def get_dirichlet_boundary_conditions(self):
""" Create and return all the strong Dirichlet boundary conditions for the Velocity and FreeSurfacePerturbation fields """
# Is the Velocity field represented by a discontinous function space?
dg = (self.W.sub(0).ufl_element().family() == "Discontinuous Lagrange")
LOG.info("Preparing strong Dirichlet boundary conditions...")
bcs = []
bc_expressions = []
for i in range(0, libspud.option_count("/system/core_fields/vector_field::Velocity/boundary_condition")):
if(libspud.have_option("/system/core_fields/vector_field::Velocity/boundary_condition[%d]/type::dirichlet" % i) and
not libspud.have_option("/system/core_fields/vector_field::Velocity/boundary_condition[%d]/type::dirichlet/apply_weakly" % i)):
expr = ExpressionFromOptions(path = ("/system/core_fields/vector_field::Velocity/boundary_condition[%d]/type::dirichlet" % i), t=0).get_expression()
# Surface IDs on the domain boundary
surface_ids = libspud.get_option("/system/core_fields/vector_field::Velocity/boundary_condition[%d]/surface_ids" % i)
method = ("geometric" if dg else "topological")
bc = DirichletBC(self.W.sub(0), expr, surface_ids, method=method)
bcs.append(bc)
bc_expressions.append(expr)
LOG.debug("Applying Velocity BC #%d strongly to surface IDs: %s" % (i, surface_ids))
for i in range(0, libspud.option_count("/system/core_fields/scalar_field::FreeSurfacePerturbation/boundary_condition/type::dirichlet")):
if(libspud.have_option("/system/core_fields/scalar_field::FreeSurfacePerturbation/boundary_condition[%d]/type::dirichlet" % i) and
not(libspud.have_option("/system/core_fields/scalar_field::FreeSurfacePerturbation/boundary_condition[%d]/type::dirichlet/apply_weakly" % i))):
expr = ExpressionFromOptions(path = ("/system/core_fields/scalar_field::FreeSurfacePerturbation/boundary_condition[%d]/type::dirichlet" % i), t=0).get_expression()
# Surface IDs on the domain boundary
surface_ids = libspud.get_option("/system/core_fields/scalar_field::FreeSurfacePerturbation/boundary_condition[%d]/surface_ids" % i)
method = ("geometric" if dg else "topological")
bc = DirichletBC(self.W.sub(1), expr, surface_ids, method=method)
bcs.append(bc)
bc_expressions.append(expr)
LOG.debug("Applying FreeSurfacePerturbation BC #%d strongly to surface IDs: %s" % (i, surface_ids))
return bcs, bc_expressions
def fill(self):
"""Fill a bucket class with data describing a set of mixedfunctionspace systems using libspud, the given optionpath."""
self.meshes = {}
# loop over the meshes in the options tree
for i in range(libspud.option_count("/geometry/mesh")):
mesh_optionpath = "/geometry/mesh["+`i`+"]"
mesh_name = libspud.get_option(mesh_optionpath+"/name")
self.meshes[mesh_name] = libspud.get_option(mesh_optionpath+"/source/cell")
visualization_optionpath = "/io/visualization/element"
self.viselementfamily = libspud.get_option(visualization_optionpath+"/family")
self.viselementdegree = libspud.get_option(visualization_optionpath+"/degree")
parameters_optionpath = "/global_parameters/ufl"
if libspud.have_option(parameters_optionpath):
self.parameters = libspud.get_option(parameters_optionpath)
self.systems = []
# loop over the systems in the options tree
for i in range(libspud.option_count("/system")):
system_optionpath = "/system["+`i`+"]"
system = buckettools.spud.SpudSystemBucket()
# get all the information about this system from the options dictionary
system.fill(system_optionpath, self)
# let the bucket know about this system
self.systems.append(system)
# done with this system
del system
def get_inlets(self):
""" Wrap the inlet data into a class """
inlets = []
options_base = '/embedded_models/particle_model/inlet'
for _ in range(libspud.option_count(options_base)):
val = None
options_key = options_base +'[%s]'%_
surface_ids = libspud.get_option(options_key+'/surface_ids')
insertion_rate = libspud.get_option(options_key+'/insertion_rate')
if libspud.have_option(options_key+'/particle_velocity/constant'):
rvel = libspud.get_option(options_key+'/particle_velocity/constant')
velocity = lambda x, t: rvel
elif libspud.have_option(options_key+'/particle_velocity/fluid_velocity'):
velocity = None
else:
exec(libspud.get_option(options_key+'/particle_velocity/python')) in globals(), locals()
velocity = val
if libspud.have_option(options_key+'/probability_density_function/constant'):
rpdf = libspud.get_option(options_key+'/probability_density_function/constant')
pdf = lambda x, t: rpdf
elif libspud.have_option(options_key+'/probability_density_function/fluid_velocity'):
pdf = None
else:
exec(libspud.get_option(options_key+'/probability_density_function/python')) in globals(), locals()
pdf = val
inlets.append(Inlet(surface_ids, insertion_rate, velocity, pdf))
return inlets
def compute_diagnostics(self):
diagnostic_field_count = libspud.option_count("/system/diagnostic_fields/diagnostic")
if(diagnostic_field_count == 0):
return
LOG.info("Computing diagnostic fields...")
d = Diagnostics(self.mesh)
for i in range(0, diagnostic_field_count):
name = libspud.get_option("/system/diagnostic_fields/diagnostic[%d]/name" % i)
try:
if(name == "grid_reynolds_number"):
viscosity = Function(self.W.sub(1)).interpolate(Expression(libspud.get_option("/system/equations/momentum_equation/stress_term/scalar_field::Viscosity/value/constant")))
field = d.grid_reynolds_number(self.u, viscosity)
elif(name == "courant_number"):
field = d.courant_number(self.u, self.options["dt"])
else:
raise ValueError("Unknown diagnostic field: %s" % name)
except ValueError as e:
LOG.exception(name)
sys.exit()
LOG.info("Diagnostic results for: %s" % name)
LOG.info("Maximum value: %f" % max(field.vector()))
LOG.info("Maximum value: %f" % min(field.vector()))
return
def fill_subforms(self, optionpath, prefix=""):
for i in range(libspud.option_count(optionpath+"/form")):
form_optionpath = optionpath+"/form["+`i`+"]"
self.form_names.append(prefix+libspud.get_option(form_optionpath+"/name"))
self.forms.append(libspud.get_option(form_optionpath)+os.linesep)
self.form_symbols.append(libspud.get_option(form_optionpath+"/ufl_symbol").split(os.linesep)[0])
self.form_ranks.append(int(libspud.get_option(form_optionpath+"/rank")))
def compute_diagnostics(self):
diagnostic_field_count = libspud.option_count(
"/system/diagnostic_fields/diagnostic")
if (diagnostic_field_count == 0):
return
LOG.info("Computing diagnostic fields...")
d = Diagnostics(self.mesh)
for i in range(0, diagnostic_field_count):
name = libspud.get_option(
"/system/diagnostic_fields/diagnostic[%d]/name" % i)
try:
if (name == "grid_reynolds_number"):
viscosity = Function(self.W.sub(1)).interpolate(
Expression(
libspud.get_option(
"/system/equations/momentum_equation/stress_term/scalar_field::Viscosity/value/constant"
)))
field = d.grid_reynolds_number(self.u, viscosity)
elif (name == "courant_number"):
field = d.courant_number(self.u, self.options["dt"])
else:
raise ValueError("Unknown diagnostic field: %s" % name)
except ValueError as e:
LOG.exception(name)
sys.exit()
LOG.info("Diagnostic results for: %s" % name)
LOG.info("Maximum value: %f" % max(field.vector()))
LOG.info("Maximum value: %f" % min(field.vector()))
return
def fill_subforms(self, optionpath, prefix=""):
for i in range(libspud.option_count(optionpath + "/form")):
form_optionpath = optionpath + "/form[" + ` i ` + "]"
self.form_names.append(prefix +
libspud.get_option(form_optionpath +
"/name"))
self.forms.append(libspud.get_option(form_optionpath) + os.linesep)
self.form_symbols.append(
libspud.get_option(form_optionpath + "/ufl_symbol").split(
os.linesep)[0])
self.form_ranks.append(
int(libspud.get_option(form_optionpath + "/rank")))
def fill_solverforms(self, optionpath, prefix=""):
schurpc_optionpath = optionpath+"/composite_type::schur/schur_preconditioner::user"
if (libspud.have_option(schurpc_optionpath)):
self.fill_subforms(schurpc_optionpath, prefix=prefix)
fs_optionpath = optionpath+"/fieldsplit"
ls_optionpath = optionpath+"/linear_solver/preconditioner"
pc_optionpath = optionpath+"/preconditioner"
if (libspud.have_option(fs_optionpath)):
for i in range(libspud.option_count(fs_optionpath)):
newoptionpath = fs_optionpath+"["+`i`+"]"
name = libspud.get_option(newoptionpath+"/name")
self.fill_solverforms(newoptionpath+"/linear_solver/preconditioner", prefix=prefix+name+"_")
elif (libspud.have_option(ls_optionpath)):
self.fill_solverforms(ls_optionpath, prefix=prefix)
elif (libspud.have_option(pc_optionpath)):
self.fill_solverforms(pc_optionpath, prefix=prefix)
def fill_solverforms(self, optionpath, prefix=""):
schurpc_optionpath = optionpath + "/composite_type::schur/schur_preconditioner::user"
if (libspud.have_option(schurpc_optionpath)):
self.fill_subforms(schurpc_optionpath, prefix=prefix)
fs_optionpath = optionpath + "/fieldsplit"
ls_optionpath = optionpath + "/linear_solver/preconditioner"
pc_optionpath = optionpath + "/preconditioner"
if (libspud.have_option(fs_optionpath)):
for i in range(libspud.option_count(fs_optionpath)):
newoptionpath = fs_optionpath + "[" + ` i ` + "]"
name = libspud.get_option(newoptionpath + "/name")
self.fill_solverforms(newoptionpath +
"/linear_solver/preconditioner",
prefix=prefix + name + "_")
elif (libspud.have_option(ls_optionpath)):
self.fill_solverforms(ls_optionpath, prefix=prefix)
elif (libspud.have_option(pc_optionpath)):
self.fill_solverforms(pc_optionpath, prefix=prefix)
def run(self, array=None, annotate=False, checkpoint=None):
""" Perform the simulation! """
# The solution field defined on the mixed function space
solution = Function(self.W, name="Solution", annotate=annotate)
# The solution from the previous time-step. At t=0, this holds the initial conditions.
solution_old = Function(self.W, name="SolutionOld", annotate=annotate)
# Assign the initial condition
initial_condition = self.get_initial_condition(checkpoint=checkpoint)
solution_old.assign(initial_condition, annotate=annotate)
# Get the test functions
test_functions = TestFunctions(self.W)
w = test_functions[0]; v = test_functions[1]
LOG.info("Test functions created.")
# These are like the TrialFunctions, but are just regular Functions here because we want to solve a non-linear problem
# 'u' and 'h' are the velocity and free surface perturbation, respectively.
functions = split(solution)
u = functions[0]; h = functions[1]
LOG.info("Trial functions created.")
functions_old = split(solution_old)
u_old = functions_old[0]; h_old = functions_old[1]
# Write initial conditions to file
LOG.info("Writing initial conditions to file...")
self.output_functions["Velocity"].assign(solution_old.split()[0], annotate=False)
self.output_files["Velocity"] << self.output_functions["Velocity"]
self.output_functions["FreeSurfacePerturbation"].assign(solution_old.split()[1], annotate=False)
self.output_files["FreeSurfacePerturbation"] << self.output_functions["FreeSurfacePerturbation"]
# Construct the collection of all the individual terms in their weak form.
LOG.info("Constructing form...")
F = 0
theta = self.options["theta"]
dt = self.options["dt"]
dimension = self.options["dimension"]
g_magnitude = self.options["g_magnitude"]
# Is the Velocity field represented by a discontinous function space?
dg = (self.W.sub(0).ufl_element().family() == "Discontinuous Lagrange")
# Mean free surface height
h_mean = Function(self.W.sub(1), name="FreeSurfaceMean", annotate=False)
h_mean.interpolate(ExpressionFromOptions(path = "/system/core_fields/scalar_field::FreeSurfaceMean/value").get_expression())
# Weight u and h by theta to obtain the theta time-stepping scheme.
assert(theta >= 0.0 and theta <= 1.0)
LOG.info("Time-stepping scheme using theta = %g" % (theta))
u_mid = (1.0 - theta) * u_old + theta * u
h_mid = (1.0 - theta) * h_old + theta * h
# The total height of the free surface.
H = h_mean + h
# Simple P1 function space, to be used in the stabilisation routines (if applicable).
P1 = FunctionSpace(self.mesh, "CG", 1)
cellsize = CellSize(self.mesh)
# Normal vector to each element facet
n = FacetNormal(self.mesh)
# Mass term
if(self.options["have_momentum_mass"]):
LOG.debug("Momentum equation: Adding mass term...")
M_momentum = (1.0/dt)*(inner(w, u) - inner(w, u_old))*dx
F += M_momentum
# Advection term
if(self.options["have_momentum_advection"]):
LOG.debug("Momentum equation: Adding advection term...")
if(self.options["integrate_advection_term_by_parts"]):
outflow = (dot(u_mid, n) + abs(dot(u_mid, n)))/2.0
A_momentum = -inner(dot(u_mid, grad(w)), u_mid)*dx - inner(dot(u_mid, grad(u_mid)), w)*dx
A_momentum += inner(w, outflow*u_mid)*ds
if(dg):
# Only add interior facet integrals if we are dealing with a discontinous Galerkin discretisation.
A_momentum += dot(outflow('+')*u_mid('+') - outflow('-')*u_mid('-'), jump(w))*dS
else:
A_momentum = inner(dot(grad(u_mid), u_mid), w)*dx
F += A_momentum
# Viscous stress term. Note that the viscosity is kinematic (not dynamic).
if(self.options["have_momentum_stress"]):
LOG.debug("Momentum equation: Adding stress term...")
viscosity = Function(self.W.sub(1))
# Background viscosity
background_viscosity = Function(self.W.sub(1)).interpolate(Expression(libspud.get_option("/system/equations/momentum_equation/stress_term/scalar_field::Viscosity/value/constant")))
viscosity.assign(background_viscosity)
# Eddy viscosity
if(self.options["have_turbulence_parameterisation"]):
LOG.debug("Momentum equation: Adding turbulence parameterisation...")
base_option_path = "/system/equations/momentum_equation/turbulence_parameterisation"
# Large eddy simulation (LES)
if(libspud.have_option(base_option_path + "/les")):
density = Constant(1.0) # We divide through by density in the momentum equation, so just set this to 1.0 for now.
smagorinsky_coefficient = Constant(libspud.get_option(base_option_path + "/les/smagorinsky/smagorinsky_coefficient"))
les = LES(self.mesh, self.W.sub(1), u_mid, density, smagorinsky_coefficient)
# Add on eddy viscosity
viscosity += les.eddy_viscosity
# Stress tensor: tau = grad(u) + transpose(grad(u)) - (2/3)*div(u)
if(not dg):
# Perform a double dot product of the stress tensor and grad(w).
K_momentum = -viscosity*inner(grad(u_mid) + grad(u_mid).T, grad(w))*dx
K_momentum += viscosity*(2.0/3.0)*inner(div(u_mid)*Identity(dimension), grad(w))*dx
else:
# Interior penalty method
cellsize = Constant(0.2) # In general, we should use CellSize(self.mesh) instead.
alpha = 1/cellsize # Penalty parameter.
K_momentum = -viscosity('+')*inner(grad(u_mid), grad(w))*dx
for dim in range(self.options["dimension"]):
K_momentum += -viscosity('+')*(alpha('+')/cellsize('+'))*dot(jump(w[dim], n), jump(u_mid[dim], n))*dS
K_momentum += viscosity('+')*dot(avg(grad(w[dim])), jump(u_mid[dim], n))*dS + viscosity('+')*dot(jump(w[dim], n), avg(grad(u_mid[dim])))*dS
F -= K_momentum # Negative sign here because we are bringing the stress term over from the RHS.
# The gradient of the height of the free surface, h
LOG.debug("Momentum equation: Adding gradient term...")
C_momentum = -g_magnitude*inner(w, grad(h_mid))*dx
F -= C_momentum
# Quadratic drag term in the momentum equation
if(self.options["have_drag"]):
LOG.debug("Momentum equation: Adding drag term...")
base_option_path = "/system/equations/momentum_equation/drag_term"
# Get the bottom drag/friction coefficient.
LOG.debug("Momentum equation: Adding bottom drag contribution...")
bottom_drag = ExpressionFromOptions(path=base_option_path+"/scalar_field::BottomDragCoefficient/value", t=0).get_expression()
bottom_drag = Function(self.W.sub(1)).interpolate(bottom_drag)
# Magnitude of the velocity field
magnitude = sqrt(dot(u_old, u_old))
# Form the drag term
if(array):
LOG.debug("Momentum equation: Adding turbine drag contribution...")
drag_coefficient = bottom_drag + array.turbine_drag()
else:
drag_coefficient = bottom_drag
D_momentum = -inner(w, (drag_coefficient*magnitude/H)*u_mid)*dx
F -= D_momentum
# The mass term in the shallow water continuity equation
# (i.e. an advection equation for the free surface height, h)
if(self.options["have_continuity_mass"]):
LOG.debug("Continuity equation: Adding mass term...")
M_continuity = (1.0/dt)*(inner(v, h) - inner(v, h_old))*dx
F += M_continuity
# Append any Expression objects for weak BCs here.
weak_bc_expressions = []
# Divergence term in the shallow water continuity equation
LOG.debug("Continuity equation: Adding divergence term...")
if(self.options["integrate_continuity_equation_by_parts"]):
LOG.debug("The divergence term is being integrated by parts.")
Ct_continuity = - H*inner(u_mid, grad(v))*dx
if(dg):
Ct_continuity += inner(jump(v, n), avg(H*u_mid))*dS
# Add in the surface integrals, but check to see if any boundary conditions need to be applied weakly here.
boundary_markers = self.mesh.exterior_facets.unique_markers
for marker in boundary_markers:
marker = int(marker) # ds() will not accept markers of type 'numpy.int32', so convert it to type 'int' here.
bc_type = None
for i in range(0, libspud.option_count("/system/core_fields/vector_field::Velocity/boundary_condition")):
bc_path = "/system/core_fields/vector_field::Velocity/boundary_condition[%d]" % i
if(not (marker in libspud.get_option(bc_path + "/surface_ids"))):
# This BC is not associated with this marker, so skip it.
continue
# Determine the BC type.
if(libspud.have_option(bc_path + "/type::no_normal_flow")):
bc_type = "no_normal_flow"
elif(libspud.have_option(bc_path + "/type::dirichlet")):
if(libspud.have_option(bc_path + "/type::dirichlet/apply_weakly")):
bc_type = "weak_dirichlet"
else:
bc_type = "dirichlet"
elif(libspud.have_option(bc_path + "/type::flather")):
bc_type = "flather"
# Apply the boundary condition...
try:
LOG.debug("Applying Velocity BC of type '%s' to surface ID %d..." % (bc_type, marker))
if(bc_type == "flather"):
# The known exterior value for the Velocity.
u_ext = ExpressionFromOptions(path = (bc_path + "/type::flather/exterior_velocity"), t=0).get_expression()
Ct_continuity += H*inner(Function(self.W.sub(0)).interpolate(u_ext), n)*v*ds(int(marker))
# The known exterior value for the FreeSurfacePerturbation.
h_ext = ExpressionFromOptions(path = (bc_path + "/type::flather/exterior_free_surface_perturbation"), t=0).get_expression()
Ct_continuity += H*sqrt(g_magnitude/H)*(h_mid - Function(self.W.sub(1)).interpolate(h_ext))*v*ds(int(marker))
weak_bc_expressions.append(u_ext)
weak_bc_expressions.append(h_ext)
elif(bc_type == "weak_dirichlet"):
u_bdy = ExpressionFromOptions(path = (bc_path + "/type::dirichlet"), t=0).get_expression()
Ct_continuity += H*(dot(Function(self.W.sub(0)).interpolate(u_bdy), n))*v*ds(int(marker))
weak_bc_expressions.append(u_bdy)
elif(bc_type == "dirichlet"):
# Add in the surface integral as it is here. The BC will be applied strongly later using a DirichletBC object.
Ct_continuity += H * inner(u_mid, n) * v * ds(int(marker))
elif(bc_type == "no_normal_flow"):
# Do nothing here since dot(u, n) is zero.
continue
else:
raise ValueError("Unknown boundary condition type!")
except ValueError as e:
LOG.exception(e)
sys.exit()
# If no boundary condition has been applied, include the surface integral as it is.
if(bc_type is None):
Ct_continuity += H * inner(u_mid, n) * v * ds(int(marker))
else:
Ct_continuity = inner(v, div(H*u_mid))*dx
F += Ct_continuity
# Add in any source terms
if(self.options["have_momentum_source"]):
LOG.debug("Momentum equation: Adding source term...")
momentum_source_expression = ExpressionFromOptions(path = "/system/equations/momentum_equation/source_term/vector_field::Source/value", t=0).get_expression()
momentum_source_function = Function(self.W.sub(0), annotate=False)
F -= inner(w, momentum_source_function.interpolate(momentum_source_expression))*dx
if(self.options["have_continuity_source"]):
LOG.debug("Continuity equation: Adding source term...")
continuity_source_expression = ExpressionFromOptions(path = "/system/equations/continuity_equation/source_term/scalar_field::Source/value", t=0).get_expression()
continuity_source_function = Function(self.W.sub(1), annotate=False)
F -= inner(v, continuity_source_function.interpolate(continuity_source_expression))*dx
# Add in any SU stabilisation
if(self.options["have_su_stabilisation"]):
LOG.debug("Momentum equation: Adding streamline-upwind stabilisation term...")
stabilisation = Stabilisation(self.mesh, P1, cellsize)
magnitude = magnitude_vector(solution_old.split()[0], P1)
# Bound the values for the magnitude below by 1.0e-9 for numerical stability reasons.
u_nodes = magnitude.vector()
near_zero = numpy.array([1.0e-9 for i in range(len(u_nodes))])
u_nodes.set_local(numpy.maximum(u_nodes.array(), near_zero))
diffusivity = ExpressionFromOptions(path = "/system/equations/momentum_equation/stress_term/scalar_field::Viscosity/value", t=self.options["t"]).get_expression()
diffusivity = Function(self.W.sub(1)).interpolate(diffusivity) # Background viscosity
grid_pe = grid_peclet_number(diffusivity, magnitude, P1, cellsize)
# Bound the values for grid_pe below by 1.0e-9 for numerical stability reasons.
grid_pe_nodes = grid_pe.vector()
values = numpy.array([1.0e-9 for i in range(len(grid_pe_nodes))])
grid_pe_nodes.set_local(numpy.maximum(grid_pe_nodes.array(), values))
F += stabilisation.streamline_upwind(w, u, magnitude, grid_pe)
LOG.info("Form construction complete.")
bcs, bc_expressions = self.get_dirichlet_boundary_conditions()
# Prepare solver_parameters dictionary
solver_parameters = self.get_solver_parameters()
# Construct the solver objects
problem = NonlinearVariationalProblem(F, solution, bcs=bcs)
solver = NonlinearVariationalSolver(problem, solver_parameters=solver_parameters)
LOG.debug("Variational problem solver created.")
# PETSc solver run-times
from petsc4py import PETSc
main_solver_stage = PETSc.Log.Stage('Main block-coupled system solve')
total_solver_time = 0.0
# Time-stepping parameters and constants
T = self.options["T"]
t = self.options["t"]
t += dt
iterations_since_dump = 1
iterations_since_checkpoint = 1
# The time-stepping loop
LOG.info("Entering the time-stepping loop...")
#if annotate: adj_start_timestep(time=t)
EPSILON = 1.0e-14
while t <= T + EPSILON: # A small value EPSILON is added here in case of round-off error.
LOG.info("t = %g" % t)
## Update any time-dependent Functions and Expressions.
# Re-compute the velocity magnitude and grid Peclet number fields.
if(self.options["have_su_stabilisation"]):
magnitude.assign(magnitude_vector(solution_old.split()[0], P1))
# Bound the values for the magnitude below by 1.0e-9 for numerical stability reasons.
u_nodes = magnitude.vector()
near_zero = numpy.array([1.0e-9 for i in range(len(u_nodes))])
u_nodes.set_local(numpy.maximum(u_nodes.array(), near_zero))
grid_pe.assign(grid_peclet_number(diffusivity, magnitude, P1, cellsize))
# Bound the values for grid_pe below by 1.0e-9 for numerical stability reasons.
grid_pe_nodes = grid_pe.vector()
values = numpy.array([1.0e-9 for i in range(len(grid_pe_nodes))])
grid_pe_nodes.set_local(numpy.maximum(grid_pe_nodes.array(), values))
if(self.options["have_turbulence_parameterisation"]):
les.solve()
# Time-dependent source terms
if(self.options["have_momentum_source"]):
momentum_source_expression.t = t
momentum_source_function.interpolate(momentum_source_expression)
if(self.options["have_continuity_source"]):
continuity_source_expression.t = t
continuity_source_function.interpolate(continuity_source_expression)
# Update any time-varying DirichletBC objects.
for expr in bc_expressions:
expr.t = t
for expr in weak_bc_expressions:
expr.t = t
# Solve the system of equations!
start_solver_time = mpi4py.MPI.Wtime()
main_solver_stage.push()
LOG.debug("Solving the system of equations...")
solver.solve(annotate=annotate)
main_solver_stage.pop()
end_solver_time = mpi4py.MPI.Wtime()
total_solver_time += (end_solver_time - start_solver_time)
# Write the solution to file.
if((self.options["dump_period"] is not None) and (dt*iterations_since_dump >= self.options["dump_period"])):
LOG.debug("Writing data to file...")
self.output_functions["Velocity"].assign(solution.split()[0], annotate=False)
self.output_files["Velocity"] << self.output_functions["Velocity"]
self.output_functions["FreeSurfacePerturbation"].assign(solution.split()[1], annotate=False)
self.output_files["FreeSurfacePerturbation"] << self.output_functions["FreeSurfacePerturbation"]
iterations_since_dump = 0 # Reset the counter.
# Print out the total power generated by turbines.
if(array):
LOG.info("Power = %.2f" % array.power(u, density=1000))
# Checkpointing
if((self.options["checkpoint_period"] is not None) and (dt*iterations_since_checkpoint >= self.options["checkpoint_period"])):
LOG.debug("Writing checkpoint data to file...")
solution.dat.save("checkpoint")
iterations_since_checkpoint = 0 # Reset the counter.
# Check whether a steady-state has been reached.
if(steady_state(solution.split()[0], solution_old.split()[0], self.options["steady_state_tolerance"]) and steady_state(solution.split()[1], solution_old.split()[1], self.options["steady_state_tolerance"])):
LOG.info("Steady-state attained. Exiting the time-stepping loop...")
break
self.compute_diagnostics()
# Move to next time step
solution_old.assign(solution, annotate=annotate)
#array.turbine_drag.assign(project(array.turbine_drag, array.turbine_drag.function_space(), annotate=annotate), annotate=annotate)
t += dt
#if annotate: adj_inc_timestep(time=t, finished=t>T)
iterations_since_dump += 1
iterations_since_checkpoint += 1
LOG.debug("Moving to next time level...")
LOG.info("Out of the time-stepping loop.")
LOG.debug("Total solver time: %.2f" % (total_solver_time))
return solution
def convert(fluidity_options_file_path, ff_options_file_path):
# Read in Fluidity simulation options
libspud.clear_options()
libspud.load_options(fluidity_options_file_path)
# Simulation name
simulation_name = libspud.get_option("/simulation_name")
# Geometry
base = "/geometry"
dimension = libspud.get_option(base + "/dimension")
mesh_path = libspud.get_option(base + "/mesh::CoordinateMesh/from_file/file_name") + ".msh" # FIXME: Always assumes gmsh format.
# Function spaces
velocity_function_space = FunctionSpace("/geometry", 1)
freesurface_function_space = FunctionSpace("/geometry", 2)
# Timestepping
base = "/timestepping"
current_time = libspud.get_option(base + "/current_time")
timestep = libspud.get_option(base + "/timestep")
finish_time = libspud.get_option(base + "/finish_time")
## Steady-state
if(libspud.have_option(base + "/steady_state")):
if(libspud.have_option(base + "/steady_state/tolerance")):
steady_state = libspud.get_option(base + "/steady_state/tolerance")
else:
steady_state = 1e-7
else:
steady_state = None
# I/O
base = "/io"
dump_format = libspud.get_option(base + "/dump_format")
if(libspud.have_option(base + "/dump_period")):
dump_period = libspud.get_option(base + "/dump_period/constant")
elif(libspud.have_option(base + "/dump_period_in_timesteps")):
dump_period = libspud.get_option(base + "/dump_period_in_timesteps/constant")*timestep
else:
print "Unable to obtain dump_period."
sys.exit()
# Gravity
g_magnitude = libspud.get_option("/physical_parameters/gravity/magnitude")
# Velocity field (momentum equation)
base = "/material_phase[0]/vector_field::Velocity"
## Depth (free surface mean height)
c = libspud.get_child_name(base + "/prognostic/equation::ShallowWater/scalar_field::BottomDepth/prescribed/value::WholeMesh/", 1)
depth = libspud.get_option(base + "/prognostic/equation::ShallowWater/scalar_field::BottomDepth/prescribed/value::WholeMesh/%s" % c)
## Bottom drag coefficient
if(libspud.have_option(base + "/prognostic/equation::ShallowWater/bottom_drag")):
c = libspud.get_child_name(base + "/prognostic/equation::ShallowWater/bottom_drag/scalar_field::BottomDragCoefficient/prescribed/value::WholeMesh/", 1)
bottom_drag = libspud.get_option(base + "/prognostic/equation::ShallowWater/bottom_drag/scalar_field::BottomDragCoefficient/prescribed/value::WholeMesh/%s" % c)
else:
bottom_drag = None
## Viscosity
if(libspud.have_option(base + "/prognostic/tensor_field::Viscosity")):
viscosity = libspud.get_option(base + "/prognostic/tensor_field::Viscosity/prescribed/value::WholeMesh/anisotropic_symmetric/constant")[0][0]
else:
viscosity = None
## Momentum source
if(libspud.have_option(base + "/prognostic/vector_field::Source")):
c = libspud.get_child_name(base + "/prognostic/vector_field::Source/prescribed/value::WholeMesh/", 1)
momentum_source = libspud.get_option(base + "/prognostic/vector_field::Source/prescribed/value::WholeMesh/%s" % c)
else:
momentum_source = None
## Initial condition
if(libspud.have_option(base + "/prognostic/initial_condition::WholeMesh")):
c = libspud.get_child_name(base + "/prognostic/initial_condition::WholeMesh/", 1)
velocity_initial_condition = libspud.get_option(base + "/prognostic/initial_condition::WholeMesh/%s" % c)
else:
velocity_initial_condition = 0.0
## Boundary conditions
number_of_bcs = libspud.option_count(base + "/prognostic/boundary_conditions")
velocity_bcs = []
for i in range(number_of_bcs):
velocity_bcs.append(VelocityBoundaryCondition(base + "/prognostic/boundary_conditions[%d]" % i))
# Pressure field (continuity equation)
base = "/material_phase[0]/scalar_field::Pressure"
integrate_by_parts = libspud.have_option(base + "/prognostic/spatial_discretisation/continuous_galerkin/integrate_continuity_by_parts")
## Initial condition
if(libspud.have_option(base + "/prognostic/initial_condition::WholeMesh")):
c = libspud.get_child_name(base + "/prognostic/initial_condition::WholeMesh/", 1)
pressure_initial_condition = libspud.get_option(base + "/prognostic/initial_condition::WholeMesh/%s" % c)
else:
pressure_initial_condition = 0.0
## Boundary conditions
number_of_bcs = libspud.option_count(base + "/prognostic/boundary_conditions")
pressure_bcs = []
for i in range(number_of_bcs):
pressure_bcs.append(PressureBoundaryCondition(base + "/prognostic/boundary_conditions[%d]" % i))
## Continuity source
if(libspud.have_option(base + "/prognostic/scalar_field::Source")):
c = libspud.get_child_name(base + "/prognostic/scalar_field::Source/prescribed/value::WholeMesh/", 1)
continuity_source = libspud.get_option(base + "/prognostic/scalar_field::Source/prescribed/value::WholeMesh/%s" % c)
else:
continuity_source = None
# Write out to a Firedrake-Fluids simulation configuration file
libspud.clear_options()
# Create a bare-bones .swml file to add to.
f = open(ff_options_file_path, "w")
f.write("<?xml version='1.0' encoding='utf-8'?>\n")
f.write("<shallow_water_options>\n")
f.write("</shallow_water_options>\n")
f.close()
libspud.load_options(ff_options_file_path)
# Simulation name
libspud.set_option("/simulation_name", simulation_name)
# Geometry
base = "/geometry"
libspud.set_option(base + "/dimension", dimension)
libspud.set_option(base + "/mesh/from_file/relative_path", mesh_path)
# Function spaces
base = "/function_spaces"
libspud.set_option(base + "/function_space::VelocityFunctionSpace/degree", velocity_function_space.degree)
libspud.set_option(base + "/function_space::VelocityFunctionSpace/family", velocity_function_space.family)
libspud.set_option(base + "/function_space::FreeSurfaceFunctionSpace/degree", freesurface_function_space.degree)
libspud.set_option(base + "/function_space::FreeSurfaceFunctionSpace/family", freesurface_function_space.family)
# I/O
base = "/io"
libspud.set_option(base + "/dump_format", dump_format)
libspud.set_option(base + "/dump_period", dump_period)
# Timestepping
base = "/timestepping"
print timestep
libspud.set_option(base + "/current_time", current_time)
try:
libspud.set_option(base + "/timestep", timestep)
except:
pass
libspud.set_option(base + "/finish_time", finish_time)
## Steady-state
if(steady_state):
libspud.set_option(base + "/steady_state/tolerance", steady_state)
# Gravity
libspud.set_option("/physical_parameters/gravity/magnitude", g_magnitude)
# System/Core Fields: Velocity
base = "/system/core_fields/vector_field::Velocity"
## Initial condition
if(isinstance(velocity_initial_condition, str)):
libspud.set_option(base + "/initial_condition/python", velocity_initial_condition)
else:
libspud.set_option(base + "/initial_condition/constant", velocity_initial_condition)
## Boundary conditions
try:
for i in range(len(velocity_bcs)):
libspud.set_option(base + "/boundary_condition::%s/surface_ids" % velocity_bcs[i].name, velocity_bcs[i].surface_ids)
libspud.set_option_attribute(base + "/boundary_condition::%s/type/name" % velocity_bcs[i].name, velocity_bcs[i].type)
if(velocity_bcs[i].type == "dirichlet"):
if(isinstance(velocity_bcs[i].value, str)):
libspud.set_option(base + "/boundary_condition::%s/type::dirichlet/value/python" % velocity_bcs[i].name, velocity_bcs[i].value)
else:
libspud.set_option(base + "/boundary_condition::%s/type::dirichlet/value/constant" % velocity_bcs[i].name, velocity_bcs[i].value)
except:
pass
# System/Core Fields: FreeSurfacePerturbation
base = "/system/core_fields/scalar_field::FreeSurfacePerturbation"
#FIXME: Pressure initial and boundary conditions are multiplied by 'g' in Fluidity, but not in Firedrake-Fluids.
## Initial condition
if(isinstance(pressure_initial_condition, str)):
libspud.set_option(base + "/initial_condition/python", pressure_initial_condition)
else:
libspud.set_option(base + "/initial_condition/constant", pressure_initial_condition)
## Boundary conditions
try:
for i in range(len(pressure_bcs)):
libspud.set_option(base + "/boundary_condition::%s/surface_ids" % pressure_bcs[i].name, pressure_bcs[i].surface_ids)
libspud.set_option(base + "/boundary_condition::%s/type/name" % pressure_bcs[i].name, pressure_bcs[i].type)
if(pressure_bcs[i].type == "dirichlet"):
if(isinstance(pressure_bcs[i].value, str)):
libspud.set_option(base + "/boundary_condition::%s/type::dirichlet/value/python" % pressure_bcs[i].name, pressure_bcs[i].value)
else:
libspud.set_option(base + "/boundary_condition::%s/type::dirichlet/value/constant" % pressure_bcs[i].name, pressure_bcs[i].value)
except:
pass
# System/Core Fields: FreeSurfaceMean
base = "/system/core_fields/scalar_field::FreeSurfaceMean"
if(isinstance(depth, str)):
libspud.set_option(base + "/value/python", depth)
else:
libspud.set_option(base + "/value/constant", depth)
# Equations: Continuity equation
base = "/system/equations/continuity_equation"
libspud.set_option(base + "/integrate_by_parts", integrate_by_parts)
## Source term
if(continuity_source is not None):
if(isinstance(continuity_source, str)):
libspud.set_option(base + "/source_term/scalar_field::Source/value/python", continuity_source)
else:
libspud.set_option(base + "/source_term/scalar_field::Source/value/constant", continuity_source)
# Equations: Momentum equation
base = "/system/equations/momentum_equation"
## Viscosity
if(viscosity is not None):
if(isinstance(viscosity, str)):
libspud.set_option(base + "/stress_term/scalar_field::Viscosity/value/python", viscosity)
else:
libspud.set_option(base + "/stress_term/scalar_field::Viscosity/value/constant", viscosity)
## Bottom drag
if(bottom_drag is not None):
if(isinstance(bottom_drag, str)):
libspud.set_option(base + "/drag_term/scalar_field::BottomDragCoefficient/value/python", bottom_drag)
else:
libspud.set_option(base + "/drag_term/scalar_field::BottomDragCoefficient/value/constant", bottom_drag)
## Source term
if(momentum_source is not None):
if(isinstance(momentum_source, str)):
libspud.set_option(base + "/source_term/vector_field::Source/value/python", momentum_source)
else:
libspud.set_option(base + "/source_term/vector_field::Source/value/constant", momentum_source)
# Write all the applied options to file.
libspud.write_options(ff_options_file_path)
return
def read_in_nirom_options(path, opal_options, nirom_options, fwd_options):
if libspud.have_option('opal_operation/nirom/snapshots_create'):
nirom_options.snapshots.create = True
fwd_options.exectuable = libspud.get_option(
'opal_operation/nirom/snapshots_create/executable')
fwd_options.path_to_results = libspud.get_option(
'opal_operation/nirom/snapshots_create/path')
fwd_options.input_file = libspud.get_option(
'opal_operation/nirom/snapshots_create/input_file')
elif libspud.have_option('opal_operation/nirom/snapshots_location'):
nirom_options.snapshots.location = True
fwd_options.path_to_results = libspud.get_option(
'opal_operation/nirom/snapshots_location/path')
fwd_options.input_file = libspud.get_option(
'opal_operation/nirom/snapshots_location/input_file')
if libspud.have_option(
'opal_operation/nirom/snapshots_location/output_filebase'):
fwd_options.results_filebase = libspud.get_option(
'opal_operation/nirom/snapshots_location/output_filebase')
if libspud.have_option(
'opal_operation/nirom/snapshots_location/extension'):
fwd_options.results_extension = libspud.get_option(
'opal_operation/nirom/snapshots_location/extension')
if libspud.have_option(
'opal_operation/nirom/snapshots_location/nParameters'):
nirom_options.snapshots.nParameters = libspud.get_option(
'opal_operation/nirom/snapshots_location/nParameters')
if libspud.have_option('/opal_operation/nirom/compression'):
if libspud.have_option('/opal_operation/nirom/compression/svd_type'):
if libspud.have_option(
'/opal_operation/nirom/compression/svd_type/svd_method'):
nirom_options.compression.svd = True
elif libspud.have_option(
'/opal_operation/nirom/compression/svd_type/eigh_method'):
nirom_options.compression.eigh = True
elif libspud.have_option(
'/opal_operation/nirom/compression/svd_type/DD_eigh_method'
):
nirom_options.compression.DD_eigh = True
nirom_options.compression.num_sub_base_2 = libspud.get_option(
'/opal_operation/nirom/compression/svd_type/DD_eigh_method/num_sub_base_2'
)
nFields = libspud.option_count(
'/opal_operation/nirom/compression/svd_type/field_name')
for ii in range(nFields):
my_string = libspud.get_option(
'/opal_operation/nirom/compression/svd_type/field_name[' +
str(ii) + ']/name')
nirom_options.compression.field.append(my_string)
value_ct = 0.0
value_nPOD = -1
if libspud.have_option(
'/opal_operation/nirom/compression/svd_type/field_name['
+ str(ii) + ']/cumulative_tol'):
value_ct = libspud.get_option(
'/opal_operation/nirom/compression/svd_type/field_name['
+ str(ii) + ']/cumulative_tol')
elif libspud.have_option(
'/opal_operation/nirom/compression/svd_type/field_name['
+ str(ii) + ']/nPOD'):
value_nPOD = libspud.get_option(
'/opal_operation/nirom/compression/svd_type/field_name['
+ str(ii) + ']/nPOD')
nirom_options.compression.cumulative_tol.append(value_ct)
nirom_options.compression.nPOD.append(value_nPOD)
# svd_autoencoder option should go here
if libspud.have_option(
'/opal_operation/nirom/compression/svd_type/svd_autoencoder'
):
nirom_options.compression.svd_autoencoder = True
nirom_options.compression.epochs = libspud.get_option(
'/opal_operation/nirom/compression/svd_type/svd_autoencoder/number_epochs'
)
nirom_options.compression.batch_size = libspud.get_option(
'/opal_operation/nirom/compression/svd_type/svd_autoencoder/batch_size'
)
nirom_options.compression.neurons_each_layer = libspud.get_option(
'/opal_operation/nirom/compression/svd_type/svd_autoencoder/neurons_each_layer'
)
elif libspud.have_option(
'/opal_operation/nirom/compression/autoencoder_type'):
nirom_options.compression.autoencoder = True
nFields = libspud.option_count(
'/opal_operation/nirom/compression/autoencoder_type/field_name'
)
for ii in range(nFields):
my_string = libspud.get_option(
'/opal_operation/nirom/compression/autoencoder_type/field_name['
+ str(ii) + ']/name')
nirom_options.compression.field.append(my_string)
batch_size = libspud.get_option(
'/opal_operation/nirom/compression/autoencoder_type/field_name['
+ str(ii) + ']/batch_size')
nirom_options.compression.batch_size.append(batch_size)
number_epochs = libspud.get_option(
'/opal_operation/nirom/compression/autoencoder_type/field_name['
+ str(ii) + ']/number_epochs')
nirom_options.compression.epochs.append(number_epochs)
neurons_each_layer = libspud.get_option(
'/opal_operation/nirom/compression/autoencoder_type/field_name['
+ str(ii) + ']/neurons_each_layer')
nirom_options.compression.neurons_each_layer.append(
neurons_each_layer) # neurons per layer
if libspud.have_option('/opal_operation/nirom/training'):
if libspud.have_option('/opal_operation/nirom/training/GPR'):
nirom_options.training.GPR = True
nirom_options.training.GPR_scaling = libspud.get_option(
'/opal_operation/nirom/training/GPR/scaling_bounds')
nirom_options.training.GPR_RBF_length_scale = libspud.get_option(
'/opal_operation/nirom/training/GPR/RBF_length_scale')
nirom_options.training.GPR_RBF_length_bounds = libspud.get_option(
'/opal_operation/nirom/training/GPR/RBF_length_scale_bounds')
nirom_options.training.GPR_constant_value = libspud.get_option(
'/opal_operation/nirom/training/GPR/constant_value')
nirom_options.training.GPR_constant_bounds = libspud.get_option(
'/opal_operation/nirom/training/GPR/constant_bounds')
if libspud.have_option('/opal_operation/nirom/training/LSTM'):
nirom_options.training.LSTM = True
if libspud.have_option('/opal_operation/nirom/training/DD_LSTM'):
nirom_options.training.DD_LSTM = True
#print "LSTM not currently implemented ... aborting"
#sys.exit(0)
if libspud.have_option('/opal_operation/nirom/training/DD_GPR'):
nirom_options.training.DD_GPR = True
if libspud.have_option('opal_operation/nirom/prediction'):
nirom_options.prediction.nTime = libspud.get_option(
'opal_operation/nirom/prediction/nTime')
return opal_options, nirom_options, fwd_options
def read_in_importance_map_options(path, opal_options):
opal_options.output_filename = libspud.get_option(path + 'Output_filename')
opal_options.executable = libspud.get_option(path + 'Executable')
opal_options.input_file = libspud.get_option(path + 'Input_file')
if (libspud.have_option(path + 'Time_window')):
opal_options.time_window = libspud.get_option(path + 'Time_window')
if (libspud.have_option(path + 'Time_window/pass_down_ginit')):
opal_options.pass_down_ginit = True
else:
opal_options.time_window = 0
opal_options.pass_down_ginit = False
if libspud.have_option(path + 'random_seed'):
opal_options.random_seed = 200
else:
opal_options.random_seed = -1
opal_options.functional.location_of_interest = libspud.get_option(
path + 'functional/location_of_interest')
if libspud.have_option(path + 'functional/all_time'):
print "has option all time"
opal_options.functional.time = "all_time"
else:
opal_options.functional.time = "end_time"
if libspud.have_option(path + 'functional/type/standard'):
opal_options.functional.type = "standard"
elif libspud.have_option(path + 'functional/type/geothermal_over_time'):
opal_options.functional.type = "geothermal_over_time"
nffields = libspud.option_count(path + 'functional/Functional_field')
for i in range(nffields):
temp_field = Functional_field()
fieldpath = path + 'functional/Functional_field[' + str(i) + ']'
temp_field.name = libspud.get_option(fieldpath + '/name')
if libspud.have_option(fieldpath + '/phase'):
temp_field.phase = libspud.get_option(fieldpath + '/phase')
if (libspud.have_option(fieldpath + '/field_type/scalar_field')):
temp_field.field_type = "scalar_field"
elif (libspud.have_option(fieldpath + '/field_type/vector_field')):
temp_field.field_type = "vector_field"
elif (libspud.have_option(fieldpath + '/field_type/tensor_field')):
temp_field.field_type = "tensor_field"
if (libspud.have_option(fieldpath + '/mesh_type/element')):
temp_field.mesh_type = "element"
elif (libspud.have_option(fieldpath + '/mesh_type/node')):
temp_field.mesh_type = "node"
opal_options.functional.Functional_field.append(temp_field)
if libspud.have_option(path + 'functional/square_integrand'):
opal_options.functional.square_integrand = True
else:
opal_options.functional.square_integrand = False
nfields = libspud.option_count(path + 'Field_to_study')
for i in range(nfields):
temp_field = Field_To_study()
fieldpath = path + 'Field_to_study[' + str(i) + ']'
temp_field.name = libspud.get_option(fieldpath + '/name')
if (libspud.have_option(fieldpath + '/field_type/scalar_field')):
temp_field.field_type = "scalar_field"
elif (libspud.have_option(fieldpath + '/field_type/vector_field')):
temp_field.field_type = "vector_field"
elif (libspud.have_option(fieldpath + '/field_type/tensor_field')):
temp_field.field_type = "tensor_field"
else:
if (libspud.have_option(fieldpath + '/field_type/scalar_field')):
temp_field.field_type = "porous_scalar"
elif (libspud.have_option(fieldpath + '/field_type/vector_field')):
temp_field.field_type = "porous_vector"
elif (libspud.have_option(fieldpath + '/field_type/tensor_field')):
temp_field.field_type = "porous_tensor"
#temp_field.location_of_interest = libspud.get_option(fieldpath+'/location_of_interest')
temp_field.perturbations_to_do = libspud.get_option(
fieldpath + '/perturbations_to_do')
temp_field.parallel_processors = 1 #Serial by default
if (libspud.have_option(fieldpath +
'/perturbations_to_do/parallel_processors')):
temp_field.parallel_processors = libspud.get_option(
fieldpath + '/perturbations_to_do/parallel_processors')
if libspud.have_option(path + '/Number_processors/MPI_runs'):
opal_options.MPI_runs = libspud.get_option(
path + '/Number_processors/MPI_runs')
opal_options.number_processors /= opal_options.MPI_runs
temp_field.initial_condition = libspud.have_option(
fieldpath + '/Initial_condition')
temp_field.boundary_condition = libspud.have_option(
fieldpath + '/Boundary_condition')
temp_field.source = libspud.have_option(fieldpath + '/source')
if (libspud.have_option(fieldpath + '/Sigma')):
temp_field.sigma = libspud.get_option(fieldpath + '/Sigma')
else:
temp_field.sigma = 0.01
if (libspud.have_option(fieldpath + '/python_function')):
temp_field.pycode = libspud.get_option(fieldpath +
'/python_function')
temp_field.phases_to_perturb = libspud.get_option(fieldpath +
'/Phases_to_perturb')
if libspud.have_option(fieldpath + '/stabilise_through_diagonal'):
temp_field.diagonal_tweak = True
temp_field.diagonal_tweak_value = libspud.get_option(
fieldpath + '/stabilise_through_diagonal/epsilon')
if libspud.have_option(
fieldpath +
'/stabilise_through_diagonal/constrain_evalue'):
temp_field.diagonal_tweak_method = 'constrain_evalue'
elif libspud.have_option(
fieldpath + '/stabilise_through_diagonal/add_to_diag'):
temp_field.diagonal_tweak_method = 'add_to_diag'
else:
print "error, option not expected", libspud.get_option(
fieldpath + '/stabilise_through_diagonal/')
else:
# can probably remove these three lines now __init__ is working....
temp_field.diagonal_tweak = False
temp_field.diagonal_tweak_method = ''
temp_field.diagonal_tweak_value = 0.0
if libspud.have_option(fieldpath + '/Gram-Schmidt'):
temp_field.gram_schmidt = True
else:
temp_field.gram_schmidt = False
if libspud.have_option(fieldpath + '/smoothing'):
temp_field.nSmooth = libspud.get_option(fieldpath + '/smoothing')
else:
temp_field.nSmooth = 0
if libspud.have_option(fieldpath + '/use_G'):
temp_field.use_G = True
temp_field.threshold_use_G = libspud.get_option(fieldpath +
'/use_G')
else:
temp_field.use_G = False
temp_field.threshold_use_G = -1
opal_options.Field_To_study_list.append(temp_field)
return opal_options
import libspud
print libspud.__file__
libspud.load_options('test.flml')
libspud.print_options()
print libspud.number_of_children('/geometry')
print libspud.get_child_name('geometry', 0)
print libspud.option_count('/problem_type')
print libspud.have_option('/problem_type')
print libspud.get_option_type('/geometry/dimension')
print libspud.get_option_type('/problem_type')
print libspud.get_option_rank('/geometry/dimension')
print libspud.get_option_rank('/physical_parameters/gravity/vector_field::GravityDirection/prescribed/value/constant')
print libspud.get_option_shape('/geometry/dimension')
print libspud.get_option_shape('/problem_type')
print libspud.get_option('/problem_type')
print libspud.get_option('/geometry/dimension')
libspud.set_option('/geometry/dimension', 3)
print libspud.get_option('/geometry/dimension')
list_path = '/material_phase::Material1/scalar_field::MaterialVolumeFraction/prognostic/boundary_conditions::LetNoOneLeave/surface_ids'
print libspud.get_option_shape(list_path)
print libspud.get_option_rank(list_path)
print libspud.get_option(list_path)
def fill(self, optionpath, bucket):
"""Fill a system class with data describing that system using libspud and the given optionpath."""
self.name = libspud.get_option(optionpath+"/name")
self.optionpath = optionpath
self.symbol = libspud.get_option(optionpath+"/ufl_symbol").split(os.linesep)[0]
self.bucket = bucket
self.mesh_name = libspud.get_option(optionpath+"/mesh/name")
mesh_optionpath = "/geometry/mesh::"+self.mesh_name
self.cell = libspud.get_option(mesh_optionpath+"/source/cell")
self.fields = []
for j in range(libspud.option_count(optionpath+"/field")):
field_optionpath = optionpath+"/field["+`j`+"]"
field = buckettools.spud.SpudFunctionBucket()
# get all the information about this field from the options dictionary
field.fill(field_optionpath, self, j)
# let the system know about this field
self.fields.append(field)
# remove the local copy of this field
del field
self.coeffs = []
for j in range(libspud.option_count(optionpath+"/coefficient")):
coeff_optionpath = optionpath+"/coefficient["+`j`+"]"
coeff = buckettools.spud.SpudFunctionBucket()
# get all the information about this coefficient from the options dictionary
coeff.fill(coeff_optionpath, self, j)
# let the system know about this coefficient
self.coeffs.append(coeff)
# remove the local copy of this coefficient
del coeff
self.special_coeffs = []
if libspud.have_option("/timestepping"):
coeff_optionpath = "/timestepping/timestep/coefficient::Timestep"
coeff = buckettools.spud.SpudFunctionBucket()
# get all the information about this coefficient from the options dictionary
coeff.fill(coeff_optionpath, self, 0)
# let the system know about this coefficient
self.special_coeffs.append(coeff)
# remove the local copy of this coefficient
del coeff
self.solvers = []
for j in range(libspud.option_count(optionpath+"/nonlinear_solver")):
solver_optionpath = optionpath+"/nonlinear_solver["+`j`+"]"
solver = buckettools.spud.SpudSolverBucket()
# get all the information about this nonlinear solver from the options dictionary
solver.fill(solver_optionpath, self)
# let the system know about this solver
self.solvers.append(solver)
# done with this nonlinear solver
del solver
self.functionals = []
for j in range(libspud.option_count(optionpath+"/functional")):
functional_optionpath = optionpath+"/functional["+`j`+"]"
functional = buckettools.spud.SpudFunctionalBucket()
# get all the information about this functional from the options dictionary
functional.fill(functional_optionpath, self)
# let the system know about this functional
self.functionals.append(functional)
# done with this functional
del functional
def fill(self, optionpath, bucket):
"""Fill a system class with data describing that system using libspud and the given optionpath."""
self.name = libspud.get_option(optionpath + "/name")
self.optionpath = optionpath
self.symbol = libspud.get_option(optionpath + "/ufl_symbol").split(
os.linesep)[0]
self.bucket = bucket
self.mesh_name = libspud.get_option(optionpath + "/mesh/name")
mesh_optionpath = "/geometry/mesh::" + self.mesh_name
self.cell = libspud.get_option(mesh_optionpath + "/source/cell")
self.fields = []
for j in range(libspud.option_count(optionpath + "/field")):
field_optionpath = optionpath + "/field[" + ` j ` + "]"
field = buckettools.spud.SpudFunctionBucket()
# get all the information about this field from the options dictionary
field.fill(field_optionpath, self, j)
# let the system know about this field
self.fields.append(field)
# remove the local copy of this field
del field
self.coeffs = []
for j in range(libspud.option_count(optionpath + "/coefficient")):
coeff_optionpath = optionpath + "/coefficient[" + ` j ` + "]"
coeff = buckettools.spud.SpudFunctionBucket()
# get all the information about this coefficient from the options dictionary
coeff.fill(coeff_optionpath, self, j)
# let the system know about this coefficient
self.coeffs.append(coeff)
# remove the local copy of this coefficient
del coeff
self.special_coeffs = []
if libspud.have_option("/timestepping"):
coeff_optionpath = "/timestepping/timestep/coefficient::Timestep"
coeff = buckettools.spud.SpudFunctionBucket()
# get all the information about this coefficient from the options dictionary
coeff.fill(coeff_optionpath, self, 0)
# let the system know about this coefficient
self.special_coeffs.append(coeff)
# remove the local copy of this coefficient
del coeff
self.solvers = []
for j in range(libspud.option_count(optionpath + "/nonlinear_solver")):
solver_optionpath = optionpath + "/nonlinear_solver[" + ` j ` + "]"
solver = buckettools.spud.SpudSolverBucket()
# get all the information about this nonlinear solver from the options dictionary
solver.fill(solver_optionpath, self)
# let the system know about this solver
self.solvers.append(solver)
# done with this nonlinear solver
del solver
self.functionals = []
for j in range(libspud.option_count(optionpath + "/functional")):
functional_optionpath = optionpath + "/functional[" + ` j ` + "]"
functional = buckettools.spud.SpudFunctionalBucket()
# get all the information about this functional from the options dictionary
functional.fill(functional_optionpath, self)
# let the system know about this functional
self.functionals.append(functional)
# done with this functional
del functional
import libspud
libspud.load_options('test.flml')
#libspud.print_options()
assert libspud.get_option('/timestepping/timestep') == 0.025
assert libspud.get_number_of_children('/geometry') == 5
assert libspud.get_child_name('geometry', 0) == "dimension"
assert libspud.option_count('/problem_type') == 1
assert libspud.have_option('/problem_type')
assert libspud.get_option_type('/geometry/dimension') is int
assert libspud.get_option_type('/problem_type') is str
assert libspud.get_option_rank('/geometry/dimension') == 0
assert libspud.get_option_rank(
'/physical_parameters/gravity/vector_field::GravityDirection/prescribed/value/constant'
) == 1
assert libspud.get_option_shape('/geometry/dimension') == (-1, -1)
assert libspud.get_option_shape('/problem_type')[0] > 1
assert libspud.get_option_shape('/problem_type')[1] == -1
assert libspud.get_option('/problem_type') == "multimaterial"
assert libspud.get_option('/geometry/dimension') == 2
libspud.set_option('/geometry/dimension', 3)
assert libspud.get_option('/geometry/dimension') == 3
def __init__(self,
tfml_file,
system_name='magma',
p_name='Pressure',
f_name='Porosity',
c_name='c',
n_name='n',
m_name='m',
d_name='d',
N_name='N',
h_squared_name='h_squared',
x0_name='x0'):
"""read the tfml_file and use libspud to populate the internal parameters
c: wavespeed
n: permeability exponent
m: bulk viscosity exponent
d: wave dimension
N: number of collocation points
x0: coordinate wave peak
h_squared: the size of the system in compaction lengths
squared (h/delta)**2
"""
# initialize libspud and extract parameters
libspud.clear_options()
libspud.load_options(tfml_file)
# get model dimension
self.dim = libspud.get_option("/geometry/dimension")
self.system_name = system_name
# get solitary wave parameters
path = "/system::" + system_name + "/coefficient::"
scalar_value = "/type::Constant/rank::Scalar/value::WholeMesh/constant"
vector_value = "/type::Constant/rank::Vector/value::WholeMesh/constant::dim"
c = libspud.get_option(path + c_name + scalar_value)
n = int(libspud.get_option(path + n_name + scalar_value))
m = int(libspud.get_option(path + m_name + scalar_value))
d = float(libspud.get_option(path + d_name + scalar_value))
N = int(libspud.get_option(path + N_name + scalar_value))
self.h = np.sqrt(
libspud.get_option(path + h_squared_name + scalar_value))
self.x0 = np.array(libspud.get_option(path + x0_name + vector_value))
self.swave = SolitaryWave(c, n, m, d, N)
self.rmax = self.swave.r[-1]
self.tfml_file = tfml_file
# check that d <= dim
assert (d <= self.dim)
# sort out appropriate index for calculating distance r
if d == 1:
self.index = [self.dim - 1]
else:
self.index = range(0, int(d))
# check that the origin point is the correct dimension
assert (len(self.x0) == self.dim)
#read in information for constructing Function space and dolfin objects
# get the mesh parameters and reconstruct the mesh
meshtype = libspud.get_option("/geometry/mesh/source[0]/name")
if meshtype == 'UnitSquare':
number_cells = libspud.get_option(
"/geometry/mesh[0]/source[0]/number_cells")
diagonal = libspud.get_option(
"/geometry/mesh[0]/source[0]/diagonal")
mesh = df.UnitSquareMesh(number_cells[0], number_cells[1],
diagonal)
elif meshtype == 'Rectangle':
x0 = libspud.get_option(
"/geometry/mesh::Mesh/source::Rectangle/lower_left")
x1 = libspud.get_option(
"/geometry/mesh::Mesh/source::Rectangle/upper_right")
number_cells = libspud.get_option(
"/geometry/mesh::Mesh/source::Rectangle/number_cells")
diagonal = libspud.get_option(
"/geometry/mesh[0]/source[0]/diagonal")
mesh = df.RectangleMesh(x0[0], x0[1], x1[0], x1[1],
number_cells[0], number_cells[1], diagonal)
elif meshtype == 'UnitCube':
number_cells = libspud.get_option(
"/geometry/mesh[0]/source[0]/number_cells")
mesh = df.UnitCubeMesh(number_cells[0], number_cells[1],
number_cells[2])
elif meshtype == 'Box':
x0 = libspud.get_option(
"/geometry/mesh::Mesh/source::Box/lower_back_left")
x1 = libspud.get_option(
"/geometry/mesh::Mesh/source::Box/upper_front_right")
number_cells = libspud.get_option(
"/geometry/mesh::Mesh/source::Box/number_cells")
mesh = df.BoxMesh(x0[0], x0[1], x0[2], x1[0], x1[1], x1[2],
number_cells[0], number_cells[1],
number_cells[2])
elif meshtype == 'UnitInterval':
number_cells = libspud.get_option(
"/geometry/mesh::Mesh/source::UnitInterval/number_cells")
mesh = df.UnitIntervalMesh(number_cells)
elif meshtype == 'Interval':
number_cells = libspud.get_option(
"/geometry/mesh::Mesh/source::Interval/number_cells")
left = libspud.get_option(
"/geometry/mesh::Mesh/source::Interval/left")
right = libspud.get_option(
"/geometry/mesh::Mesh/source::Interval/right")
mesh = df.IntervalMesh(number_cells, left, right)
elif meshtype == 'File':
mesh_filename = libspud.get_option(
"/geometry/mesh::Mesh/source::File/file")
print "tfml_file = ", self.tfml_file, "mesh_filename=", mesh_filename
mesh = df.Mesh(mesh_filename)
else:
df.error("Error: unknown mesh type " + meshtype)
#set the functionspace for n-d solitary waves
path = "/system::" + system_name + "/field::"
p_family = libspud.get_option(path + p_name +
"/type/rank/element/family")
p_degree = libspud.get_option(path + p_name +
"/type/rank/element/degree")
f_family = libspud.get_option(path + f_name +
"/type/rank/element/family")
f_degree = libspud.get_option(path + f_name +
"/type/rank/element/degree")
pe = df.FiniteElement(p_family, mesh.ufl_cell(), p_degree)
ve = df.FiniteElement(f_family, mesh.ufl_cell(), f_degree)
e = pe * ve
self.functionspace = df.FunctionSpace(mesh, e)
#work out the order of the fields
for i in xrange(
libspud.option_count("/system::" + system_name + "/field")):
name = libspud.get_option("/system::" + system_name + "/field[" +
` i ` + "]/name")
if name == f_name:
self.f_index = i
if name == p_name:
self.p_index = i
def run(self):
""" Perform the simulation! """
# Time-stepping parameters and constants
LOG.info("Setting up a few constants...")
T = self.options["T"]
t = self.options["t"]
theta = self.options["theta"]
dt = self.options["dt"]
dimension = self.options["dimension"]
g_magnitude = self.options["g_magnitude"]
# Get the function spaces
U = self.function_spaces["VelocityFunctionSpace"]
H = self.function_spaces["FreeSurfaceFunctionSpace"]
# Is the Velocity field represented by a discontinous function space?
dg = (U.ufl_element().family() == "Discontinuous Lagrange")
# Weight u and h by theta to obtain the theta time-stepping scheme.
assert (theta >= 0.0 and theta <= 1.0)
LOG.info("Time-stepping scheme using theta = %g" % (theta))
u_mid = (1.0 - theta) * self.u0 + theta * self.u
h_mid = (1.0 - theta) * self.h0 + theta * self.h
# The total height of the free surface.
self.h_total = self.h_mean + self.h0
# Non-linear approximation to the velocity
u_nl = Function(U).assign(self.u0)
# Second-order Adams-Bashforth velocity
u_bash = (3.0 / 2.0) * self.u0 - (1.0 / 2.0) * self.u00
# Simple P1 function space, to be used in the stabilisation routines (if applicable).
P1 = FunctionSpace(self.mesh, "CG", 1)
cellsize = CellSize(self.mesh)
###########################################################
################# Tentative velocity step #################
###########################################################
# The collection of all the individual terms in their weak form.
LOG.info("Constructing form...")
F = 0
# Mass term
if (self.options["have_momentum_mass"]):
LOG.debug("Momentum equation: Adding mass term...")
M_momentum = (1.0 / dt) * (inner(self.w, self.u) -
inner(self.w, self.u0)) * dx
F += M_momentum
# Append any Expression objects for weak BCs here.
weak_bc_expressions = []
# Advection term
if (self.options["have_momentum_advection"]):
LOG.debug("Momentum equation: Adding advection term...")
if (self.options["integrate_advection_term_by_parts"]):
outflow = (dot(self.u0, self.n) +
abs(dot(self.u0, self.n))) / 2.0
A_momentum = -inner(dot(u_nl, grad(self.w)),
u_bash) * dx - inner(
dot(u_bash, grad(u_nl)), self.w) * dx
A_momentum += inner(self.w, outflow * u_mid) * ds
if (dg):
# Only add interior facet integrals if we are dealing with a discontinous Galerkin discretisation.
A_momentum += dot(
outflow('+') * u_mid('+') - outflow('-') * u_mid('-'),
jump(self.w)) * dS
else:
A_momentum = inner(dot(grad(self.u), u_nl), self.w) * dx
F += A_momentum
# Viscous stress term. Note that the viscosity is kinematic (not dynamic).
if (self.options["have_momentum_stress"]):
LOG.debug("Momentum equation: Adding stress term...")
viscosity = Function(H)
# Background viscosity
background_viscosity = Function(H).interpolate(
Expression(
libspud.get_option(
"/system/equations/momentum_equation/stress_term/scalar_field::Viscosity/value/constant"
)))
viscosity.assign(background_viscosity)
# Eddy viscosity
if (self.options["have_turbulence_parameterisation"]):
LOG.debug(
"Momentum equation: Adding turbulence parameterisation...")
base_option_path = "/system/equations/momentum_equation/turbulence_parameterisation"
# Large eddy simulation (LES)
if (libspud.have_option(base_option_path + "/les")):
les = LES(self.mesh, H)
density = Constant(
1.0
) # We divide through by density in the momentum equation, so just set this to 1.0 for now.
smagorinsky_coefficient = Constant(
libspud.get_option(
base_option_path +
"/les/smagorinsky/smagorinsky_coefficient"))
eddy_viscosity = Function(H)
eddy_viscosity_lhs, eddy_viscosity_rhs = les.eddy_viscosity(
u_mid, density, smagorinsky_coefficient)
eddy_viscosity_problem = LinearVariationalProblem(
eddy_viscosity_lhs,
eddy_viscosity_rhs,
eddy_viscosity,
bcs=[])
eddy_viscosity_solver = LinearVariationalSolver(
eddy_viscosity_problem)
# Add on eddy viscosity
viscosity += eddy_viscosity
# Stress tensor: tau = grad(u) + transpose(grad(u)) - (2/3)*div(u)
if (not dg):
# Perform a double dot product of the stress tensor and grad(w).
K_momentum = -viscosity * inner(
grad(self.u) + grad(self.u).T, grad(self.w)) * dx
#K_momentum += viscosity*(2.0/3.0)*inner(div(self.u)*Identity(dimension), grad(self.w))*dx
else:
# Interior penalty method
cellsize = Constant(
0.2
) # In general, we should use CellSize(self.mesh) instead.
alpha = 1 / cellsize # Penalty parameter.
K_momentum = -viscosity('+') * inner(grad(u_mid), grad(
self.w)) * dx
for dim in range(self.options["dimension"]):
K_momentum += -viscosity('+') * (
alpha('+') / cellsize('+')) * dot(
jump(self.w[dim], self.n), jump(
u_mid[dim], self.n)) * dS
K_momentum += viscosity('+') * dot(
avg(grad(self.w[dim])), jump(u_mid[dim], self.n)
) * dS + viscosity('+') * dot(jump(self.w[dim], self.n),
avg(grad(u_mid[dim]))) * dS
F -= K_momentum # Negative sign here because we are bringing the stress term over from the RHS.
# The gradient of the height of the free surface, h
LOG.debug("Momentum equation: Adding gradient term...")
C_momentum = -g_magnitude * inner(self.w, grad(self.h0)) * dx
F -= C_momentum
# Quadratic drag term in the momentum equation
if (self.options["have_drag"]):
LOG.debug("Momentum equation: Adding drag term...")
base_option_path = "/system/equations/momentum_equation/drag_term"
# Get the bottom drag/friction coefficient.
LOG.debug("Momentum equation: Adding bottom drag contribution...")
bottom_drag = ExpressionFromOptions(
path=base_option_path +
"/scalar_field::BottomDragCoefficient/value",
t=t).get_expression()
bottom_drag = Function(H).interpolate(bottom_drag)
# Add on the turbine drag, if provided.
self.array = None
# Magnitude of the velocity field
magnitude = sqrt(dot(self.u0, self.u0))
# Form the drag term
array = sw.get_turbine_array()
if (array):
LOG.debug(
"Momentum equation: Adding turbine drag contribution...")
drag_coefficient = bottom_drag + array.turbine_drag()
else:
drag_coefficient = bottom_drag
D_momentum = -inner(
self.w,
(drag_coefficient * magnitude / self.h_total) * self.u) * dx
F -= D_momentum
# Add in any source terms
if (self.options["have_momentum_source"]):
LOG.debug("Momentum equation: Adding source term...")
momentum_source_expression = ExpressionFromOptions(
path=
"/system/equations/momentum_equation/source_term/vector_field::Source/value",
t=t).get_expression()
momentum_source_function = Function(U)
F -= inner(
self.w,
momentum_source_function.interpolate(
momentum_source_expression)) * dx
# Add in any SU stabilisation
if (self.options["have_su_stabilisation"]):
LOG.debug(
"Momentum equation: Adding streamline-upwind stabilisation term..."
)
stabilisation = Stabilisation(self.mesh, P1, cellsize)
magnitude = magnitude_vector(self.u0, P1)
# Bound the values for the magnitude below by 1.0e-9 for numerical stability reasons.
u_nodes = magnitude.vector()
near_zero = numpy.array([1.0e-9 for i in range(len(u_nodes))])
u_nodes.set_local(numpy.maximum(u_nodes.array(), near_zero))
diffusivity = ExpressionFromOptions(
path=
"/system/equations/momentum_equation/stress_term/scalar_field::Viscosity/value",
t=self.options["t"]).get_expression()
diffusivity = Function(H).interpolate(
diffusivity) # Background viscosity
grid_pe = grid_peclet_number(diffusivity, magnitude, P1, cellsize)
# Bound the values for grid_pe below by 1.0e-9 for numerical stability reasons.
grid_pe_nodes = grid_pe.vector()
values = numpy.array([1.0e-9 for i in range(len(grid_pe_nodes))])
grid_pe_nodes.set_local(
numpy.maximum(grid_pe_nodes.array(), values))
F += stabilisation.streamline_upwind(self.w, self.u0, magnitude,
grid_pe)
LOG.info("Form construction complete.")
##########################################################
################ Pressure correction step ################
##########################################################
u_tent = Function(U)
u_tent_nl = theta * u_tent + (1.0 - theta) * self.u0
F_h_corr = inner(self.v, (self.h - self.h0))*dx \
+ g_magnitude*(dt**2)*(theta**2)*self.h_total*inner(grad(self.v), grad(self.h - self.h0))*dx \
+ dt*self.v*div(self.h_total*u_tent_nl)*dx
##########################################################
################ Velocity correction step ################
##########################################################
h1 = Function(H)
u1 = Function(U)
F_u_corr = (1.0 / dt) * inner(
self.w, self.u - u_tent) * dx + g_magnitude * theta * inner(
self.w, grad(h1 - self.h0)) * dx
LOG.info("Applying strong Dirichlet boundary conditions...")
# Get all the Dirichlet boundary conditions for the Velocity field
bcs_u = []
bcs_u2 = []
bcs_h = []
bc_expressions = []
for i in range(
0,
libspud.option_count(
"/system/core_fields/vector_field::Velocity/boundary_condition"
)):
if (libspud.have_option(
"/system/core_fields/vector_field::Velocity/boundary_condition[%d]/type::dirichlet"
% i
) and not libspud.have_option(
"/system/core_fields/vector_field::Velocity/boundary_condition[%d]/type::dirichlet/apply_weakly"
% i)):
expr = ExpressionFromOptions(path=(
"/system/core_fields/vector_field::Velocity/boundary_condition[%d]/type::dirichlet"
% i),
t=t).get_expression()
# Surface IDs on the domain boundary
surface_ids = libspud.get_option(
"/system/core_fields/vector_field::Velocity/boundary_condition[%d]/surface_ids"
% i)
method = ("geometric" if dg else "topological")
bc = DirichletBC(U, expr, surface_ids, method=method)
bcs_u.append(bc)
bc_expressions.append(expr)
LOG.debug(
"Applying Velocity BC #%d strongly to surface IDs: %s" %
(i, surface_ids))
for i in range(
0,
libspud.option_count(
"/system/core_fields/vector_field::Velocity/boundary_condition"
)):
if (libspud.have_option(
"/system/core_fields/vector_field::Velocity/boundary_condition[%d]/type::dirichlet"
% i
) and not libspud.have_option(
"/system/core_fields/vector_field::Velocity/boundary_condition[%d]/type::dirichlet/apply_weakly"
% i)):
expr = ExpressionFromOptions(path=(
"/system/core_fields/vector_field::Velocity/boundary_condition[%d]/type::dirichlet"
% i),
t=t).get_expression()
# Surface IDs on the domain boundary
surface_ids = libspud.get_option(
"/system/core_fields/vector_field::Velocity/boundary_condition[%d]/surface_ids"
% i)
method = ("geometric" if dg else "topological")
bc = DirichletBC(U, expr, surface_ids, method=method)
bcs_u2.append(bc)
bc_expressions.append(expr)
LOG.debug(
"Applying Velocity BC #%d strongly to surface IDs: %s" %
(i, surface_ids))
for i in range(
0,
libspud.option_count(
"/system/core_fields/scalar_field::FreeSurfacePerturbation/boundary_condition/type::dirichlet"
)):
if (libspud.have_option(
"/system/core_fields/scalar_field::FreeSurfacePerturbation/boundary_condition[%d]/type::dirichlet"
% i
) and not (libspud.have_option(
"/system/core_fields/scalar_field::FreeSurfacePerturbation/boundary_condition[%d]/type::dirichlet/apply_weakly"
% i))):
expr = ExpressionFromOptions(path=(
"/system/core_fields/scalar_field::FreeSurfacePerturbation/boundary_condition[%d]/type::dirichlet"
% i),
t=t).get_expression()
# Surface IDs on the domain boundary
surface_ids = libspud.get_option(
"/system/core_fields/scalar_field::FreeSurfacePerturbation/boundary_condition[%d]/surface_ids"
% i)
method = ("geometric" if dg else "topological")
bc = DirichletBC(H, expr, surface_ids, method=method)
bcs_h.append(bc)
bc_expressions.append(expr)
LOG.debug(
"Applying FreeSurfacePerturbation BC #%d strongly to surface IDs: %s"
% (i, surface_ids))
# Prepare solver_parameters dictionary
LOG.debug("Defining solver_parameters dictionary...")
solver_parameters = {
'ksp_monitor': True,
'ksp_view': False,
'pc_view': False,
'snes_type': 'ksponly',
'ksp_max_it': 10000
} # NOTE: use 'snes_type': 'newtonls' for production runs.
# KSP (iterative solver) options
solver_parameters["ksp_type"] = libspud.get_option(
"/system/solver/iterative_method/name")
solver_parameters["ksp_rtol"] = libspud.get_option(
"/system/solver/relative_error")
solver_parameters['ksp_converged_reason'] = True
solver_parameters['ksp_monitor_true_residual'] = True
# Preconditioner options
solver_parameters["pc_type"] = libspud.get_option(
"/system/solver/preconditioner/name")
# Fieldsplit sub-options
if (solver_parameters["pc_type"] == "fieldsplit"):
LOG.debug("Setting up the fieldsplit preconditioner...")
solver_parameters["pc_fieldsplit_type"] = libspud.get_option(
"/system/solver/preconditioner::fieldsplit/type/name")
if (solver_parameters["pc_fieldsplit_type"] == "schur"):
solver_parameters[
"pc_fieldsplit_schur_fact_type"] = libspud.get_option(
"/system/solver/preconditioner::fieldsplit/type::schur/fact_type/name"
)
solver_parameters["fieldsplit_0_ksp_type"] = libspud.get_option(
"/system/solver/preconditioner::fieldsplit/block_0_ksp_type/iterative_method/name"
)
solver_parameters["fieldsplit_1_ksp_type"] = libspud.get_option(
"/system/solver/preconditioner::fieldsplit/block_1_ksp_type/iterative_method/name"
)
if (libspud.get_option(
"/system/solver/preconditioner::fieldsplit/block_0_pc_type/preconditioner/name"
) != "ilu"):
solver_parameters["fieldsplit_0_pc_type"] = libspud.get_option(
"/system/solver/preconditioner::fieldsplit/block_0_pc_type/preconditioner/name"
)
solver_parameters["fieldsplit_1_pc_type"] = libspud.get_option(
"/system/solver/preconditioner::fieldsplit/block_1_pc_type/preconditioner/name"
)
# Enable inner iteration monitors.
solver_parameters["fieldsplit_0_ksp_monitor"] = True
solver_parameters["fieldsplit_1_ksp_monitor"] = True
solver_parameters["fieldsplit_0_pc_factor_shift_type"] = 'INBLOCKS'
solver_parameters["fieldsplit_1_pc_factor_shift_type"] = 'INBLOCKS'
# Construct the solver objects
problem_tent = LinearVariationalProblem(lhs(F),
rhs(F),
u_tent,
bcs=bcs_u)
solver_tent = LinearVariationalSolver(problem_tent,
solver_parameters={
'ksp_monitor': False,
'ksp_view': False,
'pc_view': False,
'pc_type': 'sor',
'ksp_type': 'gmres',
'ksp_rtol': 1.0e-7
})
problem_h_corr = LinearVariationalProblem(lhs(F_h_corr),
rhs(F_h_corr),
h1,
bcs=bcs_h)
solver_h_corr = LinearVariationalSolver(problem_h_corr,
solver_parameters={
'ksp_monitor': False,
'ksp_view': False,
'pc_view': False,
'pc_type': 'sor',
'ksp_type': 'gmres',
'ksp_rtol': 1.0e-7
})
problem_u_corr = LinearVariationalProblem(lhs(F_u_corr),
rhs(F_u_corr),
u1,
bcs=bcs_u2)
solver_u_corr = LinearVariationalSolver(problem_u_corr,
solver_parameters={
'ksp_monitor': False,
'ksp_view': False,
'pc_view': False,
'pc_type': 'sor',
'ksp_type': 'gmres',
'ksp_rtol': 1.0e-7
})
t += dt
iterations_since_dump = 1
iterations_since_checkpoint = 1
# PETSc solver run-times
from petsc4py import PETSc
main_solver_stage = PETSc.Log.Stage('Main block-coupled system solve')
total_solver_time = 0.0
# The time-stepping loop
LOG.info("Entering the time-stepping loop...")
EPSILON = 1.0e-14
while t <= T + EPSILON: # A small value EPSILON is added here in case of round-off error.
LOG.info("t = %g" % t)
while True:
## Update any time-dependent Functions and Expressions.
# Re-compute the velocity magnitude and grid Peclet number fields.
if (self.options["have_su_stabilisation"]):
magnitude.assign(magnitude_vector(self.u0, P1))
# Bound the values for the magnitude below by 1.0e-9 for numerical stability reasons.
u_nodes = magnitude.vector()
near_zero = numpy.array(
[1.0e-9 for i in range(len(u_nodes))])
u_nodes.set_local(numpy.maximum(u_nodes.array(),
near_zero))
grid_pe.assign(
grid_peclet_number(diffusivity, magnitude, P1,
cellsize))
# Bound the values for grid_pe below by 1.0e-9 for numerical stability reasons.
grid_pe_nodes = grid_pe.vector()
values = numpy.array(
[1.0e-9 for i in range(len(grid_pe_nodes))])
grid_pe_nodes.set_local(
numpy.maximum(grid_pe_nodes.array(), values))
if (self.options["have_turbulence_parameterisation"]):
eddy_viscosity_solver.solve()
viscosity.assign(background_viscosity + eddy_viscosity)
# Time-dependent source terms
if (self.options["have_momentum_source"]):
momentum_source_expression.t = t
momentum_source_function.interpolate(
momentum_source_expression)
if (self.options["have_continuity_source"]):
continuity_source_expression.t = t
continuity_source_function.interpolate(
continuity_source_expression)
# Update any time-varying DirichletBC objects.
for expr in bc_expressions:
expr.t = t
for expr in weak_bc_expressions:
expr.t = t
# Solve the system of equations!
start_solver_time = mpi4py.MPI.Wtime()
main_solver_stage.push()
LOG.debug("Solving the system of equations...")
solver_tent.solve()
solver_h_corr.solve()
solver_u_corr.solve()
main_solver_stage.pop()
end_solver_time = mpi4py.MPI.Wtime()
total_solver_time += (end_solver_time - start_solver_time)
# Move to next time step
if (steady_state(u1, u_nl, 1e-7)):
break
u_nl.assign(u1)
self.u00.assign(self.u0)
self.u0.assign(u1)
self.h0.assign(h1)
t += dt
iterations_since_dump += 1
iterations_since_checkpoint += 1
LOG.debug("Moving to next time level...")
# Write the solution to file.
if ((self.options["dump_period"] is not None) and
(dt * iterations_since_dump >= self.options["dump_period"])):
LOG.debug("Writing data to file...")
self.output_functions["Velocity"].assign(u1)
self.output_files["Velocity"] << self.output_functions[
"Velocity"]
self.output_functions["FreeSurfacePerturbation"].assign(h1)
self.output_files[
"FreeSurfacePerturbation"] << self.output_functions[
"FreeSurfacePerturbation"]
iterations_since_dump = 0 # Reset the counter.
# Print out the total power generated by turbines.
if (self.options["have_drag"] and self.array is not None):
LOG.info("Power = %.2f" % self.array.power(u1, density=1000))
# Checkpointing
if ((self.options["checkpoint_period"] is not None)
and (dt * iterations_since_checkpoint >=
self.options["checkpoint_period"])):
LOG.debug("Writing checkpoint data to file...")
self.solution.dat.save("checkpoint")
iterations_since_checkpoint = 0 # Reset the counter.
# Check whether a steady-state has been reached.
if (steady_state(u1, self.u0,
self.options["steady_state_tolerance"])
and steady_state(h1, self.h0,
self.options["steady_state_tolerance"])):
LOG.info(
"Steady-state attained. Exiting the time-stepping loop...")
break
self.compute_diagnostics()
LOG.info("Out of the time-stepping loop.")
LOG.debug("Total solver time: %.2f" % (total_solver_time))
return u1, h1
def get_productions_and_injections(prod_file, geothermal, foldername, cwd):
import csv
nPhases = libspud.option_count('/material_phase')
##Get into the folder
os.chdir(foldername)
String_id = "-S"
String_prod = "- Volume rate"
#Replace spaces by commas to make it consistent
opal_options.producer_ids.replace(' ', ',')
opal_options.injector_ids.replace(' ', ',')
#Create a list with the integers
producer_list = [
int(e) if e.isdigit() else e
for e in opal_options.producer_ids.split(',')
]
injector_list = [
int(e) if e.isdigit() else e
for e in opal_options.injector_ids.split(',')
]
with open(prod_file, 'rb') as csvfile:
datareader = csv.reader(csvfile, delimiter=',', quotechar='|')
counter = -1 #To account for the header
for row in datareader:
try:
counter += 1
except:
continue
timeList = np.zeros(counter)
prod = np.zeros((nPhases, counter))
inject = np.zeros((nPhases, counter))
prod_temp = np.zeros((nPhases, counter))
inject_temp = np.zeros((nPhases, counter))
counter = 0
with open(prod_file, 'rb') as csvfile:
datareader = csv.reader(csvfile, delimiter=',', quotechar='|')
prod_cols = []
inject_cols = []
header = True
previousT = 0.0
for row in datareader:
try:
if header:
#Find the positions of interest of the producers
for ids in producer_list:
for i in range(len(row)):
if (String_id + str(ids) + String_prod) in row[i]:
prod_cols.append(i)
#Find the positions of interest of the injectors
for ids in injector_list:
for i in range(len(row)):
if (String_id + str(ids) + String_prod) in row[i]:
inject_cols.append(i)
header = False
continue
phase_prod = 0
phase_inject = 0
timeList[counter] = float(row[0])
# Calculate deltaT from absolute times
deltaT = float(row[0]) - previousT
previousT = float(row[0])
for i in range(len(row)):
# Update production
for j in range(len(prod_cols)):
if i == prod_cols[j]:
if geothermal:
#For geothermal I need to do temperature * production * rho * Cp
#CURRENTLY NOT INCLUDED Cp nor RHO
#First temperature, so we can calculate the production in this time level
prod_temp[phase_prod, counter] = abs(
float(row[i]) * deltaT *
float(row[i + nPhases * 2]))
prod[phase_prod,
counter] = abs(float(row[i]) * deltaT)
phase_prod += 1
if phase_prod == nPhases: phase_prod = 0
# Update Injection
for j in range(len(inject_cols)):
if i == inject_cols[j]:
if geothermal:
#For geothermal I need to do temperature * production * rho * Cp
#CURRENTLY NOT INCLUDED Cp nor RHO
#First temperature, so we can calculate the production in this time level
inject_temp[phase_inject, counter] = abs(
float(row[i]) * deltaT *
float(row[i + nPhases * 2]))
inject[phase_inject,
counter] = abs(float(row[i]) * deltaT)
phase_inject += 1
if phase_inject == nPhases: phase_inject = 0
counter += 1
except:
continue
##Return to original path
os.chdir(cwd)
return timeList, prod, inject, prod_temp, inject_temp
def fill(self, optionpath, system, index):
"""Fill a function class with data describing that function using libspud, the given optionpath and the system its based on."""
self.name = libspud.get_option(optionpath + "/name")
self.symbol = libspud.get_option(optionpath + "/ufl_symbol").split(
os.linesep)[0]
self.system = system
self.index = index
self.type = libspud.get_option(optionpath + "/type/name")
self.rank = libspud.get_option(optionpath + "/type/rank/name")
self.family = None
self.degree = None
self.functional = None
if self.type != "Constant":
self.family = libspud.get_option(optionpath +
"/type/rank/element/family")
self.degree = libspud.get_option(optionpath +
"/type/rank/element/degree")
self.size = None
self.shape = None
self.symmetry = None
if self.rank == "Vector":
if libspud.have_option(optionpath + "/type/rank/element/size"):
self.size = libspud.get_option(optionpath +
"/type/rank/element/size")
elif self.rank == "Tensor":
if libspud.have_option(optionpath + "/type/rank/element/shape"):
self.shape = libspud.get_option(optionpath +
"/type/rank/element/shape")
if libspud.have_option(optionpath +
"/type/rank/element/symmetric"):
self.symmetry = True
self.enrichment_family = None
self.enrichment_degree = None
if libspud.have_option(optionpath + "/type/rank/element/enrichment"):
self.enrichment_family = libspud.get_option(
optionpath + "/type/rank/element/enrichment/element/family")
self.enrichment_degree = libspud.get_option(
optionpath + "/type/rank/element/enrichment/element/degree")
if libspud.have_option(optionpath +
"/type/rank/element/quadrature_rule"):
self.quadrature_rule = libspud.get_option(
optionpath + "/type/rank/element/quadrature_rule/name")
# this should be restricted by the schema to Constant coefficients:
if libspud.have_option(optionpath + "/type/rank/value/functional"):
functional_optionpath = optionpath + "/type/rank/value/functional"
functional = buckettools.spud.SpudFunctionalBucket()
functional.fill(functional_optionpath, self.system, self)
self.functional = functional
self.cpp = []
for k in range(
libspud.option_count(optionpath +
"/type/rank/initial_condition")):
cpp_optionpath = optionpath + "/type/rank/initial_condition[" + ` k ` + "]"
if libspud.have_option(cpp_optionpath + "/cpp"):
cpp_name = libspud.get_option(cpp_optionpath + "/name")
cppexpression = buckettools.spud.SpudCppExpressionBucket()
# get all the information about this expression from the options dictionary
cppexpression.fill(cpp_optionpath, cpp_name, self)
# let the field know about this cpp expression
self.cpp.append(cppexpression)
# done with this expression
del cppexpression
for j in range(
libspud.option_count(optionpath +
"/type/rank/boundary_condition")):
bc_optionpath = optionpath + "/type/rank/boundary_condition[" + ` j ` + "]"
bc_name = libspud.get_option(bc_optionpath + "/name")
for k in range(
libspud.option_count(bc_optionpath + "/sub_components")):
bc_comp_optionpath = bc_optionpath + "/sub_components[" + ` k ` + "]"
bc_comp_name = libspud.get_option(bc_comp_optionpath + "/name")
cpp_optionpath = bc_comp_optionpath + "/type"
if libspud.have_option(cpp_optionpath + "/cpp"):
cpp_name = bc_name + bc_comp_name
cppexpression = buckettools.spud.SpudCppExpressionBucket()
# get all the information about this expression from the options dictionary
cppexpression.fill(cpp_optionpath, cpp_name, self)
# let the field know about this cpp expression
self.cpp.append(cppexpression)
# done with this expression
del cppexpression
for k in range(libspud.option_count(optionpath + "/type/rank/value")):
cpp_optionpath = optionpath + "/type/rank/value[" + ` k ` + "]"
if libspud.have_option(cpp_optionpath + "/cpp"):
cpp_name = libspud.get_option(cpp_optionpath + "/name")
cppexpression = buckettools.spud.SpudCppExpressionBucket()
# get all the information about this expression from the options dictionary
cppexpression.fill(cpp_optionpath, cpp_name, self)
# let the field know about this cpp expression
self.cpp.append(cppexpression)
# done with this expression
del cppexpression
def run(self):
""" Perform the simulation! """
# Time-stepping parameters and constants
LOG.info("Setting up a few constants...")
T = self.options["T"]
t = self.options["t"]
theta = self.options["theta"]
dt = self.options["dt"]
dimension = self.options["dimension"]
g_magnitude = self.options["g_magnitude"]
# Get the function spaces
U = self.function_spaces["VelocityFunctionSpace"]
H = self.function_spaces["FreeSurfaceFunctionSpace"]
# Is the Velocity field represented by a discontinous function space?
dg = (U.ufl_element().family() == "Discontinuous Lagrange")
# Weight u and h by theta to obtain the theta time-stepping scheme.
assert(theta >= 0.0 and theta <= 1.0)
LOG.info("Time-stepping scheme using theta = %g" % (theta))
u_mid = (1.0 - theta) * self.u0 + theta * self.u
h_mid = (1.0 - theta) * self.h0 + theta * self.h
# The total height of the free surface.
self.h_total = self.h_mean + self.h0
# Non-linear approximation to the velocity
u_nl = Function(U).assign(self.u0)
# Second-order Adams-Bashforth velocity
u_bash = (3.0/2.0)*self.u0 - (1.0/2.0)*self.u00
# Simple P1 function space, to be used in the stabilisation routines (if applicable).
P1 = FunctionSpace(self.mesh, "CG", 1)
cellsize = CellSize(self.mesh)
###########################################################
################# Tentative velocity step #################
###########################################################
# The collection of all the individual terms in their weak form.
LOG.info("Constructing form...")
F = 0
# Mass term
if(self.options["have_momentum_mass"]):
LOG.debug("Momentum equation: Adding mass term...")
M_momentum = (1.0/dt)*(inner(self.w, self.u) - inner(self.w, self.u0))*dx
F += M_momentum
# Append any Expression objects for weak BCs here.
weak_bc_expressions = []
# Advection term
if(self.options["have_momentum_advection"]):
LOG.debug("Momentum equation: Adding advection term...")
if(self.options["integrate_advection_term_by_parts"]):
outflow = (dot(self.u0, self.n) + abs(dot(self.u0, self.n)))/2.0
A_momentum = -inner(dot(u_nl, grad(self.w)), u_bash)*dx - inner(dot(u_bash, grad(u_nl)), self.w)*dx
A_momentum += inner(self.w, outflow*u_mid)*ds
if(dg):
# Only add interior facet integrals if we are dealing with a discontinous Galerkin discretisation.
A_momentum += dot(outflow('+')*u_mid('+') - outflow('-')*u_mid('-'), jump(self.w))*dS
else:
A_momentum = inner(dot(grad(self.u), u_nl), self.w)*dx
F += A_momentum
# Viscous stress term. Note that the viscosity is kinematic (not dynamic).
if(self.options["have_momentum_stress"]):
LOG.debug("Momentum equation: Adding stress term...")
viscosity = Function(H)
# Background viscosity
background_viscosity = Function(H).interpolate(Expression(libspud.get_option("/system/equations/momentum_equation/stress_term/scalar_field::Viscosity/value/constant")))
viscosity.assign(background_viscosity)
# Eddy viscosity
if(self.options["have_turbulence_parameterisation"]):
LOG.debug("Momentum equation: Adding turbulence parameterisation...")
base_option_path = "/system/equations/momentum_equation/turbulence_parameterisation"
# Large eddy simulation (LES)
if(libspud.have_option(base_option_path + "/les")):
les = LES(self.mesh, H)
density = Constant(1.0) # We divide through by density in the momentum equation, so just set this to 1.0 for now.
smagorinsky_coefficient = Constant(libspud.get_option(base_option_path + "/les/smagorinsky/smagorinsky_coefficient"))
eddy_viscosity = Function(H)
eddy_viscosity_lhs, eddy_viscosity_rhs = les.eddy_viscosity(u_mid, density, smagorinsky_coefficient)
eddy_viscosity_problem = LinearVariationalProblem(eddy_viscosity_lhs, eddy_viscosity_rhs, eddy_viscosity, bcs=[])
eddy_viscosity_solver = LinearVariationalSolver(eddy_viscosity_problem)
# Add on eddy viscosity
viscosity += eddy_viscosity
# Stress tensor: tau = grad(u) + transpose(grad(u)) - (2/3)*div(u)
if(not dg):
# Perform a double dot product of the stress tensor and grad(w).
K_momentum = -viscosity*inner(grad(self.u) + grad(self.u).T, grad(self.w))*dx
#K_momentum += viscosity*(2.0/3.0)*inner(div(self.u)*Identity(dimension), grad(self.w))*dx
else:
# Interior penalty method
cellsize = Constant(0.2) # In general, we should use CellSize(self.mesh) instead.
alpha = 1/cellsize # Penalty parameter.
K_momentum = -viscosity('+')*inner(grad(u_mid), grad(self.w))*dx
for dim in range(self.options["dimension"]):
K_momentum += -viscosity('+')*(alpha('+')/cellsize('+'))*dot(jump(self.w[dim], self.n), jump(u_mid[dim], self.n))*dS
K_momentum += viscosity('+')*dot(avg(grad(self.w[dim])), jump(u_mid[dim], self.n))*dS + viscosity('+')*dot(jump(self.w[dim], self.n), avg(grad(u_mid[dim])))*dS
F -= K_momentum # Negative sign here because we are bringing the stress term over from the RHS.
# The gradient of the height of the free surface, h
LOG.debug("Momentum equation: Adding gradient term...")
C_momentum = -g_magnitude*inner(self.w, grad(self.h0))*dx
F -= C_momentum
# Quadratic drag term in the momentum equation
if(self.options["have_drag"]):
LOG.debug("Momentum equation: Adding drag term...")
base_option_path = "/system/equations/momentum_equation/drag_term"
# Get the bottom drag/friction coefficient.
LOG.debug("Momentum equation: Adding bottom drag contribution...")
bottom_drag = ExpressionFromOptions(path=base_option_path+"/scalar_field::BottomDragCoefficient/value", t=t).get_expression()
bottom_drag = Function(H).interpolate(bottom_drag)
# Add on the turbine drag, if provided.
self.array = None
# Magnitude of the velocity field
magnitude = sqrt(dot(self.u0, self.u0))
# Form the drag term
array = sw.get_turbine_array()
if(array):
LOG.debug("Momentum equation: Adding turbine drag contribution...")
drag_coefficient = bottom_drag + array.turbine_drag()
else:
drag_coefficient = bottom_drag
D_momentum = -inner(self.w, (drag_coefficient*magnitude/self.h_total)*self.u)*dx
F -= D_momentum
# Add in any source terms
if(self.options["have_momentum_source"]):
LOG.debug("Momentum equation: Adding source term...")
momentum_source_expression = ExpressionFromOptions(path = "/system/equations/momentum_equation/source_term/vector_field::Source/value", t=t).get_expression()
momentum_source_function = Function(U)
F -= inner(self.w, momentum_source_function.interpolate(momentum_source_expression))*dx
# Add in any SU stabilisation
if(self.options["have_su_stabilisation"]):
LOG.debug("Momentum equation: Adding streamline-upwind stabilisation term...")
stabilisation = Stabilisation(self.mesh, P1, cellsize)
magnitude = magnitude_vector(self.u0, P1)
# Bound the values for the magnitude below by 1.0e-9 for numerical stability reasons.
u_nodes = magnitude.vector()
near_zero = numpy.array([1.0e-9 for i in range(len(u_nodes))])
u_nodes.set_local(numpy.maximum(u_nodes.array(), near_zero))
diffusivity = ExpressionFromOptions(path = "/system/equations/momentum_equation/stress_term/scalar_field::Viscosity/value", t=self.options["t"]).get_expression()
diffusivity = Function(H).interpolate(diffusivity) # Background viscosity
grid_pe = grid_peclet_number(diffusivity, magnitude, P1, cellsize)
# Bound the values for grid_pe below by 1.0e-9 for numerical stability reasons.
grid_pe_nodes = grid_pe.vector()
values = numpy.array([1.0e-9 for i in range(len(grid_pe_nodes))])
grid_pe_nodes.set_local(numpy.maximum(grid_pe_nodes.array(), values))
F += stabilisation.streamline_upwind(self.w, self.u0, magnitude, grid_pe)
LOG.info("Form construction complete.")
##########################################################
################ Pressure correction step ################
##########################################################
u_tent = Function(U)
u_tent_nl = theta*u_tent + (1.0-theta)*self.u0
F_h_corr = inner(self.v, (self.h - self.h0))*dx \
+ g_magnitude*(dt**2)*(theta**2)*self.h_total*inner(grad(self.v), grad(self.h - self.h0))*dx \
+ dt*self.v*div(self.h_total*u_tent_nl)*dx
##########################################################
################ Velocity correction step ################
##########################################################
h1 = Function(H)
u1 = Function(U)
F_u_corr = (1.0/dt)*inner(self.w, self.u - u_tent)*dx + g_magnitude*theta*inner(self.w, grad(h1 - self.h0))*dx
LOG.info("Applying strong Dirichlet boundary conditions...")
# Get all the Dirichlet boundary conditions for the Velocity field
bcs_u = []; bcs_u2 = []
bcs_h = []
bc_expressions = []
for i in range(0, libspud.option_count("/system/core_fields/vector_field::Velocity/boundary_condition")):
if(libspud.have_option("/system/core_fields/vector_field::Velocity/boundary_condition[%d]/type::dirichlet" % i) and
not libspud.have_option("/system/core_fields/vector_field::Velocity/boundary_condition[%d]/type::dirichlet/apply_weakly" % i)):
expr = ExpressionFromOptions(path = ("/system/core_fields/vector_field::Velocity/boundary_condition[%d]/type::dirichlet" % i), t=t).get_expression()
# Surface IDs on the domain boundary
surface_ids = libspud.get_option("/system/core_fields/vector_field::Velocity/boundary_condition[%d]/surface_ids" % i)
method = ("geometric" if dg else "topological")
bc = DirichletBC(U, expr, surface_ids, method=method)
bcs_u.append(bc)
bc_expressions.append(expr)
LOG.debug("Applying Velocity BC #%d strongly to surface IDs: %s" % (i, surface_ids))
for i in range(0, libspud.option_count("/system/core_fields/vector_field::Velocity/boundary_condition")):
if(libspud.have_option("/system/core_fields/vector_field::Velocity/boundary_condition[%d]/type::dirichlet" % i) and
not libspud.have_option("/system/core_fields/vector_field::Velocity/boundary_condition[%d]/type::dirichlet/apply_weakly" % i)):
expr = ExpressionFromOptions(path = ("/system/core_fields/vector_field::Velocity/boundary_condition[%d]/type::dirichlet" % i), t=t).get_expression()
# Surface IDs on the domain boundary
surface_ids = libspud.get_option("/system/core_fields/vector_field::Velocity/boundary_condition[%d]/surface_ids" % i)
method = ("geometric" if dg else "topological")
bc = DirichletBC(U, expr, surface_ids, method=method)
bcs_u2.append(bc)
bc_expressions.append(expr)
LOG.debug("Applying Velocity BC #%d strongly to surface IDs: %s" % (i, surface_ids))
for i in range(0, libspud.option_count("/system/core_fields/scalar_field::FreeSurfacePerturbation/boundary_condition/type::dirichlet")):
if(libspud.have_option("/system/core_fields/scalar_field::FreeSurfacePerturbation/boundary_condition[%d]/type::dirichlet" % i) and
not(libspud.have_option("/system/core_fields/scalar_field::FreeSurfacePerturbation/boundary_condition[%d]/type::dirichlet/apply_weakly" % i))):
expr = ExpressionFromOptions(path = ("/system/core_fields/scalar_field::FreeSurfacePerturbation/boundary_condition[%d]/type::dirichlet" % i), t=t).get_expression()
# Surface IDs on the domain boundary
surface_ids = libspud.get_option("/system/core_fields/scalar_field::FreeSurfacePerturbation/boundary_condition[%d]/surface_ids" % i)
method = ("geometric" if dg else "topological")
bc = DirichletBC(H, expr, surface_ids, method=method)
bcs_h.append(bc)
bc_expressions.append(expr)
LOG.debug("Applying FreeSurfacePerturbation BC #%d strongly to surface IDs: %s" % (i, surface_ids))
# Prepare solver_parameters dictionary
LOG.debug("Defining solver_parameters dictionary...")
solver_parameters = {'ksp_monitor': True, 'ksp_view': False, 'pc_view': False, 'snes_type': 'ksponly', 'ksp_max_it':10000} # NOTE: use 'snes_type': 'newtonls' for production runs.
# KSP (iterative solver) options
solver_parameters["ksp_type"] = libspud.get_option("/system/solver/iterative_method/name")
solver_parameters["ksp_rtol"] = libspud.get_option("/system/solver/relative_error")
solver_parameters['ksp_converged_reason'] = True
solver_parameters['ksp_monitor_true_residual'] = True
# Preconditioner options
solver_parameters["pc_type"] = libspud.get_option("/system/solver/preconditioner/name")
# Fieldsplit sub-options
if(solver_parameters["pc_type"] == "fieldsplit"):
LOG.debug("Setting up the fieldsplit preconditioner...")
solver_parameters["pc_fieldsplit_type"] = libspud.get_option("/system/solver/preconditioner::fieldsplit/type/name")
if(solver_parameters["pc_fieldsplit_type"] == "schur"):
solver_parameters["pc_fieldsplit_schur_fact_type"] = libspud.get_option("/system/solver/preconditioner::fieldsplit/type::schur/fact_type/name")
solver_parameters["fieldsplit_0_ksp_type"] = libspud.get_option("/system/solver/preconditioner::fieldsplit/block_0_ksp_type/iterative_method/name")
solver_parameters["fieldsplit_1_ksp_type"] = libspud.get_option("/system/solver/preconditioner::fieldsplit/block_1_ksp_type/iterative_method/name")
if(libspud.get_option("/system/solver/preconditioner::fieldsplit/block_0_pc_type/preconditioner/name") != "ilu"):
solver_parameters["fieldsplit_0_pc_type"] = libspud.get_option("/system/solver/preconditioner::fieldsplit/block_0_pc_type/preconditioner/name")
solver_parameters["fieldsplit_1_pc_type"] = libspud.get_option("/system/solver/preconditioner::fieldsplit/block_1_pc_type/preconditioner/name")
# Enable inner iteration monitors.
solver_parameters["fieldsplit_0_ksp_monitor"] = True
solver_parameters["fieldsplit_1_ksp_monitor"] = True
solver_parameters["fieldsplit_0_pc_factor_shift_type"] = 'INBLOCKS'
solver_parameters["fieldsplit_1_pc_factor_shift_type"] = 'INBLOCKS'
# Construct the solver objects
problem_tent = LinearVariationalProblem(lhs(F), rhs(F), u_tent, bcs=bcs_u)
solver_tent = LinearVariationalSolver(problem_tent, solver_parameters={'ksp_monitor': False,
'ksp_view': False,
'pc_view': False,
'pc_type': 'sor',
'ksp_type': 'gmres',
'ksp_rtol': 1.0e-7})
problem_h_corr = LinearVariationalProblem(lhs(F_h_corr), rhs(F_h_corr), h1, bcs=bcs_h)
solver_h_corr = LinearVariationalSolver(problem_h_corr, solver_parameters={'ksp_monitor': False,
'ksp_view': False,
'pc_view': False,
'pc_type': 'sor',
'ksp_type': 'gmres',
'ksp_rtol': 1.0e-7})
problem_u_corr = LinearVariationalProblem(lhs(F_u_corr), rhs(F_u_corr), u1, bcs=bcs_u2)
solver_u_corr = LinearVariationalSolver(problem_u_corr, solver_parameters={'ksp_monitor': False,
'ksp_view': False,
'pc_view': False,
'pc_type': 'sor',
'ksp_type': 'gmres',
'ksp_rtol': 1.0e-7})
t += dt
iterations_since_dump = 1
iterations_since_checkpoint = 1
# PETSc solver run-times
from petsc4py import PETSc
main_solver_stage = PETSc.Log.Stage('Main block-coupled system solve')
total_solver_time = 0.0
# The time-stepping loop
LOG.info("Entering the time-stepping loop...")
EPSILON = 1.0e-14
while t <= T + EPSILON: # A small value EPSILON is added here in case of round-off error.
LOG.info("t = %g" % t)
while True:
## Update any time-dependent Functions and Expressions.
# Re-compute the velocity magnitude and grid Peclet number fields.
if(self.options["have_su_stabilisation"]):
magnitude.assign(magnitude_vector(self.u0, P1))
# Bound the values for the magnitude below by 1.0e-9 for numerical stability reasons.
u_nodes = magnitude.vector()
near_zero = numpy.array([1.0e-9 for i in range(len(u_nodes))])
u_nodes.set_local(numpy.maximum(u_nodes.array(), near_zero))
grid_pe.assign(grid_peclet_number(diffusivity, magnitude, P1, cellsize))
# Bound the values for grid_pe below by 1.0e-9 for numerical stability reasons.
grid_pe_nodes = grid_pe.vector()
values = numpy.array([1.0e-9 for i in range(len(grid_pe_nodes))])
grid_pe_nodes.set_local(numpy.maximum(grid_pe_nodes.array(), values))
if(self.options["have_turbulence_parameterisation"]):
eddy_viscosity_solver.solve()
viscosity.assign(background_viscosity + eddy_viscosity)
# Time-dependent source terms
if(self.options["have_momentum_source"]):
momentum_source_expression.t = t
momentum_source_function.interpolate(momentum_source_expression)
if(self.options["have_continuity_source"]):
continuity_source_expression.t = t
continuity_source_function.interpolate(continuity_source_expression)
# Update any time-varying DirichletBC objects.
for expr in bc_expressions:
expr.t = t
for expr in weak_bc_expressions:
expr.t = t
# Solve the system of equations!
start_solver_time = mpi4py.MPI.Wtime()
main_solver_stage.push()
LOG.debug("Solving the system of equations...")
solver_tent.solve()
solver_h_corr.solve()
solver_u_corr.solve()
main_solver_stage.pop()
end_solver_time = mpi4py.MPI.Wtime()
total_solver_time += (end_solver_time - start_solver_time)
# Move to next time step
if(steady_state(u1, u_nl, 1e-7)):
break
u_nl.assign(u1)
self.u00.assign(self.u0)
self.u0.assign(u1)
self.h0.assign(h1)
t += dt
iterations_since_dump += 1
iterations_since_checkpoint += 1
LOG.debug("Moving to next time level...")
# Write the solution to file.
if((self.options["dump_period"] is not None) and (dt*iterations_since_dump >= self.options["dump_period"])):
LOG.debug("Writing data to file...")
self.output_functions["Velocity"].assign(u1)
self.output_files["Velocity"] << self.output_functions["Velocity"]
self.output_functions["FreeSurfacePerturbation"].assign(h1)
self.output_files["FreeSurfacePerturbation"] << self.output_functions["FreeSurfacePerturbation"]
iterations_since_dump = 0 # Reset the counter.
# Print out the total power generated by turbines.
if(self.options["have_drag"] and self.array is not None):
LOG.info("Power = %.2f" % self.array.power(u1, density=1000))
# Checkpointing
if((self.options["checkpoint_period"] is not None) and (dt*iterations_since_checkpoint >= self.options["checkpoint_period"])):
LOG.debug("Writing checkpoint data to file...")
self.solution.dat.save("checkpoint")
iterations_since_checkpoint = 0 # Reset the counter.
# Check whether a steady-state has been reached.
if(steady_state(u1, self.u0, self.options["steady_state_tolerance"]) and steady_state(h1, self.h0, self.options["steady_state_tolerance"])):
LOG.info("Steady-state attained. Exiting the time-stepping loop...")
break
self.compute_diagnostics()
LOG.info("Out of the time-stepping loop.")
LOG.debug("Total solver time: %.2f" % (total_solver_time))
return u1, h1
def post_init(model, xml_path):
model.start_time = get_optional('time_options/start_time', default=0.0)
if libspud.have_option('time_options/adaptive_timestep'):
option_path = 'time_options/adaptive_timestep/'
model.adapt_timestep = True
model.adapt_cfl = project(Constant(
libspud.get_option(option_path + 'cfl_criteria')),
model.R,
name='cfl')
else:
model.adapt_timestep = False
model.adapt_cfl = project(Constant(0.2), model.R, name='cfl')
# ts info options
if libspud.have_option('output_options/ts_info'):
model.ts_info = True
else:
model.ts_info = False
# plotting options
option_path = 'output_options/plotting/'
if libspud.have_option('output_options/plotting'):
model.plot = libspud.get_option(option_path + 'plotting_interval')
if libspud.have_option(option_path + 'output::both'):
model.show_plot = True
model.save_plot = True
elif libspud.have_option(option_path + 'output::live_plotting'):
model.show_plot = True
model.save_plot = False
elif libspud.have_option(option_path + 'output::save_plots'):
model.show_plot = False
model.save_plot = True
else:
raise Exception('unrecognised plotting output in options file')
option_path = option_path + 'dimensionalise_plots/'
else:
model.plot = None
# dimenionalisation
model.g = project(Constant(
get_optional(option_path + 'g_prime', default=1.0)),
model.R,
name='g_prime')
model.h_0 = project(Constant(get_optional(option_path + 'h_0',
default=1.0)),
model.R,
name='h_0')
model.phi_0 = project(Constant(
get_optional(option_path + 'phi_0', default=1.0)),
model.R,
name='phi_0')
# non dimensional numbers
option_path = 'non_dimensional_numbers/'
model.Fr = project(Constant(get_optional(option_path + 'Fr',
default=1.19)),
model.R,
name="Fr")
model.beta = project(Constant(
get_optional(option_path + 'beta', default=5e-3)),
model.R,
name="beta")
# initial conditions
model.form_ic = (
{
'id': 'momentum',
'function': Function(model.V, name='ic_q'),
'test_function': TestFunction(model.V)
},
{
'id': 'height',
'function': Function(model.V, name='ic_h'),
'test_function': TestFunction(model.V)
},
{
'id': 'volume_fraction',
'function': Function(model.V, name='ic_phi'),
'test_function': TestFunction(model.V)
},
{
'id': 'deposit_depth',
'function': Function(model.V, name='ic_phi_d'),
'test_function': TestFunction(model.V)
},
{
'id': 'initial_length',
'function': Function(model.R, name='ic_X_n'),
'test_function': TestFunction(model.R)
},
{
'id': 'front_velocity',
'function': Function(model.R, name='ic_u_N'),
'test_function': TestFunction(model.R)
},
{
'id': 'timestep',
'function': Function(model.R, name='ic_k'),
'test_function': TestFunction(model.R)
},
{
'id': 'phi_int',
'function': Function(model.R, name='ic_phi_int'),
'test_function': TestFunction(model.R)
},
)
option_path = 'initial_conditions/'
var_paths = 'momentum', 'height', 'volume_fraction', 'deposit_depth', \
'initial_length', 'front_velocity', 'timestep'
# form defines ic
for i, var_path in enumerate(var_paths):
path = option_path + var_path + '/form'
if libspud.have_option(path):
if libspud.have_option(path + '/additional_form_var'):
for j in range(
libspud.option_count(path +
'/additional_form_var/var')):
py_code = libspud.get_option(
path + '/additional_form_var/var[%d]' % j)
exec py_code
py_code = "model.form_ic[%d]['form'] = %s" % (
i, libspud.get_option(path))
exec py_code
# expression defined ic
model.w_ic_var = ''
if (libspud.have_option(option_path + 'variables')
and libspud.option_count(option_path + 'variables/var') > 0):
n_var = libspud.option_count(option_path + 'variables/var')
for i_var in range(n_var):
name = libspud.get_child_name(option_path + 'variables/', i_var)
var = name.split(':')[-1]
code = libspud.get_option('initial_conditions/variables/' + name +
'/code')
model.w_ic_var = model.w_ic_var + var + ' = ' + code + ', '
ic_exp = (read_ic(option_path + 'momentum', default='0.0'),
read_ic(option_path + 'height', default='1.0'),
read_ic(option_path + 'volume_fraction', default='1.0'),
read_ic(option_path + 'deposit_depth', default='0.0'),
read_ic(option_path + 'initial_length', default='1.0'),
read_ic(option_path + 'front_velocity', default='1.19'),
read_ic(option_path + 'timestep', default='1.0'), '0.0')
exp_str = ('model.w_ic_e = Expression(ic_exp, model.W.ufl_element(), %s)' %
model.w_ic_var)
exec exp_str in globals(), locals()
def __init__(self, tfml_file,system_name='magma',p_name='Pressure',f_name='Porosity',c_name='c',n_name='n',m_name='m',d_name='d',N_name='N',h_squared_name='h_squared',x0_name='x0'):
"""read the tfml_file and use libspud to populate the internal parameters
c: wavespeed
n: permeability exponent
m: bulk viscosity exponent
d: wave dimension
N: number of collocation points
x0: coordinate wave peak
h_squared: the size of the system in compaction lengths
squared (h/delta)**2
"""
# initialize libspud and extract parameters
libspud.clear_options()
libspud.load_options(tfml_file)
# get model dimension
self.dim = libspud.get_option("/geometry/dimension")
self.system_name = system_name
# get solitary wave parameters
path="/system::"+system_name+"/coefficient::"
scalar_value="/type::Constant/rank::Scalar/value::WholeMesh/constant"
vector_value="/type::Constant/rank::Vector/value::WholeMesh/constant::dim"
c = libspud.get_option(path+c_name+scalar_value)
n = int(libspud.get_option(path+n_name+scalar_value))
m = int(libspud.get_option(path+m_name+scalar_value))
d = float(libspud.get_option(path+d_name+scalar_value))
N = int(libspud.get_option(path+N_name+scalar_value))
self.h = np.sqrt(libspud.get_option(path+h_squared_name+scalar_value))
self.x0 = np.array(libspud.get_option(path+x0_name+vector_value))
self.swave = SolitaryWave(c,n,m,d,N)
self.rmax = self.swave.r[-1]
self.tfml_file = tfml_file
# check that d <= dim
assert (d <= self.dim)
# sort out appropriate index for calculating distance r
if d == 1:
self.index = [self.dim - 1]
else:
self.index = range(0,int(d))
# check that the origin point is the correct dimension
assert (len(self.x0) == self.dim)
#read in information for constructing Function space and dolfin objects
# get the mesh parameters and reconstruct the mesh
meshtype = libspud.get_option("/geometry/mesh/source[0]/name")
if meshtype == 'UnitSquare':
number_cells = libspud.get_option("/geometry/mesh[0]/source[0]/number_cells")
diagonal = libspud.get_option("/geometry/mesh[0]/source[0]/diagonal")
mesh = df.UnitSquareMesh(number_cells[0],number_cells[1],diagonal)
elif meshtype == 'Rectangle':
x0 = libspud.get_option("/geometry/mesh::Mesh/source::Rectangle/lower_left")
x1 = libspud.get_option("/geometry/mesh::Mesh/source::Rectangle/upper_right")
number_cells = libspud.get_option("/geometry/mesh::Mesh/source::Rectangle/number_cells")
diagonal = libspud.get_option("/geometry/mesh[0]/source[0]/diagonal")
mesh = df.RectangleMesh(x0[0],x0[1],x1[0],x1[1],number_cells[0],number_cells[1],diagonal)
elif meshtype == 'UnitCube':
number_cells = libspud.get_option("/geometry/mesh[0]/source[0]/number_cells")
mesh = df.UnitCubeMesh(number_cells[0],number_cells[1],number_cells[2])
elif meshtype == 'Box':
x0 = libspud.get_option("/geometry/mesh::Mesh/source::Box/lower_back_left")
x1 = libspud.get_option("/geometry/mesh::Mesh/source::Box/upper_front_right")
number_cells = libspud.get_option("/geometry/mesh::Mesh/source::Box/number_cells")
mesh = df.BoxMesh(x0[0],x0[1],x0[2],x1[0],x1[1],x1[2],number_cells[0],number_cells[1],number_cells[2])
elif meshtype == 'UnitInterval':
number_cells = libspud.get_option("/geometry/mesh::Mesh/source::UnitInterval/number_cells")
mesh = df.UnitIntervalMesh(number_cells)
elif meshtype == 'Interval':
number_cells = libspud.get_option("/geometry/mesh::Mesh/source::Interval/number_cells")
left = libspud.get_option("/geometry/mesh::Mesh/source::Interval/left")
right = libspud.get_option("/geometry/mesh::Mesh/source::Interval/right")
mesh = df.IntervalMesh(number_cells,left,right)
elif meshtype == 'File':
mesh_filename = libspud.get_option("/geometry/mesh::Mesh/source::File/file")
print "tfml_file = ",self.tfml_file, "mesh_filename=",mesh_filename
mesh = df.Mesh(mesh_filename)
else:
df.error("Error: unknown mesh type "+meshtype)
#set the functionspace for n-d solitary waves
path="/system::"+system_name+"/field::"
p_family = libspud.get_option(path+p_name+"/type/rank/element/family")
p_degree = libspud.get_option(path+p_name+"/type/rank/element/degree")
f_family = libspud.get_option(path+f_name+"/type/rank/element/family")
f_degree = libspud.get_option(path+f_name+"/type/rank/element/degree")
pe = df.FiniteElement(p_family, mesh.ufl_cell(), p_degree)
ve = df.FiniteElement(f_family, mesh.ufl_cell(), f_degree)
e = pe*ve
self.functionspace = df.FunctionSpace(mesh, e)
#work out the order of the fields
for i in xrange(libspud.option_count("/system::"+system_name+"/field")):
name = libspud.get_option("/system::"+system_name+"/field["+`i`+"]/name")
if name == f_name:
self.f_index = i
if name == p_name:
self.p_index = i
def fill(self, optionpath, system, index):
"""Fill a function class with data describing that function using libspud, the given optionpath and the system its based on."""
self.name = libspud.get_option(optionpath+"/name")
self.symbol = libspud.get_option(optionpath+"/ufl_symbol").split("\n")[0]
self.system = system
self.index = index
self.type = libspud.get_option(optionpath+"/type/name")
self.rank = libspud.get_option(optionpath+"/type/rank/name")
self.family = None
self.degree = None
self.functional = None
if self.type != "Constant":
self.family = libspud.get_option(optionpath+"/type/rank/element/family")
self.degree = libspud.get_option(optionpath+"/type/rank/element/degree")
self.size = None
self.shape = None
self.symmetry = None
if self.rank == "Vector":
if libspud.have_option(optionpath+"/type/rank/element/size"):
self.size = libspud.get_option(optionpath+"/type/rank/element/size")
elif self.rank == "Tensor":
if libspud.have_option(optionpath+"/type/rank/element/shape"):
self.shape = libspud.get_option(optionpath+"/type/rank/element/shape")
if libspud.have_option(optionpath+"/type/rank/element/symmetric"):
self.symmetry = True
self.enrichment_family = None
self.enrichment_degree = None
if libspud.have_option(optionpath+"/type/rank/element/enrichment"):
self.enrichment_family = libspud.get_option(optionpath+"/type/rank/element/enrichment/element/family")
self.enrichment_degree = libspud.get_option(optionpath+"/type/rank/element/enrichment/element/degree")
# this should be restricted by the schema to Constant coefficients:
if libspud.have_option(optionpath+"/type/rank/value/functional"):
functional_optionpath = optionpath+"/type/rank/value/functional"
functional = buckettools.spud.SpudFunctionalBucket()
functional.fill(functional_optionpath, self.system, self)
self.functional = functional
self.cpp = []
for k in range(libspud.option_count(optionpath+"/type/rank/initial_condition")):
cpp_optionpath = optionpath+"/type/rank/initial_condition["+`k`+"]"
if libspud.have_option(cpp_optionpath+"/cpp"):
cpp_name = libspud.get_option(cpp_optionpath+"/name")
cppexpression = buckettools.spud.SpudCppExpressionBucket()
# get all the information about this expression from the options dictionary
cppexpression.fill(cpp_optionpath, cpp_name, self)
# let the field know about this cpp expression
self.cpp.append(cppexpression)
# done with this expression
del cppexpression
for j in range(libspud.option_count(optionpath+"/type/rank/boundary_condition")):
bc_optionpath = optionpath+"/type/rank/boundary_condition["+`j`+"]"
bc_name = libspud.get_option(bc_optionpath+"/name")
for k in range(libspud.option_count(bc_optionpath+"/sub_components")):
bc_comp_optionpath = bc_optionpath+"/sub_components["+`k`+"]"
bc_comp_name = libspud.get_option(bc_comp_optionpath+"/name")
cpp_optionpath = bc_comp_optionpath+"/type"
if libspud.have_option(cpp_optionpath+"/cpp"):
cpp_name = bc_name + bc_comp_name
cppexpression = buckettools.spud.SpudCppExpressionBucket()
# get all the information about this expression from the options dictionary
cppexpression.fill(cpp_optionpath, cpp_name, self)
# let the field know about this cpp expression
self.cpp.append(cppexpression)
# done with this expression
del cppexpression
for k in range(libspud.option_count(optionpath+"/type/rank/value")):
cpp_optionpath = optionpath+"/type/rank/value["+`k`+"]"
if libspud.have_option(cpp_optionpath+"/cpp"):
cpp_name = libspud.get_option(cpp_optionpath+"/name")
cppexpression = buckettools.spud.SpudCppExpressionBucket()
# get all the information about this expression from the options dictionary
cppexpression.fill(cpp_optionpath, cpp_name, self)
# let the field know about this cpp expression
self.cpp.append(cppexpression)
# done with this expression
del cppexpression
def get_opal_options():
"Initialises the structure for the options."
opal_options = Opal_input()
nirom_options = Nirom_input()
fwd_options = Forward_model_options()
#Read the input data from the user
opal_input_file = str(sys.argv[1])
#Load the .opal file
libspud.load_options(opal_input_file)
##Create Opal Variable
# opal_options = Opal_input()
##Start reading options
print "reading opal input file", opal_input_file
if libspud.have_option('/avoid_perturbing_near_wells'):
opal_options.avoid_perturbing_near_wells = True
if (libspud.have_option('/opal_operation/importance_map')):
opal_options.opal_operation = 'importance_map'
im_path = '/opal_operation/importance_map/'
opal_options = read_in_importance_map_options(im_path, opal_options)
elif (libspud.have_option('/opal_operation/data_assimilation')):
opal_options.opal_operation = 'da'
opal_options.data_assimilation.fwd_input_file = libspud.get_option(
'/opal_operation/data_assimilation/fwd_input_file')
#print "opal_options.data_assimilation.fwd_input_file", opal_options.data_assimilation.fwd_input_file
elif (libspud.have_option('/opal_operation/nirom')):
opal_options.opal_operation = 'nirom'
nirom_path = 'opal_operation/nirom/'
opal_options, nirom_options, fwd_options = read_in_nirom_options(
nirom_path, opal_options, nirom_options, fwd_options)
elif (libspud.have_option('/opal_operation/second_order_da')):
opal_options.opal_operation = 'second_order_da'
da_path = '/opal_operation/second_order_da/'
opal_options = read_in_soda_options(da_path, opal_options)
elif (libspud.have_option('/opal_operation/ga_optimisation')):
opal_options.opal_operation = 'ga_optimisation'
path = '/opal_operation/ga_optimisation'
# previously these three options were at the top level
opal_options.output_filename = libspud.get_option(path +
'/Output_filename')
opal_options.executable = libspud.get_option(path + '/Executable')
opal_options.input_file = libspud.get_option(path + '/Input_file')
opal_options.ga_max_generations = libspud.get_option(
path + '/convergence_settings/Maximum_generations')
opal_options.ga_locations_to_study = libspud.get_option(
path + '/Locations_to_study/value')
if libspud.have_option(path + '/Locations_to_study/Initial_guess'):
opal_options.ga_initial_guess = libspud.get_option(
path + '/Locations_to_study/Initial_guess')
if libspud.have_option(path + '/Locations_to_study/Mind_the_gap'):
opal_options.mind_the_gap = libspud.get_option(
path + '/Locations_to_study/Mind_the_gap')
if libspud.have_option(path + '/Trelis_integration'):
opal_options.trelis_path = libspud.get_option(
path + '/Trelis_integration/trelis_path')
opal_options.trelis_input_file = libspud.get_option(
path + '/Trelis_integration/trelis_input_file')
opal_options.optimise_input = libspud.have_option(path +
'/optimise_input')
if libspud.have_option(path +
'/convergence_settings/Gradient_convergence'):
opal_options.ga_gradient_convergence = libspud.get_option(
path + '/convergence_settings/Gradient_convergence')
if libspud.have_option(path +
'/convergence_settings/Absolute_convergence'):
opal_options.ga_absolute_convergence = libspud.get_option(
path + '/convergence_settings/Absolute_convergence')
if libspud.have_option(path + '/Number_processors'):
opal_options.number_processors = libspud.get_option(
path + '/Number_processors')
if libspud.have_option(path + '/Number_processors/MPI_runs'):
opal_options.MPI_runs = libspud.get_option(
path + '/Number_processors/MPI_runs')
opal_options.number_processors /= opal_options.MPI_runs
opal_options.ga_population_generation = libspud.get_option(
path + '/Population_generation')
opal_options.ga_breeding_prob = libspud.get_option(
path + '/Breeding_probability/value')
if libspud.have_option(path +
'/Breeding_probability/Generation_method'):
opal_options.generation_method = libspud.get_option(
path + '/Breeding_probability/Generation_method')
opal_options.ga_mutation_prob = libspud.get_option(
path + '/Mutation_probability/value')
if libspud.have_option(path + '/Mutation_probability/Mutation_method'):
opal_options.mutation_method = libspud.get_option(
path + '/Mutation_probability/Mutation_method')
opal_options.precision = libspud.get_option(path + '/Precision')
if libspud.have_option(path + '/Fitness/python_function'):
opal_options.ga_fitness_functional = libspud.get_option(
path + '/Fitness/python_function')
opal_options.ga_Minimise = libspud.have_option(
path + '/Fitness/Optimisation/Minimise')
opal_options.producer_ids = libspud.get_option(path +
'/Fitness/producer_ids')
opal_options.injector_ids = libspud.get_option(path +
'/Fitness/injector_ids')
if libspud.have_option(path +
'/GA_methods/Evolutionary_algorithm/eaSimple'):
opal_options.ga_evol_algorithm = 1
elif libspud.have_option(
path + '/GA_methods/Evolutionary_algorithm/eaMuCommaLambda'):
opal_options.ga_evol_algorithm = 2
opal_options.ga_mu = libspud.get_option(
path + '/GA_methods/Evolutionary_algorithm/eaMuCommaLambda/Mu')
opal_options.ga_lambda = libspud.get_option(
path +
'/GA_methods/Evolutionary_algorithm/eaMuCommaLambda/Lambda')
elif libspud.have_option(
path + '/GA_methods/Evolutionary_algorithm/eaMuPlusLambda'):
opal_options.ga_evol_algorithm = 3
opal_options.ga_mu = libspud.get_option(
path + '/GA_methods/Evolutionary_algorithm/eaMuPlusLambda/Mu')
opal_options.ga_lambda = libspud.get_option(
path +
'/GA_methods/Evolutionary_algorithm/eaMuPlusLambda/Lambda')
if libspud.have_option(path + '/GA_methods/Selection_method/selBest'):
opal_options.ga_selection_method = 1
elif libspud.have_option(path +
'/GA_methods/Selection_method/selNSGA2'):
opal_options.ga_selection_method = 2
elif libspud.have_option(path +
'/GA_methods/Selection_method/selSPEA2'):
opal_options.ga_selection_method = 3
opal_options.ga_CMA = False
if libspud.have_option(path + '/GA_methods/Use_CMA'):
opal_options.ga_CMA = True
opal_options.ga_centroid = libspud.get_option(
path + '/GA_methods/Use_CMA/centroid')
opal_options.ga_sigma = libspud.get_option(
path + '/GA_methods/Use_CMA/sigma')
if libspud.have_option(path + 'Hall_of_fame'):
opal_options.ga_hall_of_fame = libspud.get_option(path +
'Hall_of_fame')
nfields = libspud.option_count(path + '/Variables')
for i in range(nfields):
temp_field = ga_variable()
fieldpath = path + '/Variables[' + str(i) + ']'
temp_field.name = libspud.get_option(fieldpath + '/name')
temp_field.min_limit = libspud.get_option(fieldpath + '/Min_limit')
temp_field.max_limit = libspud.get_option(fieldpath + '/Max_limit')
temp_field.variable_pattern = libspud.get_option(
fieldpath + '/Variable_pattern')
temp_field.normaliser = 1.0
if libspud.have_option(fieldpath + '/normaliser'):
temp_field.normaliser = libspud.get_option(fieldpath +
'/normaliser')
##Now append to the variables list
opal_options.ga_variables.append(temp_field)
libspud.clear_options()
return opal_options, fwd_options, nirom_options
def convert(fluidity_options_file_path, ff_options_file_path):
# Read in Fluidity simulation options
libspud.clear_options()
libspud.load_options(fluidity_options_file_path)
# Simulation name
simulation_name = libspud.get_option("/simulation_name")
# Geometry
base = "/geometry"
dimension = libspud.get_option(base + "/dimension")
mesh_path = libspud.get_option(
base + "/mesh::CoordinateMesh/from_file/file_name"
) + ".msh" # FIXME: Always assumes gmsh format.
# Function spaces
velocity_function_space = FunctionSpace("/geometry", 1)
freesurface_function_space = FunctionSpace("/geometry", 2)
# Timestepping
base = "/timestepping"
current_time = libspud.get_option(base + "/current_time")
timestep = libspud.get_option(base + "/timestep")
finish_time = libspud.get_option(base + "/finish_time")
## Steady-state
if (libspud.have_option(base + "/steady_state")):
if (libspud.have_option(base + "/steady_state/tolerance")):
steady_state = libspud.get_option(base + "/steady_state/tolerance")
else:
steady_state = 1e-7
else:
steady_state = None
# I/O
base = "/io"
dump_format = libspud.get_option(base + "/dump_format")
if (libspud.have_option(base + "/dump_period")):
dump_period = libspud.get_option(base + "/dump_period/constant")
elif (libspud.have_option(base + "/dump_period_in_timesteps")):
dump_period = libspud.get_option(
base + "/dump_period_in_timesteps/constant") * timestep
else:
print "Unable to obtain dump_period."
sys.exit()
# Gravity
g_magnitude = libspud.get_option("/physical_parameters/gravity/magnitude")
# Velocity field (momentum equation)
base = "/material_phase[0]/vector_field::Velocity"
## Depth (free surface mean height)
c = libspud.get_child_name(
base +
"/prognostic/equation::ShallowWater/scalar_field::BottomDepth/prescribed/value::WholeMesh/",
1)
depth = libspud.get_option(
base +
"/prognostic/equation::ShallowWater/scalar_field::BottomDepth/prescribed/value::WholeMesh/%s"
% c)
## Bottom drag coefficient
if (libspud.have_option(base +
"/prognostic/equation::ShallowWater/bottom_drag")):
c = libspud.get_child_name(
base +
"/prognostic/equation::ShallowWater/bottom_drag/scalar_field::BottomDragCoefficient/prescribed/value::WholeMesh/",
1)
bottom_drag = libspud.get_option(
base +
"/prognostic/equation::ShallowWater/bottom_drag/scalar_field::BottomDragCoefficient/prescribed/value::WholeMesh/%s"
% c)
else:
bottom_drag = None
## Viscosity
if (libspud.have_option(base + "/prognostic/tensor_field::Viscosity")):
viscosity = libspud.get_option(
base +
"/prognostic/tensor_field::Viscosity/prescribed/value::WholeMesh/anisotropic_symmetric/constant"
)[0][0]
else:
viscosity = None
## Momentum source
if (libspud.have_option(base + "/prognostic/vector_field::Source")):
c = libspud.get_child_name(
base +
"/prognostic/vector_field::Source/prescribed/value::WholeMesh/", 1)
momentum_source = libspud.get_option(
base +
"/prognostic/vector_field::Source/prescribed/value::WholeMesh/%s" %
c)
else:
momentum_source = None
## Initial condition
if (libspud.have_option(base +
"/prognostic/initial_condition::WholeMesh")):
c = libspud.get_child_name(
base + "/prognostic/initial_condition::WholeMesh/", 1)
velocity_initial_condition = libspud.get_option(
base + "/prognostic/initial_condition::WholeMesh/%s" % c)
else:
velocity_initial_condition = 0.0
## Boundary conditions
number_of_bcs = libspud.option_count(base +
"/prognostic/boundary_conditions")
velocity_bcs = []
for i in range(number_of_bcs):
velocity_bcs.append(
VelocityBoundaryCondition(base +
"/prognostic/boundary_conditions[%d]" %
i))
# Pressure field (continuity equation)
base = "/material_phase[0]/scalar_field::Pressure"
integrate_by_parts = libspud.have_option(
base +
"/prognostic/spatial_discretisation/continuous_galerkin/integrate_continuity_by_parts"
)
## Initial condition
if (libspud.have_option(base +
"/prognostic/initial_condition::WholeMesh")):
c = libspud.get_child_name(
base + "/prognostic/initial_condition::WholeMesh/", 1)
pressure_initial_condition = libspud.get_option(
base + "/prognostic/initial_condition::WholeMesh/%s" % c)
else:
pressure_initial_condition = 0.0
## Boundary conditions
number_of_bcs = libspud.option_count(base +
"/prognostic/boundary_conditions")
pressure_bcs = []
for i in range(number_of_bcs):
pressure_bcs.append(
PressureBoundaryCondition(base +
"/prognostic/boundary_conditions[%d]" %
i))
## Continuity source
if (libspud.have_option(base + "/prognostic/scalar_field::Source")):
c = libspud.get_child_name(
base +
"/prognostic/scalar_field::Source/prescribed/value::WholeMesh/", 1)
continuity_source = libspud.get_option(
base +
"/prognostic/scalar_field::Source/prescribed/value::WholeMesh/%s" %
c)
else:
continuity_source = None
# Write out to a Firedrake-Fluids simulation configuration file
libspud.clear_options()
# Create a bare-bones .swml file to add to.
f = open(ff_options_file_path, "w")
f.write("<?xml version='1.0' encoding='utf-8'?>\n")
f.write("<shallow_water_options>\n")
f.write("</shallow_water_options>\n")
f.close()
libspud.load_options(ff_options_file_path)
# Simulation name
libspud.set_option("/simulation_name", simulation_name)
# Geometry
base = "/geometry"
libspud.set_option(base + "/dimension", dimension)
libspud.set_option(base + "/mesh/from_file/relative_path", mesh_path)
# Function spaces
base = "/function_spaces"
libspud.set_option(base + "/function_space::VelocityFunctionSpace/degree",
velocity_function_space.degree)
libspud.set_option(base + "/function_space::VelocityFunctionSpace/family",
velocity_function_space.family)
libspud.set_option(
base + "/function_space::FreeSurfaceFunctionSpace/degree",
freesurface_function_space.degree)
libspud.set_option(
base + "/function_space::FreeSurfaceFunctionSpace/family",
freesurface_function_space.family)
# I/O
base = "/io"
libspud.set_option(base + "/dump_format", dump_format)
libspud.set_option(base + "/dump_period", dump_period)
# Timestepping
base = "/timestepping"
print timestep
libspud.set_option(base + "/current_time", current_time)
try:
libspud.set_option(base + "/timestep", timestep)
except:
pass
libspud.set_option(base + "/finish_time", finish_time)
## Steady-state
if (steady_state):
libspud.set_option(base + "/steady_state/tolerance", steady_state)
# Gravity
libspud.set_option("/physical_parameters/gravity/magnitude", g_magnitude)
# System/Core Fields: Velocity
base = "/system/core_fields/vector_field::Velocity"
## Initial condition
if (isinstance(velocity_initial_condition, str)):
libspud.set_option(base + "/initial_condition/python",
velocity_initial_condition)
else:
libspud.set_option(base + "/initial_condition/constant",
velocity_initial_condition)
## Boundary conditions
try:
for i in range(len(velocity_bcs)):
libspud.set_option(
base +
"/boundary_condition::%s/surface_ids" % velocity_bcs[i].name,
velocity_bcs[i].surface_ids)
libspud.set_option_attribute(
base +
"/boundary_condition::%s/type/name" % velocity_bcs[i].name,
velocity_bcs[i].type)
if (velocity_bcs[i].type == "dirichlet"):
if (isinstance(velocity_bcs[i].value, str)):
libspud.set_option(
base +
"/boundary_condition::%s/type::dirichlet/value/python"
% velocity_bcs[i].name, velocity_bcs[i].value)
else:
libspud.set_option(
base +
"/boundary_condition::%s/type::dirichlet/value/constant"
% velocity_bcs[i].name, velocity_bcs[i].value)
except:
pass
# System/Core Fields: FreeSurfacePerturbation
base = "/system/core_fields/scalar_field::FreeSurfacePerturbation"
#FIXME: Pressure initial and boundary conditions are multiplied by 'g' in Fluidity, but not in Firedrake-Fluids.
## Initial condition
if (isinstance(pressure_initial_condition, str)):
libspud.set_option(base + "/initial_condition/python",
pressure_initial_condition)
else:
libspud.set_option(base + "/initial_condition/constant",
pressure_initial_condition)
## Boundary conditions
try:
for i in range(len(pressure_bcs)):
libspud.set_option(
base +
"/boundary_condition::%s/surface_ids" % pressure_bcs[i].name,
pressure_bcs[i].surface_ids)
libspud.set_option(
base +
"/boundary_condition::%s/type/name" % pressure_bcs[i].name,
pressure_bcs[i].type)
if (pressure_bcs[i].type == "dirichlet"):
if (isinstance(pressure_bcs[i].value, str)):
libspud.set_option(
base +
"/boundary_condition::%s/type::dirichlet/value/python"
% pressure_bcs[i].name, pressure_bcs[i].value)
else:
libspud.set_option(
base +
"/boundary_condition::%s/type::dirichlet/value/constant"
% pressure_bcs[i].name, pressure_bcs[i].value)
except:
pass
# System/Core Fields: FreeSurfaceMean
base = "/system/core_fields/scalar_field::FreeSurfaceMean"
if (isinstance(depth, str)):
libspud.set_option(base + "/value/python", depth)
else:
libspud.set_option(base + "/value/constant", depth)
# Equations: Continuity equation
base = "/system/equations/continuity_equation"
libspud.set_option(base + "/integrate_by_parts", integrate_by_parts)
## Source term
if (continuity_source is not None):
if (isinstance(continuity_source, str)):
libspud.set_option(
base + "/source_term/scalar_field::Source/value/python",
continuity_source)
else:
libspud.set_option(
base + "/source_term/scalar_field::Source/value/constant",
continuity_source)
# Equations: Momentum equation
base = "/system/equations/momentum_equation"
## Viscosity
if (viscosity is not None):
if (isinstance(viscosity, str)):
libspud.set_option(
base + "/stress_term/scalar_field::Viscosity/value/python",
viscosity)
else:
libspud.set_option(
base + "/stress_term/scalar_field::Viscosity/value/constant",
viscosity)
## Bottom drag
if (bottom_drag is not None):
if (isinstance(bottom_drag, str)):
libspud.set_option(
base +
"/drag_term/scalar_field::BottomDragCoefficient/value/python",
bottom_drag)
else:
libspud.set_option(
base +
"/drag_term/scalar_field::BottomDragCoefficient/value/constant",
bottom_drag)
## Source term
if (momentum_source is not None):
if (isinstance(momentum_source, str)):
libspud.set_option(
base + "/source_term/vector_field::Source/value/python",
momentum_source)
else:
libspud.set_option(
base + "/source_term/vector_field::Source/value/constant",
momentum_source)
# Write all the applied options to file.
libspud.write_options(ff_options_file_path)
return
#To load the vtu files and read the coordinates of the nodes
#vtu_data = vtktools.vtu("Input_Importance_map_1.vtu") ###Hardcoded
#coordinates = vtu_data.GetLocations()
#To get the mpml file
path = os.getcwd()
mpmlfile = get_mpml_filename(path)
libspud.load_options(mpmlfile + '.mpml')
meshname_base = libspud.get_option('/geometry[0]/mesh[0]/from_file/file_name')
NDIM = libspud.get_option('/geometry/dimension')
Dt_n = libspud.get_option('/timestepping/timestep') #timestep
tlevel_begin = libspud.get_option('/timestepping/current_time') #start time
tlevel_end = libspud.get_option('/timestepping/finish_time') #end time
NSCALAR = libspud.option_count('/Field_to_study')
DELTA_T = libspud.get_option(
'/io/dump_period_in_timesteps/constant'
) ###change to point to checkpint file in unperturbed
libspud.clear_options()
DT = tlevel_end - tlevel_begin #total simulation period
NTIME = int(DT / Dt_n) + 1 # number of timelevels
def get_coordinates(vtu_filename):
vtu_data = vtktools.vtu(vtu_filename)
coordinates = vtu_data.GetLocations()
return vtu_data, coordinates
import libspud
print libspud.__file__
libspud.load_options('test.flml')
libspud.print_options()
print libspud.number_of_children('/geometry')
print libspud.get_child_name('geometry', 0)
print libspud.option_count('/problem_type')
print libspud.have_option('/problem_type')
print libspud.get_option_type('/geometry/dimension')
print libspud.get_option_type('/problem_type')
print libspud.get_option_rank('/geometry/dimension')
print libspud.get_option_rank(
'/physical_parameters/gravity/vector_field::GravityDirection/prescribed/value/constant'
)
print libspud.get_option_shape('/geometry/dimension')
print libspud.get_option_shape('/problem_type')
print libspud.get_option('/problem_type')
print libspud.get_option('/geometry/dimension')
libspud.set_option('/geometry/dimension', 3)
print libspud.get_option('/geometry/dimension')
list_path = '/material_phase::Material1/scalar_field::MaterialVolumeFraction/prognostic/boundary_conditions::LetNoOneLeave/surface_ids'
print libspud.get_option_shape(list_path)
import libspud
libspud.load_options('test.flml')
#libspud.print_options()
assert libspud.get_option('/timestepping/timestep') == 0.025
assert libspud.get_number_of_children('/geometry') == 5
assert libspud.get_child_name('geometry', 0) == "dimension"
assert libspud.option_count('/problem_type') == 1
assert libspud.have_option('/problem_type')
assert libspud.get_option_type('/geometry/dimension') is int
assert libspud.get_option_type('/problem_type') is str
assert libspud.get_option_rank('/geometry/dimension') == 0
assert libspud.get_option_rank('/physical_parameters/gravity/vector_field::GravityDirection/prescribed/value/constant') == 1
assert libspud.get_option_shape('/geometry/dimension') == (-1, -1)
assert libspud.get_option_shape('/problem_type')[0] > 1
assert libspud.get_option_shape('/problem_type')[1] == -1
assert libspud.get_option('/problem_type') == "multimaterial"
assert libspud.get_option('/geometry/dimension') == 2
libspud.set_option('/geometry/dimension', 3)
assert libspud.get_option('/geometry/dimension') == 3