ParM  parm
A molecular dynamics library
Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level 123]
 Npyparm
 CAngleGrouping
 CAngleTriples
 CArrayA fixed size array
 CAtomThe basic class for representing each particle
 CAtomGroupGroup of atoms, such as all of them (AtomVec), or a smaller group such as a molecule, sidebranch, etc
 CAtomIDA pointer to an Atom, that also knows its own index in an AtomVec
 CAtomIterFor iterating through an AtomGroup
 CAtomRefA pointer to an Atom
 CAtomVecThe main class for representing particles
 CBivariateGaussA class for generating two random numbers from a Gaussian distribution, with a given correlation
 CBondAngle
 CBondGrouping
 CBondPairs
 CBoxThe virtual interface for the shape of the space and its boundaries
 CCharged
 CChargePair
 CCharges
 CCNode
 CCNodePath
 CCollection
 CCollectionCDCollision-Driven Dynamics
 CCollectionCDBDCollision-Driven Brownian-Dynamics
 CCollectionCDBDgridCollision-Driven Brownian-Dynamics
 CCollectionCDgrid
 CCollectionDampedA damped Collection, equivalent to CollectionSol but without the random forces
 CCollectionGaussianT
 CCollectionGear3A
 CCollectionGear4A
 CCollectionGear4NPH
 CCollectionGear4NPT
 CCollectionGear5A
 CCollectionGear6A
 CCollectionNLCG
 CCollectionNLCGFixedL
 CCollectionNLCGV
 CCollectionNoseHoover
 CCollectionOverdamped
 CCollectionRK4
 CCollectionSolA Collection with a "solvent", using the Langevin equation
 CCollectionSolHT
 CCollectionVerlet
 CCollectionVerletNPT
 CCOMSpring
 CConnectivity
 CConstraint
 CContactTracker
 CCoordCOMConstraint
 CCoordConstraint
 CDihedral
 CDihedralDerivs
 CDihedralGrouping
 CDihedrals
 CDistConstraint
 CEisMclachlanAtom
 CEisMclachlanPair
 CElectricScreened
 CEnergyForce
 CEnergyTracker
 CEpsSigAtom
 CEpsSigCutAtom
 CEpsSigExpAtom
 CEpsSigExpDragAtomRepulsion 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
 CEvent
 CFixedForce
 CFixedForceAtom
 CFixedForceRegion
 CFixedForceRegionAtom
 CFixedSpring
 CFixedSpringAtom
 CForcePair
 CForcePairX
 CFPairXFunct
 CGaussVec
 CGridA fast algorithm for finding all pairs of neighboring atoms
 CGridIteratorFor iterating over all possible pairs
 CGridPairedIteratorFor iterating over all pairs of a single Atom
 CIDPair
 CIEpsISigCutAtom
 CIEpsISigExpAtom
 CIEpsRepsSigCutAtom
 CIEpsRepsSigExpCutAtom
 CIEpsSigCutAtom
 CInfiniteBoxAn infinite Box, for use with, e.g., sticky conglomerations or proteins
 CInteractionThe basic Interaction class, used to represent a potential function
 CInteractionPairsX
 CInteractPair
 CISFTracker
 CISFTracker1
 CJammingList
 CJammingListRot
 CJammingTreeA class for determining if two packings are the same
 CJammingTreeBD
 CJammingTreeRot
 CLeesEdwardsBoxLees-Edwards boundary conditions, with shear in the x-direction, relative to y
 CLennardJonesCut
 CLennardJonesCutPairTruncated and shifted Lennard-Jones, in the form \(V(r) = \epsilon \left(\frac{\sigma^6}{r^6} - 1\right)^2\)
 CLinearConstraint
 CLJAttract
 CLJAttractCut
 CLJAttractCutPair
 CLJAttractFixedRepulsePair
 CLJAttractRepulsePair
 CLJishPair
 CLJRepulsePairRepulsive LJ: \(V(r) = \epsilon \left(\frac{\sigma^6}{r^6} - 1\right)^2\)
 CLJRepulsive
 CLoisLinAtom
 CLoisLinPair
 CLoisLinPairMin
 CLoisOhernAtom
 CLoisOhernPair
 CLoisOhernPairMinCLs
 CMatrixA 3x3 matrix, with methods for adding, subtracting, dot product, etc
 CNeighborListMaintains a Verlet list of "neighbors": molecules within a 'skin radius' of each other
 CNListed
 CNListedVirial
 CNumVectorAn N-dimensional physics vector, extending NVector
 CNVectorAn N-dimensional vector, extending addition and subtraction from the type T to the NVector class
 COriginBoxA rectilinear Box, with periodic boundary conditions
 CPairListA mapping of Atom -> [list of Atom], used by NeighborList to keep track of what atoms are near what other atoms
 CRandomForce
 CRandomForceAtom
 CRDiffs
 CRelativeConstraint
 CRepulsionDragPair
 CRepulsionPairRepulsion 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
 CRigidConstraintA class that enforces rigid-body dynamics
 CRK4data
 CRsqTracker
 CRsqTracker1
 CSCAtomVec
 CSCBoxA spheocylinder box, also known as a capsule
 CSCBoxed
 CSCPair
 CSCSpringList
 CSCSpringPair
 CSimpleListed
 CSmoothLocs
 CSoftWall
 CSoftWallCylinder
 CSpheroCylinderDiff
 CSpring
 CStateTrackerThe general interface for a "tracker", a class that needs to be called every timestep
 CStaticCollecA "static" Collection, that doesn't move
 CSubGroup
 CVector2A 2D physics vector, with methods for adding, subtracting, dot product, etc
 CVector3A 3D physics vector, with methods for adding, subtracting, dot product, etc
 CWallAtom
 CWalledBox2D
 CXRPSummer