Metadata-Version: 2.1
Name: simetuc
Version: 1.8.2
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
Description: 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
        
Keywords: physics chemistry rate equations
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
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 :: 3.6
Provides-Extra: test
