PMCMCDecision will help making sample accept/reject decisions in MCMC schemes (for e.g., when performing Bayesian inference). More...

#include <PMCMCDecision.h>

Inheritance diagram for PMCMCDecision:

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Public Types
typedef DataFileName	DataFileParameterType

Public Member Functions
	PMCMCDecision (const InputParameters &parameters)

virtual void	initialize () override

virtual void	finalize () override

virtual void	execute () override

void	threadJoin (const UserObject &) final

bool	shouldStore () const override final

SubProblem &	getSubProblem () const

bool	shouldDuplicateInitialExecution () const

virtual Real	spatialValue (const Point &) const

virtual const std::vector< Point >	spatialPoints () const

void	gatherSum (T &value)

void	gatherMax (T &value)

void	gatherMin (T &value)

void	gatherProxyValueMax (T1 &proxy, T2 &value)

void	gatherProxyValueMin (T1 &proxy, T2 &value)

void	setPrimaryThreadCopy (UserObject *primary)

UserObject *	primaryThreadCopy ()

std::set< UserObjectName >	getDependObjects () const

virtual bool	needThreadedCopy () const

const std::set< std::string > &	getRequestedItems () override

const std::set< std::string > &	getSuppliedItems () override

unsigned int	systemNumber () const

virtual bool	enabled () const

std::shared_ptr< MooseObject >	getSharedPtr ()

std::shared_ptr< const MooseObject >	getSharedPtr () const

MooseApp &	getMooseApp () const

const std::string &	type () const

virtual const std::string &	name () const

std::string	typeAndName () const

std::string	errorPrefix (const std::string &error_type) const

void	callMooseError (std::string msg, const bool with_prefix) const

MooseObjectParameterName	uniqueParameterName (const std::string &parameter_name) const

const InputParameters &	parameters () const

MooseObjectName	uniqueName () const

const T &	getParam (const std::string &name) const

std::vector< std::pair< T1, T2 > >	getParam (const std::string &param1, const std::string &param2) const

const T *	queryParam (const std::string &name) const

const T &	getRenamedParam (const std::string &old_name, const std::string &new_name) const

T	getCheckedPointerParam (const std::string &name, const std::string &error_string="") const

bool	isParamValid (const std::string &name) const

bool	isParamSetByUser (const std::string &nm) const

void	paramError (const std::string &param, Args... args) const

void	paramWarning (const std::string &param, Args... args) const

void	paramInfo (const std::string &param, Args... args) const

void	connectControllableParams (const std::string &parameter, const std::string &object_type, const std::string &object_name, const std::string &object_parameter) const

void	mooseError (Args &&... args) const

void	mooseErrorNonPrefixed (Args &&... args) const

void	mooseDocumentedError (const std::string &repo_name, const unsigned int issue_num, Args &&... args) const

void	mooseWarning (Args &&... args) const

void	mooseWarningNonPrefixed (Args &&... args) const

void	mooseDeprecated (Args &&... args) const

void	mooseInfo (Args &&... args) const

std::string	getDataFileName (const std::string &param) const

std::string	getDataFileNameByName (const std::string &relative_path) const

std::string	getDataFilePath (const std::string &relative_path) const

virtual void	initialSetup ()

virtual void	timestepSetup ()

virtual void	jacobianSetup ()

virtual void	residualSetup ()

virtual void	customSetup (const ExecFlagType &)

const ExecFlagEnum &	getExecuteOnEnum () const

UserObjectName	getUserObjectName (const std::string &param_name) const

const T &	getUserObject (const std::string &param_name, bool is_dependency=true) const

const T &	getUserObjectByName (const UserObjectName &object_name, bool is_dependency=true) const

const UserObject &	getUserObjectBase (const std::string &param_name, bool is_dependency=true) const

const UserObject &	getUserObjectBaseByName (const UserObjectName &object_name, bool is_dependency=true) const

const std::vector< MooseVariableScalar *> &	getCoupledMooseScalarVars ()

const std::set< TagID > &	getScalarVariableCoupleableVectorTags () const

const std::set< TagID > &	getScalarVariableCoupleableMatrixTags () const

const GenericMaterialProperty< T, is_ad > &	getGenericMaterialProperty (const std::string &name, MaterialData &material_data, const unsigned int state=0)

const GenericMaterialProperty< T, is_ad > &	getGenericMaterialProperty (const std::string &name, const unsigned int state=0)

const GenericMaterialProperty< T, is_ad > &	getGenericMaterialProperty (const std::string &name, const unsigned int state=0)

const MaterialProperty< T > &	getMaterialProperty (const std::string &name, MaterialData &material_data, const unsigned int state=0)

const MaterialProperty< T > &	getMaterialProperty (const std::string &name, const unsigned int state=0)

const MaterialProperty< T > &	getMaterialProperty (const std::string &name, const unsigned int state=0)

const ADMaterialProperty< T > &	getADMaterialProperty (const std::string &name, MaterialData &material_data)

const ADMaterialProperty< T > &	getADMaterialProperty (const std::string &name)

const ADMaterialProperty< T > &	getADMaterialProperty (const std::string &name)

const MaterialProperty< T > &	getMaterialPropertyOld (const std::string &name, MaterialData &material_data)

const MaterialProperty< T > &	getMaterialPropertyOld (const std::string &name)

const MaterialProperty< T > &	getMaterialPropertyOld (const std::string &name)

const MaterialProperty< T > &	getMaterialPropertyOlder (const std::string &name, MaterialData &material_data)

const MaterialProperty< T > &	getMaterialPropertyOlder (const std::string &name)

const MaterialProperty< T > &	getMaterialPropertyOlder (const std::string &name)

const GenericMaterialProperty< T, is_ad > &	getGenericMaterialPropertyByName (const MaterialPropertyName &name, MaterialData &material_data, const unsigned int state)

const GenericMaterialProperty< T, is_ad > &	getGenericMaterialPropertyByName (const MaterialPropertyName &name, const unsigned int state=0)

const GenericMaterialProperty< T, is_ad > &	getGenericMaterialPropertyByName (const MaterialPropertyName &name, const unsigned int state=0)

const MaterialProperty< T > &	getMaterialPropertyByName (const MaterialPropertyName &name, MaterialData &material_data, const unsigned int state=0)

const MaterialProperty< T > &	getMaterialPropertyByName (const MaterialPropertyName &name, const unsigned int state=0)

const MaterialProperty< T > &	getMaterialPropertyByName (const MaterialPropertyName &name, const unsigned int state=0)

const ADMaterialProperty< T > &	getADMaterialPropertyByName (const MaterialPropertyName &name, MaterialData &material_data)

const ADMaterialProperty< T > &	getADMaterialPropertyByName (const MaterialPropertyName &name)

const ADMaterialProperty< T > &	getADMaterialPropertyByName (const MaterialPropertyName &name)

const MaterialProperty< T > &	getMaterialPropertyOldByName (const MaterialPropertyName &name, MaterialData &material_data)

const MaterialProperty< T > &	getMaterialPropertyOldByName (const MaterialPropertyName &name)

const MaterialProperty< T > &	getMaterialPropertyOldByName (const MaterialPropertyName &name)

const MaterialProperty< T > &	getMaterialPropertyOlderByName (const MaterialPropertyName &name, MaterialData &material_data)

const MaterialProperty< T > &	getMaterialPropertyOlderByName (const MaterialPropertyName &name)

const MaterialProperty< T > &	getMaterialPropertyOlderByName (const MaterialPropertyName &name)

std::pair< const MaterialProperty< T > *, std::set< SubdomainID > >	getBlockMaterialProperty (const MaterialPropertyName &name)

const GenericMaterialProperty< T, is_ad > &	getGenericZeroMaterialProperty (const std::string &name)

const GenericMaterialProperty< T, is_ad > &	getGenericZeroMaterialProperty ()

const GenericMaterialProperty< T, is_ad > &	getGenericZeroMaterialPropertyByName (const std::string &prop_name)

const MaterialProperty< T > &	getZeroMaterialProperty (Ts... args)

std::set< SubdomainID >	getMaterialPropertyBlocks (const std::string &name)

std::vector< SubdomainName >	getMaterialPropertyBlockNames (const std::string &name)

std::set< BoundaryID >	getMaterialPropertyBoundaryIDs (const std::string &name)

std::vector< BoundaryName >	getMaterialPropertyBoundaryNames (const std::string &name)

void	checkBlockAndBoundaryCompatibility (std::shared_ptr< MaterialBase > discrete)

std::unordered_map< SubdomainID, std::vector< MaterialBase *> >	buildRequiredMaterials (bool allow_stateful=true)

void	statefulPropertiesAllowed (bool)

bool	getMaterialPropertyCalled () const

virtual const std::unordered_set< unsigned int > &	getMatPropDependencies () const

virtual void	resolveOptionalProperties ()

const GenericMaterialProperty< T, is_ad > &	getPossiblyConstantGenericMaterialPropertyByName (const MaterialPropertyName &prop_name, MaterialData &material_data, const unsigned int state)

bool	isImplicit ()

Moose::StateArg	determineState () const

virtual void	store (nlohmann::json &json) const

virtual void	declareLateValues ()

void	buildOutputHideVariableList (std::set< std::string > variable_names)

const std::set< OutputName > &	getOutputs ()

virtual void	subdomainSetup () override

virtual void	subdomainSetup () override

bool	hasUserObject (const std::string &param_name) const

bool	hasUserObject (const std::string &param_name) const

bool	hasUserObject (const std::string &param_name) const

bool	hasUserObject (const std::string &param_name) const

bool	hasUserObjectByName (const UserObjectName &object_name) const

bool	hasUserObjectByName (const UserObjectName &object_name) const

bool	hasUserObjectByName (const UserObjectName &object_name) const

bool	hasUserObjectByName (const UserObjectName &object_name) const

const GenericOptionalMaterialProperty< T, is_ad > &	getGenericOptionalMaterialProperty (const std::string &name, const unsigned int state=0)

const GenericOptionalMaterialProperty< T, is_ad > &	getGenericOptionalMaterialProperty (const std::string &name, const unsigned int state=0)

const OptionalMaterialProperty< T > &	getOptionalMaterialProperty (const std::string &name, const unsigned int state=0)

const OptionalMaterialProperty< T > &	getOptionalMaterialProperty (const std::string &name, const unsigned int state=0)

const OptionalADMaterialProperty< T > &	getOptionalADMaterialProperty (const std::string &name)

const OptionalADMaterialProperty< T > &	getOptionalADMaterialProperty (const std::string &name)

const OptionalMaterialProperty< T > &	getOptionalMaterialPropertyOld (const std::string &name)

const OptionalMaterialProperty< T > &	getOptionalMaterialPropertyOld (const std::string &name)

const OptionalMaterialProperty< T > &	getOptionalMaterialPropertyOlder (const std::string &name)

const OptionalMaterialProperty< T > &	getOptionalMaterialPropertyOlder (const std::string &name)

MaterialBase &	getMaterial (const std::string &name)

MaterialBase &	getMaterial (const std::string &name)

MaterialBase &	getMaterialByName (const std::string &name, bool no_warn=false)

MaterialBase &	getMaterialByName (const std::string &name, bool no_warn=false)

bool	hasMaterialProperty (const std::string &name)

bool	hasMaterialProperty (const std::string &name)

bool	hasMaterialPropertyByName (const std::string &name)

bool	hasMaterialPropertyByName (const std::string &name)

bool	hasADMaterialProperty (const std::string &name)

bool	hasADMaterialProperty (const std::string &name)

bool	hasADMaterialPropertyByName (const std::string &name)

bool	hasADMaterialPropertyByName (const std::string &name)

bool	hasGenericMaterialProperty (const std::string &name)

bool	hasGenericMaterialProperty (const std::string &name)

bool	hasGenericMaterialPropertyByName (const std::string &name)

bool	hasGenericMaterialPropertyByName (const std::string &name)

const Function &	getFunction (const std::string &name) const

const Function &	getFunctionByName (const FunctionName &name) const

bool	hasFunction (const std::string &param_name) const

bool	hasFunctionByName (const FunctionName &name) const

bool	isDefaultPostprocessorValue (const std::string &param_name, const unsigned int index=0) const

bool	hasPostprocessor (const std::string &param_name, const unsigned int index=0) const

bool	hasPostprocessorByName (const PostprocessorName &name) const

std::size_t	coupledPostprocessors (const std::string &param_name) const

const PostprocessorName &	getPostprocessorName (const std::string &param_name, const unsigned int index=0) const

const VectorPostprocessorValue &	getVectorPostprocessorValue (const std::string &param_name, const std::string &vector_name) const

const VectorPostprocessorValue &	getVectorPostprocessorValue (const std::string &param_name, const std::string &vector_name, bool needs_broadcast) const

const VectorPostprocessorValue &	getVectorPostprocessorValueByName (const VectorPostprocessorName &name, const std::string &vector_name) const

const VectorPostprocessorValue &	getVectorPostprocessorValueByName (const VectorPostprocessorName &name, const std::string &vector_name, bool needs_broadcast) const

const VectorPostprocessorValue &	getVectorPostprocessorValueOld (const std::string &param_name, const std::string &vector_name) const

const VectorPostprocessorValue &	getVectorPostprocessorValueOld (const std::string &param_name, const std::string &vector_name, bool needs_broadcast) const

const VectorPostprocessorValue &	getVectorPostprocessorValueOldByName (const VectorPostprocessorName &name, const std::string &vector_name) const

const VectorPostprocessorValue &	getVectorPostprocessorValueOldByName (const VectorPostprocessorName &name, const std::string &vector_name, bool needs_broadcast) const

const ScatterVectorPostprocessorValue &	getScatterVectorPostprocessorValue (const std::string &param_name, const std::string &vector_name) const

const ScatterVectorPostprocessorValue &	getScatterVectorPostprocessorValueByName (const VectorPostprocessorName &name, const std::string &vector_name) const

const ScatterVectorPostprocessorValue &	getScatterVectorPostprocessorValueOld (const std::string &param_name, const std::string &vector_name) const

const ScatterVectorPostprocessorValue &	getScatterVectorPostprocessorValueOldByName (const VectorPostprocessorName &name, const std::string &vector_name) const

bool	hasVectorPostprocessor (const std::string &param_name, const std::string &vector_name) const

bool	hasVectorPostprocessor (const std::string &param_name) const

bool	hasVectorPostprocessorByName (const VectorPostprocessorName &name, const std::string &vector_name) const

bool	hasVectorPostprocessorByName (const VectorPostprocessorName &name) const

const VectorPostprocessorName &	getVectorPostprocessorName (const std::string &param_name) const

T &	getSampler (const std::string &name)

Sampler &	getSampler (const std::string &name)

T &	getSamplerByName (const SamplerName &name)

Sampler &	getSamplerByName (const SamplerName &name)

virtual void	meshChanged ()

virtual void	meshDisplaced ()

PerfGraph &	perfGraph ()

const PostprocessorValue &	getPostprocessorValue (const std::string &param_name, const unsigned int index=0) const

const PostprocessorValue &	getPostprocessorValue (const std::string &param_name, const unsigned int index=0) const

const PostprocessorValue &	getPostprocessorValueOld (const std::string &param_name, const unsigned int index=0) const

const PostprocessorValue &	getPostprocessorValueOld (const std::string &param_name, const unsigned int index=0) const

const PostprocessorValue &	getPostprocessorValueOlder (const std::string &param_name, const unsigned int index=0) const

const PostprocessorValue &	getPostprocessorValueOlder (const std::string &param_name, const unsigned int index=0) const

virtual const PostprocessorValue &	getPostprocessorValueByName (const PostprocessorName &name) const

virtual const PostprocessorValue &	getPostprocessorValueByName (const PostprocessorName &name) const

const PostprocessorValue &	getPostprocessorValueOldByName (const PostprocessorName &name) const

const PostprocessorValue &	getPostprocessorValueOldByName (const PostprocessorName &name) const

const PostprocessorValue &	getPostprocessorValueOlderByName (const PostprocessorName &name) const

const PostprocessorValue &	getPostprocessorValueOlderByName (const PostprocessorName &name) const

bool	isVectorPostprocessorDistributed (const std::string &param_name) const

bool	isVectorPostprocessorDistributed (const std::string &param_name) const

bool	isVectorPostprocessorDistributedByName (const VectorPostprocessorName &name) const

bool	isVectorPostprocessorDistributedByName (const VectorPostprocessorName &name) const

const Distribution &	getDistribution (const std::string &name) const

const T &	getDistribution (const std::string &name) const

const Distribution &	getDistribution (const std::string &name) const

const T &	getDistribution (const std::string &name) const

const Distribution &	getDistributionByName (const DistributionName &name) const

const T &	getDistributionByName (const std::string &name) const

const Distribution &	getDistributionByName (const DistributionName &name) const

const T &	getDistributionByName (const std::string &name) const

const Parallel::Communicator &	comm () const

processor_id_type	n_processors () const

processor_id_type	processor_id () const

Static Public Member Functions
static InputParameters	validParams ()

static void	sort (typename std::vector< T > &vector)

static void	sortDFS (typename std::vector< T > &vector)

static void	cyclicDependencyError (CyclicDependencyException< T2 > &e, const std::string &header)

Public Attributes
const ConsoleStream	_console

Static Public Attributes
static constexpr PropertyValue::id_type	default_property_id

static constexpr PropertyValue::id_type	zero_property_id

static constexpr auto	SYSTEM

static constexpr auto	NAME

Protected Member Functions
virtual void	computeEvidence (std::vector< Real > &evidence, const DenseMatrix< Real > &input_matrix)
	Compute the evidence (aka, betterness of the proposed sample vs the previous) More...

virtual void	computeTransitionVector (std::vector< Real > &tv, const std::vector< Real > &evidence)
	Compute the transition probability vector (after the computation of evidence) More...

virtual void	nextSamples (std::vector< Real > &req_inputs, DenseMatrix< Real > &input_matrix, const std::vector< Real > &tv, const unsigned int &parallel_index)
	Resample inputs given the transition vector (after transition vector computed) More...

virtual void	nextSeeds ()
	Compute the next set of seeds to facilitate proposals. More...

virtual void	addPostprocessorDependencyHelper (const PostprocessorName &name) const override

virtual void	addVectorPostprocessorDependencyHelper (const VectorPostprocessorName &name) const override

virtual void	addUserObjectDependencyHelper (const UserObject &uo) const override

void	addReporterDependencyHelper (const ReporterName &reporter_name) override

const ReporterName &	getReporterName (const std::string &param_name) const

T &	declareRestartableData (const std::string &data_name, Args &&... args)

ManagedValue< T >	declareManagedRestartableDataWithContext (const std::string &data_name, void *context, Args &&... args)

const T &	getRestartableData (const std::string &data_name) const

T &	declareRestartableDataWithContext (const std::string &data_name, void *context, Args &&... args)

T &	declareRecoverableData (const std::string &data_name, Args &&... args)

T &	declareRestartableDataWithObjectName (const std::string &data_name, const std::string &object_name, Args &&... args)

T &	declareRestartableDataWithObjectNameWithContext (const std::string &data_name, const std::string &object_name, void *context, Args &&... args)

std::string	restartableName (const std::string &data_name) const

const T &	getMeshProperty (const std::string &data_name, const std::string &prefix)

const T &	getMeshProperty (const std::string &data_name)

bool	hasMeshProperty (const std::string &data_name, const std::string &prefix) const

bool	hasMeshProperty (const std::string &data_name, const std::string &prefix) const

bool	hasMeshProperty (const std::string &data_name) const

bool	hasMeshProperty (const std::string &data_name) const

std::string	meshPropertyName (const std::string &data_name) const

PerfID	registerTimedSection (const std::string &section_name, const unsigned int level) const

PerfID	registerTimedSection (const std::string &section_name, const unsigned int level, const std::string &live_message, const bool print_dots=true) const

std::string	timedSectionName (const std::string &section_name) const

bool	isCoupledScalar (const std::string &var_name, unsigned int i=0) const

unsigned int	coupledScalarComponents (const std::string &var_name) const

unsigned int	coupledScalar (const std::string &var_name, unsigned int comp=0) const

libMesh::Order	coupledScalarOrder (const std::string &var_name, unsigned int comp=0) const

const VariableValue &	coupledScalarValue (const std::string &var_name, unsigned int comp=0) const

const ADVariableValue &	adCoupledScalarValue (const std::string &var_name, unsigned int comp=0) const

const GenericVariableValue< is_ad > &	coupledGenericScalarValue (const std::string &var_name, unsigned int comp=0) const

const GenericVariableValue< false > &	coupledGenericScalarValue (const std::string &var_name, const unsigned int comp) const

const GenericVariableValue< true > &	coupledGenericScalarValue (const std::string &var_name, const unsigned int comp) const

const VariableValue &	coupledVectorTagScalarValue (const std::string &var_name, TagID tag, unsigned int comp=0) const

const VariableValue &	coupledMatrixTagScalarValue (const std::string &var_name, TagID tag, unsigned int comp=0) const

const VariableValue &	coupledScalarValueOld (const std::string &var_name, unsigned int comp=0) const

const VariableValue &	coupledScalarValueOlder (const std::string &var_name, unsigned int comp=0) const

const VariableValue &	coupledScalarDot (const std::string &var_name, unsigned int comp=0) const

const ADVariableValue &	adCoupledScalarDot (const std::string &var_name, unsigned int comp=0) const

const VariableValue &	coupledScalarDotDot (const std::string &var_name, unsigned int comp=0) const

const VariableValue &	coupledScalarDotOld (const std::string &var_name, unsigned int comp=0) const

const VariableValue &	coupledScalarDotDotOld (const std::string &var_name, unsigned int comp=0) const

const VariableValue &	coupledScalarDotDu (const std::string &var_name, unsigned int comp=0) const

const VariableValue &	coupledScalarDotDotDu (const std::string &var_name, unsigned int comp=0) const

const MooseVariableScalar *	getScalarVar (const std::string &var_name, unsigned int comp) const

virtual void	checkMaterialProperty (const std::string &name, const unsigned int state)

void	markMatPropRequested (const std::string &)

MaterialPropertyName	getMaterialPropertyName (const std::string &name) const

void	checkExecutionStage ()

T &	declareUnusedValue (Args &&... args)

const T &	getReporterValue (const std::string &param_name, const std::size_t time_index=0)

const T &	getReporterValue (const std::string &param_name, ReporterMode mode, const std::size_t time_index=0)

const T &	getReporterValue (const std::string &param_name, const std::size_t time_index=0)

const T &	getReporterValue (const std::string &param_name, ReporterMode mode, const std::size_t time_index=0)

const T &	getReporterValueByName (const ReporterName &reporter_name, const std::size_t time_index=0)

const T &	getReporterValueByName (const ReporterName &reporter_name, ReporterMode mode, const std::size_t time_index=0)

const T &	getReporterValueByName (const ReporterName &reporter_name, const std::size_t time_index=0)

const T &	getReporterValueByName (const ReporterName &reporter_name, ReporterMode mode, const std::size_t time_index=0)

bool	hasReporterValue (const std::string &param_name) const

bool	hasReporterValue (const std::string &param_name) const

bool	hasReporterValue (const std::string &param_name) const

bool	hasReporterValue (const std::string &param_name) const

bool	hasReporterValueByName (const ReporterName &reporter_name) const

bool	hasReporterValueByName (const ReporterName &reporter_name) const

bool	hasReporterValueByName (const ReporterName &reporter_name) const

bool	hasReporterValueByName (const ReporterName &reporter_name) const

const GenericMaterialProperty< T, is_ad > *	defaultGenericMaterialProperty (const std::string &name)

const GenericMaterialProperty< T, is_ad > *	defaultGenericMaterialProperty (const std::string &name)

const MaterialProperty< T > *	defaultMaterialProperty (const std::string &name)

const MaterialProperty< T > *	defaultMaterialProperty (const std::string &name)

const ADMaterialProperty< T > *	defaultADMaterialProperty (const std::string &name)

const ADMaterialProperty< T > *	defaultADMaterialProperty (const std::string &name)

T &	declareValue (const std::string &param_name, Args &&... args)

T &	declareValue (const std::string &param_name, ReporterMode mode, Args &&... args)

T &	declareValue (const std::string &param_name, Args &&... args)

T &	declareValue (const std::string &param_name, ReporterMode mode, Args &&... args)

T &	declareValue (const std::string &param_name, Args &&... args)

T &	declareValue (const std::string &param_name, ReporterMode mode, Args &&... args)

T &	declareValue (const std::string &param_name, Args &&... args)

T &	declareValue (const std::string &param_name, ReporterMode mode, Args &&... args)

T &	declareValueByName (const ReporterValueName &value_name, Args &&... args)

T &	declareValueByName (const ReporterValueName &value_name, ReporterMode mode, Args &&... args)

T &	declareValueByName (const ReporterValueName &value_name, Args &&... args)

T &	declareValueByName (const ReporterValueName &value_name, ReporterMode mode, Args &&... args)

T &	declareValueByName (const ReporterValueName &value_name, Args &&... args)

T &	declareValueByName (const ReporterValueName &value_name, ReporterMode mode, Args &&... args)

T &	declareValueByName (const ReporterValueName &value_name, Args &&... args)

T &	declareValueByName (const ReporterValueName &value_name, ReporterMode mode, Args &&... args)

LikelihoodFunctionBase *	getLikelihoodFunctionByName (const UserObjectName &name) const
	Lookup a LikelihoodFunction object by name and return pointer. More...

Static Protected Member Functions
static std::string	meshPropertyName (const std::string &data_name, const std::string &prefix)

Protected Attributes
const std::vector< Real > &	_output_value
	Model output value from SubApp. More...

std::vector< Real > &	_outputs_required
	Transfer the right outputs to the file. More...

std::vector< std::vector< Real > > &	_inputs
	Model input data that is uncertain. More...

std::vector< Real > &	_tpm
	Transition probability matrix. More...

std::vector< Real > &	_variance
	Model variance term. More...

Real &	_noise
	Model noise term to pass to Likelihoods object. More...

std::vector< const LikelihoodFunctionBase * >	_likelihoods
	Storage for the likelihood objects to be utilized. More...

Sampler &	_sampler
	The MCMC sampler. More...

const PMCMCBase *const	_pmcmc
	MCMC sampler base. More...

dof_id_type	_props
	Storage for the number of parallel proposals. More...

const std::vector< Real > &	_rnd_vec
	Storage for the random numbers for decision making. More...

const std::vector< Real > &	_new_var_samples
	Storage for new proposed variance samples. More...

const std::vector< const Distribution * >	_priors
	Storage for the priors. More...

const Distribution *	_var_prior
	Storage for the prior over the variance. More...

dof_id_type	_num_confg_values
	Storage for the number of experimental configuration values. More...

dof_id_type	_num_confg_params
	Storage for the number of experimental configuration parameters. More...

DenseMatrix< Real >	_data_prev
	Storage for previous inputs. More...

std::vector< Real >	_var_prev
	Storage for previous variances. More...

std::vector< Real >	_outputs_prev
	Storage for previous outputs. More...

SubProblem &	_subproblem

FEProblemBase &	_fe_problem

SystemBase &	_sys

const THREAD_ID	_tid

Assembly &	_assembly

const Moose::CoordinateSystemType &	_coord_sys

const bool	_duplicate_initial_execution

std::set< std::string >	_depend_uo

const bool &	_enabled

MooseApp &	_app

const std::string	_type

const std::string	_name

const InputParameters &	_pars

Factory &	_factory

ActionFactory &	_action_factory

const ExecFlagEnum &	_execute_enum

const ExecFlagType &	_current_execute_flag

MooseApp &	_restartable_app

const std::string	_restartable_system_name

const THREAD_ID	_restartable_tid

const bool	_restartable_read_only

FEProblemBase &	_mci_feproblem

FEProblemBase &	_mdi_feproblem

MooseApp &	_pg_moose_app

const std::string	_prefix

FEProblemBase &	_sc_fe_problem

const THREAD_ID	_sc_tid

const Real &	_real_zero

const VariableValue &	_scalar_zero

const Point &	_point_zero

const InputParameters &	_mi_params

const std::string	_mi_name

const MooseObjectName	_mi_moose_object_name

FEProblemBase &	_mi_feproblem

SubProblem &	_mi_subproblem

const THREAD_ID	_mi_tid

const Moose::MaterialDataType	_material_data_type

MaterialData &	_material_data

bool	_stateful_allowed

bool	_get_material_property_called

std::vector< std::unique_ptr< PropertyValue > >	_default_properties

std::unordered_set< unsigned int >	_material_property_dependencies

const MaterialPropertyName	_get_suffix

const bool	_use_interpolated_state

const InputParameters &	_ti_params

FEProblemBase &	_ti_feproblem

bool	_is_implicit

Real &	_t

const Real &	_t_old

int &	_t_step

Real &	_dt

Real &	_dt_old

bool	_is_transient

const Parallel::Communicator &	_communicator

Static Protected Attributes
static const std::string	_interpolated_old

static const std::string	_interpolated_older

Private Attributes
libMesh::Parallel::Communicator &	_local_comm
	Communicator that was split based on samples that have rows. More...

int	_check_step
	Ensure that the MCMC algorithm proceeds in a sequential fashion. More...

Detailed Description

PMCMCDecision will help making sample accept/reject decisions in MCMC schemes (for e.g., when performing Bayesian inference).

Definition at line 22 of file PMCMCDecision.h.

Constructor & Destructor Documentation

◆ PMCMCDecision()

PMCMCDecision::PMCMCDecision ( const InputParameters & parameters )

Definition at line 39 of file PMCMCDecision.C.

   : GeneralReporter(parameters),
     LikelihoodInterface(parameters),
     _output_value(getReporterValue<std::vector<Real>>("output_value", REPORTER_MODE_DISTRIBUTED)),
     _outputs_required(declareValue<std::vector<Real>>("outputs_required")),
     _inputs(declareValue<std::vector<std::vector<Real>>>("inputs")),
     _tpm(declareValue<std::vector<Real>>("tpm")),
     _variance(declareValue<std::vector<Real>>("variance")),
     _noise(declareValue<Real>("noise")),
     _sampler(getSampler("sampler")),
     _pmcmc(dynamic_cast<const PMCMCBase *>(&_sampler)),
     _rnd_vec(_pmcmc->getRandomNumbers()),
     _new_var_samples(_pmcmc->getVarSamples()),
     _priors(_pmcmc->getPriors()),
     _var_prior(_pmcmc->getVarPrior()),
     _local_comm(_sampler.getLocalComm()),
     _check_step(std::numeric_limits<int>::max())
 {
   // Filling the `likelihoods` vector with the user-provided distributions.
   for (const UserObjectName & name : getParam<std::vector<UserObjectName>>("likelihoods"))
     _likelihoods.push_back(getLikelihoodFunctionByName(name));
 
   // Check whether the selected sampler is an MCMC sampler or not
   if (!_pmcmc)
     paramError("sampler", "The selected sampler is not of type MCMC.");
 
   // Fetching the sampler characteristics
   _props = _pmcmc->getNumParallelProposals();
   _num_confg_values = _pmcmc->getNumberOfConfigValues();
   _num_confg_params = _pmcmc->getNumberOfConfigParams();
 
   // Resizing the data arrays to transmit to the output file
   _inputs.resize(_props);
   for (unsigned int i = 0; i < _props; ++i)
     _inputs[i].resize(_sampler.getNumberOfCols() - _num_confg_params);
   _outputs_required.resize(_sampler.getNumberOfRows());
   _tpm.resize(_props);
   _variance.resize(_props);
 }

Member Function Documentation

◆ computeEvidence()

void PMCMCDecision::computeEvidence	(	std::vector< Real > &	evidence,
		const DenseMatrix< Real > &	input_matrix
	)

protectedvirtual

Compute the evidence (aka, betterness of the proposed sample vs the previous)

Parameters

evidence	The evidence vector to be filled
input_matrix	The matrix of proposed inputs that are provided

Reimplemented in IndependentMHDecision.

Definition at line 80 of file PMCMCDecision.C.

Referenced by execute().

 {
   std::vector<Real> out1(_num_confg_values);
   std::vector<Real> out2(_num_confg_values);
   for (unsigned int i = 0; i < evidence.size(); ++i)
   {
     evidence[i] = 0.0;
     for (unsigned int j = 0; j < _priors.size(); ++j)
       evidence[i] += (std::log(_priors[j]->pdf(input_matrix(i, j))) -
                       std::log(_priors[j]->pdf(_data_prev(i, j))));
     for (unsigned int j = 0; j < _num_confg_values; ++j)
     {
       out1[j] = _outputs_required[j * _props + i];
       out2[j] = _outputs_prev[j * _props + i];
     }
     if (_var_prior)
     {
       evidence[i] += (std::log(_var_prior->pdf(_new_var_samples[i])) -
                       std::log(_var_prior->pdf(_var_prev[i])));
       _noise = std::sqrt(_new_var_samples[i]);
       for (unsigned int j = 0; j < _likelihoods.size(); ++j)
         evidence[i] += _likelihoods[j]->function(out1);
       _noise = std::sqrt(_var_prev[i]);
       for (unsigned int j = 0; j < _likelihoods.size(); ++j)
         evidence[i] -= _likelihoods[j]->function(out2);
     }
     else
       for (unsigned int j = 0; j < _likelihoods.size(); ++j)
         evidence[i] += (_likelihoods[j]->function(out1) - _likelihoods[j]->function(out2));
   }
 }

◆ computeTransitionVector()

void PMCMCDecision::computeTransitionVector	(	std::vector< Real > &	tv,
		const std::vector< Real > &	evidence
	)

protectedvirtual

Compute the transition probability vector (after the computation of evidence)

Parameters

tv	The transition probability vector to be filled
evidence	The vector of evidences provided

Reimplemented in IndependentMHDecision, AffineInvariantDifferentialDecision, and AffineInvariantStretchDecision.

Definition at line 113 of file PMCMCDecision.C.

Referenced by execute().

 {
   tv.assign(_props, 1.0);
 }

◆ execute()

void PMCMCDecision::execute ( )

overridevirtual

Implements GeneralReporter.

Definition at line 146 of file PMCMCDecision.C.

 {
   if (_sampler.getNumberOfLocalRows() == 0 || _check_step == _t_step)
   {
     _check_step = _t_step;
     return;
   }
 
   // Gather inputs and outputs from the sampler and subApps
   DenseMatrix<Real> data_in(_sampler.getNumberOfRows(), _sampler.getNumberOfCols());
   for (dof_id_type ss = _sampler.getLocalRowBegin(); ss < _sampler.getLocalRowEnd(); ++ss)
   {
     const auto data = _sampler.getNextLocalRow();
     for (unsigned int j = 0; j < _sampler.getNumberOfCols(); ++j)
       data_in(ss, j) = data[j];
   }
   _local_comm.sum(data_in.get_values());
   _outputs_required = _output_value;
   _local_comm.allgather(_outputs_required);
 
   // Compute the evidence and transition vectors
   std::vector<Real> evidence(_props);
   if (_t_step > _pmcmc->decisionStep())
   {
     computeEvidence(evidence, data_in);
     computeTransitionVector(_tpm, evidence);
   }
   else
     _tpm.assign(_props, 1.0);
 
   // Accept/reject the proposed samples and assign the correct outputs
   std::vector<Real> req_inputs(_sampler.getNumberOfCols() - _num_confg_params);
   for (unsigned int i = 0; i < _props; ++i)
   {
     nextSamples(req_inputs, data_in, _tpm, i);
     _inputs[i] = req_inputs;
   }
 
   // Compute the next seeds to facilitate proposals (not always required)
   nextSeeds();
 
   // Store data from previous step
   _data_prev = data_in;
   _outputs_prev = _outputs_required;
   _var_prev = _variance;
 
   // Track the current step
   _check_step = _t_step;
 }

◆ finalize()

virtual void PMCMCDecision::finalize ( )

inlineoverridevirtual

Implements GeneralReporter.

Definition at line 28 of file PMCMCDecision.h.

28 {}

◆ getLikelihoodFunctionByName()

LikelihoodFunctionBase * LikelihoodInterface::getLikelihoodFunctionByName ( const UserObjectName & name ) const

protectedinherited

Lookup a LikelihoodFunction object by name and return pointer.

Definition at line 24 of file LikelihoodInterface.C.

Referenced by PMCMCDecision(), and TestLikelihood::TestLikelihood().

 {
   std::vector<LikelihoodFunctionBase *> models;
   _likelihood_feproblem.theWarehouse()
       .query()
       .condition<AttribName>(name)
       .condition<AttribSystem>("LikelihoodFunctionBase")
       .queryInto(models);
 
   if (models.empty())
     mooseError("Unable to find a LikelihoodFunction object with the name '" + name + "'");
   return models[0];
 }

◆ initialize()

virtual void PMCMCDecision::initialize ( )

inlineoverridevirtual

Implements GeneralReporter.

Definition at line 27 of file PMCMCDecision.h.

27 {}

◆ nextSamples()

void PMCMCDecision::nextSamples	(	std::vector< Real > &	req_inputs,
		DenseMatrix< Real > &	input_matrix,
		const std::vector< Real > &	tv,
		const unsigned int &	parallel_index
	)

protectedvirtual

Resample inputs given the transition vector (after transition vector computed)

Parameters

req_inputs	The vector of accepted samples to be filled
input_matrix	The matrix of proposed inputs provided
tv	The vector of transition probabilities provided
parallel_index	The current parallel proposal index provided

Reimplemented in IndependentMHDecision.

Definition at line 120 of file PMCMCDecision.C.

Referenced by execute().

 {
   if (tv[parallel_index] >= _rnd_vec[parallel_index])
   {
     for (unsigned int k = 0; k < _sampler.getNumberOfCols() - _num_confg_params; ++k)
       req_inputs[k] = input_matrix(parallel_index, k);
     _variance[parallel_index] = _new_var_samples[parallel_index];
   }
   else
   {
     for (unsigned int k = 0; k < _sampler.getNumberOfCols() - _num_confg_params; ++k)
     {
       req_inputs[k] = _data_prev(parallel_index, k);
       input_matrix(parallel_index, k) = _data_prev(parallel_index, k);
     }
     if (_var_prior)
       _variance[parallel_index] = _var_prev[parallel_index];
     for (unsigned int k = 0; k < _num_confg_values; ++k)
       _outputs_required[k * _props + parallel_index] = _outputs_prev[k * _props + parallel_index];
   }
 }

◆ nextSeeds()

virtual void PMCMCDecision::nextSeeds ( )

inlineprotectedvirtual

Compute the next set of seeds to facilitate proposals.

Set to empty in base to permit flexibility for MCMC samplers

Reimplemented in IndependentMHDecision.

Definition at line 63 of file PMCMCDecision.h.

Referenced by execute().

63 {}

◆ validParams()

InputParameters PMCMCDecision::validParams ( )

static

Definition at line 17 of file PMCMCDecision.C.

Referenced by AffineInvariantDifferentialDecision::validParams(), AffineInvariantStretchDecision::validParams(), and IndependentMHDecision::validParams().

 {
   InputParameters params = GeneralReporter::validParams();
   params += LikelihoodInterface::validParams();
   params.addClassDescription("Generic reporter which decides whether or not to accept a proposed "
                              "sample in parallel Markov chain Monte Carlo type of algorithms.");
   params.addRequiredParam<ReporterName>("output_value",
                                         "Value of the model output from the SubApp.");
   params.addParam<ReporterValueName>(
       "outputs_required",
       "outputs_required",
       "Modified value of the model output from this reporter class.");
   params.addParam<ReporterValueName>("inputs", "inputs", "Uncertain inputs to the model.");
   params.addParam<ReporterValueName>("tpm", "tpm", "The transition probability matrix.");
   params.addParam<ReporterValueName>("variance", "variance", "Model variance term.");
   params.addParam<ReporterValueName>(
       "noise", "noise", "Model noise term to pass to Likelihoods object.");
   params.addRequiredParam<SamplerName>("sampler", "The sampler object.");
   params.addRequiredParam<std::vector<UserObjectName>>("likelihoods", "Names of likelihoods.");
   return params;
 }

Member Data Documentation

◆ _check_step

int PMCMCDecision::_check_step

private

Ensure that the MCMC algorithm proceeds in a sequential fashion.

Definition at line 127 of file PMCMCDecision.h.

Referenced by execute().

◆ _data_prev

DenseMatrix<Real> PMCMCDecision::_data_prev

protected

Storage for previous inputs.

Definition at line 114 of file PMCMCDecision.h.

Referenced by computeEvidence(), execute(), and nextSamples().

◆ _inputs

std::vector<std::vector<Real> >& PMCMCDecision::_inputs

protected

Model input data that is uncertain.

Definition at line 72 of file PMCMCDecision.h.

Referenced by execute(), IndependentMHDecision::nextSeeds(), and PMCMCDecision().

◆ _likelihoods

std::vector<const LikelihoodFunctionBase *> PMCMCDecision::_likelihoods

protected

Storage for the likelihood objects to be utilized.

Definition at line 84 of file PMCMCDecision.h.

Referenced by IndependentMHDecision::computeEvidence(), computeEvidence(), and PMCMCDecision().

◆ _local_comm

libMesh::Parallel::Communicator& PMCMCDecision::_local_comm

private

Communicator that was split based on samples that have rows.

Definition at line 124 of file PMCMCDecision.h.

Referenced by execute().

◆ _new_var_samples

const std::vector<Real>& PMCMCDecision::_new_var_samples

protected

Storage for new proposed variance samples.

Definition at line 99 of file PMCMCDecision.h.

Referenced by computeEvidence(), IndependentMHDecision::nextSamples(), and nextSamples().

◆ _noise

Real& PMCMCDecision::_noise

protected

Model noise term to pass to Likelihoods object.

Definition at line 81 of file PMCMCDecision.h.

Referenced by computeEvidence().

◆ _num_confg_params

dof_id_type PMCMCDecision::_num_confg_params

protected

Storage for the number of experimental configuration parameters.

Definition at line 111 of file PMCMCDecision.h.

Referenced by execute(), IndependentMHDecision::nextSamples(), nextSamples(), and PMCMCDecision().

◆ _num_confg_values

dof_id_type PMCMCDecision::_num_confg_values

protected

Storage for the number of experimental configuration values.

Definition at line 108 of file PMCMCDecision.h.

Referenced by IndependentMHDecision::computeEvidence(), computeEvidence(), IndependentMHDecision::IndependentMHDecision(), IndependentMHDecision::nextSamples(), nextSamples(), IndependentMHDecision::nextSeeds(), and PMCMCDecision().

◆ _output_value

const std::vector<Real>& PMCMCDecision::_output_value

protected

Model output value from SubApp.

Definition at line 66 of file PMCMCDecision.h.

Referenced by execute().

◆ _outputs_prev

std::vector<Real> PMCMCDecision::_outputs_prev

protected

Storage for previous outputs.

Definition at line 120 of file PMCMCDecision.h.

Referenced by computeEvidence(), execute(), and nextSamples().

◆ _outputs_required

std::vector<Real>& PMCMCDecision::_outputs_required

protected

Transfer the right outputs to the file.

Definition at line 69 of file PMCMCDecision.h.

Referenced by IndependentMHDecision::computeEvidence(), computeEvidence(), IndependentMHDecision::computeTransitionVector(), execute(), IndependentMHDecision::nextSamples(), nextSamples(), IndependentMHDecision::nextSeeds(), and PMCMCDecision().

◆ _pmcmc

const PMCMCBase* const PMCMCDecision::_pmcmc

protected

MCMC sampler base.

Definition at line 90 of file PMCMCDecision.h.

Referenced by execute(), and PMCMCDecision().

◆ _priors

const std::vector<const Distribution *> PMCMCDecision::_priors

protected

Storage for the priors.

Definition at line 102 of file PMCMCDecision.h.

Referenced by IndependentMHDecision::computeEvidence(), computeEvidence(), and AffineInvariantStretchDecision::computeTransitionVector().

◆ _props

dof_id_type PMCMCDecision::_props

protected

Storage for the number of parallel proposals.

Definition at line 93 of file PMCMCDecision.h.

Referenced by IndependentMHDecision::computeEvidence(), computeEvidence(), computeTransitionVector(), execute(), IndependentMHDecision::IndependentMHDecision(), IndependentMHDecision::nextSamples(), nextSamples(), IndependentMHDecision::nextSeeds(), and PMCMCDecision().

◆ _rnd_vec

const std::vector<Real>& PMCMCDecision::_rnd_vec

protected

Storage for the random numbers for decision making.

Definition at line 96 of file PMCMCDecision.h.

Referenced by IndependentMHDecision::nextSamples(), and nextSamples().

◆ _sampler

Sampler& PMCMCDecision::_sampler

protected

The MCMC sampler.

Definition at line 87 of file PMCMCDecision.h.

Referenced by execute(), IndependentMHDecision::nextSamples(), nextSamples(), and PMCMCDecision().

◆ _tpm

std::vector<Real>& PMCMCDecision::_tpm

protected

Transition probability matrix.

Definition at line 75 of file PMCMCDecision.h.

Referenced by execute(), and PMCMCDecision().

◆ _var_prev

std::vector<Real> PMCMCDecision::_var_prev

protected

Storage for previous variances.

Definition at line 117 of file PMCMCDecision.h.

Referenced by computeEvidence(), execute(), and nextSamples().

◆ _var_prior

const Distribution* PMCMCDecision::_var_prior

protected

Storage for the prior over the variance.

Definition at line 105 of file PMCMCDecision.h.

Referenced by computeEvidence(), and nextSamples().

◆ _variance

std::vector<Real>& PMCMCDecision::_variance

protected

Model variance term.

Definition at line 78 of file PMCMCDecision.h.

Referenced by execute(), IndependentMHDecision::nextSamples(), nextSamples(), and PMCMCDecision().

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

stochastic_tools/include/reporters/PMCMCDecision.h
stochastic_tools/src/reporters/PMCMCDecision.C

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Static Public Attributes

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Static Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PMCMCDecision()

Member Function Documentation

◆ computeEvidence()

◆ computeTransitionVector()

◆ execute()

◆ finalize()

◆ getLikelihoodFunctionByName()

◆ initialize()

◆ nextSamples()

◆ nextSeeds()

◆ validParams()

Member Data Documentation

◆ _check_step

◆ _data_prev

◆ _inputs

◆ _likelihoods

◆ _local_comm

◆ _new_var_samples

◆ _noise

◆ _num_confg_params

◆ _num_confg_values

◆ _output_value

◆ _outputs_prev

◆ _outputs_required

◆ _pmcmc

◆ _priors

◆ _props

◆ _rnd_vec

◆ _sampler

◆ _tpm

◆ _var_prev

◆ _var_prior

◆ _variance