git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@560 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/compute_coord_atom.cpp

@@ -0,0 +1,128 @@
+/* ----------------------------------------------------------------------
+   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 "stdlib.h"
+#include "compute_coord_atom.h"
+#include "atom.h"
+#include "modify.h"
+#include "neighbor.h"
+#include "force.h"
+#include "pair.h"
+#include "comm.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
+  Compute(lmp, narg, arg)
+{
+  if (narg != 4) error->all("Illegal compute centro/atom command");
+
+  cutoff = atof(arg[3]);
+
+  peratom_flag = 1;
+  size_peratom = 0;
+  neigh_full_once = 1;
+
+  nmax = 0;
+  coordination = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeCoordAtom::~ComputeCoordAtom()
+{
+  memory->sfree(coordination);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeCoordAtom::init()
+{
+  if (force->pair == NULL || cutoff > force->pair->cutforce) 
+    error->all("Compute coord/atom cutoff is longer than pairwise cutoff");
+
+  int count = 0;
+  for (int i = 0; i < modify->ncompute; i++)
+    if (strcmp(modify->compute[i]->style,"coord/atom") == 0) count++;
+  if (count > 1 && comm->me == 0)
+    error->warning("More than one compute coord/atom defined");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeCoordAtom::compute_peratom()
+{
+  int j,k,jj,kk,n,numneigh;
+  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+  int *neighs;
+
+  // grow coordination array if necessary
+
+  if (atom->nlocal > nmax) {
+    memory->sfree(coordination);
+    nmax = atom->nmax;
+    coordination = (double *) 
+      memory->smalloc(nmax*sizeof(double),"compute/coord/atom:coordination");
+    scalar_atom = coordination;
+  }
+
+  // if needed, build a full neighbor list
+
+  if (!neighbor->full_every) neighbor->build_full();
+
+  // compute coordination number for each atom in group
+  // use full neighbor list to count atoms less than cutoff
+
+  double **x = atom->x;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+  int nall = atom->nlocal + atom->nghost;
+  double cutsq = cutoff*cutoff;
+
+  for (int i = 0; i < nlocal; i++)
+    if (mask[i] & groupbit) {
+      xtmp = x[i][0];
+      ytmp = x[i][1];
+      ztmp = x[i][2];
+      neighs = neighbor->firstneigh_full[i];
+      numneigh = neighbor->numneigh_full[i];
+
+      n = 0;
+      for (k = 0; k < numneigh; k++) {
+	j = neighs[k];
+	if (j >= nall) j %= nall;
+
+	delx = xtmp - x[j][0];
+	dely = ytmp - x[j][1];
+	delz = ztmp - x[j][2];
+	rsq = delx*delx + dely*dely + delz*delz;
+	if (rsq < cutsq) n++;
+      }
+
+      coordination[i] = n;
+    }
+}
+/* ----------------------------------------------------------------------
+   memory usage of local atom-based array
+------------------------------------------------------------------------- */
+
+int ComputeCoordAtom::memory_usage()
+{
+  int bytes = nmax * sizeof(double);
+  return bytes;
+}

src/compute_coord_atom.h

@@ -0,0 +1,37 @@
+/* ----------------------------------------------------------------------
+   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_COORD_ATOM_H
+#define COMPUTE_COORD_ATOM_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputeCoordAtom : public Compute {
+ public:
+  ComputeCoordAtom(class LAMMPS *, int, char **);
+  ~ComputeCoordAtom();
+  void init();
+  void compute_peratom();
+  int memory_usage();
+
+ private:
+  int nmax;
+  double cutoff;
+  double *coordination;
+};
+
+}
+
+#endif

src/style.h

@@ -73,6 +73,7 @@ CommandStyle(write_restart,WriteRestart)
 
 #ifdef ComputeInclude
 #include "compute_centro_atom.h"
+#include "compute_coord_atom.h"
 #include "compute_epair_atom.h"
 #include "compute_etotal_atom.h"
 #include "compute_ke_atom.h"
@@ -90,6 +91,7 @@ CommandStyle(write_restart,WriteRestart)
 
 #ifdef ComputeClass
 ComputeStyle(centro/atom,ComputeCentroAtom)
+ComputeStyle(coord/atom,ComputeCoordAtom)
 ComputeStyle(epair/atom,ComputeEpairAtom)
 ComputeStyle(etotal/atom,ComputeEtotalAtom)
 ComputeStyle(ke/atom,ComputeKEAtom)