def create_forward_problem(
mesh,
activation,
active_value=0.0,
active_model="active_stain",
T_ref=1.0,
):
ffun = df.MeshFunction("size_t", mesh, 2)
ffun.set_all(0)
left = df.CompiledSubDomain("on_boundary && near(x[0], 0)")
left_marker = 1
left.mark(ffun, left_marker)
# Collect the functions containing the markers
marker_functions = pulse.MarkerFunctions(ffun=ffun)
def dirichlet_bc(W):
V = W if W.sub(0).num_sub_spaces() == 0 else W.sub(0)
return da.DirichletBC(V, da.Constant((0.0, 0.0, 0.0)), left)
bcs = pulse.BoundaryConditions(dirichlet=(dirichlet_bc, ), )
f0 = df.as_vector([1, 0, 0])
microstructure = pulse.Microstructure(f0=f0)
geometry = pulse.Geometry(
mesh=mesh,
marker_functions=marker_functions,
microstructure=microstructure,
)
material_parameters = dict(
a=2.28,
a_f=1.686,
b=9.726,
b_f=15.779,
a_s=0.0,
b_s=0.0,
a_fs=0.0,
b_fs=0.0,
)
material = pulse.HolzapfelOgden(
active_model=active_model,
parameters=material_parameters,
activation=activation,
T_ref=T_ref,
)
problem = pulse.MechanicsProblem(geometry, material, bcs)
problem.solve()
if active_value > 0.0:
pulse.iterate.iterate(problem, activation, active_value)
return problem
def setup_material(material_model):
"""
Choose parameters based on
Hadjicharalambous, Myrianthi, et al. "Analysis of passive
cardiac constitutive laws for parameter estimation using 3D
tagged MRI." Biomechanics and modeling in mechanobiology 14.4
(2015): 807-828.
These parameters did not really match the Klotz curve here.
Perhaps they did some more tuning?
"""
if material_model == "guccione":
matparams = pulse.Guccione.default_parameters()
matparams["C"] = 0.18 # kPa
matparams["bf"] = 27.75
matparams["bt"] = 5.37
matparams["bfs"] = 2.445
material = pulse.Guccione(
parameters=matparams,
f0=geometry.f0,
s0=geometry.s0,
n0=geometry.n0,
)
elif material_model == "neo_hookean":
matparams = pulse.NeoHookean.default_parameters()
matparams["mu"] = 10.0 # kPa
material = pulse.NeoHookean(parameters=matparams)
elif material_model == "holzapfel_ogden":
matparams = pulse.HolzapfelOgden.default_parameters()
matparams["a"] = 4.0 # kPa
matparams["a_f"] = 10.0 # kPa
matparams["b"] = 5.0
matparams["b_f"] = 5.0
material = pulse.HolzapfelOgden(
parameters=matparams,
f0=geometry.f0,
s0=geometry.s0,
n0=geometry.n0,
)
return material
def build_problem(geometry, matparams):
activation = dolfin.Function(dolfin.FunctionSpace(geometry.mesh, "R", 0))
material = pulse.HolzapfelOgden(
activation=activation,
parameters=matparams,
f0=geometry.f0,
s0=geometry.s0,
n0=geometry.n0,
)
# LV Pressure
lvp = dolfin.Constant(0.0)
lv_marker = geometry.markers["ENDO"][0]
lv_pressure = pulse.NeumannBC(traction=lvp, marker=lv_marker, name="lv")
neumann_bc = [lv_pressure]
# Add spring term at the base with stiffness 1.0 kPa/cm^2
base_spring = 1.0
robin_bc = [
pulse.RobinBC(
value=dolfin.Constant(base_spring), marker=geometry.markers["BASE"][0]
)
]
# 0 in V.sub(0) refers to x-direction, which is the longitudinal direction
def fix_basal_plane(W):
V = W if W.sub(0).num_sub_spaces() == 0 else W.sub(0)
bc = dolfin.DirichletBC(
V.sub(0), dolfin.Constant(0.0), geometry.ffun, geometry.markers["BASE"][0]
)
return bc
dirichlet_bc = [fix_basal_plane]
# Collect boundary conditions
bcs = pulse.BoundaryConditions(
dirichlet=dirichlet_bc, neumann=neumann_bc, robin=robin_bc
)
# Create the problem
problem = pulse.MechanicsProblem(geometry, material, bcs)
return problem, activation, lvp
)
# Use the default material parameters
material_parameters = pulse.HolzapfelOgden.default_parameters()
# Select model for active contraction
active_model = pulse.ActiveModels.active_strain
# active_model = "active_stress"
# Set the activation
activation = Constant(0.0)
# Create material
material = pulse.HolzapfelOgden(
active_model=active_model,
parameters=material_parameters,
activation=activation,
)
# Make Dirichlet boundary conditions
def dirichlet_bc(W):
V = W if W.sub(0).num_sub_spaces() == 0 else W.sub(0)
return DirichletBC(V, Constant((0.0, 0.0, 0.0)), fixed)
# Make Neumann boundary conditions
neumann_bc = pulse.NeumannBC(traction=Constant(0.0), marker=free_marker)
# Collect Boundary Conditions
bcs = pulse.BoundaryConditions(dirichlet=(dirichlet_bc,), neumann=(neumann_bc,))
"""
This demo demonstrates how to unload a geometry using
the backward displament method which is an iterative
fixed point method.
"""
import matplotlib.pyplot as plt
import dolfin
import pulse
geometry = pulse.HeartGeometry.from_file(pulse.mesh_paths['simple_ellipsoid'])
material = pulse.HolzapfelOgden()
# material = pulse.Guccione()
# Parameter for the cardiac boundary conditions
bcs_parameters = pulse.MechanicsProblem.default_bcs_parameters()
bcs_parameters['base_spring'] = 1.0
bcs_parameters['base_bc'] = 'fix_x'
# Create the problem
# When performing unloading you should pass the
# bcs parameters instead of the bcs directly
problem = pulse.MechanicsProblem(geometry,
material,
bcs_parameters=bcs_parameters)
# Suppose geometry is loaded with a pressure of 1 kPa
# and create the unloader
unloader = pulse.FixedPointUnloader(problem=problem, pressure=1.0)
# Unload the geometry
microstructure = pulse.Microstructure(f0=fiber)
# Create the geometry
geometry = pulse.HeartGeometry(
mesh=mesh,
markers=markers,
marker_functions=marker_functions,
microstructure=microstructure,
)
activation = Function(dolfin.FunctionSpace(geometry.mesh, "R", 0))
activation.assign(Constant(0.0))
matparams = pulse.HolzapfelOgden.default_parameters()
material = pulse.HolzapfelOgden(
activation=activation,
parameters=matparams,
f0=geometry.f0,
)
# LV Pressure
lvp = Constant(0.0)
lv_marker = markers["ENDO"][0]
lv_pressure = pulse.NeumannBC(traction=lvp, marker=lv_marker, name="lv")
neumann_bc = [lv_pressure]
# Add spring term at the base with stiffness 1.0 kPa/cm^2
base_spring = 1.0
robin_bc = [
pulse.RobinBC(value=Constant(base_spring), marker=markers["BASE"][0])
]
def create_problem():
geometry = pulse.HeartGeometry.from_file(
pulse.mesh_paths["simple_ellipsoid"])
activation = dolfin_adjoint.Function(dolfin.FunctionSpace(
geometry.mesh, "R", 0),
name="activation")
activation.assign(dolfin_adjoint.Constant(0.0))
matparams = pulse.HolzapfelOgden.default_parameters()
V = dolfin.FunctionSpace(geometry.mesh, "R", 0)
control = dolfin_adjoint.Function(V)
control.assign(dolfin_adjoint.Constant(1.0))
# control = dolfin_adjoint.Constant(1.0, name="matparam control (a)")
matparams["a"] = control
f0 = dolfin_adjoint.Function(geometry.f0.function_space())
f0.assign(geometry.f0)
s0 = dolfin_adjoint.Function(geometry.s0.function_space())
s0.assign(geometry.s0)
n0 = dolfin_adjoint.Function(geometry.n0.function_space())
n0.assign(geometry.n0)
material = pulse.HolzapfelOgden(activation=activation,
parameters=matparams,
f0=f0,
s0=s0,
n0=n0)
# LV Pressure
lvp = dolfin_adjoint.Constant(0.0, name="lvp")
lv_marker = geometry.markers["ENDO"][0]
lv_pressure = pulse.NeumannBC(traction=lvp, marker=lv_marker, name="lv")
neumann_bc = [lv_pressure]
# Add spring term at the base with stiffness 1.0 kPa/cm^2
base_spring = 1.0
robin_bc = [
pulse.RobinBC(
value=dolfin_adjoint.Constant(base_spring, name="base_spring"),
marker=geometry.markers["BASE"][0],
)
]
# Fix the basal plane in the longitudinal direction
# 0 in V.sub(0) refers to x-direction, which is the longitudinal direction
def fix_basal_plane(W):
V = W if W.sub(0).num_sub_spaces() == 0 else W.sub(0)
bc = dolfin_adjoint.DirichletBC(
V.sub(0),
dolfin.Constant(0.0, name="fix_base"),
geometry.ffun,
geometry.markers["BASE"][0],
)
return bc
dirichlet_bc = [fix_basal_plane]
# Collect boundary conditions
bcs = pulse.BoundaryConditions(dirichlet=dirichlet_bc,
neumann=neumann_bc,
robin=robin_bc)
# Create the problem
problem = pulse.MechanicsProblem(geometry, material, bcs)
return problem, control
# Use the default material parameters from the paper
material_parameters = {
"a": 0.059,
"b": 8.023,
"a_f": 18.472,
"b_f": 16.026,
"a_s": 2.481,
"b_s": 11.120,
"a_fs": 0.216,
"b_fs": 11.436,
}
# Create material
material = pulse.HolzapfelOgden(parameters=material_parameters)
# Make a space for controling the amount of shear displacement
X_space = dolfin.VectorFunctionSpace(mesh, "R", 0)
x = Function(X_space)
zero = Constant((0.0, 0.0, 0.0))
# Make a method that will return
def create_experiment(case): # noqa: C901
if case == "fs":
def dirichlet_bc(W):
import pulse
from fenics_plotly import plot
gamma_space = "R_0"
geometry = pulse.Geometry.from_file(pulse.mesh_paths["prolate_ellipsoid"])
# geometry = pulse.geometries.prolate_ellipsoid_geometry(mesh_size_factor=3.0)
geometry.mesh.coordinates()[:] *= 0.1
# breakpoint()
activation = Function(dolfin.FunctionSpace(geometry.mesh, "R", 0))
matparams = pulse.HolzapfelOgden.default_parameters()
material = pulse.HolzapfelOgden(
active_model=pulse.ActiveModels.active_stress,
T_ref=1.0, # Total active stress should be activation * T_ref
eta=0.2, # Fraction of transverse stress
activation=activation,
parameters=matparams,
f0=geometry.f0,
s0=geometry.s0,
n0=geometry.n0,
)
# LV Pressure
lvp = Constant(0.0)
lv_marker = geometry.markers["ENDO"][0]
lv_pressure = pulse.NeumannBC(traction=lvp, marker=lv_marker, name="lv")
neumann_bc = [lv_pressure]
# Add spring term at the base with stiffness 1.0 kPa/cm^2
base_spring = 1.0
robin_bc = [
pulse.RobinBC(value=Constant(base_spring),
import matplotlib.pyplot as plt
import dolfin
import pulse
from geometry import Geometry, example_meshes
geo = Geometry.from_file(example_meshes['simple_ellipsoid'])
activation = dolfin.Function(dolfin.FunctionSpace(geo.mesh, "R", 0))
activation.assign(dolfin.Constant(0.2))
matparams = pulse.HolzapfelOgden.default_parameters()
material = pulse.HolzapfelOgden(activation=activation,
parameters=matparams,
f0=geo.f0,
s0=geo.s0,
n0=geo.n0)
# LV Pressure
lvp = dolfin.Constant(1.0)
lv_marker = geo.markers['ENDO'][0]
lv_pressure = pulse.NeumannBC(traction=lvp,
marker=lv_marker, name='lv')
neumann_bc = [lv_pressure]
# Add spring term at the base with stiffness 1.0 kPa/cm^2
base_spring = 1.0
robin_bc = [pulse.RobinBC(value=dolfin.Constant(base_spring),
marker=geo.markers["BASE"][0])]
# Fix the basal plane in the longitudinal direction