Detailed Description
An PairPotential for MD simulation.
Definition at line 36 of file MdPairPotential.h.
#include <MdPairPotential.h>
Public Member Functions | |
| MdPairPotential (System &system) | |
| Constructor. More... | |
| virtual | ~MdPairPotential () |
| Destructor. More... | |
| virtual void | addForces ()=0 |
| Calculate non-bonded pair forces for all atoms in this System. More... | |
PairList Management (non-virtual) | |
| void | buildPairList () |
| Build the internal PairList. More... | |
| bool | isPairListCurrent () |
| Return true if PairList is current, false if obsolete. More... | |
| void | clearPairListStatistics () |
| Clear all statistical accumulators stored in PairList. More... | |
| const PairList & | pairList () const |
| Return a const reference to the internal PairList. 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 | readParameters (std::istream &in) |
| Read the body of parameter block, without begin and end lines. 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::PairPotential | |
| virtual | ~PairPotential () |
| Destructor (does nothing) More... | |
| virtual double | energy (double rsq, int iAtomType, int jAtomType) const =0 |
| Return pair energy for a single pair. More... | |
| virtual double | forceOverR (double rsq, int iAtomType, int jAtomType) const =0 |
| Return force / separation for a single pair. More... | |
| virtual void | set (std::string name, int i, int j, double value)=0 |
| Modify a parameter, identified by a string. More... | |
| virtual double | get (std::string name, int i, int j) const =0 |
| Get a parameter value, identified by a string. More... | |
| virtual double | maxPairCutoff () const =0 |
| Return maximum cutoff distance. More... | |
| virtual std::string | interactionClassName () const =0 |
| Return name of pair interaction class (e.g., "LJPair"). More... | |
| Public Member Functions inherited from McMd::EnergyCalculator | |
| virtual void | computeEnergy ()=0 |
| Calculate the total nonBonded pair energy for the associated System. More... | |
| 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 | computeStress () |
| Compute and store the stress tensor. More... | |
| 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... | |
Protected Attributes | |
| PairList | pairList_ |
| Verlet neighbor pair list for nonbonded interactions. 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... | |
| SystemInterface (System &parent) | |
| Constructor. More... | |
| virtual | ~SystemInterface () |
| Destructor. More... | |
| System & | system () const |
| Get the parent System by reference. More... | |
Constructor & Destructor Documentation
| McMd::MdPairPotential::MdPairPotential | ( | System & | system | ) |
Constructor.
Definition at line 25 of file MdPairPotential.cpp.
References Util::ParamComposite::setClassName().
|
virtual |
Destructor.
Definition at line 33 of file MdPairPotential.cpp.
Member Function Documentation
|
pure virtual |
Calculate non-bonded pair forces for all atoms in this System.
Adds non-bonded pair forces to the current values of the forces for all atoms in this system. Before calculating forces, this function checks if the pair list is current, and rebuilds it if necessary.
Implemented in McMd::MdPairPotentialImpl< Interaction >, and McMd::MdEwaldPairPotentialImpl< Interaction >.
Referenced by McMd::MdSystem::calculateForces().
| void McMd::MdPairPotential::buildPairList | ( | ) |
Build the internal PairList.
Before building the PairList, this method also shifts all atom positions into the primary image of the periodic boundary. In an MD simulation, the positions are allowed to wander out of the primary image between calls to this function.
Definition at line 39 of file MdPairPotential.cpp.
References McMd::PairList::addAtom(), McMd::SystemInterface::begin(), McMd::SystemInterface::boundary(), McMd::PairList::build(), McMd::PairList::isInitialized(), Util::ArrayIterator< Data >::notEnd(), Util::PArrayIterator< Data >::notEnd(), McMd::Simulation::nSpecies(), pairList_, McMd::PairList::setup(), Simp::OrthorhombicBoundary::shift(), McMd::SystemInterface::simulation(), and UTIL_THROW.
Referenced by McMd::MdEwaldPairPotentialImpl< Interaction >::addForces(), McMd::MdPairPotentialImpl< Interaction >::addForces(), McMd::MdSimulation::analyzeConfigs(), McMd::MdSimulation::analyzeTrajectory(), McMd::MdEwaldPairPotentialImpl< Interaction >::computeEnergy(), McMd::MdPairPotentialImpl< Interaction >::computeEnergy(), McMd::MdEwaldPairPotentialImpl< Interaction >::computeStress(), McMd::MdSystem::generateMolecules(), McMd::MdSystem::loadConfig(), McMd::HybridMdMove::move(), McMd::HybridNphMdMove::move(), McMd::MdMove::move(), McMd::DpdMove::move(), McMd::MdSystem::readConfig(), McMd::MdDeformCommand::reneighbor(), McMd::NvtDpdVvIntegrator::setup(), McMd::NveVvIntegrator::step(), McMd::NvtLangevinIntegrator::step(), McMd::NvtDpdVvIntegrator::step(), McMd::NvtNhIntegrator::step(), and McMd::NphIntegrator::step().
| bool McMd::MdPairPotential::isPairListCurrent | ( | ) |
Return true if PairList is current, false if obsolete.
A PairList is considered current iff it has been built previously, and no particle has moved by a distance greater than skin/2 since the PairList was last built.
Definition at line 79 of file MdPairPotential.cpp.
References McMd::SystemInterface::boundary(), McMd::PairList::isCurrent(), and pairList_.
Referenced by McMd::MdEwaldPairPotentialImpl< Interaction >::addForces(), McMd::MdPairPotentialImpl< Interaction >::addForces(), McMd::MdEwaldPairPotentialImpl< Interaction >::computeEnergy(), McMd::MdPairPotentialImpl< Interaction >::computeEnergy(), and McMd::MdEwaldPairPotentialImpl< Interaction >::computeStress().
| void McMd::MdPairPotential::clearPairListStatistics | ( | ) |
Clear all statistical accumulators stored in PairList.
Definition at line 73 of file MdPairPotential.cpp.
References McMd::PairList::clearStatistics(), and pairList_.
Referenced by McMd::MdSystem::generateMolecules(), McMd::MdSystem::loadConfig(), McMd::MdSystem::readConfig(), and McMd::NvtDpdVvIntegrator::setup().
|
inline |
Return a const reference to the internal PairList.
Definition at line 108 of file MdPairPotential.h.
Referenced by McMd::MdSystem::isValid(), and McMd::MdSimulation::simulate().
Member Data Documentation
|
protected |
Verlet neighbor pair list for nonbonded interactions.
Definition at line 99 of file MdPairPotential.h.
Referenced by McMd::MdEwaldPairPotentialImpl< Interaction >::addForces(), McMd::MdPairPotentialImpl< Interaction >::addForces(), buildPairList(), clearPairListStatistics(), McMd::MdEwaldPairPotentialImpl< Interaction >::computeEnergy(), McMd::MdPairPotentialImpl< Interaction >::computeEnergy(), McMd::MdEwaldPairPotentialImpl< Interaction >::computeStress(), isPairListCurrent(), McMd::MdEwaldPairPotentialImpl< Interaction >::loadParameters(), McMd::MdPairPotentialImpl< Interaction >::loadParameters(), McMd::MdEwaldPairPotentialImpl< Interaction >::readParameters(), McMd::MdPairPotentialImpl< Interaction >::readParameters(), McMd::MdEwaldPairPotentialImpl< Interaction >::save(), and McMd::MdPairPotentialImpl< Interaction >::save().
The documentation for this class was generated from the following files:
