Detailed Description

Abstract base class for computing nonbonded pair forces and energies.

A PairPotential has a private CellList and PairList which it can use to calculate nonbonded pair forces. Concrete subclasses of PairPotential are constructed as instances of the PairPotentialImpl class template.

Definition at line 44 of file ddMd/potentials/pair/PairPotential.h.

#include <PairPotential.h>

Inheritance diagram for DdMd::PairPotential:

Public Member Functions
	PairPotential (Simulation &simulation)
	Constructor. More...

	PairPotential ()
	Default constructor. More...

virtual	~PairPotential ()
	Destructor. More...

double	skin () const
	Get value of the pair list skin. More...

double	cutoff () const
	Get value of the pair list cutoff (maxPairCutoff + skin). More...

int	methodId () const
	Return integer id for algorithm (0=PAIR, 1=CELL, 2=NSQ) More...

Initialization and Serialization
void	associate (Domain &domain, Boundary &boundary, AtomStorage &storage)
	Associate with related objects. More...

virtual void	setNAtomType (int nAtomType)=0
	Set the maximum number of atom types. More...

void	initialize (const Boundary &maxBoundary, double skin, int pairCapacity)
	Set parameters and allocate memory. More...

void	readParameters (std::istream &in)
	Initialize, by reading parameters and allocating memory for PairList. More...

virtual void	loadParameters (Serializable::IArchive &ar)
	Load parameters for PairList from archive, and allocate memory. More...

virtual void	save (Serializable::OArchive &ar)
	Save internal state to an output archive. More...

void	setMethodId (int methodId)
	Set id to specify algorithm for energy, force calculations. More...

Interaction interface
virtual double	pairEnergy (double rsq, int iAtomType, int jAtomType) const =0
	Return energy for a single pair. More...

virtual double	pairForceOverR (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. More...

virtual std::string	interactionClassName () const =0
	Return pair interaction class name (e.g., "LJPair"). More...

Pair and Cell Lists.
void	buildCellList ()
	Build a cell list. More...

void	buildPairList ()
	Build the Verlet Pair list. More...

virtual void	computePairEnergies (MPI::Intracomm &communicator)=0
	Compute pair energies on all processors. More...

DMatrix< double >	pairEnergies () const
	Return total pair energies, from all processors. More...

void	unsetPairEnergies ()
	Mark pair energy as unknown (nullify). More...

void	computeNPair (MPI::Intracomm &communicator)
	Compute twice the number of pairs within the force cutoff. More...

int	nPair () const
	Return twice the number of pairs within the specified force cutoff. More...

CellList &	cellList ()
	Get the CellList by reference. More...

PairList &	pairList ()
	Get the PairList by reference. More...

Public Member Functions inherited from DdMd::Potential
	Potential ()
	Constructor. More...

virtual	~Potential ()
	Destructor. More...

void	setReverseUpdateFlag (bool reverseUpdateFlag)
	Set flag to identify if reverse communication is enabled. More...

bool	reverseUpdateFlag () const
	Get flag to identify if reverse communication is enabled. More...

virtual void	computeForces ()=0
	Add force contributions to all atomic forces. More...

virtual void	computeEnergy (MPI::Intracomm &communicator)=0
	Compute potential energy on all processors. More...

double	energy () const
	Return the total potential, from all processors. More...

void	unsetEnergy ()
	Mark the energy as unknown (nullify). More...

bool	isEnergySet () const
	Is the energy set (known)? More...

virtual void	computeStress (MPI::Intracomm &communicator)
	Compute stress on all processors. More...

virtual void	computeForcesAndStress (MPI::Intracomm &communicator)
	Compute forces and stress for all processors. More...

Tensor	stress () const
	Return the stress tensor. More...

double	pressure () const
	Return the pressure. More...

void	unsetStress ()
	Mark the stress as unknown (nullify). More...

bool	isStressSet () const
	Is the stress set (known)? More...

virtual bool	isValid (MPI::Intracomm &communicator) const
	Is the potential in a valid internal state? 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 Member Functions
Boundary &	boundary ()
	Get the PairList by const reference. More...

Domain &	domain ()
	Get the PairList by const reference. More...

AtomStorage &	storage ()
	Get the AtomStorage by reference. More...

void	setPairEnergies (DMatrix< double > pairEnergies)
	Set values for pair energies. More...

Protected Member Functions inherited from DdMd::Potential
void	setEnergy (double energy)
	Set a value for the total energy. More...

void	setStress (const Tensor &stress)
	Set a value for the total stress. More...

void	incrementPairStress (const Vector &f, const Vector &dr, Tensor &stress) const
	Add a pair contribution to the stress tensor. More...

void	reduceEnergy (double localEnergy, MPI::Intracomm &communicator)
	Add local energies from all processors, set energy on master. More...

void	reduceStress (Tensor &localStress, MPI::Intracomm &communicator)
	Add local stresses from all processors, set total on master. 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 &param, bool next=true)
	Set this to the parent of a child component. More...

void	addComponent (ParamComponent &param, 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 Attributes
CellList	cellList_
	CellList to construct PairList or calculate nonbonded pair forces. More...

PairList	pairList_
	Verlet pair list, to calculate nonbonded pair forces. More...

Boundary	maxBoundary_
	Boundary used to allocate space for the cell list. More...

double	skin_
	Difference between pairlist cutoff and pair potential cutoff. More...

double	cutoff_
	Minimum cell size = pair potential cutoff + skin. More...

int	nCellCut_
	Approximate number of cells per cutoff distance in each direction. More...

int	pairCapacity_
	Maximum number of nonbonded pairs in pair list. 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...

Constructor & Destructor Documentation

DdMd::PairPotential::PairPotential ( Simulation & simulation )

Constructor.

This is the constructor used during a simulation, and is passed the parent Simulation object as a parameter.

Parameters

simulation parent Simulation object.

Definition at line 43 of file PairPotential.cpp.

References Util::ParamComposite::setClassName().

DdMd::PairPotential::PairPotential ( )

Default constructor.

This constructor is provided to simplify unit testing.

Definition at line 28 of file PairPotential.cpp.

References Util::ParamComposite::setClassName().

DdMd::PairPotential::~PairPotential ( )

virtual

Destructor.

Definition at line 69 of file PairPotential.cpp.

Member Function Documentation

void DdMd::PairPotential::associate	(	Domain &	domain,
		Boundary &	boundary,
		AtomStorage &	storage
	)

Associate with related objects.

Required iff object instantiated with default constructor. If required, it must be called before initialize, readParameters, or loadParameters.

Parameters

domain	associated Domain object.
boundary	associated Boundary object.
storage	associated AtomStorage object.

Definition at line 58 of file PairPotential.cpp.

References boundary(), domain(), and storage().

virtual void DdMd::PairPotential::setNAtomType ( int nAtomType )

pure virtual

Set the maximum number of atom types.

Required iff object instantiated with default constructor. If required, it must be called before initialize, readParameters, or loadParameters.

Parameters

nAtomType maximum number of atom types (max typeId + 1)

Implemented in DdMd::PairPotentialImpl< Interaction >.

void DdMd::PairPotential::initialize	(	const Boundary &	maxBoundary,
		double	skin,
		int	pairCapacity
	)

Set parameters and allocate memory.

This method initializes the object by assigning parameter values and allocating memory. It provides a programmatic alternative to readParameters.

Parameters

maxBoundary	largest expected Boundary (used for allocation)
skin	pair list skin length
pairCapacity	maximum number of pairs per processor

Definition at line 75 of file PairPotential.cpp.

References cutoff_, maxBoundary_, maxPairCutoff(), pairCapacity_, skin(), and skin_.

void DdMd::PairPotential::readParameters ( std::istream & in )

virtual

Initialize, by reading parameters and allocating memory for PairList.

Parameters

in	input parameter stream.

Reimplemented from Util::ParamComposite.

Reimplemented in DdMd::PairPotentialImpl< Interaction >.

Definition at line 89 of file PairPotential.cpp.

References cutoff_, maxBoundary_, maxPairCutoff(), nCellCut_, pairCapacity_, and skin_.

Referenced by DdMd::PairPotentialImpl< Interaction >::readParameters().

void DdMd::PairPotential::loadParameters ( Serializable::IArchive & ar )

virtual

Load parameters for PairList from archive, and allocate memory.

Parameters

ar	input/loading archive

Reimplemented from Util::ParamComposite.

Reimplemented in DdMd::PairPotentialImpl< Interaction >.

Definition at line 103 of file PairPotential.cpp.

References cutoff_, maxBoundary_, nCellCut_, pairCapacity_, and skin_.

Referenced by DdMd::PairPotentialImpl< Interaction >::loadParameters().

void DdMd::PairPotential::save ( Serializable::OArchive & ar )

virtual

Save internal state to an output archive.

Call only on master processor.

Parameters

ar	output/saving archive

Reimplemented from Util::ParamComposite.

Reimplemented in DdMd::PairPotentialImpl< Interaction >.

Definition at line 120 of file PairPotential.cpp.

References DdMd::PairList::allocate(), DdMd::CellList::allocate(), DdMd::AtomStorage::atomCapacity(), cellList_, cutoff_, Util::Dimension, domain(), DdMd::Domain::domainBound(), DdMd::AtomStorage::ghostCapacity(), Simp::OrthorhombicBoundary::length(), maxBoundary_, nCellCut_, pairCapacity_, pairList_, Util::Parameter::saveOptional(), skin_, and storage().

Referenced by DdMd::PairPotentialImpl< Interaction >::save().

void DdMd::PairPotential::setMethodId ( int methodId )

inline

Set id to specify algorithm for energy, force calculations.

The default algorithm, methodId=0, uses a pair list that is constructed using a cell list.

Parameters

methodId algorithm id: 0=pair list, 1=cell list, 2=N^2 loop.

Definition at line 396 of file ddMd/potentials/pair/PairPotential.h.

virtual double DdMd::PairPotential::pairEnergy	(	double	rsq,
		int	iAtomType,
		int	jAtomType
	)		const

pure virtual

Return energy for a single pair.

Parameters

rsq	square distance between atoms in pair
iAtomType	atom type index of 1st atom
jAtomType	atom type index of 2nd atom

Returns: energy of pair

Implemented in DdMd::PairPotentialImpl< Interaction >.

virtual double DdMd::PairPotential::pairForceOverR	(	double	rsq,
		int	iAtomType,
		int	jAtomType
	)		const

pure virtual

Return force / separation for a single pair.

Parameters

rsq	square distance between atoms in pair
iAtomType	atom type index of 1st atom
jAtomType	atom type index of 2nd atom

Returns: repulsive force (< 0 if attractive) over distance

Implemented in DdMd::PairPotentialImpl< Interaction >.

virtual void DdMd::PairPotential::set	(	std::string	name,
		int	i,
		int	j,
		double	value
	)

pure virtual

Modify a parameter, identified by a string.

Parameters

name	parameter name
i	type index of first atom
j	type index of first atom
value	new value of parameter

Implemented in DdMd::PairPotentialImpl< Interaction >.

virtual double DdMd::PairPotential::get	(	std::string	name,
		int	i,
		int	j
	)		const

pure virtual

Get a parameter value, identified by a string.

Parameters

name	parameter name
i	type index of first atom
j	type index of first atom

Implemented in DdMd::PairPotentialImpl< Interaction >.

virtual double DdMd::PairPotential::maxPairCutoff ( ) const

pure virtual

Return maximum cutoff.

Implemented in DdMd::PairPotentialImpl< Interaction >.

Referenced by computeNPair(), initialize(), and readParameters().

virtual std::string DdMd::PairPotential::interactionClassName ( ) const

pure virtual

Return pair interaction class name (e.g., "LJPair").

Implemented in DdMd::PairPotentialImpl< Interaction >.

void DdMd::PairPotential::buildCellList ( )

Build a cell list.

This method adds all local and ghost atoms to a cell list that is used in buildPairList() to build a Verlet pair list. On entry to this method, atomic positions must be generalized. This method should be followed by AtomStorage::transformGenToCart(Boundary& ) to transform all positions back to Cartesian coordinates.

Definition at line 159 of file PairPotential.cpp.

References DdMd::AtomStorage::begin(), DdMd::CellList::build(), cellList_, DdMd::CellList::clear(), cutoff_, Util::Dimension, domain(), DdMd::Domain::domainBound(), DdMd::AtomStorage::isCartesian(), DdMd::CellList::isValid(), Simp::OrthorhombicBoundary::length(), DdMd::CellList::makeGrid(), DdMd::AtomStorage::nAtom(), DdMd::CellList::nAtom(), nCellCut_, DdMd::AtomStorage::nGhost(), Util::PArrayIterator< Data >::notEnd(), DdMd::CellList::nReject(), DdMd::CellList::placeAtom(), storage(), and UTIL_THROW.

Referenced by DdMd::TwoStepIntegrator::run(), and DdMd::Integrator::setupAtoms().

void DdMd::PairPotential::buildPairList ( )

Build the Verlet Pair list.

Preconditions:

Cell List must have been built, by PairPotential::buildCellList.
Atomic positions must be expressed in Cartesian coordinates.

Definition at line 206 of file PairPotential.cpp.

References DdMd::PairList::build(), cellList_, pairList_, DdMd::Potential::reverseUpdateFlag(), storage(), and UTIL_THROW.

Referenced by DdMd::TwoStepIntegrator::run(), and DdMd::Integrator::setupAtoms().

virtual void DdMd::PairPotential::computePairEnergies ( MPI::Intracomm & communicator )

pure virtual

Compute pair energies on all processors.

This method must be called on all processors. The resulting total is stored on the master processor, and may be retrieved by calling the pairEnergies() function on the master processor.

Implemented in DdMd::PairPotentialImpl< Interaction >.

Referenced by DdMd::PairEnergyAnalyzer::compute().

DMatrix< double > DdMd::PairPotential::pairEnergies ( ) const

Return total pair energies, from all processors.

This method should only be called on the master (rank 0) processor, after a previous call to computePairEnergies.

Definition at line 217 of file PairPotential.cpp.

Referenced by DdMd::PairEnergyAnalyzer::value().

void DdMd::PairPotential::unsetPairEnergies ( )

Mark pair energy as unknown (nullify).

Definition at line 229 of file PairPotential.cpp.

Referenced by DdMd::PairPotentialImpl< Interaction >::computePairEnergies().

void DdMd::PairPotential::computeNPair ( MPI::Intracomm & communicator )

Compute twice the number of pairs within the force cutoff.

This method must be called on all processors.

The method for distributing pairs among processors is the same as is used to distribute the energy, and depends on the value of reverseUpdateFlag().

Definition at line 236 of file PairPotential.cpp.

References maxPairCutoff(), and methodId().

int DdMd::PairPotential::nPair ( ) const

Return twice the number of pairs within the specified force cutoff.

This method should only be called on the master (rank 0) processor. The return value is computed by a previous call to computeNPair.

Definition at line 266 of file PairPotential.cpp.

References DdMd::PairList::begin(), DdMd::CellList::begin(), DdMd::AtomStorage::begin(), cellList_, DdMd::Cell::getNeighbors(), DdMd::PairIterator::getPair(), DdMd::Atom::isGhost(), DdMd::Cell::nAtom(), DdMd::Cell::nextCellPtr(), DdMd::PairIterator::notEnd(), Util::PArrayIterator< Data >::notEnd(), pairList_, DdMd::Atom::position(), DdMd::Potential::reverseUpdateFlag(), Util::FSArray< Data, Capacity >::size(), Util::Vector::square(), storage(), and Util::Vector::subtract().

CellList & DdMd::PairPotential::cellList ( )

inline

Get the CellList by reference.

Definition at line 375 of file ddMd/potentials/pair/PairPotential.h.

PairList & DdMd::PairPotential::pairList ( )

inline

Get the PairList by reference.

Definition at line 378 of file ddMd/potentials/pair/PairPotential.h.

Referenced by DdMd::Integrator::clear(), and DdMd::Integrator::outputStatistics().

double DdMd::PairPotential::skin ( ) const

inline

Get value of the pair list skin.

Definition at line 381 of file ddMd/potentials/pair/PairPotential.h.

Referenced by initialize().

double DdMd::PairPotential::cutoff ( ) const

inline

Get value of the pair list cutoff (maxPairCutoff + skin).

Definition at line 384 of file ddMd/potentials/pair/PairPotential.h.

int DdMd::PairPotential::methodId ( ) const

inline

Return integer id for algorithm (0=PAIR, 1=CELL, 2=NSQ)

Definition at line 399 of file ddMd/potentials/pair/PairPotential.h.

Referenced by DdMd::PairPotentialImpl< Interaction >::computeEnergy(), DdMd::PairPotentialImpl< Interaction >::computeForces(), and computeNPair().

Boundary & DdMd::PairPotential::boundary ( )

inlineprotected

Get the PairList by const reference.

Definition at line 387 of file ddMd/potentials/pair/PairPotential.h.

Referenced by associate(), DdMd::PairPotentialImpl< Interaction >::computeForcesAndStress(), and DdMd::PairPotentialImpl< Interaction >::computeStress().

Domain & DdMd::PairPotential::domain ( )

inlineprotected

Get the PairList by const reference.

Definition at line 390 of file ddMd/potentials/pair/PairPotential.h.

Referenced by associate(), buildCellList(), and save().

AtomStorage & DdMd::PairPotential::storage ( )

inlineprotected

Get the AtomStorage by reference.

Definition at line 393 of file ddMd/potentials/pair/PairPotential.h.

Referenced by associate(), buildCellList(), buildPairList(), DdMd::PairPotentialImpl< Interaction >::computeEnergy(), nPair(), and save().

void DdMd::PairPotential::setPairEnergies ( DMatrix< double > pairEnergies )

protected

Set values for pair energies.

Definition at line 223 of file PairPotential.cpp.

Referenced by DdMd::PairPotentialImpl< Interaction >::computePairEnergies().

Member Data Documentation

CellList DdMd::PairPotential::cellList_

protected

CellList to construct PairList or calculate nonbonded pair forces.

Definition at line 303 of file ddMd/potentials/pair/PairPotential.h.

Referenced by buildCellList(), buildPairList(), DdMd::PairPotentialImpl< Interaction >::computeEnergy(), nPair(), and save().

PairList DdMd::PairPotential::pairList_

protected

Verlet pair list, to calculate nonbonded pair forces.

Definition at line 306 of file ddMd/potentials/pair/PairPotential.h.

Referenced by buildPairList(), DdMd::PairPotentialImpl< Interaction >::computeEnergy(), DdMd::PairPotentialImpl< Interaction >::computeForcesAndStress(), DdMd::PairPotentialImpl< Interaction >::computePairEnergies(), DdMd::PairPotentialImpl< Interaction >::computeStress(), nPair(), and save().

Boundary DdMd::PairPotential::maxBoundary_

protected

Boundary used to allocate space for the cell list.

Definition at line 309 of file ddMd/potentials/pair/PairPotential.h.

Referenced by initialize(), loadParameters(), readParameters(), and save().

double DdMd::PairPotential::skin_

protected

Difference between pairlist cutoff and pair potential cutoff.

Definition at line 312 of file ddMd/potentials/pair/PairPotential.h.

Referenced by initialize(), loadParameters(), readParameters(), and save().

double DdMd::PairPotential::cutoff_

protected

Minimum cell size = pair potential cutoff + skin.

Definition at line 315 of file ddMd/potentials/pair/PairPotential.h.

Referenced by buildCellList(), initialize(), loadParameters(), readParameters(), and save().

int DdMd::PairPotential::nCellCut_

protected

Approximate number of cells per cutoff distance in each direction.

Definition at line 318 of file ddMd/potentials/pair/PairPotential.h.

Referenced by buildCellList(), loadParameters(), readParameters(), and save().

int DdMd::PairPotential::pairCapacity_

protected

Maximum number of nonbonded pairs in pair list.

Definition at line 321 of file ddMd/potentials/pair/PairPotential.h.

Referenced by initialize(), loadParameters(), readParameters(), and save().

The documentation for this class was generated from the following files:

Detailed Description

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation