Namespaces
namespace	adjmat
namespace	analysis
namespace	bias
namespace	blas
namespace	cltools
namespace	colvar
namespace	config
namespace	crystallization
namespace	dimred
namespace	drr
namespace	eds
namespace	fisst
namespace	function
namespace	funnel
namespace	generic
namespace	gridtools
namespace	h36
	Tiny namespace for hybrid36 format.
namespace	isdb
namespace	lapack
namespace	lepton
namespace	logmfd
namespace	manyrestraints
namespace	mapping
namespace	maze
namespace	membranefusion
namespace	molfile
namespace	multicolvar
namespace	opes
namespace	pamm
namespace	piv
namespace	s2cm
namespace	sasa
namespace	secondarystructure
namespace	setup
namespace	vatom
namespace	ves
namespace	vesselbase
namespace	xdrfile

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	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
	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	PlumedHandle
	Tiny local class to load a PLUMED kernel. More...
class	PlumedMain
	Main plumed object. 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	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 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.

Functions
ActionRegister &	actionRegister ()
ActionRegister &	actionRegister ()
	Function returning a reference to the 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 ()
CLToolRegister &	cltoolRegister ()
	Function returning a reference to the 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.
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())
	Very small non-zero number.
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.
static bool	getenvMergeVectorsPriorityQueue () noexcept
	Use a priority_queue to merge unique vectors.
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)
	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)
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.
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 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)
	PI.
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.
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
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.

Function Documentation

◆ actionRegister() [1/2]

ActionRegister & PLMD::actionRegister ( )

◆ 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() [1/2]

CLToolRegister & PLMD::cltoolRegister ( )

◆ 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()

bool PLMD::dp2cutoffNoStretch ( )

inlinestatic

◆ extProduct()

template<unsigned n, unsigned m>

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

◆ getenvForceUnique()

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()

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()

OpenMPVars & PLMD::getOpenMPVars ( )

static

◆ getPointers()

template<typename T>

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()

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

◆ 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()

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()

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()

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()

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.

Namespaces

Classes

Typedefs

Functions

Variables

Function Documentation

◆ actionRegister() [1/2]

◆ add()

◆ chol_elsolve()

◆ cholesky()

◆ cltoolRegister() [1/2]

◆ copy() [1/2]

◆ copy() [2/2]

◆ crossProduct()

◆ dcrossDv1()

◆ dcrossDv2()

◆ delta()

◆ deriNorm()

◆ determinant()

◆ diagMat()

◆ diagMatSym()

◆ distance()

◆ dotProduct() [1/2]

◆ dotProduct() [2/2]

◆ dp2cutoff()

◆ dp2cutoffNoStretch()

◆ extProduct()

◆ getenvForceUnique()

◆ getenvMergeVectorsPriorityQueue()

◆ getModuleMap()

◆ getOpenMPVars()

◆ getPointers()

◆ 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()

◆ 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>()