Namespaces
	adjmat

	analysis

	bias

	blas

	cltools

	colvar

	config

	crystallization

	dimred

	drr

	eds

	function

	generic

	gridtools

	h36
	Tiny namespace for hybrid36 format.

	isdb

	lapack

	lepton

	logmfd

	manyrestraints

	mapping

	maze

	molfile

	multicolvar

	pamm

	piv

	secondarystructure

	setup

	vatom

	ves

	vesselbase

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

class	ActionAnyorder
	Action used to create a PLMD::Action that can go both before and after ActionSetup actions. More...

class	ActionAtomistic
	Action used to create objects that access the positions of the atoms from the MD code. More...

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

class	ActionPilot
	This is used to create PLMD::Action objects that are run with some set frequency. More...

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

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

class	ActionSetup
	Action used to create a PLMD::Action that do something during setup only e.g. More...

class	ActionShortcut
	Action used to create a command that expands to multiple PLMD::Action commands when read in during input More...

class	ActionWithArguments
	This is used to create PLMD::Action objects that take the output from some other Action as input. More...

class	ActionWithValue
	Used to create a PLMD::Action that has some scalar or vectorial output that may or may not have some derivatives. More...

class	ActionWithVirtualAtom
	Inherit from here if you are calculating the position of a virtual atom (eg a center of mass) More...

class	Angle
	Class to compute angles. More...

class	ArgumentOnlyDistance

class	AtomNumber
	Simple class to store the index of an atom. More...

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 taking care of bibliography. More...

class	CLTool
	This is the abstract base class to use for implementing new command line tool, within it there is information as to how to go about implemneting a new tool. More...

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

class	CLToolOptions

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

class	Colvar
	This is the abstract base class to use for implementing new collective variables, within it there is information as to how to go about implementing a new CV. More...

class	Communicator
	Class containing wrappers to MPI. More...

class	ConjugateGradient

class	DataFetchingObject

class	DataFetchingObjectTyped

class	Direction

class	DLLoader
	Class taking care of dynamic loading. More...

class	DotProductDistance

class	DRMSD

class	DynamicList
	A class for storing a list that changes which members are active as a function of time. More...

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

class	EuclideanDistance

class	Exception
	Class to deal with Plumed runtime errors. More...

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	GREX

class	Grid

class	GridBase

class	HistogramBead
	A class for calculating whether or not values are within a given range using : \( \sum_i \int_a^b G( s_i, \sigma*(b-a) ) \) More...

class	IFile
	Class for input files More...

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
	A class for doing link cells. More...

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

class	LoopUnroller
	Utiliy class for loop unrolling. More...

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
	A class that implements neighbor lists from two lists or a single list of atoms. More...

class	NormalizedEuclideanDistance

class	OFile
	Class for output files More...

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
	In many applications (e.g. More...

class	ReferenceAtoms
	In many applications (e.g. More...

class	ReferenceConfiguration
	Abstract base class for calculating the distance from a reference configuration. More...

class	ReferenceConfigurationOptions

class	ReferenceValuePack

class	RMSD
	A class that implements RMSD calculations This is a class that implements the various infrastructure to calculate the RMSD or MSD respect a given frame. More...

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	SetupMolInfo

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
	Small class to compure switching functions. More...

class	TargetDist

class	TensorChecks
	Small auxiliary class. More...

class	TensorGeneric
	Class implementing fixed size matrices of doubles More...

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

class	Tools
	Empty class which just contains several (static) tools. More...

class	Torsion
	Class to compute torsional angles. More...

class	Units
	Small utility class that contains information about units. More...

class	Value
	A class for holding the value of a function together with its derivatives. More...

class	VectorChecks
	Small auxiliary class. More...

class	VectorGeneric
	Class implementing fixed size vectors of doubles More...

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
	Alias for three dimensional vectors. More...

typedef VectorGeneric< 1 >	Vector1d
	Alias for one dimensional vectors. More...

typedef VectorGeneric< 2 >	Vector2d
	Alias for two dimensional vectors. More...

typedef VectorGeneric< 3 >	Vector3d
	Alias for three dimensional vectors. More...

typedef VectorGeneric< 4 >	Vector4d
	Alias for four dimensional vectors. More...

typedef VectorGeneric< 5 >	Vector5d
	Alias for five dimensional vectors. More...

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())
	Very small non-zero number. More...

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)
	Boltzman constant in kj/K. More...

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>
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_>
double	matmul (const VectorGeneric< n_ > &a, const VectorGeneric< n_ > &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, 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<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<typename T >
Matrix< T >	operator* (T &v, const Matrix< T > &m)
	Multiply matrix by scalar. More...

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

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

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

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

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, const TensorGeneric< n, m > &t2)

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

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

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

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

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

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

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

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

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

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

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

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

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

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)
	PI. 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 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 VectorGeneric< 3 > &v1, const TensorGeneric< 3, 3 > &v2)

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

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>

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

◆ matmul() [3/8]

template<unsigned n, unsigned m>

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

◆ matmul() [4/8]

template<unsigned n_>

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

◆ matmul() [5/8]

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() [6/8]

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() [7/8]

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() [8/8]

template<unsigned n, unsigned m>

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

◆ 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<typename T >

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

Multiply matrix by scalar.

◆ operator*() [2/5]

template<unsigned n>

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

◆ operator*() [3/5]

template<unsigned n>

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

◆ operator*() [4/5]

template<unsigned n, unsigned m>

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

◆ operator*() [5/5]

template<unsigned n, unsigned m>

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

◆ operator+() [1/2]

template<unsigned n>

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

◆ operator+() [2/2]

template<unsigned n, unsigned m>

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

◆ operator-() [1/2]

template<unsigned n>

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

◆ operator-() [2/2]

template<unsigned n, unsigned m>

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

◆ operator/() [1/2]

template<unsigned n>

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

◆ operator/() [2/2]

template<unsigned n, unsigned m>

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

◆ operator<()

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

inline

◆ operator<<() [1/10]

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

◆ operator<<() [2/10]

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<<() [3/10]

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

◆ operator<<() [4/10]

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

◆ operator<<() [5/10]

template<class T >

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

◆ operator<<() [6/10]

template<typename T >

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

◆ operator<<() [7/10]

template<class T >

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

Write using << syntax.

Formatted output with << operator.

◆ operator<<() [8/10]

template<unsigned n>

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

◆ operator<<() [9/10]

template<unsigned n, unsigned m>

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

◆ operator<<() [10/10]

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

◆ 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

◆ 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

◆ 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 VectorGeneric< 3 > &	v1,
		const TensorGeneric< 3, 3 > &	v2
	)

inline

◆ VcrossTensor() [2/2]

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

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>=()

◆ product()

◆ pseudoInvert()

◆ quotient()

◆ testThrow()

◆ transpose() [1/2]

◆ transpose() [2/2]