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https://github.com/mhoffman/kmos
kMC on steroids: A vigorous attempt to make lattice kinetic Monte Carlo modelling easier
https://github.com/mhoffman/kmos
Last synced: about 2 months ago
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kMC on steroids: A vigorous attempt to make lattice kinetic Monte Carlo modelling easier
- Host: GitHub
- URL: https://github.com/mhoffman/kmos
- Owner: mhoffman
- License: gpl-3.0
- Created: 2010-10-16T17:46:21.000Z (almost 14 years ago)
- Default Branch: master
- Last Pushed: 2018-04-30T20:28:15.000Z (over 6 years ago)
- Last Synced: 2024-07-14T14:42:56.303Z (2 months ago)
- Language: Fortran
- Homepage: http://mhoffman.github.com/kmos/
- Size: 15.7 MB
- Stars: 54
- Watchers: 14
- Forks: 34
- Open Issues: 21
-
Metadata Files:
- Readme: README.rst
- Contributing: .github/CONTRIBUTING.md
- License: COPYING
Awesome Lists containing this project
README
.. image:: https://travis-ci.org/mhoffman/kmos.png?branch=master
:target: https://travis-ci.org/mhoffman/kmos
.. image:: https://img.shields.io/badge/license-GPLv3-brightgreen.svg?style=flat-square)
:target COPYING
.. image:: https://readthedocs.org/projects/kmos/badge/?version=latest
:target: http://kmos.readthedocs.org/en/latest/?badge=latest
:alt: Documentation Status
.. image:: https://badges.gitter.im/mhoffman/kmos.svg
:alt: Join the chat at https://gitter.im/mhoffman/kmos
:target: https://gitter.im/mhoffman/kmos?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
kmos: kMC modelling on steroids
=====================================
*a vigorous attempt to make lattice kinetic Monte Carlo modelling more accessible.*
Copyright (C) 2009-13 Max J. Hoffmann
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 = [email protected]
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
#####
| ├── 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