Simp::PeriodicExternal Class Reference

Detailed Description

A clipped cosine potential that induces ordering along directions specified by waveIntVectors, w_i.

/ / / / w_i.(x-shift_[0]) w_i.(y-shift_[1]) w_i.(z-shift_[2]) \ \ \ \ u = prefactor[atomType] externalParameter tanh | clipParameter| C_ + Sum | cos | 2 pi ---------------— + ---------------— + ---------------— + phase_i | | | | \ \ i \ \ Lx Ly Lz / / / /

Prefactor (which depends on the atomType), externalParameter, waveIntVectors, interfaceWidth and periodicity are given as inputs in the parameter file. ClipParameter is the inverse of 2*pi*periodicity*interfaceWidth.

Definition at line 37 of file PeriodicExternal.h.

#include <PeriodicExternal.h>

Inheritance diagram for Simp::PeriodicExternal:

Public Member Functions
	PeriodicExternal ()
	Default constructor. More...
	PeriodicExternal (const PeriodicExternal &other)
	Copy constructor. More...
PeriodicExternal &	operator= (const PeriodicExternal &other)
	Assignment. More...
void	setNAtomType (int nAtomType)
	Set nAtomType value. More...
void	setExternalParameter (double externalParameter)
	Sets external parameter. More...
void	setBoundary (Boundary &boundary)
	Set pointer to Boundary. More...
void	readParameters (std::istream &in)
	Read potential parameters, and initialize other variables. 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...
double	externalParameter () const
	Returns external parameter. More...
double	energy (const Vector &position, int i) const
	Returns external potential energy of a single particle. More...
void	getForce (const Vector &position, int type, Vector &force) const
	Returns force caused by the external potential. More...
std::string	className () const
	Return name string "PeriodicExternal". 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 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

Simp::PeriodicExternal::PeriodicExternal

(

)

Default constructor.

Definition at line 19 of file PeriodicExternal.cpp.

References Util::ParamComposite::setClassName().

Simp::PeriodicExternal::PeriodicExternal

(

const PeriodicExternal &

other

)

Copy constructor.

Definition at line 33 of file PeriodicExternal.cpp.

References Util::DArray< Data >::allocate(), and Util::Dimension.

Member Function Documentation

PeriodicExternal & Simp::PeriodicExternal::operator=

(

const PeriodicExternal &

other

)

Assignment.

Definition at line 65 of file PeriodicExternal.cpp.

References Util::DArray< Data >::allocate(), and Util::Dimension.

void Simp::PeriodicExternal::setNAtomType

(

int

nAtomType

)

Set nAtomType value.

Parameters

nAtomType

number of atom types.

Definition at line 96 of file PeriodicExternal.cpp.

References UTIL_THROW.

void Simp::PeriodicExternal::setExternalParameter

(

double

externalParameter

)

Sets external parameter.

Parameters

externalParameter

external parameter of system

Definition at line 107 of file PeriodicExternal.cpp.

References externalParameter(), and UTIL_THROW.

void Simp::PeriodicExternal::setBoundary

(

Boundary &

boundary

)

Set pointer to Boundary.

Parameters

boundary

Boundary object (used to calculate length along perpendicular direction).

Definition at line 121 of file PeriodicExternal.cpp.

void Simp::PeriodicExternal::readParameters ( std::istream &  in )

virtual

Read potential parameters, and initialize other variables.

Precondition

nAtomType must have been set, by calling setNAtomType().

Boundary must have been set, by calling setBoundary().

Parameters

in	input stream

Reimplemented from Util::ParamComposite.

Definition at line 127 of file PeriodicExternal.cpp.

References Util::DArray< Data >::allocate(), and UTIL_CHECK.

void Simp::PeriodicExternal::loadParameters ( Serializable::IArchive &  ar )

virtual

Load internal state from an archive.

Parameters

ar	input/loading archive

Reimplemented from Util::ParamComposite.

Definition at line 152 of file PeriodicExternal.cpp.

References Util::DArray< Data >::allocate(), and UTIL_CHECK.

void Simp::PeriodicExternal::save ( Serializable::OArchive &  ar )

virtual

Save internal state to an archive.

Parameters

ar	output/saving archive

Reimplemented from Util::ParamComposite.

Definition at line 173 of file PeriodicExternal.cpp.

References UTIL_THROW.

double Simp::PeriodicExternal::externalParameter

(

)

const

Returns external parameter.

Returns

external parameter

Definition at line 230 of file PeriodicExternal.cpp.

Referenced by setExternalParameter().

double Simp::PeriodicExternal::energy ( const Vector &  position, int  i  ) const

inline

Returns external potential energy of a single particle.

Parameters

position	atomic position Vector
i	atom type.

Returns

external potential energy

Definition at line 190 of file PeriodicExternal.h.

References Util::Vector::dot().

void Simp::PeriodicExternal::getForce ( const Vector &  position, int  type, Vector &  force  ) const

inline

Returns force caused by the external potential.

Parameters

position	atom position
type	atom type id
force	force on the atom (on output)

Definition at line 214 of file PeriodicExternal.h.

References Util::Vector::dot(), and Util::Vector::zero().

std::string Simp::PeriodicExternal::className

(

)

const

Return name string "PeriodicExternal".

Definition at line 238 of file PeriodicExternal.cpp.

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

• PeriodicExternal.h
• PeriodicExternal.cpp