Adam Liwo [Thu, 4 Dec 2014 13:51:12 +0000 (14:51 +0100)]
Yet more changes in the documentation ( by Adam)
Adam Liwo [Thu, 4 Dec 2014 13:40:17 +0000 (14:40 +0100)]
Revised documentation by Adam
Dawid Jagiela [Fri, 28 Nov 2014 12:37:21 +0000 (13:37 +0100)]
changed FF preprocesor flags in src_CSA_DiL/CMakeLists.txt
Dawid Jagiela [Fri, 28 Nov 2014 11:49:03 +0000 (12:49 +0100)]
Merge branch 'prerelease-3.2.1' of mmka:unres into prerelease-3.2.1
Adam Liwo [Fri, 28 Nov 2014 11:42:27 +0000 (12:42 +0100)]
Updated INSTALL
Adam Liwo [Fri, 28 Nov 2014 11:38:33 +0000 (12:38 +0100)]
Merge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1
Dawid Jagiela [Fri, 28 Nov 2014 11:38:22 +0000 (12:38 +0100)]
fixed FF preprocesor flags for src_CSA/CMakeLists.txt
Adam Liwo [Fri, 28 Nov 2014 11:37:12 +0000 (12:37 +0100)]
Updated INSTALL
By Adam
Dawid Jagiela [Fri, 28 Nov 2014 11:24:28 +0000 (12:24 +0100)]
changed csa.f to csa.F in src_CSA/CMakeLists.txt sources
Adam Liwo [Fri, 28 Nov 2014 10:45:13 +0000 (11:45 +0100)]
Trying to bring files - continued
By Adam
Adam Liwo [Fri, 28 Nov 2014 10:37:50 +0000 (11:37 +0100)]
Trying to bring the csa.F file to the repository.
By Adam.
Adam Liwo [Thu, 27 Nov 2014 14:53:46 +0000 (15:53 +0100)]
Additional fix of xdrfpdb binaries (creation of bin/xdrf and putting
binaries there acc. to documentation.
By Adam
Adam Liwo [Thu, 27 Nov 2014 14:35:35 +0000 (15:35 +0100)]
Fixed Makefiles, handle all force fields thru appropriate options
By Adam
Dawid Jagiela [Thu, 6 Nov 2014 00:25:35 +0000 (01:25 +0100)]
fixed src_MD_DFA ala10 ctest
Dawid Jagiela [Thu, 6 Nov 2014 00:12:54 +0000 (01:12 +0100)]
1) changes for FindMPI macro in source/unres/src_MD_DFA
2) fixed broken if-then statement
Dawid Jagiela [Wed, 5 Nov 2014 22:53:39 +0000 (23:53 +0100)]
fixed marge problem
Dawid Jagiela [Wed, 5 Nov 2014 22:44:32 +0000 (23:44 +0100)]
Merge branch 'prerelease-3.2.1' into devel
Conflicts:
.gitignore
CMakeLists.txt
source/cluster/wham/src/COMMON.SCCOR
source/maxlik/src_CSA/CMakeLists.txt
source/unres/src_CSA_DiL/CMakeLists.txt
source/unres/src_MD-M/CMakeLists.txt
source/unres/src_MD-M/Makefile
source/unres/src_MD-M/energy_p_new_barrier.F
source/unres/src_MD-M/ssMD.F
source/unres/src_MD/CMakeLists.txt
source/unres/src_MIN/CMakeLists.txt
source/wham/src/DIMENSIONS.FREE
source/xdrfpdb/src/CMakeLists.txt
Dawid Jagiela [Wed, 5 Nov 2014 21:44:43 +0000 (22:44 +0100)]
Merge branch 'prerelease-3.2.1' of mmka:unres into prerelease-3.2.1
Dawid Jagiela [Wed, 5 Nov 2014 21:44:05 +0000 (22:44 +0100)]
ctest ala10 binary location fix
Dawid Jagieła [Wed, 5 Nov 2014 08:56:10 +0000 (09:56 +0100)]
Added CMake build instructions
Dawid Jagiela [Fri, 31 Oct 2014 22:48:33 +0000 (23:48 +0100)]
fix for multiple MPI include paths passed by MPI wrapper
Dawid Jagiela [Mon, 27 Oct 2014 22:19:36 +0000 (23:19 +0100)]
1) binaries are compiled into /bin subdirectory of build directory
2) added "make install" support costumizable with CMAKE_INSTALL_PREFIX
Dawid Jagiela [Sun, 26 Oct 2014 21:58:46 +0000 (22:58 +0100)]
1) Threading cleanup in src_CSA & src_CSA_DiL
2) Makefile verbose turned off for "Release" builds
3) fixed missing printmat.f in cluster/wham/src/CMakeLists.txt
Dawid Jagiela [Sun, 26 Oct 2014 16:03:50 +0000 (17:03 +0100)]
switched to CMake FindMPI module in all source files that use MPI
Dawid Jagiela [Sun, 26 Oct 2014 16:03:50 +0000 (17:03 +0100)]
switched to CMake FindMPI module in all source files that use MPI
Dawid Jagiela [Sun, 26 Oct 2014 14:33:10 +0000 (15:33 +0100)]
added missing preprocessor flags for prng_32.F
Dawid Jagiela [Sat, 25 Oct 2014 21:45:17 +0000 (23:45 +0200)]
prng.f unification
Adam Sieradzan [Thu, 23 Oct 2014 15:56:55 +0000 (17:56 +0200)]
Merge branch 'multichain' of mmka:unres into multichain
Adam Sieradzan [Thu, 23 Oct 2014 15:56:27 +0000 (17:56 +0200)]
poprawka w stochasticfric
Dawid Jagiela [Thu, 16 Oct 2014 23:51:51 +0000 (01:51 +0200)]
64-bit fix for unres/CSA and unres/CSA_DiL code
Dawid Jagieła [Tue, 14 Oct 2014 22:30:49 +0000 (00:30 +0200)]
Merge branch 'prerelease-3.2.1' of mmka:unres into prerelease-3.2.1
Dawid Jagieła [Tue, 14 Oct 2014 22:29:43 +0000 (00:29 +0200)]
fixed CMake variable typo
Cezary Czaplewski [Wed, 8 Oct 2014 10:32:04 +0000 (12:32 +0200)]
correct default option for compilers in cluster CmakeList.txt
Cezary Czaplewski [Wed, 8 Oct 2014 10:09:44 +0000 (12:09 +0200)]
correct default option for compilers in wham CmakeList.txt
Adam Kazimierz Sieradzan [Thu, 11 Sep 2014 19:14:53 +0000 (15:14 -0400)]
poprawka w triss
Adam Sieradzan [Wed, 10 Sep 2014 14:23:12 +0000 (16:23 +0200)]
correction of xdrf2pdb
Adam Kazimierz Sieradzan [Thu, 24 Jul 2014 14:22:58 +0000 (10:22 -0400)]
After long DEBUG of energy function
Dawid Jagiela [Wed, 23 Jul 2014 11:05:07 +0000 (13:05 +0200)]
added "make install" support for: unres (MD, MD-M, MIN) and maxlik
Adam Sieradzan [Tue, 22 Jul 2014 08:23:13 +0000 (10:23 +0200)]
correction in MD returnbox
Adam Kazimierz Sieradzan [Fri, 4 Jul 2014 18:40:17 +0000 (14:40 -0400)]
BUG FIX for SUMSL minimization
Adam Sieradzan [Tue, 24 Jun 2014 08:26:42 +0000 (10:26 +0200)]
bug fix for langevin dynamics
Conflicts:
.gitignore
source/unres/src_MD-M-newcorr/stochfric.F
Adam Sieradzan [Tue, 24 Jun 2014 08:41:41 +0000 (10:41 +0200)]
Merge branch 'devel' of mmka:unres into devel
Adam Sieradzan [Tue, 24 Jun 2014 08:26:42 +0000 (10:26 +0200)]
bug fix for langevin dynamics
Cezary Czaplewski [Tue, 24 Jun 2014 06:46:23 +0000 (08:46 +0200)]
Makefile without debuging
Cezary Czaplewski [Wed, 18 Jun 2014 12:56:05 +0000 (14:56 +0200)]
Merge branch 'devel' of mmka:unres into devel
Cezary Czaplewski [Wed, 18 Jun 2014 12:53:25 +0000 (14:53 +0200)]
dyn-ss in MD-M
Adam Kazimierz Sieradzan [Tue, 17 Jun 2014 19:13:00 +0000 (15:13 -0400)]
dalej wylaczona diagnostyka
Adam Kazimierz Sieradzan [Tue, 17 Jun 2014 18:18:21 +0000 (14:18 -0400)]
wylacznie diagnostyki
Adam Kazimierz Sieradzan [Tue, 17 Jun 2014 18:13:35 +0000 (14:13 -0400)]
doadany sccor_am1 do PBC (needs veryfy)
Cezary Czaplewski [Tue, 17 Jun 2014 11:18:05 +0000 (13:18 +0200)]
correcter Makefile and errors side chain parameters
Cezary Czaplewski [Tue, 17 Jun 2014 09:42:27 +0000 (11:42 +0200)]
Merge branch 'devel' of mmka:unres into devel
Cezary Czaplewski [Tue, 17 Jun 2014 09:34:30 +0000 (11:34 +0200)]
xdrf2x tests
Adam Sieradzan [Thu, 12 Jun 2014 09:21:36 +0000 (11:21 +0200)]
compiling cluster before tests
Adam Sieradzan [Tue, 10 Jun 2014 16:03:57 +0000 (18:03 +0200)]
Introduction of PBC to cluster energy and reading, turn off wham one of the debug
Adam Sieradzan [Tue, 10 Jun 2014 14:54:54 +0000 (16:54 +0200)]
Bug fix for reading single residue from pdb
Dawid Jagieła [Tue, 3 Jun 2014 15:35:28 +0000 (17:35 +0200)]
fixed typo
Dawid Jagieła [Tue, 3 Jun 2014 15:16:39 +0000 (17:16 +0200)]
fix for MD tests in E0LL2Y FF
Dawid Jagieła [Tue, 3 Jun 2014 11:57:14 +0000 (13:57 +0200)]
fixed binary name generation in unres/src_MD-M
Dawid Jagieła [Tue, 3 Jun 2014 11:54:04 +0000 (13:54 +0200)]
kolejne porzadki
Dawid Jagieła [Tue, 3 Jun 2014 11:48:09 +0000 (13:48 +0200)]
Merge branch 'devel' of mmka:unres into devel
Dawid Jagieła [Tue, 3 Jun 2014 11:47:06 +0000 (13:47 +0200)]
wywalka smieci - ludzie budujcie w katalogu build!
Bartlomiej Zaborowski [Tue, 3 Jun 2014 11:18:28 +0000 (13:18 +0200)]
Merge branch 'devel' of mmka:unres into devel
Bartlomiej Zaborowski [Tue, 3 Jun 2014 11:16:30 +0000 (13:16 +0200)]
New CMake files after cleaning
Bartlomiej Zaborowski [Tue, 3 Jun 2014 11:13:06 +0000 (13:13 +0200)]
Modification files required corresponding architecture
Bartlomiej Zaborowski [Tue, 3 Jun 2014 11:11:13 +0000 (13:11 +0200)]
Modification files required corresponding architecture
Adam Sieradzan [Sun, 25 May 2014 15:25:16 +0000 (17:25 +0200)]
zmiany w multichainie
Adam Kazimierz Sieradzan [Sun, 25 May 2014 15:23:08 +0000 (11:23 -0400)]
zmiany, wylaczenie diagnostyki, dzialajacy WHAM
Adam Kazimierz Sieradzan [Wed, 21 May 2014 11:43:27 +0000 (07:43 -0400)]
diagnoza dlaczego WHAM nie dziala
Adam Kazimierz Sieradzan [Thu, 15 May 2014 07:53:58 +0000 (03:53 -0400)]
zmiany w WHAM PBC przed sprawdzeniem differow
Adam Sieradzan [Tue, 13 May 2014 10:05:51 +0000 (12:05 +0200)]
Wylacznie timiningu i sprawdzenie gradientu
Adam Sieradzan [Mon, 12 May 2014 17:15:54 +0000 (19:15 +0200)]
po przyspieszeniu przed checkgradem i sympcheckiem
Adam Sieradzan [Thu, 8 May 2014 15:36:52 +0000 (17:36 +0200)]
wlaczenie timing
Adam Sieradzan [Thu, 8 May 2014 15:25:43 +0000 (17:25 +0200)]
Merge branch 'devel' of mmka:unres into devel
Adam Sieradzan [Thu, 8 May 2014 15:25:03 +0000 (17:25 +0200)]
Adjusted energy file (small improvement)
Adam Sieradzan [Thu, 1 May 2014 18:52:58 +0000 (20:52 +0200)]
polepszenie wydajnosci algorytmu PBC
Dawid Jagiela [Fri, 25 Apr 2014 07:54:20 +0000 (03:54 -0400)]
1) added warnings suppression if find_package(MPI) failes to find MPI
2) removed non-standardold MPI paths - should be passed by cmake variables directly
Dawid Jagiela [Fri, 25 Apr 2014 07:54:20 +0000 (03:54 -0400)]
1) added warnings suppression if find_package(MPI) failes to find MPI
2) removed non-standardold MPI paths - should be passed by cmake variables directly
Dawid Jagieła [Tue, 15 Apr 2014 11:31:34 +0000 (13:31 +0200)]
DON'T DELETE THE "git-daemon-export-ok" FILE!!!
This file is mandatory for proper git-deamon work - without it you cannot access the repository using the git protocol "git://"
Adam Liwo [Thu, 10 Apr 2014 19:57:52 +0000 (15:57 -0400)]
Merge branch 'devel' of mmka.chem.univ.gda.pl:unres into devel
Conflicts:
bin/unres/MD/unres_ifort_MPICH_GAB.exe
Adam Liwo [Thu, 10 Apr 2014 18:28:20 +0000 (14:28 -0400)]
Added new files to the NEWCORR version
Adam Liwo [Thu, 10 Apr 2014 18:24:39 +0000 (14:24 -0400)]
Added source/wham/src-NEWSC-NEWCORR/
Adam Liwo [Thu, 10 Apr 2014 11:57:44 +0000 (07:57 -0400)]
Added src_MD-M-newcorr (Adasko's source) and src-NEWSC of WHAM (with Momo's SCSC potentials)
Adam Liwo [Tue, 1 Apr 2014 04:37:15 +0000 (00:37 -0400)]
Added src_Eshel (decoy processing for threading)
Adam Liwo [Wed, 19 Mar 2014 08:06:29 +0000 (04:06 -0400)]
Fixed iatsc_s and iatscp_s for 1 residue (was 0 with MPI version)
Adam Sieradzan [Tue, 18 Mar 2014 07:21:27 +0000 (08:21 +0100)]
Devel ma zle COMMON.TORSIONAL w src_MD (single chain)
Adam Sieradzan [Tue, 4 Mar 2014 11:32:18 +0000 (12:32 +0100)]
ignorowanie build theta
Adam Sieradzan [Mon, 3 Mar 2014 05:12:50 +0000 (06:12 +0100)]
poprawka w refsysie
Adam Sieradzan [Mon, 24 Feb 2014 19:23:03 +0000 (20:23 +0100)]
Working gradient for PBC
Adam Sieradzan [Thu, 20 Feb 2014 08:37:49 +0000 (09:37 +0100)]
Drobne zmiany i dodanei parametrow dla dummy atom
Adam Sieradzan [Mon, 17 Feb 2014 18:27:57 +0000 (19:27 +0100)]
The wrong one gradient compontent...
cleaning in progress by A.Liwo other gradient OK
Adam Sieradzan [Sat, 8 Feb 2014 17:27:39 +0000 (18:27 +0100)]
zmiany w galezi multichain
Adam Sieradzan [Wed, 29 Jan 2014 20:48:46 +0000 (21:48 +0100)]
DO zmiany czytanie pisanie i cutoff
Pawel Krupa [Wed, 20 Nov 2013 15:57:39 +0000 (10:57 -0500)]
Poprawione przyklady w polu ff_gab (zmieniony potencjal SIDEPAR na:
sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k).
Pawel Krupa [Wed, 20 Nov 2013 15:53:22 +0000 (10:53 -0500)]
Poprawione przyklady do pola ff_gab (zmieniony potencjal SIDEPAR na: sc_GB_opt.1gab_3S_qclass5no310-shan2-sc-16-10-8k).
Adam Sieradzan [Mon, 18 Nov 2013 19:02:48 +0000 (20:02 +0100)]
dzialajacy gradient
Adam Sieradzan [Thu, 14 Nov 2013 22:25:51 +0000 (23:25 +0100)]
Dzialajacy gradient dla reszt 13 i 7
Adam Sieradzan [Thu, 14 Nov 2013 13:32:27 +0000 (14:32 +0100)]
zabezpieczenie przedczarkowe
Dawid Jagiela [Wed, 6 Nov 2013 10:01:12 +0000 (11:01 +0100)]
Merge branch 'devel' of mmka:unres into devel
Dawid Jagiela [Wed, 6 Nov 2013 10:00:38 +0000 (11:00 +0100)]
junk files cleanup
Adam Sieradzan [Tue, 5 Nov 2013 22:44:36 +0000 (23:44 +0100)]
Merge branch 'devel' of mmka:unres into devel
projects / unres.git / log