Source code for chaste_codegen.backward_euler_opt_model

from sympy import Eq

from chaste_codegen._lookup_tables import DEFAULT_LOOKUP_PARAMETERS, LookupTables
from chaste_codegen._partial_eval import partial_eval
from chaste_codegen.backward_euler_model import BackwardEulerModel


[docs]class BackwardEulerOptModel(BackwardEulerModel): """ Holds information specific for the Optimised Backward Euler model type.""" def __init__(self, model, file_name, **kwargs): self._lookup_tables = LookupTables(model, lookup_params=kwargs.get('lookup_table', DEFAULT_LOOKUP_PARAMETERS)) super().__init__(model, file_name, **kwargs) self._vars_for_template['model_type'] += 'Opt' self._update_formatted_deriv_eq() self._vars_for_template['lookup_parameters'] = self._lookup_tables.print_lookup_parameters(self._printer) def _get_stimulus(self): """ Get the partially evaluated stimulus currents in the model""" return_stim_eqs = super()._get_stimulus() return partial_eval(return_stim_eqs, self._model.stimulus_params | self._model.modifiable_parameters) def _get_extended_ionic_vars(self): """ Get the partially evaluated equations defining the ionic derivatives and all dependant equations""" extended_ionic_vars = partial_eval(super()._get_extended_ionic_vars(), self._model.ionic_vars) self._lookup_tables.calc_lookup_tables(extended_ionic_vars) return extended_ionic_vars def _get_derivative_equations(self): """ Get partially evaluated equations defining the derivatives including V (self._model.membrane_voltage_var)""" derivative_equations = partial_eval(super()._get_derivative_equations(), self._model.y_derivatives) self._lookup_tables.calc_lookup_tables(derivative_equations) return derivative_equations def _pre_print_hook(self): """ Retreives out linear and non-linear derivatives and the relevant jacobian for it. And calculates lookup tables for the jacobian.""" super()._pre_print_hook() # calculate lookup tables for the jacobians created by the Backward Euler self._lookup_tables.calc_lookup_tables((Eq(lhs, rhs) for lhs, rhs in self._jacobian_equations)) def _update_formatted_deriv_eq(self): """Update derivatibve equation information for lookup table printing""" for eq in self._vars_for_template['y_derivative_equations']: if not eq['linear']: with self._lookup_tables.method_being_printed('ComputeResidual'): eq['rhs'] = self._printer.doprint(eq['sympy_rhs']) if eq['in_membrane_voltage']: with self._lookup_tables.method_being_printed('UpdateTransmembranePotential'): eq['rhs'] = self._printer.doprint(eq['sympy_rhs']) def _add_printers(self): """ Initialises Printers for outputting chaste code. """ super()._add_printers(lookup_table_function=self._lookup_tables.print_lut_expr) def _format_ionic_vars(self): """ Format equations and dependant equations ionic derivatives""" with self._lookup_tables.method_being_printed('GetIIonic'): return super()._format_ionic_vars() def _format_derivative_equations(self, derivative_equations): """ Format derivative equations for chaste output""" with self._lookup_tables.method_being_printed('EvaluateYDerivatives'): return super()._format_derivative_equations(derivative_equations) def _format_derived_quant_eqs(self): """ Format equations for derived quantities based on current settings""" with self._lookup_tables.method_being_printed('ComputeDerivedQuantities'): return super()._format_derived_quant_eqs()
[docs] def format_linear_deriv_eqs(self, linear_deriv_eqs): """ Format linear derivative equations beloning, to update what belongs were""" with self._lookup_tables.method_being_printed('ComputeOneStepExceptVoltage'): return super().format_linear_deriv_eqs(linear_deriv_eqs)
[docs] def format_jacobian(self): """Format the jacobian to update what belongs were""" with self._lookup_tables.method_being_printed('ComputeJacobian'): return super().format_jacobian()