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Removed changed bond_harmonic from wrong position.

This commit is contained in:
Stefan Paquay 2017-04-10 10:06:03 -04:00
parent 1ad7d856fe
commit f19f558220
3 changed files with 19 additions and 216 deletions
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19
src/MOLECULE/bond_harmonic.cpp
View File

@ -13,6 +13,7 @@
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "bond_harmonic.h"
#include "atom.h"
#include "neighbor.h"
@ -26,7 +27,10 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
BondHarmonic::BondHarmonic(LAMMPS *lmp) : Bond(lmp) {}
BondHarmonic::BondHarmonic(LAMMPS *lmp) : Bond(lmp)
{
reinitflag = 1;
}
/* ---------------------------------------------------------------------- */
@ -196,3 +200,16 @@ double BondHarmonic::single(int type, double rsq, int i, int j,
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;
}

1
src/MOLECULE/bond_harmonic.h
View File

@ -36,6 +36,7 @@ class BondHarmonic : public Bond {
void read_restart(FILE *);
void write_data(FILE *);
double single(int, double, int, int, double &);
virtual void *extract(char *, int &);
protected:
double *k,*r0;

215
src/bond_harmonic.cpp
View File

@ -1,215 +0,0 @@
/* ----------------------------------------------------------------------
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 <math.h>
#include <stdlib.h>
#include <string.h>
#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;
}