This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel. More...

Classes
class	Accumulator
	Basic Accumulator class for numbers. More...

class	ActionCorrFunc

class	AlphaHull
	Compute alpha complex or alpha shape. More...

class	AlphaHullFinder

class	AmberImproperTorsionType
	"types/AmberImproperTorsionType.hpp" More...

class	AnalyticalModel

struct	AndParamConstraint

class	AngleR

class	AngularVelocityAutoOutProductCorrFunc

class	AngularVelVelOutProdCorrFunc

class	ApproximateModel

class	Atom

class	AtomData

class	AtomicBeadModel

struct	AtomInfo

class	AtomNameVisitor

class	AtomStamp

class	AtomType
	AtomType is what OpenMD looks to for unchanging data about an atom. More...

class	AtomTypeCompare

class	AtomTypesSectionParser
	"io/AtomTypesSectionParser.hpp" More...

class	AutoCorrFunc

class	BaseAccumulator

class	BaseAtomTypesSectionParser
	"io/BaseAtomTypesSectionParser.hpp" More...

class	BaseAtomVisitor

class	BaseRigidBodyVisitor

class	BaseVisitor

class	basic_teebuf
	As a subclass of basic_streambuf, basic_teebuf can operate on multiple stream simultaneously. More...

class	BCCLattice

class	BeadModel
	References: More...

class	Bend

struct	BendData

struct	BendDataSet

class	BendStamp

class	BendType

class	BendTypeParser

class	BendTypesSectionParser
	"io/BendTypesSectionParser.hpp" More...

class	BlockSnapshotManager

class	Bond

class	BondAngleDistribution
	BondAngleDistribution. More...

class	BondCorrFunc

class	BondOrderParameter
	Bond Order Parameter. More...

class	BondStamp

class	BondType
	BondType class is responsible for calculating the force and energy of the bond. More...

class	BondTypeParser

class	BondTypesSectionParser
	"io/BondTypesSectionParser.hpp" More...

class	BOPofR

class	BoundaryElementModel

class	BoxObjectiveFunction

class	Buckingham

struct	BuckinghamInteractionData

class	BuckinghamInteractionType
	BuckinghamInteractionType is one of the basic non-bonded interactions for representing the non-Coulombic contribution in ionic and networked solids like silica and alumina. More...

class	CenterOfMass

class	ChargeAtomTypesSectionParser

class	ChargeDensityZ

class	ChargeField

class	ChargeHistogram

class	ChargeKineticCorrFunc

class	ChargeOrientationCorrFunc

class	ChargeR

class	ChargeZ

struct	CharmmTorsionParameter

class	CharmmTorsionType
	"types/CharmmTorsionType.hpp" These torsion types are defined identically with functional form given in the following paper: More...

class	ChebyshevT
	A collection of Chebyshev Polynomials. More...

class	ChebyshevU
	A collection of Chebyshev Polynomials. More...

class	COHZ

class	CollectiveDipoleDisplacement
	Calculates the collective dipole displacement function. More...

class	Communicator

class	Comparator

class	Component

class	CompositeShape
	Combine composite pattern and visitor pattern. More...

class	CompositeVisitor

class	COMVel

struct	ConstraintData

class	ConstraintElem
	An adapter class of StuntDouble which is used at constraint algorithm. More...

class	ConstraintPair

class	ConstraintStamp

class	ConstraintWriter

class	ContactAngle1
	Calculates the contact angle of a droplet with a surface using a spherical cap approximation for the droplet. More...

class	ContactAngle2

struct	ContainsConstraint

class	ConvexHull

class	CoordinationNumber
	CoordinationNumber. More...

class	CosineBendType
	A simple harmonic bend using the cosine of the angle instead of the angle itself: More...

class	CosineSeriesBendType
	A bend used primarily in UFF that utilizes a Fourier series in terms of the cosine of the bend angle: More...

class	CrossCorrFunc

class	CubicBendType

class	CubicBondType

class	CubicLattice

class	CubicSpline

class	CubicTorsionType

class	Cuboctahedron
	Generates coordinates of atoms inside a Cuboctahedron. More...

class	CurlingStoneDecahedron

class	CurrentDensity

class	CurrentDensityAutoCorrFunc

class	CutoffGroup

class	CutoffGroupStamp

class	DataHolder

class	DataStorage

class	Decahedron
	Creates the regular decahedron, Ino decahedron, or truncated (Marks) decahedron structures (depending on the parameters). More...

class	DefaultAtomVisitor

class	DensityField

class	DensityHistogram

class	DensityPlot

class	DipoleCorrFunc

class	DipoleField

class	DipoleOrientation

class	DirectionalAdapter

class	DirectionalAtom

class	DirectionalAtomTypesSectionParser

struct	DirectionalAtypeParameters

class	DirectionalRCorrFunc

class	Displacement

class	DisplacementZ

class	DistanceFinder

class	DLM

class	DumpReader

class	DumpStatusFunction

class	DumpWriter

class	DynamicProperty
	"applications/dynamicProps/DynamicProperty" More...

class	DynamicRectMatrix
	rectangular matrix class More...

class	DynamicVector
	Dynamically-sized vector class. More...

class	EAM

class	EAMAdapter

struct	EAMAtomData

class	EAMAtomTypesSectionParser
	"io/EAMAtomTypesSectionParser.hpp" More...

struct	EAMInteractionData

class	EAMInteractionType
	EAMInteractionType is one of the basic metallic interactions for representing the bonding in metallic solids. More...

struct	EAMParameters

class	Electrostatic

struct	ElectrostaticAtomData

class	ElectrostaticInteraction
	The basic interface for electrostatic interactions. More...

class	Element

class	ElementsTable
	Periodic Table of the Elements Using element data is a place holder when we lack information about a specific atom type. More...

class	Ellipsoid
	An ellipsoid in OpenMD is restricted to having two equal equatorial semi-axes. More...

struct	EqualConstraint

struct	EqualIgnoreCaseConstraint

class	Equipartition

struct	EvenConstraint

class	FCCLattice

class	FCCOfR

class	Field

class	FixedBondType
	FixedBondType class is responsible for calculating the force and energy of the bond. More...

class	FixedChargeAdapter

struct	FixedChargeAtypeParameters

struct	FluctuatingAtypeParameters

class	FluctuatingChargeAdapter

struct	FluctuatingChargeAtomData

class	FluctuatingChargeAtomTypesSectionParser

class	FluctuatingChargeConstraints

class	FluctuatingChargeDamped

class	FluctuatingChargeForces

class	FluctuatingChargeLangevin

class	FluctuatingChargeNVE

class	FluctuatingChargeNVT

class	FluctuatingChargeObjectiveFunction

class	FluctuatingChargeParameters

class	FluctuatingChargePropagator
	abstract class for propagating fluctuating charge variables More...

class	ForceAutoCorrFunc

class	ForceDecomposition
	ForceDecomposition is an interface for passing out and collecting information from many processors at various stages of the main non-bonded ForceLoop. More...

class	ForceField

class	ForceFieldOptions

class	ForceManager
	ForceManager is responsible for calculating both the short range (bonded) interactions and long range (non-bonded) interactions. More...

class	ForceMatrixDecomposition

class	ForceModifier
	Abstract class for external ForceModifier classes. More...

class	ForTorCorrFunc

class	FragmentStamp

struct	FrameData
	FrameData is a structure for holding system-wide dynamic data about the simulation. More...

class	FreqFlucCorrFunc
	Frequency Fluctuation Correlation Function. More...

struct	FuncflParameters

class	GaussianTriangleQuadratureRule

class	GayBerneAdapter

class	GayBerneAtomTypesSectionParser

class	GB

struct	GBAtypeParameters

class	GBheadVisitor

struct	GBInteractionData

class	GBtailVisitor

class	GCN
	Generalized Coordinate Number. More...

class	GCNSeq
	Generalized Coordinate Number Sequence. More...

class	GenericData
	@ class GenericData GenericData.hpp "utils/GenericData.hpp" More...

class	GenericFactory
	GenericFactory is a template based Object Factory Factory pattern is used to define an interface for creating an object. More...

class	GhostBend

class	GhostTorsion

class	Globals

class	GofAngle2

class	GofR

class	GofRAngle

class	GofRAngle2

class	GofROmega

class	GofRTheta

class	GofRZ

class	GofXyz

class	GofZ

struct	GreaterThanConstraint

struct	GreaterThanOrEqualTo

class	Grid3D

class	gzstreambase

class	gzstreambuf

class	HarmonicBendType

class	HarmonicBondType
	HarmonicBondType is the basic OpenMD bond type. More...

class	HarmonicInversionType
	This inversion potential has the form: More...

class	HarmonicSineBendType
	A bend using the square of the sine of the angle instead of the angle itself: More...

class	HarmonicTorsionType
	These torsion types are defined identically with functional form given in equation 5 in the following paper: More...

class	HBondGeometric
	Hydrogen Bonding statistics using geometric criteria. More...

class	HBondJump

class	HBondJumpR

class	HBondJumpZ

class	HBondPersistence

class	HBondR
	Hydrogen Bonding density binned by r. More...

class	HBondRvol
	Hydrogen Bonding density binned by r. More...

class	HBondZ
	Hydrogen Bonding density binned by z. More...

class	HBondZvol
	Hydrogen Bonding density binned by z. More...

class	Hull

class	HullFinder

class	Hxy

struct	HydrodynamicsElement

class	HydrodynamicsModel

class	HydrodynamicsModelBuilder

class	HydrodynamicsModelCreator

class	HydrodynamicsModelFactory
	Factory pattern and Singleton Pattern are used to define an interface for creating an HydrodynamicsModel. More...

class	HydrogenBondingInteraction
	The basic interface for hydrogen bonding interactions. More...

class	HydroIO

class	HydroProp
	Container for information about the hydrodynamic behavior of objects interacting with surroundings. More...

class	IcosahedralOfR

class	Icosahedron
	Create the Mackay icosahedron structure. More...

class	ifstrstream
	ifstrstream class provides a stream interface to read data from files. More...

class	igzstream

struct	ImproperCosineInversionParameter

class	ImproperCosineInversionType
	"types/ImproperCosineInversionType.hpp" More...

class	IndexFinder

class	IndexListContainer

class	InoDecahedron

class	Integrator
	Declaration of the Integrator base class, which all other integrators inherit from. More...

class	IntegratorBuilder

class	IntegratorCreator

class	IntegratorFactory
	Factory pattern and Singleton Pattern are used to define an interface for creating an Integrator. More...

struct	InteractionData
	The InteractionData struct. More...

class	InteractionManager
	InteractionManager is responsible for keeping track of the non-bonded interactions (C++) More...

class	InversePowerSeries

struct	InversePowerSeriesInteractionData

class	InversePowerSeriesInteractionType
	InversePowerSeriesInteractionType is a sum of powers in the inverse of r: More...

class	Inversion

struct	InversionData

struct	InversionDataSet

class	InversionStamp

class	InversionType

class	InversionTypeParser
	"types/InversionTypeParser.hpp" More...

class	InversionTypesSectionParser
	"io/InversionTypesSectionParser.hpp" More...

class	Kirkwood

class	KirkwoodBuff

class	KirkwoodQuadrupoles

class	LangevinDynamics

class	LangevinHullDynamics

class	LangevinHullForceModifier
	Force modifier for NPT Langevin Hull Dynamics applying friction and random forces as well as torques. More...

class	LangevinPiston
	Constant pressure and temperature integrator. More...

class	Lattice

class	LatticeBuilder

class	LatticeCreator

class	LatticeFactory
	Factory pattern and Singleton Pattern are used to define an interface for creating an Lattice. More...

class	LDForceModifier
	Force modifier for Langevin Dynamics applying friction and random forces as well as torques. More...

class	LegendreCorrFunc

class	LegendreCorrFuncZ

class	LegendreGauss1d

struct	LegendreGauss1dParams

class	LegendrePolynomial
	A collection of Legendre Polynomials. More...

class	LennardJonesAdapter

class	LennardJonesAtomTypesSectionParser

class	LennardJonesInteractionType
	LennardJonesInteractionType is one of the basic interaction types. More...

struct	LessThanConstraint

struct	LessThanOrEqualToConstraint

class	LessThanPeriodicityFunctor

class	LipidHeadVisitor

class	LipidTransVisitor

class	LJ

struct	LJAtypeParameters

struct	LJInteractionData

class	LocalIndexManager
	"utils/LocalIndexManager.hpp" More...

class	MagneticField
	Applies a uniform (vector) magnetic field to the system. More...

class	MassDensityR

class	MassDensityZ

class	MatrixAccumulator

class	MAW

struct	MAWInteractionData

class	MAWInteractionType
	MAWInteractionType (Metal-Angular-Water) is one of the basic Metal-to-NonMetal interaction types. More...

class	Mesh

class	MetallicInteraction
	The basic interface for metallic interactions. More...

class	Mie

struct	MieInteractionData

class	MieInteractionType
	MieInteractionType is one of the basic interaction types. More...

class	MinimizerParameters

class	MolecularRestraint
	MolecularRestraint is the restraint (both positional and orientational) for the configuration of a flexible Molecule relative to some reference structure for the same Molecule. More...

class	Molecule

class	MoleculeACF

class	MoleculeCCF

class	MoleculeCreator

class	MoleculeStamp

class	MoLocator

class	MomAngMomCorrFunc

struct	MomentData

class	MomentumHistogram

class	Morse

class	MorseBondType
	MorseBondType is a more realistic bond potential. More...

struct	MorseInteractionData

class	MorseInteractionType
	MorseInteractionType is one of the basic non-bonded interactions. More...

class	MPITraits

class	MPITraits< RectMatrix< T, R, C > >

class	MPITraits< SquareMatrix3< T > >

class	MPITraits< Vector3< T > >

class	MPITraits< Vector< T, Dim > >

class	MSMSFormat

class	MultiComponentRDF
	Multi-Component Radial Distribution Function. More...

class	MultipoleAdapter

class	MultipoleAtomTypesSectionParser

struct	MultipoleAtypeParameters

class	MultipoleSum

class	NameFinder

class	NanoLength

class	NanoVolume

struct	NegativeConstraint

class	NgammaT
	Constant lateral surface tension integrator. More...

class	NitrileFrequencyMap

class	NodesStamp

class	NonBondedInteraction
	The basic interface for non-bonded interactions. More...

class	NonBondedInteractionsSectionParser

class	NonBondedInteractionType
	NonBondedInteractionType class is responsible for keeping track of static (unchanging) parameters for explicit non-bonded interactions. More...

struct	NonBondedInteractionTypeProperties

struct	NonNegativeConstraint

struct	NonPositiveConstraint

struct	NonZeroConstraint

class	NoStatus
	No status. More...

struct	NotEmptyConstraint

struct	NotParamConstraint

class	NPA
	Constant normal pressure and lateral surface area integrator No thermostat! More...

class	NPAT
	Constant normal pressure and lateral surface area integrator. More...

class	NPrT
	Constant normal pressure and lateral surface tension integrator. More...

class	NPT

class	NPTf

class	NPTi

class	NPTsz
	A utility integrator (much like NPTxyz) but which keeps the relative scaling of x & y fixed. More...

class	NPTxyz

class	NumberR

class	NumberZ

class	NVE

class	NVT
	Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. More...

class	ObjectACF

class	ObjectCCF

class	ObjectCount

class	ObjectRestraint
	ObjectRestraint is the basic harmonic restraint for the degrees of freedom of a StuntDouble. More...

class	ogzstream

class	OnsagerCorrFunc

class	OpenMDBitSet
	OpenMDBitSet is a wrapper class of std::vector<bool> to act as a growable std::bitset. More...

class	OpenMDException

class	OplsTorsionType
	These torsion types are defined identically with functional form given in the following paper: More...

class	OptimizationBuilder

class	OptimizationCreator

class	OptimizationFactory
	Factory pattern and Singleton Pattern are used to define an interface for creating an Optimization. More...

class	OptionSectionParser
	"io/OptionSectionParser.hpp" More...

class	OrderParameterProbZ

struct	OrParamConstraint

class	P2OrderParameter

class	P2R

class	PairList
	PairList class maintains a general purpose list of atom pairs using the global indices of the atoms. More...

class	pAngle

struct	ParamConstraintFacade
	This class allows to recognize constraint predicates, so that they can be combined using composition operators. More...

class	PipeDensity

class	Plan

class	PolarizableAdapter

class	PolarizableAtomTypesSectionParser

struct	PolarizableAtypeParameters

class	Polynomial
	A generic Polynomial class. More...

class	PolynomialBendType
	"types/PolynomialBendType.hpp" More...

class	PolynomialBondType
	"types/PolynomialBondType.hpp" More...

class	PolynomialInversionType
	"types/PolynomialInversionType.hpp" More...

class	PolynomialTorsionType
	"types/PolynomialTorsionType.hpp" More...

class	PositionZ

struct	PositiveConstraint

class	PotDiff
	Potential Energy differences with charges turned off. More...

class	PotentialEnergyObjectiveFunction

class	PotVecAccumulator

class	PrepareVisitor

class	ProgressBar

class	PropertyMap
	PropertyMap class maintains a list of GenericData. More...

class	QuarticBendType

class	QuarticBondType

class	QuarticTorsionType

class	Quaternion
	Quaternion is a sort of a higher-level complex number. More...

class	RadialDistrFunc
	Radial Distribution Function. More...

class	Rattle
	Velocity Verlet Constraint Algorithm. More...

class	RBCOMVisitor

class	RCorrFunc

class	RCorrFuncR

class	RCorrFuncZ

class	RealSphericalHarmonic

class	RealSymmetricTridiagonal
	Computes eigenvalues and eigenvectors of a real (non-complex) symmetric tridiagonal matrix by the QL method. More...

class	RectMatrix
	rectangular matrix class More...

class	RegularCuboctahedron

class	RegularDecahedron

class	ReplacementVisitor
	Replaces an atomic object with a collection atomic sites. More...

class	ReplicateVisitor

class	RepulsivePower

class	RepulsivePowerInteractionType
	RepulsivePowerInteractionType is one of the basic interaction types. More...

class	Restraint

class	RestraintForceModifier

class	RestraintStamp

class	RestReader

class	RestWriter

class	Revision

class	RhoR

class	RhoZ

class	RigidBody

class	RigidBodyStamp

class	RippleOP

class	RMSD

class	RNEMDR

class	RNEMDRTheta

class	RNEMDZ

class	RotAngleDisplacement

class	RotationAlgorithm
	abstract class for rotation More...

class	RoughShell

struct	RPInteractionData

class	SameSectionParserFunctor

class	SC

struct	SCAtomData

class	SCAtomTypesSectionParser
	"io/SCAtomTypesSectionParser.hpp" More...

struct	SCAtypeParameters

class	SCDElem

class	SCDOrderParameter

struct	SCInteractionData

class	SCLattice

class	SCN
	Secondary Coordinate Number. More...

class	SDKBend

class	SDKBendType

struct	SDShape

class	SectionParser

struct	SectionParserContext

class	SectionParserManager
	"io/SectionParserManager.hpp" SectionParserManager maintains a priority list More...

class	SelectionCompiler
	"selection/SelectionCompiler.hpp" More...

class	SelectionCorrFunc

class	SelectionEvaluator
	"selection/SelectionEvaluator" More...

class	SelectionManager

class	SelectionSet

struct	SelfData
	The SelfData struct. More...

class	SequentialAnalyzer
	"applications/sequentialProps/SequentialAnalyzer" More...

class	Shake

class	Shape

class	ShapeAtomType

class	ShapeAtomTypesSectionParser

class	ShapeBuilder

class	shapedLattice
	Returns a vector of vector3 position on a lattice truncated. More...

class	shapedLatticeEllipsoid
	Implements an ellipsoid-shaped lattice. More...

class	shapedLatticePentRod
	Implements a spherically-capped rod-shaped lattice. More...

class	shapedLatticeRod
	Implements a spherically-capped rod-shaped lattice. More...

class	shapedLatticeSpherical
	Implements a spherical lattice. More...

class	SHAPES

class	ShellStatistics

class	ShiftedMieBondType
	ShiftedMieBondType is used to correct 1-3 bend interactions in the SDK force field. More...

class	ShortRangeInteraction
	A ShortRangeInteraction holds some bookeeping data for bonded interactions (e.g. More...

class	SimCreator
	The only responsibility of SimCreator is to parse the meta-data file and create a SimInfo instance based on the information returned by parser. More...

class	SimInfo
	One of the heavy-weight classes of OpenMD, SimInfo maintains objects and variables relating to the current simulation. More...

class	SimplePreprocessor

class	SimpleTypeData
	SimpleTypeData class is a POD repository class. More...

class	SimSnapshotManager
	"brains/SimSnapshotManager.hpp" More...

class	SlabStatistics

class	Snapshot
	The Snapshot class is a repository storing dynamic data during a Simulation. More...

class	SnapshotManager
	SnapshotManager class is an abstract class which maintains a series of snapshots. More...

class	SpatialStatistics

struct	SPFData

class	SPFDynamics

class	Sphere

class	SphericalHarmonic

class	SquareMatrix
	A square matrix class. More...

class	SquareMatrix3

class	SSDAtomVisitor

class	StaticAnalyser

class	Stats

class	StatusFunction

class	StatWriter
	A configurable Statistics Writer. More...

class	Sticky

class	StickyAdapter

class	StickyAtomTypesSectionParser
	"io/StickyAtomTypesSectionParser.hpp" More...

struct	StickyAtypeParameters

struct	StickyInteractionData

class	StickyPowerAtomTypesSectionParser
	StickyPowerAtomTypesSectionParser.hpp "io/StickyAtomTypesSectionParser.hpp". More...

class	StrangFixCowperTriangleQuadratureRule

class	StressCorrFunc

class	StringTokenizer
	The string tokenizer class allows an application to break a string into tokens The set of delimiters (the characters that separate tokens) may be specified either at creation time or on a per-token basis. More...

class	StuntDouble
	"Don't move, or you're dead! Stand up! Captain, we've got them!" More...

class	SurfaceDiffusion

class	SuttonChenAdapter

class	SwitchingFunction

class	SystemACF

class	SystemCCF

class	SystemDecomposition
	SystemDecomposition is an interface for passing out and collecting information from many processors for use during integration and computation of physical properties. More...

class	SystemDipoleCorrFunc

class	TetrahedralityHBMatrix
	Tetrahedrality Hydrogen Bonding Matrix. More...

class	TetrahedralityParam
	Tetrahedrality Parameter. More...

class	TetrahedralityParamDens
	Tetrahedrality ParameterDens. More...

class	TetrahedralityParamR
	Tetrahedrality ParameterR. More...

class	TetrahedralityParamXYZ
	Tetrahedrality Parameter XYZ. More...

class	TetrahedralityParamZ
	Tetrahedrality ParameterZ. More...

class	Thermo

class	ThermoIntegrationForceModifier

class	ThetaCorrFunc

class	TimeCorrFunc
	Computes a correlation function by scanning a trajectory once to precompute quantities to be correlated. More...

class	Token

class	TokenMap

class	TorForCorrFunc

class	TorqueAutoCorrFunc

class	Torsion

struct	TorsionData

struct	TorsionDataSet

class	TorsionStamp

class	TorsionType

class	TorsionTypeParser
	"types/TorsionTypeParser.hpp" More...

class	TorsionTypesSectionParser
	"io/TorsionTypesSectionParser.hpp" More...

class	TranslationalOrderParameterR
	Translational Order ParameterR. More...

class	TrappeTorsionType
	"types/TrappeTorsionType.hpp" These torsion types are defined identically with functional form given in the following paper: More...

class	TreeNode

class	Triangle
	Triangle provides geometric data to OpenMD. More...

class	TriangleQuadrature
	A class for integrating a function using numerical quadrature over triangular domains. More...

class	TriangleQuadratureRule
	A "rule" (weights and quadrature points) for computing quadrature over triangular domains. More...

class	TruncatedCube

class	TwoDGofR

class	TypeContainer

class	UFFAdapter

class	UFFAtomTypesSectionParser

struct	UFFAtypeParameters

class	UniformField
	Applies a uniform (vector) electric field to the system. More...

class	UniformGradient
	Applies a uniform electric field gradient to the system. More...

class	UreyBradleyBend

class	UreyBradleyBendType

class	VanDerWaalsInteraction
	The basic interface for van der Waals interactions. More...

class	VCorrFunc

class	VCorrFuncR

class	VCorrFuncZ

class	Vector
	Fix length vector class. More...

class	Vector2

class	Vector3

class	VectorAccumulator

class	VectorTypeData

class	VelAngularVelOutProdCorrFunc

class	Velocitizer
	Velocity-modifying routines. More...

class	VelocityAutoOutProductCorrFunc

class	VelocityField

class	VelocityVerletIntegrator

class	VelocityZ

class	WaterTypeVisitor

class	WCorrFunc

class	WrappingVisitor

class	XiaoGimbutasTriangleQuadratureRule

struct	XYZAtom

class	XYZFormat

class	XYZVisitor

struct	ZconsData

class	ZConsReader

class	ZConsStamp

class	ZConstraintForceModifier

struct	ZconstraintMol

struct	ZconstraintParam

class	ZConsVisitor

class	ZConsWriter

struct	ZeroConstraint

struct	ZhouParameters

Typedefs
using	SnapshotBlock = std::pair<int, int>

typedef DataStorageSnapshot::*	DataStoragePointer

using	TeeBuf = basic_teebuf<char>

using	CubicSplinePtr = std::shared_ptr<CubicSpline>

using	DoublePolynomial = Polynomial<RealType>

using	Quat4d = Quaternion<RealType>

using	Mat6x6d = SquareMatrix<RealType, 6>

using	Mat3x3d = SquareMatrix3<RealType>

using	RotMat3x3d = SquareMatrix3<RealType>

typedef Vector2< int >	Vector2i

typedef Vector2< RealType >	Vector2d

using	Vector3i = Vector3<int>

using	Vector3d = Vector3<RealType>

using	potVec = Vector<RealType, N_INTERACTION_FAMILIES>

using	NonBondedInteractionPtr = std::shared_ptr<NonBondedInteraction>

using	RestraintData = SimpleTypeData<Restraint*>

using	TreeNodePtr = std::shared_ptr<TreeNode>

using	AtomTypeSet = std::set<AtomType*, AtomTypeCompare>

using	DirectionalAtypeData = SimpleTypeData<DirectionalAtypeParameters>

using	EAMData = SimpleTypeData<EAMParameters>

using	FuncflData = SimpleTypeData<FuncflParameters>

using	ZhouData = SimpleTypeData<ZhouParameters>

using	FixedChargeAtypeData = SimpleTypeData<FixedChargeAtypeParameters>

using	FluctuatingAtypeData = SimpleTypeData<FluctuatingAtypeParameters>

using	GBAtypeData = SimpleTypeData<GBAtypeParameters>

using	LJAtypeData = SimpleTypeData<LJAtypeParameters>

using	MultipoleAtypeData = SimpleTypeData<MultipoleAtypeParameters>

using	PolarizableAtypeData = SimpleTypeData<PolarizableAtypeParameters>

using	ShapeAtypeData = SimpleTypeData<ShapeAtomType*>

using	StickyAtypeData = SimpleTypeData<StickyAtypeParameters>

using	SCAtypeData = SimpleTypeData<SCAtypeParameters>

using	UFFAtypeData = SimpleTypeData<UFFAtypeParameters>

using	BoolGenericData = SimpleTypeData<bool>
	BoolGenericData is a generic data type contains a bool variable.

using	IntGenericData = SimpleTypeData<int>
	IntGenericData is a generic data type contains an integer variable.

using	FloatGenericData = SimpleTypeData<float>
	FloatGenericData is a generic data type contains a float variable.

using	DoubleGenericData = SimpleTypeData<RealType>
	DoubleGenericData is a generic data type contains a RealType variable.

using	StringGenericData = SimpleTypeData<std::string>
	A generic data type contains a std::string variable.

using	IntVectorGenericData = VectorTypeData<int>
	A generic data type contains a std::vector<int> variable.

using	FloatVectorGenericData = VectorTypeData<float>

using	DoubleVectorGenericData = VectorTypeData<RealType>

using	StringVectorGenericData = VectorTypeData<std::string>
	A generic data type contains a std::vector<string> variable.

using	ProgressBarPtr = std::unique_ptr<ProgressBar>

using	VisitorIterator = std::list<std::pair<BaseVisitor*, int>>::iterator

Enumerations
enum	CutoffMethod { HARD , SWITCHED , SHIFTED_POTENTIAL , SHIFTED_FORCE , TAYLOR_SHIFTED , EWALD_FULL }

enum	EAMMixingMethod { eamJohnson , eamDaw , eamDream1 , eamDream2 , eamUnknownMix }

enum	ElectrostaticSummationMethod { esm_HARD , esm_SWITCHING_FUNCTION , esm_SHIFTED_POTENTIAL , esm_SHIFTED_FORCE , esm_TAYLOR_SHIFTED , esm_REACTION_FIELD , esm_EWALD_FULL , esm_EWALD_PME , esm_EWALD_SPME }

enum	ElectrostaticScreeningMethod { UNDAMPED , DAMPED }

enum	InteractionFamily { NO_FAMILY = 0 , VANDERWAALS_FAMILY , ELECTROSTATIC_FAMILY = 2 , METALLIC_EMBEDDING_FAMILY , METALLIC_PAIR_FAMILY , HYDROGENBONDING_FAMILY = 5 , BONDED_FAMILY = 6 , N_INTERACTION_FAMILIES = 7 }
	The InteractionFamily enum. More...

enum	SwitchingFunctionType { cubic , fifth_order_poly }

enum	communicatorType { Global = 0 , Row = 1 , Column = 2 }

enum	SelectionType { STUNTDOUBLE = 0 , BOND = 1 , BEND = 2 , TORSION = 3 , INVERSION = 4 , MOLECULE = 5 , N_SELECTIONTYPES = 6 }
	The SelectionType enum. More...

enum	BuckinghamType { btTraditional , btModified , btUnknown }

enum	EAMType { eamFuncfl , eamZhou2001 , eamZhou2004 , eamZhou2005 , eamZhou2005Oxygen , eamZhouRose , eamOxygenFuncfl , eamUnknown }

enum	EAMiType { eamitTabulated , eamitZhou , eamitOxides }

enum	InversionKey { itAngle , itCosAngle }

enum	MorseType { mtShifted , mtRepulsive , mtUnknown }

Functions
	for (sd=seleMan1_.beginSelected(isd1);sd !=NULL;sd=seleMan1_.nextSelected(isd1))

std::ostream &	operator<< (std::ostream &o, PairList &e)

void	registerIntegrators ()
	Register all integrators.

void	registerOptimizers ()
	Register all optimizers.

void	registerLattice ()
	Register all lattice.

void	registerAll ()
	register force fields, integrators and optimizers

int	getGlobalCountOfType (AtomType *)

ostream &	operator<< (ostream &o, SimInfo &)

bool	pairCompare (const pair< RealType, int > &l, const pair< RealType, int > &r)

template<class Cont , class Predict >
void	swap_if (Cont &b1, Cont &b2, Predict predict)

std::ostream &	operator<< (std::ostream &o, HydrodynamicsModelFactory &factory)
	write out all of the type identifiers to an output stream

Mesh	operator+ (const Mesh &m1, const Mesh &m2)

std::ostream &	operator<< (std::ostream &o, IntegratorFactory &factory)
	write out all of the type identifiers to an output stream

NotEmptyConstraint	isNotEmpty ()

ZeroConstraint	isZero ()

ParamConstraintFacade< NonZeroConstraint >	isNonZero ()

PositiveConstraint	isPositive ()

NonPositiveConstraint	isNonPositive ()

NegativeConstraint	isNegative ()

NonNegativeConstraint	isNonNegative ()

EqualIgnoreCaseConstraint	isEqualIgnoreCase (std::string str)

EvenConstraint	isEven ()

template<typename Cons1T , typename Cons2T >
AndParamConstraint< Cons1T, Cons2T >	operator&& (const ParamConstraintFacade< Cons1T > &cons1, const ParamConstraintFacade< Cons2T > &cons2)

template<typename Cons1T , typename Cons2T >
OrParamConstraint< Cons1T, Cons2T >	operator\|\| (const ParamConstraintFacade< Cons1T > &cons1, const ParamConstraintFacade< Cons2T > &cons2)

template<typename ConsT >
NotParamConstraint< ConsT >	operator! (const ParamConstraintFacade< ConsT > &cons)

template<typename T >
LessThanConstraint< T >	isLessThan (T &v)

template<typename T >
LessThanOrEqualToConstraint< T >	isLessThanOrEqualTo (T &v)

template<typename T >
EqualConstraint< T >	isEqual (T &v)

template<typename T >
GreaterThanConstraint< T >	isGreaterThan (T &v)

template<typename T >
GreaterThanOrEqualTo< T >	isGreaterThanOrEqualTo (T &v)

std::ostream &	operator<< (std::ostream &o, LatticeFactory &factory)
	write out all of the type identifiers to an output stream

template<class MatrixType >
void	CholeskyDecomposition (MatrixType &A, MatrixType &L)

template<typename Real >
DynamicRectMatrix< Real >	operator- (const DynamicRectMatrix< Real > &m)
	Negate the value of every element of this matrix.

template<typename Real >
DynamicRectMatrix< Real >	operator+ (const DynamicRectMatrix< Real > &m1, const DynamicRectMatrix< Real > &m2)
	Return the sum of two matrixes (m1 + m2).

template<typename Real >
DynamicRectMatrix< Real >	operator- (const DynamicRectMatrix< Real > &m1, const DynamicRectMatrix< Real > &m2)
	Return the difference of two matrixes (m1 - m2).

template<typename Real >
DynamicRectMatrix< Real >	operator* (const DynamicRectMatrix< Real > &m, Real s)
	Return the multiplication of scalar and matrix (m * s).

template<typename Real >
DynamicRectMatrix< Real >	operator* (Real s, const DynamicRectMatrix< Real > &m)
	Return the multiplication of a scalar and a matrix (s * m).

template<typename Real >
DynamicRectMatrix< Real >	operator* (const DynamicRectMatrix< Real > &m1, const DynamicRectMatrix< Real > &m2)
	Return the multiplication of two matrixes (m1 * m2).

template<typename Real >
DynamicVector< Real >	operator* (const DynamicRectMatrix< Real > &m, const DynamicVector< Real > &v)
	Return the multiplication of a matrix and a vector (m * v).

template<typename Real >
DynamicRectMatrix< Real >	operator/ (const DynamicRectMatrix< Real > &m, Real s)
	Return the scalar division of matrix (m / s).

template<typename Real >
std::ostream &	operator<< (std::ostream &o, const DynamicRectMatrix< Real > &m)
	Write to an output stream.

template<typename Real >
DynamicVector< Real >	operator- (const DynamicVector< Real > &v1)
	unary minus

template<typename Real >
DynamicVector< Real >	operator+ (const DynamicVector< Real > &v1, const DynamicVector< Real > &v2)
	Return the sum of two vectors (v1 - v2).

template<typename Real >
DynamicVector< Real >	operator- (const DynamicVector< Real > &v1, const DynamicVector< Real > &v2)
	Return the difference of two vectors (v1 - v2).

template<typename Real >
DynamicVector< Real >	operator* (const DynamicVector< Real > &v1, Real s)
	Returns the vaule of scalar multiplication of this vector v1 (v1 * r).

template<typename Real >
DynamicVector< Real >	operator* (Real s, const DynamicVector< Real > &v1)
	Returns the vaule of scalar multiplication of this vector v1 (v1 * r).

template<typename Real >
DynamicVector< Real >	operator/ (const DynamicVector< Real > &v1, Real s)
	Returns the value of division of a vector by a scalar.

template<typename Real >
Real	dot (const DynamicVector< Real > &v1, const DynamicVector< Real > &v2)
	Returns the dot product of two DynamicVectors.

template<typename Real >
Real	distance (const DynamicVector< Real > &v1, const DynamicVector< Real > &v2)
	Returns the distance between two DynamicVectors.

template<typename Real >
Real	distanceSquare (const DynamicVector< Real > &v1, const DynamicVector< Real > &v2)
	Returns the squared distance between two DynamicVectors.

template<typename Real >
std::ostream &	operator<< (std::ostream &strm, const DynamicVector< Real > &v)
	Write to an output stream.

template<class MatrixType >
bool	invertMatrix (MatrixType &A, MatrixType &AI)
	Invert input square matrix A into matrix AI.

template<class MatrixType >
bool	invertMatrix (MatrixType &A, MatrixType &AI, unsigned int size, int *tmp1Size, typename MatrixType::ElemPoinerType tmp2Size)
	Invert input square matrix A into matrix AI (Thread safe versions).

template<class MatrixType >
int	LUFactorLinearSystem (MatrixType &A, int *index, int size, typename MatrixType::ElemPoinerType tmpSize)
	Factor linear equations Ax = b using LU decompostion A = LU where L is lower triangular matrix and U is upper triangular matrix.

template<class MatrixType >
void	LUSolveLinearSystem (MatrixType &A, int *index, typename MatrixType::ElemPoinerType x, int size)
	Solve linear equations Ax = b using LU decompostion A = LU where L is lower triangular matrix and U is upper triangular matrix.

template<typename Real >
Real	fastpow (Real x, int N)

template<typename Real >
Polynomial< Real >	operator* (const Polynomial< Real > &p1, const Polynomial< Real > &p2)
	Generates and returns the product of two given Polynomials.

template<typename Real >
Polynomial< Real >	operator* (const Polynomial< Real > &p, const Real v)

template<typename Real >
Polynomial< Real >	operator* (const Real v, const Polynomial< Real > &p)

template<typename Real >
Polynomial< Real >	operator+ (const Polynomial< Real > &p1, const Polynomial< Real > &p2)
	Generates and returns the sum of two given Polynomials.

template<typename Real >
Polynomial< Real >	operator- (const Polynomial< Real > &p1, const Polynomial< Real > &p2)
	Generates and returns the difference of two given Polynomials.

template<typename Real >
Polynomial< Real > *	getDerivative (const Polynomial< Real > &p1)
	Returns the first derivative of this polynomial.

template<typename Real >
bool	equal (const Polynomial< Real > &p1, const Polynomial< Real > &p2)
	Tests if two polynomial have the same exponents.

template<typename Real , unsigned int Dim>
Quaternion< Real >	operator* (const Quaternion< Real > &q, Real s)
	Returns the vaule of scalar multiplication of this quaterion q (q * s).

template<typename Real , unsigned int Dim>
Quaternion< Real >	operator* (const Real &s, const Quaternion< Real > &q)
	Returns the vaule of scalar multiplication of this quaterion q (q * s).

template<typename Real >
Quaternion< Real >	operator* (const Quaternion< Real > &q1, const Quaternion< Real > &q2)
	Returns the multiplication of two quaternion.

template<typename Real >
Quaternion< Real >	operator/ (Quaternion< Real > &q1, Quaternion< Real > &q2)
	Returns the division of two quaternion.

template<typename Real >
Quaternion< Real >	operator/ (const Real &s, Quaternion< Real > &q)
	Returns the value of the division of a scalar by a quaternion.

template<class T >
bool	operator== (const Quaternion< T > &lhs, const Quaternion< T > &rhs)

template<typename Real , unsigned int Row, unsigned int Col>
RectMatrix< Real, Row, Col >	operator- (const RectMatrix< Real, Row, Col > &m)
	Negate the value of every element of this matrix.

template<typename Real , unsigned int Row, unsigned int Col>
RectMatrix< Real, Row, Col >	operator+ (const RectMatrix< Real, Row, Col > &m1, const RectMatrix< Real, Row, Col > &m2)
	Return the sum of two matrixes (m1 + m2).

template<typename Real , unsigned int Row, unsigned int Col>
RectMatrix< Real, Row, Col >	operator- (const RectMatrix< Real, Row, Col > &m1, const RectMatrix< Real, Row, Col > &m2)
	Return the difference of two matrixes (m1 - m2).

template<typename Real , unsigned int Row, unsigned int Col>
RectMatrix< Real, Row, Col >	operator* (const RectMatrix< Real, Row, Col > &m, Real s)
	Return the multiplication of scalra and matrix (m * s).

template<typename Real , unsigned int Row, unsigned int Col>
RectMatrix< Real, Row, Col >	operator* (Real s, const RectMatrix< Real, Row, Col > &m)
	Return the multiplication of a scalra and a matrix (s * m).

template<typename Real , unsigned int Row, unsigned int Col, unsigned int SameDim>
RectMatrix< Real, Row, Col >	operator* (const RectMatrix< Real, Row, SameDim > &m1, const RectMatrix< Real, SameDim, Col > &m2)
	Return the multiplication of two matrixes (m1 * m2).

template<typename Real , unsigned int Row, unsigned int Col>
Vector< Real, Row >	operator* (const RectMatrix< Real, Row, Col > &m, const Vector< Real, Col > &v)
	Returns the multiplication of a matrix and a vector (m * v).

template<typename Real , unsigned int Row, unsigned int Col>
Vector< Real, Col >	operator* (const Vector< Real, Row > &v, const RectMatrix< Real, Row, Col > &m)
	Returns the multiplication of a vector transpose and a matrix (v^T * m).

template<typename Real , unsigned int Row, unsigned int Col>
RectMatrix< Real, Row, Col >	operator/ (const RectMatrix< Real, Row, Col > &m, Real s)
	Return the scalar division of matrix (m / s).

template<typename Real , unsigned int Row, unsigned int Col>
Real	doubleDot (const RectMatrix< Real, Row, Col > &t1, const RectMatrix< Real, Row, Col > &t2)
	Returns the tensor contraction (double dot product) of two rank 2 tensors (or Matrices)

template<typename Real , unsigned int Row, unsigned int Col>
Vector< Real, Row >	mCross (const RectMatrix< Real, Row, Col > &t1, const RectMatrix< Real, Row, Col > &t2)
	Returns the vector (cross) product of two matrices.

template<typename Real , unsigned int Row, unsigned int Col>
std::ostream &	operator<< (std::ostream &o, const RectMatrix< Real, Row, Col > &m)
	Write to an output stream.

template<typename Real >
SquareMatrix3< Real >	operator* (const SquareMatrix3< Real > &m1, const SquareMatrix3< Real > &m2)
	Return the multiplication of two matrixes (m1 * m2).

template<typename Real >
SquareMatrix3< Real >	outProduct (const Vector3< Real > &v1, const Vector3< Real > &v2)

template<typename T >
bool	equal (T e1, T e2)

template<typename Real , unsigned int Dim>
Vector< Real, Dim >	operator- (const Vector< Real, Dim > &v1)
	unary minus

template<typename Real , unsigned int Dim>
Vector< Real, Dim >	operator+ (const Vector< Real, Dim > &v1, const Vector< Real, Dim > &v2)
	Return the sum of two vectors (v1 - v2).

template<typename Real , unsigned int Dim>
Vector< Real, Dim >	operator- (const Vector< Real, Dim > &v1, const Vector< Real, Dim > &v2)
	Return the difference of two vectors (v1 - v2).

template<typename Real , unsigned int Dim>
Vector< Real, Dim >	operator* (const Vector< Real, Dim > &v1, Real s)
	Returns the vaule of scalar multiplication of this vector v1 (v1 * r).

template<typename Real , unsigned int Dim>
Vector< Real, Dim >	operator* (Real s, const Vector< Real, Dim > &v1)
	Returns the vaule of scalar multiplication of this vector v1 (v1 * r).

template<typename Real , unsigned int Dim>
Vector< Real, Dim >	operator/ (const Vector< Real, Dim > &v1, Real s)
	Returns the value of division of a vector by a scalar.

template<typename Real , unsigned int Dim>
Real	dot (const Vector< Real, Dim > &v1, const Vector< Real, Dim > &v2)
	Returns the dot product of two Vectors.

template<typename Real , unsigned int Dim>
Real	dot (const Vector< Real, Dim > &v1, const Vector< Real, Dim > &v2, const Vector< Real, Dim > &v3)
	Returns the wide dot product of three Vectors.

template<typename Real , unsigned int Dim>
Real	distance (const Vector< Real, Dim > &v1, const Vector< Real, Dim > &v2)
	Returns the distance between two Vectors.

template<typename Real , unsigned int Dim>
Real	distanceSquare (const Vector< Real, Dim > &v1, const Vector< Real, Dim > &v2)
	Returns the squared distance between two Vectors.

template<typename Real , unsigned int Dim>
std::ostream &	operator<< (std::ostream &o, const Vector< Real, Dim > &v)
	Write to an output stream.

std::size_t	Vlinear (const Vector2< std::size_t > &p, const Vector2< std::size_t > &s)
	Returns the linear indexing for size_t vectors.

template<typename Real >
Vector3< Real >	cross (const Vector3< Real > &v1, const Vector3< Real > &v2)
	Returns the cross product of two Vectors.

template<typename Real >
Real	Vlinear (const Vector3< Real > &p, const Vector3< Real > &s)
	Returns the linear indexing for integer vectors.

std::ostream &	operator<< (std::ostream &o, OptimizationFactory &factory)
	write out all of the type identifiers to an output stream

std::ostream &	operator<< (std::ostream &o, Molecule &mol)

SelectionManager	operator\| (const SelectionManager &sman1, const SelectionManager &sman2)

SelectionManager	operator& (const SelectionManager &sman1, const SelectionManager &sman2)

SelectionManager	operator^ (const SelectionManager &sman1, const SelectionManager &sman2)

SelectionManager	operator- (const SelectionManager &sman1, const SelectionManager &sman2)

SelectionSet	operator\| (const SelectionSet &ss1, const SelectionSet &ss2)

SelectionSet	operator& (const SelectionSet &ss1, const SelectionSet &ss2)

SelectionSet	operator^ (const SelectionSet &ss1, const SelectionSet &ss2)

SelectionSet	operator- (const SelectionSet &ss1, const SelectionSet &ss2)

bool	operator== (const SelectionSet &ss1, const SelectionSet &ss2)

std::ostream &	operator<< (std::ostream &os, const SelectionSet &ss)

std::ostream &	operator<< (std::ostream &os, AmberImproperTorsionType &ott)

template<class ContainerType >
bool	hasDuplicateElement (const ContainerType &cont)

std::ostream &	operator<< (std::ostream &os, HarmonicInversionType &hit)

std::ostream &	operator<< (std::ostream &os, HarmonicTorsionType &htt)

std::ostream &	operator<< (std::ostream &os, OplsTorsionType &ott)

std::ostream &	operator<< (std::ostream &os, PolynomialBendType &pbt)

std::ostream &	operator<< (std::ostream &os, PolynomialBondType &pbt)

std::ostream &	operator<< (std::ostream &os, TrappeTorsionType &ttt)

template<typename Container >
void	toLower (Container &cont, const std::locale &loc=std::locale())

template<typename Container >
Container	toLowerCopy (const Container &cont, const std::locale &=std::locale())

template<typename Container >
void	toUpper (Container &cont, const std::locale &loc=std::locale())

template<typename Container >
Container	toUpperCopy (const Container &cont, const std::locale &=std::locale())

template<typename O , typename I , typename C >
std::ostream &	operator<< (std::ostream &o, GenericFactory< O, I, C > &factory)
	write out all of the type identifiers to an output stream

template<class RandomAccessIterator >
bool	next_combination (std::vector< RandomAccessIterator > &iterContainer, RandomAccessIterator first, RandomAccessIterator last)
	STL next_permuation-like combination sequence generator.

OpenMDBitSet	operator\| (const OpenMDBitSet &bs1, const OpenMDBitSet &bs2)

OpenMDBitSet	operator& (const OpenMDBitSet &bs1, const OpenMDBitSet &bs2)

OpenMDBitSet	operator^ (const OpenMDBitSet &bs1, const OpenMDBitSet &bs2)

OpenMDBitSet	operator- (const OpenMDBitSet &bs1, const OpenMDBitSet &bs2)

bool	operator== (const OpenMDBitSet &bs1, const OpenMDBitSet &bs2)

std::ostream &	operator<< (std::ostream &os, const OpenMDBitSet &bs)

std::string	UpperCase (const std::string &S)
	Converts a string to UPPER CASE.

int	findBegin (std::istream &theStream, const char *startText)
	Finds the location of the string "begin <startText>" in an input stream.

int	isEndLine (char *line)
	discovers whether or not the line contains the "end" token

std::string	OpenMD_itoa (int value, unsigned int base)

std::string	getPrefix (const std::string &str)

bool	isInteger (const std::string &str)

bool	CaseInsensitiveEquals (const char ch1, const char ch2)

size_t	CaseInsensitiveFind (const std::string &str1, const std::string &str2)

template<typename T >
std::string	toString (const T &v)
	Convert a variable to a string.

template<typename T >
T	lexi_cast (const std::string &str)

template<typename T >
bool	isType (const std::string &str)

template<class ContainerType >
std::string	containerToString (const ContainerType &cont)

bool	replaceWithWildCard (std::vector< std::vector< std::string >::iterator > &cont, std::vector< std::string > &sequence, std::vector< std::string > &result, const std::string &wildCard="X")
	iteratively replace the sequence with wild cards

RealType	roundMe (const RealType &x)

Variables
const Mat3x3d	M3Zero (0.0)

static constexpr RealType	epsilon = 0.000001

const Vector2d	V2Zero (0.0, 0.0)

const Vector2d	V2X (1.0, 0.0)

const Vector2d	V2Y (0.0, 1.0)

const Vector3d	V3Zero (0.0, 0.0, 0.0)

const Vector3d	V3X (1.0, 0.0, 0.0)

const Vector3d	V3Y (0.0, 1.0, 0.0)

const Vector3d	V3Z (0.0, 0.0, 1.0)

static const int	ELECTROSTATIC_INTERACTION = (1 << 0)
	Boolean flags for the iHash_ and sHash_ data structures.

static const int	LJ_INTERACTION = (1 << 1)

static const int	EAM_INTERACTION = (1 << 2)

static const int	SC_INTERACTION = (1 << 3)

static const int	STICKY_INTERACTION = (1 << 4)

static const int	GB_INTERACTION = (1 << 5)

static const int	MORSE_INTERACTION = (1 << 6)

static const int	REPULSIVEPOWER_INTERACTION = (1 << 7)

static const int	MAW_INTERACTION = (1 << 8)

static const int	MIE_INTERACTION = (1 << 9)

static const int	BUCKINGHAM_INTERACTION = (1 << 10)

static const int	INVERSEPOWERSERIES_INTERACTION = (1 << 11)

string const	DirectionalTypeID = "Directional"

string const	EAMtypeID = "EAM"

string const	FuncflTypeID = "FUNCFL"

string const	ZhouTypeID = "ZHOU"

string const	ZhouRoseTypeID = "ZHOUROSE"

string const	FCtypeID = "Charge"

string const	FQtypeID = "FlucQ"

string const	GBtypeID = "GB"

string const	LJtypeID = "LJ"

string const	MultipoleTypeID = "Multipole"

string const	PolTypeID = "Polarizable"

string const	StickyTypeID = "Sticky"

string const	SCtypeID = "SC"

string const	UFFtypeID = "UFF"

ElementsTable	etab

const char *	progressSpinner_ = "\|/-\\"

Detailed Description

This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.

The code has been modified to match the OpenMD coding style.

We have retained the OpenBabel copyright and GPL license on this class:

This file is part of the Open Babel project. For more information, see http://openbabel.sourceforge.net/

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation version 2 of the License.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Typedef Documentation

◆ AtomTypeSet

using OpenMD::AtomTypeSet = std::set<AtomType*, AtomTypeCompare>

Definition at line 168 of file AtomType.hpp.

◆ BoolGenericData

using OpenMD::BoolGenericData = SimpleTypeData<bool>

BoolGenericData is a generic data type contains a bool variable.

Definition at line 147 of file GenericData.hpp.

◆ CubicSplinePtr

using OpenMD::CubicSplinePtr = std::shared_ptr<CubicSpline>

Definition at line 95 of file CubicSpline.hpp.

◆ DataStoragePointer

typedef DataStorageSnapshot::* OpenMD::DataStoragePointer

Definition at line 356 of file Snapshot.hpp.

◆ DirectionalAtypeData

using OpenMD::DirectionalAtypeData = SimpleTypeData<DirectionalAtypeParameters>

Definition at line 60 of file DirectionalAdapter.hpp.

◆ DoubleGenericData

using OpenMD::DoubleGenericData = SimpleTypeData<RealType>

DoubleGenericData is a generic data type contains a RealType variable.

Definition at line 156 of file GenericData.hpp.

◆ DoublePolynomial

using OpenMD::DoublePolynomial = Polynomial<RealType>

Definition at line 625 of file Polynomial.hpp.

◆ DoubleVectorGenericData

using OpenMD::DoubleVectorGenericData = VectorTypeData<RealType>

Definition at line 224 of file GenericData.hpp.

◆ EAMData

using OpenMD::EAMData = SimpleTypeData<EAMParameters>

Definition at line 128 of file EAMAdapter.hpp.

◆ FixedChargeAtypeData

using OpenMD::FixedChargeAtypeData = SimpleTypeData<FixedChargeAtypeParameters>

Definition at line 59 of file FixedChargeAdapter.hpp.

◆ FloatGenericData

using OpenMD::FloatGenericData = SimpleTypeData<float>

FloatGenericData is a generic data type contains a float variable.

Definition at line 153 of file GenericData.hpp.

◆ FloatVectorGenericData

using OpenMD::FloatVectorGenericData = VectorTypeData<float>

Definition at line 218 of file GenericData.hpp.

◆ FluctuatingAtypeData

using OpenMD::FluctuatingAtypeData = SimpleTypeData<FluctuatingAtypeParameters>

Definition at line 69 of file FluctuatingChargeAdapter.hpp.

◆ FuncflData

using OpenMD::FuncflData = SimpleTypeData<FuncflParameters>

Definition at line 129 of file EAMAdapter.hpp.

◆ GBAtypeData

using OpenMD::GBAtypeData = SimpleTypeData<GBAtypeParameters>

Definition at line 64 of file GayBerneAdapter.hpp.

◆ IntGenericData

using OpenMD::IntGenericData = SimpleTypeData<int>

IntGenericData is a generic data type contains an integer variable.

Definition at line 150 of file GenericData.hpp.

◆ IntVectorGenericData

OpenMD::IntVectorGenericData = VectorTypeData<int>

A generic data type contains a std::vector<int> variable.

A generic data type contains a std::vector<RealType> variable.

A generic data type contains a std::vector<float> variable.

Definition at line 212 of file GenericData.hpp.

◆ LJAtypeData

using OpenMD::LJAtypeData = SimpleTypeData<LJAtypeParameters>

Definition at line 61 of file LennardJonesAdapter.hpp.

◆ Mat3x3d

using OpenMD::Mat3x3d = SquareMatrix3<RealType>

Definition at line 641 of file SquareMatrix3.hpp.

◆ Mat6x6d

using OpenMD::Mat6x6d = SquareMatrix<RealType, 6>

Definition at line 444 of file SquareMatrix.hpp.

◆ MultipoleAtypeData

using OpenMD::MultipoleAtypeData = SimpleTypeData<MultipoleAtypeParameters>

Definition at line 63 of file MultipoleAdapter.hpp.

◆ NonBondedInteractionPtr

using OpenMD::NonBondedInteractionPtr = std::shared_ptr<NonBondedInteraction>

Definition at line 209 of file NonBondedInteraction.hpp.

◆ PolarizableAtypeData

using OpenMD::PolarizableAtypeData = SimpleTypeData<PolarizableAtypeParameters>

Definition at line 60 of file PolarizableAdapter.hpp.

◆ potVec

using OpenMD::potVec = Vector<RealType, N_INTERACTION_FAMILIES>

Definition at line 94 of file NonBondedInteraction.hpp.

◆ ProgressBarPtr

using OpenMD::ProgressBarPtr = std::unique_ptr<ProgressBar>

Definition at line 70 of file ProgressBar.hpp.

◆ Quat4d

using OpenMD::Quat4d = Quaternion<RealType>

Definition at line 627 of file Quaternion.hpp.

◆ RestraintData

using OpenMD::RestraintData = SimpleTypeData<Restraint*>

Definition at line 191 of file Restraint.hpp.

◆ RotMat3x3d

using OpenMD::RotMat3x3d = SquareMatrix3<RealType>

Definition at line 642 of file SquareMatrix3.hpp.

◆ SCAtypeData

using OpenMD::SCAtypeData = SimpleTypeData<SCAtypeParameters>

Definition at line 64 of file SuttonChenAdapter.hpp.

◆ ShapeAtypeData

using OpenMD::ShapeAtypeData = SimpleTypeData<ShapeAtomType*>

Definition at line 116 of file ShapeAtomType.hpp.

◆ SnapshotBlock

using OpenMD::SnapshotBlock = std::pair<int, int>

Definition at line 57 of file BlockSnapshotManager.hpp.

◆ StickyAtypeData

using OpenMD::StickyAtypeData = SimpleTypeData<StickyAtypeParameters>

Definition at line 67 of file StickyAdapter.hpp.

◆ StringGenericData

OpenMD::StringGenericData = SimpleTypeData<std::string>

A generic data type contains a std::string variable.

StringGenericData* s = new StringGenericData("MyStringGenericData");
PropertyMap propMap;
GenericData* gdata;
 
s->setData("OpenMD");
propMap->addProperty(s);
 
gdata = propMap->getPropertyByName("MyStringGenericData");
if (gdata != NULL){
  s = dynamic_cast<StringGenericData*>(gdata);
  if (s != NULL)
    std::cout << s->getData() << std::endl;
}

Definition at line 179 of file GenericData.hpp.

◆ StringVectorGenericData

OpenMD::StringVectorGenericData = VectorTypeData<std::string>

A generic data type contains a std::vector<string> variable.

 StringVectorGenericData* sv = new
StringVectorGenericData("MyStringVector"); GenericData* gdata; PropertyMap
propMap; std::vector<std::string>::iterator iter;
 
 sv->push_back("Hello World");
 sv->push_back("OpenMD");
 
 propMap.addProperty(sv);
 
 gdata = propMap.getPropertyByName("MyStringVector");
 
 if (gdata != NULL){
 
   sv = dynamic_cast<StringVectorGenericData*>(gdata);
 
   if (sv != NULL){
     for (iter = sv->begin(); iter != sv->end(); ++ iter)
       std::cout << *iter << std::endl;
   }
 }

Definition at line 253 of file GenericData.hpp.

◆ TeeBuf

using OpenMD::TeeBuf = basic_teebuf<char>

Definition at line 116 of file basic_teebuf.hpp.

◆ TreeNodePtr

using OpenMD::TreeNodePtr = std::shared_ptr<TreeNode>

Definition at line 65 of file NameFinder.hpp.

◆ UFFAtypeData

using OpenMD::UFFAtypeData = SimpleTypeData<UFFAtypeParameters>

Definition at line 70 of file UFFAdapter.hpp.

◆ Vector2d

typedef Vector2<RealType> OpenMD::Vector2d

Definition at line 118 of file Vector2.hpp.

◆ Vector2i

typedef Vector2<int> OpenMD::Vector2i

Definition at line 116 of file Vector2.hpp.

◆ Vector3d

using OpenMD::Vector3d = Vector3<RealType>

Definition at line 160 of file Vector3.hpp.

◆ Vector3i

using OpenMD::Vector3i = Vector3<int>

Definition at line 158 of file Vector3.hpp.

◆ VisitorIterator

using OpenMD::VisitorIterator = std::list<std::pair<BaseVisitor*, int>>::iterator

Definition at line 55 of file CompositeVisitor.hpp.

◆ ZhouData

using OpenMD::ZhouData = SimpleTypeData<ZhouParameters>

Definition at line 130 of file EAMAdapter.hpp.

Enumeration Type Documentation

◆ BuckinghamType

enum OpenMD::BuckinghamType

Definition at line 72 of file BuckinghamInteractionType.hpp.

◆ communicatorType

enum OpenMD::communicatorType

Definition at line 58 of file Communicator.hpp.

◆ CutoffMethod

enum OpenMD::CutoffMethod

Definition at line 50 of file Cutoffs.hpp.

◆ EAMiType

enum OpenMD::EAMiType

Definition at line 65 of file EAMInteractionType.hpp.

◆ EAMMixingMethod

enum OpenMD::EAMMixingMethod

Definition at line 82 of file EAM.hpp.

◆ EAMType

enum OpenMD::EAMType

Definition at line 61 of file EAMAdapter.hpp.

◆ ElectrostaticScreeningMethod

enum OpenMD::ElectrostaticScreeningMethod

Definition at line 86 of file Electrostatic.hpp.

◆ ElectrostaticSummationMethod

enum OpenMD::ElectrostaticSummationMethod

Enumerator
esm_EWALD_PME	PME Ewald methods aren't supported yet.
esm_EWALD_SPME	SPME Ewald methods aren't supported yet.

Definition at line 74 of file Electrostatic.hpp.

◆ InteractionFamily

enum OpenMD::InteractionFamily

The InteractionFamily enum.

This is used to sort different types of non-bonded interaction and to prevent multiple interactions in the same family from being applied to any given pair of atom types.

Enumerator
NO_FAMILY	No family defined.
VANDERWAALS_FAMILY	Long-range dispersion and short-range pauli repulsion.
ELECTROSTATIC_FAMILY	Coulombic and point-multipole interactions.
METALLIC_EMBEDDING_FAMILY	Transition metal interactions involving electron density.
METALLIC_PAIR_FAMILY	Transition metal interactions involving pair potentials.
HYDROGENBONDING_FAMILY	Short-range directional interactions.
BONDED_FAMILY	directly bonded 1-2, 1-3, or 1-4 interactions

Definition at line 62 of file NonBondedInteraction.hpp.

◆ InversionKey

enum OpenMD::InversionKey

Definition at line 59 of file InversionType.hpp.

◆ MorseType

enum OpenMD::MorseType

Definition at line 65 of file MorseInteractionType.hpp.

◆ SelectionType

enum OpenMD::SelectionType

The SelectionType enum.

This is used to sort different types of selections by object type

Enumerator
STUNTDOUBLE	StuntDoubles (Atoms & RigidBodies)
BOND	Bonds.
BEND	Bends.
TORSION	Torsions.
INVERSION	Inversions.
MOLECULE	Molecules.

Definition at line 60 of file SelectionSet.hpp.

◆ SwitchingFunctionType

enum OpenMD::SwitchingFunctionType

Definition at line 53 of file SwitchingFunction.hpp.

Function Documentation

◆ CaseInsensitiveEquals()

bool OpenMD::CaseInsensitiveEquals	(	const char	ch1,
		const char	ch2 )

Definition at line 187 of file StringUtils.cpp.

◆ CaseInsensitiveFind()

size_t OpenMD::CaseInsensitiveFind	(	const std::string &	str1,
		const std::string &	str2 )

Definition at line 191 of file StringUtils.cpp.

◆ CholeskyDecomposition()

template<class MatrixType >

void OpenMD::CholeskyDecomposition	(	MatrixType &	A,
		MatrixType &	L )

Definition at line 54 of file CholeskyDecomposition.hpp.

◆ containerToString()

template<class ContainerType >

std::string OpenMD::containerToString ( const ContainerType & cont )

Definition at line 129 of file StringUtils.hpp.

◆ cross()

template<typename Real >

Vector3< Real > OpenMD::cross	(	const Vector3< Real > &	v1,
		const Vector3< Real > &	v2 )

inline

Returns the cross product of two Vectors.

Parameters

v1	first vector
v2	second vector

Returns: the cross product of v1 and v2

Definition at line 136 of file Vector3.hpp.

References OpenMD::Vector3< Real >::x(), OpenMD::Vector3< Real >::y(), and OpenMD::Vector3< Real >::z().

Referenced by OpenMD::GhostBend::calcForce(), OpenMD::MolecularRestraint::calcForce(), OpenMD::SquareMatrix3< Real >::diagonalize(), OpenMD::Quaternion< Real >::fromShortestArc(), OpenMD::Thermo::getAngularMomentum(), OpenMD::Thermo::getInertiaTensor(), OpenMD::Inversion::getValue(), OpenMD::Torsion::getValue(), and OpenMD::Velocitizer::removeAngularDrift().

◆ distance() [1/2]

template<typename Real >

Real OpenMD::distance	(	const DynamicVector< Real > &	v1,
		const DynamicVector< Real > &	v2 )

inline

Returns the distance between two DynamicVectors.

Parameters

v1	first vector
v2	second vector

Returns: the distance between v1 and v2

Definition at line 456 of file DynamicVector.hpp.

References OpenMD::DynamicVector< Real, Alloc >::length().

Referenced by OpenMD::shapedLatticeRod::isInterior().

◆ distance() [2/2]

template<typename Real , unsigned int Dim>

Real OpenMD::distance	(	const Vector< Real, Dim > &	v1,
		const Vector< Real, Dim > &	v2 )

inline

Returns the distance between two Vectors.

Parameters

v1	first vector
v2	second vector

Returns: the distance between v1 and v2

Definition at line 546 of file Vector.hpp.

References OpenMD::Vector< Real, Dim >::length().

◆ distanceSquare() [1/2]

template<typename Real >

Real OpenMD::distanceSquare	(	const DynamicVector< Real > &	v1,
		const DynamicVector< Real > &	v2 )

inline

Returns the squared distance between two DynamicVectors.

Parameters

v1	first vector
v2	second vector

Returns: the squared distance between v1 and v2

Definition at line 469 of file DynamicVector.hpp.

References OpenMD::DynamicVector< Real, Alloc >::lengthSquare().

◆ distanceSquare() [2/2]

template<typename Real , unsigned int Dim>

Real OpenMD::distanceSquare	(	const Vector< Real, Dim > &	v1,
		const Vector< Real, Dim > &	v2 )

inline

Returns the squared distance between two Vectors.

Parameters

v1	first vector
v2	second vector

Returns: the squared distance between v1 and v2

Definition at line 559 of file Vector.hpp.

References OpenMD::Vector< Real, Dim >::lengthSquare().

◆ dot() [1/3]

template<typename Real >

Real OpenMD::dot	(	const DynamicVector< Real > &	v1,
		const DynamicVector< Real > &	v2 )

inline

Returns the dot product of two DynamicVectors.

Parameters

v1	first vector
v2	second vector

Returns: the dot product of v1 and v2

Definition at line 438 of file DynamicVector.hpp.

Referenced by OpenMD::Bend::calcForce(), OpenMD::GhostBend::calcForce(), OpenMD::MolecularRestraint::calcForce(), OpenMD::Quaternion< Real >::fromShortestArc(), OpenMD::Bend::getValue(), OpenMD::Inversion::getValue(), OpenMD::Torsion::getValue(), OpenMD::DynamicVector< Real, Alloc >::lengthSquare(), and OpenMD::Vector< Real, Dim >::lengthSquare().

◆ dot() [2/3]

template<typename Real , unsigned int Dim>

Real OpenMD::dot	(	const Vector< Real, Dim > &	v1,
		const Vector< Real, Dim > &	v2 )

inline

Returns the dot product of two Vectors.

Parameters

v1	first vector
v2	second vector

Returns: the dot product of v1 and v2

Definition at line 508 of file Vector.hpp.

◆ dot() [3/3]

template<typename Real , unsigned int Dim>

Real OpenMD::dot	(	const Vector< Real, Dim > &	v1,
		const Vector< Real, Dim > &	v2,
		const Vector< Real, Dim > &	v3 )

inline

Returns the wide dot product of three Vectors.

Compare with Rapaport's VWDot function.

Parameters

v1	first vector
v2	second vector
v3	third vector

Returns: the wide dot product of v1, v2, and v3.

Definition at line 528 of file Vector.hpp.

◆ doubleDot()

template<typename Real , unsigned int Row, unsigned int Col>

Real OpenMD::doubleDot	(	const RectMatrix< Real, Row, Col > &	t1,
		const RectMatrix< Real, Row, Col > &	t2 )

inline

Returns the tensor contraction (double dot product) of two rank 2 tensors (or Matrices)

\[ \mathbf{A} \colon \! \mathbf{B} = \sum_\alpha \sum_\beta \mathbf{A}_{\alpha \beta} B_{\alpha \beta} \]

Parameters

t1	first tensor
t2	second tensor

Returns: the tensor contraction (double dot product) of t1 and t2

Definition at line 602 of file RectMatrix.hpp.

◆ equal() [1/2]

template<typename Real >

bool OpenMD::equal	(	const Polynomial< Real > &	p1,
		const Polynomial< Real > &	p2 )

Tests if two polynomial have the same exponents.

Returns: true if all of the exponents in these Polynomial are identical

Parameters

p1	the first polynomial
p2	the second polynomial

Note: this function does not compare the coefficient

Definition at line 611 of file Polynomial.hpp.

Referenced by OpenMD::DynamicVector< Real, Alloc >::isNormalized(), OpenMD::Vector< Real, Dim >::isNormalized(), OpenMD::DynamicRectMatrix< Real >::operator==(), OpenMD::Quaternion< Real >::operator==(), OpenMD::RectMatrix< Real, Row, Col >::operator==(), and OpenMD::Vector< Real, Dim >::operator==().

◆ equal() [2/2]

template<typename T >

bool OpenMD::equal	(	T	e1,
		T	e2 )

inline

Definition at line 66 of file Vector.hpp.

◆ fastpow()

template<typename Real >

Real OpenMD::fastpow	(	Real	x,
		int	N )

Definition at line 68 of file Polynomial.hpp.

◆ findBegin()

int OpenMD::findBegin	(	std::istream &	theStream,
		const char *	startText )

Finds the location of the string "begin <startText>" in an input stream.

Parameters

theStream
startText

Returns: the line number of the block within the theStream

Definition at line 71 of file StringUtils.cpp.

◆ for()

OpenMD::for ( sd = seleMan1_.beginSelected(isd1); sd != NULL; sd = seleMan1_.nextSelected(isd1) )

Definition at line 239 of file TranslationalOrderParameterR.cpp.

◆ getDerivative()

template<typename Real >

Polynomial< Real > * OpenMD::getDerivative ( const Polynomial< Real > & p1 )

Returns the first derivative of this polynomial.

Returns: the first derivative of this polynomial

Definition at line 587 of file Polynomial.hpp.

References OpenMD::Polynomial< Real >::setCoefficient().

◆ getGlobalCountOfType()

int OpenMD::getGlobalCountOfType ( AtomType * )

Definition at line 785 of file SimInfo.cpp.

◆ getPrefix()

std::string OpenMD::getPrefix ( const std::string & str )

Todo: need implementation

Definition at line 169 of file StringUtils.cpp.

Referenced by OpenMD::PotDiff::PotDiff(), and OpenMD::ZConsVisitor::ZConsVisitor().

◆ hasDuplicateElement()

template<class ContainerType >

bool OpenMD::hasDuplicateElement ( const ContainerType & cont )

Definition at line 59 of file FragmentStamp.cpp.

◆ invertMatrix() [1/2]

template<class MatrixType >

bool OpenMD::invertMatrix	(	MatrixType &	A,
		MatrixType &	AI )

Invert input square matrix A into matrix AI.

Parameters

A	input square matrix
AI	output square matrix

Returns: true if inverse is computed, otherwise return false

Note: A is modified during the inversion

Definition at line 98 of file LU.hpp.

References invertMatrix().

Referenced by OpenMD::SquareMatrix< Real, Dim >::inverse(), and invertMatrix().

◆ invertMatrix() [2/2]

template<class MatrixType >

bool OpenMD::invertMatrix	(	MatrixType &	A,
		MatrixType &	AI,
		unsigned int	size,
		int *	tmp1Size,
		typename MatrixType::ElemPoinerType	tmp2Size )

Invert input square matrix A into matrix AI (Thread safe versions).

Parameters

A	input square matrix
AI	output square matrix
size	size of the matrix and temporary arrays
tmp1Size	temporary array
tmp2Size	temporary array

Returns: true if inverse is computed, otherwise return false

Note: A is modified during the inversion.

Definition at line 141 of file LU.hpp.

References LUFactorLinearSystem(), and LUSolveLinearSystem().

◆ isEndLine()

int OpenMD::isEndLine ( char * line )

discovers whether or not the line contains the "end" token

Parameters

line	The line to test

Returns: int (==1 if the line has "end", ==0 if not).

Definition at line 122 of file StringUtils.cpp.

◆ isEqual()

template<typename T >

EqualConstraint< T > OpenMD::isEqual ( T & v )

inline

Definition at line 366 of file ParamConstraint.hpp.

◆ isEqualIgnoreCase()

EqualIgnoreCaseConstraint OpenMD::isEqualIgnoreCase ( std::string str )

Definition at line 64 of file ParamConstraint.cpp.

◆ isEven()

EvenConstraint OpenMD::isEven ( )

Definition at line 68 of file ParamConstraint.cpp.

◆ isGreaterThan()

template<typename T >

GreaterThanConstraint< T > OpenMD::isGreaterThan ( T & v )

inline

Definition at line 371 of file ParamConstraint.hpp.

◆ isGreaterThanOrEqualTo()

template<typename T >

GreaterThanOrEqualTo< T > OpenMD::isGreaterThanOrEqualTo ( T & v )

inline

Definition at line 376 of file ParamConstraint.hpp.

◆ isInteger()

bool OpenMD::isInteger ( const std::string & str )

Definition at line 173 of file StringUtils.cpp.

◆ isLessThan()

template<typename T >

LessThanConstraint< T > OpenMD::isLessThan ( T & v )

inline

Definition at line 356 of file ParamConstraint.hpp.

◆ isLessThanOrEqualTo()

template<typename T >

LessThanOrEqualToConstraint< T > OpenMD::isLessThanOrEqualTo ( T & v )

inline

Definition at line 361 of file ParamConstraint.hpp.

◆ isNegative()

NegativeConstraint OpenMD::isNegative ( )

Definition at line 60 of file ParamConstraint.cpp.

◆ isNonNegative()

NonNegativeConstraint OpenMD::isNonNegative ( )

Definition at line 62 of file ParamConstraint.cpp.

◆ isNonPositive()

NonPositiveConstraint OpenMD::isNonPositive ( )

Definition at line 58 of file ParamConstraint.cpp.

◆ isNonZero()

ParamConstraintFacade< NonZeroConstraint > OpenMD::isNonZero ( )

Definition at line 52 of file ParamConstraint.cpp.

◆ isNotEmpty()

NotEmptyConstraint OpenMD::isNotEmpty ( )

Definition at line 48 of file ParamConstraint.cpp.

◆ isPositive()

PositiveConstraint OpenMD::isPositive ( )

Definition at line 56 of file ParamConstraint.cpp.

◆ isType()

template<typename T >

bool OpenMD::isType ( const std::string & str )

Definition at line 113 of file StringUtils.hpp.

◆ isZero()

ZeroConstraint OpenMD::isZero ( )

Definition at line 50 of file ParamConstraint.cpp.

◆ lexi_cast()

template<typename T >

T OpenMD::lexi_cast ( const std::string & str )

Definition at line 105 of file StringUtils.hpp.

◆ LUFactorLinearSystem()

template<class MatrixType >

int OpenMD::LUFactorLinearSystem	(	MatrixType &	A,
		int *	index,
		int	size,
		typename MatrixType::ElemPoinerType	tmpSize )

Factor linear equations Ax = b using LU decompostion A = LU where L is lower triangular matrix and U is upper triangular matrix.

Parameters

A	input square matrix
index	pivot indices
size	size of the matrix and temporary arrays
tmpSize	temporary array

Returns: true if inverse is computed, otherwise return false

Note: A is modified during the inversion.

Definition at line 187 of file LU.hpp.

Referenced by invertMatrix().

◆ LUSolveLinearSystem()

template<class MatrixType >

void OpenMD::LUSolveLinearSystem	(	MatrixType &	A,
		int *	index,
		typename MatrixType::ElemPoinerType	x,
		int	size )

Solve linear equations Ax = b using LU decompostion A = LU where L is lower triangular matrix and U is upper triangular matrix.

Parameters

A	input square matrix
index	pivot indices
x	vector
size	size of the matrix and temporary arrays

Returns: true if inverse is computed, otherwise return false

Note: A=LU and index[] are generated from method LUFactorLinearSystem). Also, solution vector is written directly over input load vector.

Definition at line 279 of file LU.hpp.

Referenced by invertMatrix().

◆ mCross()

template<typename Real , unsigned int Row, unsigned int Col>

Vector< Real, Row > OpenMD::mCross	(	const RectMatrix< Real, Row, Col > &	t1,
		const RectMatrix< Real, Row, Col > &	t2 )

inline

Returns the vector (cross) product of two matrices.

This operation is defined in:

W. Smith, "Point Multipoles in the Ewald Summation (Revisited)," CCP5 Newsletter No 46., pp. 18-30.

Equation 21 defines:

\[ V_alpha = \sum_\beta \left[ A_{\alpha+1,\beta} * B_{\alpha+2,\beta} -A_{\alpha+2,\beta} * B_{\alpha+2,\beta} \right] \]

where

\[\alpha+1\]

and

\[\alpha+2\]

are regarded as cyclic permuations of the matrix indices (i.e. for a 3x3 matrix, when

\[\alpha = 2\]

,

\[\alpha + 1 = 3 \]

, and

\[\alpha + 2 = 1 \]

).

Parameters

t1	first matrix
t2	second matrix

Returns: the cross product (vector product) of t1 and t2

Definition at line 636 of file RectMatrix.hpp.

◆ next_combination()

template<class RandomAccessIterator >

bool OpenMD::next_combination	(	std::vector< RandomAccessIterator > &	iterContainer,
		RandomAccessIterator	first,
		RandomAccessIterator	last )

STL next_permuation-like combination sequence generator.

Given the first and last iterator of a sequence, next_combination iteratively generates all possible combinations.

Returns: if more combination is availiable, otherwise return false

Parameters

iterContainer	iterator container
first	the first iterator
last	the last iterator

Note: first and last must be random access iterators and iterContainer must be the container of random access iterators . And all of the iteratos in iterContainer must be within the range [first, last)

std::vector<int> iv;
iv.push_back(1);
iv.push_back(8);
std::vector<std::vector<int>::iterator> ic;
while(next_combination(ic, iv.begin(), iv.end())) {
    for (i =  ic.begin(); i < ic.end(); ++i) {
        std::cout << **i << "\t";
    }
    std::cout << std::endl;
}
//output
//1
//8
//1  8

Definition at line 91 of file next_combination.hpp.

Referenced by replaceWithWildCard().

◆ OpenMD_itoa()

std::string OpenMD::OpenMD_itoa	(	int	value,
		unsigned int	base )

Definition at line 141 of file StringUtils.cpp.

◆ operator!()

template<typename ConsT >

NotParamConstraint< ConsT > OpenMD::operator! ( const ParamConstraintFacade< ConsT > & cons )

inline

Definition at line 338 of file ParamConstraint.hpp.

◆ operator&() [1/3]

OpenMDBitSet OpenMD::operator&	(	const OpenMDBitSet &	bs1,
		const OpenMDBitSet &	bs2 )

Definition at line 185 of file OpenMDBitSet.cpp.

◆ operator&() [2/3]

SelectionManager OpenMD::operator&	(	const SelectionManager &	sman1,
		const SelectionManager &	sman2 )

Definition at line 628 of file SelectionManager.cpp.

◆ operator&() [3/3]

SelectionSet OpenMD::operator&	(	const SelectionSet &	ss1,
		const SelectionSet &	ss2 )

Definition at line 197 of file SelectionSet.cpp.

◆ operator&&()

template<typename Cons1T , typename Cons2T >

AndParamConstraint< Cons1T, Cons2T > OpenMD::operator&&	(	const ParamConstraintFacade< Cons1T > &	cons1,
		const ParamConstraintFacade< Cons2T > &	cons2 )

inline

Definition at line 320 of file ParamConstraint.hpp.

◆ operator*() [1/20]

template<typename Real >

DynamicVector< Real > OpenMD::operator*	(	const DynamicRectMatrix< Real > &	m,
		const DynamicVector< Real > &	v )

inline

Return the multiplication of a matrix and a vector (m * v).

Returns: the multiplication of a matrix and a vector

Parameters

m	the matrix
v	the vector

Definition at line 578 of file DynamicRectMatrix.hpp.

◆ operator*() [2/20]

template<typename Real >

DynamicRectMatrix< Real > OpenMD::operator*	(	const DynamicRectMatrix< Real > &	m,
		Real	s )

inline

Return the multiplication of scalar and matrix (m * s).

Returns: the multiplication of a scalar and a matrix

Parameters

m	the matrix
s	the scalar

Definition at line 524 of file DynamicRectMatrix.hpp.

References OpenMD::DynamicRectMatrix< Real >::mul().

◆ operator*() [3/20]

template<typename Real >

DynamicRectMatrix< Real > OpenMD::operator*	(	const DynamicRectMatrix< Real > &	m1,
		const DynamicRectMatrix< Real > &	m2 )

inline

Return the multiplication of two matrixes (m1 * m2).

Returns: the multiplication of two matrixes

Parameters

m1	the first matrix
m2	the second matrix

Definition at line 556 of file DynamicRectMatrix.hpp.

◆ operator*() [4/20]

template<typename Real >

DynamicVector< Real > OpenMD::operator*	(	const DynamicVector< Real > &	v1,
		Real	s )

Returns the vaule of scalar multiplication of this vector v1 (v1 * r).

Returns: the vaule of scalar multiplication of this vector

Parameters

v1	the source vector
s	the scalar value

Definition at line 399 of file DynamicVector.hpp.

References OpenMD::DynamicVector< Real, Alloc >::mul().

◆ operator*() [5/20]

template<typename Real >

Polynomial< Real > OpenMD::operator*	(	const Polynomial< Real > &	p,
		const Real	v )

Definition at line 520 of file Polynomial.hpp.

◆ operator*() [6/20]

template<typename Real >

Polynomial< Real > OpenMD::operator*	(	const Polynomial< Real > &	p1,
		const Polynomial< Real > &	p2 )

Generates and returns the product of two given Polynomials.

Returns: A Polynomial containing the product of the two given Polynomial parameters

Definition at line 504 of file Polynomial.hpp.

References OpenMD::Polynomial< Real >::addCoefficient().

◆ operator*() [7/20]

template<typename Real , unsigned int Dim>

Quaternion< Real > OpenMD::operator*	(	const Quaternion< Real > &	q,
		Real	s )

Returns the vaule of scalar multiplication of this quaterion q (q * s).

Returns: the vaule of scalar multiplication of this vector

Parameters

q	the source quaternion
s	the scalar value

Definition at line 561 of file Quaternion.hpp.

References OpenMD::Quaternion< Real >::mul().

◆ operator*() [8/20]

template<typename Real >

Quaternion< Real > OpenMD::operator*	(	const Quaternion< Real > &	q1,
		const Quaternion< Real > &	q2 )

inline

Returns the multiplication of two quaternion.

Returns: the multiplication of two quaternion

Parameters

q1	the first quaternion
q2	the second quaternion

Definition at line 587 of file Quaternion.hpp.

◆ operator*() [9/20]

template<typename Real , unsigned int Dim>

Quaternion< Real > OpenMD::operator*	(	const Real &	s,
		const Quaternion< Real > &	q )

Returns the vaule of scalar multiplication of this quaterion q (q * s).

Returns: the vaule of scalar multiplication of this vector

Parameters

s	the scalar value
q	the source quaternion

Definition at line 574 of file Quaternion.hpp.

References OpenMD::Quaternion< Real >::mul().

◆ operator*() [10/20]

template<typename Real >

Polynomial< Real > OpenMD::operator*	(	const Real	v,
		const Polynomial< Real > &	p )

Definition at line 532 of file Polynomial.hpp.

◆ operator*() [11/20]

template<typename Real , unsigned int Row, unsigned int Col>

Vector< Real, Row > OpenMD::operator*	(	const RectMatrix< Real, Row, Col > &	m,
		const Vector< Real, Col > &	v )

inline

Returns the multiplication of a matrix and a vector (m * v).

Returns: the multiplication of a matrix and a vector

Parameters

m	the matrix
v	the vector

Definition at line 545 of file RectMatrix.hpp.

◆ operator*() [12/20]

template<typename Real , unsigned int Row, unsigned int Col>

RectMatrix< Real, Row, Col > OpenMD::operator*	(	const RectMatrix< Real, Row, Col > &	m,
		Real	s )

inline

Return the multiplication of scalra and matrix (m * s).

Returns: the multiplication of a scalra and a matrix

Parameters

m	the matrix
s	the scalar

Definition at line 492 of file RectMatrix.hpp.

References OpenMD::RectMatrix< Real, Row, Col >::mul().

◆ operator*() [13/20]

template<typename Real , unsigned int Row, unsigned int Col, unsigned int SameDim>

RectMatrix< Real, Row, Col > OpenMD::operator*	(	const RectMatrix< Real, Row, SameDim > &	m1,
		const RectMatrix< Real, SameDim, Col > &	m2 )

inline

Return the multiplication of two matrixes (m1 * m2).

Returns: the multiplication of two matrixes

Parameters

m1	the first matrix
m2	the second matrix

Definition at line 525 of file RectMatrix.hpp.

◆ operator*() [14/20]

template<typename Real >

SquareMatrix3< Real > OpenMD::operator*	(	const SquareMatrix3< Real > &	m1,
		const SquareMatrix3< Real > &	m2 )

inline

Return the multiplication of two matrixes (m1 * m2).

Returns: the multiplication of two matrixes

Parameters

m1	the first matrix
m2	the second matrix

Definition at line 615 of file SquareMatrix3.hpp.

◆ operator*() [15/20]

template<typename Real , unsigned int Dim>

Vector< Real, Dim > OpenMD::operator*	(	const Vector< Real, Dim > &	v1,
		Real	s )

Returns the vaule of scalar multiplication of this vector v1 (v1 * r).

Returns: the vaule of scalar multiplication of this vector

Parameters

v1	the source vector
s	the scalar value

Definition at line 469 of file Vector.hpp.

References OpenMD::Vector< Real, Dim >::mul().

◆ operator*() [16/20]

template<typename Real , unsigned int Row, unsigned int Col>

Vector< Real, Col > OpenMD::operator*	(	const Vector< Real, Row > &	v,
		const RectMatrix< Real, Row, Col > &	m )

inline

Returns the multiplication of a vector transpose and a matrix (v^T * m).

Returns: the multiplication of a vector transpose and a matrix

Parameters

v	the vector
m	the matrix

Definition at line 563 of file RectMatrix.hpp.

◆ operator*() [17/20]

template<typename Real >

DynamicRectMatrix< Real > OpenMD::operator*	(	Real	s,
		const DynamicRectMatrix< Real > &	m )

inline

Return the multiplication of a scalar and a matrix (s * m).

Returns: the multiplication of a scalar and a matrix

Parameters

s	the scalar
m	the matrix

Definition at line 540 of file DynamicRectMatrix.hpp.

References OpenMD::DynamicRectMatrix< Real >::mul().

◆ operator*() [18/20]

template<typename Real >

DynamicVector< Real > OpenMD::operator*	(	Real	s,
		const DynamicVector< Real > &	v1 )

Returns the vaule of scalar multiplication of this vector v1 (v1 * r).

Returns: the vaule of scalar multiplication of this vector

Parameters

s	the scalar value
v1	the source vector

Definition at line 412 of file DynamicVector.hpp.

References OpenMD::DynamicVector< Real, Alloc >::mul().

◆ operator*() [19/20]

template<typename Real , unsigned int Row, unsigned int Col>

RectMatrix< Real, Row, Col > OpenMD::operator*	(	Real	s,
		const RectMatrix< Real, Row, Col > &	m )

inline

Return the multiplication of a scalra and a matrix (s * m).

Returns: the multiplication of a scalra and a matrix

Parameters

s	the scalar
m	the matrix

Definition at line 508 of file RectMatrix.hpp.

References OpenMD::RectMatrix< Real, Row, Col >::mul().

◆ operator*() [20/20]

template<typename Real , unsigned int Dim>

Vector< Real, Dim > OpenMD::operator*	(	Real	s,
		const Vector< Real, Dim > &	v1 )

Returns the vaule of scalar multiplication of this vector v1 (v1 * r).

Returns: the vaule of scalar multiplication of this vector

Parameters

s	the scalar value
v1	the source vector

Definition at line 482 of file Vector.hpp.

References OpenMD::Vector< Real, Dim >::mul().

◆ operator+() [1/6]

template<typename Real >

DynamicRectMatrix< Real > OpenMD::operator+	(	const DynamicRectMatrix< Real > &	m1,
		const DynamicRectMatrix< Real > &	m2 )

inline

Return the sum of two matrixes (m1 + m2).

Returns: the sum of two matrixes

Parameters

m1	the first matrix
m2	the second matrix

Definition at line 492 of file DynamicRectMatrix.hpp.

References OpenMD::DynamicRectMatrix< Real >::add().

◆ operator+() [2/6]

template<typename Real >

DynamicVector< Real > OpenMD::operator+	(	const DynamicVector< Real > &	v1,
		const DynamicVector< Real > &	v2 )

inline

Return the sum of two vectors (v1 - v2).

Returns: the sum of two vectors

Parameters

v1	the first vector
v2	the second vector

Definition at line 369 of file DynamicVector.hpp.

References OpenMD::DynamicVector< Real, Alloc >::add().

◆ operator+() [3/6]

Mesh OpenMD::operator+	(	const Mesh &	m1,
		const Mesh &	m2 )

inline

Definition at line 203 of file Mesh.hpp.

◆ operator+() [4/6]

template<typename Real >

Polynomial< Real > OpenMD::operator+	(	const Polynomial< Real > &	p1,
		const Polynomial< Real > &	p2 )

Generates and returns the sum of two given Polynomials.

Parameters

p1	the first polynomial
p2	the second polynomial

Definition at line 549 of file Polynomial.hpp.

References OpenMD::Polynomial< Real >::addCoefficient().

◆ operator+() [5/6]

template<typename Real , unsigned int Row, unsigned int Col>

RectMatrix< Real, Row, Col > OpenMD::operator+	(	const RectMatrix< Real, Row, Col > &	m1,
		const RectMatrix< Real, Row, Col > &	m2 )

inline

Return the sum of two matrixes (m1 + m2).

Returns: the sum of two matrixes

Parameters

m1	the first matrix
m2	the second matrix

Definition at line 458 of file RectMatrix.hpp.

References OpenMD::RectMatrix< Real, Row, Col >::add().

◆ operator+() [6/6]

template<typename Real , unsigned int Dim>

Vector< Real, Dim > OpenMD::operator+	(	const Vector< Real, Dim > &	v1,
		const Vector< Real, Dim > &	v2 )

inline

Return the sum of two vectors (v1 - v2).

Returns: the sum of two vectors

Parameters

v1	the first vector
v2	the second vector

Definition at line 440 of file Vector.hpp.

References OpenMD::Vector< Real, Dim >::add().

◆ operator-() [1/12]

template<typename Real >

DynamicRectMatrix< Real > OpenMD::operator- ( const DynamicRectMatrix< Real > & m )

inline

Negate the value of every element of this matrix.

Definition at line 477 of file DynamicRectMatrix.hpp.

References OpenMD::DynamicRectMatrix< Real >::negate().

◆ operator-() [2/12]

template<typename Real >

DynamicRectMatrix< Real > OpenMD::operator-	(	const DynamicRectMatrix< Real > &	m1,
		const DynamicRectMatrix< Real > &	m2 )

inline

Return the difference of two matrixes (m1 - m2).

Returns: the sum of two matrixes

Parameters

m1	the first matrix
m2	the second matrix

Definition at line 508 of file DynamicRectMatrix.hpp.

References OpenMD::DynamicRectMatrix< Real >::sub().

◆ operator-() [3/12]

template<typename Real >

DynamicVector< Real > OpenMD::operator- ( const DynamicVector< Real > & v1 )

inline

unary minus

Definition at line 356 of file DynamicVector.hpp.

References OpenMD::DynamicVector< Real, Alloc >::negate().

◆ operator-() [4/12]

template<typename Real >

DynamicVector< Real > OpenMD::operator-	(	const DynamicVector< Real > &	v1,
		const DynamicVector< Real > &	v2 )

Return the difference of two vectors (v1 - v2).

Returns: the difference of two vectors

Parameters

v1	the first vector
v2	the second vector

Definition at line 384 of file DynamicVector.hpp.

References OpenMD::DynamicVector< Real, Alloc >::sub().

◆ operator-() [5/12]

OpenMDBitSet OpenMD::operator-	(	const OpenMDBitSet &	bs1,
		const OpenMDBitSet &	bs2 )

Definition at line 201 of file OpenMDBitSet.cpp.

◆ operator-() [6/12]

template<typename Real >

Polynomial< Real > OpenMD::operator-	(	const Polynomial< Real > &	p1,
		const Polynomial< Real > &	p2 )

Generates and returns the difference of two given Polynomials.

Returns

Parameters

p1	the first polynomial
p2	the second polynomial

Definition at line 569 of file Polynomial.hpp.

References OpenMD::Polynomial< Real >::addCoefficient().

◆ operator-() [7/12]

template<typename Real , unsigned int Row, unsigned int Col>

RectMatrix< Real, Row, Col > OpenMD::operator- ( const RectMatrix< Real, Row, Col > & m )

inline

Negate the value of every element of this matrix.

Definition at line 442 of file RectMatrix.hpp.

References OpenMD::RectMatrix< Real, Row, Col >::negate().

◆ operator-() [8/12]

template<typename Real , unsigned int Row, unsigned int Col>

RectMatrix< Real, Row, Col > OpenMD::operator-	(	const RectMatrix< Real, Row, Col > &	m1,
		const RectMatrix< Real, Row, Col > &	m2 )

inline

Return the difference of two matrixes (m1 - m2).

Returns: the sum of two matrixes

Parameters

m1	the first matrix
m2	the second matrix

Definition at line 475 of file RectMatrix.hpp.

References OpenMD::RectMatrix< Real, Row, Col >::sub().

◆ operator-() [9/12]

SelectionManager OpenMD::operator-	(	const SelectionManager &	sman1,
		const SelectionManager &	sman2 )

Definition at line 642 of file SelectionManager.cpp.

◆ operator-() [10/12]

SelectionSet OpenMD::operator-	(	const SelectionSet &	ss1,
		const SelectionSet &	ss2 )

Definition at line 211 of file SelectionSet.cpp.

◆ operator-() [11/12]

template<typename Real , unsigned int Dim>

Vector< Real, Dim > OpenMD::operator- ( const Vector< Real, Dim > & v1 )

inline

unary minus

Definition at line 427 of file Vector.hpp.

References OpenMD::Vector< Real, Dim >::negate().

◆ operator-() [12/12]

template<typename Real , unsigned int Dim>

Vector< Real, Dim > OpenMD::operator-	(	const Vector< Real, Dim > &	v1,
		const Vector< Real, Dim > &	v2 )

Return the difference of two vectors (v1 - v2).

Returns: the difference of two vectors

Parameters

v1	the first vector
v2	the second vector

Definition at line 455 of file Vector.hpp.

References OpenMD::Vector< Real, Dim >::sub().

◆ operator/() [1/6]

template<typename Real >

DynamicRectMatrix< Real > OpenMD::operator/	(	const DynamicRectMatrix< Real > &	m,
		Real	s )

inline

Return the scalar division of matrix (m / s).

Returns: the scalar division of matrix

Parameters

m	the matrix
s	the scalar

Definition at line 599 of file DynamicRectMatrix.hpp.

References OpenMD::DynamicRectMatrix< Real >::div().

◆ operator/() [2/6]

template<typename Real >

DynamicVector< Real > OpenMD::operator/	(	const DynamicVector< Real > &	v1,
		Real	s )

Returns the value of division of a vector by a scalar.

Returns: the vaule of scalar division of this vector

Parameters

v1	the source vector
s	the scalar value

Definition at line 425 of file DynamicVector.hpp.

References OpenMD::DynamicVector< Real, Alloc >::div().

◆ operator/() [3/6]

template<typename Real >

Quaternion< Real > OpenMD::operator/	(	const Real &	s,
		Quaternion< Real > &	q )

Returns the value of the division of a scalar by a quaternion.

Returns: the value of the division of a scalar by a quaternion

Parameters

s	scalar
q	quaternion

Note: for a quaternion q, 1/q = q.inverse()

Definition at line 614 of file Quaternion.hpp.

References OpenMD::Quaternion< Real >::inverse().

◆ operator/() [4/6]

template<typename Real , unsigned int Row, unsigned int Col>

RectMatrix< Real, Row, Col > OpenMD::operator/	(	const RectMatrix< Real, Row, Col > &	m,
		Real	s )

inline

Return the scalar division of matrix (m / s).

Returns: the scalar division of matrix

Parameters

m	the matrix
s	the scalar

Definition at line 581 of file RectMatrix.hpp.

References OpenMD::RectMatrix< Real, Row, Col >::div().

◆ operator/() [5/6]

template<typename Real , unsigned int Dim>

Vector< Real, Dim > OpenMD::operator/	(	const Vector< Real, Dim > &	v1,
		Real	s )

Returns the value of division of a vector by a scalar.

Returns: the vaule of scalar division of this vector

Parameters

v1	the source vector
s	the scalar value

Definition at line 495 of file Vector.hpp.

References OpenMD::Vector< Real, Dim >::div().

◆ operator/() [6/6]

template<typename Real >

Quaternion< Real > OpenMD::operator/	(	Quaternion< Real > &	q1,
		Quaternion< Real > &	q2 )

inline

Returns the division of two quaternion.

Parameters

q1	divisor
q2	dividen

Definition at line 601 of file Quaternion.hpp.

References OpenMD::Quaternion< Real >::inverse().

◆ operator<<() [1/21]

ostream & OpenMD::operator<<	(	ostream &	o,
		SimInfo &	info )

Definition at line 1025 of file SimInfo.cpp.

◆ operator<<() [2/21]

template<typename Real >

std::ostream & OpenMD::operator<<	(	std::ostream &	o,
		const DynamicRectMatrix< Real > &	m )

Write to an output stream.

Definition at line 612 of file DynamicRectMatrix.hpp.

◆ operator<<() [3/21]

template<typename Real , unsigned int Row, unsigned int Col>

std::ostream & OpenMD::operator<<	(	std::ostream &	o,
		const RectMatrix< Real, Row, Col > &	m )

Write to an output stream.

Definition at line 656 of file RectMatrix.hpp.

◆ operator<<() [4/21]

template<typename Real , unsigned int Dim>

std::ostream & OpenMD::operator<<	(	std::ostream &	o,
		const Vector< Real, Dim > &	v )

Write to an output stream.

Definition at line 569 of file Vector.hpp.

◆ operator<<() [5/21]

template<typename O , typename I , typename C >

std::ostream & OpenMD::operator<<	(	std::ostream &	o,
		GenericFactory< O, I, C > &	factory )

write out all of the type identifiers to an output stream

Definition at line 232 of file GenericFactory.hpp.

References OpenMD::GenericFactory< Object, IdentType, Creator >::getIdents().

◆ operator<<() [6/21]

std::ostream & OpenMD::operator<<	(	std::ostream &	o,
		HydrodynamicsModelFactory &	factory )

write out all of the type identifiers to an output stream

Definition at line 95 of file HydrodynamicsModelFactory.cpp.

References OpenMD::HydrodynamicsModelFactory::getIdents().

◆ operator<<() [7/21]

std::ostream & OpenMD::operator<<	(	std::ostream &	o,
		IntegratorFactory &	factory )

write out all of the type identifiers to an output stream

Definition at line 88 of file IntegratorFactory.cpp.

References OpenMD::IntegratorFactory::getIdents().

◆ operator<<() [8/21]

std::ostream & OpenMD::operator<<	(	std::ostream &	o,
		LatticeFactory &	factory )

write out all of the type identifiers to an output stream

Definition at line 85 of file LatticeFactory.cpp.

References OpenMD::LatticeFactory::getIdents().

◆ operator<<() [9/21]

std::ostream & OpenMD::operator<<	(	std::ostream &	o,
		Molecule &	mol )

Definition at line 425 of file Molecule.cpp.

◆ operator<<() [10/21]

std::ostream & OpenMD::operator<<	(	std::ostream &	o,
		OptimizationFactory &	factory )

write out all of the type identifiers to an output stream

Definition at line 88 of file OptimizationFactory.cpp.

References OpenMD::OptimizationFactory::getIdents().

◆ operator<<() [11/21]

std::ostream & OpenMD::operator<<	(	std::ostream &	o,
		PairList &	e )

Definition at line 154 of file PairList.cpp.

◆ operator<<() [12/21]

std::ostream & OpenMD::operator<<	(	std::ostream &	os,
		AmberImproperTorsionType &	ott )

Definition at line 85 of file AmberImproperTorsionType.hpp.

◆ operator<<() [13/21]

std::ostream & OpenMD::operator<<	(	std::ostream &	os,
		const OpenMDBitSet &	bs )

Definition at line 248 of file OpenMDBitSet.cpp.

◆ operator<<() [14/21]

std::ostream & OpenMD::operator<<	(	std::ostream &	os,
		const SelectionSet &	ss )

Definition at line 240 of file SelectionSet.cpp.

◆ operator<<() [15/21]

std::ostream & OpenMD::operator<<	(	std::ostream &	os,
		HarmonicInversionType &	hit )

Definition at line 86 of file HarmonicInversionType.hpp.

◆ operator<<() [16/21]

std::ostream & OpenMD::operator<<	(	std::ostream &	os,
		HarmonicTorsionType &	htt )

Definition at line 105 of file HarmonicTorsionType.hpp.

◆ operator<<() [17/21]

std::ostream & OpenMD::operator<<	(	std::ostream &	os,
		OplsTorsionType &	ott )

Definition at line 111 of file OplsTorsionType.hpp.

◆ operator<<() [18/21]

std::ostream & OpenMD::operator<<	(	std::ostream &	os,
		PolynomialBendType &	pbt )

Definition at line 91 of file PolynomialBendType.hpp.

◆ operator<<() [19/21]

std::ostream & OpenMD::operator<<	(	std::ostream &	os,
		PolynomialBondType &	pbt )

Definition at line 89 of file PolynomialBondType.hpp.

◆ operator<<() [20/21]

std::ostream & OpenMD::operator<<	(	std::ostream &	os,
		TrappeTorsionType &	ttt )

Definition at line 122 of file TrappeTorsionType.hpp.

◆ operator<<() [21/21]

template<typename Real >

std::ostream & OpenMD::operator<<	(	std::ostream &	strm,
		const DynamicVector< Real > &	v )

Write to an output stream.

Definition at line 479 of file DynamicVector.hpp.

◆ operator==() [1/3]

bool OpenMD::operator==	(	const OpenMDBitSet &	bs1,
		const OpenMDBitSet &	bs2 )

Definition at line 209 of file OpenMDBitSet.cpp.

◆ operator==() [2/3]

template<class T >

bool OpenMD::operator==	(	const Quaternion< T > &	lhs,
		const Quaternion< T > &	rhs )

inline

Definition at line 622 of file Quaternion.hpp.

◆ operator==() [3/3]

bool OpenMD::operator==	(	const SelectionSet &	ss1,
		const SelectionSet &	ss2 )

Definition at line 218 of file SelectionSet.cpp.

◆ operator^() [1/3]

OpenMDBitSet OpenMD::operator^	(	const OpenMDBitSet &	bs1,
		const OpenMDBitSet &	bs2 )

Definition at line 193 of file OpenMDBitSet.cpp.

◆ operator^() [2/3]

SelectionManager OpenMD::operator^	(	const SelectionManager &	sman1,
		const SelectionManager &	sman2 )

Definition at line 635 of file SelectionManager.cpp.

◆ operator^() [3/3]

SelectionSet OpenMD::operator^	(	const SelectionSet &	ss1,
		const SelectionSet &	ss2 )

Definition at line 204 of file SelectionSet.cpp.

◆ operator|() [1/3]

OpenMDBitSet OpenMD::operator\|	(	const OpenMDBitSet &	bs1,
		const OpenMDBitSet &	bs2 )

Definition at line 177 of file OpenMDBitSet.cpp.

◆ operator|() [2/3]

SelectionManager OpenMD::operator\|	(	const SelectionManager &	sman1,
		const SelectionManager &	sman2 )

Definition at line 621 of file SelectionManager.cpp.

◆ operator|() [3/3]

SelectionSet OpenMD::operator\|	(	const SelectionSet &	ss1,
		const SelectionSet &	ss2 )

Definition at line 190 of file SelectionSet.cpp.

◆ operator||()

template<typename Cons1T , typename Cons2T >

OrParamConstraint< Cons1T, Cons2T > OpenMD::operator\|\|	(	const ParamConstraintFacade< Cons1T > &	cons1,
		const ParamConstraintFacade< Cons2T > &	cons2 )

inline

Definition at line 329 of file ParamConstraint.hpp.

◆ outProduct()

template<typename Real >

SquareMatrix3< Real > OpenMD::outProduct	(	const Vector3< Real > &	v1,
		const Vector3< Real > &	v2 )

inline

Definition at line 628 of file SquareMatrix3.hpp.

◆ pairCompare()

bool OpenMD::pairCompare	(	const pair< RealType, int > &	l,
		const pair< RealType, int > &	r )

Definition at line 57 of file Cuboctahedron.cpp.

◆ registerAll()

void OpenMD::registerAll ( )

register force fields, integrators and optimizers

Definition at line 140 of file Register.cpp.

References registerIntegrators(), and registerOptimizers().

◆ registerIntegrators()

void OpenMD::registerIntegrators ( )

Register all integrators.

Definition at line 81 of file Register.cpp.

References OpenMD::IntegratorFactory::getInstance().

Referenced by registerAll().

◆ registerLattice()

void OpenMD::registerLattice ( )

Register all lattice.

Definition at line 131 of file Register.cpp.

References OpenMD::LatticeFactory::getInstance().

◆ registerOptimizers()

void OpenMD::registerOptimizers ( )

Register all optimizers.

Definition at line 122 of file Register.cpp.

References OpenMD::OptimizationFactory::getInstance().

Referenced by registerAll().

◆ replaceWithWildCard()

bool OpenMD::replaceWithWildCard	(	std::vector< std::vector< std::string >::iterator > &	cont,
		std::vector< std::string > &	sequence,
		std::vector< std::string > &	result,
		const std::string &	wildCard = "X" )

iteratively replace the sequence with wild cards

Returns: true if more combination sequence is avaliable, otherwise return true

Parameters

cont	iterator container, if expect the whole series of combinations, pass an empty iterator container. The user should not modify this iterator container
sequence	the whole sequence used to generate combination
result	a possible combination sequence which is set on return
wildCard	the wild card string. Its value is "X" by default

Note: since next_combination never returns an empty sequence, replaceWildCard will not generate one special combination, which is n identical wild cards (n is equal to the size of the passing sequence)

vector<string> sv;
vector<vector<string>::iterator> sic;
vector<string> resultString;
sv.push_back("H");
sv.push_back("C");
sv.push_back("N");
 
while (replaceWithWildCard(sic, sv, resultString)) {
    for(vector<string>::iterator i = resultString.begin();
         i != resultString.end(); ++i) {
        cout << *i << "\t";
    }
    cout << endl;
}
//output
//H X X
//X C X
//X X N
//H C X
//H X N
//X C N
//H C N

Definition at line 55 of file Utility.cpp.

References next_combination().

Referenced by OpenMD::TypeContainer< ElemType, SIZE >::find().

◆ roundMe()

RealType OpenMD::roundMe ( const RealType & x )

inline

Definition at line 55 of file Utility.hpp.

◆ swap_if()

template<class Cont , class Predict >

void OpenMD::swap_if	(	Cont &	b1,
		Cont &	b2,
		Predict	predict )

Definition at line 71 of file CompositeShape.cpp.

◆ toLower()

template<typename Container >

void OpenMD::toLower	(	Container &	cont,
		const std::locale &	loc = std::locale() )

Definition at line 55 of file CaseConversion.hpp.

◆ toLowerCopy()

template<typename Container >

Container OpenMD::toLowerCopy	(	const Container &	cont,
		const std::locale &	= std::locale() )

Definition at line 61 of file CaseConversion.hpp.

◆ toString()

template<typename T >

std::string OpenMD::toString ( const T & v )

Convert a variable to a string.

Template Parameters

T data type

Parameters

v	data to be converted

Returns: a string

Definition at line 98 of file StringUtils.hpp.

◆ toUpper()

template<typename Container >

void OpenMD::toUpper	(	Container &	cont,
		const std::locale &	loc = std::locale() )

Definition at line 70 of file CaseConversion.hpp.

◆ toUpperCopy()

template<typename Container >

Container OpenMD::toUpperCopy	(	const Container &	cont,
		const std::locale &	= std::locale() )

Definition at line 76 of file CaseConversion.hpp.

◆ UpperCase()

std::string OpenMD::UpperCase ( const std::string & S )

Converts a string to UPPER CASE.

Parameters

S

Definition at line 61 of file StringUtils.cpp.

◆ Vlinear() [1/2]

std::size_t OpenMD::Vlinear	(	const Vector2< std::size_t > &	p,
		const Vector2< std::size_t > &	s )

inline

Returns the linear indexing for size_t vectors.

Compare to Rapaport's VLinear

Parameters

p	first vector
s	second vector

Definition at line 111 of file Vector2.hpp.

References OpenMD::Vector2< Real >::x(), and OpenMD::Vector2< Real >::y().

◆ Vlinear() [2/2]

template<typename Real >

Real OpenMD::Vlinear	(	const Vector3< Real > &	p,
		const Vector3< Real > &	s )

inline

Returns the linear indexing for integer vectors.

Compare to Rapaport's VLinear

Parameters

p	first vector
s	second vector

Definition at line 154 of file Vector3.hpp.

References OpenMD::Vector3< Real >::x(), OpenMD::Vector3< Real >::y(), and OpenMD::Vector3< Real >::z().

Variable Documentation

◆ BUCKINGHAM_INTERACTION

const int OpenMD::BUCKINGHAM_INTERACTION = (1 << 10)

static

Definition at line 91 of file NonBondedInteraction.hpp.

◆ DirectionalTypeID

string const OpenMD::DirectionalTypeID = "Directional"

Definition at line 55 of file DirectionalAdapter.hpp.

◆ EAM_INTERACTION

const int OpenMD::EAM_INTERACTION = (1 << 2)

static

Definition at line 83 of file NonBondedInteraction.hpp.

◆ EAMtypeID

string const OpenMD::EAMtypeID = "EAM"

Definition at line 56 of file EAMAdapter.hpp.

◆ ELECTROSTATIC_INTERACTION

const int OpenMD::ELECTROSTATIC_INTERACTION = (1 << 0)

static

Boolean flags for the iHash_ and sHash_ data structures.

These are used to greatly increase the speed of looking up the low-level interaction for any given pair:

Definition at line 81 of file NonBondedInteraction.hpp.

◆ epsilon

constexpr RealType OpenMD::epsilon = 0.000001

staticconstexpr

Definition at line 63 of file Vector.hpp.

◆ etab

ElementsTable OpenMD::etab

Definition at line 56 of file ElementsTable.cpp.

◆ FCtypeID

string const OpenMD::FCtypeID = "Charge"

Definition at line 54 of file FixedChargeAdapter.hpp.

◆ FQtypeID

string const OpenMD::FQtypeID = "FlucQ"

Definition at line 55 of file FluctuatingChargeAdapter.hpp.

◆ FuncflTypeID

string const OpenMD::FuncflTypeID = "FUNCFL"

Definition at line 57 of file EAMAdapter.hpp.

◆ GB_INTERACTION

const int OpenMD::GB_INTERACTION = (1 << 5)

static

Definition at line 86 of file NonBondedInteraction.hpp.

◆ GBtypeID

string const OpenMD::GBtypeID = "GB"

Definition at line 54 of file GayBerneAdapter.hpp.

◆ INVERSEPOWERSERIES_INTERACTION

const int OpenMD::INVERSEPOWERSERIES_INTERACTION = (1 << 11)

static

Definition at line 92 of file NonBondedInteraction.hpp.

◆ LJ_INTERACTION

const int OpenMD::LJ_INTERACTION = (1 << 1)

static

Definition at line 82 of file NonBondedInteraction.hpp.

◆ LJtypeID

string const OpenMD::LJtypeID = "LJ"

Definition at line 54 of file LennardJonesAdapter.hpp.

◆ MAW_INTERACTION

const int OpenMD::MAW_INTERACTION = (1 << 8)

static

Definition at line 89 of file NonBondedInteraction.hpp.

◆ MIE_INTERACTION

const int OpenMD::MIE_INTERACTION = (1 << 9)

static

Definition at line 90 of file NonBondedInteraction.hpp.

◆ MORSE_INTERACTION

const int OpenMD::MORSE_INTERACTION = (1 << 6)

static

Definition at line 87 of file NonBondedInteraction.hpp.

◆ MultipoleTypeID

string const OpenMD::MultipoleTypeID = "Multipole"

Definition at line 55 of file MultipoleAdapter.hpp.

◆ PolTypeID

string const OpenMD::PolTypeID = "Polarizable"

Definition at line 54 of file PolarizableAdapter.hpp.

◆ progressSpinner_

const char* OpenMD::progressSpinner_ = "|/-\\"

Definition at line 72 of file ProgressBar.cpp.

◆ REPULSIVEPOWER_INTERACTION

const int OpenMD::REPULSIVEPOWER_INTERACTION = (1 << 7)

static

Definition at line 88 of file NonBondedInteraction.hpp.

◆ SC_INTERACTION

const int OpenMD::SC_INTERACTION = (1 << 3)

static

Definition at line 84 of file NonBondedInteraction.hpp.

◆ SCtypeID

string const OpenMD::SCtypeID = "SC"

Definition at line 54 of file SuttonChenAdapter.hpp.

◆ STICKY_INTERACTION

const int OpenMD::STICKY_INTERACTION = (1 << 4)

static

Definition at line 85 of file NonBondedInteraction.hpp.

◆ StickyTypeID

string const OpenMD::StickyTypeID = "Sticky"

Definition at line 54 of file StickyAdapter.hpp.

◆ UFFtypeID

string const OpenMD::UFFtypeID = "UFF"

Definition at line 54 of file UFFAdapter.hpp.

◆ ZhouRoseTypeID

string const OpenMD::ZhouRoseTypeID = "ZHOUROSE"

Definition at line 59 of file EAMAdapter.hpp.

◆ ZhouTypeID

string const OpenMD::ZhouTypeID = "ZHOU"

Definition at line 58 of file EAMAdapter.hpp.

Classes

Typedefs

Enumerations

Functions

Variables

Detailed Description

Typedef Documentation

◆ AtomTypeSet

◆ BoolGenericData

◆ CubicSplinePtr

◆ DataStoragePointer

◆ DirectionalAtypeData

◆ DoubleGenericData

◆ DoublePolynomial

◆ DoubleVectorGenericData

◆ EAMData

◆ FixedChargeAtypeData

◆ FloatGenericData

◆ FloatVectorGenericData

◆ FluctuatingAtypeData

◆ FuncflData

◆ GBAtypeData

◆ IntGenericData

◆ IntVectorGenericData

◆ LJAtypeData

◆ Mat3x3d

◆ Mat6x6d

◆ MultipoleAtypeData

◆ NonBondedInteractionPtr

◆ PolarizableAtypeData

◆ potVec

◆ ProgressBarPtr

◆ Quat4d

◆ RestraintData

◆ RotMat3x3d

◆ SCAtypeData

◆ ShapeAtypeData

◆ SnapshotBlock

◆ StickyAtypeData

◆ StringGenericData

◆ StringVectorGenericData

◆ TeeBuf

◆ TreeNodePtr

◆ UFFAtypeData

◆ Vector2d

◆ Vector2i

◆ Vector3d

◆ Vector3i

◆ VisitorIterator

◆ ZhouData

Enumeration Type Documentation

◆ BuckinghamType

◆ communicatorType

◆ CutoffMethod

◆ EAMiType

◆ EAMMixingMethod

◆ EAMType

◆ ElectrostaticScreeningMethod

◆ ElectrostaticSummationMethod

◆ InteractionFamily

◆ InversionKey

◆ MorseType

◆ SelectionType

◆ SwitchingFunctionType

Function Documentation

◆ CaseInsensitiveEquals()

◆ CaseInsensitiveFind()

◆ CholeskyDecomposition()

◆ containerToString()

◆ cross()

◆ distance() [1/2]

◆ distance() [2/2]

◆ distanceSquare() [1/2]

◆ distanceSquare() [2/2]

◆ dot() [1/3]

◆ dot() [2/3]

◆ dot() [3/3]

◆ doubleDot()

◆ equal() [1/2]

◆ equal() [2/2]