Adam Kazimierz Sieradzan [Tue, 17 Jul 2012 07:01:49 +0000 (03:01 -0400)]
D i L aminokwasy dzialajace dla src_MD
Adam Kazimierz Sieradzan [Mon, 9 Jul 2012 07:46:21 +0000 (03:46 -0400)]
D i L aminokwasy tuz przed testami
Adam Kazimierz Sieradzan [Fri, 6 Jul 2012 08:18:36 +0000 (04:18 -0400)]
Wyrowanie w COmmonie...
Adam Kazimierz Sieradzan [Fri, 6 Jul 2012 06:08:43 +0000 (02:08 -0400)]
zmiana do DiL
Adam Kazimierz Sieradzan [Thu, 5 Jul 2012 09:51:00 +0000 (05:51 -0400)]
DIL zmiana w param read
Adam Kazimierz Sieradzan [Thu, 5 Jul 2012 07:51:28 +0000 (03:51 -0400)]
dodanie do gitignor kolejnych moich poligonowy plikow
Adam Kazimierz Sieradzan [Thu, 5 Jul 2012 07:50:05 +0000 (03:50 -0400)]
Rozgrzebany DIL
Dawid Jagiela [Wed, 27 Jun 2012 12:23:49 +0000 (14:23 +0200)]
fixed broken (by adasko) alignment in COMMON.SCCOR
Adam Kazimierz Sieradzan [Wed, 27 Jun 2012 11:53:41 +0000 (07:53 -0400)]
Merge branch 'adasko' into devel
Conflicts:
.gitignore
bin/unres/MD/unres_ifort_MPICH_GAB.exe
source/cluster/wham/src/DIMENSIONS.COMPAR
source/cluster/wham/src/Makefile
source/wham/src/Makefile
source/wham/src/cinfo.f
source/wham/src/tmptmp
Adam Kazimierz Sieradzan [Wed, 27 Jun 2012 11:40:02 +0000 (07:40 -0400)]
Merge branch 'devel' of mmka.chem.univ.gda.pl:unres into devel
Adam Kazimierz Sieradzan [Wed, 27 Jun 2012 11:39:16 +0000 (07:39 -0400)]
git ignore
Adam Kazimierz Sieradzan [Wed, 27 Jun 2012 11:37:49 +0000 (07:37 -0400)]
glupia zmiana
Adam Kazimierz Sieradzan [Wed, 27 Jun 2012 11:32:25 +0000 (07:32 -0400)]
Wprowadzenie SCCOR do WHAMa i CLUSTROWNIA
Dawid Jagiela [Wed, 20 Jun 2012 20:53:36 +0000 (22:53 +0200)]
LAM/MPI boot ctest modification
Dawid Jagiela [Tue, 19 Jun 2012 13:22:11 +0000 (15:22 +0200)]
added -cpp flag to force preprocesing for all files in gfortran
Dawid Jagiela [Tue, 19 Jun 2012 13:04:51 +0000 (15:04 +0200)]
Moved ifdef MOMENT part from COMMON.CONTACTS to COMMON.CONTACTS.MOMENT and aplied preprocesor directives
Dawid Jagiela [Mon, 18 Jun 2012 20:13:38 +0000 (22:13 +0200)]
enable compiler preprocesor flags for non-standard files (COMMON.*) in gfortran for cmake
Dawid Jagiela [Mon, 18 Jun 2012 19:55:36 +0000 (21:55 +0200)]
added source/cluster/wham/src/gnmr1.f to cmake build
Dawid Jagiela [Mon, 18 Jun 2012 19:42:57 +0000 (21:42 +0200)]
added gnmr1.f to sources in cmake builds
Dawid Jagiela [Mon, 18 Jun 2012 19:31:24 +0000 (21:31 +0200)]
fixed merge conflict in readrtns_csa.F
Dawid Jagiela [Mon, 18 Jun 2012 19:16:05 +0000 (21:16 +0200)]
fixed source/xdrfpdb/src-M/xdrf2pdb-m.F
Dawid Jagiela [Mon, 18 Jun 2012 19:02:13 +0000 (21:02 +0200)]
fixed merge renamed source file: newconf.f is now newconf.F
Dawid Jagiela [Mon, 18 Jun 2012 18:55:41 +0000 (20:55 +0200)]
resolving merge conflicts
Adam Liwo [Mon, 18 Jun 2012 14:08:46 +0000 (10:08 -0400)]
Merge branch 'devel' of mmka.chem.univ.gda.pl:unres into devel
merge adam->devel (2nd attempt)
Conflicts:
.gitignore
bin/unres/MD/unres_ifort_MPICH_GAB.exe
examples/unres/MD/ff_gab/1L2Y_minim.inp
source/cluster/wham/src/DIMENSIONS.COMPAR
source/cluster/wham/src/include_unres/COMMON.INTERACT
source/cluster/wham/src/include_unres/COMMON.SBRIDGE
source/cluster/wham/src/include_unres/COMMON.TORSION
source/unres/src_MD/cinfo.f
source/unres/src_MIN/Makefile
source/xdrfpdb/src-M/xdrf
source/xdrfpdb/src/xdrf
source/xdrfpdb/src/xdrf2ang.f
source/xdrfpdb/src/xdrf2pdb-m.F
Adam Liwo [Mon, 18 Jun 2012 13:58:32 +0000 (09:58 -0400)]
Merge branch 'adam' into devel
Merging adam with devel
Conflicts:
source/unres/src_CSA/readrtns_csa.F
Dawid Jagiela [Mon, 18 Jun 2012 11:25:44 +0000 (13:25 +0200)]
fixed indent for gfortran build in source/unres/src_MD/parmread.F
Dawid Jagiela [Mon, 18 Jun 2012 10:46:01 +0000 (12:46 +0200)]
Merge branch 'devel' of mmka:unres into devel
Dawid Jagiela [Mon, 18 Jun 2012 10:43:28 +0000 (12:43 +0200)]
removed MPI form CMakeLists.txt in xdrfpdb
more verbose output in xdrf2pdb-m.F
Adam Kazimierz Sieradzan [Mon, 18 Jun 2012 10:35:12 +0000 (06:35 -0400)]
unified .gitignore
Adam Kazimierz Sieradzan [Mon, 18 Jun 2012 10:33:31 +0000 (06:33 -0400)]
small fix in .gitingnore
Adam Kazimierz Sieradzan [Mon, 18 Jun 2012 10:22:21 +0000 (06:22 -0400)]
Merge branch 'adasko' into devel
Conflicts:
.gitignore
Adam Kazimierz Sieradzan [Mon, 18 Jun 2012 10:10:09 +0000 (06:10 -0400)]
poprawka gitignore
Adam Kazimierz Sieradzan [Mon, 18 Jun 2012 10:08:32 +0000 (06:08 -0400)]
zmiana w git ignore
Adam Kazimierz Sieradzan [Mon, 18 Jun 2012 09:56:28 +0000 (05:56 -0400)]
zmiany po usunieciu diagnostyki...
Adam Liwo [Fri, 15 Jun 2012 19:09:20 +0000 (15:09 -0400)]
6/15/2012 by Adam
Minor changes; linked parallal Makefile in CSA
Adam Kazimierz Sieradzan [Fri, 15 Jun 2012 07:04:52 +0000 (03:04 -0400)]
dzialajacy grad check....
Adam Liwo [Thu, 14 Jun 2012 20:20:40 +0000 (16:20 -0400)]
6/14/12 by Adam: unnecessary files deleted
Adam Liwo [Thu, 14 Jun 2012 20:16:07 +0000 (16:16 -0400)]
6/14/12 by Adam - changes committed
Adam Liwo [Thu, 14 Jun 2012 20:10:25 +0000 (16:10 -0400)]
6/14/2012 by Adam
1. Fixed a bug in the minimization in angles im all versions; varia
was a simple variable in the calling and a vector in the called subroutine.
2. Removed (wrong) temperature scaling in the CSA snd in the MD version.
3. Added selection of printout information in SUMSL.
Adam Kazimierz Sieradzan [Thu, 14 Jun 2012 11:03:08 +0000 (07:03 -0400)]
Dzialajacy INTERTYP=1 i INTERTYP=2
Adam Liwo [Mon, 11 Jun 2012 14:43:15 +0000 (10:43 -0400)]
6/11/2012 by Adam
Yet another revision of xdrf2pdb-m. Error detected in description; directory src-M all pertains to
multi-chain systems (but the programs can also be used for single-chain systems). xdrf2pdb-m for
single-chain systems is in src
Adam Liwo [Mon, 11 Jun 2012 14:25:25 +0000 (10:25 -0400)]
6/11/2012 by Adam
xdrf-m corrected (list of arguments); changes in manual required!
Dawid Jagiela [Mon, 11 Jun 2012 12:58:33 +0000 (14:58 +0200)]
fixed iblnk in xdrf2ang
Dawid Jagiela [Mon, 11 Jun 2012 12:34:03 +0000 (14:34 +0200)]
added ctests for xdrf2ang
Dawid Jagiela [Mon, 11 Jun 2012 12:02:09 +0000 (14:02 +0200)]
fix of malloc in xdrf2pdb-m
Dawid Jagiela [Mon, 11 Jun 2012 11:56:31 +0000 (13:56 +0200)]
fix of xdrf2ang
Cezary Czaplewski [Wed, 9 May 2012 12:02:13 +0000 (14:02 +0200)]
DFA is switched off by default
Adam Liwo [Mon, 11 Jun 2012 11:07:18 +0000 (07:07 -0400)]
6/11/2012 Changes of the CSA version
Adam Liwo [Mon, 11 Jun 2012 11:06:28 +0000 (07:06 -0400)]
6/11/2012 Update of the CSA version
Dawid Jagiela [Fri, 8 Jun 2012 11:42:41 +0000 (13:42 +0200)]
added ctest/1LE1_mremd_MD000.cx for xdrf2pdb-m testing
Dawid Jagiela [Tue, 5 Jun 2012 14:05:10 +0000 (16:05 +0200)]
xdrf2pdb programs doesn't require MPI so MPI-flags ware removed
Dawid Jagiela [Tue, 5 Jun 2012 13:36:42 +0000 (15:36 +0200)]
added ctests for xdrf2pdb (one & three letter sequence )
Dawid Jagiela [Tue, 5 Jun 2012 12:50:33 +0000 (14:50 +0200)]
UNRES single MD for MPI ctest file permissions fix
Adam Kazimierz Sieradzan [Tue, 5 Jun 2012 10:40:34 +0000 (06:40 -0400)]
UDALO SIE TERAZ DEBUG
Dawid Jagiela [Tue, 5 Jun 2012 09:28:33 +0000 (11:28 +0200)]
added MPI ctest for unres single MD
Adam Kazimierz Sieradzan [Tue, 29 May 2012 12:02:25 +0000 (08:02 -0400)]
kolejna
Adam Kazimierz Sieradzan [Tue, 29 May 2012 11:18:45 +0000 (07:18 -0400)]
zmienionwe zostaly i zostal chyba tylko int to cart deriv
Adam Kazimierz Sieradzan [Tue, 29 May 2012 09:54:26 +0000 (05:54 -0400)]
sadas
Adam Liwo [Tue, 29 May 2012 08:52:17 +0000 (04:52 -0400)]
5/29/2012 by Adam
1. Fixed NaNs in wham (more stable computation of window free energies).
2. Minor fixes in cluster
3. Added exmaple with minimization in MD examples
Dawid Jagiela [Sun, 27 May 2012 21:45:02 +0000 (23:45 +0200)]
compile_definitions workaround (cmake does not pass it to last file on list) for unres/src_MD-M/CMakeLists.txt
Dawid Jagiela [Sun, 27 May 2012 19:19:37 +0000 (21:19 +0200)]
included <stdio.h> in proc_proc.c
Dawid Jagiela [Sun, 27 May 2012 19:06:40 +0000 (21:06 +0200)]
sscanf EOF fix in source/wham/src-M/proc_proc.c
Dawid Jagiela [Sun, 27 May 2012 18:56:53 +0000 (20:56 +0200)]
closing ascii art frames in energy_p_new.F
Dawid Jagiela [Sun, 27 May 2012 18:34:03 +0000 (20:34 +0200)]
flags typo fix
Dawid Jagiela [Sat, 26 May 2012 21:51:06 +0000 (23:51 +0200)]
added header for proc_proc.c
Dawid Jagiela [Sat, 26 May 2012 21:19:02 +0000 (23:19 +0200)]
wham compinfo EOF fix
Dawid Jagiela [Sat, 26 May 2012 21:12:28 +0000 (23:12 +0200)]
EOF warning fix
Dawid Jagiela [Sat, 26 May 2012 17:01:29 +0000 (19:01 +0200)]
compinfo.c rewrite
Dawid Jagiela [Sat, 26 May 2012 16:25:22 +0000 (18:25 +0200)]
void cast on fgets & fscanf in compinfo.c
Dawid Jagiela [Sat, 26 May 2012 15:50:05 +0000 (17:50 +0200)]
compinfo.c warning supresion
Dawid Jagiela [Fri, 25 May 2012 12:16:23 +0000 (14:16 +0200)]
gfortran fix for cluster/wham/src build
Dawid Jagiela [Thu, 24 May 2012 20:25:15 +0000 (22:25 +0200)]
gfortran proc_proc.c build flags fix in source/cluster/wham/src-M
Dawid Jagiela [Tue, 22 May 2012 21:33:00 +0000 (23:33 +0200)]
integer overflow fixed in xdrf2x.F
Dawid Jagiela [Tue, 22 May 2012 21:06:12 +0000 (23:06 +0200)]
more xdrfpdb fixes for gfortran build
Dawid Jagiela [Tue, 22 May 2012 20:50:22 +0000 (22:50 +0200)]
gfortran patch for xdrf2ang.f
Dawid Jagiela [Sun, 20 May 2012 22:07:12 +0000 (00:07 +0200)]
added missing source cluster/wham/src-M
Dawid Jagiela [Sun, 20 May 2012 21:36:29 +0000 (23:36 +0200)]
cluster/wham hc.f gfortran fix
Dawid Jagiela [Sun, 20 May 2012 21:16:48 +0000 (23:16 +0200)]
include typo fixed + cleanup
Adam Liwo [Sun, 20 May 2012 11:33:15 +0000 (07:33 -0400)]
5/20/2012 by Adam
1. Added distance restraints to wham and cluster
2. Fixed the bug in angle restraints to wham and added angle restraints to cluster
3. Introduced more stable procedure to calculate the dependence of ensemble averages on temperature in wham (for each temperature the lowest "free energy" is a reference to compute Boltzmann factors)
Dawid Jagiela [Fri, 18 May 2012 11:53:24 +0000 (13:53 +0200)]
deleted: PARAM/1igd.cart~
Dawid Jagiela [Fri, 18 May 2012 11:24:20 +0000 (13:24 +0200)]
Merge branch 'devel' of mmka:unres into devel
Dawid Jagiela [Fri, 18 May 2012 11:23:42 +0000 (13:23 +0200)]
fixed ascii art frames in source/cluster/wham/src-M/energy_p_new.F
Cezary Czaplewski [Fri, 18 May 2012 11:17:38 +0000 (13:17 +0200)]
Merge branch 'devel' of mmka:unres into devel
Cezary Czaplewski [Fri, 18 May 2012 11:16:06 +0000 (13:16 +0200)]
an example for MIN only version of unres, corrected paths in Makefile
Dawid Jagiela [Fri, 18 May 2012 11:13:14 +0000 (13:13 +0200)]
Merge branch 'feature-cmake' into devel
Dawid Jagiela [Fri, 18 May 2012 10:41:17 +0000 (12:41 +0200)]
another ascii art frame fix
Dawid Jagiela [Fri, 18 May 2012 10:08:31 +0000 (12:08 +0200)]
fix for gfortran build of source/cluster/unres
Dawid Jagiela [Wed, 16 May 2012 18:44:21 +0000 (20:44 +0200)]
fixed typo
Dawid Jagiela [Wed, 16 May 2012 18:33:49 +0000 (20:33 +0200)]
added CMake files to build cluster/wham/src-M
Dawid Jagiela [Tue, 15 May 2012 20:26:02 +0000 (22:26 +0200)]
added missig wham/src-M source files to cmake build
Dawid Jagiela [Tue, 15 May 2012 13:17:01 +0000 (15:17 +0200)]
Added CMake files for building source/wham/src-M
Dawid Jagiela [Mon, 14 May 2012 23:32:50 +0000 (01:32 +0200)]
ascii frames closed: unres/src_MD-M/energy_p_new_barrier.F
ascii frames closed: wham/src/energy_p_new.F
Dawid Jagiela [Mon, 14 May 2012 23:02:20 +0000 (01:02 +0200)]
1) ASCII art frame fix in unres/src_MD-M/energy_p_new_barrier.F
2) added gfortran build flags for wham/src
Dawid Jagiela [Mon, 14 May 2012 22:33:29 +0000 (00:33 +0200)]
added cmake files to build source/wham/src under ifort
Dawid Jagiela [Mon, 14 May 2012 15:02:00 +0000 (17:02 +0200)]
fixed more typos
Dawid Jagiela [Mon, 14 May 2012 13:53:46 +0000 (15:53 +0200)]
fixed typo
Dawid Jagiela [Mon, 14 May 2012 13:44:55 +0000 (15:44 +0200)]
prng_32.F/prng.f fix for intel compiler
Dawid Jagiela [Mon, 14 May 2012 13:16:23 +0000 (15:16 +0200)]
1) moved xdrf library to source/lib/xdrf - CMake files link this location when required by build binaries (Makefiles dont!)
2) added cmake files for building source/xdrfpdb/src and source/xdrfpdb/src-M
Adam Liwo [Sun, 13 May 2012 20:10:21 +0000 (16:10 -0400)]
5/13/2012 by Adam
Minor bugs in the code related to distance restraints fixed: readrtns.F
Dawid Jagiela [Sun, 13 May 2012 15:02:51 +0000 (17:02 +0200)]
linking pthreads for unres/src_MIN