Erik Lindahl [Fri, 8 Aug 2014 21:37:49 +0000 (23:37 +0200)]
Replace __LP64__ with check for pointer size
The __LP64__ define is not set e.g. on PGI compilers,
so instead we use a portable way of checking for
pointer size based on defines from stdint.h.
Change-Id: Ib2dd6e45c2b168add07f5478d59aec487a91ab9e
Berk Hess [Wed, 30 Jul 2014 12:59:17 +0000 (14:59 +0200)]
Added checks for TPI + Verlet scheme
Change-Id: I040f4cc9dbb8ff25ed97d18cca0b4a2c1e7014b0
Roland Schulz [Tue, 5 Aug 2014 02:05:04 +0000 (22:05 -0400)]
Check MD5sum for regressiontest
Because we decided it is important for FFTW we should do it for
the tests too. Is only done for non -dev versions.
Change-Id: Id7d1ee027bd302ad7cb10f46d93b0f435872c67e
Roland Schulz [Sun, 10 Aug 2014 01:59:35 +0000 (21:59 -0400)]
Merge release-4-6 into release-5-0
Conflicts:
CMakeLists.txt (version bump ignored)
Change-Id: I4ba0209b5f69b6470470530662a0b27390a02771
Erik Lindahl [Wed, 30 Jul 2014 12:46:57 +0000 (14:46 +0200)]
Fix portability issue with ArrayRef initializer overloading
Some compilers (in particular the Fujitsu compilers that are
derived from an earlier version of Clang) will not allow
overloading functions where one version uses a pointer to a
type, and the other a vector iterator to the same type - likely
because they have implemented iterators with pointers.
Regardless of what the C++ standard says, we need this working
on K computer, so this patch replaces the overloaded
initializers with non-member functions that create an ArrayRef
or ConstArrayRef either from pointers, an array,
or iterators.
Change-Id: I4c4e327c869920cc08e3f955e88cb3a5b28c7e87
Erik Lindahl [Tue, 5 Aug 2014 10:15:39 +0000 (12:15 +0200)]
Changed names of test files to avoid Fujitsu compiler bug
The Fujitsu compilers use an older version of the Clang
parser where certain static class initializers (e.g. strings)
are put in a static initializer function stub named after
the file and class. When the first such class has identical
names in two different files where the last part of the
name is identical, this will result in clashing symbols
at link time. Working around this would require an extra
(unused) class definition in each file that would pollute the
code, so for now we merely rename the files where it occurs
and hope that the compilers will be fixed (a bug report has
been submitted).
Change-Id: If552a06950facb0cdbb6e34e0b324aafa6083ae8
Berk Hess [Mon, 4 Aug 2014 12:18:36 +0000 (14:18 +0200)]
Fix hang with LJ-PME and empty domains
With LJ-PME and DD domains with 0 atoms and LJ-PME mdrun could hang.
Fixes #1571.
Change-Id: Ie205954c4f5e1a52df846a69972f735867eea15d
Roland Schulz [Tue, 29 Jul 2014 23:37:19 +0000 (19:37 -0400)]
Workaround for ICC 14
Problem was only present with BUILD_SHARED_LIBS=no
Change-Id: Ieb4377d819aa5eff3d139cdbe55775989118a738
Teemu Murtola [Sun, 3 Aug 2014 14:32:31 +0000 (17:32 +0300)]
Verify MD5 sum for FFTW download
Since ExternalProject provides confusing error messages with MD5
checking enabled, add a custom download step that works as expected.
When passed a local file as the URL, ExternalProject does the MD5
verification just fine, so the code now downloads the tarball in a
custom step and then passes that local file to ExternalProject.
This allows removing the lengthy security warning that appeared there if
one was just following the quick-and-dirty installation instructions,
and likely only confused novice users. While this change may not
improve overall security significantly, it hopefully allows everyone to
agree to remove that warning and thus improve the end-user experience.
Change-Id: I9ac5a30ae5858b7a6557ccb2d981cc909457d020
Berk Hess [Sat, 2 Aug 2014 08:53:31 +0000 (10:53 +0200)]
Fixed PME bug with high OpenMP thread count
PME energies and forces could be incorrect with combined MPI+OpenMP
parallelization. This would, only, happen when
pmegrids->nthread_comm[YY] >= 2, which can only occur with high OpenMP
thread count with multiple large prime factors.
It's unlikely that this issue affected production runs.
Fixes #1572.
Change-Id: I03b38c279c8f8ab2e111dad0976edad88b3ea93b
Erik Lindahl [Thu, 31 Jul 2014 14:32:30 +0000 (16:32 +0200)]
Added tests for denormal and underflow for simd exp()
The SIMD math functions are not expected to handle
the denormal range correctly, but it should at least
be clamped to zero rather than producing garbage
values. No changes required to the math function,
so it appears to pass these tests as-is.
Change-Id: I841c2948c81f6b62f42e60ff30ffd5e4f77926fa
Berk Hess [Thu, 31 Jul 2014 11:08:34 +0000 (13:08 +0200)]
Avoid division by 0 in nbnxn_search
Note that this issue did not affect any results.
Change-Id: I3c454783484c416b50808b9512e14072cb749784
Christian Wennberg [Mon, 28 Jul 2014 16:06:36 +0000 (18:06 +0200)]
Fix overflow in LJ-PME nbnxn kernels
The SIMD exp function in the LJ-PME nbnxn kernels could overflow
for pair distances far beyond the cut-off. Added a mask to avoid this.
Fixes #1552
Change-Id: Id87710f3815b341f53a69df0a2990d0bb4edfa74
Roland Schulz [Fri, 25 Jul 2014 22:36:17 +0000 (18:36 -0400)]
Fix build of binary package
Commit a00437 accidentally changed that the source-package error is also
printed for binary packages. Because it defined
CPACK_SOURCE_PACKAGE_FILE_NAME which we used to detect source-package.
This now uses CPACK_INSTALL_CMAKE_PROJECTS which is hopefully future-proof.
It also adds a proper warning for binary packages.
Change-Id: I842655755bed1c448f30db435a85ad1ca5844a60
Roland Schulz [Tue, 1 Jul 2014 08:54:42 +0000 (04:54 -0400)]
Add unit test for random/Threefry
Change-Id: I5f9d60c594c0d7a6925b829658119d2fdea5d113
Roland Schulz [Tue, 1 Jul 2014 10:35:53 +0000 (06:35 -0400)]
Remove Random123/features
Remove all auto-detection and replace with hard-coded
values and gmx_inline.
The purpose is that it now should compile on any hardware /
compiler. Correctness is guaranteed (as is custom in all
of Gromacs) by unit tests (separate commit).
Change-Id: I7e75ff38f7288e87817d42582ae844c1d38ef369
Erik Lindahl [Sun, 27 Jul 2014 08:54:33 +0000 (10:54 +0200)]
Fix selection of xtc groups not starting at index 0
The code to select atoms to write to the xtc file
only looped over the number of atoms selected for
output rather than all atoms. This meant that xtc
group selections that were not located at the start
of the atom indices would not be written correctly.
Fixes #1561.
Change-Id: I48886a75c682e38122dadcb2f752507b14b308fe
Roland Schulz [Sun, 13 Jul 2014 00:34:41 +0000 (20:34 -0400)]
Workaround for ICC 14 bug
ICC name-mangling is incorrect for static variable in static
member in anonymous namespace.
Fixes #1558
Change-Id: Ie861224bcc61df2f26025d1dd106bcab827308bb
Roland Schulz [Thu, 10 Jul 2014 01:11:50 +0000 (21:11 -0400)]
Fix Cygwin+Shared-Libs+FFTW
Cygwin doesn't have or require fPIC
Change-Id: If1af6f070e2cd0457f429a155e92014af51c0c33
Roland Schulz [Tue, 1 Jul 2014 08:53:53 +0000 (04:53 -0400)]
Add support for int64 in refdata
Change-Id: Ia5fedbe7593d9630a095eaf1cb6d69f0c1223ee0
Roland Schulz [Tue, 22 Jul 2014 03:35:00 +0000 (23:35 -0400)]
Fix GMX_BUILD_OWN_FFTW for Cygwin
CMAKE_BINARY_PREFIX doesn't exist and thus the previous version added just
an extra slash which doesn't work under Cygwin.
Change-Id: I285f93020d0818515fff3f2cfbf41662f03190d0
Roland Schulz [Wed, 16 Jul 2014 00:13:01 +0000 (20:13 -0400)]
Fix GMX_NONBONDED_NUM_THREADS!=GMX_PAIRSEARCH_NUM_THREADS
Change-Id: I7d5416fa299e244244d7bf48e785090da2e0b6d0
Teemu Murtola [Thu, 10 Jul 2014 03:39:59 +0000 (06:39 +0300)]
Fix HTML help and man pages for commands with dashes
Replace one case of "gmx-something" to "gmx something" conversion with
explicit construction of the latter from its component parts.
The other instance does not (easily) have the component parts available,
so only the first dash is removed when converting between
"gmx-something" and "gmx something". Add an assert for the condition
that this requires to remain functional.
Change-Id: I5bfbd1acae440af93b3b7b50a25d8782a7e60c8a
Erik Lindahl [Sat, 12 Jul 2014 08:10:36 +0000 (10:10 +0200)]
Avoid clang/32 optimization affecting IEEE endian detection
This turns the detection code into a c++ file, moves the
structure to a global one and adds volatile specifiers.
This should hopefully prevent any standard-adhering
compiler from touching the data.
Change-Id: I6f4b86ddf6b0567655466e0877bb1ba39a45ce4e
Erik Lindahl [Fri, 11 Jul 2014 08:16:27 +0000 (10:16 +0200)]
Make AVX2 check more robust
Apparently the GNU assembler version 2.20 supported some
parts of AVX2 (in particular the FMA floating-point ops),
which caused our cmake test to pass. This patch changes
it to test the integer addition instead, which isn't
supported in as-2.20 in my tests.
Change-Id: I79e516639fc78d1590d306f486eb027962388543
Teemu Murtola [Thu, 10 Jul 2014 10:57:32 +0000 (13:57 +0300)]
Fix HTML links that contain file extensions
- Consider '-' and '_' as part of a word when replacing links, so that
convert-tpr and make_ndx are considered single words, and the
extensions there are not converted into links.
- Do links.dat replacement before program links, so that the URL in the
above program name links is not processed.
Change-Id: I0ce204d3adedc56e57c1e1cd150a63d21c442eab
Roland Schulz [Thu, 10 Jul 2014 01:36:31 +0000 (21:36 -0400)]
Fix xml2 link check rerun
gmx_check_if_changed logic had a typo and thus check wasn't rerun
if LIBXML2_INCLUDE_DIR or LIBXML2_LIBRARIES changed.
Change-Id: I838f32fd6e9b62480acc4eafc4bf3d657477d09d
Mark Abraham [Sat, 5 Jul 2014 22:25:11 +0000 (00:25 +0200)]
Name the tarball how we like it
This names the tarball and the top-level directory how
GROMACS usually does it. Previously, I'd been renaming
stuff manually.
Change-Id: I485c4a4c711064a3a0ca2343ec696375cbc3de96
Mark Abraham [Thu, 3 Jul 2014 14:30:04 +0000 (16:30 +0200)]
Quieten repeated cmake runs
We should not hassle the user about optional libraries that were not
found the first time. If the user wants to detect ones found in a
different place, then they can unset the relevant cache variables to
re-trigger detection and/or related output.
Change-Id: I266268dccc46da5b098d3d5640798cbee7ee6fd0
Roland Schulz [Sun, 6 Jul 2014 04:40:14 +0000 (00:40 -0400)]
Fix Cygwin build
Doesn't work with AVX but I suspect this to be Cygwin's/GCC's fault.
GCC Bug 61730
Change-Id: I171e8414a8d65800804226034604a9973770bfdd
Erik Lindahl [Mon, 7 Jul 2014 11:43:58 +0000 (13:43 +0200)]
Make IEEE754 check more robust
This change should prevent compilers from
optimizing away the structure used for checking
strings in the binary by also using it to produce
a return values. There are now also clearer
warnings, and if IEEE754 cannot be detected we
fall by to using the OS versions of erf/erfc()
in double precision. Fixes compiles on Power7.
Change-Id: I8ed834d5b87baf33e03725d2ab93a60a76c34a12
Teemu Murtola [Sun, 6 Jul 2014 04:04:57 +0000 (07:04 +0300)]
Make selections ignore \r in input
Now the selection engine treats \r (as well as various other space
characters) the same as a space. Added a unit test for this.
There is an extra trailing space in some cases that may be more common
with \r\n than otherwise, but that is a separate, mostly cosmetic
issue.
Fixes #1555
Change-Id: I78dfe8e477133b98a98fecf1fad243262f9b30c8
Mark Abraham [Sat, 5 Jul 2014 12:24:28 +0000 (14:24 +0200)]
Fix tarball and install, particularly for INSTALL
Getting the INSTALL file generated from the markdown, into the tarball
via CPack and not otherwise installed is a bit tricky. I did this
manually for 5.0, but this automates things. CPack source archives use
a mechanism that acts on whole directories. So we put INSTALL into its
own output directory (as we do for generated HTML), and the
directory-globbing mechanism takes care of it fine. Added some
documentation for why we need to do this.
Added more CPack-time checks that the tarball will be complete.
Prevented installation of .gitattributes.
Change-Id: I77c645faf7b292a085165bdd1598741dae6972a5
Mark Abraham [Mon, 7 Jul 2014 13:28:38 +0000 (15:28 +0200)]
Version bump after 4.6.6 release
Change-Id: Ifac0db3a07caba28c123d233b54356a1db0d79ba
Magnus Lundborg [Tue, 1 Jul 2014 10:09:14 +0000 (12:09 +0200)]
Fix bug causing reading next frame not to stop.
Corresponds to commit
e6e85d562829bca in the TNG repo.
Change-Id: I89ee3e7649c4cf832798d9e2ce61b397a1757579
Magnus Lundborg [Mon, 30 Jun 2014 08:06:02 +0000 (10:06 +0200)]
Fix tng_num_frame_sets_get() with no frame sets.
When there are no frame sets the function returned an error.
This corresponds to commit
6f7862c7406b in the TNG repository.
Fixes #1540
Change-Id: I3df04d84ebd8fcdc6be76a446efa3209df363d23
Teemu Murtola [Sun, 29 Jun 2014 05:00:45 +0000 (08:00 +0300)]
Reinstantiate unsorted index group check
In most contexts, providing an index group with duplicate atoms or atom
indices not in ascending order results in the selection getting silently
evaluated incorrectly. The selection engine now detects this case and
gives a fatal error, hopefully reducing confusion if such a case arises.
The case where an unsorted index group is provided as a sole value of a
selection is still supported.
Change-Id: I0b647a26d9a1b47da10c84bdd3d073412d166a75
Roland Schulz [Thu, 3 Jul 2014 16:17:39 +0000 (12:17 -0400)]
Add running tests to install-guide
At least on architectures we don't test, it is necessary that the user
runs the tests. Because we don't have a way to query whether it is a
tested architecture every user should run the tests.
Also add a warning if unit tests cannot be build because libmxl2 wasn't
found.
Partial fix for #1548
Change-Id: I8b87cc77f909d5cf2a4ee70151096312e3191af2
Teemu Murtola [Tue, 1 Jul 2014 04:05:41 +0000 (07:05 +0300)]
Update some installation-related docs
- Add comments for installation-related variables in CMake, in
particular the RPATH section that has caused some confusion.
- Document those few variables that can be used to alter the
installation tree structure in the install guide.
- Reword some parts in the install guide about CMake iteration.
- Remove GMX_INSTALL_PREFIX, as there are other approaches to get the
desired result with CPack that are less confusing. This variable
wasn't documented or probably used anywhere outside some dormant
Jenkins jobs.
Change-Id: I199b06d905b45961313ed9fa44ae82e5987be0fe
Teemu Murtola [Tue, 1 Jul 2014 04:17:21 +0000 (07:17 +0300)]
Adjust include directory order for some corner cases
Always add headers found from the source/build tree to the beginning of
the list of include paths, such that they are preferred over those
potentially found in other non-system directories.
Fixes #1539
Change-Id: Id79634073fea5b10f250128db8ab08019a7f9e21
Mark Abraham [Sat, 28 Jun 2014 17:13:50 +0000 (19:13 +0200)]
Fix GMock to work on MSVC
This duplicates the logic of GMock's (pre-release) commit r675 in
order that GROMACS can build and test without problems on all MSVC
versions.
Change-Id: I8a7188d2d34fdfa2753a71291d8528e5c9753c6d
Mark Abraham [Sun, 29 Jun 2014 20:51:47 +0000 (22:51 +0200)]
Version bump for 5.0
Change-Id: I7ef67766e28e7ac65f9e027e61bfb9f13809d543
Mark Abraham [Sun, 29 Jun 2014 18:16:06 +0000 (20:16 +0200)]
Add forgotten licenses to COPYING
Change-Id: I3c9beffae164d0c0260d121af29db051b60ca159
Mark Abraham [Sat, 28 Jun 2014 19:57:18 +0000 (21:57 +0200)]
Refer to "mixed" precision in user-facing documentation
GROMACS has used mixed precision for many years, so we may as well be
accurate about it. In the code, we should continue to refer to single
precision for aspects of the implementation, but mdrun should not
be referred to as running in "single precision."
Also removed useless install-guide section from manual.
Change-Id: I3c26acedcdb391de50bdcb6a5e913ea0cfc32845
Berk Hess [Sun, 29 Jun 2014 09:31:14 +0000 (11:31 +0200)]
Take LJ-PME into account for table spacing
The table spacing for the grid correction for Ewald interactions
only took Coulomb and not LJ into account. Note that with default
settings LJ tables can use a coarser spacing than Coulomb.
Change-Id: Ib0f831a2177bcf10ad9e03c6764cc155e89abdbb
Erik Lindahl [Fri, 27 Jun 2014 09:04:29 +0000 (11:04 +0200)]
Fixed free energy with LJ-PME
First, Only the normal LJ part of the potential was
shifted for LJ-PME with potential-shift
modifier in the free energy kernel,
and not the Ewald component. This had an effect
of roughly 0.05% on the total energy. Second,
Berk found that the verlet nbnxn SIMD LJ-PME kernel
had an issue that caused the potential and force
to be slightly off. With this patch, both
potential and force match the non-free-energy
kernel perfectly with at lambda=0.
Change-Id: I4bc53ce1bdb96ba06656b86470dbf8dbd1e81972
Mark Abraham [Thu, 5 Jun 2014 17:20:56 +0000 (19:20 +0200)]
Convert install guide to markdown
Adds `make install-guide` to make both a plain-text INSTALL for the
tarball, and a monolithic HTML install guide for uploading to the
website. Intended for processing with pandoc, but I don't think
there's any pandoc-specific extensions used. Naturally, if the build
system doesn't have pandoc, then this make target is not available,
just like the other documentation features.
Added more description about various SIMD instruction sets,
portability, and how to use compilers and the GMX_SIMD setting.
Added summary of important CMake options for typical GROMACS
installations.
This now does some variable interpolation to keep accuracy up without
active maintenance, so setting some such variables gets changed a bit.
Mentioned more optional build components
Minor textual changes to the install guide.
Fixes #1440. Refs #1242
Change-Id: Iff8e165759fbf8cc5199c8447e912403b8a79a17
Mark Abraham [Sun, 29 Jun 2014 09:46:03 +0000 (11:46 +0200)]
Merge "Merge release-4-6 into release-5-0" into release-5-0
Berk Hess [Wed, 5 Mar 2014 22:24:30 +0000 (23:24 +0100)]
Updated LJ-PME documentation
Added a description of the more accurate treatment of the LJ
combination rule treatment for LJ-PME.
Also updated the Verlet support table.
Removed old figure describing the quality of an old approximation no
longer available in the code.
Added some usage suggestions.
Change-Id: If671536bced4a404caab10b7aa386f8f88f95c46
Rossen Apostolov [Thu, 19 Jun 2014 09:48:16 +0000 (11:48 +0200)]
Use cosistent style when referring to force fields.
Refs #677.
Change-Id: I386c6d9782c88d5af929a3230cd3beb06f2cfbd2
Teemu Murtola [Sun, 29 Jun 2014 04:39:59 +0000 (07:39 +0300)]
Remove some hardcoded selection string buffers
This removes some arbitrary limitations on the length of the input
string. The error handling would still be in the need of a bigger
overhaul (all of these were in the error handling parts).
Fixes #1538, related to #655.
Change-Id: I1112b5ccae526cf3b8fd079bbabf8d7f61e52635
Roland Schulz [Sun, 29 Jun 2014 07:32:16 +0000 (03:32 -0400)]
Merge release-4-6 into release-5-0
Change-Id: I89230f8a117d9636570e573b7b2657c79aea51c0
Roland Schulz [Sun, 29 Jun 2014 05:17:34 +0000 (01:17 -0400)]
Fix detection of i386 in tmpi
The i386 without underscore is not recommended for new code and is not
defined if -std=... (other than gnu...) is passed on the command line.
__i386__ is already present for GCC 3.2 so there is no need for the old
name. Also we use __i386__ in other places in the code already.
We dont pass such a flag by default for 4.6, but the user could.
In 5.0 this fixes tmpi if the compiler supports c++11 and we pass
std=c++11.
Fixes #1533
Change-Id: I615cb91d3e3196a90fa4ba03fa183bf47af5d444
Erik Lindahl [Tue, 24 Jun 2014 20:54:45 +0000 (22:54 +0200)]
Enable rtp angle/dihedral entries not connected by bonds
pdb2gmx has previously silently ignored any angles or
torsions not connected by bonds. This patch adds code
to mark with RTP/hackblock entries that have been
assigned in this search, and afterwards we add those
that have not yet been matched. In particular, this makes
it possible to have angles or torsions in RTP entries
even if those atoms are not connected by bonds.
Fixes #1276.
Change-Id: I61c3c3954ef8c4cd59956d88b73c6a69c1a66c65
Michael Shirts [Sun, 1 Dec 2013 01:06:10 +0000 (20:06 -0500)]
Allow printing potential energies to dhdl.xvg file
Previously, only total energies were printed out to the dhdl.xvg
file. In many cases, it is more useful to print out just
the potential energies. For example, when doing mdrun -rerun,
and comparing to output run without rerun, the velocities may not
be identical, which makes it difficult to compare the total
energies between runs when computing free energies and other
observables. dhdl-print-energy can now be 'no', 'total',
or 'potential'. The alternative 'kinetic' should generally not
be needed, since that can be done analytically in all cases.
Backwards compatible in the .tpr since gmx_bool is an int. The
old false value will be interpreted as 'no', and the 'yes' value
as 'total' energy, which will reproduce the old behavior.
Fixes #1329
Change-Id: I16828ef07c46bcfc61fe03744cbf251c00160636
David van der Spoel [Sat, 28 Jun 2014 07:33:55 +0000 (09:33 +0200)]
Fixes #1532, SEGV in g_current.
Unfortunately the tool does not do anything useful at this point
in time it seems, it just produces one graph that is non-zero
Change-Id: Ie991b8200628253ab308d36cb5afc80138b1acff
Roland Schulz [Sun, 29 Jun 2014 05:22:10 +0000 (07:22 +0200)]
Merge "Merge branch 'release-4-6' into release-5-0" into release-5-0
Mark Abraham [Sat, 28 Jun 2014 18:59:54 +0000 (20:59 +0200)]
Merge branch 'release-4-6' into release-5-0
Conflicts:
CMakeLists.txt
Left CMake version condition in favour of new fix from release-4-6;
actual settings logic from release-5-0.
Change-Id: I493571b2aca74647a7547d5c2d9463679bdd858a
Roland Schulz [Sat, 28 Jun 2014 04:58:55 +0000 (00:58 -0400)]
Fix error for no 64bit file support
Because the cache was set the error wasn't shown after
rerunning cmake.
Change-Id: I9def74eaecd02d2f2bfc6c40b7954404e2890717
Erik Lindahl [Mon, 23 Jun 2014 14:35:20 +0000 (16:35 +0200)]
Fixed CMAP generation for alanine dipeptide special residue
Fix CMAP to work for residues not detected as proteins, and
make sure we correctly process single-residue entries that
have residue-internal CMAP definitions. In particular, this
is important for the default alanine dipeptide special
residues (ALAD) in Charmm27.
Fixes #824.
Change-Id: I5538b26175f12dcac983491323b5b6ee303c8434
Magnus Lundborg [Mon, 23 Jun 2014 10:07:23 +0000 (12:07 +0200)]
Update TNG build system
GROMACS can now find and use a copy of TNG installed on the system.
The default is still to compile the version shipped with GROMACS.
That compilation is now handled using the BuildTNG.cmake script, so
there is no duplication between the GROMACS and TNG CMake code that
builds TNG, and the result is fully portable with all supported
environments and CMake versions.
Moved TNG handling into src/gromacs/CMakeLists.txt where it is
actually used.
Bumped the version of the TNG library to 1.6. Corresponds to commit
ba9aea42b01 in the TNG repository.
Renamed md5 things with GROMACS prefixes, so that there is no internal
name clash with the md5 things in TNG, and no client of libgromacs can
get unexpected behaviour.
Updated GMX_USE_TNG=off to work, and silenced unused-parameter
warnings associated with that setting.
Refs #1453 (partial fix)
Fixes #1520
Change-Id: I7ac9b578e45b8e75c67c9df9440eed968a3a9371
Mark Abraham [Tue, 20 May 2014 14:52:37 +0000 (16:52 +0200)]
Use parallel terminology more consistently
In user-facing docs, log and debug output, we should be consistent.
(Later, in master, we can fix the code and comments). Definitions:
* core: hardware that actually executes instructions
* socket: a group of cores sharing (e.g.) L3 cache
* node: a group of sockets not needing a network connection
to run in parallel
* thread: vague - an instruction stream (but should not be used
if one of the foregoing is more appropriate)
* rank: an MPI rank (of either flavour), thus containing at least
one thread
* process: in mdrun, regarding parallelism, only used when
needing to distinguish real MPI from tMPI
(These, or similar, will end up in some user docs shortly.)
The goal is to express ourselves in the most relevant abstraction, not
all of them. For example, we should talk about the number of OpenMP
threads per MPI rank without observing that there are two kinds of
implementations of MPI, unless we need to draw a relevant distinction
between those two kinds of implementations.
Where debug output seems more like dumping a data structure than
describing logical state, I've left the names in strings referring to
the members of the data structure (e.g. cr->nodeid, which refers to
the MPI rank).
Changed variable name in gmx_check_thread_affinity_set() from ncpus to
nthreads_hw_avail to make clear that the associated change to the
debug string is correct.
Doubtless there are still uses of "process" that should refer to
"rank," but we use "process" to mean very many different things, so it
is hard to use sed-like tools effectively. Ideally, clang libTooling
would make it easy to find only uses that are present in strings, but
I don't have time to learn how to do that now.
Change-Id: I4dc39dff8be81a30ce803d7833dc305d29d8d188
ngoga [Fri, 6 Dec 2013 09:30:15 +0000 (10:30 +0100)]
Default SD integrator is now sd1 by Nicu Goga
The default SD integrator is now sd1, sd2 is deprecated. grompp
and mdrun both warn about sd2, and recommend sd.
The new sd1 integrator was developed by Herman Berendsen and
implemented by Nicu Goga.
Without constraints the sd1 integrator is nearly unchanged.
With constraints the new sd1 integrator is now as accurate as normal
MD with a leap-frog integrator, whereas the sd2 integrator will give
a slightly too high temperature.
Fixes #1496
Change-Id: I02b4537b05742ed499a84b625c4d4bf8994c0304
Teemu Murtola [Sat, 28 Jun 2014 06:51:00 +0000 (09:51 +0300)]
Remove overeager selection index group check
The check for sorted groups in selections was a bit too eager, and
prevented use of many index groups that would previously have been
perfectly valid for, e.g., g_bond, with gmx distance. Remove the
check. Instead, fix the case where unsorted group is passed as the
value of a selection, and add tests for that.
Will reinstantiate the check later in another form, as currently
unsorted index groups get silently accepted and treated in a more or
less random manner in all other cases. However, this change provides
a usability improvement that could be nice to have, even if I don't
immediately have time to implement the check.
Change-Id: I86e935d8bd08e63a9e3d01fb5a4084d96c5b7006
Roland Schulz [Sat, 28 Jun 2014 05:06:58 +0000 (01:06 -0400)]
Another MacOSX rpath fix
Version comparison was wrong. 2.8.11.x is greater 2.8.11 and thus
was using the 2.8.12 method.
Change-Id: I3eda8c6239ad13194a04fa1da59e99adf2e68519
Roland Schulz [Fri, 27 Jun 2014 23:22:28 +0000 (19:22 -0400)]
Merge release-4-6 into release-5-0
Conflicts:
CMakeLists.txt
share/top/oplsaa.ff/watermodels.dat
src/gromacs/fileio/trxio.c
src/gromacs/gmxana/anadih.c
src/gromacs/gmxana/gmx_chi.c
src/gromacs/gmxana/gmx_tcaf.c
src/gromacs/gmxlib/checkpoint.c
src/gromacs/legacyheaders/tables.h
src/gromacs/mdlib/shellfc.c
src/gromacs/mdlib/tables.c
src/gromacs/pulling/pull.c
src/kernel/readpull.c -> applied to
src/gromacs/gmxpreprocess/readpull.c
src/programs/mdrun/repl_ex.c
Change ignored because was already merged:
src/gromacs/mdlib/sim_util.c
Deleted. No merge:
src/gmxlib/gpu_utils/dummy.cpp
Removal of INSTALL_NAME_DIR not necessary because
was already not there anymore:
src/gmxlib/CMakeLists.txt
src/tools/CMakeLists.txt
src/kernel/CMakeLists.txt
src/mdlib/CMakeLists.txt
Tools deleted - no merge:
src/tools/gmx_bond.c
src/tools/gmx_kinetics.c
Change-Id: Ibeb5a23cce94fb1765ebee271c9c92e001b83630
Erik Lindahl [Fri, 20 Jun 2014 15:23:06 +0000 (17:23 +0200)]
Always set b-state posres, even if identical to a-state
Previously we did not read the b-state position restraint
file (option -rb) if the name was identical to the a-state,
which caused the position restraints to be zero. Rather
than trying to be smart, we now always read it.
Fixes #1399.
Change-Id: I13d93ab667734f022e48143e4cd0672b7f303e1c
Erik Lindahl [Wed, 25 Jun 2014 12:47:17 +0000 (14:47 +0200)]
Update g_density to handle bilayers better
As suggested by Chris Neale, we now properly
perform the binning relative to the center rather than
merely shifting the center of the output. While at it,
I have also added a selection for the group to center on
(useful when the membrane is not in the center of
the system, say with a membrane protein), and an option
that allows us to perform the binning in relative
coordinates and output the average dimensions. The last
is useful when there are large box fluctuations. The
tool now also has an expanded help section with a few
recommendations for bilayers.
Fixes #1168.
Change-Id: Id132311f1d6cd4858f99e8f44a0266667100a406
Erik Lindahl [Wed, 25 Jun 2014 17:41:12 +0000 (19:41 +0200)]
Fix LJPME Lorentz-Berthelot combination rules
Christian found a bug in the way we evaluate
arithmetic combination rules for LJ-PME reciprocal
space. With this change, both group and verlet kernels
produce virtually identical total energies for both
types of reciprocal-space combination rules. It does
not affect the (default) geometric LJPME case.
Change-Id: I4bb0de1df9588dce3ca94e39a370a0b994b25b53
Rossen Apostolov [Thu, 12 Jun 2014 14:26:03 +0000 (16:26 +0200)]
Changed linking order to make Extrae work.
In addition removed redundant GMX_EXTRA_LIBRARIES linkage.
The list is already linked in libgromacs and there's no need
to include it again for mdrun and the tools.
Change-Id: I12e8d32f1f0fb2abceea2a5bd929fad563c1b609
Erik Lindahl [Sat, 21 Jun 2014 21:57:34 +0000 (23:57 +0200)]
Improve PDB I/O (keep occupancy, b-factor, element)
Retain the extra PDB info such as occupancy, b-factors,
and element name columns with trjconv when providing a
PDB structure file. If you use a TPR file, we still
write the (given atomnumbers being present).
However, we deliberately don't store the pdbinfo in the
TPR file since that is a specification for a particular
experiment, rather than something that's valid in the
simulation.
Fixes #917, #1307.
Change-Id: I80cb8f5a250ba094fe81f32c58b4eb0298164053
Carsten Kutzner [Wed, 25 Jun 2014 15:12:19 +0000 (17:12 +0200)]
Remove obsolete pull-geometry option 'position' from documentation.
Change-Id: Ie7e3e962e1b814c92ebba5de499167b3310d713f
Roland Schulz [Thu, 26 Jun 2014 03:58:19 +0000 (23:58 -0400)]
Fix Phi Platform file for MPI
The Platform file was only working without MPI. One could still
compile with MPI without using the toolchain. But now this method
described in the installguide works for MPI too.
Change-Id: I188e3e970a2d4e777ba98cb9e0ea83f6c1276c62
Erik Lindahl [Wed, 25 Jun 2014 13:28:14 +0000 (15:28 +0200)]
Avoid warnings about coupling when free_energy=no
At least during free energy testing it is irritating to
get a new warning about the molecule listed in couple-mol not
being decoupled when we disable free energy - that is why we
are disabling it. Changing the warning to a note, since it is
really a note to to help, not something that will result in a
bad simulation.
Change-Id: If56061be0ff784aeedfc31b92532927ab562392c
Rossen Apostolov [Tue, 17 Jun 2014 08:51:09 +0000 (10:51 +0200)]
Added information about dihedral restraints.
Fixes #1149.
Change-Id: Ifc6ab09d91116f3059addded11f8b0ed4f200545
Rossen Apostolov [Mon, 23 Jun 2014 12:40:57 +0000 (14:40 +0200)]
Remove install_manifest.txt during make clean.
install_manifest.txt is generated in the build tree during install.
If installation is done as root, subsequent 'make install' as
normal user will fail due to permissions issue to overwrite the file.
Change-Id: Ie29b05db3a6b4f7e07ecd88f02e61c92a99ff003
Roland Schulz [Thu, 26 Jun 2014 03:18:19 +0000 (23:18 -0400)]
Fix Visual Studio Project build
Fix two issues with project builds (the default cmake Generator on
Windows, jenkins uses jom):
- build configuration linker flags have to be defined
- only c++ flags are used
Change-Id: I773f45d0937f6bad9a2008ef1cfcbfc6c58a13a0
Mark Abraham [Thu, 26 Jun 2014 15:07:55 +0000 (17:07 +0200)]
Merge "Merge release-4-6 into release-5-0" into release-5-0
Roland Schulz [Tue, 24 Jun 2014 01:52:58 +0000 (21:52 -0400)]
Merge release-4-6 into release-5-0
This merges commit
dced970, which changes many free-energy,
modifier and table-generation code paths, and its fix
349d8056.
That patch
349d8056 contains fixes to potential-shift and
potential-switch, as well as the shift/switch interactions
in combination with free energy. Since 5.0 has undergone
changes in the same areas (both nbnxn free energy, LJ-PME
and force-switch), this commit is a likely place for
bugs to have been introduced, so we keep it as a separate
commit.
Uncrustified the result of the merge.
Conflicts:
src/gmxlib/nonbonded/nb_free_energy.c
Resolved in favour of whichever branch seemed most right; changes from
dced970,
99aa704d and
5f59569a8 were all relevant here. We have
introduced some new LJ-PME-related variables so that code path is
reasonably similar to the coulomb path. We have also fixed a small
bug where the LJPME self-energy (i==j for verlet kernels) was not
multiplied by 0.5.
src/gromacs/gmxlib/nonbonded/nonbonded.c
Resolved as for
dced970
src/gromacs/gmxpreprocess/readir.c
Resolved as for
dced970
src/gromacs/mdlib/forcerec.c
Resolved from both branches
src/gromacs/mdlib/sim_util.c
Resolved from both branches, and from
349d8056
src/gromacs/mdlib/tables.c
Resolved from both branches, and added a few lines of code
to make LJ-PME work with shift modifiers.
As noted above, to avoid breaking the 5.0 branch, we have
manually added the changes corresponding to
349d8056 to make
sure force-switch (same as vdwtype=shift) results in correct
dispersion correction, and we have added a fix for the sign
of the LJPME grid c6 term in the generic nonbonded kernels.
This means
349d8056 should not be merged in again to 5.0 later.
Change-Id: Ida29b143a1bcb727ff38f9c63bf133bf749477b1
Roland Schulz [Thu, 26 Jun 2014 05:02:47 +0000 (01:02 -0400)]
Fix MacOSX rpath
d9d2b0aa74 added rpath for MacOSX but the install rpath
was wrong for MacOSX.
Change-Id: I33984696a0800baf0c58bc13ffbdddc514008750
Erik Lindahl [Mon, 9 Jun 2014 19:06:04 +0000 (21:06 +0200)]
Updated Amber GBSA parameters
Updated parameters according to Per Larsson's post on
gmx-users in November 2012 (076230.html) that found energies
to agree to at least within 0.2kJ/mol (OK, not great).
Fixes #1161.
Change-Id: I1666238c332fb9d8cc82ab6faea672e016d78757
Erik Lindahl [Mon, 23 Jun 2014 19:30:51 +0000 (21:30 +0200)]
Make source compile under Linux X32 ABI
The X32 ABI uses 32-bit pointers in combination with all
other features of x86-64 to save memory. This requires two
minor changes to x86 inline assembly macro checks, where we
need check for __LP64__ (64-bit pointers) rather than
__x86_64__ (which is set for X32). The resulting binaries
run approximately 2% faster, but since it requires all
dependent libraries to be available in X32 format it is
not something we will enable with a simple setting for now.
To use it manually, set CFLAGS and CXXFLAGS to "-O3 -mx32".
Fixes #1263.
Change-Id: I2555b2c68d4bba24f4e581268c472a47fe7d1531
Erik Lindahl [Sun, 22 Jun 2014 06:26:40 +0000 (08:26 +0200)]
Make it harder for compiler to optimize away SIMD CMake tests
On at least one old version of Linux, a new compiler in
combination with an old assembler led to the compiler
understanding the SIMD code but optimizing it away, which made
the test pass even though the assembler could not handle it.
This changes the return value of the CMake tests to be based on
the SIMD operations, which should make them a lot more
difficult to optimize away.
Fixes #1493.
Change-Id: I3e021c3c718cf54afaadf131c5fa911b3933f61e
David van der Spoel [Wed, 25 Jun 2014 07:06:30 +0000 (09:06 +0200)]
Added check for domain decomposition and shells.
Fixes #1376 in as much as that it prevents incorrect calculations.
Can be left out when merging to 5.0 that does not support
particle decomposition. In 5.0 we can write a message about OpenMP
if that works with shells.
Change-Id: Ic07ae70cd3cd5298b6b2d579719da4d267b2d8fb
Mark Abraham [Fri, 13 Jun 2014 13:53:11 +0000 (15:53 +0200)]
Manual fixes
* updates for cut-off schemes
* used more Roman fonts for abbreviations that are not algebraic
* fixed layout and bounding boxes of figures
* removed references to removed GROMACS-87 force fields
* changed formatting of column of [moleculetype] parameter-listing
table because we now have some interactions with really long names
(and some consequent changes to how footnotes and labels
have to work)
* removed out-of-date appendix B section on Modifying GROMACS
* fixed aspects of CHARMM description, including adding the second
reference for nucleic acids, and adding a link to the CHARMM36 port
Change-Id: Icb8c0a6087af282a653bb528d71f77e1bb04fae1
Magnus Lundborg [Thu, 19 Jun 2014 08:56:00 +0000 (10:56 +0200)]
Improved check to decide if to add chain/residue.
Together with the latest TNG library updates this
fixes #1507
Change-Id: Iea7160cc1194fc398f9c4db0cc66f4bd43ce724a
David van der Spoel [Mon, 23 Jun 2014 08:42:00 +0000 (10:42 +0200)]
Added check in grompp for shells and inputrec issues.
Some combinations of inputrec settings do not work with shells,
in particular nstcalcenergy > 1 or use of a twin range cutoff.
This is now checked for in grompp. Fixes #1376.
Change-Id: I4382bcf5231920b22c725a7cf8e7b4e17c2526d9
Berk Hess [Tue, 24 Jun 2014 14:10:31 +0000 (16:10 +0200)]
Fixed the sign of mass perturbed contribution
Corrected the sign of the kinetic energy contribution to dHdl and dH.
Fixes #1527.
Change-Id: Ia1a2f708cdbba9a5a120a2ba8510cc2498f4d054
Erik Lindahl [Mon, 23 Jun 2014 00:34:37 +0000 (02:34 +0200)]
Fixed GROMOS assignment of PRO-NH terminus torsions
This patch also adjusts the parameters for torsions
over N-CA bonds in the termini, according to
suggestions by Justin Lemkul & Drazen Petrov.
Fixes #1022.
Change-Id: Ib00d69eeddf924b1e7e2de33475d774d7da54899
Erik Lindahl [Mon, 23 Jun 2014 00:01:56 +0000 (02:01 +0200)]
Make sure duplicates bondeds are set from hackblocks
Previously the rtp file could end up containing two
entries when the N/C termini databases added interactions.
These were then quicksorted, which could make the
assignment random. We now check for duplicates and
discard the rtp entry in favor of the hackblock.
Fixes #1395.
Change-Id: I505cfbb7e6c8e8050e6e2935cc417e49a515d8d8
Erik Lindahl [Mon, 23 Jun 2014 12:03:17 +0000 (14:03 +0200)]
Clean up CMAP placement in parameter list
Some of the CMAP variables were always placed into and
read from the first entry of the parameter list. While this
did not result in any errors, this patch now places them
correctly in the F_CMAP position.
Fixes #1345.
Change-Id: Ic6e09e46c352976cfc1f57ff903c082b4ec43df8
Erik Lindahl [Mon, 23 Jun 2014 21:05:53 +0000 (23:05 +0200)]
Added multisimulation info to log/output
mdrun now reports that it is part of a multisimulation
setup, how many simulations there are, and that the
detailed MPI/OpenMP data applies to the individual
simulation.
Fixes #1204.
Change-Id: I04f1edf9a7fd1eda202b83713bdd877807242dca
Erik Lindahl [Tue, 24 Jun 2014 08:32:10 +0000 (10:32 +0200)]
Fixed recent bug with disp.corr. and vdwtype=shift
The very recent commit
dced970a introduced a small error
in the dispersion correction with vdwtype=shift.
Change-Id: I23c082ed190a5eda096504a23b277fb879c5feb4
Rossen Apostolov [Thu, 19 Jun 2014 10:26:27 +0000 (12:26 +0200)]
Extend version checking/warnings for checkpoint continuation
Detect if the major/minor versions differ, and write a more
explicit warning that both explains this type of continuation
is unsupported, and recommend to use the -noappend option.
In contrast, for cases where only the patch level differs,
we now only issue a note that the binary has changed, since
this is fully supported.
Fixes #1230.
Change-Id: Ifec509de0e5a05d170ada89fd000c961e311c9ca
Erik Lindahl [Mon, 23 Jun 2014 22:28:15 +0000 (00:28 +0200)]
Enable terminus-specific atom translation
By adding protein-nterm and protein-cterm classes for atom
name translation in xlateat.dat we now avoid replacing
names such as O2 in non-standard amino acids. This patch
also corrects a cosmetic issue in the number of residues
claimed to be found in each chain by pdb2gmx.
Fixes #567.
Change-Id: I5956991e3ff3e5e1202330a857fd773f9e9b6945
Rossen Apostolov [Thu, 12 Jun 2014 15:21:10 +0000 (17:21 +0200)]
Added tip5p to the list of watermodels in some FF.
Added support for flexible tip5p to OPLSAA and parameters
were taken from the Amber/Charmm tip5p.itp files.
There are, however, various problems with that water model.
This commit doesn't resolve them so the bug report below
will need to be followed up at later stage.
watermodels.dat now includes a note about these issues
and refers users to the redmine report.
Refs #1348.
Change-Id: I3adaae21f35efbb4240716e91f1bb5d256c8853e
Erik Lindahl [Sat, 21 Jun 2014 21:30:50 +0000 (23:30 +0200)]
Enable 4-letter resname in PDB output, keeps more pdbinfo.
This still fully adheres to the PDB standard since column 21
is not used by the standard. All common programs (PyMol, VMD, etc)
understand the 4-letter format, and programs that only read three
letters will still read the same filename as they used to. In
particular, this conserves most residue names during pdb<->gro
format conversions. We have also killed the non-standard
wide pdb format to avoid writing broken PDB files.
Fixes #725. Refs #917.
Change-Id: I9b6b8f2e191acdfb65ca2b5d96f39249cd71ea98
Erik Lindahl [Thu, 12 Jun 2014 08:30:44 +0000 (10:30 +0200)]
Detect non-fatal warnings when trying CFlags for source
We now first check the flag itself (and catch warnings),
after which we check if our SIMD source compiles with it.
Fixes #1461.
Change-Id: Ic6ae99f62c5657195a59dc83ab08399d3491249a
Erik Lindahl [Mon, 23 Jun 2014 10:59:19 +0000 (12:59 +0200)]
Enable xvgr output and labels for g_principal
g_principal now writes proper xgr files instead of raw
data files, and the output has more explanatory axis
labels as well as legends for the data sets.
Fixes #609.
Change-Id: I1eb7914a25661734e6a95e70413194ef723f9635
Erik Lindahl [Fri, 20 Jun 2014 15:52:51 +0000 (17:52 +0200)]
Disallow extracting V/F from XTC files in g_traj
We now issue a fatal error if the user asks for velocities or
forces to be written to as output from g_traj when the input
XTC file does not contain these quantities.
Fixes #1298.
Change-Id: I45a12fb1e5db5b2b2e1b072444e5430373fbaaa3