Index

Symbols

~RingUpdater (C++ function)

A

absor namespace angDistDegQuaternions (C++ function) assignPolygonType (C++ function) assignPrismType (C++ function) atom_state_type (C++ enum) atom_state_type::clathrate (C++ enumerator) atom_state_type::cubic (C++ enumerator) atom_state_type::hexagonal (C++ enumerator) atom_state_type::interClathrate (C++ enumerator) atom_state_type::interfacial (C++ enumerator)

atom_state_type::reCubic (C++ enumerator) atom_state_type::reHex (C++ enumerator) atom_state_type::unclassified (C++ enumerator) atom_state_type::water (C++ enumerator) atomID (C++ member) atomIndex (C++ member) atomInSlice (C++ function) atomsFromCages (C++ function) atomsInSingleSlice (C++ function) averageRMSDatom (C++ function) avgVector (C++ function)

B

basalConditions function basalNeighbours function basalPrismConditions function basalPrismConditions (C++ function) basalRingsSeparation function BatchPeriodicDistSq function Bond group bond namespace bond_type (C++ enum) bond_type::eclipsed (C++ enumerator) bond_type::out_of_range (C++ enumerator) bond_type::staggered (C++ enumerator)

bondClassifier (C++ function) bondClassifierNames (C++ function) BondGraph (C++ enum) BondGraph::Cutoff (C++ enumerator) BondGraph::KnnMutual (C++ enumerator) BondGraph::KnnUnion (C++ enumerator) bondGraphFromName (C++ function) bondGraphName (C++ function) bonds (C++ function) box (C++ member) boxLow (C++ member) buildRefDDC (C++ function) buildRefHC (C++ function) buildRingSearchIndex function Bulk prisms group bulkPolygonRingAnalysis function

C

c_ij (C++ member) c_value (C++ member) Cage group cage namespace cage::Cage struct cage::Cage (C++ struct) cageAffiliation function cageType (C++ enum) cageType::DoubleDiaC (C++ enumerator) cageType::HexC (C++ enumerator) calcCoverageArea function calcMatrixN function calcMatrixS function calcMedian (C++ function) calcScaleFactor function centerWRTcentroid function certified variable changeDiaCageOrder function changeHexCageOrder function Chill group chill namespace chill::BondClassifier struct chill::BondClassifier (C++ struct) chill::LinearClassifier struct chill::QlmAtom struct chill::QlmAtom (C++ struct) chill::SteinhardtQl struct chill::SteinhardtQl (C++ struct)

chill::TemplateHit struct chill::VoronoiWeights struct chill::YlmAtom struct chill::YlmAtom (C++ struct) chillPlusRule (C++ function) chillRule (C++ function) class nneigh::SkinNeighborList primitive::RingUpdater ring::AffiliationUpdater classifier (C++ member) classifyBonds (C++ function) classifyTemplates function clearGraph (C++ function) clearNeighbourList (C++ function) clearPointCloud (C++ function) clearRingList (C++ function) Clump group clump namespace clusterAnalysis (C++ function) clusterCages (C++ function) commonElementsInThreeRings (C++ function) compareByAtomID (C++ function) compareRings (C++ function) conditionOneDDC function, [1] conditionThreeDDC function conditionTwoDDC function, [1] coordinationNumber (C++ member) countAllRingsFromIndex (C++ function) createBondsFromCages (C++ function) createIDMolIDmap (C++ function) createMolIDAtomIDMultiMap (C++ function) createPrismBlock function CrystalKind enum currentFrame (C++ member)

D

ddc variable, [1] deformedPrismTypes (C++ function)

discardExtraTetragonBlocks (C++ function) distance (C++ function) dropLammpsDumpIndex (C++ function)

E

eclipsedMax (C++ member) eclipsedMin (C++ member)

eigenVecAngle (C++ function) enum CrystalKind

F

file_exists (C++ function) fillPointSetPrismBlock function fillPointSetPrismRing function findBulkPrisms function findDDC function, [1] findHC function, [1] findMixedRings function findPrismatic function, [1] findPrisms (C++ function) findRings (C++ function) findsCommonElements (C++ function) findTripletInRing (C++ function) forEachLammpsFrame (C++ function) function basalConditions basalNeighbours basalPrismConditions basalRingsSeparation BatchPeriodicDistSq buildRingSearchIndex bulkPolygonRingAnalysis cageAffiliation calcCoverageArea calcMatrixN calcMatrixS calcScaleFactor centerWRTcentroid changeDiaCageOrder changeHexCageOrder classifyTemplates conditionOneDDC, [1] conditionThreeDDC conditionTwoDDC, [1] createPrismBlock fillPointSetPrismBlock fillPointSetPrismRing findBulkPrisms findDDC, [1] findHC, [1] findMixedRings findPrismatic, [1] getAtomTypesTopoBulk getAvgHeightPrismBlock getPointSetCage getPointSetRefRing getRadiusFromRings getRMSD getStrucNumbers hornAbsOrientation lastReclassified makePath matchPrism matchPrismBlock matchUntetheredPrism normHeightPercent notNeighboursOfRing printRDF projAreaSingleRing quat2RotMatrix relaxedPrismConditions relOrderDDC, [1] relOrderHC relOrderPrismBlock, [1] seededCageAffiliation soapSpectrum soapSpectrumAll steinhardtQlVoronoi topoBulkAnalysis update updatePerAtomRMSDRing updateRMSDRing voronoiFacetWeights voronoiFeature voronoiFeatures writeAllCages writeBasalRingsHex writeBasalRingsPrism writeCluster writeClusterStats writeDump writeEachCage writeHisto writeLAMMPSdata writeLAMMPSdataAllPrisms writeLAMMPSdataAllRings writeLAMMPSdataCages writeLAMMPSdataPrisms writeLAMMPSdataTopoBulk writeLAMMPSdumpCages writeLAMMPSdumpINT writeLAMMPSdumpSlice writeMoleculeIDsExpressionSelectOVITO writeMoleculeIDsInSlice writePrismNum writePrisms writeRingNum writeRingNumBulk writeRings writeTopoBulkData writeXYZcluster

G

Gen group gen namespace getAtomTypesTopoBulk function getAverageWithoutOutliers (C++ function) getAvgHeightPrismBlock function getCorrel (C++ function) getCorrelPlus (C++ function) getEdgeMoleculesInRings (C++ function) getHbondDistanceOH (C++ function) getIceType (C++ function) getIceTypeNoPrint (C++ function) getIceTypePlus (C++ function) getIceTypePlusNoPrint (C++ function) getInpFileList (C++ function) getNewNeighbourListByIndex (C++ function) getPlaneArea (C++ function) getPointCloudOneAtomType (C++ function) getPointSetCage function getPointSetRefRing function

getq6 (C++ function) getRadiusFromRings function getRMSD function getSingleRingSize (C++ function) getStrucNumbers function getSystemLengths (C++ function) global namespace graph (C++ function) group Bond Bulk prisms Cage Chill Clump Gen MolSys Nneigh Primitive Rdf2 Ring Sinp

H

halfNeighList (C++ function) hasCommonElements (C++ function)

hAtomMolList (C++ function) hornAbsOrientation function

I

iceType (C++ enum) (C++ member) iceType::ddc (C++ enumerator) iceType::dummy (C++ enumerator) iceType::hc (C++ enumerator) iceType::mixed (C++ enumerator) iceType::mixed2 (C++ enumerator) iceType::pnc (C++ enumerator) idIndexMap (C++ member)

inGraph (C++ member) inSlice (C++ member) ira namespace ira::Match struct ira::PointGroup struct isInterfacial (C++ function)

K

keepAxialRingsOnly (C++ function)

kNearestNeighbourList (C++ function) kNearestNeighbourPair (C++ function)

L

largestIceCluster (C++ function) lastBallsRefreshed (C++ function) lastChangedAtoms (C++ function) lastRebuilt (C++ function) lastReclassified function lastRecomputedSources (C++ function)

lookupTableQ3 (C++ function) lookupTableQ3Vec (C++ function) lookupTableQ4 (C++ function) lookupTableQ4Vec (C++ function) lookupTableQ6 (C++ function) lookupTableQ6Vec (C++ function) lookupTableQ8 (C++ function) lookupTableQ8Vec (C++ function)

M

makePath function match namespace matchPrism function matchPrismBlock function matchUntetheredPrism function moleculesInSingleSlice (C++ function) molID (C++ member)

MolSys group molSys namespace molSys::Point struct molSys::Point (C++ struct) molSys::PointCloud struct molSys::PointCloud (C++ struct) molSys::Result struct molSys::Result (C++ struct)

N

namespace absor bond cage chill clump gen global ira match molSys nneigh pntToPnt primitive prism3 rdf2 ring seams seams::sphericart_ylm seams::steinhardt sinp sout sph std topoparam tum3

neighbourListByIndex (C++ function) neighList (C++ function) neighListIndex (C++ member) neighListO (C++ function) nLammpsFrames (C++ function) Nneigh group nneigh namespace nneigh::SkinNeighborList class nneigh::SkinNeighborList (C++ class) nop (C++ member) normalizeRDF (C++ function) normHeightPercent function notNeighboursOfRing function numStaggered (C++ function)

O

operator= (C++ function), [1]

P

periodicDist (C++ function) periodicDistSq (C++ function) pi (C++ member) pntToPnt namespace polygonRingAnalysis (C++ function) populateBonds (C++ function), [1] populateGraphFromIndices (C++ function) populateGraphFromNListID (C++ function) populateHbonds (C++ function) populateHbondsWithInputClouds (C++ function) prettyPrintYoda (C++ function) Primitive group primitive namespace primitive::Graph struct

primitive::Graph (C++ struct) primitive::RingUpdater class primitive::RingUpdater (C++ class) primitive::Vertex struct primitive::Vertex (C++ struct) printIceType (C++ function) printRDF function printSliceGetEdgeMoleculesInRings (C++ function) prism3 namespace prismAnalysis (C++ function) projAreaSingleRing function ptq (C++ member) pts (C++ member), [1]

Q

ql (C++ member) qlBar (C++ member)

quat2RotMatrix function

R

radDeg (C++ function) radialCoord (C++ function) Rdf2 group rdf2 namespace rdf2Danalysis_AA (C++ function) readBonds (C++ function) readLammpsTrj (C++ function) readLammpsTrjO (C++ function) readLammpsTrjreduced (C++ function) readXYZ (C++ function) recenterClusterCloud (C++ function) reclassifyWater (C++ function) registerBondClassifier (C++ function) relaxedPrismConditions function relaxedPrismConditions (C++ function) relDist (C++ function) relOrderDDC function, [1]

relOrderHC function relOrderPrismBlock function, [1] removeNonSPrings (C++ function) restoreEdgesFromIndices (C++ function) Ring group ring namespace ring::AffiliationUpdater class ring::CageAffiliation struct ring::RingSearchIndex struct ring::SeededAtomLabels struct ringNetwork (C++ function) rings (C++ member), [1] RingUpdater (C++ function), [1], [2] rmAxialTranslations (C++ function)

S

sampleRDF_AA (C++ function) seams namespace seams::sphericart_ylm namespace seams::steinhardt namespace searchMolList (C++ function) seededCageAffiliation function setAtomsWithSameMolID (C++ function) shapeMatchDDC (C++ function) shapeMatchHC (C++ function) shellSeparation (C++ function) shortestPath (C++ function) singleClusterLinkedList (C++ function) Sinp group sinp namespace SkinNeighborList (C++ function) soapSpectrum function soapSpectrumAll function sout namespace sph namespace spheriHarmo (C++ function) staggeredMax (C++ member) std namespace

steinhardtQl (C++ function) steinhardtQlVoronoi function struct cage::Cage chill::BondClassifier chill::LinearClassifier chill::QlmAtom chill::SteinhardtQl chill::TemplateHit chill::VoronoiWeights chill::YlmAtom ira::Match ira::PointGroup molSys::Point molSys::PointCloud molSys::Result primitive::Graph primitive::Vertex ring::CageAffiliation ring::RingSearchIndex ring::SeededAtomLabels strucType (C++ enum) strucType::bothBasal (C++ enumerator) strucType::bothPrismatic (C++ enumerator) strucType::DDC (C++ enumerator) strucType::deformedPrism (C++ enumerator) strucType::HCbasal (C++ enumerator) strucType::HCprismatic (C++ enumerator) strucType::mixedPrismRing (C++ enumerator) strucType::Prism (C++ enumerator) strucType::unclassified (C++ enumerator)

T

tokenizer (C++ function) tokenizerDouble (C++ function) tokenizerInt (C++ function) topoBulkAnalysis function topoBulkCriteria (C++ function) topoparam namespace

topoUnitMatchingBulk (C++ function) triclinicMinImage (C++ function) trimBonds (C++ function) tum3 namespace type (C++ member), [1]

U

unwrappedCoordShift (C++ function) unWrappedDistFromPoint (C++ function) update function update (C++ function), [1]

updatePerAtomRMSDRing function updateRMSDatom (C++ function) updateRMSDRing function

V

variable certified ddc, [1] weights voronoiFacetWeights function

voronoiFeature function voronoiFeatures function

W

weights variable 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 writeMoleculeIDsExpressionSelectOVITO function writeMoleculeIDsInSlice function writePrismNum function writePrisms function writeRingNum function writeRingNumBulk function writeRings function writeTopoBulkData function writeXYZcluster function

X

x (C++ member)

Y

y (C++ member)

ylm (C++ member)

Z

z (C++ member)