Abinit: Added package(s) (#1995)

* First version of Abinit package

* Ignore *.swp files

* Add libxc, etsf_io packages

* AtomPaw package

* Make Abinit depend on mpi@2: and external version of libxc, netcdf, hdf5, etsf_io

* etsf_io: install Fortran modules in prefix.include

* Remove etsf_io from abinit requirements

* Add libxc2.2.1 (required by Abinit and atompaw)

* Cleanup

* Run make check

* Cleanup

* Use ld_flags instead of hard-coded libs, fix pep8, add copyright

* Put scalapack before lapackblas

.gitignore

@@ -15,6 +15,7 @@
 /share/spack/modules
 /share/spack/lmod
 /TAGS
+*.swp
 /htmlcov
 .coverage
 #*

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

+##############################################################################
+# 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
+##############################################################################
+#
+# Author: Matteo Giantomassi <matteo.giantomassiNOSPAM AT uclouvain.be>
+# Date: October 11, 2016
+
+from spack import *
+
+
+class Abinit(Package):
+    """ABINIT is a package whose main program allows one to find the total
+    energy, charge density and electronic structure of systems made of
+    electrons and nuclei (molecules and periodic solids) within
+    Density Functional Theory (DFT), using pseudopotentials and a planewave
+    or wavelet basis. ABINIT also includes options to optimize the geometry
+    according to the DFT forces and stresses, or to perform molecular dynamics
+    simulations using these forces, or to generate dynamical matrices,
+    Born effective charges, and dielectric tensors, based on Density-Functional
+    Perturbation Theory, and many more properties. Excited states can be
+    computed within the Many-Body Perturbation Theory (the GW approximation and
+    the Bethe-Salpeter equation), and Time-Dependent Density Functional Theory
+    (for molecules). In addition to the main ABINIT code, different utility
+    programs are provided.
+    """
+
+    homepage = "http://www.abinit.org"
+    url      = "http://ftp.abinit.org/abinit-8.0.8b.tar.gz"
+
+    # Versions before 8.0.8b are not supported.
+    version("8.0.8b", "abc9e303bfa7f9f43f95598f87d84d5d")
+
+    variant('mpi', default=True,
+            description='Builds with MPI support. Requires MPI2+')
+    variant('openmp', default=False,
+            description='Enables OpenMP threads. Use threaded FFTW3')
+    variant('scalapack', default=False,
+            description='Enables scalapack support. Requires MPI')
+    # variant('elpa', default=False,
+    # description='Uses elpa instead of scalapack. Requires MPI')
+
+    # TODO: To be tested.
+    # It was working before the last `git pull` but now all tests crash.
+    # For the time being, the default is netcdf3 and the internal fallbacks
+    variant('hdf5', default=False,
+            description='Enables HDF5+Netcdf4 with MPI. WARNING: experimental')
+
+    # Add dependencies
+    # currently one cannot forward options to virtual packages, see #1712.
+    # depends_on("blas", when="~openmp")
+    # depends_on("blas+openmp", when="+openmp")
+    depends_on('blas')
+    depends_on("lapack")
+
+    # Require MPI2+
+    depends_on("mpi@2:", when="+mpi")
+
+    depends_on("scalapack", when="+scalapack+mpi")
+    # depends_on("elpa", when="+elpa+mpi~openmp")
+    # depends_on("elpa+openmp", when="+elpa+mpi+openmp")
+
+    depends_on("fftw+float", when="~openmp")
+    depends_on("fftw+float+openmp", when="+openmp")
+
+    depends_on("netcdf-fortran", when="+hdf5")
+    depends_on("hdf5+mpi", when='+mpi+hdf5')  # required for NetCDF-4 support
+
+    # pin libxc version
+    depends_on("libxc@2.2.1")
+
+    def validate(self, spec):
+        """
+        Checks if incompatible variants have been activated at the same time
+
+        :param spec: spec of the package
+        :raises RuntimeError: in case of inconsistencies
+        """
+        error = 'you cannot ask for \'+{variant}\' when \'+mpi\' is not active'
+
+        if '+scalapack' in spec and '~mpi' in spec:
+            raise RuntimeError(error.format(variant='scalapack'))
+
+        if '+elpa' in spec and ('~mpi' in spec or '~scalapack' in spec):
+            raise RuntimeError(error.format(variant='elpa'))
+
+    def install(self, spec, prefix):
+        self.validate(spec)
+
+        options = ['--prefix=%s' % prefix]
+        oapp = options.append
+
+        if '+mpi' in spec:
+            # MPI version:
+            # let the configure script auto-detect MPI support from mpi_prefix
+            oapp("--with-mpi-prefix=%s" % spec["mpi"].prefix)
+            oapp("--enable-mpi=yes")
+            oapp("--enable-mpi-io=yes")
+
+        # Activate OpenMP in Abinit Fortran code.
+        if '+openmp' in spec:
+            oapp('--enable-openmp=yes')
+
+        # BLAS/LAPACK
+        if '+scalapack' in spec:
+            oapp("--with-linalg-flavor=custom+scalapack")
+            linalg = (spec['scalapack'].scalapack_libs +
+                      spec['lapack'].lapack_libs + spec['blas'].blas_libs)
+
+        # elif '+elpa' in spec:
+        else:
+            oapp("--with-linalg-flavor=custom")
+            linalg = spec['lapack'].lapack_libs + spec['blas'].blas_libs
+
+        oapp("--with-linalg-libs=%s" % linalg.ld_flags)
+
+        # FFTW3: use sequential or threaded version if +openmp
+        fftflavor, fftlibs = "fftw3", "-lfftw3 -lfftw3f"
+        if '+openmp' in spec:
+            fftflavor = "fftw3-threads"
+            fftlibs = "-lfftw3_omp -lfftw3 -lfftw3f"
+
+        options.extend([
+            "--with-fft-flavor=%s" % fftflavor,
+            "--with-fft-incs=-I%s" % spec["fftw"].prefix.include,
+            "--with-fft-libs=-L%s %s" % (spec["fftw"].prefix.lib, fftlibs),
+        ])
+        oapp("--with-dft-flavor=atompaw+libxc")
+
+        # LibXC library
+        options.extend([
+            "with_libxc_incs=-I%s" % spec["libxc"].prefix.include,
+            "with_libxc_libs=-L%s -lxcf90 -lxc" % spec["libxc"].prefix.lib,
+        ])
+
+        # Netcdf4/HDF5
+        if "+hdf5" in spec:
+            oapp("--with-trio-flavor=netcdf")
+            hdf_libs = "-L%s -lhdf5_hl -lhdf5" % spec["hdf5"].prefix.lib
+            options.extend([
+                "--with-netcdf-incs=-I%s" % (
+                    spec["netcdf-fortran"].prefix.include),
+                "--with-netcdf-libs=-L%s -lnetcdff -lnetcdf %s" % (
+                    spec["netcdf-fortran"].prefix.lib, hdf_libs),
+            ])
+        else:
+            # Use internal fallbacks (netcdf3)
+            oapp("--with-trio-flavor=netcdf-fallback")
+
+        configure(*options)
+        make()
+
+        # make("check")
+        # make("tests_in")
+        make("install")

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

+##############################################################################
+# 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 Atompaw(Package):
+    """A Projector Augmented Wave (PAW) code for generating
+    atom-centered functions.
+
+    Official website: http://pwpaw.wfu.edu
+
+    User's guide: ~/doc/atompaw-usersguide.pdf
+    """
+    homepage = "http://users.wfu.edu/natalie/papers/pwpaw/man.html"
+    url = "http://users.wfu.edu/natalie/papers/pwpaw/atompaw-4.0.0.13.tar.gz"
+
+    version('4.0.0.13', 'af4a042380356f6780183c4b325aad1d')
+    version('3.1.0.3', 'c996a277e11707887177f47bbb229aa6')
+
+    depends_on("lapack")
+    depends_on("blas")
+
+    # pin libxc version
+    depends_on("libxc@2.2.1")
+
+    def install(self, spec, prefix):
+        options = ['--prefix=%s' % prefix]
+
+        linalg = spec['lapack'].lapack_libs + spec['blas'].blas_libs
+        options.extend([
+            "--with-linalg-libs=%s" % linalg.ld_flags,
+            "--enable-libxc",
+            "--with-libxc-incs=-I%s" % spec["libxc"].prefix.include,
+            "--with-libxc-libs=-L%s -lxcf90 -lxc" % spec["libxc"].prefix.lib,
+        ])
+
+        configure(*options)
+        make(parallel=False)  # parallel build fails
+        make("check")
+        make("install")

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

+##############################################################################
+# 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 EtsfIo(Package):
+    """ETSF_IO is a library implementing the Nanoquanta/ETSF file
+    format specifications.
+
+    ETSF_IO enables an architecture-independent exchange of crystallographic
+    data, electronic wavefunctions, densities and potentials, as well as
+    spectroscopic data. It is meant to be used by quantum-physical and
+    quantum-chemical applications relying upon Density Functional Theory (DFT).
+    """
+
+    homepage = "http://www.etsf.eu/resources/software/libraries_and_tools"
+    url = "https://launchpad.net/etsf-io/1.0/1.0.4/+download/etsf_io-1.0.4.tar.gz"
+
+    version('1.0.4', '32d0f7143278bd925b334c69fa425da1')
+
+    depends_on("netcdf-fortran")
+    depends_on("hdf5+mpi~cxx", when='+mpi')  # required for NetCDF-4 support
+
+    def install(self, spec, prefix):
+        options = ['--prefix=%s' % prefix]
+        oapp = options.append
+
+        # Specify installation directory for Fortran module files
+        # Default is [INCLUDEDIR/FC_TYPE]
+        oapp("--with-moduledir=%s" % prefix.include)
+
+        # Netcdf4/HDF
+        hdf_libs = "-L%s -lhdf5_hl -lhdf5" % spec["hdf5"].prefix.lib
+        options.extend([
+            "--with-netcdf-incs=-I%s" % spec["netcdf-fortran"].prefix.include,
+            "--with-netcdf-libs=-L%s -lnetcdff -lnetcdf %s" % (
+                spec["netcdf-fortran"].prefix.lib, hdf_libs),
+        ])
+
+        configure(*options)
+
+        make()
+        make("check")
+        make("install")

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

@@ -34,6 +34,7 @@ class Libxc(Package):
 
     version('3.0.0', '8227fa3053f8fc215bd9d7b0d36de03c')
     version('2.2.2', 'd9f90a0d6e36df6c1312b6422280f2ec')
+    version('2.2.1', '38dc3a067524baf4f8521d5bb1cd0b8f')
 
     def install(self, spec, prefix):
         # Optimizations for the Intel compiler, suggested by CP2K