Index

_

__init__() (CrossLinkedNetwork.CrossLinkedNetwork method) (DiscretizedFiber.DiscretizedFiber method) (Domain.Domain method) (Domain.PeriodicShearedDomain method) (DoubleEndedCrossLinkedNetwork.DoubleEndedCrossLinkedNetwork method) (FibCollocationDiscretization.ChebyshevDiscretization method) (FibCollocationDiscretization.FibCollocationDiscretization method) (fiberCollection.fiberCollection method) (fiberCollection.SemiflexiblefiberCollection method) (RPYVelocityEvaluator.GPUEwaldSplitter method) (RPYVelocityEvaluator.RPYVelocityEvaluator method) (SpatialDatabase.CellLinkedList method) (SpatialDatabase.ckDSpatial method) (SpatialDatabase.SpatialDatabase method) (StericForceEvaluator.SegmentBasedStericForceEvaluator method) (StericForceEvaluator.StericForceEvaluator method)

A

averageTangentVectors() (fiberCollection.fiberCollection method) averageTau() (FibCollocationDiscretization.FibCollocationDiscretization method)

averageXsXs() (FibCollocationDiscretization.FibCollocationDiscretization method) avgBundleAlignment() (CrossLinkedNetwork.CrossLinkedNetwork method)

B

BlockDiagPrecond() (fiberCollection.fiberCollection method) BrownianUpdate() (fiberCollection.fiberCollection method) (fiberCollection.SemiflexiblefiberCollection method)

BundleOrderParameters() (CrossLinkedNetwork.CrossLinkedNetwork method)

C

calcBendMatX0() (FibCollocationDiscretization.ChebyshevDiscretization method) calcBlobTotalVel() (RPYVelocityEvaluator.GPUEwaldSplitter method) (RPYVelocityEvaluator.RPYVelocityEvaluator method) calcCurvatures() (fiberCollection.fiberCollection method) calcFibCurvature() (FibCollocationDiscretization.FibCollocationDiscretization method) calcLinkStrains() (CrossLinkedNetwork.CrossLinkedNetwork method) calcMOneHalfW() (RPYVelocityEvaluator.GPUEwaldSplitter method) (RPYVelocityEvaluator.RPYVelocityEvaluator method) calcResidualVelocity() (fiberCollection.fiberCollection method) calcShifted() (Domain.PeriodicShearedDomain method) calcXFromXsAndMP() (FibCollocationDiscretization.ChebyshevDiscretization method)

calcXFromXsMap() (FibCollocationDiscretization.ChebyshevDiscretization method) calcXsAndMPFromX() (FibCollocationDiscretization.ChebyshevDiscretization method) CellLinkedList (class in SpatialDatabase) ChebyshevDiscretization (class in FibCollocationDiscretization) CheckContacts() (StericForceEvaluator.StericForceEvaluator method) CheckIntersectWithPrev() (StericForceEvaluator.StericForceEvaluator method) CheckResiduals() (fiberCollection.fiberCollection method) ckDSpatial (class in SpatialDatabase) CLForce() (CrossLinkedNetwork.CrossLinkedNetwork method) CLStress() (CrossLinkedNetwork.CrossLinkedNetwork method) ConnectionMatrix() (CrossLinkedNetwork.CrossLinkedNetwork method) CrossLinkedNetwork (class in CrossLinkedNetwork)

D

deleteLinksFromFibers() (DoubleEndedCrossLinkedNetwork.DoubleEndedCrossLinkedNetwork method) DiscretizedFiber (class in DiscretizedFiber)

Domain (class in Domain) DoubleEndedCrossLinkedNetwork (class in DoubleEndedCrossLinkedNetwork) DriftPlusBrownianVel() (fiberCollection.SemiflexiblefiberCollection method)

E

EliminatePairsOfPointsOutsideRange() (Domain.PeriodicShearedDomain method)

evalBendForce() (fiberCollection.fiberCollection method) evalU0() (fiberCollection.fiberCollection method)

F

FactorizePreconditioner() (fiberCollection.fiberCollection method) FibCollocationDiscretization (class in FibCollocationDiscretization) FiberBirthAndDeath() (fiberCollection.fiberCollection method) fiberCollection (class in fiberCollection) FiberStress() (fiberCollection.fiberCollection method) (fiberCollection.SemiflexiblefiberCollection method)

fillPointArrays() (fiberCollection.fiberCollection method) FindBundles() (CrossLinkedNetwork.CrossLinkedNetwork method) FindEigenvalueThreshold() (FibCollocationDiscretization.ChebyshevDiscretization method) formBlockDiagRHS() (fiberCollection.fiberCollection method) (fiberCollection.SemiflexiblefiberCollection method)

G

getDownsampledVelocity() (fiberCollection.fiberCollection method) getForcesForUpsampledQuad() (fiberCollection.fiberCollection method) getg() (fiberCollection.fiberCollection method) getPairsThatCanBind() (CrossLinkedNetwork.CrossLinkedNetwork method) getPeriodicLens() (Domain.PeriodicShearedDomain method) getPointsForUpsampledQuad() (fiberCollection.fiberCollection method) getPositions() (DiscretizedFiber.DiscretizedFiber method) getSortedLinks() (CrossLinkedNetwork.CrossLinkedNetwork method)

getStackInds() (fiberCollection.fiberCollection method) getSysDimension() (fiberCollection.fiberCollection method) getTauInds() (fiberCollection.fiberCollection method) getUniformPoints() (fiberCollection.fiberCollection method) getX() (fiberCollection.fiberCollection method) getXInds() (fiberCollection.fiberCollection method) getXs() (fiberCollection.fiberCollection method) GPUEwaldSplitter (class in RPYVelocityEvaluator)

I

initD4BC() (FibCollocationDiscretization.ChebyshevDiscretization method) initFib() (DiscretizedFiber.DiscretizedFiber method) initFibList() (fiberCollection.fiberCollection method) initFPMatrix() (FibCollocationDiscretization.ChebyshevDiscretization method)

initializeLambdaForNewFibers() (fiberCollection.fiberCollection method) initIs() (FibCollocationDiscretization.FibCollocationDiscretization method) initLocalcvals() (FibCollocationDiscretization.FibCollocationDiscretization method) initPointForceVelocityArrays() (fiberCollection.fiberCollection method) initUpsamplingMatricesForDirectQuad() (FibCollocationDiscretization.ChebyshevDiscretization method)

L

LocalOrientations() (CrossLinkedNetwork.CrossLinkedNetwork method)

LocalVelocity() (fiberCollection.fiberCollection method)

M

mapFibToStartingSite() (CrossLinkedNetwork.CrossLinkedNetwork method) mapSegToFiber() (StericForceEvaluator.SegmentBasedStericForceEvaluator method) mapSiteToFiber() (CrossLinkedNetwork.CrossLinkedNetwork method)

mapUniPtToFiber() (StericForceEvaluator.StericForceEvaluator method) MHalfAndMinusHalfEta() (fiberCollection.SemiflexiblefiberCollection method) MinPrimeShiftInPrimeCoords() (Domain.PeriodicShearedDomain method) Mobility() (fiberCollection.fiberCollection method)

N

nLinksAllSites() (CrossLinkedNetwork.CrossLinkedNetwork method) nonLocalVelocity() (fiberCollection.fiberCollection method)

numLinks() (CrossLinkedNetwork.CrossLinkedNetwork method) numLinksOnEachFiber() (CrossLinkedNetwork.CrossLinkedNetwork method)

O

otherNeighborsList() (SpatialDatabase.CellLinkedList method) (SpatialDatabase.ckDSpatial method) (SpatialDatabase.SpatialDatabase method)

P

passXsandX() (DiscretizedFiber.DiscretizedFiber method) PeriodicShearedDomain (class in Domain)

PretabulateGL() (StericForceEvaluator.SegmentBasedStericForceEvaluator method) primecoords() (Domain.PeriodicShearedDomain method) primeWaveNumbersFromUnprimed() (Domain.PeriodicShearedDomain method)

R

roundg() (Domain.PeriodicShearedDomain method)

RPYVelocityEvaluator (class in RPYVelocityEvaluator) RSAFibers() (fiberCollection.fiberCollection method)

S

safetyfactor() (Domain.PeriodicShearedDomain method) SegmentBasedStericForceEvaluator (class in StericForceEvaluator) selfNeighborList() (SpatialDatabase.CellLinkedList method) (SpatialDatabase.ckDSpatial method) (SpatialDatabase.SpatialDatabase method) SemiflexiblefiberCollection (class in fiberCollection) SetForceParameters() (StericForceEvaluator.StericForceEvaluator method) setLinks() (CrossLinkedNetwork.CrossLinkedNetwork method) (DoubleEndedCrossLinkedNetwork.DoubleEndedCrossLinkedNetwork method) setLinksFromFile() (CrossLinkedNetwork.CrossLinkedNetwork method) (DoubleEndedCrossLinkedNetwork.DoubleEndedCrossLinkedNetwork method)

sigmaFromNL() (CrossLinkedNetwork.CrossLinkedNetwork method) sitesPerFib() (DoubleEndedCrossLinkedNetwork.DoubleEndedCrossLinkedNetwork method) SparseMatrixOfConnections() (CrossLinkedNetwork.CrossLinkedNetwork method) SpatialDatabase (class in SpatialDatabase) SpringCOM() (CrossLinkedNetwork.CrossLinkedNetwork method) StackedValsToCoeffsMatrix() (FibCollocationDiscretization.ChebyshevDiscretization method) StepToMidpoint() (fiberCollection.SemiflexiblefiberCollection method) StericForceEvaluator (class in StericForceEvaluator) StericForces() (StericForceEvaluator.SegmentBasedStericForceEvaluator method) (StericForceEvaluator.StericForceEvaluator method) SubtractSelfTerms() (fiberCollection.fiberCollection method) syncPythonAndCpp() (DoubleEndedCrossLinkedNetwork.DoubleEndedCrossLinkedNetwork method)

T

TotalVelocity() (fiberCollection.fiberCollection method)

TrimListEuclideanDist() (SpatialDatabase.SpatialDatabase method)

U

uniformForce() (fiberCollection.fiberCollection method) UniformUpsamplingMatrix() (FibCollocationDiscretization.ChebyshevDiscretization method) unprimecoords() (Domain.PeriodicShearedDomain method) updateAllFibers() (fiberCollection.fiberCollection method) updateFarFieldArrays() (RPYVelocityEvaluator.GPUEwaldSplitter method)

updateLambdaAlpha() (fiberCollection.fiberCollection method) updateNetwork() (DoubleEndedCrossLinkedNetwork.DoubleEndedCrossLinkedNetwork method) updateSpatialStructures() (SpatialDatabase.CellLinkedList method) (SpatialDatabase.ckDSpatial method) (SpatialDatabase.SpatialDatabase method)

W

writeFiberLocations() (fiberCollection.fiberCollection method)

writeLinks() (CrossLinkedNetwork.CrossLinkedNetwork method)

Z

ZeroLShiftInPrimeCoords() (Domain.PeriodicShearedDomain method)