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.
void	getBox (Tensor &) const override
	Retrieve box as a plumed Tensor.
void	getCharges (const std::vector< int > &index, std::vector< double > &) const override
	Retrieve selected charges.
double	getExtraCV (const std::string &name) override
	Retrieve the value of an extra CV.
void	getLocalPositions (std::vector< Vector > &p) const override
	Retrieve local positions.
void	getMasses (const std::vector< int > &index, std::vector< double > &) const override
	Retrieve selected masses.
Vector	getMDforces (const unsigned index) const override
void	getPositions (const std::vector< AtomNumber > &index, const std::vector< unsigned > &i, std::vector< Vector > &positions) const override
	Retrieve all atom positions from atom indices and local indices.
void	getPositions (const std::vector< int > &index, std::vector< Vector > &positions) const override
	Retrieve selected positions.
void	getPositions (unsigned j, unsigned k, std::vector< Vector > &positions) const override
	Retrieve all atom positions from index i to index j.
unsigned	getRealPrecision () const override
	Get the size of MD-real.
bool	isExtraCVNeeded (const std::string &name) const override
	Check if an extra CV is needed.
void	MD2double (const TypesafePtr &m, double &d) const override
	Convert a pointer to an MD-real to a double.
void	rescaleForces (const std::vector< int > &index, double factor) override
	Rescale all the forces, including the virial.
void	resetExtraCVNeeded () override
	Set all extra CV as not needed (at beginning of the step).
void	setBox (const TypesafePtr &) override
	Set a pointer to the box array (3x3) in the MD code.
void	setc (const TypesafePtr &m) override
	Set a pointer to the charge array in the MD code.
void	setExtraCV (const std::string &name, const TypesafePtr &p) override
	Set a pointer to an extra CV.
void	setExtraCVForce (const std::string &name, const TypesafePtr &p) override
	Set a pointer to an extra CV force.
void	setExtraCVNeeded (const std::string &name, bool needed=true) override
	Inform the MD code that an extra CV is needed.
void	setf (const TypesafePtr &f) override
	Set a pointer to the forces array in the MD code.
void	setf (const TypesafePtr &f, int i) override
	Set a pointer to the force array in the MD code.
void	setm (const TypesafePtr &m) override
	Set a pointer to the mass array in the MD code.
void	setp (const TypesafePtr &p) override
	Set a pointer to the positions array in the MD code.
void	setp (const TypesafePtr &p, int i) override
	Set a pointer to the position array in the MD code.
void	setUnits (const Units &, const Units &) override
	Set internal and MD units.
void	setVirial (const TypesafePtr &) override
	Set a pointer to the virial array (3x3) in the MD code.
void	updateExtraCVForce (const std::string &name, double f) override
	Update the value of an extra CV force.
void	updateForces (const std::vector< AtomNumber > &index, const std::vector< unsigned > &i, const std::vector< Vector > &forces) override
	Increment the force on selected atoms.
void	updateForces (const std::vector< int > &index, const std::vector< Vector > &) override
	Increment the force on selected atoms.
void	updateVirial (const Tensor &) const override
	Increment the virial by an amount v.

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

Private Attributes
TypesafePtr	box
TypesafePtr	c
std::map< std::string, TypesafePtr >	extraCV
std::map< std::string, TypesafePtr >	extraCVForce
std::map< std::string, bool >	extraCVNeeded
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 &	d,
		const TypesafePtr &	m ) 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::vector< 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.

◆ isExtraCVNeeded()

template<class T>

bool PLMD::MDAtomsTyped< T >::isExtraCVNeeded ( const std::string & name ) const

inlineoverridevirtual

Check if an extra CV is needed.

Implements PLMD::MDAtomsBase.

◆ MD2double()

template<class T>

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

◆ resetExtraCVNeeded()

template<class T>

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

inlineoverridevirtual

Set all extra CV as not needed (at beginning of the step).

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.

◆ setExtraCVNeeded()

template<class T>

void PLMD::MDAtomsTyped< T >::setExtraCVNeeded	(	const std::string &	name,
		bool	needed = true )

inlineoverridevirtual

Inform the MD code that an extra CV is needed.

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::vector< AtomNumber > &	index,
		const std::vector< unsigned > &	i,
		const std::vector< Vector > &	forces )