In many applications (e.g. More...

#include <ReferenceAtoms.h>

Inheritance diagram for PLMD::ReferenceAtoms:

[legend]

Public Member Functions
	ReferenceAtoms (const ReferenceConfigurationOptions &ro)

unsigned	getNumberOfReferencePositions () const
	This returns the number of reference atom positions. More...

const std::vector< Vector > &	getReferencePositions () const
	Get the reference positions. More...

unsigned	getAtomIndex (const unsigned &) const
	This allows us to use a single pos array with RMSD objects using different atom indexes. More...

virtual void	getAtomRequests (std::vector< AtomNumber > &, bool disable_checks=false)
	Get the atoms required (additional checks are required when we have multiple domains) More...

void	setAtomNumbers (const std::vector< AtomNumber > &numbers)
	Set the indices of the reference atoms. More...

virtual void	setReferenceAtoms (const std::vector< Vector > &conf, const std::vector< double > &align_in, const std::vector< double > &displace_in)=0
	Set the positions of the reference atoms. More...

void	printAtoms (OFile &ofile, const double &lunits) const
	Print the atomic positions. More...

const std::vector< AtomNumber > &	getAbsoluteIndexes ()
	Return all atom indexes. More...

unsigned	getNumberOfAtoms () const
	This returns how many atoms there should be. More...

void	displaceReferenceAtoms (const double &weight, const std::vector< Vector > &dir)
	Displace the positions of the reference atoms a bit. More...

virtual void	extractAtomicDisplacement (const std::vector< Vector > &pos, std::vector< Vector > &direction) const
	Extract a displacement from a position in space. More...

virtual double	projectAtomicDisplacementOnVector (const bool &normalized, const std::vector< Vector > &eigv, ReferenceValuePack &mypack) const
	Project the displacement on a vector. More...

const std::vector< double > &	getAlign () const
	Get the vector of alignment weights. 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...

virtual unsigned	getNumberOfReferenceArguments () const

virtual void	getArgumentRequests (std::vector< std::string > &, bool disable_checks=false)
	Retrieve the arguments that are required for this guy. More...

virtual void	set (const PDB &)
	Set the final number of arguments. More...

virtual void	read (const PDB &)=0
	Do all local business for setting the configuration. More...

void	setWeight (const double &ww)
	Set the weight for this frame. More...

double	getWeight () const
	Return the weight for this frame. 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	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 =0
	Calculate the distance from the reference configuration. 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 double	getReferenceArgument (const unsigned &i) const
	Get one of the referene arguments. More...

virtual const std::vector< double > &	getReferenceArguments () const

virtual const std::vector< double > &	getReferenceMetric ()

virtual const std::vector< std::string > &	getArgumentNames ()

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 bool	pcaIsEnabledForThisReference ()
	Stuff for pca. More...

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

virtual void	setupPCAStorage (ReferenceValuePack &mypack)
	Stuff to setup pca. More...

void	displaceReferenceConfiguration (const double &weight, Direction &dir)
	Move the reference configuration by an ammount specified using a Direction. More...

Protected Member Functions
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...

bool	parseAtomList (const std::string &, std::vector< unsigned > &)
	Read a list of atoms from the pdb input file. More...

Vector	getReferencePosition (const unsigned &iatom) const
	Get the position of the ith atom. More...

void	singleDomainRequests (std::vector< AtomNumber > &, bool disable_checks)
	Add derivatives to iatom th atom in list. More...

void	error (const std::string &msg)
	Derivatives wrt to the arguments. More...

Private Attributes
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. More...

std::vector< double >	align
	The atoms to be used to align the instantaneous atomic positions to the reference configuration. More...

std::vector< double >	displace
	The atoms to be used to calculate the distance the atoms have moved from the reference configuration. More...

std::vector< Vector >	reference_atoms
	The positions of the atoms in the reference configuration. More...

std::vector< AtomNumber >	indices
	The indices of the atoms in the pdb file. More...

std::vector< unsigned >	atom_der_index
	The indeces for setting derivatives. More...

Friends
class	Direction

class	SingleDomainRMSD

class	ReferenceConfiguration

Detailed Description

In many applications (e.g.

paths, fields, property maps) it is necessary to calculate the distance between two configurations. These distances can be calculated in a variety of different ways. For instance, one can assert that the distance between the two configuration is the distance one would have to move all the atoms to transform configuration 1 into configuration

Alternatively, one could calculate the values of a large set of collective coordinates in the two configurations and then calculate the Euclidean distances between these two points in the resulting high-dimensional vector space. Lastly, one can combine these two forms of distance calculation to calculate a hybrid distance. Plumed allows one to use all these forms of distance calculations and also to implement new forms of distance. You should inherit from this class if your distance involves reference atomic positions. This class and PLMD::ReferenceArguments mirror the functionalities in and PLMD::ActionAtomistic and PLMD::ActionWithArguments respectively but for distances.

Constructor & Destructor Documentation

◆ ReferenceAtoms()

PLMD::ReferenceAtoms::ReferenceAtoms ( const ReferenceConfigurationOptions & ro )

explicit

Member Function Documentation

◆ calc()

virtual double PLMD::ReferenceConfiguration::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

pure virtualinherited

Calculate the distance from the reference configuration.

Implemented in PLMD::MultiDomainRMSD, PLMD::ArgumentOnlyDistance, PLMD::SingleDomainRMSD, PLMD::Direction, and PLMD::FakeFrame.

◆ 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.

◆ 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.

◆ displaceReferenceAtoms()

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

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

Derivatives wrt to the arguments.

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

◆ extractAtomicDisplacement()

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

inlinevirtual

Extract a displacement from a position in space.

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

◆ 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 ( )

inlinevirtual

Return all atom indexes.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getAlign()

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

inline

Get the vector of alignment weights.

◆ getArgumentNames()

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

inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

◆ getArgumentRequests()

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

inline

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`
	)

virtual

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

inline

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

inline

This returns how many atoms there should be.

◆ getNumberOfReferenceArguments()

unsigned PLMD::ReferenceConfiguration::getNumberOfReferenceArguments ( ) const

inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

◆ getNumberOfReferencePositions()

unsigned PLMD::ReferenceAtoms::getNumberOfReferencePositions ( ) const

inlinevirtual

This returns the number of reference atom positions.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceArgument()

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

inlinevirtualinherited

Get one of the referene arguments.

Reimplemented in PLMD::ReferenceArguments.

◆ getReferenceArguments()

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

inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

◆ getReferenceMetric()

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

inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

◆ getReferencePosition()

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

inlineprotected

Get the position of the ith atom.

◆ getReferencePositions()

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

inlinevirtual

Get the reference positions.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getWeight()

double PLMD::ReferenceConfiguration::getWeight ( ) const

inlineinherited

Return the weight for this frame.

◆ 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

◆ parseAtomList()

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

protected

Read a list of atoms from the pdb input file.

◆ 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()

virtual bool PLMD::ReferenceConfiguration::pcaIsEnabledForThisReference ( )

inlinevirtualinherited

Stuff for pca.

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

◆ 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

◆ printAtoms()

void PLMD::ReferenceAtoms::printAtoms	(	OFile &	ofile,
		const double &	lunits
	)		const

Print the atomic positions.

◆ projectAtomicDisplacementOnVector()

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

inlinevirtual

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()

virtual void PLMD::ReferenceConfiguration::read ( const PDB & )

pure virtualinherited

Do all local business for setting the configuration.

Implemented in PLMD::DRMSD, PLMD::MultiDomainRMSD, PLMD::ArgumentOnlyDistance, PLMD::Direction, PLMD::OptimalRMSD, PLMD::FakeFrame, PLMD::IntermolecularDRMSD, PLMD::IntramolecularDRMSD, PLMD::SimpleRMSD, and PLMD::DotProductDistance.

◆ readAtomsFromPDB()

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

protected

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

◆ setAtomIndices()

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

protected

Add atom indices to list.

◆ setAtomNumbers()

void PLMD::ReferenceAtoms::setAtomNumbers ( const std::vector< AtomNumber > & numbers )

Set the indices of the reference atoms.

◆ 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.

◆ setReferenceAtoms()

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

pure virtual

Set the positions of the reference atoms.

Implemented in PLMD::DRMSD, PLMD::MultiDomainRMSD, PLMD::Direction, and PLMD::SingleDomainRMSD.

◆ 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()

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

inlinevirtualinherited

Stuff to setup pca.

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

◆ setWeight()

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

inlineinherited

Set the weight for this frame.

◆ singleDomainRequests()

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

protected

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

Friends And Related Function Documentation

◆ Direction

friend class Direction

friend

◆ ReferenceConfiguration

friend class ReferenceConfiguration

friend

◆ SingleDomainRMSD

friend class SingleDomainRMSD

friend

Member Data Documentation

◆ align

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

private

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

◆ atom_der_index

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

private

The indeces for setting derivatives.

◆ checks_were_disabled

bool PLMD::ReferenceAtoms::checks_were_disabled

private

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

private

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

◆ indices

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

private

The indices of the atoms in the pdb file.

◆ reference_atoms

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

private

The positions of the atoms in the reference configuration.

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

reference/ReferenceAtoms.h
reference/ReferenceAtoms.cpp

Public Member Functions

Protected Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ ReferenceAtoms()

Member Function Documentation

◆ calc()

◆ calculate()

◆ checkRead()

◆ copyDerivatives()

◆ displaceReferenceAtoms()

◆ displaceReferenceConfiguration()

◆ error()

◆ extractAtomicDisplacement()

◆ extractDisplacementVector()

◆ getAbsoluteIndexes()

◆ getAlign()

◆ getArgumentNames()

◆ getArgumentRequests()

◆ getAtomIndex()

◆ getAtomRequests()

◆ getDisplace()

◆ getName()

◆ getNumberOfAtoms()

◆ getNumberOfReferenceArguments()

◆ getNumberOfReferencePositions()

◆ getReferenceArgument()

◆ getReferenceArguments()

◆ getReferenceMetric()

◆ getReferencePosition()

◆ getReferencePositions()

◆ getWeight()

◆ parse()

◆ parseAtomList()

◆ parseFlag()

◆ parseVector()

◆ pcaIsEnabledForThisReference()

◆ print() [1/2]

◆ print() [2/2]

◆ printAtoms()

◆ projectAtomicDisplacementOnVector()

◆ projectDisplacementOnVector()

◆ read()

◆ readAtomsFromPDB()

◆ set()

◆ setAtomIndices()

◆ setAtomNumbers()

◆ setNamesAndAtomNumbers()

◆ setReferenceAtoms()

◆ setReferenceConfig()

◆ setupPCAStorage()

◆ setWeight()

◆ singleDomainRequests()

Friends And Related Function Documentation

◆ Direction

◆ ReferenceConfiguration

◆ SingleDomainRMSD

Member Data Documentation

◆ align

◆ atom_der_index

◆ checks_were_disabled

◆ displace

◆ indices

◆ reference_atoms