Package: simetuc
Simulating Energy Transfer and UpconversionInstallationPython 3.6 is required. InstallingAnacondais 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.)orpip install simetucThat 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-hfails because simetuc
wasn’t recognized as a command), usepip install simetucUpdateIf you installed it using conda, update with:conda update simetucIf you installed it with pip, update with:pip install -U simetucFeaturesCommand line interface program.Run with:simetuc config_file.txt [options]See all options below and with:simetuc-hThe 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 exampleconfiguration filein
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--averageuses standard average rate equations
instead of microscopic ones.DocumentationSee themanual.TODO[ ] Add pressure dependence option: Change the distances of the
lattice and simulate dynamics or steady-state.[ ] Read experimental data in more formats.Bugs/RequestsPlease use theGitHub issue
trackerto submit bugs or
request features.PublicationsThis 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.AcknowledgmentsThe 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.LicenseCopyright Pedro Villanueva Delgado, 2016-2018.Distributed under the terms of theMITlicense,
simetuc is free and open source software.