Rossen Apostolov [Wed, 18 Aug 2010 14:58:01 +0000 (16:58 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Rossen Apostolov [Wed, 18 Aug 2010 14:53:46 +0000 (16:53 +0200)]
Fixed the execution order in OpenMM so that the generated trajectory frames correspond to the CPU ones.
Sander Pronk [Wed, 18 Aug 2010 13:39:02 +0000 (15:39 +0200)]
Cmake tests for SIGUSR1
Rossen Apostolov [Wed, 18 Aug 2010 13:35:49 +0000 (15:35 +0200)]
Preserve the .pl extentions to scripts.
Christoph Junghans [Wed, 18 Aug 2010 13:31:18 +0000 (15:31 +0200)]
cmake: do not suffix scripts
Christoph Junghans [Wed, 18 Aug 2010 12:33:56 +0000 (14:33 +0200)]
cmake: add so version to libs
Christoph Junghans [Wed, 18 Aug 2010 11:16:36 +0000 (13:16 +0200)]
cmake: make demux.pl and xplor2gmx.pl being installed with the right permissions
Christoph Junghans [Wed, 18 Aug 2010 10:06:21 +0000 (12:06 +0200)]
port lib suffixes to cmake
Erik Lindahl [Wed, 18 Aug 2010 11:59:23 +0000 (13:59 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Erik Lindahl [Wed, 18 Aug 2010 11:59:19 +0000 (13:59 +0200)]
Fix to write GB and surface energy to separate terms, rather than putting everything in GB12
Berk Hess [Wed, 18 Aug 2010 11:16:52 +0000 (13:16 +0200)]
reduced the warning limit for Berendsen T-coupling tau_t/dt to 5 steps
Berk Hess [Wed, 18 Aug 2010 09:59:18 +0000 (11:59 +0200)]
removed the bNEMD boolean from the main MD loop and stored it in gmx_ekindata_t
Berk Hess [Wed, 18 Aug 2010 09:44:00 +0000 (11:44 +0200)]
added some comment to group grompp assignment options
Berk Hess [Wed, 18 Aug 2010 09:43:19 +0000 (11:43 +0200)]
added group comparison to gmxcheck and print groups names in gmxdump
Erik Lindahl [Wed, 18 Aug 2010 08:43:22 +0000 (10:43 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Erik Lindahl [Wed, 18 Aug 2010 08:43:14 +0000 (10:43 +0200)]
Enabled double precision all-vs-all kernels. Tested and appears to work for normal interactions, GB testing in progress.
Berk Hess [Wed, 18 Aug 2010 07:57:39 +0000 (09:57 +0200)]
fixed possible pathe string buffer overflow in get_libdir
Erik Lindahl [Wed, 18 Aug 2010 06:19:36 +0000 (08:19 +0200)]
Fixed simple typo in last commit
Erik Lindahl [Wed, 18 Aug 2010 06:18:06 +0000 (08:18 +0200)]
Fixed previous nasm-segv bug for intel-syntax SSE in the double precision SSE2 kernels too
Erik Lindahl [Tue, 17 Aug 2010 23:23:47 +0000 (01:23 +0200)]
Fixed 64-bit bug in SSE assembly (only visible with nasm)
Erik Lindahl [Tue, 17 Aug 2010 22:48:15 +0000 (00:48 +0200)]
Worked around an internal compiler error for MSVC when double was used with SSE2
Erik Lindahl [Tue, 17 Aug 2010 21:05:22 +0000 (23:05 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Erik Lindahl [Tue, 17 Aug 2010 21:05:13 +0000 (23:05 +0200)]
Deprecated -ins option to g_hbond since nobody seems to support it.
Sander Pronk [Tue, 17 Aug 2010 20:44:28 +0000 (22:44 +0200)]
Fixed thread_mpi inline assembly issue and non-optimized compiles.
Sander Pronk [Tue, 17 Aug 2010 20:25:46 +0000 (22:25 +0200)]
fsync fix for FAH core.
Erik Lindahl [Tue, 17 Aug 2010 18:14:55 +0000 (20:14 +0200)]
Copied all-vs-all change from x86-64 to ia32 kernels too
Erik Lindahl [Tue, 17 Aug 2010 18:13:37 +0000 (20:13 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Erik Lindahl [Tue, 17 Aug 2010 18:13:29 +0000 (20:13 +0200)]
Fixed potential error in coulomb energy, and maybe segfaults for small molecules in all-vs-all kernels
Christoph Junghans [Tue, 17 Aug 2010 15:44:17 +0000 (17:44 +0200)]
store custom GMX defines in pkgconfig files for cmake
Christoph Junghans [Tue, 17 Aug 2010 15:22:27 +0000 (17:22 +0200)]
fixed some out of srcdir build issue with cmake and GMXRC
Christoph Junghans [Tue, 17 Aug 2010 15:19:35 +0000 (17:19 +0200)]
store custom GMX defines in pkgconfig files for autotools
Christoph Junghans [Tue, 17 Aug 2010 14:17:14 +0000 (16:17 +0200)]
split libs in Template.mak
Christoph Junghans [Tue, 17 Aug 2010 14:02:36 +0000 (16:02 +0200)]
make cmake install a CMakeLists.txt for the template program
Berk Hess [Tue, 17 Aug 2010 13:28:56 +0000 (15:28 +0200)]
added function rescale_velocities
Roland Schulz [Tue, 17 Aug 2010 07:38:36 +0000 (03:38 -0400)]
Use always DIR_SEPARATOR
Roland Schulz [Tue, 17 Aug 2010 05:54:13 +0000 (01:54 -0400)]
Fix two Windows futil bugs:
1) Fexist for Directories
2) is_absolute with drive letter
Roland Schulz [Tue, 17 Aug 2010 01:56:35 +0000 (21:56 -0400)]
fixed spelling mistake introduced by
303d4543
Rossen Apostolov [Mon, 16 Aug 2010 20:53:36 +0000 (22:53 +0200)]
Removed the nb_kernel4xx_intel_syntax.c entries from the makefiles.
Rossen Apostolov [Mon, 16 Aug 2010 20:29:45 +0000 (22:29 +0200)]
Added support for improper dihedrals needed for CHARMM in OpenMM
Berk Hess [Mon, 16 Aug 2010 16:30:29 +0000 (18:30 +0200)]
gmx_rmpbc now guesses ePBC again for each frame
Berk Hess [Mon, 16 Aug 2010 15:57:15 +0000 (17:57 +0200)]
gmx_rmpbc gets natoms passed again, without natoms many tool could not parse trajectories of a part of the system. And added gmx_rmpbc_trxfr
Berk Hess [Mon, 16 Aug 2010 15:20:34 +0000 (17:20 +0200)]
put omp pragma's in fft5d.c between ifdef's
Sander Pronk [Mon, 16 Aug 2010 10:51:18 +0000 (12:51 +0200)]
Fixed xdr3dfcoord thread safety issues.
Sander Pronk [Mon, 16 Aug 2010 10:09:25 +0000 (12:09 +0200)]
Moved the OS-dependent part of gmx_fio_fsync() to futil.c
Berk Hess [Mon, 16 Aug 2010 09:51:47 +0000 (11:51 +0200)]
added openmp pragma's for the fft5d transpose routines
Berk Hess [Mon, 16 Aug 2010 09:41:20 +0000 (11:41 +0200)]
fixed mdrun writes tpidist.xvg on all nodes
Berk Hess [Mon, 16 Aug 2010 09:00:55 +0000 (11:00 +0200)]
fixed segv in mdrun with replica exchange
Berk Hess [Mon, 16 Aug 2010 08:59:50 +0000 (10:59 +0200)]
fixed fatal error in mdrun file appending with -multi or -seppot
Sander Pronk [Sat, 14 Aug 2010 16:01:07 +0000 (18:01 +0200)]
Fixed an issue with gmx_copy_file that would allow copies of empty files.
Teemu Murtola [Fri, 13 Aug 2010 15:14:26 +0000 (17:14 +0200)]
Cosmetic fixes for selection parsing.
The selection parser should now always replace any amount of whitespace
and line continuation with a single space in the pretty-printed
selection string. Also updated the parser generation script such that
it can be run from the root of the source tree.
Teemu Murtola [Fri, 13 Aug 2010 09:42:24 +0000 (11:42 +0200)]
Fixed CMake build with CMake 2.6.2.
Apparently, older versions of CMake do not support parentheses inside if
expressions. They were only used in cmake/gmxCFlags.cmake for clarity,
so I removed them.
Berk Hess [Fri, 13 Aug 2010 09:07:57 +0000 (11:07 +0200)]
gmxcheck now prints rmsd's as %g iso %f
Berk Hess [Fri, 13 Aug 2010 09:07:18 +0000 (11:07 +0200)]
moved full precision real format definition to simple.h
hess [Fri, 13 Aug 2010 07:47:22 +0000 (09:47 +0200)]
fixed apme bug that caused slightly incorrect results when the grid was not divisible by the number of pme nodes in x or y
Erik Lindahl [Thu, 12 Aug 2010 14:55:46 +0000 (16:55 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Erik Lindahl [Thu, 12 Aug 2010 14:55:42 +0000 (16:55 +0200)]
Added double precision SSE2 generalized born kernels. Note that these now _compile_, but they are not yet tested for accuracy (coming next week)
Berk Hess [Thu, 12 Aug 2010 14:45:06 +0000 (16:45 +0200)]
reverted the last, non-cosmetic change to pme.c
Berk Hess [Thu, 12 Aug 2010 13:29:31 +0000 (15:29 +0200)]
minor cosmetic changes in pme.c
Rossen Apostolov [Thu, 12 Aug 2010 12:22:45 +0000 (14:22 +0200)]
OpenMM: added support for AmberFF proper/improper torsion potentials.
Berk Hess [Thu, 12 Aug 2010 11:33:40 +0000 (13:33 +0200)]
made the pdb2gmx occupancy warning more obvious
Berk Hess [Thu, 12 Aug 2010 11:30:37 +0000 (13:30 +0200)]
fixed incorrect pdb2gmx output with multiple (altloc) atom entries in specbonds
Erik Lindahl [Thu, 12 Aug 2010 11:15:37 +0000 (13:15 +0200)]
Added ia32 all-vs-all kernels
Erik Lindahl [Thu, 12 Aug 2010 11:01:22 +0000 (13:01 +0200)]
Updated autoconf to work with renamed SSE2 x86-64 asm test file name too
Erik Lindahl [Thu, 12 Aug 2010 10:58:41 +0000 (12:58 +0200)]
Renamed SSE2 x86-64 asm test file to be consistent with other archs
Erik Lindahl [Thu, 12 Aug 2010 10:45:55 +0000 (12:45 +0200)]
Fixed typo to detect both x86_64->i386 and i386->x86_64 OS X architecture changes in cmake
Erik Lindahl [Thu, 12 Aug 2010 10:24:13 +0000 (12:24 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Erik Lindahl [Thu, 12 Aug 2010 10:24:09 +0000 (12:24 +0200)]
Fixed a naming error introduced yesterday in 32bit SSE GB kernel 430
Erik Lindahl [Thu, 12 Aug 2010 10:23:09 +0000 (12:23 +0200)]
Fixed compiler errors for MSVC inline intrinsics and added a test to detect incorrect CMake OS X configurations.
Erik Lindahl [Thu, 12 Aug 2010 09:53:24 +0000 (11:53 +0200)]
Fixed checkpoint problem in 32 bits. We should always check for SIZEOF_GMX_OFF_T, since the implementation _might_ use long int instead of off_t on some hosts.
Rossen Apostolov [Thu, 12 Aug 2010 09:21:11 +0000 (11:21 +0200)]
Fixed a reverted version string in configure.ac
Rossen Apostolov [Thu, 12 Aug 2010 09:11:51 +0000 (11:11 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Rossen Apostolov [Thu, 12 Aug 2010 09:09:37 +0000 (11:09 +0200)]
Warnings about using broken MPI implementations.
The build system doesn't actually check for the MPI version, it just prints a warning.
Proper checks should be implemented though.
Rossen Apostolov [Thu, 12 Aug 2010 08:39:26 +0000 (10:39 +0200)]
Updated the CMake scripts for finding CUDA, LibXml2 and MPI with the latest 2.8.2 modules.
Erik Lindahl [Thu, 12 Aug 2010 08:09:51 +0000 (10:09 +0200)]
Removed extra TER records after chains we think are polymers - this easily
leads to cluttered PDB files for selections.
Erik Lindahl [Thu, 12 Aug 2010 00:32:33 +0000 (02:32 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Erik Lindahl [Thu, 12 Aug 2010 00:32:28 +0000 (02:32 +0200)]
Fixed SSE kernels in double precision for Cmake, working in windows+osx, and fixed MSVC SSE intrinsics problems
Sander Pronk [Wed, 11 Aug 2010 18:18:40 +0000 (20:18 +0200)]
C++ type fixes in thread_mpi atomics.
Erik Lindahl [Wed, 11 Aug 2010 17:44:13 +0000 (19:44 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Erik Lindahl [Wed, 11 Aug 2010 17:44:08 +0000 (19:44 +0200)]
Cmake and Nasm support for windows
Berk Hess [Wed, 11 Aug 2010 15:32:52 +0000 (17:32 +0200)]
removed -merge from the pdb2gmx manual and clarified the new -chainsep option
Rossen Apostolov [Wed, 11 Aug 2010 13:47:09 +0000 (15:47 +0200)]
Fixed broken linking with single precision fftw3 in CMake.
Even when the single precision libraries were found, CMake would
try to link against double precision ones.
Sander Pronk [Wed, 11 Aug 2010 13:02:50 +0000 (15:02 +0200)]
Cmake now honors CFLAGS/CXXFLAGS as much as it can.
Rossen Apostolov [Wed, 11 Aug 2010 12:19:41 +0000 (14:19 +0200)]
Added a new file INSTALL.cmake with installation instructions for using CMake.
The old INSTALL was renamed INSTALL.automake
Rossen Apostolov [Wed, 11 Aug 2010 11:38:24 +0000 (13:38 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Rossen Apostolov [Wed, 11 Aug 2010 11:38:04 +0000 (13:38 +0200)]
CMake builds now install GMXRC* files.
Berk Hess [Wed, 11 Aug 2010 10:56:12 +0000 (12:56 +0200)]
fixed bug that caused a segv when snew failed
Rossen Apostolov [Wed, 11 Aug 2010 09:52:08 +0000 (11:52 +0200)]
Fix for CMake builds so that they don't fail even when version.c hasn't been generated.
Teemu Murtola [Wed, 11 Aug 2010 08:18:55 +0000 (10:18 +0200)]
Fixed non-interactive stdin selection parsing.
Providing selections non-interactively through a pipe now works as the
documentation states, i.e., identically to providing them from a file.
Erik Lindahl [Tue, 10 Aug 2010 23:25:10 +0000 (01:25 +0200)]
Moved four more SSE assembly files to avoid double extensions with intel syntax
Erik Lindahl [Tue, 10 Aug 2010 23:13:38 +0000 (01:13 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Conflicts:
src/tools/CMakeLists.txt
Erik Lindahl [Tue, 10 Aug 2010 23:07:19 +0000 (01:07 +0200)]
Changes to make Cmake work under windows again
Erik Lindahl [Tue, 10 Aug 2010 23:02:52 +0000 (01:02 +0200)]
Renamed intel syntax assembly files to avoid double extensions
Rossen Apostolov [Tue, 10 Aug 2010 18:50:10 +0000 (20:50 +0200)]
Bumped version to 4.5-beta3
Rossen Apostolov [Tue, 10 Aug 2010 18:42:51 +0000 (20:42 +0200)]
Fixed a typo in src/tools/CMakeLists.txt.
Erik Lindahl [Tue, 10 Aug 2010 17:15:32 +0000 (19:15 +0200)]
Added NASM Cmake support
Erik Lindahl [Tue, 10 Aug 2010 16:36:16 +0000 (18:36 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Teemu Murtola [Tue, 10 Aug 2010 15:46:14 +0000 (17:46 +0200)]
Fixed a segfault in selection code.
The selection parser would segfault in cleanup if certain types of
keywords were used in a selection that had a syntax error.
Rossen Apostolov [Tue, 10 Aug 2010 14:16:49 +0000 (16:16 +0200)]
Added missing NULL in chainsep enum in pdb2gmx.
Interestingly this was trigered only when compiled with icc in double precision.
Thanks to Teemu for finding it, closing bug 495.
Erik Lindahl [Tue, 10 Aug 2010 14:07:38 +0000 (16:07 +0200)]
MAYBE a fix for Berk's Heme problem. Needs testing
Berk Hess [Tue, 10 Aug 2010 12:17:53 +0000 (14:17 +0200)]
removed CYS2 from the Amber rtp files