Detailed Description
configuration bias trimer double rebridge moves, to reconnect two chains.
Definition at line 31 of file CfbDoubleRebridgeMove.h.
#include <CfbDoubleRebridgeMove.h>
Inheritance diagram for McMd::CfbDoubleRebridgeMove:
Public Member Functions | |
| CfbDoubleRebridgeMove (McSystem &system) | |
| Constructor. More... | |
| virtual void | readParameters (std::istream &in) |
| Read species to which displacement is applied. More... | |
| virtual void | loadParameters (Serializable::IArchive &ar) |
| Load internal state from an archive. More... | |
| virtual void | save (Serializable::OArchive &ar) |
| Save internal state to an archive. More... | |
| virtual bool | move () |
| Generate and accept or reject configuration bias move. More... | |
 Public Member Functions inherited from McMd::CfbRebridgeBase | |
| CfbRebridgeBase (McSystem &system) | |
| Constructor. More... | |
| virtual | ~CfbRebridgeBase () |
| Destructor. More... | |
| virtual void | setup () |
| Initialize the arrays for preferential angle, effective spring constant and normalization factor. More... | |
| Public Member Functions inherited from McMd::CfbEndBase | |
| CfbEndBase (McSystem &system) | |
| Constructor. More... | |
| virtual | ~CfbEndBase () |
| Destructor. More... | |
| void | deleteEndAtom (Atom *endPtr, Atom *pvtPtr, int bondType, double &rosenbluth, double &energy) |
| CFB algorithm for deleting an end atom from a flexible chain. More... | |
| void | addEndAtom (Atom *endPtr, Atom *pvtPtr, int bondType, double &rosenbluth, double &energy) |
| Configuration bias algorithm for adding an atom to a chain end. More... | |
| Public Member Functions inherited from McMd::SystemMove | |
| SystemMove (McSystem &system) | |
| Constructor. More... | |
| virtual | ~SystemMove () |
| Destructor. More... | |
| Public Member Functions inherited from McMd::McMove | |
| McMove (Simulation &simulation) | |
| Constructor. More... | |
| virtual | ~McMove () |
| Destructor. More... | |
| void | setProbability (double probability) |
| Set the probability for this McMove. More... | |
| double | probability () const |
| Return probability for this McMove. More... | |
| long | nAttempt () const |
| Return number of moves that have been attempted. More... | |
| long | nAccept () const |
| Return number of moves that have been accepted. More... | |
| virtual void | output () |
| Output statistics for this move (called at the end of the simulation) More... | |
| Public Member Functions inherited from Util::ParamComposite | |
| ParamComposite () | |
| Constructor. More... | |
| ParamComposite (const ParamComposite &other) | |
| Copy constructor. More... | |
| ParamComposite (int capacity) | |
| Constructor. More... | |
| virtual | ~ParamComposite () |
| Virtual destructor. More... | |
| void | resetParam () |
| Resets ParamComposite to its empty state. More... | |
| virtual void | readParam (std::istream &in) |
| Read the parameter file block. More... | |
| virtual void | readParamOptional (std::istream &in) |
| Read optional parameter file block. More... | |
| virtual void | writeParam (std::ostream &out) |
| Write all parameters to an output stream. More... | |
| virtual void | load (Serializable::IArchive &ar) |
| Load all parameters from an input archive. More... | |
| virtual void | loadOptional (Serializable::IArchive &ar) |
| Load an optional ParamComposite. More... | |
| void | saveOptional (Serializable::OArchive &ar) |
| Saves isActive flag, and then calls save() iff isActive is true. More... | |
| void | readParamComposite (std::istream &in, ParamComposite &child, bool next=true) |
| Add and read a required child ParamComposite. More... | |
| void | readParamCompositeOptional (std::istream &in, ParamComposite &child, bool next=true) |
| Add and attempt to read an optional child ParamComposite. More... | |
| template<typename Type > | |
| ScalarParam< Type > & | read (std::istream &in, const char *label, Type &value) |
| Add and read a new required ScalarParam < Type > object. More... | |
| template<typename Type > | |
| ScalarParam< Type > & | readOptional (std::istream &in, const char *label, Type &value) |
| Add and read a new optional ScalarParam < Type > object. More... | |
| template<typename Type > | |
| CArrayParam< Type > & | readCArray (std::istream &in, const char *label, Type *value, int n) |
| Add and read a required C array parameter. More... | |
| template<typename Type > | |
| CArrayParam< Type > & | readOptionalCArray (std::istream &in, const char *label, Type *value, int n) |
| Add and read an optional C array parameter. More... | |
| template<typename Type > | |
| DArrayParam< Type > & | readDArray (std::istream &in, const char *label, DArray< Type > &array, int n) |
| Add and read a required DArray < Type > parameter. More... | |
| template<typename Type > | |
| DArrayParam< Type > & | readOptionalDArray (std::istream &in, const char *label, DArray< Type > &array, int n) |
| Add and read an optional DArray < Type > parameter. More... | |
| template<typename Type , int N> | |
| FArrayParam< Type, N > & | readFArray (std::istream &in, const char *label, FArray< Type, N > &array) |
| Add and read a required FArray < Type, N > array parameter. More... | |
| template<typename Type , int N> | |
| FArrayParam< Type, N > & | readOptionalFArray (std::istream &in, const char *label, FArray< Type, N > &array) |
| Add and read an optional FArray < Type, N > array parameter. More... | |
| template<typename Type > | |
| CArray2DParam< Type > & | readCArray2D (std::istream &in, const char *label, Type *value, int m, int n, int np) |
| Add and read a required CArray2DParam < Type > 2D C-array. More... | |
| template<typename Type > | |
| CArray2DParam< Type > & | readOptionalCArray2D (std::istream &in, const char *label, Type *value, int m, int n, int np) |
| Add and read an optional CArray2DParam < Type > 2D C-array parameter. More... | |
| template<typename Type > | |
| DMatrixParam< Type > & | readDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n) |
| Add and read a required DMatrix < Type > matrix parameter. More... | |
| template<typename Type > | |
| DMatrixParam< Type > & | readOptionalDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n) |
| Add and read an optional DMatrix < Type > matrix parameter. More... | |
| template<typename Type > | |
| DSymmMatrixParam< Type > & | readDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n) |
| Add and read a required symmetrix DMatrix. More... | |
| template<typename Type > | |
| DSymmMatrixParam< Type > & | readOptionalDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n) |
| Add and read an optional DMatrix matrix parameter. More... | |
| Begin & | readBegin (std::istream &in, const char *label, bool isRequired=true) |
| Add and read a class label and opening bracket. More... | |
| End & | readEnd (std::istream &in) |
| Add and read the closing bracket. More... | |
| Blank & | readBlank (std::istream &in) |
| Add and read a new Blank object, representing a blank line. More... | |
| void | loadParamComposite (Serializable::IArchive &ar, ParamComposite &child, bool next=true) |
| Add and load a required child ParamComposite. More... | |
| void | loadParamCompositeOptional (Serializable::IArchive &ar, ParamComposite &child, bool next=true) |
| Add and load an optional child ParamComposite if isActive. More... | |
| template<typename Type > | |
| ScalarParam< Type > & | loadParameter (Serializable::IArchive &ar, const char *label, Type &value, bool isRequired) |
| Add and load a new ScalarParam < Type > object. More... | |
| template<typename Type > | |
| ScalarParam< Type > & | loadParameter (Serializable::IArchive &ar, const char *label, Type &value) |
| Add and load new required ScalarParam < Type > object. More... | |
| template<typename Type > | |
| CArrayParam< Type > & | loadCArray (Serializable::IArchive &ar, const char *label, Type *value, int n, bool isRequired) |
| Add a C array parameter and load its elements. More... | |
| template<typename Type > | |
| CArrayParam< Type > & | loadCArray (Serializable::IArchive &ar, const char *label, Type *value, int n) |
| Add and load a required CArrayParam< Type > array parameter. More... | |
| template<typename Type > | |
| DArrayParam< Type > & | loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n, bool isRequired) |
| Add an load a DArray < Type > array parameter. More... | |
| template<typename Type > | |
| DArrayParam< Type > & | loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n) |
| Add and load a required DArray< Type > array parameter. More... | |
| template<typename Type , int N> | |
| FArrayParam< Type, N > & | loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array, bool isRequired) |
| Add and load an FArray < Type, N > fixed-size array parameter. More... | |
| template<typename Type , int N> | |
| FArrayParam< Type, N > & | loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array) |
| Add and load a required FArray < Type > array parameter. More... | |
| template<typename Type > | |
| CArray2DParam< Type > & | loadCArray2D (Serializable::IArchive &ar, const char *label, Type *value, int m, int n, int np, bool isRequired) |
| Add and load a CArray2DParam < Type > C 2D array parameter. More... | |
| template<typename Type > | |
| CArray2DParam< Type > & | loadCArray2D (Serializable::IArchive &ar, const char *label, Type *value, int m, int n, int np) |
| Add and load a required < Type > matrix parameter. More... | |
| template<typename Type > | |
| DMatrixParam< Type > & | loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired) |
| Add and load a DMatrixParam < Type > matrix parameter. More... | |
| template<typename Type > | |
| DMatrixParam< Type > & | loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n) |
| Add and load a required DMatrixParam < Type > matrix parameter. More... | |
| template<typename Type > | |
| DSymmMatrixParam< Type > & | loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n, bool isRequired) |
| Add and load a symmetric DSymmMatrixParam < Type > matrix parameter. More... | |
| template<typename Type > | |
| DSymmMatrixParam< Type > & | loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n) |
| Add and load a required DSymmMatrixParam < Type > matrix parameter. More... | |
| void | addParamComposite (ParamComposite &child, bool next=true) |
| Add a child ParamComposite object to the format array. More... | |
| Begin & | addBegin (const char *label) |
| Add a Begin object representing a class name and bracket. More... | |
| End & | addEnd () |
| Add a closing bracket. More... | |
| Blank & | addBlank () |
| Create and add a new Blank object, representing a blank line. More... | |
| std::string | className () const |
| Get class name string. More... | |
| bool | isRequired () const |
| Is this ParamComposite required in the input file? More... | |
| bool | isActive () const |
| Is this parameter active? More... | |
| Public Member Functions inherited from Util::ParamComponent | |
| virtual | ~ParamComponent () |
| Destructor. More... | |
| void | setIndent (const ParamComponent &parent, bool next=true) |
| Set indent level. More... | |
| std::string | indent () const |
| Return indent string for this object (string of spaces). More... | |
| template<class Archive > | |
| void | serialize (Archive &ar, const unsigned int version) |
| Serialize this ParamComponent as a string. More... | |
| Public Member Functions inherited from Util::Serializable | |
| virtual | ~Serializable () |
| Destructor. More... | |
| Public Member Functions inherited from Util::MpiFileIo | |
| MpiFileIo () | |
| Constructor. More... | |
| MpiFileIo (const MpiFileIo &other) | |
| Copy constructor. More... | |
| bool | isIoProcessor () const |
| Can this processor do file I/O ? More... | |
| void | setIoCommunicator (MPI::Intracomm &communicator) |
| Set the communicator. More... | |
| void | clearCommunicator () |
| Clear (nullify) the communicator. More... | |
| bool | hasIoCommunicator () const |
| Does this object have an associated MPI communicator? More... | |
| MPI::Intracomm & | ioCommunicator () const |
| Get the MPI communicator by reference. More... | |
Protected Attributes | |
| DArray< Vector > | iOldPos_ |
| Array of old positions of temporarily deleted atoms (iMol). More... | |
| DArray< Vector > | jOldPos_ |
| Array of old positions of temporarily deleted atoms (jMol). More... | |
| int | speciesId_ |
| Integer index for molecular species. More... | |
| int | nRegrow_ |
| Number of particles at end to attempt to regrow. More... | |
| double | bridgeLength_ |
| upper bound for trial lenght of a bridge. More... | |
| Protected Attributes inherited from McMd::CfbRebridgeBase | |
| double | length21_ |
| Equilibrium bond lengths (2-1 bond). More... | |
| double | length10_ |
| Equilibrium bond lengths (1-0 bonds). More... | |
| double | kappa10_ |
| Spring constant (1-0 bond). More... | |
| Protected Attributes inherited from McMd::CfbEndBase | |
| int | nTrial_ |
| Actual number of trial positions for each regrown atom. More... | |
Additional Inherited Members | |
| Public Types inherited from Util::Serializable | |
| typedef BinaryFileOArchive | OArchive |
| Type of output archive used by save method. More... | |
| typedef BinaryFileIArchive | IArchive |
| Type of input archive used by load method. More... | |
| Static Public Member Functions inherited from Util::ParamComponent | |
| static void | initStatic () |
| Initialize static echo member to false. More... | |
| static void | setEcho (bool echo=true) |
| Enable or disable echoing for all subclasses of ParamComponent. More... | |
| static bool | echo () |
| Get echo parameter. More... | |
| Protected Member Functions inherited from McMd::CfbRebridgeBase | |
| void | deleteMiddleAtom (Atom *partPtr, Atom *prevPtr, Atom *nextPtr, int prevBType, int nextBType, double &rosenbluth, double &energy) |
| Configuration bias algorithm for deleting a particle between two monomers and compute the corresponding Rosenbluth factor. More... | |
| void | addMiddleAtom (Atom *partPtr, Atom *prevPtr, Atom *nextPtr, int prevBType, int nextBType, double &rosenbluth, double &energy) |
| Configuration bias algorithm for adding the last particle with special bias in favor of closing the bridge. More... | |
| void | deleteSequence (int nActive, int sign, Atom *endPtr, int *bonds, double &rosenbluth, double &energy) |
| Configuration bias algorithm for deleting a consequtive sequence of atoms. More... | |
| void | addSequence (int nActive, int sign, Atom *beginPtr, int *bonds, double &rosenbluth, double &energy) |
| Configuration bias algorithm for adding a consequtive sequence of atoms. More... | |
| Protected Member Functions inherited from McMd::SystemMove | |
| McSystem & | system () |
| Get parent McSystem. More... | |
| Boundary & | boundary () |
| Get Boundary object of parent McSystem. More... | |
| EnergyEnsemble & | energyEnsemble () |
| Get EnergyEnsemble object of parent McSystem. More... | |
| double | boltzmann (double energy) |
| Boltzmann weight associated with an energy difference. More... | |
| Protected Member Functions inherited from McMd::McMove | |
| void | incrementNAttempt () |
| Increment the number of attempted moves. More... | |
| void | incrementNAccept () |
| Increment the number of accepted moves. More... | |
| Simulation & | simulation () |
| Get parent Simulation object. More... | |
| Random & | random () |
| Get Random number generator of parent Simulation. More... | |
| void | readProbability (std::istream &in) |
| Read the probability from file. More... | |
| Protected Member Functions inherited from Util::ParamComposite | |
| void | setClassName (const char *className) |
| Set class name string. More... | |
| void | setIsRequired (bool isRequired) |
| Set or unset the isActive flag. More... | |
| void | setIsActive (bool isActive) |
| Set or unset the isActive flag. More... | |
| void | setParent (ParamComponent ¶m, bool next=true) |
| Set this to the parent of a child component. More... | |
| void | addComponent (ParamComponent ¶m, bool isLeaf=true) |
| Add a new ParamComponent object to the format array. More... | |
| template<typename Type > | |
| ScalarParam< Type > & | add (std::istream &in, const char *label, Type &value, bool isRequired=true) |
| Add a new required ScalarParam < Type > object. More... | |
| template<typename Type > | |
| CArrayParam< Type > & | addCArray (std::istream &in, const char *label, Type *value, int n, bool isRequired=true) |
| Add (but do not read) a required C array parameter. More... | |
| template<typename Type > | |
| DArrayParam< Type > & | addDArray (std::istream &in, const char *label, DArray< Type > &array, int n, bool isRequired=true) |
| Add (but do not read) a DArray < Type > parameter. More... | |
| template<typename Type , int N> | |
| FArrayParam< Type, N > & | addFArray (std::istream &in, const char *label, FArray< Type, N > &array, bool isRequired=true) |
| Add (but do not read) a FArray < Type, N > array parameter. More... | |
| template<typename Type > | |
| CArray2DParam< Type > & | addCArray2D (std::istream &in, const char *label, Type *value, int m, int n, int np, bool isRequired=true) |
| Add (but do not read) a CArray2DParam < Type > 2D C-array. More... | |
| template<typename Type > | |
| DMatrixParam< Type > & | addDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired=true) |
| Add and read a required DMatrix < Type > matrix parameter. More... | |
| Protected Member Functions inherited from Util::ParamComponent | |
| ParamComponent () | |
| Constructor. More... | |
| ParamComponent (const ParamComponent &other) | |
| Copy constructor. More... | |
| Static Protected Attributes inherited from McMd::CfbEndBase | |
| static const int | MaxTrial_ = 20 |
| Maximum allowed number of trial positions for a regrown atom. More... | |
Constructor & Destructor Documentation
| McMd::CfbDoubleRebridgeMove::CfbDoubleRebridgeMove | ( | McSystem & | system | ) |
Constructor.
Definition at line 32 of file CfbDoubleRebridgeMove.cpp.
References Util::ParamComposite::setClassName().
Member Function Documentation
|
virtual |
Read species to which displacement is applied.
Reimplemented from McMd::CfbRebridgeBase.
Definition at line 42 of file CfbDoubleRebridgeMove.cpp.
References bridgeLength_, iOldPos_, jOldPos_, nRegrow_, McMd::CfbRebridgeBase::readParameters(), McMd::McMove::readProbability(), McMd::CfbRebridgeBase::setup(), McMd::McMove::simulation(), McMd::Simulation::species(), speciesId_, and UTIL_THROW.
|
virtual |
Load internal state from an archive.
- Parameters
-
ar input/loading archive
Reimplemented from McMd::CfbRebridgeBase.
Definition at line 71 of file CfbDoubleRebridgeMove.cpp.
References bridgeLength_, iOldPos_, jOldPos_, McMd::CfbRebridgeBase::loadParameters(), McMd::McMove::loadParameters(), nRegrow_, McMd::CfbRebridgeBase::setup(), McMd::McMove::simulation(), McMd::Simulation::species(), speciesId_, and UTIL_THROW.
|
virtual |
Save internal state to an archive.
- Parameters
-
ar output/saving archive
Reimplemented from McMd::CfbRebridgeBase.
Definition at line 98 of file CfbDoubleRebridgeMove.cpp.
References bridgeLength_, nRegrow_, McMd::CfbRebridgeBase::save(), McMd::McMove::save(), and speciesId_.
|
virtual |
Generate and accept or reject configuration bias move.
Reimplemented from McMd::McMove.
Definition at line 121 of file CfbDoubleRebridgeMove.cpp.
References McMd::CfbRebridgeBase::addSequence(), McMd::Molecule::atom(), McMd::Molecule::bond(), McMd::SystemMove::boundary(), bridgeLength_, McMd::CfbRebridgeBase::deleteSequence(), Simp::OrthorhombicBoundary::distanceSq(), McMd::McMove::incrementNAccept(), McMd::McMove::incrementNAttempt(), iOldPos_, jOldPos_, Util::Random::metropolis(), McMd::System::molecule(), McMd::System::moleculeId(), McMd::Molecule::nAtom(), McMd::System::nMolecule(), nRegrow_, McMd::McSystem::pairPotential(), McMd::Atom::position(), McMd::McMove::random(), McMd::System::randomMolecule(), speciesId_, McMd::SystemMove::system(), McMd::Group< NAtom >::typeId(), Util::Random::uniformInt(), McMd::McPairPotential::updateAtomCell(), and UTIL_THROW.
Member Data Documentation
Array of old positions of temporarily deleted atoms (iMol).
Definition at line 68 of file CfbDoubleRebridgeMove.h.
Referenced by loadParameters(), move(), and readParameters().
Array of old positions of temporarily deleted atoms (jMol).
Definition at line 71 of file CfbDoubleRebridgeMove.h.
Referenced by loadParameters(), move(), and readParameters().
|
protected |
Integer index for molecular species.
Definition at line 74 of file CfbDoubleRebridgeMove.h.
Referenced by loadParameters(), move(), readParameters(), and save().
|
protected |
Number of particles at end to attempt to regrow.
Definition at line 77 of file CfbDoubleRebridgeMove.h.
Referenced by loadParameters(), move(), readParameters(), and save().
|
protected |
upper bound for trial lenght of a bridge.
Definition at line 80 of file CfbDoubleRebridgeMove.h.
Referenced by loadParameters(), move(), readParameters(), and save().
The documentation for this class was generated from the following files:
