Shear experiment#
Attempt to reproduce Figure 7 in [1].
[1] Holzapfel, Gerhard A., and Ray W. Ogden. “Constitutive modelling of passive myocardium: a structurally based framework for material characterization. “Philosophical Transactions of the Royal Society of London A: Mathematical, Physical and Engineering Sciences 367.1902 (2009): 3445-3475.
from __future__ import annotations
from pathlib import Path
import dolfin
import matplotlib.pyplot as plt
import numpy as np
try:
import ufl_legacy as ufl
except ImportError:
import ufl
import typing
import pulse
from pulse.mechanicsproblem import MechanicsProblem
try:
from dolfin_adjoint import (
Constant,
DirichletBC,
Expression,
UnitCubeMesh,
interpolate,
Function,
)
except ImportError:
from dolfin import (
Constant,
DirichletBC,
interpolate,
Expression,
UnitCubeMesh,
Function,
)
class Experiment(typing.NamedTuple):
problem: MechanicsProblem
increment: typing.Callable[[float], typing.Tuple[float, float, float]]
shear_component: typing.Callable[[ufl.tensors.ComponentTensor], float]
# Create mesh
N = 2
mesh = UnitCubeMesh(N, N, N)
Create a facet fuction in order to mark the subdomains
ffun = dolfin.MeshFunction("size_t", mesh, 2)
ffun.set_all(0)
Mark subdomains
xlow = dolfin.CompiledSubDomain("near(x[0], 0) && on_boundary")
xlow_marker = 1
xlow.mark(ffun, xlow_marker)
xhigh = dolfin.CompiledSubDomain("near(x[0], 1.0) && on_boundary")
xhigh_marker = 2
xhigh.mark(ffun, xhigh_marker)
ylow = dolfin.CompiledSubDomain("near(x[1], 0) && on_boundary")
ylow_marker = 3
ylow.mark(ffun, ylow_marker)
yhigh = dolfin.CompiledSubDomain("near(x[1], 1) && on_boundary")
yhigh_marker = 4
yhigh.mark(ffun, yhigh_marker)
zlow = dolfin.CompiledSubDomain("near(x[2], 0) && on_boundary")
zlow_marker = 5
zlow.mark(ffun, zlow_marker)
zhigh = dolfin.CompiledSubDomain("near(x[2], 1) && on_boundary")
zhigh_marker = 6
zhigh.mark(ffun, zhigh_marker)
Collect the functions containing the markers
marker_functions = pulse.MarkerFunctions(ffun=ffun)
Create mictrotructure
V_f = dolfin.VectorFunctionSpace(mesh, "CG", 1)
Fibers, sheets and fiber-sheet normal
f0 = interpolate(Expression(("1.0", "0.0", "0.0"), degree=1), V_f)
s0 = interpolate(Expression(("0.0", "1.0", "0.0"), degree=1), V_f)
n0 = interpolate(Expression(("0.0", "0.0", "1.0"), degree=1), V_f)
Collect the mictrotructure
microstructure = pulse.Microstructure(f0=f0, s0=s0, n0=n0)
Create the geometry
geometry = pulse.Geometry(
mesh=mesh,
marker_functions=marker_functions,
microstructure=microstructure,
)
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):
V = W if W.sub(0).num_sub_spaces() == 0 else W.sub(0)
return [
DirichletBC(V, zero, xlow),
DirichletBC(V, x, xhigh),
]
def increment(xi):
return (0, xi, 0)
def shear_component(T):
return dolfin.assemble(T[0, 1] * dolfin.dx)
elif case == "fn":
def dirichlet_bc(W):
V = W if W.sub(0).num_sub_spaces() == 0 else W.sub(0)
return [
DirichletBC(V, zero, xlow),
DirichletBC(V, x, xhigh),
]
def increment(xi):
return (0, 0, xi)
def shear_component(T):
return dolfin.assemble(T[0, 2] * dolfin.dx)
elif case == "sf":
def dirichlet_bc(W):
V = W if W.sub(0).num_sub_spaces() == 0 else W.sub(0)
return [
DirichletBC(V, zero, ylow),
DirichletBC(V, x, yhigh),
]
def increment(xi):
return (xi, 0, 0)
def shear_component(T):
return dolfin.assemble(T[1, 0] * dolfin.dx)
elif case == "sn":
def dirichlet_bc(W):
V = W if W.sub(0).num_sub_spaces() == 0 else W.sub(0)
return [
DirichletBC(V, zero, ylow),
DirichletBC(V, x, yhigh),
]
def increment(xi):
return (0, 0, xi)
def shear_component(T):
return dolfin.assemble(T[1, 2] * dolfin.dx)
elif case == "nf":
def dirichlet_bc(W):
V = W if W.sub(0).num_sub_spaces() == 0 else W.sub(0)
return [
DirichletBC(V, zero, zlow),
DirichletBC(V, x, zhigh),
]
def increment(xi):
return (xi, 0, 0)
def shear_component(T):
return dolfin.assemble(T[2, 0] * dolfin.dx)
elif case == "ns":
def dirichlet_bc(W):
V = W if W.sub(0).num_sub_spaces() == 0 else W.sub(0)
return [
DirichletBC(V, zero, zlow),
DirichletBC(V, x, zhigh),
]
def increment(xi):
return (0, xi, 0)
def shear_component(T):
return dolfin.assemble(T[2, 1] * dolfin.dx)
else:
raise ValueError(f"Unknown case {case}")
# Collect Boundary Conditions
bcs = pulse.BoundaryConditions(dirichlet=(dirichlet_bc,))
# Create problem
return Experiment(
problem=pulse.MechanicsProblem(geometry, material, bcs),
increment=increment,
shear_component=shear_component,
)
Loop over all modes and collect the stress values
modes = ["fs", "fn", "sf", "sn", "nf", "ns"]
stress: dict[str, dict[str, list[float]]] = {
"cauchy": {m: [] for m in modes},
"pk1": {m: [] for m in modes},
}
shear_values = np.linspace(0, 0.6, 10)
recompute = True
# Solve problem
results_file = Path("result.npy")
if recompute or not results_file.is_file():
for mode in modes:
x.assign(zero)
experiment = create_experiment(mode)
for shear in shear_values:
pulse.iterate.iterate(
experiment.problem,
x,
experiment.increment(shear),
reinit_each_step=True,
)
stress["cauchy"][mode].append(
experiment.shear_component(experiment.problem.ChachyStress()),
)
stress["pk1"][mode].append(
experiment.shear_component(experiment.problem.FirstPiolaStress()),
)
np.save(results_file, stress)
2024-09-05 12:03:03,855 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:03:03,856 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.000
2024-09-05 12:03:03,857 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.000
2024-09-05 12:03:03,950 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:03,951 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:03,952 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:03,952 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:03,953 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:03,953 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:03,954 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:03,955 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:03,955 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:03,956 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:04,419 [1037] DEBUG UFL_LEGACY: Blocks of each mode:
1 full
2024-09-05 12:03:05,045 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:05,046 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:05,046 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:05,047 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:05,047 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:05,048 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:05,048 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:05,049 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:05,049 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:05,050 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:05,177 [1037] DEBUG UFL_LEGACY: Blocks of each mode:
1 full
2024-09-05 12:03:05,668 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:03:05,669 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.000
2024-09-05 12:03:05,669 [1037] INFO pulse.iterate: Target: 0.000,0.067,0.000
2024-09-05 12:03:05,746 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:05,746 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:05,747 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:05,748 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:05,748 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:05,749 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:05,749 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:05,751 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:05,751 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:05,752 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:03:06,479 [1037] DEBUG UFL_LEGACY: Blocks of each mode:
99 full
2024-09-05 12:04:04,889 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:04,889 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:04,890 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:04,890 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:04,891 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:04,892 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:04,892 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:04,893 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:04,893 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:04,894 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:05,063 [1037] DEBUG UFL_LEGACY: Blocks of each mode:
10 full
2024-09-05 12:04:06,156 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:06,157 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.067,0.000
2024-09-05 12:04:06,157 [1037] INFO pulse.iterate: Target: 0.000,0.133,0.000
2024-09-05 12:04:06,285 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:06,286 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.133,0.000
2024-09-05 12:04:06,287 [1037] INFO pulse.iterate: Target: 0.000,0.200,0.000
2024-09-05 12:04:06,424 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:06,425 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.200,0.000
2024-09-05 12:04:06,425 [1037] INFO pulse.iterate: Target: 0.000,0.267,0.000
2024-09-05 12:04:06,564 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:06,564 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.267,0.000
2024-09-05 12:04:06,565 [1037] INFO pulse.iterate: Target: 0.000,0.333,0.000
2024-09-05 12:04:06,692 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:06,693 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.333,0.000
2024-09-05 12:04:06,693 [1037] INFO pulse.iterate: Target: 0.000,0.400,0.000
2024-09-05 12:04:06,831 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:06,832 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.400,0.000
2024-09-05 12:04:06,832 [1037] INFO pulse.iterate: Target: 0.000,0.467,0.000
2024-09-05 12:04:06,969 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:06,970 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.467,0.000
2024-09-05 12:04:06,970 [1037] INFO pulse.iterate: Target: 0.000,0.533,0.000
2024-09-05 12:04:07,117 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:07,118 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.533,0.000
2024-09-05 12:04:07,119 [1037] INFO pulse.iterate: Target: 0.000,0.600,0.000
2024-09-05 12:04:07,270 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:07,271 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.000
2024-09-05 12:04:07,272 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.000
2024-09-05 12:04:07,338 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:07,339 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:07,339 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:07,340 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:07,341 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:07,341 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:07,341 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:07,342 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:07,342 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:07,343 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:07,497 [1037] DEBUG UFL_LEGACY: Blocks of each mode:
1 full
2024-09-05 12:04:08,115 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:08,116 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:08,116 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:08,117 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:08,117 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:08,118 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:08,119 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:08,119 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:08,120 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:08,120 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:08,246 [1037] DEBUG UFL_LEGACY: Blocks of each mode:
1 full
2024-09-05 12:04:08,739 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:08,739 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.000
2024-09-05 12:04:08,740 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.067
2024-09-05 12:04:08,888 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:08,889 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.067
2024-09-05 12:04:08,890 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.133
2024-09-05 12:04:09,016 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:09,017 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.133
2024-09-05 12:04:09,018 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.200
2024-09-05 12:04:09,145 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:09,146 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.200
2024-09-05 12:04:09,146 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.267
2024-09-05 12:04:09,274 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:09,275 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.267
2024-09-05 12:04:09,275 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.333
2024-09-05 12:04:09,404 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:09,405 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.333
2024-09-05 12:04:09,406 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.400
2024-09-05 12:04:09,540 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:09,541 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.400
2024-09-05 12:04:09,542 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.467
2024-09-05 12:04:09,679 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:09,679 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.467
2024-09-05 12:04:09,680 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.533
2024-09-05 12:04:09,827 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:09,828 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.533
2024-09-05 12:04:09,828 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.600
2024-09-05 12:04:09,979 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:09,979 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.000
2024-09-05 12:04:09,980 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.000
2024-09-05 12:04:10,047 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:10,047 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:10,048 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:10,048 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:10,049 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:10,049 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:10,050 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:10,050 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:10,050 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:10,051 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:10,259 [1037] DEBUG UFL_LEGACY: Blocks of each mode:
1 full
2024-09-05 12:04:10,874 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:10,875 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:10,875 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:10,876 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:10,876 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:10,877 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:10,877 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:10,877 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:10,878 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:10,878 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:11,007 [1037] DEBUG UFL_LEGACY: Blocks of each mode:
1 full
2024-09-05 12:04:11,501 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:11,502 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.000
2024-09-05 12:04:11,502 [1037] INFO pulse.iterate: Target: 0.067,0.000,0.000
2024-09-05 12:04:11,709 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:11,710 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.067,0.000,0.000
2024-09-05 12:04:11,710 [1037] INFO pulse.iterate: Target: 0.133,0.000,0.000
2024-09-05 12:04:11,854 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:11,855 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.133,0.000,0.000
2024-09-05 12:04:11,855 [1037] INFO pulse.iterate: Target: 0.200,0.000,0.000
2024-09-05 12:04:12,006 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:12,007 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.200,0.000,0.000
2024-09-05 12:04:12,008 [1037] INFO pulse.iterate: Target: 0.267,0.000,0.000
2024-09-05 12:04:12,147 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:12,147 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.267,0.000,0.000
2024-09-05 12:04:12,148 [1037] INFO pulse.iterate: Target: 0.333,0.000,0.000
2024-09-05 12:04:12,287 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:12,287 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.333,0.000,0.000
2024-09-05 12:04:12,288 [1037] INFO pulse.iterate: Target: 0.400,0.000,0.000
2024-09-05 12:04:12,416 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:12,417 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.400,0.000,0.000
2024-09-05 12:04:12,417 [1037] INFO pulse.iterate: Target: 0.467,0.000,0.000
2024-09-05 12:04:12,568 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:12,569 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.467,0.000,0.000
2024-09-05 12:04:12,570 [1037] INFO pulse.iterate: Target: 0.533,0.000,0.000
2024-09-05 12:04:12,728 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:12,729 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.533,0.000,0.000
2024-09-05 12:04:12,729 [1037] INFO pulse.iterate: Target: 0.600,0.000,0.000
2024-09-05 12:04:12,922 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:12,923 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.000
2024-09-05 12:04:12,923 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.000
2024-09-05 12:04:12,990 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:12,991 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:12,991 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:12,992 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:12,993 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:12,993 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:12,994 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:12,994 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:12,995 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:12,996 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:13,150 [1037] DEBUG UFL_LEGACY: Blocks of each mode:
1 full
2024-09-05 12:04:13,767 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:13,768 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:13,769 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:13,769 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:13,770 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:13,771 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:13,771 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:13,772 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:13,773 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:13,775 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:13,900 [1037] DEBUG UFL_LEGACY: Blocks of each mode:
1 full
2024-09-05 12:04:14,451 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:14,452 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.000
2024-09-05 12:04:14,452 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.067
2024-09-05 12:04:14,623 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:14,623 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.067
2024-09-05 12:04:14,624 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.133
2024-09-05 12:04:14,751 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:14,752 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.133
2024-09-05 12:04:14,752 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.200
2024-09-05 12:04:14,882 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:14,882 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.200
2024-09-05 12:04:14,883 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.267
2024-09-05 12:04:15,039 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:15,040 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.267
2024-09-05 12:04:15,041 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.333
2024-09-05 12:04:15,229 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:15,230 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.333
2024-09-05 12:04:15,230 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.400
2024-09-05 12:04:15,358 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:15,359 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.400
2024-09-05 12:04:15,359 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.467
2024-09-05 12:04:15,488 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:15,489 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.467
2024-09-05 12:04:15,490 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.533
2024-09-05 12:04:15,617 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:15,618 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.533
2024-09-05 12:04:15,618 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.600
2024-09-05 12:04:15,760 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:15,761 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.000
2024-09-05 12:04:15,761 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.000
2024-09-05 12:04:15,829 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:15,830 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:15,830 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:15,831 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:15,831 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:15,832 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:15,832 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:15,834 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:15,834 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:15,835 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:15,989 [1037] DEBUG UFL_LEGACY: Blocks of each mode:
1 full
2024-09-05 12:04:16,611 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:16,612 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:16,613 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:16,613 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:16,614 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:16,614 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:16,615 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:16,615 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:16,616 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:16,616 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:16,743 [1037] DEBUG UFL_LEGACY: Blocks of each mode:
1 full
2024-09-05 12:04:17,242 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:17,243 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.000
2024-09-05 12:04:17,243 [1037] INFO pulse.iterate: Target: 0.067,0.000,0.000
2024-09-05 12:04:17,431 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:17,432 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.067,0.000,0.000
2024-09-05 12:04:17,433 [1037] INFO pulse.iterate: Target: 0.133,0.000,0.000
2024-09-05 12:04:17,570 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:17,571 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.133,0.000,0.000
2024-09-05 12:04:17,572 [1037] INFO pulse.iterate: Target: 0.200,0.000,0.000
2024-09-05 12:04:17,721 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:17,722 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.200,0.000,0.000
2024-09-05 12:04:17,722 [1037] INFO pulse.iterate: Target: 0.267,0.000,0.000
2024-09-05 12:04:17,871 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:17,872 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.267,0.000,0.000
2024-09-05 12:04:17,873 [1037] INFO pulse.iterate: Target: 0.333,0.000,0.000
2024-09-05 12:04:18,020 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:18,021 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.333,0.000,0.000
2024-09-05 12:04:18,021 [1037] INFO pulse.iterate: Target: 0.400,0.000,0.000
2024-09-05 12:04:18,158 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:18,159 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.400,0.000,0.000
2024-09-05 12:04:18,160 [1037] INFO pulse.iterate: Target: 0.467,0.000,0.000
2024-09-05 12:04:18,307 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:18,308 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.467,0.000,0.000
2024-09-05 12:04:18,309 [1037] INFO pulse.iterate: Target: 0.533,0.000,0.000
2024-09-05 12:04:18,446 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:18,447 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.533,0.000,0.000
2024-09-05 12:04:18,448 [1037] INFO pulse.iterate: Target: 0.600,0.000,0.000
2024-09-05 12:04:18,601 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:18,602 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.000
2024-09-05 12:04:18,602 [1037] INFO pulse.iterate: Target: 0.000,0.000,0.000
2024-09-05 12:04:18,669 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:18,670 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:18,670 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:18,671 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:18,672 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:18,672 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:18,673 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:18,674 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:18,674 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:18,675 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:18,829 [1037] DEBUG UFL_LEGACY: Blocks of each mode:
1 full
2024-09-05 12:04:19,505 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:19,506 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:19,507 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:19,507 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:19,508 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:19,508 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:19,509 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:19,509 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:19,510 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:19,510 [1037] INFO UFL_LEGACY: Adjusting missing element cell to tetrahedron.
2024-09-05 12:04:19,640 [1037] DEBUG UFL_LEGACY: Blocks of each mode:
1 full
2024-09-05 12:04:20,134 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:20,135 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.000,0.000
2024-09-05 12:04:20,135 [1037] INFO pulse.iterate: Target: 0.000,0.067,0.000
2024-09-05 12:04:20,333 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:20,334 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.067,0.000
2024-09-05 12:04:20,334 [1037] INFO pulse.iterate: Target: 0.000,0.133,0.000
2024-09-05 12:04:20,501 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:20,502 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.133,0.000
2024-09-05 12:04:20,503 [1037] INFO pulse.iterate: Target: 0.000,0.200,0.000
2024-09-05 12:04:20,663 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:20,664 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.200,0.000
2024-09-05 12:04:20,665 [1037] INFO pulse.iterate: Target: 0.000,0.267,0.000
2024-09-05 12:04:20,821 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:20,822 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.267,0.000
2024-09-05 12:04:20,822 [1037] INFO pulse.iterate: Target: 0.000,0.333,0.000
2024-09-05 12:04:20,979 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:20,980 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.333,0.000
2024-09-05 12:04:20,980 [1037] INFO pulse.iterate: Target: 0.000,0.400,0.000
2024-09-05 12:04:21,127 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:21,128 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.400,0.000
2024-09-05 12:04:21,129 [1037] INFO pulse.iterate: Target: 0.000,0.467,0.000
2024-09-05 12:04:21,267 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:21,268 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.467,0.000
2024-09-05 12:04:21,269 [1037] INFO pulse.iterate: Target: 0.000,0.533,0.000
2024-09-05 12:04:21,406 [1037] INFO pulse.iterate: Iterating to target control (f_32)...
2024-09-05 12:04:21,406 [1037] INFO pulse.iterate: Current control: f_32 = Current control: f_32 = 0.000,0.533,0.000
2024-09-05 12:04:21,407 [1037] INFO pulse.iterate: Target: 0.000,0.600,0.000
Plot results
stress = np.load(results_file, allow_pickle=True).item()
fig, ax = plt.subplots(1, 2, sharey=True, sharex=True)
for mode, values in stress["cauchy"].items():
ax[0].plot(shear_values, stress["cauchy"][mode], label=mode)
ax[0].set_title("Cauchy Stress")
for mode, values in stress["pk1"].items():
ax[1].plot(shear_values, stress["pk1"][mode], label=mode)
ax[1].set_title("First Piola Kirchhoff Stress")
ax[0].set_ylabel("Shear stress (kPa)")
for axi in ax:
axi.set_xlabel("Amount of shear")
axi.set_ylim((0, 16))
axi.grid()
axi.legend()
plt.show()
