| 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 | |
1.8.10
