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

#include <ReferenceAtoms.h>

Inheritance diagram for PLMD::ReferenceAtoms:

Public Member Functions
	ReferenceAtoms (const ReferenceConfigurationOptions &ro)

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
	Print the atomic positions. More...

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

std::string	getName () const
	Return the name of this metric. More...

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

virtual void	setNumberOfArguments (const unsigned &)
	Set the final number of arguments. More...

virtual void	setNumberOfAtoms (const unsigned &)
	Set the final number of atoms. More...

virtual void	set (const PDB &)
	Set the reference configuration using a PDB. 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, const bool &squared=false)
	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, const bool &squared)=0
	Calculate the distance from the reference configuration. More...

Vector	getAtomDerivative (const unsigned &) const
	Return the derivative wrt to the ith atom. More...

double	getArgumentDerivative (const unsigned &) const
	Return the derivative wrt to the ith argument. More...

bool	getVirial (Tensor &virout) const
	Return the derivatives of the distance wrt the cell vectors. More...

template<class T >
bool	parse (const std::string &key, T &t, bool ignore_missing=false)
	Parse something from the pdb remarks. 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 &old_norm)
	Print a pdb file containing the reference configuration. More...

void	print (OFile &ofile, const std::string &fmt)

virtual double	getReferenceArgument (const unsigned &i)
	Get one of the referene arguments. More...

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

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

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

Protected Member Functions
void	readAtomsFromPDB (const PDB &)
	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...

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...

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

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

void	addAtomicDerivatives (const unsigned &, const Vector &)
	Add derivatives to iatom th atom in list. More...

Vector	retrieveAtomicDerivatives (const unsigned &) const
	Get the atomic derivatives on the ith atom in the list. More...

void	addBoxDerivatives (const Tensor &)
	Add derivatives to the viral. More...

void	singleDomainRequests (std::vector< AtomNumber > &, bool disable_checks)
	This does the checks that are always required. More...

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

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

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

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

void	clearDerivatives ()
	Clear the derivatives. More...

Protected Attributes
std::vector< double >	arg_ders
	Derivatives wrt to the arguments. More...

bool	virialWasSet
	The virial contribution has to be stored. More...

Tensor	virial

std::vector< Vector >	atom_ders
	Derivatives wrt to the atoms. 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 >	der_index
	The indeces for setting derivatives. More...

Friends
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

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

Member Function Documentation

void PLMD::ReferenceAtoms::addAtomicDerivatives	(	const unsigned &	iatom,
		const Vector &	der
	)

inlineprotected

Add derivatives to iatom th atom in list.

void PLMD::ReferenceAtoms::addBoxDerivatives ( const Tensor & vir )

inlineprotected

Add derivatives to the viral.

virtual double PLMD::ReferenceConfiguration::calc	(	const std::vector< Vector > &	pos,
		const Pbc &	pbc,
		const std::vector< Value * > &	vals,
		const std::vector< double > &	args,
		const bool &	squared
	)

pure virtualinherited

Calculate the distance from the reference configuration.

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

double PLMD::ReferenceConfiguration::calculate	(	const std::vector< Vector > &	pos,
		const Pbc &	pbc,
		const std::vector< Value * > &	vals,
		const bool &	squared = `false`
	)

inherited

Calculate the distance from the reference configuration.

void PLMD::ReferenceConfiguration::checkRead ( )

inherited

Check that all the remarks in the pdb have been read in.

void PLMD::ReferenceConfiguration::clearDerivatives ( )

protectedinherited

Clear the derivatives.

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

inherited

Copy derivatives from one frame to this frame.

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

protectedinherited

Crash with an error.

const std::vector< AtomNumber > & PLMD::ReferenceAtoms::getAbsoluteIndexes ( )

inlinevirtual

Return all atom indexes.

Reimplemented from PLMD::ReferenceConfiguration.

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

inlineprotected

Get the vector of alignment weights.

double PLMD::ReferenceConfiguration::getArgumentDerivative ( const unsigned & ider ) const

inlineinherited

Return the derivative wrt to the ith argument.

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

inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

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.

Vector PLMD::ReferenceConfiguration::getAtomDerivative ( const unsigned & ider ) const

inlineinherited

Return the derivative wrt to the ith atom.

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

inlineprotected

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

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.

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

inlineprotected

Get the vector of displacement weights.

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

inherited

Return the name of this metric.

unsigned PLMD::ReferenceAtoms::getNumberOfAtoms ( ) const

inlineprotected

This returns how many atoms there should be.

unsigned PLMD::ReferenceAtoms::getNumberOfReferencePositions ( ) const

inlineprotected

This returns the number of reference atom positions.

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

inlinevirtualinherited

Get one of the referene arguments.

Reimplemented in PLMD::ReferenceArguments.

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

inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

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

inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

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

inlineprotected

Get the position of the ith atom.

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

inlineprotectedvirtual

Get the reference positions.

Reimplemented from PLMD::ReferenceConfiguration.

bool PLMD::ReferenceConfiguration::getVirial ( Tensor & virout ) const

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

double PLMD::ReferenceConfiguration::getWeight ( ) const

inlineinherited

Return the weight for this frame.

template<class T >

bool PLMD::ReferenceConfiguration::parse	(	const std::string &	key,
		T &	t,
		bool	ignore_missing = `false`
	)

inherited

Parse something from the pdb remarks.

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

protected

Read a list of atoms from the pdb input file.

void PLMD::ReferenceConfiguration::parseFlag	(	const std::string &	key,
		bool &	t
	)

inherited

Parse a flag.

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.

void PLMD::ReferenceConfiguration::print	(	OFile &	ofile,
		const double &	time,
		const double &	weight,
		const double &	old_norm
	)

inherited

Print a pdb file containing the reference configuration.

void PLMD::ReferenceConfiguration::print	(	OFile &	ofile,
		const std::string &	fmt
	)

inherited

void PLMD::ReferenceAtoms::printAtoms ( OFile & ofile ) const

Print the atomic positions.

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

pure virtualinherited

Do all local business for setting the configuration.

Implemented in PLMD::DRMSD, PLMD::MultiDomainRMSD, PLMD::SimpleRMSD, PLMD::OptimalRMSD, PLMD::FakeFrame, PLMD::SimpleRMSD, PLMD::EuclideanDistance, and PLMD::NormalizedEuclideanDistance.

void PLMD::ReferenceAtoms::readAtomsFromPDB ( const PDB & pdb )

protected

Read in the atoms from the pdb file.

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

inlineprotected

Get the atomic derivatives on the ith atom in the list.

void PLMD::ReferenceConfiguration::set ( const PDB & pdb )

virtualinherited

Set the reference configuration using a PDB.

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

protected

Add atom indices to list.

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

Set the indices of the reference atoms.

void PLMD::ReferenceConfiguration::setNamesAndAtomNumbers	(	const std::vector< AtomNumber > &	numbers,
		const std::vector< std::string > &	arg
	)

inherited

Set the atom numbers and the argument names.

void PLMD::ReferenceConfiguration::setNumberOfArguments ( const unsigned & n )

virtualinherited

Set the final number of arguments.

void PLMD::ReferenceConfiguration::setNumberOfAtoms ( const unsigned & n )

virtualinherited

Set the final number of atoms.

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

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 )

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

inlineinherited

Set the weight for this frame.

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

protected

This does the checks that are always required.

Friends And Related Function Documentation

friend class SingleDomainRMSD

friend

Member Data Documentation

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

private

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

std::vector<double> PLMD::ReferenceConfiguration::arg_ders

protectedinherited

Derivatives wrt to the arguments.

std::vector<Vector> PLMD::ReferenceConfiguration::atom_ders

protectedinherited

Derivatives wrt to the atoms.

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.

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

private

The indeces for setting derivatives.

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

private

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

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

private

The indices of the atoms in the pdb file.

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

private

The positions of the atoms in the reference configuration.

Tensor PLMD::ReferenceConfiguration::virial

protectedinherited

bool PLMD::ReferenceConfiguration::virialWasSet

protectedinherited

The virial contribution has to be stored.

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

reference/ReferenceAtoms.h
reference/ReferenceAtoms.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation