New package: qbox (#4711)

* New package: qbox

* API changes

* Use install instead of shutil for comd

* Use any BLAS library

* Fix typo

* Python2 fix

* python2 + fix backslashes

* Modified to respond to ld_flags correctly

* Modified to use ld_flags

* Add ld_flags support

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

@@ -23,7 +23,6 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 
-import shutil
 from spack import *
 
 
@@ -50,7 +49,7 @@ def edit(self, spec, prefix):
         with working_dir('src-mpi'):
             filter_file(r'^CC\s*=.*', 'CC = %s' % self.spec['mpi'].mpicc,
                         'Makefile.vanilla')
-            shutil.move('Makefile.vanilla', 'Makefile')
+            install('Makefile.vanilla', 'Makefile')
 
     def install(self, spec, prefix):
-        shutil.move('bin', prefix)
+        install_tree('bin', prefix.bin)

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

@@ -70,6 +70,11 @@ class Fftw(AutotoolsPackage):
     depends_on('autoconf', type='build', when='+pfft_patches')
     depends_on('libtool', type='build', when='+pfft_patches')
 
+    @property
+    def libs(self):
+        result = find_libraries(['libfftw3'], root=self.prefix, recurse=True)
+        return result
+
     def autoreconf(self, spec, prefix):
         if '+pfft_patches' in spec:
             autoreconf = which('autoreconf')

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

@@ -0,0 +1,93 @@
+##############################################################################
+# 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 NOTICE and LICENSE files 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
+##############################################################################
+
+import shutil
+from spack import *
+
+
+class Qbox(MakefilePackage):
+    """Qbox is a C++/MPI scalable parallel implementation of first-principles
+    molecular dynamics (FPMD) based on the plane-wave, pseudopotential
+    formalism. Qbox is designed for operation on large parallel computers."""
+
+    homepage = "http://qboxcode.org/"
+    url      = "http://qboxcode.org/download/qbox-1.63.7.tgz"
+
+    version('1.63.7', '6b0cf5656f816a1a59e22b268387af33')
+    version('1.63.5', 'da3161ab6a455793f2133dd03c04077c')
+    version('1.63.4', '8596f32c8fb7e7baa96571c655aaee07')
+    version('1.63.2', '55e8f13f37c8e1f43ca831791e3af1da')
+    version('1.63.0', '1436c884c553ab026b7f787307e5e6ed')
+    version('1.62.3', 'f07e038ab92b85956794e91a40346dbf')
+    version('1.60.9', '53b0df612e56bb65e8220d9d9dc8d395')
+    version('1.60.4', '060846c9fa03b1f3d7d5ce24a9491de2')
+    version('1.60.0', '3856cdc38a27dc17705844c4b9241a21')
+    version('1.58.0', 'ec0e6b79fa0ed06742212b1142e36b6a')
+    version('1.56.2', 'df7a4217d059a5d351d92e480ed14112')
+    version('1.54.4', '8f1a23af7d871317de93810b664ad3aa')
+    version('1.54.2', 'aeefee061255dbb36ca7e49378f63ad5')
+    version('1.52.3', '1862f2b2056cdf49ec4f746d45a7f1a6')
+    version('1.52.2', 'e406deb4c46176f1c15c226868bf61e2')
+    version('1.50.4', 'b06ff877257884e4fac321fb5a486266')
+    version('1.50.2', '171660b1bb5e57637f019fef055fb764')
+    version('1.50.1', '1da528b39da134f86f134432e8fada79')
+    version('1.47.0', '86f402651d440e05adc94168d6105da7')
+    version('1.45.3', '73b99a73dcbb1b5be9f66f3284750205')
+    version('1.45.1', '59e0c2583769b7586981c0d6ffa1b267')
+    version('1.45.0', '2c5bfbadfffd330c8c2fe294a10a08e4')
+    version('1.44.0', 'c46a2f0f68fe9229aa77779da188cea9')
+
+    depends_on('mpi')
+    depends_on('blas')
+    depends_on('scalapack')
+    depends_on('fftw')
+    depends_on('xerces-c')
+
+    build_directory = 'src'
+
+    def edit(self, spec, prefix):
+        with open('src/spack.mk', 'w') as mkfile:
+            mkfile.write('CXX = {0}\n'.format(spec['mpi'].mpicxx))
+            mkfile.write('LD = $(CXX)\n')
+            qbox_libs = spec['fftw'].libs + spec['xerces-c'].libs + \
+                spec['scalapack'].libs + spec['blas'].libs
+            mkfile.write('LDFLAGS = {0}\n'.format(qbox_libs.ld_flags))
+            mkfile.write('DFLAGS = {0}\n'.format(' -D'.join((
+                '',
+                '_LARGEFILE_SOURCE', 'USE_MPI', 'USE_XERCES',
+                'XERCESC_3', 'MPICH_IGNORE_CXX_SEEK', 'SCALAPACK',
+                'USE_FFTW3', 'FFTWMEASURE', 'FFTW3_2D', 'ADD_',
+            ))))
+            mkfile.write('CXXFLAGS = {0}\n'.format(' '.join((
+                '-g', '-O3', '$(DFLAGS)',
+            ))))
+        filter_file('$(TARGET)', 'spack', 'src/Makefile', string=True)
+
+    def install(self, spec, prefix):
+        mkdir(prefix.src)
+        install('src/qb', prefix.src)
+        shutil.move('test', prefix)
+        shutil.move('xml', prefix)
+        shutil.move('util', prefix)