def test_save():
mesh = get_mesh(3)
filename = Path("mesh.html")
if filename.is_file():
filename.unlink()
plot(mesh, filename=filename, show=False)
assert filename.is_file()
filename.unlink()
def test_plot_dirichlet_bc(dim, wireframe):
mesh = get_mesh(dim)
# Mark the first subdomain with value 1
fixed = df.CompiledSubDomain("near(x[0], 0) && on_boundary")
V = df.VectorFunctionSpace(mesh, "CG", 2)
zero = df.Constant((0.0, 0.0)) if dim == 2 else df.Constant(
(0.0, 0.0, 0.0))
bc = df.DirichletBC(V, zero, fixed)
plot(bc, wireframe=wireframe, show=False)
def test_plot_cell_function(dim, wireframe):
mesh = get_mesh(3)
ffun = df.MeshFunction("size_t", mesh, dim)
ffun.set_all(1)
# left = df.CompiledSubDomain("x[0] < 0.5")
# left_marker = 1
# Not needed since they are allready set to 1
# left.mark(ffun, left_marker)
# Mark the second subdomain with value 2
right = df.CompiledSubDomain("x[0] >= 0.5")
right_marker = 2
right.mark(ffun, right_marker)
plot(ffun, show=False)
def test_plot_cellfunction():
mesh = get_mesh(3)
ffun = df.MeshFunction("size_t", mesh, 2)
ffun.set_all(0)
# Mark the first subdomain with value 1
fixed = df.CompiledSubDomain("near(x[0], 0) && on_boundary")
fixed_marker = 1
fixed.mark(ffun, fixed_marker)
# Mark the second subdomain with value 2
free = df.CompiledSubDomain("near(x[0], 1) && on_boundary")
free_marker = 2
free.mark(ffun, free_marker)
plot(ffun, show=False)
def test_plot_vector_cg_function(dim, wireframe, norm, normalize, degree,
component):
mesh = get_mesh(dim)
V = df.VectorFunctionSpace(mesh, "CG", degree)
u = df.Function(V)
if dim == 2:
u.interpolate(df.Expression(("1 + x[0]*x[0]", "x[1]*x[1]"), degree=1))
if component == "z":
return
else:
u.interpolate(
df.Expression(("1 + x[0]*x[0]", "x[1]*x[1]", "x[2]*x[2]"),
degree=1))
plot(
u,
norm=norm,
wireframe=wireframe,
show=False,
component=component,
normalize=normalize,
)
# 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,))
# Create problem
problem = pulse.MechanicsProblem(geometry, material, bcs)
# Solve problem
pulse.iterate.iterate(problem, activation, 0.1)
# Get displacement and hydrostatic pressure
u, p = problem.state.split(deepcopy=True)
V = dolfin.VectorFunctionSpace(mesh, "CG", 1)
u_int = interpolate(u, V)
new_mesh = Mesh(mesh)
dolfin.ALE.move(new_mesh, u_int)
fig = plot(mesh, show=False)
fig.add_plot(plot(new_mesh, color="red", show=False))
fig.show()
import pulse
geometry = pulse.HeartGeometry.from_file(pulse.mesh_paths["simple_ellipsoid"])
# geometry = pulse.geometries.prolate_ellipsoid_geometry(mesh_size_factor=3.0)
material = pulse.NeoHookean()
# 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
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=3.0)
# Unload the geometry
unloader.unload()
# Get the unloaded geometry
unloaded_geometry = unloader.unloaded_geometry
fig = plot(geometry.mesh, opacity=0.0, show=False)
fig.add_plot(plot(unloaded_geometry.mesh, color="red", show=False))
fig.show()
def test_plot_scalar_cg_function_space(dim, wireframe, degree):
mesh = get_mesh(dim)
V = df.FunctionSpace(mesh, "CG", degree)
plot(V, wireframe=wireframe, show=False)
def test_plot_scalar_cg_function(dim, wireframe, scatter, degree):
mesh = get_mesh(dim)
V = df.FunctionSpace(mesh, "CG", degree)
p = df.Function(V)
p.interpolate(df.Expression("sin(x[0])", degree=1))
plot(p, scatter=scatter, wireframe=wireframe, show=False)
def test_plot_two_mesh():
mesh1 = df.UnitCubeMesh(2, 2, 2)
mesh2 = df.BoxMesh(df.MPI.comm_world, df.Point(0.0, 0.0, 0.0),
df.Point(1.2, 0.5, 1.3), 3, 3, 3)
fig = plot(mesh1, show=False)
fig.add_plot(plot(mesh2, color="red", show=False))
def test_plot_mesh(dim, wireframe):
mesh = get_mesh(dim)
plot(mesh, wireframe=wireframe, show=False)
# Collect boundary conditions
bcs = pulse.BoundaryConditions(
dirichlet=dirichlet_bc,
neumann=neumann_bc,
robin=robin_bc,
)
# Create the problem
problem = pulse.MechanicsProblem(geometry, material, bcs)
problem.solve()
# Solve the problem
pulse.iterate.iterate(problem, (lvp, activation), (1.0, 0.2))
# Get the solution
u, p = problem.state.split(deepcopy=True)
volume = geometry.cavity_volume(u=u)
print(f"Cavity volume = {volume}")
# Move mesh accoring to displacement
u_int = interpolate(u, dolfin.VectorFunctionSpace(geometry.mesh, "CG", 1))
mesh = Mesh(geometry.mesh)
dolfin.ALE.move(mesh, u_int)
fig = plot(geometry.mesh, color="red", show=False)
fig.add_plot(plot(mesh, show=False))
fig.show()
geometry = pulse.Geometry(
mesh=mesh,
microstructure=microstructure,
)
# -
activation = Function(dolfin.FunctionSpace(geometry.mesh, "R", 0))
activation.assign(Constant(0.2))
matparams = pulse.HolzapfelOgden.default_parameters()
material = pulse.HolzapfelOgden(
activation=activation,
parameters=matparams,
f0=geometry.f0,
s0=geometry.s0,
n0=geometry.n0,
)
problem = RigidMotionProblem(geometry, material)
problem.solve()
u = problem.state.split(deepcopy=True)[1]
V = dolfin.VectorFunctionSpace(mesh, "CG", 1)
u_int = interpolate(u, V)
new_mesh = Mesh(mesh)
dolfin.ALE.move(new_mesh, u_int)
fig = plot(geometry.mesh, opacity=0.4, show=False)
fig.add_plot(plot(new_mesh, color="red", show=False))
fig.show()
# dolfin.ALE.move(mesh, u_int)
# +
# Get the solution
# u, p = problem.state.split(deepcopy=True)
# dolfin.File("u.pvd") << u
# -
W = dolfin.FunctionSpace(geometry.mesh, "CG", 1)
F = pulse.kinematics.DeformationGradient(u)
E = pulse.kinematics.GreenLagrangeStrain(F)
# Green strain normal to fiber direction
Ef = project(dolfin.inner(E * geometry.f0, geometry.f0), W)
# Save to file for visualization in paraview
# dolfin.File("Ef.pvd") << Ef
plot(Ef)
P = material.FirstPiolaStress(F, p)
# First piola stress normal to fiber direction
Pf = project(dolfin.inner(P * geometry.f0, geometry.f0), W)
# Save to file for visualization in paraview
# dolfin.File("Pf.pvd") << Pf
plot(Pf, colorscale="viridis")
T = material.CauchyStress(F, p)
f = F * geometry.f0
# Cauchy fiber stress
Tf = dolfin.project(dolfin.inner(T * f, f), W)
# Save to file for visualization in paraview
# dolfin.File("Tf.pvd") << Tf
plot(Tf, colorscale="jet")
