Namespaces
	analysis

	bias

	cltools

	colvar

	config

	function

	generic

	manyrestraints

	multicolvar

	secondarystructure

	setup

	vatom

	vesselbase

Classes
class	Action
	Base class for all the input 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	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	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	CInterpolation

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	CS2Backbone
	Provides the keyword CS2BACKBONE More...

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

class	DRMSD
	A class that implements DRMSD calculations. More...

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

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

class	ExchangePatterns

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

class	FlexibleBin

class	GREX

class	Grid

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	IMD
	Provides the keyword IMD More...

class	InterpolateBicubic

class	InterpolateCubic

class	Kearsley

class	KernelFunctions

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

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

class	Log
	Class containing the log stream. 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	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	MPI_Comm
	Surrogate of MPI types when MPI library is not available. More...

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	OptimalAlignment
	A class that is intended to include or combine various optimal alignment algorithms. More...

class	Pbc

class	PDB
	Minimalistic pdb parser. More...

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

class	PlumedMain
	Main plumed object. More...

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

class	ProbWeight

class	Random

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	SetupMolInfo

class	SparseGrid

class	Stopwatch
	Class implementing stopwatch to time execution. More...

class	SwitchingFunction
	Small class to compure switching functions in the form In the future we might extend it so as to be set using a string: void set(std::string); which can then be parsed for more complex stuff, e.g. More...

class	TargetDist

class	TensorChecks
	Small auxiliary class. More...

class	TensorGeneric
	Class implementing fixed size matrices of doubles. 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 TensorGeneric< 2, 2 >	Tensor2d

typedef TensorGeneric< 3, 3 >	Tensor3d

typedef TensorGeneric< 4, 4 >	Tensor4d

typedef Tensor3d	Tensor

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 Vector3d	Vector
	Alias for three dimensional vectors. More...

Functions
ActionRegister &	actionRegister ()

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

CLToolRegister &	cltoolRegister ()

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

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

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

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

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

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

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)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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, 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)

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

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

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

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

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

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

const double	pi (3.141592653589793238462643383279502884197169399375105820974944592307)
	PI. More...

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

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

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

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

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

double	dotProduct (const VectorGeneric< 2 > &v1, const VectorGeneric< 2 > &v2)

double	dotProduct (const VectorGeneric< 3 > &v1, const VectorGeneric< 3 > &v2)

double	dotProduct (const VectorGeneric< 4 > &v1, const VectorGeneric< 4 > &v2)

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

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

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

Variables
static class PLMD::PlumedMainInitializer	RegisterMe

const double	epsilon =1e-28

static class PLMD::TensorChecks	checks

static class PLMD::VectorChecks	checks

Function Documentation

ActionRegister& PLMD::actionRegister ( )

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

Definition at line 175 of file Value.cpp.

template<typename T >

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

Definition at line 303 of file Matrix.h.

template<typename T >

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

Definition at line 282 of file Matrix.h.

CLToolRegister& PLMD::cltoolRegister ( )

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

Definition at line 159 of file Value.cpp.

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

Definition at line 167 of file Value.cpp.

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

inline

v2 Only available for size 3

Definition at line 317 of file Vector.h.

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

inline

Definition at line 401 of file Tensor.h.

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

inline

Definition at line 410 of file Tensor.h.

template<unsigned n>

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

Definition at line 262 of file Vector.h.

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

inline

Definition at line 381 of file Tensor.h.

template<typename T >

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

Definition at line 203 of file Matrix.h.

template<typename T >

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

Calculate the dot product between two vectors.

Definition at line 54 of file Matrix.h.

template<unsigned n>

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

Definition at line 274 of file Vector.h.

double PLMD::dotProduct	(	const VectorGeneric< 2 > &	v1,
		const VectorGeneric< 2 > &	v2
	)

inline

Definition at line 282 of file Vector.h.

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

inline

Definition at line 294 of file Vector.h.

double PLMD::dotProduct	(	const VectorGeneric< 4 > &	v1,
		const VectorGeneric< 4 > &	v2
	)

inline

Definition at line 306 of file Vector.h.

template<unsigned n, unsigned m>

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

Definition at line 396 of file Tensor.h.

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

inline

Definition at line 386 of file Tensor.h.

template<typename T >

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

Definition at line 246 of file Matrix.h.

template<typename T >

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

Definition at line 314 of file Matrix.h.

template<unsigned n, unsigned m, unsigned l>

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

Definition at line 343 of file Tensor.h.

template<unsigned n, unsigned m>

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

Definition at line 352 of file Tensor.h.

template<unsigned n, unsigned m>

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

Definition at line 359 of file Tensor.h.

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
	)

Definition at line 366 of file Tensor.h.

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
	)

Definition at line 371 of file Tensor.h.

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
	)

Definition at line 376 of file Tensor.h.

template<typename T >

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

Definition at line 195 of file Matrix.h.

template<unsigned n>

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

Definition at line 335 of file Vector.h.

template<unsigned n>

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

Definition at line 330 of file Vector.h.

template<typename U >

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

Definition at line 318 of file DynamicList.h.

template<typename T >

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

Definition at line 165 of file Matrix.h.

template<typename T >

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

Definition at line 171 of file Matrix.h.

template<typename T >

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

Definition at line 178 of file Matrix.h.

template<typename T >

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

Calculate the dot product between a vector and itself.

Definition at line 61 of file Matrix.h.

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

inline

Definition at line 145 of file AtomNumber.h.

template<unsigned n>

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

Definition at line 246 of file Vector.h.

template<unsigned n>

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

Definition at line 252 of file Vector.h.

template<unsigned n, unsigned m>

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

Definition at line 288 of file Tensor.h.

template<unsigned n, unsigned m>

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

Definition at line 295 of file Tensor.h.

template<unsigned n>

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

Definition at line 234 of file Vector.h.

template<unsigned n, unsigned m>

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

Definition at line 274 of file Tensor.h.

template<unsigned n>

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

Definition at line 240 of file Vector.h.

template<unsigned n, unsigned m>

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

Definition at line 281 of file Tensor.h.

template<unsigned n>

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

Definition at line 257 of file Vector.h.

template<unsigned n, unsigned m>

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

Definition at line 300 of file Tensor.h.

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

inline

Definition at line 120 of file AtomNumber.h.

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

Definition at line 41 of file Citations.cpp.

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

Definition at line 50 of file Stopwatch.cpp.

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

Definition at line 80 of file CLToolRegister.cpp.

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

Definition at line 109 of file ActionRegister.cpp.

template<typename T >

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

Definition at line 190 of file Matrix.h.

template<class T >

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

Write using << syntax.

Formatted output with << operator.

Definition at line 193 of file OFile.h.

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

Definition at line 225 of file PDB.cpp.

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

inline

Definition at line 130 of file AtomNumber.h.

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

inline

Definition at line 140 of file AtomNumber.h.

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

inline

Definition at line 125 of file AtomNumber.h.

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

inline

Definition at line 135 of file AtomNumber.h.

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

inline

Definition at line 150 of file Value.h.

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

inline

Definition at line 162 of file Value.h.

template<typename T >

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

Definition at line 185 of file Matrix.h.

template<unsigned n, unsigned m>

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

Definition at line 391 of file Tensor.h.

Variable Documentation

class PLMD::TensorChecks PLMD::checks

static

class PLMD::VectorChecks PLMD::checks

static

const double PLMD::epsilon =1e-28

Definition at line 27 of file LatticeReduction.cpp.

class PLMD::PlumedMainInitializer PLMD::RegisterMe

static

Namespaces

Classes

Typedefs

Functions

Variables

Function Documentation

Variable Documentation