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
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
Dawid Jagiela [Thu, 18 Apr 2013 14:44:24 +0000 (16:44 +0200)]
restructured examples
Cezary Czaplewski [Mon, 8 Apr 2013 13:01:54 +0000 (09:01 -0400)]
correct writing of dyn_ss for cx and x
Cezary Czaplewski [Tue, 19 Feb 2013 00:06:47 +0000 (01:06 +0100)]
dyn_ss and other finegrain printout cleaning
Cezary Czaplewski [Mon, 18 Feb 2013 12:52:01 +0000 (13:52 +0100)]
dynamic dissulfides with finegrain parallelization cont.
Cezary Czaplewski [Mon, 18 Feb 2013 07:47:34 +0000 (08:47 +0100)]
Merge branch 'prerelease-3.2.1' of mmka:unres into prerelease-3.2.1
Cezary Czaplewski [Mon, 18 Feb 2013 07:46:11 +0000 (08:46 +0100)]
dynamic dissulfides with finegrain parallelization
Adam Liwo [Mon, 18 Feb 2013 07:10:29 +0000 (02:10 -0500)]
Added refsys.f to src_CSA_DiL
Adam Liwo [Mon, 18 Feb 2013 04:49:11 +0000 (23:49 -0500)]
refsys deleted from readpdb.F in srd_CSA_DiL
Adam Liwo [Mon, 18 Feb 2013 04:41:27 +0000 (23:41 -0500)]
Added refsysy to Cmakelists
Adam Liwo [Thu, 8 Nov 2012 13:58:32 +0000 (08:58 -0500)]
8/11/12 by Adam: fixed disulfide bridge problems
Conflicts:
bin/unres/CSA/unres_csa_ifort_mpich-1.2.7p1.exe
bin/unres/MD-M/unres_Tc_procor_oldparm_em64-D-symetr.exe
bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe
bin/unres/MD/unres_ifort_MPICH_GAB.exe
bin/unres/MD/unres_ifort_single_GAB.exe
source/unres/src_MD/parmread.F
Cezary Czaplewski [Mon, 18 Feb 2013 00:23:23 +0000 (01:23 +0100)]
compilation only
Adam Liwo [Sun, 17 Feb 2013 03:34:55 +0000 (22:34 -0500)]
Fixed the addition of dummy chain ends to structures read from UNRES PDB files
Fixed the bug in arcos.f (returned alpha=0 for cos(alpha)<=-1)
Conflicts:
bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe
source/unres/src_MD-M/Makefile
Cezary Czaplewski [Sun, 17 Feb 2013 02:06:59 +0000 (03:06 +0100)]
dyn_ss writing pdb and ihpb cleaning
Cezary Czaplewski [Sat, 16 Feb 2013 13:44:13 +0000 (14:44 +0100)]
more type cleaning in DFA
Cezary Czaplewski [Sat, 16 Feb 2013 13:38:19 +0000 (14:38 +0100)]
type declaration in COMMON.DFA
Cezary Czaplewski [Sat, 16 Feb 2013 13:20:06 +0000 (14:20 +0100)]
no type declaration in common
Cezary Czaplewski [Sat, 16 Feb 2013 13:09:23 +0000 (14:09 +0100)]
no type declaration in common
Cezary Czaplewski [Sat, 16 Feb 2013 12:05:44 +0000 (13:05 +0100)]
common sccor rename to avoid conflict with torsion
Cezary Czaplewski [Sat, 16 Feb 2013 12:01:38 +0000 (13:01 +0100)]
classical Makefile cleaning
Cezary Czaplewski [Sat, 16 Feb 2013 11:20:46 +0000 (12:20 +0100)]
rename common sccorin src_CSA
Cezary Czaplewski [Sat, 16 Feb 2013 11:05:56 +0000 (12:05 +0100)]
src_MD-M compiles with old Makefile and common sccor rename
Cezary Czaplewski [Sat, 16 Feb 2013 06:34:33 +0000 (07:34 +0100)]
common name correction
Cezary Czaplewski [Sat, 16 Feb 2013 06:10:05 +0000 (07:10 +0100)]
prng and not prng_32 for gfortran
Cezary Czaplewski [Sat, 16 Feb 2013 05:31:17 +0000 (06:31 +0100)]
prng and not prng_32 for f95
Cezary Czaplewski [Sat, 16 Feb 2013 03:56:34 +0000 (04:56 +0100)]
new SCCORPAR for ctest
Cezary Czaplewski [Sat, 16 Feb 2013 03:16:00 +0000 (04:16 +0100)]
common reorder to avoid padding in gfortran
Cezary Czaplewski [Fri, 15 Feb 2013 09:16:51 +0000 (10:16 +0100)]
dynamic disulfides are working again in md
Conflicts:
bin/unres/MD/unres_ifort_MPICH_GAB.exe
examples/unres/new/MD/DYN_SS/dyn_ss/small.inp
examples/unres/new/MD/DYN_SS/dyn_ss/unres_eval.csh
examples/unres/new/MD/DYN_SS/dyn_ss_from_pdb/small.inp
examples/unres/new/MD/DYN_SS/dyn_ss_from_pdb/small.out_GB000
examples/unres/new/MD/DYN_SS/dyn_ss_from_pdb/small_000.rst
examples/unres/new/MD/DYN_SS/dyn_ss_from_pdb/small_GB000.stat
examples/unres/new/MD/DYN_SS/dyn_ss_from_pdb/small_MD000.pdb
examples/unres/new/MD/DYN_SS/no_ss/small.inp
examples/unres/new/MD/DYN_SS/no_ss/small.out_GB000
examples/unres/new/MD/DYN_SS/no_ss/small_GB000.stat
source/unres/src_MD/cinfo.f
source/unres/src_MD/energy_p_new_barrier.F
Cezary Czaplewski [Fri, 15 Feb 2013 00:50:59 +0000 (01:50 +0100)]
adding ename to statout with PRINT_COMPON
Conflicts:
bin/unres/MD/unres_ifort_MPICH_GAB.exe
examples/unres/new/MD/DYN_SS/no_ss/small.out_GB000
examples/unres/new/MD/DYN_SS/ss/small.inp
examples/unres/new/MD/DYN_SS/ss/small.out_GB000
examples/unres/new/MD/DYN_SS/ss/small_GB000.stat
source/unres/src_MD/cinfo.f
Cezary Czaplewski [Mon, 24 Sep 2012 12:02:06 +0000 (14:02 +0200)]
MULTCONF is working now
Conflicts:
bin/unres/MD/unres_ifort_MPICH_GAB.exe
Cezary Czaplewski [Mon, 24 Sep 2012 08:56:04 +0000 (10:56 +0200)]
error message when reading SCCOR corrected
Conflicts:
bin/unres/MD/unres_ifort_MPICH_E0LL2Y-test.exe
Cezary Czaplewski [Fri, 21 Sep 2012 08:41:32 +0000 (10:41 +0200)]
ss_dyn compiles with make and with cmake
Cezary Czaplewski [Thu, 20 Sep 2012 08:33:37 +0000 (10:33 +0200)]
dynamic SS from old Maurizio's code
Conflicts:
bin/unres/MD/unres_ifort_MPICH_GAB.exe
Cezary Czaplewski [Thu, 14 Feb 2013 23:48:05 +0000 (00:48 +0100)]
compilation only
Dawid Jagiela [Thu, 10 Jan 2013 10:25:21 +0000 (11:25 +0100)]
fixed missing closing bracket
Dawid Jagiela [Thu, 10 Jan 2013 10:21:22 +0000 (11:21 +0100)]
WHAM -DISNAN fix
Dawid Jagiela [Thu, 10 Jan 2013 09:56:24 +0000 (10:56 +0100)]
added UNRES_MD_FF setting for WHAM in (wham & cluster/wham)
Dawid Jagiela [Wed, 19 Dec 2012 14:13:37 +0000 (15:13 +0100)]
Merge branch 'prerelease-3.2.1' of mmka:unres into prerelease-3.2.1
Dawid Jagiela [Wed, 19 Dec 2012 13:01:49 +0000 (14:01 +0100)]
poprawki w COMMONAch
Pawel Krupa [Tue, 4 Dec 2012 08:06:08 +0000 (03:06 -0500)]
New examples based on current version of UNRES.
projects / unres.git / log