Public Member Functions | Protected Member Functions | Protected Attributes | Private Attributes | List of all members
PLMD::ArgumentOnlyDistance Class Reference

#include <ArgumentOnlyDistance.h>

Inheritance diagram for PLMD::ArgumentOnlyDistance:
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Public Member Functions

 ArgumentOnlyDistance (const ReferenceConfigurationOptions &ro)
 
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 override
 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...
 
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 copyDerivatives (const ReferenceConfiguration *)
 Parse something from the pdb remarks Copy derivatives from one frame to this frame. More...
 
void displaceReferenceArguments (const double &weight, const std::vector< double > &displace)
 Displace the positions of the reference atoms. More...
 
void displaceReferenceConfiguration (const double &weight, Direction &dir)
 Move the reference configuration by an amount specified using a Direction. 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...
 
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...
 
virtual const std::vector< AtomNumber > & getAbsoluteIndexes ()
 These are overwritten in ReferenceArguments and ReferenceAtoms to make frame copying work. More...
 
const std::vector< std::string > & getArgumentNames () override
 Return names. More...
 
void getArgumentRequests (std::vector< std::string > &, bool disable_checks=false) override
 Get the arguments required. More...
 
virtual void getAtomRequests (std::vector< AtomNumber > &, bool disable_checks=false)
 Retrieve the atoms that are required for this guy. More...
 
std::string getName () const
 Return the name of this metric. More...
 
unsigned getNumberOfReferenceArguments () const override
 Get the number of reference arguments. More...
 
virtual unsigned getNumberOfReferencePositions () const
 
double getReferenceArgument (const unsigned &i) const override
 Get the value of the ith reference argument. More...
 
const std::vector< double > & getReferenceArguments () const override
 Return all the reference arguments. More...
 
const std::vector< double > & getReferenceMetric () override
 
virtual const std::vector< Vector > & getReferencePositions () const
 These are overwritten in ReferenceArguments and ReferenceAtoms but are required here to make PLMD::distance work. More...
 
void moveReferenceArguments (const std::vector< double > &arg_vals)
 Set the positions of the reference arguments. More...
 
bool pcaIsEnabledForThisReference () override
 Stuff for pca. 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...
 
double projectDisplacementOnVector (const Direction &mydir, const std::vector< Value * > &vals, const std::vector< double > &arg, ReferenceValuePack &mypack) const
 
void read (const PDB &pdb) override
 Do all local business for setting the configuration. More...
 
void setReferenceArguments (const std::vector< double > &arg_vals, const std::vector< double > &sigma)
 Set the positions of the reference arguments. More...
 
void setupPCAStorage (ReferenceValuePack &mypack) override
 Stuff to setup pca. More...
 

Protected Member Functions

void error (const std::string &msg)
 Crash with an error. More...
 
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...
 

Protected Attributes

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

Private Attributes

std::vector< unsigned > arg_der_index
 The indices for setting derivatives. More...
 
std::vector< std::string > arg_names
 The names of the arguments. More...
 
std::vector< std::string > fake_arg_names
 
std::vector< AtomNumberfake_atom_numbers
 These are used to do fake things when we copy frames. More...
 
std::vector< double > fake_metric
 
std::vector< double > fake_refargs
 
std::vector< Vectorfake_refatoms
 These are use by the distance function above. More...
 
std::vector< std::string > line
 A vector containing all the remarks from the pdb input. More...
 
Matrix< double > metric
 The N X N matrix we are using to calculate our Malanobius distance. More...
 
std::string name
 The name of this particular config. More...
 
std::vector< double > reference_args
 The values of the colvars in the reference configuration. More...
 
std::vector< double > sqrtweight
 
std::vector< double > trig_metric
 
std::vector< double > weights
 The weights for normed euclidean distance. More...
 

Constructor & Destructor Documentation

◆ ArgumentOnlyDistance()

PLMD::ArgumentOnlyDistance::ArgumentOnlyDistance ( 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
overridevirtual

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

◆ 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.

◆ copyDerivatives()

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

Parse something from the pdb remarks 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 amount specified using a Direction.

◆ error()

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

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 ( )
inlineoverridevirtualinherited

Return names.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getArgumentRequests()

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

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
inlineoverridevirtualinherited

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
inlineoverridevirtualinherited

Get the value of the ith reference argument.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceArguments()

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

Return all the reference arguments.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceMetric()

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

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.

◆ moveReferenceArguments()

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

Set the positions of the reference arguments.

◆ pcaIsEnabledForThisReference()

bool PLMD::ArgumentOnlyDistance::pcaIsEnabledForThisReference ( )
inlineoverridevirtual

Stuff for pca.

Reimplemented from PLMD::ReferenceConfiguration.

◆ 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 )
overridevirtual

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.

◆ 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 reference arguments.

◆ setupPCAStorage()

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

Stuff to setup pca.

Reimplemented from PLMD::ReferenceConfiguration.

Member Data Documentation

◆ arg_der_index

std::vector<unsigned> PLMD::ReferenceArguments::arg_der_index
privateinherited

The indices for setting derivatives.

◆ arg_names

std::vector<std::string> PLMD::ReferenceArguments::arg_names
privateinherited

The names of the arguments.

◆ fake_arg_names

std::vector<std::string> PLMD::ReferenceConfiguration::fake_arg_names
privateinherited

◆ fake_atom_numbers

std::vector<AtomNumber> PLMD::ReferenceConfiguration::fake_atom_numbers
privateinherited

These are used to do fake things when we copy frames.

◆ fake_metric

std::vector<double> PLMD::ReferenceConfiguration::fake_metric
privateinherited

◆ fake_refargs

std::vector<double> PLMD::ReferenceConfiguration::fake_refargs
privateinherited

◆ fake_refatoms

std::vector<Vector> PLMD::ReferenceConfiguration::fake_refatoms
privateinherited

These are use by the distance function above.

◆ hasmetric

bool PLMD::ReferenceArguments::hasmetric
protectedinherited

Are we calculating a Malanobius distance.

◆ hasweights

bool PLMD::ReferenceArguments::hasweights
protectedinherited

Are we reading weights from input.

◆ line

std::vector<std::string> PLMD::ReferenceConfiguration::line
privateinherited

A vector containing all the remarks from the pdb input.

◆ metric

Matrix<double> PLMD::ReferenceArguments::metric
privateinherited

The N X N matrix we are using to calculate our Malanobius distance.

◆ name

std::string PLMD::ReferenceConfiguration::name
privateinherited

The name of this particular config.

◆ reference_args

std::vector<double> PLMD::ReferenceArguments::reference_args
privateinherited

The values of the colvars in the reference configuration.

◆ sqrtweight

std::vector<double> PLMD::ReferenceArguments::sqrtweight
privateinherited

◆ trig_metric

std::vector<double> PLMD::ReferenceArguments::trig_metric
privateinherited

◆ weights

std::vector<double> PLMD::ReferenceArguments::weights
privateinherited

The weights for normed euclidean distance.


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