def compute_steady_state(self):
names = {'Cl', 'Na', 'K'}
P1 = FiniteElement('P', fe.triangle, 1)
element = MixedElement([P1, P1, P1])
V = FunctionSpace(self.mesh, element)
self.V_conc = V
(u_cl, u_na, u_k) = TrialFunction(V)
(v_cl, v_na, v_k) = TestFunction(V)
assert (self.flow is not None)
n = fe.FacetNormal(self.mesh)
# F = ( self.F_diff_conv(u_cl, v_cl, n, grad(self.phi), 1. ,1., 0.)
# + self.F_diff_conv(u_na, v_na, n, grad(self.phi), 1. ,1., 0.)
# + self.F_diff_conv(u_k , v_k , n, grad(self.phi), 1. ,1., 0.) )
dx, ds = self.dx, self.ds
flow = self.flow
F = inner(grad(u_cl), grad(v_cl)) * dx \
+ inner(flow, grad(u_cl)) * v_cl * dx \
+ inner(grad(u_na), grad(v_na)) * dx \
+ inner(flow, grad(u_na)) * v_na * dx \
+ inner(grad(u_k), grad(v_k)) * dx \
+ inner(flow, grad(u_k)) * v_k * dx
a, L = fe.lhs(F), fe.rhs(F)
a_mat = fe.assemble(a)
L_vec = fe.assemble(L)
# solve
u = Function(V)
fe.solve(a_mat, u.vector(), L_vec)
u_cl, u_na, u_k = u.split()
output1 = fe.File('/tmp/steady_state_cl.pvd')
output1 << u_cl
output2 = fe.File('/tmp/steady_state_na.pvd')
output2 << u_na
output3 = fe.File('/tmp/steady_state_k.pvd')
output3 << u_k
self.u_cl = u_cl
self.u_na = u_na
self.u_k = u_k
def set_data_dirs(self):
if not os.path.exists(self.postprocessing_dir):
os.makedirs(self.postprocessing_dir)
if not os.path.exists(self.fem_solution_storage_dir):
os.makedirs(self.fem_solution_storage_dir)
if not os.path.exists(self.movie_dir):
os.makedirs(self.movie_dir)
if not os.path.exists(self.vtk_dir):
os.makedirs(self.vtk_dir)
if not os.path.exists(self.slope_field_dir):
os.makedirs(self.slope_field_dir)
if not os.path.exists(self.slope_field_movie_dir):
os.makedirs(self.slope_field_movie_dir)
if not os.path.exists(self.potential_dir):
os.makedirs(self.potential_dir)
if not os.path.exists(self.potential_movie_dir):
os.makedirs(self.potential_movie_dir)
txt = 'solution.pvd'
fname = os.path.join(self.vtk_dir, txt)
self.vtkfile = fe.File(fname)
def set_data_dirs(self):
with_hg = 'HG-NPs_tumor-bearing'
no_hg = 'NPS_TUMOR-BEARING'
if self.use_hg:
hg_state = with_hg
else:
hg_state = no_hg
lambda_label = str(self.lam != 0)
self.fem_opt_data_source_dir = os.path.join(os.getcwd(),\
'raw_data/Tumor-bearing',\
hg_state)
self.fem_opt_exp_data_vec_dir = os.path.join(\
self.fem_opt_data_source_dir,\
'fem_m_' + str(self.experimental_z_n))
if not os.path.exists(self.fem_opt_exp_data_vec_dir):
os.makedirs(self.fem_opt_exp_data_vec_dir)
txt = 'diffusion_' + 'lambda_' + lambda_label
self.fem_opt_img_storage_dir = os.path.join(\
self.fem_opt_data_source_dir,\
txt)
if not os.path.exists(self.fem_opt_img_storage_dir):
os.makedirs(self.fem_opt_img_storage_dir)
txt = 'solution.pvd'
fname = os.path.join(self.fem_opt_img_storage_dir, txt)
self.vtkfile = fe.File(fname)
def create_cocontinuous_mesh(self):
if self.use_previously_stored_mesh:
self.mesh = fe.Mesh(self.mesh_fname)
print('Mesh has been loaded from file')
return
p = self.L * np.ones(3)
geo = mesher.Box(fe.Point(0,0,0), fe.Point(p))
net = self.extrude_base_net()
columns = self.create_cylindrical_columns()
net += columns
if self.keep_only_network:
geo = net
else:
geo -= net
print('Finished creating the geometry')
self.mesh = mesher.generate_mesh(geo, self.mesh_density);
print('Writing mesh to file')
mesh_file = fe.File(self.mesh_fname)
mesh_file << self.mesh
print('Finished writing mesh to file')
def mfem():
files = glob.glob('data/pvd/mfem/*')
for f in files:
try:
os.remove(f)
except Exception as e:
print('Failed to delete {}, reason: {}' % (f, e))
plate = mshr.Rectangle(fe.Point(0, 0), fe.Point(100, 100))
mesh = mshr.generate_mesh(plate, 50)
# mesh = fe.RectangleMesh(fe.Point(-2, -2), fe.Point(2, 2), 50, 50)
x_hat = fe.SpatialCoordinate(mesh)
U = fe.VectorFunctionSpace(mesh, 'CG', 2)
V = fe.FunctionSpace(mesh, "CG", 1)
W = fe.FunctionSpace(mesh, "DG", 0)
# n = 21
# control_points = np.stack((np.linspace(0, 1, n), np.linspace(0, 1, n)), axis=1)
# impact_radii = np.linspace(0., 0.5, n)
rho_default = 25. / np.sqrt(5) * 2
control_points = np.array([[50., 50.], [62.5, 25.]])
impact_radii = np.array([rho_default, rho_default])
mid_point = np.array([75., 0.])
mid_point1 = np.array([100., 0.])
mid_point2 = np.array([50., 0.])
points = [mid_point, mid_point1, mid_point2]
direct_vec = np.array([1., -2])
rotated_vec = np.array([2., 1.])
direct_vec /= np.linalg.norm(direct_vec)
rotated_vec /= np.linalg.norm(rotated_vec)
directions = [direct_vec, rotated_vec]
boundary_info = [points, directions, rho_default]
# df, xi = distance_function_segments_ufl(x_hat, control_points, impact_radii)
# d = fe.project(df, V)
delta_x = map_function_ufl(x_hat, control_points, impact_radii,
boundary_info) - x_hat
u = fe.project(delta_x, U)
# e = fe.Function(U)
# int_exp = InterpolateExpression(u, control_points, impact_radii)
# e = fe.interpolate(int_exp, U)
# int_exp = InterpolateExpression(e, control_points, impact_radii)
# e = fe.project(int_exp, U)
vtkfile_u = fe.File('data/pvd/mfem/u.pvd')
u.rename("u", "u")
vtkfile_u << u
def preprocess(fname):
"""Loads mesh, defines system of equations and prepares system matrix."""
mesh = fe.Mesh(fname + ".xml")
if INPUTS['saving']['mesh']:
fe.File(fname + "_mesh.pvd") << mesh
boundaries = fe.MeshFunction('size_t', mesh, fname + '_facet_region.xml')
if INPUTS['saving']['boundaries']:
fe.File(fname + "_subdomains.pvd") << boundaries
subdomains = fe.MeshFunction('size_t', mesh,
fname + '_physical_region.xml')
if INPUTS['saving']['subdomains']:
fe.File(fname + "_subdomains.pvd") << subdomains
if INPUTS['plotting']['mesh']:
fe.plot(mesh, title='Mesh')
if INPUTS['plotting']['boundaries']:
fe.plot(boundaries, title='Boundaries')
if INPUTS['plotting']['subdomains']:
fe.plot(subdomains, title='Subdomains')
fun_space = fe.FunctionSpace(mesh,
INPUTS['element_type'],
INPUTS['element_degree'],
constrained_domain=PeriodicDomain())
if ARGS['--verbose']:
dofmap = fun_space.dofmap()
print('Number of DOFs:', len(dofmap.dofs()))
field = fe.TrialFunction(fun_space)
test_func = fe.TestFunction(fun_space)
cond = Conductivity(subdomains,
fe.Constant(INPUTS['conductivity']['gas']),
fe.Constant(INPUTS['conductivity']['solid']),
degree=0)
system_matrix = -cond * fe.inner(fe.grad(field),
fe.grad(test_func)) * fe.dx
bctop = fe.Constant(INPUTS['boundary_conditions']['top'])
bcbot = fe.Constant(INPUTS['boundary_conditions']['bottom'])
bcs = [
fe.DirichletBC(fun_space, bctop, boundaries, 1),
fe.DirichletBC(fun_space, bcbot, boundaries, 2)
]
field = fe.Function(fun_space)
return system_matrix, field, bcs, cond
def xest_second_tutorial(self):
T = 2.0 # final time
num_steps = 50 # number of time steps
dt = T / num_steps # time step size
# Create mesh and define function space
nx = ny = 30
mesh = fenics.RectangleMesh(fenics.Point(-2, -2), fenics.Point(2, 2),
nx, ny)
V = fenics.FunctionSpace(mesh, 'P', 1)
# Define boundary condition
def boundary(x, on_boundary):
return on_boundary
bc = fenics.DirichletBC(V, fenics.Constant(0), boundary)
# Define initial value
u_0 = fenics.Expression('exp(-a*pow(x[0], 2) - a*pow(x[1], 2))',
degree=2,
a=5)
u_n = fenics.interpolate(u_0, V)
# Define variational problem
u = fenics.TrialFunction(V)
v = fenics.TestFunction(V)
f = fenics.Constant(0)
F = u * v * fenics.dx + dt * fenics.dot(fenics.grad(u), fenics.grad(
v)) * fenics.dx - (u_n + dt * f) * v * fenics.dx
a, L = fenics.lhs(F), fenics.rhs(F)
# Create VTK file for saving solution
vtkfile = fenics.File(
os.path.join(os.path.dirname(__file__), 'output', 'heat_gaussian',
'solution.pvd'))
# Time-stepping
u = fenics.Function(V)
t = 0
not_initialised = True
for n in range(num_steps):
# Update current time
t += dt
# Compute solution
fenics.solve(a == L, u, bc)
# Save to file and plot solution
vtkfile << (u, t)
# Here we'll need to call tripcolor ourselves to get access to the color range
fenics.plot(u)
animation_camera.snap()
u_n.assign(u)
animation = animation_camera.animate()
animation.save(
os.path.join(os.path.dirname(__file__), 'output',
'heat_gaussian.mp4'))
def setup_fe(self):
# Define the relevant function spaces
V = d.FunctionSpace(self.mesh, "Lagrange", 1)
self.V = V
# DG0 is useful for defining piecewise constant functions
DV = d.FunctionSpace(self.mesh, "Discontinuous Lagrange", 0)
self.DV = DV
# Define test and trial functions for FE
self.z = d.TrialFunction(self.V)
self.w = d.TestFunction(self.V)
regions = self.per_tissue_constant(lambda l: l)
region_file = d.File("../%s-regions.pvd" % input_mesh)
region_file << regions
def __init__(self):
self.h = .4
# Cell properties
self.obs_length = 0.9
self.obs_height = 0.001
self.obs_ratio = self.obs_height / self.obs_length
if self.h < self.eta:
raise ValueError("Eta must be smaller than h")
self.ref_T = 0.1
self.eps = 2 * self.eta / MembraneSimulator.length
self.mesh = fe.RectangleMesh(
fe.Point(-1, 0),
fe.Point(1, 2 * self.h / MembraneSimulator.length), 50, 50)
self.cell_mesh = None
self.D = np.matrix(((4 * self.ref_T * MembraneSimulator.d1 /
MembraneSimulator.length**2, -0.05),
(+0.05, 4 * self.ref_T * MembraneSimulator.d2 /
MembraneSimulator.length**2)))
# Dirichlet boundary conditions
self.u_l = 6E-5
self.u_r = 0
self.u_boundary = fe.Expression(
'(u_l*(x[0] < - par) + u_r*(x[0] >= par))',
u_l=self.u_l,
u_r=self.u_r,
par=MembraneSimulator.w / MembraneSimulator.length,
degree=2)
self.u_0 = self.u_boundary / 2
# self.rhs = fe.Expression('(x[1]>par)*u',u=self.u_l*4,par=MembraneSimulator.eta/MembraneSimulator.length, degree=2)
self.rhs = fe.Constant(0)
self.time = 0
self.T = 1
self.dt = 0.01
self.tol = 1E-4
self.function_space = fe.FunctionSpace(self.mesh, 'P', 2)
self.solution = fe.Function(self.function_space)
self.cell_solutions = self.cell_fs = None
self.unit_vectors = [fe.Constant((1., 0.)), fe.Constant((0., 1.))]
self.eff_diff = np.zeros((2, 2))
self.file = fe.File('results/solution.pvd')
def run_solver_c(
ndim,
length,
units,
bcs,
u0,
powers,
nx,
F,
coordinates=False,
is_plot=False,
vtk=False,
):
ny = nx
nz = nx if ndim == 3 else None
u_D = fs.Constant(u0)
if len(bcs) > 0 and bcs[0] != []:
if ndim == 2:
bc_funs = [LineBoundary(line).get_boundary() for line in bcs]
else:
bc_funs = [RecBoundary(rec).get_boundary() for rec in bcs]
else:
bc_funs = [lambda x, on_boundary: on_boundary] # 边界都为 Dirichlet
f = SourceF(F, length)
u = solver(f, u_D, bc_funs, ndim, length, nx, ny, nz)
if is_plot:
import matplotlib.pyplot as plt
plt.plot(u)
if vtk:
vtkfile = fs.File("solution.pvd")
vtkfile << u
if ndim == 2:
U = u.compute_vertex_values().reshape(nx + 1, nx + 1)
else:
U = u.compute_vertex_values().reshape(nx + 1, nx + 1, nx + 1)
if coordinates:
xs, ys, zs = get_mesh_grid(length, nx, ny, nz)
else:
xs, ys, zs = None, None, None
return U, xs, ys, zs
def calculate_efield_fenics(si):
numerical_vars = si.numerical_variables
u = numerical_vars["ef_phi"]
assert u is not None, "Please calculate the potential first!"
print("Calculating the electric field... ", end="", flush=True)
fenics_field = fn.project(-fn.grad(u), solver_type='cg', preconditioner_type='ilu')
electric_field = FenicsField(fenics_field)
numerical_vars["ef_itp"] = electric_field
si.numerical_variables = numerical_vars
fieldfile = fn.File(TEMP_DIR + '/e_field.pvd')
fieldfile << fenics_field
print("Done!", flush=True)
return 0
def postprocess(fname, field, cond):
"""Postprocessing of the simulation."""
func_space = field.function_space()
mesh = func_space.mesh()
degree = func_space.ufl_element().degree()
vec_func_space = fe.VectorFunctionSpace(mesh, INPUTS['element_type'],
degree)
flux = fe.project(-cond * fe.grad(field), vec_func_space)
divergence = fe.project(-fe.div(cond * fe.grad(field)), func_space)
flux_x, flux_y, flux_z = flux.split()
av_flux = fe.assemble(flux_z * fe.dx) / ((XMAX - XMIN) * (YMAX - YMIN))
keff = av_flux * (ZMAX - ZMIN) / (INPUTS['boundary_conditions']['top'] -
INPUTS['boundary_conditions']['bottom'])
print('Effective conductivity: {0}'.format(keff))
with open(fname + "_keff.csv", 'w') as textfile:
textfile.write('keff\n')
textfile.write('{0}\n'.format(keff))
fe.File(fname + "_solution.pvd") << field
if INPUTS['saving']['flux']:
fe.File(fname + "_flux.pvd") << flux
if INPUTS['saving']['flux_divergence']:
fe.File(fname + "_flux_divergence.pvd") << divergence
if INPUTS['saving']['flux_components']:
fe.File(fname + "_flux_x.pvd") << flux_x
fe.File(fname + "_flux_y.pvd") << flux_y
fe.File(fname + "_flux_z.pvd") << flux_z
if INPUTS['plotting']['solution']:
fe.plot(field, title="Solution")
if INPUTS['plotting']['flux']:
fe.plot(flux, title="Flux")
if INPUTS['plotting']['flux_divergence']:
fe.plot(divergence, title="Divergence")
if INPUTS['plotting']['flux_components']:
fe.plot(flux_x, title='x-component of flux (-kappa*grad(u))')
fe.plot(flux_y, title='y-component of flux (-kappa*grad(u))')
fe.plot(flux_z, title='z-component of flux (-kappa*grad(u))')
if True in INPUTS['plotting'].values():
fe.interactive()
def _write_fenics_file(data, path):
fn.File(path) << data
def write_vtk(self):
"""
write the output
"""
vtkfile = FEN.File(self._vtk_filename)
vtkfile << self._u
alpha / 2 * f**2 * fa.dx)
control = da.Control(f)
rf = da.ReducedFunctional(J, control)
# set the initial value to be zero for optimization
f.vector()[:] = 0
# N = len(f.vector()[:])
# f.vector()[:] = np.random.rand(N)*2 -1
problem = da.MoolaOptimizationProblem(rf)
f_moola = moola.DolfinPrimalVector(f)
solver = moola.BFGS(problem,
f_moola,
options={
'jtol': 0,
'gtol': 1e-9,
'Hinit': "default",
'maxiter': 100,
'mem_lim': 10
})
sol = solver.solve()
f_opt = sol['control'].data
file = fa.File('f.pvd')
f_opt.rename('f', 'f')
file << f_opt
file = fa.File('g.pvd')
g.rename('g', 'g')
file << g
def _load_fct(path):
assert mesh, 'Need to specify a mesh on which to generate the region marker function'
data = fn.MeshFunction('size_t', mesh, mesh.topology().dim())
fn.File(path) >> data
return data
if MODEL:
bcSet = [
bc_1, bc_2, bc_3, bc_inflow, bc_p, bc_v_x0, bc_v_x1, bc_v_y1, bc_v_in,
bc_v_top
]
else:
bcSet = [bc_1, bc_2, bc_3, bc_inflow, bc_p]
problem = fe.NonlinearVariationalProblem(weakForm, W0, bcSet, J=dFdW)
solver = fe.NonlinearVariationalSolver(problem)
prm = solver.parameters
t = 0.0
t_end = 5.0
pFile = fe.File('Pressure.pvd')
uFile = fe.File('Velocity.pvd')
vFile = fe.File('Vorticity.pvd')
wFile = fe.File('W.pvd')
T = fe.FunctionSpace(mesh, 'CG', 1)
#solver.solve()
while t < t_end:
print("t =", t)
solver.solve()
u1, p1 = W0.split()
uFile << u1
pFile << p1
We.assign(W0)
wFile << W0
omega = fe.curl(u)
vFile << fe.project(fe.inner(omega, omega), T)
def __init__(self, optimization_problem):
"""Parent class for the optimization methods implemented in cashocs.optimization.methods
Parameters
----------
optimization_problem : cashocs.ShapeOptimizationProblem
the optimization problem
"""
self.line_search_broken = False
self.has_curvature_info = False
self.optimization_problem = optimization_problem
self.form_handler = self.optimization_problem.form_handler
self.state_problem = self.optimization_problem.state_problem
self.config = self.state_problem.config
self.adjoint_problem = self.optimization_problem.adjoint_problem
self.shape_gradient_problem = self.optimization_problem.shape_gradient_problem
self.gradient = self.shape_gradient_problem.gradient
self.cost_functional = self.optimization_problem.reduced_cost_functional
self.search_direction = fenics.Function(
self.form_handler.deformation_space)
if self.config.getboolean('Mesh', 'remesh', fallback=False):
self.iteration = self.optimization_problem.temp_dict[
'OptimizationRoutine'].get('iteration_counter', 0)
else:
self.iteration = 0
self.objective_value = 1.0
self.gradient_norm_initial = 1.0
self.relative_norm = 1.0
self.stepsize = 1.0
self.converged = False
self.converged_reason = 0
self.output_dict = dict()
try:
self.output_dict[
'cost_function_value'] = self.optimization_problem.temp_dict[
'output_dict']['cost_function_value']
self.output_dict[
'gradient_norm'] = self.optimization_problem.temp_dict[
'output_dict']['gradient_norm']
self.output_dict['stepsize'] = self.optimization_problem.temp_dict[
'output_dict']['stepsize']
self.output_dict[
'MeshQuality'] = self.optimization_problem.temp_dict[
'output_dict']['MeshQuality']
except (TypeError, KeyError):
self.output_dict['cost_function_value'] = []
self.output_dict['gradient_norm'] = []
self.output_dict['stepsize'] = []
self.output_dict['MeshQuality'] = []
self.verbose = self.config.getboolean('Output',
'verbose',
fallback=True)
self.save_results = self.config.getboolean('Output',
'save_results',
fallback=True)
self.rtol = self.config.getfloat('OptimizationRoutine',
'rtol',
fallback=1e-3)
self.atol = self.config.getfloat('OptimizationRoutine',
'atol',
fallback=0.0)
self.maximum_iterations = self.config.getint('OptimizationRoutine',
'maximum_iterations',
fallback=100)
self.soft_exit = self.config.getboolean('OptimizationRoutine',
'soft_exit',
fallback=False)
self.save_pvd = self.config.getboolean('Output',
'save_pvd',
fallback=False)
self.result_dir = self.config.get('Output',
'result_dir',
fallback='./')
if self.save_pvd:
self.state_pvd_list = []
for i in range(self.form_handler.state_dim):
if self.form_handler.state_spaces[i].num_sub_spaces() > 0:
self.state_pvd_list.append([])
for j in range(self.form_handler.state_spaces[i].
num_sub_spaces()):
if self.optimization_problem.mesh_handler.do_remesh:
self.state_pvd_list[i].append(
fenics.
File(self.result_dir + '/pvd/remesh_' + format(
self.optimization_problem.temp_dict.get(
'remesh_counter', 0), 'd') +
'_state_' + str(i) + '_' + str(j) +
'.pvd'))
else:
self.state_pvd_list[i].append(
fenics.File(self.result_dir + '/pvd/state_' +
str(i) + '_' + str(j) + '.pvd'))
else:
if self.optimization_problem.mesh_handler.do_remesh:
self.state_pvd_list.append(
fenics.File(self.result_dir + '/pvd/remesh_' +
format(
self.optimization_problem.temp_dict
.get('remesh_counter', 0), 'd') +
'_state_' + str(i) + '.pvd'))
else:
self.state_pvd_list.append(
fenics.File(self.result_dir + '/pvd/state_' +
str(i) + '.pvd'))
def forward(lmin, pml, steps, Folder):
"""
Algorithm to solve the forward problem
*Input arguments
minl: Minimum lenght of element
pml: Size of the absorbing layer in km
steps: Number of timesteps
Folder: Folder name for results
*Output arguments
c: Field of propagation speed in domain
eta: Field of damping in domain
histrec: Historical data receivers
"""
histrec = ''
# Create and define function space
V = fn.FunctionSpace(mesh, "CG", 1)
w = fn.TrialFunction(V)
v = fn.TestFunction(V)
# Boundary conditions u0 = 0.0
bc = fn.DirichletBC(V, 0.0, fn.DomainBoundary())
# State variable and source space functions
w = fn.Function(V, name="Veloc")
w_ant1 = fn.Function(V)
w_ant2 = fn.Function(V)
q = fn.Function(V, name="Sourc")
# Velocity mapping
c_func = vel_c()
c = fn.interpolate(c_func, V)
velp_file = fn.File(Folder + "/Velp.pvd")
velp_file << c
# Damping mapping
damping_func = damping(c.vector().get_local().min())
eta = fn.interpolate(damping_func, V)
damp_file = fn.File(Folder + "/Damp.pvd")
damp_file << eta
# Current time we are solving for
t = 0.
# Number of timesteps solved
ntimestep = int(0)
# dt computation
dt = critical_dt(lmin, c.vector().get_local().max(), steps)
# Final time
T = steps*dt
print("Time step:", dt, "s")
# "Bilinear term"
def aterm(u, v, dt, c, eta):
termgrad = dt**2*fn.inner(c, c)*fn.inner(fn.grad(u), fn.grad(v))*fn.dx
termvare = (1.0 + dt*eta*fn.inner(c, c))*fn.inner(u, v)*fn.dx
termboun = (dt**2*c*c)*fn.inner(fn.grad(u), n)*v*fn.ds
return termgrad + termvare - termboun
# Source term
def lsourc(u_ant1, u_ant2, v, dt, c, q, eta):
termua1 = (-2. + dt*eta*fn.inner(c, c))*fn.inner(u_ant1, v)*fn.dx
termua2 = fn.inner(u_ant2, v)*fn.dx
termsou = (dt**2*fn.inner(c, c))*fn.inner(q, v)*fn.dx
return termua1 + termua2 - termsou
# Output file names
Exct = fn.File(Folder+"/Exct.pvd")
Wave = fn.File(Folder+"/Wave.pvd")
while True:
# Update the time it is solving for
print("Step: {0:1d} - Time: {1:1.4f}".format(ntimestep, t), "s")
# Ricker source for time t
ExcSource = RickerSource(t, tol=lmin/2)
q.assign(fn.interpolate(ExcSource, V))
# Time integration loop
if ntimestep < 1:
g = fn.interpolate(fn.Expression('0.0', degree=2), V)
w.assign(g) # assign initial guess for solver
w_ant1.assign(g) # assign initial guess for solver
w_ant2.assign(g) # assign initial guess for solver
else:
a = aterm(w, v, dt, c, eta)
L = lsourc(w_ant1, w_ant2, v, dt, c, q, eta)
#solve equation
fn.solve(a + L == 0, w, bcs=bc, solver_parameters={"newton_solver":
{"maximum_iterations": forward_max_it, "absolute_tolerance": forward_tol,
"relative_tolerance": relativ_tol}})
# Cycling the variables
w_ant2.assign(w_ant1)
w_ant1.assign(w)
#Output files
# histrec += Receiver(t, posrec, pml, w)
Exct << (q, t)
Wave << (w, t)
t += dt
ntimestep += 1
if t >= T:
break
return c, eta, histrec
def _save_fct(data, path):
fn.File(path) << data
prm['newton_solver']['krylov_solver']['relative_tolerance'] = 1E-5
prm['newton_solver']['krylov_solver']['maximum_iterations'] = 1000
prm['newton_solver']['krylov_solver']['nonzero_initial_guess'] = True
if prm['newton_solver']['linear_solver'] == 'gmres':
prm['newton_solver']['preconditioner'] = 'ilu'
# Invoke the solver
#cprint("\nSOLUTION OF THE NONLINEAR PROBLEM", 'blue', attrs=['bold'])
#cprint("The solution of the nonlinear system is in progress...", 'red')
solver.solve()
############################# POST-PROCESSING ################################
#cprint("\nSOLUTION POST-PROCESSING", 'blue', attrs=['bold'])
# Save solution to file in VTK format
#cprint("Saving displacement solution to file...", 'green')
uViewer = fe.File('paraview/displacement.pvd')
uViewer << u
# Maximum and minimum displacement
u_magnitude = fe.sqrt(fe.dot(u, u))
u_magnitude = fe.project(u_magnitude, W)
print('Min/Max displacement:',
u_magnitude.vector().array().min(),
u_magnitude.vector().array().max())
# Computation of the large deformation strains
#cprint("Computing the deformation tensor and saving to file...", 'green')
epsilon_u = largeKinematics(u)
epsilon_u_project = fe.project(epsilon_u, Z)
epsilonViewer = fe.File('paraview/strain.pvd')
epsilonViewer << epsilon_u_project
def staggered_solve(self):
self.U = fe.VectorFunctionSpace(self.mesh, 'CG', 1)
self.W = fe.FunctionSpace(self.mesh, 'CG', 1)
self.WW = fe.FunctionSpace(self.mesh, 'DG', 0)
self.EE = fe.TensorFunctionSpace(self.mesh, 'DG', 0)
self.MM = fe.VectorFunctionSpace(self.mesh, 'CG', 1)
self.eta = fe.TestFunction(self.U)
self.zeta = fe.TestFunction(self.W)
q = fe.TestFunction(self.WW)
del_x = fe.TrialFunction(self.U)
del_d = fe.TrialFunction(self.W)
p = fe.TrialFunction(self.WW)
self.x_new = fe.Function(self.U, name="u")
self.d_new = fe.Function(self.W, name="d")
self.d_pre = fe.Function(self.W)
self.x_pre = fe.Function(self.U)
x_old = fe.Function(self.U)
d_old = fe.Function(self.W)
self.H_old = fe.Function(self.WW)
self.map_plot = fe.Function(self.MM, name="m")
e = fe.Function(self.EE, name="e")
self.create_custom_xdmf_files()
self.file_results = fe.XDMFFile('data/xdmf/{}/u.xdmf'.format(
self.case_name))
self.file_results.parameters["functions_share_mesh"] = True
vtkfile_e = fe.File('data/pvd/simulation/{}/e.pvd'.format(
self.case_name))
vtkfile_u = fe.File('data/pvd/simulation/{}/u.pvd'.format(
self.case_name))
vtkfile_d = fe.File('data/pvd/simulation/{}/d.pvd'.format(
self.case_name))
for i, (disp, rp) in enumerate(
zip(self.displacements, self.relaxation_parameters)):
print('\n')
print(
'================================================================================='
)
print('>> Step {}, disp boundary condition = {} [mm]'.format(
i, disp))
print(
'================================================================================='
)
self.i = i
self.update_weak_form_due_to_Model_C_bug()
if self.update_weak_form:
self.set_bcs_staggered()
print("Update weak form...")
self.build_weak_form_staggered()
print("Taking derivatives of weak form...")
J_u = fe.derivative(self.G_u, self.x_new, del_x)
J_d = fe.derivative(self.G_d, self.d_new, del_d)
print("Define nonlinear problems...")
p_u = fe.NonlinearVariationalProblem(self.G_u, self.x_new,
self.BC_u, J_u)
p_d = fe.NonlinearVariationalProblem(self.G_d, self.d_new,
self.BC_d, J_d)
print("Define solvers...")
solver_u = fe.NonlinearVariationalSolver(p_u)
solver_d = fe.NonlinearVariationalSolver(p_d)
self.update_weak_form = False
print("Update history weak form")
a = p * q * fe.dx
L = history(self.H_old, self.update_history(),
self.psi_cr) * q * fe.dx
if self.map_flag:
self.interpolate_map()
# delta_x = self.x - self.x_hat
# self.map_plot.assign(fe.project(delta_x, self.MM))
self.presLoad.t = disp
newton_prm = solver_u.parameters['newton_solver']
newton_prm['maximum_iterations'] = 100
# newton_prm['absolute_tolerance'] = 1e-8
newton_prm['relaxation_parameter'] = rp
newton_prm = solver_d.parameters['newton_solver']
newton_prm['maximum_iterations'] = 100
# newton_prm['absolute_tolerance'] = 1e-8
newton_prm['relaxation_parameter'] = rp
vtkfile_e_staggered = fe.File(
'data/pvd/simulation/{}/step{}/e.pvd'.format(
self.case_name, i))
vtkfile_u_staggered = fe.File(
'data/pvd/simulation/{}/step{}/u.pvd'.format(
self.case_name, i))
vtkfile_d_staggered = fe.File(
'data/pvd/simulation/{}/step{}/d.pvd'.format(
self.case_name, i))
iteration = 0
err = 1.
while err > self.staggered_tol:
iteration += 1
solver_d.solve()
solver_u.solve()
if self.solution_scheme == 'explicit':
break
# # Remarks(Tianju): self.x_new.vector() does not behave as expected: producing nan values
# The following lines of codes cause issues
# We use an error measure similar in https://doi.org/10.1007/s10704-019-00372-y
# np_x_new = np.asarray(self.x_new.vector())
# np_d_new = np.asarray(self.d_new.vector())
# np_x_old = np.asarray(x_old.vector())
# np_d_old = np.asarray(d_old.vector())
# err_x = np.linalg.norm(np_x_new - np_x_old) / np.sqrt(len(np_x_new))
# err_d = np.linalg.norm(np_d_new - np_d_old) / np.sqrt(len(np_d_new))
# err = max(err_x, err_d)
# # Remarks(Tianju): dolfin (2019.1.0) errornorm function has severe bugs not behave as expected
# The bug seems to be fixed in later versions
# The following sometimes produces nonzero results in dolfin (2019.1.0)
# print(fe.errornorm(self.d_new, self.d_new, norm_type='l2'))
err_x = fe.errornorm(self.x_new, x_old, norm_type='l2')
err_d = fe.errornorm(self.d_new, d_old, norm_type='l2')
err = max(err_x, err_d)
x_old.assign(self.x_new)
d_old.assign(self.d_new)
e.assign(
fe.project(strain(self.mfem_grad(self.x_new)), self.EE))
print(
'---------------------------------------------------------------------------------'
)
print(
'>> iteration. {}, err_u = {:.5}, err_d = {:.5}, error = {:.5}'
.format(iteration, err_x, err_d, err))
print(
'---------------------------------------------------------------------------------'
)
# vtkfile_e_staggered << e
# vtkfile_u_staggered << self.x_new
# vtkfile_d_staggered << self.d_new
if err < self.staggered_tol or iteration >= self.staggered_maxiter:
print(
'================================================================================='
)
print('\n')
break
print("L2 projection to update the history function...")
fe.solve(a == L, self.H_old, [])
# self.d_pre.assign(self.d_new)
# self.H_old.assign(fe.project(history(self.H_old, self.update_history(), self.psi_cr), self.WW))
if self.map_flag and not self.finish_flag:
self.update_map()
if self.compute_and_save_intermediate_results:
print("Save files...")
self.file_results.write(e, i)
self.file_results.write(self.x_new, i)
self.file_results.write(self.d_new, i)
self.file_results.write(self.map_plot, i)
vtkfile_e << e
vtkfile_u << self.x_new
vtkfile_d << self.d_new
# Assume boundary is not affected by the map.
# There's no need to use the mfem_grad wrapper so that fe.grad is used for speed-up
print("Define forces...")
sigma = cauchy_stress_plus(strain(fe.grad(self.x_new)),
self.psi)
sigma_minus = cauchy_stress_minus(strain(fe.grad(self.x_new)),
self.psi_minus)
sigma_plus = cauchy_stress_plus(strain(fe.grad(self.x_new)),
self.psi_plus)
sigma_degraded = g_d(self.d_new) * sigma_plus + sigma_minus
print("Compute forces...")
if self.case_name == 'pure_shear':
f_full = float(fe.assemble(sigma[0, 1] * self.ds(1)))
f_degraded = float(
fe.assemble(sigma_degraded[0, 1] * self.ds(1)))
else:
f_full = float(fe.assemble(sigma[1, 1] * self.ds(1)))
f_degraded = float(
fe.assemble(sigma_degraded[1, 1] * self.ds(1)))
print("Force full is {}".format(f_full))
print("Force degraded is {}".format(f_degraded))
self.delta_u_recorded.append(disp)
self.force_full.append(f_full)
self.force_degraded.append(f_degraded)
# if force_upper < 0.5 and i > 10:
# break
if self.display_intermediate_results and i % 10 == 0:
self.show_force_displacement()
self.save_data_in_loop()
if self.display_intermediate_results:
plt.ioff()
plt.show()
def run_solver(
ndim,
length,
length_unit,
bcs,
layout_list,
u0,
powers,
nx,
coordinates=False,
is_plot=False,
F=None,
vtk=False,
):
"""求解器主函数.
Args:
ndim (int): 2 or 3, 问题维数
length (float): board length
length_unit (float): unit length
bcs (list): bcs
layout_list (list): unit 位置
u0 (float): Dirichlet bc 上的值
powers (list): 功率 list
nx (int): x 方向上的单元数
coordinates (bool, optional): 是否返回坐标矩阵. Defaults to False.
is_plot (bool, optional): 是否画图. Defaults to False.
F (ndarray, optional): 热源布局矩阵 F. Defaults to None.
vtk (bool): 是否输出 vtk 文件.
Returns:
tuple: U, xs, ys, zs
"""
ny = nx
nz = nx if ndim == 3 else None
u_D = fs.Constant(u0)
if len(bcs) > 0 and bcs[0] != []:
if ndim == 2:
bc_funs = [LineBoundary(line).get_boundary() for line in bcs]
else:
bc_funs = [RecBoundary(rec).get_boundary() for rec in bcs]
else:
bc_funs = [lambda x, on_boundary: on_boundary] # 边界都为 Dirichlet
if F is None:
f = Source(layout_list, length, length_unit, powers)
else:
f = SourceF(F, length)
u = solver(f, u_D, bc_funs, ndim, length, nx, ny, nz)
if is_plot:
import matplotlib.pyplot as plt
plt.plot(u)
if vtk:
vtkfile = fs.File("solution.pvd")
vtkfile << u
if ndim == 2:
U = u.compute_vertex_values().reshape(nx + 1, nx + 1)
else:
U = u.compute_vertex_values().reshape(nx + 1, nx + 1, nx + 1)
if coordinates:
xs, ys, zs = get_mesh_grid(length, nx, ny, nz)
else:
xs, ys, zs = None, None, None
return U, xs, ys, zs
def store_solution(self):
# Store the solution to file
vtkfile = fe.File('results/solution.pvd')
vtkfile << self.solution
L = f * v * fex.dx
# Compute solution
u = fex.Function(V)
fex.solve(a == L, u, bc)
print(u)
# Plot solution and mesh
plt.subplot(2, 1, 1)
fex.plot(u)
#define the boundary conditions
plt.subplot(2, 1, 2)
fex.plot(mesh)
plt.savefig('possion_fex2.png')
#define the boundary conditions
# Save solution to file in VTK format
vtkfile = fex.File('poisson/solution.pvd')
vtkfile << u
# Compute error in L2 norm
error_L2 = fex.errornorm(u_D, u, 'L2')
# Compute maximum error at vertices
vertex_values_u_D = u_D.compute_vertex_values(mesh)
vertex_values_u = u.compute_vertex_values(mesh)
import numpy as np
error_max = np.max(np.abs(vertex_values_u_D - vertex_values_u))
# Print errors
print('error_L2 =', error_L2)
print('error_max =', error_max)
boundaries[edge.index()] = idx
idx += 1
else:
interior[key] = nodes
sections = fn.MeshFunction('size_t', mesh, dim=2)
sections.set_all(0)
for num, (key, value) in enumerate(Faces.items(), 1):
for node in value:
ver = fn.Vertex(mesh, node)
for cell in fn.cells(ver):
entity = cell.entities(0)
if all(item in value for item in entity):
sections[cell.index()] = num
fn.File("./UserFiles/boundaries.pvd") << boundaries
fn.File("./UserFiles/sections.pvd") << sections
F = fn.Function(V)
File = fn.File("./UserFiles/result.pvd")
for i in range(10):
t = 0 + (i + 1) / 10
F.interpolate(fn.Expression("x[0]+5*t*x[1]", t=t, degree=2))
File << (F, t)
''' changes made:
element numbering starts from zero
node numbering starts from zero
group node numbering is reduced by one
dimension remained at 3
'''
# currently simplifications
p_act = 0.
lmb_f = 2.
W_iso = c_10 * (I_1 - 3) + c_01 * (I_2 - 3) + 0.5 * kappa * (J - 1)**2
dx = fe.dx
ds = fe.ds
P = fe.diff(W_iso, F)
S = 2 * fe.diff(W_iso, C)
F_static = inner(S, DE(v)) * dx - rho * inner(b, v) * dx - inner(
t_bar, v) * ds + (p / kappa + J - 1) * q * dx
#F_static = inner(P, grad(v))*dx - rho*inner(b, v)*dx - inner(t_bar, v)*ds + (p/kappa + J - 1)*q*dx
file_u = fe.File("../results/displacement.pvd")
file_p = fe.File("../results/pressure.pvd")
bcul = fe.DirichletBC(V.sub(0), u_left, left)
bcur = fe.DirichletBC(V.sub(0), u_right, right)
#bcpl = fe.DirichletBC(V.sub(1), p_left, left)
bcs = [bcul, bcur] # bcpl]
J_static = fe.derivative(F_static, w, dw)
#fe.solve(F_static==0, w, bcs)
ffc_options = {"optimize": True}
problem = fe.NonlinearVariationalProblem(F_static,
w,
bcs,
solver = fe.NonlinearVariationalSolver(problem)
#usol = fe.Function(W)
prm = solver.parameters
#prm["newton_solver"]["absolute_tolerance"] = 5E-1
solver.solve()
if MODEL:
u, p, nu_t = W0.split()
else:
u, p = W0.split()
#-------------------------------------------------
# Save this solution to a file for post-processing
#-------------------------------------------------
vtkFile = fe.File('u.pvd')
vtkFile << u
vtkFile = fe.File('p.pvd')
vtkFile << p
if MODEL:
vtkFile = fe.File('nut.pvd')
vtkFile << nu_t
if MODEL:
T = fe.FunctionSpace(mesh, 'CG', 1)
#T = fe.TensorFunctionSpace(mesh, 'CG', 1)
vtkFile = fe.File('fw.pvd')
vtkFile << fe.project(fw, T)
vtkFile = fe.File('g.pvd')
vtkFile << fe.project(g, T)
vtkFile = fe.File('r.pvd')
import fenics
import pde
import rheology
from settings import *
import testcases
fenics.set_log_level(fenics.ERROR)
fluid = rheology.Sigmoid(rho, mu, ty, eps)
problem = testcases.Poiseuille(nx, ny)
u, u0 = problem.define_functions()
algorithm = pde.Abali(problem, dt, fluid, u, u0)
outdir = './output/'
file_p = fenics.File(outdir + problem.name + '_' + fluid.name + '_' +
'pressure.pvd')
file_v = fenics.File(outdir + problem.name + '_' + fluid.name + '_' +
'velocity.pvd')
t = 0.0
step = 0
change = 1
print('step\t time\t vmax\t change')
while t < t_end and change > sstol:
step += 1
t += dt
algorithm.advance(u)
pressure, velocity = u.split(deepcopy=True)
nn = fn.FacetNormal(mesh)
# Defintion of function spaces
Vh = fn.VectorElement("CG", mesh.ufl_cell(), 2)
Zh = fn.FiniteElement("CG", mesh.ufl_cell(), 1)
Qh = fn.FiniteElement("CG", mesh.ufl_cell(), 2)
# spaces for displacement and total pressure should be compatible
# whereas the space for fluid pressure can be "anything". In particular the one for total pressure
Hh = fn.FunctionSpace(mesh, fn.MixedElement([Vh, Zh, Qh]))
(u, phi, p) = fn.TrialFunctions(Hh)
(v, psi, q) = fn.TestFunctions(Hh)
fileU = fn.File(mesh.mpi_comm(), "Output/2_5_1_Footing_wall_removed/u.pvd")
filePHI = fn.File(mesh.mpi_comm(), "Output/2_5_1_Footing_wall_removed/phi.pvd")
fileP = fn.File(mesh.mpi_comm(), "Output/2_5_1_Footing_wall_removed/p.pvd")
# ******** Model constants ********** #
E = 3.0e4
nu = 0.4995
lmbda = E * nu / ((1. + nu) * (1. - 2. * nu))
mu = E / (2. * (1. + nu))
c0 = 1.0e-3
kappa = 1.0e-6
alpha = 0.1
sigma0 = 1.5e4
eta = fn.Constant(1.0)