git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9322 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/VORONOI/Install.sh

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+# Install/unInstall package files in LAMMPS
+# edit 2 Makefile.package files to include/exclude package info
+
+if (test $1 = 1) then
+
+  if (test -e ../Makefile.package) then
+    sed -i -e 's/[^ \t]*voronoi[^ \t]* //g' ../Makefile.package
+    sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(voronoi_SYSINC) |' ../Makefile.package
+    sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(voronoi_SYSLIB) |' ../Makefile.package
+    sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(voronoi_SYSPATH) |' ../Makefile.package
+  fi
+
+  if (test -e ../Makefile.package.settings) then
+    sed -i -e '/^include.*VORONOI.*$/d' ../Makefile.package.settings
+    # multiline form needed for BSD sed on Macs
+    sed -i -e '4 i \
+include ..\/VORONOI\/Makefile.lammps
+' ../Makefile.package.settings
+  fi
+
+  cp compute_voronoi_atom.h ..
+  cp compute_voronoi_atom.cpp ..
+
+elif (test $1 = 0) then
+
+  if (test -e ../Makefile.package) then
+    sed -i -e 's/[^ \t]*voronoi[^ \t]* //g' ../Makefile.package
+  fi
+
+  if (test -e ../Makefile.package.settings) then
+    sed -i -e '/^include.*VORONOI.*$/d' ../Makefile.package.settings
+  fi
+
+  rm -f ../compute_voronoi_atom.h
+  rm -f ../compute_voronoi_atom.cpp
+fi

src/VORONOI/Makefile.lammps

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+# This file contains the hooks to build and link LAMMPS with the Voro++
+# library so that a LAMMPS input script can calculate a Voronoi tesselation,
+# via the compute voronoi/atom command.
+# 
+# See the README in this directory for more info on installing Voro++.
+# 
+# When you build LAMMPS with the VORONOI package installed, it will use the
+# 3 settings in this file.  They should be set as follows.
+# 
+# voronoi_SYSINC = a path to the Voro++ include files
+# voronoi_SYSLIB = the Voro++ library
+# voronoi_SYSPATH = a path to the Voro++ library
+
+# -----------------------------------------------------------
+
+# Settings that the LAMMPS build will import when this package is installed
+
+voronoi_SYSINC = -I/usr/local/include/voro++
+voronoi_SYSLIB = -lvoro++
+voronoi_SYSPATH = -L/usr/local/lib

src/VORONOI/README

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+The VORONOI package adds a compute voronoi/atom command which
+calculates a Voronoi tesselation of the system.
+
+It uses the Voro++ library, available at http://math.lbl.gov/voro++ to
+compute the tesselation locally on each processor.  
+
+== Installation of the Voro++ library ==
+
+1.  Download Voro++ at http://math.lbl.gov/voro++/download
+    which gives instructions for using SVN to check-out the source:
+    % svn checkout https://codeforge.lbl.gov/anonscm/voro/trunk
+
+2.  compile Voro++
+    % make 
+
+3.  install Voro++ at the default location (/usr/local) 
+    % sudo make install
+
+3b. ..or change the PREFIX variable in the config.mk file 
+    to a location that is writable by the user i.e.
+    PREFIX=/home/maxuser/install/
+
+4.  In the LAMMPS src directory add the VORONOI package
+    % make yes-voronoi
+
+4b. if a different PREFIX than the default was used to install Voro++
+    update the paths in the src/VORONOI/Makefile.lammps file
+
+5.  Compile LAMMPS (you should know how that works)
+
+
+== Credits and license ==
+
+This compute was written by Daniel Schwen (daniel@schwen.de) and is
+licensed under the GPLv2 license.
+
+Please contribute changes back to the community.

src/VORONOI/compute_voronoi_atom.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: Daniel Schwen
+------------------------------------------------------------------------- */
+
+#include "math.h"
+#include "string.h"
+#include "stdlib.h"
+#include "compute_voronoi_atom.h"
+#include "atom.h"
+#include "update.h"
+#include "modify.h"
+#include "domain.h"
+#include "memory.h"
+#include "error.h"
+#include "comm.h"
+
+#include <vector>
+#include "voro++.hh"
+
+using namespace LAMMPS_NS;
+using namespace voro;
+
+/* ---------------------------------------------------------------------- */
+
+ComputeVoronoi::ComputeVoronoi(LAMMPS *lmp, int narg, char **arg) :
+  Compute(lmp, narg, arg)
+{
+  if (narg != 3) error->all(FLERR,"Illegal compute voronoi/atom command");
+
+  peratom_flag = 1;
+  size_peratom_cols = 2;
+
+  nmax = 0;
+  voro = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeVoronoi::~ComputeVoronoi()
+{
+  memory->destroy(voro);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeVoronoi::init()
+{
+  if (domain->dimension != 3)
+    error->all(FLERR,"Compute voronoi/atom not allowed for 2d systems");
+  if (domain->triclinic != 0)
+    error->all(FLERR,"Compute voronoi/atom not allowed for triclinic boxes");
+
+  int count = 0;
+  for (int i = 0; i < modify->ncompute; i++)
+    if (strcmp(modify->compute[i]->style,"voronoi/atom") == 0) count++;
+  if (count > 1 && comm->me == 0)
+    error->warning(FLERR,"More than one compute voronoi/atom command");
+}
+
+/* ----------------------------------------------------------------------
+   gather compute vector data from other nodes
+------------------------------------------------------------------------- */
+
+void ComputeVoronoi::compute_peratom()
+{
+  int i;
+
+  invoked_peratom = update->ntimestep;
+
+  // grow per atom array if necessary
+
+  int local = atom->nlocal;
+  if (nlocal > nmax) {
+    memory->destroy(voro);
+    nmax = atom->nmax;
+    memory->create(voro,nmax,size_peratom_cols,"voronoi/atom:voro");
+    array_atom = voro;
+  }
+
+  // n = # of voro++ spatial hash cells
+  // TODO: make square
+
+  int nall = nlocal + atom->nghost;
+  int n = int(floor( pow( double(nall)/8.0, 0.333333 ) ));
+  n = (n==0) ? 1 : n;
+
+  // initialize voro++ container
+  // preallocates 8 atoms per cell
+  // voro++ allocates more memory if needed
+
+  double *sublo = domain->sublo;
+  double *subhi = domain->subhi;
+  double *cut = comm->cutghost;
+
+  container con(sublo[0]-cut[0],subhi[0]+cut[0],
+                sublo[1]-cut[1],subhi[1]+cut[1],
+                sublo[2]-cut[2],subhi[2]+cut[2],
+                n,n,n,false,false,false,8); 
+
+  // pass coordinates for local and ghost atoms to voro++
+
+  double **x = atom->x;
+  for (i = 0; i < nall; i++)
+    con.put(i,x[i][0],x[i][1],x[i][2]);
+
+  // invoke voro++ and fetch results for owned atoms in group
+
+  std::vector<int> neigh;
+
+  voronoicell_neighbor c;
+  c_loop_all cl(con);
+  if (cl.start()) do if (con.compute_cell(c,cl)) {
+    i = cl.pid();
+    if (i < nlocal && (mask[i] & groupbit)) {
+      voro[i][0] = c.volume();
+      c.neighbors(neigh);
+      voro[i][1] = neigh.size();
+    } else if (i < nlocal) voro[i][0] = voro[i][1] = 0.0;
+  } while (cl.inc());
+}
+
+/* ----------------------------------------------------------------------
+   memory usage of local atom-based array
+------------------------------------------------------------------------- */
+
+double ComputeVoronoi::memory_usage()
+{
+  double bytes = size_peratom_cols * nmax * sizeof(double);
+  return bytes;
+}

src/VORONOI/compute_voronoi_atom.h

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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.
+------------------------------------------------------------------------- */
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(voronoi/atom,ComputeVoronoi)
+
+#else
+
+#ifndef LMP_COMPUTE_VORONOI_H
+#define LMP_COMPUTE_VORONOI_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputeVoronoi : public Compute {
+ public:
+  ComputeVoronoi(class LAMMPS *, int, char **);
+  ~ComputeVoronoi();
+  void init();
+  void compute_peratom();
+  double memory_usage();
+
+ private:
+  int nmax;
+  double **voro;
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+*/