David van der Spoel [Fri, 15 Jun 2012 11:47:07 +0000 (13:47 +0200)]
Fixes #882 - looping bug in trxio.c
This led to infinite output files in the case of a corrupt
input file.
Change-Id: I25d61752d901012e9ce5e6adae1679c2ef99467a
Erik Marklund [Fri, 8 Jun 2012 23:36:53 +0000 (01:36 +0200)]
Makes g_hbond -contact work
Fixes #955
Change-Id: I5d421d5f2e25d3801497efccb291425f90480a8c
Christoph Junghans [Fri, 15 Jun 2012 00:16:37 +0000 (02:16 +0200)]
Merge "Work around failure of endianness testing on BlueGene" into release-4-5-patches
Roland Schulz [Thu, 14 Jun 2012 14:14:49 +0000 (16:14 +0200)]
Merge "Made mdrun more verbose about PME split" into release-4-5-patches
Carsten Kutzner [Thu, 24 May 2012 13:18:11 +0000 (15:18 +0200)]
Small fix for g_tune_pme
Change-Id: I12fd2e48dc409f87b270f1ddaaaf2d1a83683fd1
Christoph Junghans [Fri, 8 Jun 2012 15:45:24 +0000 (17:45 +0200)]
Merge "Added more suggested strategies to error message" into release-4-5-patches
Mark Abraham [Wed, 6 Jun 2012 11:52:41 +0000 (21:52 +1000)]
Work around failure of endianness testing on BlueGene
Refs #944
Change-Id: I4bbfe9865800bbe4e407a88cdecec6678d56f3b4
Mark Abraham [Wed, 6 Jun 2012 10:15:58 +0000 (20:15 +1000)]
Fix endian test functionality
Code for big-endian systems was silently failing with CMake. This
patch brings CMake and autotools into agreement.
Partial fix of #944
Change-Id: I1f14938fd23e926e05397977963fbf968f0406e0
Mark Abraham [Mon, 4 Jun 2012 07:34:49 +0000 (17:34 +1000)]
Added more suggested strategies to error message
Change-Id: I4a68ea06697890175bb03e900664dd9bb886305c
Christoph Junghans [Fri, 1 Jun 2012 05:35:50 +0000 (07:35 +0200)]
Merge "Replace our fftpack version with Numpy's version" into release-4-5-patches
Roland Schulz [Sun, 27 May 2012 18:07:30 +0000 (14:07 -0400)]
Replace our fftpack version with Numpy's version
Fixes incorrect results for vectors with length of multiples of 12
Fixes #946
Change-Id: I9a110de7334cbb96a72d0ced73ade4d55f665fee
Mark Abraham [Thu, 31 May 2012 11:26:20 +0000 (21:26 +1000)]
Made mdrun more verbose about PME split
Change-Id: Ieda0ba5dcf08260cf94ad9aefd8937e067f2c6e2
Teemu Murtola [Wed, 30 May 2012 04:18:10 +0000 (07:18 +0300)]
Fix use after free in g_anaeig projection code.
PBC removal structure was deleted immediately after it was initialized,
and used afterwards.
Change-Id: I6126967b34e8de289370dede79cc50a9924ac34d
Sander Pronk [Tue, 22 May 2012 15:46:37 +0000 (17:46 +0200)]
Removed dependency on windows.h through commrec.h, domdec.h.
Change-Id: If40506b521a4b4690506465a3f421dab93bc9ce6
Christoph Junghans [Mon, 28 May 2012 23:25:59 +0000 (01:25 +0200)]
Merge "Continuing to fix threading on Cygwin" into release-4-5-patches
Roland Schulz [Sun, 27 May 2012 19:26:24 +0000 (15:26 -0400)]
Fix editconf real-bool misusage
Bool variable was declared as real. Caused invalid stack read
in double precision. Could have caused wrong value to be printed
for argument display but couldn't have caused wrong behavior.
Found with AddressSanitizer
Change-Id: I32553b1a898fb3a7f072ae177518dd63fad56dde
Roland Schulz [Sun, 27 May 2012 02:51:05 +0000 (22:51 -0400)]
Fix Clang 3.1 warning
grid_spacing is an integer and thus it was always set to 0
Change-Id: Id10bccdadef8f2630631d638e94bd27d78774536
Mark Abraham [Fri, 25 May 2012 09:45:09 +0000 (19:45 +1000)]
Continuing to fix threading on Cygwin
Fixes #833
Change-Id: I5d577a149ad18b295559f6d87c24dc42bffd281e
Berk Hess [Thu, 17 May 2012 22:07:46 +0000 (00:07 +0200)]
re-introduced fix for real/double issue in gmx_density
The float density histogram could overflow for large data sets.
A fix replaced 3 of the 4 pointers to floats by pointers to doubles, leading
to compilation issues. In two steps these replacements were reverted.
Now all 4 pointers have been replaced.
Change-Id: I0d8e38d27ac5c469480ff731ad191d869f5d890f
Berk Hess [Tue, 8 May 2012 09:21:56 +0000 (11:21 +0200)]
fixed mdrun -cpi SD and pcoupl initialization
With mdrun -cpi and no previous output files present SD and pressure
coupling were initialized incorrectly, leading to minor differences
at the start of a simulation. Fixes #939
Change-Id: I1ea3797ceb39760341c7c11cf74425c02dcaf235
Teemu Murtola [Fri, 4 May 2012 06:59:46 +0000 (09:59 +0300)]
Clean up cmake version generation.
- Use comparisons like ("${VAR}" STREQUAL "") for testing for empty
strings (other variants may fail in certain scenarios).
- Add some other quotes to avoid CMake errors in unusual situations.
- Remove trailing whitespace.
Related to #888.
Change-Id: Ifd1a87f0e929b4cb62db56d70ca469b73075fc2c
Teemu Murtola [Fri, 4 May 2012 06:49:56 +0000 (09:49 +0300)]
Drop support for pre-1.5.3 git for version info.
Did not touch the autoconf version, since that will anyways be obsolete
in 4.6.
Related to #888.
Change-Id: Ic7d890959e2e9a614f5d39a453c45671c3b56df4
Teemu Murtola [Fri, 4 May 2012 05:05:28 +0000 (08:05 +0300)]
Fix cmake version info generation.
Use the same logic in the cmake version info generation script as is
used in the shell script for autoconf.
Fixes #888.
Change-Id: I2a06d175a1e04e25d38b917d907cdae429743099
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
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 08:59:12 +0000 (10:59 +0200)]
changed PME MPI_Comm comparisions to MPI_COMM_NULL, fixes #931
Change-Id: I6087339c5609de0444ac578c217825b9918cb993
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
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
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 [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
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
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
Sander Pronk [Mon, 16 Apr 2012 11:31:27 +0000 (13:31 +0200)]
Merge "Permit threads build on Cygwin" into release-4-5-patches
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
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 [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 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
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
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
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
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
Christoph Junghans [Thu, 15 Mar 2012 21:10:25 +0000 (22:10 +0100)]
Merge "Clarified wording of documentation" into release-4-5-patches
Mark Abraham [Thu, 15 Mar 2012 01:27:06 +0000 (12:27 +1100)]
Clarified wording of documentation
Change-Id: I16df3e9db672f86396a22479563dc394035af5ce
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
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
Roland Schulz [Sat, 10 Mar 2012 00:30:16 +0000 (19:30 -0500)]
Fix typo in Clang CFlags
Change-Id: I4b03e585fd3f6f5d256478feef5038b2d7d13cba
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
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
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
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
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
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
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
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
Berk Hess [Mon, 6 Feb 2012 18:57:50 +0000 (19:57 +0100)]
Fixed bug with COM motion removal on part of the system
Center of mass motion removal on one group (not multiple) which is only part
of system would result in a tpr file with COM removal on the whole system.
Fixes #881
Change-Id: I181427bcad237045060000908f2c28d6e97c1ea4
Roland Schulz [Sat, 4 Feb 2012 20:18:24 +0000 (15:18 -0500)]
Fix ICC on Windows Build
Fix NASM with NMake Generator
The workaround in parser.y may not be necessary any longer when this is
merged into master.
Change-Id: I810eec3fa4a13fd912da3832279e8ab47a62bdec
Szilárd Páll [Thu, 2 Feb 2012 23:04:07 +0000 (00:04 +0100)]
Merge "Append all ICC Performance flags only to Release Flags" into release-4-5-patches