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INSTALL

For core functionality and tutorials you can simply install via

python setup.py install

or

python setup.py install --user

in order to install without admin rights. Please refer to the Manual for further instructions.

DEPENDENCIES

In general this framework has been developed and tested on Ubuntu 9.04-12.04 in conjunction with both gfortran and ifort. So things will most likely work best under a similar setup. Other than standard libraries you most likely need to fetch:

Optional (GUI Editor):

All kMC models can be built, compiled, and executed without using the GUI editor. However the GUI editor can be quite useful for spotting logical error in process definitions as models grow more complex.

  • python-gtk2: GUI toolkit

  • python-pygoocanvas

  • python-kiwi, gazpacho: frameworks for python-gtk kiwi is currently available from many repositories Unfortunately the development of gazpacho has been discontinued. If you are using an apt based distribution system you can download the last available package from

    http://packages.debian.org/squezze/all/gazpacho/download

    and install it with

    sudo dpkg -i gazpacho_*.deb

TEST INPUT

Running a minimal test case to check whether the installation was successful includes

  • Change to the examples directory

    cd examples

  • Execute the ZGB Model render script

    ./render ZGB_model.py

  • Export the Fortran90 source code and compile in one step from the generated XML file

    kmos export ZGB_model.xml

  • Change to the export directory

    cd ZGB_model_local_smart

  • Run benchmark

    kmos benchmark

If everything is working you should see the single-core CPU time to run 1 mio. steps printed on STDOUT.

GETTING STARTED

Before creating any models of your own you might take look around the examples folder and try playing with the models already specified there. Instead of kmos benchmark, try

kmos view

on an exported model and observe how it behaves for different conditions.

Create a model XML file as explained in the Tutorials or alternatively (and optionally) inspect and change it with

kmos edit [<xml-file>]

Both ways will give a XML file that contains the entire definition of your kMC model. Run

kmos export <xml-file>

and you will find a new folder under the same name with the compiled model and self-contained source code. Inside that directory run

kmos view

and readily watch your model and manipulate parameters at the same time.

For other ways of running models interactively or scripted please refer to the tutorial