python-kmos 0.3.9

kMC modeling on steroids

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

Copyright (C) 2009-13 Max J. Hoffmann <[e-mail]>

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/.

DOCUMENTATION

Please refer to

• https://www.th4.ch.tum.de/index.php?id=1321

• http://mhoffman.github.io/kmos/

• http://kmos.readthedocs.org/

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

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

├── COPYING # Copy of GPLv3

├── INSTALL.rst # installation instructions

├── README.rst # This document

├── TODO.rst # Ideas for improvement and new features

├── requirements.txt # Dependencies which can be installed via pip

├── setup.py # setuptools using setup script

├── index.html # landing website

├── kmos/ # the core kmos python modules

│   ├── cli.py # the command line interface

│   ├── config.py # configuration of some project wide paths

│   ├── fortran_src/ # static Fortran 90 source files

│   │   ├── assert.ppc # assertion macro

│   │   ├── base.f90 # the default kMC solver

│   │   ├── base_lat_int.f90 # slightly modified kMC solver for lat_int backend

│   │   ├── kind_values.f90 # definition of project wide kind values

│   │   └── main.f90 # source template for standalone Fortran 90 clients

│   ├── gui/ # kmos.gui module

│   │   ├── forms.py # view definitions (MVC) of editor GUI

│   │   └── __init__.py # controller definitions (MVC) of editor GUI

│   ├── __init__.py # root import module

│   ├── io.py # conversion between format: contains main Code Generator

│   ├── kmc_editor.glade # Glade XML definiton for form interfaces

│   ├── kmc_project_v0.1.dtd # Document Type Definition file of kMC project v0.1

│   ├── kmc_project_v0.2.dtd # Document Type Definition file of kMC project v0.2

│   ├── run.py # High-level API for compiled models

│   ├── species.py # Convenient interface for some reaction intermediates

│   ├── types.py # The basic classes for building kMC models

│   ├── units.py # Definition of conversion factor (CODATA 2010)

│   ├── utils/ # Utility function that didn’t fit elsewhere

│   │   ├── __init__.py

│   │   ├── ordered_dict.py

│   │   ├── progressbar.py

│   │   └── terminal.py

│   └── view.py # The runtime GUI for compiled models

├── doc/ # user guide, documentation, and reference

│   └── source/ # documentation source file for compilation with Sphinx

├── examples/ # demoing non-standard features and useful idioms

│   ├── AB_model.py # small demo file

│   ├── benchmark_compilers_and_backends.sh # demo file

│   ├── crowded.xml # demo file

│   ├── dreiD.xml # demo file for 3d model

│   ├── dummy.xml # mininal model

│   ├── model_Pt111_surface.py # demo file for non-rectangular lattice

│   ├── multidentate.py # basic example for multidentate adsorption

│   ├── render_bigcell.py # demo containing many sites

│   ├── render_co_oxidation_ruo2.py # demoing th CO Oxidation at RuO2(110) model

│   ├── render_diffusion_model.py # idioms for describing lateral interaction

│   ├── render_einsD.py # simple 1-dimensional model

│   ├── render_multispecies.py # render many species

│   ├── render_pairwise_interaction.py # idioms for describing lateral interaction

│   ├── render_Pt_111.py # another non-rectangular lattice

│   ├── render_sand_model.py # a neat diffusion model for non-trivial boundary conditions

│   ├── run_in_multi_process.py # an example for parallelization over processes

│   ├── run.py # a high-level run script using the ModelRunner metaclass

│   ├── ruptured_Pd.xml # a fcc(100) like surface with some sites missing

│   └── small.xml # demo file

├── tests/ # Unit tests and test data

└── tools # Entry points for command line interface

├── kmos

├── kmos.bat

├── kmos-build-standalone

└── kmos-install-dependencies-ubuntu