# ChangeLog for sci-chemistry/gromacs # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ 26 Jun 2014; Christoph Junghans gromacs-5.0.9999.ebuild: live ebuild update 14 Apr 2014; Christoph Junghans 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 +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 gromacs-9999.ebuild: fix multilib-strict 20 Feb 2014; Alexey Shvetsov gromacs-9999.ebuild: Update gromacs 5.0 16 Feb 2014; Christoph Junghans gromacs-4.6.9999.ebuild: git-r3 too smart, migrate back to git-2 05 Feb 2014; Alexey Shvetsov gromacs-9999.ebuild: Bash completion changes are comming =D 05 Feb 2014; Alexey Shvetsov gromacs-9999.ebuild: Revert back to git-2 since git-r2 gives problems 25 Jan 2014; Justin Lecher gromacs-4.6.9999.ebuild, gromacs-5.0_beta1.ebuild, gromacs-9999.ebuild: Add missing dep for USE=doc 06 Jan 2014; Justin Lecher 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 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 gromacs-5.0_beta1.ebuild, metadata.xml: Fix multilib-strict problems *gromacs-5.0_beta1 (06 Dec 2013) 06 Dec 2013; Alexey Shvetsov +gromacs-5.0_beta1.ebuild, gromacs-9999.ebuild: Add 5.0-beta1 release 05 Dec 2013; Alexey Shvetsov gromacs-9999.ebuild: Make gromacs 9999 build manual again 05 Dec 2013; Alexey Shvetsov -Manifest, -gromacs-4.5.9999.ebuild, metadata.xml: Drop 4.5 05 Dec 2013; Alexey Shvetsov gromacs-9999.ebuild: Update live ebuild to current state 03 Dec 2013; Alexey Shvetsov gromacs-9999.ebuild: make mdrun target work for gmx live 03 Dec 2013; Alexey Shvetsov gromacs-9999.ebuild: More updates #2 to gmx live 03 Dec 2013; Alexey Shvetsov gromacs-9999.ebuild: More updates to gmx live 03 Dec 2013; Alexey Shvetsov gromacs-9999.ebuild: Slightly update live ebuild for master branch 01 Jun 2013; Christoph Junghans gromacs-4.6.9999.ebuild: sync with gx86 05 May 2013; Christoph Junghans gromacs-4.5.9999.ebuild: sync with gx86 *gromacs-4.5.9999 (03 May 2013) 03 May 2013; Christoph Junghans +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 gromacs-4.6.9999.ebuild: nvcc flags dont needed anymore here 15 Mar 2013; Alexey Shvetsov gromacs-4.6.9999.ebuild, gromacs-9999.ebuild: Fix build with cuda enabled 10 Mar 2013; Christoph Junghans gromacs-4.6.9999.ebuild: added cuda build fix from gx86 09 Mar 2013; Christoph Junghans gromacs-4.6.9999.ebuild: fixed deps + doc build on darwin 06 Mar 2013; Christoph Junghans -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 gromacs-4.6.9999.ebuild, gromacs-9999.ebuild, metadata.xml: sse41 -> sse4_1 (bug #456886) + ninja has missing keywords 30 Jan 2013; Christoph Junghans gromacs-4.6.9999.ebuild, gromacs-9999.ebuild: added subslot, removed gromacs-manual blocker 30 Jan 2013; Christoph Junghans gromacs-4.6.9999.ebuild: clean up 28 Jan 2013; Christoph Junghans gromacs-4.6.9999.ebuild: added app-doc/gromacs-manual in here 21 Jan 2013; Christoph Junghans gromacs-4.6.9999.ebuild: sci-chemistry/gromacs: use cuda.eclass 21 Jan 2013; Christoph Junghans gromacs-4.6.9999.ebuild: fixed sci-chemistry/gromacs[test] 21 Jan 2013; Alexey Shvetsov gromacs-4.6.9999.ebuild: [sci-chemistry/gromacs] Drop restrict test for 4.6 21 Jan 2013; Alexey Shvetsov gromacs-4.6.9999.ebuild: [sci-chemistry/gromacs] Update 4.6 series ebuild 18 Jan 2013; Christoph Junghans gromacs-4.6.9999.ebuild: yet another update for git 18 Jan 2013; Christoph Junghans gromacs-4.6.9999.ebuild: live ebuild update 30 Dec 2012; Christoph Junghans gromacs-4.6.9999.ebuild: further clean up 29 Dec 2012; Christoph Junghans gromacs-4.6.9999.ebuild: fixed build with newer mkl 27 Dec 2012; Christoph Junghans gromacs-4.6.9999.ebuild: sci-chemistry/gromacs: clean up 26 Dec 2012; Christoph Junghans gromacs-4.6.9999.ebuild: fixed openmm suffix 26 Dec 2012; Christoph Junghans gromacs-4.6.9999.ebuild: fixed another typo 26 Dec 2012; Christoph Junghans gromacs-4.6.9999.ebuild: fixed typo 26 Dec 2012; Christoph Junghans gromacs-4.6.9999.ebuild, metadata.xml: Added mkl support 22 Dec 2012; Christoph Junghans gromacs-4.6.9999.ebuild, gromacs-9999.ebuild, metadata.xml: sync with gx86 20 Dec 2012; Christoph Junghans gromacs-4.6.9999.ebuild: fortran is gone 08 Dec 2012; Christoph Junghans gromacs-4.5.9999.ebuild, gromacs-4.6.9999.ebuild, gromacs-9999.ebuild: CMAKE_BUILD_DIR -> BUILD_DIR 30 Nov 2012; Christoph Junghans gromacs-4.6.9999.ebuild: sync with gx86 27 Nov 2012; Christoph Junghans gromacs-4.6.9999.ebuild, metadata.xml: added openmm support 19 Nov 2012; Christoph Junghans gromacs-4.6.9999.ebuild: live ebuild update 04 Oct 2012; Christoph Junghans gromacs-4.6.9999.ebuild, gromacs-9999.ebuild: live ebuild update 03 Oct 2012; Christoph Junghans gromacs-4.6.9999.ebuild, metadata.xml: hybrid stuff got merged 09 Aug 2012; Christoph Junghans gromacs-4.6.9999.ebuild: use ninja if available 25 Jul 2012; Christoph Junghans gromacs-4.5.9999.ebuild, gromacs-4.6.9999.ebuild, gromacs-9999.ebuild: added ~x86-macos 19 Jun 2012; Alexey Shvetsov 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 gromacs-4.6.9999.ebuild, metadata.xml: add support for new hybrid kernels 28 Apr 2012; Christoph Junghans gromacs-4.6.9999.ebuild: [sci-chemistry/gromacs] add more mirrors 19 Apr 2012; Alexey Shvetsov 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 gromacs-4.5.9999.ebuild, gromacs-9999.ebuild: removed obsolete call to env-update 04 Mar 2012; Christoph Junghans gromacs-4.6.9999.ebuild: reworked fortran and openmp support 12 Feb 2012; Christoph Junghans gromacs-4.6.9999.ebuild: sci-chemistry/gromacs: clean up 12 Feb 2012; Christoph Junghans gromacs-4.6.9999.ebuild: fixed threads and mpi 05 Feb 2012; Christoph Junghans gromacs-4.6.9999.ebuild: handle new vmd detection 05 Feb 2012; Christoph Junghans gromacs-4.6.9999.ebuild: added openmp support *gromacs-4.6.9999 (28 Sep 2011) 28 Sep 2011; Christoph Junghans +gromacs-4.6.9999.ebuild: Added gromacs-4.6 live version 10 Sep 2011; Christoph Junghans gromacs-4.5.9999.ebuild, gromacs-9999.ebuild: Migrate to the bash-completion-r1 eclass 18 Jul 2011; Christoph Junghans gromacs-4.5.9999.ebuild, gromacs-9999.ebuild: sync with tree 25 Jun 2011; Christoph Junghans gromacs-4.5.9999.ebuild, gromacs-9999.ebuild: migrate to git-2 25 Jun 2011; Justin Lecher gromacs-4.5.9999.ebuild, gromacs-9999.ebuild, metadata.xml: migrate from 'git' to 'git-2' 21 Jun 2011; Christoph Junghans gromacs-4.5.9999.ebuild, gromacs-9999.ebuild: only USE=fkernels needs fortran 21 Jun 2011; Justin Lecher gromacs-4.5.9999.ebuild, gromacs-9999.ebuild: Added fortran-2.eclass support 19 Jun 2011; Christoph Junghans gromacs-4.5.9999.ebuild, metadata.xml: autotools is broken 10 Apr 2011; Christoph Junghans -gromacs-4.0.9999.ebuild: remove 4.0.* (EOM) 08 Mar 2011; Christoph Junghans gromacs-4.5.9999.ebuild, gromacs-9999.ebuild: added fixes from 4.5.3-r4 07 Mar 2011; Justin Lecher 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 -gromacs-4.5.3-r3.ebuild: InCVS *gromacs-4.5.3-r3 (17 Feb 2011) 17 Feb 2011; Christoph Junghans -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 -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 gromacs-9999.ebuild: add back live manual 17 Jan 2011; Christoph Junghans gromacs-9999.ebuild: QA fixes 16 Dec 2010; Justin Lecher gromacs-4.0.9999.ebuild, gromacs-4.5.9999.ebuild, gromacs-9999.ebuild: Removal of fortran.eclass, #348851 25 Nov 2010; Alexey Shvetsov -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 +gromacs-4.5.3.ebuild: version bump *gromacs-4.5.2 (30 Oct 2010) 30 Oct 2010; Christoph Junghans +gromacs-4.5.2.ebuild: Version bump 25 Oct 2010; Christoph Junghans gromacs-4.5.9999.ebuild, gromacs-9999.ebuild, metadata.xml: added natural vmd support (bug #340651#c8) 21 Oct 2010; Christoph Junghans gromacs-4.5.9999.ebuild, metadata.xml: added vmd use flag 17 Oct 2010; Christoph Junghans gromacs-4.0.7-r5.ebuild, gromacs-4.0.9999.ebuild: rename manual in distfiles 16 Oct 2010; Christoph Junghans 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 +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 -gromacs-4.5_beta3.ebuild, +gromacs-4.5.1.ebuild: version bump *gromacs-4.5_beta3 (11 Aug 2010) 11 Aug 2010; Alexey Shvetsov 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 -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 +gromacs-4.5_beta1.ebuild, +gromacs-4.5.9999.ebuild, gromacs-9999.ebuild: Version bump 24 Jul 2010; Alexey Shvetsov gromacs-9999.ebuild: ffamber officialy shipped with gromacs from now on 08 Jul 2010; Christoph Junghans gromacs-4.0.9999.ebuild, gromacs-9999.ebuild: fix for bug #301854 04 Jul 2010; Christoph Junghans 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 gromacs-4.0.9999.ebuild, gromacs-9999.ebuild: Fixes for Bug #326331 28 Jun 2010; Christoph Junghans 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 +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 +gromacs-4.0.7-r2.ebuild: Add ffamber port to gromacs 18 Feb 2010; Alexey Shvetsov gromacs-9999.ebuild, -files/gromacs-9999-dirent.patch: Dropped unneded patches. They all were applied to git master 18 Feb 2010; Alexey Shvetsov 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 gromacs-9999.ebuild, +files/gromacs-9999-as-needed.patch: added as-needed fix 06 Feb 2010; Christoph Junghans -gromacs-4.0.7-r1.ebuild, -files/gromacs-4.0.9999-docdir.patch: InCvs 06 Feb 2010; Christoph Junghans gromacs-4.0.9999.ebuild, gromacs-9999.ebuild: docdir patch went upstream 01 Feb 2010; Christoph Junghans 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 -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 gromacs-4.0.9999.ebuild, gromacs-9999.ebuild: fixed --as-needed confusion 21 Jan 2010; Christoph Junghans -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 files/gromacs-4.0.5-docdir.patch: docdir -> htmldir 30 Nov 2009; Christoph Junghans 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 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 +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 +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 gromacs-4.0.4.ebuild: Fixed some repoman errors 22 Feb 2009; Jeff Gardner 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 -gromacs-4.0.3-r1.ebuild, +gromacs-4.0.4.ebuild: Version bump\! 20 Feb 2009; Alexey Shvetsov gromacs-4.0.3-r1.ebuild: Fix typo *gromacs-4.0.3-r1 (20 Feb 2009) 20 Feb 2009; Alexey Shvetsov +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 -gromacs-3.3.3.ebuild, +gromacs-4.0.3.ebuild: Version bump