Szilard Pall [Fri, 10 Sep 2010 15:54:47 +0000 (17:54 +0200)]
Merge branch 'master' of git.gromacs.org:gromacs
Szilard Pall [Fri, 10 Sep 2010 10:13:40 +0000 (12:13 +0200)]
Merge remote branch 'origin/release-4-5-patches'
Berk Hess [Fri, 10 Sep 2010 09:35:13 +0000 (11:35 +0200)]
removed tip5p from charmm27.ff/watermodels.dat, since several other files would need to be updated as well and we don't want to encourage the use of tip5p
Berk Hess [Fri, 10 Sep 2010 09:28:26 +0000 (11:28 +0200)]
made sure the energy history from a checkpoint file is ignored when not appending mdrun output
Teemu Murtola [Fri, 10 Sep 2010 07:08:50 +0000 (09:08 +0200)]
CMake documentation improvements (bug #539).
Added a bit of information to CMake cache documentation strings as
discussed in bug #539.
Mark Abraham [Thu, 9 Sep 2010 23:17:20 +0000 (09:17 +1000)]
Added TIP5p to CHARMM forcefield by analogy with AMBER03 TIP5p and existing CHARMM TIP[34]p
Mark Abraham [Wed, 8 Sep 2010 04:59:04 +0000 (14:59 +1000)]
Spelling fix
Szilard Pall [Thu, 9 Sep 2010 19:37:32 +0000 (21:37 +0200)]
Merge branch 'master' of git.gromacs.org:gromacs
Sander Pronk [Thu, 9 Sep 2010 15:18:50 +0000 (17:18 +0200)]
Fixed a deadlock while closing files.
Berk Hess [Thu, 9 Sep 2010 14:49:46 +0000 (16:49 +0200)]
added SSE overflow check for TPI
Berk Hess [Thu, 9 Sep 2010 14:44:15 +0000 (16:44 +0200)]
the force tables are now continued linearly from nearly 0 to 0 to treat completely overlapping atoms in energy minimization or TPI
Sander Pronk [Thu, 9 Sep 2010 13:56:16 +0000 (15:56 +0200)]
Fixed segv in trajana due to wrong cell index calculation.
Szilard Pall [Thu, 9 Sep 2010 10:57:10 +0000 (12:57 +0200)]
added gmx_membed.c to CMakeLists.txt for mdrun
Gerrit Groenhof [Thu, 9 Sep 2010 07:13:31 +0000 (09:13 +0200)]
added environment variable to run orca in parallel
Gerrit Groenhof [Thu, 9 Sep 2010 07:11:59 +0000 (09:11 +0200)]
added environment variable to run orca in parallel
Sander Pronk [Wed, 8 Sep 2010 19:43:41 +0000 (21:43 +0200)]
Fixed segv while reading overly long lines in xvgr.c
hess [Wed, 8 Sep 2010 14:48:02 +0000 (16:48 +0200)]
mdrun now also generates a fatal error for nnodes with large prime divisors (when -dd is not set)
Szilard Pall [Wed, 8 Sep 2010 14:11:50 +0000 (16:11 +0200)]
Merge branch 'release-4-5-patches'
Szilard Pall [Wed, 8 Sep 2010 14:10:23 +0000 (16:10 +0200)]
Fixed binary/lib suffixing inconsistencies (bug 539)
Berk Hess [Wed, 8 Sep 2010 11:51:28 +0000 (13:51 +0200)]
improved the automatic choice of the number of PME nodes
Per Larsson [Wed, 8 Sep 2010 11:41:43 +0000 (13:41 +0200)]
Fixed atomtype H0 for GBSA in amber03
Berk Hess [Wed, 8 Sep 2010 09:39:18 +0000 (11:39 +0200)]
added MCH3S atom type for Charmm for virtual sites in Met
Mark Abraham [Wed, 8 Sep 2010 01:56:52 +0000 (11:56 +1000)]
Added note to g_covar about memory costs and managing segfaults
Berk Hess [Tue, 7 Sep 2010 14:32:40 +0000 (16:32 +0200)]
changed the order of the outer loops in the fft5d transpose routines
Rossen Apostolov [Tue, 7 Sep 2010 13:19:40 +0000 (15:19 +0200)]
Merge branch 'release-4-5-patches'
Berk Hess [Tue, 7 Sep 2010 11:16:20 +0000 (13:16 +0200)]
removed empty edr and xtc files with nm
Berk Hess [Tue, 7 Sep 2010 11:15:50 +0000 (13:15 +0200)]
removed (nan) average printing with normal modes
Berk Hess [Tue, 7 Sep 2010 11:15:10 +0000 (13:15 +0200)]
fixed crash with parallel nm with cut-off's
Szilard Pall [Tue, 7 Sep 2010 08:31:48 +0000 (10:31 +0200)]
fixed warnings caused by some uninitialized variables
Sander Pronk [Tue, 7 Sep 2010 07:55:59 +0000 (09:55 +0200)]
Fixed segfault in g_bar with unequally distributed sample numbers.
Szilard Pall [Mon, 6 Sep 2010 21:17:55 +0000 (23:17 +0200)]
Merge branch 'release-4-5-patches'
Szilard Pall [Mon, 6 Sep 2010 21:16:54 +0000 (23:16 +0200)]
Mark advanced variables/options that are not relevant for the OpenMM build
Szilard Pall [Mon, 6 Sep 2010 21:13:59 +0000 (23:13 +0200)]
Mark advanced GMX_BINARY_SUFFIX and GMX_LIBS_SUFFIX when GMX_DEFAULT_SUFFIX=ON
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 10:39:25 +0000 (12:39 +0200)]
Merge branch 'release-4-5-patches'
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
Christoph Junghans [Tue, 31 Aug 2010 07:56:23 +0000 (09:56 +0200)]
Revert "Disabled building template because it does not compile !"
This reverts commit
860cdb58313a3b37d01454b8aa5cd693bf49e2a2.
The issue was fixed in commit
8e147cde59251bbf0d68033c0cca4dd5a0da3414
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
David van der Spoel [Mon, 30 Aug 2010 19:04:58 +0000 (21:04 +0200)]
Disabled compilation of g_membed for the time being.
David van der Spoel [Mon, 30 Aug 2010 18:33:02 +0000 (20:33 +0200)]
Merge branch 'release-4-5-patches'
David van der Spoel [Mon, 30 Aug 2010 17:18:24 +0000 (19:18 +0200)]
Added one quote.
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.