git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6643 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/USER-MISC/bond_harmonic_shift.cpp

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+/* ----------------------------------------------------------------------
+   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.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;
+
+/* ---------------------------------------------------------------------- */
+
+BondHarmonicShift::BondHarmonicShift(LAMMPS *lmp) : Bond(lmp) {}
+
+/* ---------------------------------------------------------------------- */
+
+BondHarmonicShift::~BondHarmonicShift()
+{
+  if (allocated) {
+    memory->destroy(setflag);
+    memory->destroy(k);
+    memory->destroy(r0);
+    memory->destroy(r1);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void BondHarmonicShift::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];
+    domain->minimum_image(delx,dely,delz);
+
+    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 = 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 BondHarmonicShift::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 BondHarmonicShift::coeff(int narg, char **arg)
+{
+  if (narg != 4) error->all("Incorrect args for bond coefficients");
+  if (!allocated) allocate();
+
+  int ilo,ihi;
+  force->bounds(arg[0],atom->nbondtypes,ilo,ihi);
+
+  double Umin = force->numeric(arg[1]);   // energy at minimum
+  double r0_one = force->numeric(arg[2]); // position of minimum
+  double r1_one = force->numeric(arg[3]);  // position where energy = 0
+
+  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("Incorrect args for bond coefficients");
+}
+
+/* ----------------------------------------------------------------------
+   return an equilbrium bond length 
+------------------------------------------------------------------------- */
+
+double BondHarmonicShift::equilibrium_distance(int i)
+{
+  return r0[i];
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes out coeffs to restart file 
+------------------------------------------------------------------------- */
+
+void BondHarmonicShift::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 BondHarmonicShift::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;
+}
+
+/* ---------------------------------------------------------------------- */
+
+double BondHarmonicShift::single(int type, double rsq, int i, int j)
+{
+  double r = sqrt(rsq);  
+  double dr = r - r0[type];
+  double dr2=r0[type]-r1[type];
+  
+  return k[type]*(dr*dr - dr2*dr2);
+}