Computational Modeling & Simulation of Atria with Fibrotic Remodeling - Example

Computational Modeling & Simulation of Atria with Fibrotic RemodelingExample prepared by Dr. Patrick M. Boyle ([e-mail]) 2021-02-24
Update 2021-05-03: removed junk OSX files from zip; updated to reflect testing info (openCARP on OSX works!), and added version number (v2.2) to meshalyzer documentation.
Available in perpetuity via fig share doi: 10.6084/m9.figshare.14347979
###############################################################################Step 1: Download the publicly available mesh###############################################################################
This should be obtained from the following repository:https://zenodo.org/record/3764917#.YDc13XVKjS8If this work is re-used, please attribute the original source properly:Roney et al. Med Image Anal. 2019 Jul;55:65-75. PMID: 31026761.
Only one of the meshes will be used (LA_Epi/A/Labelled_A_6_1)... but the whole .zip archive should be downloaded and decompressed in thesame directory as this file.
###############################################################################Step 2: Run the included shell script to modify the mesh###############################################################################
$ bash -u CreateMesh_AvgFibroticLA.sh
If any required files are missing, the script should output an informative error
###############################################################################Step 3: Run the simulations using a compiled version of openCARP###############################################################################
The model has been tested using openCARP v5.0 compiled on various linux systemswith default settings. It was also recently tested with a compiled version onMac OSX. Only built-in components of the simulator are used. openCARP is freeto use for non-commercial applications, but use of the simulator is governed bythe terms of use outlined at https://opencarp.org/
Recommended syntax to run:$ [mpi prefix] [carp path] +F [name].par |tee [name].log 2>&1
Example wrapper code for running all 15 simulations:$ for F in AvgFibroticLA_Stim*par; do mpiexec -n 32 /opt/openCARPv5.0/bin/openCARP.opt +F $F \ |tee $(basename $F .par).log 2>&1;done;
Each simulation will take several minutes to run (e.g., max. 15 minutes when runon a supercomputer node with 32 cores). Based on testing at the time of examplepreparation, the RIPV1 pacing site should induce reentry sustained by a rotor inthe vicinity of the RSPV region (with meander in the LA roof).
###############################################################################Step 4: Visualize results using meshalyzer (state files supplied)###############################################################################
Compile and install meshalyzer (also available via openCARP site).This version of the example has been tested with meshalyzer v2.2; if you use anolder version, the visualization should still work but you may see warnings atlaunch time regarding items in the .mshz file (these can be ignored).
Example command for visualizing mesh only:$ meshalyzer AvgFibroticLA. fib.mshz
Example command for visualizing simulation results:$ meshalyzer AvgFibroticLA. AvgFibroticLA_LSPV1/vm.igb vm.mshz