DdMd Namespace Reference

Parallel domain decomposition (DD) MD simulation. More...

Classes
class	Analyzer
	Abstract base for periodic output and/or analysis actions. More...
class	AnalyzerFactory
	Factory for DdMd::Analyzer objects. More...
class	AnalyzerManager
	Manager for a list of Analyzer objects. More...
class	AngleFactory
	Factory for AnglePotential objects. More...
class	AnglePotential
	Abstract base class for computation of angle force and energies. More...
class	AnglePotentialImpl
	Implementation template for a AnglePotential. More...
class	AngleStorage
	Container for Group<3> (angle) objects. More...
class	Atom
	A point particle in an MD simulation. More...
class	AtomArray
	An array of Atom objects. More...
class	AtomCollector
	Class for collecting Atoms from processors to master processor. More...
struct	AtomContext
	Descriptor for context of an Atom within a molecule and species. More...
class	AtomDistributor
	Class for distributing Atoms among processors. More...
class	AtomIterator
	Iterator for all atoms owned by an AtomStorage. More...
class	AtomMap
	Associative container for finding atoms identified by integer id. More...
class	AtomStorage
	A container for all the atoms and ghost atoms on this processor. More...
class	AtomType
	Descriptor for a type of Atom. More...
class	AutoCorrAnalyzer
	Compute an autocorrelation function for a sequence of Data values. More...
class	AverageAnalyzer
	Analyze average and block averages of a single floating point variable. More...
class	BondFactory
	Factory for BondPotential objects. More...
class	BondPotential
	Abstract base class for computing bond forces and energies. More...
class	BondPotentialImpl
	Implementation template for a BondPotential. More...
class	BondStorage
	Container for for Group<2> (bond) objects. More...
class	BondTensorAutoCorr
	Calculate stress autocorrelation function. More...
class	Buffer
	Buffer for interprocessor communication. More...
class	Cell
	A single Cell in a CellList. More...
class	CellAtom
	Data for an atom in a CellList. More...
class	CellList
	A cell list used only to identify nearby atom pairs. More...
class	ConfigIo
	Abstract reader/writer for configuration files. More...
class	ConfigIoFactory
	Default Factory for subclasses of ConfigIo. More...
class	ConfigWriter
	Periodically write simulation configuration to a new file. More...
class	ConstAtomIterator
	Const iterator for all atoms owned by an AtomStorage. More...
class	ConstGhostIterator
	Iterator for all ghost atoms owned by an AtomStorage. More...
class	ConstGroupIterator
	Const iterator for all Group < N > objects owned by a GroupStorage < N >. More...
class	DdMdConfigIo
	Native / default format for configuration files. More...
class	DdMdGroupTrajectoryWriter
	Native binary trajectory format for ddSim, for one group. More...
class	DdMdOrderedConfigIo
	Native / default format for configuration files. More...
class	DdMdTrajectoryWriter
	Native binary trajectory format for ddSim. More...
class	DdTimer
	Class for measuring time intervals. More...
class	DihedralFactory
	Factory for DihedralPotential objects. More...
class	DihedralPotential
	Abstract base class for computing dihedral forces and energies. More...
class	DihedralPotentialImpl
	Implementation template for a DihedralPotential. More...
class	DihedralStorage
	Container for Group<4> (dihedral) objects. More...
class	Domain
	Decomposition of the system into domains associated with processors. More...
class	EnergyAnalyzer
	Compute averages and output block averages of energy components. More...
class	Exchanger
	Class for exchanging Atoms, Ghosts and Groups between processors. More...
class	ExternalEnergyAnalyzer
	Output and evaluate average of external energy. More...
class	ExternalEnergyAverage
	Periodically write simulation energies to Log output. More...
class	ExternalFactory
	Factory for ExternalPotential objects. More...
class	ExternalPotential
	Calculates external forces and energies for a parent Simulation. More...
class	ExternalPotentialImpl
	Implementation template for a ExternalPotential. More...
class	GhostIterator
	Iterator for all ghost atoms owned by an AtomStorage. More...
class	Group
	A group of covalently interacting atoms. More...
class	GroupCollector
	Class for collecting Groups from processors to master processor. More...
class	GroupDistributor
	Class template for distributing Group<N> objects among processors. More...
class	GroupExchanger
	Interface for a GroupStorage<N> for use in Exchanger. More...
class	GroupIterator
	Iterator for all Group < N > objects owned by a GroupStorage< N >. More...
class	GroupStorage
	A container for all the Group<N> objects on this processor. More...
class	Integrator
	An Integrator numerically integrates the equations of motion. More...
class	IntegratorFactory
	Factory for subclasses of Integrator (i.e., MD integrators). More...
class	KineticEnergyAnalyzer
	Output and evaluate average of kinetic energy. More...
class	LammpsConfigIo
	Lammps data file format for configuration files. More...
class	LammpsDumpWriter
	Write a trajectory in the Lammps dump format. More...
class	LogEnergy
	Periodically write simulation energies to Log output. More...
class	Mask
	Set of Atoms for which pair interactions with a parent Atom are "masked". More...
class	Modifier
	A Modifier can modify the time evolution of the simulation. More...
class	ModifierFactory
	Factory for DdMd::Modifier objects. More...
class	ModifierManager
	Manager for a set of Modifier objects. More...
class	NphIntegrator
	A reversible, symplectic NPH integrator (Anderson barostat). More...
class	NptIntegrator
	A reversible symplectic NPT integrator. More...
class	NveIntegrator
	A velocity-Verlet constant energy integrator. More...
class	NvtIntegrator
	A Nose-Hoover constant temperature, constant volume integrator. More...
class	NvtLangevinIntegrator
	A NVT molecular dynamics integrator with a Langevin thermostat. More...
class	OrderParamNucleation
	OrderParamNucleation is designed to evaluate a sort of composition profile in the specific case of nucleating a lamellar ordered phase in a small region at the center of a simulation cell. More...
class	OutputBoxdim
	Periodically write Boundary dimensions to file. More...
class	OutputEnergy
	Periodically write simulation energies to file. More...
class	OutputPairEnergies
	Periodically write pair energies to file. More...
class	OutputPressure
	Periodically write (scalar) pressure to file. More...
class	OutputStressTensor
	Periodically write (tensor) StressTensor to file. More...
class	OutputTemperature
	Periodically output kinetic temperature to file. More...
class	PairEnergyAnalyzer
	Compute and analyze pair energies. More...
class	PairEnergyAverage
	Compute average of pair energy. More...
class	PairFactory
	Factory for PairPotential objects. More...
class	PairIterator
	Iterator for pairs in a PairList. More...
class	PairList
	A Verlet nonbonded pair list. More...
class	PairPotential
	Abstract base class for computing nonbonded pair forces and energies. More...
class	PairPotentialImpl
	Implementation template for a PairPotential. More...
class	Plan
	Communication plan. More...
class	Potential
	A Potential represents a potential energy contribution. More...
class	PressureAnalyzer
	Sample and evaluate average of total pressure. More...
class	SerializeConfigIo
	Save / load configuration from / to an archive. More...
class	Simulation
	Main object for a domain-decomposition MD simulation. More...
class	SimulationAccess
	Provides access to members of Simulation object. More...
class	StressAnalyzer
	Output and evaluate average of stress tensor. More...
class	StressAutoCorr
	Compute stress autocorrelation function for a liquid. More...
class	StressAutoCorrelation
	Compute the shear stress autocorrelation function. More...
class	StructureFactor
	StructureFactor evaluates structure factors in Fourier space. More...
class	StructureFactorGrid
	StructureFactorGrid evaluates structure factors in Fourier space. More...
class	SymmTensorAverageAnalyzer
	Analyzer that computes average of a sequence of symmetric Tensor values. More...
class	TensorAverageAnalyzer
	Analyzer that computes averages and block averages of a single Tensor. More...
class	TrajectoryWriter
	Base class to write a trajectory to a single file. More...
class	TwoStepIntegrator
	A two-step velocity-Verlet style integrator. More...
class	VanHove
	Evaluates the van Hove function S(k,t) for one or more wavevector k. More...
class	VirialStressAnalyzer
	Output and evaluate average of virial stress tensor. More...
class	VirialStressTensor
	Periodically write virial stress tensor components to file. More...
class	VirialStressTensorAverage
	Compute average and output block averages of virial stress tensor. More...

Enumerations

Functions
std::istream &	operator>> (std::istream &in, AtomType &atomType)
	istream extractor (>>) for an AtomType. More...
std::ostream &	operator<< (std::ostream &out, const AtomType &atomType)
	ostream inserter (<<) for an AtomType. More...
template<class Archive >
void	serialize (Archive &ar, AtomType &atomType, const unsigned int version)
	Serialize an AtomType. More...
template<int N>
std::istream &	operator>> (std::istream &in, Group< N > &group)
	istream extractor (>>) for a Group. More...
template<int N>
std::ostream &	operator<< (std::ostream &out, const Group< N > &group)
	ostream inserter (<<) for a Group. More...
template<class Archive , int N>
void	serialize (Archive &ar, Group< N > &group, const unsigned int version)
	Serialize one Group<N>. More...
std::istream &	operator>> (std::istream &in, MaskPolicy &policy)
	istream extractor for a MaskPolicy. More...
std::ostream &	operator<< (std::ostream &out, MaskPolicy policy)
	ostream inserter for an MaskPolicy. More...
template<class Archive >
void	serialize (Archive &ar, MaskPolicy &policy, const unsigned int version)
	Serialize a MaskPolicy. More...
std::istream &	operator>> (std::istream &in, Plan &plan)
	istream extractor (>>) for a Plan. More...
std::ostream &	operator<< (std::ostream &out, const Plan &plan)
	ostream inserter (<<) for a Plan. More...
void	initStatic ()
	Guarantee initialization of all static class members in DdMd namespace. More...

Detailed Description

Parallel domain decomposition (DD) MD simulation.

Function Documentation

std::istream & DdMd::operator>>	(	std::istream &	in,
		AtomType &	atomType
	)

istream extractor (>>) for an AtomType.

Format:

name mass

Parameters

in	input stream
atomType	AtomType to be read from stream

Returns

modified input stream

Definition at line 34 of file ddMd/chemistry/AtomType.cpp.

std::ostream & DdMd::operator<<	(	std::ostream &	out,
		const AtomType &	atomType
	)

ostream inserter (<<) for an AtomType.

Format, one one line with no line break:

name mass

Parameters

out	output stream
atomType	AtomType to be written to stream

Returns

modified output stream

Definition at line 44 of file ddMd/chemistry/AtomType.cpp.

References Util::Parameter::Precision, and Util::Parameter::Width.

template<class Archive >

void DdMd::serialize	(	Archive &	ar,
		AtomType &	atomType,
		const unsigned int	version
	)

Serialize an AtomType.

Parameters

ar	archive
atomType	object to be serialized
version	archive version id

Definition at line 161 of file ddMd/chemistry/AtomType.h.

template<int N>

std::istream & DdMd::operator>>	(	std::istream &	in,
		Group< N > &	group
	)

istream extractor (>>) for a Group.

Parameters

in	input stream
group	Group to be read from stream

Returns

modified input stream

Definition at line 378 of file ddMd/chemistry/Group.h.

template<int N>

std::ostream & DdMd::operator<<	(	std::ostream &	out,
		const Group< N > &	group
	)

ostream inserter (<<) for a Group.

Format on one line with no line break:

Parameters

out	output stream
group	Group to be written to stream

Returns

modified output stream

Definition at line 392 of file ddMd/chemistry/Group.h.

References DdMd::Group< N >::serialize.

template<class Archive , int N>

void DdMd::serialize	(	Archive &	ar,
		Group< N > &	group,
		const unsigned int	version
	)

Serialize one Group<N>.

Default implementation calls serialize method of data object. Can be overridden by any explicit specialization.

Parameters

ar	archive object
group	object to be serialized
version	archive version id

std::istream & DdMd::operator>>	(	std::istream &	in,
		MaskPolicy &	policy
	)

istream extractor for a MaskPolicy.

Parameters

in	input stream
policy	MaskPolicy to be read

Returns

modified input stream

Definition at line 31 of file ddMd/chemistry/MaskPolicy.cpp.

References UTIL_THROW.

std::ostream & DdMd::operator<<	(	std::ostream &	out,
		MaskPolicy	policy
	)

ostream inserter for an MaskPolicy.

Parameters

out	output stream
policy	MaskPolicy to be written

Returns

modified output stream

Definition at line 49 of file ddMd/chemistry/MaskPolicy.cpp.

References UTIL_THROW.

template<class Archive >

void DdMd::serialize	(	Archive &	ar,
		MaskPolicy &	policy,
		const unsigned int	version
	)

Serialize a MaskPolicy.

Parameters

ar	archive object
policy	MaskPolicy enum value to be serialized
version	archive version id

Definition at line 57 of file ddMd/chemistry/MaskPolicy.h.

References Util::serializeEnum().

std::istream & DdMd::operator>>	(	std::istream &	in,
		Plan &	plan
	)

istream extractor (>>) for a Plan.

Parameters

in	input stream
plan	Plan to be read from stream

Returns

modified input stream

Definition at line 22 of file Plan.cpp.

References DdMd::Plan::clearExchange(), DdMd::Plan::clearGhost(), Util::Dimension, DdMd::Plan::setExchange(), and DdMd::Plan::setGhost().

std::ostream & DdMd::operator<<	(	std::ostream &	out,
		const Plan &	plan
	)

ostream inserter (<<) for a Plan.

Format, one one line with no line break:

Parameters

out	output stream
plan	Plan to be written to stream

Returns

modified output stream

Definition at line 58 of file Plan.cpp.

References Util::Dimension, DdMd::Plan::exchange(), and DdMd::Plan::ghost().

void DdMd::initStatic

(

)

Guarantee initialization of all static class members in DdMd namespace.

Definition at line 18 of file ddMd/misc/initStatic.cpp.

References DdMd::Modifier::initStatic().