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 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
Martin Hoefling [Wed, 13 Jun 2012 12:29:24 +0000 (14:29 +0200)]
gmx_dyecoupl: check selected groups from user
check if the user accidentally selected the same group twice. Abort
with error, since this will not produce any meaningful results.
Change-Id: Iace69c473e5f1b815e35d20a39845533297ad208
Erik Lindahl [Mon, 28 May 2012 18:54:17 +0000 (20:54 +0200)]
New CPU detection & AVX/SSE code, removed raw assembly files.
Removed all raw assembly files and deprecated altivec support.
Removed support for NASM and other assemblers, and replaced
previous SSE detection code with a new module using CPUID instead.
Added detection for SSE2, SSE4.1, AVX 128-bit with FMA, and AVX 256-bit.
Added Cmake detection of build platform based on CPUID, and output this
to the log file. The executables now compare the compile-time platform
and selected acceleration with the run-time platform and most suitable
acceleration and warns the user if they do not match. The compiler
detection code has also been reordered slightly to produce more readable
warnings when OpenMP is not available, and correctly disable pragma
warnings.
Added intrinsics code and math functions for SSE2, SSE4.1, AVX128/256
both in single and double precision. All math functions and permutation
code have been tested & verified. Single precision math functions are
correct apart from the least significant bit, and double precision has
roughly twice the accuracy.
This has forced me to temporarily disable the SSE & Fortran acceleration.
SSE will be added back soon based on new intrinsics-only kernels currently
in testing, and we will test if Fortran still makes sense then.
Finally, the patch includes a modification to gmx_rmsdist where
a regression issue was introduced recently by using sqrtf() for
the norm function. This caused the intel compiler to produce slightly
different results at high optimization leves, which got evident here.
Closes #926 - Raw assembly code has been removed.
Refs #923 - Old kernels removed, new will be added shortly.
Fixes #914 - Cmake now does architecture-speficic optimization.
Fixes #912, #913
Fixes #857 - We detect rdtscp support with CPUID and use it if possible.
Fixes #750
Closes #537, #574 - Altivec is now deprecated.
Change-Id: Icfca5a940762f8d82ae67b59c65b2d2ac683256d
Justin Lemkul [Thu, 7 Jun 2012 00:11:26 +0000 (20:11 -0400)]
Simple patch for openmm_wrapper.cpp
The naming of several variables is changed to be consistent with the
latest free energy changes. Allows mdrun-gpu to be compiled, which
otherwise fails (as reported on gmx-developers).
Change-Id: I497ba07ee6883ef78d23022450f6c3d971b2127e
Michael Shirts [Tue, 17 Jan 2012 14:51:13 +0000 (09:51 -0500)]
Merging in free energy, exp. ensemble, & andersen t-control to 4.6
Conflicts:
src/gmxlib/mvdata.c
src/gmxlib/txtdump.c
src/kernel/readir.c
src/mdlib/sim_util.c
src/tools/gmx_membed.c
include/mdrun.h
src/kernel/md.c
src/kernel/md_openmm.c
src/kernel/md_openmm.h
src/kernel/runner.c
src/mdlib/minimize.c
src/mdlib/tpi.c
src/tools/gmx_membed.c
src/kernel/md.c
Change-Id: Ide69a8dbfb96072d5c55d0a051dc9db788cbe144
Roland Schulz [Fri, 1 Jun 2012 06:24:10 +0000 (02:24 -0400)]
Merge release-4-5-patches into release-4-6
Changes in 4.5 for removed lines/files in 4.6:
Makefile.am
include/domdec.h
include/domdec_network.h
Trivial conflict:
include/types/commrec.h
Fixed GMX_THREADS into GMX_THREAD_MPI for those added in 4.5 in:
include/mdrun.h
src/gmxlib/shift_util.c
src/mdlib/gmx_fft_fftw3.c
Change-Id: Id37bfbbacc945a7cf184fa21313c05e2680e1fba
Christoph Junghans [Fri, 1 Jun 2012 06:04:28 +0000 (08:04 +0200)]
Merge "Use External BLAS/LAPACK by default" into release-4-6
Christoph Junghans [Fri, 1 Jun 2012 05:35:50 +0000 (07:35 +0200)]
Merge "Replace our fftpack version with Numpy's version" into release-4-5-patches
Roland Schulz [Sun, 27 May 2012 18:07:30 +0000 (14:07 -0400)]
Replace our fftpack version with Numpy's version
Fixes incorrect results for vectors with length of multiples of 12
Fixes #946
Change-Id: I9a110de7334cbb96a72d0ced73ade4d55f665fee
Teemu Murtola [Wed, 30 May 2012 04:18:10 +0000 (07:18 +0300)]
Fix use after free in g_anaeig projection code.
PBC removal structure was deleted immediately after it was initialized,
and used afterwards.
Change-Id: I6126967b34e8de289370dede79cc50a9924ac34d
Sander Pronk [Tue, 22 May 2012 15:46:37 +0000 (17:46 +0200)]
Removed dependency on windows.h through commrec.h, domdec.h.
Change-Id: If40506b521a4b4690506465a3f421dab93bc9ce6
Christoph Junghans [Tue, 29 May 2012 16:26:52 +0000 (18:26 +0200)]
Merge "Revised g_tune_pme" into release-4-6
Christoph Junghans [Mon, 28 May 2012 23:25:59 +0000 (01:25 +0200)]
Merge "Continuing to fix threading on Cygwin" into release-4-5-patches
Roland Schulz [Sun, 27 May 2012 19:26:24 +0000 (15:26 -0400)]
Fix editconf real-bool misusage
Bool variable was declared as real. Caused invalid stack read
in double precision. Could have caused wrong value to be printed
for argument display but couldn't have caused wrong behavior.
Found with AddressSanitizer
Change-Id: I32553b1a898fb3a7f072ae177518dd63fad56dde
David van der Spoel [Sun, 27 May 2012 08:49:56 +0000 (10:49 +0200)]
Merge "added explicit sqrtf to the float version of norm" into release-4-6
Roland Schulz [Sun, 27 May 2012 02:51:05 +0000 (22:51 -0400)]
Fix Clang 3.1 warning
grid_spacing is an integer and thus it was always set to 0
Change-Id: Id10bccdadef8f2630631d638e94bd27d78774536
Mark Abraham [Fri, 25 May 2012 09:45:09 +0000 (19:45 +1000)]
Continuing to fix threading on Cygwin
Fixes #833
Change-Id: I5d577a149ad18b295559f6d87c24dc42bffd281e
Roland Schulz [Mon, 21 May 2012 18:21:23 +0000 (14:21 -0400)]
Make load_vmd_library static
Was already used only within the same file
Change-Id: I43276424d51021bc8247c04a3c3647f7fc1565f7
Roland Schulz [Thu, 17 May 2012 22:23:25 +0000 (18:23 -0400)]
Made all vmdio headers private
- Made vmdio struct in trx a pointer
- No need for vmdio to be in the public API
Change-Id: Ic142a6900d0cbc803e8c24139efbfbc072b46c22
Roland Schulz [Fri, 25 May 2012 14:47:21 +0000 (16:47 +0200)]
Merge "fixed [dd] and [TT] typos in documentation of mdrun and gmx_sans" into release-4-6
David van der Spoel [Fri, 25 May 2012 14:26:50 +0000 (16:26 +0200)]
Merge "grompp now retains the order of bonds converted to constraints" into release-4-6
Martin Hoefling [Fri, 25 May 2012 10:09:07 +0000 (12:09 +0200)]
fixed [dd] and [TT] typos in documentation of mdrun and gmx_sans
Change-Id: Ia51f67b2b056f66072875d2c7a366ae4685bf9d4
Christoph Junghans [Fri, 25 May 2012 07:17:48 +0000 (09:17 +0200)]
Merge "Fix that sigaction mask wasn't zeroed" into release-4-6
Berk Hess [Wed, 23 May 2012 16:23:12 +0000 (18:23 +0200)]
now mdrun always initializes MPI
MPI was only initialized with more than one process. This required
checks everywhere. Now MPI is also initialized with one process.
Change-Id: I4d0f543d5c1ae5a6136a0ba34f0f83ac27604b14
Teemu Murtola [Thu, 24 May 2012 17:02:36 +0000 (19:02 +0200)]
Merge "Code cleanup to avoid name collisions" into release-4-6
Carsten Kutzner [Tue, 22 May 2012 08:07:42 +0000 (10:07 +0200)]
Revised g_tune_pme
1. Now, g_tune_pme only duplicates mdrun options where necessary,
options not understood by g_tune_pme are simply passed over to mdrun.
2. Users can now set minimum and maximum Coulomb radius iso scaling
factors for rcoulomb and the Fourier grid.
3. As a result of 1 and 2, some cleanup of the code was possible and
unneeded code was removed.
4. For -npme auto, the tool now derives a reasonable number of PME-
only nodes from the .tpr file settings and tests values around this
number.
Change-Id: I88af5d38a61e0409613f5f3fd4272f7f43823f64
Roland Schulz [Wed, 23 May 2012 09:30:50 +0000 (05:30 -0400)]
Fix that sigaction mask wasn't zeroed
Change-Id: I84a1f77e6320538730cc367ed722eadf22046a68
Roland Schulz [Wed, 23 May 2012 00:30:08 +0000 (20:30 -0400)]
Code cleanup to avoid name collisions
- Adding missing prepropessor guards
- Renaming functions defined using same name as other function
- Removing unused magic.h
Change-Id: I1375097eb7eced2dafb30222c9986ac24f45fb08
Roland Schulz [Tue, 22 May 2012 21:38:12 +0000 (17:38 -0400)]
Use External BLAS/LAPACK by default
Check if Blas/Lapack is available and only use internal
if it isn't found
Updated FindLAPACK to 2.8.8. and included FindBLAS
so that it works without Fortran enabled.
Change-Id: I6d1df8a03196d9c14436d5b70c731d36b4ddf823
Szilard Pall [Mon, 21 May 2012 20:33:11 +0000 (22:33 +0200)]
added explicit sqrtf to the float version of norm
Additionally, as inlining is not a concern nowadays, also cleaned up the
code by using iprod in norm.
Change-Id: Iabc237906380f848e16ed158809bf22b1de9ddd0
Berk Hess [Mon, 21 May 2012 17:07:09 +0000 (19:07 +0200)]
grompp now retains the order of bonds converted to constraints
With the constraint mdp option grompp used to write tpr files where
the order of the constraints was reversed with respect to the order
of the bonds. This reordering has been removed.
Change-Id: I094c5001ccad1e80f46b61c4fbcfa400fd5c1e74
Berk Hess [Thu, 17 May 2012 22:07:46 +0000 (00:07 +0200)]
re-introduced fix for real/double issue in gmx_density
The float density histogram could overflow for large data sets.
A fix replaced 3 of the 4 pointers to floats by pointers to doubles, leading
to compilation issues. In two steps these replacements were reverted.
Now all 4 pointers have been replaced.
Change-Id: I0d8e38d27ac5c469480ff731ad191d869f5d890f
Roland Schulz [Fri, 18 May 2012 00:00:22 +0000 (20:00 -0400)]
Rename BOOL to EBOOL
- All other ENUM_NAME functions start with E
- BOOL can easily collide with other names (e.g. on Windows)
Change-Id: I6cb9438386dfb0c93299dfc5a161e4294e7834a3
Teemu Murtola [Thu, 17 May 2012 15:15:25 +0000 (17:15 +0200)]
Merge "Fixing more clang warnings" into release-4-6
Maarten Wolf [Wed, 16 May 2012 08:16:43 +0000 (10:16 +0200)]
mv membed.h from include to src/kernel
,because membed function calls are not part of gmxlib
Created an abstract datatype gmx_membed_t in include/types
mv all struct declaration to file that uses them (membed.c)
made membed init print conditional on MASTER(cr)
Change-Id: I8bb23403415f1c35a31f06c2fb0fae2148ee15f6
Roland Schulz [Sun, 13 May 2012 03:49:24 +0000 (23:49 -0400)]
Fixing more clang warnings
Change-Id: I1359503f61e1fa003c078c98a99420249b915e9c
Christoph Junghans [Wed, 9 May 2012 21:08:35 +0000 (23:08 +0200)]
Merge "Backporting "moving membed to mdrun" from master" into release-4-6
Alexey Shvetsov [Tue, 8 May 2012 18:17:50 +0000 (22:17 +0400)]
[tools] g_sans - add OpenMP based parallelism
This commit adds OpenMP based parallelism for
calc_radial_distribution_histogram function
Also it adds check for mcover parameter which should be -1 or (0,1]
Change-Id: Ic14267782c69c25364b69a91719cb451fd8e3a89
Signed-off-by: Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru>
Maarten Wolf [Fri, 27 Aug 2010 12:40:26 +0000 (14:40 +0200)]
Backporting "moving membed to mdrun" from master
commit 1: cherry pick
45181651
Moved g_membed functionality to mdrun
commit 2: cherry pick
21a84994
Moved g_membed functionality to mdrun bug fix
commit 3: cherry pick
34471042
added gmx_membed.c to CMakeLists.txt for mdrun
commit 4: cherry pick
1a72f4c8
membed renaming and adding tools wrapper again
commit 5:
Fixes necessary after membed to mdrun cherry picking
commit 6: cherry pick
a52f8c45
bugfix #697 for g_membed
commit 7:
deleted unused code, changed fclose to ffclose in membed.c
Change-Id: Ia3ba001b338cadcadc9b2bf1f4c728c5ffc1414b
Berk Hess [Tue, 8 May 2012 09:21:56 +0000 (11:21 +0200)]
fixed mdrun -cpi SD and pcoupl initialization
With mdrun -cpi and no previous output files present SD and pressure
coupling were initialized incorrectly, leading to minor differences
at the start of a simulation. Fixes #939
Change-Id: I1ea3797ceb39760341c7c11cf74425c02dcaf235
Roland Schulz [Tue, 8 May 2012 02:19:12 +0000 (22:19 -0400)]
Fixing more Clang warnings
Change-Id: Ic2189579eaaa262d4907d912d59a3e78274bd4ed
Teemu Murtola [Mon, 7 May 2012 14:22:50 +0000 (17:22 +0300)]
Merge branch 'gerrit/release-4-5-patches' into release-4-6
Conflicts:
CMakeLists.txt
cmake/gmxGenerateVersionInfo.cmake
Change-Id: I82c2429f9b1d8441edb19f6287dbbe446fc07233
Teemu Murtola [Fri, 4 May 2012 06:59:46 +0000 (09:59 +0300)]
Clean up cmake version generation.
- Use comparisons like ("${VAR}" STREQUAL "") for testing for empty
strings (other variants may fail in certain scenarios).
- Add some other quotes to avoid CMake errors in unusual situations.
- Remove trailing whitespace.
Related to #888.
Change-Id: Ifd1a87f0e929b4cb62db56d70ca469b73075fc2c
Teemu Murtola [Fri, 4 May 2012 06:49:56 +0000 (09:49 +0300)]
Drop support for pre-1.5.3 git for version info.
Did not touch the autoconf version, since that will anyways be obsolete
in 4.6.
Related to #888.
Change-Id: Ic7d890959e2e9a614f5d39a453c45671c3b56df4
Teemu Murtola [Fri, 4 May 2012 05:05:28 +0000 (08:05 +0300)]
Fix cmake version info generation.
Use the same logic in the cmake version info generation script as is
used in the shell script for autoconf.
Fixes #888.
Change-Id: I2a06d175a1e04e25d38b917d907cdae429743099
Teemu Murtola [Sat, 5 May 2012 06:06:19 +0000 (09:06 +0300)]
Removed autoconf version info generation.
Since autoconf is no longer supported, there is no need for this shell
script either.
IssueID #645
Change-Id: I5607d52817122dfdf9ea33e784a50abc7941ba0e
Szilard Pall [Wed, 2 May 2012 12:59:00 +0000 (14:59 +0200)]
removed -finline-functions from the release gcc flags
All gcc versions >= v4.1 include -finline-functions with -O3.
Change-Id: Iecdf906162400863329bbe2d57fc110c9c2c7a9a
Teemu Murtola [Wed, 2 May 2012 05:10:19 +0000 (08:10 +0300)]
Remove #include <config.h> from pull_rotation.h.
There is nothing in the header that needs it, and installed headers
should not include something that is not installed.
Change-Id: I563fa21f3a6ecce8f728feb9656bccfef5edaa73
Roland Schulz [Sat, 28 Apr 2012 15:27:23 +0000 (11:27 -0400)]
Fix Windows specific cmake hacks
MT/MD related:
- Only use MT instead of MD if GMX_PREFER_STATIC_LIBS
Gromacs compiles fine with MD and produces smaller binaries.
- Fix that MT is also used with C++ and Intel
Workaroud for cmake 13174:
- Replace GZ with RTC1 also for C++
- Replace GX with EHsc for C++
Remove of set(GMX_EXTRA_LIBRARIES):
- This has no effect because it isn't set before.
Change-Id: I911c88e099c1faaa896b54b791a952c1265dd89e
Roland Schulz [Tue, 1 May 2012 14:56:49 +0000 (16:56 +0200)]
Merge "Disable OpenMP for llvm-gcc 4.2.x" into release-4-6
Roland Schulz [Mon, 30 Apr 2012 02:20:20 +0000 (22:20 -0400)]
Fix gmxdump error introduced by
553d4b1369
Change-Id: Ib3ebe7231e3be0f2bdeda21cf5c589f6d5144c5c
Roland Schulz [Sun, 29 Apr 2012 15:10:51 +0000 (11:10 -0400)]
Disable OpenMP for llvm-gcc 4.2.x
Fixes #900
Change-Id: Ibd80b2e3768e25f5091441a65785f539dc3b7050
Roland Schulz [Sun, 29 Apr 2012 12:41:36 +0000 (08:41 -0400)]
Merge release-4-5-patches into release-4-6
Change-Id: I420226d869a1d755c731b9f65b66a29c233e9b6e
David van der Spoel [Sun, 29 Apr 2012 07:26:00 +0000 (09:26 +0200)]
Merge "changed number of iatoms for F_SETTLE from 1 to 3" into release-4-6
David van der Spoel [Sun, 29 Apr 2012 07:06:19 +0000 (09:06 +0200)]
Merge "added support for graphs not starting at 0" into release-4-6
Roland Schulz [Sun, 29 Apr 2012 04:29:44 +0000 (00:29 -0400)]
Don't enable ASM if no asm kernel is selected
Caused that -DGMX_ACCELERATION=none didn't compile without
asm installed.
Change-Id: I572d64b94af89516ef35336190636ead6a256c0f
Roland Schulz [Sun, 29 Apr 2012 01:45:00 +0000 (21:45 -0400)]
Merge release-4-5-patches into release-4-6
Conflicts:
src/mdlib/pme.c
Change-Id: I0a77a63162168d3a07ab957a9bf7b367a9f05eac
Berk Hess [Fri, 27 Apr 2012 09:15:24 +0000 (11:15 +0200)]
fixed PME forces with FE, fixes #929 introduced in recent merge
Change-Id: I4f3bc59ed8c0351c4c59feceb3c2116b2f063daf
Teemu Murtola [Sat, 28 Apr 2012 14:12:15 +0000 (16:12 +0200)]
Merge "Fix for sigaction" into release-4-6
Roland Schulz [Fri, 27 Apr 2012 18:36:56 +0000 (14:36 -0400)]
Fix srenew/sfree_aligned misuse in PME
denom was first allocated with srenew and then freed with
sfree_aligned. This is illegal and crashes on Windows.
Change-Id: I83d8c35973ed0be1bb23396d6b97bf1d4b0f5f06
Mark Abraham [Sat, 28 Apr 2012 12:44:44 +0000 (14:44 +0200)]
Merge "Remove checks based on Generator" into release-4-5-patches
Mark Abraham [Sat, 28 Apr 2012 12:43:22 +0000 (14:43 +0200)]
Merge "Fix version info generation for autoconf." into release-4-5-patches
Berk Hess [Fri, 27 Apr 2012 12:35:48 +0000 (14:35 +0200)]
fixed segv in TPI with PME, fixes #927
Change-Id: Ie465c7300e491f4e67cacd0fa7186a253ee46cad
Berk Hess [Fri, 27 Apr 2012 08:59:12 +0000 (10:59 +0200)]
changed PME MPI_Comm comparisions to MPI_COMM_NULL, fixes #931
Change-Id: I6087339c5609de0444ac578c217825b9918cb993
Berk Hess [Thu, 26 Apr 2012 18:35:41 +0000 (20:35 +0200)]
changed number of iatoms for F_SETTLE from 1 to 3
Change-Id: Ia0cb1f277b5d3e8988c6fd1fb26896fa68c2fb3c
Teemu Murtola [Fri, 27 Apr 2012 07:25:10 +0000 (10:25 +0300)]
Fix version info generation for autoconf.
Should now work with a repository cheched out both from git.gromacs.org
and gerrit.gromacs.org. The pattern for finding the remotes may be
better with some finetuning, but it works for me. However, not that
much effort should be spent for the autoconf part since it will be
removed for 4.6.
Partial fix for IssueID #888.
Change-Id: I3f0caf440067b3eceba28845c1061c0642c0226b
Roland Schulz [Fri, 27 Apr 2012 06:26:29 +0000 (02:26 -0400)]
Remove checks based on Generator
OS dependending checks should not depend on Generator
Change-Id: I3c682c8b5ec82fe2a2b78744c6f56dccd655ee5c
Roland Schulz [Fri, 27 Apr 2012 04:09:17 +0000 (00:09 -0400)]
Fix for sigaction
Commit "Restart IO operations when interrupter by signal"
didn't actually activate sigaction because config.h.cmakein
change was missing.
Fixes #798
Change-Id: Id5c7e3344688c32ec4c51d84ccbc66658ed928f9
Berk Hess [Wed, 10 Aug 2011 09:31:30 +0000 (11:31 +0200)]
added support for graphs not starting at 0
It has always been implicitly assumed that graph->start==0.
This assumption would only fail for a topology starting with
single atom molecules followed by multi-atom molecules.
Furthermore, for mk_graph at_start could only be 0, a check
has been added for this, and at_end was not stored.
In t_graph start is now replaced by at_start and end by at_end,
where at_end is end+1, now the first atom not part of the graph.
Change-Id: I0d4c09c90cbba1a7f4a1d84cf1f90a7643c17cd8
Berk Hess [Thu, 26 Apr 2012 18:56:22 +0000 (20:56 +0200)]
Merge "Merge release-4-5-patches into release-4-6" into release-4-6
Berk Hess [Thu, 26 Apr 2012 15:40:34 +0000 (17:40 +0200)]
Merge release-4-5-patches into release-4-6
Change-Id: Id1c62a482c6c3467704cc9b657b53f7df493b7ba
David van der Spoel [Thu, 26 Apr 2012 18:07:01 +0000 (20:07 +0200)]
Merge "[tools] g_sans - splited out fixes and added citation" into release-4-6
Berk Hess [Wed, 18 Apr 2012 10:47:29 +0000 (12:47 +0200)]
fixed the reported temperature with Brownian dynamics
Reduced the (meaningless) masses with BD by a factor 2.
Since v with BD is defined as dx/dt, the reported Ekin and T are
now correct (and if there are too high, dt is too large).
Fixes #797
Change-Id: Iee8613ff9637deb58600ad03289f7bcce7f32df2
Berk Hess [Thu, 26 Apr 2012 12:40:13 +0000 (14:40 +0200)]
fixed dispersion correction with parallel EM
With EM the energy and pressure dispersion correction terms
were multiplied by the number of nodes. Fixes #901
Change-Id: I289ac0de7d7a9c1f72e939b840c549c1cb49a52a
Szilard Pall [Thu, 26 Apr 2012 11:54:37 +0000 (13:54 +0200)]
Corrected fourierspacing description
Change-Id: I5cb577f0750cea3481f766330096d5b2bca7eb6f
Szilárd Páll [Thu, 26 Apr 2012 11:48:42 +0000 (13:48 +0200)]
Merge "fixed initial COM motion removal with multiple groups" into release-4-5-patches
Alexey Shvetsov [Wed, 25 Apr 2012 21:38:40 +0000 (01:38 +0400)]
[tools] g_sans - splited out fixes and added citation
This commit contains fixes splited out from postponed g_nse commit.
1. Added citation
2. Fixed detection of triclinic boxes (needed for largest possible
distance)
3. mc runs uses monte carlo coverage
Change-Id: I6190fa9f7f710426f3d0bcf5c77013fe0d20eecc
Signed-off-by: Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru>
David van der Spoel [Thu, 26 Apr 2012 07:05:10 +0000 (09:05 +0200)]
Merge "Various improvements to shell code" into release-4-5-patches
Berk Hess [Tue, 24 Apr 2012 07:48:49 +0000 (09:48 +0200)]
replaced PPPM by P3M-AD: a few lines in pme.c
The deprecated PPPM method has been replaced by P3M-AD: a PPPM method
with analytical derivative. The full code path of P3M-AD is identical
to PME, except for the moduli calculation, which use the influence
function optimized for the grid.
Change-Id: I53d08d9ff4e909dc1a34dce668f4dea8f26f728e
Berk Hess [Thu, 19 Apr 2012 13:49:22 +0000 (15:49 +0200)]
fixed initial COM motion removal with multiple groups
Seperate COM motion removal code before step 0 has been replaced by
a call to the normal vcm code. This require some cglo flag changes.
Fixes #925
Change-Id: Ia6b8637b133c343c7e503307f00b557f7ad7409c
Berk Hess [Tue, 24 Apr 2012 11:35:33 +0000 (13:35 +0200)]
Merge "allow -append to overrule unsupported file locking" into release-4-5-patches
Christoph Junghans [Mon, 23 Apr 2012 15:39:42 +0000 (17:39 +0200)]
Merge "compiler flag fixes" into release-4-6
Roland Schulz [Sun, 11 Mar 2012 11:18:19 +0000 (07:18 -0400)]
Resolving a couple of clang analyzer warnings
Most of these are real errors or potential problems.
It's only a small start ~100 warnings are left and quite a few
false positives are within those remaining ones.
Change-Id: I7c83afa84c52362ecc1b7c992591d82f8262a6ac
Roland Schulz [Sun, 22 Apr 2012 16:41:33 +0000 (18:41 +0200)]
Merge "enable command line option cheking in mdrun" into release-4-6
Szilard Pall [Wed, 18 Apr 2012 01:12:24 +0000 (03:12 +0200)]
compiler flag fixes
- added patched Check{C,CXX}CompilerFlag.cmake scripts to enable invalid
option detection with Intel Compilers 12.x; the patches have been
submitted to CMake (will be included in 2.8.9:
http://cmake.org/gitweb?p=cmake.git;a=commit;h=
bbb895959f54a9dec9f5132313f4a71fafc458e5),
these files should be removed when the required CMake version will
contain the fixes
- moved compiler option generation after the default cmake variable
setting to add -Wunknown-pragmas only when GMX_OPENMP=OFF
- moved optimization options to release flags
- enabled warnings with the Intel Compilers
Change-Id: I767aea7f043255ee95eef5e7cb597c1c99feb05a
Mark Abraham [Wed, 18 Apr 2012 16:07:16 +0000 (02:07 +1000)]
Various improvements to shell code
Tested for binary equality only when appropriate. Increased verbosity
of error message. Clarified code that interpolates a scale factor for
a steepest-descent step size.
Change-Id: Ia386390e3a1b7690bf446342e55a3559da1e67eb
Berk Hess [Wed, 18 Apr 2012 11:23:42 +0000 (13:23 +0200)]
fixed segfault in graph code with coordinate subsets
The graph code checked for atom indices above the subset size,
but not for settle. The check for settle has been added.
Fixes #809
Change-Id: I67ddbd3dab5a34f57a29f54f4b07918a6d74c38c
Mark Abraham [Wed, 18 Apr 2012 03:07:32 +0000 (13:07 +1000)]
Removed outdated #includes
isnan() is no longer used in the code (although I can't find the
commit in src/kernel/md.c where it disappeared). Removed references
to gmx_header_config.h, since these are also no longer required.
Change-Id: Id9fcd3f221526c528cace86279e533c6581b26f7
Berk Hess [Wed, 18 Apr 2012 08:28:54 +0000 (10:28 +0200)]
allow -append to overrule unsupported file locking
This is a change to the previous change to let mdrun append anyhow
when file locking is not supported. Now a fatal error is generated,
unless -append is specified explicitly.
This commit refs #924
Change-Id: I98fa201fb5bd62c0de58c3c2d7e17e8b3f727c2f
Szilard Pall [Tue, 17 Apr 2012 22:56:56 +0000 (00:56 +0200)]
added missing #ifdef around #include "thread_mpi.h"
Due to the the missing #ifdef mdrun was not compiling with compilers
that don't like thread_mpi.h (e.g. Cray compiler).
Change-Id: Ibf980b46aaf56b81fffec5ada7cb3d93492a2220
Berk Hess [Tue, 17 Apr 2012 15:08:27 +0000 (17:08 +0200)]
changed mdrun file locking not supported error to a note
On some (file) systems file locking is not supported.
This should not prevent users from using the append option of mdrun,
Fixes #924
Change-Id: I99c0d38eb702b316df0027df3d33befc562a0a7a
Mark Abraham [Wed, 11 Apr 2012 02:26:22 +0000 (12:26 +1000)]
Added Windows-specific #defines, and use them
The lack of an elegant way to code "do this on Windows/
Cygwin/whatever" may have contributed to 4.5.5 not compiling with
threading under Cygwin (IssueID #833, which was fixed elsewhere).
Change-Id: I07fa69825181e2b04cb89798898898f1d258d371