OpenMD  2.5
Molecular Dynamics in the Open
OpenMD Namespace Reference

Namespaces

 Constants
 

Classes

class  Accumulator
 
class  ActionCorrFunc
 
class  AlphaHull
 
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  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...
 
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  Buckingham
 
struct  BuckinghamInteractionData
 
class  BuckinghamInteractionType
 
class  CenterOfMass
 
struct  CharClassification
 
class  ChargeAtomTypesSectionParser
 
class  ChargeField
 
struct  CharmmTorsionParameter
 
class  CharmmTorsionType
 
class  ChebyshevT
 
class  ChebyshevU
 
class  COHZ
 
class  Communicator
 
class  Comparator
 
class  Component
 
class  CompositeShape
 
class  CompositeVisitor
 
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  CutoffGroup
 
class  CutoffGroupStamp
 
class  DataHolder
 
class  DataStorage
 
class  Decahedron
 
class  DefaultAtomVisitor
 
class  DensityField
 
class  DensityPlot
 
class  DipoleCorrFunc
 
class  DipoleField
 
class  DirectionalAdapter
 
class  DirectionalAtom
 
class  DirectionalAtomTypesSectionParser
 
struct  DirectionalAtypeParameters
 
class  DirectionalRCorrFunc
 
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
 
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  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  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
 Base class of Integrator. More...
 
class  IntegratorBuilder
 
class  IntegratorCreator
 
class  IntegratorFactory
 
struct  InteractionData
 
class  InteractionManager
 
class  InteractionTimeCorrFunc
 
struct  InteriorFunctor
 
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  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
 
class  MomentumCorrFunc
 
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  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  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
 
class  VelocityField
 
class  VelocityVerletIntegrator
 Velocity-Verlet Family Integrator Template pattern is used in VelocityVerletIntegrator class. More...
 
class  WaterTypeVisitor
 
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_FAMILIESpotVec
 
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, 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_FAMILY = 3,
  HYDROGENBONDING_FAMILY = 4, BONDED_FAMILY = 5, N_INTERACTION_FAMILIES = 6
}
 
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, 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)
 
snap setThermostat (thermostat)
 
NotEmptyConstraint isNotEmpty ()
 
ZeroConstraint isZero ()
 
ParamConstraintFacade< NonZeroConstraintisNonZero ()
 
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, Rowoperator* (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, RowmCross (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 >
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

void NVT
 
void RealType thermostat = snap->getThermostat()
 
RealType instTemp = thermo.getTemperature()
 
thermostat first = dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_)
 
thermostat second = thermostat.first * dt2
 
 oldChi_ = thermostat.first
 
 oldChiInt_ = thermostat.second
 
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)
 
string const DirectionalTypeID = "Directional"
 
string const EAMtypeID = "EAM"
 
string const FuncflTypeID = "FUNCFL"
 
string const ZhouTypeID = "ZHOU"
 
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

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 319 of file Snapshot.hpp.

◆ DirectionalAtypeData

◆ DoubleGenericData

DoubleGenericData is a generic data type contains a RealType variable

Definition at line 153 of file GenericData.hpp.

◆ DoublePolynomial

Definition at line 669 of file Polynomial.hpp.

◆ DoubleVectorGenericData

Definition at line 223 of file GenericData.hpp.

◆ EAMData

Definition at line 119 of file EAMAdapter.hpp.

◆ FixedChargeAtypeData

◆ FloatGenericData

FloatGenericData is a generic data type contains a float variable

Definition at line 150 of file GenericData.hpp.

◆ FloatVectorGenericData

Definition at line 217 of file GenericData.hpp.

◆ FluctuatingAtypeData

◆ FuncflData

Definition at line 120 of file EAMAdapter.hpp.

◆ GBAtypeData

◆ 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

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

◆ Mat3x3d

typedef SquareMatrix3<RealType> OpenMD::Mat3x3d

Definition at line 583 of file SquareMatrix3.hpp.

◆ Mat6x6d

typedef SquareMatrix<RealType, 6> OpenMD::Mat6x6d

Definition at line 408 of file SquareMatrix.hpp.

◆ MultipoleAtypeData

◆ PolarizableAtypeData

◆ potVec

Definition at line 86 of file NonBondedInteraction.hpp.

◆ Quat4d

typedef Quaternion<RealType> OpenMD::Quat4d

Definition at line 651 of file Quaternion.hpp.

◆ RestraintData

Definition at line 174 of file Restraint.hpp.

◆ RotMat3x3d

typedef SquareMatrix3<RealType> OpenMD::RotMat3x3d

Definition at line 584 of file SquareMatrix3.hpp.

◆ SCAtypeData

◆ ShapeAtypeData

◆ SnapshotBlock

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

Definition at line 50 of file BlockSnapshotManager.hpp.

◆ StickyAtypeData

◆ 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

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

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

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

Definition at line 121 of file EAMAdapter.hpp.

Enumeration Type Documentation

◆ BuckinghamType

Enumerator
btTraditional 
btModified 
btUnknown 

Definition at line 68 of file BuckinghamInteractionType.hpp.

◆ communicatorType

Enumerator
Global 
Row 
Column 

Definition at line 61 of file Communicator.hpp.

◆ CutoffMethod

Enumerator
HARD 
SWITCHED 
SHIFTED_POTENTIAL 
SHIFTED_FORCE 
TAYLOR_SHIFTED 
EWALD_FULL 

Definition at line 48 of file Cutoffs.hpp.

◆ EAMiType

Enumerator
eamitTabulated 
eamitZhou 

Definition at line 63 of file EAMInteractionType.hpp.

◆ EAMMixingMethod

Enumerator
eamJohnson 
eamDaw 
eamUnknownMix 

Definition at line 70 of file EAM.hpp.

◆ EAMType

Enumerator
eamFuncfl 
eamZhou2001 
eamZhou2004 
eamZhou2005 
eamZhou2005Oxygen 
eamUnknown 

Definition at line 56 of file EAMAdapter.hpp.

◆ ElectrostaticScreeningMethod

Enumerator
UNDAMPED 
DAMPED 

Definition at line 87 of file Electrostatic.hpp.

◆ 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 75 of file Electrostatic.hpp.

◆ 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_FAMILY 

Transition metal interactions involving electron density

HYDROGENBONDING_FAMILY 

Short-range directional interactions

BONDED_FAMILY 

directly bonded 1-2, 1-3, or 1-4 interactions

N_INTERACTION_FAMILIES 

Definition at line 59 of file NonBondedInteraction.hpp.

◆ InversionKey

Enumerator
itAngle 
itCosAngle 

Definition at line 55 of file InversionType.hpp.

◆ MorseType

Enumerator
mtShifted 
mtRepulsive 
mtUnknown 

Definition at line 63 of file MorseInteractionType.hpp.

◆ OutputDataHandling

Enumerator
odhAverage 
odhTotal 
odhLastValue 
odhMax 
odhUnknownDataHandling 

Definition at line 58 of file StaticAnalyser.hpp.

◆ OutputDataType

Enumerator
odtReal 
odtVector3 
odtArray2d 
odtUnknownDataType 

Definition at line 51 of file StaticAnalyser.hpp.

◆ 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

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 
)

◆ containerToString()

◆ 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.

References first.

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
v1first vector
v2second 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().

Referenced by OpenMD::Quaternion< Real >::align(), OpenMD::UniformField::applyPerturbation(), OpenMD::UniformGradient::applyPerturbation(), OpenMD::ForceMatrixDecomposition::buildNeighborList(), OpenMD::SHAPES::calcForce(), OpenMD::GhostBend::calcForce(), OpenMD::GhostTorsion::calcForce(), OpenMD::GB::calcForce(), OpenMD::Inversion::calcForce(), OpenMD::Torsion::calcForce(), OpenMD::MolecularRestraint::calcForce(), OpenMD::Electrostatic::calcForce(), OpenMD::SCDElem::calcSCD(), OpenMD::Electrostatic::calcSurfaceTerm(), OpenMD::RNEMD::collectData(), OpenMD::Triangle::computeHydrodynamicTensor(), OpenMD::Triangle::computeNormal(), OpenMD::MomAngMomCorrFunc::computeProperty2(), OpenMD::Triangle::computeUnitNormal(), OpenMD::SquareMatrix3< RealType >::diagonalize(), OpenMD::RNEMD::doVSS(), OpenMD::Field< Vector3d >::Field(), OpenMD::Quaternion< Real >::fromShortestArc(), OpenMD::Thermo::getAngularMomentum(), OpenMD::Thermo::getInertiaTensor(), OpenMD::Inversion::getValue(), OpenMD::Torsion::getValue(), OpenMD::Snapshot::getXYarea(), OpenMD::GofXyz::initializeHistogram(), OpenMD::LDForceManager::postCalculation(), OpenMD::Field< Vector3d >::processFrame(), OpenMD::RNEMDR::processFrame(), OpenMD::RNEMDRTheta::processFrame(), OpenMD::Electrostatic::ReciprocalSpaceSum(), OpenMD::Velocitizer::removeAngularDrift(), and OpenMD::LipidTransVisitor::update().

◆ distance() [1/2]

◆ 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
v1first vector
v2second 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
v1first vector
v2second 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
v1first vector
v2second 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
v1first vector
v2second vector
Returns
the dot product of v1 and v2

Definition at line 412 of file DynamicVector.hpp.

Referenced by OpenMD::Quaternion< Real >::align(), OpenMD::UniformField::applyPerturbation(), OpenMD::UniformGradient::applyPerturbation(), OpenMD::ForceMatrixDecomposition::buildNeighborList(), OpenMD::ThetaCorrFunc::calcCorrVal(), OpenMD::VCorrFunc::calcCorrVal(), OpenMD::DipoleCorrFunc::calcCorrVal(), OpenMD::MomAngMomCorrFunc::calcCorrVal(), OpenMD::FreqFlucCorrFunc::calcCorrVal(), OpenMD::DirectionalRCorrFunc::calcCorrVals(), OpenMD::LegendreCorrFunc::calcCorrVals(), OpenMD::LegendreCorrFuncZ::calcCorrVals(), OpenMD::COHZ::calcCorrVals(), OpenMD::SHAPES::calcForce(), OpenMD::GhostBend::calcForce(), OpenMD::GhostTorsion::calcForce(), OpenMD::GB::calcForce(), OpenMD::Inversion::calcForce(), OpenMD::Torsion::calcForce(), OpenMD::Bend::calcForce(), OpenMD::MolecularRestraint::calcForce(), OpenMD::Electrostatic::calcForce(), OpenMD::SCDElem::calcSCD(), OpenMD::Electrostatic::calcSurfaceTerm(), OpenMD::RMSD::calculate_rmsd(), OpenMD::GofRAngle2::collectHistogram(), OpenMD::Kirkwood::collectHistogram(), OpenMD::GofAngle2::collectHistogram(), OpenMD::HBondJump::computeFrame(), QuantLib::Problem::computeGradientNormValue(), OpenMD::VCorrFuncR::computeProperty1(), OpenMD::Rattle::constraintPairA(), OpenMD::Rattle::constraintPairB(), OpenMD::Shake::constraintPairF(), OpenMD::Shake::constraintPairR(), OpenMD::SystemDipoleCorrFunc::correlateFrames(), QuantLib::Problem::DotProduct(), OpenMD::RNEMD::doVSS(), OpenMD::GofRTheta::evaluateAngle(), OpenMD::GofROmega::evaluateAngle(), OpenMD::Field< Vector3d >::Field(), OpenMD::Quaternion< Real >::fromShortestArc(), OpenMD::RNEMDRTheta::getBins(), OpenMD::NanoLength::getLength(), OpenMD::Electrostatic::getSitePotentials(), OpenMD::Inversion::getValue(), OpenMD::Torsion::getValue(), OpenMD::Bend::getValue(), OpenMD::UniformGradient::initialize(), OpenMD::DynamicVector< Real >::lengthSquare(), OpenMD::Vector< RealType, N_INTERACTION_FAMILIES >::lengthSquare(), OpenMD::ForceManager::longRangeInteractions(), OpenMD::LDForceManager::postCalculation(), OpenMD::FreqFlucCorrFunc::preCorrelate(), OpenMD::MultipoleSum::process(), OpenMD::P2OrderParameter::process(), OpenMD::NitrileFrequencyMap::process(), OpenMD::AngleR::process(), OpenMD::BondAngleDistribution::process(), OpenMD::pAngle::process(), OpenMD::HBondGeometric::process(), OpenMD::TetrahedralityHBMatrix::process(), OpenMD::TetrahedralityParamXYZ::process(), OpenMD::TetrahedralityParam::process(), OpenMD::TetrahedralityParamZ::process(), OpenMD::TetrahedralityParamDens::process(), OpenMD::Field< Vector3d >::processFrame(), OpenMD::RNEMDRTheta::processFrame(), and OpenMD::Electrostatic::ReciprocalSpaceSum().

◆ 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
v1first vector
v2second 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
v1first vector
v2second vector
v3third 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
t1first tensor
t2second tensor
Returns
the tensor contraction (double dot product) of t1 and t2

Definition at line 569 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 ( e1,
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 
)

◆ fastpow()

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

◆ 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.

Referenced by OpenMD::SimInfo::getUseAtomicVirial().

◆ getPrefix()

std::string OpenMD::getPrefix ( const std::string &  str)
Todo:
need implementation

Definition at line 229 of file StringUtils.cpp.

Referenced by OpenMD::ActionCorrFunc::ActionCorrFunc(), OpenMD::AngleR::AngleR(), OpenMD::BondAngleDistribution::BondAngleDistribution(), OpenMD::BondCorrFunc::BondCorrFunc(), OpenMD::BondOrderParameter::BondOrderParameter(), OpenMD::BOPofR::BOPofR(), OpenMD::CenterOfMass::CenterOfMass(), OpenMD::ChargeField::ChargeField(), OpenMD::COHZ::COHZ(), OpenMD::ContactAngle1::ContactAngle1(), OpenMD::ContactAngle2::ContactAngle2(), OpenMD::CoordinationNumber::CoordinationNumber(), OpenMD::DensityField::DensityField(), OpenMD::DensityPlot::DensityPlot(), OpenMD::DipoleCorrFunc::DipoleCorrFunc(), OpenMD::DipoleField::DipoleField(), OpenMD::DirectionalRCorrFunc::DirectionalRCorrFunc(), OpenMD::EnergyCorrFunc::EnergyCorrFunc(), OpenMD::Field< Vector3d >::Field(), OpenMD::ForceAutoCorrFunc::ForceAutoCorrFunc(), OpenMD::ForTorCorrFunc::ForTorCorrFunc(), OpenMD::FreqFlucCorrFunc::FreqFlucCorrFunc(), OpenMD::SimCreator::gatherParameters(), OpenMD::GCN::GCN(), OpenMD::GCNSeq::GCNSeq(), OpenMD::GofAngle2::GofAngle2(), OpenMD::GofR::GofR(), OpenMD::GofRAngle2::GofRAngle2(), OpenMD::GofROmega::GofROmega(), OpenMD::GofRTheta::GofRTheta(), OpenMD::GofRZ::GofRZ(), OpenMD::GofXyz::GofXyz(), OpenMD::GofZ::GofZ(), OpenMD::HBondGeometric::HBondGeometric(), OpenMD::HBondJump::HBondJump(), OpenMD::Hxy::Hxy(), OpenMD::Kirkwood::Kirkwood(), OpenMD::KirkwoodQuadrupoles::KirkwoodQuadrupoles(), OpenMD::LegendreCorrFunc::LegendreCorrFunc(), OpenMD::LegendreCorrFuncZ::LegendreCorrFuncZ(), main(), OpenMD::MomAngMomCorrFunc::MomAngMomCorrFunc(), OpenMD::MomentumCorrFunc::MomentumCorrFunc(), OpenMD::MultipoleSum::MultipoleSum(), OpenMD::NanoLength::NanoLength(), OpenMD::NanoVolume::NanoVolume(), OpenMD::NitrileFrequencyMap::NitrileFrequencyMap(), OpenMD::ObjectCount::ObjectCount(), OpenMD::P2OrderParameter::P2OrderParameter(), OpenMD::pAngle::pAngle(), OpenMD::PotDiff::PotDiff(), OpenMD::SurfaceDiffusion::process(), OpenMD::Rattle::Rattle(), OpenMD::RCorrFunc::RCorrFunc(), OpenMD::RCorrFuncR::RCorrFuncR(), OpenMD::RCorrFuncZ::RCorrFuncZ(), OpenMD::RestraintForceManager::RestraintForceManager(), OpenMD::RhoR::RhoR(), OpenMD::RhoZ::RhoZ(), OpenMD::RippleOP::RippleOP(), OpenMD::RNEMD::RNEMD(), OpenMD::RNEMDR::RNEMDR(), OpenMD::RNEMDRTheta::RNEMDRTheta(), OpenMD::RNEMDZ::RNEMDZ(), OpenMD::SCDOrderParameter::SCDOrderParameter(), OpenMD::SCN::SCN(), OpenMD::SelectionCorrFunc::SelectionCorrFunc(), OpenMD::Shake::Shake(), OpenMD::SpatialStatistics::SpatialStatistics(), OpenMD::StressCorrFunc::StressCorrFunc(), OpenMD::SystemDipoleCorrFunc::SystemDipoleCorrFunc(), OpenMD::TetrahedralityHBMatrix::TetrahedralityHBMatrix(), OpenMD::TetrahedralityParam::TetrahedralityParam(), OpenMD::TetrahedralityParamDens::TetrahedralityParamDens(), OpenMD::TetrahedralityParamXYZ::TetrahedralityParamXYZ(), OpenMD::TetrahedralityParamZ::TetrahedralityParamZ(), OpenMD::ThetaCorrFunc::ThetaCorrFunc(), to_string(), OpenMD::TorForCorrFunc::TorForCorrFunc(), OpenMD::TorqueAutoCorrFunc::TorqueAutoCorrFunc(), OpenMD::TwoDGofR::TwoDGofR(), OpenMD::VCorrFunc::VCorrFunc(), OpenMD::VCorrFuncR::VCorrFuncR(), OpenMD::VCorrFuncZ::VCorrFuncZ(), OpenMD::VelocityField::VelocityField(), OpenMD::ZConsReader::ZConsReader(), OpenMD::ZconstraintForceManager::ZconstraintForceManager(), and OpenMD::ZConsVisitor::ZConsVisitor().

◆ getSuffix()

std::string OpenMD::getSuffix ( const std::string &  str)
Todo:
need implementation

Definition at line 233 of file StringUtils.cpp.

Referenced by to_string().

◆ hasDuplicateElement()

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

◆ invertMatrix() [1/2]

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

Invert input square matrix A into matrix AI.

Parameters
Ainput square matrix
AIoutput square matrix
Returns
true if inverse is computed, otherwise return false
Note
A is modified during the inversion

Definition at line 93 of file LU.hpp.

Referenced by OpenMD::ApproximationModel::calcHydroPropsAtCD(), OpenMD::ApproximationModel::calcHydroPropsAtCR(), OpenMD::Sphere::getHydroProp(), and OpenMD::Ellipsoid::getHydroProp().

◆ 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
Ainput square matrix
AIoutput square matrix
sizesize of the matrix and temporary arrays
tmp1Sizetemporary array
tmp2Sizetemporary array
Returns
true if inverse is computed, otherwise return false
Note
A is modified during the inversion.

Definition at line 136 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
lineThe 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()

◆ isEven()

EvenConstraint OpenMD::isEven ( )

Definition at line 78 of file ParamConstraint.cpp.

Referenced by operator!().

◆ 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.

◆ isGreaterThanOrEqualTo()

template<typename T >
GreaterThanOrEqualTo<T> OpenMD::isGreaterThanOrEqualTo ( T &  v)
inline

Definition at line 378 of file ParamConstraint.hpp.

References isEqualIgnoreCase().

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

◆ isInteger()

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

◆ 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().

◆ 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.

Referenced by operator!().

◆ isNonNegative()

◆ isNonPositive()

NonPositiveConstraint OpenMD::isNonPositive ( )

Definition at line 62 of file ParamConstraint.cpp.

Referenced by operator!().

◆ isNonZero()

ParamConstraintFacade< NonZeroConstraint > OpenMD::isNonZero ( )

Definition at line 54 of file ParamConstraint.cpp.

Referenced by operator!().

◆ isNotEmpty()

◆ isPositive()

◆ 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.

Referenced by operator!().

◆ lexi_cast()

◆ 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
Ainput square matrix
indexpivot indices
sizesize of the matrix and temporary arrays
tmpSizetemporary array
Returns
true if inverse is computed, otherwise return false
Note
A is modified during the inversion.

Definition at line 181 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
Ainput square matrix
indexpivot indices
xvector
sizesize 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 275 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 
)

◆ 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
t1first matrix
t2second matrix
Returns
the cross product (vector product) of t1 and t2

Definition at line 605 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
ptrWhere parse begins
retptr(output) Pointer to next char after parse completes

Parses a string into a number. The number stored at

Parameters
ptris 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 containerToString(), and 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
iterContaineriterator container
firstthe first iterator
lastthe 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.

References first.

Referenced by replaceWithWildCard().

◆ OpenMD_itoa()

◆ 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 526 of file SelectionManager.cpp.

◆ operator &&()

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!() [1/2]

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

Definition at line 178 of file Predicate.hpp.

◆ operator!() [2/2]

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

◆ operator&&()

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

Definition at line 320 of file ParamConstraint.hpp.

◆ operator*() [1/20]

template<typename Real >
DynamicVector<Real> OpenMD::operator* ( const 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
v1the source vector
sthe 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
sthe scalar value
v1the source vector

Definition at line 386 of file DynamicVector.hpp.

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

◆ operator*() [3/20]

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
mthe matrix
sthe scalar

Definition at line 467 of file RectMatrix.hpp.

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

◆ operator*() [4/20]

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
v1the source vector
sthe scalar value

Definition at line 476 of file Vector.hpp.

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

◆ operator*() [5/20]

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
sthe scalar
mthe matrix

Definition at line 482 of file RectMatrix.hpp.

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

◆ operator*() [6/20]

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
sthe scalar value
v1the source vector

Definition at line 489 of file Vector.hpp.

References OpenMD::Vector< Real, Dim >::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
m1the first matrix
m2the second matrix

Definition at line 497 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 scalra and matrix (m * s).

Returns
the multiplication of a scalra and a matrix
Parameters
mthe matrix
sthe scalar

Definition at line 510 of file DynamicRectMatrix.hpp.

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

◆ operator*() [9/20]

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
mthe matrix
vthe vector

Definition at line 515 of file RectMatrix.hpp.

References Row.

◆ operator*() [10/20]

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

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

Returns
the multiplication of a scalra and a matrix
Parameters
sthe scalar
mthe matrix

Definition at line 525 of file DynamicRectMatrix.hpp.

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

◆ operator*() [11/20]

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
vthe vector
mthe matrix

Definition at line 532 of file RectMatrix.hpp.

References Row.

◆ operator*() [12/20]

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
m1the first matrix
m2the second matrix

Definition at line 540 of file DynamicRectMatrix.hpp.

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

◆ 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 >
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
m1the first matrix
m2the second matrix

Definition at line 558 of file SquareMatrix3.hpp.

◆ operator*() [15/20]

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

◆ operator*() [16/20]

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
mthe matrix
vthe vector

Definition at line 561 of file DynamicRectMatrix.hpp.

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

◆ operator*() [17/20]

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

◆ operator*() [18/20]

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
qthe source quaternion
sthe scalar value

Definition at line 587 of file Quaternion.hpp.

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

◆ operator*() [19/20]

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
sthe scalar value
qthe source quaternion

Definition at line 600 of file Quaternion.hpp.

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

◆ 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
q1the first quaternion
q2the second quaternion

Definition at line 613 of file Quaternion.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
v1the first vector
v2the 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
m1the first matrix
m2the second matrix

Definition at line 437 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
v1the first vector
v2the 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
m1the first matrix
m2the second matrix

Definition at line 479 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
p1the first polynomial
p2the 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-() [1/12]

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

Definition at line 187 of file OpenMDBitSet.cpp.

References OpenMD::OpenMDBitSet::size().

◆ operator-() [2/12]

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-() [3/12]

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-() [4/12]

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

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

Returns
the difference of two vectors
Parameters
v1the first vector
v2the second vector

Definition at line 359 of file DynamicVector.hpp.

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

◆ operator-() [5/12]

template<typename Real , unsigned int Row, unsigned int Col>
RectMatrix<Real, Row, Col> OpenMD::operator- ( const RectMatrix< Real, Row, Col > &  m)
inline

Negate the value of every element of this matrix.

Definition at line 422 of file RectMatrix.hpp.

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

◆ operator-() [6/12]

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-() [7/12]

template<typename Real , unsigned int Row, unsigned int Col>
RectMatrix<Real, Row, Col> OpenMD::operator- ( const RectMatrix< Real, Row, Col > &  m1,
const RectMatrix< Real, Row, Col > &  m2 
)
inline

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

Returns
the sum of two matrixes
Parameters
m1the first matrix
m2the second matrix

Definition at line 452 of file RectMatrix.hpp.

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

◆ operator-() [8/12]

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

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

Returns
the difference of two vectors
Parameters
v1the first vector
v2the second vector

Definition at line 463 of file Vector.hpp.

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

◆ operator-() [9/12]

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

Negate the value of every element of this matrix.

Definition at line 464 of file DynamicRectMatrix.hpp.

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

◆ operator-() [10/12]

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

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

Returns
the sum of two matrixes
Parameters
m1the first matrix
m2the second matrix

Definition at line 495 of file DynamicRectMatrix.hpp.

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

◆ operator-() [11/12]

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

Definition at line 540 of file SelectionManager.cpp.

◆ operator-() [12/12]

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

Generates and returns the difference of two given Polynomials.

Returns
Parameters
p1the first polynomial
p2the 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/() [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
v1the source vector
sthe 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
v1the source vector
sthe 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
mthe matrix
sthe scalar

Definition at line 549 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
mthe matrix
sthe scalar

Definition at line 581 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
q1divisor
q2dividen

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

Definition at line 638 of file Quaternion.hpp.

References OpenMD::Quaternion< Real >::inverse(), and OpenMD::Quaternion< Real >::x().

◆ 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.

◆ 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.

◆ operator<<() [1/22]

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

◆ operator<<() [2/22]

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

◆ 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,
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<<() [5/22]

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<<() [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().

Referenced by OpenMD::SimInfo::getUseAtomicVirial(), and antlr::AST::~AST().

◆ operator<<() [7/22]

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

◆ operator<<() [8/22]

◆ operator<<() [9/22]

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

◆ operator<<() [10/22]

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

◆ operator<<() [11/22]

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

◆ 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.

◆ 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]

◆ operator<<() [17/22]

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

◆ 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 593 of file DynamicRectMatrix.hpp.

◆ 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 626 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 
)

◆ 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

◆ 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 533 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 519 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()

◆ 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 108 of file Register.cpp.

References registerIntegrators(), and registerOptimizers().

Referenced by main().

◆ registerIntegrators()

void OpenMD::registerIntegrators ( )

Register all integrators

Definition at line 77 of file Register.cpp.

Referenced by registerAll().

◆ registerLattice()

void OpenMD::registerLattice ( )

Register all lattice

Definition at line 104 of file Register.cpp.

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

◆ registerOptimizers()

void OpenMD::registerOptimizers ( )

Register all optimizers

Definition at line 98 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
contiterator container, if expect the whole series of combinations, pass an empty iterator container. The user should not modify this iterator container
sequencethe whole sequence used to generate combination
resulta possible combination sequence which is set on return
wildCardthe 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(), and roundMe().

◆ roundMe()

RealType OpenMD::roundMe ( const RealType &  x)
inline

◆ setThermostat()

snap OpenMD::setThermostat ( thermostat  )

◆ 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()

◆ toLower()

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

◆ 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
Tdata type
Parameters
vdata to be converted
Returns
a string

Definition at line 119 of file StringUtils.hpp.

Referenced by antlr::RecognitionException::getColumn(), OpenMD::SelectionEvaluator::invalidIndex(), OpenMD::SelectionEvaluator::invalidIndexRange(), antlr::CommonToken::setColumn(), antlr::AST::~AST(), and antlr::Token::~Token().

◆ toUpper()

◆ toUpperCopy()

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

◆ trim()

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

Remove all leading and trailing spaces in-place

Parameters
strAn input sequence

Definition at line 54 of file Trim.cpp.

References isSpace(), and trimIf().

Referenced by trimCopyIf().

◆ 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
inputAn input sequence

Definition at line 66 of file Trim.cpp.

References isSpace(), and trimCopyIf().

Referenced by trimCopyIf().

◆ trimCopyIf()

template<typename P >
std::string OpenMD::trimCopyIf ( const std::string &  input,
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
inputAn input sequence
predThe unary predicate identifying spaces

Definition at line 149 of file Trim.hpp.

References trim(), trimCopy(), trimIf(), trimLeft(), trimLeftCopy(), trimRight(), and trimRightCopy().

Referenced by trimCopy().

◆ trimIf()

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

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

Parameters
strAn input sequence
predThe 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
strAn input sequence

Definition at line 46 of file Trim.cpp.

References isSpace(), and trimLeftIf().

Referenced by trimCopyIf().

◆ trimLeftCopy()

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

Remove all leading spaces from the input.

Returns
A trimmed copy of the input
Parameters
inputAn 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(), OpenMD::SectionParserManager::parse(), and trimCopyIf().

◆ trimLeftCopyIf()

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

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

Parameters
strAn input sequence
predThe 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
strAn input sequence

Definition at line 50 of file Trim.cpp.

References isSpace(), and trimRightIf().

Referenced by trimCopyIf().

◆ trimRightCopy()

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

Remove all trailing spaces from the input.

Returns
A trimmed copy of the input
Parameters
inputAn input sequence

Definition at line 62 of file Trim.cpp.

References isSpace(), and trimRightCopyIf().

Referenced by trimCopyIf().

◆ trimRightCopyIf()

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

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

Parameters
strAn input sequence
predThe 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
strString 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
pfirst vector
ssecond 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"

◆ EAM_INTERACTION

◆ EAMtypeID

◆ 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().

◆ epsilon

const RealType OpenMD::epsilon = 0.000001
static

Definition at line 59 of file Vector.hpp.

Referenced by OpenMD::LJ::addExplicitInteraction(), OpenMD::RepulsivePower::addExplicitInteraction(), OpenMD::Mie::addExplicitInteraction(), OpenMD::Buckingham::addExplicitInteraction(), OpenMD::SC::addExplicitInteraction(), OpenMD::GhostTorsion::calcForce(), OpenMD::LJ::calcForce(), OpenMD::RepulsivePower::calcForce(), OpenMD::Mie::calcForce(), OpenMD::Buckingham::calcForce(), OpenMD::Torsion::calcForce(), OpenMD::RigidBody::calcRefCoords(), CholeskyDecomposition(), OpenMD::DirectionalAtom::DirectionalAtom(), equal(), getSTOZeta(), OpenMD::Torsion::getValue(), OpenMD::LJ::initialize(), OpenMD::RepulsivePower::initialize(), OpenMD::Mie::initialize(), OpenMD::SquareMatrix3< RealType >::inverse(), OpenMD::SquareMatrix< RealType, 6 >::isDiagonal(), OpenMD::SquareMatrix< RealType, 6 >::isSymmetric(), OpenMD::SquareMatrix< RealType, 6 >::isUnitMatrix(), OpenMD::LennardJonesAdapter::LennardJonesAdapter(), LUFactorLinearSystem(), OpenMD::LennardJonesAdapter::makeLennardJones(), OpenMD::SuttonChenAdapter::makeSuttonChen(), QuantLib::LineSearchBasedMethod::minimize(), OpenMD::DumpReader::parseDumpLine(), OpenMD::RestReader::parseDumpLine(), OpenMD::LennardJonesAtomTypesSectionParser::parseLine(), OpenMD::BendTypeParser::parseLine(), OpenMD::BondTypeParser::parseLine(), OpenMD::SCAtomTypesSectionParser::parseLine(), OpenMD::NonBondedInteractionsSectionParser::parseLine(), OpenMD::VelocityVerletIntegrator::preStep(), OpenMD::LJ::setSimulatedAtomTypes(), OpenMD::RepulsivePower::setSimulatedAtomTypes(), OpenMD::Mie::setSimulatedAtomTypes(), OpenMD::Buckingham::setSimulatedAtomTypes(), sSTOCoulInt(), sSTOOvInt(), OpenMD::SuttonChenAdapter::SuttonChenAdapter(), and OpenMD::SquareMatrix3< RealType >::toQuaternion().

◆ etab

◆ FCtypeID

◆ first

◆ FQtypeID

◆ FuncflTypeID

string const OpenMD::FuncflTypeID = "FUNCFL"

◆ GB_INTERACTION

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

◆ GBtypeID

◆ instTemp

RealType OpenMD::instTemp = thermo.getTemperature()

◆ LJ_INTERACTION

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

◆ LJtypeID

◆ M3Zero

◆ MAW_INTERACTION

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

◆ MIE_INTERACTION

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

◆ MORSE_INTERACTION

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

◆ MultipoleTypeID

string const OpenMD::MultipoleTypeID = "Multipole"

◆ NVT

Definition at line 90 of file myNVT.cpp.

◆ oldChi_

OpenMD::oldChi_ = thermostat.first

Definition at line 95 of file myNVT.cpp.

◆ oldChiInt_

OpenMD::oldChiInt_ = thermostat.second

Definition at line 96 of file myNVT.cpp.

◆ PolTypeID

◆ progressSpinner_

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

Definition at line 68 of file ProgressBar.cpp.

◆ REPULSIVEPOWER_INTERACTION

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

◆ SC_INTERACTION

◆ SCtypeID

◆ second

◆ STICKY_INTERACTION

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

◆ StickyTypeID

string const OpenMD::StickyTypeID = "Sticky"

◆ thermostat

◆ V3X

◆ V3Y

◆ V3Z

◆ V3Zero

const Vector3d OpenMD::V3Zero(0.0, 0.0, 0.0)

Referenced by OpenMD::SHAPES::calcForce(), OpenMD::GB::calcForce(), OpenMD::Sticky::calcForce(), OpenMD::RMSD::calculate_rmsd(), OpenMD::VectorAccumulator::clear(), OpenMD::Snapshot::clearDerivedProperties(), OpenMD::RNEMD::collectData(), OpenMD::ForceMatrixDecomposition::collectData(), OpenMD::ForceMatrixDecomposition::collectIntermediateData(), OpenMD::AlphaHull::computeHull(), OpenMD::ConvexHull::computeHull(), OpenMD::CenterOfMass::doFrame(), OpenMD::ContactAngle1::doFrame(), OpenMD::RNEMD::doVSS(), OpenMD::ForceAutoCorrFunc::ForceAutoCorrFunc(), OpenMD::ForTorCorrFunc::ForTorCorrFunc(), OpenMD::StuntDouble::freeze(), OpenMD::LangevinHullForceManager::genTriangleForces(), OpenMD::Thermo::getHeatFlux(), OpenMD::Sphere::getHydroProp(), OpenMD::CompositeShape::getHydroProp(), OpenMD::Ellipsoid::getHydroProp(), OpenMD::Lattice::Lattice(), OpenMD::LDForceManager::LDForceManager(), main(), OpenMD::NitrileFrequencyMap::NitrileFrequencyMap(), OpenMD::RMSD::optimal_superposition(), OpenMD::MultipoleAtomTypesSectionParser::parseLine(), OpenMD::MoLocator::placeMol(), OpenMD::LangevinHullForceManager::postCalculation(), OpenMD::MultipoleSum::process(), OpenMD::RNEMDZ::processFrame(), OpenMD::RNEMDR::processFrame(), OpenMD::Electrostatic::ReciprocalSpaceSum(), OpenMD::RNEMD::RNEMD(), OpenMD::RMSD::set_reference_structure(), OpenMD::ShellStatistics::ShellStatistics(), OpenMD::TorForCorrFunc::TorForCorrFunc(), OpenMD::TorqueAutoCorrFunc::TorqueAutoCorrFunc(), OpenMD::CutoffGroup::updateCOM(), OpenMD::ReplacementVisitor::visit(), OpenMD::DefaultAtomVisitor::visit(), OpenMD::RNEMD::writeOutputFile(), OpenMD::StuntDouble::zeroForcesAndTorques(), and OpenMD::ForceMatrixDecomposition::zeroWorkArrays().

◆ ZhouTypeID