2013-02-04  Potapov Ilya  <elias.potapov@gmail.com>

	* everywhere printf Qualifiers giving warning messages on Mac were replaced
	with more correct ones.

	* src/din_main.c (main): Changed compilation LDFLAGS from
	-L/usr/local/lib(Linux) to -L/opt/local/lib(Mac). This should be
	arranged automatically in the future.

	* src/read_ode.c (read_source): All realloc's on the NULL pointers
	must be substituted with malloc: dinamica fails to run on Mac
	without this.

	* Makefile (LDFLAGS+CPPFLAGS): Started maintainance of the program
	in Mac OS X. There are some issues on the Mac I have never
	encountered in Linux. There is a strong need in Autoconf scripts
	for the program.

2013-01-30  Ilya Potapov  <elias.potapov@gmail.com>

	* Makefile (SUBVER): Removed sub-sub-version of the program. The
	current release is 0.9.

	* src/trajectory.c (slope): Introduced the slope amplitude array
	size since it can be changed by check_slope_ampl(...).

2013-01-29  Ilya Potapov  <elias.potapov@gmail.com>

	* src/input_interpreter.c (numerics_interp): BSIMP method in the
	menu.

	* src/integrator.c (run): Bulirsch-Stoer implicit method for the
	stiff systems.

2013-01-28  Ilya Potapov  <elias.potapov@gmail.com>

	* src/trajectory.c (slope): Criteria for the oscillatory
	regime. Compare the last slope amplitude to the rest one by
	one. We are on the oscillatory regime if the last amplitude equal
	to any previous one.

2013-01-27  Ilya Potapov  <elias.potapov@gmail.com>

	* src/trajectory.c (slope): Detect the steady state by the
	computing the decrease in the slope amplitudes along the
	trajectory. This happens if the trajectory is not within the
	tolerance boundaries for being at the steady state, but tends to
	it.
	(slope): 50% of slopes demonstrating the monotonical decrease is
	the criterion for the steady state.
	(slope): Compare monotonical decrease with
	D(abs_am,rel_am,sl_ampl[i]) rather than with the absolute
	tolerance level(like in case of the very small amplitudes). The
	same criterion but of the opposite sing is applied to find
	oscillations.
	(slope): >50% slopes demonstrate monotonical decrease in amplitude
	AND >50% of the amplitude drop allows to claim the SS was observed.

2013-01-26  Ilya Potapov  <elias.potapov@gmail.com>

	* src/trajectory.c (slope): Detect the steady state by comparing
	with the system-wide tolerance level = eps_abs_am, in other word,
	this could be also interpreted as the computational error of the
	integration.

	* src/input_interpreter.c (periods_interp): Recompute common
	entities within the periodics menu.

2013-01-21  Ilya Potapov  <elias.potapov@gmail.com>

	* src/trajectory.c (slope): This new function gets the info about
	the slopes of the trajectory. Slope is the part of the trajectory
	between the peak and the trough or vice versa.
	(slope_ampl): Given the struct trajPeak of the trajectory the
	function computes the amplitudes of the slopes. This info can be
	used to assert the steady state and oscillatory attractors
	convergence.

	* src/cross.c (peak_trough): The function determines the peaks and
	troughs of the deterministic time series. This info is kept in the
	special struct trajPeak defined in the trajectory.h.

2013-01-14  Ilya Potapov  <elias.potapov@gmail.com>

	* src/graph.c (graph_set_labels): Graph: X11 first window for the
	kinetics/phase portraits, the second window is for the histograms
	"thist" and "mdist" types.

2013-01-12  Ilya Potapov  <elias.potapov@gmail.com>

	* src/graph.c (init_graph): Enhanced mode for X11 terminal of gnuplot.

	* src/input_interpreter.c (periods_interp): Do not print variable
	for periods calculation when no runs were performed.
	(periods_interp): perVarInd --> per_var.

	* src/init.h: We cannot remove per_var!!! It is a flag, while
	perVarInd is a real index.

2013-01-11  Ilya Potapov  <elias.potapov@gmail.com>

	* src/trajectory.c (mol_dist): Automatic detection of the variable
	during the creation of a molecular histogram.

	* src/input_interpreter.c (traj_interp): Molecular distribution in
	trajectory menu.

	* src/trajectory.c (mol_dist): free_frame was killing frame before
	it is used.

	* src/input_interpreter.c (traj_interp): Trajectory menu.

	* src/trajectory.c (mol_dist): New function to compute molecular
	distributions. First simple implementation.

	* src/cross.c (compute_period): perVarInd used everywhere instead
	of per_var.

	* src/input_interpreter.c (load_initials): New function for
	loading the initial conditions. Simple fscanf() implementation.
	(traj_interp): New trajectory menu is introduced.

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

	NEW YEAR STARTS!

	* Makefile (SUBVER): 0.9.4a release.

