Simp::EnergyEnsemble Class Reference

Detailed Description

A statistical ensemble for energy.

An energy ensemble has a type, which can be adiabatic or isothermal, and stores a temperature and inverse temperature beta if the type is isothermal.

Definition at line 29 of file EnergyEnsemble.h.

#include <EnergyEnsemble.h>

Inheritance diagram for Simp::EnergyEnsemble:

Public Types
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...

Public Member Functions
	EnergyEnsemble (Type type=UNKNOWN)
	Constructor. More...
	~EnergyEnsemble ()
	Destructor. More...
void	setTemperature (double temperature)
	Set the temperature. More...
virtual void	readParameters (std::istream &in)
	Read the type and (if necessary) temperature from file. 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...
Accessors
bool	isAdiabatic () const
	Is this an Adiabatic ensemble? More...
bool	isIsothermal () const
	Is this an Isothermal ensemble? More...
double	temperature () const
	Return the temperature. More...
double	beta () const
	Return the inverse temperature. 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...

Static Public Member Functions
static void	commitMpiType ()
	Commit MPI data type for an EnergyEnsemble. 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...

Additional Inherited Members
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...

Member Enumeration Documentation

enum Simp::EnergyEnsemble::Type

Enumeration of the allowed types of EnergyEnsemble.

Definition at line 37 of file EnergyEnsemble.h.

Constructor & Destructor Documentation

Simp::EnergyEnsemble::EnergyEnsemble

(

Type

type = UNKNOWN

)

Constructor.

Definition at line 22 of file EnergyEnsemble.cpp.

References Util::ParamComposite::setClassName().

Simp::EnergyEnsemble::~EnergyEnsemble

(

)

Destructor.

Definition at line 31 of file EnergyEnsemble.cpp.

Member Function Documentation

void Simp::EnergyEnsemble::setTemperature

(

double

temperature

)

Set the temperature.

Definition at line 37 of file EnergyEnsemble.cpp.

References isIsothermal(), temperature(), and UTIL_THROW.

Referenced by McMd::McEnergyPerturbation::setParameter().

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

virtual

Read the type and (if necessary) temperature from file.

The type is specified in the input file by a string literal "adiabatic" or "isothermal".

Reimplemented from Util::ParamComposite.

Definition at line 49 of file EnergyEnsemble.cpp.

References isIsothermal().

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

virtual

Load internal state from an archive.

Parameters

ar	input/loading archive

Reimplemented from Util::ParamComposite.

Definition at line 61 of file EnergyEnsemble.cpp.

References isIsothermal().

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

virtual

Save internal state to an archive.

Parameters

ar	output/saving archive

Reimplemented from Util::ParamComposite.

Definition at line 73 of file EnergyEnsemble.cpp.

References isIsothermal().

Referenced by McMd::System::saveEnsembles().

bool Simp::EnergyEnsemble::isAdiabatic ( ) const

inline

Is this an Adiabatic ensemble?

Definition at line 157 of file EnergyEnsemble.h.

bool Simp::EnergyEnsemble::isIsothermal ( ) const

inline

Is this an Isothermal ensemble?

Definition at line 163 of file EnergyEnsemble.h.

Referenced by McMd::McExternalPerturbation< Interaction >::derivative(), McMd::McPairExternalPerturbation< PairInteraction, ExternalInteraction >::derivative(), McMd::McPairPerturbation< Interaction >::derivative(), loadParameters(), McMd::NvtDpdVvIntegrator::NvtDpdVvIntegrator(), DdMd::NvtIntegrator::NvtIntegrator(), McMd::NvtNhIntegrator::NvtNhIntegrator(), readParameters(), save(), setTemperature(), McMd::NvtLangevinIntegrator::setup(), and DdMd::NvtLangevinIntegrator::setup().

double Simp::EnergyEnsemble::temperature ( ) const

inline

Return the temperature.

Definition at line 145 of file EnergyEnsemble.h.

Referenced by DdMd::NvtIntegrator::integrateStep1(), DdMd::NptIntegrator::integrateStep1(), DdMd::NvtIntegrator::integrateStep2(), McMd::HybridNphMdMove::move(), McMd::NvtDpdVvIntegrator::NvtDpdVvIntegrator(), McMd::NvtNhIntegrator::NvtNhIntegrator(), McMd::McEnergyPerturbation::parameter(), McMd::NvtNhIntegrator::readParameters(), setTemperature(), DdMd::NvtIntegrator::setup(), DdMd::NptIntegrator::setup(), McMd::NvtLangevinIntegrator::setup(), DdMd::NvtLangevinIntegrator::setup(), McMd::NvtDpdVvIntegrator::setup(), McMd::NvtNhIntegrator::setup(), McMd::NvtNhIntegrator::step(), McMd::McSystem::unsetPotentialEnergies(), and McMd::McStressAutoCorrelation::~McStressAutoCorrelation().

double Simp::EnergyEnsemble::beta ( ) const

inline

Return the inverse temperature.

Definition at line 151 of file EnergyEnsemble.h.

Referenced by McMd::CfbLinear::addAtom(), McMd::CfbEndBase::addEndAtom(), McMd::CfbRebridgeBase::addMiddleAtom(), McMd::McExternalPerturbation< Interaction >::derivative(), McMd::McPairPerturbation< Interaction >::derivative(), McMd::McPairExternalPerturbation< PairInteraction, ExternalInteraction >::derivative(), McMd::McNVTChemicalPotential::load(), McMd::McNVTChemicalPotential::sample(), and McMd::McMuExchange::sample().

void Simp::EnergyEnsemble::commitMpiType ( )

static

Commit MPI data type for an EnergyEnsemble.

Definition at line 119 of file EnergyEnsemble.cpp.

References Util::MpiStructBuilder::addMember(), Util::MpiStructBuilder::commit(), and Util::MpiStructBuilder::setBase().

---

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

• EnergyEnsemble.h
• EnergyEnsemble.cpp