PLMD Namespace Reference

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
	membranefusion
	molfile
	multicolvar
	opes
	pamm
	piv
	s2cm
	sasa
	secondarystructure
	setup
	vatom
	ves
	vesselbase
	xdrfile

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	ExceptionTypeError
	Class representing a type error in the PLMD::Plumed interface. 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	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	TensorGeneric
class	TensorGenericAux
	Small class to contain local utilities. More...
class	Tools
class	Torsion
class	Tree
class	TypesafePtr
class	Units
class	Value
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	dp2cutoff (6.25)
static bool	dp2cutoffNoStretch ()
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 const char *	getenvForceUnique () noexcept
	Use unique list of atoms to manipulate forces and positions. More...
static bool	getenvMergeVectorsPriorityQueue () noexcept
	Use a priority_queue to merge unique vectors. More...
const std::map< std::string, std::string > &	getModuleMap ()
static OpenMPVars &	getOpenMPVars ()
template<typename T >
static void	getPointers (const TypesafePtr &p, const TypesafePtr &px, const TypesafePtr &py, const TypesafePtr &pz, unsigned maxel, T *&ppx, T *&ppy, T *&ppz, unsigned &stride)
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)
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 __PLUMED_WRAPPER_ANONYMOUS_BEGIN 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)
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
const double	dp2cutoffA =1.00193418799744762399
const double	dp2cutoffB =-.00193418799744762399
const double	epsilon =1e-14
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 ( )

related

add()

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 ( )

related

copy() [1/2]

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
	)

dp2cutoff()

const double PLMD::dp2cutoff

(

6.

25

)

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
	)

getenvForceUnique()

static const char* PLMD::getenvForceUnique ( )

staticnoexcept

Use unique list of atoms to manipulate forces and positions.

A unique list of atoms is used to manipulate forces and positions in MPI parallel runs. In serial runs, this is done if convenient. The code currently contain some heuristic to decide if the unique list should be used or not. An env var can be used to override this decision. export PLUMED_FORCE_UNIQUE=yes # enforce using the unique list in serial runs export PLUMED_FORCE_UNIQUE=no # enforce not using the unique list in serial runs export PLUMED_FORCE_UNIQUE=auto # choose heuristically default: auto

getenvMergeVectorsPriorityQueue()

static bool PLMD::getenvMergeVectorsPriorityQueue ( )

staticnoexcept

Use a priority_queue to merge unique vectors.

export PLUMED_MERGE_VECTORS_PRIORITY_QUEUE=yes to use a priority_queue. Might be faster with some settings, but appears to not be in practice. This option is for testing and might be removed.

getModuleMap()

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

(

)

getOpenMPVars()

static OpenMPVars& PLMD::getOpenMPVars ( )

static

getPointers()

template<typename T >

static void PLMD::getPointers ( const TypesafePtr &  p, const TypesafePtr &  px, const TypesafePtr &  py, const TypesafePtr &  pz, unsigned  maxel, T *&  ppx, T *&  ppy, T *&  ppz, unsigned &  stride  )

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
	)

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 __PLUMED_WRAPPER_ANONYMOUS_BEGIN 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

)

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

const double PLMD::dp2cutoffA =1.00193418799744762399

dp2cutoffB

const double PLMD::dp2cutoffB =-.00193418799744762399

epsilon

const double PLMD::epsilon =1e-14

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.