Carsten Kutzner [Mon, 8 Nov 2010 10:40:08 +0000 (11:40 +0100)]
Merge branch 'master' into rotation
Conflicts:
src/tools/Makefile.am
Carsten Kutzner [Mon, 8 Nov 2010 10:34:42 +0000 (11:34 +0100)]
Merge branch 'rotation-4-5' into rotation
Carsten Kutzner [Mon, 8 Nov 2010 10:33:26 +0000 (11:33 +0100)]
Enforced rotatin: Put in check for acos value; enhanced output file description
Carsten Kutzner [Mon, 8 Nov 2010 08:58:10 +0000 (09:58 +0100)]
Merge branch 'release-4-5-patches' into rotation-4-5
Mark Abraham [Sun, 7 Nov 2010 01:36:37 +0000 (12:36 +1100)]
Made mdrun exit with a fatal error for EM or NM with -rerun
Mark Abraham [Sat, 6 Nov 2010 11:55:56 +0000 (22:55 +1100)]
Fixed .xvg legends for g_sas options -or and -oa
Teemu Murtola [Fri, 5 Nov 2010 17:53:07 +0000 (19:53 +0200)]
Merge branch 'release-4-5-patches'
Conflicts:
src/tools/Makefile.am
David van der Spoel [Fri, 5 Nov 2010 13:10:25 +0000 (14:10 +0100)]
Fixed compilation issue.
David van der Spoel [Fri, 5 Nov 2010 13:05:55 +0000 (14:05 +0100)]
Fixed compilation issue.
David van der Spoel [Fri, 5 Nov 2010 12:56:06 +0000 (13:56 +0100)]
Added flag to gmx_stats_get_point
Pär Bjelkmar [Fri, 5 Nov 2010 12:38:11 +0000 (13:38 +0100)]
More atom-based charge groups in CHARMM (termini and hard-coded residues).
Carsten Kutzner [Fri, 5 Nov 2010 11:56:31 +0000 (12:56 +0100)]
Merge branch 'rotation-4-5' into rotation
Carsten Kutzner [Fri, 5 Nov 2010 11:55:44 +0000 (12:55 +0100)]
Flexible RMSD fitting is now optionally mass-weighted
Carsten Kutzner [Fri, 5 Nov 2010 10:02:06 +0000 (11:02 +0100)]
Print warning when reference file is set but could not be found
Berk Hess [Fri, 5 Nov 2010 09:18:29 +0000 (10:18 +0100)]
pdb2gmx now puts atoms with cgnr=-1 in separate charge groups
Carsten Kutzner [Fri, 5 Nov 2010 08:54:34 +0000 (09:54 +0100)]
Merge branch 'release-4-5-patches' into rotation-4-5
Roland Schulz [Thu, 4 Nov 2010 08:14:56 +0000 (04:14 -0400)]
print more information in case of lock error
Carsten Kutzner [Thu, 4 Nov 2010 10:51:56 +0000 (11:51 +0100)]
Merge branch 'rotation-4-5' into rotation
Conflicts:
src/tools/Makefile.am
Carsten Kutzner [Thu, 4 Nov 2010 10:45:40 +0000 (11:45 +0100)]
Doxygen comment for dd_make_local_rotation_groups
Berk Hess [Thu, 4 Nov 2010 10:19:35 +0000 (11:19 +0100)]
Fixed md.log being opened twice when appending, which prevented file locking.
Added check for -seppot and -append.
Carsten Kutzner [Thu, 4 Nov 2010 09:42:45 +0000 (10:42 +0100)]
Merge branch 'master' into rotation
Conflicts:
src/kernel/runner.c
Carsten Kutzner [Thu, 4 Nov 2010 09:33:40 +0000 (10:33 +0100)]
Merge branch 'release-4-5-patches' into rotation-4-5
Carsten Kutzner [Thu, 4 Nov 2010 09:31:24 +0000 (10:31 +0100)]
Merge branch 'rotation-4-5' into rotation
Carsten Kutzner [Thu, 4 Nov 2010 09:28:38 +0000 (10:28 +0100)]
Updated normalization factor
hess [Thu, 4 Nov 2010 08:42:54 +0000 (09:42 +0100)]
added GB params for charmm MCH3S
hess [Thu, 4 Nov 2010 08:42:18 +0000 (09:42 +0100)]
clarified GB parameter error messages in grompp
Berk Hess [Tue, 2 Nov 2010 17:29:26 +0000 (18:29 +0100)]
fixed incorrect print in fatal error on charge group size
Berk Hess [Tue, 2 Nov 2010 17:16:13 +0000 (18:16 +0100)]
proper defined of MAX_CHARGEGROUP_SIZE=32 in a single include file
David van der Spoel [Tue, 2 Nov 2010 15:09:35 +0000 (16:09 +0100)]
Fixed bug 608 by throwing a fatal error in grompp.
Sander Pronk [Tue, 2 Nov 2010 12:27:01 +0000 (13:27 +0100)]
Fixed double precision energy file reading + box matrix writing to ener.edr
- double precision energy files can now be read back
- All non-zero elements of the box matrix are now correctly written out
when needed
hess [Tue, 2 Nov 2010 07:50:33 +0000 (08:50 +0100)]
fixed incorrect y result in mvmul_ur0, only used in g_vanhove
Rossen Apostolov [Sat, 30 Oct 2010 20:07:36 +0000 (22:07 +0200)]
Added back the "-dev" suffixes to the version strings.
Rossen Apostolov [Sat, 30 Oct 2010 19:22:54 +0000 (21:22 +0200)]
New bugfix release: 4.5.2
Rossen Apostolov [Sat, 30 Oct 2010 17:27:54 +0000 (19:27 +0200)]
For MPI builds, CMake will first try to compile a sample MPI program.
On some systems such as Cray the FindMPI.cmake module can't find the proper
libraries to link to. Therefore we now test whether the given C compiler
is an MPI wrapper and skip the rest of the tests.
Thanks to Roland Schulz for the patch.
Sander Pronk [Sat, 30 Oct 2010 15:11:18 +0000 (17:11 +0200)]
Added Windows macro for snprintf.
Rossen Apostolov [Fri, 29 Oct 2010 19:24:17 +0000 (21:24 +0200)]
added g_kinetics to the CMake build scripts
Szilard Pall [Fri, 29 Oct 2010 17:06:10 +0000 (19:06 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Szilard Pall [Fri, 29 Oct 2010 17:04:44 +0000 (19:04 +0200)]
enabled GMX_PREFER_STATIC_LIBS CMake option for CYGWIN
As it turns out that Cygwin also uses ".a" for static libraries,
the it is safe to enable this option.
Carsten Kutzner [Fri, 29 Oct 2010 16:38:33 +0000 (18:38 +0200)]
Fixed segv in gmx_hbond
Szilard Pall [Fri, 29 Oct 2010 15:24:06 +0000 (17:24 +0200)]
fixed the default for OpenMM plugin dir location (bug #606)
The OpenMM plugin lookup mechanism works again, so when running mdrun-gpu
on the same machine/OS where the binaries were built, the plugins are picked
up from the OpenMM installation used for building (but the env.var.
OPENMM_PLUGIN_DIR still has priority over all defaults!).
Szilard Pall [Fri, 29 Oct 2010 15:28:02 +0000 (17:28 +0200)]
fixed make install-mdrun issue (bug #605)
Szilard Pall [Fri, 29 Oct 2010 14:18:01 +0000 (16:18 +0200)]
(re)added "-dev" suffix for the CMake hardcoded version number
This avoids the potential confusion when the source from a git
release banch is used on machines without git. In these cases the
version reported by gromacs binaries would be the same as the
version of an official release, while former might actually
differ from the release in some patches from git.
Szilard Pall [Fri, 29 Oct 2010 13:44:31 +0000 (15:44 +0200)]
added CMake option GMX_PREFER_STATIC_LIBS (also fixes bug #541)
This option instructs CMake to prefer static external libs when both static
and shared version available. This makes possible linking statically against
external libraries (e.g. fftw, xml2).
The option only available on *NIX platforms, except APPLE and CYGWIN.
Note, that when the option is enabled UILD_SHARED_LIBS gets disabled.
Also note, that with this option on, the binaries built will still be
dynamically linked against system libraries.
David van der Spoel [Thu, 28 Oct 2010 20:26:28 +0000 (22:26 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
David van der Spoel [Thu, 28 Oct 2010 20:23:45 +0000 (22:23 +0200)]
Fixed bug 604 as requested.
Per Larsson [Thu, 28 Oct 2010 18:44:59 +0000 (20:44 +0200)]
Fixed a bug in the all-vs-all sse gb kernels, where an exclusion mask was
calculated incorrectly. Also fixes to loop indeces in the all-vs-all non-sse
code.
Berk Hess [Thu, 28 Oct 2010 10:12:24 +0000 (12:12 +0200)]
added HEM to HEME renaming for Gromos and Charmm ff's
Berk Hess [Thu, 28 Oct 2010 10:09:13 +0000 (12:09 +0200)]
fixed pdb2gmx chain merging bug (bugzilla 544)
hess [Wed, 27 Oct 2010 21:23:58 +0000 (23:23 +0200)]
changed fftw2_empty to fftw3_empty in gmx_fft_fftw3.c
Berk Hess [Tue, 26 Oct 2010 09:04:41 +0000 (11:04 +0200)]
fixed cycle print type cast issue on certain platforms, fixes bugzilla 601
Mark Abraham [Sun, 24 Oct 2010 16:19:10 +0000 (03:19 +1100)]
Don't sprintf variable-sized input into fixed-size buffers
Mark Abraham [Fri, 22 Oct 2010 16:01:00 +0000 (05:01 +1300)]
Re-enabled for BlueGene/L an optimization in the BG kernels that works for BG/L but not always for BG/P. Bugzilla 429 says this optimization is not stable for use in BG/P, however the work-around in
764d171c36b32c0497090531a11de disables it for BG/P too, which is undesirable.
Mark Abraham [Fri, 22 Oct 2010 15:58:34 +0000 (04:58 +1300)]
Rearranged cmake+BlueGene solution to have the same form as the other GMX_ACCELERATION solutions
Mark Abraham [Fri, 22 Oct 2010 15:57:04 +0000 (04:57 +1300)]
Made GMX_POWERPC_INVSQRT work properly on Power6 and BlueGene
Mark Abraham [Fri, 22 Oct 2010 06:02:25 +0000 (19:02 +1300)]
Power6 FORTRAN kernels do not work on PPC440 or PPC450 (these are the BlueGene chips)
Mark Abraham [Fri, 22 Oct 2010 05:50:47 +0000 (18:50 +1300)]
Carsten Kutzner [Fri, 22 Oct 2010 09:51:32 +0000 (11:51 +0200)]
Fixed segv in g_potential. Field output has now also the correct prefactor for V/nm
Per Larsson [Fri, 22 Oct 2010 08:31:02 +0000 (10:31 +0200)]
Added a check in grompp for the case with particles having a non-zero
charge while all GB-parameters are set to zero. This fixes bug #599.
Berk Hess [Thu, 21 Oct 2010 07:45:44 +0000 (09:45 +0200)]
clarified make_ndx error message
Mark Abraham [Wed, 20 Oct 2010 13:16:31 +0000 (02:16 +1300)]
Fixed cmake to work with BlueGene/L. This fix does not work for BlueGene/P.
Sander Pronk [Wed, 20 Oct 2010 13:00:57 +0000 (15:00 +0200)]
file reading error messages in g_bar less confusing.
Per Larsson [Wed, 20 Oct 2010 07:07:25 +0000 (09:07 +0200)]
Removed code for calculating logarithms using a table
This was not much faster than the builtin c-function,
and also only used in the non-sse loops
Berk Hess [Tue, 19 Oct 2010 13:36:01 +0000 (15:36 +0200)]
changed enxio warning into fatal errors by default, can be overridden with an env var
Per Larsson [Tue, 19 Oct 2010 08:32:21 +0000 (10:32 +0200)]
Fixed a compiler warning introduced by commit
9ccc786e4...
Per Larsson [Tue, 19 Oct 2010 05:52:58 +0000 (07:52 +0200)]
Replaced _mm_castsi128_pd with gmx_mm_castsi128_pd everywhere
in gmx_sse2_double
Per Larsson [Mon, 18 Oct 2010 19:50:40 +0000 (21:50 +0200)]
Double precision GB energies are now summed corrently (bug #585)
The issue was that __m128d _mm_add_sd(a,b) should give back r0 = a0 + b0
and r1 = a0, but it gives back r1 = 0. But since this is not true for
all architectures, it is also important to carefully zeroing out of some
variables in the code (explained in the kernel4XX-comments).
Sander Pronk [Mon, 18 Oct 2010 12:50:43 +0000 (14:50 +0200)]
Tries recovery during errors in .edr files.
Sander Pronk [Mon, 18 Oct 2010 12:12:50 +0000 (14:12 +0200)]
Better time checks in .edrs wihtout version numbers.
Sander Pronk [Mon, 18 Oct 2010 12:11:23 +0000 (14:11 +0200)]
More stringent .edr file data checks.
Berk Hess [Mon, 18 Oct 2010 11:55:54 +0000 (13:55 +0200)]
fixed atom type name case for methanol.itp in gromos43a1.ff
Teemu Murtola [Mon, 18 Oct 2010 10:47:18 +0000 (12:47 +0200)]
Use CMake install for install-mdrun (bugs #549, #555)
The custom target install-mdrun now invokes the cmake_install.cmake
script that is generated by CMake to perform the actual installation.
Adds support for DESTDIR and RPATH rewriting (see bug #570).
To implement this, all installation targets are now grouped into
components: "data" for shared data, "development" for headers and
pkgconfig files, "libraries" for libraries needed by mdrun, "mdrun" for
mdrun itself, and "runtime" for other binaries and libraries. Only
"mdrun" and "libraries" are used at the moment (the latter only when
installing with shared libraries).
Haven't tested this with Visual Studio, but if it doesn't work, it
should be easy to adapt.
Berk Hess [Mon, 18 Oct 2010 08:56:04 +0000 (10:56 +0200)]
fixed possible overflow of unused variable in lincs
Berk Hess [Mon, 18 Oct 2010 08:45:59 +0000 (10:45 +0200)]
added checks for rare events that would make variables in the v-rescale thermostat out of range
Berk Hess [Fri, 15 Oct 2010 10:34:12 +0000 (12:34 +0200)]
more fixes for TPI with PME, now really fixed bugzilla 590
Teemu Murtola [Thu, 14 Oct 2010 14:25:46 +0000 (16:25 +0200)]
Merge branch 'release-4-5-patches'
Berk Hess [Wed, 13 Oct 2010 12:50:10 +0000 (14:50 +0200)]
fixed g_velacc -m not automatically using -s
Teemu Murtola [Wed, 13 Oct 2010 12:20:25 +0000 (14:20 +0200)]
Fixed selection problems with a minus sign.
Negative values should now work consistently, independent of where the
value appears and whether it is an integer or not. Also, changed
precedence of operations such that "x-1" is interpreted as subtraction
and not as "x equals -1". The latter must now be written x {-1}.
Curly braces can also be used elsewhere to delimit value lists in
parameters (a yet undocumented feature).
For technical reasons and clarity, also changed static positions to use
square brackets ("[1.2, 2.0, 3.4]") instead of normal parentheses.
Teemu Murtola [Wed, 13 Oct 2010 12:11:29 +0000 (14:11 +0200)]
Fixed valgrind warnings in selections.
Arithmetic expressions that used a ^ operator on dynamic values resulted
in (mostly harmless) valgrind warnings about uninitialized values.
Dynamic numerical values are now initialized to zero to avoid this.
Teemu Murtola [Wed, 13 Oct 2010 11:56:52 +0000 (13:56 +0200)]
Fixed more selection negation segfaults.
Teemu Murtola [Wed, 13 Oct 2010 07:31:11 +0000 (09:31 +0200)]
Fixed segfaults with negations in selections.
Roland Schulz [Wed, 13 Oct 2010 00:58:54 +0000 (20:58 -0400)]
make sure that the MANPATH is not set to only GMXMANPATH
under ubuntu it is empty which means getting the system path
it has to include the empty string to keep finding the system man pages
Berk Hess [Tue, 12 Oct 2010 10:56:02 +0000 (12:56 +0200)]
added note to g_density for using g_energy for normal densities
Berk Hess [Tue, 12 Oct 2010 07:38:14 +0000 (09:38 +0200)]
fixed incorrect dispersion correction for TPI with multiple atoms, bugzilla 592
Roland Schulz [Mon, 11 Oct 2010 22:52:24 +0000 (18:52 -0400)]
fixed spelling
Erik Lindahl [Sat, 9 Oct 2010 09:56:58 +0000 (11:56 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Erik Lindahl [Sat, 9 Oct 2010 09:56:53 +0000 (11:56 +0200)]
Fixed uninitialized variable warning in grompp.c
Roland Shulz [Sat, 9 Oct 2010 00:23:54 +0000 (20:23 -0400)]
fixed
d3b582c73
this commit accidential disabled IA32 and X86_64 ASM kernels
Roland Shulz [Sat, 9 Oct 2010 00:02:04 +0000 (20:02 -0400)]
fixed
624db1bb
applied those change also to autoconf GMXRC templates
Berk Hess [Fri, 8 Oct 2010 12:06:21 +0000 (14:06 +0200)]
fixed typo in checkpoint warning
Berk Hess [Fri, 8 Oct 2010 12:04:44 +0000 (14:04 +0200)]
made combination of tpi and pme work again in parallel
Berk Hess [Fri, 8 Oct 2010 11:41:39 +0000 (13:41 +0200)]
fixed combination of tpic with pme, pme mesh energy would be incorrect, always around 0
David van der Spoel [Fri, 8 Oct 2010 11:37:24 +0000 (13:37 +0200)]
Merge branch 'release-4-5-patches' of git.gromacs.org:gromacs into release-4-5-patches
Roland Schulz [Fri, 8 Oct 2010 09:30:42 +0000 (05:30 -0400)]
Merge remote branch 'origin/release-4-5-patches'
Christoph Junghans [Fri, 8 Oct 2010 08:34:59 +0000 (10:34 +0200)]
CMake: another fortran fix
Sander Pronk [Fri, 8 Oct 2010 07:25:43 +0000 (09:25 +0200)]
Now really fixed locking of log file.
Roland Schulz [Fri, 8 Oct 2010 06:04:17 +0000 (02:04 -0400)]
Merge branch 'release-4-5-patches'
Conflicts:
src/tools/gmx_membed.c
Roland Schulz [Fri, 8 Oct 2010 05:48:00 +0000 (01:48 -0400)]
fixed locking of log file - broken by
d750b9ce
hess [Thu, 7 Oct 2010 17:59:59 +0000 (19:59 +0200)]
Made Charmm27 DNA and RNA termini (Michel Cuendet) and atom renaming work
Sander Pronk [Thu, 7 Oct 2010 14:55:25 +0000 (16:55 +0200)]
cmake LIB environment variable check, and GMXRC check due to Klaus Kaempf.
David van der Spoel [Thu, 7 Oct 2010 14:05:41 +0000 (16:05 +0200)]
Fixed compilation issues with C99 compatibility.