Namespaces | |
| namespace | adjmat |
| namespace | bias |
| namespace | blas |
| namespace | cltools |
| namespace | clusters |
| namespace | colvar |
| namespace | config |
| namespace | contour |
| namespace | crystdistrib |
| namespace | dimred |
| namespace | drr |
| namespace | eds |
| namespace | enum_traits |
| namespace | envsim |
| namespace | fisst |
| namespace | fourier |
| namespace | function |
| namespace | funnel |
| namespace | gch |
| namespace | generic |
| namespace | gridtools |
| namespace | h36 |
| Tiny namespace for hybrid36 format. | |
| namespace | helpers |
| namespace | isdb |
| namespace | landmarks |
| namespace | lapack |
| namespace | lepton |
| namespace | liquid_crystal |
| namespace | logmfd |
| namespace | mapping |
| namespace | matrixtools |
| namespace | maze |
| namespace | membranefusion |
| namespace | mergeVectorTools |
| namespace | metatomic |
| namespace | molfile |
| namespace | multicolvar |
| namespace | OpenACC |
| namespace | OpenMP |
| namespace | opes |
| namespace | pamm |
| namespace | piv |
| namespace | refdist |
| namespace | s2cm |
| namespace | sasa |
| namespace | secondarystructure |
| namespace | setup |
| namespace | sizeshape |
| namespace | sprint |
| namespace | switchContainers |
| namespace | symfunc |
| namespace | valtools |
| namespace | vatom |
| namespace | Versors |
| namespace | ves |
| namespace | volumes |
| namespace | wham |
| namespace | xdrfile |
Classes | |
| class | Accelerator |
| class | Action |
| Base class for all the input Actions. More... | |
| class | ActionAnyorder |
| Action used to create a PLMD::Action that can go both before and after ActionSetup actions. More... | |
| class | ActionAtomistic |
| Action used to create objects that access the positions of the atoms from the MD code. More... | |
| class | ActionForInterface |
| 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... | |
| struct | ActionRegisterPointers |
| class | ActionRegistration |
| Each instance of this specialized class represents an action that can be called with the specified directive. 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 | ActionShortcut |
| Action used to create a command that expands to multiple PLMD::Action commands when read in during input. More... | |
| class | ActionToGetData |
| Provides the keyword GET More... | |
| class | ActionToPutData |
| Provides the keyword PUT More... | |
| class | ActionWithArguments |
| class | ActionWithMatrix |
| 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 | ActionWithVector |
| 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... | |
| struct | ArgumentBookeepingHolder |
| struct | ArgumentsBookkeeping |
| struct | AtomDistribution |
| tested in regtest/tools/rt-make-AtomicDistribution Acts as a template for any distribution More... | |
| class | AtomNumber |
| Simple class to store the index of an atom. 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 | Brent1DRootSearch |
| A class for doing parabolic interpolation and minimisation of 1D functions using Brent's method. More... | |
| class | CheckInRange |
| 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... | |
| struct | CLToolRegisterPointers |
| 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 | ColvarOutput |
| class | Communicator |
| Class containing wrappers to MPI. More... | |
| class | ConjugateGradient |
| class | DataPassingObject |
| class | DataPassingObjectTyped |
| class | DataPassingTools |
| class | DataPassingToolsTyped |
| class | DLLoader |
| Class taking care of dynamic loading. More... | |
| class | DomainDecomposition |
| class | ERMSD |
| A class that implements ERMSD calculations. More... | |
| class | Exception |
| Class to deal with Plumed runtime errors. More... | |
| class | ExceptionDebug |
| Class representing a debug error (can only be thrown when using debug options) More... | |
| class | ExceptionError |
| Class representing a generic error. More... | |
| class | ExceptionRegisterError |
| Class representing an error in a register. More... | |
| class | ExceptionTypeError |
| Class representing a type error in the PLMD::Plumed interface. More... | |
| class | ExchangePatterns |
| class | F1dim |
| class | FileBase |
| Base class for dealing with files. More... | |
| struct | fileDeleter |
| class | fileParser |
| class | fileTraj |
| atomic distribution from a trajectory file More... | |
| class | FlexibleBin |
| struct | ForceIndexHolder |
| class | ForceInput |
| struct | ForceOutput |
| class | ForwardDecl |
| Utility class for forward declaration of references. More... | |
| class | GenericMolInfo |
| class | GREX |
| class | Grid |
| class | GridBase |
| class | Group |
| Provides the keyword GROUP More... | |
| 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 | KernelFunctions |
| class | Keywords |
| This class holds the keywords and their documentation. More... | |
| class | LatticeReduction |
| Class implementing algorithms for lattice reduction. More... | |
| class | LeptonCall |
| class | LinkCells |
| A class for doing link cells. More... | |
| class | Log |
| Class containing the log stream. More... | |
| class | LoopUnroller |
| Utiliy class for loop unrolling. More... | |
| class | Matrix |
| This class stores a full matrix and allows one to do some simple matrix operations. More... | |
| class | MatrixElementOutput |
| class | MatrixSquareBracketsAccess |
| Utility class to add [][] access. More... | |
| class | Minimise1DBrent |
| A class for doing parabolic interpolation and minimisation of 1D functions using Brent's method. More... | |
| class | MinimiseBase |
| 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 | NeighborList |
| A class that implements neighbor lists from two lists or a single list of atoms. More... | |
| class | OFile |
| Class for output files. More... | |
| struct | ParallelActionsInput |
| struct | ParallelActionsOutput |
| class | ParallelTaskManager |
| class | Pbc |
| class | PbcAction |
| Provides the keyword PBC More... | |
| class | PDB |
| Minimalistic pdb parser. More... | |
| class | PlumedHandle |
| Tiny local class to load a PLUMED kernel. More... | |
| class | PlumedMain |
| Main plumed object. More... | |
| class | ProbWeight |
| class | Random |
| class | Register |
| Base class, with type independent information. More... | |
| class | RegisterBase |
| General register. More... | |
| class | repliedTrajectory |
| a decorator for replicate the atomic distribution More... | |
| class | RequiredMatrixElements |
| class | RequiredMatrixElementsUpdater |
| 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 | RMSDCoreData |
| this is a class which is needed to share information across the various non-threadsafe routines so that the public function of rmsd are threadsafe while the inner core can safely share information More... | |
| class | RootFindingBase |
| class | SparseGrid |
| class | Stopwatch |
| class | Subprocess |
| Class managing a subprocess. More... | |
| class | SubprocessPid |
| Small utility class, used to avoid inclusion of unistd.h> in a header file. More... | |
| class | SwitchingFunction |
| Small class to compute switching functions. More... | |
| class | SwitchingFunctionAccelerable |
| Small class to compute switching functions. More... | |
| class | TargetDist |
| struct | TensorGenericAux |
| Small class to contain local utilities. More... | |
| class | TensorTyped |
| Class implementing fixed size matrices of doubles. More... | |
| struct | theLine |
| A wiggly line of atoms. More... | |
| struct | tiledSimpleCubic |
| class | TokenizedLine |
| This class abstracts the input line in tokens. More... | |
| class | Tools |
| Empty class which just contains several (static) tools. More... | |
| class | Torsion |
| Class to compute torsional angles. More... | |
| class | TrajectoryParser |
| class | Tree |
| struct | twoGlobs |
| Atom randomly distribuited between two not overlapping a spheres. More... | |
| class | TypesafePtr |
| Class to deal with propoagation of typesafe pointers. More... | |
| struct | uniformCube |
| struct | uniformSphere |
| Atom randomly distribuited in a sphere. More... | |
| class | UniformSphericalVector |
| 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 | VectorTyped |
| Class implementing fixed size vectors of doubles. More... | |
| class | View |
| A not-owning view for generic data. More... | |
| class | View2D |
| A not-owning view for accessing array witha 2D interface. More... | |
| class | WeightBase |
| class | WithCmd |
| Base for classes with cmd() method. More... | |
Typedefs | |
| template<std::size_t N = helpers::dynamic_extent, std::size_t STRIDE = 3> | |
| using | mdMemoryView = View2D<double,N,STRIDE> |
| template<std::size_t N = 3> | |
| using | MemoryView = View<double,N> |
| typedef Tensor3d | Tensor |
| typedef TensorGeneric< 1, 1 > | Tensor1d |
| typedef TensorTyped< float, 1, 1 > | Tensor1f |
| typedef TensorGeneric< 2, 2 > | Tensor2d |
| typedef TensorTyped< float, 2, 2 > | Tensor2f |
| typedef TensorGeneric< 3, 3 > | Tensor3d |
| typedef TensorTyped< float, 3, 3 > | Tensor3f |
| typedef TensorGeneric< 4, 4 > | Tensor4d |
| typedef TensorTyped< float, 4, 4 > | Tensor4f |
| typedef TensorGeneric< 5, 5 > | Tensor5d |
| typedef TensorTyped< float, 5, 5 > | Tensor5f |
| template<unsigned n, unsigned m> | |
| using | TensorGeneric = TensorTyped<double,n,m> |
| template<typename T> | |
| using | TensorT = TensorTyped<T,3,3> |
| Alias for three by three Tensor of any type: | |
| using | unique_FILE = std::unique_ptr<FILE,fileDeleter> |
| typedef Vector3d | Vector |
| Alias for three dimensional vectors. | |
| typedef VectorGeneric< 1 > | Vector1d |
| Alias for one dimensional vectors. | |
| typedef VectorTyped< float, 1 > | Vector1f |
| Alias for one dimensional vectors. | |
| typedef VectorGeneric< 2 > | Vector2d |
| Alias for two dimensional vectors. | |
| typedef VectorTyped< float, 2 > | Vector2f |
| Alias for two dimensional vectors. | |
| typedef VectorGeneric< 3 > | Vector3d |
| Alias for three dimensional vectors. | |
| typedef VectorTyped< float, 3 > | Vector3f |
| Alias for three dimensional vectors. | |
| typedef VectorGeneric< 4 > | Vector4d |
| Alias for four dimensional vectors. | |
| typedef VectorTyped< float, 4 > | Vector4f |
| Alias for four dimensional vectors. | |
| typedef VectorGeneric< 5 > | Vector5d |
| Alias for five dimensional vectors. | |
| typedef VectorTyped< float, 5 > | Vector5f |
| Alias for five dimensional vectors. | |
| template<unsigned n> | |
| using | VectorGeneric = VectorTyped<double, n> |
| template<typename T> | |
| using | VectorT = VectorTyped<T,3> |
| Alias for three dimensional vectors of any type: | |
| using | VectorView = mdMemoryView<helpers::dynamic_extent, 3> |
Functions | |
| ActionRegister & | actionRegister () |
| ActionRegister & | actionRegister () |
| Function returning a reference to the ActionRegister. | |
| template<typename T> | |
| void | chol_elsolve (const Matrix< T > &M, const std::vector< T > &b, std::vector< T > &y) |
| template<typename T> | |
| void | cholesky (const Matrix< T > &A, Matrix< T > &B) |
| CLToolRegister & | cltoolRegister () |
| CLToolRegister & | cltoolRegister () |
| Function returning a reference to the CLToolRegister. | |
| template<typename T> | |
| constexpr VectorTyped< T, 3 > | crossProduct (const VectorTyped< T, 3 > &v1, const VectorTyped< T, 3 > &v2) |
| template<typename T> | |
| constexpr TensorTyped< T, 3, 3 > | dcrossDv1 (const VectorTyped< T, 3 > &v1, const VectorTyped< T, 3 > &v2) |
| template<typename T> | |
| constexpr TensorTyped< T, 3, 3 > | dcrossDv2 (const VectorTyped< T, 3 > &v1, const VectorTyped< T, 3 > &v2) |
| template<typename T, unsigned n> | |
| constexpr VectorTyped< T, n > | delta (const VectorTyped< T, n > &v1, const VectorTyped< T, n > &v2) |
| template<typename T> | |
| VectorTyped< std::remove_const_t< T >, 3 > | delta (const View< T, 3 > v1, const View< T, 3 > v2) noexcept |
| template<typename T> | |
| TensorTyped< T, 3, 3 > | deriNorm (const VectorTyped< T, 3 > &v1, const TensorTyped< T, 3, 3 > &v2) |
| template<typename T> | |
| constexpr T | determinant (const TensorTyped< T, 3, 3 > &t) |
| template<typename T> | |
| int | diagMat (const Matrix< T > &A, std::vector< T > &eigenvals, Matrix< T > &eigenvecs) |
| template<typename precision, unsigned n, unsigned m> | |
| void | diagMatSym (const TensorTyped< precision, n, n > &mat, VectorTyped< precision, m > &evals, TensorTyped< precision, m, n > &evec) |
| Diagonalize tensor. | |
| template<typename T, unsigned n, unsigned m> | |
| void | diagMatSym (const TensorTyped< T, n, n > &, VectorTyped< T, m > &evals, TensorTyped< T, m, n > &evec) |
| Diagonalize tensor. | |
| template<typename T> | |
| T | dotProduct (const std::vector< T > &A, const std::vector< T > &B) |
| Calculate the dot product between two vectors. | |
| template<typename T, unsigned n> | |
| constexpr T | dotProduct (const VectorTyped< T, n > &v1, const VectorTyped< T, n > &v2) |
| constexpr double | dp2cutoff (6.25) |
| static bool | dp2cutoffNoStretch () |
| constexpr double | epsilon (std::numeric_limits< double >::epsilon()) |
| Very small non-zero number. | |
| template<typename T, unsigned n, unsigned m> | |
| constexpr TensorTyped< T, n, m > | extProduct (const VectorTyped< T, n > &v1, const VectorTyped< T, m > &v2) |
| returns the transpose of a tensor (same as TensorGeneric(const VectorGeneric&,const VectorGeneric&)) | |
| template<typename T, unsigned n, unsigned m> | |
| T | frobeniusNorm (const TensorTyped< T, m, n > &t) |
| Compute the Frobenius norm 2. | |
| const std::map< std::string, std::string > & | getModuleMap () |
| template<typename T> | |
| static void | getPointer (const TypesafePtr &p, const std::vector< std::size_t > &shape, const unsigned &start, const unsigned &stride, T *&pp) |
| void | getWords_replicas (gch::small_vector< std::string_view > &words, std::string_view line, const std::string_view separators) |
| bool | indexed_lt (std::pair< Grid::index_t, double > const &x, std::pair< Grid::index_t, double > const &y) |
| template<typename T> | |
| constexpr TensorTyped< T, 3, 3 > | inverse (const TensorTyped< T, 3, 3 > &t) |
| template<typename T> | |
| int | Invert (const Matrix< T > &A, Matrix< T > &inverse) |
| static bool | isZero (const ExpressionTreeNode &node) |
| constexpr double | kBoltzmann (0.0083144621) |
| Boltzman constant in kj/K. | |
| template<typename T> | |
| int | logdet (const Matrix< T > &M, T &ldet) |
| template<typename T, unsigned n> | |
| T | lowestEigenpairSym (const TensorTyped< T, n, n > &K, VectorTyped< T, n > &eigenvector, unsigned niter=24) |
| Compute lowest eigenvalue and eigenvector, using a branchless iterative implementation. | |
| template<typename CT> | |
| constexpr View< const typename CT::value_type > | make_const_view (const CT &container) |
| Returns a complete constant dynamic view of a container. | |
| template<typename T> | |
| View< T > | make_view (const std::vector< T > &d) |
| template<typename CT> | |
| constexpr View< typename CT::value_type > | make_view (CT &container) |
| Returns a complete dynamic view of a container. | |
| template<typename IT> | |
| auto | mapCreator (IT k, IT const end) |
| template<typename T, unsigned n, unsigned m, unsigned l> | |
| constexpr TensorTyped< T, n, l > | matmul (const TensorTyped< T, n, m > &a, const TensorTyped< T, m, l > &b) |
| matrix-matrix multiplication | |
| template<typename T, unsigned n, unsigned m, unsigned l, unsigned i> | |
| constexpr TensorTyped< T, n, i > | matmul (const TensorTyped< T, n, m > &a, const TensorTyped< T, m, l > &b, const TensorTyped< T, l, i > &c) |
| matrix-matrix-matrix multiplication | |
| template<typename T, unsigned n, unsigned m, unsigned l> | |
| constexpr VectorTyped< T, n > | matmul (const TensorTyped< T, n, m > &a, const TensorTyped< T, m, l > &b, const VectorTyped< T, l > &c) |
| matrix-matrix-vector multiplication | |
| template<typename T, typename TT, unsigned n, unsigned m> | |
| constexpr VectorTyped< T, n > | matmul (const TensorTyped< T, n, m > &a, const VectorTyped< TT, m > &b) |
| matrix-vector multiplicationi, the first argument determines the type of the result | |
| template<typename T, typename TT, unsigned n, unsigned m> | |
| constexpr VectorTyped< T, n > | matmul (const VectorTyped< T, m > &a, const TensorTyped< TT, m, n > &b) |
| vector-matrix multiplication, the first argument determines the type of the result | |
| template<typename T, unsigned n, unsigned m, unsigned l> | |
| constexpr VectorTyped< T, l > | matmul (const VectorTyped< T, n > &a, const TensorTyped< T, n, m > &b, const TensorTyped< T, m, l > &c) |
| vector-matrix-matrix multiplication | |
| template<typename T, unsigned n, unsigned m> | |
| constexpr T | matmul (const VectorTyped< T, n > &a, const TensorTyped< T, n, m > &b, const VectorTyped< T, m > &c) |
| vector-matrix-vector multiplication | |
| template<typename T, unsigned n_> | |
| constexpr T | matmul (const VectorTyped< T, n_ > &a, const VectorTyped< T, n_ > &b) |
| vector-vector multiplication (maps to dotProduct) | |
| template<typename T> | |
| void | matrixOut (Log &ostr, const Matrix< T > &mat) |
| constexpr int | max_cell (int celn, const int ncells, const bool usePBC) |
| constexpr int | min_cell (int celn, const int ncells, const bool usePBC) |
| template<typename T, unsigned n> | |
| constexpr T | modulo (const VectorTyped< T, n > &v) |
| template<typename T, unsigned n> | |
| constexpr T | modulo2 (const VectorTyped< T, n > &v) |
| 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> | |
| T | norm (const std::vector< T > &A) |
| Calculate the dot product between a vector and itself. | |
| bool | operator!= (const AtomNumber &a, const AtomNumber &b) |
| template<typename enumtype> | |
| constexpr std::enable_if_t< enum_traits::BitmaskEnum< enumtype >::has_bit_and, enumtype > | operator& (enumtype a, enumtype b) |
| Perform a bitwise AND between two enum values. | |
| template<typename T, typename J, unsigned n, unsigned m> | |
| constexpr TensorTyped< T, n, m > | operator* (const TensorTyped< T, n, m > &t1, J s) |
| template<typename T, typename J, unsigned n, unsigned m> | |
| constexpr TensorTyped< T, n, m > | operator* (J s, const TensorTyped< T, n, m > &t1) |
| template<typename T, typename J, unsigned n> | |
| constexpr VectorTyped< T, n > | operator* (J s, VectorTyped< T, n >v) |
| template<typename T> | |
| Matrix< T > | operator* (T &v, const Matrix< T > &m) |
| Multiply matrix by scalar. | |
| template<typename T, typename J, unsigned n> | |
| constexpr VectorTyped< T, n > | operator* (VectorTyped< T, n > v, J s) |
| template<typename T, unsigned n, unsigned m> | |
| constexpr TensorTyped< T, n, m > | operator+ (const TensorTyped< T, n, m > &t1, const TensorTyped< T, n, m > &t2) |
| template<typename T, unsigned n> | |
| constexpr VectorTyped< T, n > | operator+ (const VectorTyped< T, n > &v1, const VectorTyped< T, n > &v2) |
| template<typename T, unsigned n, unsigned m> | |
| constexpr TensorTyped< T, n, m > | operator- (const TensorTyped< T, n, m > &t1, const TensorTyped< T, n, m > &t2) |
| template<typename T, unsigned n> | |
| constexpr VectorTyped< T, n > | operator- (VectorTyped< T, n >v1, const VectorTyped< T, n > &v2) |
| template<typename T, typename J, unsigned n, unsigned m> | |
| constexpr TensorTyped< T, n, m > | operator/ (const TensorTyped< T, n, m > &t1, J s) |
| template<typename T, typename J, unsigned n> | |
| constexpr VectorTyped< T, n > | operator/ (const VectorTyped< T, n > &v, J s) |
| bool | operator< (const AtomNumber &a, const AtomNumber &b) |
| template<typename T> | |
| Log & | operator<< (Log &ostr, const Matrix< T > &mat) |
| Log & | operator<< (Log &ostr, const PDB &pdb) |
| template<class T> | |
| OFile & | operator<< (OFile &of, const T &t) |
| Write using << syntax. | |
| std::ostream & | operator<< (std::ostream &log, const Citations &cit) |
| std::ostream & | operator<< (std::ostream &log, const Register ®) |
| std::ostream & | operator<< (std::ostream &os, const Stopwatch &sw) |
| template<typename T, unsigned n, unsigned m> | |
| std::ostream & | operator<< (std::ostream &os, const TensorTyped< T, n, m > &t) |
| template<typename T, unsigned n> | |
| std::ostream & | operator<< (std::ostream &os, const VectorTyped< T, n > &v) |
| template<class T> | |
| Subprocess & | operator<< (Subprocess &ep, const T &t) |
| 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) |
| template<typename enumtype> | |
| constexpr std::enable_if_t< enum_traits::BitmaskEnum< enumtype >::has_bit_or, enumtype > | operator| (enumtype a, enumtype b) |
| Perform a bitwise OR between two enum values. | |
| constexpr double | pi (3.141592653589793238462643383279502884197169399375105820974944592307) |
| PI. | |
| template<typename T> | |
| int | pseudoInvert (const Matrix< T > &A, Matrix< T > &pseudoinverse) |
| auto | render (const TokenizedLine::line &l) |
| Keywords::argType | stoat (std::string_view str) |
| Converts a string to the corresponding Keywords::argType. | |
| Keywords::componentType | stoct (std::string_view str) |
| Converts a string to the corresponding Keywords::componentType. | |
| static const std::string & | StopwatchEmptyString () noexcept |
| Return an empty string. | |
| static bool | SubprocessPidGetenvSignals () noexcept |
| Retrieve PLUMED_ENABLE_SIGNALS. | |
| template<typename T, typename TT, unsigned n> | |
| constexpr VectorTyped< T, n > | sumT (const VectorTyped< T, n > &v1, const VectorTyped< TT, n > &v2) |
| static void | testThrow (const char *what) |
| Small utility just used in this file to throw arbitrary exceptions. | |
| std::string | toString (Keywords::argType at) |
| std::string | toString (Keywords::componentType at) |
| template<typename T> | |
| void | transpose (const Matrix< T > &A, Matrix< T > &AT) |
| template<typename T, unsigned n, unsigned m> | |
| constexpr TensorTyped< T, n, m > | transpose (const TensorTyped< T, m, n > &t) |
| returns the transpose of a tensor (same as TensorGeneric::transpose()) | |
| template<class T> | |
| std::size_t | typesafePtrSizeof () |
| template<> | |
| std::size_t | typesafePtrSizeof< const void > () |
| template<> | |
| std::size_t | typesafePtrSizeof< void > () |
| static bool | typesafePtrSkipCheck () |
| template<typename enumtype> | |
| constexpr std::enable_if_t< enum_traits::BitmaskEnum< enumtype >::has_valid, bool > | valid (enumtype a) |
| Test if an enum value is valid. | |
| template<typename T> | |
| TensorTyped< T, 3, 3 > | VcrossTensor (const TensorTyped< T, 3, 3 > &v2, const VectorTyped< T, 3 > &v1) |
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| TensorTyped< T, 3, 3 > | VcrossTensor (const VectorTyped< T, 3 > &v1, const TensorTyped< T, 3, 3 > &v2) |
| TokenizedLine::line | wholeLineReplicas (const std::string &myLine) |
Variables | |
| static const Tools::FastStringUnorderedMap< std::string > | doi_map |
| constexpr double | DP2CUTOFF =6.25 |
| constexpr double | dp2cutoffA =1.00193418799744762399 |
| constexpr double | dp2cutoffB =-.00193418799744762399 |
| const double | epsilon =1e-14 |
| constexpr double | halfpi =PLMD::pi*0.5 |
| PI / 2. | |
| template<typename T> | |
| constexpr bool | isActionType = std::is_base_of<Action, T>::value |
| constexpr double | twopi =PLMD::pi*2.0 |
| PI * 2. | |
| using PLMD::mdMemoryView = View2D<double,N,STRIDE> |
| using PLMD::MemoryView = View<double,N> |
| using PLMD::TensorGeneric = TensorTyped<double,n,m> |
| using PLMD::unique_FILE = std::unique_ptr<FILE,fileDeleter> |
| using PLMD::VectorGeneric = VectorTyped<double, n> |
| using PLMD::VectorView = mdMemoryView<helpers::dynamic_extent, 3> |
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| void PLMD::chol_elsolve | ( | const Matrix< T > & | M, |
| const std::vector< T > & | b, | ||
| std::vector< T > & | y ) |
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| int PLMD::diagMat | ( | const Matrix< T > & | A, |
| std::vector< T > & | eigenvals, | ||
| Matrix< T > & | eigenvecs ) |
| void PLMD::diagMatSym | ( | const TensorTyped< precision, n, n > & | mat, |
| VectorTyped< precision, m > & | evals, | ||
| TensorTyped< precision, m, n > & | evec ) |
Diagonalize tensor.
Syntax is the same as Matrix::diagMat. In addition, it is possible to call if with m_ smaller than n_. In this case, only the first (smaller) m_ eigenvalues and eigenvectors are retrieved. If case lapack fails (info!=0) it throws an exception. Notice that tensor is assumed to be symmetric!!!
| void PLMD::diagMatSym | ( | const TensorTyped< T, n, n > & | , |
| VectorTyped< T, m > & | evals, | ||
| TensorTyped< T, m, n > & | evec ) |
Diagonalize tensor.
Syntax is the same as Matrix::diagMat. In addition, it is possible to call if with m smaller than n. In this case, only the first (smaller) m eigenvalues and eigenvectors are retrieved. If case lapack fails (info!=0) it throws an exception. Notice that tensor is assumed to be symmetric!!!
| T PLMD::dotProduct | ( | const std::vector< T > & | A, |
| const std::vector< T > & | B ) |
Calculate the dot product between two vectors.
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returns the transpose of a tensor (same as TensorGeneric(const VectorGeneric&,const VectorGeneric&))
| T PLMD::frobeniusNorm | ( | const TensorTyped< T, m, n > & | t | ) |
Compute the Frobenius norm 2.
| const std::map< std::string, std::string > & PLMD::getModuleMap | ( | ) |
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| void PLMD::getWords_replicas | ( | gch::small_vector< std::string_view > & | words, |
| std::string_view | line, | ||
| const std::string_view | separators ) |
| bool PLMD::indexed_lt | ( | std::pair< Grid::index_t, double > const & | x, |
| std::pair< Grid::index_t, double > const & | y ) |
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| int PLMD::logdet | ( | const Matrix< T > & | M, |
| T & | ldet ) |
| T PLMD::lowestEigenpairSym | ( | const TensorTyped< T, n, n > & | K, |
| VectorTyped< T, n > & | eigenvector, | ||
| unsigned | niter = 24 ) |
Compute lowest eigenvalue and eigenvector, using a branchless iterative implementation.
This function is amenable for running on openACC. The accuracy could be controlled increasing the number of iterations. The default value (24) seems sufficient for most applications. In principle, it could be extended to compute m eigenvalues by:
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Returns a complete constant dynamic view of a container.
The container must have defined the methods data() and size() Also the container must have defined a public type value_type For example a std::vector is compatible
| View< T > PLMD::make_view | ( | const std::vector< T > & | d | ) |
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Returns a complete dynamic view of a container.
The container must have defined the methods data() and size() Also the container must have defined a public type value_type For example a std::vector is compatible A const std::vector is not compatible with this signature, to avoid confusion
| auto PLMD::mapCreator | ( | IT | k, |
| IT const | end ) |
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matrix-matrix multiplication
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matrix-matrix-matrix multiplication
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matrix-matrix-vector multiplication
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matrix-vector multiplicationi, the first argument determines the type of the result
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vector-matrix multiplication, the first argument determines the type of the result
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vector-matrix-matrix multiplication
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vector-matrix-vector multiplication
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vector-vector multiplication (maps to dotProduct)
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| void PLMD::mult | ( | const Matrix< T > & | A, |
| const Matrix< T > & | B, | ||
| Matrix< T > & | C ) |
| void PLMD::mult | ( | const Matrix< T > & | A, |
| const std::vector< T > & | B, | ||
| std::vector< T > & | C ) |
| void PLMD::mult | ( | const std::vector< T > & | A, |
| const Matrix< T > & | B, | ||
| std::vector< T > & | C ) |
| T PLMD::norm | ( | const std::vector< T > & | A | ) |
Calculate the dot product between a vector and itself.
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Perform a bitwise AND between two enum values.
| a | The first enum value. |
| b | The second enum value. |
This operator is only available for enum types that have a specialization of enum_traits::BitmaskEnum with the has_bit_and trait enabled.
Useful for checking composed values agains masks.
Note that the value may be a 0, and if you do not have defined the 0 as a named value you should use valid(enumtype) to check it.
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Multiply matrix by scalar.
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Write using << syntax.
Formatted output with << operator.
| 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 & | log, |
| const Register & | reg ) |
| std::ostream & PLMD::operator<< | ( | std::ostream & | os, |
| const Stopwatch & | sw ) |
| std::ostream & PLMD::operator<< | ( | std::ostream & | os, |
| const TensorTyped< T, n, m > & | t ) |
Allows printing tensor t with std::cout<<t;
| std::ostream & PLMD::operator<< | ( | std::ostream & | os, |
| const VectorTyped< T, n > & | v ) |
Allows printing vector v with std::cout<<v;
| Subprocess & PLMD::operator<< | ( | Subprocess & | ep, |
| const T & | t ) |
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Perform a bitwise OR between two enum values.
| a | The first enum value. |
| b | The second enum value. |
This operator is only available for enum types that have a specialization of enum_traits::BitmaskEnum with the has_bit_or trait enabled.
The principal use is to compose named enum values into masks or combined options.
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| Keywords::argType PLMD::stoat | ( | std::string_view | str | ) |
Converts a string to the corresponding Keywords::argType.
| str | The string to convert. |
| std::invalid_argument | If the string does not match any enum value. |
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Converts a string to the corresponding Keywords::componentType.
| str | The string to convert. |
| std::invalid_argument | if the string does not match any enum value. |
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Return an empty string.
Inline static so that it can store a static variable (for quicker access) without adding a unique global symbol to a library including this header file.
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inlinestaticnoexcept |
Retrieve PLUMED_ENABLE_SIGNALS.
Inline static so that it can store a static variable (for quicker access) without adding a unique global symbol to a library including this header file.
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Small utility just used in this file to throw arbitrary exceptions.
| std::string PLMD::toString | ( | Keywords::argType | at | ) |
| std::string PLMD::toString | ( | Keywords::componentType | at | ) |
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returns the transpose of a tensor (same as TensorGeneric::transpose())
| std::size_t PLMD::typesafePtrSizeof | ( | ) |
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inlinestatic |
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Test if an enum value is valid.
| a | The enum value to test. |
This operator is only available for enum types that have a specialization of enum_traits::BitmaskEnum with the has_valid trait enabled.
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| TokenizedLine::line PLMD::wholeLineReplicas | ( | const std::string & | myLine | ) |
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| const double PLMD::epsilon =1e-14 |
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Hosted by GitHub
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1.13.2
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