Public Member Functions | Static Public Member Functions | Public Attributes | Protected Member Functions | Protected Attributes | List of all members
PLMD::vesselbase::Histogram Class Reference
Inheritance diagram for PLMD::vesselbase::Histogram:
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Public Member Functions

 Histogram (const VesselOptions &da)
 
std::string description ()
 Return a description of the vessel contents. More...
 
void resize ()
 Reset the size of the buffers. More...
 
bool calculate (const unsigned &taskCode, MultiValue &myvals, std::vector< double > &buffer, std::vector< unsigned > &der_index) const
 Calculate the part of the vessel that is done in the loop. More...
 
void finish (const std::vector< double > &buffer)
 Complete the calculation once the loop is finished. More...
 
bool applyForce (std::vector< double > &forces)
 Retrieve the forces on the quantities in the vessel. More...
 
std::string getName () const
 Return the name. More...
 
std::string getLabel () const
 Return the label. More...
 
void checkRead ()
 Check that readin was fine. More...
 
virtual void setBufferStart (unsigned &start)
 Set the start of the buffer. More...
 
virtual void prepare ()
 Do something before the loop. More...
 
virtual MultiValuetransformDerivatives (const unsigned &current, MultiValue &myvals, MultiValue &bvals)
 This is replaced in bridges so we can transform the derivatives. More...
 

Static Public Member Functions

static void registerKeywords (Keywords &keys)
 
static void reserveKeyword (Keywords &keys)
 
static std::string transformName (const std::string &name)
 Convert the name to the label of the component. More...
 

Public Attributes

Loglog
 Reference to the log on which to output details. More...
 

Protected Member Functions

void addVessel (const std::string &name, const std::string &intput)
 
int getNumericalLabel () const
 Return the numerical label. More...
 
void error (const std::string &errmsg)
 Report an error. More...
 
template<class T >
void parse (const std::string &key, T &t)
 Parse something from the input. More...
 
template<class T >
void parseVector (const std::string &key, std::vector< T > &t)
 Parse one keyword as std::vector. More...
 
void parseFlag (const std::string &key, bool &t)
 Parse one keyword as boolean flag. More...
 
std::string getAllInput ()
 This returns the whole input line (it is used for less_than/more_than/between) More...
 
ActionWithVesselgetAction () const
 Return a pointer to the action we are working in. More...
 
double getTolerance () const
 Return the value of the tolerance. More...
 
double getNLTolerance () const
 Return the value of the neighbor list tolerance. More...
 
void resizeBuffer (const unsigned &n)
 Set the size of the data buffer. More...
 

Protected Attributes

unsigned bufstart
 The start of this Vessel's buffer in buffer in the underlying ActionWithVessel. More...
 
Communicatorcomm
 A copy of the communicator. More...
 

Constructor & Destructor Documentation

PLMD::vesselbase::Histogram::Histogram ( const VesselOptions da)
explicit

Member Function Documentation

void PLMD::vesselbase::ShortcutVessel::addVessel ( const std::string &  name,
const std::string &  intput 
)
protectedinherited
bool PLMD::vesselbase::ShortcutVessel::applyForce ( std::vector< double > &  forces)
inlinevirtualinherited

Retrieve the forces on the quantities in the vessel.

Implements PLMD::vesselbase::Vessel.

bool PLMD::vesselbase::ShortcutVessel::calculate ( const unsigned &  current,
MultiValue myvals,
std::vector< double > &  buffer,
std::vector< unsigned > &  der_list 
) const
inlinevirtualinherited

Calculate the part of the vessel that is done in the loop.

Implements PLMD::vesselbase::Vessel.

void PLMD::vesselbase::Vessel::checkRead ( )
inherited

Check that readin was fine.

std::string PLMD::vesselbase::ShortcutVessel::description ( )
inlinevirtualinherited

Return a description of the vessel contents.

Implements PLMD::vesselbase::Vessel.

void PLMD::vesselbase::Vessel::error ( const std::string &  errmsg)
protectedinherited

Report an error.

void PLMD::vesselbase::ShortcutVessel::finish ( const std::vector< double > &  )
inlinevirtualinherited

Complete the calculation once the loop is finished.

Implements PLMD::vesselbase::Vessel.

ActionWithVessel * PLMD::vesselbase::Vessel::getAction ( ) const
inlineprotectedinherited

Return a pointer to the action we are working in.

std::string PLMD::vesselbase::Vessel::getAllInput ( )
protectedinherited

This returns the whole input line (it is used for less_than/more_than/between)

std::string PLMD::vesselbase::Vessel::getLabel ( ) const
inherited

Return the label.

std::string PLMD::vesselbase::Vessel::getName ( ) const
inherited

Return the name.

double PLMD::vesselbase::Vessel::getNLTolerance ( ) const
inlineprotectedinherited

Return the value of the neighbor list tolerance.

int PLMD::vesselbase::Vessel::getNumericalLabel ( ) const
inlineprotectedinherited

Return the numerical label.

double PLMD::vesselbase::Vessel::getTolerance ( ) const
inlineprotectedinherited

Return the value of the tolerance.

template<class T >
void PLMD::vesselbase::Vessel::parse ( const std::string &  key,
T &  t 
)
protectedinherited

Parse something from the input.

void PLMD::vesselbase::Vessel::parseFlag ( const std::string &  key,
bool &  t 
)
protectedinherited

Parse one keyword as boolean flag.

template<class T >
void PLMD::vesselbase::Vessel::parseVector ( const std::string &  key,
std::vector< T > &  t 
)
protectedinherited

Parse one keyword as std::vector.

virtual void PLMD::vesselbase::Vessel::prepare ( )
inlinevirtualinherited
void PLMD::vesselbase::Histogram::registerKeywords ( Keywords keys)
static
void PLMD::vesselbase::Histogram::reserveKeyword ( Keywords keys)
static
void PLMD::vesselbase::ShortcutVessel::resize ( )
inlinevirtualinherited

Reset the size of the buffers.

Implements PLMD::vesselbase::Vessel.

void PLMD::vesselbase::Vessel::resizeBuffer ( const unsigned &  n)
inlineprotectedinherited

Set the size of the data buffer.

void PLMD::vesselbase::Vessel::setBufferStart ( unsigned &  start)
inlinevirtualinherited

Set the start of the buffer.

Reimplemented in PLMD::vesselbase::BridgeVessel, and PLMD::multicolvar::AdjacencyMatrixVessel.

MultiValue & PLMD::vesselbase::Vessel::transformDerivatives ( const unsigned &  current,
MultiValue myvals,
MultiValue bvals 
)
inlinevirtualinherited

This is replaced in bridges so we can transform the derivatives.

Reimplemented in PLMD::vesselbase::BridgeVessel.

std::string PLMD::vesselbase::Vessel::transformName ( const std::string &  name)
staticinherited

Convert the name to the label of the component.

Member Data Documentation

unsigned PLMD::vesselbase::Vessel::bufstart
protectedinherited

The start of this Vessel's buffer in buffer in the underlying ActionWithVessel.

Communicator& PLMD::vesselbase::Vessel::comm
protectedinherited

A copy of the communicator.

Log& PLMD::vesselbase::Vessel::log
inherited

Reference to the log on which to output details.


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