A class for integrating ODEs with CVODES. More...

#include <ODE.h>

Inheritance diagram for muq::Modeling::ODE:

Detailed Description

A class for integrating ODEs with CVODES.

Configuration Parameters:

Parameter Key	Type	Default Value	Description
"NonlinearSolver"	ptree	-	A child tree of options for the nonlinear solver. See ODEPiece::NonlinearSolverOptions.
"LinearSolver"	ptree	-	A child tree of options for the linear solver. See ODEPiece::LinearSolverOptions.
"Integrator"	ptree	-	A child tree of options for the nonlinear solver See ODEPiece::IntegratorOptions.

Definition at line 31 of file ODE.h.

Classes
struct	IntegratorOptions

struct	Interface

struct	LinearSolverOptions

struct	NonlinearSolverOptions

Public Member Functions
	ODE (std::shared_ptr< ModPiece > const &rhsIn, Eigen::VectorXd const &evalTimesIn, boost::property_tree::ptree opts=boost::property_tree::ptree())

	ODE (std::shared_ptr< ModPiece > const &rhsIn, Eigen::VectorXd const &evalTimesIn, bool isAuto, boost::property_tree::ptree opts=boost::property_tree::ptree())

virtual	~ODE ()=default

Public Member Functions inherited from muq::Modeling::ModPiece
	ModPiece (std::vector< int > const &inputSizes, std::vector< int > const &outputSizes)

	ModPiece (Eigen::VectorXi const &inputSizes, Eigen::VectorXi const &outputSizes)

virtual	~ModPiece ()=default

virtual double	GetRunTime (const std::string &method="Evaluate") const override
	Get the average run time for one of the implemented methods. More...

virtual void	ResetCallTime () override
	Resets the number of call and times. More...

virtual unsigned long int	GetNumCalls (const std::string &method="Evaluate") const override
	get the number of times one of the implemented methods has been called. More...

virtual std::vector< Eigen::VectorXd > const &	Evaluate (std::vector< Eigen::VectorXd > const &input)
	Evaluate the ModPiece. More...

virtual std::vector< Eigen::VectorXd > const &	Evaluate (ref_vector< Eigen::VectorXd > const &input)

	VARIADIC_TO_REFVECTOR (Evaluate, Eigen::VectorXd, std::vector< Eigen::VectorXd > const &)

virtual Eigen::VectorXd const &	Gradient (unsigned int const outputDimWrt, unsigned int const inputDimWrt, std::vector< Eigen::VectorXd > const &input, Eigen::VectorXd const &sensitivity)
	Compute the Gradient \(J^Tv\). More...

virtual Eigen::VectorXd const &	Gradient (unsigned int const outputDimWrt, unsigned int const inputDimWrt, ref_vector< Eigen::VectorXd > const &input, Eigen::VectorXd const &sensitivity)

Eigen::VectorXd const &	Gradient (unsigned int outWrt, unsigned int inWrt, Eigen::VectorXd const &last, Eigen::VectorXd const &sens)

template<typename... Args>
Eigen::VectorXd const &	Gradient (unsigned int wrtOut, unsigned int wrtIn, Args const &... args)

Eigen::VectorXd const &	ApplyHessian (unsigned int outWrt, unsigned int inWrt1, unsigned int inWrt2, Eigen::VectorXd const &last, Eigen::VectorXd const &sens, Eigen::VectorXd const &vec)

template<typename... Args>
Eigen::VectorXd const &	ApplyHessian (unsigned int wrtOut, unsigned int wrtIn1, unsigned int wrtIn2, Args const &... args)

virtual Eigen::MatrixXd const &	Jacobian (unsigned int const outputDimWrt, unsigned int const inputDimWrt, std::vector< Eigen::VectorXd > const &input)
	Compute the Jacobian of this ModPiece. More...

virtual Eigen::MatrixXd const &	Jacobian (unsigned int const outputDimWrt, unsigned int const inputDimWrt, ref_vector< Eigen::VectorXd > const &input)

template<typename... Args>
Eigen::MatrixXd const &	Jacobian (unsigned int outWrt, unsigned int inWrt, Args const &... args)

template<typename... Args>
Eigen::MatrixXd	JacobianByFD (unsigned int outWrt, unsigned int inWrt, Args const &... args)

template<typename... Args>
Eigen::MatrixXd	ApplyJacobianByFD (unsigned int outWrt, unsigned int inWrt, Args const &... args)

virtual Eigen::VectorXd const &	ApplyJacobian (unsigned int const outputDimWrt, unsigned int const inputDimWrt, std::vector< Eigen::VectorXd > const &input, Eigen::VectorXd const &vec)
	Apply the Jacobian of this ModPiece to a vector. More...

virtual Eigen::VectorXd const &	ApplyJacobian (unsigned int const outputDimWrt, unsigned int const inputDimWrt, ref_vector< Eigen::VectorXd > const &input, Eigen::VectorXd const &vec)

Eigen::VectorXd const &	ApplyJacobian (unsigned int outWrt, unsigned int inWrt, Eigen::VectorXd const &last, Eigen::VectorXd const &sens)

template<typename... Args>
Eigen::VectorXd const &	ApplyJacobian (unsigned int wrtOut, unsigned int wrtIn, Args const &... args)

virtual Eigen::VectorXd	GradientByFD (unsigned int const outputDimWrt, unsigned int const inputDimWrt, std::vector< Eigen::VectorXd > const &input, Eigen::VectorXd const &sensitivity)

virtual Eigen::VectorXd	GradientByFD (unsigned int const outputDimWrt, unsigned int const inputDimWrt, ref_vector< Eigen::VectorXd > const &input, Eigen::VectorXd const &sensitivity)

virtual Eigen::MatrixXd	JacobianByFD (unsigned int const outputDimWrt, unsigned int const inputDimWrt, std::vector< Eigen::VectorXd > const &input)

virtual Eigen::MatrixXd	JacobianByFD (unsigned int const outputDimWrt, unsigned int const inputDimWrt, ref_vector< Eigen::VectorXd > const &input)

virtual Eigen::VectorXd	ApplyJacobianByFD (unsigned int const outputDimWrt, unsigned int const inputDimWrt, std::vector< Eigen::VectorXd > const &input, Eigen::VectorXd const &vec)

virtual Eigen::VectorXd	ApplyJacobianByFD (unsigned int const outputDimWrt, unsigned int const inputDimWrt, ref_vector< Eigen::VectorXd > const &input, Eigen::VectorXd const &vec)

virtual Eigen::VectorXd const &	ApplyHessian (unsigned int const outWrt, unsigned int const inWrt1, unsigned int const inWrt2, std::vector< Eigen::VectorXd > const &input, Eigen::VectorXd const &sens, Eigen::VectorXd const &vec)

virtual Eigen::VectorXd const &	ApplyHessian (unsigned int const outWrt, unsigned int const inWrt1, unsigned int const inWrt2, ref_vector< Eigen::VectorXd > const &input, Eigen::VectorXd const &sens, Eigen::VectorXd const &vec)

virtual Eigen::VectorXd	ApplyHessianByFD (unsigned int const outWrt, unsigned int const inWrt1, unsigned int const inWrt2, std::vector< Eigen::VectorXd > const &input, Eigen::VectorXd const &sens, Eigen::VectorXd const &vec)

virtual Eigen::VectorXd	ApplyHessianByFD (unsigned int const outWrt, unsigned int const inWrt1, unsigned int const inWrt2, ref_vector< Eigen::VectorXd > const &input, Eigen::VectorXd const &sens, Eigen::VectorXd const &vec)

void	EnableCache ()

void	DisableCache ()

bool	CacheStatus () const

virtual void	SetWarnLevel (unsigned int newLevel)

Public Member Functions inherited from muq::Modeling::WorkPiece
	WorkPiece ()
	Create a muq::Modeling::WorkPiece with no fixed number of inputs and outputs and variable input/output types. More...

	WorkPiece (int const num, WorkPiece::Fix const fix=WorkPiece::Fix::Inputs)
	Create a muq::Modeling::WorkPiece with either a fixed number of inputs or outputs and variable input/output types. More...

	WorkPiece (int const numIns, int const numOuts)
	Create a muq::Modeling::WorkPiece with a fixed number of inputs and outputs but variable input/output types. More...

	WorkPiece (std::vector< std::string > const &types, WorkPiece::Fix const fix=WorkPiece::Fix::Inputs)
	Create a muq::Modeling::WorkPiece with either a fixed number of inputs with specified types or a fixed number of outputs with specified types. More...

	WorkPiece (std::map< unsigned int, std::string > const &types, WorkPiece::Fix const fix=WorkPiece::Fix::Inputs)
	Create a muq::Modeling::WorkPiece where either some of the inputs have specified types or some of the outputs have specified types. More...

	WorkPiece (std::map< unsigned int, std::string > const &types, int const num, WorkPiece::Fix const fixTypes=WorkPiece::Fix::Inputs, WorkPiece::Fix const fixNum=WorkPiece::Fix::Inputs)
	Create a muq::Modeling::WorkPiece where either some of the inputs have specified types or some of the outputs have specified types and either the number of inputs or the number of outputs is fixed. More...

	WorkPiece (std::vector< std::string > const &types, int const num)
	Create a muq::Modeling::WorkPiece with a fixed number of inputs with specified types and a fixed number of outputs (of uknown type) More...

	WorkPiece (int const num, std::vector< std::string > const &types)
	Create a muq::Modeling::WorkPiece with a fixed number of outputs with specified types and a fixed number of inputs (of uknown type) More...

	WorkPiece (std::map< unsigned int, std::string > const &inTypes, int const numIns, int const numOuts)
	Create a muq::Modeling::WorkPiece where some of the inputs are known and we know the input and output numbers. More...

	WorkPiece (int const numIns, std::map< unsigned int, std::string > const &outTypes, int const numOuts)
	Create a muq::Modeling::WorkPiece where some of the outputs are known and we know the input and output numbers. More...

	WorkPiece (std::vector< std::string > const &inTypes, std::vector< std::string > const &outTypes)
	Create a muq::Modeling::WorkPiece with a fixed number of inputs and outputs with specified types. More...

	WorkPiece (std::map< unsigned int, std::string > const &inTypes, std::vector< std::string > const &outTypes)
	Create a muq::Modeling::WorkPiece where some of the inputs are known and all of the outputs have specified types. More...

	WorkPiece (std::map< unsigned int, std::string > const &inTypes, int const num, std::vector< std::string > const &outTypes)
	Create a muq::Modeling::WorkPiece where some of the inputs are known with a known number of inputs and all of the outputs have specified types. More...

	WorkPiece (std::vector< std::string > const &inTypes, std::map< unsigned int, std::string > const &outTypes)
	Create a muq::Modeling::WorkPiece where some of the outputs and all of the inputs have specified types. More...

	WorkPiece (std::vector< std::string > const &inTypes, std::map< unsigned int, std::string > const &outTypes, int const num)
	Create a muq::Modeling::WorkPiece where some of the outputs with a known number of outputs and all of the inputs have specified types. More...

	WorkPiece (std::map< unsigned int, std::string > const &inTypes, std::map< unsigned int, std::string > const &outTypes)
	Create a muq::Mdoeling::WorkPiece where some of the inputs and some of the outputs have specified types. More...

	WorkPiece (std::map< unsigned int, std::string > const &inTypes, int const numIn, std::map< unsigned int, std::string > const &outTypes)
	Create a muq::Mdoeling::WorkPiece where some of the inputs and some of the outputs have specified types with a fixed number of inputs. More...

	WorkPiece (std::map< unsigned int, std::string > const &inTypes, std::map< unsigned int, std::string > const &outTypes, int const numOut)
	Create a muq::Mdoeling::WorkPiece where some of the inputs and some of the outputs have specified types with a fixed number of outputs. More...

	WorkPiece (std::map< unsigned int, std::string > const &inTypes, int const numIn, std::map< unsigned int, std::string > const &outTypes, int const numOut)
	Create a muq::Mdoeling::WorkPiece where some of the inputs and some of the outputs have specified types with a fixed number of inputs and outputs. More...

virtual	~WorkPiece ()
	Default destructor. More...

std::vector< boost::any > const &	Evaluate (std::vector< boost::any > const &ins)
	Evaluate this muq::Modeling::WorkPiece. More...

std::vector< boost::any > const &	Evaluate (ref_vector< boost::any > const &ins)
	Evaluate this muq::Modeling::WorkPiece using references to the inputs. More...

std::vector< boost::any > const &	Evaluate ()
	Evaluate this muq::Modeling::WorkPiece in the case that there are no inputs. More...

template<typename... Args>
std::vector< boost::any > const &	Evaluate (Args... args)
	Evalaute this muq::Modeling::WorkPiece using multiple arguments. More...

std::string const &	Name ()
	Get the (unique) name of this work piece. More...

void	SetName (std::string const &newName)
	Set the name of this work piece. More...

std::string	InputType (unsigned int inputNum, bool const demangle=true) const
	Get the input type (if we know it) for a specific input. More...

int	InputSize (unsigned int inputNum) const
	Get the length of a vector valued input with fixed size. More...

void	SetInputSize (unsigned int inputNum, int newSize)

std::string	OutputType (unsigned int outputNum, bool const demangle=true) const
	Get the output type (if we know it) for a specific output. More...

std::map< unsigned int, std::string >	OutputTypes () const
	Get the output types. More...

std::map< unsigned int, std::string >	InputTypes () const
	Get the input types. More...

unsigned int	ID () const
	Get the unique ID number. More...

Public Attributes
const bool	isAutonomous
	Does the RHS explicitly depend on time? More...

const double	startTime
	The time when this simulation starts – either set in the opts ptree or set to the minimum of evalTimes. More...

Public Attributes inherited from muq::Modeling::ModPiece
const Eigen::VectorXi	inputSizes

const Eigen::VectorXi	outputSizes

Public Attributes inherited from muq::Modeling::WorkPiece
int	numInputs
	The number of inputs. More...

int	numOutputs
	The number of outputs. More...

Additional Inherited Members
Static Public Member Functions inherited from muq::Modeling::WorkPiece
static ref_vector< const boost::any >	ToRefVector (std::vector< boost::any > const &anyVec)
	Create vector of references from a vector of boost::any's. More...

static ref_vector< const Eigen::VectorXd >	ToRefVector (std::vector< Eigen::VectorXd > const &anyVec)

Constructor & Destructor Documentation

◆ ODE() [1/2]

muq::Modeling::ODE::ODE	(	std::shared_ptr< ModPiece > const &	rhsIn,
		Eigen::VectorXd const &	evalTimesIn,
		boost::property_tree::ptree	opts = `boost::property_tree::ptree()`
	)

inline

Definition at line 35 of file ODE.h.

◆ ODE() [2/2]

ODE::ODE	(	std::shared_ptr< ModPiece > const &	rhsIn,
		Eigen::VectorXd const &	evalTimesIn,
		bool	isAuto,
		boost::property_tree::ptree	opts = `boost::property_tree::ptree()`
	)

Definition at line 24 of file ODE.cpp.

References intOpts, linOpts, nonlinOpts, muq::Modeling::ODE::NonlinearSolverOptions::SetOptions(), muq::Modeling::ODE::LinearSolverOptions::SetOptions(), and muq::Modeling::ODE::IntegratorOptions::SetOptions().

◆ ~ODE()

virtual muq::Modeling::ODE::~ODE ( )

virtualdefault

Member Function Documentation

◆ ApplyJacobianImpl()

void ODE::ApplyJacobianImpl	(	unsigned int	outWrt,
		unsigned int	inWrt,
		ref_vector< Eigen::VectorXd > const &	inputs,
		Eigen::VectorXd const &	vec
	)

overrideprotectedvirtual

◆ CheckFlag()

void ODE::CheckFlag	(	void *	returnvalue,
		const char *	funcname,
		int	opt
	)

staticprivate

Checks the return value produced by CVODES. Throws and exception if error occured.

Definition at line 1212 of file ODE.cpp.

Referenced by ApplyJacobianImpl(), CreateAdjointLinearSolver(), CreateAdjointNonlinearSolver(), CreateLinearSolver(), CreateNonlinearSolver(), EvaluateImpl(), GradientImpl(), and JacobianImpl().

◆ CreateAdjointLinearSolver()

std::pair< SUNLinearSolver, SUNMatrix > ODE::CreateAdjointLinearSolver	(	void *	cvode_mem,
		N_Vector const &	state,
		int	indexB
	)

private

Definition at line 218 of file ODE.cpp.

References CheckFlag(), linOpts, muq::Modeling::ODE::LinearSolverOptions::maxIters, muq::Modeling::ODE::NonlinearSolverOptions::method, muq::Modeling::ODE::LinearSolverOptions::method, and nonlinOpts.

Referenced by GradientImpl().

◆ CreateAdjointNonlinearSolver()

SUNNonlinearSolver ODE::CreateAdjointNonlinearSolver	(	void *	cvode_mem,
		N_Vector const &	state,
		int	indexB
	)

private

Definition at line 273 of file ODE.cpp.

References CheckFlag(), muq::Modeling::ODE::NonlinearSolverOptions::maxIters, muq::Modeling::ODE::NonlinearSolverOptions::method, and nonlinOpts.

Referenced by GradientImpl().

◆ CreateLinearSolver()

std::pair< SUNLinearSolver, SUNMatrix > ODE::CreateLinearSolver	(	void *	cvode_mem,
		N_Vector const &	state
	)

private

Creates a linear solver and, if necessary, a dense matrix for storing the Jacobian. If the nonlinear solver is fixed point iteration, then no linear solver is necessary and this function returns an empty linear solver. If no Jacobian is needed, either because a fixed point nonlinear solver is specified or because an iterative linear solver is specified, then NULL is returned. The options read by the constructor and stored in linOpts are used to construct the solver.

Definition at line 133 of file ODE.cpp.

References CheckFlag(), linOpts, muq::Modeling::ODE::LinearSolverOptions::maxIters, muq::Modeling::ODE::NonlinearSolverOptions::method, muq::Modeling::ODE::LinearSolverOptions::method, nonlinOpts, muq::Modeling::ODE::Interface::RHSJacobian(), and muq::Modeling::ODE::Interface::RHSJacobianAction().

Referenced by ApplyJacobianImpl(), EvaluateImpl(), GradientImpl(), and JacobianImpl().

◆ CreateNonlinearSolver()

SUNNonlinearSolver ODE::CreateNonlinearSolver	(	void *	cvode_mem,
		N_Vector const &	state
	)

private

Definition at line 189 of file ODE.cpp.

References CheckFlag(), muq::Modeling::ODE::NonlinearSolverOptions::maxIters, muq::Modeling::ODE::NonlinearSolverOptions::method, and nonlinOpts.

Referenced by ApplyJacobianImpl(), EvaluateImpl(), GradientImpl(), and JacobianImpl().

◆ EvaluateImpl()

void ODE::EvaluateImpl ( ref_vector< Eigen::VectorXd > const & inputs )

overrideprotectedvirtual

Integrates the ODE forward in time.

Implements muq::Modeling::ModPiece.

Definition at line 302 of file ODE.cpp.

References muq::Modeling::ODE::IntegratorOptions::abstol, CheckFlag(), CreateLinearSolver(), CreateNonlinearSolver(), nlohmann::detail::dtoa_impl::e, evalTimes, intOpts, isAutonomous, muq::Modeling::ODE::IntegratorOptions::maxNumSteps, muq::Modeling::ODE::IntegratorOptions::method, muq::Modeling::ModPiece::outputs, muq::Modeling::ModPiece::outputSizes, muq::Modeling::ODE::IntegratorOptions::reltol, muq::Modeling::ODE::Interface::RHS(), rhs, and startTime.

◆ GetInputSizes()

Eigen::VectorXi ODE::GetInputSizes	(	std::shared_ptr< ModPiece > const &	rhsIn,
		bool	isAuto
	)

staticprivate

Definition at line 77 of file ODE.cpp.

◆ GetOutputSizes()

Eigen::VectorXi ODE::GetOutputSizes	(	std::shared_ptr< ModPiece > const &	rhsIn,
		Eigen::VectorXd const &	evalTimes
	)

staticprivate

Definition at line 87 of file ODE.cpp.

References evalTimes.

◆ GetStartTime()

double ODE::GetStartTime	(	Eigen::VectorXd const &	evalTimesIn,
		boost::property_tree::ptree const &	opts
	)

staticprivate

Definition at line 48 of file ODE.cpp.

References startTime.

◆ GradientImpl()

void ODE::GradientImpl	(	unsigned int	outWrt,
		unsigned int	inWrt,
		ref_vector< Eigen::VectorXd > const &	inputs,
		Eigen::VectorXd const &	sens
	)

overrideprotectedvirtual

◆ JacobianImpl()

void ODE::JacobianImpl	(	unsigned int	outWrt,
		unsigned int	inWrt,
		ref_vector< Eigen::VectorXd > const &	inputs
	)

overrideprotectedvirtual

Reimplemented from muq::Modeling::ModPiece.

Definition at line 638 of file ODE.cpp.

References muq::Modeling::ODE::IntegratorOptions::abstol, muq::Modeling::ModPiece::cacheEnabled, muq::Modeling::ModPiece::cacheInput, CheckFlag(), CreateLinearSolver(), CreateNonlinearSolver(), nlohmann::detail::dtoa_impl::e, evalTimes, muq::Modeling::ModPiece::inputSizes, intOpts, isAutonomous, muq::Modeling::ModPiece::jacobian, muq::Modeling::ODE::IntegratorOptions::maxNumSteps, muq::Modeling::ODE::NonlinearSolverOptions::method, muq::Modeling::ODE::IntegratorOptions::method, nonlinOpts, muq::Modeling::ModPiece::outputs, muq::Modeling::ModPiece::outputSizes, muq::Modeling::ODE::IntegratorOptions::reltol, muq::Modeling::ODE::Interface::RHS(), rhs, muq::Modeling::ODE::IntegratorOptions::sensAbsTol, muq::Modeling::ODE::IntegratorOptions::sensRelTol, and startTime.

Member Data Documentation

◆ evalTimes

const Eigen::VectorXd muq::Modeling::ODE::evalTimes

protected

Definition at line 189 of file ODE.h.

Referenced by ApplyJacobianImpl(), EvaluateImpl(), GetOutputSizes(), GradientImpl(), and JacobianImpl().

◆ intOpts

IntegratorOptions muq::Modeling::ODE::intOpts

protected

Definition at line 186 of file ODE.h.

Referenced by ApplyJacobianImpl(), EvaluateImpl(), GradientImpl(), JacobianImpl(), and ODE().

◆ isAutonomous

const bool muq::Modeling::ODE::isAutonomous

Does the RHS explicitly depend on time?

Definition at line 48 of file ODE.h.

Referenced by ApplyJacobianImpl(), EvaluateImpl(), GradientImpl(), and JacobianImpl().

◆ linOpts

LinearSolverOptions muq::Modeling::ODE::linOpts

protected

Definition at line 185 of file ODE.h.

Referenced by CreateAdjointLinearSolver(), CreateLinearSolver(), and ODE().

◆ nonlinOpts

NonlinearSolverOptions muq::Modeling::ODE::nonlinOpts

protected

Definition at line 184 of file ODE.h.

Referenced by ApplyJacobianImpl(), CreateAdjointLinearSolver(), CreateAdjointNonlinearSolver(), CreateLinearSolver(), CreateNonlinearSolver(), JacobianImpl(), and ODE().

◆ rhs

std::shared_ptr<ModPiece> muq::Modeling::ODE::rhs

protected

Definition at line 192 of file ODE.h.

Referenced by ApplyJacobianImpl(), EvaluateImpl(), GradientImpl(), and JacobianImpl().

◆ startTime

const double muq::Modeling::ODE::startTime

The time when this simulation starts – either set in the opts ptree or set to the minimum of evalTimes.

Definition at line 51 of file ODE.h.

Referenced by ApplyJacobianImpl(), EvaluateImpl(), GetStartTime(), GradientImpl(), and JacobianImpl().

The documentation for this class was generated from the following files:

doxygen_prep/MUQ/Modeling/ODE.h
doxygen_prep/modules/Modeling/src/ODE.cpp

Detailed Description

Classes

Public Member Functions

Public Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ ODE() [1/2]

◆ ODE() [2/2]

◆ ~ODE()

Member Function Documentation

◆ ApplyJacobianImpl()

◆ CheckFlag()

◆ CreateAdjointLinearSolver()

◆ CreateAdjointNonlinearSolver()

◆ CreateLinearSolver()

◆ CreateNonlinearSolver()

◆ EvaluateImpl()

◆ GetInputSizes()

◆ GetOutputSizes()

◆ GetStartTime()

◆ GradientImpl()

◆ JacobianImpl()

Member Data Documentation

◆ evalTimes

◆ intOpts

◆ isAutonomous

◆ linOpts

◆ nonlinOpts

◆ rhs

◆ startTime