amici.ode_model.ConservationLaw

class amici.ode_model.ConservationLaw(identifier, name, value, coefficients, state_id)[source]

A conservation law defines the absolute the total amount of a (weighted) sum of states

__init__(identifier, name, value, coefficients, state_id)[source]

Create a new ConservationLaw instance.

Parameters

identifier (sympy.core.symbol.Symbol) – unique identifier of the ConservationLaw
name (str) – individual name of the ConservationLaw (does not need to be unique)
value (sympy.core.expr.Expr) – formula (sum of states)
coefficients (typing.Dict[sympy.core.symbol.Symbol, sympy.core.expr.Expr]) – coefficients of the states in the sum
state_id (sympy.core.symbol.Symbol) – identifier of the state that this conservation law replaces

Methods Summary

`__init__`(identifier, name, value, ...)	Create a new ConservationLaw instance.
`get_id`()	ModelQuantity identifier
`get_name`()	ModelQuantity name
`get_ncoeff`(state_id)	Computes the normalized coefficient a_i/a_j where i is the index of the provided state_id and j is the index of the state that is replaced by this conservation law.
`get_val`()	ModelQuantity value
`get_x_rdata`()	Returns the expression that allows computation of x_rdata for the state that this conservation law replaces.
`set_val`(val)	Set ModelQuantity value

Methods

__init__(identifier, name, value, coefficients, state_id)[source]

Create a new ConservationLaw instance.

Parameters

identifier (sympy.core.symbol.Symbol) – unique identifier of the ConservationLaw
name (str) – individual name of the ConservationLaw (does not need to be unique)
value (sympy.core.expr.Expr) – formula (sum of states)
coefficients (typing.Dict[sympy.core.symbol.Symbol, sympy.core.expr.Expr]) – coefficients of the states in the sum
state_id (sympy.core.symbol.Symbol) – identifier of the state that this conservation law replaces

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_ncoeff(state_id)[source]

Computes the normalized coefficient a_i/a_j where i is the index of the provided state_id and j is the index of the state that is replaced by this conservation law. This can be used to compute both dtotal_cl/dx_rdata (=ncoeff) and dx_rdata/dx_solver (=-ncoeff).

Parameters: state_id – identifier of the state
Return type: typing.Union[sympy.core.expr.Expr, int, float]
Returns: normalized coefficent of the state

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 the state that this conservation law replaces.

Returns: x_rdata expression

set_val(val)

Set ModelQuantity value

Returns: value of the ModelQuantity