Package: kmcos
kmcos: Kinetic Monte Carlo of Systemskmcos is designed for lattice based Kinetic Monte Carlo simulations to understand chemical kinetics and mechanisms. It has been used to produce more than 10 scientific publications. Links to tutorials and other documentation are below.DOCUMENTATIONPlease refer toDocumentation (including installation):http://kmcos.readthedocs.org/Exampleshttps://github.com/kmcos/kmcos/tree/master/examplesWorkshop files:https://github.com/kmcos/intro2kmcos[the later part of the document are for advanced users and may require an instructor]HELP, BUGS, ISSUES, TROUBLEThis 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 themailing list, or open anissue.CONTRIBUTORSCurrent Project Leaders:Karsten ReuterAditya (Ashi) SavaraCreator:Max J. HoffmannDevelopers:Sebastian MateraJuan M. LorenziMie AndersenMichal BajdichAndreas GarhammerOther:
* Martin Deimel
* Thomas Danielson
* Jonathan Sutton
* Joseba Alberdi
* Steve Erwin & NB
* Meelod WaheedTHANKSThis project draws on several other great Python modules, which are in turn
each free software and we would like to thank each of these projects for
making their code freely avalaible, namely:PythonASENumpyf2pykiwi, gazpacholxml and in particularElementTreeFILESâ”œâ”€â”€ COPYING                                      # Copy of GPLv3â”œâ”€â”€ INSTALL.rst                                  # installation instructionsâ”œâ”€â”€ README.rst                                   # This documentâ”œâ”€â”€ TODO.rst                                     # Ideas for improvement and new featuresâ”œâ”€â”€ requirements.txt                             # Dependencies which can be installed via pipâ”œâ”€â”€ setup.py                                     # setuptools using setup scriptâ”œâ”€â”€ index.html                                   # landing websiteâ”œâ”€â”€ kmcos/                                        # the core kmcos python modulesâ”‚Â Â  â”œâ”€â”€ cli.py                                   # the command line interfaceâ”‚Â Â  â”œâ”€â”€ config.py                                # configuration of some project wide pathsâ”‚Â Â  â”œâ”€â”€ fortran_src/                             # static Fortran 90 source filesâ”‚Â Â  â”‚Â Â  â”œâ”€â”€ assert.ppc                           # assertion macroâ”‚Â Â  â”‚Â Â  â”œâ”€â”€ base.f90                             # the default kMC solverâ”‚Â Â  â”‚Â Â  â”œâ”€â”€ base_lat_int.f90                     # slightly modified kMC solver for lat_int backendâ”‚Â Â  â”‚Â Â  â”œâ”€â”€ kind_values.f90                      # definition of project wide kind valuesâ”‚Â Â  â”‚Â Â  â””â”€â”€ main.f90                             # source template for standalone Fortran 90 clientsâ”‚Â Â  â”œâ”€â”€ gui/                                     # kmcos.gui moduleâ”‚Â Â  â”‚Â Â  â”œâ”€â”€ forms.py                             # view definitions (MVC) of editor GUIâ”‚Â Â  â”‚Â Â  â””â”€â”€ __init__.py                          # controller definitions (MVC) of editor GUIâ”‚Â Â  â”œâ”€â”€ __init__.py                              # root import moduleâ”‚Â Â  â”œâ”€â”€ io.py                                    # conversion between format: contains main Code Generatorâ”‚Â Â  â”œâ”€â”€ kmc_editor.glade                         # Glade XML definiton for form interfacesâ”‚Â Â  â”œâ”€â”€ kmc_project_v0.1.dtd                     # Document Type Definition file of kMC project v0.1â”‚Â Â  â”œâ”€â”€ kmc_project_v0.2.dtd                     # Document Type Definition file of kMC project v0.2â”‚Â Â  â”œâ”€â”€ run.py                                   # High-level API for compiled modelsâ”‚Â Â  â”œâ”€â”€ species.py                               # Convenient interface for some reaction intermediatesâ”‚Â Â  â”œâ”€â”€ types.py                                 # The basic classes for building kMC modelsâ”‚Â Â  â”œâ”€â”€ units.py                                 # Definition of conversion factor (CODATA 2010)â”‚Â Â  â”œâ”€â”€ utils/                                   # Utility function that didn’t fit elsewhereâ”‚Â Â  â”‚Â Â  â”œâ”€â”€ __init__.pyâ”‚Â Â  â”‚Â Â  â”œâ”€â”€ ordered_dict.pyâ”‚Â Â  â”‚Â Â  â”œâ”€â”€ progressbar.pyâ”‚Â Â  â”‚Â Â  â””â”€â”€ terminal.pyâ”‚Â Â  â””â”€â”€ view.py                                  # The runtime GUI for compiled modelsâ”œâ”€â”€ doc/                                         # user guide, documentation, and referenceâ”‚Â Â  â””â”€â”€ source/                                  # documentation source file for compilation with Sphinxâ”œâ”€â”€ examples/                                    # demoing non-standard features and useful idiomsâ”‚Â Â  â”œâ”€â”€ AB_model.py                              # small demo fileâ”‚Â Â  â”œâ”€â”€ benchmark_compilers_and_backends.sh      # demo fileâ”‚Â Â  â”œâ”€â”€ crowded.xml                              # demo fileâ”‚Â Â  â”œâ”€â”€ dreiD.xml                                # demo file for 3d modelâ”‚Â Â  â”œâ”€â”€ dummy.xml                                # mininal modelâ”‚Â Â  â”œâ”€â”€ model_Pt111_surface.py                   # demo file for non-rectangular latticeâ”‚Â Â  â”œâ”€â”€ multidentate.py                          # basic example for multidentate adsorptionâ”‚Â Â  â”œâ”€â”€ render_bigcell.py                        # demo containing many sitesâ”‚Â Â  â”œâ”€â”€ render_co_oxidation_ruo2.py              # demoing th CO Oxidation at RuO2(110) modelâ”‚Â Â  â”œâ”€â”€ render_diffusion_model.py                # idioms for describing lateral interactionâ”‚Â Â  â”œâ”€â”€ render_einsD.py                          # simple 1-dimensional modelâ”‚Â Â  â”œâ”€â”€ render_multispecies.py                   # render many speciesâ”‚Â Â  â”œâ”€â”€ render_pairwise_interaction.py           # idioms for describing lateral interactionâ”‚Â Â  â”œâ”€â”€ render_Pt_111.py                         # another non-rectangular latticeâ”‚Â Â  â”œâ”€â”€ render_sand_model.py                     # a neat diffusion model for non-trivial boundary conditionsâ”‚Â Â  â”œâ”€â”€ run_in_multi_process.py                  # an example for parallelization over processesâ”‚Â Â  â”œâ”€â”€ run.py                                   # a high-level run script using the ModelRunner metaclassâ”‚Â Â  â”œâ”€â”€ ruptured_Pd.xml                          # a fcc(100) like surface with some sites missingâ”‚Â Â  â””â”€â”€ small.xml                                # demo fileâ”œâ”€â”€ tests/                                       # Unit tests and test dataâ”œâ”€â”€ tools                                        # Entry points for command line interfaceâ”‚Â Â  â”œâ”€â”€ kmcosâ”‚Â Â  â”œâ”€â”€ kmcos.batâ”‚Â Â  â”œâ”€â”€ kmcos-build-standaloneâ”‚Â Â  â””â”€â”€ kmcos-install-dependencies-ubuntuCOPYRIGHT AND LICENSECopyright (C) 2009-13 Max J. HoffmannThis 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, seehttp://www.gnu.org/licenses/.