PLMD Namespace Reference

Namespaces
	analysis
	bias
	cltools
	colvar
	config
	crystallization
	function
	generic
	manyrestraints
	mapping
	molfile
	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	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	CH3Shifts
	Provides the keyword CH3SHIFTS More...
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
class	DynamicList
	A class for storing a list that changes which members are active as a function of time. More...
class	EuclideanDistance
class	Exception
	Class to deal with Plumed runtime errors. More...
class	ExchangePatterns
class	FakeFrame
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	LinkCells
	A class for doing link cells. 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	MetricRegister
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	MultiReferenceBase
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	OptimalAlignment
	A class that is intended to include or combine various optimal alignment algorithms. More...
class	OptimalRMSD
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	PointWiseMapping
class	ProbWeight
class	Random
class	RDC
	Provides the keyword RDC More...
class	ReferenceArguments
	In many applications (e.g. More...
class	ReferenceAtoms
	In many applications (e.g. More...
class	ReferenceConfiguration
class	ReferenceConfigurationOptions
	Abstract base class for calculating the distance from a reference configuration. 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	RMSDBase
class	SetupMolInfo
class	SimpleRMSD
class	SingleDomainRMSD
class	SparseGrid
class	Stopwatch
	Class implementing stopwatch to time execution. More...
class	SwitchingFunction
	Small class to compure switching functions. More...
class	TargetDist
class	TensorChecks
	Small auxiliary class. More...
class	TensorGeneric
	Class implementing fixed size matrices of doubles. More...
class	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)
MetricRegister &	metricRegister ()
double	distance (const Pbc &pbc, const std::vector< Value * > &vals, ReferenceConfiguration *ref1, ReferenceConfiguration *ref2, const bool &squared)
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 >
Matrix< T >	operator* (T &v, const Matrix< T > &m)
	Multiply matrix by scalar. 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	pseudoInvert (const Matrix< T > &A, Matrix< double > &pseudoinverse)
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 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...
static class PLMD::PlumedMainInitializer	RegisterMe
const double	epsilon =1e-14
static class PLMD::TensorChecks	checks
static class PLMD::VectorChecks	checks

Function Documentation

ActionRegister& PLMD::actionRegister ( )

related

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

template<typename T >

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

template<typename T >

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

CLToolRegister& PLMD::cltoolRegister ( )

related

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

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

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

inline

v2 Only available for size 3

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

inline

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

inline

template<unsigned n>

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

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

inline

template<typename T >

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

double PLMD::distance	(	const Pbc &	pbc,
		const std::vector< Value * > &	vals,
		ReferenceConfiguration *	ref1,
		ReferenceConfiguration *	ref2,
		const bool &	squared
	)

template<typename T >

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

Calculate the dot product between two vectors.

template<unsigned n>

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

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

inline

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

inline

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

inline

template<unsigned n, unsigned m>

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

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

inline

template<typename T >

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

template<typename T >

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

template<unsigned n, unsigned m, unsigned l>

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

template<unsigned n, unsigned m>

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

template<unsigned n, unsigned m>

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

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
	)

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
	)

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
	)

template<typename T >

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

MetricRegister & PLMD::metricRegister

(

)

template<unsigned n>

double PLMD::modulo

(

const VectorGeneric< n > &

v

)

template<unsigned n>

double PLMD::modulo2

(

const VectorGeneric< n > &

v

)

template<typename U >

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

template<typename T >

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

template<typename T >

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

template<typename T >

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

template<typename T >

T PLMD::norm

(

const std::vector< T > &

A

)

Calculate the dot product between a vector and itself.

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

inline

template<typename T >

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

Multiply matrix by scalar.

template<unsigned n>

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

template<unsigned n>

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

template<unsigned n, unsigned m>

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

template<unsigned n, unsigned m>

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

template<unsigned n>

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

template<unsigned n, unsigned m>

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

template<unsigned n>

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

template<unsigned n, unsigned m>

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

template<unsigned n>

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

template<unsigned n, unsigned m>

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

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

inline

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

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

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

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

template<typename T >

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

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

template<class T >

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

Write using << syntax.

Formatted output with << operator.

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

inline

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

inline

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

inline

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

inline

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

inline

template<typename T >

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

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

inline

template<typename T >

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

template<unsigned n, unsigned m>

TensorGeneric<n,m> PLMD::transpose

(

const TensorGeneric< m, n > &

t

)

Variable Documentation

class PLMD::TensorChecks PLMD::checks

static

class PLMD::VectorChecks PLMD::checks

static

const double PLMD::epsilon =1e-14

class PLMD::PlumedMainInitializer PLMD::RegisterMe

static

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.