simetuc: Simulating Energy Transfer and Upconversion
Simulating Energy Transfer and Upconversion
Python 3.6 is required. Installing Anaconda 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.)
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
If you installed it using conda, update with:
conda update simetuc
If you installed it with pip, update with:
pip install -U simetuc
- 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
- 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).
- Cooperative processes.
- Energy transfer from sensitizers to activators.
- Back transfer from activators to sensitizers.
- See the example configuration file 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.
- For all options --average uses standard average rate equations instead of microscopic ones.
See the manual.
- [ ] Add pressure dependence option: Change the distances of the lattice and simulate dynamics or steady-state.
- [ ] Read experimental data in more formats.
Please use the GitHub issue tracker to submit bugs or request features.
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+
- Villanueva-Delgado, P.; KrÃ¤mer, K. W.; Valiente, R.; de Jong, M. & Meijerink, A. Modeling Blue to UV Upconversion in Î²-NaYF4: Tm3+
If you use this software in a scientific publication, please cite the appropriate articles above.
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.
Copyright Pedro Villanueva Delgado, 2016-2017.
Distributed under the terms of the MIT license, simetuc is free and open source software.
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