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
behaviour. Proc. R. Soc. A. 2015 Dec 8;471(2184):20150641.
"""
import matplotlib.pyplot as plt
import dolfin
import pulse
geometry = pulse.HeartGeometry.from_file(pulse.mesh_paths['benchmark'])
# Create the material
material_parameters = pulse.Guccione.default_parameters()
material_parameters['CC'] = 10.0
material_parameters['bf'] = 1.0
material_parameters['bfs'] = 1.0
material_parameters['bt'] = 1.0
material = pulse.Guccione(params=material_parameters)
# Define Dirichlet boundary. Fix the base_spring
def dirichlet_bc(W):
V = W if W.sub(0).num_sub_spaces() == 0 else W.sub(0)
return dolfin.DirichletBC(V, dolfin.Constant((0.0, 0.0, 0.0)),
geometry.ffun, geometry.markers['BASE'][0])
# Traction at the bottom of the beam
lvp = dolfin.Constant(0.0)
neumann_bc = pulse.NeumannBC(traction=lvp, marker=geometry.markers['ENDO'][0])
# Collect Boundary Conditions
bcs = pulse.BoundaryConditions(dirichlet=(dirichlet_bc, ),
import matplotlib.pyplot as plt
import dolfin
import pulse
from problem import Problem
from force import ca_transient
# pulse.parameters['log_level'] = dolfin.WARNING
geometry = pulse.HeartGeometry.from_file(pulse.mesh_paths['simple_ellipsoid'])
# Scale mesh to fit Windkessel parameters
geometry.mesh.coordinates()[:] *= 2.4
activation = dolfin.Constant(0.0)
matparams = pulse.Guccione.default_parameters()
material = pulse.Guccione(activation=activation,
parameters=matparams)
# 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])]
# 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.DirichletBC(V.sub(0),
dolfin.Constant(0.0),
geometry.ffun, geometry.markers["BASE"][0])
from fenics_plotly import plot
geometry = pulse.HeartGeometry.from_file(pulse.mesh_paths["benchmark"])
# geometry = pulse.geometries.benchmark_ellipsoid_geometry()
# Create the material
material_parameters = pulse.Guccione.default_parameters()
material_parameters["CC"] = 2.0
material_parameters["bf"] = 8.0
material_parameters["bfs"] = 4.0
material_parameters["bt"] = 2.0
activation = Constant(0.0)
material = pulse.Guccione(
parameters=material_parameters,
active_model=pulse.ActiveModels.active_stress,
activation=activation,
)
# Define Dirichlet boundary. Fix the base_spring
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)),
geometry.ffun,
geometry.markers["BASE"][0],
)
def solve(
geometry,
EDP=1.0,
ESP=15.0,
Ta=60,
material_parameters=None,
):
"""
Arguments
---------
EDP : float
End diastolic pressure
ESP : float
End systolic pressure
Ta : float
Peak active tension (at ES)
material_parameters : dict
A dictionart with parameter in the Guccione model.
Default: {'C': 2.0, 'bf': 8.0, 'bt': 2.0, 'bfs': 4.0}
filename : str
Filname where to store the results
"""
# Create model
activation = df.Function(df.FunctionSpace(geometry.mesh, "R", 0))
matparams = pulse.Guccione.default_parameters()
if material_parameters is not None:
matparams.update(material_parameters)
material = pulse.Guccione(activation=activation,
parameters=matparams,
active_model="active_stress",
f0=geometry.f0,
s0=geometry.s0,
n0=geometry.n0)
lvp = df.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=df.Constant(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 = df.DirichletBC(V.sub(0), df.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)
xdmf = df.XDMFFile(df.mpi_comm_world(), 'output.xdmf')
# Solve the problem
print(("Do an initial solve with pressure = 0 kPa "
"and active tension = 0 kPa"))
problem.solve()
u, p = problem.state.split()
xdmf.write(u, 0.0)
print("LV cavity volume = {} ml".format(geometry.cavity_volume(u=u)))
# Solve for ED
print(("Solver for ED with pressure = {} kPa and active tension = 0 kPa"
"".format(EDP)))
pulse.iterate.iterate(problem, lvp, EDP, initial_number_of_steps=20)
u, p = problem.state.split(deepcopy=True)
xdmf.write(u, 1.0)
df.File("ED_displacement.xml") << u
print("LV cavity volume = {} ml".format(geometry.cavity_volume(u=u)))
# Solve for ES
print(("Solver for ES with pressure = {} kPa and active tension = {} kPa"
"".format(ESP, Ta)))
pulse.iterate.iterate(problem, lvp, ESP, initial_number_of_steps=50)
pulse.iterate.iterate(problem,
activation,
Ta,
adapt_step=False,
max_iters=100,
initial_number_of_steps=40)
u, p = problem.state.split(deepcopy=True)
xdmf.write(u, 2.0)
df.File("ES_displacement.xml") << u
print("LV cavity volume = {} ml".format(geometry.cavity_volume(u=u)))
import dolfin
import pulse
geometry = pulse.HeartGeometry.from_file(pulse.mesh_paths['benchmark'])
# Create the material
material_parameters = pulse.Guccione.default_parameters()
material_parameters['CC'] = 2.0
material_parameters['bf'] = 8.0
material_parameters['bfs'] = 4.0
material_parameters['bt'] = 2.0
activation = dolfin.Constant(0.0)
material = pulse.Guccione(params=material_parameters,
active_model='active_stress',
activation=activation)
# Define Dirichlet boundary. Fix the base_spring
def dirichlet_bc(W):
V = W if W.sub(0).num_sub_spaces() == 0 else W.sub(0)
return dolfin.DirichletBC(V, dolfin.Constant((0.0, 0.0, 0.0)),
geometry.ffun, geometry.markers['BASE'][0])
# Traction at the bottom of the beam
lvp = dolfin.Constant(0.0)
neumann_bc = pulse.NeumannBC(traction=lvp,
marker=geometry.markers['ENDO'][0])