System

System(
    porosity,
    discharge,
    cells,
    advection,
    dispersion,
    species_is_mobile,
    reactions=list(),
    bcs=list(),
    parameters=None,
)

Represents a 1D reactive transport system.

This class encapsulates all the components needed to model reactive transport in a 1D domain, including spatial discretization, advection, dispersion, species mobility, reactions, and boundary conditions.

Parameters

Name	Type	Description	Default
porosity	jax.Array	Porosity of the medium, either scalar or per cell.	required
discharge	Callable[[jax.Array], jax.Array]	Function that computes discharge given time.	required
cells	Cells	Spatial discretization of the domain.	required
advection	Advection	Advection scheme parameters.	required
dispersion	Dispersion	Dispersion scheme parameters.	required
species_is_mobile	AbstractSpecies	Species mobility information.	required
reactions	list[KineticReaction]	List of kinetic reactions. Default is empty list.	list()
bcs	list[BoundaryCondition]	List of boundary conditions. Default is empty list.	list()
parameters	Any	Additional system parameters. Default is None. Must be created with @user_system_parameters for spatial awareness and JAX compatibility.	None

Methods

Name	Description
build	Build a configured reactive transport system.
cell_velocity	Compute the pore-water velocity in each cell.

build

System.build(
    cells,
    advection,
    dispersion,
    bcs=None,
    species_is_mobile,
    reactions=None,
    discharge,
    porosity,
    parameters=None,
)

Build a configured reactive transport system.

This convenience constructor validates input shapes and normalizes scalar inputs before creating a System instance.

Parameters

Name	Type	Description	Default
cells	Cells	Spatial discretization of the domain.	required
advection	Advection	Advection scheme parameters.	required
dispersion	Dispersion	Dispersion scheme parameters.	required
bcs	list[BoundaryCondition] or None	List of boundary conditions. Default is None.	None
species_is_mobile	AbstractSpecies	Species mobility information.	required
reactions	list[BoundaryCondition] or None	List of kinetic reactions. Default is None.	None
discharge	Callable[[jax.Array], jax.Array] or jax.Array	Discharge function or scalar discharge value.	required
porosity	jax.Array	Porosity of the medium, either scalar or per cell.	required
parameters	Any or None	Additional system parameters. Default is None. Must be created with @user_system_parameters for spatial operations.	None

Returns

Name	Type	Description
	System	Configured reactive transport system.

Raises

Name	Type	Description
	ValueError	If porosity has an invalid shape or a boundary condition is incompatible with the selected species.

cell_velocity

System.cell_velocity(t)

Compute the pore-water velocity in each cell.

Parameters

Name	Type	Description	Default
t	jax.Array	Current simulation time.	required

Returns

Name	Type	Description
	jax.Array	Velocity in each cell.