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

 NormalizedEuclideanDistance (const ReferenceConfigurationOptions &ro)
 
void read (const PDB &pdb)
 Do all local business for setting the configuration. More...
 
bool pcaIsEnabledForThisReference ()
 Stuff for pca. More...
 
void setupPCAStorage (ReferenceValuePack &mypack)
 Stuff to setup pca. More...
 
double calc (const std::vector< Vector > &pos, const Pbc &pbc, const std::vector< Value *> &vals, const std::vector< double > &arg, ReferenceValuePack &myder, const bool &squared) const
 Calculate the distance from the reference configuration. More...
 
double calculate (const std::vector< Value *> &vals, ReferenceValuePack &myder, const bool &squared) const
 
double calculate (const std::vector< Vector > &pos, const Pbc &pbc, const std::vector< Value *> &vals, ReferenceValuePack &myder, const bool &squared=false) const
 Calculate the distance from the reference configuration. More...
 
void setReferenceArguments (const std::vector< double > &arg_vals, const std::vector< double > &sigma)
 Set the positions of the refernce arguments. More...
 
unsigned getNumberOfReferenceArguments () const
 Get the number of reference arguments. More...
 
void getArgumentRequests (std::vector< std::string > &, bool disable_checks=false)
 Get the arguments required. More...
 
void setArgumentNames (const std::vector< std::string > &arg_vals)
 Set the names of the arguments. More...
 
void moveReferenceArguments (const std::vector< double > &arg_vals)
 Set the positions of the reference arguments. More...
 
double getReferenceArgument (const unsigned &i) const
 Get the value of the ith reference argument. More...
 
void printArguments (OFile &ofile, const std::string &fmt) const
 Print the arguments out. More...
 
const std::vector< double > & getReferenceArguments () const
 Return all the reference arguments. More...
 
const std::vector< double > & getReferenceMetric ()
 
const std::vector< std::string > & getArgumentNames ()
 Return names. More...
 
virtual double calculateArgumentDistance (const std::vector< Value *> &vals, const std::vector< double > &arg, ReferenceValuePack &myder, const bool &squared) const
 Calculate the euclidean/malanobius distance the atoms have moved from the reference configuration in CV space. More...
 
void displaceReferenceArguments (const double &weight, const std::vector< double > &displace)
 Displace the positions of the reference atoms. More...
 
virtual void extractArgumentDisplacement (const std::vector< Value *> &vals, const std::vector< double > &arg, std::vector< double > &dirout) const
 Extract the displacement from a position in a space. More...
 
double projectArgDisplacementOnVector (const std::vector< double > &eigv, const std::vector< Value *> &vals, const std::vector< double > &arg, ReferenceValuePack &mypack) const
 Project the displacement of the arguments on a vector. More...
 
std::string getName () const
 Return the name of this metric. More...
 
virtual unsigned getNumberOfReferencePositions () const
 
virtual void getAtomRequests (std::vector< AtomNumber > &, bool disable_checks=false)
 Retrieve the atoms that are required for this guy. More...
 
virtual void set (const PDB &)
 Set the final number of arguments. More...
 
void setWeight (const double &ww)
 Set the weight for this frame. More...
 
double getWeight () const
 Return the weight for this frame. More...
 
template<class T >
bool parse (const std::string &key, T &t, bool ignore_missing=false)
 Return the derivatives of the distance wrt the cell vectors. More...
 
template<class T >
bool parseVector (const std::string &key, std::vector< T > &t, bool ignore_missing=false)
 Parse vector from the pdb remarks. More...
 
void parseFlag (const std::string &key, bool &t)
 Parse a flag. More...
 
void checkRead ()
 Check that all the remarks in the pdb have been read in. More...
 
void copyDerivatives (const ReferenceConfiguration *)
 Copy derivatives from one frame to this frame. More...
 
void setNamesAndAtomNumbers (const std::vector< AtomNumber > &numbers, const std::vector< std::string > &arg)
 Set the atom numbers and the argument names. More...
 
void setReferenceConfig (const std::vector< Vector > &pos, const std::vector< double > &arg, const std::vector< double > &metric)
 Set the reference structure (perhaps should also pass the pbc and align and displace ) More...
 
void print (OFile &ofile, const double &time, const double &weight, const double &lunits, const double &old_norm)
 Print a pdb file containing the reference configuration. More...
 
void print (OFile &ofile, const std::string &fmt, const double &lunits)
 
virtual const std::vector< Vector > & getReferencePositions () const
 These are overwritten in ReferenceArguments and ReferenceAtoms but are required here to make PLMD::distance work. More...
 
virtual const std::vector< AtomNumber > & getAbsoluteIndexes ()
 These are overwritten in ReferenceArguments and ReferenceAtoms to make frame copying work. More...
 
void extractDisplacementVector (const std::vector< Vector > &pos, const std::vector< Value *> &vals, const std::vector< double > &arg, const bool &nflag, Direction &mydir) const
 Extract a Direction giving you the displacement from some position. More...
 
double projectDisplacementOnVector (const Direction &mydir, const std::vector< Value *> &vals, const std::vector< double > &arg, ReferenceValuePack &mypack) const
 
void displaceReferenceConfiguration (const double &weight, Direction &dir)
 Move the reference configuration by an ammount specified using a Direction. More...
 

Protected Member Functions

void readArgumentsFromPDB (const PDB &pdb)
 Read in the atoms from the pdb file. More...
 
void setReferenceArguments ()
 Set the values of the colvars based on their current instantanous values (used in Analysis) More...
 
void error (const std::string &msg)
 Derivatives wrt to the arguments. More...
 

Protected Attributes

bool hasweights
 Are we reading weights from input. More...
 
bool hasmetric
 Are we calculating a Malanobius distance. More...
 

Constructor & Destructor Documentation

◆ NormalizedEuclideanDistance()

PLMD::NormalizedEuclideanDistance::NormalizedEuclideanDistance ( const ReferenceConfigurationOptions ro)
explicit

Member Function Documentation

◆ calc()

double PLMD::ArgumentOnlyDistance::calc ( const std::vector< Vector > &  pos,
const Pbc pbc,
const std::vector< Value *> &  vals,
const std::vector< double > &  args,
ReferenceValuePack myder,
const bool &  squared 
) const
virtualinherited

Calculate the distance from the reference configuration.

Implements PLMD::ReferenceConfiguration.

◆ calculate() [1/2]

double PLMD::ArgumentOnlyDistance::calculate ( const std::vector< Value *> &  vals,
ReferenceValuePack myder,
const bool &  squared 
) const
inherited

◆ calculate() [2/2]

double PLMD::ReferenceConfiguration::calculate ( const std::vector< Vector > &  pos,
const Pbc pbc,
const std::vector< Value *> &  vals,
ReferenceValuePack myder,
const bool &  squared = false 
) const
inherited

Calculate the distance from the reference configuration.

◆ calculateArgumentDistance()

double PLMD::ReferenceArguments::calculateArgumentDistance ( const std::vector< Value *> &  vals,
const std::vector< double > &  arg,
ReferenceValuePack myder,
const bool &  squared 
) const
virtualinherited

Calculate the euclidean/malanobius distance the atoms have moved from the reference configuration in CV space.

Reimplemented in PLMD::DotProductDistance.

◆ checkRead()

void PLMD::ReferenceConfiguration::checkRead ( )
inherited

Check that all the remarks in the pdb have been read in.

◆ copyDerivatives()

void PLMD::ReferenceConfiguration::copyDerivatives ( const ReferenceConfiguration )
inherited

Copy derivatives from one frame to this frame.

◆ displaceReferenceArguments()

void PLMD::ReferenceArguments::displaceReferenceArguments ( const double &  weight,
const std::vector< double > &  displace 
)
inherited

Displace the positions of the reference atoms.

◆ displaceReferenceConfiguration()

void PLMD::ReferenceConfiguration::displaceReferenceConfiguration ( const double &  weight,
Direction dir 
)
inherited

Move the reference configuration by an ammount specified using a Direction.

◆ error()

void PLMD::ReferenceConfiguration::error ( const std::string &  msg)
protectedinherited

Derivatives wrt to the arguments.

The virial contribution has to be stored Derivatives wrt to the atoms Crash with an error

◆ extractArgumentDisplacement()

void PLMD::ReferenceArguments::extractArgumentDisplacement ( const std::vector< Value *> &  vals,
const std::vector< double > &  arg,
std::vector< double > &  dirout 
) const
virtualinherited

Extract the displacement from a position in a space.

Reimplemented in PLMD::Direction.

◆ extractDisplacementVector()

void PLMD::ReferenceConfiguration::extractDisplacementVector ( const std::vector< Vector > &  pos,
const std::vector< Value *> &  vals,
const std::vector< double > &  arg,
const bool &  nflag,
Direction mydir 
) const
inherited

Extract a Direction giving you the displacement from some position.

◆ getAbsoluteIndexes()

const std::vector< AtomNumber > & PLMD::ReferenceConfiguration::getAbsoluteIndexes ( )
inlinevirtualinherited

These are overwritten in ReferenceArguments and ReferenceAtoms to make frame copying work.

Reimplemented in PLMD::ReferenceAtoms.

◆ getArgumentNames()

const std::vector< std::string > & PLMD::ReferenceArguments::getArgumentNames ( )
inlinevirtualinherited

Return names.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getArgumentRequests()

void PLMD::ReferenceArguments::getArgumentRequests ( std::vector< std::string > &  argout,
bool  disable_checks = false 
)
virtualinherited

Get the arguments required.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getAtomRequests()

virtual void PLMD::ReferenceConfiguration::getAtomRequests ( std::vector< AtomNumber > &  ,
bool  disable_checks = false 
)
inlinevirtualinherited

Retrieve the atoms that are required for this guy.

Reimplemented in PLMD::ReferenceAtoms.

◆ getName()

std::string PLMD::ReferenceConfiguration::getName ( ) const
inherited

Return the name of this metric.

◆ getNumberOfReferenceArguments()

unsigned PLMD::ReferenceArguments::getNumberOfReferenceArguments ( ) const
inlinevirtualinherited

Get the number of reference arguments.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getNumberOfReferencePositions()

unsigned PLMD::ReferenceConfiguration::getNumberOfReferencePositions ( ) const
inlinevirtualinherited

Reimplemented in PLMD::ReferenceAtoms.

◆ getReferenceArgument()

double PLMD::ReferenceArguments::getReferenceArgument ( const unsigned &  i) const
inlinevirtualinherited

Get the value of the ith reference argument.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceArguments()

const std::vector< double > & PLMD::ReferenceArguments::getReferenceArguments ( ) const
inlinevirtualinherited

Return all the reference arguments.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceMetric()

const std::vector< double > & PLMD::ReferenceArguments::getReferenceMetric ( )
virtualinherited

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferencePositions()

const std::vector< Vector > & PLMD::ReferenceConfiguration::getReferencePositions ( ) const
inlinevirtualinherited

These are overwritten in ReferenceArguments and ReferenceAtoms but are required here to make PLMD::distance work.

Reimplemented in PLMD::ReferenceAtoms.

◆ getWeight()

double PLMD::ReferenceConfiguration::getWeight ( ) const
inlineinherited

Return the weight for this frame.

◆ moveReferenceArguments()

void PLMD::ReferenceArguments::moveReferenceArguments ( const std::vector< double > &  arg_vals)
inherited

Set the positions of the reference arguments.

◆ parse()

template<class T >
bool PLMD::ReferenceConfiguration::parse ( const std::string &  key,
T &  t,
bool  ignore_missing = false 
)
inherited

Return the derivatives of the distance wrt the cell vectors.

This returns false for everything other than DRMSD as these sort of calculations have to be done separately when you use RMSD Parse something from the pdb remarks

◆ parseFlag()

void PLMD::ReferenceConfiguration::parseFlag ( const std::string &  key,
bool &  t 
)
inherited

Parse a flag.

◆ parseVector()

template<class T >
bool PLMD::ReferenceConfiguration::parseVector ( const std::string &  key,
std::vector< T > &  t,
bool  ignore_missing = false 
)
inherited

Parse vector from the pdb remarks.

◆ pcaIsEnabledForThisReference()

bool PLMD::ArgumentOnlyDistance::pcaIsEnabledForThisReference ( )
inlinevirtualinherited

Stuff for pca.

Reimplemented from PLMD::ReferenceConfiguration.

◆ print() [1/2]

void PLMD::ReferenceConfiguration::print ( OFile ofile,
const double &  time,
const double &  weight,
const double &  lunits,
const double &  old_norm 
)
inherited

Print a pdb file containing the reference configuration.

◆ print() [2/2]

void PLMD::ReferenceConfiguration::print ( OFile ofile,
const std::string &  fmt,
const double &  lunits 
)
inherited

◆ printArguments()

void PLMD::ReferenceArguments::printArguments ( OFile ofile,
const std::string &  fmt 
) const
inherited

Print the arguments out.

◆ projectArgDisplacementOnVector()

double PLMD::ReferenceArguments::projectArgDisplacementOnVector ( const std::vector< double > &  eigv,
const std::vector< Value *> &  vals,
const std::vector< double > &  arg,
ReferenceValuePack mypack 
) const
inherited

Project the displacement of the arguments on a vector.

◆ projectDisplacementOnVector()

double PLMD::ReferenceConfiguration::projectDisplacementOnVector ( const Direction mydir,
const std::vector< Value *> &  vals,
const std::vector< double > &  arg,
ReferenceValuePack mypack 
) const
inherited

◆ read()

void PLMD::ArgumentOnlyDistance::read ( const PDB )
virtualinherited

Do all local business for setting the configuration.

Implements PLMD::ReferenceConfiguration.

Reimplemented in PLMD::DotProductDistance.

◆ readArgumentsFromPDB()

void PLMD::ReferenceArguments::readArgumentsFromPDB ( const PDB pdb)
protectedinherited

Read in the atoms from the pdb file.

◆ set()

void PLMD::ReferenceConfiguration::set ( const PDB pdb)
virtualinherited

Set the final number of arguments.

Set the final number of atoms Set the reference configuration using a PDB

◆ setArgumentNames()

void PLMD::ReferenceArguments::setArgumentNames ( const std::vector< std::string > &  arg_vals)
inherited

Set the names of the arguments.

◆ setNamesAndAtomNumbers()

void PLMD::ReferenceConfiguration::setNamesAndAtomNumbers ( const std::vector< AtomNumber > &  numbers,
const std::vector< std::string > &  arg 
)
inherited

Set the atom numbers and the argument names.

◆ setReferenceArguments() [1/2]

void PLMD::ReferenceArguments::setReferenceArguments ( )
protectedinherited

Set the values of the colvars based on their current instantanous values (used in Analysis)

◆ setReferenceArguments() [2/2]

void PLMD::ReferenceArguments::setReferenceArguments ( const std::vector< double > &  arg_vals,
const std::vector< double > &  sigma 
)
inherited

Set the positions of the refernce arguments.

◆ setReferenceConfig()

void PLMD::ReferenceConfiguration::setReferenceConfig ( const std::vector< Vector > &  pos,
const std::vector< double > &  arg,
const std::vector< double > &  metric 
)
inherited

Set the reference structure (perhaps should also pass the pbc and align and displace )

◆ setupPCAStorage()

void PLMD::ArgumentOnlyDistance::setupPCAStorage ( ReferenceValuePack mypack)
inlinevirtualinherited

Stuff to setup pca.

Reimplemented from PLMD::ReferenceConfiguration.

◆ setWeight()

void PLMD::ReferenceConfiguration::setWeight ( const double &  ww)
inlineinherited

Set the weight for this frame.

Member Data Documentation

◆ hasmetric

bool PLMD::ReferenceArguments::hasmetric
protectedinherited

Are we calculating a Malanobius distance.

◆ hasweights

bool PLMD::ReferenceArguments::hasweights
protectedinherited

Are we reading weights from input.


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