git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@716 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/compute_ebond_atom.cpp

@@ -0,0 +1,163 @@
+/* ----------------------------------------------------------------------
+   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 "string.h"
+#include "compute_ebond_atom.h"
+#include "atom.h"
+#include "neighbor.h"
+#include "comm.h"
+#include "update.h"
+#include "force.h"
+#include "bond.h"
+#include "modify.h"
+#include "domain.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define MIN(a,b) ((a) < (b) ? (a) : (b))
+#define MAX(a,b) ((a) > (b) ? (a) : (b))
+
+/* ---------------------------------------------------------------------- */
+
+ComputeEbondAtom::ComputeEbondAtom(LAMMPS *lmp, int narg, char **arg) :
+  Compute(lmp, narg, arg)
+{
+  if (narg != 3) error->all("Illegal compute ebond/atom command");
+
+  peratom_flag = 1;
+  size_peratom = 0;
+  comm_reverse = 1;
+
+  nmax = 0;
+  energy = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeEbondAtom::~ComputeEbondAtom()
+{
+  memory->sfree(energy);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeEbondAtom::init()
+{
+  if (force->bond == NULL)
+    error->all("Bond style does not support computing per-atom energy");
+
+  int count = 0;
+  for (int i = 0; i < modify->ncompute; i++)
+    if (strcmp(modify->compute[i]->style,"ebond/atom") == 0) count++;
+  if (count > 1 && comm->me == 0)
+    error->warning("More than one compute ebond/atom");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeEbondAtom::compute_peratom()
+{
+  int i,n,i1,i2,type;
+  double delx,dely,delz,rsq,fforce,eng;
+
+  // grow energy array if necessary
+
+  if (atom->nmax > nmax) {
+    memory->sfree(energy);
+    nmax = atom->nmax;
+    energy = (double *) 
+      memory->smalloc(nmax*sizeof(double),"compute/epair/atom:energy");
+    scalar_atom = energy;
+  }
+
+  // clear energy array
+  // n includes ghosts only if newton_bond flag is set
+
+  int nlocal = atom->nlocal;
+  int newton_bond = force->newton_bond;
+
+  if (newton_bond) n = nlocal + atom->nghost;
+  else n = nlocal;
+
+  for (i = 0; i < n; i++) energy[i] = 0.0;
+
+  // compute bond energy for atoms via bond->single()
+  // if neither atom is in compute group, skip that bond
+
+  double **x = atom->x;
+  int *mask = atom->mask;
+  int **bondlist = neighbor->bondlist;
+  int nbondlist = neighbor->nbondlist;
+
+  for (n = 0; n < nbondlist; n++) {
+    i1 = bondlist[n][0];
+    i2 = bondlist[n][1];
+    type = bondlist[n][2];
+    if ((mask[i1] & groupbit) == 0 && (mask[i2] & groupbit) == 0) continue;
+
+    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;
+    force->bond->single(type,rsq,i1,i2,0,fforce,eng);
+    energy[i] += eng;
+    if (newton_bond || i2 < nlocal) energy[i2] += eng;
+  }
+
+  // communicate energy between neigchbor procs
+
+  if (newton_bond) comm->reverse_comm_compute(this);
+
+  // remove double counting of per-atom energy
+
+  for (i = 0; i < nlocal; i++) energy[i] *= 0.5;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int ComputeEbondAtom::pack_reverse_comm(int n, int first, double *buf)
+{
+  int i,m,last;
+
+  m = 0;
+  last = first + n;
+  for (i = first; i < last; i++) buf[m++] = energy[i];
+  return 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeEbondAtom::unpack_reverse_comm(int n, int *list, double *buf)
+{
+  int i,j,m;
+
+  m = 0;
+  for (i = 0; i < n; i++) {
+    j = list[i];
+    energy[j] += buf[m++];
+  }
+}
+
+/* ----------------------------------------------------------------------
+   memory usage of local atom-based array
+------------------------------------------------------------------------- */
+
+int ComputeEbondAtom::memory_usage()
+{
+  int bytes = nmax * sizeof(double);
+  return bytes;
+}

src/compute_ebond_atom.h

@@ -0,0 +1,38 @@
+/* ----------------------------------------------------------------------
+   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.
+------------------------------------------------------------------------- */
+
+#ifndef COMPUTE_EBOND_ATOM_H
+#define COMPUTE_EBOND_ATOM_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputeEbondAtom : public Compute {
+ public:
+  ComputeEbondAtom(class LAMMPS *, int, char **);
+  ~ComputeEbondAtom();
+  void init();
+  void compute_peratom();
+  int pack_reverse_comm(int, int, double *);
+  void unpack_reverse_comm(int, int *, double *);
+  int memory_usage();
+
+ private:
+  int nmax;
+  double *energy;
+};
+
+}
+
+#endif