ParM
parm
A molecular dynamics library

►Npyparm  
CAngleGrouping  
CAngleTriples  
CArray  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 
CAtomID  A pointer to an Atom, that also knows its own index in an AtomVec 
CAtomIter  For iterating through an AtomGroup 
CAtomRef  A pointer to an Atom 
CAtomVec  The main class for representing particles 
CBivariateGauss  A class for generating two random numbers from a Gaussian distribution, with a given correlation 
CBondAngle  
CBondGrouping  
CBondPairs  
CBox  The virtual interface for the shape of the space and its boundaries 
CCharged  
CChargePair  
CCharges  
CCNode  
CCNodePath  
CCollection  
CCollectionCD  CollisionDriven Dynamics 
CCollectionCDBD  CollisionDriven BrownianDynamics 
CCollectionCDBDgrid  CollisionDriven BrownianDynamics 
CCollectionCDgrid  
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  
CCOMSpring  
CConnectivity  
CConstraint  
CContactTracker  
CCoordCOMConstraint  
CCoordConstraint  
CDihedral  
CDihedralDerivs  
CDihedralGrouping  
CDihedrals  
CDistConstraint  
CEisMclachlanAtom  
CEisMclachlanPair  
CElectricScreened  
CEnergyForce  
CEnergyTracker  
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 
CEvent  
CFixedForce  
CFixedForceAtom  
CFixedForceRegion  
CFixedForceRegionAtom  
CFixedSpring  
CFixedSpringAtom  
CForcePair  
CForcePairX  
CFPairXFunct  
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  
CIEpsISigCutAtom  
CIEpsISigExpAtom  
CIEpsRepsSigCutAtom  
CIEpsRepsSigExpCutAtom  
CIEpsSigCutAtom  
CInfiniteBox  An infinite Box, for use with, e.g., sticky conglomerations or proteins 
CInteraction  The basic Interaction class, used to represent a potential function 
CInteractionPairsX  
CInteractPair  
CISFTracker  
CISFTracker1  
CJammingList  
CJammingListRot  
CJammingTree  A class for determining if two packings are the same 
CJammingTreeBD  
CJammingTreeRot  
CLeesEdwardsBox  LeesEdwards boundary conditions, with shear in the xdirection, relative to y 
CLennardJonesCut  
CLennardJonesCutPair  Truncated and shifted LennardJones, in the form \(V(r) = \epsilon \left(\frac{\sigma^6}{r^6}  1\right)^2\) 
CLinearConstraint  
CLJAttract  
CLJAttractCut  
CLJAttractCutPair  
CLJAttractFixedRepulsePair  
CLJAttractRepulsePair  
CLJishPair  
CLJRepulsePair  Repulsive LJ: \(V(r) = \epsilon \left(\frac{\sigma^6}{r^6}  1\right)^2\) 
CLJRepulsive  
CLoisLinAtom  
CLoisLinPair  
CLoisLinPairMin  
CLoisOhernAtom  
CLoisOhernPair  
CLoisOhernPairMinCLs  
CMatrix  A 3x3 matrix, with methods for adding, subtracting, dot product, etc 
CNeighborList  Maintains a Verlet list of "neighbors": molecules within a 'skin radius' of each other 
CNListed  
CNListedVirial  
CNumVector  An Ndimensional physics vector, extending NVector 
CNVector  An Ndimensional vector, extending addition and subtraction from the type T to the NVector class 
COriginBox  A rectilinear Box, with periodic boundary conditions 
CPairList  A 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  
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 
CRigidConstraint  A class that enforces rigidbody dynamics 
CRK4data  
CRsqTracker  
CRsqTracker1  
CSCAtomVec  
CSCBox  A spheocylinder box, also known as a capsule 
CSCBoxed  
CSCPair  
CSCSpringList  
CSCSpringPair  
CSimpleListed  
CSmoothLocs  
CSoftWall  
CSoftWallCylinder  
CSpheroCylinderDiff  
CSpring  
CStateTracker  The general interface for a "tracker", a class that needs to be called every timestep 
CStaticCollec  A "static" Collection, that doesn't move 
CSubGroup  
CVector2  A 2D physics vector, with methods for adding, subtracting, dot product, etc 
CVector3  A 3D physics vector, with methods for adding, subtracting, dot product, etc 
CWallAtom  
CWalledBox2D  
CXRPSummer 