Tool Box

Classes providing basic tools in plumed. More...

Classes
class	PLMD::Value
	A class for holding the value of a function together with its derivatives. More...
class	PLMD::ReferenceArguments
	In many applications (e.g. More...
class	PLMD::ReferenceAtoms
	In many applications (e.g. More...
class	PLMD::Angle
	Class to compute angles. More...
class	PLMD::AtomNumber
	Simple class to store the index of an atom. More...
class	PLMD::Citations
	Class taking care of bibliography. More...
struct	PLMD::Communicator::Data
	Structure defining a buffer for MPI. More...
struct	PLMD::Communicator::ConstData
	Const version of Communicator::Data See Communicator::Data documentation. More...
class	PLMD::Communicator::Status
	Wrapper class for MPI_Status. More...
class	PLMD::Communicator::Request
	Wrapper class for MPI_Request. More...
class	PLMD::Communicator
	Class containing wrappers to MPI. More...
class	PLMD::DLLoader
	Class taking care of dynamic loading. More...
class	PLMD::DynamicList< T >
	A class for storing a list that changes which members are active as a function of time. More...
class	PLMD::Exception
	Class to deal with Plumed runtime errors. More...
class	PLMD::Grid
class	PLMD::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	PLMD::IFile::Field
class	PLMD::IFile
	Class for input files. More...
class	PLMD::LinkCells
	A class for doing link cells. More...
class	PLMD::LoopUnroller< n >
	Utiliy class for loop unrolling. More...
class	PLMD::NeighborList
	A class that implements neighbor lists from two lists or a single list of atoms. More...
class	PLMD::OFile::Field
	Class identifying a single field for fielded output. More...
class	PLMD::OFile
	Class for output files. More...
class	PLMD::Random
class	PLMD::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	PLMD::Stopwatch::Time
	Class to hold the value of absolute time. More...
class	PLMD::Stopwatch::Watch
	Class to store a single stopwatch. More...
class	PLMD::Stopwatch
	Class implementing stopwatch to time execution. More...
class	PLMD::SwitchingFunction
	Small class to compure switching functions. More...
class	PLMD::TensorGeneric< n, m >
	Class implementing fixed size matrices of doubles. More...
class	PLMD::Tools
	Empty class which just contains several (static) tools. More...
class	PLMD::Torsion
	Class to compute torsional angles. More...
class	PLMD::Units
	Small utility class that contains information about units. More...
class	PLMD::VectorGeneric< n >
	Class implementing fixed size vectors of doubles. More...
class	PLMD::vesselbase::BridgeVessel
	This class allows you to calculate the vessel in one ActionWithVessel. More...
class	PLMD::vesselbase::FunctionVessel
	Objects that inherit from FunctionVessel can be used (in tandem with PLMD::vesselbase::ActionWithVessel) to calculate functions of the form \(\prod_k H_k[ \sum_j \prod_i g_i(x) ]\). More...
class	PLMD::vesselbase::StoreDataVessel
	Objects that inherit from FunctionVessel can be used (in tandem with PLMD::vesselbase::ActionWithVessel) to store values and derivatives for a set of scalars or vectors that are calculated by a PLMD::vesselbase::ActionWithVessel. More...

Typedefs
typedef TensorGeneric< 2, 2 >	PLMD::Tensor2d
typedef TensorGeneric< 3, 3 >	PLMD::Tensor3d
typedef TensorGeneric< 4, 4 >	PLMD::Tensor4d
typedef Tensor3d	PLMD::Tensor
typedef VectorGeneric< 2 >	PLMD::Vector2d
	Alias for two dimensional vectors. More...
typedef VectorGeneric< 3 >	PLMD::Vector3d
	Alias for three dimensional vectors. More...
typedef VectorGeneric< 4 >	PLMD::Vector4d
	Alias for four dimensional vectors. More...
typedef Vector3d	PLMD::Vector
	Alias for three dimensional vectors. More...

Functions
const double	PLMD::epsilon (std::numeric_limits< double >::epsilon())
	Very small non-zero number. More...
const double	PLMD::kBoltzmann (0.0083144621)
	Boltzman constant in kj/K. More...
const double	PLMD::pi (3.141592653589793238462643383279502884197169399375105820974944592307)
	PI. More...

Detailed Description

Classes providing basic tools in plumed.

Classes of this group are designed to be reusable and to incorporate all sorts of functionality in plumed. We try to keep their documentation as complete and clear as possible so as to increase the chance that they will be reused.

If you implement a new class that you think might be useful to others please add it to the list by including the following inside the header file.

\ingroup TOOLBOX

Typedef Documentation

typedef Tensor3d PLMD::Tensor

typedef TensorGeneric<2,2> PLMD::Tensor2d

typedef TensorGeneric<3,3> PLMD::Tensor3d

typedef TensorGeneric<4,4> PLMD::Tensor4d

typedef Vector3d PLMD::Vector

Alias for three dimensional vectors.

typedef VectorGeneric<2> PLMD::Vector2d

Alias for two dimensional vectors.

typedef VectorGeneric<3> PLMD::Vector3d

Alias for three dimensional vectors.

typedef VectorGeneric<4> PLMD::Vector4d

Alias for four dimensional vectors.

Function Documentation

const double PLMD::epsilon

(

std::numeric_limits< double >::

epsilon()

)

Very small non-zero number.

const double PLMD::kBoltzmann

(

0.

0083144621

)

Boltzman constant in kj/K.

const double PLMD::pi

(

3.

141592653589793238462643383279502884197169399375105820974944592307

)

PI.