Classes | Typedefs | Functions
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.