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
Christoph Junghans [Wed, 8 Feb 2012 00:04:07 +0000 (01:04 +0100)]
Merge "fixed confusing nonbonded kernel pointer initialization" into release-4-6
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
Roland Schulz [Fri, 3 Feb 2012 18:43:09 +0000 (13:43 -0500)]
Merge remote-tracking branch 'gerrit/release-4-5-patches' into release-4-6
Change-Id: I825d441cf0d13d53ea8b460cb97e2e7775f2e8ce
David van der Spoel [Fri, 3 Feb 2012 07:54:53 +0000 (08:54 +0100)]
Merge "Improved the accuracy of the sd1 integrator" into release-4-6
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
Szilárd Páll [Thu, 2 Feb 2012 21:25:51 +0000 (22:25 +0100)]
Merge "Merges in threading branch as one squashed commit" into release-4-6
Szilard Pall [Thu, 2 Feb 2012 20:36:36 +0000 (21:36 +0100)]
fixed confusing nonbonded kernel pointer initialization
Change-Id: I590c7c08d77491f05c798ccc4abf4de988b950f5
Roland Schulz [Sun, 15 Jan 2012 06:18:38 +0000 (01:18 -0500)]
Merges in threading branch as one squashed commit
Implements OpenMP threading for PME
All PME (including SSE) code by Berk.
FFT, timer, and CPU affinity code by Roland.
Two bugfixes by Szilard.
Conflicts:
include/gmx_wallcycle.h
src/gmxlib/trxio.c
src/mdlib/Makefile.am
src/mdlib/fft5d.c
src/mdlib/gmx_wallcycle.c
src/tools/acf.test.c
Change-Id: I4bdd0e29caf135ba6b4cc7297640f29f0d136656
Teemu Murtola [Thu, 2 Feb 2012 16:10:18 +0000 (17:10 +0100)]
Merge "Revert "Fix ICC on Windows Build"" into release-4-5-patches
Berk Hess [Thu, 2 Feb 2012 14:25:43 +0000 (15:25 +0100)]
Improved the accuracy of the sd1 integrator
There was a small error in one of the coefficients of the sd1 integrator.
Correcting this makes sd1 as accurate as sd, unless constraints are used.
Change-Id: I2f71a80cc0487d92fd151c6ea4f243feb228626c
Christoph Junghans [Wed, 1 Feb 2012 17:44:28 +0000 (10:44 -0700)]
initialize adress_do_hybridpairs=FALSE by default
fr->adress_do_hybridpairs is evaluated in nonbonded.c:1028 even if
adress is actually off, so it could be used uninitialized, set it
to false for this case.
Change-Id: I6868e7ecc5c484c95483f5bc94f8205350e39028
David van der Spoel [Wed, 1 Feb 2012 16:28:33 +0000 (17:28 +0100)]
Merge "g_sans - tool to compute SANS spectra" into release-4-6
David van der Spoel [Wed, 1 Feb 2012 08:10:58 +0000 (09:10 +0100)]
Merge "Fixed error message to identify the correct file" into release-4-5-patches
David van der Spoel [Wed, 1 Feb 2012 07:58:54 +0000 (08:58 +0100)]
Merge "Fixed trjconv -sub" into release-4-5-patches
David van der Spoel [Wed, 1 Feb 2012 07:57:14 +0000 (08:57 +0100)]
Merge "Improved error message" into release-4-5-patches
Mark Abraham [Wed, 1 Feb 2012 05:57:08 +0000 (16:57 +1100)]
Fixed trjconv -sub
If the index group contains 1..100, then clust->maxframe == 99,
and thus when frame == clust->maxframe it should be included
in the cluster.
Change-Id: I6e093d9f76d0952b31ea9ee1516bade9e9b4419b
Mark Abraham [Wed, 1 Feb 2012 04:45:41 +0000 (15:45 +1100)]
Fixed error message to identify the correct file
When a frame exists, that file has *not* run out of frames.
Change-Id: Ief52d5a17ef73ab318f6d8e00d1f5acb71b69f52
Christoph Junghans [Wed, 1 Feb 2012 04:52:29 +0000 (05:52 +0100)]
Merge "Fix signed/unsigned warnings" into release-4-5-patches
Mark Abraham [Tue, 31 Jan 2012 13:43:18 +0000 (00:43 +1100)]
Improved error message
Users would be confused by "Atom N3 is used in an interaction of
type atom in the topology database..." so when "atom" is the
bondtype we don't mention the fact.
Also changed variable name from bDontQuit to bAllowMissing for
consistency with variable names used in pdb2gmx when calling
this code.
Change-Id: Ie8cb3ba64f39d3746b470fa6ae44f5a6f4b6a16c
Roland Schulz [Tue, 31 Jan 2012 23:47:52 +0000 (00:47 +0100)]
Revert "Fix ICC on Windows Build"
This reverts commit
e8e495fe4317c2e489acb4e82e004afdac618e92
Martin Hoefling [Fri, 20 Jan 2012 21:04:30 +0000 (22:04 +0100)]
implemented -intra switch for g_dist (now based on release-4-6)
Change-Id: I7fc226a71bd5bd5e1be866177fbecf5dd443dbd1
Roland Schulz [Tue, 31 Jan 2012 11:01:29 +0000 (06:01 -0500)]
Append all ICC Performance flags only to Release Flags
Some of the ICC performance flags were appended to GMXC_CFLAGS
and thus also used e.g. for Debug.
Change-Id: Iadfaa29fb347f24208e6f2406e0d1ad41f037804
David van der Spoel [Tue, 31 Jan 2012 18:38:42 +0000 (19:38 +0100)]
Merge "Fix ICC on Windows Build" into release-4-5-patches
David van der Spoel [Tue, 31 Jan 2012 15:39:34 +0000 (16:39 +0100)]
Changed order of parameters in top file
For linear angles. Now the distance parameter comes
first, and then the force constant, like in other
bonded potentials. In addition, the angle defined by
the same atom types but with the opposite order of
atoms now gets a modified constant (1-a).
Change-Id: I6db408be01b0cbb795edaa9943b72dbe149e3f97
Mark Abraham [Tue, 31 Jan 2012 13:51:19 +0000 (14:51 +0100)]
Merge "Corrected use of ?: in conditional" into release-4-5-patches
Roland Schulz [Mon, 30 Jan 2012 07:34:03 +0000 (02:34 -0500)]
Fix signed/unsigned warnings
Change-Id: I3318f06f303a08068849d820381e99267543b4f5
Mark Abraham [Tue, 31 Jan 2012 07:10:55 +0000 (18:10 +1100)]
Made error message even more explicit
Change-Id: Ib1f2e01ca24c5fb305fe220e34797d6991c3f080
Roland Schulz [Mon, 30 Jan 2012 07:11:48 +0000 (02:11 -0500)]
Fix ICC on Windows Build
The workaround in parser.y may not be necessary any longer when this is
merged into master.
Change-Id: I48199b55ede5d786a69c41ab008ef3055101d3b0
Mark Abraham [Tue, 31 Jan 2012 05:20:16 +0000 (16:20 +1100)]
Corrected use of ?: in conditional
Patch contributed by Matthew Zwier to fix the incorrect use of
precedence of ?: and != operators.
Fixes #872
Change-Id: Ie4bbc3cbdaf33fc0386d12c2e142a9c076c2e946
Alexey Shvetsov [Sun, 6 Nov 2011 20:17:53 +0000 (00:17 +0400)]
g_sans - tool to compute SANS spectra
This tool can compute sans spectra from tpr files
using Debye method (both direct evalution of g(r) and
Monte carlo one).
Change-Id: Ia2eaed81294d0f5ddc3d79e532dc1f616fdde381
Signed-off-by: Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru>
Roland Schulz [Wed, 25 Jan 2012 18:37:02 +0000 (19:37 +0100)]
Merge "Merge release-4-5-patches into release-4-6" into release-4-6
Roland Schulz [Wed, 25 Jan 2012 18:36:49 +0000 (19:36 +0100)]
Merge "New approach for GerritBuild script" into release-4-5-patches
Berk Hess [Wed, 25 Jan 2012 11:25:49 +0000 (12:25 +0100)]
Merge "Added two new bonded functions." into release-4-6
David van der Spoel [Thu, 19 Jan 2012 19:20:46 +0000 (20:20 +0100)]
Added two new bonded functions.
The first one implements a potential for linear angles without any
discontinuities at 180 degrees. A paper is being written about this. The
potential has [ angles ] type 9 or F_LINEAR_ANGLES internally.
A free energy option has been implemented as well for the linear angles.
The second is an anharmonic polarization function, based on the normal harmonic
term plus a forth order term, as introduced by the Roux group in
J. Chem. Theor. Comput. 6 (2010) p. 774-786. The potential has [ polarization ]
type 2 or F_ANHARM_POL internally.
Change-Id: I0497ed20baf1c1c0b2a6c2354eed77bc9ed75c6d
Christoph Junghans [Wed, 25 Jan 2012 00:27:39 +0000 (17:27 -0700)]
make gromacs manual build again
* bug was introduced in
78534fcaabfc8e3990ea50b1a798dc7713995745
* updated ref to make it consistent with the manual
Change-Id: I9664bfa5e4d6487ed664d2f38bebd1daa92496ba
Sebastian Fritsch [Tue, 24 Jan 2012 21:57:14 +0000 (22:57 +0100)]
Merge "document AdResS mdp options" into release-4-6
Christoph Junghans [Mon, 23 Jan 2012 20:17:18 +0000 (13:17 -0700)]
document AdResS mdp options
* 1st version
* incl. Sebastian's comments
Change-Id: Ifa5a3d979078de1e1a08d3eb3e50b80b5b71cdce
Carsten Kutzner [Tue, 20 Dec 2011 17:53:32 +0000 (18:53 +0100)]
New tool that extracts dye dynamics from trajectories
Change-Id: Ie2007a60ad612938160197c0ec091e474e7091d2
David van der Spoel [Fri, 20 Jan 2012 08:15:33 +0000 (09:15 +0100)]
Merge "Fixed timing measurements." into release-4-5-patches
Roland Schulz [Thu, 19 Jan 2012 06:11:18 +0000 (01:11 -0500)]
Merge release-4-5-patches into release-4-6
Conflicts:
admin/GerritBuild
admin/GerritBuild.bat
Change-Id: I812540cbc8c076aae9f21c52eb035b920430e033
Roland Schulz [Wed, 18 Jan 2012 09:21:18 +0000 (04:21 -0500)]
New approach for GerritBuild script
- Allows to make changes to build in seperate RelEng repository
- Replaces Matrix view by a linear list of configurations
Change-Id: I7f5c76805836c4cd06527b949ab7ac68f27a31b5
Roland Schulz [Wed, 18 Jan 2012 08:05:54 +0000 (09:05 +0100)]
Revert "Replace stderr by stdout in editconf terminal output for easier scripting."
This reverts commit
bc2fbe9b50a8a39a185cb6a448dea43c8ad9ed7b
Szilard Pall [Mon, 16 Jan 2012 20:46:59 +0000 (21:46 +0100)]
Fixed timing measurements.
With the VV integrator, kinetic energy calculations are done before the
main MD loop. These should be excluded from the timing measurements.
Change-Id: Ib06b1154965735adc0ff2e20802f78d96ed6fca4
David van der Spoel [Tue, 17 Jan 2012 10:56:28 +0000 (11:56 +0100)]
Replace stderr by stdout in editconf terminal output for easier scripting.
Change-Id: If477f6148d347fbbed16d37db62e2e12f1444ece
Sander Pronk [Mon, 16 Jan 2012 16:50:42 +0000 (17:50 +0100)]
Thread affinity and x86 assembly fixes for thread_mpi
set_affinity_np now fails silently (shouldn't do much on recent linux
systems, anyway)
x86 asm changes for llvm compatibility.
Change-Id: Id1e71d3e693bc39f5a5e84b0e949fb41c7b7d0e3
Christoph Junghans [Sun, 15 Jan 2012 01:47:41 +0000 (02:47 +0100)]
Merge "Added CMake Toolchain file for BlueGene/P" into release-4-5-patches
Mark Abraham [Sat, 14 Jan 2012 05:37:18 +0000 (06:37 +0100)]
Merge "Remove use of FindMPI.cmake" into release-4-6
Mark Abraham [Sat, 14 Jan 2012 05:18:14 +0000 (06:18 +0100)]
Merge "Removing outdated vsite comment" into release-4-6
Mark Abraham [Mon, 9 Jan 2012 09:38:33 +0000 (20:38 +1100)]
Remove use of FindMPI.cmake
The functionality of FindMPI.cmake should not be needed for GROMACS,
since the wrapper compiler will do the complete job. This already
worked for Cray and BlueGene, and so far this new version is known
to work for OpenMPI wrapping icc and gcc.
CMake now warns the user about possible unsuitable versions of
OpenMPI and MVAPICH2.
The process of managing MPI is more modular than it used to be.
To use:
cmake .. -DGMX_MPI=ON -DCMAKE_C_COMPILER=`which mpicc`
or with bash
CC=mpicc cmake .. -DGMX_MPI=ON
and whatever else suits your setup.
Fixes #851 and #636.
Change-Id: Ibe41206bed8b70b83a25da1e4e29dd87b61ea17d
Christoph Junghans [Fri, 13 Jan 2012 18:00:13 +0000 (11:00 -0700)]
CMake improvements
* make CMake quiet again, when running for the second time
* remember that VMD was found before
* removed duplicate definition of HAVE_FSEEKO
Change-Id: If2a2cc600fd14e67c6169e12172e7c5aa8ebedfc
Roland Schulz [Fri, 13 Jan 2012 22:08:04 +0000 (23:08 +0100)]
Merge "Fixed MSVC compiling with plug-in support" into release-4-6
Roland Schulz [Fri, 13 Jan 2012 18:54:42 +0000 (13:54 -0500)]
Removing outdated vsite comment
Vsite parameters were replace by Berk in commit
14bc4ad9 by
calculated parameters. Since then the comment was outdated.
Change-Id: I6ddacfbdcf40e11db9d2d3091d9c34f4872816bc
Christoph Junghans [Thu, 9 Jun 2011 09:16:58 +0000 (11:16 +0200)]
Adds AdResS feature to gromacs
This is actually a rebase of the following commits:
* backport adress to 4.5, was ported from adress branch, which is based on the master
* update init_forcerec in gmx_membed.c due to adress
* energy terms in AdreS only caclulated for meaningful properties.
* adress variables only printed if adress is used
* grompp checks to prevent adress being used with lr coulomb or pressure coupling
* Windows/C90 fixes
* put inputrec variables into adress struct
* increases tpx_version from 74 to 75 (as enforced rotation was 74)
* rebase to recent 4.6 branch
* bAdress to false for tpx < 75 (disabled by default)
Change-Id: Ica1d121f8edb9086ac2d5d456b1037a3d57a24e4
Mark Abraham [Wed, 4 Jan 2012 03:47:05 +0000 (14:47 +1100)]
Fixed use of isfinite and _isfinite
Implemented proper CMake tests for the above functionality.
Catered for MSVC idiosyncratic _finite() function. Removed
erroneous use of HAS_ISFINITE and HAS__ISFINITE.
Encapsulated the use of preprocessor directives into the new
gmx_isfinite() function so the programmer doesn't need to
know about the foregoing mess.
The previous versions resulted in unreachable code.
Change-Id: I7471388ed8f402c3f8b664e7846465de4b85f578
Mark Abraham [Mon, 9 Jan 2012 13:55:58 +0000 (00:55 +1100)]
Fixed MSVC compiling with plug-in support
Fixes #598
Change-Id: I8fe274a83c4965466f1241d2237ca3e77b93b038
Mark Abraham [Mon, 9 Jan 2012 13:50:56 +0000 (00:50 +1100)]
Fixed use of _snprintf_s with MSVC
Change-Id: I807ef17e8b4eb07861600c6a1d9d03f330f17218
Roland Schulz [Sat, 7 Jan 2012 16:52:32 +0000 (11:52 -0500)]
Check for VMD plugins that they are at least abi-version 10
All plugins with VMD 1.8 are abi-version 10. Plugin support is
untested for older versions.
Change-Id: I98fe11313d7115d476e44bff0bc729c7380c52f0
Mark Abraham [Thu, 5 Jan 2012 06:21:14 +0000 (17:21 +1100)]
Made use of VMD plugins more robust
Attempt to use VMD trajectory-reading plugins only if plugin
loading functionality exists and shared libraries are being used
(else dlopen can be unreliable).
Also, for helping to find those plugins, the user can supply the plug-in
path in a CMake cache variable. If not, the code can now fall back
on the run-time value of the environment variable VMDDIR, or its
value at configuration time. Previously only an explicit run-time
environment variable or a hard-coded path was available on non-Windows
platforms.
Also printed diagnostic text when GROMACS cannot tell if the
trajectory being read by a plug-in might have atom velocities.
Fixes #598
Change-Id: I44267e115267772dae2c1d754895f8ff25c98a6a
Christoph Junghans [Wed, 4 Jan 2012 15:52:39 +0000 (16:52 +0100)]
Merge "Documented the function of g_cluster -cl -noav" into release-4-5-patches
David van der Spoel [Wed, 4 Jan 2012 09:58:22 +0000 (10:58 +0100)]
Introduced fatal error in grompp for incorrect use of settle and charge groups.
Change-Id: I02dfe3f3454a6fc329d9b5ecb2fd4b544c8d2cd1
Mark Abraham [Fri, 16 Dec 2011 04:02:52 +0000 (15:02 +1100)]
Added CMake Toolchain file for BlueGene/P
Change-Id: Iff9b5fe3cccc4d18fc252856a1b50ee64630b54a
Mark Abraham [Thu, 29 Dec 2011 22:39:34 +0000 (09:39 +1100)]
Documented the function of g_cluster -cl -noav
A definition was needed for the center of a cluster.
Change-Id: Id1c6d2f229feb27b7981c2d616e78e510d215a9a
Roland Schulz [Tue, 27 Dec 2011 09:29:19 +0000 (10:29 +0100)]
Merge "Added -dhdl to tpr file list, fixes #855" into release-4-5-patches
Roland Schulz [Mon, 26 Dec 2011 14:06:22 +0000 (09:06 -0500)]
Merge remote-tracking branch 'gerrit/release-4-5-patches' into release-4-6
Conflicts:
src/tools/gmx_tune_pme.c
Change-Id: I0cb93d965cd30a6d0e158eac595fac7c8b891492
Carsten Kutzner [Mon, 19 Dec 2011 14:42:29 +0000 (15:42 +0100)]
Added -dhdl to tpr file list, fixes #855
Change-Id: I2621c7bb44daa01e25831e2d44c22cdcf47f58e7
Roland Schulz [Tue, 20 Dec 2011 12:28:48 +0000 (07:28 -0500)]
Merge release-4-5-patches into release-4-6
Conflicts:
admin/GerritBuild.bat
include/gstat.h
src/tools/anadih.c
src/tools/gmx_chi.c
Change-Id: If70475e8f38978aeb52652afce2ca2a62d355987
Roland Schulz [Tue, 20 Dec 2011 07:52:33 +0000 (08:52 +0100)]
Merge "Using MinSizeRel configuration and Release target on Windows" into release-4-5-patches
Roland Schulz [Tue, 20 Dec 2011 07:52:06 +0000 (08:52 +0100)]
Merge changes Iaf4c56b7,Ibabed87f into release-4-5-patches
* changes:
Testing external BLAS/LAPACK
Using 2 cores per build on Windows
Christoph Junghans [Mon, 19 Dec 2011 18:23:25 +0000 (11:23 -0700)]
Set GMX_*_ASM true if GMX_ACCELERATION != auto
In case GMX_ACCELERATION was set to SSE manually (like in Gentoo Linux)
GMX_*_ASM would never be set (false), so sse kernel will not be build.
Change-Id: Icf04707c6174a0182fe4472536b568e1d2d91166
Carsten Kutzner [Wed, 23 Nov 2011 17:37:38 +0000 (18:37 +0100)]
Enforced rotation
Change-Id: Ia2d3b409c197fd2a6bd5922b636bd40a47046918
Roland Schulz [Thu, 15 Dec 2011 12:01:55 +0000 (07:01 -0500)]
Using MinSizeRel configuration and Release target on Windows
Faster build:
no need to compute debug symbols
dynamic library
low optimization level
Also fixing MSVC warnings with this configuration
Change-Id: Ic87da40f1e78e2ac70ef543525b49f4cf1a3f639
Roland Schulz [Thu, 15 Dec 2011 08:20:17 +0000 (03:20 -0500)]
Testing external BLAS/LAPACK
Change-Id: Iaf4c56b7e62654425801cd8d3272c4028b016a2a
Roland Schulz [Thu, 15 Dec 2011 06:27:08 +0000 (01:27 -0500)]
Using 2 cores per build on Windows
Windows build is much slower than Linux build. Don't understand why
but hopefully using 2 cores will help narrow that gap.
Change-Id: Ibabed87f2f4d6c931fbb1ebd25c571be9a2cb9ee
Roland Schulz [Wed, 14 Dec 2011 01:49:28 +0000 (02:49 +0100)]
Merge "Re-fixed static linking of maths libraries under UNIX" into release-4-5-patches
Mark Abraham [Wed, 14 Dec 2011 01:10:26 +0000 (12:10 +1100)]
Re-fixed static linking of maths libraries under UNIX
In commit
5e51ffa9 I submitted a patch for the above case, and
suggested the same to CMake. The CMake developers have refined
this and I'm back-porting their fix here.
See http://public.kitware.com/Bug/view.php?id=12477 for details
Change-Id: Ib48bc6b5a87b66b51c893e24aa42e4cd4db32a38
Roland Schulz [Tue, 13 Dec 2011 07:29:42 +0000 (08:29 +0100)]
Merge "Converted macro usage for readability" into release-4-6
Mark Abraham [Sun, 4 Dec 2011 23:58:54 +0000 (10:58 +1100)]
Converted macro usage for readability
Replaced some helper macros with inline functions, and expanded
the macro that was implementing three nested loops.
Change-Id: I48e1d6a5401e21cd99b51158e3ddcb1729f842b3
Roland Schulz [Tue, 13 Dec 2011 02:04:29 +0000 (03:04 +0100)]
Merge "Relaxed some assumptions about trajectory times" into release-4-5-patches
Mark Abraham [Tue, 13 Dec 2011 00:04:04 +0000 (11:04 +1100)]
Relaxed some assumptions about trajectory times
Counting of dihedral transitions used to assume that each frame was
equally spaced in time. This is only necessary for making a
subsequent histogram of those transition times (unless more
elaborate machinery was written for that histogram).
Also documented what g_angle -ot and -oh do.
Change-Id: I587dba94c40a1a69e5aa227d09271166db055595
Mark Abraham [Sun, 4 Dec 2011 22:50:25 +0000 (09:50 +1100)]
Fixed macros that ended in semicolons
These now don't end in semicolons, which makes life much simpler
when using parsing tools that are not (fully) macro-aware.
Also replaced some compound-statement macros with inline functions.
Change-Id: Ic83d9419a67d82665ff250e0568a85cf9a8f1c32
Roland Schulz [Sun, 11 Dec 2011 20:05:19 +0000 (15:05 -0500)]
Merge release-4-5-patches into release-4-6
Conflicts:
admin/GerritBuild.bat
Change-Id: Ib62e8f5949cc8e65342cd1826888901d11032474
Roland Schulz [Sun, 11 Dec 2011 19:47:54 +0000 (20:47 +0100)]
Merge "Set -DMPI only if compiled for FAH" into release-4-5-patches
Roland Schulz [Sun, 11 Dec 2011 18:51:07 +0000 (13:51 -0500)]
Set -DMPI only if compiled for FAH
MPI conflicts with C++ MPI namespace.
This allows to compile with FAH or with C++ and MPI.
Compiling with FAH and C++ and MPI will still have a name conflict.
Resolves #849
Change-Id: I73ccb7b0e682ae6d12352c76e26c6d79e93ea798
Roland Schulz [Sun, 11 Dec 2011 02:35:47 +0000 (21:35 -0500)]
Fixing MSVC unsigned/signed warnings
Change-Id: I110b591cfd8c8078f3b7853bdf2db6a705e9e453
Roland Schulz [Sat, 10 Dec 2011 00:53:12 +0000 (19:53 -0500)]
Run tests also on Windows
Change-Id: Iab166b5cc8e394e3d330afffd86aced00aa7e0a2
Roland Schulz [Tue, 11 Oct 2011 21:32:42 +0000 (17:32 -0400)]
Only check those atoms for PBC which are part of selection (Issue #809)
Change-Id: I2afccb82c3b761890f4d1f53d842606bb8404c98
Roland Schulz [Thu, 8 Dec 2011 19:59:20 +0000 (20:59 +0100)]
Merge "Added an option to easily compile contrib programs with cmake" into release-4-6
Roland Schulz [Thu, 8 Dec 2011 19:57:05 +0000 (20:57 +0100)]
Merge "Fix selection parsing in double precision." into release-4-5-patches
Roland Schulz [Thu, 8 Dec 2011 19:53:08 +0000 (20:53 +0100)]
Merge "Avoid possible warnings if HUGE_VAL != infinity." into release-4-5-patches
Roland Schulz [Fri, 25 Nov 2011 11:34:06 +0000 (06:34 -0500)]
Remove RETSIGTYPE. C89 defines return value to be void.
Because it is defined in C89 no sane system should require this anymore.
Checked for Windows.
See e.g. http://lists.gnu.org/archive/html/emacs-devel/2011-03/msg01076.html
Change-Id: If24fa3d47a1ddec189784f49e3e59e1936fe263d
Roland Schulz [Fri, 2 Dec 2011 21:48:17 +0000 (16:48 -0500)]
Adding support for Windows build and different CMake Versions
Ant doesn't work very well - trying shell script instead
Change-Id: Ia08e6979c0e0734c33183840c9d34c3a7367af4a
Roland Schulz [Fri, 2 Dec 2011 21:48:17 +0000 (16:48 -0500)]
Adding support for Windows build and different CMake Versions
Ant doesn't work very well - trying shell script instead
Change-Id: Ia08e6979c0e0734c33183840c9d34c3a7367af4a
Teemu Murtola [Thu, 1 Dec 2011 16:00:09 +0000 (18:00 +0200)]
Fix selection parsing in double precision.
Fixes #850.
Change-Id: Ifd0bf1f5401ca4d62571c8c2fc39e67cac537ecf
Teemu Murtola [Thu, 1 Dec 2011 15:52:28 +0000 (17:52 +0200)]
Avoid possible warnings if HUGE_VAL != infinity.
Replaced HUGE_VAL by GMX_REAL_MAX in one source file for trajectory
analysis library source file, since it seemed to cause compiler warnings
on some systems.
Reported by Chris Neale on gmx-users.
Change-Id: Ic52a01c5bcedb244d1453117f626ef4f0d46df78
Roland Schulz [Wed, 30 Nov 2011 10:10:25 +0000 (05:10 -0500)]
Adding Gerrit Build description
Change-Id: Ib9e88333967178c8f0962a72e5f8432067094e77
Roland Schulz [Wed, 30 Nov 2011 10:10:25 +0000 (05:10 -0500)]
Adding Gerrit Build description
Change-Id: Ib9e88333967178c8f0962a72e5f8432067094e77
Roland Schulz [Sun, 27 Nov 2011 21:30:25 +0000 (16:30 -0500)]
Removing TestBuildAll test
No need for it because ctest automtically tests building anyhow
It does not work under Windows (using msbuild not make)
Change-Id: I02c7152d61cbe5b536c86c406f37ed78db94ee11
Roland Schulz [Wed, 30 Nov 2011 05:37:37 +0000 (06:37 +0100)]
Merge "Merge remote-tracking branch 'gerrit/release-4-5-patches' into release-4-6" into release-4-6