OpenMD 3.2
Molecular Dynamics in the Open
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OpenMD::MoleculeACF< T > Class Template Referenceabstract
Inheritance diagram for OpenMD::MoleculeACF< T >:

Public Member Functions

 MoleculeACF (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2)
 MoleculeACF (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2)
Public Member Functions inherited from OpenMD::AutoCorrFunc< T >
 AutoCorrFunc (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2)
 AutoCorrFunc (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2)
Public Member Functions inherited from OpenMD::TimeCorrFunc< T >
 TimeCorrFunc (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2)
virtual void doCorrelate ()
const std::string & getCorrFuncType () const
void setCorrFuncType (const std::string &type)
void setParameterString (const std::string &params)
void setLabelString (const std::string &label)
 TimeCorrFunc (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2)
void setWindowingParameters (RealType tcorr_fs, int nStart, RealType tsep_fs)
virtual void doCorrelate ()
const std::string & getCorrFuncType () const
void setCorrFuncType (const std::string &type)
void setParameterString (const std::string &params)
void setLabelString (const std::string &label)
Public Member Functions inherited from OpenMD::DynamicProperty
void setOutputName (const std::string &filename)
const std::string & getOutputFileName () const
void setSelectionModeRestart ()

Protected Member Functions

virtual int computeProperty1 (int frame, Molecule *mol)=0
virtual T calcCorrVal (int frame1, int frame2, int id1, int id2)=0
virtual void computeProperty1 (int)
virtual int computeProperty1 (int, StuntDouble *)
virtual int computeProperty1 (int, Bond *)
virtual void computeProperty2 (int)
virtual int computeProperty2 (int, Molecule *)
virtual int computeProperty2 (int, StuntDouble *)
virtual int computeProperty2 (int, Bond *)
virtual T calcCorrVal (int, int)
virtual int computeProperty1 (int frame, Molecule *mol)=0
virtual T calcCorrVal (int frame1, int frame2, int id1, int id2)=0
virtual void computeProperty1 (int)
virtual int computeProperty1 (int, StuntDouble *)
virtual int computeProperty1 (int, Bond *)
virtual void computeProperty2 (int)
virtual int computeProperty2 (int, Molecule *)
virtual int computeProperty2 (int, StuntDouble *)
virtual int computeProperty2 (int, Bond *)
virtual T calcCorrVal (int, int)
Protected Member Functions inherited from OpenMD::TimeCorrFunc< T >
virtual void preCorrelate ()
virtual void correlation ()
virtual void postCorrelate ()
virtual void computeFrame (int frame)
virtual void validateSelection (SelectionManager &seleMan)
virtual void correlateFrames (int frame1, int frame2, int timeBin)
virtual void writeCorrelate ()
virtual void preCorrelate ()
virtual void correlation ()
virtual void postCorrelate ()
virtual void computeFrame (int frame)
virtual void validateSelection (SelectionManager &seleMan)
virtual void correlateFrames (int frame1, int frame2, int timeBin)
virtual void writeCorrelate ()
void writeCorrelate ()
void writeCorrelate ()
void writeCorrelate ()
void writeCorrelate ()

Additional Inherited Members

Protected Attributes inherited from OpenMD::TimeCorrFunc< T >
RealType deltaTime_
unsigned int nTimeBins_
int nFrames_
std::vector< T > histogram_
std::vector< int > count_
std::vector< RealType > times_
RealType dtMean_ {}
RealType dtSigma_ {}
SimInfo * info_ {nullptr}
DumpReader * reader_
std::string dumpFilename_
SelectionManager seleMan1_
SelectionManager seleMan2_
Snapshot * currentSnapshot_
std::string selectionScript1_
std::string selectionScript2_
SelectionEvaluator evaluator1_
SelectionEvaluator evaluator2_
bool uniqueSelections_
bool autoCorrFunc_
bool doSystemProperties_
bool doMolecularProperties_
bool doObjectProperties_
bool doAtomicProperties_
bool doBondProperties_
bool allowTimeFuzz_
std::string corrFuncType_
std::string paramString_
std::string labelString_
std::vector< std::vector< int > > sele1ToIndex_
std::vector< std::vector< int > > sele2ToIndex_
ProgressBarPtr progressBar_
std::vector< std::vector< int > > GIDtoSele1_
std::vector< std::vector< int > > GIDtoSele2_
std::vector< std::vector< int > > selection1StartFrame_
std::vector< std::vector< int > > selection2StartFrame_
int nStart_ {0}
int nSep_ {0}
int nStride_ {1}
int navg_ {0}
bool useWindowing_ {false}
Protected Attributes inherited from OpenMD::DynamicProperty
std::string outputFilename_
bool selectionModeRestart_

Detailed Description

template<typename T>
class OpenMD::MoleculeACF< T >

Definition at line 279 of file TimeCorrFunc.hpp.

Constructor & Destructor Documentation

◆ MoleculeACF()

template<typename T>
OpenMD::MoleculeACF< T >::MoleculeACF ( SimInfo * info,
const std::string & filename,
const std::string & sele1,
const std::string & sele2 )

Definition at line 596 of file TimeCorrFunc.cpp.

Member Function Documentation

◆ calcCorrVal() [1/4]

template<typename T>
virtual T OpenMD::MoleculeACF< T >::calcCorrVal ( int frame1,
int frame2,
int id1,
int id2 )
protectedpure virtual

Implements OpenMD::TimeCorrFunc< T >.

◆ calcCorrVal() [2/4]

template<typename T>
virtual T OpenMD::MoleculeACF< T >::calcCorrVal ( int frame1,
int frame2,
int id1,
int id2 )
protectedpure virtual

Implements OpenMD::TimeCorrFunc< T >.

◆ calcCorrVal() [3/4]

template<typename T>
virtual T OpenMD::MoleculeACF< T >::calcCorrVal ( int ,
int  )
inlineprotectedvirtual

Implements OpenMD::TimeCorrFunc< T >.

Definition at line 297 of file TimeCorrFunc.hpp.

◆ calcCorrVal() [4/4]

template<typename T>
virtual T OpenMD::MoleculeACF< T >::calcCorrVal ( int ,
int  )
inlineprotectedvirtual

Implements OpenMD::TimeCorrFunc< T >.

Definition at line 378 of file TimeCorrFunc.hpp.

◆ computeProperty1() [1/8]

template<typename T>
virtual int OpenMD::MoleculeACF< T >::computeProperty1 ( int frame,
Molecule * mol )
protectedpure virtual

Implements OpenMD::AutoCorrFunc< T >.

◆ computeProperty1() [2/8]

template<typename T>
virtual int OpenMD::MoleculeACF< T >::computeProperty1 ( int frame,
Molecule * mol )
protectedpure virtual

Implements OpenMD::AutoCorrFunc< T >.

◆ computeProperty1() [3/8]

template<typename T>
virtual void OpenMD::MoleculeACF< T >::computeProperty1 ( int )
inlineprotectedvirtual

Implements OpenMD::AutoCorrFunc< T >.

Definition at line 288 of file TimeCorrFunc.hpp.

◆ computeProperty1() [4/8]

template<typename T>
virtual void OpenMD::MoleculeACF< T >::computeProperty1 ( int )
inlineprotectedvirtual

Implements OpenMD::AutoCorrFunc< T >.

Definition at line 369 of file TimeCorrFunc.hpp.

◆ computeProperty1() [5/8]

template<typename T>
virtual int OpenMD::MoleculeACF< T >::computeProperty1 ( int ,
Bond *  )
inlineprotectedvirtual

Implements OpenMD::AutoCorrFunc< T >.

Definition at line 290 of file TimeCorrFunc.hpp.

◆ computeProperty1() [6/8]

template<typename T>
virtual int OpenMD::MoleculeACF< T >::computeProperty1 ( int ,
Bond *  )
inlineprotectedvirtual

Implements OpenMD::AutoCorrFunc< T >.

Definition at line 371 of file TimeCorrFunc.hpp.

◆ computeProperty1() [7/8]

template<typename T>
virtual int OpenMD::MoleculeACF< T >::computeProperty1 ( int ,
StuntDouble *  )
inlineprotectedvirtual

Implements OpenMD::AutoCorrFunc< T >.

Definition at line 289 of file TimeCorrFunc.hpp.

◆ computeProperty1() [8/8]

template<typename T>
virtual int OpenMD::MoleculeACF< T >::computeProperty1 ( int ,
StuntDouble *  )
inlineprotectedvirtual

Implements OpenMD::AutoCorrFunc< T >.

Definition at line 370 of file TimeCorrFunc.hpp.

◆ computeProperty2() [1/8]

template<typename T>
virtual void OpenMD::MoleculeACF< T >::computeProperty2 ( int )
inlineprotectedvirtual

Reimplemented from OpenMD::AutoCorrFunc< T >.

Definition at line 292 of file TimeCorrFunc.hpp.

◆ computeProperty2() [2/8]

template<typename T>
virtual void OpenMD::MoleculeACF< T >::computeProperty2 ( int )
inlineprotectedvirtual

Reimplemented from OpenMD::AutoCorrFunc< T >.

Definition at line 373 of file TimeCorrFunc.hpp.

◆ computeProperty2() [3/8]

template<typename T>
virtual int OpenMD::MoleculeACF< T >::computeProperty2 ( int ,
Bond *  )
inlineprotectedvirtual

Reimplemented from OpenMD::AutoCorrFunc< T >.

Definition at line 295 of file TimeCorrFunc.hpp.

◆ computeProperty2() [4/8]

template<typename T>
virtual int OpenMD::MoleculeACF< T >::computeProperty2 ( int ,
Bond *  )
inlineprotectedvirtual

Reimplemented from OpenMD::AutoCorrFunc< T >.

Definition at line 376 of file TimeCorrFunc.hpp.

◆ computeProperty2() [5/8]

template<typename T>
virtual int OpenMD::MoleculeACF< T >::computeProperty2 ( int ,
Molecule *  )
inlineprotectedvirtual

Reimplemented from OpenMD::AutoCorrFunc< T >.

Definition at line 293 of file TimeCorrFunc.hpp.

◆ computeProperty2() [6/8]

template<typename T>
virtual int OpenMD::MoleculeACF< T >::computeProperty2 ( int ,
Molecule *  )
inlineprotectedvirtual

Reimplemented from OpenMD::AutoCorrFunc< T >.

Definition at line 374 of file TimeCorrFunc.hpp.

◆ computeProperty2() [7/8]

template<typename T>
virtual int OpenMD::MoleculeACF< T >::computeProperty2 ( int ,
StuntDouble *  )
inlineprotectedvirtual

Reimplemented from OpenMD::AutoCorrFunc< T >.

Definition at line 294 of file TimeCorrFunc.hpp.

◆ computeProperty2() [8/8]

template<typename T>
virtual int OpenMD::MoleculeACF< T >::computeProperty2 ( int ,
StuntDouble *  )
inlineprotectedvirtual

Reimplemented from OpenMD::AutoCorrFunc< T >.

Definition at line 375 of file TimeCorrFunc.hpp.

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