gentoo resync : 27.10.2018

18 files changed, 105 insertions, 90 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index dd8fa32bf085..28cbe7717ba5 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index cc18d9debf2f..51c9344b4905 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,28 +1,26 @@
 DIST gromacs-2016.2.tar.gz 27339623 BLAKE2B c3548f4abdc4c1b09a79a3da99d7ca8060daca7307e4c5b81bd97d54adfb9621fbccf1ea7fd96c3676d6b44c20f9f4cd2168ce131799792512fad3b8b1ac0522 SHA512 f5e74bb8c126823c90d205ac0f0835e61fdd13a4550bc15aa9c972ee9b187f6451cdc90877c17276d2f889d61abb5eaa5ea1b54f7cbf3da67074146c749c1aa6
 DIST gromacs-2016.5.tar.gz 27369491 BLAKE2B 4a8bf1ae3e298ac2e26ec476130720dc3ef00db5d999e3a45fdbfd7fbfe7e94fbc86be6ff0f2f23552769c8bc851ce49c73f6fc1ab13f372523279b93e7794d7 SHA512 9cb8ff88871aa5df0967c60ba303c03296c6fa3c215cd01b26259df7753f0014f04222078ab4b84a66a1f709997837134d5c0f74da19b78322e410010c9d9e10
-DIST gromacs-2018.1.tar.gz 29895119 BLAKE2B 45cc674bd78dc7dc56388a899ae50da9f10eb4dc80dad461f7e298894ee845eae744010013e682f3be4b03c1f04624111266e84cd9721415b23f87d544846827 SHA512 d29f152e9f115c7de07881c6af4cc05481e0a5520bd33142a09507e8c4df9f8b6c9d6d96efcb7adaaf4e0127b76ab247421d43918bd7e7779d6e71f5984db715
-DIST gromacs-2018.2.tar.gz 29899294 BLAKE2B a4d7111fdfb2c6919ef7a94aded634c5e14c4ca6ee6411c6c84289a9c88c39d731e89d3b01f14b2370d7de7782964e8db378aa6baabdd85cf46b689504f0738a SHA512 d444b503e24a9875b0ab7622772946ef73ab2c897da6ff45ac908f147ea398ba2404b064a8784996fd34b25e188e36f12a492e0070427e0929f422d934205d28
 DIST gromacs-2018.3.tar.gz 29915626 BLAKE2B 6e6eeafecdd923a25b4a2a78a8e89f793639b57ffbd63f19d133d8474302f9a381041f138a509dadb42b36e25fe508729e860efb6b0c75cdbf01d924b0a8fd83 SHA512 3c4d6eb3942d7b54d01c94c6f6f5ae706e0f5d4f9901ea11a56fde4df97b1a9112007f2cb13feea0f19f30c89f57ae80ff53a8f5203b8cdff103aa903cd0dc8f
+DIST gromacs-2019-beta1.tar.gz 33549950 BLAKE2B 667246f9a7cb136efca3fbda21aabe5ab0a759aa42896f8a9ddc86fafbfb1906e31fe46688c98477a5841e8fe5708b960c2a26abe754b8d793046734cd509377 SHA512 9f8bec3671f6f7421dc45cab1b5edb8ba8f2ebc34cd19ebd3d5d534be1f84135a112f49733a3f8c79e93ffc2b09c5053ae0dea31e95832a2b98acaee47f7d1af
 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 regressiontests-2016.5.tar.gz 67641413 BLAKE2B 4fcd30c198f3acbbabf1104c040d9a686de49536a97dbeb14732bfa0ed3cf37aa61b1b0f45393668985b993d1f1862a8985e416af819cf9793f5964f3e4f43cc SHA512 31764fd99cc4185d61de5d4443ee482c27b13533451a24aa0e4899997ce275a63685424eafacae38b1a3ffd4ce0d5ebe02a90348953b04c104f91376f0edfdff
-DIST regressiontests-2018.1.tar.gz 67859956 BLAKE2B f561eb9373b4e0e5faae2aa91e3cb3911c096c1fce96755fc7a8a7b3a25b53bda88ef90d04d3a6fce414bf9dba44d0933827f080949306d5c98f60e5a1797412 SHA512 81c9a62fca859923c1e27214b32b0cff1dd48224dd4ad9301554036b842ccc400a2729752ba71b284e0c5b6c1769ce7de5fe2c9ba4fc7cf0917fd4ced9883112
-DIST regressiontests-2018.2.tar.gz 67855795 BLAKE2B 32504a7d9315f404b4a57fd45dd59540166b0e73d51ad5938b6a18cafc491cda5c00fe204dedba9c51a3f859759fb1d8c894c0607d71d49701269cf909617584 SHA512 6cc4bd4716f8b7aba69b840facd160f1abb32def2349cc441b89e12bf8df21dc4a4ca23acc4e47bf7ec3ae55b8e3f9a28beab044833b9d8ddfcf5e21d2878a5a
 DIST regressiontests-2018.3.tar.gz 67857855 BLAKE2B acd7a05ae79d1b4eb47d0c68a3fec9ee19f028a5019f39c37a033f48cf6da2a468375180ad6ceca9ac4f685a8bead38550663a47d6427b51f84c32a5c810e5f0 SHA512 57980d49efe6dcc3b3d14b5913a30c68fc1de5b679ef986fec1a149c76f67139b0299c3ee2825451461294fab5f345c7ad4f42e90f8991b81aafe9c369f3ff0b
+DIST regressiontests-2019-beta1.tar.gz 67604794 BLAKE2B 163046e54206d3406d39e6bd9552dcce5a9a05a73e14249bf371d2432d902a3e336c0caa3e0c83353ac4566d91f4f805724f8eb996a831f8d3b712f65b1d1c42 SHA512 eef7eaacf56ba9358bfb0a3e34da4bc00d2a65564da81d144f57ee8a732081882b8e1c96f7006b966455105b834271715273e7590d3d4310209ee0324e7fa585
 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 90510b56d31e59f2f7f76e7772b55e4acdb825af6e8df46da40c7aeb6b7d4b986253b10ac71fbd04c749dd3935b1eeb154e7d0aac7b21147859fb03b57e4e687 SHA512 7a85084cc29da0d3da6c9aabf65320edb38cd682146cc1b739120b728c6704c3e20941b9022c846b84a111e3ca88f29ca21cdbcdf4c5b7204989ac194bf15725
-EBUILD gromacs-2016.5.ebuild 7987 BLAKE2B 02bfdcce78718a1e16ad0cdf63e521d656eaa886ddf2ef7016f22abc398b95e240ecb4705a894609f188afbf4ec17c96ee9441ee7510cfaeb02c0ceced4e1b17 SHA512 5d762c0f9212ec0b91fba7565c15787201b1fcd923111b7055d6362b813d92b850f67becff023c57d3846c2f01a7df29e2b5e52d1bd643f797305c59449b1f46
-EBUILD gromacs-2016.9999.ebuild 7987 BLAKE2B 45d8b50b3ee54c8c701eb8c6533c1dc7d680eb0f5c40cdf1a75e81b59bd2d603b4235f6e4942e40211b748b7cf8239c90f8d613b20bdc44fca48d23f9c45ae14 SHA512 ce2b0d2730e87831a517468033cada7097ba431d8a60dcef77a04c9e05bf4cfacb6eb500a5196e378f4c69e5020f8e9f871eac6e61dd2776834aee006ecb167f
-EBUILD gromacs-2018.1.ebuild 7899 BLAKE2B f70665f54e2103275dbf7466d15c15ce41593264bb768b542a49eebd76b1764871ac9b82e9eacee5db1a413cac8863a6e87d751cdb2196ff5a431a096c7f6f3f SHA512 3cb7bab30e822420e308b15af997f01ab3ce3072ddefc752d5f0d314040f699febcd804d983cf9af160d1388b38a62e81c9ee6fc7a6647a5d7e199262b3afec9
-EBUILD gromacs-2018.2.ebuild 7859 BLAKE2B 43d1ce476e49201e337c214fa6fcd5fdd83d0f8f209057ee00edffbcbdbfd7cc08177f029702dc26eb111c725b3347e72623a1008857911b1866142395e0d066 SHA512 f080df3b8befb1b6de337f297b561dd76069d15e4053149d1e6e3d98938349ce6e6acab8a73286dd239798be79d0ee9f081b9631aeac5e671de582e68099f574
-EBUILD gromacs-2018.3.ebuild 7859 BLAKE2B 43d1ce476e49201e337c214fa6fcd5fdd83d0f8f209057ee00edffbcbdbfd7cc08177f029702dc26eb111c725b3347e72623a1008857911b1866142395e0d066 SHA512 f080df3b8befb1b6de337f297b561dd76069d15e4053149d1e6e3d98938349ce6e6acab8a73286dd239798be79d0ee9f081b9631aeac5e671de582e68099f574
-EBUILD gromacs-2018.9999.ebuild 7859 BLAKE2B 43d1ce476e49201e337c214fa6fcd5fdd83d0f8f209057ee00edffbcbdbfd7cc08177f029702dc26eb111c725b3347e72623a1008857911b1866142395e0d066 SHA512 f080df3b8befb1b6de337f297b561dd76069d15e4053149d1e6e3d98938349ce6e6acab8a73286dd239798be79d0ee9f081b9631aeac5e671de582e68099f574
+EBUILD gromacs-2016.2.ebuild 7971 BLAKE2B 889ded117d36d17c224bdf65ddc8a2e5fcbdb5cdbf58b5774e308fc45e42a7b3734aae1f87d1d95fb3751c18342025a86317e2bf05a82ffa7f9dfaeb47533e5b SHA512 a2ad66f58d79b03e0832ae0daf9b6cbcdceae2873d25318ee7fb9235a41acc1403708206682848c35d2c347ad2ccb72f75c38df38e8899ba07033040b296eb81
+EBUILD gromacs-2016.5.ebuild 7989 BLAKE2B 1f4673c38c33675dc1e12e84a50d50ca34e04bd0562017a2fcd4b8865313f4de6d3a718ef2809080aef1609d17368cfab8470d743780b8a73b9c77d65337f2f6 SHA512 c2fe28bc3e8483a796ed4ea6cdd31d5fac6f754f2bee9be7014ef0c378f24c9a42bde36f5c4ba0a0715d0312819b49c6998005af127dc3905731a8c9552eee99
+EBUILD gromacs-2016.9999.ebuild 7987 BLAKE2B c048a6f661441fb98bc12cafbbb7194924dda12325195c565045679fb8e3b9a3aa32ec9c3823f307256a0c0679d7dc73dbf0af27e8a34b3d69c94538ee125ded SHA512 6473d8b666f5b99193c3ed4ab49b81b3a3f3e5a34597c382c8f95d32f22447e6c40a481f43a7970c55ffb74ceaa8e27353d0219fec1b7891f0c1c6a828196f8d
+EBUILD gromacs-2018.3.ebuild 7840 BLAKE2B 8d78d3b3dbb870f1b21e67143b272734a487d6448a07f619726e97676a774bcbf871c3bf93dda302346359c812adad296743d887152406582776ece827c566e2 SHA512 ea7b38264bb665d3c08268cafd23004a474ddd58a509c7e8be578b157a3ef38cf0790f640e86d0404077f8f8a2304d9c42286d927651ea87cbd990468329ffb4
+EBUILD gromacs-2018.9999.ebuild 7838 BLAKE2B ea4fd716f9de3228df842d3c642ce2cba3b0f2a56c979c328d9a0a6720943b723873b5fa76ac057e869e5cd3273d52a26cb0985319bf6e05301619c92162c3c5 SHA512 4637f96407363bf3eb048de5fc075e7a3df3865641f37e62ed85a7dc5f368c230324f68634729f2ef063a265ca4ae2834853537bb10a616978dc3489b05ed1d1
+EBUILD gromacs-2019.9999.ebuild 8241 BLAKE2B 6892211d932a008b0dadad4ae8d696c882d8ec1f1b76b448e35d727b1f64996e461e4b6e76e4164182fadc707c98167679aa39b282ed0c685f11838a3262929d SHA512 952f5926bd01f66b7f1eae9c16b3bbf5e20896b928c85806b3d39de400418b1b221397ed9107d5a5d958ab15211f6bcd7bc06f1fd963a1495f64aef940440ce5
+EBUILD gromacs-2019_beta1.ebuild 8112 BLAKE2B 56a88efcf6b1b97fe0ba90d8765a83060aa2327e110d1d6be65744e044a7687484e9ae0d21e88711d532df85cec92b8df7cd07f23e6a96c727bd1137304cd093 SHA512 b021200072381da492d37257845e30851e224515438b174361abf15053025c3db600b4719f9dccbc652d276ad7686294bc28d6bba7bf5ef06ef71abcf1ddf01a
 EBUILD gromacs-4.6.9999.ebuild 8110 BLAKE2B dd8ac9cbc4abfcc75a3a188c59cdbe5111f363404ff5a787f64b05d4bd411deebb50f172f09963800ed87997788b2e678617805e65a523bed19aa6ef18fe2b96 SHA512 2206e257f0b29b6f3a90c5d7739079b9add3e04f2a3acbd58c814811b389b5d51b3594815a94529d1de43deb380504029c302d18fc16d63a81c92727254e863e
 EBUILD gromacs-5.0.4.ebuild 8429 BLAKE2B c06c423365fa79befd5a4f0b6314e77b96d983c84df776ce84fddc79d35ce735d856d1184e5913af0c8cd3a0c4e9087110af9bd4402e2bce1f014e64a8a585a7 SHA512 d1e91cc25c5f90bd0fbad15060cae9c8bf1235ca45a2b72521b3a4f5f091bdd7d32ec2e6ff2bb22cd3fe165092f11a24ea148ae8000b8517f0b8671f6c2af6f2
 EBUILD gromacs-5.0.9999.ebuild 8439 BLAKE2B 33d51254e62593a58c636bd902f43edc553ad11af306d1d022278b223eda15b0772097f26565df74a1118bd5b144e5b93aac09cdb995123ccbae2856889c31b2 SHA512 6756116cdeae9c21b094f74ea1b1d9f41617467dc736878cdcff27fed9f53b338830a608e23e87238d0756884799fbc5d62f02685774ea86c239ecc3e8804814
-EBUILD gromacs-5.1.3.ebuild 7783 BLAKE2B d8154b902324d1f47d4b0d4d316bb0e1154379e3c9e3732e195f269386fe9666ba546ab624df95b201c1dbf63c0d7c24cab0e5be92ac70180c53a362e37e71c9 SHA512 8cf9573ec5dfa09e283b1d50513863214ca216007ad76cce15bc54caa2f1e55de8c992db8bd4b2e4fa95bc3f5d50eef32fce78ca61bc09cae2fe37e35a4cee68
-EBUILD gromacs-5.1.9999.ebuild 7783 BLAKE2B d8154b902324d1f47d4b0d4d316bb0e1154379e3c9e3732e195f269386fe9666ba546ab624df95b201c1dbf63c0d7c24cab0e5be92ac70180c53a362e37e71c9 SHA512 8cf9573ec5dfa09e283b1d50513863214ca216007ad76cce15bc54caa2f1e55de8c992db8bd4b2e4fa95bc3f5d50eef32fce78ca61bc09cae2fe37e35a4cee68
-EBUILD gromacs-9999.ebuild 7710 BLAKE2B efd556f55dc198d8526df775fed3c2aa55fa88794ea9618a222d67886ee46371c19c7ac0b58d37c11b5e0605e08caaeb42de9883db2bdab86c8baacbc372b639 SHA512 a3cb96cf8ada5f278b4b932fafac93659ca2c65ab530337567bf87be53ddea7123e2e03c0c3fefd2faca8bc3ce9494ebf960f1fdf9cff000b548790b5e0c9d81
-MISC metadata.xml 1251 BLAKE2B 324e432ebfca2fea64aa5ec331c51263422f22ef6f326f7034fd0d3e97ff0a408b8bf06e09d488fea89176b2996ec9a7f02597ef5dd65ee718c16c38298d0acb SHA512 b84b070eb8d6e264e036945c9903020cb1b9b8407c9c136ccbac0387f659c2943eb1c3f5c74c2627873bab7eb68d637152da759830f18a996aaa09e63d546e37
+EBUILD gromacs-5.1.3.ebuild 7759 BLAKE2B 77239a47dc1d1a93c4f8a679e0ab3571729b7f69f66eb3a97d1c812ec56289c7b35b14e23e39f47fd2bcdd140eea28bba58353002923b737c9707fddeebfc3ea SHA512 681c76b9224c6a21a443362dbe13fe38a96b0af7349e221b34bab303c8af4401c760fbc8047ad49c932d230ffcebc69d73f90a817efa7585ccadabd6fb62193f
+EBUILD gromacs-5.1.9999.ebuild 7759 BLAKE2B 77239a47dc1d1a93c4f8a679e0ab3571729b7f69f66eb3a97d1c812ec56289c7b35b14e23e39f47fd2bcdd140eea28bba58353002923b737c9707fddeebfc3ea SHA512 681c76b9224c6a21a443362dbe13fe38a96b0af7349e221b34bab303c8af4401c760fbc8047ad49c932d230ffcebc69d73f90a817efa7585ccadabd6fb62193f
+EBUILD gromacs-9999.ebuild 8105 BLAKE2B a7946a54f0fb54aee44f97f0bf3e6f14cbf842823d7d0dfa6759eb6146deaa3c82771192cb34584340da0bbadf9aa03f7a0b90c217038fdd5cb9e57cf24d619f SHA512 fd8e54b639d355d60269ba4f1a913f38798e33e76359cd75632863725f550d603bf84a444394ab70cf5a65a30f7ee8c394c3f4d13e673883fd23b0831c0d732b
+MISC metadata.xml 1378 BLAKE2B 74d5e63ad45455ea441cd4546c2063587be8cff2977f8c0b9e1f92b3ba02481589ca314cf5cba43f61806638e5be336dbc679cc00d5ef96afd6edd0083120791 SHA512 dfbfa2b9199074310d0a959998cdd30def0a32213763aa6e0756b33dbd8d3946981eb8167b68a8669ba9f3799f9c685a786d423014e6b9fcd959a133f8a1b151
diff --git a/sci-chemistry/gromacs/gromacs-2016.2.ebuild b/sci-chemistry/gromacs/gromacs-2016.2.ebuild
index 3b371d273088..15acf0b2cf75 100644
--- a/sci-chemistry/gromacs/gromacs-2016.2.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2016.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -41,7 +41,7 @@ CDEPEND="
 	blas? ( virtual/blas )
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
 	fftw? ( sci-libs/fftw:3.0 )
-	hwloc? ( sys-apps/hwloc )
+	hwloc? ( <sys-apps/hwloc-2 )
 	lapack? ( virtual/lapack )
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
diff --git a/sci-chemistry/gromacs/gromacs-2016.5.ebuild b/sci-chemistry/gromacs/gromacs-2016.5.ebuild
index e86fdf946c7c..65d0315dc5ce 100644
--- a/sci-chemistry/gromacs/gromacs-2016.5.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2016.5.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -14,11 +14,11 @@ if [[ $PV = *9999* ]]; then
 		http://repo.or.cz/r/gromacs.git"
 	[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
 	inherit git-r3
-	KEYWORDS=""
+	KEYWORDS="x86"
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
 		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
-	KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+	KEYWORDS="~amd64 ~arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 fi
 
 ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
@@ -42,7 +42,7 @@ CDEPEND="
 	blas? ( virtual/blas )
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
 	fftw? ( sci-libs/fftw:3.0 )
-	hwloc? ( sys-apps/hwloc )
+	hwloc? ( <sys-apps/hwloc-2 )
 	lapack? ( virtual/lapack )
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
diff --git a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild b/sci-chemistry/gromacs/gromacs-2016.9999.ebuild
index 7e426ddfdf5a..69ec80d2cbef 100644
--- a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2016.9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -42,7 +42,7 @@ CDEPEND="
 	blas? ( virtual/blas )
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
 	fftw? ( sci-libs/fftw:3.0 )
-	hwloc? ( sys-apps/hwloc )
+	hwloc? ( <sys-apps/hwloc-2 )
 	lapack? ( virtual/lapack )
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
diff --git a/sci-chemistry/gromacs/gromacs-2018.3.ebuild b/sci-chemistry/gromacs/gromacs-2018.3.ebuild
index d4ea677a994c..4437231ca268 100644
--- a/sci-chemistry/gromacs/gromacs-2018.3.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2018.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -14,11 +14,11 @@ if [[ $PV = *9999* ]]; then
 		http://repo.or.cz/r/gromacs.git"
 	[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
 	inherit git-r3
-	KEYWORDS=""
+	KEYWORDS="x86"
 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"
+	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"
@@ -43,7 +43,7 @@ CDEPEND="
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
 	opencl? ( virtual/opencl )
 	fftw? ( sci-libs/fftw:3.0 )
-	hwloc? ( sys-apps/hwloc )
+	hwloc? ( <sys-apps/hwloc-2 )
 	lapack? ( virtual/lapack )
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
diff --git a/sci-chemistry/gromacs/gromacs-2018.9999.ebuild b/sci-chemistry/gromacs/gromacs-2018.9999.ebuild
index d4ea677a994c..73c49fd596da 100644
--- a/sci-chemistry/gromacs/gromacs-2018.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2018.9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -18,7 +18,7 @@ if [[ $PV = *9999* ]]; then
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
 		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
-	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+	KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 fi
 
 ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
@@ -43,7 +43,7 @@ CDEPEND="
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
 	opencl? ( virtual/opencl )
 	fftw? ( sci-libs/fftw:3.0 )
-	hwloc? ( sys-apps/hwloc )
+	hwloc? ( <sys-apps/hwloc-2 )
 	lapack? ( virtual/lapack )
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
diff --git a/sci-chemistry/gromacs/gromacs-2018.2.ebuild b/sci-chemistry/gromacs/gromacs-2019.9999.ebuild
index d4ea677a994c..2fde5b4b55b7 100644
--- a/sci-chemistry/gromacs/gromacs-2018.2.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019.9999.ebuild
@@ -1,11 +1,13 @@
-# Copyright 1999-2018 Gentoo Foundation
+# 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
+PYTHON_COMPAT=( python2_7 )
+
+inherit bash-completion-r1 cmake-utils cuda eutils multilib python-any-r1 readme.gentoo-r1 toolchain-funcs xdg-utils
 
 if [[ $PV = *9999* ]]; then
 	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
@@ -18,7 +20,7 @@ if [[ $PV = *9999* ]]; then
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
 		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
-	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+	KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 fi
 
 ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
@@ -31,7 +33,7 @@ HOMEPAGE="http://www.gromacs.org/"
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -40,11 +42,12 @@ CDEPEND="
 		x11-libs/libICE
 		)
 	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 )
 	opencl? ( virtual/opencl )
 	fftw? ( sci-libs/fftw:3.0 )
 	hwloc? ( sys-apps/hwloc )
 	lapack? ( virtual/lapack )
+	lmfit? ( sci-libs/lmfit )
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
 	"
@@ -52,6 +55,9 @@ DEPEND="${CDEPEND}
 	virtual/pkgconfig
 	doc? (
 		app-doc/doxygen
+		${PYTHON_DEPS}
+		$(python_gen_any_dep 'dev-python/sphinx[${PYTHON_USEDEP}]')
+		media-gfx/mscgen
 		dev-texlive/texlive-latex
 		dev-texlive/texlive-latexextra
 		media-gfx/imagemagick
@@ -146,8 +152,15 @@ src_configure() {
 		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=$(usex lapack)
@@ -155,6 +168,7 @@ src_configure() {
 		-DGMX_COOL_QUOTES=$(usex offensive)
 		-DGMX_USE_TNG=$(usex tng)
 		-DGMX_BUILD_MANUAL=$(usex doc)
+		-DPYTHON_EXECUTABLE="${PYTHON}"
 		-DGMX_HWLOC=$(usex hwloc)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_SIMD="$acce"
@@ -181,6 +195,7 @@ src_configure() {
 			${mycmakeargs_pre[@]} ${p}
 			-DGMX_MPI=OFF
 			-DGMX_THREAD_MPI=$(usex threads)
+			-DGMXAPI=$(usex gmxapi)
 			"${opencl[@]}"
 			"${cuda[@]}"
 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
@@ -197,6 +212,7 @@ src_configure() {
 			-DGMX_THREAD_MPI=OFF
 			-DGMX_MPI=ON ${cuda}
 			-DGMX_OPENMM=OFF
+			-DGMXAPI=OFF
 			-DGMX_BUILD_MDRUN_ONLY=ON
 			-DBUILD_SHARED_LIBS=OFF
 			-DGMX_BUILD_MANUAL=OFF
diff --git a/sci-chemistry/gromacs/gromacs-2018.1.ebuild b/sci-chemistry/gromacs/gromacs-2019_beta1.ebuild
index 11f2b2483a38..b59d3312f446 100644
--- a/sci-chemistry/gromacs/gromacs-2018.1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019_beta1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -18,7 +18,7 @@ if [[ $PV = *9999* ]]; then
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
 		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
-	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+	KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 fi
 
 ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
@@ -31,7 +31,7 @@ HOMEPAGE="http://www.gromacs.org/"
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -40,11 +40,12 @@ CDEPEND="
 		x11-libs/libICE
 		)
 	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 )
 	opencl? ( virtual/opencl )
 	fftw? ( sci-libs/fftw:3.0 )
 	hwloc? ( sys-apps/hwloc )
 	lapack? ( virtual/lapack )
+	lmfit? ( sci-libs/lmfit )
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
 	"
@@ -52,6 +53,8 @@ DEPEND="${CDEPEND}
 	virtual/pkgconfig
 	doc? (
 		app-doc/doxygen
+		dev-python/sphinx
+		media-gfx/mscgen
 		dev-texlive/texlive-latex
 		dev-texlive/texlive-latexextra
 		media-gfx/imagemagick
@@ -146,8 +149,15 @@ src_configure() {
 		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=$(usex lapack)
@@ -158,7 +168,6 @@ src_configure() {
 		-DGMX_HWLOC=$(usex hwloc)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_SIMD="$acce"
-		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
 		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
 		-DBUILD_TESTING=$(usex test)
 		-DGMX_BUILD_UNITTESTS=$(usex test)
@@ -182,6 +191,7 @@ src_configure() {
 			${mycmakeargs_pre[@]} ${p}
 			-DGMX_MPI=OFF
 			-DGMX_THREAD_MPI=$(usex threads)
+			-DGMXAPI=$(usex gmxapi)
 			"${opencl[@]}"
 			"${cuda[@]}"
 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
@@ -198,6 +208,7 @@ src_configure() {
 			-DGMX_THREAD_MPI=OFF
 			-DGMX_MPI=ON ${cuda}
 			-DGMX_OPENMM=OFF
+			-DGMXAPI=OFF
 			-DGMX_BUILD_MDRUN_ONLY=ON
 			-DBUILD_SHARED_LIBS=OFF
 			-DGMX_BUILD_MANUAL=OFF
@@ -216,10 +227,10 @@ src_compile() {
 		BUILD_DIR="${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}_${x}"\
-				cmake-utils_src_compile manual
-		fi
+		#if use doc; then
+		#	BUILD_DIR="${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"\
@@ -238,9 +249,9 @@ 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-${PV}.pdf"
-		fi
+		#if use doc; then
+		#	newdoc "${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
diff --git a/sci-chemistry/gromacs/gromacs-5.1.3.ebuild b/sci-chemistry/gromacs/gromacs-5.1.3.ebuild
index b08ea7c3af7f..eba3bfc8c094 100644
--- a/sci-chemistry/gromacs/gromacs-5.1.3.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.1.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -18,7 +18,7 @@ if [[ $PV = *9999* ]]; then
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
 		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
-	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+	KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 fi
 
 ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
diff --git a/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild
index b08ea7c3af7f..eba3bfc8c094 100644
--- a/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -18,7 +18,7 @@ if [[ $PV = *9999* ]]; then
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
 		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )"
-	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+	KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 fi
 
 ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index b38e62cc3e58..8a643e0fb30d 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -18,7 +18,7 @@ if [[ $PV = *9999* ]]; then
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
 		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
-	KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+	KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 fi
 
 ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
@@ -31,7 +31,7 @@ HOMEPAGE="http://www.gromacs.org/"
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -40,10 +40,12 @@ CDEPEND="
 		x11-libs/libICE
 		)
 	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 )
+	opencl? ( virtual/opencl )
 	fftw? ( sci-libs/fftw:3.0 )
 	hwloc? ( sys-apps/hwloc )
 	lapack? ( virtual/lapack )
+	lmfit? ( sci-libs/lmfit )
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
 	"
@@ -51,6 +53,8 @@ DEPEND="${CDEPEND}
 	virtual/pkgconfig
 	doc? (
 		app-doc/doxygen
+		dev-python/sphinx
+		media-gfx/mscgen
 		dev-texlive/texlive-latex
 		dev-texlive/texlive-latexextra
 		media-gfx/imagemagick
@@ -60,6 +64,7 @@ RDEPEND="${CDEPEND}"
 REQUIRED_USE="
 	|| ( single-precision double-precision )
 	cuda? ( single-precision )
+	cuda? ( !opencl )
 	mkl? ( !blas !fftw !lapack )"
 
 DOCS=( AUTHORS README )
@@ -144,8 +149,15 @@ src_configure() {
 		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=$(usex lapack)
@@ -156,7 +168,6 @@ src_configure() {
 		-DGMX_HWLOC=$(usex hwloc)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_SIMD="$acce"
-		-DGMX_LIB_INSTALL_DIR="$(get_libdir)"
 		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
 		-DBUILD_TESTING=$(usex test)
 		-DGMX_BUILD_UNITTESTS=$(usex test)
@@ -173,11 +184,15 @@ src_configure() {
 		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
 		local cuda=( "-DGMX_GPU=OFF" )
 		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( -DGMX_GPU=ON )
+			cuda=( "-DGMX_GPU=ON" )
+		local opencl=( "-DGMX_USE_OPENCL=OFF" )
+		use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" )
 		mycmakeargs=(
 			${mycmakeargs_pre[@]} ${p}
 			-DGMX_MPI=OFF
 			-DGMX_THREAD_MPI=$(usex threads)
+			-DGMXAPI=$(usex gmxapi)
+			"${opencl[@]}"
 			"${cuda[@]}"
 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
 			-DGMX_BINARY_SUFFIX="${suffix}"
@@ -193,6 +208,7 @@ src_configure() {
 			-DGMX_THREAD_MPI=OFF
 			-DGMX_MPI=ON ${cuda}
 			-DGMX_OPENMM=OFF
+			-DGMXAPI=OFF
 			-DGMX_BUILD_MDRUN_ONLY=ON
 			-DBUILD_SHARED_LIBS=OFF
 			-DGMX_BUILD_MANUAL=OFF
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 844b34dd014b..0dcc6a6c4d7f 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -22,6 +22,8 @@
 		<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>
 		<!-- 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>
diff --git a/sci-chemistry/tm-align/Manifest b/sci-chemistry/tm-align/Manifest
index 8260fae5754a..f8a2ec5e7dd3 100644
--- a/sci-chemistry/tm-align/Manifest
+++ b/sci-chemistry/tm-align/Manifest
@@ -1,6 +1,4 @@
 AUX CMakeLists.txt 182 BLAKE2B a6bd5aedcbeb2b8019d59123da91cf668c3717a3e41c2259b2e023a4661aefeb2e4334d10ba7b236bfb6fb1cf52c87aae393c9af8b5e3d2f12663799aeccab32 SHA512 1e77edbfb2184e11c09fc2133eb40bd9d4b2fb04a30139134939482f4e817ebfa5c316e8d75a6fd5aa866ef1f6f56d65df924dc41cfb698330943e0bc433948d
-DIST TMtools20140601.tar.gz 934391 BLAKE2B 4dfe18501bfd26b0c12f734175b908f65e97cea9cf2c620c100aa2f68f10fb288c8973c71c9fc6364a635f0275d3a04d7eaffdd5833345dda57e7a318e7c4e5f SHA512 99b90425ff051c836e19225601ddfb1576bec9c8f233aafeba96075f924a3c0892b5b1cfef36254ff5ef468a6dbf64f7fcc9a3ce24a0d869b3c1eb87c0149765
 DIST TMtools20150914.tar.gz 982948 BLAKE2B 788f43040c1262c7e9eae2b47b0035d320a30fe7194e340d682b78e5961b82e46eef2b0a43d1ae458b9d5da6570f9c0ec0aca51b6ec3e25f0447fd43d629f592 SHA512 5fda29f6437ac9b0216a037496a01502de07e5a36736815833cb09217158a959370e750b75c55a54a49c733e4bd28be53b2dcbb25d71e2897273a4280ed3b530
-EBUILD tm-align-20140601.ebuild 720 BLAKE2B 169462fabc7fb255e1746ae1f692b6f989591787ca53023ded771f56489c4c8a2407d40d45186b8fa89ba3750d51e45ab889e4ca6b4f768fa28f1f8eea004f4b SHA512 04d20ceb4a1a33277af7cee7ec49e1902eceb5cb33361020a56f6b9bad62b0c423867104fb6b4bda8b0197d3b7d0a0e057cea87907ab43d69cf10961ca082543
-EBUILD tm-align-20150914.ebuild 719 BLAKE2B 085ff1781394ded54c8f8759c5dcb3c74f92283cfe94ab6f6f85b5d6f8e09eeb84d539aacfe998384870db0f7f34f7cb3c560d316eb55ffb9628d6cfb343dbbf SHA512 e725f7d70953c620a4082049e435647d2ead74359912e0028ef065d6fb428e4ac885f8c13f7c4d72fbe91367853066b2451d351c4aa0a4ab82339bac85608ef0
+EBUILD tm-align-20150914.ebuild 717 BLAKE2B 45ca4e8358af29d5e4f8890548515a15aace7549d85a988699e5aaffa9f8657617c77b62a67794147b64ba36499f83cf9b7e1a89fa54c66d3a7c7df557ea3979 SHA512 b89bac74a0fea20b4bcf35b552465144beab620372ce6ae368dab49118f6ae773e569d17b7fbff2abc6455b3ddd353dcd9eb343b78cd4bf58614089d60b5f21b
 MISC metadata.xml 1294 BLAKE2B 7972c0f1c379a3929c3d561756099a2071ddc9a6ff35a905a30807f1d724100aa39e98bf549ab4614a7f7b95628246fde7f44d655dceebb0e8f4a4f70686123d SHA512 e1b90b61682c3c1099c3b2d5d5fad166e408b14aca67e49521f470b2df1c746aa4c1eeae06f4f67fe6ccf8ded94c5fbe7a194a441fae8fab450f69acdcb49663
diff --git a/sci-chemistry/tm-align/tm-align-20140601.ebuild b/sci-chemistry/tm-align/tm-align-20140601.ebuild
deleted file mode 100644
index a0010e5ebfcb..000000000000
--- a/sci-chemistry/tm-align/tm-align-20140601.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils flag-o-matic fortran-2
-
-DESCRIPTION="Quick & Accurate Structural Alignment"
-HOMEPAGE="http://zhanglab.ccmb.med.umich.edu/TM-align/"
-SRC_URI="http://zhanglab.ccmb.med.umich.edu/TM-align/TMtools${PV}.tar.gz"
-
-LICENSE="tm-align"
-SLOT="0"
-KEYWORDS="amd64 ppc ppc64 x86 ~amd64-linux ~x86-linux"
-IUSE="static custom-cflags"
-
-S="${WORKDIR}"
-
-src_prepare() {
-	cmake-utils_src_prepare
-
-	cp "${FILESDIR}"/CMakeLists.txt . || die
-	use static && append-fflags -static && append-ldflags -static
-	# recommended by upstream
-	use custom-cflags || replace-flags -O* -O3 && append-fflags -ffast-math
-}
diff --git a/sci-chemistry/tm-align/tm-align-20150914.ebuild b/sci-chemistry/tm-align/tm-align-20150914.ebuild
index a19b8da0b4c1..26eb0fd6597f 100644
--- a/sci-chemistry/tm-align/tm-align-20150914.ebuild
+++ b/sci-chemistry/tm-align/tm-align-20150914.ebuild
@@ -11,7 +11,7 @@ SRC_URI="http://zhanglab.ccmb.med.umich.edu/TM-align/TMtools${PV}.tar.gz"
 
 LICENSE="tm-align"
 SLOT="0"
-KEYWORDS="~amd64 ppc ppc64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="amd64 ppc ppc64 x86 ~amd64-linux ~x86-linux"
 IUSE="custom-cflags static"
 
 S="${WORKDIR}"
diff --git a/sci-chemistry/votca-csg/Manifest b/sci-chemistry/votca-csg/Manifest
index 60874d84d6e4..c9dfe8ebe96a 100644
--- a/sci-chemistry/votca-csg/Manifest
+++ b/sci-chemistry/votca-csg/Manifest
@@ -4,7 +4,7 @@ DIST votca-csg-manual-1.4.1.pdf 1282641 BLAKE2B 370b7c8997649555fd2360b999cf381c
 DIST votca-csg-manual-1.4.pdf 1281983 BLAKE2B 5659c2e327ba7bb00fac15adfb578288d546b509366863f593776a62dd3064662535d4fd525f1063f5ccaf47446822f13fefd7f66aa9d68cd1a4a7c99d66a790 SHA512 2e1f4a4375d83df9bd357d4d17e79d26a3a31c9177f008de86721427ffc6f43a5000ec840691108b52a8aecf962321ba6363cd975c7445d7230ee5b0b151b3fa
 DIST votca-csg-tutorials-1.4.1.tar.gz 6339417 BLAKE2B e9acf8e421f6fce4d97be2d51fb559979c6fd3e6b042525cedf32cadeab1dddc5b1aaf80bbbfd387da3bce71672759c2e84d317c789f616dc71834c72a581fff SHA512 896ec9d6b2537a06301046a74c1957708eb96d9854b3ec855fe3457208c142f6fb26a03e323a2644862a1efd0030fcceb1189f73655b984462f0f7127a02de90
 DIST votca-csg-tutorials-1.4.tar.gz 6348417 BLAKE2B 612fcbc4457a57be74e5306bf86d6e031ea8cd55ebe3f4d246c0876e272e6e6dd535c8dd2f24f7593cb1ef31fbc18111269d29cb69120368ddef7b1b7d25825c SHA512 f3eb28a133ebc04eed07f84d5962943cb9c547c1099638127f15e0015dfdf3f0b25aab4c97d009d6040bf1d69d408cc178edd6e803d33bf1d831e12dca0671c7
-EBUILD votca-csg-1.4.1.ebuild 3195 BLAKE2B 62369b40fac01281c4bb4e790d30638d83c7a5f105c941e462c36a316b13130245027423f99ef571b2f3ce78adaefe03eccb76a142682e93f0e7ce4d484e869c SHA512 9648303d65c86c2643f4f0892128c09d97ce4aa75a843644bc87cc7fbae0dc272d126ebe5a712d1640365ef31578c97da960edcc559561c56f303870fcb104ad
+EBUILD votca-csg-1.4.1.ebuild 3198 BLAKE2B 47ee7941de81e6de211b945ddb95f27c7d9cd7509e84784a57222e4acbca1f15181042d74ebec9198a1074e1eae553438ea073f10385e8c016b947ed6618d332 SHA512 093ae1b82f6498df6befbd24ae3146c275257ec20dd9d466bc5dd93d5ca5a4e48650b2a16d0e7d750b82bd5e3d5bce85fe8ac7ad428f91a1376a0be4b3e8b3de
 EBUILD votca-csg-1.4.ebuild 3191 BLAKE2B 93981bf3302b4c0feaaf1e45005df343ab5e12011a461e0f9729a9e6d50f1268fb016ce2bbe397a2b673fb0172a9971bc9e67fb806fa9a56fb7ab4e05235bd56 SHA512 ddeed3f96f097e73ad3593daebab448ae992a3f0d4ba9d46b9027c79c9654457ba3611af51049741f8ff04c0f8425eb097a6115f75d1ec7704f48c46a71ea088
 EBUILD votca-csg-9999.ebuild 2540 BLAKE2B 605ea77ddd320c1e0af4c93468261e3a44ef49fa1073568d64521a1557f5cdbd18fbf66e82be235b2e221adddacbc731fde63233d2ecb05e37528d0ce16be79c SHA512 932e5be7cf66118e246a56fa4420d4a5df07fc1ebb82ce6a5331b3ca71eace4ac79a7a84bc5186515e7bbd6856de6c604bc8b1351020146d466f4bd229f7446c
 MISC metadata.xml 676 BLAKE2B b3f2e43f5cb505876216b0a329410c9cef1b44a9bbd7e1c61faa4acd00dbe87ea0cebb00ed78dc00b9e1d2b08b95e3c40d25fecc0738c992a3f933e430f94e2b SHA512 14ecd498eeeed1576923d8da9bc5dc98e47c1d162173b7f2419ad367fa84e227555bd0365709be8a456dc5388ea6fa6734fa7df3c82fd4efcd1cf3460c7e12a1
diff --git a/sci-chemistry/votca-csg/votca-csg-1.4.1.ebuild b/sci-chemistry/votca-csg/votca-csg-1.4.1.ebuild
index c83eac6e62bb..47c989751bff 100644
--- a/sci-chemistry/votca-csg/votca-csg-1.4.1.ebuild
+++ b/sci-chemistry/votca-csg/votca-csg-1.4.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -29,7 +29,7 @@ SLOT="0"
 
 RDEPEND="
 	~sci-libs/votca-tools-${PV}
-	gromacs? ( sci-chemistry/gromacs:= )
+	gromacs? ( <sci-chemistry/gromacs-2019:= )
 	hdf5? ( sci-libs/hdf5 )
 	dev-lang/perl
 	app-shells/bash:*"