BiV Geometry

In this demo we will show how you can generate fibers using the ldrb algorithm on a BiV mesh. In order to run this demo you also need to install mshr if you haven’t already.

To run the demo in serial do

python demo_biv.py

If you want to run the demo in parallel you should first comment out the lines that don’t work in serial. Say you want to run on 4 cpu’s, you run the command:

mpirun -n 4 python demo_biv.py

import dolfin as df
import ldrb

# Here we just create a lv mesh. Here you can use yor own mesh instead.
geometry = ldrb.create_biv_mesh()
#
# The mesh
mesh = geometry.mesh
# The facet function (function with marking for the boundaries)
ffun = geometry.ffun
# A dictionary with keys and values for the markers
markers = geometry.markers

# Also if you want to to this demo in parallell you should create the mesh
# in serial and save it to e.g xml
# df.File('biv_mesh.xml') << mesh


# And when you run the code in paralall you should load the mesh from the file.
# mesh = df.Mesh('biv_mesh.xml')

# Since the markers are the default markers and the facet function is
# stored within the mesh itself, you can just set
# markers = None
# ffun = None


# Decide on the angles you want to use
angles = dict(alpha_endo_lv=30,    # Fiber angle on the LV endocardium
              alpha_epi_lv=-30,    # Fiber angle on the LV epicardium
              beta_endo_lv=0,      # Sheet angle on the LV endocardium
              beta_epi_lv=0,       # Sheet angle on the LV epicardium
              alpha_endo_sept=60,  # Fiber angle on the Septum endocardium
              alpha_epi_sept=-60,  # Fiber angle on the Septum epicardium
              beta_endo_sept=0,   # Sheet angle on the Septum endocardium
              beta_epi_sept=0,   # Sheet angle on the Septum epicardium
              alpha_endo_rv=80,    # Fiber angle on the RV endocardium
              alpha_epi_rv=-80,    # Fiber angle on the RV epicardium
              beta_endo_rv=0,      # Sheet angle on the RV endocardium
              beta_epi_rv=0)        # Sheet angle on the RV epicardium

# Choose space for the fiber fields.
# This is a string on the form {family}_{degree}
fiber_space = 'Quadrature_2'
# fiber_space = 'Lagrange_1'

# Compute the microstructure
fiber, sheet, sheet_normal = ldrb.dolfin_ldrb(mesh=mesh,
                                              fiber_space=fiber_space,
                                              ffun=ffun,
                                              markers=markers,
                                              log_level=df.debug,
                                              **angles)

# # Store the results
df.File('biv_fiber.xml') << fiber
df.File('biv_sheet.xml') << sheet
df.File('biv_sheet_normal.xml') << sheet_normal

# If you run in parallel you should skip the visualization step and do that in
# serial in stead. In that case you can read the the functions from the xml
# Using the following code
# V = ldrb.space_from_string(fiber_space, mesh, dim=3)
# fiber = df.Function(V, 'biv_fiber.xml')
# sheet = df.Function(V, 'biv_sheet.xml')
# sheet_normal = df.Function(V, 'biv_sheet_normal.xml')

# Store files in XDMF to be visualized in Paraview
# (These function are not tested in parallel)
ldrb.fiber_to_xdmf(fiber, 'biv_fiber')
ldrb.fiber_to_xdmf(sheet, 'biv_sheet')
ldrb.fiber_to_xdmf(sheet_normal, 'biv_sheet_normal')

BiV Fiber