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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Private Attributes
double	scalep

double	scalef

double	scaleb

double	scalev

int	stride

T *	m

T *	c

T *	px

T *	py

T *	pz

T *	fx

T *	fy

T *	fz

T *	box

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

Definition at line 36 of file MDAtoms.cpp.

Constructor & Destructor Documentation

template<class T >

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

Definition at line 206 of file MDAtoms.cpp.

Member Function Documentation

MDAtomsBase * PLMD::MDAtomsBase::create ( unsigned n )

staticinherited

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

Definition at line 224 of file MDAtoms.cpp.

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.

Definition at line 62 of file MDAtoms.cpp.

template<class T >

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

virtual

Retrieve box as a plumed Tensor.

Implements PLMD::MDAtomsBase.

Definition at line 88 of file MDAtoms.cpp.

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.

Definition at line 109 of file MDAtoms.cpp.

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.

Definition at line 103 of file MDAtoms.cpp.

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.

Definition at line 94 of file MDAtoms.cpp.

template<class T >

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

virtual

Get the size of MD-real.

Implements PLMD::MDAtomsBase.

Definition at line 139 of file MDAtoms.cpp.

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.

Definition at line 59 of file MDAtoms.cpp.

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

Attention: the virial is not scaled indeed... is it a bug??

Implements PLMD::MDAtomsBase.

Definition at line 129 of file MDAtoms.cpp.

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.

Definition at line 154 of file MDAtoms.cpp.

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.

Definition at line 201 of file MDAtoms.cpp.

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.

Definition at line 160 of file MDAtoms.cpp.

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.

Definition at line 186 of file MDAtoms.cpp.

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.

Definition at line 196 of file MDAtoms.cpp.

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.

Definition at line 144 of file MDAtoms.cpp.

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.

Definition at line 170 of file MDAtoms.cpp.

template<class T >

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

virtual

Set internal and MD units.

Implements PLMD::MDAtomsBase.

Definition at line 76 of file MDAtoms.cpp.

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.

Definition at line 180 of file MDAtoms.cpp.

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.

Definition at line 120 of file MDAtoms.cpp.

template<class T >

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

virtual

Increment the virial by an amount v.

Implements PLMD::MDAtomsBase.

Definition at line 115 of file MDAtoms.cpp.

Member Data Documentation

template<class T >

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

private

Definition at line 46 of file MDAtoms.cpp.

template<class T >

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

private

Definition at line 43 of file MDAtoms.cpp.

template<class T >

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

private

Definition at line 45 of file MDAtoms.cpp.

template<class T >

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

private

Definition at line 45 of file MDAtoms.cpp.

template<class T >

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

private

Definition at line 45 of file MDAtoms.cpp.

template<class T >

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

private

Definition at line 42 of file MDAtoms.cpp.

template<class T >

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

private

Definition at line 44 of file MDAtoms.cpp.

template<class T >

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

private

Definition at line 44 of file MDAtoms.cpp.

template<class T >

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

private

Definition at line 44 of file MDAtoms.cpp.

template<class T >

double PLMD::MDAtomsTyped< T >::scaleb

private

Definition at line 40 of file MDAtoms.cpp.

template<class T >

double PLMD::MDAtomsTyped< T >::scalef

private

Definition at line 39 of file MDAtoms.cpp.

template<class T >

double PLMD::MDAtomsTyped< T >::scalep

private

Definition at line 39 of file MDAtoms.cpp.

template<class T >

double PLMD::MDAtomsTyped< T >::scalev

private

Definition at line 40 of file MDAtoms.cpp.

template<class T >

int PLMD::MDAtomsTyped< T >::stride

private

Definition at line 41 of file MDAtoms.cpp.

template<class T >

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

private

Definition at line 47 of file MDAtoms.cpp.

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

Member Function Documentation

Member Data Documentation

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