This repository contains scripts for launching and post-processing the simulations in the paper The importance of geometry in the corneal micropocket assay.

Requirements to run simulations:

• Microvessel Chaste Python package (and its dependencies)

Requirements to do postprocessing:

• Microvessel Chaste Python package (and its dependencies)
• VTK Python package

The simulation launcher is in test/python/batch_simulation.py. To run simulations do:

mpirun -np $NUM_CPUS python test/python/batch_simulation.py

The collection of different simulations is in src/python/cornea/simulations. To change the simulation run by the launcher modify the line:

from cornea.simulations.fixed_case5 import study, master_work_dir, study_data

in test/python/batch_simulation.py to the desired simulation. Results will be in the directory specified by the $CHASTE_TEST_OUTPUT environment variable.

To postprocess simulations do:

mpirun -np $NUM_CPUS python test/python/batch_postprocess.py

Change the line work_dir = "Python/Cornea/Submission/Fixed_Case5" to the desired output directory. Some postprocessing operations will work in parallel, but most only work in serial (requiring mpirun -np 2).

After postprocessing the plots used in the paper will be included in the simulation folders. Screenshots have been generated in Paraview using the vtp, vti and vtu files produced during the simulations.