def get_solver_parameters(self):
""" Get the parameters for the SNES and linear solvers. """
LOG.debug("Defining solver_parameters dictionary...")
# NOTE: use 'snes_type': 'newtonls' for production runs.
solver_parameters = {'ksp_monitor': True, 'ksp_view': False, 'pc_view': False, 'snes_type': 'ksponly', 'snes_rtol': 1e-7, 'ksp_max_it': 10000}
# 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'
return solver_parameters
def __init__(self, base_option_path, mesh):
""" Create an array of turbines.
:param str base_option_path: The top-most level of the turbine options in the simulation's configuration/options file.
:param mesh: The Mesh object.
:returns: None
"""
fs = FunctionSpace(mesh, "CG", 1)
turbine_type = libspud.get_option(base_option_path + "/array/turbine_type/name")
turbine_coords = eval(libspud.get_option(base_option_path + "/array/turbine_coordinates"))
turbine_radius = eval(libspud.get_option(base_option_path + "/array/turbine_radius"))
K = libspud.get_option(base_option_path + "/array/scalar_field::TurbineDragCoefficient/value/constant")
self.drag = Function(fs).interpolate(Expression("0"))
for coords in turbine_coords:
# For each coordinate tuple in the list, create a new turbine.
# FIXME: This assumes that all turbines are of the same type.
try:
if(turbine_type == "bump"):
turbine = BumpTurbine(K=K, coords=coords, r=turbine_radius)
elif(turbine_type == "tophat"):
turbine = TopHatTurbine(K=K, coords=coords, r=turbine_radius)
else:
raise ValueError("Unknown turbine type '%s'." % turbine_type)
except ValueError as e:
LOG.exception(e)
sys.exit()
self.drag += Function(fs).interpolate(turbine)
LOG.info("Added %s turbine at %s..." % (turbine_type, coords))
self.optimise = libspud.have_option(base_option_path + "/optimise")
return
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 populate_options(self):
""" Add simulation options related to the shallow water model to a dictionary object.
:returns: None
"""
# A dictionary storing all the options
self.options = {}
LOG.info("Populating options dictionary...")
self.options["simulation_name"] = libspud.get_option("/simulation_name")
self.options["dimension"] = libspud.get_option("/geometry/dimension")
# Time-stepping parameters
self.options["T"] = libspud.get_option("/timestepping/finish_time")
self.options["t"] = libspud.get_option("/timestepping/current_time")
self.options["dt"] = libspud.get_option("/timestepping/timestep")
self.options["theta"] = libspud.get_option("/timestepping/theta")
if(libspud.have_option("/timestepping/steady_state")):
self.options["steady_state_tolerance"] = libspud.get_option("/timestepping/steady_state/tolerance")
else:
self.options["steady_state_tolerance"] = -1000
# I/O parameters
if(libspud.have_option("/io/dump_period")):
self.options["dump_period"] = libspud.get_option("/io/dump_period")
else:
self.options["dump_period"] = None
if(libspud.have_option("/io/checkpoint")):
self.options["checkpoint_period"] = libspud.get_option("/io/checkpoint/dump_period")
else:
self.options["checkpoint_period"] = None
# Physical parameters
self.options["g_magnitude"] = libspud.get_option("/physical_parameters/gravity/magnitude")
# Enable/disable terms in the shallow water equations
self.options["have_momentum_mass"] = (not libspud.have_option("/system/equations/momentum_equation/mass_term/exclude_mass_term"))
self.options["have_momentum_advection"] = (not libspud.have_option("/system/equations/momentum_equation/advection_term/exclude_advection_term"))
self.options["have_momentum_stress"] = libspud.have_option("/system/equations/momentum_equation/stress_term")
# Source terms for the momentum and continuity equations
self.options["have_momentum_source"] = libspud.have_option("/system/equations/momentum_equation/source_term")
self.options["have_continuity_source"] = libspud.have_option("/system/equations/continuity_equation/source_term")
# Check for any SU stabilisation
self.options["have_su_stabilisation"] = libspud.have_option("/system/equations/momentum_equation/spatial_discretisation/continuous_galerkin/stabilisation/streamline_upwind")
# Turbulence parameterisation
self.options["have_turbulence_parameterisation"] = libspud.have_option("/system/equations/momentum_equation/turbulence_parameterisation")
# Drag parameterisation
self.options["have_drag"] = libspud.have_option("/system/equations/momentum_equation/drag_term")
# Integration by parts
self.options["integrate_continuity_equation_by_parts"] = libspud.have_option("/system/equations/continuity_equation/integrate_by_parts")
self.options["integrate_advection_term_by_parts"] = libspud.have_option("/system/equations/momentum_equation/advection_term/integrate_by_parts")
return
def __init__(self, path, t=None):
""" Retrieve the expression's value from the options file.
:param str path: The path to the expression's definition in the options file.
:param float t: The current time. """
try:
if(libspud.have_option(path + "/constant")):
self.val = libspud.get_option(path + "/constant")
self.type = "constant"
elif(libspud.have_option(path + "/python")):
v = libspud.get_option(path + "/python")
self.type = "python"
exec v # Make the 'val' function that the user has defined available for calling.
self.val = val
self.t = t
elif(libspud.have_option(path + "/cpp")):
# For C++ expressions.
self.type = "cpp"
v = libspud.get_option(path + "/cpp")
exec v
self.val = val
self.t = t
else:
raise ValueError("Unknown expression type.")
except ValueError as e:
LOG.exception(e)
sys.exit()
return
def get_expression(self):
""" Create a UFL Expression object, whose value is obtained from self.val.
Note that for time-dependent Expressions, the variable 't' will need to be updated manually.
:returns: A UFL Expression object.
:rtype: ufl.Expression
"""
try:
if(self.type == "constant"):
return Expression(self.val)
elif(self.type == "cpp"):
return Expression(code=self.val(), t=self.t)
elif(self.type == "python"):
val = self.val
t = self.t
# Determine the value shape by plugging in some dummy coordinate and time.
s = val(x = [0,0,0], t=t)
class PythonExpression(Expression):
def eval(self, value, x, t=None):
value[:] = val(x, t)
if(not isinstance(s, float) and not isinstance(s, int)):
def value_shape(self):
return (len(s),)
e = PythonExpression(t=t)
return e
else:
raise ValueError("Unknown expression type: %s." % self.type)
except ValueError as e:
LOG.exception(e)
sys.exit()
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 get_mesh(self, path):
""" Create or load a mesh, given a configuration specified in the simulation configuration file.
:param str path: The path to the mesh file.
:returns: A Mesh object.
"""
LOG.info("Creating/loading mesh...")
dimension = self.options["dimension"]
try:
# Unit mesh whose vertex coordinates lie in the range [0, 1] along all axes.
if (libspud.have_option("/geometry/mesh/unit_mesh")):
number_of_nodes = libspud.get_option(
"/geometry/mesh/unit_mesh/number_of_nodes")
if (dimension == 1):
mesh = UnitIntervalMesh(number_of_nodes[0])
elif (dimension == 2):
mesh = UnitSquareMesh(number_of_nodes[0],
number_of_nodes[1])
elif (dimension == 3):
mesh = UnitCubeMesh(number_of_nodes[0], number_of_nodes[1],
number_of_nodes[2])
else:
raise ValueError("Unsupported dimension.")
# Interval mesh whose vertex coordinates lie in the range [0, L].
elif (libspud.have_option("/geometry/mesh/interval_mesh")):
L = libspud.get_option("/geometry/mesh/interval_mesh/length")
n = libspud.get_option(
"/geometry/mesh/interval_mesh/number_of_cells")
mesh = IntervalMesh(n, L)
# A user-defined mesh file (currently only supports Gmsh format).
elif (libspud.have_option("/geometry/mesh/from_file")):
absolute_path_to_config = os.path.dirname(
os.path.abspath(path))
# This is the path relative to the directory where the configuration file is stored.
relative_path_to_mesh = libspud.get_option(
"/geometry/mesh/from_file/relative_path")
absolute_path_to_mesh = os.path.join(absolute_path_to_config,
relative_path_to_mesh)
if (not os.path.exists(absolute_path_to_mesh)):
raise ValueError(
"The path to the mesh file '%s' does not exist." %
absolute_path_to_mesh)
else:
mesh = Mesh(absolute_path_to_mesh)
# Unknown mesh format.
else:
raise ValueError("Unsupported input mesh type.")
except ValueError as e:
LOG.exception(e)
sys.exit()
return mesh
def write_turbine_drag(self, options):
""" Write the turbine drag field to a file for visualisation.
:param dict options: The options dictionary created when the simulation was being set up.
:returns: None
"""
LOG.debug("Integral of the turbine drag field: %.2f" % (assemble(self.turbine_drag*dx)))
LOG.debug("Writing turbine drag field to file...")
f = File("%s_%s.pvd" % (options["simulation_name"], "TurbineDrag"))
f << self.turbine_drag
return
def create_output_streams(self):
# Set up the functions used to write fields to file.
self.output_functions = {}
self.output_functions["Velocity"] = Function(self.W.sub(0), name="VelocityOutput", annotate=False)
self.output_functions["FreeSurfacePerturbation"] = Function(self.W.sub(1), name="FreeSurfacePerturbationOutput", annotate=False)
# Set up the output stream
LOG.info("Initialising output file streams...")
self.output_files = {}
for field in self.output_functions.keys():
self.output_files[field] = File("%s_%s.pvd" % (self.options["simulation_name"], field))
return
def write_turbine_drag(self, options):
""" Write the turbine drag field to a file for visualisation.
:param dict options: The options dictionary created when the simulation was being set up.
:returns: None
"""
LOG.debug("Integral of the turbine drag field: %.2f" %
(assemble(self.turbine_drag * dx)))
LOG.debug("Writing turbine drag field to file...")
f = File("%s_%s.pvd" % (options["simulation_name"], "TurbineDrag"))
f << self.turbine_drag
return
def get_mesh(self, path):
""" Create or load a mesh, given a configuration specified in the simulation configuration file.
:param str path: The path to the mesh file.
:returns: A Mesh object.
"""
LOG.info("Creating/loading mesh...")
dimension = self.options["dimension"]
try:
# Unit mesh whose vertex coordinates lie in the range [0, 1] along all axes.
if(libspud.have_option("/geometry/mesh/unit_mesh")):
number_of_nodes = libspud.get_option("/geometry/mesh/unit_mesh/number_of_nodes")
if(dimension == 1):
mesh = UnitIntervalMesh(number_of_nodes[0])
elif(dimension == 2):
mesh = UnitSquareMesh(number_of_nodes[0], number_of_nodes[1])
elif(dimension == 3):
mesh = UnitCubeMesh(number_of_nodes[0], number_of_nodes[1], number_of_nodes[2])
else:
raise ValueError("Unsupported dimension.")
# Interval mesh whose vertex coordinates lie in the range [0, L].
elif(libspud.have_option("/geometry/mesh/interval_mesh")):
L = libspud.get_option("/geometry/mesh/interval_mesh/length")
n = libspud.get_option("/geometry/mesh/interval_mesh/number_of_cells")
mesh = IntervalMesh(n, L)
# A user-defined mesh file (currently only supports Gmsh format).
elif(libspud.have_option("/geometry/mesh/from_file")):
absolute_path_to_config = os.path.dirname(os.path.abspath(path))
# This is the path relative to the directory where the configuration file is stored.
relative_path_to_mesh = libspud.get_option("/geometry/mesh/from_file/relative_path")
absolute_path_to_mesh = os.path.join(absolute_path_to_config, relative_path_to_mesh)
if(not os.path.exists(absolute_path_to_mesh)):
raise ValueError("The path to the mesh file '%s' does not exist." % absolute_path_to_mesh)
else:
mesh = Mesh(absolute_path_to_mesh)
# Unknown mesh format.
else:
raise ValueError("Unsupported input mesh type.")
except ValueError as e:
LOG.exception(e)
sys.exit()
return mesh
def get_git_revision(cwd=None):
""" Return the Git HEAD revision in the form of a SHA-1 hash.
:param str cwd: The current working directory that Git should look in for version information.
:returns: The SHA-1 hash corresponding to the HEAD revision in the Git repository.
:rtype: str
"""
# Adapted from the pybench code by Florian Rathgeber.
# https://github.com/firedrakeproject/pybench/blob/master/pybench.py
try:
revision = subprocess.check_output(['git', 'rev-parse', 'HEAD'], cwd=cwd).strip()
except OSError as e:
LOG.exception(e)
revision = None
return revision
def get_initial_condition(self, checkpoint=None):
""" Set up the initial conditions for the simulation. """
LOG.info("Setting initial conditions...")
h_initial = ExpressionFromOptions(path = "/system/core_fields/scalar_field::FreeSurfacePerturbation/initial_condition").get_expression()
u_initial = ExpressionFromOptions(path = "/system/core_fields/vector_field::Velocity/initial_condition").get_expression()
initial_condition = Function(self.W, name="InitialCondition", annotate=False)
initial_condition.sub(0).assign(Function(self.W.sub(0), annotate=False).interpolate(u_initial))
initial_condition.sub(1).assign(Function(self.W.sub(1), annotate=False).interpolate(h_initial))
# Load initial conditions from the specified checkpoint file if desired.
if(checkpoint is not None):
initial_condition.dat.load(checkpoint)
LOG.debug("Loaded initial condition from checkpoint file.")
return initial_condition
def get_git_revision(cwd=None):
""" Return the Git HEAD revision in the form of a SHA-1 hash.
:param str cwd: The current working directory that Git should look in for version information.
:returns: The SHA-1 hash corresponding to the HEAD revision in the Git repository.
:rtype: str
"""
# Adapted from the pybench code by Florian Rathgeber.
# https://github.com/firedrakeproject/pybench/blob/master/pybench.py
try:
revision = subprocess.check_output(['git', 'rev-parse', 'HEAD'],
cwd=cwd).strip()
except OSError as e:
LOG.exception(e)
revision = None
return revision
def get_turbine_array(self):
""" Create and return an array of turbines, if desired by the user. """
base_option_path = "/system/equations/momentum_equation/turbines"
# Parameterise the turbine array.
if(libspud.have_option(base_option_path)):
array_type = libspud.get_option(base_option_path + "/array/name")
try:
if(array_type == "individual"):
array = IndividualArray(base_option_path, self.mesh)
elif(array_type == "continuum"):
array = ContinuumArray(base_option_path, self.mesh)
else:
raise ValueError("Unknown turbine array type.")
except ValueError as e:
LOG.exception(e)
else:
array = None
return array
def get_turbine_array(self):
""" Create and return an array of turbines, if desired by the user. """
base_option_path = "/system/equations/momentum_equation/turbines"
# Parameterise the turbine array.
if (libspud.have_option(base_option_path)):
array_type = libspud.get_option(base_option_path + "/array/name")
try:
if (array_type == "individual"):
array = IndividualArray(base_option_path, self.mesh)
elif (array_type == "continuum"):
array = ContinuumArray(base_option_path, self.mesh)
else:
raise ValueError("Unknown turbine array type.")
except ValueError as e:
LOG.exception(e)
else:
array = None
return array
def __init__(self, base_option_path, mesh):
""" Create an array of turbines.
:param str base_option_path: The top-most level of the turbine options in the simulation's configuration/options file.
:param mesh: The Mesh object.
:returns: None
"""
fs = FunctionSpace(mesh, "CG", 1)
turbine_type = libspud.get_option(base_option_path +
"/array/turbine_type/name")
turbine_coords = eval(
libspud.get_option(base_option_path +
"/array/turbine_coordinates"))
turbine_radius = eval(
libspud.get_option(base_option_path + "/array/turbine_radius"))
K = libspud.get_option(
base_option_path +
"/array/scalar_field::TurbineDragCoefficient/value/constant")
self.drag = Function(fs).interpolate(Expression("0"))
for coords in turbine_coords:
# For each coordinate tuple in the list, create a new turbine.
# FIXME: This assumes that all turbines are of the same type.
try:
if (turbine_type == "bump"):
turbine = BumpTurbine(K=K, coords=coords, r=turbine_radius)
elif (turbine_type == "tophat"):
turbine = TopHatTurbine(K=K,
coords=coords,
r=turbine_radius)
else:
raise ValueError("Unknown turbine type '%s'." %
turbine_type)
except ValueError as e:
LOG.exception(e)
sys.exit()
self.drag += Function(fs).interpolate(turbine)
LOG.info("Added %s turbine at %s..." % (turbine_type, coords))
self.optimise = libspud.have_option(base_option_path + "/optimise")
return
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 populate_options(self):
""" Add simulation options related to the shallow water model to a dictionary object.
:returns: None
"""
# A dictionary storing all the options
self.options = {}
LOG.info("Populating options dictionary...")
self.options["simulation_name"] = libspud.get_option(
"/simulation_name")
self.options["dimension"] = libspud.get_option("/geometry/dimension")
# Time-stepping parameters
self.options["T"] = libspud.get_option("/timestepping/finish_time")
self.options["t"] = libspud.get_option("/timestepping/current_time")
self.options["dt"] = libspud.get_option("/timestepping/timestep")
self.options["theta"] = libspud.get_option("/timestepping/theta")
if (libspud.have_option("/timestepping/steady_state")):
self.options["steady_state_tolerance"] = libspud.get_option(
"/timestepping/steady_state/tolerance")
else:
self.options["steady_state_tolerance"] = -1000
# I/O parameters
if (libspud.have_option("/io/dump_period")):
self.options["dump_period"] = libspud.get_option("/io/dump_period")
else:
self.options["dump_period"] = None
if (libspud.have_option("/io/checkpoint")):
self.options["checkpoint_period"] = libspud.get_option(
"/io/checkpoint/dump_period")
else:
self.options["checkpoint_period"] = None
# Physical parameters
self.options["g_magnitude"] = libspud.get_option(
"/physical_parameters/gravity/magnitude")
# Enable/disable terms in the shallow water equations
self.options["have_momentum_mass"] = (not libspud.have_option(
"/system/equations/momentum_equation/mass_term/exclude_mass_term"))
self.options["have_momentum_advection"] = (not libspud.have_option(
"/system/equations/momentum_equation/advection_term/exclude_advection_term"
))
self.options["have_momentum_stress"] = libspud.have_option(
"/system/equations/momentum_equation/stress_term")
# Source terms for the momentum and continuity equations
self.options["have_momentum_source"] = libspud.have_option(
"/system/equations/momentum_equation/source_term")
self.options["have_continuity_source"] = libspud.have_option(
"/system/equations/continuity_equation/source_term")
# Check for any SU stabilisation
self.options["have_su_stabilisation"] = libspud.have_option(
"/system/equations/momentum_equation/spatial_discretisation/continuous_galerkin/stabilisation/streamline_upwind"
)
# Turbulence parameterisation
self.options["have_turbulence_parameterisation"] = libspud.have_option(
"/system/equations/momentum_equation/turbulence_parameterisation")
# Drag parameterisation
self.options["have_drag"] = libspud.have_option(
"/system/equations/momentum_equation/drag_term")
# Integration by parts
self.options[
"integrate_continuity_equation_by_parts"] = libspud.have_option(
"/system/equations/continuity_equation/integrate_by_parts")
self.options["integrate_advection_term_by_parts"] = libspud.have_option(
"/system/equations/momentum_equation/advection_term/integrate_by_parts"
)
return
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 __init__(self, path):
""" Initialise a new shallow water simulation, using an options file.
:param str path: The path to the simulation's configuration/options file.
:returns: None
"""
LOG.info("Initialising simulation...")
# Remove any stored options.
libspud.clear_options()
# Load the options from the options tree.
libspud.load_options(path)
# Populate the options dictionary
self.populate_options()
# Read in the input mesh (or construct one)
self.mesh = self.get_mesh(path)
# Create a dictionary containing all the function spaces
LOG.info("Creating function spaces...")
self.function_spaces = {}
# The Velocity field's function space
name = "VelocityFunctionSpace"
path = "/function_spaces/function_space::%s" % name
family = libspud.get_option(path+"/family")
degree = libspud.get_option(path+"/degree")
try:
if(family == "Continuous Lagrange"):
self.function_spaces[name] = VectorFunctionSpace(self.mesh, "CG", degree)
elif(family == "Discontinuous Lagrange"):
self.function_spaces[name] = VectorFunctionSpace(self.mesh, "DG", degree)
else:
raise ValueError("Unknown element family: %s." % family)
except ValueError as e:
LOG.exception(e)
sys.exit()
LOG.debug("Created a new %s function space of degree %d for Velocity" % (family, degree))
# The FreeSurfacePerturbation field's function space
name = "FreeSurfaceFunctionSpace"
path = "/function_spaces/function_space::%s" % name
family = libspud.get_option(path+"/family")
degree = libspud.get_option(path+"/degree")
try:
if(family == "Continuous Lagrange"):
self.function_spaces[name] = FunctionSpace(self.mesh, "CG", degree)
elif(family == "Discontinuous Lagrange"):
self.function_spaces[name] = FunctionSpace(self.mesh, "DG", degree)
else:
raise ValueError("Unknown element family: %s." % family)
except ValueError as e:
LOG.exception(e)
sys.exit()
LOG.debug("Created a new %s function space of degree %d for FreeSurfacePerturbation" % (family, degree))
# Define the mixed function space
U = self.function_spaces["VelocityFunctionSpace"]
H = self.function_spaces["FreeSurfaceFunctionSpace"]
self.W = MixedFunctionSpace([U, H])
# Set up the output streams
self.create_output_streams()
return
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 __init__(self, path, checkpoint=None):
""" Initialise a new shallow water simulation, using an options file.
:param str path: The path to the simulation's configuration/options file.
:param str checkpoint: The path to a checkpoint file.
:returns: None
"""
LOG.info("Initialising simulation...")
# Remove any stored options.
libspud.clear_options()
# Load the options from the options tree.
libspud.load_options(path)
# Populate the options dictionary
self.populate_options()
# Read in the input mesh (or construct one)
self.mesh = self.get_mesh(path)
# Create a dictionary containing all the function spaces
LOG.info("Creating function spaces...")
self.function_spaces = {}
# The Velocity field's function space
name = "VelocityFunctionSpace"
path = "/function_spaces/function_space::%s" % name
family = libspud.get_option(path + "/family")
degree = libspud.get_option(path + "/degree")
try:
if (family == "Continuous Lagrange"):
self.function_spaces[name] = VectorFunctionSpace(
self.mesh, "CG", degree)
elif (family == "Discontinuous Lagrange"):
self.function_spaces[name] = VectorFunctionSpace(
self.mesh, "DG", degree)
else:
raise ValueError("Unknown element family: %s." % family)
except ValueError as e:
LOG.exception(e)
sys.exit()
LOG.debug("Created a new %s function space of degree %d for Velocity" %
(family, degree))
# The FreeSurfacePerturbation field's function space
name = "FreeSurfaceFunctionSpace"
path = "/function_spaces/function_space::%s" % name
family = libspud.get_option(path + "/family")
degree = libspud.get_option(path + "/degree")
try:
if (family == "Continuous Lagrange"):
self.function_spaces[name] = FunctionSpace(
self.mesh, "CG", degree)
elif (family == "Discontinuous Lagrange"):
self.function_spaces[name] = FunctionSpace(
self.mesh, "DG", degree)
else:
raise ValueError("Unknown element family: %s." % family)
except ValueError as e:
LOG.exception(e)
sys.exit()
LOG.debug(
"Created a new %s function space of degree %d for FreeSurfacePerturbation"
% (family, degree))
# Get the function spaces
U = self.function_spaces["VelocityFunctionSpace"]
H = self.function_spaces["FreeSurfaceFunctionSpace"]
# Test functions
self.w = TestFunction(U)
self.v = TestFunction(H)
LOG.info("Test functions created.")
# Trial functions (i.e. the solutions for time n+1)
self.u = TrialFunction(U)
self.h = TrialFunction(H)
LOG.info("Trial functions created.")
# Normal vector to each element facet
self.n = FacetNormal(self.mesh)
# Set up initial conditions
LOG.info("Setting initial conditions...")
h_initial = ExpressionFromOptions(
path=
"/system/core_fields/scalar_field::FreeSurfacePerturbation/initial_condition"
).get_expression()
u_initial = ExpressionFromOptions(
path="/system/core_fields/vector_field::Velocity/initial_condition"
).get_expression()
# The solution at time n.
self.u0 = Function(U).interpolate(u_initial)
self.h0 = Function(H).interpolate(h_initial)
# The solution at time n-1.
self.u00 = Function(U)
self.u00.assign(self.u0)
# Load initial conditions from the specified checkpoint file if desired.
if (checkpoint is not None):
self.solution_old.dat.load(checkpoint)
LOG.debug("Loaded initial condition from checkpoint file.")
# Mean free surface height
self.h_mean = Function(H)
self.h_mean.interpolate(
ExpressionFromOptions(
path="/system/core_fields/scalar_field::FreeSurfaceMean/value"
).get_expression())
# Set up the functions used to write fields to file.
self.output_functions = {}
self.output_functions["Velocity"] = Function(U, name="Velocity")
self.output_functions["FreeSurfacePerturbation"] = Function(
H, name="FreeSurfacePerturbation")
# Set up the output stream
LOG.info("Initialising output file streams...")
self.output_files = {}
for field in self.output_functions.keys():
self.output_files[field] = File(
"%s_%s.pvd" % (self.options["simulation_name"], field))
# Write initial conditions to file
LOG.info("Writing initial conditions to file...")
self.output_functions["Velocity"].assign(self.u0)
self.output_files["Velocity"] << self.output_functions["Velocity"]
self.output_functions["FreeSurfacePerturbation"].assign(self.h0)
self.output_files["FreeSurfacePerturbation"] << self.output_functions[
"FreeSurfacePerturbation"]
return
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 __init__(self, path, checkpoint=None):
""" Initialise a new shallow water simulation, using an options file.
:param str path: The path to the simulation's configuration/options file.
:param str checkpoint: The path to a checkpoint file.
:returns: None
"""
LOG.info("Initialising simulation...")
# Remove any stored options.
libspud.clear_options()
# Load the options from the options tree.
libspud.load_options(path)
# Populate the options dictionary
self.populate_options()
# Read in the input mesh (or construct one)
self.mesh = self.get_mesh(path)
# Create a dictionary containing all the function spaces
LOG.info("Creating function spaces...")
self.function_spaces = {}
# The Velocity field's function space
name = "VelocityFunctionSpace"
path = "/function_spaces/function_space::%s" % name
family = libspud.get_option(path+"/family")
degree = libspud.get_option(path+"/degree")
try:
if(family == "Continuous Lagrange"):
self.function_spaces[name] = VectorFunctionSpace(self.mesh, "CG", degree)
elif(family == "Discontinuous Lagrange"):
self.function_spaces[name] = VectorFunctionSpace(self.mesh, "DG", degree)
else:
raise ValueError("Unknown element family: %s." % family)
except ValueError as e:
LOG.exception(e)
sys.exit()
LOG.debug("Created a new %s function space of degree %d for Velocity" % (family, degree))
# The FreeSurfacePerturbation field's function space
name = "FreeSurfaceFunctionSpace"
path = "/function_spaces/function_space::%s" % name
family = libspud.get_option(path+"/family")
degree = libspud.get_option(path+"/degree")
try:
if(family == "Continuous Lagrange"):
self.function_spaces[name] = FunctionSpace(self.mesh, "CG", degree)
elif(family == "Discontinuous Lagrange"):
self.function_spaces[name] = FunctionSpace(self.mesh, "DG", degree)
else:
raise ValueError("Unknown element family: %s." % family)
except ValueError as e:
LOG.exception(e)
sys.exit()
LOG.debug("Created a new %s function space of degree %d for FreeSurfacePerturbation" % (family, degree))
# Get the function spaces
U = self.function_spaces["VelocityFunctionSpace"]
H = self.function_spaces["FreeSurfaceFunctionSpace"]
# Test functions
self.w = TestFunction(U)
self.v = TestFunction(H)
LOG.info("Test functions created.")
# Trial functions (i.e. the solutions for time n+1)
self.u = TrialFunction(U)
self.h = TrialFunction(H)
LOG.info("Trial functions created.")
# Normal vector to each element facet
self.n = FacetNormal(self.mesh)
# Set up initial conditions
LOG.info("Setting initial conditions...")
h_initial = ExpressionFromOptions(path = "/system/core_fields/scalar_field::FreeSurfacePerturbation/initial_condition").get_expression()
u_initial = ExpressionFromOptions(path = "/system/core_fields/vector_field::Velocity/initial_condition").get_expression()
# The solution at time n.
self.u0 = Function(U).interpolate(u_initial)
self.h0 = Function(H).interpolate(h_initial)
# The solution at time n-1.
self.u00 = Function(U)
self.u00.assign(self.u0)
# Load initial conditions from the specified checkpoint file if desired.
if(checkpoint is not None):
self.solution_old.dat.load(checkpoint)
LOG.debug("Loaded initial condition from checkpoint file.")
# Mean free surface height
self.h_mean = Function(H)
self.h_mean.interpolate(ExpressionFromOptions(path = "/system/core_fields/scalar_field::FreeSurfaceMean/value").get_expression())
# Set up the functions used to write fields to file.
self.output_functions = {}
self.output_functions["Velocity"] = Function(U, name="Velocity")
self.output_functions["FreeSurfacePerturbation"] = Function(H, name="FreeSurfacePerturbation")
# Set up the output stream
LOG.info("Initialising output file streams...")
self.output_files = {}
for field in self.output_functions.keys():
self.output_files[field] = File("%s_%s.pvd" % (self.options["simulation_name"], field))
# Write initial conditions to file
LOG.info("Writing initial conditions to file...")
self.output_functions["Velocity"].assign(self.u0)
self.output_files["Velocity"] << self.output_functions["Velocity"]
self.output_functions["FreeSurfacePerturbation"].assign(self.h0)
self.output_files["FreeSurfacePerturbation"] << self.output_functions["FreeSurfacePerturbation"]
return
# along with Firedrake-Fluids. If not, see <http://www.gnu.org/licenses/>.
import sys, os
from firedrake_fluids import LOG
# PETSc environment variables
try:
if (os.environ["PETSC_OPTIONS"] == ""):
os.environ["PETSC_OPTIONS"] = "-log_summary"
else:
os.environ[
"PETSC_OPTIONS"] = os.environ["PETSC_OPTIONS"] + " -log_summary"
except KeyError:
# Environment variable does not exist, so let's set it now.
os.environ["PETSC_OPTIONS"] = "-log_summary"
LOG.debug("Environment variable PETSC_OPTIONS set to: %s" %
(os.environ["PETSC_OPTIONS"]))
import numpy
import mpi4py
import libspud
LOG.debug("libspud successfully imported")
from pyop2 import *
LOG.debug("PyOP2 successfully imported")
from firedrake import *
LOG.debug("Firedrake successfully imported")
# COFFEE, PyOP2 and FFC parameters
op2.init(lazy_evaluation=False)
parameters['form_compiler']['quadrature_degree'] = 4
parameters["coffee"]["O2"] = False
# You should have received a copy of the GNU General Public License
# along with Firedrake-Fluids. If not, see <http://www.gnu.org/licenses/>.
import sys, os
from firedrake_fluids import LOG
# PETSc environment variables
try:
if(os.environ["PETSC_OPTIONS"] == ""):
os.environ["PETSC_OPTIONS"] = "-log_summary"
else:
os.environ["PETSC_OPTIONS"] = os.environ["PETSC_OPTIONS"] + " -log_summary"
except KeyError:
# Environment variable does not exist, so let's set it now.
os.environ["PETSC_OPTIONS"] = "-log_summary"
LOG.debug("Environment variable PETSC_OPTIONS set to: %s" % (os.environ["PETSC_OPTIONS"]))
import numpy
import mpi4py
import libspud
LOG.debug("libspud successfully imported")
from pyop2 import *
LOG.debug("PyOP2 successfully imported")
from firedrake import *
LOG.debug("Firedrake successfully imported")
# COFFEE, PyOP2 and FFC parameters
op2.init(lazy_evaluation=False)
parameters['form_compiler']['quadrature_degree'] = 4
#parameters["coffee"]["O2"] = False # FIXME: Remove this one this issue has been fixed: https://github.com/firedrakeproject/firedrake/issues/425