Add experimental python bindings

Package-Manager: portage-2.2.15

3 files changed, 838 insertions, 0 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
new file mode 100644
index 0000000..da2baae
--- /dev/null
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -0,0 +1,532 @@
+# ChangeLog for sci-chemistry/gromacs
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  21 Dec 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
+  sync with gx86
+
+  25 Nov 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-5.0.9999.ebuild, gromacs-9999.ebuild:
+  fixed a typo preventing AVX2 support (bug #530454)
+
+  09 Oct 2014; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+  Fix doc install
+
+  07 Sep 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
+  fix completion install
+
+  06 Sep 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
+  sync with gx86
+
+  04 Sep 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
+  sync with gx86
+
+  03 Sep 2014; Christoph Junghans <ottxor@gentoo.org> -Manifest,
+  -gromacs-5.0_rc1.ebuild:
+  drop old
+
+  03 Sep 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
+  live update
+
+  07 Jul 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-5.0.9999.ebuild:
+  sync with gx86, fix FEATURES=test
+
+  26 Jun 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
+  live ebuild update
+
+  14 Apr 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild,
+  gromacs-5.0_rc1.ebuild, gromacs-9999.ebuild, metadata.xml:
+  added make-symlinks use flag, multilib-strict fix
+
+*gromacs-5.0.9999 (08 Apr 2014)
+*gromacs-5.0_rc1 (08 Apr 2014)
+
+  08 Apr 2014; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-5.0.9999.ebuild,
+  +gromacs-5.0_rc1.ebuild, -gromacs-5.0_beta1.ebuild, gromacs-9999.ebuild,
+  metadata.xml:
+  [sci-chemistry/gromacs] New ebuilds
+
+  05 Mar 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-9999.ebuild:
+  fix multilib-strict
+
+  20 Feb 2014; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+  Update gromacs 5.0
+
+  16 Feb 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  git-r3 too smart, migrate back to git-2
+
+  05 Feb 2014; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+  Bash completion changes are comming =D
+
+  05 Feb 2014; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+  Revert back to git-2 since git-r2  gives problems
+
+  25 Jan 2014; Justin Lecher <jlec@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-5.0_beta1.ebuild, gromacs-9999.ebuild:
+  Add missing dep for USE=doc
+
+  06 Jan 2014; Justin Lecher <jlec@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-5.0_beta1.ebuild, gromacs-9999.ebuild:
+  Switch from git-2 to git-r3
+
+  06 Jan 2014; Justin Lecher <jlec@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-5.0_beta1.ebuild, gromacs-9999.ebuild:
+  Switch from git-2 to git-r3
+
+  07 Dec 2013; Justin Lecher <jlec@gentoo.org> gromacs-5.0_beta1.ebuild,
+  metadata.xml:
+  Fix multilib-strict problems
+
+*gromacs-5.0_beta1 (06 Dec 2013)
+
+  06 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-5.0_beta1.ebuild,
+  gromacs-9999.ebuild:
+  Add 5.0-beta1 release
+
+  05 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+  Make gromacs 9999 build manual again
+
+  05 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> -Manifest,
+  -gromacs-4.5.9999.ebuild, metadata.xml:
+  Drop 4.5
+
+  05 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+  Update live ebuild to current state
+
+  03 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+  make mdrun target work for gmx live
+
+  03 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+  More updates #2 to gmx live
+
+  03 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+  More updates to gmx live
+
+  03 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+  Slightly update live ebuild for master branch
+
+  01 Jun 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  sync with gx86
+
+  05 May 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild:
+  sync with gx86
+
+*gromacs-4.5.9999 (03 May 2013)
+
+  03 May 2013; Christoph Junghans <ottxor@gentoo.org>
+  +files/gromacs-4.5.7-cmake-cpp-asm.patch, +gromacs-4.5.9999.ebuild,
+  metadata.xml:
+  added recent 4.5.x version from gx86 (bug #468454)
+
+  15 Mar 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.6.9999.ebuild:
+  nvcc flags dont needed anymore here
+
+  15 Mar 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-9999.ebuild:
+  Fix build with cuda enabled
+
+  10 Mar 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  added cuda build fix from gx86
+
+  09 Mar 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  fixed deps + doc build on darwin
+
+  06 Mar 2013; Christoph Junghans <ottxor@gentoo.org> -Manifest,
+  -gromacs-4.5.9999.ebuild, gromacs-4.6.9999.ebuild, gromacs-9999.ebuild,
+  metadata.xml:
+  sync with gx86 + clean up
+
+  12 Feb 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-9999.ebuild, metadata.xml:
+  sse41 -> sse4_1 (bug #456886) + ninja has missing keywords
+
+  30 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-9999.ebuild:
+  added subslot, removed gromacs-manual blocker
+
+  30 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  clean up
+
+  28 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  added app-doc/gromacs-manual in here
+
+  21 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  sci-chemistry/gromacs: use cuda.eclass
+
+  21 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  fixed sci-chemistry/gromacs[test]
+
+  21 Jan 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.6.9999.ebuild:
+  [sci-chemistry/gromacs] Drop restrict test for 4.6
+
+  21 Jan 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.6.9999.ebuild:
+  [sci-chemistry/gromacs] Update 4.6 series ebuild
+
+  18 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  yet another update for git
+
+  18 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  live ebuild update
+
+  30 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  further clean up
+
+  29 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  fixed build with newer mkl
+
+  27 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  sci-chemistry/gromacs: clean up
+
+  26 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  fixed openmm suffix
+
+  26 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  fixed another typo
+
+  26 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  fixed typo
+
+  26 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  metadata.xml:
+  Added mkl support
+
+  22 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-9999.ebuild, metadata.xml:
+  sync with gx86
+
+  20 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  fortran is gone
+
+  08 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+  gromacs-4.6.9999.ebuild, gromacs-9999.ebuild:
+  CMAKE_BUILD_DIR -> BUILD_DIR
+
+  30 Nov 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  sync with gx86
+
+  27 Nov 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  metadata.xml:
+  added openmm support
+
+  19 Nov 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  live ebuild update
+
+  04 Oct 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-9999.ebuild:
+  live ebuild update
+
+  03 Oct 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  metadata.xml:
+  hybrid stuff got merged
+
+  09 Aug 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  use ninja if available
+
+  25 Jul 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+  gromacs-4.6.9999.ebuild, gromacs-9999.ebuild:
+  added ~x86-macos
+
+  19 Jun 2012; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.6.9999.ebuild,
+  gromacs-9999.ebuild, metadata.xml:
+  [sci-chemistry/gromacs] Add new acceleration use flags for gromacs
+
+  11 Jun 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+  metadata.xml:
+  add support for new hybrid kernels
+
+  28 Apr 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  [sci-chemistry/gromacs] add more mirrors
+
+  19 Apr 2012; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.5.9999.ebuild,
+  gromacs-4.6.9999.ebuild, gromacs-9999.ebuild:
+  [sci-chemistry/gromacs] Also add http mirror git uri
+
+  04 Mar 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+  gromacs-9999.ebuild:
+  removed obsolete call to env-update
+
+  04 Mar 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  reworked fortran and openmp support
+
+  12 Feb 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  sci-chemistry/gromacs: clean up
+
+  12 Feb 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  fixed threads and mpi
+
+  05 Feb 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  handle new vmd detection
+
+  05 Feb 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+  added openmp support
+
+*gromacs-4.6.9999 (28 Sep 2011)
+
+  28 Sep 2011; Christoph Junghans <ottxor@gentoo.org> +gromacs-4.6.9999.ebuild:
+  Added gromacs-4.6 live version
+
+  10 Sep 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+  gromacs-9999.ebuild:
+  Migrate to the bash-completion-r1 eclass
+
+  18 Jul 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+  gromacs-9999.ebuild:
+  sync with tree
+
+  25 Jun 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+  gromacs-9999.ebuild:
+  migrate to git-2
+
+  25 Jun 2011; Justin Lecher <jlec@gentoo.org> gromacs-4.5.9999.ebuild,
+  gromacs-9999.ebuild, metadata.xml:
+  migrate from 'git' to 'git-2'
+
+  21 Jun 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+  gromacs-9999.ebuild:
+  only USE=fkernels needs fortran
+
+  21 Jun 2011; Justin Lecher <jlec@gentoo.org> gromacs-4.5.9999.ebuild,
+  gromacs-9999.ebuild:
+  Added fortran-2.eclass support
+
+  19 Jun 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+  metadata.xml:
+  autotools is broken
+
+  10 Apr 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.0.9999.ebuild:
+  remove 4.0.* (EOM)
+
+  08 Mar 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+  gromacs-9999.ebuild:
+  added fixes from 4.5.3-r4
+
+  07 Mar 2011; Justin Lecher <jlec@gentoo.org> gromacs-4.0.9999.ebuild,
+  gromacs-4.5.9999.ebuild, gromacs-9999.ebuild:
+  Correct Slots for gtk 3 introduction to tree
+
+  19 Feb 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.5.3-r3.ebuild:
+  InCVS
+
+*gromacs-4.5.3-r3 (17 Feb 2011)
+
+  17 Feb 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.5.3-r2.ebuild,
+  +gromacs-4.5.3-r3.ebuild:
+  version bump
+
+*gromacs-4.5.3-r2 (14 Feb 2011)
+
+  14 Feb 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.5.3-r1.ebuild,
+  +gromacs-4.5.3-r2.ebuild, gromacs-4.5.9999.ebuild, gromacs-9999.ebuild:
+  bring back sse/sse2 useflag (bug #339837)
+
+  20 Jan 2011; Christoph Junghans <kleiner_otti@gmx.de> gromacs-9999.ebuild:
+  add back live manual
+
+  17 Jan 2011; Christoph Junghans <kleiner_otti@gmx.de> gromacs-9999.ebuild:
+  QA fixes
+
+  16 Dec 2010; Justin Lecher <jlec@gentoo.org> gromacs-4.0.9999.ebuild,
+  gromacs-4.5.9999.ebuild, gromacs-9999.ebuild:
+  Removal of fortran.eclass, #348851
+
+  25 Nov 2010; Alexey Shvetsov <alexxy@gentoo.org> -gromacs-4.0.7-r5.ebuild,
+  -files/gromacs-4.0.7_missing_distfiles.patch.gz,
+  -files/gromacs-4.0.7_upstream2010-09-15.patch.gz, -gromacs-4.5.2.ebuild,
+  -gromacs-4.5.3.ebuild:
+  Moved to tree
+
+*gromacs-4.5.3 (23 Nov 2010)
+
+  23 Nov 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  +gromacs-4.5.3.ebuild:
+  version bump
+
+*gromacs-4.5.2 (30 Oct 2010)
+
+  30 Oct 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  +gromacs-4.5.2.ebuild:
+  Version bump
+
+  25 Oct 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  gromacs-4.5.9999.ebuild, gromacs-9999.ebuild, metadata.xml:
+  added natural vmd support (bug #340651#c8)
+
+  21 Oct 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  gromacs-4.5.9999.ebuild, metadata.xml:
+  added vmd use flag
+
+  17 Oct 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  gromacs-4.0.7-r5.ebuild, gromacs-4.0.9999.ebuild:
+  rename manual in distfiles
+
+  16 Oct 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  gromacs-4.0.9999.ebuild, gromacs-4.5.9999.ebuild, gromacs-9999.ebuild:
+  Live ebuild updates
+
+*gromacs-4.0.7-r5 (16 Oct 2010)
+
+  16 Oct 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  +gromacs-4.0.7-r5.ebuild, +files/gromacs-4.0.7_missing_distfiles.patch.gz,
+  +files/gromacs-4.0.7_upstream2010-09-15.patch.gz:
+  Version bump
+
+*gromacs-4.5.1 (02 Sep 2010)
+
+  02 Sep 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  -gromacs-4.5_beta3.ebuild, +gromacs-4.5.1.ebuild:
+  version bump
+
+*gromacs-4.5_beta3 (11 Aug 2010)
+
+  11 Aug 2010; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.0.9999.ebuild,
+  -gromacs-4.5_beta2.ebuild, +gromacs-4.5_beta3.ebuild,
+  gromacs-4.5.9999.ebuild, gromacs-9999.ebuild:
+  Add epatch_user
+
+*gromacs-4.5_beta2 (02 Aug 2010)
+
+  02 Aug 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  -gromacs-4.5_beta1.ebuild, +gromacs-4.5_beta2.ebuild,
+  gromacs-4.5.9999.ebuild, gromacs-9999.ebuild:
+  Version bump + new manual
+
+*gromacs-4.5.9999 (31 Jul 2010)
+*gromacs-4.5_beta1 (31 Jul 2010)
+
+  31 Jul 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  +gromacs-4.5_beta1.ebuild, +gromacs-4.5.9999.ebuild, gromacs-9999.ebuild:
+  Version bump
+
+  24 Jul 2010; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+  ffamber officialy shipped with gromacs from now on
+
+  08 Jul 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  gromacs-4.0.9999.ebuild, gromacs-9999.ebuild:
+  fix for bug #301854
+
+  04 Jul 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  gromacs-4.0.9999.ebuild, -files/gromacs-4.0.9999-ccache.patch,
+  -files/gromacs-4.0.9999-configure-gfortran.patch, gromacs-9999.ebuild:
+  make it compile without fortran again
+
+  04 Jul 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  gromacs-4.0.9999.ebuild, gromacs-9999.ebuild:
+  Fixes for Bug #326331
+
+  28 Jun 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  gromacs-4.0.9999.ebuild, +files/gromacs-4.0.9999-docdir.patch:
+  docdir patch is still not in 4.0 branch
+
+*gromacs-4.0.7-r3 (22 Jun 2010)
+
+  22 Jun 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  +gromacs-4.0.7-r3.ebuild, +files/gromacs-4.0.7to2010-06-08.patch.gz:
+  added patches from stable branch
+
+*gromacs-4.0.7-r2 (26 Feb 2010)
+
+  26 Feb 2010; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-4.0.7-r2.ebuild:
+  Add ffamber port to gromacs
+
+  18 Feb 2010; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild,
+  -files/gromacs-9999-dirent.patch:
+  Dropped unneded patches. They all were applied to git master
+
+  18 Feb 2010; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild,
+  -files/gromacs-9999-as-needed.patch,
+  -files/gromacs-9999-install-mdrun.patch:
+  Dropped unneded patches. They all were applied to git master
+
+  09 Feb 2010; Christoph Junghans <kleiner_otti@gmx.de> gromacs-9999.ebuild,
+  +files/gromacs-9999-as-needed.patch:
+  added as-needed fix
+
+  06 Feb 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  -gromacs-4.0.7-r1.ebuild, -files/gromacs-4.0.9999-docdir.patch:
+  InCvs
+
+  06 Feb 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  gromacs-4.0.9999.ebuild, gromacs-9999.ebuild:
+  docdir patch went upstream
+
+  01 Feb 2010; Christoph Junghans <kleiner_otti@gmx.de> gromacs-9999.ebuild,
+  +files/gromacs-9999-install-mdrun.patch:
+  update live ebuild
+
+*gromacs-4.0.7-r1 (24 Jan 2010)
+
+  24 Jan 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  -files/gromacs-4.0.4-configure-gfortran.patch, +gromacs-4.0.7-r1.ebuild,
+  gromacs-4.0.9999.ebuild, +files/gromacs-4.0.9999-ccache.patch,
+  +files/gromacs-4.0.9999-configure-gfortran.patch, gromacs-9999.ebuild:
+  Fixes bug #302048
+
+  23 Jan 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  gromacs-4.0.9999.ebuild, gromacs-9999.ebuild:
+  fixed --as-needed confusion
+
+  21 Jan 2010; Christoph Junghans <kleiner_otti@gmx.de>
+  -gromacs-3.3.9999.ebuild, -gromacs-4.0.4.ebuild,
+  -files/gromacs-4.0.4-sparc-cyclecounter.patch, -gromacs-4.0.5-r1.ebuild,
+  -files/gromacs-4.0.5-docdir.patch,
+  -files/gromacs-4.0.5-path-overflow.patch, gromacs-4.0.9999.ebuild,
+  +files/gromacs-4.0.9999-docdir.patch, gromacs-9999.ebuild:
+  sync with tree and removed old ebuilds
+
+  30 Nov 2009; Christoph Junghans <kleiner_otti@gmx.de>
+  files/gromacs-4.0.5-docdir.patch:
+  docdir -> htmldir
+
+  30 Nov 2009; Christoph Junghans <kleiner_otti@gmx.de>
+  gromacs-4.0.5-r1.ebuild, +files/gromacs-4.0.5-docdir.patch:
+  htmldoc was installed in the wrong path
+
+  22 Nov 2009; Christoph Junghans <kleiner_otti@gmx.de>
+  gromacs-4.0.5-r1.ebuild:
+  build mpi and non-mpi libs, enable gsl by default
+
+*gromacs-4.0.5-r1 (14 Nov 2009)
+
+  14 Nov 2009; Christoph Junghans <kleiner_otti@gmx.de>
+  +files/gromacs-4.0.4-sparc-cyclecounter.patch, +gromacs-4.0.5-r1.ebuild,
+  +files/gromacs-4.0.5-path-overflow.patch:
+  fixes bug #284431
+
+*gromacs-9999 (21 Jun 2009)
+*gromacs-4.0.9999 (21 Jun 2009)
+*gromacs-3.3.9999 (21 Jun 2009)
+
+  21 Jun 2009; Christoph Junghans <kleiner_otti@gmx.de>
+  +gromacs-3.3.9999.ebuild, +files/gromacs-4.0.4-configure-gfortran.patch,
+  +gromacs-4.0.9999.ebuild, +gromacs-9999.ebuild, metadata.xml:
+  added live ebuilds for old, stable, experimental branch
+
+  21 Jun 2009; Christoph Junghans <kleiner_otti@gmx.de>
+  gromacs-4.0.4.ebuild:
+  Fixed some repoman errors
+
+  22 Feb 2009; Jeff Gardner <je_fro@gentoo.org>
+  gromacs-4.0.4.ebuild:
+  Add 'append-ldflags' to facilitate building for users with --as-needed.
+
+*gromacs-4.0.4 (20 Feb 2009)
+
+  20 Feb 2009; Alexey Shvetsov <alexxy@gentoo.org> -gromacs-4.0.3-r1.ebuild,
+  +gromacs-4.0.4.ebuild:
+  Version bump\!
+
+  20 Feb 2009; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.0.3-r1.ebuild:
+  Fix typo
+
+*gromacs-4.0.3-r1 (20 Feb 2009)
+
+  20 Feb 2009; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-4.0.3-r1.ebuild,
+  -gromacs-4.0.3.ebuild:
+  Add support for qm/mm with mopac7 for gromacs
+
+*gromacs-4.0.3 (20 Jan 2009)
+
+  20 Jan 2009; Alexey Shvetsov <alexxy@gentoo.org> -gromacs-3.3.3.ebuild,
+  +gromacs-4.0.3.ebuild:
+  Version bump
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
new file mode 100644
index 0000000..d26c345
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -0,0 +1,279 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+TEST_PV="5.0-rc1"
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+PYTHON_COMPAT=( python{3_2,3_3,3_4} )
+
+inherit bash-completion-r1 cmake-utils cuda eutils multilib python-single-r1 readme.gentoo toolchain-funcs
+
+if [[ $PV = *9999* ]]; then
+	if use python; then
+		EGIT_REPO_URI="git://biod.pnpi.spb.ru/alexxy/gromacs.git"
+		EGIT_BRANCH="pygromacs"
+	else
+		EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
+			https://gerrit.gromacs.org/gromacs.git
+			git://github.com/gromacs/gromacs.git
+			http://repo.or.cz/r/gromacs.git"
+		EGIT_BRANCH="master"
+	fi
+	inherit git-r3
+else
+	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
+		test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )"
+fi
+
+ACCE_IUSE="sse2 sse4_1 avx_128_fma avx_256 avx2_256"
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+
+# see COPYING for details
+# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
+#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
+LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
+SLOT="0/${PV}"
+KEYWORDS=""
+IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp python +single-precision test +threads +tng ${ACCE_IUSE}"
+
+CDEPEND="
+	X? (
+		x11-libs/libX11
+		x11-libs/libSM
+		x11-libs/libICE
+		)
+	blas? ( virtual/blas )
+	boost? ( >=dev-libs/boost-1.55 )
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
+	fftw? ( sci-libs/fftw:3.0 )
+	lapack? ( virtual/lapack )
+	mkl? ( sci-libs/mkl )
+	mpi? ( virtual/mpi )
+	python? (
+		dev-python/numpy
+		dev-python/sip
+		)
+	"
+DEPEND="${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 )
+	python? ( ${PYTHON_REQUIRED_USE} )"
+
+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"
+}
+
+pkg_setup() {
+	use python && python-single-r1_pkg_setup
+}
+
+src_unpack() {
+	if [[ ${PV} != *9999 ]]; then
+		default
+	else
+		git-r3_src_unpack
+		if use test; then
+			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
+			EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \
+			EGIT_SOURCEDIR="${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 sse2 && acce="SSE2"
+	use sse4_1 && acce="SSE4.1"
+	use avx_128_fma && acce="AVX_128_FMA"
+	use avx_256 && acce="AVX_256"
+	use avx2_256 && 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)
+		$(cmake-utils_use python GMX_PYTHON_BINDINGS)
+		-DGMX_DEFAULT_SUFFIX=off
+		-DGMX_SIMD="$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
+		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
+	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
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake-utils_src_compile completion
+		if use doc; then
+			BUILD_DIR="${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-${PV}.pdf"
+		fi
+		newbashcomp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash gromacs
+		use mpi || continue
+		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+			cmake-utils_src_install
+	done
+	# drop unneeded stuff
+	rm -f "${ED}"usr/bin/gmx-completion*
+	rm -f "${ED}"usr/bin/g_options*
+	rm -f "${ED}"usr/bin/GMXRC*
+	rm -f "${ED}"usr/lib*/libtng*.a
+
+	readme.gentoo_create_doc
+}
+
+pkg_postinst() {
+	einfo
+	einfo  "Please read and cite:"
+	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
+	einfo  "http://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
new file mode 100644
index 0000000..87e0f0a
--- /dev/null
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>ottxor@gentoo.org</email>
+    <name>Christoph Junghans</name>
+  </maintainer>
+  <use>
+    <flag name="cuda">Enable cuda 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="tng">Enable new trajectory format - tng</flag>
+	<flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag>
+    <!-- acceleration optimization flags -->
+    <flag name="sse4_1">Enable sse4.1 acceleration</flag>
+	<flag name="avx128fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
+	<flag name="avx_128_fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
+	<flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
+	<flag name="avx_256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
+	<flag name="avx2_256">Enable 256bit avx2 (e.g. Intel Haswell)</flag>
+    <flag name="offensive">Enable gromacs partly offensive quotes</flag>
+    <flag name="openmm">Add acceleration through <pkg>sci-libs/openmm</pkg></flag>
+    <flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag>
+  </use>
+</pkgmetadata>