ProtoMol - an object-oriented component based framework for Molecular Dynamics simulations.
Main Page | Namespace List | Class Hierarchy | Alphabetical List | Class List | File List | Namespace Members | Class Members | File Members

ProtoMol Namespace Reference


Classes

class  AbstractEnumType
class  Angle
 This class contains the information for one Angle. More...

class  AngleInfo
class  AngleSystemForce
class  AngleSystemForceBase
class  Array
class  Array::RefArray
class  Array::RefArray< 1 >
class  Array< T, 0 >
class  Array< T, 1 >
class  ArrayCellListStructure
class  ArraySize
class  ArraySizes
struct  Atom
struct  AtomType
struct  BankLennardJonesParameterTable
class  BBKIntegrator
class  Bond
struct  Bond::Constraint
class  BondSystemForce
class  BondSystemForceBase
class  BSpline
class  BSplineEnum
 BSpline MOLLY types. More...

class  BSplineMOLLYIntegrator
struct  BSplineMOLLYIntegrator::AngleIndex
struct  BSplineMOLLYIntegrator::BondIndex
class  C1SwitchingFunction
class  C1SwitchingFunctionBase
class  C2SwitchingFunction
class  C2SwitchingFunctionBase
class  CellListEnumerator
class  CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >
struct  CellListEnumerator< PeriodicBoundaryConditions, CubicCellManager >::CellPair
class  CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >
struct  CellListEnumerator< VacuumBoundaryConditions, CubicCellManager >::CellPair
class  CompareForce
struct  CompareForce::CompareError
class  ComplementSwitchingFunction
class  ComplementSwitchingFunctionBase
class  Configuration
class  ConfigurationReader
class  ConstraintValueEnum
 Map of Value constraints. More...

struct  ConstraintValueEnum::Enum2Type
class  CoulombEwaldRealForce
class  CoulombEwaldRealTableForce
class  CoulombForce
class  CoulombForce::C1
class  CoulombForce::C2
class  CoulombForce::C3
class  CoulombForce::C4
class  CoulombMultiGridDirectForce
class  CoulombMultiGridDirectForceBase
class  CoulombMultiGridDirectTableForce
class  CoulombMultiGridDirectTableForceBase
class  CubicCellLocation
class  CubicCellManager
class  CutoffSwitchingFunction
class  CutoffSwitchingFunctionBase
class  Cycles
class  DCDTrajectoryReader
class  DCDTrajectoryWriter
struct  DebugPostConstraint
struct  DebugPreConstraint
class  DihedralHMCIntegrator
class  DihedralSystemForce
class  DihedralSystemForceBase
class  DLMCIntegrator
class  DMDLeapfrogIntegrator
class  ElectricFieldSystemForce
class  ElectricFieldSystemForceBase
struct  Endian
struct  Enum2ValueTraits< ValueType::BOOL >
struct  Enum2ValueTraits< ValueType::FORCE >
struct  Enum2ValueTraits< ValueType::INT >
struct  Enum2ValueTraits< ValueType::INTEGRATOR >
struct  Enum2ValueTraits< ValueType::REAL >
struct  Enum2ValueTraits< ValueType::STRING >
struct  Enum2ValueTraits< ValueType::UINT >
struct  Enum2ValueTraits< ValueType::VECTOR >
struct  Enum2ValueTraits< ValueType::VECTOR3D >
class  EquilibriumMOLLYIntegrator
struct  EquilibriumMOLLYIntegrator::HydrogenBond
class  ExclusionEnum
struct  ExclusionPair
class  ExclusionTable
class  ExtendedCompareForce
class  ExtendedForce
class  ExtendedTimeForce
class  ExternalGravitationSystemForce
class  ExternalMagneticFieldExtendedForce
class  Factory
class  FactoryBase
class  FactoryTraits< Force >
class  FactoryTraits< GenericTopology >
class  FactoryTraits< Integrator >
class  FactoryTraits< Output >
class  FFTComplex
class  FFTInternal
class  File
class  Force
class  ForceFactoryDetails
struct  ForceFactoryDetails::ForceType
class  ForceGroup
class  FrictionExtendedForce
class  GenericTopology
class  GravitationForce
class  Grid
struct  Grid::Int3D
struct  Grid::Interpolation3D
 3d interpolation More...

class  HapticSystemForce
class  HarmDihedralSystemForce
class  HarmDihedralSystemForceBase
struct  HBondConstraint
struct  HelpText
class  HelpTextFactory
class  Hermite
class  HMCIntegrator
class  IMDElf
class  ImproperSystemForce
class  ImproperSystemForceBase
class  ImpulseIntegrator
struct  InputBoundaryConditionsIdentifier
struct  InputCellManagerIdentifier
struct  InputConfigIdentifier
struct  InputDebugIdentifier
struct  InputDihedralMultPSFIdentifier
struct  InputFirststepIdentifier
struct  InputIntegratorIdentifier
struct  InputMaxPackagesIdentifier
struct  InputMolVirialCalcIdentifier
struct  InputNumstepsIdentifier
struct  InputOutputfreqIdentifier
struct  InputOutputIdentifier
struct  InputParallelModeIdentifier
struct  InputParallelPipeIdentifier
struct  InputPARIdentifier
struct  InputPDBScalingIdentifier
struct  InputPositionsIdentifier
class  InputPosVel
class  InputPosVelEnum
struct  InputPSFIdentifier
struct  InputRattleEpsilonIdentifier
struct  InputRattleIdentifier
struct  InputRattleMaxIterIdentifier
struct  InputReducedImageIdentifier
struct  InputRemoveAngularMomentumIdentifier
struct  InputRemoveLinearMomentumIdentifier
struct  InputSeedIdentifier
struct  InputShakeEpsilonIdentifier
struct  InputShakeIdentifier
struct  InputShakeMaxIterIdentifier
struct  InputTemperatureIdentifier
struct  InputUseBarrierIdentifier
class  InputValue
struct  InputVelocitiesIdentifier
struct  InputVirialCalcIdentifier
class  Integrator
struct  IntegratorDefinition
class  IntegratorFactoryDetails
struct  IntegratorFactoryDetails::IntegratorInput
class  iSGAngleSystemForce
class  iSGAngleSystemForceBase
class  iSGBondSystemForce
class  iSGBondSystemForceBase
class  iSGCoulombEwaldRealForce
class  iSGCoulombEwaldRealTableForce
class  iSGCoulombForce
class  iSGCoulombForce::C1
class  iSGCoulombForce::C2
class  iSGCoulombForce::C3
class  iSGCoulombForce::C4
class  iSGDihedralSystemForce
class  iSGDihedralSystemForceBase
class  iSGGrid
struct  iSGGrid::Int3D
struct  iSGGrid::Interpolation3D
class  iSGIdealGasCoulombForce
class  iSGIdealGasCoulombForce::C1
class  iSGIdealGasCoulombForce::C2
class  iSGIdealGasCoulombForce::C3
class  iSGIdealGasCoulombForce::C4
class  iSGIdealGasLennardJonesForce
class  iSGImproperSystemForce
class  iSGImproperSystemForceBase
class  iSGIntegrator
class  iSGLennardJonesForce
class  iSGLennardJonesTableForce
class  iSGModifierPostForceChemostat
class  iSGModifierPreForceChemostat
class  iSGMTorsionSystemForce
class  iSGNonbondedFullEwaldSystemForce
class  iSGNonbondedFullEwaldSystemForceBase
class  iSGNonbondedPMEwaldSystemForce
class  iSGNonbondedPMEwaldSystemForceBase
class  iSGOneAtomPair
class  iSGOneAtomPairFull
class  iSGOneAtomPairTwo
class  iSGOneAtomPairTwoFull
class  iSGPAR
struct  iSGPAR::Angle
struct  iSGPAR::AtomType
 This class contains information common to one type of atom. More...

struct  iSGPAR::Bond
struct  iSGPAR::Dihedral
struct  iSGPAR::Improper
struct  iSGPAR::Nonbonded
 This structure holds data for an atom's nonbonded parameters. More...

class  iSGPARReader
class  Lagrange
class  LangevinImpulseIntegrator
class  LeapfrogIntegrator
class  LennardJonesForce
struct  LennardJonesParameters
 The Lennard-Jones parameters for one pair of atom types. More...

class  LennardJonesParameterTable
class  LennardJonesTableForce
struct  ltstrNocase
class  MagneticDipoleForce
class  MagneticDipoleMirrorSystemForce
class  MagneticDipoleMirrorSystemForceBase
class  Makeable
struct  MakeableDefinition
class  Matrix3by3
class  MCIntegrator
class  MetaForce
class  Modifier
class  ModifierAveraging
class  ModifierFriction
class  ModifierIncrementTimestep
class  ModifierISG
struct  ModifierISG::TransformMap
class  ModifierMetaRattle
class  ModifierMetaRattleShake
class  ModifierMetaShake
class  ModifierMollification
class  ModifierNPTRattle
class  ModifierNPTRattleDetails
class  ModifierNPTShake
class  ModifierNPTShakeDetails
class  ModifierNVTRattle
class  ModifierNVTRattleDetails
class  ModifierNVTShake
class  ModifierNVTShakeDetails
class  ModifierPostForceBarostat
class  ModifierPostForceThermostat
class  ModifierPreForceBarostat
class  ModifierPreForceThermostat
class  ModifierRattle
class  ModifierRemoveAngularMomentum
class  ModifierRemoveLinearMomentum
class  ModifierShake
class  ModifierUmbrella
class  ModifierUpdateBeta
class  ModifierUpdateBetaAndPush
struct  Molecule
class  MollyForce
class  MOLLYIntegrator
class  MTorsionSystemForce
class  MTSIntegrator
class  MultiGrid
struct  MultiGrid::Int3D
struct  MultiGrid::Interpolation3D
 3D interpolation More...

struct  NoConstraint
class  NonbondedCutoffForce
class  NonbondedCutoffForceBase
class  NonbondedCutoffMollyForce
class  NonbondedCutoffSystemForce
class  NonbondedFullEwaldSystemForce
class  NonbondedFullEwaldSystemForceBase
class  NonbondedFullSystemForce
class  NonbondedFullSystemForceBase
class  NonbondedMultiGridSystemForce
class  NonbondedMultiGridSystemForceBase
class  NonbondedPMEwaldSystemForce
class  NonbondedPMEwaldSystemForceBase
class  NonbondedSimpleFullSystemForce
class  NonbondedSimpleFullSystemForceBase
class  NonStandardIntegrator
class  NoseNVTLeapfrogIntegrator
struct  NotSameMoleculeConstraint
class  NPTVerletIntegrator
class  NVTVerletIntegrator
struct  ObjectDefinition
class  OneAtomPair
class  OneAtomPairFull
class  OneAtomPairTwo
class  OneAtomPairTwoFull
class  OneMollyPair
class  OneMollyPairTwo
class  Output
class  OutputCache
class  OutputCollection
class  OutputDCDTrajectory
class  OutputDiffusion
class  OutputDihedrals
class  OutputEnergies
class  OutputFactoryDetails
class  OutputFile
class  OutputFinalPDBPos
class  OutputFinalPSF
class  OutputFinalXSC
class  OutputFinalXYZBinPos
class  OutputFinalXYZBinVel
class  OutputFinalXYZPos
class  OutputFinalXYZVel
class  OutputISGProperties
class  OutputMomentum
class  OutputPaulTrap
class  OutputPDBFramePos
class  OutputScreen
class  OutputTemperatures
class  OutputXYZTrajectoryForce
class  OutputXYZTrajectoryPos
class  OutputXYZTrajectoryVel
struct  PairIntSorted
 Pair of sorted int, where first <= second. More...

class  PAR
struct  PAR::Angle
struct  PAR::Bond
struct  PAR::Dihedral
struct  PAR::Hbond
 This structure holds data for hydrogen bonds, including the well depth and the minimum radius. More...

struct  PAR::Improper
struct  PAR::Nbfix
struct  PAR::Nonbonded
 This structure holds data for a nonbonded - including. More...

class  Parallel
class  ParallelEnum
struct  Parameter
class  PARReader
class  PARWriter
class  PaulTrapExtendedForce
class  PaulTrapExtendedForceBase
class  PaulTrapIntegrator
struct  PDB
struct  PDB::PDBAtom
class  PDBReader
class  PDBWriter
class  PeriodicBoundaryConditions
class  PGM
class  PGMReader
class  PGMWriter
class  PLeapfrogIntegrator
class  PNGWriter
class  PPM
class  PPMReader
class  PPMWriter
class  Proxy
class  PSF
struct  PSF::Acceptor
struct  PSF::Angle
struct  PSF::Atom
struct  PSF::Bond
struct  PSF::Dihedral
struct  PSF::Donor
struct  PSF::Improper
struct  PSF::Ngrp
struct  PSF::Nonbonded
class  PSFReader
class  PSFWriter
class  RangeSwitchingFunction
class  RangeSwitchingFunctionBase
class  Reader
class  ReducedHessAngle
class  ReducedHessCoulomb
class  ReducedHessLennardJones
struct  ReducedHessTraits< CoulombForce >
struct  ReducedHessTraits< LennardJonesForce >
class  RefArray
class  RefArray< T, 1 >
struct  SameMoleculeConstraint
class  ScalarStructure
class  SemiGenericTopology
class  ShadowHMCIntegrator
class  ShiftSwitchingFunction
class  ShiftSwitchingFunctionBase
class  SphericalSystemForce
class  Stack
class  StandardIntegrator
class  STSIntegrator
class  SystemCompareForce
class  SystemForce
class  SystemTimeForce
struct  Text
class  ThermostatEnum
class  TimeForce
class  Timer
class  TimeRep
class  TimerStatistic
class  Topology
class  TopologyFactoryDetails
class  Torsion
class  TRANS
struct  TRANS::AtomType
class  TRANSReader
struct  TripleInt
 Triple of int. More...

class  UmbrellaIntegrator
class  UniversalSwitchingFunction
class  UniversalSwitchingFunctionBase
class  VacuumBoundaryConditions
class  Value
class  Value::Holder
class  Value::PlaceHolder
struct  Value::Undefined
class  ValueEnum
struct  ValueEnum::Enum2ValueType
struct  ValueTraits< bool >
 BOOL. More...

struct  ValueTraits< char[n]>
struct  ValueTraits< const char[n]>
struct  ValueTraits< int >
 INT. More...

struct  ValueTraits< Real >
 REAL. More...

struct  ValueTraits< std::string >
 STRING. More...

struct  ValueTraits< std::vector< Real > >
 VECTOR. More...

struct  ValueTraits< unsigned int >
 UINT. More...

struct  ValueTraits< ValueType::Force >
 FORCE. More...

struct  ValueTraits< ValueType::Integrator >
 INTEGRATOR. More...

struct  ValueTraits< Vector3D >
 VECTOR3D. More...

class  Vector
class  Vector3D
class  Vector3DBlock
class  VectorPacker
class  WrapperMetaForce
class  Writer
class  XFigWriter
struct  XSC
class  XSCReader
class  XSCWriter
struct  XYZ
class  XYZBinReader
class  XYZBinWriter
class  XYZReader
class  XYZTrajectoryReader
class  XYZTrajectoryWriter
class  XYZWriter

Typedefs

typedef AbstractEnumType<
BSplineEnum > 		BSplineType
typedef AbstractEnumType<
ConstraintValueEnum > 		ConstraintValueType
typedef double Real
typedef std::pair< std::string,
std::string > 		PairString
typedef std::pair< int, int > PairInt
typedef std::pair< unsigned
int, unsigned int > 		PairUInt
typedef AbstractEnumType<
ValueEnum > 		ValueType
typedef Factory< Force > ForceFactory
typedef AbstractEnumType<
InputPosVelEnum > 		InputPosVelType
typedef InputValue< InputOutputIdentifier,
ValueType::BOOL,ConstraintValueType::NOCONSTRAINTS > 		InputOutput
typedef InputValue< InputDebugIdentifier,
ValueType::INT,ConstraintValueType::NOCONSTRAINTS > 		InputDebug
typedef InputValue< InputTemperatureIdentifier,
ValueType::REAL,ConstraintValueType::NOTNEGATIVE > 		InputTemperature
typedef InputValue< InputSeedIdentifier,
ValueType::INT,ConstraintValueType::NOTNEGATIVE > 		InputSeed
typedef InputValue< InputConfigIdentifier,
ValueType::STRING,ConstraintValueType::NOTEMPTY > 		InputConfig
typedef InputValue< InputFirststepIdentifier,
ValueType::INT,ConstraintValueType::NOCONSTRAINTS > 		InputFirststep
typedef InputValue< InputNumstepsIdentifier,
ValueType::INT,ConstraintValueType::NOTNEGATIVE > 		InputNumsteps
typedef InputValue< InputOutputfreqIdentifier,
ValueType::INT,ConstraintValueType::NOTNEGATIVE > 		InputOutputfreq
typedef InputValue< InputIntegratorIdentifier,
ValueType::INTEGRATOR,ConstraintValueType::NOTEMPTY > 		InputIntegrator
typedef InputValue< InputPositionsIdentifier,
ValueType::STRING,ConstraintValueType::NOTEMPTY > 		InputPositions
typedef InputValue< InputVelocitiesIdentifier,
ValueType::STRING,ConstraintValueType::NOTEMPTY > 		InputVelocities
typedef InputValue< InputPSFIdentifier,
ValueType::STRING,ConstraintValueType::NOTEMPTY > 		InputPSF
typedef InputValue< InputPARIdentifier,
ValueType::STRING,ConstraintValueType::NOTEMPTY > 		InputPAR
typedef InputValue< InputRemoveLinearMomentumIdentifier,
ValueType::INT,ConstraintValueType::NOCONSTRAINTS > 		InputRemoveLinearMomentum
typedef InputValue< InputRemoveAngularMomentumIdentifier,
ValueType::INT,ConstraintValueType::NOCONSTRAINTS > 		InputRemoveAngularMomentum
typedef InputValue< InputUseBarrierIdentifier,
ValueType::BOOL,ConstraintValueType::NOCONSTRAINTS > 		InputUseBarrier
typedef InputValue< InputParallelPipeIdentifier,
ValueType::INT,ConstraintValueType::NOCONSTRAINTS > 		InputParallelPipe
typedef InputValue< InputParallelModeIdentifier,
ValueType::STRING,ConstraintValueType::NOTEMPTY > 		InputParallelMode
typedef InputValue< InputMaxPackagesIdentifier,
ValueType::INT,ConstraintValueType::NOCONSTRAINTS > 		InputMaxPackages
typedef InputValue< InputPDBScalingIdentifier,
ValueType::BOOL,ConstraintValueType::NOCONSTRAINTS > 		InputPDBScaling
typedef InputValue< InputBoundaryConditionsIdentifier,
ValueType::STRING,ConstraintValueType::NOTEMPTY > 		InputBoundaryConditions
typedef InputValue< InputCellManagerIdentifier,
ValueType::STRING,ConstraintValueType::NOTEMPTY > 		InputCellManager
typedef InputValue< InputDihedralMultPSFIdentifier,
ValueType::BOOL,ConstraintValueType::NOCONSTRAINTS > 		InputDihedralMultPSF
typedef InputValue< InputVirialCalcIdentifier,
ValueType::BOOL,ConstraintValueType::NOCONSTRAINTS > 		InputVirialCalc
typedef InputValue< InputMolVirialCalcIdentifier,
ValueType::BOOL,ConstraintValueType::NOCONSTRAINTS > 		InputMolVirialCalc
typedef InputValue< InputShakeIdentifier,
ValueType::BOOL,ConstraintValueType::NOCONSTRAINTS > 		InputShake
typedef InputValue< InputShakeEpsilonIdentifier,
ValueType::REAL,ConstraintValueType::NOTNEGATIVE > 		InputShakeEpsilon
typedef InputValue< InputShakeMaxIterIdentifier,
ValueType::INT,ConstraintValueType::NOTNEGATIVE > 		InputShakeMaxIter
typedef InputValue< InputRattleIdentifier,
ValueType::BOOL,ConstraintValueType::NOCONSTRAINTS > 		InputRattle
typedef InputValue< InputRattleEpsilonIdentifier,
ValueType::REAL,ConstraintValueType::NOTNEGATIVE > 		InputRattleEpsilon
typedef InputValue< InputRattleMaxIterIdentifier,
ValueType::INT,ConstraintValueType::NOTNEGATIVE > 		InputRattleMaxIter
typedef InputValue< InputReducedImageIdentifier,
ValueType::BOOL,ConstraintValueType::NOCONSTRAINTS > 		InputReducedImage
typedef Factory< Integrator > IntegratorFactory
typedef Factory< Output > OutputFactory
typedef Factory< GenericTopology > TopologyFactory
typedef AbstractEnumType<
ThermostatEnum > 		ThermostatType
typedef AbstractEnumType<
ParallelEnum > 		ParallelType
typedef AbstractEnumType<
ExclusionEnum > 		ExclusionType

Enumerations

enum  ExclusionClass {
  EXCLUSION_NONE = 0,
  EXCLUSION_MODIFIED = 1,
  EXCLUSION_FULL = 2
}
enum  {
  X_AXIS,
  Y_AXIS,
  Z_AXIS
}
enum  waterOption {
  IGNORE_WATER,
  ONLY_WATER,
  ALL
}

Functions

template<typename T, size_t N> bool operator== (const Array< T, N > &A, const Array< T, N > &B)
template<typename T, size_t N> bool operator!= (const Array< T, N > &A, const Array< T, N > &B)
MyStreamer & operator<< (MyStreamer &OS, const iSGPAR::Bond &p)
MyStreamer & operator<< (MyStreamer &OS, const iSGPAR::Angle &p)
MyStreamer & operator<< (MyStreamer &OS, const iSGPAR::Dihedral &p)
MyStreamer & operator<< (MyStreamer &OS, const iSGPAR::Improper &p)
MyStreamer & operator<< (MyStreamer &OS, const iSGPAR::Nonbonded &p)
MyStreamer & operator<< (MyStreamer &OS, const iSGPAR::Nbfix &p)
MyStreamer & operator<< (MyStreamer &OS, const iSGPAR::Hbond &p)
Real myerf (Real x)
Real poly5 (Real ar)
vector< Real > rtod (const vector< Real > &rad)
vector< Real > dtor (const vector< Real > &deg)
void sincos (Real alpha, Real &sinAlpha, Real &cosAlpha)
Real power (Real x, int n)
Real norm (Real a, Real b)
Real randomNumber (unsigned int seed)
Real randomGaussian (Real sdv, unsigned int seed)
Real randomGaussianNumber (unsigned int seed)
Real randomGaussianNumber (Real mean, Real stdev, unsigned int iseed)
int getTimerSeed ()
void splitRangeQuadratic (unsigned int p, unsigned int from, unsigned int to, vector< PairUInt > &fromRange, vector< PairUInt > &toRange)
void splitRangeArea (unsigned int p, unsigned int from, unsigned int to, vector< PairUInt > &fromRange, vector< PairUInt > &toRange)
Real square (Real x)
template<int _power> Real power (Real x)
template<> Real power< 0 > (Real)
template<> Real power< 1 > (Real x)
template<> Real power<-1 > (Real x)
int fact (int n)
Real dtor (Real degree)
Real rtod (Real rad)
std::vector< Real > rtod (const std::vector< Real > &rad)
std::vector< Real > dtor (const std::vector< Real > &deg)
bool equal (Real x, Real y)
bool equal (Real x, Real y, Real epsilon)
template<class T> int sign (T a)
Real sign (Real a, Real b)
template<class T> T max (const T &a, const T &b, const T &c)
template<class T> T max (const T &a, const T &b, const T &c, const T &d)
template<class T> T min (const T &a, const T &b, const T &c)
template<class T> T min (const T &a, const T &b, const T &c, const T &d)
std::ostream & operator<< (std::ostream &os, const Matrix3by3 &tm)
Vector3D operator * (const Vector3D &point, const Matrix3by3 &tm)
void convert (const Matrix3by3 &from, float to[9])
void convert (const Matrix3by3 &from, double to[16])
void convert (const Matrix3by3 &from, double to[9])
MyStreamer & operator<< (MyStreamer &OS, const PDB::PDBAtom &p)
ostream & operator<< (ostream &os, const ReducedHessAngle &tm)
Matrix3by3 reducedHessBond (const Vector3D &atom_i, const Vector3D &atom_j, const Real _k, const Real _r0)
string uppercase (const string &word)
string lowercase (const string &word)
bool equal (const string &s1, const string &s2)
bool equalNocase (const string &s1, const string &s2)
bool equalBegin (const string &s1, const string &s2)
bool equalBeginNocase (const string &s1, const string &s2)
bool equalStart (const string &s1, const string &s2)
bool equalStartNocase (const string &s1, const string &s2)
bool equalEnd (const string &s1, const string &s2)
bool equalEndNocase (const string &s1, const string &s2)
bool equalTerminate (const string &s1, const string &s2)
bool equalTerminateNocase (const string &s1, const string &s2)
template<class T> string toStringGeneric (T x)
string toString (Real x)
string toString (Real x, unsigned int n, unsigned int m)
string toString (bool x)
string toString (const Vector3D &c)
string toString (const vector< Real > &v)
bool isReal (const string &word)
Real toReal (const string &word)
bool toReal (const string &word, Real &r)
bool isInt (const string &word)
int toInt (const string &word)
bool toInt (const string &word, int &i)
bool isUInt (const string &word)
unsigned int toUInt (const string &word)
bool toUInt (const string &word, unsigned int &i)
bool isBool (const string &word)
bool toBool (const string &word)
bool toBool (const string &word, bool &b)
bool isVector3D (const string &word)
Vector3D toVector3D (const string &word)
bool toVector3D (const string &word, Vector3D &c)
bool isVector (const string &word)
vector< Real > toVector (const string &word)
bool toVector (const string &word, vector< Real > &v)
bool isBlank (const string &word)
bool isblankchar (char c)
bool isPrintable (const string &word)
bool isprintablechar (char c)
string getBegin (const string &s, string::size_type n)
string getEnd (const string &s, string::size_type n)
string getRightFill (const string &s, string::size_type n)
string getLeftFill (const string &s, string::size_type n)
string removeBeginEndBlanks (const string &s)
bool ltstrNocaseOp (const string &s1, const string &s2)
int equalWildcard (const string &wildcard, const string &name)
vector< string > splitString (const string &id)
string mergeString (const vector< string > &id)
string normalizeString (const string &word)
std::string uppercase (const std::string &word)
std::string lowercase (const std::string &word)
bool equal (const std::string &s1, const std::string &s2)
bool equalNocase (const std::string &s1, const std::string &s2)
bool equalBegin (const std::string &s1, const std::string &s2)
bool equalBeginNocase (const std::string &s1, const std::string &s2)
bool equalStart (const std::string &s1, const std::string &s2)
bool equalStartNocase (const std::string &s1, const std::string &s2)
bool equalEnd (const std::string &s1, const std::string &s2)
bool equalEndNocase (const std::string &s1, const std::string &s2)
bool equalTerminate (const std::string &s1, const std::string &s2)
bool equalTerminateNocase (const std::string &s1, const std::string &s2)
bool isReal (const std::string &word)
bool toReal (const std::string &word, Real &r)
Real toReal (const std::string &word)
bool isInt (const std::string &word)
bool toInt (const std::string &word, int &i)
int toInt (const std::string &word)
bool isUInt (const std::string &word)
bool toUInt (const std::string &word, unsigned int &i)
unsigned int toUInt (const std::string &word)
bool isBool (const std::string &word)
bool toBool (const std::string &word, bool &b)
bool toBool (const std::string &word)
bool isVector3D (const std::string &word)
bool toVector3D (const std::string &word, Vector3D &c)
Vector3D toVector3D (const std::string &word)
bool isVector (const std::string &word)
std::vector< Real > toVector (const std::string &word)
bool toVector (const std::string &word, std::vector< Real > &c)
std::string toString (const std::vector< Real > &x)
const std::string & toString (const std::string &x)
template<class T> std::string toString (T x)
bool isBlank (const std::string &word)
bool isPrintable (const std::string &word)
std::string getBegin (const std::string &s, std::string::size_type n)
std::string getEnd (const std::string &s, std::string::size_type n)
std::string getRightFill (const std::string &s, std::string::size_type n)
std::string getLeftFill (const std::string &s, std::string::size_type n)
std::string removeBeginEndBlanks (const std::string &s)
bool ltstrNocaseOp (const std::string &s1, const std::string &s2)
int equalWildcard (const std::string &wildcard, const std::string &name)
std::vector< std::string > splitString (const std::string &str)
std::string mergeString (const std::vector< std::string > &str)
std::string normalizeString (const std::string &str)
bool changeDirectory (const string &fileName)
bool isAccessible (const string &fileName)
void protomolAbort ()
void setProtomolAbort (void(*abortFunction)())
void protomolExit ()
void setProtomolExit (void(*exitFunction)())
void protomolStartSerial (bool exludeMaster)
void setProtomolStartSerial (void(*startSerialFunction)(bool))
void protomolEndSerial (bool exludeMaster)
void setProtomolEndSerial (void(*endSerialFunction)(bool))
string getUserName ()
bool changeDirectory (const std::string &fileName)
bool isAccessible (const std::string &fileName)
template<typename T> void swapBytes (T &t)
void shift (Real &a, Real &b, Real &c, const Real d)
template<typename T> void realclear (T &t)
template<typename T> void shrink (T &t)
Report::MyStreamer & operator<< (Report::MyStreamer &os, const TimeRep &time)
Report::MyStreamer & operator<< (Report::MyStreamer &os, const Timer &timer)
Report::MyStreamer & operator<< (Report::MyStreamer &os, const TimerStatistic &)
bool operator== (const Value &v1, const Value &v2)
bool operator< (const Value &v1, const Value &v2)
bool operator<= (const Value &v1, const Value &v2)
bool operator> (const Value &v1, const Value &v2)
bool operator>= (const Value &v1, const Value &v2)
MyStreamer & operator<< (MyStreamer &OS, const Value &v)
template<typename BC, typename CM> void registerForceExemplarsDispatch (const Topology< BC, CM > *topo)
void registerForceExemplars (const GenericTopology *topo)
void registerForceExemplarsBonded (const PeriodicBoundaryConditions *)
void registerForceExemplarsBonded (const VacuumBoundaryConditions *)
void registerForceExemplarsCutoff (const PeriodicBoundaryConditions *, const CubicCellManager *)
void registerForceExemplarsCutoff (const VacuumBoundaryConditions *, const CubicCellManager *)
void registerForceExemplarsFastElectrostatic (const PeriodicBoundaryConditions *, const CubicCellManager *)
void registerForceExemplarsFastElectrostatic (const VacuumBoundaryConditions *, const CubicCellManager *)
void registerForceExemplarsFull (const PeriodicBoundaryConditions *)
void registerForceExemplarsFull (const VacuumBoundaryConditions *)
void registerForceExemplarsOther (const PeriodicBoundaryConditions *, const CubicCellManager *)
void registerForceExemplarsOther (const PeriodicBoundaryConditions *)
void registerForceExemplarsOther (const VacuumBoundaryConditions *, const CubicCellManager *)
void registerForceExemplarsOther ()
void registerForceExemplarsOther (const VacuumBoundaryConditions *)
void registerForceExemplarsSimpleFull (const PeriodicBoundaryConditions *)
void registerForceExemplarsSimpleFull (const VacuumBoundaryConditions *)
void registerIntegratorExemplars ()
void registerOutputExemplars ()
void registerTopologyExemplars ()
void findNextNeighbor (int a, vector< int > &v, vector< PairInt > &p, vector< bool > &unused, const vector< vector< int > > &graph, set< PairInt > &pairs)
void buildTopology (GenericTopology *topo, const PSF &psf, const PAR &par, bool dihedralMultPSF)
void buildMoleculeTable (GenericTopology *topo)
void buildExclusionTable (GenericTopology *topo, const ExclusionType &exclusionType)
InputPosVel & operator>> (InputPosVel &posReader, PDB &pdb)
InputPosVel & operator>> (InputPosVel &posReader, XYZ &xyz)
InputPosVel & operator>> (InputPosVel &posReader, Vector3DBlock &coords)
vector< vector< string > > parseCommandLine (int argc, char **argv, const Configuration *config, void(*registerForceExemplarsFunction)(const GenericTopology *))
ConfigurationReader & operator>> (ConfigurationReader &configReader, Configuration &config)
DCDTrajectoryReader & operator>> (DCDTrajectoryReader &dcdTrajectoryReader, XYZ &xyz)
DCDTrajectoryReader & operator>> (DCDTrajectoryReader &dcdTrajectoryReader, Vector3DBlock &coords)
DCDTrajectoryWriter & operator<< (DCDTrajectoryWriter &dcdWriter, const Vector3DBlock &coords)
DCDTrajectoryWriter & operator<< (DCDTrajectoryWriter &dcdWriter, const XYZ &xyz)
PARReader & operator>> (PARReader &parReader, PAR &par)
PARWriter & operator<< (PARWriter &parWriter, const PAR &par)
PDBReader & operator>> (PDBReader &pdbReader, PDB &pdb)
PDBReader & operator>> (PDBReader &pdbReader, Vector3DBlock &coords)
PDBReader & operator>> (PDBReader &pdbReader, XYZ &xyz)
PDBWriter & operator<< (PDBWriter &pdbWriter, const PDB &pdb)
PGMReader & operator>> (PGMReader &pgmReader, PGM &pgm)
PGMReader & operator>> (PGMReader &pgmReader, PPM &ppm)
PGMWriter & operator<< (PGMWriter &pgmWriter, const PGM &pgm)
PGMWriter & operator<< (PGMWriter &pgmWriter, const PPM &ppm)
PNGWriter & operator<< (PNGWriter &PNGWriter, const PPM &ppm)
PNGWriter & operator<< (PNGWriter &pngWriter, const PGM &pgm)
PPMReader & operator>> (PPMReader &ppmReader, PPM &ppm)
PPMReader & operator>> (PPMReader &ppmReader, PGM &pgm)
PPMWriter & operator<< (PPMWriter &ppmWriter, const PPM &ppm)
PPMWriter & operator<< (PPMWriter &ppmWriter, const PGM &pgm)
PSFReader & operator>> (PSFReader &psfReader, PSF &psf)
PSFWriter & operator<< (PSFWriter &psfWriter, const PSF &psf)
XFigWriter & operator<< (XFigWriter &xyzWriter, const XYZ &xyz)
XYZBinReader & operator>> (XYZBinReader &xyzbinReader, XYZ &xyz)
XYZBinReader & operator>> (XYZBinReader &xyzbinReader, Vector3DBlock &coords)
XYZBinWriter & operator<< (XYZBinWriter &xyzWriter, const XYZ &xyz)
XYZBinWriter & operator<< (XYZBinWriter &xyzWriter, const Vector3DBlock &coords)
XYZReader & operator>> (XYZReader &xyzReader, XYZ &xyz)
XYZReader & operator>> (XYZReader &xyzReader, Vector3DBlock &coords)
XYZTrajectoryReader & operator>> (XYZTrajectoryReader &xyzReader, XYZ &xyz)
XYZTrajectoryReader & operator>> (XYZTrajectoryReader &xyzReader, Vector3DBlock &coords)
XYZTrajectoryWriter & operator<< (XYZTrajectoryWriter &xyzWriter, const XYZ &xyz)
XYZTrajectoryWriter & operator<< (XYZTrajectoryWriter &xyzWriter, const Vector3DBlock &coords)
XYZWriter & operator<< (XYZWriter &xyzWriter, const XYZ &xyz)
void mpiAbort ()
void mpiExit ()
void mpiStartSerial (bool exludeMaster)
void mpiEndSerial (bool exludeMaster)
void buildCellLists (const Topology< PeriodicBoundaryConditions, CubicCellManager > *topo, const Vector3DBlock *positions)
void buildCellLists (const Topology< VacuumBoundaryConditions, CubicCellManager > *topo, const Vector3DBlock *positions)
bool normVector3DOp (const Vector3D &v1, const Vector3D &v2)
void randomVelocity (Real temperature, const GenericTopology *topology, Vector3DBlock *velocities, unsigned int seed)
void randomVelocity (Real temperatureFrom, Real temperatureTo, const GenericTopology *topology, Vector3DBlock *velocities, unsigned int seed)
Real temperature (const GenericTopology *topology, const Vector3DBlock *velocities)
Real temperature (Real kineticEnergy, unsigned int degreesOfFreedom)
Real temperatureForAtomType (const GenericTopology *topology, const Vector3DBlock *velocities, int atomType, waterOption option)
Real temperatureForWater (const GenericTopology *topology, const Vector3DBlock *velocities)
Real temperatureForNonWater (const GenericTopology *topology, const Vector3DBlock *velocities)
Real kineticEnergy (const GenericTopology *topology, const Vector3DBlock *velocities)
Real kineticEnergyForAtomType (const GenericTopology *topology, const Vector3DBlock *velocities, int atomType, waterOption option)
Real kineticEnergyForAtomType (const GenericTopology *topology, const Vector3DBlock *velocities, int atomType, waterOption option, int &atomCount)
Real kineticEnergyForWater (const GenericTopology *topology, const Vector3DBlock *velocities)
Real kineticEnergyForWater (const GenericTopology *topology, const Vector3DBlock *velocities, int &waterCount)
Real kineticEnergyForNonWater (const GenericTopology *topology, const Vector3DBlock *velocities)
Real kineticEnergyForNonWater (const GenericTopology *topology, const Vector3DBlock *velocities, int &nonWaterCount)
Real molecularKineticEnergy (const GenericTopology *topology, const Vector3DBlock *velocities)
ScalarStructure velocityVirial (const GenericTopology *topology, const Vector3DBlock *velocities)
void addVelocityVirial (ScalarStructure *energies, const GenericTopology *topology, const Vector3DBlock *velocities)
string atomTypeToSymbolName (const string &type)
Vector3D linearMomentum (const Vector3DBlock *velocities, const GenericTopology *topo)
Vector3D removeLinearMomentum (Vector3DBlock *velocities, const GenericTopology *topo)
Vector3D centerOfMass (const Vector3DBlock *positions, const GenericTopology *topo)
Vector3D angularMomentum (const Vector3DBlock *positions, const Vector3DBlock *velocities, const GenericTopology *topo)
Vector3D angularMomentum (const Vector3DBlock *positions, const Vector3DBlock *velocities, const GenericTopology *topo, const Vector3D &centerOfMass)
Matrix3by3 inertiaMomentum (const Vector3DBlock *positions, const GenericTopology *topo, const Vector3D &centerOfMass)
Vector3D removeAngularMomentum (const Vector3DBlock *positions, Vector3DBlock *velocities, const GenericTopology *topo)
Real computePressure (const GenericTopology *topology, const Vector3DBlock *positions, const Vector3DBlock *velocities, const ScalarStructure *energies)
Real computePressure (const ScalarStructure *energies, Real volume, Real kineticEnergy)
Real computeMolecularPressure (const ScalarStructure *energies, Real volume, Real kineticEnergy)
Vector3D molecularMomentum (const vector< int > &atomList, const Vector3DBlock *velocities, const GenericTopology *topo)
Vector3D molecularCenterOfMass (const vector< int > &atomList, const Vector3DBlock *positions, const GenericTopology *topo)
void buildMolecularCenterOfMass (const Vector3DBlock *positions, GenericTopology *topo)
void buildMolecularMomentum (const Vector3DBlock *velocities, GenericTopology *topo)
void buildRattleShakeBondConstraintList (GenericTopology *topology, vector< Bond::Constraint > &bondConstraints)
void getAtomsBondedtoDihedral (const GenericTopology *topology, set< int, std::less< int > > *atomSet, const int atomID, const int inAtomID, const int outAtomID, const int exclAtomID)
void rotateDihedral (const GenericTopology *topology, Vector3DBlock *positions, Vector3DBlock *velocities, const int dihedralID, Real angle)
void rotateDihedral (const GenericTopology *topology, Vector3DBlock *positions, const int dihedralID, Real angle)
void set_angles (Stack< unsigned int > *nodeStack, vector< AngleInfo > *angles, bool lastIsInnerAtom, Real wholeAngle)
void build_angle_list (const GenericTopology *topo, const unsigned int atomID, const unsigned int inAtomID, const unsigned int outAtomID, const unsigned int exclAtomID, Real rotAngle, vector< AngleInfo > *angles)
Real computePhiDihedral (const GenericTopology *topo, const Vector3DBlock *positions, int index)
Real computePhiDihedralEnergy (const GenericTopology *topo, int index, Real phi)
void general_rotation (unsigned int innerAtom1, unsigned int innerAtom2, Vector3DBlock *positions, vector< AngleInfo > *angles)
void general_rotation (unsigned int innerAtom1, unsigned int innerAtom2, Vector3DBlock *positions, Vector3DBlock *velocities, vector< AngleInfo > *angles)
void getAtomsBondedtoDihedral (const GenericTopology *topology, std::set< int > *atomSet, const int atomID, const int inAtomID, const int outAtomID, const int exclAtomID)
std::string atomTypeToSymbolName (const std::string &type)
Vector3D molecularMomentum (const std::vector< int > &, const Vector3DBlock *, const GenericTopology *)
Vector3D molecularCenterOfMass (const std::vector< int > &, const Vector3DBlock *, const GenericTopology *)
template<typename BC, typename CM> void iSGregisterForceExemplarsDispatch (const Topology< BC, CM > *topo)
void iSGregisterForceExemplars (const GenericTopology *topo)
void iSGregisterForceExemplarsBonded (const PeriodicBoundaryConditions *)
void iSGregisterForceExemplarsBonded (const VacuumBoundaryConditions *)
void iSGregisterForceExemplarsCutoff (const PeriodicBoundaryConditions *, const CubicCellManager *)
void iSGregisterForceExemplarsCutoff (const VacuumBoundaryConditions *, const CubicCellManager *)
void iSGregisterForceExemplarsFastElectrostatic (const PeriodicBoundaryConditions *, const CubicCellManager *)
void iSGregisterForceExemplarsFastElectrostatic (const VacuumBoundaryConditions *, const CubicCellManager *)
void iSGregisterForceExemplarsFull (const PeriodicBoundaryConditions *)
void iSGregisterForceExemplarsFull (const VacuumBoundaryConditions *)
void iSGregisterForceExemplarsIdealGas (const PeriodicBoundaryConditions *, const CubicCellManager *)
void iSGregisterForceExemplarsIdealGas (const VacuumBoundaryConditions *, const CubicCellManager *)
void iSGregisterForceExemplarsSimpleFull (const PeriodicBoundaryConditions *)
void iSGregisterForceExemplarsSimpleFull (const VacuumBoundaryConditions *)
void iSGregisterOutputExemplars ()
void buildISGTopology (GenericTopology *topo, const PSF &psf, const iSGPAR &par)
void buildMoleculeBondingLists (GenericTopology *topo)
iSGPARReader & operator>> (iSGPARReader &parReader, iSGPAR &par)
TRANSReader & operator>> (TRANSReader &transReader, TRANS &trans)
XSCReader & operator>> (XSCReader &xscReader, XSC &xsc)
XSCWriter & operator<< (XSCWriter &xscWriter, const XSC &xsc)
unsigned int openglToPlain (ostream &output, void(*display)())
unsigned int openglToEPS (ostream &output, void(*display)())
void openglToPPM (PPM &ppm)
void openglToPGM (PGM &pgm)

Variables

const Real E1 = 0.254829592
const Real E2 = -0.284496736
const Real E3 = 1.421413741
const Real E4 = -1.453152027
const Real E5 = 1.061405429
const Real PP = 0.3275911
const Real BORDER_TOLERANCE = 0.0001
const int BORDER = 2
void(* myAbortFunction )()=NULL
void(* myExitFunction )()=NULL
void(* myStartSerial )(bool)=NULL
void(* myEndSerial )(bool)=NULL
const bool ISLITTLEENDIAN = Endian::isLittleEndian()
const Real SI_FACTOR = 1e-3*Constant::SI::KCAL/Constant::SI::LENGTH_AA
const Real SI_FORCE_FACTOR = Constant::SI::ELECTRON_CHARGE*Constant::SI::AVOGADRO*Constant::SI::KCAL/Constant::SI::LENGTH_AA*(1e8/sqrt(4184.0))
const Real defaultScale = 1000.0
const int xFigXMax = 12500
const int xFigYMax = 9700
const int xFigColorsN = 32
const int xFigColors [xFigColorsN] = {0,20,13,10,31,1,2,3,4,5,6,7,8,9,11,12,14,15,16,17,18,19,21,22,23,24,25,26,27,28,29,30}
const int xFigBWN = 4
const std::string xFigBW1 [xFigBWN]
const std::string xFigBW2 [xFigBWN]
const int master = 0

Typedef Documentation

typedef AbstractEnumType<BSplineEnum> ProtoMol::BSplineType
 

typedef AbstractEnumType<ConstraintValueEnum> ProtoMol::ConstraintValueType
 

typedef AbstractEnumType<ExclusionEnum> ProtoMol::ExclusionType
 

typedef Factory<Force> ProtoMol::ForceFactory
 

typedef InputValue< InputBoundaryConditionsIdentifier,ValueType:: STRING ,ConstraintValueType:: NOTEMPTY > ProtoMol::InputBoundaryConditions
 

typedef InputValue< InputCellManagerIdentifier,ValueType:: STRING ,ConstraintValueType:: NOTEMPTY > ProtoMol::InputCellManager
 

typedef InputValue< InputConfigIdentifier,ValueType:: STRING ,ConstraintValueType:: NOTEMPTY > ProtoMol::InputConfig
 

typedef InputValue< InputDebugIdentifier,ValueType:: INT ,ConstraintValueType:: NOCONSTRAINTS > ProtoMol::InputDebug
 

typedef InputValue< InputDihedralMultPSFIdentifier,ValueType:: BOOL ,ConstraintValueType:: NOCONSTRAINTS > ProtoMol::InputDihedralMultPSF
 

typedef InputValue< InputFirststepIdentifier,ValueType:: INT ,ConstraintValueType:: NOCONSTRAINTS > ProtoMol::InputFirststep
 

typedef InputValue< InputIntegratorIdentifier,ValueType:: INTEGRATOR ,ConstraintValueType:: NOTEMPTY > ProtoMol::InputIntegrator
 

typedef InputValue< InputMaxPackagesIdentifier,ValueType:: INT ,ConstraintValueType:: NOCONSTRAINTS > ProtoMol::InputMaxPackages
 

typedef InputValue< InputMolVirialCalcIdentifier,ValueType:: BOOL ,ConstraintValueType:: NOCONSTRAINTS > ProtoMol::InputMolVirialCalc
 

typedef InputValue< InputNumstepsIdentifier,ValueType:: INT ,ConstraintValueType:: NOTNEGATIVE > ProtoMol::InputNumsteps
 

typedef InputValue< InputOutputIdentifier,ValueType:: BOOL ,ConstraintValueType:: NOCONSTRAINTS > ProtoMol::InputOutput
 

typedef InputValue< InputOutputfreqIdentifier,ValueType:: INT ,ConstraintValueType:: NOTNEGATIVE > ProtoMol::InputOutputfreq
 

typedef InputValue< InputPARIdentifier,ValueType:: STRING ,ConstraintValueType:: NOTEMPTY > ProtoMol::InputPAR
 

typedef InputValue< InputParallelModeIdentifier,ValueType:: STRING ,ConstraintValueType:: NOTEMPTY > ProtoMol::InputParallelMode
 

typedef InputValue< InputParallelPipeIdentifier,ValueType:: INT ,ConstraintValueType:: NOCONSTRAINTS > ProtoMol::InputParallelPipe
 

typedef InputValue< InputPDBScalingIdentifier,ValueType:: BOOL ,ConstraintValueType:: NOCONSTRAINTS > ProtoMol::InputPDBScaling
 

typedef InputValue< InputPositionsIdentifier,ValueType:: STRING ,ConstraintValueType:: NOTEMPTY > ProtoMol::InputPositions
 

typedef AbstractEnumType<InputPosVelEnum> ProtoMol::InputPosVelType
 

typedef InputValue< InputPSFIdentifier,ValueType:: STRING ,ConstraintValueType:: NOTEMPTY > ProtoMol::InputPSF
 

typedef InputValue< InputRattleIdentifier,ValueType:: BOOL ,ConstraintValueType:: NOCONSTRAINTS > ProtoMol::InputRattle
 

typedef InputValue< InputRattleEpsilonIdentifier,ValueType:: REAL ,ConstraintValueType:: NOTNEGATIVE > ProtoMol::InputRattleEpsilon
 

typedef InputValue< InputRattleMaxIterIdentifier,ValueType:: INT ,ConstraintValueType:: NOTNEGATIVE > ProtoMol::InputRattleMaxIter
 

typedef InputValue< InputReducedImageIdentifier,ValueType:: BOOL ,ConstraintValueType:: NOCONSTRAINTS > ProtoMol::InputReducedImage
 

typedef InputValue< InputRemoveAngularMomentumIdentifier,ValueType:: INT ,ConstraintValueType:: NOCONSTRAINTS > ProtoMol::InputRemoveAngularMomentum
 

typedef InputValue< InputRemoveLinearMomentumIdentifier,ValueType:: INT ,ConstraintValueType:: NOCONSTRAINTS > ProtoMol::InputRemoveLinearMomentum
 

typedef InputValue< InputSeedIdentifier,ValueType:: INT ,ConstraintValueType:: NOTNEGATIVE > ProtoMol::InputSeed
 

typedef InputValue< InputShakeIdentifier,ValueType:: BOOL ,ConstraintValueType:: NOCONSTRAINTS > ProtoMol::InputShake
 

typedef InputValue< InputShakeEpsilonIdentifier,ValueType:: REAL ,ConstraintValueType:: NOTNEGATIVE > ProtoMol::InputShakeEpsilon
 

typedef InputValue< InputShakeMaxIterIdentifier,ValueType:: INT ,ConstraintValueType:: NOTNEGATIVE > ProtoMol::InputShakeMaxIter
 

typedef InputValue< InputTemperatureIdentifier,ValueType:: REAL ,ConstraintValueType:: NOTNEGATIVE > ProtoMol::InputTemperature
 

typedef InputValue< InputUseBarrierIdentifier,ValueType:: BOOL ,ConstraintValueType:: NOCONSTRAINTS > ProtoMol::InputUseBarrier
 

typedef InputValue< InputVelocitiesIdentifier,ValueType:: STRING ,ConstraintValueType:: NOTEMPTY > ProtoMol::InputVelocities
 

typedef InputValue< InputVirialCalcIdentifier,ValueType:: BOOL ,ConstraintValueType:: NOCONSTRAINTS > ProtoMol::InputVirialCalc
 

typedef Factory<Integrator> ProtoMol::IntegratorFactory
 

typedef Factory<Output> ProtoMol::OutputFactory
 

typedef std::pair<int, int> ProtoMol::PairInt
 

Pair of int.

typedef std::pair<std::string, std::string> ProtoMol::PairString
 

Pair of std::string.

typedef std::pair<unsigned int, unsigned int> ProtoMol::PairUInt
 

Pair of unsigned int.

typedef AbstractEnumType<ParallelEnum> ProtoMol::ParallelType
 

typedef double ProtoMol::Real
 

The standard Real number type, settable by the user: double.

typedef AbstractEnumType<ThermostatEnum> ProtoMol::ThermostatType
 

typedef Factory<GenericTopology> ProtoMol::TopologyFactory
 

typedef AbstractEnumType<ValueEnum> ProtoMol::ValueType
 

Enumeration Type Documentation

anonymous enum
 

Enumeration values:
X_AXIS 
Y_AXIS 
Z_AXIS 

enum ProtoMol::ExclusionClass
 

Defines exclusions between two atoms, intra-molecular They are used to implement (bulding blocks) the exclusion type of system: ONE2, ONE3, ONE4 and ONE4MODIFIED

Enumeration values:
EXCLUSION_NONE  do not exclude
EXCLUSION_MODIFIED  do not exlcude, but modify
EXCLUSION_FULL  do exclude

enum ProtoMol::waterOption
 

Enumeration values:
IGNORE_WATER 
ONLY_WATER 
ALL 

Function Documentation

void ProtoMol::addVelocityVirial (  ScalarStructure *  energies,
const GenericTopology *  topology,
const Vector3DBlock *  velocities
) 
 

Vector3D ProtoMol::angularMomentum (  const Vector3DBlock *  positions,
const Vector3DBlock *  velocities,
const GenericTopology *  topo,
const Vector3D &  centerOfMass
) 
 

Vector3D ProtoMol::angularMomentum (  const Vector3DBlock *  positions,
const Vector3DBlock *  velocities,
const GenericTopology *  topo
) 
 

std::string atomTypeToSymbolName (  const std::string &  type  ) 
 

string atomTypeToSymbolName (  const string &  type  ) 
 

void ProtoMol::build_angle_list (  const GenericTopology *  topo,
const unsigned int  atomID,
const unsigned int  inAtomID,
const unsigned int  outAtomID,
const unsigned int  exclAtomID,
Real  rotAngle,
std::vector< AngleInfo > *  angles
) 
 

void ProtoMol::buildCellLists (  const Topology< VacuumBoundaryConditions, CubicCellManager > *  topo,
const Vector3DBlock *  positions
) 
 

build the cell list for vacuum

void ProtoMol::buildCellLists (  const Topology< PeriodicBoundaryConditions, CubicCellManager > *  topo,
const Vector3DBlock *  positions
) 
 

builds the cell list for periodic boundary conditions

void ProtoMol::buildExclusionTable (  GenericTopology *  topo,
const ExclusionType &  exclusionType
) 
 

void ProtoMol::buildISGTopology (  GenericTopology *  topo,
const PSF &  psf,
const iSGPAR &  par
) 
 

void ProtoMol::buildMolecularCenterOfMass (  const Vector3DBlock *  positions,
GenericTopology *  topo
) 
 

void ProtoMol::buildMolecularMomentum (  const Vector3DBlock *  positions,
GenericTopology *  topo
) 
 

void ProtoMol::buildMoleculeBondingLists (  GenericTopology *  topo  ) 
 

void ProtoMol::buildMoleculeTable (  GenericTopology *  topo  ) 
 

void ProtoMol::buildRattleShakeBondConstraintList (  GenericTopology *  topo,
vector< Bond::Constraint > &  bondConstraints
) 
 

void ProtoMol::buildTopology (  GenericTopology *  topo,
const PSF &  psf,
const PAR &  par,
bool  dihedralMultPSF
) 
 

Vector3D ProtoMol::centerOfMass (  const Vector3DBlock *  positions,
const GenericTopology *  topo
) 
 

bool changeDirectory (  const std::string &  fileName  ) 
 

Changes to the actual directory of the file name.

bool changeDirectory (  const string &  fileName  ) 
 

Real ProtoMol::computeMolecularPressure (  const ScalarStructure *  energies,
Real  volume,
Real  kineticEnergy
) 
 

Real ProtoMol::computePhiDihedral (  const GenericTopology *  topo,
const Vector3DBlock *  positions,
int  index
) 
 

Real ProtoMol::computePhiDihedralEnergy (  const GenericTopology *  topo,
int  index,
Real  phi
) 
 

Real ProtoMol::computePressure (  const ScalarStructure *  energies,
Real  volume,
Real  kineticEnergy
) 
 

Real ProtoMol::computePressure (  const GenericTopology *  topology,
const Vector3DBlock *  positions,
const Vector3DBlock *  velocities,
const ScalarStructure *  energies
) 
 

void convert (  const Matrix3by3 &  from,
double  to[9]
) 
 

void convert (  const Matrix3by3 &  from,
double  to[16]
) 
 

void ProtoMol::convert (  const Matrix3by3 &  from,
float  to[9]
) 
 

std::vector<Real> dtor (  const std::vector< Real > &  deg  ) 
 

Real dtor (  Real  degree  )  [inline]
 

vector<Real> dtor (  const vector< Real > &  deg  ) 
 

bool equal (  const std::string &  s1,
const std::string &  s2
) 
 

bool equal (  const string &  s1,
const string &  s2
) 
 

bool equal (  Real  x,
Real  y,
Real  epsilon
)  [inline]
 

bool equal (  Real  x,
Real  y
)  [inline]
 

bool equalBegin (  const std::string &  s1,
const std::string &  s2
) 
 

bool equalBegin (  const string &  s1,
const string &  s2
) 
 

bool equalBeginNocase (  const std::string &  s1,
const std::string &  s2
) 
 

bool equalBeginNocase (  const string &  s1,
const string &  s2
) 
 

bool equalEnd (  const std::string &  s1,
const std::string &  s2
) 
 

bool equalEnd (  const string &  s1,
const string &  s2
) 
 

bool equalEndNocase (  const std::string &  s1,
const std::string &  s2
) 
 

bool equalEndNocase (  const string &  s1,
const string &  s2
) 
 

bool equalNocase (  const std::string &  s1,
const std::string &  s2
) 
 

bool equalNocase (  const string &  s1,
const string &  s2
) 
 

bool equalStart (  const std::string &  s1,
const std::string &  s2
) 
 

bool equalStart (  const string &  s1,
const string &  s2
) 
 

bool equalStartNocase (  const std::string &  s1,
const std::string &  s2
) 
 

bool equalStartNocase (  const string &  s1,
const string &  s2
) 
 

bool equalTerminate (  const std::string &  s1,
const std::string &  s2
) 
 

bool equalTerminate (  const string &  s1,
const string &  s2
) 
 

bool equalTerminateNocase (  const std::string &  s1,
const std::string &  s2
) 
 

bool equalTerminateNocase (  const string &  s1,
const string &  s2
) 
 

int equalWildcard (  const std::string &  wildcard,
const std::string &  name
) 
 

Wildcard specifications:

  • * : matches any string of characters (including none),
  • % : matches any single character,
  • # : matches any string of digits (including none),
  • + : matches any single digit.

Return:

  • 2 : match without wildcards
  • 1 : match with wildcards
  • 0 : no match at all

int equalWildcard (  const string &  wildcard,
const string &  name
) 
 

int fact (  int  n  )  [inline]
 

void ProtoMol::findNextNeighbor (  int  a,
vector< int > &  v,
vector< PairInt > &  p,
vector< bool > &  unused,
const vector< vector< int > > &  graph,
set< PairInt > &  pairs
)  [static]
 

void ProtoMol::general_rotation (  unsigned int  innerAtom1,
unsigned int  innerAtom2,
Vector3DBlock *  positions,
Vector3DBlock *  velocities,
std::vector< AngleInfo > *  angles
) 
 

void ProtoMol::general_rotation (  unsigned int  innerAtom1,
unsigned int  innerAtom2,
Vector3DBlock *  positions,
std::vector< AngleInfo > *  angles
) 
 

void getAtomsBondedtoDihedral (  const GenericTopology *  topology,
std::set< int > *  atomSet,
const int  atomID,
const int  inAtomID,
const int  outAtomID,
const int  exclAtomID
) 
 

this function gets all the atoms bonded to ONE side of the dihedral

void getAtomsBondedtoDihedral (  const GenericTopology *  topology,
set< int, std::less< int > > *  atomSet,
const int  atomID,
const int  inAtomID,
const int  outAtomID,
const int  exclAtomID
) 
 

std::string getBegin (  const std::string &  s,
std::string::size_type  n
) 
 

string getBegin (  const string &  s,
string::size_type  n
) 
 

std::string getEnd (  const std::string &  s,
std::string::size_type  n
) 
 

string getEnd (  const string &  s,
string::size_type  n
) 
 

std::string getLeftFill (  const std::string &  s,
std::string::size_type  n
) 
 

string getLeftFill (  const string &  s,
string::size_type  n
) 
 

std::string getRightFill (  const std::string &  s,
std::string::size_type  n
) 
 

string getRightFill (  const string &  s,
string::size_type  n
) 
 

int ProtoMol::getTimerSeed (   ) 
 

Computes a seed based on the actual time.

std::string ProtoMol::getUserName (   ) 
 

Returns the username or user id.

Matrix3by3 ProtoMol::inertiaMomentum (  const Vector3DBlock *  positions,
const GenericTopology *  topo,
const Vector3D &  centerOfMass
) 
 

bool isAccessible (  const std::string &  fileName  ) 
 

Test if the file is accessible.

bool isAccessible (  const string &  fileName  ) 
 

bool isBlank (  const std::string &  word  ) 
 

bool isBlank (  const string &  word  ) 
 

bool ProtoMol::isblankchar (  char  c  ) 
 

bool isBool (  const std::string &  word  ) 
 

bool isBool (  const string &  word  ) 
 

void ProtoMol::iSGregisterForceExemplars (  const GenericTopology *  topo  ) 
 

void ProtoMol::iSGregisterForceExemplarsBonded (  const VacuumBoundaryConditions *   ) 
 

void ProtoMol::iSGregisterForceExemplarsBonded (  const PeriodicBoundaryConditions *   ) 
 

void ProtoMol::iSGregisterForceExemplarsCutoff (  const VacuumBoundaryConditions *  ,
const CubicCellManager * 
) 
 

void ProtoMol::iSGregisterForceExemplarsCutoff (  const PeriodicBoundaryConditions *  ,
const CubicCellManager * 
) 
 

template<typename BC, typename CM>
void iSGregisterForceExemplarsDispatch (  const Topology< BC, CM > *  topo  )  [inline]
 

void ProtoMol::iSGregisterForceExemplarsFastElectrostatic (  const VacuumBoundaryConditions *  ,
const CubicCellManager * 
) 
 

void ProtoMol::iSGregisterForceExemplarsFastElectrostatic (  const PeriodicBoundaryConditions *  ,
const CubicCellManager * 
) 
 

void ProtoMol::iSGregisterForceExemplarsFull (  const VacuumBoundaryConditions *   ) 
 

void ProtoMol::iSGregisterForceExemplarsFull (  const PeriodicBoundaryConditions *   ) 
 

void ProtoMol::iSGregisterForceExemplarsIdealGas (  const VacuumBoundaryConditions *  ,
const CubicCellManager * 
) 
 

void ProtoMol::iSGregisterForceExemplarsIdealGas (  const PeriodicBoundaryConditions *  ,
const CubicCellManager * 
) 
 

void ProtoMol::iSGregisterForceExemplarsSimpleFull (  const VacuumBoundaryConditions *   ) 
 

void ProtoMol::iSGregisterForceExemplarsSimpleFull (  const PeriodicBoundaryConditions *   ) 
 

void ProtoMol::iSGregisterOutputExemplars (   ) 
 

bool isInt (  const std::string &  word  ) 
 

bool isInt (  const string &  word  ) 
 

bool isPrintable (  const std::string &  word  ) 
 

bool isPrintable (  const string &  word  ) 
 

bool ProtoMol::isprintablechar (  char  c  ) 
 

bool isReal (  const std::string &  word  ) 
 

bool isReal (  const string &  word  ) 
 

bool isUInt (  const std::string &  word  ) 
 

bool isUInt (  const string &  word  ) 
 

bool isVector (  const std::string &  word  ) 
 

bool isVector (  const string &  word  ) 
 

bool isVector3D (  const std::string &  word  ) 
 

bool isVector3D (  const string &  word  ) 
 

Real ProtoMol::kineticEnergy (  const GenericTopology *  topology,
const Vector3DBlock *  velocities
) 
 

Real ProtoMol::kineticEnergyForAtomType (  const GenericTopology *  topology,
const Vector3DBlock *  velocities,
int  atomType,
waterOption  option,
int &  atomCount
) 
 

Real ProtoMol::kineticEnergyForAtomType (  const GenericTopology *  topology,
const Vector3DBlock *  velocities,
int  atomType,
waterOption  option
) 
 

Real ProtoMol::kineticEnergyForNonWater (  const GenericTopology *  topology,
const Vector3DBlock *  velocities,
int &  nonWaterCount
) 
 

Real ProtoMol::kineticEnergyForNonWater (  const GenericTopology *  topology,
const Vector3DBlock *  velocities
) 
 

Real ProtoMol::kineticEnergyForWater (  const GenericTopology *  topology,
const Vector3DBlock *  velocities,
int &  waterCount
) 
 

Real ProtoMol::kineticEnergyForWater (  const GenericTopology *  topology,
const Vector3DBlock *  velocities
) 
 

Vector3D ProtoMol::linearMomentum (  const Vector3DBlock *  velocities,
const GenericTopology *  topo
) 
 

std::string lowercase (  const std::string &  word  ) 
 

string lowercase (  const string &  word  ) 
 

bool ltstrNocaseOp (  const std::string &  s1,
const std::string &  s2
) 
 

bool ltstrNocaseOp (  const string &  s1,
const string &  s2
) 
 

template<class T>
T max (  const T &  a,
const T &  b,
const T &  c,
const T &  d
)  [inline]
 

return the largest of the numbers a, b, c, and d

template<class T>
T max (  const T &  a,
const T &  b,
const T &  c
)  [inline]
 

return the largest of the numbers a, b, and c

std::string mergeString (  const std::vector< std::string > &  str  ) 
 

string mergeString (  const vector< string > &  id  ) 
 

template<class T>
T min (  const T &  a,
const T &  b,
const T &  c,
const T &  d
)  [inline]
 

return the smallest of the numbers a, b, c, and d

template<class T>
T min (  const T &  a,
const T &  b,
const T &  c
)  [inline]
 

return the smallest of the numbers a, b, and c

Vector3D molecularCenterOfMass (  const std::vector< int > &  ,
const Vector3DBlock *  ,
const GenericTopology * 
) 
 

Vector3D molecularCenterOfMass (  const vector< int > &  atomList,
const Vector3DBlock *  positions,
const GenericTopology *  topo
) 
 

Real ProtoMol::molecularKineticEnergy (  const GenericTopology *  topology,
const Vector3DBlock *  velocitiies
) 
 

Vector3D molecularMomentum (  const std::vector< int > &  ,
const Vector3DBlock *  ,
const GenericTopology * 
) 
 

Vector3D molecularMomentum (  const vector< int > &  atomList,
const Vector3DBlock *  velocities,
const GenericTopology *  topo
) 
 

void ProtoMol::mpiAbort (   )  [static]
 

void ProtoMol::mpiEndSerial (  bool  exludeMaster  )  [static]
 

void ProtoMol::mpiExit (   )  [static]
 

void ProtoMol::mpiStartSerial (  bool  exludeMaster  )  [static]
 

Real ProtoMol::myerf (  Real  x  ) 
 

Polynomial approximation of the error function with fractional error everywhere less than 1.2*10-7.

Real ProtoMol::norm (  Real  a,
Real  b
) 
 

2-norm

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

string normalizeString (  const string &  word  ) 
 

bool normVector3DOp (  const Vector3D &  v1,
const Vector3D &  v2
)  [static]
 

unsigned int ProtoMol::openglToEPS (  std::ostream &  output,
void(*  display)()
) 
 

void ProtoMol::openglToPGM (  PGM &  pgm  ) 
 

unsigned int ProtoMol::openglToPlain (  std::ostream &  output,
void(*  display)()
) 
 

void ProtoMol::openglToPPM (  PPM &  ppm  ) 
 

Vector3D ProtoMol::operator * (  const Vector3D &  point,
const Matrix3by3 &  tm
) 
 

template<typename T, size_t N>
bool ProtoMol::operator!= (  const Array< T, N > &  A,
const Array< T, N > &  B
)  [inline]
 

bool operator< (  const Value &  v1,
const Value &  v2
) 
 

XSCWriter& operator<< (  XSCWriter &  xscWriter,
const XSC &  xsc
) 
 

XYZWriter& operator<< (  XYZWriter &  xyzWriter,
const XYZ &  xyz
) 
 

XYZTrajectoryWriter& operator<< (  XYZTrajectoryWriter &  xyzWriter,
const Vector3DBlock &  coords
) 
 

XYZTrajectoryWriter& operator<< (  XYZTrajectoryWriter &  xyzWriter,
const XYZ &  xyz
) 
 

XYZBinWriter& operator<< (  XYZBinWriter &  xyzWriter,
const Vector3DBlock &  coords
) 
 

XYZBinWriter& operator<< (  XYZBinWriter &  xyzWriter,
const XYZ &  xyz
) 
 

XFigWriter& operator<< (  XFigWriter &  xyzWriter,
const XYZ &  xyz
) 
 

PSFWriter& operator<< (  PSFWriter &  psfWriter,
const PSF &  psf
) 
 

PPMWriter& operator<< (  PPMWriter &  ppmWriter,
const PGM &  pgm
) 
 

PPMWriter& operator<< (  PPMWriter &  ppmWriter,
const PPM &  ppm
) 
 

PNGWriter& operator<< (  PNGWriter &  pngWriter,
const PGM &  pgm
) 
 

PNGWriter& operator<< (  PNGWriter &  PNGWriter,
const PPM &  ppm
) 
 

PGMWriter& operator<< (  PGMWriter &  pgmWriter,
const PPM &  ppm
) 
 

PGMWriter& operator<< (  PGMWriter &  pgmWriter,
const PGM &  pgm
) 
 

PDBWriter& operator<< (  PDBWriter &  pdbWriter,
const PDB &  pdb
) 
 

PARWriter& operator<< (  PARWriter &  parWriter,
const PAR &  par
) 
 

DCDTrajectoryWriter& operator<< (  DCDTrajectoryWriter &  dcdWriter,
const XYZ &  xyz
) 
 

DCDTrajectoryWriter& operator<< (  DCDTrajectoryWriter &  dcdWriter,
const Vector3DBlock &  coords
) 
 

MyStreamer& operator<< (  MyStreamer &  OS,
const Value &  v
) 
 

Report::MyStreamer& operator<< (  Report::MyStreamer &  os,
const TimerStatistic & 
) 
 

Report::MyStreamer& operator<< (  Report::MyStreamer &  os,
const Timer &  timer
) 
 

Report::MyStreamer& operator<< (  Report::MyStreamer &  os,
const TimeRep &  time
) 
 

ostream& operator<< (  std::ostream &  os,
const ReducedHessAngle &  tm
) 
 

MyStreamer& operator<< (  MyStreamer &  OS,
const PDB::PDBAtom &  p
) 
 

std::ostream & ProtoMol::operator<< (  std::ostream &  os,
const Matrix3by3 &  tm
) 
 

MyStreamer& operator<< (  MyStreamer &  OS,
const iSGPAR::Hbond &  p
) 
 

MyStreamer& operator<< (  MyStreamer &  OS,
const iSGPAR::Nbfix &  p
) 
 

MyStreamer& operator<< (  MyStreamer &  OS,
const iSGPAR::Nonbonded &  p
) 
 

MyStreamer& operator<< (  MyStreamer &  OS,
const iSGPAR::Improper &  p
) 
 

MyStreamer& operator<< (  MyStreamer &  OS,
const iSGPAR::Dihedral &  p
) 
 

MyStreamer& operator<< (  MyStreamer &  OS,
const iSGPAR::Angle &  p
) 
 

MyStreamer& operator<< (  MyStreamer &  OS,
const iSGPAR::Bond &  p
) 
 

bool operator<= (  const Value &  v1,
const Value &  v2
) 
 

bool operator== (  const Value &  v1,
const Value &  v2
) 
 

template<typename T, size_t N>
bool ProtoMol::operator== (  const Array< T, N > &  A,
const Array< T, N > &  B
)  [inline]
 

bool operator> (  const Value &  v1,
const Value &  v2
) 
 

bool operator>= (  const Value &  v1,
const Value &  v2
) 
 

XSCReader& operator>> (  XSCReader &  xscReader,
XSC &  xsc
) 
 

TRANSReader& operator>> (  TRANSReader &  transReader,
TRANS &  trans
) 
 

iSGPARReader& operator>> (  iSGPARReader &  parReader,
iSGPAR &  par
) 
 

XYZTrajectoryReader& operator>> (  XYZTrajectoryReader &  xyzReader,
Vector3DBlock &  coords
) 
 

XYZTrajectoryReader& operator>> (  XYZTrajectoryReader &  xyzReader,
XYZ &  xyz
) 
 

XYZReader& operator>> (  XYZReader &  xyzReader,
Vector3DBlock &  coords
) 
 

XYZReader& operator>> (  XYZReader &  xyzReader,
XYZ &  xyz
) 
 

XYZBinReader& operator>> (  XYZBinReader &  xyzbinReader,
Vector3DBlock &  coords
) 
 

XYZBinReader& operator>> (  XYZBinReader &  xyzbinReader,
XYZ &  xyz
) 
 

PSFReader& operator>> (  PSFReader &  psfReader,
PSF &  psf
) 
 

PPMReader& operator>> (  PPMReader &  ppmReader,
PGM &  pgm
) 
 

PPMReader& operator>> (  PPMReader &  ppmReader,
PPM &  ppm
) 
 

PGMReader& operator>> (  PGMReader &  pgmReader,
PPM &  ppm
) 
 

PGMReader& operator>> (  PGMReader &  pgmReader,
PGM &  pgm
) 
 

PDBReader& operator>> (  PDBReader &  pdbReader,
XYZ &  xyz
) 
 

PDBReader& operator>> (  PDBReader &  pdbReader,
Vector3DBlock &  coords
) 
 

PDBReader& operator>> (  PDBReader &  pdbReader,
PDB &  pdb
) 
 

PARReader& operator>> (  PARReader &  parReader,
PAR &  par
) 
 

DCDTrajectoryReader& operator>> (  DCDTrajectoryReader &  dcdTrajectoryReader,
Vector3DBlock &  coords
) 
 

DCDTrajectoryReader& operator>> (  DCDTrajectoryReader &  dcdTrajectoryReader,
XYZ &  xyz
) 
 

ConfigurationReader& operator>> (  ConfigurationReader &  configReader,
Configuration &  config
) 
 

InputPosVel& operator>> (  InputPosVel &  posReader,
Vector3DBlock &  coords
) 
 

InputPosVel& operator>> (  InputPosVel &  posReader,
XYZ &  xyz
) 
 

InputPosVel& operator>> (  InputPosVel &  posReader,
PDB &  pdb
) 
 

std::vector< std::vector< std::string > > ProtoMol::parseCommandLine (  int  argc,
char **  argv,
const Configuration *  config = NULL,
void(*  registerForceExemplarsFunction)(const GenericTopology *) = NULL
) 
 

Real ProtoMol::poly5 (  Real  ar  ) 
 

Polynomial constants used in evaluation of the complementary error function.

template<int _power>
Real power (  Real  x  )  [inline]
 

Real ProtoMol::power (  Real  x,
int  n
) 
 

template<>
Real power< 0 > (  Real   )  [inline]
 

template<>
Real power< 1 > (  Real  x  )  [inline]
 

template<>
Real power<-1 > (  Real  x  )  [inline]
 

void ProtoMol::protomolAbort (   ) 
 

Does an abort, calling the adequate abort system function.

void ProtoMol::protomolEndSerial (  bool  exludeMaster  ) 
 

Finializes the serialization block.

void ProtoMol::protomolExit (   ) 
 

Does an exit, calling the adequate exit system function.

void ProtoMol::protomolStartSerial (  bool  exludeMaster  ) 
 

Initiates the serialization block, e.g., used by Report.

Real ProtoMol::randomGaussian (  Real  sdv,
unsigned int  seed = 1234
) 
 

Real ProtoMol::randomGaussianNumber (  Real  mean,
Real  stdev,
unsigned int  seed = 1234
) 
 

Generates a number from a near-Gaussian distribution using the Box-Muller method.

Real ProtoMol::randomGaussianNumber (  unsigned int  seed = 1234  ) 
 

Real ProtoMol::randomNumber (  unsigned int  seed = 1234  ) 
 

void ProtoMol::randomVelocity (  Real  temperatureFrom,
Real  temperatureTo,
const GenericTopology *  topology,
Vector3DBlock *  velocities,
unsigned int  seed = 1234
) 
 

void ProtoMol::randomVelocity (  Real  temperature,
const GenericTopology *  topology,
Vector3DBlock *  velocities,
unsigned int  seed = 1234
) 
 

template<typename T>
void realclear (  T &  t  )  [inline]
 

Clears a container explicitly.

Matrix3by3 ProtoMol::reducedHessBond (  const Vector3D &  atom_i,
const Vector3D &  atom_j,
const Real  _k,
const Real  _r0
) 
 

void ProtoMol::registerForceExemplars (  const GenericTopology *  topo  ) 
 

registers all force prototypes by calling all registerForceExemplars* to be recognized by the parser

void ProtoMol::registerForceExemplarsBonded (  const VacuumBoundaryConditions *   ) 
 

registers bond force method prototypes (vacuum) to be recognized by the parser

void ProtoMol::registerForceExemplarsBonded (  const PeriodicBoundaryConditions *   ) 
 

registers bond force method prototypes (periodic boundary conditions) to be recognized by the parser

void ProtoMol::registerForceExemplarsCutoff (  const VacuumBoundaryConditions *  ,
const CubicCellManager * 
) 
 

registers cutoff force method prototypes(vacuum) to be recognized by the parser

void ProtoMol::registerForceExemplarsCutoff (  const PeriodicBoundaryConditions *  ,
const CubicCellManager * 
) 
 

registers cutoff force method prototypes (periodic boundary conditions) to be recognized by the parser

template<typename BC, typename CM>
void registerForceExemplarsDispatch (  const Topology< BC, CM > *  topo  )  [inline]
 

void ProtoMol::registerForceExemplarsFastElectrostatic (  const VacuumBoundaryConditions *  ,
const CubicCellManager * 
) 
 

registers fast electrostatic force method prototypes (vacuum) to be recognized by the parser

void ProtoMol::registerForceExemplarsFastElectrostatic (  const PeriodicBoundaryConditions *  ,
const CubicCellManager * 
) 
 

registers fast electrostatic force method prototypes (periodic boundary conditions) to be recognized by the parser

void ProtoMol::registerForceExemplarsFull (  const VacuumBoundaryConditions *   ) 
 

registers direct force method prototypes for multiple images (vacuum) to be recognized by the parser should performe as SimpleFull!

void ProtoMol::registerForceExemplarsFull (  const PeriodicBoundaryConditions *   ) 
 

registers direct force method prototypes for multiple images (periodic boundary conditions) prototypes to be recognized by the parser

void ProtoMol::registerForceExemplarsOther (  const VacuumBoundaryConditions *   ) 
 

registers special force prototypes (vacuum) to be recognized by the parser

void ProtoMol::registerForceExemplarsOther (   ) 
 

registers special force prototypes (independent of boundary condtions and cell list manager) to be recognized by the parser

void ProtoMol::registerForceExemplarsOther (  const VacuumBoundaryConditions *  ,
const CubicCellManager * 
) 
 

registers special force prototypes (vacuum and cell list manager) to be recognized by the parser

void ProtoMol::registerForceExemplarsOther (  const PeriodicBoundaryConditions *   ) 
 

registers special force prototypes (periodic boundary conditions) to be recognized by the parser

void ProtoMol::registerForceExemplarsOther (  const PeriodicBoundaryConditions *  ,
const CubicCellManager * 
) 
 

registers special force prototypes (periodic boundary conditionsand cell list manager) to be recognized by the parser

void ProtoMol::registerForceExemplarsSimpleFull (  const VacuumBoundaryConditions *   ) 
 

registers direct force method prototypes (vacuum) to be recognized by the parser

void ProtoMol::registerForceExemplarsSimpleFull (  const PeriodicBoundaryConditions *   ) 
 

registers direct force method prototypes (periodic boundary conditions) to be recognized by the parser

void ProtoMol::registerIntegratorExemplars (   ) 
 

registers Integrator prototypes to be recognized by the parser

void ProtoMol::registerOutputExemplars (   ) 
 

registers Output prototypes to be recognized by the parser

void ProtoMol::registerTopologyExemplars (   ) 
 

registers Topology prototypes to be recognized by the parser

Vector3D ProtoMol::removeAngularMomentum (  const Vector3DBlock *  positions,
Vector3DBlock *  velocities,
const GenericTopology *  topo
) 
 

std::string removeBeginEndBlanks (  const std::string &  s  ) 
 

string removeBeginEndBlanks (  const string &  s  ) 
 

Vector3D ProtoMol::removeLinearMomentum (  Vector3DBlock *  positions,
const GenericTopology *  topo
) 
 

void ProtoMol::rotateDihedral (  const GenericTopology *  topology,
Vector3DBlock *  positions,
const int  dihedralID,
Real  angle
) 
 

this function rotates all the atoms bonded to ONE side of the dihedral

void ProtoMol::rotateDihedral (