def get_residual_form(u, v, rho_e, method='RAMP'):
df.dx = df.dx(metadata={"quadrature_degree": 4})
# stiffness = rho_e/(1 + 8. * (1. - rho_e))
if method == 'SIMP':
stiffness = rho_e**3
else: #RAMP
stiffness = rho_e / (1 + 8. * (1. - rho_e))
# print('the value of stiffness is:', rho_e.vector().get_local())
# Kinematics
k = 3e1
E = k * stiffness
nu = 0.3
mu, lmbda = (E / (2 * (1 + nu))), (E * nu / ((1 + nu) * (1 - 2 * nu)))
d = len(u)
I = df.Identity(d) # Identity tensor
F = I + df.grad(u) # Deformation gradient
C = F.T * F # Right Cauchy-Green tensor
E_ = 0.5 * (C - I) # Green--Lagrange strain
S = 2.0 * mu * E_ + lmbda * df.tr(E_) * df.Identity(
d) # stress tensor (C:eps)
psi = 0.5 * df.inner(S, E_) # 0.5*eps:C:eps
# Total potential energy
Pi = psi * df.dx
# Solve weak problem obtained by differentiating Pi:
res = df.derivative(Pi, u, v)
return res
def get_residual_form(u, v, rho_e, T, T_hat, KAPPA, k, alpha, mode='plane_stress', method='RAMP', T_r=df.Constant(20.)):
if method=='RAMP':
p =8
C = rho_e/(1 + p * (1. - rho_e))
else:
C = rho_e**3
E = k * C
# C is the design variable, its values is from 0 to 1
nu = 0.3 # Poisson's ratio
lambda_ = E * nu/(1. + nu)/(1 - 2 * nu)
mu = E / 2 / (1 + nu) #lame's parameters
if mode == 'plane_stress':
lambda_ = 2*mu*lambda_/(lambda_+2*mu)
# Th = df.Constant(7)
I = df.Identity(len(u))
T_0 = df.Constant(20.)
w_ij = 0.5 * (df.grad(u) + df.grad(u).T) - C * alpha * I * (T-T_0)
v_ij = 0.5 * (df.grad(v) + df.grad(v).T)
d = len(u)
sigm = lambda_*df.div(u)*df.Identity(d) + 2*mu*w_ij
a = df.inner(sigm, v_ij) * df.dx + \
df.dot(C*KAPPA* df.grad(T), df.grad(T_hat)) * df.dx
print("get a-------")
return a
def Fa(self):
if self.model == ActiveModels.active_stress:
return dolfin.Identity(self.dim)
f0 = self.f0
f0f0 = dolfin.outer(f0, f0)
Id = dolfin.Identity(self.dim)
mgamma = 1 - self.activation_field
Fa = mgamma * f0f0 + pow(mgamma,
-1.0 / float(self.dim - 1)) * (Id - f0f0)
return Fa
def get_volume(geometry, u=None, chamber="lv"):
if "ENDO" in geometry.markers:
lv_endo_marker = geometry.markers["ENDO"]
rv_endo_marker = None
else:
lv_endo_marker = geometry.markers["ENDO_LV"]
rv_endo_marker = geometry.markers["ENDO_RV"]
marker = lv_endo_marker if chamber == "lv" else rv_endo_marker
if marker is None:
return None
if hasattr(marker, "__len__"):
marker = marker[0]
ds = df.Measure(
"exterior_facet", subdomain_data=geometry.ffun, domain=geometry.mesh
)(marker)
X = df.SpatialCoordinate(geometry.mesh)
N = df.FacetNormal(geometry.mesh)
if u is None:
vol = df.assemble((-1.0 / 3.0) * df.dot(X, N) * ds)
else:
F = df.grad(u) + df.Identity(3)
J = df.det(F)
vol = df.assemble((-1.0 / 3.0) * df.dot(X + u, J * df.inv(F).T * N) * ds)
return vol
def __init__(
self,
mesh,
field,
strain_tensor="E",
dmu=None,
approx="original",
F_ref=None,
isochoric=True,
displacement_space="CG_2",
interpolation_space="CG_1",
description="",
):
ModelObservation.__init__(self,
mesh,
target_space="R_0",
description=description)
# Check that the given field is a vector of the same dim as the mesh
dim = mesh.geometry().dim()
# assert isinstance(field, (dolfin.Function, dolfin.Constant)
assert field.ufl_shape[0] == dim
approxs = ["project", "interpolate", "original"]
msg = 'Expected "approx" for be one of {}, got {}'.format(
approxs, approx)
self.field = field
assert approx in approxs, msg
self._approx = approx
self._F_ref = F_ref if F_ref is not None else dolfin.Identity(dim)
self._isochoric = isochoric
tensors = ["gradu", "E", "almansi"]
msg = "Expected strain tensor to be one of {}, got {}".format(
tensors, strain_tensor)
assert strain_tensor in tensors, msg
self._tensor = strain_tensor
if dmu is None:
dmu = dolfin.dx(domain=mesh)
assert isinstance(dmu, dolfin.Measure)
self._dmu = dmu
self._vol = dolfin_adjoint.Constant(
dolfin.assemble(dolfin.Constant(1.0) * dmu))
# These spaces are only used if you want to project
# or interpolate the displacement before assigning it
# Space for interpolating the displacement if needed
family, degree = interpolation_space.split("_")
self._interpolation_space = dolfin.VectorFunctionSpace(
mesh, family, int(degree))
# Displacement space
family, degree = displacement_space.split("_")
self._displacement_space = dolfin.VectorFunctionSpace(
mesh, family, int(degree))
def get_residual_form(u, v, rho_e, E = 1, method='SIMP'):
if method =='SIMP':
C = rho_e**3
else:
C = rho_e/(1 + 8. * (1. - rho_e))
E = 1. * C # C is the design variable, its values is from 0 to 1
nu = 0.3 # Poisson's ratio
lambda_ = E * nu/(1. + nu)/(1 - 2 * nu)
mu = E / 2 / (1 + nu) #lame's parameters
w_ij = 0.5 * (df.grad(u) + df.grad(u).T)
v_ij = 0.5 * (df.grad(v) + df.grad(v).T)
d = len(u)
sigm = lambda_*df.div(u)*df.Identity(d) + 2*mu*w_ij
a = df.inner(sigm, v_ij) * df.dx
return a
def get_residual_form(u, v, rho_e, Th, k=199.5e9, alpha=15.4e-6):
C = rho_e / (1 + 8. * (1. - rho_e))
E = k * C # C is the design variable, its values is from 0 to 1
nu = 0.3 # Poisson's ratio
Th = Th - df.Constant(20.)
Th = 0.
lambda_ = E * nu / (1. + nu) / (1 - 2 * nu)
mu = E / 2 / (1 + nu) #lame's parameters
# Th = df.Constant(7)
w_ij = 0.5 * (df.grad(u) + df.grad(u).T)
v_ij = 0.5 * (df.grad(v) + df.grad(v).T)
d = len(u)
sigm = (lambda_ * df.tr(w_ij) - alpha *
(3. * lambda_ + 2. * mu) * Th) * df.Identity(d) + 2 * mu * w_ij
a = df.inner(sigm, v_ij) * df.dx
return a
def normal_stresses(self):
k = self.bc_dict["obstacle"]
n = df.FacetNormal(self.mesh)
tau = (self.mu * (df.grad(self.u_) + df.grad(self.u_).T) -
self.p_ * df.Identity(2))
normal_stresses_x = -df.assemble(df.dot(tau, n)[0] * self.ds_(k))
normal_stresses_y = df.assemble(df.dot(tau, n)[1] * self.ds_(k))
return np.array([normal_stresses_x, normal_stresses_y])
def stf3d3(rank3_3d):
r"""
Return the symmetric and trace-free part of a 3D 3-tensor.
Return the symmetric and trace-free part of a 3D 3-tensor. (dev(sym(.)))
Returns the STF part :math:`A_{\langle i j k\rangle}` of a rank-3 tensor
:math:`A \in \mathbb{R}^{3 \times 3 \times 3}` [TOR2018]_.
.. math::
A_{\langle i j k\rangle}=A_{(i j k)}-\frac{1}{5}\left[A_{(i l l)}
\delta_{j k}+A_{(l j l)} \delta_{i k}+A_{(l l k)} \delta_{i j}\right]
A gradient :math:`\frac{\partial S_{\langle i j}}{\partial x_{k \rangle}}`
of a symmetric 2-tensor :math:`S \in \mathbb{R}^{3 \times 3}` has the
deviator [STR2005]_:
.. math::
\frac{\partial S_{\langle i j}}{\partial x_{k \rangle}}
=&
\frac{1}{3}\left(
\frac{\partial S_{i j}}{\partial x_{k}}
+\frac{\partial S_{i k}}{\partial x_{j}}
+\frac{\partial S_{j k}}{\partial x_{i}}
\right)
-\frac{1}{15}
\biggl[
\left(
\frac{\partial S_{i r}}{\partial x_{r}}
+\frac{\partial S_{i r}}{\partial x_{r}}
+\frac{\partial S_{r r}}{\partial x_{i}}
\right) \delta_{j k}
\\
&+
\left(
\frac{\partial S_{j r}}{\partial x_{r}}
+\frac{\partial S_{j r}}{\partial x_{r}}
+\frac{\partial S_{r r}}{\partial x_{j}}
\right) \delta_{i k}
+\left(
\frac{\partial S_{k r}}{\partial x_{r}}
+\frac{\partial S_{k r}}{\partial x_{r}}
+\frac{\partial S_{r r}}{\partial x_{k}}
\right) \delta_{i j}
\biggr]
"""
i, j, k, L = ufl.indices(4)
delta = df.Identity(3)
sym_ijk = sym3d3(rank3_3d)[i, j, k]
traces_ijk = 1 / 5 * (+sym3d3(rank3_3d)[i, L, L] * delta[j, k] +
sym3d3(rank3_3d)[L, j, L] * delta[i, k] +
sym3d3(rank3_3d)[L, L, k] * delta[i, j])
tracefree_ijk = sym_ijk - traces_ijk
return ufl.as_tensor(tracefree_ijk, (i, j, k))
def molecular_stress_tensor(self, u, p):
r"""Define the molecular stress tensor:
.. math:: \bar{\pi} = 2\mu\bar{\epsilon}-p\bar{I}
:param u: The velocity field.
:param p: The pressure field.
:return: The molecular stress tensor.
"""
mu = self._mu.magnitude
return 2 * mu * self.strain_rate_tensor(u) - p * dolfin.Identity(3)
def update_vector_field(
f0, new_mesh, u=None, name="fiber", normalize=True, regen_fibers=False
):
df.parameters["form_compiler"]["representation"] = "quadrature"
df.parameters["form_compiler"]["quadrature_degree"] = 4
ufl_elem = f0.function_space().ufl_element()
f0_new = df.Function(df.FunctionSpace(new_mesh, ufl_elem), name=name)
mpi_size = df.mpi_comm_world().getSize()
if regen_fibers and mpi_size == 1:
from mesh_generation.generate_mesh import setup_fiber_parameters
from mesh_generation.mesh_utils import load_geometry_from_h5, generate_fibers
fiber_params = setup_fiber_parameters()
fields = generate_fibers(new_mesh, fiber_params)
f0_new = fields[0]
else:
if regen_fibers:
msg = (
"Warning fibers can only be regenerated in serial. "
+ "Use Piola transformation instead.\n"
)
logger.warning(msg)
if u is not None:
f0_mesh = f0.function_space().mesh()
u_elm = u.function_space().ufl_element()
V = df.FunctionSpace(f0_mesh, u_elm)
u0 = df.Function(V)
arr = gather_broadcast(u.vector().array())
assign_to_vector(u0.vector(), arr)
F = df.grad(u0) + df.Identity(3)
f0_updated = df.project(F * f0, f0.function_space())
if normalize:
f0_updated = normalize_vector_field(f0_updated)
f0_arr = gather_broadcast(f0_updated.vector().array())
assign_to_vector(f0_new.vector(), f0_arr)
else:
f0_arr = gather_broadcast(f0.vector().array())
assign_to_vector(f0_new.vector(), f0_arr)
return f0_new
def define_deformation_tensors(self):
"""
Define kinematic tensors needed for constitutive equations. Tensors
that are irrelevant to the current problem are set to 0, e.g. the
deformation gradient is set to 0 when simulating fluid flow. Secondary
tensors are added with the suffix "0" if the problem is time-dependent.
The names of member data added to an instance of the MechanicsProblem
class are:
- :code:`deformationGradient`
- :code:`deformationGradient0`
- :code:`velocityGradient`
- :code:`velocityGradient0`
- :code:`jacobian`
- :code:`jacobian0`
"""
# Exit function if tensors have already been defined.
if hasattr(self, 'deformationGradient') \
or hasattr(self, 'deformationRateGradient'):
return None
# Checks the type of material to determine which deformation
# tensors to define.
if self.config['material']['type'] == 'elastic':
I = dlf.Identity(self.mesh.geometry().dim())
self.deformationGradient = I + dlf.grad(self.displacement)
self.jacobian = dlf.det(self.deformationGradient)
if self.config['formulation']['time']['unsteady']:
self.velocityGradient = dlf.grad(self.velocity)
self.deformationGradient0 = I + dlf.grad(self.displacement0)
self.velocityGradient0 = dlf.grad(self.velocity0)
self.jacobian0 = dlf.det(self.deformationGradient0)
else:
self.velocityGradient = 0
self.deformationGradient0 = 0
self.velocityGradient0 = 0
self.jacobian0 = 0
else:
self.deformationGradient = 0
self.deformationGradient0 = 0
self.jacobian = 0
self.jacobian0 = 0
self.velocityGradient = dlf.grad(self.velocity)
if self.config['formulation']['time']['unsteady']:
self.velocityGradient0 = dlf.grad(self.velocity0)
else:
self.velocityGradient0 = 0
return None
def set_parameters(self, mesh, elastic_ratio):
assert isinstance(mesh, dlfn.Mesh)
self._mesh = mesh
self._space_dim = self._mesh.geometry().dim()
self._I = dlfn.Identity(self._space_dim)
assert isinstance(elastic_ratio, (dlfn.Constant, float))
assert float(elastic_ratio) > 0.
self._elastic_ratio = elastic_ratio
def strain_energy(self, F_):
F = self.Fe(F_)
dim = get_dimesion(F)
gradu = F - dolfin.Identity(dim)
epsilon = 0.5 * (gradu + gradu.T)
W = self.lmbda / 2 * (dolfin.tr(epsilon)**2) + self.mu * dolfin.tr(
epsilon * epsilon, )
# Active stress
Wactive = self.Wactive(F, diff=0)
return W + Wactive
def get_residual_form(u, v, rho_e, T, T_hat, KAPPA, k, alpha, mode='plane_stress', method='RAMP'):
if method=='RAMP':
C = rho_e/(1 + 8. * (1. - rho_e))
else:
C = rho_e**3
E = k * C
# C is the design variable, its values is from 0 to 1
nu = 0.3 # Poisson's ratio
lambda_ = E * nu/(1. + nu)/(1 - 2 * nu)
mu = E / 2 / (1 + nu) #lame's parameters
if mode == 'plane_stress':
lambda_ = 2*mu*lambda_/(lambda_+2*mu)
# Th = df.Constant(7)
I = df.Identity(len(u))
# w_ij = 0.5 * (df.grad(u) + df.grad(u).T) - alpha * I * T
# change May 23 penalize on alpha
T_0 = df.Constant(20)
w_ij = 0.5 * (df.grad(u) + df.grad(u).T) - C*alpha * I * (T-T_0)
v_ij = 0.5 * (df.grad(v) + df.grad(v).T)
d = len(u)
# kappa = alpha*(2*mu + 3*lambda_)
sigm = lambda_*df.div(u)*df.Identity(d) + 2*mu*w_ij
# eps_u = df.sym(df.grad(u))
# sigm = (lambda_*df.tr(eps_u)-kappa*T)*df.Identity(d) + 2*mu*eps_u
a = df.inner(sigm, v_ij) * df.dx + \
df.dot(C*KAPPA* df.grad(T-T_0), df.grad(T_hat)) * df.dx
print("get a-------")
return a
def get_residual_form(u,
v,
rho_e,
phi_angle,
k,
alpha,
method='RAMP',
Th=df.Constant(1.)):
if method == 'SIMP':
C = rho_e**3
else:
C = rho_e / (1 + 8. * (1. - rho_e))
E = k
# C is the design variable, its values is from 0 to 1
nu = 0.49 # Poisson's ratio
lambda_ = E * nu / (1. + nu) / (1 - 2 * nu)
mu = E / 2 / (1 + nu) #lame's parameters
# Th = df.Constant(5e1)
# Th = df.Constant(1.)
# Th = df.Constant(5e0)
w_ij = 0.5 * (df.grad(u) + df.grad(u).T)
v_ij = 0.5 * (df.grad(v) + df.grad(v).T)
S = df.as_matrix([[-2., 0., 0.], [0., 1., 0.], [0., 0., 1.]])
L = df.as_matrix([[df.cos(phi_angle),
df.sin(phi_angle), 0.],
[-df.sin(phi_angle),
df.cos(phi_angle), 0.], [0., 0., 1.]])
alpha_e = alpha * C
eps = w_ij - alpha_e * Th * L.T * S * L
d = len(u)
sigm = lambda_ * df.div(u) * df.Identity(d) + 2 * mu * eps
a = df.inner(sigm, v_ij) * df.dx
return a
def stress_tensor(self, L, p):
"""
Return the Cauchy stress tensor for an incompressible Newtonian fluid,
namely
.. math::
\mathbf{T} = -p\mathbf{I} + 2\mu\\text{Sym}(\mathbf{L}),
where :math:`\mathbf{L} = \\text{grad}(\mathbf{v})`, :math:`\mathbf{I}`
is the identity tensor, :math:`p` is the hydrostatic pressure, and
:math:`\mu` is the dynamic viscosity.
Parameters
----------
L : ufl.differentiation.Grad
The velocity gradient.
p : dolfin.Function, ufl.indexed.Indexed
The hydrostatic pressure.
Returns
-------
T : ufl.algebra.Sum
The Cauchy stress tensor defined above.
"""
params = self._parameters
dim = ufl.domain.find_geometric_dimension(L)
mu = dlf.Constant(params['mu'], name='mu')
I = dlf.Identity(dim)
D = dlf.sym(L)
return -p * I + dlf.Constant(2.0) * mu * D
def stress_strain(eps, lambda_, mu):
I = dolfin.Identity(DIM)
return lambda_ * dolfin.tr(eps) * I + 2 * mu * eps
def sigma(self, uu): return 2.*self.mu*self.epsilon(uu) + self.ll*dolfin.tr(self.epsilon(uu))*dolfin.Identity(self.basedim)
h = d/16.
atol = 1.e-8
mesh = dolfin.RectangleMesh(dolfin.Point(0., -0.5*d), dolfin.Point(ell, 0.5*d), int(ell/h), int(d/h))
left = dolfin.CompiledSubDomain('on_boundary && x[0] <= atol', atol=atol)#dolfin.plot(mesh)
#plt.savefig("mesh.png")
# Variational formulation
degree = 1
element = dolfin.VectorElement('P', cell="triangle", degree=degree, dim=mesh.geometric_dimension())
V = dolfin.FunctionSpace(mesh, element)
u = dolfin.Function(V,name="displacement")
u_trial = dolfin.TrialFunction(V)
v = dolfin.TestFunction(V)
E = 1.0
nu = 0.3
I2 = dolfin.Identity(mesh.geometric_dimension())
mu = dolfin.Constant(E/2./(1.+nu))
lambda_ = dolfin.Constant(E*nu/(1.+nu)/(1.-2.*nu))
def strain_displacement(u):
return dolfin.sym(dolfin.grad(u))
def stress_strain(eps):
return lambda_*dolfin.tr(eps)*I2+2*mu*eps
bilinear_form = dolfin.inner(stress_strain(strain_displacement(u_trial)),
strain_displacement(v))*dolfin.dx
traction = dolfin.Expression(('x[0] < x_right ? 0.0 : -12.*M/d/d/d*x[1]', '0.0'),
x_right=ell-atol, M=1.0, d=d, degree=degree)
def main(dt,
tEnd,
length=10.0,
height=5.0,
numElementsFilm=2.0,
reGen=True,
ratLame=5.0,
ratFilmSub=100.0):
#fileDir = ("results-dt-%.2f-tEnd-%.0f-L-%.1f-H-%.1f-ratioLame-%.0f-ratioFilm-%.0f" %
# (dt, tEnd, length, height, ratLame, ratFilmSub))
fileDir = "results-1"
# create geometry
rectDomain = Geometry(length=length, height=height, filmHeight=0.05)
rectDomain.read_mesh(numElementsFilm, reGen)
# define periodic boundary conditions
periodicBC = PeriodicBoundary(rectDomain)
# specify physical parameters
physParams = Physical_Params(lmbdaSub=ratLame, muSub=1.0, ratFilmSub=100.0)
physParams.create_Lame(rectDomain)
# create discrete function space
element = create_vector_element(rectDomain, order=1)
W = dl.FunctionSpace(rectDomain.mesh,
element,
constrained_domain=periodicBC)
# define boundaries
def left(x, on_boundary):
return dl.near(x[0], 0.) and on_boundary
def right(x, on_boundary):
return dl.near(x[0], rectDomain.length) and on_boundary
def bottom(x, on_boundary):
return dl.near(x[1], 0.0) and on_boundary
def top(x, on_boundary):
return dl.near(x[1], rectDomain.height) and on_boundary
def corner(x, on_boundary):
return dl.near(x[0], 0.0) and dl.near(x[1], 0.0)
# define fixed boundary
bcs = [
dl.DirichletBC(W.sub(0), dl.Constant(0), left),
dl.DirichletBC(W.sub(0), dl.Constant(0), right),
dl.DirichletBC(W.sub(1), dl.Constant(0), bottom),
dl.DirichletBC(W.sub(0), dl.Constant(0), corner, method="pointwise")
]
bcs = bcs[-2:]
# the variable to solve for
w = dl.Function(W, name="Variables at current step")
# test and trial function
dw = dl.TrialFunction(W)
w_ = dl.TestFunction(W)
# dealing with physics of growth
growthFactor = create_growthFactor(rectDomain, filmGrowth=1, subGrowth=0)
Fg = create_Fg(growthFactor, "uniaxial")
# kinematics
I = dl.Identity(2)
F = I + dl.grad(w)
Fe = F * dl.inv(Fg)
# write the variational form from potential energy
psi = cal_neoHookean(Fe, physParams)
Energy = psi * dl.dx
Residual = dl.derivative(Energy, w, w_)
Jacobian = dl.derivative(Residual, w, dw)
problem = BucklingProblem(w, Energy, Residual, Jacobian)
wLowerBound, wUpperBound = create_bounds(wMin=[-0.5, -0.5],
wMax=[0.5, 0.5],
functionSpace=W,
boundaryCondtions=bcs)
# Create the PETScTAOSolver
solver = dl.PETScTAOSolver()
TAOSolverParameters = {
"method": "tron",
"maximum_iterations": 1000,
"monitor_convergence": True
}
solver.parameters.update(TAOSolverParameters)
#solver.parameters["report"] = False
#solver.parameters["linear_solver"] = "umfpack"
#solver.parameters["line_search"] = "gpcg"
#solver.parameters["preconditioner"] = "ml_amg"
growthRate = 0.1
growthEnd = growthRate * tEnd
gF = 0.0
outDisp = dl.File(fileDir + "/displacement.pvd")
outDisp << (w, 0.0)
iCounter = 0
wArray = w.compute_vertex_values()
while gF <= growthEnd - tol:
gF += growthRate * dt
iCounter += 1
growthFactor.gF = gF
w.vector()[:] += 2e-04 * np.random.uniform(-1, 1,
w.vector().local_size())
nIters, converged = solver.solve(problem, w.vector(),
wLowerBound.vector(),
wUpperBound.vector())
wArray[:] = w.compute_vertex_values()
np.save(fileDir + "/w-{}.npy".format(iCounter), wArray)
print("--- growth = %.4f, niters = %d, dt = %.5f -----" %
(1 + gF, nIters, dt))
outDisp << (w, gF)
def __init__(self, domain, *args, **kwargs):
self._domain = domain
self.geometric_dimension = self.domain.mesh.ufl_cell(
).geometric_dimension()
self.identity_tensor = dolf.Identity(self.geometric_dimension)
self._complex_forms_flag = "real"
def get_residual_form(u,
v,
rho_e,
V_density,
tractionBC,
T,
iteration_number,
additive='strain',
k=8.,
method='RAMP'):
df.dx = df.dx(metadata={"quadrature_degree": 4})
# stiffness = rho_e/(1 + 8. * (1. - rho_e))
if method == 'SIMP':
stiffness = rho_e**3
else:
stiffness = rho_e / (1 + 8. * (1. - rho_e))
# print('the value of stiffness is:', rho_e.vector().get_local())
# Kinematics
d = len(u)
I = df.Identity(d) # Identity tensor
F = I + df.grad(u) # Deformation gradient
C = F.T * F # Right Cauchy-Green tensor
# Invariants of deformation tensors
Ic = df.tr(C)
J = df.det(F)
stiffen_pow = 1.
threshold_vol = 1.
eps_star = 0.05
# print("eps_star--------")
if additive == 'strain':
print("additive == strain")
if iteration_number == 1:
print('iteration_number == 1')
eps = df.sym(df.grad(u))
eps_dev = eps - 1 / 3 * df.tr(eps) * df.Identity(2)
eps_eq = df.sqrt(2.0 / 3.0 * df.inner(eps_dev, eps_dev))
# eps_eq_proj = df.project(eps_eq, density_function_space)
ratio = eps_eq / eps_star
ratio_proj = df.project(ratio, V_density)
c1_e = k * (5.e-2) / (1 + 8. * (1. - (5.e-2))) / 6
c2_e = df.Function(V_density)
c2_e.vector().set_local(5e-4 * np.ones(V_density.dim()))
fFile = df.HDF5File(df.MPI.comm_world, "c2_e_proj.h5", "w")
fFile.write(c2_e, "/f")
fFile.close()
fFile = df.HDF5File(df.MPI.comm_world, "ratio_proj.h5", "w")
fFile.write(ratio_proj, "/f")
fFile.close()
iteration_number += 1
E = k * stiffness
phi_add = (1 - stiffness) * ((c1_e * (Ic - 3)) + (c2_e *
(Ic - 3))**2)
else:
ratio_proj = df.Function(V_density)
fFile = df.HDF5File(df.MPI.comm_world, "ratio_proj.h5", "r")
fFile.read(ratio_proj, "/f")
fFile.close()
c2_e = df.Function(V_density)
fFile = df.HDF5File(df.MPI.comm_world, "c2_e_proj.h5", "r")
fFile.read(c2_e, "/f")
fFile.close()
c1_e = k * (5.e-2) / (1 + 8. * (1. - (5.e-2))) / 6
c2_e = df.conditional(df.le(ratio_proj, eps_star),
c2_e * df.sqrt(ratio_proj),
c2_e * (ratio_proj**3))
phi_add = (1 - stiffness) * ((c1_e * (Ic - 3)) + (c2_e *
(Ic - 3))**2)
E = k * stiffness
c2_e_proj = df.project(c2_e, V_density)
print('c2_e projected -------------')
eps = df.sym(df.grad(u))
eps_dev = eps - 1 / 3 * df.tr(eps) * df.Identity(2)
eps_eq = df.sqrt(2.0 / 3.0 * df.inner(eps_dev, eps_dev))
# eps_eq_proj = df.project(eps_eq, V_density)
ratio = eps_eq / eps_star
ratio_proj = df.project(ratio, V_density)
fFile = df.HDF5File(df.MPI.comm_world, "c2_e_proj.h5", "w")
fFile.write(c2_e_proj, "/f")
fFile.close()
fFile = df.HDF5File(df.MPI.comm_world, "ratio_proj.h5", "w")
fFile.write(ratio_proj, "/f")
fFile.close()
elif additive == 'vol':
print("additive == vol")
stiffness = stiffness / (df.det(F)**stiffen_pow)
# stiffness = df.conditional(df.le(df.det(F),threshold_vol), (stiffness/(df.det(F)/threshold_vol))**stiffen_pow, stiffness)
E = k * stiffness
elif additive == 'False':
print("additive == False")
E = k * stiffness # rho_e is the design variable, its values is from 0 to 1
nu = 0.4 # Poisson's ratio
lambda_ = E * nu / (1. + nu) / (1 - 2 * nu)
mu = E / 2 / (1 + nu) #lame's parameters
# Stored strain energy density (compressible neo-Hookean model)
psi = (mu / 2) * (Ic - 3) - mu * df.ln(J) + (lambda_ / 2) * (df.ln(J))**2
# print('the length of psi is:',len(psi.vector()))
if additive == 'strain':
psi += phi_add
B = df.Constant((0.0, 0.0))
# Total potential energy
'''The first term in this equation provided this error'''
Pi = psi * df.dx - df.dot(B, u) * df.dx - df.dot(T, u) * tractionBC
res = df.derivative(Pi, u, v)
return res
'fiber_files': fiber_files,
'fiber_names': fiber_names,
'element': 'p%i' % pd
}
from fenicsmechanics.materials.solid_materials import AnisotropicMaterial, FungMaterial
mat1 = AnisotropicMaterial(fiber_dict1, mesh)
hdf5_name = "fibers/n_all.h5"
f = dlf.HDF5File(MPI_COMM_WORLD, hdf5_name, 'w')
f.write(n1, "n1")
f.write(n2, "n2")
f.close()
fiber_dict2 = {
'fiber_files': hdf5_name,
'fiber_names': fiber_names[:2],
'element': 'p%i' % pd
}
mat2 = AnisotropicMaterial(fiber_dict2, mesh)
material_dict = {'kappa': 1e4, 'fibers': fiber_dict2}
mat3 = FungMaterial(mesh, inverse=True, incompressible=False, **material_dict)
u = dlf.Function(W)
F = dlf.Identity(2) + dlf.grad(u)
J = dlf.det(F)
P = mat3.stress_tensor(F, J)
def sigma(u, p, mu):
# Define stress tensor
return 2 * mu * epsilon(u) - p * dolfin.Identity(len(u))
bcs.append(DirichletBC(Vx, zero, boundary_markers, id_subdomain_fix))
bcs.append(DirichletBC(Vx, uxD_msr, boundary_markers, id_subdomain_msr))
bcs.append(DirichletBC(V, zeros, fixed_vertex_000, "pointwise"))
bcs.append(DirichletBC(Vz, zero, fixed_vertex_010, "pointwise"))
### Define hyperelastic material model
material_parameters = {'E': Constant(1.0), 'nu': Constant(0.0)}
E, nu = material_parameters.values()
d = len(u) # Displacement dimension
I = dolfin.Identity(d)
F = dolfin.variable(I + dolfin.grad(u))
C = F.T * F
J = dolfin.det(F)
I1 = dolfin.tr(C)
# Lame material parameters
lm = E * nu / ((1.0 + nu) * (1.0 - 2.0 * nu))
mu = E / (2.0 + 2.0 * nu)
# Energy density of a Neo-Hookean material model
psi = (mu / 2.0) * (I1 - d - 2.0 * dolfin.ln(J)) + (lm / 2.0) * dolfin.ln(J)**2
# First Piola-Kirchhoff
pk1 = dolfin.diff(psi, F)
def numerical_test(
user_parameters
):
time_data = []
time_data_pd = []
spacetime = []
lmbda_min_prev = 1e-6
bifurcated = False
bifurcation_loads = []
save_current_bifurcation = False
bifurcation_loads = []
comm = MPI.comm_world
default_parameters = getDefaultParameters()
default_parameters.update(user_parameters)
parameters = default_parameters
parameters['code']['script'] = __file__
signature = hashlib.md5(str(parameters).encode('utf-8')).hexdigest()
outdir = '../output/traction/{}-{}CPU'.format(signature, size)
Path(outdir).mkdir(parents=True, exist_ok=True)
log(LogLevel.INFO, 'Outdir is: '+outdir)
BASE_DIR = os.path.dirname(os.path.realpath(__file__))
print(parameters['geometry'])
d={'Lx': parameters['geometry']['Lx'],'Ly': parameters['geometry']['Ly'],
'h': parameters['material']['ell']/parameters['geometry']['n']}
geom_signature = hashlib.md5(str(d).encode('utf-8')).hexdigest()
Lx = parameters['geometry']['Lx']
Ly = parameters['geometry']['Ly']
n = parameters['geometry']['n']
ell = parameters['material']['ell']
fname = os.path.join('../meshes', 'strip-{}'.format(geom_signature))
resolution = max(parameters['geometry']['n'] * Lx / ell, 5/(Ly*10))
resolution = 3
geom = mshr.Rectangle(dolfin.Point(-Lx/2., -Ly/2.), dolfin.Point(Lx/2., Ly/2.))
mesh = mshr.generate_mesh(geom, resolution)
log(LogLevel.INFO, 'Number of dofs: {}'.format(mesh.num_vertices()*(1+parameters['general']['dim'])))
if size == 1:
meshf = dolfin.File(os.path.join(outdir, "mesh.xml"))
plot(mesh)
plt.savefig(os.path.join(outdir, "mesh.pdf"), bbox_inches='tight')
with open(os.path.join(outdir, 'parameters.yaml'), "w") as f:
yaml.dump(parameters, f, default_flow_style=False)
Lx = parameters['geometry']['Lx']
ell = parameters['material']['ell']
savelag = 1
# Function Spaces
V_u = dolfin.VectorFunctionSpace(mesh, "CG", 1)
V_alpha = dolfin.FunctionSpace(mesh, "CG", 1)
L2 = dolfin.FunctionSpace(mesh, "DG", 0)
u = dolfin.Function(V_u, name="Total displacement")
u.rename('u', 'u')
alpha = Function(V_alpha)
alpha_old = dolfin.Function(alpha.function_space())
alpha.rename('alpha', 'alpha')
dalpha = TrialFunction(V_alpha)
alpha_bif = dolfin.Function(V_alpha)
alpha_bif_old = dolfin.Function(V_alpha)
state = {'u': u, 'alpha': alpha}
Z = dolfin.FunctionSpace(mesh,
dolfin.MixedElement([u.ufl_element(),alpha.ufl_element()]))
z = dolfin.Function(Z)
v, beta = dolfin.split(z)
left = dolfin.CompiledSubDomain("near(x[0], -Lx/2.)", Lx=Lx)
right = dolfin.CompiledSubDomain("near(x[0], Lx/2.)", Lx=Lx)
bottom = dolfin.CompiledSubDomain("near(x[1],-Ly/2.)", Ly=Ly)
top = dolfin.CompiledSubDomain("near(x[1],Ly/2.)", Ly=Ly)
left_bottom_pt = dolfin.CompiledSubDomain("near(x[0],-Lx/2.) && near(x[1],-Ly/2.)", Lx=Lx, Ly=Ly)
mf = dolfin.MeshFunction("size_t", mesh, 1, 0)
right.mark(mf, 1)
left.mark(mf, 2)
bottom.mark(mf, 3)
ut = dolfin.Expression("t", t=0.0, degree=0)
bcs_u = [dolfin.DirichletBC(V_u.sub(0), dolfin.Constant(0), left),
dolfin.DirichletBC(V_u.sub(0), ut, right),
dolfin.DirichletBC(V_u, (0, 0), left_bottom_pt, method="pointwise")]
bcs_alpha = []
bcs = {"damage": bcs_alpha, "elastic": bcs_u}
ds = dolfin.Measure("ds", subdomain_data=mf)
dx = dolfin.Measure("dx", metadata=parameters['compiler'], domain=mesh)
ell = parameters['material']['ell']
# -----------------------
# Problem definition
k_res = parameters['material']['k_res']
a = (1 - alpha) ** 2. + k_res
w_1 = parameters['material']['sigma_D0'] ** 2 / parameters['material']['E']
w = w_1 * alpha
eps = sym(grad(u))
eps0t=Expression([['t', 0.],[0.,'t']], t=0., degree=0)
lmbda0 = parameters['material']['E'] * parameters['material']['nu'] /(1. - parameters['material']['nu'])**2.
mu0 = parameters['material']['E']/ 2. / (1.0 + parameters['material']['nu'])
nu = parameters['material']['nu']
sigma0 = lmbda0 * tr(eps)*dolfin.Identity(parameters['general']['dim']) + 2*mu0*eps
e1 = Constant((1., 0))
_sigma = ((1 - alpha) ** 2. + k_res)*sigma0
_snn = dolfin.dot(dolfin.dot(_sigma, e1), e1)
# -------------------
ell = parameters['material']['ell']
E = parameters['material']['E']
def elastic_energy(u,alpha, E=E, nu=nu, eps0t=eps0t, k_res=k_res):
a = (1 - alpha) ** 2. + k_res
eps = sym(grad(u))
Wt = a*E*nu/(2*(1-nu**2.)) * tr(eps)**2. \
+ a*E/(2.*(1+nu))*(inner(eps, eps))
return Wt * dx
def dissipated_energy(alpha,w_1=w_1,ell=ell):
return w_1 *( alpha + ell** 2.*inner(grad(alpha), grad(alpha)))*dx
def total_energy(u, alpha, k_res=k_res, w_1=w_1,
E=E,
nu=nu,
ell=ell,
eps0t=eps0t):
elastic_energy_ = elastic_energy(u,alpha, E=E, nu=nu, eps0t=eps0t, k_res=k_res)
dissipated_energy_ = dissipated_energy(alpha,w_1=w_1,ell=ell)
return elastic_energy_ + dissipated_energy_
def energy_1d(h, perturbation_v=Function(u.function_space()), perturbation_beta=Function(alpha.function_space())):
return assemble(total_energy(u + float(h) * perturbation_v,
alpha + float(h) * perturbation_beta))
energy = total_energy(u,alpha)
def create_output(outdir):
file_out = dolfin.XDMFFile(os.path.join(outdir, "output.xdmf"))
file_out.parameters["functions_share_mesh"] = True
file_out.parameters["flush_output"] = True
file_postproc = dolfin.XDMFFile(os.path.join(outdir, "postprocess.xdmf"))
file_postproc.parameters["functions_share_mesh"] = True
file_postproc.parameters["flush_output"] = True
file_eig = dolfin.XDMFFile(os.path.join(outdir, "perturbations.xdmf"))
file_eig.parameters["functions_share_mesh"] = True
file_eig.parameters["flush_output"] = True
file_bif = dolfin.XDMFFile(os.path.join(outdir, "bifurcation.xdmf"))
file_bif.parameters["functions_share_mesh"] = True
file_bif.parameters["flush_output"] = True
file_bif_postproc = dolfin.XDMFFile(os.path.join(outdir, "bifurcation_postproc.xdmf"))
file_bif_postproc.parameters["functions_share_mesh"] = True
file_bif_postproc.parameters["flush_output"] = True
file_ealpha = dolfin.XDMFFile(os.path.join(outdir, "elapha.xdmf"))
file_ealpha.parameters["functions_share_mesh"] = True
file_ealpha.parameters["flush_output"] = True
files = {'output': file_out,
'postproc': file_postproc,
'eigen': file_eig,
'bifurcation': file_bif,
'ealpha': file_ealpha}
return files
files = create_output(outdir)
solver = EquilibriumAM(energy, state, bcs, parameters=parameters)
stability = StabilitySolver(energy, state, bcs, parameters = parameters)
linesearch = LineSearch(energy, state)
load_steps = np.linspace(parameters['loading']['load_min'],
parameters['loading']['load_max'],
parameters['loading']['n_steps'])
tc = (parameters['material']['sigma_D0']/parameters['material']['E'])**(.5)
_eps = 1e-3
load_steps = [0., tc-_eps, tc+_eps]
time_data = []
time_data_pd = []
bifurcation_loads = []
save_current_bifurcation = False
alpha_bif = dolfin.Function(V_alpha)
alpha_bif_old = dolfin.Function(V_alpha)
bifurcation_loads = []
save_bifurcation = 1
log(LogLevel.INFO, '{}'.format(parameters))
for step, load in enumerate(load_steps):
plt.clf()
mineigs = []
exhaust_modes = []
log(LogLevel.CRITICAL, '====================== STEPPING ==========================')
log(LogLevel.CRITICAL, 'Solving load t = {:.2f}'.format(load))
alpha_old.assign(alpha)
ut.t = load
(time_data_i, am_iter) = solver.solve()
# Second order stability
(stable, negev) = stability.solve(solver.damage.problem.lb)
log(LogLevel.CRITICAL, 'Current state is{}stable'.format(' ' if stable else ' un'))
if stable:
solver.update()
else:
log(LogLevel.INFO, 'About to bifurcate load {:.3f} step {}'.format(load, step))
iteration = 1
mineigs.append(stability.mineig)
while stable == False:
log(LogLevel.INFO, 'Continuation iteration {}'.format(iteration))
iteration += 1
# plotstep()
cont_data_pre = compile_continuation_data(state, energy)
opt_mode = 0
perturbation_v = stability.perturbations_v[opt_mode]
perturbation_beta = stability.perturbations_beta[opt_mode]
(hmin, hmax) = linesearch.admissible_interval(alpha, alpha_old, perturbation_beta)
hs = np.linspace(hmin, hmax, 20)
energy_vals = np.array([energy_1d(h, perturbation_v, perturbation_beta) for h in hs])
h_opt = hs[np.argmin(energy_vals)]
log(LogLevel.INFO, 'Computed h_opt {}'.format(h_opt))
perturbation = {'v': stability.perturbations_v[opt_mode],
'beta': stability.perturbations_beta[opt_mode],
'h': h_opt}
perturbState(state, perturbation)
(time_data_i, am_iter) = solver.solve(outdir)
(stable, negev) = stability.solve(solver.damage.problem.lb)
mineigs.append(stability.mineig)
log(LogLevel.INFO, 'Continuation iteration {}, current state is{}stable'.format(iteration, ' ' if stable else ' un'))
cont_data_post = compile_continuation_data(state, energy)
# continuation criterion
if abs(np.diff(mineigs)[-1]) > parameters['stability']['cont_rtol']:
log(LogLevel.INFO, 'Continuing perturbations')
else:
log(LogLevel.CRITICAL, 'We are stuck in the matrix')
log(LogLevel.WARNING, 'Continuing load program')
break
solver.update()
if save_current_bifurcation:
plotPerturbationData()
savePerturbationData()
save_current_bifurcation = False
def compileTimeData(time_data_i, load):
time_data_i["load"] = load
time_data_i["alpha_max"] = max(alpha.vector()[:])
time_data_i["elastic_energy"] = dolfin.assemble(elastic_energy(
u,alpha, E=E, nu=nu, eps0t=eps0t, k_res=k_res))
time_data_i["dissipated_energy"] = dolfin.assemble(
(w + w_1 * parameters['material']['ell'] ** 2. * inner(grad(alpha), grad(alpha)))*dx)
time_data_i["stable"] = stability.stable
time_data_i["# neg ev"] = stability.negev
time_data_i["eigs"] = stability.eigs if hasattr(stability, 'eigs') else np.inf
time_data_i["sigma"] = 1/Ly * dolfin.assemble(_snn*ds(1))
log(LogLevel.INFO,
"Load/time step {:.4g}: converged in iterations: {:3d}, err_alpha={:.4e}".format(
time_data_i["load"],
time_data_i["iterations"][0],
time_data_i["alpha_error"][0]))
return time_data_i
time_data.append(compileTimeData(time_data_i, load))
time_data_pd = pd.DataFrame(time_data)
def outputData():
np.save(os.path.join(outdir, 'bifurcation_loads'), bifurcation_loads, allow_pickle=True, fix_imports=True)
with files['output'] as file:
file.write(alpha, load)
file.write(u, load)
with files['postproc'] as file:
file.write_checkpoint(alpha, "alpha-{}".format(step), step, append = True)
file.write_checkpoint(u, "u-{}".format(step), step, append = True)
log(LogLevel.INFO, 'Written postprocessing step {}'.format(step))
time_data_pd.to_json(os.path.join(outdir, "time_data.json"))
outputData()
return time_data_pd, outdir
#Define HDG element and function space
element_cls = geopart.stokes.incompressible.HDG2()
W = element_cls.function_space(mesh)
ds = dolfin.Measure('ds', domain=mesh, subdomain_data=boundaries)
n = dolfin.FacetNormal(mesh)
#Define boundary condition
U = element_cls.create_solution_variable(W)
p_in = dolfin.Constant(1.0) # pressure inlet
p_out = dolfin.Constant(0.0) # pressure outlet
noslip = dolfin.Constant([0.0] * mesh.geometry().dim()) # no-slip wall
#Boundary conditions
gN1 = (-p_out * dolfin.Identity(mesh.geometry().dim())) * n
Neumann_outlet = dg.DGNeumannBC(ds(mark["outlet"]), gN1)
gN2 = (-p_in * dolfin.Identity(mesh.geometry().dim())) * n
Neumann_inlet = dg.DGNeumannBC(ds(mark["inlet"]), gN2)
Dirichlet_wall = dg.DGDirichletBC(ds(mark["wall"]), noslip)
weak_bcs = [Dirichlet_wall, Neumann_inlet, Neumann_outlet]
#Body force term
f = dolfin.Constant([0.0] * mesh.geometry().dim())
model = geopart.stokes.StokesModel(eta=mu, f=f)
#Form and solve Stokes
A, b = dolfin.PETScMatrix(), dolfin.PETScVector()
element_cls.solve_stokes(W, U, (A, b), weak_bcs, model)
uh, ph = element_cls.get_velocity(U), element_cls.get_pressure(U)
print("Add output-compliance-------")
# Add output-compliance to the PDE problem:
C = density_function / (1 + 8. * (1. - density_function))
E = K * C # C is the design variable, its values is from 0 to 1
nu = 0.3 # Poisson's ratio
# Th = Th - df.Constant(20.)
lambda_ = E * nu / (1. + nu) / (1 - 2 * nu)
mu = E / 2 / (1 + nu) #lame's parameters
lambda_ = 2 * mu * lambda_ / (lambda_ + 2 * mu)
# Th = df.Constant(7)
I = df.Identity(len(displacements_function))
# w_ij = 0.5 * (df.grad(displacements_function) + df.grad(displacements_function).T) - ALPHA * I * temperature_function
# sigm = lambda_*df.div(displacements_function)* I + 2*mu*w_ij
# s = sigm - (1./3)*df.tr(sigm)*I
# von_Mises = df.sqrt(3./2*df.inner(s, s))
# von_Mises_form = (1/df.CellVolume(mesh)) * von_Mises * df.TestFunction(density_function_space) * df.dx
# T = df.TensorFunctionSpace(mesh, "CG", 1)
# T.vector.set_local()
T_00 = df.Constant(20)
w_ij = 0.5 * (df.grad(displacements_function) + df.grad(
displacements_function).T) - C * ALPHA * I * (temperature_function - T_00)
sigm = lambda_ * df.div(displacements_function) * I + 2 * mu * w_ij
s = sigm - (1. / 3) * df.tr(sigm) * I
scalar_ = 5e8
def stress(u, p, mu):
return 2 * mu * epsilon(u) - p * df.Identity(len(u))