Base Model#
- class pybamm.BaseModel(name='Unnamed model')[source]#
Base model class for other models to extend.
- rhs#
A dictionary that maps expressions (variables) to expressions that represent the rhs.
- Type:
- algebraic#
A dictionary that maps expressions (variables) to expressions that represent the algebraic equations. The algebraic expressions are assumed to equate to zero. Note that all the variables in the model must exist in the keys of rhs or algebraic.
- Type:
- initial_conditions#
A dictionary that maps expressions (variables) to expressions that represent the initial conditions for the state variables y. The initial conditions for algebraic variables are provided as initial guesses to a root finding algorithm that calculates consistent initial conditions.
- Type:
- boundary_conditions#
A dictionary that maps expressions (variables) to expressions that represent the boundary conditions.
- Type:
- variables#
A dictionary that maps strings to expressions that represent the useful variables.
- Type:
- events#
A list of events. Each event can either cause the solver to terminate (e.g. concentration goes negative), or be used to inform the solver of the existance of a discontinuity (e.g. discontinuity in the input current).
- Type:
list of
pybamm.Event
- concatenated_rhs#
After discretisation, contains the expressions representing the rhs equations concatenated into a single expression.
- Type:
- concatenated_algebraic#
After discretisation, contains the expressions representing the algebraic equations concatenated into a single expression.
- Type:
- concatenated_initial_conditions#
After discretisation, contains the vector of initial conditions.
- Type:
numpy.array
- mass_matrix#
After discretisation, contains the mass matrix for the model. This is computed automatically.
- Type:
- mass_matrix_inv#
After discretisation, contains the inverse mass matrix for the differential (rhs) part of model. This is computed automatically.
- Type:
- jacobian#
Contains the Jacobian for the model. If model.use_jacobian is True, the Jacobian is computed automatically during solver set up.
- Type:
- jacobian_rhs#
Contains the Jacobian for the part of the model which contains time derivatives. If model.use_jacobian is True, the Jacobian is computed automatically during solver set up.
- Type:
- jacobian_algebraic#
Contains the Jacobian for the algebraic part of the model. This may be used by the solver when calculating consistent initial conditions. If model.use_jacobian is True, the Jacobian is computed automatically during solver set up.
- Type:
- convert_to_format#
Whether to convert the expression trees representing the rhs and algebraic equations, Jacobain (if using) and events into a different format:
None: keep PyBaMM expression tree structure.
“python”: convert into pure python code that will calculate the result of calling evaluate(t, y) on the given expression treeself.
“casadi”: convert into CasADi expression tree, which then uses CasADi’s algorithm to calculate the Jacobian.
Default is “casadi”.
- Type:
- check_algebraic_equations(post_discretisation)[source]#
Check that the algebraic equations are well-posed. After discretisation, there must be at least one StateVector in each algebraic equation.
- check_discretised_or_discretise_inplace_if_0D()[source]#
Discretise model if it isn’t already discretised This only works with purely 0D models, as otherwise the mesh and spatial method should be specified by the user
- check_well_determined(post_discretisation)[source]#
Check that the model is not under- or over-determined.
- check_well_posedness(post_discretisation=False)[source]#
Check that the model is well-posed by executing the following tests: - Model is not over- or underdetermined, by comparing keys and equations in rhs and algebraic. Overdetermined if more equations than variables, underdetermined if more variables than equations. - There is an initial condition in self.initial_conditions for each variable/equation pair in self.rhs - There are appropriate boundary conditions in self.boundary_conditions for each variable/equation pair in self.rhs and self.algebraic
- Parameters:
post_discretisation (boolean) – A flag indicating tests to be skipped after discretisation
- property default_solver#
Return default solver based on whether model is ODE/DAE or algebraic
- classmethod deserialise(properties: dict)[source]#
Create a model instance from a serialised object.
- export_casadi_objects(variable_names, input_parameter_order=None)[source]#
Export the constituent parts of the model (rhs, algebraic, initial conditions, etc) as casadi objects.
- Parameters:
variable_names (list) – Variables to be exported alongside the model structure
input_parameter_order (list, optional) – Order in which the input parameters should be stacked. If input_parameter_order=None and len(self.input_parameters) > 1, a ValueError is raised (this helps to avoid accidentally using the wrong order)
- Returns:
casadi_dict – Dictionary of {str: casadi object} pairs representing the model in casadi format
- Return type:
- generate(filename, variable_names, input_parameter_order=None, cg_options=None)[source]#
Generate the model in C, using CasADi.
- Parameters:
filename (str) – Name of the file to which to save the code
variable_names (list) – Variables to be exported alongside the model structure
input_parameter_order (list, optional) – Order in which the input parameters should be stacked. If input_parameter_order=None and len(self.input_parameters) > 1, a ValueError is raised (this helps to avoid accidentally using the wrong order)
cg_options (dict) – Options to pass to the code generator. See https://web.casadi.org/docs/#generating-c-code
- get_parameter_info()[source]#
Extracts the parameter information and returns it as a dictionary. To get a list of all parameter-like objects without extra information, use
model.parameters
.
- info(symbol_name)[source]#
Provides helpful summary information for a symbol.
- Parameters:
parameter_name (str) –
- property input_parameters#
Returns all the input parameters in the model
- latexify(filename=None, newline=True, output_variables=None)[source]#
Converts all model equations in latex.
- Parameters:
filename (str (optional)) – Accepted file formats - any image format, pdf and tex Default is None, When None returns all model equations in latex If not None, returns all model equations in given file format.
newline (bool (optional)) – Default is True, If True, returns every equation in a new line. If False, returns the list of all the equations.
model (Load) –
pybamm.lithium_ion.SPM() (>>> model =) –
png (This will returns all model equations in) –
model.latexify("equations.png") (>>>) –
latex (This will return all the model equations in) –
model.latexify() (>>>) –
equations (This will return first five model) –
model.latexify(newline=False) (>>>) –
equations –
model.latexify(newline=False)[1 (>>>) –
- new_copy()[source]#
Creates a copy of the model, explicitly copying all the mutable attributes to avoid issues with shared objects.
- property parameters#
Returns all the parameters in the model
- print_parameter_info()[source]#
Print parameter information in a formatted table from a dictionary of parameters
- process_parameters_and_discretise(symbol, parameter_values, disc)[source]#
Process parameters and discretise a symbol using supplied parameter values and discretisation. Note: care should be taken if using spatial operators on dimensional symbols. Operators in pybamm are written in non-dimensional form, so may need to be scaled by the appropriate length scale. It is recommended to use this method on non-dimensional symbols.
- Parameters:
symbol (
pybamm.Symbol
) – Symbol to be processedparameter_values (
pybamm.ParameterValues
) – The parameter values to use during processingdisc (
pybamm.Discretisation
) – The discrisation to use
- Returns:
Processed symbol
- Return type:
- save_model(filename=None, mesh=None, variables=None)[source]#
Write out a discretised model to a JSON file
- Parameters:
filename (str, optional) –
provided (The desired name of the JSON file. If no name is) –
created (one will be) –
name (based on the model) –
datetime. (and the current) –
- set_initial_conditions_from(solution, inplace=True, return_type='model')[source]#
Update initial conditions with the final states from a Solution object or from a dictionary. This assumes that, for each variable in self.initial_conditions, there is a corresponding variable in the solution with the same name and size.
- Parameters:
solution (
pybamm.Solution
, or dict) – The solution to use to initialize the modelinplace (bool, optional) – Whether to modify the model inplace or create a new model (default True)
return_type (str, optional) – Whether to return the model (default) or initial conditions (“ics”)
- update(*submodels)[source]#
Update model to add new physics from submodels
- Parameters:
submodel (iterable of
pybamm.BaseModel
) – The submodels from which to create new model
- property variables_and_events#
Returns variables and events in a single dictionary