Computational Modeling & Simulation of Atria with Fibrotic Remodeling - Example

Computational Modeling &amp; Simulation of Atria with Fibrotic RemodelingExample prepared by Dr. Patrick M. Boyle ([e-mail]) 2021-02-24<br>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.<br>Available in perpetuity via fig share doi: 10.6084/m9.figshare.14347979<br>###############################################################################Step 1: Download the publicly available mesh###############################################################################<br>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.<br>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.<br>###############################################################################Step 2: Run the included shell script to modify the mesh###############################################################################<br>$ bash -u CreateMesh_AvgFibroticLA.sh<br>If any required files are missing, the script should output an informative error<br>###############################################################################Step 3: Run the simulations using a compiled version of openCARP###############################################################################<br>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/<br>Recommended syntax to run:$ [mpi prefix] [carp path] +F [name].par |tee [name].log 2&gt;&amp;1<br>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 $F .par).log 2&gt;&amp;1;done;<br>Each simulation will take several minutes to run (e.g., max. 15 minutes when runon a supercomputer node with 32 cores). Based on testing at the time of examplepreparation, the RIPV1 pacing site should induce reentry sustained by a rotor inthe vicinity of the RSPV region (with meander in the LA roof).<br>###############################################################################Step 4: Visualize results using meshalyzer (state files supplied)###############################################################################<br>Compile and install meshalyzer (also available via openCARP site).This version of the example has been tested with meshalyzer v2.2; if you use anolder version, the visualization should still work but you may see warnings atlaunch time regarding items in the .mshz file (these can be ignored).<br>Example command for visualizing mesh only:$ meshalyzer AvgFibroticLA. fib.mshz<br>Example command for visualizing simulation results:$ meshalyzer AvgFibroticLA. AvgFibroticLA_LSPV1/vm.igb vm.mshz