queso-0.51.1
Private Member Functions | Private Attributes | List of all members
QUESO::SequenceOfVectors< V, M > Class Template Reference

Class for handling vector samples (sequence of vectors). More...

#include <SequenceOfVectors.h>

Inheritance diagram for QUESO::SequenceOfVectors< V, M >:
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Collaboration diagram for QUESO::SequenceOfVectors< V, M >:
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Public Types

Class typedefs
typedef std::vector< const V * >
::const_iterator 		seqVectorPositionConstIteratorTypedef
 
typedef std::vector< const V * >
::iterator 		seqVectorPositionIteratorTypedef
 

Public Member Functions

Constructor/Destructor methods
 SequenceOfVectors (const VectorSpace< V, M > &vectorSpace, unsigned int subSequenceSize, const std::string &name)
 Default constructor. More...
 
 ~SequenceOfVectors ()
 Destructor. More...
 
Set methods
SequenceOfVectors< V, M > & operator= (const SequenceOfVectors< V, M > &rhs)
 Copies values from rhs to this. More...
 
Sequence methods
unsigned int subSequenceSize () const
 Size of the sub-sequence of vectors. More...
 
void resizeSequence (unsigned int newSubSequenceSize)
 Resizes the sequence. More...
 
void resetValues (unsigned int initialPos, unsigned int numPos)
 Resets a total of numPos values of the sequence starting at position initialPos. More...
 
void erasePositions (unsigned int initialPos, unsigned int numPos)
 Erases numPos elements of the sequence starting at position initialPos. More...
 
void getPositionValues (unsigned int posId, V &vec) const
 Gets the values of the sequence at position posId and stores them at vec. More...
 
void setPositionValues (unsigned int posId, const V &vec)
 Set the values in vec at position posId of the sequence. More...
 
void subUniformlySampledCdf (const V &numEvaluationPointsVec, ArrayOfOneDGrids< V, M > &cdfGrids, ArrayOfOneDTables< V, M > &cdfValues) const
 Uniformly samples from the CDF from the sub-sequence. More...
 
void unifiedUniformlySampledCdf (const V &numEvaluationPointsVec, ArrayOfOneDGrids< V, M > &unifiedCdfGrids, ArrayOfOneDTables< V, M > &unifiedCdfValues) const
 Uniformly samples from the CDF from the sub-sequence. More...
 
void subMeanExtra (unsigned int initialPos, unsigned int numPos, V &meanVec) const
 Finds the mean value of the sub-sequence, considering numPos positions starting at position initialPos. More...
 
void unifiedMeanExtra (unsigned int initialPos, unsigned int numPos, V &unifiedMeanVec) const
 Finds the mean value of the unified sequence, considering numPos positions starting at position initialPos. More...
 
void subMedianExtra (unsigned int initialPos, unsigned int numPos, V &medianVec) const
 Finds the median value of the sub-sequence, considering numPos positions starting at position initialPos. More...
 
void unifiedMedianExtra (unsigned int initialPos, unsigned int numPos, V &unifiedMedianVec) const
 Finds the median value of the unfed sequence, considering numPos positions starting at position initialPos. More...
 
void subSampleVarianceExtra (unsigned int initialPos, unsigned int numPos, const V &meanVec, V &samVec) const
 Finds the sample variance of the sub-sequence, considering numPos positions starting at position initialPos and of mean meanVec. More...
 
void unifiedSampleVarianceExtra (unsigned int initialPos, unsigned int numPos, const V &unifiedMeanVec, V &unifiedSamVec) const
 Finds the sample variance of the unified sequence, considering numPos positions starting at position initialPos and of mean meanVec. More...
 
void subSampleStd (unsigned int initialPos, unsigned int numPos, const V &meanVec, V &stdVec) const
 Finds the sample standard deviation of the sub-sequence, considering numPos positions starting at position initialPos and of mean meanVec. More...
 
void unifiedSampleStd (unsigned int initialPos, unsigned int numPos, const V &unifiedMeanVec, V &unifiedStdVec) const
 Finds the sample standard deviation of the unified sequence, considering numPos positions starting at position initialPos and of mean meanVec. More...
 
void subPopulationVariance (unsigned int initialPos, unsigned int numPos, const V &meanVec, V &popVec) const
 Finds the population variance of the sub-sequence, considering numPos positions starting at position initialPos and of mean meanVec. More...
 
void unifiedPopulationVariance (unsigned int initialPos, unsigned int numPos, const V &unifiedMeanVec, V &unifiedPopVec) const
 Finds the population variance of the unified sequence, considering numPos positions starting at position initialPos and of mean meanVec. More...
 
void autoCovariance (unsigned int initialPos, unsigned int numPos, const V &meanVec, unsigned int lag, V &covVec) const
 Calculates the autocovariance. More...
 
void autoCorrViaDef (unsigned int initialPos, unsigned int numPos, unsigned int lag, V &corrVec) const
 Calculates the autocorrelation via definition. More...
 
void autoCorrViaFft (unsigned int initialPos, unsigned int numPos, const std::vector< unsigned int > &lags, std::vector< V * > &corrVecs) const
 Calculates the autocorrelation via Fast Fourier transforms (FFT). More...
 
void autoCorrViaFft (unsigned int initialPos, unsigned int numPos, unsigned int numSum, V &autoCorrsSumVec) const
 Calculates the autocorrelation via Fast Fourier transforms (FFT). More...
 
void subMinMaxExtra (unsigned int initialPos, unsigned int numPos, V &minVec, V &maxVec) const
 Finds the minimum and the maximum values of the sub-sequence, considering numPos positions starting at position initialPos. More...
 
void unifiedMinMaxExtra (unsigned int initialPos, unsigned int numPos, V &unifiedMinVec, V &unifiedMaxVec) const
 Finds the minimum and the maximum values of the unified sequence, considering numPos positions starting at position initialPos. More...
 
void subHistogram (unsigned int initialPos, const V &minVec, const V &maxVec, std::vector< V * > &centersForAllBins, std::vector< V * > &quanttsForAllBins) const
 Calculates the histogram of the sub-sequence. More...
 
void unifiedHistogram (unsigned int initialPos, const V &unifiedMinVec, const V &unifiedMaxVec, std::vector< V * > &unifiedCentersForAllBins, std::vector< V * > &unifiedQuanttsForAllBins) const
 Calculates the histogram of the unified sequence. More...
 
void subInterQuantileRange (unsigned int initialPos, V &iqrVec) const
 Returns the interquartile range of the values in the sub-sequence. More...
 
void unifiedInterQuantileRange (unsigned int initialPos, V &unifiedIqrVec) const
 Returns the interquartile range of the values in the unified sequence. More...
 
void subScalesForKde (unsigned int initialPos, const V &iqrVec, unsigned int kdeDimension, V &scaleVec) const
 Selects the scales (bandwidth, scaleVec) for the kernel density estimation, considering only the sub-sequence. More...
 
void unifiedScalesForKde (unsigned int initialPos, const V &unifiedIqrVec, unsigned int kdeDimension, V &unifiedScaleVec) const
 Selects the scales (bandwidth) for the kernel density estimation, considering the unified sequence. More...
 
void subGaussian1dKde (unsigned int initialPos, const V &scaleVec, const std::vector< V * > &evalParamVecs, std::vector< V * > &densityVecs) const
 Gaussian kernel for the KDE estimate of the sub-sequence. More...
 
void unifiedGaussian1dKde (unsigned int initialPos, const V &unifiedScaleVec, const std::vector< V * > &unifiedEvalParamVecs, std::vector< V * > &unifiedDensityVecs) const
 Gaussian kernel for the KDE estimate of the unified sequence. More...
 
void subWriteContents (unsigned int initialPos, unsigned int numPos, const std::string &fileName, const std::string &fileType, const std::set< unsigned int > &allowedSubEnvIds) const
 Writes the sub-sequence to a file. More...
 
void subWriteContents (unsigned int initialPos, unsigned int numPos, FilePtrSetStruct &filePtrSet, const std::string &fileType) const
 Writes the sub-sequence to a file. More...
 
void subWriteContents (unsigned int initialPos, unsigned int numPos, std::ofstream &ofs, const std::string &fileType) const
 Writes the sub-sequence to a file. More...
 
void unifiedWriteContents (const std::string &fileName, const std::string &fileType) const
 
void unifiedReadContents (const std::string &fileName, const std::string &fileType, const unsigned int subSequenceSize)
 Reads the unified sequence from a file. More...
 
void select (const std::vector< unsigned int > &idsOfUniquePositions)
 TODO: It shall select positions in the sequence of vectors. More...
 
void filter (unsigned int initialPos, unsigned int spacing)
 Filters positions in the sequence of vectors. More...
 
double estimateConvBrooksGelman (unsigned int initialPos, unsigned int numPos) const
 Estimates convergence rate using Brooks & Gelman method. More...
 
void extractScalarSeq (unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
 Extracts a sequence of scalars. More...
 
- Public Member Functions inherited from QUESO::BaseVectorSequence< V, M >
 BaseVectorSequence (const VectorSpace< V, M > &vectorSpace, unsigned int subSequenceSize, const std::string &name)
 Default constructor. More...
 
virtual ~BaseVectorSequence ()
 Destructor. 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...
 
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...
 
void computeFilterParams (std::ofstream *passedOfs, unsigned int &initialPos, unsigned int &spacing)
 Computes the filtering parameters spacing for the sequence of vectors. More...
 

Private Member Functions

void copy (const SequenceOfVectors< V, M > &src)
 Copies vector sequence src to this. More...
 
void extractRawData (unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, std::vector< double > &rawData) const
 Extracts the raw data. More...
 

Private Attributes

std::vector< const V * > m_seq
 Sequence of vectors. More...
 

Additional Inherited Members

- Protected Member Functions inherited from QUESO::BaseVectorSequence< V, M >
void copy (const BaseVectorSequence< V, M > &src)
 Copies vector sequence src to this. More...
 
- Protected Attributes inherited from QUESO::BaseVectorSequence< V, M >
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, class M>
class QUESO::SequenceOfVectors< V, M >

Class for handling vector samples (sequence of vectors).

This class handles vector samples generated by an algorithm, as well as operations that can be carried over them, e.g., calculation of means, correlation and covariance matrices. It is derived from and implements BaseVectorSequence<V,M>.

Definition at line 46 of file SequenceOfVectors.h.

Member Typedef Documentation

template<class V, class M>
typedef std::vector<const V*>::const_iterator QUESO::SequenceOfVectors< V, M >::seqVectorPositionConstIteratorTypedef

Definition at line 52 of file SequenceOfVectors.h.

template<class V, class M>
typedef std::vector<const V*>::iterator QUESO::SequenceOfVectors< V, M >::seqVectorPositionIteratorTypedef

Definition at line 53 of file SequenceOfVectors.h.

Constructor & Destructor Documentation

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

Default constructor.

Definition at line 33 of file SequenceOfVectors.C.

37  :
38  BaseVectorSequence<V,M>(vectorSpace,subSequenceSize,name),
39  m_seq (subSequenceSize,NULL)
40 #ifdef UQ_CODE_HAS_MONITORS
41  ,
42  m_subMeanMonitorPosSeq (NULL),
43  m_subMeanVecSeq (NULL),
44  m_subMeanCltStdSeq (NULL),
45  m_subMeanInter0MonitorPosSeq (NULL),
46  m_subMeanInter0Mean (NULL),
47  m_subMeanInter0Clt95 (NULL),
48  m_subMeanInter0Empirical90 (NULL),
49  m_subMeanInter0Min (NULL),
50  m_subMeanInter0Max (NULL),
51  m_unifiedMeanMonitorPosSeq (NULL),
52  m_unifiedMeanVecSeq (NULL),
53  m_unifiedMeanCltStdSeq (NULL)
54 #endif
55 {
56  //if (m_env.subDisplayFile()) {
57  // *m_env.subDisplayFile() << "Entering SequenceOfVectors<V,M>::constructor()"
58  // << std::endl;
59  //}
60 
61  //if (m_env.subDisplayFile()) {
62  // *m_env.subDisplayFile() << "Leaving SequenceOfVectors<V,M>::constructor()"
63  // << std::endl;
64  //}
65 }
QUESO::BaseVectorSequence::name
const std::string & name() const
Access to protected attribute m_name: name of the sequence of vectors.
Definition: VectorSequence.C:121
QUESO::SequenceOfVectors::m_seq
std::vector< const V * > m_seq
Sequence of vectors.
Definition: SequenceOfVectors.h:417
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:114
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
QUESO::SequenceOfVectors< V, M >::~SequenceOfVectors ( )

Destructor.

Definition at line 68 of file SequenceOfVectors.C.

69 {
70 #ifdef UQ_CODE_HAS_MONITORS
71  if (m_subMeanMonitorPosSeq) delete m_subMeanMonitorPosSeq;
72  if (m_subMeanVecSeq ) delete m_subMeanVecSeq;
73  if (m_subMeanCltStdSeq ) delete m_subMeanCltStdSeq;
74 
75  if (m_subMeanInter0MonitorPosSeq) delete m_subMeanInter0MonitorPosSeq;
76  if (m_subMeanInter0Mean ) delete m_subMeanInter0Mean;
77  if (m_subMeanInter0Clt95 ) delete m_subMeanInter0Clt95;
78  if (m_subMeanInter0Empirical90 ) delete m_subMeanInter0Empirical90;
79  if (m_subMeanInter0Min ) delete m_subMeanInter0Min;
80  if (m_subMeanInter0Max ) delete m_subMeanInter0Max;
81 
82  if (m_unifiedMeanMonitorPosSeq) delete m_unifiedMeanMonitorPosSeq;
83  if (m_unifiedMeanVecSeq ) delete m_unifiedMeanVecSeq;
84  if (m_unifiedMeanCltStdSeq ) delete m_unifiedMeanCltStdSeq;
85 #endif
86 
87  for (unsigned int i = 0; i < (unsigned int) m_seq.size(); ++i) {
88  if (m_seq[i]) delete m_seq[i];
89  }
90 }
QUESO::SequenceOfVectors::m_seq
std::vector< const V * > m_seq
Sequence of vectors.
Definition: SequenceOfVectors.h:417

Member Function Documentation

template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::autoCorrViaDef ( unsigned int  initialPos,
unsigned int  numPos,
unsigned int  lag,
V &  corrVec 
) const
virtual

Calculates the autocorrelation via definition.

Autocorrelation is the cross-correlation of a variable with itself; it describes the correlation between values of the process at different times, as a function of the two times. It is calculated over a sequence of vectors with initial position initialPos, considering numPos positions, a lag of lag, with mean given by meanVec. Output:

Parameters
corrVecis the vector of the calculated autocorrelations of the sequence of vectors.

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 820 of file SequenceOfVectors.C.

References UQ_FATAL_TEST_MACRO.

825 {
826  bool bRC = ((initialPos < this->subSequenceSize()) &&
827  (0 < numPos ) &&
828  ((initialPos+numPos) <= this->subSequenceSize()) &&
829  (lag < numPos ) && // lag should not be too large
830  (this->vectorSizeLocal() == corrVec.sizeLocal() ));
831  UQ_FATAL_TEST_MACRO(bRC == false,
832  m_env.worldRank(),
833  "SequenceOfVectors<V,M>::autoCorrViaDef()",
834  "invalid input data");
835 
836  ScalarSequence<double> data(m_env,0,"");
837 
838  unsigned int numParams = this->vectorSizeLocal();
839  for (unsigned int i = 0; i < numParams; ++i) {
840  this->extractScalarSeq(initialPos,
841  1, // spacing
842  numPos,
843  i,
844  data);
845  corrVec[i] = data.autoCorrViaDef(0,
846  numPos,
847  lag);
848  }
849 
850  return;
851 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::autoCorrViaFft ( unsigned int  initialPos,
unsigned int  numPos,
const std::vector< unsigned int > &  lags,
std::vector< V * > &  corrVecs 
) const
virtual

Calculates the autocorrelation via Fast Fourier transforms (FFT).

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 855 of file SequenceOfVectors.C.

References QUESO::ScalarSequence< T >::autoCorrViaFft(), and UQ_FATAL_TEST_MACRO.

860 {
861  bool bRC = ((initialPos < this->subSequenceSize()) &&
862  (0 < numPos ) &&
863  ((initialPos+numPos) <= this->subSequenceSize()) &&
864  (0 < lags.size() ) &&
865  (lags[lags.size()-1] < numPos )); // lag should not be too large
866  UQ_FATAL_TEST_MACRO(bRC == false,
867  m_env.worldRank(),
868  "SequenceOfVectors<V,M>::autoCorrViaFft()",
869  "invalid input data");
870 
871  for (unsigned int j = lags.size(); j < corrVecs.size(); ++j) {
872  if (corrVecs[j] != NULL) {
873  delete corrVecs[j];
874  corrVecs[j] = NULL;
875  }
876  }
877  corrVecs.resize(lags.size(),NULL);
878  for (unsigned int j = 0; j < corrVecs.size(); ++j) {
879  if (corrVecs[j] == NULL) corrVecs[j] = new V(m_vectorSpace.zeroVector());
880  }
881 
882  ScalarSequence<double> data(m_env,0,"");
883  unsigned int maxLag = lags[lags.size()-1];
884  std::vector<double> autoCorrs(maxLag+1,0.); // Yes, +1
885 
886  unsigned int numParams = this->vectorSizeLocal();
887  for (unsigned int i = 0; i < numParams; ++i) {
888  this->extractScalarSeq(initialPos,
889  1, // spacing
890  numPos,
891  i,
892  data);
893 
894  //if (m_env.subDisplayFile()) {
895  // *m_env.subDisplayFile() << "In SequenceOfVectors<V,M>::autoCorrViaFft()"
896  // << ": about to call data.autoCorrViaFft() for paramId = " << i
897  // << ", with numPos = " << numPos
898  // << ", maxLag = " << maxLag
899  // << ", autoCorrs.size() = " << autoCorrs.size()
900  // << std::endl;
901  //}
902  data.autoCorrViaFft(0,
903  numPos,
904  maxLag,
905  autoCorrs);
906 
907  for (unsigned int j = 0; j < lags.size(); ++j) {
908  (*(corrVecs[j]))[i] = autoCorrs[lags[j]];
909  }
910  }
911 
912  return;
913 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:424
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::autoCorrViaFft ( unsigned int  initialPos,
unsigned int  numPos,
unsigned int  numSum,
V &  autoCorrsSumVec 
) const
virtual

Calculates the autocorrelation via Fast Fourier transforms (FFT).

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 917 of file SequenceOfVectors.C.

References UQ_FATAL_TEST_MACRO.

922 {
923  bool bRC = ((initialPos < this->subSequenceSize()) &&
924  (0 < numPos ) &&
925  ((initialPos+numPos) <= this->subSequenceSize()) &&
926  (0 < numSum ) &&
927  (numSum <= numPos ) &&
928  (autoCorrsSumVec.sizeLocal() == this->vectorSizeLocal()));
929  UQ_FATAL_TEST_MACRO(bRC == false,
930  m_env.worldRank(),
931  "SequenceOfVectors<V,M>::autoCorrViaFft(), for sum",
932  "invalid input data");
933 
934  ScalarSequence<double> data(m_env,0,"");
935 
936  unsigned int numParams = this->vectorSizeLocal();
937  for (unsigned int i = 0; i < numParams; ++i) {
938  this->extractScalarSeq(initialPos,
939  1, // spacing
940  numPos,
941  i,
942  data);
943 
944  data.autoCorrViaFft(0,
945  numPos,
946  numSum,
947  autoCorrsSumVec[i]);
948  }
949 
950  return;
951 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::autoCovariance ( unsigned int  initialPos,
unsigned int  numPos,
const V &  meanVec,
unsigned int  lag,
V &  covVec 
) const
virtual

Calculates the autocovariance.

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. Output:

Parameters
covVecis the vector of the calculated autocovariances of the sequence of vectors.

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 782 of file SequenceOfVectors.C.

References UQ_FATAL_TEST_MACRO.

788 {
789  bool bRC = ((initialPos < this->subSequenceSize()) &&
790  (0 < numPos ) &&
791  ((initialPos+numPos) <= this->subSequenceSize()) &&
792  (this->vectorSizeLocal() == meanVec.sizeLocal() ) &&
793  (lag < numPos ) && // lag should not be too large
794  (this->vectorSizeLocal() == covVec.sizeLocal() ));
795  UQ_FATAL_TEST_MACRO(bRC == false,
796  m_env.worldRank(),
797  "SequenceOfVectors<V,M>::autoCovariance()",
798  "invalid input data");
799 
800  ScalarSequence<double> data(m_env,0,"");
801 
802  unsigned int numParams = this->vectorSizeLocal();
803  for (unsigned int i = 0; i < numParams; ++i) {
804  this->extractScalarSeq(initialPos,
805  1, // spacing
806  numPos,
807  i,
808  data);
809  covVec[i] = data.autoCovariance(0,
810  numPos,
811  meanVec[i],
812  lag);
813  }
814 
815  return;
816 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::copy ( const SequenceOfVectors< V, M > &  src)
private

Copies vector sequence src to this.

Definition at line 2274 of file SequenceOfVectors.C.

References QUESO::BaseVectorSequence< V, M >::copy(), QUESO::SequenceOfVectors< V, M >::m_seq, and QUESO::SequenceOfVectors< V, M >::subSequenceSize().

2275 {
2276  BaseVectorSequence<V,M>::copy(src);
2277  for (unsigned int i = 0; i < (unsigned int) m_seq.size(); ++i) {
2278  if (m_seq[i]) {
2279  delete m_seq[i];
2280  m_seq[i] = NULL;
2281  }
2282  }
2283  m_seq.resize(src.subSequenceSize(),NULL);
2284  for (unsigned int i = 0; i < m_seq.size(); ++i) {
2285  m_seq[i] = new V(*(src.m_seq[i]));
2286  }
2287 
2288  return;
2289 }
QUESO::SequenceOfVectors::m_seq
std::vector< const V * > m_seq
Sequence of vectors.
Definition: SequenceOfVectors.h:417
QUESO::BaseVectorSequence::copy
void copy(const BaseVectorSequence< V, M > &src)
Copies vector sequence src to this.
Definition: VectorSequence.C:681
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::erasePositions ( unsigned int  initialPos,
unsigned int  numPos 
)
virtual

Erases numPos elements of the sequence starting at position initialPos.

This routine deletes all stored computed vectors

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 157 of file SequenceOfVectors.C.

References QUESO::BaseVectorSequence< V, M >::deleteStoredVectors(), and UQ_FATAL_TEST_MACRO.

158 {
159  bool bRC = ((initialPos < this->subSequenceSize()) &&
160  (0 < numPos ) &&
161  ((initialPos+numPos) <= this->subSequenceSize()));
162  UQ_FATAL_TEST_MACRO(bRC == false,
163  m_env.worldRank(),
164  "SequenceOfVectors<V,M>::erasePositions()",
165  "invalid input data");
166 
167  for (unsigned int j = 0; j < numPos; ++j) {
168  if (m_seq[initialPos+j] != NULL) {
169  delete m_seq[initialPos+j];
170  m_seq[initialPos+j] = NULL;
171  }
172  }
173 
174  seqVectorPositionIteratorTypedef posIteratorBegin = m_seq.begin();
175  if (initialPos < this->subSequenceSize()) std::advance(posIteratorBegin,initialPos);
176  else posIteratorBegin = m_seq.end();
177 
178  unsigned int posEnd = initialPos + numPos - 1;
179  seqVectorPositionIteratorTypedef posIteratorEnd = m_seq.begin();
180  if (posEnd < this->subSequenceSize()) std::advance(posIteratorEnd,posEnd);
181  else posIteratorEnd = m_seq.end();
182 
183  unsigned int oldSubSequenceSize = this->subSequenceSize();
184  m_seq.erase(posIteratorBegin,posIteratorEnd);
185  UQ_FATAL_TEST_MACRO((oldSubSequenceSize - numPos) != this->subSequenceSize(),
186  m_env.worldRank(),
187  "SequenceOfVectors::erasePositions()",
188  "(oldSubSequenceSize - numPos) != this->subSequenceSize()");
189 
190  BaseVectorSequence<V,M>::deleteStoredVectors();
191 
192  return;
193 }
QUESO::BaseVectorSequence::deleteStoredVectors
void deleteStoredVectors()
Deletes all the stored vectors.
Definition: VectorSequence.C:301
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::SequenceOfVectors::seqVectorPositionIteratorTypedef
std::vector< const V * >::iterator seqVectorPositionIteratorTypedef
Definition: SequenceOfVectors.h:53
QUESO::SequenceOfVectors::m_seq
std::vector< const V * > m_seq
Sequence of vectors.
Definition: SequenceOfVectors.h:417
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
double QUESO::SequenceOfVectors< V, M >::estimateConvBrooksGelman ( unsigned int  initialPos,
unsigned int  numPos 
) const
virtual

Estimates convergence rate using Brooks & Gelman method.

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 2120 of file SequenceOfVectors.C.

References QUESO::matrixProduct(), and UQ_FATAL_RC_MACRO.

2123 {
2124  // This method requires *at least* two sequences. Error if there is only one.
2125  UQ_FATAL_RC_MACRO((m_env.numSubEnvironments() < 2),
2126  m_env.worldRank(),
2127  "SequenceOfVectors<V,M>::estimateConvBrooksGelman()",
2128  "At least two sequences required for Brooks-Gelman convergence test.");
2129 
2130  // TODO: Need special case for 1-dimensional parameter space.
2131 
2132  // Initialize with garbage to give the user a clue something is funky.
2133  double convMeasure = -1.0;
2134 
2135  // We only do the work on the subenvironment where the sequence data
2136  // is stashed.
2137  if( m_env.inter0Rank() >= 0 )
2138  {
2139  // Sanity Checks
2140 
2141  // REMEMBER: \psi is a *vector* of parameters
2142  // Get quantities we will use several times
2143  V psi_j_dot = m_vectorSpace.zeroVector();
2144  V psi_dot_dot = m_vectorSpace.zeroVector();
2145  V work = m_vectorSpace.zeroVector();
2146 
2147  // m = number of chains > 1
2148  // n = number of steps for which we are computing the metric
2149  int m = m_env.numSubEnvironments();
2150  int n = numPos;
2151 
2152  this->subMeanExtra ( initialPos, numPos, psi_j_dot );
2153  this->unifiedMeanExtra( initialPos, numPos, psi_dot_dot );
2154 
2155 #if 0
2156  std::cout << "psi_j_dot = " << psi_j_dot << std::endl;
2157  std::cout << "psi_dot_dot = " << psi_dot_dot << std::endl;
2158 #endif
2159 
2160  /* W = \frac{1}{m*(n-1)}*\sum_{j=1}^m \sum{t=1}^n
2161  (\psi_{jt} - \overline{\psi_{j\cdot}})*(\psi_{jt} - \overline{\psi_{j\cdot}})^T
2162  This corresponds to the "within-sequence" covariance matrix. */
2163  M* W_local = m_vectorSpace.newDiagMatrix( m_vectorSpace.zeroVector() );
2164  M* W = m_vectorSpace.newDiagMatrix( m_vectorSpace.zeroVector() );
2165  V psi_j_t = m_vectorSpace.zeroVector();
2166 
2167  // Sum within the chain
2168  for( unsigned int t = initialPos; t < initialPos+numPos; ++t )
2169  {
2170  psi_j_t = *(m_seq[t]);
2171 
2172  work = psi_j_t - psi_j_dot;
2173 
2174  (*W_local) += matrixProduct( work, work );
2175  }
2176 
2177  // Now do the sum over the chains
2178  // W will be available on all inter0 processors
2179  W_local->mpiSum( m_env.inter0Comm(), (*W) );
2180 
2181  (*W) = 1.0/(double(m)*(double(n)-1.0)) * (*W);
2182 
2183 #if 0
2184  std::cout << "n, m = " << n << ", " << m << std::endl;
2185  std::cout << "W_local = " << *W_local << std::endl;
2186  std::cout << "W = " << *W << std::endl;
2187 #endif
2188 
2189  // Need to delete pointers to temporary covariance matrices
2190  delete W_local;
2191 
2192  /* B/n = \frac{1}{m-1}\sum_{j=1}^m
2193  (\overline{\psi_{j\cdot}} - \overline{\psi_{\cdot \cdot}})*
2194  (\overline{\psi_{j\cdot}} - \overline{\psi_{\cdot \cdot}})^T
2195  This corresponds to the "between-sequence" covariance matrix. */
2196  M* B_over_n_local = m_vectorSpace.newDiagMatrix( m_vectorSpace.zeroVector() );
2197  M* B_over_n = m_vectorSpace.newDiagMatrix( m_vectorSpace.zeroVector() );
2198 
2199  work = psi_j_dot - psi_dot_dot;
2200  (*B_over_n_local) = matrixProduct( work, work );
2201 
2202  B_over_n_local->mpiSum( m_env.inter0Comm(), (*B_over_n) );
2203 
2204  // Need to delete pointers to temporary covariance matrices
2205  delete B_over_n_local;
2206 
2207  (*B_over_n) = 1.0/(double(m)-1.0) * (*B_over_n);
2208 
2209 #if 0
2210  std::cout << "B_over_n = " << *B_over_n << std::endl;
2211 #endif
2212 
2213 
2214  /* R_p = (n-1)/n + (m+1)/m * \lambda
2215  \lambda = largest eigenvalue of W^{-1}*B/n */
2216  M* A = m_vectorSpace.newDiagMatrix( m_vectorSpace.zeroVector() );
2217 
2218  W->invertMultiply( *B_over_n, *A );
2219 
2220 #if 0
2221  std::cout << "A = " << *A << std::endl;
2222  std::cout.flush();
2223 #endif
2224  // Need to delete pointers to temporary covariance matrices
2225  delete W;
2226  delete B_over_n;
2227 
2228  double eigenValue;
2229  V eigenVector = m_vectorSpace.zeroVector();
2230 
2231  A->largestEigen( eigenValue, eigenVector );
2232 
2233  // Need to delete pointers to temporary covariance matrices
2234  delete A;
2235 
2236  // Now, finally compute the final convMeasure
2237  convMeasure = (double(n)-1.0)/double(n) + (double(m)+1.0)/double(m)*eigenValue;
2238 
2239  } // End of check on inter0Rank
2240 
2241  //TODO: Do we need a Barrier here?
2242  //TODO: Error checking on MPI.
2243  //m_env.fullComm().Barrier(); // Dangerous to barrier on fullComm ...
2244 
2245  return convMeasure;
2246 }
QUESO::SequenceOfVectors::subMeanExtra
void subMeanExtra(unsigned int initialPos, unsigned int numPos, V &meanVec) const
Finds the mean value of the sub-sequence, considering numPos positions starting at position initialPo...
Definition: SequenceOfVectors.C:329
QUESO::BaseEnvironment::inter0Rank
int inter0Rank() const
Returns the process inter0 rank.
Definition: Environment.C:289
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:424
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
UQ_FATAL_RC_MACRO
#define UQ_FATAL_RC_MACRO(macroIRc, givenRank, where, what)
Definition: Defines.h:207
QUESO::SequenceOfVectors::unifiedMeanExtra
void unifiedMeanExtra(unsigned int initialPos, unsigned int numPos, V &unifiedMeanVec) const
Finds the mean value of the unified sequence, considering numPos positions starting at position initi...
Definition: SequenceOfVectors.C:387
QUESO::SequenceOfVectors::m_seq
std::vector< const V * > m_seq
Sequence of vectors.
Definition: SequenceOfVectors.h:417
QUESO::BaseEnvironment::numSubEnvironments
unsigned int numSubEnvironments() const
Access function to the number of sub-environments.
Definition: Environment.C:319
QUESO::BaseEnvironment::inter0Comm
const MpiComm & inter0Comm() const
Access function for MpiComm inter0-communicator.
Definition: Environment.C:295
QUESO::matrixProduct
GslMatrix matrixProduct(const GslVector &v1, const GslVector &v2)
Definition: GslMatrix.C:2409
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::extractRawData ( unsigned int  initialPos,
unsigned int  spacing,
unsigned int  numPos,
unsigned int  paramId,
std::vector< double > &  rawData 
) const
privatevirtual

Extracts the raw data.

This method saves in rawData the data from the sequence of vectors (in private attribute m_seq) starting at position (initialPos,paramId) , with a spacing of spacing until numPos positions have been extracted.

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 2293 of file SequenceOfVectors.C.

2299 {
2300  rawData.resize(numPos);
2301  if (spacing == 1) {
2302  for (unsigned int j = 0; j < numPos; ++j) {
2303  rawData[j] = (*(m_seq[initialPos+j ]))[paramId];
2304  }
2305  }
2306  else {
2307  for (unsigned int j = 0; j < numPos; ++j) {
2308  rawData[j] = (*(m_seq[initialPos+j*spacing]))[paramId];
2309  }
2310  }
2311 
2312  return;
2313 }
QUESO::SequenceOfVectors::m_seq
std::vector< const V * > m_seq
Sequence of vectors.
Definition: SequenceOfVectors.h:417
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::extractScalarSeq ( unsigned int  initialPos,
unsigned int  spacing,
unsigned int  numPos,
unsigned int  paramId,
ScalarSequence< double > &  scalarSeq 
) const
virtual

Extracts a sequence of scalars.

The sequence of scalars has size numPos, and it will be extracted starting at position (initialPos, paramId ) of this sequences of vectors, given spacing spacing.

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 2250 of file SequenceOfVectors.C.

References QUESO::ScalarSequence< T >::resizeSequence().

2256 {
2257  scalarSeq.resizeSequence(numPos);
2258  if (spacing == 1) {
2259  for (unsigned int j = 0; j < numPos; ++j) {
2260  scalarSeq[j] = (*(m_seq[initialPos+j ]))[paramId];
2261  }
2262  }
2263  else {
2264  for (unsigned int j = 0; j < numPos; ++j) {
2265  scalarSeq[j] = (*(m_seq[initialPos+j*spacing]))[paramId];
2266  }
2267  }
2268 
2269  return;
2270 }
QUESO::SequenceOfVectors::m_seq
std::vector< const V * > m_seq
Sequence of vectors.
Definition: SequenceOfVectors.h:417
QUESO::ScalarSequence::resizeSequence
void resizeSequence(unsigned int newSequenceSize)
Resizes the size of the sequence of scalars.
Definition: ScalarSequence.C:181
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::filter ( unsigned int  initialPos,
unsigned int  spacing 
)
virtual

Filters positions in the sequence of vectors.

Filtered positions will starting at initialPos, and with spacing given by spacing.

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 2079 of file SequenceOfVectors.C.

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

2082 {
2083  if (m_env.subDisplayFile()) {
2084  *m_env.subDisplayFile() << "Entering SequenceOfVectors<V,M>::filter()"
2085  << ": initialPos = " << initialPos
2086  << ", spacing = " << spacing
2087  << ", subSequenceSize = " << this->subSequenceSize()
2088  << std::endl;
2089  }
2090 
2091  unsigned int i = 0;
2092  unsigned int j = initialPos;
2093  unsigned int originalSubSequenceSize = this->subSequenceSize();
2094  while (j < originalSubSequenceSize) {
2095  if (i != j) {
2096  //*m_env.subDisplayFile() << i << "--" << j << " ";
2097  delete m_seq[i];
2098  m_seq[i] = new V(*(m_seq[j]));
2099  }
2100  i++;
2101  j += spacing;
2102  }
2103 
2104  this->resetValues(i,originalSubSequenceSize-i);
2105  this->resizeSequence(i);
2106 
2107  if (m_env.subDisplayFile()) {
2108  *m_env.subDisplayFile() << "Leaving SequenceOfVectors<V,M>::filter()"
2109  << ": initialPos = " << initialPos
2110  << ", spacing = " << spacing
2111  << ", subSequenceSize = " << this->subSequenceSize()
2112  << std::endl;
2113  }
2114 
2115  return;
2116 }
QUESO::SequenceOfVectors::resetValues
void resetValues(unsigned int initialPos, unsigned int numPos)
Resets a total of numPos values of the sequence starting at position initialPos.
Definition: SequenceOfVectors.C:126
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:305
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::SequenceOfVectors::m_seq
std::vector< const V * > m_seq
Sequence of vectors.
Definition: SequenceOfVectors.h:417
QUESO::SequenceOfVectors::resizeSequence
void resizeSequence(unsigned int newSubSequenceSize)
Resizes the sequence.
Definition: SequenceOfVectors.C:110
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::getPositionValues ( unsigned int  posId,
V &  vec 
) const
virtual

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

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 197 of file SequenceOfVectors.C.

References UQ_FATAL_TEST_MACRO.

Referenced by QUESO::MLSampling< P_V, P_M >::generateBalLinkedChains_all(), QUESO::MLSampling< P_V, P_M >::generateSequence(), QUESO::MetropolisHastingsSG< P_V, P_M >::generateSequence(), QUESO::MLSampling< P_V, P_M >::generateSequence_Step02_inter0(), QUESO::MLSampling< P_V, P_M >::generateSequence_Step04_inter0(), QUESO::MLSampling< P_V, P_M >::generateUnbLinkedChains_all(), and QUESO::MLSampling< P_V, P_M >::mpiExchangePositions_inter0().

198 {
199  UQ_FATAL_TEST_MACRO((posId >= this->subSequenceSize()),
200  m_env.worldRank(),
201  "SequenceOfVectorss<V,M>::getPositionValues()",
202  "posId > subSequenceSize()");
203 
204  UQ_FATAL_TEST_MACRO(m_seq[posId] == NULL,
205  m_env.worldRank(),
206  "SequenceOfVectorss<V,M>::getPositionValues()",
207  "posId is NULL");
208 
209  //if (posId == 0) { // mox
210  // std::cout << "In SequenceOfVectors<V,M>::getPositionValues(): m_seq[0] = " << m_seq[0] << ", *(m_seq[0]) = " << *(m_seq[0])
211  // << std::endl;
212  //}
213 
214  vec = *(m_seq[posId]); // *(const_cast<V*>(m_seq[posId])); // prudenci 2010-06-17 mox
215 
216  return;
217 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::SequenceOfVectors::m_seq
std::vector< const V * > m_seq
Sequence of vectors.
Definition: SequenceOfVectors.h:417
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
SequenceOfVectors< V, M > & QUESO::SequenceOfVectors< V, M >::operator= ( const SequenceOfVectors< V, M > &  rhs)

Copies values from rhs to this.

Definition at line 94 of file SequenceOfVectors.C.

95 {
96  this->copy(rhs);
97  return *this;
98 }
QUESO::SequenceOfVectors::copy
void copy(const SequenceOfVectors< V, M > &src)
Copies vector sequence src to this.
Definition: SequenceOfVectors.C:2274
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::resetValues ( unsigned int  initialPos,
unsigned int  numPos 
)
virtual

Resets a total of numPos values of the sequence starting at position initialPos.

This routine deletes all stored computed vectors

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 126 of file SequenceOfVectors.C.

References QUESO::BaseVectorSequence< V, M >::deleteStoredVectors(), and UQ_FATAL_TEST_MACRO.

127 {
128  bool bRC = ((initialPos < this->subSequenceSize()) &&
129  (0 < numPos ) &&
130  ((initialPos+numPos) <= this->subSequenceSize()));
131  if ((bRC == false) && (m_env.subDisplayFile())) {
132  *m_env.subDisplayFile() << "In SequenceOfVectors<V,M>::resetValues()"
133  << ", initialPos = " << initialPos
134  << ", this->subSequenceSize() = " << this->subSequenceSize()
135  << ", numPos = " << numPos
136  << std::endl;
137  }
138  UQ_FATAL_TEST_MACRO(bRC == false,
139  m_env.worldRank(),
140  "SequenceOfVectors<V,M>::resetValues()",
141  "invalid input data");
142 
143  for (unsigned int j = 0; j < numPos; ++j) {
144  if (m_seq[initialPos+j] != NULL) {
145  delete m_seq[initialPos+j];
146  m_seq[initialPos+j] = NULL;
147  }
148  }
149 
150  BaseVectorSequence<V,M>::deleteStoredVectors();
151 
152  return;
153 }
QUESO::BaseVectorSequence::deleteStoredVectors
void deleteStoredVectors()
Deletes all the stored vectors.
Definition: VectorSequence.C:301
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:305
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::SequenceOfVectors::m_seq
std::vector< const V * > m_seq
Sequence of vectors.
Definition: SequenceOfVectors.h:417
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::resizeSequence ( unsigned int  newSubSequenceSize)
virtual

Resizes the sequence.

This routine deletes all stored computed vectors

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 110 of file SequenceOfVectors.C.

References QUESO::BaseVectorSequence< V, M >::deleteStoredVectors().

Referenced by QUESO::MetropolisHastingsSG< P_V, P_M >::generateFullChain(), and QUESO::MLSampling< P_V, P_M >::generateSequence_Level0_all().

111 {
112  if (newSubSequenceSize != this->subSequenceSize()) {
113  if (newSubSequenceSize < this->subSequenceSize()) {
114  this->resetValues(newSubSequenceSize,this->subSequenceSize()-newSubSequenceSize);
115  }
116  m_seq.resize(newSubSequenceSize,NULL);
117  std::vector<const V*>(m_seq).swap(m_seq);
118  BaseVectorSequence<V,M>::deleteStoredVectors();
119  }
120 
121  return;
122 }
QUESO::BaseVectorSequence::deleteStoredVectors
void deleteStoredVectors()
Deletes all the stored vectors.
Definition: VectorSequence.C:301
QUESO::SequenceOfVectors::resetValues
void resetValues(unsigned int initialPos, unsigned int numPos)
Resets a total of numPos values of the sequence starting at position initialPos.
Definition: SequenceOfVectors.C:126
QUESO::SequenceOfVectors::m_seq
std::vector< const V * > m_seq
Sequence of vectors.
Definition: SequenceOfVectors.h:417
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::select ( const std::vector< unsigned int > &  idsOfUniquePositions)
virtual

TODO: It shall select positions in the sequence of vectors.

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 2065 of file SequenceOfVectors.C.

References UQ_FATAL_RC_MACRO.

2066 {
2067  UQ_FATAL_RC_MACRO(true,
2068  m_env.worldRank(),
2069  "SequenceOfVectors<V,M>::select()",
2070  "Code is not complete yet");
2071 
2072  if (&idsOfUniquePositions) {}; // just to remove compiler warning
2073 
2074  return;
2075 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
UQ_FATAL_RC_MACRO
#define UQ_FATAL_RC_MACRO(macroIRc, givenRank, where, what)
Definition: Defines.h:207
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::setPositionValues ( unsigned int  posId,
const V &  vec 
)
virtual

Set the values in vec at position posId of the sequence.

This routine deletes all stored computed vectors

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 221 of file SequenceOfVectors.C.

References QUESO::BaseVectorSequence< V, M >::deleteStoredVectors(), and UQ_FATAL_TEST_MACRO.

Referenced by QUESO::MetropolisHastingsSG< P_V, P_M >::generateFullChain(), and QUESO::MLSampling< P_V, P_M >::generateSequence_Level0_all().

222 {
223  UQ_FATAL_TEST_MACRO((posId >= this->subSequenceSize()),
224  m_env.worldRank(),
225  "SequenceOfVectorss<V,M>::setPositionValues()",
226  "posId > subSequenceSize()");
227 
228  UQ_FATAL_TEST_MACRO(vec.sizeLocal() != m_vectorSpace.zeroVector().sizeLocal(),
229  m_env.worldRank(),
230  "SequenceOfVectorss<V,M>::setPositionValues()",
231  "invalid vec");
232 
233  if (m_seq[posId] != NULL) delete m_seq[posId];
234  m_seq[posId] = new V(vec);
235 
236  //if (posId == 0) { // mox
237  // std::cout << "In SequenceOfVectors<V,M>::setPositionValues(): m_seq[0] = " << m_seq[0] << ", *(m_seq[0]) = " << *(m_seq[0])
238  // << std::endl;
239  //}
240 
241  BaseVectorSequence<V,M>::deleteStoredVectors();
242 
243  return;
244 }
QUESO::BaseVectorSequence::deleteStoredVectors
void deleteStoredVectors()
Deletes all the stored vectors.
Definition: VectorSequence.C:301
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:424
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::SequenceOfVectors::m_seq
std::vector< const V * > m_seq
Sequence of vectors.
Definition: SequenceOfVectors.h:417
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::subGaussian1dKde ( unsigned int  initialPos,
const V &  scaleVec,
const std::vector< V * > &  evalParamVecs,
std::vector< V * > &  densityVecs 
) const
virtual

Gaussian kernel for the KDE estimate of the sub-sequence.

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).

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 1252 of file SequenceOfVectors.C.

References QUESO::ScalarSequence< T >::subGaussian1dKde(), and UQ_FATAL_TEST_MACRO.

1257 {
1258  bool bRC = ((initialPos < this->subSequenceSize()) &&
1259  (this->vectorSizeLocal() == scaleVec.sizeLocal() ) &&
1260  (0 < evalParamVecs.size() ) &&
1261  (evalParamVecs.size() == densityVecs.size() ));
1262  UQ_FATAL_TEST_MACRO(bRC == false,
1263  m_env.worldRank(),
1264  "SequenceOfVectors<V,M>::subGaussian1dKde()",
1265  "invalid input data");
1266 
1267  unsigned int numPos = this->subSequenceSize() - initialPos;
1268  ScalarSequence<double> data(m_env,0,"");
1269 
1270  unsigned int numEvals = evalParamVecs.size();
1271  for (unsigned int j = 0; j < numEvals; ++j) {
1272  densityVecs[j] = new V(m_vectorSpace.zeroVector());
1273  }
1274  std::vector<double> evalParams(numEvals,0.);
1275  std::vector<double> densities (numEvals,0.);
1276 
1277  unsigned int numParams = this->vectorSizeLocal();
1278  for (unsigned int i = 0; i < numParams; ++i) {
1279  this->extractScalarSeq(initialPos,
1280  1, // spacing
1281  numPos,
1282  i,
1283  data);
1284 
1285  for (unsigned int j = 0; j < numEvals; ++j) {
1286  evalParams[j] = (*evalParamVecs[j])[i];
1287  }
1288 
1289  data.subGaussian1dKde(0,
1290  scaleVec[i],
1291  evalParams,
1292  densities);
1293 
1294  for (unsigned int j = 0; j < numEvals; ++j) {
1295  (*densityVecs[j])[i] = densities[j];
1296  }
1297  }
1298 
1299  return;
1300 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:424
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::subHistogram ( unsigned int  initialPos,
const V &  minVec,
const V &  maxVec,
std::vector< V * > &  centersForAllBins,
std::vector< V * > &  quanttsForAllBins 
) const
virtual

Calculates the histogram of the sub-sequence.

It requires the specification of the number of bins that the histogram will have, the center of each bin and the initial position where the data will be considered.

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 1025 of file SequenceOfVectors.C.

References QUESO::ScalarSequence< T >::subHistogram(), and UQ_FATAL_TEST_MACRO.

1031 {
1032  bool bRC = ((initialPos < this->subSequenceSize() ) &&
1033  (this->vectorSizeLocal() == minVec.sizeLocal() ) &&
1034  (this->vectorSizeLocal() == maxVec.sizeLocal() ) &&
1035  (0 < centersForAllBins.size()) &&
1036  (centersForAllBins.size() == quanttsForAllBins.size()));
1037  UQ_FATAL_TEST_MACRO(bRC == false,
1038  m_env.worldRank(),
1039  "SequenceOfVectors<V,M>::subHistogram()",
1040  "invalid input data");
1041 
1042  for (unsigned int j = 0; j < quanttsForAllBins.size(); ++j) {
1043  centersForAllBins[j] = new V(m_vectorSpace.zeroVector());
1044  quanttsForAllBins [j] = new V(m_vectorSpace.zeroVector());
1045  }
1046 
1047  unsigned int dataSize = this->subSequenceSize() - initialPos;
1048  unsigned int numParams = this->vectorSizeLocal();
1049  for (unsigned int i = 0; i < numParams; ++i) {
1050  ScalarSequence<double> data(m_env,dataSize,"");
1051  for (unsigned int j = 0; j < dataSize; ++j) {
1052  data[j] = (*(m_seq[initialPos+j]))[i];
1053  }
1054 
1055  std::vector<double > centers(centersForAllBins.size(),0.);
1056  std::vector<unsigned int> quantts(quanttsForAllBins.size(), 0 );
1057  data.subHistogram(0,
1058  minVec[i],
1059  maxVec[i],
1060  centers,
1061  quantts);
1062 
1063  for (unsigned int j = 0; j < quantts.size(); ++j) {
1064  (*(centersForAllBins[j]))[i] = centers[j];
1065  (*(quanttsForAllBins[j]))[i] = (double) quantts[j];
1066  }
1067  }
1068 
1069  return;
1070 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:424
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::SequenceOfVectors::m_seq
std::vector< const V * > m_seq
Sequence of vectors.
Definition: SequenceOfVectors.h:417
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::subInterQuantileRange ( unsigned int  initialPos,
V &  iqrVec 
) const
virtual

Returns the interquartile range of the values in the sub-sequence.

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)

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 1124 of file SequenceOfVectors.C.

References QUESO::ScalarSequence< T >::subInterQuantileRange(), and UQ_FATAL_TEST_MACRO.

1127 {
1128  bool bRC = ((initialPos < this->subSequenceSize()) &&
1129  (this->vectorSizeLocal() == iqrVec.sizeLocal() ));
1130  UQ_FATAL_TEST_MACRO(bRC == false,
1131  m_env.worldRank(),
1132  "SequenceOfVectors<V,M>::subInterQuantileRange()",
1133  "invalid input data");
1134 
1135  unsigned int numPos = this->subSequenceSize() - initialPos;
1136  ScalarSequence<double> data(m_env,0,"");
1137 
1138  unsigned int numParams = this->vectorSizeLocal();
1139  for (unsigned int i = 0; i < numParams; ++i) {
1140  this->extractScalarSeq(initialPos,
1141  1, // spacing
1142  numPos,
1143  i,
1144  data);
1145  iqrVec[i] = data.subInterQuantileRange(0);
1146  }
1147 
1148  return;
1149 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::subMeanExtra ( unsigned int  initialPos,
unsigned int  numPos,
V &  meanVec 
) const
virtual

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

Output:

Parameters
meanVecis the vector of the calculated means of the sub-sequence of vectors.

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 329 of file SequenceOfVectors.C.

References UQ_FATAL_TEST_MACRO.

333 {
334  if ((m_env.subDisplayFile()) && (m_env.displayVerbosity() >= 5)) {
335  *m_env.subDisplayFile() << "Entering SequenceOfVectors<V,M>::subMeanExtra()"
336  << ": initialPos = " << initialPos
337  << ", numPos = " << numPos
338  << ", sub sequence size = " << this->subSequenceSize()
339  << std::endl;
340  }
341 
342  bool bRC = ((initialPos < this->subSequenceSize()) &&
343  (0 < numPos ) &&
344  ((initialPos+numPos) <= this->subSequenceSize()) &&
345  (this->vectorSizeLocal() == meanVec.sizeLocal() ));
346  if ((bRC == false) && (m_env.subDisplayFile())) {
347  *m_env.subDisplayFile() << "In SequenceOfVectors<V,M>::subMeanExtra()"
348  << ", initialPos = " << initialPos
349  << ", this->subSequenceSize() = " << this->subSequenceSize()
350  << ", numPos = " << numPos
351  << ", this->vectorSizeLocal() = " << this->vectorSizeLocal()
352  << ", meanVec.sizeLocal() = " << meanVec.sizeLocal()
353  << std::endl;
354  }
355  UQ_FATAL_TEST_MACRO(bRC == false,
356  m_env.worldRank(),
357  "SequenceOfVectors<V,M>::subMeanExtra()",
358  "invalid input data");
359 
360  ScalarSequence<double> data(m_env,0,"");
361 
362  unsigned int numParams = this->vectorSizeLocal();
363  for (unsigned int i = 0; i < numParams; ++i) {
364  this->extractScalarSeq(initialPos,
365  1, // spacing
366  numPos,
367  i,
368  data);
369  meanVec[i] = data.subMeanExtra(0,
370  numPos);
371  }
372 
373  if ((m_env.subDisplayFile()) && (m_env.displayVerbosity() >= 5)) {
374  *m_env.subDisplayFile() << "Leaving SequenceOfVectors<V,M>::subMeanExtra()"
375  << ": initialPos = " << initialPos
376  << ", numPos = " << numPos
377  << ", sub sequence size = " << this->subSequenceSize()
378  << ", meanVec = " << meanVec
379  << std::endl;
380  }
381 
382  return;
383 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:305
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
QUESO::BaseEnvironment::displayVerbosity
unsigned int displayVerbosity() const
Definition: Environment.C:436
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::subMedianExtra ( unsigned int  initialPos,
unsigned int  numPos,
V &  medianVec 
) const
virtual

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

Output:

Parameters
medianVecis the vector of the calculated medians of the sub-sequence of vectors.

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 449 of file SequenceOfVectors.C.

References UQ_FATAL_TEST_MACRO.

453 {
454  if (this->subSequenceSize() == 0) return;
455 
456  bool bRC = ((initialPos < this->subSequenceSize()) &&
457  (0 < numPos ) &&
458  ((initialPos+numPos) <= this->subSequenceSize()));
459  if (bRC == false) {
460  std::cerr << "In SequenceOfVectors<V,M>::subMedianExtra()"
461  << ": ERROR at fullRank " << m_env.fullRank()
462  << ", initialPos = " << initialPos
463  << ", numPos = " << numPos
464  << ", this->subSequenceSize() = " << this->subSequenceSize()
465  << std::endl;
466  if (m_env.subDisplayFile()) {
467  *m_env.subDisplayFile() << "In SequenceOfVectors<V,M>::subMedianExtra()"
468  << ": ERROR at fullRank " << m_env.fullRank()
469  << ", initialPos = " << initialPos
470  << ", numPos = " << numPos
471  << ", this->subSequenceSize() = " << this->subSequenceSize()
472  << std::endl;
473  }
474  }
475  UQ_FATAL_TEST_MACRO(bRC == false,
476  m_env.worldRank(),
477  "SequenceOfVectors<V,M>::subMedianExtra()",
478  "invalid input data");
479 
480  ScalarSequence<double> data(m_env,0,"");
481 
482  unsigned int numParams = this->vectorSizeLocal();
483  for (unsigned int i = 0; i < numParams; ++i) {
484  this->extractScalarSeq(initialPos,
485  1, // spacing
486  numPos,
487  i,
488  data);
489  medianVec[i] = data.subMedianExtra(0,
490  numPos);
491  }
492 
493  if ((m_env.subDisplayFile()) && (m_env.displayVerbosity() >= 5)) {
494  *m_env.subDisplayFile() << "Leaving SequenceOfVectors<V,M>::subMedianExtra()"
495  << ": initialPos = " << initialPos
496  << ", numPos = " << numPos
497  << ", sub sequence size = " << this->subSequenceSize()
498  << ", medianVec = " << medianVec
499  << std::endl;
500  }
501 
502  return;
503 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:305
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
QUESO::BaseEnvironment::fullRank
int fullRank() const
Returns the process full rank.
Definition: Environment.C:241
QUESO::BaseEnvironment::displayVerbosity
unsigned int displayVerbosity() const
Definition: Environment.C:436
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::subMinMaxExtra ( unsigned int  initialPos,
unsigned int  numPos,
V &  minVec,
V &  maxVec 
) const
virtual

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

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 955 of file SequenceOfVectors.C.

References QUESO::ScalarSequence< T >::subMinMaxExtra(), and UQ_FATAL_TEST_MACRO.

960 {
961  bool bRC = ((0 < numPos ) &&
962  ((initialPos+numPos) <= this->subSequenceSize()) &&
963  (this->vectorSizeLocal() == minVec.sizeLocal() ) &&
964  (this->vectorSizeLocal() == maxVec.sizeLocal() ));
965  UQ_FATAL_TEST_MACRO(bRC == false,
966  m_env.worldRank(),
967  "SequenceOfVectors<V,M>::subMinMaxExtra()",
968  "invalid input data");
969 
970  //unsigned int numPos = this->subSequenceSize() - initialPos;
971  unsigned int numParams = this->vectorSizeLocal();
972  ScalarSequence<double> data(m_env,0,"");
973 
974  for (unsigned int i = 0; i < numParams; ++i) {
975  this->extractScalarSeq(initialPos,
976  1, // spacing
977  numPos,
978  i,
979  data);
980  data.subMinMaxExtra(0,numPos,minVec[i],maxVec[i]);
981  }
982 
983  return;
984 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::subPopulationVariance ( unsigned int  initialPos,
unsigned int  numPos,
const V &  meanVec,
V &  popVec 
) const
virtual

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

Output:

Parameters
popVecis the vector of the calculated population variance of the sub-sequence of vectors. The population variance $ \sigma^2 $ is defined by $ \sigma^2 = \frac{1}{n-1} \sum_{i=1}^n \left(y_i - \mu \right)^2 $, where $ \mu $ is the sample mean and $ n $ is the sample size. This procedure lets the users choose the initial position and the number of elements of the sequence which will be used to evaluate the population variance .

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 711 of file SequenceOfVectors.C.

References UQ_FATAL_TEST_MACRO.

716 {
717  bool bRC = ((initialPos < this->subSequenceSize()) &&
718  (0 < numPos ) &&
719  ((initialPos+numPos) <= this->subSequenceSize()) &&
720  (this->vectorSizeLocal() == meanVec.sizeLocal() ) &&
721  (this->vectorSizeLocal() == popVec.sizeLocal() ));
722  UQ_FATAL_TEST_MACRO(bRC == false,
723  m_env.worldRank(),
724  "SequenceOfVectors<V,M>::subPopulationVariance()",
725  "invalid input data");
726 
727  ScalarSequence<double> data(m_env,0,"");
728 
729  unsigned int numParams = this->vectorSizeLocal();
730  for (unsigned int i = 0; i < numParams; ++i) {
731  this->extractScalarSeq(initialPos,
732  1, // spacing
733  numPos,
734  i,
735  data);
736  popVec[i] = data.subPopulationVariance(0,
737  numPos,
738  meanVec[i]);
739  }
740 
741  return;
742 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::subSampleStd ( unsigned int  initialPos,
unsigned int  numPos,
const V &  meanVec,
V &  stdVec 
) const

Finds the sample standard deviation of the sub-sequence, considering numPos positions starting at position initialPos and of mean meanVec.

Output:

Parameters
stdVecis the vector of the calculated sample standard deviation of the sub-sequence of vectors.

Definition at line 640 of file SequenceOfVectors.C.

References UQ_FATAL_TEST_MACRO.

645 {
646  bool bRC = ((initialPos < this->subSequenceSize()) &&
647  (0 < numPos ) &&
648  ((initialPos+numPos) <= this->subSequenceSize()) &&
649  (this->vectorSizeLocal() == meanVec.sizeLocal() ) &&
650  (this->vectorSizeLocal() == stdvec.sizeLocal() ));
651  UQ_FATAL_TEST_MACRO(bRC == false,
652  m_env.worldRank(),
653  "SequenceOfVectors<V,M>::subSampleStd()",
654  "invalid input data");
655 
656  ScalarSequence<double> data(m_env,0,"");
657 
658  unsigned int numParams = this->vectorSizeLocal();
659  for (unsigned int i = 0; i < numParams; ++i) {
660  this->extractScalarSeq(initialPos,
661  1, // spacing
662  numPos,
663  i,
664  data);
665  stdvec[i] = data.subSampleStd(0,
666  numPos,
667  meanVec[i]);
668  }
669 
670  return;
671 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::subSampleVarianceExtra ( unsigned int  initialPos,
unsigned int  numPos,
const V &  meanVec,
V &  samVec 
) const
virtual

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

Output:

Parameters
samVecis the vector of the calculated sample variance of the sub-sequence of vectors. The sample variance $ \sigma_y^2 $ is the second sample central moment and is defined by $ \sigma_y^2 = \frac{1}{n} \sum_{i=1}^n \left(y_i - \mu \right)^2 $, where $ \mu $ is the sample mean and $ n $ is the sample size. This procedure lets the users choose the initial position and the number of elements of the sequence which will be used to evaluate the sample variance.

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 569 of file SequenceOfVectors.C.

References UQ_FATAL_TEST_MACRO.

574 {
575  bool bRC = ((initialPos < this->subSequenceSize()) &&
576  (0 < numPos ) &&
577  ((initialPos+numPos) <= this->subSequenceSize()) &&
578  (this->vectorSizeLocal() == meanVec.sizeLocal() ) &&
579  (this->vectorSizeLocal() == samVec.sizeLocal() ));
580  UQ_FATAL_TEST_MACRO(bRC == false,
581  m_env.worldRank(),
582  "SequenceOfVectors<V,M>::subSampleVarianceExtra()",
583  "invalid input data");
584 
585  ScalarSequence<double> data(m_env,0,"");
586 
587  unsigned int numParams = this->vectorSizeLocal();
588  for (unsigned int i = 0; i < numParams; ++i) {
589  this->extractScalarSeq(initialPos,
590  1, // spacing
591  numPos,
592  i,
593  data);
594  samVec[i] = data.subSampleVarianceExtra(0,
595  numPos,
596  meanVec[i]);
597  }
598 
599  return;
600 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::subScalesForKde ( unsigned int  initialPos,
const V &  iqrVec,
unsigned int  kdeDimension,
V &  scaleVec 
) const
virtual

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

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.

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 1183 of file SequenceOfVectors.C.

References QUESO::ScalarSequence< T >::subScaleForKde(), and UQ_FATAL_TEST_MACRO.

1188 {
1189  bool bRC = ((initialPos < this->subSequenceSize()) &&
1190  (this->vectorSizeLocal() == iqrVec.sizeLocal() ) &&
1191  (this->vectorSizeLocal() == scaleVec.sizeLocal() ));
1192  UQ_FATAL_TEST_MACRO(bRC == false,
1193  m_env.worldRank(),
1194  "SequenceOfVectors<V,M>::subScalesForKde()",
1195  "invalid input data");
1196 
1197  unsigned int numPos = this->subSequenceSize() - initialPos;
1198  ScalarSequence<double> data(m_env,0,"");
1199 
1200  unsigned int numParams = this->vectorSizeLocal();
1201  for (unsigned int i = 0; i < numParams; ++i) {
1202  this->extractScalarSeq(initialPos,
1203  1, // spacing
1204  numPos,
1205  i,
1206  data);
1207  scaleVec[i] = data.subScaleForKde(0,
1208  iqrVec[i],
1209  kdeDimension);
1210  }
1211 
1212  return;
1213 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
unsigned int QUESO::SequenceOfVectors< V, M >::subSequenceSize ( ) const
virtual

Size of the sub-sequence of vectors.

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 103 of file SequenceOfVectors.C.

Referenced by QUESO::SequenceOfVectors< V, M >::copy(), QUESO::MLSampling< P_V, P_M >::generateBalLinkedChains_all(), QUESO::MetropolisHastingsSG< P_V, P_M >::generateFullChain(), 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::MLSampling< P_V, P_M >::generateUnbLinkedChains_all().

104 {
105  return m_seq.size();
106 }
QUESO::SequenceOfVectors::m_seq
std::vector< const V * > m_seq
Sequence of vectors.
Definition: SequenceOfVectors.h:417
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::subUniformlySampledCdf ( const V &  numEvaluationPointsVec,
ArrayOfOneDGrids< V, M > &  cdfGrids,
ArrayOfOneDTables< V, M > &  cdfValues 
) const

Uniformly samples from the CDF from the sub-sequence.

Definition at line 248 of file SequenceOfVectors.C.

References QUESO::ArrayOfOneDTables< V, M >::setOneDTable(), and QUESO::ArrayOfOneDGrids< V, M >::setUniformGrids().

Referenced by QUESO::StatisticalForwardProblem< P_V, P_M, Q_V, Q_M >::solveWithMonteCarlo().

252 {
253  V minDomainValues(m_vectorSpace.zeroVector());
254  V maxDomainValues(m_vectorSpace.zeroVector());
255 
256  ScalarSequence<double> data(m_env,0,"");
257 
258  unsigned int numParams = this->vectorSizeLocal();
259  for (unsigned int i = 0; i < numParams; ++i) {
260  this->extractScalarSeq(0, // initialPos
261  1, // spacing
262  subSequenceSize(), // numPos
263  i,
264  data);
265 
266  std::vector<double> aCdf(0);
267  data.subUniformlySampledCdf((unsigned int) numEvaluationPointsVec[i],
268  minDomainValues[i],
269  maxDomainValues[i],
270  aCdf);
271  cdfValues.setOneDTable(i,aCdf);
272  }
273 
274  cdfGrids.setUniformGrids(numEvaluationPointsVec,
275  minDomainValues,
276  maxDomainValues);
277 
278  return;
279 }
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:424
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::subWriteContents ( unsigned int  initialPos,
unsigned int  numPos,
const std::string &  fileName,
const std::string &  fileType,
const std::set< unsigned int > &  allowedSubEnvIds 
) const
virtual

Writes the sub-sequence to a file.

Given the allowed sub environments (allowedSubEnvIds) that are allowed to write to file, together with the file name and type (fileName, fileType), it writes the entire sub- sequence to the file. The sum of the initial position of the sequence (initialPos) with the number of positions that will be written (numPos) must equal the size of the sequence. This procedure calls void subWriteContents (unsigned int initialPos, unsigned int numPos, FilePtrSetStruct& filePtrSet, const std::string& fileType).

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 1357 of file SequenceOfVectors.C.

References UQ_FATAL_TEST_MACRO.

1363 {
1364  UQ_FATAL_TEST_MACRO(m_env.subRank() < 0,
1365  m_env.worldRank(),
1366  "SequenceOfVectors<V,M>::subWriteContents(1)",
1367  "unexpected subRank");
1368 
1369  FilePtrSetStruct filePtrSet;
1370  if ((m_env.subDisplayFile()) && (m_env.displayVerbosity() >= 99)) {
1371  *m_env.subDisplayFile() << "In SequenceOfVectors<V,M>::subWriteContents()"
1372  << ": about to try to open file '" << fileName << "." << fileType
1373  << "'"
1374  << ", initialPos = " << initialPos
1375  << ", numPos = " << numPos
1376  << std::endl;
1377  }
1378  if (m_env.openOutputFile(fileName,
1379  fileType,
1380  allowedSubEnvIds,
1381  false, // A 'true' causes problems when the user chooses (via options
1382  // in the input file) to use just one file for all outputs.
1383  filePtrSet)) {
1384  if ((m_env.subDisplayFile()) && (m_env.displayVerbosity() >= 99)) {
1385  *m_env.subDisplayFile() << "In SequenceOfVectors<V,M>::subWriteContents()"
1386  << ": successfully opened file '" << fileName << "." << fileType
1387  << "'"
1388  << std::endl;
1389  }
1390  this->subWriteContents(initialPos,
1391  numPos,
1392  filePtrSet,
1393  fileType);
1394  m_env.closeFile(filePtrSet,fileType);
1395  }
1396  if ((m_env.subDisplayFile()) && (m_env.displayVerbosity() >= 99)) {
1397  *m_env.subDisplayFile() << "In SequenceOfVectors<V,M>::subWriteContents()"
1398  << ": before Barrier()"
1399  << std::endl;
1400  }
1401  m_env.subComm().Barrier();
1402 
1403  return;
1404 }
QUESO::BaseEnvironment::subRank
int subRank() const
Access function for sub-rank.
Definition: Environment.C:263
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::BaseEnvironment::subComm
const MpiComm & subComm() const
Access function for MpiComm sub communicator.
Definition: Environment.C:269
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:305
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::MpiComm::Barrier
void Barrier() const
Pause every process in *this communicator until all the processes reach this point.
Definition: MpiComm.C:143
QUESO::BaseEnvironment::closeFile
void closeFile(FilePtrSetStruct &filePtrSet, const std::string &fileType) const
Closes the file.
Definition: Environment.C:1117
QUESO::BaseEnvironment::displayVerbosity
unsigned int displayVerbosity() const
Definition: Environment.C:436
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subWriteContents
void subWriteContents(unsigned int initialPos, unsigned int numPos, const std::string &fileName, const std::string &fileType, const std::set< unsigned int > &allowedSubEnvIds) const
Writes the sub-sequence to a file.
Definition: SequenceOfVectors.C:1357
QUESO::BaseEnvironment::openOutputFile
bool openOutputFile(const std::string &fileName, const std::string &fileType, const std::set< unsigned int > &allowedSubEnvIds, bool writeOver, FilePtrSetStruct &filePtrSet) const
Opens an output file for each sub-environment that was chosen to send data to the file...
Definition: Environment.C:516
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::subWriteContents ( unsigned int  initialPos,
unsigned int  numPos,
FilePtrSetStruct &  filePtrSet,
const std::string &  fileType 
) const

Writes the sub-sequence to a file.

Uses additional variable of the type FilePtrSetStruct& to operate on files.

Definition at line 1408 of file SequenceOfVectors.C.

References UQ_FATAL_TEST_MACRO, UQ_FILE_EXTENSION_FOR_HDF_FORMAT, and UQ_FILE_EXTENSION_FOR_MATLAB_FORMAT.

1413 {
1414  UQ_FATAL_TEST_MACRO(filePtrSet.ofsVar == NULL,
1415  m_env.worldRank(),
1416  "SequenceOfVectors<V,M>::subWriteContents(2)",
1417  "filePtrSet.ofsVar should not be NULL");
1418 
1419  if (fileType == UQ_FILE_EXTENSION_FOR_MATLAB_FORMAT) {
1420  this->subWriteContents(initialPos,
1421  numPos,
1422  *filePtrSet.ofsVar,
1423  fileType);
1424  }
1425  else if (fileType == UQ_FILE_EXTENSION_FOR_HDF_FORMAT) {
1426  UQ_FATAL_TEST_MACRO(true,
1427  m_env.worldRank(),
1428  "SequenceOfVectors<V,M>::subWriteContents(2)",
1429  "hdf file type not supported yet");
1430  }
1431  else {
1432  UQ_FATAL_TEST_MACRO(true,
1433  m_env.worldRank(),
1434  "SequenceOfVectors<V,M>::subWriteContents(2)",
1435  "invalid file type");
1436  }
1437 
1438  return;
1439 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
UQ_FILE_EXTENSION_FOR_MATLAB_FORMAT
#define UQ_FILE_EXTENSION_FOR_MATLAB_FORMAT
Definition: Defines.h:89
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
UQ_FILE_EXTENSION_FOR_HDF_FORMAT
#define UQ_FILE_EXTENSION_FOR_HDF_FORMAT
Definition: Defines.h:90
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subWriteContents
void subWriteContents(unsigned int initialPos, unsigned int numPos, const std::string &fileName, const std::string &fileType, const std::set< unsigned int > &allowedSubEnvIds) const
Writes the sub-sequence to a file.
Definition: SequenceOfVectors.C:1357
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::subWriteContents ( unsigned int  initialPos,
unsigned int  numPos,
std::ofstream &  ofs,
const std::string &  fileType 
) const
virtual

Writes the sub-sequence to a file.

Uses object of the type std::ofstream.

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 1443 of file SequenceOfVectors.C.

References UQ_FATAL_TEST_MACRO.

1448 {
1449  UQ_FATAL_TEST_MACRO((initialPos+numPos) > this->subSequenceSize(),
1450  m_env.worldRank(),
1451  "SequenceOfVectors<V,M>::subWriteContents(3)",
1452  "invalid routine input parameters");
1453 
1454  if (fileType.c_str()) {}; // just to avoid compiler warning
1455 
1456  if (initialPos == 0) {
1457  ofs << m_name << "_sub" << m_env.subIdString() << " = zeros(" << this->subSequenceSize()
1458  << "," << this->vectorSizeLocal()
1459  << ");"
1460  << std::endl;
1461  ofs << m_name << "_sub" << m_env.subIdString() << " = [";
1462  }
1463 
1464  for (unsigned int j = initialPos; j < initialPos+numPos; ++j) {
1465  bool savedVectorPrintScientific = m_seq[j]->getPrintScientific();
1466  bool savedVectorPrintState = m_seq[j]->getPrintHorizontally();
1467  m_seq[j]->setPrintScientific (true);
1468  m_seq[j]->setPrintHorizontally(true);
1469 
1470  ofs << *(m_seq[j])
1471  << std::endl;
1472 
1473  m_seq[j]->setPrintHorizontally(savedVectorPrintState);
1474  m_seq[j]->setPrintScientific (savedVectorPrintScientific);
1475  }
1476  if ((initialPos+numPos) == this->subSequenceSize()) {
1477  ofs << "];\n";
1478  }
1479 
1480  return;
1481 }
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:335
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::SequenceOfVectors::m_seq
std::vector< const V * > m_seq
Sequence of vectors.
Definition: SequenceOfVectors.h:417
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::unifiedGaussian1dKde ( unsigned int  initialPos,
const V &  unifiedScaleVec,
const std::vector< V * > &  unifiedEvalParamVecs,
std::vector< V * > &  unifiedDensityVecs 
) const
virtual

Gaussian kernel for the KDE estimate of the unified sequence.

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 1304 of file SequenceOfVectors.C.

References QUESO::ScalarSequence< T >::unifiedGaussian1dKde(), and UQ_FATAL_TEST_MACRO.

1309 {
1310  bool bRC = ((initialPos < this->subSequenceSize() ) &&
1311  (this->vectorSizeLocal() == unifiedScaleVec.sizeLocal()) &&
1312  (0 < unifiedEvalParamVecs.size()) &&
1313  (unifiedEvalParamVecs.size() == unifiedDensityVecs.size() ));
1314  UQ_FATAL_TEST_MACRO(bRC == false,
1315  m_env.worldRank(),
1316  "SequenceOfVectors<V,M>::unifiedGaussian1dKde()",
1317  "invalid input data");
1318 
1319  unsigned int numPos = this->subSequenceSize() - initialPos;
1320  ScalarSequence<double> data(m_env,0,"");
1321 
1322  unsigned int numEvals = unifiedEvalParamVecs.size();
1323  for (unsigned int j = 0; j < numEvals; ++j) {
1324  unifiedDensityVecs[j] = new V(m_vectorSpace.zeroVector());
1325  }
1326  std::vector<double> unifiedEvalParams(numEvals,0.);
1327  std::vector<double> unifiedDensities (numEvals,0.);
1328 
1329  unsigned int numParams = this->vectorSizeLocal();
1330  for (unsigned int i = 0; i < numParams; ++i) {
1331  this->extractScalarSeq(initialPos,
1332  1, // spacing
1333  numPos,
1334  i,
1335  data);
1336 
1337  for (unsigned int j = 0; j < numEvals; ++j) {
1338  unifiedEvalParams[j] = (*unifiedEvalParamVecs[j])[i];
1339  }
1340 
1341  data.unifiedGaussian1dKde(m_vectorSpace.numOfProcsForStorage() == 1,
1342  0,
1343  unifiedScaleVec[i],
1344  unifiedEvalParams,
1345  unifiedDensities);
1346 
1347  for (unsigned int j = 0; j < numEvals; ++j) {
1348  (*unifiedDensityVecs[j])[i] = unifiedDensities[j];
1349  }
1350  }
1351 
1352  return;
1353 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:424
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::unifiedHistogram ( unsigned int  initialPos,
const V &  unifiedMinVec,
const V &  unifiedMaxVec,
std::vector< V * > &  unifiedCentersForAllBins,
std::vector< V * > &  unifiedQuanttsForAllBins 
) const
virtual

Calculates the histogram of the unified sequence.

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 1074 of file SequenceOfVectors.C.

References QUESO::ScalarSequence< T >::unifiedHistogram(), and UQ_FATAL_TEST_MACRO.

1080 {
1081  bool bRC = ((initialPos < this->subSequenceSize() ) &&
1082  (this->vectorSizeLocal() == unifiedMinVec.sizeLocal() ) &&
1083  (this->vectorSizeLocal() == unifiedMaxVec.sizeLocal() ) &&
1084  (0 < unifiedCentersForAllBins.size()) &&
1085  (unifiedCentersForAllBins.size() == unifiedQuanttsForAllBins.size()));
1086  UQ_FATAL_TEST_MACRO(bRC == false,
1087  m_env.worldRank(),
1088  "SequenceOfVectors<V,M>::unifiedHistogram()",
1089  "invalid input data");
1090 
1091  for (unsigned int j = 0; j < unifiedQuanttsForAllBins.size(); ++j) {
1092  unifiedCentersForAllBins[j] = new V(m_vectorSpace.zeroVector());
1093  unifiedQuanttsForAllBins [j] = new V(m_vectorSpace.zeroVector());
1094  }
1095 
1096  unsigned int dataSize = this->subSequenceSize() - initialPos;
1097  unsigned int numParams = this->vectorSizeLocal();
1098  for (unsigned int i = 0; i < numParams; ++i) {
1099  ScalarSequence<double> data(m_env,dataSize,"");
1100  for (unsigned int j = 0; j < dataSize; ++j) {
1101  data[j] = (*(m_seq[initialPos+j]))[i];
1102  }
1103 
1104  std::vector<double > unifiedCenters(unifiedCentersForAllBins.size(),0.);
1105  std::vector<unsigned int> unifiedQuantts(unifiedQuanttsForAllBins.size(), 0 );
1106  data.unifiedHistogram(m_vectorSpace.numOfProcsForStorage() == 1,
1107  0,
1108  unifiedMinVec[i],
1109  unifiedMaxVec[i],
1110  unifiedCenters,
1111  unifiedQuantts);
1112 
1113  for (unsigned int j = 0; j < unifiedQuantts.size(); ++j) {
1114  (*(unifiedCentersForAllBins[j]))[i] = unifiedCenters[j];
1115  (*(unifiedQuanttsForAllBins[j]))[i] = (double) unifiedQuantts[j];
1116  }
1117  }
1118 
1119  return;
1120 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:424
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::SequenceOfVectors::m_seq
std::vector< const V * > m_seq
Sequence of vectors.
Definition: SequenceOfVectors.h:417
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::unifiedInterQuantileRange ( unsigned int  initialPos,
V &  unifiedIqrVec 
) const
virtual

Returns the interquartile range of the values in the unified sequence.

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 1153 of file SequenceOfVectors.C.

References QUESO::ScalarSequence< T >::unifiedInterQuantileRange(), and UQ_FATAL_TEST_MACRO.

1156 {
1157  bool bRC = ((initialPos < this->subSequenceSize() ) &&
1158  (this->vectorSizeLocal() == unifiedIqrVec.sizeLocal()));
1159  UQ_FATAL_TEST_MACRO(bRC == false,
1160  m_env.worldRank(),
1161  "SequenceOfVectors<V,M>::unifiedInterQuantileRange()",
1162  "invalid input data");
1163 
1164  unsigned int numPos = this->subSequenceSize() - initialPos;
1165  ScalarSequence<double> data(m_env,0,"");
1166 
1167  unsigned int numParams = this->vectorSizeLocal();
1168  for (unsigned int i = 0; i < numParams; ++i) {
1169  this->extractScalarSeq(initialPos,
1170  1, // spacing
1171  numPos,
1172  i,
1173  data);
1174  unifiedIqrVec[i] = data.unifiedInterQuantileRange(m_vectorSpace.numOfProcsForStorage() == 1,
1175  0);
1176  }
1177 
1178  return;
1179 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:424
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::unifiedMeanExtra ( unsigned int  initialPos,
unsigned int  numPos,
V &  unifiedMeanVec 
) const
virtual

Finds the mean value of the unified sequence, considering numPos positions starting at position initialPos.

Output:

Parameters
meanVecis the vector of the calculated means of the unified sequence of vectors.

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 387 of file SequenceOfVectors.C.

References UQ_FATAL_TEST_MACRO.

391 {
392  unsigned int tmpUnif = this->unifiedSequenceSize();
393  if ((m_env.subDisplayFile()) && (m_env.displayVerbosity() >= 5)) {
394  *m_env.subDisplayFile() << "Entering SequenceOfVectors<V,M>::unifiedMeanExtra()"
395  << ": initialPos = " << initialPos
396  << ", numPos = " << numPos
397  << ", sub sequence size = " << this->subSequenceSize()
398  << ", unified sequence size = " << tmpUnif
399  << std::endl;
400  }
401 
402  bool bRC = ((initialPos < this->subSequenceSize() ) &&
403  (0 < numPos ) &&
404  ((initialPos+numPos) <= this->subSequenceSize() ) &&
405  (this->vectorSizeLocal() == unifiedMeanVec.sizeLocal()));
406  if ((bRC == false) && (m_env.subDisplayFile())) {
407  *m_env.subDisplayFile() << "In SequenceOfVectors<V,M>::unifiedMeanExtra()"
408  << ", initialPos = " << initialPos
409  << ", this->subSequenceSize() = " << this->subSequenceSize()
410  << ", numPos = " << numPos
411  << ", this->vectorSizeLocal() = " << this->vectorSizeLocal()
412  << ", unifiedMeanVec.sizeLocal() = " << unifiedMeanVec.sizeLocal()
413  << std::endl;
414  }
415  UQ_FATAL_TEST_MACRO(bRC == false,
416  m_env.worldRank(),
417  "SequenceOfVectors<V,M>::unifiedMeanExtra()",
418  "invalid input data");
419 
420  ScalarSequence<double> data(m_env,0,"");
421 
422  unsigned int numParams = this->vectorSizeLocal();
423  for (unsigned int i = 0; i < numParams; ++i) {
424  this->extractScalarSeq(initialPos,
425  1, // spacing
426  numPos,
427  i,
428  data);
429  unifiedMeanVec[i] = data.unifiedMeanExtra(m_vectorSpace.numOfProcsForStorage() == 1,
430  0,
431  numPos);
432  }
433 
434  if ((m_env.subDisplayFile()) && (m_env.displayVerbosity() >= 5)) {
435  *m_env.subDisplayFile() << "Leaving SequenceOfVectors<V,M>::unifiedMeanExtra()"
436  << ": initialPos = " << initialPos
437  << ", numPos = " << numPos
438  << ", sub sequence size = " << this->subSequenceSize()
439  << ", unified sequence size = " << tmpUnif
440  << ", unifiedMeanVec = " << unifiedMeanVec
441  << std::endl;
442  }
443 
444  return;
445 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:305
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:424
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
QUESO::BaseEnvironment::displayVerbosity
unsigned int displayVerbosity() const
Definition: Environment.C:436
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::BaseVectorSequence::unifiedSequenceSize
unsigned int unifiedSequenceSize() const
Calculates the size of the unified sequence of vectors.
Definition: VectorSequence.C:70
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::unifiedMedianExtra ( unsigned int  initialPos,
unsigned int  numPos,
V &  unifiedMedianVec 
) const
virtual

Finds the median value of the unfed sequence, considering numPos positions starting at position initialPos.

Output:

Parameters
medianVecis the vector of the calculated medians of the unified sequence of vectors.

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 507 of file SequenceOfVectors.C.

References UQ_FATAL_TEST_MACRO.

511 {
512  unsigned int tmpUnif = this->unifiedSequenceSize();
513  if ((m_env.subDisplayFile()) && (m_env.displayVerbosity() >= 5)) {
514  *m_env.subDisplayFile() << "Entering SequenceOfVectors<V,M>::unifiedMedianExtra()"
515  << ": initialPos = " << initialPos
516  << ", numPos = " << numPos
517  << ", sub sequence size = " << this->subSequenceSize()
518  << ", unified sequence size = " << tmpUnif
519  << std::endl;
520  }
521 
522  bool bRC = ((initialPos < this->subSequenceSize() ) &&
523  (0 < numPos ) &&
524  ((initialPos+numPos) <= this->subSequenceSize() ) &&
525  (this->vectorSizeLocal() == unifiedMedianVec.sizeLocal()));
526  if ((bRC == false) && (m_env.subDisplayFile())) {
527  *m_env.subDisplayFile() << "In SequenceOfVectors<V,M>::unifiedMedianExtra()"
528  << ", initialPos = " << initialPos
529  << ", this->subSequenceSize() = " << this->subSequenceSize()
530  << ", numPos = " << numPos
531  << ", this->vectorSizeLocal() = " << this->vectorSizeLocal()
532  << ", unifiedMedianVec.sizeLocal() = " << unifiedMedianVec.sizeLocal()
533  << std::endl;
534  }
535  UQ_FATAL_TEST_MACRO(bRC == false,
536  m_env.worldRank(),
537  "SequenceOfVectors<V,M>::unifiedMedianExtra()",
538  "invalid input data");
539 
540  ScalarSequence<double> data(m_env,0,"");
541 
542  unsigned int numParams = this->vectorSizeLocal();
543  for (unsigned int i = 0; i < numParams; ++i) {
544  this->extractScalarSeq(initialPos,
545  1, // spacing
546  numPos,
547  i,
548  data);
549  unifiedMedianVec[i] = data.unifiedMedianExtra(m_vectorSpace.numOfProcsForStorage() == 1,
550  0,
551  numPos);
552  }
553 
554  if ((m_env.subDisplayFile()) && (m_env.displayVerbosity() >= 5)) {
555  *m_env.subDisplayFile() << "Leaving SequenceOfVectors<V,M>::unifiedMedianExtra()"
556  << ": initialPos = " << initialPos
557  << ", numPos = " << numPos
558  << ", sub sequence size = " << this->subSequenceSize()
559  << ", unified sequence size = " << tmpUnif
560  << ", unifiedMedianVec = " << unifiedMedianVec
561  << std::endl;
562  }
563 
564  return;
565 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:305
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:424
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
QUESO::BaseEnvironment::displayVerbosity
unsigned int displayVerbosity() const
Definition: Environment.C:436
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::BaseVectorSequence::unifiedSequenceSize
unsigned int unifiedSequenceSize() const
Calculates the size of the unified sequence of vectors.
Definition: VectorSequence.C:70
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::unifiedMinMaxExtra ( unsigned int  initialPos,
unsigned int  numPos,
V &  unifiedMinVec,
V &  unifiedMaxVec 
) const
virtual

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

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 988 of file SequenceOfVectors.C.

References QUESO::ScalarSequence< T >::unifiedMinMaxExtra(), and UQ_FATAL_TEST_MACRO.

993 {
994  bool bRC = ((0 < numPos ) &&
995  ((initialPos+numPos) <= this->subSequenceSize() ) &&
996  (this->vectorSizeLocal() == unifiedMinVec.sizeLocal()) &&
997  (this->vectorSizeLocal() == unifiedMaxVec.sizeLocal()));
998  UQ_FATAL_TEST_MACRO(bRC == false,
999  m_env.worldRank(),
1000  "SequenceOfVectors<V,M>::unifiedMinMaxExtra()",
1001  "invalid input data");
1002 
1003  //unsigned int numPos = this->subSequenceSize() - initialPos;
1004  unsigned int numParams = this->vectorSizeLocal();
1005  ScalarSequence<double> data(m_env,0,"");
1006 
1007  for (unsigned int i = 0; i < numParams; ++i) {
1008  this->extractScalarSeq(initialPos,
1009  1, // spacing
1010  numPos,
1011  i,
1012  data);
1013  data.unifiedMinMaxExtra(m_vectorSpace.numOfProcsForStorage() == 1,
1014  0,
1015  numPos,
1016  unifiedMinVec[i],
1017  unifiedMaxVec[i]);
1018  }
1019 
1020  return;
1021 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:424
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::unifiedPopulationVariance ( unsigned int  initialPos,
unsigned int  numPos,
const V &  unifiedMeanVec,
V &  unifiedPopVec 
) const
virtual

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

Output:

Parameters
popVecis the vector of the calculated population variance of the unified sequence of vectors.

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 746 of file SequenceOfVectors.C.

References UQ_FATAL_TEST_MACRO.

751 {
752  bool bRC = ((initialPos < this->subSequenceSize() ) &&
753  (0 < numPos ) &&
754  ((initialPos+numPos) <= this->subSequenceSize() ) &&
755  (this->vectorSizeLocal() == unifiedMeanVec.sizeLocal()) &&
756  (this->vectorSizeLocal() == unifiedPopVec.sizeLocal() ));
757  UQ_FATAL_TEST_MACRO(bRC == false,
758  m_env.worldRank(),
759  "SequenceOfVectors<V,M>::unifiedPopulationVariance()",
760  "invalid input data");
761 
762  ScalarSequence<double> data(m_env,0,"");
763 
764  unsigned int numParams = this->vectorSizeLocal();
765  for (unsigned int i = 0; i < numParams; ++i) {
766  this->extractScalarSeq(initialPos,
767  1, // spacing
768  numPos,
769  i,
770  data);
771  unifiedPopVec[i] = data.unifiedPopulationVariance(m_vectorSpace.numOfProcsForStorage() == 1,
772  0,
773  numPos,
774  unifiedMeanVec[i]);
775  }
776 
777  return;
778 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:424
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::unifiedReadContents ( const std::string &  fileName,
const std::string &  fileType,
const unsigned int  subSequenceSize 
)
virtual

Reads the unified sequence from a file.

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 1760 of file SequenceOfVectors.C.

References QUESO::FilePtrSetStruct::ifsVar, QUESO::MiscGetEllapsedSeconds(), UQ_FATAL_TEST_MACRO, UQ_FILE_EXTENSION_FOR_HDF_FORMAT, UQ_FILE_EXTENSION_FOR_MATLAB_FORMAT, and QUESO::UQ_OK_RC.

Referenced by QUESO::MLSampling< P_V, P_M >::restartML().

1764 {
1765  std::string fileType(inputFileType);
1766 #ifdef QUESO_HAS_HDF5
1767  // Do nothing
1768 #else
1769  if (fileType == UQ_FILE_EXTENSION_FOR_HDF_FORMAT) {
1770  if (m_env.subDisplayFile()) {
1771  *m_env.subDisplayFile() << "WARNING in SequenceOfVectors<V,M>::unifiedReadContents()"
1772  << ": file format '" << UQ_FILE_EXTENSION_FOR_HDF_FORMAT
1773  << "' has been requested, but this QUESO library has not been built with 'hdf5'"
1774  << ". Code will therefore process the file format '" << UQ_FILE_EXTENSION_FOR_HDF_FORMAT
1775  << "' instead..."
1776  << std::endl;
1777  }
1778  if (m_env.subRank() == 0) {
1779  std::cerr << "WARNING in SequenceOfVectors<V,M>::unifiedReadContents()"
1780  << ": file format '" << UQ_FILE_EXTENSION_FOR_HDF_FORMAT
1781  << "' has been requested, but this QUESO library has not been built with 'hdf5'"
1782  << ". Code will therefore process the file format '" << UQ_FILE_EXTENSION_FOR_HDF_FORMAT
1783  << "' instead..."
1784  << std::endl;
1785  }
1786  fileType = UQ_FILE_EXTENSION_FOR_MATLAB_FORMAT;
1787  }
1788 #endif
1789 
1790  //m_env.fullComm().Barrier(); // Dangerous to barrier on fullComm ...
1791  if (m_env.subDisplayFile()) {
1792  *m_env.subDisplayFile() << "Entering SequenceOfVectors<V,M>::unifiedReadContents()"
1793  << ": worldRank " << m_env.worldRank()
1794  << ", fullRank " << m_env.fullRank()
1795  << ", subEnvironment " << m_env.subId()
1796  << ", subRank " << m_env.subRank()
1797  << ", inter0Rank " << m_env.inter0Rank()
1798  //<< ", m_env.inter0Comm().NumProc() = " << m_env.inter0Comm().NumProc()
1799  << ", fileName = " << fileName
1800  << ", subReadSize = " << subReadSize
1801  //<< ", unifiedReadSize = " << unifiedReadSize
1802  << std::endl;
1803  }
1804 
1805  this->resizeSequence(subReadSize);
1806 
1807  if (m_env.inter0Rank() >= 0) {
1808  double unifiedReadSize = subReadSize*m_env.inter0Comm().NumProc();
1809 
1810  // In the logic below, the id of a line' begins with value 0 (zero)
1811  unsigned int idOfMyFirstLine = 1 + m_env.inter0Rank()*subReadSize;
1812  unsigned int idOfMyLastLine = (1 + m_env.inter0Rank())*subReadSize;
1813  unsigned int numParams = this->vectorSizeLocal();
1814 
1815  for (unsigned int r = 0; r < (unsigned int) m_env.inter0Comm().NumProc(); ++r) { // "m or hdf"
1816  if (m_env.inter0Rank() == (int) r) {
1817  // My turn
1818  FilePtrSetStruct unifiedFilePtrSet;
1819  if (m_env.openUnifiedInputFile(fileName,
1820  fileType,
1821  unifiedFilePtrSet)) {
1822  if (fileType == UQ_FILE_EXTENSION_FOR_MATLAB_FORMAT) {
1823  if (r == 0) {
1824  // Read number of chain positions in the file by taking care of the first line,
1825  // which resembles something like 'variable_name = zeros(n_positions,m_params);'
1826  std::string tmpString;
1827 
1828  // Read 'variable name' string
1829  *unifiedFilePtrSet.ifsVar >> tmpString;
1830  //std::cout << "Just read '" << tmpString << "'" << std::endl;
1831 
1832  // Read '=' sign
1833  *unifiedFilePtrSet.ifsVar >> tmpString;
1834  //std::cout << "Just read '" << tmpString << "'" << std::endl;
1835  UQ_FATAL_TEST_MACRO(tmpString != "=",
1836  m_env.worldRank(),
1837  "SequenceOfVectors<V,M>::unifiedReadContents()",
1838  "string should be the '=' sign");
1839 
1840  // Read 'zeros(n_positions,n_params)' string
1841  *unifiedFilePtrSet.ifsVar >> tmpString;
1842  //std::cout << "Just read '" << tmpString << "'" << std::endl;
1843  unsigned int posInTmpString = 6;
1844 
1845  // Isolate 'n_positions' in a string
1846  //char nPositionsString[tmpString.size()-posInTmpString+1]; // avoid compiler warning
1847  std::string nPositionsString((size_t) (tmpString.size()-posInTmpString+1),' ');
1848  unsigned int posInPositionsString = 0;
1849  do {
1850  UQ_FATAL_TEST_MACRO(posInTmpString >= tmpString.size(),
1851  m_env.worldRank(),
1852  "SequenceOfVectors<V,M>::unifiedReadContents()",
1853  "symbol ',' not found in first line of file");
1854  nPositionsString[posInPositionsString++] = tmpString[posInTmpString++];
1855  } while (tmpString[posInTmpString] != ',');
1856  nPositionsString[posInPositionsString] = '\0';
1857 
1858  // Isolate 'n_params' in a string
1859  posInTmpString++; // Avoid reading ',' char
1860  //char nParamsString[tmpString.size()-posInTmpString+1]; // avoid compiler warning
1861  std::string nParamsString((size_t) (tmpString.size()-posInTmpString+1),' ');
1862  unsigned int posInParamsString = 0;
1863  do {
1864  UQ_FATAL_TEST_MACRO(posInTmpString >= tmpString.size(),
1865  m_env.worldRank(),
1866  "SequenceOfVectors<V,M>::unifiedReadContents()",
1867  "symbol ')' not found in first line of file");
1868  nParamsString[posInParamsString++] = tmpString[posInTmpString++];
1869  } while (tmpString[posInTmpString] != ')');
1870  nParamsString[posInParamsString] = '\0';
1871 
1872  // Convert 'n_positions' and 'n_params' strings to numbers
1873  unsigned int sizeOfChainInFile = (unsigned int) strtod(nPositionsString.c_str(),NULL);
1874  unsigned int numParamsInFile = (unsigned int) strtod(nParamsString.c_str(), NULL);
1875  if (m_env.subDisplayFile()) {
1876  *m_env.subDisplayFile() << "In SequenceOfVectors<V,M>::unifiedReadContents()"
1877  << ": worldRank " << m_env.worldRank()
1878  << ", fullRank " << m_env.fullRank()
1879  << ", sizeOfChainInFile = " << sizeOfChainInFile
1880  << ", numParamsInFile = " << numParamsInFile
1881  << std::endl;
1882  }
1883 
1884  // Check if [size of chain in file] >= [requested unified sequence size]
1885  UQ_FATAL_TEST_MACRO(sizeOfChainInFile < unifiedReadSize,
1886  m_env.worldRank(),
1887  "SequenceOfVectors<V,M>::unifiedReadContents()",
1888  "size of chain in file is not big enough");
1889 
1890  // Check if [num params in file] == [num params in current chain]
1891  UQ_FATAL_TEST_MACRO(numParamsInFile != numParams,
1892  m_env.worldRank(),
1893  "SequenceOfVectors<V,M>::unifiedReadContents()",
1894  "number of parameters of chain in file is different than number of parameters in this chain object");
1895  } // if (r == 0)
1896 
1897  // Code common to any core in 'inter0Comm', including core of rank 0
1898  unsigned int maxCharsPerLine = 64*numParams; // Up to about 60 characters to represent each parameter value
1899 
1900  unsigned int lineId = 0;
1901  while (lineId < idOfMyFirstLine) {
1902  unifiedFilePtrSet.ifsVar->ignore(maxCharsPerLine,'\n');
1903  lineId++;
1904  };
1905 
1906  if (r == 0) {
1907  // Take care of initial part of the first data line,
1908  // which resembles something like 'variable_name = [value1 value2 ...'
1909  std::string tmpString;
1910 
1911  // Read 'variable name' string
1912  *unifiedFilePtrSet.ifsVar >> tmpString;
1913  //std::cout << "Core 0 just read '" << tmpString << "'" << std::endl;
1914 
1915  // Read '=' sign
1916  *unifiedFilePtrSet.ifsVar >> tmpString;
1917  //std::cout << "Core 0 just read '" << tmpString << "'" << std::endl;
1918  UQ_FATAL_TEST_MACRO(tmpString != "=",
1919  m_env.worldRank(),
1920  "SequenceOfVectors<V,M>::unifiedReadContents()",
1921  "in core 0, string should be the '=' sign");
1922 
1923  // Take into account the ' [' portion
1924  std::streampos tmpPos = unifiedFilePtrSet.ifsVar->tellg();
1925  unifiedFilePtrSet.ifsVar->seekg(tmpPos+(std::streampos)2);
1926  }
1927 
1928  V tmpVec(m_vectorSpace.zeroVector());
1929  while (lineId <= idOfMyLastLine) {
1930  for (unsigned int i = 0; i < numParams; ++i) {
1931  *unifiedFilePtrSet.ifsVar >> tmpVec[i];
1932  }
1933  this->setPositionValues(lineId - idOfMyFirstLine, tmpVec);
1934  lineId++;
1935  };
1936  }
1937 #ifdef QUESO_HAS_HDF5
1938  else if (fileType == UQ_FILE_EXTENSION_FOR_HDF_FORMAT) {
1939  if (r == 0) {
1940  hid_t dataset = H5Dopen2(unifiedFilePtrSet.h5Var,
1941  "seq_of_vectors",
1942  H5P_DEFAULT); // Dataset access property list
1943  hid_t datatype = H5Dget_type(dataset);
1944  H5T_class_t t_class = H5Tget_class(datatype);
1945  UQ_FATAL_TEST_MACRO(t_class != H5T_FLOAT,
1946  m_env.worldRank(),
1947  "SequenceOfVectors<V,M>::unifiedReadContents()",
1948  "t_class is not H5T_DOUBLE");
1949  hid_t dataspace = H5Dget_space(dataset);
1950  int rank = H5Sget_simple_extent_ndims(dataspace);
1951  UQ_FATAL_TEST_MACRO(rank != 2,
1952  m_env.worldRank(),
1953  "SequenceOfVectors<V,M>::unifiedReadContents()",
1954  "hdf rank is not 2");
1955  hsize_t dims_in[2];
1956  int status_n;
1957  status_n = H5Sget_simple_extent_dims(dataspace, dims_in, NULL);
1958  if (status_n) {}; // just to remover compiler warning
1959  //std::cout << "In SequenceOfVectors<V,M>::unifiedReadContents()"
1960  // << ": dims_in[0] = " << dims_in[0]
1961  // << ", dims_in[1] = " << dims_in[1]
1962  // << std::endl;
1963  UQ_FATAL_TEST_MACRO(dims_in[0] != numParams,
1964  m_env.worldRank(),
1965  "SequenceOfVectors<V,M>::unifiedReadContents()",
1966  "dims_in[0] is not equal to 'numParams'");
1967  UQ_FATAL_TEST_MACRO(dims_in[1] < subReadSize,
1968  m_env.worldRank(),
1969  "SequenceOfVectors<V,M>::unifiedReadContents()",
1970  "dims_in[1] is smaller that requested 'subReadSize'");
1971 
1972  struct timeval timevalBegin;
1973  int iRC = UQ_OK_RC;
1974  iRC = gettimeofday(&timevalBegin,NULL);
1975  if (iRC) {}; // just to remover compiler warning
1976 
1977  unsigned int chainSizeIn = (unsigned int) dims_in[1];
1978  //double* dataIn[numParams]; // avoid compiler warning
1979  std::vector<double*> dataIn((size_t) numParams,NULL);
1980  dataIn[0] = (double*) malloc(numParams*chainSizeIn*sizeof(double));
1981  for (unsigned int i = 1; i < numParams; ++i) { // Yes, from '1'
1982  dataIn[i] = dataIn[i-1] + chainSizeIn; // Yes, just 'chainSizeIn', not 'chainSizeIn*sizeof(double)'
1983  }
1984  //std::cout << "In SequenceOfVectors<V,M>::unifiedReadContents(): h5 case, memory allocated" << std::endl;
1985  herr_t status;
1986  status = H5Dread(dataset,
1987  H5T_NATIVE_DOUBLE,
1988  H5S_ALL,
1989  dataspace,
1990  H5P_DEFAULT,
1991  dataIn[0]);
1992  if (status) {}; // just to remover compiler warning
1993  //std::cout << "In SequenceOfVectors<V,M>::unifiedReadContents(): h5 case, data read" << std::endl;
1994  V tmpVec(m_vectorSpace.zeroVector());
1995  for (unsigned int j = 0; j < subReadSize; ++j) { // Yes, 'subReadSize', not 'chainSizeIn'
1996  for (unsigned int i = 0; i < numParams; ++i) {
1997  tmpVec[i] = dataIn[i][j];
1998  }
1999  this->setPositionValues(j, tmpVec);
2000  }
2001 
2002  double readTime = MiscGetEllapsedSeconds(&timevalBegin);
2003  if ((m_env.subDisplayFile()) && (m_env.displayVerbosity() >= 2)) {
2004  *m_env.subDisplayFile() << "In SequenceOfVectors<V,M>::unifiedReadContents()"
2005  << ": worldRank " << m_env.worldRank()
2006  << ", fullRank " << m_env.fullRank()
2007  << ", subEnvironment " << m_env.subId()
2008  << ", subRank " << m_env.subRank()
2009  << ", inter0Rank " << m_env.inter0Rank()
2010  << ", fileName = " << fileName
2011  << ", numParams = " << numParams
2012  << ", chainSizeIn = " << chainSizeIn
2013  << ", subReadSize = " << subReadSize
2014  << ", readTime = " << readTime << " seconds"
2015  << std::endl;
2016  }
2017 
2018  H5Sclose(dataspace);
2019  H5Tclose(datatype);
2020  H5Dclose(dataset);
2021  //free(dataIn[0]); // related to the changes above for compiler warning
2022  for (unsigned int tmpIndex = 0; tmpIndex < dataIn.size(); tmpIndex++) {
2023  free (dataIn[tmpIndex]);
2024  }
2025  }
2026  else {
2027  UQ_FATAL_TEST_MACRO(true,
2028  m_env.worldRank(),
2029  "SequenceOfVectors<V,M>::unifiedReadContents()",
2030  "hdf file type not supported for multiple sub-environments yet");
2031  }
2032  }
2033 #endif
2034  else {
2035  UQ_FATAL_TEST_MACRO(true,
2036  m_env.worldRank(),
2037  "SequenceOfVectors<V,M>::unifiedReadContents()",
2038  "invalid file type");
2039  }
2040  m_env.closeFile(unifiedFilePtrSet,fileType);
2041  } // if (m_env.openUnifiedInputFile())
2042  } // if (m_env.inter0Rank() == (int) r)
2043  m_env.inter0Comm().Barrier();
2044  } // for r
2045  } // if (m_env.inter0Rank() >= 0)
2046  else {
2047  V tmpVec(m_vectorSpace.zeroVector());
2048  for (unsigned int i = 1; i < subReadSize; ++i) {
2049  this->setPositionValues(i,tmpVec);
2050  }
2051  }
2052 
2053  if (m_env.subDisplayFile()) {
2054  *m_env.subDisplayFile() << "Leaving SequenceOfVectors<V,M>::unifiedReadContents()"
2055  << ", fileName = " << fileName
2056  << std::endl;
2057  }
2058  //m_env.fullComm().Barrier(); // Dangerous to barrier on fullComm ...
2059 
2060  return;
2061 }
QUESO::BaseEnvironment::subRank
int subRank() const
Access function for sub-rank.
Definition: Environment.C:263
QUESO::SequenceOfVectors::setPositionValues
void setPositionValues(unsigned int posId, const V &vec)
Set the values in vec at position posId of the sequence.
Definition: SequenceOfVectors.C:221
QUESO::BaseEnvironment::openUnifiedInputFile
bool openUnifiedInputFile(const std::string &fileName, const std::string &fileType, FilePtrSetStruct &filePtrSet) const
Opens the unified input file.
Definition: Environment.C:1016
QUESO::BaseEnvironment::inter0Rank
int inter0Rank() const
Returns the process inter0 rank.
Definition: Environment.C:289
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
UQ_FILE_EXTENSION_FOR_MATLAB_FORMAT
#define UQ_FILE_EXTENSION_FOR_MATLAB_FORMAT
Definition: Defines.h:89
QUESO::MpiComm::NumProc
int NumProc() const
Returns total number of processes.
Definition: MpiComm.C:121
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:305
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:424
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::MpiComm::Barrier
void Barrier() const
Pause every process in *this communicator until all the processes reach this point.
Definition: MpiComm.C:143
QUESO::BaseEnvironment::closeFile
void closeFile(FilePtrSetStruct &filePtrSet, const std::string &fileType) const
Closes the file.
Definition: Environment.C:1117
QUESO::SequenceOfVectors::resizeSequence
void resizeSequence(unsigned int newSubSequenceSize)
Resizes the sequence.
Definition: SequenceOfVectors.C:110
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
QUESO::BaseEnvironment::fullRank
int fullRank() const
Returns the process full rank.
Definition: Environment.C:241
UQ_FILE_EXTENSION_FOR_HDF_FORMAT
#define UQ_FILE_EXTENSION_FOR_HDF_FORMAT
Definition: Defines.h:90
QUESO::BaseEnvironment::displayVerbosity
unsigned int displayVerbosity() const
Definition: Environment.C:436
QUESO::BaseEnvironment::inter0Comm
const MpiComm & inter0Comm() const
Access function for MpiComm inter0-communicator.
Definition: Environment.C:295
QUESO::UQ_OK_RC
const int UQ_OK_RC
Definition: Defines.h:76
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::BaseEnvironment::subId
unsigned int subId() const
Access function to the number of each sub-environment Id: m_subId.
Definition: Environment.C:329
QUESO::MiscGetEllapsedSeconds
double MiscGetEllapsedSeconds(struct timeval *timeval0)
Definition: Miscellaneous.C:287
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::unifiedSampleStd ( unsigned int  initialPos,
unsigned int  numPos,
const V &  unifiedMeanVec,
V &  unifiedStdVec 
) const

Finds the sample standard deviation of the unified sequence, considering numPos positions starting at position initialPos and of mean meanVec.

Output:

Parameters
stdVecis the vector of the calculated sample standard deviation of the unified sequence of vectors.

Definition at line 675 of file SequenceOfVectors.C.

References UQ_FATAL_TEST_MACRO.

680 {
681  bool bRC = ((initialPos < this->subSequenceSize() ) &&
682  (0 < numPos ) &&
683  ((initialPos+numPos) <= this->subSequenceSize() ) &&
684  (this->vectorSizeLocal() == unifiedMeanVec.sizeLocal()) &&
685  (this->vectorSizeLocal() == unifiedStdVec.sizeLocal() ));
686  UQ_FATAL_TEST_MACRO(bRC == false,
687  m_env.worldRank(),
688  "SequenceOfVectors<V,M>::unifiedSampleStd()",
689  "invalid input data");
690 
691  ScalarSequence<double> data(m_env,0,"");
692 
693  unsigned int numParams = this->vectorSizeLocal();
694  for (unsigned int i = 0; i < numParams; ++i) {
695  this->extractScalarSeq(initialPos,
696  1, // spacing
697  numPos,
698  i,
699  data);
700  unifiedStdVec[i] = data.unifiedSampleStd(m_vectorSpace.numOfProcsForStorage() == 1,
701  0,
702  numPos,
703  unifiedMeanVec[i]);
704  }
705 
706  return;
707 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:424
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::unifiedSampleVarianceExtra ( unsigned int  initialPos,
unsigned int  numPos,
const V &  unifiedMeanVec,
V &  unifiedSamVec 
) const
virtual

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

Output:

Parameters
samVecis the vector of the calculated sample variance of the unified sequence of vectors.

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 604 of file SequenceOfVectors.C.

References UQ_FATAL_TEST_MACRO.

609 {
610  bool bRC = ((initialPos < this->subSequenceSize() ) &&
611  (0 < numPos ) &&
612  ((initialPos+numPos) <= this->subSequenceSize() ) &&
613  (this->vectorSizeLocal() == unifiedMeanVec.sizeLocal()) &&
614  (this->vectorSizeLocal() == unifiedSamVec.sizeLocal() ));
615  UQ_FATAL_TEST_MACRO(bRC == false,
616  m_env.worldRank(),
617  "SequenceOfVectors<V,M>::unifiedSampleVarianceExtra()",
618  "invalid input data");
619 
620  ScalarSequence<double> data(m_env,0,"");
621 
622  unsigned int numParams = this->vectorSizeLocal();
623  for (unsigned int i = 0; i < numParams; ++i) {
624  this->extractScalarSeq(initialPos,
625  1, // spacing
626  numPos,
627  i,
628  data);
629  unifiedSamVec[i] = data.unifiedSampleVarianceExtra(m_vectorSpace.numOfProcsForStorage() == 1,
630  0,
631  numPos,
632  unifiedMeanVec[i]);
633  }
634 
635  return;
636 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:424
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::unifiedScalesForKde ( unsigned int  initialPos,
const V &  unifiedIqrVec,
unsigned int  kdeDimension,
V &  unifiedScaleVec 
) const
virtual

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

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 1217 of file SequenceOfVectors.C.

References QUESO::ScalarSequence< T >::unifiedScaleForKde(), and UQ_FATAL_TEST_MACRO.

1222 {
1223  bool bRC = ((initialPos < this->subSequenceSize() ) &&
1224  (this->vectorSizeLocal() == unifiedIqrVec.sizeLocal() ) &&
1225  (this->vectorSizeLocal() == unifiedScaleVec.sizeLocal()));
1226  UQ_FATAL_TEST_MACRO(bRC == false,
1227  m_env.worldRank(),
1228  "SequenceOfVectors<V,M>::unifiedScalesForKde()",
1229  "invalid input data");
1230 
1231  unsigned int numPos = this->subSequenceSize() - initialPos;
1232  ScalarSequence<double> data(m_env,0,"");
1233 
1234  unsigned int numParams = this->vectorSizeLocal();
1235  for (unsigned int i = 0; i < numParams; ++i) {
1236  this->extractScalarSeq(initialPos,
1237  1, // spacing
1238  numPos,
1239  i,
1240  data);
1241  unifiedScaleVec[i] = data.unifiedScaleForKde(m_vectorSpace.numOfProcsForStorage() == 1,
1242  0,
1243  unifiedIqrVec[i],
1244  kdeDimension);
1245  }
1246 
1247  return;
1248 }
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:424
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::unifiedUniformlySampledCdf ( const V &  numEvaluationPointsVec,
ArrayOfOneDGrids< V, M > &  unifiedCdfGrids,
ArrayOfOneDTables< V, M > &  unifiedCdfValues 
) const

Uniformly samples from the CDF from the sub-sequence.

Definition at line 283 of file SequenceOfVectors.C.

References QUESO::ArrayOfOneDTables< V, M >::setOneDTable(), and QUESO::ArrayOfOneDGrids< V, M >::setUniformGrids().

Referenced by QUESO::StatisticalForwardProblem< P_V, P_M, Q_V, Q_M >::solveWithMonteCarlo().

287 {
288  if ((m_env.subDisplayFile()) && (m_env.displayVerbosity() >= 10)) {
289  *m_env.subDisplayFile() << "Entering SequenceOfVectors<V,M>::unifiedUniformlySampledCdf()"
290  << std::endl;
291  }
292 
293  V unifiedMinDomainValues(m_vectorSpace.zeroVector());
294  V unifiedMaxDomainValues(m_vectorSpace.zeroVector());
295 
296  ScalarSequence<double> data(m_env,0,"");
297 
298  unsigned int numParams = this->vectorSizeLocal();
299  for (unsigned int i = 0; i < numParams; ++i) {
300  this->extractScalarSeq(0, // initialPos
301  1, // spacing
302  subSequenceSize(), // numPos
303  i,
304  data);
305 
306  std::vector<double> aCdf(0);
307  data.unifiedUniformlySampledCdf(m_vectorSpace.numOfProcsForStorage() == 1,
308  (unsigned int) numEvaluationPointsVec[i],
309  unifiedMinDomainValues[i],
310  unifiedMaxDomainValues[i],
311  aCdf);
312  unifiedCdfValues.setOneDTable(i,aCdf);
313  }
314 
315  unifiedCdfGrids.setUniformGrids(numEvaluationPointsVec,
316  unifiedMinDomainValues,
317  unifiedMaxDomainValues);
318 
319  if ((m_env.subDisplayFile()) && (m_env.displayVerbosity() >= 10)) {
320  *m_env.subDisplayFile() << "Leaving SequenceOfVectors<V,M>::unifiedUniformlySampledCdf()"
321  << std::endl;
322  }
323 
324  return;
325 }
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:305
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:424
QUESO::SequenceOfVectors::extractScalarSeq
void extractScalarSeq(unsigned int initialPos, unsigned int spacing, unsigned int numPos, unsigned int paramId, ScalarSequence< double > &scalarSeq) const
Extracts a sequence of scalars.
Definition: SequenceOfVectors.C:2250
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
QUESO::BaseEnvironment::displayVerbosity
unsigned int displayVerbosity() const
Definition: Environment.C:436
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103
template<class V , class M >
void QUESO::SequenceOfVectors< V, M >::unifiedWriteContents ( const std::string &  fileName,
const std::string &  fileType 
) const
virtual

Writes the unfed sequence to a file. Writes the unified sequence in Matlab/Octave format or, if enabled, in HDF5 format.

Implements QUESO::BaseVectorSequence< V, M >.

Definition at line 1485 of file SequenceOfVectors.C.

References QUESO::MiscGetEllapsedSeconds(), QUESO::FilePtrSetStruct::ofsVar, UQ_FATAL_TEST_MACRO, UQ_FILE_EXTENSION_FOR_HDF_FORMAT, UQ_FILE_EXTENSION_FOR_MATLAB_FORMAT, and QUESO::UQ_OK_RC.

Referenced by QUESO::MLSampling< P_V, P_M >::checkpointML(), QUESO::MLSampling< P_V, P_M >::generateSequence(), QUESO::MLSampling< P_V, P_M >::generateSequence_Level0_all(), and QUESO::MLSampling< P_V, P_M >::generateSequence_Step11_inter0().

1488 {
1489  std::string fileType(inputFileType);
1490 #ifdef QUESO_HAS_HDF5
1491  // Do nothing
1492 #else
1493  if (fileType == UQ_FILE_EXTENSION_FOR_HDF_FORMAT) {
1494  if (m_env.subDisplayFile()) {
1495  *m_env.subDisplayFile() << "WARNING in SequenceOfVectors<V,M>::unifiedWriteContents()"
1496  << ": file format '" << UQ_FILE_EXTENSION_FOR_HDF_FORMAT
1497  << "' has been requested, but this QUESO library has not been built with 'hdf5'"
1498  << ". Code will therefore process the file format '" << UQ_FILE_EXTENSION_FOR_HDF_FORMAT
1499  << "' instead..."
1500  << std::endl;
1501  }
1502  if (m_env.subRank() == 0) {
1503  std::cerr << "WARNING in SequenceOfVectors<V,M>::unifiedWriteContents()"
1504  << ": file format '" << UQ_FILE_EXTENSION_FOR_HDF_FORMAT
1505  << "' has been requested, but this QUESO library has not been built with 'hdf5'"
1506  << ". Code will therefore process the file format '" << UQ_FILE_EXTENSION_FOR_HDF_FORMAT
1507  << "' instead..."
1508  << std::endl;
1509  }
1510  fileType = UQ_FILE_EXTENSION_FOR_MATLAB_FORMAT;
1511  }
1512 #endif
1513 
1514  // All processors in 'fullComm' should call this routine...
1515 
1516  //m_env.fullComm().Barrier(); // Dangerous to barrier on fullComm ... // prudenci-2011-01-17
1517  if ((m_env.subDisplayFile()) && (m_env.displayVerbosity() >= 10)) {
1518  *m_env.subDisplayFile() << "Entering SequenceOfVectors<V,M>::unifiedWriteContents()"
1519  << ": worldRank " << m_env.worldRank()
1520  << ", fullRank " << m_env.fullRank()
1521  << ", subEnvironment " << m_env.subId()
1522  << ", subRank " << m_env.subRank()
1523  << ", inter0Rank " << m_env.inter0Rank()
1524  //<< ", m_env.inter0Comm().NumProc() = " << m_env.inter0Comm().NumProc()
1525  << ", fileName = " << fileName
1526  << std::endl;
1527  }
1528 
1529  if (m_env.inter0Rank() >= 0) {
1530  for (unsigned int r = 0; r < (unsigned int) m_env.inter0Comm().NumProc(); ++r) {
1531  if (m_env.inter0Rank() == (int) r) {
1532  // My turn
1533  if ((m_env.subDisplayFile()) && (m_env.displayVerbosity() >= 10)) {
1534  *m_env.subDisplayFile() << "In SequenceOfVectors<V,M>::unifiedWriteContents()"
1535  << ": worldRank " << m_env.worldRank()
1536  << ", fullRank " << m_env.fullRank()
1537  << ", subEnvironment " << m_env.subId()
1538  << ", subRank " << m_env.subRank()
1539  << ", inter0Rank " << m_env.inter0Rank()
1540  //<< ", m_env.inter0Comm().NumProc() = " << m_env.inter0Comm().NumProc()
1541  << ", fileName = " << fileName
1542  << ", about to open file for r = " << r
1543  << std::endl;
1544  }
1545 
1546  // bool writeOver = (r == 0);
1547  bool writeOver = false; // A 'true' causes problems when the user chooses (via options
1548  // in the input file) to use just one file for all outputs.
1549  FilePtrSetStruct unifiedFilePtrSet;
1550  if (m_env.openUnifiedOutputFile(fileName,
1551  fileType, // "m or hdf"
1552  writeOver,
1553  unifiedFilePtrSet)) {
1554  if ((m_env.subDisplayFile()) && (m_env.displayVerbosity() >= 10)) { // 2013-02-23
1555  *m_env.subDisplayFile() << "In SequenceOfVectors<V,M>::unifiedWriteContents()"
1556  << ": worldRank " << m_env.worldRank()
1557  << ", fullRank " << m_env.fullRank()
1558  << ", subEnvironment " << m_env.subId()
1559  << ", subRank " << m_env.subRank()
1560  << ", inter0Rank " << m_env.inter0Rank()
1561  //<< ", m_env.inter0Comm().NumProc() = " << m_env.inter0Comm().NumProc()
1562  << ", fileName = " << fileName
1563  << ", just opened file for r = " << r
1564  << std::endl;
1565  }
1566 
1567  unsigned int chainSize = this->subSequenceSize();
1568  if (fileType == UQ_FILE_EXTENSION_FOR_MATLAB_FORMAT) {
1569  if (r == 0) {
1570  *unifiedFilePtrSet.ofsVar << m_name << "_unified" << " = zeros(" << this->subSequenceSize()*m_env.inter0Comm().NumProc()
1571  << "," << this->vectorSizeLocal()
1572  << ");"
1573  << std::endl;
1574  *unifiedFilePtrSet.ofsVar << m_name << "_unified" << " = [";
1575  }
1576 
1577  for (unsigned int j = 0; j < chainSize; ++j) { // 2013-02-23
1578  //std::cout << "In SequenceOfVectors<V,M>::unifiedWriteContents(): m_seq[" << j << "] = " << m_seq[j]
1579  // << std::endl;
1580  //std::cout << "In SequenceOfVectors<V,M>::unifiedWriteContents(): &(m_seq[" << j << "].map()) = " << &(m_seq[j]->map())
1581  // << std::endl;
1582  //std::cout << "In SequenceOfVectors<V,M>::unifiedWriteContents(): (m_seq[" << j << "].map().NumMyElements = " << m_seq[j]->map().NumMyElements()
1583  // << std::endl;
1584  //V tmpVec(*(m_seq[j]));
1585  //std::cout << "*(m_seq[" << j << "]) = " << tmpVec
1586  // << std::endl;
1587  //std::cout << "*(m_seq[" << j << "]) = " << *(m_seq[j])
1588  // << std::endl;
1589 
1590  bool savedVectorPrintScientific = m_seq[j]->getPrintScientific();
1591  bool savedVectorPrintState = m_seq[j]->getPrintHorizontally();
1592  m_seq[j]->setPrintScientific (true);
1593  m_seq[j]->setPrintHorizontally(true);
1594 
1595  *unifiedFilePtrSet.ofsVar << *(m_seq[j])
1596  << std::endl;
1597 
1598  m_seq[j]->setPrintHorizontally(savedVectorPrintState);
1599  m_seq[j]->setPrintScientific (savedVectorPrintScientific);
1600  }
1601  }
1602 #ifdef QUESO_HAS_HDF5
1603  else if (fileType == UQ_FILE_EXTENSION_FOR_HDF_FORMAT) {
1604  unsigned int numParams = m_vectorSpace.dimLocal();
1605  if (r == 0) {
1606  hid_t datatype = H5Tcopy(H5T_NATIVE_DOUBLE);
1607  //std::cout << "In SequenceOfVectors<V,M>::unifiedWriteContents(): h5 case, data type created" << std::endl;
1608  hsize_t dimsf[2];
1609  dimsf[0] = numParams;
1610  dimsf[1] = chainSize;
1611  hid_t dataspace = H5Screate_simple(2, dimsf, NULL); // HDF5_rank = 2
1612  //std::cout << "In SequenceOfVectors<V,M>::unifiedWriteContents(): h5 case, data space created" << std::endl;
1613  hid_t dataset = H5Dcreate2(unifiedFilePtrSet.h5Var,
1614  "seq_of_vectors",
1615  datatype,
1616  dataspace,
1617  H5P_DEFAULT, // Link creation property list
1618  H5P_DEFAULT, // Dataset creation property list
1619  H5P_DEFAULT); // Dataset access property list
1620  //std::cout << "In SequenceOfVectors<V,M>::unifiedWriteContents(): h5 case, data set created" << std::endl;
1621 
1622  struct timeval timevalBegin;
1623  int iRC = UQ_OK_RC;
1624  iRC = gettimeofday(&timevalBegin,NULL);
1625  if (iRC) {}; // just to remover compiler warning
1626 
1627  //double* dataOut[numParams]; // avoid compiler warning
1628  std::vector<double*> dataOut((size_t) numParams,NULL);
1629  dataOut[0] = (double*) malloc(numParams*chainSize*sizeof(double));
1630  for (unsigned int i = 1; i < numParams; ++i) { // Yes, from '1'
1631  dataOut[i] = dataOut[i-1] + chainSize; // Yes, just 'chainSize', not 'chainSize*sizeof(double)'
1632  }
1633  //std::cout << "In SequenceOfVectors<V,M>::unifiedWriteContents(): h5 case, memory allocated" << std::endl;
1634  for (unsigned int j = 0; j < chainSize; ++j) {
1635  V tmpVec(*(m_seq[j]));
1636  for (unsigned int i = 0; i < numParams; ++i) {
1637  dataOut[i][j] = tmpVec[i];
1638  }
1639  }
1640  //std::cout << "In SequenceOfVectors<V,M>::unifiedWriteContents(): h5 case, memory filled" << std::endl;
1641 
1642  herr_t status;
1643  status = H5Dwrite(dataset,
1644  H5T_NATIVE_DOUBLE,
1645  H5S_ALL,
1646  H5S_ALL,
1647  H5P_DEFAULT,
1648  (void*) dataOut[0]);
1649  if (status) {}; // just to remover compiler warning
1650  //std::cout << "In SequenceOfVectors<V,M>::unifiedWriteContents(): h5 case, data written" << std::endl;
1651 
1652  double writeTime = MiscGetEllapsedSeconds(&timevalBegin);
1653  if ((m_env.subDisplayFile()) && (m_env.displayVerbosity() >= 2)) {
1654  *m_env.subDisplayFile() << "In SequenceOfVectors<V,M>::unifiedWriteContents()"
1655  << ": worldRank " << m_env.worldRank()
1656  << ", fullRank " << m_env.fullRank()
1657  << ", subEnvironment " << m_env.subId()
1658  << ", subRank " << m_env.subRank()
1659  << ", inter0Rank " << m_env.inter0Rank()
1660  << ", fileName = " << fileName
1661  << ", numParams = " << numParams
1662  << ", chainSize = " << chainSize
1663  << ", writeTime = " << writeTime << " seconds"
1664  << std::endl;
1665  }
1666 
1667  H5Dclose(dataset);
1668  //std::cout << "In SequenceOfVectors<V,M>::unifiedWriteContents(): h5 case, data set closed" << std::endl;
1669  H5Sclose(dataspace);
1670  //std::cout << "In SequenceOfVectors<V,M>::unifiedWriteContents(): h5 case, data space closed" << std::endl;
1671  H5Tclose(datatype);
1672  //std::cout << "In SequenceOfVectors<V,M>::unifiedWriteContents(): h5 case, data type closed" << std::endl;
1673  //free(dataOut[0]); // related to the changes above for compiler warning
1674  for (unsigned int tmpIndex = 0; tmpIndex < dataOut.size(); tmpIndex++) {
1675  free (dataOut[tmpIndex]);
1676  }
1677  }
1678  else {
1679  UQ_FATAL_TEST_MACRO(true,
1680  m_env.worldRank(),
1681  "SequenceOfVectors<V,M>::unifiedWriteContents()",
1682  "hdf file type not supported for multiple sub-environments yet");
1683  }
1684  }
1685 #endif
1686  else {
1687  UQ_FATAL_TEST_MACRO(true,
1688  m_env.worldRank(),
1689  "SequenceOfVectors<V,M>::unifiedWriteContents()",
1690  "invalid file type");
1691  }
1692 
1693  if ((m_env.subDisplayFile()) && (m_env.displayVerbosity() >= 10)) {
1694  *m_env.subDisplayFile() << "In SequenceOfVectors<V,M>::unifiedWriteContents()"
1695  << ": worldRank " << m_env.worldRank()
1696  << ", fullRank " << m_env.fullRank()
1697  << ", subEnvironment " << m_env.subId()
1698  << ", subRank " << m_env.subRank()
1699  << ", inter0Rank " << m_env.inter0Rank()
1700  //<< ", m_env.inter0Comm().NumProc() = " << m_env.inter0Comm().NumProc()
1701  << ", fileName = " << fileName
1702  << ", about to close file for r = " << r
1703  << std::endl;
1704  }
1705 
1706  m_env.closeFile(unifiedFilePtrSet,fileType);
1707 
1708  if ((m_env.subDisplayFile()) && (m_env.displayVerbosity() >= 10)) {
1709  *m_env.subDisplayFile() << "In SequenceOfVectors<V,M>::unifiedWriteContents()"
1710  << ": worldRank " << m_env.worldRank()
1711  << ", fullRank " << m_env.fullRank()
1712  << ", subEnvironment " << m_env.subId()
1713  << ", subRank " << m_env.subRank()
1714  << ", inter0Rank " << m_env.inter0Rank()
1715  //<< ", m_env.inter0Comm().NumProc() = " << m_env.inter0Comm().NumProc()
1716  << ", fileName = " << fileName
1717  << ", just closed file for r = " << r
1718  << std::endl;
1719  }
1720  } // if (m_env.openUnifiedOutputFile())
1721  } // if (m_env.inter0Rank() == (int) r)
1722  m_env.inter0Comm().Barrier();
1723  } // for r
1724 
1725  if (m_env.inter0Rank() == 0) {
1726  if (fileType == UQ_FILE_EXTENSION_FOR_MATLAB_FORMAT) {
1727  FilePtrSetStruct unifiedFilePtrSet;
1728  if (m_env.openUnifiedOutputFile(fileName,
1729  fileType,
1730  false, // Yes, 'writeOver = false' in order to close the array for matlab
1731  unifiedFilePtrSet)) {
1732  *unifiedFilePtrSet.ofsVar << "];\n";
1733  m_env.closeFile(unifiedFilePtrSet,fileType);
1734  }
1735  }
1736  else if (fileType == UQ_FILE_EXTENSION_FOR_HDF_FORMAT) {
1737  // Do nothing
1738  }
1739  else {
1740  UQ_FATAL_TEST_MACRO(true,
1741  m_env.worldRank(),
1742  "SequenceOfVectors<V,M>::unifiedWriteContents(), final",
1743  "invalid file type");
1744  }
1745  }
1746  } // if (m_env.inter0Rank() >= 0)
1747 
1748  if ((m_env.subDisplayFile()) && (m_env.displayVerbosity() >= 10)) {
1749  *m_env.subDisplayFile() << "Leaving SequenceOfVectors<V,M>::unifiedWriteContents()"
1750  << ", fileName = " << fileName
1751  << std::endl;
1752  }
1753  //m_env.fullComm().Barrier(); // Dangerous to barrier on fullComm ... // prudenci-2011-01-17
1754 
1755  return;
1756 }
QUESO::BaseEnvironment::subRank
int subRank() const
Access function for sub-rank.
Definition: Environment.C:263
QUESO::BaseEnvironment::inter0Rank
int inter0Rank() const
Returns the process inter0 rank.
Definition: Environment.C:289
QUESO::BaseEnvironment::worldRank
int worldRank() const
Returns the process world rank.
Definition: Environment.C:235
UQ_FILE_EXTENSION_FOR_MATLAB_FORMAT
#define UQ_FILE_EXTENSION_FOR_MATLAB_FORMAT
Definition: Defines.h:89
QUESO::MpiComm::NumProc
int NumProc() const
Returns total number of processes.
Definition: MpiComm.C:121
QUESO::BaseEnvironment::subDisplayFile
std::ofstream * subDisplayFile() const
Access function for m_subDisplayFile (displays file on stream).
Definition: Environment.C:305
QUESO::BaseVectorSequence::m_vectorSpace
const VectorSpace< V, M > & m_vectorSpace
Definition: VectorSequence.h:424
QUESO::BaseVectorSequence::m_env
const BaseEnvironment & m_env
Definition: VectorSequence.h:423
QUESO::MpiComm::Barrier
void Barrier() const
Pause every process in *this communicator until all the processes reach this point.
Definition: MpiComm.C:143
QUESO::BaseEnvironment::closeFile
void closeFile(FilePtrSetStruct &filePtrSet, const std::string &fileType) const
Closes the file.
Definition: Environment.C:1117
QUESO::SequenceOfVectors::m_seq
std::vector< const V * > m_seq
Sequence of vectors.
Definition: SequenceOfVectors.h:417
QUESO::BaseVectorSequence::vectorSizeLocal
unsigned int vectorSizeLocal() const
Local dimension (size) of the vector space.
Definition: VectorSequence.C:100
QUESO::BaseEnvironment::fullRank
int fullRank() const
Returns the process full rank.
Definition: Environment.C:241
UQ_FILE_EXTENSION_FOR_HDF_FORMAT
#define UQ_FILE_EXTENSION_FOR_HDF_FORMAT
Definition: Defines.h:90
QUESO::BaseEnvironment::openUnifiedOutputFile
bool openUnifiedOutputFile(const std::string &fileName, const std::string &fileType, bool writeOver, FilePtrSetStruct &filePtrSet) const
Opens a unified output file, that will contain data from all sub-environments.
Definition: Environment.C:733
QUESO::BaseEnvironment::displayVerbosity
unsigned int displayVerbosity() const
Definition: Environment.C:436
QUESO::BaseEnvironment::inter0Comm
const MpiComm & inter0Comm() const
Access function for MpiComm inter0-communicator.
Definition: Environment.C:295
QUESO::UQ_OK_RC
const int UQ_OK_RC
Definition: Defines.h:76
UQ_FATAL_TEST_MACRO
#define UQ_FATAL_TEST_MACRO(test, givenRank, where, what)
Definition: Defines.h:223
QUESO::BaseEnvironment::subId
unsigned int subId() const
Access function to the number of each sub-environment Id: m_subId.
Definition: Environment.C:329
QUESO::MiscGetEllapsedSeconds
double MiscGetEllapsedSeconds(struct timeval *timeval0)
Definition: Miscellaneous.C:287
QUESO::SequenceOfVectors::subSequenceSize
unsigned int subSequenceSize() const
Size of the sub-sequence of vectors.
Definition: SequenceOfVectors.C:103

Member Data Documentation

template<class V, class M>
std::vector<const V*> QUESO::SequenceOfVectors< V, M >::m_seq
private

Sequence of vectors.

Definition at line 417 of file SequenceOfVectors.h.

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

The documentation for this class was generated from the following files:
Generated on Thu Apr 23 2015 19:26:17 for queso-0.51.1 by  doxygen 1.8.5