Szilard Pall [Mon, 3 Sep 2012 10:40:56 +0000 (12:40 +0200)]
Merge branch 'release-4-5-patches' into release-4-6
Conflicts:
src/mdlib/tpi.c
Change-Id: I1b5d92291ece7cf3194b4e1d88cd686a5aa18696
Roland Schulz [Sun, 2 Sep 2012 16:26:22 +0000 (12:26 -0400)]
Fix stack error in grompp
vsiteatoms array was one to short
Fixes #997
Change-Id: I0897694dfc431a20bd1ebf769b24d09038d588b2
Berk Hess [Wed, 29 Aug 2012 16:00:08 +0000 (18:00 +0200)]
bug fix for pme.c MPI_COMM_NULL fix
dcf8b67e
Change-Id: Idb233db1337bcb881041caec96572e5df6183e6e
Sander Pronk [Tue, 21 Aug 2012 11:10:45 +0000 (13:10 +0200)]
Newer version of thread_mpi, with various fixes, including tMPI_Scan()
- Implements tMPI_Scan()
- Many doxygen fixes
- removed unused variables from atomic operations
- Added C++11 compatible thread and mutex class
Change-Id: I4cce48627fa846da3c599a7de64d3898c358390b
Bogdan Iorga [Wed, 22 Aug 2012 16:30:26 +0000 (18:30 +0200)]
Added PGLU entry in aminoacids.n.tdb for OPLS-AA.
Previously, pdb2gmx would fail during terminus selection for this residue.
Change submitted initially on the master branch, then abandoned.
(https://gerrit.gromacs.org/#/c/1290/)
Fixes #804.
Change-Id: Ic810242dc65019858c0332d352ef1ba96d4662d6
Christoph Junghans [Mon, 20 Aug 2012 17:52:48 +0000 (19:52 +0200)]
Merge "Fixing of things associated with aminoacid.rtp header" into release-4-6
Christoph Junghans [Mon, 20 Aug 2012 17:51:08 +0000 (19:51 +0200)]
Merge "Clean up some variable naming for eigensolving" into release-4-6
Christoph Junghans [Mon, 20 Aug 2012 17:50:53 +0000 (19:50 +0200)]
Merge "Fix coordinate is zero check in gmxcheck" into release-4-5-patches
Christoph Junghans [Mon, 20 Aug 2012 17:50:35 +0000 (19:50 +0200)]
Merge "Explicitly noted an issue with use of genbox -maxsol" into release-4-6
Roland Schulz [Sat, 18 Aug 2012 19:30:09 +0000 (21:30 +0200)]
Merge "fix AdResS and long-range electrostatics warning" into release-4-6
Roland Schulz [Thu, 16 Aug 2012 23:50:15 +0000 (19:50 -0400)]
Fix coordinate is zero check in gmxcheck
Change-Id: I7504d235edc659b586d61243f3cbf72add2f92b2
David van der Spoel [Thu, 16 Aug 2012 07:45:41 +0000 (09:45 +0200)]
Optional computation of fluct. props in g_energy. Fixes #954
Added a command line option -fluct_props to turn on the computation
of heat capacity etc. in g_energy. This prevents a warning message
from appearing on the screen each time the program is run.
Change-Id: I0cac44494ec5a366762d4d0a915146298d2ce1e0
Mark Abraham [Tue, 14 Aug 2012 05:02:34 +0000 (15:02 +1000)]
Explicitly noted an issue with use of genbox -maxsol
Change-Id: I6f16c94296e7e17150331e4d3072d6430fb87bff
Mark Abraham [Tue, 14 Aug 2012 04:59:11 +0000 (14:59 +1000)]
Don't silently accept genbox -nmol without -ci
Change-Id: Ia50da1ee741eec9ea49ec04eb9fd14dd6b3116fc
Christoph Junghans [Mon, 13 Aug 2012 01:57:56 +0000 (19:57 -0600)]
fix AdResS and long-range electrostatics warning
Change-Id: Ibe6615e327a1a386f2fec5746e843fcf8fba5401
Mark Abraham [Fri, 10 Aug 2012 01:41:25 +0000 (11:41 +1000)]
Clean up some variable naming for eigensolving
Change-Id: I42c1751f505e931c7245a4804c1609d0e369e23f
Roland Schulz [Sat, 28 Jul 2012 18:32:18 +0000 (14:32 -0400)]
Make GCC OpenMP libraries static if GMX_PREFER_STATIC_OPENMP
Change-Id: I9ef26070c289f83f9d0f9e76635bb3a3dd493570
Roland Schulz [Sat, 28 Jul 2012 17:25:34 +0000 (13:25 -0400)]
Guarantee OpenMP flags for linker and make them user modifiable
- Linker files were set only C/C++ compiler flags. For Fortran
language it wasn't guranteed that the linker had the correct flags.
- The FindOpenMP module doesn't check for correct openmp linker flags
and we assumed that compiler, library-linker, and executable linker
flags are all the same.
- This also allows to create binaries with OpenMP linked in
statically.
Change-Id: Ifde1d3f875bb779f04aa44a969138fe04620f224
Mark Abraham [Sat, 5 May 2012 03:54:18 +0000 (13:54 +1000)]
Fixing of things associated with aminoacid.rtp header
Code, commenting and documentation changes, including
* expanded self-documention boolean variable names
* clean up of dihedral generation code
* more reuse of output code
* more use of t_restp objects
* documentation in every force field's .rtp files
* clarified why and when generated dihedrals get superseded
Change-Id: I384f498f1124795e33c0ec1707ad52558bf15eb1
Mark Abraham [Tue, 31 Jul 2012 01:05:19 +0000 (11:05 +1000)]
Added TIP4P back into CHARMM27
I think Par erroneously removed this in
73b6d636a
Change-Id: Ie9f64636b1b28030ec86248649acad343b7c9a76
Berk Hess [Thu, 9 Aug 2012 12:25:24 +0000 (14:25 +0200)]
fixed trjconv not writing velocities with cpt input
Fixes #930
Change-Id: I554dd729484a4238620f2773b5c3b3672cab72ee
Christoph Junghans [Tue, 7 Aug 2012 16:10:56 +0000 (18:10 +0200)]
Merge "fixed incorrect TPI results with dynamic box" into release-4-5-patches
Carsten Kutzner [Tue, 7 Aug 2012 09:15:59 +0000 (11:15 +0200)]
Fixed essential dynamics / flooding group PBC serial
In former versions, the PBC representation of essential dynamics /
flooding group atoms could be incorrect in serial runs if the ED group
contained more than a single molecule. In multi-molecule cases, the required
steps to choose the correct PBC image in communicate_group_positions()
therefore need to be performed also in serial runs. Since the PBC representation
can only change in neigborsearching steps, we only need to check the
shifts then. In parallel, NS is signalled by the bUpdateShifts
variable, which is set in dd_make_local_ed_indices(). The latter
function is however not called in serial runs; but still we can pass
the bNS boolean to do_flood() to signal the NS status. For essential
dynamics, unfortunately, since do_edsam() is called from constrain(), there
is no information about the NS status at that point. Until someone
comes up with a better idea, we therefore do the PBC check in every step
in serial essential dynamics - the performance impact will be negligible
anyway.
Change-Id: I86336a5e34131bdeac7e28f35b1ccb633450e54e
Berk Hess [Mon, 6 Aug 2012 18:52:59 +0000 (20:52 +0200)]
fixed incorrect TPI results with dynamic box
TPI with a box in the -rerun file different from the tpr gave systematic
errors. In Gromacs 4.0 there was a minor error, but not systematic.
Now TPI with any box setup is fully correct. Fixes #799
Change-Id: I69279874c2d1192e63efa224a0f035d43e919e88
Christoph Junghans [Mon, 6 Aug 2012 17:18:50 +0000 (19:18 +0200)]
Merge "Added comment in get_structure about which structures are included" into release-4-5-patches
Carsten Kutzner [Mon, 6 Aug 2012 13:45:08 +0000 (15:45 +0200)]
Fixed calculation of projection for STAR and/or SORI
Both for STAR and for SORI, if provided to make_edi, the
fit structure and the average structure can be the same
(in these cases the old code works fine), or one can do
the fit on another (possibly larger) part of the molecule.
In the latter case, STAR (or SORI) contains first the fit and
then the average structure (concatenated). Here, the fit has to
be performed using the fit structure while the projection(s) have
to be calculated using the average structure. This is now
taken care of by the 'avindex' index variable.
Change-Id: Id97235030f3394df2931e30249083ad439dbe791
Carsten Kutzner [Mon, 6 Aug 2012 12:26:53 +0000 (14:26 +0200)]
Added comment in get_structure about which structures are included
This patch just adds a comment and refactors natoms -> nav to better
clarify when we deal with the AVERAGE and when with the REFERENCE (fit)
structure. 'natoms' is not a good choice if we are talking about
the number of atoms in the average structure only.
Change-Id: I7025fb6ea59af0a7bcd7953a25abd09be0dd2979
Roland Schulz [Sun, 5 Aug 2012 23:01:45 +0000 (19:01 -0400)]
Remove share/tutor
Not up-to-date and better tutorials exists.
Fixes #811
Change-Id: I52708a534e641039ccb05538e0a5387079370761
Roland Schulz [Sat, 4 Aug 2012 18:12:18 +0000 (20:12 +0200)]
Merge "Fixed segv in essential dynamics module" into release-4-5-patches
Carsten Kutzner [Thu, 2 Aug 2012 09:52:41 +0000 (11:52 +0200)]
Fixed segv in essential dynamics module
Change-Id: Ia5657a535e7e31d55bf2b310a20dfee2a5e3b7f4
Roland Schulz [Fri, 3 Aug 2012 02:02:09 +0000 (22:02 -0400)]
Fix overlapping memcpy
The memcpy were not neccessary.
Fixes #984
Change-Id: Iea1d34756444cba2493940ab3f2252e7c108323f
Christoph Junghans [Wed, 1 Aug 2012 23:32:17 +0000 (17:32 -0600)]
Add note about SD integrator and t-coupling
Change-Id: I6c2bd1a332abbaf5312c9ad46de24bcd7205a085
Roland Schulz [Wed, 1 Aug 2012 00:38:43 +0000 (20:38 -0400)]
Fix use after free memory error with adress
Change-Id: I481a55704a0a93235df531269bbbe40240dd12dc
Michael Shirts [Mon, 30 Jul 2012 03:19:19 +0000 (21:19 -0600)]
Added a check for efep that was missing.
Fixes #983
Change-Id: Icdc1dd68f782fd6385fd55b616993fadea0c4448
Christoph Junghans [Tue, 31 Jul 2012 00:24:04 +0000 (02:24 +0200)]
Merge "Clarified reasons for termination of EM" into release-4-6
Mark Abraham [Thu, 26 Jul 2012 14:34:11 +0000 (00:34 +1000)]
Clarified reasons for termination of EM
"Step size too small" can be misinterpreted as nsteps is too small,
and so the error message is now more explicit.
Change-Id: I5680b3d13f34f7186ce28c553ac5736c4a74818e
Michael Shirts [Wed, 18 Jul 2012 13:59:53 +0000 (09:59 -0400)]
Fix in when to call the constraints for andersen.
Change-Id: Ifa7eebd3a23312cb5abe66f7bf0d7a3299740f9a
Roland Schulz [Sun, 29 Jul 2012 07:24:26 +0000 (03:24 -0400)]
Fix Segfaults in Genion
Introduced by
babdd87c and
c7a82654f
Change-Id: Id42042966931f3b7dfbd2eebcde29d659f80c0f0
Fixes: 982
Roland Schulz [Tue, 3 Jul 2012 00:05:19 +0000 (20:05 -0400)]
Fix that VMD version check was performed for binary not plugin
Gromacs is not using the VMD binary and thus it is not very
insightful to check the VMD binary version. Also checking the VMD
binary version was potential very slow.
The new code tries to find and load one of the VMD plugins and
check the version of the plugin.
Change-Id: Iba7be9cb742c530ce4edb8963597b8ea467e5520
Roland Schulz [Wed, 25 Jul 2012 23:27:56 +0000 (01:27 +0200)]
Merge "cmake: allow switch between single and double" into release-4-6
Roland Schulz [Wed, 25 Jul 2012 23:24:54 +0000 (01:24 +0200)]
Merge "fix a segfault in sse_mask_init" into release-4-6
Roland Schulz [Tue, 24 Jul 2012 11:44:07 +0000 (07:44 -0400)]
Fix installation rules for man pages: don't install gromacs.7.cmakein
8c87e60 added gromacs.7.cmakein and didn't add an exclusion rule.
Change to CPackInit.cmake: Removing wrong (incorrect path) and unnessary file in message.
Change-Id: I8fe7436b8164d80ad6db64eb54dc81424cd44e4a
Roland Schulz [Tue, 24 Jul 2012 11:26:07 +0000 (07:26 -0400)]
Add default root folder to cpack archives
Fixes that source archives had no root folder. If non-default
root folder for binary archives is wanted, this still can be
achived by:
cmake -DGMX_INSTALL_PREFIX={path}/ -DCPACK_INCLUDE_TOPLEVEL_DIRECTORY=0
Fixes #977
Change-Id: Iaf42afd3617873e5c1e5e7cb7c327986efa20fcd
Mark Abraham [Tue, 24 Jul 2012 00:16:27 +0000 (10:16 +1000)]
Clean up of environment variables
In particular, reduce ambiguous usage of "force".
Refs #974
Change-Id: Ia6178ce3392f66451341dd7a4af98312f9e72c0f
Christoph Junghans [Thu, 19 Jul 2012 22:34:54 +0000 (16:34 -0600)]
cmake: allow switch between single and double
* only use FFTW_INCLUDE_DIR and FFTW_LIBRARY if user set them
* otherwise do not initialize them
* description will still show up in ccmake as advanced
* fixes #971 (linking error when switching without "make rebuild_cache")
Change-Id: Idfce7d912c3d432f48fd3a7021c8c04d6311569b
Berk Hess [Wed, 18 Jul 2012 12:36:01 +0000 (14:36 +0200)]
fixed DD charge group displacement error check
One of the two checks for large charge group displacement during
domain decomposition mixed the dimension index and the dimension.
The check was correct for decomposition in x, xy or xyz. Other setups
could lead to false positives and false negatives (unlikely).
Fixes #959
Change-Id: I9e38c43f931e6ca8149faae40f49f675a7ae9664
Berk Hess [Tue, 17 Jul 2012 16:50:24 +0000 (10:50 -0600)]
fix a segfault in sse_mask_init
* work array was unaligned in some cases
* fixes #970
Change-Id: I1b474019bf93e6ef6f7cc935aa3f73f2597a91a8
Christoph Junghans [Mon, 16 Jul 2012 15:26:35 +0000 (17:26 +0200)]
Merge "Removed commas from gmx_hbond OpenMP constructs." into release-4-6
Christoph Junghans [Mon, 16 Jul 2012 15:25:35 +0000 (17:25 +0200)]
Merge "Enforced rotation: PBC/restart fix" into release-4-6
Roland Schulz [Wed, 11 Jul 2012 19:31:33 +0000 (15:31 -0400)]
Take first description if programs.txt has more than one entry
26bd5f7ac took the last description of programs.txt. I wasn't
aware at the time that programs.txt can have more than one
description for one program. I think this is not a particularly
good to allow more than one description, and then somewhat
arbitrary take the first one. But this is how mknroff.pl behaved
and I don't want to change more then needed at this point.
Change-Id: Ia4fba1b1a66baab8b409fbb3932ee099cec80298
David van der Spoel [Sun, 15 Jul 2012 12:44:04 +0000 (14:44 +0200)]
Merge "Autogenerate gromacs.7 from programs.txt" into release-4-6
Roland Schulz [Tue, 10 Jul 2012 16:49:32 +0000 (12:49 -0400)]
Adding missing entries in programs.txt
Change-Id: I323524d32f07409c02de6066a24e73fb8a966481
Teemu Murtola [Sun, 15 Jul 2012 09:44:39 +0000 (12:44 +0300)]
Removed commas from gmx_hbond OpenMP constructs.
Commas between clauses within #pragma omp caused compilation to fail
with some compilers (e.g., gcc 4.2 on OS X 10.5), even with OpenMP
disabled.
Change-Id: I089d67a6442a745faa3bf5e3be1c779855725a67
Roland Schulz [Fri, 13 Jul 2012 13:04:58 +0000 (09:04 -0400)]
Merge release-4.5-patches into HEAD
Conflicts:
src/mdlib/mdebin.c
src/mdlib/minimize.c
src/tools/gmx_hbond.c
src/tools/gmx_tune_pme.c
Change-Id: I114f1ab4d58c9ccca0261e8588b61c39feaae874
Roland Schulz [Tue, 10 Jul 2012 16:32:05 +0000 (12:32 -0400)]
Adding missing entries in programs.txt
Change-Id: I3b7879fc93d9b3a7c5eed5f14825331a12589b25
Roland Schulz [Tue, 10 Jul 2012 07:28:24 +0000 (03:28 -0400)]
Use relative rpath to support relocatable binary packages
Change-Id: I7ec8707acf021b0f168691014fb0ba2f68ae29a6
Roland Schulz [Sun, 8 Jul 2012 16:56:05 +0000 (12:56 -0400)]
Allow usage of relative install paths
Relative install paths is recommended(*) and required by some
cpack generators (e.g. NSIS). Using relative install paths should
always work, but to take no risks the absolute install paths are
still the default.
*) http://www.cmake.org/pipermail/cmake/2008-May/021663.html
Change-Id: Ie656d5fcfa62f9c7e0fee605c90251084a421a72
Christoph Junghans [Mon, 9 Jul 2012 23:44:01 +0000 (01:44 +0200)]
Merge "Fixed bug in sfactor.c that makes g_rdf -sq give wrong results." into release-4-5-patches
Jochen Hub [Mon, 9 Jul 2012 19:46:02 +0000 (21:46 +0200)]
Fixed bug in sfactor.c that makes g_rdf -sq give wrong results.
The number of neutrons is not any more in sfactor.dat, but the
respective sscanf line in sfactor.c has still a placeholder for it.
Consequently, the Cromer-Mann parameter were read incorrectly.
I left the element n (for number of neurons) in gmx_structurefactors_t
for now, but the variable is at present not used.
Fixes Bug #919
Change-Id: I20a78b0b1cf4bf2271ba0ce8c785d900502d7656
Teemu Murtola [Fri, 22 Jun 2012 06:25:59 +0000 (09:25 +0300)]
Fix memory error with complex boolean selections.
Backported from
dd3a102.
Conflicts:
src/gmxlib/selection/compiler.c
Fixes #968.
Change-Id: If92b5b1eb8cf6b3acb510ba43f64fc82b63ab82a
Roland Schulz [Sat, 7 Jul 2012 03:25:08 +0000 (23:25 -0400)]
Autogenerate gromacs.7 from programs.txt
Change-Id: I958906dc9967155bccd3f43e5a6882632a829951
Carsten Kutzner [Fri, 15 Jun 2012 12:43:35 +0000 (14:43 +0200)]
Enforced rotation: PBC/restart fix
... for rot groups consisting of >1 molecule. This commit fixes a problem with checkpoint-restarts
when using a rotation group consisting of more than a single molecule.
Change-Id: I7378047b5cd0909b864a62200ded747682f627a1
Erik Marklund [Fri, 6 Jul 2012 07:32:32 +0000 (09:32 +0200)]
Bugfix for the segfault that occurs with g_hbond -hbm -contact.
Fixes #967
Change-Id: I23968ca45683b5867f919bf32e588058bd391c67
Roland Schulz [Thu, 5 Jul 2012 23:08:41 +0000 (19:08 -0400)]
Don't prevent GMX_PREFER_STATIC_LIBS with BUILD_SHARED_LIBS
In general it seems better to not overwrite the user requested
settings unless the settings are not possible.
In this case the combination makes sense for binary packages.
Static external libraries make them easier to distribute and
shared gromacs libraries make them much smaller.
Change-Id: Icb9c4dfa2e7d211ab6bd2efcb2f2437504a87cfe
Roland Schulz [Wed, 4 Jul 2012 01:55:29 +0000 (21:55 -0400)]
Build man-pages instead of distributing them in the source
One less thing to do manual for releasing the code. And thus
avoiding to accidental releasing which old version of man-pages.
Writing copyright notice to stderr for all programs (was inconsistent)
and caused copyright notice to be displayed during build.
The CPack source package continues to contain the man pages pre-build.
CPack verifies that they are genenerated before building the source
package.
Added .isreposource to distinquish code obtained from git from code
downloaded as CPack source package.
Related to #645, #854, #735
Fixes #878
Change-Id: I7d7145fb99d3f1991d0f3992ca4f3ea20668dd9a
Christoph Junghans [Thu, 5 Jul 2012 19:45:36 +0000 (21:45 +0200)]
Merge "Don't rerun checks and be quiet 2nd time cmake is run" into release-4-6
Christoph Junghans [Thu, 5 Jul 2012 19:42:15 +0000 (21:42 +0200)]
Merge "Allow also FindMPI for cmake<2.8.5" into release-4-6
Christoph Junghans [Thu, 5 Jul 2012 19:26:41 +0000 (21:26 +0200)]
Merge "Finalized and extended Szilard's openMP cleanup of gmx_hbond.c:" into release-4-6
Roland Schulz [Tue, 26 Jun 2012 19:23:38 +0000 (15:23 -0400)]
Don't rerun checks and be quiet 2nd time cmake is run
Change-Id: I86f8cb4dfb73898e74d320ae8ef3676e62ebde51
Erik Marklund [Thu, 28 Jun 2012 19:02:00 +0000 (21:02 +0200)]
Finalized and extended Szilard's openMP cleanup of gmx_hbond.c:
* Changed HAVE_OPENMP into GMX_OPENMP
* Fixed incorrect use of OpenMP API functions
* Made variables shared by default in parallel sections
This also avoids problems with stderr being a macro in certain
implementations, which caused compilation errors on some systems
when stderr occurs explicitly in pragmas.
* Protected a block where reallocation of hbdata occurs with a critical section
* Cleaned out some output that was commented out anyway.
* Removed redundant preprocessor directives
Change-Id: I452ab2e873434086e6bc616d9d24a8d890147220
Roland Schulz [Wed, 4 Jul 2012 05:18:46 +0000 (07:18 +0200)]
Merge "Add FindGROMACS.cmake to template's CMakeLists.txt" into release-4-6
Roland Schulz [Wed, 4 Jul 2012 05:16:56 +0000 (07:16 +0200)]
Merge "Fixed bug in free energy calculation for Morse potentials" into release-4-6
Berk Hess [Mon, 2 Jul 2012 17:08:41 +0000 (19:08 +0200)]
set default for rcoulomb, rvdw and rlist to -1
To avoid users using the default values and to force them to think
about the cut-offs, all default values are now -1.
This also avoids grompp notes with the new Verlet scheme,
where the rlist value can be generated automatically.
Change-Id: I99bc7eee76953d06767f9c9916d1c9289badf74f
Elton Carvalho [Thu, 28 Jun 2012 15:13:03 +0000 (17:13 +0200)]
Fixed L-BFGS trajectory output.
This bug made mdrun ignore nstxout and nstfout when running l_bfgs.
When calling write_traj, MDOF_X|MDOF_F was given as mdof_flags to write
the trajetory, thus ignoring do_x and do_f evaluated on the previous
lines.
Fixes #905.
Change-Id: Id3ff7b090efd23fd28d8c27ea99992d1647f1ed6
Szilárd Páll [Tue, 3 Jul 2012 09:35:35 +0000 (11:35 +0200)]
Merge "Minor formatting and consistency changes to txtdump.c" into release-4-6
Christoph Junghans [Mon, 2 Jul 2012 20:20:10 +0000 (14:20 -0600)]
Do not print disabled pressures and virials
* For some methods pressure and virial calculation is disabled
* md.bVir and md.bPress was added in
*
d870cd31bee97e277f48ba982da85303bce98611
* At this point only AdResS has md.bVir=md.bPress=FALSE
Change-Id: I6abe24a5c286d20dcf554831ade9540674df9d77
David van der Spoel [Sat, 30 Jun 2012 13:18:31 +0000 (15:18 +0200)]
Fixed bug in free energy calculation for Morse potentials
Introduced recently when FEP was added to the Morse potential.
Change-Id: I90edfd13835637c872af31f2c7abf900ce8a8e5f
Christoph Junghans [Fri, 29 Jun 2012 20:18:17 +0000 (14:18 -0600)]
Add FindGROMACS.cmake to template's CMakeLists.txt
Change-Id: Id5adec8aa057f1d56021b06aaedd35dab108ead7
Michael Shirts [Fri, 29 Jun 2012 17:35:59 +0000 (11:35 -0600)]
Minor formatting and consistency changes to txtdump.c
Change-Id: I2992a927ccf49b407fa985eb2283c37818bbd2a5
Michael Shirts [Fri, 29 Jun 2012 17:28:37 +0000 (11:28 -0600)]
Corrected checkpoint version issues with free energy changes.
Change-Id: If9494aa0bdbd6f83cc2a8a57a5c7e399aaa787f4
Sebastian Fritsch [Fri, 29 Jun 2012 10:05:18 +0000 (12:05 +0200)]
Merge "Fixed adress kernel for double precision" into release-4-6
Christoph Junghans [Thu, 28 Jun 2012 17:27:58 +0000 (11:27 -0600)]
Fixed adress kernel for double precision
Change-Id: I5145ced14d59f7186dd8ef47fe6877fe00cbd94b
Roland Schulz [Thu, 28 Jun 2012 16:29:02 +0000 (12:29 -0400)]
Allow also FindMPI for cmake<2.8.5
Using FindMPI instead of mpi-wrapper makes it easier to compile
with CUDA. While FindMPI of cmake<2.8.5 is unreliable it depends
on the OS whether it works. With this change FindMPI is attemted
if no mpi wrapper is used and if it fails, mpi-wrapper or cmake
upgrade is recommended.
Change-Id: I20c0ac3958724feecaaef5c20279d340ecca4b1a
Christoph Junghans [Thu, 28 Jun 2012 16:22:44 +0000 (18:22 +0200)]
Merge "Fix MPI build for MPI library without mpi wrapper" into release-4-6
Roland Schulz [Wed, 27 Jun 2012 07:31:12 +0000 (03:31 -0400)]
Fix MPI build for MPI library without mpi wrapper
Some MPI library (e.g. MPICH and OpenMPI on Windows) don't
contain any MPI wrappers and thus
417d0afff broke the support for
those MPI libraries.
This change uses the FindMPI module if the compiler is not a
mpi wrapper and cmake >= 2.8.5. Requiring mpi wrappers for
cmake < 2.8.5 avoids reintroducing the problems of #851.
To avoid any confusion of different behavior with older and newer
versions of cmake, all documentation should recommend the mpi wrapper
approach, which works for all versions. The FindMPI approach should
only be discussed for advanced users (to support e.g. Windows).
As a side effect this change makes it more convinient to use with
cmake>=2.8.5. No need to speciy mpi wrapper and less problems with
nvcc.
Fixes #958
Change-Id: Ic53d8125c5a58edc6789fe16f2b710e7e2568d4f
Szilard Pall [Tue, 26 Jun 2012 11:30:59 +0000 (13:30 +0200)]
fixes typo gmx_omp introduced by
697bcdc
Also removes an unnecessary include and replaces a few remaining
HAVE_OPENMP-s with GMX_OPENMP.
Change-Id: I8a92a5f1849d170951719b29b17e0ec6134ee556
Roland Schulz [Tue, 26 Jun 2012 18:50:55 +0000 (14:50 -0400)]
Fix that rerunning cmake gives the same result as 1st run
- SetBuildInformation: strip was missing for 3 of 6 CPU_* variables
Not sure why this caused only for the first run an extra newline.
Extra newline doesn't change the build but causes unnessray
complete rebuild.
- IsFinite: The cached value of whether one of the 3 isfinite
function was found wasn't set the 2nd time. Thus after reruninng
cmake the isfinite function wasn't used anymore.
Change-Id: I988763e6b26cc5bae62c4da66cc7b30f2f93c128
Roland Schulz [Tue, 26 Jun 2012 01:32:58 +0000 (03:32 +0200)]
Merge "Fix gmx_fatal for serial compilation" into release-4-6
Szilard Pall [Fri, 15 Jun 2012 15:03:41 +0000 (17:03 +0200)]
introduce gmx_omp wrapper for the OpenMP API
The gmx_omp_* OpenMP API wrappers should be used instead of directly
calling OpenMP functions. Therefore, gmx_omp.h should be included
instead of omp.h so OpenMP API functions don't need #ifdef-ing.
Additionally, moved GMX_OPENMP from command-line define to config.h.
Change-Id: If30f433946fef908c26a29f1bff3671580e90629
Berk Hess [Mon, 25 Jun 2012 09:39:03 +0000 (11:39 +0200)]
fixed segv/hang with EM and foreign lambda values
Energy minimization with nstcalcenergy=-1, foreign lambda values
and no separate dhdl.xvg output file called malloc with negative count.
Fixes #962
Change-Id: I3d6b636ddba80fc2ae400590c48642c217325293
Berk Hess [Mon, 25 Jun 2012 08:03:11 +0000 (10:03 +0200)]
added check for log fp!=NULL when disabling acceleration
Change-Id: I79d16574b6c4cb039afa01240e7d3aa816b3f337
Christoph Junghans [Sun, 24 Jun 2012 20:26:37 +0000 (22:26 +0200)]
Merge "Remove MPI define for FAH" into release-4-6
Michael Shirts [Sun, 24 Jun 2012 17:27:15 +0000 (19:27 +0200)]
Merge "Fix mdp_opt formatting of expanded ensemble" into release-4-6
Roland Schulz [Sun, 24 Jun 2012 15:07:04 +0000 (11:07 -0400)]
Fix mdp_opt formatting of expanded ensemble
Was introduced with
c7a82654f2e. Broke the build of the manual
because dl tag wasn't closed.
Change-Id: I86afd4a2bdc638fb910cb0afa827b3f56447bb36
Roland Schulz [Sun, 24 Jun 2012 05:11:58 +0000 (01:11 -0400)]
Remove MPI define for FAH
FAH will use with 4.6 the standard GMX_MPI define instead of MPI.
This removes problems with C++ compile.
This fixes #849 and is related to #853.
Change-Id: I63bfc14400cda096350aba9a94a676e9c0952d56
Roland Schulz [Thu, 21 Jun 2012 16:28:36 +0000 (12:28 -0400)]
Fix illegal usage of MPI_Comm_create
Bug was introduced by
8cd25f0d45567
Illegal to call MPI_Comm_create with different group arguments
Change-Id: Ia70f81862fa50b03ab127e8796226369f6732942
Christoph Junghans [Fri, 22 Jun 2012 21:04:20 +0000 (23:04 +0200)]
Merge "Simple patch for openmm_wrapper.cpp" into release-4-6
Erik Lindahl [Thu, 21 Jun 2012 09:38:12 +0000 (11:38 +0200)]
Fixed gcc inline assembly issue with PIC and older gcc compilers
Some gcc versions had problems with the recently introduced inline
assembly for cpuid (clobbering of ebx register), and since we used
a slightly different inline assembly instruction test in cmake we
did not detect it properly. This patch both makes the inline asm
itself much more portable, and we also test with exactly the same
instruction in cmake so we don't set the flag for supporting inline
asm unless we know this instruction works.
Change-Id: Ib479e2706024abb5e3f66d0249291ce55f1257b1
David van der Spoel [Thu, 21 Jun 2012 16:14:33 +0000 (18:14 +0200)]
Fixes #961 - Shake reports wrong error
The constraint index reported by shake was off by 1.
Change-Id: I6f4d0c013b30f5963fb312b41fb87e90e6314619
Roland Schulz [Thu, 14 Jun 2012 23:16:06 +0000 (19:16 -0400)]
Fix gmx_fatal for serial compilation
With neither GMX_MPI nor GMX_THREAD_MPI gmx_fatal
called gmx_abort which called gmx_fatal.
Change-Id: Id18c3bc94f19a8008fa2aaa8335c221f115fcd8b