Szilard Pall [Wed, 2 May 2012 12:59:00 +0000 (14:59 +0200)]
removed -finline-functions from the release gcc flags
All gcc versions >= v4.1 include -finline-functions with -O3.
Change-Id: Iecdf906162400863329bbe2d57fc110c9c2c7a9a
Teemu Murtola [Wed, 2 May 2012 05:10:19 +0000 (08:10 +0300)]
Remove #include <config.h> from pull_rotation.h.
There is nothing in the header that needs it, and installed headers
should not include something that is not installed.
Change-Id: I563fa21f3a6ecce8f728feb9656bccfef5edaa73
Roland Schulz [Sat, 28 Apr 2012 15:27:23 +0000 (11:27 -0400)]
Fix Windows specific cmake hacks
MT/MD related:
- Only use MT instead of MD if GMX_PREFER_STATIC_LIBS
Gromacs compiles fine with MD and produces smaller binaries.
- Fix that MT is also used with C++ and Intel
Workaroud for cmake 13174:
- Replace GZ with RTC1 also for C++
- Replace GX with EHsc for C++
Remove of set(GMX_EXTRA_LIBRARIES):
- This has no effect because it isn't set before.
Change-Id: I911c88e099c1faaa896b54b791a952c1265dd89e
Roland Schulz [Tue, 1 May 2012 14:56:49 +0000 (16:56 +0200)]
Merge "Disable OpenMP for llvm-gcc 4.2.x" into release-4-6
Roland Schulz [Mon, 30 Apr 2012 02:20:20 +0000 (22:20 -0400)]
Fix gmxdump error introduced by
553d4b1369
Change-Id: Ib3ebe7231e3be0f2bdeda21cf5c589f6d5144c5c
Roland Schulz [Sun, 29 Apr 2012 15:10:51 +0000 (11:10 -0400)]
Disable OpenMP for llvm-gcc 4.2.x
Fixes #900
Change-Id: Ibd80b2e3768e25f5091441a65785f539dc3b7050
Roland Schulz [Sun, 29 Apr 2012 12:41:36 +0000 (08:41 -0400)]
Merge release-4-5-patches into release-4-6
Change-Id: I420226d869a1d755c731b9f65b66a29c233e9b6e
David van der Spoel [Sun, 29 Apr 2012 07:26:00 +0000 (09:26 +0200)]
Merge "changed number of iatoms for F_SETTLE from 1 to 3" into release-4-6
David van der Spoel [Sun, 29 Apr 2012 07:06:19 +0000 (09:06 +0200)]
Merge "added support for graphs not starting at 0" into release-4-6
Roland Schulz [Sun, 29 Apr 2012 04:29:44 +0000 (00:29 -0400)]
Don't enable ASM if no asm kernel is selected
Caused that -DGMX_ACCELERATION=none didn't compile without
asm installed.
Change-Id: I572d64b94af89516ef35336190636ead6a256c0f
Roland Schulz [Sun, 29 Apr 2012 01:45:00 +0000 (21:45 -0400)]
Merge release-4-5-patches into release-4-6
Conflicts:
src/mdlib/pme.c
Change-Id: I0a77a63162168d3a07ab957a9bf7b367a9f05eac
Berk Hess [Fri, 27 Apr 2012 09:15:24 +0000 (11:15 +0200)]
fixed PME forces with FE, fixes #929 introduced in recent merge
Change-Id: I4f3bc59ed8c0351c4c59feceb3c2116b2f063daf
Teemu Murtola [Sat, 28 Apr 2012 14:12:15 +0000 (16:12 +0200)]
Merge "Fix for sigaction" into release-4-6
Roland Schulz [Fri, 27 Apr 2012 18:36:56 +0000 (14:36 -0400)]
Fix srenew/sfree_aligned misuse in PME
denom was first allocated with srenew and then freed with
sfree_aligned. This is illegal and crashes on Windows.
Change-Id: I83d8c35973ed0be1bb23396d6b97bf1d4b0f5f06
Mark Abraham [Sat, 28 Apr 2012 12:44:44 +0000 (14:44 +0200)]
Merge "Remove checks based on Generator" into release-4-5-patches
Mark Abraham [Sat, 28 Apr 2012 12:43:22 +0000 (14:43 +0200)]
Merge "Fix version info generation for autoconf." into release-4-5-patches
Berk Hess [Fri, 27 Apr 2012 12:35:48 +0000 (14:35 +0200)]
fixed segv in TPI with PME, fixes #927
Change-Id: Ie465c7300e491f4e67cacd0fa7186a253ee46cad
Berk Hess [Fri, 27 Apr 2012 08:59:12 +0000 (10:59 +0200)]
changed PME MPI_Comm comparisions to MPI_COMM_NULL, fixes #931
Change-Id: I6087339c5609de0444ac578c217825b9918cb993
Berk Hess [Thu, 26 Apr 2012 18:35:41 +0000 (20:35 +0200)]
changed number of iatoms for F_SETTLE from 1 to 3
Change-Id: Ia0cb1f277b5d3e8988c6fd1fb26896fa68c2fb3c
Teemu Murtola [Fri, 27 Apr 2012 07:25:10 +0000 (10:25 +0300)]
Fix version info generation for autoconf.
Should now work with a repository cheched out both from git.gromacs.org
and gerrit.gromacs.org. The pattern for finding the remotes may be
better with some finetuning, but it works for me. However, not that
much effort should be spent for the autoconf part since it will be
removed for 4.6.
Partial fix for IssueID #888.
Change-Id: I3f0caf440067b3eceba28845c1061c0642c0226b
Roland Schulz [Fri, 27 Apr 2012 06:26:29 +0000 (02:26 -0400)]
Remove checks based on Generator
OS dependending checks should not depend on Generator
Change-Id: I3c682c8b5ec82fe2a2b78744c6f56dccd655ee5c
Roland Schulz [Fri, 27 Apr 2012 04:09:17 +0000 (00:09 -0400)]
Fix for sigaction
Commit "Restart IO operations when interrupter by signal"
didn't actually activate sigaction because config.h.cmakein
change was missing.
Fixes #798
Change-Id: Id5c7e3344688c32ec4c51d84ccbc66658ed928f9
Berk Hess [Wed, 10 Aug 2011 09:31:30 +0000 (11:31 +0200)]
added support for graphs not starting at 0
It has always been implicitly assumed that graph->start==0.
This assumption would only fail for a topology starting with
single atom molecules followed by multi-atom molecules.
Furthermore, for mk_graph at_start could only be 0, a check
has been added for this, and at_end was not stored.
In t_graph start is now replaced by at_start and end by at_end,
where at_end is end+1, now the first atom not part of the graph.
Change-Id: I0d4c09c90cbba1a7f4a1d84cf1f90a7643c17cd8
Berk Hess [Thu, 26 Apr 2012 18:56:22 +0000 (20:56 +0200)]
Merge "Merge release-4-5-patches into release-4-6" into release-4-6
Berk Hess [Thu, 26 Apr 2012 15:40:34 +0000 (17:40 +0200)]
Merge release-4-5-patches into release-4-6
Change-Id: Id1c62a482c6c3467704cc9b657b53f7df493b7ba
David van der Spoel [Thu, 26 Apr 2012 18:07:01 +0000 (20:07 +0200)]
Merge "[tools] g_sans - splited out fixes and added citation" into release-4-6
Berk Hess [Wed, 18 Apr 2012 10:47:29 +0000 (12:47 +0200)]
fixed the reported temperature with Brownian dynamics
Reduced the (meaningless) masses with BD by a factor 2.
Since v with BD is defined as dx/dt, the reported Ekin and T are
now correct (and if there are too high, dt is too large).
Fixes #797
Change-Id: Iee8613ff9637deb58600ad03289f7bcce7f32df2
Berk Hess [Thu, 26 Apr 2012 12:40:13 +0000 (14:40 +0200)]
fixed dispersion correction with parallel EM
With EM the energy and pressure dispersion correction terms
were multiplied by the number of nodes. Fixes #901
Change-Id: I289ac0de7d7a9c1f72e939b840c549c1cb49a52a
Szilard Pall [Thu, 26 Apr 2012 11:54:37 +0000 (13:54 +0200)]
Corrected fourierspacing description
Change-Id: I5cb577f0750cea3481f766330096d5b2bca7eb6f
Szilárd Páll [Thu, 26 Apr 2012 11:48:42 +0000 (13:48 +0200)]
Merge "fixed initial COM motion removal with multiple groups" into release-4-5-patches
Alexey Shvetsov [Wed, 25 Apr 2012 21:38:40 +0000 (01:38 +0400)]
[tools] g_sans - splited out fixes and added citation
This commit contains fixes splited out from postponed g_nse commit.
1. Added citation
2. Fixed detection of triclinic boxes (needed for largest possible
distance)
3. mc runs uses monte carlo coverage
Change-Id: I6190fa9f7f710426f3d0bcf5c77013fe0d20eecc
Signed-off-by: Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru>
David van der Spoel [Thu, 26 Apr 2012 07:05:10 +0000 (09:05 +0200)]
Merge "Various improvements to shell code" into release-4-5-patches
Berk Hess [Tue, 24 Apr 2012 07:48:49 +0000 (09:48 +0200)]
replaced PPPM by P3M-AD: a few lines in pme.c
The deprecated PPPM method has been replaced by P3M-AD: a PPPM method
with analytical derivative. The full code path of P3M-AD is identical
to PME, except for the moduli calculation, which use the influence
function optimized for the grid.
Change-Id: I53d08d9ff4e909dc1a34dce668f4dea8f26f728e
Berk Hess [Thu, 19 Apr 2012 13:49:22 +0000 (15:49 +0200)]
fixed initial COM motion removal with multiple groups
Seperate COM motion removal code before step 0 has been replaced by
a call to the normal vcm code. This require some cglo flag changes.
Fixes #925
Change-Id: Ia6b8637b133c343c7e503307f00b557f7ad7409c
Berk Hess [Tue, 24 Apr 2012 11:35:33 +0000 (13:35 +0200)]
Merge "allow -append to overrule unsupported file locking" into release-4-5-patches
Christoph Junghans [Mon, 23 Apr 2012 15:39:42 +0000 (17:39 +0200)]
Merge "compiler flag fixes" into release-4-6
Roland Schulz [Sun, 11 Mar 2012 11:18:19 +0000 (07:18 -0400)]
Resolving a couple of clang analyzer warnings
Most of these are real errors or potential problems.
It's only a small start ~100 warnings are left and quite a few
false positives are within those remaining ones.
Change-Id: I7c83afa84c52362ecc1b7c992591d82f8262a6ac
Roland Schulz [Sun, 22 Apr 2012 16:41:33 +0000 (18:41 +0200)]
Merge "enable command line option cheking in mdrun" into release-4-6
Szilard Pall [Wed, 18 Apr 2012 01:12:24 +0000 (03:12 +0200)]
compiler flag fixes
- added patched Check{C,CXX}CompilerFlag.cmake scripts to enable invalid
option detection with Intel Compilers 12.x; the patches have been
submitted to CMake (will be included in 2.8.9:
http://cmake.org/gitweb?p=cmake.git;a=commit;h=
bbb895959f54a9dec9f5132313f4a71fafc458e5),
these files should be removed when the required CMake version will
contain the fixes
- moved compiler option generation after the default cmake variable
setting to add -Wunknown-pragmas only when GMX_OPENMP=OFF
- moved optimization options to release flags
- enabled warnings with the Intel Compilers
Change-Id: I767aea7f043255ee95eef5e7cb597c1c99feb05a
Mark Abraham [Wed, 18 Apr 2012 16:07:16 +0000 (02:07 +1000)]
Various improvements to shell code
Tested for binary equality only when appropriate. Increased verbosity
of error message. Clarified code that interpolates a scale factor for
a steepest-descent step size.
Change-Id: Ia386390e3a1b7690bf446342e55a3559da1e67eb
Berk Hess [Wed, 18 Apr 2012 11:23:42 +0000 (13:23 +0200)]
fixed segfault in graph code with coordinate subsets
The graph code checked for atom indices above the subset size,
but not for settle. The check for settle has been added.
Fixes #809
Change-Id: I67ddbd3dab5a34f57a29f54f4b07918a6d74c38c
Mark Abraham [Wed, 18 Apr 2012 03:07:32 +0000 (13:07 +1000)]
Removed outdated #includes
isnan() is no longer used in the code (although I can't find the
commit in src/kernel/md.c where it disappeared). Removed references
to gmx_header_config.h, since these are also no longer required.
Change-Id: Id9fcd3f221526c528cace86279e533c6581b26f7
Berk Hess [Wed, 18 Apr 2012 08:28:54 +0000 (10:28 +0200)]
allow -append to overrule unsupported file locking
This is a change to the previous change to let mdrun append anyhow
when file locking is not supported. Now a fatal error is generated,
unless -append is specified explicitly.
This commit refs #924
Change-Id: I98fa201fb5bd62c0de58c3c2d7e17e8b3f727c2f
Szilard Pall [Tue, 17 Apr 2012 22:56:56 +0000 (00:56 +0200)]
added missing #ifdef around #include "thread_mpi.h"
Due to the the missing #ifdef mdrun was not compiling with compilers
that don't like thread_mpi.h (e.g. Cray compiler).
Change-Id: Ibf980b46aaf56b81fffec5ada7cb3d93492a2220
Berk Hess [Tue, 17 Apr 2012 15:08:27 +0000 (17:08 +0200)]
changed mdrun file locking not supported error to a note
On some (file) systems file locking is not supported.
This should not prevent users from using the append option of mdrun,
Fixes #924
Change-Id: I99c0d38eb702b316df0027df3d33befc562a0a7a
Mark Abraham [Wed, 11 Apr 2012 02:26:22 +0000 (12:26 +1000)]
Added Windows-specific #defines, and use them
The lack of an elegant way to code "do this on Windows/
Cygwin/whatever" may have contributed to 4.5.5 not compiling with
threading under Cygwin (IssueID #833, which was fixed elsewhere).
Change-Id: I07fa69825181e2b04cb89798898898f1d258d371
Mark Abraham [Tue, 17 Apr 2012 09:09:12 +0000 (19:09 +1000)]
Rename gmxconfig.h to gmx_header_config.h
Change-Id: I756afd4c9a05666ca89f82726132ba5d15eaec2b
Roland Schulz [Mon, 16 Apr 2012 21:59:18 +0000 (23:59 +0200)]
Merge "changed default for nstxout, nstvout and nstlog" into release-4-6
Roland Schulz [Mon, 16 Apr 2012 21:29:09 +0000 (23:29 +0200)]
Merge "checkpoint files now contain a double precision flag" into release-4-6
David van der Spoel [Mon, 16 Apr 2012 19:21:05 +0000 (21:21 +0200)]
Merge "Added support for dssp2.X with the -ver option" into release-4-6
David van der Spoel [Mon, 16 Apr 2012 19:18:14 +0000 (21:18 +0200)]
Merge "Expanded the help text regarding the -r2 and -ac options." into release-4-6
Erik Marklund [Mon, 16 Apr 2012 15:14:53 +0000 (17:14 +0200)]
Expanded the help text regarding the -r2 and -ac options.
Fixes #862
Change-Id: If7ff131648881da8b1749bc736e141ff0b307ca6
Berk Hess [Mon, 16 Apr 2012 14:43:44 +0000 (16:43 +0200)]
changed default for nstxout, nstvout and nstlog
trr output is not useful in many cases, so the default is now 0.
nstlog has been increased from 100 to 1000.
Change-Id: I705a3cd6e33dc8db8efe5fa780d699196853da20
Berk Hess [Mon, 16 Apr 2012 13:31:37 +0000 (15:31 +0200)]
checkpoint files now contain a double precision flag
It was difficult to extract the precision from a checkpoint file.
Now a double precision flag has been added, as well as a fatal error
when mdrun tries to append output files of different precision.
Fixes #884
Change-Id: If333d13639ce80147ee1f6cd0cc34ad1f69afa03
Roland Schulz [Wed, 11 Apr 2012 15:39:02 +0000 (11:39 -0400)]
Restart IO operations when interrupter by signal
Fixes #798
Change-Id: I762412abf8138bbbe3d386d015e6af3522bd5235
Sander Pronk [Mon, 16 Apr 2012 11:31:27 +0000 (13:31 +0200)]
Merge "Permit threads build on Cygwin" into release-4-5-patches
Erik Marklund [Tue, 27 Mar 2012 17:42:39 +0000 (19:42 +0200)]
Added support for dssp2.X with the -ver option
Fixes #891
Change-Id: If274058aa776f64b04cb6f5a3c8303f8c567ef97
Szilard Pall [Thu, 12 Apr 2012 15:13:59 +0000 (17:13 +0200)]
enable command line option cheking in mdrun
Command line option checking has been disabled in mdrun. This can cause
unexpected issues e.g. when mdrun disregards an option with a typo.
Note that a few tools (g_tune_pme, g_pme_error, and g_membed) also omit
option checking, but these either rely on this "feature" or are in process
of rewriting/fixing for 4.6 which will implement the checkin. refs #922
Change-Id: I855c2dc0f2ebb09edfce92eb4a7b63fa144a5f4d
Teemu Murtola [Sat, 14 Apr 2012 16:29:20 +0000 (18:29 +0200)]
Merge "Clarified warning message" into release-4-5-patches
Teemu Murtola [Sat, 14 Apr 2012 16:28:32 +0000 (18:28 +0200)]
Merge "Clarified warning string" into release-4-5-patches
Mark Abraham [Sat, 14 Apr 2012 15:58:01 +0000 (01:58 +1000)]
Described default output behaviour
Change-Id: I62d48961277255192d2f1709fbb992e0673337c8
Mark Abraham [Sat, 14 Apr 2012 15:53:46 +0000 (01:53 +1000)]
Clarified warning message
Change-Id: I6fb5ba3cc42604e2445b4cb48093227478e6a613
Mark Abraham [Sat, 14 Apr 2012 15:47:07 +0000 (01:47 +1000)]
Clarified warning string
Change-Id: I65d422d342b946a548e9a29234d1803a13b1a9f0
Teemu Murtola [Thu, 12 Apr 2012 18:45:51 +0000 (21:45 +0300)]
Read PDB information in read_tps_conf().
Fixes #916.
Change-Id: Iaa2bed444b632b4596c6a4e9a4c527a6bc0236b8
Christoph Junghans [Tue, 3 Apr 2012 17:59:58 +0000 (11:59 -0600)]
Reworked FindFFTW.cmake
* make user input FFTW_{LIBRARY|INCLUDE_DIR} work and advanced
* ade more documentation
* reconsider test if failed in the last run
* improve error messages to the user
* check if fftw is compiled with sse support
* fixed detection on Cray
Change-Id: I0b7d440d372da7cf897ca956ccd882e21b109591
Roland Schulz [Sat, 31 Mar 2012 22:16:51 +0000 (18:16 -0400)]
Fix that directory is not mistaken for binary
The smart searching for the library path searched for an existing
inode with the name of the binary. If a directory with that name
existed, it was mistaken for the binary.
E.g.:
$ mkdir pdb2gmx
$ pdb2gmx
Fatal error:
No force fields found
This patch replaces gmx_fexist with gmx_is_file which checks that
the inode with the name of the binary is not a directory.
Change-Id: I78cdf8136db9ed69b75dcb1d4d0582ab388ef1d8
Mark Abraham [Wed, 11 Apr 2012 01:56:16 +0000 (11:56 +1000)]
Introduce include/gmxconfig.h
This header file is for #defines that should be available in an installed
header file that can be used by projects that depend on GROMACS. The
src/config.h used in building GROMACS is not installed, and so is not
available to such projects. CMake is used to configure
include/gmxconfig.h.cmakein and create include/gmxconfig.h.
Change-Id: Ide36fb4c0958d5faa647263411b3cfb91baa1d61
Mark Abraham [Tue, 10 Apr 2012 01:37:03 +0000 (11:37 +1000)]
Made g_helix sensitive to CHARMM atom naming
Peptide N-H atoms named HN in CHARMM were not recognized as backbone
atoms.
Fixes #896
Change-Id: I205b8dc5c895f20e6cde61ee2a1640fc6414b030
Mark Abraham [Tue, 10 Apr 2012 00:55:41 +0000 (10:55 +1000)]
Permit threads build on Cygwin
Fixes #833
Change-Id: I1429629417132c164e9b017721c0035583d7d6bf
Christoph Junghans [Mon, 9 Apr 2012 22:06:27 +0000 (00:06 +0200)]
Merge "Documentation and error message enhancements" into release-4-5-patches
Mark Abraham [Mon, 9 Apr 2012 19:15:37 +0000 (05:15 +1000)]
Documentation and error message enhancements
Change-Id: I4282e37c6b070607351cdafba56441b43fb04cd1
Mark Abraham [Fri, 6 Apr 2012 04:57:19 +0000 (14:57 +1000)]
Lots of manual updates
Accompanies changes in the manual project
Change-Id: I4c64d660f2a0dc2c265efb2f983d4ffbaf432fd4
Christoph Junghans [Mon, 9 Apr 2012 17:05:27 +0000 (19:05 +0200)]
Merge "Consolidated documentation of .mdp restraint options" into release-4-5-patches
Mark Abraham [Thu, 5 Apr 2012 06:24:09 +0000 (16:24 +1000)]
Consolidated documentation of .mdp restraint options
Change-Id: I04164a0e9a36338c5e412cdf73da78ef58299920
Roland Schulz [Fri, 6 Apr 2012 01:09:15 +0000 (21:09 -0400)]
Fix domain decomposition setup for >46k cores
Fixing int overflow in line 701:
ldiv*ldiv*ldiv > nnodes_div*nnodes_div
Change-Id: Ic97960caededeee255e874b81d9bbd2fc71d2ae6
Roland Schulz [Tue, 3 Apr 2012 17:02:10 +0000 (13:02 -0400)]
Merge remote-tracking branch 'gerrit/release-4-5-patches' into release-4-6
Conflicts:
CMakeLists.txt
Change-Id: I67d65e260f68442841d8b901d77780b8d1505340
Roland Schulz [Tue, 3 Apr 2012 16:45:46 +0000 (18:45 +0200)]
Merge "Fixes problems with g_msd and g_energy" into release-4-5-patches
Michael Shirts [Fri, 30 Mar 2012 18:05:59 +0000 (14:05 -0400)]
Fixes problems with g_msd and g_energy
* Fixes a problem where g_msd will stall on reading a file
with xy periodic boxes.
* Fixes a problem with gmx_energy ignoring the -skip option.
Was correct in 4.0.7, but was wrong by 4.5.5. Redmine issue #910
Change-Id: I4247a4bd1cf1ab15ea6157646c97452216a887aa
David van der Spoel [Mon, 2 Apr 2012 18:02:36 +0000 (20:02 +0200)]
Merge "Improved pdb2gmx error message" into release-4-5-patches
Mark Abraham [Mon, 2 Apr 2012 07:04:45 +0000 (17:04 +1000)]
Improved pdb2gmx error message
Increased the extent to which pdb2gmx makes use of the encapsulation
available with the t_atoms struct. Now the function that writes the
error message has an easier time being more descriptive of what
is wrong when the atoms in the input coordinate file do not match
those of the .rtp entry.
Change-Id: Ie39dea18efa358f90decad6491ddc04e3756ac39
Mark Abraham [Mon, 2 Apr 2012 06:56:54 +0000 (16:56 +1000)]
Keep CMake quiet about a Cygwin issue
The CMake warning that is suppressed by this does not affect GROMACS
builds.
Change-Id: I6a19f55868b6363cb2be328286b4716659cc270b
Szilard Pall [Wed, 28 Mar 2012 16:18:10 +0000 (18:18 +0200)]
Merge branch 'release-4-5-patches' into release-4-6
Change-Id: Id4fc52b784ac55c2e57669af391b8d2a70a56695
Christoph Junghans [Wed, 28 Mar 2012 16:01:40 +0000 (18:01 +0200)]
Merge "Resolving clang analyzer warnings in analysis" into release-4-6
Roland Schulz [Sun, 11 Mar 2012 11:17:14 +0000 (07:17 -0400)]
Resolving clang analyzer warnings in analysis
Backporting fixes in selection and trajana from
9b0c1478b93867550d4a126421bf85d35ad8c0e0
Conflicts:
src/gmxlib/selection/compiler.c
src/gmxlib/selection/selmethod.c
src/gromacs/fatalerror/gmxassert.h
src/gromacs/options/tests/abstractoptionstorage.cpp
src/programs/g_ana/g_ana.cpp
Change-Id: Ia3a74d5079b2e5dccac4499de9c4b65fdd3868e1
Berk Hess [Tue, 27 Mar 2012 11:35:13 +0000 (13:35 +0200)]
added correction for PME virial with non-linear virtual sites
With non-linear virtual site constructs the virial nees to be corrected
when it is not calculated from the particle coordinates and masses.
Currently this is only a problem for the PME mesh contribution.
This would lead to an incorrect virial and pressure. The error was small
for unordered systems, but could be significant for e.g. an all-atom
bilayer with hydrogens replaced by virtual sites. Fixes #908
Change-Id: I27a06019aa09734a14f3630ef296aaaacb9c5f0b
Roland Schulz [Mon, 26 Mar 2012 19:47:27 +0000 (15:47 -0400)]
Warn when a value is unused
Change-Id: I306062c791daf41b0791d0609c666af1b2910524
Berk Hess [Fri, 23 Mar 2012 13:58:36 +0000 (14:58 +0100)]
fixed g_bar xvg reading issue
Due to a comparison between temperatures in single and double precision
g_bar could give a fatal error when processing xvg files.
Change-Id: Ie63187261b3f20f8e241bf606cc9f23fdd93ec2b
Roland Schulz [Mon, 19 Mar 2012 06:12:59 +0000 (02:12 -0400)]
Removing unused code
Change-Id: Ic3eb509b2438c2dc5b022aed0974a400e75e8e02
Roland Schulz [Mon, 19 Mar 2012 06:37:48 +0000 (02:37 -0400)]
Fix incorrect fclose usage
fclose should not be used files opened with
- ffopen
- xvgropen
- gmx_fio_fopen
- fflib_open
Change-Id: I18d8e506f2763812d8193a92c67f25028e450cc1
Christoph Junghans [Sun, 18 Mar 2012 20:06:35 +0000 (21:06 +0100)]
Merge "Warnings against equilibrating with P-R P-coupling" into release-4-5-patches
David van der Spoel [Sun, 18 Mar 2012 11:30:31 +0000 (12:30 +0100)]
Merge "Fix typo in Clang CFlags" into release-4-5-patches
Mark Abraham [Wed, 14 Mar 2012 12:38:12 +0000 (23:38 +1100)]
Warnings against equilibrating with P-R P-coupling
Hopefully this will inhibit some people from doing Parrinello-Rahman
pressure coupling during their equilibration stage. If there's a
legitimate reason for P-R to have volume changes greater than 1%
we can reconsider the verbosity and/or frequency of the warning.
Change-Id: Icaeafa2fad37dfaa4b63ba69be3a3f804d957e7c
David van der Spoel [Sun, 18 Mar 2012 08:08:44 +0000 (09:08 +0100)]
Merge "Merge release-4-5-patches into release-4-6" into release-4-6
Berk Hess [Sat, 17 Mar 2012 20:46:06 +0000 (21:46 +0100)]
fixed increasing memory usage with SHAKE and DD
With domain decompostion SHAKE would be reinitialized every DD step.
This is now only done at initialization. Fixes #899
Change-Id: I4bcb162fa97271f602c5733ba04c7314456fcfa4
David van der Spoel [Sat, 17 Mar 2012 11:09:30 +0000 (12:09 +0100)]
Removed qhop files from this branch.
Change-Id: I7b6038571caaf47313d3edcf7111b3d2d0a3420c
Berk Hess [Fri, 16 Mar 2012 16:27:45 +0000 (17:27 +0100)]
fixed incorrect table allocation
This caused problems after commit
553d4b13.
The bug was already in older versions, but was hidden due to
the over allocation for pointer alignment.
Change-Id: Ifc50ee66fd4e963aab20ff1231c90a472fd5c443
Roland Schulz [Fri, 16 Mar 2012 01:24:37 +0000 (21:24 -0400)]
Merge release-4-5-patches into release-4-6
Change-Id: I5a7f695d49e3b7d1a5b4a0aeb099e5d3cc100faa
Christoph Junghans [Thu, 15 Mar 2012 21:10:25 +0000 (22:10 +0100)]
Merge "Clarified wording of documentation" into release-4-5-patches
Roland Schulz [Sun, 11 Mar 2012 03:26:39 +0000 (22:26 -0500)]
Fix most errors found by cppcheck
While some are only style issues (e.g. include "" instead of <>),
it includes a couple of real bugs.
- Not correct handling of '\0' termination of string
- assignment in if statement
- using of variable before checking that it isn't null
Warnings from a couple of non-critical categories aren't fixed.
To run cppcheck (tested with latest 1.53):
cppcheck -j8 `find src -name '*.c' -o -name '*.cpp' -o -name '*.cu'` \
-DHAVE_CONFIG_H -DSIZEOF_LONG_LONG_INT=8 -DSIZEOF_INT=4 -DLINUX -I include \
--enable=style \
--suppress=variableScope --suppress=unusedVariable --suppress=unreadVariable \
--suppress=invalidscanf --suppress=unusedStructMember --suppress=sizeofCalculation \
--suppress=unnecessaryForwardDeclaration --suppress=*:src/gmxlib/gmx_lapack/* \
--suppress=*:src/contrib/* --suppress=missingInclude \
--template gcc --inline-suppr
Change-Id: I1eabfce3e6cf8a6bed0f1282868667e290159279
Mark Abraham [Thu, 15 Mar 2012 01:27:06 +0000 (12:27 +1100)]
Clarified wording of documentation
Change-Id: I16df3e9db672f86396a22479563dc394035af5ce