simetuc

Simulating Energy Transfer and Upconversion

Installation

Python 3.6 is required. Installing Anaconda <https://www.continuum.io/downloads>__ is recommended; it works with Windows (64/32 bits), Linux (64/32 bits) and Mac (64 bits).

After installing Anaconda execute the following commands at the command prompt (cmd.exe for Windows, shell for Linux and Mac):

::

conda config --add channels conda-forge
conda config --add channels pedvide
conda install simetuc
pip install settings_parser

(The first two commands add packages repositories with up-to-date versions of all needed packages.)

or

::

pip install simetuc

That will download and install all necessary files.

Note: Some OSX users report problems using conda, if after installing you can't use the program (i.e., simetuc -h fails because simetuc wasn't recognized as a command), use pip install simetuc

Update ~~~~~~

If you installed it using conda, update with:

::

conda update simetuc

If you installed it with pip, update with:

::

pip install -U simetuc

Features

Command line interface program.
- Run with: simetuc config_file.txt [options]
- See all options below and with: simetuc -h
The simulations are controlled by a configuration text file that the user can edit with the parameters adequate to its system of study. It includes:
- Information about the host lattice.
- Energy states labels.
- Absorption and excitation (including ESA).
- Decay (including branching ratios).
- Energy transfer.
- Other settings for the power and concentration dependence or optimization.
simetuc works with any sensitizer and activator ion kind.
- The examples are given for the Yb-Tm system.
All kinds of energy transfer processes are supported:
- Energy migration.
- Upconversion (ETU).
- Downconversion.
- Cross-relaxation.
- Cooperative processes.
- Energy transfer from sensitizers to activators.
- Back transfer from activators to sensitizers.
See the example configuration file <https://github.com/pedvide/simetuc/blob/master/simetuc/config_file.cfg>__ in the simetuc folder.
Add decay experimental data as two column text data, separated by tabs or spaces.
Different options:
- Create the lattice.
- Simulate the dynamics (rise and decay).
- Optimize the energy transfer parameters.
  - Minimize the deviation between experiment and simulation.
- Simulate the steady state.
- Simulate the power dependence of each emission.
- Simulate the concentration dependence of the dynamics or the steady state.
All results are plotted and saved in the .hdf5 format. A summary of the results is saved as a text file.
For all options --average uses standard average rate equations instead of microscopic ones.

Documentation

See the manual <https://github.com/pedvide/simetuc/blob/master/docs/manual/simetuc_user_manual.pdf>__.

TODO

[ ] Add pressure dependence option: Change the distances of the lattice and simulate dynamics or steady-state.
[ ] Read experimental data in more formats.

Bugs/Requests

Please use the GitHub issue tracker <https://github.com/pedvide/simetuc/issues>__ to submit bugs or request features.

Publications

This software has been described and used in these publications:

Villanueva-Delgado, P.; KrÃ¤mer, K. W. & Valiente, R. Simulating Energy Transfer and Upconversion in Î²-NaYF4: Yb3+, Tm3+ <http://pubs.acs.org/doi/10.1021/acs.jpcc.5b06770>__
Villanueva-Delgado, P.; KrÃ¤mer, K. W.; Valiente, R.; de Jong, M. & Meijerink, A. Modeling Blue to UV Upconversion in Î²-NaYF4: Tm3+ <http://pubs.rsc.org/en/Content/ArticleLanding/2016/CP/C6CP04347J#!divAbstract>__

If you use this software in a scientific publication, please cite the appropriate articles above.

Acknowledgments

The financial support of the EU FP7 ITN LUMINET (Grant agreement No. 316906) and the SNSF (grant number: P2BEP2_172238) are gratefully acknowledged.

This work was started at the University of Cantabria under Prof. Rafael Valiente, continued at the University of Bern under PD Dr. Karl KrÃ¤mer and then at the Utrecht University under Prof. Andries Meijerink.

License

Copyright Pedro Villanueva Delgado, 2016-2017.

Distributed under the terms of the MIT <https://github.com/pedvide/simetuc/blob/master/LICENSE.txt>__ license, simetuc is free and open source software.

.. |License| image:: https://img.shields.io/github/license/pedvide/simetuc.svg :target: https://github.com/pedvide/simetuc/blob/master/LICENSE.txt .. |Python version| image:: https://img.shields.io/pypi/pyversions/simetuc.svg :target: https://pypi.python.org/pypi/simetuc .. |Pypi version| image:: https://img.shields.io/pypi/v/simetuc.svg :target: https://pypi.python.org/pypi/simetuc .. |Anaconda version| image:: https://anaconda.org/pedvide/simetuc/badges/version.svg :target: https://anaconda.org/pedvide/simetuc .. |Build Status| image:: https://travis-ci.org/pedvide/simetuc.svg?branch=master :target: https://travis-ci.org/pedvide/simetuc .. |Coverage Status| image:: https://coveralls.io/repos/github/pedvide/simetuc/badge.svg?branch=master :target: https://coveralls.io/github/pedvide/simetuc?branch=master