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QUESO::BaseVectorSequence< V, M > Class Template Referenceabstract

Base class for handling vector and array samples (sequence of vectors or arrays). More...

#include <VectorSequence.h>

Inheritance diagram for QUESO::BaseVectorSequence< V, M >:
QUESO::ArrayOfSequences< V, M > QUESO::SequenceOfVectors< V, M >

Public Member Functions

Constructor/Destructor methods
 BaseVectorSequence (const VectorSpace< V, M > &vectorSpace, unsigned int subSequenceSize, const std::string &name)
 Default constructor. More...
 
virtual ~BaseVectorSequence ()
 Destructor. More...
 
Sequence methods
virtual unsigned int subSequenceSize () const =0
 Size of the sub-sequence of vectors. See template specialization. More...
 
unsigned int unifiedSequenceSize () const
 Calculates the size of the unified sequence of vectors. More...
 
unsigned int vectorSizeLocal () const
 Local dimension (size) of the vector space. More...
 
unsigned int vectorSizeGlobal () const
 Global dimension (size) of the vector space. More...
 
const VectorSpace< V, M > & vectorSpace () const
 Vector space; access to protected attribute VectorSpace<V,M>& m_vectorSpace. More...
 
const std::string & name () const
 Access to protected attribute m_name: name of the sequence of vectors. More...
 
void setName (const std::string &newName)
 Changes the name of the sequence of vectors. More...
 
void clear ()
 Reset the values and the size of the sequence of vectors. More...
 
const V & subMinPlain () const
 Finds the minimum value of the sub-sequence. More...
 
const V & unifiedMinPlain () const
 Finds the minimum value of the unified sequence. More...
 
const V & subMaxPlain () const
 Finds the maximum value of the sub-sequence. More...
 
const V & unifiedMaxPlain () const
 Finds the maximum value of the unified sequence. More...
 
const V & subMeanPlain () const
 Finds the mean value of the sub-sequence. More...
 
const V & unifiedMeanPlain () const
 Finds the mean value of the unified sequence. More...
 
const V & subMedianPlain () const
 Finds the median value of the sub-sequence. More...
 
const V & unifiedMedianPlain () const
 Finds the median value of the unified sequence. More...
 
const V & subSampleVariancePlain () const
 Finds the variance of a sample of the sub-sequence. More...
 
const V & unifiedSampleVariancePlain () const
 Finds the variance of a sample of the unified sequence. More...
 
const BoxSubset< V, M > & subBoxPlain () const
 Finds a box subset of the sub-sequence (given by its min and max values calculated via subMinPlain and subMaxPlain). More...
 
const BoxSubset< V, M > & unifiedBoxPlain () const
 Finds a box subset of the unified-sequence (given by the min and max values of the unified sequence calculated via unifiedMinPlain and unifiedMaxPlain). More...
 
void deleteStoredVectors ()
 Deletes all the stored vectors. More...
 
void append (const BaseVectorSequence< V, M > &src, unsigned int initialPos, unsigned int numPos)
 Appends the vector src to this vector. More...
 
double subPositionsOfMaximum (const ScalarSequence< double > &subCorrespondingScalarValues, BaseVectorSequence< V, M > &subPositionsOfMaximum)
 Finds the positions where the maximum element occurs in the sub-sequence. More...
 
double unifiedPositionsOfMaximum (const ScalarSequence< double > &subCorrespondingScalarValues, BaseVectorSequence< V, M > &unifiedPositionsOfMaximum)
 Finds the positions where the maximum element occurs in the unified sequence. More...
 
virtual void resizeSequence (unsigned int newSubSequenceSize)=0
 Resize the sequence. See template specialization. More...
 
virtual void resetValues (unsigned int initialPos, unsigned int numPos)=0
 Reset the values of the sequence. See template specialization. More...
 
virtual void erasePositions (unsigned int initialPos, unsigned int numPos)=0
 Erase numPos positions in the sequence, starting at position initialPos. More...
 
virtual void getPositionValues (unsigned int posId, V &vec) const =0
 Gets the values of the sequence at position posId and stores them at vec. See template specialization. More...
 
virtual void setPositionValues (unsigned int posId, const V &vec)=0
 Set the values in vec at position posId of the sequence. See template specialization. More...
 
void setGaussian (const V &meanVec, const V &stdDevVec)
 Sets the values of the sequence as a Gaussian distribution of mean given by meanVec and standard deviation by stdDevVec. More...
 
void setUniform (const V &aVec, const V &bVec)
 Sets the values of the sequence as a uniform distribution between the values given by vectors aVec and bVec. More...
 
virtual void subMeanExtra (unsigned int initialPos, unsigned int numPos, V &meanVec) const =0
 Finds the mean value of the sub-sequence, considering numPos positions starting at position initialPos. See template specialization. More...
 
virtual void unifiedMeanExtra (unsigned int initialPos, unsigned int numPos, V &unifiedMeanVec) const =0
 Finds the mean value of the unified sequence of numPos positions starting at position initialPos. See template specialization. More...
 
virtual void subMedianExtra (unsigned int initialPos, unsigned int numPos, V &medianVec) const =0
 Finds the median value of the sub-sequence, considering numPos positions starting at position initialPos. See template specialization. More...
 
virtual void unifiedMedianExtra (unsigned int initialPos, unsigned int localNumPos, V &unifiedMedianVec) const =0
 Finds the median value of the unified sequence, considering numPos positions starting at position initialPos. See template specialization. More...
 
virtual void subSampleVarianceExtra (unsigned int initialPos, unsigned int numPos, const V &meanVec, V &samVec) const =0
 Finds the sample variance of the sub-sequence, considering numPos positions starting at position initialPos and of mean meanVec. See template specialization. More...
 
virtual void unifiedSampleVarianceExtra (unsigned int initialPos, unsigned int numPos, const V &unifiedMeanVec, V &unifiedSamVec) const =0
 Finds the sample variance of the unified sequence, considering numPos positions starting at position initialPos and of mean meanVec. See template specialization. More...
 
virtual void subPopulationVariance (unsigned int initialPos, unsigned int numPos, const V &meanVec, V &popVec) const =0
 Finds the population variance of the sub-sequence, considering numPos positions starting at position initialPos and of mean meanVec. See template specialization. More...
 
virtual void unifiedPopulationVariance (unsigned int initialPos, unsigned int numPos, const V &unifiedMeanVec, V &unifiedPopVec) const =0
 Finds the population variance of the unified-sequence, considering numPos positions starting at position initialPos and of mean meanVec. See template specialization. More...
 
virtual void autoCovariance (unsigned int initialPos, unsigned int numPos, const V &meanVec, unsigned int lag, V &covVec) const =0
 Calculates the autocovariance. See template specialization. More...
 
virtual void autoCorrViaDef (unsigned int initialPos, unsigned int numPos, unsigned int lag, V &corrVec) const =0
 Calculates autocorrelation via definition. See template specialization. More...
 
virtual void autoCorrViaFft (unsigned int initialPos, unsigned int numPos, const std::vector< unsigned int > &lags, std::vector< V * > &corrVecs) const =0
 Calculates autocorrelation via Fast Fourier transforms (FFT). See template specialization. More...
 
virtual void autoCorrViaFft (unsigned int initialPos, unsigned int numPos, unsigned int numSum, V &autoCorrsSumVec) const =0
 Calculates autocorrelation via Fast Fourier transforms (FFT). See template specialization. More...
 
virtual void subMinMaxExtra (unsigned int initialPos, unsigned int numPos, V &minVec, V &maxVec) const =0
 Finds the minimum and the maximum values of the sub-sequence, considering numPos positions starting at position initialPos. See template specialization. More...
 
virtual void unifiedMinMaxExtra (unsigned int initialPos, unsigned int numPos, V &unifiedMinVec, V &unifiedMaxVec) const =0
 Finds the minimum and the maximum values of the unified sequence, considering numPos positions starting at position initialPos. See template specialization. More...
 
virtual void subHistogram (unsigned int initialPos, const V &minVec, const V &maxVec, std::vector< V * > &centersForAllBins, std::vector< V * > &quanttsForAllBins) const =0
 Calculates the histogram of the sub-sequence. See template specialization. More...
 
virtual void unifiedHistogram (unsigned int initialPos, const V &unifiedMinVec, const V &unifiedMaxVec, std::vector< V * > &unifiedCentersForAllBins, std::vector< V * > &unifiedQuanttsForAllBins) const =0
 Calculates the histogram of the unified sequence. See template specialization. More...
 
virtual void subInterQuantileRange (unsigned int initialPos, V &iqrVec) const =0
 Returns the interquartile range of the values in the sub-sequence. See template specialization. More...
 
virtual void unifiedInterQuantileRange (unsigned int initialPos, V &unifiedIqrVec) const =0
 Returns the interquartile range of the values in the unified sequence. See template specialization. More...
 
virtual void subScalesForKde (unsigned int initialPos, const V &iqrVec, unsigned int kdeDimension, V &scaleVec) const =0
 Selects the scales (bandwidth, scaleVec) for the kernel density estimation, considering only the sub-sequence. See template specialization. More...
 
virtual void unifiedScalesForKde (unsigned int initialPos, const V &unifiedIqrVec, unsigned int kdeDimension, V &unifiedScaleVec) const =0
 Selects the scales (bandwidth) for the kernel density estimation, considering the unified sequence. See template specialization. More...
 
virtual void subGaussian1dKde (unsigned int initialPos, const V &scaleVec, const std::vector< V * > &evaluationParamVecs, std::vector< V * > &densityVecs) const =0
 Gaussian kernel for the KDE estimate of the sub-sequence. See template specialization. More...
 
virtual void unifiedGaussian1dKde (unsigned int initialPos, const V &unifiedScaleVec, const std::vector< V * > &unifiedEvaluationParamVecs, std::vector< V * > &unifiedDensityVecs) const =0
 Gaussian kernel for the KDE estimate of the unified sequence. See template specialization. More...
 
virtual void subWriteContents (unsigned int initialPos, unsigned int numPos, const std::string &fileName, const std::string &fileType, const std::set< unsigned int > &allowedSubEnvIds) const =0
 Writes info of the sub-sequence to a file. See template specialization. More...
 
virtual void subWriteContents (unsigned int initialPos, unsigned int numPos, std::ofstream &ofsvar, const std::string &fileType) const =0
 Writes info of the sub-sequence to a file. See template specialization. More...
 
virtual void unifiedWriteContents (const std::string &fileName, const std::string &fileType) const =0
 Writes info of the unified sequence to a file. See template specialization. More...
 
virtual void unifiedReadContents (const std::string &fileName, const std::string &fileType, const unsigned int subSequenceSize)=0
 Reads info of the unified sequence from a file. See template specialization. More...
 
virtual void select (const std::vector< unsigned int > &idsOfUniquePositions)=0
 Select positions in the sequence of vectors. See template specialization. More...
 
virtual void filter (unsigned int initialPos, unsigned int spacing)=0
 Filters positions in the sequence of vectors, starting at initialPos, and with spacing given by spacing. See template specialization. More...
 
void computeFilterParams (std::ofstream *passedOfs, unsigned int &initialPos, unsigned int &spacing)
 Computes the filtering parameters spacing for the sequence of vectors. More...
 
virtual double estimateConvBrooksGelman (unsigned int initialPos, unsigned int numPos) const =0
 Estimates convergence rate using Brooks & Gelman method. See template specialization. More...
 
virtual void extractScalarSeq (unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const =0
 Extracts a sequence of scalars of size numPos, starting at position initialPos, given spacing spacing. See template specialization. More...
 
virtual void subUniformlySampledCdf (const V &numEvaluationPointsVec, ArrayOfOneDGrids< V, M > &cdfGrids, ArrayOfOneDTables< V, M > &cdfValues) const =0
 
virtual void unifiedUniformlySampledCdf (const V &numEvaluationPointsVec, ArrayOfOneDGrids< V, M > &unifiedCdfGrids, ArrayOfOneDTables< V, M > &unifieddfValues) const =0
 
virtual void bmm (unsigned int initialPos, unsigned int batchLength, V &bmmVec) const =0
 
virtual void fftForward (unsigned int initialPos, unsigned int fftSize, unsigned int paramId, std::vector< std::complex< double > > &fftResult) const =0
 
virtual void psd (unsigned int initialPos, unsigned int numBlocks, double hopSizeRatio, unsigned int paramId, std::vector< double > &psdResult) const =0
 
virtual void psdAtZero (unsigned int initialPos, unsigned int numBlocks, double hopSizeRatio, V &psdVec) const =0
 
virtual void geweke (unsigned int initialPos, double ratioNa, double ratioNb, V &gewVec) const =0
 
virtual void meanStacc (unsigned int initialPos, V &meanStaccVec) const =0
 
virtual void subCdfStacc (unsigned int initialPos, const std::vector< V * > &evalPositionsVecs, std::vector< V * > &cdfStaccVecs) const =0
 
void computeHistCdfstaccKde (const SequenceStatisticalOptions &statisticalOptions, std::ofstream *passedOfs)
 
void computeStatistics (const SequenceStatisticalOptions &statisticalOptions, std::ofstream *passedOfs)
 
void computeHistCdfstaccKde (const SsOptionsValues &statisticalOptions, std::ofstream *passedOfs)
 
void computeStatistics (const SsOptionsValues &statisticalOptions, std::ofstream *passedOfs)
 
virtual void subUniformlySampledMdf (const V &numEvaluationPointsVec, ArrayOfOneDGrids< V, M > &mdfGrids, ArrayOfOneDTables< V, M > &mdfValues) const =0
 

Protected Member Functions

void copy (const BaseVectorSequence< V, M > &src)
 Copies vector sequence src to this. More...
 
virtual void extractRawData (unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, std::vector< double > &rawData) const =0
 Extracts the raw data. See template specialization. More...
 
virtual void subMeanMonitorAlloc (unsigned int numberOfMonitorPositions)=0
 
virtual void subMeanInter0MonitorAlloc (unsigned int numberOfMonitorPositions)=0
 
virtual void unifiedMeanMonitorAlloc (unsigned int numberOfMonitorPositions)=0
 
virtual void subMeanMonitorRun (unsigned int monitorPosition, V &subMeanVec, V &subMeanCltStd)=0
 
virtual void subMeanInter0MonitorRun (unsigned int monitorPosition, V &subMeanInter0Mean, V &subMeanInter0Clt95, V &subMeanInter0Empirical90, V &subMeanInter0Min, V &subMeanInter0Max)=0
 
virtual void unifiedMeanMonitorRun (unsigned int monitorPosition, V &unifiedMeanVec, V &unifiedMeanCltStd)=0
 
virtual void subMeanMonitorStore (unsigned int i, unsigned int monitorPosition, const V &subMeanVec, const V &subMeanCltStd)=0
 
virtual void subMeanInter0MonitorStore (unsigned int i, unsigned int monitorPosition, const V &subMeanInter0Mean, const V &subMeanInter0Clt95, const V &subMeanInter0Empirical90, const V &subMeanInter0Min, const V &subMeanInter0Max)=0
 
virtual void unifiedMeanMonitorStore (unsigned int i, unsigned int monitorPosition, V &unifiedMeanVec, V &unifiedMeanCltStd)=0
 
virtual void subMeanMonitorWrite (std::ofstream &ofs)=0
 
virtual void subMeanInter0MonitorWrite (std::ofstream &ofs)=0
 
virtual void unifiedMeanMonitorWrite (std::ofstream &ofs)=0
 
virtual void subMeanMonitorFree ()=0
 
virtual void subMeanInter0MonitorFree ()=0
 
virtual void unifiedMeanMonitorFree ()=0
 
void computeMeanEvolution (const SequenceStatisticalOptions &statisticalOptions, std::ofstream *passedOfs)
 
void computeMeanEvolution (const SsOptionsValues &statisticalOptions, std::ofstream *passedOfs)
 
void computeBMM (const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
 
void computeFFT (const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
 
void computePSD (const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
 
void computePSDAtZero (const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
 
void computeGeweke (const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
 
void computeMeanStacc (const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
 
void computeBMM (const SsOptionsValues &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
 
void computeFFT (const SsOptionsValues &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
 
void computePSD (const SsOptionsValues &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
 
void computePSDAtZero (const SsOptionsValues &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
 
void computeGeweke (const SsOptionsValues &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
 
void computeMeanStacc (const SsOptionsValues &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
 
void computeMeanVars (const SequenceStatisticalOptions &statisticalOptions, std::ofstream *passedOfs, V *subMeanPtr, V *subMedianPtr, V *subSampleVarPtr, V *subPopulVarPtr)
 
void computeAutoCorrViaDef (const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, const std::vector< unsigned int > &lagsForCorrs, std::ofstream *passedOfs)
 
void computeAutoCorrViaFFT (const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, const std::vector< unsigned int > &lagsForCorrs, std::ofstream *passedOfs)
 
void computeCovCorrMatrices (const SequenceStatisticalOptions &statisticalOptions, std::ofstream *passedOfs)
 
void computeMeanVars (const SsOptionsValues &statisticalOptions, std::ofstream *passedOfs, V *subMeanPtr, V *subMedianPtr, V *subSampleVarPtr, V *subPopulVarPtr)
 
void computeAutoCorrViaDef (const SsOptionsValues &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, const std::vector< unsigned int > &lagsForCorrs, std::ofstream *passedOfs)
 
void computeAutoCorrViaFFT (const SsOptionsValues &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, const std::vector< unsigned int > &lagsForCorrs, std::ofstream *passedOfs)
 
void computeCovCorrMatrices (const SsOptionsValues &statisticalOptions, std::ofstream *passedOfs)
 

Protected Attributes

const BaseEnvironment & m_env
 
const VectorSpace< V, M > & m_vectorSpace
 
std::string m_name
 
Fft< double > * m_fftObj
 
V * m_subMinPlain
 
V * m_unifiedMinPlain
 
V * m_subMaxPlain
 
V * m_unifiedMaxPlain
 
V * m_subMeanPlain
 
V * m_unifiedMeanPlain
 
V * m_subMedianPlain
 
V * m_unifiedMedianPlain
 
V * m_subSampleVariancePlain
 
V * m_unifiedSampleVariancePlain
 
BoxSubset< V, M > * m_subBoxPlain
 
BoxSubset< V, M > * m_unifiedBoxPlain
 

Detailed Description

template<class V = GslVector, class M = GslMatrix>
class QUESO::BaseVectorSequence< V, M >

Base class for handling vector and array samples (sequence of vectors or arrays).

This class handles either vector or array samples generated by an algorithm, as well as operations that can be carried over them, e.g., calculation of means, correlation and covariance matrices.

Definition at line 56 of file VectorSequence.h.

Constructor & Destructor Documentation

template<class V, class M>
QUESO::BaseVectorSequence< V, M >::BaseVectorSequence ( const VectorSpace< V, M > &  vectorSpace,
unsigned int  subSequenceSize,
const std::string &  name 
)

Default constructor.

Definition at line 34 of file VectorSequence.C.

38  :
39  m_env (vectorSpace.env()),
40  m_vectorSpace (vectorSpace),
41  m_name (name),
42  m_fftObj (new Fft<double>(m_env)),
43  m_subMinPlain (NULL),
44  m_unifiedMinPlain (NULL),
45  m_subMaxPlain (NULL),
46  m_unifiedMaxPlain (NULL),
47  m_subMeanPlain (NULL),
48  m_unifiedMeanPlain (NULL),
49  m_subMedianPlain (NULL),
50  m_unifiedMedianPlain (NULL),
51  m_subSampleVariancePlain (NULL),
52  m_unifiedSampleVariancePlain(NULL),
53  m_subBoxPlain (NULL),
54  m_unifiedBoxPlain (NULL)
55 {
56  if (subSequenceSize) {}; // just to avoid compiler warning
57 }
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
QUESO::BaseVectorSequence::m_unifiedBoxPlain
BoxSubset< V, M > * m_unifiedBoxPlain
Definition: VectorSequence.h:447
QUESO::BaseVectorSequence::name
const std::string & name() const
Access to protected attribute m_name: name of the sequence of vectors.
Definition: VectorSequence.C:118
QUESO::BaseVectorSequence::m_subBoxPlain
BoxSubset< V, M > * m_subBoxPlain
Definition: VectorSequence.h:446
QUESO::BaseVectorSequence::vectorSpace
const VectorSpace< V, M > & vectorSpace() const
Vector space; access to protected attribute VectorSpace&lt;V,M&gt;&amp; m_vectorSpace.
Definition: VectorSequence.C:111
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:431
template<class V , class M >
QUESO::BaseVectorSequence< V, M >::~BaseVectorSequence ( )
virtual

Destructor.

Definition at line 60 of file VectorSequence.C.

61 {
62  //clear();
63  this->deleteStoredVectors();
64  if (m_fftObj != NULL) delete m_fftObj;
65 }
QUESO::BaseVectorSequence::deleteStoredVectors
void deleteStoredVectors()
Deletes all the stored vectors.
Definition: VectorSequence.C:298

Member Function Documentation

template<class V, class M>
void QUESO::BaseVectorSequence< V, M >::append ( const BaseVectorSequence< V, M > &  src,
unsigned int  initialPos,
unsigned int  numPos 
)

Appends the vector src to this vector.

This routine deletes all stored computed vectors

Definition at line 354 of file VectorSequence.C.

References QUESO::BaseVectorSequence< V, M >::getPositionValues(), QUESO::BaseVectorSequence< V, M >::subSequenceSize(), and QUESO::BaseVectorSequence< V, M >::vectorSpace().

Referenced by QUESO::MLSampling< P_V, P_M >::generateBalLinkedChains_all(), and QUESO::MLSampling< P_V, P_M >::generateUnbLinkedChains_all().

358 {
359  queso_require_greater_equal_msg(src.subSequenceSize(), (initialPos+1), "initialPos is too big");
360 
361  queso_require_greater_equal_msg(src.subSequenceSize(), (initialPos+numPos), "numPos is too big");
362 
363  this->deleteStoredVectors();
364  unsigned int currentSize = this->subSequenceSize();
365  this->resizeSequence(currentSize+numPos);
366  V tmpVec(src.vectorSpace().zeroVector());
367  for (unsigned int i = 0; i < numPos; ++i) {
368  src.getPositionValues(initialPos+i,tmpVec);
369  this->setPositionValues(currentSize+i,tmpVec);
370  }
371 
372  return;
373 }
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::BaseVectorSequence::deleteStoredVectors
void deleteStoredVectors()
Deletes all the stored vectors.
Definition: VectorSequence.C:298
QUESO::BaseVectorSequence::resizeSequence
virtual void resizeSequence(unsigned int newSubSequenceSize)=0
Resize the sequence. See template specialization.
QUESO::BaseVectorSequence::setPositionValues
virtual void setPositionValues(unsigned int posId, const V &vec)=0
Set the values in vec at position posId of the sequence. See template specialization.
template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::autoCorrViaDef ( unsigned int  initialPos,
unsigned int  numPos,
unsigned int  lag,
V &  corrVec 
) const
pure virtual

Calculates autocorrelation via definition. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >, and QUESO::ArrayOfSequences< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::autoCorrViaFft ( unsigned int  initialPos,
unsigned int  numPos,
const std::vector< unsigned int > &  lags,
std::vector< V * > &  corrVecs 
) const
pure virtual

Calculates autocorrelation via Fast Fourier transforms (FFT). See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >, and QUESO::ArrayOfSequences< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::autoCorrViaFft ( unsigned int  initialPos,
unsigned int  numPos,
unsigned int  numSum,
V &  autoCorrsSumVec 
) const
pure virtual

Calculates autocorrelation via Fast Fourier transforms (FFT). See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >, and QUESO::ArrayOfSequences< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::autoCovariance ( unsigned int  initialPos,
unsigned int  numPos,
const V &  meanVec,
unsigned int  lag,
V &  covVec 
) const
pure virtual

Calculates the autocovariance. See template specialization.

The autocovariance is the covariance of a variable with itself at some other time. It is calculated over a sequence of vectors with initial position initialPos, considering numPos positions, a lag of lag, with mean given by meanVec. The results are saved in the output vector covVec/

Implemented in QUESO::SequenceOfVectors< V, M >, and QUESO::ArrayOfSequences< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::bmm ( unsigned int  initialPos,
unsigned int  batchLength,
V &  bmmVec 
) const
pure virtual

Implemented in QUESO::SequenceOfVectors< V, M >, and QUESO::ArrayOfSequences< V, M >.

template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::clear ( )

Reset the values and the size of the sequence of vectors.

Definition at line 133 of file VectorSequence.C.

Referenced by QUESO::MLSampling< P_V, P_M >::generateSequence(), and QUESO::MLSampling< P_V, P_M >::generateSequence_Step02_inter0().

134 {
135  unsigned int numPos = this->subSequenceSize();
136  if (numPos) {
137  this->resetValues(0,numPos);
138  this->resizeSequence(0);
139  }
140 
141  return;
142 }
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::BaseVectorSequence::resetValues
virtual void resetValues(unsigned int initialPos, unsigned int numPos)=0
Reset the values of the sequence. See template specialization.
QUESO::BaseVectorSequence::resizeSequence
virtual void resizeSequence(unsigned int newSubSequenceSize)=0
Resize the sequence. See template specialization.
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computeAutoCorrViaDef ( const SequenceStatisticalOptions &  statisticalOptions,
const std::vector< unsigned int > &  initialPosForStatistics,
const std::vector< unsigned int > &  lagsForCorrs,
std::ofstream *  passedOfs 
)
protected

Definition at line 1093 of file VectorSequence.C.

References SequenceStatisticalOptions::m_ov.

1098 {
1099  queso_deprecated();
1100  computeAutoCorrViaDef(statisticalOptions.m_ov, initialPosForStatistics,
1101  lagsForCorrs, passedOfs);
1102 }
QUESO::BaseVectorSequence::computeAutoCorrViaDef
void computeAutoCorrViaDef(const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, const std::vector< unsigned int > &lagsForCorrs, std::ofstream *passedOfs)
Definition: VectorSequence.C:1093
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computeAutoCorrViaDef ( const SsOptionsValues &  statisticalOptions,
const std::vector< unsigned int > &  initialPosForStatistics,
const std::vector< unsigned int > &  lagsForCorrs,
std::ofstream *  passedOfs 
)
protected

Definition at line 1106 of file VectorSequence.C.

References QUESO::MiscGetEllapsedSeconds(), QUESO::TwoDArray< T >::setLocation(), and QUESO::UQ_OK_RC.

1111 {
1112  int iRC = UQ_OK_RC;
1113  struct timeval timevalTmp;
1114  iRC = gettimeofday(&timevalTmp, NULL);
1115  double tmpRunTime = 0.;
1116 
1117  if (m_env.subDisplayFile()) {
1118  *m_env.subDisplayFile() << "\n-----------------------------------------------------"
1119  << "\nComputing autocorrelation coefficients (via def)"
1120  << std::endl;
1121  }
1122 
1123  if (statisticalOptions.autoCorrDisplay() && (m_env.subDisplayFile())) {
1124  *m_env.subDisplayFile() << "In BaseVectorSequence<V,M>::computeAutoCorrViaDef(): lags for autocorrelation (via def) = ";
1125  for (unsigned int i = 0; i < lagsForCorrs.size(); ++i) {
1126  *m_env.subDisplayFile() << " " << lagsForCorrs[i];
1127  }
1128  *m_env.subDisplayFile() << std::endl;
1129  }
1130 
1131  TwoDArray<V> _2dArrayOfAutoCorrs(initialPosForStatistics.size(),lagsForCorrs.size());
1132  for (unsigned int i = 0; i < _2dArrayOfAutoCorrs.numRows(); ++i) {
1133  for (unsigned int j = 0; j < _2dArrayOfAutoCorrs.numCols(); ++j) {
1134  _2dArrayOfAutoCorrs.setLocation(i,j,new V(m_vectorSpace.zeroVector()) /*.*/);
1135  }
1136  }
1137  //V corrVec(m_vectorSpace.zeroVector());
1138  for (unsigned int initialPosId = 0; initialPosId < initialPosForStatistics.size(); initialPosId++) {
1139  unsigned int initialPos = initialPosForStatistics[initialPosId];
1140  for (unsigned int lagId = 0; lagId < lagsForCorrs.size(); lagId++) {
1141  unsigned int lag = lagsForCorrs[lagId];
1142  this->autoCorrViaDef(initialPos,
1143  this->subSequenceSize()-initialPos,
1144  lag,
1145  _2dArrayOfAutoCorrs(initialPosId,lagId));
1146  //_2dArrayOfAutoCorrs(initialPosId,lagId) = corrVec;
1147  }
1148  }
1149 
1150  // It is not practical to compute the variance of sample mean by computing the autocorrelations via definition for each lag
1151  // The code computes the variance of sample mean by computing the autocorrelations via fft, below, in another routine
1152 
1153  if ((statisticalOptions.autoCorrDisplay()) && (m_env.subDisplayFile())) {
1154  for (unsigned int initialPosId = 0; initialPosId < initialPosForStatistics.size(); initialPosId++) {
1155  *m_env.subDisplayFile() << "\nComputed autocorrelation coefficients (via def), for subchain beginning at position " << initialPosForStatistics[initialPosId]
1156  << " (each column corresponds to a different lag)"
1157  << std::endl;
1158  char line[512];
1159  sprintf(line,"%s",
1160  "Parameter");
1161  *m_env.subDisplayFile() << line;
1162  for (unsigned int lagId = 0; lagId < lagsForCorrs.size(); lagId++) {
1163  sprintf(line,"%10s%3d",
1164  " ",
1165  lagsForCorrs[lagId]);
1166  *m_env.subDisplayFile() << line;
1167  }
1168 
1169  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
1170  sprintf(line,"\n%9.9s",
1171  m_vectorSpace.localComponentName(i).c_str() /*.*/);
1172  *m_env.subDisplayFile() << line;
1173  for (unsigned int lagId = 0; lagId < lagsForCorrs.size(); lagId++) {
1174  sprintf(line,"%2s%11.4e",
1175  " ",
1176  _2dArrayOfAutoCorrs(initialPosId,lagId)[i]);
1177  *m_env.subDisplayFile() << line;
1178  }
1179  }
1180  *m_env.subDisplayFile() << std::endl;
1181  }
1182  }
1183 
1184  tmpRunTime += MiscGetEllapsedSeconds(&timevalTmp);
1185  if (m_env.subDisplayFile()) {
1186  *m_env.subDisplayFile() << "Chain autocorrelation (via def) took " << tmpRunTime
1187  << " seconds"
1188  << std::endl;
1189  }
1190 
1191  // Write autocorrelations
1192  if (statisticalOptions.autoCorrWrite() && passedOfs) {
1193  std::ofstream& ofsvar = *passedOfs;
1194  ofsvar << m_name << "_corrViaDefLags_sub" << m_env.subIdString() << " = zeros(" << 1
1195  << "," << lagsForCorrs.size()
1196  << ");"
1197  << std::endl;
1198  for (unsigned int lagId = 0; lagId < lagsForCorrs.size(); lagId++) {
1199  ofsvar << m_name << "_corrViaDefLags_sub" << m_env.subIdString() << "(" << 1
1200  << "," << lagId+1
1201  << ") = " << lagsForCorrs[lagId]
1202  << ";"
1203  << std::endl;
1204  }
1205 
1206  for (unsigned int initialPosId = 0; initialPosId < initialPosForStatistics.size(); initialPosId++) {
1207  ofsvar << m_name << "_corrViaDefInitPos" << initialPosForStatistics[initialPosId] << "_sub" << m_env.subIdString() << " = zeros(" << this->vectorSizeLocal() /*.*/
1208  << "," << lagsForCorrs.size()
1209  << ");"
1210  << std::endl;
1211  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
1212  for (unsigned int lagId = 0; lagId < lagsForCorrs.size(); lagId++) {
1213  ofsvar << m_name << "_corrViaDefInitPos" << initialPosForStatistics[initialPosId] << "_sub" << m_env.subIdString() << "(" << i+1
1214  << "," << lagId+1
1215  << ") = " << _2dArrayOfAutoCorrs(initialPosId,lagId)[i]
1216  << ";"
1217  << std::endl;
1218  }
1219  }
1220  }
1221  }
1222 
1223  return;
1224 }
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::UQ_OK_RC
const int UQ_OK_RC
Definition: Defines.h:92
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
QUESO::BaseVectorSequence::autoCorrViaDef
virtual void autoCorrViaDef(unsigned int initialPos, unsigned int numPos, unsigned int lag, V &corrVec) const =0
Calculates autocorrelation via definition. See template specialization.
QUESO::BaseEnvironment::subIdString
const std::string & subIdString() const
Access to the attribute m_subIdString; which stores the string for the sub-environment, and it will be used, for instance, to create the output files for each sub-environment.
Definition: Environment.C:348
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:97
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:431
QUESO::MiscGetEllapsedSeconds
double MiscGetEllapsedSeconds(struct timeval *timeval0)
Definition: Miscellaneous.C:282
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:320
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computeAutoCorrViaFFT ( const SequenceStatisticalOptions &  statisticalOptions,
const std::vector< unsigned int > &  initialPosForStatistics,
const std::vector< unsigned int > &  lagsForCorrs,
std::ofstream *  passedOfs 
)
protected

Definition at line 1228 of file VectorSequence.C.

References SequenceStatisticalOptions::m_ov.

1233 {
1234  queso_deprecated();
1235  computeAutoCorrViaFFT(statisticalOptions.m_ov, initialPosForStatistics,
1236  lagsForCorrs, passedOfs);
1237 }
QUESO::BaseVectorSequence::computeAutoCorrViaFFT
void computeAutoCorrViaFFT(const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, const std::vector< unsigned int > &lagsForCorrs, std::ofstream *passedOfs)
Definition: VectorSequence.C:1228
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computeAutoCorrViaFFT ( const SsOptionsValues &  statisticalOptions,
const std::vector< unsigned int > &  initialPosForStatistics,
const std::vector< unsigned int > &  lagsForCorrs,
std::ofstream *  passedOfs 
)
protected

Definition at line 1241 of file VectorSequence.C.

References QUESO::MiscGetEllapsedSeconds(), QUESO::TwoDArray< T >::setLocation(), and QUESO::UQ_OK_RC.

1246 {
1247  int iRC = UQ_OK_RC;
1248  struct timeval timevalTmp;
1249  iRC = gettimeofday(&timevalTmp, NULL);
1250  double tmpRunTime = 0.;
1251 
1252  if (m_env.subDisplayFile()) {
1253  *m_env.subDisplayFile() << "\n-----------------------------------------------------"
1254  << "\nComputing autocorrelation coefficients (via fft)"
1255  << std::endl;
1256  }
1257 
1258  if (statisticalOptions.autoCorrDisplay() && (m_env.subDisplayFile())) {
1259  *m_env.subDisplayFile() << "In BaseVectorSequence<V,M>::computeAutoCorrViaFFT(): lags for autocorrelation (via fft) = ";
1260  for (unsigned int i = 0; i < lagsForCorrs.size(); ++i) {
1261  *m_env.subDisplayFile() << " " << lagsForCorrs[i];
1262  }
1263  *m_env.subDisplayFile() << std::endl;
1264  }
1265 
1266  TwoDArray<V> _2dArrayOfAutoCorrs(initialPosForStatistics.size(),lagsForCorrs.size());
1267  for (unsigned int i = 0; i < _2dArrayOfAutoCorrs.numRows(); ++i) {
1268  for (unsigned int j = 0; j < _2dArrayOfAutoCorrs.numCols(); ++j) {
1269  _2dArrayOfAutoCorrs.setLocation(i,j,new V(m_vectorSpace.zeroVector()) /*.*/);
1270  }
1271  }
1272  std::vector<V*> corrVecs(lagsForCorrs.size(),NULL);
1273  std::vector<V*> corrSumVecs(initialPosForStatistics.size(),NULL);
1274  for (unsigned int initialPosId = 0; initialPosId < initialPosForStatistics.size(); initialPosId++) {
1275  corrSumVecs[initialPosId] = new V(m_vectorSpace.zeroVector()) /*.*/;
1276  unsigned int initialPos = initialPosForStatistics[initialPosId];
1277  for (unsigned int lagId = 0; lagId < lagsForCorrs.size(); lagId++) {
1278  corrVecs[lagId] = new V(m_vectorSpace.zeroVector()) /*.*/;
1279  }
1280  if (m_env.subDisplayFile()) {
1281  *m_env.subDisplayFile() << "In BaseVectorSequence<V,M>::computeAutoCorrViaFFT()"
1282  << ": about to call chain.autoCorrViaFft()"
1283  << " with initialPos = " << initialPos
1284  << ", numPos = " << this->subSequenceSize()-initialPos
1285  << ", lagsForCorrs.size() = " << lagsForCorrs.size()
1286  << ", corrVecs.size() = " << corrVecs.size()
1287  << std::endl;
1288  }
1289  this->autoCorrViaFft(initialPos,
1290  this->subSequenceSize()-initialPos, // Use all possible data positions
1291  lagsForCorrs,
1292  corrVecs);
1293  this->autoCorrViaFft(initialPos,
1294  this->subSequenceSize()-initialPos, // Use all possible data positions
1295  (unsigned int) (1.0 * (double) (this->subSequenceSize()-initialPos)), // CHECK
1296  *corrSumVecs[initialPosId]); // Sum of all possibly computable autocorrelations, not only the asked ones in lagsForCorrs
1297  for (unsigned int lagId = 0; lagId < lagsForCorrs.size(); lagId++) {
1298  _2dArrayOfAutoCorrs(initialPosId,lagId) = *(corrVecs[lagId]);
1299  }
1300  }
1301  for (unsigned int j = 0; j < corrVecs.size(); ++j) {
1302  if (corrVecs[j] != NULL) delete corrVecs[j];
1303  }
1304 
1305  if (statisticalOptions.autoCorrDisplay()) {
1306  V subChainMean (m_vectorSpace.zeroVector());
1307  V subChainSampleVariance (m_vectorSpace.zeroVector());
1308  V estimatedVarianceOfSampleMean(m_vectorSpace.zeroVector());
1309  for (unsigned int initialPosId = 0; initialPosId < initialPosForStatistics.size(); initialPosId++) {
1310  unsigned int initialPos = initialPosForStatistics[initialPosId];
1311 
1312  this->subMeanExtra(initialPos,
1313  this->subSequenceSize()-initialPos,
1314  subChainMean);
1315 
1316  this->subSampleVarianceExtra(initialPos,
1317  this->subSequenceSize()-initialPos,
1318  subChainMean,
1319  subChainSampleVariance);
1320 
1321  if (m_env.subDisplayFile()) {
1322  *m_env.subDisplayFile() << "\nEstimated variance of sample mean, through autocorrelation (via fft), for subchain beginning at position " << initialPosForStatistics[initialPosId]
1323  << std::endl;
1324  }
1325  estimatedVarianceOfSampleMean.cwSet(-1.); // Yes, '-1' because the autocorrelation at lag 0, which values '+1', is already counted in the sum
1326  estimatedVarianceOfSampleMean += 2.* (*corrSumVecs[initialPosId]);
1327  estimatedVarianceOfSampleMean *= subChainSampleVariance;
1328  estimatedVarianceOfSampleMean /= (double) (this->subSequenceSize() - initialPos);
1329  bool savedVectorPrintState = estimatedVarianceOfSampleMean.getPrintHorizontally();
1330  estimatedVarianceOfSampleMean.setPrintHorizontally(false);
1331  if (m_env.subDisplayFile()) {
1332  *m_env.subDisplayFile() << estimatedVarianceOfSampleMean
1333  << std::endl;
1334  }
1335  estimatedVarianceOfSampleMean.setPrintHorizontally(savedVectorPrintState);
1336 
1337  if (m_env.subDisplayFile()) {
1338  *m_env.subDisplayFile() << "\nComputed autocorrelation coefficients (via fft), for subchain beginning at position " << initialPosForStatistics[initialPosId]
1339  << " (each column corresponds to a different lag)"
1340  << std::endl;
1341 
1342  char line[512];
1343  sprintf(line,"%s",
1344  "Parameter");
1345  *m_env.subDisplayFile() << line;
1346  for (unsigned int lagId = 0; lagId < lagsForCorrs.size(); lagId++) {
1347  sprintf(line,"%10s%3d",
1348  " ",
1349  lagsForCorrs[lagId]);
1350  *m_env.subDisplayFile() << line;
1351  }
1352 
1353  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
1354  sprintf(line,"\n%9.9s",
1355  m_vectorSpace.localComponentName(i).c_str() /*.*/);
1356  *m_env.subDisplayFile() << line;
1357  for (unsigned int lagId = 0; lagId < lagsForCorrs.size(); lagId++) {
1358  sprintf(line,"%2s%11.4e",
1359  " ",
1360  _2dArrayOfAutoCorrs(initialPosId,lagId)[i]);
1361  *m_env.subDisplayFile() << line;
1362  }
1363  }
1364  *m_env.subDisplayFile() << std::endl;
1365  }
1366  }
1367  }
1368 
1369  tmpRunTime += MiscGetEllapsedSeconds(&timevalTmp);
1370  if (m_env.subDisplayFile()) {
1371  *m_env.subDisplayFile() << "Chain autocorrelation (via fft) took " << tmpRunTime
1372  << " seconds"
1373  << std::endl;
1374  }
1375 
1376  // Write autocorrelations
1377  if (statisticalOptions.autoCorrWrite() && passedOfs) {
1378  std::ofstream& ofsvar = *passedOfs;
1379  ofsvar << m_name << "_corrViaFftLags_sub" << m_env.subIdString() << " = zeros(" << 1
1380  << "," << lagsForCorrs.size()
1381  << ");"
1382  << std::endl;
1383  for (unsigned int lagId = 0; lagId < lagsForCorrs.size(); lagId++) {
1384  ofsvar << m_name << "_corrViaFftLags_sub" << m_env.subIdString() << "(" << 1
1385  << "," << lagId+1
1386  << ") = " << lagsForCorrs[lagId]
1387  << ";"
1388  << std::endl;
1389  }
1390 
1391  for (unsigned int initialPosId = 0; initialPosId < initialPosForStatistics.size(); initialPosId++) {
1392  ofsvar << m_name << "_corrViaFftInitPos" << initialPosForStatistics[initialPosId] << "_sub" << m_env.subIdString() << " = zeros(" << this->vectorSizeLocal() /*.*/
1393  << "," << lagsForCorrs.size()
1394  << ");"
1395  << std::endl;
1396  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
1397  for (unsigned int lagId = 0; lagId < lagsForCorrs.size(); lagId++) {
1398  ofsvar << m_name << "_corrViaFftInitPos" << initialPosForStatistics[initialPosId] << "_sub" << m_env.subIdString() << "(" << i+1
1399  << "," << lagId+1
1400  << ") = " << _2dArrayOfAutoCorrs(initialPosId,lagId)[i]
1401  << ";"
1402  << std::endl;
1403  }
1404  }
1405  }
1406  }
1407 
1408  return;
1409 }
QUESO::BaseVectorSequence::subMeanExtra
virtual void subMeanExtra(unsigned int initialPos, unsigned int numPos, V &meanVec) const =0
Finds the mean value of the sub-sequence, considering numPos positions starting at position initialPo...
QUESO::BaseVectorSequence::autoCorrViaFft
virtual void autoCorrViaFft(unsigned int initialPos, unsigned int numPos, const std::vector< unsigned int > &lags, std::vector< V * > &corrVecs) const =0
Calculates autocorrelation via Fast Fourier transforms (FFT). See template specialization.
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::UQ_OK_RC
const int UQ_OK_RC
Definition: Defines.h:92
QUESO::BaseVectorSequence::subSampleVarianceExtra
virtual void subSampleVarianceExtra(unsigned int initialPos, unsigned int numPos, const V &meanVec, V &samVec) const =0
Finds the sample variance of the sub-sequence, considering numPos positions starting at position init...
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
QUESO::BaseEnvironment::subIdString
const std::string & subIdString() const
Access to the attribute m_subIdString; which stores the string for the sub-environment, and it will be used, for instance, to create the output files for each sub-environment.
Definition: Environment.C:348
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:97
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:431
QUESO::MiscGetEllapsedSeconds
double MiscGetEllapsedSeconds(struct timeval *timeval0)
Definition: Miscellaneous.C:282
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:320
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computeBMM ( const SequenceStatisticalOptions &  statisticalOptions,
const std::vector< unsigned int > &  initialPosForStatistics,
std::ofstream *  passedOfs 
)
protected

Definition at line 2203 of file VectorSequence.C.

References SequenceStatisticalOptions::m_ov.

2207 {
2208  queso_deprecated();
2209  computeMeanStacc(statisticalOptions.m_ov, initialPosForStatistics, passedOfs);
2210 }
QUESO::BaseVectorSequence::computeMeanStacc
void computeMeanStacc(const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
Definition: VectorSequence.C:2691
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computeBMM ( const SsOptionsValues &  statisticalOptions,
const std::vector< unsigned int > &  initialPosForStatistics,
std::ofstream *  passedOfs 
)
protected

Definition at line 2311 of file VectorSequence.C.

References QUESO::Fft< T >::inverse(), QUESO::MiscGetEllapsedSeconds(), and QUESO::UQ_OK_RC.

2315 {
2316  int iRC = UQ_OK_RC;
2317  struct timeval timevalTmp;
2318  iRC = gettimeofday(&timevalTmp, NULL);
2319  double tmpRunTime = 0.;
2320 
2321  if (m_env.subDisplayFile()) {
2322  *m_env.subDisplayFile() << "\n-----------------------------------------------------"
2323  << "\nComputing FFT of chain on parameter of id = " << statisticalOptions.fftParamId()
2324  << std::endl;
2325  }
2326 
2327  std::vector<std::complex<double> > forwardResult(0,std::complex<double>(0.,0.));
2328  std::vector<std::complex<double> > inverseResult(0,std::complex<double>(0.,0.));
2329  Fft<std::complex<double> > fftObj(m_env);
2330  for (unsigned int initialPosId = 0; initialPosId < initialPosForStatistics.size(); initialPosId++) {
2331  unsigned int initialPosition = initialPosForStatistics[initialPosId];
2332  this->fftForward(initialPosition,
2333  statisticalOptions.fftSize(),
2334  statisticalOptions.fftParamId(),
2335  forwardResult);
2336 
2337  if (statisticalOptions.fftWrite() && passedOfs) {
2338  std::ofstream& ofsvar = *passedOfs;
2339  ofsvar << m_name << "_fftInitPos" << initialPosForStatistics[initialPosId] << "_sub" << m_env.subIdString() << " = zeros(" << 1
2340  << "," << forwardResult.size()
2341  << ");"
2342  << std::endl;
2343  for (unsigned int j = 0; j < forwardResult.size(); ++j) {
2344  ofsvar << m_name << "_fftInitPos" << initialPosForStatistics[initialPosId] << "_sub" << m_env.subIdString() << "(" << 1
2345  << "," << j+1
2346  << ") = " << forwardResult[j].real()
2347  << " + i*" << forwardResult[j].imag()
2348  << ";"
2349  << std::endl;
2350  }
2351  } // if write
2352 
2353  if (statisticalOptions.fftTestInversion()) {
2354  fftObj.inverse(forwardResult,
2355  statisticalOptions.fftSize(),
2356  inverseResult);
2357  if (statisticalOptions.fftWrite() && passedOfs) {
2358  std::ofstream& ofsvar = *passedOfs;
2359  ofsvar << m_name << "_iftInitPos" << initialPosForStatistics[initialPosId] << "_sub" << m_env.subIdString() << " = zeros(" << 1
2360  << "," << inverseResult.size()
2361  << ");"
2362  << std::endl;
2363  for (unsigned int j = 0; j < inverseResult.size(); ++j) {
2364  ofsvar << m_name << "_iftInitPos" << initialPosForStatistics[initialPosId] << "_sub" << m_env.subIdString() << "(" << 1
2365  << "," << j+1
2366  << ") = " << inverseResult[j].real()
2367  << " + i*" << inverseResult[j].imag()
2368  << ";"
2369  << std::endl;
2370  }
2371  } // if write
2372  }
2373  } // for initialPosId
2374 
2375  tmpRunTime += MiscGetEllapsedSeconds(&timevalTmp);
2376  if (m_env.subDisplayFile()) {
2377  *m_env.subDisplayFile() << "Chain FFT took " << tmpRunTime
2378  << " seconds"
2379  << std::endl;
2380  }
2381 
2382  return;
2383 }
QUESO::BaseVectorSequence::fftForward
virtual void fftForward(unsigned int initialPos, unsigned int fftSize, unsigned int paramId, std::vector< std::complex< double > > &fftResult) const =0
QUESO::UQ_OK_RC
const int UQ_OK_RC
Definition: Defines.h:92
QUESO::BaseEnvironment::subIdString
const std::string & subIdString() const
Access to the attribute m_subIdString; which stores the string for the sub-environment, and it will be used, for instance, to create the output files for each sub-environment.
Definition: Environment.C:348
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:431
QUESO::MiscGetEllapsedSeconds
double MiscGetEllapsedSeconds(struct timeval *timeval0)
Definition: Miscellaneous.C:282
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:320
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computeCovCorrMatrices ( const SequenceStatisticalOptions &  statisticalOptions,
std::ofstream *  passedOfs 
)
protected

Definition at line 2000 of file VectorSequence.C.

References SequenceStatisticalOptions::m_ov.

2003 {
2004  queso_deprecated();
2005  computeCovCorrMatrices(statisticalOptions.m_ov, passedOfs);
2006 }
QUESO::BaseVectorSequence::computeCovCorrMatrices
void computeCovCorrMatrices(const SequenceStatisticalOptions &statisticalOptions, std::ofstream *passedOfs)
Definition: VectorSequence.C:2000
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computeCovCorrMatrices ( const SsOptionsValues &  statisticalOptions,
std::ofstream *  passedOfs 
)
protected

Definition at line 2010 of file VectorSequence.C.

References QUESO::ComputeCovCorrMatricesBetweenVectorSequences().

2013 {
2014  if (m_env.subDisplayFile()) {
2015  *m_env.subDisplayFile() << "\n"
2016  << "\n-----------------------------------------------------"
2017  << "\n Computing covariance and correlation matrices for chain '" << m_name << "' ..."
2018  << "\n-----------------------------------------------------"
2019  << "\n"
2020  << std::endl;
2021  }
2022 
2023  //int iRC = UQ_OK_RC;
2024  //struct timeval timevalTmp;
2025  M* covarianceMatrix = new M(m_env,
2026  m_vectorSpace.map(), // number of rows
2027  m_vectorSpace.dimGlobal()); // number of cols
2028  M* correlationMatrix = new M(m_env,
2029  m_vectorSpace.map(), // number of rows
2030  m_vectorSpace.dimGlobal()); // number of cols
2031 
2032  ComputeCovCorrMatricesBetweenVectorSequences(*this,
2033  *this,
2034  this->subSequenceSize(),
2035  *covarianceMatrix,
2036  *correlationMatrix);
2037 
2038  if (m_env.subDisplayFile()) {
2039  if (m_vectorSpace.numOfProcsForStorage() == 1) {
2040  // Only unified covariance matrix is written. And only one processor writes it.
2041  if (m_env.inter0Rank() == 0) {
2042  *m_env.subDisplayFile() << "\nBaseVectorSequence<V,M>::computeCovCorrMatrices"
2043  << ", chain " << m_name
2044  << ": contents of covariance matrix are\n" << *covarianceMatrix
2045  << std::endl;
2046 
2047  *m_env.subDisplayFile() << "\nBaseVectorSequence<V,M>::computeCovCorrMatrices"
2048  << ", chain " << m_name
2049  << ": contents of correlation matrix are\n" << *correlationMatrix
2050  << std::endl;
2051  }
2052  }
2053  else {
2054  queso_error_msg("parallel vectors not supported yet");
2055  }
2056  }
2057 
2058  delete correlationMatrix;
2059  delete covarianceMatrix;
2060 
2061  if (m_env.subDisplayFile()) {
2062  *m_env.subDisplayFile() << "\n-----------------------------------------------------"
2063  << "\n Finished computing covariance and correlation matrices for chain '" << m_name << "'"
2064  << "\n-----------------------------------------------------"
2065  << "\n"
2066  << std::endl;
2067  }
2068 
2069  return;
2070 }
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:431
QUESO::BaseEnvironment::inter0Rank
int inter0Rank() const
Returns the process inter0 rank.
Definition: Environment.C:307
QUESO::ComputeCovCorrMatricesBetweenVectorSequences
void ComputeCovCorrMatricesBetweenVectorSequences(const BaseVectorSequence< P_V, P_M > &subPSeq, const BaseVectorSequence< Q_V, Q_M > &subQSeq, unsigned int subNumSamples, P_M &pqCovMatrix, P_M &pqCorrMatrix)
Definition: VectorSequence.C:2774
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:320
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computeFFT ( const SequenceStatisticalOptions &  statisticalOptions,
const std::vector< unsigned int > &  initialPosForStatistics,
std::ofstream *  passedOfs 
)
protected

Definition at line 2300 of file VectorSequence.C.

References SequenceStatisticalOptions::m_ov.

2304 {
2305  queso_deprecated();
2306  computeBMM(statisticalOptions.m_ov, initialPosForStatistics, passedOfs);
2307 }
QUESO::BaseVectorSequence::computeBMM
void computeBMM(const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
Definition: VectorSequence.C:2203
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computeFFT ( const SsOptionsValues &  statisticalOptions,
const std::vector< unsigned int > &  initialPosForStatistics,
std::ofstream *  passedOfs 
)
protected

Definition at line 2398 of file VectorSequence.C.

References QUESO::MiscGetEllapsedSeconds(), and QUESO::UQ_OK_RC.

2402 {
2403  int iRC = UQ_OK_RC;
2404  struct timeval timevalTmp;
2405  iRC = gettimeofday(&timevalTmp, NULL);
2406  double tmpRunTime = 0.;
2407 
2408  if (m_env.subDisplayFile()) {
2409  *m_env.subDisplayFile() << "\n-----------------------------------------------------"
2410  << "\nComputing PSD of chain on parameter of id = " << statisticalOptions.psdParamId()
2411  << std::endl;
2412  }
2413 
2414  std::vector<double> psdResult(0,0.);
2415  for (unsigned int initialPosId = 0; initialPosId < initialPosForStatistics.size(); initialPosId++) {
2416  unsigned int initialPosition = initialPosForStatistics[initialPosId];
2417  this->psd(initialPosition,
2418  statisticalOptions.psdNumBlocks(),
2419  statisticalOptions.psdHopSizeRatio(),
2420  statisticalOptions.psdParamId(),
2421  psdResult);
2422 
2423  if (statisticalOptions.psdWrite() && passedOfs) {
2424  std::ofstream& ofsvar = *passedOfs;
2425  ofsvar << m_name << "_psdInitPos" << initialPosForStatistics[initialPosId] << "_sub" << m_env.subIdString() << " = zeros(" << 1
2426  << "," << psdResult.size()
2427  << ");"
2428  << std::endl;
2429  for (unsigned int j = 0; j < psdResult.size(); ++j) {
2430  ofsvar << m_name << "_psdInitPos" << initialPosForStatistics[initialPosId] << "_sub" << m_env.subIdString() << "(" << 1
2431  << "," << j+1
2432  << ") = " << psdResult[j]
2433  << ";"
2434  << std::endl;
2435  }
2436  } // if write
2437  }
2438 
2439  tmpRunTime += MiscGetEllapsedSeconds(&timevalTmp);
2440  if (m_env.subDisplayFile()) {
2441  *m_env.subDisplayFile() << "Chain PSD took " << tmpRunTime
2442  << " seconds"
2443  << std::endl;
2444  }
2445 
2446  return;
2447 }
QUESO::UQ_OK_RC
const int UQ_OK_RC
Definition: Defines.h:92
QUESO::BaseEnvironment::subIdString
const std::string & subIdString() const
Access to the attribute m_subIdString; which stores the string for the sub-environment, and it will be used, for instance, to create the output files for each sub-environment.
Definition: Environment.C:348
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:431
QUESO::BaseVectorSequence::psd
virtual void psd(unsigned int initialPos, unsigned int numBlocks, double hopSizeRatio, unsigned int paramId, std::vector< double > &psdResult) const =0
QUESO::MiscGetEllapsedSeconds
double MiscGetEllapsedSeconds(struct timeval *timeval0)
Definition: Miscellaneous.C:282
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:320
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computeFilterParams ( std::ofstream *  passedOfs,
unsigned int &  initialPos,
unsigned int &  spacing 
)

Computes the filtering parameters spacing for the sequence of vectors.

Definition at line 615 of file VectorSequence.C.

Referenced by QUESO::MLSampling< P_V, P_M >::generateSequence(), QUESO::MetropolisHastingsSG< P_V, P_M >::generateSequence(), and QUESO::MLSampling< P_V, P_M >::generateSequence_Step11_inter0().

619 {
620  if (m_env.subDisplayFile()) {
621  *m_env.subDisplayFile() << "\n"
622  << "\n-----------------------------------------------------"
623  << "\n Computing filter parameters for chain '" << m_name << "' ..."
624  << "\n-----------------------------------------------------"
625  << "\n"
626  << std::endl;
627  }
628 
629  bool okSituation = ((passedOfs == NULL ) ||
630  ((passedOfs != NULL) && (m_env.subRank() >= 0)));
631  queso_require_msg(!(!okSituation), "unexpected combination of file pointer and subRank");
632 
633  //initialPos = 0;
634  spacing = 1;
635 
636  if (m_env.subDisplayFile()) {
637  *m_env.subDisplayFile() << "\n-----------------------------------------------------"
638  << "\n Finished computing filter parameters for chain '" << m_name << "'"
639  << ": initialPos = " << initialPos
640  << ", spacing = " << spacing
641  << "\n-----------------------------------------------------"
642  << "\n"
643  << std::endl;
644  }
645 
646  return;
647 }
QUESO::BaseEnvironment::subRank
int subRank() const
Returns the rank of the MPI process in the sub-communicator subComm()
Definition: Environment.C:287
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:431
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:320
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computeGeweke ( const SequenceStatisticalOptions &  statisticalOptions,
const std::vector< unsigned int > &  initialPosForStatistics,
std::ofstream *  passedOfs 
)
protected

Definition at line 2611 of file VectorSequence.C.

References SequenceStatisticalOptions::m_ov.

2615 {
2616  queso_deprecated();
2617  computePSDAtZero(statisticalOptions.m_ov, initialPosForStatistics, passedOfs);
2618 }
QUESO::BaseVectorSequence::computePSDAtZero
void computePSDAtZero(const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
Definition: VectorSequence.C:2451
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computeGeweke ( const SsOptionsValues &  statisticalOptions,
const std::vector< unsigned int > &  initialPosForStatistics,
std::ofstream *  passedOfs 
)
protected

Definition at line 2702 of file VectorSequence.C.

References QUESO::MiscGetEllapsedSeconds(), and QUESO::UQ_OK_RC.

2706 {
2707  int iRC = UQ_OK_RC;
2708  struct timeval timevalTmp;
2709  iRC = gettimeofday(&timevalTmp, NULL);
2710  double tmpRunTime = 0.;
2711 
2712  if (m_env.subDisplayFile()) {
2713  *m_env.subDisplayFile() << "\n-----------------------------------------------------"
2714  << "\nComputing mean statistical accuracy"
2715  << std::endl;
2716  }
2717 
2718  std::vector<V*> vectorOfMeanStacc(initialPosForStatistics.size(),NULL);
2719  V meanStaccVec(m_vectorSpace.zeroVector());
2720  for (unsigned int initialPosId = 0; initialPosId < initialPosForStatistics.size(); initialPosId++) {
2721  unsigned int initialPosition = initialPosForStatistics[initialPosId];
2722  this->meanStacc(initialPosition,
2723  meanStaccVec);
2724  vectorOfMeanStacc[initialPosId] = new V(meanStaccVec);
2725  }
2726 
2727  if (m_env.subDisplayFile()) {
2728  *m_env.subDisplayFile() << "\nComputed mean statistical accuracy"
2729  << " (each column corresponds to a different initial position on the full chain)"
2730  << std::endl;
2731 
2732  char line[512];
2733  sprintf(line,"%s",
2734  "Parameter");
2735  *m_env.subDisplayFile() << line;
2736  for (unsigned int initialPosId = 0; initialPosId < initialPosForStatistics.size(); initialPosId++) {
2737  sprintf(line,"%10s%3d",
2738  " ",
2739  initialPosForStatistics[initialPosId]);
2740  *m_env.subDisplayFile() << line;
2741  }
2742 
2743  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
2744  sprintf(line,"\n%9.9s",
2745  m_vectorSpace.localComponentName(i).c_str() /*.*/);
2746  *m_env.subDisplayFile() << line;
2747  for (unsigned int initialPosId = 0; initialPosId < initialPosForStatistics.size(); initialPosId++) {
2748  sprintf(line,"%2s%11.4e",
2749  " ",
2750  (*(vectorOfMeanStacc[initialPosId]))[i]);
2751  *m_env.subDisplayFile() << line;
2752  }
2753  }
2754  *m_env.subDisplayFile() << std::endl;
2755  }
2756 
2757  tmpRunTime += MiscGetEllapsedSeconds(&timevalTmp);
2758  if (m_env.subDisplayFile()) {
2759  *m_env.subDisplayFile() << "Chain mean statistical accuracy took " << tmpRunTime
2760  << " seconds"
2761  << std::endl;
2762  }
2763 
2764  return;
2765 }
QUESO::UQ_OK_RC
const int UQ_OK_RC
Definition: Defines.h:92
QUESO::BaseVectorSequence::meanStacc
virtual void meanStacc(unsigned int initialPos, V &meanStaccVec) const =0
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:97
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:431
QUESO::MiscGetEllapsedSeconds
double MiscGetEllapsedSeconds(struct timeval *timeval0)
Definition: Miscellaneous.C:282
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:320
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computeHistCdfstaccKde ( const SequenceStatisticalOptions &  statisticalOptions,
std::ofstream *  passedOfs 
)

Definition at line 1413 of file VectorSequence.C.

References SequenceStatisticalOptions::m_ov.

1416 {
1417  queso_deprecated();
1418  computeHistCdfstaccKde(statisticalOptions.m_ov, passedOfs);
1419 }
QUESO::BaseVectorSequence::computeHistCdfstaccKde
void computeHistCdfstaccKde(const SequenceStatisticalOptions &statisticalOptions, std::ofstream *passedOfs)
Definition: VectorSequence.C:1413
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computeHistCdfstaccKde ( const SsOptionsValues &  statisticalOptions,
std::ofstream *  passedOfs 
)

Definition at line 1423 of file VectorSequence.C.

References QUESO::MiscComputePositionsBetweenMinMax(), QUESO::MiscGetEllapsedSeconds(), and QUESO::UQ_OK_RC.

1426 {
1427  if (m_env.subDisplayFile()) {
1428  *m_env.subDisplayFile() << "\n"
1429  << "\n-----------------------------------------------------"
1430  << "\n Computing histogram and/or cdf stacc and/or Kde for chain '" << m_name << "' ..."
1431  << "\n-----------------------------------------------------"
1432  << "\n"
1433  << std::endl;
1434  }
1435 
1436  int iRC = UQ_OK_RC;
1437  struct timeval timevalTmp;
1438 
1439  //****************************************************
1440  // Compute MIN and MAX: for histograms and Kde
1441  //****************************************************
1442  double tmpRunTime = 0.;
1443  iRC = gettimeofday(&timevalTmp, NULL);
1444  if (m_env.subDisplayFile()) {
1445  *m_env.subDisplayFile() << "\n-----------------------------------------------------"
1446  << "\nComputing min and max for histograms and Kde"
1447  << std::endl;
1448  }
1449 
1450  V statsMinPositions(m_vectorSpace.zeroVector());
1451  V statsMaxPositions(m_vectorSpace.zeroVector());
1452  this->subMinMaxExtra(0, // Use the whole chain
1453  this->subSequenceSize(),
1454  statsMinPositions,
1455  statsMaxPositions);
1456 
1457  if (m_env.subDisplayFile()) {
1458  *m_env.subDisplayFile() << "\nComputed min values and max values for chain '" << m_name << "'"
1459  << std::endl;
1460 
1461  char line[512];
1462  sprintf(line,"%s",
1463  "Parameter");
1464  *m_env.subDisplayFile() << line;
1465 
1466  sprintf(line,"%9s%s%9s%s",
1467  " ",
1468  "min",
1469  " ",
1470  "max");
1471  *m_env.subDisplayFile() << line;
1472 
1473  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
1474  sprintf(line,"\n%8.8s",
1475  m_vectorSpace.localComponentName(i).c_str() /*.*/);
1476  *m_env.subDisplayFile() << line;
1477 
1478  sprintf(line,"%2s%11.4e%2s%11.4e",
1479  " ",
1480  statsMinPositions[i],
1481  " ",
1482  statsMaxPositions[i]);
1483  *m_env.subDisplayFile() << line;
1484  }
1485  *m_env.subDisplayFile() << std::endl;
1486  }
1487 
1488  V unifiedStatsMinPositions(statsMinPositions);
1489  V unifiedStatsMaxPositions(statsMaxPositions);
1490  if (m_env.numSubEnvironments() > 1) {
1491  // Compute unified min-max
1492  this->unifiedMinMaxExtra(0, // Use the whole chain
1493  this->subSequenceSize(),
1494  unifiedStatsMinPositions,
1495  unifiedStatsMaxPositions);
1496 
1497  // Write unified min-max
1498  if (m_env.subDisplayFile()) {
1499  if (m_vectorSpace.numOfProcsForStorage() == 1) {
1500  if (m_env.inter0Rank() == 0) {
1501  *m_env.subDisplayFile() << "\nComputed unified min values and max values for chain '" << m_name << "'"
1502  << std::endl;
1503 
1504  char line[512];
1505  sprintf(line,"%s",
1506  "Parameter");
1507  *m_env.subDisplayFile() << line;
1508 
1509  sprintf(line,"%9s%s%9s%s",
1510  " ",
1511  "min",
1512  " ",
1513  "max");
1514  *m_env.subDisplayFile() << line;
1515 
1516  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
1517  sprintf(line,"\n%8.8s",
1518  m_vectorSpace.localComponentName(i).c_str() /*.*/);
1519  *m_env.subDisplayFile() << line;
1520 
1521  sprintf(line,"%2s%11.4e%2s%11.4e",
1522  " ",
1523  unifiedStatsMinPositions[i],
1524  " ",
1525  unifiedStatsMaxPositions[i]);
1526  *m_env.subDisplayFile() << line;
1527  }
1528  *m_env.subDisplayFile() << std::endl;
1529  }
1530  }
1531  else {
1532  queso_error_msg("unified min-max writing, parallel vectors not supported yet");
1533  }
1534  } // if subDisplayFile
1535  } // if numSubEnvs > 1
1536 
1537  //m_env.fullComm().Barrier(); // Dangerous to barrier on fullComm ...
1538  tmpRunTime += MiscGetEllapsedSeconds(&timevalTmp);
1539  if (m_env.subDisplayFile()) {
1540  *m_env.subDisplayFile() << "Chain min and max took " << tmpRunTime
1541  << " seconds"
1542  << std::endl;
1543  }
1544 
1545  //****************************************************
1546  // Compute histograms
1547  //****************************************************
1548 #ifdef QUESO_COMPUTES_EXTRA_POST_PROCESSING_STATISTICS
1549  if ((statisticalOptions.histCompute() ) &&
1550  (statisticalOptions.histNumInternalBins() > 0)) {
1551  tmpRunTime = 0.;
1552  iRC = gettimeofday(&timevalTmp, NULL);
1553  if (m_env.subDisplayFile()) {
1554  *m_env.subDisplayFile() << "\n-----------------------------------------------------"
1555  << "\nComputing histograms"
1556  << std::endl;
1557  }
1558 
1559  std::string subCoreName_HistCenters((std::string)( "_HistCenters_sub")+m_env.subIdString());
1560  std::string uniCoreName_HistCenters((std::string)("_unifHistCenters_sub")+m_env.subIdString());
1561  if (m_env.numSubEnvironments() == 1) subCoreName_HistCenters = uniCoreName_HistCenters;
1562 
1563  std::string subCoreName_HistQuantts((std::string)( "_HistQuantts_sub")+m_env.subIdString());
1564  std::string uniCoreName_HistQuantts((std::string)("_unifHistQuantts_sub")+m_env.subIdString());
1565  if (m_env.numSubEnvironments() == 1) subCoreName_HistQuantts = uniCoreName_HistQuantts;
1566 
1567  for (unsigned int i = 0; i < statsMaxPositions.sizeLocal(); ++i) {
1568  statsMaxPositions[i] *= (1. + 1.e-15);
1569  }
1570 
1571  // Compute histograms
1572  std::vector<V*> histCentersForAllBins(statisticalOptions.histNumInternalBins()+2,NULL); // IMPORTANT: +2
1573  std::vector<V*> histQuanttsForAllBins(statisticalOptions.histNumInternalBins()+2,NULL); // IMPORTANT: +2
1574  this->subHistogram(0, // Use the whole chain
1575  statsMinPositions,
1576  statsMaxPositions,
1577  histCentersForAllBins,
1578  histQuanttsForAllBins);
1579 
1580  // Write histograms
1581  if (passedOfs) {
1582  std::ofstream& ofsvar = *passedOfs;
1583  ofsvar << m_name << subCoreName_HistCenters << " = zeros(" << this->vectorSizeLocal() /*.*/
1584  << "," << histCentersForAllBins.size()
1585  << ");"
1586  << std::endl;
1587  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
1588  for (unsigned int j = 0; j < histCentersForAllBins.size(); ++j) {
1589  ofsvar << m_name << subCoreName_HistCenters << "(" << i+1
1590  << "," << j+1
1591  << ") = " << (*(histCentersForAllBins[j]))[i]
1592  << ";"
1593  << std::endl;
1594  }
1595  }
1596 
1597  ofsvar << m_name << subCoreName_HistQuantts << " = zeros(" << this->vectorSizeLocal() /*.*/
1598  << "," << histQuanttsForAllBins.size()
1599  << ");"
1600  << std::endl;
1601  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
1602  for (unsigned int j = 0; j < histQuanttsForAllBins.size(); ++j) {
1603  ofsvar << m_name << subCoreName_HistQuantts << "(" << i+1
1604  << "," << j+1
1605  << ") = " << (*(histQuanttsForAllBins[j]))[i]
1606  << ";"
1607  << std::endl;
1608  }
1609  }
1610  }
1611 
1612  for (unsigned int i = 0; i < histQuanttsForAllBins.size(); ++i) {
1613  if (histQuanttsForAllBins[i] != NULL) delete histQuanttsForAllBins[i];
1614  }
1615  for (unsigned int i = 0; i < histCentersForAllBins.size(); ++i) {
1616  if (histCentersForAllBins[i] != NULL) delete histCentersForAllBins[i];
1617  }
1618 
1619  std::vector<V*> unifiedHistCentersForAllBins(statisticalOptions.histNumInternalBins()+2,NULL); // IMPORTANT: +2
1620  std::vector<V*> unifiedHistQuanttsForAllBins(statisticalOptions.histNumInternalBins()+2,NULL); // IMPORTANT: +2
1621  if (m_env.numSubEnvironments() > 1) {
1622  // Compute unified histogram
1623  this->unifiedHistogram(0, // Use the whole chain
1624  unifiedStatsMinPositions,
1625  unifiedStatsMaxPositions,
1626  unifiedHistCentersForAllBins,
1627  unifiedHistQuanttsForAllBins);
1628 
1629  // Write unified histogram
1630  if (passedOfs) {
1631  if (m_vectorSpace.numOfProcsForStorage() == 1) {
1632  if (m_env.inter0Rank() == 0) {
1633  std::ofstream& ofsvar = *passedOfs;
1634  ofsvar << m_name << uniCoreName_HistCenters << " = zeros(" << this->vectorSizeLocal() /*.*/
1635  << "," << unifiedHistCentersForAllBins.size()
1636  << ");"
1637  << std::endl;
1638  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
1639  for (unsigned int j = 0; j < unifiedHistCentersForAllBins.size(); ++j) {
1640  ofsvar << m_name << uniCoreName_HistCenters << "(" << i+1
1641  << "," << j+1
1642  << ") = " << (*(unifiedHistCentersForAllBins[j]))[i]
1643  << ";"
1644  << std::endl;
1645  }
1646  }
1647 
1648  ofsvar << m_name << uniCoreName_HistQuantts << " = zeros(" << this->vectorSizeLocal() /*.*/
1649  << "," << unifiedHistQuanttsForAllBins.size()
1650  << ");"
1651  << std::endl;
1652  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
1653  for (unsigned int j = 0; j < unifiedHistQuanttsForAllBins.size(); ++j) {
1654  ofsvar << m_name << uniCoreName_HistQuantts << "(" << i+1
1655  << "," << j+1
1656  << ") = " << (*(unifiedHistQuanttsForAllBins[j]))[i]
1657  << ";"
1658  << std::endl;
1659  }
1660  }
1661  }
1662  }
1663  else {
1664  queso_error_msg("unified histogram writing, parallel vectors not supported yet");
1665  }
1666  } // if passedOfs
1667 
1668  for (unsigned int i = 0; i < unifiedHistQuanttsForAllBins.size(); ++i) {
1669  if (unifiedHistQuanttsForAllBins[i] != NULL) delete unifiedHistQuanttsForAllBins[i];
1670  }
1671  for (unsigned int i = 0; i < unifiedHistCentersForAllBins.size(); ++i) {
1672  if (unifiedHistCentersForAllBins[i] != NULL) delete unifiedHistCentersForAllBins[i];
1673  }
1674  } // if numSubEnvs > 1
1675 
1676  //m_env.fullComm().Barrier(); // Dangerous to barrier on fullComm ...
1677  tmpRunTime += MiscGetEllapsedSeconds(&timevalTmp);
1678  if (m_env.subDisplayFile()) {
1679  *m_env.subDisplayFile() << "Chain histograms took " << tmpRunTime
1680  << " seconds"
1681  << std::endl;
1682  }
1683  }
1684 #endif
1685 #ifdef QUESO_COMPUTES_EXTRA_POST_PROCESSING_STATISTICS
1686  //****************************************************
1687  // Compute cdf statistical accuracy
1688  //****************************************************
1689  if ((statisticalOptions.cdfStaccCompute() ) &&
1690  (statisticalOptions.cdfStaccNumEvalPositions() > 0)) {
1691  tmpRunTime = 0.;
1692  iRC = gettimeofday(&timevalTmp, NULL);
1693  if (m_env.subDisplayFile()) {
1694  *m_env.subDisplayFile() << "\n-----------------------------------------------------"
1695  << "\nComputing cdf statistical accuracy"
1696  << std::endl;
1697  }
1698 
1699  std::vector<V*> cdfStaccEvalPositions(statisticalOptions.cdfStaccNumEvalPositions(),NULL);
1700  MiscComputePositionsBetweenMinMax(statsMinPositions,
1701  statsMaxPositions,
1702  cdfStaccEvalPositions);
1703 
1704  std::vector<V*> cdfStaccValues(statisticalOptions.cdfStaccNumEvalPositions(),NULL);
1705  this->subCdfStacc(0, // Use the whole chain
1706  cdfStaccEvalPositions,
1707  cdfStaccValues);
1708 
1709  //m_env.fullComm().Barrier(); // Dangerous to barrier on fullComm ...
1710  tmpRunTime += MiscGetEllapsedSeconds(&timevalTmp);
1711  if (m_env.subDisplayFile()) {
1712  *m_env.subDisplayFile() << "Chain cdf statistical accuracy took " << tmpRunTime
1713  << " seconds"
1714  << std::endl;
1715  }
1716  }
1717 #endif
1718  //****************************************************
1719  // Compute estimations of probability densities
1720  //****************************************************
1721  if ((statisticalOptions.kdeCompute() ) &&
1722  (statisticalOptions.kdeNumEvalPositions() > 0)) {
1723  tmpRunTime = 0.;
1724  iRC = gettimeofday(&timevalTmp, NULL);
1725  if (m_env.subDisplayFile()) {
1726  *m_env.subDisplayFile() << "\n-----------------------------------------------------"
1727  << "\nComputing Kde"
1728  << std::endl;
1729  }
1730 
1731  std::string subCoreName_GaussianKdePositions((std::string)( "_GkdePosits_sub")+m_env.subIdString());
1732  std::string uniCoreName_GaussianKdePositions((std::string)("_unifGkdePosits_sub")+m_env.subIdString());
1733  if (m_env.numSubEnvironments() == 1) subCoreName_GaussianKdePositions = uniCoreName_GaussianKdePositions; // avoid temporarily (see '< -1' below)
1734 
1735  std::string subCoreName_GaussianKdeScaleVec ((std::string)( "_GkdeScalev_sub")+m_env.subIdString());
1736  std::string uniCoreName_GaussianKdeScaleVec ((std::string)("_unifGkdeScalev_sub")+m_env.subIdString());
1737  if (m_env.numSubEnvironments() == 1) subCoreName_GaussianKdeScaleVec = uniCoreName_GaussianKdeScaleVec; // avoid temporarily (see '< -1' below)
1738 
1739  std::string subCoreName_GaussianKdeValues ((std::string)( "_GkdeValues_sub")+m_env.subIdString());
1740  std::string uniCoreName_GaussianKdeValues ((std::string)("_unifGkdeValues_sub")+m_env.subIdString());
1741  if (m_env.numSubEnvironments() == 1) subCoreName_GaussianKdeValues = uniCoreName_GaussianKdeValues; // avoid temporarily (see '< -1' below)
1742 
1743  V iqrVec(m_vectorSpace.zeroVector());
1744  this->subInterQuantileRange(0, // Use the whole chain
1745  iqrVec);
1746 
1747  V gaussianKdeScaleVec(m_vectorSpace.zeroVector());
1748  this->subScalesForKde(0, // Use the whole chain
1749  iqrVec,
1750  1,
1751  gaussianKdeScaleVec);
1752 
1753  std::vector<V*> kdeEvalPositions(statisticalOptions.kdeNumEvalPositions(),NULL);
1754  MiscComputePositionsBetweenMinMax(statsMinPositions,
1755  statsMaxPositions,
1756  kdeEvalPositions);
1757 
1758  std::vector<V*> gaussianKdeDensities(statisticalOptions.kdeNumEvalPositions(),NULL);
1759  this->subGaussian1dKde(0, // Use the whole chain
1760  gaussianKdeScaleVec,
1761  kdeEvalPositions,
1762  gaussianKdeDensities);
1763 
1764  // Write iqr
1765  if (m_env.subDisplayFile()) {
1766  *m_env.subDisplayFile() << "\nComputed inter quantile ranges for chain '" << m_name << "'"
1767  << std::endl;
1768 
1769  char line[512];
1770  sprintf(line,"%s",
1771  "Parameter");
1772  *m_env.subDisplayFile() << line;
1773 
1774  sprintf(line,"%9s%s",
1775  " ",
1776  "iqr");
1777  *m_env.subDisplayFile() << line;
1778 
1779  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
1780  sprintf(line,"\n%8.8s",
1781  m_vectorSpace.localComponentName(i).c_str() /*.*/);
1782  *m_env.subDisplayFile() << line;
1783 
1784  sprintf(line,"%2s%11.4e",
1785  " ",
1786  iqrVec[i]);
1787  *m_env.subDisplayFile() << line;
1788  }
1789  *m_env.subDisplayFile() << std::endl;
1790  }
1791 
1792  // Write Kde
1793  if ((m_env.subDisplayFile()) && (m_env.displayVerbosity() > 10)) { // output debug
1794  *m_env.subDisplayFile() << "In BaseVectorSequence<V,M>::computeHistCdfstaccKde()"
1795  << ", for chain '" << m_name << "'"
1796  << ", about to write sub kde to ofstream with pointer = " << passedOfs
1797  << std::endl;
1798  }
1799  if (passedOfs) {
1800  std::ofstream& ofsvar = *passedOfs;
1801  ofsvar << m_name << subCoreName_GaussianKdePositions << " = zeros(" << this->vectorSizeLocal() /*.*/
1802  << "," << kdeEvalPositions.size()
1803  << ");"
1804  << std::endl;
1805  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
1806  for (unsigned int j = 0; j < kdeEvalPositions.size(); ++j) {
1807  ofsvar << m_name << subCoreName_GaussianKdePositions << "(" << i+1
1808  << "," << j+1
1809  << ") = " << (*(kdeEvalPositions[j]))[i]
1810  << ";"
1811  << std::endl;
1812  }
1813  }
1814 
1815  ofsvar << m_name << subCoreName_GaussianKdeScaleVec << " = zeros(" << this->vectorSizeLocal() /*.*/
1816  << ");"
1817  << std::endl;
1818  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
1819  ofsvar << m_name << subCoreName_GaussianKdeScaleVec << "(" << i+1
1820  << ") = " << gaussianKdeScaleVec[i]
1821  << ";"
1822  << std::endl;
1823  }
1824 
1825  ofsvar << m_name << subCoreName_GaussianKdeValues << " = zeros(" << this->vectorSizeLocal() /*.*/
1826  << "," << gaussianKdeDensities.size()
1827  << ");"
1828  << std::endl;
1829  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
1830  for (unsigned int j = 0; j < gaussianKdeDensities.size(); ++j) {
1831  ofsvar << m_name << subCoreName_GaussianKdeValues << "(" << i+1
1832  << "," << j+1
1833  << ") = " << (*(gaussianKdeDensities[j]))[i]
1834  << ";"
1835  << std::endl;
1836  }
1837  }
1838  }
1839 
1840  for (unsigned int i = 0; i < gaussianKdeDensities.size(); ++i) {
1841  if (gaussianKdeDensities[i] != NULL) delete gaussianKdeDensities[i];
1842  }
1843  for (unsigned int i = 0; i < kdeEvalPositions.size(); ++i) {
1844  if (kdeEvalPositions[i] != NULL) delete kdeEvalPositions[i];
1845  }
1846 
1847  if ((int) m_env.numSubEnvironments() > 1) { // avoid code temporarily
1848  // Compute unified Kde
1849  V unifiedIqrVec(m_vectorSpace.zeroVector());
1850  this->unifiedInterQuantileRange(0, // Use the whole chain
1851  unifiedIqrVec);
1852  //m_env.fullComm().Barrier(); // Dangerous to barrier on fullComm ...
1853 
1854  V unifiedGaussianKdeScaleVec(m_vectorSpace.zeroVector());
1855  this->unifiedScalesForKde(0, // Use the whole chain
1856  unifiedIqrVec,
1857  1,
1858  unifiedGaussianKdeScaleVec);
1859  //m_env.fullComm().Barrier(); // Dangerous to barrier on fullComm ...
1860 
1861  std::vector<V*> unifiedKdeEvalPositions(statisticalOptions.kdeNumEvalPositions(),NULL);
1862  MiscComputePositionsBetweenMinMax(unifiedStatsMinPositions,
1863  unifiedStatsMaxPositions,
1864  unifiedKdeEvalPositions);
1865 
1866  std::vector<V*> unifiedGaussianKdeDensities(statisticalOptions.kdeNumEvalPositions(),NULL);
1867  this->unifiedGaussian1dKde(0, // Use the whole chain
1868  unifiedGaussianKdeScaleVec,
1869  unifiedKdeEvalPositions,
1870  unifiedGaussianKdeDensities);
1871  //m_env.fullComm().Barrier(); // Dangerous to barrier on fullComm ...
1872 
1873  // Write unified iqr
1874  if (m_env.subDisplayFile()) {
1875  if (m_vectorSpace.numOfProcsForStorage() == 1) {
1876  if (m_env.inter0Rank() == 0) {
1877  *m_env.subDisplayFile() << "\nComputed unified inter quantile ranges for chain '" << m_name << "'"
1878  << std::endl;
1879 
1880  char line[512];
1881  sprintf(line,"%s",
1882  "Parameter");
1883  *m_env.subDisplayFile() << line;
1884 
1885  sprintf(line,"%9s%s",
1886  " ",
1887  "iqr");
1888  *m_env.subDisplayFile() << line;
1889 
1890  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
1891  sprintf(line,"\n%8.8s",
1892  m_vectorSpace.localComponentName(i).c_str() /*.*/);
1893  *m_env.subDisplayFile() << line;
1894 
1895  sprintf(line,"%2s%11.4e",
1896  " ",
1897  unifiedIqrVec[i]);
1898  *m_env.subDisplayFile() << line;
1899  }
1900  *m_env.subDisplayFile() << std::endl;
1901  }
1902  }
1903  else {
1904  queso_error_msg("unified iqr writing, parallel vectors not supported yet");
1905  }
1906  }
1907 
1908  // Write unified Kde
1909  if ((m_env.subDisplayFile()) && (m_env.displayVerbosity() > 10)) { // output debug
1910  *m_env.subDisplayFile() << "In BaseVectorSequence<V,M>::computeHistCdfstaccKde()"
1911  << ", for chain '" << m_name << "'"
1912  << ", about to write unified kde to ofstream with pointer = " << passedOfs
1913  << std::endl;
1914  }
1915  if (passedOfs) {
1916  if (m_vectorSpace.numOfProcsForStorage() == 1) {
1917  if (m_env.inter0Rank() == 0) {
1918  std::ofstream& ofsvar = *passedOfs;
1919  ofsvar << m_name << uniCoreName_GaussianKdePositions << " = zeros(" << this->vectorSizeLocal() /*.*/
1920  << "," << unifiedKdeEvalPositions.size()
1921  << ");"
1922  << std::endl;
1923  if ((m_env.subDisplayFile()) && (m_env.displayVerbosity() > 10)) { // output debug
1924  *m_env.subDisplayFile() << "In BaseVectorSequence<V,M>::computeHistCdfstaccKde()"
1925  << ", for chain '" << m_name << "'"
1926  << ": just wrote '... = zeros(.,.);' line to output file, which has pointer = " << passedOfs
1927  << std::endl;
1928  }
1929  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
1930  for (unsigned int j = 0; j < unifiedKdeEvalPositions.size(); ++j) {
1931  ofsvar << m_name << uniCoreName_GaussianKdePositions << "(" << i+1
1932  << "," << j+1
1933  << ") = " << (*(unifiedKdeEvalPositions[j]))[i]
1934  << ";"
1935  << std::endl;
1936  }
1937  }
1938 
1939  ofsvar << m_name << uniCoreName_GaussianKdeScaleVec << " = zeros(" << this->vectorSizeLocal() /*.*/
1940  << ");"
1941  << std::endl;
1942  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
1943  ofsvar << m_name << uniCoreName_GaussianKdeScaleVec << "(" << i+1
1944  << ") = " << unifiedGaussianKdeScaleVec[i]
1945  << ";"
1946  << std::endl;
1947  }
1948 
1949  ofsvar << m_name << uniCoreName_GaussianKdeValues << " = zeros(" << this->vectorSizeLocal() /*.*/
1950  << "," << unifiedGaussianKdeDensities.size()
1951  << ");"
1952  << std::endl;
1953  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
1954  for (unsigned int j = 0; j < unifiedGaussianKdeDensities.size(); ++j) {
1955  ofsvar << m_name << uniCoreName_GaussianKdeValues << "(" << i+1
1956  << "," << j+1
1957  << ") = " << (*(unifiedGaussianKdeDensities[j]))[i]
1958  << ";"
1959  << std::endl;
1960  }
1961  }
1962  }
1963  }
1964  else {
1965  queso_error_msg("unified Kde writing, parallel vectors not supported yet");
1966  }
1967  }
1968 
1969  for (unsigned int i = 0; i < unifiedGaussianKdeDensities.size(); ++i) {
1970  if (unifiedGaussianKdeDensities[i] != NULL) delete unifiedGaussianKdeDensities[i];
1971  }
1972  for (unsigned int i = 0; i < unifiedKdeEvalPositions.size(); ++i) {
1973  if (unifiedKdeEvalPositions[i] != NULL) delete unifiedKdeEvalPositions[i];
1974  }
1975  }
1976 
1977  //m_env.fullComm().Barrier(); // Dangerous to barrier on fullComm ...
1978  tmpRunTime += MiscGetEllapsedSeconds(&timevalTmp);
1979  if (m_env.subDisplayFile()) {
1980  *m_env.subDisplayFile() << "Chain Kde took " << tmpRunTime
1981  << " seconds"
1982  << std::endl;
1983  }
1984  }
1985 
1986  if (m_env.subDisplayFile()) {
1987  *m_env.subDisplayFile() << "\n-----------------------------------------------------"
1988  << "\n Finished computing histogram and/or cdf stacc and/or Kde for chain '" << m_name << "'"
1989  << "\n-----------------------------------------------------"
1990  << "\n"
1991  << std::endl;
1992  }
1993 
1994  return;
1995 }
QUESO::BaseVectorSequence::unifiedMinMaxExtra
virtual void unifiedMinMaxExtra(unsigned int initialPos, unsigned int numPos, V &unifiedMinVec, V &unifiedMaxVec) const =0
Finds the minimum and the maximum values of the unified sequence, considering numPos positions starti...
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::BaseVectorSequence::subMinMaxExtra
virtual void subMinMaxExtra(unsigned int initialPos, unsigned int numPos, V &minVec, V &maxVec) const =0
Finds the minimum and the maximum values of the sub-sequence, considering numPos positions starting a...
QUESO::BaseVectorSequence::subInterQuantileRange
virtual void subInterQuantileRange(unsigned int initialPos, V &iqrVec) const =0
Returns the interquartile range of the values in the sub-sequence. See template specialization.
QUESO::UQ_OK_RC
const int UQ_OK_RC
Definition: Defines.h:92
QUESO::BaseVectorSequence::unifiedScalesForKde
virtual void unifiedScalesForKde(unsigned int initialPos, const V &unifiedIqrVec, unsigned int kdeDimension, V &unifiedScaleVec) const =0
Selects the scales (bandwidth) for the kernel density estimation, considering the unified sequence...
QUESO::BaseVectorSequence::subGaussian1dKde
virtual void subGaussian1dKde(unsigned int initialPos, const V &scaleVec, const std::vector< V * > &evaluationParamVecs, std::vector< V * > &densityVecs) const =0
Gaussian kernel for the KDE estimate of the sub-sequence. See template specialization.
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
QUESO::BaseVectorSequence::unifiedInterQuantileRange
virtual void unifiedInterQuantileRange(unsigned int initialPos, V &unifiedIqrVec) const =0
Returns the interquartile range of the values in the unified sequence. See template specialization...
QUESO::MiscComputePositionsBetweenMinMax
void MiscComputePositionsBetweenMinMax(V minValues, V maxValues, std::vector< V * > &positions)
Definition: Miscellaneous.C:537
QUESO::BaseVectorSequence::unifiedHistogram
virtual void unifiedHistogram(unsigned int initialPos, const V &unifiedMinVec, const V &unifiedMaxVec, std::vector< V * > &unifiedCentersForAllBins, std::vector< V * > &unifiedQuanttsForAllBins) const =0
Calculates the histogram of the unified sequence. See template specialization.
QUESO::BaseVectorSequence::subCdfStacc
virtual void subCdfStacc(unsigned int initialPos, const std::vector< V * > &evalPositionsVecs, std::vector< V * > &cdfStaccVecs) const =0
QUESO::BaseVectorSequence::subHistogram
virtual void subHistogram(unsigned int initialPos, const V &minVec, const V &maxVec, std::vector< V * > &centersForAllBins, std::vector< V * > &quanttsForAllBins) const =0
Calculates the histogram of the sub-sequence. See template specialization.
QUESO::BaseEnvironment::displayVerbosity
unsigned int displayVerbosity() const
Definition: Environment.C:450
QUESO::BaseEnvironment::subIdString
const std::string & subIdString() const
Access to the attribute m_subIdString; which stores the string for the sub-environment, and it will be used, for instance, to create the output files for each sub-environment.
Definition: Environment.C:348
QUESO::BaseVectorSequence::subScalesForKde
virtual void subScalesForKde(unsigned int initialPos, const V &iqrVec, unsigned int kdeDimension, V &scaleVec) const =0
Selects the scales (bandwidth, scaleVec) for the kernel density estimation, considering only the sub-...
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:97
QUESO::BaseVectorSequence::unifiedGaussian1dKde
virtual void unifiedGaussian1dKde(unsigned int initialPos, const V &unifiedScaleVec, const std::vector< V * > &unifiedEvaluationParamVecs, std::vector< V * > &unifiedDensityVecs) const =0
Gaussian kernel for the KDE estimate of the unified sequence. See template specialization.
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:431
QUESO::BaseEnvironment::numSubEnvironments
unsigned int numSubEnvironments() const
Access function to the number of sub-environments.
Definition: Environment.C:335
QUESO::MiscGetEllapsedSeconds
double MiscGetEllapsedSeconds(struct timeval *timeval0)
Definition: Miscellaneous.C:282
QUESO::BaseEnvironment::inter0Rank
int inter0Rank() const
Returns the process inter0 rank.
Definition: Environment.C:307
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:320
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computeMeanEvolution ( const SequenceStatisticalOptions &  statisticalOptions,
std::ofstream *  passedOfs 
)
protected

Definition at line 2080 of file VectorSequence.C.

References SequenceStatisticalOptions::m_ov.

2083 {
2084  queso_deprecated();
2085  computeMeanEvolution(statisticalOptions.m_ov, passedOfs);
2086 }
QUESO::BaseVectorSequence::computeMeanEvolution
void computeMeanEvolution(const SequenceStatisticalOptions &statisticalOptions, std::ofstream *passedOfs)
Definition: VectorSequence.C:2080
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computeMeanEvolution ( const SsOptionsValues &  statisticalOptions,
std::ofstream *  passedOfs 
)
protected

Definition at line 2090 of file VectorSequence.C.

References QUESO::MiscGetEllapsedSeconds(), and QUESO::UQ_OK_RC.

2093 {
2094  int iRC = UQ_OK_RC;
2095  struct timeval timevalTmp;
2096  iRC = gettimeofday(&timevalTmp, NULL);
2097  double tmpRunTime = 0.;
2098 
2099  if (m_env.subDisplayFile()) {
2100  *m_env.subDisplayFile() << "\n-----------------------------------------------------"
2101  << "\nComputing mean evolution"
2102  << std::endl;
2103  }
2104 
2105  unsigned int monitorPeriod = statisticalOptions.meanMonitorPeriod();
2106  unsigned int iMin = 0;
2107  unsigned int iMax = (unsigned int) ( ((double) this->subSequenceSize())/((double) monitorPeriod) );
2108 
2109  if (monitorPeriod == 1) {
2110  iMin = 1;
2111  }
2112 
2113  if (m_env.subDisplayFile()) {
2114  *m_env.subDisplayFile() << " Sub sequence size = " << this->subSequenceSize()
2115  << "\n Monitor period = " << monitorPeriod
2116  << "\n Number of monitoring positions = " << iMax
2117  << std::endl;
2118  }
2119 
2120  this->subMeanMonitorAlloc(iMax);
2121  if (m_env.numSubEnvironments() > 1) {
2122  this->subMeanInter0MonitorAlloc(iMax);
2123  this->unifiedMeanMonitorAlloc(iMax);
2124  }
2125 
2126  for (unsigned int i = iMin; i < iMax; ++i) {
2127  unsigned int currentMonitoredFinalPosition = (i+1)*monitorPeriod - 1; // Yes, '-1'
2128  V subMeanVec (m_vectorSpace.zeroVector());
2129  V subMeanCltStd(m_vectorSpace.zeroVector());
2130  this->subMeanMonitorRun(currentMonitoredFinalPosition,
2131  subMeanVec,
2132  subMeanCltStd);
2133  this->subMeanMonitorStore(i,
2134  currentMonitoredFinalPosition,
2135  subMeanVec,
2136  subMeanCltStd);
2137 
2138  if (m_env.numSubEnvironments() > 1) {
2139  V subMeanInter0Mean (m_vectorSpace.zeroVector());
2140  V subMeanInter0Clt95 (m_vectorSpace.zeroVector());
2141  V subMeanInter0Empirical90(m_vectorSpace.zeroVector());
2142  V subMeanInter0Min (m_vectorSpace.zeroVector());
2143  V subMeanInter0Max (m_vectorSpace.zeroVector());
2144  this->subMeanInter0MonitorRun(currentMonitoredFinalPosition,
2145  subMeanInter0Mean,
2146  subMeanInter0Clt95,
2147  subMeanInter0Empirical90,
2148  subMeanInter0Min,
2149  subMeanInter0Max);
2150  this->subMeanInter0MonitorStore(i,
2151  currentMonitoredFinalPosition,
2152  subMeanInter0Mean,
2153  subMeanInter0Clt95,
2154  subMeanInter0Empirical90,
2155  subMeanInter0Min,
2156  subMeanInter0Max);
2157 
2158  V unifiedMeanVec (m_vectorSpace.zeroVector());
2159  V unifiedMeanCltStd(m_vectorSpace.zeroVector());
2160  this->unifiedMeanMonitorRun(currentMonitoredFinalPosition,
2161  unifiedMeanVec,
2162  unifiedMeanCltStd);
2163  this->unifiedMeanMonitorStore(i,
2164  currentMonitoredFinalPosition,
2165  unifiedMeanVec,
2166  unifiedMeanCltStd);
2167  }
2168  }
2169 
2170  if (passedOfs) {
2171  this->subMeanMonitorWrite(*passedOfs);
2172  if (m_env.numSubEnvironments() > 1) {
2173  this->subMeanInter0MonitorWrite(*passedOfs);
2174  this->unifiedMeanMonitorWrite(*passedOfs); // Yes, call 'unified' even though not all nodes might have 'passedOfs != NULL' ????????????? Ernesto
2175  }
2176  }
2177 
2178  this->subMeanMonitorFree();
2179  if (m_env.numSubEnvironments() > 1) {
2180  this->subMeanInter0MonitorFree();
2181  this->unifiedMeanMonitorFree();
2182  }
2183 
2184  tmpRunTime += MiscGetEllapsedSeconds(&timevalTmp);
2185  if (m_env.subDisplayFile()) {
2186  *m_env.subDisplayFile() << "Mean evolution took " << tmpRunTime
2187  << " seconds"
2188  << std::endl;
2189  }
2190 
2191  return;
2192 }
QUESO::BaseVectorSequence::subMeanMonitorWrite
virtual void subMeanMonitorWrite(std::ofstream &ofs)=0
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::BaseVectorSequence::subMeanMonitorFree
virtual void subMeanMonitorFree()=0
QUESO::BaseVectorSequence::unifiedMeanMonitorStore
virtual void unifiedMeanMonitorStore(unsigned int i, unsigned int monitorPosition, V &unifiedMeanVec, V &unifiedMeanCltStd)=0
QUESO::BaseVectorSequence::subMeanInter0MonitorStore
virtual void subMeanInter0MonitorStore(unsigned int i, unsigned int monitorPosition, const V &subMeanInter0Mean, const V &subMeanInter0Clt95, const V &subMeanInter0Empirical90, const V &subMeanInter0Min, const V &subMeanInter0Max)=0
QUESO::UQ_OK_RC
const int UQ_OK_RC
Definition: Defines.h:92
QUESO::BaseVectorSequence::unifiedMeanMonitorFree
virtual void unifiedMeanMonitorFree()=0
QUESO::BaseVectorSequence::unifiedMeanMonitorWrite
virtual void unifiedMeanMonitorWrite(std::ofstream &ofs)=0
QUESO::BaseVectorSequence::subMeanMonitorRun
virtual void subMeanMonitorRun(unsigned int monitorPosition, V &subMeanVec, V &subMeanCltStd)=0
QUESO::BaseVectorSequence::unifiedMeanMonitorAlloc
virtual void unifiedMeanMonitorAlloc(unsigned int numberOfMonitorPositions)=0
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
QUESO::BaseVectorSequence::subMeanInter0MonitorFree
virtual void subMeanInter0MonitorFree()=0
QUESO::BaseVectorSequence::subMeanInter0MonitorWrite
virtual void subMeanInter0MonitorWrite(std::ofstream &ofs)=0
QUESO::BaseVectorSequence::unifiedMeanMonitorRun
virtual void unifiedMeanMonitorRun(unsigned int monitorPosition, V &unifiedMeanVec, V &unifiedMeanCltStd)=0
QUESO::BaseVectorSequence::subMeanMonitorAlloc
virtual void subMeanMonitorAlloc(unsigned int numberOfMonitorPositions)=0
QUESO::BaseVectorSequence::subMeanInter0MonitorRun
virtual void subMeanInter0MonitorRun(unsigned int monitorPosition, V &subMeanInter0Mean, V &subMeanInter0Clt95, V &subMeanInter0Empirical90, V &subMeanInter0Min, V &subMeanInter0Max)=0
QUESO::BaseVectorSequence::subMeanMonitorStore
virtual void subMeanMonitorStore(unsigned int i, unsigned int monitorPosition, const V &subMeanVec, const V &subMeanCltStd)=0
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:431
QUESO::BaseVectorSequence::subMeanInter0MonitorAlloc
virtual void subMeanInter0MonitorAlloc(unsigned int numberOfMonitorPositions)=0
QUESO::BaseEnvironment::numSubEnvironments
unsigned int numSubEnvironments() const
Access function to the number of sub-environments.
Definition: Environment.C:335
QUESO::MiscGetEllapsedSeconds
double MiscGetEllapsedSeconds(struct timeval *timeval0)
Definition: Miscellaneous.C:282
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:320
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computeMeanStacc ( const SequenceStatisticalOptions &  statisticalOptions,
const std::vector< unsigned int > &  initialPosForStatistics,
std::ofstream *  passedOfs 
)
protected

Definition at line 2691 of file VectorSequence.C.

References SequenceStatisticalOptions::m_ov.

2695 {
2696  queso_deprecated();
2697  computeGeweke(statisticalOptions.m_ov, initialPosForStatistics, passedOfs);
2698 }
QUESO::BaseVectorSequence::computeGeweke
void computeGeweke(const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
Definition: VectorSequence.C:2611
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computeMeanStacc ( const SsOptionsValues &  statisticalOptions,
const std::vector< unsigned int > &  initialPosForStatistics,
std::ofstream *  passedOfs 
)
protected

Definition at line 2214 of file VectorSequence.C.

References QUESO::MiscGetEllapsedSeconds(), QUESO::TwoDArray< T >::setLocation(), and QUESO::UQ_OK_RC.

2218 {
2219  int iRC = UQ_OK_RC;
2220  struct timeval timevalTmp;
2221  iRC = gettimeofday(&timevalTmp, NULL);
2222  double tmpRunTime = 0.;
2223 
2224  if (m_env.subDisplayFile()) {
2225  *m_env.subDisplayFile() << "\n-----------------------------------------------------"
2226  << "\nComputing variance of sample mean through BMM"
2227  << std::endl;
2228  }
2229 
2230  if (m_env.subDisplayFile()) {
2231  *m_env.subDisplayFile() << "In BaseVectorSequence<V,M>::computeBMM(): lengths for batchs in BMM =";
2232  for (unsigned int i = 0; i < statisticalOptions.bmmLengths().size(); ++i) {
2233  *m_env.subDisplayFile() << " " << statisticalOptions.bmmLengths()[i];
2234  }
2235  *m_env.subDisplayFile() << std::endl;
2236  }
2237 
2238  TwoDArray<V> _2dArrayOfBMM(initialPosForStatistics.size(),statisticalOptions.bmmLengths().size());
2239  for (unsigned int i = 0; i < _2dArrayOfBMM.numRows(); ++i) {
2240  for (unsigned int j = 0; j < _2dArrayOfBMM.numCols(); ++j) {
2241  _2dArrayOfBMM.setLocation(i,j,new V(m_vectorSpace.zeroVector()) /*.*/);
2242  }
2243  }
2244  V bmmVec(m_vectorSpace.zeroVector());
2245  for (unsigned int initialPosId = 0; initialPosId < initialPosForStatistics.size(); initialPosId++) {
2246  unsigned int initialPos = initialPosForStatistics[initialPosId];
2247  for (unsigned int batchLengthId = 0; batchLengthId < statisticalOptions.bmmLengths().size(); batchLengthId++) {
2248  unsigned int batchLength = statisticalOptions.bmmLengths()[batchLengthId];
2249  this->bmm(initialPos,
2250  batchLength,
2251  bmmVec);
2252  _2dArrayOfBMM(initialPosId,batchLengthId) = bmmVec;
2253  }
2254  }
2255 
2256  if (m_env.subDisplayFile()) {
2257  for (unsigned int initialPosId = 0; initialPosId < initialPosForStatistics.size(); initialPosId++) {
2258  *m_env.subDisplayFile() << "\nEstimated variance of sample mean, through batch means method, for subchain beginning at position " << initialPosForStatistics[initialPosId]
2259  << " (each column corresponds to a batch length)"
2260  << std::endl;
2261 
2262  char line[512];
2263  sprintf(line,"%s",
2264  "Parameter");
2265  *m_env.subDisplayFile() << line;
2266  for (unsigned int batchLengthId = 0; batchLengthId < statisticalOptions.bmmLengths().size(); batchLengthId++) {
2267  sprintf(line,"%10s%3d",
2268  " ",
2269  statisticalOptions.bmmLengths()[batchLengthId]);
2270  *m_env.subDisplayFile() << line;
2271  }
2272 
2273  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
2274  sprintf(line,"\n%9.9s",
2275  m_vectorSpace.localComponentName(i).c_str() /*.*/);
2276  *m_env.subDisplayFile() << line;
2277  for (unsigned int batchLengthId = 0; batchLengthId < statisticalOptions.bmmLengths().size(); batchLengthId++) {
2278  sprintf(line,"%2s%11.4e",
2279  " ",
2280  _2dArrayOfBMM(initialPosId,batchLengthId)[i]);
2281  *m_env.subDisplayFile() << line;
2282  }
2283  }
2284  *m_env.subDisplayFile() << std::endl;
2285  }
2286  }
2287 
2288  tmpRunTime += MiscGetEllapsedSeconds(&timevalTmp);
2289  if (m_env.subDisplayFile()) {
2290  *m_env.subDisplayFile() << "Chain BMM took " << tmpRunTime
2291  << " seconds"
2292  << std::endl;
2293  }
2294 
2295  return;
2296 }
QUESO::UQ_OK_RC
const int UQ_OK_RC
Definition: Defines.h:92
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
QUESO::BaseVectorSequence::bmm
virtual void bmm(unsigned int initialPos, unsigned int batchLength, V &bmmVec) const =0
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:97
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:431
QUESO::MiscGetEllapsedSeconds
double MiscGetEllapsedSeconds(struct timeval *timeval0)
Definition: Miscellaneous.C:282
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:320
template<class V, class M >
void QUESO::BaseVectorSequence< V, M >::computeMeanVars ( const SequenceStatisticalOptions &  statisticalOptions,
std::ofstream *  passedOfs,
V *  subMeanPtr,
V *  subMedianPtr,
V *  subSampleVarPtr,
V *  subPopulVarPtr 
)
protected

Definition at line 882 of file VectorSequence.C.

References SequenceStatisticalOptions::m_ov.

889 {
890  queso_deprecated();
891  computeMeanVars(statisticalOptions.m_ov, passedOfs, subMeanPtr, subMedianPtr,
892  subSampleVarPtr, subPopulVarPtr);
893 }
QUESO::BaseVectorSequence::computeMeanVars
void computeMeanVars(const SequenceStatisticalOptions &statisticalOptions, std::ofstream *passedOfs, V *subMeanPtr, V *subMedianPtr, V *subSampleVarPtr, V *subPopulVarPtr)
Definition: VectorSequence.C:882
template<class V, class M >
void QUESO::BaseVectorSequence< V, M >::computeMeanVars ( const SsOptionsValues &  statisticalOptions,
std::ofstream *  passedOfs,
V *  subMeanPtr,
V *  subMedianPtr,
V *  subSampleVarPtr,
V *  subPopulVarPtr 
)
protected

Definition at line 897 of file VectorSequence.C.

References QUESO::MiscGetEllapsedSeconds(), and QUESO::UQ_OK_RC.

904 {
905  int iRC = UQ_OK_RC;
906  struct timeval timevalTmp;
907  iRC = gettimeofday(&timevalTmp, NULL);
908  double tmpRunTime = 0.;
909 
910  if (m_env.subDisplayFile()) {
911  *m_env.subDisplayFile() << "\n-----------------------------------------------------"
912  << "\nComputing mean, sample variance and population variance"
913  << std::endl;
914  }
915 
916  V subChainMean(m_vectorSpace.zeroVector());
917  this->subMeanExtra(0,
918  this->subSequenceSize(),
919  subChainMean);
920 
921  V subChainMedian(m_vectorSpace.zeroVector());
922  this->subMedianExtra(0,
923  this->subSequenceSize(),
924  subChainMedian);
925 
926  V subChainSampleVariance(m_vectorSpace.zeroVector());
927  this->subSampleVarianceExtra(0,
928  this->subSequenceSize(),
929  subChainMean,
930  subChainSampleVariance);
931 
932  if ((m_env.displayVerbosity() >= 5) && (m_env.subDisplayFile())) {
933  *m_env.subDisplayFile() << "In BaseVectorSequence<V,M>::computeMeanVars()"
934  << ": subChainMean.sizeLocal() = " << subChainMean.sizeLocal()
935  << ", subChainMean = " << subChainMean
936  << ", subChainMedian = " << subChainMedian
937  << ", subChainSampleVariance.sizeLocal() = " << subChainSampleVariance.sizeLocal()
938  << ", subChainSampleVariance = " << subChainSampleVariance
939  << std::endl;
940  }
941 
942  V estimatedVarianceOfSampleMean(subChainSampleVariance);
943  estimatedVarianceOfSampleMean /= (double) this->subSequenceSize();
944  bool savedVectorPrintState = estimatedVarianceOfSampleMean.getPrintHorizontally();
945  estimatedVarianceOfSampleMean.setPrintHorizontally(false);
946  if (m_env.subDisplayFile()) {
947  *m_env.subDisplayFile() << "\nEstimated variance of sample mean for the whole chain '" << m_name << "'"
948  << ", under independence assumption:"
949  << "\n"
950  << estimatedVarianceOfSampleMean
951  << std::endl;
952  }
953  estimatedVarianceOfSampleMean.setPrintHorizontally(savedVectorPrintState);
954 
955  V estimatedStdOfSampleMean(estimatedVarianceOfSampleMean);
956  estimatedStdOfSampleMean.cwSqrt();
957  savedVectorPrintState = estimatedStdOfSampleMean.getPrintHorizontally();
958  estimatedStdOfSampleMean.setPrintHorizontally(false);
959  if (m_env.subDisplayFile()) {
960  *m_env.subDisplayFile() << "\nEstimated standard deviation of sample mean for the whole chain '" << m_name << "'"
961  << ", under independence assumption:"
962  << "\n"
963  << estimatedStdOfSampleMean
964  << std::endl;
965  }
966  estimatedStdOfSampleMean.setPrintHorizontally(savedVectorPrintState);
967 
968  V subChainPopulationVariance(m_vectorSpace.zeroVector());
969  this->subPopulationVariance(0,
970  this->subSequenceSize(),
971  subChainMean,
972  subChainPopulationVariance);
973 
974  tmpRunTime += MiscGetEllapsedSeconds(&timevalTmp);
975  if (m_env.subDisplayFile()) {
976  *m_env.subDisplayFile() << "Sub Mean, median, and variances took " << tmpRunTime
977  << " seconds"
978  << std::endl;
979  }
980 
981  if (m_env.subDisplayFile()) {
982  *m_env.subDisplayFile() << "\nSub mean, median, sample std, population std"
983  << std::endl;
984  char line[512];
985  sprintf(line,"%s%4s%s%6s%s%9s%s%9s%s",
986  "Parameter",
987  " ",
988  "Mean",
989  " ",
990  "Median",
991  " ",
992  "SampleStd",
993  " ",
994  "Popul.Std");
995  *m_env.subDisplayFile() << line;
996 
997  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
998  sprintf(line,"\n%8.8s%2s%11.4e%2s%11.4e%2s%11.4e%2s%11.4e",
999  m_vectorSpace.localComponentName(i).c_str(), /*.*/
1000  " ",
1001  subChainMean[i],
1002  " ",
1003  subChainMedian[i],
1004  " ",
1005  std::sqrt(subChainSampleVariance[i]),
1006  " ",
1007  std::sqrt(subChainPopulationVariance[i]));
1008  *m_env.subDisplayFile() << line;
1009  }
1010  *m_env.subDisplayFile() << std::endl;
1011  }
1012 
1013  if (subMeanPtr ) *subMeanPtr = subChainMean;
1014  if (subMedianPtr ) *subMedianPtr = subChainMedian;
1015  if (subSampleVarPtr) *subSampleVarPtr = subChainSampleVariance;
1016  if (subPopulVarPtr ) *subPopulVarPtr = subChainPopulationVariance;
1017 
1018  if (m_env.numSubEnvironments() > 1) {
1019  // Write unified min-max
1020  if (m_vectorSpace.numOfProcsForStorage() == 1) {
1021  V unifiedChainMean(m_vectorSpace.zeroVector());
1022  this->unifiedMeanExtra(0,
1023  this->subSequenceSize(),
1024  unifiedChainMean);
1025 
1026  V unifiedChainMedian(m_vectorSpace.zeroVector());
1027  this->unifiedMedianExtra(0,
1028  this->subSequenceSize(),
1029  unifiedChainMedian);
1030 
1031  V unifiedChainSampleVariance(m_vectorSpace.zeroVector());
1032  this->unifiedSampleVarianceExtra(0,
1033  this->subSequenceSize(),
1034  unifiedChainMean,
1035  unifiedChainSampleVariance);
1036 
1037  V unifiedChainPopulationVariance(m_vectorSpace.zeroVector());
1038  this->unifiedPopulationVariance(0,
1039  this->subSequenceSize(),
1040  unifiedChainMean,
1041  unifiedChainPopulationVariance);
1042 
1043  if (m_env.inter0Rank() == 0) {
1044  if (m_env.subDisplayFile()) {
1045  *m_env.subDisplayFile() << "\nUnif mean, median, sample std, population std"
1046  << std::endl;
1047  char line[512];
1048  sprintf(line,"%s%4s%s%6s%s%9s%s%9s%s",
1049  "Parameter",
1050  " ",
1051  "Mean",
1052  " ",
1053  "Median",
1054  " ",
1055  "SampleStd",
1056  " ",
1057  "Popul.Std");
1058  *m_env.subDisplayFile() << line;
1059 
1060  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
1061  sprintf(line,"\n%8.8s%2s%11.4e%2s%11.4e%2s%11.4e%2s%11.4e",
1062  m_vectorSpace.localComponentName(i).c_str(), /*.*/
1063  " ",
1064  unifiedChainMean[i],
1065  " ",
1066  unifiedChainMedian[i],
1067  " ",
1068  std::sqrt(unifiedChainSampleVariance[i]),
1069  " ",
1070  std::sqrt(unifiedChainPopulationVariance[i]));
1071  *m_env.subDisplayFile() << line;
1072  }
1073  *m_env.subDisplayFile() << std::endl;
1074  } // if subDisplayFile
1075  }
1076  }
1077  else {
1078  queso_error_msg("unified min-max writing, parallel vectors not supported yet");
1079  }
1080  } // if numSubEnvs > 1
1081 
1082  if (m_env.subDisplayFile()) {
1083  *m_env.subDisplayFile() << "\nEnded computing mean, sample variance and population variance"
1084  << "\n-----------------------------------------------------"
1085  << std::endl;
1086  }
1087 
1088  return;
1089 }
QUESO::BaseVectorSequence::unifiedMedianExtra
virtual void unifiedMedianExtra(unsigned int initialPos, unsigned int localNumPos, V &unifiedMedianVec) const =0
Finds the median value of the unified sequence, considering numPos positions starting at position ini...
QUESO::BaseVectorSequence::subMeanExtra
virtual void subMeanExtra(unsigned int initialPos, unsigned int numPos, V &meanVec) const =0
Finds the mean value of the sub-sequence, considering numPos positions starting at position initialPo...
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::BaseVectorSequence::unifiedMeanExtra
virtual void unifiedMeanExtra(unsigned int initialPos, unsigned int numPos, V &unifiedMeanVec) const =0
Finds the mean value of the unified sequence of numPos positions starting at position initialPos...
QUESO::BaseVectorSequence::unifiedSampleVarianceExtra
virtual void unifiedSampleVarianceExtra(unsigned int initialPos, unsigned int numPos, const V &unifiedMeanVec, V &unifiedSamVec) const =0
Finds the sample variance of the unified sequence, considering numPos positions starting at position ...
QUESO::UQ_OK_RC
const int UQ_OK_RC
Definition: Defines.h:92
QUESO::BaseVectorSequence::subSampleVarianceExtra
virtual void subSampleVarianceExtra(unsigned int initialPos, unsigned int numPos, const V &meanVec, V &samVec) const =0
Finds the sample variance of the sub-sequence, considering numPos positions starting at position init...
QUESO::BaseVectorSequence::unifiedPopulationVariance
virtual void unifiedPopulationVariance(unsigned int initialPos, unsigned int numPos, const V &unifiedMeanVec, V &unifiedPopVec) const =0
Finds the population variance of the unified-sequence, considering numPos positions starting at posit...
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
QUESO::BaseVectorSequence::subPopulationVariance
virtual void subPopulationVariance(unsigned int initialPos, unsigned int numPos, const V &meanVec, V &popVec) const =0
Finds the population variance of the sub-sequence, considering numPos positions starting at position ...
QUESO::BaseEnvironment::displayVerbosity
unsigned int displayVerbosity() const
Definition: Environment.C:450
QUESO::BaseVectorSequence::subMedianExtra
virtual void subMedianExtra(unsigned int initialPos, unsigned int numPos, V &medianVec) const =0
Finds the median value of the sub-sequence, considering numPos positions starting at position initial...
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:97
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:431
QUESO::BaseEnvironment::numSubEnvironments
unsigned int numSubEnvironments() const
Access function to the number of sub-environments.
Definition: Environment.C:335
QUESO::MiscGetEllapsedSeconds
double MiscGetEllapsedSeconds(struct timeval *timeval0)
Definition: Miscellaneous.C:282
QUESO::BaseEnvironment::inter0Rank
int inter0Rank() const
Returns the process inter0 rank.
Definition: Environment.C:307
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:320
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computePSD ( const SequenceStatisticalOptions &  statisticalOptions,
const std::vector< unsigned int > &  initialPosForStatistics,
std::ofstream *  passedOfs 
)
protected

Definition at line 2387 of file VectorSequence.C.

References SequenceStatisticalOptions::m_ov.

2391 {
2392  queso_deprecated();
2393  computeFFT(statisticalOptions.m_ov, initialPosForStatistics, passedOfs);
2394 }
QUESO::BaseVectorSequence::computeFFT
void computeFFT(const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
Definition: VectorSequence.C:2300
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computePSD ( const SsOptionsValues &  statisticalOptions,
const std::vector< unsigned int > &  initialPosForStatistics,
std::ofstream *  passedOfs 
)
protected

Definition at line 2462 of file VectorSequence.C.

References QUESO::MiscGetEllapsedSeconds(), QUESO::TwoDArray< T >::setLocation(), and QUESO::UQ_OK_RC.

2466 {
2467  int iRC = UQ_OK_RC;
2468  struct timeval timevalTmp;
2469  iRC = gettimeofday(&timevalTmp, NULL);
2470  double tmpRunTime = 0.;
2471 
2472  if (m_env.subDisplayFile()) {
2473  *m_env.subDisplayFile() << "\n-----------------------------------------------------"
2474  << "\nComputing PSD at frequency zero for all parameters"
2475  << std::endl;
2476  }
2477 
2478  TwoDArray<V> _2dArrayOfPSDAtZero(initialPosForStatistics.size(),statisticalOptions.psdAtZeroNumBlocks().size());
2479  for (unsigned int i = 0; i < _2dArrayOfPSDAtZero.numRows(); ++i) {
2480  for (unsigned int j = 0; j < _2dArrayOfPSDAtZero.numCols(); ++j) {
2481  _2dArrayOfPSDAtZero.setLocation(i,j,new V(m_vectorSpace.zeroVector()) /*.*/);
2482  }
2483  }
2484  V psdVec(m_vectorSpace.zeroVector());
2485  for (unsigned int initialPosId = 0; initialPosId < initialPosForStatistics.size(); initialPosId++) {
2486  unsigned int initialPosition = initialPosForStatistics[initialPosId];
2487  for (unsigned int numBlocksId = 0; numBlocksId < statisticalOptions.psdAtZeroNumBlocks().size(); numBlocksId++) {
2488  unsigned int numBlocks = statisticalOptions.psdAtZeroNumBlocks()[numBlocksId];
2489  this->psdAtZero(initialPosition,
2490  numBlocks,
2491  statisticalOptions.psdAtZeroHopSizeRatio(),
2492  psdVec);
2493  _2dArrayOfPSDAtZero(initialPosId,numBlocksId) = psdVec;
2494  }
2495  }
2496 
2497  // Display PSD at frequency zero
2498  if ((statisticalOptions.psdAtZeroDisplay()) && (m_env.subDisplayFile())) {
2499  for (unsigned int initialPosId = 0; initialPosId < initialPosForStatistics.size(); initialPosId++) {
2500  unsigned int initialPos = initialPosForStatistics[initialPosId];
2501  *m_env.subDisplayFile() << "\nComputed PSD at frequency zero for subchain beginning at position " << initialPos
2502  << ", so effective data size = " << this->subSequenceSize() - initialPos
2503  << " (each column corresponds to a number of blocks)"
2504  << std::endl;
2505 
2506  char line[512];
2507  sprintf(line,"%s",
2508  "Parameter");
2509  *m_env.subDisplayFile() << line;
2510  for (unsigned int numBlocksId = 0; numBlocksId < statisticalOptions.psdAtZeroNumBlocks().size(); numBlocksId++) {
2511  sprintf(line,"%10s%3d",
2512  " ",
2513  statisticalOptions.psdAtZeroNumBlocks()[numBlocksId]);
2514  *m_env.subDisplayFile() << line;
2515  }
2516 
2517  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
2518  sprintf(line,"\n%9.9s",
2519  m_vectorSpace.localComponentName(i).c_str() /*.*/);
2520  *m_env.subDisplayFile() << line;
2521  for (unsigned int numBlocksId = 0; numBlocksId < statisticalOptions.psdAtZeroNumBlocks().size(); numBlocksId++) {
2522  sprintf(line,"%2s%11.4e",
2523  " ",
2524  _2dArrayOfPSDAtZero(initialPosId,numBlocksId)[i]);
2525  *m_env.subDisplayFile() << line;
2526  }
2527  }
2528  *m_env.subDisplayFile() << std::endl;
2529  }
2530  }
2531 
2532  // Display estimated variance of sample mean through PSD
2533  if (/*(statisticalOptions.psdAtZeroDisplay()) &&*/ (m_env.subDisplayFile())) {
2534  for (unsigned int initialPosId = 0; initialPosId < initialPosForStatistics.size(); initialPosId++) {
2535  unsigned int initialPos = initialPosForStatistics[initialPosId];
2536  *m_env.subDisplayFile() << "\nEstimated variance of sample mean, through psd, for subchain beginning at position " << initialPos
2537  << ", so effective data size = " << this->subSequenceSize() - initialPos
2538  << " (each column corresponds to a number of blocks)"
2539  << std::endl;
2540 
2541  char line[512];
2542  sprintf(line,"%s",
2543  "Parameter");
2544  *m_env.subDisplayFile() << line;
2545  for (unsigned int numBlocksId = 0; numBlocksId < statisticalOptions.psdAtZeroNumBlocks().size(); numBlocksId++) {
2546  sprintf(line,"%10s%3d",
2547  " ",
2548  statisticalOptions.psdAtZeroNumBlocks()[numBlocksId]);
2549  *m_env.subDisplayFile() << line;
2550  }
2551 
2552  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
2553  sprintf(line,"\n%9.9s",
2554  m_vectorSpace.localComponentName(i).c_str() /*.*/);
2555  *m_env.subDisplayFile() << line;
2556  for (unsigned int numBlocksId = 0; numBlocksId < statisticalOptions.psdAtZeroNumBlocks().size(); numBlocksId++) {
2557  sprintf(line,"%2s%11.4e",
2558  " ",
2559  2.*M_PI*_2dArrayOfPSDAtZero(initialPosId,numBlocksId)[i]/(double) (this->subSequenceSize() - initialPos));
2560  *m_env.subDisplayFile() << line;
2561  }
2562  }
2563  *m_env.subDisplayFile() << std::endl;
2564  }
2565  }
2566 
2567  tmpRunTime += MiscGetEllapsedSeconds(&timevalTmp);
2568  if (m_env.subDisplayFile()) {
2569  *m_env.subDisplayFile() << "Chain PSD at frequency zero took " << tmpRunTime
2570  << " seconds"
2571  << std::endl;
2572  }
2573 
2574  // Write PSD at frequency zero
2575  if (statisticalOptions.psdAtZeroWrite() && passedOfs) {
2576  std::ofstream& ofsvar = *passedOfs;
2577  ofsvar << m_name << "_psdAtZeroNumBlocks_sub" << m_env.subIdString() << " = zeros(" << 1
2578  << "," << statisticalOptions.psdAtZeroNumBlocks().size()
2579  << ");"
2580  << std::endl;
2581  for (unsigned int numBlocksId = 0; numBlocksId < statisticalOptions.psdAtZeroNumBlocks().size(); numBlocksId++) {
2582  ofsvar << m_name << "_psdAtZeroNumBlocks_sub" << m_env.subIdString() << "(" << 1
2583  << "," << numBlocksId+1
2584  << ") = " << statisticalOptions.psdAtZeroNumBlocks()[numBlocksId]
2585  << ";"
2586  << std::endl;
2587  }
2588 
2589  for (unsigned int initialPosId = 0; initialPosId < initialPosForStatistics.size(); initialPosId++) {
2590  ofsvar << m_name << "_psdAtZeroInitPos" << initialPosForStatistics[initialPosId] << "_sub" << m_env.subIdString() << " = zeros(" << this->vectorSizeLocal() /*.*/
2591  << "," << statisticalOptions.psdAtZeroNumBlocks().size()
2592  << ");"
2593  << std::endl;
2594  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
2595  for (unsigned int numBlocksId = 0; numBlocksId < statisticalOptions.psdAtZeroNumBlocks().size(); numBlocksId++) {
2596  ofsvar << m_name << "_psdAtZeroInitPos" << initialPosForStatistics[initialPosId] << "_sub" << m_env.subIdString() << "(" << i+1
2597  << "," << numBlocksId+1
2598  << ") = " << _2dArrayOfPSDAtZero(initialPosId,numBlocksId)[i]
2599  << ";"
2600  << std::endl;
2601  }
2602  }
2603  }
2604  }
2605 
2606  return;
2607 }
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::UQ_OK_RC
const int UQ_OK_RC
Definition: Defines.h:92
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
QUESO::BaseEnvironment::subIdString
const std::string & subIdString() const
Access to the attribute m_subIdString; which stores the string for the sub-environment, and it will be used, for instance, to create the output files for each sub-environment.
Definition: Environment.C:348
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:97
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:431
QUESO::BaseVectorSequence::psdAtZero
virtual void psdAtZero(unsigned int initialPos, unsigned int numBlocks, double hopSizeRatio, V &psdVec) const =0
QUESO::MiscGetEllapsedSeconds
double MiscGetEllapsedSeconds(struct timeval *timeval0)
Definition: Miscellaneous.C:282
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:320
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computePSDAtZero ( const SequenceStatisticalOptions &  statisticalOptions,
const std::vector< unsigned int > &  initialPosForStatistics,
std::ofstream *  passedOfs 
)
protected

Definition at line 2451 of file VectorSequence.C.

References SequenceStatisticalOptions::m_ov.

2455 {
2456  queso_deprecated();
2457  computePSD(statisticalOptions.m_ov, initialPosForStatistics, passedOfs);
2458 }
QUESO::BaseVectorSequence::computePSD
void computePSD(const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
Definition: VectorSequence.C:2387
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computePSDAtZero ( const SsOptionsValues &  statisticalOptions,
const std::vector< unsigned int > &  initialPosForStatistics,
std::ofstream *  passedOfs 
)
protected

Definition at line 2622 of file VectorSequence.C.

References QUESO::MiscGetEllapsedSeconds(), and QUESO::UQ_OK_RC.

2626 {
2627  int iRC = UQ_OK_RC;
2628  struct timeval timevalTmp;
2629  iRC = gettimeofday(&timevalTmp, NULL);
2630  double tmpRunTime = 0.;
2631 
2632  if (m_env.subDisplayFile()) {
2633  *m_env.subDisplayFile() << "\n-----------------------------------------------------"
2634  << "\nComputing Geweke coefficients"
2635  << std::endl;
2636  }
2637 
2638  std::vector<V*> vectorOfGeweke(initialPosForStatistics.size(),NULL);
2639  V gewVec(m_vectorSpace.zeroVector());
2640  for (unsigned int initialPosId = 0; initialPosId < initialPosForStatistics.size(); initialPosId++) {
2641  unsigned int initialPosition = initialPosForStatistics[initialPosId];
2642  this->geweke(initialPosition,
2643  statisticalOptions.gewekeNaRatio(),
2644  statisticalOptions.gewekeNbRatio(),
2645  gewVec);
2646  vectorOfGeweke[initialPosId] = new V(gewVec);
2647  }
2648 
2649  if (m_env.subDisplayFile()) {
2650  *m_env.subDisplayFile() << "\nComputed Geweke coefficients with 10% and 50% percentages"
2651  << " (each column corresponds to a different initial position on the full chain)"
2652  << std::endl;
2653 
2654  char line[512];
2655  sprintf(line,"%s",
2656  "Parameter");
2657  *m_env.subDisplayFile() << line;
2658  for (unsigned int initialPosId = 0; initialPosId < initialPosForStatistics.size(); initialPosId++) {
2659  sprintf(line,"%10s%3d",
2660  " ",
2661  initialPosForStatistics[initialPosId]);
2662  *m_env.subDisplayFile() << line;
2663  }
2664 
2665  for (unsigned int i = 0; i < this->vectorSizeLocal() /*.*/; ++i) {
2666  sprintf(line,"\n%9.9s",
2667  m_vectorSpace.localComponentName(i).c_str() /*.*/);
2668  *m_env.subDisplayFile() << line;
2669  for (unsigned int initialPosId = 0; initialPosId < initialPosForStatistics.size(); initialPosId++) {
2670  sprintf(line,"%2s%11.4e",
2671  " ",
2672  (*(vectorOfGeweke[initialPosId]))[i]);
2673  *m_env.subDisplayFile() << line;
2674  }
2675  }
2676  *m_env.subDisplayFile() << std::endl;
2677  }
2678 
2679  tmpRunTime += MiscGetEllapsedSeconds(&timevalTmp);
2680  if (m_env.subDisplayFile()) {
2681  *m_env.subDisplayFile() << "Chain Geweke took " << tmpRunTime
2682  << " seconds"
2683  << std::endl;
2684  }
2685 
2686  return;
2687 }
QUESO::BaseVectorSequence::geweke
virtual void geweke(unsigned int initialPos, double ratioNa, double ratioNb, V &gewVec) const =0
QUESO::UQ_OK_RC
const int UQ_OK_RC
Definition: Defines.h:92
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:97
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:431
QUESO::MiscGetEllapsedSeconds
double MiscGetEllapsedSeconds(struct timeval *timeval0)
Definition: Miscellaneous.C:282
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:320
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computeStatistics ( const SequenceStatisticalOptions &  statisticalOptions,
std::ofstream *  passedOfs 
)

Definition at line 672 of file VectorSequence.C.

References SequenceStatisticalOptions::m_ov.

Referenced by QUESO::MLSampling< P_V, P_M >::generateSequence(), QUESO::MetropolisHastingsSG< P_V, P_M >::generateSequence(), QUESO::MLSampling< P_V, P_M >::generateSequence_Level0_all(), QUESO::MLSampling< P_V, P_M >::generateSequence_Step11_inter0(), and QUESO::MonteCarloSG< P_V, P_M, Q_V, Q_M >::internGenerateSequence().

675 {
676  queso_deprecated();
677  computeStatistics(statisticalOptions.m_ov, passedOfs);
678 }
QUESO::BaseVectorSequence::computeStatistics
void computeStatistics(const SequenceStatisticalOptions &statisticalOptions, std::ofstream *passedOfs)
Definition: VectorSequence.C:672
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::computeStatistics ( const SsOptionsValues &  statisticalOptions,
std::ofstream *  passedOfs 
)

Definition at line 682 of file VectorSequence.C.

References QUESO::MiscGetEllapsedSeconds(), and QUESO::UQ_OK_RC.

685 {
686  if (m_env.subDisplayFile()) {
687  *m_env.subDisplayFile() << "\n"
688  << "\n-----------------------------------------------------"
689  << "\n Computing statistics for chain '" << m_name << "' ..."
690  << "\n-----------------------------------------------------"
691  << "\n"
692  << std::endl;
693  }
694 
695  bool okSituation = ((passedOfs == NULL ) ||
696  ((passedOfs != NULL) && (m_env.subRank() >= 0)));
697  queso_require_msg(!(!okSituation), "unexpected combination of file pointer and subRank");
698 
699  int iRC = UQ_OK_RC;
700  struct timeval timevalTmp;
701  iRC = gettimeofday(&timevalTmp, NULL);
702  double tmpRunTime = 0.;
703 
704  // Set initial positions for the computation of chain statistics
705  std::vector<unsigned int> initialPosForStatistics(statisticalOptions.initialDiscardedPortions().size(),0);
706  for (unsigned int i = 0; i < initialPosForStatistics.size(); ++i) {
707  initialPosForStatistics[i] = (unsigned int) (statisticalOptions.initialDiscardedPortions()[i] * (double) (this->subSequenceSize()-1));
708  if (m_env.subDisplayFile()) {
709  *m_env.subDisplayFile() << "In BaseVectorSequence<V,M>::computeStatistics()"
710  << ": statisticalOptions.initialDiscardedPortions()[" << i << "] = " << statisticalOptions.initialDiscardedPortions()[i]
711  << ", initialPosForStatistics[" << i << "] = " << initialPosForStatistics[i]
712  << std::endl;
713  }
714  }
715  if (m_env.subDisplayFile()) {
716  *m_env.subDisplayFile() << "In BaseVectorSequence<V,M>::computeStatistics(): initial positions for statistics =";
717  for (unsigned int i = 0; i < initialPosForStatistics.size(); ++i) {
718  *m_env.subDisplayFile() << " " << initialPosForStatistics[i];
719  }
720  *m_env.subDisplayFile() << std::endl;
721  }
722 
723  //****************************************************
724  // Compute mean, median, sample std, population std
725  //****************************************************
726  this->computeMeanVars(statisticalOptions,
727  passedOfs,
728  NULL,
729  NULL,
730  NULL,
731  NULL);
732 
733 #ifdef UQ_CODE_HAS_MONITORS
734  if (statisticalOptions.meanMonitorPeriod() != 0) {
735  this->computeMeanEvolution(statisticalOptions,
736  passedOfs);
737  }
738 #endif
739 
740  //****************************************************
741  // Compute variance of sample mean through the 'batch means method' (BMM)
742  //****************************************************
743 #ifdef QUESO_COMPUTES_EXTRA_POST_PROCESSING_STATISTICS
744  if ((statisticalOptions.bmmRun() ) &&
745  (initialPosForStatistics.size() > 0) &&
746  (statisticalOptions.bmmLengths().size() > 0)) {
747  this->computeBMM(statisticalOptions,
748  initialPosForStatistics,
749  passedOfs);
750  }
751 #endif
752  //****************************************************
753  // Compute FFT of chain, for one parameter only
754  //****************************************************
755 #ifdef QUESO_COMPUTES_EXTRA_POST_PROCESSING_STATISTICS
756  if ((statisticalOptions.fftCompute() ) &&
757  (initialPosForStatistics.size() > 0)) {
758  this->computeFFT(statisticalOptions,
759  initialPosForStatistics,
760  passedOfs);
761  }
762 #endif
763  //****************************************************
764  // Compute power spectral density (PSD) of chain, for one parameter only
765  //****************************************************
766 #ifdef QUESO_COMPUTES_EXTRA_POST_PROCESSING_STATISTICS
767  if ((statisticalOptions.psdCompute() ) &&
768  (initialPosForStatistics.size() > 0)) {
769  this->computePSD(statisticalOptions,
770  initialPosForStatistics,
771  passedOfs);
772  }
773 #endif
774  //****************************************************
775  // Compute power spectral density (PSD) of chain at zero frequency
776  //****************************************************
777 #ifdef QUESO_COMPUTES_EXTRA_POST_PROCESSING_STATISTICS
778  if ((statisticalOptions.psdAtZeroCompute() ) &&
779  (initialPosForStatistics.size() > 0) &&
780  (statisticalOptions.psdAtZeroNumBlocks().size() > 0)) {
781  this->computePSDAtZero(statisticalOptions,
782  initialPosForStatistics,
783  passedOfs);
784  }
785 #endif
786  //****************************************************
787  // Compute Geweke
788  //****************************************************
789 #ifdef QUESO_COMPUTES_EXTRA_POST_PROCESSING_STATISTICS
790  if ((statisticalOptions.gewekeCompute()) &&
791  (initialPosForStatistics.size() > 0)) {
792  this->computeGeweke(statisticalOptions,
793  initialPosForStatistics,
794  passedOfs);
795  }
796 #endif
797  //****************************************************
798  // Compute mean statistical accuracy
799  //****************************************************
800 #ifdef QUESO_COMPUTES_EXTRA_POST_PROCESSING_STATISTICS
801  if ((statisticalOptions.meanStaccCompute()) &&
802  (initialPosForStatistics.size() > 0 )) {
803  this->computeMeanStacc(statisticalOptions,
804  initialPosForStatistics,
805  passedOfs);
806  }
807 #endif
808  // Set lags for the computation of chain autocorrelations
809  std::vector<unsigned int> lagsForCorrs(statisticalOptions.autoCorrNumLags(),1);
810  for (unsigned int i = 1; i < lagsForCorrs.size(); ++i) {
811  lagsForCorrs[i] = statisticalOptions.autoCorrSecondLag() + (i-1)*statisticalOptions.autoCorrLagSpacing();
812  }
813 
814  //****************************************************
815  // Compute autocorrelation coefficients via definition
816  //****************************************************
817  if ((statisticalOptions.autoCorrComputeViaDef()) &&
818  (initialPosForStatistics.size() > 0 ) &&
819  (lagsForCorrs.size() > 0 )) {
820  this->computeAutoCorrViaDef(statisticalOptions,
821  initialPosForStatistics,
822  lagsForCorrs,
823  passedOfs);
824  }
825 
826  //****************************************************
827  // Compute autocorrelation coefficients via FFT
828  //****************************************************
829  if ((statisticalOptions.autoCorrComputeViaFft()) &&
830  (initialPosForStatistics.size() > 0 ) &&
831  (lagsForCorrs.size() > 0 )) {
832  this->computeAutoCorrViaFFT(statisticalOptions,
833  initialPosForStatistics,
834  lagsForCorrs,
835  passedOfs);
836  }
837 
838  //****************************************************
839  // Compute histogram and/or cdf stacc and/or Kde
840  //****************************************************
841 #ifdef QUESO_COMPUTES_EXTRA_POST_PROCESSING_STATISTICS
842  if ((statisticalOptions.histCompute ()) ||
843  (statisticalOptions.cdfStaccCompute()) ||
844  (statisticalOptions.kdeCompute ())) {
845 #else
846  if (statisticalOptions.kdeCompute()) //kemelli deleted single '{' on 5/28/13 - compare to queso-0.45.2
847 #endif
848  this->computeHistCdfstaccKde(statisticalOptions,
849  passedOfs);
850  }
851 
852  //****************************************************
853  // Compute covariance and correlation matrices
854  //****************************************************
855  if ((statisticalOptions.covMatrixCompute ()) ||
856  (statisticalOptions.corrMatrixCompute())) {
857  this->computeCovCorrMatrices(statisticalOptions,
858  passedOfs);
859  }
860 
861  tmpRunTime += MiscGetEllapsedSeconds(&timevalTmp);
862  if (m_env.subDisplayFile()) {
863  *m_env.subDisplayFile() << "All statistics of chain '" << m_name << "'"
864  << " took " << tmpRunTime
865  << " seconds"
866  << std::endl;
867  }
868 
869  if (m_env.subDisplayFile()) {
870  *m_env.subDisplayFile() << "\n-----------------------------------------------------"
871  << "\n Finished computing statistics for chain '" << m_name << "'"
872  << "\n-----------------------------------------------------"
873  << "\n"
874  << std::endl;
875  }
876 
877  return;
878 }
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::BaseVectorSequence::computeAutoCorrViaDef
void computeAutoCorrViaDef(const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, const std::vector< unsigned int > &lagsForCorrs, std::ofstream *passedOfs)
Definition: VectorSequence.C:1093
QUESO::BaseVectorSequence::computeBMM
void computeBMM(const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
Definition: VectorSequence.C:2203
QUESO::UQ_OK_RC
const int UQ_OK_RC
Definition: Defines.h:92
QUESO::BaseEnvironment::subRank
int subRank() const
Returns the rank of the MPI process in the sub-communicator subComm()
Definition: Environment.C:287
QUESO::BaseVectorSequence::computeGeweke
void computeGeweke(const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
Definition: VectorSequence.C:2611
QUESO::BaseVectorSequence::computeCovCorrMatrices
void computeCovCorrMatrices(const SequenceStatisticalOptions &statisticalOptions, std::ofstream *passedOfs)
Definition: VectorSequence.C:2000
QUESO::BaseVectorSequence::computeMeanEvolution
void computeMeanEvolution(const SequenceStatisticalOptions &statisticalOptions, std::ofstream *passedOfs)
Definition: VectorSequence.C:2080
QUESO::BaseVectorSequence::computeHistCdfstaccKde
void computeHistCdfstaccKde(const SequenceStatisticalOptions &statisticalOptions, std::ofstream *passedOfs)
Definition: VectorSequence.C:1413
QUESO::BaseVectorSequence::computePSDAtZero
void computePSDAtZero(const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
Definition: VectorSequence.C:2451
QUESO::BaseVectorSequence::computeFFT
void computeFFT(const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
Definition: VectorSequence.C:2300
QUESO::BaseVectorSequence::computeMeanVars
void computeMeanVars(const SequenceStatisticalOptions &statisticalOptions, std::ofstream *passedOfs, V *subMeanPtr, V *subMedianPtr, V *subSampleVarPtr, V *subPopulVarPtr)
Definition: VectorSequence.C:882
QUESO::BaseVectorSequence::computeMeanStacc
void computeMeanStacc(const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
Definition: VectorSequence.C:2691
QUESO::BaseVectorSequence::computePSD
void computePSD(const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, std::ofstream *passedOfs)
Definition: VectorSequence.C:2387
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:431
QUESO::MiscGetEllapsedSeconds
double MiscGetEllapsedSeconds(struct timeval *timeval0)
Definition: Miscellaneous.C:282
QUESO::BaseVectorSequence::computeAutoCorrViaFFT
void computeAutoCorrViaFFT(const SequenceStatisticalOptions &statisticalOptions, const std::vector< unsigned int > &initialPosForStatistics, const std::vector< unsigned int > &lagsForCorrs, std::ofstream *passedOfs)
Definition: VectorSequence.C:1228
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:320
template<class V, class M>
void QUESO::BaseVectorSequence< V, M >::copy ( const BaseVectorSequence< V, M > &  src)
protected

Copies vector sequence src to this.

This routine deletes all stored computed vectors

Definition at line 652 of file VectorSequence.C.

References QUESO::BaseVectorSequence< V, M >::m_name, QUESO::BaseVectorSequence< V, M >::m_vectorSpace, and QUESO::queso_require_equal_to_msg.

Referenced by QUESO::SequenceOfVectors< V, M >::copy().

653 {
654  // FIX ME: should check environments as well ???
655 
656  queso_require_equal_to_msg(m_vectorSpace.dimLocal(), src.m_vectorSpace.dimLocal(), "incompatible vector space dimensions");
657 
658  m_name = src.m_name;
659  this->deleteStoredVectors();
660 
661  return;
662 }
QUESO::BaseVectorSequence::deleteStoredVectors
void deleteStoredVectors()
Deletes all the stored vectors.
Definition: VectorSequence.C:298
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
QUESO::queso_require_equal_to_msg
MonteCarloSGOptions::MonteCarloSGOptions(const BaseEnvironment &env, const char *prefix, const McOptionsValues &alternativeOptionsValues queso_require_equal_to_msg)(m_env.optionsInputFileName(), std::string(""), std::string("this constructor is incompatible with the existence of an options input file"))
Definition: MonteCarloSGOptions.C:460
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::deleteStoredVectors ( )

Deletes all the stored vectors.

It deletes all stored vectors and assigns NULL value to the pointers: m_subMinPlain, m_unifiedMinPlain, m_subMaxPlain, m_unifiedMaxPlain, m_subMeanPlain, m_unifiedMeanPlain, m_subMedianPlain, m_unifiedMedianPlain, m_subBoxPlain, m_unifiedBoxPlain, m_subSampleVariancePlain, m_unifiedSampleVariancePlain.

Definition at line 298 of file VectorSequence.C.

Referenced by QUESO::ArrayOfSequences< V, M >::erasePositions(), QUESO::SequenceOfVectors< V, M >::erasePositions(), QUESO::ArrayOfSequences< V, M >::resetValues(), QUESO::SequenceOfVectors< V, M >::resetValues(), QUESO::ArrayOfSequences< V, M >::resizeSequence(), QUESO::SequenceOfVectors< V, M >::resizeSequence(), QUESO::ArrayOfSequences< V, M >::setGaussian(), QUESO::ArrayOfSequences< V, M >::setPositionValues(), QUESO::SequenceOfVectors< V, M >::setPositionValues(), and QUESO::ArrayOfSequences< V, M >::setUniform().

299 {
300  if (m_subMinPlain) {
301  delete m_subMinPlain;
302  m_subMinPlain = NULL;
303  }
304  if (m_unifiedMinPlain) {
305  delete m_unifiedMinPlain;
306  m_unifiedMinPlain = NULL;
307  }
308  if (m_subMaxPlain) {
309  delete m_subMaxPlain;
310  m_subMaxPlain = NULL;
311  }
312  if (m_unifiedMaxPlain) {
313  delete m_unifiedMaxPlain;
314  m_unifiedMaxPlain = NULL;
315  }
316  if (m_subMeanPlain) {
317  delete m_subMeanPlain;
318  m_subMeanPlain = NULL;
319  }
320  if (m_unifiedMeanPlain) {
321  delete m_unifiedMeanPlain;
322  m_unifiedMeanPlain = NULL;
323  }
324  if (m_subMedianPlain) {
325  delete m_subMedianPlain;
326  m_subMedianPlain = NULL;
327  }
328  if (m_unifiedMedianPlain) {
329  delete m_unifiedMedianPlain;
330  m_unifiedMedianPlain = NULL;
331  }
332  if (m_subSampleVariancePlain) {
333  delete m_subSampleVariancePlain;
334  m_subSampleVariancePlain = NULL;
335  }
336  if (m_unifiedSampleVariancePlain) {
337  delete m_unifiedSampleVariancePlain;
338  m_unifiedSampleVariancePlain = NULL;
339  }
340  if (m_subBoxPlain) {
341  delete m_subBoxPlain;
342  m_subBoxPlain = NULL;
343  }
344  if (m_unifiedBoxPlain) {
345  delete m_unifiedBoxPlain;
346  m_unifiedBoxPlain = NULL;
347  }
348 
349  return;
350 }
QUESO::BaseVectorSequence::m_unifiedBoxPlain
BoxSubset< V, M > * m_unifiedBoxPlain
Definition: VectorSequence.h:447
QUESO::BaseVectorSequence::m_subBoxPlain
BoxSubset< V, M > * m_subBoxPlain
Definition: VectorSequence.h:446
template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::erasePositions ( unsigned int  initialPos,
unsigned int  numPos 
)
pure virtual

Erase numPos positions in the sequence, starting at position initialPos.

This routine deletes all stored computed vectors

Implemented in QUESO::SequenceOfVectors< V, M >, and QUESO::ArrayOfSequences< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual double QUESO::BaseVectorSequence< V, M >::estimateConvBrooksGelman ( unsigned int  initialPos,
unsigned int  numPos 
) const
pure virtual

Estimates convergence rate using Brooks & Gelman method. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >.

Referenced by QUESO::MetropolisHastingsSG< P_V, P_M >::generateFullChain().

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::extractRawData ( unsigned int  initialPos,
unsigned int  spacing,
unsigned int  numPos,
unsigned int  paramId,
std::vector< double > &  rawData 
) const
protectedpure virtual

Extracts the raw data. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >, and QUESO::ArrayOfSequences< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::extractScalarSeq ( unsigned int  initialPos,
unsigned int  spacing,
unsigned int  numPos,
unsigned int  paramId,
ScalarSequence< double > &  scalarSeq 
) const
pure virtual

Extracts a sequence of scalars of size numPos, starting at position initialPos, given spacing spacing. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >, and QUESO::ArrayOfSequences< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::fftForward ( unsigned int  initialPos,
unsigned int  fftSize,
unsigned int  paramId,
std::vector< std::complex< double > > &  fftResult 
) const
pure virtual

Implemented in QUESO::SequenceOfVectors< V, M >, and QUESO::ArrayOfSequences< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::filter ( unsigned int  initialPos,
unsigned int  spacing 
)
pure virtual

Filters positions in the sequence of vectors, starting at initialPos, and with spacing given by spacing. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >, and QUESO::ArrayOfSequences< V, M >.

Referenced by QUESO::MetropolisHastingsSG< P_V, P_M >::generateSequence().

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::getPositionValues ( unsigned int  posId,
V &  vec 
) const
pure virtual

Gets the values of the sequence at position posId and stores them at vec. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >, and QUESO::ArrayOfSequences< V, M >.

Referenced by QUESO::MonteCarloSG< P_V, P_M, Q_V, Q_M >::actualGenerateSequence(), QUESO::MetropolisHastingsSG< P_V, P_M >::adapt(), QUESO::BaseVectorSequence< V, M >::append(), QUESO::ComputeCovCorrMatricesBetweenVectorSequences(), QUESO::BaseVectorSequence< V, M >::unifiedPositionsOfMaximum(), and QUESO::MetropolisHastingsSG< P_V, P_M >::updateAdaptedCovMatrix().

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::geweke ( unsigned int  initialPos,
double  ratioNa,
double  ratioNb,
V &  gewVec 
) const
pure virtual

Implemented in QUESO::SequenceOfVectors< V, M >, and QUESO::ArrayOfSequences< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::meanStacc ( unsigned int  initialPos,
V &  meanStaccVec 
) const
pure virtual

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V , class M >
const std::string & QUESO::BaseVectorSequence< V, M >::name ( ) const

Access to protected attribute m_name: name of the sequence of vectors.

This method is used, for instance, to recover the name of a sequence of vector samples, such as the 'rawChain' for the raw chain of samples used in an Monte Carlo algorithm.

Definition at line 118 of file VectorSequence.C.

Referenced by QUESO::MonteCarloSG< P_V, P_M, Q_V, Q_M >::actualGenerateSequence(), QUESO::MetropolisHastingsSG< P_V, P_M >::generateFullChain(), QUESO::MetropolisHastingsSG< P_V, P_M >::generateSequence(), QUESO::MonteCarloSG< P_V, P_M, Q_V, Q_M >::internGenerateSequence(), and QUESO::MetropolisHastingsSG< P_V, P_M >::writeInfo().

119 {
120  return m_name;
121 }
template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::psd ( unsigned int  initialPos,
unsigned int  numBlocks,
double  hopSizeRatio,
unsigned int  paramId,
std::vector< double > &  psdResult 
) const
pure virtual

Implemented in QUESO::SequenceOfVectors< V, M >, and QUESO::ArrayOfSequences< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::psdAtZero ( unsigned int  initialPos,
unsigned int  numBlocks,
double  hopSizeRatio,
V &  psdVec 
) const
pure virtual

Implemented in QUESO::SequenceOfVectors< V, M >, and QUESO::ArrayOfSequences< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::resetValues ( unsigned int  initialPos,
unsigned int  numPos 
)
pure virtual

Reset the values of the sequence. See template specialization.

This routine deletes all stored computed vectors

Implemented in QUESO::SequenceOfVectors< V, M >, and QUESO::ArrayOfSequences< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::resizeSequence ( unsigned int  newSubSequenceSize)
pure virtual

Resize the sequence. See template specialization.

This routine deletes all stored computed vectors

Implemented in QUESO::SequenceOfVectors< V, M >, and QUESO::ArrayOfSequences< V, M >.

Referenced by QUESO::MonteCarloSG< P_V, P_M, Q_V, Q_M >::actualGenerateSequence(), QUESO::MonteCarloSG< P_V, P_M, Q_V, Q_M >::actualReadSequence(), QUESO::MetropolisHastingsSG< P_V, P_M >::generateFullChain(), QUESO::MLSampling< P_V, P_M >::generateSequence(), QUESO::BaseVectorSequence< V, M >::subPositionsOfMaximum(), and QUESO::BaseVectorSequence< V, M >::unifiedPositionsOfMaximum().

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::select ( const std::vector< unsigned int > &  idsOfUniquePositions)
pure virtual

Select positions in the sequence of vectors. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >, and QUESO::ArrayOfSequences< V, M >.

template<class V, class M >
void QUESO::BaseVectorSequence< V, M >::setGaussian ( const V &  meanVec,
const V &  stdDevVec 
)

Sets the values of the sequence as a Gaussian distribution of mean given by meanVec and standard deviation by stdDevVec.

This routine deletes all stored computed vectors

Definition at line 585 of file VectorSequence.C.

586 {
587  V gaussianVector(m_vectorSpace.zeroVector());
588  for (unsigned int j = 0; j < this->subSequenceSize(); ++j) {
589  gaussianVector.cwSetGaussian(meanVec,stdDevVec);
590  this->setPositionValues(j,gaussianVector);
591  }
592 
593  this->deleteStoredVectors();
594 
595  return;
596 }
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::BaseVectorSequence::deleteStoredVectors
void deleteStoredVectors()
Deletes all the stored vectors.
Definition: VectorSequence.C:298
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
QUESO::BaseVectorSequence::setPositionValues
virtual void setPositionValues(unsigned int posId, const V &vec)=0
Set the values in vec at position posId of the sequence. See template specialization.
template<class V , class M >
void QUESO::BaseVectorSequence< V, M >::setName ( const std::string &  newName)

Changes the name of the sequence of vectors.

Definition at line 125 of file VectorSequence.C.

Referenced by QUESO::MLSampling< P_V, P_M >::generateSequence(), QUESO::MetropolisHastingsSG< P_V, P_M >::generateSequence(), QUESO::MLSampling< P_V, P_M >::generateSequence_Level0_all(), QUESO::MLSampling< P_V, P_M >::generateSequence_Step02_inter0(), QUESO::MLSampling< P_V, P_M >::generateSequence_Step11_inter0(), and QUESO::MonteCarloSG< P_V, P_M, Q_V, Q_M >::internGenerateSequence().

126 {
127  m_name = newName;
128  return;
129 }
template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::setPositionValues ( unsigned int  posId,
const V &  vec 
)
pure virtual

Set the values in vec at position posId of the sequence. See template specialization.

This routine deletes all stored computed vectors

Implemented in QUESO::SequenceOfVectors< V, M >, and QUESO::ArrayOfSequences< V, M >.

Referenced by QUESO::MonteCarloSG< P_V, P_M, Q_V, Q_M >::actualGenerateSequence(), QUESO::MonteCarloSG< P_V, P_M, Q_V, Q_M >::actualReadSequence(), QUESO::MetropolisHastingsSG< P_V, P_M >::generateFullChain(), QUESO::MLSampling< P_V, P_M >::generateSequence(), QUESO::BaseVectorSequence< V, M >::subPositionsOfMaximum(), and QUESO::BaseVectorSequence< V, M >::unifiedPositionsOfMaximum().

template<class V, class M >
void QUESO::BaseVectorSequence< V, M >::setUniform ( const V &  aVec,
const V &  bVec 
)

Sets the values of the sequence as a uniform distribution between the values given by vectors aVec and bVec.

This routine deletes all stored computed vectors

Definition at line 600 of file VectorSequence.C.

601 {
602  V uniformVector(m_vectorSpace.zeroVector());
603  for (unsigned int j = 0; j < this->subSequenceSize(); ++j) {
604  uniformVector.cwSetUniform(aVec,bVec);
605  this->setPositionValues(j,uniformVector);
606  }
607 
608  this->deleteStoredVectors();
609 
610  return;
611 }
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::BaseVectorSequence::deleteStoredVectors
void deleteStoredVectors()
Deletes all the stored vectors.
Definition: VectorSequence.C:298
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
QUESO::BaseVectorSequence::setPositionValues
virtual void setPositionValues(unsigned int posId, const V &vec)=0
Set the values in vec at position posId of the sequence. See template specialization.
template<class V , class M >
const BoxSubset< V, M > & QUESO::BaseVectorSequence< V, M >::subBoxPlain ( ) const

Finds a box subset of the sub-sequence (given by its min and max values calculated via subMinPlain and subMaxPlain).

Definition at line 270 of file VectorSequence.C.

271 {
272  if (m_subBoxPlain == NULL) {
273  m_subBoxPlain = new BoxSubset<V,M>(m_name.c_str(),
274  m_vectorSpace,
275  this->subMinPlain(),
276  this->subMaxPlain());
277  }
278 
279  return *m_subBoxPlain;
280 }
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
QUESO::BaseVectorSequence::subMaxPlain
const V & subMaxPlain() const
Finds the maximum value of the sub-sequence.
Definition: VectorSequence.C:172
QUESO::BaseVectorSequence::m_subBoxPlain
BoxSubset< V, M > * m_subBoxPlain
Definition: VectorSequence.h:446
QUESO::BaseVectorSequence::subMinPlain
const V & subMinPlain() const
Finds the minimum value of the sub-sequence.
Definition: VectorSequence.C:146
template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subCdfStacc ( unsigned int  initialPos,
const std::vector< V * > &  evalPositionsVecs,
std::vector< V * > &  cdfStaccVecs 
) const
pure virtual

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subGaussian1dKde ( unsigned int  initialPos,
const V &  scaleVec,
const std::vector< V * > &  evaluationParamVecs,
std::vector< V * > &  densityVecs 
) const
pure virtual

Gaussian kernel for the KDE estimate of the sub-sequence. See template specialization.

Computes a probability density estimate of the sample in this sub-sequence, starting at position initialPos. densityVecs is the vector of density values evaluated at the points in evaluationParamVecs. The estimate is based on Gaussian (normal) kernel function, using a window parameter (scaleVec).

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subHistogram ( unsigned int  initialPos,
const V &  minVec,
const V &  maxVec,
std::vector< V * > &  centersForAllBins,
std::vector< V * > &  quanttsForAllBins 
) const
pure virtual

Calculates the histogram of the sub-sequence. See template specialization.

The IQR is a robust estimate of the spread of the data, since changes in the upper and lower 25% of the data do not affect it. If there are outliers in the data, then the IQR is more representative than the standard deviation as an estimate of the spread of the body of the data. The IQR is less efficient than the standard deviation as an estimate of the spread when the data is all from the normal distribution. (from Matlab)

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subInterQuantileRange ( unsigned int  initialPos,
V &  iqrVec 
) const
pure virtual

Returns the interquartile range of the values in the sub-sequence. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V , class M >
const V & QUESO::BaseVectorSequence< V, M >::subMaxPlain ( ) const

Finds the maximum value of the sub-sequence.

Definition at line 172 of file VectorSequence.C.

173 {
174  if (m_subMaxPlain == NULL) {
175  if (m_subMinPlain == NULL) m_subMinPlain = m_vectorSpace.newVector();
176  m_subMaxPlain = m_vectorSpace.newVector();
177  subMinMaxExtra(0,this->subSequenceSize(),*m_subMinPlain,*m_subMaxPlain);
178  }
179 
180  return *m_subMaxPlain;
181 }
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::BaseVectorSequence::subMinMaxExtra
virtual void subMinMaxExtra(unsigned int initialPos, unsigned int numPos, V &minVec, V &maxVec) const =0
Finds the minimum and the maximum values of the sub-sequence, considering numPos positions starting a...
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subMeanExtra ( unsigned int  initialPos,
unsigned int  numPos,
V &  meanVec 
) const
pure virtual

Finds the mean value of the sub-sequence, considering numPos positions starting at position initialPos. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >.

Referenced by QUESO::MetropolisHastingsSG< P_V, P_M >::updateAdaptedCovMatrix().

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subMeanInter0MonitorAlloc ( unsigned int  numberOfMonitorPositions)
protectedpure virtual

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subMeanInter0MonitorFree ( )
protectedpure virtual

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subMeanInter0MonitorRun ( unsigned int  monitorPosition,
V &  subMeanInter0Mean,
V &  subMeanInter0Clt95,
V &  subMeanInter0Empirical90,
V &  subMeanInter0Min,
V &  subMeanInter0Max 
)
protectedpure virtual

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subMeanInter0MonitorStore ( unsigned int  i,
unsigned int  monitorPosition,
const V &  subMeanInter0Mean,
const V &  subMeanInter0Clt95,
const V &  subMeanInter0Empirical90,
const V &  subMeanInter0Min,
const V &  subMeanInter0Max 
)
protectedpure virtual

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subMeanInter0MonitorWrite ( std::ofstream &  ofs)
protectedpure virtual

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subMeanMonitorAlloc ( unsigned int  numberOfMonitorPositions)
protectedpure virtual

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subMeanMonitorFree ( )
protectedpure virtual

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subMeanMonitorRun ( unsigned int  monitorPosition,
V &  subMeanVec,
V &  subMeanCltStd 
)
protectedpure virtual

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subMeanMonitorStore ( unsigned int  i,
unsigned int  monitorPosition,
const V &  subMeanVec,
const V &  subMeanCltStd 
)
protectedpure virtual

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subMeanMonitorWrite ( std::ofstream &  ofs)
protectedpure virtual

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V , class M >
const V & QUESO::BaseVectorSequence< V, M >::subMeanPlain ( ) const

Finds the mean value of the sub-sequence.

Definition at line 198 of file VectorSequence.C.

Referenced by QUESO::MetropolisHastingsSG< P_V, P_M >::updateAdaptedCovMatrix().

199 {
200  if (m_subMeanPlain == NULL) {
201  m_subMeanPlain = m_vectorSpace.newVector();
202  subMeanExtra(0,subSequenceSize(),*m_subMeanPlain);
203  }
204 
205  return *m_subMeanPlain;
206 }
QUESO::BaseVectorSequence::subMeanExtra
virtual void subMeanExtra(unsigned int initialPos, unsigned int numPos, V &meanVec) const =0
Finds the mean value of the sub-sequence, considering numPos positions starting at position initialPo...
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subMedianExtra ( unsigned int  initialPos,
unsigned int  numPos,
V &  medianVec 
) const
pure virtual

Finds the median value of the sub-sequence, considering numPos positions starting at position initialPos. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V , class M >
const V & QUESO::BaseVectorSequence< V, M >::subMedianPlain ( ) const

Finds the median value of the sub-sequence.

Definition at line 222 of file VectorSequence.C.

223 {
224  if (m_subMedianPlain == NULL) {
225  m_subMedianPlain = m_vectorSpace.newVector();
226  subMedianExtra(0, subSequenceSize(), *m_subMedianPlain);
227  }
228 
229  return *m_subMedianPlain;
230 }
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
QUESO::BaseVectorSequence::subMedianExtra
virtual void subMedianExtra(unsigned int initialPos, unsigned int numPos, V &medianVec) const =0
Finds the median value of the sub-sequence, considering numPos positions starting at position initial...
template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subMinMaxExtra ( unsigned int  initialPos,
unsigned int  numPos,
V &  minVec,
V &  maxVec 
) const
pure virtual

Finds the minimum and the maximum values of the sub-sequence, considering numPos positions starting at position initialPos. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V , class M >
const V & QUESO::BaseVectorSequence< V, M >::subMinPlain ( ) const

Finds the minimum value of the sub-sequence.

Definition at line 146 of file VectorSequence.C.

147 {
148  if (m_subMinPlain == NULL) {
149  m_subMinPlain = m_vectorSpace.newVector();
150  if (m_subMaxPlain == NULL) m_subMaxPlain = m_vectorSpace.newVector();
151  subMinMaxExtra(0,this->subSequenceSize(),*m_subMinPlain,*m_subMaxPlain);
152  }
153 
154  return *m_subMinPlain;
155 }
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::BaseVectorSequence::subMinMaxExtra
virtual void subMinMaxExtra(unsigned int initialPos, unsigned int numPos, V &minVec, V &maxVec) const =0
Finds the minimum and the maximum values of the sub-sequence, considering numPos positions starting a...
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subPopulationVariance ( unsigned int  initialPos,
unsigned int  numPos,
const V &  meanVec,
V &  popVec 
) const
pure virtual

Finds the population variance of the sub-sequence, considering numPos positions starting at position initialPos and of mean meanVec. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V, class M>
double QUESO::BaseVectorSequence< V, M >::subPositionsOfMaximum ( const ScalarSequence< double > &  subCorrespondingScalarValues,
BaseVectorSequence< V, M > &  subPositionsOfMaximum 
)

Finds the positions where the maximum element occurs in the sub-sequence.

Definition at line 377 of file VectorSequence.C.

References QUESO::queso_require_equal_to_msg, QUESO::BaseVectorSequence< V, M >::resizeSequence(), QUESO::BaseVectorSequence< V, M >::setPositionValues(), QUESO::ScalarSequence< T >::subMaxPlain(), and QUESO::ScalarSequence< T >::subSequenceSize().

Referenced by QUESO::MetropolisHastingsSG< P_V, P_M >::generateSequence().

380 {
381  if (m_env.subDisplayFile()) {
382  *m_env.subDisplayFile() << "Entering BaseVectorSequence<V,M>::subPositionsOfMaximum()"
383  << ": subCorrespondingScalarValues,subSequenceSize() = " << subCorrespondingScalarValues.subSequenceSize()
384  << ", this->subSequenceSize = " << this->subSequenceSize()
385  << std::endl;
386  }
387 
388  queso_require_equal_to_msg(subCorrespondingScalarValues.subSequenceSize(), this->subSequenceSize(), "invalid input");
389 
390  double subMaxValue = subCorrespondingScalarValues.subMaxPlain();
391  unsigned int iMax = subCorrespondingScalarValues.subSequenceSize();
392 
393  unsigned int subNumPos = 0;
394  for (unsigned int i = 0; i < iMax; ++i) {
395  if (subCorrespondingScalarValues[i] == subMaxValue) {
396  subNumPos++;
397  }
398  }
399 
400  V tmpVec(this->vectorSpace().zeroVector());
401  subPositionsOfMaximum.resizeSequence(subNumPos);
402  unsigned int j = 0;
403  for (unsigned int i = 0; i < iMax; ++i) {
404  if (subCorrespondingScalarValues[i] == subMaxValue) {
405  this->getPositionValues (i,tmpVec);
406  subPositionsOfMaximum.setPositionValues(j,tmpVec);
407  j++;
408  }
409  }
410 
411  if (m_env.subDisplayFile()) {
412  *m_env.subDisplayFile() << "Leaving BaseVectorSequence<V,M>::subPositionsOfMaximum()"
413  << std::endl;
414  }
415 
416  return subMaxValue;
417 }
QUESO::ScalarSequence::subMaxPlain
const T & subMaxPlain() const
Finds the maximum value of the sub-sequence of scalars.
Definition: ScalarSequence.C:369
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::BaseVectorSequence::subPositionsOfMaximum
double subPositionsOfMaximum(const ScalarSequence< double > &subCorrespondingScalarValues, BaseVectorSequence< V, M > &subPositionsOfMaximum)
Finds the positions where the maximum element occurs in the sub-sequence.
Definition: VectorSequence.C:377
QUESO::BaseVectorSequence::getPositionValues
virtual void getPositionValues(unsigned int posId, V &vec) const =0
Gets the values of the sequence at position posId and stores them at vec. See template specialization...
QUESO::BaseVectorSequence::vectorSpace
const VectorSpace< V, M > & vectorSpace() const
Vector space; access to protected attribute VectorSpace&lt;V,M&gt;&amp; m_vectorSpace.
Definition: VectorSequence.C:111
QUESO::queso_require_equal_to_msg
MonteCarloSGOptions::MonteCarloSGOptions(const BaseEnvironment &env, const char *prefix, const McOptionsValues &alternativeOptionsValues queso_require_equal_to_msg)(m_env.optionsInputFileName(), std::string(""), std::string("this constructor is incompatible with the existence of an options input file"))
Definition: MonteCarloSGOptions.C:460
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:431
QUESO::ScalarSequence::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of scalars.
Definition: ScalarSequence.C:136
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:320
template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subSampleVarianceExtra ( unsigned int  initialPos,
unsigned int  numPos,
const V &  meanVec,
V &  samVec 
) const
pure virtual

Finds the sample variance of the sub-sequence, considering numPos positions starting at position initialPos and of mean meanVec. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V , class M >
const V & QUESO::BaseVectorSequence< V, M >::subSampleVariancePlain ( ) const

Finds the variance of a sample of the sub-sequence.

Definition at line 246 of file VectorSequence.C.

247 {
248  if (m_subSampleVariancePlain == NULL) {
249  m_subSampleVariancePlain = m_vectorSpace.newVector();
250  subSampleVarianceExtra(0,subSequenceSize(),subMeanPlain(),*m_subSampleVariancePlain);
251  }
252 
253  return *m_subSampleVariancePlain;
254 }
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::BaseVectorSequence::subMeanPlain
const V & subMeanPlain() const
Finds the mean value of the sub-sequence.
Definition: VectorSequence.C:198
QUESO::BaseVectorSequence::subSampleVarianceExtra
virtual void subSampleVarianceExtra(unsigned int initialPos, unsigned int numPos, const V &meanVec, V &samVec) const =0
Finds the sample variance of the sub-sequence, considering numPos positions starting at position init...
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subScalesForKde ( unsigned int  initialPos,
const V &  iqrVec,
unsigned int  kdeDimension,
V &  scaleVec 
) const
pure virtual

Selects the scales (bandwidth, scaleVec) for the kernel density estimation, considering only the sub-sequence. See template specialization.

The bandwidth of the kernel is a free parameter which exhibits a strong influence on the resulting estimate. Silverman (1986) suggests the following normal-based estimates: S1 = 1.06 × (standard deviation) × n^{-1/5} S2 = 0.79 × (iqrVec) × n^{-1/5}, where iqrVec is the interquartile range scaleVec = 0.90 × minimum(standard deviation, iqrVec /1.34) × n^{-1/5}. These estimates are popular due to their simplicity, and are used in QUESO with the adaptation of the exponent oven the sample size n (-1/5) with -1/(4 + kdeDimension) where kdeDimension is the KDE dimension.

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual unsigned int QUESO::BaseVectorSequence< V, M >::subSequenceSize ( ) const
pure virtual

Size of the sub-sequence of vectors. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >, and QUESO::ArrayOfSequences< V, M >.

Referenced by QUESO::MonteCarloSG< P_V, P_M, Q_V, Q_M >::actualGenerateSequence(), QUESO::BaseVectorSequence< V, M >::append(), QUESO::ComputeCovCorrMatricesBetweenVectorSequences(), QUESO::MetropolisHastingsSG< P_V, P_M >::generateFullChain(), QUESO::MLSampling< P_V, P_M >::generateSequence(), QUESO::MetropolisHastingsSG< P_V, P_M >::generateSequence(), QUESO::MonteCarloSG< P_V, P_M, Q_V, Q_M >::internGenerateSequence(), QUESO::MetropolisHastingsSG< P_V, P_M >::updateAdaptedCovMatrix(), and QUESO::MetropolisHastingsSG< P_V, P_M >::writeInfo().

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subUniformlySampledCdf ( const V &  numEvaluationPointsVec,
ArrayOfOneDGrids< V, M > &  cdfGrids,
ArrayOfOneDTables< V, M > &  cdfValues 
) const
pure virtual

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subUniformlySampledMdf ( const V &  numEvaluationPointsVec,
ArrayOfOneDGrids< V, M > &  mdfGrids,
ArrayOfOneDTables< V, M > &  mdfValues 
) const
pure virtual

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subWriteContents ( unsigned int  initialPos,
unsigned int  numPos,
const std::string &  fileName,
const std::string &  fileType,
const std::set< unsigned int > &  allowedSubEnvIds 
) const
pure virtual

Writes info of the sub-sequence to a file. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >.

Referenced by QUESO::MonteCarloSG< P_V, P_M, Q_V, Q_M >::actualGenerateSequence(), QUESO::MetropolisHastingsSG< P_V, P_M >::generateFullChain(), QUESO::MetropolisHastingsSG< P_V, P_M >::generateSequence(), and QUESO::MonteCarloSG< P_V, P_M, Q_V, Q_M >::internGenerateSequence().

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::subWriteContents ( unsigned int  initialPos,
unsigned int  numPos,
std::ofstream &  ofsvar,
const std::string &  fileType 
) const
pure virtual

Writes info of the sub-sequence to a file. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V , class M >
const BoxSubset< V, M > & QUESO::BaseVectorSequence< V, M >::unifiedBoxPlain ( ) const

Finds a box subset of the unified-sequence (given by the min and max values of the unified sequence calculated via unifiedMinPlain and unifiedMaxPlain).

Definition at line 284 of file VectorSequence.C.

285 {
286  if (m_unifiedBoxPlain == NULL) {
287  m_unifiedBoxPlain = new BoxSubset<V,M>(m_name.c_str(),
288  m_vectorSpace,
289  this->unifiedMinPlain(),
290  this->unifiedMaxPlain());
291  }
292 
293  return *m_unifiedBoxPlain;
294 }
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
QUESO::BaseVectorSequence::m_unifiedBoxPlain
BoxSubset< V, M > * m_unifiedBoxPlain
Definition: VectorSequence.h:447
QUESO::BaseVectorSequence::unifiedMinPlain
const V & unifiedMinPlain() const
Finds the minimum value of the unified sequence.
Definition: VectorSequence.C:159
QUESO::BaseVectorSequence::unifiedMaxPlain
const V & unifiedMaxPlain() const
Finds the maximum value of the unified sequence.
Definition: VectorSequence.C:185
template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::unifiedGaussian1dKde ( unsigned int  initialPos,
const V &  unifiedScaleVec,
const std::vector< V * > &  unifiedEvaluationParamVecs,
std::vector< V * > &  unifiedDensityVecs 
) const
pure virtual

Gaussian kernel for the KDE estimate of the unified sequence. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::unifiedHistogram ( unsigned int  initialPos,
const V &  unifiedMinVec,
const V &  unifiedMaxVec,
std::vector< V * > &  unifiedCentersForAllBins,
std::vector< V * > &  unifiedQuanttsForAllBins 
) const
pure virtual

Calculates the histogram of the unified sequence. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::unifiedInterQuantileRange ( unsigned int  initialPos,
V &  unifiedIqrVec 
) const
pure virtual

Returns the interquartile range of the values in the unified sequence. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V , class M >
const V & QUESO::BaseVectorSequence< V, M >::unifiedMaxPlain ( ) const

Finds the maximum value of the unified sequence.

Definition at line 185 of file VectorSequence.C.

186 {
187  if (m_unifiedMaxPlain == NULL) {
188  if (m_unifiedMinPlain == NULL) m_unifiedMinPlain = m_vectorSpace.newVector();
189  m_unifiedMaxPlain = m_vectorSpace.newVector();
190  unifiedMinMaxExtra(0,this->subSequenceSize(),*m_unifiedMinPlain,*m_unifiedMaxPlain);
191  }
192 
193  return *m_unifiedMaxPlain;
194 }
QUESO::BaseVectorSequence::unifiedMinMaxExtra
virtual void unifiedMinMaxExtra(unsigned int initialPos, unsigned int numPos, V &unifiedMinVec, V &unifiedMaxVec) const =0
Finds the minimum and the maximum values of the unified sequence, considering numPos positions starti...
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::unifiedMeanExtra ( unsigned int  initialPos,
unsigned int  numPos,
V &  unifiedMeanVec 
) const
pure virtual

Finds the mean value of the unified sequence of numPos positions starting at position initialPos. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >.

Referenced by QUESO::ComputeCovCorrMatricesBetweenVectorSequences().

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::unifiedMeanMonitorAlloc ( unsigned int  numberOfMonitorPositions)
protectedpure virtual

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::unifiedMeanMonitorFree ( )
protectedpure virtual

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::unifiedMeanMonitorRun ( unsigned int  monitorPosition,
V &  unifiedMeanVec,
V &  unifiedMeanCltStd 
)
protectedpure virtual

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::unifiedMeanMonitorStore ( unsigned int  i,
unsigned int  monitorPosition,
V &  unifiedMeanVec,
V &  unifiedMeanCltStd 
)
protectedpure virtual

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::unifiedMeanMonitorWrite ( std::ofstream &  ofs)
protectedpure virtual

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V , class M >
const V & QUESO::BaseVectorSequence< V, M >::unifiedMeanPlain ( ) const

Finds the mean value of the unified sequence.

Definition at line 210 of file VectorSequence.C.

211 {
212  if (m_unifiedMeanPlain == NULL) {
213  m_unifiedMeanPlain = m_vectorSpace.newVector();
214  unifiedMeanExtra(0,subSequenceSize(),*m_unifiedMeanPlain);
215  }
216 
217  return *m_unifiedMeanPlain;
218 }
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::BaseVectorSequence::unifiedMeanExtra
virtual void unifiedMeanExtra(unsigned int initialPos, unsigned int numPos, V &unifiedMeanVec) const =0
Finds the mean value of the unified sequence of numPos positions starting at position initialPos...
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::unifiedMedianExtra ( unsigned int  initialPos,
unsigned int  localNumPos,
V &  unifiedMedianVec 
) const
pure virtual

Finds the median value of the unified sequence, considering numPos positions starting at position initialPos. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V , class M >
const V & QUESO::BaseVectorSequence< V, M >::unifiedMedianPlain ( ) const

Finds the median value of the unified sequence.

Definition at line 234 of file VectorSequence.C.

235 {
236  if (m_unifiedMedianPlain == NULL) {
237  m_unifiedMedianPlain = m_vectorSpace.newVector();
238  unifiedMedianExtra(0, subSequenceSize(), *m_unifiedMedianPlain);
239  }
240 
241  return *m_unifiedMedianPlain;
242 }
QUESO::BaseVectorSequence::unifiedMedianExtra
virtual void unifiedMedianExtra(unsigned int initialPos, unsigned int localNumPos, V &unifiedMedianVec) const =0
Finds the median value of the unified sequence, considering numPos positions starting at position ini...
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::unifiedMinMaxExtra ( unsigned int  initialPos,
unsigned int  numPos,
V &  unifiedMinVec,
V &  unifiedMaxVec 
) const
pure virtual

Finds the minimum and the maximum values of the unified sequence, considering numPos positions starting at position initialPos. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V , class M >
const V & QUESO::BaseVectorSequence< V, M >::unifiedMinPlain ( ) const

Finds the minimum value of the unified sequence.

Definition at line 159 of file VectorSequence.C.

160 {
161  if (m_unifiedMinPlain == NULL) {
162  m_unifiedMinPlain = m_vectorSpace.newVector();
163  if (m_unifiedMaxPlain == NULL) m_unifiedMaxPlain = m_vectorSpace.newVector();
164  unifiedMinMaxExtra(0,this->subSequenceSize(),*m_unifiedMinPlain,*m_unifiedMaxPlain);
165  }
166 
167  return *m_unifiedMinPlain;
168 }
QUESO::BaseVectorSequence::unifiedMinMaxExtra
virtual void unifiedMinMaxExtra(unsigned int initialPos, unsigned int numPos, V &unifiedMinVec, V &unifiedMaxVec) const =0
Finds the minimum and the maximum values of the unified sequence, considering numPos positions starti...
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::unifiedPopulationVariance ( unsigned int  initialPos,
unsigned int  numPos,
const V &  unifiedMeanVec,
V &  unifiedPopVec 
) const
pure virtual

Finds the population variance of the unified-sequence, considering numPos positions starting at position initialPos and of mean meanVec. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V, class M>
double QUESO::BaseVectorSequence< V, M >::unifiedPositionsOfMaximum ( const ScalarSequence< double > &  subCorrespondingScalarValues,
BaseVectorSequence< V, M > &  unifiedPositionsOfMaximum 
)

Finds the positions where the maximum element occurs in the unified sequence.

Parameters
thisThe underlying sequence of vectors
subCorrespondingScalarValuesFor a given process, a scalar sequence where element i corresponds to element i of this.
unifiedPositionsOfMaximumUpon returning, on process 0 on chain 0, this will contain states that correspond to the unique maximum value in subCorrespondingScalarValues over all processes.
Returns
Maximum element of subCorrespondingScalarValues over all processes.

Definition at line 421 of file VectorSequence.C.

References QUESO::BaseVectorSequence< V, M >::getPositionValues(), QUESO::queso_require_equal_to_msg, QUESO::BaseVectorSequence< V, M >::resizeSequence(), QUESO::BaseVectorSequence< V, M >::setPositionValues(), QUESO::ScalarSequence< T >::subMaxPlain(), and QUESO::ScalarSequence< T >::subSequenceSize().

Referenced by QUESO::MetropolisHastingsSG< P_V, P_M >::generateSequence().

424 {
425  if (m_env.subDisplayFile()) {
426  *m_env.subDisplayFile() << "Entering BaseVectorSequence<V,M>::unifiedPositionsOfMaximum()"
427  << ": subCorrespondingScalarValues,subSequenceSize() = " << subCorrespondingScalarValues.subSequenceSize()
428  << ", this->subSequenceSize = " << this->subSequenceSize()
429  << std::endl;
430  }
431 
432  queso_require_equal_to_msg(subCorrespondingScalarValues.subSequenceSize(), this->subSequenceSize(), "invalid input");
433 
434  // Compute the max on each process
435  double subMaxValue = subCorrespondingScalarValues.subMaxPlain();
436 
437  //******************************************************************
438  // Get overall max
439  //******************************************************************
440  double unifiedMaxValue;
441  std::vector<double> sendbufPos(1,0.);
442  for (unsigned int i = 0; i < sendbufPos.size(); ++i) {
443  sendbufPos[i] = subMaxValue;
444  }
445  m_env.inter0Comm().template Allreduce<double>(&sendbufPos[0], &unifiedMaxValue, (int) sendbufPos.size(), RawValue_MPI_MAX,
446  "BaseVectorSequence<V,M>::unifiedPositionsOfMaximum()",
447  "failed MPI.Allreduce() for max");
448 
449  // Find number of elements (subNumPos) on each process that attain the
450  // global max. This could be zero.
451  unsigned int iMax = subCorrespondingScalarValues.subSequenceSize();
452  int subNumPos = 0; // Yes, 'int', due to MPI to be used soon
453  for (unsigned int i = 0; i < iMax; ++i) {
454  if (subCorrespondingScalarValues[i] == unifiedMaxValue) {
455  subNumPos++;
456  }
457  }
458 
459  // Fill up unifiedPositionsOfMaximum with the states that attain maxima
460  // (if they exist)
461  V tmpVec(this->vectorSpace().zeroVector());
462  unifiedPositionsOfMaximum.resizeSequence(subNumPos); // subNumPos could be 0
463  unsigned int j = 0;
464  for (unsigned int i = 0; i < iMax; ++i) {
465  // This 'if' statement is false if subNumPos == 0
466  if (subCorrespondingScalarValues[i] == unifiedMaxValue) {
467  this->getPositionValues (i,tmpVec);
468  unifiedPositionsOfMaximum.setPositionValues(j,tmpVec);
469  j++;
470  }
471  }
472 
473  // Compute total (over all processes) number of elements that attain maxima
474  std::vector<int> auxBuf(1,0);
475  int unifiedNumPos = 0; // Yes, 'int', due to MPI to be used soon
476  auxBuf[0] = subNumPos;
477  m_env.inter0Comm().template Allreduce<int>(&auxBuf[0], &unifiedNumPos, (int) auxBuf.size(), RawValue_MPI_SUM,
478  "BaseVectorSequence<V,M>::unifiedPositionsOfMaximum()",
479  "failed MPI.Allreduce() for sum");
480 
481  // Resize positions to hold all elements that attain maxima
482  unifiedPositionsOfMaximum.resizeSequence(unifiedNumPos);
483 
484  //******************************************************************
485  // Use MPI_Gatherv for number of positions
486  //******************************************************************
487  // Gather up *number* of maxima on each chain and store in recvcntsPos
488  unsigned int Np = (unsigned int) m_env.inter0Comm().NumProc();
489 
490  std::vector<int> recvcntsPos(Np,0); // '0' is NOT the correct value for recvcntsPos[0]
491  m_env.inter0Comm().template Gather<int>(&subNumPos, 1, &recvcntsPos[0], (int) 1, 0,
492  "BaseVectorSequence<V,M>::unifiedPositionsOfMaximum()",
493  "failed MPI.Gatherv()");
494  if (m_env.inter0Rank() == 0) {
495  queso_require_equal_to_msg(recvcntsPos[0], (int) subNumPos, "failed MPI.Gather() result at proc 0 (recvcntsPos[0])");
496  }
497 
498  // Construct offset indices based on number of maxima
499  std::vector<int> displsPos(Np,0);
500  for (unsigned int nodeId = 1; nodeId < Np; ++nodeId) { // Yes, from '1' on
501  displsPos[nodeId] = displsPos[nodeId-1] + recvcntsPos[nodeId-1];
502  }
503  if (m_env.inter0Rank() == 0) {
504  queso_require_equal_to_msg(unifiedNumPos, (displsPos[Np - 1] + recvcntsPos[Np - 1]), "failed MPI.Gather() result at proc 0 (unifiedNumPos)");
505  }
506 
507  //******************************************************************
508  // Use MPI_Gatherv for number of doubles
509  //******************************************************************
510  // Gather up number of states that attain maxima multiplied by the size of
511  // the state (on each process). Store this in recvcntsDbs.
512  // So recvcntsDbs[i] is the number of states that attain maxima on chain i
513  // multiplied by the size of the state (a state could be a vector of length
514  // > 1).
515  unsigned int dimSize = m_vectorSpace.dimLocal();
516  int subNumDbs = subNumPos * dimSize; // Yes, 'int', due to MPI to be used soon
517  std::vector<int> recvcntsDbs(Np,0); // '0' is NOT the correct value for recvcntsDbs[0]
518  m_env.inter0Comm().template Gather<int>(&subNumDbs, 1, &recvcntsDbs[0], (int) 1, 0,
519  "BaseVectorSequence<V,M>::unifiedPositionsOfMaximum()",
520  "failed MPI.Gatherv()");
521  if (m_env.inter0Rank() == 0) {
522  queso_require_equal_to_msg(recvcntsDbs[0], (int) subNumDbs, "failed MPI.Gather() result at proc 0 (recvcntsDbs[0])");
523  }
524 
525  // Now gather up the offsets based on the number of states (mulitplied by the
526  // size of the state)
527  std::vector<int> displsDbs(Np,0);
528  for (unsigned int nodeId = 1; nodeId < Np; ++nodeId) { // Yes, from '1' on
529  displsDbs[nodeId] = displsDbs[nodeId-1] + recvcntsDbs[nodeId-1];
530  }
531  if (m_env.inter0Rank() == 0) {
532  queso_require_equal_to_msg(((int) (unifiedNumPos*dimSize)), (displsDbs[Np - 1] + recvcntsDbs[Np - 1]), "failed MPI.Gather() result at proc 0 (unifiedNumPos*dimSize)");
533  }
534 
535  //******************************************************************
536  // Prepare counters and buffers for gatherv of maximum positions
537  //******************************************************************
538  // Take all the states on all chains that attain maxima, and put them in a
539  // send buffer ready for MPI
540  std::vector<double> sendbufDbs(subNumDbs,0.);
541  for (unsigned int i = 0; i < (unsigned int) subNumPos; ++i) {
542  unifiedPositionsOfMaximum.getPositionValues(i,tmpVec);
543  for (unsigned int j = 0; j < dimSize; ++j) {
544  sendbufDbs[i*dimSize + j] = tmpVec[j];
545  }
546  }
547 
548  std::vector<double> recvbufDbs(unifiedNumPos * dimSize);
549 
550  // Gather up all states that attain maxima and store then in recvbufDbs
551  m_env.inter0Comm().template Gatherv<double>(&sendbufDbs[0], (int) subNumDbs,
552  &recvbufDbs[0], (int *) &recvcntsDbs[0], (int *) &displsDbs[0], 0,
553  "BaseVectorSequence<V,M>::unifiedPositionsOfMaximum()",
554  "failed MPI.Gatherv()");
555 
556  //******************************************************************
557  // Transfer data from 'recvbuf' to 'unifiedPositionsOfMaximum'
558  //******************************************************************
559  // Copy over all the gathered states to the unifiedPositionsOfMaximum
560  // variable on process 0. Process 0 now contains everything.
561  if (m_env.inter0Rank() == (int) 0) {
562  for (unsigned int i = 0; i < (unsigned int) unifiedNumPos; ++i) {
563  for (unsigned int j = 0; j < dimSize; ++j) {
564  tmpVec[j] = recvbufDbs[i*dimSize + j];
565  }
566  unifiedPositionsOfMaximum.setPositionValues(i,tmpVec);
567  }
568  }
569  else {
570  // Process zero has all the states that attain maxima, so let's nuke the
571  // others rather than letting them contain NULL pointers
572  unifiedPositionsOfMaximum.resizeSequence(0);
573  }
574 
575  if (m_env.subDisplayFile()) {
576  *m_env.subDisplayFile() << "Leaving BaseVectorSequence<V,M>::unifiedPositionsOfMaximum()"
577  << std::endl;
578  }
579 
580  return unifiedMaxValue;
581 }
QUESO::ScalarSequence::subMaxPlain
const T & subMaxPlain() const
Finds the maximum value of the sub-sequence of scalars.
Definition: ScalarSequence.C:369
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::BaseEnvironment::inter0Comm
const MpiComm & inter0Comm() const
Access function for MpiComm communicator for processes with subRank() 0.
Definition: Environment.C:313
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
QUESO::BaseVectorSequence::getPositionValues
virtual void getPositionValues(unsigned int posId, V &vec) const =0
Gets the values of the sequence at position posId and stores them at vec. See template specialization...
QUESO::BaseVectorSequence::vectorSpace
const VectorSpace< V, M > & vectorSpace() const
Vector space; access to protected attribute VectorSpace&lt;V,M&gt;&amp; m_vectorSpace.
Definition: VectorSequence.C:111
QUESO::queso_require_equal_to_msg
MonteCarloSGOptions::MonteCarloSGOptions(const BaseEnvironment &env, const char *prefix, const McOptionsValues &alternativeOptionsValues queso_require_equal_to_msg)(m_env.optionsInputFileName(), std::string(""), std::string("this constructor is incompatible with the existence of an options input file"))
Definition: MonteCarloSGOptions.C:460
QUESO::MpiComm::NumProc
int NumProc() const
Returns total number of processes.
Definition: MpiComm.C:133
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:431
QUESO::BaseEnvironment::inter0Rank
int inter0Rank() const
Returns the process inter0 rank.
Definition: Environment.C:307
QUESO::BaseVectorSequence::unifiedPositionsOfMaximum
double unifiedPositionsOfMaximum(const ScalarSequence< double > &subCorrespondingScalarValues, BaseVectorSequence< V, M > &unifiedPositionsOfMaximum)
Finds the positions where the maximum element occurs in the unified sequence.
Definition: VectorSequence.C:421
QUESO::ScalarSequence::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of scalars.
Definition: ScalarSequence.C:136
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:320
template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::unifiedReadContents ( const std::string &  fileName,
const std::string &  fileType,
const unsigned int  subSequenceSize 
)
pure virtual

Reads info of the unified sequence from a file. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >, and QUESO::ArrayOfSequences< V, M >.

Referenced by QUESO::MonteCarloSG< P_V, P_M, Q_V, Q_M >::actualReadSequence(), and QUESO::MetropolisHastingsSG< P_V, P_M >::readFullChain().

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::unifiedSampleVarianceExtra ( unsigned int  initialPos,
unsigned int  numPos,
const V &  unifiedMeanVec,
V &  unifiedSamVec 
) const
pure virtual

Finds the sample variance of the unified sequence, considering numPos positions starting at position initialPos and of mean meanVec. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >.

Referenced by QUESO::ComputeCovCorrMatricesBetweenVectorSequences().

template<class V , class M >
const V & QUESO::BaseVectorSequence< V, M >::unifiedSampleVariancePlain ( ) const

Finds the variance of a sample of the unified sequence.

Definition at line 258 of file VectorSequence.C.

259 {
260  if (m_unifiedSampleVariancePlain == NULL) {
261  m_unifiedSampleVariancePlain = m_vectorSpace.newVector();
262  unifiedSampleVarianceExtra(0,subSequenceSize(),unifiedMeanPlain(),*m_unifiedSampleVariancePlain);
263  }
264 
265  return *m_unifiedSampleVariancePlain;
266 }
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::BaseVectorSequence::unifiedSampleVarianceExtra
virtual void unifiedSampleVarianceExtra(unsigned int initialPos, unsigned int numPos, const V &unifiedMeanVec, V &unifiedSamVec) const =0
Finds the sample variance of the unified sequence, considering numPos positions starting at position ...
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
QUESO::BaseVectorSequence::unifiedMeanPlain
const V & unifiedMeanPlain() const
Finds the mean value of the unified sequence.
Definition: VectorSequence.C:210
template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::unifiedScalesForKde ( unsigned int  initialPos,
const V &  unifiedIqrVec,
unsigned int  kdeDimension,
V &  unifiedScaleVec 
) const
pure virtual

Selects the scales (bandwidth) for the kernel density estimation, considering the unified sequence. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V , class M >
unsigned int QUESO::BaseVectorSequence< V, M >::unifiedSequenceSize ( ) const

Calculates the size of the unified sequence of vectors.

TODO: this procedure does not support parallel vectors yet.

Definition at line 70 of file VectorSequence.C.

Referenced by QUESO::MLSampling< P_V, P_M >::checkpointML(), and QUESO::MLSampling< P_V, P_M >::generateSequence_Step02_inter0().

71 {
72  unsigned int unifiedNumSamples = 0;
73 
74  bool useOnlyInter0Comm = (m_vectorSpace.numOfProcsForStorage() == 1);
75 
76  if (useOnlyInter0Comm) {
77  if (m_env.inter0Rank() >= 0) {
78  unsigned int subNumSamples = this->subSequenceSize();
79  m_env.inter0Comm().template Allreduce<unsigned int>(&subNumSamples, &unifiedNumSamples, (int) 1, RawValue_MPI_SUM,
80  "BaseVectorSequence<V,M>::unifiedSequenceSize()",
81  "failed MPI.Allreduce() for unifiedSequenceSize()");
82  }
83  else {
84  // Node not in the 'inter0' communicator
85  unifiedNumSamples = this->subSequenceSize();
86  }
87  }
88  else {
89  queso_require_msg(useOnlyInter0Comm, "parallel vectors not supported yet");
90  }
91 
92  return unifiedNumSamples;
93 }
QUESO::BaseVectorSequence::subSequenceSize
virtual unsigned int subSequenceSize() const =0
Size of the sub-sequence of vectors. See template specialization.
QUESO::BaseEnvironment::inter0Comm
const MpiComm & inter0Comm() const
Access function for MpiComm communicator for processes with subRank() 0.
Definition: Environment.C:313
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:431
QUESO::BaseEnvironment::inter0Rank
int inter0Rank() const
Returns the process inter0 rank.
Definition: Environment.C:307
template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::unifiedUniformlySampledCdf ( const V &  numEvaluationPointsVec,
ArrayOfOneDGrids< V, M > &  unifiedCdfGrids,
ArrayOfOneDTables< V, M > &  unifieddfValues 
) const
pure virtual

Implemented in QUESO::SequenceOfVectors< V, M >.

template<class V = GslVector, class M = GslMatrix>
virtual void QUESO::BaseVectorSequence< V, M >::unifiedWriteContents ( const std::string &  fileName,
const std::string &  fileType 
) const
pure virtual

Writes info of the unified sequence to a file. See template specialization.

Implemented in QUESO::SequenceOfVectors< V, M >, and QUESO::ArrayOfSequences< V, M >.

Referenced by QUESO::MetropolisHastingsSG< P_V, P_M >::generateSequence(), and QUESO::MonteCarloSG< P_V, P_M, Q_V, Q_M >::internGenerateSequence().

template<class V , class M >
unsigned int QUESO::BaseVectorSequence< V, M >::vectorSizeGlobal ( ) const

Global dimension (size) of the vector space.

Definition at line 104 of file VectorSequence.C.

105 {
106  return m_vectorSpace.dimGlobal();
107 }
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
template<class V , class M >
unsigned int QUESO::BaseVectorSequence< V, M >::vectorSizeLocal ( ) const

Local dimension (size) of the vector space.

Definition at line 97 of file VectorSequence.C.

Referenced by QUESO::MonteCarloSG< P_V, P_M, Q_V, Q_M >::generateSequence(), and QUESO::MetropolisHastingsSG< P_V, P_M >::generateSequence().

98 {
99  return m_vectorSpace.dimLocal();
100 }
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432
template<class V , class M >
const VectorSpace< V, M > & QUESO::BaseVectorSequence< V, M >::vectorSpace ( ) const

Vector space; access to protected attribute VectorSpace<V,M>& m_vectorSpace.

Definition at line 111 of file VectorSequence.C.

Referenced by QUESO::BaseVectorSequence< V, M >::append(), and QUESO::ComputeCovCorrMatricesBetweenVectorSequences().

112 {
113  return m_vectorSpace;
114 }
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:432

Member Data Documentation

template<class V = GslVector, class M = GslMatrix>
const BaseEnvironment& QUESO::BaseVectorSequence< V, M >::m_env
protected

Definition at line 431 of file VectorSequence.h.

Referenced by QUESO::ArrayOfSequences< V, M >::ArrayOfSequences().

template<class V = GslVector, class M = GslMatrix>
Fft<double>* QUESO::BaseVectorSequence< V, M >::m_fftObj
mutableprotected

Definition at line 435 of file VectorSequence.h.

template<class V = GslVector, class M = GslMatrix>
std::string QUESO::BaseVectorSequence< V, M >::m_name
protected

Definition at line 433 of file VectorSequence.h.

Referenced by QUESO::BaseVectorSequence< V, M >::copy().

template<class V = GslVector, class M = GslMatrix>
BoxSubset<V,M>* QUESO::BaseVectorSequence< V, M >::m_subBoxPlain
mutableprotected

Definition at line 446 of file VectorSequence.h.

template<class V = GslVector, class M = GslMatrix>
V* QUESO::BaseVectorSequence< V, M >::m_subMaxPlain
mutableprotected

Definition at line 438 of file VectorSequence.h.

template<class V = GslVector, class M = GslMatrix>
V* QUESO::BaseVectorSequence< V, M >::m_subMeanPlain
mutableprotected

Definition at line 440 of file VectorSequence.h.

template<class V = GslVector, class M = GslMatrix>
V* QUESO::BaseVectorSequence< V, M >::m_subMedianPlain
mutableprotected

Definition at line 442 of file VectorSequence.h.

template<class V = GslVector, class M = GslMatrix>
V* QUESO::BaseVectorSequence< V, M >::m_subMinPlain
mutableprotected

Definition at line 436 of file VectorSequence.h.

template<class V = GslVector, class M = GslMatrix>
V* QUESO::BaseVectorSequence< V, M >::m_subSampleVariancePlain
mutableprotected

Definition at line 444 of file VectorSequence.h.

template<class V = GslVector, class M = GslMatrix>
BoxSubset<V,M>* QUESO::BaseVectorSequence< V, M >::m_unifiedBoxPlain
mutableprotected

Definition at line 447 of file VectorSequence.h.

template<class V = GslVector, class M = GslMatrix>
V* QUESO::BaseVectorSequence< V, M >::m_unifiedMaxPlain
mutableprotected

Definition at line 439 of file VectorSequence.h.

template<class V = GslVector, class M = GslMatrix>
V* QUESO::BaseVectorSequence< V, M >::m_unifiedMeanPlain
mutableprotected

Definition at line 441 of file VectorSequence.h.

template<class V = GslVector, class M = GslMatrix>
V* QUESO::BaseVectorSequence< V, M >::m_unifiedMedianPlain
mutableprotected

Definition at line 443 of file VectorSequence.h.

template<class V = GslVector, class M = GslMatrix>
V* QUESO::BaseVectorSequence< V, M >::m_unifiedMinPlain
mutableprotected

Definition at line 437 of file VectorSequence.h.

template<class V = GslVector, class M = GslMatrix>
V* QUESO::BaseVectorSequence< V, M >::m_unifiedSampleVariancePlain
mutableprotected

Definition at line 445 of file VectorSequence.h.

template<class V = GslVector, class M = GslMatrix>
const VectorSpace<V,M>& QUESO::BaseVectorSequence< V, M >::m_vectorSpace
protected

Definition at line 432 of file VectorSequence.h.

Referenced by QUESO::BaseVectorSequence< V, M >::copy().

The documentation for this class was generated from the following files:
Generated on Tue Jun 5 2018 19:49:02 for queso-0.57.1 by  doxygen 1.8.5