anuga.Domain

class anuga.Domain(coordinates=None, vertices=None, boundary=None, tagged_elements=None, geo_reference=None, use_inscribed_circle=False, mesh_filename=None, use_cache=False, verbose=False, conserved_quantities=None, evolved_quantities=None, other_quantities=None, full_send_dict=None, ghost_recv_dict=None, starttime=0, processor=0, numproc=1, number_of_full_nodes=None, number_of_full_triangles=None, ghost_layer_width=2, **kwargs)

Object which encapulates the shallow water model

This class is a specialization of class Generic_Domain from module generic_domain.py consisting of methods specific to the Shallow Water Wave Equation

Shallow Water Wave Equation

\[U_t + E_x + G_y = S\]

where

\[U = [w, uh, vh]^T\]

\[E = [uh, u^2h + gh^2/2, uvh]\]

\[G = [vh, uvh, v^2h + gh^2/2]\]

S represents source terms forcing the system (e.g. gravity, friction, wind stress, …)

and _t, _x, _y denote the derivative with respect to t, x and y respectively.

The quantities are

symbol	variable name	explanation
x	x	horizontal distance from origin [m]
y	y	vertical distance from origin [m]
z	elevation	elevation of bed on which flow is modelled [m]
h	height	water height above z [m]
w	stage	absolute water level, w = z+h [m]
u		speed in the x direction [m/s]
v		speed in the y direction [m/s]
uh	xmomentum	momentum in the x direction [m^2/s]
vh	ymomentum	momentum in the y direction [m^2/s]
eta		mannings friction coefficient [to appear]
nu		wind stress coefficient [to appear]

The conserved quantities are w, uh, vh

__init__(coordinates=None, vertices=None, boundary=None, tagged_elements=None, geo_reference=None, use_inscribed_circle=False, mesh_filename=None, use_cache=False, verbose=False, conserved_quantities=None, evolved_quantities=None, other_quantities=None, full_send_dict=None, ghost_recv_dict=None, starttime=0, processor=0, numproc=1, number_of_full_nodes=None, number_of_full_triangles=None, ghost_layer_width=2, **kwargs)

Instantiate a shallow water domain.

Parameters:

• coordinates – vertex locations for the mesh

• vertices – vertex indices defining the triangles of the mesh

• boundary – boundaries of the mesh

Methods

__init__([coordinates, vertices, boundary, ...])	Instantiate a shallow water domain.
add_quantity(name, *args, **kwargs)	Add values to a named quantity
apply_fractional_steps()
apply_protection_against_isolated_degenerate_timesteps()
backup_conserved_quantities()
balance_deep_and_shallow()	Compute linear combination between stage as computed by gradient-limiters limiting using w, and stage computed by gradient-limiters limiting using h (h-limiter).
boundary_statistics([quantities, tags])	Output statistics about boundary forcing at each timestep
build_tagged_elements_dictionary(*args, **kwargs)
centroid_norm(quantity, normfunc)	Calculate the norm of the centroid values of a specific quantity, using normfunc.
check_integrity()	Run integrity checks on shallow water domain.
compute_boundary_flows()	Compute boundary flows at current timestep.
compute_flux_update_frequency()	Update the 'flux_update_frequency' and 'update_extrapolate' variables Used to control updating of fluxes / extrapolation for 'local-time-stepping'
compute_fluxes()	Compute fluxes and timestep suitable for all volumes in domain.
compute_forcing_terms()	If there are any forcing functions driving the system they should be defined in Domain subclass and appended to the list self.forcing_terms
compute_total_volume()	Compute total volume (m^3) of water in entire domain
conserved_values_to_evolved_values(q_cons, ...)	Needs to be overridden by Domain subclass
create_quantity_from_expression(expression)	Create new quantity from other quantities using arbitrary expression.
distribute_to_vertices_and_edges()	extrapolate centroid values to vertices and edges
distribute_using_edge_limiter()	Distribution from centroids to edges specific to the SWW eqn.
distribute_using_vertex_limiter()	Distribution from centroids to vertices specific to the SWW equation.
dump_triangulation([filename])	Get vertex coordinates, partition full and ghost triangles based on self.tri_full_flag
evolve([yieldstep, outputstep, finaltime, ...])	Evolve method from Domain class.
evolve_one_euler_step(yieldstep, finaltime)	One Euler Time Step Q^{n+1} = E(h) Q^n
evolve_one_rk2_step(yieldstep, finaltime)	One 2nd order RK timestep Q^{n+1} = 0.5 Q^n + 0.5 E(h)^2 Q^n
evolve_one_rk3_step(yieldstep, finaltime)	One 3rd order RK timestep Q^(1) = 3/4 Q^n + 1/4 E(h)^2 Q^n (at time t^n + h/2) Q^{n+1} = 1/3 Q^n + 2/3 E(h) Q^(1) (at time t^{n+1})
evolve_to_end([finaltime])	Iterate evolve all the way to the end.
extrapolate_second_order_sw()	Fast version of extrapolation from centroids to edges
get_CFL()	get CFL
get_algorithm_parameters()	Get the standard parameter that are currently set (as a dictionary)
get_area(*args, **kwargs)
get_areas(*args, **kwargs)
get_beta()	Get default beta for limiting.
get_boundary_flux_integral()	Compute the boundary flux integral.
get_boundary_polygon(*args, **kwargs)
get_boundary_tags(*args, **kwargs)
get_centroid_coordinates(*args, **kwargs)
get_centroid_transmissive_bc()	Get value of centroid_transmissive_bc flag.
get_cfl()	get CFL
get_compute_fluxes_method()	Get method for computing fluxes.
get_conserved_quantities(vol_id[, vertex, edge])	Get conserved quantities at volume vol_id.
get_datadir()
get_datetime([timestamp])	Retrieve datetime corresponding to current timestamp wrt to domain timezone
get_disconnected_triangles(*args, **kwargs)
get_distribute_to_vertices_and_edges_method()	Get method for distribute_to_vertices_and_edges.
get_edge_midpoint_coordinate(*args, **kwargs)
get_edge_midpoint_coordinates(*args, **kwargs)
get_energy_through_cross_section(polyline[, ...])	Obtain average energy head [m] across specified cross section.
get_evolve_max_timestep()	Set default max_timestep for evolving.
get_evolve_min_timestep()	Set default max_timestep for evolving.
get_evolve_starttime()
get_evolved_quantities(vol_id[, vertex, edge])	Get evolved quantities at volume vol_id.
get_extent(*args, **kwargs)
get_flow_algorithm()	Get method used for timestepping and spatial discretisation
get_flow_through_cross_section(polyline[, ...])	Get the total flow through an arbitrary poly line.
get_fractional_step_volume_integral()	Compute the integrated flows from fractional steps.
get_full_centroid_coordinates(*args, **kwargs)
get_full_nodes(*args, **kwargs)
get_full_triangles(*args, **kwargs)
get_full_vertex_coordinates(*args, **kwargs)
get_georeference(*args, **kwargs)
get_global_name()
get_hemisphere()
get_interpolation_object(*args, **kwargs)
get_intersecting_segments(*args, **kwargs)
get_inv_tri_map()
get_lone_vertices(*args, **kwargs)
get_maximum_inundation_elevation([indices, ...])	Return highest elevation where h > 0
get_maximum_inundation_location([indices])	Return location of highest elevation where h > 0
get_minimum_allowed_height()
get_minimum_storable_height()
get_name()
get_nodes(*args, **kwargs)
get_normal(*args, **kwargs)
get_number_of_full_triangles(*args, **kwargs)
get_number_of_nodes(*args, **kwargs)
get_number_of_triangles(*args, **kwargs)
get_number_of_triangles_per_node(*args, **kwargs)
get_quantity(name[, location, indices])	Get pointer to quantity object.
get_quantity_names()	Get a list of all the quantity names that this domain is aware of.
get_radii(*args, **kwargs)
get_relative_time()	Set internal relative time
get_starttime([datetime])	return starttime, either as timestamp, or as a datetime
get_store()	Get whether data saved to sww file.
get_store_centroids()	Get whether data saved to sww file.
get_tagged_elements(*args, **kwargs)
get_time()	Get the absolute model time (seconds).
get_timestep()	get current timestep (seconds).
get_timestepping_method()
get_timezone()	Retrieve current domain timezone
get_tri_map()
get_triangle_containing_point(*args, **kwargs)
get_triangles(*args, **kwargs)
get_triangles_and_vertices_per_node(*args, ...)
get_triangles_inside_polygon(*args, **kwargs)
get_unique_vertices(*args, **kwargs)
get_using_centroid_averaging()
get_using_discontinuous_elevation()	Return boolean indicating whether algorithm is using dicontinuous elevation
get_vertex_coordinate(*args, **kwargs)
get_vertex_coordinates(*args, **kwargs)
get_water_volume()
get_wet_elements([indices, minimum_height])	Return indices for elements where h > minimum_allowed_height
get_zone()	get zone for domain Geo_reference
initialise_storage()	Create and initialise self.writer object for storing data.
log_operator_timestepping_statistics()
maximum_quantity(name, *args, **kwargs)	max of values to a named quantity
minimum_quantity(name, *args, **kwargs)	min of values to a named quantity
print_algorithm_parameters()	Print the standard parameters that are curently set (as a dictionary)
print_boundary_statistics([quantities, tags])
print_operator_statistics()
print_operator_timestepping_statistics()
print_statistics(*args, **kwargs)
print_timestepping_statistics(*args, **kwargs)	Print time stepping statistics
print_volumetric_balance_statistics()
protect_against_infinitesimal_and_negative_heights()	Clean up the stage and momentum values to ensure non-negative heights
quantity_statistics([precision])	Return string with statistics about quantities for printing or logging
report_cells_with_small_local_timestep([...])	Convenience function to print the locations of cells with a small local timestep.
report_water_volume_statistics([verbose, ...])	Compute the volume, boundary flux integral, fractional step volume integral, and their difference
saxpy_conserved_quantities(a, b)
set_CFL([cfl])	Set CFL parameter, warn if greater than 2.0
set_beta(beta)	Shorthand to assign one constant value [0,2] to all limiters.
set_betas(beta_w, beta_w_dry, beta_uh, ...)	Assign beta values in the range [0,2] to all limiters.
set_boundary(boundary_map)	Associate boundary objects with tagged boundary segments.
set_centroid_transmissive_bc(flag)	Set behaviour of the transmissive boundary condition, namely calculate the BC using the centroid value of neighbouring cell or the calculated edge value.
set_cfl([cfl])	Set CFL parameter, warn if greater than 2.0
set_checkpointing([checkpoint, ...])	Set up checkpointing.
set_compute_fluxes_method([flag])	Set method for computing fluxes.
set_datadir(name)
set_default_order(n)	Set default (spatial) order to either 1 or 2.
set_distribute_to_vertices_and_edges_method([flag])	Set method for computing fluxes.
set_evolve_max_timestep(max_timestep)	Set default max_timestep for evolving.
set_evolve_min_timestep(min_timestep)	Set default min_timestep for evolving.
set_evolve_starttime(time)
set_extrapolate_velocity([flag])	Extrapolation routine uses momentum by default, can change to velocity extrapolation which seems to work better.
set_fixed_flux_timestep([flux_timestep])	Disable variable timestepping and manually set a fixed flux_timestep
set_flow_algorithm([flag])	Set combination of slope limiting and time stepping
set_fractional_step_operator(operator)
set_georeference(*args, **kwargs)
set_gravity_method()	Gravity method is determined by the compute_fluxes_method This is now not used, as gravity is combine in the compute_fluxes method
set_hemisphere(hemisphere)
set_institution(institution)
set_local_extrapolation_and_flux_updating([...])	Use local flux and extrapolation updating
set_low_froude([low_froude])	For low Froude problems the standard flux calculations can lead to excessive damping.
set_maximum_allowed_speed(maximum_allowed_speed)	Set the maximum particle speed that is allowed in water shallower than minimum_allowed_height.
set_minimum_allowed_height(...)	Set minimum depth that will be recognised in the numerical scheme.
set_minimum_storable_height(...)	Set the minimum depth that will be written to an SWW file.
set_name([name, timestamp])	Assign a name to this simulation.
set_points_file_block_line_size(...)
set_quantities_to_be_monitored(q[, polygon, ...])	Specify which quantities will be monitored for extrema.
set_quantities_to_be_stored(q)	Specify which quantities will be stored in the SWW file.
set_quantity(name, *args, **kwargs)	Set values for named quantity
set_quantity_vertices_dict(quantity_dict)	Set values for named quantities.
set_relative_time([time])	Set internal relative time
set_sloped_mannings_function([flag])	Set mannings friction function to use the sloped wetted area.
set_starttime([timestamp])	Set the starttime for the evolution
set_store([flag])	Set whether data saved to sww file.
set_store_centroids([flag])	Set whether centroid data is saved to sww file.
set_store_vertices_smoothly([flag, reduction])	Decide whether vertex values should be stored smoothly (one value per vertex) or uniquely as computed in the model (False).
set_store_vertices_uniquely([flag, reduction])	Decide whether vertex values should be stored uniquely as computed in the model (True) or whether they should be reduced to one value per vertex using self.reduction (False).
set_tag_region(*args, **kwargs)	Set quantities based on a regional tag.
set_time([time])	Set the model time (seconds).
set_timestepping_method(timestepping_method)
set_timezone([tz])	Set timezone for domain
set_use_edge_limiter([flag])	Extrapolation routine uses vertex values by default, for limiting, can change to edge limiting which seems to work better in some cases.
set_use_kinematic_viscosity([flag])
set_use_optimise_dry_cells([flag])	Try to optimize calculations where region is dry
set_using_centroid_averaging([flag])	Set flag to use centroid averaging in output of smoothed vertex values.
set_using_discontinuous_elevation([flag])	Set flag to show whether compute flux algorithm is allowing discontinuous elevation.
set_zone(zone)	Set zone for domain.
statistics(*args, **kwargs)
store_timestep()	Store time dependent quantities and time.
sww_merge(*args, **kwargs)	Dummy function for sequential algorithms where the sww produced is the final products.
timestepping_statistics([track_speeds, ...])	Return string with time stepping statistics for printing or logging
update_boundary()	Go through list of boundary objects and update boundary values for all conserved quantities on boundary.
update_boundary_old()	Go through list of boundary objects and update boundary values for all conserved quantities on boundary.
update_boundary_old_2()	Go through list of boundary objects and update boundary values for all conserved quantities on boundary.
update_centroids_of_momentum_from_velocity()	Calculate the centroid value of x and y momentum from height and velocities
update_centroids_of_velocities_and_height()	Calculate the centroid values of velocities and height based on the values of the quantities stage and x and y momentum
update_conserved_quantities()	Update vectors of conserved quantities using previously computed fluxes and specified forcing functions.
update_extrema()	Update extrema if requested by set_quantities_to_be_monitored.
update_ghosts([quantities])	We must send the information from the full cells and receive the information for the ghost cells We have a list with ghosts expecting updates
update_other_quantities()	There may be a need to calculates some of the other quantities based on the new values of conserved quantities
update_special_conditions()
update_timestep(yieldstep, finaltime)	Calculate the next timestep to take
volumetric_balance_statistics()	Create volumetric balance report suitable for printing or logging.
write_boundary_statistics([quantities, tags])
write_time([track_speeds])