pogona.objects.ObjectTube

class pogona.objects.ObjectTube[source]

Bases: 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: 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: ndarray) → Optional[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[ndarray]

get_current_mesh_local() → Optional[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: SimulationKernel, position_global: 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() → Transformation

get_tube_mesh_index(flow_rate_mlpmin: float) → str[source]

get_vector_field_manager() → Optional[VectorFieldManager]

initialize(simulation_kernel: SimulationKernel, init_stage: InitStages)[source]: Use InitStages to initialize this Component instance.

load_current_vector_field(simulation_kernel: SimulationKernel)

process_changed_inlet_flow_rate(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: SimulationKernel, notification_stage: 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