 |
 |
 |
Namespaces | |
| analysis | |
| bias | |
| blas | |
| cltools | |
| colvar | |
| config | |
| crystallisation | |
| crystallization | |
| function | |
| generic | |
| lapack | |
| manyrestraints | |
| mapping | |
| molfile | |
| multicolvar | |
| secondarystructure | |
| setup | |
| vatom | |
| vesselbase | |
Classes | |
| class | Action |
| Base class for all the input Actions. More... | |
| class | ActionAtomistic |
| Action used to create objects that access the positions of the atoms from the MD code. More... | |
| 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... | |
| 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 | ActionWithArguments |
| This is used to create PLMD::Action objects that take the output from some other Action as input. More... | |
| 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 | 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... | |
| class | ArgumentOnlyDistance |
| class | AtomNumber |
| Simple class to store the index of an atom. More... | |
| class | Atoms |
| Class containing atom related quantities from the MD code. 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 | CH3Shifts |
| Provides the keyword CH3SHIFTS More... | |
| class | CInterpolation |
| 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... | |
| 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 | Communicator |
| Class containing wrappers to MPI. More... | |
| class | CS2Backbone |
| Provides the keyword CS2BACKBONE More... | |
| class | Direction |
| class | DLLoader |
| Class taking care of dynamic loading. More... | |
| class | DotProductDistance |
| class | DRMSD |
| class | DynamicList |
| A class for storing a list that changes which members are active as a function of time. More... | |
| class | EuclideanDistance |
| class | Exception |
| Class to deal with Plumed runtime errors. More... | |
| class | ExchangePatterns |
| class | FakeFrame |
| class | FileBase |
| Base class for dealing with files. More... | |
| class | FlexibleBin |
| class | GREX |
| class | Grid |
| 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 | IMD |
| Provides the keyword IMD More... | |
| class | InterpolateBicubic |
| class | InterpolateCubic |
| class | Kearsley |
| class | KernelFunctions |
| class | Keywords |
| This class holds the keywords and their documentation. More... | |
| class | LatticeReduction |
| Class implementing algorithms for lattice reduction. More... | |
| 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 | MahalanobisDistance |
| class | Matrix |
| This class stores a full matrix and allows one to do some simple matrix operations. More... | |
| class | MatrixSquareBracketsAccess |
| Utility class to add [][] access. More... | |
| class | MDAtomsBase |
| Class containing interface to MDAtomsTyped. More... | |
| class | MDAtomsTyped |
| Class containing the pointers to the MD data It is templated so that single and double precision versions coexist IT IS STILL UNDOCUMENTED. More... | |
| class | MetricRegister |
| 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 | MultiDomainRMSD |
| class | MultiReferenceBase |
| class | MultiValue |
| class | NeighborList |
| A class that implements neighbor lists from two lists or a single list of atoms. More... | |
| class | NormalizedEuclideanDistance |
| class | OFile |
| Class for output files. More... | |
| class | OpenMP |
| class | OptimalAlignment |
| A class that is intended to include or combine various optimal alignment algorithms. More... | |
| class | OptimalRMSD |
| class | Pbc |
| class | PDB |
| Minimalistic pdb parser. More... | |
| class | Plumed |
| C++ wrapper for plumed. More... | |
| class | PlumedMain |
| Main plumed object. More... | |
| class | PlumedMainInitializer |
| Static object which registers Plumed. More... | |
| class | PointWiseMapping |
| class | ProbWeight |
| class | Random |
| class | RDC |
| Provides the keyword RDC More... | |
| class | ReferenceArguments |
| In many applications (e.g. More... | |
| class | ReferenceAtoms |
| In many applications (e.g. More... | |
| class | ReferenceConfiguration |
| Abstract base class for calculating the distance from a reference configuration. More... | |
| class | ReferenceConfigurationOptions |
| class | ReferenceValuePack |
| 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 | RMSDBase |
| 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 | SetupMolInfo |
| class | SimpleRMSD |
| class | SingleDomainRMSD |
| class | SparseGrid |
| class | Stopwatch |
| Class implementing stopwatch to time execution. More... | |
| class | SwitchingFunction |
| Small class to compure switching functions. More... | |
| class | TargetDist |
| class | TensorChecks |
| Small auxiliary class. More... | |
| class | TensorGeneric |
| Class implementing fixed size matrices of doubles. More... | |
| class | Tools |
| Empty class which just contains several (static) tools. More... | |
| class | Torsion |
| Class to compute torsional angles. More... | |
| 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 | VectorChecks |
| Small auxiliary class. More... | |
| class | VectorGeneric |
| Class implementing fixed size vectors of doubles. More... | |
| class | WeightBase |
| class | WithCmd |
| Base for classes with cmd() method. More... | |
Typedefs | |
| typedef TensorGeneric< 2, 2 > | Tensor2d |
| typedef TensorGeneric< 3, 3 > | Tensor3d |
| typedef TensorGeneric< 4, 4 > | Tensor4d |
| typedef Tensor3d | Tensor |
| typedef VectorGeneric< 2 > | Vector2d |
| Alias for two dimensional vectors. More... | |
| typedef VectorGeneric< 3 > | Vector3d |
| Alias for three dimensional vectors. More... | |
| typedef VectorGeneric< 4 > | Vector4d |
| Alias for four dimensional vectors. More... | |
| typedef Vector3d | Vector |
| Alias for three dimensional vectors. More... | |
Functions | |
| ActionRegister & | actionRegister () |
| std::ostream & | operator<< (std::ostream &log, const ActionRegister &ar) |
| CLToolRegister & | cltoolRegister () |
| std::ostream & | operator<< (std::ostream &log, const CLToolRegister &ar) |
| void | copy (const Value &val1, Value &val2) |
| void | copy (const Value &val1, Value *val2) |
| void | add (const Value &val1, Value *val2) |
| void | product (const Value &val1, const Value &val2, Value &valout) |
| void | quotient (const Value &val1, const Value &val2, Value *valout) |
| MetricRegister & | metricRegister () |
| double | distance (const Pbc &pbc, const std::vector< Value * > &vals, ReferenceConfiguration *ref1, ReferenceConfiguration *ref2, const bool &squared) |
| 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) |
| bool | operator== (const AtomNumber &a, const AtomNumber &b) |
| bool | operator!= (const AtomNumber &a, const AtomNumber &b) |
| std::ostream & | operator<< (std::ostream &log, const Citations &cit) |
| template<typename U > | |
| void | mpi_gatherActiveMembers (Communicator &comm, std::vector< DynamicList< U > > &ll) |
| template<typename T > | |
| T | dotProduct (const std::vector< T > &A, const std::vector< T > &B) |
| Calculate the dot product between two vectors. More... | |
| template<typename T > | |
| T | norm (const std::vector< T > &A) |
| Calculate the dot product between a vector and itself. More... | |
| template<typename T > | |
| Matrix< T > | operator* (T &v, const Matrix< T > &m) |
| Multiply matrix by scalar. More... | |
| 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 > | |
| void | transpose (const Matrix< T > &A, Matrix< T > &AT) |
| template<typename T > | |
| Log & | operator<< (Log &ostr, const Matrix< T > &mat) |
| template<typename T > | |
| void | matrixOut (Log &ostr, const Matrix< T > &mat) |
| template<typename T > | |
| int | diagMat (const Matrix< T > &A, std::vector< double > &eigenvals, Matrix< double > &eigenvecs) |
| template<typename T > | |
| int | pseudoInvert (const Matrix< T > &A, Matrix< double > &pseudoinverse) |
| template<typename T > | |
| int | Invert (const Matrix< T > &A, Matrix< double > &inverse) |
| template<typename T > | |
| void | cholesky (const Matrix< T > &A, Matrix< T > &B) |
| template<typename T > | |
| void | chol_elsolve (const Matrix< T > &M, const std::vector< T > &b, std::vector< T > &y) |
| template<typename T > | |
| int | logdet (const Matrix< T > &M, double &ldet) |
| template<class T > | |
| OFile & | operator<< (OFile &of, const T &t) |
| Write using << syntax. More... | |
| Log & | operator<< (Log &ostr, const PDB &pdb) |
| std::ostream & | operator<< (std::ostream &os, const Stopwatch &sw) |
| template<unsigned n, unsigned m> | |
| TensorGeneric< n, m > | operator+ (const TensorGeneric< n, m > &t1, const TensorGeneric< n, m > &t2) |
| template<unsigned n, unsigned m> | |
| TensorGeneric< n, m > | operator- (const TensorGeneric< n, m > &t1, const TensorGeneric< n, m > &t2) |
| template<unsigned n, unsigned m> | |
| TensorGeneric< n, m > | operator* (const TensorGeneric< n, m > &t1, double s) |
| template<unsigned n, unsigned m> | |
| TensorGeneric< n, m > | operator* (double s, const TensorGeneric< n, m > &t1) |
| template<unsigned n, unsigned m> | |
| TensorGeneric< n, m > | operator/ (const TensorGeneric< n, m > &t1, double s) |
| template<unsigned n, unsigned m, unsigned l> | |
| TensorGeneric< n, l > | matmul (const TensorGeneric< n, m > &a, const TensorGeneric< m, l > &b) |
| template<unsigned n, unsigned m> | |
| VectorGeneric< n > | matmul (const TensorGeneric< n, m > &a, const VectorGeneric< m > &b) |
| template<unsigned n, unsigned m> | |
| VectorGeneric< n > | matmul (const VectorGeneric< m > &a, const TensorGeneric< m, n > &b) |
| template<unsigned n_> | |
| double | matmul (const VectorGeneric< n_ > &a, const VectorGeneric< n_ > &b) |
| template<unsigned n, unsigned m, unsigned l, unsigned i> | |
| TensorGeneric< n, i > | matmul (const TensorGeneric< n, m > &a, const TensorGeneric< m, l > &b, const TensorGeneric< l, i > &c) |
| template<unsigned n, unsigned m, unsigned l> | |
| VectorGeneric< n > | matmul (const TensorGeneric< n, m > &a, const TensorGeneric< m, l > &b, const VectorGeneric< l > &c) |
| template<unsigned n, unsigned m, unsigned l> | |
| VectorGeneric< l > | matmul (const VectorGeneric< n > &a, const TensorGeneric< n, m > &b, const TensorGeneric< m, l > &c) |
| template<unsigned n, unsigned m> | |
| double | matmul (const VectorGeneric< n > &a, const TensorGeneric< n, m > &b, const VectorGeneric< m > &c) |
| double | determinant (const TensorGeneric< 3, 3 > &t) |
| TensorGeneric< 3, 3 > | inverse (const TensorGeneric< 3, 3 > &t) |
| template<unsigned n, unsigned m> | |
| TensorGeneric< n, m > | transpose (const TensorGeneric< m, n > &t) |
| template<unsigned n, unsigned m> | |
| TensorGeneric< n, m > | extProduct (const VectorGeneric< n > &v1, const VectorGeneric< m > &v2) |
| TensorGeneric< 3, 3 > | dcrossDv1 (const VectorGeneric< 3 > &v1, const VectorGeneric< 3 > &v2) |
| TensorGeneric< 3, 3 > | dcrossDv2 (const VectorGeneric< 3 > &v1, const VectorGeneric< 3 > &v2) |
| template<unsigned n, unsigned m> | |
| std::ostream & | operator<< (std::ostream &os, const TensorGeneric< n, m > &t) |
| const double | epsilon (std::numeric_limits< double >::epsilon()) |
| Very small non-zero number. More... | |
| const double | kBoltzmann (0.0083144621) |
| Boltzman constant in kj/K. More... | |
| const double | pi (3.141592653589793238462643383279502884197169399375105820974944592307) |
| PI. More... | |
| template<unsigned n> | |
| VectorGeneric< n > | operator+ (const VectorGeneric< n > &v1, const VectorGeneric< n > &v2) |
| template<unsigned n> | |
| VectorGeneric< n > | operator- (const VectorGeneric< n > &v1, const VectorGeneric< n > &v2) |
| template<unsigned n> | |
| VectorGeneric< n > | operator* (double s, const VectorGeneric< n > &v) |
| template<unsigned n> | |
| VectorGeneric< n > | operator* (const VectorGeneric< n > &v, double s) |
| template<unsigned n> | |
| VectorGeneric< n > | operator/ (const VectorGeneric< n > &v, double s) |
| template<unsigned n> | |
| VectorGeneric< n > | delta (const VectorGeneric< n > &v1, const VectorGeneric< n > &v2) |
| template<unsigned n> | |
| double | dotProduct (const VectorGeneric< n > &v1, const VectorGeneric< n > &v2) |
| VectorGeneric< 3 > | crossProduct (const VectorGeneric< 3 > &v1, const VectorGeneric< 3 > &v2) |
| template<unsigned n> | |
| double | modulo2 (const VectorGeneric< n > &v) |
| template<unsigned n> | |
| double | modulo (const VectorGeneric< n > &v) |
| template<unsigned n> | |
| std::ostream & | operator<< (std::ostream &os, const VectorGeneric< n > &v) |
Variables | |
| static const bool | shareMassAndChargeOnlyAtFirstStep =true |
| We assume that charges and masses are constant along the simulation Set this to false if you want to revert to the original (expensive) behavior. More... | |
| static class PLMD::PlumedMainInitializer | RegisterMe |
| const double | epsilon =1e-14 |
| static class PLMD::TensorChecks | checks |
| static class PLMD::VectorChecks | checks |
|
related |
| void PLMD::chol_elsolve | ( | const Matrix< T > & | M, |
| const std::vector< T > & | b, | ||
| std::vector< T > & | y | ||
| ) |
|
related |
|
inline |
v2 Only available for size 3
|
inline |
|
inline |
| VectorGeneric<n> PLMD::delta | ( | const VectorGeneric< n > & | v1, |
| const VectorGeneric< n > & | v2 | ||
| ) |
|
inline |
| int PLMD::diagMat | ( | const Matrix< T > & | A, |
| std::vector< double > & | eigenvals, | ||
| Matrix< double > & | eigenvecs | ||
| ) |
| double PLMD::distance | ( | const Pbc & | pbc, |
| const std::vector< Value * > & | vals, | ||
| ReferenceConfiguration * | ref1, | ||
| ReferenceConfiguration * | ref2, | ||
| const bool & | squared | ||
| ) |
| T PLMD::dotProduct | ( | const std::vector< T > & | A, |
| const std::vector< T > & | B | ||
| ) |
Calculate the dot product between two vectors.
| double PLMD::dotProduct | ( | const VectorGeneric< n > & | v1, |
| const VectorGeneric< n > & | v2 | ||
| ) |
| TensorGeneric<n,m> PLMD::extProduct | ( | const VectorGeneric< n > & | v1, |
| const VectorGeneric< m > & | v2 | ||
| ) |
|
inline |
| int PLMD::logdet | ( | const Matrix< T > & | M, |
| double & | ldet | ||
| ) |
| TensorGeneric<n,l> PLMD::matmul | ( | const TensorGeneric< n, m > & | a, |
| const TensorGeneric< m, l > & | b | ||
| ) |
| VectorGeneric<n> PLMD::matmul | ( | const TensorGeneric< n, m > & | a, |
| const VectorGeneric< m > & | b | ||
| ) |
| VectorGeneric<n> PLMD::matmul | ( | const VectorGeneric< m > & | a, |
| const TensorGeneric< m, n > & | b | ||
| ) |
| double PLMD::matmul | ( | const VectorGeneric< n_ > & | a, |
| const VectorGeneric< n_ > & | b | ||
| ) |
| TensorGeneric<n,i> PLMD::matmul | ( | const TensorGeneric< n, m > & | a, |
| const TensorGeneric< m, l > & | b, | ||
| const TensorGeneric< l, i > & | c | ||
| ) |
| VectorGeneric<n> PLMD::matmul | ( | const TensorGeneric< n, m > & | a, |
| const TensorGeneric< m, l > & | b, | ||
| const VectorGeneric< l > & | c | ||
| ) |
| VectorGeneric<l> PLMD::matmul | ( | const VectorGeneric< n > & | a, |
| const TensorGeneric< n, m > & | b, | ||
| const TensorGeneric< m, l > & | c | ||
| ) |
| double PLMD::matmul | ( | const VectorGeneric< n > & | a, |
| const TensorGeneric< n, m > & | b, | ||
| const VectorGeneric< m > & | c | ||
| ) |
| MetricRegister & PLMD::metricRegister | ( | ) |
| double PLMD::modulo | ( | const VectorGeneric< n > & | v | ) |
| double PLMD::modulo2 | ( | const VectorGeneric< n > & | v | ) |
| void PLMD::mpi_gatherActiveMembers | ( | Communicator & | comm, |
| std::vector< DynamicList< U > > & | ll | ||
| ) |
| 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.
|
inline |
Multiply matrix by scalar.
| VectorGeneric<n> PLMD::operator* | ( | double | s, |
| const VectorGeneric< n > & | v | ||
| ) |
| VectorGeneric<n> PLMD::operator* | ( | const VectorGeneric< n > & | v, |
| double | s | ||
| ) |
| TensorGeneric<n,m> PLMD::operator* | ( | const TensorGeneric< n, m > & | t1, |
| double | s | ||
| ) |
| TensorGeneric<n,m> PLMD::operator* | ( | double | s, |
| const TensorGeneric< n, m > & | t1 | ||
| ) |
| VectorGeneric<n> PLMD::operator+ | ( | const VectorGeneric< n > & | v1, |
| const VectorGeneric< n > & | v2 | ||
| ) |
| TensorGeneric<n,m> PLMD::operator+ | ( | const TensorGeneric< n, m > & | t1, |
| const TensorGeneric< n, m > & | t2 | ||
| ) |
| VectorGeneric<n> PLMD::operator- | ( | const VectorGeneric< n > & | v1, |
| const VectorGeneric< n > & | v2 | ||
| ) |
| TensorGeneric<n,m> PLMD::operator- | ( | const TensorGeneric< n, m > & | t1, |
| const TensorGeneric< n, m > & | t2 | ||
| ) |
| VectorGeneric<n> PLMD::operator/ | ( | const VectorGeneric< n > & | v, |
| double | s | ||
| ) |
| TensorGeneric<n,m> PLMD::operator/ | ( | const TensorGeneric< n, m > & | t1, |
| double | s | ||
| ) |
|
inline |
| 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 & | os, |
| const Stopwatch & | sw | ||
| ) |
| std::ostream & PLMD::operator<< | ( | std::ostream & | log, |
| const CLToolRegister & | ar | ||
| ) |
| std::ostream & PLMD::operator<< | ( | std::ostream & | log, |
| const ActionRegister & | ar | ||
| ) |
Write using << syntax.
Formatted output with << operator.
| std::ostream& PLMD::operator<< | ( | std::ostream & | os, |
| const VectorGeneric< n > & | v | ||
| ) |
| std::ostream& PLMD::operator<< | ( | std::ostream & | os, |
| const TensorGeneric< n, m > & | t | ||
| ) |
|
inline |
|
inline |
|
inline |
|
inline |
| int PLMD::pseudoInvert | ( | const Matrix< T > & | A, |
| Matrix< double > & | pseudoinverse | ||
| ) |
| TensorGeneric<n,m> PLMD::transpose | ( | const TensorGeneric< m, n > & | t | ) |
|
static |
|
static |
| const double PLMD::epsilon =1e-14 |
|
static |
|
static |
We assume that charges and masses are constant along the simulation Set this to false if you want to revert to the original (expensive) behavior.
Hosted by GitHub
|
1.8.10
|
