File List

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

accumulators.mod
Activate.cpp
Activate.h
mcMd/analyzers/Analyzer.cpp
ddMd/analyzers/Analyzer.cpp
tools/analyzers/Analyzer.cpp
mcMd/analyzers/Analyzer.h
ddMd/analyzers/Analyzer.h
tools/analyzers/Analyzer.h
mcMd/analyzers/analyzer.mod
ddMd/analyzers/analyzer.mod
tools/analyzers/analyzer.mod
ddMd/analyzers/AnalyzerFactory.cpp
tools/analyzers/AnalyzerFactory.cpp
AnalyzerFactory.h
mcMd/analyzers/AnalyzerManager.cpp
ddMd/analyzers/AnalyzerManager.cpp
tools/analyzers/AnalyzerManager.cpp
mcMd/analyzers/AnalyzerManager.h
ddMd/analyzers/AnalyzerManager.h
tools/analyzers/AnalyzerManager.h
mcMd/chemistry/Angle.h
ddMd/chemistry/Angle.h
angle.mod
mcMd/potentials/angle/AngleFactory.cpp
ddMd/potentials/angle/AngleFactory.cpp
mcMd/potentials/angle/AngleFactory.h
ddMd/potentials/angle/AngleFactory.h
mcMd/potentials/angle/AnglePotential.cpp
ddMd/potentials/angle/AnglePotential.cpp
mcMd/potentials/angle/AnglePotential.h
ddMd/potentials/angle/AnglePotential.h
mcMd/potentials/angle/AnglePotentialImpl.h
ddMd/potentials/angle/AnglePotentialImpl.h
AngleStorage.cpp
AngleStorage.h
Ar1Process.cpp
Ar1Process.h
Array.h
ArrayIterator.h
ArraySet.h
ArrayStack.h
mcMd/chemistry/Atom.cpp
ddMd/chemistry/Atom.cpp
mcMd/chemistry/Atom.h
ddMd/chemistry/Atom.h
tools/chemistry/Atom.h
AtomArray.cpp
AtomArray.h
AtomCollector.cpp
AtomCollector.h
AtomContext.h
AtomDisplaceMove.cpp
AtomDisplaceMove.h
AtomDistributor.cpp
AtomDistributor.h
AtomIterator.h
AtomMap.cpp
AtomMap.h
mcMd/analyzers/system/AtomMSD.cpp
tools/analyzers/AtomMSD.cpp
mcMd/analyzers/system/AtomMSD.h
tools/analyzers/AtomMSD.h
ddMd/storage/AtomStorage.cpp
tools/storage/AtomStorage.cpp
ddMd/storage/AtomStorage.h
tools/storage/AtomStorage.h
mcMd/chemistry/AtomType.cpp
ddMd/chemistry/AtomType.cpp
mcMd/chemistry/AtomType.h
ddMd/chemistry/AtomType.h
AutoCorr.h
AutoCorrAnalyzer.h
AutoCorrAnalyzer.tpp
AutoCorrArray.h
AutoCorrelation.h
AutoCorrelation.tpp
AutoCorrStage.h
AutoCorrStage.tpp
Average.cpp
Average.h
AverageAnalyzer.cpp
mcMd/analyzers/util/AverageAnalyzer.h
ddMd/analyzers/AverageAnalyzer.h
AverageStage.cpp
AverageStage.h
Begin.cpp
Begin.h
Bend.h
BendForce.h
BennettsMethod.cpp
BennettsMethod.h
BinaryFileIArchive.cpp
BinaryFileIArchive.h
BinaryFileOArchive.cpp
BinaryFileOArchive.h
Binomial.cpp
Binomial.h
Bit.cpp
Bit.h
Blank.cpp
Blank.h
BlockRadiusGyration.cpp
BlockRadiusGyration.h
mcMd/chemistry/Bond.h
ddMd/chemistry/Bond.h
bond.mod
mcMd/potentials/bond/BondFactory.cpp
ddMd/potentials/bond/BondFactory.cpp
mcMd/potentials/bond/BondFactory.h
ddMd/potentials/bond/BondFactory.h
BondLengthDist.cpp
BondLengthDist.h
mcMd/potentials/bond/BondPotential.cpp
ddMd/potentials/bond/BondPotential.cpp
mcMd/potentials/bond/BondPotential.h
ddMd/potentials/bond/BondPotential.h
mcMd/potentials/bond/BondPotentialImpl.h
ddMd/potentials/bond/BondPotentialImpl.h
BondStorage.cpp
BondStorage.h
BondTensorAutoCorr.cpp
BondTensorAutoCorr.h
Bool.cpp
Bool.h
Boundary.h
boundary.mod
BoundaryAverage.cpp
BoundaryAverage.h
BoundaryEnsemble.cpp
BoundaryEnsemble.h
BoxExternal.cpp
BoxExternal.h
Buffer.cpp
Buffer.h
Byte.h
CardinalBSpline.cpp
CardinalBSpline.h
CArray2DParam.h
CArrayParam.h
mcMd/neighbor/Cell.cpp
ddMd/neighbor/Cell.cpp
tools/neighbor/Cell.cpp
mcMd/neighbor/Cell.h
ddMd/neighbor/Cell.h
tools/neighbor/Cell.h
ddMd/neighbor/CellAtom.h
tools/neighbor/CellAtom.h
mcMd/neighbor/CellList.cpp
ddMd/neighbor/CellList.cpp
tools/neighbor/CellList.cpp
mcMd/neighbor/CellList.h
ddMd/neighbor/CellList.h
tools/neighbor/CellList.h
CellTag.h
CfbDoubleRebridgeMove.cpp
CfbDoubleRebridgeMove.h
CfbEndBase.cpp
CfbEndBase.h
CfbEndMove.cpp
CfbEndMove.h
CfbLinear.cpp
CfbLinear.h
CfbLinearEndMove.cpp
CfbLinearEndMove.h
CfbRebridgeBase.cpp
CfbRebridgeBase.h
CfbRebridgeMove.cpp
CfbRebridgeMove.h
CfbReptateMove.cpp
CfbReptateMove.h
CfbReptationMove.cpp
CfbReptationMove.h
CfbRingRebridgeMove.cpp
CfbRingRebridgeMove.h
ChainMaker.cpp
ChainMaker.h
mcMd/chemistry/chemistry.mod
ddMd/chemistry/chemistry.mod
tools/chemistry/chemistry.mod
Cluster.cpp
Cluster.h
ClusterHistogram.cpp
ClusterHistogram.h
ClusterIdentifier.cpp
ClusterIdentifier.h
ClusterLink.h
ColVar.cpp
ColVar.h
ColVarPotentialTmpl.h
ColVarPotentialTmpl.tpp
Command.cpp
Command.h
command.mod
CommandLine.h
CommandManager.cpp
CommandManager.h
ComMSD.cpp
ComMSD.h
communicate.mod
CompensatedPair.h
CompositeBond.h
CompositeTestRunner.h
CompositionProfile.cpp
CompositionProfile.h
config.mod
mcMd/configIos/ConfigIo.cpp
ddMd/configIos/ConfigIo.cpp
mcMd/configIos/ConfigIo.h
ddMd/configIos/ConfigIo.h
mcMd/configIos/configIo.mod
ddMd/configIos/configIo.mod
mcMd/configIos/ConfigIoFactory.cpp
ddMd/configIos/ConfigIoFactory.cpp
mcMd/configIos/ConfigIoFactory.h
ddMd/configIos/ConfigIoFactory.h
ConfigReader.cpp
ConfigReader.h
configReader.mod
ConfigReaderFactory.cpp
ConfigReaderFactory.h
Configuration.cpp
Configuration.h
mcMd/analyzers/system/ConfigWriter.cpp
ddMd/analyzers/trajectory/ConfigWriter.cpp
tools/config/ConfigWriter.cpp
mcMd/analyzers/system/ConfigWriter.h
ddMd/analyzers/trajectory/ConfigWriter.h
tools/config/ConfigWriter.h
configWriter.mod
ConfigWriterFactory.cpp
ConfigWriterFactory.h
Constants.cpp
Constants.h
ConstArrayIterator.h
ConstAtomIterator.h
ConstGhostIterator.h
ConstGroupIterator.h
ConstPArrayIterator.h
containers.mod
CosineAngle.cpp
CosineAngle.h
CosineDihedral.cpp
CosineDihedral.h
CosineSqAngle.cpp
CosineSqAngle.h
CoulombFactory.cpp
CoulombFactory.h
Crosslinker.cpp
Crosslinker.h
crystal.mod
CvBias.cpp
CvBias.h
DArray.h
DArrayParam.h
Dbl.cpp
Dbl.h
DCDTrajectoryReader.cpp
DCDTrajectoryReader.h
ddMd.mod
mcMd/configIos/DdMdConfigIo.cpp
ddMd/configIos/DdMdConfigIo.cpp
mcMd/configIos/DdMdConfigIo.h
ddMd/configIos/DdMdConfigIo.h
DdMdConfigReader.cpp
DdMdConfigReader.h
DdMdConfigWriter.cpp
DdMdConfigWriter.h
DdMdGroupTrajectoryWriter.cpp
DdMdGroupTrajectoryWriter.h
DdMdOrderedConfigIo.cpp
DdMdOrderedConfigIo.h
mcMd/trajectory/DdMdTrajectoryReader.cpp
tools/trajectory/DdMdTrajectoryReader.cpp
mcMd/trajectory/DdMdTrajectoryReader.h
tools/trajectory/DdMdTrajectoryReader.h
DdMdTrajectoryWriter.cpp
DdMdTrajectoryWriter.h
ddSim.cpp
DdTimer.cpp
DdTimer.h
DeformCommand.cpp
DeformCommand.h
Diblock.cpp
Diblock.h
mcMd/chemistry/Dihedral.h
ddMd/chemistry/Dihedral.h
dihedral.mod
mcMd/potentials/dihedral/DihedralFactory.cpp
ddMd/potentials/dihedral/DihedralFactory.cpp
mcMd/potentials/dihedral/DihedralFactory.h
ddMd/potentials/dihedral/DihedralFactory.h
mcMd/potentials/dihedral/DihedralPotential.cpp
ddMd/potentials/dihedral/DihedralPotential.cpp
mcMd/potentials/dihedral/DihedralPotential.h
ddMd/potentials/dihedral/DihedralPotential.h
mcMd/potentials/dihedral/DihedralPotentialImpl.h
ddMd/potentials/dihedral/DihedralPotentialImpl.h
DihedralStorage.cpp
DihedralStorage.h
Dimension.h
Distribution.cpp
Distribution.h
DMatrix.h
DMatrixParam.h
Domain.cpp
Domain.h
DPArray.h
DpdMove.cpp
DpdMove.h
DpdPair.cpp
DpdPair.h
DRaggedMatrix.h
DSArray.h
DSymmMatrixParam.h
End.cpp
End.h
EndSwapMove.cpp
EndSwapMove.h
EndtoEnd.cpp
EndtoEnd.h
EndtoEndXYZ.cpp
EndtoEndXYZ.h
energy.mod
EnergyAnalyzer.cpp
EnergyAnalyzer.h
EnergyCalculator.cpp
EnergyCalculator.h
EnergyEnsemble.cpp
EnergyEnsemble.h
ensemble.mod
EwaldInteraction.cpp
EwaldInteraction.h
EwaldRSpaceAccumulator.cpp
EwaldRSpaceAccumulator.h
example1.cpp
example2.cpp
example3.cpp
Exception.cpp
Exception.h
Exchanger.cpp
Exchanger.h
external.mod
ExternalEnergyAnalyzer.cpp
ExternalEnergyAnalyzer.h
ExternalEnergyAverage.cpp
ExternalEnergyAverage.h
mcMd/potentials/external/ExternalFactory.cpp
ddMd/potentials/external/ExternalFactory.cpp
mcMd/potentials/external/ExternalFactory.h
ddMd/potentials/external/ExternalFactory.h
ExternalPotential.cpp
mcMd/potentials/external/ExternalPotential.h
ddMd/potentials/external/ExternalPotential.h
mcMd/potentials/external/ExternalPotentialImpl.h
ddMd/potentials/external/ExternalPotentialImpl.h
Factory.h
FArray.h
FArrayParam.h
FeneBond.cpp
FeneBond.h
feq.h
FileMaster.cpp
FileMaster.h
FlagSet.cpp
FlagSet.h
FlexPtr.h
FMatrix.h
Format.cpp
Format.h
format.mod
FPArray.h
FSArray.h
G1MSD.cpp
G1MSD.h
GArray.h
gcd.h
GcSliplinkMove.cpp
GcSliplinkMove.h
GeneralPeriodicExternal.cpp
GeneralPeriodicExternal.h
Generator.cpp
Generator.h
generator.mod
generatorFactory.cpp
generatorFactory.h
getAtomGroups.cpp
getAtomGroups.h
GhostIterator.h
global.h	File containing preprocessor macros for error handling
GPArray.h
Grid.cpp
Grid.h
GridArray.h
mcMd/chemistry/Group.h
ddMd/chemistry/Group.h
tools/chemistry/Group.h
GroupCollector.h
GroupCollector.tpp
GroupDistributor.h
GroupDistributor.tpp
GroupExchanger.cpp
GroupExchanger.h
GroupIterator.h
GroupRebridgeBase.cpp
GroupRebridgeBase.h
ddMd/storage/GroupStorage.h
tools/storage/GroupStorage.h
GroupStorage.tpp
GStack.h
HarmonicAngle.cpp
HarmonicAngle.h
HarmonicBond.cpp
HarmonicBond.h
HarmonicCvBias.cpp
HarmonicCvBias.h
HarmonicL0Bond.cpp
HarmonicL0Bond.h
Homopolymer.cpp
Homopolymer.h
HomopolymerSemiGrandMove.cpp
HomopolymerSemiGrandMove.h
HomopolymerSG.cpp
HomopolymerSG.h
HomoRing.cpp
HomoRing.h
HoomdConfigReader.cpp
HoomdConfigReader.h
HoomdConfigWriter.cpp
HoomdConfigWriter.h
HybridMdMove.cpp
HybridMdMove.h
HybridNphMdMove.cpp
HybridNphMdMove.h
IFunctor.h
util/misc/initStatic.cpp
ddMd/misc/initStatic.cpp
util/misc/initStatic.h
ddMd/misc/initStatic.h
Int.cpp
Int.h
IntDistribution.cpp
IntDistribution.h
Integrator.cpp
Integrator.h
integrator.mod
IntegratorFactory.cpp
IntegratorFactory.h
interaction.mod
InterIntraLink.cpp
InterIntraLink.h
IntraBondStressAutoCorr.h
IntraBondStressAutoCorr.tpp
IntraBondTensorAutoCorr.h
IntraBondTensorAutoCorr.tpp
IntraPairAutoCorr.cpp
IntraPairAutoCorr.h
IntraStructureFactor.cpp
IntraStructureFactor.h
IntraStructureFactorGrid.cpp
IntraStructureFactorGrid.h
IntVector.cpp
IntVector.h
ioUtil.cpp
ioUtil.h
isNull.h
KineticEnergyAnalyzer.cpp
KineticEnergyAnalyzer.h
Label.cpp
Label.h
LamellarOrderingExternal.cpp
LamellarOrderingExternal.h
mcMd/configIos/LammpsConfigIo.cpp
ddMd/configIos/LammpsConfigIo.cpp
mcMd/configIos/LammpsConfigIo.h
ddMd/configIos/LammpsConfigIo.h
mcMd/trajectory/LammpsDumpReader.cpp
tools/trajectory/LammpsDumpReader.cpp
mcMd/trajectory/LammpsDumpReader.h
tools/trajectory/LammpsDumpReader.h
mcMd/analyzers/trajectory/LammpsDumpWriter.cpp
ddMd/analyzers/trajectory/LammpsDumpWriter.cpp
tools/analyzers/LammpsDumpWriter.cpp
mcMd/analyzers/trajectory/LammpsDumpWriter.h
ddMd/analyzers/trajectory/LammpsDumpWriter.h
tools/analyzers/LammpsDumpWriter.h
LatticeSystem.cpp
LatticeSystem.h
Linear.cpp
Linear.h
LinearCvBias.cpp
LinearCvBias.h
LinearGenerator.cpp
LinearGenerator.h
LinearPerturbation.h
LinearRouseAutoCorr.cpp
LinearRouseAutoCorr.h
LinearSG.cpp
LinearSG.h
Link.h
LinkEvents.h
LinkFactory.cpp
LinkFactory.h
LinkLengthDist.cpp
LinkLengthDist.h
LinkLifeTime.cpp
LinkLifeTime.h
LinkLTPos.cpp
LinkLTPos.h
LinkMaster.cpp
LinkMaster.h
LinkMSD.cpp
LinkMSD.h
LinkPotentialImpl.h
List.h
ListArray.h
ListIterator.h
LJPair.cpp
LJPair.h
Lng.cpp
Lng.h
LocalLamellarOrderingExternal.cpp
LocalLamellarOrderingExternal.h
Log.cpp
Log.h
LogEnergy.cpp
LogEnergy.h
LogProgress.cpp
LogProgress.h
LogStep.h
Manager.h
util/param/manager.mod
mcMd/simulation/manager.mod
mcMd/chemistry/Mask.cpp
ddMd/chemistry/Mask.cpp
mcMd/chemistry/Mask.h
ddMd/chemistry/Mask.h
mcMd/chemistry/MaskPolicy.cpp
ddMd/chemistry/MaskPolicy.cpp
mcMd/chemistry/MaskPolicy.h
ddMd/chemistry/MaskPolicy.h
math.mod
Matrix.h
mc_potentials.h	Include this file to include all MC potential energy classes at once
McAnalyzerFactory.cpp
McAnalyzerFactory.h
McAnalyzerManager.cpp
McAnalyzerManager.h
McBondEnergyAverage.cpp
McBondEnergyAverage.h
McCommandFactory.cpp
McCommandFactory.h
McCommandManager.cpp
McCommandManager.h
McConfigIo.cpp
McConfigIo.h
McCoulombPotential.h
McDeformCommand.cpp
McDeformCommand.h
McEnergyAnalyzer.cpp
McEnergyAnalyzer.h
McEnergyAverage.cpp
McEnergyAverage.h
McEnergyOutput.cpp
McEnergyOutput.h
McEnergyPerturbation.cpp
McEnergyPerturbation.h
McExternalEnergyAverage.cpp
McExternalEnergyAverage.h
McExternalPerturbation.cpp
McExternalPerturbation.h
McIntraBondStressAutoCorr.cpp
McIntraBondStressAutoCorr.h
McIntraBondTensorAutoCorr.cpp
McIntraBondTensorAutoCorr.h
mcmd.mod
McMd_mpi.cpp
McMd_mpi.h
McMdConfigIo.cpp
McMdConfigIo.h
McMove.cpp
McMove.h
mcmove.mod
McMoveFactory.cpp
McMoveFactory.h
McMoveManager.cpp
McMoveManager.h
McMuExchange.cpp
McMuExchange.h
McNVTChemicalPotential.cpp
McNVTChemicalPotential.h
McPairEnergyAverage.cpp
McPairEnergyAverage.h
McPairExternalPerturbation.h
McPairPerturbation.h
McPairPotential.cpp
McPairPotential.h
McPairPotentialImpl.h
McPerturbationFactory.cpp
McPerturbationFactory.h
McPressureAverage.cpp
McPressureAverage.h
mcSim.cpp
modules/sliplink/mcSim.cpp
McSimulation.cpp
McSimulation.h
McStressAutoCorrelation.cpp
McStressAutoCorrelation.h
McSystem.cpp
McSystem.h
McSystemInterface.cpp
McSystemInterface.h
McVirialStressTensorAverage.cpp
McVirialStressTensorAverage.h
md_potentials.h	Include this file to include all MD potentials at once
MdAnalyzerFactory.cpp
MdAnalyzerFactory.h
MdAnalyzerManager.cpp
MdAnalyzerManager.h
MdColVar.cpp
MdColVar.h
MdCommandFactory.cpp
MdCommandFactory.h
MdCommandManager.cpp
MdCommandManager.h
MdConfigIo.cpp
MdConfigIo.h
MdCoulombPotential.cpp
MdCoulombPotential.h
MdDeformCommand.cpp
MdDeformCommand.h
MdEnergyAnalyzer.cpp
MdEnergyAnalyzer.h
MdEnergyOutput.cpp
MdEnergyOutput.h
MdEwaldPairPotentialImpl.h
MdEwaldPotential.cpp
MdEwaldPotential.h
MdIntegrator.cpp
MdIntegrator.h
mdIntegrator.mod
MdIntegratorFactory.cpp
MdIntegratorFactory.h
MdIntraBondStressAutoCorr.cpp
MdIntraBondStressAutoCorr.h
MdIntraBondTensorAutoCorr.cpp
MdIntraBondTensorAutoCorr.h
MdKineticEnergyAverage.cpp
MdKineticEnergyAverage.h
MdMove.cpp
MdMove.h
MdPairEnergyCoefficients.cpp
MdPairEnergyCoefficients.h
MdPairPotential.cpp
MdPairPotential.h
MdPairPotentialImpl.h
MdPotentialEnergyAverage.cpp
MdPotentialEnergyAverage.h
mdPp.cpp
MdPressureAverage.cpp
MdPressureAverage.h
mdSim.cpp
modules/sliplink/mdSim.cpp
MdSimulation.cpp
MdSimulation.h
MdSpmePotential.cpp
MdSpmePotential.h
MdStressAutoCorr.cpp
MdStressAutoCorr.h
MdSystem.cpp
MdSystem.h
MdSystemInterface.cpp
MdSystemInterface.h
MdVirialStressTensorAverage.cpp
MdVirialStressTensorAverage.h
MeanSqDispArray.h
Memory.cpp
Memory.h
MemoryCounter.cpp
MemoryCounter.h
MemoryIArchive.cpp
MemoryIArchive.h
MemoryOArchive.cpp
MemoryOArchive.h
MethodFunctor.h
util/misc/misc.mod
ddMd/analyzers/misc/misc.mod
Modifier.cpp
Modifier.h
modifier.mod
ModifierFactory.cpp
ModifierFactory.h
ModifierManager.cpp
ModifierManager.h
mcMd/chemistry/Molecule.cpp
tools/chemistry/Molecule.cpp
mcMd/chemistry/Molecule.h
tools/chemistry/Molecule.h
MonoclinicBoundary.cpp
MonoclinicBoundary.h
MpiFileIo.cpp
MpiFileIo.h
MpiLoader.h
MpiLogger.cpp
MpiLogger.h
MpiSendRecv.cpp
MpiSendRecv.h	This file contains templates for global functions send<T>, recv<T> and bcast<T>
MpiStructBuilder.cpp
MpiStructBuilder.h
MpiTraits.cpp
MpiTraits.h
mtrand.cpp
mtrand.h
Multiblock.cpp
Multiblock.h
MultiHarmonicDihedral.cpp
MultiHarmonicDihedral.h
mcMd/neighbor/neighbor.mod
ddMd/neighbor/neighbor.mod
tools/neighbor/neighbor.mod
NLinkAverage.cpp
NLinkAverage.h
Node.h
Notifier.h
mcMd/mdIntegrators/NphIntegrator.cpp
ddMd/integrators/NphIntegrator.cpp
mcMd/mdIntegrators/NphIntegrator.h
ddMd/integrators/NphIntegrator.h
NptIntegrator.cpp
NptIntegrator.h
NucleationExternal.cpp
NucleationExternal.h
NveIntegrator.cpp
NveIntegrator.h
NveVvIntegrator.cpp
NveVvIntegrator.h
NvtDpdVvIntegrator.cpp
NvtDpdVvIntegrator.h
NvtIntegrator.cpp
NvtIntegrator.h
mcMd/mdIntegrators/NvtLangevinIntegrator.cpp
ddMd/integrators/NvtLangevinIntegrator.cpp
mcMd/mdIntegrators/NvtLangevinIntegrator.h
ddMd/integrators/NvtLangevinIntegrator.h
NvtNhIntegrator.cpp
NvtNhIntegrator.h
Observer.h
Offset.h
OptionalLabel.cpp
OptionalLabel.h
OrderParamNucleation.cpp
OrderParamNucleation.h
OrthoBoxExternal.cpp
OrthoBoxExternal.h
OrthoRegion.cpp
OrthoRegion.h
OrthorhombicBoundary.cpp
OrthorhombicBoundary.h
OutputBoxdim.cpp
OutputBoxdim.h
OutputEnergy.cpp
OutputEnergy.h
OutputPairEnergies.cpp
OutputPairEnergies.h
OutputPressure.cpp
OutputPressure.h
OutputStressTensor.cpp
OutputStressTensor.h
OutputTemperature.cpp
OutputTemperature.h
pack.h
Pair.h
pair.mod
PairEnergy.cpp
PairEnergy.h
PairEnergyAnalyzer.cpp
PairEnergyAnalyzer.h
PairEnergyAverage.cpp
PairEnergyAverage.h
mcMd/potentials/pair/PairFactory.cpp
ddMd/potentials/pair/PairFactory.cpp
mcMd/potentials/pair/PairFactory.h
ddMd/potentials/pair/PairFactory.h
mcMd/neighbor/PairIterator.h
ddMd/neighbor/PairIterator.h
mcMd/neighbor/PairList.cpp
ddMd/neighbor/PairList.cpp
mcMd/neighbor/PairList.h
ddMd/neighbor/PairList.h
PairPotential.cpp
mcMd/potentials/pair/PairPotential.h
ddMd/potentials/pair/PairPotential.h
PairPotentialImpl.h
PairSelector.cpp
PairSelector.h
param.mod
ParamComponent.cpp
ParamComponent.h
ParamComposite.cpp
ParamComposite.h
Parameter.cpp
Parameter.h
ParamFileTest.h
PArray.h
PArrayIterator.h
PeriodicExternal.cpp
PeriodicExternal.h
perturb.mod
Perturbation.cpp
Perturbation.h
PerturbDerivative.cpp
PerturbDerivative.h
Plan.cpp
Plan.h
Point.cpp
Point.h
PointGenerator.cpp
PointGenerator.h
PointGroup.cpp
PointGroup.h
PointSymmetry.cpp
PointSymmetry.h
Polynomial.cpp
Polynomial.h
Potential.cpp
Potential.h
mcMd/potentials/potentials.mod
ddMd/potentials/potentials.mod
PressureAnalyzer.cpp
PressureAnalyzer.h
PressureAverage.h
Processor.cpp
Processor.h
ProcessorAnalyzerFactory.cpp
ProcessorAnalyzerFactory.h
ProcessorAnalyzerManager.cpp
ProcessorAnalyzerManager.h
product.h
programs.mod
RadialDistribution.cpp
RadialDistribution.h
RadiusGyration.cpp
RadiusGyration.h
RaggedMatrix.h
Random.cpp
Random.h
random.mod
RArray.h
Rational.cpp
Rational.h
RDF.cpp
RDF.h
ReplicaMove.cpp
ReplicaMove.h
RigidDisplaceMove.cpp
RigidDisplaceMove.h
Ring.cpp
Ring.h
RingBuffer.h
RingOctaRebridgeMove.cpp
RingOctaRebridgeMove.h
RingRouseAutoCorr.cpp
RingRouseAutoCorr.h
RingTetraRebridgeMove.cpp
RingTetraRebridgeMove.h
ScalarParam.h
scattering.mod
ScopedPtr.h
SemiGrandDistribution.cpp
SemiGrandDistribution.h
Serializable.h
Serializable_includes.h
serialize.h
serialize.mod
SerializeConfigIo.cpp
SerializeConfigIo.h
Setable.h
setToZero.h
Signal.cpp
Signal.h
signal.mod
simp.mod
SimplePeriodicExternal.cpp
SimplePeriodicExternal.h
mcMd/simulation/Simulation.cpp
ddMd/simulation/Simulation.cpp
mcMd/simulation/Simulation.h
ddMd/simulation/Simulation.h
mcMd/simulation/simulation.mod
ddMd/simulation/simulation.mod
SimulationAccess.cpp
SimulationAccess.h
Sliplinker.cpp
Sliplinker.h
SliplinkerAll.cpp
SliplinkerAll.h
SliplinkerEnd.cpp
SliplinkerEnd.h
SliplinkMcAnalyzerFactory.cpp
SliplinkMcAnalyzerFactory.h
SliplinkMcModule.cpp
SliplinkMcModule.h
SliplinkMcMoveFactory.cpp
SliplinkMcMoveFactory.h
SliplinkMdAnalyzerFactory.cpp
SliplinkMdAnalyzerFactory.h
SliplinkMove.cpp
SliplinkMove.h
SlitExternal.cpp
SlitExternal.h
SmpConfigIo.cpp
SmpConfigIo.h
space.mod
SpecialExternal.cpp
SpecialExternal.h
SpecialFactory.cpp
SpecialFactory.h
SpecialPotential.cpp
SpecialPotential.h
SpecialPotentialFacade.h
SpecialPotentialFacade.tpp
simp/species/Species.cpp
tools/chemistry/Species.cpp
simp/species/Species.h
tools/chemistry/Species.h
species.mod
SpeciesEnsemble.cpp
SpeciesEnsemble.h
SpeciesFactory.cpp
SpeciesFactory.h
SpeciesGroup.cpp
SpeciesGroup.h
SpeciesGroup.tpp
SpeciesManager.cpp
SpeciesManager.h
SpeciesMutator.cpp
SpeciesMutator.h
SphericalTabulatedExternal.cpp
SphericalTabulatedExternal.h
SSChainDist.cpp
SSChainDist.h
SSet.h
ddMd/storage/storage.mod
tools/storage/storage.mod
Str.cpp
Str.h
stress.h
stress.mod
StressAnalyzer.cpp
StressAnalyzer.h
StressAutoCorr.cpp
mcMd/analyzers/system/StressAutoCorr.h
ddMd/analyzers/stress/StressAutoCorr.h
StressAutoCorrelation.cpp
StressAutoCorrelation.h
StressCalculator.cpp
StressCalculator.h
StressTensorAverage.h
mcMd/analyzers/system/StructureFactor.cpp
ddMd/analyzers/scattering/StructureFactor.cpp
mcMd/analyzers/system/StructureFactor.h
ddMd/analyzers/scattering/StructureFactor.h
mcMd/analyzers/system/StructureFactorGrid.cpp
ddMd/analyzers/scattering/StructureFactorGrid.cpp
mcMd/analyzers/system/StructureFactorGrid.h
ddMd/analyzers/scattering/StructureFactorGrid.h
StructureFactorP.cpp
StructureFactorP.h
StructureFactorPGrid.cpp
StructureFactorPGrid.h
SymmetryGroup.h
SymmTensorAverage.cpp
SymmTensorAverage.h
SymmTensorAverageAnalyzer.cpp
SymmTensorAverageAnalyzer.h
System.cpp
System.h
system.mod
SystemAnalyzer.h
SystemAnalyzerFactory.cpp
SystemAnalyzerFactory.h
SystemInterface.cpp
SystemInterface.h
SystemMove.cpp
SystemMove.h
Tensor.cpp
Tensor.h
TensorAverage.cpp
TensorAverage.h
TensorAverageAnalyzer.cpp
TensorAverageAnalyzer.h
test.mod
TestException.h
TestRunner.h
TextFileIArchive.cpp
TextFileIArchive.h
TextFileOArchive.cpp
TextFileOArchive.h
Timer.h
tools.mod
Torsion.h
TorsionForce.h
mcMd/trajectory/trajectory.mod
ddMd/analyzers/trajectory/trajectory.mod
tools/trajectory/trajectory.mod
mcMd/trajectory/TrajectoryReader.cpp
tools/trajectory/TrajectoryReader.cpp
mcMd/trajectory/TrajectoryReader.h
tools/trajectory/TrajectoryReader.h
mcMd/trajectory/TrajectoryReaderFactory.cpp
tools/trajectory/TrajectoryReaderFactory.cpp
mcMd/trajectory/TrajectoryReaderFactory.h
tools/trajectory/TrajectoryReaderFactory.h
mcMd/analyzers/trajectory/TrajectoryWriter.cpp
ddMd/analyzers/trajectory/TrajectoryWriter.cpp
tools/analyzers/TrajectoryWriter.cpp
mcMd/analyzers/trajectory/TrajectoryWriter.h
ddMd/analyzers/trajectory/TrajectoryWriter.h
tools/analyzers/TrajectoryWriter.h
TwoStepIntegrator.cpp
TwoStepIntegrator.h
TypeDistribution.cpp
TypeDistribution.h
TypeMap.cpp
TypeMap.h
UnitTest.h
UnitTestRunner.h
util.mod
mcMd/analyzers/system/VanHove.cpp
ddMd/analyzers/scattering/VanHove.cpp
mcMd/analyzers/system/VanHove.h
ddMd/analyzers/scattering/VanHove.h
Vector.cpp
Vector.h
VelProf.cpp
VelProf.h
VirialStressAnalyzer.cpp
VirialStressAnalyzer.h
VirialStressTensor.cpp
VirialStressTensor.h
VirialStressTensorAverage.cpp
VirialStressTensorAverage.h
WcaPair.cpp
WcaPair.h
write.cpp
write.h
XdrFileIArchive.cpp
XdrFileIArchive.h
XdrFileOArchive.cpp
XdrFileOArchive.h
XmlAttribute.cpp
XmlAttribute.h
XmlBase.cpp
XmlBase.h
XmlEndTag.cpp
XmlEndTag.h
XmlStartTag.cpp
XmlStartTag.h
xmltag.mod
XmlXmlTag.cpp
XmlXmlTag.h