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	getLocalMasses (std::vector< double > &)
void	getLocalPositions (std::vector< Vector > &)
void	getLocalForces (std::vector< Vector > &)
void	getLocalMDForces (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 (ActionAtomistic *)
void	remove (ActionAtomistic *)
double	getEnergy () const
bool	isEnergyNeeded () const
void	setMDEnergyUnits (double d)
void	setMDLengthUnits (double d)
void	setMDTimeUnits (double d)
void	setMDChargeUnits (double d)
void	setMDMassUnits (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::set< AtomNumber >	unique
std::vector< unsigned >	uniq_index
std::vector< int >	g2l
	Map global indexes to local indexes E.g. More...
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< 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

Atoms()

PLMD::Atoms::Atoms ( PlumedMain &  plumed )

explicit

~Atoms()

PLMD::Atoms::~Atoms

(

)

Member Function Documentation

add()

void PLMD::Atoms::add

(

ActionAtomistic *

a

)

addVirtualAtom()

AtomNumber PLMD::Atoms::addVirtualAtom

(

ActionWithVirtualAtom *

a

)

boxWasSet()

bool PLMD::Atoms::boxWasSet ( ) const

inline

chargesWereSet()

bool PLMD::Atoms::chargesWereSet ( ) const

inline

clearFullList()

void PLMD::Atoms::clearFullList

(

)

createFullList()

void PLMD::Atoms::createFullList

(

int *

n

)

double2MD()

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

getDdStep()

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

inline

getEnergy()

double PLMD::Atoms::getEnergy ( ) const

inline

getFullList()

void PLMD::Atoms::getFullList

(

int **

x

)

getGatindex()

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

inline

getKBoltzmann()

double PLMD::Atoms::getKBoltzmann

(

)

const

getKbT()

double PLMD::Atoms::getKbT

(

)

const

getLocalForces()

void PLMD::Atoms::getLocalForces

(

std::vector< Vector > &

localForces

)

getLocalMasses()

void PLMD::Atoms::getLocalMasses

(

std::vector< double > &

localMasses

)

getLocalMDForces()

void PLMD::Atoms::getLocalMDForces

(

std::vector< Vector > &

localForces

)

getLocalPositions()

void PLMD::Atoms::getLocalPositions

(

std::vector< Vector > &

localPositions

)

getMDKBoltzmann()

double PLMD::Atoms::getMDKBoltzmann

(

)

const

getMDUnits()

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

inline

getNatoms()

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

inline

getPbc()

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

inline

getRealPrecision()

int PLMD::Atoms::getRealPrecision

(

)

const

getTimeStep()

double PLMD::Atoms::getTimeStep

(

)

const

getUnits()

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

inline

getVirial()

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

inline

getVirtualAtomsAction()

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

inline

init()

void PLMD::Atoms::init

(

)

insertGroup()

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

isEnergyNeeded()

bool PLMD::Atoms::isEnergyNeeded ( ) const

inline

isVirtualAtom()

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

inline

MD2double()

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

readBinary()

void PLMD::Atoms::readBinary

(

std::istream &

i

)

remove()

void PLMD::Atoms::remove

(

ActionAtomistic *

a

)

removeGroup()

void PLMD::Atoms::removeGroup

(

const std::string &

name

)

removeVirtualAtom()

void PLMD::Atoms::removeVirtualAtom

(

ActionWithVirtualAtom *

a

)

resizeVectors()

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

private

setAtomsContiguous()

void PLMD::Atoms::setAtomsContiguous

(

int

start

)

setAtomsGatindex()

void PLMD::Atoms::setAtomsGatindex	(	int *	g,
		bool	fortran
	)

setAtomsNlocal()

void PLMD::Atoms::setAtomsNlocal

(

int

n

)

setBox()

void PLMD::Atoms::setBox

(

void *

p

)

setCharges()

void PLMD::Atoms::setCharges

(

void *

p

)

setCollectEnergy()

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

inline

setDomainDecomposition()

void PLMD::Atoms::setDomainDecomposition

(

Communicator &

comm

)

setEnergy()

void PLMD::Atoms::setEnergy

(

void *

p

)

setForces() [1/2]

void PLMD::Atoms::setForces

(

void *

p

)

setForces() [2/2]

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

setKbT()

void PLMD::Atoms::setKbT

(

void *

p

)

setMasses()

void PLMD::Atoms::setMasses

(

void *

p

)

setMDChargeUnits()

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

inline

setMDEnergyUnits()

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

inline

setMDLengthUnits()

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

inline

setMDMassUnits()

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

inline

setMDNaturalUnits()

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

inline

setMDTimeUnits()

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

inline

setNatoms()

void PLMD::Atoms::setNatoms

(

int

n

)

setNaturalUnits()

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

inline

setPositions() [1/2]

void PLMD::Atoms::setPositions

(

void *

p

)

setPositions() [2/2]

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

setRealPrecision()

void PLMD::Atoms::setRealPrecision

(

int

p

)

setTimeStep()

void PLMD::Atoms::setTimeStep

(

void *

p

)

setUnits()

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

inline

setVirial()

void PLMD::Atoms::setVirial

(

void *

p

)

share() [1/2]

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

private

share() [2/2]

void PLMD::Atoms::share

(

)

shareAll()

void PLMD::Atoms::shareAll

(

)

startStep()

void PLMD::Atoms::startStep

(

)

updateForces()

void PLMD::Atoms::updateForces

(

)

updateUnits()

void PLMD::Atoms::updateUnits

(

)

usingNaturalUnits()

bool PLMD::Atoms::usingNaturalUnits ( ) const

inline

wait()

void PLMD::Atoms::wait

(

)

writeBinary()

void PLMD::Atoms::writeBinary

(

std::ostream &

o

)

const

Friends And Related Function Documentation

ActionAtomistic

friend class ActionAtomistic

friend

ActionWithVirtualAtom

friend class ActionWithVirtualAtom

friend

Member Data Documentation

actions

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

private

asyncSent

bool PLMD::Atoms::asyncSent

private

atomsNeeded

bool PLMD::Atoms::atomsNeeded

private

box

Tensor PLMD::Atoms::box

private

boxHasBeenSet

bool PLMD::Atoms::boxHasBeenSet

private

charges

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

private

chargesHaveBeenSet

bool PLMD::Atoms::chargesHaveBeenSet

private

collectEnergy

bool PLMD::Atoms::collectEnergy

private

dataCanBeSet

bool PLMD::Atoms::dataCanBeSet

private

dd

DomainDecomposition PLMD::Atoms::dd

private

ddStep

long int PLMD::Atoms::ddStep

private

energy

double PLMD::Atoms::energy

private

energyHasBeenSet

bool PLMD::Atoms::energyHasBeenSet

private

forceOnEnergy

double PLMD::Atoms::forceOnEnergy

private

forces

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

private

forcesHaveBeenSet

unsigned PLMD::Atoms::forcesHaveBeenSet

private

fullList

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

private

g2l

std::vector<int> PLMD::Atoms::g2l

private

Map global indexes to local indexes E.g.

g2l[i] is the position of atom i in the array passed from the MD engine. Called "global to local" since originally it was used to map global indexes to local ones used in domain decomposition. However, it is now also used for the NAMD-like interface, where only a small number of atoms is passed to plumed.

gatindex

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

private

groups

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

private

kbT

double PLMD::Atoms::kbT

private

massAndChargeOK

bool PLMD::Atoms::massAndChargeOK

private

masses

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

private

massesHaveBeenSet

bool PLMD::Atoms::massesHaveBeenSet

private

md_energy

double PLMD::Atoms::md_energy

private

mdatoms

MDAtomsBase* PLMD::Atoms::mdatoms

private

MDnaturalUnits

bool PLMD::Atoms::MDnaturalUnits

private

MDUnits

Units PLMD::Atoms::MDUnits

private

natoms

int PLMD::Atoms::natoms

private

naturalUnits

bool PLMD::Atoms::naturalUnits

private

pbc

Pbc& PLMD::Atoms::pbc

private

plumed

PlumedMain& PLMD::Atoms::plumed

private

positions

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

private

positionsHaveBeenSet

unsigned PLMD::Atoms::positionsHaveBeenSet

private

shuffledAtoms

unsigned PLMD::Atoms::shuffledAtoms

private

timestep

double PLMD::Atoms::timestep

private

uniq_index

std::vector<unsigned> PLMD::Atoms::uniq_index

private

unique

std::set<AtomNumber> PLMD::Atoms::unique

private

units

Units PLMD::Atoms::units

private

virial

Tensor PLMD::Atoms::virial

private

virialHasBeenSet

bool PLMD::Atoms::virialHasBeenSet

private

virtualAtomsActions

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

private

zeroallforces

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