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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::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::Communicator::Status |
| class | PLMD::Communicator::Request |
| 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::IFile::Field |
| 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::Stopwatch::Time |
| Class to hold the value of absolute time. More... | |
| class | PLMD::Stopwatch::Watch |
| Class to store a single stopwatch. More... | |
| class | PLMD::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 | 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::ActionWithVessel) to calculate functions of the form \(\prod_k H_k[ \sum_j \prod_i g_i(x) ]\). 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... | |
Enumerations | |
| enum | { PLMD::Value::unset, PLMD::Value::periodic, PLMD::Value::notperiodic } |
| Is this quantity periodic. More... | |
| enum | { PLMD::HistogramBead::gaussian, PLMD::HistogramBead::triangular } |
| enum | { PLMD::HistogramBead::unset, PLMD::HistogramBead::periodic, PLMD::HistogramBead::notperiodic } |
| enum | PLMD::RMSD::AlignmentMethod { PLMD::RMSD::SIMPLE, PLMD::RMSD::OPTIMAL, PLMD::RMSD::OPTIMAL_FAST } |
| enum | { PLMD::SwitchingFunction::spline, PLMD::SwitchingFunction::exponential, PLMD::SwitchingFunction::gaussian, PLMD::SwitchingFunction::smap } |
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... | |
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 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 |
| typedef VectorGeneric<2> PLMD::Vector2d |
| typedef VectorGeneric<3> PLMD::Vector3d |
| typedef VectorGeneric<4> PLMD::Vector4d |
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private |
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private |
| Enumerator | |
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| gaussian | |
| triangular | |
Definition at line 47 of file HistogramBead.h.
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private |
| Enumerator | |
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| unset | |
| periodic | |
| notperiodic | |
Definition at line 48 of file HistogramBead.h.
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private |
| Enumerator | |
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| spline | |
| exponential | |
| gaussian | |
| smap | |
Definition at line 41 of file SwitchingFunction.h.
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private |
| 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.
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1.8.8
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