AtomEye an efficient atomistic configuration viewer

AtomEye an efficient atomistic configuration viewer

INSTITUTEOFPHYSICSPUBLISHINGMODELLINGANDSIMULATIONINMATERIALSSCIENCEANDENGINEERING

PII:S0965-0393(03)57873-1ModellingSimul.Mater.Sci.Eng.11(2003)173–177

AtomEye:anef cientatomisticcon gurationviewer

JuLi

DepartmentofMaterialsScienceandEngineering,OhioStateUniversity,Columbus,

OH43210,USA

Received10December2002

Published30January2003

http://doc.guandang.net/MSMSE/11/173

Abstract

AtomEyeisfreeatomisticvisualizationsoftwareforallmajorUNIXplatforms.

Itisbasedonanewlydevelopedgraphicscorelibraryofhigherquality

thantheX-windowstandard,witharea-weightedanti-aliasing.Anorder-N

neighbourlistalgorithmisusedtocomputethebondconnectivity.The

functionalitiesofAtomEyeinclude:parallelandperspectiveprojectionswith

fullthree-dimensionalnavigation;customizablebondandcoordinationnumber

calculation;colour-encodingofarbitraryuser-de nedquantities;localatomic

straininvariant;colouredatomtilingandtracing;upto16cuttingplanes;

periodicboundaryconditiontranslations;high-qualityJPEG,PNGandEPS

screenshots;andanimationscripting.Theprogramisef cientcomparedto

OpenGLhardwareaccelerationbyemployingspecialalgorithmstotreatspheres

(atoms)andcylinders(bonds),inwhichtheyarerenderedasprimitiveobjects

ratherthanascompositesofpolygons.AtomEyecanhandlemorethanone

millionatomsonaPCwith1GBmemory.Itisarobust,low-costtoolfor

surveyingnanostructuresandfollowingtheirevolutions.

1.Introduction

Modellingphysicalprocessesatthenanoscaleisevermoreimportantasexperimentaltechniquessuchasatomicforcemicroscopy(AFM)andhigh-resolutiontransmissionelectronmicroscopy(HRTEM)overlapinlengthscalewithwhichachievableindirectatomisticcalculations[1].Inaway,visualizationofsimulationresultsplaysthesameroleasmicroscopyinexperiments:werelyonittoextractmechanisticinformation,beforewedecidewhattodonext(morecalculationsorexperiments)toaccentuateacertain ndingortheory.Inthisfeedback,thecapabilitiesandease-of-useofthevisualizationsoftwareemployedareactuallyimportanttowardsscienti cdiscovery,eventhoughonemayinitiallyconsideritasmerelyatechnicaldetail.

VerypowerfulcommercialsoftwarepackagessuchasMaterialsStudio andChemOf ce arecurrentlyavailable,buttheircostsofentryarequitehigh.HereIwouldliketointroduceAtomEye,alow-orno-costgeneralvisualizationtoolwhosepurposeissimilartothatofRASMOL[2],aground-breakingsoftwarethathasbroadimpact,although0965-0393/03/020173+05$30.00©2003IOPPublishingLtdPrintedintheUK173

AtomEye an efficient atomistic configuration viewer

174JuLimanifestingde cienciesathandlinglargenumberofatoms(>50000).Atpresent,therearehigh-qualityvisualizationprogramssuchasXCrySDen[3]fordisplayingcrystalstructuresandelectrondensities,MOLSCRIPT[4]forcreatingvectorgraphicsoutputs,andRaster3D

[5]forray-tracingstill-frames,butAtomEye’smainfunctionisclosertothatofRASMOLandXMol[6],whichisreal-timesurveyingoflarge-scaleatomicstructures.AleaderinthisaspectisVMD[7]whichisbasedonOpenGL-drivenhardwareacceleration[8].

2.Concepts

Forgeneral-purposerealtimethree-dimensionalgraphicssuchasthoseusedincomputergames,thereisnoquestionthathardwareacceleration,takingadvantageofthemoderngraphicscards,isthebestsolution.Currently,thistechnologyismainlybasedontheassemblageofpolygons,whosetransformandlighting,vertexshadingandtexturemapping,etcareallperformedinthegraphicspipelines(hardware).Yetforcertaincategoriesofatomisticvisualization,ifalmostallonerendersarespheres(foratoms)andcylinders(forbonds),thentheaboveapproachmaynotbetheoptimalsolution.Particularly,asphererequiresalargenumberofpolygons(～20)torepresent,whichleadstodrawbacksinbothspeed(whenthereare～106atomsonthescene)andquality.

Analternativeapproachistoregardspheresandcylindersasprimitivesandusespecializedalgorithmstorenderthemdirectlywithout rstdecomposingthemintopolygons.InAtomEye,itisdonebymemorycaching,whereatthestartoftheprogramoneusesmathematicalformulaetoshadearangeofspheresinveryhigh-qualitypixelmapswitharea-weightedanti-aliasingattheborder[9],keepthesepixelmapsinthemainmemory,andinusesimplypastethemapstothescenewithz-buffering.Becauseonlysimpleoperations(mostlymemorycopying)areperformedinreal-time,thisisveryfast.Also,thespheresandcylindershavetopassafewfastvisibilityscreeningtestsbeforebeingcommittedtothez-buffer.Insceneswith>104spheres,thisapproachhasbeencon rmedtobecompetitivecomparedtothegeneralhardwareaccelerationapproachusingOpenGL[8],anditgivesoverallhigherqualityoutputs

[10]eventhoughthelightingandshadingisnot100%physical.Graphicscardtechnologyhasevolved,butsohasCPU/mainmemory,astheyarefromthesamemicrofabricationtechnology.Intheforeseeablefuture,itisunlikelythatthisapproachlosestothehardwareaccelerationapproacheswhichperformgeneralpolygonassemblage.

X-window[11]isthecommongraphicsstandardonUNIXandLinuxplatforms.Butitscoredrawingfunctionsareseverelyoutdated.Ihaverewrittenalltwo-dimensionaldrawingandclippingfunctions(fordisplayingwireframes,etcinAtomEye)withgeometricallyexactarea-weightedanti-aliasing[9],andtheentiresceneimageisgeneratedinthemainmemory rstwithoutcallinganyoftheoldX-windowdrawingfunctions.X-windowisusedonlyasaninput-eventshandleandforremotedisplayovernetwork.Ifsharedmemoryextension(forlocaldisplay)isavailable,thenitisinvokedautomatically.Italsoqueriesandhandlesdifferentdisplaycolourdepthsandbig/smallendianissuesautomatically.

TheProteinDataBank(PDB)[12]atomicstructure leformat,thoughwidespreadwithgreatimpact,doeshavedrawbackssuchas xed(andthereforepossiblyinsuf cient)digits/accuracy,novelocityspeci cationstandard(formoleculardynamics),andisuncompressed.AtomEyesupportsPDBformat,butalsoanewatomiccon guration leformatCFG[10]whichaddressestheaboveproblems.Allinputcon guration lescanbecompressedbygzip[13]orbzip2[14];AtomEyerecognizescompressionbymagicnumbersandautomaticallydecompressthe le(temporarily,wi …… 此处隐藏：11279字，全部文档内容请下载后查看。喜欢就下载吧 ……