| ►CUtil::Array< Atom > | |
| CDdMd::AtomArray | An array of Atom objects |
| ►CUtil::Array< DdMd::Atom * > | |
| CUtil::DArray< DdMd::Atom * > | |
| ►CUtil::Array< DdMd::AtomType > | |
| CUtil::DArray< DdMd::AtomType > | |
| CUtil::RArray< DdMd::AtomType > | |
| ►CUtil::Array< DdMd::CellAtom > | |
| CUtil::DArray< DdMd::CellAtom > | |
| ►CUtil::Array< DdMd::Group< N > * > | |
| CUtil::DArray< DdMd::Group< N > * > | |
| ►CUtil::Array< DdMd::Group< N > > | |
| CUtil::DArray< DdMd::Group< N > > | |
| ►CUtil::Array< double > | |
| CUtil::DArray< double > | |
| ►CUtil::Array< float > | |
| CUtil::DArray< float > | |
| ►CUtil::Array< int > | |
| CUtil::DArray< int > | |
| ►CUtil::Array< long > | |
| CUtil::DArray< long > | |
| ►CUtil::Array< McMd::Atom * > | |
| CUtil::DArray< McMd::Atom * > | |
| ►CUtil::Array< McMd::AtomType > | |
| CUtil::DArray< McMd::AtomType > | |
| ►CUtil::Array< McMd::Cell > | |
| CUtil::DArray< McMd::Cell > | |
| ►CUtil::Array< McMd::CellTag > | |
| CUtil::DArray< McMd::CellTag > | |
| ►CUtil::Array< McMd::ClusterLink > | |
| CUtil::DArray< McMd::ClusterLink > | |
| ►CUtil::Array< McMd::Group > | |
| CUtil::DArray< McMd::Group > | |
| ►CUtil::Array< McMd::Link > | |
| CUtil::DArray< McMd::Link > | |
| ►CUtil::Array< McMd::Molecule > | |
| CUtil::DArray< McMd::Molecule > | |
| ►CUtil::Array< McMd::System::MoleculeSet > | |
| CUtil::DArray< McMd::System::MoleculeSet > | |
| ►CUtil::Array< Product > | |
| CUtil::DArray< Product > | |
| ►CUtil::Array< Simp::MultiHarmonicDihedral::Parameter > | |
| CUtil::DArray< Simp::MultiHarmonicDihedral::Parameter > | |
| ►CUtil::Array< Simp::Species > | |
| CUtil::DArray< Simp::Species > | |
| ►CUtil::Array< Simp::SpeciesGroup > | |
| CUtil::DArray< Simp::SpeciesGroup > | |
| ►CUtil::Array< std::complex< double > > | |
| CUtil::DArray< std::complex< double > > | |
| ►CUtil::Array< std::ofstream > | |
| CUtil::DArray< std::ofstream > | |
| ►CUtil::Array< Tag > | |
| CUtil::DArray< Tag > | |
| ►CUtil::Array< Tools::Atom * > | |
| CUtil::DArray< Tools::Atom * > | |
| ►CUtil::Array< Tools::CellAtom > | |
| CUtil::DArray< Tools::CellAtom > | |
| ►CUtil::Array< Type > | |
| CUtil::DArray< Type > | |
| ►CUtil::Array< Util::ArraySet > | |
| CUtil::DArray< Util::ArraySet > | |
| ►CUtil::Array< Util::ArrayStack< McMd::Molecule > > | |
| CUtil::DArray< Util::ArrayStack< McMd::Molecule > > | |
| ►CUtil::Array< Util::AutoCorr< double, double > > | |
| CUtil::DArray< Util::AutoCorr< double, double > > | |
| ►CUtil::Array< Util::AutoCorr< std::complex< double >, std::complex< double > > > | |
| CUtil::DArray< Util::AutoCorr< std::complex< double >, std::complex< double > > > | |
| ►CUtil::Array< Util::Average > | |
| CUtil::DArray< Util::Average > | |
| ►CUtil::Array< Util::DArray< double > > | |
| CUtil::DArray< Util::DArray< double > > | |
| ►CUtil::Array< Util::DArray< Util::DSArray< Util::Pair< McMd::Atom * > > > > | |
| CUtil::DArray< Util::DArray< Util::DSArray< Util::Pair< McMd::Atom * > > > > | |
| ►CUtil::Array< Util::Distribution > | |
| CUtil::DArray< Util::Distribution > | |
| ►CUtil::Array< Util::DSArray< Util::Pair< McMd::Atom * > > > | |
| CUtil::DArray< Util::DSArray< Util::Pair< McMd::Atom * > > > | |
| ►CUtil::Array< Util::FSArray > | |
| CUtil::DArray< Util::FSArray > | |
| ►CUtil::Array< Util::IntVector > | |
| CUtil::DArray< Util::IntVector > | |
| ►CUtil::Array< Util::Pair< int > > | |
| CUtil::DArray< Util::Pair< int > > | |
| ►CUtil::Array< Util::Polynomial< double > > | |
| CUtil::DArray< Util::Polynomial< double > > | |
| ►CUtil::Array< Util::RingBuffer< Data > > | |
| CUtil::DArray< Util::RingBuffer< Data > > | |
| ►CUtil::Array< Util::RingBuffer< Util::Tensor > > | |
| CUtil::DArray< Util::RingBuffer< Util::Tensor > > | |
| ►CUtil::Array< Util::RingBuffer< Util::Vector > > | |
| CUtil::DArray< Util::RingBuffer< Util::Vector > > | |
| ►CUtil::Array< Util::SSet > | |
| CUtil::DArray< Util::SSet > | |
| ►CUtil::Array< Util::Tensor > | |
| CUtil::DArray< Util::Tensor > | |
| ►CUtil::Array< Util::Vector > | |
| CUtil::DArray< Util::Vector > | |
| CUtil::ArrayStack< DdMd::Atom > | |
| CUtil::ArrayStack< DdMd::Group< N > > | |
| CUtil::ArrayStack< McMd::Link > | |
| CUtil::ArrayStack< McMd::Molecule > | |
| ►CUtil::AutoCorrStage< Tensor, double > | |
| CUtil::AutoCorrelation< Tensor, double > | |
| ►CUtil::AutoCorrStage< Util::Tensor, double > | |
| CUtil::AutoCorrelation< Util::Tensor, double > | |
| CCommandLine | Abstraction of a C array of command line arguments |
| ►CUtil::ConstPArrayIterator< Atom > | |
| CDdMd::ConstAtomIterator | Const iterator for all atoms owned by an AtomStorage |
| CDdMd::ConstGhostIterator | Iterator for all ghost atoms owned by an AtomStorage |
| ►CUtil::ConstPArrayIterator< Group< N > > | |
| CDdMd::ConstGroupIterator< N > | Const iterator for all Group < N > objects owned by a GroupStorage < N > |
| ►CCoulombPotential | |
| CMcMd::McCoulombPotential | Long-range part of Coulomb potential for MC |
| CDdMd::Atom | A point particle in an MD simulation |
| CDdMd::AtomContext | Descriptor for context of an Atom within a molecule and species |
| CDdMd::AtomMap | Associative container for finding atoms identified by integer id |
| CDdMd::AtomType | Descriptor for a type of Atom |
| CDdMd::Cell | A single Cell in a CellList |
| CDdMd::CellAtom | Data for an atom in a CellList |
| CDdMd::CellList | A cell list used only to identify nearby atom pairs |
| CDdMd::DdTimer | Class for measuring time intervals |
| CDdMd::Exchanger | Class for exchanging Atoms, Ghosts and Groups between processors |
| CDdMd::Group< N > | A group of covalently interacting atoms |
| ►CDdMd::GroupExchanger | Interface for a GroupStorage<N> for use in Exchanger |
| CDdMd::GroupStorage< N > | A container for all the Group<N> objects on this processor |
| ►CDdMd::GroupStorage< 2 > | |
| CDdMd::BondStorage | Container for for Group<2> (bond) objects |
| ►CDdMd::GroupStorage< 3 > | |
| CDdMd::AngleStorage | Container for Group<3> (angle) objects |
| ►CDdMd::GroupStorage< 4 > | |
| CDdMd::DihedralStorage | Container for Group<4> (dihedral) objects |
| CDdMd::Mask | Set of Atoms for which pair interactions with a parent Atom are "masked" |
| CDdMd::Modifier::Flags | Bit flag constants associated with particular actions |
| CDdMd::PairIterator | Iterator for pairs in a PairList |
| CDdMd::PairList | A Verlet nonbonded pair list |
| CDdMd::Plan | Communication plan |
| ►CDdMd::SimulationAccess | Provides access to members of Simulation object |
| ►CDdMd::Integrator | An Integrator numerically integrates the equations of motion |
| ►CDdMd::TwoStepIntegrator | A two-step velocity-Verlet style integrator |
| CDdMd::NphIntegrator | A reversible, symplectic NPH integrator (Anderson barostat) |
| CDdMd::NptIntegrator | A reversible symplectic NPT integrator |
| CDdMd::NveIntegrator | A velocity-Verlet constant energy integrator |
| CDdMd::NvtIntegrator | A Nose-Hoover constant temperature, constant volume integrator |
| CDdMd::NvtLangevinIntegrator | A NVT molecular dynamics integrator with a Langevin thermostat |
| ►CUtil::DSArray< Group< N > > | |
| CTools::GroupStorage< 2 > | |
| CTools::GroupStorage< 3 > | |
| CTools::GroupStorage< 4 > | |
| CTools::GroupStorage< N > | A container for Group<N> objects |
| CUtil::DSArray< int > | |
| CUtil::DSArray< Tools::Atom > | |
| CUtil::DSArray< Tools::Molecule > | |
| CUtil::DSArray< Util::Pair< McMd::Atom * > > | |
| ►CUtil::Factory< Analyzer > | |
| CDdMd::AnalyzerFactory | Factory for DdMd::Analyzer objects |
| ►CMcMd::McAnalyzerFactory | AnalyzerFactory for an McSimulation |
| CMcMd::SliplinkMcAnalyzerFactory | Custom AnalyzerFactory for an McSimulation |
| ►CMcMd::MdAnalyzerFactory | AnalyzerFactory for an MdSimulation |
| CMcMd::SliplinkMdAnalyzerFactory | Custom AnalyzerFactory for an MdSimulation |
| CMcMd::SystemAnalyzerFactory | AnalyzerFactory for any System (for mc or md) |
| CTools::ProcessorAnalyzerFactory | Factory for Tools::Analyzer objects |
| ►CUtil::Factory< AnglePotential > | |
| CDdMd::AngleFactory | Factory for AnglePotential objects |
| CMcMd::AngleFactory | Factory for subclasses of AnglePotential |
| ►CUtil::Factory< BondPotential > | |
| CDdMd::BondFactory | Factory for BondPotential objects |
| CMcMd::BondFactory | Factory for BondPotential objects |
| CMcMd::LinkFactory | Factory for subclasses of MdBondPotential or McBondPotential |
| ►CUtil::Factory< Command > | |
| CMcMd::McCommandFactory | CommandFactory for an McSimulation |
| CMcMd::MdCommandFactory | CommandFactory for an MdSimulation |
| ►CUtil::Factory< ConfigIo > | |
| CDdMd::ConfigIoFactory | Default Factory for subclasses of ConfigIo |
| CMcMd::ConfigIoFactory | Default Factory for subclasses of ConfigIo |
| ►CUtil::Factory< ConfigReader > | |
| CTools::ConfigReaderFactory | Default Factory for subclasses of ConfigReader |
| ►CUtil::Factory< ConfigWriter > | |
| CTools::ConfigWriterFactory | Default Factory for subclasses of ConfigWriter |
| CUtil::Factory< DdMd::AnglePotential > | |
| CUtil::Factory< DdMd::BondPotential > | |
| CUtil::Factory< DdMd::ConfigIo > | |
| CUtil::Factory< DdMd::DihedralPotential > | |
| CUtil::Factory< DdMd::ExternalPotential > | |
| CUtil::Factory< DdMd::Integrator > | |
| CUtil::Factory< DdMd::PairPotential > | |
| ►CUtil::Factory< DihedralPotential > | |
| CDdMd::DihedralFactory | Factory for DihedralPotential objects |
| CMcMd::DihedralFactory | Factory for subclasses of DihedralPotential |
| ►CUtil::Factory< ExternalPotential > | |
| CDdMd::ExternalFactory | Factory for ExternalPotential objects |
| CMcMd::ExternalFactory | Factory for subclasses MdExternalPotential or McExternalPotential |
| ►CUtil::Factory< Integrator > | |
| CDdMd::IntegratorFactory | Factory for subclasses of Integrator (i.e., MD integrators) |
| CUtil::Factory< McMd::AnglePotential > | |
| CUtil::Factory< McMd::BondPotential > | |
| CUtil::Factory< McMd::ConfigIo > | |
| CUtil::Factory< McMd::DihedralPotential > | |
| CUtil::Factory< McMd::ExternalPotential > | |
| CUtil::Factory< McMd::MdIntegrator > | |
| CUtil::Factory< McMd::Perturbation > | |
| CUtil::Factory< McMd::TrajectoryReader > | |
| ►CUtil::Factory< McMove > | |
| ►CMcMd::McMoveFactory | McMoveFactory for an McSimulation |
| CMcMd::SliplinkMcMoveFactory | Custom McMoveFactory |
| ►CUtil::Factory< MdCoulombPotential > | |
| CMcMd::CoulombFactory | Factory for CoulombPotential objects |
| ►CUtil::Factory< MdIntegrator > | |
| CMcMd::MdIntegratorFactory | Default Factory for subclasses of MdIntegrator |
| ►CUtil::Factory< Modifier > | |
| CDdMd::ModifierFactory | Factory for DdMd::Modifier objects |
| ►CUtil::Factory< PairPotential > | |
| CDdMd::PairFactory | Factory for PairPotential objects |
| ►CUtil::Factory< Perturbation > | |
| CMcMd::McPerturbationFactory | Default Factory for subclasses of Perturbation |
| ►CUtil::Factory< Simp::Species > | |
| CMcMd::SpeciesFactory | Default Factory for subclasses of Species |
| ►CUtil::Factory< TrajectoryReader > | |
| CMcMd::TrajectoryReaderFactory | Default Factory for subclasses of TrajectoryReader |
| CTools::TrajectoryReaderFactory | Default Factory for subclasses of TrajectoryReader |
| CUtil::FArray< bool, Dimension > | |
| ►CUtil::FArray< Data, 2 > | |
| CUtil::Pair< Data > | An array of exactly 2 objects |
| ►CUtil::FArray< int, 2 > | |
| CUtil::Pair< int > | |
| ►CUtil::FArray< McMd::Atom *, 2 > | |
| CUtil::Pair< McMd::Atom * > | |
| CUtil::FArray< Type, N > | |
| CUtil::FArray< Util::Average, Dimension *(Dimension+1)/2 > | |
| CUtil::FArray< Util::Average, Dimension *Dimension > | |
| CUtil::FSArray< Atom *, MaxNeighbor > | |
| CUtil::FSArray< std::pair< int, int >, OffSetArrayCapacity > | |
| CUtil::FSArray< Util::Vector, Dimension > | |
| CUtil::GArray< DCMPLX > | |
| CUtil::GArray< DdMd::Atom * > | |
| CUtil::GArray< DdMd::Cell > | |
| ►CUtil::GArray< double > | |
| CUtil::Polynomial< double > | |
| CUtil::GArray< int > | |
| CUtil::GArray< McMd::Cluster > | |
| ►CUtil::GArray< T > | |
| CUtil::Polynomial< T > | A Polynomial (i.e, |
| CUtil::GArray< Tools::Cell > | |
| CUtil::GArray< Util::AutoCorrStage< Data, Product > * > | |
| CUtil::GArray< Util::AutoCorrStage< Tensor, double > * > | |
| CUtil::GArray< Util::AutoCorrStage< Util::Tensor, double > * > | |
| CUtil::GArray< Util::IntVector > | |
| CUtil::GArray< Util::Vector > | |
| CUtil::GridArray< DCMPLX > | |
| CUtil::GridArray< double > | |
| CUtil::GridArray< Util::Vector > | |
| CUtil::GStack< McMd::ClusterLink > | |
| CUtil::IFunctor<> | |
| ►CUtil::Matrix< DdMd::Atom * > | |
| CUtil::DMatrix< DdMd::Atom * > | |
| ►CUtil::Matrix< double > | |
| CUtil::DMatrix< double > | |
| CUtil::FMatrix< double, Dimension, 2 > | |
| ►CUtil::Matrix< int > | |
| CUtil::DMatrix< int > | |
| CUtil::FMatrix< int, Dimension, 2 > | |
| CUtil::FMatrix< int, Dimension, Dimension > | |
| ►CUtil::Matrix< std::complex< double > > | |
| CUtil::DMatrix< std::complex< double > > | |
| ►CUtil::Matrix< Type > | |
| CUtil::DMatrix< Type > | |
| CMcMd::Activate | Static member functions to de-active and re-active atoms |
| CMcMd::Atom | A point particle within a Molecule |
| CMcMd::AtomType | Descriptor for a type of Atom |
| CMcMd::Cell | A set of Atoms in a small region |
| CMcMd::CellList | A cell list for Atom objects in a periodic system boundary |
| CMcMd::CellTag | Location of the pointer to a particular Atom in a CellList |
| CMcMd::Cluster | Cluster of molecules |
| CMcMd::ClusterIdentifier | Identifies clusters of molecules, such as micelles |
| CMcMd::ClusterLink | Molecule in a cluster |
| ►CMcMd::ConfigIo | System configuration file reader and writer |
| CMcMd::DdMdConfigIo | ConfigIo for DdMd data files |
| CMcMd::LammpsConfigIo | ConfigIo for Lammps data files |
| ►CMcMd::McMdConfigIo | Base class for default Mc and Md configIos |
| CMcMd::McConfigIo | ConfigIo for MC simulations (no atom velocities) |
| CMcMd::MdConfigIo | ConfigIo for MD simulations (includes velocities) |
| CMcMd::SmpConfigIo | Common configuration file format for simpatico |
| ►CMcMd::EnergyCalculator | Interface for a class that calculates a total energy |
| ►CMcMd::AnglePotential | Interface for a Angle Interaction |
| CMcMd::AnglePotentialImpl< Interaction > | Implementation template for an AnglePotential |
| ►CMcMd::BondPotential | Abstract Bond Potential class |
| CMcMd::BondPotentialImpl< Interaction > | Implementation template for a BondPotential |
| CMcMd::LinkPotentialImpl< Interaction > | Template implementation of an BondPotential for links |
| ►CMcMd::DihedralPotential | Interface for a Dihedral Potential |
| CMcMd::DihedralPotentialImpl< Interaction > | Implementation template for an DihedralPotential |
| ►CMcMd::ExternalPotential | Abstract External Potential class |
| CMcMd::ExternalPotentialImpl< Interaction > | Template implementation of ExternalPotential |
| ►CMcMd::PairPotential | Interface for a Pair Potential |
| ►CMcMd::McPairPotential | A PairPotential for MC simulations (abstract) |
| CMcMd::McPairPotentialImpl< Interaction > | Implementation template for an McPairPotential |
| ►CMcMd::MdPairPotential | An PairPotential for MD simulation |
| CMcMd::MdEwaldPairPotentialImpl< Interaction > | Implementation of a pair potential for a charged system |
| CMcMd::MdPairPotentialImpl< Interaction > | Implementation template for an MdPairPotential |
| ►CMcMd::SpecialPotential | Specialized potential for an MD simulation |
| CMcMd::ColVarPotentialTmpl< ColVarType, BiasType > | SpecialPotential that is a function of a collective variable |
| CMcMd::SpecialPotentialFacade< PotentialType, FactoryType > | SpecialPotential interface to an existing potential |
| ►CMcMd::SpecialPotentialFacade< ExternalPotential, ExternalFactory > | |
| CMcMd::SpecialExternal | Potential for testing purposes |
| CMcMd::EwaldRSpaceAccumulator | Utility class to store r-space Coulomb energy and stress |
| ►CMcMd::Generator | Generates initial configurations for molecules of one species |
| CMcMd::LinearGenerator | Generates random configurations for linear molecules |
| CMcMd::PointGenerator | Generator for monoatomic molecules (atoms) |
| CMcMd::Group< NAtom > | A sequence of NAtom covalently interacting atoms |
| CMcMd::Link | A Link represents a crosslink between two Atoms |
| CMcMd::LinkAddEvent | Event signalling addition of Link to the LinkMaster |
| CMcMd::LinkRemoveEvent | Event signalling removal of a Link from the LinkMaster |
| CMcMd::LinkResetEvent | Event signalling reset of Link to the LinkMaster |
| CMcMd::Mask | Set of Atoms for which pair interactions with a target Atom are "masked" |
| CMcMd::Molecule | A physical molecule (a set of covalently bonded Atoms) |
| CMcMd::MoleculeSetObserver | Observer interface |
| CMcMd::PairFactory | Factory for subclasses MdPairPotential or McPairPotential |
| CMcMd::PairIterator | Iterator for pairs in a PairList |
| CMcMd::PairSelector | Selection rule for pairs of Atoms |
| CMcMd::ReSetAtomEvent | Event signalling the reset of an atom from the LinkMaster |
| CMcMd::SliplinkMcModule | Module for slip link simulation |
| CMcMd::SpecialFactory | Factory for specialized subclasses of SpecialPotential |
| ►CMcMd::SpeciesMutator | Mix-in class for mutable subclasses of Species |
| CMcMd::HomopolymerSG | A Homopolymer with a mutable type, for semigrand ensemble |
| CMcMd::LinearSG | A mutable linear polymer, for semigrand ensemble |
| ►CMcMd::StressCalculator | Interface for a stress calculator |
| CMcMd::AnglePotential | Interface for a Angle Interaction |
| CMcMd::BondPotential | Abstract Bond Potential class |
| CMcMd::DihedralPotential | Interface for a Dihedral Potential |
| CMcMd::PairPotential | Interface for a Pair Potential |
| CMcMd::SpecialPotential | Specialized potential for an MD simulation |
| ►CMcMd::SystemInterface | An interface to a System |
| CMcMd::AnglePotentialImpl< Interaction > | Implementation template for an AnglePotential |
| CMcMd::BondPotentialImpl< Interaction > | Implementation template for a BondPotential |
| ►CMcMd::DeformCommand | Command to deform the unit cell |
| CMcMd::McDeformCommand | Command to deform the unit cell |
| CMcMd::MdDeformCommand | Command to deform the unit cell |
| CMcMd::DihedralPotentialImpl< Interaction > | Implementation template for an DihedralPotential |
| CMcMd::ExternalPotentialImpl< Interaction > | Template implementation of ExternalPotential |
| CMcMd::LinkPotentialImpl< Interaction > | Template implementation of an BondPotential for links |
| CMcMd::McPairPotential | A PairPotential for MC simulations (abstract) |
| CMcMd::McSystemInterface | An interface to an McSystem |
| CMcMd::MdPairPotential | An PairPotential for MD simulation |
| CMcMd::MdSystemInterface | An interface to an MdSystem |
| ►CMcMd::TrajectoryReader | Trajectory file reader (base class) |
| CMcMd::DCDTrajectoryReader | TrajectoryReader for CHARMM ".dcd" data files |
| CMcMd::DdMdTrajectoryReader | TrajectoryReader for a DdMd trajectory file |
| CMcMd::LammpsDumpReader | TrajectoryReader for Lammps dump trajectory files |
| ►CUtil::Notifier< LinkAddEvent > | |
| CMcMd::LinkMaster | Manages all Link objects in a System |
| ►CUtil::Notifier< LinkRemoveEvent > | |
| CMcMd::LinkMaster | Manages all Link objects in a System |
| ►CUtil::Notifier< LinkResetEvent > | |
| CMcMd::LinkMaster | Manages all Link objects in a System |
| ►CUtil::Notifier< ReSetAtomEvent > | |
| CMcMd::LinkMaster | Manages all Link objects in a System |
| ►CUtil::Notifier< sendRecvPair > | |
| CMcMd::ReplicaMove | Replica exchange Monte Carlo move using Gibbs sampling |
| ►CUtil::Observer< LinkAddEvent > | |
| CMcMd::LinkLifeTime | LinkLifeTime evaluates how long the slip-springs live |
| CMcMd::LinkLTPos | LinkLTPos evaluates how long the slip-springs live as a function of position along the chain |
| CMcMd::LinkMSD | Evaluates msd of link ends along the chains |
| ►CUtil::Observer< LinkRemoveEvent > | |
| CMcMd::LinkLifeTime | LinkLifeTime evaluates how long the slip-springs live |
| CMcMd::LinkLTPos | LinkLTPos evaluates how long the slip-springs live as a function of position along the chain |
| CMcMd::LinkMSD | Evaluates msd of link ends along the chains |
| CUtil::Observer< LinkResetEvent > | |
| ►CUtil::Observer< ReSetAtomEvent > | |
| CMcMd::LinkLTPos | LinkLTPos evaluates how long the slip-springs live as a function of position along the chain |
| CUtil::Observer< sendRecvPair > | |
| ►CUtil::PArrayIterator< Atom > | |
| CDdMd::AtomIterator | Iterator for all atoms owned by an AtomStorage |
| CDdMd::GhostIterator | Iterator for all ghost atoms owned by an AtomStorage |
| ►CUtil::PArrayIterator< Group< N > > | |
| CDdMd::GroupIterator< N > | Iterator for all Group < N > objects owned by a GroupStorage< N > |
| CUtil::RingBuffer< double > | |
| CUtil::RingBuffer< std::complex< double > > | |
| CUtil::RingBuffer< Tensor > | |
| CUtil::RingBuffer< Util::Tensor > | |
| CUtil::RingBuffer< Util::Vector > | |
| CUtil::Setable< double > | |
| CUtil::Setable< int > | |
| CUtil::Setable< Util::DMatrix< double > > | |
| CUtil::Setable< Util::Tensor > | |
| ►CSimp::Bend | A Bend calculates the angle between two vectors |
| CSimp::BendForce | A BendForce computes derivatives of the angle between two vectors |
| CSimp::MonoclinicBoundary | A monoclinic periodic unit cell |
| ►CSimp::OrthoRegion | A region with orthogonal edges parallel to the x, y, and z axes |
| CSimp::OrthorhombicBoundary | An orthorhombic periodic unit cell |
| CSimp::SpeciesGroup< NAtom > | A Group of covalently interacting atoms within any molecule of one Species |
| ►CSimp::Torsion | Computes dihedral / torsion angle involving 3 bonds |
| CSimp::TorsionForce | Computes derivatives of dihedral angle with respect to bond vectors |
| ►CStressAutoCorrelation | |
| CMcMd::McStressAutoCorrelation | Analyzer to calculate average isotropic pressure |
| ►CUtil::SymmetryGroup< PointSymmetry > | |
| CUtil::PointGroup | Group of crystal symmetries with no translations |
| CTestException | An exception thrown by a failed unit test |
| ►CTestRunner | Abstract base class for classes that run tests |
| CCompositeTestRunner | A TestRunner comprised of one or more child TestRunners |
| CUnitTestRunner< UnitTestClass > | Template for a TestRunner that runs test methods of an associated UnitTest |
| CTools::Atom | A point particle in an MD simulation |
| CTools::AtomStorage | Container for a set of atoms |
| CTools::Cell | A single cell in a CellList |
| CTools::CellAtom | Data for an atom in a CellList |
| CTools::CellList | A cell list used only to identify nearby atom pairs |
| CTools::Group< N > | A group of covalently interacting atoms |
| CTools::Molecule | An Molecule has a sequence of atoms, and belongs to an Species |
| CTools::Species | A set of identical molecules |
| CTools::TypeMap | Map between type names and type ids |
| ►CUnitTest | UnitTest is a base class for classes that define unit tests |
| CParamFileTest | A UnitTest with a built-in input file |
| CTestA | This example shows how to construct and run a single UnitTest class |
| CTestA | This example shows how to construct and run a single UnitTest class |
| CTestA | This example shows how to construct and run a single UnitTest class |
| CTestB | Trivial UnitTest B |
| CUtil::Ar1Process | Generator for a discrete AR(1) Markov process |
| ►CUtil::Array< Data > | Array container class template |
| CUtil::RArray< McMd::Atom > | |
| CUtil::DArray< Data > | Dynamically allocatable contiguous array template |
| CUtil::RArray< Data > | An Array that acts as a reference to another Array or C array |
| CUtil::ArrayIterator< Data > | Forward iterator for an Array or a C array |
| CUtil::ArrayStack< Data > | A stack of fixed capacity |
| ►CUtil::AutoCorrStage< Data, Product > | Hierarchical auto-correlation function algorithm |
| CUtil::AutoCorrelation< Data, Product > | Auto-correlation function, using hierarchical algorithm |
| ►CUtil::AverageStage | Evaluate average with hierarchical blocking error analysis |
| CUtil::Average | Calculates the average and variance of a sampled property |
| CUtil::BinaryFileIArchive | Saving archive for binary istream |
| CUtil::BinaryFileOArchive | Saving / output archive for binary ostream |
| CUtil::Binomial | Class for binomial coefficients (all static members) |
| CUtil::Bit | Represents a specific bit location within an unsigned int |
| CUtil::Bool | Wrapper for an bool value, for formatted ostream output |
| CUtil::CardinalBSpline | A cardinal B-spline basis function |
| CUtil::Constants | Mathematical constants |
| CUtil::ConstArrayIterator< Data > | Forward const iterator for an Array or a C array |
| CUtil::ConstPArrayIterator< Data > | Forward iterator for a PArray |
| CUtil::Dbl | Wrapper for a double precision number, for formatted ostream output |
| CUtil::DSArray< Data > | Dynamically allocated array with variable logical size |
| CUtil::Exception | A user-defined exception |
| CUtil::Factory< Data > | Factory template |
| CUtil::FArray< Data, Capacity > | A fixed size (static) contiguous array template |
| CUtil::FlagSet | A set of boolean variables represented by characters |
| CUtil::FlexPtr< T > | A pointer that may or may not own the object to which it points |
| CUtil::Format | Base class for output wrappers for formatted C++ ostream output |
| CUtil::FPArray< Data, Capacity > | Statically allocated pointer array |
| CUtil::FSArray< Data, Capacity > | A fixed capacity (static) contiguous array with a variable logical size |
| CUtil::GArray< Data > | An automatically growable array, analogous to a std::vector |
| CUtil::Grid | A grid of points indexed by integer coordinates |
| CUtil::GridArray< Data > | Multi-dimensional array with the dimensionality of space |
| CUtil::GStack< Data > | An automatically growable Stack |
| ►CUtil::IFunctor< T > | Interface for functor that wraps a void function with one argument (abstract) |
| CUtil::MethodFunctor< Object, T > | Functor that wraps a one-argument class member function |
| ►CUtil::IFunctor< void > | Interface for functor that wraps a void function with no arguments (abstract) |
| CUtil::MethodFunctor< Object, void > | Functor that wraps a class member function with no arguments |
| CUtil::Int | Wrapper for an int, for formatted ostream output |
| CUtil::IntVector | An IntVector is an integer Cartesian vector |
| ►CUtil::Label | A label string in a file format |
| CUtil::OptionalLabel | An optional Label string in a file format |
| CUtil::List< Data > | Linked list class template |
| CUtil::ListArray< Data > | An array of objects that are accessible by one or more linked List objects |
| CUtil::ListIterator< Data > | Bidirectional iterator for a List |
| CUtil::Lng | Wrapper for a long int, for formatted ostream output |
| CUtil::Log | A static class that holds a log output stream |
| ►CUtil::Matrix< Data > | Two-dimensional array container template (abstract) |
| CUtil::FMatrix< Util::GPArray< DdMd::Atom >, Dimension, 2 > | |
| CUtil::DMatrix< Data > | Dynamically allocated Matrix |
| CUtil::FMatrix< Data, M, N > | Fixed Size Matrix |
| CUtil::Memory | Provides method to allocate array |
| CUtil::MemoryCounter | Archive to computed packed size of a sequence of objects, in bytes |
| CUtil::MemoryIArchive | Input archive for packed heterogeneous binary data |
| CUtil::MemoryOArchive | Save archive for packed heterogeneous binary data |
| ►CUtil::MpiFileIo | Identifies whether this processor may do file I/O |
| ►CUtil::ParamComponent | Abstract base class for classes that input and ouput parameters to file |
| CUtil::Begin | Beginning line of a composite parameter block |
| CUtil::Blank | An empty line within a parameter file |
| CUtil::End | End bracket of a ParamComposite parameter block |
| ►CUtil::ParamComposite | An object that can read multiple parameters from file |
| CUtil::AutoCorr< double, double > | |
| CUtil::AutoCorr< std::complex< double >, std::complex< double > > | |
| CUtil::AutoCorrArray< Util::Tensor, double > | |
| CUtil::AutoCorrArray< Util::Vector, double > | |
| CUtil::AutoCorrelation< Tensor, double > | |
| CUtil::AutoCorrelation< Util::Tensor, double > | |
| ►CDdMd::Analyzer | Abstract base for periodic output and/or analysis actions |
| ►CDdMd::AutoCorrAnalyzer< Tensor, double > | |
| CDdMd::BondTensorAutoCorr | Calculate stress autocorrelation function |
| CDdMd::StressAutoCorrelation | Compute the shear stress autocorrelation function |
| CDdMd::AutoCorrAnalyzer< Data, Product > | Compute an autocorrelation function for a sequence of Data values |
| ►CDdMd::AverageAnalyzer | Analyze average and block averages of a single floating point variable |
| CDdMd::ExternalEnergyAnalyzer | Output and evaluate average of external energy |
| CDdMd::KineticEnergyAnalyzer | Output and evaluate average of kinetic energy |
| CDdMd::PairEnergyAnalyzer | Compute and analyze pair energies |
| CDdMd::PressureAnalyzer | Sample and evaluate average of total pressure |
| CDdMd::ConfigWriter | Periodically write simulation configuration to a new file |
| CDdMd::EnergyAnalyzer | Compute averages and output block averages of energy components |
| CDdMd::ExternalEnergyAverage | Periodically write simulation energies to Log output |
| CDdMd::LogEnergy | Periodically write simulation energies to Log output |
| CDdMd::OrderParamNucleation | 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 |
| CDdMd::OutputBoxdim | Periodically write Boundary dimensions to file |
| CDdMd::OutputEnergy | Periodically write simulation energies to file |
| CDdMd::OutputPairEnergies | Periodically write pair energies to file |
| CDdMd::OutputPressure | Periodically write (scalar) pressure to file |
| CDdMd::OutputStressTensor | Periodically write (tensor) StressTensor to file |
| CDdMd::OutputTemperature | Periodically output kinetic temperature to file |
| CDdMd::PairEnergyAverage | Compute average of pair energy |
| CDdMd::StressAutoCorr | Compute stress autocorrelation function for a liquid |
| ►CDdMd::StructureFactor | StructureFactor evaluates structure factors in Fourier space |
| CDdMd::StructureFactorGrid | StructureFactorGrid evaluates structure factors in Fourier space |
| ►CDdMd::SymmTensorAverageAnalyzer | Analyzer that computes average of a sequence of symmetric Tensor values |
| CDdMd::StressAnalyzer | Output and evaluate average of stress tensor |
| CDdMd::VirialStressAnalyzer | Output and evaluate average of virial stress tensor |
| CDdMd::TensorAverageAnalyzer | Analyzer that computes averages and block averages of a single Tensor |
| ►CDdMd::TrajectoryWriter | Base class to write a trajectory to a single file |
| CDdMd::DdMdGroupTrajectoryWriter | Native binary trajectory format for ddSim, for one group |
| CDdMd::DdMdTrajectoryWriter | Native binary trajectory format for ddSim |
| CDdMd::LammpsDumpWriter | Write a trajectory in the Lammps dump format |
| CDdMd::VanHove | Evaluates the van Hove function S(k,t) for one or more wavevector k |
| CDdMd::VirialStressTensor | Periodically write virial stress tensor components to file |
| CDdMd::VirialStressTensorAverage | Compute average and output block averages of virial stress tensor |
| CDdMd::AtomCollector | Class for collecting Atoms from processors to master processor |
| CDdMd::AtomDistributor | Class for distributing Atoms among processors |
| CDdMd::AtomStorage | A container for all the atoms and ghost atoms on this processor |
| CDdMd::Buffer | Buffer for interprocessor communication |
| ►CDdMd::ConfigIo | Abstract reader/writer for configuration files |
| CDdMd::DdMdConfigIo | Native / default format for configuration files |
| CDdMd::DdMdOrderedConfigIo | Native / default format for configuration files |
| CDdMd::LammpsConfigIo | Lammps data file format for configuration files |
| CDdMd::SerializeConfigIo | Save / load configuration from / to an archive |
| CDdMd::Domain | Decomposition of the system into domains associated with processors |
| CDdMd::GroupCollector< N > | Class for collecting Groups from processors to master processor |
| CDdMd::GroupDistributor< N > | Class template for distributing Group<N> objects among processors |
| CDdMd::GroupStorage< N > | A container for all the Group<N> objects on this processor |
| CDdMd::Integrator | An Integrator numerically integrates the equations of motion |
| CDdMd::Modifier | A Modifier can modify the time evolution of the simulation |
| ►CDdMd::Potential | A Potential represents a potential energy contribution |
| ►CDdMd::AnglePotential | Abstract base class for computation of angle force and energies |
| CDdMd::AnglePotentialImpl< Interaction > | Implementation template for a AnglePotential |
| ►CDdMd::BondPotential | Abstract base class for computing bond forces and energies |
| CDdMd::BondPotentialImpl< Interaction > | Implementation template for a BondPotential |
| ►CDdMd::DihedralPotential | Abstract base class for computing dihedral forces and energies |
| CDdMd::DihedralPotentialImpl< Interaction > | Implementation template for a DihedralPotential |
| ►CDdMd::ExternalPotential | Calculates external forces and energies for a parent Simulation |
| CDdMd::ExternalPotentialImpl< Interaction > | Implementation template for a ExternalPotential |
| ►CDdMd::PairPotential | Abstract base class for computing nonbonded pair forces and energies |
| CDdMd::PairPotentialImpl< Interaction > | Implementation template for a PairPotential |
| CDdMd::Simulation | Main object for a domain-decomposition MD simulation |
| CDdMd::GroupStorage< 2 > | |
| CDdMd::GroupStorage< 3 > | |
| CDdMd::GroupStorage< 4 > | |
| ►CUtil::Manager< Analyzer > | |
| CDdMd::AnalyzerManager | Manager for a list of Analyzer objects |
| ►CMcMd::AnalyzerManager | Manager for a list of Analyzer objects |
| CMcMd::McAnalyzerManager | Manager for Analyzer objects in an McSimulation |
| CMcMd::MdAnalyzerManager | Manager for Analyzer objects in an MdSimulation |
| ►CTools::AnalyzerManager | Manager for a list of Analyzer objects |
| CTools::ProcessorAnalyzerManager | Manager for a list of Analyzer objects |
| ►CUtil::Manager< Command > | |
| ►CMcMd::CommandManager | Manager for Command objects in an MdSimulation |
| CMcMd::McCommandManager | Command interpreter and Manager for an McSimulation |
| CMcMd::MdCommandManager | Command interpreter and Command Manager for an MdSimulation |
| ►CUtil::Manager< McMove > | |
| CMcMd::McMoveManager | Manager for a set of McMove objects |
| ►CUtil::Manager< Modifier > | |
| CDdMd::ModifierManager | Manager for a set of Modifier objects |
| ►CUtil::Manager< Simp::Species > | |
| CMcMd::SpeciesManager | A Manager for a set of Species objects |
| ►CMcMd::Analyzer | Abstract base for periodic output and/or analysis actions |
| CMcMd::LogProgress | Periodically write step number to a Log file |
| ►CMcMd::SystemAnalyzer< SystemType > | Template for Analyzer associated with one System |
| CMcMd::AverageAnalyzer< SystemType > | AverageAnalyzer averages of total potential energy |
| CMcMd::IntraBondStressAutoCorr< SystemType > | Autocorrelation for bond stress of a molecule |
| CMcMd::IntraBondTensorAutoCorr< SystemType > | Autocorrelation for bond stress of a molecule |
| CMcMd::PressureAverage< SystemType > | PressureAverage evaluates average pressure |
| CMcMd::StressAutoCorr< SystemType > | Compute stress autocorrelation for an isotropic system |
| CMcMd::StressTensorAverage< SystemType > | Periodically write (tensor) StressTensor to file |
| ►CMcMd::SystemAnalyzer< McSystem > | |
| ►CMcMd::AverageAnalyzer< McSystem > | |
| CMcMd::McBondEnergyAverage | McBondEnergyAverage averages of bond potential energy |
| CMcMd::McEnergyAverage | McEnergyAverage averages of total potential energy |
| CMcMd::McExternalEnergyAverage | McExternalEnergyAverage averages of total external energy |
| ►CMcMd::IntraBondStressAutoCorr< McSystem > | |
| CMcMd::McIntraBondStressAutoCorr | Autocorrelation for bond stress of a molecule |
| ►CMcMd::IntraBondTensorAutoCorr< McSystem > | |
| CMcMd::McIntraBondTensorAutoCorr | Autocorrelation for bond stress of a molecule |
| CMcMd::McEnergyAnalyzer | Compute averages and output block averages of energy components |
| CMcMd::McEnergyOutput | Analyzer to output total potential energy |
| CMcMd::McMuExchange | Exchange chemical potential for semigrand ensemble |
| CMcMd::McNVTChemicalPotential | McNVTChemicalPotential uses configuration bias algorithm to calculate the chemical potential of a linear chain |
| CMcMd::McPairEnergyAverage | McPairEnergyAverage averages of total potential energy |
| CMcMd::McVirialStressTensorAverage | Periodically write (tensor) StressTensor to file |
| CMcMd::SemiGrandDistribution | Calculate distribution of type indices for mutable species |
| CMcMd::TypeDistribution | Calculate distribution of type indices for mutable species |
| ►CMcMd::PressureAverage< McSystem > | |
| CMcMd::McPressureAverage | Analyzer to calculate average isotropic pressure |
| ►CMcMd::SystemAnalyzer< MdSystem > | |
| ►CMcMd::IntraBondStressAutoCorr< MdSystem > | |
| CMcMd::MdIntraBondStressAutoCorr | Autocorrelation for bond stress of a molecule |
| ►CMcMd::IntraBondTensorAutoCorr< MdSystem > | |
| CMcMd::MdIntraBondTensorAutoCorr | Autocorrelation for bond orientation of of a molecule |
| CMcMd::MdEnergyAnalyzer | Compute averages and output block averages of energy components |
| CMcMd::MdEnergyOutput | Analyzer to output total potential and kinetic energies |
| CMcMd::MdKineticEnergyAverage | MdKineticEnergyAverage averages of total kinetic energy |
| CMcMd::MdPairEnergyCoefficients | Analyzer to output the total pair energy and the sum of squares of the monomeric and molecular pair energy |
| CMcMd::MdPotentialEnergyAverage | MdPotentialEnergyAverage averages of total potential energy |
| CMcMd::MdVirialStressTensorAverage | Periodically write (tensor) StressTensor to file |
| ►CMcMd::PressureAverage< MdSystem > | |
| CMcMd::MdPressureAverage | Calculate average scalar pressure for an MdSystem |
| ►CMcMd::StressAutoCorr< MdSystem > | |
| CMcMd::MdStressAutoCorr | Analyzer to calculate average isotropic pressure |
| ►CMcMd::SystemAnalyzer< System > | |
| CMcMd::AtomMSD | Autocorrelation for vector separation of two atoms on a molecule |
| CMcMd::BennettsMethod | Bennett's method estimates free energy difference between two states |
| CMcMd::BlockRadiusGyration | Radius of gyration of different blocks in a molecule |
| CMcMd::BondLengthDist | BondLengthDist evaluates the distribution function of the lengths of the bonds |
| CMcMd::BoundaryAverage | Average of boundary lengths and volume of simulation cell |
| CMcMd::ClusterHistogram | Identify micelle clusters in polymeric systems |
| CMcMd::ComMSD | Molecular center of mass mean squared displacement |
| CMcMd::CompositionProfile | CompositionProfile evaluates the distribution of monomer positions along several user-specified directions |
| CMcMd::ConfigWriter | Periodically dump system configuration to a new file |
| CMcMd::Crosslinker | Analyzer to create crosslinks and output the resulting configuration |
| CMcMd::EndtoEnd | End to end distance of a molecule |
| CMcMd::EndtoEndXYZ | Mean square end to end distance of a molecule |
| CMcMd::G1MSD | Autocorrelation for vector separation of any two monomers on a molecule |
| CMcMd::InterIntraLink | Number of inter and intramolecular links |
| CMcMd::IntraPairAutoCorr | Autocorrelation for vector separation of any two monomers on a molecule |
| ►CMcMd::IntraStructureFactor | Intramolecular contribution to the structure factor S(k) |
| CMcMd::IntraStructureFactorGrid | IntraStructureFactorGrid evaluates structure factors in Fourier space |
| CMcMd::LammpsDumpWriter | Periodically write snapshots to a lammps dump (i.e., trajectory) file |
| CMcMd::LinearRouseAutoCorr | Autocorrelation for Rouse mode coefficients of a linear molecule |
| CMcMd::LinkLengthDist | LinkLengthDist evaluates the distribution function of the lengths of the links |
| CMcMd::LinkLifeTime | LinkLifeTime evaluates how long the slip-springs live |
| CMcMd::LinkLTPos | LinkLTPos evaluates how long the slip-springs live as a function of position along the chain |
| CMcMd::LinkMSD | Evaluates msd of link ends along the chains |
| CMcMd::NLinkAverage | Average number of crosslinks |
| CMcMd::PerturbDerivative | PerturbDerivative returns average value of Perturbation::derivative() |
| CMcMd::RadiusGyration | Radius of gyration of a molecule |
| CMcMd::RDF | RDF evaluates the atomic radial distribution function |
| CMcMd::RingRouseAutoCorr | Autocorrelation for Rouse mode coefficients of a ring molecule |
| CMcMd::SSChainDist | SSChainDist evaluates the distribution of slip-springs along the chains |
| ►CMcMd::StructureFactor | StructureFactor evaluates structure factors in Fourier space |
| CMcMd::StructureFactorGrid | StructureFactorGrid evaluates structure factors in Fourier space |
| ►CMcMd::StructureFactorP | StructureFactorP evaluates partial structure factors in Fourier space |
| CMcMd::StructureFactorPGrid | StructureFactorPGrid evaluates structure factors in Fourier space |
| CMcMd::TrajectoryWriter | Periodically write snapshots to a lammps dump (i.e., trajectory) file |
| CMcMd::VanHove | Evaluates the van Hove function S(k,t) for one or more wavevector k |
| CMcMd::VelProf | Evaluates x-velocity profile as a function of z |
| CMcMd::AnglePotential | Interface for a Angle Interaction |
| CMcMd::BondPotential | Abstract Bond Potential class |
| ►CMcMd::ColVar | Abstract base class for collective variables |
| CMcMd::MdColVar | Collective variables for MD simulation, with atom forces |
| ►CMcMd::Command | Command is an object that can be invoked from the command script |
| CMcMd::DeformCommand | Command to deform the unit cell |
| ►CMcMd::CvBias | Bias potential as a function of a collective variable (CV) |
| CMcMd::HarmonicCvBias | Harmonic function of a collective variable (CV) |
| CMcMd::LinearCvBias | Linear function of a collective variable (CV) |
| CMcMd::DihedralPotential | Interface for a Dihedral Potential |
| CMcMd::ExternalPotential | Abstract External Potential class |
| CMcMd::LinkMaster | Manages all Link objects in a System |
| ►CMcMd::McMove | McMove is an abstract base class for Monte Carlo moves |
| ►CMcMd::SystemMove | An McMove that acts on one McSystem |
| CMcMd::AtomDisplaceMove | Random displacement of one atom |
| ►CMcMd::CfbEndBase | Base class for configuration bias (CFB) end regrowth moves |
| CMcMd::CfbEndMove | Configuration bias end regrowth move for flexible linear chains |
| ►CMcMd::CfbRebridgeBase | Base class configuration bias moves internal segment regrowth moves |
| CMcMd::CfbDoubleRebridgeMove | Configuration bias trimer double rebridge moves, to reconnect two chains |
| CMcMd::CfbRebridgeMove | Config-bias move for internal segment of a flexible linear polymer |
| CMcMd::CfbRingRebridgeMove | Configuration bias rebridge moves for ring molecules |
| CMcMd::CfbReptationMove | Configuration bias reptation move for a Linear species |
| ►CMcMd::CfbLinear | Base class for configuration bias (CFB) end regrowth moves |
| CMcMd::CfbLinearEndMove | Configuration bias end regrowth move for flexible linear chains |
| CMcMd::CfbReptateMove | Configuration bias reptation move for a Linear species |
| CMcMd::DpdMove | DpdMove is a short dissipative particle dynamics (DPD) simulation |
| CMcMd::EndSwapMove | A move that swaps the ends of a linear hetero-polymer |
| CMcMd::GcSliplinkMove | Move to evolve the slip-springs |
| ►CMcMd::GroupRebridgeBase | Base class for rebridging a group of atoms forming a tetrahedron |
| CMcMd::RingOctaRebridgeMove | Molecule rebridging move for a Ring species |
| CMcMd::RingTetraRebridgeMove | Molecule move that attempt the exchange of interior pieces of one close rings |
| CMcMd::HomopolymerSemiGrandMove | A move that changes the type of a HomopolymerSG molecule |
| CMcMd::HybridMdMove | HybridMdMove is a hybrid Molecular Dynamics MC move |
| CMcMd::HybridNphMdMove | HybridNphMove is a hybrid Molecular Dynamics MC move for NPT ensemble |
| CMcMd::MdMove | MdMove is a simple NVE molecular Dynamics MC move |
| CMcMd::RigidDisplaceMove | Random rigid displacement of a molecule |
| CMcMd::Sliplinker | Move to create and destroy slip-springs |
| CMcMd::SliplinkerAll | Move to create and destroy slip-springs |
| CMcMd::SliplinkerEnd | Move to create and destroy slip-springs |
| CMcMd::SliplinkMove | Move to evolve the slip-springs |
| CMcMd::McPairPotential | A PairPotential for MC simulations (abstract) |
| ►CMcMd::MdCoulombPotential | Coulomb potential for an Md simulation |
| CMcMd::MdEwaldPotential | Ewald Coulomb potential class for MD simulations |
| CMcMd::MdSpmePotential | Smooth Particle-Mesh Ewald Coulomb potential for MD simulations |
| ►CMcMd::MdIntegrator | Abstract base for molecular dynamics integrators |
| CMcMd::NphIntegrator | An explictly reversible/measure-preserving Parrinello-Rahman type NPH integrator |
| CMcMd::NveVvIntegrator | An NVE Verlet molecular dynamics integrator |
| CMcMd::NvtDpdVvIntegrator | A velocity-Verlet dissipative particle dynamics (DPD) integrator |
| CMcMd::NvtLangevinIntegrator | A NVT molecular dynamics integrator with a Langevin thermostat |
| CMcMd::NvtNhIntegrator | A Nose-Hoover NVT molecular dynamics integrator |
| CMcMd::MdPairPotential | An PairPotential for MD simulation |
| CMcMd::PairList | A Verlet neighbor list |
| ►CMcMd::Perturbation | Model of parameter dependence in a free energy perturbation theory |
| ►CMcMd::LinearPerturbation< McSystem > | |
| CMcMd::McEnergyPerturbation | A Perturbation with a variable inverse temperature |
| CMcMd::McExternalPerturbation< Interaction > | A Perturbation in the external potential external parameter |
| CMcMd::McPairExternalPerturbation< PairInteraction, ExternalInteraction > | 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() |
| CMcMd::McPairPerturbation< Interaction > | A Perturbation in the pair interaction epsilon(0,1) for any pair potential supporting setEpsilon() |
| CMcMd::LinearPerturbation< SystemType > | A Perturbation that is a linear function of a parameter |
| CMcMd::ReplicaMove | Replica exchange Monte Carlo move using Gibbs sampling |
| ►CMcMd::Simulation | The main object in a simulation, which coordinates others |
| CMcMd::McSimulation | A Monte-Carlo simulation of one McSystem |
| CMcMd::MdSimulation | A molecular dynamics simulation of a single MdSystem |
| CMcMd::SpecialPotential | Specialized potential for an MD simulation |
| ►CMcMd::System | A set of interacting Molecules enclosed by a Boundary |
| CMcMd::McSystem | A System for use in a Markov chain Monte Carlo simulation |
| CMcMd::MdSystem | A System for Molecular Dynamics simulation |
| CUtil::MeanSqDispArray< Util::Vector > | |
| CSimp::BoundaryEnsemble | Statistical ensemble for changes in the periodic unit cell size |
| CSimp::BoxExternal | A repulsive 9-3 potential confining particles within a box |
| CSimp::CompensatedPair< BarePair, LinkPotential > | Compensated pair potential for transient gel |
| CSimp::CompositeBond< BareBond, BarePair > | Composite bond potential |
| CSimp::CosineAngle | A three body angle potential, as a function of angle cosine |
| CSimp::CosineDihedral | A dihedral potential proportional to cos(phi) |
| CSimp::CosineSqAngle | A three body angle potential, as a function of angle cosine |
| CSimp::DpdPair | Soft pair potential used in dissipative particle dynamics (DPD) simulations of Groot, Warren et al |
| CSimp::EnergyEnsemble | A statistical ensemble for energy |
| CSimp::EwaldInteraction | Implementation of r-space and k-space Ewald Coulomb interactions |
| CSimp::FeneBond | A finitely-extensible nonlinear element (FENE) bond potential |
| CSimp::GeneralPeriodicExternal | A clipped cosine potential that induces ordering along directions specified by waveIntVectors, w_i |
| CSimp::HarmonicAngle | A angle potential that is harmonic in the angle |
| CSimp::HarmonicBond | A harmonic covalent bond potential |
| CSimp::HarmonicL0Bond | A harmonic bond potential with zero rest length |
| CSimp::LamellarOrderingExternal | A clipped cosine potential that induces lamellar ordering along the direction specified by perpDirection_ |
| ►CSimp::LJPair | A cutoff, shifted Lennard-Jones nonbonded pair interaction |
| CSimp::WcaPair | A Weeks-Chandler-Anderson (WCA) repulsive LJ interaction |
| CSimp::LocalLamellarOrderingExternal | 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_ |
| CSimp::MultiHarmonicDihedral | A truncated Fourier series dihedral potential |
| CSimp::NucleationExternal | A clipped cosine potential that induces ordering along directions specified by waveIntVectors, w_i |
| CSimp::OrthoBoxExternal | A repulsive 9-3 potential confining particles inside an orthogonal box along directions specified by indConfine_ |
| CSimp::PeriodicExternal | A clipped cosine potential that induces ordering along directions specified by waveIntVectors, w_i |
| CSimp::SimplePeriodicExternal | A clipped cosine potential that induces ordering along directions specified by waveIntVectors, w_i |
| CSimp::SlitExternal | A repulsive 9-3 potential confining particles along the z direction |
| ►CSimp::Species | A Species represents a set of chemically similar molecules |
| ►CSimp::Linear | A Species of linear polymers (abstract) |
| CMcMd::HomopolymerSG | A Homopolymer with a mutable type, for semigrand ensemble |
| CMcMd::LinearSG | A mutable linear polymer, for semigrand ensemble |
| CSimp::Diblock | A linear diblock copolymer chain |
| CSimp::Homopolymer | A Homopolymer species of chain molecules |
| CSimp::Multiblock | A linear MULTIBLOCK copolymer chain |
| CSimp::Point | A Species in which each Molecule contains only one Atom |
| ►CSimp::Ring | A Species of ring polymers (abstract) |
| CSimp::HomoRing | A species of homogeneous ring molecules |
| CSimp::SpeciesEnsemble | An ensemble for the number of molecules of one Species |
| CSimp::SphericalTabulatedExternal | The potential is independent on the type of atoms |
| ►CTools::Analyzer | Abstract base for periodic output and/or analysis actions |
| CTools::AtomMSD | Mean-squared displacement of specific atoms in specific species |
| CTools::LogStep | Write step number to log |
| CTools::PairEnergy | Analyzer to compute total nonbonded pair energy |
| ►CTools::TrajectoryWriter | Based class for classes that write trajectories to a single file |
| CTools::LammpsDumpWriter | Write a trajectory in the Lammps dump format |
| CTools::ChainMaker | Generates a simulation box full of randomly generated linear polymers |
| ►CTools::ConfigReader | Abstract reader/writer for configuration files |
| CTools::DdMdConfigReader | Native / default DdMd format for configuration files |
| CTools::HoomdConfigReader | Reader for Hoomd-blue XML configuration files |
| ►CTools::Configuration | An instantaneous molecular dynamics configuration |
| CTools::Processor | A post-processor for analyzing outputs of MD simulations |
| ►CTools::ConfigWriter | Abstract reader/writer for configuration files |
| CTools::DdMdConfigWriter | Native / default DdMd format for configuration files |
| CTools::HoomdConfigWriter | Hoomd-blue XML format for configuration files |
| ►CTools::TrajectoryReader | Abstract trajectory file reader |
| CTools::DdMdTrajectoryReader | Reader for lammps dump trajectory file format |
| CTools::LammpsDumpReader | Reader for lammps dump trajectory file format |
| CUtil::AutoCorr< Data, Product > | Auto-correlation function for one sequence of Data values |
| CUtil::AutoCorrArray< Data, Product > | Auto-correlation function for an ensemble of sequences |
| CUtil::AutoCorrelation< Data, Product > | Auto-correlation function, using hierarchical algorithm |
| CUtil::Average | Calculates the average and variance of a sampled property |
| ►CUtil::Distribution | A distribution (or histogram) of values for a real variable |
| CUtil::RadialDistribution | Distribution (or histogram) of values for particle separations |
| CUtil::FileMaster | A FileMaster manages input and output files for a simulation |
| CUtil::IntDistribution | A distribution (or histogram) of values for an int variable |
| CUtil::Manager< Data > | Template container for pointers to objects with a common base class |
| CUtil::MeanSqDispArray< Data > | Mean-squared displacement (MSD) vs |
| CUtil::Random | Random number generator |
| CUtil::SymmTensorAverage | Calculates averages of all components of a Tensor-valued variable |
| CUtil::TensorAverage | Calculates averages of all components of a Tensor-valued variable |
| ►CUtil::Parameter | A single variable in a parameter file |
| CUtil::CArray2DParam< Type > | A Parameter associated with a 2D built-in C array |
| CUtil::CArrayParam< Type > | A Parameter associated with a 1D C array |
| CUtil::DArrayParam< Type > | A Parameter associated with a DArray container |
| CUtil::DMatrixParam< Type > | A Parameter associated with a 2D built-in C array |
| CUtil::DSymmMatrixParam< Type > | A Parameter associated with a symmetric DMatrix |
| CUtil::FArrayParam< Type, N > | A Parameter associated with a FArray container |
| CUtil::ScalarParam< Type > | Template for a Parameter object associated with a scalar variable |
| CUtil::MpiLoader< IArchive > | Provides methods for MPI-aware loading of data from input archive |
| CUtil::MpiLogger | Allows information from every processor in a communicator, to be output in rank sequence |
| CUtil::MpiStructBuilder | A MpiStructBuilder objects is used to create an MPI Struct datatype |
| CUtil::MpiTraits< bool > | MpiTraits<bool> explicit specialization |
| CUtil::MpiTraits< char > | MpiTraits<char> explicit specialization |
| CUtil::MpiTraits< DdMd::AtomType > | Explicit specialization MpiTraits<AtomType> |
| CUtil::MpiTraits< DdMd::MaskPolicy > | Explicit specialization MpiTraits<MaskPolicy> |
| CUtil::MpiTraits< double > | MpiTraits<double> explicit specialization |
| CUtil::MpiTraits< float > | MpiTraits<float> explicit specialization |
| CUtil::MpiTraits< int > | MpiTraits<int> explicit specialization |
| CUtil::MpiTraits< IntVector > | Explicit specialization MpiTraits<IntVector> |
| CUtil::MpiTraits< long > | MpiTraits<long> explicit specialization |
| CUtil::MpiTraits< long double > | MpiTraits<long double> explicit specialization |
| CUtil::MpiTraits< McMd::AtomType > | Explicit specialization MpiTraits<AtomType> |
| CUtil::MpiTraits< McMd::MaskPolicy > | Explicit specialization MpiTraits<MaskPolicy> |
| CUtil::MpiTraits< McMd::PairSelector > | Explicit specialization MpiTraits<PairSelector> |
| CUtil::MpiTraits< McMd::PairSelector::PairType > | Explicit specialization MpiTraits<PairSelector::PairType> |
| CUtil::MpiTraits< MonoclinicBoundary > | Explicit specialization MpiTraits<MonoclinicBoundary> |
| CUtil::MpiTraits< Pair< int > > | Explicit specialization MpiTraits< Pair<int> > |
| CUtil::MpiTraits< Rational > | Explicit specialization MpiTraits<Rational> |
| CUtil::MpiTraits< short > | MpiTraits<short> explicit specialization |
| CUtil::MpiTraits< Simp::BoundaryEnsemble > | Explicit specialization MpiTraits<Simp::BoundaryEnsemble> |
| CUtil::MpiTraits< Simp::BoundaryEnsemble::Type > | Explicit specialization MpiTraits<Simp::BoundaryEnsemble::Type> |
| CUtil::MpiTraits< Simp::EnergyEnsemble > | Explicit specialization MpiTraits<Simp::EnergyEnsemble> |
| CUtil::MpiTraits< Simp::EnergyEnsemble::Type > | Explicit specialization MpiTraits<Simp::EnergyEnsemble::Type> |
| CUtil::MpiTraits< Simp::OrthorhombicBoundary > | Explicit specialization MpiTraits<OrthorhombicBoundary> |
| CUtil::MpiTraits< Simp::SpeciesEnsemble > | Explicit specialization MpiTraits<Simp::SpeciesEnsemble> |
| CUtil::MpiTraits< Simp::SpeciesEnsemble::Type > | Explicit specialization MpiTraits<Simp::SpeciesEnsemble::Type> |
| CUtil::MpiTraits< Simp::SpeciesGroup< 2 > > | Explicit specialization MpiTraits< SpeciesGroup<2> > |
| CUtil::MpiTraits< Simp::SpeciesGroup< 3 > > | Explicit specialization MpiTraits< SpeciesGroup<3> > |
| CUtil::MpiTraits< Simp::SpeciesGroup< 4 > > | Explicit specialization MpiTraits< SpeciesGroup<4> > |
| CUtil::MpiTraits< Tensor > | Explicit specialization MpiTraits<Tensor> |
| CUtil::MpiTraits< unsigned char > | MpiTraits<unsigned char> explicit specialization |
| CUtil::MpiTraits< unsigned int > | MpiTraits<unsigned int> explicit specialization |
| CUtil::MpiTraits< unsigned long > | MpiTraits<unsigned long> explicit specialization |
| CUtil::MpiTraits< unsigned short > | MpiTraits<unsigned short> explicit specialization |
| CUtil::MpiTraits< Util::LatticeSystem > | Explicit specialization MpiTraits<LatticeSystem> |
| CUtil::MpiTraits< Vector > | Explicit specialization MpiTraits<Vector> |
| ►CUtil::MpiTraitsNoType | Base class for MpiTraits with no type |
| CUtil::MpiTraits< T > | Default MpiTraits class |
| ►CUtil::MTRand_int32 | Mersenne Twister random number generator engine |
| CUtil::MTRand | Generates double floating point numbers in the half-open interval [0, 1) |
| CUtil::MTRand53 | Generates 53 bit resolution doubles in the half-open interval [0, 1) |
| CUtil::MTRand_closed | Generates double floating point numbers in the closed interval [0, 1] |
| CUtil::MTRand_open | Generates double floating point numbers in the open interval (0, 1) |
| CUtil::Node< Data > | Linked List Node, class template |
| CUtil::Notifier< Event > | Abstract template for a notifier (or subject) in the Observer design pattern |
| CUtil::Observer< Event > | Abstract class template for observer in the observer design pattern |
| ►CUtil::PArray< Data > | An array that only holds pointers to its elements |
| CUtil::ArraySet< DdMd::Atom > | |
| CUtil::ArraySet< DdMd::Group< N > > | |
| CUtil::ArraySet< McMd::Link > | |
| CUtil::GPArray< DdMd::Atom > | |
| CUtil::GPArray< DdMd::Group< N > > | |
| CUtil::GPArray< DdMd::GroupExchanger > | |
| CUtil::GPArray< DdMd::Modifier > | |
| CUtil::ArraySet< Data > | A container for pointers to a subset of elements of an associated array |
| CUtil::DPArray< Data > | A dynamic array that only holds pointers to its elements |
| CUtil::GPArray< Data > | An automatically growable PArray |
| CUtil::PArrayIterator< Data > | Forward iterator for a PArray |
| CUtil::PointSymmetry | A PointSymmetry represents a crystallographic point group symmetry |
| ►CUtil::RaggedMatrix< Data > | A 2D array in which different rows can have different lengths |
| CUtil::DRaggedMatrix< Data > | Dynamically allocated RaggedMatrix |
| CUtil::Rational | A Rational number (a ratio of integers) |
| CUtil::RingBuffer< Data > | Class for storing history of previous values in an array |
| CUtil::ScopedPtr< T > | A very simple RAII pointer |
| ►CUtil::Serializable | Abstract class for serializable objects |
| CUtil::ParamComponent | Abstract base class for classes that input and ouput parameters to file |
| CUtil::Setable< T > | Template for a value that can be set or declared null (i.e., unknown) |
| CUtil::Signal< T > | Notifier (or subject) in the Observer design pattern |
| CUtil::Signal< void > | Notifier (or subject) in the Observer design pattern (zero parameters) |
| CUtil::SSet< Data, Capacity > | Statically allocated array of pointers to an unordered set |
| CUtil::Str | Wrapper for a std::string, for formatted ostream output |
| CUtil::SymmetryGroup< Symmetry > | Class template for a group of elements of type Symmetry |
| CUtil::Tensor | A Tensor represents a Cartesian tensor |
| CUtil::TextFileIArchive | Loading archive for text istream |
| CUtil::TextFileOArchive | Saving archive for character based ostream |
| CUtil::Timer | Wall clock timer |
| CUtil::Vector | A Vector is a Cartesian vector |
| CUtil::XdrFileIArchive | Loading / input archive for binary XDR file |
| CUtil::XdrFileOArchive | Saving / output archive for binary XDR file |
| ►CUtil::XmlBase | Base class for classes that parse XML markup tags |
| CUtil::XmlAttribute | Parser for an XML attribute |
| CUtil::XmlEndTag | Parser for an XML end tag |
| CUtil::XmlStartTag | Parser for an XML start tag |
| CUtil::XmlXmlTag | Parser for an XML file declaration tag (first line in file) |
