Detailed Description

Coulomb potential for an Md simulation.

This class computes the long-range k-space part of the Coulomb forces and energies in a molecular dynamics (MD) simulation, and provides accessors for both r-space and k-space contributions to the Coulomb energy and stress.

Definition at line 33 of file MdCoulombPotential.h.

#include <MdCoulombPotential.h>

Inheritance diagram for McMd::MdCoulombPotential:

Public Member Functions
	MdCoulombPotential ()
	Constructor. More...

virtual	~MdCoulombPotential ()
	Destructor (does nothing). More...

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

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

Waves (data that depends on Boundary).
bool	hasWaves ()
	Are wavevectors and k-space influence function up to date? More...

virtual void	makeWaves ()=0
	Generate wavevectors and influence function for this boundary. More...

void	unsetWaves ()
	Unset all data that depends on the Boundary. More...

virtual int	nWave () const =0
	Current number of wavevectors. More...

Forces and Energy
virtual void	addForces ()=0
	Add k-space Coulomb forces to forces on all atoms. More...

virtual void	computeEnergy ()=0
	Calculate the long range kspace part of Coulomb energy. More...

virtual void	unsetEnergy ()
	Unset k-space energy. More...

double	kSpaceEnergy ()
	Get long-range k-space part of Coulomb energy. More...

double	rSpaceEnergy ()
	Return short-range r-space part of Coulomb energy. More...

double	energy ()
	Get total Coulomb energy. More...

Stress
virtual void	computeStress ()=0
	Compute kspace part of Coulomb stress. More...

virtual void	unsetStress ()
	Unset k-space stress. More...

Tensor	kSpaceStress ()
	Get long-range k-space part of Coulomb stress. More...

Tensor	rSpaceStress ()
	Return short-range r-space part of Coulomb stress. More...

Tensor	stress ()
	Get total Coulomb stress. More...

void	computeStress (Tensor &stress)
	Get total Coulomb stress. More...

void	computeStress (Vector &pressures)
	Get diagonal components of Coulomb stress. More...

double	pressure ()
	Get total Coulomb pressure. More...

void	computeStress (double &pressure)
	Get the total Coulomb pressure. More...

Public Member Functions inherited from Util::ParamComposite
	ParamComposite ()
	Constructor. More...

	ParamComposite (const ParamComposite &other)
	Copy constructor. More...

	ParamComposite (int capacity)
	Constructor. More...

virtual	~ParamComposite ()
	Virtual destructor. More...

void	resetParam ()
	Resets ParamComposite to its empty state. More...

virtual void	readParam (std::istream &in)
	Read the parameter file block. More...

virtual void	readParamOptional (std::istream &in)
	Read optional parameter file block. More...

virtual void	readParameters (std::istream &in)
	Read the body of parameter block, without begin and end lines. More...

virtual void	writeParam (std::ostream &out)
	Write all parameters to an output stream. More...

virtual void	load (Serializable::IArchive &ar)
	Load all parameters from an input archive. More...

virtual void	loadOptional (Serializable::IArchive &ar)
	Load an optional ParamComposite. More...

virtual void	loadParameters (Serializable::IArchive &ar)
	Load state from archive, without adding Begin and End lines. More...

virtual void	save (Serializable::OArchive &ar)
	Saves all parameters to an archive. More...

void	saveOptional (Serializable::OArchive &ar)
	Saves isActive flag, and then calls save() iff isActive is true. More...

void	readParamComposite (std::istream &in, ParamComposite &child, bool next=true)
	Add and read a required child ParamComposite. More...

void	readParamCompositeOptional (std::istream &in, ParamComposite &child, bool next=true)
	Add and attempt to read an optional child ParamComposite. More...

template<typename Type >
ScalarParam< Type > &	read (std::istream &in, const char *label, Type &value)
	Add and read a new required ScalarParam < Type > object. More...

template<typename Type >
ScalarParam< Type > &	readOptional (std::istream &in, const char *label, Type &value)
	Add and read a new optional ScalarParam < Type > object. More...

template<typename Type >
CArrayParam< Type > &	readCArray (std::istream &in, const char label, Type value, int n)
	Add and read a required C array parameter. More...

template<typename Type >
CArrayParam< Type > &	readOptionalCArray (std::istream &in, const char label, Type value, int n)
	Add and read an optional C array parameter. More...

template<typename Type >
DArrayParam< Type > &	readDArray (std::istream &in, const char *label, DArray< Type > &array, int n)
	Add and read a required DArray < Type > parameter. More...

template<typename Type >
DArrayParam< Type > &	readOptionalDArray (std::istream &in, const char *label, DArray< Type > &array, int n)
	Add and read an optional DArray < Type > parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	readFArray (std::istream &in, const char *label, FArray< Type, N > &array)
	Add and read a required FArray < Type, N > array parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	readOptionalFArray (std::istream &in, const char *label, FArray< Type, N > &array)
	Add and read an optional FArray < Type, N > array parameter. More...

template<typename Type >
CArray2DParam< Type > &	readCArray2D (std::istream &in, const char label, Type value, int m, int n, int np)
	Add and read a required CArray2DParam < Type > 2D C-array. More...

template<typename Type >
CArray2DParam< Type > &	readOptionalCArray2D (std::istream &in, const char label, Type value, int m, int n, int np)
	Add and read an optional CArray2DParam < Type > 2D C-array parameter. More...

template<typename Type >
DMatrixParam< Type > &	readDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n)
	Add and read a required DMatrix < Type > matrix parameter. More...

template<typename Type >
DMatrixParam< Type > &	readOptionalDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n)
	Add and read an optional DMatrix < Type > matrix parameter. More...

template<typename Type >
DSymmMatrixParam< Type > &	readDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n)
	Add and read a required symmetrix DMatrix. More...

template<typename Type >
DSymmMatrixParam< Type > &	readOptionalDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n)
	Add and read an optional DMatrix matrix parameter. More...

Begin &	readBegin (std::istream &in, const char *label, bool isRequired=true)
	Add and read a class label and opening bracket. More...

End &	readEnd (std::istream &in)
	Add and read the closing bracket. More...

Blank &	readBlank (std::istream &in)
	Add and read a new Blank object, representing a blank line. More...

void	loadParamComposite (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
	Add and load a required child ParamComposite. More...

void	loadParamCompositeOptional (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
	Add and load an optional child ParamComposite if isActive. More...

template<typename Type >
ScalarParam< Type > &	loadParameter (Serializable::IArchive &ar, const char *label, Type &value, bool isRequired)
	Add and load a new ScalarParam < Type > object. More...

template<typename Type >
ScalarParam< Type > &	loadParameter (Serializable::IArchive &ar, const char *label, Type &value)
	Add and load new required ScalarParam < Type > object. More...

template<typename Type >
CArrayParam< Type > &	loadCArray (Serializable::IArchive &ar, const char label, Type value, int n, bool isRequired)
	Add a C array parameter and load its elements. More...

template<typename Type >
CArrayParam< Type > &	loadCArray (Serializable::IArchive &ar, const char label, Type value, int n)
	Add and load a required CArrayParam< Type > array parameter. More...

template<typename Type >
DArrayParam< Type > &	loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n, bool isRequired)
	Add an load a DArray < Type > array parameter. More...

template<typename Type >
DArrayParam< Type > &	loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n)
	Add and load a required DArray< Type > array parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array, bool isRequired)
	Add and load an FArray < Type, N > fixed-size array parameter. More...

template<typename Type , int N>
FArrayParam< Type, N > &	loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array)
	Add and load a required FArray < Type > array parameter. More...

template<typename Type >
CArray2DParam< Type > &	loadCArray2D (Serializable::IArchive &ar, const char label, Type value, int m, int n, int np, bool isRequired)
	Add and load a CArray2DParam < Type > C 2D array parameter. More...

template<typename Type >
CArray2DParam< Type > &	loadCArray2D (Serializable::IArchive &ar, const char label, Type value, int m, int n, int np)
	Add and load a required < Type > matrix parameter. More...

template<typename Type >
DMatrixParam< Type > &	loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired)
	Add and load a DMatrixParam < Type > matrix parameter. More...

template<typename Type >
DMatrixParam< Type > &	loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n)
	Add and load a required DMatrixParam < Type > matrix parameter. More...

template<typename Type >
DSymmMatrixParam< Type > &	loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n, bool isRequired)
	Add and load a symmetric DSymmMatrixParam < Type > matrix parameter. More...

template<typename Type >
DSymmMatrixParam< Type > &	loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n)
	Add and load a required DSymmMatrixParam < Type > matrix parameter. More...

void	addParamComposite (ParamComposite &child, bool next=true)
	Add a child ParamComposite object to the format array. More...

Begin &	addBegin (const char *label)
	Add a Begin object representing a class name and bracket. More...

End &	addEnd ()
	Add a closing bracket. More...

Blank &	addBlank ()
	Create and add a new Blank object, representing a blank line. More...

std::string	className () const
	Get class name string. More...

bool	isRequired () const
	Is this ParamComposite required in the input file? More...

bool	isActive () const
	Is this parameter active? More...

Public Member Functions inherited from Util::ParamComponent
virtual	~ParamComponent ()
	Destructor. More...

void	setIndent (const ParamComponent &parent, bool next=true)
	Set indent level. More...

std::string	indent () const
	Return indent string for this object (string of spaces). More...

template<class Archive >
void	serialize (Archive &ar, const unsigned int version)
	Serialize this ParamComponent as a string. More...

Public Member Functions inherited from Util::Serializable
virtual	~Serializable ()
	Destructor. More...

Public Member Functions inherited from Util::MpiFileIo
	MpiFileIo ()
	Constructor. More...

	MpiFileIo (const MpiFileIo &other)
	Copy constructor. More...

bool	isIoProcessor () const
	Can this processor do file I/O ? More...

void	setIoCommunicator (MPI::Intracomm &communicator)
	Set the communicator. More...

void	clearCommunicator ()
	Clear (nullify) the communicator. More...

bool	hasIoCommunicator () const
	Does this object have an associated MPI communicator? More...

MPI::Intracomm &	ioCommunicator () const
	Get the MPI communicator by reference. More...

Protected Attributes
EwaldRSpaceAccumulator	rSpaceAccumulator_
	Short-range real space energy and stress contributions. More...

Setable< double >	kSpaceEnergy_
	K-space part of Coulomb energy. More...

Setable< Tensor >	kSpaceStress_
	K-space part of Coulomb stress. More...

bool	isInitialized_
	Have parameters been set? More...

bool	hasWaves_
	Are waves and k-space potential up to date? Unset if boundary or parameters change. 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

McMd::MdCoulombPotential::MdCoulombPotential ( )

Constructor.

Definition at line 23 of file MdCoulombPotential.cpp.

References Util::ParamComposite::setClassName().

McMd::MdCoulombPotential::~MdCoulombPotential ( )

virtual

Destructor (does nothing).

Definition at line 31 of file MdCoulombPotential.cpp.

Member Function Documentation

void McMd::MdCoulombPotential::set	(	std::string	name,
		double	value
	)

virtual

Modify an interaction parameter, identified by a string.

Parameters

name	parameter name
value	new value of parameter

Reimplemented in McMd::MdEwaldPotential, and McMd::MdSpmePotential.

Definition at line 41 of file MdCoulombPotential.cpp.

References UTIL_THROW.

double McMd::MdCoulombPotential::get ( std::string name ) const

virtual

Get an interaction parameter value, identified by a string.

Parameters

name	parameter name

Reimplemented in McMd::MdEwaldPotential, and McMd::MdSpmePotential.

Definition at line 53 of file MdCoulombPotential.cpp.

References UTIL_THROW.

bool McMd::MdCoulombPotential::hasWaves ( )

inline

Are wavevectors and k-space influence function up to date?

Definition at line 216 of file MdCoulombPotential.h.

Referenced by McMd::MdEwaldPotential::makeWaves(), and McMd::MdSpmePotential::makeWaves().

virtual void McMd::MdCoulombPotential::makeWaves ( )

pure virtual

Generate wavevectors and influence function for this boundary.

Implemented in McMd::MdEwaldPotential, and McMd::MdSpmePotential.

Referenced by McMd::MdSystem::generateMolecules(), McMd::MdSystem::loadConfig(), McMd::MdSystem::readConfig(), and McMd::MdSimulation::simulate().

void McMd::MdCoulombPotential::unsetWaves ( )

Unset all data that depends on the Boundary.

Unsets stored values of waves, influence function, energy and stress.

Definition at line 62 of file MdCoulombPotential.cpp.

References hasWaves_, unsetEnergy(), and unsetStress().

Referenced by McMd::MdEwaldPotential::set(), and McMd::MdSpmePotential::set().

virtual int McMd::MdCoulombPotential::nWave ( ) const

pure virtual

Current number of wavevectors.

Implemented in McMd::MdEwaldPotential, and McMd::MdSpmePotential.

Referenced by McMd::MdSystem::readConfig().

virtual void McMd::MdCoulombPotential::addForces ( )

pure virtual

Add k-space Coulomb forces to forces on all atoms.

Implemented in McMd::MdEwaldPotential, and McMd::MdSpmePotential.

Referenced by McMd::MdSystem::calculateForces().

virtual void McMd::MdCoulombPotential::computeEnergy ( )

pure virtual

Calculate the long range kspace part of Coulomb energy.

Implemented in McMd::MdEwaldPotential, and McMd::MdSpmePotential.

Referenced by kSpaceEnergy().

void McMd::MdCoulombPotential::unsetEnergy ( )

virtual

Unset k-space energy.

Definition at line 72 of file MdCoulombPotential.cpp.

References kSpaceEnergy_, and Util::Setable< T >::unset().

Referenced by McMd::MdSystem::unsetPotentialEnergy(), and unsetWaves().

double McMd::MdCoulombPotential::kSpaceEnergy ( )

Get long-range k-space part of Coulomb energy.

Recomputes iff necessary (i.e., if not set).

Definition at line 78 of file MdCoulombPotential.cpp.

References computeEnergy(), Util::Setable< T >::isSet(), kSpaceEnergy_, and Util::Setable< T >::value().

Referenced by energy(), and McMd::MdEnergyAnalyzer::sample().

double McMd::MdCoulombPotential::rSpaceEnergy ( )

Return short-range r-space part of Coulomb energy.

Uses associated pair potential to recompute iff necessary.

Definition at line 89 of file MdCoulombPotential.cpp.

References rSpaceAccumulator_, and McMd::EwaldRSpaceAccumulator::rSpaceEnergy().

Referenced by energy(), and McMd::MdEnergyAnalyzer::sample().

double McMd::MdCoulombPotential::energy ( )

Get total Coulomb energy.

Invokes kSpaceEnergy() and rSpaceEnergy() internally, and thus recomputes k-space and r-space components as needed.

Definition at line 95 of file MdCoulombPotential.cpp.

References kSpaceEnergy(), and rSpaceEnergy().

Referenced by McMd::MdEwaldPotential::computeEnergy(), McMd::MdSpmePotential::computeEnergy(), McMd::MdSystem::potentialEnergy(), McMd::MdEnergyOutput::sample(), and McMd::MdEnergyAnalyzer::sample().

virtual void McMd::MdCoulombPotential::computeStress ( )

pure virtual

Compute kspace part of Coulomb stress.

Implemented in McMd::MdEwaldPotential, and McMd::MdSpmePotential.

Referenced by McMd::MdSystem::kineticEnergy(), and kSpaceStress().

void McMd::MdCoulombPotential::unsetStress ( )

virtual

Unset k-space stress.

Definition at line 106 of file MdCoulombPotential.cpp.

References kSpaceStress_.

Referenced by McMd::MdSystem::unsetVirialStress(), and unsetWaves().

Tensor McMd::MdCoulombPotential::kSpaceStress ( )

Get long-range k-space part of Coulomb stress.

Recomputes iff necessary.

Definition at line 112 of file MdCoulombPotential.cpp.

References computeStress(), and kSpaceStress_.

Referenced by computeStress(), and stress().

Tensor McMd::MdCoulombPotential::rSpaceStress ( )

Return short-range r-space part of Coulomb stress.

Directs associated pair potential to recompute if necessary.

Definition at line 123 of file MdCoulombPotential.cpp.

References rSpaceAccumulator_, and McMd::EwaldRSpaceAccumulator::rSpaceStress().

Tensor McMd::MdCoulombPotential::stress ( )

Get total Coulomb stress.

Calls kSpaceStress() and rSpaceStress() internally, and thus recomputes k-space and r-space components as needed.

Definition at line 129 of file MdCoulombPotential.cpp.

References kSpaceStress(), rSpaceAccumulator_, and McMd::EwaldRSpaceAccumulator::rSpaceStress().

Referenced by McMd::MdSpmePotential::computeStress(), computeStress(), and pressure().

void McMd::MdCoulombPotential::computeStress ( Tensor & stress )

Get total Coulomb stress.

Equivalent to Tensor stress().

Definition at line 153 of file MdCoulombPotential.cpp.

References kSpaceStress(), rSpaceAccumulator_, and McMd::EwaldRSpaceAccumulator::rSpaceStress().

void McMd::MdCoulombPotential::computeStress ( Vector & pressures )

Get diagonal components of Coulomb stress.

Definition at line 162 of file MdCoulombPotential.cpp.

References Util::Dimension, and stress().

double McMd::MdCoulombPotential::pressure ( )

Get total Coulomb pressure.

Definition at line 140 of file MdCoulombPotential.cpp.

References Util::Dimension, and stress().

void McMd::MdCoulombPotential::computeStress ( double & pressure )

Get the total Coulomb pressure.

Get Coulomb pressure.

Equivalent to double pressure().

Definition at line 175 of file MdCoulombPotential.cpp.

References Util::Dimension, and stress().

Member Data Documentation

EwaldRSpaceAccumulator McMd::MdCoulombPotential::rSpaceAccumulator_

protected

Short-range real space energy and stress contributions.

Definition at line 195 of file MdCoulombPotential.h.

Referenced by computeStress(), rSpaceEnergy(), rSpaceStress(), and stress().

Setable<double> McMd::MdCoulombPotential::kSpaceEnergy_

protected

K-space part of Coulomb energy.

Definition at line 198 of file MdCoulombPotential.h.

Referenced by McMd::MdEwaldPotential::computeEnergy(), McMd::MdSpmePotential::computeEnergy(), kSpaceEnergy(), and unsetEnergy().

Setable<Tensor> McMd::MdCoulombPotential::kSpaceStress_

protected

K-space part of Coulomb stress.

Definition at line 201 of file MdCoulombPotential.h.

Referenced by McMd::MdEwaldPotential::computeStress(), McMd::MdSpmePotential::computeStress(), kSpaceStress(), and unsetStress().

bool McMd::MdCoulombPotential::isInitialized_

protected

Have parameters been set?

Definition at line 204 of file MdCoulombPotential.h.

bool McMd::MdCoulombPotential::hasWaves_

protected

Are waves and k-space potential up to date? Unset if boundary or parameters change.

Definition at line 208 of file MdCoulombPotential.h.

Referenced by McMd::MdEwaldPotential::makeWaves(), McMd::MdSpmePotential::makeWaves(), and unsetWaves().

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

Detailed Description

Public Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation