#
# ChangeLog for /
#
# Generated by Trac 1.5.4
# 05/13/24 03:18:31

Thu, 15 Sep 2011 13:38:37 GMT j.meinke@…> [87ddcf7]
	* INCL.H (modified)

	Rename common block log to logging.


Thu, 02 Sep 2010 11:22:59 GMT Jan Meinke <j.meinke@…> [225475c]
	* pysmmp/ParallelTempering.py (added)
	* pysmmp/__init__.py (added)
	* pysmmp/algorithms.py (moved)
	* pysmmp/interactionscan.py (added)
	* pysmmp/main.py (moved)
	* pysmmp/pPySMMP.py (added)
	* pysmmp/protein.py (moved)
	* pysmmp/universe.py (moved)

	Move pysmmp in its own subdirectory.


Thu, 02 Sep 2010 08:25:36 GMT Jan Meinke <j.meinke@…> [5fef0d7]
	* Makefile (modified)
	* algorithms.py (modified)
	* enysol_p.f (modified)
	* protein.py (modified)

	Changed module name from smmp to smmp_p.

	Fixed conversion to ...


Wed, 16 Jun 2010 06:25:47 GMT Jan Meinke <j.meinke@…> [3fbbfbb]
	* EXAMPLES/1bdd.seq (modified)
	* INCL.H (modified)
	* algorithms.py (modified)
	* enyshe.f (modified)
	* enyshe_p.f (modified)
	* main.f (modified)
	* partem_p.f (modified)
	* protein.py (modified)
	* rgyr.f (modified)
	* timer.F90 (modified)
	* universe.py (modified)
	* utilities.f (modified)

	Move to doxygen comments and smmp_p.

	Doxygen comments in Fortran ...


Tue, 15 Jun 2010 19:58:34 GMT Jan Meinke <j.meinke@…> [9f146fa]
	* Makefile (modified)

	Added comment describing how to compile a minimal interface.


Tue, 15 Jun 2010 19:58:07 GMT Jan Meinke <j.meinke@…> [281b862]
	* Makefile (modified)

	Merged Makefile


Tue, 15 Jun 2010 07:29:31 GMT Jan Meinke <j.meinke@…> [5272e0d]
	* Makefile (modified)
	* init_molecule.f (modified)

	Added ppybind target to Makefile

	Added a new target for creating ...


Thu, 01 Apr 2010 10:10:52 GMT Jan Meinke <j.meinke@…> [7137e5d]
	* Makefile (modified)
	* enyshe_simple.f90 (added)
	* timer.F90 (added)

	Added timer and enyshe using double loop.


Thu, 19 Nov 2009 10:29:48 GMT baerbaer <baerbaer@…> [38d77eb]
	* INCL.H (modified)
	* INCP.H (modified)
	* addend.f (modified)
	* anneal.f (modified)
	* bgs.f (modified)
	* bldmol.f (modified)
	* canon.f (modified)
	* cnteny.f (modified)
	* contacts.f (modified)
	* dihedr.f (modified)
	* enyflx.f (modified)
	* enyshe.f (modified)
	* enyshe_p.f (modified)
	* enysol.f (modified)
	* enysol_p.f (modified)
	* esolan.f (modified)
	* getmol.f (modified)
	* gradient.f (modified)
	* hbond.f (modified)
	* init_energy.f (modified)
	* main.f (modified)
	* main_bgl_p.f (modified)
	* main_p.f (modified)
	* metropolis.f (modified)
	* mincjg.f (modified)
	* minim.f (modified)
	* minqsn.f (modified)
	* mklist.f (modified)
	* mulcan_par.f (modified)
	* mulcan_par_mod.f90 (modified)
	* mulcan_sim.f (modified)
	* nursvr.f (modified)
	* opeflx.f (modified)
	* opereg.f (modified)
	* opeshe.f (modified)
	* opesol.f (modified)
	* outpdb.f (modified)
	* outvar.f (modified)
	* partem_p.f (modified)
	* partem_s.f (modified)
	* pdbread.f (modified)
	* redseq.f (modified)
	* redstr.f (modified)
	* redvar.f (modified)
	* regul.f (modified)
	* rgyr.f (modified)
	* rmsdfun.f (modified)
	* setmvs.f (modified)
	* utilities.f (modified)

	Redirected standard out to logString.

	SMMP produced a lot of log ...


Thu, 19 Nov 2009 10:29:41 GMT baerbaer <baerbaer@…> [32289cd]
	* INCL.H (modified)
	* bgs.f (modified)
	* cnteny.f (modified)
	* difang.f (modified)
	* energy.f (modified)
	* eninteract.f (modified)
	* enylun.f (modified)
	* enyreg.f (modified)
	* enyshe.f (modified)
	* enyshe_p.f (modified)
	* enysol.f (modified)
	* enysol_p.f (modified)
	* esolan.f (modified)
	* eyabgn.f (modified)
	* gradient.f (modified)
	* init_energy.f (modified)
	* init_molecule.f (modified)
	* main.f (modified)
	* main_p.f (modified)
	* metropolis.f (modified)
	* mincjg.f (modified)
	* nursvr.f (modified)
	* opereg.f (modified)
	* opesol.f (modified)
	* outpdb.f (modified)
	* outvar.f (modified)
	* partem_p.f (modified)
	* partem_s.f (modified)
	* pdbread.f (modified)
	* regul.f (modified)
	* rgyr.f (modified)
	* rmsdfun.f (modified)
	* twister.f (modified)
	* utilities.f (modified)
	* zimmer.f (modified)

	Explicitly declare variables.

	git-svn-id: ...


Thu, 19 Nov 2009 10:29:38 GMT baerbaer <baerbaer@…> [6650a56]
	* EXAMPLES/Makefile (modified)
	* EXAMPLES/multicanonical.f (modified)
	* INCP.H (modified)
	* anneal.f (modified)
	* canon.f (modified)
	* doc/manual.lyx (modified)
	* helix.f (modified)
	* incl_lund.h (modified)
	* init_lund.f90 (modified)
	* minqsn.f (modified)
	* mklist.f (modified)
	* mulcan_par_mod.f90 (modified)
	* opesol.f (modified)
	* partem_p.f (modified)
	* redstr.f (modified)

	Explicitly declare variables.

	git-svn-id: ...


Thu, 19 Nov 2009 10:29:35 GMT baerbaer <baerbaer@…> [30644a9]
	* init_lund.f90 (added)

	Put init_lund in separate file.

	git-svn-id: ...


Thu, 19 Nov 2009 10:29:33 GMT baerbaer <baerbaer@…> [6012d3f]
	* Makefile (modified)

	Include init_lund in dependencies.

	git-svn-id: ...


Thu, 19 Nov 2009 10:29:31 GMT baerbaer <baerbaer@…> [c021909]
	* partem_p.f (modified)

	Changed asap to asa_p to avoid shadowing

	The global variable asap ...


Thu, 19 Nov 2009 10:29:29 GMT baerbaer <baerbaer@…> [08edfcf]
	* INCL.H (modified)

	Charges need to be floating point numbers.

	While explicitely typing ...


Thu, 19 Nov 2009 10:29:26 GMT baerbaer <baerbaer@…> [2019dff]
	* contacts.f (modified)
	* hbond.f (modified)
	* minim.f (modified)
	* opeshe.f (modified)

	Explicitly declare variables.

	git-svn-id: ...


Thu, 19 Nov 2009 10:29:24 GMT baerbaer <baerbaer@…> [2d5d396]
	* opeflx.f (modified)

	Explicitly declare variables.

	git-svn-id: ...


Thu, 19 Nov 2009 10:29:16 GMT baerbaer <baerbaer@…> [cb47b9c]
	* addend.f (modified)
	* bgs.f (modified)
	* bldmol.f (modified)
	* canon.f (modified)
	* dihedr.f (modified)
	* enyflx.f (modified)
	* enysol.f (modified)
	* getmol.f (modified)
	* incl_lund.h (modified)
	* init_molecule.f (modified)
	* main.f (modified)
	* mklist.f (modified)
	* mulcan_par_mod.f90 (modified)
	* redseq.f (modified)
	* redstr.f (modified)
	* redvar.f (modified)
	* regul.f (modified)
	* setmvs.f (modified)
	* setvar.f (modified)
	* utilities.f (modified)

	Explicitly declare variables.

	All variables should be declared so ...


Thu, 19 Nov 2009 10:29:13 GMT baerbaer <baerbaer@…> [ffd2d46]
	* smmp.pyf (modified)

	Added bindings to setvar and enysol.

	For the trajectory analysis, I ...


Thu, 19 Nov 2009 10:29:11 GMT baerbaer <baerbaer@…> [8d0e6d6]
	* esolan.f (modified)

	Make grad an allocatable rather than a static array.

	The array ...


Thu, 19 Nov 2009 10:29:09 GMT baerbaer <baerbaer@…> [5ae43a7]
	* INCL.H (modified)

	Set implicit none and declare variables.

	git-svn-id: ...


Thu, 19 Nov 2009 10:29:07 GMT baerbaer <baerbaer@…> [31550cb]
	* INCL.H (modified)
	* partem_p.f (modified)

	Extrema stored per replica not temperature.

	Tracking of the minimum ...


Thu, 19 Nov 2009 10:25:06 GMT baerbaer <baerbaer@…> [0f06b4a]
	* INCL.H (modified)

	Declared some more variable in INCL.H.

	git-svn-id: ...


Wed, 24 Sep 2008 16:48:41 GMT sandipan <sandipan@…> [ba939c7]
	* SMMP/lib.lun (modified)
	* init_molecule.f (modified)

	Fixing omega when structure is read from a PDB file

	For Lund force ...


Wed, 24 Sep 2008 13:27:04 GMT sandipan <sandipan@…> [4fd4338]
	* enylun.f (modified)
	* init_molecule.f (modified)

	Array index overrun in if statements with "and" and "or" operators ...


Wed, 24 Sep 2008 13:27:03 GMT sandipan <sandipan@…> [c076b43]
	* SMMP/lib.lun (added)
	* enylun.f (modified)
	* init_energy.f (modified)

	Updated version of Lund force field functions

	The Lund force field ...


Fri, 05 Sep 2008 09:49:44 GMT baerbaer <baerbaer@…> [a52fb83]
	* Makefile (modified)

	Removed extraneous FLAGS from ifort options.


	git-svn-id: ...


Fri, 05 Sep 2008 09:49:43 GMT baerbaer <baerbaer@…> [4e219a3]
	* EXAMPLES/parallel_tempering_p.f (modified)
	* Makefile (modified)
	* SMMP.kdevelop.filelist (modified)
	* contacts.f (modified)
	* main_p.f (modified)
	* protein.py (modified)
	* setmvs.f (modified)

	Update Lund init and BG/P compatibility.

	* Moved call of ...


Fri, 05 Sep 2008 09:49:43 GMT baerbaer <baerbaer@…> [229cc35]
	* metropolis.f (modified)

	Removed unnecessary call to energy in metropolis.


	git-svn-id: ...


Fri, 05 Sep 2008 09:49:43 GMT baerbaer <baerbaer@…> [fafe4d6]
	* energy.f (modified)

	Call enyflx() in energy() if ientyp is 1.

	The function energy() ...


Fri, 05 Sep 2008 09:49:42 GMT baerbaer <baerbaer@…> [bd2278d]
	* EXAMPLES/parallel_tempering_s.f (modified)
	* EXAMPLES/partem_p.f (modified)
	* INCP.H (modified)
	* SMMP.kdevelop (modified)
	* SMMP.kdevelop.filelist (added)
	* addend.f (modified)
	* anneal.f (modified)
	* bgs.f (modified)
	* bldmol.f (modified)
	* callbacktest.f (modified)
	* canon.f (modified)
	* cnteny.f (modified)
	* contacts.f (modified)
	* difang.f (modified)
	* dihedr.f (modified)
	* eninteract.f (modified)
	* enyflx.f (modified)
	* enylun.f (modified)
	* enyreg.f (modified)
	* enyshe.f (modified)
	* enyshe_p.f (modified)
	* enysol.f (modified)
	* enysol_p.f (modified)
	* esolan.f (modified)
	* eyabgn.f (modified)
	* getmol.f (modified)
	* gradient.f (modified)
	* hbond.f (modified)
	* helix.f (modified)
	* incl_lund.h (modified)
	* init_energy.f (modified)
	* init_molecule.f (modified)
	* main.f (modified)
	* main_bgl_p.f (modified)
	* main_p.f (modified)
	* metropolis.f (modified)
	* mincjg.f (modified)
	* minim.f (modified)
	* minqsn.f (modified)
	* mklist.f (modified)
	* mulcan_par.f (modified)
	* mulcan_sim.f (modified)
	* nursvr.f (modified)
	* opeflx.f (modified)
	* opereg.f (modified)
	* opeshe.f (modified)
	* opesol.f (modified)
	* outpdb.f (modified)
	* outvar.f (modified)
	* partem_p.f (modified)
	* partem_s.f (modified)
	* pdbread.f (modified)
	* redseq.f (modified)
	* redstr.f (modified)
	* redvar.f (modified)
	* regul.f (modified)
	* rgyr.f (modified)
	* rmsdfun.f (modified)
	* setmvs.f (modified)
	* setvar.f (modified)
	* universe.py (modified)
	* utilities.f (modified)
	* zimmer.f (modified)

	Reformatting comments and continuation marks.

	Fortran 90 and higher ...


Fri, 05 Sep 2008 09:49:42 GMT baerbaer <baerbaer@…> [2ebb8b6]
	* .gitignore (added)

	Added .gitignore to repository.


	git-svn-id: ...


Fri, 05 Sep 2008 09:49:41 GMT baerbaer <baerbaer@…> [b477fe8]
	* energy.f (modified)
	* esolan.f (modified)

	Fixed handling of nmol = 0 in esolan.

	The function energy calls ...


Sun, 22 Jun 2008 12:33:26 GMT baerbaer <baerbaer@…> [078aff3]
	* energy.f (modified)

	Uncomment lines related to analytic solvent calculation.

 ...


Sun, 22 Jun 2008 12:33:25 GMT baerbaer <baerbaer@…> [621e10f]

	* INCL.H: Corrected formatting

	* INCL.H: zero and one are doubles ...


Sun, 22 Jun 2008 12:33:25 GMT baerbaer <baerbaer@…> [f3074b0]
	* INCL.H (modified)
	* smmp.pyf (modified)

	* INCL.H: Corrected formatting
	* INCL.H: zero and one are doubles ...


Sun, 22 Jun 2008 12:33:24 GMT baerbaer <baerbaer@…> [81c1ffc]

	* Type definition of the first set of parameters.


	git-svn-id: ...


Sun, 22 Jun 2008 12:33:24 GMT baerbaer <baerbaer@…> [9e4fc47]
	* INCL.H (modified)

	* Type definition of the first set of parameters.


	git-svn-id: ...


Tue, 17 Jun 2008 11:45:04 GMT baerbaer <baerbaer@…> [17e791d]
	* EXAMPLES/Makefile (modified)
	* EXAMPLES/multicanonical.mod (added)

	* Changed compiler in EXAMPLES/Makefile to gfortran.
	* Added link to ...


Thu, 29 May 2008 11:30:27 GMT baerbaer <baerbaer@…> [e40e335]
	* ChangeLog (added)
	* EXAMPLES/1bdd.pdb (added)
	* EXAMPLES/1bdd.ref (added)
	* EXAMPLES/1bdd.seq (added)
	* EXAMPLES/1bdd.var (added)
	* EXAMPLES/Makefile (added)
	* EXAMPLES/Python/SMMP/charges (added)
	* EXAMPLES/Python/SMMP/lib.flx (added)
	* EXAMPLES/Python/SMMP/lib.sh2 (added)
	* EXAMPLES/Python/SMMP/lib.sh3 (added)
	* EXAMPLES/Python/SMMP/tes.dat (added)
	* EXAMPLES/Python/annealing.py (added)
	* EXAMPLES/Python/best.pml (added)
	* EXAMPLES/Python/enkefa.ref (added)
	* EXAMPLES/Python/gui_example.py (added)
	* EXAMPLES/Python/minimization.py (added)
	* EXAMPLES/Python/muca.py (added)
	* EXAMPLES/Python/regularization.py (added)
	* EXAMPLES/abeta.ref (added)
	* EXAMPLES/abeta.seq (added)
	* EXAMPLES/abeta.var (added)
	* EXAMPLES/annealing.f (added)
	* EXAMPLES/annealing.out (added)
	* EXAMPLES/dfnkf.seq (added)
	* EXAMPLES/enkefa.ann (added)
	* EXAMPLES/enkefa.ref (added)
	* EXAMPLES/enkefa.seq (added)
	* EXAMPLES/enkefa.var (added)
	* EXAMPLES/enkefatimes2.seq (added)
	* EXAMPLES/minimization.f (added)
	* EXAMPLES/multicanonical.f (added)
	* EXAMPLES/par_R.in (added)
	* EXAMPLES/parallel_tempering_p.f (added)
	* EXAMPLES/parallel_tempering_s.f (added)
	* EXAMPLES/partem_p.f (added)
	* EXAMPLES/regularization.f (added)
	* EXAMPLES/smmp.cmd (added)
	* EXAMPLES/smmp.run (added)
	* EXAMPLES/temperatures (added)
	* EXAMPLES/temperatures_abeta (added)
	* EXAMPLES/val10.seq (added)
	* INCL.H (added)
	* INCP.H (added)
	* Makefile (added)
	* README (added)
	* SMMP.kdevelop (added)
	* SMMP.kdevelop.spec (added)
	* SMMP.spec (added)
	* SMMP.tag (added)
	* SMMP/charges (added)
	* SMMP/lib.flx (added)
	* SMMP/lib.sh2 (added)
	* SMMP/lib.sh3 (added)
	* SMMP/tes.dat (added)
	* addend.f (added)
	* algorithms.py (added)
	* anneal.f (added)
	* bgs.f (added)
	* bldmol.f (added)
	* callbacktest.f (added)
	* canon.f (added)
	* cnteny.f (added)
	* contacts.f (added)
	* difang.f (added)
	* dihedr.f (added)
	* doc/Makefile (added)
	* doc/angle_defs.svg (added)
	* doc/atom_numbering.svg (added)
	* doc/dihedral_defs.svg (added)
	* doc/license.txt (added)
	* doc/manual.lyx (added)
	* energy.f (added)
	* eninteract.f (added)
	* enyflx.f (added)
	* enylun.f (added)
	* enyreg.f (added)
	* enyshe.f (added)
	* enyshe_p.f (added)
	* enysol.f (added)
	* enysol_p.f (added)
	* esolan.f (added)
	* eyabgn.f (added)
	* getmol.f (added)
	* gradient.f (added)
	* hbond.f (added)
	* helix.f (added)
	* incl_lund.h (added)
	* init_energy.f (added)
	* init_molecule.f (added)
	* main.f (added)
	* main.py (added)
	* main_bgl_p.f (added)
	* main_p.f (added)
	* metropolis.f (added)
	* mincjg.f (added)
	* minim.f (added)
	* minqsn.f (added)
	* mklist.f (added)
	* mulcan_par.f (added)
	* mulcan_par_mod.f90 (added)
	* mulcan_sim.f (added)
	* nursvr.f (added)
	* opeflx.f (added)
	* opereg.f (added)
	* opeshe.f (added)
	* opesol.f (added)
	* outpdb.f (added)
	* outvar.f (added)
	* partem_p.f (added)
	* partem_s.f (added)
	* pdbread.f (added)
	* protein.py (added)
	* pySMMP.doxygen (added)
	* redseq.f (added)
	* redstr.f (added)
	* redvar.f (added)
	* regul.f (added)
	* restoreexclpoint.py (added)
	* rgyr.f (added)
	* rmexclpoint.py (added)
	* rmsdfun.f (added)
	* setmvs.f (added)
	* setvar.f (added)
	* smmp.pyf (added)
	* twister.f (added)
	* universe.py (added)
	* utilities.f (added)
	* zimmer.f (added)

	Initial import to BerliOS corresponding to 3.0.4

	git-svn-id: ...