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
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>
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The deprecated PPPM method has been replaced by P3M-AD: a PPPM method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
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 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
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
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
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
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
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
Szilard Pall [Wed, 14 Mar 2012 18:43:29 +0000 (19:43 +0100)]
fixed appending OpenMP compiler option to flag list
GROMACS_C_FLAGS and GROMACS_CXX_FLAGS is treated as a string and
therefore appending to it using list append operation will result in an
extra semicolon.
Change-Id: I39f768b48bb8c029f8c7b21f0fc3c5e8c2309199
Mark Abraham [Wed, 14 Mar 2012 06:08:20 +0000 (17:08 +1100)]
Changed cryptic error messages about disk quota
People who have never had a disk quota don't understand what "out
of quota" could possibly mean. They understand running out of
disk space much more often.
Change-Id: I988cd038e74cf4e914075a748f9f66038ab37882
Roland Schulz [Tue, 13 Mar 2012 20:13:04 +0000 (21:13 +0100)]
Merge "mdrun -npme without PME or with PD now generates a fatal error" into release-4-6
Christoph Junghans [Tue, 13 Mar 2012 19:49:18 +0000 (20:49 +0100)]
Merge "Vibration spectra from velocity ACF or Normal modes." into release-4-6
Berk Hess [Tue, 13 Mar 2012 18:10:59 +0000 (19:10 +0100)]
mdrun -npme without PME or with PD now generates a fatal error
Change-Id: I887f2030e76a2932afd2989e17d7f14acefd18b1
Christoph Junghans [Mon, 12 Mar 2012 17:03:22 +0000 (18:03 +0100)]
Merge "More editorial fixes to tool documentation" into release-4-5-patches
Teemu Murtola [Mon, 12 Mar 2012 09:36:48 +0000 (10:36 +0100)]
Merge "Made description string for g_select -select clearer" into release-4-5-patches
David van der Spoel [Tue, 28 Feb 2012 20:53:28 +0000 (21:53 +0100)]
Vibration spectra from velocity ACF or Normal modes.
The velocity autocorrelation function can be converted into
a vibrational spectrum by performing a fourier transform
and plotting the amplitude squared as a function of
frequency or wavenumber. This has now been automated in
g_velacc with the -os flag. Likewise, an option -os
has been added to the g_nmeig program to produce a spectrum
based on the harmonic approximation.
Change-Id: I7e3d669b9108e3a91856ff20688f6216a035bf4a
Roland Schulz [Sat, 10 Mar 2012 02:22:00 +0000 (21:22 -0500)]
Activating more GCC warnings
- Removing very odd "else" in assert to remove empty body warning
- Ideally we wouldn't need to exclude:
- missing-field-initializers: only first 4 fields of t_filenm
are initialized in all places. Not easy to change.
- sign-compare: used in several places. Not sure worth to fix.
Change-Id: I137482c8c0cbdd75b6406bc6c61cffdd45af2ad8
Roland Schulz [Sat, 10 Mar 2012 00:30:16 +0000 (19:30 -0500)]
Fix typo in Clang CFlags
Change-Id: I4b03e585fd3f6f5d256478feef5038b2d7d13cba
Roland Schulz [Fri, 9 Mar 2012 16:40:53 +0000 (17:40 +0100)]
Merge "Improve FindFFTW" into release-4-6
David van der Spoel [Fri, 9 Mar 2012 16:25:22 +0000 (17:25 +0100)]
Merge "Improved cryptic error message" into release-4-5-patches
Carsten Kutzner [Fri, 9 Mar 2012 09:10:17 +0000 (10:10 +0100)]
Merge "Improved warning note with DD and periodic molecules" into release-4-5-patches
Mark Abraham [Fri, 9 Mar 2012 06:03:47 +0000 (17:03 +1100)]
More editorial fixes to tool documentation
Needed to add better treatment of <averages> and
|magnitudes| for LaTeX versions.
Change-Id: I5e8e3a8d685715af38117a762327d41a8bedf391
Mark Abraham [Fri, 9 Mar 2012 02:22:22 +0000 (13:22 +1100)]
Editorial changes to tools documentation
Made LaTeX type-setting of maths in documentation of tools more
sophisticated, without changing the presentation of maths in
plain text mode.
Various spelling and typographical fixes also.
Change-Id: Ia0c13e1f2ba825911c6e0673af6b940aba9efa21
Christoph Junghans [Thu, 8 Mar 2012 23:51:31 +0000 (16:51 -0700)]
Make finite checks remember theirs results
* saves time on rerun of cmake
* makes cmake quiet on rerun
Change-Id: I2120d8f13d2b7c5baa52d5aa8f06d6eb9ca2bb26
Mark Abraham [Thu, 8 Mar 2012 22:10:51 +0000 (09:10 +1100)]
Improved warning note with DD and periodic molecules
Change-Id: I3f7f201edcce1b70a360d0462e5103dfc144b2d7
Mark Abraham [Thu, 8 Mar 2012 22:07:53 +0000 (09:07 +1100)]
Made description string for g_select -select clearer
New UNIX users wouldn't guess they had to enclose the selection
string in quotes to get around their shell.
Change-Id: I8dd7fdd237e4290ad830a168b4880739aa5dc425
Mark Abraham [Thu, 8 Mar 2012 22:04:35 +0000 (09:04 +1100)]
Improved cryptic error message
Change-Id: Idd3f7a9ce36e155c61009b16da9a1f2b1a98e93e
Christoph Junghans [Thu, 8 Mar 2012 18:55:09 +0000 (11:55 -0700)]
Improve FindFFTW
* mark internally used variables INTERNAL
* make pkg-config search quiet on 2nd run to avoid confusion
Change-Id: I8b91adea1af8a14dffb88438fb2620df738f5a76
David van der Spoel [Thu, 8 Mar 2012 07:28:30 +0000 (08:28 +0100)]
Merge "Minimal support for Clang" into release-4-5-patches
Berk Hess [Mon, 5 Mar 2012 11:18:58 +0000 (12:18 +0100)]
fixed g_anaeig incorrect multiple extremes, fixes #870
Change-Id: Id06f267c1da300f2a940778833ec35b85fecd3f1
Berk Hess [Mon, 5 Mar 2012 10:57:22 +0000 (11:57 +0100)]
added check for mass-weighting with g_anaeig -entropy, fixes #785
Change-Id: I7a1623ba7a7c7987078901876fb4717d8c0a7261
Berk Hess [Mon, 5 Mar 2012 10:43:48 +0000 (11:43 +0100)]
removed initial temperature with OpenMM, fixes #757
Change-Id: Ifc661ce3ece3dfcd2e4bad862392b96d64e70c18
Roland Schulz [Sat, 3 Mar 2012 20:16:03 +0000 (15:16 -0500)]
Minimal support for Clang
Change-Id: I4c6fb22ef8b5d596527eb8fe0991c3c573be606c
Alexey Shvetsov [Tue, 28 Feb 2012 13:13:50 +0000 (17:13 +0400)]
[tools] Move common functions from gmx_sans.c to nsfactor.c
This commit moves common functions to gmx_sans and gmx_nse to nsfcator.c
Change-Id: Ifcf8e87203dd8721bb91807cd96d0e21f797b918
Signed-off-by: Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru>
Szilard Pall [Wed, 29 Feb 2012 16:50:32 +0000 (17:50 +0100)]
Merge branch 'release-4-5-patches' into release-4-6
Also fixed uninitialized variable warning in pdb2top.c with gcc 4.3.
Conflicts:
share/html/online/mdp_opt.html
Change-Id: I8e499a77a3ce71c2063f453348330e2aad38669b
Berk Hess [Mon, 27 Feb 2012 14:05:25 +0000 (15:05 +0100)]
fixed array index out of bounds in EM force trr storage
The partially implemented force copy was a leftover from a different way
of copying, which should never have been committed.
Change-Id: I026aa79158afcc327185f2f0cf6167d040eccede
Berk Hess [Sun, 26 Feb 2012 13:11:33 +0000 (14:11 +0100)]
use separate PME nodes with #nodes>18
PME nodes were used with #nodes>=10, but with 2D PME decomposition,
introduced already in 4.5, PME nodes are not faster with 12 or 16 nodes.
Change-Id: I9c5c8ac225df9d4b81f451074b74d35f002205ee
David van der Spoel [Sat, 25 Feb 2012 13:36:54 +0000 (14:36 +0100)]
Merge "Minor formatting fixes to .mdp option documentation" into release-4-5-patches
Mark Abraham [Fri, 24 Feb 2012 00:29:21 +0000 (11:29 +1100)]
Minor formatting fixes to .mdp option documentation
Change-Id: I71762463880e4cb650f680a2ed83125e450f003a
Roland Schulz [Thu, 23 Feb 2012 21:49:35 +0000 (16:49 -0500)]
Merge remote-tracking branch 'gerrit/release-4-5-patches' into release-4-6
Conflicts:
admin/GerritBuild.bat
Change-Id: Ie04e9e5932aa2a154712a17efb03538648b4b817
Berk Hess [Thu, 23 Feb 2012 15:52:36 +0000 (16:52 +0100)]
added tpx file tag string
The tpx file now contains a tag, such that feature branches can increase
the tpx version without the risk of later having tpx files with the same
version number but different format which can not be distinguised on read.
Change-Id: I07e804133bb1e55de6f25fd355bd79a7cb2fe141
Mark Abraham [Tue, 21 Feb 2012 06:03:39 +0000 (17:03 +1100)]
Fix pdb2gmx -cmap in corner cases
CMAP torsions are only generated when the atoms are from the same chain
(pdb2gmx -merge allows multiple chains to be present in the
moleculetype), and their residues are in residuetypes.dat as
"Protein".
Fixes #800, #885
Change-Id: Idc4f9a867beedc0be6a4c153606c0731eec86f5f
Sander Pronk [Wed, 22 Feb 2012 08:01:19 +0000 (09:01 +0100)]
Fixed ABI warning for thread_mpi on gcc 4.6 for x86.
Atomic operation data structures are now padded to the size of a cache
line instead of aligned to the start of a cache line. This works just
as well, but eliminates a warning in gcc 4.6.
Change-Id: I8d00778dcfea41cdb518b083a9c0732e8d978c66
Teemu Murtola [Tue, 21 Feb 2012 18:52:10 +0000 (19:52 +0100)]
Merge "Use Git server (mirror) to avoid fetching problems" into release-4-5-patches
Roland Schulz [Tue, 21 Feb 2012 04:37:26 +0000 (23:37 -0500)]
Use Git server (mirror) to avoid fetching problems
Change-Id: I144082bd01cf6a5f0583feac0e7877e8e1b163ff
Christoph Junghans [Tue, 21 Feb 2012 03:26:51 +0000 (04:26 +0100)]
Merge "changed default epsilon-rf value to 0" into release-4-6
Berk Hess [Mon, 20 Feb 2012 13:46:47 +0000 (14:46 +0100)]
changed default epsilon-rf value to 0
The default for epsilon-rf used to be 1, now it has been changed to infinity.
Infinity is a sensible value and gives 0 potential and force at the cut-off.
Change-Id: I3884085b687002edff4b4b96f21851e182268a55
Berk Hess [Sun, 19 Feb 2012 21:50:49 +0000 (22:50 +0100)]
Merge "Generate warnings for QMMM usage" into release-4-6
Gerrit Groenhof [Mon, 6 Feb 2012 10:39:23 +0000 (11:39 +0100)]
Generate warnings for QMMM usage
Change-Id: Ic6088f765cb0bfbb6f85e3da53421ef6a2167d94
Christoph Junghans [Wed, 15 Feb 2012 04:48:23 +0000 (21:48 -0700)]
Removed FFTw2 support
Change-Id: I04a702577ceb9f15ed9ec3fdc83bed0caef0fda1
Roland Schulz [Wed, 15 Feb 2012 03:47:02 +0000 (04:47 +0100)]
Merge "Cmake: unite FindFFTW3* into one file" into release-4-6
Sander Pronk [Mon, 13 Feb 2012 17:28:56 +0000 (18:28 +0100)]
Fixed an allocation issue with dH histograms.
Change-Id: Ifc6ed94d77664e3b3afb7fe8dbd1016444d86bc3
Szilárd Páll [Sat, 11 Feb 2012 16:45:25 +0000 (17:45 +0100)]
Merge changes If0c2f9d9,Ic2a8ad82 into release-4-5-patches
* changes:
Fixed g_sham using more than three dimensions
Integer multiplication that checks for overflow
Berk Hess [Fri, 10 Feb 2012 10:25:45 +0000 (11:25 +0100)]
fixed gmxcheck segv with tpr files without AdResS
Change-Id: If337862e4247b3ecada73f5d0cec20f27a0d9a50
Mark Abraham [Thu, 9 Feb 2012 02:48:35 +0000 (13:48 +1100)]
Fixed g_sham using more than three dimensions
When the value given with g_sham -n was greater than 3, arrays used to
overflow and pick_minima() did not work. pick_minima() has been updated
to treat an arbitrary number of dimensions, but retains the particular
code for the two- and three-dimensional cases in the hope that these
are faster. The logic of the complex conditionals has hopefully been
made easier to follow without compromising performance with modern
compilers. Index variables are now of gmx_large_int_t type, as
high-dimensional cases can have large numbers of grid points very fast.
Change-Id: If0c2f9d9ceaf2b5c4c8b1a28a942fae8349fb600
Mark Abraham [Fri, 10 Feb 2012 04:10:34 +0000 (15:10 +1100)]
Integer multiplication that checks for overflow
Integer multiplication overflows silently in C, and sometimes we need to
know when it would. For example, when computing the size of
multi-dimensional arrays, we can need to manage the case when the number
of dimensions and their size is too large to represent in the available
type.
Change-Id: Ic2a8ad820838cf314bb985511e483fc397ba35e2
Christoph Junghans [Fri, 10 Feb 2012 01:14:01 +0000 (02:14 +0100)]
Merge "Fixed bug with COM motion removal on part of the system" into release-4-5-patches
Christoph Junghans [Fri, 10 Feb 2012 01:08:20 +0000 (18:08 -0700)]
Cmake: unite FindFFTW3* into one file
* easier to maintain
* leave space to add support for fftw2
* leave space to add support for other modules like fftw_omp
Change-Id: I30e1f7a6fff26b924b29fe37a34a8ce5c5177153
Szilard Pall [Fri, 3 Feb 2012 01:36:59 +0000 (02:36 +0100)]
renamed GMX_THREADS to GMX_THREAD_MPI
The aim is to better differentiate between the two types of threading:
OpenMP and thread-MPI.
Both CMake cache variable and preprocessor definitons were renamed.
Change-Id: Ie905a572cc9c02cacdcce6f80497a078131d253e
Roland Schulz [Wed, 8 Feb 2012 00:14:57 +0000 (19:14 -0500)]
Merge remote-tracking branch 'gerrit/release-4-5-patches' into release-4-6
Change-Id: I13898484048384500e946fc4dddaaca3281a8819