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

#include <Atoms.h>

Classes
class	DomainDecomposition

Public Member Functions
	Atoms (PlumedMain &plumed)
	~Atoms ()
void	add (ActionAtomistic *)
AtomNumber	addVirtualAtom (ActionWithVirtualAtom *)
bool	boxWasSet () const
bool	chargesWereSet () const
void	clearFullList ()
void	createFullList (const TypesafePtr &)
void	double2MD (const double &d, const TypesafePtr &m) const
const long long int &	getDdStep () const
double	getEnergy () const
double	getExtraCV (const std::string &name)
void	getFullList (const TypesafePtr &)
const std::vector< int > &	getGatindex () const
double	getKBoltzmann () const
double	getKbT () const
void	getLocalForces (std::vector< Vector > &)
void	getLocalMasses (std::vector< double > &)
void	getLocalMDForces (std::vector< Vector > &)
void	getLocalPositions (std::vector< Vector > &)
double	getMDKBoltzmann () const
const Units &	getMDUnits ()
int	getNatoms () const
int	getNVirtualAtoms () const
const Pbc &	getPbc () const
int	getRealPrecision () const
double	getTimeStep () const
const Units &	getUnits ()
const Tensor &	getVirial () const
ActionWithVirtualAtom *	getVirtualAtomsAction (AtomNumber) const
void	init ()
void	insertGroup (const std::string &name, const std::vector< AtomNumber > &a)
bool	isEnergyNeeded () const
bool	isExtraCVNeeded (const std::string &name) const
bool	isVirtualAtom (AtomNumber) const
void	MD2double (const TypesafePtr &m, double &d) const
void	readBinary (std::istream &)
void	remove (ActionAtomistic *)
void	removeGroup (const std::string &name)
void	removeVirtualAtom (ActionWithVirtualAtom *)
void	resetExtraCVNeeded ()
void	setAtomsContiguous (int)
void	setAtomsGatindex (const TypesafePtr &, bool)
void	setAtomsNlocal (int)
void	setBox (const TypesafePtr &)
void	setCharges (const TypesafePtr &)
void	setCollectEnergy (bool b)
void	setDomainDecomposition (Communicator &)
void	setEnergy (const TypesafePtr &)
void	setExtraCV (const std::string &name, const TypesafePtr &p)
void	setExtraCVForce (const std::string &name, const TypesafePtr &p)
void	setExtraCVNeeded (const std::string &name, bool needed=true)
void	setForces (const TypesafePtr &)
void	setForces (const TypesafePtr &, int)
void	setKbT (const TypesafePtr &)
void	setMasses (const TypesafePtr &)
void	setMDChargeUnits (double d)
void	setMDEnergyUnits (double d)
void	setMDLengthUnits (double d)
void	setMDMassUnits (double d)
void	setMDNaturalUnits (bool n)
void	setMDTimeUnits (double d)
void	setNatoms (int)
void	setNaturalUnits (bool n)
void	setPositions (const TypesafePtr &)
void	setPositions (const TypesafePtr &, int)
void	setRealPrecision (int)
void	setTimeStep (const TypesafePtr &)
void	setUnits (const Units &u)
void	setVirial (const TypesafePtr &)
void	share ()
void	shareAll ()
void	startStep ()
void	updateExtraCVForce (const std::string &name, double f)
void	updateForces ()
void	updateUnits ()
bool	usingNaturalUnits () const
void	wait ()
void	writeBinary (std::ostream &) const

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

Private Attributes
std::vector< ActionAtomistic * >	actions
bool	asyncSent
bool	atomsNeeded
Tensor	box
bool	boxHasBeenSet
std::vector< double >	charges
bool	chargesHaveBeenSet
bool	collectEnergy
bool	dataCanBeSet
DomainDecomposition	dd
long long int	ddStep
double	energy
bool	energyHasBeenSet
double	forceOnEnergy
std::vector< Vector >	forces
unsigned	forcesHaveBeenSet
std::vector< int >	fullList
std::vector< int >	g2l
	Map global indexes to local indexes E.g.
std::vector< int >	gatindex
std::map< std::string, std::vector< AtomNumber > >	groups
double	kbT
bool	massAndChargeOK
std::vector< double >	masses
bool	massesHaveBeenSet
double	md_energy
std::unique_ptr< MDAtomsBase >	mdatoms
bool	MDnaturalUnits
Units	MDUnits
int	natoms
bool	naturalUnits
Pbc &	pbc =*pbc_fwd
ForwardDecl< Pbc >	pbc_fwd
PlumedMain &	plumed
std::vector< Vector >	positions
unsigned	positionsHaveBeenSet
unsigned	shuffledAtoms
double	timestep
std::vector< unsigned >	uniq_index
std::vector< AtomNumber >	unique
bool	unique_serial =false
Units	units
Tensor	virial
bool	virialHasBeenSet
std::vector< ActionWithVirtualAtom * >	virtualAtomsActions
bool	zeroallforces
	if set to true, all the forces in the global array are zeroes at every step.

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 ( const TypesafePtr & n )

◆ double2MD()

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

◆ getDdStep()

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

inline

◆ getEnergy()

double PLMD::Atoms::getEnergy ( ) const

inline

◆ getExtraCV()

double PLMD::Atoms::getExtraCV ( const std::string & name )

◆ getFullList()

void PLMD::Atoms::getFullList ( const TypesafePtr & 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()

int PLMD::Atoms::getNatoms ( ) const

inline

◆ getNVirtualAtoms()

int PLMD::Atoms::getNVirtualAtoms ( ) 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

◆ isExtraCVNeeded()

bool PLMD::Atoms::isExtraCVNeeded ( const std::string & name ) const

◆ isVirtualAtom()

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

inline

◆ MD2double()

void PLMD::Atoms::MD2double	(	const TypesafePtr &	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 )

◆ resetExtraCVNeeded()

void PLMD::Atoms::resetExtraCVNeeded ( )

◆ resizeVectors()

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

private

◆ setAtomsContiguous()

void PLMD::Atoms::setAtomsContiguous ( int start )

◆ setAtomsGatindex()

void PLMD::Atoms::setAtomsGatindex	(	const TypesafePtr &	g,
		bool	fortran )

◆ setAtomsNlocal()

void PLMD::Atoms::setAtomsNlocal ( int n )

◆ setBox()

void PLMD::Atoms::setBox ( const TypesafePtr & p )

◆ setCharges()

void PLMD::Atoms::setCharges ( const TypesafePtr & p )

◆ setCollectEnergy()

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

inline

◆ setDomainDecomposition()

void PLMD::Atoms::setDomainDecomposition ( Communicator & comm )

◆ setEnergy()

void PLMD::Atoms::setEnergy ( const TypesafePtr & p )

◆ setExtraCV()

void PLMD::Atoms::setExtraCV	(	const std::string &	name,
		const TypesafePtr &	p )

◆ setExtraCVForce()

void PLMD::Atoms::setExtraCVForce	(	const std::string &	name,
		const TypesafePtr &	p )

◆ setExtraCVNeeded()

void PLMD::Atoms::setExtraCVNeeded	(	const std::string &	name,
		bool	needed = true )

◆ setForces() [1/2]

void PLMD::Atoms::setForces ( const TypesafePtr & p )

◆ setForces() [2/2]

void PLMD::Atoms::setForces	(	const TypesafePtr &	p,
		int	i )

◆ setKbT()

void PLMD::Atoms::setKbT ( const TypesafePtr & p )

◆ setMasses()

void PLMD::Atoms::setMasses ( const TypesafePtr & 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 ( const TypesafePtr & p )

◆ setPositions() [2/2]

void PLMD::Atoms::setPositions	(	const TypesafePtr &	p,
		int	i )

◆ setRealPrecision()

void PLMD::Atoms::setRealPrecision ( int p )

◆ setTimeStep()

void PLMD::Atoms::setTimeStep ( const TypesafePtr & p )

◆ setUnits()

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

inline

◆ setVirial()

void PLMD::Atoms::setVirial ( const TypesafePtr & p )

◆ share() [1/2]

void PLMD::Atoms::share ( )

◆ share() [2/2]

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

private

◆ shareAll()

void PLMD::Atoms::shareAll ( )

◆ startStep()

void PLMD::Atoms::startStep ( )

◆ updateExtraCVForce()

void PLMD::Atoms::updateExtraCVForce	(	const std::string &	name,
		double	f )

◆ 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

◆ 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 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

std::unique_ptr<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 =*pbc_fwd

private

◆ pbc_fwd

ForwardDecl<Pbc> PLMD::Atoms::pbc_fwd

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::vector<AtomNumber> PLMD::Atoms::unique

private

◆ unique_serial

bool PLMD::Atoms::unique_serial =false

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

Classes

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ Atoms()

◆ ~Atoms()

Member Function Documentation

◆ add()

◆ addVirtualAtom()

◆ boxWasSet()

◆ chargesWereSet()

◆ clearFullList()

◆ createFullList()

◆ double2MD()

◆ getDdStep()

◆ getEnergy()

◆ getExtraCV()

◆ getFullList()

◆ getGatindex()

◆ getKBoltzmann()

◆ getKbT()

◆ getLocalForces()

◆ getLocalMasses()

◆ getLocalMDForces()

◆ getLocalPositions()

◆ getMDKBoltzmann()

◆ getMDUnits()

◆ getNatoms()

◆ getNVirtualAtoms()

◆ getPbc()

◆ getRealPrecision()

◆ getTimeStep()

◆ getUnits()

◆ getVirial()

◆ getVirtualAtomsAction()

◆ init()

◆ insertGroup()

◆ isEnergyNeeded()

◆ isExtraCVNeeded()

◆ isVirtualAtom()

◆ MD2double()

◆ readBinary()

◆ remove()

◆ removeGroup()

◆ removeVirtualAtom()

◆ resetExtraCVNeeded()

◆ resizeVectors()

◆ setAtomsContiguous()

◆ setAtomsGatindex()

◆ setAtomsNlocal()

◆ setBox()

◆ setCharges()

◆ setCollectEnergy()

◆ setDomainDecomposition()

◆ setEnergy()

◆ setExtraCV()

◆ setExtraCVForce()

◆ setExtraCVNeeded()

◆ setForces() [1/2]

◆ setForces() [2/2]

◆ setKbT()

◆ setMasses()

◆ setMDChargeUnits()

◆ setMDEnergyUnits()

◆ setMDLengthUnits()

◆ setMDMassUnits()

◆ setMDNaturalUnits()

◆ setMDTimeUnits()

◆ setNatoms()

◆ setNaturalUnits()

◆ setPositions() [1/2]

◆ setPositions() [2/2]

◆ setRealPrecision()

◆ setTimeStep()

◆ setUnits()

◆ setVirial()

◆ share() [1/2]