pogona.objects.ObjectTube

class pogona.objects.ObjectTube[source]

Bases: pogona.object.Object

Attributes

component_name

Unique name of this component, unless it is "Generic component".

dummy_boundary_points

Whether to insert dummy points at the boundary of the mesh, and where exactly.

fallback_flow_rate

Fallback flow rate for making sensor subscriptions possible in the case that this Object starts with an overall flow rate of 0 (i.e., is_active == False).

flow_rate

Flow rate in ml/min.

inlet_zone

Length of the inlet zone in m.

is_active

length

Length of the tube in m.

mesh_resolution

Mesh resolution, defined as number of 'radius cells' in the OpenFOAM blockMeshDict.

name

The name of this type of object.

object_id

Object index, set by the scene manager.

openfoam_cases_path

Path to all OpenFOAM simulation cases.

outlet_zone

For teleporting: If a molecule enters this zone at the end of the tube, it will be teleported to a connected object.

radius

Radius of the tube in m.

rotation

scale

translation

use_sensor_subscriptions

Notify subscribed sensors based on object mesh cells.

variant

Additional variant information.

walls_patch_names

__init__()[source]

Methods

__init__()

finalize(simulation_kernel)

find_latest_time_step(path)

return

The highest-valued subdirectory of path that is named

get_closest_cell_centre_id(position_global)

returns

Array of closest cell centers to position.

get_current_mesh_global()

get_current_mesh_local()

get_fallback_mesh_index()

If an Object supports sensor subscriptions, some OpenFOAM case with a non-zero flow rate should exist (i.e., a vector field for which this Object has self.is_active == True).

get_flow(simulation_kernel, position_global, ...)

get_mesh_index()

returns

A unique string for the current configuration of this object.

get_outlet_area(outlet_name)

get_path([use_latest_time_step, fallback])

param use_latest_time_step

Find the latest time step in path.

get_transformation()

get_tube_mesh_index(flow_rate_mlpmin)

get_vector_field_manager()

initialize(simulation_kernel, init_stage)

Use InitStages to initialize this Component instance.

load_current_vector_field(simulation_kernel)

process_changed_inlet_flow_rate(...)

Update the flow rate inside this Object based on the changed flow rate of the inlet with name inlet_name, then propagate this change to any Object connected to this Object's outlets.

process_new_time_step(simulation_kernel, ...)

set_arguments(**kwargs)

Read arguments as key value pairs and set this component's member variables accordingly.

__init__()[source]
finalize(simulation_kernel: pogona.simulation_kernel.SimulationKernel)
static find_latest_time_step(path: str) str
Returns

The highest-valued subdirectory of path that is named only after a floating point value. E.g., if there are ‘{path}/0/’ and ‘{path}/0.1/’, this will return ‘0.1’.

get_closest_cell_centre_id(position_global: numpy.ndarray) Optional[numpy.ndarray]
Returns

Array of closest cell centers to position. If there’s only one position, output is squeezed. None if this Object is inactive. See documentation of cKDTree.query().

get_current_mesh_global() Optional[numpy.ndarray]
get_current_mesh_local() Optional[numpy.ndarray]
get_fallback_mesh_index() Optional[str][source]

If an Object supports sensor subscriptions, some OpenFOAM case with a non-zero flow rate should exist (i.e., a vector field for which this Object has self.is_active == True). If this object is initially inactive, however, we still need to know where to find this mesh for the initialization of the SensorManager.

Returns

A valid mesh index independent of this Object’s is_active status. None if this Object does not support sensor subscriptions.

get_flow(simulation_kernel: pogona.simulation_kernel.SimulationKernel, position_global: numpy.ndarray, sim_time: float)
get_mesh_index()[source]
Returns

A unique string for the current configuration of this object. Used for caching.

get_outlet_area(outlet_name: str)[source]
get_path(use_latest_time_step=False, fallback=False) str
Parameters
  • use_latest_time_step – Find the latest time step in path. If False, use this Object’s _default_time_str, which may still be set to ‘latest’, which has the same effect.

  • fallback – Use get_fallback_mesh_index instead of get_mesh_index.

Returns

Path to the OpenFOAM files for this object.

get_transformation() pogona.transformation.Transformation
get_tube_mesh_index(flow_rate_mlpmin: float) str[source]
get_vector_field_manager() Optional[pogona.vector_field_manager.VectorFieldManager]
initialize(simulation_kernel: pogona.simulation_kernel.SimulationKernel, init_stage: pogona.component.InitStages)[source]

Use InitStages to initialize this Component instance.

load_current_vector_field(simulation_kernel: pogona.simulation_kernel.SimulationKernel)
process_changed_inlet_flow_rate(simulation_kernel: pogona.simulation_kernel.SimulationKernel, inlet_name: str, flow_rate: float)[source]

Update the flow rate inside this Object based on the changed flow rate of the inlet with name inlet_name, then propagate this change to any Object connected to this Object’s outlets.

Should also update is_active accordingly.

process_new_time_step(simulation_kernel: pogona.simulation_kernel.SimulationKernel, notification_stage: pogona.component.NotificationStages)
set_arguments(**kwargs)

Read arguments as key value pairs and set this component’s member variables accordingly. Validity of the argument values will be checked in initialize().

component_name = 'Generic component'

Unique name of this component, unless it is “Generic component”.

dummy_boundary_points = 'NONE'

Whether to insert dummy points at the boundary of the mesh, and where exactly. This may help with interpolation.

fallback_flow_rate = 5.0

Fallback flow rate for making sensor subscriptions possible in the case that this Object starts with an overall flow rate of 0 (i.e., is_active == False).

flow_rate = 5.0

Flow rate in ml/min.

id

Unique integer component ID

inlet_zone = 0.05

Length of the inlet zone in m.

This segment at the start of the tube mesh will be cut off, since the OpenFOAM simulation showed that the flow profile before this threshold does not yet match the analytically determined profile of a tube to a sufficient degree.

‘Cut off’ here means that this ObjectTube will be shifted along its axis such that it will appear as though you are dealing with a tube that is simply inlet_zone metres shorter.

inlets: List[str]

Names of the inlets in the OpenFOAM mesh.

property is_active
length = 0.05

Length of the tube in m.

mesh_resolution = 11

Mesh resolution, defined as number of ‘radius cells’ in the OpenFOAM blockMeshDict.

name: str = 'Tube'

The name of this type of object. Not a unique identifier like Component.component_name!

object_id = -1

Object index, set by the scene manager.

openfoam_cases_path = ''

Path to all OpenFOAM simulation cases. Subclasses may use this as the base path to find their respective meshes via get_path().

outlet_zone = 0.005

For teleporting: If a molecule enters this zone at the end of the tube, it will be teleported to a connected object.

outlets: List[str]

Names of the outlets in the OpenFOAM mesh.

radius = 0.00075

Radius of the tube in m.

rotation = [0, 0, 0]
scale = [1, 1, 1]
translation = [0, 0, 0]
use_sensor_subscriptions = 'USE_DEFAULT'

Notify subscribed sensors based on object mesh cells. This speeds up simulation. Only disable this if you are constrained by memory or if the object does not have a mesh in the first place. If None, use the SensorManager’s default_use_sensor_subscriptions.

variant = ''

Additional variant information.

If given, look for an OpenFOAM case with ‘_<variant>’ appended to its path name.

property walls_patch_names