Detailed Description

A System for use in a Markov chain Monte Carlo simulation.

McSystem provides methods to evaluate energies of individual atoms, and other functions needed in MC simulations.

Definition at line 52 of file McSystem.h.

#include <McSystem.h>

Inheritance diagram for McMd::McSystem:

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

virtual	~McSystem ()
	Destructor. More...

Parameter IO
virtual void	readParameters (std::istream &in)
	Read parameters from input file. More...

virtual void	loadParameters (Serializable::IArchive &ar)
	Load parameters from an archive, without configuration. More...

virtual void	saveParameters (Serializable::OArchive &ar)
	Save parameters to an archive, without configuration. More...

Initial Configurations
virtual void	readConfig (std::istream &in)
	Read system configuration from file. More...

virtual void	loadConfig (Serializable::IArchive &ar)
	Load the system configuration from an archive. More...

virtual void	generateMolecules (Array< int > const &capacities, Array< double > const &diameters)
	Generate molecules for all species. More...

Energy and Stress calculators
double	atomPotentialEnergy (const Atom &atom) const
	Calculate the total potential energy for one Atom. More...

double	potentialEnergy () const
	Return total potential energy of this System. More...

template<typename T >
void	computeVirialStress (T &stress) const
	Compute total virial stress (excludes kinetic contribution). More...

template<typename T >
void	computeStress (T &stress) const
	Compute total pressure (T=double), xyz pressures (T=Vector) or stress (T=Tensor). More...

void	unsetPotentialEnergies ()
	Unset potential precomputed potential energy components. More...

void	unsetVirialStress ()
	Unset precomputed virial stress components. More...

Potential Energy Accessors
McPairPotential &	pairPotential () const
	Return the McPairPotential by reference. More...

bool	hasBondPotential () const
	Does a bond potential exist?. More...

BondPotential &	bondPotential () const
	Return the BondPotential by reference. More...

bool	hasAnglePotential () const
	Does angle potential exist?. More...

AnglePotential &	anglePotential () const
	Return AnglePotential by reference. More...

bool	hasDihedralPotential () const
	Does a dihedral potential exist?. More...

DihedralPotential &	dihedralPotential () const
	Return the DihedralPotential by reference. More...

bool	hasCoulombPotential () const
	Does a Coulomb potential exist?. More...

CoulombPotential &	coulombPotential () const
	Return CoulombPotential by reference. More...

bool	hasExternalPotential () const
	Does an external potential exist?. More...

ExternalPotential &	externalPotential () const
	Return ExternalPotential by reference. More...

bool	hasLinkPotential () const
	Does a link potential exist?. More...

BondPotential &	linkPotential () const
	Return the McLinkPotential by reference. More...

Miscellaneous
Signal &	positionSignal ()
	Signal to indicate change in atomic positions. More...

virtual bool	isValid () const
	Return true if McSystem is valid, or throw Exception. More...

Public Member Functions inherited from McMd::System
	System ()
	Default constructor. More...

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

virtual	~System ()
	Destructor. More...

void	setId (int Id)
	Set the integer Id for this System. More...

void	setSimulation (Simulation &simulation)
	Set the parent Simulation. More...

void	setFileMaster (FileMaster &filemaster)
	Set the FileMaster. More...

void	saveParameters (Serializable::OArchive &ar)
	Save internal state from an archive. More...

Factory< ConfigIo > &	configIoFactory ()
	Get the configuration file reader/writer factory by reference. More...

void	setConfigIo (std::string &classname)
	Create a new configuration file reader/writer. More...

void	readConfig (std::string filename)
	Open, read and close configuration file. More...

void	writeConfig (std::ostream &out)
	Write system configuration to a specified ostream. More...

void	writeConfig (std::string filename)
	Open, write and close a configuration file. More...

void	saveConfig (Serializable::OArchive &ar)
	Save configuration. More...

Factory< TrajectoryReader > &	trajectoryReaderFactory ()
	Get the trajectory reader/writer factory by reference. More...

void	addMolecule (Molecule &molecule)
	Add a Molecule to this System. More...

void	removeMolecule (Molecule &molecule)
	Remove a specific molecule from this System. More...

void	removeAllMolecules ()
	Remove all molecules from this System. More...

void	subscribeMoleculeSetChange (MoleculeSetObserver &observer)
	Subscribe to moleculeSet change signal. More...

void	unsubscribeMoleculeSetChange (MoleculeSetObserver &observer)
	Unsubscribe from moleculeSet change signal. More...

int	nMolecule (int speciesId) const
	Get the number of molecules of one Species in this System. More...

int	nAtom () const
	Return the total number of atoms in this System. More...

bool	isEmpty () const
	Is this an empty System (i.e., one with no molecules) ? More...

int	moleculeId (const Molecule &molecule) const
	Get the index of a Molecule within its Species in this System. More...

Molecule &	molecule (int speciesId, int moleculeId)
	Get a specific Molecule in this System, by integer index. More...

Molecule &	randomMolecule (int speciesId)
	Get a random Molecule of a specified species in this System. More...

void	begin (int speciesId, MoleculeIterator &iterator)
	Initialize an iterator for molecules of one species in this System. More...

void	begin (int speciesId, ConstMoleculeIterator &iterator) const
	Initialize a const iterator for molecules of one species in this System. More...

PairFactory &	pairFactory ()
	Get the PairFactory by reference. More...

std::string	pairStyle () const
	Return nonbonded pair style string. More...

Factory< BondPotential > &	bondFactory ()
	Get the associated Factory<BondPotential> by reference. More...

std::string	bondStyle () const
	Return covalent bond style string. More...

Factory< AnglePotential > &	angleFactory ()
	Get the associated AngleFactory by reference. More...

std::string	angleStyle () const
	Return angle potential style string. More...

Factory< DihedralPotential > &	dihedralFactory ()
	Get the associated Dihedral Factory by reference. More...

std::string	dihedralStyle () const
	Return dihedral potential style string. More...

CoulombFactory &	coulombFactory ()
	Get the associated Coulomb Factory by reference. More...

std::string	coulombStyle () const
	Return coulomb potential style string. More...

Factory< ExternalPotential > &	externalFactory ()
	Get the associated ExternalPotential factory by reference. More...

std::string	externalStyle () const
	Return external potential style string. More...

Factory< BondPotential > &	linkFactory ()
	Get the associated Link factory by reference. More...

std::string	linkStyle () const
	Return link potential style string. More...

LinkMaster &	linkMaster () const
	Get the LinkMaster by reference. More...

Factory< Perturbation > &	perturbationFactory ()
	Get the perturbation factory by reference. More...

void	setExpectPerturbation ()
	Set to expect a Perturbation in the parameter file. More...

bool	expectPerturbation () const
	Return true if we expect a perturbation. More...

bool	hasPerturbation () const
	Does this system have an associated Perturbation? More...

Perturbation &	perturbation () const
	Get the associated Perturbation by reference. More...

bool	hasReplicaMove () const
	Does this system have an associated ReplicaMove? More...

ReplicaMove &	replicaMove () const
	Get the associated ReplicaMove by reference. More...

int	id () const
	Get integer index for this System. More...

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

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

EnergyEnsemble &	energyEnsemble () const
	Get the EnergyEnsemble by reference. More...

BoundaryEnsemble &	boundaryEnsemble () const
	Get the BoundaryEnsemble by reference. More...

FileMaster &	fileMaster () const
	Get the associated FileMaster by reference. More...

bool	isCopy () const
	Was this System instantiated with the copy constructor? 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...

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 Member Functions
virtual Factory< Perturbation > *	newDefaultPerturbationFactory ()
	Return a pointer to a new McPerturbationFactory. More...

void	setPairPotential (McPairPotential *pairPotentialPtr)
	Set the PairPotential. More...

Protected Member Functions inherited from McMd::System
Boundary &	maxBoundary () const
	Get the maximum Boundary by reference. More...

virtual ConfigIo *	newDefaultConfigIo ()
	Return a pointer to a new default ConfigIo. More...

virtual Factory< ConfigIo > *	newDefaultConfigIoFactory ()
	Return a pointer to a new default ConfigIoFactory. More...

virtual Factory< TrajectoryReader > *	newDefaultTrajectoryReaderFactory ()
	Return a pointer to a new default TrajectoryReaderFactory. More...

void	readPerturbation (std::istream &in)
	Read the perturbation parameter block (if any) More...

void	loadPerturbation (Serializable::IArchive &ar)
	Load the perturbation parameter block (if any) More...

void	savePerturbation (Serializable::OArchive &ar)
	Save the perturbation parameter block (if any) More...

void	readReplicaMove (std::istream &in)
	Read the ReplicaMove parameter block (if any) More...

void	loadReplicaMove (Serializable::IArchive &ar)
	Read the ReplicaMove parameter block (if any) More...

void	saveReplicaMove (Serializable::OArchive &ar)
	Save the ReplicaMove parameter block (if any) More...

void	allocateMoleculeSets ()
	Allocate and initialize molecule sets for all species. More...

void	readFileMaster (std::istream &in)
	Read FileMaster parameters, if none yet exists. More...

void	loadFileMaster (Serializable::IArchive &ar)
	Load FileMaster data from archive, if necessary. More...

void	saveFileMaster (Serializable::OArchive &ar)
	If necessary, save FileMaster to archive. More...

void	readPotentialStyles (std::istream &in)
	Read potential style parameter strings. More...

void	loadPotentialStyles (Serializable::IArchive &ar)
	Load potential style strings from an archive. More...

void	savePotentialStyles (Serializable::OArchive &ar)
	Save potential style strings. More...

void	readEnsembles (std::istream &in)
	Read energy and boundary ensemble parameters. More...

void	loadEnsembles (Serializable::IArchive &ar)
	Load energy and boundary ensembles from archive. More...

void	saveEnsembles (Serializable::OArchive &ar)
	Save energy and boundary ensembles. More...

void	readLinkMaster (std::istream &in)
	Read the LinkMaster parameters. More...

void	loadLinkMaster (Serializable::IArchive &ar)
	Load the LinkMaster. More...

void	saveLinkMaster (Serializable::OArchive &ar)
	Save the LinkMaster. 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...

Additional Inherited Members
Public Types inherited from McMd::System
typedef ArraySet< Molecule >	MoleculeSet
	A set of molecules of one Species in a System. More...

typedef PArrayIterator< Molecule >	MoleculeIterator
	Iterator for a MoleculeSet. More...

typedef ConstPArrayIterator< Molecule >	ConstMoleculeIterator
	Const Iterator for a MoleculeSet. More...

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...

Constructor & Destructor Documentation

McMd::McSystem::McSystem ( )

Constructor.

Definition at line 64 of file McSystem.cpp.

References Util::Signal< T >::addObserver(), McMd::System::isCopy(), positionSignal(), Util::ParamComposite::setClassName(), unsetPotentialEnergies(), unsetVirialStress(), and UTIL_CHECK.

McMd::McSystem::~McSystem ( )

virtual

Destructor.

Definition at line 101 of file McSystem.cpp.

Member Function Documentation

void McMd::McSystem::readParameters ( std::istream & in )

virtual

Read parameters from input file.

This method first calls System::readParameters(in).

Finally, it allocates a CellList, and builds the new CellList if an initial configuration has been read previously by System::readParam. The number of cells allocated for the CellList is determined by the dimensions of maxBoundary and the maximum nonbonded cutoff distance.

Parameters

in	file stream.

Reimplemented from McMd::System.

Definition at line 132 of file McSystem.cpp.

void McMd::McSystem::loadParameters ( Serializable::IArchive & ar )

virtual

Load parameters from an archive, without configuration.

Parameters

ar	input/loading archive

Reimplemented from McMd::System.

Definition at line 233 of file McSystem.cpp.

References McMd::System::allocateMoleculeSets(), McMd::System::angleFactory(), McMd::System::angleStyle(), McMd::System::bondFactory(), McMd::System::bondStyle(), McMd::System::dihedralFactory(), McMd::System::dihedralStyle(), McMd::System::externalFactory(), McMd::System::externalStyle(), Util::Factory< Data >::factory(), McMd::System::hasPerturbation(), McMd::System::linkFactory(), McMd::System::linkStyle(), McMd::System::loadEnsembles(), McMd::System::loadFileMaster(), McMd::System::loadLinkMaster(), Util::ParamComposite::loadParamComposite(), McMd::System::loadPerturbation(), McMd::System::loadPotentialStyles(), McMd::System::loadReplicaMove(), McMd::PairFactory::mcFactory(), McMd::System::pairFactory(), McMd::System::pairStyle(), McMd::System::simulation(), and UTIL_THROW.

void McMd::McSystem::saveParameters ( Serializable::OArchive & ar )

virtual

Save parameters to an archive, without configuration.

Parameters

ar	output/saving archive

Definition at line 331 of file McSystem.cpp.

References anglePotential(), bondPotential(), dihedralPotential(), McMd::System::hasPerturbation(), pairPotential(), Util::ParamComposite::save(), McMd::System::saveEnsembles(), McMd::System::saveFileMaster(), McMd::System::saveLinkMaster(), McMd::System::savePerturbation(), McMd::System::savePotentialStyles(), McMd::System::saveReplicaMove(), and McMd::System::simulation().

Referenced by McMd::McSimulation::save().

void McMd::McSystem::readConfig ( std::istream & in )

virtual

Read system configuration from file.

Calls System::readConfig() and then builds CellList.

Parameters

in	configuration file input stream

Reimplemented from McMd::System.

Definition at line 393 of file McSystem.cpp.

References McMd::McPairPotential::buildCellList(), pairPotential(), and McMd::System::readConfig().

Referenced by McMd::McSimulation::analyzeConfigs(), and McMd::McCommandManager::readStandardCommand().

void McMd::McSystem::loadConfig ( Serializable::IArchive & ar )

virtual

Load the system configuration from an archive.

Parameters

ar	input (loading) archive object.

Reimplemented from McMd::System.

Definition at line 404 of file McSystem.cpp.

References McMd::McPairPotential::buildCellList(), McMd::System::loadConfig(), and pairPotential().

Referenced by McMd::McSimulation::loadParameters().

void McMd::McSystem::generateMolecules	(	Array< int > const &	capacities,
		Array< double > const &	diameters
	)

virtual

Generate molecules for all species.

The array capacities contains at least nSpecies elements, in which element i contains the number of molecules to generate for species i.

The array capacities contains at least nAtomType elements, in which element i contains the steric diameter used for atom i in the packing algorithm.

Parameters

capacities	number of molecules in each species
diameters	diameter of each atom type

Definition at line 415 of file McSystem.cpp.

References McMd::System::boundary(), McMd::McPairPotential::buildCellList(), Util::Log::file(), McMd::Generator::generate(), McMd::generatorFactory(), isValid(), McMd::Simulation::nSpecies(), pairPotential(), McMd::Generator::setupCellList(), McMd::System::simulation(), and UTIL_CHECK.

Referenced by McMd::McCommandManager::readStandardCommand().

double McMd::McSystem::atomPotentialEnergy ( const Atom & atom ) const

Calculate the total potential energy for one Atom.

Parameters

atom	Atom object of interest

Returns: potential energy of atom

Definition at line 459 of file McSystem.cpp.

References anglePotential(), McMd::McPairPotential::atomEnergy(), McMd::ExternalPotential::atomEnergy(), McMd::BondPotential::atomEnergy(), McMd::DihedralPotential::atomEnergy(), McMd::AnglePotential::atomEnergy(), bondPotential(), dihedralPotential(), externalPotential(), hasAnglePotential(), hasBondPotential(), hasDihedralPotential(), hasExternalPotential(), hasLinkPotential(), linkPotential(), and pairPotential().

Referenced by McMd::AtomDisplaceMove::move(), and McMd::RingOctaRebridgeMove::move().

double McMd::McSystem::potentialEnergy ( ) const

Return total potential energy of this System.

Definition at line 503 of file McSystem.cpp.

References anglePotential(), bondPotential(), dihedralPotential(), McMd::PairPotential::energy(), McMd::BondPotential::energy(), McMd::AnglePotential::energy(), McMd::ExternalPotential::energy(), McMd::DihedralPotential::energy(), externalPotential(), hasAnglePotential(), hasBondPotential(), hasDihedralPotential(), hasExternalPotential(), hasLinkPotential(), linkPotential(), and pairPotential().

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

template<typename T >

void McMd::McSystem::computeVirialStress ( T & stress ) const

Compute total virial stress (excludes kinetic contribution).

The virial stress is the sum of all pair and bonded stress components. It excludes the kinetic stress.

See also: McSystem::computeStress(T&) regarding allowed types for T.

Parameters

stress (output) pressure, pressures or Tensor.

Referenced by McMd::McVirialStressTensorAverage::sample(), unsetPotentialEnergies(), and McMd::McStressAutoCorrelation::~McStressAutoCorrelation().

template<typename T >

void McMd::McSystem::computeStress ( T & stress ) const

Compute total pressure (T=double), xyz pressures (T=Vector) or stress (T=Tensor).

In this and all other stress / pressure calculators, typename T must be double to obtain total pressure, Util::Vector to obtain the diagonal pressure components, or Util::Tensor to obtain the full stress tensor. These templates work only for these three types. The parameter stress contains the desired value when the function returns.

The total stress is the sum of the virial stress arising from interatomic forces and an ideal gas kinetic stress.

Parameters

stress (output) pressure, xyz pressures or stress Tensor.

Referenced by McMd::McStressAutoCorrelation::~McStressAutoCorrelation().

void McMd::McSystem::unsetPotentialEnergies ( )

Unset potential precomputed potential energy components.

Definition at line 545 of file McSystem.cpp.

References anglePotential(), bondPotential(), McMd::System::boundary(), McMd::StressCalculator::computeStress(), computeVirialStress(), dihedralPotential(), Util::Dimension, McMd::System::energyEnsemble(), externalPotential(), hasAnglePotential(), hasBondPotential(), hasDihedralPotential(), hasExternalPotential(), hasLinkPotential(), linkPotential(), McMd::System::nAtom(), pairPotential(), Util::setToZero(), Simp::EnergyEnsemble::temperature(), McMd::EnergyCalculator::unsetEnergy(), and Simp::OrthorhombicBoundary::volume().