Detailed Description
template<class Interaction>
class McMd::LinkPotentialImpl< Interaction >
Template implementation of an BondPotential for links.
A LinkPotential implements the BondPotential interface, and uses an instance of a bond interaction class, but uses the LinkMaster of the parent System to identify linked atoms.
Definition at line 39 of file LinkPotentialImpl.h.
#include <LinkPotentialImpl.h>
Inheritance diagram for McMd::LinkPotentialImpl< Interaction >:
Public Member Functions | |
| LinkPotentialImpl (System &system) | |
| Constructor. More... | |
| LinkPotentialImpl (LinkPotentialImpl< Interaction > &other) | |
| Copy constructor. More... | |
| virtual | ~LinkPotentialImpl () |
| Destructor. More... | |
| virtual void | readParameters (std::istream &in) |
| Read potential energy. More... | |
| Interaction & | interaction () |
| Return bond interaction by reference. More... | |
| const Interaction & | interaction () const |
| Return bond interaction by const reference. More... | |
Bond interaction interface. | |
| virtual double | energy (double rsq, int bondTypeId) const |
| Return pair energy for a single pair. More... | |
| virtual double | forceOverR (double rsq, int bondTypeId) const |
| Return force / separation for a single pair. More... | |
| virtual double | randomBondLength (Random *random, double beta, int bondTypeId) const |
| Return force / separation for a single pair. More... | |
| void | set (std::string name, int type, double value) |
| Modify a parameter, identified by a string. More... | |
| double | get (std::string name, int type) const |
| Get a parameter value, identified by a string. More... | |
| virtual std::string | interactionClassName () const |
| Return pair interaction class name (e.g., "HarmonicBond"). More... | |
System energy, force and stress. | |
| virtual double | atomEnergy (const Atom &atom) const |
| Calculate the link potential energy for one Atom. More... | |
| virtual void | addForces () |
| Compute and increment link forces for all atoms. More... | |
| virtual void | computeEnergy () |
| Calculate and store pair energy for this System. More... | |
| virtual void | computeStress () |
| Compute and store the total nonbonded pressure. More... | |
 Public Member Functions inherited from McMd::BondPotential | |
| BondPotential () | |
| Constructor . More... | |
| virtual | ~BondPotential () |
| Destructor (does nothing) 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... | |
| virtual void | loadParameters (Serializable::IArchive &ar) |
| Load state from archive, without adding Begin and End lines. More... | |
| virtual void | save (Serializable::OArchive &ar) |
| Saves all parameters to an archive. 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... | |
| Public Member Functions inherited from McMd::EnergyCalculator | |
| virtual void | unsetEnergy () |
| Mark the energy as unknown. More... | |
| double | energy () |
| Return the energy contribution, compute if necessary. More... | |
| Public Member Functions inherited from McMd::StressCalculator | |
| virtual void | unsetStress () |
| Mark the stress as unknown. More... | |
| void | computeStress (Tensor &stress) |
| Get pair stress tensor. More... | |
| void | computeStress (Vector &pressures) |
| Get the xx, yy, zz non-Coulomb pair pressures. More... | |
| void | computeStress (double &pressure) |
| Get the scalar pressure. More... | |
| bool | createsStress () const |
| Return false if subclass does not generate stress. More... | |
| Public Member Functions inherited from McMd::SystemInterface | |
| SystemInterface (System &parent) | |
| Constructor. More... | |
| virtual | ~SystemInterface () |
| Destructor. More... | |
| System & | system () const |
| Get the parent System by reference. 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 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... | |
| Protected Member Functions inherited from McMd::StressCalculator | |
| StressCalculator (bool createsStress=true) | |
| Constructor (protected to prevent direct instantiation). More... | |
| Protected Member Functions inherited from McMd::SystemInterface | |
| Boundary & | boundary () const |
| Get the Boundary by reference. More... | |
| Simulation & | simulation () const |
| Get the parent Simulation by reference. More... | |
| int | nMolecule (int speciesId) const |
| Get the number of molecules of one Species in this SystemInterface. More... | |
| int | nAtom () const |
| Return the total number of atoms in this SystemInterface. More... | |
| bool | isEmpty () const |
| Is this an empty SystemInterface (i.e., one with no molecules) ? More... | |
| void | begin (int speciesId, System::MoleculeIterator &iterator) |
| Initialize an iterator for molecules of one species in this SystemInterface. More... | |
| void | begin (int speciesId, System::ConstMoleculeIterator &iterator) const |
| Initialize a const iterator for molecules of one species in this SystemInterface. More... | |
| bool | hasBonds () const |
| Does a bond potential exist? More... | |
| bool | hasAngles () const |
| Does an angle potential exist? More... | |
| bool | hasDihedrals () const |
| Does a dihedral potential exist? More... | |
| bool | hasLinks () const |
| Does a link potential exist? More... | |
| bool | hasExternal () const |
| Does an external potential exist? More... | |
Constructor & Destructor Documentation
template<class Interaction >
| McMd::LinkPotentialImpl< Interaction >::LinkPotentialImpl | ( | System & | system | ) |
Constructor.
Definition at line 195 of file LinkPotentialImpl.h.
References Util::ParamComposite::setClassName().
template<class Interaction >
| McMd::LinkPotentialImpl< Interaction >::LinkPotentialImpl | ( | LinkPotentialImpl< Interaction > & | other | ) |
Copy constructor.
Definition at line 210 of file LinkPotentialImpl.h.
References Util::ParamComposite::setClassName().
template<class Interaction >
|
virtual |
Destructor.
Definition at line 223 of file LinkPotentialImpl.h.
Member Function Documentation
template<class Interaction >
|
virtual |
Read potential energy.
This method reads the bond potential Interaction parameter block. Before calling Interaction::readParameters(), it passes simulation().nBondType() to Interaction::setNBondType().
Reimplemented from Util::ParamComposite.
Definition at line 230 of file LinkPotentialImpl.h.
References Util::ParamComposite::addParamComposite(), McMd::LinkPotentialImpl< Interaction >::interaction(), and McMd::SystemInterface::simulation().
template<class Interaction >
|
virtual |
Return pair energy for a single pair.
Implements McMd::BondPotential.
Definition at line 245 of file LinkPotentialImpl.h.
References McMd::LinkPotentialImpl< Interaction >::interaction().
template<class Interaction >
|
virtual |
Return force / separation for a single pair.
Implements McMd::BondPotential.
Definition at line 253 of file LinkPotentialImpl.h.
References McMd::LinkPotentialImpl< Interaction >::interaction(), and McMd::LinkPotentialImpl< Interaction >::randomBondLength().
template<class Interaction >
|
virtual |
Return force / separation for a single pair.
Implements McMd::BondPotential.
Definition at line 262 of file LinkPotentialImpl.h.
References McMd::LinkPotentialImpl< Interaction >::interaction().
Referenced by McMd::LinkPotentialImpl< Interaction >::forceOverR().
template<class Interaction>
|
inlinevirtual |
Modify a parameter, identified by a string.
- Parameters
-
name parameter name type bond type index value new value of parameter
Implements McMd::BondPotential.
Definition at line 95 of file LinkPotentialImpl.h.
template<class Interaction>
|
inlinevirtual |
Get a parameter value, identified by a string.
- Parameters
-
name parameter name type bond type index 1
Implements McMd::BondPotential.
Definition at line 104 of file LinkPotentialImpl.h.
template<class Interaction >
|
virtual |
Return pair interaction class name (e.g., "HarmonicBond").
Implements McMd::BondPotential.
Definition at line 391 of file LinkPotentialImpl.h.
References McMd::LinkPotentialImpl< Interaction >::interaction().
template<class Interaction >
|
virtual |
Calculate the link potential energy for one Atom.
- Parameters
-
atom Atom object of interest
- Returns
- bond energy of one atom.
Implements McMd::BondPotential.
Definition at line 269 of file LinkPotentialImpl.h.
References McMd::Link::atom0(), McMd::Link::atom1(), McMd::LinkMaster::atomLinkSet(), McMd::SystemInterface::boundary(), Simp::OrthorhombicBoundary::distanceSq(), McMd::EnergyCalculator::energy(), McMd::LinkPotentialImpl< Interaction >::interaction(), McMd::Atom::position(), Util::SSet< Data, Capacity >::size(), and McMd::Link::typeId().
template<class Interaction >
|
virtual |
Compute and increment link forces for all atoms.
Implements McMd::BondPotential.
Definition at line 294 of file LinkPotentialImpl.h.
References McMd::Link::atom0(), McMd::Link::atom1(), McMd::SystemInterface::boundary(), McMd::Atom::force(), McMd::LinkPotentialImpl< Interaction >::interaction(), McMd::LinkMaster::link(), McMd::LinkMaster::nLink(), McMd::Atom::position(), and McMd::Link::typeId().
template<class Interaction >
|
virtual |
Calculate and store pair energy for this System.
Implements McMd::EnergyCalculator.
Definition at line 319 of file LinkPotentialImpl.h.
References McMd::Link::atom0(), McMd::Link::atom1(), McMd::SystemInterface::boundary(), Simp::OrthorhombicBoundary::distanceSq(), McMd::EnergyCalculator::energy(), McMd::LinkPotentialImpl< Interaction >::interaction(), McMd::LinkMaster::link(), McMd::LinkMaster::nLink(), McMd::Atom::position(), Util::Setable< T >::set(), Util::setToZero(), McMd::Link::typeId(), and Simp::OrthorhombicBoundary::volume().
template<class Interaction >
|
virtual |
Compute and store the total nonbonded pressure.
Reimplemented from McMd::StressCalculator.
Definition at line 370 of file LinkPotentialImpl.h.
template<class Interaction >
|
inline |
Return bond interaction by reference.
Definition at line 380 of file LinkPotentialImpl.h.
Referenced by McMd::LinkPotentialImpl< Interaction >::addForces(), McMd::LinkPotentialImpl< Interaction >::atomEnergy(), McMd::LinkPotentialImpl< Interaction >::computeEnergy(), McMd::LinkPotentialImpl< Interaction >::energy(), McMd::LinkPotentialImpl< Interaction >::forceOverR(), McMd::LinkPotentialImpl< Interaction >::interactionClassName(), McMd::LinkPotentialImpl< Interaction >::randomBondLength(), and McMd::LinkPotentialImpl< Interaction >::readParameters().
template<class Interaction >
|
inline |
Return bond interaction by const reference.
Definition at line 384 of file LinkPotentialImpl.h.
The documentation for this class was generated from the following file:
