Public Member Functions | Static Public Member Functions | Public Attributes | Protected Member Functions | Protected Attributes | Private Attributes | List of all members
PLMD::mapping::SpathVessel Class Reference
Inheritance diagram for PLMD::mapping::SpathVessel:
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Public Member Functions

 SpathVessel (const vesselbase::VesselOptions &da)
 
std::string value_descriptor ()
 
void prepare ()
 Do something before the loop. More...
 
bool calculate (const unsigned &current, MultiValue &myvals, std::vector< double > &buffer, std::vector< unsigned > &der_index) const
 Do the calcualtion. More...
 
virtual void resize ()
 This does the resizing of the buffer. More...
 
virtual double calcTransform (const double &val, double &df) const
 Do any transformations of the value that are required. More...
 
virtual void finish (const std::vector< double > &buffer)
 Finish the calculation of the quantity. More...
 
virtual double finalTransform (const double &val, double &dv)
 Finish with any transforms required. More...
 
std::string description ()
 Return a description of the vessel contents. 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 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

ValuegetFinalValue () const
 
void setOutputValue (const double &val)
 Set the final value. More...
 
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

bool diffweight
 Are the derivatives differentiable. More...
 
bool norm
 Are we normalising by the weight. More...
 
bool usetol
 Are we using the tolerance. More...
 
unsigned bufstart
 The start of this Vessel's buffer in buffer in the underlying ActionWithVessel. More...
 
Communicatorcomm
 A copy of the communicator. More...
 

Private Attributes

bool foundoneclose
 
unsigned mycoordnumber
 
Mappingmymap
 

Constructor & Destructor Documentation

PLMD::mapping::SpathVessel::SpathVessel ( const vesselbase::VesselOptions da)
explicit

Member Function Documentation

bool PLMD::vesselbase::ValueVessel::applyForce ( std::vector< double > &  forces)
virtualinherited

Retrieve the forces on the quantities in the vessel.

Implements PLMD::vesselbase::Vessel.

double PLMD::vesselbase::FunctionVessel::calcTransform ( const double &  val,
double &  df 
) const
virtualinherited
bool PLMD::mapping::SpathVessel::calculate ( const unsigned &  current,
MultiValue myvals,
std::vector< double > &  buffer,
std::vector< unsigned > &  der_list 
) const
virtual

Do the calcualtion.

Reimplemented from PLMD::vesselbase::FunctionVessel.

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

Check that readin was fine.

std::string PLMD::vesselbase::ValueVessel::description ( )
virtualinherited

Return a description of the vessel contents.

Implements PLMD::vesselbase::Vessel.

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

Report an error.

double PLMD::vesselbase::FunctionVessel::finalTransform ( const double &  val,
double &  dv 
)
virtualinherited

Finish with any transforms required.

Reimplemented in PLMD::mapping::ZpathVessel, PLMD::vesselbase::Max, PLMD::vesselbase::Min, and PLMD::mapping::AltMin.

void PLMD::vesselbase::FunctionVessel::finish ( const std::vector< double > &  buffer)
virtualinherited
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)

Value * PLMD::vesselbase::ValueVessel::getFinalValue ( ) const
inlineprotectedinherited
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.

void PLMD::mapping::SpathVessel::prepare ( )
virtual

Do something before the loop.

Reimplemented from PLMD::vesselbase::Vessel.

void PLMD::mapping::SpathVessel::registerKeywords ( Keywords keys)
static
void PLMD::mapping::SpathVessel::reserveKeyword ( Keywords keys)
static
void PLMD::vesselbase::FunctionVessel::resize ( )
virtualinherited
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.

void PLMD::vesselbase::ValueVessel::setOutputValue ( const double &  val)
inlineprotectedinherited

Set the final value.

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.

std::string PLMD::mapping::SpathVessel::value_descriptor ( )
virtual

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.

bool PLMD::vesselbase::FunctionVessel::diffweight
protectedinherited

Are the derivatives differentiable.

bool PLMD::mapping::SpathVessel::foundoneclose
private
Log& PLMD::vesselbase::Vessel::log
inherited

Reference to the log on which to output details.

unsigned PLMD::mapping::SpathVessel::mycoordnumber
private
Mapping* PLMD::mapping::SpathVessel::mymap
private
bool PLMD::vesselbase::FunctionVessel::norm
protectedinherited

Are we normalising by the weight.

bool PLMD::vesselbase::FunctionVessel::usetol
protectedinherited

Are we using the tolerance.


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