Class containing the pointers to the MD data It is templated so that single and double precision versions coexist IT IS STILL UNDOCUMENTED. More...

Inheritance diagram for PLMD::MDAtomsTyped< T >:

[legend]

Public Member Functions
void	double2MD (const double &d, const TypesafePtr &m) const override
	Convert a double to a pointer to an MD-real. More...

void	getBox (Tensor &) const override
	Retrieve box as a plumed Tensor. More...

void	getCharges (const std::vector< int > &index, std::vector< double > &) const override
	Retrieve selected charges. More...

double	getExtraCV (const std::string &name) override
	Retrieve the value of an extra CV. More...

void	getLocalPositions (std::vector< Vector > &p) const override
	Retrieve local positions. More...

void	getMasses (const std::vector< int > &index, std::vector< double > &) const override
	Retrieve selected masses. More...

Vector	getMDforces (const unsigned index) const override

void	getPositions (const std::set< AtomNumber > &index, const std::vector< unsigned > &i, std::vector< Vector > &positions) const override
	Retrieve all atom positions from atom indices and local indices. More...

void	getPositions (const std::vector< int > &index, std::vector< Vector > &positions) const override
	Retrieve selected positions. More...

void	getPositions (unsigned j, unsigned k, std::vector< Vector > &positions) const override
	Retrieve all atom positions from index i to index j. More...

unsigned	getRealPrecision () const override
	Get the size of MD-real. More...

void	MD2double (const TypesafePtr &m, double &d) const override
	Convert a pointer to an MD-real to a double. More...

void	rescaleForces (const std::vector< int > &index, double factor) override
	Rescale all the forces, including the virial. More...

void	setBox (const TypesafePtr &) override
	Set a pointer to the box array (3x3) in the MD code. More...

void	setc (const TypesafePtr &m) override
	Set a pointer to the charge array in the MD code. More...

void	setExtraCV (const std::string &name, const TypesafePtr &p) override
	Set a pointer to an extra CV. More...

void	setExtraCVForce (const std::string &name, const TypesafePtr &p) override
	Set a pointer to an extra CV force. More...

void	setf (const TypesafePtr &f) override
	Set a pointer to the forces array in the MD code. More...

void	setf (const TypesafePtr &f, int i) override
	Set a pointer to the force array in the MD code. More...

void	setm (const TypesafePtr &m) override
	Set a pointer to the mass array in the MD code. More...

void	setp (const TypesafePtr &p) override
	Set a pointer to the positions array in the MD code. More...

void	setp (const TypesafePtr &p, int i) override
	Set a pointer to the position array in the MD code. More...

void	setUnits (const Units &, const Units &) override
	Set internal and MD units. More...

void	setVirial (const TypesafePtr &) override
	Set a pointer to the virial array (3x3) in the MD code. More...

void	updateExtraCVForce (const std::string &name, double f) override
	Update the value of an extra CV force. More...

void	updateForces (const std::set< AtomNumber > &index, const std::vector< unsigned > &i, const std::vector< Vector > &forces) override
	Increment the force on selected atoms. More...

void	updateForces (const std::vector< int > &index, const std::vector< Vector > &) override
	Increment the force on selected atoms. More...

void	updateVirial (const Tensor &) const override
	Increment the virial by an amount v. More...

Static Public Member Functions
static std::unique_ptr< MDAtomsBase >	create (unsigned n)
	Creates an MDAtomsTyped<T> object such that sizeof(T)==n. More...

Private Attributes
TypesafePtr	box

TypesafePtr	c

std::map< std::string, TypesafePtr >	extraCV

std::map< std::string, TypesafePtr >	extraCVForce

TypesafePtr	f

TypesafePtr	fx

TypesafePtr	fy

TypesafePtr	fz

TypesafePtr	m

TypesafePtr	p

TypesafePtr	px

TypesafePtr	py

TypesafePtr	pz

T	scaleb =1.0

T	scalec =1.0

T	scalef =1.0

T	scalem =1.0

T	scalep =1.0

T	scalev =1.0

TypesafePtr	virial

Detailed Description

template<class T>
class PLMD::MDAtomsTyped< T >

Class containing the pointers to the MD data It is templated so that single and double precision versions coexist IT IS STILL UNDOCUMENTED.

IT PROBABLY NEEDS A STRONG CLEANUP

Member Function Documentation

◆ create()

std::unique_ptr< MDAtomsBase > PLMD::MDAtomsBase::create ( unsigned n )

staticinherited

Creates an MDAtomsTyped<T> object such that sizeof(T)==n.

◆ double2MD()

template<class T >

void PLMD::MDAtomsTyped< T >::double2MD	(	const double &	,
		const TypesafePtr &
	)		const

inlineoverridevirtual

Convert a double to a pointer to an MD-real.

Implements PLMD::MDAtomsBase.

◆ getBox()

template<class T >

void PLMD::MDAtomsTyped< T >::getBox ( Tensor & ) const

overridevirtual

Retrieve box as a plumed Tensor.

Implements PLMD::MDAtomsBase.

◆ getCharges()

template<class T >

void PLMD::MDAtomsTyped< T >::getCharges	(	const std::vector< int > &	index,
		std::vector< double > &	c
	)		const

overridevirtual

Retrieve selected charges.

The operation is done in such a way that c[index[i]] is equal to the charge of atom i

Implements PLMD::MDAtomsBase.

◆ getExtraCV()

template<class T >

double PLMD::MDAtomsTyped< T >::getExtraCV ( const std::string & name )

inlineoverridevirtual

Retrieve the value of an extra CV.

Implements PLMD::MDAtomsBase.

◆ getLocalPositions()

template<class T >

void PLMD::MDAtomsTyped< T >::getLocalPositions ( std::vector< Vector > & p ) const

overridevirtual

Retrieve local positions.

Implements PLMD::MDAtomsBase.

◆ getMasses()

template<class T >

void PLMD::MDAtomsTyped< T >::getMasses	(	const std::vector< int > &	index,
		std::vector< double > &	m
	)		const

overridevirtual

Retrieve selected masses.

The operation is done in such a way that m[index[i]] is equal to the mass of atom i

Implements PLMD::MDAtomsBase.

◆ getMDforces()

template<class T >

Vector PLMD::MDAtomsTyped< T >::getMDforces ( const unsigned index ) const

inlineoverridevirtual

Implements PLMD::MDAtomsBase.

◆ getPositions() [1/3]

template<class T >

void PLMD::MDAtomsTyped< T >::getPositions	(	const std::set< AtomNumber > &	index,
		const std::vector< unsigned > &	i,
		std::vector< Vector > &	p
	)		const

overridevirtual

Retrieve all atom positions from atom indices and local indices.

Implements PLMD::MDAtomsBase.

◆ getPositions() [2/3]

template<class T >

void PLMD::MDAtomsTyped< T >::getPositions	(	const std::vector< int > &	index,
		std::vector< Vector > &	p
	)		const

overridevirtual

Retrieve selected positions.

The operation is done in such a way that p[index[i]] is equal to the coordinates of atom i

Implements PLMD::MDAtomsBase.

◆ getPositions() [3/3]

template<class T >

void PLMD::MDAtomsTyped< T >::getPositions	(	unsigned	i,
		unsigned	j,
		std::vector< Vector > &	p
	)		const

overridevirtual

Retrieve all atom positions from index i to index j.

Implements PLMD::MDAtomsBase.

◆ getRealPrecision()

template<class T >

unsigned PLMD::MDAtomsTyped< T >::getRealPrecision ( ) const

overridevirtual

Get the size of MD-real.

Implements PLMD::MDAtomsBase.

◆ MD2double()

template<class T >

void PLMD::MDAtomsTyped< T >::MD2double	(	const TypesafePtr &	,
		double &
	)		const

inlineoverridevirtual

Convert a pointer to an MD-real to a double.

Implements PLMD::MDAtomsBase.

◆ rescaleForces()

template<class T >

void PLMD::MDAtomsTyped< T >::rescaleForces	(	const std::vector< int > &	index,
		double	factor
	)

overridevirtual

Rescale all the forces, including the virial.

It is applied to all atoms with local index going from 0 to index.size()-1

Implements PLMD::MDAtomsBase.

◆ setBox()

template<class T >

void PLMD::MDAtomsTyped< T >::setBox ( const TypesafePtr & )

overridevirtual

Set a pointer to the box array (3x3) in the MD code.

Implements PLMD::MDAtomsBase.

◆ setc()

template<class T >

void PLMD::MDAtomsTyped< T >::setc ( const TypesafePtr & m )

overridevirtual

Set a pointer to the charge array in the MD code.

Implements PLMD::MDAtomsBase.

◆ setExtraCV()

template<class T >

void PLMD::MDAtomsTyped< T >::setExtraCV	(	const std::string &	name,
		const TypesafePtr &	p
	)

inlineoverridevirtual

Set a pointer to an extra CV.

Implements PLMD::MDAtomsBase.

◆ setExtraCVForce()

template<class T >

void PLMD::MDAtomsTyped< T >::setExtraCVForce	(	const std::string &	name,
		const TypesafePtr &	p
	)

inlineoverridevirtual

Set a pointer to an extra CV force.

Implements PLMD::MDAtomsBase.

◆ setf() [1/2]

template<class T >

void PLMD::MDAtomsTyped< T >::setf ( const TypesafePtr & f )

overridevirtual

Set a pointer to the forces array in the MD code.

Implements PLMD::MDAtomsBase.

◆ setf() [2/2]

template<class T >

void PLMD::MDAtomsTyped< T >::setf	(	const TypesafePtr &	f,
		int	i
	)

overridevirtual

Set a pointer to the force array in the MD code.

Implements PLMD::MDAtomsBase.

◆ setm()

template<class T >

void PLMD::MDAtomsTyped< T >::setm ( const TypesafePtr & m )

overridevirtual

Set a pointer to the mass array in the MD code.

Implements PLMD::MDAtomsBase.

◆ setp() [1/2]

template<class T >

void PLMD::MDAtomsTyped< T >::setp ( const TypesafePtr & p )

overridevirtual

Set a pointer to the positions array in the MD code.

Implements PLMD::MDAtomsBase.

◆ setp() [2/2]

template<class T >

void PLMD::MDAtomsTyped< T >::setp	(	const TypesafePtr &	p,
		int	i
	)

overridevirtual

Set a pointer to the position array in the MD code.

Implements PLMD::MDAtomsBase.

◆ setUnits()

template<class T >

void PLMD::MDAtomsTyped< T >::setUnits	(	const Units &	units,
		const Units &	MDUnits
	)

overridevirtual

Set internal and MD units.

Implements PLMD::MDAtomsBase.

◆ setVirial()

template<class T >

void PLMD::MDAtomsTyped< T >::setVirial ( const TypesafePtr & )

overridevirtual

Set a pointer to the virial array (3x3) in the MD code.

Implements PLMD::MDAtomsBase.

◆ updateExtraCVForce()

template<class T >

void PLMD::MDAtomsTyped< T >::updateExtraCVForce	(	const std::string &	name,
		double	f
	)

inlineoverridevirtual

Update the value of an extra CV force.

Todo:: check if this should also be scaled when acting on total energy

Implements PLMD::MDAtomsBase.

◆ updateForces() [1/2]

template<class T >

void PLMD::MDAtomsTyped< T >::updateForces	(	const std::set< AtomNumber > &	index,
		const std::vector< unsigned > &	i,
		const std::vector< Vector > &	forces
	)