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Atomeye Manual.docx

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Atomeye Manual.docx

AtomeyeManual

AtomEyeManual

OrignizedbyLIUXuefengformhttp:

//li.mit.edu/Archive/Graphics/A/

Usage:

DownloadbinaryfrombrowserandsaveasA

%chmod755A

%./Afilename

Youmustensurethatthe"xterm"commandisinyourshellPATHandcanbedirectlycalled.Seealsohereifyourconfigurationfilehasbeencompressed.

NumLock:

Ingeneral,yourNumLockkeyshouldbeinthe'off'state.Otherwise,AtomEyewillregarditasequivalenttohavingCapsLock'on',whichisequivalenttohavingMeta+modifierforeverykeyyoupress.

HelpKey:

Press'F1'or'h'forhelp.

RotateObject（orsoyouthink）:

Thiscanbeaccomplishedeitherwitharrowkeysormousedrag.PressLeft,Right,Up,Downkeystorotateobjectasifyouarerollingacrystalballwiththeobjectembeddedinit.Forin-planerotation,useShift+Up（clockwise）andShift+Down（counter-clockwise）.Theangleofrotationcorrespondingtoonekeystrokeiscontrolledbythegearboxvaluemultipliedbypi.Therefore,atgear-9correspondingtogearboxvalueof0.5,eachkeystrokewillfliptheobjectbypi/2,whichcomesinhandywhenviewinglargeconfigurations.

Onecanalsorotatetheviewportbypressingleftbuttonanddragthemouse.The"crystalball"canbeimaginedasbeinghingedattheviewportcenterandwhosediameterissomewhatsmallerthantheviewport.Ifthepointershouldfallontothecrystalball'ssurface,therotationfollowsageodesicpathconnectingAandBontheball'ssurface.Ontheotherhand,ifthepointerfallsoutsideoftheball,thendraggingthemousewilljustrotatetheobjectclockwise/counter-clockwisein-plane.

Itcanbeforeseenthatwhentheconfigurationislarge,itismuchmoreefficienttorotatetheviewportthantorotatetheobject.Infact,contrarytowhattheheadingsuggests,thisishowIimplementtherotation.Togetthecorrectlookandfeel,onemustalsotranslatetheviewportaftertherotation.Itisdonebythefollowingrule:

westipulatethatthereexistsalocationinspacewherebythecombinedeffectofrotationandtranslationwouldnotchangeitssubjectivepositionwithrespecttotheviewport.Thislocationiscalledtheanchor,namedsobecausewhenwe"rotatetheobject",itappearstobehingingontheanchor.Pleasevisitanchorcontroltoseehowtochangetheanchorposition.

AnchorControl:

Atthestartofasession,theanchoristakentobethecenterofthebox,sotheobjectappearstobehingedattheboxcenterifrotated.Thisstatecanberecoveredwhenever'w'ispressed.

Ontheotherhand,right-clickingonanatomtransferstheanchortothatatom'sposition.Thisallowsastreamlinedrightclick+dragactionthatpullstheviewportclosertoanyatomyouwanttoseeindetail.Also,onceyouright-clickedonanatom,ensuingrotationswillbehingedonthatatom,whichisconvenientforstudyinglocalatomicarrangements.

Ifyouareinthebondmode,thenright-clickingonabondwillalsosettheanchorpositiontothebondcenter.

Press'a'toshifttheviewportsotheanchorisseenrightatthemiddleoftheviewport.

ToggleBondMode:

Press'b'totogglewhethertodrawbondsornot.Tochangethebondingcutoffbetweentwospeciesofatoms,visitCutoffControl.

ToggleBetweenParallel/PerspectiveProjection:

Press'Tab'totogglebetweenparallelandperspectiveprojectionrenderingmethods.Parallelprojectionisalimitingcaseofperspectiveprojection,wheretheviewpointisveryfarawayfromtheobjectbuttheviewangleisalsoturnedverysmall.Itisusefulfordiscerningatomicrowsandplanes.

ScaleAtomRadii:

Press'PageUp'toincreaseatomradiiand'PageDown'todecreaseatomradiirenderedonscreenbyacommonfactor.Therateofchangeiscontrolledbythegearbox.

ChangeBondRadius:

Press'Home'toincreasebondradiusand'End'todecreasebondradiusdrawnonthescreen.Therateofchangeiscontrolledbythegearbox.

ToggleWireframeMode:

Press'i'totogglewireframemodethatdetermineshowtorenderthePBCbox.Youhavethefreedomtoselectnowireframe,monochromaticwireframe,RGBwireframe,andsoon.InthecaseoftheRGBwireframe,thethreeaxescorrespondto（s1,0,0）,（0,s2,0）,（0,0,s3）,respectively;thepointtheymeetcorrespondstotheorigin（0,0,0）.

CutoffControl:

Press'r'forcutoffcontrol,whichdecideshowclosetwoatomsneedtobewitheachothertobeconsiderednearestneighbor（iftheyare,theneachatom'scoordinationnumberwillbeincreasedby1,andabondwillbedrawnbetweenthemifunderthebondmode）.

Youwillbefirstinquiredaboutwhichtwospecies.Forexample,ifyouwanttochangethecutoffdistancebetweensiliconandcarbon,thenyoushouldenter"SiC"andpressenter.Then,witheachCtrl+Home/Ctrl+End,thecutoffdistancewillbeincreased/decreased;therateofchangeiscontrolledbythegearbox.Whenyouaresatisfied,youshouldpress'r'againtoclosethechange,soyoucan'tmodifytwopairingtypesatthesametime.

MakeViewframeUpright:

Sometimestoomuchrotationisabadthing,andyouwanttheviewframeuprightagainjustlikeatthebeginning.Press'u'.

InquireAtomInformation:

Rightclickonanatomtodisplayrelevantinformationaboutitinthexterm.Thiswillalsosettheanchortothisatom.

Right-clickingonabondwilldisplayinformationaboutthisbond.Thiswillsettheanchortothebondcenter.

InquireGeometricalInformation:

AtomEyeremembersthelastfouratomsthatyouhaveclickedon.

Pressing','（comma）wouldprintouttheCartesianseparationanddistancebetweenthelasttwoatomsclicked.

Pressing'.'（period）wouldprintoutthebondanglebetweenthelastthreeatomsclicked.

Pressing'/'（slash）wouldprintoutthedihedralanglebetweenthelastfouratomsclicked.

PullViewportCloser/AwayfromtheAnchor:

Rightclickinthewindowanddragmousetopullcloser.Alternatively,useIMWheel（orCtrl+IMWheelforquickeraction）topullviewportcloser/awayfromtheanchor.Ifyouclickonanatom,thatatomwillautomaticallybecometheanchor.Ifyouclickonabond,thebondcenterwillalsobecometheanchor.

ShiftObject（orsoyouthink）:

Ctrl+Left,Ctrl+Right,Ctrl+Up,Ctrl+Downwillshifttheobjectinplane.Ctrl+Shift+Upwillsendtheobjectfurtherfromviewport,Ctrl+Shift+Downwillpullitcloser.

ChangingGearboxValue:

Pressnumeralkeys'0'to'9',andthegearboxvaluewillbeswitchedto,

[1]0.001[2]0.002[3]0.005[4]0.010[5]0.020

[6]0.050[7]0.100[8]0.200[9]0.500[0]0.150

Thegearboxvaluecontrolsallrateofchange,suchasangleofrotation,amountoftranslation,therateofatomradiuschange,etc.

CoordinationNumberColoring:

Press'k'totogglecoordinationnumbercoloring.Coordinationnumberisanempiricalmeasureofhowmanynearestneighbors（couldbeofvariousspecies）thereareforaparticularatom.Thedefinitionof"nearestneighbors"canbechangedbycutoffcontrol.

Toclearlyseedefectcores,youoftenneedtoremovetheperfectlycoordinatedatoms.ThisisdoneinMakeAtomsInvisible.

AtomisticLocalvonMisesShearStrainInvariantColoring:

Meta+gwillcolor-encodetheatomsaccordingtotheirlocalvonMisesshearstraininvariant.Shift+gwilltoggletheflagcontrollingwhethertosubtractoffthesystem-averagedstraintensorornotbeforecomputingtheinvariant;thedefaultisno.Thecontrolsofcolormap,visibilitiesetc.areidenticaltothatofauxiliarypropertiescoloring.

CentralSymmetryParameterColoring:

Meta+hwillcolor-encodetheatomsaccordingtotheircentralsymmetryparameterc's.Shift+hwillprompttheusertochangethemaximumnumberofneighborsMusedinthecomputation;thedefaultbeingthemostpopularcoordinationnumberoftheconfigurationroundedeven.Thecontrolsofcolormap,visibilitiesetc.areidenticaltothatofauxiliarypropertiescoloring.

Becausecalculatingthecentralsymmetryparametersrequiresaneighborlistwithoutpairwisesaving,itisnotcalculatedbydefaultwhentheconfigurationisloaded,butonlycomputedafterMeta+hispressed.cisbetween[0,1],anditsaverageisusuallylessthan0.5evenforamorphousstructures.AnintrinsicstackingfaultinFCCcrystalwouldpossesstwolayersofatomswithc'satabout0.042,andaperfectcrystalshouldhavec'slessthan0.01evenwiththermalfluctuations.Soarecommendedthresholdvalueforvisualizingplanarfaultsis0.01,whichcanbesetbyshiftingthegearboxtolevel-4andpressingCtrl+PageUponce.Also,asauxiliarypropertiescoloringexplains,oneneedstopress'Ctrl+T'tokeeptheabovesetthresholdsforensuingconfigurations.Seealsoauxiliarypropertiescoloringforfurthercontrols.

Least-SquareAtomicLocalStrain

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