Detailed Description

A set of interacting Molecules enclosed by a Boundary.

a Boundary, which defines the System dimensions.
an ArraySet of Molecule objects of each Species.
an EnergyEnsemble and a BoundaryEnsemble
a ConfigIo, which can read and write a configuration file
a FileMaster, to manage associated input and output files

A System must be associated with a parent Simulation, which owns many of the data structures used by a System.

The MdSystem and McSystem subclasses of System are designed for use in MD and MC simulations, respectively, and provide methods to evaluate energies and forces.

Definition at line 115 of file System.h.

#include <System.h>

Inheritance diagram for McMd::System:

Public Types
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...

Public Member Functions
	System ()
	Default constructor. More...

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

virtual	~System ()
	Destructor. More...

Initialization
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...

virtual void	readParameters (std::istream &in)
	Read parameter file. More...

virtual void	loadParameters (Serializable::IArchive &ar)
	Load internal state from an archive. More...

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

Config File IO
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...

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

virtual void	loadConfig (Serializable::IArchive &ar)
	Load configuration. More...

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

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

Molecule Set Mutators
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...

Molecule Set Accessors
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...

Potential Energy Factories and Styles
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...

Free Energy Perturbation Theory
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...

Accessors (Miscellaneous)
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...

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

virtual Factory< Perturbation > *	newDefaultPerturbationFactory ()
	Return a pointer to the default perturbation Factory. 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
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...

Member Typedef Documentation

typedef ArraySet<Molecule> McMd::System::MoleculeSet

A set of molecules of one Species in a System.

Definition at line 123 of file System.h.

typedef PArrayIterator<Molecule> McMd::System::MoleculeIterator

Iterator for a MoleculeSet.

Definition at line 126 of file System.h.

typedef ConstPArrayIterator<Molecule> McMd::System::ConstMoleculeIterator

Const Iterator for a MoleculeSet.

Definition at line 129 of file System.h.

Constructor & Destructor Documentation

McMd::System::System ( )

Default constructor.

Definition at line 78 of file System.cpp.

McMd::System::System ( const System & other )

Copy constructor.

This is intended to be used to create the System subobject of an MdSystem that is created by a hybrid MD/MC move within a parent MC simulation. The constructor creates a shallow copy, in which the child has pointers to most of the same objects as those owned by the parent. Specifically, the child will have pointers to the same molecule sets for each species, the same Boundary, and the same energy and boundary ensembles as the parent system. A System created by copying a parent that has a Perturbation or Replica Exchange move will, however, not have pointers to these objects.

Parameters

other System object being copied.

Definition at line 177 of file System.cpp.

McMd::System::~System ( )

virtual

Destructor.

Definition at line 272 of file System.cpp.

References isCopy().

Member Function Documentation

void McMd::System::setId ( int Id )

Set the integer Id for this System.

Set id to zero for Simulation objects with one System.

Parameters

Id	integer System index.

Definition at line 862 of file System.cpp.

References id().

Referenced by McMd::McSimulation::McSimulation(), and McMd::MdSimulation::MdSimulation().

void McMd::System::setSimulation ( Simulation & simulation )

Set the parent Simulation.

Parameters

simulation parent Simulation object.

Definition at line 872 of file System.cpp.

References simulation().

Referenced by McMd::McSimulation::McSimulation(), and McMd::MdSimulation::MdSimulation().

void McMd::System::setFileMaster ( FileMaster & filemaster )

Set the FileMaster.

Is normally used to set the FileMaster to that of the parent Simulation.

Parameters

filemaster FileMaster object.

Definition at line 881 of file System.cpp.

References fileMaster().

Referenced by McMd::McSimulation::McSimulation(), and McMd::MdSimulation::MdSimulation().

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

virtual

Read parameter file.

Only reads parameters if this System is not a copy (i.e., was not constructed with the copy constructor). If it is a copy, this function does nothing and returns normally.

Parameters

in	pararameter file input stream

Reimplemented from Util::ParamComposite.

Reimplemented in McMd::MdSystem, and McMd::McSystem.

Definition at line 368 of file System.cpp.

References allocateMoleculeSets(), isCopy(), readEnsembles(), readFileMaster(), readLinkMaster(), and readPotentialStyles().

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

virtual

Load internal state from an archive.

Parameters

ar	input/loading archive

Reimplemented from Util::ParamComposite.

Reimplemented in McMd::MdSystem, and McMd::McSystem.

Definition at line 390 of file System.cpp.

References allocateMoleculeSets(), isCopy(), loadEnsembles(), loadFileMaster(), loadLinkMaster(), and loadPotentialStyles().

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

Save internal state from an archive.

Parameters

ar	output/saving archive

Definition at line 409 of file System.cpp.

References isCopy(), saveEnsembles(), saveFileMaster(), saveLinkMaster(), and savePotentialStyles().

Factory< ConfigIo > & McMd::System::configIoFactory ( )

Get the configuration file reader/writer factory by reference.

Definition at line 892 of file System.cpp.

References newDefaultConfigIoFactory().

void McMd::System::setConfigIo ( std::string & classname )

Create a new configuration file reader/writer.

This function allows one to choose from among several subclasses of ConfigIo, identified by subclass name. The implementation uses a Factory<ConfigIo> object to instantiate a new object. If setConfigIoFactory() has not been called, an instance of the default class ConfigIoFactory is created and used.

Parameters

classname name of desired ConfigIo subclass.

Definition at line 909 of file System.cpp.

References Util::Factory< Data >::factory(), newDefaultConfigIoFactory(), and UTIL_THROW.

Referenced by McMd::McCommandManager::readStandardCommand(), and McMd::MdCommandManager::readStandardCommand().

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

virtual

Read system configuration from file.

The configuration file contains the dimensions of the Boundary, the number of molecules of each Species, and the atomic positions for all atoms of all molecules in this System.

This function uses a ConfigIo object that is registered with this System. If a ConfigIo object has not been registered by calling setConfigIo(std::string&), this function creates and uses an instance of the ConfigIo base class.

Precondition: The System and its Parent Simulation must have been initialized by calling their readParam function.

Parameters

in	configuration file input stream

Reimplemented in McMd::MdSystem, and McMd::McSystem.

Definition at line 808 of file System.cpp.

References isEmpty(), isValid(), newDefaultConfigIo(), McMd::ConfigIo::read(), and removeAllMolecules().

Referenced by McMd::McSystem::readConfig(), McMd::MdSystem::readConfig(), and readConfig().

void McMd::System::readConfig ( std::string filename )

Open, read and close configuration file.

Uses FileMaster::openInputFile(filename) to open the file, which appends an input file prefix to the path. Calls the function readConfig(std::istream& ) internally.

Parameters

filename configuration file name

Definition at line 825 of file System.cpp.

References fileMaster(), Util::FileMaster::openInputFile(), and readConfig().

void McMd::System::writeConfig ( std::ostream & out )

Write system configuration to a specified ostream.

Like readConfig(), this function will create and use a ConfigIo object if none has been registered previously.

Parameters

out	configuration file output stream

Definition at line 836 of file System.cpp.

References newDefaultConfigIo(), and McMd::ConfigIo::write().

Referenced by McMd::McCommandManager::readStandardCommand(), McMd::MdCommandManager::readStandardCommand(), McMd::Crosslinker::sample(), McMd::LammpsDumpWriter::sample(), McMd::ConfigWriter::sample(), and writeConfig().

void McMd::System::writeConfig ( std::string filename )

Open, write and close a configuration file.

Uses FileMaster::openOutputFile(filename) to open the file, which appends a output file prefix to the path. Calls the function readConfig(std::istream& ) internally.

Parameters

filename configuration file name

Definition at line 847 of file System.cpp.

References fileMaster(), Util::FileMaster::openOutputFile(), and writeConfig().

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

virtual

Load configuration.

Parameters

ar	input/loading archive

Reimplemented in McMd::MdSystem, and McMd::McSystem.

Definition at line 706 of file System.cpp.

References addMolecule(), McMd::Molecule::begin(), boundary(), McMd::Simulation::getMolecule(), molecule(), Simp::Species::mutator(), Util::ArrayIterator< Data >::notEnd(), McMd::Simulation::nSpecies(), McMd::SpeciesMutator::setMoleculeState(), Simp::OrthorhombicBoundary::shift(), simulation(), McMd::Simulation::species(), and UTIL_THROW.

Referenced by McMd::McSystem::loadConfig(), and McMd::MdSystem::loadConfig().

void McMd::System::saveConfig ( Serializable::OArchive & ar )

Save configuration.

Parameters

ar	output/save archive

Definition at line 756 of file System.cpp.

References begin(), boundary(), McMd::SpeciesMutator::moleculeStateId(), Simp::Species::mutator(), nMolecule(), Util::ArrayIterator< Data >::notEnd(), Util::PArrayIterator< Data >::notEnd(), McMd::Simulation::nSpecies(), Simp::OrthorhombicBoundary::shift(), simulation(), and McMd::Simulation::species().

Referenced by McMd::McSimulation::save(), and McMd::MdSimulation::save().

Factory< TrajectoryReader > & McMd::System::trajectoryReaderFactory ( )

Get the trajectory reader/writer factory by reference.

Definition at line 929 of file System.cpp.

References newDefaultTrajectoryReaderFactory().

Referenced by McMd::MdSimulation::analyzeTrajectory(), and McMd::McSimulation::analyzeTrajectory().

void McMd::System::addMolecule ( Molecule & molecule )

Add a Molecule to this System.

This function adds a Molecule to the set of Molecules of the same Species in this System, and calls Molecule::setSystem(*this).

The molecule to be added should first be popped off the Species reservoir or removed from another System.

Parameters

molecule Molecule to be added to this System.

Definition at line 1111 of file System.cpp.

References Simp::Species::id(), McMd::Molecule::setSystem(), McMd::Molecule::species(), and UTIL_THROW.

Referenced by McMd::TrajectoryReader::addMolecules(), McMd::Generator::generate(), loadConfig(), McMd::McMdConfigIo::read(), McMd::SmpConfigIo::read(), McMd::DdMdConfigIo::read(), McMd::LammpsConfigIo::read(), and McMd::McNVTChemicalPotential::sample().

void McMd::System::removeMolecule ( Molecule & molecule )

Remove a specific molecule from this System.

This function removes a Molecule from the set of molecules of the same Species in this System, and calls Molecule::unsetSystem().

The removed Molecule should be pushed onto the Species reservoir or added to another System.

Parameters

molecule Molecule to be removed from this System.

Definition at line 1129 of file System.cpp.

References Simp::Species::id(), McMd::Molecule::species(), McMd::Molecule::system(), McMd::Molecule::unsetSystem(), and UTIL_THROW.

Referenced by McMd::Generator::generate(), removeAllMolecules(), and McMd::McNVTChemicalPotential::sample().

void McMd::System::removeAllMolecules ( )

Remove all molecules from this System.

Remove all molecules of every species from this System, and push each onto the reservoir for the appropriate Species.

Definition at line 1163 of file System.cpp.

References McMd::LinkMaster::clear(), linkMaster(), molecule(), nMolecule(), McMd::Simulation::nSpecies(), removeMolecule(), McMd::Simulation::returnMolecule(), and simulation().

Referenced by McMd::MdSimulation::analyzeConfigs(), McMd::McSimulation::analyzeConfigs(), and readConfig().

void McMd::System::subscribeMoleculeSetChange ( MoleculeSetObserver & observer )

inline

Subscribe to moleculeSet change signal.

Parameters

observer the observer

Definition at line 1212 of file System.h.

void McMd::System::unsubscribeMoleculeSetChange ( MoleculeSetObserver & observer )

inline

Unsubscribe from moleculeSet change signal.

Parameters

observer the observer

Definition at line 1218 of file System.h.

int McMd::System::nMolecule ( int speciesId ) const

inline

Get the number of molecules of one Species in this System.

Parameters

speciesId integer Id for a Species.

Returns: number of molecules of specified Species in this System.

Definition at line 1128 of file System.h.

Referenced by isEmpty(), McMd::ClusterIdentifier::isValid(), isValid(), McMd::SliplinkerEnd::move(), McMd::GcSliplinkMove::move(), McMd::CfbDoubleRebridgeMove::move(), nAtom(), McMd::CfbReptationMove::output(), McMd::CfbReptateMove::output(), randomMolecule(), removeAllMolecules(), McMd::EndtoEndXYZ::sample(), McMd::EndtoEnd::sample(), McMd::BlockRadiusGyration::sample(), McMd::RadiusGyration::sample(), saveConfig(), McMd::G1MSD::setup(), McMd::McMuExchange::setup(), McMd::AtomMSD::setup(), McMd::ComMSD::setup(), McMd::RingRouseAutoCorr::setup(), McMd::LinearRouseAutoCorr::setup(), McMd::IntraPairAutoCorr::setup(), McMd::SmpConfigIo::write(), McMd::McMdConfigIo::write(), McMd::DdMdConfigIo::write(), and McMd::LammpsConfigIo::write().

int McMd::System::nAtom ( ) const

Return the total number of atoms in this System.

Definition at line 1216 of file System.cpp.

References Simp::Species::nAtom(), nMolecule(), McMd::Simulation::nSpecies(), simulation(), and McMd::Simulation::species().

Referenced by McMd::MdSystem::removeDriftVelocity(), McMd::NvtNhIntegrator::setup(), McMd::NvtNhIntegrator::step(), and McMd::McSystem::unsetPotentialEnergies().

bool McMd::System::isEmpty ( ) const

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

Definition at line 1147 of file System.cpp.

References nMolecule(), McMd::Simulation::nSpecies(), and simulation().

Referenced by readConfig().

int McMd::System::moleculeId ( const Molecule & molecule ) const

Get the index of a Molecule within its Species in this System.

This function returns the current (mutable) index of the molecule within the set of molecules of the same Species in this System, in the range 0 <= moleculeId < nMolecule(speciesId). This is the index required as the second argument of molecule(int, int).

Note: The id returned by this function is not the same as the id returned by Molecule::id(), which is a permanent identifier for each molecule that is set immediately after allocation.

Parameters

molecule Molecule object of interest.

Returns: index for molecule within its Species and System.

Definition at line 1189 of file System.cpp.

References Simp::Species::id(), and McMd::Molecule::species().

Referenced by McMd::Sliplinker::move(), McMd::SliplinkMove::move(), McMd::CfbDoubleRebridgeMove::move(), randomMolecule(), McMd::InterIntraLink::sample(), and McMd::McMdConfigIo::write().

Molecule & McMd::System::molecule	(	int	speciesId,
		int	moleculeId
	)

inline

Get a specific Molecule in this System, by integer index.

The moleculeId must be in range 0 <= moleculeId < nMolecule(speciesId). The index associated with a molecule is mutable, and can change when another molecule of the same Species is removed from this System. The value of this index is returned by System::moleculeId().

Parameters

speciesId	integer id of the desired Species
moleculeId	integer id of molecule within Species and System

Returns: reference to the molecule

Definition at line 1137 of file System.h.

Referenced by loadConfig(), McMd::CfbDoubleRebridgeMove::move(), McMd::RingOctaRebridgeMove::move(), McMd::ComMSD::output(), randomMolecule(), McMd::McMdConfigIo::read(), McMd::LammpsDumpReader::readFrame(), McMd::DdMdTrajectoryReader::readFrame(), McMd::DCDTrajectoryReader::readFrame(), removeAllMolecules(), McMd::G1MSD::sample(), McMd::AtomMSD::sample(), McMd::ComMSD::sample(), McMd::RingRouseAutoCorr::sample(), McMd::EndtoEndXYZ::sample(), McMd::LinearRouseAutoCorr::sample(), McMd::EndtoEnd::sample(), McMd::BlockRadiusGyration::sample(), McMd::IntraPairAutoCorr::sample(), McMd::RadiusGyration::sample(), McMd::RingOctaRebridgeMove::scanBridge(), McMd::G1MSD::setup(), McMd::AtomMSD::setup(), and McMd::ComMSD::setup().

Molecule & McMd::System::randomMolecule ( int speciesId )

Get a random Molecule of a specified species in this System.

Parameters

speciesId integer id of the desired Species.

Returns: const reference to the chosen molecule

Definition at line 1200 of file System.cpp.

References Util::Log::file(), molecule(), moleculeId(), nMolecule(), McMd::Simulation::random(), simulation(), Util::Random::uniformInt(), and UTIL_THROW.

void McMd::System::begin	(	int	speciesId,
		MoleculeIterator &	iterator
	)

inline

Initialize an iterator for molecules of one species in this System.

Parameters

speciesId	integer Id for the desired Species (input)
iterator	molecule iterator (output)

Definition at line 1147 of file System.h.

Referenced by McMd::MdEwaldPotential::addForces(), McMd::MdSpmePotential::addForces(), McMd::MdEwaldPotential::computeEnergy(), McMd::MdSpmePotential::computeEnergy(), McMd::McExternalPerturbation< Interaction >::derivative(), McMd::McPairExternalPerturbation< PairInteraction, ExternalInteraction >::derivative(), McMd::ClusterIdentifier::identifyClusters(), McMd::ClusterIdentifier::isValid(), McMd::MdSystem::kineticEnergy(), McMd::MdEwaldPotential::makeWaves(), McMd::MdSpmePotential::makeWaves(), McMd::HybridMdMove::move(), McMd::HybridNphMdMove::move(), McMd::ReplicaMove::move(), McMd::McCommandManager::readStandardCommand(), McMd::MdSystem::removeDriftVelocity(), McMd::Crosslinker::sample(), McMd::McExternalEnergyAverage::sample(), McMd::McMuExchange::sample(), McMd::CompositionProfile::sample(), McMd::RDF::sample(), McMd::StructureFactor::sample(), McMd::VanHove::sample(), McMd::StructureFactorP::sample(), McMd::IntraStructureFactor::sample(), saveConfig(), McMd::MdSystem::setBoltzmannVelocities(), McMd::MdSystem::setZeroForces(), McMd::MdSystem::setZeroVelocities(), McMd::MdSystem::shiftAtoms(), McMd::NveVvIntegrator::step(), McMd::NvtLangevinIntegrator::step(), McMd::NvtDpdVvIntegrator::step(), McMd::NvtNhIntegrator::step(), McMd::NphIntegrator::step(), McMd::McMdConfigIo::write(), McMd::SmpConfigIo::write(), McMd::DdMdConfigIo::write(), and McMd::LammpsConfigIo::write().

void McMd::System::begin	(	int	speciesId,
		ConstMoleculeIterator &	iterator
	)		const

inline

Initialize a const iterator for molecules of one species in this System.

Parameters

speciesId	integer Id for the desired Species (input)
iterator	molecule iterator (output)

Definition at line 1157 of file System.h.

PairFactory & McMd::System::pairFactory ( )

Get the PairFactory by reference.

Definition at line 1229 of file System.cpp.

Referenced by McMd::McSystem::loadParameters(), McMd::MdSystem::loadParameters(), McMd::MdSystem::MdSystem(), McMd::McSystem::readParameters(), and McMd::MdSystem::readParameters().

std::string McMd::System::pairStyle ( ) const

Return nonbonded pair style string.

Definition at line 1241 of file System.cpp.

Referenced by McMd::McSystem::loadParameters(), McMd::MdSystem::loadParameters(), McMd::McSystem::readParameters(), and McMd::MdSystem::readParameters().

Factory< BondPotential > & McMd::System::bondFactory ( )

Get the associated Factory<BondPotential> by reference.

Definition at line 1249 of file System.cpp.

Referenced by McMd::McSystem::loadParameters(), McMd::MdSystem::loadParameters(), McMd::McSystem::readParameters(), and McMd::MdSystem::readParameters().

std::string McMd::System::bondStyle ( ) const

Return covalent bond style string.

Definition at line 1261 of file System.cpp.

Referenced by McMd::McSystem::loadParameters(), McMd::MdSystem::loadParameters(), McMd::McSystem::readParameters(), and McMd::MdSystem::readParameters().

Factory< AnglePotential > & McMd::System::angleFactory ( )

Get the associated AngleFactory by reference.

Definition at line 1269 of file System.cpp.

Referenced by McMd::McSystem::loadParameters(), McMd::MdSystem::loadParameters(), McMd::McSystem::readParameters(), and McMd::MdSystem::readParameters().

std::string McMd::System::angleStyle ( ) const

Return angle potential style string.

Definition at line 1281 of file System.cpp.

Referenced by McMd::McSystem::loadParameters(), McMd::MdSystem::loadParameters(), McMd::McSystem::readParameters(), and McMd::MdSystem::readParameters().

Factory< DihedralPotential > & McMd::System::dihedralFactory ( )

Get the associated Dihedral Factory by reference.

Definition at line 1289 of file System.cpp.

Referenced by McMd::McSystem::loadParameters(), McMd::MdSystem::loadParameters(), McMd::McSystem::readParameters(), and McMd::MdSystem::readParameters().

std::string McMd::System::dihedralStyle ( ) const

Return dihedral potential style string.

Definition at line 1301 of file System.cpp.

Referenced by McMd::McSystem::loadParameters(), McMd::MdSystem::loadParameters(), McMd::McSystem::readParameters(), and McMd::MdSystem::readParameters().

CoulombFactory & McMd::System::coulombFactory ( )

Get the associated Coulomb Factory by reference.

Definition at line 1309 of file System.cpp.

Referenced by McMd::MdSystem::loadParameters(), and McMd::MdSystem::readParameters().

std::string McMd::System::coulombStyle ( ) const

Return coulomb potential style string.

Definition at line 1321 of file System.cpp.

Referenced by McMd::MdSystem::loadParameters(), McMd::MdEwaldPairPotentialImpl< Interaction >::MdEwaldPairPotentialImpl(), and McMd::MdSystem::readParameters().

Factory< ExternalPotential > & McMd::System::externalFactory ( )

Get the associated ExternalPotential factory by reference.

Definition at line 1329 of file System.cpp.

Referenced by McMd::McSystem::loadParameters(), McMd::MdSystem::loadParameters(), McMd::McSystem::readParameters(), and McMd::MdSystem::readParameters().

std::string McMd::System::externalStyle ( ) const

Return external potential style string.

Definition at line 1341 of file System.cpp.

Referenced by McMd::McSystem::loadParameters(), McMd::MdSystem::loadParameters(), McMd::McSystem::readParameters(), and McMd::MdSystem::readParameters().

Factory< BondPotential > & McMd::System::linkFactory ( )

Get the associated Link factory by reference.

Definition at line 1366 of file System.cpp.

Referenced by McMd::McSystem::loadParameters(), McMd::MdSystem::loadParameters(), McMd::McSystem::readParameters(), and McMd::MdSystem::readParameters().

std::string McMd::System::linkStyle ( ) const

Return link potential style string.

Definition at line 1378 of file System.cpp.

Referenced by McMd::McSystem::loadParameters(), McMd::MdSystem::loadParameters(), McMd::McSystem::readParameters(), and McMd::MdSystem::readParameters().

LinkMaster & McMd::System::linkMaster ( ) const

inline

Factory< Perturbation > & McMd::System::perturbationFactory ( )

inline

Get the perturbation factory by reference.

Return the perturbation factory by reference.

Definition at line 1173 of file System.h.

void McMd::System::setExpectPerturbation ( )

Set to expect a Perturbation in the parameter file.

Definition at line 948 of file System.cpp.

References hasPerturbation(), newDefaultPerturbationFactory(), and UTIL_THROW.

Referenced by loadPerturbation(), McMd::MdSimulation::setOptions(), and McMd::McSimulation::setOptions().

bool McMd::System::expectPerturbation ( ) const

inline

Return true if we expect a perturbation.

Should this system create a Perturbation?

Definition at line 1167 of file System.h.

Referenced by McMd::McSystem::readParameters().

bool McMd::System::hasPerturbation ( ) const

inline

Does this system have an associated Perturbation?

Definition at line 1179 of file System.h.

Referenced by McMd::McSystem::loadParameters(), loadPerturbation(), loadReplicaMove(), McMd::McSystem::readParameters(), readPerturbation(), readReplicaMove(), McMd::ReplicaMove::ReplicaMove(), McMd::McSystem::saveParameters(), savePerturbation(), saveReplicaMove(), and setExpectPerturbation().

Perturbation & McMd::System::perturbation ( ) const

inline

Get the associated Perturbation by reference.

Definition at line 1185 of file System.h.

Referenced by McMd::BennettsMethod::BennettsMethod(), McMd::ReplicaMove::move(), McMd::ReplicaMove::ReplicaMove(), and McMd::BennettsMethod::sample().

bool McMd::System::hasReplicaMove ( ) const

inline

Does this system have an associated ReplicaMove?

Definition at line 1195 of file System.h.

ReplicaMove & McMd::System::replicaMove ( ) const

inline

Get the associated ReplicaMove by reference.

Definition at line 1201 of file System.h.

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

int McMd::System::id ( ) const

inline

Get integer index for this System.

Definition at line 1049 of file System.h.

Referenced by setId().

Simulation & McMd::System::simulation ( ) const

inline

Get the parent Simulation by reference.

Definition at line 1055 of file System.h.

Boundary & McMd::System::boundary ( ) const

inline

Get the Boundary by reference.

Definition at line 1064 of file System.h.

Referenced by McMd::McPairExternalPerturbation< PairInteraction, ExternalInteraction >::derivative(), McMd::McPairPerturbation< Interaction >::derivative(), McMd::DeformCommand::execute(), McMd::McSystem::generateMolecules(), McMd::MdSystem::generateMolecules(), McMd::ClusterIdentifier::identifyClusters(), McMd::ClusterIdentifier::initialize(), McMd::MdSystem::kineticEnergy(), loadConfig(), McMd::CompositionProfile::makeWaveVectors(), McMd::StructureFactor::makeWaveVectors(), McMd::StructureFactorP::makeWaveVectors(), McMd::SliplinkerAll::move(), McMd::Sliplinker::move(), McMd::SliplinkMove::move(), McMd::SliplinkerEnd::move(), McMd::HybridNphMdMove::move(), McMd::ReplicaMove::move(), McMd::VelProf::output(), McMd::ComMSD::output(), McMd::DdMdConfigIo::read(), McMd::McCommandManager::readStandardCommand(), McMd::MdCommandManager::readStandardCommand(), McMd::Crosslinker::sample(), McMd::LinkLengthDist::sample(), McMd::G1MSD::sample(), McMd::VelProf::sample(), McMd::CompositionProfile::sample(), McMd::BoundaryAverage::sample(), McMd::AtomMSD::sample(), McMd::BondLengthDist::sample(), McMd::McPairEnergyAverage::sample(), McMd::ComMSD::sample(), McMd::RingRouseAutoCorr::sample(), McMd::EndtoEndXYZ::sample(), McMd::LinearRouseAutoCorr::sample(), McMd::EndtoEnd::sample(), McMd::RDF::sample(), McMd::BlockRadiusGyration::sample(), McMd::StructureFactor::sample(), McMd::IntraPairAutoCorr::sample(), McMd::RadiusGyration::sample(), McMd::StructureFactorGrid::sample(), McMd::VanHove::sample(), McMd::StructureFactorP::sample(), McMd::IntraStructureFactor::sample(), saveConfig(), McMd::RingTetraRebridgeMove::scanBridge(), McMd::G1MSD::setup(), McMd::VelProf::setup(), McMd::AtomMSD::setup(), McMd::ComMSD::setup(), McMd::MdSystem::shiftAtoms(), McMd::NphIntegrator::step(), McMd::McSystem::unsetPotentialEnergies(), and McMd::DdMdConfigIo::write().

EnergyEnsemble & McMd::System::energyEnsemble ( ) const

inline

Get the EnergyEnsemble by reference.

Definition at line 1095 of file System.h.

Referenced by McMd::McExternalPerturbation< Interaction >::derivative(), McMd::McPairExternalPerturbation< PairInteraction, ExternalInteraction >::derivative(), McMd::McPairPerturbation< Interaction >::derivative(), McMd::HybridNphMdMove::move(), McMd::NvtDpdVvIntegrator::NvtDpdVvIntegrator(), McMd::NvtNhIntegrator::NvtNhIntegrator(), McMd::McEnergyPerturbation::parameter(), McMd::McMuExchange::sample(), McMd::McEnergyPerturbation::setParameter(), McMd::NvtLangevinIntegrator::setup(), McMd::NvtDpdVvIntegrator::setup(), McMd::SystemMove::SystemMove(), McMd::McSystem::unsetPotentialEnergies(), and McMd::McStressAutoCorrelation::~McStressAutoCorrelation().

BoundaryEnsemble & McMd::System::boundaryEnsemble ( ) const

inline

Get the BoundaryEnsemble by reference.

Definition at line 1104 of file System.h.

Referenced by McMd::HybridNphMdMove::move(), and McMd::NphIntegrator::step().

FileMaster & McMd::System::fileMaster ( ) const

inline

Get the associated FileMaster by reference.

Definition at line 1113 of file System.h.

Referenced by McMd::CfbReptationMove::output(), McMd::CfbReptateMove::output(), readConfig(), McMd::MdVirialStressTensorAverage::readParameters(), McMd::McVirialStressTensorAverage::readParameters(), McMd::ReplicaMove::ReplicaMove(), setFileMaster(), and writeConfig().

bool McMd::System::isCopy ( ) const

inline

Was this System instantiated with the copy constructor?

Definition at line 1122 of file System.h.

Referenced by loadEnsembles(), McMd::MdSystem::loadParameters(), loadParameters(), loadPerturbation(), loadPotentialStyles(), McMd::McSystem::McSystem(), readEnsembles(), McMd::MdSystem::readParameters(), readParameters(), readPotentialStyles(), saveEnsembles(), McMd::MdSystem::saveParameters(), saveParameters(), savePerturbation(), savePotentialStyles(), McMd::MdSystem::~MdSystem(), and ~System().

bool McMd::System::isValid ( ) const

virtual

Return true if valid, or throw Exception.

Reimplemented in McMd::MdSystem, and McMd::McSystem.

Definition at line 1405 of file System.cpp.

References McMd::LinkMaster::isValid(), nMolecule(), McMd::Simulation::nSpecies(), simulation(), McMd::Molecule::system(), and UTIL_THROW.

Referenced by McMd::McSystem::isValid(), McMd::MdSystem::isValid(), and readConfig().

Boundary& McMd::System::maxBoundary ( ) const

protected

Get the maximum Boundary by reference.

ConfigIo * McMd::System::newDefaultConfigIo ( )

protectedvirtual

Return a pointer to a new default ConfigIo.

Reimplemented in McMd::MdSystem.

Definition at line 802 of file System.cpp.

Referenced by readConfig(), and writeConfig().

Factory< ConfigIo > * McMd::System::newDefaultConfigIoFactory ( )

protectedvirtual

Return a pointer to a new default ConfigIoFactory.

Definition at line 903 of file System.cpp.

Referenced by configIoFactory(), and setConfigIo().

Factory< TrajectoryReader > * McMd::System::newDefaultTrajectoryReaderFactory ( )

protectedvirtual

Return a pointer to a new default TrajectoryReaderFactory.

Definition at line 940 of file System.cpp.

Referenced by trajectoryReaderFactory().

virtual Factory<Perturbation>* McMd::System::newDefaultPerturbationFactory ( )

inlineprotectedvirtual

Return a pointer to the default perturbation Factory.

Reimplemented in McMd::McSystem.

Definition at line 678 of file System.h.

Referenced by setExpectPerturbation().

void McMd::System::readPerturbation ( std::istream & in )

protected

Read the perturbation parameter block (if any)

Parameters

in	input parameter stream

Definition at line 980 of file System.cpp.

References Util::ParamComposite::className(), Util::MpiFileIo::hasIoCommunicator(), hasPerturbation(), Util::Factory< Data >::readObject(), UTIL_CHECK, and UTIL_THROW.

Referenced by McMd::McSystem::readParameters(), and McMd::MdSystem::readParameters().

void McMd::System::loadPerturbation ( Serializable::IArchive & ar )

protected

Load the perturbation parameter block (if any)

Parameters

ar	input/saving archive

Definition at line 1003 of file System.cpp.

References Util::ParamComposite::className(), hasPerturbation(), isCopy(), Util::Factory< Data >::loadObject(), setExpectPerturbation(), UTIL_CHECK, and UTIL_THROW.

Referenced by McMd::McSystem::loadParameters(), and McMd::MdSystem::loadParameters().

void McMd::System::savePerturbation ( Serializable::OArchive & ar )

protected

Save the perturbation parameter block (if any)

Parameters

ar	output/saving archive

Definition at line 1028 of file System.cpp.

References Util::ParamComposite::className(), hasPerturbation(), isCopy(), McMd::Perturbation::save(), and UTIL_CHECK.

Referenced by McMd::McSystem::saveParameters(), and McMd::MdSystem::saveParameters().

void McMd::System::readReplicaMove ( std::istream & in )

protected

Read the ReplicaMove parameter block (if any)

Parameters

in	input parameter stream

Definition at line 1044 of file System.cpp.

References hasPerturbation(), and Util::ParamComposite::readParamComposite().

Referenced by McMd::McSystem::readParameters().

void McMd::System::loadReplicaMove ( Serializable::IArchive & ar )

protected

Read the ReplicaMove parameter block (if any)

Parameters

ar	input/loading archive

Definition at line 1061 of file System.cpp.

References hasPerturbation(), and Util::ParamComposite::loadParamComposite().

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

void McMd::System::saveReplicaMove ( Serializable::OArchive & ar )

protected

Save the ReplicaMove parameter block (if any)

Parameters

ar	output/saving archive

Definition at line 1078 of file System.cpp.

References hasPerturbation(), and McMd::ReplicaMove::save().

Referenced by McMd::McSystem::saveParameters().

void McMd::System::allocateMoleculeSets ( )

protected

Allocate and initialize molecule sets for all species.

This function is called within the Simulation::initialize() private member function to allocate and initialize an array of MoleculeSet objects for all Species for this System.

Preconditions: This System must be associated with a parent Simulation, and all Species objects must have been initialized by calling SpeciesManager::readParameters().

Definition at line 1093 of file System.cpp.

References McMd::Simulation::allocateMoleculeSet(), McMd::Simulation::nSpecies(), and simulation().

Referenced by McMd::McSystem::loadParameters(), McMd::MdSystem::loadParameters(), loadParameters(), McMd::McSystem::readParameters(), McMd::MdSystem::readParameters(), and readParameters().