queso-0.53.0
Public Attributes | Private Member Functions | Private Attributes | List of all members
QUESO::MetropolisHastingsSGOptions Class Reference

This class reads the options for the Metropolis-Hastings generator of samples from an input file. More...

#include <MetropolisHastingsSGOptions.h>

Collaboration diagram for QUESO::MetropolisHastingsSGOptions:
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Public Member Functions

Constructor/Destructor methods
 MetropolisHastingsSGOptions (const BaseEnvironment &env, const char *prefix)
 Constructor: reads options from the input file. More...
 
 MetropolisHastingsSGOptions (const BaseEnvironment &env, const char *prefix, const MhOptionsValues &alternativeOptionsValues)
 Constructor: with alternative option values. More...
 
 MetropolisHastingsSGOptions (const MLSamplingLevelOptions &mlOptions)
 Copy constructor. More...
 
 ~MetropolisHastingsSGOptions ()
 Destructor. More...
 
I/O methods
void scanOptionsValues ()
 It scans the option values from the options input file. More...
 
void print (std::ostream &os) const
 It prints the option values. More...
 

Public Attributes

MhOptionsValues m_ov
 This class is where the actual options are stored. More...
 
std::string m_prefix
 

Private Member Functions

void defineMyOptions (boost::program_options::options_description &optionsDesc) const
 Defines the options for the Metropolis-Hastings generator of samples as the default options. More...
 
void getMyOptionValues (boost::program_options::options_description &optionsDesc)
 Gets the sequence options defined to the Metropolis-Hastings algorithm. More...
 

Private Attributes

const BaseEnvironment & m_env
 
boost::program_options::options_description * m_optionsDesc
 
std::string m_option_help
 
std::string m_option_dataOutputFileName
 
std::string m_option_dataOutputAllowAll
 
std::string m_option_dataOutputAllowedSet
 
std::string m_option_totallyMute
 
std::string m_option_initialPosition_dataInputFileName
 
std::string m_option_initialPosition_dataInputFileType
 
std::string m_option_initialProposalCovMatrix_dataInputFileName
 
std::string m_option_initialProposalCovMatrix_dataInputFileType
 
std::string m_option_listOfDisabledParameters
 
std::string m_option_rawChain_dataInputFileName
 
std::string m_option_rawChain_dataInputFileType
 
std::string m_option_rawChain_size
 
std::string m_option_rawChain_generateExtra
 
std::string m_option_rawChain_displayPeriod
 
std::string m_option_rawChain_measureRunTimes
 
std::string m_option_rawChain_dataOutputPeriod
 
std::string m_option_rawChain_dataOutputFileName
 
std::string m_option_rawChain_dataOutputFileType
 
std::string m_option_rawChain_dataOutputAllowAll
 
std::string m_option_rawChain_dataOutputAllowedSet
 
std::string m_option_filteredChain_generate
 
std::string m_option_filteredChain_discardedPortion
 
std::string m_option_filteredChain_lag
 
std::string m_option_filteredChain_dataOutputFileName
 
std::string m_option_filteredChain_dataOutputFileType
 
std::string m_option_filteredChain_dataOutputAllowAll
 
std::string m_option_filteredChain_dataOutputAllowedSet
 
std::string m_option_displayCandidates
 
std::string m_option_putOutOfBoundsInChain
 
std::string m_option_tk_useLocalHessian
 
std::string m_option_tk_useNewtonComponent
 
std::string m_option_dr_maxNumExtraStages
 
std::string m_option_dr_listOfScalesForExtraStages
 
std::string m_option_dr_duringAmNonAdaptiveInt
 
std::string m_option_am_keepInitialMatrix
 
std::string m_option_am_initialNonAdaptInterval
 
std::string m_option_am_adaptInterval
 
std::string m_option_am_adaptedMatrices_dataOutputPeriod
 
std::string m_option_am_adaptedMatrices_dataOutputFileName
 
std::string m_option_am_adaptedMatrices_dataOutputFileType
 
std::string m_option_am_adaptedMatrices_dataOutputAllowAll
 
std::string m_option_am_adaptedMatrices_dataOutputAllowedSet
 
std::string m_option_am_eta
 See MhOptionsValues::m_amEta. More...
 
std::string m_option_am_epsilon
 See MhOptionsValues::m_amEpsilon. More...
 
std::string m_option_enableBrooksGelmanConvMonitor
 
std::string m_option_BrooksGelmanLag
 
std::string m_option_outputLogLikelihood
 
std::string m_option_outputLogTarget
 
std::string m_option_doLogitTransform
 

Detailed Description

This class reads the options for the Metropolis-Hastings generator of samples from an input file.

This class implements a Metropolis-Hastings generator of samples. 'SG' stands for 'Sequence Generator'. Metropolis-Hastings generator of samples expects some options to be fully defined. This class reads the options for the Metropolis-Hastings generator of samples from an input file provided by the user. The class expects the prefix '<prefix>_mh_'. For instance, if 'prefix' is 'foo_775_fp_', then the constructor will read all options that begin with 'foo_775_fp_mh_'. Options reading is hpandled by class 'MetropolisHastingsOptions'. To set options by hand, use the MhOptionsValues class.

Definition at line 733 of file MetropolisHastingsSGOptions.h.

Constructor & Destructor Documentation

QUESO::MetropolisHastingsSGOptions::MetropolisHastingsSGOptions ( const BaseEnvironment &  env,
const char *  prefix 
)

Constructor: reads options from the input file.

Definition at line 641 of file MetropolisHastingsSGOptions.C.

References m_env, QUESO::BaseEnvironment::optionsInputFileName(), queso_deprecated, and queso_require_not_equal_to_msg.

644  :
645 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
646  m_ov (NULL,NULL), // dakota
647  m_rawChainStatisticalOptionsObj (NULL),
648  m_rawChainStatOptsInstantiated (false),
649  m_filteredChainStatisticalOptionsObj (NULL),
650  m_filteredChainStatOptsInstantiated (false),
651 #else
652  m_ov (),
653 #endif
654  m_prefix ((std::string)(prefix) + "mh_"),
655  m_env (env),
656  m_optionsDesc (new boost::program_options::options_description("Bayesian Metropolis-Hastings options")),
657  m_option_help (m_prefix + "help" ),
658  m_option_dataOutputFileName (m_prefix + "dataOutputFileName" ),
659  m_option_dataOutputAllowAll (m_prefix + "dataOutputAllowAll" ),
660  m_option_dataOutputAllowedSet (m_prefix + "dataOutputAllowedSet" ),
661  m_option_totallyMute (m_prefix + "totallyMute" ),
662  m_option_initialPosition_dataInputFileName (m_prefix + "initialPosition_dataInputFileName" ),
663  m_option_initialPosition_dataInputFileType (m_prefix + "initialPosition_dataInputFileType" ),
664  m_option_initialProposalCovMatrix_dataInputFileName(m_prefix + "initialProposalCovMatrix_dataInputFileName"),
665  m_option_initialProposalCovMatrix_dataInputFileType(m_prefix + "initialProposalCovMatrix_dataInputFileType"),
666  m_option_listOfDisabledParameters (m_prefix + "listOfDisabledParameters" ),
667  m_option_rawChain_dataInputFileName (m_prefix + "rawChain_dataInputFileName" ),
668  m_option_rawChain_dataInputFileType (m_prefix + "rawChain_dataInputFileType" ),
669  m_option_rawChain_size (m_prefix + "rawChain_size" ),
670  m_option_rawChain_generateExtra (m_prefix + "rawChain_generateExtra" ),
671  m_option_rawChain_displayPeriod (m_prefix + "rawChain_displayPeriod" ),
672  m_option_rawChain_measureRunTimes (m_prefix + "rawChain_measureRunTimes" ),
673  m_option_rawChain_dataOutputPeriod (m_prefix + "rawChain_dataOutputPeriod" ),
674  m_option_rawChain_dataOutputFileName (m_prefix + "rawChain_dataOutputFileName" ),
675  m_option_rawChain_dataOutputFileType (m_prefix + "rawChain_dataOutputFileType" ),
676  m_option_rawChain_dataOutputAllowAll (m_prefix + "rawChain_dataOutputAllowAll" ),
677  m_option_rawChain_dataOutputAllowedSet (m_prefix + "rawChain_dataOutputAllowedSet" ),
678 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
679  m_option_rawChain_computeStats (m_prefix + "rawChain_computeStats" ),
680 #endif
681  m_option_filteredChain_generate (m_prefix + "filteredChain_generate" ),
682  m_option_filteredChain_discardedPortion (m_prefix + "filteredChain_discardedPortion" ),
683  m_option_filteredChain_lag (m_prefix + "filteredChain_lag" ),
684  m_option_filteredChain_dataOutputFileName (m_prefix + "filteredChain_dataOutputFileName" ),
685  m_option_filteredChain_dataOutputFileType (m_prefix + "filteredChain_dataOutputFileType" ),
686  m_option_filteredChain_dataOutputAllowAll (m_prefix + "filteredChain_dataOutputAllowAll" ),
687  m_option_filteredChain_dataOutputAllowedSet (m_prefix + "filteredChain_dataOutputAllowedSet" ),
688 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
689  m_option_filteredChain_computeStats (m_prefix + "filteredChain_computeStats" ),
690 #endif
691  m_option_displayCandidates (m_prefix + "displayCandidates" ),
692  m_option_putOutOfBoundsInChain (m_prefix + "putOutOfBoundsInChain" ),
693  m_option_tk_useLocalHessian (m_prefix + "tk_useLocalHessian" ),
694  m_option_tk_useNewtonComponent (m_prefix + "tk_useNewtonComponent" ),
695  m_option_dr_maxNumExtraStages (m_prefix + "dr_maxNumExtraStages" ),
696  m_option_dr_listOfScalesForExtraStages (m_prefix + "dr_listOfScalesForExtraStages" ),
697  m_option_dr_duringAmNonAdaptiveInt (m_prefix + "dr_duringAmNonAdaptiveInt" ),
698  m_option_am_keepInitialMatrix (m_prefix + "am_keepInitialMatrix" ),
699  m_option_am_initialNonAdaptInterval (m_prefix + "am_initialNonAdaptInterval" ),
700  m_option_am_adaptInterval (m_prefix + "am_adaptInterval" ),
701  m_option_am_adaptedMatrices_dataOutputPeriod (m_prefix + "am_adaptedMatrices_dataOutputPeriod" ),
702  m_option_am_adaptedMatrices_dataOutputFileName (m_prefix + "am_adaptedMatrices_dataOutputFileName" ),
703  m_option_am_adaptedMatrices_dataOutputFileType (m_prefix + "am_adaptedMatrices_dataOutputFileType" ),
704  m_option_am_adaptedMatrices_dataOutputAllowAll (m_prefix + "am_adaptedMatrices_dataOutputAllowAll" ),
705  m_option_am_adaptedMatrices_dataOutputAllowedSet (m_prefix + "am_adaptedMatrices_dataOutputAllowedSet" ),
706  m_option_am_eta (m_prefix + "am_eta" ),
707  m_option_am_epsilon (m_prefix + "am_epsilon" ),
708  m_option_enableBrooksGelmanConvMonitor (m_prefix + "enableBrooksGelmanConvMonitor" ),
709  m_option_BrooksGelmanLag (m_prefix + "BrooksGelmanLag" ),
710  m_option_outputLogLikelihood (m_prefix + "outputLogLikelihood" ),
711  m_option_outputLogTarget (m_prefix + "outputLogTarget" ),
712  m_option_doLogitTransform (m_prefix + "doLogitTransform" )
713 {
714  queso_deprecated();
715 
716  queso_require_not_equal_to_msg(m_env.optionsInputFileName(), "", "this constructor is incompatible with the absence of an options input file");
717 }
queso_require_not_equal_to_msg
#define queso_require_not_equal_to_msg(expr1, expr2, msg)
Definition: asserts.h:86
QUESO::BaseEnvironment::optionsInputFileName
std::string optionsInputFileName() const
Access to the attribute m_optionsInputFileName, which stores the name of the input file passed by the...
Definition: Environment.C:307
QUESO::MetropolisHastingsSGOptions::m_option_am_eta
std::string m_option_am_eta
See MhOptionsValues::m_amEta.
Definition: MetropolisHastingsSGOptions.h:835
queso_deprecated
#define queso_deprecated()
Definition: Defines.h:120
QUESO::MetropolisHastingsSGOptions::m_option_am_epsilon
std::string m_option_am_epsilon
See MhOptionsValues::m_amEpsilon.
Definition: MetropolisHastingsSGOptions.h:837
QUESO::MetropolisHastingsSGOptions::m_optionsDesc
boost::program_options::options_description * m_optionsDesc
Definition: MetropolisHastingsSGOptions.h:780
QUESO::MetropolisHastingsSGOptions::m_ov
MhOptionsValues m_ov
This class is where the actual options are stored.
Definition: MetropolisHastingsSGOptions.h:762
QUESO::MetropolisHastingsSGOptions::MetropolisHastingsSGOptions ( const BaseEnvironment &  env,
const char *  prefix,
const MhOptionsValues &  alternativeOptionsValues 
)

Constructor: with alternative option values.

In this constructor, the input options are given by alternativeOptionsValues.

Definition at line 719 of file MetropolisHastingsSGOptions.C.

References m_env, m_ov, m_prefix, QUESO::MhOptionsValues::m_totallyMute, QUESO::BaseEnvironment::optionsInputFileName(), queso_deprecated, queso_require_equal_to_msg, and QUESO::BaseEnvironment::subDisplayFile().

723  :
724  m_ov (alternativeOptionsValues),
725 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
726  m_rawChainStatisticalOptionsObj (NULL),
727  m_rawChainStatOptsInstantiated (false),
728  m_filteredChainStatisticalOptionsObj (NULL),
729  m_filteredChainStatOptsInstantiated (false),
730 #endif
731  m_prefix ((std::string)(prefix) + "mh_"),
732  m_env (env),
733  m_optionsDesc (NULL),
734  m_option_help (m_prefix + "help" ),
735  m_option_dataOutputFileName (m_prefix + "dataOutputFileName" ),
736  m_option_dataOutputAllowAll (m_prefix + "dataOutputAllowAll" ),
737  m_option_dataOutputAllowedSet (m_prefix + "dataOutputAllowedSet" ),
738  m_option_totallyMute (m_prefix + "totallyMute" ),
739  m_option_initialPosition_dataInputFileName (m_prefix + "initialPosition_dataInputFileName" ),
740  m_option_initialPosition_dataInputFileType (m_prefix + "initialPosition_dataInputFileType" ),
741  m_option_initialProposalCovMatrix_dataInputFileName(m_prefix + "initialProposalCovMatrix_dataInputFileName"),
742  m_option_initialProposalCovMatrix_dataInputFileType(m_prefix + "initialProposalCovMatrix_dataInputFileType"),
743  m_option_listOfDisabledParameters (m_prefix + "listOfDisabledParameters" ),
744  m_option_rawChain_dataInputFileName (m_prefix + "rawChain_dataInputFileName" ),
745  m_option_rawChain_dataInputFileType (m_prefix + "rawChain_dataInputFileType" ),
746  m_option_rawChain_size (m_prefix + "rawChain_size" ),
747  m_option_rawChain_generateExtra (m_prefix + "rawChain_generateExtra" ),
748  m_option_rawChain_displayPeriod (m_prefix + "rawChain_displayPeriod" ),
749  m_option_rawChain_measureRunTimes (m_prefix + "rawChain_measureRunTimes" ),
750  m_option_rawChain_dataOutputPeriod (m_prefix + "rawChain_dataOutputPeriod" ),
751  m_option_rawChain_dataOutputFileName (m_prefix + "rawChain_dataOutputFileName" ),
752  m_option_rawChain_dataOutputFileType (m_prefix + "rawChain_dataOutputFileType" ),
753  m_option_rawChain_dataOutputAllowAll (m_prefix + "rawChain_dataOutputAllowAll" ),
754  m_option_rawChain_dataOutputAllowedSet (m_prefix + "rawChain_dataOutputAllowedSet" ),
755 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
756  m_option_rawChain_computeStats (m_prefix + "rawChain_computeStats" ),
757 #endif
758  m_option_filteredChain_generate (m_prefix + "filteredChain_generate" ),
759  m_option_filteredChain_discardedPortion (m_prefix + "filteredChain_discardedPortion" ),
760  m_option_filteredChain_lag (m_prefix + "filteredChain_lag" ),
761  m_option_filteredChain_dataOutputFileName (m_prefix + "filteredChain_dataOutputFileName" ),
762  m_option_filteredChain_dataOutputFileType (m_prefix + "filteredChain_dataOutputFileType" ),
763  m_option_filteredChain_dataOutputAllowAll (m_prefix + "filteredChain_dataOutputAllowAll" ),
764  m_option_filteredChain_dataOutputAllowedSet (m_prefix + "filteredChain_dataOutputAllowedSet" ),
765 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
766  m_option_filteredChain_computeStats (m_prefix + "filteredChain_computeStats" ),
767 #endif
768  m_option_displayCandidates (m_prefix + "displayCandidates" ),
769  m_option_putOutOfBoundsInChain (m_prefix + "putOutOfBoundsInChain" ),
770  m_option_tk_useLocalHessian (m_prefix + "tk_useLocalHessian" ),
771  m_option_tk_useNewtonComponent (m_prefix + "tk_useNewtonComponent" ),
772  m_option_dr_maxNumExtraStages (m_prefix + "dr_maxNumExtraStages" ),
773  m_option_dr_listOfScalesForExtraStages (m_prefix + "dr_listOfScalesForExtraStages" ),
774  m_option_dr_duringAmNonAdaptiveInt (m_prefix + "dr_duringAmNonAdaptiveInt" ),
775  m_option_am_keepInitialMatrix (m_prefix + "am_keepInitialMatrix" ),
776  m_option_am_initialNonAdaptInterval (m_prefix + "am_initialNonAdaptInterval" ),
777  m_option_am_adaptInterval (m_prefix + "am_adaptInterval" ),
778  m_option_am_adaptedMatrices_dataOutputPeriod (m_prefix + "am_adaptedMatrices_dataOutputPeriod" ),
779  m_option_am_adaptedMatrices_dataOutputFileName (m_prefix + "am_adaptedMatrices_dataOutputFileName" ),
780  m_option_am_adaptedMatrices_dataOutputFileType (m_prefix + "am_adaptedMatrices_dataOutputFileType" ),
781  m_option_am_adaptedMatrices_dataOutputAllowAll (m_prefix + "am_adaptedMatrices_dataOutputAllowAll" ),
782  m_option_am_adaptedMatrices_dataOutputAllowedSet (m_prefix + "am_adaptedMatrices_dataOutputAllowedSet" ),
783  m_option_am_eta (m_prefix + "am_eta" ),
784  m_option_am_epsilon (m_prefix + "am_epsilon" ),
785  m_option_enableBrooksGelmanConvMonitor (m_prefix + "enableBrooksGelmanConvMonitor" ),
786  m_option_BrooksGelmanLag (m_prefix + "BrooksGelmanLag" ),
787  m_option_outputLogLikelihood (m_prefix + "outputLogLikelihood" ),
788  m_option_outputLogTarget (m_prefix + "outputLogTarget" ),
789  m_option_doLogitTransform (m_prefix + "doLogitTransform" )
790 {
791  queso_deprecated();
792 
793  queso_require_equal_to_msg(m_env.optionsInputFileName(), "", "this constructor is incompatible with the existence of an options input file");
794 
795  if ((m_env.subDisplayFile() != NULL ) &&
796  (m_ov.m_totallyMute == false)) {
797  *m_env.subDisplayFile() << "In MetropolisHastingsSGOptions::constructor(2)"
798  << ": after setting values of options with prefix '" << m_prefix
799  << "', state of object is:"
800  << "\n" << *this
801  << std::endl;
802  }
803 
804 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
805  if (m_ov.m_rawChainComputeStats) {
806  m_rawChainStatisticalOptionsObj = new SequenceStatisticalOptions(m_env,m_prefix + "rawChain_",m_ov.m_alternativeRawSsOptionsValues);
807  m_rawChainStatOptsInstantiated = true;
808  }
809  if (m_ov.m_filteredChainComputeStats) {
810  m_filteredChainStatisticalOptionsObj = new SequenceStatisticalOptions(m_env,m_prefix + "filteredChain_",m_ov.m_alternativeFilteredSsOptionsValues);
811  m_filteredChainStatOptsInstantiated = true;
812  }
813 #endif
814 }
queso_require_equal_to_msg
#define queso_require_equal_to_msg(expr1, expr2, msg)
Definition: asserts.h:85
QUESO::BaseEnvironment::optionsInputFileName
std::string optionsInputFileName() const
Access to the attribute m_optionsInputFileName, which stores the name of the input file passed by the...
Definition: Environment.C:307
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:274
QUESO::MetropolisHastingsSGOptions::m_option_am_eta
std::string m_option_am_eta
See MhOptionsValues::m_amEta.
Definition: MetropolisHastingsSGOptions.h:835
QUESO::MhOptionsValues::m_totallyMute
bool m_totallyMute
If true, zero output is written to files. Default is false.
Definition: MetropolisHastingsSGOptions.h:194
queso_deprecated
#define queso_deprecated()
Definition: Defines.h:120
QUESO::MetropolisHastingsSGOptions::m_option_am_epsilon
std::string m_option_am_epsilon
See MhOptionsValues::m_amEpsilon.
Definition: MetropolisHastingsSGOptions.h:837
QUESO::MetropolisHastingsSGOptions::m_optionsDesc
boost::program_options::options_description * m_optionsDesc
Definition: MetropolisHastingsSGOptions.h:780
QUESO::MetropolisHastingsSGOptions::m_ov
MhOptionsValues m_ov
This class is where the actual options are stored.
Definition: MetropolisHastingsSGOptions.h:762
QUESO::MetropolisHastingsSGOptions::MetropolisHastingsSGOptions ( const MLSamplingLevelOptions &  mlOptions)

Copy constructor.

Definition at line 816 of file MetropolisHastingsSGOptions.C.

References QUESO::MLSamplingLevelOptions::m_amAdaptedMatricesDataOutputAllowAll, QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputAllowAll, QUESO::MLSamplingLevelOptions::m_amAdaptedMatricesDataOutputAllowedSet, QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputAllowedSet, QUESO::MLSamplingLevelOptions::m_amAdaptedMatricesDataOutputFileName, QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputFileName, QUESO::MLSamplingLevelOptions::m_amAdaptedMatricesDataOutputFileType, QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputFileType, QUESO::MLSamplingLevelOptions::m_amAdaptedMatricesDataOutputPeriod, QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputPeriod, QUESO::MLSamplingLevelOptions::m_amAdaptInterval, QUESO::MhOptionsValues::m_amAdaptInterval, QUESO::MLSamplingLevelOptions::m_amEpsilon, QUESO::MhOptionsValues::m_amEpsilon, QUESO::MLSamplingLevelOptions::m_amEta, QUESO::MhOptionsValues::m_amEta, QUESO::MLSamplingLevelOptions::m_amInitialNonAdaptInterval, QUESO::MhOptionsValues::m_amInitialNonAdaptInterval, QUESO::MLSamplingLevelOptions::m_amKeepInitialMatrix, QUESO::MhOptionsValues::m_amKeepInitialMatrix, QUESO::MhOptionsValues::m_BrooksGelmanLag, QUESO::MLSamplingLevelOptions::m_dataOutputAllowAll, QUESO::MhOptionsValues::m_dataOutputAllowAll, QUESO::MLSamplingLevelOptions::m_dataOutputAllowedSet, QUESO::MhOptionsValues::m_dataOutputAllowedSet, QUESO::MLSamplingLevelOptions::m_dataOutputFileName, QUESO::MhOptionsValues::m_dataOutputFileName, QUESO::MLSamplingLevelOptions::m_displayCandidates, QUESO::MhOptionsValues::m_displayCandidates, QUESO::MLSamplingLevelOptions::m_doLogitTransform, QUESO::MhOptionsValues::m_doLogitTransform, QUESO::MLSamplingLevelOptions::m_drDuringAmNonAdaptiveInt, QUESO::MhOptionsValues::m_drDuringAmNonAdaptiveInt, QUESO::MLSamplingLevelOptions::m_drMaxNumExtraStages, QUESO::MhOptionsValues::m_drMaxNumExtraStages, QUESO::MLSamplingLevelOptions::m_drScalesForExtraStages, QUESO::MhOptionsValues::m_drScalesForExtraStages, QUESO::MhOptionsValues::m_enableBrooksGelmanConvMonitor, m_env, QUESO::MLSamplingLevelOptions::m_filteredChainDataOutputAllowAll, QUESO::MhOptionsValues::m_filteredChainDataOutputAllowAll, QUESO::MLSamplingLevelOptions::m_filteredChainDataOutputAllowedSet, QUESO::MhOptionsValues::m_filteredChainDataOutputAllowedSet, QUESO::MLSamplingLevelOptions::m_filteredChainDataOutputFileName, QUESO::MhOptionsValues::m_filteredChainDataOutputFileName, QUESO::MLSamplingLevelOptions::m_filteredChainDataOutputFileType, QUESO::MhOptionsValues::m_filteredChainDataOutputFileType, QUESO::MLSamplingLevelOptions::m_filteredChainDiscardedPortion, QUESO::MhOptionsValues::m_filteredChainDiscardedPortion, QUESO::MLSamplingLevelOptions::m_filteredChainGenerate, QUESO::MhOptionsValues::m_filteredChainGenerate, QUESO::MLSamplingLevelOptions::m_filteredChainLag, QUESO::MhOptionsValues::m_filteredChainLag, QUESO::MhOptionsValues::m_initialPositionDataInputFileName, QUESO::MLSamplingLevelOptions::m_initialPositionDataInputFileName, QUESO::MhOptionsValues::m_initialPositionDataInputFileType, QUESO::MLSamplingLevelOptions::m_initialPositionDataInputFileType, QUESO::MLSamplingLevelOptions::m_initialProposalCovMatrixDataInputFileName, QUESO::MhOptionsValues::m_initialProposalCovMatrixDataInputFileName, QUESO::MLSamplingLevelOptions::m_initialProposalCovMatrixDataInputFileType, QUESO::MhOptionsValues::m_initialProposalCovMatrixDataInputFileType, QUESO::MhOptionsValues::m_outputLogLikelihood, QUESO::MhOptionsValues::m_outputLogTarget, m_ov, QUESO::MLSamplingLevelOptions::m_parameterDisabledSet, QUESO::MhOptionsValues::m_parameterDisabledSet, m_prefix, QUESO::MLSamplingLevelOptions::m_putOutOfBoundsInChain, QUESO::MhOptionsValues::m_putOutOfBoundsInChain, QUESO::MLSamplingLevelOptions::m_rawChainDataInputFileName, QUESO::MhOptionsValues::m_rawChainDataInputFileName, QUESO::MLSamplingLevelOptions::m_rawChainDataInputFileType, QUESO::MhOptionsValues::m_rawChainDataInputFileType, QUESO::MLSamplingLevelOptions::m_rawChainDataOutputAllowAll, QUESO::MhOptionsValues::m_rawChainDataOutputAllowAll, QUESO::MLSamplingLevelOptions::m_rawChainDataOutputAllowedSet, QUESO::MhOptionsValues::m_rawChainDataOutputAllowedSet, QUESO::MLSamplingLevelOptions::m_rawChainDataOutputFileName, QUESO::MhOptionsValues::m_rawChainDataOutputFileName, QUESO::MLSamplingLevelOptions::m_rawChainDataOutputFileType, QUESO::MhOptionsValues::m_rawChainDataOutputFileType, QUESO::MLSamplingLevelOptions::m_rawChainDataOutputPeriod, QUESO::MhOptionsValues::m_rawChainDataOutputPeriod, QUESO::MLSamplingLevelOptions::m_rawChainDisplayPeriod, QUESO::MhOptionsValues::m_rawChainDisplayPeriod, QUESO::MLSamplingLevelOptions::m_rawChainGenerateExtra, QUESO::MhOptionsValues::m_rawChainGenerateExtra, QUESO::MLSamplingLevelOptions::m_rawChainMeasureRunTimes, QUESO::MhOptionsValues::m_rawChainMeasureRunTimes, QUESO::MLSamplingLevelOptions::m_rawChainSize, QUESO::MhOptionsValues::m_rawChainSize, QUESO::MLSamplingLevelOptions::m_tkUseLocalHessian, QUESO::MhOptionsValues::m_tkUseLocalHessian, QUESO::MLSamplingLevelOptions::m_tkUseNewtonComponent, QUESO::MhOptionsValues::m_tkUseNewtonComponent, QUESO::MhOptionsValues::m_totallyMute, QUESO::MLSamplingLevelOptions::m_totallyMute, queso_deprecated, QUESO::BaseEnvironment::subDisplayFile(), UQ_MH_SG_BROOKS_GELMAN_LAG, UQ_MH_SG_ENABLE_BROOKS_GELMAN_CONV_MONITOR, UQ_MH_SG_OUTPUT_LOG_LIKELIHOOD, and UQ_MH_SG_OUTPUT_LOG_TARGET.

818  :
819 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
820  m_ov (NULL,NULL), // dakota
821  m_rawChainStatisticalOptionsObj (NULL),
822  m_rawChainStatOptsInstantiated (false),
823  m_filteredChainStatisticalOptionsObj (NULL),
824  m_filteredChainStatOptsInstantiated (false),
825 #else
826  m_ov (),
827 #endif
828  m_prefix (mlOptions.m_prefix),
829  m_env (mlOptions.env()),
830  m_optionsDesc (NULL),
831  m_option_help (m_prefix + "help" ),
832  m_option_dataOutputFileName (m_prefix + "dataOutputFileName" ),
833  m_option_dataOutputAllowAll (m_prefix + "dataOutputAllowAll" ),
834  m_option_dataOutputAllowedSet (m_prefix + "dataOutputAllowedSet" ),
835  m_option_totallyMute (m_prefix + "totallyMute" ),
836  m_option_initialPosition_dataInputFileName (m_prefix + "initialPosition_dataInputFileName" ),
837  m_option_initialPosition_dataInputFileType (m_prefix + "initialPosition_dataInputFileType" ),
838  m_option_initialProposalCovMatrix_dataInputFileName(m_prefix + "initialProposalCovMatrix_dataInputFileName"),
839  m_option_initialProposalCovMatrix_dataInputFileType(m_prefix + "initialProposalCovMatrix_dataInputFileType"),
840  m_option_listOfDisabledParameters (m_prefix + "listOfDisabledParameters" ),
841  m_option_rawChain_dataInputFileName (m_prefix + "rawChain_dataInputFileName" ),
842  m_option_rawChain_dataInputFileType (m_prefix + "rawChain_dataInputFileType" ),
843  m_option_rawChain_size (m_prefix + "rawChain_size" ),
844  m_option_rawChain_generateExtra (m_prefix + "rawChain_generateExtra" ),
845  m_option_rawChain_displayPeriod (m_prefix + "rawChain_displayPeriod" ),
846  m_option_rawChain_measureRunTimes (m_prefix + "rawChain_measureRunTimes" ),
847  m_option_rawChain_dataOutputPeriod (m_prefix + "rawChain_dataOutputPeriod" ),
848  m_option_rawChain_dataOutputFileName (m_prefix + "rawChain_dataOutputFileName" ),
849  m_option_rawChain_dataOutputFileType (m_prefix + "rawChain_dataOutputFileType" ),
850  m_option_rawChain_dataOutputAllowAll (m_prefix + "rawChain_dataOutputAllowAll" ),
851  m_option_rawChain_dataOutputAllowedSet (m_prefix + "rawChain_dataOutputAllowedSet" ),
852 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
853  m_option_rawChain_computeStats (m_prefix + "rawChain_computeStats" ),
854 #endif
855  m_option_filteredChain_generate (m_prefix + "filteredChain_generate" ),
856  m_option_filteredChain_discardedPortion (m_prefix + "filteredChain_discardedPortion" ),
857  m_option_filteredChain_lag (m_prefix + "filteredChain_lag" ),
858  m_option_filteredChain_dataOutputFileName (m_prefix + "filteredChain_dataOutputFileName" ),
859  m_option_filteredChain_dataOutputFileType (m_prefix + "filteredChain_dataOutputFileType" ),
860  m_option_filteredChain_dataOutputAllowAll (m_prefix + "filteredChain_dataOutputAllowAll" ),
861  m_option_filteredChain_dataOutputAllowedSet (m_prefix + "filteredChain_dataOutputAllowedSet" ),
862 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
863  m_option_filteredChain_computeStats (m_prefix + "filteredChain_computeStats" ),
864 #endif
865  m_option_displayCandidates (m_prefix + "displayCandidates" ),
866  m_option_putOutOfBoundsInChain (m_prefix + "putOutOfBoundsInChain" ),
867  m_option_tk_useLocalHessian (m_prefix + "tk_useLocalHessian" ),
868  m_option_tk_useNewtonComponent (m_prefix + "tk_useNewtonComponent" ),
869  m_option_dr_maxNumExtraStages (m_prefix + "dr_maxNumExtraStages" ),
870  m_option_dr_listOfScalesForExtraStages (m_prefix + "dr_listOfScalesForExtraStages" ),
871  m_option_dr_duringAmNonAdaptiveInt (m_prefix + "dr_duringAmNonAdaptiveInt" ),
872  m_option_am_keepInitialMatrix (m_prefix + "am_keepInitialMatrix" ),
873  m_option_am_initialNonAdaptInterval (m_prefix + "am_initialNonAdaptInterval" ),
874  m_option_am_adaptInterval (m_prefix + "am_adaptInterval" ),
875  m_option_am_adaptedMatrices_dataOutputPeriod (m_prefix + "am_adaptedMatrices_dataOutputPeriod" ),
876  m_option_am_adaptedMatrices_dataOutputFileName (m_prefix + "am_adaptedMatrices_dataOutputFileName" ),
877  m_option_am_adaptedMatrices_dataOutputFileType (m_prefix + "am_adaptedMatrices_dataOutputFileType" ),
878  m_option_am_adaptedMatrices_dataOutputAllowAll (m_prefix + "am_adaptedMatrices_dataOutputAllowAll" ),
879  m_option_am_adaptedMatrices_dataOutputAllowedSet (m_prefix + "am_adaptedMatrices_dataOutputAllowedSet" ),
880  m_option_am_eta (m_prefix + "am_eta" ),
881  m_option_am_epsilon (m_prefix + "am_epsilon" ),
882  m_option_enableBrooksGelmanConvMonitor (m_prefix + "enableBrooksGelmanConvMonitor" ),
883  m_option_BrooksGelmanLag (m_prefix + "BrooksGelmanLag" ),
884  m_option_outputLogLikelihood (m_prefix + "outputLogLikelihood" ),
885  m_option_outputLogTarget (m_prefix + "outputLogTarget" ),
886  m_option_doLogitTransform (m_prefix + "doLogitTransform" )
887 {
888  queso_deprecated();
889 
890  m_ov.m_dataOutputFileName = mlOptions.m_dataOutputFileName;
891  m_ov.m_dataOutputAllowAll = mlOptions.m_dataOutputAllowAll;
892  m_ov.m_dataOutputAllowedSet = mlOptions.m_dataOutputAllowedSet;
893  m_ov.m_totallyMute = mlOptions.m_totallyMute;
894  m_ov.m_initialPositionDataInputFileName = mlOptions.m_initialPositionDataInputFileName;
895  m_ov.m_initialPositionDataInputFileType = mlOptions.m_initialPositionDataInputFileType;
896  m_ov.m_initialProposalCovMatrixDataInputFileName = mlOptions.m_initialProposalCovMatrixDataInputFileName;
897  m_ov.m_initialProposalCovMatrixDataInputFileType = mlOptions.m_initialProposalCovMatrixDataInputFileType;
898  m_ov.m_parameterDisabledSet = mlOptions.m_parameterDisabledSet;
899  m_ov.m_rawChainDataInputFileName = mlOptions.m_rawChainDataInputFileName;
900  m_ov.m_rawChainDataInputFileType = mlOptions.m_rawChainDataInputFileType;
901  m_ov.m_rawChainSize = mlOptions.m_rawChainSize;
902  m_ov.m_rawChainGenerateExtra = mlOptions.m_rawChainGenerateExtra;
903  m_ov.m_rawChainDisplayPeriod = mlOptions.m_rawChainDisplayPeriod;
904  m_ov.m_rawChainMeasureRunTimes = mlOptions.m_rawChainMeasureRunTimes;
905  m_ov.m_rawChainDataOutputPeriod = mlOptions.m_rawChainDataOutputPeriod;
906  m_ov.m_rawChainDataOutputFileName = mlOptions.m_rawChainDataOutputFileName;
907  m_ov.m_rawChainDataOutputFileType = mlOptions.m_rawChainDataOutputFileType;
908  m_ov.m_rawChainDataOutputAllowAll = mlOptions.m_rawChainDataOutputAllowAll;
909  m_ov.m_rawChainDataOutputAllowedSet = mlOptions.m_rawChainDataOutputAllowedSet;
910 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
911  m_ov.m_rawChainComputeStats = mlOptions.m_rawChainComputeStats;
912 #endif
913  m_ov.m_filteredChainGenerate = mlOptions.m_filteredChainGenerate;
914  m_ov.m_filteredChainDiscardedPortion = mlOptions.m_filteredChainDiscardedPortion;
915  m_ov.m_filteredChainLag = mlOptions.m_filteredChainLag;
916  m_ov.m_filteredChainDataOutputFileName = mlOptions.m_filteredChainDataOutputFileName;
917  m_ov.m_filteredChainDataOutputFileType = mlOptions.m_filteredChainDataOutputFileType;
918  m_ov.m_filteredChainDataOutputAllowAll = mlOptions.m_filteredChainDataOutputAllowAll;
919  m_ov.m_filteredChainDataOutputAllowedSet = mlOptions.m_filteredChainDataOutputAllowedSet;
920 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
921  m_ov.m_filteredChainComputeStats = mlOptions.m_filteredChainComputeStats;
922 #endif
923  m_ov.m_displayCandidates = mlOptions.m_displayCandidates;
924  m_ov.m_putOutOfBoundsInChain = mlOptions.m_putOutOfBoundsInChain;
925  m_ov.m_tkUseLocalHessian = mlOptions.m_tkUseLocalHessian;
926  m_ov.m_tkUseNewtonComponent = mlOptions.m_tkUseNewtonComponent;
927  m_ov.m_drMaxNumExtraStages = mlOptions.m_drMaxNumExtraStages;
928  m_ov.m_drScalesForExtraStages = mlOptions.m_drScalesForExtraStages;
929  m_ov.m_drDuringAmNonAdaptiveInt = mlOptions.m_drDuringAmNonAdaptiveInt;
930  m_ov.m_amKeepInitialMatrix = mlOptions.m_amKeepInitialMatrix;
931  m_ov.m_amInitialNonAdaptInterval = mlOptions.m_amInitialNonAdaptInterval;
932  m_ov.m_amAdaptInterval = mlOptions.m_amAdaptInterval;
933  m_ov.m_amAdaptedMatricesDataOutputPeriod = mlOptions.m_amAdaptedMatricesDataOutputPeriod;
934  m_ov.m_amAdaptedMatricesDataOutputFileName = mlOptions.m_amAdaptedMatricesDataOutputFileName;
935  m_ov.m_amAdaptedMatricesDataOutputFileType = mlOptions.m_amAdaptedMatricesDataOutputFileType;
936  m_ov.m_amAdaptedMatricesDataOutputAllowAll = mlOptions.m_amAdaptedMatricesDataOutputAllowAll;
937  m_ov.m_amAdaptedMatricesDataOutputAllowedSet = mlOptions.m_amAdaptedMatricesDataOutputAllowedSet;
938  m_ov.m_amEta = mlOptions.m_amEta;
939  m_ov.m_amEpsilon = mlOptions.m_amEpsilon;
940  m_ov.m_enableBrooksGelmanConvMonitor = UQ_MH_SG_ENABLE_BROOKS_GELMAN_CONV_MONITOR;
941  m_ov.m_BrooksGelmanLag = UQ_MH_SG_BROOKS_GELMAN_LAG;
942  m_ov.m_outputLogLikelihood = UQ_MH_SG_OUTPUT_LOG_LIKELIHOOD;
943  m_ov.m_outputLogTarget = UQ_MH_SG_OUTPUT_LOG_TARGET;
944  m_ov.m_doLogitTransform = mlOptions.m_doLogitTransform;
945 
946 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
947 //m_ov.m_alternativeRawSsOptionsValues = mlOptions.; // dakota
948 //m_ov.m_alternativeFilteredSsOptionsValues = mlOptions.; // dakota
949 #endif
950 
951 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
952  m_rawChainStatisticalOptionsObj = mlOptions.m_rawChainStatisticalOptionsObj; // dakota
953  m_rawChainStatOptsInstantiated = false;
954  m_filteredChainStatisticalOptionsObj = mlOptions.m_filteredChainStatisticalOptionsObj; // dakota
955  m_filteredChainStatOptsInstantiated = false;
956 #endif
957  if ((m_env.subDisplayFile() != NULL ) &&
958  (m_ov.m_totallyMute == false)) {
959  *m_env.subDisplayFile() << "In MetropolisHastingsSGOptions::constructor(3)"
960  << ": after copying values of options with prefix '" << m_prefix
961  << "', state of object is:"
962  << "\n" << *this
963  << std::endl;
964  }
965 }
QUESO::MhOptionsValues::m_filteredChainDataOutputFileType
std::string m_filteredChainDataOutputFileType
The filetype of m_filteredChainDataOutputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:350
QUESO::MhOptionsValues::m_doLogitTransform
bool m_doLogitTransform
Flag for deciding whether or not to do logit transform of bounded domains Default is true...
Definition: MetropolisHastingsSGOptions.h:583
QUESO::MhOptionsValues::m_rawChainGenerateExtra
bool m_rawChainGenerateExtra
If true, extra chain information is computed/stored.
Definition: MetropolisHastingsSGOptions.h:250
UQ_MH_SG_OUTPUT_LOG_LIKELIHOOD
#define UQ_MH_SG_OUTPUT_LOG_LIKELIHOOD
Definition: MetropolisHastingsSGOptions.h:93
QUESO::MhOptionsValues::m_amEpsilon
double m_amEpsilon
Regularisation parameter for the DRAM covariance matrix.
Definition: MetropolisHastingsSGOptions.h:548
QUESO::MhOptionsValues::m_tkUseNewtonComponent
bool m_tkUseNewtonComponent
This option is a no-op. Default is true.
Definition: MetropolisHastingsSGOptions.h:416
QUESO::MhOptionsValues::m_filteredChainDataOutputAllowedSet
std::set< unsigned int > m_filteredChainDataOutputAllowedSet
The set of MPI ranks that will write filtered Markov chain output to a file. See also m_filteredChain...
Definition: MetropolisHastingsSGOptions.h:365
QUESO::MhOptionsValues::m_initialPositionDataInputFileType
std::string m_initialPositionDataInputFileType
The filetype of m_initialPositionDataInputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:203
QUESO::MhOptionsValues::m_rawChainDataInputFileName
std::string m_rawChainDataInputFileName
Filename for reading an already-produced Markov chain.
Definition: MetropolisHastingsSGOptions.h:235
QUESO::MhOptionsValues::m_filteredChainDataOutputFileName
std::string m_filteredChainDataOutputFileName
If not &quot;.&quot;, file name to save the filtered chain to. Default is &quot;.&quot;.
Definition: MetropolisHastingsSGOptions.h:347
QUESO::MhOptionsValues::m_amAdaptInterval
unsigned int m_amAdaptInterval
The frequency at which to adapt the proposal covariance matrix.
Definition: MetropolisHastingsSGOptions.h:491
QUESO::MhOptionsValues::m_amEta
double m_amEta
Proposal covariance scaling factor, usually 2.4 * 2.4 / d.
Definition: MetropolisHastingsSGOptions.h:536
QUESO::MhOptionsValues::m_rawChainDataOutputPeriod
unsigned int m_rawChainDataOutputPeriod
The frequency with which to write chain output. Defaults to 0.
Definition: MetropolisHastingsSGOptions.h:280
UQ_MH_SG_ENABLE_BROOKS_GELMAN_CONV_MONITOR
#define UQ_MH_SG_ENABLE_BROOKS_GELMAN_CONV_MONITOR
Definition: MetropolisHastingsSGOptions.h:91
QUESO::MhOptionsValues::m_outputLogTarget
bool m_outputLogTarget
Flag for deciding whether or not to dump log target values in output Default is true.
Definition: MetropolisHastingsSGOptions.h:580
QUESO::MhOptionsValues::m_drScalesForExtraStages
std::vector< double > m_drScalesForExtraStages
The vector of scale factors for the proposal covariance matrix to use for delayed rejection...
Definition: MetropolisHastingsSGOptions.h:445
QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputAllowedSet
std::set< unsigned int > m_amAdaptedMatricesDataOutputAllowedSet
This option is a no-op. The default is the empty set.
Definition: MetropolisHastingsSGOptions.h:523
QUESO::MhOptionsValues::m_filteredChainLag
unsigned int m_filteredChainLag
Set the lag for the filtered chain. Default is 1.
Definition: MetropolisHastingsSGOptions.h:338
QUESO::MhOptionsValues::m_dataOutputAllowedSet
std::set< unsigned int > m_dataOutputAllowedSet
The set of MPI ranks that can write output. See m_dataOutputAllowAll.
Definition: MetropolisHastingsSGOptions.h:191
QUESO::MhOptionsValues::m_rawChainDataOutputAllowAll
bool m_rawChainDataOutputAllowAll
Toggle for whether or not to allow all processes to write Markov chain output to a file...
Definition: MetropolisHastingsSGOptions.h:306
QUESO::MhOptionsValues::m_rawChainSize
unsigned int m_rawChainSize
The size of the chain (number of posterior samples) to generate. Default is 100.
Definition: MetropolisHastingsSGOptions.h:241
QUESO::MhOptionsValues::m_drMaxNumExtraStages
unsigned int m_drMaxNumExtraStages
The number of delayed rejection stages to do. Default is 0.
Definition: MetropolisHastingsSGOptions.h:426
UQ_MH_SG_BROOKS_GELMAN_LAG
#define UQ_MH_SG_BROOKS_GELMAN_LAG
Definition: MetropolisHastingsSGOptions.h:92
QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputAllowAll
bool m_amAdaptedMatricesDataOutputAllowAll
This option is a no-op. The default is false.
Definition: MetropolisHastingsSGOptions.h:520
QUESO::MhOptionsValues::m_putOutOfBoundsInChain
bool m_putOutOfBoundsInChain
Flag to tell QUESO how chains should be upon generating a proposal that is out of the problem domain...
Definition: MetropolisHastingsSGOptions.h:387
QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputPeriod
unsigned int m_amAdaptedMatricesDataOutputPeriod
The frequency (after m_amInitialNonAdaptInterval samples are done) of printing the last adapted propo...
Definition: MetropolisHastingsSGOptions.h:508
QUESO::MhOptionsValues::m_amKeepInitialMatrix
bool m_amKeepInitialMatrix
This option is a no-op. The default is false.
Definition: MetropolisHastingsSGOptions.h:470
QUESO::MhOptionsValues::m_rawChainDisplayPeriod
unsigned int m_rawChainDisplayPeriod
The frequency with which to output diagnostic information.
Definition: MetropolisHastingsSGOptions.h:260
QUESO::MhOptionsValues::m_initialProposalCovMatrixDataInputFileName
std::string m_initialProposalCovMatrixDataInputFileName
If not &quot;.&quot;, reads the contents of the file as the initial proposal covariance matrix.
Definition: MetropolisHastingsSGOptions.h:215
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:274
QUESO::MhOptionsValues::m_dataOutputAllowAll
bool m_dataOutputAllowAll
If true, all processes write output and m_dataOutputAllowedSet is ignored.
Definition: MetropolisHastingsSGOptions.h:185
QUESO::MhOptionsValues::m_amInitialNonAdaptInterval
unsigned int m_amInitialNonAdaptInterval
The number of initial samples to do without adapting the proposal covariance matrix.
Definition: MetropolisHastingsSGOptions.h:481
QUESO::MhOptionsValues::m_BrooksGelmanLag
unsigned int m_BrooksGelmanLag
The lag with which to compute the Brooks-Gelman convergence statistic.
Definition: MetropolisHastingsSGOptions.h:574
QUESO::MhOptionsValues::m_filteredChainDiscardedPortion
double m_filteredChainDiscardedPortion
What initial fraction of the filtered chain is discarded.
Definition: MetropolisHastingsSGOptions.h:331
UQ_MH_SG_OUTPUT_LOG_TARGET
#define UQ_MH_SG_OUTPUT_LOG_TARGET
Definition: MetropolisHastingsSGOptions.h:94
QUESO::MhOptionsValues::m_drDuringAmNonAdaptiveInt
bool m_drDuringAmNonAdaptiveInt
Do delayed rejection during the initial non-adaptive part of sampling?
Definition: MetropolisHastingsSGOptions.h:467
QUESO::MhOptionsValues::m_rawChainDataOutputFileName
std::string m_rawChainDataOutputFileName
If not &quot;.&quot;, filename to write the Markov chain to.
Definition: MetropolisHastingsSGOptions.h:291
QUESO::MhOptionsValues::m_rawChainDataOutputFileType
std::string m_rawChainDataOutputFileType
The filetype of m_rawChainDataOutputFileName. Only &quot;m&quot; (matlab) is currently supported. Default is &quot;m&quot;.
Definition: MetropolisHastingsSGOptions.h:294
QUESO::MetropolisHastingsSGOptions::m_option_am_eta
std::string m_option_am_eta
See MhOptionsValues::m_amEta.
Definition: MetropolisHastingsSGOptions.h:835
QUESO::MhOptionsValues::m_totallyMute
bool m_totallyMute
If true, zero output is written to files. Default is false.
Definition: MetropolisHastingsSGOptions.h:194
queso_deprecated
#define queso_deprecated()
Definition: Defines.h:120
QUESO::MhOptionsValues::m_initialPositionDataInputFileName
std::string m_initialPositionDataInputFileName
If not &quot;.&quot;, reads the contents of the file and uses that to start the MCMC. Default is &quot;...
Definition: MetropolisHastingsSGOptions.h:200
QUESO::MetropolisHastingsSGOptions::m_option_am_epsilon
std::string m_option_am_epsilon
See MhOptionsValues::m_amEpsilon.
Definition: MetropolisHastingsSGOptions.h:837
QUESO::MhOptionsValues::m_filteredChainDataOutputAllowAll
bool m_filteredChainDataOutputAllowAll
Toggle for whether or not to allow all processes to write filtered Markov chain output to a file...
Definition: MetropolisHastingsSGOptions.h:362
QUESO::MhOptionsValues::m_displayCandidates
bool m_displayCandidates
Toggle to tell QUESO whether or not to write proposal (candidate) state to output file...
Definition: MetropolisHastingsSGOptions.h:372
QUESO::MetropolisHastingsSGOptions::m_optionsDesc
boost::program_options::options_description * m_optionsDesc
Definition: MetropolisHastingsSGOptions.h:780
QUESO::MhOptionsValues::m_parameterDisabledSet
std::set< unsigned int > m_parameterDisabledSet
Set of parameters that don&#39;t get sampled.
Definition: MetropolisHastingsSGOptions.h:224
QUESO::MetropolisHastingsSGOptions::m_ov
MhOptionsValues m_ov
This class is where the actual options are stored.
Definition: MetropolisHastingsSGOptions.h:762
QUESO::MhOptionsValues::m_enableBrooksGelmanConvMonitor
unsigned int m_enableBrooksGelmanConvMonitor
The frequency with which to compute the Brooks-Gelman convergence statistic.
Definition: MetropolisHastingsSGOptions.h:564
QUESO::MhOptionsValues::m_rawChainMeasureRunTimes
bool m_rawChainMeasureRunTimes
If true, measures timings spent in various chain computions and writes them to the output file...
Definition: MetropolisHastingsSGOptions.h:277
QUESO::MhOptionsValues::m_rawChainDataInputFileType
std::string m_rawChainDataInputFileType
The filetype of m_rawChainDataInputFileName. Only &quot;m&quot; (matlab) is currently supported. Default is &quot;m&quot;.
Definition: MetropolisHastingsSGOptions.h:238
QUESO::MhOptionsValues::m_tkUseLocalHessian
bool m_tkUseLocalHessian
Flag to tell QUESO whether or not to use Hessian information for the proposal covariance matrix...
Definition: MetropolisHastingsSGOptions.h:413
QUESO::MhOptionsValues::m_filteredChainGenerate
bool m_filteredChainGenerate
Toggle the option to save a filtered chain.
Definition: MetropolisHastingsSGOptions.h:322
QUESO::MhOptionsValues::m_rawChainDataOutputAllowedSet
std::set< unsigned int > m_rawChainDataOutputAllowedSet
The set of MPI ranks that will write Markov chain output to a file. See also m_rawChainDataOutputAllo...
Definition: MetropolisHastingsSGOptions.h:309
QUESO::MhOptionsValues::m_initialProposalCovMatrixDataInputFileType
std::string m_initialProposalCovMatrixDataInputFileType
The filetype of m_initialProposalCovMatrixDataInputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:218
QUESO::MhOptionsValues::m_outputLogLikelihood
bool m_outputLogLikelihood
Flag for deciding whether or not to dump log likelihood values in output. Default is true...
Definition: MetropolisHastingsSGOptions.h:577
QUESO::MhOptionsValues::m_dataOutputFileName
std::string m_dataOutputFileName
The base name of output files where the chain (and related information) will be written.
Definition: MetropolisHastingsSGOptions.h:176
QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputFileName
std::string m_amAdaptedMatricesDataOutputFileName
If not &quot;.&quot;, this is the file to write adapted proposal covariance matrices to. Default is &quot;...
Definition: MetropolisHastingsSGOptions.h:514
QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputFileType
std::string m_amAdaptedMatricesDataOutputFileType
The filetype of m_amAdaptedMatricesDataOutputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:517
QUESO::MetropolisHastingsSGOptions::~MetropolisHastingsSGOptions ( )

Destructor.

Definition at line 967 of file MetropolisHastingsSGOptions.C.

References m_optionsDesc, and queso_deprecated.

968 {
969  queso_deprecated();
970 
971 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
972  if (m_filteredChainStatOptsInstantiated) delete m_filteredChainStatisticalOptionsObj;
973  if (m_rawChainStatOptsInstantiated ) delete m_rawChainStatisticalOptionsObj;
974 #endif
975  if (m_optionsDesc ) delete m_optionsDesc;
976 }
queso_deprecated
#define queso_deprecated()
Definition: Defines.h:120
QUESO::MetropolisHastingsSGOptions::m_optionsDesc
boost::program_options::options_description * m_optionsDesc
Definition: MetropolisHastingsSGOptions.h:780

Member Function Documentation

void QUESO::MetropolisHastingsSGOptions::defineMyOptions ( boost::program_options::options_description &  optionsDesc) const
private

Defines the options for the Metropolis-Hastings generator of samples as the default options.

Definition at line 1100 of file MetropolisHastingsSGOptions.C.

References m_option_am_adaptedMatrices_dataOutputAllowAll, m_option_am_adaptedMatrices_dataOutputAllowedSet, m_option_am_adaptedMatrices_dataOutputFileName, m_option_am_adaptedMatrices_dataOutputFileType, m_option_am_adaptedMatrices_dataOutputPeriod, m_option_am_adaptInterval, m_option_am_epsilon, m_option_am_eta, m_option_am_initialNonAdaptInterval, m_option_am_keepInitialMatrix, m_option_BrooksGelmanLag, m_option_dataOutputAllowAll, m_option_dataOutputAllowedSet, m_option_dataOutputFileName, m_option_displayCandidates, m_option_doLogitTransform, m_option_dr_duringAmNonAdaptiveInt, m_option_dr_listOfScalesForExtraStages, m_option_dr_maxNumExtraStages, m_option_enableBrooksGelmanConvMonitor, m_option_filteredChain_dataOutputAllowAll, m_option_filteredChain_dataOutputAllowedSet, m_option_filteredChain_dataOutputFileName, m_option_filteredChain_dataOutputFileType, m_option_filteredChain_discardedPortion, m_option_filteredChain_generate, m_option_filteredChain_lag, m_option_help, m_option_initialPosition_dataInputFileName, m_option_initialPosition_dataInputFileType, m_option_initialProposalCovMatrix_dataInputFileName, m_option_initialProposalCovMatrix_dataInputFileType, m_option_listOfDisabledParameters, m_option_outputLogLikelihood, m_option_outputLogTarget, m_option_putOutOfBoundsInChain, m_option_rawChain_dataInputFileName, m_option_rawChain_dataInputFileType, m_option_rawChain_dataOutputAllowAll, m_option_rawChain_dataOutputAllowedSet, m_option_rawChain_dataOutputFileName, m_option_rawChain_dataOutputFileType, m_option_rawChain_dataOutputPeriod, m_option_rawChain_displayPeriod, m_option_rawChain_generateExtra, m_option_rawChain_measureRunTimes, m_option_rawChain_size, m_option_tk_useLocalHessian, m_option_tk_useNewtonComponent, m_option_totallyMute, queso_deprecated, UQ_MH_SG_AM_ADAPT_INTERVAL_ODV, UQ_MH_SG_AM_ADAPTED_MATRICES_DATA_OUTPUT_ALLOW_ALL_ODV, UQ_MH_SG_AM_ADAPTED_MATRICES_DATA_OUTPUT_ALLOWED_SET_ODV, UQ_MH_SG_AM_ADAPTED_MATRICES_DATA_OUTPUT_FILE_NAME_ODV, UQ_MH_SG_AM_ADAPTED_MATRICES_DATA_OUTPUT_FILE_TYPE_ODV, UQ_MH_SG_AM_ADAPTED_MATRICES_DATA_OUTPUT_PERIOD_ODV, UQ_MH_SG_AM_EPSILON_ODV, UQ_MH_SG_AM_ETA_ODV, UQ_MH_SG_AM_INIT_NON_ADAPT_INT_ODV, UQ_MH_SG_AM_KEEP_INITIAL_MATRIX_ODV, UQ_MH_SG_BROOKS_GELMAN_LAG, UQ_MH_SG_DATA_OUTPUT_ALLOW_ALL_ODV, UQ_MH_SG_DATA_OUTPUT_ALLOWED_SET_ODV, UQ_MH_SG_DATA_OUTPUT_FILE_NAME_ODV, UQ_MH_SG_DISPLAY_CANDIDATES_ODV, UQ_MH_SG_DO_LOGIT_TRANSFORM, UQ_MH_SG_DR_DURING_AM_NON_ADAPTIVE_INT_ODV, UQ_MH_SG_DR_LIST_OF_SCALES_FOR_EXTRA_STAGES_ODV, UQ_MH_SG_DR_MAX_NUM_EXTRA_STAGES_ODV, UQ_MH_SG_ENABLE_BROOKS_GELMAN_CONV_MONITOR, UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_ALLOW_ALL_ODV, UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_ALLOWED_SET_ODV, UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_FILE_NAME_ODV, UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_FILE_TYPE_ODV, UQ_MH_SG_FILTERED_CHAIN_DISCARDED_PORTION_ODV, UQ_MH_SG_FILTERED_CHAIN_GENERATE_ODV, UQ_MH_SG_FILTERED_CHAIN_LAG_ODV, UQ_MH_SG_INITIAL_POSITION_DATA_INPUT_FILE_NAME_ODV, UQ_MH_SG_INITIAL_POSITION_DATA_INPUT_FILE_TYPE_ODV, UQ_MH_SG_INITIAL_PROPOSAL_COV_MATRIX_DATA_INPUT_FILE_NAME_ODV, UQ_MH_SG_INITIAL_PROPOSAL_COV_MATRIX_DATA_INPUT_FILE_TYPE_ODV, UQ_MH_SG_LIST_OF_DISABLED_PARAMETERS_ODV, UQ_MH_SG_OUTPUT_LOG_LIKELIHOOD, UQ_MH_SG_OUTPUT_LOG_TARGET, UQ_MH_SG_PUT_OUT_OF_BOUNDS_IN_CHAIN_ODV, UQ_MH_SG_RAW_CHAIN_DATA_INPUT_FILE_NAME_ODV, UQ_MH_SG_RAW_CHAIN_DATA_INPUT_FILE_TYPE_ODV, UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_ALLOW_ALL_ODV, UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_ALLOWED_SET_ODV, UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_FILE_NAME_ODV, UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_FILE_TYPE_ODV, UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_PERIOD_ODV, UQ_MH_SG_RAW_CHAIN_DISPLAY_PERIOD_ODV, UQ_MH_SG_RAW_CHAIN_GENERATE_EXTRA_ODV, UQ_MH_SG_RAW_CHAIN_MEASURE_RUN_TIMES_ODV, UQ_MH_SG_RAW_CHAIN_SIZE_ODV, UQ_MH_SG_TK_USE_LOCAL_HESSIAN_ODV, UQ_MH_SG_TK_USE_NEWTON_COMPONENT_ODV, and UQ_MH_SG_TOTALLY_MUTE_ODV.

Referenced by scanOptionsValues().

1101 {
1102  queso_deprecated();
1103 
1104  optionsDesc.add_options()
1105  (m_option_help.c_str(), "produce help msg for Bayesian Metropolis-Hastings" )
1106  (m_option_dataOutputFileName.c_str(), boost::program_options::value<std::string >()->default_value(UQ_MH_SG_DATA_OUTPUT_FILE_NAME_ODV ), "name of generic output file" )
1107  (m_option_dataOutputAllowAll.c_str(), boost::program_options::value<bool >()->default_value(UQ_MH_SG_DATA_OUTPUT_ALLOW_ALL_ODV ), "allow all subEnvs write to a generic output file" )
1108  (m_option_dataOutputAllowedSet.c_str(), boost::program_options::value<std::string >()->default_value(UQ_MH_SG_DATA_OUTPUT_ALLOWED_SET_ODV ), "subEnvs that will write to generic output file" )
1109  (m_option_totallyMute.c_str(), boost::program_options::value<bool >()->default_value(UQ_MH_SG_TOTALLY_MUTE_ODV ), "totally mute (no printout msg)" )
1110  (m_option_initialPosition_dataInputFileName.c_str(), boost::program_options::value<std::string >()->default_value(UQ_MH_SG_INITIAL_POSITION_DATA_INPUT_FILE_NAME_ODV ), "name of input file for raw chain " )
1111  (m_option_initialPosition_dataInputFileType.c_str(), boost::program_options::value<std::string >()->default_value(UQ_MH_SG_INITIAL_POSITION_DATA_INPUT_FILE_TYPE_ODV ), "type of input file for raw chain " )
1112  (m_option_initialProposalCovMatrix_dataInputFileName.c_str(), boost::program_options::value<std::string >()->default_value(UQ_MH_SG_INITIAL_PROPOSAL_COV_MATRIX_DATA_INPUT_FILE_NAME_ODV), "name of input file for raw chain " )
1113  (m_option_initialProposalCovMatrix_dataInputFileType.c_str(), boost::program_options::value<std::string >()->default_value(UQ_MH_SG_INITIAL_PROPOSAL_COV_MATRIX_DATA_INPUT_FILE_TYPE_ODV), "type of input file for raw chain " )
1114  (m_option_listOfDisabledParameters.c_str(), boost::program_options::value<std::string >()->default_value(UQ_MH_SG_LIST_OF_DISABLED_PARAMETERS_ODV ), "list of disabled parameters" )
1115  (m_option_rawChain_dataInputFileName.c_str(), boost::program_options::value<std::string >()->default_value(UQ_MH_SG_RAW_CHAIN_DATA_INPUT_FILE_NAME_ODV ), "name of input file for raw chain " )
1116  (m_option_rawChain_dataInputFileType.c_str(), boost::program_options::value<std::string >()->default_value(UQ_MH_SG_RAW_CHAIN_DATA_INPUT_FILE_TYPE_ODV ), "type of input file for raw chain " )
1117  (m_option_rawChain_size.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_MH_SG_RAW_CHAIN_SIZE_ODV ), "size of raw chain" )
1118  (m_option_rawChain_generateExtra.c_str(), boost::program_options::value<bool >()->default_value(UQ_MH_SG_RAW_CHAIN_GENERATE_EXTRA_ODV ), "generate extra information about raw chain" )
1119  (m_option_rawChain_displayPeriod.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_MH_SG_RAW_CHAIN_DISPLAY_PERIOD_ODV ), "period of msg display during raw chain generation" )
1120  (m_option_rawChain_measureRunTimes.c_str(), boost::program_options::value<bool >()->default_value(UQ_MH_SG_RAW_CHAIN_MEASURE_RUN_TIMES_ODV ), "measure run times" )
1121  (m_option_rawChain_dataOutputPeriod.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_PERIOD_ODV ), "period of msg display during raw chain generation" )
1122  (m_option_rawChain_dataOutputFileName.c_str(), boost::program_options::value<std::string >()->default_value(UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_FILE_NAME_ODV ), "name of output file for raw chain " )
1123  (m_option_rawChain_dataOutputFileType.c_str(), boost::program_options::value<std::string >()->default_value(UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_FILE_TYPE_ODV ), "type of output file for raw chain " )
1124  (m_option_rawChain_dataOutputAllowAll.c_str(), boost::program_options::value<bool >()->default_value(UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_ALLOW_ALL_ODV ), "allow all subEnvs to write raw chain to an output file" )
1125  (m_option_rawChain_dataOutputAllowedSet.c_str(), boost::program_options::value<std::string >()->default_value(UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_ALLOWED_SET_ODV ), "subEnvs that will write raw chain to output file" )
1126 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
1127  (m_option_rawChain_computeStats.c_str(), boost::program_options::value<bool >()->default_value(UQ_MH_SG_RAW_CHAIN_COMPUTE_STATS_ODV ), "compute statistics on raw chain" )
1128 #endif
1129  (m_option_filteredChain_generate.c_str(), boost::program_options::value<bool >()->default_value(UQ_MH_SG_FILTERED_CHAIN_GENERATE_ODV ), "generate filtered chain" )
1130  (m_option_filteredChain_discardedPortion.c_str(), boost::program_options::value<double >()->default_value(UQ_MH_SG_FILTERED_CHAIN_DISCARDED_PORTION_ODV ), "initial discarded portion for chain filtering" )
1131  (m_option_filteredChain_lag.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_MH_SG_FILTERED_CHAIN_LAG_ODV ), "spacing for chain filtering" )
1132  (m_option_filteredChain_dataOutputFileName.c_str(), boost::program_options::value<std::string >()->default_value(UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_FILE_NAME_ODV ), "name of output file for filtered chain" )
1133  (m_option_filteredChain_dataOutputFileType.c_str(), boost::program_options::value<std::string >()->default_value(UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_FILE_TYPE_ODV ), "type of output file for filtered chain" )
1134  (m_option_filteredChain_dataOutputAllowAll.c_str(), boost::program_options::value<bool >()->default_value(UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_ALLOW_ALL_ODV ), "allow all subEnvs to write filt chain to an output file" )
1135  (m_option_filteredChain_dataOutputAllowedSet.c_str(), boost::program_options::value<std::string >()->default_value(UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_ALLOWED_SET_ODV ), "subEnvs that will write filt chain to output file" )
1136 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
1137  (m_option_filteredChain_computeStats.c_str(), boost::program_options::value<bool >()->default_value(UQ_MH_SG_FILTERED_CHAIN_COMPUTE_STATS_ODV ), "compute statistics on filtered chain" )
1138 #endif
1139  (m_option_displayCandidates.c_str(), boost::program_options::value<bool >()->default_value(UQ_MH_SG_DISPLAY_CANDIDATES_ODV ), "display candidates in the core MH algorithm" )
1140  (m_option_putOutOfBoundsInChain.c_str(), boost::program_options::value<bool >()->default_value(UQ_MH_SG_PUT_OUT_OF_BOUNDS_IN_CHAIN_ODV ), "put 'out of bound' candidates in chain as well" )
1141  (m_option_tk_useLocalHessian.c_str(), boost::program_options::value<bool >()->default_value(UQ_MH_SG_TK_USE_LOCAL_HESSIAN_ODV ), "'proposal' use local Hessian" )
1142  (m_option_tk_useNewtonComponent.c_str(), boost::program_options::value<bool >()->default_value(UQ_MH_SG_TK_USE_NEWTON_COMPONENT_ODV ), "'proposal' use Newton component" )
1143  (m_option_dr_maxNumExtraStages.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_MH_SG_DR_MAX_NUM_EXTRA_STAGES_ODV ), "'dr' maximum number of extra stages" )
1144  (m_option_dr_listOfScalesForExtraStages.c_str(), boost::program_options::value<std::string >()->default_value(UQ_MH_SG_DR_LIST_OF_SCALES_FOR_EXTRA_STAGES_ODV ), "'dr' scales for prop cov matrices from 2nd stage on" )
1145  (m_option_dr_duringAmNonAdaptiveInt.c_str(), boost::program_options::value<bool >()->default_value(UQ_MH_SG_DR_DURING_AM_NON_ADAPTIVE_INT_ODV ), "'dr' used during 'am' non adaptive interval" )
1146  (m_option_am_keepInitialMatrix.c_str(), boost::program_options::value<bool >()->default_value(UQ_MH_SG_AM_KEEP_INITIAL_MATRIX_ODV ), "'am' keep initial (given) matrix" )
1147  (m_option_am_initialNonAdaptInterval.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_MH_SG_AM_INIT_NON_ADAPT_INT_ODV ), "'am' initial non adaptation interval" )
1148  (m_option_am_adaptInterval.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_MH_SG_AM_ADAPT_INTERVAL_ODV ), "'am' adaptation interval" )
1149  (m_option_am_adaptedMatrices_dataOutputPeriod.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_MH_SG_AM_ADAPTED_MATRICES_DATA_OUTPUT_PERIOD_ODV ), "period for outputting 'am' adapted matrices" )
1150  (m_option_am_adaptedMatrices_dataOutputFileName.c_str(), boost::program_options::value<std::string >()->default_value(UQ_MH_SG_AM_ADAPTED_MATRICES_DATA_OUTPUT_FILE_NAME_ODV ), "name of output file for 'am' adapted matrices" )
1151  (m_option_am_adaptedMatrices_dataOutputFileType.c_str(), boost::program_options::value<std::string >()->default_value(UQ_MH_SG_AM_ADAPTED_MATRICES_DATA_OUTPUT_FILE_TYPE_ODV ), "type of output file for 'am' adapted matrices" )
1152  (m_option_am_adaptedMatrices_dataOutputAllowAll.c_str(), boost::program_options::value<bool >()->default_value(UQ_MH_SG_AM_ADAPTED_MATRICES_DATA_OUTPUT_ALLOW_ALL_ODV ), "type of output file for 'am' adapted matrices" )
1153  (m_option_am_adaptedMatrices_dataOutputAllowedSet.c_str(), boost::program_options::value<std::string >()->default_value(UQ_MH_SG_AM_ADAPTED_MATRICES_DATA_OUTPUT_ALLOWED_SET_ODV ), "type of output file for 'am' adapted matrices" )
1154  (m_option_am_eta.c_str(), boost::program_options::value<double >()->default_value(UQ_MH_SG_AM_ETA_ODV ), "'am' eta" )
1155  (m_option_am_epsilon.c_str(), boost::program_options::value<double >()->default_value(UQ_MH_SG_AM_EPSILON_ODV ), "'am' epsilon" )
1156  (m_option_enableBrooksGelmanConvMonitor.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_MH_SG_ENABLE_BROOKS_GELMAN_CONV_MONITOR ), "assess convergence using Brooks-Gelman metric" )
1157  (m_option_BrooksGelmanLag.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_MH_SG_BROOKS_GELMAN_LAG ), "number of chain positions before starting to compute metric")
1158  (m_option_outputLogLikelihood.c_str(), boost::program_options::value<bool >()->default_value(UQ_MH_SG_OUTPUT_LOG_LIKELIHOOD ), "flag to toggle output of log likelihood values" )
1159  (m_option_outputLogTarget.c_str(), boost::program_options::value<bool >()->default_value(UQ_MH_SG_OUTPUT_LOG_TARGET ), "flag to toggle output of log target values" )
1160  (m_option_doLogitTransform.c_str(), boost::program_options::value<bool >()->default_value(UQ_MH_SG_DO_LOGIT_TRANSFORM ), "flag to toggle logit transform for bounded domains" )
1161  ;
1162 
1163  return;
1164 }
UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_FILE_TYPE_ODV
#define UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_FILE_TYPE_ODV
Definition: MetropolisHastingsSGOptions.h:58
UQ_MH_SG_INITIAL_POSITION_DATA_INPUT_FILE_NAME_ODV
#define UQ_MH_SG_INITIAL_POSITION_DATA_INPUT_FILE_NAME_ODV
Definition: MetropolisHastingsSGOptions.h:45
UQ_MH_SG_OUTPUT_LOG_LIKELIHOOD
#define UQ_MH_SG_OUTPUT_LOG_LIKELIHOOD
Definition: MetropolisHastingsSGOptions.h:93
UQ_MH_SG_LIST_OF_DISABLED_PARAMETERS_ODV
#define UQ_MH_SG_LIST_OF_DISABLED_PARAMETERS_ODV
Definition: MetropolisHastingsSGOptions.h:49
UQ_MH_SG_DR_MAX_NUM_EXTRA_STAGES_ODV
#define UQ_MH_SG_DR_MAX_NUM_EXTRA_STAGES_ODV
Definition: MetropolisHastingsSGOptions.h:78
UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_ALLOW_ALL_ODV
#define UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_ALLOW_ALL_ODV
Definition: MetropolisHastingsSGOptions.h:59
UQ_MH_SG_AM_KEEP_INITIAL_MATRIX_ODV
#define UQ_MH_SG_AM_KEEP_INITIAL_MATRIX_ODV
Definition: MetropolisHastingsSGOptions.h:81
UQ_MH_SG_DATA_OUTPUT_ALLOW_ALL_ODV
#define UQ_MH_SG_DATA_OUTPUT_ALLOW_ALL_ODV
Definition: MetropolisHastingsSGOptions.h:41
UQ_MH_SG_DR_LIST_OF_SCALES_FOR_EXTRA_STAGES_ODV
#define UQ_MH_SG_DR_LIST_OF_SCALES_FOR_EXTRA_STAGES_ODV
Definition: MetropolisHastingsSGOptions.h:79
UQ_MH_SG_RAW_CHAIN_MEASURE_RUN_TIMES_ODV
#define UQ_MH_SG_RAW_CHAIN_MEASURE_RUN_TIMES_ODV
Definition: MetropolisHastingsSGOptions.h:55
UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_FILE_TYPE_ODV
#define UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_FILE_TYPE_ODV
Definition: MetropolisHastingsSGOptions.h:68
UQ_MH_SG_RAW_CHAIN_GENERATE_EXTRA_ODV
#define UQ_MH_SG_RAW_CHAIN_GENERATE_EXTRA_ODV
Definition: MetropolisHastingsSGOptions.h:53
UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_ALLOWED_SET_ODV
#define UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_ALLOWED_SET_ODV
Definition: MetropolisHastingsSGOptions.h:70
UQ_MH_SG_ENABLE_BROOKS_GELMAN_CONV_MONITOR
#define UQ_MH_SG_ENABLE_BROOKS_GELMAN_CONV_MONITOR
Definition: MetropolisHastingsSGOptions.h:91
UQ_MH_SG_RAW_CHAIN_DATA_INPUT_FILE_NAME_ODV
#define UQ_MH_SG_RAW_CHAIN_DATA_INPUT_FILE_NAME_ODV
Definition: MetropolisHastingsSGOptions.h:50
UQ_MH_SG_DR_DURING_AM_NON_ADAPTIVE_INT_ODV
#define UQ_MH_SG_DR_DURING_AM_NON_ADAPTIVE_INT_ODV
Definition: MetropolisHastingsSGOptions.h:80
UQ_MH_SG_FILTERED_CHAIN_GENERATE_ODV
#define UQ_MH_SG_FILTERED_CHAIN_GENERATE_ODV
Definition: MetropolisHastingsSGOptions.h:64
UQ_MH_SG_DISPLAY_CANDIDATES_ODV
#define UQ_MH_SG_DISPLAY_CANDIDATES_ODV
Definition: MetropolisHastingsSGOptions.h:74
UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_FILE_NAME_ODV
#define UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_FILE_NAME_ODV
Definition: MetropolisHastingsSGOptions.h:67
UQ_MH_SG_BROOKS_GELMAN_LAG
#define UQ_MH_SG_BROOKS_GELMAN_LAG
Definition: MetropolisHastingsSGOptions.h:92
UQ_MH_SG_PUT_OUT_OF_BOUNDS_IN_CHAIN_ODV
#define UQ_MH_SG_PUT_OUT_OF_BOUNDS_IN_CHAIN_ODV
Definition: MetropolisHastingsSGOptions.h:75
UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_PERIOD_ODV
#define UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_PERIOD_ODV
Definition: MetropolisHastingsSGOptions.h:56
UQ_MH_SG_RAW_CHAIN_SIZE_ODV
#define UQ_MH_SG_RAW_CHAIN_SIZE_ODV
Definition: MetropolisHastingsSGOptions.h:52
UQ_MH_SG_INITIAL_POSITION_DATA_INPUT_FILE_TYPE_ODV
#define UQ_MH_SG_INITIAL_POSITION_DATA_INPUT_FILE_TYPE_ODV
Definition: MetropolisHastingsSGOptions.h:46
UQ_MH_SG_AM_ADAPTED_MATRICES_DATA_OUTPUT_ALLOWED_SET_ODV
#define UQ_MH_SG_AM_ADAPTED_MATRICES_DATA_OUTPUT_ALLOWED_SET_ODV
Definition: MetropolisHastingsSGOptions.h:88
UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_ALLOW_ALL_ODV
#define UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_ALLOW_ALL_ODV
Definition: MetropolisHastingsSGOptions.h:69
UQ_MH_SG_DATA_OUTPUT_ALLOWED_SET_ODV
#define UQ_MH_SG_DATA_OUTPUT_ALLOWED_SET_ODV
Definition: MetropolisHastingsSGOptions.h:42
UQ_MH_SG_AM_ADAPTED_MATRICES_DATA_OUTPUT_FILE_TYPE_ODV
#define UQ_MH_SG_AM_ADAPTED_MATRICES_DATA_OUTPUT_FILE_TYPE_ODV
Definition: MetropolisHastingsSGOptions.h:86
UQ_MH_SG_RAW_CHAIN_DISPLAY_PERIOD_ODV
#define UQ_MH_SG_RAW_CHAIN_DISPLAY_PERIOD_ODV
Definition: MetropolisHastingsSGOptions.h:54
UQ_MH_SG_TOTALLY_MUTE_ODV
#define UQ_MH_SG_TOTALLY_MUTE_ODV
Definition: MetropolisHastingsSGOptions.h:44
UQ_MH_SG_OUTPUT_LOG_TARGET
#define UQ_MH_SG_OUTPUT_LOG_TARGET
Definition: MetropolisHastingsSGOptions.h:94
UQ_MH_SG_AM_ADAPT_INTERVAL_ODV
#define UQ_MH_SG_AM_ADAPT_INTERVAL_ODV
Definition: MetropolisHastingsSGOptions.h:83
UQ_MH_SG_INITIAL_PROPOSAL_COV_MATRIX_DATA_INPUT_FILE_NAME_ODV
#define UQ_MH_SG_INITIAL_PROPOSAL_COV_MATRIX_DATA_INPUT_FILE_NAME_ODV
Definition: MetropolisHastingsSGOptions.h:47
UQ_MH_SG_AM_ADAPTED_MATRICES_DATA_OUTPUT_FILE_NAME_ODV
#define UQ_MH_SG_AM_ADAPTED_MATRICES_DATA_OUTPUT_FILE_NAME_ODV
Definition: MetropolisHastingsSGOptions.h:85
UQ_MH_SG_AM_ADAPTED_MATRICES_DATA_OUTPUT_ALLOW_ALL_ODV
#define UQ_MH_SG_AM_ADAPTED_MATRICES_DATA_OUTPUT_ALLOW_ALL_ODV
Definition: MetropolisHastingsSGOptions.h:87
UQ_MH_SG_DO_LOGIT_TRANSFORM
#define UQ_MH_SG_DO_LOGIT_TRANSFORM
Definition: MetropolisHastingsSGOptions.h:95
UQ_MH_SG_AM_INIT_NON_ADAPT_INT_ODV
#define UQ_MH_SG_AM_INIT_NON_ADAPT_INT_ODV
Definition: MetropolisHastingsSGOptions.h:82
UQ_MH_SG_TK_USE_NEWTON_COMPONENT_ODV
#define UQ_MH_SG_TK_USE_NEWTON_COMPONENT_ODV
Definition: MetropolisHastingsSGOptions.h:77
QUESO::MetropolisHastingsSGOptions::m_option_am_eta
std::string m_option_am_eta
See MhOptionsValues::m_amEta.
Definition: MetropolisHastingsSGOptions.h:835
queso_deprecated
#define queso_deprecated()
Definition: Defines.h:120
QUESO::MetropolisHastingsSGOptions::m_option_am_epsilon
std::string m_option_am_epsilon
See MhOptionsValues::m_amEpsilon.
Definition: MetropolisHastingsSGOptions.h:837
UQ_MH_SG_RAW_CHAIN_DATA_INPUT_FILE_TYPE_ODV
#define UQ_MH_SG_RAW_CHAIN_DATA_INPUT_FILE_TYPE_ODV
Definition: MetropolisHastingsSGOptions.h:51
UQ_MH_SG_AM_ADAPTED_MATRICES_DATA_OUTPUT_PERIOD_ODV
#define UQ_MH_SG_AM_ADAPTED_MATRICES_DATA_OUTPUT_PERIOD_ODV
Definition: MetropolisHastingsSGOptions.h:84
UQ_MH_SG_FILTERED_CHAIN_DISCARDED_PORTION_ODV
#define UQ_MH_SG_FILTERED_CHAIN_DISCARDED_PORTION_ODV
Definition: MetropolisHastingsSGOptions.h:65
UQ_MH_SG_INITIAL_PROPOSAL_COV_MATRIX_DATA_INPUT_FILE_TYPE_ODV
#define UQ_MH_SG_INITIAL_PROPOSAL_COV_MATRIX_DATA_INPUT_FILE_TYPE_ODV
Definition: MetropolisHastingsSGOptions.h:48
UQ_MH_SG_DATA_OUTPUT_FILE_NAME_ODV
#define UQ_MH_SG_DATA_OUTPUT_FILE_NAME_ODV
Definition: MetropolisHastingsSGOptions.h:40
UQ_MH_SG_AM_EPSILON_ODV
#define UQ_MH_SG_AM_EPSILON_ODV
Definition: MetropolisHastingsSGOptions.h:90
UQ_MH_SG_AM_ETA_ODV
#define UQ_MH_SG_AM_ETA_ODV
Definition: MetropolisHastingsSGOptions.h:89
UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_FILE_NAME_ODV
#define UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_FILE_NAME_ODV
Definition: MetropolisHastingsSGOptions.h:57
UQ_MH_SG_TK_USE_LOCAL_HESSIAN_ODV
#define UQ_MH_SG_TK_USE_LOCAL_HESSIAN_ODV
Definition: MetropolisHastingsSGOptions.h:76
UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_ALLOWED_SET_ODV
#define UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_ALLOWED_SET_ODV
Definition: MetropolisHastingsSGOptions.h:60
UQ_MH_SG_FILTERED_CHAIN_LAG_ODV
#define UQ_MH_SG_FILTERED_CHAIN_LAG_ODV
Definition: MetropolisHastingsSGOptions.h:66
void QUESO::MetropolisHastingsSGOptions::getMyOptionValues ( boost::program_options::options_description &  optionsDesc)
private

Gets the sequence options defined to the Metropolis-Hastings algorithm.

Definition at line 1167 of file MetropolisHastingsSGOptions.C.

References QUESO::BaseEnvironment::allOptionsMap(), QUESO::BaseEnvironment::fullRank(), QUESO::BaseEnvironment::inter0Rank(), QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputAllowAll, QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputAllowedSet, QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputFileName, QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputFileType, QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputPeriod, QUESO::MhOptionsValues::m_amAdaptInterval, QUESO::MhOptionsValues::m_amEpsilon, QUESO::MhOptionsValues::m_amEta, QUESO::MhOptionsValues::m_amInitialNonAdaptInterval, QUESO::MhOptionsValues::m_amKeepInitialMatrix, QUESO::MhOptionsValues::m_BrooksGelmanLag, QUESO::MhOptionsValues::m_dataOutputAllowAll, QUESO::MhOptionsValues::m_dataOutputAllowedSet, QUESO::MhOptionsValues::m_dataOutputFileName, QUESO::MhOptionsValues::m_displayCandidates, QUESO::MhOptionsValues::m_doLogitTransform, QUESO::MhOptionsValues::m_drDuringAmNonAdaptiveInt, QUESO::MhOptionsValues::m_drMaxNumExtraStages, QUESO::MhOptionsValues::m_drScalesForExtraStages, QUESO::MhOptionsValues::m_enableBrooksGelmanConvMonitor, m_env, QUESO::MhOptionsValues::m_filteredChainDataOutputAllowAll, QUESO::MhOptionsValues::m_filteredChainDataOutputAllowedSet, QUESO::MhOptionsValues::m_filteredChainDataOutputFileName, QUESO::MhOptionsValues::m_filteredChainDataOutputFileType, QUESO::MhOptionsValues::m_filteredChainDiscardedPortion, QUESO::MhOptionsValues::m_filteredChainGenerate, QUESO::MhOptionsValues::m_filteredChainLag, QUESO::MhOptionsValues::m_initialPositionDataInputFileName, QUESO::MhOptionsValues::m_initialPositionDataInputFileType, QUESO::MhOptionsValues::m_initialProposalCovMatrixDataInputFileName, QUESO::MhOptionsValues::m_initialProposalCovMatrixDataInputFileType, m_option_am_adaptedMatrices_dataOutputAllowAll, m_option_am_adaptedMatrices_dataOutputAllowedSet, m_option_am_adaptedMatrices_dataOutputFileName, m_option_am_adaptedMatrices_dataOutputFileType, m_option_am_adaptedMatrices_dataOutputPeriod, m_option_am_adaptInterval, m_option_am_epsilon, m_option_am_eta, m_option_am_initialNonAdaptInterval, m_option_am_keepInitialMatrix, m_option_BrooksGelmanLag, m_option_dataOutputAllowAll, m_option_dataOutputAllowedSet, m_option_dataOutputFileName, m_option_displayCandidates, m_option_doLogitTransform, m_option_dr_duringAmNonAdaptiveInt, m_option_dr_listOfScalesForExtraStages, m_option_dr_maxNumExtraStages, m_option_enableBrooksGelmanConvMonitor, m_option_filteredChain_dataOutputAllowAll, m_option_filteredChain_dataOutputAllowedSet, m_option_filteredChain_dataOutputFileName, m_option_filteredChain_dataOutputFileType, m_option_filteredChain_discardedPortion, m_option_filteredChain_generate, m_option_filteredChain_lag, m_option_help, m_option_initialPosition_dataInputFileName, m_option_initialPosition_dataInputFileType, m_option_initialProposalCovMatrix_dataInputFileName, m_option_initialProposalCovMatrix_dataInputFileType, m_option_listOfDisabledParameters, m_option_outputLogLikelihood, m_option_outputLogTarget, m_option_putOutOfBoundsInChain, m_option_rawChain_dataInputFileName, m_option_rawChain_dataInputFileType, m_option_rawChain_dataOutputAllowAll, m_option_rawChain_dataOutputAllowedSet, m_option_rawChain_dataOutputFileName, m_option_rawChain_dataOutputFileType, m_option_rawChain_dataOutputPeriod, m_option_rawChain_displayPeriod, m_option_rawChain_generateExtra, m_option_rawChain_measureRunTimes, m_option_rawChain_size, m_option_tk_useLocalHessian, m_option_tk_useNewtonComponent, m_option_totallyMute, QUESO::MhOptionsValues::m_outputLogLikelihood, QUESO::MhOptionsValues::m_outputLogTarget, m_ov, QUESO::MhOptionsValues::m_parameterDisabledSet, QUESO::MhOptionsValues::m_putOutOfBoundsInChain, QUESO::MhOptionsValues::m_rawChainDataInputFileName, QUESO::MhOptionsValues::m_rawChainDataInputFileType, QUESO::MhOptionsValues::m_rawChainDataOutputAllowAll, QUESO::MhOptionsValues::m_rawChainDataOutputAllowedSet, QUESO::MhOptionsValues::m_rawChainDataOutputFileName, QUESO::MhOptionsValues::m_rawChainDataOutputFileType, QUESO::MhOptionsValues::m_rawChainDataOutputPeriod, QUESO::MhOptionsValues::m_rawChainDisplayPeriod, QUESO::MhOptionsValues::m_rawChainGenerateExtra, QUESO::MhOptionsValues::m_rawChainMeasureRunTimes, QUESO::MhOptionsValues::m_rawChainSize, QUESO::MhOptionsValues::m_tkUseLocalHessian, QUESO::MhOptionsValues::m_tkUseNewtonComponent, QUESO::MhOptionsValues::m_totallyMute, QUESO::MiscReadDoublesFromString(), queso_deprecated, scale, QUESO::BaseEnvironment::subDisplayFile(), QUESO::BaseEnvironment::subId(), QUESO::BaseEnvironment::subRank(), and QUESO::BaseEnvironment::worldRank().

Referenced by scanOptionsValues().

1168 {
1169  queso_deprecated();
1170 
1171  if (m_env.allOptionsMap().count(m_option_help)) {
1172  if ((m_env.subDisplayFile()) &&
1173  (m_ov.m_totallyMute == false)) {
1174  *m_env.subDisplayFile() << optionsDesc
1175  << std::endl;
1176  }
1177  }
1178 
1179  if (m_env.allOptionsMap().count(m_option_dataOutputFileName)) {
1180  m_ov.m_dataOutputFileName = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_dataOutputFileName]).as<std::string>();
1181  }
1182 
1183  if (m_env.allOptionsMap().count(m_option_dataOutputAllowAll.c_str())) {
1184  m_ov.m_dataOutputAllowAll = m_env.allOptionsMap()[m_option_dataOutputAllowAll].as<bool>();
1185  }
1186 
1187  if (m_ov.m_dataOutputAllowAll) {
1188  m_ov.m_dataOutputAllowedSet.insert(m_env.subId());
1189  }
1190  else if (m_env.allOptionsMap().count(m_option_dataOutputAllowedSet)) {
1191  m_ov.m_dataOutputAllowedSet.clear();
1192  std::vector<double> tmpAllow(0,0.);
1193  std::string inputString = m_env.allOptionsMap()[m_option_dataOutputAllowedSet].as<std::string>();
1194  MiscReadDoublesFromString(inputString,tmpAllow);
1195 
1196  if (tmpAllow.size() > 0) {
1197  for (unsigned int i = 0; i < tmpAllow.size(); ++i) {
1198  m_ov.m_dataOutputAllowedSet.insert((unsigned int) tmpAllow[i]);
1199  }
1200  }
1201  }
1202 
1203  if (m_env.allOptionsMap().count(m_option_totallyMute)) {
1204  m_ov.m_totallyMute = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_totallyMute]).as<bool>();
1205  }
1206 
1207  if (m_env.allOptionsMap().count(m_option_initialPosition_dataInputFileName)) {
1208  m_ov.m_initialPositionDataInputFileName = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_initialPosition_dataInputFileName]).as<std::string>();
1209  }
1210 
1211  if (m_env.allOptionsMap().count(m_option_initialPosition_dataInputFileType)) {
1212  m_ov.m_initialPositionDataInputFileType = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_initialPosition_dataInputFileType]).as<std::string>();
1213  }
1214 
1215  if (m_env.allOptionsMap().count(m_option_initialProposalCovMatrix_dataInputFileName)) {
1216  m_ov.m_initialProposalCovMatrixDataInputFileName = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_initialProposalCovMatrix_dataInputFileName]).as<std::string>();
1217  }
1218 
1219  if (m_env.allOptionsMap().count(m_option_initialProposalCovMatrix_dataInputFileType)) {
1220  m_ov.m_initialProposalCovMatrixDataInputFileType = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_initialProposalCovMatrix_dataInputFileType]).as<std::string>();
1221  }
1222 
1223  if (m_env.allOptionsMap().count(m_option_listOfDisabledParameters)) {
1224  m_ov.m_parameterDisabledSet.clear();
1225  std::vector<double> tmpAllow(0,0.);
1226  std::string inputString = m_env.allOptionsMap()[m_option_listOfDisabledParameters].as<std::string>();
1227  MiscReadDoublesFromString(inputString,tmpAllow);
1228  if (tmpAllow.size() > 0) {
1229  for (unsigned int i = 0; i < tmpAllow.size(); ++i) {
1230  m_ov.m_parameterDisabledSet.insert((unsigned int) tmpAllow[i]);
1231  }
1232  }
1233  }
1234 
1235  if (m_env.allOptionsMap().count(m_option_rawChain_dataInputFileName)) {
1236  m_ov.m_rawChainDataInputFileName = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_rawChain_dataInputFileName]).as<std::string>();
1237  }
1238 
1239  if (m_env.allOptionsMap().count(m_option_rawChain_dataInputFileType)) {
1240  m_ov.m_rawChainDataInputFileType = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_rawChain_dataInputFileType]).as<std::string>();
1241  }
1242 
1243  if (m_env.allOptionsMap().count(m_option_rawChain_size)) {
1244  m_ov.m_rawChainSize = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_rawChain_size]).as<unsigned int>();
1245  }
1246 
1247  if (m_env.allOptionsMap().count(m_option_rawChain_displayPeriod)) {
1248  m_ov.m_rawChainDisplayPeriod = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_rawChain_displayPeriod]).as<unsigned int>();
1249  }
1250 
1251  if (m_env.allOptionsMap().count(m_option_rawChain_measureRunTimes)) {
1252  m_ov.m_rawChainMeasureRunTimes = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_rawChain_measureRunTimes]).as<bool>();
1253  }
1254 
1255  if (m_env.allOptionsMap().count(m_option_rawChain_dataOutputPeriod)) {
1256  m_ov.m_rawChainDataOutputPeriod = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_rawChain_dataOutputPeriod]).as<unsigned int>();
1257  }
1258 
1259  if (m_env.allOptionsMap().count(m_option_rawChain_dataOutputFileName)) {
1260  m_ov.m_rawChainDataOutputFileName = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_rawChain_dataOutputFileName]).as<std::string>();
1261  }
1262 
1263  if (m_env.allOptionsMap().count(m_option_rawChain_dataOutputFileType)) {
1264  m_ov.m_rawChainDataOutputFileType = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_rawChain_dataOutputFileType]).as<std::string>();
1265  }
1266 
1267  if (m_env.allOptionsMap().count(m_option_rawChain_dataOutputAllowAll.c_str())) {
1268  m_ov.m_rawChainDataOutputAllowAll = m_env.allOptionsMap()[m_option_rawChain_dataOutputAllowAll].as<bool>();
1269  }
1270 
1271  if (m_ov.m_rawChainDataOutputAllowAll) {
1272  m_ov.m_rawChainDataOutputAllowedSet.insert(m_env.subId());
1273  }
1274  else if (m_env.allOptionsMap().count(m_option_rawChain_dataOutputAllowedSet)) {
1275  m_ov.m_rawChainDataOutputAllowedSet.clear();
1276  std::vector<double> tmpAllow(0,0.);
1277  std::string inputString = m_env.allOptionsMap()[m_option_rawChain_dataOutputAllowedSet].as<std::string>();
1278  MiscReadDoublesFromString(inputString,tmpAllow);
1279 
1280  if (tmpAllow.size() > 0) {
1281  for (unsigned int i = 0; i < tmpAllow.size(); ++i) {
1282  m_ov.m_rawChainDataOutputAllowedSet.insert((unsigned int) tmpAllow[i]);
1283  }
1284  }
1285  }
1286 
1287 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
1288  if (m_env.allOptionsMap().count(m_option_rawChain_computeStats)) {
1289  m_ov.m_rawChainComputeStats = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_rawChain_computeStats]).as<bool>();
1290  }
1291 #endif
1292  if (m_env.allOptionsMap().count(m_option_rawChain_generateExtra)) {
1293  m_ov.m_rawChainGenerateExtra = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_rawChain_generateExtra]).as<bool>();
1294  }
1295 
1296  if (m_env.allOptionsMap().count(m_option_filteredChain_generate)) {
1297  m_ov.m_filteredChainGenerate = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_filteredChain_generate]).as<bool>();
1298  }
1299 
1300  if (m_env.allOptionsMap().count(m_option_filteredChain_discardedPortion)) {
1301  m_ov.m_filteredChainDiscardedPortion = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_filteredChain_discardedPortion]).as<double>();
1302  }
1303 
1304  if (m_env.allOptionsMap().count(m_option_filteredChain_lag)) {
1305  m_ov.m_filteredChainLag = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_filteredChain_lag]).as<unsigned int>();
1306  }
1307  if ((m_ov.m_filteredChainGenerate == true) &&
1308  (m_ov.m_filteredChainLag < 2 )) {
1309  std::cerr << "WARNING In MetropolisHastingsSG<P_V,P_M>::getMyOptionsValues()"
1310  << ", worldRank " << m_env.worldRank()
1311  << ", fullRank " << m_env.fullRank()
1312  << ", subEnvironment " << m_env.subId()
1313  << ", subRank " << m_env.subRank()
1314  << ", inter0Rank " << m_env.inter0Rank()
1315  << ": forcing the value of '" << m_option_filteredChain_lag
1316  << "' from " << m_ov.m_filteredChainLag
1317  << " to " << 2
1318  << std::endl;
1319  m_ov.m_filteredChainLag = 2;
1320  }
1321 
1322  if (m_env.allOptionsMap().count(m_option_filteredChain_dataOutputFileName)) {
1323  m_ov.m_filteredChainDataOutputFileName = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_filteredChain_dataOutputFileName]).as<std::string>();
1324  }
1325 
1326  if (m_env.allOptionsMap().count(m_option_filteredChain_dataOutputFileType)) {
1327  m_ov.m_filteredChainDataOutputFileType = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_filteredChain_dataOutputFileType]).as<std::string>();
1328  }
1329 
1330  if (m_env.allOptionsMap().count(m_option_filteredChain_dataOutputAllowAll.c_str())) {
1331  m_ov.m_filteredChainDataOutputAllowAll = m_env.allOptionsMap()[m_option_filteredChain_dataOutputAllowAll].as<bool>();
1332  }
1333 
1334  if (m_ov.m_filteredChainDataOutputAllowAll) {
1335  m_ov.m_filteredChainDataOutputAllowedSet.insert(m_env.subId());
1336  }
1337  else if (m_env.allOptionsMap().count(m_option_filteredChain_dataOutputAllowedSet)) {
1338  m_ov.m_filteredChainDataOutputAllowedSet.clear();
1339  std::vector<double> tmpAllow(0,0.);
1340  std::string inputString = m_env.allOptionsMap()[m_option_filteredChain_dataOutputAllowedSet].as<std::string>();
1341  MiscReadDoublesFromString(inputString,tmpAllow);
1342 
1343  if (tmpAllow.size() > 0) {
1344  for (unsigned int i = 0; i < tmpAllow.size(); ++i) {
1345  m_ov.m_filteredChainDataOutputAllowedSet.insert((unsigned int) tmpAllow[i]);
1346  }
1347  }
1348  }
1349 
1350 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
1351  if (m_env.allOptionsMap().count(m_option_filteredChain_computeStats)) {
1352  m_ov.m_filteredChainComputeStats = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_filteredChain_computeStats]).as<bool>();
1353  }
1354 #endif
1355  if (m_env.allOptionsMap().count(m_option_displayCandidates)) {
1356  m_ov.m_displayCandidates = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_displayCandidates]).as<bool>();
1357  }
1358 
1359  if (m_env.allOptionsMap().count(m_option_putOutOfBoundsInChain)) {
1360  m_ov.m_putOutOfBoundsInChain = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_putOutOfBoundsInChain]).as<bool>();
1361  }
1362 
1363  if (m_env.allOptionsMap().count(m_option_tk_useLocalHessian)) {
1364  m_ov.m_tkUseLocalHessian = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_tk_useLocalHessian]).as<bool>();
1365  }
1366 
1367  if (m_env.allOptionsMap().count(m_option_tk_useNewtonComponent)) {
1368  m_ov.m_tkUseNewtonComponent = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_tk_useNewtonComponent]).as<bool>();
1369  }
1370 
1371  if (m_env.allOptionsMap().count(m_option_dr_maxNumExtraStages)) {
1372  m_ov.m_drMaxNumExtraStages = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_dr_maxNumExtraStages]).as<unsigned int>();
1373  }
1374 
1375  std::vector<double> tmpScales(0,0.);
1376  if (m_env.allOptionsMap().count(m_option_dr_listOfScalesForExtraStages)) {
1377  std::string inputString = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_dr_listOfScalesForExtraStages]).as<std::string>();
1378  MiscReadDoublesFromString(inputString,tmpScales);
1379  //if (m_env.subDisplayFile()) {
1380  // *m_env.subDisplayFile() << "In MetropolisHastingsSG<P_V,P_M>::getMyOptionValues(): scales =";
1381  // for (unsigned int i = 0; i < tmpScales.size(); ++i) {
1382  // *m_env.subDisplayFile() << " " << tmpScales[i];
1383  // }
1384  // *m_env.subDisplayFile() << std::endl;
1385  //}
1386  }
1387 
1388  if (m_ov.m_drMaxNumExtraStages > 0) {
1389  double scale = 1.0;
1390  unsigned int tmpSize = tmpScales.size();
1391 
1392  m_ov.m_drScalesForExtraStages.clear();
1393  m_ov.m_drScalesForExtraStages.resize(m_ov.m_drMaxNumExtraStages,1.);
1394  for (unsigned int i = 0; i < m_ov.m_drMaxNumExtraStages; ++i) {
1395  if (i < tmpSize) scale = tmpScales[i];
1396  m_ov.m_drScalesForExtraStages[i] = scale;
1397  }
1398  //updateTK();
1399  }
1400 
1401  if (m_env.allOptionsMap().count(m_option_dr_duringAmNonAdaptiveInt)) {
1402  m_ov.m_drDuringAmNonAdaptiveInt = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_dr_duringAmNonAdaptiveInt]).as<bool>();
1403  }
1404 
1405  if (m_env.allOptionsMap().count(m_option_am_keepInitialMatrix)) {
1406  m_ov.m_amKeepInitialMatrix = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_am_keepInitialMatrix]).as<bool>();
1407  }
1408 
1409  if (m_env.allOptionsMap().count(m_option_am_initialNonAdaptInterval)) {
1410  m_ov.m_amInitialNonAdaptInterval = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_am_initialNonAdaptInterval]).as<unsigned int>();
1411  }
1412 
1413  if (m_env.allOptionsMap().count(m_option_am_adaptInterval)) {
1414  m_ov.m_amAdaptInterval = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_am_adaptInterval]).as<unsigned int>();
1415  }
1416 
1417  if (m_env.allOptionsMap().count(m_option_am_adaptedMatrices_dataOutputPeriod)) {
1418  m_ov.m_amAdaptedMatricesDataOutputPeriod = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_am_adaptedMatrices_dataOutputPeriod]).as<unsigned int>();
1419  }
1420 
1421  if (m_env.allOptionsMap().count(m_option_am_adaptedMatrices_dataOutputFileName)) {
1422  m_ov.m_amAdaptedMatricesDataOutputFileName = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_am_adaptedMatrices_dataOutputFileName]).as<std::string>();
1423  }
1424 
1425  if (m_env.allOptionsMap().count(m_option_am_adaptedMatrices_dataOutputFileType)) {
1426  m_ov.m_amAdaptedMatricesDataOutputFileType = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_am_adaptedMatrices_dataOutputFileType]).as<std::string>();
1427  }
1428 
1429  if (m_env.allOptionsMap().count(m_option_am_adaptedMatrices_dataOutputAllowAll.c_str())) {
1430  m_ov.m_amAdaptedMatricesDataOutputAllowAll = m_env.allOptionsMap()[m_option_am_adaptedMatrices_dataOutputAllowAll].as<bool>();
1431  }
1432 
1433  if (m_ov.m_amAdaptedMatricesDataOutputAllowAll) {
1434  m_ov.m_amAdaptedMatricesDataOutputAllowedSet.insert(m_env.subId());
1435  }
1436  else if (m_env.allOptionsMap().count(m_option_am_adaptedMatrices_dataOutputAllowedSet)) {
1437  m_ov.m_amAdaptedMatricesDataOutputAllowedSet.clear();
1438  std::vector<double> tmpAllow(0,0.);
1439  std::string inputString = m_env.allOptionsMap()[m_option_am_adaptedMatrices_dataOutputAllowedSet].as<std::string>();
1440  MiscReadDoublesFromString(inputString,tmpAllow);
1441 
1442  if (tmpAllow.size() > 0) {
1443  for (unsigned int i = 0; i < tmpAllow.size(); ++i) {
1444  m_ov.m_amAdaptedMatricesDataOutputAllowedSet.insert((unsigned int) tmpAllow[i]);
1445  }
1446  }
1447  }
1448 
1449  if (m_env.allOptionsMap().count(m_option_am_eta)) {
1450  m_ov.m_amEta = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_am_eta]).as<double>();
1451  }
1452 
1453  if (m_env.allOptionsMap().count(m_option_am_epsilon)) {
1454  m_ov.m_amEpsilon = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_am_epsilon]).as<double>();
1455  }
1456 
1457  if (m_env.allOptionsMap().count(m_option_enableBrooksGelmanConvMonitor)) {
1458  m_ov.m_enableBrooksGelmanConvMonitor = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_enableBrooksGelmanConvMonitor]).as<unsigned int>();
1459  }
1460 
1461  if (m_env.allOptionsMap().count(m_option_BrooksGelmanLag)) {
1462  m_ov.m_BrooksGelmanLag = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_BrooksGelmanLag]).as<unsigned int>();
1463  }
1464 
1465  if (m_env.allOptionsMap().count(m_option_outputLogLikelihood)) {
1466  m_ov.m_outputLogLikelihood = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_outputLogLikelihood]).as<bool>();
1467  }
1468 
1469  if (m_env.allOptionsMap().count(m_option_outputLogTarget)) {
1470  m_ov.m_outputLogTarget = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_outputLogTarget]).as<bool>();
1471  }
1472 
1473  if (m_env.allOptionsMap().count(m_option_doLogitTransform)) {
1474  m_ov.m_doLogitTransform = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_doLogitTransform]).as<bool>();
1475  }
1476 }
QUESO::MhOptionsValues::m_filteredChainDataOutputFileType
std::string m_filteredChainDataOutputFileType
The filetype of m_filteredChainDataOutputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:350
QUESO::MhOptionsValues::m_doLogitTransform
bool m_doLogitTransform
Flag for deciding whether or not to do logit transform of bounded domains Default is true...
Definition: MetropolisHastingsSGOptions.h:583
QUESO::MhOptionsValues::m_rawChainGenerateExtra
bool m_rawChainGenerateExtra
If true, extra chain information is computed/stored.
Definition: MetropolisHastingsSGOptions.h:250
QUESO::BaseEnvironment::subRank
int subRank() const
Access function for sub-rank.
Definition: Environment.C:241
QUESO::MhOptionsValues::m_amEpsilon
double m_amEpsilon
Regularisation parameter for the DRAM covariance matrix.
Definition: MetropolisHastingsSGOptions.h:548
QUESO::MhOptionsValues::m_tkUseNewtonComponent
bool m_tkUseNewtonComponent
This option is a no-op. Default is true.
Definition: MetropolisHastingsSGOptions.h:416
QUESO::MhOptionsValues::m_filteredChainDataOutputAllowedSet
std::set< unsigned int > m_filteredChainDataOutputAllowedSet
The set of MPI ranks that will write filtered Markov chain output to a file. See also m_filteredChain...
Definition: MetropolisHastingsSGOptions.h:365
QUESO::MhOptionsValues::m_initialPositionDataInputFileType
std::string m_initialPositionDataInputFileType
The filetype of m_initialPositionDataInputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:203
QUESO::MhOptionsValues::m_rawChainDataInputFileName
std::string m_rawChainDataInputFileName
Filename for reading an already-produced Markov chain.
Definition: MetropolisHastingsSGOptions.h:235
QUESO::MhOptionsValues::m_filteredChainDataOutputFileName
std::string m_filteredChainDataOutputFileName
If not &quot;.&quot;, file name to save the filtered chain to. Default is &quot;.&quot;.
Definition: MetropolisHastingsSGOptions.h:347
QUESO::BaseEnvironment::fullRank
int fullRank() const
Returns the process full rank.
Definition: Environment.C:222
QUESO::MhOptionsValues::m_amAdaptInterval
unsigned int m_amAdaptInterval
The frequency at which to adapt the proposal covariance matrix.
Definition: MetropolisHastingsSGOptions.h:491
QUESO::MhOptionsValues::m_amEta
double m_amEta
Proposal covariance scaling factor, usually 2.4 * 2.4 / d.
Definition: MetropolisHastingsSGOptions.h:536
QUESO::MhOptionsValues::m_rawChainDataOutputPeriod
unsigned int m_rawChainDataOutputPeriod
The frequency with which to write chain output. Defaults to 0.
Definition: MetropolisHastingsSGOptions.h:280
QUESO::MhOptionsValues::m_outputLogTarget
bool m_outputLogTarget
Flag for deciding whether or not to dump log target values in output Default is true.
Definition: MetropolisHastingsSGOptions.h:580
QUESO::MhOptionsValues::m_drScalesForExtraStages
std::vector< double > m_drScalesForExtraStages
The vector of scale factors for the proposal covariance matrix to use for delayed rejection...
Definition: MetropolisHastingsSGOptions.h:445
QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputAllowedSet
std::set< unsigned int > m_amAdaptedMatricesDataOutputAllowedSet
This option is a no-op. The default is the empty set.
Definition: MetropolisHastingsSGOptions.h:523
QUESO::BaseEnvironment::allOptionsMap
boost::program_options::variables_map & allOptionsMap() const
Definition: Environment.C:336
QUESO::MhOptionsValues::m_filteredChainLag
unsigned int m_filteredChainLag
Set the lag for the filtered chain. Default is 1.
Definition: MetropolisHastingsSGOptions.h:338
QUESO::BaseEnvironment::inter0Rank
int inter0Rank() const
Returns the process inter0 rank.
Definition: Environment.C:261
QUESO::MhOptionsValues::m_dataOutputAllowedSet
std::set< unsigned int > m_dataOutputAllowedSet
The set of MPI ranks that can write output. See m_dataOutputAllowAll.
Definition: MetropolisHastingsSGOptions.h:191
QUESO::MhOptionsValues::m_rawChainDataOutputAllowAll
bool m_rawChainDataOutputAllowAll
Toggle for whether or not to allow all processes to write Markov chain output to a file...
Definition: MetropolisHastingsSGOptions.h:306
QUESO::MhOptionsValues::m_rawChainSize
unsigned int m_rawChainSize
The size of the chain (number of posterior samples) to generate. Default is 100.
Definition: MetropolisHastingsSGOptions.h:241
QUESO::MhOptionsValues::m_drMaxNumExtraStages
unsigned int m_drMaxNumExtraStages
The number of delayed rejection stages to do. Default is 0.
Definition: MetropolisHastingsSGOptions.h:426
scale
double scale
Definition: ann2fig.cpp:85
QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputAllowAll
bool m_amAdaptedMatricesDataOutputAllowAll
This option is a no-op. The default is false.
Definition: MetropolisHastingsSGOptions.h:520
QUESO::MhOptionsValues::m_putOutOfBoundsInChain
bool m_putOutOfBoundsInChain
Flag to tell QUESO how chains should be upon generating a proposal that is out of the problem domain...
Definition: MetropolisHastingsSGOptions.h:387
QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputPeriod
unsigned int m_amAdaptedMatricesDataOutputPeriod
The frequency (after m_amInitialNonAdaptInterval samples are done) of printing the last adapted propo...
Definition: MetropolisHastingsSGOptions.h:508
QUESO::MhOptionsValues::m_amKeepInitialMatrix
bool m_amKeepInitialMatrix
This option is a no-op. The default is false.
Definition: MetropolisHastingsSGOptions.h:470
QUESO::MhOptionsValues::m_rawChainDisplayPeriod
unsigned int m_rawChainDisplayPeriod
The frequency with which to output diagnostic information.
Definition: MetropolisHastingsSGOptions.h:260
QUESO::MhOptionsValues::m_initialProposalCovMatrixDataInputFileName
std::string m_initialProposalCovMatrixDataInputFileName
If not &quot;.&quot;, reads the contents of the file as the initial proposal covariance matrix.
Definition: MetropolisHastingsSGOptions.h:215
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:274
QUESO::MhOptionsValues::m_dataOutputAllowAll
bool m_dataOutputAllowAll
If true, all processes write output and m_dataOutputAllowedSet is ignored.
Definition: MetropolisHastingsSGOptions.h:185
QUESO::MhOptionsValues::m_amInitialNonAdaptInterval
unsigned int m_amInitialNonAdaptInterval
The number of initial samples to do without adapting the proposal covariance matrix.
Definition: MetropolisHastingsSGOptions.h:481
QUESO::MhOptionsValues::m_BrooksGelmanLag
unsigned int m_BrooksGelmanLag
The lag with which to compute the Brooks-Gelman convergence statistic.
Definition: MetropolisHastingsSGOptions.h:574
QUESO::MhOptionsValues::m_filteredChainDiscardedPortion
double m_filteredChainDiscardedPortion
What initial fraction of the filtered chain is discarded.
Definition: MetropolisHastingsSGOptions.h:331
QUESO::MhOptionsValues::m_drDuringAmNonAdaptiveInt
bool m_drDuringAmNonAdaptiveInt
Do delayed rejection during the initial non-adaptive part of sampling?
Definition: MetropolisHastingsSGOptions.h:467
QUESO::BaseEnvironment::subId
unsigned int subId() const
Access function to the number of each sub-environment Id: m_subId.
Definition: Environment.C:295
QUESO::MhOptionsValues::m_rawChainDataOutputFileName
std::string m_rawChainDataOutputFileName
If not &quot;.&quot;, filename to write the Markov chain to.
Definition: MetropolisHastingsSGOptions.h:291
QUESO::MhOptionsValues::m_rawChainDataOutputFileType
std::string m_rawChainDataOutputFileType
The filetype of m_rawChainDataOutputFileName. Only &quot;m&quot; (matlab) is currently supported. Default is &quot;m&quot;.
Definition: MetropolisHastingsSGOptions.h:294
QUESO::MiscReadDoublesFromString
void MiscReadDoublesFromString(const std::string &inputString, std::vector< double > &outputDoubles)
Definition: Miscellaneous.C:40
QUESO::MetropolisHastingsSGOptions::m_option_am_eta
std::string m_option_am_eta
See MhOptionsValues::m_amEta.
Definition: MetropolisHastingsSGOptions.h:835
QUESO::MhOptionsValues::m_totallyMute
bool m_totallyMute
If true, zero output is written to files. Default is false.
Definition: MetropolisHastingsSGOptions.h:194
queso_deprecated
#define queso_deprecated()
Definition: Defines.h:120
QUESO::MhOptionsValues::m_initialPositionDataInputFileName
std::string m_initialPositionDataInputFileName
If not &quot;.&quot;, reads the contents of the file and uses that to start the MCMC. Default is &quot;...
Definition: MetropolisHastingsSGOptions.h:200
QUESO::MetropolisHastingsSGOptions::m_option_am_epsilon
std::string m_option_am_epsilon
See MhOptionsValues::m_amEpsilon.
Definition: MetropolisHastingsSGOptions.h:837
QUESO::MhOptionsValues::m_filteredChainDataOutputAllowAll
bool m_filteredChainDataOutputAllowAll
Toggle for whether or not to allow all processes to write filtered Markov chain output to a file...
Definition: MetropolisHastingsSGOptions.h:362
QUESO::MhOptionsValues::m_displayCandidates
bool m_displayCandidates
Toggle to tell QUESO whether or not to write proposal (candidate) state to output file...
Definition: MetropolisHastingsSGOptions.h:372
QUESO::MhOptionsValues::m_parameterDisabledSet
std::set< unsigned int > m_parameterDisabledSet
Set of parameters that don&#39;t get sampled.
Definition: MetropolisHastingsSGOptions.h:224
QUESO::MetropolisHastingsSGOptions::m_ov
MhOptionsValues m_ov
This class is where the actual options are stored.
Definition: MetropolisHastingsSGOptions.h:762
QUESO::MhOptionsValues::m_enableBrooksGelmanConvMonitor
unsigned int m_enableBrooksGelmanConvMonitor
The frequency with which to compute the Brooks-Gelman convergence statistic.
Definition: MetropolisHastingsSGOptions.h:564
QUESO::MhOptionsValues::m_rawChainMeasureRunTimes
bool m_rawChainMeasureRunTimes
If true, measures timings spent in various chain computions and writes them to the output file...
Definition: MetropolisHastingsSGOptions.h:277
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:216
QUESO::MhOptionsValues::m_rawChainDataInputFileType
std::string m_rawChainDataInputFileType
The filetype of m_rawChainDataInputFileName. Only &quot;m&quot; (matlab) is currently supported. Default is &quot;m&quot;.
Definition: MetropolisHastingsSGOptions.h:238
QUESO::MhOptionsValues::m_tkUseLocalHessian
bool m_tkUseLocalHessian
Flag to tell QUESO whether or not to use Hessian information for the proposal covariance matrix...
Definition: MetropolisHastingsSGOptions.h:413
QUESO::MhOptionsValues::m_filteredChainGenerate
bool m_filteredChainGenerate
Toggle the option to save a filtered chain.
Definition: MetropolisHastingsSGOptions.h:322
QUESO::MhOptionsValues::m_rawChainDataOutputAllowedSet
std::set< unsigned int > m_rawChainDataOutputAllowedSet
The set of MPI ranks that will write Markov chain output to a file. See also m_rawChainDataOutputAllo...
Definition: MetropolisHastingsSGOptions.h:309
QUESO::MhOptionsValues::m_initialProposalCovMatrixDataInputFileType
std::string m_initialProposalCovMatrixDataInputFileType
The filetype of m_initialProposalCovMatrixDataInputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:218
QUESO::MhOptionsValues::m_outputLogLikelihood
bool m_outputLogLikelihood
Flag for deciding whether or not to dump log likelihood values in output. Default is true...
Definition: MetropolisHastingsSGOptions.h:577
QUESO::MhOptionsValues::m_dataOutputFileName
std::string m_dataOutputFileName
The base name of output files where the chain (and related information) will be written.
Definition: MetropolisHastingsSGOptions.h:176
QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputFileName
std::string m_amAdaptedMatricesDataOutputFileName
If not &quot;.&quot;, this is the file to write adapted proposal covariance matrices to. Default is &quot;...
Definition: MetropolisHastingsSGOptions.h:514
QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputFileType
std::string m_amAdaptedMatricesDataOutputFileType
The filetype of m_amAdaptedMatricesDataOutputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:517
void QUESO::MetropolisHastingsSGOptions::print ( std::ostream &  os) const

It prints the option values.

Definition at line 1014 of file MetropolisHastingsSGOptions.C.

References QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputAllowAll, QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputAllowedSet, QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputFileName, QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputFileType, QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputPeriod, QUESO::MhOptionsValues::m_amAdaptInterval, QUESO::MhOptionsValues::m_amEpsilon, QUESO::MhOptionsValues::m_amEta, QUESO::MhOptionsValues::m_amInitialNonAdaptInterval, QUESO::MhOptionsValues::m_amKeepInitialMatrix, QUESO::MhOptionsValues::m_BrooksGelmanLag, QUESO::MhOptionsValues::m_dataOutputAllowAll, QUESO::MhOptionsValues::m_dataOutputAllowedSet, QUESO::MhOptionsValues::m_dataOutputFileName, QUESO::MhOptionsValues::m_displayCandidates, QUESO::MhOptionsValues::m_doLogitTransform, QUESO::MhOptionsValues::m_drDuringAmNonAdaptiveInt, QUESO::MhOptionsValues::m_drMaxNumExtraStages, QUESO::MhOptionsValues::m_drScalesForExtraStages, QUESO::MhOptionsValues::m_enableBrooksGelmanConvMonitor, QUESO::MhOptionsValues::m_filteredChainDataOutputAllowAll, QUESO::MhOptionsValues::m_filteredChainDataOutputAllowedSet, QUESO::MhOptionsValues::m_filteredChainDataOutputFileName, QUESO::MhOptionsValues::m_filteredChainDataOutputFileType, QUESO::MhOptionsValues::m_filteredChainDiscardedPortion, QUESO::MhOptionsValues::m_filteredChainGenerate, QUESO::MhOptionsValues::m_filteredChainLag, QUESO::MhOptionsValues::m_initialPositionDataInputFileName, QUESO::MhOptionsValues::m_initialPositionDataInputFileType, QUESO::MhOptionsValues::m_initialProposalCovMatrixDataInputFileName, QUESO::MhOptionsValues::m_initialProposalCovMatrixDataInputFileType, m_option_am_adaptedMatrices_dataOutputAllowAll, m_option_am_adaptedMatrices_dataOutputAllowedSet, m_option_am_adaptedMatrices_dataOutputFileName, m_option_am_adaptedMatrices_dataOutputFileType, m_option_am_adaptedMatrices_dataOutputPeriod, m_option_am_adaptInterval, m_option_am_epsilon, m_option_am_eta, m_option_am_initialNonAdaptInterval, m_option_am_keepInitialMatrix, m_option_BrooksGelmanLag, m_option_dataOutputAllowAll, m_option_dataOutputAllowedSet, m_option_dataOutputFileName, m_option_displayCandidates, m_option_doLogitTransform, m_option_dr_duringAmNonAdaptiveInt, m_option_dr_listOfScalesForExtraStages, m_option_dr_maxNumExtraStages, m_option_enableBrooksGelmanConvMonitor, m_option_filteredChain_dataOutputAllowAll, m_option_filteredChain_dataOutputAllowedSet, m_option_filteredChain_dataOutputFileName, m_option_filteredChain_dataOutputFileType, m_option_filteredChain_discardedPortion, m_option_filteredChain_generate, m_option_filteredChain_lag, m_option_initialPosition_dataInputFileName, m_option_initialPosition_dataInputFileType, m_option_initialProposalCovMatrix_dataInputFileName, m_option_initialProposalCovMatrix_dataInputFileType, m_option_listOfDisabledParameters, m_option_outputLogLikelihood, m_option_outputLogTarget, m_option_putOutOfBoundsInChain, m_option_rawChain_dataInputFileName, m_option_rawChain_dataInputFileType, m_option_rawChain_dataOutputAllowAll, m_option_rawChain_dataOutputAllowedSet, m_option_rawChain_dataOutputFileName, m_option_rawChain_dataOutputFileType, m_option_rawChain_dataOutputPeriod, m_option_rawChain_displayPeriod, m_option_rawChain_generateExtra, m_option_rawChain_measureRunTimes, m_option_rawChain_size, m_option_tk_useLocalHessian, m_option_tk_useNewtonComponent, m_option_totallyMute, QUESO::MhOptionsValues::m_outputLogLikelihood, QUESO::MhOptionsValues::m_outputLogTarget, m_ov, QUESO::MhOptionsValues::m_parameterDisabledSet, QUESO::MhOptionsValues::m_putOutOfBoundsInChain, QUESO::MhOptionsValues::m_rawChainDataInputFileName, QUESO::MhOptionsValues::m_rawChainDataInputFileType, QUESO::MhOptionsValues::m_rawChainDataOutputAllowAll, QUESO::MhOptionsValues::m_rawChainDataOutputAllowedSet, QUESO::MhOptionsValues::m_rawChainDataOutputFileName, QUESO::MhOptionsValues::m_rawChainDataOutputFileType, QUESO::MhOptionsValues::m_rawChainDataOutputPeriod, QUESO::MhOptionsValues::m_rawChainDisplayPeriod, QUESO::MhOptionsValues::m_rawChainGenerateExtra, QUESO::MhOptionsValues::m_rawChainMeasureRunTimes, QUESO::MhOptionsValues::m_rawChainSize, QUESO::MhOptionsValues::m_tkUseLocalHessian, QUESO::MhOptionsValues::m_tkUseNewtonComponent, QUESO::MhOptionsValues::m_totallyMute, and queso_deprecated.

Referenced by QUESO::operator<<().

1015 {
1016  queso_deprecated();
1017 
1018  os << m_option_dataOutputFileName << " = " << m_ov.m_dataOutputFileName
1019  << "\n" << m_option_dataOutputAllowAll << " = " << m_ov.m_dataOutputAllowAll
1020  << "\n" << m_option_dataOutputAllowedSet << " = ";
1021  for (std::set<unsigned int>::iterator setIt = m_ov.m_dataOutputAllowedSet.begin(); setIt != m_ov.m_dataOutputAllowedSet.end(); ++setIt) {
1022  os << *setIt << " ";
1023  }
1024  os << "\n" << m_option_totallyMute << " = " << m_ov.m_totallyMute
1025  << "\n" << m_option_initialPosition_dataInputFileName << " = " << m_ov.m_initialPositionDataInputFileName
1026  << "\n" << m_option_initialPosition_dataInputFileType << " = " << m_ov.m_initialPositionDataInputFileType
1027  << "\n" << m_option_initialProposalCovMatrix_dataInputFileName << " = " << m_ov.m_initialProposalCovMatrixDataInputFileName
1028  << "\n" << m_option_initialProposalCovMatrix_dataInputFileType << " = " << m_ov.m_initialProposalCovMatrixDataInputFileType
1029  << "\n" << m_option_listOfDisabledParameters << " = ";
1030  for (std::set<unsigned int>::iterator setIt = m_ov.m_parameterDisabledSet.begin(); setIt != m_ov.m_parameterDisabledSet.end(); ++setIt) {
1031  os << *setIt << " ";
1032  }
1033  os << "\n" << m_option_rawChain_dataInputFileName << " = " << m_ov.m_rawChainDataInputFileName
1034  << "\n" << m_option_rawChain_dataInputFileType << " = " << m_ov.m_rawChainDataInputFileType
1035  << "\n" << m_option_rawChain_size << " = " << m_ov.m_rawChainSize
1036  << "\n" << m_option_rawChain_generateExtra << " = " << m_ov.m_rawChainGenerateExtra
1037  << "\n" << m_option_rawChain_displayPeriod << " = " << m_ov.m_rawChainDisplayPeriod
1038  << "\n" << m_option_rawChain_measureRunTimes << " = " << m_ov.m_rawChainMeasureRunTimes
1039  << "\n" << m_option_rawChain_dataOutputPeriod << " = " << m_ov.m_rawChainDataOutputPeriod
1040  << "\n" << m_option_rawChain_dataOutputFileName << " = " << m_ov.m_rawChainDataOutputFileName
1041  << "\n" << m_option_rawChain_dataOutputFileType << " = " << m_ov.m_rawChainDataOutputFileType
1042  << "\n" << m_option_rawChain_dataOutputAllowAll << " = " << m_ov.m_rawChainDataOutputAllowAll
1043  << "\n" << m_option_rawChain_dataOutputAllowedSet << " = ";
1044  for (std::set<unsigned int>::iterator setIt = m_ov.m_rawChainDataOutputAllowedSet.begin(); setIt != m_ov.m_rawChainDataOutputAllowedSet.end(); ++setIt) {
1045  os << *setIt << " ";
1046  }
1047  os
1048 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
1049  << "\n" << m_option_rawChain_computeStats << " = " << m_ov.m_rawChainComputeStats
1050 #endif
1051  << "\n" << m_option_filteredChain_generate << " = " << m_ov.m_filteredChainGenerate
1052  << "\n" << m_option_filteredChain_discardedPortion << " = " << m_ov.m_filteredChainDiscardedPortion
1053  << "\n" << m_option_filteredChain_lag << " = " << m_ov.m_filteredChainLag
1054  << "\n" << m_option_filteredChain_dataOutputFileName << " = " << m_ov.m_filteredChainDataOutputFileName
1055  << "\n" << m_option_filteredChain_dataOutputFileType << " = " << m_ov.m_filteredChainDataOutputFileType
1056  << "\n" << m_option_filteredChain_dataOutputAllowAll << " = " << m_ov.m_filteredChainDataOutputAllowAll
1057  << "\n" << m_option_filteredChain_dataOutputAllowedSet << " = ";
1058  for (std::set<unsigned int>::iterator setIt = m_ov.m_filteredChainDataOutputAllowedSet.begin(); setIt != m_ov.m_filteredChainDataOutputAllowedSet.end(); ++setIt) {
1059  os << *setIt << " ";
1060  }
1061  os
1062 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
1063  << "\n" << m_option_filteredChain_computeStats << " = " << m_ov.m_filteredChainComputeStats
1064 #endif
1065  << "\n" << m_option_displayCandidates << " = " << m_ov.m_displayCandidates
1066  << "\n" << m_option_putOutOfBoundsInChain << " = " << m_ov.m_putOutOfBoundsInChain
1067  << "\n" << m_option_tk_useLocalHessian << " = " << m_ov.m_tkUseLocalHessian
1068  << "\n" << m_option_tk_useNewtonComponent << " = " << m_ov.m_tkUseNewtonComponent
1069  << "\n" << m_option_dr_maxNumExtraStages << " = " << m_ov.m_drMaxNumExtraStages
1070  << "\n" << m_option_dr_listOfScalesForExtraStages << " = ";
1071  for (unsigned int i = 0; i < m_ov.m_drScalesForExtraStages.size(); ++i) {
1072  os << m_ov.m_drScalesForExtraStages[i] << " ";
1073  }
1074  os << "\n" << m_option_dr_duringAmNonAdaptiveInt << " = " << m_ov.m_drDuringAmNonAdaptiveInt
1075  << "\n" << m_option_am_keepInitialMatrix << " = " << m_ov.m_amKeepInitialMatrix
1076  << "\n" << m_option_am_initialNonAdaptInterval << " = " << m_ov.m_amInitialNonAdaptInterval
1077  << "\n" << m_option_am_adaptInterval << " = " << m_ov.m_amAdaptInterval
1078  << "\n" << m_option_am_adaptedMatrices_dataOutputPeriod << " = " << m_ov.m_amAdaptedMatricesDataOutputPeriod
1079  << "\n" << m_option_am_adaptedMatrices_dataOutputFileName << " = " << m_ov.m_amAdaptedMatricesDataOutputFileName
1080  << "\n" << m_option_am_adaptedMatrices_dataOutputFileType << " = " << m_ov.m_amAdaptedMatricesDataOutputFileType
1081  << "\n" << m_option_am_adaptedMatrices_dataOutputAllowAll << " = " << m_ov.m_amAdaptedMatricesDataOutputAllowAll
1082  << "\n" << m_option_am_adaptedMatrices_dataOutputAllowedSet << " = ";
1083  for (std::set<unsigned int>::iterator setIt = m_ov.m_amAdaptedMatricesDataOutputAllowedSet.begin(); setIt != m_ov.m_amAdaptedMatricesDataOutputAllowedSet.end(); ++setIt) {
1084  os << *setIt << " ";
1085  }
1086  os << "\n" << m_option_am_eta << " = " << m_ov.m_amEta
1087  << "\n" << m_option_am_epsilon << " = " << m_ov.m_amEpsilon
1088  << "\n" << m_option_enableBrooksGelmanConvMonitor << " = " << m_ov.m_enableBrooksGelmanConvMonitor
1089  << "\n" << m_option_BrooksGelmanLag << " = " << m_ov.m_BrooksGelmanLag
1090  << "\n" << m_option_outputLogLikelihood << " = " << m_ov.m_outputLogLikelihood
1091  << "\n" << m_option_outputLogTarget << " = " << m_ov.m_outputLogTarget
1092  << "\n" << m_option_doLogitTransform << " = " << m_ov.m_doLogitTransform
1093  << std::endl;
1094 
1095  return;
1096 }
QUESO::MhOptionsValues::m_filteredChainDataOutputFileType
std::string m_filteredChainDataOutputFileType
The filetype of m_filteredChainDataOutputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:350
QUESO::MhOptionsValues::m_doLogitTransform
bool m_doLogitTransform
Flag for deciding whether or not to do logit transform of bounded domains Default is true...
Definition: MetropolisHastingsSGOptions.h:583
QUESO::MhOptionsValues::m_rawChainGenerateExtra
bool m_rawChainGenerateExtra
If true, extra chain information is computed/stored.
Definition: MetropolisHastingsSGOptions.h:250
QUESO::MhOptionsValues::m_amEpsilon
double m_amEpsilon
Regularisation parameter for the DRAM covariance matrix.
Definition: MetropolisHastingsSGOptions.h:548
QUESO::MhOptionsValues::m_tkUseNewtonComponent
bool m_tkUseNewtonComponent
This option is a no-op. Default is true.
Definition: MetropolisHastingsSGOptions.h:416
QUESO::MhOptionsValues::m_filteredChainDataOutputAllowedSet
std::set< unsigned int > m_filteredChainDataOutputAllowedSet
The set of MPI ranks that will write filtered Markov chain output to a file. See also m_filteredChain...
Definition: MetropolisHastingsSGOptions.h:365
QUESO::MhOptionsValues::m_initialPositionDataInputFileType
std::string m_initialPositionDataInputFileType
The filetype of m_initialPositionDataInputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:203
QUESO::MhOptionsValues::m_rawChainDataInputFileName
std::string m_rawChainDataInputFileName
Filename for reading an already-produced Markov chain.
Definition: MetropolisHastingsSGOptions.h:235
QUESO::MhOptionsValues::m_filteredChainDataOutputFileName
std::string m_filteredChainDataOutputFileName
If not &quot;.&quot;, file name to save the filtered chain to. Default is &quot;.&quot;.
Definition: MetropolisHastingsSGOptions.h:347
QUESO::MhOptionsValues::m_amAdaptInterval
unsigned int m_amAdaptInterval
The frequency at which to adapt the proposal covariance matrix.
Definition: MetropolisHastingsSGOptions.h:491
QUESO::MhOptionsValues::m_amEta
double m_amEta
Proposal covariance scaling factor, usually 2.4 * 2.4 / d.
Definition: MetropolisHastingsSGOptions.h:536
QUESO::MhOptionsValues::m_rawChainDataOutputPeriod
unsigned int m_rawChainDataOutputPeriod
The frequency with which to write chain output. Defaults to 0.
Definition: MetropolisHastingsSGOptions.h:280
QUESO::MhOptionsValues::m_outputLogTarget
bool m_outputLogTarget
Flag for deciding whether or not to dump log target values in output Default is true.
Definition: MetropolisHastingsSGOptions.h:580
QUESO::MhOptionsValues::m_drScalesForExtraStages
std::vector< double > m_drScalesForExtraStages
The vector of scale factors for the proposal covariance matrix to use for delayed rejection...
Definition: MetropolisHastingsSGOptions.h:445
QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputAllowedSet
std::set< unsigned int > m_amAdaptedMatricesDataOutputAllowedSet
This option is a no-op. The default is the empty set.
Definition: MetropolisHastingsSGOptions.h:523
QUESO::MhOptionsValues::m_filteredChainLag
unsigned int m_filteredChainLag
Set the lag for the filtered chain. Default is 1.
Definition: MetropolisHastingsSGOptions.h:338
QUESO::MhOptionsValues::m_dataOutputAllowedSet
std::set< unsigned int > m_dataOutputAllowedSet
The set of MPI ranks that can write output. See m_dataOutputAllowAll.
Definition: MetropolisHastingsSGOptions.h:191
QUESO::MhOptionsValues::m_rawChainDataOutputAllowAll
bool m_rawChainDataOutputAllowAll
Toggle for whether or not to allow all processes to write Markov chain output to a file...
Definition: MetropolisHastingsSGOptions.h:306
QUESO::MhOptionsValues::m_rawChainSize
unsigned int m_rawChainSize
The size of the chain (number of posterior samples) to generate. Default is 100.
Definition: MetropolisHastingsSGOptions.h:241
QUESO::MhOptionsValues::m_drMaxNumExtraStages
unsigned int m_drMaxNumExtraStages
The number of delayed rejection stages to do. Default is 0.
Definition: MetropolisHastingsSGOptions.h:426
QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputAllowAll
bool m_amAdaptedMatricesDataOutputAllowAll
This option is a no-op. The default is false.
Definition: MetropolisHastingsSGOptions.h:520
QUESO::MhOptionsValues::m_putOutOfBoundsInChain
bool m_putOutOfBoundsInChain
Flag to tell QUESO how chains should be upon generating a proposal that is out of the problem domain...
Definition: MetropolisHastingsSGOptions.h:387
QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputPeriod
unsigned int m_amAdaptedMatricesDataOutputPeriod
The frequency (after m_amInitialNonAdaptInterval samples are done) of printing the last adapted propo...
Definition: MetropolisHastingsSGOptions.h:508
QUESO::MhOptionsValues::m_amKeepInitialMatrix
bool m_amKeepInitialMatrix
This option is a no-op. The default is false.
Definition: MetropolisHastingsSGOptions.h:470
QUESO::MhOptionsValues::m_rawChainDisplayPeriod
unsigned int m_rawChainDisplayPeriod
The frequency with which to output diagnostic information.
Definition: MetropolisHastingsSGOptions.h:260
QUESO::MhOptionsValues::m_initialProposalCovMatrixDataInputFileName
std::string m_initialProposalCovMatrixDataInputFileName
If not &quot;.&quot;, reads the contents of the file as the initial proposal covariance matrix.
Definition: MetropolisHastingsSGOptions.h:215
QUESO::MhOptionsValues::m_dataOutputAllowAll
bool m_dataOutputAllowAll
If true, all processes write output and m_dataOutputAllowedSet is ignored.
Definition: MetropolisHastingsSGOptions.h:185
QUESO::MhOptionsValues::m_amInitialNonAdaptInterval
unsigned int m_amInitialNonAdaptInterval
The number of initial samples to do without adapting the proposal covariance matrix.
Definition: MetropolisHastingsSGOptions.h:481
QUESO::MhOptionsValues::m_BrooksGelmanLag
unsigned int m_BrooksGelmanLag
The lag with which to compute the Brooks-Gelman convergence statistic.
Definition: MetropolisHastingsSGOptions.h:574
QUESO::MhOptionsValues::m_filteredChainDiscardedPortion
double m_filteredChainDiscardedPortion
What initial fraction of the filtered chain is discarded.
Definition: MetropolisHastingsSGOptions.h:331
QUESO::MhOptionsValues::m_drDuringAmNonAdaptiveInt
bool m_drDuringAmNonAdaptiveInt
Do delayed rejection during the initial non-adaptive part of sampling?
Definition: MetropolisHastingsSGOptions.h:467
QUESO::MhOptionsValues::m_rawChainDataOutputFileName
std::string m_rawChainDataOutputFileName
If not &quot;.&quot;, filename to write the Markov chain to.
Definition: MetropolisHastingsSGOptions.h:291
QUESO::MhOptionsValues::m_rawChainDataOutputFileType
std::string m_rawChainDataOutputFileType
The filetype of m_rawChainDataOutputFileName. Only &quot;m&quot; (matlab) is currently supported. Default is &quot;m&quot;.
Definition: MetropolisHastingsSGOptions.h:294
QUESO::MetropolisHastingsSGOptions::m_option_am_eta
std::string m_option_am_eta
See MhOptionsValues::m_amEta.
Definition: MetropolisHastingsSGOptions.h:835
QUESO::MhOptionsValues::m_totallyMute
bool m_totallyMute
If true, zero output is written to files. Default is false.
Definition: MetropolisHastingsSGOptions.h:194
queso_deprecated
#define queso_deprecated()
Definition: Defines.h:120
QUESO::MhOptionsValues::m_initialPositionDataInputFileName
std::string m_initialPositionDataInputFileName
If not &quot;.&quot;, reads the contents of the file and uses that to start the MCMC. Default is &quot;...
Definition: MetropolisHastingsSGOptions.h:200
QUESO::MetropolisHastingsSGOptions::m_option_am_epsilon
std::string m_option_am_epsilon
See MhOptionsValues::m_amEpsilon.
Definition: MetropolisHastingsSGOptions.h:837
QUESO::MhOptionsValues::m_filteredChainDataOutputAllowAll
bool m_filteredChainDataOutputAllowAll
Toggle for whether or not to allow all processes to write filtered Markov chain output to a file...
Definition: MetropolisHastingsSGOptions.h:362
QUESO::MhOptionsValues::m_displayCandidates
bool m_displayCandidates
Toggle to tell QUESO whether or not to write proposal (candidate) state to output file...
Definition: MetropolisHastingsSGOptions.h:372
QUESO::MhOptionsValues::m_parameterDisabledSet
std::set< unsigned int > m_parameterDisabledSet
Set of parameters that don&#39;t get sampled.
Definition: MetropolisHastingsSGOptions.h:224
QUESO::MetropolisHastingsSGOptions::m_ov
MhOptionsValues m_ov
This class is where the actual options are stored.
Definition: MetropolisHastingsSGOptions.h:762
QUESO::MhOptionsValues::m_enableBrooksGelmanConvMonitor
unsigned int m_enableBrooksGelmanConvMonitor
The frequency with which to compute the Brooks-Gelman convergence statistic.
Definition: MetropolisHastingsSGOptions.h:564
QUESO::MhOptionsValues::m_rawChainMeasureRunTimes
bool m_rawChainMeasureRunTimes
If true, measures timings spent in various chain computions and writes them to the output file...
Definition: MetropolisHastingsSGOptions.h:277
QUESO::MhOptionsValues::m_rawChainDataInputFileType
std::string m_rawChainDataInputFileType
The filetype of m_rawChainDataInputFileName. Only &quot;m&quot; (matlab) is currently supported. Default is &quot;m&quot;.
Definition: MetropolisHastingsSGOptions.h:238
QUESO::MhOptionsValues::m_tkUseLocalHessian
bool m_tkUseLocalHessian
Flag to tell QUESO whether or not to use Hessian information for the proposal covariance matrix...
Definition: MetropolisHastingsSGOptions.h:413
QUESO::MhOptionsValues::m_filteredChainGenerate
bool m_filteredChainGenerate
Toggle the option to save a filtered chain.
Definition: MetropolisHastingsSGOptions.h:322
QUESO::MhOptionsValues::m_rawChainDataOutputAllowedSet
std::set< unsigned int > m_rawChainDataOutputAllowedSet
The set of MPI ranks that will write Markov chain output to a file. See also m_rawChainDataOutputAllo...
Definition: MetropolisHastingsSGOptions.h:309
QUESO::MhOptionsValues::m_initialProposalCovMatrixDataInputFileType
std::string m_initialProposalCovMatrixDataInputFileType
The filetype of m_initialProposalCovMatrixDataInputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:218
QUESO::MhOptionsValues::m_outputLogLikelihood
bool m_outputLogLikelihood
Flag for deciding whether or not to dump log likelihood values in output. Default is true...
Definition: MetropolisHastingsSGOptions.h:577
QUESO::MhOptionsValues::m_dataOutputFileName
std::string m_dataOutputFileName
The base name of output files where the chain (and related information) will be written.
Definition: MetropolisHastingsSGOptions.h:176
QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputFileName
std::string m_amAdaptedMatricesDataOutputFileName
If not &quot;.&quot;, this is the file to write adapted proposal covariance matrices to. Default is &quot;...
Definition: MetropolisHastingsSGOptions.h:514
QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputFileType
std::string m_amAdaptedMatricesDataOutputFileType
The filetype of m_amAdaptedMatricesDataOutputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:517
void QUESO::MetropolisHastingsSGOptions::scanOptionsValues ( )

It scans the option values from the options input file.

Definition at line 980 of file MetropolisHastingsSGOptions.C.

References defineMyOptions(), getMyOptionValues(), m_env, m_optionsDesc, m_ov, m_prefix, QUESO::MhOptionsValues::m_totallyMute, queso_deprecated, queso_require_msg, QUESO::BaseEnvironment::scanInputFileForMyOptions(), and QUESO::BaseEnvironment::subDisplayFile().

981 {
982  queso_deprecated();
983 
984  queso_require_msg(m_optionsDesc, "m_optionsDesc variable is NULL");
985 
986  defineMyOptions (*m_optionsDesc);
987  m_env.scanInputFileForMyOptions(*m_optionsDesc);
988  getMyOptionValues (*m_optionsDesc);
989 
990  if ((m_env.subDisplayFile() != NULL) &&
991  (m_ov.m_totallyMute == false )) {
992  *m_env.subDisplayFile() << "In MetropolisHastingsSGOptions::scanOptionsValues()"
993  << ": after reading values of options with prefix '" << m_prefix
994  << "', state of object is:"
995  << "\n" << *this
996  << std::endl;
997  }
998 
999 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
1000  if (m_ov.m_rawChainComputeStats) {
1001  m_rawChainStatisticalOptionsObj = new SequenceStatisticalOptions(m_env,m_prefix + "rawChain_");
1002  m_rawChainStatOptsInstantiated = true;
1003  }
1004  if (m_ov.m_filteredChainComputeStats) {
1005  m_filteredChainStatisticalOptionsObj = new SequenceStatisticalOptions(m_env,m_prefix + "filteredChain_");
1006  m_filteredChainStatOptsInstantiated = true;
1007  }
1008 #endif
1009 
1010  return;
1011 }
QUESO::MetropolisHastingsSGOptions::defineMyOptions
void defineMyOptions(boost::program_options::options_description &optionsDesc) const
Defines the options for the Metropolis-Hastings generator of samples as the default options...
Definition: MetropolisHastingsSGOptions.C:1100
QUESO::BaseEnvironment::scanInputFileForMyOptions
void scanInputFileForMyOptions(const boost::program_options::options_description &optionsDesc) const
This method scans the input file provided by the user to QUESO.
Definition: Environment.C:345
queso_require_msg
#define queso_require_msg(asserted, msg)
Definition: asserts.h:69
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:274
QUESO::MhOptionsValues::m_totallyMute
bool m_totallyMute
If true, zero output is written to files. Default is false.
Definition: MetropolisHastingsSGOptions.h:194
queso_deprecated
#define queso_deprecated()
Definition: Defines.h:120
QUESO::MetropolisHastingsSGOptions::m_optionsDesc
boost::program_options::options_description * m_optionsDesc
Definition: MetropolisHastingsSGOptions.h:780
QUESO::MetropolisHastingsSGOptions::m_ov
MhOptionsValues m_ov
This class is where the actual options are stored.
Definition: MetropolisHastingsSGOptions.h:762
QUESO::MetropolisHastingsSGOptions::getMyOptionValues
void getMyOptionValues(boost::program_options::options_description &optionsDesc)
Gets the sequence options defined to the Metropolis-Hastings algorithm.
Definition: MetropolisHastingsSGOptions.C:1167

Member Data Documentation

const BaseEnvironment& QUESO::MetropolisHastingsSGOptions::m_env
private

Definition at line 779 of file MetropolisHastingsSGOptions.h.

Referenced by getMyOptionValues(), MetropolisHastingsSGOptions(), and scanOptionsValues().

std::string QUESO::MetropolisHastingsSGOptions::m_option_am_adaptedMatrices_dataOutputAllowAll
private

Definition at line 831 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_am_adaptedMatrices_dataOutputAllowedSet
private

Definition at line 832 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_am_adaptedMatrices_dataOutputFileName
private

Definition at line 829 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_am_adaptedMatrices_dataOutputFileType
private

Definition at line 830 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_am_adaptedMatrices_dataOutputPeriod
private

Definition at line 828 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_am_adaptInterval
private

Definition at line 827 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_am_epsilon
private

See MhOptionsValues::m_amEpsilon.

Definition at line 837 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_am_eta
private

See MhOptionsValues::m_amEta.

Definition at line 835 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_am_initialNonAdaptInterval
private

Definition at line 826 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_am_keepInitialMatrix
private

Definition at line 825 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_BrooksGelmanLag
private

Definition at line 840 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_dataOutputAllowAll
private

Definition at line 785 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_dataOutputAllowedSet
private

Definition at line 786 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_dataOutputFileName
private

Definition at line 784 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_displayCandidates
private

Definition at line 818 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_doLogitTransform
private

Definition at line 844 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_dr_duringAmNonAdaptiveInt
private

Definition at line 824 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_dr_listOfScalesForExtraStages
private

Definition at line 823 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_dr_maxNumExtraStages
private

Definition at line 822 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_enableBrooksGelmanConvMonitor
private

Definition at line 839 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_filteredChain_dataOutputAllowAll
private

Definition at line 813 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_filteredChain_dataOutputAllowedSet
private

Definition at line 814 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_filteredChain_dataOutputFileName
private

Definition at line 811 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_filteredChain_dataOutputFileType
private

Definition at line 812 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_filteredChain_discardedPortion
private

Definition at line 809 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_filteredChain_generate
private

Definition at line 808 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_filteredChain_lag
private

Definition at line 810 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_help
private

Definition at line 782 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), and getMyOptionValues().

std::string QUESO::MetropolisHastingsSGOptions::m_option_initialPosition_dataInputFileName
private

Definition at line 789 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_initialPosition_dataInputFileType
private

Definition at line 790 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_initialProposalCovMatrix_dataInputFileName
private

Definition at line 791 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_initialProposalCovMatrix_dataInputFileType
private

Definition at line 792 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_listOfDisabledParameters
private

Definition at line 793 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_outputLogLikelihood
private

Definition at line 842 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_outputLogTarget
private

Definition at line 843 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_putOutOfBoundsInChain
private

Definition at line 819 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_rawChain_dataInputFileName
private

Definition at line 794 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_rawChain_dataInputFileType
private

Definition at line 795 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_rawChain_dataOutputAllowAll
private

Definition at line 803 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_rawChain_dataOutputAllowedSet
private

Definition at line 804 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_rawChain_dataOutputFileName
private

Definition at line 801 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_rawChain_dataOutputFileType
private

Definition at line 802 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_rawChain_dataOutputPeriod
private

Definition at line 800 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_rawChain_displayPeriod
private

Definition at line 798 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_rawChain_generateExtra
private

Definition at line 797 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_rawChain_measureRunTimes
private

Definition at line 799 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_rawChain_size
private

Definition at line 796 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_tk_useLocalHessian
private

Definition at line 820 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_tk_useNewtonComponent
private

Definition at line 821 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

std::string QUESO::MetropolisHastingsSGOptions::m_option_totallyMute
private

Definition at line 788 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), getMyOptionValues(), and print().

boost::program_options::options_description* QUESO::MetropolisHastingsSGOptions::m_optionsDesc
private

Definition at line 780 of file MetropolisHastingsSGOptions.h.

Referenced by scanOptionsValues(), and ~MetropolisHastingsSGOptions().

MhOptionsValues QUESO::MetropolisHastingsSGOptions::m_ov

This class is where the actual options are stored.

Definition at line 762 of file MetropolisHastingsSGOptions.h.

Referenced by getMyOptionValues(), QUESO::MetropolisHastingsSG< P_V, P_M >::MetropolisHastingsSG(), MetropolisHastingsSGOptions(), print(), and scanOptionsValues().

std::string QUESO::MetropolisHastingsSGOptions::m_prefix

Definition at line 770 of file MetropolisHastingsSGOptions.h.

Referenced by MetropolisHastingsSGOptions(), and scanOptionsValues().

The documentation for this class was generated from the following files:
Generated on Thu Jun 11 2015 13:52:36 for queso-0.53.0 by  doxygen 1.8.5