iDMC

Installing iDMC on Ubuntu-linux

2009-04-15T16:42:00.002+01:00

After several requests about precise instructions on how to install iDMC on Ubuntu-linux, I finally decided to write down basic, generic instructions on how to do that. You can find it there.
It should work on any debian-based linux distribution.

Released a minor new version of iDMC

2008-07-11T15:48:00.004+01:00

As the title suggests, a minor new version of iDMC has been released. The version 2.0.10 can be download from here, and has the following changes w.r.t. version 2.0.9:

fixed legend in Lyap.exp. map plot: 'NA' instead of 'divergent'
fixed bug in trajectory initialization code
misc internal code cleaning
silent error message is reported when 'NaN' values on trajectory rendering

So, if you have some problems with trajectory plots, try out this new version.
Thanks to prof. M. Lines for suggesting point (1), and to prof. A. Medio for pointing out issue (2).

Released idmclib 0.10.0

2008-05-30T12:44:00.006+01:00

A new version of the idmclib has been released.
The API is backward compatible, so that any project using previous versions of the library can switch to this new release efforthlessy.

Beside the usual (minor) bug fixes, this release display some important changes:

added TCL bindings
added a new 'attractor' module
upgraded documentation
upgraded dependency on the 5.1.x series of the Lua library

As a demo of the capabilities of the new TCL bindings, a command line script which computes trajectories of discrete and continuous models has been added to the source distribution.
TCL bindings will allow much easier testing of old and new C code, and the eventual development of special purpose, cross-platform applications. In this respect, the Tk toolkit is also a valid option for prototyping GUIs around crude library functionalities.

The new attractor module has been added mostly for internal use, and provides data structures and methods for handling sets of arbitrary-dimensional points (which can be read, for instance, as 'attractors'), and lists of those lists of points.

Finally, some words on the Lua upgrade. Until version 0.9.0, the idmclib was based on the release 5.0.x of the Lua library. This was released on April 2003, and got last update on on 26 Jun 2006. Now development of series 5.0.x seems to be stalled, so the need to upgrade to the more recent release of the Lua library: 5.1.3. This new version has some interesting new features, is considerably easier to compile and, most important, is actively maintained.

Models archive

2008-05-13T17:20:00.003+01:00

A web space has been prepared for collecting iDMC models. Submission of models from all iDMC users is strongly encouraged.

To submit, send a message to the iDMC mailing list:
idmc-discussion_at_googlegroups_dot_com
with the lua file attached and a link to model documentation (a related paper or at least a file with model description and typical initial and parameter values). Model files are made freely available to the public under the GPLv2 license.

iDMC - version 2.0.9 released

2008-04-16T09:48:00.004+01:00

iDMC version 2.0.9 has been released.
That version sees the core numerical idmclib upgraded to version 0.9.0 (which in turn fixes a serious numerical bug affecting computation of Lyapunov exponents on systems with no jacobian information).
Fixed also a minor bug affecting trajectory plot with manual chart bounds.

iDMC - version 2.0.8 released

2008-03-24T12:47:00.002+01:00

A minor new version of iDMC has been released (previous release was on 2/11/2007).
That fixes a regression introduced in 2.0.7, causing problems in handling trajectory plots of models with more than 2 dimensions, and uses a more recent version of the idmclib (0.8.0).

Thanks again, Marji, for pointing me the bug!

RiDMC 0.9-0 released

2008-02-18T21:28:00.003+01:00

Following the recent release of the 0.9.0 version of idmclib, RiDMC 0.9-0 has been released. As usual, platform independent sources and windows binary packages can be downloaded.

This version is more a development snapshot than a milestone release. However, there are some interesting changes:

upgraded idmclib to version 0.9.0
added some as.matrix methods (now all idmc_xxx classes have an as.matrix method)
fixed (many) bugs in Trajectory, TrajectoryList, LyapunpovExponents plotting functions
added detailed LUA syntax errors reporting

Released idmclib 0.9.0

2008-02-16T16:38:00.003+01:00

A new version of the idmclib has been released.

From the change log:
- added tutorial chapter to documentation
- added intro section to documentation
- fixes and additions to documentation
- robustified IDMC_EPS_VALUE definition
- added pkg-config support
- added C++ compatibility directives to include files

The online html developers guide has been updated accordingly.

idmclib developers guide now online

2008-02-04T00:22:00.000+01:00

After some delay, I've finally put online the html version of the idmclib developers guide.
The idmclib manual is already shipped with the idmclib, and can be compiled in html and pdf format. However, potential users which might want to just give a brief look to what idmclib is can now look at the developers guide without ever downloading the source package.

Note that the published guide is relative to the latest release of the library. I will try to keep it up-to-date with future releases. However, for older/newer versions, one can always look at the distributed idmclib packages.

iDMC 3D: a demo C++ application which uses the idmclib

2008-01-18T15:05:00.000+01:00

I've written from scratch a new application, tentativly called iDMC-3D, a demo application based on the idmclib, largely inspired by iDMC, which lets you visualize trajectories of continuous-time dynamical systems in a 3D space. You can download the win32 binary package here, and package sources with compiling instructions here. It doesn't require Java or something else, so windows users can just unzip on their desktop and launch the binary 'idmc.exe'.

The application is essentially GUI and some logic, and uses the powerful, small and fast FOX library for cross-platform GUI building and OpenGL handling.

This application is to be intended as just a demo: is likely to be full of bugs, but working correctly with shipped models in most common situations. Moreover, it isn't officially supported by anyone, even if I appreciate feedback, comments and suggestions. Note that this is my first FOX application, as well as my first C++ program after a couple of years, so please be gentle in reviewing the sources:-)

Lets see how it works with a couple of screenshots...

This is how it looks when started on my linux box:

After opening a model (here the Rossler model), a new subordinate window pops up:

Now we can compute a trajectory:

Feed in sensible starting values, parameters, time span (in time units), transient and step size to be used in numerical integration:
After clicking 'Ok', you can watch the result:
You can interactively drag with the mouse pointer to rotate, right-click for the above shown menu, mouse wheel for zooming.
On the left side, you can choose which variables to show. Here the model has just 3 variables, named 'x','y' and 'z', so not many options. But you can always include the time axis in the plot:

That's all. Have fun!

Released RiDMC 0.8-2

2007-12-01T17:13:00.000+01:00

I have rolled up a new version of RiDMC some moments ago.

In this version, all plotting functions have been completely redesigned, for allowing easier plot customization. The online demo has been updated accordingly.
Here an example adapted from the Basin man page:

m <- Model(exModelFile('henon'))
b1 <- Basin(m, c(1.42,0.3), c(-2,2), 200, c(-2, 2), 200, 1000, 1000)
plot(b1, legend=TRUE)

Among other things, package source size have been reduced considerably (from 2.5Mb to 842Kb), and the configure script (needed on *nix platforms) slightly robustified.

Released RiDMC 0.8-0

2007-11-24T16:06:00.000+01:00

As already anticipated, I've released a new version of RiDMC, which now depends on idmclib-0.8.0. There are no important changes for the end user.

Packages sources and windows binaries can be downloaded here.

Released a new version of idmclib

2007-11-16T21:41:00.000+01:00

A new version of the idmclib (version 0.8.0) have just been released. You can grab it from the usual place.
This new version now depends on GSL version >= 1.9 (instead of 1.7).
This version of the GSL library finally have functions for the computation of eigenvalues of real nonsymmetric matrices. This frees idmclib from the need of Fortran LAPACK code for this specific task.

So, what does this means in practice?
To the end user of the idmclib library, nothing, except that now a different algorithm is used for jacobian eigenvalues computation in the periodic cycles routine.
For anyone who wants to compile idmclib on his platform, means that you don't need a fortran compiler anymore: CMake + gcc will be enough!

This change should facilitate redistribution of idmclib, and its use in other projects.
I'm already working on upgrading RiDMC to this new version of the idmclib. Then will be the turn of the stand-alone iDMC.

iDMC - version 2.0.7 released

2007-11-02T12:21:00.000+01:00

A minor new version of iDMC has been released.
For the end user, this fixes a bug pointed out by some Marji Lines students: in trajectory plots, when using the 'automatic bounds' option, you get an incorrect starting value in the plot.
Here an example with the Solow model (sample model in 'Economic' folder).
With 2.0.6 you get:
With 2.0.7:

2007-10-07T21:55:00.000+01:00

iDMC, version 2.0.6 has been released.

This is a minor release, with bugfixes:

fixed bug in trajectory plot when 'Variation' option activated
fixed Lyapunov exponents plot in parameters space when there are diverging exponents
now there is one installer file working for both windows and linux

Here's a screenshot related to point 1:

As usual, you can download the installer from here, and report bugs to
idmc-discussion _at_ googlegroups.com

iDMC - version 2.0.5 released

2007-07-11T12:42:00.000+01:00

iDMC, version 2.0.5 has been released.

The most evident change, is the new cross-platform java installer:

This works under Windows and Linux-i386.
Some other changes w.r.t. version 2.0.4:

internal code cleaning
removed broken ODE solver option from trajectory plot
fixed 'Save Data as...' menu item enabling/disabling, improved related error messages
upgraded idmclib to version 0.7.0
idmclib version number retrieved at runtime

Report bugs to project mailing list: idmc-discussion _at_ googlegroups.com.

iDMC sources again online

2007-07-09T10:55:00.000+01:00

iDMC, idmclib and RiDMC sources have been moved on repo.or.cz.
Here you can keep track of projects development, as well as make contributions.

By the way, googlecode source repository service is no more used.
Many reasons for that, the most important: now I can work offline, and publish changes from time to time.

Now you can get a full copy of the iDMC repository by:
$ git clone http://repo.or.cz/r/iDMC.git
Similar commands for idmclib and RiDMC.

idmclib and RiDMC 0.7.0

2007-07-07T09:39:00.000+01:00

A new version of idmclib and of RiDMC have been released.
They're both named 0.7.0.

idmclib has a bug fix in the new 'slow' basin algorithm and improved and cleaned dynamic version info retrievial functions. This lets other software (i.e. idmclib and RiDMC) getting idmclib version number at runtime.

RiDMC has many improvements. Among others:

cleaned and unified continuous and discrete trajectory functions in one generic function
added more details in package man pages
GUI dialog for selection of sample model file
better interface for customizing basins of attraction plot

The online demo has been upgraded accordingly. Download and enjoy it!

Static linux binary released

2007-06-22T12:31:00.000+01:00

I've released the Linux static binary of iDMC-2.0.4, for i386, 32bit systems.

This has no external dependencies so, if you have Sun Java 6, you can run it by typing from a shell prompt:

tar xjf iDmc-2.0.4-linux-i386-32.tar.bz2
cd iDmc-2.0.4
java -jar iDmc-2.0.4.jar

As usual, you can download it from the downloads section.

New BoA algorithm for idmclib and RiDMC

2007-06-15T13:59:00.000+01:00

First of all, the news: idmclib-0.6.0 and RiDMC-0.6-0 released. They can be downloaded from the downloads section of the idmclib home page.

Special thanks to Marji Lines who, after trying out RiDMC-0.5-3, pointed out that there are interesting cases where the 'fast' BoA (Basins of Attraction) algorithm provided by idmclib simply doesn't work at all.

Following her suggestions, the slower (but sometimes more precise) algorithm already developed in the stand-alone version of iDMC has been added to the idmclib C library .

In brief, the main difference w.r.t. the faster algorithm is that there is a preliminary phase where all attractors are found, before actual plotting.

Now idmclib has a small set of new function dedicated to the new BoA algorithm, while the RiDMC package has been uppgraded accordingly, by adding 3 more options to the Basin R function. A nice example has been added to the Basin help page to illustrate this change. Have fun with it!

RiDMC demo online

2007-06-11T20:09:00.000+01:00

I've just put online a short demo of the (work-in-progress) RiDMC R package.
It's based on RiDMC version 0.5-3, which can be downloaded from the downloads section of the idmclib project website.

Note for non-windows users: for compiling RiDMC, you will need lua-5.0 and gsl-1.8 (or compatible) development libraries available on your system.

Started development of RiDMC

2007-05-28T15:11:00.000+01:00

Dear all,
I've started the development of RiDMC, an R package which will bring idmclib capabilities to R users.
A first source development snapshot can be downloaded from here.

Have fun with RiDMC!

Uploaded a new linux binary of iDMC

2007-04-15T09:52:00.000+01:00

I've uploaded a new linux binary version of iDMC, named '2.0.5-preview'.
You can download it here.

It's a 'preview', just for keeping linux users up-to-date with recent additions made to iDMC (last official linux release was on 21/01/07). With this 'preview', linux users are aligned with windows ones.

Released idmclib 0.5.0

2007-04-13T14:35:00.000+01:00

Dear all,
a new version of the idmclib library was just released.
It has no relevant changes in its contents w.r.t. previous releases, but introduces the use of a new cross-platform build system: CMake.
Now, especially on linux systems, compiling idmclib should be as easy as typing:

# cmake .
# make

from the shell prompt. This should ease a lot the distribution of idmclib (and, consequently, iDMC) on a wide variety of platforms, for which no official binaries are distributed.

In all that, no differences will be seen by the final user.
By the way, next iDMC releases will start using this new version of the idmclib support library.

Released RTisean 3.0-7

2007-03-23T15:16:00.000+01:00

As anticipated some days ago, I've found the time to release a new version of RTisean compatible with the latest TISEAN version. It should be on CRAN in a few hours. Enjoy it!

TISEAN 3.0.0 is out!

2007-03-08T09:39:00.000+01:00

After more than 6 years from the last upgrade, a new TISEAN version was released last 22 february! Many thanks to all the TISEAN developers for continuing their work on it. You can see more about it from the project web site.

Among others, the most relevant changes are:

now the software is explicitely GPL-ed
more functions handling multivariate data
some general code cleaning, bug fixing

I'm currently working on the RTisean R package for making it compatible with this new release.

released iDMC-2.0.4 and idmclib-0.4.0

2007-03-03T12:05:00.000+01:00

A new version of iDMC (2.0.4) and of the idmclib library (0.4.0) have been released.

The idmclib library introduces some important fixes:

runtime error messages are now much more detailed (with line number reference)
R and Java interface have been upgraded accordingly
RNG seed can now be set from the R interface

The new iDMC version has a bug fix (see issue 5) and the upgrade to the new idmclib version.

iDMC - version 2.0.3 released

2007-02-23T18:32:00.000+01:00

A new minor version (2.0.3) of iDMC was released. Package sources and windows binaries are available in the downloads section of the project web site.

This new release fixes some plotting bugs, and improves a little lua errors reporting to the user (see issues 2, 3 and 4).

Especially for making the last improvement possible, a new idmclib version (0.3.0) is used.

Static 32 and 64bit linux released

2007-01-21T17:22:00.000+01:00

Working static binary packages of the 2.0.2 version have been just uploaded. The cited bug disappeared when re-packing the jar file with the 32bit version of the jdk...

Bug in 32bit linux binary

2007-01-20T22:44:00.000+01:00

A subtle bug (which causes a jvm crash) was just discovered in the last version of the native binary of iDMC, affecting linux systems running the 32bit JRE distributed by SUN.

I will try to detect where the problem is. In the meanwhile, I've uploaded a 32bit-linux binary package of the 'old' 1.10.3 release, which is working as usual.

iDMC - blog started

2007-01-19T18:46:00.000+01:00

Dear reader,
this blog was started now for publishing news and comments about the iDMC software.

Hope this will be useful.