Life X - 01_strocchi_LV¶

Life X recently published their own implementation of the LDRB algorithm and with that they also publushed a lot of example meshes. This demo aims to try out this implementation of the LDRB algorithm on these example meshes. The LifeX example meshes can be found at https://zenodo.org/record/5810269#.YeEjWi8w1B0, which also contains a DOI: https://doi.org/10.5281/zenodo.5810269.

This demo assumes that you have downloaded the folder with the meshes in the same format as they are uploaded on zenodo, so that the gmsh files are located in a folder called lifex_fiber_generation_examples/mesh.

First we import the necessary packages. Note that we also import meshio which is used for converted from .msh (gmsh) to .xdmf (FEnICS).

import dolfin

import ldrb

Load the mesh and markers. This is a large mesh that you probably want to run in parallel, but you need to first convert the mesh to a fenics mesh and that has to be done in serial. You can make sure that the mesh is saved by setting unlink = False

# Last argument here is the markers, but these are not used
mesh, ffun, _ = ldrb.gmsh2dolfin(
    "lifex_fiber_generation_examples/mesh/01_strocchi_LV.msh",
    unlink=False,
)
# Run this first in serial and exit here
# exit()

To run the in paralell you can do

mpirun -n 4 python demo_lifex_strocchi_LV.py

These are the actualy markers (but we only supprt one base at the moment)

original_markers = {"epi": 10, "endo": 20, "aortic_valve": 50, "mitral_valve": 60}

So we just use these markers instead

markers = {"epi": 10, "lv": 20, "base": 40}

And update the markers accordingly

ffun.array()[ffun.array() == original_markers["aortic_valve"]] = markers["base"]
ffun.array()[ffun.array() == original_markers["mitral_valve"]] = markers["base"]

Select linear langange elements

fiber_space = "P_1"

Compute the fiber-sheet system

fiber, sheet, sheet_normal = ldrb.dolfin_ldrb(
    mesh=mesh,
    fiber_space=fiber_space,
    ffun=ffun,
    markers=markers,
    alpha_endo_lv=60,  # Fiber angle on the endocardium
    alpha_epi_lv=-60,  # Fiber angle on the epicardium
    beta_endo_lv=0,  # Sheet angle on the endocardium
    beta_epi_lv=0,  # Sheet angle on the epicardium
)

And save the results

with dolfin.XDMFFile(mesh.mpi_comm(), "01_strocchi_LV_fiber.xdmf") as xdmf:
    xdmf.write(fiber)