Dinamica is intended to provide a general interface to the analysis of the Dynamical Systems. However, the specific set of aims ranges from the determining of the dynamical regime of the Deterministic (Coupled Symmetric) Dynamical systems written in the ODE form to the comparative analysis of the deterministic and stochastic (both discrete and continuous) representations of the same system. The aims are achieved by calculating various errors and comparing them with user-defined levels. Thus, the user ought to have some experience in scientific terms, although the algorithms are straightforward.
Dinamica treats both the stationary and oscillatory dynamical regimes. Additionally, there are algorithmic ways to calculate various oscillatory regimes: simple self-oscillations, coupled synchronized and non-synchronized, homogeneous and non-homogenous regimes, to name a few.
Additionally, there are many techniques used assisting the user in the analysis of dynamical systems. For example, period calculation with several methods, lyapunov exponents, continuation over parameters of the system, different statistical tools, period distributions etc.
Dinamica uses the powerful scientific library GSL (GNU Scientific Library) for the routine operations like e.g. numerical integration, random number generation, finding max and min etc. So one needs the GSL library pre-installed in order to use Dinamica.
- Unix/Linux OS.
- gcc compatible C compiler, needed for Dinamica functioning (not only compilation).
- GNU Scientific Library (GSL) installed.
- Gnuplot plotting utility installed (optional, but advisable).
Quick installation:
- Dowload the archive (usually .zip or .tar.gz) and uncompress it.
1a. NOTE: this repository contains the configuration files generated with ver. 1-14 of the GNU autotools.
If your version differs you need to run
aclocalandautomakefirst to regenerate the configuration files for the updated autotools. - Configure the systemm by typing
./configure. This will check for all the requirements and complain if any of those is not found. You may considerCPPFLAGSandLDFLAGSvariables, as well as--prefixoption to./configure, before configuring the system (see below). - Type
maketo compile thelibdin.aand the dinamica itself. The two must appear under thesrc/directory in the root. - Type
make installto install dinamica executable andlibdin.alibrary to the usual destinations (/usr/local/binand/usr/local/lib, respectively). This might require the root password. You may uninstall the program later by typingmake uninstallto remove those two files from the system. After the installation one might want to remove all the files extracted from the archive.
Dinamica processes the input from the user (equations, parameters, variables, constants etc.) in the form of the .ode file. The result of the processing is the output .c file with C language definitions and functions for the user system and the binary configuration .bcf file. This output .c file is then compiled with the dinamica library (libdin.*) generating the final executable .din. This executable is then invoked to read the .bcf file and, finally, the program fires up.
It is important to understand that the compilation and linking of the libraries take place during the functioning of Dinamica. Thus, the compiler and the right path for the required libraries are needed to be properly set when Dinamica is first compiled. One should take care of this before the configuration starts.
The way Dinamica can obtain the full set of the paths is to specify CPPFLAGS,
LDFLAGS and --prefix option, together or one by one when needed. These three
variables are passed to the Dinamica compilation command, so they are crucial. The
current directory where Dinamica is invoked is always checked for the dinamica
library (libdin.*).
This variable is important for the preprocessor, a program checking the included,
so called header, files. During the configuring the ./configure script checks for
several .h files from the GSL and the standard C libraries whether they are
available. Sometimes it fails to find them in the standard locations. In this case,
the CPPFLAGS is needed. The usage is simple: if one knows that the GSL headers are
located, for example, in /usr/local/include/, e.g. the full path to gsl_odeiv2.h
file is /usr/local/include/gsl/gsl_odeiv2.h (similarly for all other gsl *.h
files), then one could type:
CPPFLAGS=-I/usr/local/include ./configure
in the shell prompt. This sets the environment variable for the ./configure script.
Next, in Dinamica this option will be set, i.e. will be used as a path to the header
files to find. Note, that the path to the GSL header files is always gsl/*.h, so omit
the gsl/ directory when specifying the CPPFLAGS.
This variable shows the path to the GSL library (and possibly the standard C
libraries). If the gsl library files are located in /usr/local/lib then combining
with CPPFLAGS one could type
CPPFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib ./configure
which should do the trick. Additionally, Dinamica will compile the output .c file
using these options or the one specified by --prefix (see below) to find the
libdin.* library.
./configure script accepts the --prefix option, which specifies the installation
directory for make install command. Namely,
./configure --prefix=/usr/local
would install all the files produced by the package to the corresponding
subdirectories of /usr/local. For example, binary files, i.e dinamica, would go
into /usr/local/bin and libraries, i.e. libdin.a, --- into /usr/local/lib. This
variable is set after the -L flag to the compiler in Dinamica.
The main input from the user of Dinamica is represented by the ode-files. The
ode-file syntax in many ways resembles that of the XPPAUT .ode files (Bard
Ermentrout's program for exploring the dynamical systems, see
http://www.math.pitt.edu/~bard/xpp/xpp.html). However, there are many Dinamica
specific options, like, for example, #system directive which instructs Dinamica how
many physical coupled systems are there. See more on how to write ode-files in the
manual. To launch the program type:
dinamica <your_file>.ode
this should process the file, compile and fire up Dinamica. There are several command line options and many other things one can do with Dinamica. For those, consult the manual
Bug reports, any questions and suggestions can be sent to: [email protected]