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	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)
Vector &	modifyPosition (AtomNumber i)

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
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
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

Definition at line 45 of file Atoms.h.

Constructor & Destructor Documentation

PLMD::Atoms::Atoms

(

PlumedMain &

plumed

)

Definition at line 37 of file Atoms.cpp.

PLMD::Atoms::~Atoms

(

)

Definition at line 58 of file Atoms.cpp.

Member Function Documentation

void PLMD::Atoms::add

(

const ActionAtomistic *

a

)

Definition at line 261 of file Atoms.cpp.

AtomNumber PLMD::Atoms::addVirtualAtom

(

ActionWithVirtualAtom *

a

)

Definition at line 370 of file Atoms.cpp.

bool PLMD::Atoms::boxWasSet ( ) const

inline

Definition at line 226 of file Atoms.h.

bool PLMD::Atoms::chargesWereSet ( ) const

inline

Definition at line 221 of file Atoms.h.

void PLMD::Atoms::clearFullList

(

)

Definition at line 346 of file Atoms.cpp.

void PLMD::Atoms::createFullList

(

int *

n

)

Definition at line 330 of file Atoms.cpp.

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

Definition at line 314 of file Atoms.cpp.

double PLMD::Atoms::getEnergy ( ) const

inline

Definition at line 172 of file Atoms.h.

void PLMD::Atoms::getFullList

(

int **

x

)

Definition at line 341 of file Atoms.cpp.

double PLMD::Atoms::getKBoltzmann

(

)

const

Definition at line 407 of file Atoms.cpp.

double PLMD::Atoms::getMDKBoltzmann

(

)

const

Definition at line 412 of file Atoms.cpp.

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

inline

Definition at line 179 of file Atoms.h.

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

inline

Definition at line 201 of file Atoms.h.

int PLMD::Atoms::getRealPrecision

(

)

const

Definition at line 307 of file Atoms.cpp.

double PLMD::Atoms::getTimeStep

(

)

const

Definition at line 326 of file Atoms.cpp.

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

inline

Definition at line 181 of file Atoms.h.

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

inline

Definition at line 211 of file Atoms.h.

void PLMD::Atoms::init

(

)

Definition at line 350 of file Atoms.cpp.

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

Definition at line 384 of file Atoms.cpp.

bool PLMD::Atoms::isEnergyNeeded ( ) const

inline

Definition at line 174 of file Atoms.h.

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

inline

Definition at line 206 of file Atoms.h.

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

Definition at line 311 of file Atoms.cpp.

Vector& PLMD::Atoms::modifyPosition ( AtomNumber  i )

inline

Definition at line 197 of file Atoms.h.

void PLMD::Atoms::readBinary

(

std::istream &

i

)

Definition at line 400 of file Atoms.cpp.

void PLMD::Atoms::remove

(

const ActionAtomistic *

a

)

Definition at line 265 of file Atoms.cpp.

void PLMD::Atoms::removeGroup

(

const std::string &

name

)

Definition at line 389 of file Atoms.cpp.

void PLMD::Atoms::removeVirtualAtom

(

ActionWithVirtualAtom *

a

)

Definition at line 377 of file Atoms.cpp.

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

private

Definition at line 363 of file Atoms.cpp.

void PLMD::Atoms::setAtomsContiguous

(

int

start

)

Definition at line 296 of file Atoms.cpp.

void PLMD::Atoms::setAtomsGatindex

(

int *

g

)

Definition at line 289 of file Atoms.cpp.

void PLMD::Atoms::setAtomsNlocal

(

int

n

)

Definition at line 278 of file Atoms.cpp.

void PLMD::Atoms::setBox

(

void *

p

)

Definition at line 72 of file Atoms.cpp.

void PLMD::Atoms::setCharges

(

void *

p

)

Definition at line 90 of file Atoms.cpp.

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

inline

Definition at line 142 of file Atoms.h.

void PLMD::Atoms::setDomainDecomposition

(

Communicator &

comm

)

Definition at line 359 of file Atoms.cpp.

void PLMD::Atoms::setEnergy

(

void *

p

)

Definition at line 102 of file Atoms.cpp.

void PLMD::Atoms::setForces

(

void *

p

)

Definition at line 109 of file Atoms.cpp.

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

Definition at line 122 of file Atoms.cpp.

void PLMD::Atoms::setMasses

(

void *

p

)

Definition at line 83 of file Atoms.cpp.

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

inline

Definition at line 176 of file Atoms.h.

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

inline

Definition at line 177 of file Atoms.h.

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

inline

Definition at line 196 of file Atoms.h.

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

inline

Definition at line 178 of file Atoms.h.

void PLMD::Atoms::setNatoms

(

int

n

)

Definition at line 250 of file Atoms.cpp.

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

inline

Definition at line 195 of file Atoms.h.

void PLMD::Atoms::setPositions

(

void *

p

)

Definition at line 77 of file Atoms.cpp.

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

Definition at line 116 of file Atoms.cpp.

void PLMD::Atoms::setRealPrecision

(

int

p

)

Definition at line 302 of file Atoms.cpp.

void PLMD::Atoms::setTimeStep

(

void *

p

)

Definition at line 322 of file Atoms.cpp.

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

inline

Definition at line 180 of file Atoms.h.

void PLMD::Atoms::setVirial

(

void *

p

)

Definition at line 96 of file Atoms.cpp.

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

private

Definition at line 145 of file Atoms.cpp.

void PLMD::Atoms::share

(

)

Definition at line 128 of file Atoms.cpp.

void PLMD::Atoms::shareAll

(

)

Definition at line 138 of file Atoms.cpp.

void PLMD::Atoms::startStep

(

)

Definition at line 66 of file Atoms.cpp.

void PLMD::Atoms::updateForces

(

)

Definition at line 237 of file Atoms.cpp.

void PLMD::Atoms::updateUnits

(

)

Definition at line 318 of file Atoms.cpp.

bool PLMD::Atoms::usingNaturalUnits ( ) const

inline

Definition at line 216 of file Atoms.h.

void PLMD::Atoms::wait

(

)

Definition at line 204 of file Atoms.cpp.

void PLMD::Atoms::writeBinary

(

std::ostream &

o

)

const

Definition at line 394 of file Atoms.cpp.

Friends And Related Function Documentation

friend class ActionAtomistic

friend

Definition at line 47 of file Atoms.h.

friend class ActionWithVirtualAtom

friend

Definition at line 48 of file Atoms.h.

Member Data Documentation

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

private

Definition at line 92 of file Atoms.h.

Tensor PLMD::Atoms::box

private

Definition at line 55 of file Atoms.h.

bool PLMD::Atoms::boxHasBeenSet

private

Definition at line 69 of file Atoms.h.

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

private

Definition at line 53 of file Atoms.h.

bool PLMD::Atoms::chargesHaveBeenSet

private

Definition at line 68 of file Atoms.h.

bool PLMD::Atoms::collectEnergy

private

Definition at line 64 of file Atoms.h.

bool PLMD::Atoms::dataCanBeSet

private

Definition at line 63 of file Atoms.h.

DomainDecomposition PLMD::Atoms::dd

private

Definition at line 117 of file Atoms.h.

double PLMD::Atoms::energy

private

Definition at line 61 of file Atoms.h.

bool PLMD::Atoms::energyHasBeenSet

private

Definition at line 65 of file Atoms.h.

double PLMD::Atoms::forceOnEnergy

private

Definition at line 90 of file Atoms.h.

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

private

Definition at line 51 of file Atoms.h.

unsigned PLMD::Atoms::forcesHaveBeenSet

private

Definition at line 70 of file Atoms.h.

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

private

Definition at line 77 of file Atoms.h.

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

private

Definition at line 93 of file Atoms.h.

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

private

Definition at line 73 of file Atoms.h.

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

private

Definition at line 52 of file Atoms.h.

bool PLMD::Atoms::massesHaveBeenSet

private

Definition at line 67 of file Atoms.h.

double PLMD::Atoms::md_energy

private

Definition at line 59 of file Atoms.h.

MDAtomsBase* PLMD::Atoms::mdatoms

private

Definition at line 79 of file Atoms.h.

bool PLMD::Atoms::MDnaturalUnits

private

Definition at line 87 of file Atoms.h.

Units PLMD::Atoms::MDUnits

private

Definition at line 83 of file Atoms.h.

int PLMD::Atoms::natoms

private

Definition at line 49 of file Atoms.h.

bool PLMD::Atoms::naturalUnits

private

Definition at line 86 of file Atoms.h.

Pbc& PLMD::Atoms::pbc

private

Definition at line 56 of file Atoms.h.

PlumedMain& PLMD::Atoms::plumed

private

Definition at line 81 of file Atoms.h.

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

private

Definition at line 50 of file Atoms.h.

unsigned PLMD::Atoms::positionsHaveBeenSet

private

Definition at line 66 of file Atoms.h.

double PLMD::Atoms::timestep

private

Definition at line 89 of file Atoms.h.

Units PLMD::Atoms::units

private

Definition at line 84 of file Atoms.h.

Tensor PLMD::Atoms::virial

private

Definition at line 57 of file Atoms.h.

bool PLMD::Atoms::virialHasBeenSet

private

Definition at line 71 of file Atoms.h.

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

private

Definition at line 54 of file Atoms.h.

---

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

• core/Atoms.h
• core/Atoms.cpp