == 0) {
|
|
fp = force->open_potential(file);
|
|
if (fp == NULL) {
|
|
char str[128];
|
|
snprintf(str,128,"Cannot open EDIP potential file %s",file);
|
|
error->one(FLERR,str);
|
|
}
|
|
}
|
|
|
|
// read each set of params from potential file
|
|
// one set of params can span multiple lines
|
|
// store params if all 3 element tags are in element list
|
|
|
|
int n,nwords,ielement,jelement,kelement;
|
|
char line[MAXLINE],*ptr;
|
|
int eof = 0;
|
|
|
|
while (1) {
|
|
if (comm->me == 0) {
|
|
ptr = fgets(line,MAXLINE,fp);
|
|
if (ptr == NULL) {
|
|
eof = 1;
|
|
fclose(fp);
|
|
} else n = strlen(line) + 1;
|
|
}
|
|
MPI_Bcast(&eof,1,MPI_INT,0,world);
|
|
if (eof) break;
|
|
MPI_Bcast(&n,1,MPI_INT,0,world);
|
|
MPI_Bcast(line,n,MPI_CHAR,0,world);
|
|
|
|
// strip comment, skip line if blank
|
|
|
|
if ((ptr = strchr(line,'#'))) *ptr = '\0';
|
|
nwords = utils::count_words(line);
|
|
if (nwords == 0) continue;
|
|
|
|
// concatenate additional lines until have params_per_line words
|
|
|
|
while (nwords < params_per_line) {
|
|
n = strlen(line);
|
|
if (comm->me == 0) {
|
|
ptr = fgets(&line[n],MAXLINE-n,fp);
|
|
if (ptr == NULL) {
|
|
eof = 1;
|
|
fclose(fp);
|
|
} else n = strlen(line) + 1;
|
|
}
|
|
MPI_Bcast(&eof,1,MPI_INT,0,world);
|
|
if (eof) break;
|
|
MPI_Bcast(&n,1,MPI_INT,0,world);
|
|
MPI_Bcast(line,n,MPI_CHAR,0,world);
|
|
if ((ptr = strchr(line,'#'))) *ptr = '\0';
|
|
nwords = utils::count_words(line);
|
|
}
|
|
|
|
if (nwords != params_per_line)
|
|
error->all(FLERR,"Incorrect format in EDIP potential file");
|
|
|
|
// words = ptrs to all words in line
|
|
|
|
nwords = 0;
|
|
words[nwords++] = strtok(line," \t\n\r\f");
|
|
while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
|
|
|
|
// ielement,jelement,kelement = 1st args
|
|
// if all 3 args are in element list, then parse this line
|
|
// else skip to next entry in file
|
|
|
|
for (ielement = 0; ielement < nelements; ielement++)
|
|
if (strcmp(words[0],elements[ielement]) == 0) break;
|
|
if (ielement == nelements) continue;
|
|
for (jelement = 0; jelement < nelements; jelement++)
|
|
if (strcmp(words[1],elements[jelement]) == 0) break;
|
|
if (jelement == nelements) continue;
|
|
for (kelement = 0; kelement < nelements; kelement++)
|
|
if (strcmp(words[2],elements[kelement]) == 0) break;
|
|
if (kelement == nelements) continue;
|
|
|
|
// load up parameter settings and error check their values
|
|
|
|
if (nparams == maxparam) {
|
|
maxparam += DELTA;
|
|
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
|
|
"pair:params");
|
|
|
|
// make certain all addional allocated storage is initialized
|
|
// to avoid false positives when checking with valgrind
|
|
|
|
memset(params + nparams, 0, DELTA*sizeof(Param));
|
|
}
|
|
|
|
params[nparams].ielement = ielement;
|
|
params[nparams].jelement = jelement;
|
|
params[nparams].kelement = kelement;
|
|
params[nparams].A = atof(words[3]);
|
|
params[nparams].B = atof(words[4]);
|
|
params[nparams].cutoffA = atof(words[5]);
|
|
params[nparams].cutoffC = atof(words[6]);
|
|
params[nparams].alpha = atof(words[7]);
|
|
params[nparams].beta = atof(words[8]);
|
|
params[nparams].eta = atof(words[9]);
|
|
params[nparams].gamm = atof(words[10]);
|
|
params[nparams].lambda = atof(words[11]);
|
|
params[nparams].mu = atof(words[12]);
|
|
params[nparams].rho = atof(words[13]);
|
|
params[nparams].sigma = atof(words[14]);
|
|
params[nparams].Q0 = atof(words[15]);
|
|
params[nparams].u1 = atof(words[16]);
|
|
params[nparams].u2 = atof(words[17]);
|
|
params[nparams].u3 = atof(words[18]);
|
|
params[nparams].u4 = atof(words[19]);
|
|
|
|
if (params[nparams].A < 0.0 || params[nparams].B < 0.0 ||
|
|
params[nparams].cutoffA < 0.0 || params[nparams].cutoffC < 0.0 ||
|
|
params[nparams].alpha < 0.0 || params[nparams].beta < 0.0 ||
|
|
params[nparams].eta < 0.0 || params[nparams].gamm < 0.0 ||
|
|
params[nparams].lambda < 0.0 || params[nparams].mu < 0.0 ||
|
|
params[nparams].rho < 0.0 || params[nparams].sigma < 0.0)
|
|
error->all(FLERR,"Illegal EDIP parameter");
|
|
|
|
nparams++;
|
|
}
|
|
|
|
delete [] words;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void PairEDIP::setup_params()
|
|
{
|
|
int i,j,k,m,n;
|
|
double rtmp;
|
|
|
|
// set elem2param for all triplet combinations
|
|
// must be a single exact match to lines read from file
|
|
// do not allow for ACB in place of ABC
|
|
|
|
memory->destroy(elem2param);
|
|
memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param");
|
|
|
|
for (i = 0; i < nelements; i++)
|
|
for (j = 0; j < nelements; j++)
|
|
for (k = 0; k < nelements; k++) {
|
|
n = -1;
|
|
for (m = 0; m < nparams; m++) {
|
|
if (i == params[m].ielement && j == params[m].jelement &&
|
|
k == params[m].kelement) {
|
|
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
|
|
n = m;
|
|
}
|
|
}
|
|
if (n < 0) error->all(FLERR,"Potential file is missing an entry");
|
|
elem2param[i][j][k] = n;
|
|
}
|
|
|
|
// set cutoff square
|
|
|
|
for (m = 0; m < nparams; m++) {
|
|
params[m].cutsq = params[m].cutoffA*params[m].cutoffA;
|
|
}
|
|
|
|
// set cutmax to max of all params
|
|
|
|
cutmax = 0.0;
|
|
for (m = 0; m < nparams; m++) {
|
|
rtmp = sqrt(params[m].cutsq);
|
|
if (rtmp > cutmax) cutmax = rtmp;
|
|
}
|
|
|
|
// this should be removed for multi species parameterization
|
|
|
|
A = params[0].A;
|
|
B = params[0].B;
|
|
rho = params[0].rho;
|
|
cutoffA = params[0].cutoffA;
|
|
cutoffC = params[0].cutoffC;
|
|
sigma = params[0].sigma;
|
|
lambda = params[0].lambda;
|
|
gamm = params[0].gamm;
|
|
eta = params[0].eta;
|
|
Q0 = params[0].Q0;
|
|
mu = params[0].mu;
|
|
beta = params[0].beta;
|
|
alpha = params[0].alpha;
|
|
u1 = params[0].u1;
|
|
u2 = params[0].u2;
|
|
u3 = params[0].u3;
|
|
u4 = params[0].u4;
|
|
}
|