diff --git a/src/bond_harmonic.cpp b/src/bond_harmonic.cpp new file mode 100644 index 0000000000..f0b6d96cc8 --- /dev/null +++ b/src/bond_harmonic.cpp @@ -0,0 +1,215 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "bond_harmonic.h" +#include "atom.h" +#include "neighbor.h" +#include "domain.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +BondHarmonic::BondHarmonic(LAMMPS *lmp) : Bond(lmp) +{ + reinitflag = 1; +} + +/* ---------------------------------------------------------------------- */ + +BondHarmonic::~BondHarmonic() +{ + if (allocated && !copymode) { + memory->destroy(setflag); + memory->destroy(k); + memory->destroy(r0); + } +} + +/* ---------------------------------------------------------------------- */ + +void BondHarmonic::compute(int eflag, int vflag) +{ + int i1,i2,n,type; + double delx,dely,delz,ebond,fbond; + double rsq,r,dr,rk; + + ebond = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = 0; + + double **x = atom->x; + double **f = atom->f; + int **bondlist = neighbor->bondlist; + int nbondlist = neighbor->nbondlist; + int nlocal = atom->nlocal; + int newton_bond = force->newton_bond; + + for (n = 0; n < nbondlist; n++) { + i1 = bondlist[n][0]; + i2 = bondlist[n][1]; + type = bondlist[n][2]; + + delx = x[i1][0] - x[i2][0]; + dely = x[i1][1] - x[i2][1]; + delz = x[i1][2] - x[i2][2]; + + rsq = delx*delx + dely*dely + delz*delz; + r = sqrt(rsq); + dr = r - r0[type]; + rk = k[type] * dr; + + // force & energy + + if (r > 0.0) fbond = -2.0*rk/r; + else fbond = 0.0; + + if (eflag) ebond = rk*dr; + + // apply force to each of 2 atoms + + if (newton_bond || i1 < nlocal) { + f[i1][0] += delx*fbond; + f[i1][1] += dely*fbond; + f[i1][2] += delz*fbond; + } + + if (newton_bond || i2 < nlocal) { + f[i2][0] -= delx*fbond; + f[i2][1] -= dely*fbond; + f[i2][2] -= delz*fbond; + } + + if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz); + } +} + +/* ---------------------------------------------------------------------- */ + +void BondHarmonic::allocate() +{ + allocated = 1; + int n = atom->nbondtypes; + + memory->create(k,n+1,"bond:k"); + memory->create(r0,n+1,"bond:r0"); + + memory->create(setflag,n+1,"bond:setflag"); + for (int i = 1; i <= n; i++) setflag[i] = 0; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more types +------------------------------------------------------------------------- */ + +void BondHarmonic::coeff(int narg, char **arg) +{ + if (narg != 3) error->all(FLERR,"Incorrect args for bond coefficients"); + if (!allocated) allocate(); + + int ilo,ihi; + force->bounds(FLERR,arg[0],atom->nbondtypes,ilo,ihi); + + double k_one = force->numeric(FLERR,arg[1]); + double r0_one = force->numeric(FLERR,arg[2]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + k[i] = k_one; + r0[i] = r0_one; + setflag[i] = 1; + count++; + } + + if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients"); +} + +/* ---------------------------------------------------------------------- + return an equilbrium bond length +------------------------------------------------------------------------- */ + +double BondHarmonic::equilibrium_distance(int i) +{ + return r0[i]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void BondHarmonic::write_restart(FILE *fp) +{ + fwrite(&k[1],sizeof(double),atom->nbondtypes,fp); + fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void BondHarmonic::read_restart(FILE *fp) +{ + allocate(); + + if (comm->me == 0) { + fread(&k[1],sizeof(double),atom->nbondtypes,fp); + fread(&r0[1],sizeof(double),atom->nbondtypes,fp); + } + MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world); + MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); + + for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void BondHarmonic::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->nbondtypes; i++) + fprintf(fp,"%d %g %g\n",i,k[i],r0[i]); +} + +/* ---------------------------------------------------------------------- */ + +double BondHarmonic::single(int type, double rsq, int i, int j, + double &fforce) +{ + double r = sqrt(rsq); + double dr = r - r0[type]; + double rk = k[type] * dr; + fforce = 0; + if (r > 0.0) fforce = -2.0*rk/r; + return rk*dr; +} + +/* ---------------------------------------------------------------------- + Return ptr to internal members upon request. +------------------------------------------------------------------------ */ +void *BondHarmonic::extract( char *str, int &dim ) +{ + dim = 1; + if( strcmp(str,"kappa") == 0 ) return (void*) k; + if( strcmp(str,"r0") == 0 ) return (void*) r0; + return NULL; +} + +