Adam Liwo [Sun, 10 May 2015 02:31:17 +0000 (04:31 +0200)]
Merge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1
Conflicts:
source/unres/src_MD/intcartderiv.F
Adam Liwo [Wed, 6 May 2015 13:17:29 +0000 (15:17 +0200)]
Fixed Makefiles in clust/src_MD-M
Adam Sieradzan [Wed, 6 May 2015 10:33:08 +0000 (12:33 +0200)]
correction in readpdb (bugfix)
Adam Liwo [Wed, 8 Apr 2015 19:11:13 +0000 (21:11 +0200)]
By Adam
Cezary Czaplewski [Wed, 25 Mar 2015 18:49:45 +0000 (19:49 +0100)]
changes to avoid PMPI_Scatterv: Invalid buffer pointer in Intel MPI
for src_MD-M (multichain)
Cezary Czaplewski [Fri, 13 Mar 2015 13:38:56 +0000 (14:38 +0100)]
changes to avoid PMPI_Scatterv: Invalid buffer pointer in Intel MPI
Adam Sieradzan [Wed, 25 Feb 2015 09:36:46 +0000 (10:36 +0100)]
Finding undefined tua...
Adam Sieradzan [Tue, 24 Feb 2015 11:01:21 +0000 (12:01 +0100)]
zmiany przywracajace TURN dla dummy i rozszerzajace SCCORR
Adam Sieradzan [Mon, 23 Feb 2015 19:00:58 +0000 (20:00 +0100)]
poprawka turn3 i turn4 uwaga moga byc wlaczone diagnostki
Adam Sieradzan [Thu, 19 Feb 2015 17:41:51 +0000 (18:41 +0100)]
EBE change in prerealese-3.2.1 make dummy atom idependent
Adam Sieradzan [Mon, 16 Feb 2015 12:36:45 +0000 (13:36 +0100)]
poprawka w src_MD
Adam Sieradzan [Mon, 16 Feb 2015 12:34:30 +0000 (13:34 +0100)]
Poprawiony src_MD-M gradient
Adam Sieradzan [Wed, 11 Feb 2015 16:06:45 +0000 (17:06 +0100)]
Merge branch 'prerelease-3.2.1' of mmka:unres into prerelease-3.2.1
Adam Sieradzan [Wed, 11 Feb 2015 16:05:21 +0000 (17:05 +0100)]
rozgrzebana minimalizacja
Adam Sieradzan [Wed, 11 Feb 2015 11:23:12 +0000 (12:23 +0100)]
intro of SCCOR into src_MIN
Adam Liwo [Fri, 23 Jan 2015 20:34:54 +0000 (21:34 +0100)]
refsys
Adam Liwo [Fri, 23 Jan 2015 20:30:52 +0000 (21:30 +0100)]
Merge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1
Conflicts:
source/unres/src_MD-M/cinfo.f
source/unres/src_MD-M/refsys.f
Adam Liwo [Fri, 23 Jan 2015 20:29:12 +0000 (21:29 +0100)]
Corrected refsys.f in src_MD-M
Adam Sieradzan [Thu, 22 Jan 2015 10:18:23 +0000 (11:18 +0100)]
Merge branch 'prerelease-3.2.1' of mmka:unres into prerelease-3.2.1
Adam Sieradzan [Mon, 19 Jan 2015 13:32:01 +0000 (14:32 +0100)]
dzialajacy wham+poprawka w funckji energi+ poprawka w czytaniu
Cezary Czaplewski [Thu, 8 Jan 2015 07:49:23 +0000 (08:49 +0100)]
Makefiles for mpich2 and some corrections to Makefiles
Adam Liwo [Mon, 5 Jan 2015 05:50:09 +0000 (06:50 +0100)]
Merge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1
Conflicts:
source/unres/src_MD-M/cinfo.f
source/wham/src-M/cinfo.f
Adam Liwo [Mon, 5 Jan 2015 05:46:39 +0000 (06:46 +0100)]
Added cinfo
Adam Liwo [Mon, 5 Jan 2015 05:43:41 +0000 (06:43 +0100)]
MREMD corrected; Langevin mode (bcast instead of scatter i2rep)
Adam Sieradzan [Sun, 4 Jan 2015 11:33:52 +0000 (12:33 +0100)]
poprawka gradientu w CSA
Adam Sieradzan [Sun, 4 Jan 2015 10:54:16 +0000 (11:54 +0100)]
Naprawienie wham'a oraz wprowadzenie SCcorr do CSA
Adam Sieradzan [Tue, 30 Dec 2014 11:04:30 +0000 (12:04 +0100)]
wprowadzenie do multichaina SCcorr
Adam Sieradzan [Fri, 19 Dec 2014 12:29:56 +0000 (13:29 +0100)]
debug w poszukiwaniu bledu w ostatniej reszcie
Adam Kazimierz Sieradzan [Tue, 30 Oct 2012 11:33:45 +0000 (07:33 -0400)]
dodanie czytania wagi wsccor do clustrowania-M
Conflicts:
bin/cluster/unres_clustMD-mult_MPICH-GAB.exe
source/cluster/wham/src-M/readrtns.o
Adam Kazimierz Sieradzan [Tue, 30 Oct 2012 11:16:58 +0000 (07:16 -0400)]
Wstawnieni SCCOR dla clustrowania. Nie wiadomo czy jest czytana waga
Conflicts:
bin/cluster/unres_clustMD-mult_MPICH-GAB.exe
bin/wham_multparm-D-sccor-oldparm
source/cluster/wham/src-M/COMMON.SCCOR
source/cluster/wham/src-M/chainbuild.o
source/cluster/wham/src-M/convert.o
source/cluster/wham/src-M/energy_p_new.F
source/cluster/wham/src-M/energy_p_new.o
source/cluster/wham/src-M/geomout.o
source/cluster/wham/src-M/initialize_p.o
source/cluster/wham/src-M/int_from_cart1.o
source/cluster/wham/src-M/main_clust.o
source/cluster/wham/src-M/parmread.o
source/cluster/wham/src-M/permut.o
source/cluster/wham/src-M/read_coords.o
source/cluster/wham/src-M/read_ref_str.o
source/cluster/wham/src-M/readpdb.o
source/cluster/wham/src-M/readrtns.o
source/cluster/wham/src-M/setup_var.o
source/cluster/wham/src-M/wrtclust.o
source/cluster/wham/src-M/xdrf/libxdrf.a
Adam Kazimierz Sieradzan [Mon, 29 Oct 2012 12:37:44 +0000 (08:37 -0400)]
Wprowadzenie SCCOR dla wham-M
Conflicts:
bin/unres/MD-M/unres_Tc_procor_oldparm_em64-D-symetr.exe
bin/wham_multparm-D-sccor-oldparm
source/unres/src_MD-M/cinfo.f
source/wham/src-M/COMMON.ALLPARM
source/wham/src-M/cinfo.f
source/wham/src-M/energy_p_new.F
source/wham/src-M/include_unres/COMMON.LOCAL
source/wham/src-M/include_unres/COMMON.SCCOR
source/wham/src/include_unres/COMMON.SCCOR
Adam Kazimierz Sieradzan [Fri, 26 Oct 2012 09:47:18 +0000 (05:47 -0400)]
Rozgrzebany SCCOR dla wham-M
Conflicts:
source/wham/src-M/energy_p_new.F
Adam Kazimierz Sieradzan [Fri, 5 Oct 2012 11:17:17 +0000 (07:17 -0400)]
Poprawiony SCR_MD-M i dzialajacy
Conflicts:
source/unres/src_MD-M/initialize_p.F
source/unres/src_MD-M/parmread.F
Adam Kazimierz Sieradzan [Thu, 4 Oct 2012 14:52:15 +0000 (10:52 -0400)]
Wprowadznie potencjalow SC-COR do multichain oraz ich pseudosymetrii dla
D aminokwasow
Conflicts:
bin/unres/MD-M/unres_Tc_procor_oldparm_em64-D-symetr.exe
source/unres/src_MD-M/COMMON.SCCOR
source/unres/src_MD-M/Makefile
source/unres/src_MD-M/cinfo.f
source/unres/src_MD-M/energy_p_new_barrier.F
source/unres/src_MD-M/lagrangian_lesyng.F
source/unres/src_MD-M/moments.f
source/unres/src_MD-M/parmread.F
source/unres/src_MD-M/stochfric.F
source/unres/src_MD/COMMON.SCCOR
Adam Sieradzan [Wed, 17 Dec 2014 10:06:19 +0000 (11:06 +0100)]
Merge branch 'prerelease-3.2.1' of mmka:unres into prerelease-3.2.1
Dawid Jagiela [Fri, 12 Dec 2014 14:15:37 +0000 (15:15 +0100)]
removed source/maxlik/src_CSA dir from CMake
Adam Liwo [Fri, 12 Dec 2014 00:48:20 +0000 (01:48 +0100)]
Again, documentation updated
Adam Liwo [Fri, 12 Dec 2014 00:43:11 +0000 (01:43 +0100)]
Documentation updated
Adam Liwo [Thu, 11 Dec 2014 14:37:42 +0000 (15:37 +0100)]
Minor change in documentation (installman)
Adam Liwo [Thu, 11 Dec 2014 14:36:04 +0000 (15:36 +0100)]
Updated changelog, added minimization-only version binaries
Adam Liwo [Thu, 11 Dec 2014 14:14:41 +0000 (15:14 +0100)]
Created binaries and fixed bugs when compiling single-processor version of the multichain code.
Dawid Jagieła [Sun, 7 Dec 2014 15:30:55 +0000 (16:30 +0100)]
removed CSA_DiL sources from CMake
Cezary Czaplewski [Fri, 5 Dec 2014 13:32:31 +0000 (14:32 +0100)]
correction to 4P energy and csa examples
Cezary Czaplewski [Fri, 5 Dec 2014 13:16:25 +0000 (14:16 +0100)]
corrected example CSA run with 4P
Cezary Czaplewski [Fri, 5 Dec 2014 12:44:53 +0000 (13:44 +0100)]
new options for mpich2 with gfortran Makefile
Cezary Czaplewski [Fri, 5 Dec 2014 10:39:17 +0000 (11:39 +0100)]
src_CSA_DiL removed from prerelease, current version in devel
Adam Liwo [Thu, 4 Dec 2014 13:54:48 +0000 (14:54 +0100)]
Added the change docs by Adam
Adam Liwo [Thu, 4 Dec 2014 13:52:45 +0000 (14:52 +0100)]
Merge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1
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 [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 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
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 Sieradzan [Thu, 11 Sep 2014 11:07:33 +0000 (13:07 +0200)]
dodanie parametrow
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
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 [Tue, 5 Nov 2013 16:30:27 +0000 (17:30 +0100)]
Debug part 1
Adam Sieradzan [Mon, 7 Oct 2013 17:45:58 +0000 (19:45 +0200)]
small correctian in wham
Cezary Czaplewski [Mon, 2 Sep 2013 13:02:33 +0000 (15:02 +0200)]
Merge branch 'prerelease-3.2.1' of mmka:unres into prerelease-3.2.1
Cezary Czaplewski [Mon, 2 Sep 2013 13:01:15 +0000 (15:01 +0200)]
dynamic disulfides in multichain
Adam Kazimierz Sieradzan [Sat, 31 Aug 2013 09:32:31 +0000 (05:32 -0400)]
wylaczenie diagnostyki
Adam Kazimierz Sieradzan [Sat, 31 Aug 2013 09:28:36 +0000 (05:28 -0400)]
Merge branch 'prerelease-3.2.1' of mmka.chem.univ.gda.pl:unres into prerelease-3.2.1
Adam Kazimierz Sieradzan [Sat, 31 Aug 2013 09:27:48 +0000 (05:27 -0400)]
zmiany w prereleasie drobne
Adam Sieradzan [Mon, 12 Aug 2013 20:28:23 +0000 (22:28 +0200)]
changes for DIMENSION for smaller size MEMory
Adam Sieradzan [Thu, 8 Aug 2013 00:16:23 +0000 (02:16 +0200)]
Merge branch 'prerelease-3.2.1' of mmka:unres into prerelease-3.2.1
Cezary Czaplewski [Wed, 7 Aug 2013 21:54:08 +0000 (23:54 +0200)]
decrease of Max_Parm to 32 necessary for 4GB machine
Adam Sieradzan [Wed, 7 Aug 2013 16:05:10 +0000 (18:05 +0200)]
merge...
Merge branch 'prerelease-3.2.1' of mmka:unres into prerelease-3.2.1
Conflicts:
source/wham/src/energy_p_new.F
Adam Sieradzan [Wed, 7 Aug 2013 16:03:22 +0000 (18:03 +0200)]
usuniecie diagnostyki
Cezary Czaplewski [Mon, 5 Aug 2013 07:09:27 +0000 (09:09 +0200)]
Merge branch 'prerelease-3.2.1' of mmka:unres into prerelease-3.2.1
Cezary Czaplewski [Mon, 5 Aug 2013 07:07:47 +0000 (09:07 +0200)]
only new xdrf2pdb binary
Dawid Jagiela [Thu, 25 Jul 2013 08:14:18 +0000 (10:14 +0200)]
fixed WHAM for gfortran: src/energy_p_new.F
Adam Kazimierz Sieradzan [Fri, 28 Jun 2013 18:12:54 +0000 (14:12 -0400)]
Just few comments added to WHAM to clarify
Adam Kazimierz Sieradzan [Fri, 28 Jun 2013 01:00:10 +0000 (21:00 -0400)]
Bugfix for SS wham and introduction SS to cluster analysis
Adam Kazimierz Sieradzan [Tue, 25 Jun 2013 23:37:52 +0000 (19:37 -0400)]
Dodanie dynamic disulfide to WHAM
Cezary Czaplewski [Tue, 7 May 2013 13:39:45 +0000 (15:39 +0200)]
some corrections in xdrf2pdb-m for dyn_ss
Cezary Czaplewski [Tue, 30 Apr 2013 07:10:32 +0000 (09:10 +0200)]
Merge branch 'prerelease-3.2.1' of mmka:unres into prerelease-3.2.1
Cezary Czaplewski [Tue, 30 Apr 2013 07:08:54 +0000 (09:08 +0200)]
testing ssbond in cx