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:
.. code::
mpirun -n 4 python demo_lv.py
"""
import dolfin as df
import pulse
import ldrb
# comm = ldrb.utils.mpi_comm_world()
# Here we just create a lv mesh. Here you can use yor own mesh instead.
geometry = ldrb.create_lv_mesh()
# Make fiber field
fiber_params = df.Parameters("Fibers")
fiber_params.add("fiber_space", "CG_1")
# fiber_params.add("fiber_space", "Quadrature_4")
fiber_params.add("include_sheets", False)
fiber_params.add("fiber_angle_epi", -60)
fiber_params.add("fiber_angle_endo", 60)
pulse.geometry_utils.generate_fibers(geometry.mesh, fiber_params)
# The mesh
mesh = geometry.mesh
# The facet function (function with marking for the boundaries)
# ffun = geometry.ffun
def create_geometry(h5name):
"""
Create an lv-ellipsoidal mesh and fiber fields using LDRB algorithm
An ellipsoid is given by the equation
.. math::
\frac{x^2}{a} + \frac{y^2}{b} + \frac{z^2}{c} = 1
We create two ellipsoids, one for the endocardium and one
for the epicardium and subtract them and then cut the base.
For simplicity we assume that the longitudinal axis is in
in :math:`x`-direction and as default the base is located
at the :math:`x=0` plane.
"""
# Number of subdivision (higher -> finer mesh)
N = 13
# Parameter for the endo ellipsoid
a_endo = 1.5
b_endo = 0.5
c_endo = 0.5
# Parameter for the epi ellipsoid
a_epi = 2.0
b_epi = 1.0
c_epi = 1.0
# Center of the ellipsoid (same of endo and epi)
center = (0.0, 0.0, 0.0)
# Location of the base
base_x = 0.0
# Create a lv ellipsoid mesh with longitudinal axis along the x-axis
geometry = ldrb.create_lv_mesh(N=N,
a_endo=a_endo,
b_endo=b_endo,
c_endo=c_endo,
a_epi=a_epi,
b_epi=b_epi,
c_epi=c_epi,
center=center,
base_x=base_x)
# Select fiber angles for rule based algorithm
angles = dict(
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
fiber_space = 'Lagrange_1'
# Compte the microstructure
fiber, sheet, sheet_normal = ldrb.dolfin_ldrb(mesh=geometry.mesh,
fiber_space=fiber_space,
ffun=geometry.ffun,
markers=geometry.markers,
**angles)
# Compute focal point
focal = np.sqrt(a_endo**2 - (0.5 * (b_endo + c_endo))**2)
# Make mesh according to AHA-zons
pulse.geometry_utils.mark_strain_regions(mesh=geometry.mesh, foc=focal)
mapper = {'lv': 'ENDO', 'epi': 'EPI', 'rv': 'ENDO_RV', 'base': 'BASE'}
m = {mapper[k]: (v, 2) for k, v in geometry.markers.items()}
pulse.geometry_utils.save_geometry_to_h5(
geometry.mesh, h5name, markers=m, fields=[fiber, sheet, sheet_normal])
def lv_geometry():
return ldrb.create_lv_mesh()
def lv_mesh():
return ldrb.create_lv_mesh().mesh