sci-chemistry/gromacs: add first beta for 2025 release

Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>

4 files changed, 710 insertions, 2 deletions

diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 6409f7133958..1debfdf404f1 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -4,15 +4,18 @@ DIST gromacs-2022.6.tar.gz 40330705 BLAKE2B fdafbd5b2a92d6022dec3e79e961fef220f1
 DIST gromacs-2023.5.tar.gz 42079310 BLAKE2B e50dbe76396230f4a886280bdebcf7b131506679240e77d2a2263c3b5dbfe7ef754c4265fc04e9acad7932c7691de7f694cc23140a25d0d5be649a4120f45b0c SHA512 f3a34cf0d379d6d4964d7494af6c6617c0c092293ea38a3a248af2dd2a90cae04696d52e68126176065efc480977942b00efa441028e526e1555c7e84551fc0c
 DIST gromacs-2024.3.tar.gz 42373103 BLAKE2B f45af72ecdf119b423d98b84818eaca1aa2e3f43eaf1aff7435de2a5891079a880f19a654627ee2f43e3a38c9dcfa0638bc6eb6da201b3c9ce89b2dc32fc683b SHA512 13f23e581c2b63f6262e8359e7bed6a1a5f3164047ea38d2b6a44bcd2b20b61332705167435fe2ad30fe6f24f8ab49b982388550cdecb49167e4156e36286d3d
 DIST gromacs-2024.tar.gz 42455653 BLAKE2B 86446c5e95f9ddaf718126c409389730ee1642f36c3e0d844eb4b3a640c275e7979581365dacb57ac66daec296bbd94be6d5c0376f7255d3d3950f6759f8d69a SHA512 d64bf3cbe579003ce37dfd3d27c68746a04360d9d5491c638f3f2bd9af2c938504b0c9710c62e85225370ddf5418e6ebc2422033e46af5eee6e4aaa53699fed7
+DIST gromacs-2025.0-beta.tar.gz 45067499 BLAKE2B 661607007af6d1f697f5aec72a88cefec5546dee2c0facaf2776354665f56fd71b1a7a2ea92185b4d64e764cd0ac10e865b740dda6d7438318acbbadd1bd7fd0 SHA512 831b4ba2631f5dd65c1b48d4ba0455af0b101af22d8cc78c246e7b36f4ce3c8f33f1cb8d94e42559741dbe1585c75a6e05a2538708d7e57c86ac2174aca302b9
 DIST manual-2020.7.pdf 11850780 BLAKE2B 38594e87993badfbbcf47d6010a7f67d3c3426dab85e1462916b4d62be27b5764953f912cf2b71ee24877e0bfa27b3f74431da2da81b4977d58cb66b2cc795a3 SHA512 4f184f2c90e0bac01a48069cc546cd5b04fa5f543f90dd2d68c6d17be278152fd09456b6a6c5c8236f8fb85a174d6ec7a1c7b44d437b4e6fea5d0ada73cec0f6
 DIST manual-2021.7.pdf 12256526 BLAKE2B 6f298d7dac142f66914bbc2ea7d6ca70c4aeafaf33ccf12336d5cec64b1f1097b5332c767bb411ccef706ec6184479a84bcf59bda21c4249d45d8ce3dea08e79 SHA512 197765accb8ab6c5f1cc94b2697ff1817e157d85fa231dfe36a85036076e04da2a8035de66aba4f46c6dd7f553176357b94c92e1da5d1dabc574c627deee5279
 DIST manual-2022.6.pdf 13081140 BLAKE2B e7ae3f23ddc076c295be2c464fe2177d6d6848d070ee5eba2b572e996ae08adead898ec6432b123802907f64983aa4d2e17426be8d540c48d12398a479519f9e SHA512 4724888b3c33c4fa4a035d5fb2f8c51496f67e1ee312676510d5ba74bc3cc1571e71e84464585b87ad0133e8e736343ae382bf8f7b556633f86a99560213d271
 DIST manual-2023.5.pdf 13579081 BLAKE2B 42f687ebcdb79bfc77aabac4fd382940c23ba27da380b8eff342c2e9255a58fc11a0458220d1f71f3c13ab1cf6fdabad00ac1bad741781d0b787899165bea2cc SHA512 0661f166f7a8dc24b4244c0139f366832ddfc1298129df2a6e29800b5d1567318781ab547bc7e9ee54de7a62abba4996f8e3010c91d6917c248117e5711d7dbb
 DIST manual-2024.3.pdf 13676383 BLAKE2B fa5b310ee8977c525781492c70a18d40f8842f5fa43831ad0283c033f39968ba98e74ea618a4a9c25d88c3ed694071327220617b17f316ba2f29777c3edc95ca SHA512 8dd09913b89213a6673a5f5e3462fb963d1f30d68e0d58b846b7e2cf2f73baacb14fabab6591b680849607f4ca617cf288899729939b2c32021b4ee5ba06835f
 DIST manual-2024.pdf 13644437 BLAKE2B 19d547686d5c5be5e1236aba648e8afb174b281802ab76e020466953ab5d2dd98701f21eb4736cb449b61960b5b7aadce6711b2b0309a41dd1997d7383bce09e SHA512 b00048651f1f81f9024ba5c4c02ad66d2b07eb7b816f0489568fb64859cac515b885a5cb4640c8b5bd7c3620655a7ebc5fc2e4e4cbb8e952ffb0c9b5815ae661
+DIST manual-2025.0-beta.pdf 13788093 BLAKE2B 40652f32f35d73964dfb8146b916c0249d8b7044595114986108f209e98e3a0a402ead18842822ce12c9cdd24a224bb95f80fbe5eec908f013b1eddc14d2a2fd SHA512 eafc1fd060f4a5dd5e7317f0f0fa45cfd5ccc20518a9d67b9055a87c324893d92573dfd416fcbf0fc9b7a932a47e3a592fbc38837bccdd237466bb62cd3ad9ed
 DIST regressiontests-2020.7.tar.gz 48541487 BLAKE2B 255608b52158c6c01e7c7c4dcf075128ecf22b2f26d32e8c203de8a4bc69c60ec95f49cf8ccd64abc3073c5e8dca9d6b01daed9dfb8f67bce2dd068ed01acd05 SHA512 2458582f94f3c9f4e1454824ce3940b4f5b6cb2151d06846c42e7a9448296fd2a6df4f53be9624e0d3317d2b59f89bb5348eb8b2970d7b46ac22ca989ef3458a
 DIST regressiontests-2021.7.tar.gz 48537500 BLAKE2B b0c97fa652cb9b972c50f29822f530fcaa2ec9acb6d6442114fc6446c54aade5eb1bfa153c69a7e8bf64b66e8b041d7f8e0d51e7f7b0516f9e03f3d9ad626193 SHA512 7cbead90aa6d62346dcf7c2249c3cfa179884b987a749624444d2f59d93e0322f7721143bf6eb44d26102635dc70a73546ef82d4647558b6320bfdd459074017
 DIST regressiontests-2022.6.tar.gz 48615697 BLAKE2B 566adafbc36d3c1faae322fca9cf451f57245c4ceed63f90f26208025937dae0c1bbb8c372bce618f63305d0368113fecd96c7275a75d8b9c19c22a6e5aa9b96 SHA512 68aa9bedffbea37fb7703c18c3f66f607a91f16ece4bec58ced6e42a481156b2fe83760d0e40cecbdcaf87b168441b8ebde27cec30d98c89f516360ea45ddd43
 DIST regressiontests-2023.5.tar.gz 48619605 BLAKE2B f2549a34750c6866f054614a00a3360a09b82306e6bd5e5b848e18cdd3a3fabaac6203c5ca734901019403225dd47e0d662838abe9a1db7d07662f1c745b8e4f SHA512 3ccaf9db7dfba641a5e98ebff3d735cae3f679926aba443ffedec20dd6c85e67f0e9711ebad5dfa8105122d5411f5de6ded1802a7da4ddf0599657832c8c597a
 DIST regressiontests-2024.3.tar.gz 32776961 BLAKE2B 6a74977a396f8e82f7aba7a384cc840275b86d470597a4bbb93e97f1c13cd8fcf6d86ab26bdd4a89464b863954c9ed7dbd49af095e821573845f7bda43c2b90b SHA512 1c4afbbca82c9b9ad371713ef5e7e093ca766f25f6fbda55c79ea1aecb2f0a06bdb042d3c8a86e3d9bf9e8b8091244827dbff544f66037ffa56b0bcb341a9d2c
 DIST regressiontests-2024.tar.gz 48142685 BLAKE2B e24c29c2b534f2fe42e4abc122578ba618279f3182f83be604516e6ee2a34ff037b2604b4cda7a9b7e2ea9fce0a386b3efb7c8aa0cac378d6d8c1595be884c76 SHA512 6c4a847c379603590f618a4da7c691b51bbe180ca9dc59abf885ef8599e1b66758171eb05b7d7709d968f559b209c2fa4cfec8f15cc5d072fafe952567002c2e
+DIST regressiontests-2025.0-beta.tar.gz 32653220 BLAKE2B 9f7388d7dfc59d89e719d693733f7ff2b3085e9c6b526238f62dc89ba9c30f9c778d99952ca170bf0ffc1d09fff6e4cd1bf1f0dc77c5b45e8613229043ebe409 SHA512 f3786ef08a54cc4a525a8af4ca7276dc6dfb624f13a82b9a9f168253729dd2e7161cecc5540b805bdfdaface8e272cea430bb561d0694970f5a394a718cdd8c3
diff --git a/sci-chemistry/gromacs/gromacs-2025.0_beta.ebuild b/sci-chemistry/gromacs/gromacs-2025.0_beta.ebuild
new file mode 100644
index 000000000000..4382a7dba81e
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-2025.0_beta.ebuild
@@ -0,0 +1,352 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+PYTHON_COMPAT=( python3_{10..12} )
+
+DISTUTILS_OPTIONAL=1
+DISTUTILS_USE_PEP517=no
+DISTUTILS_SINGLE_IMPL=1
+
+inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils
+
+if [[ ${PV} = *9999* ]]; then
+	EGIT_REPO_URI="
+		https://gitlab.com/gromacs/gromacs.git
+		https://github.com/gromacs/gromacs.git
+		"
+	[[ ${PV} = 9999 ]] && EGIT_BRANCH="main" || EGIT_BRANCH="release-${PV:0:4}"
+	inherit git-r3
+else
+	SRC_URI="
+		https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
+		doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
+		test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
+	# since 2022 arm support was dropped (but not arm64)
+	# since 2025 x86-32 support was dropped
+	KEYWORDS="~amd64 -arm ~arm64 ~riscv -x86 ~amd64-linux ~x86-linux ~x64-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 cpu_flags_x86_avx512f cpu_flags_arm_neon"
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="https://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="blas clang clang-cuda cuda  +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy hdf5 +hwloc lapack mkl mpi nnpot +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
+
+CDEPEND="
+	blas? ( virtual/blas )
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
+	opencl? ( virtual/opencl )
+	openmp? (
+		sys-devel/gcc[openmp]
+		sys-devel/clang-runtime[openmp]
+	)
+	fftw? ( sci-libs/fftw:3.0= )
+	hdf5? ( sci-libs/hdf5 )
+	hwloc? ( sys-apps/hwloc:= )
+	lapack? ( virtual/lapack )
+	mkl? ( sci-libs/mkl )
+	mpi? ( virtual/mpi[cxx] )
+	nnpot? ( sci-libs/caffe2[cuda=,opencl=] )
+	sci-libs/lmfit:=
+	>=dev-cpp/muParser-2.3:=
+	${PYTHON_DEPS}
+	"
+BDEPEND="${CDEPEND}
+	virtual/pkgconfig
+	clang? ( >=sys-devel/clang-6:* )
+	build-manual? (
+		app-text/doxygen
+		$(python_gen_cond_dep '
+			dev-python/sphinx[${PYTHON_USEDEP}]
+			dev-python/sphinx-copybutton[${PYTHON_USEDEP}]
+			dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]
+			dev-python/sphinx-argparse[${PYTHON_USEDEP}]
+			dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}]
+		')
+		media-gfx/mscgen
+		media-gfx/graphviz
+		dev-texlive/texlive-latex
+		dev-texlive/texlive-latexextra
+		media-gfx/imagemagick
+	)"
+RDEPEND="${CDEPEND}"
+
+REQUIRED_USE="
+	|| ( single-precision double-precision )
+	doc? ( !build-manual )
+	cuda? ( single-precision )
+	opencl? ( single-precision )
+	cuda? ( !opencl )
+	clang-cuda? ( clang cuda )
+	mkl? ( !blas !fftw !lapack )
+	${PYTHON_REQUIRED_USE}"
+
+DOCS=( AUTHORS README )
+
+RESTRICT="!test? ( test )"
+
+if [[ ${PV} != *9999 ]]; then
+	S="${WORKDIR}/${PN}-${PV/_/-}"
+fi
+
+pkg_pretend() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+	python-single-r1_pkg_setup
+}
+
+src_unpack() {
+	if [[ ${PV} != *9999 ]]; then
+		default
+	else
+		git-r3_src_unpack
+		if use test; then
+			EGIT_REPO_URI="https://gitlab.com/gromacs/gromacs-regressiontests.git" \
+			EGIT_BRANCH="${EGIT_BRANCH}" \
+			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
+				git-r3_src_unpack
+		fi
+	fi
+}
+
+src_prepare() {
+	#notes/todos
+	# -on apple: there is framework support
+
+	xdg_environment_reset #591952
+
+	# we can use clang as default
+	if use clang && ! tc-is-clang ; then
+		export CC=${CHOST}-clang
+		export CXX=${CHOST}-clang++
+	else
+		tc-export CXX CC
+	fi
+	# clang-cuda need to filter mfpmath
+	if use clang-cuda ; then
+		filter-mfpmath sse
+		filter-mfpmath i386
+	fi
+
+	cmake_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"
+	if use build-manual; then
+		# 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
+	fi
+}
+
+src_configure() {
+	local mycmakeargs_pre=( ) extra fft_opts=( )
+	local acce="AUTO"
+	local nnpot="OFF"
+
+	if use nnpot; then
+		nnpot="TORCH"
+	fi
+
+	if use custom-cflags; then
+		#go from slowest to fastest acceleration
+		acce="None"
+		if (use amd64 || use x86); then
+			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"
+			use cpu_flags_x86_avx512f && acce="AVX_512"
+		elif (use arm); then
+			use cpu_flags_arm_neon && acce="ARM_NEON"
+		elif (use arm64); then
+			use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD"
+		fi
+	else
+		strip-flags
+	fi
+
+	#to create man pages, build tree binaries are executed (bug #398437)
+	[[ ${CHOST} = *-darwin* ]] && \
+		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
+
+	if use fftw; then
+		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
+	elif use mkl; then
+		local bits=$(get_libdir)
+		fft_opts=( -DGMX_FFT_LIBRARY=mkl
+			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
+			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
+		)
+	else
+		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
+	fi
+
+	mycmakeargs_pre+=(
+		"${fft_opts[@]}"
+		"${lmfit_opts[@]}"
+		-DGMX_USE_LMFIT=EXTERNAL
+		-DGMX_USE_MUPARSER=EXTERNAL
+		-DGMX_EXTERNAL_BLAS=$(usex blas)
+		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
+		-DGMX_OPENMP=$(usex openmp)
+		-DGMX_COOL_QUOTES=$(usex offensive)
+		-DGMX_USE_TNG=$(usex tng)
+		-DGMX_BUILD_MANUAL=$(usex build-manual)
+		-DGMX_USE_HDF5=$(usex hdf5)
+		-DGMX_HWLOC=$(usex hwloc)
+		-DGMX_DEFAULT_SUFFIX=off
+		-DGMX_BUILD_HELP=on
+		-DGMX_SIMD="$acce"
+		-DGMX_NNPOT="$nnpot"
+		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
+		-DBUILD_TESTING=$(usex test)
+		-DGMX_BUILD_UNITTESTS=$(usex test)
+		-DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
+		${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 gpu=( "-DGMX_GPU=OFF" )
+		[[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
+		[[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" )
+		use opencl && gpu=( "-DGMX_GPU=OPENCL" )
+		local mycmakeargs=(
+			${mycmakeargs_pre[@]} ${p}
+			-DGMX_MPI=$(usex mpi)
+			-DGMX_THREAD_MPI=$(usex threads)
+			-DGMXAPI=$(usex gmxapi)
+			-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
+			"${gpu[@]}"
+			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
+			-DGMX_BINARY_SUFFIX="${suffix}"
+			-DGMX_LIBS_SUFFIX="${suffix}"
+			-DGMX_PYTHON_PACKAGE=$(usex python)
+		)
+		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
+		[[ ${CHOST} != *-darwin* ]] || \
+		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
+	done
+}
+
+src_compile() {
+	for x in ${GMX_DIRS}; do
+		einfo "Compiling for ${x} precision"
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake_src_compile
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake_src_compile man
+		if use python; then
+			BUILD_DIR="${WORKDIR}/${P}_${x}"\
+				cmake_src_compile	python_packaging/all
+			BUILD_DIR="${WORKDIR}/${P}" \
+				distutils-r1_src_compile
+		fi
+		# not 100% necessary for rel ebuilds as available from website
+		if use build-manual; then
+			BUILD_DIR="${WORKDIR}/${P}_${x}"\
+				cmake_src_compile manual
+		fi
+	done
+}
+
+src_test() {
+	for x in ${GMX_DIRS}; do
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake_src_compile check
+	done
+}
+
+src_install() {
+	for x in ${GMX_DIRS}; do
+		BUILD_DIR="${WORKDIR}/${P}_${x}" \
+			cmake_src_install
+		if use python; then
+			BUILD_DIR="${WORKDIR}/${P}_${x}" \
+				cmake_src_install	python_packaging/install
+		fi
+		if use build-manual; then
+			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
+		fi
+
+		if use doc; then
+			if [[ ${PV} != *9999* ]]; then
+				newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
+			fi
+		fi
+	done
+
+	if use tng; then
+		insinto /usr/include/tng
+		doins src/external/tng_io/include/tng/*h
+	fi
+	# drop unneeded stuff
+	rm "${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 gromacs related papers from list:"
+	einfo  "https://www.gromacs.org/articles.html"
+	einfo
+	readme.gentoo_print_elog
+}
diff --git a/sci-chemistry/gromacs/gromacs-2025.9999.ebuild b/sci-chemistry/gromacs/gromacs-2025.9999.ebuild
new file mode 100644
index 000000000000..4382a7dba81e
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-2025.9999.ebuild
@@ -0,0 +1,352 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+PYTHON_COMPAT=( python3_{10..12} )
+
+DISTUTILS_OPTIONAL=1
+DISTUTILS_USE_PEP517=no
+DISTUTILS_SINGLE_IMPL=1
+
+inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils
+
+if [[ ${PV} = *9999* ]]; then
+	EGIT_REPO_URI="
+		https://gitlab.com/gromacs/gromacs.git
+		https://github.com/gromacs/gromacs.git
+		"
+	[[ ${PV} = 9999 ]] && EGIT_BRANCH="main" || EGIT_BRANCH="release-${PV:0:4}"
+	inherit git-r3
+else
+	SRC_URI="
+		https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
+		doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
+		test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
+	# since 2022 arm support was dropped (but not arm64)
+	# since 2025 x86-32 support was dropped
+	KEYWORDS="~amd64 -arm ~arm64 ~riscv -x86 ~amd64-linux ~x86-linux ~x64-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 cpu_flags_x86_avx512f cpu_flags_arm_neon"
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="https://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="blas clang clang-cuda cuda  +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy hdf5 +hwloc lapack mkl mpi nnpot +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
+
+CDEPEND="
+	blas? ( virtual/blas )
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
+	opencl? ( virtual/opencl )
+	openmp? (
+		sys-devel/gcc[openmp]
+		sys-devel/clang-runtime[openmp]
+	)
+	fftw? ( sci-libs/fftw:3.0= )
+	hdf5? ( sci-libs/hdf5 )
+	hwloc? ( sys-apps/hwloc:= )
+	lapack? ( virtual/lapack )
+	mkl? ( sci-libs/mkl )
+	mpi? ( virtual/mpi[cxx] )
+	nnpot? ( sci-libs/caffe2[cuda=,opencl=] )
+	sci-libs/lmfit:=
+	>=dev-cpp/muParser-2.3:=
+	${PYTHON_DEPS}
+	"
+BDEPEND="${CDEPEND}
+	virtual/pkgconfig
+	clang? ( >=sys-devel/clang-6:* )
+	build-manual? (
+		app-text/doxygen
+		$(python_gen_cond_dep '
+			dev-python/sphinx[${PYTHON_USEDEP}]
+			dev-python/sphinx-copybutton[${PYTHON_USEDEP}]
+			dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]
+			dev-python/sphinx-argparse[${PYTHON_USEDEP}]
+			dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}]
+		')
+		media-gfx/mscgen
+		media-gfx/graphviz
+		dev-texlive/texlive-latex
+		dev-texlive/texlive-latexextra
+		media-gfx/imagemagick
+	)"
+RDEPEND="${CDEPEND}"
+
+REQUIRED_USE="
+	|| ( single-precision double-precision )
+	doc? ( !build-manual )
+	cuda? ( single-precision )
+	opencl? ( single-precision )
+	cuda? ( !opencl )
+	clang-cuda? ( clang cuda )
+	mkl? ( !blas !fftw !lapack )
+	${PYTHON_REQUIRED_USE}"
+
+DOCS=( AUTHORS README )
+
+RESTRICT="!test? ( test )"
+
+if [[ ${PV} != *9999 ]]; then
+	S="${WORKDIR}/${PN}-${PV/_/-}"
+fi
+
+pkg_pretend() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+	python-single-r1_pkg_setup
+}
+
+src_unpack() {
+	if [[ ${PV} != *9999 ]]; then
+		default
+	else
+		git-r3_src_unpack
+		if use test; then
+			EGIT_REPO_URI="https://gitlab.com/gromacs/gromacs-regressiontests.git" \
+			EGIT_BRANCH="${EGIT_BRANCH}" \
+			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
+				git-r3_src_unpack
+		fi
+	fi
+}
+
+src_prepare() {
+	#notes/todos
+	# -on apple: there is framework support
+
+	xdg_environment_reset #591952
+
+	# we can use clang as default
+	if use clang && ! tc-is-clang ; then
+		export CC=${CHOST}-clang
+		export CXX=${CHOST}-clang++
+	else
+		tc-export CXX CC
+	fi
+	# clang-cuda need to filter mfpmath
+	if use clang-cuda ; then
+		filter-mfpmath sse
+		filter-mfpmath i386
+	fi
+
+	cmake_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"
+	if use build-manual; then
+		# 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
+	fi
+}
+
+src_configure() {
+	local mycmakeargs_pre=( ) extra fft_opts=( )
+	local acce="AUTO"
+	local nnpot="OFF"
+
+	if use nnpot; then
+		nnpot="TORCH"
+	fi
+
+	if use custom-cflags; then
+		#go from slowest to fastest acceleration
+		acce="None"
+		if (use amd64 || use x86); then
+			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"
+			use cpu_flags_x86_avx512f && acce="AVX_512"
+		elif (use arm); then
+			use cpu_flags_arm_neon && acce="ARM_NEON"
+		elif (use arm64); then
+			use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD"
+		fi
+	else
+		strip-flags
+	fi
+
+	#to create man pages, build tree binaries are executed (bug #398437)
+	[[ ${CHOST} = *-darwin* ]] && \
+		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
+
+	if use fftw; then
+		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
+	elif use mkl; then
+		local bits=$(get_libdir)
+		fft_opts=( -DGMX_FFT_LIBRARY=mkl
+			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
+			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
+		)
+	else
+		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
+	fi
+
+	mycmakeargs_pre+=(
+		"${fft_opts[@]}"
+		"${lmfit_opts[@]}"
+		-DGMX_USE_LMFIT=EXTERNAL
+		-DGMX_USE_MUPARSER=EXTERNAL
+		-DGMX_EXTERNAL_BLAS=$(usex blas)
+		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
+		-DGMX_OPENMP=$(usex openmp)
+		-DGMX_COOL_QUOTES=$(usex offensive)
+		-DGMX_USE_TNG=$(usex tng)
+		-DGMX_BUILD_MANUAL=$(usex build-manual)
+		-DGMX_USE_HDF5=$(usex hdf5)
+		-DGMX_HWLOC=$(usex hwloc)
+		-DGMX_DEFAULT_SUFFIX=off
+		-DGMX_BUILD_HELP=on
+		-DGMX_SIMD="$acce"
+		-DGMX_NNPOT="$nnpot"
+		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
+		-DBUILD_TESTING=$(usex test)
+		-DGMX_BUILD_UNITTESTS=$(usex test)
+		-DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
+		${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 gpu=( "-DGMX_GPU=OFF" )
+		[[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
+		[[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" )
+		use opencl && gpu=( "-DGMX_GPU=OPENCL" )
+		local mycmakeargs=(
+			${mycmakeargs_pre[@]} ${p}
+			-DGMX_MPI=$(usex mpi)
+			-DGMX_THREAD_MPI=$(usex threads)
+			-DGMXAPI=$(usex gmxapi)
+			-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
+			"${gpu[@]}"
+			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
+			-DGMX_BINARY_SUFFIX="${suffix}"
+			-DGMX_LIBS_SUFFIX="${suffix}"
+			-DGMX_PYTHON_PACKAGE=$(usex python)
+		)
+		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
+		[[ ${CHOST} != *-darwin* ]] || \
+		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
+	done
+}
+
+src_compile() {
+	for x in ${GMX_DIRS}; do
+		einfo "Compiling for ${x} precision"
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake_src_compile
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake_src_compile man
+		if use python; then
+			BUILD_DIR="${WORKDIR}/${P}_${x}"\
+				cmake_src_compile	python_packaging/all
+			BUILD_DIR="${WORKDIR}/${P}" \
+				distutils-r1_src_compile
+		fi
+		# not 100% necessary for rel ebuilds as available from website
+		if use build-manual; then
+			BUILD_DIR="${WORKDIR}/${P}_${x}"\
+				cmake_src_compile manual
+		fi
+	done
+}
+
+src_test() {
+	for x in ${GMX_DIRS}; do
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake_src_compile check
+	done
+}
+
+src_install() {
+	for x in ${GMX_DIRS}; do
+		BUILD_DIR="${WORKDIR}/${P}_${x}" \
+			cmake_src_install
+		if use python; then
+			BUILD_DIR="${WORKDIR}/${P}_${x}" \
+				cmake_src_install	python_packaging/install
+		fi
+		if use build-manual; then
+			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
+		fi
+
+		if use doc; then
+			if [[ ${PV} != *9999* ]]; then
+				newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
+			fi
+		fi
+	done
+
+	if use tng; then
+		insinto /usr/include/tng
+		doins src/external/tng_io/include/tng/*h
+	fi
+	# drop unneeded stuff
+	rm "${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 "${ED}"/usr/bin/gmx-completion*.bash || die
+	readme.gentoo_create_doc
+}
+
+pkg_postinst() {
+	einfo
+	einfo  "Please read and cite gromacs related papers from list:"
+	einfo  "https://www.gromacs.org/articles.html"
+	einfo
+	readme.gentoo_print_elog
+}
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 01ebc8ab87b7..4382a7dba81e 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -26,7 +26,8 @@ else
 		doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
 		test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
 	# since 2022 arm support was dropped (but not arm64)
-	KEYWORDS="~amd64 -arm ~arm64 ~riscv ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+	# since 2025 x86-32 support was dropped
+	KEYWORDS="~amd64 -arm ~arm64 ~riscv -x86 ~amd64-linux ~x86-linux ~x64-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 cpu_flags_x86_avx512f cpu_flags_arm_neon"
@@ -39,7 +40,7 @@ HOMEPAGE="https://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="blas clang clang-cuda cuda  +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hdf5 +hwloc lapack mkl mpi nnpot +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="blas clang clang-cuda cuda  +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy hdf5 +hwloc lapack mkl mpi nnpot +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
 	blas? ( virtual/blas )