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Simpatico
v1.10
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Single-processor Monte Carlo (MC) and molecular dynamics (MD). More...
Classes | |
| class | Activate |
| Static member functions to de-active and re-active atoms. More... | |
| class | Analyzer |
| Abstract base for periodic output and/or analysis actions. More... | |
| class | AnalyzerManager |
| Manager for a list of Analyzer objects. More... | |
| class | AngleFactory |
| Factory for subclasses of AnglePotential. More... | |
| class | AnglePotential |
| Interface for a Angle Interaction. More... | |
| class | AnglePotentialImpl |
| Implementation template for an AnglePotential. More... | |
| class | Atom |
| A point particle within a Molecule. More... | |
| class | AtomDisplaceMove |
| Random displacement of one atom. More... | |
| class | AtomMSD |
| Autocorrelation for vector separation of two atoms on a molecule. More... | |
| class | AtomType |
| Descriptor for a type of Atom. More... | |
| class | AverageAnalyzer |
| AverageAnalyzer averages of total potential energy. More... | |
| class | BennettsMethod |
| Bennett's method estimates free energy difference between two states. More... | |
| class | BlockRadiusGyration |
| Radius of gyration of different blocks in a molecule. More... | |
| class | BondFactory |
| Factory for BondPotential objects. More... | |
| class | BondLengthDist |
| BondLengthDist evaluates the distribution function of the lengths of the bonds. More... | |
| class | BondPotential |
| Abstract Bond Potential class. More... | |
| class | BondPotentialImpl |
| Implementation template for a BondPotential. More... | |
| class | BoundaryAverage |
| Average of boundary lengths and volume of simulation cell. More... | |
| class | Cell |
| A set of Atoms in a small region. More... | |
| class | CellList |
| A cell list for Atom objects in a periodic system boundary. More... | |
| class | CellTag |
| Location of the pointer to a particular Atom in a CellList. More... | |
| class | CfbDoubleRebridgeMove |
| configuration bias trimer double rebridge moves, to reconnect two chains. More... | |
| class | CfbEndBase |
| Base class for configuration bias (CFB) end regrowth moves. More... | |
| class | CfbEndMove |
| Configuration bias end regrowth move for flexible linear chains. More... | |
| class | CfbLinear |
| Base class for configuration bias (CFB) end regrowth moves. More... | |
| class | CfbLinearEndMove |
| Configuration bias end regrowth move for flexible linear chains. More... | |
| class | CfbRebridgeBase |
| Base class configuration bias moves internal segment regrowth moves. More... | |
| class | CfbRebridgeMove |
| Config-bias move for internal segment of a flexible linear polymer. More... | |
| class | CfbReptateMove |
| Configuration bias reptation move for a Linear species. More... | |
| class | CfbReptationMove |
| Configuration bias reptation move for a Linear species. More... | |
| class | CfbRingRebridgeMove |
| Configuration bias rebridge moves for ring molecules. More... | |
| class | Cluster |
| Cluster of molecules. More... | |
| class | ClusterHistogram |
| Identify micelle clusters in polymeric systems. More... | |
| class | ClusterIdentifier |
| Identifies clusters of molecules, such as micelles. More... | |
| struct | ClusterLink |
| Molecule in a cluster. More... | |
| class | ColVar |
| Abstract base class for collective variables. More... | |
| class | ColVarPotentialTmpl |
| SpecialPotential that is a function of a collective variable. More... | |
| class | Command |
| Command is an object that can be invoked from the command script. More... | |
| class | CommandManager |
| Manager for Command objects in an MdSimulation. More... | |
| class | ComMSD |
| Molecular center of mass mean squared displacement. More... | |
| class | CompositionProfile |
| CompositionProfile evaluates the distribution of monomer positions along several user-specified directions. More... | |
| class | ConfigIo |
| System configuration file reader and writer. More... | |
| class | ConfigIoFactory |
| Default Factory for subclasses of ConfigIo. More... | |
| class | ConfigWriter |
| Periodically dump system configuration to a new file. More... | |
| class | CoulombFactory |
| Factory for CoulombPotential objects. More... | |
| class | Crosslinker |
| Analyzer to create crosslinks and output the resulting configuration. More... | |
| class | CvBias |
| Bias potential as a function of a collective variable (CV). More... | |
| class | DCDTrajectoryReader |
| TrajectoryReader for CHARMM ".dcd" data files. More... | |
| class | DdMdConfigIo |
| ConfigIo for DdMd data files. More... | |
| class | DdMdTrajectoryReader |
| TrajectoryReader for a DdMd trajectory file. More... | |
| class | DeformCommand |
| Command to deform the unit cell. More... | |
| class | DihedralFactory |
| Factory for subclasses of DihedralPotential. More... | |
| class | DihedralPotential |
| Interface for a Dihedral Potential. More... | |
| class | DihedralPotentialImpl |
| Implementation template for an DihedralPotential. More... | |
| class | DpdMove |
| DpdMove is a short dissipative particle dynamics (DPD) simulation. More... | |
| class | EndSwapMove |
| A move that swaps the ends of a linear hetero-polymer. More... | |
| class | EndtoEnd |
| End to end distance of a molecule. More... | |
| class | EndtoEndXYZ |
| Mean square end to end distance of a molecule. More... | |
| class | EnergyCalculator |
| Interface for a class that calculates a total energy. More... | |
| class | EwaldRSpaceAccumulator |
| Utility class to store r-space Coulomb energy and stress. More... | |
| class | ExternalFactory |
| Factory for subclasses MdExternalPotential or McExternalPotential. More... | |
| class | ExternalPotential |
| Abstract External Potential class. More... | |
| class | ExternalPotentialImpl |
| Template implementation of ExternalPotential. More... | |
| class | G1MSD |
| Autocorrelation for vector separation of any two monomers on a molecule. More... | |
| class | GcSliplinkMove |
| Move to evolve the slip-springs. More... | |
| class | Generator |
| Generates initial configurations for molecules of one species. More... | |
| class | Group |
| A sequence of NAtom covalently interacting atoms. More... | |
| class | GroupRebridgeBase |
| Base class for rebridging a group of atoms forming a tetrahedron. More... | |
| class | HarmonicCvBias |
| Harmonic function of a collective variable (CV). More... | |
| class | HomopolymerSemiGrandMove |
| A move that changes the type of a HomopolymerSG molecule. More... | |
| class | HomopolymerSG |
| A Homopolymer with a mutable type, for semigrand ensemble. More... | |
| class | HybridMdMove |
| HybridMdMove is a hybrid Molecular Dynamics MC move. More... | |
| class | HybridNphMdMove |
| HybridNphMove is a hybrid Molecular Dynamics MC move for NPT ensemble. More... | |
| class | InterIntraLink |
| Number of inter and intramolecular links. More... | |
| class | IntraBondStressAutoCorr |
| Autocorrelation for bond stress of a molecule. More... | |
| class | IntraBondTensorAutoCorr |
| Autocorrelation for bond stress of a molecule. More... | |
| class | IntraPairAutoCorr |
| Autocorrelation for vector separation of any two monomers on a molecule. More... | |
| class | IntraStructureFactor |
| Intramolecular contribution to the structure factor S(k) More... | |
| class | IntraStructureFactorGrid |
| IntraStructureFactorGrid evaluates structure factors in Fourier space. More... | |
| class | LammpsConfigIo |
| ConfigIo for Lammps data files. More... | |
| class | LammpsDumpReader |
| TrajectoryReader for Lammps dump trajectory files. More... | |
| class | LammpsDumpWriter |
| Periodically write snapshots to a lammps dump (i.e., trajectory) file. More... | |
| class | LinearCvBias |
| Linear function of a collective variable (CV). More... | |
| class | LinearGenerator |
| Generates random configurations for linear molecules. More... | |
| class | LinearPerturbation |
| A Perturbation that is a linear function of a parameter. More... | |
| class | LinearRouseAutoCorr |
| Autocorrelation for Rouse mode coefficients of a linear molecule. More... | |
| class | LinearSG |
| A mutable linear polymer, for semigrand ensemble. More... | |
| class | Link |
| A Link represents a crosslink between two Atoms. More... | |
| class | LinkAddEvent |
| Event signalling addition of Link to the LinkMaster. More... | |
| class | LinkFactory |
| Factory for subclasses of MdBondPotential or McBondPotential. More... | |
| class | LinkLengthDist |
| LinkLengthDist evaluates the distribution function of the lengths of the links. More... | |
| class | LinkLifeTime |
| LinkLifeTime evaluates how long the slip-springs live. More... | |
| class | LinkLTPos |
| LinkLTPos evaluates how long the slip-springs live as a function of position along the chain. More... | |
| class | LinkMaster |
| Manages all Link objects in a System. More... | |
| class | LinkMSD |
| Evaluates msd of link ends along the chains. More... | |
| class | LinkPotentialImpl |
| Template implementation of an BondPotential for links. More... | |
| struct | LinkRemoveEvent |
| Event signalling removal of a Link from the LinkMaster. More... | |
| class | LinkResetEvent |
| Event signalling reset of Link to the LinkMaster. More... | |
| class | LogProgress |
| Periodically write step number to a Log file. More... | |
| class | Mask |
| Set of Atoms for which pair interactions with a target Atom are "masked". More... | |
| class | McAnalyzerFactory |
| AnalyzerFactory for an McSimulation. More... | |
| class | McAnalyzerManager |
| Manager for Analyzer objects in an McSimulation. More... | |
| class | McBondEnergyAverage |
| McBondEnergyAverage averages of bond potential energy. More... | |
| class | McCommandFactory |
| CommandFactory for an McSimulation. More... | |
| class | McCommandManager |
| Command interpreter and Manager for an McSimulation. More... | |
| class | McConfigIo |
| ConfigIo for MC simulations (no atom velocities). More... | |
| class | McCoulombPotential |
| Long-range part of Coulomb potential for MC. More... | |
| class | McDeformCommand |
| Command to deform the unit cell. More... | |
| class | McEnergyAnalyzer |
| Compute averages and output block averages of energy components. More... | |
| class | McEnergyAverage |
| McEnergyAverage averages of total potential energy. More... | |
| class | McEnergyOutput |
| Analyzer to output total potential energy. More... | |
| class | McEnergyPerturbation |
| A Perturbation with a variable inverse temperature. More... | |
| class | McExternalEnergyAverage |
| McExternalEnergyAverage averages of total external energy. More... | |
| class | McExternalPerturbation |
| A Perturbation in the external potential external parameter. More... | |
| class | McIntraBondStressAutoCorr |
| Autocorrelation for bond stress of a molecule. More... | |
| class | McIntraBondTensorAutoCorr |
| Autocorrelation for bond stress of a molecule. More... | |
| class | McMdConfigIo |
| Base class for default Mc and Md configIos. More... | |
| class | McMove |
| McMove is an abstract base class for Monte Carlo moves. More... | |
| class | McMoveFactory |
| McMoveFactory for an McSimulation. More... | |
| class | McMoveManager |
| Manager for a set of McMove objects. More... | |
| class | McMuExchange |
| Exchange chemical potential for semigrand ensemble. More... | |
| class | McNVTChemicalPotential |
| McNVTChemicalPotential uses configuration bias algorithm to calculate the chemical potential of a linear chain. More... | |
| class | McPairEnergyAverage |
| McPairEnergyAverage averages of total potential energy. More... | |
| class | McPairExternalPerturbation |
| 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(). More... | |
| class | McPairPerturbation |
| A Perturbation in the pair interaction epsilon(0,1) for any pair potential supporting setEpsilon(). More... | |
| class | McPairPotential |
| A PairPotential for MC simulations (abstract). More... | |
| class | McPairPotentialImpl |
| Implementation template for an McPairPotential. More... | |
| class | McPerturbationFactory |
| Default Factory for subclasses of Perturbation. More... | |
| class | McPressureAverage |
| Analyzer to calculate average isotropic pressure. More... | |
| class | McSimulation |
| A Monte-Carlo simulation of one McSystem. More... | |
| class | McStressAutoCorrelation |
| Analyzer to calculate average isotropic pressure. More... | |
| class | McSystem |
| A System for use in a Markov chain Monte Carlo simulation. More... | |
| class | McSystemInterface |
| An interface to an McSystem. More... | |
| class | McVirialStressTensorAverage |
| Periodically write (tensor) StressTensor to file. More... | |
| class | MdAnalyzerFactory |
| AnalyzerFactory for an MdSimulation. More... | |
| class | MdAnalyzerManager |
| Manager for Analyzer objects in an MdSimulation. More... | |
| class | MdColVar |
| Collective variables for MD simulation, with atom forces. More... | |
| class | MdCommandFactory |
| CommandFactory for an MdSimulation. More... | |
| class | MdCommandManager |
| Command interpreter and Command Manager for an MdSimulation. More... | |
| class | MdConfigIo |
| ConfigIo for MD simulations (includes velocities). More... | |
| class | MdCoulombPotential |
| Coulomb potential for an Md simulation. More... | |
| class | MdDeformCommand |
| Command to deform the unit cell. More... | |
| class | MdEnergyAnalyzer |
| Compute averages and output block averages of energy components. More... | |
| class | MdEnergyOutput |
| Analyzer to output total potential and kinetic energies. More... | |
| class | MdEwaldPairPotentialImpl |
| Implementation of a pair potential for a charged system. More... | |
| class | MdEwaldPotential |
| Ewald Coulomb potential class for MD simulations. More... | |
| class | MdIntegrator |
| Abstract base for molecular dynamics integrators. More... | |
| class | MdIntegratorFactory |
| Default Factory for subclasses of MdIntegrator. More... | |
| class | MdIntraBondStressAutoCorr |
| Autocorrelation for bond stress of a molecule. More... | |
| class | MdIntraBondTensorAutoCorr |
| Autocorrelation for bond orientation of of a molecule. More... | |
| class | MdKineticEnergyAverage |
| MdKineticEnergyAverage averages of total kinetic energy. More... | |
| class | MdMove |
| MdMove is a simple NVE molecular Dynamics MC move. More... | |
| class | MdPairEnergyCoefficients |
| Analyzer to output the total pair energy and the sum of squares of the monomeric and molecular pair energy. More... | |
| class | MdPairPotential |
| An PairPotential for MD simulation. More... | |
| class | MdPairPotentialImpl |
| Implementation template for an MdPairPotential. More... | |
| class | MdPotentialEnergyAverage |
| MdPotentialEnergyAverage averages of total potential energy. More... | |
| class | MdPressureAverage |
| Calculate average scalar pressure for an MdSystem. More... | |
| class | MdSimulation |
| A molecular dynamics simulation of a single MdSystem. More... | |
| class | MdSpmePotential |
| Smooth Particle-Mesh Ewald Coulomb potential for MD simulations. More... | |
| class | MdStressAutoCorr |
| Analyzer to calculate average isotropic pressure. More... | |
| class | MdSystem |
| A System for Molecular Dynamics simulation. More... | |
| class | MdSystemInterface |
| An interface to an MdSystem. More... | |
| class | MdVirialStressTensorAverage |
| Periodically write (tensor) StressTensor to file. More... | |
| class | Molecule |
| A physical molecule (a set of covalently bonded Atoms). More... | |
| class | MoleculeSetObserver |
| Observer interface. More... | |
| class | NLinkAverage |
| Average number of crosslinks. More... | |
| class | NphIntegrator |
| An explictly reversible/measure-preserving Parrinello-Rahman type NPH integrator. More... | |
| class | NveVvIntegrator |
| An NVE Verlet molecular dynamics integrator. More... | |
| class | NvtDpdVvIntegrator |
| A velocity-Verlet dissipative particle dynamics (DPD) integrator. More... | |
| class | NvtLangevinIntegrator |
| A NVT molecular dynamics integrator with a Langevin thermostat. More... | |
| class | NvtNhIntegrator |
| A Nose-Hoover NVT molecular dynamics integrator. More... | |
| class | PairFactory |
| Factory for subclasses MdPairPotential or McPairPotential. More... | |
| class | PairIterator |
| Iterator for pairs in a PairList. More... | |
| class | PairList |
| A Verlet neighbor list. More... | |
| class | PairPotential |
| Interface for a Pair Potential. More... | |
| class | PairSelector |
| Selection rule for pairs of Atoms. More... | |
| class | Perturbation |
| Model of parameter dependence in a free energy perturbation theory. More... | |
| class | PerturbDerivative |
| PerturbDerivative returns average value of Perturbation::derivative(). More... | |
| class | PointGenerator |
| Generator for monoatomic molecules (atoms). More... | |
| class | PressureAverage |
| PressureAverage evaluates average pressure. More... | |
| class | RadiusGyration |
| Radius of gyration of a molecule. More... | |
| class | RDF |
| RDF evaluates the atomic radial distribution function. More... | |
| class | ReplicaMove |
| Replica exchange Monte Carlo move using Gibbs sampling. More... | |
| struct | ReSetAtomEvent |
| Event signalling the reset of an atom from the LinkMaster. More... | |
| class | RigidDisplaceMove |
| Random rigid displacement of a molecule. More... | |
| class | RingOctaRebridgeMove |
| Molecule rebridging move for a Ring species. More... | |
| class | RingRouseAutoCorr |
| Autocorrelation for Rouse mode coefficients of a ring molecule. More... | |
| class | RingTetraRebridgeMove |
| Molecule move that attempt the exchange of interior pieces of one close rings. More... | |
| class | SemiGrandDistribution |
| Calculate distribution of type indices for mutable species. More... | |
| class | Simulation |
| The main object in a simulation, which coordinates others. More... | |
| class | Sliplinker |
| Move to create and destroy slip-springs. More... | |
| class | SliplinkerAll |
| Move to create and destroy slip-springs. More... | |
| class | SliplinkerEnd |
| Move to create and destroy slip-springs. More... | |
| class | SliplinkMcAnalyzerFactory |
| Custom AnalyzerFactory for an McSimulation. More... | |
| class | SliplinkMcModule |
| Module for slip link simulation. More... | |
| class | SliplinkMcMoveFactory |
| Custom McMoveFactory. More... | |
| class | SliplinkMdAnalyzerFactory |
| Custom AnalyzerFactory for an MdSimulation. More... | |
| class | SliplinkMove |
| Move to evolve the slip-springs. More... | |
| class | SmpConfigIo |
| Common configuration file format for simpatico. More... | |
| class | SpecialExternal |
| Potential for testing purposes. More... | |
| class | SpecialFactory |
| Factory for specialized subclasses of SpecialPotential. More... | |
| class | SpecialPotential |
| Specialized potential for an MD simulation. More... | |
| class | SpecialPotentialFacade |
| SpecialPotential interface to an existing potential. More... | |
| class | SpeciesFactory |
| Default Factory for subclasses of Species. More... | |
| class | SpeciesManager |
| A Manager for a set of Species objects. More... | |
| class | SpeciesMutator |
| Mix-in class for mutable subclasses of Species. More... | |
| class | SSChainDist |
| SSChainDist evaluates the distribution of slip-springs along the chains. More... | |
| class | StressAutoCorr |
| Compute stress autocorrelation for an isotropic system. More... | |
| class | StressCalculator |
| Interface for a stress calculator. More... | |
| class | StressTensorAverage |
| Periodically write (tensor) StressTensor to file. More... | |
| class | StructureFactor |
| StructureFactor evaluates structure factors in Fourier space. More... | |
| class | StructureFactorGrid |
| StructureFactorGrid evaluates structure factors in Fourier space. More... | |
| class | StructureFactorP |
| StructureFactorP evaluates partial structure factors in Fourier space. More... | |
| class | StructureFactorPGrid |
| StructureFactorPGrid evaluates structure factors in Fourier space. More... | |
| class | System |
| A set of interacting Molecules enclosed by a Boundary. More... | |
| class | SystemAnalyzer |
| Template for Analyzer associated with one System. More... | |
| class | SystemAnalyzerFactory |
| AnalyzerFactory for any System (for mc or md). More... | |
| class | SystemInterface |
| An interface to a System. More... | |
| class | SystemMove |
| An McMove that acts on one McSystem. More... | |
| class | TrajectoryReader |
| Trajectory file reader (base class). More... | |
| class | TrajectoryReaderFactory |
| Default Factory for subclasses of TrajectoryReader. More... | |
| class | TrajectoryWriter |
| Periodically write snapshots to a lammps dump (i.e., trajectory) file. More... | |
| class | TypeDistribution |
| Calculate distribution of type indices for mutable species. More... | |
| class | VanHove |
| Evaluates the van Hove function S(k,t) for one or more wavevector k. More... | |
| class | VelProf |
| Evaluates x-velocity profile as a function of z. More... | |
Typedefs | |
| typedef Group< 3 > | Angle |
| Group of 3 Atoms involved in an angle potential. More... | |
| typedef Group< 2 > | Bond |
| A Group of 2 covalently bonded Atoms. More... | |
| typedef Group< 4 > | Dihedral |
| Group of the 4 Atoms in a dihedral interaction. More... | |
| typedef FSArray< const Bond *, Species::MaxBondPerAtom > | AtomBondArray |
| Array to hold pointers to bonds that contain a specific atom. More... | |
| typedef FSArray< const Angle *, Simp::Species::MaxAnglePerAtom > | AtomAngleArray |
| Array to hold pointers to angles that contain a specific atom. More... | |
| typedef FSArray< const Dihedral *, Simp::Species::MaxDihedralPerAtom > | AtomDihedralArray |
| Array to hold pointers to Dihedrals that contain a specific atom. More... | |
| typedef Pair< int > | sendRecvPair |
| A pair of receiving and sending partner ranks. More... | |
Enumerations |
Functions | |
| std::istream & | operator>> (std::istream &in, PairSelector &selector) |
| istream extractor (>>) for a PairSelector object. More... | |
| std::ostream & | operator<< (std::ostream &out, const PairSelector &selector) |
| ostream inserter (<<) for a PairSelector object. More... | |
| std::istream & | operator>> (std::istream &in, PairSelector::PairType &type) |
| istream extractor (>>) for a PairSelector::PairType enum. More... | |
| std::ostream & | operator<< (std::ostream &out, const PairSelector::PairType &type) |
| ostream inserter (<<) for a PairSelector::PairType enum. More... | |
| template<class Archive > | |
| void | serialize (Archive &ar, PairSelector &selector, const unsigned int version) |
| Serialize a PairSelector. More... | |
| template<class Archive > | |
| void | serialize (Archive &ar, PairSelector::PairType &type, const unsigned int version) |
| Serialize a PairSelector. More... | |
| std::istream & | operator>> (std::istream &in, AtomType &atomType) |
| istream extractor (>>) for an AtomType. More... | |
| std::ostream & | operator<< (std::ostream &out, const AtomType &atomType) |
| ostream inserter (<<) for an AtomType. More... | |
| template<class Archive > | |
| void | serialize (Archive &ar, AtomType &atomType, const unsigned int version) |
| Serialize an AtomType. More... | |
| void | getAtomBonds (const Atom &atom, AtomBondArray &bonds) |
| Fill an array of pointers to Bonds that contain an Atom. More... | |
| void | getAtomAngles (const Atom &atom, AtomAngleArray &angles) |
| Fill an array of pointers to Angles that contain an Atom. More... | |
| void | getAtomDihedrals (const Atom &atom, AtomDihedralArray &dihedrals) |
| Fill an array of pointers to Dihedrals that contain an Atom. More... | |
| std::istream & | operator>> (std::istream &in, MaskPolicy &policy) |
| istream extractor for a MaskPolicy. More... | |
| std::ostream & | operator<< (std::ostream &out, MaskPolicy policy) |
| ostream inserter for an MaskPolicy. More... | |
| template<class Archive > | |
| void | serialize (Archive &ar, MaskPolicy &policy, const unsigned int version) |
| Serialize a MaskPolicy. More... | |
| Generator * | generatorFactory (Species &species, McSystem &system) |
| Instantiates generator for on species in an McSystem. More... | |
| Generator * | generatorFactory (Species &species, MdSystem &system) |
| Instantiates generator for on species in an MdSystem. More... | |
| void | commitMpiTypes () |
| Commit all MPI data types needed for Mc and Md simulations. More... | |
Single-processor Monte Carlo (MC) and molecular dynamics (MD).
| typedef FSArray<const Bond*, Species::MaxBondPerAtom> McMd::AtomBondArray |
Array to hold pointers to bonds that contain a specific atom.
Definition at line 30 of file getAtomGroups.h.
| typedef FSArray<const Angle*, Simp::Species::MaxAnglePerAtom> McMd::AtomAngleArray |
Array to hold pointers to angles that contain a specific atom.
Definition at line 53 of file getAtomGroups.h.
| typedef FSArray<const Dihedral*, Simp::Species::MaxDihedralPerAtom> McMd::AtomDihedralArray |
Array to hold pointers to Dihedrals that contain a specific atom.
Definition at line 69 of file getAtomGroups.h.
| typedef Pair<int> McMd::sendRecvPair |
A pair of receiving and sending partner ranks.
Definition at line 29 of file ReplicaMove.h.
| std::istream & McMd::operator>> | ( | std::istream & | in, |
| PairSelector & | selector | ||
| ) |
istream extractor (>>) for a PairSelector object.
Format: pairType atom1TypeId atom2TypeId
| in | input stream |
| selector | PairSelector to be read from stream |
Definition at line 82 of file PairSelector.cpp.
Referenced by McMd::AtomType::charge().
| std::ostream & McMd::operator<< | ( | std::ostream & | out, |
| const PairSelector & | selector | ||
| ) |
ostream inserter (<<) for a PairSelector object.
Format: pairType atom1TypeId atom2TypeId
| out | output stream |
| selector | PairSelector to be written to stream |
Definition at line 93 of file PairSelector.cpp.
References Util::Parameter::Width.
Referenced by McMd::AtomType::charge().
| std::istream & McMd::operator>> | ( | std::istream & | in, |
| PairSelector::PairType & | type | ||
| ) |
istream extractor (>>) for a PairSelector::PairType enum.
| in | input stream |
| type | PairType to be read from stream |
Definition at line 107 of file PairSelector.cpp.
References UTIL_THROW.
| std::ostream & McMd::operator<< | ( | std::ostream & | out, |
| const PairSelector::PairType & | type | ||
| ) |
ostream inserter (<<) for a PairSelector::PairType enum.
| out | output stream |
| type | PairSelector::PairType to be written to stream |
Definition at line 128 of file PairSelector.cpp.
References UTIL_THROW.
| void McMd::serialize | ( | Archive & | ar, |
| PairSelector & | selector, | ||
| const unsigned int | version | ||
| ) |
Serialize a PairSelector.
Default implementation calls serialize method of data object. Can be overridden by any explicit specialization.
| ar | archive object |
| selector | object to be serialized |
| version | archive version id |
Definition at line 167 of file PairSelector.h.
References McMd::PairSelector::operator<<, and McMd::PairSelector::operator>>.
Referenced by McMd::ConfigWriter::~ConfigWriter(), McMd::LammpsDumpWriter::~LammpsDumpWriter(), McMd::StressTensorAverage< SystemType >::~StressTensorAverage(), and McMd::TrajectoryWriter::~TrajectoryWriter().
| void McMd::serialize | ( | Archive & | ar, |
| PairSelector::PairType & | type, | ||
| const unsigned int | version | ||
| ) |
Serialize a PairSelector.
Default implementation calls serialize method of data object. Can be overridden by any explicit specialization.
| ar | archive object |
| type | object to be serialized |
| version | archive version id |
Definition at line 203 of file PairSelector.h.
References Util::serializeEnum().
| std::istream & McMd::operator>> | ( | std::istream & | in, |
| AtomType & | atomType | ||
| ) |
istream extractor (>>) for an AtomType.
Format:
name [string] mass [double] charge [double]
| in | input stream |
| atomType | AtomType to be read from stream |
Definition at line 69 of file mcMd/chemistry/AtomType.cpp.
| std::ostream & McMd::operator<< | ( | std::ostream & | out, |
| const AtomType & | atomType | ||
| ) |
ostream inserter (<<) for an AtomType.
Format, one one line with no line break:
name mass [charge]
| out | output stream |
| atomType | AtomType to be written to stream |
Definition at line 84 of file mcMd/chemistry/AtomType.cpp.
References Util::Parameter::Precision, and Util::Parameter::Width.
| void McMd::serialize | ( | Archive & | ar, |
| AtomType & | atomType, | ||
| const unsigned int | version | ||
| ) |
Serialize an AtomType.
| ar | archive object |
| atomType | object to be serialized |
| version | archive version id |
Definition at line 235 of file mcMd/chemistry/AtomType.h.
| void McMd::getAtomBonds | ( | const Atom & | atom, |
| AtomBondArray & | bonds | ||
| ) |
Fill an array of pointers to Bonds that contain an Atom.
| atom | the Atom of interest |
| bonds | an array to fill with pointers to bonds |
Definition at line 21 of file getAtomGroups.cpp.
References Util::FSArray< Data, Capacity >::append(), McMd::Molecule::atom(), Simp::Species::atomBondIds(), McMd::Molecule::bond(), Util::FSArray< Data, Capacity >::clear(), McMd::Atom::molecule(), McMd::Molecule::nBond(), Util::FSArray< Data, Capacity >::size(), and McMd::Molecule::species().
Referenced by McMd::BondPotentialImpl< Interaction >::atomEnergy(), and McMd::GroupRebridgeBase::tetraEnergy().
| void McMd::getAtomAngles | ( | const Atom & | atom, |
| AtomAngleArray & | angles | ||
| ) |
Fill an array of pointers to Angles that contain an Atom.
| atom | the Atom of interest |
| angles | an array to fill with pointers to angles |
Definition at line 42 of file getAtomGroups.cpp.
References McMd::Molecule::angle(), Util::FSArray< Data, Capacity >::append(), McMd::Molecule::atom(), Simp::Species::atomAngleIds(), Util::FSArray< Data, Capacity >::clear(), McMd::Atom::molecule(), McMd::Molecule::nAngle(), Util::FSArray< Data, Capacity >::size(), and McMd::Molecule::species().
Referenced by McMd::CfbEndBase::addEndAtom(), McMd::AnglePotentialImpl< Interaction >::atomEnergy(), McMd::CfbEndBase::deleteEndAtom(), and McMd::GroupRebridgeBase::tetraEnergy().
| void McMd::getAtomDihedrals | ( | const Atom & | atom, |
| AtomDihedralArray & | dihedrals | ||
| ) |
Fill an array of pointers to Dihedrals that contain an Atom.
| atom | the Atom of interest |
| dihedrals | an array to fill with pointers to dihedrals |
Definition at line 63 of file getAtomGroups.cpp.
References Util::FSArray< Data, Capacity >::append(), McMd::Molecule::atom(), Simp::Species::atomDihedralIds(), Util::FSArray< Data, Capacity >::clear(), McMd::Molecule::dihedral(), McMd::Atom::molecule(), McMd::Molecule::nDihedral(), Util::FSArray< Data, Capacity >::size(), and McMd::Molecule::species().
Referenced by McMd::DihedralPotentialImpl< Interaction >::atomEnergy().
| std::istream & McMd::operator>> | ( | std::istream & | in, |
| MaskPolicy & | policy | ||
| ) |
istream extractor for a MaskPolicy.
| in | input stream |
| policy | MaskPolicy to be read |
Definition at line 31 of file mcMd/chemistry/MaskPolicy.cpp.
References UTIL_THROW.
| std::ostream & McMd::operator<< | ( | std::ostream & | out, |
| MaskPolicy | policy | ||
| ) |
ostream inserter for an MaskPolicy.
| out | output stream |
| policy | MaskPolicy to be written |
Definition at line 49 of file mcMd/chemistry/MaskPolicy.cpp.
| void McMd::serialize | ( | Archive & | ar, |
| MaskPolicy & | policy, | ||
| const unsigned int | version | ||
| ) |
Serialize a MaskPolicy.
| ar | archive object |
| policy | object to be serialized |
| version | archive version id |
Definition at line 57 of file mcMd/chemistry/MaskPolicy.h.
References Util::serializeEnum().
| void McMd::commitMpiTypes | ( | ) |
Commit all MPI data types needed for Mc and Md simulations.
Definition at line 31 of file McMd_mpi.cpp.
References Simp::commitMpiSpeciesGroupTypes(), Util::Pair< Data >::commitMpiType(), Util::Vector::commitMpiType(), Util::IntVector::commitMpiType(), and commitMpiTypes().
Referenced by commitMpiTypes(), and McMd::Simulation::Simulation().
1.8.11