queso-0.56.0
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
 
std::string m_option_algorithm
 
std::string m_option_tk
 

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 772 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 825 of file MetropolisHastingsSGOptions.C.

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

828  :
829 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
830  m_ov (NULL,NULL), // dakota
831  m_rawChainStatisticalOptionsObj (NULL),
832  m_rawChainStatOptsInstantiated (false),
833  m_filteredChainStatisticalOptionsObj (NULL),
834  m_filteredChainStatOptsInstantiated (false),
835 #else
836  m_ov (),
837 #endif
838  m_prefix ((std::string)(prefix) + "mh_"),
839  m_env (env),
840 #ifndef DISABLE_BOOST_PROGRAM_OPTIONS
841  m_optionsDesc (new boost::program_options::options_description("Bayesian Metropolis-Hastings options")),
842 #endif // DISABLE_BOOST_PROGRAM_OPTIONS
843  m_option_help (m_prefix + "help" ),
844  m_option_dataOutputFileName (m_prefix + "dataOutputFileName" ),
845  m_option_dataOutputAllowAll (m_prefix + "dataOutputAllowAll" ),
846  m_option_dataOutputAllowedSet (m_prefix + "dataOutputAllowedSet" ),
847  m_option_totallyMute (m_prefix + "totallyMute" ),
848  m_option_initialPosition_dataInputFileName (m_prefix + "initialPosition_dataInputFileName" ),
849  m_option_initialPosition_dataInputFileType (m_prefix + "initialPosition_dataInputFileType" ),
850  m_option_initialProposalCovMatrix_dataInputFileName(m_prefix + "initialProposalCovMatrix_dataInputFileName"),
851  m_option_initialProposalCovMatrix_dataInputFileType(m_prefix + "initialProposalCovMatrix_dataInputFileType"),
852  m_option_listOfDisabledParameters (m_prefix + "listOfDisabledParameters" ),
853  m_option_rawChain_dataInputFileName (m_prefix + "rawChain_dataInputFileName" ),
854  m_option_rawChain_dataInputFileType (m_prefix + "rawChain_dataInputFileType" ),
855  m_option_rawChain_size (m_prefix + "rawChain_size" ),
856  m_option_rawChain_generateExtra (m_prefix + "rawChain_generateExtra" ),
857  m_option_rawChain_displayPeriod (m_prefix + "rawChain_displayPeriod" ),
858  m_option_rawChain_measureRunTimes (m_prefix + "rawChain_measureRunTimes" ),
859  m_option_rawChain_dataOutputPeriod (m_prefix + "rawChain_dataOutputPeriod" ),
860  m_option_rawChain_dataOutputFileName (m_prefix + "rawChain_dataOutputFileName" ),
861  m_option_rawChain_dataOutputFileType (m_prefix + "rawChain_dataOutputFileType" ),
862  m_option_rawChain_dataOutputAllowAll (m_prefix + "rawChain_dataOutputAllowAll" ),
863  m_option_rawChain_dataOutputAllowedSet (m_prefix + "rawChain_dataOutputAllowedSet" ),
864 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
865  m_option_rawChain_computeStats (m_prefix + "rawChain_computeStats" ),
866 #endif
867  m_option_filteredChain_generate (m_prefix + "filteredChain_generate" ),
868  m_option_filteredChain_discardedPortion (m_prefix + "filteredChain_discardedPortion" ),
869  m_option_filteredChain_lag (m_prefix + "filteredChain_lag" ),
870  m_option_filteredChain_dataOutputFileName (m_prefix + "filteredChain_dataOutputFileName" ),
871  m_option_filteredChain_dataOutputFileType (m_prefix + "filteredChain_dataOutputFileType" ),
872  m_option_filteredChain_dataOutputAllowAll (m_prefix + "filteredChain_dataOutputAllowAll" ),
873  m_option_filteredChain_dataOutputAllowedSet (m_prefix + "filteredChain_dataOutputAllowedSet" ),
874 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
875  m_option_filteredChain_computeStats (m_prefix + "filteredChain_computeStats" ),
876 #endif
877  m_option_displayCandidates (m_prefix + "displayCandidates" ),
878  m_option_putOutOfBoundsInChain (m_prefix + "putOutOfBoundsInChain" ),
879  m_option_tk_useLocalHessian (m_prefix + "tk_useLocalHessian" ),
880  m_option_tk_useNewtonComponent (m_prefix + "tk_useNewtonComponent" ),
881  m_option_dr_maxNumExtraStages (m_prefix + "dr_maxNumExtraStages" ),
882  m_option_dr_listOfScalesForExtraStages (m_prefix + "dr_listOfScalesForExtraStages" ),
883  m_option_dr_duringAmNonAdaptiveInt (m_prefix + "dr_duringAmNonAdaptiveInt" ),
884  m_option_am_keepInitialMatrix (m_prefix + "am_keepInitialMatrix" ),
885  m_option_am_initialNonAdaptInterval (m_prefix + "am_initialNonAdaptInterval" ),
886  m_option_am_adaptInterval (m_prefix + "am_adaptInterval" ),
887  m_option_am_adaptedMatrices_dataOutputPeriod (m_prefix + "am_adaptedMatrices_dataOutputPeriod" ),
888  m_option_am_adaptedMatrices_dataOutputFileName (m_prefix + "am_adaptedMatrices_dataOutputFileName" ),
889  m_option_am_adaptedMatrices_dataOutputFileType (m_prefix + "am_adaptedMatrices_dataOutputFileType" ),
890  m_option_am_adaptedMatrices_dataOutputAllowAll (m_prefix + "am_adaptedMatrices_dataOutputAllowAll" ),
891  m_option_am_adaptedMatrices_dataOutputAllowedSet (m_prefix + "am_adaptedMatrices_dataOutputAllowedSet" ),
892  m_option_am_eta (m_prefix + "am_eta" ),
893  m_option_am_epsilon (m_prefix + "am_epsilon" ),
894  m_option_enableBrooksGelmanConvMonitor (m_prefix + "enableBrooksGelmanConvMonitor" ),
895  m_option_BrooksGelmanLag (m_prefix + "BrooksGelmanLag" ),
896  m_option_outputLogLikelihood (m_prefix + "outputLogLikelihood" ),
897  m_option_outputLogTarget (m_prefix + "outputLogTarget" ),
898  m_option_doLogitTransform (m_prefix + "doLogitTransform" ),
899  m_option_algorithm (m_prefix + "algorithm" ),
900  m_option_tk (m_prefix + "tk" )
901 {
902  queso_deprecated();
903 
904  queso_require_not_equal_to_msg(m_env.optionsInputFileName(), std::string(""), std::string("this constructor is incompatible with the absence of an options input file"));
905 }
QUESO::MetropolisHastingsSGOptions::m_ov
MhOptionsValues m_ov
This class is where the actual options are stored.
Definition: MetropolisHastingsSGOptions.h:801
QUESO::MetropolisHastingsSGOptions::m_option_am_eta
std::string m_option_am_eta
See MhOptionsValues::m_amEta.
Definition: MetropolisHastingsSGOptions.h:878
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:353
QUESO::MetropolisHastingsSGOptions::m_option_am_epsilon
std::string m_option_am_epsilon
See MhOptionsValues::m_amEpsilon.
Definition: MetropolisHastingsSGOptions.h:880
queso_deprecated
#define queso_deprecated()
Definition: Defines.h:134
queso_require_not_equal_to_msg
#define queso_require_not_equal_to_msg(expr1, expr2, msg)
Definition: asserts.h:74
QUESO::MetropolisHastingsSGOptions::m_optionsDesc
boost::program_options::options_description * m_optionsDesc
Definition: MetropolisHastingsSGOptions.h:822
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 907 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().

911  :
912  m_ov (alternativeOptionsValues),
913 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
914  m_rawChainStatisticalOptionsObj (NULL),
915  m_rawChainStatOptsInstantiated (false),
916  m_filteredChainStatisticalOptionsObj (NULL),
917  m_filteredChainStatOptsInstantiated (false),
918 #endif
919  m_prefix ((std::string)(prefix) + "mh_"),
920  m_env (env),
921 #ifndef DISABLE_BOOST_PROGRAM_OPTIONS
922  m_optionsDesc (NULL),
923 #endif // DISABLE_BOOST_PROGRAM_OPTIONS
924  m_option_help (m_prefix + "help" ),
925  m_option_dataOutputFileName (m_prefix + "dataOutputFileName" ),
926  m_option_dataOutputAllowAll (m_prefix + "dataOutputAllowAll" ),
927  m_option_dataOutputAllowedSet (m_prefix + "dataOutputAllowedSet" ),
928  m_option_totallyMute (m_prefix + "totallyMute" ),
929  m_option_initialPosition_dataInputFileName (m_prefix + "initialPosition_dataInputFileName" ),
930  m_option_initialPosition_dataInputFileType (m_prefix + "initialPosition_dataInputFileType" ),
931  m_option_initialProposalCovMatrix_dataInputFileName(m_prefix + "initialProposalCovMatrix_dataInputFileName"),
932  m_option_initialProposalCovMatrix_dataInputFileType(m_prefix + "initialProposalCovMatrix_dataInputFileType"),
933  m_option_listOfDisabledParameters (m_prefix + "listOfDisabledParameters" ),
934  m_option_rawChain_dataInputFileName (m_prefix + "rawChain_dataInputFileName" ),
935  m_option_rawChain_dataInputFileType (m_prefix + "rawChain_dataInputFileType" ),
936  m_option_rawChain_size (m_prefix + "rawChain_size" ),
937  m_option_rawChain_generateExtra (m_prefix + "rawChain_generateExtra" ),
938  m_option_rawChain_displayPeriod (m_prefix + "rawChain_displayPeriod" ),
939  m_option_rawChain_measureRunTimes (m_prefix + "rawChain_measureRunTimes" ),
940  m_option_rawChain_dataOutputPeriod (m_prefix + "rawChain_dataOutputPeriod" ),
941  m_option_rawChain_dataOutputFileName (m_prefix + "rawChain_dataOutputFileName" ),
942  m_option_rawChain_dataOutputFileType (m_prefix + "rawChain_dataOutputFileType" ),
943  m_option_rawChain_dataOutputAllowAll (m_prefix + "rawChain_dataOutputAllowAll" ),
944  m_option_rawChain_dataOutputAllowedSet (m_prefix + "rawChain_dataOutputAllowedSet" ),
945 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
946  m_option_rawChain_computeStats (m_prefix + "rawChain_computeStats" ),
947 #endif
948  m_option_filteredChain_generate (m_prefix + "filteredChain_generate" ),
949  m_option_filteredChain_discardedPortion (m_prefix + "filteredChain_discardedPortion" ),
950  m_option_filteredChain_lag (m_prefix + "filteredChain_lag" ),
951  m_option_filteredChain_dataOutputFileName (m_prefix + "filteredChain_dataOutputFileName" ),
952  m_option_filteredChain_dataOutputFileType (m_prefix + "filteredChain_dataOutputFileType" ),
953  m_option_filteredChain_dataOutputAllowAll (m_prefix + "filteredChain_dataOutputAllowAll" ),
954  m_option_filteredChain_dataOutputAllowedSet (m_prefix + "filteredChain_dataOutputAllowedSet" ),
955 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
956  m_option_filteredChain_computeStats (m_prefix + "filteredChain_computeStats" ),
957 #endif
958  m_option_displayCandidates (m_prefix + "displayCandidates" ),
959  m_option_putOutOfBoundsInChain (m_prefix + "putOutOfBoundsInChain" ),
960  m_option_tk_useLocalHessian (m_prefix + "tk_useLocalHessian" ),
961  m_option_tk_useNewtonComponent (m_prefix + "tk_useNewtonComponent" ),
962  m_option_dr_maxNumExtraStages (m_prefix + "dr_maxNumExtraStages" ),
963  m_option_dr_listOfScalesForExtraStages (m_prefix + "dr_listOfScalesForExtraStages" ),
964  m_option_dr_duringAmNonAdaptiveInt (m_prefix + "dr_duringAmNonAdaptiveInt" ),
965  m_option_am_keepInitialMatrix (m_prefix + "am_keepInitialMatrix" ),
966  m_option_am_initialNonAdaptInterval (m_prefix + "am_initialNonAdaptInterval" ),
967  m_option_am_adaptInterval (m_prefix + "am_adaptInterval" ),
968  m_option_am_adaptedMatrices_dataOutputPeriod (m_prefix + "am_adaptedMatrices_dataOutputPeriod" ),
969  m_option_am_adaptedMatrices_dataOutputFileName (m_prefix + "am_adaptedMatrices_dataOutputFileName" ),
970  m_option_am_adaptedMatrices_dataOutputFileType (m_prefix + "am_adaptedMatrices_dataOutputFileType" ),
971  m_option_am_adaptedMatrices_dataOutputAllowAll (m_prefix + "am_adaptedMatrices_dataOutputAllowAll" ),
972  m_option_am_adaptedMatrices_dataOutputAllowedSet (m_prefix + "am_adaptedMatrices_dataOutputAllowedSet" ),
973  m_option_am_eta (m_prefix + "am_eta" ),
974  m_option_am_epsilon (m_prefix + "am_epsilon" ),
975  m_option_enableBrooksGelmanConvMonitor (m_prefix + "enableBrooksGelmanConvMonitor" ),
976  m_option_BrooksGelmanLag (m_prefix + "BrooksGelmanLag" ),
977  m_option_outputLogLikelihood (m_prefix + "outputLogLikelihood" ),
978  m_option_outputLogTarget (m_prefix + "outputLogTarget" ),
979  m_option_doLogitTransform (m_prefix + "doLogitTransform" ),
980  m_option_algorithm (m_prefix + "algorithm" ),
981  m_option_tk (m_prefix + "tk" )
982 {
983  queso_deprecated();
984 
985  queso_require_equal_to_msg(m_env.optionsInputFileName(), std::string(""), std::string("this constructor is incompatible with the existence of an options input file"));
986 
987  if ((m_env.subDisplayFile() != NULL ) &&
988  (m_ov.m_totallyMute == false)) {
989  *m_env.subDisplayFile() << "In MetropolisHastingsSGOptions::constructor(2)"
990  << ": after setting values of options with prefix '" << m_prefix
991  << "', state of object is:"
992  << "\n" << *this
993  << std::endl;
994  }
995 
996 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
997  if (m_ov.m_rawChainComputeStats) {
998  m_rawChainStatisticalOptionsObj = new SequenceStatisticalOptions(m_env,m_prefix + "rawChain_",m_ov.m_alternativeRawSsOptionsValues);
999  m_rawChainStatOptsInstantiated = true;
1000  }
1001  if (m_ov.m_filteredChainComputeStats) {
1002  m_filteredChainStatisticalOptionsObj = new SequenceStatisticalOptions(m_env,m_prefix + "filteredChain_",m_ov.m_alternativeFilteredSsOptionsValues);
1003  m_filteredChainStatOptsInstantiated = true;
1004  }
1005 #endif
1006 }
QUESO::MhOptionsValues::m_totallyMute
bool m_totallyMute
If true, zero output is written to files. Default is false.
Definition: MetropolisHastingsSGOptions.h:201
QUESO::MetropolisHastingsSGOptions::m_ov
MhOptionsValues m_ov
This class is where the actual options are stored.
Definition: MetropolisHastingsSGOptions.h:801
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:320
QUESO::MetropolisHastingsSGOptions::m_option_am_eta
std::string m_option_am_eta
See MhOptionsValues::m_amEta.
Definition: MetropolisHastingsSGOptions.h:878
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:353
QUESO::MetropolisHastingsSGOptions::m_option_am_epsilon
std::string m_option_am_epsilon
See MhOptionsValues::m_amEpsilon.
Definition: MetropolisHastingsSGOptions.h:880
queso_require_equal_to_msg
#define queso_require_equal_to_msg(expr1, expr2, msg)
Definition: asserts.h:73
queso_deprecated
#define queso_deprecated()
Definition: Defines.h:134
QUESO::MetropolisHastingsSGOptions::m_optionsDesc
boost::program_options::options_description * m_optionsDesc
Definition: MetropolisHastingsSGOptions.h:822
QUESO::MetropolisHastingsSGOptions::MetropolisHastingsSGOptions ( const MLSamplingLevelOptions &  mlOptions)

Copy constructor.

Definition at line 1008 of file MetropolisHastingsSGOptions.C.

References QUESO::MLSamplingLevelOptions::m_algorithm, QUESO::MhOptionsValues::m_algorithm, 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::MLSamplingLevelOptions::m_initialPositionDataInputFileName, QUESO::MhOptionsValues::m_initialPositionDataInputFileName, QUESO::MLSamplingLevelOptions::m_initialPositionDataInputFileType, QUESO::MhOptionsValues::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_tk, QUESO::MhOptionsValues::m_tk, 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.

1010  :
1011 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
1012  m_ov (NULL,NULL), // dakota
1013  m_rawChainStatisticalOptionsObj (NULL),
1014  m_rawChainStatOptsInstantiated (false),
1015  m_filteredChainStatisticalOptionsObj (NULL),
1016  m_filteredChainStatOptsInstantiated (false),
1017 #else
1018  m_ov (),
1019 #endif
1020  m_prefix (mlOptions.m_prefix),
1021  m_env (mlOptions.env()),
1022 #ifndef DISABLE_BOOST_PROGRAM_OPTIONS
1023  m_optionsDesc (NULL),
1024 #endif // DISABLE_BOOST_PROGRAM_OPTIONS
1025  m_option_help (m_prefix + "help" ),
1026  m_option_dataOutputFileName (m_prefix + "dataOutputFileName" ),
1027  m_option_dataOutputAllowAll (m_prefix + "dataOutputAllowAll" ),
1028  m_option_dataOutputAllowedSet (m_prefix + "dataOutputAllowedSet" ),
1029  m_option_totallyMute (m_prefix + "totallyMute" ),
1030  m_option_initialPosition_dataInputFileName (m_prefix + "initialPosition_dataInputFileName" ),
1031  m_option_initialPosition_dataInputFileType (m_prefix + "initialPosition_dataInputFileType" ),
1032  m_option_initialProposalCovMatrix_dataInputFileName(m_prefix + "initialProposalCovMatrix_dataInputFileName"),
1033  m_option_initialProposalCovMatrix_dataInputFileType(m_prefix + "initialProposalCovMatrix_dataInputFileType"),
1034  m_option_listOfDisabledParameters (m_prefix + "listOfDisabledParameters" ),
1035  m_option_rawChain_dataInputFileName (m_prefix + "rawChain_dataInputFileName" ),
1036  m_option_rawChain_dataInputFileType (m_prefix + "rawChain_dataInputFileType" ),
1037  m_option_rawChain_size (m_prefix + "rawChain_size" ),
1038  m_option_rawChain_generateExtra (m_prefix + "rawChain_generateExtra" ),
1039  m_option_rawChain_displayPeriod (m_prefix + "rawChain_displayPeriod" ),
1040  m_option_rawChain_measureRunTimes (m_prefix + "rawChain_measureRunTimes" ),
1041  m_option_rawChain_dataOutputPeriod (m_prefix + "rawChain_dataOutputPeriod" ),
1042  m_option_rawChain_dataOutputFileName (m_prefix + "rawChain_dataOutputFileName" ),
1043  m_option_rawChain_dataOutputFileType (m_prefix + "rawChain_dataOutputFileType" ),
1044  m_option_rawChain_dataOutputAllowAll (m_prefix + "rawChain_dataOutputAllowAll" ),
1045  m_option_rawChain_dataOutputAllowedSet (m_prefix + "rawChain_dataOutputAllowedSet" ),
1046 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
1047  m_option_rawChain_computeStats (m_prefix + "rawChain_computeStats" ),
1048 #endif
1049  m_option_filteredChain_generate (m_prefix + "filteredChain_generate" ),
1050  m_option_filteredChain_discardedPortion (m_prefix + "filteredChain_discardedPortion" ),
1051  m_option_filteredChain_lag (m_prefix + "filteredChain_lag" ),
1052  m_option_filteredChain_dataOutputFileName (m_prefix + "filteredChain_dataOutputFileName" ),
1053  m_option_filteredChain_dataOutputFileType (m_prefix + "filteredChain_dataOutputFileType" ),
1054  m_option_filteredChain_dataOutputAllowAll (m_prefix + "filteredChain_dataOutputAllowAll" ),
1055  m_option_filteredChain_dataOutputAllowedSet (m_prefix + "filteredChain_dataOutputAllowedSet" ),
1056 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
1057  m_option_filteredChain_computeStats (m_prefix + "filteredChain_computeStats" ),
1058 #endif
1059  m_option_displayCandidates (m_prefix + "displayCandidates" ),
1060  m_option_putOutOfBoundsInChain (m_prefix + "putOutOfBoundsInChain" ),
1061  m_option_tk_useLocalHessian (m_prefix + "tk_useLocalHessian" ),
1062  m_option_tk_useNewtonComponent (m_prefix + "tk_useNewtonComponent" ),
1063  m_option_dr_maxNumExtraStages (m_prefix + "dr_maxNumExtraStages" ),
1064  m_option_dr_listOfScalesForExtraStages (m_prefix + "dr_listOfScalesForExtraStages" ),
1065  m_option_dr_duringAmNonAdaptiveInt (m_prefix + "dr_duringAmNonAdaptiveInt" ),
1066  m_option_am_keepInitialMatrix (m_prefix + "am_keepInitialMatrix" ),
1067  m_option_am_initialNonAdaptInterval (m_prefix + "am_initialNonAdaptInterval" ),
1068  m_option_am_adaptInterval (m_prefix + "am_adaptInterval" ),
1069  m_option_am_adaptedMatrices_dataOutputPeriod (m_prefix + "am_adaptedMatrices_dataOutputPeriod" ),
1070  m_option_am_adaptedMatrices_dataOutputFileName (m_prefix + "am_adaptedMatrices_dataOutputFileName" ),
1071  m_option_am_adaptedMatrices_dataOutputFileType (m_prefix + "am_adaptedMatrices_dataOutputFileType" ),
1072  m_option_am_adaptedMatrices_dataOutputAllowAll (m_prefix + "am_adaptedMatrices_dataOutputAllowAll" ),
1073  m_option_am_adaptedMatrices_dataOutputAllowedSet (m_prefix + "am_adaptedMatrices_dataOutputAllowedSet" ),
1074  m_option_am_eta (m_prefix + "am_eta" ),
1075  m_option_am_epsilon (m_prefix + "am_epsilon" ),
1076  m_option_enableBrooksGelmanConvMonitor (m_prefix + "enableBrooksGelmanConvMonitor" ),
1077  m_option_BrooksGelmanLag (m_prefix + "BrooksGelmanLag" ),
1078  m_option_outputLogLikelihood (m_prefix + "outputLogLikelihood" ),
1079  m_option_outputLogTarget (m_prefix + "outputLogTarget" ),
1080  m_option_doLogitTransform (m_prefix + "doLogitTransform" ),
1081  m_option_algorithm (m_prefix + "algorithm" ),
1082  m_option_tk (m_prefix + "tk" )
1083 {
1084  queso_deprecated();
1085 
1086  m_ov.m_dataOutputFileName = mlOptions.m_dataOutputFileName;
1087  m_ov.m_dataOutputAllowAll = mlOptions.m_dataOutputAllowAll;
1088  m_ov.m_dataOutputAllowedSet = mlOptions.m_dataOutputAllowedSet;
1089  m_ov.m_totallyMute = mlOptions.m_totallyMute;
1090  m_ov.m_initialPositionDataInputFileName = mlOptions.m_initialPositionDataInputFileName;
1091  m_ov.m_initialPositionDataInputFileType = mlOptions.m_initialPositionDataInputFileType;
1092  m_ov.m_initialProposalCovMatrixDataInputFileName = mlOptions.m_initialProposalCovMatrixDataInputFileName;
1093  m_ov.m_initialProposalCovMatrixDataInputFileType = mlOptions.m_initialProposalCovMatrixDataInputFileType;
1094  m_ov.m_parameterDisabledSet = mlOptions.m_parameterDisabledSet;
1095  m_ov.m_rawChainDataInputFileName = mlOptions.m_rawChainDataInputFileName;
1096  m_ov.m_rawChainDataInputFileType = mlOptions.m_rawChainDataInputFileType;
1097  m_ov.m_rawChainSize = mlOptions.m_rawChainSize;
1098  m_ov.m_rawChainGenerateExtra = mlOptions.m_rawChainGenerateExtra;
1099  m_ov.m_rawChainDisplayPeriod = mlOptions.m_rawChainDisplayPeriod;
1100  m_ov.m_rawChainMeasureRunTimes = mlOptions.m_rawChainMeasureRunTimes;
1101  m_ov.m_rawChainDataOutputPeriod = mlOptions.m_rawChainDataOutputPeriod;
1102  m_ov.m_rawChainDataOutputFileName = mlOptions.m_rawChainDataOutputFileName;
1103  m_ov.m_rawChainDataOutputFileType = mlOptions.m_rawChainDataOutputFileType;
1104  m_ov.m_rawChainDataOutputAllowAll = mlOptions.m_rawChainDataOutputAllowAll;
1105  m_ov.m_rawChainDataOutputAllowedSet = mlOptions.m_rawChainDataOutputAllowedSet;
1106 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
1107  m_ov.m_rawChainComputeStats = mlOptions.m_rawChainComputeStats;
1108 #endif
1109  m_ov.m_filteredChainGenerate = mlOptions.m_filteredChainGenerate;
1110  m_ov.m_filteredChainDiscardedPortion = mlOptions.m_filteredChainDiscardedPortion;
1111  m_ov.m_filteredChainLag = mlOptions.m_filteredChainLag;
1112  m_ov.m_filteredChainDataOutputFileName = mlOptions.m_filteredChainDataOutputFileName;
1113  m_ov.m_filteredChainDataOutputFileType = mlOptions.m_filteredChainDataOutputFileType;
1114  m_ov.m_filteredChainDataOutputAllowAll = mlOptions.m_filteredChainDataOutputAllowAll;
1115  m_ov.m_filteredChainDataOutputAllowedSet = mlOptions.m_filteredChainDataOutputAllowedSet;
1116 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
1117  m_ov.m_filteredChainComputeStats = mlOptions.m_filteredChainComputeStats;
1118 #endif
1119  m_ov.m_displayCandidates = mlOptions.m_displayCandidates;
1120  m_ov.m_putOutOfBoundsInChain = mlOptions.m_putOutOfBoundsInChain;
1121  m_ov.m_tkUseLocalHessian = mlOptions.m_tkUseLocalHessian;
1122  m_ov.m_tkUseNewtonComponent = mlOptions.m_tkUseNewtonComponent;
1123  m_ov.m_drMaxNumExtraStages = mlOptions.m_drMaxNumExtraStages;
1124  m_ov.m_drScalesForExtraStages = mlOptions.m_drScalesForExtraStages;
1125  m_ov.m_drDuringAmNonAdaptiveInt = mlOptions.m_drDuringAmNonAdaptiveInt;
1126  m_ov.m_amKeepInitialMatrix = mlOptions.m_amKeepInitialMatrix;
1127  m_ov.m_amInitialNonAdaptInterval = mlOptions.m_amInitialNonAdaptInterval;
1128  m_ov.m_amAdaptInterval = mlOptions.m_amAdaptInterval;
1129  m_ov.m_amAdaptedMatricesDataOutputPeriod = mlOptions.m_amAdaptedMatricesDataOutputPeriod;
1130  m_ov.m_amAdaptedMatricesDataOutputFileName = mlOptions.m_amAdaptedMatricesDataOutputFileName;
1131  m_ov.m_amAdaptedMatricesDataOutputFileType = mlOptions.m_amAdaptedMatricesDataOutputFileType;
1132  m_ov.m_amAdaptedMatricesDataOutputAllowAll = mlOptions.m_amAdaptedMatricesDataOutputAllowAll;
1133  m_ov.m_amAdaptedMatricesDataOutputAllowedSet = mlOptions.m_amAdaptedMatricesDataOutputAllowedSet;
1134  m_ov.m_amEta = mlOptions.m_amEta;
1135  m_ov.m_amEpsilon = mlOptions.m_amEpsilon;
1136  m_ov.m_enableBrooksGelmanConvMonitor = UQ_MH_SG_ENABLE_BROOKS_GELMAN_CONV_MONITOR;
1137  m_ov.m_BrooksGelmanLag = UQ_MH_SG_BROOKS_GELMAN_LAG;
1138  m_ov.m_outputLogLikelihood = UQ_MH_SG_OUTPUT_LOG_LIKELIHOOD;
1139  m_ov.m_outputLogTarget = UQ_MH_SG_OUTPUT_LOG_TARGET;
1140  m_ov.m_doLogitTransform = mlOptions.m_doLogitTransform;
1141  m_ov.m_algorithm = mlOptions.m_algorithm;
1142  m_ov.m_tk = mlOptions.m_tk;
1143 
1144 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
1145 //m_ov.m_alternativeRawSsOptionsValues = mlOptions.; // dakota
1146 //m_ov.m_alternativeFilteredSsOptionsValues = mlOptions.; // dakota
1147 #endif
1148 
1149 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
1150  m_rawChainStatisticalOptionsObj = mlOptions.m_rawChainStatisticalOptionsObj; // dakota
1151  m_rawChainStatOptsInstantiated = false;
1152  m_filteredChainStatisticalOptionsObj = mlOptions.m_filteredChainStatisticalOptionsObj; // dakota
1153  m_filteredChainStatOptsInstantiated = false;
1154 #endif
1155  if ((m_env.subDisplayFile() != NULL ) &&
1156  (m_ov.m_totallyMute == false)) {
1157  *m_env.subDisplayFile() << "In MetropolisHastingsSGOptions::constructor(3)"
1158  << ": after copying values of options with prefix '" << m_prefix
1159  << "', state of object is:"
1160  << "\n" << *this
1161  << std::endl;
1162  }
1163 }
QUESO::MhOptionsValues::m_filteredChainDiscardedPortion
double m_filteredChainDiscardedPortion
What initial fraction of the filtered chain is discarded.
Definition: MetropolisHastingsSGOptions.h:355
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:469
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:396
QUESO::MhOptionsValues::m_rawChainDataOutputFileName
std::string m_rawChainDataOutputFileName
If not &quot;.&quot;, filename to write the Markov chain to.
Definition: MetropolisHastingsSGOptions.h:298
QUESO::MhOptionsValues::m_totallyMute
bool m_totallyMute
If true, zero output is written to files. Default is false.
Definition: MetropolisHastingsSGOptions.h:201
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:411
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:547
QUESO::MetropolisHastingsSGOptions::m_ov
MhOptionsValues m_ov
This class is where the actual options are stored.
Definition: MetropolisHastingsSGOptions.h:801
QUESO::MhOptionsValues::m_rawChainDataOutputPeriod
unsigned int m_rawChainDataOutputPeriod
The frequency with which to write chain output. Defaults to 0.
Definition: MetropolisHastingsSGOptions.h:287
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:371
QUESO::MhOptionsValues::m_rawChainDataOutputFileType
std::string m_rawChainDataOutputFileType
The filetype of m_rawChainDataOutputFileName.
Definition: MetropolisHastingsSGOptions.h:318
QUESO::MhOptionsValues::m_drDuringAmNonAdaptiveInt
bool m_drDuringAmNonAdaptiveInt
Do delayed rejection during the initial non-adaptive part of sampling?
Definition: MetropolisHastingsSGOptions.h:491
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:320
QUESO::MetropolisHastingsSGOptions::m_option_am_eta
std::string m_option_am_eta
See MhOptionsValues::m_amEta.
Definition: MetropolisHastingsSGOptions.h:878
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:207
QUESO::MhOptionsValues::m_BrooksGelmanLag
unsigned int m_BrooksGelmanLag
The lag with which to compute the Brooks-Gelman convergence statistic.
Definition: MetropolisHastingsSGOptions.h:598
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:604
QUESO::MhOptionsValues::m_rawChainDisplayPeriod
unsigned int m_rawChainDisplayPeriod
The frequency with which to output diagnostic information.
Definition: MetropolisHastingsSGOptions.h:267
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:222
QUESO::MetropolisHastingsSGOptions::m_option_am_epsilon
std::string m_option_am_epsilon
See MhOptionsValues::m_amEpsilon.
Definition: MetropolisHastingsSGOptions.h:880
QUESO::MhOptionsValues::m_enableBrooksGelmanConvMonitor
unsigned int m_enableBrooksGelmanConvMonitor
The frequency with which to compute the Brooks-Gelman convergence statistic.
Definition: MetropolisHastingsSGOptions.h:588
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:437
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:183
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:386
QUESO::MhOptionsValues::m_parameterDisabledSet
std::set< unsigned int > m_parameterDisabledSet
Set of parameters that don&#39;t get sampled.
Definition: MetropolisHastingsSGOptions.h:231
QUESO::MhOptionsValues::m_filteredChainGenerate
bool m_filteredChainGenerate
Toggle the option to save a filtered chain.
Definition: MetropolisHastingsSGOptions.h:346
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:245
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:538
QUESO::MhOptionsValues::m_initialProposalCovMatrixDataInputFileType
std::string m_initialProposalCovMatrixDataInputFileType
The filetype of m_initialProposalCovMatrixDataInputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:225
queso_deprecated
#define queso_deprecated()
Definition: Defines.h:134
QUESO::MhOptionsValues::m_amInitialNonAdaptInterval
unsigned int m_amInitialNonAdaptInterval
The number of initial samples to do without adapting the proposal covariance matrix.
Definition: MetropolisHastingsSGOptions.h:505
UQ_MH_SG_OUTPUT_LOG_LIKELIHOOD
#define UQ_MH_SG_OUTPUT_LOG_LIKELIHOOD
Definition: MetropolisHastingsSGOptions.h:96
QUESO::MhOptionsValues::m_tk
std::string m_tk
Which transition kernel to use for MCMC. Default is &quot;random_walk&quot;.
Definition: MetropolisHastingsSGOptions.h:613
QUESO::MhOptionsValues::m_algorithm
std::string m_algorithm
Which algorithm to use for the MCMC. Default is &quot;random_walk&quot;.
Definition: MetropolisHastingsSGOptions.h:610
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:601
QUESO::MhOptionsValues::m_drMaxNumExtraStages
unsigned int m_drMaxNumExtraStages
The number of delayed rejection stages to do. Default is 0.
Definition: MetropolisHastingsSGOptions.h:450
UQ_MH_SG_OUTPUT_LOG_TARGET
#define UQ_MH_SG_OUTPUT_LOG_TARGET
Definition: MetropolisHastingsSGOptions.h:97
QUESO::MhOptionsValues::m_initialPositionDataInputFileType
std::string m_initialPositionDataInputFileType
The filetype of m_initialPositionDataInputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:210
QUESO::MhOptionsValues::m_rawChainDataInputFileName
std::string m_rawChainDataInputFileName
Filename for reading an already-produced Markov chain.
Definition: MetropolisHastingsSGOptions.h:242
QUESO::MhOptionsValues::m_filteredChainDataOutputFileType
std::string m_filteredChainDataOutputFileType
The filetype of m_filteredChainDataOutputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:374
QUESO::MetropolisHastingsSGOptions::m_optionsDesc
boost::program_options::options_description * m_optionsDesc
Definition: MetropolisHastingsSGOptions.h:822
QUESO::MhOptionsValues::m_dataOutputAllowAll
bool m_dataOutputAllowAll
If true, all processes write output and m_dataOutputAllowedSet is ignored.
Definition: MetropolisHastingsSGOptions.h:192
QUESO::MhOptionsValues::m_rawChainGenerateExtra
bool m_rawChainGenerateExtra
If true, extra chain information is computed/stored.
Definition: MetropolisHastingsSGOptions.h:257
QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputFileType
std::string m_amAdaptedMatricesDataOutputFileType
The filetype of m_amAdaptedMatricesDataOutputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:541
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:330
QUESO::MhOptionsValues::m_filteredChainLag
unsigned int m_filteredChainLag
Set the lag for the filtered chain. Default is 1.
Definition: MetropolisHastingsSGOptions.h:362
QUESO::MhOptionsValues::m_amEta
double m_amEta
Proposal covariance scaling factor, usually 2.4 * 2.4 / d.
Definition: MetropolisHastingsSGOptions.h:560
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:198
QUESO::MhOptionsValues::m_tkUseNewtonComponent
bool m_tkUseNewtonComponent
This option is a no-op. Default is true.
Definition: MetropolisHastingsSGOptions.h:440
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:248
UQ_MH_SG_BROOKS_GELMAN_LAG
#define UQ_MH_SG_BROOKS_GELMAN_LAG
Definition: MetropolisHastingsSGOptions.h:95
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:389
QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputAllowAll
bool m_amAdaptedMatricesDataOutputAllowAll
This option is a no-op. The default is false.
Definition: MetropolisHastingsSGOptions.h:544
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:284
QUESO::MhOptionsValues::m_amEpsilon
double m_amEpsilon
Regularisation parameter for the DRAM covariance matrix.
Definition: MetropolisHastingsSGOptions.h:572
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:607
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:333
UQ_MH_SG_ENABLE_BROOKS_GELMAN_CONV_MONITOR
#define UQ_MH_SG_ENABLE_BROOKS_GELMAN_CONV_MONITOR
Definition: MetropolisHastingsSGOptions.h:94
QUESO::MhOptionsValues::m_amAdaptInterval
unsigned int m_amAdaptInterval
The frequency at which to adapt the proposal covariance matrix.
Definition: MetropolisHastingsSGOptions.h:515
QUESO::MhOptionsValues::m_amKeepInitialMatrix
bool m_amKeepInitialMatrix
This option is a no-op. The default is false.
Definition: MetropolisHastingsSGOptions.h:494
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:532
QUESO::MetropolisHastingsSGOptions::~MetropolisHastingsSGOptions ( )

Destructor.

Definition at line 1165 of file MetropolisHastingsSGOptions.C.

References m_optionsDesc, and queso_deprecated.

1166 {
1167  queso_deprecated();
1168 
1169 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
1170  if (m_filteredChainStatOptsInstantiated) delete m_filteredChainStatisticalOptionsObj;
1171  if (m_rawChainStatOptsInstantiated ) delete m_rawChainStatisticalOptionsObj;
1172 #endif
1173 #ifndef DISABLE_BOOST_PROGRAM_OPTIONS
1174  if (m_optionsDesc ) delete m_optionsDesc;
1175 #endif // DISABLE_BOOST_PROGRAM_OPTIONS
1176 }
queso_deprecated
#define queso_deprecated()
Definition: Defines.h:134
QUESO::MetropolisHastingsSGOptions::m_optionsDesc
boost::program_options::options_description * m_optionsDesc
Definition: MetropolisHastingsSGOptions.h:822

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 1305 of file MetropolisHastingsSGOptions.C.

References m_option_algorithm, 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, m_option_tk_useLocalHessian, m_option_tk_useNewtonComponent, m_option_totallyMute, queso_deprecated, UQ_MH_SG_ALGORITHM, 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, 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().

1306 {
1307  queso_deprecated();
1308 
1309  optionsDesc.add_options()
1310  (m_option_help.c_str(), "produce help msg for Bayesian Metropolis-Hastings" )
1311  (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" )
1312  (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" )
1313  (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" )
1314  (m_option_totallyMute.c_str(), boost::program_options::value<bool >()->default_value(UQ_MH_SG_TOTALLY_MUTE_ODV ), "totally mute (no printout msg)" )
1315  (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 " )
1316  (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 " )
1317  (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 " )
1318  (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 " )
1319  (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" )
1320  (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 " )
1321  (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 " )
1322  (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" )
1323  (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" )
1324  (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" )
1325  (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" )
1326  (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" )
1327  (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 " )
1328  (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 " )
1329  (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" )
1330  (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" )
1331 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
1332  (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" )
1333 #endif
1334  (m_option_filteredChain_generate.c_str(), boost::program_options::value<bool >()->default_value(UQ_MH_SG_FILTERED_CHAIN_GENERATE_ODV ), "generate filtered chain" )
1335  (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" )
1336  (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" )
1337  (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" )
1338  (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" )
1339  (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" )
1340  (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" )
1341 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
1342  (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" )
1343 #endif
1344  (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" )
1345  (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" )
1346  (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" )
1347  (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" )
1348  (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" )
1349  (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" )
1350  (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" )
1351  (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" )
1352  (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" )
1353  (m_option_am_adaptInterval.c_str(), boost::program_options::value<unsigned int>()->default_value(UQ_MH_SG_AM_ADAPT_INTERVAL_ODV ), "'am' adaptation interval" )
1354  (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" )
1355  (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" )
1356  (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" )
1357  (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" )
1358  (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" )
1359  (m_option_am_eta.c_str(), boost::program_options::value<double >()->default_value(UQ_MH_SG_AM_ETA_ODV ), "'am' eta" )
1360  (m_option_am_epsilon.c_str(), boost::program_options::value<double >()->default_value(UQ_MH_SG_AM_EPSILON_ODV ), "'am' epsilon" )
1361  (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" )
1362  (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")
1363  (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" )
1364  (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" )
1365  (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" )
1366  (m_option_algorithm.c_str(), boost::program_options::value<std::string >()->default_value(UQ_MH_SG_ALGORITHM ), "which mcmc algorithm to use" )
1367  (m_option_tk.c_str(), boost::program_options::value<std::string >()->default_value(UQ_MH_SG_TK ), "which mcmc tk to use" )
1368  ;
1369 
1370  return;
1371 }
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:90
UQ_MH_SG_INITIAL_POSITION_DATA_INPUT_FILE_NAME_ODV
#define UQ_MH_SG_INITIAL_POSITION_DATA_INPUT_FILE_NAME_ODV
Definition: MetropolisHastingsSGOptions.h:48
UQ_MH_SG_TK
#define UQ_MH_SG_TK
Definition: MetropolisHastingsSGOptions.h:100
UQ_MH_SG_LIST_OF_DISABLED_PARAMETERS_ODV
#define UQ_MH_SG_LIST_OF_DISABLED_PARAMETERS_ODV
Definition: MetropolisHastingsSGOptions.h:52
UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_PERIOD_ODV
#define UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_PERIOD_ODV
Definition: MetropolisHastingsSGOptions.h:59
UQ_MH_SG_RAW_CHAIN_SIZE_ODV
#define UQ_MH_SG_RAW_CHAIN_SIZE_ODV
Definition: MetropolisHastingsSGOptions.h:55
UQ_MH_SG_DR_MAX_NUM_EXTRA_STAGES_ODV
#define UQ_MH_SG_DR_MAX_NUM_EXTRA_STAGES_ODV
Definition: MetropolisHastingsSGOptions.h:81
UQ_MH_SG_ALGORITHM
#define UQ_MH_SG_ALGORITHM
Definition: MetropolisHastingsSGOptions.h:99
QUESO::MetropolisHastingsSGOptions::m_option_am_eta
std::string m_option_am_eta
See MhOptionsValues::m_amEta.
Definition: MetropolisHastingsSGOptions.h:878
UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_ALLOW_ALL_ODV
#define UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_ALLOW_ALL_ODV
Definition: MetropolisHastingsSGOptions.h:62
UQ_MH_SG_DATA_OUTPUT_ALLOW_ALL_ODV
#define UQ_MH_SG_DATA_OUTPUT_ALLOW_ALL_ODV
Definition: MetropolisHastingsSGOptions.h:44
QUESO::MetropolisHastingsSGOptions::m_option_am_epsilon
std::string m_option_am_epsilon
See MhOptionsValues::m_amEpsilon.
Definition: MetropolisHastingsSGOptions.h:880
UQ_MH_SG_RAW_CHAIN_GENERATE_EXTRA_ODV
#define UQ_MH_SG_RAW_CHAIN_GENERATE_EXTRA_ODV
Definition: MetropolisHastingsSGOptions.h:56
UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_FILE_TYPE_ODV
#define UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_FILE_TYPE_ODV
Definition: MetropolisHastingsSGOptions.h:71
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:88
UQ_MH_SG_RAW_CHAIN_DATA_INPUT_FILE_NAME_ODV
#define UQ_MH_SG_RAW_CHAIN_DATA_INPUT_FILE_NAME_ODV
Definition: MetropolisHastingsSGOptions.h:53
UQ_MH_SG_TK_USE_NEWTON_COMPONENT_ODV
#define UQ_MH_SG_TK_USE_NEWTON_COMPONENT_ODV
Definition: MetropolisHastingsSGOptions.h:80
UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_FILE_NAME_ODV
#define UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_FILE_NAME_ODV
Definition: MetropolisHastingsSGOptions.h:70
queso_deprecated
#define queso_deprecated()
Definition: Defines.h:134
UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_FILE_TYPE_ODV
#define UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_FILE_TYPE_ODV
Definition: MetropolisHastingsSGOptions.h:61
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:51
UQ_MH_SG_DATA_OUTPUT_FILE_NAME_ODV
#define UQ_MH_SG_DATA_OUTPUT_FILE_NAME_ODV
Definition: MetropolisHastingsSGOptions.h:43
UQ_MH_SG_AM_EPSILON_ODV
#define UQ_MH_SG_AM_EPSILON_ODV
Definition: MetropolisHastingsSGOptions.h:93
UQ_MH_SG_OUTPUT_LOG_LIKELIHOOD
#define UQ_MH_SG_OUTPUT_LOG_LIKELIHOOD
Definition: MetropolisHastingsSGOptions.h:96
UQ_MH_SG_PUT_OUT_OF_BOUNDS_IN_CHAIN_ODV
#define UQ_MH_SG_PUT_OUT_OF_BOUNDS_IN_CHAIN_ODV
Definition: MetropolisHastingsSGOptions.h:78
UQ_MH_SG_INITIAL_POSITION_DATA_INPUT_FILE_TYPE_ODV
#define UQ_MH_SG_INITIAL_POSITION_DATA_INPUT_FILE_TYPE_ODV
Definition: MetropolisHastingsSGOptions.h:49
UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_ALLOW_ALL_ODV
#define UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_ALLOW_ALL_ODV
Definition: MetropolisHastingsSGOptions.h:72
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:89
UQ_MH_SG_RAW_CHAIN_DISPLAY_PERIOD_ODV
#define UQ_MH_SG_RAW_CHAIN_DISPLAY_PERIOD_ODV
Definition: MetropolisHastingsSGOptions.h:57
UQ_MH_SG_DATA_OUTPUT_ALLOWED_SET_ODV
#define UQ_MH_SG_DATA_OUTPUT_ALLOWED_SET_ODV
Definition: MetropolisHastingsSGOptions.h:45
UQ_MH_SG_OUTPUT_LOG_TARGET
#define UQ_MH_SG_OUTPUT_LOG_TARGET
Definition: MetropolisHastingsSGOptions.h:97
UQ_MH_SG_AM_ADAPT_INTERVAL_ODV
#define UQ_MH_SG_AM_ADAPT_INTERVAL_ODV
Definition: MetropolisHastingsSGOptions.h:86
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:82
UQ_MH_SG_DO_LOGIT_TRANSFORM
#define UQ_MH_SG_DO_LOGIT_TRANSFORM
Definition: MetropolisHastingsSGOptions.h:98
UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_ALLOWED_SET_ODV
#define UQ_MH_SG_FILTERED_CHAIN_DATA_OUTPUT_ALLOWED_SET_ODV
Definition: MetropolisHastingsSGOptions.h:73
UQ_MH_SG_AM_INIT_NON_ADAPT_INT_ODV
#define UQ_MH_SG_AM_INIT_NON_ADAPT_INT_ODV
Definition: MetropolisHastingsSGOptions.h:85
UQ_MH_SG_RAW_CHAIN_DATA_INPUT_FILE_TYPE_ODV
#define UQ_MH_SG_RAW_CHAIN_DATA_INPUT_FILE_TYPE_ODV
Definition: MetropolisHastingsSGOptions.h:54
UQ_MH_SG_AM_KEEP_INITIAL_MATRIX_ODV
#define UQ_MH_SG_AM_KEEP_INITIAL_MATRIX_ODV
Definition: MetropolisHastingsSGOptions.h:84
UQ_MH_SG_AM_ADAPTED_MATRICES_DATA_OUTPUT_PERIOD_ODV
#define UQ_MH_SG_AM_ADAPTED_MATRICES_DATA_OUTPUT_PERIOD_ODV
Definition: MetropolisHastingsSGOptions.h:87
UQ_MH_SG_FILTERED_CHAIN_GENERATE_ODV
#define UQ_MH_SG_FILTERED_CHAIN_GENERATE_ODV
Definition: MetropolisHastingsSGOptions.h:67
UQ_MH_SG_FILTERED_CHAIN_DISCARDED_PORTION_ODV
#define UQ_MH_SG_FILTERED_CHAIN_DISCARDED_PORTION_ODV
Definition: MetropolisHastingsSGOptions.h:68
UQ_MH_SG_DISPLAY_CANDIDATES_ODV
#define UQ_MH_SG_DISPLAY_CANDIDATES_ODV
Definition: MetropolisHastingsSGOptions.h:77
UQ_MH_SG_BROOKS_GELMAN_LAG
#define UQ_MH_SG_BROOKS_GELMAN_LAG
Definition: MetropolisHastingsSGOptions.h:95
UQ_MH_SG_AM_ETA_ODV
#define UQ_MH_SG_AM_ETA_ODV
Definition: MetropolisHastingsSGOptions.h:92
UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_FILE_NAME_ODV
#define UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_FILE_NAME_ODV
Definition: MetropolisHastingsSGOptions.h:60
UQ_MH_SG_RAW_CHAIN_MEASURE_RUN_TIMES_ODV
#define UQ_MH_SG_RAW_CHAIN_MEASURE_RUN_TIMES_ODV
Definition: MetropolisHastingsSGOptions.h:58
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:91
UQ_MH_SG_TK_USE_LOCAL_HESSIAN_ODV
#define UQ_MH_SG_TK_USE_LOCAL_HESSIAN_ODV
Definition: MetropolisHastingsSGOptions.h:79
UQ_MH_SG_ENABLE_BROOKS_GELMAN_CONV_MONITOR
#define UQ_MH_SG_ENABLE_BROOKS_GELMAN_CONV_MONITOR
Definition: MetropolisHastingsSGOptions.h:94
UQ_MH_SG_TOTALLY_MUTE_ODV
#define UQ_MH_SG_TOTALLY_MUTE_ODV
Definition: MetropolisHastingsSGOptions.h:47
UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_ALLOWED_SET_ODV
#define UQ_MH_SG_RAW_CHAIN_DATA_OUTPUT_ALLOWED_SET_ODV
Definition: MetropolisHastingsSGOptions.h:63
UQ_MH_SG_DR_DURING_AM_NON_ADAPTIVE_INT_ODV
#define UQ_MH_SG_DR_DURING_AM_NON_ADAPTIVE_INT_ODV
Definition: MetropolisHastingsSGOptions.h:83
UQ_MH_SG_FILTERED_CHAIN_LAG_ODV
#define UQ_MH_SG_FILTERED_CHAIN_LAG_ODV
Definition: MetropolisHastingsSGOptions.h:69
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:50
void QUESO::MetropolisHastingsSGOptions::getMyOptionValues ( boost::program_options::options_description &  optionsDesc)
private

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

Definition at line 1377 of file MetropolisHastingsSGOptions.C.

References QUESO::BaseEnvironment::allOptionsMap(), QUESO::BaseEnvironment::fullRank(), QUESO::BaseEnvironment::inter0Rank(), QUESO::MhOptionsValues::m_algorithm, 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_algorithm, 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, 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_tk, 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().

1378 {
1379  queso_deprecated();
1380 
1381  if (m_env.allOptionsMap().count(m_option_help)) {
1382  if ((m_env.subDisplayFile()) &&
1383  (m_ov.m_totallyMute == false)) {
1384  *m_env.subDisplayFile() << optionsDesc
1385  << std::endl;
1386  }
1387  }
1388 
1389  if (m_env.allOptionsMap().count(m_option_dataOutputFileName)) {
1390  m_ov.m_dataOutputFileName = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_dataOutputFileName]).as<std::string>();
1391  }
1392 
1393  if (m_env.allOptionsMap().count(m_option_dataOutputAllowAll.c_str())) {
1394  m_ov.m_dataOutputAllowAll = m_env.allOptionsMap()[m_option_dataOutputAllowAll].as<bool>();
1395  }
1396 
1397  if (m_ov.m_dataOutputAllowAll) {
1398  m_ov.m_dataOutputAllowedSet.insert(m_env.subId());
1399  }
1400  else if (m_env.allOptionsMap().count(m_option_dataOutputAllowedSet)) {
1401  m_ov.m_dataOutputAllowedSet.clear();
1402  std::vector<double> tmpAllow(0,0.);
1403  std::string inputString = m_env.allOptionsMap()[m_option_dataOutputAllowedSet].as<std::string>();
1404  MiscReadDoublesFromString(inputString,tmpAllow);
1405 
1406  if (tmpAllow.size() > 0) {
1407  for (unsigned int i = 0; i < tmpAllow.size(); ++i) {
1408  m_ov.m_dataOutputAllowedSet.insert((unsigned int) tmpAllow[i]);
1409  }
1410  }
1411  }
1412 
1413  if (m_env.allOptionsMap().count(m_option_totallyMute)) {
1414  m_ov.m_totallyMute = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_totallyMute]).as<bool>();
1415  }
1416 
1417  if (m_env.allOptionsMap().count(m_option_initialPosition_dataInputFileName)) {
1418  m_ov.m_initialPositionDataInputFileName = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_initialPosition_dataInputFileName]).as<std::string>();
1419  }
1420 
1421  if (m_env.allOptionsMap().count(m_option_initialPosition_dataInputFileType)) {
1422  m_ov.m_initialPositionDataInputFileType = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_initialPosition_dataInputFileType]).as<std::string>();
1423  }
1424 
1425  if (m_env.allOptionsMap().count(m_option_initialProposalCovMatrix_dataInputFileName)) {
1426  m_ov.m_initialProposalCovMatrixDataInputFileName = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_initialProposalCovMatrix_dataInputFileName]).as<std::string>();
1427  }
1428 
1429  if (m_env.allOptionsMap().count(m_option_initialProposalCovMatrix_dataInputFileType)) {
1430  m_ov.m_initialProposalCovMatrixDataInputFileType = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_initialProposalCovMatrix_dataInputFileType]).as<std::string>();
1431  }
1432 
1433  if (m_env.allOptionsMap().count(m_option_listOfDisabledParameters)) {
1434  m_ov.m_parameterDisabledSet.clear();
1435  std::vector<double> tmpAllow(0,0.);
1436  std::string inputString = m_env.allOptionsMap()[m_option_listOfDisabledParameters].as<std::string>();
1437  MiscReadDoublesFromString(inputString,tmpAllow);
1438  if (tmpAllow.size() > 0) {
1439  for (unsigned int i = 0; i < tmpAllow.size(); ++i) {
1440  m_ov.m_parameterDisabledSet.insert((unsigned int) tmpAllow[i]);
1441  }
1442  }
1443  }
1444 
1445  if (m_env.allOptionsMap().count(m_option_rawChain_dataInputFileName)) {
1446  m_ov.m_rawChainDataInputFileName = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_rawChain_dataInputFileName]).as<std::string>();
1447  }
1448 
1449  if (m_env.allOptionsMap().count(m_option_rawChain_dataInputFileType)) {
1450  m_ov.m_rawChainDataInputFileType = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_rawChain_dataInputFileType]).as<std::string>();
1451  }
1452 
1453  if (m_env.allOptionsMap().count(m_option_rawChain_size)) {
1454  m_ov.m_rawChainSize = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_rawChain_size]).as<unsigned int>();
1455  }
1456 
1457  if (m_env.allOptionsMap().count(m_option_rawChain_displayPeriod)) {
1458  m_ov.m_rawChainDisplayPeriod = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_rawChain_displayPeriod]).as<unsigned int>();
1459  }
1460 
1461  if (m_env.allOptionsMap().count(m_option_rawChain_measureRunTimes)) {
1462  m_ov.m_rawChainMeasureRunTimes = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_rawChain_measureRunTimes]).as<bool>();
1463  }
1464 
1465  if (m_env.allOptionsMap().count(m_option_rawChain_dataOutputPeriod)) {
1466  m_ov.m_rawChainDataOutputPeriod = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_rawChain_dataOutputPeriod]).as<unsigned int>();
1467  }
1468 
1469  if (m_env.allOptionsMap().count(m_option_rawChain_dataOutputFileName)) {
1470  m_ov.m_rawChainDataOutputFileName = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_rawChain_dataOutputFileName]).as<std::string>();
1471  }
1472 
1473  if (m_env.allOptionsMap().count(m_option_rawChain_dataOutputFileType)) {
1474  m_ov.m_rawChainDataOutputFileType = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_rawChain_dataOutputFileType]).as<std::string>();
1475  }
1476 
1477  if (m_env.allOptionsMap().count(m_option_rawChain_dataOutputAllowAll.c_str())) {
1478  m_ov.m_rawChainDataOutputAllowAll = m_env.allOptionsMap()[m_option_rawChain_dataOutputAllowAll].as<bool>();
1479  }
1480 
1481  if (m_ov.m_rawChainDataOutputAllowAll) {
1482  m_ov.m_rawChainDataOutputAllowedSet.insert(m_env.subId());
1483  }
1484  else if (m_env.allOptionsMap().count(m_option_rawChain_dataOutputAllowedSet)) {
1485  m_ov.m_rawChainDataOutputAllowedSet.clear();
1486  std::vector<double> tmpAllow(0,0.);
1487  std::string inputString = m_env.allOptionsMap()[m_option_rawChain_dataOutputAllowedSet].as<std::string>();
1488  MiscReadDoublesFromString(inputString,tmpAllow);
1489 
1490  if (tmpAllow.size() > 0) {
1491  for (unsigned int i = 0; i < tmpAllow.size(); ++i) {
1492  m_ov.m_rawChainDataOutputAllowedSet.insert((unsigned int) tmpAllow[i]);
1493  }
1494  }
1495  }
1496 
1497 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
1498  if (m_env.allOptionsMap().count(m_option_rawChain_computeStats)) {
1499  m_ov.m_rawChainComputeStats = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_rawChain_computeStats]).as<bool>();
1500  }
1501 #endif
1502  if (m_env.allOptionsMap().count(m_option_rawChain_generateExtra)) {
1503  m_ov.m_rawChainGenerateExtra = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_rawChain_generateExtra]).as<bool>();
1504  }
1505 
1506  if (m_env.allOptionsMap().count(m_option_filteredChain_generate)) {
1507  m_ov.m_filteredChainGenerate = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_filteredChain_generate]).as<bool>();
1508  }
1509 
1510  if (m_env.allOptionsMap().count(m_option_filteredChain_discardedPortion)) {
1511  m_ov.m_filteredChainDiscardedPortion = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_filteredChain_discardedPortion]).as<double>();
1512  }
1513 
1514  if (m_env.allOptionsMap().count(m_option_filteredChain_lag)) {
1515  m_ov.m_filteredChainLag = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_filteredChain_lag]).as<unsigned int>();
1516  }
1517  if ((m_ov.m_filteredChainGenerate == true) &&
1518  (m_ov.m_filteredChainLag < 2 )) {
1519  std::cerr << "WARNING In MetropolisHastingsSG<P_V,P_M>::getMyOptionsValues()"
1520  << ", worldRank " << m_env.worldRank()
1521  << ", fullRank " << m_env.fullRank()
1522  << ", subEnvironment " << m_env.subId()
1523  << ", subRank " << m_env.subRank()
1524  << ", inter0Rank " << m_env.inter0Rank()
1525  << ": forcing the value of '" << m_option_filteredChain_lag
1526  << "' from " << m_ov.m_filteredChainLag
1527  << " to " << 2
1528  << std::endl;
1529  m_ov.m_filteredChainLag = 2;
1530  }
1531 
1532  if (m_env.allOptionsMap().count(m_option_filteredChain_dataOutputFileName)) {
1533  m_ov.m_filteredChainDataOutputFileName = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_filteredChain_dataOutputFileName]).as<std::string>();
1534  }
1535 
1536  if (m_env.allOptionsMap().count(m_option_filteredChain_dataOutputFileType)) {
1537  m_ov.m_filteredChainDataOutputFileType = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_filteredChain_dataOutputFileType]).as<std::string>();
1538  }
1539 
1540  if (m_env.allOptionsMap().count(m_option_filteredChain_dataOutputAllowAll.c_str())) {
1541  m_ov.m_filteredChainDataOutputAllowAll = m_env.allOptionsMap()[m_option_filteredChain_dataOutputAllowAll].as<bool>();
1542  }
1543 
1544  if (m_ov.m_filteredChainDataOutputAllowAll) {
1545  m_ov.m_filteredChainDataOutputAllowedSet.insert(m_env.subId());
1546  }
1547  else if (m_env.allOptionsMap().count(m_option_filteredChain_dataOutputAllowedSet)) {
1548  m_ov.m_filteredChainDataOutputAllowedSet.clear();
1549  std::vector<double> tmpAllow(0,0.);
1550  std::string inputString = m_env.allOptionsMap()[m_option_filteredChain_dataOutputAllowedSet].as<std::string>();
1551  MiscReadDoublesFromString(inputString,tmpAllow);
1552 
1553  if (tmpAllow.size() > 0) {
1554  for (unsigned int i = 0; i < tmpAllow.size(); ++i) {
1555  m_ov.m_filteredChainDataOutputAllowedSet.insert((unsigned int) tmpAllow[i]);
1556  }
1557  }
1558  }
1559 
1560 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
1561  if (m_env.allOptionsMap().count(m_option_filteredChain_computeStats)) {
1562  m_ov.m_filteredChainComputeStats = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_filteredChain_computeStats]).as<bool>();
1563  }
1564 #endif
1565  if (m_env.allOptionsMap().count(m_option_displayCandidates)) {
1566  m_ov.m_displayCandidates = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_displayCandidates]).as<bool>();
1567  }
1568 
1569  if (m_env.allOptionsMap().count(m_option_putOutOfBoundsInChain)) {
1570  m_ov.m_putOutOfBoundsInChain = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_putOutOfBoundsInChain]).as<bool>();
1571  }
1572 
1573  if (m_env.allOptionsMap().count(m_option_tk_useLocalHessian)) {
1574  m_ov.m_tkUseLocalHessian = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_tk_useLocalHessian]).as<bool>();
1575  }
1576 
1577  if (m_env.allOptionsMap().count(m_option_tk_useNewtonComponent)) {
1578  m_ov.m_tkUseNewtonComponent = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_tk_useNewtonComponent]).as<bool>();
1579  }
1580 
1581  if (m_env.allOptionsMap().count(m_option_dr_maxNumExtraStages)) {
1582  m_ov.m_drMaxNumExtraStages = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_dr_maxNumExtraStages]).as<unsigned int>();
1583  }
1584 
1585  std::vector<double> tmpScales(0,0.);
1586  if (m_env.allOptionsMap().count(m_option_dr_listOfScalesForExtraStages)) {
1587  std::string inputString = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_dr_listOfScalesForExtraStages]).as<std::string>();
1588  MiscReadDoublesFromString(inputString,tmpScales);
1589  //if (m_env.subDisplayFile()) {
1590  // *m_env.subDisplayFile() << "In MetropolisHastingsSG<P_V,P_M>::getMyOptionValues(): scales =";
1591  // for (unsigned int i = 0; i < tmpScales.size(); ++i) {
1592  // *m_env.subDisplayFile() << " " << tmpScales[i];
1593  // }
1594  // *m_env.subDisplayFile() << std::endl;
1595  //}
1596  }
1597 
1598  if (m_ov.m_drMaxNumExtraStages > 0) {
1599  double scale = 1.0;
1600  unsigned int tmpSize = tmpScales.size();
1601 
1602  m_ov.m_drScalesForExtraStages.clear();
1603  m_ov.m_drScalesForExtraStages.resize(m_ov.m_drMaxNumExtraStages,1.);
1604  for (unsigned int i = 0; i < m_ov.m_drMaxNumExtraStages; ++i) {
1605  if (i < tmpSize) scale = tmpScales[i];
1606  m_ov.m_drScalesForExtraStages[i] = scale;
1607  }
1608  //updateTK();
1609  }
1610 
1611  if (m_env.allOptionsMap().count(m_option_dr_duringAmNonAdaptiveInt)) {
1612  m_ov.m_drDuringAmNonAdaptiveInt = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_dr_duringAmNonAdaptiveInt]).as<bool>();
1613  }
1614 
1615  if (m_env.allOptionsMap().count(m_option_am_keepInitialMatrix)) {
1616  m_ov.m_amKeepInitialMatrix = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_am_keepInitialMatrix]).as<bool>();
1617  }
1618 
1619  if (m_env.allOptionsMap().count(m_option_am_initialNonAdaptInterval)) {
1620  m_ov.m_amInitialNonAdaptInterval = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_am_initialNonAdaptInterval]).as<unsigned int>();
1621  }
1622 
1623  if (m_env.allOptionsMap().count(m_option_am_adaptInterval)) {
1624  m_ov.m_amAdaptInterval = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_am_adaptInterval]).as<unsigned int>();
1625  }
1626 
1627  if (m_env.allOptionsMap().count(m_option_am_adaptedMatrices_dataOutputPeriod)) {
1628  m_ov.m_amAdaptedMatricesDataOutputPeriod = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_am_adaptedMatrices_dataOutputPeriod]).as<unsigned int>();
1629  }
1630 
1631  if (m_env.allOptionsMap().count(m_option_am_adaptedMatrices_dataOutputFileName)) {
1632  m_ov.m_amAdaptedMatricesDataOutputFileName = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_am_adaptedMatrices_dataOutputFileName]).as<std::string>();
1633  }
1634 
1635  if (m_env.allOptionsMap().count(m_option_am_adaptedMatrices_dataOutputFileType)) {
1636  m_ov.m_amAdaptedMatricesDataOutputFileType = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_am_adaptedMatrices_dataOutputFileType]).as<std::string>();
1637  }
1638 
1639  if (m_env.allOptionsMap().count(m_option_am_adaptedMatrices_dataOutputAllowAll.c_str())) {
1640  m_ov.m_amAdaptedMatricesDataOutputAllowAll = m_env.allOptionsMap()[m_option_am_adaptedMatrices_dataOutputAllowAll].as<bool>();
1641  }
1642 
1643  if (m_ov.m_amAdaptedMatricesDataOutputAllowAll) {
1644  m_ov.m_amAdaptedMatricesDataOutputAllowedSet.insert(m_env.subId());
1645  }
1646  else if (m_env.allOptionsMap().count(m_option_am_adaptedMatrices_dataOutputAllowedSet)) {
1647  m_ov.m_amAdaptedMatricesDataOutputAllowedSet.clear();
1648  std::vector<double> tmpAllow(0,0.);
1649  std::string inputString = m_env.allOptionsMap()[m_option_am_adaptedMatrices_dataOutputAllowedSet].as<std::string>();
1650  MiscReadDoublesFromString(inputString,tmpAllow);
1651 
1652  if (tmpAllow.size() > 0) {
1653  for (unsigned int i = 0; i < tmpAllow.size(); ++i) {
1654  m_ov.m_amAdaptedMatricesDataOutputAllowedSet.insert((unsigned int) tmpAllow[i]);
1655  }
1656  }
1657  }
1658 
1659  if (m_env.allOptionsMap().count(m_option_am_eta)) {
1660  m_ov.m_amEta = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_am_eta]).as<double>();
1661  }
1662 
1663  if (m_env.allOptionsMap().count(m_option_am_epsilon)) {
1664  m_ov.m_amEpsilon = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_am_epsilon]).as<double>();
1665  }
1666 
1667  if (m_env.allOptionsMap().count(m_option_enableBrooksGelmanConvMonitor)) {
1668  m_ov.m_enableBrooksGelmanConvMonitor = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_enableBrooksGelmanConvMonitor]).as<unsigned int>();
1669  }
1670 
1671  if (m_env.allOptionsMap().count(m_option_BrooksGelmanLag)) {
1672  m_ov.m_BrooksGelmanLag = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_BrooksGelmanLag]).as<unsigned int>();
1673  }
1674 
1675  if (m_env.allOptionsMap().count(m_option_outputLogLikelihood)) {
1676  m_ov.m_outputLogLikelihood = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_outputLogLikelihood]).as<bool>();
1677  }
1678 
1679  if (m_env.allOptionsMap().count(m_option_outputLogTarget)) {
1680  m_ov.m_outputLogTarget = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_outputLogTarget]).as<bool>();
1681  }
1682 
1683  if (m_env.allOptionsMap().count(m_option_doLogitTransform)) {
1684  m_ov.m_doLogitTransform = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_doLogitTransform]).as<bool>();
1685  }
1686 
1687  if (m_env.allOptionsMap().count(m_option_algorithm)) {
1688  m_ov.m_algorithm = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_algorithm]).as<std::string>();
1689  }
1690 
1691  if (m_env.allOptionsMap().count(m_option_tk)) {
1692  m_ov.m_tk = ((const boost::program_options::variable_value&) m_env.allOptionsMap()[m_option_tk]).as<std::string>();
1693  }
1694 }
QUESO::MhOptionsValues::m_filteredChainDiscardedPortion
double m_filteredChainDiscardedPortion
What initial fraction of the filtered chain is discarded.
Definition: MetropolisHastingsSGOptions.h:355
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:469
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:396
QUESO::MhOptionsValues::m_rawChainDataOutputFileName
std::string m_rawChainDataOutputFileName
If not &quot;.&quot;, filename to write the Markov chain to.
Definition: MetropolisHastingsSGOptions.h:298
QUESO::MhOptionsValues::m_totallyMute
bool m_totallyMute
If true, zero output is written to files. Default is false.
Definition: MetropolisHastingsSGOptions.h:201
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:411
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:547
QUESO::MetropolisHastingsSGOptions::m_ov
MhOptionsValues m_ov
This class is where the actual options are stored.
Definition: MetropolisHastingsSGOptions.h:801
QUESO::MhOptionsValues::m_rawChainDataOutputPeriod
unsigned int m_rawChainDataOutputPeriod
The frequency with which to write chain output. Defaults to 0.
Definition: MetropolisHastingsSGOptions.h:287
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:262
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:371
QUESO::MhOptionsValues::m_rawChainDataOutputFileType
std::string m_rawChainDataOutputFileType
The filetype of m_rawChainDataOutputFileName.
Definition: MetropolisHastingsSGOptions.h:318
QUESO::MhOptionsValues::m_drDuringAmNonAdaptiveInt
bool m_drDuringAmNonAdaptiveInt
Do delayed rejection during the initial non-adaptive part of sampling?
Definition: MetropolisHastingsSGOptions.h:491
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:320
QUESO::MetropolisHastingsSGOptions::m_option_am_eta
std::string m_option_am_eta
See MhOptionsValues::m_amEta.
Definition: MetropolisHastingsSGOptions.h:878
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:207
QUESO::BaseEnvironment::subRank
int subRank() const
Access function for sub-rank.
Definition: Environment.C:287
QUESO::MhOptionsValues::m_BrooksGelmanLag
unsigned int m_BrooksGelmanLag
The lag with which to compute the Brooks-Gelman convergence statistic.
Definition: MetropolisHastingsSGOptions.h:598
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:604
QUESO::MhOptionsValues::m_rawChainDisplayPeriod
unsigned int m_rawChainDisplayPeriod
The frequency with which to output diagnostic information.
Definition: MetropolisHastingsSGOptions.h:267
scale
double scale
Definition: ann2fig.cpp:85
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:222
QUESO::MetropolisHastingsSGOptions::m_option_am_epsilon
std::string m_option_am_epsilon
See MhOptionsValues::m_amEpsilon.
Definition: MetropolisHastingsSGOptions.h:880
QUESO::MhOptionsValues::m_enableBrooksGelmanConvMonitor
unsigned int m_enableBrooksGelmanConvMonitor
The frequency with which to compute the Brooks-Gelman convergence statistic.
Definition: MetropolisHastingsSGOptions.h:588
QUESO::BaseEnvironment::inter0Rank
int inter0Rank() const
Returns the process inter0 rank.
Definition: Environment.C:307
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:437
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:183
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:386
QUESO::MiscReadDoublesFromString
void MiscReadDoublesFromString(const std::string &inputString, std::vector< double > &outputDoubles)
Definition: Miscellaneous.C:40
QUESO::MhOptionsValues::m_parameterDisabledSet
std::set< unsigned int > m_parameterDisabledSet
Set of parameters that don&#39;t get sampled.
Definition: MetropolisHastingsSGOptions.h:231
QUESO::MhOptionsValues::m_filteredChainGenerate
bool m_filteredChainGenerate
Toggle the option to save a filtered chain.
Definition: MetropolisHastingsSGOptions.h:346
QUESO::BaseEnvironment::allOptionsMap
boost::program_options::variables_map & allOptionsMap() const
Definition: Environment.C:385
QUESO::BaseEnvironment::subId
unsigned int subId() const
Access function to the number of each sub-environment Id: m_subId.
Definition: Environment.C:341
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:245
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:538
QUESO::MhOptionsValues::m_initialProposalCovMatrixDataInputFileType
std::string m_initialProposalCovMatrixDataInputFileType
The filetype of m_initialProposalCovMatrixDataInputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:225
queso_deprecated
#define queso_deprecated()
Definition: Defines.h:134
QUESO::MhOptionsValues::m_amInitialNonAdaptInterval
unsigned int m_amInitialNonAdaptInterval
The number of initial samples to do without adapting the proposal covariance matrix.
Definition: MetropolisHastingsSGOptions.h:505
QUESO::MhOptionsValues::m_tk
std::string m_tk
Which transition kernel to use for MCMC. Default is &quot;random_walk&quot;.
Definition: MetropolisHastingsSGOptions.h:613
QUESO::MhOptionsValues::m_algorithm
std::string m_algorithm
Which algorithm to use for the MCMC. Default is &quot;random_walk&quot;.
Definition: MetropolisHastingsSGOptions.h:610
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:601
QUESO::MhOptionsValues::m_drMaxNumExtraStages
unsigned int m_drMaxNumExtraStages
The number of delayed rejection stages to do. Default is 0.
Definition: MetropolisHastingsSGOptions.h:450
QUESO::BaseEnvironment::fullRank
int fullRank() const
Returns the process full rank.
Definition: Environment.C:268
QUESO::MhOptionsValues::m_initialPositionDataInputFileType
std::string m_initialPositionDataInputFileType
The filetype of m_initialPositionDataInputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:210
QUESO::MhOptionsValues::m_rawChainDataInputFileName
std::string m_rawChainDataInputFileName
Filename for reading an already-produced Markov chain.
Definition: MetropolisHastingsSGOptions.h:242
QUESO::MhOptionsValues::m_filteredChainDataOutputFileType
std::string m_filteredChainDataOutputFileType
The filetype of m_filteredChainDataOutputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:374
QUESO::MhOptionsValues::m_dataOutputAllowAll
bool m_dataOutputAllowAll
If true, all processes write output and m_dataOutputAllowedSet is ignored.
Definition: MetropolisHastingsSGOptions.h:192
QUESO::MhOptionsValues::m_rawChainGenerateExtra
bool m_rawChainGenerateExtra
If true, extra chain information is computed/stored.
Definition: MetropolisHastingsSGOptions.h:257
QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputFileType
std::string m_amAdaptedMatricesDataOutputFileType
The filetype of m_amAdaptedMatricesDataOutputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:541
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:330
QUESO::MhOptionsValues::m_filteredChainLag
unsigned int m_filteredChainLag
Set the lag for the filtered chain. Default is 1.
Definition: MetropolisHastingsSGOptions.h:362
QUESO::MhOptionsValues::m_amEta
double m_amEta
Proposal covariance scaling factor, usually 2.4 * 2.4 / d.
Definition: MetropolisHastingsSGOptions.h:560
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:198
QUESO::MhOptionsValues::m_tkUseNewtonComponent
bool m_tkUseNewtonComponent
This option is a no-op. Default is true.
Definition: MetropolisHastingsSGOptions.h:440
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:248
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:389
QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputAllowAll
bool m_amAdaptedMatricesDataOutputAllowAll
This option is a no-op. The default is false.
Definition: MetropolisHastingsSGOptions.h:544
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:284
QUESO::MhOptionsValues::m_amEpsilon
double m_amEpsilon
Regularisation parameter for the DRAM covariance matrix.
Definition: MetropolisHastingsSGOptions.h:572
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:607
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:333
QUESO::MhOptionsValues::m_amAdaptInterval
unsigned int m_amAdaptInterval
The frequency at which to adapt the proposal covariance matrix.
Definition: MetropolisHastingsSGOptions.h:515
QUESO::MhOptionsValues::m_amKeepInitialMatrix
bool m_amKeepInitialMatrix
This option is a no-op. The default is false.
Definition: MetropolisHastingsSGOptions.h:494
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:532
void QUESO::MetropolisHastingsSGOptions::print ( std::ostream &  os) const

It prints the option values.

Definition at line 1216 of file MetropolisHastingsSGOptions.C.

References QUESO::MhOptionsValues::m_algorithm, 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_algorithm, 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, 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_tk, QUESO::MhOptionsValues::m_tkUseLocalHessian, QUESO::MhOptionsValues::m_tkUseNewtonComponent, QUESO::MhOptionsValues::m_totallyMute, and queso_deprecated.

Referenced by QUESO::operator<<().

1217 {
1218  queso_deprecated();
1219 
1220  os << m_option_dataOutputFileName << " = " << m_ov.m_dataOutputFileName
1221  << "\n" << m_option_dataOutputAllowAll << " = " << m_ov.m_dataOutputAllowAll
1222  << "\n" << m_option_dataOutputAllowedSet << " = ";
1223  for (std::set<unsigned int>::iterator setIt = m_ov.m_dataOutputAllowedSet.begin(); setIt != m_ov.m_dataOutputAllowedSet.end(); ++setIt) {
1224  os << *setIt << " ";
1225  }
1226  os << "\n" << m_option_totallyMute << " = " << m_ov.m_totallyMute
1227  << "\n" << m_option_initialPosition_dataInputFileName << " = " << m_ov.m_initialPositionDataInputFileName
1228  << "\n" << m_option_initialPosition_dataInputFileType << " = " << m_ov.m_initialPositionDataInputFileType
1229  << "\n" << m_option_initialProposalCovMatrix_dataInputFileName << " = " << m_ov.m_initialProposalCovMatrixDataInputFileName
1230  << "\n" << m_option_initialProposalCovMatrix_dataInputFileType << " = " << m_ov.m_initialProposalCovMatrixDataInputFileType
1231  << "\n" << m_option_listOfDisabledParameters << " = ";
1232  for (std::set<unsigned int>::iterator setIt = m_ov.m_parameterDisabledSet.begin(); setIt != m_ov.m_parameterDisabledSet.end(); ++setIt) {
1233  os << *setIt << " ";
1234  }
1235  os << "\n" << m_option_rawChain_dataInputFileName << " = " << m_ov.m_rawChainDataInputFileName
1236  << "\n" << m_option_rawChain_dataInputFileType << " = " << m_ov.m_rawChainDataInputFileType
1237  << "\n" << m_option_rawChain_size << " = " << m_ov.m_rawChainSize
1238  << "\n" << m_option_rawChain_generateExtra << " = " << m_ov.m_rawChainGenerateExtra
1239  << "\n" << m_option_rawChain_displayPeriod << " = " << m_ov.m_rawChainDisplayPeriod
1240  << "\n" << m_option_rawChain_measureRunTimes << " = " << m_ov.m_rawChainMeasureRunTimes
1241  << "\n" << m_option_rawChain_dataOutputPeriod << " = " << m_ov.m_rawChainDataOutputPeriod
1242  << "\n" << m_option_rawChain_dataOutputFileName << " = " << m_ov.m_rawChainDataOutputFileName
1243  << "\n" << m_option_rawChain_dataOutputFileType << " = " << m_ov.m_rawChainDataOutputFileType
1244  << "\n" << m_option_rawChain_dataOutputAllowAll << " = " << m_ov.m_rawChainDataOutputAllowAll
1245  << "\n" << m_option_rawChain_dataOutputAllowedSet << " = ";
1246  for (std::set<unsigned int>::iterator setIt = m_ov.m_rawChainDataOutputAllowedSet.begin(); setIt != m_ov.m_rawChainDataOutputAllowedSet.end(); ++setIt) {
1247  os << *setIt << " ";
1248  }
1249  os
1250 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
1251  << "\n" << m_option_rawChain_computeStats << " = " << m_ov.m_rawChainComputeStats
1252 #endif
1253  << "\n" << m_option_filteredChain_generate << " = " << m_ov.m_filteredChainGenerate
1254  << "\n" << m_option_filteredChain_discardedPortion << " = " << m_ov.m_filteredChainDiscardedPortion
1255  << "\n" << m_option_filteredChain_lag << " = " << m_ov.m_filteredChainLag
1256  << "\n" << m_option_filteredChain_dataOutputFileName << " = " << m_ov.m_filteredChainDataOutputFileName
1257  << "\n" << m_option_filteredChain_dataOutputFileType << " = " << m_ov.m_filteredChainDataOutputFileType
1258  << "\n" << m_option_filteredChain_dataOutputAllowAll << " = " << m_ov.m_filteredChainDataOutputAllowAll
1259  << "\n" << m_option_filteredChain_dataOutputAllowedSet << " = ";
1260  for (std::set<unsigned int>::iterator setIt = m_ov.m_filteredChainDataOutputAllowedSet.begin(); setIt != m_ov.m_filteredChainDataOutputAllowedSet.end(); ++setIt) {
1261  os << *setIt << " ";
1262  }
1263  os
1264 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
1265  << "\n" << m_option_filteredChain_computeStats << " = " << m_ov.m_filteredChainComputeStats
1266 #endif
1267  << "\n" << m_option_displayCandidates << " = " << m_ov.m_displayCandidates
1268  << "\n" << m_option_putOutOfBoundsInChain << " = " << m_ov.m_putOutOfBoundsInChain
1269  << "\n" << m_option_tk_useLocalHessian << " = " << m_ov.m_tkUseLocalHessian
1270  << "\n" << m_option_tk_useNewtonComponent << " = " << m_ov.m_tkUseNewtonComponent
1271  << "\n" << m_option_dr_maxNumExtraStages << " = " << m_ov.m_drMaxNumExtraStages
1272  << "\n" << m_option_dr_listOfScalesForExtraStages << " = ";
1273  for (unsigned int i = 0; i < m_ov.m_drScalesForExtraStages.size(); ++i) {
1274  os << m_ov.m_drScalesForExtraStages[i] << " ";
1275  }
1276  os << "\n" << m_option_dr_duringAmNonAdaptiveInt << " = " << m_ov.m_drDuringAmNonAdaptiveInt
1277  << "\n" << m_option_am_keepInitialMatrix << " = " << m_ov.m_amKeepInitialMatrix
1278  << "\n" << m_option_am_initialNonAdaptInterval << " = " << m_ov.m_amInitialNonAdaptInterval
1279  << "\n" << m_option_am_adaptInterval << " = " << m_ov.m_amAdaptInterval
1280  << "\n" << m_option_am_adaptedMatrices_dataOutputPeriod << " = " << m_ov.m_amAdaptedMatricesDataOutputPeriod
1281  << "\n" << m_option_am_adaptedMatrices_dataOutputFileName << " = " << m_ov.m_amAdaptedMatricesDataOutputFileName
1282  << "\n" << m_option_am_adaptedMatrices_dataOutputFileType << " = " << m_ov.m_amAdaptedMatricesDataOutputFileType
1283  << "\n" << m_option_am_adaptedMatrices_dataOutputAllowAll << " = " << m_ov.m_amAdaptedMatricesDataOutputAllowAll
1284  << "\n" << m_option_am_adaptedMatrices_dataOutputAllowedSet << " = ";
1285  for (std::set<unsigned int>::iterator setIt = m_ov.m_amAdaptedMatricesDataOutputAllowedSet.begin(); setIt != m_ov.m_amAdaptedMatricesDataOutputAllowedSet.end(); ++setIt) {
1286  os << *setIt << " ";
1287  }
1288  os << "\n" << m_option_am_eta << " = " << m_ov.m_amEta
1289  << "\n" << m_option_am_epsilon << " = " << m_ov.m_amEpsilon
1290  << "\n" << m_option_enableBrooksGelmanConvMonitor << " = " << m_ov.m_enableBrooksGelmanConvMonitor
1291  << "\n" << m_option_BrooksGelmanLag << " = " << m_ov.m_BrooksGelmanLag
1292  << "\n" << m_option_outputLogLikelihood << " = " << m_ov.m_outputLogLikelihood
1293  << "\n" << m_option_outputLogTarget << " = " << m_ov.m_outputLogTarget
1294  << "\n" << m_option_doLogitTransform << " = " << m_ov.m_doLogitTransform
1295  << "\n" << m_option_algorithm << " = " << m_ov.m_algorithm
1296  << "\n" << m_option_tk << " = " << m_ov.m_tk
1297  << std::endl;
1298 
1299  return;
1300 }
QUESO::MhOptionsValues::m_filteredChainDiscardedPortion
double m_filteredChainDiscardedPortion
What initial fraction of the filtered chain is discarded.
Definition: MetropolisHastingsSGOptions.h:355
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:469
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:396
QUESO::MhOptionsValues::m_rawChainDataOutputFileName
std::string m_rawChainDataOutputFileName
If not &quot;.&quot;, filename to write the Markov chain to.
Definition: MetropolisHastingsSGOptions.h:298
QUESO::MhOptionsValues::m_totallyMute
bool m_totallyMute
If true, zero output is written to files. Default is false.
Definition: MetropolisHastingsSGOptions.h:201
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:411
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:547
QUESO::MetropolisHastingsSGOptions::m_ov
MhOptionsValues m_ov
This class is where the actual options are stored.
Definition: MetropolisHastingsSGOptions.h:801
QUESO::MhOptionsValues::m_rawChainDataOutputPeriod
unsigned int m_rawChainDataOutputPeriod
The frequency with which to write chain output. Defaults to 0.
Definition: MetropolisHastingsSGOptions.h:287
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:371
QUESO::MhOptionsValues::m_rawChainDataOutputFileType
std::string m_rawChainDataOutputFileType
The filetype of m_rawChainDataOutputFileName.
Definition: MetropolisHastingsSGOptions.h:318
QUESO::MhOptionsValues::m_drDuringAmNonAdaptiveInt
bool m_drDuringAmNonAdaptiveInt
Do delayed rejection during the initial non-adaptive part of sampling?
Definition: MetropolisHastingsSGOptions.h:491
QUESO::MetropolisHastingsSGOptions::m_option_am_eta
std::string m_option_am_eta
See MhOptionsValues::m_amEta.
Definition: MetropolisHastingsSGOptions.h:878
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:207
QUESO::MhOptionsValues::m_BrooksGelmanLag
unsigned int m_BrooksGelmanLag
The lag with which to compute the Brooks-Gelman convergence statistic.
Definition: MetropolisHastingsSGOptions.h:598
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:604
QUESO::MhOptionsValues::m_rawChainDisplayPeriod
unsigned int m_rawChainDisplayPeriod
The frequency with which to output diagnostic information.
Definition: MetropolisHastingsSGOptions.h:267
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:222
QUESO::MetropolisHastingsSGOptions::m_option_am_epsilon
std::string m_option_am_epsilon
See MhOptionsValues::m_amEpsilon.
Definition: MetropolisHastingsSGOptions.h:880
QUESO::MhOptionsValues::m_enableBrooksGelmanConvMonitor
unsigned int m_enableBrooksGelmanConvMonitor
The frequency with which to compute the Brooks-Gelman convergence statistic.
Definition: MetropolisHastingsSGOptions.h:588
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:437
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:183
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:386
QUESO::MhOptionsValues::m_parameterDisabledSet
std::set< unsigned int > m_parameterDisabledSet
Set of parameters that don&#39;t get sampled.
Definition: MetropolisHastingsSGOptions.h:231
QUESO::MhOptionsValues::m_filteredChainGenerate
bool m_filteredChainGenerate
Toggle the option to save a filtered chain.
Definition: MetropolisHastingsSGOptions.h:346
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:245
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:538
QUESO::MhOptionsValues::m_initialProposalCovMatrixDataInputFileType
std::string m_initialProposalCovMatrixDataInputFileType
The filetype of m_initialProposalCovMatrixDataInputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:225
queso_deprecated
#define queso_deprecated()
Definition: Defines.h:134
QUESO::MhOptionsValues::m_amInitialNonAdaptInterval
unsigned int m_amInitialNonAdaptInterval
The number of initial samples to do without adapting the proposal covariance matrix.
Definition: MetropolisHastingsSGOptions.h:505
QUESO::MhOptionsValues::m_tk
std::string m_tk
Which transition kernel to use for MCMC. Default is &quot;random_walk&quot;.
Definition: MetropolisHastingsSGOptions.h:613
QUESO::MhOptionsValues::m_algorithm
std::string m_algorithm
Which algorithm to use for the MCMC. Default is &quot;random_walk&quot;.
Definition: MetropolisHastingsSGOptions.h:610
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:601
QUESO::MhOptionsValues::m_drMaxNumExtraStages
unsigned int m_drMaxNumExtraStages
The number of delayed rejection stages to do. Default is 0.
Definition: MetropolisHastingsSGOptions.h:450
QUESO::MhOptionsValues::m_initialPositionDataInputFileType
std::string m_initialPositionDataInputFileType
The filetype of m_initialPositionDataInputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:210
QUESO::MhOptionsValues::m_rawChainDataInputFileName
std::string m_rawChainDataInputFileName
Filename for reading an already-produced Markov chain.
Definition: MetropolisHastingsSGOptions.h:242
QUESO::MhOptionsValues::m_filteredChainDataOutputFileType
std::string m_filteredChainDataOutputFileType
The filetype of m_filteredChainDataOutputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:374
QUESO::MhOptionsValues::m_dataOutputAllowAll
bool m_dataOutputAllowAll
If true, all processes write output and m_dataOutputAllowedSet is ignored.
Definition: MetropolisHastingsSGOptions.h:192
QUESO::MhOptionsValues::m_rawChainGenerateExtra
bool m_rawChainGenerateExtra
If true, extra chain information is computed/stored.
Definition: MetropolisHastingsSGOptions.h:257
QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputFileType
std::string m_amAdaptedMatricesDataOutputFileType
The filetype of m_amAdaptedMatricesDataOutputFileName. Only &quot;m&quot; (matlab) is currently supported...
Definition: MetropolisHastingsSGOptions.h:541
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:330
QUESO::MhOptionsValues::m_filteredChainLag
unsigned int m_filteredChainLag
Set the lag for the filtered chain. Default is 1.
Definition: MetropolisHastingsSGOptions.h:362
QUESO::MhOptionsValues::m_amEta
double m_amEta
Proposal covariance scaling factor, usually 2.4 * 2.4 / d.
Definition: MetropolisHastingsSGOptions.h:560
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:198
QUESO::MhOptionsValues::m_tkUseNewtonComponent
bool m_tkUseNewtonComponent
This option is a no-op. Default is true.
Definition: MetropolisHastingsSGOptions.h:440
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:248
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:389
QUESO::MhOptionsValues::m_amAdaptedMatricesDataOutputAllowAll
bool m_amAdaptedMatricesDataOutputAllowAll
This option is a no-op. The default is false.
Definition: MetropolisHastingsSGOptions.h:544
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:284
QUESO::MhOptionsValues::m_amEpsilon
double m_amEpsilon
Regularisation parameter for the DRAM covariance matrix.
Definition: MetropolisHastingsSGOptions.h:572
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:607
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:333
QUESO::MhOptionsValues::m_amAdaptInterval
unsigned int m_amAdaptInterval
The frequency at which to adapt the proposal covariance matrix.
Definition: MetropolisHastingsSGOptions.h:515
QUESO::MhOptionsValues::m_amKeepInitialMatrix
bool m_amKeepInitialMatrix
This option is a no-op. The default is false.
Definition: MetropolisHastingsSGOptions.h:494
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:532
void QUESO::MetropolisHastingsSGOptions::scanOptionsValues ( )

It scans the option values from the options input file.

Definition at line 1180 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().

1181 {
1182  queso_deprecated();
1183 
1184 #ifndef DISABLE_BOOST_PROGRAM_OPTIONS
1185  queso_require_msg(m_optionsDesc, "m_optionsDesc variable is NULL");
1186 
1187  defineMyOptions (*m_optionsDesc);
1188  m_env.scanInputFileForMyOptions(*m_optionsDesc);
1189  getMyOptionValues (*m_optionsDesc);
1190 #endif // DISABLE_BOOST_PROGRAM_OPTIONS
1191 
1192  if ((m_env.subDisplayFile() != NULL) &&
1193  (m_ov.m_totallyMute == false )) {
1194  *m_env.subDisplayFile() << "In MetropolisHastingsSGOptions::scanOptionsValues()"
1195  << ": after reading values of options with prefix '" << m_prefix
1196  << "', state of object is:"
1197  << "\n" << *this
1198  << std::endl;
1199  }
1200 
1201 #ifdef QUESO_USES_SEQUENCE_STATISTICAL_OPTIONS
1202  if (m_ov.m_rawChainComputeStats) {
1203  m_rawChainStatisticalOptionsObj = new SequenceStatisticalOptions(m_env,m_prefix + "rawChain_");
1204  m_rawChainStatOptsInstantiated = true;
1205  }
1206  if (m_ov.m_filteredChainComputeStats) {
1207  m_filteredChainStatisticalOptionsObj = new SequenceStatisticalOptions(m_env,m_prefix + "filteredChain_");
1208  m_filteredChainStatOptsInstantiated = true;
1209  }
1210 #endif
1211 
1212  return;
1213 }
QUESO::MhOptionsValues::m_totallyMute
bool m_totallyMute
If true, zero output is written to files. Default is false.
Definition: MetropolisHastingsSGOptions.h:201
QUESO::MetropolisHastingsSGOptions::m_ov
MhOptionsValues m_ov
This class is where the actual options are stored.
Definition: MetropolisHastingsSGOptions.h:801
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:320
QUESO::MetropolisHastingsSGOptions::getMyOptionValues
void getMyOptionValues(boost::program_options::options_description &optionsDesc)
Gets the sequence options defined to the Metropolis-Hastings algorithm.
Definition: MetropolisHastingsSGOptions.C:1377
queso_deprecated
#define queso_deprecated()
Definition: Defines.h:134
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:396
QUESO::MetropolisHastingsSGOptions::m_optionsDesc
boost::program_options::options_description * m_optionsDesc
Definition: MetropolisHastingsSGOptions.h:822
queso_require_msg
#define queso_require_msg(asserted, msg)
Definition: asserts.h:69
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:1305

Member Data Documentation

const BaseEnvironment& QUESO::MetropolisHastingsSGOptions::m_env
private

Definition at line 820 of file MetropolisHastingsSGOptions.h.

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

std::string QUESO::MetropolisHastingsSGOptions::m_option_algorithm
private

Definition at line 888 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 874 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 875 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 872 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 873 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 871 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 870 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 880 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 878 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 869 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 868 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 883 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 828 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 829 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 827 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 861 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 887 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 867 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 866 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 865 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 882 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 856 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 857 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 854 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 855 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 852 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 851 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 853 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 825 of file MetropolisHastingsSGOptions.h.

Referenced by defineMyOptions(), and getMyOptionValues().

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

Definition at line 832 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 833 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 834 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 835 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 836 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 885 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 886 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 862 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 837 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 838 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 846 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 847 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 844 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 845 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 843 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 841 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 840 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 842 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 839 of file MetropolisHastingsSGOptions.h.

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

std::string QUESO::MetropolisHastingsSGOptions::m_option_tk
private

Definition at line 889 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 863 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 864 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 831 of file MetropolisHastingsSGOptions.h.

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

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

Definition at line 822 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 801 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 809 of file MetropolisHastingsSGOptions.h.

Referenced by MetropolisHastingsSGOptions(), and scanOptionsValues().

The documentation for this class was generated from the following files:
Generated on Tue Nov 29 2016 10:53:15 for queso-0.56.0 by  doxygen 1.8.5