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
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
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
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 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.
David van der Spoel [Thu, 7 Oct 2010 11:53:09 +0000 (13:53 +0200)]
Fixes and small additions to g_wham, due to Jochen Hub.
hess [Thu, 7 Oct 2010 08:27:04 +0000 (10:27 +0200)]
fixed genbox producing incorrect residue names with mixed solvents, bugzilla 576
Roland Schulz [Thu, 7 Oct 2010 05:41:42 +0000 (01:41 -0400)]
added a comment about assumptions of aligned memory
Christoph Junghans [Wed, 6 Oct 2010 12:38:45 +0000 (14:38 +0200)]
CMake: fortran fix
Szilard Pall [Wed, 6 Oct 2010 07:27:57 +0000 (09:27 +0200)]
fixed syntax error from commit
bd5b2724
Christoph Junghans [Tue, 5 Oct 2010 15:53:04 +0000 (17:53 +0200)]
cmake: give openmm default suffixes
Christoph Junghans [Tue, 5 Oct 2010 15:16:54 +0000 (17:16 +0200)]
cmake: install-mdrun should not install pkg-config files (bug #586)
Sander Pronk [Tue, 5 Oct 2010 15:18:40 +0000 (17:18 +0200)]
Modified FORTRAN and threads warning.
Szilard Pall [Tue, 5 Oct 2010 13:25:36 +0000 (15:25 +0200)]
improved option compatibility checking with OpenMM
(cherry picked from commit
eba3b450aba044c55aae5e49d5068d7fc05adbbb)
Berk Hess [Tue, 5 Oct 2010 13:01:50 +0000 (15:01 +0200)]
made grompp mdp input file non-optional, fixes bugzilla 577
Berk Hess [Tue, 5 Oct 2010 12:24:53 +0000 (14:24 +0200)]
added fail-safe check for OpenMM with double precision
Berk Hess [Tue, 5 Oct 2010 10:50:54 +0000 (12:50 +0200)]
renamed mdp setting Ace-approx to Ace-approximation
Berk Hess [Tue, 5 Oct 2010 10:35:59 +0000 (12:35 +0200)]
fixed completely incorrect pressure scaling with nstlist=-1, bugzilla 579
Mark Abraham [Tue, 5 Oct 2010 01:50:44 +0000 (12:50 +1100)]
Fix manual references for 'continuation', rather than 'unconstrained_start', even though they are equivalient and the latter is legal
Mark Abraham [Thu, 23 Sep 2010 05:09:08 +0000 (15:09 +1000)]
mk_dlist() changed its parameter list, so its declaration here needed to change, even though it's never used.
Roland Schulz [Mon, 4 Oct 2010 19:55:28 +0000 (15:55 -0400)]
fix broken check for dlopen (by Christoph Junghans, thanks!)
Roland Schulz [Fri, 1 Oct 2010 22:31:59 +0000 (18:31 -0400)]
fix FFTW3 interface for non aligned memory
(FFT5D doesn't use non-aligned memory thus this didn't cause any errors in 4.5
unknown to me whether this caused errors in 4.0)
Szilard Pall [Fri, 1 Oct 2010 16:42:38 +0000 (18:42 +0200)]
make install-mdrun now installes shared libs (fix for bugzilla 549) + mnir fixes
"make install-mdrun" correctly installing the shared gromacs libraries
when the case, including the pkgconfig data and symbolic links.
Also made the openmm_wrapper and gmgx_gpu_utils libraries always build
and link staticlally (no need for these externally).
Christoph Junghans [Thu, 30 Sep 2010 10:01:20 +0000 (12:01 +0200)]
configure: added '--disable-la-files' option
Berk Hess [Thu, 30 Sep 2010 14:07:01 +0000 (16:07 +0200)]
changed the grompp charge group radii to always check against rlist iso againt rlistlong
Sander Pronk [Thu, 30 Sep 2010 08:56:22 +0000 (10:56 +0200)]
Error message on enabling FORTRAN and threads.
Roland Schulz [Thu, 30 Sep 2010 02:49:55 +0000 (22:49 -0400)]
made vmdio work with older api version (e.g. vmd 1.8.6)
improved error message
David van der Spoel [Tue, 28 Sep 2010 19:59:25 +0000 (21:59 +0200)]
Re-added g_kinetics to src/tools/Makefile.am
Roland Schulz [Mon, 27 Sep 2010 22:27:57 +0000 (18:27 -0400)]
include "error.h" was not neccessary and caused problems with xlc (bug 575)
Roland Schulz [Sun, 26 Sep 2010 05:41:40 +0000 (01:41 -0400)]
1) gmx_fio_seek was not returning correct return value, thus trjacat thought the seek failed and trjcat -overwrite wasn't working
2) checkpoint didn't check the return value of gmx_fio_seek
3) log file wasn't truncated if md5 file was available in checkpoint
4) made comments more clear
Rossen Apostolov [Sat, 25 Sep 2010 19:59:20 +0000 (21:59 +0200)]
Reverted changes to md_openmm.c, get rid of 'nan' in averages.
David van der Spoel [Sat, 25 Sep 2010 13:13:36 +0000 (15:13 +0200)]
Added software-related quote
Rossen Apostolov [Sat, 25 Sep 2010 12:21:52 +0000 (14:21 +0200)]
mdrun-gpu now doesn't output individual energy term, only the totals.
Closes bug 568.
Berk Hess [Sat, 25 Sep 2010 07:37:42 +0000 (09:37 +0200)]
fixed case of opls atom types in share/top/ions.itp to make old opls topologies work with the new ff setup
David van der Spoel [Fri, 24 Sep 2010 06:45:52 +0000 (08:45 +0200)]
Updated to reflect bug 557.
Mark Abraham [Thu, 23 Sep 2010 04:41:41 +0000 (14:41 +1000)]
Fixes for g_chi for bugzilla 569, so that it now uses the GROMACS 4.5 residuetypes.dat database, not the old aminoacids.dat. These fixes use the new gmx_residuetypes API functions contained in the previous commit (
bbf195d).
Mark Abraham [Thu, 23 Sep 2010 04:40:30 +0000 (14:40 +1000)]
Extensions to the gmx_residuetypes_t API to meet the needs of g_chi
Roland Schulz [Thu, 23 Sep 2010 04:05:01 +0000 (00:05 -0400)]
vmdio read the box but didn't mark it as beeing read (bBox)
Roland Shulz [Wed, 22 Sep 2010 21:33:39 +0000 (17:33 -0400)]
MCH3S was missing
Sander Pronk [Wed, 22 Sep 2010 14:51:29 +0000 (16:51 +0200)]
Added missing includes to gmx_tune_pme.c
Berk Hess [Wed, 22 Sep 2010 14:22:29 +0000 (16:22 +0200)]
added a warning/note for bond oscillational periods of a few times the time step
Berk Hess [Tue, 21 Sep 2010 15:43:33 +0000 (17:43 +0200)]
added check for tau_t<=0 with integrator sd
Berk Hess [Tue, 21 Sep 2010 15:19:32 +0000 (17:19 +0200)]
fixed incorrect gmxcheck comparison of ir->separate_dhdl_file
Carsten Kutzner [Tue, 21 Sep 2010 14:40:45 +0000 (16:40 +0200)]
Added missing #ifdef around MPI directive
Rossen Apostolov [Tue, 21 Sep 2010 14:06:04 +0000 (16:06 +0200)]
Fixed missing installation of the openmm_api_wrapper; added INSTALL.*make* for distribution.
Berk Hess [Tue, 21 Sep 2010 13:28:32 +0000 (15:28 +0200)]
improved the initial guess and fitting weights for autocorrelation fitting with -beginfit>0
Berk Hess [Tue, 21 Sep 2010 13:27:53 +0000 (15:27 +0200)]
removed g_analyze confusing fitting messages about fitting the function when fitting only the acf
Szilard Pall [Mon, 20 Sep 2010 21:26:23 +0000 (23:26 +0200)]
FindFFT?[F] scripts can use a path provided in FFTWx[F]_ROOT_DIR environment variable when looking for libs/headers
Berk Hess [Mon, 20 Sep 2010 14:50:01 +0000 (16:50 +0200)]
fixed too small fixed array in grompp top reading (only used with incorrect input
Rossen Apostolov [Mon, 20 Sep 2010 12:27:15 +0000 (14:27 +0200)]
Added do_multiprot in src/contrib, thanks to Ran Friedman
David van der Spoel [Mon, 20 Sep 2010 11:54:17 +0000 (13:54 +0200)]
Merge branch 'release-4-5-patches' of git@git.gromacs.org:gromacs into release-4-5-patches