Inheritance diagram for CellMLToNektar.pycml.mathml_diff:

[legend]

Public Member Functions
def	independent_variable (self)

def	dependent_variable (self)

Public Member Functions inherited from CellMLToNektar.pycml.mathml_operator
def	wrong_number_of_operands (self, found, wanted)

Public Member Functions inherited from CellMLToNektar.pycml.mathml
def	__init__ (self)

def	__repr__ (self)

def	__deepcopy__ (self, memo)

def	clone_self (self, register=False)

def	get_original_of_clone (self)

def	get_component (self)

def	model (self)

def	eval (self, elt)

Public Member Functions inherited from CellMLToNektar.pycml.element_base
def	__init__ (self)

def	__delattr__ (self, key)

def	__setattr__ (self, key, value)

def	rootNode (self)

def	cmeta_id (self)

def	xml_remove_child_at (self, index=-1)

def	xml_doc (self)

def	xml_properties (self)

Static Public Member Functions
def	create_new (elt, bvar, state_var, rhs)

Static Public Member Functions inherited from CellMLToNektar.pycml.mathml
def	clone (expr)

Private Member Functions
def	_set_var_types (self)

def	_get_binding_time (self)

def	_reduce (self)

Additional Inherited Members
Public Attributes inherited from CellMLToNektar.pycml.element_base
	xml_attributes

Properties inherited from CellMLToNektar.pycml.mathml
	component = property(get_component)

Detailed Description

Class representing the diff element, containing some useful methods.

Definition at line 5416 of file pycml.py.

Member Function Documentation

◆ _get_binding_time()

def CellMLToNektar.pycml.mathml_diff._get_binding_time ( self )

private

Return the binding time of the enclosing <apply> element.

This is the binding time of the expression defining this ODE.

Definition at line 5483 of file pycml.py.

    def _get_binding_time(self):
        """Return the binding time of the enclosing <apply> element.
 
        This is the binding time of the expression defining this ODE.
        """
        expr = self.dependent_variable.get_ode_dependency(
            self.independent_variable)
        return expr._get_binding_time()
 

References CellMLToNektar.pycml.mathml_diff.dependent_variable(), and CellMLToNektar.pycml.mathml_diff.independent_variable().

Referenced by CellMLToNektar.pycml.mathml_ci._reduce(), CellMLToNektar.pycml.mathml_apply._reduce(), CellMLToNektar.pycml.mathml_piecewise._reduce(), CellMLToNektar.pycml.cellml_variable.get_value(), and CellMLToNektar.pycml.cellml_variable.is_statically_const().

◆ _reduce()

def CellMLToNektar.pycml.mathml_diff._reduce ( self )

private

Reduce this expression by evaluating its static parts.

If the whole expression is static, proceed as normal for an
<apply>.  Otherwise just rename the variable references.  We
can't instantiate the definition, because there will always be
another user - external code.

This operator is special cased because we need to alter its
qualifier, but mathml_apply only considers operands.  MathML
data binding can be annoying at times!

Definition at line 5492 of file pycml.py.

    def _reduce(self):
        """Reduce this expression by evaluating its static parts.
 
        If the whole expression is static, proceed as normal for an
        <apply>.  Otherwise just rename the variable references.  We
        can't instantiate the definition, because there will always be
        another user - external code.
        
        This operator is special cased because we need to alter its
        qualifier, but mathml_apply only considers operands.  MathML
        data binding can be annoying at times!
        """
        app = self.xml_parent
        bt = app._get_binding_time()
        if bt == BINDING_TIMES.static:
            # Evaluate this expression as normal
            app._reduce(check_operator=False)
        else:
            # Just update names to be canonical.
            for ci in [app.ci, app.bvar.ci]:
                ci._set_variable_obj(ci.variable.get_source_variable(recurse=True))
                ci._rename()
 

◆ _set_var_types()

def CellMLToNektar.pycml.mathml_diff._set_var_types ( self )

private

Set the types of the dependent & independent variables: State for
the dependent variable and Free for the independent variable.
Gives a validation warning if they already have 'incompatible'
types.

Definition at line 5441 of file pycml.py.

    def _set_var_types(self):
        """
        Set the types of the dependent & independent variables: State for
        the dependent variable and Free for the independent variable.
        Gives a validation warning if they already have 'incompatible'
        types.
        """
        dep, indep = self.dependent_variable, self.independent_variable
        model = self.xml_parent.model
        
        # The dependent variable should have an initial value
        if not dep.get_type() == VarTypes.Mapped and \
               not hasattr(dep, u'initial_value'):
            model.validation_warning(u' '.join([
                u'The state variable',dep.fullname(),
                u'does not have an initial value given.']),
                                     level=logging.WARNING_TRANSLATE_ERROR)
        # It doesn't make sense to compute a state variable
        if dep.get_type(follow_maps=True) == VarTypes.Computed:
            model.validation_warning(u' '.join([
                u'The state variable',dep.fullname(),
                u'is also assigned to directly.']),
                                     level=logging.WARNING_TRANSLATE_ERROR)
        dep._set_type(VarTypes.State)
        
        t = indep.get_type(follow_maps=True)
        if t != VarTypes.Free:
            if t != VarTypes.Unknown:
                if t == VarTypes.Computed:
                    reason = u'is computed in an expression.'
                elif t == VarTypes.State:
                    reason = u'is a state variable itself.'
                else:
                    reason = u'has an initial value specified.'
                model.validation_warning(u' '.join([
                    u'The derivative of',dep.fullname(),
                    u'is taken with respect to',indep.fullname(),
                    u'but the latter', reason]),
                                         level=logging.WARNING_TRANSLATE_ERROR)
            # TODO: Add to list of independent vars?
            indep._set_type(VarTypes.Free)
 

References CellMLToNektar.pycml.mathml_diff.dependent_variable(), and CellMLToNektar.pycml.mathml_diff.independent_variable().

◆ create_new()

def CellMLToNektar.pycml.mathml_diff.create_new	(	elt,
		bvar,
		state_var,
		rhs
	)

static

Construct an ODE expression: d(state_var)/d(bvar) = rhs.

Definition at line 5516 of file pycml.py.

    def create_new(elt, bvar, state_var, rhs):
        """Construct an ODE expression: d(state_var)/d(bvar) = rhs."""
        bvar_elt = elt.xml_create_element(u'bvar', NSS[u'm'])
        bvar_elt.xml_append(mathml_ci.create_new(elt, bvar))
        diff = mathml_apply.create_new(elt, u'diff', [state_var], [bvar_elt])
        ode = mathml_apply.create_new(elt, u'eq', [diff, rhs])
        return ode
 

◆ dependent_variable()

def CellMLToNektar.pycml.mathml_diff.dependent_variable ( self )

Return the variable object being differentiated.

Definition at line 5431 of file pycml.py.

    def dependent_variable(self):
        """
        Return the variable object being differentiated.
        """
        apply_elt = self.xml_parent
        operand = apply_elt.operands().next()
        if not operand.localName == u'ci':
            raise MathsError(apply_elt, u'Derivatives of non-variables are not supported.')
        return operand.variable
 

Referenced by CellMLToNektar.pycml.mathml_diff._get_binding_time(), and CellMLToNektar.pycml.mathml_diff._set_var_types().

◆ independent_variable()

def CellMLToNektar.pycml.mathml_diff.independent_variable ( self )

Return the variable object w.r.t which we are differentiating.

Definition at line 5419 of file pycml.py.

    def independent_variable(self):
        """
        Return the variable object w.r.t which we are differentiating.
        """
        # Note that after units checking the <bvar> qualifier can be
        # assumed to exist.
        apply_elt = self.xml_parent
        if not hasattr(apply_elt.bvar, u'ci'):
            raise MathsError(apply_elt, u'Differential operator does not have a variable element as bound variable.')
        return apply_elt.bvar.ci.variable
 

Referenced by CellMLToNektar.pycml.mathml_diff._get_binding_time(), and CellMLToNektar.pycml.mathml_diff._set_var_types().

Public Member Functions

Static Public Member Functions

Private Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ _get_binding_time()

◆ _reduce()

◆ _set_var_types()

◆ create_new()

◆ dependent_variable()

◆ independent_variable()