https://github.com/pedvide/simetuc

Simulating Energy Transfer and Upconversion
https://github.com/pedvide/simetuc

anaconda chemistry physics physics-simulation python simulation

Last synced: 3 months ago
JSON representation

Simulating Energy Transfer and Upconversion

• Host: GitHub
• URL: https://github.com/pedvide/simetuc
• Owner: pedvide
• License: mit
• Created: 2016-11-01T15:04:34.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2018-07-26T16:36:51.000Z (almost 8 years ago)
• Last Synced: 2025-12-15T08:55:21.405Z (6 months ago)
• Topics: anaconda, chemistry, physics, physics-simulation, python, simulation
• Language: Python
• Size: 36.8 MB
• Stars: 4
• Watchers: 1
• Forks: 1
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

Awesome Lists containing this project

README

          
# simetuc

Simulating Energy Transfer and Upconversion

------

[![License](https://img.shields.io/github/license/pedvide/simetuc.svg)](https://github.com/pedvide/simetuc/blob/master/LICENSE.txt)

[![Python version](https://img.shields.io/pypi/pyversions/simetuc.svg)](https://pypi.python.org/pypi/simetuc)

[![Pypi version](https://img.shields.io/pypi/v/simetuc.svg)](https://pypi.python.org/pypi/simetuc)

[![Anaconda version](https://anaconda.org/pedvide/simetuc/badges/version.svg)](https://anaconda.org/pedvide/simetuc)

[![Build Status](https://travis-ci.org/pedvide/simetuc.svg?branch=master)](https://travis-ci.org/pedvide/simetuc)

[![Coverage Status](https://coveralls.io/repos/github/pedvide/simetuc/badge.svg?branch=master)](https://coveralls.io/github/pedvide/simetuc?branch=master)

## 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](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](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.; Krämer, K. W. & Valiente, R. [Simulating Energy Transfer and Upconversion in β-NaYF4: Yb3+, Tm3+](http://pubs.acs.org/doi/10.1021/acs.jpcc.5b06770)

 - Villanueva-Delgado, P.; Krämer, K. W.; Valiente, R.; de Jong, M. & Meijerink, A. [Modeling Blue to UV Upconversion in β-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 Krämer and then at the Utrecht University under Prof. Andries Meijerink.

## License

Copyright Pedro Villanueva Delgado, 2016-2018.

Distributed under the terms of the [MIT](LICENSE.txt) license, simetuc is free and open source software.