gentoo resync : 25.08.2018

3 files changed, 161 insertions, 0 deletions

diff --git a/sci-physics/lammps/Manifest b/sci-physics/lammps/Manifest
index e7c2f930b8d4..98e454a1ac8a 100644
--- a/sci-physics/lammps/Manifest
+++ b/sci-physics/lammps/Manifest
@@ -1,3 +1,4 @@
+AUX 1080.patch 922 BLAKE2B 59325abb5d2f9d9e501c34b539a98efea521ee38872f1e2d3850442aac82adaea3a3c32e644f3d2982aa9aa86dbdfb5bd1373175a89acffac63d87ac542919a7 SHA512 a94bba2ad992f85db0f7d7d04cef235a79e4600e353897032d78ffc3e1f899bc340a5ad8aa1d8da41f9783b67d912dab8c3cd2f83a605a9e0c0ef51bdb909279
 AUX fm_exp.patch 347 BLAKE2B 230da9c04160d445a3da1c813453a788ad04b1d174c494ab9dd1de628ba3c1bf7f9aeb5070b165ec545a280208f07254afaa4d9120fffff5ee98975233d9fc9e SHA512 d0c8303bfe623fe766a545e1614f7576709381597e56f7c7634e90768376bccb9fbe37d4c0eeb6491c9b45d911a913a37386e0280ec3f05a90388aad7bb23c3e
 AUX gcc-6.patch 397 BLAKE2B 7ef1bf4e884763d84ea661ad09dc1e373db10a177e1bf09f617edfc6bcefef5d494def037ba62a8ea76d83cb2eba172dc0188ba4f0ad1877b7cadd3a91d1f583 SHA512 eebb9041347dbe260be6028d9462183188ce95f3114873b2a776990aa77c71dd4b0ba37d2fe3fbf0b8bff64f85dfafaec93ad7234502791a1048ab6bfd1d06ed
 AUX lammps-python3-r1.patch 544 BLAKE2B dcde498a0d886f941aefef6818429efe2a9d253285239a122b983a5bc6ab7b7c053f3fa78b24b995b21891c190f3c82d7032d07015f9baf3c525320e7421a3c4 SHA512 833ec755ba4dadf072ced646220a7a68147023548da9eeebdd1d4a6c198ee48fed1e60a7fc26de7093b5d9b77a906e162a7ef4f5f929918196943564f69037d5
@@ -27,6 +28,7 @@ DIST lammps-9Jan17.tar.gz 109694893 BLAKE2B dc3af18d4a7db43d22bc4d2ed79366f7f1b7
 DIST lammps-patch_16Mar2018.tar.gz 91908414 BLAKE2B 0d2363ba507765d439988be9f17390889539ecf22132145f5f5f5411c6c3bf097b278b24b005374e4b176efcfbd01edb48b55076bfa41403718ad14d3905e062 SHA512 2847f9ffa368b966cba4792ebe86ea38dfc1e147647e2b738753121a09689901cea7197d3d95fa69cd065cd1d30aa37cbeffcb78b62ec85d88cd9f3ab25e25c2
 DIST lammps-patch_17Jan2018.tar.gz 91721592 BLAKE2B d606a5fd699f3e7aaa777065532f778e96a5b21b88de3fcce69e79c4931fea233ed1ad68f56120865061623c6e33282b9f23f927a7a9820f8f824a241e5cd823 SHA512 533ada073882e9bfc6431db62c4899005983d9efbbb043bcb50b2b0a7af2b11c411bbcc6523b2ffbd5d46531b24573f4b98a07dc757bacbc2f27bb056d7956ff
 DIST lammps-patch_1Sep2017.tar.gz 88751184 BLAKE2B 013ba612c67767c0e11b64f0b726a81c534ceb763ac9eba9a94ef9e02166278c28cb5937162b83f783b80fef6471b0e265e45245cc5594eaa2b27ec2d5f972cf SHA512 01b56484d6e9d03c0cdc2f8100f571d6e0a354b08bda7f22176744f2724e566443514e7d8abb0571d4207709155441644d4c6dbcf17ee2a8dc4f10cb6c3e8ac1
+DIST lammps-patch_22Aug2018.tar.gz 108761265 BLAKE2B fc509ccd8f5fda9fea9cf7f54b888df235b5d499a0aa3eee24bba81d35c95355cfc72ebb60f32a4adb879c0ab176659ebe634f9bbaeefd54ffc0d02329054f9f SHA512 bb1c11ef9c287b101b9f3483d6b90e55dc69a048529e5076f6f7d46e54802d0d75efc899865d462f9dd76937089e1080a126c1dc4bbb2648eda91cb38ba142b0
 DIST lammps-patch_22Feb2018.tar.gz 91869050 BLAKE2B 09d364b489d4402145b879ca40b290a4e33f39b6e5e4183bcccb09001002cb742917c8792f942a8b64bd992cde5c0f8dcd8b76506048f1392d33d1192aa4551d SHA512 8d4ac0f9cdcf4caa10bfb48129eec21cf31f7ce881b4cbd803c20fb638f7e55a1e645d314e172fe70eab473a4976c7f482e8c059e0c4e82527eb9438437ae146
 DIST lammps-patch_8Mar2018.tar.gz 91878683 BLAKE2B a4cf307769b1ac27c9cbe781a70f307d5275d2ccd4f6f77a2a21f00413ffa0af499577207afd23afd95ef6126071e8b779f6c52d50ff7117afb63161613c9f5b SHA512 57885d12e9e0ea9a6735cc2f7a2a8a9314dacbe9eaf5a46cb6d20fd7e2d0e8b0ebb3e24731eb750861973efe4d3cf0cf5a739cc9d51407f26bf3d556243c186f
 EBUILD lammps-20150210.ebuild 4832 BLAKE2B f857d2e0e82c2e5b05fe89c62fda44b917d8be0a184171235eadee85c97699de5d4f22a1ea20c12a5523702ab376df9c80d486a7751cd3fbc9527a6954e59026 SHA512 fbbfd6768d9ee99f49aea6abb030486a7f80c4aad95412407031499681a2a36997c31cb4873e0ab867425678b952a44284129accde9abe60c1bfb891c38d2dfa
@@ -56,4 +58,5 @@ EBUILD lammps-20180117.ebuild 3040 BLAKE2B 74b48a09ab862dc1fb0d7b1fc927b16250926
 EBUILD lammps-20180222.ebuild 3040 BLAKE2B 74b48a09ab862dc1fb0d7b1fc927b16250926d7b528d1d36a8cbe1fb3ce1fd58522355bb7559f7a4ae999b5748d0b66e2982c218a8acd40435243825d6a07cc2 SHA512 6965f3a6102e86b375482a35061ffbd6d1b3ee2bd7e8023f66c639af9630e29face9be627196cb0658e28b9b09a19f55b5bd62688370a8f01cc78152b5952b80
 EBUILD lammps-20180308.ebuild 3040 BLAKE2B 74b48a09ab862dc1fb0d7b1fc927b16250926d7b528d1d36a8cbe1fb3ce1fd58522355bb7559f7a4ae999b5748d0b66e2982c218a8acd40435243825d6a07cc2 SHA512 6965f3a6102e86b375482a35061ffbd6d1b3ee2bd7e8023f66c639af9630e29face9be627196cb0658e28b9b09a19f55b5bd62688370a8f01cc78152b5952b80
 EBUILD lammps-20180316.ebuild 3038 BLAKE2B a212f0fa069fb7e116ce13b44dc9351dbd59fbc9da4fb70994b5bf182c3eb2456029fa75e0640d5225ae87e7fa77185962a6feb19a26222dfe736b582feb651a SHA512 860d93f1837193c778d14b3d77c5b64aace3161501159d364002037b92e3179c2fcac408bbb1f3aa1ffcc52106530c326f14551762e25eb38c5c8713a226b906
+EBUILD lammps-20180822.ebuild 2808 BLAKE2B c627112df16849842409b56a6be66ea52b79a848b5279bcc321e770ad854365d51863464e3f0cf2454a61caac809c80353114829b1fa4985ad4e311d38a48beb SHA512 ca505928c1c73438f89b1ddf2d80fd0277ce5745bb92b76343a82891f4efff9702cede0a469b1897cccd4d12c733db19e4c2a4b878449b0026e6a4b06e1cea39
 MISC metadata.xml 1338 BLAKE2B 553629a0b3221db88a37cd6b0bfa806da9265caf2df038736211351a87ac34af5a98f0e7f3e34246d814a378cd64b1ed82d69f4c26e18c3a7700441f8be6fa2d SHA512 b3556e8444b4cb42d1fa80cc8735e11e07cd2928af67104d4518b874e167d5755840c3585e3ffefa88057f84d711cafe0a60405323b4ad6a9546c19d4a5d94bd
diff --git a/sci-physics/lammps/files/1080.patch b/sci-physics/lammps/files/1080.patch
new file mode 100644
index 000000000000..85538b2a638c
--- /dev/null
+++ b/sci-physics/lammps/files/1080.patch
@@ -0,0 +1,29 @@
+From a10bb4b96f40f3b5574b0fade2cfece8bf4c6fc9 Mon Sep 17 00:00:00 2001
+From: Christoph Junghans <junghans@lanl.gov>
+Date: Thu, 23 Aug 2018 15:02:36 -0600
+Subject: [PATCH] cmake: fix link issue with --as-needed
+
+---
+ cmake/CMakeLists.txt | 5 ++++-
+ 1 file changed, 4 insertions(+), 1 deletion(-)
+
+diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
+index 460d177c92..51997593db 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -276,11 +276,14 @@ endif()
+ 
+ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
+   find_package(LAPACK)
+-  if(NOT LAPACK_FOUND)
++  find_package(BLAS)
++  if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
+     enable_language(Fortran)
+     file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.[fF])
+     add_library(linalg STATIC ${LAPACK_SOURCES})
+     set(LAPACK_LIBRARIES linalg)
++  else()
++    list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
+   endif()
+ endif()
+ 
diff --git a/sci-physics/lammps/lammps-20180822.ebuild b/sci-physics/lammps/lammps-20180822.ebuild
new file mode 100644
index 000000000000..dfa18f8327bf
--- /dev/null
+++ b/sci-physics/lammps/lammps-20180822.ebuild
@@ -0,0 +1,129 @@
+# Copyright 1999-2018 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? ( ${PYTHON_REQUIRED_USE} )"
+
+# https://github.com/lammps/lammps/pull/1080
+PATCHES=( "${FILESDIR}/1080.patch" )
+
+S="${WORKDIR}/${MY_P}/cmake"
+
+src_configure() {
+	local mycmakeargs=(
+	    -DCMAKE_INSTALL_SYSCONFDIR="${EPREFIX}/etc"
+	    -DBUILD_SHARED_LIBS=ON
+		-DBUILD_MPI=$(usex mpi)
+		-DPKG_GPU=$(usex cuda)
+		-DGPU_API=CUDA
+		-DENABLE_TESTING=$(usex test)
+		-DPKG_ASPHERE=ON
+		-DPKG_BODY=ON
+		-DPKG_CLASS2=ON
+		-DPKG_COLLOID=ON
+		-DPKG_COMPRESS=ON
+		-DPKG_CORESHELL=ON
+		-DPKG_DIPOLE=ON
+		-DPKG_GRANULAR=ON
+		-DPKG_KSPACE=ON
+		-DFFT=FFTW3
+		-DPKG_MANYBODY=ON
+		-DPKG_MC=ON
+		-DPKG_MEAM=ON
+		-DPKG_MISC=ON
+		-DPKG_MOLECULE=ON
+		-DPKG_PERI=ON
+		-DPKG_QEQ=ON
+		-DPKG_REAX=ON
+		-DPKG_REPLICA=ON
+		-DPKG_RIGID=ON
+		-DPKG_SHOCK=ON
+		-DPKG_SNAP=ON
+		-DPKG_SRD=ON
+		-DPKG_PYTHON=ON
+		-DPKG_MPIIO=$(usex mpi)
+		-DPKG_VORONOI=ON
+		-DPKG_USER-ATC=ON
+		-DPKG_USER-AWPMD=ON
+		-DPKG_USER-CGDNA=ON
+		-DPKG_USER-CGSDK=ON
+		-DPKG_USER-COLVARS=ON
+		-DPKG_USER-DIFFRACTION=ON
+		-DPKG_USER-DPD=ON
+		-DPKG_USER-DRUDE=ON
+		-DPKG_USER-EFF=ON
+		-DPKG_USER-FEP=ON
+		-DPKG_USER-H5MD=$(usex mpi)
+		-DPKG_USER-LB=$(usex mpi)
+		-DPKG_USER-MANIFOLD=ON
+		-DPKG_USER-MEAMC=ON
+		-DPKG_USER-MGPT=ON
+		-DPKG_USER-MISC=ON
+		-DPKG_USER-MOLFILE=ON
+		-DPKG_USER-NETCDF=$(usex netcdf)
+		-DPKG_USER-PHONON=ON
+		-DPKG_USER-QTB=ON
+		-DPKG_USER-REAXC=ON
+		-DPKG_USER-SMD=ON
+		-DPKG_USER-SMTBQ=ON
+		-DPKG_USER-SPH=ON
+		-DPKG_USER-TALLY=ON
+	)
+	cmake-utils_src_configure
+}
+
+src_install() {
+	cmake-utils_src_install
+
+	# 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
+}