From 1ad7d856feeefbe5056ea295903e7f154e280f36 Mon Sep 17 00:00:00 2001
From: Stefan Paquay <stefanpaquay@gmail.com>
Date: Mon, 10 Apr 2017 09:57:54 -0400
Subject: [PATCH] Added forgotten #include string to bond_harmonic.cpp
---
src/bond_harmonic.cpp | 215 ++++++++++++++++++++++++++++++++++++++++++
1 file changed, 215 insertions(+)
create mode 100644 src/bond_harmonic.cpp
diff --git a/src/bond_harmonic.cpp b/src/bond_harmonic.cpp
new file mode 100644
index 0000000000..f0b6d96cc8
--- /dev/null
+++ b/src/bond_harmonic.cpp
@@ -0,0 +1,215 @@
+/* ----------------------------------------------------------------------
+ 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;
+}
+
+
--
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