Rossen Apostolov [Mon, 6 Sep 2010 19:39:36 +0000 (21:39 +0200)]
Added a note that running in double precision is slower.
Rossen Apostolov [Mon, 6 Sep 2010 18:47:04 +0000 (20:47 +0200)]
A lot of CMake options are now marked as advanced since most users won't need to modify them.
Sander Pronk [Mon, 6 Sep 2010 12:43:05 +0000 (14:43 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Sander Pronk [Mon, 6 Sep 2010 12:42:51 +0000 (14:42 +0200)]
Fixed reading of older .xvg file formats in g_bar
Teemu Murtola [Mon, 6 Sep 2010 11:03:05 +0000 (13:03 +0200)]
Improved package version handling in CMake.
Options related to versioning are now marked as advanced (bug #539).
PROJECT_VERSION is no longer cached to keep build trees automatically
up-to-date when the version is increased. To override the default
version, there is a new cache variable CUSTOM_VERSION_STRING.
Also updated CPack version to match the actual version.
Sander Pronk [Mon, 6 Sep 2010 10:51:18 +0000 (12:51 +0200)]
Fixed misinterpretation of -b and -e in g_bar.
Sander Pronk [Fri, 3 Sep 2010 07:08:12 +0000 (09:08 +0200)]
Added missing windows thread files to distribution list.
Rossen Apostolov [Thu, 2 Sep 2010 12:18:13 +0000 (14:18 +0200)]
Another missing CMake file.
Rossen Apostolov [Thu, 2 Sep 2010 10:16:17 +0000 (12:16 +0200)]
Updated the version numbers to 4.5.1.
Accidentally tagged the previous commit as 4.5.1 before
updating them.
Rossen Apostolov [Thu, 2 Sep 2010 09:57:09 +0000 (11:57 +0200)]
Added for distribution missing CMake specific files.
Mark Abraham [Thu, 2 Sep 2010 05:52:40 +0000 (15:52 +1000)]
Fix spelling error
Rossen Apostolov [Wed, 1 Sep 2010 20:01:49 +0000 (22:01 +0200)]
New release: 4.5 (final). Yay!!!
Erik Lindahl [Wed, 1 Sep 2010 18:56:08 +0000 (20:56 +0200)]
Removed lots of unnecessary messages to stdout from g_hbond
Erik Lindahl [Wed, 1 Sep 2010 18:55:27 +0000 (20:55 +0200)]
Added Gerrit to the list of authors. Sorry for forgetting you Gerrit :-)
Rossen Apostolov [Wed, 1 Sep 2010 16:44:01 +0000 (18:44 +0200)]
Added g_rmsdist and g_rotmat to the CMake build system
Sander Pronk [Wed, 1 Sep 2010 13:51:37 +0000 (15:51 +0200)]
Shared libraries off by default on Windows.
Carsten Kutzner [Wed, 1 Sep 2010 13:27:34 +0000 (15:27 +0200)]
Fixed make_edi when no fitting was done in g_covar
Sander Pronk [Wed, 1 Sep 2010 12:23:53 +0000 (14:23 +0200)]
Added support for PGI atomics in thread_mpi.
Szilard Pall [Wed, 1 Sep 2010 10:42:14 +0000 (12:42 +0200)]
Updated list of supported GPUs
Mark Abraham [Wed, 1 Sep 2010 09:58:32 +0000 (19:58 +1000)]
Formatting fixes to documentation
Sander Pronk [Wed, 1 Sep 2010 09:41:27 +0000 (11:41 +0200)]
Final thread_mpi fixes (ppc works, no deadlocks on any system).
Mark Abraham [Wed, 1 Sep 2010 09:10:02 +0000 (19:10 +1000)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Mark Abraham [Wed, 1 Sep 2010 08:48:11 +0000 (18:48 +1000)]
make_opt.html now doesn't use <h4>, rather it uses <b>. This makes things more consistent for turning all the relevant bold bits into monospace for the LaTeX manual. mkmdp has been updated accordingly.
Mark Abraham [Wed, 1 Sep 2010 08:47:03 +0000 (18:47 +1000)]
General fixes
Rossen Apostolov [Wed, 1 Sep 2010 07:31:25 +0000 (09:31 +0200)]
Small update of the GPU related documentation.
Sander Pronk [Wed, 1 Sep 2010 07:26:12 +0000 (09:26 +0200)]
Code reorg in thread_mpi
hess [Wed, 1 Sep 2010 08:46:33 +0000 (10:46 +0200)]
cleaner implementation of close_nblist with comments on the assembly kernel requirement
Rossen Apostolov [Wed, 1 Sep 2010 07:31:25 +0000 (09:31 +0200)]
Small update of the GPU related documentation.
Rossen Apostolov [Wed, 1 Sep 2010 07:30:11 +0000 (09:30 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Sander Pronk [Wed, 1 Sep 2010 07:26:12 +0000 (09:26 +0200)]
Code reorg in thread_mpi
Rossen Apostolov [Wed, 1 Sep 2010 07:23:02 +0000 (09:23 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Erik Lindahl [Tue, 31 Aug 2010 19:48:22 +0000 (21:48 +0200)]
Made the options program for the latex manual compile again
Erik Lindahl [Tue, 31 Aug 2010 19:43:05 +0000 (21:43 +0200)]
Fixed typo in src/contrib/Makefile.am
Rossen Apostolov [Tue, 31 Aug 2010 19:35:38 +0000 (21:35 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Erik Lindahl [Tue, 31 Aug 2010 19:20:41 +0000 (21:20 +0200)]
Fixed incorrect call to gmx_finalize() in gmx_pme_error()
Erik Lindahl [Tue, 31 Aug 2010 18:49:28 +0000 (20:49 +0200)]
Added final newline to avoid compiler warning in sfactor.h
Rossen Apostolov [Tue, 31 Aug 2010 18:19:43 +0000 (20:19 +0200)]
OpenMM now accepts cut-off method, since it's needed for implicit solvent calculations.
Erik Lindahl [Tue, 31 Aug 2010 18:10:10 +0000 (20:10 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Erik Lindahl [Tue, 31 Aug 2010 18:10:04 +0000 (20:10 +0200)]
Added Cpack support
Sander Pronk [Tue, 31 Aug 2010 17:51:39 +0000 (19:51 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Sander Pronk [Tue, 31 Aug 2010 17:51:01 +0000 (19:51 +0200)]
Fixed memory ordering issue on ppc with gcc&xlc.
Szilard Pall [Tue, 31 Aug 2010 15:25:37 +0000 (17:25 +0200)]
Merge branch 'release-4-5-patches' of git://git.gromacs.org/gromacs into release-4-5-patches
Szilard Pall [Tue, 31 Aug 2010 15:20:22 +0000 (17:20 +0200)]
Improved option disabling on switching to OpenMM build in a non-clean build tree
When switching from CPU->GPU in a non-clean build tree it seems to work fine,
a few options are disabled/modified from the default values.
However, when doings GPU->CPU switch, the code builds, but the default values
(fftw3, threads, SSE) are not restores and need to be changed manually.
Szilard Pall [Tue, 31 Aug 2010 15:18:24 +0000 (17:18 +0200)]
fixed/improved cmake FFTW3 detection
Sander Pronk [Tue, 31 Aug 2010 14:56:39 +0000 (16:56 +0200)]
thread_mpi fixes: gcc works on power7, xlc still does not..
Szilard [Tue, 31 Aug 2010 14:43:37 +0000 (16:43 +0200)]
Removed leftover debug message from openmm_wrapper
Teemu Murtola [Tue, 31 Aug 2010 09:56:52 +0000 (11:56 +0200)]
Fixed CMake libxml2 detection.
Berk Hess [Tue, 31 Aug 2010 09:46:10 +0000 (11:46 +0200)]
avoided creation of neighborlists without j-particles
Erik Lindahl [Tue, 31 Aug 2010 08:29:56 +0000 (10:29 +0200)]
Added label writing capability to editconf when used with an index file
Erik Lindahl [Tue, 31 Aug 2010 07:48:52 +0000 (09:48 +0200)]
Added check for <2 frames when autocorrelation is requested in g_hbond()
Erik Lindahl [Tue, 31 Aug 2010 06:52:52 +0000 (08:52 +0200)]
Moved buggy and unsupported g_sdf to contrib directory and removed its documentation from default build
Sander Pronk [Tue, 31 Aug 2010 06:24:42 +0000 (08:24 +0200)]
Fixed warning in gmx_energy
hess [Mon, 30 Aug 2010 21:03:12 +0000 (23:03 +0200)]
g_rms now allows for more atoms in trx than tpr
hess [Mon, 30 Aug 2010 19:26:44 +0000 (21:26 +0200)]
small changes to grompp documentation
Christoph Junghans [Mon, 30 Aug 2010 15:02:19 +0000 (17:02 +0200)]
fixed Template.mak
Christoph Junghans [Mon, 30 Aug 2010 13:21:44 +0000 (15:21 +0200)]
fixed a typo in old libxdrf fortran wrapper
Erik Lindahl [Mon, 30 Aug 2010 13:00:38 +0000 (15:00 +0200)]
Improved handling of include paths in gmxcpp from Teemu
Christoph Junghans [Mon, 30 Aug 2010 12:05:01 +0000 (14:05 +0200)]
forcerec.c: added missing int
Teemu Murtola [Mon, 30 Aug 2010 11:00:14 +0000 (13:00 +0200)]
Cosmetic fix to include/CMakeLists.txt.
Now uses INCL_INSTALL_DIR for consistency instead of specifying the
directory explicitly; all other subdirectories use the corresponding
variables.
Sander Pronk [Mon, 30 Aug 2010 09:53:42 +0000 (11:53 +0200)]
grompp calculates output size with dh data estimate.
Sander Pronk [Mon, 30 Aug 2010 08:05:10 +0000 (10:05 +0200)]
Clearer error messages in g_energy.
Sander Pronk [Mon, 30 Aug 2010 07:55:59 +0000 (09:55 +0200)]
Fixed the g_energy -odh option to be less confusing.
hess [Mon, 30 Aug 2010 06:40:44 +0000 (08:40 +0200)]
Corrected trjconv check for topology presence, see bugzilla 526
Mark Abraham [Mon, 30 Aug 2010 04:59:48 +0000 (14:59 +1000)]
Made a pdb2gmx message less cryptic when it finds multiple copies of a force field
Sander Pronk [Sun, 29 Aug 2010 16:58:48 +0000 (18:58 +0200)]
Made the dhdl_derivatives option do something when separate_dhdl_file=yes
Erik Lindahl [Fri, 27 Aug 2010 21:20:45 +0000 (23:20 +0200)]
Added longer list of authors...
Erik Lindahl [Fri, 27 Aug 2010 20:22:54 +0000 (22:22 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Erik Lindahl [Fri, 27 Aug 2010 20:22:40 +0000 (22:22 +0200)]
Added check for SSE2 support to use generalized born kernels
Christoph Junghans [Fri, 27 Aug 2010 19:09:51 +0000 (21:09 +0200)]
added a missing include to sighandler.h
Roland Schulz [Thu, 26 Aug 2010 22:44:46 +0000 (15:44 -0700)]
Revert "Parenthesis around comparisons and no <= or >= for xlc"
This reverts commit
51c81c1e7c833a5b947019ab8840a75407590b16.
Roland Schulz [Fri, 27 Aug 2010 19:06:37 +0000 (15:06 -0400)]
fix logic to convert GMX_INTEGER_BIG_ENDIAN to ARCH_IS_BIG_ENDIAN
Erik Lindahl [Fri, 27 Aug 2010 18:44:04 +0000 (20:44 +0200)]
Added trjconv check for topology prescence, see bugzilla 526
Rossen Apostolov [Fri, 27 Aug 2010 18:17:06 +0000 (20:17 +0200)]
New release 4.5-beta4
Erik Lindahl [Fri, 27 Aug 2010 17:45:23 +0000 (19:45 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Erik Lindahl [Fri, 27 Aug 2010 17:45:07 +0000 (19:45 +0200)]
Fixed gmxcpp to always use unix path separators in internal names (just like cpp)
Roland Schulz [Fri, 27 Aug 2010 17:11:07 +0000 (13:11 -0400)]
Parenthesis around comparisons and no <= or >= for xlc
Sander Pronk [Fri, 27 Aug 2010 16:41:33 +0000 (18:41 +0200)]
Fixed begin and end times in g_bar.
Erik Lindahl [Fri, 27 Aug 2010 16:40:53 +0000 (18:40 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Erik Lindahl [Fri, 27 Aug 2010 16:40:41 +0000 (18:40 +0200)]
Fixed another uninitialized variable warning in gmx_energy.c
Erik Lindahl [Fri, 27 Aug 2010 14:59:00 +0000 (16:59 +0200)]
Add current path (./) to topol.top include when force field was local
Sander Pronk [Fri, 27 Aug 2010 09:59:46 +0000 (11:59 +0200)]
More documentation for g_bar.
Erik Lindahl [Fri, 27 Aug 2010 09:49:29 +0000 (11:49 +0200)]
Dont write EOF warnings to stdout every time we checkpoint if the file size==0
Erik Lindahl [Fri, 27 Aug 2010 08:58:48 +0000 (10:58 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Erik Lindahl [Fri, 27 Aug 2010 08:58:36 +0000 (10:58 +0200)]
Fixed first statemement occuring before variable declarations in gmx_pme_error()
Sander Pronk [Fri, 27 Aug 2010 08:49:17 +0000 (10:49 +0200)]
Some documentation changes.
Sander Pronk [Fri, 27 Aug 2010 07:57:35 +0000 (09:57 +0200)]
Some documentation changes.
Erik Lindahl [Thu, 26 Aug 2010 22:21:02 +0000 (00:21 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Erik Lindahl [Thu, 26 Aug 2010 22:18:55 +0000 (00:18 +0200)]
Modified pdb2gmx to automatically pick the force field from the current directory
if a choice is specified with the -ff option, even if others exist. We still
print a notice about it. The full include paths were also removed from the topology,
but we now print information about where the FF was picked up from, and a notice
that this location must be included when processing it if it is a non-standard one.
Rossen Apostolov [Thu, 26 Aug 2010 21:09:18 +0000 (23:09 +0200)]
Modified the OpenMM wrapper interface to support the strange CUDA platform implementation.
The CUDA platform in OpenMM does not allow the user to generate more
than one instance of a force kernel object. That requires to pack
force field terms that have the same form into one instance,
e.g. Urey-Bradley and Bond/Angle, and the harmonic dihedrals.
Rossen Apostolov [Thu, 26 Aug 2010 20:51:48 +0000 (22:51 +0200)]
Added the g_pme_error tool from Florian Dommert. Thanks!
Rossen Apostolov [Thu, 26 Aug 2010 18:02:56 +0000 (20:02 +0200)]
Fixed hardcoded OpenMM library name.
If OpenMM is compiled with debugging information, the build
attaches _d to the library names. Now CMake will be able to
link against them also.
Sander Pronk [Thu, 26 Aug 2010 16:20:55 +0000 (18:20 +0200)]
gmx_bar now works with derivative histogram sets.
Fixed several warnings.
Erik Lindahl [Thu, 26 Aug 2010 15:59:48 +0000 (17:59 +0200)]
Fixed pointer typo in patch from Alexey Shvetsov
Erik Lindahl [Thu, 26 Aug 2010 15:57:32 +0000 (17:57 +0200)]
Added PBC checking patch to g_cluster from Alexey Shvetsov (Bugzilla 526)
Erik Lindahl [Thu, 26 Aug 2010 15:44:23 +0000 (17:44 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Erik Lindahl [Thu, 26 Aug 2010 15:44:19 +0000 (17:44 +0200)]
Modified pdb2gmx to not accept extra hydrogen atoms at the N-terminus
Sander Pronk [Thu, 26 Aug 2010 15:16:01 +0000 (17:16 +0200)]
Free energy histogram bug fixes.
Erik Lindahl [Thu, 26 Aug 2010 15:03:32 +0000 (17:03 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Erik Lindahl [Thu, 26 Aug 2010 15:03:29 +0000 (17:03 +0200)]
true/false input settings should be called bool instead of gmx_bool
Berk Hess [Thu, 26 Aug 2010 14:29:11 +0000 (16:29 +0200)]
fixed bug that caused corrupted checkpoint files