CAngleGrouping | |

CArray< T, N > | A fixed size array |

CAtom | The basic class for representing each particle |

►CAtomGroup | Group of atoms, such as all of them (AtomVec), or a smaller group such as a molecule, sidebranch, etc |

CAtomVec | The main class for representing particles |

CSCAtomVec | |

CSubGroup | |

CAtomIter | For iterating through an AtomGroup |

►CAtomRef | A pointer to an Atom |

►CAtomID | A pointer to an Atom, that also knows its own index in an AtomVec |

CCharged | |

CEisMclachlanAtom | |

►CEpsSigAtom | |

CEpsSigCutAtom | |

CEpsSigExpAtom | |

CEpsSigExpDragAtom | Repulsion potential with drag, with ε = √(ε₁ ε₂) and σ = (σ₁ + σ₂)/2 Potential is V(r) = ε/n (1 - r/σ)^n, with n = 5/2 usually cutoff at r = σ drag is f = -γv in the normal direction |

CFixedForceRegionAtom | |

CIEpsISigCutAtom | |

CIEpsISigExpAtom | |

CIEpsRepsSigCutAtom | |

CIEpsRepsSigExpCutAtom | |

CIEpsSigCutAtom | |

CLoisLinAtom | |

CLoisOhernAtom | |

CRandomForceAtom | |

CWallAtom | |

CBivariateGauss | A class for generating two random numbers from a Gaussian distribution, with a given correlation |

CBondAngle | |

CBondGrouping | |

►CBox | The virtual interface for the shape of the space and its boundaries |

CInfiniteBox | An infinite Box, for use with, e.g., sticky conglomerations or proteins |

►COriginBox | A rectilinear Box, with periodic boundary conditions |

CLeesEdwardsBox | Lees-Edwards boundary conditions, with shear in the x-direction, relative to y |

CWalledBox2D | |

CSCBox | A spheocylinder box, also known as a capsule |

CChargePair | |

CCNode | |

CCNodePath | |

►CCollection | |

►CCollectionCD | Collision-Driven Dynamics |

CCollectionCDBD | Collision-Driven Brownian-Dynamics |

►CCollectionCDgrid | |

CCollectionCDBDgrid | Collision-Driven Brownian-Dynamics |

CCollectionDamped | A damped Collection, equivalent to `CollectionSol` but without the random forces |

CCollectionGaussianT | |

CCollectionGear3A | |

CCollectionGear4A | |

CCollectionGear4NPH | |

CCollectionGear4NPT | |

CCollectionGear5A | |

CCollectionGear6A | |

►CCollectionNLCG | |

CCollectionNLCGFixedL | |

CCollectionNLCGV | |

CCollectionNoseHoover | |

CCollectionOverdamped | |

CCollectionRK4 | |

CCollectionSol | A Collection with a "solvent", using the Langevin equation |

CCollectionSolHT | |

CCollectionVerlet | |

CCollectionVerletNPT | |

CStaticCollec | A "static" Collection, that doesn't move |

CConnectivity | |

►CConstraint | |

CCoordCOMConstraint | |

CCoordConstraint | |

CDistConstraint | |

CLinearConstraint | |

CRelativeConstraint | |

CRigidConstraint | A class that enforces rigid-body dynamics |

CDihedral | |

CDihedralDerivs | |

CDihedralGrouping | |

CEisMclachlanPair | |

CEnergyForce | |

CEvent | |

CFixedForceAtom | |

CFixedSpringAtom | |

CForcePair | |

CForcePairX | |

►CFPairXFunct | |

CXRPSummer | |

CGaussVec | |

CGrid | A fast algorithm for finding all pairs of neighboring atoms |

CGridIterator | For iterating over all possible pairs |

CGridPairedIterator | For iterating over all pairs of a single Atom |

CIDPair | |

►CInteraction | The basic Interaction class, used to represent a potential function |

CAngleTriples | |

CBondPairs | |

CCharges | |

CCOMSpring | |

CDihedrals | |

CFixedForce | |

CFixedForceRegion | |

CFixedSpring | |

►CInteractionPairsX | |

CNListedVirial< A, P > | |

CNListed< A, P > | |

CRandomForce | |

CSCBoxed< A, P > | |

CSCSpringList | |

CSimpleListed< A, P > | |

CSoftWall | |

CSoftWallCylinder | |

►CInteractPair | |

CElectricScreened | |

CSpring | |

CISFTracker1 | |

►CJammingList | |

CJammingListRot | |

CJammingTree | A class for determining if two packings are the same |

►CJammingTreeRot | |

CJammingTreeBD | |

CLennardJonesCut | |

CLennardJonesCutPair | Truncated and shifted Lennard-Jones, in the form \(V(r) = \epsilon \left(\frac{\sigma^6}{r^6} - 1\right)^2\) |

CLJAttract | |

CLJAttractCut | |

CLJAttractCutPair | |

CLJAttractFixedRepulsePair | |

CLJAttractRepulsePair | |

CLJishPair | |

CLJRepulsePair | Repulsive LJ: \(V(r) = \epsilon \left(\frac{\sigma^6}{r^6} - 1\right)^2\) |

CLJRepulsive | |

►CLoisLinPair | |

CLoisLinPairMin | |

►CLoisOhernPair | |

CLoisOhernPairMinCLs | |

Cpyparm.packmin.Minimizer | |

►CNVector< T, N > | An N-dimensional vector, extending addition and subtraction from the type T to the NVector class |

CNumVector< T, N > | An N-dimensional physics vector, extending NVector |

►CNumVector< T, 2 > | |

CVector2< T > | A 2D physics vector, with methods for adding, subtracting, dot product, etc |

►CNumVector< T, 3 > | |

CVector3< T > | A 3D physics vector, with methods for adding, subtracting, dot product, etc |

►CNVector< C, N > | |

►CNumVector< C, 3 > | |

CVector3< C > | |

►CNVector< Vector3< C >, 3 > | |

CMatrix< C > | A 3x3 matrix, with methods for adding, subtracting, dot product, etc |

CPairList | A mapping of Atom -> [list of Atom], used by NeighborList to keep track of what atoms are near what other atoms |

CRepulsionDragPair | |

CRepulsionPair | Repulsion potential, with ε = √(ε₁ ε₂) and σ = (σ₁ + σ₂)/2 Potential is V(r) = ε/n (1 - r/σ)^n, with n = 5/2 usually cutoff at r = σ |

CRK4data | |

CRsqTracker1 | |

►CSCPair | |

CSCSpringPair | |

CSpheroCylinderDiff | |

►CStateTracker | The general interface for a "tracker", a class that needs to be called every timestep |

CContactTracker | |

CEnergyTracker | |

CISFTracker | |

CNeighborList | Maintains a Verlet list of "neighbors": molecules within a 'skin radius' of each other |

CRDiffs | |

CRsqTracker | |

CSmoothLocs | |