ContractingGeometry Class Reference

Contracting geometry model in the context of solid-state reaction kinetics. More...

Detailed Description

Contracting geometry model in the context of solid-state reaction kinetics.

#include <ContractingGeometry.h>

Inheritance diagram for ContractingGeometry:

Public Member Functions
	ContractingGeometry (const OptionSet &options)
Public Member Functions inherited from ReactionMechanism
	ReactionMechanism (const OptionSet &options)
Public Member Functions inherited from Model
	Model (const OptionSet &options)
	Construct a new Model object.
void	setup () override
	Setup this object.
void	diagnose () const override
	Check for common problems.
virtual bool	defines_values () const
	Whether this model defines output values.
virtual bool	defines_derivatives () const
	Whether this model defines first derivatives.
virtual bool	defines_second_derivatives () const
	Whether this model defines second derivatives.
virtual bool	is_jit_enabled () const
	Whether JIT is enabled.
virtual void	to (const TensorOptions &options)
	Send model to a different device or dtype.
const std::vector< std::shared_ptr< Model > > &	registered_models () const
	The models that may be used during the evaluation of this model.
std::shared_ptr< Model >	registered_model (const std::string &name) const
	Get a registered model by its name.
void	register_nonlinear_parameter (const std::string &pname, const NonlinearParameter &param)
	Register a nonlinear parameter.
bool	has_nl_param (bool recursive=false) const
	Whether this parameter store has any nonlinear parameter.
const VariableBase *	nl_param (const std::string &) const
	Query the existence of a nonlinear parameter.
virtual std::map< std::string, NonlinearParameter >	named_nonlinear_parameters (bool recursive=false) const
	Get all nonlinear parameters.
std::set< VariableName >	consumed_items () const override
	The variables that this model depends on.
std::set< VariableName >	provided_items () const override
	The variables that this model defines as part of its output.
void	request_AD (VariableBase &y, const VariableBase &u)
	Request to use AD to compute the first derivative of a variable.
void	request_AD (VariableBase &y, const VariableBase &u1, const VariableBase &u2)
	Request to use AD to compute the second derivative of a variable.
void	clear_input () override
void	clear_output () override
void	zero_undefined_input () override
	Fill undefined input variables with zeros.
void	forward_maybe_jit (bool out, bool dout, bool d2out)
	Forward operator with jit.
std::string	variable_name_lookup (const ATensor &var) const
	Look up the name of a variable in the traced graph.
virtual ValueMap	value (const ValueMap &in)
	Convenient shortcut to construct and return the model value.
virtual std::tuple< ValueMap, DerivMap >	value_and_dvalue (const ValueMap &in)
	Convenient shortcut to construct and return the model value and its derivative.
virtual DerivMap	dvalue (const ValueMap &in)
	Convenient shortcut to construct and return the derivative.
virtual std::tuple< ValueMap, DerivMap, SecDerivMap >	value_and_dvalue_and_d2value (const ValueMap &in)
	Convenient shortcut to construct and return the model's value, first and second derivative.
virtual SecDerivMap	d2value (const ValueMap &in)
	Convenient shortcut to construct and return the model's second derivative.
virtual std::tuple< DerivMap, SecDerivMap >	dvalue_and_d2value (const ValueMap &in)
	Convenient shortcut to construct and return the model's first and second derivative.
Public Member Functions inherited from Data
	Data (const OptionSet &options)
	Construct a new Data object.
const std::vector< std::shared_ptr< Data > > &	registered_data () const
	All the registered data objects.
Public Member Functions inherited from NEML2Object
	NEML2Object ()=delete
	NEML2Object (NEML2Object &&)=delete
	NEML2Object (const NEML2Object &)=delete
NEML2Object &	operator= (NEML2Object &&)=delete
NEML2Object &	operator= (const NEML2Object &)=delete
virtual	~NEML2Object ()=default
	NEML2Object (const OptionSet &options)
	Construct a new NEML2Object object.
const OptionSet &	input_options () const
const std::string &	name () const
	A readonly reference to the object's name.
const std::string &	type () const
	A readonly reference to the object's type.
const std::string &	path () const
	A readonly reference to the object's path.
const std::string &	doc () const
	A readonly reference to the object's docstring.
Factory *	factory () const
	Get the factory that created this object.
const Settings &	settings () const
	Settings.
template<typename T = NEML2Object>
const T *	host () const
	Get a readonly pointer to the host.
template<typename T = NEML2Object>
T *	host ()
	Get a writable pointer to the host.
template<typename T>
const T &	resolve_tensor (const std::string &name)
	Resolve a TensorName to a Tensor.
template<class T>
std::shared_ptr< T >	get_object (const std::string &section, const std::string &name)
template<class T = EquationSystem>
std::shared_ptr< T >	get_es (const std::string &name)
	Get an equation system from the factory.
template<class T = Solver>
std::shared_ptr< T >	get_solver (const std::string &name)
	Get a solver from the factory.
template<class T = Data>
std::shared_ptr< T >	get_data (const std::string &name)
	Get a data from the factory.
template<class T = Model>
std::shared_ptr< T >	get_model (const std::string &name)
	Get a model from the factory.
template<class T = Driver>
std::shared_ptr< T >	get_driver (const std::string &name)
	Get a driver from the factory.
template<class T = WorkScheduler>
std::shared_ptr< T >	get_scheduler (const std::string &name)
	Get a scheduler from the factory.
Public Member Functions inherited from BufferStore
	BufferStore (NEML2Object *object)
	BufferStore (const BufferStore &)=delete
	BufferStore (BufferStore &&)=delete
BufferStore &	operator= (const BufferStore &)=delete
BufferStore &	operator= (BufferStore &&)=delete
virtual	~BufferStore ()=default
const std::map< std::string, std::unique_ptr< TensorValueBase > > &	named_buffers () const
std::map< std::string, std::unique_ptr< TensorValueBase > > &	named_buffers ()
const TensorValueBase &	get_buffer (const std::string &name) const
	}@
TensorValueBase &	get_buffer (const std::string &name)
	Get a writable reference of a buffer.
Public Member Functions inherited from ParameterStore
	ParameterStore (NEML2Object *object)
	ParameterStore (const ParameterStore &)=delete
	ParameterStore (ParameterStore &&)=delete
ParameterStore &	operator= (const ParameterStore &)=delete
ParameterStore &	operator= (ParameterStore &&)=delete
virtual	~ParameterStore ()=default
const std::map< std::string, std::unique_ptr< TensorValueBase > > &	named_parameters () const
std::map< std::string, std::unique_ptr< TensorValueBase > > &	named_parameters ()
const TensorValueBase &	get_parameter (const std::string &name) const
	}@
TensorValueBase &	get_parameter (const std::string &name)
	Get a writable reference of a parameter.
void	set_parameter (const std::string &, const Tensor &)
	Set the value for a parameter.
void	set_parameters (const std::map< std::string, Tensor > &)
	Set values for parameters.
Public Member Functions inherited from VariableStore
	VariableStore (Model *object)
	VariableStore (const VariableStore &)=delete
	VariableStore (VariableStore &&)=delete
VariableStore &	operator= (const VariableStore &)=delete
VariableStore &	operator= (VariableStore &&)=delete
virtual	~VariableStore ()=default
LabeledAxis &	declare_axis (const std::string &name)
const TensorOptions &	variable_options () const
	Current tensor options for variables.
LabeledAxis &	input_axis ()
const LabeledAxis &	input_axis () const
LabeledAxis &	output_axis ()
const LabeledAxis &	output_axis () const
VariableStorage &	input_variables ()
const VariableStorage &	input_variables () const
VariableStorage &	output_variables ()
const VariableStorage &	output_variables () const
VariableBase &	input_variable (const VariableName &)
const VariableBase &	input_variable (const VariableName &) const
VariableBase &	output_variable (const VariableName &)
const VariableBase &	output_variable (const VariableName &) const
virtual void	clear_derivatives ()
void	cache_derivative_sparsity ()
void	cache_second_derivative_sparsity ()
	Cache sparsity of second derivatives.
const std::optional< DerivSparsity > &	derivative_sparsity () const
	Derivative sparsity.
const std::optional< SecDerivSparsity > &	second_derivative_sparsity () const
	Second derivative sparsity.
void	assign_input (const ValueMap &vals)
void	assign_input (const std::vector< VariableName > &, const SparseTensorList &)
	Assign input variable values for the given variable names.
void	assign_output (const ValueMap &vals)
	Assign output variable values.
void	assign_output (const std::vector< VariableName > &, const SparseTensorList &)
	Assign output variable values for the given variable names.
void	assign_output_derivatives (const DerivMap &derivs)
	Assign variable derivatives.
void	assign_output_derivatives (const std::vector< VariableName > &, const std::vector< VariableName > &, const SparseTensorList &)
	Assign variable derivatives for the given variable names.
ValueMap	collect_input () const
SparseTensorList	collect_input (const std::vector< VariableName > &) const
	Collect input variable values for the given variable names.
ValueMap	collect_output () const
	Collect output variable values.
SparseTensorList	collect_output (const std::vector< VariableName > &) const
	Collect output variable values for the given variable names.
DerivMap	collect_output_derivatives () const
	Collect variable derivatives.
SparseTensorList	collect_output_derivatives (const std::vector< VariableName > &, const std::vector< VariableName > &) const
	Collect variable derivatives for the given variable names.
SecDerivMap	collect_output_second_derivatives () const
	Collect variable second derivatives.
Public Member Functions inherited from DependencyDefinition< VariableName >
	DependencyDefinition ()=default
DependencyDefinition &	operator= (const DependencyDefinition &)=delete
virtual	~DependencyDefinition ()=default
Public Member Functions inherited from DiagnosticsInterface
	DiagnosticsInterface ()=delete
	DiagnosticsInterface (NEML2Object *object)
	DiagnosticsInterface (DiagnosticsInterface &&)=delete
	DiagnosticsInterface (const DiagnosticsInterface &)=delete
DiagnosticsInterface &	operator= (const DiagnosticsInterface &)=delete
DiagnosticsInterface &	operator= (DiagnosticsInterface &&)=delete
virtual	~DiagnosticsInterface ()=default
const NEML2Object &	object () const
	Get the object.

Static Public Member Functions
static OptionSet	expected_options ()
Static Public Member Functions inherited from ReactionMechanism
static OptionSet	expected_options ()
Static Public Member Functions inherited from Model
static OptionSet	expected_options ()
Static Public Member Functions inherited from Data
static OptionSet	expected_options ()
Static Public Member Functions inherited from NEML2Object
static OptionSet	expected_options ()

Protected Member Functions
void	set_value (bool out, bool dout_din, bool d2out_din2) override
	The map between input -> output, and optionally its derivatives.
Protected Member Functions inherited from Model
void	diagnostic_assert_state (const VariableBase &v) const
void	diagnostic_assert_old_state (const VariableBase &v) const
void	diagnostic_assert_force (const VariableBase &v) const
void	diagnostic_assert_old_force (const VariableBase &v) const
void	diagnostic_assert_residual (const VariableBase &v) const
void	diagnostic_check_input_variable (const VariableBase &v) const
void	diagnostic_check_output_variable (const VariableBase &v) const
virtual void	link_input_variables ()
virtual void	link_input_variables (Model *submodel)
virtual void	link_output_variables ()
virtual void	link_output_variables (Model *submodel)
void	check_precision () const
	Check the current default precision and warn if it's not double precision.
virtual std::string	failed_graph_execution_hint () const
	Additional hint to include in the error message when an exception is encountered during execution of the traced graph.
virtual void	request_AD ()
void	forward (bool out, bool dout, bool d2out)
	Forward operator without jit.
template<typename T = Model, typename = typename std::enable_if_t<std::is_base_of_v<Model, T>>>
T &	register_model (const std::string &name, bool merge_input=true)
	Register a model that the current model may use during its evaluation.
template<typename T = Model, typename = typename std::enable_if_t<std::is_base_of_v<Model, T>>>
void	register_model (const std::shared_ptr< T > &model, bool merge_input=true)
	Register a model that the current model may use during its evaluation.
void	assign_input_stack (jit::Stack &stack)
jit::Stack	collect_input_stack () const
Protected Member Functions inherited from Data
template<typename T, typename = typename std::enable_if_t<std::is_base_of_v<Data, T>>>
T &	register_data (const std::string &name)
virtual void	send_buffers_to (const TensorOptions &options)
	Send all buffers to options.
template<typename T, typename = typename std::enable_if_t<std::is_base_of_v<TensorBase<T>, T>>>
const T &	declare_buffer (const std::string &name, const T &rawval)
	Declare a buffer.
template<typename T, typename = typename std::enable_if_t<std::is_base_of_v<TensorBase<T>, T>>>
const T &	declare_buffer (const std::string &name, const TensorName< T > &tensorname)
	Declare a buffer.
template<typename T, typename = typename std::enable_if_t<std::is_base_of_v<TensorBase<T>, T>>>
const T &	declare_buffer (const std::string &name, const std::string &input_option_name)
	Declare a buffer.
void	assign_buffer_stack (jit::Stack &stack)
	Assign stack to buffers.
jit::Stack	collect_buffer_stack () const
	Collect stack from buffers.
virtual void	send_parameters_to (const TensorOptions &options)
	Send parameters to options.
template<typename T, typename = typename std::enable_if_t<std::is_base_of_v<TensorBase<T>, T>>>
const T &	declare_parameter (const std::string &name, const T &rawval)
	Declare a parameter.
template<typename T, typename = typename std::enable_if_t<std::is_base_of_v<TensorBase<T>, T>>>
const T &	declare_parameter (const std::string &name, const TensorName< T > &tensorname, bool allow_nonlinear)
	Declare a parameter.
template<typename T, typename = typename std::enable_if_t<std::is_base_of_v<TensorBase<T>, T>>>
const T &	declare_parameter (const std::string &name, const std::string &input_option_name, bool allow_nonlinear=false)
	Declare a parameter.
void	assign_parameter_stack (jit::Stack &stack)
	Assign stack to parameters.
jit::Stack	collect_parameter_stack () const
	Collect stack from parameters.
Protected Member Functions inherited from VariableStore
virtual void	send_variables_to (const TensorOptions &options)
	Send padding variables to options.
template<typename T>
const Variable< T > &	declare_input_variable (const char *name, bool allow_duplicate=false)
	Declare an input variable.
template<typename T>
const Variable< T > &	declare_input_variable (const VariableName &name, bool allow_duplicate=false)
	Declare an input variable.
template<typename T>
Variable< T > &	declare_output_variable (const char *name)
	Declare an output variable.
template<typename T>
Variable< T > &	declare_output_variable (const VariableName &name)
	Declare an output variable.
const VariableBase *	clone_input_variable (const VariableBase &var, const VariableName &new_name={})
	Clone a variable and put it on the input axis.
VariableBase *	clone_output_variable (const VariableBase &var, const VariableName &new_name={})
	Clone a variable and put it on the output axis.
void	assign_input_stack (jit::Stack &stack)
	Assign stack to input variables.
void	assign_output_stack (jit::Stack &stack, bool out, bool dout, bool d2out)
	Assign stack to output variables and derivatives.
jit::Stack	collect_input_stack () const
	Collect stack from input variables.
jit::Stack	collect_output_stack (bool out, bool dout, bool d2out) const
	Collect stack from output variables and derivatives.

Protected Attributes
const Scalar &	_k
	Rate coefficient.
const Scalar &	_n
	Reaction order.
Protected Attributes inherited from ReactionMechanism
const Variable< Scalar > &	_a
Variable< Scalar > &	_f
Protected Attributes inherited from Model
std::vector< std::shared_ptr< Model > >	_registered_models
	Models this model may use during its evaluation.
Protected Attributes inherited from Data
std::vector< std::shared_ptr< Data > >	_registered_data
	Registered Data objects.

Additional Inherited Members
Public Types inherited from VariableStore
using	VariableStorage = std::map<VariableName, std::unique_ptr<VariableBase>>
using	DerivSparsity = std::vector<std::pair<VariableBase *, const VariableBase *>>
using	SecDerivSparsity

Constructor & Destructor Documentation

ContractingGeometry()

ContractingGeometry

(

const OptionSet &

options

)

Member Function Documentation

expected_options()

OptionSet expected_options ( )

static

set_value()

void set_value ( bool out, bool dout_din, bool d2out_din2 )

overrideprotectedvirtual

The map between input -> output, and optionally its derivatives.

Implements Model.

Member Data Documentation

_k

const Scalar& _k

protected

Rate coefficient.

_n

const Scalar& _n

protected

Reaction order.