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 | |