PLMD::Atoms Class Reference

Class containing atom related quantities from the MD code. More...

#include <Atoms.h>

Classes
class	DomainDecomposition

Public Member Functions
	Atoms (PlumedMain &plumed)
	~Atoms ()
void	init ()
void	share ()
void	shareAll ()
void	wait ()
void	updateForces ()
void	setRealPrecision (int)
int	getRealPrecision () const
void	setTimeStep (void *)
double	getTimeStep () const
void	setKbT (void *)
double	getKbT () const
void	setNatoms (int)
const int &	getNatoms () const
void	setCollectEnergy (bool b)
void	setDomainDecomposition (Communicator &)
void	setAtomsGatindex (int *)
void	setAtomsContiguous (int)
void	setAtomsNlocal (int)
void	startStep ()
void	setEnergy (void *)
void	setBox (void *)
void	setVirial (void *)
void	setPositions (void *)
void	setPositions (void *, int)
void	setForces (void *)
void	setForces (void *, int)
void	setMasses (void *)
void	setCharges (void *)
bool	chargesWereSet () const
bool	boxWasSet () const
void	MD2double (const void *m, double &d) const
void	double2MD (const double &d, void *m) const
void	createFullList (int *)
void	getFullList (int **)
void	clearFullList ()
void	add (const ActionAtomistic *)
void	remove (const ActionAtomistic *)
double	getEnergy () const
bool	isEnergyNeeded () const
void	setMDEnergyUnits (double d)
void	setMDLengthUnits (double d)
void	setMDTimeUnits (double d)
const Units &	getMDUnits ()
void	setUnits (const Units &u)
const Units &	getUnits ()
void	updateUnits ()
AtomNumber	addVirtualAtom (ActionWithVirtualAtom *)
void	removeVirtualAtom (ActionWithVirtualAtom *)
ActionWithVirtualAtom *	getVirtualAtomsAction (AtomNumber) const
bool	isVirtualAtom (AtomNumber) const
void	insertGroup (const std::string &name, const std::vector< AtomNumber > &a)
void	removeGroup (const std::string &name)
void	writeBinary (std::ostream &) const
void	readBinary (std::istream &)
double	getKBoltzmann () const
double	getMDKBoltzmann () const
bool	usingNaturalUnits () const
void	setNaturalUnits (bool n)
void	setMDNaturalUnits (bool n)

Private Member Functions
void	resizeVectors (unsigned)
void	share (const std::set< AtomNumber > &)

Private Attributes
int	natoms
std::vector< Vector >	positions
std::vector< Vector >	forces
std::vector< double >	masses
std::vector< double >	charges
std::vector < ActionWithVirtualAtom * >	virtualAtomsActions
Tensor	box
Pbc &	pbc
Tensor	virial
double	md_energy
double	energy
bool	dataCanBeSet
bool	collectEnergy
bool	energyHasBeenSet
unsigned	positionsHaveBeenSet
bool	massesHaveBeenSet
bool	chargesHaveBeenSet
bool	boxHasBeenSet
unsigned	forcesHaveBeenSet
bool	virialHasBeenSet
bool	massAndChargeOK
unsigned	shuffledAtoms
std::map< std::string, std::vector< AtomNumber > >	groups
std::vector< int >	fullList
MDAtomsBase *	mdatoms
PlumedMain &	plumed
Units	MDUnits
Units	units
bool	naturalUnits
bool	MDnaturalUnits
double	timestep
double	forceOnEnergy
double	kbT
std::vector< const ActionAtomistic * >	actions
std::vector< int >	gatindex
DomainDecomposition	dd

Friends
class	ActionAtomistic
class	ActionWithVirtualAtom

Detailed Description

Class containing atom related quantities from the MD code.

IT IS STILL UNDOCUMENTED. IT PROBABLY NEEDS A STRONG CLEANUP

Constructor & Destructor Documentation

PLMD::Atoms::Atoms

(

PlumedMain &

plumed

)

PLMD::Atoms::~Atoms

(

)

Member Function Documentation

void PLMD::Atoms::add

(

const ActionAtomistic *

a

)

AtomNumber PLMD::Atoms::addVirtualAtom

(

ActionWithVirtualAtom *

a

)

bool PLMD::Atoms::boxWasSet ( ) const

inline

bool PLMD::Atoms::chargesWereSet ( ) const

inline

void PLMD::Atoms::clearFullList

(

)

void PLMD::Atoms::createFullList

(

int *

n

)

void PLMD::Atoms::double2MD	(	const double &	d,
		void *	m
	)		const

double PLMD::Atoms::getEnergy ( ) const

inline

void PLMD::Atoms::getFullList

(

int **

x

)

double PLMD::Atoms::getKBoltzmann

(

)

const

double PLMD::Atoms::getKbT

(

)

const

double PLMD::Atoms::getMDKBoltzmann

(

)

const

const Units& PLMD::Atoms::getMDUnits ( )

inline

const int & PLMD::Atoms::getNatoms ( ) const

inline

int PLMD::Atoms::getRealPrecision

(

)

const

double PLMD::Atoms::getTimeStep

(

)

const

const Units& PLMD::Atoms::getUnits ( )

inline

ActionWithVirtualAtom * PLMD::Atoms::getVirtualAtomsAction ( AtomNumber  i ) const

inline

void PLMD::Atoms::init

(

)

void PLMD::Atoms::insertGroup	(	const std::string &	name,
		const std::vector< AtomNumber > &	a
	)

bool PLMD::Atoms::isEnergyNeeded ( ) const

inline

bool PLMD::Atoms::isVirtualAtom ( AtomNumber  i ) const

inline

void PLMD::Atoms::MD2double	(	const void *	m,
		double &	d
	)		const

void PLMD::Atoms::readBinary

(

std::istream &

i

)

void PLMD::Atoms::remove

(

const ActionAtomistic *

a

)

void PLMD::Atoms::removeGroup

(

const std::string &

name

)

void PLMD::Atoms::removeVirtualAtom

(

ActionWithVirtualAtom *

a

)

void PLMD::Atoms::resizeVectors ( unsigned  n )

private

void PLMD::Atoms::setAtomsContiguous

(

int

start

)

void PLMD::Atoms::setAtomsGatindex

(

int *

g

)

void PLMD::Atoms::setAtomsNlocal

(

int

n

)

void PLMD::Atoms::setBox

(

void *

p

)

void PLMD::Atoms::setCharges

(

void *

p

)

void PLMD::Atoms::setCollectEnergy ( bool  b )

inline

void PLMD::Atoms::setDomainDecomposition

(

Communicator &

comm

)

void PLMD::Atoms::setEnergy

(

void *

p

)

void PLMD::Atoms::setForces

(

void *

p

)

void PLMD::Atoms::setForces	(	void *	p,
		int	i
	)

void PLMD::Atoms::setKbT

(

void *

p

)

void PLMD::Atoms::setMasses

(

void *

p

)

void PLMD::Atoms::setMDEnergyUnits ( double  d )

inline

void PLMD::Atoms::setMDLengthUnits ( double  d )

inline

void PLMD::Atoms::setMDNaturalUnits ( bool  n )

inline

void PLMD::Atoms::setMDTimeUnits ( double  d )

inline

void PLMD::Atoms::setNatoms

(

int

n

)

void PLMD::Atoms::setNaturalUnits ( bool  n )

inline

void PLMD::Atoms::setPositions

(

void *

p

)

void PLMD::Atoms::setPositions	(	void *	p,
		int	i
	)

void PLMD::Atoms::setRealPrecision

(

int

p

)

void PLMD::Atoms::setTimeStep

(

void *

p

)

void PLMD::Atoms::setUnits ( const Units &  u )

inline

void PLMD::Atoms::setVirial

(

void *

p

)

void PLMD::Atoms::share ( const std::set< AtomNumber > &  unique )

private

void PLMD::Atoms::share

(

)

void PLMD::Atoms::shareAll

(

)

void PLMD::Atoms::startStep

(

)

void PLMD::Atoms::updateForces

(

)

void PLMD::Atoms::updateUnits

(

)

bool PLMD::Atoms::usingNaturalUnits ( ) const

inline

void PLMD::Atoms::wait

(

)

void PLMD::Atoms::writeBinary

(

std::ostream &

o

)

const

Friends And Related Function Documentation

friend class ActionAtomistic

friend

friend class ActionWithVirtualAtom

friend

Member Data Documentation

std::vector<const ActionAtomistic*> PLMD::Atoms::actions

private

Tensor PLMD::Atoms::box

private

bool PLMD::Atoms::boxHasBeenSet

private

std::vector<double> PLMD::Atoms::charges

private

bool PLMD::Atoms::chargesHaveBeenSet

private

bool PLMD::Atoms::collectEnergy

private

bool PLMD::Atoms::dataCanBeSet

private

DomainDecomposition PLMD::Atoms::dd

private

double PLMD::Atoms::energy

private

bool PLMD::Atoms::energyHasBeenSet

private

double PLMD::Atoms::forceOnEnergy

private

std::vector<Vector> PLMD::Atoms::forces

private

unsigned PLMD::Atoms::forcesHaveBeenSet

private

std::vector<int> PLMD::Atoms::fullList

private

std::vector<int> PLMD::Atoms::gatindex

private

std::map<std::string,std::vector<AtomNumber> > PLMD::Atoms::groups

private

double PLMD::Atoms::kbT

private

bool PLMD::Atoms::massAndChargeOK

private

std::vector<double> PLMD::Atoms::masses

private

bool PLMD::Atoms::massesHaveBeenSet

private

double PLMD::Atoms::md_energy

private

MDAtomsBase* PLMD::Atoms::mdatoms

private

bool PLMD::Atoms::MDnaturalUnits

private

Units PLMD::Atoms::MDUnits

private

int PLMD::Atoms::natoms

private

bool PLMD::Atoms::naturalUnits

private

Pbc& PLMD::Atoms::pbc

private

PlumedMain& PLMD::Atoms::plumed

private

std::vector<Vector> PLMD::Atoms::positions

private

unsigned PLMD::Atoms::positionsHaveBeenSet

private

unsigned PLMD::Atoms::shuffledAtoms

private

double PLMD::Atoms::timestep

private

Units PLMD::Atoms::units

private

Tensor PLMD::Atoms::virial

private

bool PLMD::Atoms::virialHasBeenSet

private

std::vector<ActionWithVirtualAtom*> PLMD::Atoms::virtualAtomsActions

private

---

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

• core/Atoms.h
• core/Atoms.cpp