gentoo resync : 12.01.2019

author: V3n3RiX <venerix@redcorelinux.org> 2019-01-12 16:58:08 +0000
committer: V3n3RiX <venerix@redcorelinux.org> 2019-01-12 16:58:08 +0000
commit: c8a77dfe4d3d307c1d5dd2650b7297447d8b609d (patch)
tree: 9ea78393bc3ecd6ab4de449383d4e97e5f3648ae /sci-chemistry
parent: 2891d29af8907ce881662f4a02844926d7a293c7 (diff)
14 files changed, 55 insertions, 1700 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index feb6155bab04..a385cff1f710 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest
index d83109851ca0..1b33c2abb01e 100644
--- a/sci-chemistry/apbs/Manifest
+++ b/sci-chemistry/apbs/Manifest
@@ -1,6 +1,6 @@
-AUX apbs-1.4.1-manip.patch 1522 BLAKE2B 4a30aadc2d80fef5d813ea29f20073b6c4d1cefe24578624faca4fef19418bca64768653b5c3ba7ff935f79885432480b46f7a5fef407d8951be76386e5a62c2 SHA512 b2517b86b688091a9ae6a78132e8cd5a451eff6150211459dae6919bf2ee61edcf2cf1b95d8b2922050a3a7a3aaaa9ce8e2be6766116a1e66d413339b291326b
+AUX apbs-1.4.1-manip.patch 1462 BLAKE2B f4559008a1fc4dc367bc770ed29b7fa9ae9489ab57cfc8dd6e5cff358e27e2ac71b1e786bf9a4e3d96dfb4eea3596305beb5078746324769b582abf8a702a1c5 SHA512 70679623621fb56eeffc79166aa6fd35b5fa2fec828f6800a27b795a4e94c9eee673a7ba5f872c3266c9e78af8935d684fb5c4679b57da6a969189ce45e31468
 AUX apbs-1.4.1-multilib.patch 3301 BLAKE2B 4268a21ec878d780c7a1efe433bf2c82ef2e72f49a6071b6df695bf672ee999be9c29fed06e949b80cc230333d8deca1094c946662ec657d31e3b6f86e873969 SHA512 cdd72fd23a57ee8413f72bf674ae246543b1c9f326727ff07c3b8848d59f98ab7d2daf28677460cb4726f919832079c1d280bcdc86a8bef5c0875583c789b7c0
-AUX apbs-1.4.1-python.patch 4109 BLAKE2B 25193eb227ab9d34f3f636b6264bdbaecdbe48747220582b39798c5c6631bdc7731645f66096dbf659c9eea7f31c8e20c0944796f8f89d995a4cd2712be91a3b SHA512 369c0fa08187ba80d8ce72542fc2942f28426beed39619dd6a90a9ef8dfecb47ea6dc7aa20994629a69d63b55d72d1f837c442744bf5499a942bf312f6723092
+AUX apbs-1.4.1-python.patch 3979 BLAKE2B b21633655df329f5d445c4e53140367b0a8a6cfbfafccba8943206ed9bae46839bae532e3efd19d75e89bc70a1fa59d05f3ed977b1a59f949649d3e89b887a96 SHA512 a38ca3bbf692f42268d192aff61949ece95d9b043ac10b4eec33e383773beec1c60425a12e84843a602e828528f6cf0ed6b8c90e99aeea679c5abc8c093c68ae
 DIST apbs-1.4.1.zip 37999283 BLAKE2B 2301deb7ab4eb2f20098cf63df180bb53189e42a89cd5559357cdcf08e84d27a44eafe8557bb460574802d24d29741ad4606dc3bd7f32911d0d0f2c7453d6470 SHA512 3a127af3940054e5a43b3c0c620507f4f9baa69049e5a0933d8e8825458ad2faba840392752de49fe68d91e2054fb1394cf87bb5bb1c0b48305368e2f404cf6a
-EBUILD apbs-1.4.1-r2.ebuild 3140 BLAKE2B b31ecbf8ddb9e8824917cb7c79ba5239957e1723c56a60b9b20aa6d818a0140ce0e4ace7691ac9663d0e38f99b5d851b529b1355b965d071d7e6b65566763bf9 SHA512 e97100de2ed58f60b414cead8aea44d53178f2b28ca016c9fa4a783993b3be0c66a53eb541e4679f58bc3054e18ab8866bef1a31b817cf62031b65ad3044e1a5
+EBUILD apbs-1.4.1-r2.ebuild 3038 BLAKE2B 52199b0b53f146f7ed915b0cf65e48de40b39e5df10fde56ab89fb43324e3d98e66ba9d09a85d4cc209427d0cd0fc24f7472bc55393703b4c8aa2a13c3d23cdd SHA512 d5b3e8008db4f59618dc08d7e5289929a4852856aea51e2b08e6151d8530f6dab882a0b7229b079afd4ef336023b0f0a0ff19accce91f980fe2a6aea71a6399c
 MISC metadata.xml 1048 BLAKE2B 53a61bd7e05e53b294f0cbd1a21b86f391429ad5f23a545e7cbb27625b152589247a08db06c5d7f6658425de032be970fae0230ad1ac14ac4f6de42663d6c97c SHA512 7d68049cb9b044676430fe879890cc4cd869b99f85696f579d9cbf3b156081301792fd7f03205a9b9d429d71c9a35b4815f4236573f68d3ef6b4718e6e1f0bb3
diff --git a/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild
index 108e43bf904b..b3c4f192894b 100644
--- a/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild
+++ b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild
@@ -1,19 +1,17 @@
 # Copyright 1999-2018 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=6
 
 PYTHON_COMPAT=( python2_7 )
 DISTUTILS_SINGLE_IMPL=true
-
-inherit cmake-utils distutils-r1 flag-o-matic multilib toolchain-funcs
-
-GITHUB_REV="74fcb8676de69ed04ddab8976a8b05a6caaf4d65"
+COMMIT="74fcb8676de69ed04ddab8976a8b05a6caaf4d65"
+inherit cmake-utils distutils-r1 flag-o-matic toolchain-funcs
 
 DESCRIPTION="Evaluation of electrostatic properties of nanoscale biomolecular systems"
 HOMEPAGE="https://www.poissonboltzmann.org/apbs/"
 #SRC_URI="mirror://sourceforge/${PN}/${P}-source.tar.gz"
-SRC_URI="https://github.com/Electrostatics/apbs-pdb2pqr/archive/${GITHUB_REV}.zip -> ${P}.zip"
+SRC_URI="https://github.com/Electrostatics/apbs-pdb2pqr/archive/${COMMIT}.zip -> ${P}.zip"
 
 SLOT="0"
 LICENSE="BSD"
@@ -44,7 +42,7 @@ DEPEND="${RDEPEND}
 	doc? ( app-doc/doxygen )
 "
 
-S="${WORKDIR}"/${PN}-pdb2pqr-${GITHUB_REV}/${PN}
+S="${WORKDIR}"/${PN}-pdb2pqr-${COMMIT}/${PN}
 
 PATCHES=(
 	"${FILESDIR}"/${P}-multilib.patch
@@ -71,24 +69,24 @@ src_prepare() {
 src_configure() {
 	local mycmakeargs=(
 		-DCMAKE_SKIP_RPATH=ON
-		-DTOOLS_PATH="${ED}"/usr
+		-DTOOLS_PATH="${ED%/}"/usr
 		-DSYS_LIBPATHS="${EPREFIX}"/usr/$(get_libdir)
 		-DLIBRARY_INSTALL_PATH=$(get_libdir)
 		-DFETK_PATH="${EPREFIX}"/usr/
 		-DBUILD_SHARED_LIBS=ON
 		-DENABLE_QUIT=OFF
-		$(cmake-utils_use_build doc DOC)
-		$(cmake-utils_use_build tools TOOLS)
+		-DBUILD_DOC=$(usex doc)
+		-DBUILD_TOOLS=$(usex tools)
 		-DENABLE_BEM=OFF
 # ENABLE_BEM: Boundary element method using TABIPB
-		$(cmake-utils_use_enable debug DEBUG)
-		$(cmake-utils_use_enable debug VERBOSE_DEBUG)
-		$(cmake-utils_use_enable fast FAST)
-		$(cmake-utils_use_enable fetk FETK)
-		$(cmake-utils_use_enable mpi MPI)
-		$(cmake-utils_use_enable python PYTHON)
+		-DENABLE_DEBUG=$(usex debug)
+		-DENABLE_VERBOSE_DEBUG=$(usex debug)
+		-DENABLE_FAST=$(usex fast)
+		-DENABLE_FETK=$(usex fetk)
+		-DENABLE_MPI=$(usex mpi)
+		-DENABLE_PYTHON=$(usex python)
 # ENABLE_TINKER: Enable TINKER support
-		$(cmake-utils_use_enable iapbs iAPBS)
+		-DENABLE_iAPBS=$(usex iapbs)
 # MAX_MEMORY: Set the maximum memory (in MB) to be used for a job
 	)
 	cmake-utils_src_configure
diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch b/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch
index 378223397594..090a27d8a5a6 100644
--- a/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch
+++ b/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch
@@ -3,10 +3,10 @@
  apbs/tools/mesh/CMakeLists.txt  | 4 ++--
  4 files changed, 5 insertions(+), 9 deletions(-)
 
-diff --git a/apbs/CMakeLists.txt b/apbs/CMakeLists.txt
+diff --git a/CMakeLists.txt b/CMakeLists.txt
 index 8917fc4..5152008 100644
---- a/apbs/CMakeLists.txt
-+++ b/apbs/CMakeLists.txt
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
 @@ -293,7 +293,7 @@ option(ENABLE_FETK "Enable the finite element solver" OFF)
  
  if(ENABLE_FETK)
@@ -16,10 +16,10 @@ index 8917fc4..5152008 100644
  
      list(APPEND APBS_LIBS "-lstdc++")
      list(APPEND APBS_LIBS "-L${FETK_PATH}/lib")
-diff --git a/apbs/tools/manip/CMakeLists.txt b/apbs/tools/manip/CMakeLists.txt
+diff --git a/tools/manip/CMakeLists.txt b/tools/manip/CMakeLists.txt
 index 937dac7..5768cc5 100644
---- a/apbs/tools/manip/CMakeLists.txt
-+++ b/apbs/tools/manip/CMakeLists.txt
+--- a/tools/manip/CMakeLists.txt
++++ b/tools/manip/CMakeLists.txt
 @@ -4,9 +4,9 @@ set(LIBS "")
  list(APPEND LIBS "apbs_generic")
  list(APPEND LIBS "apbs_mg")
@@ -32,10 +32,10 @@ index 937dac7..5768cc5 100644
  
  message(STATUS "libraries: ${LIBS}")
  
-diff --git a/apbs/tools/mesh/CMakeLists.txt b/apbs/tools/mesh/CMakeLists.txt
+diff --git a/tools/mesh/CMakeLists.txt b/tools/mesh/CMakeLists.txt
 index 1406377..6e6dfb9 100644
---- a/apbs/tools/mesh/CMakeLists.txt
-+++ b/apbs/tools/mesh/CMakeLists.txt
+--- a/tools/mesh/CMakeLists.txt
++++ b/tools/mesh/CMakeLists.txt
 @@ -4,9 +4,9 @@ set(LIBS "")
  list(APPEND LIBS "apbs_generic")
  list(APPEND LIBS "apbs_mg")
diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-python.patch b/sci-chemistry/apbs/files/apbs-1.4.1-python.patch
index db9f86ba120a..5ad6613615f2 100644
--- a/sci-chemistry/apbs/files/apbs-1.4.1-python.patch
+++ b/sci-chemistry/apbs/files/apbs-1.4.1-python.patch
@@ -7,10 +7,10 @@
  apbs/tools/python/setup.py           | 16 ++++++++++++++++
  7 files changed, 26 insertions(+), 8 deletions(-)
 
-diff --git a/apbs/contrib/iapbs/src/apbs_driver.c b/apbs/contrib/iapbs/src/apbs_driver.c
+diff --git a/contrib/iapbs/src/apbs_driver.c b/contrib/iapbs/src/apbs_driver.c
 index c9e443b..e1ad67f 100644
---- a/apbs/contrib/iapbs/src/apbs_driver.c
-+++ b/apbs/contrib/iapbs/src/apbs_driver.c
+--- a/contrib/iapbs/src/apbs_driver.c
++++ b/contrib/iapbs/src/apbs_driver.c
 @@ -595,7 +595,7 @@ int apbsdrv_(
  		printPBEPARM(pbeparm);
  
@@ -38,10 +38,10 @@ index c9e443b..e1ad67f 100644
  		    }
  		    bytesTotal = Vmem_bytesTotal();
  		    highWater = Vmem_highWaterTotal();
-diff --git a/apbs/src/CMakeLists.txt b/apbs/src/CMakeLists.txt
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
 index 44d20fa..2577343 100644
---- a/apbs/src/CMakeLists.txt
-+++ b/apbs/src/CMakeLists.txt
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
 @@ -68,6 +68,7 @@ configure_file(
  
  if(ENABLE_iAPBS)
@@ -50,10 +50,10 @@ index 44d20fa..2577343 100644
      INSTALL(TARGETS apbs_routines DESTINATION ${LIBRARY_INSTALL_PATH})
      INSTALL(FILES apbscfg.h DESTINATION ${HEADER_INSTALL_PATH})
  endif()
-diff --git a/apbs/tools/CMakeLists.txt b/apbs/tools/CMakeLists.txt
+diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
 index 1982a3c..4acbe68 100644
---- a/apbs/tools/CMakeLists.txt
-+++ b/apbs/tools/CMakeLists.txt
+--- a/tools/CMakeLists.txt
++++ b/tools/CMakeLists.txt
 @@ -4,5 +4,5 @@ add_subdirectory(mesh)
  add_subdirectory(manip)
  
@@ -61,17 +61,17 @@ index 1982a3c..4acbe68 100644
 -    add_subdirectory(manip)
 +    add_subdirectory(python)
  endif(ENABLE_PYTHON)
-diff --git a/apbs/tools/python/CMakeLists.txt b/apbs/tools/python/CMakeLists.txt
+diff --git a/tools/python/CMakeLists.txt b/tools/python/CMakeLists.txt
 new file mode 100644
 index 0000000..8b13789
 --- /dev/null
-+++ b/apbs/tools/python/CMakeLists.txt
++++ b/tools/python/CMakeLists.txt
 @@ -0,0 +1 @@
 +
-diff --git a/apbs/tools/python/apbslib.c b/apbs/tools/python/apbslib.c
+diff --git a/tools/python/apbslib.c b/tools/python/apbslib.c
 index fef5cc8..feaaa2c 100644
---- a/apbs/tools/python/apbslib.c
-+++ b/apbs/tools/python/apbslib.c
+--- a/tools/python/apbslib.c
++++ b/tools/python/apbslib.c
 @@ -2504,8 +2504,8 @@ static swig_module_info swig_module = {swig_types, 24, 0, 0, 0, 0};
  #include "maloc/maloc.h"
  #include "apbscfg.h" 
@@ -83,10 +83,10 @@ index fef5cc8..feaaa2c 100644
  
  
  #include <limits.h>
-diff --git a/apbs/tools/python/apbslib.i b/apbs/tools/python/apbslib.i
+diff --git a/tools/python/apbslib.i b/tools/python/apbslib.i
 index 17fe521..44d05ea 100644
---- a/apbs/tools/python/apbslib.i
-+++ b/apbs/tools/python/apbslib.i
+--- a/tools/python/apbslib.i
++++ b/tools/python/apbslib.i
 @@ -15,8 +15,8 @@ Header files:
  #include "maloc/maloc.h"
  #include "apbscfg.h" 
@@ -98,11 +98,11 @@ index 17fe521..44d05ea 100644
  %} 
  
  /* 
-diff --git a/apbs/tools/python/setup.py b/apbs/tools/python/setup.py
+diff --git a/tools/python/setup.py b/tools/python/setup.py
 new file mode 100644
 index 0000000..4a20198
 --- /dev/null
-+++ b/apbs/tools/python/setup.py
++++ b/tools/python/setup.py
 @@ -0,0 +1,16 @@
 +from distutils.core import setup, Extension
 +setup(name='apbs',
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 8583c5f536e6..713bea7304a7 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,18 +1,11 @@
-DIST gromacs-2016.2.tar.gz 27339623 BLAKE2B c3548f4abdc4c1b09a79a3da99d7ca8060daca7307e4c5b81bd97d54adfb9621fbccf1ea7fd96c3676d6b44c20f9f4cd2168ce131799792512fad3b8b1ac0522 SHA512 f5e74bb8c126823c90d205ac0f0835e61fdd13a4550bc15aa9c972ee9b187f6451cdc90877c17276d2f889d61abb5eaa5ea1b54f7cbf3da67074146c749c1aa6
 DIST gromacs-2016.5.tar.gz 27369491 BLAKE2B 4a8bf1ae3e298ac2e26ec476130720dc3ef00db5d999e3a45fdbfd7fbfe7e94fbc86be6ff0f2f23552769c8bc851ce49c73f6fc1ab13f372523279b93e7794d7 SHA512 9cb8ff88871aa5df0967c60ba303c03296c6fa3c215cd01b26259df7753f0014f04222078ab4b84a66a1f709997837134d5c0f74da19b78322e410010c9d9e10
 DIST gromacs-2018.3.tar.gz 29915626 BLAKE2B 6e6eeafecdd923a25b4a2a78a8e89f793639b57ffbd63f19d133d8474302f9a381041f138a509dadb42b36e25fe508729e860efb6b0c75cdbf01d924b0a8fd83 SHA512 3c4d6eb3942d7b54d01c94c6f6f5ae706e0f5d4f9901ea11a56fde4df97b1a9112007f2cb13feea0f19f30c89f57ae80ff53a8f5203b8cdff103aa903cd0dc8f
 DIST gromacs-2018.4.tar.gz 29918276 BLAKE2B daf3f91e47bab61befee4ecd91e4885835fc5ded408462c239c824567e64b5710fb252456c6be2bf0e4ce1a2119747fca9d8fb0532286bb93d6ccdd289fe57ab SHA512 8ef0b90b2c266bb706c8fdba12e763de9c21aad197c1c71f48c06378644a734a3694172804db6c916a4974a9832b128512f2445d0b72783811e64edd22d27955
-DIST gromacs-2019-rc1.tar.gz 33426863 BLAKE2B 8de7eeee128389652922dafe2a6f73fadfeb463a9a1ffea898ac34cfe056500113a12c795aa9ba1304d6e4a737dcfa7bd537bab2f1d49c0951f8b68714c13458 SHA512 ade6e9df653f1212540ca969d0b70b046fe30de866ca899ecb463d2c96e6dd70ac8a5ff08df801728332357abefee2d73cd3e77cae4b2b586a827c69e0257654
-DIST gromacs-5.0.4.tar.gz 26342095 BLAKE2B 27a2483e23533ad627114c0005fa0d49a311b359c31aed6378bdd768c9dda03c3b19f11d961f0bd3b82a1711737d4b7dce13cad5fc56d058dd0110fe21421ee3 SHA512 bc62b623bf71dcaa948aaf7563a3d3afa973da0702062848a20323db202e862dcee413197dacd1472866ccb40fce7709e283177b1c6c49514064f23e6c46b5ee
-DIST gromacs-5.1.3.tar.gz 27095702 BLAKE2B b7fd8fa10e8c4f4368ac551338c59374dc35f85c9fdae5d64eec62929b8f04ea724a084959b3618cd8a151bf3e0a0c84c8f75de953722effca82a4928941ce73 SHA512 9ab26e1b2268f8d567b89b2d99d0b75b937b28edceaec56d17ca3243c76faa31255ffc0c45d762c7c693fe500b00e36ad43b80572d1d7f92dc87f9d2d98c0ba6
-DIST regressiontests-2016.2.tar.gz 67095329 BLAKE2B fec8a663845ad67374c8a230d1590fa9e5079460198f41cee3b788aaa1c72e8ec9dcda48bc68a594f15003d11bf6617d46cc1a09c16b7a333587b43904a16ba6 SHA512 e0aceb56d1f38a7e6ab9fdaac5063fd20c5b3a162ffb6eddd0e6dc7dff9b724bfe31363493a9437e9f9d5421a534b375960fcb31e903a4901a0fa94ed8511294
+DIST gromacs-2019.tar.gz 33428725 BLAKE2B 307838a5ee1a85554d6f2ef8cd9c9dd2f3d9cacd32c534545c23483b5f3a1c7d027bfbdf224b90661cd8cd3fb85c0c99c66cbd619698245a0cb45ebd512dec5d SHA512 54b11530e8ff671461e3ae9418d991fe242957943c944798cddf6efe740eee670a562cd5201dbba68b045f4bafd3afa2dc8de27e0643c7def4e05eaf0ccb5769
 DIST regressiontests-2016.5.tar.gz 67641413 BLAKE2B 4fcd30c198f3acbbabf1104c040d9a686de49536a97dbeb14732bfa0ed3cf37aa61b1b0f45393668985b993d1f1862a8985e416af819cf9793f5964f3e4f43cc SHA512 31764fd99cc4185d61de5d4443ee482c27b13533451a24aa0e4899997ce275a63685424eafacae38b1a3ffd4ce0d5ebe02a90348953b04c104f91376f0edfdff
 DIST regressiontests-2018.3.tar.gz 67857855 BLAKE2B acd7a05ae79d1b4eb47d0c68a3fec9ee19f028a5019f39c37a033f48cf6da2a468375180ad6ceca9ac4f685a8bead38550663a47d6427b51f84c32a5c810e5f0 SHA512 57980d49efe6dcc3b3d14b5913a30c68fc1de5b679ef986fec1a149c76f67139b0299c3ee2825451461294fab5f345c7ad4f42e90f8991b81aafe9c369f3ff0b
 DIST regressiontests-2018.4.tar.gz 67860326 BLAKE2B 0160f701a8fa14ba4f175f4fca9894104bc5cc6aa5f02ac57200fd5a8f74a29b595df609e704cb70fcd9a03529bcf758fb4547e35557a45c0546d819c2681983 SHA512 baaac0c918684216ada5254a7c3a1f5b3ea00b1a63d6085d569095139b2a0c9de4ed330d4694f7eaedab729ed5dcea547390781b3d2f7c2ffdf02e0541a90efe
-DIST regressiontests-2019-rc1.tar.gz 67606596 BLAKE2B e614b21fdf73e205c6ad870e19998f9fdb52cb0c54f878a0ab924772f8a710b7ac3d68faf8b77a043f03f3302f829de61e729e69d04abb38de761022dcb7aa7c SHA512 7521bc03a410d2532ee8681a0a3544f3a33f1aaff83513765ed1a28a756f24812955a44c0d8ae88988e23c347c4df455dd4bd3db7b9bb6d3d7d0bf0cc57bbebb
-DIST regressiontests-5.0.4.tar.gz 65193251 BLAKE2B c5e5f23adcc2639fe652bc252533307c7fda44453d506603242968bd8588c7394028b2c3c7a9252f807a050d40e8f78735e904dfe517d3db8ae962051f4826c1 SHA512 747725fa28c1c9525596bdeeb8809e45268e19036c11dac67d043aa1c51748688ca37eb6014eb7e819eb927a8b9ca2631d0ace4cdff8ed491b08c316c530ab65
-DIST regressiontests-5.1.3.tar.gz 66994083 BLAKE2B 7009f65ad0138664ac84e57f8bc7cce5d18a59f99943e56b6642583120bfce279e005ac0bacd2db8904ea477a48e2b938c64de46a65fa5d08fce6009d53583c3 SHA512 486e86eb3b75bae822abe82dac4e1098aa13723bd04214021f835a2f0b847303f015a9ececc33aa5ae63d31a2eeae07e512f22464b6c0e26d1286b0781578022
-EBUILD gromacs-2016.2.ebuild 7971 BLAKE2B 889ded117d36d17c224bdf65ddc8a2e5fcbdb5cdbf58b5774e308fc45e42a7b3734aae1f87d1d95fb3751c18342025a86317e2bf05a82ffa7f9dfaeb47533e5b SHA512 a2ad66f58d79b03e0832ae0daf9b6cbcdceae2873d25318ee7fb9235a41acc1403708206682848c35d2c347ad2ccb72f75c38df38e8899ba07033040b296eb81
+DIST regressiontests-2019.tar.gz 67597618 BLAKE2B fb950d8518cf1e28db5ebb99bdda8d269c5e43dd49a117bdaae9f00857abc7c096766fb90ff1d2d95a12a875ba2e243b707bfc81a45d07fc8b340a154cf2ad0f SHA512 081e56d052c0a0d021a8a1566f802911e261e1f2b5b2141350fe2372bcad0844042f26121167ed31a31490bd4e042068690c4905fcbc80b539686a074621fc5e
 EBUILD gromacs-2016.5.ebuild 7971 BLAKE2B 889ded117d36d17c224bdf65ddc8a2e5fcbdb5cdbf58b5774e308fc45e42a7b3734aae1f87d1d95fb3751c18342025a86317e2bf05a82ffa7f9dfaeb47533e5b SHA512 a2ad66f58d79b03e0832ae0daf9b6cbcdceae2873d25318ee7fb9235a41acc1403708206682848c35d2c347ad2ccb72f75c38df38e8899ba07033040b296eb81
 EBUILD gromacs-2016.9999.ebuild 7974 BLAKE2B 5568ed9513fd44da7382370e418ffe456db73076c0000101c96bba4e704e6eece7ef6131379ddbe95c42e9fa4b082346db2ee4f6bb15a25d8c6afd9209db2e5c SHA512 911a5f71d9dde20d11a13cff416db12d6722cf9fb9609895a3d3bd2381c36a875f80f1617f6960deae2ceaa951f60a14738dfe5065f41560cfeecf7ad26b7c70
 EBUILD gromacs-2018.3-r1.ebuild 7825 BLAKE2B 359b7f832c98d897e9ccaa1ecbe39f7b8e7077bbdc2f32b1b722c2a221ebf4c187ed691a14dcb5c044a3d243d319963e50297bcb347c6433e4ddeafb0ba1c1fd SHA512 730eef3897293939c0b00a236b3f8d0964354fba7cf89170e2b028510f7c0aee8a0925f4c0b7d765d5631bedd90e8a3010e190f08dd8ed71505710b79d9061d5
@@ -20,11 +13,6 @@ EBUILD gromacs-2018.3.ebuild 7822 BLAKE2B af732727b7050314a4d4d38f5d4b753f96f26b
 EBUILD gromacs-2018.4.ebuild 7825 BLAKE2B 359b7f832c98d897e9ccaa1ecbe39f7b8e7077bbdc2f32b1b722c2a221ebf4c187ed691a14dcb5c044a3d243d319963e50297bcb347c6433e4ddeafb0ba1c1fd SHA512 730eef3897293939c0b00a236b3f8d0964354fba7cf89170e2b028510f7c0aee8a0925f4c0b7d765d5631bedd90e8a3010e190f08dd8ed71505710b79d9061d5
 EBUILD gromacs-2018.9999.ebuild 7825 BLAKE2B 359b7f832c98d897e9ccaa1ecbe39f7b8e7077bbdc2f32b1b722c2a221ebf4c187ed691a14dcb5c044a3d243d319963e50297bcb347c6433e4ddeafb0ba1c1fd SHA512 730eef3897293939c0b00a236b3f8d0964354fba7cf89170e2b028510f7c0aee8a0925f4c0b7d765d5631bedd90e8a3010e190f08dd8ed71505710b79d9061d5
 EBUILD gromacs-2019.9999.ebuild 9112 BLAKE2B 0b972db0fe7e4c4730e9b480ea981b01a9930d128cef5fd589ad06b3f245d845721f74d0ac7b9e08dbed8f85985d3a0a84f361b02221318daf809ef37df9413f SHA512 363db0dfce3fa8459e6f8a07f6c5e5061d143deebc78fdb852557b101cee3fc342cc3c342a878153ced8edb8d8c567b9ab91bb275d3190034dcef6255003c9d7
-EBUILD gromacs-2019_rc1.ebuild 9112 BLAKE2B 0b972db0fe7e4c4730e9b480ea981b01a9930d128cef5fd589ad06b3f245d845721f74d0ac7b9e08dbed8f85985d3a0a84f361b02221318daf809ef37df9413f SHA512 363db0dfce3fa8459e6f8a07f6c5e5061d143deebc78fdb852557b101cee3fc342cc3c342a878153ced8edb8d8c567b9ab91bb275d3190034dcef6255003c9d7
-EBUILD gromacs-4.6.9999.ebuild 8094 BLAKE2B b5d89654043667e88e275270bc3d79fa5b6168cb76450cecc6e143a19d606ddfadeb7cb2d97a3a623e5069159151017afa0ced6080264ecd09de9afb4652457e SHA512 0701afb0d0ccb977aad8cf69209299db91babdcbc3d8b1abc2f727637956e2d86cbb7c36f38be35f793a8abd684f51bc68ab8f107006f02e0975a2b05f317c58
-EBUILD gromacs-5.0.4.ebuild 8413 BLAKE2B 3e78b8d41d4499293ec54c3442d6412e9c1c6fd33f5830d2a4dbf7a369f896f0be2f9407eb3c2a444a29677e261cdf14589e8a80c8b64f5beeaa24800a4e1cce SHA512 b5ed004538c3fdfc4a265ccdc0771f5cd49e21d84d0af916e7dfeb6e32a083c2fe2d93d83c14bc1e657abfafe7204e7a2f337bb639b727eafc71c6525abe9626
-EBUILD gromacs-5.0.9999.ebuild 8423 BLAKE2B c3b636e32170f00ce77260e7d58bc2a36a6fcc1e2220045a51f151fff9cf3aac617a755fbfd647b262bf6cd44ef4201ac8716b942f71a868679eef6498e29229 SHA512 7cee51a8d1809f2c111acfda77525dd02b853735c0af31d5439c80943dddc2d8a50b5c00999c1808c2eb8daa6f158003048e6348d683b5c9d93fd3c383c73423
-EBUILD gromacs-5.1.3.ebuild 7746 BLAKE2B b97b9d8dd5f6111383e140b51df01136d443f11005d342df4ab35e4008fb6e02b90db7871acf30396ecb0e69ff9b4a1b2bb744a0d0c88e9ecc962a07dbb37b7d SHA512 6c1c868ae4c2c04313b16fa5db0786e65dafa4f6131423f1cbfb505b95165ea1e85fa9cdbfb2fb2d5ef63b04bc89fe27873293b67d123c34527a250bff6c0f3f
-EBUILD gromacs-5.1.9999.ebuild 7746 BLAKE2B b97b9d8dd5f6111383e140b51df01136d443f11005d342df4ab35e4008fb6e02b90db7871acf30396ecb0e69ff9b4a1b2bb744a0d0c88e9ecc962a07dbb37b7d SHA512 6c1c868ae4c2c04313b16fa5db0786e65dafa4f6131423f1cbfb505b95165ea1e85fa9cdbfb2fb2d5ef63b04bc89fe27873293b67d123c34527a250bff6c0f3f
+EBUILD gromacs-2019.ebuild 9112 BLAKE2B 0b972db0fe7e4c4730e9b480ea981b01a9930d128cef5fd589ad06b3f245d845721f74d0ac7b9e08dbed8f85985d3a0a84f361b02221318daf809ef37df9413f SHA512 363db0dfce3fa8459e6f8a07f6c5e5061d143deebc78fdb852557b101cee3fc342cc3c342a878153ced8edb8d8c567b9ab91bb275d3190034dcef6255003c9d7
 EBUILD gromacs-9999.ebuild 8092 BLAKE2B 42eef753c8cc34bfef79a710311a0eab2b445cfc2a88a552a729692a89d3c73348c9fbe210feaa299adc232be2f2b7548a262c3a16f43df31a0797e7007ac40a SHA512 d51775e52a42f01b95d829b6efc083de3a919778384fbf986b47c56459cd25a9b620fc8ae3a6237330989a763d8f0b7f9a7c4cc9878a725bb9a08d5c2fcaa234
-MISC metadata.xml 1264 BLAKE2B b6314076f02de8a49a6837f1c2ad298cc14c25107658cdad9b2eda09a1d9f06a9353d2a5844f0c5bc6d9ce68db5897c565a8c0d264ba7e64b6c3af8d32a55807 SHA512 d941d17586df7301802862db0f1134f65f6b6fadf0242b8f7353822f6b32c1e955bf7c94b2b6a977346725d4139f0d8d12f19ca3952fdb61c1dc562aad570458
+MISC metadata.xml 1123 BLAKE2B 5e945fdf580821b62aaf40c5b4b3252b366284f2df16f02e7c3cf913e5ad498a6a8548bc2e4275d8b80373f88d9879ab59d401e619595014262dcebfe8660f9f SHA512 bac0c94aee957487d8af8a1e06323cb286c8773cef2070d91aff9fdad63eb1bd55f2678dd58dca21b33d8d3e7110d2526e280abd538e3653aee638f6de72090d
diff --git a/sci-chemistry/gromacs/gromacs-2016.2.ebuild b/sci-chemistry/gromacs/gromacs-2016.2.ebuild
deleted file mode 100644
index 15acf0b2cf75..000000000000
--- a/sci-chemistry/gromacs/gromacs-2016.2.ebuild
+++ /dev/null
@@ -1,275 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
-
-if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
-		https://github.com/gromacs/gromacs.git
-		http://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
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
-	fftw? ( sci-libs/fftw:3.0 )
-	hwloc? ( <sys-apps/hwloc-2 )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )
-	"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	doc? (
-		app-doc/doxygen
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)
-	dev-libs/tinyxml2
-	"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	cuda? ( single-precision )
-	mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
-	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
-	use openmp && ! tc-has-openmp && \
-		die "Please switch to an openmp compatible compiler"
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="${EGIT_BRANCH}" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	xdg_environment_reset #591952
-
-	cmake-utils_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use cpu_flags_x86_sse2 && acce="SSE2"
-	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-	use cpu_flags_x86_avx && acce="AVX_256"
-	use cpu_flags_x86_avx2 && acce="AVX2_256"
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl && has_version "=sci-libs/mkl-10*"; then
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
-			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
-		)
-	elif use mkl && has_version "<sci-libs/mkl-11.3"; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/linux/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/linux/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		-DGMX_X11=$(usex X)
-		-DGMX_EXTERNAL_BLAS=$(usex blas)
-		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-		-DGMX_OPENMP=$(usex openmp)
-		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_USE_TNG=$(usex tng)
-		-DGMX_BUILD_MANUAL=$(usex doc)
-		-DGMX_HWLOC=$(usex hwloc)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_SIMD="$acce"
-		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DBUILD_TESTING=OFF
-		-DGMX_BUILD_UNITTESTS=OFF
-		-DGMX_EXTERNAL_TINYXML2=ON
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local cuda=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( -DGMX_GPU=ON )
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=OFF
-			-DGMX_THREAD_MPI=$(usex threads)
-			"${cuda[@]}"
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda}
-			-DGMX_OPENMM=OFF
-			-DGMX_BUILD_MDRUN_ONLY=ON
-			-DBUILD_SHARED_LIBS=OFF
-			-DGMX_BUILD_MANUAL=OFF
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		# not 100% necessary for rel ebuilds as available from website
-		if use doc; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile manual
-		fi
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		if use doc; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-		use mpi || continue
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_install
-	done
-
-	if use tng; then
-		insinto /usr/include/tng
-		doins src/external/tng_io/include/tng/*h
-	fi
-	# drop unneeded stuff
-	rm "${ED}"usr/bin/GMXRC* || die
-	for x in "${ED}"usr/bin/gmx-completion-*.bash ; do
-		local n=${x##*/gmx-completion-}
-		n="${n%.bash}"
-		cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
-		newbashcomp "${T}"/"${n}" "${n}"
-	done
-	rm "${ED}"usr/bin/gmx-completion*.bash || die
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite:"
-	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	einfo  "https://dx.doi.org/10.1021/ct700301q"
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-2019_rc1.ebuild b/sci-chemistry/gromacs/gromacs-2019.ebuild
index c090fc6b03ef..c090fc6b03ef 100644
--- a/sci-chemistry/gromacs/gromacs-2019_rc1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019.ebuild
diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
deleted file mode 100644
index 3fba885a4926..000000000000
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ /dev/null
@@ -1,261 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-TEST_PV="4.6.6"
-MANUAL_PV="4.6.6"
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs
-
-if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
-		https://github.com/gromacs/gromacs.git
-		http://repo.or.cz/r/gromacs.git"
-	EGIT_BRANCH="release-4-6"
-	inherit git-r3
-	LIVE_DEPEND="doc? (
-		app-doc/doxygen
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-		sys-apps/coreutils
-	)"
-else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
-		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf )
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )"
-	LIVE_DEPEND=""
-	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
-	fftw? ( sci-libs/fftw:3.0 )
-	gsl? ( sci-libs/gsl )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	${LIVE_DEPEND}
-	doc? ( app-doc/doxygen )"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	cuda? ( single-precision )
-	mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-HTML_DOCS=( "${ED}"/usr/share/gromacs/html/ )
-
-pkg_pretend() {
-	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
-	use openmp && ! tc-has-openmp && \
-		die "Please switch to an openmp compatible compiler"
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use doc; then
-			EGIT_REPO_URI="git://git.gromacs.org/manual.git" \
-			EGIT_BRANCH="release-4-6" EGIT_COMMIT="release-4-6" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/manual"\
-				git-r3_src_unpack
-		fi
-		if use test; then
-			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="release-4-6" EGIT_COMMIT="release-4-6" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	cmake-utils_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use cpu_flags_x86_sse2 && acce="SSE2"
-	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-	use cpu_flags_x86_avx && acce="AVX_256"
-
-	#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
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		-DGMX_X11=$(usex X)
-		-DGMX_EXTERNAL_BLAS=$(usex blas)
-		-DGMX_GSL=$(usex gsl)
-		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-		-DGMX_OPENMP=$(usex openmp)
-		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_ACCELERATION="$acce"
-		-DGMXLIB="$(get_libdir)"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DGMX_PREFIX_LIBMD=ON
-		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
-		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local cuda=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( -DGMX_GPU=ON )
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
-			-DGMX_THREAD_MPI=$(usex threads) "${cuda[@]}" -DGMX_OPENMM=OFF
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda} -DGMX_OPENMM=OFF
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile mdrun
-	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
-		#manual can only be build after gromacs was installed once in image
-		if use doc && [[ $PV = *9999*  && ! -d ${WORKDIR}/manual_build ]]; then
-			mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" )
-			BUILD_DIR="${WORKDIR}"/manual_build \
-				CMAKE_USE_DIR="${WORKDIR}/manual" cmake-utils_src_configure
-			[[ ${CHOST} = *-darwin* ]] && \
-				export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}${DYLD_LIBRARY_PATH:+:}${ED}/usr/$(get_libdir)"
-			BUILD_DIR="${WORKDIR}"/manual_build cmake-utils_src_make
-			[[ ${CHOST} = *-darwin* ]] && DYLD_LIBRARY_PATH="${ED}/usr/$(get_libdir)"
-			newdoc "${WORKDIR}"/manual_build/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-		use mpi || continue
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			DESTDIR="${D}" cmake-utils_src_make install-mdrun
-	done
-
-	use doc && [[ $PV != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf"
-	newbashcomp "${ED}"/usr/bin/completion.bash ${PN}
-	if use zsh-completion ; then
-		insinto /usr/share/zsh/site-functions
-		newins "${ED}"/usr/bin/completion.zsh _${PN}
-	fi
-	rm -f "${ED}"usr/bin/completion.*
-	rm -rf "${ED}"usr/share/gromacs/html
-	rm -f "${ED}"usr/bin/g_options*
-	rm -f "${ED}"usr/bin/GMXRC*
-
-	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"
-	if use offensive; then
-		einfo
-		einfo  $(g_luck)
-		einfo  "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc"
-	fi
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-5.0.4.ebuild b/sci-chemistry/gromacs/gromacs-5.0.4.ebuild
deleted file mode 100644
index ac00ea29ca72..000000000000
--- a/sci-chemistry/gromacs/gromacs-5.0.4.ebuild
+++ /dev/null
@@ -1,277 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo toolchain-funcs
-
-if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
-		https://github.com/gromacs/gromacs.git
-		http://repo.or.cz/r/gromacs.git"
-	EGIT_BRANCH="release-5-0"
-	inherit git-r3
-else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
-	KEYWORDS="~alpha amd64 arm ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	boost? ( >=dev-libs/boost-1.55 )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
-	fftw? ( sci-libs/fftw:3.0 )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )
-	"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	doc? (
-		app-doc/doxygen
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	cuda? ( single-precision )
-	mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
-	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
-	use openmp && ! tc-has-openmp && \
-		die "Please switch to an openmp compatible compiler"
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="master" EGIT_COMMIT="master" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	cmake-utils_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use cpu_flags_x86_sse2 && acce="SSE2"
-	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-	use cpu_flags_x86_avx && acce="AVX_256"
-	use cpu_flags_x86_avx2 && acce="AVX2_256"
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl && has_version "=sci-libs/mkl-10*"; then
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
-			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
-		)
-	elif use mkl; 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[@]}"
-		$(cmake-utils_use X GMX_X11)
-		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
-		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
-		$(cmake-utils_use openmp GMX_OPENMP)
-		$(cmake-utils_use offensive GMX_COOL_QUOTES)
-		$(cmake-utils_use boost GMX_EXTERNAL_BOOST)
-		$(cmake-utils_use tng GMX_USE_TNG)
-		$(cmake-utils_use doc GMX_BUILD_MANUAL)
-		$(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_SIMD="$acce"
-		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
-		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
-		-DBUILD_TESTING=OFF
-		-DGMX_BUILD_UNITTESTS=OFF
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local cuda=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( -DGMX_GPU=ON )
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=OFF
-			$(cmake-utils_use threads GMX_THREAD_MPI)
-			"${cuda[@]}"
-			-DGMX_OPENMM=OFF
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda}
-			-DGMX_OPENMM=OFF
-			-DGMX_BUILD_MDRUN_ONLY=ON
-			-DBUILD_SHARED_LIBS=OFF
-			-DGMX_BUILD_MANUAL=OFF
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		# generate bash completion, not 100% necessary for
-		# rel ebuilds as bundled
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile completion
-		# not 100% necessary for rel ebuilds as available from website
-		if use doc; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile manual
-		fi
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		if use doc; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-		#release ebuild does this automatically
-		if [[ $PV = *9999* ]]; then
-			cp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash "${ED}/usr/bin" || die
-			echo "complete -o nospace -F _gmx_compl gmx" > "${ED}/usr/bin/gmx-completion-gmx.bash" || die
-		fi
-		use mpi || continue
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_install
-	done
-	# drop unneeded stuff
-	rm "${ED}"usr/bin/GMXRC* || die
-	#concatenate all gmx-completion*, starting with gmx-completion.bash (fct defs)
-	#little hacckery as some gmx-completion* newlines ,so cat won't work
-	for x in "${ED}"usr/bin/gmx-completion{,?*}.bash ; do
-		echo $(<${x})
-	done > "${T}"/gmx-bashcomp || die
-	newbashcomp "${T}"/gmx-bashcomp gmx
-	bashcomp_alias gmx mdrun
-	rm "${ED}"usr/bin/gmx-completion{,?*}.bash || die
-	if use double-precision && use single-precision; then
-		bashcomp_alias gmx gmx_d
-		bashcomp_alias gmx mdrun_d
-	fi
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite:"
-	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	einfo  "https://dx.doi.org/10.1021/ct700301q"
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
deleted file mode 100644
index bb4000f2520d..000000000000
--- a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild
+++ /dev/null
@@ -1,282 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs
-
-if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
-		https://github.com/gromacs/gromacs.git
-		http://repo.or.cz/r/gromacs.git"
-	EGIT_BRANCH="release-5-0"
-	inherit git-r3
-else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
-	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	boost? ( >=dev-libs/boost-1.55 )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
-	fftw? ( sci-libs/fftw:3.0 )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )
-	"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	doc? (
-		app-doc/doxygen
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	cuda? ( single-precision )
-	mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
-	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
-	use openmp && ! tc-has-openmp && \
-		die "Please switch to an openmp compatible compiler"
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="master" EGIT_COMMIT="master" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	cmake-utils_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use cpu_flags_x86_sse2 && acce="SSE2"
-	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-	use cpu_flags_x86_avx && acce="AVX_256"
-	use cpu_flags_x86_avx2 && acce="AVX2_256"
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl && has_version "=sci-libs/mkl-10*"; then
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
-			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
-		)
-	elif use mkl; 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+=(
-		"${fft_opts[@]}"
-		-DGMX_X11=$(usex X)
-		-DGMX_EXTERNAL_BLAS=$(usex blas)
-		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-		-DGMX_OPENMP=$(usex openmp)
-		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_EXTERNAL_BOOST=$(usex boost)
-		-DGMX_USE_TNG=$(usex tng)
-		-DGMX_BUILD_MANUAL=$(usex doc)
-		-DGMX_SYMLINK_OLD_BINARY_NAMES=$(usex make-symlinks)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_SIMD="$acce"
-		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
-		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
-		-DBUILD_TESTING=OFF
-		-DGMX_BUILD_UNITTESTS=OFF
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local cuda=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( -DGMX_GPU=ON )
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=OFF
-			-DGMX_THREAD_MPI=$(usex threads)
-			"${cuda[@]}"
-			-DGMX_OPENMM=OFF
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda}
-			-DGMX_OPENMM=OFF
-			-DGMX_BUILD_MDRUN_ONLY=ON
-			-DBUILD_SHARED_LIBS=OFF
-			-DGMX_BUILD_MANUAL=OFF
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		# generate bash completion, not 100% necessary for
-		# rel ebuilds as bundled
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile completion
-		# not 100% necessary for rel ebuilds as available from website
-		if use doc; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile manual
-		fi
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		if use doc; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-		#release ebuild does this automatically
-		if [[ $PV = *9999* ]]; then
-			cp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash "${ED}/usr/bin" || die
-			echo "complete -o nospace -F _gmx_compl gmx" > "${ED}/usr/bin/gmx-completion-gmx.bash" || die
-		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
-	#concatenate all gmx-completion*, starting with gmx-completion.bash (fct defs)
-	#little hacckery as some gmx-completion* newlines ,so cat won't work
-	for x in "${ED}"usr/bin/gmx-completion{,?*}.bash ; do
-		echo $(<${x})
-	done > "${T}"/gmx-bashcomp || die
-	newbashcomp "${T}"/gmx-bashcomp gmx
-	bashcomp_alias gmx mdrun
-	rm "${ED}"usr/bin/gmx-completion{,?*}.bash || die
-	if use double-precision && use single-precision; then
-		bashcomp_alias gmx gmx_d
-		bashcomp_alias gmx mdrun_d
-	fi
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite:"
-	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	einfo  "https://dx.doi.org/10.1021/ct700301q"
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-5.1.3.ebuild b/sci-chemistry/gromacs/gromacs-5.1.3.ebuild
deleted file mode 100644
index 0b84b86b413a..000000000000
--- a/sci-chemistry/gromacs/gromacs-5.1.3.ebuild
+++ /dev/null
@@ -1,267 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs
-
-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
-		http://repo.or.cz/r/gromacs.git"
-	[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}"
-	inherit git-r3
-else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
-	KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	boost? ( >=dev-libs/boost-1.55 )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
-	fftw? ( sci-libs/fftw:3.0 )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )
-	"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	doc? (
-		app-doc/doxygen
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	cuda? ( single-precision )
-	mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
-	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
-	use openmp && ! tc-has-openmp && \
-		die "Please switch to an openmp compatible compiler"
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="${EGIT_BRANCH}" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	cmake-utils_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use cpu_flags_x86_sse2 && acce="SSE2"
-	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-	use cpu_flags_x86_avx && acce="AVX_256"
-	use cpu_flags_x86_avx2 && acce="AVX2_256"
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl && has_version "=sci-libs/mkl-10*"; then
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
-			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
-		)
-	elif use mkl; 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+=(
-		"${fft_opts[@]}"
-		-DGMX_X11=$(usex X)
-		-DGMX_EXTERNAL_BLAS=$(usex blas)
-		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-		-DGMX_OPENMP=$(usex openmp)
-		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_EXTERNAL_BOOST=$(usex boost)
-		-DGMX_USE_TNG=$(usex tng)
-		-DGMX_BUILD_MANUAL=$(usex doc)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_SIMD="$acce"
-		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
-		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
-		-DBUILD_TESTING=$(usex test)
-		-DGMX_BUILD_UNITTESTS=$(usex test)
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local cuda=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( -DGMX_GPU=ON )
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=OFF
-			-DGMX_THREAD_MPI=$(usex threads)
-			"${cuda[@]}"
-			-DGMX_OPENMM=OFF
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda}
-			-DGMX_OPENMM=OFF
-			-DGMX_BUILD_MDRUN_ONLY=ON
-			-DBUILD_SHARED_LIBS=OFF
-			-DGMX_BUILD_MANUAL=OFF
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		# not 100% necessary for rel ebuilds as available from website
-		if use doc; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile manual
-		fi
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		if use doc; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-		use mpi || continue
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_install
-	done
-
-	if use tng; then
-		insinto /usr/include/tng
-		doins src/external/tng_io/include/tng/*h
-	fi
-	# drop unneeded stuff
-	rm "${ED}"usr/bin/GMXRC* || die
-	for x in "${ED}"usr/bin/gmx-completion-*.bash ; do
-		local n=${x##*/gmx-completion-}
-		n="${n%.bash}"
-		cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
-		newbashcomp "${T}"/"${n}" "${n}"
-	done
-	rm "${ED}"usr/bin/gmx-completion*.bash || die
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite:"
-	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	einfo  "https://dx.doi.org/10.1021/ct700301q"
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild
deleted file mode 100644
index 0b84b86b413a..000000000000
--- a/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild
+++ /dev/null
@@ -1,267 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs
-
-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
-		http://repo.or.cz/r/gromacs.git"
-	[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}"
-	inherit git-r3
-else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
-	KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	boost? ( >=dev-libs/boost-1.55 )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
-	fftw? ( sci-libs/fftw:3.0 )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )
-	"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	doc? (
-		app-doc/doxygen
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	cuda? ( single-precision )
-	mkl? ( !blas !fftw !lapack )"
-
-DOCS=( AUTHORS README )
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
-	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
-	use openmp && ! tc-has-openmp && \
-		die "Please switch to an openmp compatible compiler"
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="${EGIT_BRANCH}" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	cmake-utils_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use cpu_flags_x86_sse2 && acce="SSE2"
-	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-	use cpu_flags_x86_avx && acce="AVX_256"
-	use cpu_flags_x86_avx2 && acce="AVX2_256"
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl && has_version "=sci-libs/mkl-10*"; then
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
-			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
-		)
-	elif use mkl; 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+=(
-		"${fft_opts[@]}"
-		-DGMX_X11=$(usex X)
-		-DGMX_EXTERNAL_BLAS=$(usex blas)
-		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-		-DGMX_OPENMP=$(usex openmp)
-		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_EXTERNAL_BOOST=$(usex boost)
-		-DGMX_USE_TNG=$(usex tng)
-		-DGMX_BUILD_MANUAL=$(usex doc)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_SIMD="$acce"
-		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
-		-DGMX_USE_GCC44_BUG_WORKAROUND=OFF
-		-DBUILD_TESTING=$(usex test)
-		-DGMX_BUILD_UNITTESTS=$(usex test)
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local cuda=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( -DGMX_GPU=ON )
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=OFF
-			-DGMX_THREAD_MPI=$(usex threads)
-			"${cuda[@]}"
-			-DGMX_OPENMM=OFF
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda}
-			-DGMX_OPENMM=OFF
-			-DGMX_BUILD_MDRUN_ONLY=ON
-			-DBUILD_SHARED_LIBS=OFF
-			-DGMX_BUILD_MANUAL=OFF
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		# not 100% necessary for rel ebuilds as available from website
-		if use doc; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile manual
-		fi
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		if use doc; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-		use mpi || continue
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_install
-	done
-
-	if use tng; then
-		insinto /usr/include/tng
-		doins src/external/tng_io/include/tng/*h
-	fi
-	# drop unneeded stuff
-	rm "${ED}"usr/bin/GMXRC* || die
-	for x in "${ED}"usr/bin/gmx-completion-*.bash ; do
-		local n=${x##*/gmx-completion-}
-		n="${n%.bash}"
-		cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
-		newbashcomp "${T}"/"${n}" "${n}"
-	done
-	rm "${ED}"usr/bin/gmx-completion*.bash || die
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite:"
-	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	einfo  "https://dx.doi.org/10.1021/ct700301q"
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index fca9b4acc974..7c756657ae42 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -11,17 +11,15 @@
 	</maintainer>
 	<use>
 		<flag name="cuda">Enable cuda non-bonded kernels</flag>
-		<flag name="opencl">Enable opencl non-bonded kernels</flag>
 		<flag name="double-precision">More precise calculations at the expense of speed</flag>
-		<flag name="single-precision">Single precision version of gromacs (default)</flag>
-		<flag name="boost">Enable external boost library</flag>
+		<flag name="gmxapi">Add support for gmxapi library</flag>
 		<flag name="hwloc">Enable HWLoc lib support</flag>
-		<flag name="tng">Enable new trajectory format - tng</flag>
-		<flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag>
 		<flag name="lmfit">Use external <pkg>sci-libs/lmfit</pkg></flag>
-		<flag name="gmxapi">Add support for gmxapi library</flag>
+		<flag name="opencl">Enable opencl non-bonded kernels</flag>
+		<flag name="single-precision">Single precision version of gromacs (default)</flag>
+		<flag name="tng">Enable new trajectory format - tng</flag>
 		<!-- acceleration optimization flags -->
-		<flag name="offensive">Enable gromacs partly offensive quotes</flag>
 		<flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag>
+		<flag name="offensive">Enable gromacs partly offensive quotes</flag>
 	</use>
 </pkgmetadata>
author	V3n3RiX <venerix@redcorelinux.org>	2019-01-12 16:58:08 +0000
committer	V3n3RiX <venerix@redcorelinux.org>	2019-01-12 16:58:08 +0000
commit	c8a77dfe4d3d307c1d5dd2650b7297447d8b609d (patch)
tree	9ea78393bc3ecd6ab4de449383d4e97e5f3648ae /sci-chemistry
parent	2891d29af8907ce881662f4a02844926d7a293c7 (diff)