gentoo Easter resync : 12.04.2020

author: V3n3RiX <venerix@redcorelinux.org> 2020-04-12 03:41:30 +0100
committer: V3n3RiX <venerix@redcorelinux.org> 2020-04-12 03:41:30 +0100
commit: 623ee73d661e5ed8475cb264511f683407d87365 (patch)
tree: 993eb27c93ec7a2d2d19550300d888fc1fed9e69 /sci-chemistry
parent: ceeeb463cc1eef97fd62eaee8bf2196ba04bc384 (diff)
25 files changed, 1380 insertions, 140 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index c2c2183fe140..e76a1b1a0191 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/avogadro2/Manifest b/sci-chemistry/avogadro2/Manifest
index 6065c99351f1..c47e8dd7bad9 100644
--- a/sci-chemistry/avogadro2/Manifest
+++ b/sci-chemistry/avogadro2/Manifest
@@ -1,4 +1,6 @@
 AUX avogadro2-1.90.0_p20180211-qt-5.11b3.patch 1134 BLAKE2B ff96a5b19d17768de242490e555679270d568ce41b321e549e88986c66c931e7275c88697ee71600cdab7990f473f6c214f903771754d292ff0766874a82f810 SHA512 5362a64709127b30656f1f7830d902ac00291cdf39160c4639f121568666fe1249f2f92c9378f75b2fc6cf44cecf74e92e207b73c029a9c9d997ac852f02ed86
 DIST avogadro2-1.90.0_p20180211.tar.gz 1099312 BLAKE2B fbf8e2006c46114632587615b48ac130e45a46ce2859a9c34270714091bc8397d9d7a93c3166bf58833f100e3e40afd1962012e479a8f92ba8ff9078200d51c5 SHA512 db9b0983d2161df493138ddf18c5dbda54cf2f8b75ebc944f1f57dab0f1e2048582362e5f46a78b1610aba080aaac8a66d2b2b71db748e031ffde306d3609856
+DIST avogadro2-1.93.0.tar.gz 2905461 BLAKE2B db51e4574fdf2a31657b8bef7b06eb0d563484deaae1a6d75649187d6f5fd7b02a99506cfb850e09792555d7c27d9937d0df0f7172fafc3ddcbccaa7502c5bb6 SHA512 8e4e15b6c2d1935f8c585c83761b28a6397bc1dc22cd5f66464d59dd25327b1cffec809af492586be4b56793448f94f9375c16e8a4c4969f7b8f2591049cc5fc
 EBUILD avogadro2-1.90.0_p20180211.ebuild 1273 BLAKE2B b0f9d795978e059158ae4929cdbe97425f58f84da99f67407b858e0b59672d35dbd83864d0e08d23fd0f3a1cb7d7ef70f9db0475e94e7b6a837f376313b9209e SHA512 d790a4f9c61937bf832c48ee7551ca9e63061732507e771d6ad9cf9b024da318ae83b7879f344360aff60a98473791cb741264c5cc73e4f930a8a3256fb65970
+EBUILD avogadro2-1.93.0.ebuild 1224 BLAKE2B 13b6f9bb19f20fb638cae69b4dd556563b749935a79735a4ad55fdcafe0b590320c6040bf8d147cfa657b7c79560fcb40c13993343bf54ecd750da707c23f142 SHA512 c27577dce2314671c15c47d9dfd4b1c0288503d418cb43b22dfa6c240e70c17f21d99f91915a6d6bd1d529426f7f99843954b69d24f08c42e90ecf6fec9b1846
 MISC metadata.xml 513 BLAKE2B f721104691759eb8a87d9cb6dd56bef45ac151e180caa68376406274a57df6c04e3fec6ba6d7e2aabf4355356002d27dd92e5b850c55103b3b23340d9b64d891 SHA512 4209c0681f7055b240f1054a10d58d5c22dca467903096ab1f5eb1b8cf276990f694b2033b4e9b4e4838cce65dd7c7660633079764248f394e32ece0048f09a0
diff --git a/sci-chemistry/avogadro2/avogadro2-1.93.0.ebuild b/sci-chemistry/avogadro2/avogadro2-1.93.0.ebuild
new file mode 100644
index 000000000000..b4a2a037987e
--- /dev/null
+++ b/sci-chemistry/avogadro2/avogadro2-1.93.0.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+MY_PN=avogadroapp
+
+inherit desktop cmake-utils xdg
+
+DESCRIPTION="Advanced molecule editor and visualizer 2"
+HOMEPAGE="https://www.openchemistry.org/"
+SRC_URI="https://github.com/OpenChemistry/${MY_PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD GPL-2+"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc rpc test vtk"
+
+RDEPEND="
+	dev-qt/qtcore:5
+	dev-qt/qtgui:5
+	dev-qt/qtwidgets:5
+	>=sci-libs/avogadrolibs-${PV}[qt5,vtk?]
+	sci-libs/hdf5:=
+	rpc? ( sci-chemistry/molequeue )
+"
+DEPEND="${DEPEND}
+	dev-cpp/eigen:3
+	test? ( dev-qt/qttest:5 )
+"
+
+RESTRICT="test"
+
+S="${WORKDIR}/${MY_PN}-${PV}"
+
+src_prepare() {
+	cmake-utils_src_prepare
+	sed -e "/LICENSE/d" -i CMakeLists.txt || die
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DCMAKE_INSTALL_DOCDIR="${EPREFIX}/usr/share/doc/${PF}"
+		-DBUILD_DOCUMENTATION=$(usex doc)
+		-DAvogadro_ENABLE_RPC=$(usex rpc)
+		-DENABLE_TESTING=$(usex test)
+		-DUSE_VTK=$(usex vtk)
+	)
+	cmake-utils_src_configure
+}
+
+src_install() {
+	cmake-utils_src_install
+	for size in 64 128 256 512; do
+		newicon -s "${size}" avogadro/icons/"${PN}"_"${size}".png "${PN}".png
+	done
+}
diff --git a/sci-chemistry/chemical-mime-data/Manifest b/sci-chemistry/chemical-mime-data/Manifest
index 1a972a59a0fa..0d50b7faa712 100644
--- a/sci-chemistry/chemical-mime-data/Manifest
+++ b/sci-chemistry/chemical-mime-data/Manifest
@@ -1,9 +1,9 @@
 AUX chemical-mime-data-0.1.94-drop-turbomole-vibrational.patch 934 BLAKE2B 8c35adddc5dbed044a68c1f0f485faf01ae4d6fb4724e82956e9e73292e2b7e37f527a8225fce3fa4b3c6629038086f30912b8bce21d704244dc18ba52673f8a SHA512 f1ca2c08b33f77ccc1355edbbba53971e4c09ed004ec35554617d57cb6dd90c9a8a712ebfe1c7e0b01d9a97790004a048029a9e96323e7a105e9b15408a0d4cd
 AUX chemical-mime-data-0.1.94-namespace-svg.patch 798 BLAKE2B 4ab826dd3c76234c903a740b2e59dd4403d01aff856327d31c6707ab4563931d9fe4d9d57bdc19d6102d63d860eb2d88220844b934aa63cc3be984621ac52d28 SHA512 64addfac817a7f056f381515561b4311936410dc46385a3ded8c65f8fbc3d5dda731c4ec02e9369299c8122e7c43a6dc53005a4957e4165bbf958f683708513d
 AUX chemical-mime-data-0.1.94-pigz.patch 481 BLAKE2B dee47e41645b5d196326fb7439e1a96b3d46983fa9c9ec4295b17676d51f966f48ff51668203e59f18580939337d83d5ae904ef33fe2044dcc62fedd90fcb82e SHA512 a16839c1b88486ed26b4987a22594d0c3d45254d31157560135bdba008e5caa0a372d11e7db858564f1eca75452d2e43509899a91c2a8872465ea06277a1fb6c
+AUX chemical-mime-data-0.1.94-rsvg-convert-r2.patch 1305 BLAKE2B 22809dbd6c769a0dcc88d65c3454702021d9d6e082a50fce9a5f3a28743aafdbcb5e153a90ee43f7a42d4ccd5f98465f91f872e7fabf69086b8ecf1336a60e49 SHA512 4bea8dae65e28657ff75b5b613137c0f89f6de185db79297642616f208e841ba56181044eee194c619bad2c3bfb62454b7839b720d2f32fca0e768b75c842683
 AUX chemical-mime-data-0.1.94-rsvg-convert.patch 1039 BLAKE2B 2eff2aa39206181f56bc802c30b4b043a0aeccef55c5d4e34755dcca69cc3afadd6cac364307729d8d83c88b7ba1d91d7200a80c7bd577e22c6ec5aec3b1921d SHA512 9c12f96f16e7982a5ba11fc546293a2e74f8918ef6eb274e3b1a618fc28aff244402c9b28ffebc2e01c8f6eb0e9e2516da82852bd0f9142c10e97f027670e60d
 AUX chemical-mime-data-0.1.94-turbomole.patch 2451 BLAKE2B 86b4b08b2af4503e0f8a525ebaa4231a3d0d3727c951b9e957c9fdac790bc41b7f01092350099a64cce66dbb61bc4cbd3654ef91834310c6c7cd1dc156ca87e8 SHA512 1bfa8818d159f0f917a24a06b0bfe926f0854f4242d8c2dbbedcd4210ffd38a459298862dc1d1aedbbe648a933db99c5d647c5409af74f88b03dd3033946df54
 DIST chemical-mime-data-0.1.94.tar.bz2 146077 BLAKE2B 9996c240446dc9571b6b4afbcdc6cf16a08e11314da9f785490b1b20933b6d18a333132492e30315c08f4441c048ec593a111815253050cfb5ab562aadb784f1 SHA512 7f3d967149f27ab1de53c948dc055959e661e1be9d778e3d56d06bea95769da7770ab5fb66afab6607747ef91ffb1dbbcf921e5f06e3303351781968594b5f00
-EBUILD chemical-mime-data-0.1.94-r3.ebuild 924 BLAKE2B 16f1360fe9d074a4eb52d40e3951ec334780664e8fef794362ce1d48e582ac1b70fa1a150be610a4f41bba2fe606336f5b6221aafe1f40296467c2d14d48e3d1 SHA512 c90b05d4fecc6649b1449f42d1cb520867c3ec2991e87b00a83d1fa32001d4971b8c2f44834c17b2cd9fa63783d514f1d1dc4e2efa2a9c5973f97523065d7893
-EBUILD chemical-mime-data-0.1.94-r4.ebuild 1091 BLAKE2B d48e62af64089a866ffc7fa07d7165a934039e4289fffb914b2dd351397ffaa7a7ca97950ce398bb20b7786b844863d4d0709ac428e2cd6f5aa8e589b9dbcd21 SHA512 f0bd3338089a3897ac41903411314fc3df2200a1c057e5cc7bba10ec4f70bd631c607f23ce4db0d29ae99555e687d3b3eb1821287f2800e895d1892daed37014
+EBUILD chemical-mime-data-0.1.94-r4.ebuild 1091 BLAKE2B 2014dc00aed88c563263444a32fa008b440413ddacca3a8e08a9f07191a0595f5166715e12f31c5454b32fe0561476b4b4400aeee6e7a99c9d791f923bd8b4fa SHA512 6760106eb5303b951b3a245de3da8356cf73a7bc6ba788554b308fd31c004ff18729e7c223264df011ac2a3493e201525e394b4f2a63bc4e7fbade9f0056663f
 MISC metadata.xml 474 BLAKE2B c4d6ffbdf66f856fc9e404202d9a9956d8bbfaeb31eb1eb056300ca5049c02d0499ead32a2013080e397eba272bd3a290b81f343baab1fb40204364bfa5208ec SHA512 59cfe759a75bf49fb020652168434fb610c2d5ba56507945253f556b5542a119bc9c9dc4f2b71ceed93f6672b31e5713cc9d76c433e95b0a08c51e9e577bac00
diff --git a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r3.ebuild b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r3.ebuild
deleted file mode 100644
index 7989cf9ef6dc..000000000000
--- a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r3.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit autotools xdg
-
-DESCRIPTION="A collection of data files to add support for chemical MIME types"
-HOMEPAGE="https://github.com/dleidert/chemical-mime"
-SRC_URI="mirror://sourceforge/${PN/-data/}/${P}.tar.bz2"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="amd64 arm arm64 x86"
-IUSE=""
-
-RDEPEND="
-	gnome-base/gnome-mime-data
-	x11-misc/shared-mime-info"
-DEPEND="${RDEPEND}
-	dev-util/intltool
-	dev-util/desktop-file-utils
-	dev-libs/libxslt
-	|| (
-		gnome-base/librsvg
-		media-gfx/imagemagick[xml,png,svg]
-	)
-	media-gfx/imagemagick[png]
-	virtual/pkgconfig"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-turbomole.patch
-	"${FILESDIR}"/${P}-pigz.patch
-	"${FILESDIR}"/${P}-namespace-svg.patch
-	"${FILESDIR}"/${P}-rsvg-convert.patch
-	)
-
-src_prepare() {
-	xdg_src_prepare
-	eautoreconf
-}
-
-src_configure() {
-	econf --disable-update-database
-}
diff --git a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r4.ebuild b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r4.ebuild
index 3abec36ba7d1..bbc0bfb9e26e 100644
--- a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r4.ebuild
+++ b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.94-r4.ebuild
@@ -10,7 +10,7 @@ SRC_URI="mirror://sourceforge/${PN/-data/}/${P}.tar.bz2"
 
 LICENSE="LGPL-2.1"
 SLOT="0"
-KEYWORDS="amd64 ~arm ~arm64 ~x86"
+KEYWORDS="amd64 arm arm64 x86"
 IUSE=""
 
 RDEPEND="
@@ -33,7 +33,7 @@ PATCHES=(
 	"${FILESDIR}"/${P}-turbomole.patch
 	"${FILESDIR}"/${P}-pigz.patch
 	"${FILESDIR}"/${P}-namespace-svg.patch
-	"${FILESDIR}"/${P}-rsvg-convert.patch
+	"${FILESDIR}"/${P}-rsvg-convert-r2.patch
 	# https://github.com/dleidert/chemical-mime/issues/1
 	"${FILESDIR}"/${P}-drop-turbomole-vibrational.patch
 )
diff --git a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-rsvg-convert-r2.patch b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-rsvg-convert-r2.patch
new file mode 100644
index 000000000000..55039f8be07e
--- /dev/null
+++ b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.94-rsvg-convert-r2.patch
@@ -0,0 +1,36 @@
+--- a/configure.ac.old	2020-03-20 23:32:05.866604992 +0100
++++ b/configure.ac	2020-03-20 23:32:30.866022834 +0100
+@@ -97,14 +97,12 @@
+ AC_PATH_PROG([CONVERT], [convert], [no])
+ AC_SUBST([CONVERT])
+ 
+-if test "x$enable_convert" != "xyes" -a "x$CONVERT" = "xno" ; then
+-	AC_ARG_VAR(
+-		[RSVG],
+-		[The 'rsvg' binary with path. Use it to define or override the location of 'rsvg'.]
+-	)
+-	AC_PATH_PROG([RSVG], [rsvg], [no])
+-	AC_SUBST([RSVG])
+-fi
++AC_ARG_VAR(
++	[RSVG],
++	[The 'rsvg' binary with path. Use it to define or override the location of 'rsvg'.]
++)
++AC_PATH_PROG([RSVG], [rsvg-convert], [no])
++AC_SUBST([RSVG])
+ 
+ if test "x$RSVG" = "xno" -a "x$CONVERT" = "xno" ; then
+ 	AC_MSG_ERROR([Cannot find rsvg (librsvg binary) or convert (imagemagick). Please install one of them.])
+--- a/icons/hicolor/Makefile.am.old	2020-03-20 23:32:54.292414381 +0100
++++ b/icons/hicolor/Makefile.am	2020-03-20 23:33:40.052179227 +0100
+@@ -23,8 +23,8 @@
+ .svg.svgz:
+ 	gzip $< -c > $@
+ 	for size in $(icon_sizes) ; do \
+-		if test "x$(RSVG)" != "x" ; then \
+-			$(RSVG) -w $${size} -h $${size} -f png $< $*_$${size}.png ; \
++		if test "x$(RSVG)" != "xno" ; then \
++			$(RSVG) -w $${size} -h $${size} -f png $< --output $*_$${size}.png ; \
+ 		else \
+ 			$(CONVERT) $< -resize $${size}x$${size} $*_$${size}.png ; \
+ 		fi \
diff --git a/sci-chemistry/gnome-chemistry-utils/Manifest b/sci-chemistry/gnome-chemistry-utils/Manifest
new file mode 100644
index 000000000000..af81a2074285
--- /dev/null
+++ b/sci-chemistry/gnome-chemistry-utils/Manifest
@@ -0,0 +1,4 @@
+AUX gnome-chemistry-utils-0.14.17-gnumeric.patch 2242 BLAKE2B 1fef5e8aa58e26d22cf2b3e57250f335950e1ddca635f72c00d4f09d1b3a7654691b53628d7628d9ff33690542d99d42a885a596c2a5484478e0455af2d2b757 SHA512 3f723f5bce350f8b2c778755c323c2d6009e761c16634ec40764a330ddfdfa057b5d9eabadeb212cedab300b44f09ae4778530d599c1c989ed4046b5da8b2cd2
+DIST gnome-chemistry-utils-0.14.17.tar.xz 5911248 BLAKE2B 5d3bb4afbe3d3f620912e810717f08674d56a11c384b1fb239788cfbbb625797e8c52de2b6d940ae7f3d83847533afedd6ed961b1fa0ea1cec62dda88de1a6df SHA512 01bb964e1484e028c5965f1de74798422b448823047fcadf668dc76e98b3e214939a2f031d0182c717c4376f490e5969a4604ee66d1763e6b480032d7ae97468
+EBUILD gnome-chemistry-utils-0.14.17.ebuild 1376 BLAKE2B a8208b91a1126d43b638d60a7c8ae13bbc4f14dee21df8b114af5be271e9e1e1a9815cc220418eb185d58bc6d50e3153dc8470813089182dcc1d97535468f9e0 SHA512 56d2721c19ad1416b559cfe9c278b4034801ed3e59354a54e35a494cdc045264c83a2a357f0f756b8f9379f462bf9c28e58bfa0298725cb0489d7e7bbc44178b
+MISC metadata.xml 336 BLAKE2B 3a1270d31b630b57fc2fc272992b191bba7106355dd176c8fc8ebfe2a92f3aae68284448df2dc43682c6663d8e087320c979d2539a3d10ae5706be2e5b8c35e7 SHA512 eddb0149bf60d2149ab99cd49486c9252815787cb6b1c41e1cd11ea2897df619d4186e6f84cda414f977f8877b7d23ce92b92fcee5918de8b3441fdebe834bb8
diff --git a/sci-chemistry/gnome-chemistry-utils/files/gnome-chemistry-utils-0.14.17-gnumeric.patch b/sci-chemistry/gnome-chemistry-utils/files/gnome-chemistry-utils-0.14.17-gnumeric.patch
new file mode 100644
index 000000000000..826d9b056df8
--- /dev/null
+++ b/sci-chemistry/gnome-chemistry-utils/files/gnome-chemistry-utils-0.14.17-gnumeric.patch
@@ -0,0 +1,47 @@
+Index: gchemutils/configure.ac
+===================================================================
+--- gchemutils/configure.ac	(revision 2072)
++++ gchemutils/configure.ac	(revision 2073)
+@@ -352,7 +352,7 @@
+   libspreadsheet=libspreadsheet-1.12
+ fi
+ 
+-PKG_CHECK_MODULES(gnumeric, [$libspreadsheet >= 1.11.6], [build_gnumeric_plugin=yes],
++PKG_CHECK_MODULES(gnumeric, [$libspreadsheet >= 1.12.42], [build_gnumeric_plugin=yes],
+ 		[build_gnumeric_plugin=no])
+ dnl --without is not handled
+ 
+Index: gchemutils/gnumeric/functions.cc
+===================================================================
+--- gchemutils/gnumeric/functions.cc	(revision 2072)
++++ gchemutils/gnumeric/functions.cc	(revision 2073)
+@@ -195,23 +195,23 @@
+ const GnmFuncDescriptor Chemistry_functions[] = {
+ 
+         { N_("molarmass"),       "s",
+-			help_molarmass, gnumeric_molarmass, NULL, NULL, NULL,
++			help_molarmass, gnumeric_molarmass, NULL,
+ 			GNM_FUNC_SIMPLE, GNM_FUNC_IMPL_STATUS_COMPLETE, GNM_FUNC_TEST_STATUS_NO_TESTSUITE},
+         { N_("monoisotopicmass"),       "s",
+-			help_monoisotopicmass, gnumeric_monoisotopicmass, NULL, NULL, NULL,
++			help_monoisotopicmass, gnumeric_monoisotopicmass, NULL,
+ 			GNM_FUNC_SIMPLE, GNM_FUNC_IMPL_STATUS_COMPLETE, GNM_FUNC_TEST_STATUS_NO_TESTSUITE},
+         { N_("chemcomposition"),       "ss",
+-			help_chemcomposition, gnumeric_chemcomposition, NULL, NULL, NULL,
++			help_chemcomposition, gnumeric_chemcomposition, NULL,
+ 			GNM_FUNC_SIMPLE, GNM_FUNC_IMPL_STATUS_COMPLETE, GNM_FUNC_TEST_STATUS_NO_TESTSUITE},
+         { N_("elementnumber"),       "s",
+-			help_elementnumber, gnumeric_elementnumber, NULL, NULL, NULL,
++			help_elementnumber, gnumeric_elementnumber, NULL,
+ 			GNM_FUNC_SIMPLE, GNM_FUNC_IMPL_STATUS_COMPLETE, GNM_FUNC_TEST_STATUS_NO_TESTSUITE},
+         { N_("elementsymbol"),       "f",
+-			help_elementsymbol, gnumeric_elementsymbol, NULL, NULL, NULL,
++			help_elementsymbol, gnumeric_elementsymbol, NULL,
+ 			GNM_FUNC_SIMPLE, GNM_FUNC_IMPL_STATUS_COMPLETE, GNM_FUNC_TEST_STATUS_NO_TESTSUITE},
+ 
+ 
+-        {NULL, NULL, NULL, NULL, NULL, NULL, NULL,
++        {NULL, NULL, NULL, NULL, NULL,
+ 			GNM_FUNC_IS_PLACEHOLDER,  GNM_FUNC_IMPL_STATUS_UNIMPLEMENTED, GNM_FUNC_TEST_STATUS_NO_TESTSUITE}
+ };
+ 
diff --git a/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.17.ebuild b/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.17.ebuild
new file mode 100644
index 000000000000..40a653132cd5
--- /dev/null
+++ b/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.17.ebuild
@@ -0,0 +1,62 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+inherit autotools xdg
+
+DESCRIPTION="Programs and library containing GTK widgets and C++ classes related to chemistry"
+HOMEPAGE="http://gchemutils.nongnu.org/"
+SRC_URI="http://download.savannah.gnu.org/releases/gchemutils/$(ver_cut 1-2)/${P}.tar.xz"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+LICENSE="GPL-3"
+IUSE="gnumeric"
+
+RDEPEND="
+	>=app-text/gnome-doc-utils-0.3.2
+	>=dev-libs/glib-2.36.0:2
+	>=dev-libs/libxml2-2.4.16:2
+	>=gnome-extra/libgsf-1.14.9
+	>=sci-chemistry/bodr-5
+	>=sci-chemistry/chemical-mime-data-0.1.94
+	>=sci-chemistry/openbabel-2.3.0:0
+	>=x11-libs/cairo-1.6.0
+	>=x11-libs/gdk-pixbuf-2.22.0
+	>=x11-libs/goffice-0.10.12
+	x11-libs/gtk+:3
+	>=x11-libs/libX11-1.0.0
+	gnumeric? ( >=app-office/gnumeric-1.12.42 )
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	app-doc/doxygen
+	gnome-base/gnome-common
+	virtual/pkgconfig
+"
+
+src_prepare() {
+	xdg_src_prepare
+
+	# From Debian
+	eapply "${FILESDIR}/${P}-gnumeric.patch"
+	eautoreconf
+}
+
+src_configure() {
+	# lasem is not in the tree
+	econf \
+		--without-lasem \
+		--disable-mozilla-plugin \
+		--disable-scrollkeeper \
+		--disable-update-databases
+}
+
+src_install() {
+	default
+
+	mv "${ED}"/usr/share/appdata "${ED}"/usr/share/metainfo || die
+	rm -rf "${ED}"/usr/share/mimelnk/ || die
+
+	find "${D}" -name '*.la' -type f -delete || die
+}
diff --git a/sci-chemistry/gnome-chemistry-utils/metadata.xml b/sci-chemistry/gnome-chemistry-utils/metadata.xml
new file mode 100644
index 000000000000..0d27f618fe33
--- /dev/null
+++ b/sci-chemistry/gnome-chemistry-utils/metadata.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>pacho@gentoo.org</email>
+	</maintainer>
+	<use>
+		<flag name="gnumeric">Add a Gnumeric plugin to provide a molarmass function for the spreadsheet</flag>
+	</use>
+</pkgmetadata>
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index a4dbd284f957..82f44f00612e 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -2,10 +2,12 @@ AUX gromacs-2020_beta1-pytest.patch 630 BLAKE2B 1036e06589c24459006f0b579ee89c9d
 DIST gromacs-2018.8.tar.gz 29913703 BLAKE2B 8780032305928067fbfe1559efe9eedc4d47e27ab2f6ab54d6dba39edfcbeefbee4673d8910009048a850620b5a08ba8feb622db652c439cfa50a149ec5f0015 SHA512 6717895942f2ab7b54019511ed2aebadadde8e96d3c4b7414bb9168ffe418432d2dee330192e199f7b9d2f665c71f5d4f1ef0911aa7243d525a2ca182ef5b122
 DIST gromacs-2019.5.tar.gz 33445791 BLAKE2B 1e2e2764b0c8774c878abf4f32c2fa7ddd9b46f464cf1256deb48335433d92ef1b315f5534cdec9f766ae928a71361b5a4dd4a4def638269eb260ff98dbbe8bb SHA512 fdd177e4dfd29629b72bfbb4d61ff7bcdb37279f534883a9df8fd57569212fe1e9f8b8c9cec347fcc607539f31412d604d11ee3c0eb797251960435962b1bec6
 DIST gromacs-2019.6.tar.gz 33446147 BLAKE2B adc21fb6b841b06d499607f8c0166a673645ef5af0b40bd823d0fff5ea24397e6301c5e1e0070986ae1ce1deba8a42052b66da148b071c1e21f2fe3908fee275 SHA512 7c227a9539e5775d5d128ae9e872a24181d79cdcd2852b86453597987e8d7332ecec371da65d089f6e610c54aafbccc8824ce298743383dd6240719ebee692a8
+DIST gromacs-2020.1.tar.gz 29153989 BLAKE2B b1c0313da945c57c74040c2bcd50495b238b0e131cc4ebecd74ae0d01465b47d732ea456a52a2f9d998cd37e2bfdb93d52bd15177328c4b7a14e6b1d8bc00117 SHA512 130394ec70e5d75ea451e9fa77c4ea2dd4adb0c51cc7663ac8579972bab7a0b75d9143d0eebb21802fc93305deca8831393a8cb3f51b6d01f9477f3dadece037
 DIST gromacs-2020.tar.gz 28928068 BLAKE2B 72d4ff8f6b383284e61df9d3b2b53c51300f6961d4c19810670c8ee9ba2f1864d2a325e2774093b9338db785cb91a94461bf93f16cdf4caf0f690298a672d51c SHA512 15f0d58cd8d217eab39ef8e3535dec34127708797eaf6575fb340292cbee2303cd25deb84b3d4417a787076f4ae7be9e4958ec3a347a3aa9aed52ef337a4587c
 DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb
 DIST regressiontests-2019.5.tar.gz 67643634 BLAKE2B c4d9535d9a8a650869d67544ad5f367324f45e55325bb5074ece9b010f232f2f0dd97c9af97924d3f2368ed63015ca7330baff1cc681310e1439ec330b70ee8d SHA512 7c0917b76e7db35ab4e3271d523d268e0e2d858091e68ead863bfe6d1e56b381e30fdbf44f479f6e065c029e2eb27cfa0dbaa1b243f185144321aaf5084c55ce
 DIST regressiontests-2019.6.tar.gz 67643195 BLAKE2B 1e054e24b187946f7ea28090d4f20cf8e1d79a26253f57ba07d130e0773d8541b8a1552a38023d31a68ce8bc62d8e0af1d98609234bb3e7d3e6d567307ebb386 SHA512 eacf1c55b982515a305c29459fe80a7cd558a8481e5689962aa956148af542568b1d1ce59c6784ecb0afd4768c2b664afa21e12af2d89ae2b06b1ba61ad72036
+DIST regressiontests-2020.1.tar.gz 48541809 BLAKE2B 0fec2f0fb7fad0ad48bb790d7df6487e2c1931a0a2134795bf7da4a9087f0f2a3743288fc4ec057fa6b22412c2d8f312cfa3af38be8c5bea51d7a06afb5ac9f0 SHA512 664d29ce39629ed218de65179ce4a73e479d73d30bc96f5ae57624d7e4447298c6122dc09e7873b8cad458eaee0530866411fab20e009e46bf39b133e0de47e8
 DIST regressiontests-2020.tar.gz 48536146 BLAKE2B 9511db78b5d6a5ea431fdb73782f28dde4b94655139886c0ad519888ef3e435fe81807f158d66c1a4284cb88fe730f62d039ac23549f17d0ce5984764ef35f10 SHA512 5a35aaf6fe2f3b146c7045e9c967dc1c8bf754748cc1f2a7300193ae3f206a9f5058329380ae7b03b181410303bcd434584571e6161a75f99e52bd48f8ba1821
 EBUILD gromacs-2018.8.ebuild 8784 BLAKE2B 8c08b6c4f4278ed6455a0489b765c97c748835e49973bb83b7fe8e15d9453c8c9b6c6e26cd27a2d5a927aa87a36bfdef3874020f6658c9b2dcb774043e4547e3 SHA512 b66644847daa453b9a764faaa7f3145e16f3819d0d7ffdad12c1209a398cd03dbf7c2d60e0510f514b18f6ed8c09dfadb77bca6ff2f1eb044c65632842a7499a
 EBUILD gromacs-2018.9999.ebuild 8787 BLAKE2B 9edbb2ae0bd3f76af41cee9971b70fdc957f22bb61ec131abd3cf44a2da56c208b0b103f72754e17cccfa054d79c1e95a9477228b0c14f4476e58bd7656b641a SHA512 c4548c8436dadf1daaf7f4f41e3c957029a10f5eb7fd11c5c8f42046d2ba38c6baf9f47e69fb8e8eeef550e0463d76bf738d6f708ffce6b4cf556e29d725ed5a
@@ -13,6 +15,7 @@ EBUILD gromacs-2019.5-r1.ebuild 9270 BLAKE2B 7bc19e1950bb824a0d30b6340ea181f0089
 EBUILD gromacs-2019.6.ebuild 9273 BLAKE2B f60f3d2c19fcbb406cee16e3ca0743eb72fffcfe7d0565ec69299c4315f72786197d83ae88b32b7f51312e82453555df3a82ea6d28f7ea40ab9f4628e66d62bb SHA512 5d5fb26afbd6c17ecf39685706337fe893171048bd745c4b6b2a6cf5d62a25c6b48f5b0ebff00b7d3a00d6731b0ef56701ed5236ac7ac1abf1d431a426638be5
 EBUILD gromacs-2019.9999.ebuild 9272 BLAKE2B 6d6484a75d2f6ec9d97a33766ff42f0a3b364f8d71f9d8c0af8265e1dffd9eee93dce6a4e7edf93fe316abef0dd8ec1ee0beb9b7cfa04f0ffbe8aa15cefb6c04 SHA512 c0e81e4312accad7377e9e221b636c1870fdf85928ca221c8272b7af6d2d422c2c44b4e6e3cca9818b922e7f194f1e45208e545d5a65e77d57aa29df1d0474dc
 EBUILD gromacs-2020-r1.ebuild 9831 BLAKE2B 0d20f9e04a318eb2313d1b84adb9a747f4b70cc57446031da410e05bc37d2e3b53489110b803b69bcb235ea87dd913e9a7de6531c2e32b6afb9505c44a4d2dbe SHA512 c2edca500cd77e9b88f6b83cb4b3f11819adf313e4b68250d8b446466187e963bdd925665ca3aa532ae2c88b611f15b860f722cdf17c2b145d7cd58a56cb2c17
+EBUILD gromacs-2020.1.ebuild 9831 BLAKE2B 0d20f9e04a318eb2313d1b84adb9a747f4b70cc57446031da410e05bc37d2e3b53489110b803b69bcb235ea87dd913e9a7de6531c2e32b6afb9505c44a4d2dbe SHA512 c2edca500cd77e9b88f6b83cb4b3f11819adf313e4b68250d8b446466187e963bdd925665ca3aa532ae2c88b611f15b860f722cdf17c2b145d7cd58a56cb2c17
 EBUILD gromacs-2020.9999.ebuild 9831 BLAKE2B 0d20f9e04a318eb2313d1b84adb9a747f4b70cc57446031da410e05bc37d2e3b53489110b803b69bcb235ea87dd913e9a7de6531c2e32b6afb9505c44a4d2dbe SHA512 c2edca500cd77e9b88f6b83cb4b3f11819adf313e4b68250d8b446466187e963bdd925665ca3aa532ae2c88b611f15b860f722cdf17c2b145d7cd58a56cb2c17
 EBUILD gromacs-9999.ebuild 9827 BLAKE2B 20a6e2e5b0d70a1c0ada0cafcb12eb170b99ebb37778f467dda1800cabb05d6a34d0dfef9bfaa04b5e6f3b781ed2e5eb97a1f61044e54e526559a9f9093be648 SHA512 19c73f34eda0ed83e58b67c7feb87e6540fb441806c27ae3b6b7d0e59c33cd220d87873fa3b3b9b5c72e8f9f73b778d41d69f21a3fded51a030d1ac6854bc2a2
 MISC metadata.xml 1192 BLAKE2B 560c1c792102747fc16c22d475114480b9897263405da05946721dae5b781c599a02e1401adfa4d929bfb41b4d52791376438aa37d33de18beabc9edbeb779fa SHA512 136c49bfaca76e714e811077c7f7d214a5984c7b6c891c79ad4a754c304752e17450c9aee100dafce04d7bf3893a53224ef9b54504a278654d59fae9acdd0f77
diff --git a/sci-chemistry/gromacs/gromacs-2020.1.ebuild b/sci-chemistry/gromacs/gromacs-2020.1.ebuild
new file mode 100644
index 000000000000..a2dcda755c8b
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-2020.1.ebuild
@@ -0,0 +1,337 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+PYTHON_COMPAT=( python3_{6,7} )
+
+DISTUTILS_SINGLE_IMPL=1
+
+inherit bash-completion-r1 cmake-utils cuda distutils-r1 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 +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +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-6.5.14 )
+	opencl? ( virtual/opencl )
+	fftw? ( sci-libs/fftw:3.0 )
+	hwloc? ( sys-apps/hwloc )
+	lapack? ( virtual/lapack )
+	lmfit? ( sci-libs/lmfit )
+	mkl? ( sci-libs/mkl )
+	mpi? ( virtual/mpi )
+	${PYTHON_DEPS}
+	!sci-chemistry/gmxapi
+	"
+BDEPEND="${CDEPEND}
+	virtual/pkgconfig
+	doc? (
+		app-doc/doxygen
+		$(python_gen_cond_dep '
+			dev-python/sphinx[${PYTHON_MULTI_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 )
+	cuda? ( single-precision )
+	cuda? ( !opencl )
+	mkl? ( !blas !fftw !lapack )
+	${PYTHON_REQUIRED_USE}"
+
+DOCS=( AUTHORS README )
+
+RESTRICT="!test? ( test )"
+
+if [[ ${PV} != *9999 ]]; then
+	S="${WORKDIR}/${PN}-${PV/_/-}"
+fi
+
+PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" )
+
+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"
+}
+
+pkg_setup() {
+	python-single-r1_pkg_setup
+}
+
+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"
+
+	# 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() {
+	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; 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
+
+	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=$(usex lapack)
+		-DGMX_OPENMP=$(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="$acce"
+		-DGMX_VMD_PLUGIN_PATH="${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 cuda=( "-DGMX_GPU=OFF" )
+		[[ ${x} = "float" ]] && use cuda && \
+			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=$(usex gmxapi)
+			-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
+			"${opencl[@]}"
+			"${cuda[@]}"
+			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
+			-DGMX_BINARY_SUFFIX="${suffix}"
+			-DGMX_LIBS_SUFFIX="${suffix}"
+			-DGMX_PYTHON_PACKAGE=$(usex python)
+			)
+		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-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[@]} ${p}
+			-DGMX_THREAD_MPI=OFF
+			-DGMX_MPI=ON
+			-DGMX_OPENMM=OFF
+			-DGMXAPI=OFF
+			"${opencl[@]}"
+			"${cuda[@]}"
+			-DGMX_BUILD_MDRUN_ONLY=ON
+			-DBUILD_SHARED_LIBS=OFF
+			-DGMX_BUILD_MANUAL=OFF
+			-DGMX_BINARY_SUFFIX="_mpi${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
+		if use python; then
+			BUILD_DIR="${WORKDIR}/${P}_${x}"\
+				cmake-utils_src_compile	python_packaging/all
+			BUILD_DIR="${WORKDIR}/${P}" \
+				distutils-r1_src_compile
+		fi
+		# not 100% necessary for rel ebuilds as available from website
+		if use doc; then
+			BUILD_DIR="${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 python; then
+			BUILD_DIR="${WORKDIR}/${P}_${x}" \
+				cmake-utils_src_install	python_packaging/install
+		fi
+		if use doc; then
+			newdoc "${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-gmx.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/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 2b6e1d1125bd..1f4e55620fe5 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,4 +1,5 @@
 DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c
 DIST pymol-2.3.0.tar.gz 10448674 BLAKE2B 0d508587d880ce7f2e8a0481bf664e6bfe6eb1d68b0f48b9266cde756824bd8c0144d7243e958bbc5e571d60fca9dafff125d81a8a3d32107e78ad2ff8dffc05 SHA512 e1dcea1c97bcd9045d3543e92902f240e6affbf61a38e8d2a0be04309e3dbabfe1a869847d1423b3151008978d4c305bbf3ce994fc9d453c0063ce020100c133
-EBUILD pymol-2.3.0-r2.ebuild 3225 BLAKE2B bd378cf0a461ce741ee375bc9e4a2db7153a060125292905e4e050244de22c9ac4df2d32e3c8c049c04cdf256a6240beba9955878419fd574ce2b7965200924b SHA512 6c4ead16743147b4e983e2e626f19e489cd4676ea8610db33104e987e52759d6edd0f355675f723053eb234399b8cf7d7f8235ae479ad38ac48fe980e6cfa292
+EBUILD pymol-2.3.0-r2.ebuild 3189 BLAKE2B b696daab150edc9c5b69e330f68d0a79bb825d39d69e6b149a90be7f12a3956525b91373f330e528178b2732b84b86f6e9ae1624c8cad48eb1580e81b4bde38a SHA512 4c4c4e94c768325728584e6c424e7c7d87e4daab291c0f6bad2c6f527645056d0b9b4fefc822543542f27431f51a1f1a6cda1ab7fb9136d0f44a11c6129060be
+EBUILD pymol-2.3.0-r3.ebuild 3003 BLAKE2B 8e629b5cd104f6fcf1ba885c59f41e4f9ccd564af9d2a6cd273eb5e1faf5af84b2d550dd7157e2f856788f8d96a7cc212aa8a84cfd4320a8500ac28f93b305f2 SHA512 c41a31a5123bdadeb8da8f6fb6ac0cbbc81ef3ecf49ecbbf3c8b4884c01f1bf1c04f63c0872aadca85adb831d8510ec0d7a41f18c0da923524c2380ec2d4d1e6
 MISC metadata.xml 439 BLAKE2B 68df7dfc8ca3d4d4b18b419532bade69491f2e9362f10ae2397c804132b7fc9cd08dcf9703c0a89c44588c570e0c0c1bb9bffb7394d51faf1283142dbc5f70b3 SHA512 f5a3eded9b12fa715ba2e6e10b41c75d9bd823ca0dd40acbffc3f5bfc4b36c687f720b1a4e119b4540a31faf849985778cbd72b0b2cd35af8c52ca0f808d71e4
diff --git a/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild b/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild
index 36cc913f7b09..5eadc9a8512d 100644
--- a/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild
+++ b/sci-chemistry/pymol/pymol-2.3.0-r2.ebuild
@@ -29,7 +29,6 @@ DEPEND="
 	dev-python/pmw:py2[${PYTHON_USEDEP}]
 	dev-python/pyopengl[${PYTHON_USEDEP}]
 	dev-python/PyQt5[opengl,${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
 	media-libs/freetype:2
 	media-libs/glew:0=
 	media-libs/glm
diff --git a/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild b/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
new file mode 100644
index 000000000000..675c8b368801
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-2.3.0-r3.ebuild
@@ -0,0 +1,113 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{6,7} )
+
+inherit distutils-r1 desktop eutils flag-o-matic xdg-utils
+
+DESCRIPTION="A Python-extensible molecular graphics system"
+HOMEPAGE="https://www.pymol.org/"
+SRC_URI="
+	https://dev.gentoo.org/~jlec/distfiles/${PN}-1.8.4.0.png.xz
+	https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz
+	"
+RESTRICT="mirror"
+LICENSE="PSF-2.2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="web"
+
+DEPEND="
+	dev-libs/msgpack[cxx]
+	dev-libs/mmtf-cpp
+	dev-python/pyopengl[${PYTHON_USEDEP}]
+	dev-python/PyQt5[opengl,${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	media-libs/freetype:2
+	media-libs/glew:0=
+	media-libs/glm
+	media-libs/libpng:0=
+	media-video/mpeg-tools
+	sys-libs/zlib
+"
+RDEPEND="${DEPEND}
+	sci-chemistry/chemical-mime-data
+"
+
+S="${WORKDIR}"/${PN}-open-source-${PV}
+
+python_prepare_all() {
+	sed \
+		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
+		-e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
+		-e "/import/s:argparse:argparseX:g" \
+		-i setup.py || die
+
+	sed \
+		-e "s:/opt/local:${EPREFIX}/usr:g" \
+		-e '/ext_comp_args/s:\[.*\]:[]:g' \
+		-i setup.py || die
+	sed \
+		-e "s:\['msgpackc'\]:\['msgpack'\]:g" \
+		-i setup.py || die
+
+	append-cxxflags -std=c++0x
+
+	distutils-r1_python_prepare_all
+}
+
+python_install() {
+	distutils-r1_python_install \
+		--pymol-path="${EPREFIX}/usr/share/pymol"
+
+	sed \
+		-e '1d' \
+		-e "/APBS_BINARY_LOCATION/s:None:\"${EPREFIX}/usr/bin/apbs\":g" \
+		-e "/APBS_PSIZE_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/src/\":g" \
+		-e "/APBS_PDB2PQR_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/\":g" \
+		-i "${D}/$(python_get_sitedir)"/pmg_tk/startup/apbs_tools.py || die
+}
+
+python_install_all() {
+	distutils-r1_python_install_all
+
+	sed \
+		-e '1i#!/usr/bin/env python' \
+		"${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die
+
+	python_foreach_impl python_doscript "${T}"/${PN}
+
+	# These environment variables should not go in the wrapper script, or else
+	# it will be impossible to use the PyMOL libraries from Python.
+	cat >> "${T}"/20pymol <<- EOF
+		PYMOL_PATH="${EPREFIX}/usr/share/pymol"
+		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
+		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
+	EOF
+
+	doenvd "${T}"/20pymol
+
+	newicon "${WORKDIR}"/${PN}-1.8.4.0.png ${PN}.png
+	make_desktop_entry ${PN} PyMol ${PN} \
+		"Graphics;Education;Science;Chemistry;" \
+		"MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;"
+
+	if ! use web; then
+		rm -rf "${D}/$(python_get_sitedir)/web" || die
+	fi
+
+	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
+}
+
+pkg_postinst() {
+	xdg_desktop_database_update
+	xdg_mimeinfo_database_update
+	optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr
+}
+
+pkg_postrm() {
+	xdg_desktop_database_update
+	xdg_mimeinfo_database_update
+}
diff --git a/sci-chemistry/shelx/Manifest b/sci-chemistry/shelx/Manifest
deleted file mode 100644
index 775ffdc94cee..000000000000
--- a/sci-chemistry/shelx/Manifest
+++ /dev/null
@@ -1,20 +0,0 @@
-DIST anode_amd64.bz2 8758937 BLAKE2B a5ef69be49149d7dddaa99a51f435a22df6820a8a8c9b641335bc5fa4b969e470454523b6cc34fe64d03f447af946cdbdad22ef6784a49dbb2261650c221c9b5 SHA512 6d9f0e506531e14956a95ed23c4c5ccfabaf79b92feba237923db2731e9f3861163f6039e556a6976d910075558fae120088c4805f09880ff33955eff86cc2e1
-DIST anode_x86.bz2 4310241 BLAKE2B 5220c6b0438a08af27cc0094178f0dfecd3b528c324f79f3dedffda40facd502cbe8d65c8bd2338f9246c8eb215d22e2cfddbe2117bc8e6320573a8fa39db82d SHA512 344e25564d4e0d94764c536625c9be3f4a4b8be74153f17f07254f798e9ebbfe416d069a082906187ba0ec7ab958adf8c7c1ec0afab7a6b146fe02a0b5b88505
-DIST ciftab_amd64.bz2 1409694 BLAKE2B bfc56d37954f3571eb0419e525c79576023b54fee40db9d29fa9e1b7d1145c13dc73de362e16cffdb6cba1cb28960c0fd0d5fca5abeeb8bd6f953d5ad17d803f SHA512 7f2439cf5d7afefaf9df0a2e0ab970076ea3f65d1e394aa0a81340e4cae0cbcbd25169a5e490c8269cfdc92fe9d1240d9d0a2949322b48c339f7556173e83428
-DIST ciftab_x86.bz2 510941 BLAKE2B eaf458bb7123ca2e8d6c7525f5796f1062b4b94974754e4e340caf5c580ca4ca6b714090c21a7371bbe15d777e48853e9a6b96da8e5155f11ecbeba81593f9f0 SHA512 185628c888e74e7f7ae69eccb3195d841eab83616449c3358dd3fb49605f6bb9e86e97959cf6d20b424037746b67332ad98b9a41ca2a7fae7e3cbe503bf71127
-DIST shelxc_amd64.bz2 1512555 BLAKE2B 6bdddb74b719f73d1225ca2956e3ef86ac38fcdeebf3b56899d4c73213295d60efb5526a8fb2b9db7c2891ff36a83d596d9416d6e2f4be2e86cc031637666100 SHA512 11b382c6a8440052ffaf136f5c4695d7f6d10e184334810d0f9b7ff25a782c424ae3509a0bbacabddb152b56e6fdfea7266f9c395d0a39994a8c02bd650625ca
-DIST shelxc_x86.bz2 614564 BLAKE2B 8b45373bf8392cea08c816acda7af0ba4a3ad776d88cafe8ca1cd4ba3c6a241493b5f403e48c5526458a7eb93de808c6bdeb04da8eed801f149eb19f6c95adae SHA512 5be05948e5b79a44e4ead25deba9b1b08857a4636e4c2f8cdc832f6bb2c2407122adff393035f91ce24b48b025191582b919771052f56ebd7a06aaf66dc82115
-DIST shelxd_amd64.bz2 8773698 BLAKE2B 4cdd16ab39c2be996f282d70b247abd391de59814c3330d46ce446bcf8a9dee5464d95c74ee87b087d3ebb2227c5b7c8b4f852a5f09db8a55460a4656ffa4d0e SHA512 6cb881a937e461edf9c9e7736bfab164e6dc16c4df4291b8dce69b3abf98ce27fadb8079cc5142d2b77eb94ac42c0bb375f3ac21b45f590d535839cc7f8cd762
-DIST shelxd_x86.bz2 4406371 BLAKE2B 78f083b86c05b2081d80310d1a10ad24a2c1ad581423fc32cb7e83dba482076143d3bf23edd2a109d70d3ae5b615563a10fd8f6fbdf7e85bfafee5d123eaae94 SHA512 68d11983f98984bfaca089b839d38cc9607857d2bb6d2cff306d9efa2f34ea8d741220eb01a99d2ecdd832dde1794b4bb228ceae3fc0e87e3210dfa491e6a402
-DIST shelxe_amd64.bz2 8302570 BLAKE2B 7a662c9d1ac3ab73d6266b763b5bab2ce9d865d4dfc742485032406711e4ecbf5e3b733cdaf0726111d30b39d2390ae976fcc69187a721cdba5987d82b4e213c SHA512 cbafde59ba1d9943f74e8c66cc012168f1f8062e978d2f9103adb4d130c9a024e3e8b170af5b5207168f23db4742b4a99ce3b550e897c59e1dfd3631d7d6c6ab
-DIST shelxe_x86.bz2 4177233 BLAKE2B 48ad55d206c9e6ff40c136bce798b6b0ef2d3b17468911b0ecaa5a2e668972c7b46ea6a4f5408b016d298fd17ef7122e3b32238feb095dc7e2e251e7bb6cdcec SHA512 67d56beef36918ec6b5d86109d2e61a0dc5a34ed73174ba5cdf96e0db8d8d41cdf20bffdee138f6f177e30a9df32aa1494c18221139538e5c778d61d5f558c51
-DIST shelxl_amd64.bz2 2985452 BLAKE2B cd5e64c07a302735c771a7fa29612d75134bedf9af443be6218632bcd11f33ba355e67a0b690b2d66bf4014d629d4928146d28d536f672630d7f7286dbee0577 SHA512 0c5b5e4bf6041399221a2f321a3e8f3def952a6eb9af26652a8af04c4bedf5cb98aa529c11e84da20c061028701a49af960135ac697ae157609ca8ae8acde219
-DIST shelxl_x86.bz2 1610822 BLAKE2B 027c1f52175446a6952695df2c9869cb4d38813e92e782920d75e40299f1883f562d465bfe52b8eeab6de9aa2e516d3651ff8fbe716e4646a8250c33ae4d7cc8 SHA512 deaeed15676f294088ce07dc3760e2eecca503f87a537e3e9598d1de6102e82f25b2bd46c080e5140a35046847c345845a88adf159197be640ba52b1a790cfec
-DIST shelxs_amd64.bz2 1606403 BLAKE2B adaf69454a60832daa27f73801f7fe43e704231c9a6a0af9eea45b4a04a0dc239a5962f9fc1fd686cde6ec9797241c8172fde5233b731cee2829ba1bfdcc16de SHA512 3d26e8bc10f0004ee52a564be567db0cdf41f7d05d457e66c12e117bb82550066bf7333830f8dcd56ea987de677f365db25a51f4c22efda9c911fda03d49086e
-DIST shelxs_x86.bz2 746352 BLAKE2B d391c82a284321e23c150ebeeb2d8b6ce26c18b2ba208431cba72d5369e932fc712eee21169c95fd3bf28296c235cf7193cef28861237efc4d58d18614a23258 SHA512 9ecf1e8da8df2280a1982c210dea5418004492047fdd3ab004eade39d247199f3c757d00a56d179eadc7a1ce434c8019c39af865b641ae3c370a8461a950140c
-DIST shelxt_amd64.bz2 8862210 BLAKE2B 9ed422923af05a21933ebc53fd15223291e6672a8c0b56757201d20c555eec60f98c4d94d7230e588083bf00a1775d447d9de24be13a99221b045109239efd17 SHA512 49cb7b5e9f3a1cab153dd04ce4ab424f3331790df2e4acf0584263edcd28e20f6225a6f48161469e1569ae0d6eeed5389db0c9a66d7853ea34b798364a346e27
-DIST shelxt_x86.bz2 4441488 BLAKE2B 5b51964c24a24af6c96acca547efad75b95a7896550bf3e8de6a6811f6879a28ff4f5cb1f08a01fd022774a6ea1f4e13c98529eeebfc6548de4879faafff2f3a SHA512 83027d24d58863030a284e5e573df27db760ce61f7c8d7da5741471bd814256ae5ade1316aa3e262a54c4c4fb6ad231dacfcef043c3279d381d2969e0b73dd14
-DIST shredcif_amd64.bz2 461442 BLAKE2B 547335d13a57a22693f361183bac8d8f9564202bb219b8a419949ce2d9487f940fa5d5b840c2b2fe50adce0b0ff79a780e660757373d27d888b1bb545f9bf900 SHA512 8097b6285d3e9269989663e52a4d903b279f9cdd0a5650c91d605dd324c62361de619c0873968a3178d3c125f59a9b448465a09542e2582779fbb8cca1f9ebf7
-DIST shredcif_x86.bz2 461442 BLAKE2B 547335d13a57a22693f361183bac8d8f9564202bb219b8a419949ce2d9487f940fa5d5b840c2b2fe50adce0b0ff79a780e660757373d27d888b1bb545f9bf900 SHA512 8097b6285d3e9269989663e52a4d903b279f9cdd0a5650c91d605dd324c62361de619c0873968a3178d3c125f59a9b448465a09542e2582779fbb8cca1f9ebf7
-EBUILD shelx-20141228.ebuild 1104 BLAKE2B 0a956ee2c0afa625a865dc7277d5ba14c493818cb66cb97012dba3bddd3a129b89b1d85f5c32bfbe903293f34a0e3b38cd7932dafa24f4f93848a2ffb1f83de2 SHA512 5344381a22c23b847b845395dc4985a5838ba282635e97dcb440fcc9815d1794e42e21501574cd9a0b7b294b58e3825af6c3fd8a0f23c0a981c2dc2d044cd679
-MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-chemistry/shelx/metadata.xml b/sci-chemistry/shelx/metadata.xml
deleted file mode 100644
index 8937bad0b175..000000000000
--- a/sci-chemistry/shelx/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/shelx/shelx-20141228.ebuild b/sci-chemistry/shelx/shelx-20141228.ebuild
deleted file mode 100644
index 156c08fefdd4..000000000000
--- a/sci-chemistry/shelx/shelx-20141228.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Crystal structure determination from single-crystal diffraction data"
-HOMEPAGE="http://shelx.uni-ac.gwdg.de/SHELX/"
-SRC_URI="
-	amd64? (
-		anode_amd64.bz2
-		ciftab_amd64.bz2
-		shelxc_amd64.bz2
-		shelxd_amd64.bz2
-		shelxe_amd64.bz2
-		shelxl_amd64.bz2
-		shelxs_amd64.bz2
-		shelxt_amd64.bz2
-		shredcif_amd64.bz2
-	)
-	x86? (
-		anode_x86.bz2
-		ciftab_x86.bz2
-		shelxc_x86.bz2
-		shelxd_x86.bz2
-		shelxe_x86.bz2
-		shelxl_x86.bz2
-		shelxs_x86.bz2
-		shelxt_x86.bz2
-		shredcif_x86.bz2
-	)
-"
-
-SLOT="0"
-LICENSE="free-noncomm"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-S="${WORKDIR}"
-
-RESTRICT="fetch"
-
-QA_PREBUILT="opt/bin/*"
-
-pkg_nofetch() {
-	elog "Go to ${HOMEPAGE}"
-	elog "Fill out the application form, and send it in."
-	elog "Download ${A} and rename them to"
-	use amd64 && elog "*_amd64.bz2"
-	use x86 && elog "*_x86.bz2"
-	elog "and place renamed tarballs into your DISTDIR directory."
-}
-
-src_install() {
-	local i
-	into /opt
-	for i in *; do
-		newbin ${i} ${i/_*/}
-	done
-}
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index 92abd3614dc7..1cd5411f26dc 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,6 +1,7 @@
 AUX vmd-1.9.1-cuda-device_ptr.patch 894 BLAKE2B 96aeab7c2b9d29e5cd3558e69d1365d6b7dc2d78284bb1185d63a57300a83a4c7c0b8f1c1718027ff33333d34bba116d6898fbee74ab23dfd1a77c560160d659 SHA512 9a561773562873dad077f0f2903299952cb935c69ae4bd1463a5f79d6f27ae3845ac5a24ee295ff3569d9c65ae00a9fe3974f4ead003109246f97d130c2c48bf
 AUX vmd-1.9.2-format-security.patch 550 BLAKE2B d50d05d8697c345f5888b1344c827be1282c5b2e06cfddac022d562688550a728a91a943f9b31c4247f683dcd062ab8fe8ed360aa97a202f20af0467a3148cd3 SHA512 81a71ee4c4c438d18f3a393ebad5c9a08f1a7bb95fa58b78a8798955a34ae2494f80fa074b973a1b595862080e9103d21e509443742cfe2bc3cf77f10c0e3c9d
 AUX vmd-1.9.3-configure-libtachyon.patch 613 BLAKE2B 5717e941102c4d759d6985087f74724df21312a61313d397da1bbac1969b76590117c70bc3b7fac6c7a84483df433d03613b245a05db8bb10bf7b8807369f415 SHA512 1eafa38022588e9b9bba3a15394a432f66693e64ba62c27e7aebf759d279cb04326f76bcc6545ef34cbcbd7446aead1a05a18072e99aa7df0940f11173ab3c00
+AUX vmd-1.9.3-cuda.patch 15569 BLAKE2B a26ce893fd2808b7ce1ad36f6d2d690be482d24805f44030434fd3aadaa9f9a834ae8b73d7f1c759161e20041c2372181b90ae17f71eab50c94e6b38e3b133a3 SHA512 ba6f435601a53d5ed26ceab9ab86a9734e6a3b60f9cb61be5c9f59676a5145a4c64a538ddadf446e82608ade5a3d86ec6b8cb7257d9c402e245f845371feb571
 AUX vmd-1.9.3-tmpdir.patch 673 BLAKE2B 074456a8a68a36f16a804aeb8caee9abf14505cb76a2661b03ad97119bf4afb13a994c9cf22eeb952a79a980fcf03bd3dee5c93cf63bf82a19831f71bcbd83c2 SHA512 f7f570c729259f9133fb6411047266312c3d5f802d4cffe316cfdc4094f0fd0830c3eaae6408f56ea17dadba283e1a1fdf86fec858a5211b1c00ed927f160ea4
 DIST vmd-1.9.2-gentoo-patches.tar.xz 14896 BLAKE2B eb7c7fb982602f37bd8374bf8458a0a2ea2202161248caffd0d4e0f8124d627755304bb778976e1cf5598b6bfbbe5d8c8e6016c9ec562204d6782aaaf179b185 SHA512 0516b9e57b256ce822a64df420ebf3ab7391722757caeaa7e615526242043e9375fee8f4ee86fb4eb8de7a50d5cfc8f8d973ace5fa082e6f9010eb692cd6ee51
 DIST vmd-1.9.2.src.tar.gz 34903084 BLAKE2B f7f7048ef7bb72a8b0dcae955c7f90691085158c38a59229d5b929a4b52d3148bdb2f40084cf8c4544f01cb8bcb57de1d98a90bd17568a07c4ebb8f6985cec9b SHA512 b232b743d4ea97dcf76e3005e1c8716d7138602edc078c4846026ab67759c8559af956182cb1acf3c85890db10b6f658ac9c269d432f2595612cf376d6d505ef
@@ -9,5 +10,6 @@ DIST vmd-1.9.3.src.tar 129566720 BLAKE2B 848f3280d51765dcd18722dd233e0cdee3b7c0a
 EBUILD vmd-1.9.2.ebuild 7255 BLAKE2B d59ea537a43555104edd2effc973274abae483d739bf5051efce7c1ad15e131ff0156ce2129cf882c88194f359c69eb163571e23f47025ae26cc6f85ab4999a2 SHA512 bafeb7c0448920feaa77855d29cffd2e3d9df1994c528bb738ac01551d6eb5fea4d3e681f5d4c189366e8dff973c9f8c5633f18648c31026ce749041eb5358ee
 EBUILD vmd-1.9.3-r1.ebuild 7612 BLAKE2B 62e0208cbe8fac390d942885f1e12713a88dc29eac68aa708dacfa9a2c0c0eff94982795ddc3bce47c459e8153692978744efdf520518705db0892208761dd9d SHA512 4529071928c4b63ebc35d92ff9ef7713a38d49d5579cf4351a979806ae81eb9ce3e02c438a9ce127eba217039341ae2c53e74710aa0151d4e9b0db865458facb
 EBUILD vmd-1.9.3-r4.ebuild 7793 BLAKE2B 9f023e8efb5a095d2d6b46198a4137298d7e61c697e7f1eeb57ecfa5f1df7102840b9c42f4ceeb8c5052c59031d572a50eda0a2799a11432487b15a21e97eb5c SHA512 22326601bd6908b3495ebef7e9b45f3482dbd73c8b6bd54582d02e4721bcc483ef02ea67d8e582b59777cbfc923e4464a707281a06b6459de64a7f1e301d9268
+EBUILD vmd-1.9.3-r5.ebuild 7822 BLAKE2B 2a3933c1008dcde65b37846ae5cfc993036d387a9a62a4cb207865187a22e8cf41401000171d083e059abc17c43adf773490aafcfbc576480b241fd359f6fb88 SHA512 9abc8facc673387ee0fcc77b27e4f421f2c7cb590b451b5d8ce4165a66be27ad1b69a45d9c939718a4359f1c76591855219bdb5956947aa2408d61f338eb78ca
 EBUILD vmd-1.9.3.ebuild 7210 BLAKE2B a4c7a26b5c137c67adb5ea4b49acf0b8866a5b5a30840816a7c5a62c12355dfbb3bf17b2dfff39501c9d63e5bf3b479624c9186f7eaef65db455a9f29fe543a3 SHA512 fea1bf7019ae20f796be0c9fb9a5f912a491de16ecabeb6327b366120621c65401f8b4d32a575cf8d231b2c40d54f7c38537f3ce6a217856e1ec44fe49420e38
 MISC metadata.xml 778 BLAKE2B 6c4202950f57a4d7a3004e966c761325a0a31ab19fe06a6bd69882bd685e41424953104ff653c03d6cbbcb60bb9aba45fbcec43cd228c4bb57fcb1c63a2bd881 SHA512 b967b71fb9f1b47a9d3b69e6958dfb0314a9f071dade7ed1876e91dfa73188748faf11ef832d240a71745b36a30422bde79de2e9ff8e5ec6b6da4b11b40d19c9
diff --git a/sci-chemistry/vmd/files/vmd-1.9.3-cuda.patch b/sci-chemistry/vmd/files/vmd-1.9.3-cuda.patch
new file mode 100644
index 000000000000..258efb777caf
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.9.3-cuda.patch
@@ -0,0 +1,426 @@
+--- a/src/CUDAMarchingCubes.cu	2018-03-30 18:52:25.467189457 +0300
++++ b/src/CUDAMarchingCubes.cu	2018-03-30 18:52:02.387136244 +0300
+@@ -10,7 +10,7 @@
+  *
+  *      $RCSfile: CUDAMarchingCubes.cu,v $
+  *      $Author: johns $        $Locker:  $             $State: Exp $
+- *      $Revision: 1.30 $       $Date: 2016/11/28 03:04:58 $
++ *      $Revision: 1.32 $       $Date: 2018/02/15 05:15:02 $
+  *
+  ***************************************************************************
+  * DESCRIPTION:
+@@ -25,14 +25,17 @@
+ //
+ // Description: This class computes an isosurface for a given density grid
+ //              using a CUDA Marching Cubes (MC) alorithm. 
+-//              The implementation is based on the MC demo from the 
+-//              Nvidia GPU Computing SDK, but has been improved 
+-//              and extended.  This implementation achieves higher 
+-//              performance by reducing the number of temporary memory
+-//              buffers, reduces the number of scan calls by using vector
+-//              integer types, and allows extraction of per-vertex normals 
+-//              optionally computes per-vertex colors if provided with a 
+-//              volumetric texture map.
++//
++//              The implementation is loosely based on the MC demo from 
++//              the Nvidia GPU Computing SDK, but the design has been 
++//              improved and extended in several ways.  
++//
++//              This implementation achieves higher performance
++//              by reducing the number of temporary memory
++//              buffers, reduces the number of scan calls by using 
++//              vector integer types, and allows extraction of 
++//              per-vertex normals and optionally computes 
++//              per-vertex colors if a volumetric texture map is provided.
+ //
+ // Author: Michael Krone <michael.krone@visus.uni-stuttgart.de>
+ //         John Stone <johns@ks.uiuc.edu>
+@@ -48,7 +51,7 @@
+ #include <thrust/functional.h>
+ 
+ //
+-// Restrict macro to make it easy to do perf tuning tess
++// Restrict macro to make it easy to do perf tuning tests
+ //
+ #if 0
+ #define RESTRICT __restrict__
+@@ -171,6 +174,11 @@
+ texture<float, 3, cudaReadModeElementType> volumeTex;
+ 
+ // sample volume data set at a point p, p CAN NEVER BE OUT OF BOUNDS
++// XXX The sampleVolume() call underperforms vs. peak memory bandwidth
++//     because we don't strictly enforce coalescing requirements in the
++//     layout of the input volume presently.  If we forced X/Y dims to be
++//     warp-multiple it would become possible to use wider fetches and
++//     a few other tricks to improve global memory bandwidth 
+ __device__ float sampleVolume(const float * RESTRICT data, 
+                               uint3 p, uint3 gridSize) {
+     return data[(p.z*gridSize.x*gridSize.y) + (p.y*gridSize.x) + p.x];
+@@ -592,6 +600,30 @@
+     cudaBindTextureToArray(volumeTex, d_vol, desc);
+ }
+ 
++#if CUDART_VERSION >= 9000
++//
++// XXX CUDA 9.0RC breaks the usability of Thrust scan() prefix sums when
++//     used with the built-in uint2 vector integer types.  To workaround
++//     the problem we have to define our own type and associated conversion
++//     routines etc.
++//
++
++// XXX workaround for uint2 breakage in CUDA 9.0RC
++struct myuint2 : uint2 {
++  __host__ __device__ myuint2() : uint2(make_uint2(0, 0)) {}
++  __host__ __device__ myuint2(int val) : uint2(make_uint2(val, val)) {}
++  __host__ __device__ myuint2(uint2 val) : uint2(make_uint2(val.x, val.y)) {}
++};
++
++void ThrustScanWrapperUint2(uint2* output, uint2* input, unsigned int numElements) {
++    const uint2 zero = make_uint2(0, 0);
++    thrust::exclusive_scan(thrust::device_ptr<myuint2>((myuint2*)input),
++                           thrust::device_ptr<myuint2>((myuint2*)input + numElements),
++                           thrust::device_ptr<myuint2>((myuint2*)output),
++                           (myuint2) zero);
++}
++
++#else
+ 
+ void ThrustScanWrapperUint2(uint2* output, uint2* input, unsigned int numElements) {
+     const uint2 zero = make_uint2(0, 0);
+@@ -601,6 +633,7 @@
+                            zero);
+ }
+ 
++#endif
+ 
+ void ThrustScanWrapperArea(float* output, float* input, unsigned int numElements) {
+     thrust::inclusive_scan(thrust::device_ptr<float>(input), 
+@@ -639,11 +672,9 @@
+ }
+ 
+ 
+-///////////////////////////////////////////////////////////////////////////////
+ //
+ // class CUDAMarchingCubes
+ //
+-///////////////////////////////////////////////////////////////////////////////
+ 
+ CUDAMarchingCubes::CUDAMarchingCubes() {
+     // initialize values
+@@ -713,9 +744,6 @@
+ }
+ 
+ 
+-////////////////////////////////////////////////////////////////////////////////
+-//! Run the Cuda part of the computation
+-////////////////////////////////////////////////////////////////////////////////
+ void CUDAMarchingCubes::computeIsosurfaceVerts(float3* vertOut, unsigned int maxverts, dim3 & grid3) {
+     // check if data is available
+     if (!this->setdata)
+
+--- a/src/CUDAMDFF.cu	2016-12-01 10:11:56.000000000 +0300
++++ b/src/CUDAMDFF.cu	2018-03-30 18:56:44.352937599 +0300
+@@ -11,7 +11,7 @@
+  *
+  *      $RCSfile: CUDAMDFF.cu,v $
+  *      $Author: johns $        $Locker:  $             $State: Exp $
+- *      $Revision: 1.75 $      $Date: 2015/04/07 20:41:26 $
++ *      $Revision: 1.78 $      $Date: 2018/02/19 07:10:37 $
+  *
+  ***************************************************************************
+  * DESCRIPTION:
+@@ -28,12 +28,16 @@
+ #include <stdlib.h>
+ #include <string.h>
+ #include <cuda.h>
+-#include <float.h> // FLT_MAX etc
+-
++#if CUDART_VERSION >= 9000
++#include <cuda_fp16.h> // need to explicitly include for CUDA 9.0
++#endif
+ #if CUDART_VERSION < 4000
+ #error The VMD MDFF feature requires CUDA 4.0 or later
+ #endif
+ 
++#include <float.h> // FLT_MAX etc
++
++
+ #include "Inform.h"
+ #include "utilities.h"
+ #include "WKFThreads.h"
+@@ -588,6 +592,43 @@
+ }
+ 
+ 
++
++// #define VMDUSESHUFFLE 1
++#if defined(VMDUSESHUFFLE) && __CUDA_ARCH__ >= 300 && CUDART_VERSION >= 9000
++// New warp shuffle-based CC sum reduction for Kepler and later GPUs.
++inline __device__ void cc_sumreduction(int tid, int totaltb, 
++                                float4 &total_cc_sums,
++                                float &total_lcc,
++                                int &total_lsize,
++                                float4 *tb_cc_sums,
++                                float *tb_lcc,
++                                int *tb_lsize) {
++  total_cc_sums = make_float4(0.0f, 0.0f, 0.0f, 0.0f);
++  total_lcc = 0.0f;
++  total_lsize = 0;
++
++  // use precisely one warp to do the final reduction
++  if (tid < warpSize) {
++    for (int i=tid; i<totaltb; i+=warpSize) {
++      total_cc_sums += tb_cc_sums[i];
++      total_lcc     += tb_lcc[i];
++      total_lsize   += tb_lsize[i];
++    }
++
++    // perform intra-warp parallel reduction...
++    // general loop version of parallel sum-reduction
++    for (int mask=warpSize/2; mask>0; mask>>=1) {
++      total_cc_sums.x += __shfl_xor_sync(0xffffffff, total_cc_sums.x, mask);
++      total_cc_sums.y += __shfl_xor_sync(0xffffffff, total_cc_sums.y, mask);
++      total_cc_sums.z += __shfl_xor_sync(0xffffffff, total_cc_sums.z, mask);
++      total_cc_sums.w += __shfl_xor_sync(0xffffffff, total_cc_sums.w, mask);
++      total_lcc     += __shfl_xor_sync(0xffffffff, total_lcc, mask);
++      total_lsize   += __shfl_xor_sync(0xffffffff, total_lsize, mask);
++    }
++  }
++}
++#else
++// shared memory based CC sum reduction 
+ inline __device__ void cc_sumreduction(int tid, int totaltb, 
+                                 float4 &total_cc_sums,
+                                 float &total_lcc,
+@@ -629,6 +670,7 @@
+   total_lcc = tb_lcc[0];
+   total_lsize = tb_lsize[0];
+ }
++#endif
+ 
+ 
+ inline __device__ void thread_cc_sum(float ref, float density,
+@@ -750,6 +792,92 @@
+   }
+ 
+ 
++#if defined(VMDUSESHUFFLE) && __CUDA_ARCH__ >= 300 && CUDART_VERSION >= 9000
++  // all threads write their local sums to shared memory...
++  __shared__ float2 tb_cc_means_s[TOTALBLOCKSZ];
++  __shared__ float2 tb_cc_squares_s[TOTALBLOCKSZ];
++  __shared__ float tb_lcc_s[TOTALBLOCKSZ];
++  __shared__ int tb_lsize_s[TOTALBLOCKSZ];
++
++  tb_cc_means_s[tid] = thread_cc_means;
++  tb_cc_squares_s[tid] = thread_cc_squares;
++  tb_lcc_s[tid] = thread_lcc;
++  tb_lsize_s[tid] = thread_lsize;
++  __syncthreads(); // all threads must hit syncthreads call...
++
++  // use precisely one warp to do the thread-block-wide reduction
++  if (tid < warpSize) {
++    float2 tmp_cc_means = make_float2(0.0f, 0.0f);
++    float2 tmp_cc_squares = make_float2(0.0f, 0.0f);
++    float tmp_lcc = 0.0f;
++    int tmp_lsize = 0;
++    for (int i=tid; i<TOTALBLOCKSZ; i+=warpSize) {
++      tmp_cc_means   += tb_cc_means_s[i];
++      tmp_cc_squares += tb_cc_squares_s[i];
++      tmp_lcc        += tb_lcc_s[i];
++      tmp_lsize      += tb_lsize_s[i];
++    }
++
++    // perform intra-warp parallel reduction...
++    // general loop version of parallel sum-reduction
++    for (int mask=warpSize/2; mask>0; mask>>=1) {
++      tmp_cc_means.x   += __shfl_xor_sync(0xffffffff, tmp_cc_means.x, mask);
++      tmp_cc_means.y   += __shfl_xor_sync(0xffffffff, tmp_cc_means.y, mask);
++      tmp_cc_squares.x += __shfl_xor_sync(0xffffffff, tmp_cc_squares.x, mask);
++      tmp_cc_squares.y += __shfl_xor_sync(0xffffffff, tmp_cc_squares.y, mask);
++      tmp_lcc          += __shfl_xor_sync(0xffffffff, tmp_lcc, mask);
++      tmp_lsize        += __shfl_xor_sync(0xffffffff, tmp_lsize, mask);
++    }
++
++    // write per-thread-block partial sums to global memory,
++    // if a per-thread-block CC output array is provided, write the 
++    // local CC for this thread block out, and finally, check if we 
++    // are the last thread block to finish, and finalize the overall
++    // CC results for the entire grid of thread blocks.
++    if (tid == 0) {   
++      unsigned int bid = blockIdx.z * gridDim.x * gridDim.y +
++                         blockIdx.y * gridDim.x + blockIdx.x;
++
++      tb_cc_sums[bid] = make_float4(tmp_cc_means.x, tmp_cc_means.y,
++                                    tmp_cc_squares.x, tmp_cc_squares.y);
++      tb_lcc[bid]     = tmp_lcc;
++      tb_lsize[bid]   = tmp_lsize;
++
++      if (tb_CC != NULL) {
++        float cc = calc_cc(tb_cc_means_s[0].x, tb_cc_means_s[0].y,
++                           tb_cc_squares_s[0].x, tb_cc_squares_s[0].y,
++                           tb_lsize_s[0], tb_lcc_s[0]);
++
++        // write local per-thread-block CC to global memory
++        tb_CC[bid]   = cc;
++      }
++
++      __threadfence();
++
++      unsigned int value = atomicInc(&tbcatomic[0], totaltb);
++      isLastBlockDone = (value == (totaltb - 1));
++    }
++  }
++  __syncthreads();
++
++  if (isLastBlockDone) {
++    float4 total_cc_sums;
++    float total_lcc;
++    int total_lsize;
++    cc_sumreduction(tid, totaltb, total_cc_sums, total_lcc, total_lsize,
++                    tb_cc_sums, tb_lcc, tb_lsize); 
++
++    if (tid == 0) {
++      tb_cc_sums[totaltb] = total_cc_sums;
++      tb_lcc[totaltb] = total_lcc;
++      tb_lsize[totaltb] = total_lsize;
++    }
++ 
++    reset_atomic_counter(&tbcatomic[0]);
++  }
++
++#else
++
+   // all threads write their local sums to shared memory...
+   __shared__ float2 tb_cc_means_s[TOTALBLOCKSZ];
+   __shared__ float2 tb_cc_squares_s[TOTALBLOCKSZ];
+@@ -794,6 +922,7 @@
+     }
+     __syncthreads(); // all threads must hit syncthreads call...
+   }
++//#endif
+ 
+   // write per-thread-block partial sums to global memory,
+   // if a per-thread-block CC output array is provided, write the 
+@@ -847,6 +976,7 @@
+     }
+ #endif
+   }
++#endif
+ }
+ 
+ 
+
+--- a/src/CUDAQuickSurf.cu	2016-12-01 10:11:56.000000000 +0300
++++ b/src/CUDAQuickSurf.cu	2018-03-30 19:01:38.777196233 +0300
+@@ -11,7 +11,7 @@
+  *
+  *      $RCSfile: CUDAQuickSurf.cu,v $
+  *      $Author: johns $        $Locker:  $             $State: Exp $
+- *      $Revision: 1.81 $      $Date: 2016/04/20 04:57:46 $
++ *      $Revision: 1.84 $      $Date: 2018/02/15 04:59:15 $
+  *
+  ***************************************************************************
+  * DESCRIPTION:
+@@ -22,6 +22,9 @@
+ #include <stdlib.h>
+ #include <string.h>
+ #include <cuda.h>
++#if CUDART_VERSION >= 9000
++#include <cuda_fp16.h>  // need to explicitly include for CUDA 9.0
++#endif
+ 
+ #if CUDART_VERSION < 4000
+ #error The VMD QuickSurf feature requires CUDA 4.0 or later
+@@ -130,14 +133,14 @@
+ #define GUNROLL      1
+ #endif
+ 
+-#if __CUDA_ARCH__ >= 300
+ #define MAXTHRDENS  ( GBLOCKSZX * GBLOCKSZY * GBLOCKSZZ )
+-#define MINBLOCKDENS 1
++#if __CUDA_ARCH__ >= 600
++#define MINBLOCKDENS 16
++#elif __CUDA_ARCH__ >= 300
++#define MINBLOCKDENS 16
+ #elif __CUDA_ARCH__ >= 200
+-#define MAXTHRDENS  ( GBLOCKSZX * GBLOCKSZY * GBLOCKSZZ )
+ #define MINBLOCKDENS 1
+ #else
+-#define MAXTHRDENS  ( GBLOCKSZX * GBLOCKSZY * GBLOCKSZZ )
+ #define MINBLOCKDENS 1
+ #endif
+ 
+@@ -150,7 +153,7 @@
+ //
+ template<class DENSITY, class VOLTEX>
+ __global__ static void 
+-// __launch_bounds__ ( MAXTHRDENS, MINBLOCKDENS )
++__launch_bounds__ ( MAXTHRDENS, MINBLOCKDENS )
+ gaussdensity_fast_tex_norm(int natoms,
+                       const float4 * RESTRICT sorted_xyzr, 
+                       const float4 * RESTRICT sorted_color, 
+@@ -217,6 +220,8 @@
+     for (yab=yabmin; yab<=yabmax; yab++) {
+       for (xab=xabmin; xab<=xabmax; xab++) {
+         int abcellidx = zab * acplanesz + yab * acncells.x + xab;
++        // this biggest latency hotspot in the kernel, if we could improve
++        // packing of the grid cell map, we'd likely improve performance 
+         uint2 atomstartend = cellStartEnd[abcellidx];
+         if (atomstartend.x != GRID_CELL_EMPTY) {
+           unsigned int atomid;
+@@ -296,7 +301,7 @@
+ 
+ 
+ __global__ static void 
+-// __launch_bounds__ ( MAXTHRDENS, MINBLOCKDENS )
++__launch_bounds__ ( MAXTHRDENS, MINBLOCKDENS )
+ gaussdensity_fast_tex3f(int natoms,
+                         const float4 * RESTRICT sorted_xyzr, 
+                         const float4 * RESTRICT sorted_color, 
+@@ -363,6 +368,8 @@
+     for (yab=yabmin; yab<=yabmax; yab++) {
+       for (xab=xabmin; xab<=xabmax; xab++) {
+         int abcellidx = zab * acplanesz + yab * acncells.x + xab;
++        // this biggest latency hotspot in the kernel, if we could improve
++        // packing of the grid cell map, we'd likely improve performance 
+         uint2 atomstartend = cellStartEnd[abcellidx];
+         if (atomstartend.x != GRID_CELL_EMPTY) {
+           unsigned int atomid;
+@@ -550,7 +557,6 @@
+ 
+ // per-GPU handle with various memory buffer pointers, etc.
+ typedef struct {
+-  /// max grid sizes and attributes the current allocations will support
+   int verbose;
+   long int natoms;
+   int colorperatom;
+@@ -561,18 +567,18 @@
+   int gy;
+   int gz;
+ 
+-  CUDAMarchingCubes *mc;     ///< Marching cubes class used to extract surface
++  CUDAMarchingCubes *mc;     
+ 
+-  float *devdensity;         ///< density map stored in GPU memory
+-  void *devvoltexmap;        ///< volumetric texture map
+-  float4 *xyzr_d;            ///< atom coords and radii
+-  float4 *sorted_xyzr_d;     ///< cell-sorted coords and radii
+-  float4 *color_d;           ///< colors
+-  float4 *sorted_color_d;    ///< cell-sorted colors
+-
+-  unsigned int *atomIndex_d; ///< cell index for each atom
+-  unsigned int *atomHash_d;  ///<  
+-  uint2 *cellStartEnd_d;     ///< cell start/end indices 
++  float *devdensity;         
++  void *devvoltexmap;        
++  float4 *xyzr_d;            
++  float4 *sorted_xyzr_d;     
++  float4 *color_d;           
++  float4 *sorted_color_d;    
++
++  unsigned int *atomIndex_d; 
++  unsigned int *atomHash_d;  
++  uint2 *cellStartEnd_d;     
+ 
+   void *safety;
+   float3 *v3f_d;
diff --git a/sci-chemistry/vmd/vmd-1.9.3-r5.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r5.ebuild
new file mode 100644
index 000000000000..a4e0e6db49b0
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.9.3-r5.ebuild
@@ -0,0 +1,272 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+PYTHON_COMPAT=( python2_7 )
+
+inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs xdg
+
+DESCRIPTION="Visual Molecular Dynamics"
+HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
+SRC_URI="
+	https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz
+	${P}.src.tar
+"
+
+SLOT="0"
+LICENSE="vmd"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RESTRICT="fetch"
+
+# currently, tk-8.5* with USE=truetype breaks some
+# tk apps such as Sequence Viewer or Timeline.
+CDEPEND="
+	>=dev-lang/tk-8.6.1:0=
+	dev-lang/perl
+	dev-libs/expat
+	$(python_gen_cond_dep '
+		|| (
+			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
+			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
+		)
+	')
+	sci-libs/netcdf:0=
+	virtual/opengl
+	>=x11-libs/fltk-1.1.10-r2:1
+	x11-libs/libXft
+	x11-libs/libXi
+	${PYTHON_DEPS}
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= )
+	gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] )
+	sqlite? ( dev-db/sqlite:3= )
+	tachyon? ( >=media-gfx/tachyon-0.99_beta6 )
+	xinerama? ( x11-libs/libXinerama )
+"
+DEPEND="${CDEPEND}"
+BDEPEND="
+	virtual/pkgconfig
+	dev-lang/swig
+"
+RDEPEND="${CDEPEND}
+	sci-biology/stride
+	sci-chemistry/chemical-mime-data
+	sci-chemistry/surf
+	x11-terms/xterm
+	msms? ( sci-chemistry/msms-bin )
+	povray? ( media-gfx/povray )
+"
+
+VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
+# Binary only plugin!!
+QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so"
+QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
+QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
+
+pkg_nofetch() {
+	elog "Please download ${P}.src.tar from"
+	elog "${VMD_DOWNLOAD}"
+	elog "after agreeing to the license and get"
+	elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz"
+	elog "Place both into your DISTDIR directory"
+	elog
+	elog "Due to an upstream bug (https://bugs.gentoo.org/640440) sources"
+	elog "file may get downloaded as a compressed tarball or not. In that case"
+	elog "you will need to ensure you uncompress the file and rename it"
+	elog "as ${P}.src.tar"
+}
+
+src_prepare() {
+	xdg_src_prepare
+
+	use cuda && cuda_sanitize
+
+	# Compat with newer CUDA versions (from Arch)
+	eapply "${FILESDIR}"/${P}-cuda.patch
+
+	cd "${WORKDIR}"/plugins || die
+
+	eapply -p2 "${WORKDIR}"/${P}-gentoo-plugins.patch
+
+	[[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile)
+
+	sed \
+		-e "s:CC = gcc:CC = $(tc-getCC):" \
+		-e "s:CXX = g++:CXX = $(tc-getCXX):" \
+		-e "s:COPTO =.*\":COPTO = -fPIC -o \":" \
+		-e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \
+		-e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \
+		-e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \
+		-e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \
+		-e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \
+		-e "s:-ltcl8.5:-ltcl:" \
+		-i Make-arch || die "Failed to set up plugins Makefile"
+
+	sed \
+		-e '/^AR /s:=:?=:g' \
+		-e '/^RANLIB /s:=:?=:g' \
+		-i ../plugins/*/Makefile || die
+
+	tc-export AR RANLIB
+
+	sed \
+		-e "s:\$(CXXFLAGS)::g" \
+		-i hesstrans/Makefile || die
+
+	# prepare vmd itself
+	cd "${S}" || die
+
+	eapply -p2 "${WORKDIR}"/${P}-gentoo-base.patch
+	eapply "${FILESDIR}"/${P}-configure-libtachyon.patch
+	eapply "${FILESDIR}"/${P}-tmpdir.patch
+
+	# PREFIX
+	sed \
+		-e "s:/usr/include/:${EPREFIX}/usr/include:g" \
+		-i configure || die
+
+	sed \
+		-e "s:gentoo-bindir:${ED}/usr/bin:g" \
+		-e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \
+		-e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \
+		-e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:gentoo-gcc:$(tc-getCC):g" \
+		-e "s:gentoo-g++:$(tc-getCXX):g" \
+		-e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \
+		-e "s:gentoo-cflags:${CFLAGS}:g" \
+		-e "s:gentoo-cxxflags:${CXXFLAGS}:g" \
+		-e "s:gentoo-nvflags::g" \
+		-e "s:gentoo-ldflags:${LDFLAGS}:g" \
+		-e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \
+		-e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \
+		-e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \
+		-e "s:gentoo-libtachyon-include:${EPREFIX}/usr/include/tachyon:g" \
+		-e "s:gentoo-libtachyon-libs:${EPREFIX}/usr/$(get_libdir):g" \
+		-e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \
+		-e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \
+		-i configure || die
+
+	if use cuda; then
+		sed \
+			-e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \
+			-e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \
+			-i configure src/Makefile || die
+		sed \
+			-e '/compute_/d' \
+			-i configure || die
+		sed \
+			-e 's:-gencode .*code=sm_..::' \
+			-i src/Makefile || die
+	fi
+
+	sed \
+		-e "s:LINUXPPC:LINUX:g" \
+		-e "s:LINUXALPHA:LINUX:g" \
+		-e "s:LINUXAMD64:LINUX:g" \
+		-e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \
+		-e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \
+		-e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \
+		-i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script"
+
+	EMAKEOPTS=(
+		TCLINC="-I${EPREFIX}/usr/include"
+		TCLLIB="-L${EPREFIX}/usr/$(get_libdir)"
+		TCLLDFLAGS="-shared"
+		NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf)${EPREFIX}/usr/$(get_libdir)/libnetcdf.so"
+		NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf)${EPREFIX}/usr/include"
+		NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)"
+		NETCDFDYNAMIC=1
+		EXPATINC="-I${EPREFIX}/usr/include"
+		EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)"
+		EXPATLDFLAGS="-shared"
+		EXPATDYNAMIC=1
+	)
+	if use gromacs; then
+		EMAKEOPTS+=(
+			TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)"
+			TNGINC="-I${EPREFIX}/usr/include"
+			TNGLDFLAGS="-shared"
+			TNGDYNAMIC=1
+		)
+	fi
+	if use sqlite; then
+		EMAKEOPTS+=(
+			SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)"
+			SQLITEINC="-I${EPREFIX}/usr/include"
+			SQLITELDFLAGS="-shared"
+			SQLITEDYNAMIC=1
+		)
+	fi
+}
+
+src_configure() {
+	local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT"
+	rm -f configure.options && echo $myconf >> configure.options
+
+	use cuda && myconf+=" CUDA"
+#	use mpi && myconf+=" MPI"
+	use tachyon && myconf+=" LIBTACHYON"
+	use xinerama && myconf+=" XINERAMA"
+
+	export \
+		PYTHON_INCLUDE_DIR="$(python_get_includedir)" \
+		PYTHON_LIBRARY_DIR="$(python_get_library_path)" \
+		PYTHON_LIBRARY="$(python_get_LIBS)" \
+		NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \
+		NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include"
+
+	perl ./configure LINUX \
+		${myconf} || die
+}
+
+src_compile() {
+	# build plugins
+	cd "${WORKDIR}"/plugins || die
+
+	emake \
+		${EMAKEOPTS[@]} \
+		LINUX
+
+	# build vmd
+	cd "${S}"/src || die
+	emake
+}
+
+src_install() {
+	# install plugins
+	cd "${WORKDIR}"/plugins || die
+	emake \
+			PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \
+			distrib
+
+	# install vmd
+	cd "${S}"/src || die
+	emake install
+
+	# install docs
+	cd "${S}" || die
+	dodoc Announcement README doc/ig.pdf doc/ug.pdf
+
+	# remove some of the things we don't want and need in
+	# /usr/lib
+	cd "${ED}"/usr/$(get_libdir)/vmd || die
+	rm -fr doc README Announcement LICENSE || \
+		die "failed to clean up /usr/lib/vmd directory"
+
+	# adjust path in vmd wrapper
+	sed \
+		-e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \
+		-e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \
+		|| die "failed to set up vmd wrapper script"
+
+	# install icon and generate desktop entry
+	insinto /usr/share/pixmaps
+	doins "${WORKDIR}"/vmd.png
+	eprefixify "${WORKDIR}"/vmd.desktop
+	sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die
+	# Open PDB files with VMD
+	echo "MimeType=chemical/x-pdb;" >> "${WORKDIR}"/vmd.desktop || die
+	domenu "${WORKDIR}"/vmd.desktop
+}
diff --git a/sci-chemistry/votca-xtp/Manifest b/sci-chemistry/votca-xtp/Manifest
index 34950fb4ccb2..74504cca2946 100644
--- a/sci-chemistry/votca-xtp/Manifest
+++ b/sci-chemistry/votca-xtp/Manifest
@@ -11,6 +11,6 @@ EBUILD votca-xtp-1.4.1.ebuild 1622 BLAKE2B 1358e16a21b653584fefdf8eb673744f18ba7
 EBUILD votca-xtp-1.4.ebuild 1618 BLAKE2B bab1c2d4cd442bc2208f87ff16ed1218aaf6c34ccb229c63d9de14086055684ee9440102b0c9a5bf807ddad69d22ee1b680120f493f18891e8719211509a418f SHA512 affe412a6c4cb8139530d559ae4c12d519eb6b9190075743ed7806c2975a4647f48282893d71b4bef3477b0d35ee07815e416c33095be819967d235c9623a48a
 EBUILD votca-xtp-1.5.1.ebuild 1628 BLAKE2B a89ea389a31edce013d2e41eca4a0a818fd3f0b359aa9e770ecf3e04089b99063106d8b20562b36ad83fdc318c6cc6ffc119a589d995db08175e704ff7ce53f1 SHA512 a90fd6523ef6d42af25b99509718511cf0303bef2e0b083b6e4e8cbb5160bf1cc802b0e60a682c7bd1301f5b17cbaf78c2d2e593d2528f9c24b5f6c3c1aa984f
 EBUILD votca-xtp-1.5.ebuild 1626 BLAKE2B 15b3e63d11348ac376e15769b6106c98144a0ce88bbc7149fcf98bede2f7a29ee4ea066cea67fadf14e60e6dbc6745de4bffa4cf11d6ce6f08d5631fad0af347 SHA512 ac39f8f262a40683ff267dd13ea17cdfb9bd3ba62d698e8e20c98ee1adce53bd002a10dd7805a4ba419ca80a4a3ffd0b3b5c8f9e4b040182eaa6ffd069df114e
-EBUILD votca-xtp-1.6_rc1.ebuild 961 BLAKE2B daa3640486b6405ae8542d99aacb9c3db9c0e30ba69fba949047fd85be8d47748fb363a5ef3790d647468e851bdbf88a3b8dc4cceb89b3ea1cb4962cbc138e7c SHA512 d23d65d51e1a585d42cd42d75bf96a8fa90db1c6977a76712cc372177cd5c9715053e4ea0873d2df2c24446766212032ee6e47f9b0dfc4ef8a37081e3ee97e88
-EBUILD votca-xtp-9999.ebuild 961 BLAKE2B daa3640486b6405ae8542d99aacb9c3db9c0e30ba69fba949047fd85be8d47748fb363a5ef3790d647468e851bdbf88a3b8dc4cceb89b3ea1cb4962cbc138e7c SHA512 d23d65d51e1a585d42cd42d75bf96a8fa90db1c6977a76712cc372177cd5c9715053e4ea0873d2df2c24446766212032ee6e47f9b0dfc4ef8a37081e3ee97e88
+EBUILD votca-xtp-1.6_rc1.ebuild 981 BLAKE2B 029f87e4554e2d353b5ce31f3901b5d18ae56ae4165878066e93d2de5f4ff4c65b9532be077127ec4e605b22ff0c765b841a6f9978cc7e503e50554b0e7ff7b7 SHA512 e2d58abe5b8f8d6b3e2a696a0b0a0f7b27f0af4a88d00d2fc59053dbccd9b7fa840579a5bc3b854bcdf3ce9266d10bacd962d4bada0b5ed325e0074c2d873d3d
+EBUILD votca-xtp-9999.ebuild 981 BLAKE2B 029f87e4554e2d353b5ce31f3901b5d18ae56ae4165878066e93d2de5f4ff4c65b9532be077127ec4e605b22ff0c765b841a6f9978cc7e503e50554b0e7ff7b7 SHA512 e2d58abe5b8f8d6b3e2a696a0b0a0f7b27f0af4a88d00d2fc59053dbccd9b7fa840579a5bc3b854bcdf3ce9266d10bacd962d4bada0b5ed325e0074c2d873d3d
 MISC metadata.xml 453 BLAKE2B 51ee11d9c55f15fd0382a7c422d1c12364901a5ac257f57d04b91b8ca77acf9c1eb709879bfc6042b577961352cbc4e31b01ece3a8c650eaffa9b4ebc6d385fb SHA512 892c8f84df6bd19e969b372def9a485be9121d8f7ab410b532529980298e57d0705f73fac409d8f251449cf2119dd3f28133e08d21d0e73b27d5ec0e9a3f205e
diff --git a/sci-chemistry/votca-xtp/votca-xtp-1.6_rc1.ebuild b/sci-chemistry/votca-xtp/votca-xtp-1.6_rc1.ebuild
index 4de1f7f7474f..9e3b8ca0fa6d 100644
--- a/sci-chemistry/votca-xtp/votca-xtp-1.6_rc1.ebuild
+++ b/sci-chemistry/votca-xtp/votca-xtp-1.6_rc1.ebuild
@@ -27,6 +27,7 @@ SLOT="0"
 RDEPEND="
 	~sci-libs/votca-tools-${PV}
 	>=dev-cpp/eigen-3.3
+	sci-libs/hdf5[cxx]
 	~sci-chemistry/votca-csg-${PV}
 	sci-libs/libxc"
 
diff --git a/sci-chemistry/votca-xtp/votca-xtp-9999.ebuild b/sci-chemistry/votca-xtp/votca-xtp-9999.ebuild
index 4de1f7f7474f..9e3b8ca0fa6d 100644
--- a/sci-chemistry/votca-xtp/votca-xtp-9999.ebuild
+++ b/sci-chemistry/votca-xtp/votca-xtp-9999.ebuild
@@ -27,6 +27,7 @@ SLOT="0"
 RDEPEND="
 	~sci-libs/votca-tools-${PV}
 	>=dev-cpp/eigen-3.3
+	sci-libs/hdf5[cxx]
 	~sci-chemistry/votca-csg-${PV}
 	sci-libs/libxc"
author	V3n3RiX <venerix@redcorelinux.org>	2020-04-12 03:41:30 +0100
committer	V3n3RiX <venerix@redcorelinux.org>	2020-04-12 03:41:30 +0100
commit	623ee73d661e5ed8475cb264511f683407d87365 (patch)
tree	993eb27c93ec7a2d2d19550300d888fc1fed9e69 /sci-chemistry
parent	ceeeb463cc1eef97fd62eaee8bf2196ba04bc384 (diff)