Metadata-Version: 2.0
Name: simetuc
Version: 1.0.0
Summary: simetuc: Simulating Energy Transfer and Upconversion
Home-page: https://github.com/pedvide/simetuc
Author: Pedro Villanueva Delgado
Author-email: pedvide@gmail.com
License: MIT
Keywords: physics chemistry rate equations
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Physics
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.5
Requires-Dist: PyYAML (>=3.12)
Requires-Dist: ase (>=3.9)
Requires-Dist: colorama
Requires-Dist: h5py (>=2.6)
Requires-Dist: matplotlib (>=1.5)
Requires-Dist: numba
Requires-Dist: numpy (>=1.11)
Requires-Dist: scipy (>=0.18)
Requires-Dist: tqdm (>=4.8)
Provides-Extra: test
Requires-Dist: flake8; extra == 'test'
Requires-Dist: mypy-lang; extra == 'test'
Requires-Dist: pytest; extra == 'test'
Requires-Dist: pytest-benchmark; extra == 'test'
Requires-Dist: pytest-cov; extra == 'test'
Requires-Dist: pytest-mock; extra == 'test'
Requires-Dist: pytest-xdist; extra == 'test'
Requires-Dist: python-coveralls; extra == 'test'

simetuc
=======

Simulating Energy Transfer and Upconversion

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

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

Installation
------------

Python 3.5 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 command at the command
prompt (cmd.exe for Windows, shell for Linux and Mac):

::

    conda install -c pedvide simetuc

or

::

    pip install simetuc

That will download and install all necessary files.

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 adecuate 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 setings 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 tranfer processes are supported:

   -  Energy migration.
   -  Upconversion (ETU).
   -  Downconversion.
   -  Cross-relaxation.
   -  Cooperative processes.
   -  Energy tranfer from sensitizers to activators
   -  Back transfer from activators to sensitizers.

-  See the example `configuration file <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 can be plotted and saved in .hdf5 format.
-  For all options --average uses standard average rate equations
   instead of microscopic ones.

Documentation
-------------

See the powerpoint `presentation <docs/simetuc_presentation>`__.

TODO
----

-  [ ] Add pressure dependence option: Change the distances of the
   lattice and simulate dynamics or steady-state.
-  [ ] Read experimental data in more formats.
-  [x] Add cooperative sensitization (work in progress).
-  [ ] Include pulse frequency for steady state simulations using a non
   cw laser

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 sofware in a scientific publication, please cite the
appropiate articles above.

Acknowledgements
----------------

The financial support of the EU FP7 ITN LUMINET (Grant agreement No.
316906) is gratefully acknowledged.

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

License
-------

Copyright Pedro Villanueva Delgado, 2016.

Distributed under the terms of the `MIT <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


