#include <Direction.h>

Inheritance diagram for PLMD::Direction:

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.
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.
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.
void	copyDerivatives (const ReferenceConfiguration *)
	Parse something from the pdb remarks Copy derivatives from one frame to this frame.
void	displaceReferenceArguments (const double &weight, const std::vector< double > &displace)
	Displace the positions of the reference atoms.
void	displaceReferenceAtoms (const double &weight, const std::vector< Vector > &dir)
	Displace the positions of the reference atoms a bit.
void	displaceReferenceConfiguration (const double &weight, Direction &dir)
	Move the reference configuration by an amount specified using a Direction.
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.
void	extractAtomicDisplacement (const std::vector< Vector > &pos, std::vector< Vector > &dirout) const override
	Extract a displacement from a position in space.
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.
const std::vector< AtomNumber > &	getAbsoluteIndexes () override
	Return all atom indexes.
const std::vector< double > &	getAlign () const
	Get the vector of alignment weights.
const std::vector< std::string > &	getArgumentNames () override
	Return names.
void	getArgumentRequests (std::vector< std::string > &, bool disable_checks=false) override
	Get the arguments required.
unsigned	getAtomIndex (const unsigned &) const
	This allows us to use a single pos array with RMSD objects using different atom indexes.
void	getAtomRequests (std::vector< AtomNumber > &, bool disable_checks=false) override
	Get the atoms required (additional checks are required when we have multiple domains).
const std::vector< double > &	getDisplace () const
	Get the vector of displacement weights.
std::string	getName () const
	Return the name of this metric.
unsigned	getNumberOfAtoms () const
	This returns how many atoms there should be.
unsigned	getNumberOfReferenceArguments () const override
	Get the number of reference arguments.
unsigned	getNumberOfReferencePositions () const override
	This returns the number of reference atom positions.
double	getReferenceArgument (const unsigned &i) const override
	Get the value of the ith reference argument.
const std::vector< double > &	getReferenceArguments () const override
	Return all the reference arguments.
const std::vector< double > &	getReferenceMetric () override
const std::vector< Vector > &	getReferencePositions () const override
	Get the reference positions.
void	moveReferenceArguments (const std::vector< double > &arg_vals)
	Set the positions of the reference arguments.
virtual bool	pcaIsEnabledForThisReference ()
	Stuff for pca.
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.
virtual double	projectAtomicDisplacementOnVector (const bool &normalized, const std::vector< Vector > &eigv, ReferenceValuePack &mypack) const
	Project the displacement on a vector.
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.
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 reference arguments.
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.
virtual void	setupPCAStorage (ReferenceValuePack &mypack)
	Stuff to setup pca.
void	zeroDirection ()

Public Attributes
bool	normalized

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

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

Private Attributes
std::vector< double >	align
	The atoms to be used to align the instantaneous atomic positions to the reference configuration.
std::vector< unsigned >	arg_der_index
	The indices for setting derivatives.
std::vector< std::string >	arg_names
	The names of the arguments.
std::vector< unsigned >	atom_der_index
	The indeces for setting derivatives.
bool	checks_were_disabled
	This flag tells us if the user has disabled checking of the input in order to do fancy paths with weird inputs.
std::vector< double >	displace
	The atoms to be used to calculate the distance the atoms have moved from the reference configuration.
std::vector< AtomNumber >	indices
	The indices of the atoms in the pdb file.
Matrix< double >	metric
	The N X N matrix we are using to calculate our Malanobius distance.
std::vector< double >	reference_args
	The values of the colvars in the reference configuration.
std::vector< Vector >	reference_atoms
	The positions of the atoms in the reference configuration.
std::vector< double >	sqrtweight
std::vector< double >	trig_metric
std::vector< double >	weights
	The weights for normed euclidean distance.

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 amount 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()

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.

◆ 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()

unsigned PLMD::ReferenceArguments::getNumberOfReferenceArguments ( ) const

inlineoverridevirtualinherited

Get the number of reference arguments.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getNumberOfReferencePositions()

unsigned PLMD::ReferenceAtoms::getNumberOfReferencePositions ( ) const

inlineoverridevirtualinherited

This returns the number of reference atom positions.

Reimplemented from PLMD::ReferenceConfiguration.

◆ 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.

◆ 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

Stuff for pca.

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

◆ 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 reference 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

Stuff to setup pca.

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

◆ 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

◆ align

std::vector<double> PLMD::ReferenceAtoms::align

privateinherited

The atoms to be used to align the instantaneous atomic positions to the reference configuration.

◆ 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.

◆ atom_der_index

std::vector<unsigned> PLMD::ReferenceAtoms::atom_der_index

privateinherited

The indeces for setting derivatives.

◆ checks_were_disabled

bool PLMD::ReferenceAtoms::checks_were_disabled

privateinherited

This flag tells us if the user has disabled checking of the input in order to do fancy paths with weird inputs.

◆ displace

std::vector<double> PLMD::ReferenceAtoms::displace

privateinherited

The atoms to be used to calculate the distance the atoms have moved from the reference configuration.

◆ hasmetric

bool PLMD::ReferenceArguments::hasmetric

protectedinherited

Are we calculating a Malanobius distance.

◆ hasweights

bool PLMD::ReferenceArguments::hasweights

protectedinherited

Are we reading weights from input.

◆ indices

std::vector<AtomNumber> PLMD::ReferenceAtoms::indices

privateinherited

The indices of the atoms in the pdb file.

◆ metric

Matrix<double> PLMD::ReferenceArguments::metric

privateinherited

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

◆ normalized

bool PLMD::Direction::normalized

◆ reference_args

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

privateinherited

The values of the colvars in the reference configuration.

◆ reference_atoms

std::vector<Vector> PLMD::ReferenceAtoms::reference_atoms

privateinherited

The positions of the atoms 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:

reference/Direction.h
reference/Direction.cpp

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Attributes

Constructor & Destructor Documentation

◆ Direction()

Member Function Documentation

◆ addDirection()

◆ calc()

◆ calculate()

◆ calculateArgumentDistance()

◆ copyDerivatives()

◆ displaceReferenceArguments()

◆ displaceReferenceAtoms()

◆ displaceReferenceConfiguration()

◆ error()

◆ extractArgumentDisplacement()

◆ extractAtomicDisplacement()

◆ extractDisplacementVector()

◆ getAbsoluteIndexes()

◆ getAlign()

◆ getArgumentNames()

◆ getArgumentRequests()

◆ getAtomIndex()

◆ getAtomRequests()

◆ getDisplace()

◆ getName()

◆ getNumberOfAtoms()

◆ getNumberOfReferenceArguments()

◆ getNumberOfReferencePositions()

◆ getReferenceArgument()

◆ getReferenceArguments()

◆ getReferenceMetric()

◆ getReferencePosition()

◆ getReferencePositions()

◆ moveReferenceArguments()

◆ parseAtomList()

◆ pcaIsEnabledForThisReference()

◆ projectArgDisplacementOnVector()

◆ projectAtomicDisplacementOnVector()

◆ projectDisplacementOnVector()

◆ read()

◆ readArgumentsFromPDB()

◆ readAtomsFromPDB()

◆ setAtomIndices()

◆ setDirection()

◆ setReferenceArguments() [1/2]

◆ setReferenceArguments() [2/2]

◆ setReferenceAtoms()

◆ setupPCAStorage()

◆ singleDomainRequests()

◆ zeroDirection()

Member Data Documentation

◆ align

◆ arg_der_index

◆ arg_names

◆ atom_der_index

◆ checks_were_disabled

◆ displace

◆ hasmetric

◆ hasweights

◆ indices

◆ metric

◆ normalized

◆ reference_args

◆ reference_atoms

◆ sqrtweight

◆ trig_metric

◆ weights