simetuc 1.8.2
simetuc: Simulating Energy Transfer and Upconversion
License: MIT
Keywords: physics chemistry rate equations

simetuc
=======

Simulating Energy Transfer and Upconversion

--------------

|License| |Python version| |Pypi version| |Anaconda version| |Build
Status| |Coverage Status|

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 (Use "Anaconda Prompt" 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, 2016-2018.

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