gentoo resync : 16.06.2019

9 files changed, 62 insertions, 484 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index afcb5812232c..cd635dc327b8 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 7b4a1c176053..ba4761ab8503 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,17 +1,16 @@
-DIST gromacs-2016.5.tar.gz 27369491 BLAKE2B 4a8bf1ae3e298ac2e26ec476130720dc3ef00db5d999e3a45fdbfd7fbfe7e94fbc86be6ff0f2f23552769c8bc851ce49c73f6fc1ab13f372523279b93e7794d7 SHA512 9cb8ff88871aa5df0967c60ba303c03296c6fa3c215cd01b26259df7753f0014f04222078ab4b84a66a1f709997837134d5c0f74da19b78322e410010c9d9e10
 DIST gromacs-2018.3.tar.gz 29915626 BLAKE2B 6e6eeafecdd923a25b4a2a78a8e89f793639b57ffbd63f19d133d8474302f9a381041f138a509dadb42b36e25fe508729e860efb6b0c75cdbf01d924b0a8fd83 SHA512 3c4d6eb3942d7b54d01c94c6f6f5ae706e0f5d4f9901ea11a56fde4df97b1a9112007f2cb13feea0f19f30c89f57ae80ff53a8f5203b8cdff103aa903cd0dc8f
 DIST gromacs-2018.7.tar.gz 29912662 BLAKE2B 0714b28ec2443f3201275fc2fa6db1202a059161362134d4de03a900a3a67fe9d31ba8c058d5ee971198fecd69379fcd389f03d25c61f50b8460c43ba5c564d5 SHA512 fbc3b847b70b1396f412b8f4a1b977268651f8d53a222dcf6349fe563ff6319e096484209a24351e382bc9162a949b3900591f5b469c32dd9effeb894f03c172
 DIST gromacs-2019.2.tar.gz 33437869 BLAKE2B bebe4942688dace148856d4491b687b8e0fd2c86d7fbd9eecdb46824d316a0fc3854464ecafa79d8db92327ee8467be204b050c11f1e71132184efd812c3bf09 SHA512 da7ff24e8485774e22d1c2464fbe64675c3305ef0e21a3d17e363201031952e5d4a9b81f572d5284fb6f2596ed99daf62fe78d653387d9d714274f46bc750183
-DIST regressiontests-2016.5.tar.gz 67641413 BLAKE2B 4fcd30c198f3acbbabf1104c040d9a686de49536a97dbeb14732bfa0ed3cf37aa61b1b0f45393668985b993d1f1862a8985e416af819cf9793f5964f3e4f43cc SHA512 31764fd99cc4185d61de5d4443ee482c27b13533451a24aa0e4899997ce275a63685424eafacae38b1a3ffd4ce0d5ebe02a90348953b04c104f91376f0edfdff
+DIST gromacs-2019.3.tar.gz 33441419 BLAKE2B 79319dd23982c65c7c4d8e5f633cef0c7fd99a38a4e0cc9030a3ffb0fdfc07a4fbfbcfa942896f23a143b747e044fae645498a3e6992497d1f1a7d966f80b2b0 SHA512 de9f54d095b45ea7efd1043f83a40f6c778a6e3e2067a01f48d1ce843d68d226061933ca28a3edb635b795a8ddd5ef9deb8ed1114aa3235bc8039db8ff7d0218
 DIST regressiontests-2018.3.tar.gz 67857855 BLAKE2B acd7a05ae79d1b4eb47d0c68a3fec9ee19f028a5019f39c37a033f48cf6da2a468375180ad6ceca9ac4f685a8bead38550663a47d6427b51f84c32a5c810e5f0 SHA512 57980d49efe6dcc3b3d14b5913a30c68fc1de5b679ef986fec1a149c76f67139b0299c3ee2825451461294fab5f345c7ad4f42e90f8991b81aafe9c369f3ff0b
 DIST regressiontests-2018.7.tar.gz 67856738 BLAKE2B 955ae8b5e74f90fec704cf41fbd00bd8c09d754f950551fe0adfcd407db6fdb4491a3815149ea37d36c747316c79d462e823b9f6b26f2376bf90d87aad95731b SHA512 c2ff390750bd99faebcd8d5dd8ad6dbf2b00113ed888bddddf985dbf95d7f347093adb67f3c396547b3e2990de330fddb7efe83ded91a72cf97c82a1dac7e826
 DIST regressiontests-2019.2.tar.gz 67643003 BLAKE2B 4178de5d62f194a81f97e442c10f123dc59c5e63f2078f7f07135709f3f6e530e0d237bf40264b285c084519d5ace75dfcbcddc16dc740c4f17233dc33542e45 SHA512 c1f25bc770d3f0a873c887d5563c1cd88179e81211b70ce6f5015696e6fa0b6931a8da7a449f2b223f3105b9e2e7eca67248e96fbfc2a7fd5fb360ba616f22ff
-EBUILD gromacs-2016.5.ebuild 7973 BLAKE2B 72b0552595f3187c91bfff89cbe49ac5dbfa1396d82f32428e1519e98aff243f5a68e1c7679386abc8eb0bbb62f40f594def4fa2bf8460134631f5c9e734c456 SHA512 a269b5bc8a484bd27b75f0301267d432d1d0ffa3389f190779acf474410401f8b81fd5ae4fec286472c99e75076da592f06566a777773518b25f2b2b29f9967c
-EBUILD gromacs-2016.9999.ebuild 7976 BLAKE2B 24237f4e253faef5df7600baafa01ac9db0e7eacee6c4a5cef6e9e17961e159c701ef8573b3cea4703511f759d7659c5bbd925c8739c1bcf172f9fdf296c7cb2 SHA512 80307361e6b22dcf182bf77c587c31089eb1e85cbda69276bcc90fd85f10a143f69b2568b4ace41104d602793de3fd7219271ca28228ae0b621e23e7c7b58227
+DIST regressiontests-2019.3.tar.gz 67640462 BLAKE2B ed6c176a144e0407be66585be5d6090c31c047498bc5f48f59685108de91f2f9ddb2d22b291a15e6ffa1db848aae19b94a79c8c3d34b1067680f759a179953dd SHA512 822e905fb488ce308eb9324d93f78106da5252c773c7941d49c6162e73bdff109aeca1f0d57216c6dd6536a4c41d80013fa1cee2f5206b0c4160a3e5b4a31315
 EBUILD gromacs-2018.3.ebuild 7824 BLAKE2B cc5ec314f5338c269d00bb8ec7af34f38134c59dd7009fc593cfa559cc68e69753f17bd8b77f5156f08999a83980d1e1c5684fd9ed489386af309f1babf850aa SHA512 d47c8c6e1e4c1dc5cd2429e5c77f04af822b5995cdd1f93a1331442dfe95d0192bda5565d3837575100f2fe841f1006cd38698ced727525c716d1925c0e65579
 EBUILD gromacs-2018.7.ebuild 7825 BLAKE2B 8ec9d3451720801d0249a6964b3df6dfd774e66a6ec790a0ebaba967d9d9fa23785ed5c229e8821de40f663d6adfaaab1c056ac36b78ebb1ce8213b0bffee7f7 SHA512 5e39cf72d8344c4690161a1ce4a6961ff2fa492167d4dc768de623c3ead7bb40d42a808f5a20386c39530bc33e9d74feca69181929a387c2fb1d41e69dfe7f91
 EBUILD gromacs-2018.9999.ebuild 7827 BLAKE2B 97a2437061a55854dd2799c8bdbec6a342586fc480785ea52de8d6b612c747ace1fba0a1fc3dbec9904cafcb3abdabd363ba0d6285cfc44f60964047c52f5b74 SHA512 975f2bcfdd93df006ec2a8f439a2a90e4c9079c58209ec2828b5647d96c29f7eef7fd0c79da844cc8d4e449b573a75884b19c951649c0028133d3fa87b03934c
-EBUILD gromacs-2019.2.ebuild 9113 BLAKE2B 9e111d428ab09ddabe000b17e645a1d35de5efb88cfc3989a2119be9e3533eb8c4c3d8df9e396e0dc8140081e6cdfa8e70323e32e0a56c8b88e39b5d27482fc0 SHA512 b8f234c0dfe092a26d86e6ac856fd9c3221dbda55686d2ea341ba42883fa0b29ed188dfee37bb7859ba069a90a83ddaa2ab117f8694c696ceb58350d25fe393f
+EBUILD gromacs-2019.2.ebuild 9112 BLAKE2B 54e93c462fec627d154f385ec910c682a3b57fcded8bec082d1dddc73d774e876422d9b24cd50f9984f1a412db7e85e1e862fd94ac295d6e0318d24e07d53a6c SHA512 4c4906a7a982cfe9fffd4375c469b8f637b3e73ea4dde7ce37d517e916b59418a2f80a007ae516be7611b4a6f6379ac444df6946f70968671bccdf0060d85e97
+EBUILD gromacs-2019.3.ebuild 9114 BLAKE2B 9286e7663d622e30ca491577c880827006f3bb2a68d2e3fd9c26fdc97541c12ebef06ab9d3b73ea89e0bbb079e79188c10b387366948920ee631c37da0be4ac5 SHA512 70fd567f7cdb9d8f2c7609b56c4522b5c3cc8094856ace84c001daeae390de788ff3c103987a44f09a11bf9cc6802a071511140bbd881423cefb8e70d1f8189c
 EBUILD gromacs-2019.9999.ebuild 9114 BLAKE2B 9286e7663d622e30ca491577c880827006f3bb2a68d2e3fd9c26fdc97541c12ebef06ab9d3b73ea89e0bbb079e79188c10b387366948920ee631c37da0be4ac5 SHA512 70fd567f7cdb9d8f2c7609b56c4522b5c3cc8094856ace84c001daeae390de788ff3c103987a44f09a11bf9cc6802a071511140bbd881423cefb8e70d1f8189c
 EBUILD gromacs-9999.ebuild 8094 BLAKE2B 932061da2ed5e2e20d1ca0c1ef9000fd946bbe3720cea6d585863e4bf2d7821b7e7b934d4d33d20a4c6040865c58c61c11f5bc8ce98812ad4f946a95b1c1fb83 SHA512 e3987a36622751c20e6a5b3fa88d43c94e24a30cd513eb2e9f9375457413c9ad131ec3f3012ec94e7574d50233c00d9edd357a44413ac0873edb88df82487ba0
 MISC metadata.xml 1123 BLAKE2B 5e945fdf580821b62aaf40c5b4b3252b366284f2df16f02e7c3cf913e5ad498a6a8548bc2e4275d8b80373f88d9879ab59d401e619595014262dcebfe8660f9f SHA512 bac0c94aee957487d8af8a1e06323cb286c8773cef2070d91aff9fdad63eb1bd55f2678dd58dca21b33d8d3e7110d2526e280abd538e3653aee638f6de72090d
diff --git a/sci-chemistry/gromacs/gromacs-2016.5.ebuild b/sci-chemistry/gromacs/gromacs-2016.5.ebuild
deleted file mode 100644
index bef5457975aa..000000000000
--- a/sci-chemistry/gromacs/gromacs-2016.5.ebuild
+++ /dev/null
@@ -1,275 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
-
-if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
-		https://github.com/gromacs/gromacs.git
-		https://repo.or.cz/r/gromacs.git"
-	[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
-	inherit git-r3
-else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
-	KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
-	fftw? ( sci-libs/fftw:3.0 )
-	hwloc? ( <sys-apps/hwloc-2 )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )
-	"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	doc? (
-		app-doc/doxygen
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)
-	dev-libs/tinyxml2
-	"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	cuda? ( single-precision )
-	mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
-	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
-	use openmp && ! tc-has-openmp && \
-		die "Please switch to an openmp compatible compiler"
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="${EGIT_BRANCH}" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	xdg_environment_reset #591952
-
-	cmake-utils_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use cpu_flags_x86_sse2 && acce="SSE2"
-	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-	use cpu_flags_x86_avx && acce="AVX_256"
-	use cpu_flags_x86_avx2 && acce="AVX2_256"
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl && has_version "=sci-libs/mkl-10*"; then
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
-			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
-		)
-	elif use mkl && has_version "<sci-libs/mkl-11.3"; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/linux/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/linux/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		-DGMX_X11=$(usex X)
-		-DGMX_EXTERNAL_BLAS=$(usex blas)
-		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-		-DGMX_OPENMP=$(usex openmp)
-		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_USE_TNG=$(usex tng)
-		-DGMX_BUILD_MANUAL=$(usex doc)
-		-DGMX_HWLOC=$(usex hwloc)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_SIMD="$acce"
-		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DBUILD_TESTING=OFF
-		-DGMX_BUILD_UNITTESTS=OFF
-		-DGMX_EXTERNAL_TINYXML2=ON
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local cuda=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( -DGMX_GPU=ON )
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=OFF
-			-DGMX_THREAD_MPI=$(usex threads)
-			"${cuda[@]}"
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda}
-			-DGMX_OPENMM=OFF
-			-DGMX_BUILD_MDRUN_ONLY=ON
-			-DBUILD_SHARED_LIBS=OFF
-			-DGMX_BUILD_MANUAL=OFF
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		# not 100% necessary for rel ebuilds as available from website
-		if use doc; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile manual
-		fi
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		if use doc; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-		use mpi || continue
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_install
-	done
-
-	if use tng; then
-		insinto /usr/include/tng
-		doins src/external/tng_io/include/tng/*h
-	fi
-	# drop unneeded stuff
-	rm "${ED}"usr/bin/GMXRC* || die
-	for x in "${ED}"usr/bin/gmx-completion-*.bash ; do
-		local n=${x##*/gmx-completion-}
-		n="${n%.bash}"
-		cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
-		newbashcomp "${T}"/"${n}" "${n}"
-	done
-	rm "${ED}"usr/bin/gmx-completion*.bash || die
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite:"
-	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	einfo  "https://dx.doi.org/10.1021/ct700301q"
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-2019.2.ebuild b/sci-chemistry/gromacs/gromacs-2019.2.ebuild
index 066004be22c5..df6c7eaf37ff 100644
--- a/sci-chemistry/gromacs/gromacs-2019.2.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019.2.ebuild
@@ -19,7 +19,7 @@ if [[ $PV = *9999* ]]; then
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
 		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
-	KEYWORDS="~amd64 ~arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+	KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 fi
 
 ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
diff --git a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild b/sci-chemistry/gromacs/gromacs-2019.3.ebuild
index 937bdf673d2a..dc5c8185316e 100644
--- a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019.3.ebuild
@@ -5,7 +5,9 @@ EAPI=6
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+PYTHON_COMPAT=( python2_7 )
+
+inherit bash-completion-r1 cmake-utils cuda eutils multilib python-single-r1 readme.gentoo-r1 toolchain-funcs xdg-utils
 
 if [[ $PV = *9999* ]]; then
 	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
@@ -30,7 +32,7 @@ HOMEPAGE="http://www.gromacs.org/"
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -39,10 +41,12 @@ CDEPEND="
 		x11-libs/libICE
 		)
 	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 )
+	opencl? ( virtual/opencl )
 	fftw? ( sci-libs/fftw:3.0 )
-	hwloc? ( <sys-apps/hwloc-2 )
+	hwloc? ( sys-apps/hwloc )
 	lapack? ( virtual/lapack )
+	lmfit? ( sci-libs/lmfit )
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
 	"
@@ -50,17 +54,18 @@ DEPEND="${CDEPEND}
 	virtual/pkgconfig
 	doc? (
 		app-doc/doxygen
+		dev-python/sphinx[${PYTHON_USEDEP}]
+		media-gfx/mscgen
 		dev-texlive/texlive-latex
 		dev-texlive/texlive-latexextra
 		media-gfx/imagemagick
-	)
-	dev-libs/tinyxml2
-	"
+	)"
 RDEPEND="${CDEPEND}"
 
 REQUIRED_USE="
 	|| ( single-precision double-precision )
 	cuda? ( single-precision )
+	cuda? ( !opencl )
 	mkl? ( !blas !fftw !lapack )"
 
 DOCS=( AUTHORS README )
@@ -111,6 +116,28 @@ src_prepare() {
 	fi
 
 	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
+
+	# try to create policy for imagemagik
+	mkdir -p ${HOME}/.config/ImageMagick
+	cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF
+	<?xml version="1.0" encoding="UTF-8"?>
+	<!DOCTYPE policymap [
+	<!ELEMENT policymap (policy)+>
+	!ATTLIST policymap xmlns CDATA #FIXED ''>
+	<!ELEMENT policy EMPTY>
+	<!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
+			name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
+			stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
+	]>
+	<policymap>
+		<policy domain="coder" rights="read | write" pattern="PS" />
+		<policy domain="coder" rights="read | write" pattern="PS2" />
+		<policy domain="coder" rights="read | write" pattern="PS3" />
+		<policy domain="coder" rights="read | write" pattern="EPS" />
+		<policy domain="coder" rights="read | write" pattern="PDF" />
+		<policy domain="coder" rights="read | write" pattern="XPS" />
+	</policymap>
+	EOF
 }
 
 src_configure() {
@@ -135,24 +162,25 @@ src_configure() {
 			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
 			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
 		)
-	elif use mkl && has_version "<sci-libs/mkl-11.3"; then
+	elif use mkl; then
 		local bits=$(get_libdir)
 		fft_opts=( -DGMX_FFT_LIBRARY=mkl
 			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
 			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
 		)
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/linux/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/linux/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
 	else
 		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
 	fi
 
+	if use lmfit; then
+		local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL )
+	else
+		local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL )
+	fi
+
 	mycmakeargs_pre+=(
 		"${fft_opts[@]}"
+		"${lmfit_opts[@]}"
 		-DGMX_X11=$(usex X)
 		-DGMX_EXTERNAL_BLAS=$(usex blas)
 		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
@@ -163,11 +191,10 @@ src_configure() {
 		-DGMX_HWLOC=$(usex hwloc)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_SIMD="$acce"
-		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
 		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DBUILD_TESTING=OFF
-		-DGMX_BUILD_UNITTESTS=OFF
-		-DGMX_EXTERNAL_TINYXML2=ON
+		-DBUILD_TESTING=$(usex test)
+		-DGMX_BUILD_UNITTESTS=$(usex test)
+		-DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
 		${extra}
 	)
 
@@ -181,11 +208,15 @@ src_configure() {
 		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
 		local cuda=( "-DGMX_GPU=OFF" )
 		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( -DGMX_GPU=ON )
+			cuda=( "-DGMX_GPU=ON" )
+		local opencl=( "-DGMX_USE_OPENCL=OFF" )
+		use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" )
 		mycmakeargs=(
 			${mycmakeargs_pre[@]} ${p}
 			-DGMX_MPI=OFF
 			-DGMX_THREAD_MPI=$(usex threads)
+			-DGMXAPI=$(usex gmxapi)
+			"${opencl[@]}"
 			"${cuda[@]}"
 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
 			-DGMX_BINARY_SUFFIX="${suffix}"
@@ -201,6 +232,7 @@ src_configure() {
 			-DGMX_THREAD_MPI=OFF
 			-DGMX_MPI=ON ${cuda}
 			-DGMX_OPENMM=OFF
+			-DGMXAPI=OFF
 			-DGMX_BUILD_MDRUN_ONLY=ON
 			-DBUILD_SHARED_LIBS=OFF
 			-DGMX_BUILD_MANUAL=OFF
diff --git a/sci-chemistry/molequeue/Manifest b/sci-chemistry/molequeue/Manifest
index 5297d5f0b10b..d70775668870 100644
--- a/sci-chemistry/molequeue/Manifest
+++ b/sci-chemistry/molequeue/Manifest
@@ -1,7 +1,4 @@
-AUX molequeue-0.8.0-cmake.patch 4285 BLAKE2B 916f0c248f487b6d7c11dd34e20364b5dfb494d2e27e657bc5a13f9d6c3f71ae2ab6818bace7df04c0a1388f6f85c42e3e0ab96fc5d3d892c0a95612532baf28 SHA512 9031fd3e5efe0a9332db4b1f46d82486fc804cef55c9fab35030bc562d1a40f5f16a02a5eb8c31bf4c50c7a0abcf22c11da5bdd4e2a45a37a8b6f4ff994d3ad6
 AUX molequeue-0.9.0-qt-5.11b3.patch 6380 BLAKE2B 8d4a66dab1b233880269559cff9b566593ec271fc2b0982a92eec1d60a7c2c42e7186c0007be2afc956200d28c250822b36d3146d1a9ff1fb33b574f97969c60 SHA512 09429566422a1490c2621fd895238d4aeba3c324563cab411290a60942c749e9fa967dd6399f4f4efdc635fa77c339d08824def3e6a175aadc1061893df7df9c
-DIST molequeue-0.8.0.tar.gz 643072 BLAKE2B c9ba0a93e4dac3027de1aeb5ae6c62fc3e4229786973d6c3b56af4b70476b0ed54a563837d489912a40c76b9ce0013e13633a327eb314c34305ba17d7f0b4cf7 SHA512 b9539d2ad2c67188ad254f186c1d67c122a15a32047801c632a1613a4f9c887f38baf2da1bb80cb123391948c2a44604fb1082e475ca6de1e683fbe51266ac84
 DIST molequeue-0.9.0.tar.gz 604015 BLAKE2B 37e7f404a0fefb40defb198295659372121fbe770269c2f9fb92e856aceb8222bec5e83939ecea061b76f925c0cbde1be0a854db41f992a92a2b2b9e0651f2e1 SHA512 87ddd8ca59227cab60c0ce2643e5bd435d9ac7e23b929659b95f190478734a5b71d4935f37d03eeadbc39939cbffb3604e0a283d50b0a23a1a000b57c1fce335
-EBUILD molequeue-0.8.0.ebuild 1613 BLAKE2B 21ddbe84fb9ad674cc796330ee2a26f5fdcfc7f6187869d2775e5679bbb2bf2dc147d80c79617867f9b1424bf07eb797315fb5cab3cb59359c39171315cf353c SHA512 6971db16063f3c1dfad7a780adae7aaf438c2957f46698a1739a65ac3d658ccac501f687db18eddc1305a4e6a220cac206d781f5783cdcb0d38b4e952c550ed7
-EBUILD molequeue-0.9.0.ebuild 1471 BLAKE2B ace497ea7a4c5ebaae14755f27ac18348fc7190246f7292318d50d2f1b120152fb626af0efd735f27b9d1aed4d615912261f304b589f4f947f3461d6989f26cb SHA512 05afccaad6d36c69a8838278a9e4d5af3257aff61c99467958fd62074c7e4823100d15e80c86521e626fc3625d1333c5cdaea78a16f51fa3ed9a166f34ea3325
+EBUILD molequeue-0.9.0.ebuild 1479 BLAKE2B f00bb04fa08a720367daa464399daa71f47c4fe34263dc699811cc9ea0683a065d06a30e8be9d0ccd46071329829cae739a8c3fa5773998c1c3b8fb6d53653a1 SHA512 a6a5643849c85231652e9d1ff1c93e599a539eca0cc5572bab8ae9b837cc2f6ad8f5c04d96774493187f3f3cb216f163e7990a9d62abb60caefcde9ad610aedb
 MISC metadata.xml 1257 BLAKE2B 181f9234f11d0cb14fd6b93b42ef153c089d4df8dcb7cf72bc710dbee11bf4bb573f37ea703d02dbe17fa1f39c0aaf591c6d28ad1429abced5108b9ce39f2030 SHA512 10e3dd48ec1e54bc0d47d4c2f0aca427875cc0ceb59a93ab41ab2734607aa6474e80f3ae622e45fa319753591f16439118dd0b301068cb3e16fd79ff11a4f058
diff --git a/sci-chemistry/molequeue/files/molequeue-0.8.0-cmake.patch b/sci-chemistry/molequeue/files/molequeue-0.8.0-cmake.patch
deleted file mode 100644
index 3fd8a9db76be..000000000000
--- a/sci-chemistry/molequeue/files/molequeue-0.8.0-cmake.patch
+++ /dev/null
@@ -1,106 +0,0 @@
-From 45cbc9f167d1158bc73e87618cc08ede2e3f2911 Mon Sep 17 00:00:00 2001
-From: "Marcus D. Hanwell" <marcus.hanwell@kitware.com>
-Date: Thu, 1 Jun 2017 13:17:20 -0400
-Subject: [PATCH] Removed GenerateExportHeader, bumped CMake min
-
-Removed the GenerateExportHeader copy we had, use CMake's, and bump the
-minimum to ensure it has the features we expect.
----
- CMakeLists.txt                   |   2 +-
- cmake/GenerateExportHeader.cmake | 375 ---------------------------------------
- cmake/exportheader.cmake.in      |  35 ----
- 3 files changed, 1 insertion(+), 411 deletions(-)
- delete mode 100644 cmake/GenerateExportHeader.cmake
- delete mode 100644 cmake/exportheader.cmake.in
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index df93bc8..a107c8f 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -1,4 +1,4 @@
--cmake_minimum_required(VERSION 2.8.8 FATAL_ERROR)
-+cmake_minimum_required(VERSION 3.3 FATAL_ERROR)
- 
- project(MoleQueue)
- 
-From aae92632d10fe98728c3e73bfd891e502e8712fd Mon Sep 17 00:00:00 2001
-From: "Marcus D. Hanwell" <marcus.hanwell@kitware.com>
-Date: Thu, 16 Nov 2017 15:10:25 -0500
-Subject: [PATCH] Remove deprecated calls for export flags
-
-Move them to the project default variables in the top level.
----
- CMakeLists.txt                      | 8 ++++++++
- molequeue/client/CMakeLists.txt     | 1 -
- molequeue/servercore/CMakeLists.txt | 1 -
- molequeue/zeromq/CMakeLists.txt     | 1 -
- thirdparty/qt5json/CMakeLists.txt   | 1 -
- 5 files changed, 8 insertions(+), 4 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index a107c8f..e68d81f 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -4,6 +4,14 @@ project(MoleQueue)
- 
- set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
- 
-+# Request C++11 standard, using new CMake variables.
-+set(CMAKE_CXX_STANDARD 11)
-+set(CMAKE_CXX_STANDARD_REQUIRED True)
-+set(CMAKE_CXX_EXTENSIONS False)
-+# Set symbol visibility defaults for all targets.
-+set(CMAKE_CXX_VISIBILITY_PRESET "hidden")
-+set(CMAKE_VISIBILITY_INLINES_HIDDEN True)
-+
- include(BuildType)
- include(BuildLocation)
- include(CompilerFlags)
-diff --git a/molequeue/client/CMakeLists.txt b/molequeue/client/CMakeLists.txt
-index 674f91a..8cb131a 100644
---- a/molequeue/client/CMakeLists.txt
-+++ b/molequeue/client/CMakeLists.txt
-@@ -20,7 +20,6 @@ set_target_properties(MoleQueueClient PROPERTIES AUTOMOC TRUE)
- include(GenerateExportHeader)
- generate_export_header(MoleQueueClient EXPORT_FILE_NAME molequeueclientexport.h)
- list(APPEND headers "${CMAKE_CURRENT_BINARY_DIR}/molequeueclientexport.h")
--add_compiler_export_flags(molequeue_export_flags)
- set_property(TARGET MoleQueueClient APPEND
-     PROPERTY COMPILE_FLAGS ${molequeue_export_flags})
- 
-diff --git a/molequeue/servercore/CMakeLists.txt b/molequeue/servercore/CMakeLists.txt
-index 8d4f7ee..aab0bec 100644
---- a/molequeue/servercore/CMakeLists.txt
-+++ b/molequeue/servercore/CMakeLists.txt
-@@ -30,7 +30,6 @@ set(hdrs
- generate_export_header(MoleQueueServerCore
-   EXPORT_FILE_NAME molequeueservercoreexport.h)
- include_directories(${CMAKE_CURRENT_BINARY_DIR})
--add_compiler_export_flags(molequeue_export_flags)
- set_property(TARGET MoleQueueServerCore APPEND
-   PROPERTY COMPILE_FLAGS ${molequeue_export_flags})
- 
-diff --git a/molequeue/zeromq/CMakeLists.txt b/molequeue/zeromq/CMakeLists.txt
-index bc1e893..188f437 100644
---- a/molequeue/zeromq/CMakeLists.txt
-+++ b/molequeue/zeromq/CMakeLists.txt
-@@ -20,7 +20,6 @@ target_link_libraries(MoleQueueZeroMq MoleQueueServerCore ${ZeroMQ_LIBRARIES})
- generate_export_header(MoleQueueZeroMq
-   EXPORT_FILE_NAME molequeuezeromqexport.h)
- include_directories(${CMAKE_CURRENT_BINARY_DIR})
--add_compiler_export_flags(molequeue_export_flags)
- set_property(TARGET MoleQueueZeroMq APPEND
-   PROPERTY COMPILE_FLAGS ${molequeue_export_flags})
- 
-diff --git a/thirdparty/qt5json/CMakeLists.txt b/thirdparty/qt5json/CMakeLists.txt
-index 6d00685..52f5df2 100644
---- a/thirdparty/qt5json/CMakeLists.txt
-+++ b/thirdparty/qt5json/CMakeLists.txt
-@@ -54,7 +54,6 @@ include(GenerateExportHeader)
- generate_export_header(${QT5_JSON_LIBRARY_NAME}
-   EXPORT_FILE_NAME qt5jsonexport.h
-   EXPORT_MACRO_NAME QT5JSON_EXPORT)
--add_compiler_export_flags(qt5json_export_flags)
- 
- set_property(TARGET ${QT5_JSON_LIBRARY_NAME} APPEND
-   PROPERTY COMPILE_FLAGS ${qt5json_export_flags})
diff --git a/sci-chemistry/molequeue/molequeue-0.8.0.ebuild b/sci-chemistry/molequeue/molequeue-0.8.0.ebuild
deleted file mode 100644
index 2c20c0bfeeac..000000000000
--- a/sci-chemistry/molequeue/molequeue-0.8.0.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils python-single-r1 versionator virtualx
-
-DESCRIPTION="Abstract, manage and coordinate execution of tasks"
-HOMEPAGE="https://www.openchemistry.org/projects/molequeue/"
-SRC_URI="https://github.com/OpenChemistry/molequeue/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+client doc server test +zeromq"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}
-	server? ( client )
-	test? ( server )"
-
-RDEPEND="${PYTHON_DEPS}
-	dev-qt/qtcore:5
-	dev-qt/qtgui:5
-	dev-qt/qtnetwork:5
-	dev-qt/qtwidgets:5
-	zeromq? ( net-libs/cppzmq:0= )"
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen )"
-
-PATCHES=( "${FILESDIR}"/${P}-cmake.patch )
-
-src_prepare() {
-	cmake-utils_src_prepare
-
-	rm cmake/{GenerateExportHeader.cmake,exportheader.cmake.in} || die
-
-	# delete bundled Qt5Json library
-	rm -r thirdparty || die
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DBUILD_DOCUMENTATION=$(usex doc)
-		-DMoleQueue_BUILD_CLIENT=$(usex client)
-		-DoleQueue_BUILD_APPLICATION=$(usex server)
-		-DENABLE_TESTING=$(usex test)
-		-DUSE_ZERO_MQ=$(usex zeromq)
-		-DINSTALL_LIBRARY_DIR=$(get_libdir)
-	)
-	use zeromq && \
-		mycmakeargs+=( -DZeroMQ_ROOT_DIR=\"${EPREFIX}/usr\" )
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile all $(usex doc documentation "")
-}
-
-src_test() {
-	VIRTUALX_COMMAND=cmake-utils_src_test
-	virtualmake
-}
-
-src_install() {
-	use doc && HTML_DOCS=( "${BUILD_DIR}"/docs/html/. )
-	cmake-utils_src_install
-}
diff --git a/sci-chemistry/molequeue/molequeue-0.9.0.ebuild b/sci-chemistry/molequeue/molequeue-0.9.0.ebuild
index 1f484848233a..71e253b4283a 100644
--- a/sci-chemistry/molequeue/molequeue-0.9.0.ebuild
+++ b/sci-chemistry/molequeue/molequeue-0.9.0.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 PYTHON_COMPAT=( python2_7 )
 
@@ -20,14 +20,15 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}
 	server? ( client )
 	test? ( server )"
 
+BDEPEND="
+	doc? ( app-doc/doxygen )"
 RDEPEND="${PYTHON_DEPS}
 	dev-qt/qtcore:5
 	dev-qt/qtgui:5
 	dev-qt/qtnetwork:5
 	dev-qt/qtwidgets:5
 	zeromq? ( net-libs/cppzmq:0= )"
-DEPEND="${RDEPEND}
-	doc? ( app-doc/doxygen )"
+DEPEND="${RDEPEND}"
 
 PATCHES=( "${FILESDIR}"/${P}-qt-5.11b3.patch )