From f19f5582209c34363c3072b08bafc9de3ac0205b Mon Sep 17 00:00:00 2001
From: Stefan Paquay <stefanpaquay@gmail.com>
Date: Mon, 10 Apr 2017 10:06:03 -0400
Subject: [PATCH] Removed changed bond_harmonic from wrong position.
---
src/MOLECULE/bond_harmonic.cpp | 19 ++-
src/MOLECULE/bond_harmonic.h | 1 +
src/bond_harmonic.cpp | 215 ---------------------------------
3 files changed, 19 insertions(+), 216 deletions(-)
delete mode 100644 src/bond_harmonic.cpp
diff --git a/src/MOLECULE/bond_harmonic.cpp b/src/MOLECULE/bond_harmonic.cpp
index f164a51de4..0763d7d3e2 100644
--- a/src/MOLECULE/bond_harmonic.cpp
+++ b/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;
+}
+
+
diff --git a/src/MOLECULE/bond_harmonic.h b/src/MOLECULE/bond_harmonic.h
index 7c7125b04c..a0fd24577a 100644
--- a/src/MOLECULE/bond_harmonic.h
+++ b/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;
diff --git a/src/bond_harmonic.cpp b/src/bond_harmonic.cpp
deleted file mode 100644
index f0b6d96cc8..0000000000
--- a/src/bond_harmonic.cpp
+++ /dev/null
@@ -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;
-}
-
-
--
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