From e5547724996360c986a6fbcc938d2522cf18f3ae Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Fri, 25 Jan 2013 16:33:31 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9322
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/VORONOI/Install.sh | 36 +++++++
src/VORONOI/Makefile.lammps | 20 ++++
src/VORONOI/README | 37 +++++++
src/VORONOI/compute_voronoi_atom.cpp | 143 +++++++++++++++++++++++++++
src/VORONOI/compute_voronoi_atom.h | 53 ++++++++++
5 files changed, 289 insertions(+)
create mode 100755 src/VORONOI/Install.sh
create mode 100644 src/VORONOI/Makefile.lammps
create mode 100644 src/VORONOI/README
create mode 100644 src/VORONOI/compute_voronoi_atom.cpp
create mode 100644 src/VORONOI/compute_voronoi_atom.h
diff --git a/src/VORONOI/Install.sh b/src/VORONOI/Install.sh
new file mode 100755
index 0000000000..0942ac6cfb
--- /dev/null
+++ b/src/VORONOI/Install.sh
@@ -0,0 +1,36 @@
+# 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
diff --git a/src/VORONOI/Makefile.lammps b/src/VORONOI/Makefile.lammps
new file mode 100644
index 0000000000..33f33d095d
--- /dev/null
+++ b/src/VORONOI/Makefile.lammps
@@ -0,0 +1,20 @@
+# 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
diff --git a/src/VORONOI/README b/src/VORONOI/README
new file mode 100644
index 0000000000..89cf838b45
--- /dev/null
+++ b/src/VORONOI/README
@@ -0,0 +1,37 @@
+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.
diff --git a/src/VORONOI/compute_voronoi_atom.cpp b/src/VORONOI/compute_voronoi_atom.cpp
new file mode 100644
index 0000000000..4d430dea3c
--- /dev/null
+++ b/src/VORONOI/compute_voronoi_atom.cpp
@@ -0,0 +1,143 @@
+/* ----------------------------------------------------------------------
+ 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;
+}
diff --git a/src/VORONOI/compute_voronoi_atom.h b/src/VORONOI/compute_voronoi_atom.h
new file mode 100644
index 0000000000..d285860e6c
--- /dev/null
+++ b/src/VORONOI/compute_voronoi_atom.h
@@ -0,0 +1,53 @@
+/* ----------------------------------------------------------------------
+ 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.
+
+*/
--
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