Namespaces
	Constants

Classes
class	Accumulator

class	ActionCorrFunc

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

class	AlphaHullFinder

class	AmberImproperTorsionType

class	AnalyticalModel

struct	AndParamConstraint

class	AngleR

class	ApproximationModel

class	Atom

class	AtomData

struct	AtomInfo

class	AtomNameVisitor

class	AtomStamp

class	AtomType

class	AtomTypesSectionParser

class	AutoCorrFunc

class	BAOAB
	Declaration of the Langevin Dynamics BAOAB Integrator. More...

class	BaseAccumulator

class	BaseAtomTypesSectionParser

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

struct	BeadLattice

class	BeadModel

struct	BeadParam

class	Bend

struct	BendData

struct	BendDataSet

class	BendStamp

class	BendType

class	BendTypeParser

class	BendTypesSectionParser

class	BlockSnapshotManager

class	Bond

class	BondAngleDistribution
	BondAngleDistribution. More...

class	BondCorrFunc

class	BondOrderParameter
	Bond Order Parameter. More...

class	BondStamp

class	BondType

class	BondTypeParser

class	BondTypesSectionParser

class	BOPofR

class	BoxObjectiveFunction

class	Buckingham

struct	BuckinghamInteractionData

class	BuckinghamInteractionType

class	CenterOfMass

struct	CharClassification

class	ChargeAtomTypesSectionParser

class	ChargeField

class	ChargeHistogram

struct	CharmmTorsionParameter

class	CharmmTorsionType

class	ChebyshevT

class	ChebyshevU

class	COHZ

class	Communicator

class	Comparator

class	Component

class	CompositeShape

class	CompositeVisitor

class	COMVel

struct	ConstraintData

class	ConstraintElem

class	ConstraintPair

class	ConstraintStamp

class	ConstraintWriter

class	ContactAngle1

class	ContactAngle2

struct	ContainsConstraint

class	ConvexHull

class	CoordinationNumber
	CoordinationNumber. More...

class	CosineBendType

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	CutoffGroup

class	CutoffGroupStamp

class	DataHolder

class	DataStorage

class	Decahedron

class	DefaultAtomVisitor

class	DensityField

class	DensityHistogram

class	DensityPlot

class	DipoleCorrFunc

class	DipoleField

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
	Base class for Dynamic properties. More...

class	DynamicRectMatrix
	rectangular matrix class More...

class	DynamicVector
	Fix length vector class. More...

class	EAM

class	EAMAdapter

struct	EAMAtomData

class	EAMAtomTypesSectionParser

struct	EAMInteractionData

class	EAMInteractionType

struct	EAMParameters

class	Electrostatic

struct	ElectrostaticAtomData

class	ElectrostaticInteraction

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. In particular, the Langevin algorithms must assume specific atomic radii to predict drag and random forces on those atoms. For force fields which do not specify Lennard-Jones radii, the element's van der Waals radius is used instead. The ElementsTable class (etab) is declared as external in ElementsTable.cpp. Source files that include the header file ElementsTable.hpp automatically have an extern definition to etab. The following code sample demonstrates the use of the ElementsTable class: More...

class	Ellipsoid

class	EnergyCorrFunc

struct	EqualConstraint

struct	EqualIgnoreCaseConstraint

class	Equipartition

struct	EvenConstraint

struct	ExteriorFunctor

class	FCCLattice

class	FCCOfR

class	Field

class	FixedBondType

class	FixedChargeAdapter

struct	FixedChargeAtypeParameters

struct	FluctuatingAtypeParameters

class	FluctuatingChargeAdapter

struct	FluctuatingChargeAtomData

class	FluctuatingChargeAtomTypesSectionParser

class	FluctuatingChargeConstraints

class	FluctuatingChargeDamped

class	FluctuatingChargeForces

class	FluctuatingChargeLangevin

class	FluctuatingChargeNVE

class	FluctuatingChargeNVT

class	FluctuatingChargeObjectiveFunction

class	FluctuatingChargeParameters

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

class	ForceAutoCorrFunc

class	ForceDecomposition

class	ForceField

class	ForceFieldOptions

class	ForceManager

class	ForceMatrixDecomposition

class	ForTorCorrFunc

class	FragmentStamp

struct	FrameData

class	FrameTimeCorrFunc

class	FreqFlucCorrFunc
	Frequency Fluctuation Correlation Function. More...

struct	FromRangeFunctor

struct	FuncflParameters

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
	Base class for generic data which is associated with an id. 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

class	HarmonicInversionType

class	HarmonicTorsionType

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

class	HBondJump

class	HBondJumpZ

class	HBondPersistence

class	Hull

class	HullFinder

class	Hxy

class	HydrodynamicsModel

class	HydrodynamicsModelBuilder

class	HydrodynamicsModelCreator

class	HydrodynamicsModelFactory

class	HydrogenBondingInteraction

class	HydroProp

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

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

struct	InteractionData

class	InteractionManager

class	InteractionTimeCorrFunc

struct	InteriorFunctor

class	InversePowerSeries

struct	InversePowerSeriesInteractionData

class	InversePowerSeriesInteractionType

class	Inversion

struct	InversionData

struct	InversionDataSet

class	InversionStamp

class	InversionType

class	InversionTypeParser

class	InversionTypesSectionParser

class	Kirkwood

class	KirkwoodQuadrupoles

class	LangevinDynamics

class	LangevinHullDynamics

class	LangevinHullForceManager

class	Lattice

class	LatticeBuilder

class	LatticeCreator

class	LatticeFactory

class	LDForceManager

class	LegendreCorrFunc

class	LegendreCorrFuncZ

class	LegendrePolynomial

class	LennardJonesAdapter

class	LennardJonesAtomTypesSectionParser

class	LennardJonesInteractionType

struct	LessThanConstraint

struct	LessThanOrEqualToConstraint

class	LessThanPeriodicityFunctor

class	LipidHeadVisitor

class	LipidTransVisitor

class	LJ

struct	LJAtypeParameters

struct	LJInteractionData

class	LocalIndexManager

struct	logical_xor

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

class	MatrixAccumulator

class	MAW

struct	MAWInteractionData

class	MAWInteractionType

class	MemoryUtils

class	MetallicInteraction

class	Mie

struct	MieInteractionData

class	MieInteractionType

class	MinimizerParameters

class	MolecularRestraint

class	Molecule

class	MoleculeCreator

class	MoleculeStamp

class	MoLocator

class	MomAngMomCorrFunc

struct	MomentData

class	MomentumCorrFunc

class	MomentumHistogram

class	Morse

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

struct	MorseInteractionData

class	MorseInteractionType

class	MPITraits

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

class	MPITraits< SquareMatrix3< T > >

class	MPITraits< Vector3< T > >

class	MPITraits< Vector< T, Dim > >

class	MTRand

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

class	MultipoleAdapter

class	MultipoleAtomTypesSectionParser

struct	MultipoleAtypeParameters

class	MultipoleSum

class	NameFinder

class	NanoLength

class	NanoVolume

struct	NegativeConstraint

class	NgammaT

class	NitrileFrequencyMap

class	NonBondedInteraction

class	NonBondedInteractionsSectionParser

class	NonBondedInteractionType

struct	NonBondedInteractionTypeProperties

struct	NonNegativeConstraint

struct	NonPositiveConstraint

struct	NonZeroConstraint

class	NoStatus
	No status. More...

struct	NotEmptyConstraint

struct	NotParamConstraint

class	NPA

class	NPAT

class	NPrT

class	NPT

class	NPTf

class	NPTi

class	NPTsz

class	NPTxyz

class	NVE

class	NVT

class	ObjectCount

class	ObjectRestraint

class	ogzstream

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

class	OpenMDException

class	OplsTorsionType

class	OptimizationBuilder

class	OptimizationCreator

class	OptimizationFactory

class	OptionSectionParser

struct	OrParamConstraint

struct	OutputData

class	P2OrderParameter

class	PairList
	PairList class maintains a general purpose list of atom pairs using the global indices of the atoms. This structure is the general form for exclude lists as well as 1-4, 1-3, and 1-2 lists. More...

class	pAngle

class	ParallelRandNumGen
	a parallel random number generator More...

struct	ParamConstraintFacade

class	ParticleTimeCorrFunc

class	Perturbation
	Abstract class for external perturbation classes. More...

class	PipeDensity

class	Plan

class	PolarizableAdapter

class	PolarizableAtomTypesSectionParser

struct	PolarizableAtypeParameters

class	Polynomial

class	PolynomialBendType

class	PolynomialBondType

class	PolynomialInversionType

class	PolynomialTorsionType

struct	PositiveConstraint

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

class	PotentialEnergyObjectiveFunction

class	PotVecAccumulator

struct	PredAndFunctor

struct	PredFacade

struct	PredNotFunctor

struct	PredOrFunctor

class	PrepareVisitor

class	ProgressBar

class	PropertyMap

class	QuarticBendType

class	QuarticBondType

class	QuarticTorsionType

class	Quaternion

class	RadialDistrFunc
	Radial Distribution Function. More...

class	RandNumGen
	a random number generator class More...

class	Rattle

class	RBCOMVisitor

class	RCorrFunc

class	RCorrFuncR

class	RCorrFuncZ

class	RealSphericalHarmonic

class	RealSymmetricTridiagonal

class	RectMatrix
	rectangular matrix class More...

class	RegularCuboctahedron

class	RegularDecahedron

class	ReplacementVisitor

class	ReplicateVisitor

class	RepulsivePower

class	RepulsivePowerInteractionType

class	Restraint

class	RestraintForceManager

class	RestraintStamp

class	RestReader

class	RestWriter

class	Revision

class	RhoR

class	RhoZ

class	RigidBody

class	RigidBodyStamp

class	RippleOP

class	RMSD

class	RNEMD

class	RNEMDParameters

class	RNEMDR

class	RNEMDRTheta

class	RNEMDZ

class	RotationAlgorithm
	abstract class for rotation More...

class	RoughShell

struct	RPInteractionData

class	SameSectionParserFunctor

class	SC

struct	SCAtomData

class	SCAtomTypesSectionParser

struct	SCAtypeParameters

class	SCDElem

class	SCDOrderParameter

struct	SCInteractionData

class	SCLattice

class	SCN
	Secondary Coordinate Number. More...

class	SDKBend

class	SDKBendType

struct	SDShape

class	SectionParser

struct	SectionParserContext

class	SectionParserManager

class	SelectionCompiler
	compile a selection script to tokens More...

class	SelectionCorrFunc

class	SelectionEvaluator
	Evalute the tokens compiled by SelectionCompiler and return a OpenMDBitSet. More...

class	SelectionManager

class	SelectionSet

struct	SelfData

class	SeqRandNumGen
	a sequential random number generator More...

class	SequentialAnalyzer
	Base class for Sequence Analyzer. More...

class	Shake

class	Shape

class	ShapeAtomType

class	ShapeAtomTypesSectionParser

class	ShapeBuilder

class	shapedLattice

class	shapedLatticeEllipsoid

class	shapedLatticePentRod

class	shapedLatticeRod

class	shapedLatticeSpherical

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. Bonds, Bends, Torsions, Inversions). More...

class	SimCreator

class	SimInfo
	One of the heavy-weight classes of OpenMD, SimInfo maintains objects and variables relating to the current simulation. This includes the master list of Molecules. The Molecule class maintains all of the concrete objects (Atoms, Bond, Bend, Torsions, Inversions, RigidBodies, CutoffGroups, Constraints). In both the single and parallel versions, Atoms and RigidBodies have both global and local indices. More...

class	SimplePreprocessor

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

class	SimSnapshotManager
	SimSnapshotManager class is the concrete snapshot manager for actual simulation SimSnapshotManager only maintains two snapshots. More...

class	SlabStatistics

class	Snapshot
	The Snapshot class is a repository storing dynamic data during a Simulation. Every Snapshot contains FrameData (for global information) as well as DataStorage (one for Atoms, one for RigidBodies, and one for CutoffGroups). More...

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

class	SpatialStatistics

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

struct	StickyAtypeParameters

struct	StickyInteractionData

class	StickyPowerAtomTypesSectionParser

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. An instance of StringTokenizer behaves in one of two ways, depending on whether it was created with the returnTokens flag having the value true or false. 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	SystemDecomposition

class	SystemDipoleCorrFunc

class	TetrahedralityHBMatrix
	Tetrahedrality Hydrogen Bonding Matrix. More...

class	TetrahedralityParam
	Tetrahedrality Parameter. More...

class	TetrahedralityParamDens
	Tetrahedrality ParameterDens. More...

class	TetrahedralityParamXYZ
	Tetrahedrality Parameter XYZ. More...

class	TetrahedralityParamZ
	Tetrahedrality ParameterZ. More...

class	Thermo

class	ThermoIntegrationForceManager

class	ThetaCorrFunc

class	TimeCorrFunc
	Base class for Correlation function. More...

struct	to_bool

class	Token

class	TokenMap

struct	toLowerFunctor

class	TorForCorrFunc

class	TorqueAutoCorrFunc

class	Torsion

struct	TorsionData

struct	TorsionDataSet

class	TorsionStamp

class	TorsionType

class	TorsionTypeParser

class	TorsionTypesSectionParser

struct	toUpperFunctor

class	TrappeTorsionType

class	TreeNode

class	Triangle

class	TruncatedCube

struct	tuple3

struct	tuple4

class	TupleMatcher

class	TwoDGofR

class	TypeContainer

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

class	VCorrFunc

class	VCorrFuncR

class	VCorrFuncZ

class	Vector
	Fix length vector class. More...

class	Vector3

class	VectorAccumulator

class	VectorTypeData

class	Velocitizer
	Velocity-modifying routines. More...

class	VelocityField

class	VelocityVerletIntegrator

class	VelocityZ

class	WaterTypeVisitor

class	WCorrFunc

class	WrappingVisitor

class	XYZVisitor

struct	ZconsData

class	ZConsReader

class	ZConsStamp

class	ZconstraintForceManager

struct	ZconstraintMol

struct	ZconstraintParam

class	ZConsVisitor

class	ZConsWriter

struct	ZeroConstraint

struct	ZhouParameters

Typedefs
typedef std::pair< int, int >	SnapshotBlock

typedef DataStorageSnapshot::*	DataStoragePointer

typedef basic_teebuf< char >	TeeBuf

typedef Polynomial< RealType >	DoublePolynomial

typedef Quaternion< RealType >	Quat4d

typedef SquareMatrix< RealType, 6 >	Mat6x6d

typedef SquareMatrix3< RealType >	Mat3x3d

typedef SquareMatrix3< RealType >	RotMat3x3d

typedef Vector3< int >	Vector3i

typedef Vector3< RealType >	Vector3d

typedef Vector< RealType, N_INTERACTION_FAMILIES >	potVec

typedef SimpleTypeData< Restraint * >	RestraintData

typedef SimpleTypeData< DirectionalAtypeParameters * >	DirectionalAtypeData

typedef SimpleTypeData< EAMParameters * >	EAMData

typedef SimpleTypeData< FuncflParameters * >	FuncflData

typedef SimpleTypeData< ZhouParameters * >	ZhouData

typedef SimpleTypeData< FixedChargeAtypeParameters * >	FixedChargeAtypeData

typedef SimpleTypeData< FluctuatingAtypeParameters * >	FluctuatingAtypeData

typedef SimpleTypeData< GBAtypeParameters * >	GBAtypeData

typedef SimpleTypeData< LJAtypeParameters * >	LJAtypeData

typedef SimpleTypeData< MultipoleAtypeParameters * >	MultipoleAtypeData

typedef SimpleTypeData< PolarizableAtypeParameters * >	PolarizableAtypeData

typedef SimpleTypeData< ShapeAtomType * >	ShapeAtypeData

typedef SimpleTypeData< StickyAtypeParameters * >	StickyAtypeData

typedef SimpleTypeData< SCAtypeParameters * >	SCAtypeData

typedef SimpleTypeData< bool >	BoolGenericData

typedef SimpleTypeData< int >	IntGenericData

typedef SimpleTypeData< float >	FloatGenericData

typedef SimpleTypeData< RealType >	DoubleGenericData

typedef SimpleTypeData< std::string >	StringGenericData

typedef VectorTypeData< int >	IntVectorGenericData

typedef VectorTypeData< float >	FloatVectorGenericData

typedef VectorTypeData< RealType >	DoubleVectorGenericData

typedef VectorTypeData< std::string >	StringVectorGenericData

typedef tuple3< int, int, int >	IntTuple3

typedef tuple4< int, int, int, int >	IntTuple4

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

Enumerations
enum	OutputDataType { odtReal, odtVector3, odtArray2d, odtUnknownDataType }

enum	OutputDataHandling { odhAverage, odhTotal, odhLastValue, odhMax, odhUnknownDataHandling }

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 = 1, ELECTROSTATIC_FAMILY = 2, METALLIC_EMBEDDING_FAMILY = 3, METALLIC_PAIR_FAMILY = 4, HYDROGENBONDING_FAMILY = 5, BONDED_FAMILY = 6, N_INTERACTION_FAMILIES = 7 }

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 }

enum	BuckinghamType { btTraditional, btModified, btUnknown }

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

enum	EAMiType { eamitTabulated, eamitZhou }

enum	InversionKey { itAngle, itCosAngle }

enum	MorseType { mtShifted, mtRepulsive, mtUnknown }

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

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

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

void	registerIntegrators ()

void	registerOptimizers ()

void	registerLattice ()

void	registerAll ()

int	getGlobalCountOfType (AtomType *atype)

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

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

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

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)

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

template<typename Real >
DynamicRectMatrix< Real >	operator - (const DynamicRectMatrix< Real > &m)

template<typename Real >
DynamicRectMatrix< Real >	operator+ (const DynamicRectMatrix< Real > &m1, const DynamicRectMatrix< Real > &m2)

template<typename Real >
DynamicRectMatrix< Real >	operator - (const DynamicRectMatrix< Real > &m1, const DynamicRectMatrix< Real > &m2)

template<typename Real >
DynamicRectMatrix< Real >	operator * (const DynamicRectMatrix< Real > &m, Real s)

template<typename Real >
DynamicRectMatrix< Real >	operator * (Real s, const DynamicRectMatrix< Real > &m)

template<typename Real >
DynamicRectMatrix< Real >	operator * (const DynamicRectMatrix< Real > &m1, const DynamicRectMatrix< Real > &m2)

template<typename Real >
DynamicVector< Real >	operator * (const DynamicRectMatrix< Real > &m, const DynamicVector< Real > &v)

template<typename Real >
DynamicRectMatrix< Real >	operator/ (const DynamicRectMatrix< Real > &m, Real s)

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

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

template<typename Real >
DynamicVector< Real >	operator+ (const DynamicVector< Real > &v1, const DynamicVector< Real > &v2)

template<typename Real >
DynamicVector< Real >	operator - (const DynamicVector< Real > &v1, const DynamicVector< Real > &v2)

template<typename Real >
DynamicVector< Real >	operator * (const DynamicVector< Real > &v1, Real s)

template<typename Real >
DynamicVector< Real >	operator * (Real s, const DynamicVector< Real > &v1)

template<typename Real >
DynamicVector< Real >	operator/ (const DynamicVector< Real > &v1, Real s)

template<typename Real >
Real	dot (const DynamicVector< Real > &v1, const DynamicVector< Real > &v2)

template<typename Real >
Real	distance (const DynamicVector< Real > &v1, const DynamicVector< Real > &v2)

template<typename Real >
Real	distanceSquare (const DynamicVector< Real > &v1, const DynamicVector< Real > &v2)

template<typename Real >
std::ostream &	operator<< (std::ostream &o, const DynamicVector< Real > &v)

template<class MatrixType >
bool	invertMatrix (MatrixType &A, MatrixType &AI)

template<class MatrixType >
bool	invertMatrix (MatrixType &A, MatrixType &AI, unsigned int size, int *tmp1Size, typename MatrixType::ElemPoinerType tmp2Size)

template<class MatrixType >
int	LUFactorLinearSystem (MatrixType &A, int *index, int size, typename MatrixType::ElemPoinerType tmpSize)

template<class MatrixType >
void	LUSolveLinearSystem (MatrixType &A, int *index, typename MatrixType::ElemPoinerType x, int size)

std::ostream &	operator<< (std::ostream &os, const MTRand &mtrand)

std::istream &	operator>> (std::istream &is, MTRand &mtrand)

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

template<typename Real >
Polynomial< Real >	operator * (const Polynomial< Real > &p1, const Polynomial< Real > &p2)

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)

template<typename Real >
Polynomial< Real >	operator - (const Polynomial< Real > &p1, const Polynomial< Real > &p2)

template<typename Real >
Polynomial< Real > *	getDerivative (const Polynomial< Real > &p1)

template<typename Real >
bool	equal (const Polynomial< Real > &p1, const Polynomial< Real > &p2)

template<typename Real , unsigned int Dim>
Quaternion< Real >	operator * (const Quaternion< Real > &q, Real s)

template<typename Real , unsigned int Dim>
Quaternion< Real >	operator * (const Real &s, const Quaternion< Real > &q)

template<typename Real >
Quaternion< Real >	operator * (const Quaternion< Real > &q1, const Quaternion< Real > &q2)

template<typename Real >
Quaternion< Real >	operator/ (Quaternion< Real > &q1, Quaternion< Real > &q2)

template<typename Real >
Quaternion< Real >	operator/ (const Real &s, Quaternion< Real > &q)

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)

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)

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)

template<typename Real , unsigned int Row, unsigned int Col>
RectMatrix< Real, Row, Col >	operator * (const RectMatrix< Real, Row, Col > &m, Real s)

template<typename Real , unsigned int Row, unsigned int Col>
RectMatrix< Real, Row, Col >	operator * (Real s, const RectMatrix< Real, Row, Col > &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)

template<typename Real , unsigned int Row, unsigned int Col>
Vector< Real, Row >	operator * (const RectMatrix< Real, Row, Col > &m, const Vector< Real, Col > &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)

template<typename Real , unsigned int Row, unsigned int Col>
RectMatrix< Real, Row, Col >	operator/ (const RectMatrix< Real, Row, Col > &m, Real s)

template<typename Real , unsigned int Row, unsigned int Col>
Real	doubleDot (const RectMatrix< Real, Row, Col > &t1, const RectMatrix< Real, Row, Col > &t2)

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)

template<typename Real , unsigned int Row, unsigned int Col>
std::ostream &	operator<< (std::ostream &o, const RectMatrix< Real, Row, Col > &m)

template<typename Real >
SquareMatrix3< Real >	operator * (const SquareMatrix3< Real > &m1, const SquareMatrix3< Real > &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<>
bool	equal (RealType e1, RealType e2)

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

template<typename Real , unsigned int Dim>
Vector< Real, Dim >	operator+ (const Vector< Real, Dim > &v1, const Vector< Real, Dim > &v2)

template<typename Real , unsigned int Dim>
Vector< Real, Dim >	operator - (const Vector< Real, Dim > &v1, const Vector< Real, Dim > &v2)

template<typename Real , unsigned int Dim>
Vector< Real, Dim >	operator * (const Vector< Real, Dim > &v1, Real s)

template<typename Real , unsigned int Dim>
Vector< Real, Dim >	operator * (Real s, const Vector< Real, Dim > &v1)

template<typename Real , unsigned int Dim>
Vector< Real, Dim >	operator/ (const Vector< Real, Dim > &v1, Real s)

template<typename Real , unsigned int Dim>
Real	dot (const Vector< Real, Dim > &v1, const Vector< Real, Dim > &v2)

template<typename Real , unsigned int Dim>
Real	dot (const Vector< Real, Dim > &v1, const Vector< Real, Dim > &v2, const Vector< Real, Dim > &v3)

template<typename Real , unsigned int Dim>
Real	distance (const Vector< Real, Dim > &v1, const Vector< Real, Dim > &v2)

template<typename Real , unsigned int Dim>
Real	distanceSquare (const Vector< Real, Dim > &v1, const Vector< Real, Dim > &v2)

template<typename Real , unsigned int Dim>
std::ostream &	operator<< (std::ostream &o, const Vector< Real, Dim > &v)

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

template<typename Real >
Real	Vlinear (const Vector3< Real > &p, const Vector3< Real > &s)

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

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)

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

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

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

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 InputIterator , typename OutputIterator , typename Predicate >
OutputIterator	copy_if (InputIterator first, InputIterator last, OutputIterator result, Predicate p)

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

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

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

template<class RandomAccessIterator >
bool	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. More...

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)

CharClassification	isSpace (const std::locale &loc=std::locale())

CharClassification	isAlnum (const std::locale &loc=std::locale())

CharClassification	isAlpha (const std::locale &loc=std::locale())

CharClassification	isCntrl (const std::locale &loc=std::locale())

CharClassification	isDigit (const std::locale &loc=std::locale())

CharClassification	isGraph (const std::locale &loc=std::locale())

CharClassification	isLower (const std::locale &loc=std::locale())

CharClassification	isPrint (const std::locale &loc=std::locale())

CharClassification	isPunct (const std::locale &loc=std::locale())

CharClassification	isUpper (const std::locale &loc=std::locale())

CharClassification	isXDigit (const std::locale &loc=std::locale())

template<typename CharT >
FromRangeFunctor< CharT >	isFromRange (CharT from, CharT to)

template<typename Pred1T , typename Pred2T >
PredAndFunctor< Pred1T, Pred2T >	operator && (const PredFacade< Pred1T > &Pred1, const PredFacade< Pred2T > &Pred2)

template<typename Pred1T , typename Pred2T >
PredOrFunctor< Pred1T, Pred2T >	operator\|\| (const PredFacade< Pred1T > &Pred1, const PredFacade< Pred2T > &Pred2)

template<typename PredT >
PredNotFunctor< PredT >	operator! (const PredFacade< PredT > &Pred)

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

std::string	LowerCase (const std::string &S)

char *	trimSpaces (char *str)

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

int	countTokens (char line, char delimiters)

int	isEndLine (char *line)

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

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

std::string	getSuffix (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)

unsigned long long	memparse (char ptr, char *retptr)

template<typename T >
std::string	toString (const T &v)

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

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

template<typename T >
std::string	to_string (T value)

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

void	trimLeft (std::string &str)

void	trimRight (std::string &str)

void	trim (std::string &str)

std::string	trimLeftCopy (const std::string &input)

std::string	trimRightCopy (const std::string &input)

std::string	trimCopy (const std::string &input)

template<typename P >
void	trimLeftIf (std::string &str, P pred)

template<typename P >
void	trimRightIf (std::string &str, P pred)

template<typename P >
void	trimIf (std::string &str, P pred)

template<typename P >
std::string	trimLeftCopyIf (const std::string &input, P pred)

template<typename P >
std::string	trimRightCopyIf (const std::string &input, P pred)

template<typename P >
std::string	trimCopyIf (const std::string &input, P pred)

template<class T1 , class T2 , class T3 >
tuple3< T1, T2, T3 >	make_tuple3 (T1 t1, T2 t2, T3 t3)

template<class T1 , class T2 , class T3 , class T4 >
tuple4< T1, T2, T3, T4 >	make_tuple4 (T1 t1, T2 t2, T3 t3, T4 t4)

template<class T1 , class T2 , class T3 >
bool	operator< (const tuple3< T1, T2, T3 > &t1, const tuple3< T1, T2, T3 > &t2)

bool	operator< (const tuple3< int, int, std::vector< std::string > > &t1, const tuple3< int, int, std::vector< std::string > > &t2)

template<class T1 , class T2 , class T3 , class T4 >
bool	operator< (const tuple4< T1, T2, T3, T4 > &t1, const tuple4< T1, T2, T3, T4 > &t2)

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

RealType	roundMe (const RealType &x)

Variables
const Mat3x3d	M3Zero (0.0)

static const RealType	epsilon = 0.000001

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)

static const int	LJ_INTERACTION = (1 << 1)

static const int	EAM_INTERACTION = (1 << 2)

static const int	SC_INTERACTION = (1 << 3)

static const int	STICKY_INTERACTION = (1 << 4)

static const int	GB_INTERACTION = (1 << 5)

static const int	MORSE_INTERACTION = (1 << 6)

static const int	REPULSIVEPOWER_INTERACTION = (1 << 7)

static const int	MAW_INTERACTION = (1 << 8)

static const int	MIE_INTERACTION = (1 << 9)

static const int	BUCKINGHAM_INTERACTION = (1 << 10)

static const int	INVERSEPOWERSERIES_INTERACTION = (1 << 11)

string const	DirectionalTypeID = "Directional"

string const	EAMtypeID = "EAM"

string const	FuncflTypeID = "FUNCFL"

string const	ZhouTypeID = "ZHOU"

string const	ZhouRoseTypeID = "ZHOUROSE"

string const	FCtypeID = "Charge"

string const	FQtypeID = "FlucQ"

string const	GBtypeID = "GB"

string const	LJtypeID = "LJ"

string const	MultipoleTypeID = "Multipole"

string const	PolTypeID = "Polarizable"

string const	StickyTypeID = "Sticky"

string const	SCtypeID = "SC"

ElementsTable	etab

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

Typedef Documentation

◆ BoolGenericData

typedef SimpleTypeData<bool> OpenMD::BoolGenericData

BoolGenericData is a generic data type contains a bool variable

Definition at line 144 of file GenericData.hpp.

◆ DataStoragePointer

typedef DataStorageSnapshot::* OpenMD::DataStoragePointer

Definition at line 331 of file Snapshot.hpp.

◆ DirectionalAtypeData

typedef SimpleTypeData<DirectionalAtypeParameters*> OpenMD::DirectionalAtypeData

Definition at line 58 of file DirectionalAdapter.hpp.

◆ DoubleGenericData

typedef SimpleTypeData<RealType> OpenMD::DoubleGenericData

DoubleGenericData is a generic data type contains a RealType variable

Definition at line 153 of file GenericData.hpp.

◆ DoublePolynomial

typedef Polynomial<RealType> OpenMD::DoublePolynomial

Definition at line 669 of file Polynomial.hpp.

◆ DoubleVectorGenericData

typedef VectorTypeData<RealType> OpenMD::DoubleVectorGenericData

Definition at line 223 of file GenericData.hpp.

◆ EAMData

typedef SimpleTypeData<EAMParameters*> OpenMD::EAMData

Definition at line 124 of file EAMAdapter.hpp.

◆ FixedChargeAtypeData

typedef SimpleTypeData<FixedChargeAtypeParameters*> OpenMD::FixedChargeAtypeData

Definition at line 57 of file FixedChargeAdapter.hpp.

◆ FloatGenericData

typedef SimpleTypeData<float> OpenMD::FloatGenericData

FloatGenericData is a generic data type contains a float variable

Definition at line 150 of file GenericData.hpp.

◆ FloatVectorGenericData

typedef VectorTypeData<float> OpenMD::FloatVectorGenericData

Definition at line 217 of file GenericData.hpp.

◆ FluctuatingAtypeData

typedef SimpleTypeData<FluctuatingAtypeParameters*> OpenMD::FluctuatingAtypeData

Definition at line 69 of file FluctuatingChargeAdapter.hpp.

◆ FuncflData

typedef SimpleTypeData<FuncflParameters*> OpenMD::FuncflData

Definition at line 125 of file EAMAdapter.hpp.

◆ GBAtypeData

typedef SimpleTypeData<GBAtypeParameters*> OpenMD::GBAtypeData

Definition at line 62 of file GayBerneAdapter.hpp.

◆ IntGenericData

typedef SimpleTypeData<int> OpenMD::IntGenericData

IntGenericData is a generic data type contains an integer variable

Definition at line 147 of file GenericData.hpp.

◆ IntTuple3

typedef tuple3<int, int, int> OpenMD::IntTuple3

Definition at line 122 of file Tuple.hpp.

◆ IntTuple4

typedef tuple4<int, int, int, int> OpenMD::IntTuple4

Definition at line 123 of file Tuple.hpp.

◆ IntVectorGenericData

OpenMD::IntVectorGenericData

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

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

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

Definition at line 211 of file GenericData.hpp.

◆ LJAtypeData

typedef SimpleTypeData<LJAtypeParameters*> OpenMD::LJAtypeData

Definition at line 59 of file LennardJonesAdapter.hpp.

◆ Mat3x3d

typedef SquareMatrix3<RealType> OpenMD::Mat3x3d

Definition at line 635 of file SquareMatrix3.hpp.

◆ Mat6x6d

typedef SquareMatrix<RealType, 6> OpenMD::Mat6x6d

Definition at line 452 of file SquareMatrix.hpp.

◆ MultipoleAtypeData

typedef SimpleTypeData<MultipoleAtypeParameters*> OpenMD::MultipoleAtypeData

Definition at line 61 of file MultipoleAdapter.hpp.

◆ PolarizableAtypeData

typedef SimpleTypeData<PolarizableAtypeParameters*> OpenMD::PolarizableAtypeData

Definition at line 57 of file PolarizableAdapter.hpp.

◆ potVec

typedef Vector<RealType, N_INTERACTION_FAMILIES> OpenMD::potVec

Definition at line 87 of file NonBondedInteraction.hpp.

◆ Quat4d

typedef Quaternion<RealType> OpenMD::Quat4d

Definition at line 651 of file Quaternion.hpp.

◆ RestraintData

typedef SimpleTypeData<Restraint*> OpenMD::RestraintData

Definition at line 174 of file Restraint.hpp.

◆ RotMat3x3d

typedef SquareMatrix3<RealType> OpenMD::RotMat3x3d

Definition at line 636 of file SquareMatrix3.hpp.

◆ SCAtypeData

typedef SimpleTypeData<SCAtypeParameters*> OpenMD::SCAtypeData

Definition at line 61 of file SuttonChenAdapter.hpp.

◆ ShapeAtypeData

typedef SimpleTypeData<ShapeAtomType*> OpenMD::ShapeAtypeData

Definition at line 108 of file ShapeAtomType.hpp.

◆ SnapshotBlock

typedef std::pair<int, int> OpenMD::SnapshotBlock

Definition at line 50 of file BlockSnapshotManager.hpp.

◆ StickyAtypeData

typedef SimpleTypeData<StickyAtypeParameters*> OpenMD::StickyAtypeData

Definition at line 64 of file StickyAdapter.hpp.

◆ StringGenericData

OpenMD::StringGenericData

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 176 of file GenericData.hpp.

◆ StringVectorGenericData

OpenMD::StringVectorGenericData

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

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

Definition at line 253 of file GenericData.hpp.

◆ TeeBuf

typedef basic_teebuf<char> OpenMD::TeeBuf

Definition at line 117 of file basic_teebuf.hpp.

◆ Vector3d

typedef Vector3<RealType> OpenMD::Vector3d

Definition at line 160 of file Vector3.hpp.

◆ Vector3i

typedef Vector3<int> OpenMD::Vector3i

Definition at line 158 of file Vector3.hpp.

◆ VisitorIterator

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

Definition at line 53 of file CompositeVisitor.hpp.

◆ ZhouData

typedef SimpleTypeData<ZhouParameters*> OpenMD::ZhouData

Definition at line 126 of file EAMAdapter.hpp.

Enumeration Type Documentation

◆ BuckinghamType

enum OpenMD::BuckinghamType

Enumerator
btTraditional
btModified
btUnknown

Definition at line 68 of file BuckinghamInteractionType.hpp.

◆ communicatorType

enum OpenMD::communicatorType

Enumerator
Global
Row
Column

Definition at line 61 of file Communicator.hpp.

◆ CutoffMethod

enum OpenMD::CutoffMethod

Enumerator
HARD
SWITCHED
SHIFTED_POTENTIAL
SHIFTED_FORCE
TAYLOR_SHIFTED
EWALD_FULL

Definition at line 48 of file Cutoffs.hpp.

◆ EAMiType

enum OpenMD::EAMiType

Enumerator
eamitTabulated
eamitZhou

Definition at line 63 of file EAMInteractionType.hpp.

◆ EAMMixingMethod

enum OpenMD::EAMMixingMethod

Enumerator
eamJohnson
eamDaw
eamDream1
eamDream2
eamUnknownMix

Definition at line 73 of file EAM.hpp.

◆ EAMType

enum OpenMD::EAMType

Enumerator
eamFuncfl
eamZhou2001
eamZhou2004
eamZhou2005
eamZhou2005Oxygen
eamZhouRose
eamUnknown

Definition at line 57 of file EAMAdapter.hpp.

◆ ElectrostaticScreeningMethod

enum OpenMD::ElectrostaticScreeningMethod

Enumerator
UNDAMPED
DAMPED

Definition at line 85 of file Electrostatic.hpp.

◆ ElectrostaticSummationMethod

enum OpenMD::ElectrostaticSummationMethod

Enumerator
esm_HARD
esm_SWITCHING_FUNCTION
esm_SHIFTED_POTENTIAL
esm_SHIFTED_FORCE
esm_TAYLOR_SHIFTED
esm_REACTION_FIELD
esm_EWALD_FULL
esm_EWALD_PME	PME Ewald methods aren't supported yet
esm_EWALD_SPME	SPME Ewald methods aren't supported yet

Definition at line 73 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
N_INTERACTION_FAMILIES

Definition at line 58 of file NonBondedInteraction.hpp.

◆ InversionKey

enum OpenMD::InversionKey

Enumerator
itAngle
itCosAngle

Definition at line 55 of file InversionType.hpp.

◆ MorseType

enum OpenMD::MorseType

Enumerator
mtShifted
mtRepulsive
mtUnknown

Definition at line 63 of file MorseInteractionType.hpp.

◆ OutputDataHandling

enum OpenMD::OutputDataHandling

Enumerator
odhAverage
odhTotal
odhLastValue
odhMax
odhUnknownDataHandling

Definition at line 58 of file StaticAnalyser.hpp.

◆ OutputDataType

enum OpenMD::OutputDataType

Enumerator
odtReal
odtVector3
odtArray2d
odtUnknownDataType

Definition at line 51 of file StaticAnalyser.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
N_SELECTIONTYPES

Definition at line 57 of file SelectionSet.hpp.

◆ SwitchingFunctionType

enum OpenMD::SwitchingFunctionType

Enumerator
cubic
fifth_order_poly

Definition at line 51 of file SwitchingFunction.hpp.

Function Documentation

◆ CaseInsensitiveEquals()

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

Definition at line 253 of file StringUtils.cpp.

Referenced by CaseInsensitiveFind().

◆ CaseInsensitiveFind()

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

Definition at line 257 of file StringUtils.cpp.

References CaseInsensitiveEquals().

Referenced by OpenMD::SimCreator::createSim().

◆ CholeskyDecomposition()

template<class MatrixType >

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

Definition at line 52 of file CholeskyDecomposition.hpp.

References epsilon.

Referenced by OpenMD::HydroProp::complete(), OpenMD::BAOAB::getMomentData(), OpenMD::HydroProp::HydroProp(), and OpenMD::LangevinHullForceManager::postCalculation().

◆ containerToString()

template<class ContainerType >

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

Definition at line 168 of file StringUtils.hpp.

Referenced by OpenMD::MoleculeStamp::checkBends(), OpenMD::MoleculeStamp::checkInversions(), OpenMD::MoleculeStamp::checkTorsions(), OpenMD::BondStamp::setMembers(), OpenMD::ConstraintStamp::setMembers(), OpenMD::TorsionStamp::setMembers(), OpenMD::BendStamp::setMembers(), OpenMD::AtomStamp::setOrientation(), and OpenMD::AtomStamp::setPosition().

◆ copy_if()

template<typename InputIterator , typename OutputIterator , typename Predicate >

OutputIterator OpenMD::copy_if	(	InputIterator	first,
		InputIterator	last,
		OutputIterator	result,
		Predicate	p
	)

copy_if is one of the missing functions in STL. copy_if copies elements from the range [first, last) to the range [result, result + (last-first)), except that any element for which pred is false is not copied.

Definition at line 53 of file Algorithm.hpp.

Referenced by OpenMD::BlockSnapshotManager::getActiveBlocks().

◆ countTokens()

int OpenMD::countTokens	(	char *	line,
		char *	delimiters
	)

Counts the number of tokens on line which are delimited by the characters listed in delimiters

Parameters

line
delimiters

Definition at line 157 of file StringUtils.cpp.

◆ 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 135 of file Vector3.hpp.

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

◆ 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 429 of file DynamicVector.hpp.

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

◆ 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 556 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 441 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 568 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 412 of file DynamicVector.hpp.

◆ 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 515 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 538 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 580 of file RectMatrix.hpp.

References Row.

Referenced by OpenMD::UniformGradient::applyPerturbation(), OpenMD::KirkwoodQuadrupoles::collectHistogram(), and OpenMD::MultipoleSum::process().

◆ equal() [1/3]

template<typename T >

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

inline

Definition at line 62 of file Vector.hpp.

◆ equal() [2/3]

template<>

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

inline

Definition at line 72 of file Vector.hpp.

References epsilon.

◆ equal() [3/3]

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 649 of file Polynomial.hpp.

References OpenMD::Polynomial< Real >::begin(), OpenMD::Polynomial< Real >::end(), and OpenMD::Polynomial< Real >::size().

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

◆ fastpow()

template<typename Real >

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

Definition at line 63 of file Polynomial.hpp.

Referenced by OpenMD::RNEMD::doNIVS(), OpenMD::Polynomial< RealType >::evaluate(), and OpenMD::Polynomial< RealType >::evaluateDerivative().

◆ 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 107 of file StringUtils.cpp.

Referenced by OpenMD::ShapeAtomTypesSectionParser::parseShapeFile().

◆ 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 625 of file Polynomial.hpp.

References OpenMD::Polynomial< Real >::begin(), OpenMD::Polynomial< Real >::end(), and OpenMD::Polynomial< Real >::setCoefficient().

◆ getGlobalCountOfType()

int OpenMD::getGlobalCountOfType ( AtomType * atype )

Definition at line 803 of file SimInfo.cpp.

◆ getPrefix()

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

Todo:: need implementation

Definition at line 229 of file StringUtils.cpp.

◆ getSuffix()

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

Todo:: need implementation

Definition at line 233 of file StringUtils.cpp.

◆ hasDuplicateElement()

template<class ContainerType >

bool OpenMD::hasDuplicateElement ( const ContainerType & cont )

Definition at line 52 of file MoleculeStamp.cpp.

Referenced by OpenMD::MoleculeStamp::checkBends(), OpenMD::MoleculeStamp::checkInversions(), and OpenMD::MoleculeStamp::checkTorsions().

◆ 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 94 of file LU.hpp.

Referenced by OpenMD::ApproximationModel::calcHydroPropsAtCD(), OpenMD::ApproximationModel::calcHydroPropsAtCR(), OpenMD::Sphere::getHydroProp(), OpenMD::Ellipsoid::getHydroProp(), OpenMD::SquareMatrix< RealType, 6 >::inverse(), and main().

◆ 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 137 of file LU.hpp.

References LUFactorLinearSystem(), and LUSolveLinearSystem().

◆ isAlnum()

CharClassification OpenMD::isAlnum ( const std::locale & loc = std::locale() )

inline

Definition at line 107 of file Predicate.hpp.

◆ isAlpha()

CharClassification OpenMD::isAlpha ( const std::locale & loc = std::locale() )

inline

Definition at line 111 of file Predicate.hpp.

◆ isCntrl()

CharClassification OpenMD::isCntrl ( const std::locale & loc = std::locale() )

inline

Definition at line 115 of file Predicate.hpp.

◆ isDigit()

CharClassification OpenMD::isDigit ( const std::locale & loc = std::locale() )

inline

Definition at line 119 of file Predicate.hpp.

◆ 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 177 of file StringUtils.cpp.

Referenced by OpenMD::ShapeAtomTypesSectionParser::parseShapeFile().

◆ isEqual()

template<typename T >

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

inline

Definition at line 368 of file ParamConstraint.hpp.

◆ isEqualIgnoreCase()

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

Definition at line 74 of file ParamConstraint.cpp.

Referenced by OpenMD::MinimizerParameters::validate(), OpenMD::RestraintStamp::validate(), OpenMD::FluctuatingChargeParameters::validate(), OpenMD::RNEMDParameters::validate(), OpenMD::Globals::validate(), and OpenMD::ForceFieldOptions::validateOptions().

◆ isEven()

EvenConstraint OpenMD::isEven ( )

Definition at line 78 of file ParamConstraint.cpp.

◆ isFromRange()

template<typename CharT >

FromRangeFunctor<CharT> OpenMD::isFromRange	(	CharT	from,
		CharT	to
	)

inline

Definition at line 149 of file Predicate.hpp.

◆ isGraph()

CharClassification OpenMD::isGraph ( const std::locale & loc = std::locale() )

inline

Definition at line 123 of file Predicate.hpp.

◆ isGreaterThan()

template<typename T >

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

inline

Definition at line 373 of file ParamConstraint.hpp.

Referenced by OpenMD::MinimizerParameters::validate(), and OpenMD::FluctuatingChargeParameters::validate().

◆ isGreaterThanOrEqualTo()

template<typename T >

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

inline

Definition at line 378 of file ParamConstraint.hpp.

Referenced by OpenMD::MinimizerParameters::validate().

◆ isInteger()

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

Definition at line 237 of file StringUtils.cpp.

Referenced by OpenMD::SelectionCompiler::lookingAtInteger(), and OpenMD::ForceFieldOptions::setData().

◆ isLessThan()

template<typename T >

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

inline

Definition at line 358 of file ParamConstraint.hpp.

◆ isLessThanOrEqualTo()

template<typename T >

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

inline

Definition at line 363 of file ParamConstraint.hpp.

Referenced by OpenMD::MinimizerParameters::validate(), and OpenMD::FluctuatingChargeParameters::validate().

◆ isLower()

CharClassification OpenMD::isLower ( const std::locale & loc = std::locale() )

inline

Definition at line 127 of file Predicate.hpp.

◆ isNegative()

NegativeConstraint OpenMD::isNegative ( )

Definition at line 66 of file ParamConstraint.cpp.

◆ isNonNegative()

NonNegativeConstraint OpenMD::isNonNegative ( )

Definition at line 70 of file ParamConstraint.cpp.

Referenced by OpenMD::Component::validate(), OpenMD::ZConsStamp::validate(), OpenMD::RestraintStamp::validate(), OpenMD::FluctuatingChargeParameters::validate(), OpenMD::ConstraintStamp::validate(), OpenMD::BendStamp::validate(), OpenMD::TorsionStamp::validate(), and OpenMD::Globals::validate().

◆ isNonPositive()

NonPositiveConstraint OpenMD::isNonPositive ( )

Definition at line 62 of file ParamConstraint.cpp.

◆ isNonZero()

ParamConstraintFacade< NonZeroConstraint > OpenMD::isNonZero ( )

Definition at line 54 of file ParamConstraint.cpp.

◆ isNotEmpty()

NotEmptyConstraint OpenMD::isNotEmpty ( )

Definition at line 46 of file ParamConstraint.cpp.

Referenced by OpenMD::FragmentStamp::validate(), OpenMD::Component::validate(), OpenMD::AtomStamp::validate(), and OpenMD::Globals::validate().

◆ isPositive()

PositiveConstraint OpenMD::isPositive ( )

Definition at line 58 of file ParamConstraint.cpp.

Referenced by OpenMD::Component::validate(), OpenMD::MinimizerParameters::validate(), OpenMD::FluctuatingChargeParameters::validate(), OpenMD::RNEMDParameters::validate(), and OpenMD::Globals::validate().

◆ isPrint()

CharClassification OpenMD::isPrint ( const std::locale & loc = std::locale() )

inline

Definition at line 131 of file Predicate.hpp.

◆ isPunct()

CharClassification OpenMD::isPunct ( const std::locale & loc = std::locale() )

inline

Definition at line 135 of file Predicate.hpp.

◆ isSpace()

CharClassification OpenMD::isSpace ( const std::locale & loc = std::locale() )

inline

Definition at line 103 of file Predicate.hpp.

Referenced by trim(), trimCopy(), trimLeft(), trimLeftCopy(), trimRight(), and trimRightCopy().

◆ isType()

template<typename T >

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

Definition at line 139 of file StringUtils.hpp.

◆ isUpper()

CharClassification OpenMD::isUpper ( const std::locale & loc = std::locale() )

inline

Definition at line 139 of file Predicate.hpp.

◆ isXDigit()

CharClassification OpenMD::isXDigit ( const std::locale & loc = std::locale() )

inline

Definition at line 143 of file Predicate.hpp.

◆ isZero()

ZeroConstraint OpenMD::isZero ( )

Definition at line 50 of file ParamConstraint.cpp.

◆ lexi_cast()

template<typename T >

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

Definition at line 128 of file StringUtils.hpp.

◆ LowerCase()

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

Converts a string to lower case

Parameters

S

Definition at line 69 of file StringUtils.cpp.

◆ 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 183 of file LU.hpp.

References epsilon.

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 277 of file LU.hpp.

Referenced by invertMatrix().

◆ make_tuple3()

template<class T1 , class T2 , class T3 >

tuple3<T1,T2,T3> OpenMD::make_tuple3	(	T1	t1,
		T2	t2,
		T3	t3
	)

Definition at line 61 of file Tuple.hpp.

Referenced by OpenMD::ForceField::getBendType(), OpenMD::ForceField::getInversionType(), OpenMD::ForceField::getTorsionType(), OpenMD::Icosahedron::Icosahedron(), and OpenMD::SCDElem::SCDElem().

◆ make_tuple4()

template<class T1 , class T2 , class T3 , class T4 >

tuple4<T1,T2,T3,T4> OpenMD::make_tuple4	(	T1	t1,
		T2	t2,
		T3	t3,
		T4	t4
	)

Definition at line 83 of file Tuple.hpp.

◆ 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 616 of file RectMatrix.hpp.

References Row.

Referenced by OpenMD::UniformGradient::applyPerturbation(), and OpenMD::Electrostatic::calcForce().

◆ memparse()

unsigned long long OpenMD::memparse	(	char *	ptr,
		char **	retptr
	)

memparse - parse a string with mem suffixes into a number

Parameters

ptr	Where parse begins
retptr	(output) Pointer to next char after parse completes

Parses a string into a number. The number stored at ptr is potentially suffixed with K (for kilobytes, or 1024 bytes), M (for megabytes, or 1048576 bytes), or G (for gigabytes, or 1073741824). If the number is suffixed with K, M, or G, then the return value is the number multiplied by one kilobyte, one megabyte, or one gigabyte, respectively.

Definition at line 277 of file StringUtils.cpp.

Referenced by main().

◆ 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 87 of file next_combination.hpp.

Referenced by replaceWithWildCard().

◆ OpenMD_itoa()

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

Definition at line 198 of file StringUtils.cpp.

References MATPACK::sign().

Referenced by OpenMD::MoleculeCreator::createBend(), OpenMD::MoleculeCreator::createBond(), OpenMD::MoleculeCreator::createInversion(), OpenMD::MoleculeCreator::createRigidBody(), OpenMD::MoleculeCreator::createTorsion(), and OpenMD::SCDOrderParameter::SCDOrderParameter().

◆ operator !()

template<typename ConsT >

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

inline

Definition at line 339 of file ParamConstraint.hpp.

◆ operator &() [1/3]

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

Definition at line 171 of file OpenMDBitSet.cpp.

References OpenMD::OpenMDBitSet::size().

◆ operator &() [2/3]

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

Definition at line 196 of file SelectionSet.cpp.

References OpenMD::SelectionSet::bitsets_, and N_SELECTIONTYPES.

◆ operator &() [3/3]

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

Definition at line 615 of file SelectionManager.cpp.

◆ operator &&() [1/2]

template<typename Pred1T , typename Pred2T >

PredAndFunctor<Pred1T, Pred2T> OpenMD::operator &&	(	const PredFacade< Pred1T > &	Pred1,
		const PredFacade< Pred2T > &	Pred2
	)

inline

Definition at line 155 of file Predicate.hpp.

◆ operator &&() [2/2]

template<typename Cons1T , typename Cons2T >

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

inline

Definition at line 320 of file ParamConstraint.hpp.

◆ operator *() [1/20]

template<typename Real >

DynamicVector<Real> OpenMD::operator *	(	const 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 373 of file DynamicVector.hpp.

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

◆ operator *() [2/20]

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 386 of file DynamicVector.hpp.

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

◆ operator *() [3/20]

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 476 of file Vector.hpp.

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

◆ operator *() [4/20]

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 478 of file RectMatrix.hpp.

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

◆ operator *() [5/20]

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 489 of file Vector.hpp.

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

◆ operator *() [6/20]

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 493 of file RectMatrix.hpp.

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

◆ operator *() [7/20]

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 508 of file RectMatrix.hpp.

References Row.

◆ operator *() [8/20]

template<typename Real >

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

inline

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

Returns: the multiplication of a scalar and a matrix

Parameters

m	the matrix
s	the scalar

Definition at line 511 of file DynamicRectMatrix.hpp.

References OpenMD::DynamicRectMatrix< Real >::getNCol(), OpenMD::DynamicRectMatrix< Real >::getNRow(), and OpenMD::DynamicRectMatrix< Real >::mul().

◆ operator *() [9/20]

template<typename Real >

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

inline

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

Returns: the multiplication of a scalar and a matrix

Parameters

s	the scalar
m	the matrix

Definition at line 526 of file DynamicRectMatrix.hpp.

References OpenMD::DynamicRectMatrix< Real >::getNCol(), OpenMD::DynamicRectMatrix< Real >::getNRow(), and OpenMD::DynamicRectMatrix< Real >::mul().

◆ operator *() [10/20]

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 526 of file RectMatrix.hpp.

References Row.

◆ operator *() [11/20]

template<typename Real >

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

inline

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

Returns: the multiplication of two matrixes

Parameters

m1	the first matrix
m2	the second matrix

Definition at line 541 of file DynamicRectMatrix.hpp.

References OpenMD::DynamicRectMatrix< Real >::getNCol(), and OpenMD::DynamicRectMatrix< Real >::getNRow().

◆ operator *() [12/20]

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 543 of file RectMatrix.hpp.

References Row.

◆ operator *() [13/20]

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 543 of file Polynomial.hpp.

References OpenMD::Polynomial< Real >::addCoefficient(), OpenMD::Polynomial< Real >::begin(), and OpenMD::Polynomial< Real >::end().

◆ operator *() [14/20]

template<typename Real >

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

Definition at line 558 of file Polynomial.hpp.

References OpenMD::Polynomial< Real >::begin(), OpenMD::Polynomial< Real >::end(), and OpenMD::Polynomial< Real >::setCoefficient().

◆ operator *() [15/20]

template<typename Real >

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

inline

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

Returns: the multiplication of a matrix and a vector

Parameters

m	the matrix
v	the vector

Definition at line 562 of file DynamicRectMatrix.hpp.

References OpenMD::DynamicRectMatrix< Real >::getNCol(), and OpenMD::DynamicRectMatrix< Real >::getNRow().

◆ operator *() [16/20]

template<typename Real >

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

Definition at line 570 of file Polynomial.hpp.

References OpenMD::Polynomial< Real >::begin(), OpenMD::Polynomial< Real >::end(), and OpenMD::Polynomial< Real >::setCoefficient().

◆ operator *() [17/20]

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 587 of file Quaternion.hpp.

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

◆ operator *() [18/20]

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 600 of file Quaternion.hpp.

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

◆ operator *() [19/20]

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 610 of file SquareMatrix3.hpp.

◆ operator *() [20/20]

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 613 of file Quaternion.hpp.

◆ operator -() [1/9]

template<typename Real >

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

inline

unary minus

Definition at line 332 of file DynamicVector.hpp.

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

◆ operator -() [2/9]

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 359 of file DynamicVector.hpp.

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

◆ operator -() [3/9]

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 433 of file RectMatrix.hpp.

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

◆ operator -() [4/9]

template<typename Real , unsigned int Dim>

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

inline

unary minus

Definition at line 436 of file Vector.hpp.

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

◆ operator -() [5/9]

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 463 of file RectMatrix.hpp.

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

◆ operator -() [6/9]

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 463 of file Vector.hpp.

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

◆ operator -() [7/9]

template<typename Real >

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

inline

Negate the value of every element of this matrix.

Definition at line 465 of file DynamicRectMatrix.hpp.

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

◆ operator -() [8/9]

template<typename Real >

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

inline

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

Returns: the sum of two matrixes

Parameters

m1	the first matrix
m2	the second matrix

Definition at line 496 of file DynamicRectMatrix.hpp.

References OpenMD::DynamicRectMatrix< Real >::getNCol(), OpenMD::DynamicRectMatrix< Real >::getNRow(), and OpenMD::DynamicRectMatrix< Real >::sub().

◆ operator -() [9/9]

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 607 of file Polynomial.hpp.

References OpenMD::Polynomial< Real >::addCoefficient(), OpenMD::Polynomial< Real >::begin(), and OpenMD::Polynomial< Real >::end().

◆ operator!()

template<typename PredT >

PredNotFunctor<PredT> OpenMD::operator! ( const PredFacade< PredT > & Pred )

inline

Definition at line 178 of file Predicate.hpp.

◆ operator+() [1/5]

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 345 of file DynamicVector.hpp.

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

◆ operator+() [2/5]

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 448 of file RectMatrix.hpp.

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

◆ operator+() [3/5]

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 449 of file Vector.hpp.

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

◆ operator+() [4/5]

template<typename Real >

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

inline

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

Returns: the sum of two matrixes

Parameters

m1	the first matrix
m2	the second matrix

Definition at line 480 of file DynamicRectMatrix.hpp.

References OpenMD::DynamicRectMatrix< Real >::add(), OpenMD::DynamicRectMatrix< Real >::getNCol(), and OpenMD::DynamicRectMatrix< Real >::getNRow().

◆ operator+() [5/5]

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 587 of file Polynomial.hpp.

References OpenMD::Polynomial< Real >::addCoefficient(), OpenMD::Polynomial< Real >::begin(), and OpenMD::Polynomial< Real >::end().

◆ operator-() [1/3]

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

Definition at line 187 of file OpenMDBitSet.cpp.

References OpenMD::OpenMDBitSet::size().

◆ operator-() [2/3]

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

Definition at line 210 of file SelectionSet.cpp.

References OpenMD::SelectionSet::bitsets_, and N_SELECTIONTYPES.

◆ operator-() [3/3]

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

Definition at line 629 of file SelectionManager.cpp.

◆ operator/() [1/6]

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 399 of file DynamicVector.hpp.

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

◆ operator/() [2/6]

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 502 of file Vector.hpp.

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

◆ operator/() [3/6]

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 560 of file RectMatrix.hpp.

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

◆ operator/() [4/6]

template<typename Real >

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

inline

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

Returns: the scalar division of matrix

Parameters

m	the matrix
s	the scalar

Definition at line 582 of file DynamicRectMatrix.hpp.

References OpenMD::DynamicRectMatrix< Real >::div(), OpenMD::DynamicRectMatrix< Real >::getNCol(), and OpenMD::DynamicRectMatrix< Real >::getNRow().

◆ operator/() [5/6]

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 626 of file Quaternion.hpp.

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

◆ operator/() [6/6]

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 638 of file Quaternion.hpp.

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

◆ operator<() [1/3]

template<class T1 , class T2 , class T3 >

bool OpenMD::operator<	(	const tuple3< T1, T2, T3 > &	t1,
		const tuple3< T1, T2, T3 > &	t2
	)

inline

Definition at line 88 of file Tuple.hpp.

References OpenMD::tuple3< T1, T2, T3 >::first, OpenMD::tuple3< T1, T2, T3 >::second, and OpenMD::tuple3< T1, T2, T3 >::third.

◆ operator<() [2/3]

bool OpenMD::operator<	(	const tuple3< int, int, std::vector< std::string > > &	t1,
		const tuple3< int, int, std::vector< std::string > > &	t2
	)

inline

Definition at line 96 of file Tuple.hpp.

◆ operator<() [3/3]

template<class T1 , class T2 , class T3 , class T4 >

bool OpenMD::operator<	(	const tuple4< T1, T2, T3, T4 > &	t1,
		const tuple4< T1, T2, T3, T4 > &	t2
	)

inline

Definition at line 115 of file Tuple.hpp.

References OpenMD::tuple4< T1, T2, T3, T4 >::first, OpenMD::tuple4< T1, T2, T3, T4 >::fourth, OpenMD::tuple4< T1, T2, T3, T4 >::second, and OpenMD::tuple4< T1, T2, T3, T4 >::third.

◆ operator<<() [1/22]

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

Definition at line 86 of file AmberImproperTorsionType.hpp.

References OpenMD::AmberImproperTorsionType::v2_.

◆ operator<<() [2/22]

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

Definition at line 86 of file HarmonicInversionType.hpp.

References OpenMD::HarmonicInversionType::d0_, and OpenMD::HarmonicInversionType::phi0_.

◆ operator<<() [3/22]

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

write out all of the type identifiers to an output stream

Definition at line 89 of file IntegratorFactory.cpp.

References OpenMD::IntegratorFactory::getIdents().

◆ operator<<() [4/22]

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

write out all of the type identifiers to an output stream

Definition at line 89 of file OptimizationFactory.cpp.

References OpenMD::OptimizationFactory::getIdents().

◆ operator<<() [5/22]

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

write out all of the type identifiers to an output stream

Definition at line 89 of file LatticeFactory.cpp.

References OpenMD::LatticeFactory::getIdents().

◆ operator<<() [6/22]

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

write out all of the type identifiers to an output stream

Definition at line 90 of file HydrodynamicsModelFactory.cpp.

References OpenMD::HydrodynamicsModelFactory::getIdents().

◆ operator<<() [7/22]

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

Definition at line 90 of file PolynomialBendType.hpp.

References OpenMD::Polynomial< Real >::begin(), OpenMD::Polynomial< Real >::end(), OpenMD::BendType::getTheta(), and OpenMD::PolynomialBendType::polynomial_.

◆ operator<<() [8/22]

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

Definition at line 90 of file PolynomialBondType.hpp.

References OpenMD::Polynomial< Real >::begin(), OpenMD::Polynomial< Real >::end(), OpenMD::BondType::getEquilibriumBondLength(), and OpenMD::PolynomialBondType::polynomial_.

◆ operator<<() [9/22]

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

Definition at line 111 of file HarmonicTorsionType.hpp.

References OpenMD::HarmonicTorsionType::d0_, and OpenMD::HarmonicTorsionType::phi0_.

◆ operator<<() [10/22]

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

Definition at line 113 of file OplsTorsionType.hpp.

References OpenMD::OplsTorsionType::v1_, OpenMD::OplsTorsionType::v2_, and OpenMD::OplsTorsionType::v3_.

◆ operator<<() [11/22]

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

Definition at line 123 of file TrappeTorsionType.hpp.

References OpenMD::TrappeTorsionType::c0_, OpenMD::TrappeTorsionType::c1_, OpenMD::TrappeTorsionType::c2_, and OpenMD::TrappeTorsionType::c3_.

◆ operator<<() [12/22]

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

write out the exclusion list to an ostream

Definition at line 153 of file PairList.cpp.

References OpenMD::PairList::pairSet_.

◆ operator<<() [13/22]

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 220 of file GenericFactory.hpp.

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

◆ operator<<() [14/22]

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

Definition at line 233 of file OpenMDBitSet.cpp.

References OpenMD::OpenMDBitSet::bitset_.

◆ operator<<() [15/22]

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

Definition at line 243 of file SelectionSet.cpp.

References OpenMD::SelectionSet::bitsets_, and N_SELECTIONTYPES.

◆ operator<<() [16/22]

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

Definition at line 413 of file Molecule.cpp.

References OpenMD::Molecule::getGlobalIndex(), OpenMD::Molecule::getNAtoms(), OpenMD::Molecule::getNBends(), OpenMD::Molecule::getNBonds(), OpenMD::Molecule::getNConstraintPairs(), OpenMD::Molecule::getNCutoffGroups(), OpenMD::Molecule::getNFluctuatingCharges(), OpenMD::Molecule::getNIntegrableObjects(), OpenMD::Molecule::getNInversions(), OpenMD::Molecule::getNRigidBodies(), and OpenMD::Molecule::getNTorsions().

◆ operator<<() [17/22]

std::ostream& OpenMD::operator<<	(	std::ostream &	os,
		const MTRand &	mtrand
	)

inline

Definition at line 425 of file MersenneTwister.hpp.

References OpenMD::MTRand::left, OpenMD::MTRand::N, and OpenMD::MTRand::state.

◆ operator<<() [18/22]

template<typename Real >

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

Write to an output stream

Definition at line 450 of file DynamicVector.hpp.

◆ operator<<() [19/22]

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 577 of file Vector.hpp.

◆ operator<<() [20/22]

template<typename Real >

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

Write to an output stream

Definition at line 594 of file DynamicRectMatrix.hpp.

References OpenMD::DynamicRectMatrix< Real >::getNCol(), and OpenMD::DynamicRectMatrix< Real >::getNRow().

◆ operator<<() [21/22]

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 637 of file RectMatrix.hpp.

References Row.

◆ operator<<() [22/22]

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

Definition at line 1060 of file SimInfo.cpp.

◆ operator==() [1/3]

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

Definition at line 195 of file OpenMDBitSet.cpp.

References OpenMD::OpenMDBitSet::bitset_, equal(), and OpenMD::OpenMDBitSet::size().

◆ operator==() [2/3]

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

Definition at line 217 of file SelectionSet.cpp.

References OpenMD::SelectionSet::bitsets_, and N_SELECTIONTYPES.

◆ operator==() [3/3]

template<class T >

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

inline

Definition at line 647 of file Quaternion.hpp.

References equal().

◆ operator>>()

std::istream& OpenMD::operator>>	(	std::istream &	is,
		MTRand &	mtrand
	)

inline

Definition at line 434 of file MersenneTwister.hpp.

References OpenMD::MTRand::left, OpenMD::MTRand::N, OpenMD::MTRand::pNext, and OpenMD::MTRand::state.

◆ operator^() [1/3]

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

Definition at line 179 of file OpenMDBitSet.cpp.

References OpenMD::OpenMDBitSet::size().

◆ operator^() [2/3]

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

Definition at line 203 of file SelectionSet.cpp.

References OpenMD::SelectionSet::bitsets_, and N_SELECTIONTYPES.

◆ operator^() [3/3]

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

Definition at line 622 of file SelectionManager.cpp.

◆ operator|() [1/3]

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

Definition at line 163 of file OpenMDBitSet.cpp.

References OpenMD::OpenMDBitSet::size().

◆ operator|() [2/3]

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

Definition at line 189 of file SelectionSet.cpp.

References OpenMD::SelectionSet::bitsets_, and N_SELECTIONTYPES.

◆ operator|() [3/3]

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

Definition at line 608 of file SelectionManager.cpp.

◆ operator||() [1/2]

template<typename Pred1T , typename Pred2T >

PredOrFunctor<Pred1T, Pred2T> OpenMD::operator\|\|	(	const PredFacade< Pred1T > &	Pred1,
		const PredFacade< Pred2T > &	Pred2
	)

inline

Definition at line 167 of file Predicate.hpp.

◆ operator||() [2/2]

template<typename Cons1T , typename Cons2T >

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

inline

Definition at line 329 of file ParamConstraint.hpp.

◆ outProduct()

template<typename Real >

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

inline

Definition at line 622 of file SquareMatrix3.hpp.

Referenced by OpenMD::ForceAutoCorrFunc::calcCorrVal(), OpenMD::TorqueAutoCorrFunc::calcCorrVal(), OpenMD::TorForCorrFunc::calcCorrVal(), OpenMD::ForTorCorrFunc::calcCorrVal(), OpenMD::MolecularRestraint::calcForce(), OpenMD::ApproximationModel::calcHydroPropsAtCD(), OpenMD::ApproximationModel::calcHydroPropsAtCR(), OpenMD::RigidBody::calcRefCoords(), OpenMD::RMSD::calculate_rmsd(), OpenMD::RNEMD::collectData(), OpenMD::ActionCorrFunc::correlateFrames(), OpenMD::StressCorrFunc::correlateFrames(), OpenMD::MomentumCorrFunc::correlateFrames(), OpenMD::RNEMD::doVSS(), OpenMD::NanoLength::getLength(), OpenMD::LDForceManager::getMomentData(), OpenMD::BAOAB::getMomentData(), OpenMD::Thermo::getPressureTensor(), OpenMD::Thermo::getSystemQuadrupole(), OpenMD::Triangle::hydro_tensor(), OpenMD::ForceManager::longRangeInteractions(), OpenMD::RMSD::optimal_superposition(), OpenMD::ForceAutoCorrFunc::postCorrelate(), OpenMD::TorqueAutoCorrFunc::postCorrelate(), OpenMD::TorForCorrFunc::postCorrelate(), OpenMD::ForTorCorrFunc::postCorrelate(), OpenMD::RippleOP::process(), OpenMD::P2OrderParameter::process(), OpenMD::RNEMDR::processFrame(), OpenMD::RNEMDRTheta::processFrame(), OpenMD::Electrostatic::ReciprocalSpaceSum(), and OpenMD::ForceManager::selectedLongRangeInteractions().

◆ pairCompare()

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

Definition at line 53 of file Cuboctahedron.cpp.

Referenced by OpenMD::Cuboctahedron::getPoints().

◆ registerAll()

void OpenMD::registerAll ( )

register force fields, integrators and optimizers

Definition at line 112 of file Register.cpp.

References registerIntegrators(), and registerOptimizers().

Referenced by main().

◆ registerIntegrators()

void OpenMD::registerIntegrators ( )

Register all integrators

Definition at line 79 of file Register.cpp.

Referenced by registerAll().

◆ registerLattice()

void OpenMD::registerLattice ( )

Register all lattice

Definition at line 106 of file Register.cpp.

Referenced by main(), and OpenMD::shapedLattice::shapedLattice().

◆ registerOptimizers()

void OpenMD::registerOptimizers ( )

Register all optimizers

Definition at line 100 of file Register.cpp.

Referenced by registerAll().

◆ replaceWithWildCard()

bool OpenMD::replaceWithWildCard	(	vector< vector< string >::iterator > &	cont,
		vector< string > &	sequence,
		vector< string > &	result,
		const 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 48 of file Utility.cpp.

References next_combination().

Referenced by OpenMD::TypeContainer< BendType, 3 >::find().

◆ roundMe()

RealType OpenMD::roundMe ( const RealType & x )

inline

Definition at line 52 of file Utility.hpp.

Referenced by OpenMD::ForceMatrixDecomposition::buildNeighborList(), OpenMD::Hxy::process(), OpenMD::Field< Vector3d >::processFrame(), and OpenMD::Snapshot::wrapVector().

◆ swap_if()

template<class Cont , class Predict >

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

Definition at line 65 of file CompositeShape.cpp.

Referenced by OpenMD::CompositeShape::getBoundingBox().

◆ to_string()

template<typename T >

std::string OpenMD::to_string ( T value )

Definition at line 150 of file StringUtils.hpp.

Referenced by OpenMD::BendTypeParser::parseTypeAndPars(), OpenMD::BondTypeParser::parseTypeAndPars(), OpenMD::InversionTypeParser::parseTypeAndPars(), and OpenMD::TorsionTypeParser::parseTypeAndPars().

◆ toLower()

template<typename Container >

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

Definition at line 74 of file CaseConversion.hpp.

Referenced by ParameterTraits< bool >::convert(), main(), OpenMD::ShapeAtomTypesSectionParser::parseShapeFile(), and toLowerCopy().

◆ toLowerCopy()

template<typename Container >

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

Definition at line 79 of file CaseConversion.hpp.

References toLower().

◆ 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 119 of file StringUtils.hpp.

Referenced by OpenMD::SelectionEvaluator::invalidIndex(), and OpenMD::SelectionEvaluator::invalidIndexRange().

◆ toUpper()

template<typename Container >

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

Definition at line 86 of file CaseConversion.hpp.

Referenced by OpenMD::GB::addType(), OpenMD::SimCreator::createSim(), OpenMD::Cuboctahedron::Cuboctahedron(), OpenMD::SC::getAlpha(), OpenMD::LJ::getSigma(), OpenMD::Electrostatic::initialize(), OpenMD::EAM::initialize(), OpenMD::EAMAdapter::makeZhou2001(), OpenMD::EAMAdapter::makeZhou2004(), OpenMD::EAMAdapter::makeZhou2005(), OpenMD::TorsionTypesSectionParser::parseLine(), OpenMD::EAMAtomTypesSectionParser::parseLine(), OpenMD::NonBondedInteractionsSectionParser::parseLine(), OpenMD::RNEMD::parseOutputFileFormat(), OpenMD::Stats::parseStatFileFormat(), OpenMD::ForceManager::setupCutoffs(), and toUpperCopy().

◆ toUpperCopy()

template<typename Container >

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

Definition at line 91 of file CaseConversion.hpp.

References toUpper().

Referenced by OpenMD::ForceManager::initialize(), OpenMD::Integrator::Integrator(), main(), OpenMD::EqualIgnoreCaseConstraint::operator()(), OpenMD::ContainsConstraint::operator()(), OpenMD::RestraintForceManager::RestraintForceManager(), and OpenMD::ForceManager::setupCutoffs().

◆ trim()

void OpenMD::trim ( std::string & str )

Remove all leading and trailing spaces in-place

Parameters

str	An input sequence

Definition at line 54 of file Trim.cpp.

References isSpace(), and trimIf().

◆ trimCopy()

std::string OpenMD::trimCopy ( const std::string & input )

Remove all leading and trailing spaces from the input.

Returns: A trimmed copy of the input

Parameters

input An input sequence

Definition at line 66 of file Trim.cpp.

References isSpace(), and trimCopyIf().

◆ trimCopyIf()

template<typename P >

std::string OpenMD::trimCopyIf	(	const std::string &	input,
		P	pred
	)

Remove all leading and trailing spaces from the input. The supplied predicate is used to determine which characters are considered spaces

Returns: A trimmed copy of the input

Parameters

input	An input sequence
pred	The unary predicate identifying spaces

Definition at line 149 of file Trim.hpp.

References trimIf().

Referenced by trimCopy().

◆ trimIf()

template<typename P >

void OpenMD::trimIf	(	std::string &	str,
		P	pred
	)

Remove all leading and trailing spaces in-place. The supplied predicate is used to determine which characters are considered spaces

Parameters

str	An input sequence
pred	The unary predicate identifying spaces

Definition at line 108 of file Trim.hpp.

References trimLeftIf(), and trimRightIf().

Referenced by trim(), and trimCopyIf().

◆ trimLeft()

void OpenMD::trimLeft ( std::string & str )

Remove all leading spaces in-place.

Parameters

str	An input sequence

Definition at line 46 of file Trim.cpp.

References isSpace(), and trimLeftIf().

◆ trimLeftCopy()

std::string OpenMD::trimLeftCopy ( const std::string & input )

Remove all leading spaces from the input.

Returns: A trimmed copy of the input

Parameters

input An input sequence

Definition at line 58 of file Trim.cpp.

References isSpace(), and trimLeftCopyIf().

Referenced by OpenMD::SimCreator::createSim(), OpenMD::SimplePreprocessor::doPreprocess(), OpenMD::SectionParser::parse(), and OpenMD::SectionParserManager::parse().

◆ trimLeftCopyIf()

template<typename P >

std::string OpenMD::trimLeftCopyIf	(	const std::string &	input,
		P	pred
	)

Remove all leading spaces from the input. The supplied predicate is used to determine which characters are considered spaces

Returns: A trimmed copy of the input

Parameters

input	An input sequence
pred	The unary predicate identifying spaces

Definition at line 121 of file Trim.hpp.

References trimLeftIf().

Referenced by trimLeftCopy().

◆ trimLeftIf()

template<typename P >

void OpenMD::trimLeftIf	(	std::string &	str,
		P	pred
	)

Remove all leading spaces in-place. The supplied predicate is used to determine which characters are considered spaces

Parameters

str	An input sequence
pred	The unary predicate identifying spaces

std::string str = "  acb  trimLeftIf test case"
trimLeftIf(str, pred() || isFromRange('a', 'c')); 
std::cout << str << std::endl; //print "trimLeft test case"

Definition at line 69 of file Trim.hpp.

Referenced by trimIf(), trimLeft(), and trimLeftCopyIf().

◆ trimRight()

void OpenMD::trimRight ( std::string & str )

Remove all trailing spaces in-place.

Parameters

str	An input sequence

Definition at line 50 of file Trim.cpp.

References isSpace(), and trimRightIf().

◆ trimRightCopy()

std::string OpenMD::trimRightCopy ( const std::string & input )

Remove all trailing spaces from the input.

Returns: A trimmed copy of the input

Parameters

input An input sequence

Definition at line 62 of file Trim.cpp.

References isSpace(), and trimRightCopyIf().

◆ trimRightCopyIf()

template<typename P >

std::string OpenMD::trimRightCopyIf	(	const std::string &	input,
		P	pred
	)

Remove all trailing spaces from the input. The supplied predicate is used to determine which characters are considered spaces

Returns: A trimmed copy of the input

Parameters

input	An input sequence
pred	The unary predicate identifying spaces

Definition at line 135 of file Trim.hpp.

References trimRightIf().

Referenced by trimRightCopy().

◆ trimRightIf()

template<typename P >

void OpenMD::trimRightIf	(	std::string &	str,
		P	pred
	)

Remove all trailing spaces in-place. The supplied predicate is used to determine which characters are considered spaces

Parameters

str	An input sequence
pred	The unary predicate identifying spaces

Definition at line 88 of file Trim.hpp.

Referenced by trimIf(), trimRight(), and trimRightCopyIf().

◆ trimSpaces()

char * OpenMD::trimSpaces ( char * str )

Removes left and right spaces from a string

Parameters

str	String to trim

Returns: char* to the trimed string

Definition at line 79 of file StringUtils.cpp.

◆ UpperCase()

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

Converts a string to UPPER CASE

Parameters

S

Definition at line 59 of file StringUtils.cpp.

Referenced by OpenMD::Molecule::complete().

◆ Vlinear()

template<typename Real >

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

inline

Returns the linear indexing for integer vectors. Compare to Rapaport's VLinear

Parameters

p	first vector
s	second vector

Definition at line 154 of file Vector3.hpp.

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

Referenced by OpenMD::ForceMatrixDecomposition::buildNeighborList().

Variable Documentation

◆ BUCKINGHAM_INTERACTION

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

static

Definition at line 84 of file NonBondedInteraction.hpp.

Referenced by OpenMD::Buckingham::getHash().

◆ DirectionalTypeID

string const OpenMD::DirectionalTypeID = "Directional"

Definition at line 53 of file DirectionalAdapter.hpp.

Referenced by OpenMD::DirectionalAdapter::getDirectionalParam(), OpenMD::DirectionalAdapter::isDirectional(), and OpenMD::DirectionalAdapter::makeDirectional().

◆ EAM_INTERACTION

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

static

Definition at line 76 of file NonBondedInteraction.hpp.

Referenced by OpenMD::InteractionManager::doPair(), OpenMD::InteractionManager::doPreForce(), OpenMD::InteractionManager::doPrePair(), OpenMD::EAM::getHash(), and OpenMD::InteractionManager::initialize().

◆ EAMtypeID

string const OpenMD::EAMtypeID = "EAM"

Definition at line 52 of file EAMAdapter.hpp.

Referenced by OpenMD::EAMAdapter::getEAMParam(), OpenMD::EAMAdapter::isEAM(), OpenMD::EAMAdapter::makeFuncfl(), OpenMD::EAMAdapter::makeZhou2001(), OpenMD::EAMAdapter::makeZhou2004(), OpenMD::EAMAdapter::makeZhou2005(), OpenMD::EAMAdapter::makeZhou2005Oxygen(), and OpenMD::EAMAdapter::makeZhouRose().

◆ 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 74 of file NonBondedInteraction.hpp.

Referenced by OpenMD::InteractionManager::doPair(), OpenMD::InteractionManager::doSelfCorrection(), OpenMD::ElectrostaticInteraction::getHash(), and OpenMD::InteractionManager::initialize().