Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/USER-MISC/bond_harmonic_shift_cut.cpp
0f6d21acda7befficient_neuronet

Last Change
Raw File

bond_harmonic_shift_cut.cpp
View Options

/* ----------------------------------------------------------------------
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 author: Carsten Svaneborg, science@zqex.dk
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include "bond_harmonic_shift_cut.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;
/* ---------------------------------------------------------------------- */
BondHarmonicShiftCut::BondHarmonicShiftCut(LAMMPS *lmp) : Bond(lmp) {}
/* ---------------------------------------------------------------------- */
BondHarmonicShiftCut::~BondHarmonicShiftCut()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(k);
memory->destroy(r0);
memory->destroy(r1);
}
}
/* ---------------------------------------------------------------------- */
void BondHarmonicShiftCut::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);
if (r>r1[type]) continue;
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 = k[type]*(dr*dr -(r0[type]-r1[type])*(r0[type]-r1[type]));
// 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 BondHarmonicShiftCut::allocate()
{
allocated = 1;
int n = atom->nbondtypes;
memory->create(k , n+1,"bond:k");
memory->create(r0, n+1,"bond:r0");
memory->create(r1, n+1,"bond:r1");
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 BondHarmonicShiftCut::coeff(int narg, char **arg)
{
if (narg != 4) error->all(FLERR,"Incorrect args for bond coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->nbondtypes,ilo,ihi);
double Umin = force->numeric(FLERR,arg[1]); // energy at minimum
double r0_one = force->numeric(FLERR,arg[2]); // position of minimum
double r1_one = force->numeric(FLERR,arg[3]); // position where energy = 0 = cutoff
if (r0_one == r1_one)
error->all(FLERR,"Bond harmonic/shift/cut r0 and r1 must be different");
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = Umin/((r0_one-r1_one)*(r0_one-r1_one));
r0[i] = r0_one;
r1[i] = r1_one;
setflag[i] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients");
}
/* ----------------------------------------------------------------------
return an equilbrium bond length
------------------------------------------------------------------------- */
double BondHarmonicShiftCut::equilibrium_distance(int i)
{
return r0[i];
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void BondHarmonicShiftCut::write_restart(FILE *fp)
{
fwrite(&k[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&r1[1],sizeof(double),atom->nbondtypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void BondHarmonicShiftCut::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);
fread(&r1[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);
MPI_Bcast(&r1[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 BondHarmonicShiftCut::write_data(FILE *fp)
{
for (int i = 1; i <= atom->nbondtypes; i++) {
double d2 = (r0[i]-r1[i])*(r0[i]-r1[i]);
fprintf(fp,"%d %g %g %g\n",i,k[i]*d2,r0[i],r1[i]);
}
}
/* ---------------------------------------------------------------------- */
double BondHarmonicShiftCut::single(int type, double rsq, int i, int j,
double &fforce)
{
fforce = 0.0;
double r = sqrt(rsq);
if (r>r1[type]) return 0.0;
double dr = r - r0[type];
double dr2=r0[type]-r1[type];
fforce = -2.0*k[type]*dr/r;
return k[type]*(dr*dr - dr2*dr2);
}
c4science · Help