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ChangeLog2011
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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.