| ►NDdMd | Parallel domain decomposition (DD) MD simulation |
| CAnalyzer | Abstract base for periodic output and/or analysis actions |
| CAnalyzerFactory | Factory for DdMd::Analyzer objects |
| CAnalyzerManager | Manager for a list of Analyzer objects |
| CAngleFactory | Factory for AnglePotential objects |
| CAnglePotential | Abstract base class for computation of angle force and energies |
| CAnglePotentialImpl | Implementation template for a AnglePotential |
| CAngleStorage | Container for Group<3> (angle) objects |
| CAtom | A point particle in an MD simulation |
| CAtomArray | An array of Atom objects |
| CAtomCollector | Class for collecting Atoms from processors to master processor |
| CAtomContext | Descriptor for context of an Atom within a molecule and species |
| CAtomDistributor | Class for distributing Atoms among processors |
| CAtomIterator | Iterator for all atoms owned by an AtomStorage |
| CAtomMap | Associative container for finding atoms identified by integer id |
| CAtomStorage | A container for all the atoms and ghost atoms on this processor |
| CAtomType | Descriptor for a type of Atom |
| CAutoCorrAnalyzer | Compute an autocorrelation function for a sequence of Data values |
| CAverageAnalyzer | Analyze average and block averages of a single floating point variable |
| CBondFactory | Factory for BondPotential objects |
| CBondPotential | Abstract base class for computing bond forces and energies |
| CBondPotentialImpl | Implementation template for a BondPotential |
| CBondStorage | Container for for Group<2> (bond) objects |
| CBondTensorAutoCorr | Calculate stress autocorrelation function |
| CBuffer | Buffer for interprocessor communication |
| CCell | A single Cell in a CellList |
| CCellAtom | Data for an atom in a CellList |
| CCellList | A cell list used only to identify nearby atom pairs |
| CConfigIo | Abstract reader/writer for configuration files |
| CConfigIoFactory | Default Factory for subclasses of ConfigIo |
| CConfigWriter | Periodically write simulation configuration to a new file |
| CConstAtomIterator | Const iterator for all atoms owned by an AtomStorage |
| CConstGhostIterator | Iterator for all ghost atoms owned by an AtomStorage |
| CConstGroupIterator | Const iterator for all Group < N > objects owned by a GroupStorage < N > |
| CDdMdConfigIo | Native / default format for configuration files |
| CDdMdGroupTrajectoryWriter | Native binary trajectory format for ddSim, for one group |
| CDdMdOrderedConfigIo | Native / default format for configuration files |
| CDdMdTrajectoryWriter | Native binary trajectory format for ddSim |
| CDdTimer | Class for measuring time intervals |
| CDihedralFactory | Factory for DihedralPotential objects |
| CDihedralPotential | Abstract base class for computing dihedral forces and energies |
| CDihedralPotentialImpl | Implementation template for a DihedralPotential |
| CDihedralStorage | Container for Group<4> (dihedral) objects |
| CDomain | Decomposition of the system into domains associated with processors |
| CEnergyAnalyzer | Compute averages and output block averages of energy components |
| CExchanger | Class for exchanging Atoms, Ghosts and Groups between processors |
| CExternalEnergyAnalyzer | Output and evaluate average of external energy |
| CExternalEnergyAverage | Periodically write simulation energies to Log output |
| CExternalFactory | Factory for ExternalPotential objects |
| CExternalPotential | Calculates external forces and energies for a parent Simulation |
| CExternalPotentialImpl | Implementation template for a ExternalPotential |
| CGhostIterator | Iterator for all ghost atoms owned by an AtomStorage |
| CGroup | A group of covalently interacting atoms |
| CGroupCollector | Class for collecting Groups from processors to master processor |
| CGroupDistributor | Class template for distributing Group<N> objects among processors |
| CGroupExchanger | Interface for a GroupStorage<N> for use in Exchanger |
| CGroupIterator | Iterator for all Group < N > objects owned by a GroupStorage< N > |
| CGroupStorage | A container for all the Group<N> objects on this processor |
| CIntegrator | An Integrator numerically integrates the equations of motion |
| CIntegratorFactory | Factory for subclasses of Integrator (i.e., MD integrators) |
| CKineticEnergyAnalyzer | Output and evaluate average of kinetic energy |
| CLammpsConfigIo | Lammps data file format for configuration files |
| CLammpsDumpWriter | Write a trajectory in the Lammps dump format |
| CLogEnergy | Periodically write simulation energies to Log output |
| CMask | Set of Atoms for which pair interactions with a parent Atom are "masked" |
| ►CModifier | A Modifier can modify the time evolution of the simulation |
| CFlags | Bit flag constants associated with particular actions |
| CModifierFactory | Factory for DdMd::Modifier objects |
| CModifierManager | Manager for a set of Modifier objects |
| CNphIntegrator | A reversible, symplectic NPH integrator (Anderson barostat) |
| CNptIntegrator | A reversible symplectic NPT integrator |
| CNveIntegrator | A velocity-Verlet constant energy integrator |
| CNvtIntegrator | A Nose-Hoover constant temperature, constant volume integrator |
| CNvtLangevinIntegrator | A NVT molecular dynamics integrator with a Langevin thermostat |
| COrderParamNucleation | OrderParamNucleation is designed to evaluate a sort of composition profile in the specific case of nucleating a lamellar ordered phase in a small region at the center of a simulation cell |
| COutputBoxdim | Periodically write Boundary dimensions to file |
| COutputEnergy | Periodically write simulation energies to file |
| COutputPairEnergies | Periodically write pair energies to file |
| COutputPressure | Periodically write (scalar) pressure to file |
| COutputStressTensor | Periodically write (tensor) StressTensor to file |
| COutputTemperature | Periodically output kinetic temperature to file |
| CPairEnergyAnalyzer | Compute and analyze pair energies |
| CPairEnergyAverage | Compute average of pair energy |
| CPairFactory | Factory for PairPotential objects |
| CPairIterator | Iterator for pairs in a PairList |
| CPairList | A Verlet nonbonded pair list |
| CPairPotential | Abstract base class for computing nonbonded pair forces and energies |
| CPairPotentialImpl | Implementation template for a PairPotential |
| CPlan | Communication plan |
| CPotential | A Potential represents a potential energy contribution |
| CPressureAnalyzer | Sample and evaluate average of total pressure |
| CSerializeConfigIo | Save / load configuration from / to an archive |
| CSimulation | Main object for a domain-decomposition MD simulation |
| CSimulationAccess | Provides access to members of Simulation object |
| CStressAnalyzer | Output and evaluate average of stress tensor |
| CStressAutoCorr | Compute stress autocorrelation function for a liquid |
| CStressAutoCorrelation | Compute the shear stress autocorrelation function |
| CStructureFactor | StructureFactor evaluates structure factors in Fourier space |
| CStructureFactorGrid | StructureFactorGrid evaluates structure factors in Fourier space |
| CSymmTensorAverageAnalyzer | Analyzer that computes average of a sequence of symmetric Tensor values |
| CTensorAverageAnalyzer | Analyzer that computes averages and block averages of a single Tensor |
| CTrajectoryWriter | Base class to write a trajectory to a single file |
| CTwoStepIntegrator | A two-step velocity-Verlet style integrator |
| CVanHove | Evaluates the van Hove function S(k,t) for one or more wavevector k |
| CVirialStressAnalyzer | Output and evaluate average of virial stress tensor |
| CVirialStressTensor | Periodically write virial stress tensor components to file |
| CVirialStressTensorAverage | Compute average and output block averages of virial stress tensor |
| ►NMcMd | Single-processor Monte Carlo (MC) and molecular dynamics (MD) |
| CActivate | Static member functions to de-active and re-active atoms |
| CAnalyzer | Abstract base for periodic output and/or analysis actions |
| CAnalyzerManager | Manager for a list of Analyzer objects |
| CAngleFactory | Factory for subclasses of AnglePotential |
| CAnglePotential | Interface for a Angle Interaction |
| CAnglePotentialImpl | Implementation template for an AnglePotential |
| CAtom | A point particle within a Molecule |
| CAtomDisplaceMove | Random displacement of one atom |
| CAtomMSD | Autocorrelation for vector separation of two atoms on a molecule |
| CAtomType | Descriptor for a type of Atom |
| CAverageAnalyzer | AverageAnalyzer averages of total potential energy |
| CBennettsMethod | Bennett's method estimates free energy difference between two states |
| CBlockRadiusGyration | Radius of gyration of different blocks in a molecule |
| CBondFactory | Factory for BondPotential objects |
| CBondLengthDist | BondLengthDist evaluates the distribution function of the lengths of the bonds |
| CBondPotential | Abstract Bond Potential class |
| CBondPotentialImpl | Implementation template for a BondPotential |
| CBoundaryAverage | Average of boundary lengths and volume of simulation cell |
| CCell | A set of Atoms in a small region |
| CCellList | A cell list for Atom objects in a periodic system boundary |
| CCellTag | Location of the pointer to a particular Atom in a CellList |
| CCfbDoubleRebridgeMove | Configuration bias trimer double rebridge moves, to reconnect two chains |
| CCfbEndBase | Base class for configuration bias (CFB) end regrowth moves |
| CCfbEndMove | Configuration bias end regrowth move for flexible linear chains |
| CCfbLinear | Base class for configuration bias (CFB) end regrowth moves |
| CCfbLinearEndMove | Configuration bias end regrowth move for flexible linear chains |
| CCfbRebridgeBase | Base class configuration bias moves internal segment regrowth moves |
| CCfbRebridgeMove | Config-bias move for internal segment of a flexible linear polymer |
| CCfbReptateMove | Configuration bias reptation move for a Linear species |
| CCfbReptationMove | Configuration bias reptation move for a Linear species |
| CCfbRingRebridgeMove | Configuration bias rebridge moves for ring molecules |
| CCluster | Cluster of molecules |
| CClusterHistogram | Identify micelle clusters in polymeric systems |
| CClusterIdentifier | Identifies clusters of molecules, such as micelles |
| CClusterLink | Molecule in a cluster |
| CColVar | Abstract base class for collective variables |
| CColVarPotentialTmpl | SpecialPotential that is a function of a collective variable |
| CCommand | Command is an object that can be invoked from the command script |
| CCommandManager | Manager for Command objects in an MdSimulation |
| CComMSD | Molecular center of mass mean squared displacement |
| CCompositionProfile | CompositionProfile evaluates the distribution of monomer positions along several user-specified directions |
| CConfigIo | System configuration file reader and writer |
| CConfigIoFactory | Default Factory for subclasses of ConfigIo |
| CConfigWriter | Periodically dump system configuration to a new file |
| CCoulombFactory | Factory for CoulombPotential objects |
| CCrosslinker | Analyzer to create crosslinks and output the resulting configuration |
| CCvBias | Bias potential as a function of a collective variable (CV) |
| CDCDTrajectoryReader | TrajectoryReader for CHARMM ".dcd" data files |
| CDdMdConfigIo | ConfigIo for DdMd data files |
| CDdMdTrajectoryReader | TrajectoryReader for a DdMd trajectory file |
| CDeformCommand | Command to deform the unit cell |
| CDihedralFactory | Factory for subclasses of DihedralPotential |
| CDihedralPotential | Interface for a Dihedral Potential |
| CDihedralPotentialImpl | Implementation template for an DihedralPotential |
| CDpdMove | DpdMove is a short dissipative particle dynamics (DPD) simulation |
| CEndSwapMove | A move that swaps the ends of a linear hetero-polymer |
| CEndtoEnd | End to end distance of a molecule |
| CEndtoEndXYZ | Mean square end to end distance of a molecule |
| CEnergyCalculator | Interface for a class that calculates a total energy |
| CEwaldRSpaceAccumulator | Utility class to store r-space Coulomb energy and stress |
| CExternalFactory | Factory for subclasses MdExternalPotential or McExternalPotential |
| CExternalPotential | Abstract External Potential class |
| CExternalPotentialImpl | Template implementation of ExternalPotential |
| CG1MSD | Autocorrelation for vector separation of any two monomers on a molecule |
| CGcSliplinkMove | Move to evolve the slip-springs |
| CGenerator | Generates initial configurations for molecules of one species |
| CGroup | A sequence of NAtom covalently interacting atoms |
| CGroupRebridgeBase | Base class for rebridging a group of atoms forming a tetrahedron |
| CHarmonicCvBias | Harmonic function of a collective variable (CV) |
| CHomopolymerSemiGrandMove | A move that changes the type of a HomopolymerSG molecule |
| CHomopolymerSG | A Homopolymer with a mutable type, for semigrand ensemble |
| CHybridMdMove | HybridMdMove is a hybrid Molecular Dynamics MC move |
| CHybridNphMdMove | HybridNphMove is a hybrid Molecular Dynamics MC move for NPT ensemble |
| CInterIntraLink | Number of inter and intramolecular links |
| CIntraBondStressAutoCorr | Autocorrelation for bond stress of a molecule |
| CIntraBondTensorAutoCorr | Autocorrelation for bond stress of a molecule |
| CIntraPairAutoCorr | Autocorrelation for vector separation of any two monomers on a molecule |
| CIntraStructureFactor | Intramolecular contribution to the structure factor S(k) |
| CIntraStructureFactorGrid | IntraStructureFactorGrid evaluates structure factors in Fourier space |
| CLammpsConfigIo | ConfigIo for Lammps data files |
| CLammpsDumpReader | TrajectoryReader for Lammps dump trajectory files |
| CLammpsDumpWriter | Periodically write snapshots to a lammps dump (i.e., trajectory) file |
| CLinearCvBias | Linear function of a collective variable (CV) |
| CLinearGenerator | Generates random configurations for linear molecules |
| CLinearPerturbation | A Perturbation that is a linear function of a parameter |
| CLinearRouseAutoCorr | Autocorrelation for Rouse mode coefficients of a linear molecule |
| CLinearSG | A mutable linear polymer, for semigrand ensemble |
| CLink | A Link represents a crosslink between two Atoms |
| CLinkAddEvent | Event signalling addition of Link to the LinkMaster |
| CLinkFactory | Factory for subclasses of MdBondPotential or McBondPotential |
| CLinkLengthDist | LinkLengthDist evaluates the distribution function of the lengths of the links |
| CLinkLifeTime | LinkLifeTime evaluates how long the slip-springs live |
| CLinkLTPos | LinkLTPos evaluates how long the slip-springs live as a function of position along the chain |
| CLinkMaster | Manages all Link objects in a System |
| CLinkMSD | Evaluates msd of link ends along the chains |
| CLinkPotentialImpl | Template implementation of an BondPotential for links |
| CLinkRemoveEvent | Event signalling removal of a Link from the LinkMaster |
| CLinkResetEvent | Event signalling reset of Link to the LinkMaster |
| CLogProgress | Periodically write step number to a Log file |
| CMask | Set of Atoms for which pair interactions with a target Atom are "masked" |
| CMcAnalyzerFactory | AnalyzerFactory for an McSimulation |
| CMcAnalyzerManager | Manager for Analyzer objects in an McSimulation |
| CMcBondEnergyAverage | McBondEnergyAverage averages of bond potential energy |
| CMcCommandFactory | CommandFactory for an McSimulation |
| CMcCommandManager | Command interpreter and Manager for an McSimulation |
| CMcConfigIo | ConfigIo for MC simulations (no atom velocities) |
| CMcCoulombPotential | Long-range part of Coulomb potential for MC |
| CMcDeformCommand | Command to deform the unit cell |
| CMcEnergyAnalyzer | Compute averages and output block averages of energy components |
| CMcEnergyAverage | McEnergyAverage averages of total potential energy |
| CMcEnergyOutput | Analyzer to output total potential energy |
| CMcEnergyPerturbation | A Perturbation with a variable inverse temperature |
| CMcExternalEnergyAverage | McExternalEnergyAverage averages of total external energy |
| CMcExternalPerturbation | A Perturbation in the external potential external parameter |
| CMcIntraBondStressAutoCorr | Autocorrelation for bond stress of a molecule |
| CMcIntraBondTensorAutoCorr | Autocorrelation for bond stress of a molecule |
| CMcMdConfigIo | Base class for default Mc and Md configIos |
| CMcMove | McMove is an abstract base class for Monte Carlo moves |
| CMcMoveFactory | McMoveFactory for an McSimulation |
| CMcMoveManager | Manager for a set of McMove objects |
| CMcMuExchange | Exchange chemical potential for semigrand ensemble |
| CMcNVTChemicalPotential | McNVTChemicalPotential uses configuration bias algorithm to calculate the chemical potential of a linear chain |
| CMcPairEnergyAverage | McPairEnergyAverage averages of total potential energy |
| CMcPairExternalPerturbation | A Perturbation in the pair interaction epsilon(0,1) for any pair potential supporting setEpsilon() and in the external parameter for any external potential supporting setExternalParameter() |
| CMcPairPerturbation | A Perturbation in the pair interaction epsilon(0,1) for any pair potential supporting setEpsilon() |
| CMcPairPotential | A PairPotential for MC simulations (abstract) |
| CMcPairPotentialImpl | Implementation template for an McPairPotential |
| CMcPerturbationFactory | Default Factory for subclasses of Perturbation |
| CMcPressureAverage | Analyzer to calculate average isotropic pressure |
| CMcSimulation | A Monte-Carlo simulation of one McSystem |
| CMcStressAutoCorrelation | Analyzer to calculate average isotropic pressure |
| CMcSystem | A System for use in a Markov chain Monte Carlo simulation |
| CMcSystemInterface | An interface to an McSystem |
| CMcVirialStressTensorAverage | Periodically write (tensor) StressTensor to file |
| CMdAnalyzerFactory | AnalyzerFactory for an MdSimulation |
| CMdAnalyzerManager | Manager for Analyzer objects in an MdSimulation |
| CMdColVar | Collective variables for MD simulation, with atom forces |
| CMdCommandFactory | CommandFactory for an MdSimulation |
| CMdCommandManager | Command interpreter and Command Manager for an MdSimulation |
| CMdConfigIo | ConfigIo for MD simulations (includes velocities) |
| CMdCoulombPotential | Coulomb potential for an Md simulation |
| CMdDeformCommand | Command to deform the unit cell |
| CMdEnergyAnalyzer | Compute averages and output block averages of energy components |
| CMdEnergyOutput | Analyzer to output total potential and kinetic energies |
| CMdEwaldPairPotentialImpl | Implementation of a pair potential for a charged system |
| CMdEwaldPotential | Ewald Coulomb potential class for MD simulations |
| CMdIntegrator | Abstract base for molecular dynamics integrators |
| CMdIntegratorFactory | Default Factory for subclasses of MdIntegrator |
| CMdIntraBondStressAutoCorr | Autocorrelation for bond stress of a molecule |
| CMdIntraBondTensorAutoCorr | Autocorrelation for bond orientation of of a molecule |
| CMdKineticEnergyAverage | MdKineticEnergyAverage averages of total kinetic energy |
| CMdMove | MdMove is a simple NVE molecular Dynamics MC move |
| CMdPairEnergyCoefficients | Analyzer to output the total pair energy and the sum of squares of the monomeric and molecular pair energy |
| CMdPairPotential | An PairPotential for MD simulation |
| CMdPairPotentialImpl | Implementation template for an MdPairPotential |
| CMdPotentialEnergyAverage | MdPotentialEnergyAverage averages of total potential energy |
| CMdPressureAverage | Calculate average scalar pressure for an MdSystem |
| CMdSimulation | A molecular dynamics simulation of a single MdSystem |
| CMdSpmePotential | Smooth Particle-Mesh Ewald Coulomb potential for MD simulations |
| CMdStressAutoCorr | Analyzer to calculate average isotropic pressure |
| CMdSystem | A System for Molecular Dynamics simulation |
| CMdSystemInterface | An interface to an MdSystem |
| CMdVirialStressTensorAverage | Periodically write (tensor) StressTensor to file |
| CMolecule | A physical molecule (a set of covalently bonded Atoms) |
| CMoleculeSetObserver | Observer interface |
| CNLinkAverage | Average number of crosslinks |
| CNphIntegrator | An explictly reversible/measure-preserving Parrinello-Rahman type NPH integrator |
| CNveVvIntegrator | An NVE Verlet molecular dynamics integrator |
| CNvtDpdVvIntegrator | A velocity-Verlet dissipative particle dynamics (DPD) integrator |
| CNvtLangevinIntegrator | A NVT molecular dynamics integrator with a Langevin thermostat |
| CNvtNhIntegrator | A Nose-Hoover NVT molecular dynamics integrator |
| CPairFactory | Factory for subclasses MdPairPotential or McPairPotential |
| CPairIterator | Iterator for pairs in a PairList |
| CPairList | A Verlet neighbor list |
| CPairPotential | Interface for a Pair Potential |
| CPairSelector | Selection rule for pairs of Atoms |
| CPerturbation | Model of parameter dependence in a free energy perturbation theory |
| CPerturbDerivative | PerturbDerivative returns average value of Perturbation::derivative() |
| CPointGenerator | Generator for monoatomic molecules (atoms) |
| CPressureAverage | PressureAverage evaluates average pressure |
| CRadiusGyration | Radius of gyration of a molecule |
| CRDF | RDF evaluates the atomic radial distribution function |
| CReplicaMove | Replica exchange Monte Carlo move using Gibbs sampling |
| CReSetAtomEvent | Event signalling the reset of an atom from the LinkMaster |
| CRigidDisplaceMove | Random rigid displacement of a molecule |
| CRingOctaRebridgeMove | Molecule rebridging move for a Ring species |
| CRingRouseAutoCorr | Autocorrelation for Rouse mode coefficients of a ring molecule |
| CRingTetraRebridgeMove | Molecule move that attempt the exchange of interior pieces of one close rings |
| CSemiGrandDistribution | Calculate distribution of type indices for mutable species |
| CSimulation | The main object in a simulation, which coordinates others |
| CSliplinker | Move to create and destroy slip-springs |
| CSliplinkerAll | Move to create and destroy slip-springs |
| CSliplinkerEnd | Move to create and destroy slip-springs |
| CSliplinkMcAnalyzerFactory | Custom AnalyzerFactory for an McSimulation |
| CSliplinkMcModule | Module for slip link simulation |
| CSliplinkMcMoveFactory | Custom McMoveFactory |
| CSliplinkMdAnalyzerFactory | Custom AnalyzerFactory for an MdSimulation |
| CSliplinkMove | Move to evolve the slip-springs |
| CSmpConfigIo | Common configuration file format for simpatico |
| CSpecialExternal | Potential for testing purposes |
| CSpecialFactory | Factory for specialized subclasses of SpecialPotential |
| CSpecialPotential | Specialized potential for an MD simulation |
| CSpecialPotentialFacade | SpecialPotential interface to an existing potential |
| CSpeciesFactory | Default Factory for subclasses of Species |
| CSpeciesManager | A Manager for a set of Species objects |
| CSpeciesMutator | Mix-in class for mutable subclasses of Species |
| CSSChainDist | SSChainDist evaluates the distribution of slip-springs along the chains |
| CStressAutoCorr | Compute stress autocorrelation for an isotropic system |
| CStressCalculator | Interface for a stress calculator |
| CStressTensorAverage | Periodically write (tensor) StressTensor to file |
| CStructureFactor | StructureFactor evaluates structure factors in Fourier space |
| CStructureFactorGrid | StructureFactorGrid evaluates structure factors in Fourier space |
| CStructureFactorP | StructureFactorP evaluates partial structure factors in Fourier space |
| CStructureFactorPGrid | StructureFactorPGrid evaluates structure factors in Fourier space |
| CSystem | A set of interacting Molecules enclosed by a Boundary |
| CSystemAnalyzer | Template for Analyzer associated with one System |
| CSystemAnalyzerFactory | AnalyzerFactory for any System (for mc or md) |
| CSystemInterface | An interface to a System |
| CSystemMove | An McMove that acts on one McSystem |
| CTrajectoryReader | Trajectory file reader (base class) |
| CTrajectoryReaderFactory | Default Factory for subclasses of TrajectoryReader |
| CTrajectoryWriter | Periodically write snapshots to a lammps dump (i.e., trajectory) file |
| CTypeDistribution | Calculate distribution of type indices for mutable species |
| CVanHove | Evaluates the van Hove function S(k,t) for one or more wavevector k |
| CVelProf | Evaluates x-velocity profile as a function of z |
| ►NSimp | Classes used by all simpatico molecular simulations |
| CBend | A Bend calculates the angle between two vectors |
| CBendForce | A BendForce computes derivatives of the angle between two vectors |
| CBoundaryEnsemble | Statistical ensemble for changes in the periodic unit cell size |
| CBoxExternal | A repulsive 9-3 potential confining particles within a box |
| CCompensatedPair | Compensated pair potential for transient gel |
| CCompositeBond | Composite bond potential |
| CCosineAngle | A three body angle potential, as a function of angle cosine |
| CCosineDihedral | A dihedral potential proportional to cos(phi) |
| CCosineSqAngle | A three body angle potential, as a function of angle cosine |
| CDiblock | A linear diblock copolymer chain |
| CDpdPair | Soft pair potential used in dissipative particle dynamics (DPD) simulations of Groot, Warren et al |
| CEnergyEnsemble | A statistical ensemble for energy |
| CEwaldInteraction | Implementation of r-space and k-space Ewald Coulomb interactions |
| CFeneBond | A finitely-extensible nonlinear element (FENE) bond potential |
| CGeneralPeriodicExternal | A clipped cosine potential that induces ordering along directions specified by waveIntVectors, w_i |
| CHarmonicAngle | A angle potential that is harmonic in the angle |
| CHarmonicBond | A harmonic covalent bond potential |
| CHarmonicL0Bond | A harmonic bond potential with zero rest length |
| CHomopolymer | A Homopolymer species of chain molecules |
| CHomoRing | A species of homogeneous ring molecules |
| CLamellarOrderingExternal | A clipped cosine potential that induces lamellar ordering along the direction specified by perpDirection_ |
| CLinear | A Species of linear polymers (abstract) |
| CLJPair | A cutoff, shifted Lennard-Jones nonbonded pair interaction |
| CLocalLamellarOrderingExternal | A clipped cosine potential that induces lamellar ordering along the direction specified by perpDirection_ in only a fraction of box specified by the parameter fraction along box length in parallelDirection_ |
| CMonoclinicBoundary | A monoclinic periodic unit cell |
| CMultiblock | A linear MULTIBLOCK copolymer chain |
| CMultiHarmonicDihedral | A truncated Fourier series dihedral potential |
| CNucleationExternal | A clipped cosine potential that induces ordering along directions specified by waveIntVectors, w_i |
| COrthoBoxExternal | A repulsive 9-3 potential confining particles inside an orthogonal box along directions specified by indConfine_ |
| COrthoRegion | A region with orthogonal edges parallel to the x, y, and z axes |
| COrthorhombicBoundary | An orthorhombic periodic unit cell |
| CPeriodicExternal | A clipped cosine potential that induces ordering along directions specified by waveIntVectors, w_i |
| CPoint | A Species in which each Molecule contains only one Atom |
| CRing | A Species of ring polymers (abstract) |
| CSimplePeriodicExternal | A clipped cosine potential that induces ordering along directions specified by waveIntVectors, w_i |
| CSlitExternal | A repulsive 9-3 potential confining particles along the z direction |
| CSpecies | A Species represents a set of chemically similar molecules |
| CSpeciesEnsemble | An ensemble for the number of molecules of one Species |
| CSpeciesGroup | A Group of covalently interacting atoms within any molecule of one Species |
| CSphericalTabulatedExternal | The potential is independent on the type of atoms |
| CTorsion | Computes dihedral / torsion angle involving 3 bonds |
| CTorsionForce | Computes derivatives of dihedral angle with respect to bond vectors |
| CWcaPair | A Weeks-Chandler-Anderson (WCA) repulsive LJ interaction |
| ►NTools | Single-processor classes for pre- and post-processing MD trajectories |
| CAnalyzer | Abstract base for periodic output and/or analysis actions |
| CAnalyzerManager | Manager for a list of Analyzer objects |
| CAtom | A point particle in an MD simulation |
| CAtomMSD | Mean-squared displacement of specific atoms in specific species |
| CAtomStorage | Container for a set of atoms |
| CCell | A single cell in a CellList |
| CCellAtom | Data for an atom in a CellList |
| CCellList | A cell list used only to identify nearby atom pairs |
| CChainMaker | Generates a simulation box full of randomly generated linear polymers |
| CConfigReader | Abstract reader/writer for configuration files |
| CConfigReaderFactory | Default Factory for subclasses of ConfigReader |
| CConfiguration | An instantaneous molecular dynamics configuration |
| CConfigWriter | Abstract reader/writer for configuration files |
| CConfigWriterFactory | Default Factory for subclasses of ConfigWriter |
| CDdMdConfigReader | Native / default DdMd format for configuration files |
| CDdMdConfigWriter | Native / default DdMd format for configuration files |
| CDdMdTrajectoryReader | Reader for lammps dump trajectory file format |
| CGroup | A group of covalently interacting atoms |
| CGroupStorage | A container for Group<N> objects |
| CHoomdConfigReader | Reader for Hoomd-blue XML configuration files |
| CHoomdConfigWriter | Hoomd-blue XML format for configuration files |
| CLammpsDumpReader | Reader for lammps dump trajectory file format |
| CLammpsDumpWriter | Write a trajectory in the Lammps dump format |
| CLogStep | Write step number to log |
| CMolecule | An Molecule has a sequence of atoms, and belongs to an Species |
| CPairEnergy | Analyzer to compute total nonbonded pair energy |
| CProcessor | A post-processor for analyzing outputs of MD simulations |
| CProcessorAnalyzerFactory | Factory for Tools::Analyzer objects |
| CProcessorAnalyzerManager | Manager for a list of Analyzer objects |
| CSpecies | A set of identical molecules |
| CTrajectoryReader | Abstract trajectory file reader |
| CTrajectoryReaderFactory | Default Factory for subclasses of TrajectoryReader |
| CTrajectoryWriter | Based class for classes that write trajectories to a single file |
| CTypeMap | Map between type names and type ids |
| ►NUtil | Utility classes for scientific computation |
| CAr1Process | Generator for a discrete AR(1) Markov process |
| CArray | Array container class template |
| CArrayIterator | Forward iterator for an Array or a C array |
| CArraySet | A container for pointers to a subset of elements of an associated array |
| CArrayStack | A stack of fixed capacity |
| CAutoCorr | Auto-correlation function for one sequence of Data values |
| CAutoCorrArray | Auto-correlation function for an ensemble of sequences |
| CAutoCorrelation | Auto-correlation function, using hierarchical algorithm |
| CAutoCorrStage | Hierarchical auto-correlation function algorithm |
| CAverage | Calculates the average and variance of a sampled property |
| CAverageStage | Evaluate average with hierarchical blocking error analysis |
| CBegin | Beginning line of a composite parameter block |
| CBinaryFileIArchive | Saving archive for binary istream |
| CBinaryFileOArchive | Saving / output archive for binary ostream |
| CBinomial | Class for binomial coefficients (all static members) |
| CBit | Represents a specific bit location within an unsigned int |
| CBlank | An empty line within a parameter file |
| CBool | Wrapper for an bool value, for formatted ostream output |
| CCardinalBSpline | A cardinal B-spline basis function |
| CCArray2DParam | A Parameter associated with a 2D built-in C array |
| CCArrayParam | A Parameter associated with a 1D C array |
| CConstants | Mathematical constants |
| CConstArrayIterator | Forward const iterator for an Array or a C array |
| CConstPArrayIterator | Forward iterator for a PArray |
| CDArray | Dynamically allocatable contiguous array template |
| CDArrayParam | A Parameter associated with a DArray container |
| CDbl | Wrapper for a double precision number, for formatted ostream output |
| CDistribution | A distribution (or histogram) of values for a real variable |
| CDMatrix | Dynamically allocated Matrix |
| CDMatrixParam | A Parameter associated with a 2D built-in C array |
| CDPArray | A dynamic array that only holds pointers to its elements |
| CDRaggedMatrix | Dynamically allocated RaggedMatrix |
| CDSArray | Dynamically allocated array with variable logical size |
| CDSymmMatrixParam | A Parameter associated with a symmetric DMatrix |
| CEnd | End bracket of a ParamComposite parameter block |
| CException | A user-defined exception |
| CFactory | Factory template |
| CFArray | A fixed size (static) contiguous array template |
| CFArrayParam | A Parameter associated with a FArray container |
| CFileMaster | A FileMaster manages input and output files for a simulation |
| CFlagSet | A set of boolean variables represented by characters |
| CFlexPtr | A pointer that may or may not own the object to which it points |
| CFMatrix | Fixed Size Matrix |
| CFormat | Base class for output wrappers for formatted C++ ostream output |
| CFPArray | Statically allocated pointer array |
| CFSArray | A fixed capacity (static) contiguous array with a variable logical size |
| CGArray | An automatically growable array, analogous to a std::vector |
| CGPArray | An automatically growable PArray |
| CGrid | A grid of points indexed by integer coordinates |
| CGridArray | Multi-dimensional array with the dimensionality of space |
| CGStack | An automatically growable Stack |
| CIFunctor | Interface for functor that wraps a void function with one argument (abstract) |
| CIFunctor< void > | Interface for functor that wraps a void function with no arguments (abstract) |
| CInt | Wrapper for an int, for formatted ostream output |
| CIntDistribution | A distribution (or histogram) of values for an int variable |
| CIntVector | An IntVector is an integer Cartesian vector |
| CLabel | A label string in a file format |
| CList | Linked list class template |
| CListArray | An array of objects that are accessible by one or more linked List objects |
| CListIterator | Bidirectional iterator for a List |
| CLng | Wrapper for a long int, for formatted ostream output |
| CLog | A static class that holds a log output stream |
| CManager | Template container for pointers to objects with a common base class |
| CMatrix | Two-dimensional array container template (abstract) |
| CMeanSqDispArray | Mean-squared displacement (MSD) vs |
| CMemory | Provides method to allocate array |
| CMemoryCounter | Archive to computed packed size of a sequence of objects, in bytes |
| CMemoryIArchive | Input archive for packed heterogeneous binary data |
| CMemoryOArchive | Save archive for packed heterogeneous binary data |
| CMethodFunctor | Functor that wraps a one-argument class member function |
| CMethodFunctor< Object, void > | Functor that wraps a class member function with no arguments |
| CMpiFileIo | Identifies whether this processor may do file I/O |
| CMpiLoader | Provides methods for MPI-aware loading of data from input archive |
| CMpiLogger | Allows information from every processor in a communicator, to be output in rank sequence |
| CMpiStructBuilder | A MpiStructBuilder objects is used to create an MPI Struct datatype |
| CMpiTraits | Default MpiTraits class |
| CMpiTraits< bool > | MpiTraits<bool> explicit specialization |
| CMpiTraits< char > | MpiTraits<char> explicit specialization |
| CMpiTraits< DdMd::AtomType > | Explicit specialization MpiTraits<AtomType> |
| CMpiTraits< DdMd::MaskPolicy > | Explicit specialization MpiTraits<MaskPolicy> |
| CMpiTraits< double > | MpiTraits<double> explicit specialization |
| CMpiTraits< float > | MpiTraits<float> explicit specialization |
| CMpiTraits< int > | MpiTraits<int> explicit specialization |
| CMpiTraits< IntVector > | Explicit specialization MpiTraits<IntVector> |
| CMpiTraits< long > | MpiTraits<long> explicit specialization |
| CMpiTraits< long double > | MpiTraits<long double> explicit specialization |
| CMpiTraits< McMd::AtomType > | Explicit specialization MpiTraits<AtomType> |
| CMpiTraits< McMd::MaskPolicy > | Explicit specialization MpiTraits<MaskPolicy> |
| CMpiTraits< McMd::PairSelector > | Explicit specialization MpiTraits<PairSelector> |
| CMpiTraits< McMd::PairSelector::PairType > | Explicit specialization MpiTraits<PairSelector::PairType> |
| CMpiTraits< MonoclinicBoundary > | Explicit specialization MpiTraits<MonoclinicBoundary> |
| CMpiTraits< Pair< int > > | Explicit specialization MpiTraits< Pair<int> > |
| CMpiTraits< Rational > | Explicit specialization MpiTraits<Rational> |
| CMpiTraits< short > | MpiTraits<short> explicit specialization |
| CMpiTraits< Simp::BoundaryEnsemble > | Explicit specialization MpiTraits<Simp::BoundaryEnsemble> |
| CMpiTraits< Simp::BoundaryEnsemble::Type > | Explicit specialization MpiTraits<Simp::BoundaryEnsemble::Type> |
| CMpiTraits< Simp::EnergyEnsemble > | Explicit specialization MpiTraits<Simp::EnergyEnsemble> |
| CMpiTraits< Simp::EnergyEnsemble::Type > | Explicit specialization MpiTraits<Simp::EnergyEnsemble::Type> |
| CMpiTraits< Simp::OrthorhombicBoundary > | Explicit specialization MpiTraits<OrthorhombicBoundary> |
| CMpiTraits< Simp::SpeciesEnsemble > | Explicit specialization MpiTraits<Simp::SpeciesEnsemble> |
| CMpiTraits< Simp::SpeciesEnsemble::Type > | Explicit specialization MpiTraits<Simp::SpeciesEnsemble::Type> |
| CMpiTraits< Simp::SpeciesGroup< 2 > > | Explicit specialization MpiTraits< SpeciesGroup<2> > |
| CMpiTraits< Simp::SpeciesGroup< 3 > > | Explicit specialization MpiTraits< SpeciesGroup<3> > |
| CMpiTraits< Simp::SpeciesGroup< 4 > > | Explicit specialization MpiTraits< SpeciesGroup<4> > |
| CMpiTraits< Tensor > | Explicit specialization MpiTraits<Tensor> |
| CMpiTraits< unsigned char > | MpiTraits<unsigned char> explicit specialization |
| CMpiTraits< unsigned int > | MpiTraits<unsigned int> explicit specialization |
| CMpiTraits< unsigned long > | MpiTraits<unsigned long> explicit specialization |
| CMpiTraits< unsigned short > | MpiTraits<unsigned short> explicit specialization |
| CMpiTraits< Util::LatticeSystem > | Explicit specialization MpiTraits<LatticeSystem> |
| CMpiTraits< Vector > | Explicit specialization MpiTraits<Vector> |
| CMpiTraitsNoType | Base class for MpiTraits with no type |
| CMTRand | Generates double floating point numbers in the half-open interval [0, 1) |
| CMTRand53 | Generates 53 bit resolution doubles in the half-open interval [0, 1) |
| CMTRand_closed | Generates double floating point numbers in the closed interval [0, 1] |
| CMTRand_int32 | Mersenne Twister random number generator engine |
| CMTRand_open | Generates double floating point numbers in the open interval (0, 1) |
| CNode | Linked List Node, class template |
| CNotifier | Abstract template for a notifier (or subject) in the Observer design pattern |
| CObserver | Abstract class template for observer in the observer design pattern |
| COptionalLabel | An optional Label string in a file format |
| CPair | An array of exactly 2 objects |
| CParamComponent | Abstract base class for classes that input and ouput parameters to file |
| CParamComposite | An object that can read multiple parameters from file |
| CParameter | A single variable in a parameter file |
| CPArray | An array that only holds pointers to its elements |
| CPArrayIterator | Forward iterator for a PArray |
| CPointGroup | Group of crystal symmetries with no translations |
| CPointSymmetry | A PointSymmetry represents a crystallographic point group symmetry |
| CPolynomial | A Polynomial (i.e, |
| CRadialDistribution | Distribution (or histogram) of values for particle separations |
| CRaggedMatrix | A 2D array in which different rows can have different lengths |
| CRandom | Random number generator |
| CRArray | An Array that acts as a reference to another Array or C array |
| CRational | A Rational number (a ratio of integers) |
| CRingBuffer | Class for storing history of previous values in an array |
| CScalarParam | Template for a Parameter object associated with a scalar variable |
| CScopedPtr | A very simple RAII pointer |
| CSerializable | Abstract class for serializable objects |
| CSetable | Template for a value that can be set or declared null (i.e., unknown) |
| CSignal | Notifier (or subject) in the Observer design pattern |
| CSignal< void > | Notifier (or subject) in the Observer design pattern (zero parameters) |
| CSSet | Statically allocated array of pointers to an unordered set |
| CStr | Wrapper for a std::string, for formatted ostream output |
| CSymmetryGroup | Class template for a group of elements of type Symmetry |
| CSymmTensorAverage | Calculates averages of all components of a Tensor-valued variable |
| CTensor | A Tensor represents a Cartesian tensor |
| CTensorAverage | Calculates averages of all components of a Tensor-valued variable |
| CTextFileIArchive | Loading archive for text istream |
| CTextFileOArchive | Saving archive for character based ostream |
| CTimer | Wall clock timer |
| CVector | A Vector is a Cartesian vector |
| CXdrFileIArchive | Loading / input archive for binary XDR file |
| CXdrFileOArchive | Saving / output archive for binary XDR file |
| CXmlAttribute | Parser for an XML attribute |
| CXmlBase | Base class for classes that parse XML markup tags |
| CXmlEndTag | Parser for an XML end tag |
| CXmlStartTag | Parser for an XML start tag |
| CXmlXmlTag | Parser for an XML file declaration tag (first line in file) |
| CCommandLine | Abstraction of a C array of command line arguments |
| CCompositeTestRunner | A TestRunner comprised of one or more child TestRunners |
| CParamFileTest | A UnitTest with a built-in input file |
| CTestA | This example shows how to construct and run a single UnitTest class |
| CTestB | Trivial UnitTest B |
| CTestException | An exception thrown by a failed unit test |
| CTestRunner | Abstract base class for classes that run tests |
| CUnitTest | UnitTest is a base class for classes that define unit tests |
| CUnitTestRunner | Template for a TestRunner that runs test methods of an associated UnitTest |
