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

2 files changed, 144 insertions, 13 deletions

diff --git a/sci-physics/lammps/lammps-20170901-r1.ebuild b/sci-physics/lammps/lammps-20170901-r1.ebuild
new file mode 100644
index 000000000000..6d06f933adae
--- /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 8f2d53d1312a..be0e36d7abee 100644
--- 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>