Removed changed bond_harmonic from wrong position.

src/MOLECULE/bond_harmonic.cpp

@@ -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;
+}
+
+

src/MOLECULE/bond_harmonic.h

@@ -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;

src/bond_harmonic.cpp

-/* ----------------------------------------------------------------------
-   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;
-}
-
-