added plumed

* plumed : first version
* plumed : added dependencies and docs

var/spack/repos/builtin/packages/plumed/package.py

@@ -0,0 +1,82 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+
+class Plumed(Package):
+    """PLUMED is an open source library for free energy calculations in
+    molecular systems which works together with some of the most popular
+    molecular dynamics engines.
+
+    Free energy calculations can be performed as a function of many order
+    parameters with a particular focus on biological problems, using state
+    of the art methods such as metadynamics, umbrella sampling and
+    Jarzynski-equation based steered MD.
+
+    The software, written in C++, can be easily interfaced with both fortran
+    and C/C++ codes.
+    """
+    homepage = 'http://www.plumed.org/'
+    url = 'https://github.com/plumed/plumed2/archive/v2.2.3.tar.gz'
+
+    version('2.2.3', 'a6e3863e40aac07eb8cf739cbd14ecf8')
+
+
+    variant('shared', default=True, description='Builds shared libraries')
+    variant('mpi', default=True, description='Activates MPI support')
+    variant('gsl', default=True, description='Activates GSL support')
+
+    depends_on('zlib')
+    depends_on('blas')
+    depends_on('lapack')
+
+    depends_on('mpi', when='+mpi')
+    depends_on('gsl', when='+gsl')
+
+    def setup_dependent_package(self, module, ext_spec):
+        # Make plumed visible from dependent packages
+        module.plumed = Executable(join_path(self.spec.prefix.bin, 'plumed'))
+
+    def install(self, spec, prefix):
+        # From plumed docs :
+        # Also consider that this is different with respect to what some other
+        # configure script does in that variables such as MPICXX are
+        # completely ignored here. In case you work on a machine where CXX is
+        # set to a serial compiler and MPICXX to a MPI compiler, to compile with
+        # MPI you should use:
+        #
+        # > ./configure CXX="$MPICXX"
+        configure_opts = ['CXX={0}'.format(spec['mpi'].mpicxx)] if '+mpi' in self.spec else []
+        configure_opts.extend([
+            '--prefix={0}'.format(prefix),
+            '--enable-shared={0}'.format('yes' if '+shared' in spec else 'no'),
+            '--enable-mpi={0}'.format('yes' if '+mpi' in spec else 'no'),
+            '--enable-gsl={0}'.format('yes' if '+gsl' in spec else 'no')
+        ])
+
+        configure(*configure_opts)
+        make()
+        make('install')