Index

A

absor namespace addToLibrary function analyzeResident function

applyFile function atomKeys variable atomType variable

B

basalConditions function, [1], [2] basalNeighbours function basalPrismConditions function basalRingsSeparation function Bond group

bond namespace brokenRings function buildRingSearchIndex function, [1] Bulk prisms group bulkPolygonRingAnalysis function

C

Cage group cage namespace cage::Cage struct cage::CageShape struct cage::EdgeWindow struct cage::FormerRow struct cage::FoundCage struct cage::Signature struct cageAffiliation function cageCounts function cageOfGuest variable cageRings function calcCoverageArea function calcMatrixN function calcMatrixS function calcScaleFactor function cappedRings function centerWRTcentroid function centreDistance variable certificate variable certified variable changeDiaCageOrder function changeHexCageOrder function Chill group chill namespace chill::BondClassifier struct

chill::ChillPlusResult struct chill::LinearClassifier struct chill::QlmAtom struct chill::SteinhardtQl struct chill::TemplateHit struct chill::VoronoiWeights struct chill::YlmAtom struct class nneigh::SkinNeighborList primitive::RingUpdater ring::AffiliationUpdater ring::NeighBond classes variable classifyTemplates function closed variable Clump group clump namespace clump::Domain struct clusterOf variable clusterOfIon variable coloured variable, [1] conditionOneDDC function, [1] contractibleRings function coordsOfVertices function counts variable createPrismBlock function crossings variable CrystalKind enum

D

danglingEdges variable ddc variable, [1] ddcFrom function

decompose function densityZ function, [1] depth variable

E

edges variable edgeWindowSpec function emitBasalFrom function enum CrystalKind Family GlassKind Int8Backend IonState Kind Mode Reduction

enumSixFrom function equatorial variable equatorialConditions function exportEnviron function

F

faces variable Family enum fillPointSetPrismBlock function fillPointSetPrismRing function findBulkPrisms function findBySignature function, [1], [2], [3] findBySignatures function findDDC function, [1] findHC function, [1] findIncompleteBySignature function findMixedRings function findPrismatic function, [1] fingerprint function formerRows function frameDensity function, [1] free variable function addToLibrary analyzeResident applyFile basalConditions, [1], [2] basalNeighbours basalPrismConditions basalRingsSeparation brokenRings buildRingSearchIndex, [1] bulkPolygonRingAnalysis cageAffiliation cageCounts cageRings calcCoverageArea calcMatrixN calcMatrixS calcScaleFactor cappedRings centerWRTcentroid changeDiaCageOrder changeHexCageOrder classifyTemplates conditionOneDDC, [1] contractibleRings coordsOfVertices createPrismBlock ddcFrom decompose densityZ, [1] edgeWindowSpec emitBasalFrom enumSixFrom equatorialConditions exportEnviron fillPointSetPrismBlock fillPointSetPrismRing findBulkPrisms findBySignature, [1], [2], [3] findBySignatures findDDC, [1] findHC, [1] findIncompleteBySignature findMixedRings findPrismatic, [1] fingerprint formerRows frameDensity, [1] getAtomTypesTopoBulk getAvgHeightPrismBlock getPointSetCage getPointSetRefRing getRadiusFromRings getRMSD getStrucNumbers glassFromDensity, [1], [2] guestOccupancy guestOccupancyInside hex hilbertKey hopBoundPrimitiveSix hopNeighbourhood hopsAtMost hornAbsOrientation hostCageCounts hostChillPlus hydrogenMSD incrementalFingerprint insideRayDirections invertOneRing ionEnvironment isClosedPolyhedron isSpherePolyhedron jumpRotorTau90 lastReclassified load localDensity localKey makePath matchLibraries matchLibrary matchPrism matchPrismBlock matchUntetheredPrism maximumEquators meanFinite normHeightPercent notNeighboursOfRing openChannelCount overlayVertices parseEdgeWindow pathFromArgv periodicCentroid pointInFacesTrace positionRank preferOffload printRDF projAreaSingleRing protonKey quat2RotMatrix relaxedPrismConditions relOrderDDC, [1] relOrderHC relOrderPrismBlock, [1] ringAdjacentCompletion rings rodgerF4 sameNetwork seededCageAffiliation, [1] seenEarlier setBatchFraction shapeOfVertices shellRingCensus soapSpectrum soapSpectrumAll specializedCageCounts, [1] specializedChillPlus speciesCycleMatches steinhardtQlVoronoi subCloud summarize topoBulkAnalysis tumLayerStack update updatePerAtomRMSDRing updateRMSDRing voronoiFacetWeights voronoiFeature voronoiFeatures wlHash writeAllCages writeBasalRingsHex writeBasalRingsPrism writeCluster writeClusterStats writeDump writeEachCage writeHisto writeLAMMPSdata writeLAMMPSdataAllPrisms writeLAMMPSdataAllRings writeLAMMPSdataCages writeLAMMPSdataPrisms writeLAMMPSdataTopoBulk writeLAMMPSdumpCages writeLAMMPSdumpINT writeLAMMPSdumpSlice writeLibrary writeMoleculeIDsExpressionSelectOVITO writeMoleculeIDsInSlice writePrismNum writePrisms writeRingNum writeRingNumBulk writeRings writeTopoBulkData writeXYZcluster

G

Gen group gen namespace gen::FracBox struct gen::mic namespace getAtomTypesTopoBulk function getAvgHeightPrismBlock function getPointSetCage function getPointSetRefRing function getRadiusFromRings function getRMSD function getStrucNumbers function glassFromDensity function, [1], [2] GlassKind enum global namespace gpu namespace

gpu::BatchResult struct gpu::DeviceInfo struct gpu::Footprint struct gpu::Plan struct group Bond Bulk prisms Cage Chill Clump Gen MolSys Nneigh Primitive Rdf Rdf2 Ring Sinp guestOccupancy function guestOccupancyInside function guestsPerCage variable

H

hex function hilbertKey function hopBoundPrimitiveSix function hopNeighbourhood function hopsAtMost function

hornAbsOrientation function hostCageCounts function hostChillPlus function hydrogenMSD function

I

iceFraction variable incrementalFingerprint function insideRayDirections function Int8Backend enum invertOneRing function ion variable ionEnvironment function

ionsInCluster variable IonState enum ira namespace ira::Match struct ira::PointGroup struct isClosedPolyhedron function isSpherePolyhedron function

J

jumpRotorTau90 function

K

key variable, [1] Kind enum

kInsideRelTol variable kRowCap variable

L

labelOf variable labels variable lastReclassified function load function

local variable localDensity function localKey function

M

makePath function match namespace matchLibraries function matchLibrary function matchPrism function matchPrismBlock function matchUntetheredPrism function maximumEquators function meanFinite function

members variable method variable, [1], [2] Mode enum MolSys group molSys namespace molSys::Point struct molSys::PointCloud struct molSys::Result struct multiply variable

N

namespace absor bond cage chill clump gen gen::mic global gpu ira match molSys nneigh phase pntToPnt primitive prism3 rdf rdf2 ring seams seams::cfg seams::domain seams::product seams::sphericart_ylm seams::steinhardt sinp site sout sph std topo topoparam tum tum3 tum::device

Nneigh group nneigh namespace nneigh::SkinNeighborList class normHeightPercent function notNeighboursOfRing function

O

occupancyHistogram variable occupied variable onFace variable openChannelCount function

overlayVertices function owned variable owner variable

P

parseEdgeWindow function pathFromArgv function periodicCentroid function phase namespace phase::IceXXIHit struct pntToPnt namespace pointInFacesTrace function positionRank function preferOffload function

Primitive group primitive namespace primitive::Graph struct primitive::RingUpdater class primitive::Vertex struct printRDF function prism3 namespace projAreaSingleRing function protonKey function

Q

quat2RotMatrix function

R

rays variable Rdf group rdf namespace Rdf2 group rdf2 namespace rdf::PartialRdf struct Reduction enum relaxedPrismConditions function relOrderDDC function, [1] relOrderHC function relOrderPrismBlock function, [1] rho variable Ring group ring namespace

ring::AffiliationUpdater class ring::CageAffiliation struct ring::EquatorChoice struct ring::NeighBond class ring::PackingCertificate struct ring::RingSearchIndex struct ring::SeededAtomLabels struct ring::StackingPlanes struct ringAdjacentCompletion function ringCensus variable rings function ringShift variable rodgerF4 function Rows typedef

S

sameNetwork function seams namespace seams::cfg namespace seams::cfg::Runtime struct seams::domain namespace seams::domain::RingSummary struct seams::domain::Share struct seams::product namespace seams::product::Cij struct seams::product::ComplexDot struct seams::product::GemmInfo struct seams::product::RealDot struct seams::sphericart_ylm namespace seams::steinhardt namespace seededCageAffiliation function, [1] seenEarlier function setBatchFraction function shapeOfVertices function shell variable shellRingCensus function Sinp group sinp namespace site namespace site::DensityZ struct site::GuestOccupancy struct site::IceClusterIons struct site::InsideTrace struct site::IonEnvironment struct site::Table struct sizeCount variable soapSpectrum function soapSpectrumAll function sout namespace specializedCageCounts function, [1] specializedChillPlus function

speciesCycleMatches function sph namespace std namespace steinhardtQlVoronoi function struct cage::Cage cage::CageShape cage::EdgeWindow cage::FormerRow cage::FoundCage cage::Signature chill::BondClassifier chill::ChillPlusResult chill::LinearClassifier chill::QlmAtom chill::SteinhardtQl chill::TemplateHit chill::VoronoiWeights chill::YlmAtom clump::Domain gen::FracBox gpu::BatchResult gpu::DeviceInfo gpu::Footprint gpu::Plan ira::Match ira::PointGroup molSys::Point molSys::PointCloud molSys::Result phase::IceXXIHit primitive::Graph primitive::Vertex rdf::PartialRdf ring::CageAffiliation ring::EquatorChoice ring::PackingCertificate ring::RingSearchIndex ring::SeededAtomLabels ring::StackingPlanes seams::cfg::Runtime seams::domain::RingSummary seams::domain::Share seams::product::Cij seams::product::ComplexDot seams::product::GemmInfo seams::product::RealDot site::DensityZ site::GuestOccupancy site::IceClusterIons site::InsideTrace site::IonEnvironment site::Table topo::FrameFingerprint topo::KeyLibrary topo::LibraryMatch topo::LocalKey topoparam::LayerStack tum::CageCounts tum::SpecializedCaps subCloud function summarize function

T

topo namespace topo::FrameFingerprint struct topo::KeyLibrary struct topo::LibraryMatch struct topo::LocalKey struct topoBulkAnalysis function topoparam namespace topoparam::LayerStack struct

tum namespace tum3 namespace tum::CageCounts struct tum::device namespace tum::SpecializedCaps struct tumLayerStack function type variable typedef Rows

U

update function updatePerAtomRMSDRing function

updateRMSDRing function

V

variable atomKeys atomType cageOfGuest centreDistance certificate certified classes closed clusterOf clusterOfIon coloured, [1] counts crossings danglingEdges ddc, [1] depth edges equatorial faces free guestsPerCage iceFraction ion ionsInCluster key, [1] kInsideRelTol kRowCap labelOf labels local members method, [1], [2] multiply occupancyHistogram occupied onFace owned owner rays rho ringCensus ringShift shell sizeCount type vertices, [1] weights wlAtom

vertices variable, [1] voronoiFacetWeights function voronoiFeature function voronoiFeatures function

W

weights variable wlAtom variable wlHash function writeAllCages function writeBasalRingsHex function writeBasalRingsPrism function writeCluster function writeClusterStats function writeDump function writeEachCage function writeHisto function writeLAMMPSdata function writeLAMMPSdataAllPrisms function writeLAMMPSdataAllRings function writeLAMMPSdataCages function

writeLAMMPSdataPrisms function writeLAMMPSdataTopoBulk function writeLAMMPSdumpCages function writeLAMMPSdumpINT function writeLAMMPSdumpSlice function writeLibrary function writeMoleculeIDsExpressionSelectOVITO function writeMoleculeIDsInSlice function writePrismNum function writePrisms function writeRingNum function writeRingNumBulk function writeRings function writeTopoBulkData function writeXYZcluster function