Life X - idealized_LV

Life X recently published their own implementation of the LDRB algorithm and with that they also published 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

import cardiac_geometries

Load the mesh and markers.

mesh, markers, marker_functions = cardiac_geometries.gmsh2dolfin(
    "lifex_fiber_generation_examples/mesh/idealized_LV.msh",
)

Here the markers are actually parsed with meshio, but they have the wrong name so we just rename them

ldrb_markers = {
    "epi": markers["Epicardium"][0],
    "lv": markers["Endocardium"][0],
    "base": markers["Basal plane"][0],
}

Select linear Lagrange elements

fiber_space = "P_1"

Compute the fiber-sheet system

fiber, sheet, sheet_normal = ldrb.dolfin_ldrb(
    mesh=mesh,
    fiber_space=fiber_space,
    ffun=marker_functions.ffun,
    markers=ldrb_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(), "idealized_LV_fiber.xdmf") as xdmf:
    xdmf.write(fiber)