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

#include <ReferenceAtoms.h>

Inheritance diagram for PLMD::ReferenceAtoms:

Public Member Functions
	ReferenceAtoms (const ReferenceConfigurationOptions &ro)
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.
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.
void	copyDerivatives (const ReferenceConfiguration *)
	Parse something from the pdb remarks Copy derivatives from one frame to this frame.
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.
virtual void	extractAtomicDisplacement (const std::vector< Vector > &pos, std::vector< Vector > &direction) const
	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.
virtual const std::vector< std::string > &	getArgumentNames ()
virtual void	getArgumentRequests (std::vector< std::string > &, bool disable_checks=false)
	Retrieve the arguments that are required for this guy.
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.
virtual unsigned	getNumberOfReferenceArguments () const
unsigned	getNumberOfReferencePositions () const override
	This returns the number of reference atom positions.
virtual double	getReferenceArgument (const unsigned &i) const
	Get one of the referene arguments.
virtual const std::vector< double > &	getReferenceArguments () const
virtual const std::vector< double > &	getReferenceMetric ()
const std::vector< Vector > &	getReferencePositions () const override
	Get the reference positions.
virtual bool	pcaIsEnabledForThisReference ()
	Stuff for pca.
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
virtual void	read (const PDB &)=0
	Do all local business for setting the configuration.
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.
virtual void	setupPCAStorage (ReferenceValuePack &mypack)
	Stuff to setup pca.

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

Private Attributes
std::vector< double >	align
	The atoms to be used to align the instantaneous atomic positions to the reference configuration.
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< std::string >	fake_arg_names
std::vector< AtomNumber >	fake_atom_numbers
	These are used to do fake things when we copy frames.
std::vector< double >	fake_metric
std::vector< double >	fake_refargs
std::vector< Vector >	fake_refatoms
	These are use by the distance function above.
std::vector< AtomNumber >	indices
	The indices of the atoms in the pdb file.
std::vector< std::string >	line
	A vector containing all the remarks from the pdb input.
std::string	name
	The name of this particular config.
std::vector< Vector >	reference_atoms
	The positions of the atoms in the reference configuration.

Friends
class	Direction
class	MultiDomainRMSD
class	ReferenceConfiguration
class	SingleDomainRMSD

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::ArgumentOnlyDistance, PLMD::Direction, PLMD::FakeFrame, PLMD::MultiDomainRMSD, PLMD::RMSDBase, and PLMD::SingleDomainRMSD.

◆ 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.

◆ copyDerivatives()

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

inherited

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

◆ error()

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

protectedinherited

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::Direction, PLMD::MultiDomainRMSD, 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 ( )

inlineoverridevirtual

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 )

overridevirtual

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

inlineoverridevirtual

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

inlineoverridevirtual

Get the reference positions.

Reimplemented from PLMD::ReferenceConfiguration.

◆ parseAtomList()

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

protected

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.

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

◆ readAtomsFromPDB()

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

protected

Read in the atoms from the pdb file.

◆ setAtomIndices()

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

protected

Add atom indices to list.

◆ 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::Direction, PLMD::DRMSD, PLMD::MultiDomainRMSD, and PLMD::SingleDomainRMSD.

◆ 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 )

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

◆ Direction

friend class Direction

friend

◆ MultiDomainRMSD

friend class MultiDomainRMSD

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.

◆ 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.

◆ indices

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

private

The indices of the atoms in the pdb file.

◆ line

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

privateinherited

A vector containing all the remarks from the pdb input.

◆ name

std::string PLMD::ReferenceConfiguration::name

privateinherited

The name of this particular config.

◆ 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()

◆ copyDerivatives()

◆ displaceReferenceAtoms()

◆ displaceReferenceConfiguration()

◆ error()

◆ extractAtomicDisplacement()

◆ extractDisplacementVector()

◆ getAbsoluteIndexes()

◆ getAlign()

◆ getArgumentNames()

◆ getArgumentRequests()

◆ getAtomIndex()

◆ getAtomRequests()

◆ getDisplace()

◆ getName()

◆ getNumberOfAtoms()

◆ getNumberOfReferenceArguments()

◆ getNumberOfReferencePositions()

◆ getReferenceArgument()

◆ getReferenceArguments()

◆ getReferenceMetric()

◆ getReferencePosition()

◆ getReferencePositions()

◆ parseAtomList()

◆ pcaIsEnabledForThisReference()

◆ projectAtomicDisplacementOnVector()

◆ projectDisplacementOnVector()

◆ read()

◆ readAtomsFromPDB()

◆ setAtomIndices()

◆ setReferenceAtoms()

◆ setupPCAStorage()

◆ singleDomainRequests()

Friends And Related Symbol Documentation

◆ Direction

◆ MultiDomainRMSD

◆ ReferenceConfiguration

◆ SingleDomainRMSD

Member Data Documentation

◆ align

◆ atom_der_index

◆ checks_were_disabled

◆ displace

◆ fake_arg_names

◆ fake_atom_numbers

◆ fake_metric

◆ fake_refargs

◆ fake_refatoms

◆ indices

◆ line

◆ name

◆ reference_atoms