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ChangeLog2009
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ChangeLog2009
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2009-12-30 Elias Potapov <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* src/input_interpreter.c (sing_interp): Singularity menu. Added
technical parameters to menu. They may be changed now.
2009-11-28 Elias Potapov <[email protected]>
* src/input_interpreter.c (sing_interp): `show' command for
singularity menu.
2009-11-27 Elias Potapov <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
***********************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 <[email protected]>
***********************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 <[email protected]>
* src/init.c (init): Config file reading with error open
handling.
2009-10-28 Elias Potapov <[email protected]>
* 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 <[email protected]>
* src/main.c (copyleft): Added 2009 year to copyright.
2009-09-04 Elias Potapov <[email protected]>
* 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 <[email protected]>
* src/input_interpreter.c (errors_interp): Completed ERRORS menu.
2009-08-18 Elias Potapov <[email protected]>
* src/input_interpreter.c (parameters): Some additional changes in
parameters reading from menu. More desired behaviour and errors
handling.
2009-08-15 Elias Potapov <[email protected]>
* 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 <[email protected]>
* src/trajectory.c (traj): Added zeroing regime_ratio at each new
invocation of traj().
2009-08-07 Elias Potapov <[email protected]>
*****************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 <[email protected]>
* src/read_config.c (read_config): More extensive read of config
file par section.
2009-08-04 Elias Potapov <[email protected]>
* Makefile (.PHONY): Upgraded Makefile.
*****************VER 0.1 RELEASE******************
2009-08-02 Elias Potapov <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
START LOGGING: Actually, started to write log in ChangeLog for
"din'amica" project today!