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

#include <Direction.h>

Inheritance diagram for PLMD::Direction:
Inheritance graph
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Public Member Functions

 Direction (const ReferenceConfigurationOptions &ro)
 
void addDirection (const double &weight, const Direction &dir)
 
double 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 override
 Calculate the distance from the reference configuration. More...
 
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 displaceReferenceAtoms (const double &weight, const std::vector< Vector > &dir)
 Displace the positions of the reference atoms a bit. More...
 
void displaceReferenceConfiguration (const double &weight, Direction &dir)
 Move the reference configuration by an ammount specified using a Direction. More...
 
void extractArgumentDisplacement (const std::vector< Value *> &vals, const std::vector< double > &arg, std::vector< double > &dirout) const override
 This allows us to extract the reference positions, which are the direction in this case. More...
 
void extractAtomicDisplacement (const std::vector< Vector > &pos, std::vector< Vector > &dirout) const override
 Extract a displacement from a position in 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...
 
const std::vector< AtomNumber > & getAbsoluteIndexes () override
 Return all atom indexes. More...
 
const std::vector< double > & getAlign () const
 Get the vector of alignment weights. More...
 
const std::vector< std::string > & getArgumentNames () override
 Return names. More...
 
virtual const std::vector< std::string > & getArgumentNames ()
 
void getArgumentRequests (std::vector< std::string > &, bool disable_checks=false) override
 Get the arguments required. More...
 
virtual void getArgumentRequests (std::vector< std::string > &, bool disable_checks=false)
 Retrieve the arguments that are required for this guy. More...
 
unsigned getAtomIndex (const unsigned &) const
 This allows us to use a single pos array with RMSD objects using different atom indexes. More...
 
void getAtomRequests (std::vector< AtomNumber > &, bool disable_checks=false) override
 Get the atoms required (additional checks are required when we have multiple domains) More...
 
const std::vector< double > & getDisplace () const
 Get the vector of displacement weights. More...
 
std::string getName () const
 Return the name of this metric. More...
 
unsigned getNumberOfAtoms () const
 This returns how many atoms there should be. More...
 
unsigned getNumberOfReferenceArguments () const override
 Get the number of reference arguments. More...
 
virtual unsigned getNumberOfReferenceArguments () const
 
unsigned getNumberOfReferencePositions () const override
 This returns the number of reference atom positions. More...
 
double getReferenceArgument (const unsigned &i) const override
 Get the value of the ith reference argument. More...
 
virtual double getReferenceArgument (const unsigned &i) const
 Get one of the referene arguments. More...
 
const std::vector< double > & getReferenceArguments () const override
 Return all the reference arguments. More...
 
virtual const std::vector< double > & getReferenceArguments () const
 
const std::vector< double > & getReferenceMetric () override
 
virtual const std::vector< double > & getReferenceMetric ()
 
const std::vector< Vector > & getReferencePositions () const override
 Get the reference positions. More...
 
void moveReferenceArguments (const std::vector< double > &arg_vals)
 Set the positions of the reference arguments. More...
 
virtual bool pcaIsEnabledForThisReference ()
 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...
 
virtual double projectAtomicDisplacementOnVector (const bool &normalized, const std::vector< Vector > &eigv, ReferenceValuePack &mypack) const
 Project the displacement 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 &) override
 Do all local business for setting the configuration. More...
 
void setDirection (const std::vector< Vector > &conf, const std::vector< double > &args)
 
void setReferenceArguments (const std::vector< double > &arg_vals, const std::vector< double > &sigma)
 Set the positions of the refernce arguments. More...
 
void setReferenceAtoms (const std::vector< Vector > &conf, const std::vector< double > &align_in, const std::vector< double > &displace_in) override
 Set the positions of the reference atoms. More...
 
virtual void setupPCAStorage (ReferenceValuePack &mypack)
 Stuff to setup pca. More...
 
void zeroDirection ()
 

Public Attributes

bool normalized
 

Protected Member Functions

void error (const std::string &msg)
 Crash with an error. More...
 
Vector getReferencePosition (const unsigned &iatom) const
 Get the position of the ith atom. More...
 
bool parseAtomList (const std::string &, std::vector< unsigned > &)
 Read a list of atoms from the pdb input file. More...
 
void readArgumentsFromPDB (const PDB &pdb)
 Read in the atoms from the pdb file. More...
 
void readAtomsFromPDB (const PDB &, const bool allowblocks=false)
 Read in the atoms from the pdb file. More...
 
void setAtomIndices (const std::vector< AtomNumber > &atomnumbers)
 Add atom indices to list. More...
 
void setReferenceArguments ()
 Set the values of the colvars based on their current instantanous values (used in Analysis) More...
 
void singleDomainRequests (std::vector< AtomNumber > &, bool disable_checks)
 Add derivatives to iatom th atom in list. More...
 

Protected Attributes

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

Constructor & Destructor Documentation

◆ Direction()

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

Member Function Documentation

◆ addDirection()

void PLMD::Direction::addDirection ( const double &  weight,
const Direction dir 
)

◆ calc()

double PLMD::Direction::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()

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.

◆ displaceReferenceAtoms()

void PLMD::ReferenceAtoms::displaceReferenceAtoms ( const double &  weight,
const std::vector< Vector > &  dir 
)
inherited

Displace the positions of the reference atoms a bit.

◆ 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

Crash with an error.

◆ extractArgumentDisplacement()

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

This allows us to extract the reference positions, which are the direction in this case.

Reimplemented from PLMD::ReferenceArguments.

◆ extractAtomicDisplacement()

void PLMD::Direction::extractAtomicDisplacement ( const std::vector< Vector > &  pos,
std::vector< Vector > &  direction 
) const
overridevirtual

Extract a displacement from a position in space.

Reimplemented from PLMD::ReferenceAtoms.

◆ 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::ReferenceAtoms::getAbsoluteIndexes ( )
inlineoverridevirtualinherited

Return all atom indexes.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getAlign()

const std::vector< double > & PLMD::ReferenceAtoms::getAlign ( ) const
inlineinherited

Get the vector of alignment weights.

◆ getArgumentNames() [1/2]

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

Return names.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getArgumentNames() [2/2]

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

Reimplemented in PLMD::ReferenceArguments.

◆ getArgumentRequests() [1/2]

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

Get the arguments required.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getArgumentRequests() [2/2]

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

Retrieve the arguments that are required for this guy.

Reimplemented in PLMD::ReferenceArguments.

◆ getAtomIndex()

unsigned PLMD::ReferenceAtoms::getAtomIndex ( const unsigned &  iatom) const
inlineinherited

This allows us to use a single pos array with RMSD objects using different atom indexes.

◆ getAtomRequests()

void PLMD::ReferenceAtoms::getAtomRequests ( std::vector< AtomNumber > &  numbers,
bool  disable_checks = false 
)
overridevirtualinherited

Get the atoms required (additional checks are required when we have multiple domains)

Reimplemented from PLMD::ReferenceConfiguration.

◆ getDisplace()

const std::vector< double > & PLMD::ReferenceAtoms::getDisplace ( ) const
inlineinherited

Get the vector of displacement weights.

◆ getName()

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

Return the name of this metric.

◆ getNumberOfAtoms()

unsigned PLMD::ReferenceAtoms::getNumberOfAtoms ( ) const
inlineinherited

This returns how many atoms there should be.

◆ getNumberOfReferenceArguments() [1/2]

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

Get the number of reference arguments.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getNumberOfReferenceArguments() [2/2]

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

Reimplemented in PLMD::ReferenceArguments.

◆ getNumberOfReferencePositions()

unsigned PLMD::ReferenceAtoms::getNumberOfReferencePositions ( ) const
inlineoverridevirtualinherited

This returns the number of reference atom positions.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceArgument() [1/2]

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

Get the value of the ith reference argument.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceArgument() [2/2]

virtual double PLMD::ReferenceConfiguration::getReferenceArgument ( const unsigned &  i) const
inlinevirtualinherited

Get one of the referene arguments.

Reimplemented in PLMD::ReferenceArguments.

◆ getReferenceArguments() [1/2]

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

Return all the reference arguments.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceArguments() [2/2]

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

Reimplemented in PLMD::ReferenceArguments.

◆ getReferenceMetric() [1/2]

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

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceMetric() [2/2]

const std::vector< double > & PLMD::ReferenceConfiguration::getReferenceMetric ( )
inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

◆ getReferencePosition()

Vector PLMD::ReferenceAtoms::getReferencePosition ( const unsigned &  iatom) const
inlineprotectedinherited

Get the position of the ith atom.

◆ getReferencePositions()

const std::vector< Vector > & PLMD::ReferenceAtoms::getReferencePositions ( ) const
inlineoverridevirtualinherited

Get the reference positions.

Reimplemented from PLMD::ReferenceConfiguration.

◆ moveReferenceArguments()

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

Set the positions of the reference arguments.

◆ parseAtomList()

bool PLMD::ReferenceAtoms::parseAtomList ( const std::string &  ,
std::vector< unsigned > &   
)
protectedinherited

Read a list of atoms from the pdb input file.

◆ pcaIsEnabledForThisReference()

virtual bool PLMD::ReferenceConfiguration::pcaIsEnabledForThisReference ( )
inlinevirtualinherited

◆ 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.

◆ projectAtomicDisplacementOnVector()

virtual double PLMD::ReferenceAtoms::projectAtomicDisplacementOnVector ( const bool &  normalized,
const std::vector< Vector > &  eigv,
ReferenceValuePack mypack 
) const
inlinevirtualinherited

Project the displacement on a vector.

Reimplemented in PLMD::MultiDomainRMSD, PLMD::OptimalRMSD, and PLMD::SimpleRMSD.

◆ 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::Direction::read ( const PDB )
overridevirtual

Do all local business for setting the configuration.

Implements PLMD::ReferenceConfiguration.

◆ readArgumentsFromPDB()

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

Read in the atoms from the pdb file.

◆ readAtomsFromPDB()

void PLMD::ReferenceAtoms::readAtomsFromPDB ( const PDB pdb,
const bool  allowblocks = false 
)
protectedinherited

Read in the atoms from the pdb file.

◆ setAtomIndices()

void PLMD::ReferenceAtoms::setAtomIndices ( const std::vector< AtomNumber > &  atomnumbers)
protectedinherited

Add atom indices to list.

◆ setDirection()

void PLMD::Direction::setDirection ( const std::vector< Vector > &  conf,
const std::vector< double > &  args 
)

◆ 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.

◆ setReferenceAtoms()

void PLMD::Direction::setReferenceAtoms ( const std::vector< Vector > &  conf,
const std::vector< double > &  align_in,
const std::vector< double > &  displace_in 
)
inlineoverridevirtual

Set the positions of the reference atoms.

Implements PLMD::ReferenceAtoms.

◆ setupPCAStorage()

virtual void PLMD::ReferenceConfiguration::setupPCAStorage ( ReferenceValuePack mypack)
inlinevirtualinherited

◆ singleDomainRequests()

void PLMD::ReferenceAtoms::singleDomainRequests ( std::vector< AtomNumber > &  numbers,
bool  disable_checks 
)
protectedinherited

Add derivatives to iatom th atom in list.

Get the atomic derivatives on the ith atom in the list Add derivatives to the viral This does the checks that are always required

◆ zeroDirection()

void PLMD::Direction::zeroDirection ( )

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.

◆ normalized

bool PLMD::Direction::normalized

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