amici.ode_model.State

class amici.ode_model.State(identifier, name, init, dt)[source]

A State variable defines an entity that evolves with time according to the provided time derivative, abbreviated by x.

Variables

_conservation_law – algebraic formula that allows computation of this state according to a conservation law
_dt – algebraic formula that defines the temporal derivative of this state

__init__(identifier, name, init, dt)[source]

Create a new State instance. Extends ModelQuantity.__init__() by dt

Parameters

identifier (sympy.core.symbol.Symbol) – unique identifier of the state
name (str) – individual name of the state (does not need to be unique)
init (sympy.core.expr.Expr) – initial value
dt (sympy.core.expr.Expr) – time derivative

Methods Summary

`__init__`(identifier, name, init, dt)	Create a new State instance.
`get_dt`()	Gets the time derivative
`get_dx_rdata_dx_solver`(state_id)	Returns the expression that allows computation of `dx_rdata_dx_solver` for this state, accounting for conservation laws.
`get_free_symbols`()	Gets the set of free symbols in time derivative and initial conditions
`get_id`()	ModelQuantity identifier
`get_name`()	ModelQuantity name
`get_val`()	ModelQuantity value
`get_x_rdata`()	Returns the expression that allows computation of x_rdata for this state, accounting for conservation laws.
`has_conservation_law`()	Checks whether this state has a conservation law assigned.
`set_conservation_law`(law)	Sets the conservation law of a state.
`set_dt`(dt)	Sets the time derivative
`set_val`(val)	Set ModelQuantity value

Methods

__init__(identifier, name, init, dt)[source]

Create a new State instance. Extends ModelQuantity.__init__() by dt

Parameters

identifier (sympy.core.symbol.Symbol) – unique identifier of the state
name (str) – individual name of the state (does not need to be unique)
init (sympy.core.expr.Expr) – initial value
dt (sympy.core.expr.Expr) – time derivative

get_dt()[source]

Gets the time derivative

Return type: sympy.core.expr.Expr
Returns: time derivative

get_dx_rdata_dx_solver(state_id)[source]

Returns the expression that allows computation of dx_rdata_dx_solver for this state, accounting for conservation laws.

Returns: dx_rdata_dx_solver expression

get_free_symbols()[source]

Gets the set of free symbols in time derivative and initial conditions

Return type: typing.Set[sympy.core.basic.Basic]
Returns: free symbols

get_id()

ModelQuantity identifier

Return type: sympy.core.symbol.Symbol
Returns: identifier of the ModelQuantity

get_name()

ModelQuantity name

Return type: str
Returns: name of the ModelQuantity

get_val()

ModelQuantity value

Return type: sympy.core.expr.Expr
Returns: value of the ModelQuantity

get_x_rdata()[source]

Returns the expression that allows computation of x_rdata for this state, accounting for conservation laws.

Returns: x_rdata expression

has_conservation_law()[source]

Checks whether this state has a conservation law assigned.

Returns: True if assigned, False otherwise

set_conservation_law(law)[source]

Sets the conservation law of a state.

If a conservation law is set, the respective state will be replaced by an algebraic formula according to the respective conservation law.

Parameters: law (amici.ode_model.ConservationLaw) – linear sum of states that if added to this state remain constant over time
Return type: None

set_dt(dt)[source]

Sets the time derivative

Parameters: dt (sympy.core.expr.Expr) – time derivative
Return type: None

set_val(val)

Set ModelQuantity value

Returns: value of the ModelQuantity