Namespaces
	adjmat

	analysis

	bias

	blas

	cltools

	colvar

	config

	crystallization

	dimred

	drr

	eds

	fisst

	function

	funnel

	generic

	gridtools

	h36
	Tiny namespace for hybrid36 format.

	isdb

	lapack

	lepton

	logmfd

	manyrestraints

	mapping

	maze

	molfile

	multicolvar

	opes

	pamm

	piv

	secondarystructure

	setup

	vatom

	ves

	vesselbase

Classes
class	Action
	Base class for all the input Actions. More...

class	ActionAnyorder

class	ActionAtomistic

class	ActionOptions
	This class is used to bring the relevant information to the Action constructor. More...

class	ActionPilot

class	ActionRegister
	Register holding all the allowed keywords. More...

class	ActionSet
	std::vector containing the sequence of Action to be done. More...

class	ActionSetup

class	ActionShortcut

class	ActionWithArguments

class	ActionWithValue

class	ActionWithVirtualAtom
	Class to add a single virtual atom to the system. More...

class	Angle

class	ArgumentOnlyDistance

class	AtomNumber

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

class	BiasRepresentation
	this class implements a general purpose class that aims to provide a Grid/list transparently add gaussians to a bias More...

class	BiasWeight

class	Brent1DRootSearch
	A class for doing parabolic interpolation and minimisation of 1D functions using Brent's method. More...

class	Citations

class	CLTool

class	CLToolMain
	Class providing cmd() access to command line tools. More...

class	CLToolOptions

class	CLToolRegister
	Same as ActionRegister, but for CLTools. More...

class	Colvar

class	Communicator

class	ConjugateGradient

class	DataFetchingObject

class	DataFetchingObjectTyped

class	Direction

class	DLLoader

class	DotProductDistance

class	DRMSD

class	DynamicList

class	ERMSD
	A class that implements ERMSD calculations. More...

class	EuclideanDistance

class	Exception

class	ExceptionDebug
	Class representing a debug error (can only be thrown when using debug options) More...

class	ExceptionError
	Class representing a generic error. More...

class	ExchangePatterns

class	F1dim

class	FakeFrame

class	FileBase
	Base class for dealing with files. More...

class	FlexibleBin

class	ForwardDecl
	Utility class for forward declaration of references. More...

class	GenericMolInfo

class	GREX

class	Grid

class	GridBase

class	HistogramBead

class	IFile

class	IntermolecularDRMSD

class	IntramolecularDRMSD

class	KernelFunctions

class	Keywords
	This class holds the keywords and their documentation. More...

class	LatticeReduction
	Class implementing algorithms for lattice reduction. More...

class	LinkCells

class	Log
	Class containing the log stream. More...

class	LoopUnroller

class	MahalanobisDistance

class	Matrix
	This class stores a full matrix and allows one to do some simple matrix operations. More...

class	MatrixSquareBracketsAccess
	Utility class to add [][] access. More...

class	MDAtomsBase
	Class containing interface to MDAtomsTyped. More...

class	MDAtomsTyped
	Class containing the pointers to the MD data It is templated so that single and double precision versions coexist IT IS STILL UNDOCUMENTED. More...

class	MetricRegister

class	Minimise1DBrent
	A class for doing parabolic interpolation and minimisation of 1D functions using Brent's method. More...

class	MinimiseBase

class	MolDataClass
	This class provides information on various kinds of molecules for instance the kinds of residues that are in a protein the atoms involved in the backbone of a particular residue etc. More...

class	MPI_Comm
	Surrogate of MPI_Comm when MPI library is not available. More...

class	MPI_Datatype
	Surrogate of MPI_Datatype when MPI library is not available. More...

class	MPI_Request
	Surrogate of MPI_Request when MPI library is not available. More...

class	MPI_Status
	Surrogate of MPI_Status when MPI library is not available. More...

class	MultiDomainRMSD

class	MultiValue

class	NeighborList

class	NormalizedEuclideanDistance

class	OFile

class	OpenMP

struct	OpenMPVars

class	OptimalRMSD

class	Pbc

class	PDB
	Minimalistic pdb parser. More...

class	Plumed
	C++ wrapper for plumed. More...

class	PlumedHandle
	Tiny local class to load a PLUMED kernel. More...

class	PlumedMain
	Main plumed object. More...

class	PlumedMainInitializer
	Static object which registers Plumed. More...

class	ProbWeight

class	Random

class	ReferenceArguments

class	ReferenceAtoms

class	ReferenceConfiguration

class	ReferenceConfigurationOptions

class	ReferenceValuePack

class	RMSD

class	RMSDBase

class	RMSDCoreData
	this is a class which is needed to share information across the various non-threadsafe routines so that the public function of rmsd are threadsafe while the inner core can safely share information More...

class	RootFindingBase

class	SimpleRMSD

class	SingleDomainRMSD

class	SparseGrid

class	Stopwatch

class	Subprocess
	Class managing a subprocess. More...

class	SubprocessPid
	Small utility class, used to avoid inclusion of unistd.h> in a header file. More...

class	SwitchingFunction

class	TargetDist

class	TensorChecks
	Small auxiliary class. More...

class	TensorGeneric

class	TensorGenericAux
	Small class to contain local utilities. More...

class	Tools

class	Torsion

class	Units

class	Value

class	VectorChecks
	Small auxiliary class. More...

class	VectorGeneric

class	WeightBase

class	WithCmd
	Base for classes with cmd() method. More...

Typedefs
typedef Tensor3d	Tensor

typedef TensorGeneric< 1, 1 >	Tensor1d

typedef TensorGeneric< 2, 2 >	Tensor2d

typedef TensorGeneric< 3, 3 >	Tensor3d

typedef TensorGeneric< 4, 4 >	Tensor4d

typedef TensorGeneric< 5, 5 >	Tensor5d

typedef Vector3d	Vector

typedef VectorGeneric< 1 >	Vector1d

typedef VectorGeneric< 2 >	Vector2d

typedef VectorGeneric< 3 >	Vector3d

typedef VectorGeneric< 4 >	Vector4d

typedef VectorGeneric< 5 >	Vector5d

Functions
ActionRegister &	actionRegister ()

void	add (const Value &val1, Value *val2)

template<typename T >
void	chol_elsolve (const Matrix< T > &M, const std::vector< T > &b, std::vector< T > &y)

template<typename T >
void	cholesky (const Matrix< T > &A, Matrix< T > &B)

CLToolRegister &	cltoolRegister ()

void	copy (const Value &val1, Value &val2)

void	copy (const Value &val1, Value *val2)

VectorGeneric< 3 >	crossProduct (const VectorGeneric< 3 > &v1, const VectorGeneric< 3 > &v2)

TensorGeneric< 3, 3 >	dcrossDv1 (const VectorGeneric< 3 > &v1, const VectorGeneric< 3 > &v2)

TensorGeneric< 3, 3 >	dcrossDv2 (const VectorGeneric< 3 > &v1, const VectorGeneric< 3 > &v2)

template<unsigned n>
VectorGeneric< n >	delta (const VectorGeneric< n > &v1, const VectorGeneric< n > &v2)

TensorGeneric< 3, 3 >	deriNorm (const VectorGeneric< 3 > &v1, const TensorGeneric< 3, 3 > &v2)

double	determinant (const TensorGeneric< 3, 3 > &t)

template<typename T >
int	diagMat (const Matrix< T > &A, std::vector< double > &eigenvals, Matrix< double > &eigenvecs)

template<unsigned n, unsigned m>
void	diagMatSym (const TensorGeneric< n, n > &mat, VectorGeneric< m > &evals, TensorGeneric< m, n > &evec)

double	distance (const Pbc &pbc, const std::vector< Value * > &vals, ReferenceConfiguration ref1, ReferenceConfiguration ref2, const bool &squared)

template<typename T >
T	dotProduct (const std::vector< T > &A, const std::vector< T > &B)
	Calculate the dot product between two vectors. More...

template<unsigned n>
double	dotProduct (const VectorGeneric< n > &v1, const VectorGeneric< n > &v2)

const double	epsilon (std::numeric_limits< double >::epsilon())

template<unsigned n, unsigned m>
TensorGeneric< n, m >	extProduct (const VectorGeneric< n > &v1, const VectorGeneric< m > &v2)

static OpenMPVars &	getOpenMPVars ()

bool	indexed_lt (pair< Grid::index_t, double > const &x, pair< Grid::index_t, double > const &y)

TensorGeneric< 3, 3 >	inverse (const TensorGeneric< 3, 3 > &t)

template<typename T >
int	Invert (const Matrix< T > &A, Matrix< double > &inverse)

const double	kBoltzmann (0.0083144621)

template<typename T >
int	logdet (const Matrix< T > &M, double &ldet)

template<unsigned n, unsigned m, unsigned l>
TensorGeneric< n, l >	matmul (const TensorGeneric< n, m > &a, const TensorGeneric< m, l > &b)

template<unsigned n, unsigned m, unsigned l, unsigned i>
TensorGeneric< n, i >	matmul (const TensorGeneric< n, m > &a, const TensorGeneric< m, l > &b, const TensorGeneric< l, i > &c)

template<unsigned n, unsigned m, unsigned l>
VectorGeneric< n >	matmul (const TensorGeneric< n, m > &a, const TensorGeneric< m, l > &b, const VectorGeneric< l > &c)

template<unsigned n, unsigned m>
VectorGeneric< n >	matmul (const TensorGeneric< n, m > &a, const VectorGeneric< m > &b)

template<unsigned n, unsigned m>
VectorGeneric< n >	matmul (const VectorGeneric< m > &a, const TensorGeneric< m, n > &b)

template<unsigned n, unsigned m, unsigned l>
VectorGeneric< l >	matmul (const VectorGeneric< n > &a, const TensorGeneric< n, m > &b, const TensorGeneric< m, l > &c)

template<unsigned n, unsigned m>
double	matmul (const VectorGeneric< n > &a, const TensorGeneric< n, m > &b, const VectorGeneric< m > &c)

template<unsigned n_>
double	matmul (const VectorGeneric< n_ > &a, const VectorGeneric< n_ > &b)

template<typename T >
void	matrixOut (Log &ostr, const Matrix< T > &mat)

MetricRegister &	metricRegister ()

template<unsigned n>
double	modulo (const VectorGeneric< n > &v)

template<unsigned n>
double	modulo2 (const VectorGeneric< n > &v)

template<typename U >
void	mpi_gatherActiveMembers (Communicator &comm, std::vector< DynamicList< U > > &ll)

template<typename T >
void	mult (const Matrix< T > &A, const Matrix< T > &B, Matrix< T > &C)

template<typename T >
void	mult (const Matrix< T > &A, const std::vector< T > &B, std::vector< T > &C)

template<typename T >
void	mult (const std::vector< T > &A, const Matrix< T > &B, std::vector< T > &C)

template<typename T >
T	norm (const std::vector< T > &A)
	Calculate the dot product between a vector and itself. More...

bool	operator!= (const AtomNumber &a, const AtomNumber &b)

template<unsigned n, unsigned m>
TensorGeneric< n, m >	operator* (const TensorGeneric< n, m > &t1, double s)

template<unsigned n>
VectorGeneric< n >	operator* (const VectorGeneric< n > &v, double s)

template<unsigned n, unsigned m>
TensorGeneric< n, m >	operator* (double s, const TensorGeneric< n, m > &t1)

template<unsigned n>
VectorGeneric< n >	operator* (double s, const VectorGeneric< n > &v)

template<typename T >
Matrix< T >	operator* (T &v, const Matrix< T > &m)
	Multiply matrix by scalar. More...

template<unsigned n, unsigned m>
TensorGeneric< n, m >	operator+ (const TensorGeneric< n, m > &t1, const TensorGeneric< n, m > &t2)

template<unsigned n>
VectorGeneric< n >	operator+ (const VectorGeneric< n > &v1, const VectorGeneric< n > &v2)

template<unsigned n, unsigned m>
TensorGeneric< n, m >	operator- (const TensorGeneric< n, m > &t1, const TensorGeneric< n, m > &t2)

template<unsigned n>
VectorGeneric< n >	operator- (const VectorGeneric< n > &v1, const VectorGeneric< n > &v2)

template<unsigned n, unsigned m>
TensorGeneric< n, m >	operator/ (const TensorGeneric< n, m > &t1, double s)

template<unsigned n>
VectorGeneric< n >	operator/ (const VectorGeneric< n > &v, double s)

bool	operator< (const AtomNumber &a, const AtomNumber &b)

template<typename T >
Log &	operator<< (Log &ostr, const Matrix< T > &mat)

Log &	operator<< (Log &ostr, const PDB &pdb)

template<class T >
OFile &	operator<< (OFile &of, const T &t)
	Write using << syntax. More...

std::ostream &	operator<< (std::ostream &log, const ActionRegister &ar)

std::ostream &	operator<< (std::ostream &log, const Citations &cit)

std::ostream &	operator<< (std::ostream &log, const CLToolRegister &ar)

std::ostream &	operator<< (std::ostream &os, const Stopwatch &sw)

template<unsigned n, unsigned m>
std::ostream &	operator<< (std::ostream &os, const TensorGeneric< n, m > &t)

template<unsigned n>
std::ostream &	operator<< (std::ostream &os, const VectorGeneric< n > &v)

template<class T >
Subprocess &	operator<< (Subprocess &ep, const T &t)

bool	operator<= (const AtomNumber &a, const AtomNumber &b)

bool	operator== (const AtomNumber &a, const AtomNumber &b)

bool	operator> (const AtomNumber &a, const AtomNumber &b)

bool	operator>= (const AtomNumber &a, const AtomNumber &b)

const double	pi (3.141592653589793238462643383279502884197169399375105820974944592307)

static bool	PlumedGetenvExceptionsDebug () noexcept
	Retrieve PLUMED_EXCEPTIONS_DEBUG (internal utility). More...

void	product (const Value &val1, const Value &val2, Value &valout)

template<typename T >
int	pseudoInvert (const Matrix< T > &A, Matrix< double > &pseudoinverse)

void	quotient (const Value &val1, const Value &val2, Value *valout)

static const std::string &	StopwatchEmptyString () noexcept
	Return an empty string. More...

static bool	SubprocessPidGetenvSignals () noexcept
	Retrieve PLUMED_ENABLE_SIGNALS. More...

static void	testThrow (const char *what)
	Small utility just used in this file to throw arbitrary exceptions. More...

template<typename T >
void	transpose (const Matrix< T > &A, Matrix< T > &AT)

template<unsigned n, unsigned m>
TensorGeneric< n, m >	transpose (const TensorGeneric< m, n > &t)

TensorGeneric< 3, 3 >	VcrossTensor (const TensorGeneric< 3, 3 > &v2, const VectorGeneric< 3 > &v1)

TensorGeneric< 3, 3 >	VcrossTensor (const VectorGeneric< 3 > &v1, const TensorGeneric< 3, 3 > &v2)

Variables
static class PLMD::TensorChecks	checks

static class PLMD::VectorChecks	checks

const double	epsilon =1e-14

static class PLMD::PlumedMainInitializer	PlumedMainInitializerRegisterMe

static const bool	shareMassAndChargeOnlyAtFirstStep =true
	We assume that charges and masses are constant along the simulation Set this to false if you want to revert to the original (expensive) behavior. More...

Function Documentation

◆ actionRegister()

ActionRegister& PLMD::actionRegister ( )

void PLMD::add	(	const Value &	val1,
		Value *	val2
	)

◆ chol_elsolve()

template<typename T >

void PLMD::chol_elsolve	(	const Matrix< T > &	M,
		const std::vector< T > &	b,
		std::vector< T > &	y
	)

◆ cholesky()

template<typename T >

void PLMD::cholesky	(	const Matrix< T > &	A,
		Matrix< T > &	B
	)

◆ cltoolRegister()

CLToolRegister& PLMD::cltoolRegister ( )

void PLMD::copy	(	const Value &	val1,
		Value &	val2
	)

◆ copy() [2/2]

void PLMD::copy	(	const Value &	val1,
		Value *	val2
	)

◆ crossProduct()

VectorGeneric<3> PLMD::crossProduct	(	const VectorGeneric< 3 > &	v1,
		const VectorGeneric< 3 > &	v2
	)

inline

v2 Only available for size 3

◆ dcrossDv1()

TensorGeneric<3,3> PLMD::dcrossDv1	(	const VectorGeneric< 3 > &	v1,
		const VectorGeneric< 3 > &	v2
	)

inline

◆ dcrossDv2()

TensorGeneric<3,3> PLMD::dcrossDv2	(	const VectorGeneric< 3 > &	v1,
		const VectorGeneric< 3 > &	v2
	)

inline

◆ delta()

template<unsigned n>

VectorGeneric<n> PLMD::delta	(	const VectorGeneric< n > &	v1,
		const VectorGeneric< n > &	v2
	)

◆ deriNorm()

TensorGeneric<3,3> PLMD::deriNorm	(	const VectorGeneric< 3 > &	v1,
		const TensorGeneric< 3, 3 > &	v2
	)

inline

◆ determinant()

double PLMD::determinant ( const TensorGeneric< 3, 3 > & t )

inline

◆ diagMat()

template<typename T >

int PLMD::diagMat	(	const Matrix< T > &	A,
		std::vector< double > &	eigenvals,
		Matrix< double > &	eigenvecs
	)

◆ diagMatSym()

template<unsigned n, unsigned m>

void PLMD::diagMatSym	(	const TensorGeneric< n, n > &	mat,
		VectorGeneric< m > &	evals,
		TensorGeneric< m, n > &	evec
	)

◆ distance()

double PLMD::distance	(	const Pbc &	pbc,
		const std::vector< Value * > &	vals,
		ReferenceConfiguration *	ref1,
		ReferenceConfiguration *	ref2,
		const bool &	squared
	)

◆ dotProduct() [1/2]

template<typename T >

T PLMD::dotProduct	(	const std::vector< T > &	A,
		const std::vector< T > &	B
	)

Calculate the dot product between two vectors.

◆ dotProduct() [2/2]

template<unsigned n>

double PLMD::dotProduct	(	const VectorGeneric< n > &	v1,
		const VectorGeneric< n > &	v2
	)

◆ extProduct()

template<unsigned n, unsigned m>

TensorGeneric<n,m> PLMD::extProduct	(	const VectorGeneric< n > &	v1,
		const VectorGeneric< m > &	v2
	)

◆ getOpenMPVars()

static OpenMPVars& PLMD::getOpenMPVars ( )

static

◆ indexed_lt()

bool PLMD::indexed_lt	(	pair< Grid::index_t, double > const &	x,
		pair< Grid::index_t, double > const &	y
	)

◆ inverse()

TensorGeneric<3,3> PLMD::inverse ( const TensorGeneric< 3, 3 > & t )

inline

◆ Invert()

template<typename T >

int PLMD::Invert	(	const Matrix< T > &	A,
		Matrix< double > &	inverse
	)

◆ logdet()

template<typename T >

int PLMD::logdet	(	const Matrix< T > &	M,
		double &	ldet
	)

◆ matmul() [1/8]

template<unsigned n, unsigned m, unsigned l>

TensorGeneric<n,l> PLMD::matmul	(	const TensorGeneric< n, m > &	a,
		const TensorGeneric< m, l > &	b
	)

◆ matmul() [2/8]

template<unsigned n, unsigned m, unsigned l, unsigned i>

TensorGeneric<n,i> PLMD::matmul	(	const TensorGeneric< n, m > &	a,
		const TensorGeneric< m, l > &	b,
		const TensorGeneric< l, i > &	c
	)

◆ matmul() [3/8]

template<unsigned n, unsigned m, unsigned l>

VectorGeneric<n> PLMD::matmul	(	const TensorGeneric< n, m > &	a,
		const TensorGeneric< m, l > &	b,
		const VectorGeneric< l > &	c
	)

◆ matmul() [4/8]

template<unsigned n, unsigned m>

VectorGeneric<n> PLMD::matmul	(	const TensorGeneric< n, m > &	a,
		const VectorGeneric< m > &	b
	)

◆ matmul() [5/8]

template<unsigned n, unsigned m>

VectorGeneric<n> PLMD::matmul	(	const VectorGeneric< m > &	a,
		const TensorGeneric< m, n > &	b
	)

◆ matmul() [6/8]

template<unsigned n, unsigned m, unsigned l>

VectorGeneric<l> PLMD::matmul	(	const VectorGeneric< n > &	a,
		const TensorGeneric< n, m > &	b,
		const TensorGeneric< m, l > &	c
	)

◆ matmul() [7/8]

template<unsigned n, unsigned m>

double PLMD::matmul	(	const VectorGeneric< n > &	a,
		const TensorGeneric< n, m > &	b,
		const VectorGeneric< m > &	c
	)

◆ matmul() [8/8]

template<unsigned n_>

double PLMD::matmul	(	const VectorGeneric< n_ > &	a,
		const VectorGeneric< n_ > &	b
	)

◆ matrixOut()

template<typename T >

void PLMD::matrixOut	(	Log &	ostr,
		const Matrix< T > &	mat
	)

◆ metricRegister()

MetricRegister & PLMD::metricRegister ( )

◆ modulo()

template<unsigned n>

double PLMD::modulo ( const VectorGeneric< n > & v )

◆ modulo2()

template<unsigned n>

double PLMD::modulo2 ( const VectorGeneric< n > & v )

◆ mpi_gatherActiveMembers()

template<typename U >

void PLMD::mpi_gatherActiveMembers	(	Communicator &	comm,
		std::vector< DynamicList< U > > &	ll
	)

◆ mult() [1/3]

template<typename T >

void PLMD::mult	(	const Matrix< T > &	A,
		const Matrix< T > &	B,
		Matrix< T > &	C
	)

◆ mult() [2/3]

template<typename T >

void PLMD::mult	(	const Matrix< T > &	A,
		const std::vector< T > &	B,
		std::vector< T > &	C
	)

◆ mult() [3/3]

template<typename T >

void PLMD::mult	(	const std::vector< T > &	A,
		const Matrix< T > &	B,
		std::vector< T > &	C
	)

◆ norm()

template<typename T >

T PLMD::norm ( const std::vector< T > & A )

Calculate the dot product between a vector and itself.

◆ operator!=()

bool PLMD::operator!=	(	const AtomNumber &	a,
		const AtomNumber &	b
	)

inline

◆ operator*() [1/5]

template<unsigned n, unsigned m>

TensorGeneric<n,m> PLMD::operator*	(	const TensorGeneric< n, m > &	t1,
		double	s
	)

◆ operator*() [2/5]

template<unsigned n>

VectorGeneric<n> PLMD::operator*	(	const VectorGeneric< n > &	v,
		double	s
	)

◆ operator*() [3/5]

template<unsigned n, unsigned m>

TensorGeneric<n,m> PLMD::operator*	(	double	s,
		const TensorGeneric< n, m > &	t1
	)

◆ operator*() [4/5]

template<unsigned n>

VectorGeneric<n> PLMD::operator*	(	double	s,
		const VectorGeneric< n > &	v
	)

◆ operator*() [5/5]

template<typename T >

Matrix<T> PLMD::operator*	(	T &	v,
		const Matrix< T > &	m
	)

Multiply matrix by scalar.

◆ operator+() [1/2]

template<unsigned n, unsigned m>

TensorGeneric<n,m> PLMD::operator+	(	const TensorGeneric< n, m > &	t1,
		const TensorGeneric< n, m > &	t2
	)

◆ operator+() [2/2]

template<unsigned n>

VectorGeneric<n> PLMD::operator+	(	const VectorGeneric< n > &	v1,
		const VectorGeneric< n > &	v2
	)

◆ operator-() [1/2]

template<unsigned n, unsigned m>

TensorGeneric<n,m> PLMD::operator-	(	const TensorGeneric< n, m > &	t1,
		const TensorGeneric< n, m > &	t2
	)

◆ operator-() [2/2]

template<unsigned n>

VectorGeneric<n> PLMD::operator-	(	const VectorGeneric< n > &	v1,
		const VectorGeneric< n > &	v2
	)

◆ operator/() [1/2]

template<unsigned n, unsigned m>

TensorGeneric<n,m> PLMD::operator/	(	const TensorGeneric< n, m > &	t1,
		double	s
	)

◆ operator/() [2/2]

template<unsigned n>

VectorGeneric<n> PLMD::operator/	(	const VectorGeneric< n > &	v,
		double	s
	)

◆ operator<()

bool PLMD::operator<	(	const AtomNumber &	a,
		const AtomNumber &	b
	)

inline

◆ operator<<() [1/10]

template<typename T >

Log& PLMD::operator<<	(	Log &	ostr,
		const Matrix< T > &	mat
	)

◆ operator<<() [2/10]

Log& PLMD::operator<<	(	Log &	ostr,
		const PDB &	pdb
	)

◆ operator<<() [3/10]

template<class T >

OFile& PLMD::operator<<	(	OFile &	of,
		const T &	t
	)

Write using << syntax.

Formatted output with << operator.

◆ operator<<() [4/10]

std::ostream & PLMD::operator<<	(	std::ostream &	log,
		const ActionRegister &	ar
	)

◆ operator<<() [5/10]

std::ostream & PLMD::operator<<	(	std::ostream &	log,
		const Citations &	cit
	)

It writes on the ostream the list of all the bibliographic items prefixed with their reference number

◆ operator<<() [6/10]

std::ostream & PLMD::operator<<	(	std::ostream &	log,
		const CLToolRegister &	ar
	)

◆ operator<<() [7/10]

std::ostream& PLMD::operator<<	(	std::ostream &	os,
		const Stopwatch &	sw
	)

◆ operator<<() [8/10]

template<unsigned n, unsigned m>

std::ostream& PLMD::operator<<	(	std::ostream &	os,
		const TensorGeneric< n, m > &	t
	)

◆ operator<<() [9/10]

template<unsigned n>

std::ostream& PLMD::operator<<	(	std::ostream &	os,
		const VectorGeneric< n > &	v
	)

◆ operator<<() [10/10]

template<class T >

Subprocess& PLMD::operator<<	(	Subprocess &	ep,
		const T &	t
	)

◆ operator<=()

bool PLMD::operator<=	(	const AtomNumber &	a,
		const AtomNumber &	b
	)

inline

◆ operator==()

bool PLMD::operator==	(	const AtomNumber &	a,
		const AtomNumber &	b
	)

inline

◆ operator>()

bool PLMD::operator>	(	const AtomNumber &	a,
		const AtomNumber &	b
	)

inline

◆ operator>=()

bool PLMD::operator>=	(	const AtomNumber &	a,
		const AtomNumber &	b
	)

inline

◆ PlumedGetenvExceptionsDebug()

static bool PLMD::PlumedGetenvExceptionsDebug ( )

inlinestaticnoexcept

Retrieve PLUMED_EXCEPTIONS_DEBUG (internal utility).

This function should not be used by external programs. It is defined as inline static so that it can store a static variable (for quicker access) without adding a unique global symbol to a library including this header file.

◆ product()

void PLMD::product	(	const Value &	val1,
		const Value &	val2,
		Value &	valout
	)

inline

◆ pseudoInvert()

template<typename T >

int PLMD::pseudoInvert	(	const Matrix< T > &	A,
		Matrix< double > &	pseudoinverse
	)

◆ quotient()

void PLMD::quotient	(	const Value &	val1,
		const Value &	val2,
		Value *	valout
	)

inline

◆ StopwatchEmptyString()

static const std::string& PLMD::StopwatchEmptyString ( )

inlinestaticnoexcept

Return an empty string.

Inline static so that it can store a static variable (for quicker access) without adding a unique global symbol to a library including this header file.

◆ SubprocessPidGetenvSignals()

static bool PLMD::SubprocessPidGetenvSignals ( )

inlinestaticnoexcept

Retrieve PLUMED_ENABLE_SIGNALS.

Inline static so that it can store a static variable (for quicker access) without adding a unique global symbol to a library including this header file.

◆ testThrow()

static void PLMD::testThrow ( const char * what )

static

Small utility just used in this file to throw arbitrary exceptions.

◆ transpose() [1/2]

template<typename T >

void PLMD::transpose	(	const Matrix< T > &	A,
		Matrix< T > &	AT
	)

◆ transpose() [2/2]

template<unsigned n, unsigned m>

TensorGeneric<n,m> PLMD::transpose ( const TensorGeneric< m, n > & t )

◆ VcrossTensor() [1/2]

TensorGeneric<3,3> PLMD::VcrossTensor	(	const TensorGeneric< 3, 3 > &	v2,
		const VectorGeneric< 3 > &	v1
	)

inline

◆ VcrossTensor() [2/2]

TensorGeneric<3,3> PLMD::VcrossTensor	(	const VectorGeneric< 3 > &	v1,
		const TensorGeneric< 3, 3 > &	v2
	)

inline

Variable Documentation

◆ checks [1/2]

class PLMD::TensorChecks PLMD::checks

static

◆ checks [2/2]

class PLMD::VectorChecks PLMD::checks

static

◆ epsilon

const double PLMD::epsilon =1e-14

◆ PlumedMainInitializerRegisterMe

class PLMD::PlumedMainInitializer PLMD::PlumedMainInitializerRegisterMe

static

◆ shareMassAndChargeOnlyAtFirstStep

const bool PLMD::shareMassAndChargeOnlyAtFirstStep =true

static

We assume that charges and masses are constant along the simulation Set this to false if you want to revert to the original (expensive) behavior.

Namespaces

Classes

Typedefs

Functions

Variables

Function Documentation

◆ actionRegister()

◆ add()

◆ chol_elsolve()

◆ cholesky()

◆ cltoolRegister()

◆ copy() [1/2]

◆ copy() [2/2]

◆ crossProduct()

◆ dcrossDv1()

◆ dcrossDv2()

◆ delta()

◆ deriNorm()

◆ determinant()

◆ diagMat()

◆ diagMatSym()

◆ distance()

◆ dotProduct() [1/2]

◆ dotProduct() [2/2]

◆ extProduct()

◆ getOpenMPVars()

◆ indexed_lt()

◆ inverse()

◆ Invert()

◆ logdet()

◆ matmul() [1/8]

◆ matmul() [2/8]

◆ matmul() [3/8]

◆ matmul() [4/8]

◆ matmul() [5/8]

◆ matmul() [6/8]

◆ matmul() [7/8]

◆ matmul() [8/8]

◆ matrixOut()

◆ metricRegister()

◆ modulo()

◆ modulo2()

◆ mpi_gatherActiveMembers()

◆ mult() [1/3]

◆ mult() [2/3]

◆ mult() [3/3]

◆ norm()

◆ operator!=()

◆ operator*() [1/5]

◆ operator*() [2/5]

◆ operator*() [3/5]

◆ operator*() [4/5]

◆ operator*() [5/5]

◆ operator+() [1/2]

◆ operator+() [2/2]

◆ operator-() [1/2]

◆ operator-() [2/2]

◆ operator/() [1/2]

◆ operator/() [2/2]

◆ operator<()

◆ operator<<() [1/10]

◆ operator<<() [2/10]

◆ operator<<() [3/10]

◆ operator<<() [4/10]

◆ operator<<() [5/10]

◆ operator<<() [6/10]

◆ operator<<() [7/10]

◆ operator<<() [8/10]

◆ operator<<() [9/10]

◆ operator<<() [10/10]

◆ operator<=()

◆ operator==()

◆ operator>()

◆ operator>=()

◆ PlumedGetenvExceptionsDebug()

◆ product()

◆ pseudoInvert()

◆ quotient()

◆ StopwatchEmptyString()

◆ SubprocessPidGetenvSignals()