Added forgotten #include string to bond_harmonic.cpp

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;
+}
+
+