Detailed Description

The main object in a simulation, which coordinates others.

A Simulation object is the main object in a simulation. Which is instantiated in the main program, and coordinates creation and actions of other objects. Simulation is a base class, which has subclasses McSimulation and MdSimulation designed for MC and MD simulations.

A Simulation has the following publicly accessible members:

An array of AtomType descriptor objects.
A SpeciesManager, which has one or more Species objects.
An AnalyzerManager, which has one or more Analyzer objects.
A CommandManager, which has one or more Command objects.
A FileMaster to manage associated input and output files.
A random number generator object (an instances of Util::Random).
An MPI communicator (if compiled with UTIL_MPI defined).

A Simulation also contains several global data structures.

An array of all allocated Atom objects.
An array of all allocated Molecule objects, for all Species.
Arrays of all Bond, Angle, and Dihedral Group objects.

Each Molecule is associated with a block of Atom objects, and blocks of Group objects (Bond, Angle, and Dihedral). These associations are created during initialization, and are permanent.

Each subclass of Simulation also has one or more System objects. An MdSimulation has one MdSystem. An McSimulation has one McSystem. A System represents a set of molecules surrounded by a Boundary. A System holds a set of pointers to Molecule objects in the array of Molecules owned by parent Simulation.

Definition at line 101 of file mcMd/simulation/Simulation.h.

#include <Simulation.h>

Inheritance diagram for McMd::Simulation:

Public Member Functions
	Simulation (MPI::Intracomm &communicator)
	Constructor. More...

	Simulation ()
	Constructor. More...

virtual	~Simulation ()
	Destructor. More...

void	outputOptions (std::ostream &out) const
	Output a list of options enabled and disabled during compilation. More...

Initialization
virtual void	setIoCommunicator (MPI::Intracomm &communicator)
	Set MPI job to read one parameter file and one command file. More...

void	setIoCommunicator ()
	Set MPI job to read one parameter file and one command file. More...

virtual void	readParameters (std::istream &in)
	Read parameter file block and initialize simulation. More...

void	writeParam (std::string filename)
	Open output, write and close an output parameter file. More...

void	allocateMoleculeSet (Util::ArraySet< Molecule > &set, int speciesId) const
	Allocate and initialize a molecule set for one Species. More...

Serialization (Load / Save)
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...

Molecule Management
Molecule &	getMolecule (int speciesId)
	Get a new molecule from a reservoir of unused Molecule objects. More...

void	returnMolecule (Molecule &molecule)
	Return a molecule to a reservoir of unused molecules. More...

Read-write accessors (return by non-const reference)
Random &	random ()
	Get the random number generator by reference. More...

Species &	species (int i)
	Get a specific Species by reference. More...

Factory< Analyzer > &	analyzerFactory ()
	Return the Analyzer factory by reference. More...

Factory< Species > &	speciesFactory ()
	Return the Species Factory by reference. More...

FileMaster &	fileMaster ()
	Get the FileMaster object. More...

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

Read-only accessors (return by value or const reference)
int	iStep () const
	Get value of step index for main MC or MD loop. More...

int	nAtomType () const
	Get the number of atom types. More...

const AtomType &	atomType (int i) const
	Get a single AtomType object by const reference. More...

const Array< AtomType > &	atomTypes () const
	Get a const Array of all AtomType objects. More...

int	nSpecies () const
	Get the number of Species in this Simulation. More...

const Species &	species (int i) const
	Get a specific Species by const reference. More...

int	moleculeCapacity () const
	Get the total number of Molecules allocated. More...

int	atomCapacity () const
	Get the total number of Atoms allocated. More...

int	nSystem () const
	Get the number of Systems in this Simulation. More...

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

bool	hasSpecies () const
	Has data for all species structures and capacities. More...

MaskPolicy	maskedPairPolicy () const
	Return the value of the mask policy (MaskNone or MaskBonded). More...

int	nBondType () const
	Get the number of bond types. More...

int	bondCapacity () const
	Get the total number of Bonds allocated. More...

int	nAngleType () const
	Get the number of angle types. More...

int	angleCapacity () const
	Get the total number of Angles allocated. More...

int	nDihedralType () const
	Get the number of dihedral types. More...

int	dihedralCapacity () const
	Get the total number of Dihedrals allocated. More...

int	hasCoulomb () const
	Does a Coulomb potential exist? More...

int	hasExternal () const
	Does an external potential exist? More...

int	nLinkType () const
	Get the number of link types. More...

bool	hasCommunicator () const
	Does the simulation have an associated MPI communicator? 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...

Protected Member Functions
void	setAnalyzerManager (AnalyzerManager *ptr)
	Set the associated AnalyzerManager. More...

AnalyzerManager &	analyzerManager ()
	Get the associated AnalyzerManager by reference. More...

void	setCommandManager (CommandManager *ptr)
	Set the associated CommandManager. More...

CommandManager &	commandManager ()
	Get the associated CommandManager by reference. 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...

Protected Attributes
int	iStep_
	Step index for main MC or MD loop. More...

int	nSystem_
	Number of Systems of interacting molecules (> 1 in Gibbs ensemble). More...

Additional Inherited Members
Public Types inherited from Util::Serializable
typedef BinaryFileOArchive	OArchive
	Type of output archive used by save method. More...

typedef BinaryFileIArchive	IArchive
	Type of input archive used by load method. More...

Static Public Member Functions inherited from Util::ParamComponent
static void	initStatic ()
	Initialize static echo member to false. More...

static void	setEcho (bool echo=true)
	Enable or disable echoing for all subclasses of ParamComponent. More...

static bool	echo ()
	Get echo parameter. More...

Constructor & Destructor Documentation

McMd::Simulation::Simulation ( MPI::Intracomm & communicator )

Constructor.

Definition at line 39 of file mcMd/simulation/Simulation.cpp.

References McMd::commitMpiTypes(), Util::initStatic(), McMd::Analyzer::initStatic(), McMd::Atom::initStatic(), Util::FileMaster::openOutputFile(), Util::ParamComposite::setClassName(), Util::FileMaster::setDirectoryId(), Util::Log::setFile(), and UTIL_THROW.

McMd::Simulation::Simulation ( )

Constructor.

Definition at line 107 of file mcMd/simulation/Simulation.cpp.

References Util::initStatic(), McMd::Analyzer::initStatic(), McMd::Atom::initStatic(), and Util::ParamComposite::setClassName().

McMd::Simulation::~Simulation ( )

virtual

Destructor.

Definition at line 161 of file mcMd/simulation/Simulation.cpp.

References McMd::Atom::deallocate().

Member Function Documentation

void McMd::Simulation::setIoCommunicator ( MPI::Intracomm & communicator )

virtual

Set MPI job to read one parameter file and one command file.

Call this function before readParam() to allow a single parameter and command file to be used in multi-processor free energy perturbation simulations, and to read the parameter file from std in. It calls Util::ParamComposite:setIoCommunicator() and Util::FileMaster::setCommonControl().

Parameters

communicator MPI communicator used for parameter file.

Definition at line 190 of file mcMd/simulation/Simulation.cpp.

References hasCommunicator(), Util::FileMaster::setCommonControl(), Util::MpiFileIo::setIoCommunicator(), and UTIL_THROW.

void McMd::Simulation::setIoCommunicator ( )

Set MPI job to read one parameter file and one command file.

Equivalent to Simulation::setIoCommunicator(communicator()).

Definition at line 205 of file mcMd/simulation/Simulation.cpp.

References communicator().

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

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

virtual

Read parameter file block and initialize simulation.

Parameters

in	parameter input stream

Reimplemented from Util::ParamComposite.

Reimplemented in McMd::McSimulation, and McMd::MdSimulation.

Definition at line 212 of file mcMd/simulation/Simulation.cpp.

References hasSpecies(), nSpecies(), Util::ParamComposite::readParamComposite(), Simp::Species::setId(), species(), UTIL_ASSERT, and UTIL_THROW.

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

void McMd::Simulation::writeParam ( std::string filename )

Open output, write and close an output parameter file.

Calls ParamComposite::writeParam internally. Opens file using FileMaster::openOutputFile function, with adds output prefix to filename.

Parameters

filename name of output parameter file

Definition at line 313 of file mcMd/simulation/Simulation.cpp.

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

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

void McMd::Simulation::allocateMoleculeSet	(	Util::ArraySet< Molecule > &	set,
		int	speciesId
	)		const

Allocate and initialize a molecule set for one Species.

This function is called during initialization by the readParam() function of an associated System.

Parameters

set	molecule set for one Species in a System.
speciesId	integer index of the relevant Species.

Definition at line 901 of file mcMd/simulation/Simulation.cpp.

References Simp::Species::capacity(), and species().

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

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

virtual

Load internal state from an archive.

Parameters

ar	input/loading archive

Reimplemented from Util::ParamComposite.

Reimplemented in McMd::McSimulation, and McMd::MdSimulation.

Definition at line 324 of file mcMd/simulation/Simulation.cpp.

References hasSpecies(), Util::ParamComposite::loadParamComposite(), nSpecies(), Simp::Species::setId(), species(), and UTIL_ASSERT.

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

void McMd::Simulation::save ( Serializable::OArchive & ar )

virtual

Save internal state to an archive.

Parameters

ar	output/saving archive

Reimplemented from Util::ParamComposite.

Reimplemented in McMd::MdSimulation, and McMd::McSimulation.

Definition at line 386 of file mcMd/simulation/Simulation.cpp.

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

Molecule & McMd::Simulation::getMolecule ( int speciesId )

Get a new molecule from a reservoir of unused Molecule objects.

Parameters

speciesId integer index of the relevant Species.

Definition at line 912 of file mcMd/simulation/Simulation.cpp.

References McMd::Activate::activate().

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

void McMd::Simulation::returnMolecule ( Molecule & molecule )

Return a molecule to a reservoir of unused molecules.

Parameters

molecule Molecule object to be returned.

Definition at line 922 of file mcMd/simulation/Simulation.cpp.

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

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

Random & McMd::Simulation::random ( )

inline

Get the random number generator by reference.

Definition at line 837 of file mcMd/simulation/Simulation.h.

Referenced by McMd::LinearGenerator::attemptPlaceMolecule(), McMd::HybridNphMdMove::move(), McMd::ReplicaMove::move(), McMd::System::randomMolecule(), McMd::MdSystem::setBoltzmannVelocities(), and McMd::NvtLangevinIntegrator::step().

Species & McMd::Simulation::species ( int i )

Get a specific Species by reference.

Parameters

i	integer index of desired Species

Returns: reference to species with index i

Definition at line 939 of file mcMd/simulation/Simulation.cpp.

Factory< Analyzer > & McMd::Simulation::analyzerFactory ( )

Return the Analyzer factory by reference.

Definition at line 1330 of file mcMd/simulation/Simulation.cpp.

References Util::Manager< Data >::factory(), and UTIL_CHECK.

Referenced by McMd::SliplinkMcModule::SliplinkMcModule().

Factory< Species > & McMd::Simulation::speciesFactory ( )

Return the Species Factory by reference.

Definition at line 1321 of file mcMd/simulation/Simulation.cpp.

References Util::Manager< Data >::factory(), and UTIL_CHECK.

FileMaster & McMd::Simulation::fileMaster ( )

inline

MPI::Intracomm & McMd::Simulation::communicator ( )

inline

Get the MPI communicator by reference.

Definition at line 847 of file mcMd/simulation/Simulation.h.

Referenced by McMd::BennettsMethod::BennettsMethod(), McMd::McPerturbationFactory::factory(), McMd::MdSimulation::readCommands(), McMd::McSimulation::readCommands(), McMd::ReplicaMove::ReplicaMove(), and setIoCommunicator().

int McMd::Simulation::iStep ( ) const

inline

Get value of step index for main MC or MD loop.

Definition at line 856 of file mcMd/simulation/Simulation.h.

Referenced by McMd::VelProf::output(), McMd::LinkLifeTime::sample(), and McMd::LinkLTPos::sample().

int McMd::Simulation::nAtomType ( ) const

inline

Get the number of atom types.

Definition at line 768 of file mcMd/simulation/Simulation.h.

const AtomType & McMd::Simulation::atomType ( int i ) const

inline

Get a single AtomType object by const reference.

Parameters

i	integer index of desired AtomType

Definition at line 780 of file mcMd/simulation/Simulation.h.

Referenced by McMd::MdSystem::kineticEnergy(), McMd::MdSystem::setBoltzmannVelocities(), McMd::NveVvIntegrator::setup(), McMd::NvtLangevinIntegrator::setup(), McMd::NvtDpdVvIntegrator::setup(), McMd::NvtNhIntegrator::setup(), and McMd::NphIntegrator::setup().

const Array< AtomType > & McMd::Simulation::atomTypes ( ) const

inline

Get a const Array of all AtomType objects.

Definition at line 777 of file mcMd/simulation/Simulation.h.

int McMd::Simulation::nSpecies ( ) const

Get the number of Species in this Simulation.

Definition at line 933 of file mcMd/simulation/Simulation.cpp.

References Util::Manager< Data >::size().

Referenced by McMd::ExternalPotentialImpl< Interaction >::addForces(), McMd::MdSpmePotential::addForces(), McMd::MdEwaldPotential::addForces(), McMd::BondPotentialImpl< Interaction >::addForces(), McMd::DihedralPotentialImpl< Interaction >::addForces(), McMd::AnglePotentialImpl< Interaction >::addForces(), McMd::TrajectoryReader::addMolecules(), McMd::System::allocateMoleculeSets(), McMd::McPairPotential::buildCellList(), McMd::MdPairPotential::buildPairList(), McMd::ExternalPotentialImpl< Interaction >::computeEnergy(), McMd::MdEwaldPotential::computeEnergy(), McMd::MdSpmePotential::computeEnergy(), McMd::BondPotentialImpl< Interaction >::computeEnergy(), McMd::DihedralPotentialImpl< Interaction >::computeEnergy(), McMd::AnglePotentialImpl< Interaction >::computeEnergy(), McMd::McExternalPerturbation< Interaction >::derivative(), McMd::McPairExternalPerturbation< PairInteraction, ExternalInteraction >::derivative(), McMd::DeformCommand::execute(), McMd::McSystem::generateMolecules(), McMd::MdSystem::generateMolecules(), McMd::SystemInterface::isEmpty(), McMd::System::isEmpty(), isValid(), McMd::System::isValid(), McMd::MdSystem::kineticEnergy(), McMd::System::loadConfig(), McMd::SemiGrandDistribution::loadParameters(), McMd::TypeDistribution::loadParameters(), loadParameters(), McMd::MdEwaldPotential::makeWaves(), McMd::MdSpmePotential::makeWaves(), McMd::HybridMdMove::move(), McMd::HybridNphMdMove::move(), McMd::ReplicaMove::move(), McMd::SystemInterface::nAtom(), McMd::System::nAtom(), McMd::McMdConfigIo::read(), McMd::SmpConfigIo::read(), McMd::DdMdConfigIo::read(), McMd::LammpsConfigIo::read(), McMd::LammpsDumpReader::readFrame(), McMd::DdMdTrajectoryReader::readFrame(), McMd::DCDTrajectoryReader::readFrame(), readParameters(), McMd::McCommandManager::readStandardCommand(), McMd::MdCommandManager::readStandardCommand(), McMd::System::removeAllMolecules(), McMd::MdSystem::removeDriftVelocity(), McMd::Crosslinker::sample(), McMd::McExternalEnergyAverage::sample(), McMd::CompositionProfile::sample(), McMd::RDF::sample(), McMd::StructureFactor::sample(), McMd::VanHove::sample(), McMd::StructureFactorP::sample(), save(), McMd::System::saveConfig(), McMd::MdSystem::setBoltzmannVelocities(), McMd::VelProf::setup(), 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::SmpConfigIo::write(), McMd::McMdConfigIo::write(), McMd::DdMdConfigIo::write(), and McMd::LammpsConfigIo::write().

const Species & McMd::Simulation::species ( int i ) const

Get a specific Species by const reference.

Parameters

i	integer index of desired Species

Definition at line 945 of file mcMd/simulation/Simulation.cpp.

int McMd::Simulation::moleculeCapacity ( ) const

inline

Get the total number of Molecules allocated.

Definition at line 771 of file mcMd/simulation/Simulation.h.

int McMd::Simulation::atomCapacity ( ) const

inline

Get the total number of Atoms allocated.

Definition at line 774 of file mcMd/simulation/Simulation.h.

Referenced by McMd::Generator::generate(), McMd::ClusterIdentifier::initialize(), McMd::ReplicaMove::loadParameters(), McMd::SliplinkerAll::move(), McMd::Sliplinker::move(), McMd::ReplicaMove::readParameters(), and McMd::ReplicaMove::save().

int McMd::Simulation::nSystem ( ) const

inline

Get the number of Systems in this Simulation.

This will return 1 for an McSimulation or MdSimulation.

Definition at line 765 of file mcMd/simulation/Simulation.h.

bool McMd::Simulation::isValid ( ) const

virtual

Return true if Simulation is valid, or throw an Exception.

Reimplemented in McMd::McSimulation, and McMd::MdSimulation.

Definition at line 951 of file mcMd/simulation/Simulation.cpp.

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

bool McMd::Simulation::hasSpecies ( ) const

inline

Has data for all species structures and capacities.

Definition at line 840 of file mcMd/simulation/Simulation.h.

Referenced by loadParameters(), and readParameters().

MaskPolicy McMd::Simulation::maskedPairPolicy ( ) const

inline

Return the value of the mask policy (MaskNone or MaskBonded).

Definition at line 833 of file mcMd/simulation/Simulation.h.

Referenced by McMd::CfbReptationMove::readParameters(), and McMd::CfbReptateMove::readParameters().

int McMd::Simulation::nBondType ( ) const

inline

Get the number of bond types.

Definition at line 784 of file mcMd/simulation/Simulation.h.

Referenced by McMd::System::loadPotentialStyles(), McMd::System::readPotentialStyles(), and McMd::LammpsConfigIo::write().

int McMd::Simulation::bondCapacity ( ) const

inline

Get the total number of Bonds allocated.

Definition at line 787 of file mcMd/simulation/Simulation.h.

int McMd::Simulation::nAngleType ( ) const

inline

Get the number of angle types.

Definition at line 792 of file mcMd/simulation/Simulation.h.

Referenced by McMd::System::loadPotentialStyles(), McMd::System::readPotentialStyles(), and McMd::LammpsConfigIo::write().

int McMd::Simulation::angleCapacity ( ) const

inline

Get the total number of Angles allocated.

Definition at line 795 of file mcMd/simulation/Simulation.h.

int McMd::Simulation::nDihedralType ( ) const

inline

Get the number of dihedral types.

Definition at line 800 of file mcMd/simulation/Simulation.h.

Referenced by McMd::System::loadPotentialStyles(), McMd::System::readPotentialStyles(), and McMd::LammpsConfigIo::write().

int McMd::Simulation::dihedralCapacity ( ) const

inline

Get the total number of Dihedrals allocated.

Definition at line 803 of file mcMd/simulation/Simulation.h.

int McMd::Simulation::hasCoulomb ( ) const

inline

Does a Coulomb potential exist?

Definition at line 808 of file mcMd/simulation/Simulation.h.

Referenced by McMd::System::loadPotentialStyles(), McMd::PairFactory::mdFactory(), and McMd::System::readPotentialStyles().

int McMd::Simulation::hasExternal ( ) const

inline

Does an external potential exist?

Definition at line 813 of file mcMd/simulation/Simulation.h.

Referenced by McMd::System::loadPotentialStyles(), and McMd::System::readPotentialStyles().

int McMd::Simulation::nLinkType ( ) const

inline

Get the number of link types.

Definition at line 818 of file mcMd/simulation/Simulation.h.

Referenced by McMd::System::loadPotentialStyles(), and McMd::System::readPotentialStyles().

bool McMd::Simulation::hasCommunicator ( ) const

inline

Does the simulation have an associated MPI communicator?

Definition at line 844 of file mcMd/simulation/Simulation.h.

Referenced by setIoCommunicator().

void McMd::Simulation::outputOptions ( std::ostream & out ) const

Output a list of options enabled and disabled during compilation.

Parameters

out	output stream

Definition at line 1257 of file mcMd/simulation/Simulation.cpp.

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

void McMd::Simulation::setAnalyzerManager ( AnalyzerManager * ptr )

protected

Set the associated AnalyzerManager.

This should be called in the constructor for each subclass of Simulation (e.g., in McSimulation and MdSimulation) by register an instance of an appropriate subclass of AnalyzerManager.

Definition at line 177 of file mcMd/simulation/Simulation.cpp.

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

AnalyzerManager & McMd::Simulation::analyzerManager ( )

inlineprotected

Get the associated AnalyzerManager by reference.

Definition at line 862 of file mcMd/simulation/Simulation.h.

References UTIL_CHECK.

Referenced by McMd::MdSimulation::analyzeConfigs(), McMd::McSimulation::analyzeConfigs(), McMd::MdSimulation::analyzeTrajectory(), McMd::McSimulation::analyzeTrajectory(), McMd::MdSimulation::loadParameters(), McMd::McSimulation::loadParameters(), McMd::MdSimulation::readParameters(), McMd::McSimulation::readParameters(), McMd::McSimulation::save(), McMd::MdSimulation::save(), McMd::MdSimulation::simulate(), and McMd::McSimulation::simulate().