OpenMD  2.5
Molecular Dynamics in the Open
OpenMD::MultipassCorrFunc< T > Class Template Referenceabstract

Computes a correlation function by scanning a trajectory once to precompute quantities to be correlated. More...

#include <MultipassCorrFunc.hpp>

Inheritance diagram for OpenMD::MultipassCorrFunc< T >:
OpenMD::DynamicProperty OpenMD::AutoCorrFunc< T > OpenMD::CrossCorrFunc< T >

Public Member Functions

 MultipassCorrFunc (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2, int storageLayout)
 
virtual ~MultipassCorrFunc ()
 
virtual void doCorrelate ()
 
const std::string & getCorrFuncType () const
 
void setCorrFuncType (const std::string &type)
 
void setParameterString (const std::string &params)
 
- Public Member Functions inherited from OpenMD::DynamicProperty
 DynamicProperty ()
 
virtual ~DynamicProperty ()
 
void setOutputName (const std::string &filename)
 
const std::string & getOutputFileName () const
 

Protected Member Functions

virtual void preCorrelate ()
 
virtual void correlation ()
 
virtual void postCorrelate ()
 
virtual void computeFrame (int frame)
 
virtual void validateSelection (SelectionManager &seleMan)
 
virtual int computeProperty1 (int frame, StuntDouble *sd)=0
 
virtual int computeProperty2 (int frame, StuntDouble *sd)=0
 
virtual void correlateFrames (int frame1, int frame2, int timeBin)
 
virtual T calcCorrVal (int frame1, int frame2, int id1, int id2)=0
 
virtual void writeCorrelate ()
 
template<>
void writeCorrelate ()
 
template<>
void writeCorrelate ()
 

Protected Attributes

int storageLayout_
 
RealType deltaTime_
 
int nTimeBins_
 
int nFrames_
 
std::vector< T > histogram_
 
std::vector< int > count_
 
std::vector< RealType > times_
 
bool uniqueSelections_
 
SimInfoinfo_
 
DumpReaderreader_
 
std::string dumpFilename_
 
SelectionManager seleMan1_
 
SelectionManager seleMan2_
 
SnapshotcurrentSnapshot_
 
std::string selectionScript1_
 
std::string selectionScript2_
 
SelectionEvaluator evaluator1_
 
SelectionEvaluator evaluator2_
 
bool autoCorrFunc_
 
std::string corrFuncType_
 
std::string paramString_
 
std::vector< std::vector< int > > sele1ToIndex_
 
std::vector< std::vector< int > > sele2ToIndex_
 
- Protected Attributes inherited from OpenMD::DynamicProperty
std::string outputFilename_
 

Detailed Description

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

Computes a correlation function by scanning a trajectory once to precompute quantities to be correlated.

Definition at line 60 of file MultipassCorrFunc.hpp.

Constructor & Destructor Documentation

◆ MultipassCorrFunc()

template<typename T >
OpenMD::MultipassCorrFunc< T >::MultipassCorrFunc ( SimInfo info,
const std::string &  filename,
const std::string &  sele1,
const std::string &  sele2,
int  storageLayout 
)

Definition at line 52 of file MultipassCorrFunc.cpp.

◆ ~MultipassCorrFunc()

template<typename T>
virtual OpenMD::MultipassCorrFunc< T >::~MultipassCorrFunc ( )
inlinevirtual

Definition at line 66 of file MultipassCorrFunc.hpp.

Member Function Documentation

◆ calcCorrVal()

◆ computeFrame()

template<typename T >
void OpenMD::MultipassCorrFunc< T >::computeFrame ( int  frame)
protectedvirtual

◆ computeProperty1()

◆ computeProperty2()

◆ correlateFrames()

template<typename T >
void OpenMD::MultipassCorrFunc< T >::correlateFrames ( int  frame1,
int  frame2,
int  timeBin 
)
protectedvirtual

◆ correlation()

template<typename T >
void OpenMD::MultipassCorrFunc< T >::correlation ( )
protectedvirtual

Reimplemented in OpenMD::HBondJump.

Definition at line 204 of file MultipassCorrFunc.cpp.

Referenced by OpenMD::MultipassCorrFunc< Mat3x3d >::setParameterString().

◆ doCorrelate()

template<typename T >
void OpenMD::MultipassCorrFunc< T >::doCorrelate ( )
virtual

◆ getCorrFuncType()

template<typename T>
const std::string& OpenMD::MultipassCorrFunc< T >::getCorrFuncType ( ) const
inline

Definition at line 69 of file MultipassCorrFunc.hpp.

◆ postCorrelate()

◆ preCorrelate()

template<typename T >
void OpenMD::MultipassCorrFunc< T >::preCorrelate ( )
protectedvirtual

◆ setCorrFuncType()

template<typename T>
void OpenMD::MultipassCorrFunc< T >::setCorrFuncType ( const std::string &  type)
inline

Definition at line 73 of file MultipassCorrFunc.hpp.

◆ setParameterString()

template<typename T>
void OpenMD::MultipassCorrFunc< T >::setParameterString ( const std::string &  params)
inline

Definition at line 77 of file MultipassCorrFunc.hpp.

◆ validateSelection()

template<typename T >
void OpenMD::MultipassCorrFunc< T >::validateSelection ( SelectionManager seleMan)
protectedvirtual

◆ writeCorrelate() [1/3]

template<typename T >
void OpenMD::MultipassCorrFunc< T >::writeCorrelate ( )
protectedvirtual

◆ writeCorrelate() [2/3]

template<>
void OpenMD::MultipassCorrFunc< Vector3d >::writeCorrelate ( )
protected

Definition at line 329 of file MultipassCorrFunc.cpp.

◆ writeCorrelate() [3/3]

template<>
void OpenMD::MultipassCorrFunc< Mat3x3d >::writeCorrelate ( )
protected

Definition at line 367 of file MultipassCorrFunc.cpp.

Member Data Documentation

◆ autoCorrFunc_

template<typename T>
bool OpenMD::MultipassCorrFunc< T >::autoCorrFunc_
protected

Definition at line 119 of file MultipassCorrFunc.hpp.

◆ corrFuncType_

template<typename T>
std::string OpenMD::MultipassCorrFunc< T >::corrFuncType_
protected

◆ count_

template<typename T>
std::vector<int> OpenMD::MultipassCorrFunc< T >::count_
protected

Definition at line 100 of file MultipassCorrFunc.hpp.

◆ currentSnapshot_

template<typename T>
Snapshot* OpenMD::MultipassCorrFunc< T >::currentSnapshot_
protected

Definition at line 111 of file MultipassCorrFunc.hpp.

◆ deltaTime_

template<typename T>
RealType OpenMD::MultipassCorrFunc< T >::deltaTime_
protected

Definition at line 96 of file MultipassCorrFunc.hpp.

◆ dumpFilename_

template<typename T>
std::string OpenMD::MultipassCorrFunc< T >::dumpFilename_
protected

Definition at line 106 of file MultipassCorrFunc.hpp.

◆ evaluator1_

template<typename T>
SelectionEvaluator OpenMD::MultipassCorrFunc< T >::evaluator1_
protected

Definition at line 116 of file MultipassCorrFunc.hpp.

◆ evaluator2_

template<typename T>
SelectionEvaluator OpenMD::MultipassCorrFunc< T >::evaluator2_
protected

Definition at line 117 of file MultipassCorrFunc.hpp.

◆ histogram_

template<typename T>
std::vector<T> OpenMD::MultipassCorrFunc< T >::histogram_
protected

Definition at line 99 of file MultipassCorrFunc.hpp.

◆ info_

template<typename T>
SimInfo* OpenMD::MultipassCorrFunc< T >::info_
protected

Definition at line 104 of file MultipassCorrFunc.hpp.

◆ nFrames_

template<typename T>
int OpenMD::MultipassCorrFunc< T >::nFrames_
protected

Definition at line 98 of file MultipassCorrFunc.hpp.

◆ nTimeBins_

template<typename T>
int OpenMD::MultipassCorrFunc< T >::nTimeBins_
protected

Definition at line 97 of file MultipassCorrFunc.hpp.

◆ paramString_

template<typename T>
std::string OpenMD::MultipassCorrFunc< T >::paramString_
protected

◆ reader_

template<typename T>
DumpReader* OpenMD::MultipassCorrFunc< T >::reader_
protected

Definition at line 105 of file MultipassCorrFunc.hpp.

◆ sele1ToIndex_

template<typename T>
std::vector<std::vector<int> > OpenMD::MultipassCorrFunc< T >::sele1ToIndex_
protected

Definition at line 124 of file MultipassCorrFunc.hpp.

◆ sele2ToIndex_

template<typename T>
std::vector<std::vector<int> > OpenMD::MultipassCorrFunc< T >::sele2ToIndex_
protected

Definition at line 125 of file MultipassCorrFunc.hpp.

◆ selectionScript1_

template<typename T>
std::string OpenMD::MultipassCorrFunc< T >::selectionScript1_
protected

Definition at line 113 of file MultipassCorrFunc.hpp.

◆ selectionScript2_

template<typename T>
std::string OpenMD::MultipassCorrFunc< T >::selectionScript2_
protected

Definition at line 114 of file MultipassCorrFunc.hpp.

◆ seleMan1_

template<typename T>
SelectionManager OpenMD::MultipassCorrFunc< T >::seleMan1_
protected

Definition at line 107 of file MultipassCorrFunc.hpp.

◆ seleMan2_

template<typename T>
SelectionManager OpenMD::MultipassCorrFunc< T >::seleMan2_
protected

Definition at line 108 of file MultipassCorrFunc.hpp.

◆ storageLayout_

template<typename T>
int OpenMD::MultipassCorrFunc< T >::storageLayout_
protected

Definition at line 94 of file MultipassCorrFunc.hpp.

◆ times_

template<typename T>
std::vector<RealType> OpenMD::MultipassCorrFunc< T >::times_
protected

Definition at line 101 of file MultipassCorrFunc.hpp.

◆ uniqueSelections_

template<typename T>
bool OpenMD::MultipassCorrFunc< T >::uniqueSelections_
protected

Definition at line 102 of file MultipassCorrFunc.hpp.


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