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MonoAlg3D build

The MonoAlg3D is a program for solving the 3D monodomain equation by applying the Finite Volume Method.

Pre-Requisites

  • Linux-based operating system
  • Nvidia Driver
  • CUDA library

Setting the enviroment

Ubuntu: Refer to the ubuntu guide

Fedora: Refer to the fedora guide

Compile

$ ./build.sh

The binary files will be saved in the bin folder.

Running examples

$ bin/MonoAlg3D -c example_configs/cuboid_ohara.ini

The output will be saved in the VTK format. In order to see the results you can use Paraview (https://www.paraview.org/) or the compiled visualization tool in bin/MonoAlg3D_visualizer. You can also set the output to plain text, by changing the section save_result in example_configs/cuboid_ohara.ini to:

[save_result]
print_rate=250
output_dir=./outputs/tmp_cube
main_function=save_as_text_or_binary
binary=false

In the plain text format we have:

  • Each line represents a Volume
  • Each volume is represented by its center point (X, Y, and Z), the value of half of its side length on x, y and z and the calculated V

Example file:

850,850,950,50,50,50, -85
850,950,950,50,50,50, -85
850,950,850,50,50,50, -85

This file represents 3 volumes with 100 micrometer of side. The first volume is centered at at 850,850,950 and the calculated V is -85 mV.

Contributors:

@rsachetto Rafael Sachetto Oliveira

@bergolho Lucas Arantes Berg

@Rodrigo-Weber-dos-Santos Rodrigo Weber dos Santos

Among others.

How to cite:

Oliveira RS, Rocha BM, Burgarelli D, Meira Jr W, Constantinides C, dos Santos RW. Performance evaluation of GPU parallelization, space‐time adaptive algorithms, and their combination for simulating cardiac electrophysiology. Int J Numer Meth Biomed Engng. 2018;34:e2913. https://doi.org/10.1002/cnm.2913

Credits

Heart icons created by phatplus - Flaticon