emulsim.actors.autonomous.fields module

Provides actors that influence scalar fields.

`LocalReactionsActor`	Actor simulating a local chemical reactions in a field.
`ScalarPDEActor`	Actor evolving a field according to a PDE.
`DiffusionActor`	Actor evolving a field according to a simple diffusion equation.
`ReactionDiffusionActor`	Actor evolving a field according to a reaction-diffusion equation.
`CollectionPDEActor`	Actor evolving a field collection according to a PDE.

class CollectionPDEActor(pde: PDEBase, parameters: dict[str, Any] | None = None)[source]

Bases: ActorBase

Actor evolving a field collection according to a PDE.

Initialize the actor and its PDE.

Parameters:

pde (PDEBase) – The partial differential equation describing the dynamics of the scalar field.
parameters (dict) – Parameters affecting the actor. Call show_parameters() for details.

copy() → CollectionPDEActor[source]: Returns a copy the actor.

element_classes: tuple[type[_ElementBase] | tuple[type[_ElementBase], ...], ...] | EllipsisType = (<class 'emulsim.elements.fields.FieldCollectionElement'>,)

defines the elements this actor handles and in what order they need to be supplied. An ellipsis (…) indicates that all elements and lists of elements are accepted. Setting this attribute allows internal consistency checks.

Type:: tuple

evolve(elements: tuple[FieldCollectionElement], t: float, dt: float)[source]

Evolve the field from time t to t + dt

Parameters:

elements (tuple of ScalarFieldElement) – The element affected by the actor
t (float) – The current time point
dt (float) – The time step used to evolve the element

property info: dict[str, Any]

information about the actor

Type:: dict

make_evolver_numba(elements: tuple[FieldCollectionElement]) → Callable[[tuple[ndarray], float, float], None][source]

Return a function evolving the field from time t to t + dt

Parameters:

elements (tuple of ScalarFieldElement) – The element affected by the actor

Returns:

A function with signature (field_data, t: float,: dt: float), which evolves the field_data.

Return type:

callable

class DiffusionActor(parameters: dict[str, Any] | None = None)[source]

Bases: ScalarPDEActor

Actor evolving a field according to a simple diffusion equation.

Parameters Dictionary:

boundary_conditions: Defines the boundary conditions on the field.Boundary conditions are generally given as a dictionary with one condition for

each axis side (default=’auto_periodic_neumann’)

diffusivity: Diffusivity in the field (default=1.0)

Parameters:: parameters (dict) – Parameters affecting the actor. Call show_parameters() for details.

Parameters of DiffusionActor:

diffusivity: Diffusivity in the field. This actor only supports constant diffusivities. Diffusivities depending on local concentration are supported by ReactionDiffusionActor. (Default value: 1.0)
boundary_conditions: Defines the boundary conditions on the field.Boundary conditions are generally given as a dictionary with one condition for each axis side. For periodic axes, only periodic boundary conditions are allowed (indicated by ‘periodic’ and ‘anti-periodic’). For non-periodic axes, different boundary conditions can be specified for the lower and upper end (using specific identifiers, like x- and y+). For instance, Dirichlet conditions enforcing a value NUM (specified by {‘value’: NUM}) and Neumann conditions enforcing the value DERIV for the derivative in the normal direction (specified by {‘derivative’: DERIV}) are supported. Note that the special value ‘auto_periodic_neumann’ imposes periodic boundary conditions for periodic axis and a vanishing derivative otherwise. More information can be found in the boundaries documentation. (Default value: 'auto_periodic_neumann')

estimate_dt(elements: tuple[ScalarFieldElement]) → float[source]

Get the optimal time step for the simulation of the actor.

Parameters:: elements (tuple of ScalarFieldElement) – The element affected by the actor
Returns:: the time step
Return type:: float

class LocalReactionsActor(parameters: dict[str, Any] | None = None)[source]

Bases: ActorBase

Actor simulating a local chemical reactions in a field.

Parameters Dictionary:

reaction_flux: An expression for the reaction flux in the mean field (default=’0’)

Parameters:: parameters (dict) – Parameters affecting the actor. Call show_parameters() for details.

Parameters of LocalReactionsActor:

reaction_flux: An expression for the reaction flux in the mean field. The expression may depend on the concentration and time, which are denoted by the variables c and t respectively. (Default value: '0')

element_classes: tuple[type[_ElementBase] | tuple[type[_ElementBase], ...], ...] | EllipsisType = (<class 'emulsim.elements.fields.FieldElementBase'>,)

defines the elements this actor handles and in what order they need to be supplied. An ellipsis (…) indicates that all elements and lists of elements are accepted. Setting this attribute allows internal consistency checks.

Type:: tuple

estimate_dt(elements: tuple[FieldElementBase]) → float[source]

Get the optimal time step for the simulation of the actor.

Parameters:: elements (tuple of MeanfieldElement) – The element affected by the actor

evolve(elements: tuple[FieldElementBase], t: float, dt: float)[source]

Evolve the field from time t to t + dt

Parameters:

elements (tuple of MeanfieldElement) – The element affected by the actor
t (float) – The current time point
dt (float) – The time step used to evolve the element

make_evolver_numba(elements: tuple[FieldElementBase]) → Callable[[tuple[ndarray], float, float], None][source]

Return a function evolve the field from time t to t + dt

Parameters:

elements (tuple of MeanfieldElement) – The element affected by the actor

Returns:

A function with signature (field_data, t: float,: dt: float), which evolves the field_data.

Return type:

callable

class MeanfieldActor(parameters: dict[str, Any] | None = None)[source]

Bases: LocalReactionsActor

Parameters Dictionary: * reaction_flux: An expression for the reaction flux in the mean field (default=’0’)

Parameters:: parameters (dict) – Parameters affecting the actor. Call show_parameters() for details.

Parameters of MeanfieldActor:

reaction_flux: An expression for the reaction flux in the mean field. The expression may depend on the concentration and time, which are denoted by the variables c and t respectively. (Default value: '0')

class ReactionDiffusionActor(parameters: dict[str, Any] | None = None)[source]

Bases: ScalarPDEActor

Actor evolving a field according to a reaction-diffusion equation.

This class relies on the optional phasesep package, which needs to be installed separately.

Parameters Dictionary:

boundary_conditions: Defines the boundary conditions on the field.Boundary conditions are generally given as a dictionary with one condition for

each axis side (default=’auto_periodic_neumann’)

diffusivity: Diffusivity in the field (default=’1’)
expression_constants: A dictionary defining values of constants that can be used in expressions, e.g., the parameter reaction_flux. (default={})
reaction_flux: An expression for the reaction flux in the field, which can depend on the concentration (denoted by c or phi), spatial coordinates (denoted by x[i], where i is the dimension), and time t. (default=’0’)

Parameters:: parameters (dict) – Parameters affecting the actor. Call show_parameters() for details

Parameters of ReactionDiffusionActor:

diffusivity: Diffusivity in the field. This can be an expression depending on the local concentration that is parsed by sympy. Alternatively, simple numbers are also supported. (Default value: '1')
reaction_flux: An expression for the reaction flux in the field, which can depend on the concentration (denoted by c or phi), spatial coordinates (denoted by x[i], where i is the dimension), and time t. (Default value: '0')
boundary_conditions: Defines the boundary conditions on the field.Boundary conditions are generally given as a dictionary with one condition for each axis side. For periodic axes, only periodic boundary conditions are allowed (indicated by ‘periodic’ and ‘anti-periodic’). For non-periodic axes, different boundary conditions can be specified for the lower and upper end (using specific identifiers, like x- and y+). For instance, Dirichlet conditions enforcing a value NUM (specified by {‘value’: NUM}) and Neumann conditions enforcing the value DERIV for the derivative in the normal direction (specified by {‘derivative’: DERIV}) are supported. Note that the special value ‘auto_periodic_neumann’ imposes periodic boundary conditions for periodic axis and a vanishing derivative otherwise. More information can be found in the boundaries documentation. (Default value: 'auto_periodic_neumann')
expression_constants: A dictionary defining values of constants that can be used in expressions, e.g., the parameter reaction_flux. (Default value: {})

estimate_dt(elements: tuple[ScalarFieldElement]) → float[source]

Get the optimal time step for the simulation of the actor.

Parameters:: elements (tuple of ScalarFieldElement) – The element affected by the actor
Returns:: the time step
Return type:: float

class ScalarPDEActor(pde: PDEBase, parameters: dict[str, Any] | None = None)[source]

Bases: ActorBase

Actor evolving a field according to a PDE.

Initialize the actor and its PDE.

Parameters:

pde (PDEBase) – The partial differential equation describing the dynamics of the scalar field.
parameters (dict) – Parameters affecting the actor. Call show_parameters() for details.

copy() → ScalarPDEActor[source]: Returns a copy the actor.

element_classes: tuple[type[_ElementBase] | tuple[type[_ElementBase], ...], ...] | EllipsisType = (<class 'emulsim.elements.fields.ScalarFieldElement'>,)

defines the elements this actor handles and in what order they need to be supplied. An ellipsis (…) indicates that all elements and lists of elements are accepted. Setting this attribute allows internal consistency checks.

Type:: tuple

evolve(elements: tuple[ScalarFieldElement], t: float, dt: float)[source]

Evolve the field from time t to t + dt

Parameters:

elements (tuple of ScalarFieldElement) – The element affected by the actor
t (float) – The current time point
dt (float) – The time step used to evolve the element

property info: dict[str, Any]

information about the actor

Type:: dict

make_evolver_numba(elements: tuple[ScalarFieldElement]) → Callable[[tuple[ndarray], float, float], None][source]

Return a function evolving the field from time t to t + dt

Parameters:

elements (tuple of ScalarFieldElement) – The element affected by the actor

Returns:

A function with signature (field_data, t: float,: dt: float), which evolves the field_data.

Return type:

callable

pde: PDEBase