git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12900 f3b2605a-c512-4ea7-a41b-209d697bcdaa

lib/README

@@ -1,11 +1,11 @@
 This directory contains libraries that can be linked with when
 building LAMMPS, if particular packages are included in a LAMMPS
-build.  The library itself must be built first, so that a lib*.a file
+build.  The library itself must be built first, so that a library file
 exists for LAMMPS to link against.
 
 Each library directory contains a README with additional info about
-how to build the library.  This may require you to edit one of the
+how to acquire and/or build the library.  This may require you to edit
-provided Makefiles to make it suitable for your machine.
+one of the provided Makefiles to make it suitable for your machine.
 
 The libraries included in the LAMMPS distribution are the following:
 
@@ -19,6 +19,8 @@ cuda	      NVIDIA GPU routines, USER-CUDA package
                 from Christian Trott (U Tech Ilmenau)
 gpu	      general GPU routines, GPU package
 	        from Mike Brown (ORNL)
+kim           hooks to KIM library, used by KIM package
+                from Ryan Elliott and Ellad Tadmor (U Minn)
 kokkos        Kokkos package for GPU and many-core acceleration
                 from Kokkos development team (Sandia)
 linalg        set of BLAS and LAPACK routines needed by USER-ATC package
@@ -31,3 +33,5 @@ qmmm	      quantum mechanics/molecular mechanics coupling interface
                 from Axel Kohlmeyer (Temple U)
 reax          ReaxFF potential, REAX package
 	        from Adri van Duin (Penn State) and Aidan Thompson (Sandia)
+voronoi       hooks to Voro++ library, used by compute voronoi/atom command
+	        from Daniel Schwen (LANL)

lib/voronoi/Makefile.lammps

@@ -0,0 +1,5 @@
+# Settings that the LAMMPS build will import when this package is installed
+
+voronoi_SYSINC = 
+voronoi_SYSLIB = 
+voronoi_SYSPATH = 

lib/voronoi/README

@@ -0,0 +1,57 @@
+This directory contains links to the Voro++ library which is required
+to use the VORONOI package and its compute voronoi/atom command in a
+LAMMPS input script.
+
+The Voro++ library is available at http://math.lbl.gov/voro++ and was
+developed by Chris H. Rycroft while at UC Berkeley / Lawrence Berkeley
+Laboratory.
+
+You must perform the following steps yourself, or you can use the
+install.py Python script to automate any or all steps of the process.
+Type "python install.py" for instructions.
+
+1.  Download Voro++ at http://math.lbl.gov/voro++/download
+    either as a tarball or via SVN, and unpack the
+    tarball either in this /lib/voronoi directory
+    or somewhere else on your system.
+
+2.  compile Voro++ from within its home directory
+    % make 
+
+3.  There is no need to install Voro++ if you only wish
+    to use it from LAMMPS.  You can install it if you
+    wish to use it stand-alone or from other codes:
+    a) install under the default /usr/local
+       % sudo make install
+    b) install under a user-writeable location by first
+         changing the PREFIX variable in the config.mk file, then
+       % make install
+
+4.  Create two soft links in this dir (lib/voronoi)
+    to where the Voro++ src directory is.  E.g if you
+    built Voro++ it in this dir:
+      % ln -s voro++-0.4.6/src includelink
+      % ln -s voro++-0.4.6/src liblink
+    Note that these links could also be set to the include and lib
+    directories created by a Voro++ install, if you prefer, e.g.
+      % ln -s /usr/local/include includelink
+      % ln -s /usr/local/lib liblink
+
+When these steps are complete you can build LAMMPS
+with the VORONOI package installed:
+
+% cd lammps/src
+% make yes-voronoi
+% make g++ (or whatever target you wish)
+
+Note that if you download and unpack a new LAMMPS tarball,
+the "includelink" and "liblink" files will be lost
+and you will need to re-create them (step 4).  If you
+built Voro++ in this directory (as opposed to somewhere
+else on your system) and did not install it somewhere
+else, you will also need to repeat steps 1,2,3.
+
+The Makefile.lammps file in this directory is there for compatibility
+with the way other libraries under the lib dir are linked with by
+LAMMPS.  However, Voro++ requires no auxiliary files or
+settings, so its variables are blank.

lib/voronoi/install.py

@@ -0,0 +1,127 @@
+#!usr/local/python
+
+# install.py tool to download, unpack, build, and link to the Voro++ library
+# used to automate the steps described in the README file in this dir
+
+import sys,os,urllib,commands
+
+help = """
+Syntax: install.py -d dir -v version -g -b -i installdir -l incdir libdir
+        specify one or more options, order does not matter
+        -d = dir to download tarball to, unpack tarball in, perform build in
+             dir will be created if it doesn't exist (only last level)
+             default = this dir
+        -v = version of Voro++ to download and work with
+             default = voro++-0.4.6 (current as of Jan 2015)
+        -g = download (grab) tarball from
+             http://math.lbl.gov/voro++/download/dir/version
+        -b = build Voro++ by invoking "make" in its home dir
+             no default
+        -i = install Voro++ by invoking "make install" in its home dir
+             installdir arg is optional:
+               if not specified, installs at PREFIX defined in config.mk file
+               if specified, will overwrite PREFIX and install there
+             if PREFIX starts with /usr, will invoke "sudo make install"
+        -l = create two links to incdir and libdir
+             incdir and libdir are optional (specify neither or both):
+               if specified, includelink and liblink are to those two dirs
+               if not specified and no install, links are to Voro++ src dir
+               if not specified and install performed,
+                 links are to include and lib dirs under PREFIX
+"""
+
+def error():
+  print help
+  sys.exit()
+  
+# parse args
+
+args = sys.argv
+
+if len(args) == 1: error()
+
+dir = "."
+version = "voro++-0.4.6"
+grabflag = 0
+buildflag = 0
+installflag = 0
+linkflag = 0
+
+iarg = 1
+while iarg < len(args):
+  if args[iarg] == "-d":
+    if iarg+2 > len(args): error()
+    dir = args[iarg+1]
+    iarg += 2  
+  elif args[iarg] == "-v":
+    if iarg+2 > len(args): error()
+    version = args[iarg+1]
+    iarg += 2  
+  elif args[iarg] == "-g":
+    grabflag = 1
+    iarg += 1
+  elif args[iarg] == "-b":
+    buildflag = 1
+    iarg += 1
+  elif args[iarg] == "-i":
+    if iarg+2 > len(args): error()
+    if iarg+1 == len(args) or args[iarg+1][0] == '-':
+      installdir = ""
+      iarg += 1
+    else:
+      installdir = args[iarg+1]
+      iarg += 2  
+  elif args[iarg] == "-l":
+    if iarg+2 > len(args): error()
+    if iarg+1 == len(args) or args[iarg+1][0] == '-':
+      incdir = libdir = ""
+      iarg += 1
+    else:
+      incdir = args[iarg+1]
+      libdir = args[iarg+2]
+      iarg += 3
+  else: error()
+
+url = "http://math.lbl.gov/voro++/download/dir/%s.tar.gz" % version
+
+# create dir if does not exist
+
+if not os.path.isdir(dir):
+  if os.path.isfile(dir):
+    print "ERROR: Dir already exists as file"
+    sys.exit()
+  os.mkdir(dir)
+  if not os.path.isdir(dir):
+    print "ERROR: Unable to create dir"
+    sys.exit()
+
+# download and unpack tarball
+
+if grabflag:
+  print "Downloading Voro++ tarball ..."
+  urllib.urlretrieve(url,"%s/%s.tar.gz" % (dir,version))
+  print "Unpacking Voro++ tarball ..."
+  cmd = "cd %s; tar zxvf %s.tar.gz" % (dir,version)
+  txt = commands.getoutput(cmd)
+
+# build Voro++
+
+if buildflag:
+  print "Building Voro++ ..."
+  cmd = "cd %s/%s; make" % (dir,version)
+  txt = commands.getoutput(cmd)
+  print txt
+
+# install Voro++
+
+
+
+  
+# create links in this dir to Voro++ include and lib files
+
+if linkflag:
+  print "Creating links to Voro++ include and lib files"
+  cmd = "ln -s %s/src includelink" % version
+  txt = commands.getoutput(cmd)
+  cmd = "ln -s %s/src liblink" % version
+  txt = commands.getoutput(cmd)