Index

A

absor namespace addToLibrary function analyzeResident function

applyFile function atomKeys variable

B

basalConditions function basalNeighbours function basalPrismConditions function basalRingsSeparation function Bond group

bond namespace buildRingSearchIndex function Bulk prisms group bulkPolygonRingAnalysis function

C

Cage group cage namespace cage::Cage struct cage::FoundCage struct cage::Signature struct cageAffiliation function cageOfGuest variable calcCoverageArea function calcMatrixN function calcMatrixS function calcScaleFactor function centerWRTcentroid function centreDistance variable certificate variable certified variable changeDiaCageOrder function changeHexCageOrder function Chill group chill namespace chill::BondClassifier 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 classes variable classifyTemplates function Clump group clump namespace clump::Domain struct coloured variable, [1] conditionOneDDC function, [1] conditionThreeDDC function conditionTwoDDC function, [1] counts variable createPrismBlock function CrystalKind enum

D

ddc variable, [1] densityZ function, [1]

depth variable

E

edges variable enum CrystalKind Family IonState Kind

exportEnviron function

F

faces variable Family enum fillPointSetPrismBlock function fillPointSetPrismRing function findBulkPrisms function findBySignature function, [1] findDDC function, [1] findHC function, [1] findMixedRings function findPrismatic function, [1] fingerprint function free variable function addToLibrary analyzeResident applyFile basalConditions basalNeighbours basalPrismConditions basalRingsSeparation buildRingSearchIndex bulkPolygonRingAnalysis cageAffiliation calcCoverageArea calcMatrixN calcMatrixS calcScaleFactor centerWRTcentroid changeDiaCageOrder changeHexCageOrder classifyTemplates conditionOneDDC, [1] conditionThreeDDC conditionTwoDDC, [1] createPrismBlock densityZ, [1] exportEnviron fillPointSetPrismBlock fillPointSetPrismRing findBulkPrisms findBySignature, [1] findDDC, [1] findHC, [1] findMixedRings findPrismatic, [1] fingerprint getAtomTypesTopoBulk getAvgHeightPrismBlock getPointSetCage getPointSetRefRing getRadiusFromRings getRMSD getStrucNumbers guestOccupancy hex hopNeighbourhood hornAbsOrientation ionEnvironment isClosedPolyhedron lastReclassified load localKey makePath matchLibraries matchLibrary matchPrism matchPrismBlock matchUntetheredPrism normHeightPercent notNeighboursOfRing pathFromArgv periodicCentroid printRDF projAreaSingleRing quat2RotMatrix relaxedPrismConditions relOrderDDC, [1] relOrderHC relOrderPrismBlock, [1] ringAdjacentCompletion seededCageAffiliation shellRingCensus soapSpectrum soapSpectrumAll steinhardtQlVoronoi topoBulkAnalysis 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 getAtomTypesTopoBulk function getAvgHeightPrismBlock function getPointSetCage function getPointSetRefRing function getRadiusFromRings function getRMSD function getStrucNumbers function 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 guestsPerCage variable

H

hex function hopNeighbourhood function

hornAbsOrientation function

I

iceFraction variable ion variable ionEnvironment function IonState enum

ira namespace ira::Match struct ira::PointGroup struct isClosedPolyhedron function

K

key variable, [1]

Kind enum

L

labelOf variable labels variable lastReclassified function

load function localKey function

M

makePath function match namespace matchLibraries function matchLibrary function matchPrism function matchPrismBlock function matchUntetheredPrism function members variable

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

N

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

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

O

occupied variable

P

pathFromArgv function periodicCentroid function pntToPnt namespace Primitive group primitive namespace primitive::Graph struct

primitive::RingUpdater class primitive::Vertex struct printRDF function prism3 namespace projAreaSingleRing function

Q

quat2RotMatrix function

R

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

Ring group ring namespace ring::AffiliationUpdater class ring::CageAffiliation struct ring::RingSearchIndex struct ring::SeededAtomLabels struct ringAdjacentCompletion function ringCensus variable Rows typedef

S

seams namespace seams::cfg namespace seams::cfg::Runtime struct seams::sphericart_ylm namespace seams::steinhardt namespace seededCageAffiliation function shell variable shellRingCensus function Sinp group sinp namespace site namespace site::DensityZ struct site::GuestOccupancy struct site::IonEnvironment struct site::Table struct soapSpectrum function soapSpectrumAll function sout namespace sph namespace std namespace

steinhardtQlVoronoi function struct cage::Cage cage::FoundCage cage::Signature chill::BondClassifier chill::LinearClassifier chill::QlmAtom chill::SteinhardtQl chill::TemplateHit chill::VoronoiWeights chill::YlmAtom clump::Domain gpu::BatchResult gpu::DeviceInfo gpu::Footprint gpu::Plan ira::Match ira::PointGroup molSys::Point molSys::PointCloud molSys::Result primitive::Graph primitive::Vertex rdf::PartialRdf ring::CageAffiliation ring::RingSearchIndex ring::SeededAtomLabels seams::cfg::Runtime site::DensityZ site::GuestOccupancy site::IonEnvironment site::Table topo::FrameFingerprint topo::KeyLibrary topo::LibraryMatch topo::LocalKey

T

topo namespace topo::FrameFingerprint struct topo::KeyLibrary struct topo::LibraryMatch struct topo::LocalKey struct

topoBulkAnalysis function topoparam namespace tum3 namespace type variable typedef Rows

U

update function updatePerAtomRMSDRing function

updateRMSDRing function

V

variable atomKeys cageOfGuest centreDistance certificate certified classes coloured, [1] counts ddc, [1] depth edges faces free guestsPerCage iceFraction ion key, [1] labelOf labels members method, [1], [2] multiply occupied rho ringCensus shell type vertices, [1] weights

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

W

weights 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