Classes | Typedefs | Functions
Tool Box

Classes

class  PLMD::Value
 A class for holding the value of a function together with its derivatives. More...
 
class  PLMD::mapping::PathReparameterization
 This class can be used to make a set of reference configurations equidistant. 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...
 
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
 
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
 
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
 
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::ves::CoeffsBase
 
class  PLMD::ves::FermiSwitchingFunction
 Small class to compute fermi switching function. 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

◆ Tensor

◆ Tensor2d

◆ Tensor3d

◆ Tensor4d

◆ Vector

Alias for three dimensional vectors.

◆ Vector2d

Alias for two dimensional vectors.

◆ Vector3d

Alias for three dimensional vectors.

◆ Vector4d

Alias for four dimensional vectors.

Function Documentation

◆ epsilon()

const double PLMD::epsilon ( std::numeric_limits< double >  ::epsilon())

Very small non-zero number.

◆ kBoltzmann()

const double PLMD::kBoltzmann ( 0.  0083144621)

Boltzman constant in kj/K.

◆ pi()

const double PLMD::pi ( 3.  141592653589793238462643383279502884197169399375105820974944592307)

PI.