Namespaces
namespace	adjmat

namespace	bias

namespace	blas

namespace	cltools

namespace	clusters

namespace	colvar

namespace	config

namespace	contour

namespace	crystdistrib

namespace	dimred

namespace	drr

namespace	eds

namespace	envsim

namespace	fisst

namespace	fourier

namespace	function

namespace	funnel

namespace	gch

namespace	generic

namespace	gridtools

namespace	h36
	Tiny namespace for hybrid36 format.

namespace	helpers

namespace	isdb

namespace	landmarks

namespace	lapack

namespace	lepton

namespace	logmfd

namespace	mapping

namespace	matrixtools

namespace	maze

namespace	membranefusion

namespace	mergeVectorTools

namespace	metatomic

namespace	molfile

namespace	multicolvar

namespace	OpenMP

namespace	opes

namespace	pamm

namespace	piv

namespace	refdist

namespace	s2cm

namespace	sasa

namespace	secondarystructure

namespace	setup

namespace	sizeshape

namespace	sprint

namespace	switchContainers

namespace	symfunc

namespace	valtools

namespace	vatom

namespace	ves

namespace	volumes

namespace	wham

namespace	xdrfile

Classes
class	Accelerator

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	ActionForInterface

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...

struct	ActionRegisterPointers

class	ActionRegistration
	Each instance of this specialized class represents an action that can be called with the specified directive. 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	ActionToGetData
	Provides the keyword GET More...

class	ActionToPutData
	Provides the keyword PUT More...

class	ActionWithArguments

class	ActionWithMatrix

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	ActionWithVector

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

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...

struct	CLToolRegisterPointers

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	DataPassingObject

class	DataPassingObjectTyped

class	DataPassingTools

class	DataPassingToolsTyped

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

class	DomainDecomposition

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

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	ExceptionRegisterError
	Class representing an error in a register. More...

class	ExceptionTypeError
	Class representing a type error in the PLMD::Plumed interface. More...

class	ExchangePatterns

class	F1dim

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	Group
	Provides the keyword GROUP More...

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	KernelFunctions

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

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

class	LeptonCall

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	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	mdMemoryView

class	MemoryView

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	MultiValue

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

class	OFile
	Class for output files. More...

class	Pbc

class	PbcAction
	Provides the keyword PBC More...

class	PDB
	Minimalistic pdb parser. More...

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

class	PlumedMain
	Main plumed object. More...

class	ProbWeight

class	Random

class	Register
	Base class, with type independent information. More...

class	RegisterBase
	General register. More...

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	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	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 compute switching functions. More...

class	TargetDist

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	Tree

class	TypesafePtr
	Class to deal with propoagation of typesafe pointers. 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	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.

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

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

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

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

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

using	VectorView = mdMemoryView<helpers::dynamic_extent, 3>

Functions
ActionRegister &	actionRegister ()

ActionRegister &	actionRegister ()
	Function returning a reference to the ActionRegister.

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 ()

CLToolRegister &	cltoolRegister ()
	Function returning a reference to the CLToolRegister.

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)

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

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

constexpr double	dp2cutoff (6.25)

static bool	dp2cutoffNoStretch ()

constexpr double	epsilon (std::numeric_limits< double >::epsilon())
	Very small non-zero number.

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

const std::map< std::string, std::string > &	getModuleMap ()

template<typename T>
static void	getPointer (const TypesafePtr &p, const std::vector< unsigned > &shape, const unsigned &start, const unsigned &stride, T *&pp)

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

static bool	isZero (const ExpressionTreeNode &node)

constexpr double	kBoltzmann (0.0083144621)
	Boltzman constant in kj/K.

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)

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

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

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.

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.

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.

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

std::ostream &	operator<< (std::ostream &log, const Register &reg)

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)

constexpr double	pi (3.141592653589793238462643383279502884197169399375105820974944592307)
	PI.

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

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

static bool	SubprocessPidGetenvSignals () noexcept
	Retrieve PLUMED_ENABLE_SIGNALS.

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

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)

template<class T>
std::size_t	typesafePtrSizeof ()

template<>
std::size_t	typesafePtrSizeof< const void > ()

template<>
std::size_t	typesafePtrSizeof< void > ()

static bool	typesafePtrSkipCheck ()

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
constexpr double	dp2cutoffA =1.00193418799744762399

constexpr double	dp2cutoffB =-.00193418799744762399

const double	epsilon =1e-14

template<typename T>
constexpr bool	isActionType = std::is_base_of<Action, T>::value

Typedef Documentation

◆ VectorView

using PLMD::VectorView = mdMemoryView<helpers::dynamic_extent, 3>

Function Documentation

◆ actionRegister() [1/2]

ActionRegister & PLMD::actionRegister ( )

◆ 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() [1/2]

CLToolRegister & PLMD::cltoolRegister ( )

◆ 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 )

◆ 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 )

◆ dp2cutoff()

double PLMD::dp2cutoff ( 6. 25 )

constexpr

◆ dp2cutoffNoStretch()

static bool PLMD::dp2cutoffNoStretch ( )

inlinestatic

◆ extProduct()

template<unsigned n, unsigned m>

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

◆ getModuleMap()

const std::map< std::string, std::string > & PLMD::getModuleMap ( )

◆ getPointer()

template<typename T>

static void PLMD::getPointer	(	const TypesafePtr &	p,
		const std::vector< unsigned > &	shape,
		const unsigned &	start,
		const unsigned &	stride,
		T *&	pp )

static

◆ indexed_lt()

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

◆ isZero()

static bool PLMD::isZero ( const ExpressionTreeNode & node )

static

◆ 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 )

◆ modulo()

template<unsigned n>

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

◆ modulo2()

template<unsigned n>

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

◆ 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<<() [1/9]

template<typename T>

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

◆ operator<<() [2/9]

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

◆ operator<<() [3/9]

template<class T>

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

Write using << syntax.

Formatted output with << operator.

◆ operator<<() [4/9]

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<<() [5/9]

std::ostream & PLMD::operator<<	(	std::ostream &	log,
		const Register &	reg )

◆ operator<<() [6/9]

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

◆ operator<<() [7/9]

template<unsigned n, unsigned m>

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

◆ operator<<() [8/9]

template<unsigned n>

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

◆ operator<<() [9/9]

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

◆ pseudoInvert()

template<typename T>

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

◆ 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 )

◆ typesafePtrSizeof()

template<class T>

std::size_t PLMD::typesafePtrSizeof ( )

◆ typesafePtrSizeof< const void >()

template<>

std::size_t PLMD::typesafePtrSizeof< const void > ( )

inline

◆ typesafePtrSizeof< void >()

template<>

std::size_t PLMD::typesafePtrSizeof< void > ( )

inline

◆ typesafePtrSkipCheck()

static bool PLMD::typesafePtrSkipCheck ( )

inlinestatic

◆ 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

◆ dp2cutoffA

double PLMD::dp2cutoffA =1.00193418799744762399

constexpr

◆ dp2cutoffB

double PLMD::dp2cutoffB =-.00193418799744762399

constexpr

◆ epsilon

const double PLMD::epsilon =1e-14

◆ isActionType

template<typename T>

bool PLMD::isActionType = std::is_base_of<Action, T>::value

inlineconstexpr

Namespaces

Classes

Typedefs

Functions

Variables

Typedef Documentation

◆ VectorView

Function Documentation

◆ actionRegister() [1/2]

◆ chol_elsolve()

◆ cholesky()

◆ cltoolRegister() [1/2]

◆ crossProduct()

◆ dcrossDv1()

◆ dcrossDv2()

◆ delta()

◆ deriNorm()

◆ determinant()

◆ diagMat()

◆ diagMatSym()

◆ dotProduct() [1/2]

◆ dotProduct() [2/2]

◆ dp2cutoff()

◆ dp2cutoffNoStretch()

◆ extProduct()

◆ getModuleMap()

◆ getPointer()

◆ indexed_lt()

◆ inverse()

◆ Invert()

◆ isZero()

◆ 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()

◆ modulo()

◆ modulo2()

◆ 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<<() [1/9]

◆ operator<<() [2/9]

◆ operator<<() [3/9]

◆ operator<<() [4/9]

◆ operator<<() [5/9]

◆ operator<<() [6/9]

◆ operator<<() [7/9]

◆ operator<<() [8/9]

◆ operator<<() [9/9]

◆ operator<=()

◆ operator==()

◆ operator>()

◆ operator>=()

◆ pseudoInvert()

◆ StopwatchEmptyString()

◆ SubprocessPidGetenvSignals()

◆ testThrow()

◆ transpose() [1/2]

◆ transpose() [2/2]

◆ typesafePtrSizeof()