kmos: kMC modelling on steroids

a vigorous attempt to make lattice kinetic Monte Carlo modelling more accessible.

Copyright (C) 2009-13 Max J. Hoffmann <mjhoffmann@gmail.com>

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, see http://www.gnu.org/licenses/.

QUICKSTART

Prepare a minimal input file with the following content and save it as mini_101.ini

[Meta]
author = Your Name
email = you@server.com
model_dimension = 2
model_name = fcc_100

[Species empty]
color = #FFFFFF

[Species CO]
representation = Atoms("CO", [[0, 0, 0], [0, 0, 1.17]])
color = #FF0000

[Lattice]
cell_size = 3.5 3.5 10.0

[Layer simple_cubic]
site hollow = (0.5, 0.5, 0.5)
color = #FFFFFF

[Parameter k_CO_ads]
value = 100
adjustable = True
min = 1
max = 1e13
scale = log

[Parameter k_CO_des]
value = 100
adjustable = True
min = 1
max = 1e13
scale = log

[Process CO_ads]
rate_constant = k_CO_ads
conditions = empty@hollow
actions = CO@hollow
tof_count = {'adsorption':1}

[Process CO_des]
rate_constant = k_CO_des
conditions = CO@hollow
actions = empty@hollow
tof_count = {'desorption':1}

In the same directory run kmos export mini_101.ini. You should now have a folder mini_101_local_smart in the same directory. cd into it and run kmos benchmark. If everything went well you should see something like

Using the [local_smart] backend.
1000000 steps took 1.51 seconds
Or 6.62e+05 steps/s

In the same directory try running kmos view to watch the model run or fire up kmos shell to interact with the model interactively. Explore more commands with kmos help and please refer to the documentation how to build complex model and evaluate them systematically. To test all bells and whistles try kmos edit mini_101.ini and inspect the model visually.

DOCUMENTATION

Please refer to

• https://www.th4.ch.tum.de/index.php?id=1321
• http://mhoffman.github.io/kmos/
• http://kmos.readthedocs.org/
• https://github.com/jmlorenzi/intro2kmos

or links therein for tutorials, user guide, reference, and troubleshooting hints.

BUGS, ISSUES, TROUBLE

This code is research code for scientists by scientists. If you believe you have hit a bug, have a feature request get in touch with us either via the mailing list, Gitter, or open an issue .

THANKS

This project draws on several other great Python modules, which are in turn each free software and I would like to thank each of these projects for making their code freely avalaible, namely:

• Python
• ASE
• Numpy
• f2py
• kiwi, gazpacho
• lxml and in particular ElementTree

FILES