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	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	CountDifference
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 with contiguous flat storage. 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	FluxOut
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	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	LHDForceModifier
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	MeanDisplacement
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	MoleculeCount
class	MoleculeCreator
class	MoleculeStamp
class	MoleculeStampCompare
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	NEP
struct	NEPAtoms
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	OHFrequencyMap
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	P2Z
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	Qsurf
	Tetrahedral order parameter Q field, output frame-by-frame as OpenDX volumetric data files. 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	RPYMobility
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	SDVelocityField
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	SFG
	Computes the vibrational SFG susceptibility spectrum Im χ²(ω) in the OH-stretch region using the exciton Hamiltonian approach with an ADIABATIC quantum propagator. More...
class	SFGTimeAvg
	Computes vibrational SFG spectra in the OH-stretch region using the TIME-AVERAGING APPROXIMATION (TAA) of Auer & Skinner, rather than the dynamical adiabatic-propagator method implemented in the SFG dynamic property. 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
	Storage specific to the SPF-RNEMD method that allows for a new simulation to pick up where an old one left off. More...
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	TetrahedralityParamRAngle
	Tetrahedrality ParameterRAngle. 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	TranslationalOrderParamZ
	TranslationalOrder ParameterZ. 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
	A linear (homogeneous) ambient velocity field, v(r) = v0 + K . r. More...
class	VelocityVerletIntegrator
class	VelocityZ
class	WaterTypeVisitor
class	WCorrFunc
class	WrappingVisitor
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	MoleculeStampSet = std::set<MoleculeStamp*, MoleculeStampCompare>
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
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 &info)
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 matrices (m1 + m2).
template<typename Real>
DynamicRectMatrix< Real >	operator- (const DynamicRectMatrix< Real > &m1, const DynamicRectMatrix< Real > &m2)
	Return the difference of two matrices (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 matrices (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	stripComments (const std::string &S)
	Strip comments from a string.
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
bool	replaceWithWildCardSkippingFirstElement (std::vector< std::vector< std::string >::iterator > &cont, std::vector< std::string > &sequence, std::vector< std::string > &result, const std::string &wildCard)
RealType	roundMe (const RealType &x)

Variables
static constexpr double	HBAR_CM_PS = 5.3088373
constexpr double	SMALL_NUMBER = 1.0e-12
constexpr int	MAX_SCRATCH_ARRAY_SIZE = 10
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)
static const TokenEntry	tokenTable []
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
template<class Object, typename IdentType, typename Creator>
GenericFactory< Object, IdentType, Creator > *	GenericFactory< Object, IdentType, Creator >::instance_
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 171 of file AtomType.hpp.

◆ BoolGenericData

using OpenMD::BoolGenericData = SimpleTypeData<bool>

BoolGenericData is a generic data type contains a bool variable.

Definition at line 150 of file GenericData.hpp.

◆ CubicSplinePtr

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

Definition at line 89 of file CubicSpline.hpp.

◆ DataStoragePointer

typedef DataStorageSnapshot::* OpenMD::DataStoragePointer

Definition at line 375 of file Snapshot.hpp.

◆ DirectionalAtypeData

using OpenMD::DirectionalAtypeData = SimpleTypeData<DirectionalAtypeParameters>

Definition at line 63 of file DirectionalAdapter.hpp.

◆ DoubleGenericData

using OpenMD::DoubleGenericData = SimpleTypeData<RealType>

DoubleGenericData is a generic data type contains a RealType variable.

Definition at line 159 of file GenericData.hpp.

◆ DoublePolynomial

using OpenMD::DoublePolynomial = Polynomial<RealType>

Definition at line 628 of file Polynomial.hpp.

◆ DoubleVectorGenericData

using OpenMD::DoubleVectorGenericData = VectorTypeData<RealType>

Definition at line 227 of file GenericData.hpp.

◆ EAMData

using OpenMD::EAMData = SimpleTypeData<EAMParameters>

Definition at line 131 of file EAMAdapter.hpp.

◆ FixedChargeAtypeData

using OpenMD::FixedChargeAtypeData = SimpleTypeData<FixedChargeAtypeParameters>

Definition at line 62 of file FixedChargeAdapter.hpp.

◆ FloatGenericData

using OpenMD::FloatGenericData = SimpleTypeData<float>

FloatGenericData is a generic data type contains a float variable.

Definition at line 156 of file GenericData.hpp.

◆ FloatVectorGenericData

using OpenMD::FloatVectorGenericData = VectorTypeData<float>

Definition at line 221 of file GenericData.hpp.

◆ FluctuatingAtypeData

using OpenMD::FluctuatingAtypeData = SimpleTypeData<FluctuatingAtypeParameters>

Definition at line 72 of file FluctuatingChargeAdapter.hpp.

◆ FuncflData

using OpenMD::FuncflData = SimpleTypeData<FuncflParameters>

Definition at line 132 of file EAMAdapter.hpp.

◆ GBAtypeData

using OpenMD::GBAtypeData = SimpleTypeData<GBAtypeParameters>

Definition at line 67 of file GayBerneAdapter.hpp.

◆ IntGenericData

using OpenMD::IntGenericData = SimpleTypeData<int>

IntGenericData is a generic data type contains an integer variable.

Definition at line 153 of file GenericData.hpp.

◆ IntVectorGenericData

using 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 215 of file GenericData.hpp.

◆ LJAtypeData

using OpenMD::LJAtypeData = SimpleTypeData<LJAtypeParameters>

Definition at line 67 of file LennardJonesAdapter.hpp.

◆ Mat3x3d

using OpenMD::Mat3x3d = SquareMatrix3<RealType>

Definition at line 647 of file SquareMatrix3.hpp.

◆ Mat6x6d

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

Definition at line 461 of file SquareMatrix.hpp.

◆ MoleculeStampSet

using OpenMD::MoleculeStampSet = std::set<MoleculeStamp*, MoleculeStampCompare>

Definition at line 185 of file MoleculeStamp.hpp.

◆ MultipoleAtypeData

using OpenMD::MultipoleAtypeData = SimpleTypeData<MultipoleAtypeParameters>

Definition at line 66 of file MultipoleAdapter.hpp.

◆ NonBondedInteractionPtr

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

Definition at line 212 of file NonBondedInteraction.hpp.

◆ PolarizableAtypeData

using OpenMD::PolarizableAtypeData = SimpleTypeData<PolarizableAtypeParameters>

Definition at line 63 of file PolarizableAdapter.hpp.

◆ potVec

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

Definition at line 97 of file NonBondedInteraction.hpp.

◆ ProgressBarPtr

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

Definition at line 73 of file ProgressBar.hpp.

◆ Quat4d

using OpenMD::Quat4d = Quaternion<RealType>

Definition at line 630 of file Quaternion.hpp.

◆ RestraintData

using OpenMD::RestraintData = SimpleTypeData<Restraint*>

Definition at line 219 of file Restraint.hpp.

◆ RotMat3x3d

using OpenMD::RotMat3x3d = SquareMatrix3<RealType>

Definition at line 648 of file SquareMatrix3.hpp.

◆ SCAtypeData

using OpenMD::SCAtypeData = SimpleTypeData<SCAtypeParameters>

Definition at line 67 of file SuttonChenAdapter.hpp.

◆ ShapeAtypeData

using OpenMD::ShapeAtypeData = SimpleTypeData<ShapeAtomType*>

Definition at line 119 of file ShapeAtomType.hpp.

◆ SnapshotBlock

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

Definition at line 60 of file BlockSnapshotManager.hpp.

◆ StickyAtypeData

using OpenMD::StickyAtypeData = SimpleTypeData<StickyAtypeParameters>

Definition at line 70 of file StickyAdapter.hpp.

◆ StringGenericData

using 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 182 of file GenericData.hpp.

◆ StringVectorGenericData

using 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 256 of file GenericData.hpp.

◆ TeeBuf

using OpenMD::TeeBuf = basic_teebuf<char>

Definition at line 119 of file basic_teebuf.hpp.

◆ TreeNodePtr

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

Definition at line 68 of file NameFinder.hpp.

◆ UFFAtypeData

using OpenMD::UFFAtypeData = SimpleTypeData<UFFAtypeParameters>

Definition at line 73 of file UFFAdapter.hpp.

◆ Vector2d

typedef Vector2<RealType> OpenMD::Vector2d

Definition at line 121 of file Vector2.hpp.

◆ Vector2i

typedef Vector2<int> OpenMD::Vector2i

Definition at line 119 of file Vector2.hpp.

◆ Vector3d

using OpenMD::Vector3d = Vector3<RealType>

Definition at line 163 of file Vector3.hpp.

◆ Vector3i

using OpenMD::Vector3i = Vector3<int>

Definition at line 161 of file Vector3.hpp.

◆ VisitorIterator

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

Definition at line 58 of file CompositeVisitor.hpp.

◆ ZhouData

using OpenMD::ZhouData = SimpleTypeData<ZhouParameters>

Definition at line 133 of file EAMAdapter.hpp.

Enumeration Type Documentation

◆ BuckinghamType

enum OpenMD::BuckinghamType

Definition at line 75 of file BuckinghamInteractionType.hpp.

◆ communicatorType

enum OpenMD::communicatorType

Definition at line 61 of file Communicator.hpp.

◆ CutoffMethod

enum OpenMD::CutoffMethod

Definition at line 53 of file Cutoffs.hpp.

◆ EAMiType

enum OpenMD::EAMiType

Definition at line 68 of file EAMInteractionType.hpp.

◆ EAMMixingMethod

enum OpenMD::EAMMixingMethod

Definition at line 85 of file EAM.hpp.

◆ EAMType

enum OpenMD::EAMType

Definition at line 64 of file EAMAdapter.hpp.

◆ ElectrostaticScreeningMethod

enum OpenMD::ElectrostaticScreeningMethod

Definition at line 89 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 77 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 65 of file NonBondedInteraction.hpp.

◆ InversionKey

enum OpenMD::InversionKey

Definition at line 62 of file InversionType.hpp.

◆ MorseType

enum OpenMD::MorseType

Definition at line 68 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 63 of file SelectionSet.hpp.

◆ SwitchingFunctionType

enum OpenMD::SwitchingFunctionType

Definition at line 56 of file SwitchingFunction.hpp.

Function Documentation

◆ CaseInsensitiveEquals()

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

Definition at line 225 of file StringUtils.cpp.

◆ CaseInsensitiveFind()

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

Definition at line 229 of file StringUtils.cpp.

◆ CholeskyDecomposition()

template<class MatrixType>

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

Definition at line 57 of file CholeskyDecomposition.hpp.

◆ containerToString()

template<class ContainerType>

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

Definition at line 138 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 139 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< RealType >::fromShortestArc(), OpenMD::Thermo::getAngularMomentum(), OpenMD::Thermo::getInertiaTensor(), OpenMD::Inversion::getValue(), OpenMD::Torsion::getValue(), OpenMD::RPY::muRD_dot_E(), 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 470 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 547 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 483 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 560 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 452 of file DynamicVector.hpp.

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

◆ 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 509 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 529 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 605 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 614 of file Polynomial.hpp.

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

◆ equal() [2/2]

template<typename T>

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

inline

Definition at line 69 of file Vector.hpp.

◆ fastpow()

template<typename Real>

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

Definition at line 71 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 109 of file StringUtils.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 590 of file Polynomial.hpp.

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

◆ getGlobalCountOfType()

int OpenMD::getGlobalCountOfType ( AtomType * )

Definition at line 789 of file SimInfo.cpp.

◆ getPrefix()

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

Todo: need implementation

Definition at line 207 of file StringUtils.cpp.

Referenced by OpenMD::PotDiff::PotDiff().

◆ hasDuplicateElement()

template<class ContainerType>

bool OpenMD::hasDuplicateElement ( const ContainerType & cont )

Definition at line 62 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 101 of file LU.hpp.

References invertMatrix().

Referenced by OpenMD::SquareMatrix< RealType, 6 >::inverse(), invertMatrix(), and OpenMD::RPYMobility::update().

◆ 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 138 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 160 of file StringUtils.cpp.

◆ isEqual()

template<typename T>

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

inline

Definition at line 369 of file ParamConstraint.hpp.

◆ isEqualIgnoreCase()

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

Definition at line 67 of file ParamConstraint.cpp.

◆ isEven()

EvenConstraint OpenMD::isEven ( )

Definition at line 71 of file ParamConstraint.cpp.

◆ isGreaterThan()

template<typename T>

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

inline

Definition at line 374 of file ParamConstraint.hpp.

◆ isGreaterThanOrEqualTo()

template<typename T>

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

inline

Definition at line 379 of file ParamConstraint.hpp.

◆ isInteger()

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

Definition at line 211 of file StringUtils.cpp.

◆ isLessThan()

template<typename T>

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

inline

Definition at line 359 of file ParamConstraint.hpp.

◆ isLessThanOrEqualTo()

template<typename T>

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

inline

Definition at line 364 of file ParamConstraint.hpp.

◆ isNegative()

NegativeConstraint OpenMD::isNegative ( )

Definition at line 63 of file ParamConstraint.cpp.

◆ isNonNegative()

NonNegativeConstraint OpenMD::isNonNegative ( )

Definition at line 65 of file ParamConstraint.cpp.

◆ isNonPositive()

NonPositiveConstraint OpenMD::isNonPositive ( )

Definition at line 61 of file ParamConstraint.cpp.

◆ isNonZero()

ParamConstraintFacade< NonZeroConstraint > OpenMD::isNonZero ( )

Definition at line 55 of file ParamConstraint.cpp.

◆ isNotEmpty()

NotEmptyConstraint OpenMD::isNotEmpty ( )

Definition at line 51 of file ParamConstraint.cpp.

◆ isPositive()

PositiveConstraint OpenMD::isPositive ( )

Definition at line 59 of file ParamConstraint.cpp.

◆ isType()

template<typename T>

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

Definition at line 122 of file StringUtils.hpp.

◆ isZero()

ZeroConstraint OpenMD::isZero ( )

Definition at line 53 of file ParamConstraint.cpp.

◆ lexi_cast()

template<typename T>

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

Definition at line 114 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 184 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 274 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 639 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 94 of file next_combination.hpp.

Referenced by replaceWithWildCard().

◆ OpenMD_itoa()

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

Definition at line 179 of file StringUtils.cpp.

◆ operator!()

template<typename ConsT>

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

inline

Definition at line 341 of file ParamConstraint.hpp.

◆ operator&() [1/3]

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

Definition at line 188 of file OpenMDBitSet.cpp.

◆ operator&() [2/3]

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

Definition at line 752 of file SelectionManager.cpp.

◆ operator&() [3/3]

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

Definition at line 200 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 323 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).

Parameters

m	the matrix
v	the vector

Definition at line 501 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).

Parameters

m	the matrix
s	the scalar

Definition at line 455 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 matrices (m1 * m2).

Parameters

m1	the first matrix
m2	the second matrix

Definition at line 481 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 413 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 523 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 507 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 564 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 590 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 577 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 535 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 548 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 495 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 528 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 621 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 470 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 566 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).

Parameters

s	the scalar
m	the matrix

Definition at line 468 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 426 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 511 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 483 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 matrices (m1 + m2).

Parameters

m1	the first matrix
m2	the second matrix

Definition at line 429 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 383 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 206 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 552 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 461 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 441 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 417 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 matrices (m1 - m2).

Parameters

m1	the first matrix
m2	the second matrix

Definition at line 442 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 370 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 398 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 204 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 572 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 445 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 478 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 766 of file SelectionManager.cpp.

◆ operator-() [10/12]

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

Definition at line 214 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 428 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 456 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).

Parameters

m	the matrix
s	the scalar

Definition at line 519 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 439 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 617 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 584 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 496 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 604 of file Quaternion.hpp.

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

◆ operator<<() [1/21]

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

Definition at line 1029 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 530 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 659 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 570 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 235 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 98 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 91 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 88 of file LatticeFactory.cpp.

References OpenMD::LatticeFactory::getIdents().

◆ operator<<() [9/21]

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

Definition at line 442 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 91 of file OptimizationFactory.cpp.

References OpenMD::OptimizationFactory::getIdents().

◆ operator<<() [11/21]

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

Definition at line 157 of file PairList.cpp.

◆ operator<<() [12/21]

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

Definition at line 88 of file AmberImproperTorsionType.hpp.

◆ operator<<() [13/21]

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

Definition at line 251 of file OpenMDBitSet.cpp.

◆ operator<<() [14/21]

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

Definition at line 243 of file SelectionSet.cpp.

◆ operator<<() [15/21]

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

Definition at line 89 of file HarmonicInversionType.hpp.

◆ operator<<() [16/21]

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

Definition at line 108 of file HarmonicTorsionType.hpp.

◆ operator<<() [17/21]

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

Definition at line 114 of file OplsTorsionType.hpp.

◆ operator<<() [18/21]

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

Definition at line 94 of file PolynomialBendType.hpp.

◆ operator<<() [19/21]

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

Definition at line 92 of file PolynomialBondType.hpp.

◆ operator<<() [20/21]

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

Definition at line 125 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 493 of file DynamicVector.hpp.

◆ operator==() [1/3]

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

Definition at line 212 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 625 of file Quaternion.hpp.

◆ operator==() [3/3]

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

Definition at line 221 of file SelectionSet.cpp.

◆ operator^() [1/3]

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

Definition at line 196 of file OpenMDBitSet.cpp.

◆ operator^() [2/3]

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

Definition at line 759 of file SelectionManager.cpp.

◆ operator^() [3/3]

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

Definition at line 207 of file SelectionSet.cpp.

◆ operator|() [1/3]

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

Definition at line 180 of file OpenMDBitSet.cpp.

◆ operator|() [2/3]

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

Definition at line 745 of file SelectionManager.cpp.

◆ operator|() [3/3]

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

Definition at line 193 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 332 of file ParamConstraint.hpp.

◆ outProduct()

template<typename Real>

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

inline

Definition at line 634 of file SquareMatrix3.hpp.

◆ pairCompare()

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

Definition at line 60 of file Cuboctahedron.cpp.

◆ registerAll()

void OpenMD::registerAll ( )

register force fields, integrators and optimizers

Definition at line 143 of file Register.cpp.

References registerIntegrators(), and registerOptimizers().

◆ registerIntegrators()

void OpenMD::registerIntegrators ( )

Register all integrators.

Definition at line 80 of file Register.cpp.

References OpenMD::IntegratorFactory::getInstance(), and OpenMD::IntegratorFactory::registerIntegrator().

Referenced by registerAll().

◆ registerLattice()

void OpenMD::registerLattice ( )

Register all lattice.

Definition at line 134 of file Register.cpp.

References OpenMD::LatticeFactory::getInstance(), and OpenMD::LatticeFactory::registerLattice().

◆ registerOptimizers()

void OpenMD::registerOptimizers ( )

Register all optimizers.

Definition at line 125 of file Register.cpp.

References OpenMD::OptimizationFactory::getInstance(), and OpenMD::OptimizationFactory::registerOptimization().

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 58 of file Utility.cpp.

References next_combination().

Referenced by OpenMD::TypeContainer< AtomType, 1 >::find().

◆ replaceWithWildCardSkippingFirstElement()

bool OpenMD::replaceWithWildCardSkippingFirstElement	(	std::vector< std::vector< std::string >::iterator > &	cont,
		std::vector< std::string > &	sequence,
		std::vector< std::string > &	result,
		const std::string &	wildCard )

Definition at line 81 of file Utility.cpp.

◆ roundMe()

RealType OpenMD::roundMe ( const RealType & x )

inline

Definition at line 58 of file Utility.hpp.

◆ stripComments()

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

Strip comments from a string.

Parameters

S

Definition at line 64 of file StringUtils.cpp.

◆ swap_if()

template<class Cont, class Predict>

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

Definition at line 74 of file CompositeShape.cpp.

◆ toLower()

template<typename Container>

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

Definition at line 58 of file CaseConversion.hpp.

◆ toLowerCopy()

template<typename Container>

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

Definition at line 64 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 107 of file StringUtils.hpp.

◆ toUpper()

template<typename Container>

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

Definition at line 73 of file CaseConversion.hpp.

◆ toUpperCopy()

template<typename Container>

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

Definition at line 79 of file CaseConversion.hpp.

◆ UpperCase()

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

Converts a string to UPPER CASE.

Parameters

S

Definition at line 99 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 114 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 157 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 94 of file NonBondedInteraction.hpp.

◆ DirectionalTypeID

string const OpenMD::DirectionalTypeID = "Directional"

Definition at line 58 of file DirectionalAdapter.hpp.

◆ EAM_INTERACTION

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

static

Definition at line 86 of file NonBondedInteraction.hpp.

◆ EAMtypeID

string const OpenMD::EAMtypeID = "EAM"

Definition at line 59 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 84 of file NonBondedInteraction.hpp.

◆ epsilon

RealType OpenMD::epsilon = 0.000001

staticconstexpr

Definition at line 66 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 57 of file FixedChargeAdapter.hpp.

◆ FQtypeID

string const OpenMD::FQtypeID = "FlucQ"

Definition at line 58 of file FluctuatingChargeAdapter.hpp.

◆ FuncflTypeID

string const OpenMD::FuncflTypeID = "FUNCFL"

Definition at line 60 of file EAMAdapter.hpp.

◆ GB_INTERACTION

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

static

Definition at line 89 of file NonBondedInteraction.hpp.

◆ GBtypeID

string const OpenMD::GBtypeID = "GB"

Definition at line 57 of file GayBerneAdapter.hpp.

◆ GenericFactory< Object, IdentType, Creator >::instance_

template<class Object, typename IdentType, typename Creator>

GenericFactory<Object, IdentType, Creator>* OpenMD::GenericFactory< Object, IdentType, Creator >::instance_

Definition at line 252 of file GenericFactory.hpp.

◆ HBAR_CM_PS

double OpenMD::HBAR_CM_PS = 5.3088373

staticconstexpr

Definition at line 78 of file SFG.cpp.

◆ INVERSEPOWERSERIES_INTERACTION

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

static

Definition at line 95 of file NonBondedInteraction.hpp.

◆ LJ_INTERACTION

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

static

Definition at line 85 of file NonBondedInteraction.hpp.

◆ LJtypeID

string const OpenMD::LJtypeID = "LJ"

Definition at line 57 of file LennardJonesAdapter.hpp.

◆ MAW_INTERACTION

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

static

Definition at line 92 of file NonBondedInteraction.hpp.

◆ MAX_SCRATCH_ARRAY_SIZE

int OpenMD::MAX_SCRATCH_ARRAY_SIZE = 10

constexpr

Definition at line 91 of file LU.hpp.

◆ MIE_INTERACTION

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

static

Definition at line 93 of file NonBondedInteraction.hpp.

◆ MORSE_INTERACTION

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

static

Definition at line 90 of file NonBondedInteraction.hpp.

◆ MultipoleTypeID

string const OpenMD::MultipoleTypeID = "Multipole"

Definition at line 58 of file MultipoleAdapter.hpp.

◆ PolTypeID

string const OpenMD::PolTypeID = "Polarizable"

Definition at line 57 of file PolarizableAdapter.hpp.

◆ progressSpinner_

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

Definition at line 76 of file ProgressBar.cpp.

◆ REPULSIVEPOWER_INTERACTION

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

static

Definition at line 91 of file NonBondedInteraction.hpp.

◆ SC_INTERACTION

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

static

Definition at line 87 of file NonBondedInteraction.hpp.

◆ SCtypeID

string const OpenMD::SCtypeID = "SC"

Definition at line 57 of file SuttonChenAdapter.hpp.

◆ SMALL_NUMBER

double OpenMD::SMALL_NUMBER = 1.0e-12

constexpr

Definition at line 90 of file LU.hpp.

◆ STICKY_INTERACTION

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

static

Definition at line 88 of file NonBondedInteraction.hpp.

◆ StickyTypeID

string const OpenMD::StickyTypeID = "Sticky"

Definition at line 57 of file StickyAdapter.hpp.

◆ tokenTable

const TokenEntry OpenMD::tokenTable[]

static

Definition at line 60 of file TokenMap.cpp.

◆ UFFtypeID

string const OpenMD::UFFtypeID = "UFF"

Definition at line 57 of file UFFAdapter.hpp.

◆ ZhouRoseTypeID

string const OpenMD::ZhouRoseTypeID = "ZHOUROSE"

Definition at line 62 of file EAMAdapter.hpp.

◆ ZhouTypeID

string const OpenMD::ZhouTypeID = "ZHOU"

Definition at line 61 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

◆ MoleculeStampSet

◆ 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]