ChangeLog2012

2012-12-31  Ilya Potapov  <elias.potapov@gmail.com>

	* src/input_interpreter.c (file_interp): Graphics is updated when
	new data is loaded through file menu.
	(file_interp): Longer symbuf string for the filenames with
	diretories specifications.

	Complete usage of read_input_line(...).

	* src/read_ode.c (gen_conf): cross_level can be set from ode file
	under internal par section (@).

2012-12-30  Ilya Potapov  <elias.potapov@gmail.com>

	* src/graph.c (send_to_eps): Resetting to the X11 graph after
	dumping to the eps.

2012-12-29  Ilya Potapov  <elias.potapov@gmail.com>

	* src/cross.c (compute_period): per_var is in the function.

	* src/input_interpreter.c (periods_interp): per_var is the
	variable for which the periods are calculated. per_var = -1 is
	automatic detection by the max amplitude, as before was the only
	method.

	* src/read_ode.c (process_inter_par): var names for axis labels in
	ode file. yax=X or yax=1 are both possible.
	(process_inter_par): Error check for the axes specification.

	* src/file.c (get_info_data): It takes one array of integers
	indicators from the time series technical line.
	(convert_data_file): Number of data sets is got from the info line
	of the data source.
	(convert_data_file): The function does no longer need the number
	of data sets as its input. Plus, some additional corrections to
	the temporary strings are made.

	* src/integrator.c (run): Added lang_flag to the technical line of
	the timeseries. It is redundant, we dont need it for now, for the
	future uses.

2012-12-28  Ilya Potapov  <elias.potapov@gmail.com>

	* src/integrator.c (run): Removed storage arrays. Not completely,
	only from the run().

	* src/random.c (load_frame): Skips the first technical line in the
	time series data file.

	* src/integrator.c (analyze_traj): nPerStoch/nPerDet = 0 for non
	complex det/stoch method(s). In order to avoid printing of period
	of older runs.

2012-12-21  Ilya Potapov  <elias.potapov@gmail.com>

	* src/trajectory.c (get_index_trans): Gets the index of the frame
	time which is closest to the specified time threshold.

	* Makefile (SUBVER): .3a subversion.

	* src/init.h: no cross_interp(). There is no need in this
	function. We have added new global entity cross_level that can be
	changed within the periodics menu. This entity alone completely
	substitutes all items in the cross menu.

2012-12-19  Ilya Potapov  <elias.potapov@gmail.com>

	* src/file.c (get_info_data): pure_det is taken into account.

	* src/integrator.c (run): Introducing 'pure_determ_flag' to the
	technical parameters of the data file.

	* src/file.c (convert_data_file): Correct slightly the function to
	reflect changes in the time series data file format.
	(get_info_data): new function intended to read first technical
	line in the time series source data file.

	* src/integrator.c (run): Printing for multiple runs to the user,
	every 0.2 part of the simulation is reported.
	(run): Put some technical info in the header of the time series
	data file. For now "#complex,nruns" where complex is true if the
	method is complex and false otherwise.

2012-12-17  Ilya Potapov  <elias.potapov@gmail.com>

	* src/input_interpreter.c (graphics_interp): Dumping to the eps is
	under graphics menu.

	* src/graph.c (send_to_eps): Fast dump the current file to the eps.

	* src/submenu.c (periodics_hist_interp): Plotting the histogram of
	periods when it is computed.

	* src/graph.c (graph_set_labels): New style of graph_set_labels()
	which depens on the type of the plot: "tsphase" -- time series or
	phase space and "thist" -- histogram of periods.

	* src/input_interpreter.c (graphics_interp): Graphics flag in the
	graphics menu.
	(get_parameter): Par-initial link is now checked in this
	function. The current value of a var is set immediately after the
	paramter, linked to this var, gets new value.

	* src/graph.c: libplot is disabled completely.

2012-12-16  Ilya Potapov  <elias.potapov@gmail.com>

	* Makefile (install): `make install' copies the .so.<ver> lib file
	to /usr/local/lib and makes link inside this directory.

	* README: Updated installation instructions.

	* src/input_interpreter.c (graphics_interp): X- and Y-axes can be
	set from inside the graphics menu.
	(graphics_interp): Grid toggle.

	* Makefile (SUBVER): New graphics update up to version 0.9.2a.

	* src/graph.c (gnuplot_interp): Gnuplot interactive command line.

	* src/input_interpreter.c (graphics_interp): Graphics menu.

	* src/graph.c (graph_set_labels): set labels to the graph if the
	plotting x- or y-axis is changed.
	(gplot_results): primitive function for multiple variables plots.

	* src/read_ode.c (process_inter_par): graph_flag within @parameters.

	* src/init.c (din_close): xs, xs[i] and ts are freed.

2012-12-15  Ilya Potapov  <elias.potapov@gmail.com>

	* src/input_interpreter.c (periods_interp): New period
	representation under periodics menu.

	* src/integrator.c (analyze_traj): periods computation

2012-12-14  Ilya Potapov  <elias.potapov@gmail.com>

	* src/read_ode.c (read_source): "d" letter is synonym for "done"
	in ode file.

	* src/cross.c (compute_period): Debugged enough, seems working
	very fine.

2012-12-13  Ilya Potapov  <elias.potapov@gmail.com>

	* src/cross.c (crossing): Completely new function.
	(crossing): The function is finalized.

	* src/integrator.c (run): The function finalized.
	(analyze_traj): The function is intended for summary analysis of
	the trajectory computed from the run(...) run.

2012-12-12  Ilya Potapov  <elias.potapov@gmail.com>

	* src/integrator.c (run): Rearrangements in the run()
	function. Make it more clear. Start introducing a universal
	analysis of the trajectories function.

	* src/cross.c (compute_period): this function is universal
	computing period/distribution from all the data both deterministic
	and stochastic.

	* src/random.c (load_frame): realloc is better than malloc, since
	it frees the memory if the pointer was malloc-ed before.

2012-12-09  Ilya Potapov  <elias.potapov@gmail.com>

	* src/input_interpreter.c (numerics_interp): strcpy instead of
	just assignment of method strings. This serves the memory
	allocation and can be freed in the end of the program by
	din_close().

	* src/main.c (copyleft): Thanks to gnuplot_i library.

	* Makefile (SUBVER): 0.9 version release with simple graphics
	capability of Dinamica.

	* src/graph.c (init_graph): Initial graphics set up. Gnuplot
	and/or GNU libplot... We use gnuplot_i interface for Gnuplot
	within C programs, written by N.Devillard.
	(gplot_results): Plotting with Gnuplot.

2012-12-08  Ilya Potapov  <elias.potapov@gmail.com>

	* src/init.c (din_close): Added a function finalizing the work
	with Dinamica, i.e. closing all streams, cleaning memory etc.

2012-11-14  Ilya Potapov  <elias.potapov@gmail.com>

	* src/read_ode.c (process_init1): Temporary function to include
	parameter initial conditions. The old one process_init(...) is
	kept for a trial period.
	(get_parameter_name): Very useful function: gets the index of
	existing parameter name or copies the new name returning the index
	of it, given the string of characters.
	(process_par1): Temporary function to process parameters. The old
	one process_par(...) is kept for a trial period.

2012-11-12  Ilya Potapov  <elias.potapov@gmail.com>

	* src/integrator.c (run): Transient run problem fixed. fprintf to
	the data source was done when trans. flag is even zero. This caused
	the stream corruption problem.
	(run): Removed random generator initialization and free-ing when
	the deterministic run is performed.

2012-11-11  Ilya Potapov  <elias.potapov@gmail.com>

	* src/cross.c (compute_hist_per): Histogram of the periods.

2012-11-10  Ilya Potapov  <elias.potapov@gmail.com>

	* src/random.c (compute_autocorrelation): frame_size-1 is the last
	element. Ignore the real last one, making NaN, since covariation
	is normalized by (frame_size-1).

	* src/cross.c (compute_perStoch_autocorr): Computes the period for
	a given variable(all too expensive) from a set of data(a number of
	frames) in the source file
	(get_var_perStoch): The function determines which variable to
	compute period from. The estimator uses the difference between max
	and min values, the variable with the max of the difference is
	preferable.

	* src/random.c (write_autocorr_file): Writes the autocorrelation
	computed to the specified output.

2012-11-09  Ilya Potapov  <elias.potapov@gmail.com>

	* src/input_interpreter.c (read_input_line): function reading the
	input for different command, release the input from the newline
	and checks the length of the input.

2012-11-08  Ilya Potapov  <elias.potapov@gmail.com>

	* src/integrator.c (run): stochastic periods, global variables
	along with numPerStoch, i.e. number of periods computed for the
	stochastic trajectory.

	* src/cross.c (compute_peak_autocorr): Function determining the
	first peak of the autocorrelation function.

2012-11-07  Ilya Potapov  <elias.potapov@gmail.com>

	* src/random.c (compute_autocorrelation): Function computing the
	autocorrelation of the signal, based on the sequential calls to
	the gsl_stats_covariance() function.

2012-11-06  Ilya Potapov  <elias.potapov@gmail.com>

	* src/random.c (load_frame): For analyzing ensembles of the
	stochastic trajectories we have introduced the function reading
	only a frame (single trajectory data) from the source data file.
	(write_frame): writes the frame.
	(load_frame): Reallocation memory for the frame.

2012-11-05  Ilya Potapov  <elias.potapov@gmail.com>

	* src/input_interpreter.c (get_parameter): More complex parameter
	assignment function get_parameter().
	(read_menu): no nargin argument to the function. Setting zero's
	for all MAX_N_ARG command line argin's.
	(read_menu): no nargin anymore.

2012-11-02  Ilya Potapov  <elias.potapov@gmail.com>

	* src/integrator.c (write_data_file): Shortened the file, by
	introducing new functions, like write_data_array().

2012-11-01  Ilya Potapov  <elias.potapov@gmail.com>

	* src/integrator.c (run): the function is shorter and gsl_odeiv2
	is now used instead of old gsl_odeiv.

	* src/input_interpreter.c (check_next_arg): new function checking
	the next argument existence of the command line
	buffer. Additionally all strncat are substituted with strncpy in
	menu reading system.

2012-10-31  Ilya Potapov  <elias.potapov@gmail.com>

	* src/input_interpreter.c (errors_interp): Few minor correction in
	reading menu input.

	* Makefile (SUBVER): 0.8.6a is released. Enhanced menu handling.

	* src/input_interpreter.c (errors_interp): correct reading. no use
	of external temporal buffers.
	(numerics_interp): some correction in reading input in numerics_interp().

2012-10-26  Ilya Potapov  <elias.potapov@gmail.com>

	* src/din_main.c (main): Correctly prepared .c file can define the
	system skipping the complete writing of .ode file. Minimalistic
	.ode file, however, is required. It must contain #include
	statement specifying the external .c source, definition of the
	variables (dX/dt=<whatever>) and parameters (par statement). It
	may contain some other stuff as usual .ode file, only the transfer
	of the system to the corresponding .c source is disabled.

	* src/read_ode.c (read_source): init() moved back to read_source().

	* src/din_main.c (main): Initialization init() moved to dinamica main.

	* src/read_ode.c (process_update_vector): New update vectory
	specification system. One needs to specify number and var
	name. For example, g:x*y;-2x,+1y,-z. Single + and - are allowed to
	mean +1 and -1, respectively.

2012-10-25  Ilya Potapov  <elias.potapov@gmail.com>

	* src/read_ode.c (read_source): Allocation for upstr was 1 too
	short. This caused that invalid pointer problem.
	(read_source): New copying method using memcpy.
	(buf_strip): changed the function. buf_check() from libdin.a is
	the similar to this (except removal of newlines '\n').

2012-10-23  Ilya Potapov  <elias.potapov@gmail.com>

	* src/din_main.c (main): Correctly prepared .c file can be
	compiled with -s option to dinamica without reading the
	corresponding .ode file.
	(extr_base): the function extracts basename from .c files from now
	as well as .ode files.

2012-10-16  Ilya Potapov  <elias.potapov@gmail.com>

	* src/trajectory.c (attr_conv): New atrr_conv function trying to
	determine the convergence to an attractor by computing euclidean
	distances between all points and comparing them to some
	threshold (0.01 for now found to be O.K.). Being on the
	attractor the system must pass close to the vicinity
	of some points,	i.e. must repeat its path in the phase space.

2012-09-12  Ilya Potapov  <elias.potapov@gmail.com>

	* src/file.c (convert_data_file): 10 digits are not enough per
	single value, now it is 20 and is in #define MAX_N_DIG.

2012-09-09  Ilya Potapov  <elias.potapov@gmail.com>

	* src/read_ode.c (read_source): init() function initialize all
	values, like DIM,LDIM,NREAC etc.

2012-09-07  Ilya Potapov  <elias.potapov@gmail.com>

	* src/input_interpreter.c (read_ode): Langeven flag and
	complex method are possible to set up from within the .ode file.

2012-09-05  Ilya Potapov  <elias.potapov@gmail.com>

	* src/input_interpreter.c (main_interp): Multiple operations by
	single command. For example, 'n tt' will set up total time of
	integration and 'f d' command will set up new name for the data
	file. Actually, main_interp(...) combines consecutive commands
	into a single one.
	(numerics_interp): no longer accepts additional argument of
	pointer to struct num. No need in this, all variables are global
	in init.h.
	(numerics_interp): Complete new design of menus, provided with the
	depth_level, determining at what menu and command level the
	program is. This provides extensive multiple operations commands
	in single command. This is totally done for numerics menu. Other
	menus are just waiting.

2012-07-03  Ilya Potapov  <elias.potapov@gmail.com>

	* src/read_ode.c (process_odefile): print jacobian only when
	jac_flag is TRUE.

	* src/integrator.c (run): Additional fclose(...) caused memory
	violation. Fixed.

	* src/solver.c (ss_stab): Completed analysis of the steady state
	stability by computation of eigenvalues.

2012-06-25  Ilya Potapov  <elias.potapov@gmail.com>

	* src/solver.c (ss_stab): Stability analysis of the steady states
	by eigenvalues computation.

2012-06-15  Ilya Potapov  <elias.potapov@gmail.com>

	* src/input_interpreter.c (show_initials): New show_initials
	function, taking as many init conditions as wanted.
	(main_interp): New call to the initial condition function: it
	takes all init. conditions and start simulation, for each
	init. cond. new data file is created, which is <basename>-<i>, where
	<i> is the number of init. condition and <basename> is the
	`data_name' string, used as a basename. Not enough specified
	init. points are compensated with zeros.

2012-06-14  Ilya Potapov  <elias.potapov@gmail.com>

	* src/integrator.c (run): Preliminary added additional loop over
	number of runs for the deterministic methods. This is needed for
	Langevin.

2012-06-03  Ilya Potapov  <elias.potapov@gmail.com>

	* src/input_interpreter.c (lyap_interp): realloc problems, changed
	to malloc.

	* src/solver.c (ss_stab): GSL eigensystems tools are implemented.

2012-06-02  Ilya Potapov  <elias.potapov@gmail.com>

	* src/singularity.c (multiroot_find): Reports about stability. Not
	reliable yet, see below notes about ss_stab(...). it is not still
	complete.

	* src/solver.c (ss_stab): Not finished yet. Computes the Jacobian
	at the steady state. What is next?

	* src/ode.c (jac): Jacobian numerical computation if
	jac_flag=0. Based on five points stencil computation of
	derivatives. Step is taken from mynum.step.

	* src/read_config.c (read_conf): auxillary entities names are
	allocated now differently. Also affected is read_ode.c/gen_conf
	function.

2012-06-01  Ilya Potapov  <elias.potapov@gmail.com>

	* src/ode.c (jac): If jac_flag is true, then call jacobian(...),
	otherwise compute derivatives numerically.

	* src/read_ode.c (read_source): jacobian statements. Several
	checks for incomplete jacobian statements specified. Jacobian
	flag (jac_flag) added (global in init.h), determining if user has
	specified the jacobian.

2012-05-30  Ilya Potapov  <elias.potapov@gmail.com>

	* src/read_ode.c (read_source): realloc() problems. Actual
	var_name[i] and odestr[i] do not need realloc, the malloc is
	better and sufficient.

	* src/read_config.c (read_conf): method allocation(in
	read_ode.c/gen_conf and reading.

	* src/din_main.c (extr_base): additional argument to the function
	specifying outcoming string.
	(extr_base): Fatal error: did not put trailing zero to basename
	string when copying. Fixed. Now use strncpy, but own code is
	provided as well.

	* src/din_main.c (app_ext): additional argument to the function
	specifying outcoming string.

2012-05-29  Ilya Potapov  <elias.potapov@gmail.com>

	* src/input_interpreter.c (read_menu): New input argument reading
	system. Uses MAX_N_ARG and MAX_ARG_LEN global variables defined in
	init.h. If user input exceeds the MAX_N_ARG the error message is
	displayed and the program takes only first MAX_N_ARG
	arguments. For the rest of the arguments the behavior is undefined.

2012-05-05  Ilya Potapov  <elias.potapov@gmail.com>

	* src/file.c (convert_data_file): converter modification in case
	of complex method: first deterministic data set is converted
	without a number appended(not a stochastic realization).
	(convert_data_file): minor changes to converter

2012-05-04  Ilya Potapov  <elias.potapov@gmail.com>

	* src/file.c (convert_data_file): New file converter: single data
	set as well as multiple data sets to multiple .csv (default) file.

	* src/input_interpreter.c (file_interp): file converter + new data
	file name

2012-04-29  Ilya Potapov  <elias.potapov@gmail.com>

	* src/integrator.c (run): Removed period notification at the end
	of simulations

	* src/input_interpreter.c (parameters): added memset(buf...) to
	erase previous data in buf and buf2

2012-04-28  Ilya Potapov  <elias.potapov@gmail.com>

	* src/integrator.c (run): New complex method approach

2012-04-09  Ilya Potapov  <elias.potapov@gmail.com>

	* src/integrator.c (run): Single run function including the
	Gillespie procedure.

	* src/input_interpreter.c (read_menu): Menu reading function takes
	additional argument of num of arguments read to erase the memory
	from the old calls to the function.

2012-03-22  Ilya Potapov  <elias.potapov@gmail.com>

	* src/read_ode.c (isVar): Accepts size argument to check the size
	of var_list. It is needed if one applies process_odestr(...) to,
	e.g. functions' right hand sides, where the list of search for the
	variables is not "global" var list, but list of arguments of the function.
	(process_odestr): Accepts size argument for the same reason as above.
	REMARKS: If someone at any time decides to include variable
	`t'(time) to the system (regardless if any such a system exists)
	then DIM argument for the `size' parameter must be at least
	changed to (DIM+1)

2012-03-21  Ilya Potapov  <elias.potapov@gmail.com>

	* src/main.c (max_min_x): Fatal error in computing start and stop
	points! Now fixed. Periods are determined correct by peak method.

2012-01-07  Ilya Potapov  <elias.potapov@gmail.com>

	* src/integrator.c (run): Gillespie algorithm full implementation
	is done.

2012-01-06  Ilya Potapov  <elias.potapov@gmail.com>

	* src/init.c (init): Some dynamically allocated arrays added.

	* src/read_config.c (read_conf): Binary configuration file .bcf,
	no ASCII config file is support from now on.

2012-01-04  Ilya Potapov  <elias.potapov@gmail.com>

	* src/read_ode.c (gen_conf): First implementaion(testing) of the
	binary configuration file

2012-01-02  Ilya Potapov  <elias.potapov@gmail.com>

	* src/init.c (init): dynamic allocation of memory for variables
	`y',`ksi',`pr'.