2009-12-30  Elias Potapov  <elias.potapov@gmail.com>

	* src/integrator.c (run): Integrator structure simplified. More
	readable. 

	* src/cross.c (peak_def): Resolved problem: integrator stops when
	reaches max number of intersec or peaks(depends on period
	method). This caused early stop when on SS regime, because peaks
	are defined there as well. Now fixed. No early integrator stop
	when on SS regime. This also involved files integrator.c,
	trajectory.c, init.h.

2009-12-20  Elias Potapov  <elias.potapov@gmail.com>

	* src/singularity.c (multiroot_find): New random seed formulae.

	* src/input_interpreter.c (rand_interp): Slightly different
	formulae for creating seed for random generator. Hope it will help
	to overcome the same seed when one starts generator sequentially.
	(rand_interp): New random seed formulae.

	* src/singularity.c (multiroot_find): Seed and generator type in
	singularity menu can be changed now.

2009-12-05  Elias Potapov  <elias.potapov@gmail.com>

	* src/input_interpreter.c (sing_interp): Singularity menu. Added
	technical parameters to menu. They may be changed now.

2009-11-28  Elias Potapov  <elias.potapov@gmail.com>

	* src/input_interpreter.c (sing_interp): `show' command for
	singularity menu.

2009-11-27  Elias Potapov  <elias.potapov@gmail.com>

	* src/singularity.c (multiroot_find): Printig solution to stdout
	non only to the file. Fclose of stream added(is crucial for
	writing data).

	* src/input_interpreter.c (sing_interp): file name input:
	allocating memory for char* pointer is done via calloc instead of malloc

2009-11-25  Elias Potapov  <elias.potapov@gmail.com>

	* src/input_interpreter.c (numerics_interp): No warning message in
	numerics menu in case of write step ==0, when computed amount of
	points(in run-kut integrator) are more than global buffer.

2009-11-18  Elias Potapov  <elias.potapov@gmail.com>

	***********************Version 0.2.1 RELEASE**********************
	
	* src/input_interpreter.c (sing_interp): Now dinamica is able to
	find roots(steady state solutions of the system of ODEs).

	* src/singularity.c (func_multiroot): Added new file and functions
	for root finding.
	(multiroot_find): Basic algorithm for finding roots established.

2009-11-01  Elias Potapov  <elias.potapov@gmail.com>

	***********************Version 0.2 RELEASE************************
	
	* src/init.h (MAX_N_ISEC): Discovered memory conflicts with too
	big MAX_N_ISEC and MAX_N_PEAKS values. Function traj() doesnt want
	to work. ALL should be changed from static allocation to dynamic
	memory allocation(see TODO).

	* src/input_interpreter.c (numerics_interp): write step can be
	equal to zero, in such a way there is no writing output to storage
	arrays, but first(initial) point. This is another way to overcome
	storage array problem.

2009-10-31  Elias Potapov  <elias.potapov@gmail.com>

	* src/init.c (init): Config file reading with error open
	handling.

2009-10-28  Elias Potapov  <elias.potapov@gmail.com>

	* src/* (*): Added a great opportunity to compute period consequent map and
	periods histogram. This helps to analyze complex trajectory with
	many periods as we encountered in Repressilator(A) model.

	* src/submenu.c (*): This file added for the
	first time.

2009-09-12  Elias Potapov  <elias.potapov@gmail.com>

	* src/main.c (copyleft): Added 2009 year to copyright.

2009-09-04  Elias Potapov  <elias.potapov@gmail.com>

	* src/read_config.c (buf_check): Replaced global looping vars(i,j)
	with local one, defined inside the function---lp1 and lp2.

	* src/input_interpreter.c (parameters): Added checking for
	character input for par value(returning correspond. error).
	Par name now case sensitive.
	Added buf_check there, instead of direct checking.

2009-08-19  Elias Potapov  <elias.potapov@gmail.com>

	* src/input_interpreter.c (errors_interp): Completed ERRORS menu.

2009-08-18  Elias Potapov  <elias.potapov@gmail.com>

	* src/input_interpreter.c (parameters): Some additional changes in
	parameters reading from menu. More desired behaviour and errors
	handling. 

2009-08-15  Elias Potapov  <elias.potapov@gmail.com>

	* src/input_interpreter.c (errors_interp): Added ERRORS menu to
	MAIN one. All errors listed there and may be changed there.

2009-08-14  Elias Potapov  <elias.potapov@gmail.com>

	* src/trajectory.c (traj): Added zeroing regime_ratio at each new
	invocation of traj().

2009-08-07  Elias Potapov  <elias.potapov@gmail.com>

	*****************VER 0.1.1 RELEASE*******************
	
	* src/read_config.c (read_config): Moer extensive read of config
	file var section.
	(read_config): Comments support in config file.

2009-08-05  Elias Potapov  <elias.potapov@gmail.com>

	* src/read_config.c (read_config): More extensive read of config
	file par section.

2009-08-04  Elias Potapov  <elias.potapov@gmail.com>

	* Makefile (.PHONY): Upgraded Makefile.
	*****************VER 0.1 RELEASE******************

2009-08-02  Elias Potapov  <elias.potapov@gmail.com>

	* src/trajectory.c (traj): Added regime = NULL and reg[i] = NULL,
	allocating (null) solution before any new run of traj().

	* src/cross.c (cross): Not correcto computing Poincare sections' average.

2009-08-01  Elias Potapov  <elias.potapov@gmail.com>

	* src/integrator.c (run): Leaved sole function run(), added
	parameters to it. Now it is no run_trans() and run_write() functions.

	* src/cross.c (intersec): Changed func(...) with func_odeiv().

	* src/solver.c (solver): Removed func(...). Using func_odeiv() instead.

	* src/integrator.c (run): Completely removed func(...) from this file.
	

	* src/cross.c: Removed first occurence of func(...), changed it
	for func_odeiv in peak_def(). Added pointer to function as a
	paramter to pead_def(); removed (double f[]) from there. It is the
	first step, next will be remove func() all over the programm.

2009-07-31  Elias Potapov  <elias.potapov@gmail.com>

	* src/init.c (init): Removed init_after_conf() no need in it.

	* src/ode.c: Since this time, src/ode.c is the file for defining
	ODE system to solve.

2009-07-30  Elias Potapov  <elias.potapov@gmail.com>

	* src/input_interpreter.c (cont_interp): Some cosmetics to
	continue menu.

	* src/init.c (init): Moved cont_init() and rand_init() after the
	whole config file is read.

	* src/input_interpreter.c (cont_interp): Added HSS and IHSS as
	solution to track.

	* src/trajectory.c (traj): Moved out any memory allocations for
	*regime and *reg[i]. Because I do its contents constant
	string(like PANTI or PIN or IHLC) and if it is NULL I do check for it.

	* src/input_interpreter.c (rand_interp): Changes in all
	menu_interpreter functions. Wrong command prints the message "No
	such command" for each menu. Enter hit doesn't count for wrong
	command, instead new prompt printed again silently.

	* src/main.c (copyleft): Copylefted the program...with GNU GPL.

	* src/init.h: init_command_line() prototyping was incorrect. 

2009-07-29  Elias Potapov  <elias.potapov@gmail.com>

	* src/read_config.c (read_config): Did the same. See below for
	input_interpreter.c file.

	* src/input_interpreter.c (numerics_interp): Change comparison
	section for "run-kut4" string. It is now using strcasecmp()
	function, not simply string1==string2.

	*** SINCE THIS TIME I keep all *.c and *.h files in src/
	directory. ***

2009-07-27  Elias Potapov  <elias.potapov@gmail.com>

	* input_interpreter.c (rand_interp): Some attributes to out file
	for report of desired solution(rnd_out)---how many points got
	desired solution and total attempts. Removed 'break' statement
	if max-min is equal to zero, for getting SS solutions in count.

2009-07-26  Elias Potapov  <elias.potapov@gmail.com>

	* read_config.c (read_config): Checking for rnd_solution
	item. There was a reason for crash before when memory allocation
	for rnd_solution was in random_init(). See also comment in
	read_config in rndsol item.
	(buf_check): Now spaces, tabs are allowed when writing config
	file. Moreover they are allowed even between characters of each
	single word. For example, 'r n d so l' becomes 'rndsol', numbers
	like '7 0 9' ---> '709' and so forth.

	* random.c (random_init): Added memory allocation to rnd_solution,
	removed it from  previous place in init.c(init()).

2009-07-23  Elias Potapov  <elias.potapov@gmail.com>

	* trajectory.c (subper): Initialize n_subperiods,spectrum_per
	elements to zero and per_ratio elements to unity(not convergence)
	BEFORE any new run.
	(traj): If any of regime is PANTIALL then total REGIME is the
	same,but if any regime is IHLC then total REGIME is the IHLC(IHLC
	dominance).
	
	* cross.c (intersec): Initialize t_peak,x_peak,tper to 0.0(zero)
	before any new run.

	* input_interpreter.c (rand_interp): Menu item for selecting
	desired solution in RANDOM menu.
	(rand_interp): Convert string of desired solution (in
	RANDOM/SOLUTION) menu item to upper case if any of entered
	characters is lower case.

	* trajectory.c (traj): Added "continue" statement to Reporting of
	various regimes. More clear in determining specific regime.
	(traj): If any of trajectory is IHLC then total REGIME is IHLC.

2009-07-17  Elias Potapov  <elias.potapov@gmail.com>

	* init.c (init): Memory allocation for rnd_solution.

	* read_config.c (read_config): Added checking for fixed solution
	to watch in random initial points generating mechanism.

	* input_interpreter.c (rand_interp): char *rnd_solution instead of
	simple char *word for solution which initial points wanted to be
	written to "rand" file. Of course added declaration to init.h.

2009-07-16  Elias Potapov  <elias.potapov@gmail.com>

	* input_interpreter.c (rand_interp): More correct random initial
	points. Changed from (max-min)*u to (max-min)*u+min.

2009-07-07  Elias Potapov  <elias.potapov@gmail.com>

	* init.h: Removed array of pointer to vars(x) and RHS(f) all over
	the program.
	   Removed array pointer for max and min of vars(p_max_x
	and p_min_x). Everywhere they occur in rest of the program.
	   Removed array of pointers for Poincare level(p_x_cross). 
	   Removed array of pointers for p_n_isec,p_n_peaks,p_n_subperiods.

2009-07-06  Elias Potapov  <elias.potapov@gmail.com>

	* read_config.c (read_config): Made changed to read vars and pars
	initial values  and their names from config file. Needed to do
	changes in declarations of par_name and var_name in init.h

2009-07-05  Elias Potapov  <elias.potapov@gmail.com>

	* trajectory.c (traj): Added new names for regimes. PIN---Periodic
	INphase. PANTI---Periodic ANTIphase. PANTIALL---Periodic ANTIphase
	for ALL vars. IHSS,HSS,IHLC leaved unchanged.
	(traj): Changed some terminal output information.
	(traj): Changed 'cnt' with 'cmppairs' and 'MAX_N_CNT' with
	'MAX_N_CMPPAIRS'. That should be clearer than it was. 

2009-07-04  Elias Potapov  <elias.potapov@gmail.com>

	* trajectory.c (traj): ERRORS FORMING. Serious mistake in
	algorithm. Forming 'cnt'(actually, number of compared
	variables. Cnts were not correctly formed. They were formed both
	for isec and peak method, not checking for what period determining
	method is. As a result, not correct formation of
	count[k]s... Added if(per_method == ..) for ERRORS FORMATION.
	

	* init.h: Added a functions prototypes. No comments.  Created TAGS
	file. All functions can be found there.
	

2009-07-04  Elias Potapov  <elias.potapoc@gmail.com>

	START LOGGING: Actually, started to write log in ChangeLog for
	"din'amica" project today!
