Detailed Description

template<class Interaction>
class DdMd::PairPotentialImpl< Interaction >

Implementation template for a PairPotential.

This template provides a concrete implementation of the PairPotential base class for a specific nonbonded pair interaction class, representing a specific functional form for the pair potential (e.g., cutoff Lennard-Jones). The template argument Interaction represents the specified pair interaction class (e.g., LJPair for cutoff Lennard-Jones), which is normally a class in the Simp namespace from the src/simp/pair directory.

Definition at line 42 of file PairPotentialImpl.h.

#include <PairPotentialImpl.h>

Inheritance diagram for DdMd::PairPotentialImpl< Interaction >:

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

	PairPotentialImpl ()
	Default constructor (for unit testing). More...

virtual	~PairPotentialImpl ()
	Destructor. More...

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

virtual void	readParameters (std::istream &in)
	Read pair potential interaction and pair list blocks. 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...

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

virtual double	pairForceOverR (double rsq, int iAtomType, int jAtomType) const
	Return force / separation for a single pair. More...

void	set (std::string name, int i, int j, double value)
	Modify a pair interaction parameter, identified by a string. More...

double	get (std::string name, int i, int j) const
	Get a parameter value, identified by a string. More...

virtual double	maxPairCutoff () const
	Return maximum cutoff. More...

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

const Interaction &	interaction () const
	Return underlying pair interaction object by const reference. More...

Interaction &	interaction ()
	Return underlying pair interaction object by reference. More...

Total Energy, Force and Stress
virtual void	computeForces ()
	Compute non-bonded pair forces for all atoms in this Simulation. More...

virtual void	computeEnergy (MPI::Intracomm &communicator)
	Compute the total nonBonded pair energy for all processors. More...

virtual void	computeStress (MPI::Intracomm &communicator)
	Compute the total nonBonded stress for all processors. More...

virtual void	computePairEnergies (MPI::Intracomm &communicator)
	Compute total pair energies for all processors Compute nonbonded forces and sress for all processors. More...

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

Public Member Functions inherited from DdMd::PairPotential
	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...

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

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

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

void	buildCellList ()
	Build a cell list. More...

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

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...

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...

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 DdMd::PairPotential
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 inherited from DdMd::PairPotential
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...

Constructor & Destructor Documentation

template<class Interaction >

DdMd::PairPotentialImpl< Interaction >::PairPotentialImpl ( Simulation & simulation )

Constructor.

Sets nNAtomType to simulation.nAtomType().

Parameters

simulation parent Simulation object.

Definition at line 338 of file PairPotentialImpl.h.

References DdMd::Simulation::nAtomType(), and DdMd::PairPotentialImpl< Interaction >::setNAtomType().

template<class Interaction >

DdMd::PairPotentialImpl< Interaction >::PairPotentialImpl ( )

Default constructor (for unit testing).

Definition at line 351 of file PairPotentialImpl.h.

template<class Interaction >

DdMd::PairPotentialImpl< Interaction >::~PairPotentialImpl ( )

virtual

Destructor.

Definition at line 361 of file PairPotentialImpl.h.

Member Function Documentation

template<class Interaction >

void DdMd::PairPotentialImpl< Interaction >::setNAtomType ( int nAtomType )

virtual

Set the maximum number of atom types.

This function is required iff the object is instantiated using the default constructor, which is intended for use only for unit testing. It is called internally by the constructor PairPotentialImpl(Simulation& ) that is used during a simulation.

Implements DdMd::PairPotential.

Definition at line 372 of file PairPotentialImpl.h.

References DdMd::PairPotentialImpl< Interaction >::interaction(), and UTIL_CHECK.

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

template<class Interaction >

void DdMd::PairPotentialImpl< Interaction >::readParameters ( std::istream & in )

virtual

Read pair potential interaction and pair list blocks.

This method initializes the pair potential. It reads the the maxBoundary, PairList and pair potential Interaction parameter blocks, in that order, and initializes an internal PairList.

Precondition: nAtomType must be set to a positive value; This object may not already be initialized

Parameters

in	input parameter stream.

Reimplemented from DdMd::PairPotential.

Definition at line 383 of file PairPotentialImpl.h.

References Util::ParamComposite::addParamComposite(), DdMd::PairPotentialImpl< Interaction >::interaction(), DdMd::PairPotential::readParameters(), and UTIL_CHECK.

template<class Interaction >

void DdMd::PairPotentialImpl< Interaction >::loadParameters ( Serializable::IArchive & ar )

virtual

Load internal state from an archive.

This function initializes the pair potential during a restart.

Precondition: nAtomType must be set to a positive value; This object may not already be initialized

Parameters

ar	input/loading archive

Reimplemented from DdMd::PairPotential.

Definition at line 403 of file PairPotentialImpl.h.

References Util::ParamComposite::addParamComposite(), DdMd::PairPotentialImpl< Interaction >::interaction(), DdMd::PairPotential::loadParameters(), and UTIL_CHECK.

template<class Interaction >

void DdMd::PairPotentialImpl< Interaction >::save ( Serializable::OArchive & ar )

virtual

Save internal state to an archive.

Call only on master processor.

Parameters

ar	output/saving archive

Reimplemented from DdMd::PairPotential.

Definition at line 419 of file PairPotentialImpl.h.

References DdMd::PairPotentialImpl< Interaction >::interaction(), and DdMd::PairPotential::save().

template<class Interaction >

double DdMd::PairPotentialImpl< Interaction >::pairEnergy	(	double	rsq,
		int	iAtomType,
		int	jAtomType
	)		const

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

Implements DdMd::PairPotential.

Definition at line 429 of file PairPotentialImpl.h.

References DdMd::PairPotentialImpl< Interaction >::interaction().

template<class Interaction >

double DdMd::PairPotentialImpl< Interaction >::pairForceOverR	(	double	rsq,
		int	iAtomType,
		int	jAtomType
	)		const

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

Implements DdMd::PairPotential.

Definition at line 437 of file PairPotentialImpl.h.

References DdMd::PairPotentialImpl< Interaction >::interaction().

template<class Interaction>

void DdMd::PairPotentialImpl< Interaction >::set	(	std::string	name,
		int	i,
		int	j,
		double	value
	)

inlinevirtual

Modify a pair interaction 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

Implements DdMd::PairPotential.

Definition at line 147 of file PairPotentialImpl.h.

template<class Interaction>

double DdMd::PairPotentialImpl< Interaction >::get	(	std::string	name,
		int	i,
		int	j
	)		const

inlinevirtual

Get a parameter value, identified by a string.

Parameters

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

Implements DdMd::PairPotential.

Definition at line 157 of file PairPotentialImpl.h.

template<class Interaction >

double DdMd::PairPotentialImpl< Interaction >::maxPairCutoff ( ) const

virtual

Return maximum cutoff.

Implements DdMd::PairPotential.

Definition at line 451 of file PairPotentialImpl.h.

References DdMd::PairPotentialImpl< Interaction >::interaction().

template<class Interaction >

std::string DdMd::PairPotentialImpl< Interaction >::interactionClassName ( ) const

virtual

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

Implements DdMd::PairPotential.

Definition at line 458 of file PairPotentialImpl.h.

References DdMd::PairPotentialImpl< Interaction >::interaction().

template<class Interaction>

const Interaction& DdMd::PairPotentialImpl< Interaction >::interaction ( ) const

inline

Return underlying pair interaction object by const reference.

Definition at line 173 of file PairPotentialImpl.h.

Referenced by DdMd::PairPotentialImpl< Interaction >::interactionClassName(), DdMd::PairPotentialImpl< Interaction >::loadParameters(), DdMd::PairPotentialImpl< Interaction >::maxPairCutoff(), DdMd::PairPotentialImpl< Interaction >::pairEnergy(), DdMd::PairPotentialImpl< Interaction >::pairForceOverR(), DdMd::PairPotentialImpl< Interaction >::readParameters(), DdMd::PairPotentialImpl< Interaction >::save(), and DdMd::PairPotentialImpl< Interaction >::setNAtomType().

template<class Interaction>

Interaction& DdMd::PairPotentialImpl< Interaction >::interaction ( )

inline

Return underlying pair interaction object by reference.

Definition at line 179 of file PairPotentialImpl.h.

template<class Interaction >

void DdMd::PairPotentialImpl< Interaction >::computeForces ( )

virtual

Compute non-bonded pair forces for all atoms in this Simulation.

Adds non-bonded pair forces to the current values of the forces for all atoms in this simulation. Before calculating forces, the method checks if the pair list is current, and rebuilds it if necessary.

Implements DdMd::Potential.

Definition at line 465 of file PairPotentialImpl.h.

References DdMd::PairPotential::methodId().

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

template<class Interaction >

void DdMd::PairPotentialImpl< Interaction >::computeEnergy ( MPI::Intracomm & communicator )

virtual

Compute the total nonBonded pair energy for all processors.

Call on all processors.

Implements DdMd::Potential.

Definition at line 483 of file PairPotentialImpl.h.

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