2016-07-10  Potapov Ilya  <elias.potapov@gmail.com>

	* src/lyapunov.c (mle): load_frame() function used to load
	"frames" to replace the old-convention of ts/xs storage arrays.

2015-01-04  Potapov Ilya  <elias.potapov@gmail.com>

	* src/main.c (main): Resolve reading from stdin when EOF reached
	in the script file (.di).

2014-11-09  Potapov Ilya  <elias.potapov@gmail.com>

	* src/input_interpreter.c (get_parameter): Got rid from the
	dynamically allocated symbuf in the command line parsing. This
	caused some bad allocation/bad freeing problems.

2014-10-11  Potapov Ilya  <elias.potapov@gmail.com>

	* src/read_ode.c (process_odefile): Include "double t" specifier
	to the propensity() function (transferred after the
	processing). This is done to use user-defined functions in the
	propensity() function. Also, "const" specifier is removed before
	"double P[]", for the same reason.

2014-07-01  Potapov Ilya  <elias.potapov@gmail.com>

	* src/random.c (rnd_init_cond_run): Report translation to the
	output of random throwing.

2014-06-30  Potapov Ilya  <elias.potapov@gmail.com>

	* src/random.h: Only initial condition to write to the
	output. Flag for this.

2014-06-25  Potapov Ilya  <elias.potapov@gmail.com>

	* src/integrator.c (write_data_file): Do not proceed writing to
	the file, when NaN is calculated.

2014-06-12  Potapov Ilya  <elias.potapov@gmail.com>

	* src/trajectory.h: T-system own tolerance values: absolute and
	relative.

	* src/continue.c (run_extend_rnd): Continue by the parameter along
	with random throwing.

	* src/trajectory.c (statND_to_file): Fixed the problem with the
	array of regStat structs.
	(perdcty_in_stat_array): Sort by all possible unique periodicities
	for all regStat structs.

2014-06-06  Potapov Ilya  <elias.potapov@gmail.com>

	* src/trajectory.h (struct): Distinct separation between SS and OS
	regimes without determination of SS through OS.

	* src/trajectory.c (statND_to_file): General statistics for
	multiple regStat values. Classification by all criteria.

2014-06-04  Potapov Ilya  <elias.potapov@gmail.com>

	* src/trajectory.c (regime_stat): Output file to report and
	statistics type to report. First type added.
	(ss_by_frame): New function determining SS by the fact of equal
	values in the trajectory for over than 50% of the time.

2014-06-03  Potapov Ilya  <elias.potapov@gmail.com>

	* src/trajectory.c (regime_stat): Periodicity report in the regime
	statistics.
	(free_regime_stat): Special free-ing of the regime stat structure
	regStat.

	* src/random.c (rnd_init_cond_run): A single function performing
	random initial conditions throwing.

2014-05-30  Potapov Ilya  <elias.potapov@gmail.com>

	* src/init.h (FRAME_LINE_LEN): Frame constants are in the globale
	init.h.

	* src/cross.c (write_autocorr_file): Autocorrelation handling
	functions in cross.c.

	* src/file.c (load_frame): Frame handling functions in file.c.

2014-05-29  Potapov Ilya  <elias.potapov@gmail.com>

	* src/trajectory.c (mol_dist): Only the first frame is analyzed
	for molecular species function.
	(mol_dist): Correct handling of the variable for the distribution
	calculation.

	* src/cross.c (peak_ampl): New amplitude calculating
	function. Jumps over the peaks and calculates the min of preceding
	and next troughs, then amplitude is the result of subtraction from
	peak value and the min value.

	* src/input_interpreter.c (periods_interp): Number of bins of the
	amplitude histogram can be specified from the command line.

	* src/cross.c (peak_ampl): Simple function to calculate amplitudes
	from the peak information (trajPeak object).
	(ampl_multi_frames): Calculate amplitudes from multiple
	frames. For stochastic purposes.

	* src/input_interpreter.c (periods_interp): Amplitude calculation
	in the Periods Menu restored.

	* src/trajectory.c (mol_dist): Bug is detected in the
	function. Should be fixed in the future. Only last imported frame
	is analyzed and NOT a number of them.

2014-04-24  Potapov Ilya  <elias.potapov@gmail.com>

	* src/trajectory.h (struct): Indicator of the ascending/descending
	slope.

2014-04-21  Potapov Ilya  <elias.potapov@gmail.com>

	* src/trajectory.c (get_dynamics_nd): Period for each subsystem
	printed. All phase shifts are reported.

2014-04-16  Potapov Ilya  <elias.potapov@gmail.com>

	* src/input_interpreter.c (rand_interp): Constraints can be set
	from one-line command.
	(load_initials): Take the ceiling instead of round for the
	discrete initial conditions.

2014-04-15  Potapov Ilya  <elias.potapov@gmail.com>

	* src/trajectory.c (regime_stat): The In-/Out-of-phase statistic
	is included.

2014-04-14  Potapov Ilya  <elias.potapov@gmail.com>

	* src/input_interpreter.c (load_initials): Make the round
	operation when reading the initial conditions for the discrete system.

	* src/din_main.c (main): Get the $PWD system variable to resolve
	the current directory name instead of the previous "./" identificator.

2014-03-30  Potapov Ilya  <elias.potapov@gmail.com>

	* src/trajectory.c (report_translate): No phase and no homogeneity
	reports are shown in case of LDIM=1.

2014-03-29  Potapov Ilya  <elias.potapov@gmail.com>

	* src/trajectory.c (get_dynamics_nd): Reformulation of the ND T-system.

2014-03-28  Potapov Ilya  <elias.potapov@gmail.com>

	* src/din_main.c (main): Deleting unnecessary files: make sure the
	files exist.

	* src/input_interpreter.c (load_initials): Copy the initial
	conditions to the correspong discrete array of initial
	conditions.

2014-03-27  Potapov Ilya  <elias.potapov@gmail.com>

	* src/init.c (din_close): More freeing at the end.

	* src/lyapunov.c (lyap_free): Freeing Lyapunov entities.

	* src/input_interpreter.c (rand_interp): Parameters and variables
	in the header of the random throwing output file.

2014-03-26  Potapov Ilya  <elias.potapov@gmail.com>

	* src/input_interpreter.c (parse_command_line): The new command
	line parsing system which includes the possibility of reading the
	commands from the script file. The latter can be specified to the
	program using -f flag.
	(rand_interp): Empty args for the random throwing
	constraints. Plus, no limitation for DIM number of iterations:
	given the empty args there can be more than DIM iterations.

2014-03-14  Potapov Ilya  <elias.potapov@gmail.com>

	* src/trajectory.c (find_lag_nd): The new way of determining the
	sub-system lag to check the out-of-phase regimes. This way also
	includes the definition of the homogeneous vs. in-homogeneous by
	the nature of it.

2014-03-11  Potapov Ilya  <elias.potapov@gmail.com>

	* src/trajectory.c (check_slope_ampl): No boom appeared treatment
	in the slope amplitudes checking. Very important issue left unseen
	in the code. Now fixed.

	* src/read_ode.c (read_source): The new possibility to define
	number of physical systems in .ode files: "%system"
	directive. This will deprecate in near future old "#system"
	directive, which is kept for backward compatibility.
	(read_source): The same as above for "%include"
	directive. "#include" is to be deprecated in near future.

2014-02-20  Potapov Ilya  <elias.potapov@gmail.com>

	* src/input_interpreter.c (read_next_command_wrapper): New wrapper
	function starts the new shorter way of reading the user-input.

2014-02-17  Potapov Ilya  <elias.potapov@gmail.com>

	* src/input_interpreter.c (rand_interp): Random throwing for the
	stochastic system.

	* src/trajectory.c (get_dynamics_1d): Redefined the attractor
	approaching rate, that is, now, showing how much (in %) of the
	last slope amplitude has changed over time from slope to
	slope. Defined by analogy of the derivative of a function.

2014-02-13  Potapov Ilya  <elias.potapov@gmail.com>

	* src/trajectory.c (get_dynamics_1d): Trying to avoid returning
	meaningless NULL and save the dynamics regime checking in case of
	sl_ampl_size == 1.

	* src/cross.c (compute_period): Appending mode for writing the
	autocorrelation function to the file.

	* src/input_interpreter.c (periods_interp): Plotting the
	autocorrelation function.

	* src/trajectory.c (get_dynamics_1d): Simple rules to overcome SS
	(or not enough points) situation when all the values in the data
	file are equal to each other and no peak/trough as well as slope
	information can be computed.

2014-02-11  Potapov Ilya  <elias.potapov@gmail.com>

	* src/trajectory.c (get_dynamics_1d): The iterative check of the
	slope amplitudes to support OS lag value.

2014-02-10  Potapov Ilya  <elias.potapov@gmail.com>

	* src/trajectory.c (get_dynamics_1d): Attractor approaching rate
	-- how fast you need to reach the attractor.

2014-02-06  Potapov Ilya  <elias.potapov@gmail.com>

	* src/trajectory.c (get_dynamics_1d): Define the descending rate
	before any slope comparisons. This will indicate the descending of
	the slope amplitudes. NOTE: negative values will show the
	ascending, which is checked in the OS regime.

	* src/read_ode.c (process_odefile): Minor bugs about NLANG value
	in the processing to .c file.

2014-02-04  Potapov Ilya  <elias.potapov@gmail.com>

	* src/read_ode.c (read_source): The new format for the langevin
	amendments: "lang x=0.1,y=0.4,z=1.3" .

2014-01-31  Potapov Ilya  <elias.potapov@gmail.com>

	* src/cross.c (crossing): The new way to allocate tisec in the
	function. It gets allocated from within the function and then gets
	returned. Additionally, the memory gets allocated by the big
	chunks, whose size is determined via the constant TISEC_CHUNK_SIZE
	[defined in the same file]. This avoids too many calls to the
	realloc function, which is advisable to avoid.

2014-01-30  Potapov Ilya  <elias.potapov@gmail.com>

	* src/integrator.c (analyze_traj): The new output extension. No
	more information of the cross level in the output file name. The
	output extension is ".do" = (d)inamica (o)utput. The cross level
	information is written in the file itself anyway.
	(analyze_traj): Single .do output for all cross levels (up to
	three). The output is just appended to the file.

2014-01-29  Potapov Ilya  <elias.potapov@gmail.com>

	* src/input_interpreter.c (main_interp): Minor bugs with memory
	allocation under the "Calculate" menu of the Main Menu.

2014-01-23  Potapov Ilya  <elias.potapov@gmail.com>

	* src/input_interpreter.c (rand_interp): Random menu receives the
	new command line treatment procedures. See read_command_line and
	read_next_command functions. Additionally, this menu receives the
	functionality to constrain the random throwing intervals for the
	specific variables set by the user.
	(graphics_interp): Free-ing symbuf variable under all *_interp
	function before every return statement withing those functions. Or
	as a partial solution, remove all return 0; statement under all
	else if conditionals in those menus and replace all of them with
	one single return 0; at the end of the functions. Except for the
	return 1000; statements indicating the exit from the menus.
	(rand_interp): Menu for specifying the constraints for the random
	throwing.

	* src/random.c (random_free): First, "freeing" function. For the
	Random stuff. It is invoked in the din_close() function closing
	the program.
	(random_init): New boundaries for the random throwing for each
	variable. Which variable is limited by the special constraints is
	determined in the logical array.

2014-01-21  Potapov Ilya  <elias.potapov@gmail.com>

	* Some declarations missing fixed. Plus, some minor mistypos in
	the code as well as some headers were undefined. New compiler, when
	moved to the new OS, has complained about all of this.
