Detailed Description

A System for Molecular Dynamics simulation.

An MdSystem is a System that also has:

Associated Potential objects (MdPairPotential, BondPotential, etc.)
Associated MdIntegrator and MdIntegratorFactory objects.

It provides methods to compute forces, total energy, and stress.

Definition at line 68 of file MdSystem.h.

#include <MdSystem.h>

Inheritance diagram for McMd::MdSystem:

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

	MdSystem (McSystem &system)
	Constructor, copy from McSystem. More...

virtual	~MdSystem ()
	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 MdSystem configuration from an archive. More...

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

Force, Energy and Stress calculators
void	calculateForces ()
	Compute all forces in this System. More...

double	kineticEnergy () const
	Compute and return total kinetic energy. More...

double	potentialEnergy ()
	Compute and return total potential energy. More...

void	unsetPotentialEnergy ()
	Unset all precomputed potential energy components. More...

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

template<typename T >
void	computeVirialStress (T &stress) const
	Compute total virial stress, from all forces. More...

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

template<typename T >
void	computeKineticStress (T &stress) const
	Compute kinetic stress mvv, arising from velocities. More...

Potential energy accessors
MdPairPotential &	pairPotential () const
	Return MdPairPotential by reference. More...

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

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

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

MdCoulombPotential &	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 link potential by reference. More...

Mutators
void	setZeroForces ()
	Set all atomic forces to zero. More...

void	setZeroVelocities ()
	Set all atomic velocities to zero. More...

void	setBoltzmannVelocities (double temperature)
	Set all velocities to Boltzmann distributed random values. More...

Vector	removeDriftVelocity ()
	Subtract average velocity from all atomic velocities. More...

void	shiftAtoms ()
	Shift all atoms into primary cell. More...

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

Signal &	velocitySignal ()
	Signal to indicate change in atomic velocities. More...

Accessors
MdIntegrator &	mdIntegrator ()
	Return the MdIntegrator by reference. More...

Factory< MdIntegrator > &	mdIntegratorFactory ()
	Return the MdIntegrator Factory by reference. More...

virtual bool	isValid () const
	Return true if 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 ConfigIo *	newDefaultConfigIo ()
	Return a pointer to a new MdConfigIo object. More...

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

Default constructor.

If an MdSystem was created by this constructor, the inherited function System::isCopy() returns false.

Definition at line 73 of file MdSystem.cpp.

References Util::Signal< T >::addObserver(), positionSignal(), Util::ParamComposite::setClassName(), unsetPotentialEnergy(), and unsetVirialStress().

McMd::MdSystem::MdSystem ( McSystem & system )

Constructor, copy from McSystem.

Used to create child MdSystem for Hybrid MD/MC move. The resulting object has pointers to the same array of molecule sets for all species, the same Boundary, and the same set of potential energy or (for pair potentials) interaction objects as those used by the parent MdSystem. All computations by the child MdSystem thus reflect the state of the parent McSystem, and can directly modify the state of the parent system (e.g., my updating atomic positions).

If an MdSystem was created by this constructor, the inherited function System::isCopy() returns true.

Parameters

system System object to be cloned.

Definition at line 116 of file MdSystem.cpp.

McMd::MdSystem::~MdSystem ( )

virtual

Destructor.

Definition at line 224 of file MdSystem.cpp.

References McMd::System::isCopy().

Member Function Documentation

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

virtual

Read parameters from input file.

This method calls System::readParameters(in), reads potentials, and allocates the pairList.

Parameters

in	file stream.

Reimplemented from McMd::System.

Definition at line 277 of file MdSystem.cpp.

References McMd::System::allocateMoleculeSets(), McMd::System::angleFactory(), McMd::System::angleStyle(), McMd::System::bondFactory(), McMd::System::bondStyle(), Util::ParamComposite::className(), McMd::System::coulombFactory(), McMd::System::coulombStyle(), McMd::System::dihedralFactory(), McMd::System::dihedralStyle(), McMd::System::externalFactory(), McMd::System::externalStyle(), McMd::CoulombFactory::factory(), Util::Factory< Data >::factory(), McMd::System::isCopy(), McMd::System::linkFactory(), McMd::System::linkStyle(), McMd::PairFactory::mdFactory(), McMd::System::pairFactory(), McMd::System::pairStyle(), McMd::System::readEnsembles(), McMd::System::readFileMaster(), McMd::System::readLinkMaster(), Util::Factory< Data >::readObject(), Util::ParamComposite::readParamComposite(), McMd::System::readPerturbation(), McMd::System::readPotentialStyles(), McMd::System::simulation(), and UTIL_THROW.

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

virtual

Load parameters from an archive, without configuration.

Parameters

ar	input/loading archive

Reimplemented from McMd::System.

Definition at line 430 of file MdSystem.cpp.

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

virtual

Save parameters to an archive, without configuration.

Parameters

ar	output/saving archive

Definition at line 582 of file MdSystem.cpp.

References anglePotential(), bondPotential(), Util::ParamComposite::className(), dihedralPotential(), externalPotential(), McMd::System::isCopy(), linkPotential(), pairPotential(), Util::ParamComposite::save(), McMd::System::saveEnsembles(), McMd::System::saveFileMaster(), McMd::System::saveLinkMaster(), McMd::System::savePerturbation(), McMd::System::savePotentialStyles(), and McMd::System::simulation().

Referenced by McMd::HybridMdMove::save(), McMd::HybridNphMdMove::save(), McMd::DpdMove::save(), McMd::MdMove::save(), and McMd::MdSimulation::save().

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

virtual

Read system configuration from file.

This calls System::readConfig(), followed by pairPotential().buildPairList() and calculateForces().

Parameters

in	configuration file input stream

Reimplemented from McMd::System.

Definition at line 655 of file MdSystem.cpp.

References McMd::MdPairPotential::buildPairList(), calculateForces(), McMd::MdPairPotential::clearPairListStatistics(), coulombPotential(), Util::Log::file(), hasCoulombPotential(), McMd::MdCoulombPotential::makeWaves(), McMd::MdCoulombPotential::nWave(), pairPotential(), and McMd::System::readConfig().

Referenced by McMd::MdSimulation::analyzeConfigs(), and McMd::MdCommandManager::readStandardCommand().

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

virtual

Load the MdSystem configuration from an archive.

This calls System::loadConfig(ar), followed by pairPotential().buildPairList() and calculateForces().

Parameters

ar	input (loading) archive object.

Reimplemented from McMd::System.

Definition at line 676 of file MdSystem.cpp.

References McMd::MdPairPotential::buildPairList(), calculateForces(), McMd::MdPairPotential::clearPairListStatistics(), coulombPotential(), hasCoulombPotential(), McMd::System::loadConfig(), McMd::MdCoulombPotential::makeWaves(), and pairPotential().

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

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

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 695 of file MdSystem.cpp.

References McMd::System::boundary(), McMd::MdPairPotential::buildPairList(), calculateForces(), McMd::MdPairPotential::clearPairListStatistics(), coulombPotential(), Util::Log::file(), McMd::Generator::generate(), McMd::generatorFactory(), hasCoulombPotential(), isValid(), McMd::MdCoulombPotential::makeWaves(), McMd::Simulation::nSpecies(), pairPotential(), McMd::Generator::setupCellList(), McMd::System::simulation(), and UTIL_CHECK.

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

void McMd::MdSystem::calculateForces ( )

Compute all forces in this System.

This method zero all forces and then calls the addForces() method of each of the potential objects (pair, bond, etc.). The McPairPotential::addForces() method updates the pair list if necessary before calculating pair forces. On exit, all atomic forces are updated to values corresponding to current positions.

Definition at line 857 of file MdSystem.cpp.

References McMd::MdPairPotential::addForces(), McMd::ExternalPotential::addForces(), McMd::MdCoulombPotential::addForces(), McMd::DihedralPotential::addForces(), McMd::BondPotential::addForces(), McMd::AnglePotential::addForces(), anglePotential(), bondPotential(), coulombPotential(), dihedralPotential(), externalPotential(), hasAnglePotential(), hasBondPotential(), hasCoulombPotential(), hasDihedralPotential(), hasExternalPotential(), hasLinkPotential(), linkPotential(), pairPotential(), and setZeroForces().

Referenced by generateMolecules(), loadConfig(), McMd::HybridMdMove::move(), McMd::HybridNphMdMove::move(), McMd::MdMove::move(), McMd::DpdMove::move(), readConfig(), McMd::NvtDpdVvIntegrator::setup(), McMd::MdSimulation::simulate(), McMd::NveVvIntegrator::step(), McMd::NvtLangevinIntegrator::step(), McMd::NvtDpdVvIntegrator::step(), McMd::NvtNhIntegrator::step(), and McMd::NphIntegrator::step().

double McMd::MdSystem::kineticEnergy ( ) const

Compute and return total kinetic energy.

Definition at line 1003 of file MdSystem.cpp.

References anglePotential(), McMd::Simulation::atomType(), McMd::System::begin(), bondPotential(), McMd::System::boundary(), computeKineticStress(), McMd::StressCalculator::computeStress(), McMd::MdCoulombPotential::computeStress(), computeVirialStress(), coulombPotential(), dihedralPotential(), hasAnglePotential(), hasBondPotential(), hasCoulombPotential(), hasDihedralPotential(), hasLinkPotential(), linkPotential(), McMd::AtomType::mass(), Util::Vector::multiply(), Util::ConstArrayIterator< Data >::notEnd(), Util::ConstPArrayIterator< Data >::notEnd(), McMd::Simulation::nSpecies(), pairPotential(), Util::setToZero(), McMd::System::simulation(), and Simp::OrthorhombicBoundary::volume().

Referenced by McMd::HybridMdMove::move(), McMd::HybridNphMdMove::move(), McMd::MdEnergyOutput::sample(), McMd::MdEnergyAnalyzer::sample(), McMd::NvtNhIntegrator::setup(), and McMd::NvtNhIntegrator::step().

double McMd::MdSystem::potentialEnergy ( )

Compute and return total potential energy.

Definition at line 910 of file MdSystem.cpp.

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

Referenced by McMd::HybridMdMove::move(), and McMd::HybridNphMdMove::move().

void McMd::MdSystem::unsetPotentialEnergy ( )

Unset all precomputed potential energy components.

Definition at line 963 of file MdSystem.cpp.

References anglePotential(), bondPotential(), coulombPotential(), dihedralPotential(), externalPotential(), hasAnglePotential(), hasBondPotential(), hasCoulombPotential(), hasDihedralPotential(), hasExternalPotential(), pairPotential(), McMd::EnergyCalculator::unsetEnergy(), and McMd::MdCoulombPotential::unsetEnergy().

Referenced by MdSystem().

template<typename T >

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

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

In this and all other stress / pressure calculator method templates, typename T must be double to obtain total pressure, Util::Vector to obtain the x, y, and z diagonal pressure components, or Util::Tensor to obtain the full stress tensor. These templates work only for these three types. The function parameter "stress" is set to the desired value.

The total stress is the sum of the virial stress, from interatomic forces, and a kinetic stress arising from the atomic velocities.

Parameters

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

Referenced by McMd::NphIntegrator::step().

template<typename T >

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

Compute total virial stress, from all forces.

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

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

Parameters

stress (output) pressure, pressures or Tensor.

Referenced by McMd::MdStressAutoCorr::computeStress(), kineticEnergy(), and McMd::MdVirialStressTensorAverage::sample().

void McMd::MdSystem::unsetVirialStress ( )

Unset precomputed virial stress components.

Definition at line 1170 of file MdSystem.cpp.

References anglePotential(), bondPotential(), coulombPotential(), dihedralPotential(), hasAnglePotential(), hasBondPotential(), hasCoulombPotential(), hasDihedralPotential(), pairPotential(), McMd::StressCalculator::unsetStress(), and McMd::MdCoulombPotential::unsetStress().

Referenced by MdSystem().

template<typename T >

void McMd::MdSystem::computeKineticStress ( T & stress ) const

Compute kinetic stress mvv, arising from velocities.

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

Parameters

stress (output) pressure, pressures or Tensor.

Referenced by McMd::MdStressAutoCorr::computeStress(), and kineticEnergy().

MdPairPotential & McMd::MdSystem::pairPotential ( ) const

inline

Return MdPairPotential by reference.

Definition at line 520 of file MdSystem.h.

Referenced by McMd::MdSimulation::analyzeConfigs(), McMd::MdSimulation::analyzeTrajectory(), calculateForces(), generateMolecules(), isValid(), kineticEnergy(), loadConfig(), McMd::NvtDpdVvIntegrator::loadParameters(), McMd::MdSystemInterface::MdSystemInterface(), McMd::HybridMdMove::move(), McMd::HybridNphMdMove::move(), McMd::MdMove::move(), McMd::DpdMove::move(), potentialEnergy(), readConfig(), McMd::NvtDpdVvIntegrator::readParameters(), McMd::MdCommandManager::readStandardCommand(), McMd::MdEnergyOutput::sample(), McMd::MdEnergyAnalyzer::sample(), saveParameters(), McMd::NvtDpdVvIntegrator::setup(), McMd::MdSimulation::simulate(), McMd::NveVvIntegrator::step(), McMd::NvtLangevinIntegrator::step(), McMd::NvtDpdVvIntegrator::step(), McMd::NvtNhIntegrator::step(), McMd::NphIntegrator::step(), unsetPotentialEnergy(), and unsetVirialStress().

bool McMd::MdSystem::hasBondPotential ( ) const

inline

Does a bond potential exist?.

Definition at line 531 of file MdSystem.h.

Referenced by calculateForces(), McMd::MdEnergyAnalyzer::clear(), kineticEnergy(), McMd::MdEnergyAnalyzer::loadParameters(), McMd::MdEnergyAnalyzer::output(), potentialEnergy(), McMd::MdEnergyAnalyzer::readParameters(), McMd::MdEnergyAnalyzer::sample(), McMd::MdEnergyAnalyzer::save(), McMd::MdEnergyAnalyzer::setup(), unsetPotentialEnergy(), and unsetVirialStress().

BondPotential & McMd::MdSystem::bondPotential ( ) const

inline

Return BondPotential by reference.

Definition at line 537 of file MdSystem.h.

Referenced by calculateForces(), McMd::generatorFactory(), kineticEnergy(), McMd::MdSystemInterface::MdSystemInterface(), potentialEnergy(), McMd::MdCommandManager::readStandardCommand(), McMd::MdEnergyOutput::sample(), McMd::MdEnergyAnalyzer::sample(), saveParameters(), unsetPotentialEnergy(), and unsetVirialStress().

bool McMd::MdSystem::hasAnglePotential ( ) const

inline

Does angle potential exist?.

Definition at line 548 of file MdSystem.h.

Referenced by calculateForces(), McMd::MdEnergyAnalyzer::clear(), kineticEnergy(), McMd::MdEnergyAnalyzer::loadParameters(), McMd::MdEnergyAnalyzer::output(), potentialEnergy(), McMd::MdEnergyAnalyzer::readParameters(), McMd::MdEnergyAnalyzer::sample(), McMd::MdEnergyAnalyzer::save(), McMd::MdEnergyAnalyzer::setup(), unsetPotentialEnergy(), and unsetVirialStress().

AnglePotential & McMd::MdSystem::anglePotential ( ) const

inline

Return AnglePotential by reference.

Definition at line 554 of file MdSystem.h.

Referenced by calculateForces(), kineticEnergy(), McMd::MdSystemInterface::MdSystemInterface(), potentialEnergy(), McMd::MdCommandManager::readStandardCommand(), McMd::MdEnergyOutput::sample(), McMd::MdEnergyAnalyzer::sample(), saveParameters(), unsetPotentialEnergy(), and unsetVirialStress().

bool McMd::MdSystem::hasDihedralPotential ( ) const

inline

Does a dihedral potential exist?.

Definition at line 565 of file MdSystem.h.

Referenced by calculateForces(), McMd::MdEnergyAnalyzer::clear(), kineticEnergy(), McMd::MdEnergyAnalyzer::loadParameters(), McMd::MdEnergyAnalyzer::output(), potentialEnergy(), McMd::MdEnergyAnalyzer::readParameters(), McMd::MdEnergyAnalyzer::sample(), McMd::MdEnergyAnalyzer::save(), McMd::MdEnergyAnalyzer::setup(), unsetPotentialEnergy(), and unsetVirialStress().

DihedralPotential & McMd::MdSystem::dihedralPotential ( ) const

inline

Return DihedralPotential by reference.

Definition at line 571 of file MdSystem.h.

Referenced by calculateForces(), kineticEnergy(), McMd::MdSystemInterface::MdSystemInterface(), potentialEnergy(), McMd::MdCommandManager::readStandardCommand(), McMd::MdEnergyOutput::sample(), McMd::MdEnergyAnalyzer::sample(), saveParameters(), unsetPotentialEnergy(), and unsetVirialStress().

bool McMd::MdSystem::hasCoulombPotential ( ) const

inline

Does a Coulomb potential exist?.

Definition at line 582 of file MdSystem.h.

Referenced by calculateForces(), McMd::MdEnergyAnalyzer::clear(), generateMolecules(), kineticEnergy(), loadConfig(), McMd::MdEnergyAnalyzer::loadParameters(), McMd::MdEnergyAnalyzer::output(), potentialEnergy(), readConfig(), McMd::MdEnergyAnalyzer::readParameters(), McMd::MdEnergyAnalyzer::sample(), McMd::MdEnergyAnalyzer::save(), McMd::MdEnergyAnalyzer::setup(), unsetPotentialEnergy(), and unsetVirialStress().

MdCoulombPotential & McMd::MdSystem::coulombPotential ( ) const

inline

Return CoulombPotential by reference.

Definition at line 588 of file MdSystem.h.

Referenced by calculateForces(), generateMolecules(), kineticEnergy(), loadConfig(), McMd::MdEwaldPairPotentialImpl< Interaction >::MdEwaldPairPotentialImpl(), potentialEnergy(), readConfig(), McMd::MdEnergyOutput::sample(), McMd::MdEnergyAnalyzer::sample(), McMd::MdSimulation::simulate(), unsetPotentialEnergy(), and unsetVirialStress().

bool McMd::MdSystem::hasExternalPotential ( ) const

inline

Does an external potential exist?.

Definition at line 599 of file MdSystem.h.

Referenced by calculateForces(), McMd::MdEnergyAnalyzer::clear(), McMd::MdEnergyAnalyzer::loadParameters(), McMd::MdEnergyAnalyzer::output(), potentialEnergy(), McMd::MdEnergyAnalyzer::readParameters(), McMd::MdEnergyAnalyzer::sample(), McMd::MdEnergyAnalyzer::save(), McMd::MdEnergyAnalyzer::setup(), and unsetPotentialEnergy().

ExternalPotential & McMd::MdSystem::externalPotential ( ) const

inline

Return ExternalPotential by reference.

Definition at line 605 of file MdSystem.h.

Referenced by calculateForces(), McMd::MdSystemInterface::MdSystemInterface(), potentialEnergy(), McMd::MdEnergyOutput::sample(), McMd::MdEnergyAnalyzer::sample(), saveParameters(), and unsetPotentialEnergy().

bool McMd::MdSystem::hasLinkPotential ( ) const

inline

Does a link potential exist?.

Definition at line 633 of file MdSystem.h.

Referenced by calculateForces(), kineticEnergy(), and potentialEnergy().

BondPotential & McMd::MdSystem::linkPotential ( ) const

inline

Return link potential by reference.

Definition at line 639 of file MdSystem.h.

Referenced by calculateForces(), kineticEnergy(), potentialEnergy(), McMd::MdEnergyOutput::sample(), and saveParameters().

void McMd::MdSystem::setZeroForces ( )

Set all atomic forces to zero.

Definition at line 764 of file MdSystem.cpp.

References McMd::System::begin(), Util::ArrayIterator< Data >::notEnd(), Util::PArrayIterator< Data >::notEnd(), McMd::Simulation::nSpecies(), and McMd::System::simulation().

Referenced by calculateForces().

void McMd::MdSystem::setZeroVelocities ( )

Set all atomic velocities to zero.

Definition at line 780 of file MdSystem.cpp.

References McMd::System::begin(), Util::ArrayIterator< Data >::notEnd(), Util::PArrayIterator< Data >::notEnd(), McMd::Simulation::nSpecies(), and McMd::System::simulation().

void McMd::MdSystem::setBoltzmannVelocities ( double temperature )

Set all velocities to Boltzmann distributed random values.

Parameters

temperature temperature used in Boltzmann distribution

Definition at line 797 of file MdSystem.cpp.

References McMd::Simulation::atomType(), McMd::System::begin(), Util::Dimension, Util::Random::gaussian(), Util::ArrayIterator< Data >::notEnd(), Util::PArrayIterator< Data >::notEnd(), McMd::Simulation::nSpecies(), McMd::Simulation::random(), and McMd::System::simulation().

Referenced by McMd::HybridMdMove::move(), McMd::HybridNphMdMove::move(), McMd::MdMove::move(), and McMd::MdCommandManager::readStandardCommand().

Vector McMd::MdSystem::removeDriftVelocity ( )

Subtract average velocity from all atomic velocities.

Upon return, the system has a vanishing center-of-mass momentum.

Returns: value of drift velocity before subtraction

Definition at line 825 of file MdSystem.cpp.

References McMd::System::begin(), McMd::System::nAtom(), Util::ArrayIterator< Data >::notEnd(), Util::PArrayIterator< Data >::notEnd(), McMd::Simulation::nSpecies(), and McMd::System::simulation().

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

void McMd::MdSystem::shiftAtoms ( )

Shift all atoms into primary cell.

Shifts all atom positions into the primary image of the periodic boundary.

Definition at line 743 of file MdSystem.cpp.

References McMd::System::begin(), McMd::System::boundary(), Util::ArrayIterator< Data >::notEnd(), Util::PArrayIterator< Data >::notEnd(), McMd::Simulation::nSpecies(), Simp::OrthorhombicBoundary::shift(), and McMd::System::simulation().

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

Signal & McMd::MdSystem::positionSignal ( )

inline

Signal to indicate change in atomic positions.

Definition at line 669 of file MdSystem.h.

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

Signal & McMd::MdSystem::velocitySignal ( )

inline

Signal to indicate change in atomic velocities.

Definition at line 675 of file MdSystem.h.

Referenced by McMd::NveVvIntegrator::setup(), McMd::NvtLangevinIntegrator::setup(), McMd::NvtDpdVvIntegrator::setup(), McMd::NvtNhIntegrator::setup(), McMd::NphIntegrator::setup(), McMd::NveVvIntegrator::step(), McMd::NvtLangevinIntegrator::step(), McMd::NvtDpdVvIntegrator::step(), McMd::NvtNhIntegrator::step(), and McMd::NphIntegrator::step().

MdIntegrator & McMd::MdSystem::mdIntegrator ( )

inline

Return the MdIntegrator by reference.

Definition at line 660 of file MdSystem.h.

Referenced by McMd::HybridNphMdMove::loadParameters(), McMd::HybridMdMove::move(), McMd::MdMove::move(), McMd::DpdMove::move(), McMd::HybridNphMdMove::readParameters(), McMd::DpdMove::setup(), and McMd::MdSimulation::simulate().

Factory< MdIntegrator > & McMd::MdSystem::mdIntegratorFactory ( )

Return the MdIntegrator Factory by reference.

Definition at line 265 of file MdSystem.cpp.

bool McMd::MdSystem::isValid ( ) const

virtual

Return true if valid, or throw Exception.

Reimplemented from McMd::System.

Definition at line 1210 of file MdSystem.cpp.

References McMd::PairList::isValid(), McMd::System::isValid(), McMd::MdPairPotential::pairList(), and pairPotential().

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

ConfigIo * McMd::MdSystem::newDefaultConfigIo ( )

protectedvirtual

Return a pointer to a new MdConfigIo object.

Reimplemented from McMd::System.

Definition at line 1222 of file MdSystem.cpp.

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

Detailed Description

Public Member Functions

Protected Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation