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
	MDAtomsTyped ()

void	double2MD (const double &d, void *m) const
	Convert a double to a pointer to an MD-real. More...

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

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

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

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

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

Vector	getMDforces (const unsigned index) const

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

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

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

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

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

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

void	setBox (void *)
	Set a pointer to the box array (3x3) in the MD code. More...

void	setc (void *m)
	Set a pointer to the charge array in the MD code. More...

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

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

void	setf (void *f)
	Set a pointer to the forces array in the MD code. More...

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

void	setm (void *m)
	Set a pointer to the mass array in the MD code. More...

void	setp (void *p)
	Set a pointer to the positions array in the MD code. More...

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

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

void	setVirial (void *)
	Set a pointer to the virial array (3x3) in the MD code. More...

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

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

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

void	updateVirial (const Tensor &) const
	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
T *	box

T *	c

std::map< std::string, T * >	extraCV

std::map< std::string, T * >	extraCVForce

T *	fx

T *	fy

T *	fz

T *	m

T *	px

T *	py

T *	pz

T	scaleb

T	scalec

T	scalef

T	scalem

T	scalep

T	scalev

int	stride

T *	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

Constructor & Destructor Documentation

◆ MDAtomsTyped()

template<class T >

PLMD::MDAtomsTyped< T >::MDAtomsTyped ( )

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 &	,
		void *
	)		const

inlinevirtual

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

Implements PLMD::MDAtomsBase.

◆ getBox()

template<class T >

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

virtual

Retrieve box as a plumed Tensor.

Implements PLMD::MDAtomsBase.

◆ getCharges()

template<class T >

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

virtual

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 )

inlinevirtual

Retrieve the value of an extra CV.

Implements PLMD::MDAtomsBase.

◆ getLocalPositions()

template<class T >

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

virtual

Retrieve local positions.

Implements PLMD::MDAtomsBase.

◆ getMasses()

template<class T >

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

virtual

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

inlinevirtual

Implements PLMD::MDAtomsBase.

◆ getPositions() [1/3]

template<class T >

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

virtual

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() [2/3]

template<class T >

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

virtual

Retrieve all atom positions from atom indices and local indices.

Implements PLMD::MDAtomsBase.

◆ getPositions() [3/3]

template<class T >

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

virtual

Retrieve all atom positions from index i to index j.

Implements PLMD::MDAtomsBase.

◆ getRealPrecision()

template<class T >

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

virtual

Get the size of MD-real.

Implements PLMD::MDAtomsBase.

◆ MD2double()

template<class T >

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

inlinevirtual

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

Implements PLMD::MDAtomsBase.

◆ rescaleForces()

template<class T >

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

virtual

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 ( void * )

virtual

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

Implements PLMD::MDAtomsBase.

◆ setc()

template<class T >

void PLMD::MDAtomsTyped< T >::setc ( void * m )

virtual

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,
		void *	p
	)

inlinevirtual

Set a pointer to an extra CV.

Implements PLMD::MDAtomsBase.

◆ setExtraCVForce()

template<class T >

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

inlinevirtual

Set a pointer to an extra CV force.

Implements PLMD::MDAtomsBase.

◆ setf() [1/2]

template<class T >

void PLMD::MDAtomsTyped< T >::setf ( void * f )

virtual

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	(	void *	f,
		int	i
	)

virtual

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

Implements PLMD::MDAtomsBase.

◆ setm()

template<class T >

void PLMD::MDAtomsTyped< T >::setm ( void * m )

virtual

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 ( void * p )

virtual

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	(	void *	p,
		int	i
	)

virtual

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
	)

virtual

Set internal and MD units.

Implements PLMD::MDAtomsBase.

◆ setVirial()

template<class T >

void PLMD::MDAtomsTyped< T >::setVirial ( void * )

virtual

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
	)

inlinevirtual

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 vector< int > &	index,
		const vector< Vector > &	f
	)

virtual

Increment the force on selected atoms.

The operation is done in such a way that f[index[i]] is added to the force on atom i

Implements PLMD::MDAtomsBase.

◆ updateForces() [2/2]

template<class T >

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

virtual

Increment the force on selected atoms.

The operation is done only for local atoms used in an action

Implements PLMD::MDAtomsBase.

◆ updateVirial()

template<class T >

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

virtual

Increment the virial by an amount v.

Implements PLMD::MDAtomsBase.

Member Data Documentation

◆ box

template<class T >

T* PLMD::MDAtomsTyped< T >::box

private

◆ c

template<class T >

T* PLMD::MDAtomsTyped< T >::c

private

◆ extraCV

template<class T >

std::map<std::string,T*> PLMD::MDAtomsTyped< T >::extraCV

private

◆ extraCVForce

template<class T >

std::map<std::string,T*> PLMD::MDAtomsTyped< T >::extraCVForce

private

◆ fx

template<class T >

T* PLMD::MDAtomsTyped< T >::fx

private

◆ fy

template<class T >

T* PLMD::MDAtomsTyped< T >::fy

private

◆ fz

template<class T >

T* PLMD::MDAtomsTyped< T >::fz

private

◆ m

template<class T >

T* PLMD::MDAtomsTyped< T >::m

private

◆ px

template<class T >

T* PLMD::MDAtomsTyped< T >::px

private

◆ py

template<class T >

T* PLMD::MDAtomsTyped< T >::py

private

◆ pz

template<class T >

T* PLMD::MDAtomsTyped< T >::pz

private

◆ scaleb

template<class T >

T PLMD::MDAtomsTyped< T >::scaleb

private

◆ scalec

template<class T >

T PLMD::MDAtomsTyped< T >::scalec

private

◆ scalef

template<class T >

T PLMD::MDAtomsTyped< T >::scalef

private

◆ scalem

template<class T >

T PLMD::MDAtomsTyped< T >::scalem

private

◆ scalep

template<class T >

T PLMD::MDAtomsTyped< T >::scalep

private

◆ scalev

template<class T >

T PLMD::MDAtomsTyped< T >::scalev

private

◆ stride

template<class T >

int PLMD::MDAtomsTyped< T >::stride

private

◆ virial

template<class T >

T* PLMD::MDAtomsTyped< T >::virial

private

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

core/MDAtoms.cpp

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

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

Constructor & Destructor Documentation

◆ MDAtomsTyped()

Member Function Documentation

◆ create()

◆ double2MD()

◆ getBox()

◆ getCharges()

◆ getExtraCV()

◆ getLocalPositions()

◆ getMasses()

◆ getMDforces()

◆ getPositions() [1/3]

◆ getPositions() [2/3]

◆ getPositions() [3/3]

◆ getRealPrecision()

◆ MD2double()

◆ rescaleForces()

◆ setBox()

◆ setc()

◆ setExtraCV()

◆ setExtraCVForce()

◆ setf() [1/2]

◆ setf() [2/2]

◆ setm()

◆ setp() [1/2]

◆ setp() [2/2]

◆ setUnits()

◆ setVirial()

◆ updateExtraCVForce()

◆ updateForces() [1/2]

◆ updateForces() [2/2]

◆ updateVirial()

Member Data Documentation

◆ box

◆ c

◆ extraCV

◆ extraCVForce

◆ fx

◆ fy

◆ fz

◆ m

◆ px

◆ py

◆ pz

◆ scaleb

◆ scalec

◆ scalef

◆ scalem

◆ scalep

◆ scalev

◆ stride

◆ virial

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