path: root/sci-chemistry/gromacs/ChangeLog

# ChangeLog for sci-chemistry/gromacs
# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.80 2011/04/04 21:26:20 alexxy Exp $

*gromacs-4.5.4-r1 (04 Apr 2011)

  04 Apr 2011; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-4.5.4-r1.ebuild:
  Fix QA execstack bug #361687

  04 Apr 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.0.7-r5.ebuild,
  -gromacs-4.5.3.ebuild, -gromacs-4.5.3-r3.ebuild:
  Removed old

  04 Apr 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.4.ebuild:
  Removed sse use flag (fixed bug #361933)

  02 Apr 2011; Raúl Porcel <armin76@gentoo.org> gromacs-4.5.3-r4.ebuild:
  alpha/sparc stable wrt #357017

  02 Apr 2011; Kacper Kowalik <xarthisius@gentoo.org> gromacs-4.5.4.ebuild:
  Bump to EAPI=4 for REQUIRED_USE on fkernels and threads wrt #361687. Mark
  ppc64 stable wrt #357017

  02 Apr 2011; Samuli Suominen <ssuominen@gentoo.org> gromacs-4.5.4.ebuild:
  Remove illegal QA_EXECSTACK for source based package.

  02 Apr 2011; Kacper Kowalik <xarthisius@gentoo.org> gromacs-4.5.4.ebuild:
  Revert to ~ppc64

  25 Mar 2011; Kacper Kowalik <xarthisius@gentoo.org> gromacs-4.5.4.ebuild:
  ppc64 stable wrt #357017

  22 Mar 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.4.ebuild:
  New manual, added back pkg-config to DEPEND

*gromacs-4.5.4 (21 Mar 2011)

  21 Mar 2011; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-4.5.4.ebuild:
  Version bump

  17 Mar 2011; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.5.3-r4.ebuild:
  Clean up ebuild a bit

  09 Mar 2011; Thomas Kahle <tomka@gentoo.org> gromacs-4.5.3-r4.ebuild:
  x86 stable per bug 357017

  08 Mar 2011; Markos Chandras <hwoarang@gentoo.org> gromacs-4.5.3-r4.ebuild:
  Stable on amd64 wrt bug #357017

*gromacs-4.5.3-r4 (05 Mar 2011)

  05 Mar 2011; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-4.5.3-r4.ebuild:
  Rework using of external blas & lapack. Also fix issues with prefix and mpi
  build

  02 Mar 2011; Justin Lecher <jlec@gentoo.org> gromacs-4.0.7-r4.ebuild,
  gromacs-4.0.7-r5.ebuild, gromacs-4.5.3.ebuild, gromacs-4.5.3-r3.ebuild:
  Correct Slots for gtk 3 introduction to tree

*gromacs-4.5.3-r3 (19 Feb 2011)

  19 Feb 2011; Christoph Junghans <ottxor@gentoo.org> +gromacs-4.5.3-r3.ebuild:
  Version bump (fixes bug #339837)

  04 Jan 2011; Jeremy Olexa <darkside@gentoo.org> metadata.xml:
  QA: Remove redundant local use flag description

  16 Dec 2010; Justin Lecher <jlec@gentoo.org> gromacs-4.0.7-r4.ebuild,
  gromacs-4.0.7-r5.ebuild, gromacs-4.5.3.ebuild:
  Removal of fortran.eclass, #348851

*gromacs-4.5.3 (25 Nov 2010)
*gromacs-4.0.7-r5 (25 Nov 2010)

  25 Nov 2010; Alexey Shvetsov <alexxy@gentoo.org> -gromacs-4.0.4.ebuild,
  -files/gromacs-4.0.4-configure-gfortran.patch,
  -files/gromacs-4.0.4-sparc-cyclecounter.patch, -gromacs-4.0.5.ebuild,
  gromacs-4.0.7-r4.ebuild, +gromacs-4.0.7-r5.ebuild,
  -files/gromacs-4.0.9999-ccache.patch,
  -files/gromacs-4.0.9999-configure-gfortran.patch, -gromacs-4.5.1.ebuild,
  +gromacs-4.5.3.ebuild:
  Version bump. Clean up old versions. Thanks to Christoph Junghans

  25 Oct 2010; Samuli Suominen <ssuominen@gentoo.org>
  gromacs-4.0.7-r4.ebuild:
  ppc64 stable wrt #326151

  12 Oct 2010; Raúl Porcel <armin76@gentoo.org> gromacs-4.0.7-r4.ebuild:
  sparc stable wrt #326151

*gromacs-4.5.1 (14 Sep 2010)

  14 Sep 2010; Alexey Shvetsov <alexxy@gentoo.org> -gromacs-4.0.7-r3.ebuild,
  +gromacs-4.5.1.ebuild:
  Version bump. Now it can use ffambber. And threads. Many thanks to
  Christoph Junghans

  11 Sep 2010; Tobias Klausmann <klausman@gentoo.org>
  gromacs-4.0.7-r4.ebuild:
  Stable on alpha, bug #326151

  17 Jul 2010; Kacper Kowalik <xarthisius@gentoo.org>
  gromacs-4.0.7-r3.ebuild, gromacs-4.0.7-r4.ebuild,
  -files/gromacs-4.0.7_upstream2010-06-08.patch.gz:
  Move gromacs-4.0.7_upstream2010-06-08.patch.gz to gentoo mirrors. Fixes
  bug 328659. Thanks to Samuli for the report

  10 Jul 2010; Christian Faulhammer <fauli@gentoo.org>
  gromacs-4.0.7-r4.ebuild:
  stable x86, bug 326151

  09 Jul 2010; Pacho Ramos <pacho@gentoo.org> gromacs-4.0.7-r4.ebuild:
  amd64 stable, bug 326151

  08 Jul 2010; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.0.7-r4.ebuild:
  Fix typo in ebuild for prefix setup

*gromacs-4.0.7-r4 (04 Jul 2010)

  04 Jul 2010; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-4.0.7-r4.ebuild:
  Fix bug #326331. thanks to Christoph Junghans

  05 Jul 2010; Alexey Shvetsov <alexxy@gentoo.org> -gromacs-3.3.1-r1.ebuild,
  -gromacs-3.3.3.ebuild:
  Gromacs 3.x moved to sci overlay since its unmaintained and no longer
  supported

*gromacs-4.0.7-r3 (27 Jun 2010)

  27 Jun 2010; Alexey Shvetsov <alexxy@gentoo.org> -gromacs-4.0.7.ebuild,
  -gromacs-4.0.7-r1.ebuild, +gromacs-4.0.7-r3.ebuild,
  -files/gromacs-4.0.7-docdir.patch,
  +files/gromacs-4.0.7_upstream2010-06-08.patch:
  Added patches from upstream stable branch. Added ffamber ports. Also fixed
  bugs #301854 and #284431. Big thank to Christoph Junghans

  24 Jun 2010; Justin Lecher <jlec@gentoo.org> gromacs-3.3.1-r1.ebuild,
  gromacs-3.3.3.ebuild:
  Blocking sci-mathematics/num-utils, #257566

*gromacs-4.0.7-r1 (24 Jan 2010)

  24 Jan 2010; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-4.0.7-r1.ebuild,
  +files/gromacs-4.0.9999-ccache.patch,
  +files/gromacs-4.0.9999-configure-gfortran.patch,
  +files/gromacs-4.0.9999-docdir.patch:
  Fix bug #302048. thanks to Christoph Junghans

  18 Jan 2010; Raúl Porcel <armin76@gentoo.org> gromacs-4.0.5.ebuild:
  alpha stable

  08 Dec 2009; Alexey Shvetsov <alexxy@gentoo.org>
  +files/gromacs-4.0.7-docdir.patch:
  Add missing patch. thanks to rei4dan

*gromacs-4.0.7 (07 Dec 2009)

  07 Dec 2009; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-4.0.7.ebuild:
  Version bump

  31 Oct 2009; Raúl Porcel <armin76@gentoo.org> gromacs-4.0.5.ebuild:
  sparc stable wrt #260995

  30 Oct 2009; Markus Meier <maekke@gentoo.org> gromacs-4.0.5.ebuild:
  amd64/x86 stable, bug #260995

  26 Sep 2009; Brent Baude <ranger@gentoo.org> gromacs-4.0.4.ebuild:
  Marking gromacs-4.0.4 ppc64 for bug 260995

  28 Aug 2009; William Hubbs <williamh@gentoo.org> metadata.xml:
  new global use flag "zsh-completion"

  15 May 2009; Markus Meier <maekke@gentoo.org> gromacs-4.0.4.ebuild:
  amd64 stable, bug #260995

  14 May 2009; Alexey Shvetsov <alexxy@gentoo.org> -gromacs-4.0.3.ebuild,
  +gromacs-4.0.5.ebuild:
  Drop old version; Fix keywords for 4.0.5. Sorry =)

*gromacs-4.0.5 (14 May 2009)

  14 May 2009; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-4.0.5.ebuild:
  Bump new version with bugfixes. Bug #269754

  14 May 2009; Christian Faulhammer <fauli@gentoo.org> gromacs-4.0.4.ebuild:
  stable x86, bug 260995

  13 May 2009; Tobias Klausmann <klausman@gentoo.org> gromacs-4.0.4.ebuild:
  Stable on alpha, bug #260995

  10 May 2009; Ferris McCormick <fmccor@gentoo.org> gromacs-4.0.4.ebuild:
  Sparc stable, Bug #260995, which see for discussion.

  10 May 2009; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.0.4.ebuild,
  +files/gromacs-4.0.4-sparc-cyclecounter.patch:
  Add upstream fix for sparc bug #260995

*gromacs-4.0.4 (20 Apr 2009)

  20 Apr 2009; Alexey Shvetsov <alexxy@gentoo.org>
  +files/gromacs-4.0.4-configure-gfortran.patch, metadata.xml,
  -gromacs-4.0.ebuild, -gromacs-4.0.2.ebuild, +gromacs-4.0.4.ebuild:
  Add new gromacs 4.0.4

  08 Mar 2009; Markus Meier <maekke@gentoo.org> gromacs-4.0.3.ebuild:
  amd64/x86 stable, bug #260995

  22 Jan 2009; Jeff Gardner <je_fro@gentoo.org> +gromacs-4.0.3.ebuild:
  Latest version.

*gromacs-4.0.2 (04 Jan 2009)

  04 Jan 2009; Jeff Gardner <je_fro@gentoo.org> +gromacs-4.0.2.ebuild:
  Latest version, thanks to Alexxy for the prod :)

*gromacs-4.0 (12 Oct 2008)

  12 Oct 2008; Jeff Gardner <je_fro@gentoo.org> +gromacs-4.0.ebuild:
  Latest version, closing bug #241474 thanks to Alexey Shvetsov

  06 Oct 2008; Jeff Gardner <je_fro@gentoo.org> ChangeLog, Manifest:
  Fixing changelog to reflect addition of gromacs-3.3.3.ebuild

*gromacs-3.3.3 (06 Oct 2008)

  06 Oct 2008; Jeff Gardner <je_fro@gentoo.org> +gromacs-3.3.3.ebuild:
  Latest stable version, thanks to Alexey Shvetsov, closing bug #193532

  06 Aug 2008; Ulrich Mueller <ulm@gentoo.org> metadata.xml:
  Add USE flag description to metadata wrt GLEP 56.

  27 Jun 2008; Ulrich Mueller <ulm@gentoo.org> gromacs-3.3.1-r1.ebuild:
  Change dependency from virtual/motif to x11-libs/openmotif, bug 224749.

  23 Jun 2008; Jeff Gardner <je_fro@gentoo.org>
  -files/gromacs-alpha-axp_asm.patch, -files/gromacs-ppc64-altivec.patch,
  -gromacs-3.2.1-r1.ebuild, gromacs-3.3.1-r1.ebuild:
  Moving disco manpage to g_disco, fixing bug 210083.

  03 Jun 2008; Jeff Gardner <je_fro@gentoo.org> gromacs-3.3.1-r1.ebuild:
  No altivec patching with this gromacs version. Thanks to Maik Nijhuis in
  bug #224773.

  13 Jun 2007; Raúl Porcel <armin76@gentoo.org> gromacs-3.3.1-r1.ebuild:
  Modify the ebuild so it compiles on alpha and mark stable wrt #168182

  17 Mar 2007; Steve Dibb <beandog@gentoo.org> gromacs-3.3.1-r1.ebuild:
  amd64 stable, bug 168182

  11 Mar 2007; Sven Wegener <swegener@gentoo.org> gromacs-3.3.1-r1.ebuild:
  Properly indent src_compile, thanks to ferringb.

  08 Mar 2007; Jason Wever <weeve@gentoo.org> gromacs-3.3.1-r1.ebuild:
  Stable on SPARC wrt bug #168182.

  07 Mar 2007; Jeff Gardner <je_fro@gentoo.org> gromacs-3.3.1-r1.ebuild:
  Fix up the demo script so the xterms stay open.

  24 Feb 2007; Raúl Porcel <armin76@gentoo.org> gromacs-3.3.1-r1.ebuild:
  x86 stable wrt bug 168182

  23 Feb 2007; Markus Rothe <corsair@gentoo.org> gromacs-3.3.1-r1.ebuild:
  Stable on ppc64; bug #168182

  07 Jan 2007; Danny van Dyk <kugelfang@gentoo.org> -gromacs-3.2.1.ebuild,
  -gromacs-3.3.ebuild, -gromacs-3.3.1.ebuild:
  QA: Removed unused versions.

  20 Dec 2006; Jeff Gardner <je_fro@gentoo.org> gromacs-3.3.1-r1.ebuild:
  Small fix of DEPEND

  20 Dec 2006; Jeff Gardner <je_fro@gentoo.org> ChangeLog:
  Many thanks to Rene Meier, Shvetsov Alexey Mathias Weigt, dawe, and Mike
  Hlavac for their contributions to gromacs-3.3.1-r1.

*gromacs-3.3.1-r1 (17 Dec 2006)

  17 Dec 2006; Jeff Gardner <je_fro@gentoo.org> +gromacs-3.3.1-r1.ebuild:
  Fixup to address bugs 135146 118421 and 147614.

  20 Sep 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
  (#148281) Change herd to sci-chemistry from sci.

*gromacs-3.3.1 (08 Aug 2006)

  08 Aug 2006; Markus Dittrich <markusle@gentoo.org> +gromacs-3.3.1.ebuild:
  Version bump. Ebuild now inherits the fortran.eclass and forces
  the use of g77 since gfortran is presently missing some of the 
  fortran intrinsics needed by gromacs. See bug #141672.

  05 Aug 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
  Remove myself as maintainer, anyone feel free to work on this, although I'll
  continue to do so as well.

  07 Jul 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
  Update to my new email address.

  25 Jun 2006; Donnie Berkholz <dberkholz@gentoo.org>; gromacs-3.2.1.ebuild,
  gromacs-3.2.1-r1.ebuild, gromacs-3.3.ebuild:
  (#116346) Change xml2 USE flag to xml.

  07 May 2006; Markus Rothe <corsair@gentoo.org> gromacs-3.2.1-r1.ebuild:
  Stable on ppc64; bug #89969

*gromacs-3.3 (14 Oct 2005)

  14 Oct 2005; Donnie Berkholz <dberkholz@gentoo.org>; +gromacs-3.3.ebuild:
  (#109184) Bump. Main change in ebuild is adding a check for fftw built w/
  mpi if trying to build w/ mpi. One of the more interesting upstream changes
  is the addition of x86-64 and ia64 assembly.

  05 Aug 2005; <omkhar@gentoo.org> +files/gromacs-ppc64-altivec.patch,
  gromacs-3.2.1-r1.ebuild:
  Added patch back as binary due to metatags. Made sure patch only applies when ppc64 && altivec

*gromacs-3.2.1-r1 (04 Aug 2005)

  04 Aug 2005; <omkhar@gentoo.org> +files/gromacs-ppc64-altivec.patch,
  +gromacs-3.2.1-r1.ebuild:
  Added ppc64 support and altivec support

  24 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
  +gromacs-3.2.1.ebuild:
  Moved from app-sci/gromacs to sci-chemistry/gromacs.

  06 Jun 2004; Danny van Dyk <kugelfang@gentoo.org> gromacs-3.2.1.ebuild:
  Marked stable on amd64.

  22 Apr 2004; Donnie Berkholz <dberkholz@gentoo.org>;
  -files/gromacs-3.2-all-static-fix.patch, -gromacs-3.1.4-r1.ebuild,
  -gromacs-3.1.4-r2.ebuild, gromacs-3.2.1.ebuild, -gromacs-3.2.ebuild:
  Mark 3.2.1 stable on x86. Remove old versions.

  22 Apr 2004; Donnie Berkholz <dberkholz@gentoo.org>;
  gromacs-3.1.4-r1.ebuild, gromacs-3.2.1.ebuild:
  Add app-shells/tcsh to dependencies (#48691).

  22 Apr 2004; Danny van Dyk <kugelfang@gentoo.org> gromacs-3.2.1.ebuild:
  marked ~amd64

*gromacs-3.2.1 (02 Apr 2004)

  02 Apr 2004; Donnie Berkholz <dberkholz@gentoo.org>; gromacs-3.2.1.ebuild:
  Version bump, closes #44377.

*gromacs-3.2 (29 Feb 2004)

  29 Feb 2004; Donnie Berkholz <dberkholz@gentoo.org>; gromacs-3.2.ebuild,
  files/gromacs-3.2-all-static-fix.patch:
  Version bump. New xml2 USE flag.

*gromacs-3.1.4-r2 (28 Feb 2004)

  28 Feb 2004; Donnie Berkholz <dberkholz@gentoo.org>;
  gromacs-3.1.4-r2.ebuild:
  Closing bug #42989 by installing binaries to /usr/bin. Also discovered libs
  needed to be installed to /usr/lib. Enabled assembly for Alphas too, if any
  Alpha user ever tries this.

  04 Oct 2003; Donnie Berkholz <dberkholz@gentoo.org>; gromacs-3.1.3.ebuild,
  gromacs-3.1.4.ebuild:
  Pulling old versions.

  04 Oct 2003; Donnie Berkholz <dberkholz@gentoo.org>;
  gromacs-3.1.4-r1.ebuild:
  Fixing fftw dep. Won't compile against fftw-3 yet, in part because it looks
  for fftw3.h instead of fftw.h, and in part because MPI doesn't work in fftw-3
  yet.

*gromacs-3.1.4-r1 (23 Mar 2003)

  23 Mar 2003; George Shapovalov <george@gentoo.org> gromacs-3.1.4-r1.ebuild :
  added mpi support, lam-mpi is the only working implementation at the moment.
  !IMPORTANT!:
  Since portage cannot at present check whether optional dependencies of dependencies were turned on, 
  please check yourself that gromacs and fftw have identical mpi setting.
  Generally USE="mpi" emerge gromacs should work fine if you did not install fftw previously (with 
  different mpi off for example).

*gromacs-3.1.4 (08 Nov 2002)

  08 Nov 2002; George Shapovalov <george@gentoo.org> gromacs-3.1.4.ebuild, files/digest-gromacs-3.1.4 :

  new version.
  !!!IMPORTANT!!!
  I changed --prefix to point to /usr for FHS compliance.
  Now the binaries and the libs are getting installed into
  /usr/i686-pc-linux-gnu/{bin,lib} correspondingly and the data into /usr/share/gromacs-${PV}
  This seems to fit well in the existing direcory structure and does not conflict with gcc.

*gromacs-3.1.3 (27 Apr 2002)
  
  27 Apr 2002; George Shapovalov <george@gentoo.org> all_files :

  initial release.