This version of MonoAlg3D contains custom functions necessary to reproduce the results in Riebel et al., Scientific Reports (2024), https://doi.org/10.1038/s41598-024-67951-5.
Accompanying Purkinje and biventricular infarction mesh files can be found in https://doi.org/10.5281/zenodo.14699735.
Example configuration files for the above study are provided in custom_configs/.
NOTE:
- If you WANT TO USE the STEM CELL functionality, please edit lines 806 and following of the src/models_library/ToROrd/Paci_ToRORd_dynCl_PhiCaL_IKCa_mixed_apicobasal_infarctionRemod_RL.common.c file. To test the stem cell model, a test case initilisation file and single-cube-mesh are available in this repository in custom_configs/ and meshes/.
- If you DO NOT WANT TO USE the STEM CELL functionality, please note that some changes may be required in the code (it should work but I haven't thoroughly tested it without stem cells). To make sure, remove mention of stem cells or Paci in the src/models_library/ToROrd/Paci_ToRORd..., src/domains_library/custom_functions.c, src/domains_library/custom_mesh_info_data.h, src/extra_data_library/custom_functions.c, src/matrix_assembly_library/custom_functions.c, and src/matrix_assembly_library/purkinje_coupling_matrix_assembly.c files.
The MonoAlg3D is a program for solving the 3D monodomain equation by applying the Finite Volume Method.
- Linux-based operating system
- Nvidia Driver
- CUDA library
Ubuntu: Refer to the ubuntu guide
Fedora: Refer to the fedora guide
$ ./build.shThe binary files will be saved in the bin folder.
$ 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.
@rsachetto Rafael Sachetto Oliveira
@bergolho Lucas Arantes Berg
@Rodrigo-Weber-dos-Santos Rodrigo Weber dos Santos
Among others.
For the updates made in Riebel et al., 2024: Riebel LL, Wang, ZJ, Martinez-Navarro H, Trovato C, Camps J, Berg LA, Zhou X, Doste R, Sachetto Oliveira, R Weber dos Santos R, Biasetti J, Rodriguez B. In Silico Evaluation of Cell Therapy in Acute versus Chronic Infarction: Role of Automaticity, Heterogeneity and Purkinje in Human. Sci Rep, 14 21584 (2024). https://doi.org/10.1038/s41598-024-67951-5
For MonoAlg3D: 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