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
const long int &	getDdStep () const
const std::vector< int > &	getGatindex () const
const Pbc &	getPbc () const
void	getLocalPositions (std::vector< Vector > &)
void	getLocalForces (std::vector< Vector > &)
const Tensor &	getVirial () const
void	setCollectEnergy (bool b)
void	setDomainDecomposition (Communicator &)
void	setAtomsGatindex (int *, bool)
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
bool	zeroallforces
	if set to true, all the forces in the global array are zeroes at every step. More...
double	kbT
std::vector< const ActionAtomistic * >	actions
std::vector< int >	gatindex
bool	asyncSent
bool	atomsNeeded
DomainDecomposition	dd
long int	ddStep

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 )

explicit

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

const long int & PLMD::Atoms::getDdStep ( ) const

inline

double PLMD::Atoms::getEnergy ( ) const

inline

void PLMD::Atoms::getFullList

(

int **

x

)

const std::vector< int > & PLMD::Atoms::getGatindex ( ) const

inline

double PLMD::Atoms::getKBoltzmann

(

)

const

double PLMD::Atoms::getKbT

(

)

const

void PLMD::Atoms::getLocalForces

(

std::vector< Vector > &

localForces

)

void PLMD::Atoms::getLocalPositions

(

std::vector< Vector > &

localPositions

)

double PLMD::Atoms::getMDKBoltzmann

(

)

const

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

inline

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

inline

const Pbc & PLMD::Atoms::getPbc ( ) const

inline

int PLMD::Atoms::getRealPrecision

(

)

const

double PLMD::Atoms::getTimeStep

(

)

const

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

inline

const Tensor & PLMD::Atoms::getVirial ( ) const

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,
		bool	fortran
	)

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

bool PLMD::Atoms::asyncSent

private

bool PLMD::Atoms::atomsNeeded

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

long int PLMD::Atoms::ddStep

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

bool PLMD::Atoms::zeroallforces

private

if set to true, all the forces in the global array are zeroes at every step.

It should not be necessary in general, but it is for actions accessing to modifyGlobalForce() (e.g. FIT_TO_TEMPLATE).

---

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

• core/Atoms.h
• core/Atoms.cpp