sci-physics/lammps: Include bench subdirectory

Using the `examples` USE flag did not include the `bench` subdirectory,
which is needed for some of the examples.

Fixes: #637672
Package-Manager: Portage-2.3.13, Repoman-2.3.3

diff --git a/sci-physics/lammps/lammps-20170901-r1.ebuild b/sci-physics/lammps/lammps-20170901-r1.ebuild
new file mode 100644 (file)
index 0000000..6d06f93
--- /dev/null
+++ b/sci-physics/lammps/lammps-20170901-r1.ebuild
@@ -0,0 +1,131 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
+
+inherit cmake-utils fortran-2 python-r1
+
+convert_month() {
+       local months=( "" Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec )
+       echo ${months[${1#0}]}
+}
+
+MY_PV="patch_$((10#${PV:6:2}))$(convert_month ${PV:4:2})${PV:0:4}"
+MY_P="${PN}-${MY_PV}"
+
+DESCRIPTION="Large-scale Atomic/Molecular Massively Parallel Simulator"
+HOMEPAGE="http://lammps.sandia.gov/"
+SRC_URI="https://github.com/lammps/lammps/archive/${MY_PV}.tar.gz -> ${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="cuda examples gzip lammps-memalign mpi netcdf python test"
+
+DEPEND="
+       app-arch/gzip
+       media-libs/libpng:0
+       sys-libs/zlib
+       mpi? (
+               virtual/mpi
+               sci-libs/hdf5[mpi]
+       )
+       python? ( ${PYTHON_DEPS} )
+       sci-libs/voro++
+       virtual/blas
+       virtual/lapack
+       sci-libs/fftw:3.0
+       netcdf? ( sci-libs/netcdf )
+       cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
+       dev-cpp/eigen:3
+       "
+RDEPEND="${DEPEND}"
+
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+S="${WORKDIR}/${MY_P}/cmake"
+
+src_configure() {
+       local mycmakeargs=(
+           -DBUILD_SHARED_LIBS=ON
+               -DENABLE_MPI=$(usex mpi)
+               -DENABLE_GPU=$(usex cuda)
+               -DENABLE_TESTING=$(usex test)
+               -DENABLE_ASPHERE=ON
+               -DENABLE_BODY=ON
+               -DENABLE_CLASS2=ON
+               -DENABLE_COLLOID=ON
+               -DENABLE_COMPRESS=ON
+               -DENABLE_CORESHELL=ON
+               -DENABLE_DIPOLE=ON
+               -DENABLE_GRANULAR=ON
+               -DENABLE_KSPACE=ON
+               -DFFT=FFTW3
+               -DENABLE_MANYBODY=ON
+               -DENABLE_MC=ON
+               -DENABLE_MEAM=ON
+               -DENABLE_MISC=ON
+               -DLAMMPS_XDR=ON #630444
+               -DENABLE_MOLECULE=ON
+               -DENABLE_PERI=ON
+               -DENABLE_QEQ=ON
+               -DENABLE_REAX=ON
+               -DENABLE_REPLICA=ON
+               -DENABLE_RIGID=ON
+               -DENABLE_SHOCK=ON
+               -DENABLE_SNAP=ON
+               -DENABLE_SRD=ON
+               -DENABLE_PYTHON=ON
+               -DENABLE_MPIIO=$(usex mpi)
+               -DENABLE_VORONOI=ON
+               -DENABLE_USER-ATC=ON
+               -DENABLE_USER-AWPMD=ON
+               -DENABLE_USER-CGDNA=ON
+               -DENABLE_USER-CGSDK=ON
+               -DENABLE_USER-COLVARS=ON
+               -DENABLE_USER-DIFFRACTION=ON
+               -DENABLE_USER-DPD=ON
+               -DENABLE_USER-DRUDE=ON
+               -DENABLE_USER-EFF=ON
+               -DENABLE_USER-FEP=ON
+               -DENABLE_USER-H5MD=$(usex mpi)
+               -DENABLE_USER-LB=$(usex mpi)
+               -DENABLE_USER-MANIFOLD=ON
+               -DENABLE_USER-MEAMC=ON
+               -DENABLE_USER-MGPT=ON
+               -DENABLE_USER-MISC=ON
+               -DENABLE_USER-MOLFILE=ON
+               -DENABLE_USER-NETCDF=$(usex netcdf)
+               -DENABLE_USER-PHONON=ON
+               -DENABLE_USER-QTB=ON
+               -DENABLE_USER-REAXC=ON
+               -DENABLE_USER-SMD=ON
+               -DENABLE_USER-SMTBQ=ON
+               -DENABLE_USER-SPH=ON
+               -DENABLE_USER-TALLY=ON
+       )
+       cmake-utils_src_configure
+}
+
+src_install() {
+       cmake-utils_src_install
+
+       local LAMMPS_POTENTIALS="usr/share/${PN}/potentials"
+       insinto "/${LAMMPS_POTENTIALS}"
+       doins "${S}"/../potentials/*
+       echo "LAMMPS_POTENTIALS=${EROOT}${LAMMPS_POTENTIALS}" > 99lammps
+       doenvd 99lammps
+
+       # Install python script.
+       use python && python_foreach_impl python_domodule "${S}"/../python/lammps.py
+
+       if use examples; then
+               for d in examples bench; do
+                       local LAMMPS_EXAMPLES="/usr/share/${PN}/${d}"
+                       insinto "${LAMMPS_EXAMPLES}"
+                       doins -r "${S}"/../${d}/*
+               done
+       fi
+}

diff --git a/sci-physics/lammps/metadata.xml b/sci-physics/lammps/metadata.xml
index 8f2d53d1312a603b05077772d357827d18010a9f..be0e36d7abee7789af861abd05a472c3fe811de2 100644 (file)
--- a/sci-physics/lammps/metadata.xml
+++ b/sci-physics/lammps/metadata.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-  <longdescription lang="en">
+       <longdescription lang="en">
                LAMMPS is a classical molecular dynamics code, and an acronym for
                Large-scale Atomic/Molecular Massively Parallel Simulator.
 
@@ -15,18 +15,18 @@
                techniques and a spatial-decomposition of the simulation domain. The
                code is designed to be easy to modify or extend with new functionality. 
        </longdescription>
-  <use>
-    <flag name="lammps-memalign">Enables the use of the posix_memalign()
+       <use>
+               <flag name="lammps-memalign">Enables the use of the posix_memalign()
                        call instead of malloc() when large chunks or memory are allocated
                        by LAMMPS. Aliengnment is on 16 byte boundaries.</flag>
-    <flag name="cuda">Enable cuda non-bonded kernels</flag>
-  </use>
-  <maintainer type="person">
-    <email>nicolasbock@gentoo.org</email>
-       <name>Nicolas Bock</name>
-  </maintainer>
-<maintainer type="project">
-    <email>sci-physics@gentoo.org</email>
-    <name>Gentoo Physics Project</name>
-  </maintainer>
+               <flag name="cuda">Enable cuda non-bonded kernels</flag>
+       </use>
+       <maintainer type="person">
+               <email>nicolasbock@gentoo.org</email>
+               <name>Nicolas Bock</name>
+       </maintainer>
+       <maintainer type="project">
+               <email>sci-physics@gentoo.org</email>
+               <name>Gentoo Physics Project</name>
+       </maintainer>
 </pkgmetadata>