File List

Here is a list of all documented files with brief descriptions:

[detail level 123]

► antlr
ANTLRException.hpp
ANTLRUtil.cpp
ANTLRUtil.hpp
AST.hpp
ASTArray.hpp
ASTFactory.cpp
ASTFactory.hpp
ASTNULLType.cpp
ASTNULLType.hpp
ASTPair.hpp
ASTRefCount.cpp
ASTRefCount.hpp
BaseAST.cpp
BaseAST.hpp
BitSet.cpp
BitSet.hpp
CharBuffer.cpp
CharBuffer.hpp
CharInputBuffer.hpp
CharScanner.cpp
CharScanner.hpp
CharStreamException.hpp
CharStreamIOException.hpp
CircularQueue.hpp
CommonAST.cpp
CommonAST.hpp
CommonASTWithHiddenTokens.cpp
CommonASTWithHiddenTokens.hpp
CommonHiddenStreamToken.cpp
CommonHiddenStreamToken.hpp
CommonToken.cpp
CommonToken.hpp
config.hpp
InputBuffer.cpp
InputBuffer.hpp
IOException.hpp
LexerSharedInputState.hpp
LLkParser.cpp
LLkParser.hpp
MismatchedCharException.cpp
MismatchedCharException.hpp
MismatchedTokenException.cpp
MismatchedTokenException.hpp
NoViableAltException.cpp
NoViableAltException.hpp
NoViableAltForCharException.cpp
NoViableAltForCharException.hpp
Parser.cpp
Parser.hpp
ParserSharedInputState.hpp
RecognitionException.cpp
RecognitionException.hpp
RefCount.hpp
SemanticException.hpp
String.cpp
String.hpp
Token.cpp
Token.hpp
TokenBuffer.cpp
TokenBuffer.hpp
TokenRefCount.cpp
TokenRefCount.hpp
TokenStream.hpp
TokenStreamBasicFilter.cpp
TokenStreamBasicFilter.hpp
TokenStreamException.hpp
TokenStreamHiddenTokenFilter.cpp
TokenStreamHiddenTokenFilter.hpp
TokenStreamIOException.hpp
TokenStreamRecognitionException.hpp
TokenStreamRetryException.hpp
TokenStreamRewriteEngine.cpp
TokenStreamRewriteEngine.hpp
TokenStreamSelector.cpp
TokenStreamSelector.hpp
TokenWithIndex.hpp
TreeParser.cpp
TreeParser.hpp
TreeParserSharedInputState.hpp
► applications
► atom2omd
atom2omd.cpp
openmdformat.cpp
► dump2Xyz
Dump2XYZ.cpp
Dump2XYZCmd.cpp
Dump2XYZCmd.hpp	The header file for the command line option parser generated by GNU Gengetopt version 2.22.6 http://www.gnu.org/software/gengetopt
► dynamicProps
ActionCorrFunc.cpp
ActionCorrFunc.hpp
AngularVelocityAutoOutProductCorrFunc.cpp
AngularVelocityAutoOutProductCorrFunc.hpp
AngularVelVelOutProdCorrFunc.cpp
AngularVelVelOutProdCorrFunc.hpp
BondCorrFunc.cpp
BondCorrFunc.hpp
ChargeKineticCorrFunc.cpp
ChargeKineticCorrFunc.hpp
ChargeOrientationCorrFunc.cpp
ChargeOrientationCorrFunc.hpp
cOHz.cpp
cOHz.hpp
CollectiveDipoleDisplacement.cpp
CollectiveDipoleDisplacement.hpp
CurrentDensityAutoCorrFunc.cpp
CurrentDensityAutoCorrFunc.hpp
DipoleCorrFunc.cpp
DipoleCorrFunc.hpp
DirectionalRCorrFunc.cpp
DirectionalRCorrFunc.hpp
Displacement.cpp
Displacement.hpp
DynamicProperty.hpp
DynamicProps.cpp
DynamicPropsCmd.cpp
DynamicPropsCmd.hpp	The header file for the command line option parser generated by GNU Gengetopt version 2.23 http://www.gnu.org/software/gengetopt
ForceAutoCorrFunc.cpp
ForceAutoCorrFunc.hpp
ForTorCorrFunc.cpp
ForTorCorrFunc.hpp
FreqFlucCorrFunc.cpp
FreqFlucCorrFunc.hpp	Frequency Fluctuation Correlation Function
HBondJump.cpp
HBondJump.hpp
HBondPersistence.cpp
HBondPersistence.hpp
LegendreCorrFunc.cpp
LegendreCorrFunc.hpp
LegendreCorrFuncZ.cpp
LegendreCorrFuncZ.hpp
MomAngMomCorrFunc.cpp
MomAngMomCorrFunc.hpp
OnsagerCorrFunc.cpp
OnsagerCorrFunc.hpp
RCorrFunc.cpp
RCorrFunc.hpp
RotAngleDisplacement.cpp
RotAngleDisplacement.hpp
SelectionCorrFunc.cpp
SelectionCorrFunc.hpp
StressCorrFunc.cpp
StressCorrFunc.hpp
SystemDipoleCorrFunc.cpp
SystemDipoleCorrFunc.hpp
ThetaCorrFunc.cpp
ThetaCorrFunc.hpp
TimeCorrFunc.cpp
TimeCorrFunc.hpp
TorForCorrFunc.cpp
TorForCorrFunc.hpp
TorqueAutoCorrFunc.cpp
TorqueAutoCorrFunc.hpp
VCorrFunc.cpp
VCorrFunc.hpp
VelAngularVelOutProdCorrFunc.cpp
VelAngularVelOutProdCorrFunc.hpp
VelocityAutoOutProductCorrFunc.cpp
VelocityAutoOutProductCorrFunc.hpp
WCorrFunc.cpp
WCorrFunc.hpp
► elasticConstants
elasticConstants.cpp
elasticConstantsCmd.cpp
elasticConstantsCmd.hpp	The header file for the command line option parser generated by GNU Gengetopt version 2.22.6 http://www.gnu.org/software/gengetopt
► eos
equationofstate.cpp
equationofstateCmd.cpp
equationofstateCmd.hpp	The header file for the command line option parser generated by GNU Gengetopt version 2.23 http://www.gnu.org/software/gengetopt
► hydrodynamics
Hydro.cpp
HydroCmd.cpp
HydroCmd.hpp	The header file for the command line option parser generated by GNU Gengetopt version 2.23 http://www.gnu.org/software/gengetopt
► nanoparticleBuilder
icosahedralBuilder.cpp
icosahedralBuilderCmd.cpp
icosahedralBuilderCmd.hpp	The header file for the command line option parser generated by GNU Gengetopt version 2.22.6 http://www.gnu.org/software/gengetopt
nanoparticleBuilder.cpp
nanoparticleBuilderCmd.cpp
nanoparticleBuilderCmd.hpp	The header file for the command line option parser generated by GNU Gengetopt version 2.22.6 http://www.gnu.org/software/gengetopt
nanorod_pentBuilder.cpp
nanorod_pentBuilderCmd.cpp
nanorod_pentBuilderCmd.hpp	The header file for the command line option parser generated by GNU Gengetopt version 2.22.6 http://www.gnu.org/software/gengetopt
nanorodBuilder.cpp
nanorodBuilderCmd.cpp
nanorodBuilderCmd.hpp	The header file for the command line option parser generated by GNU Gengetopt version 2.22.6 http://www.gnu.org/software/gengetopt
shapedLatticeEllipsoid.cpp
shapedLatticeEllipsoid.hpp
shapedLatticePentRod.cpp
shapedLatticePentRod.hpp
shapedLatticeRod.cpp
shapedLatticeRod.hpp
shapedLatticeSpherical.cpp
shapedLatticeSpherical.hpp
► omd2omd
omd2omd.cpp
omd2omdCmd.cpp
omd2omdCmd.hpp	The header file for the command line option parser generated by GNU Gengetopt version 2.23 http://www.gnu.org/software/gengetopt
► openmd
openmd.cpp
► randomBuilder
randomBuilder.cpp
randomBuilderCmd.cpp
randomBuilderCmd.hpp	The header file for the command line option parser generated by GNU Gengetopt version 2.22.6 http://www.gnu.org/software/gengetopt
► recenter
recenter.cpp
recenterCmd.cpp
recenterCmd.hpp	The header file for the command line option parser generated by GNU Gengetopt version 2.22.6 http://www.gnu.org/software/gengetopt
► sequentialProps
CenterOfMass.cpp
CenterOfMass.hpp
COMVel.cpp
COMVel.hpp
ContactAngle1.cpp
ContactAngle1.hpp
ContactAngle2.cpp
ContactAngle2.hpp
equipartitionTest.cpp
equipartitionTest.hpp
GCNSeq.cpp
GCNSeq.hpp
SequentialAnalyzer.cpp
SequentialAnalyzer.hpp
SequentialProps.cpp
SequentialPropsCmd.cpp
SequentialPropsCmd.hpp	The header file for the command line option parser generated by GNU Gengetopt version 2.22.6 http://www.gnu.org/software/gengetopt
► simpleBuilder
simpleBuilder.cpp
simpleBuilderCmd.cpp
simpleBuilderCmd.hpp	The header file for the command line option parser generated by GNU Gengetopt version 2.22.6 http://www.gnu.org/software/gengetopt
► staticProps
AngleR.cpp
AngleR.hpp
BondAngleDistribution.cpp
BondAngleDistribution.hpp
BondOrderParameter.cpp
BondOrderParameter.hpp
BOPofR.cpp
BOPofR.hpp
ChargeDensityZ.cpp
ChargeDensityZ.hpp
ChargeHistogram.cpp
ChargeHistogram.hpp
ChargeR.cpp
ChargeR.hpp
ChargeZ.cpp
ChargeZ.hpp
CoordinationNumber.cpp
CoordinationNumber.hpp
CurrentDensity.cpp
CurrentDensity.hpp
DensityHistogram.cpp
DensityHistogram.hpp
DensityPlot.cpp
DensityPlot.hpp
DipoleOrientation.cpp
DipoleOrientation.hpp
Field.cpp
Field.hpp
GofAngle2.cpp
GofAngle2.hpp
GofR.cpp
GofR.hpp
GofRAngle.cpp
GofRAngle.hpp
GofRAngle2.cpp
GofRAngle2.hpp
GofRZ.cpp
GofRZ.hpp
GofXyz.cpp
GofXyz.hpp
GofZ.cpp
GofZ.hpp
HBondGeometric.cpp
HBondGeometric.hpp
HBondR.cpp
HBondR.hpp
HBondRvol.cpp
HBondRvol.hpp
HBondZ.cpp
HBondZ.hpp
HBondZvol.cpp
HBondZvol.hpp
Hxy.cpp
Hxy.hpp
Kirkwood.cpp
Kirkwood.hpp
KirkwoodBuff.cpp
KirkwoodBuff.hpp
MassDensityR.cpp
MassDensityR.hpp
MassDensityZ.cpp
MassDensityZ.hpp
MomentumHistogram.cpp
MomentumHistogram.hpp
MultiComponentRDF.cpp
MultiComponentRDF.hpp
MultipoleSum.cpp
MultipoleSum.hpp
NanoLength.cpp
NanoLength.hpp
NanoVolume.cpp
NanoVolume.hpp
NitrileFrequencyMap.cpp
NitrileFrequencyMap.hpp
NumberR.cpp
NumberR.hpp
NumberZ.cpp
NumberZ.hpp
ObjectCount.cpp
ObjectCount.hpp
OrderParameterProbZ.cpp
OrderParameterProbZ.hpp
P2OrderParameter.cpp
P2OrderParameter.hpp
P2R.cpp
P2R.hpp
pAngle.cpp
pAngle.hpp
PipeDensity.cpp
PipeDensity.hpp
PositionZ.cpp
PositionZ.hpp
PotDiff.cpp
PotDiff.hpp	StaticAnalyser for Potential Energy changes with charges turned off
RadialDistrFunc.cpp
RadialDistrFunc.hpp
RhoAngleR.cpp
RhoAngleR.hpp
RhoR.cpp
RhoR.hpp
RhoZ.cpp
RhoZ.hpp
RippleOP.cpp
RippleOP.hpp
RNEMDStats.cpp
RNEMDStats.hpp
SCDOrderParameter.cpp
SCDOrderParameter.hpp
SpatialStatistics.cpp
SpatialStatistics.hpp
StaticAnalyser.cpp
StaticAnalyser.hpp
StaticProps.cpp
StaticPropsCmd.cpp
StaticPropsCmd.hpp	The header file for the command line option parser generated by GNU Gengetopt version 2.23 http://www.gnu.org/software/gengetopt
SurfaceDiffusion.cpp
SurfaceDiffusion.hpp
TetrahedralityHBMatrix.cpp
TetrahedralityHBMatrix.hpp
TetrahedralityParam.cpp
TetrahedralityParam.hpp
TetrahedralityParamDens.cpp
TetrahedralityParamDens.hpp
TetrahedralityParamR.cpp
TetrahedralityParamR.hpp
TetrahedralityParamXYZ.cpp
TetrahedralityParamXYZ.hpp
TetrahedralityParamZ.cpp
TetrahedralityParamZ.hpp
TranslationalOrderParameterR.cpp
TranslationalOrderParameterR.hpp
TwoDGofR.cpp
TwoDGofR.hpp
VelocityZ.cpp
VelocityZ.hpp
► thermalizer
thermalizer.cpp
thermalizerCmd.cpp
thermalizerCmd.hpp	The header file for the command line option parser generated by GNU Gengetopt version 2.22.6 http://www.gnu.org/software/gengetopt
► utilities
affineScale
dumpConverter
funcflExtractor
hbtetAnalyzer
lcorrzFit
omd-solvator
omdCombined
omdLast
omdShrink
omdSplit
pack2omd
principalAxisCalculator
protonSampler
slabBuilder
slipLength
solLiqFricCalc
solvator
stat2dielectric
stat2dipolecorr
stat2pcorr
stat2tension
stat2thcond
stat2visco
vcorr2spectrum
waterBoxer
waterReplacer
waterRotator
waterSphere
wcorr2spectrum
► brains
BlockSnapshotManager.cpp
BlockSnapshotManager.hpp
DataStorage.cpp
DataStorage.hpp
ForceField.cpp
ForceField.hpp
ForceManager.cpp
ForceManager.hpp
ForceModifier.hpp
MoleculeCreator.cpp
MoleculeCreator.hpp
PairList.cpp
PairList.hpp
Register.cpp
Register.hpp
SimCreator.cpp
SimCreator.hpp
SimInfo.cpp
SimInfo.hpp
SimSnapshotManager.cpp
SimSnapshotManager.hpp
Snapshot.cpp
Snapshot.hpp
SnapshotManager.hpp
Stats.cpp
Stats.hpp
Thermo.cpp
Thermo.hpp
Velocitizer.cpp
Velocitizer.hpp
► clusters
Cuboctahedron.cpp
Cuboctahedron.hpp	Cuboctahedron cluster structure generator
Decahedron.cpp
Decahedron.hpp	Decahedron cluster structure generator
Icosahedron.cpp
Icosahedron.hpp	Icosahedron cluster structure generator
► constraints
ConstraintElem.hpp
ConstraintPair.hpp
Rattle.cpp
Rattle.hpp
Shake.cpp
Shake.hpp
ZconsStruct.hpp
ZconstraintForceModifier.cpp
ZconstraintForceModifier.hpp
► flucq
FluctuatingChargeConstraints.cpp
FluctuatingChargeConstraints.hpp
FluctuatingChargeDamped.cpp
FluctuatingChargeDamped.hpp
FluctuatingChargeForces.cpp
FluctuatingChargeForces.hpp
FluctuatingChargeLangevin.cpp
FluctuatingChargeLangevin.hpp
FluctuatingChargeNVE.cpp
FluctuatingChargeNVE.hpp
FluctuatingChargeNVT.cpp
FluctuatingChargeNVT.hpp
FluctuatingChargeObjectiveFunction.cpp
FluctuatingChargeObjectiveFunction.hpp
FluctuatingChargeParameters.cpp
FluctuatingChargeParameters.hpp
FluctuatingChargePropagator.cpp
FluctuatingChargePropagator.hpp
► hydrodynamics
AnalyticalModel.cpp
AnalyticalModel.hpp
ApproximateModel.cpp
ApproximateModel.hpp
AtomicBeadModel.cpp
AtomicBeadModel.hpp
BeadModel.cpp
BeadModel.hpp
BoundaryElementModel.cpp
BoundaryElementModel.hpp
CompositeShape.cpp
CompositeShape.hpp
Ellipsoid.cpp
Ellipsoid.hpp
HydrodynamicsModel.cpp
HydrodynamicsModel.hpp
HydrodynamicsModelCreator.hpp
HydrodynamicsModelFactory.cpp
HydrodynamicsModelFactory.hpp
HydroIO.cpp
HydroIO.hpp
HydroProp.cpp
HydroProp.hpp
Mesh.hpp
RoughShell.cpp
RoughShell.hpp
Shape.hpp
ShapeBuilder.cpp
ShapeBuilder.hpp
Sphere.cpp
Sphere.hpp
► integrators
DLM.cpp
DLM.hpp
Integrator.cpp
Integrator.hpp
IntegratorCreator.hpp
IntegratorFactory.cpp
IntegratorFactory.hpp
LangevinDynamics.cpp
LangevinDynamics.hpp
LangevinHullDynamics.cpp
LangevinHullDynamics.hpp
LangevinHullForceModifier.cpp
LangevinHullForceModifier.hpp
LangevinPiston.cpp
LangevinPiston.hpp
LDForceModifier.cpp
LDForceModifier.hpp
LP.cpp
NgammaT.cpp
NgammaT.hpp
NPA.cpp
NPA.hpp
NPAT.cpp
NPAT.hpp
NPrT.cpp
NPrT.hpp
NPT.cpp
NPT.hpp
NPTf.cpp
NPTf.hpp
NPTi.cpp
NPTi.hpp
NPTsz.cpp
NPTsz.hpp
NPTxyz.cpp
NPTxyz.hpp
NVE.cpp
NVE.hpp
NVT.cpp
NVT.hpp
RotationAlgorithm.hpp
SPFDynamics.cpp
SPFDynamics.hpp
VelocityVerletIntegrator.cpp
VelocityVerletIntegrator.hpp
► io
AtomTypesSectionParser.cpp
AtomTypesSectionParser.hpp
BaseAtomTypesSectionParser.cpp
BaseAtomTypesSectionParser.hpp
basic_teebuf.hpp
BendTypesSectionParser.cpp
BendTypesSectionParser.hpp
BondTypesSectionParser.cpp
BondTypesSectionParser.hpp
ChargeAtomTypesSectionParser.cpp
ChargeAtomTypesSectionParser.hpp
ConstraintWriter.cpp
ConstraintWriter.hpp
DirectionalAtomTypesSectionParser.cpp
DirectionalAtomTypesSectionParser.hpp
DumpReader.cpp
DumpReader.hpp
DumpWriter.cpp
DumpWriter.hpp
EAMAtomTypesSectionParser.cpp
EAMAtomTypesSectionParser.hpp
FluctuatingChargeAtomTypesSectionParser.cpp
FluctuatingChargeAtomTypesSectionParser.hpp
ForceFieldOptions.cpp
ForceFieldOptions.hpp
GayBerneAtomTypesSectionParser.cpp
GayBerneAtomTypesSectionParser.hpp
Globals.cpp
Globals.hpp
gzstream.cpp
gzstream.hpp
ifstrstream.cpp
ifstrstream.hpp
InversionTypesSectionParser.cpp
InversionTypesSectionParser.hpp
LennardJonesAtomTypesSectionParser.cpp
LennardJonesAtomTypesSectionParser.hpp
MSMSFormat.hpp
MultipoleAtomTypesSectionParser.cpp
MultipoleAtomTypesSectionParser.hpp
NonBondedInteractionsSectionParser.cpp
NonBondedInteractionsSectionParser.hpp
OptionSectionParser.cpp
OptionSectionParser.hpp
ParamConstraint.cpp
ParamConstraint.hpp
PolarizableAtomTypesSectionParser.cpp
PolarizableAtomTypesSectionParser.hpp
RestReader.cpp
RestReader.hpp
RestWriter.cpp
RestWriter.hpp
SCAtomTypesSectionParser.cpp
SCAtomTypesSectionParser.hpp
SectionParser.cpp
SectionParser.hpp
SectionParserManager.cpp
SectionParserManager.hpp
ShapeAtomTypesSectionParser.cpp
ShapeAtomTypesSectionParser.hpp
StatWriter.cpp
StatWriter.hpp
StickyAtomTypesSectionParser.cpp
StickyAtomTypesSectionParser.hpp
StickyPowerAtomTypesSectionParser.cpp
StickyPowerAtomTypesSectionParser.hpp
TorsionTypesSectionParser.cpp
TorsionTypesSectionParser.hpp
UFFAtomTypesSectionParser.cpp
UFFAtomTypesSectionParser.hpp
XYZFormat.cpp
XYZFormat.hpp
ZConsReader.cpp
ZConsReader.hpp
ZConsWriter.cpp
ZConsWriter.hpp
► lattice
BCCLattice.cpp
BCCLattice.hpp
CubicLattice.cpp
CubicLattice.hpp
FCCLattice.cpp
FCCLattice.hpp
Lattice.cpp
Lattice.hpp
LatticeCreator.hpp
LatticeFactory.cpp
LatticeFactory.hpp
SCLattice.cpp
SCLattice.hpp
shapedLattice.cpp
shapedLattice.hpp
► math
► integration
GaussianTriangleQuadrature.hpp
LegendreGauss1d.hpp
StrangFixCowperTriangleQuadrature.hpp
TriangleQuadrature.hpp
TriangleQuadratureRule.hpp
XiaoGimbutasTriangleQuadrature.hpp
AlphaHull.cpp
AlphaHull.hpp
ChebyshevT.cpp
ChebyshevT.hpp
ChebyshevU.cpp
ChebyshevU.hpp
CholeskyDecomposition.hpp
ConvexHull.cpp
ConvexHull.hpp
CubicSpline.cpp
CubicSpline.hpp
DynamicRectMatrix.hpp
DynamicVector.hpp
Eigenvalue.hpp
erfc.hpp
Factorials.hpp
Hull.hpp
LegendrePolynomial.cpp
LegendrePolynomial.hpp
LU.hpp
Polynomial.hpp
qhull.hpp
QR.hpp
Quaternion.hpp
RealSphericalHarmonic.cpp
RealSphericalHarmonic.hpp
RealSymmetricTridiagonal.hpp
RectMatrix.hpp
RMSD.cpp
RMSD.hpp
SphericalHarmonic.cpp
SphericalHarmonic.hpp
SquareMatrix.hpp
SquareMatrix3.hpp
SVD.hpp
Triangle.cpp
Triangle.hpp
Vector.hpp
Vector2.hpp
Vector3.hpp
Wigner3jm.cpp
Wigner3jm.hpp
► mdParser
FilenameObserver.cpp
FilenameObserver.hpp
MDLexer.cpp
MDLexer.hpp
MDParser.cpp
MDParser.hpp
MDTokenTypes.hpp
MDTreeParser.cpp
MDTreeParser.hpp
MDTreeParserTokenTypes.hpp
SimplePreprocessor.hpp
► nonbonded
Buckingham.cpp
Buckingham.hpp
Cutoffs.hpp
EAM.cpp
EAM.hpp
Electrostatic.cpp
Electrostatic.hpp
GB.cpp
GB.hpp
InteractionManager.cpp
InteractionManager.hpp
InversePowerSeries.cpp
InversePowerSeries.hpp
LJ.cpp
LJ.hpp
MAW.cpp
MAW.hpp
Mie.cpp
Mie.hpp
Morse.cpp
Morse.hpp
NonBondedInteraction.hpp
RepulsivePower.cpp
RepulsivePower.hpp
SC.cpp
SC.hpp
SHAPES.cpp
SHAPES.hpp
SlaterIntegrals.hpp
Sticky.cpp
Sticky.hpp
SwitchingFunction.cpp
SwitchingFunction.hpp
► optimization
Armijo.cpp
Armijo.hpp	Armijo line-search class
BFGS.cpp
BFGS.hpp	Broyden-Fletcher-Goldfarb-Shanno optimization method
BoxObjectiveFunction.cpp
BoxObjectiveFunction.hpp
ConjugateGradient.cpp
ConjugateGradient.hpp	Conjugate gradient optimization method
Constraint.cpp
Constraint.hpp	Abstract constraint class
EndCriteria.cpp
EndCriteria.hpp	Optimization criteria class
LineSearch.cpp
LineSearch.hpp	Line search abstract class
LineSearchBasedMethod.cpp
LineSearchBasedMethod.hpp	Abstract optimization method class
Method.hpp	Abstract optimization method class
MinimizerParameters.cpp
MinimizerParameters.hpp
ObjectiveFunction.hpp	Optimization objective function class
OptimizationCreator.hpp
OptimizationFactory.cpp
OptimizationFactory.hpp
PotentialEnergyObjectiveFunction.cpp
PotentialEnergyObjectiveFunction.hpp
Problem.cpp
Problem.hpp	Abstract optimization problem class
StatusFunction.hpp
SteepestDescent.cpp
SteepestDescent.hpp	Steepest descent optimization method
► parallel
Communicator.hpp
ForceDecomposition.cpp
ForceDecomposition.hpp
ForceMatrixDecomposition.cpp
ForceMatrixDecomposition.hpp
SystemDecomposition.hpp
► perturbations
MagneticField.cpp
MagneticField.hpp	Uniform Magnetic Field perturbation
UniformField.cpp
UniformField.hpp	Uniform Electric Field perturbation
UniformGradient.cpp
UniformGradient.hpp	Uniform Electric Field Gradient perturbation
► primitives
Atom.cpp
Atom.hpp
Bend.cpp
Bend.hpp
Bond.hpp
CutoffGroup.hpp
DirectionalAtom.cpp
DirectionalAtom.hpp
Element.hpp	This basic Element data-holding class was originally taken from the data.h file in OpenBabel
GhostBend.cpp
GhostBend.hpp
GhostTorsion.cpp
GhostTorsion.hpp
Inversion.cpp
Inversion.hpp
Molecule.cpp
Molecule.hpp
RigidBody.cpp
RigidBody.hpp
SDKBend.cpp
SDKBend.hpp
ShortRangeInteraction.cpp
ShortRangeInteraction.hpp
StuntDouble.cpp
StuntDouble.hpp
Torsion.cpp
Torsion.hpp
UreyBradleyBend.cpp
UreyBradleyBend.hpp
► restraints
MolecularRestraint.cpp
MolecularRestraint.hpp
ObjectRestraint.cpp
ObjectRestraint.hpp
Restraint.hpp
RestraintForceModifier.cpp
RestraintForceModifier.hpp
ThermoIntegrationForceModifier.cpp
ThermoIntegrationForceModifier.hpp
► rnemd
MethodFactory.hpp
NIVS.cpp
NIVS.hpp
RNEMD.cpp
RNEMD.hpp
RNEMDParameters.cpp
RNEMDParameters.hpp
SPF.cpp
SPF.hpp
SPFForceManager.cpp
SPFForceManager.hpp
Swap.cpp
Swap.hpp
VSS.cpp
VSS.hpp
► selection
DistanceFinder.cpp
DistanceFinder.hpp
HullFinder.cpp
HullFinder.hpp
IndexFinder.cpp
IndexFinder.hpp
NameFinder.cpp
NameFinder.hpp
SelectionCompiler.cpp
SelectionCompiler.hpp
SelectionEvaluator.cpp
SelectionEvaluator.hpp
SelectionManager.cpp
SelectionManager.hpp
SelectionSet.cpp
SelectionSet.hpp
SelectionToken.cpp
SelectionToken.hpp
TokenMap.cpp
TokenMap.hpp
► types
AmberImproperTorsionType.hpp
AtomStamp.cpp
AtomStamp.hpp
AtomType.cpp
AtomType.hpp
BendStamp.cpp
BendStamp.hpp
BendType.hpp
BendTypeParser.cpp
BendTypeParser.hpp
BondStamp.cpp
BondStamp.hpp
BondType.hpp
BondTypeParser.cpp
BondTypeParser.hpp
BuckinghamInteractionType.hpp
CharmmTorsionType.cpp
CharmmTorsionType.hpp
Component.cpp
Component.hpp
ConstraintStamp.cpp
ConstraintStamp.hpp
CosineBendType.hpp
CosineSeriesBendType.hpp
CubicBendType.hpp
CubicBondType.hpp
CubicTorsionType.hpp
CutoffGroupStamp.cpp
CutoffGroupStamp.hpp
DataHolder.hpp
DirectionalAdapter.cpp
DirectionalAdapter.hpp
EAMAdapter.cpp
EAMAdapter.hpp
EAMInteractionType.hpp
FixedBondType.hpp
FixedChargeAdapter.cpp
FixedChargeAdapter.hpp
FluctuatingChargeAdapter.cpp
FluctuatingChargeAdapter.hpp
FragmentStamp.cpp
FragmentStamp.hpp
GayBerneAdapter.cpp
GayBerneAdapter.hpp
HarmonicBendType.hpp
HarmonicBondType.hpp
HarmonicInversionType.hpp
HarmonicSineBendType.hpp
HarmonicTorsionType.hpp
ImproperCosineInversionType.cpp
ImproperCosineInversionType.hpp
InversePowerSeriesInteractionType.hpp
InversionStamp.cpp
InversionStamp.hpp
InversionType.hpp
InversionTypeParser.cpp
InversionTypeParser.hpp
LennardJonesAdapter.cpp
LennardJonesAdapter.hpp
LennardJonesInteractionType.hpp
MAWInteractionType.hpp
MieInteractionType.hpp
MoleculeStamp.cpp
MoleculeStamp.hpp
MorseBondType.hpp
MorseInteractionType.hpp
MultipoleAdapter.cpp
MultipoleAdapter.hpp
NodesStamp.cpp
NodesStamp.hpp
NonBondedInteractionType.cpp
NonBondedInteractionType.hpp
OplsTorsionType.hpp
PolarizableAdapter.cpp
PolarizableAdapter.hpp
PolynomialBendType.hpp
PolynomialBondType.hpp
PolynomialInversionType.hpp
PolynomialTorsionType.hpp
QuarticBendType.hpp
QuarticBondType.hpp
QuarticTorsionType.hpp
RepulsivePowerInteractionType.hpp
RestraintStamp.cpp
RestraintStamp.hpp
RigidBodyStamp.cpp
RigidBodyStamp.hpp
SDKBendType.hpp
ShapeAtomType.cpp
ShapeAtomType.hpp
ShiftedMieBondType.hpp
StickyAdapter.cpp
StickyAdapter.hpp
SuttonChenAdapter.cpp
SuttonChenAdapter.hpp
TorsionStamp.cpp
TorsionStamp.hpp
TorsionType.hpp
TorsionTypeParser.cpp
TorsionTypeParser.hpp
TrappeTorsionType.hpp
UFFAdapter.cpp
UFFAdapter.hpp
UreyBradleyBendType.hpp
ZconsStamp.cpp
ZconsStamp.hpp
► utils
Accumulator.hpp
AccumulatorView.hpp
BaseAccumulator.hpp
CaseConversion.hpp
CI_String.hpp
Constants.hpp
ElementsTable.cpp	This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel
ElementsTable.hpp	This basic Periodic Table class was originally taken from the data.h file in OpenBabel
GenericData.hpp
GenericFactory.hpp
Grid3d.hpp
LocalIndexManager.hpp
MemoryUtils.hpp
MoLocator.cpp
MoLocator.hpp
next_combination.hpp
OldAccumulator.hpp
OpenMDBitSet.cpp
OpenMDBitSet.hpp
OpenMDException.hpp
ParameterManager.hpp
ProgressBar.cpp
ProgressBar.hpp
PropertyMap.cpp
PropertyMap.hpp
RandNumGen.cpp
RandNumGen.hpp
Revision.hpp
simError.cpp
simError.h
StringTokenizer.cpp
StringTokenizer.hpp
StringUtils.cpp
StringUtils.hpp
Trim.hpp
TypeContainer.hpp
Utility.cpp
Utility.hpp
wildcards.cpp
wildcards.hpp
wingetopt.cpp
wingetopt.h
► visitors
AtomData.hpp
AtomNameVisitor.cpp
AtomNameVisitor.hpp
AtomVisitor.cpp
AtomVisitor.hpp
BaseVisitor.hpp
CompositeVisitor.cpp
CompositeVisitor.hpp
LipidTransVisitor.cpp
LipidTransVisitor.hpp
OtherVisitor.cpp
OtherVisitor.hpp
ReplacementVisitor.cpp
ReplacementVisitor.hpp
RigidBodyVisitor.cpp
RigidBodyVisitor.hpp
ZconsVisitor.cpp
ZconsVisitor.hpp