Detailed Description

template<class Interaction>
class DdMd::ExternalPotentialImpl< Interaction >

Implementation template for a ExternalPotential.

Definition at line 33 of file ddMd/potentials/external/ExternalPotentialImpl.h.

#include <ExternalPotentialImpl.h>

Inheritance diagram for DdMd::ExternalPotentialImpl< Interaction >:

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

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

virtual	~ExternalPotentialImpl ()
	Destructor. More...

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

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

virtual void	readParameters (std::istream &in)
	Read external potential interaction. More...

virtual void	loadParameters (Serializable::IArchive &ar)
	Load internal state from archive and initialize, for restart. More...

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

Interaction interface
virtual double	externalEnergy (const Vector &position, int typeId) const
	Returns external potential energy of a single atom. More...

virtual void	getExternalForce (const Vector &position, int typeId, Vector &force) const
	Computes external force on one atom. More...

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

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

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

Interaction &	interaction ()
	Return external interaction by reference. More...

const Interaction &	interaction () const
	Return external interaction by const reference. More...

Total Energy and Forces
virtual void	computeForces ()
	Calculate external forces for all atoms in this Simulation. More...

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

Public Member Functions inherited from DdMd::ExternalPotential
	ExternalPotential (Simulation &simulation)
	Constructor. More...

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

virtual	~ExternalPotential ()
	Destructor. 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...

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...

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::ExternalPotential
Simulation &	simulation ()
	Get the parent Simulation by reference. More...

Boundary &	boundary ()
	Get the Boundary by reference. More...

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

Constructor & Destructor Documentation

template<class Interaction >

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

Constructor.

Definition at line 211 of file ddMd/potentials/external/ExternalPotentialImpl.h.

References DdMd::Simulation::boundary(), DdMd::ExternalPotentialImpl< Interaction >::interaction(), DdMd::Simulation::nAtomType(), and DdMd::ExternalPotentialImpl< Interaction >::setNAtomType().

template<class Interaction >

DdMd::ExternalPotentialImpl< Interaction >::ExternalPotentialImpl ( )

Default constructor (for unit testing).

Definition at line 225 of file ddMd/potentials/external/ExternalPotentialImpl.h.

template<class Interaction >

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

virtual

Destructor.

Definition at line 235 of file ddMd/potentials/external/ExternalPotentialImpl.h.

Member Function Documentation

template<class Interaction >

void DdMd::ExternalPotentialImpl< Interaction >::associate	(	Boundary &	boundary,
		AtomStorage &	storage
	)

virtual

Associate with related objects.

Call iff object instantiated with default constructor.

Parameters

boundary	associated Boundary object.
storage	associated AtomStorage object.

Reimplemented from DdMd::ExternalPotential.

Definition at line 249 of file ddMd/potentials/external/ExternalPotentialImpl.h.

References DdMd::ExternalPotential::associate(), and DdMd::ExternalPotentialImpl< Interaction >::interaction().

template<class Interaction >

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

virtual

Set the maximum number of atom types.

Set the maximum number of atom types (for unit testing).

Call iff object instantiated with default constructor.

Parameters

nAtomType maximum number of atomTypes (max index+1)

Implements DdMd::ExternalPotential.

Definition at line 259 of file ddMd/potentials/external/ExternalPotentialImpl.h.

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

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

template<class Interaction >

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

virtual

Read external potential interaction.

Parameters

in	input parameter stream

Reimplemented from Util::ParamComposite.

Definition at line 266 of file ddMd/potentials/external/ExternalPotentialImpl.h.

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

template<class Interaction >

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

virtual

Load internal state from archive and initialize, for restart.

Parameters

ar	input/loading archive

Reimplemented from Util::ParamComposite.

Definition at line 279 of file ddMd/potentials/external/ExternalPotentialImpl.h.

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

template<class Interaction >

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

virtual

Save internal state to an archive, for restart.

Call only on master processor.

Parameters

ar	output/saving archive

Reimplemented from Util::ParamComposite.

Definition at line 292 of file ddMd/potentials/external/ExternalPotentialImpl.h.

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

template<class Interaction >

double DdMd::ExternalPotentialImpl< Interaction >::externalEnergy	(	const Vector &	position,
		int	typeId
	)		const

virtual

Returns external potential energy of a single atom.

Parameters

position	atomic position Vector
typeId	atom type index

Returns: external potential energy

Implements DdMd::ExternalPotential.

Definition at line 300 of file ddMd/potentials/external/ExternalPotentialImpl.h.

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

template<class Interaction >

void DdMd::ExternalPotentialImpl< Interaction >::getExternalForce	(	const Vector &	position,
		int	typeId,
		Vector &	force
	)		const

virtual

Computes external force on one atom.

Parameters

position	atom position (input)
typeId	atom type index (input)
force	force on the atom (output)

Implements DdMd::ExternalPotential.

Definition at line 309 of file ddMd/potentials/external/ExternalPotentialImpl.h.

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

template<class Interaction>

void DdMd::ExternalPotentialImpl< Interaction >::set	(	std::string	name,
		double	value
	)

inlinevirtual

Modify a pair interaction parameter, identified by a string.

Parameters

name	parameter name
value	new value of parameter

Implements DdMd::ExternalPotential.

Definition at line 123 of file ddMd/potentials/external/ExternalPotentialImpl.h.

template<class Interaction>

double DdMd::ExternalPotentialImpl< Interaction >::get ( std::string name ) const

inlinevirtual

Get a parameter value, identified by a string.

Parameters

name	parameter name

Implements DdMd::ExternalPotential.

Definition at line 131 of file ddMd/potentials/external/ExternalPotentialImpl.h.

template<class Interaction >

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

virtual

Return external interaction class name (e.g., "LamellarOrderingExternal").

Implements DdMd::ExternalPotential.

Definition at line 317 of file ddMd/potentials/external/ExternalPotentialImpl.h.

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

template<class Interaction >

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

Return external interaction by reference.

Return underlying interaction object by reference.

Definition at line 334 of file ddMd/potentials/external/ExternalPotentialImpl.h.

template<class Interaction >

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

Return external interaction by const reference.

Return underlying interaction object by const reference.

Definition at line 324 of file ddMd/potentials/external/ExternalPotentialImpl.h.

template<class Interaction >

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

virtual

Calculate external forces for all atoms in this Simulation.

Implements DdMd::Potential.

Definition at line 344 of file ddMd/potentials/external/ExternalPotentialImpl.h.

Referenced by DdMd::ExternalPotentialImpl< Interaction >::computeEnergy().

template<class Interaction >

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

virtual

Compute the total external energy for all processors.

Call on all processors.

Implements DdMd::Potential.

Definition at line 353 of file ddMd/potentials/external/ExternalPotentialImpl.h.

References DdMd::AtomStorage::begin(), DdMd::ExternalPotentialImpl< Interaction >::computeForces(), DdMd::Potential::energy(), Util::PArrayIterator< Data >::notEnd(), DdMd::Potential::reduceEnergy(), DdMd::Potential::setEnergy(), and DdMd::ExternalPotential::storage().

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

ddMd/potentials/external/ExternalPotentialImpl.h

Detailed Description

template<class Interaction> class DdMd::ExternalPotentialImpl< Interaction >

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

template<class Interaction>
class DdMd::ExternalPotentialImpl< Interaction >