OpenMD 3.0
Molecular Dynamics in the Open
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Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
OpenMD::TimeCorrFunc< T > Class Template Referenceabstract

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

#include <TimeCorrFunc.hpp>

+ Inheritance diagram for OpenMD::TimeCorrFunc< T >:

Public Member Functions

 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)
 
- Public Member Functions inherited from OpenMD::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 void correlateFrames (int frame1, int frame2, int timeBin)
 
virtual void writeCorrelate ()
 
virtual void computeProperty1 (int frame)=0
 
virtual void computeProperty2 (int frame)=0
 
virtual T calcCorrVal (int frame1, int frame2)=0
 
virtual int computeProperty1 (int frame, Molecule *mol)=0
 
virtual int computeProperty2 (int frame, Molecule *mol)=0
 
virtual int computeProperty1 (int frame, StuntDouble *sd)=0
 
virtual int computeProperty2 (int frame, StuntDouble *sd)=0
 
virtual int computeProperty1 (int frame, Bond *b)=0
 
virtual int computeProperty2 (int frame, Bond *b)=0
 
virtual T calcCorrVal (int frame1, int frame2, int id1, int id2)=0
 
void writeCorrelate ()
 
void writeCorrelate ()
 

Protected Attributes

RealType deltaTime_
 
unsigned int nTimeBins_
 
int nFrames_
 
std::vector< T > histogram_
 
std::vector< int > count_
 
std::vector< RealType > times_
 
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_
 
std::string corrFuncType_
 
std::string paramString_
 
std::string labelString_
 
std::vector< std::vector< int > > sele1ToIndex_
 
std::vector< std::vector< int > > sele2ToIndex_
 
ProgressBarPtr progressBar_
 
- Protected Attributes inherited from OpenMD::DynamicProperty
std::string outputFilename_
 

Detailed Description

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

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

Definition at line 65 of file TimeCorrFunc.hpp.

Constructor & Destructor Documentation

◆ TimeCorrFunc()

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

Definition at line 58 of file TimeCorrFunc.cpp.

◆ ~TimeCorrFunc()

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

Definition at line 70 of file TimeCorrFunc.hpp.

Member Function Documentation

◆ computeFrame()

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

Definition at line 131 of file TimeCorrFunc.cpp.

◆ correlateFrames()

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

Definition at line 326 of file TimeCorrFunc.cpp.

◆ correlation()

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

Definition at line 278 of file TimeCorrFunc.cpp.

◆ doCorrelate()

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

Implements OpenMD::DynamicProperty.

Definition at line 254 of file TimeCorrFunc.cpp.

◆ getCorrFuncType()

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

Definition at line 73 of file TimeCorrFunc.hpp.

◆ postCorrelate()

template<typename T >
void OpenMD::TimeCorrFunc< T >::postCorrelate ( )
protectedvirtual

Definition at line 373 of file TimeCorrFunc.cpp.

◆ preCorrelate()

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

Definition at line 100 of file TimeCorrFunc.cpp.

◆ setCorrFuncType()

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

Definition at line 75 of file TimeCorrFunc.hpp.

◆ setLabelString()

template<typename T >
void OpenMD::TimeCorrFunc< T >::setLabelString ( const std::string & label)
inline

Definition at line 81 of file TimeCorrFunc.hpp.

◆ setParameterString()

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

Definition at line 77 of file TimeCorrFunc.hpp.

◆ validateSelection()

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

Definition at line 385 of file TimeCorrFunc.cpp.

◆ writeCorrelate() [1/3]

void OpenMD::TimeCorrFunc< Vector3d >::writeCorrelate ( )
protected

Definition at line 423 of file TimeCorrFunc.cpp.

◆ writeCorrelate() [2/3]

void OpenMD::TimeCorrFunc< Mat3x3d >::writeCorrelate ( )
protected

Definition at line 462 of file TimeCorrFunc.cpp.

◆ writeCorrelate() [3/3]

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

Definition at line 388 of file TimeCorrFunc.cpp.

Member Data Documentation

◆ autoCorrFunc_

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

Definition at line 132 of file TimeCorrFunc.hpp.

◆ corrFuncType_

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

Definition at line 139 of file TimeCorrFunc.hpp.

◆ count_

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

Definition at line 114 of file TimeCorrFunc.hpp.

◆ currentSnapshot_

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

Definition at line 123 of file TimeCorrFunc.hpp.

◆ deltaTime_

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

Definition at line 110 of file TimeCorrFunc.hpp.

◆ doAtomicProperties_

template<typename T >
bool OpenMD::TimeCorrFunc< T >::doAtomicProperties_
protected

Definition at line 136 of file TimeCorrFunc.hpp.

◆ doBondProperties_

template<typename T >
bool OpenMD::TimeCorrFunc< T >::doBondProperties_
protected

Definition at line 137 of file TimeCorrFunc.hpp.

◆ doMolecularProperties_

template<typename T >
bool OpenMD::TimeCorrFunc< T >::doMolecularProperties_
protected

Definition at line 134 of file TimeCorrFunc.hpp.

◆ doObjectProperties_

template<typename T >
bool OpenMD::TimeCorrFunc< T >::doObjectProperties_
protected

Definition at line 135 of file TimeCorrFunc.hpp.

◆ doSystemProperties_

template<typename T >
bool OpenMD::TimeCorrFunc< T >::doSystemProperties_
protected

Definition at line 133 of file TimeCorrFunc.hpp.

◆ dumpFilename_

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

Definition at line 119 of file TimeCorrFunc.hpp.

◆ evaluator1_

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

Definition at line 128 of file TimeCorrFunc.hpp.

◆ evaluator2_

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

Definition at line 129 of file TimeCorrFunc.hpp.

◆ histogram_

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

Definition at line 113 of file TimeCorrFunc.hpp.

◆ info_

template<typename T >
SimInfo* OpenMD::TimeCorrFunc< T >::info_ {nullptr}
protected

Definition at line 117 of file TimeCorrFunc.hpp.

◆ labelString_

template<typename T >
std::string OpenMD::TimeCorrFunc< T >::labelString_
protected

Definition at line 141 of file TimeCorrFunc.hpp.

◆ nFrames_

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

Definition at line 112 of file TimeCorrFunc.hpp.

◆ nTimeBins_

template<typename T >
unsigned int OpenMD::TimeCorrFunc< T >::nTimeBins_
protected

Definition at line 111 of file TimeCorrFunc.hpp.

◆ paramString_

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

Definition at line 140 of file TimeCorrFunc.hpp.

◆ progressBar_

template<typename T >
ProgressBarPtr OpenMD::TimeCorrFunc< T >::progressBar_
protected

Definition at line 146 of file TimeCorrFunc.hpp.

◆ reader_

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

Definition at line 118 of file TimeCorrFunc.hpp.

◆ sele1ToIndex_

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

Definition at line 143 of file TimeCorrFunc.hpp.

◆ sele2ToIndex_

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

Definition at line 144 of file TimeCorrFunc.hpp.

◆ selectionScript1_

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

Definition at line 125 of file TimeCorrFunc.hpp.

◆ selectionScript2_

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

Definition at line 126 of file TimeCorrFunc.hpp.

◆ seleMan1_

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

Definition at line 120 of file TimeCorrFunc.hpp.

◆ seleMan2_

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

Definition at line 121 of file TimeCorrFunc.hpp.

◆ times_

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

Definition at line 115 of file TimeCorrFunc.hpp.

◆ uniqueSelections_

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

Definition at line 131 of file TimeCorrFunc.hpp.

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