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SimEMTher: I wrote this software in Matlab to solve problems of bio-heat propagation in two-dimensions. It has a graphical user interface but it not maintained anymore. License GNU GPL V3.
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MEFiSToTM Electromagnetic Simulations: Commercial software to solve 2D and 3D electromagnetic scattering problems using TLM. The 2D version (MEFiSTo-2D Classic) can be obtained free of charge. This software does not seem to be maintained anymore.
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emGine: Free for non-commercial purposes, emGine solves time-domain full-wave 3D electromagnetic problems. It does not seem to be maintained anymore (last version is from 2011 and the last website updated was in 2014). Tri-license MPL/GPL/LGPL.
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CST TLM solver: Active commercial software that provides the TLM solver for electromagnetic simulations.
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Transmission Line Matrix for Acoustic Simulations. This is a implementation by Kenneth Haugland of the TLM method applied to acoustic simulations. The code was written in VB and C#. The license is The Code Project Open License (CPOL).
Do you another software not listed here? Let me know and I will include it!