pogona.objects.ObjectYPiece

class pogona.objects.ObjectYPiece[source]

Bases: Object

Attributes

`angle`	Angle between outlet and particle inlet in degrees.
`background_inlet_length`	Length of the background flow inlet in meters.
`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_background_rate_mlpmin`	Fallback background 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).
`fallback_injection_rate_mlpmin`	Fallback injection 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_background`	Background flow rate in ml/min.
`flow_rate_injection`	Flow rate in the injection tube in ml/min.
`injection_inlet_length`	Length of the particle injection inlet tube in meters.
`is_active`
`name`	The name of this object.
`object_id`	Object index, set by the scene manager.
`openfoam_cases_path`	Path to all OpenFOAM simulation cases.
`outlet_length`	Length of the outlet tube in meters.
`outlet_zone`	For teleporting: If a molecule enters this zone at the end of the outlet tube, it will be teleported to a connected object.
`radius`	Radius of the outlet tube in meters.
`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_vector_field_manager`()
`get_ypiece_mesh_index`(injection_rate_mlpmin, ...)
`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_vector_field_manager() → Optional[VectorFieldManager]

get_ypiece_mesh_index(injection_rate_mlpmin: float, background_rate_mlpmin: float) → str[source]

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().

angle = 30.0: Angle between outlet and particle inlet in degrees.

background_inlet_length = 0.01: Length of the background flow inlet in meters.

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_background_rate_mlpmin = 5.0: Fallback background 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).

fallback_injection_rate_mlpmin = 0.0: Fallback injection 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_background = 5.0: Background flow rate in ml/min.

flow_rate_injection = 0.0: Flow rate in the injection tube in ml/min.

id: Unique integer component ID

injection_inlet_length = 0.04: Length of the particle injection inlet tube in meters.

inlets: List[str]: Names of the inlets in the OpenFOAM mesh.

property is_active

name: str = 'Y-Piece': The name of this object.

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_length = 0.04: Length of the outlet tube in meters.

outlet_zone = 0.005: For teleporting: If a molecule enters this zone at the end of the outlet 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 outlet tube in meters.

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