2011-12-30  Ilya Potapov  <elias.potapov@gmail.com>

	* src/read_ode.c: Added the statements defining
	the input of the discrete system(Gillespie).

2011-12-28  Ilya Potapov  <elias.potapov@gmail.com>

	* src/read_ode.c (read_source): fixed memory allocating bug for
	initstr 

2011-11-18  Ilya Potapov  <elias.potapov@gmail.com>

	* src/lyapunov.c (lyap_spec_cont): LCE spectrum continuation over
	parameter algorithm

2011-11-17  Ilya Potapov  <elias.potapov@gmail.com>

	* src/lyapunov.c (lyap_spec): Fixed main bug about Lyapunov
	Exponents spectrum algorithm. (0.8.5 release)

2011-11-14  Ilya Potapov  <elias.potapov@gmail.com>

	* src/lyapunov.c (lyap_spec): Lyapunov Exponents spectrum
	algorithm from Wolf et al, 1985.

	* src/din_main.c (app_ext): additional '\0' character for a new
	output name. It was detected to be other symbols in the end
	without ending '\0' char.

	* src/ode.c (ode_lin): Linear ODEs.

	* src/ode.c (jac): Jacobian.

2011-11-03  Ilya Potapov  <elias.potapov@gmail.com>

	* src/solver.c (solver): Euler method is introduced.

	* src/ode.c (jac): dfdx and dfdt hold the values of Jacobian and
	2nd time derivatives in the core routines.

	* src/din_main.c (main): Only compilation is possible with `-c'
	flag to dinamica.

	* src/read_ode.c (read_source): New syntax for defining the
	Jacobian for the ODE system and second time derivative of
	variables(which means we have not ODE system). But Jacobian is
	still not supported by the core routines from the din library. It
	waits its implementation.

2011-11-01  Ilya Potapov  <elias.potapov@gmail.com>

	* src/lyapunov.c (lyap_cont): New algorithm computing the Main
	Lyapunov Exponent when on of the system's parameter is
	varied. Continuation along the parameter is done with a fixed step
	size.

2011-10-27  Ilya Potapov  <elias.potapov@gmail.com>

	* src/lyapunov.c (mle): Added is a new function mle(...) computing
	the Main Lyapunov Exponent. The function is intended to study
	chaos. Before use one needs to get the attractor with fixed step
	integrator with write_step=1, then run mle(...) with defined
	threshold and initial distances.
	

2011-02-17  Ilya Potapov  <elias.potapov@gmail.com>

	Totally changed n_steps  to  write_count in cross, peak functions
	for ability to use the write_step. It takes a lot of time to
	compute Langevin stoch equations.

	* src/main.c (max_min_x): Max and min computing: no comparing with
	the fixed error, just more or less then specified time. Because of
	write_count which writes not all points to storage arrays.

	* src/read_ode.c (isVar): Minor fix of "Segmentation fault"
	discovered for some systems. Now switched to using of DIM in
	isVar() function.

2011-01-10  Ilya Potapov  <elias.potapov@gmail.com>

	* Makefile: Ver 0.8.1a release. Langevin approach is now available
	in the program. At this point it only accepts random generation
	from gaussian distribution, so it is possible to add white noise
	to the RHS.

	* src/input_interpreter.c (numerics_interp): We have added the
	buffer increment menu item. Buffer increment is number of points
	to be stored by additional integration when storage array is full
	and incrementing is required.

	* src/ode.c (func_odeiv): Added new noisy terms to RHS. There are
	amplitude coefficients in front of numbers from random
	generator. By setting these conefficients to zero it is possible
	to reduce noise effect or introduce noise only for several
	variables. These conefficients are constants so we have additive
	noise.

	* src/random.c (generate_seed): Slight changes in random generator
	seed creation: in now multiplies the seconds of computer's uptime
	by 100. For ex.: 123.45 seconds of uptime => 12345 seed. This is
	done for preventing the same seed for multiple runs in a second.

2011-01-05  Ilya Potapov  <elias.potapov@gmail.com>

        ********************** Ver 0.8.0a RELEASE **********************
	SUMMARY: New extended ode file parser created.
	****************************************************************
	
	* src/input_interpreter.c (rand_interp): Now it is possible to set
	the seed for the random generator manually and automatically(from
	system's uptime)

	* src/random.c (random_d): More general function to obtain random
	values.

	* src/init.c (init): New initiation process: there is no dynamical
	and statical initialization as we totally define DIM, LDIM and
	PARDIM from within ode file. Also those values are not allowed to
	be changed anymore.

	* src/input_interpreter.c (rand_interp): New procedure for getting
	the seed number for the random generator. The source of the seed
	did not change. 

	* src/integrator.c (run): Printing info is different for two types
	of runs: transient and normal.

2011-01-02  Ilya Potapov  <elias.potapov@gmail.com>

	* src/integrator.c (run): Auxillary and fixed entities are now
	stored in the data file. NOTE: we do not use storage arrays for
	those values.

	* src/main.c (main): `-c' flag is still possible to pass to the
	system executable to specify configuration file.

	* src/read_config.c (set): AUXNUM and FNUM are now available
	through configuration file.

	* src/read_ode.c (read_source): Reading fixed entities. See XPPAUT
	manual for details.

	* src/din_main.c (main): Now system executable accepts
	configuration file without `-c' flag in front of the file name.

2011-01-01  Ilya Potapov  <elias.potapov@gmail.com>

	* src/read_ode.c (process_odestr): fgets function changed to read
	the correct number of characters.
	(gen_conf): Added functionality to read auxillary entities from
	.ode file.

