Pogona API Documentation

Core

Face(face_id, position, normalized_normal, ...)

EmbeddedRungeKuttaMethod()

Butcher tableau for a specific Runge-Kutta method as defined here: https://web.archive.org/save/https://en.wikipedia.org/wiki/List_of_Runge–Kutta_methods

Geometry(shape)

Common functions defined for various shapes centered around the origin (0, 0, 0) with a maximum width, height, and depth of 1.

InitStages(value)

Initialization stages for ensuring that Component instances are initialized in the right order.

Integration(value)

An enumeration.

Interpolation(value)

An enumeration.

KnownSensors(value)

An enumeration.

MeshManager()

Molecule(position, velocity, object_id)

MoleculeManager()

MovementPredictor()

NotificationStages(value)

An enumeration.

RKFehlberg45()

DOI: 10.1007/BF02241732

SceneManager()

Shapes(value)

An enumeration.

SensorManager()

SensorSubscriptionsUsage(value)

An enumeration.

SimulationKernel()

The simulation kernel that is responsible for starting and coordinating how a simulation is run.

Transformation([translation, rotation, ...])

VectorField(cell_centres, flow, at_boundary, ...)

VectorFieldParser()

Components

BitstreamGenerator()

Component()

Base class for simulation components that can be configured via YAML files.

Injector()

An injector spawns particles within its defined volume in every time step in which it is turned on.

Modulation()

ModulationOOK()

ModulationPPM()

Separates the symbol duration into N chips for N-PPM.

Object()

PlotterCSV()

Writes molecule positions to CSVs.

PlotterTerminal()

Produces additional logging output in each time step.

Sensor()

SensorCounting()

SensorDestructing()

SensorEmpirical()

Sensor based on empirical measurements of susceptibility variations within a susceptometer.

SensorEmpiricalRadialTest()

Sensor based on empirical measurements in a magnetic field simulation.

SensorFlowRate()

At the beginning of the simulation, the position of N sample points will be randomly set inside this sensor's Geometry.

SensorTeleporting()

Teleports molecules from one object to another.

SprayNozzle()

Objects

ObjectPumpPeristaltic()

Model for a peristaltic pump that tries to avoid overdosing by ramping down the flow speed towards the end of an injection.

ObjectPumpTimed()

ObjectTube()

ObjectTubeAnalytical()

ObjectYPiece()

Properties

AbstractProperty(default, required, *args, ...)

BoolProperty(default, required, *args, **kwargs)

ComponentReferenceProperty(default, ...)

EnumProperty(default, name, required, ...)

FloatArrayProperty(default, required, *args, ...)

Reserved for lists of floats of arbitrary lengths.

FloatProperty(default, required, *args, **kwargs)

IntProperty(default, required, *args, **kwargs)

ListOfVectorsProperty(default, required, ...)

List of length-3 lists of floats.

StrProperty(default, required, *args, **kwargs)

VectorProperty(default, required, *args, ...)

Reserved for lists of floats of length 3.

Utility Functions

assemble_config_recursively(conf[, ...])

param conf

Either the filename of a YAML config file or a dictionary

update_dict_recursively(to_update, to_read)

param to_update

Dictionary to update in-place.

write_config(conf, filename)

util

Miscellaneous utility functions for the Pogona simulator.