Dawid Jagiela [Mon, 20 Aug 2012 10:56:05 +0000 (12:56 +0200)]
added CMake build file for source/maxlik/src_CSA/
Dawid Jagiela [Mon, 20 Aug 2012 08:39:57 +0000 (10:39 +0200)]
1. cmake cinfo.f generation for all sources 2. deleted old cinfo.f
Bartlomiej Zaborowski [Wed, 8 Aug 2012 12:11:06 +0000 (14:11 +0200)]
Maximum likelihood parameters optimization program for CSA added without examples.
Bartlomiej Zaborowski [Wed, 8 Aug 2012 11:22:22 +0000 (13:22 +0200)]
New examples for GAB force fields (restrained, unrestrained, CLUSTER,
energy minimization, energy reminimization, local CSA)
Bartlomiej Zaborowski [Wed, 8 Aug 2012 10:25:53 +0000 (12:25 +0200)]
CASP3 force field deleted. Fixed merge conflicts.
Merge branch 'devel' of mmka:unres into devel
Conflicts:
.gitignore
examples/unres/CSA/CASP3/ENERGY/unres_casp3.csh
source/unres/src_CSA/Makefile
Bartlomiej Zaborowski [Wed, 8 Aug 2012 10:07:04 +0000 (12:07 +0200)]
Old force fields removed, new ones (GAB, E0LL2Y) added.
Adam Kazimierz Sieradzan [Tue, 31 Jul 2012 11:12:37 +0000 (07:12 -0400)]
poprawka clustrowania z potencjalami wsccor (zle czytanie wagi)
Adam Kazimierz Sieradzan [Mon, 30 Jul 2012 06:07:50 +0000 (02:07 -0400)]
Merge branch 'devel' of mmka.chem.univ.gda.pl:unres into devel
Adam Kazimierz Sieradzan [Mon, 30 Jul 2012 06:06:57 +0000 (02:06 -0400)]
poprawka w cluster dla potencjalow shelleya
Dawid Jagiela [Thu, 19 Jul 2012 23:49:02 +0000 (01:49 +0200)]
Merge branch 'devel' of mmka:unres into devel
Dawid Jagiela [Thu, 19 Jul 2012 23:47:47 +0000 (01:47 +0200)]
cinfo.f generation and macro for unres MD
Adam Liwo [Wed, 18 Jul 2012 10:34:03 +0000 (06:34 -0400)]
Merge branch 'devel' into adam
Conflicts:
bin/wham/wham_ifort_MPICH_GAB.exe
source/cluster/wham/src/Makefile
source/unres/src_MD/cinfo.f
source/wham/src/cinfo.f
Adam Liwo [Wed, 18 Jul 2012 10:31:10 +0000 (06:31 -0400)]
cinfo
Adam Kazimierz Sieradzan [Wed, 18 Jul 2012 09:56:32 +0000 (05:56 -0400)]
modified Makefile
Adam Kazimierz Sieradzan [Wed, 18 Jul 2012 09:55:48 +0000 (05:55 -0400)]
hotfix parmread
Adam Liwo [Wed, 18 Jul 2012 09:34:44 +0000 (05:34 -0400)]
Implement minor changes on branch adam
Adam Kazimierz Sieradzan [Wed, 18 Jul 2012 09:23:47 +0000 (05:23 -0400)]
Revert "Merge branch 'adasko' into devel"
This reverts commit
a20d7ba73b9caa74140350c4c97fa62d83711703, reversing
changes made to
d39961a524eb1bf7968c3d46f34cef44774ad491.
Adam Kazimierz Sieradzan [Wed, 18 Jul 2012 09:20:17 +0000 (05:20 -0400)]
Revert "poprawka przy liczeniu tau w clustrze"
This reverts commit
ffcc28c7645550e2a62c0d066271fa1ee8323310.
Adam Kazimierz Sieradzan [Tue, 17 Jul 2012 08:40:16 +0000 (04:40 -0400)]
Merge branch 'adasko' into devel
Dzialajacy D i L aminokwasy dla src_MD
Conflicts:
bin/unres/MD/unres_ifort_MPICH_GAB.exe
bin/wham/wham_multparm-ham_rep-oldparm
source/unres/src_MD/Makefile
source/unres/src_MD/Makefile_MPICH_ifort
source/unres/src_MD/cinfo.f
source/wham/src/Makefile
source/wham/src/cinfo.f
Adam Kazimierz Sieradzan [Tue, 17 Jul 2012 07:03:58 +0000 (03:03 -0400)]
Merge branch 'devel' of mmka.chem.univ.gda.pl:unres into devel
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
Dawid Jagiela [Fri, 6 Jul 2012 09:52:30 +0000 (11:52 +0200)]
Merge branch 'devel' of mmka:unres into devel
Dawid Jagiela [Fri, 6 Jul 2012 09:51:03 +0000 (11:51 +0200)]
added CMake install documentation
Dawid Jagiela [Fri, 6 Jul 2012 09:14:55 +0000 (05:14 -0400)]
Merge branch 'devel' of mmka.chem.univ.gda.pl:unres into devel
Dawid Jagiela [Fri, 6 Jul 2012 09:13:49 +0000 (05:13 -0400)]
aditional MPI search lib path added
Adam Kazimierz Sieradzan [Fri, 6 Jul 2012 08:25:58 +0000 (04:25 -0400)]
poprawki makefile ktore i tak zostan zmienione
Adam Kazimierz Sieradzan [Fri, 6 Jul 2012 08:20:04 +0000 (04:20 -0400)]
wyrowanie COMMON>SCCOR
Adam Kazimierz Sieradzan [Fri, 6 Jul 2012 08:18:36 +0000 (04:18 -0400)]
Wyrowanie w COmmonie...
Adam Kazimierz Sieradzan [Fri, 6 Jul 2012 07:59:29 +0000 (03:59 -0400)]
poprawka przy liczeniu tau w clustrze
Adam Kazimierz Sieradzan [Fri, 6 Jul 2012 07:42:07 +0000 (03:42 -0400)]
proba pullowania
Merge branch 'devel' of mmka.chem.univ.gda.pl:unres into devel
Conflicts:
bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe
source/unres/src_MD/cinfo.f
source/wham/src/cinfo.f
Adam Kazimierz Sieradzan [Fri, 6 Jul 2012 07:34:57 +0000 (03:34 -0400)]
Zabijanie robakow znalezionych przez Pawla w WHAMie
dodanie licznie katow tau w int_from_cart oraz diagonostyki w przypadku
gdy liczona energia jest odmienna od energii czytanej
Adam Kazimierz Sieradzan [Fri, 6 Jul 2012 06:08:43 +0000 (02:08 -0400)]
zmiana do DiL
Adam Liwo [Thu, 5 Jul 2012 10:19:09 +0000 (06:19 -0400)]
Merge branch 'adam' into devel
Conflicts:
source/unres/src_MD/Makefile_MPICH_ifort
Adam Liwo [Thu, 5 Jul 2012 10:17:09 +0000 (06:17 -0400)]
Minor change
Adam Liwo [Thu, 5 Jul 2012 10:15:57 +0000 (06:15 -0400)]
Minor change
Adam Kazimierz Sieradzan [Thu, 5 Jul 2012 10:13:29 +0000 (06:13 -0400)]
zmiana binarki...
Adam Liwo [Thu, 5 Jul 2012 10:02:39 +0000 (06:02 -0400)]
Merge branch 'adam' into devel
Minor fixed in cxread diagnostics in wham
Conflicts:
source/unres/src_MD/Makefile
source/unres/src_MD/cinfo.f
source/wham/src/Makefile
source/wham/src/cinfo.f
Adam Liwo [Thu, 5 Jul 2012 09:55:42 +0000 (05:55 -0400)]
5/7/2012 by Adam
Minor optional diagnostics in wham
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 08:06:02 +0000 (04:06 -0400)]
hotfix of SCCOR potentials
Adam Kazimierz Sieradzan [Thu, 5 Jul 2012 07:54:52 +0000 (03:54 -0400)]
Merge branch 'devel' of mmka.chem.univ.gda.pl:unres into devel
Adam Kazimierz Sieradzan [Thu, 5 Jul 2012 07:54:04 +0000 (03:54 -0400)]
hotfix do potencjalow AM1
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 13:57:01 +0000 (15:57 +0200)]
1) added ctests for xdrf2pdb-m 2) cleanup
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
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