diff --git a/src/pair_zbl.cpp b/src/pair_zbl.cpp new file mode 100644 index 0000000000..a9882f1fe7 --- /dev/null +++ b/src/pair_zbl.cpp @@ -0,0 +1,428 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Stephen Foiles, Aidan Thompson (SNL) +------------------------------------------------------------------------- */ + +#include "math.h" +#include "stdio.h" +#include "stdlib.h" +#include "string.h" +#include "pair_zbl.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "update.h" +#include "integrate.h" +#include "respa.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" + +// From J.F. Zeigler, J. P. Biersack and U. Littmark, +// "The Stopping and Range of Ions in Matter" volume 1, Pergamon, 1985. + +using namespace LAMMPS_NS; +using namespace MathConst; +using namespace PairZBLConstants; + +/* ---------------------------------------------------------------------- */ + +PairZBL::PairZBL(LAMMPS *lmp) : Pair(lmp) {} + +/* ---------------------------------------------------------------------- */ + +PairZBL::~PairZBL() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(z); + memory->destroy(d1a); + memory->destroy(d2a); + memory->destroy(d3a); + memory->destroy(d4a); + memory->destroy(zze); + memory->destroy(sw1); + memory->destroy(sw2); + memory->destroy(sw3); + memory->destroy(sw4); + memory->destroy(sw5); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairZBL::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; + double rsq,r,t,fswitch,eswitch; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cut_globalsq) { + r = sqrt(rsq); + fpair = dzbldr(r, itype, jtype); + + if (rsq > cut_innersq) { + t = r - cut_inner; + fswitch = t*t * + (sw1[itype][jtype] + sw2[itype][jtype]*t); + fpair += fswitch; + } + + fpair *= -1.0/r; + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (eflag) { + evdwl = e_zbl(r, itype, jtype); + evdwl += sw5[itype][jtype]; + if (rsq > cut_innersq) { + eswitch = t*t*t * + (sw3[itype][jtype] + sw4[itype][jtype]*t); + evdwl += eswitch; + } + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,0.0,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairZBL::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(z,n+1,"pair:z"); + memory->create(d1a,n+1,n+1,"pair:d1a"); + memory->create(d2a,n+1,n+1,"pair:d2a"); + memory->create(d3a,n+1,n+1,"pair:d3a"); + memory->create(d4a,n+1,n+1,"pair:d4a"); + memory->create(zze,n+1,n+1,"pair:zze"); + memory->create(sw1,n+1,n+1,"pair:sw1"); + memory->create(sw2,n+1,n+1,"pair:sw2"); + memory->create(sw3,n+1,n+1,"pair:sw3"); + memory->create(sw4,n+1,n+1,"pair:sw4"); + memory->create(sw5,n+1,n+1,"pair:sw5"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairZBL::settings(int narg, char **arg) +{ + if (narg != 2) error->all(FLERR,"Illegal pair_style command"); + + cut_inner = force->numeric(FLERR,arg[0]); + cut_global = force->numeric(FLERR,arg[1]); + + if (cut_inner <= 0.0 ) + error->all(FLERR,"Illegal pair_style command"); + if (cut_inner > cut_global) + error->all(FLERR,"Illegal pair_style command"); +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairZBL::coeff(int narg, char **arg) +{ + if (narg != 3) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi; + force->bounds(arg[0],atom->ntypes,ilo,ihi); + + int jlo,jhi; + force->bounds(arg[1],atom->ntypes,jlo,jhi); + + double z_one = force->numeric(FLERR,arg[2]); + + // Set flag for each i-j pair + // Set z-parameter only for i-i pairs + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + if (i == j) z[i] = z_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairZBL::init_style() +{ + neighbor->request(this); + + cut_innersq = cut_inner * cut_inner; + cut_globalsq = cut_global * cut_global; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairZBL::init_one(int i, int j) +{ + + double ainv = (pow(z[i],pzbl) + pow(z[j],pzbl))/a0; + d1a[i][j] = d1*ainv; + d2a[i][j] = d2*ainv; + d3a[i][j] = d3*ainv; + d4a[i][j] = d4*ainv; + zze[i][j] = z[i]*z[j]*econv; + + d1a[j][i] = d1a[i][j]; + d2a[j][i] = d2a[i][j]; + d3a[j][i] = d3a[i][j]; + d4a[j][i] = d4a[i][j]; + zze[j][i] = zze[i][j]; + + // e = t^3 (sw3 + sw4*t) + sw5 + // = A/3*t^3 + B/4*t^4 + C + // sw3 = A/3 + // sw4 = B/4 + // sw5 = C + + // dedr = t^2 (sw1 + sw2*t) + // = A*t^2 + B*t^3 + // sw1 = A + // sw2 = B + + // A = (-3Fc' + tc*Fc'')/tc^2 + // B = ( 2Fc' - tc*Fc'')/tc^3 + // C = = -Fc + tc/2*Fc' - tc^2/12*Fc'' + + double tc = cut_global - cut_inner; + double fc = e_zbl(cut_global, i, j); + double fcp = dzbldr(cut_global, i, j); + double fcpp = d2zbldr2(cut_global, i, j); + + double swa = (-3.0*fcp + tc*fcpp)/(tc*tc); + double swb = ( 2.0*fcp - tc*fcpp)/(tc*tc*tc); + double swc = -fc + (tc/2.0)*fcp - (tc*tc/12.0)*fcpp; + + sw1[i][j] = swa; + sw2[i][j] = swb; + sw3[i][j] = swa/3.0; + sw4[i][j] = swb/4.0; + sw5[i][j] = swc; + + sw1[j][i] = sw1[i][j]; + sw2[j][i] = sw2[i][j]; + sw3[j][i] = sw3[i][j]; + sw4[j][i] = sw4[i][j]; + sw5[j][i] = sw5[i][j]; + + return cut_global; +} + +/* ---------------------------------------------------------------------- */ + +double PairZBL::single(int i, int j, int itype, int jtype, double rsq, + double dummy1, double dummy2, + double &fforce) +{ + double phi,r,t,eswitch,fswitch; + + r = sqrt(rsq); + fforce = dzbldr(r, itype, jtype); + if (rsq > cut_innersq) { + t = r - cut_inner; + fswitch = t*t * + (sw1[itype][jtype] + sw2[itype][jtype]*t); + fforce += fswitch; + } + fforce *= -1.0/r; + + phi = e_zbl(r, itype, jtype); + phi += sw5[itype][jtype]; + if (rsq > cut_innersq) { + eswitch = t*t*t * + (sw3[itype][jtype] + sw4[itype][jtype]*t); + phi += eswitch; + } + + return phi; +} + +/* ---------------------------------------------------------------------- + compute ZBL pair energy +------------------------------------------------------------------------- */ + +double PairZBL::e_zbl(double r, int i, int j) { + + double d1aij = d1a[i][j]; + double d2aij = d2a[i][j]; + double d3aij = d3a[i][j]; + double d4aij = d4a[i][j]; + double zzeij = zze[i][j]; + double rinv = 1.0/r; + + double sum = c1*exp(-d1aij*r); + sum += c2*exp(-d2aij*r); + sum += c3*exp(-d3aij*r); + sum += c4*exp(-d4aij*r); + + double result = zzeij*sum*rinv; + + return result; +}; + + +/* ---------------------------------------------------------------------- + compute ZBL first derivative +------------------------------------------------------------------------- */ + +double PairZBL::dzbldr(double r, int i, int j) { + + double d1aij = d1a[i][j]; + double d2aij = d2a[i][j]; + double d3aij = d3a[i][j]; + double d4aij = d4a[i][j]; + double zzeij = zze[i][j]; + double rinv = 1.0/r; + + double e1 = exp(-d1aij*r); + double e2 = exp(-d2aij*r); + double e3 = exp(-d3aij*r); + double e4 = exp(-d4aij*r); + + double sum = c1*e1; + sum += c2*e2; + sum += c3*e3; + sum += c4*e4; + + double sum_p = -c1*d1aij*e1; + sum_p -= c2*d2aij*e2; + sum_p -= c3*d3aij*e3; + sum_p -= c4*d4aij*e4; + + double result = zzeij*(sum_p - sum*rinv)*rinv; + + return result; +}; + +/* ---------------------------------------------------------------------- + compute ZBL second derivative +------------------------------------------------------------------------- */ + +double PairZBL::d2zbldr2(double r, int i, int j) { + + double d1aij = d1a[i][j]; + double d2aij = d2a[i][j]; + double d3aij = d3a[i][j]; + double d4aij = d4a[i][j]; + double zzeij = zze[i][j]; + double rinv = 1.0/r; + + double e1 = exp(-d1aij*r); + double e2 = exp(-d2aij*r); + double e3 = exp(-d3aij*r); + double e4 = exp(-d4aij*r); + + double sum = c1*e1; + sum += c2*e2; + sum += c3*e3; + sum += c4*e4; + + double sum_p = c1*e1*d1aij; + sum_p += c2*e2*d2aij; + sum_p += c3*e3*d3aij; + sum_p += c4*e4*d4aij; + + double sum_pp = c1*e1*d1aij*d1aij; + sum_pp += c2*e2*d2aij*d2aij; + sum_pp += c3*e3*d3aij*d3aij; + sum_pp += c4*e4*d4aij*d4aij; + + double result = zzeij*(sum_pp + 2.0*sum_p*rinv + + 2.0*sum*rinv*rinv)*rinv; + + return result; +}; + diff --git a/src/pair_zbl.h b/src/pair_zbl.h new file mode 100644 index 0000000000..690ae8107d --- /dev/null +++ b/src/pair_zbl.h @@ -0,0 +1,88 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(zbl,PairZBL) + +#else + +#ifndef LMP_PAIR_ZBL_H +#define LMP_PAIR_ZBL_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairZBL : public Pair { + public: + PairZBL(class LAMMPS *); + virtual ~PairZBL(); + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + void init_style(); + double init_one(int, int); + double single(int, int, int, int, double, double, double, double &); + + protected: + double cut_global, cut_inner; + double cut_globalsq, cut_innersq; + double *z; + double **d1a,**d2a,**d3a,**d4a,**zze; + double **sw1,**sw2,**sw3,**sw4,**sw5; + + void allocate(); + double e_zbl(double, int, int); + double dzbldr(double, int, int); + double d2zbldr2(double, int, int); +}; + +namespace PairZBLConstants { + + // ZBL constants + + static const double pzbl = 0.23; + static const double a0 = 0.46850; + static const double c1 = 0.02817; + static const double c2 = 0.28022; + static const double c3 = 0.50986; + static const double c4 = 0.18175; + static const double d1 = 0.20162; + static const double d2 = 0.40290; + static const double d3 = 0.94229; + static const double d4 = 3.19980; + + // units: e^2/angstrom = 2*Ryd*bohr + + static const double econv = 2.0*13.6058*0.529177; +} + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +*/