Lab2

InthislabwewillbeusingQuantumEspressotorundensityfunctionaltheory(DFT)calculations. QuantumEspressocontainsmanysoftwarepackagesthathavebeenintegratedtogether,andthe componentusedforDFTcalculationsiscalledPlanewaveselfconsistentfield(PWscf).For reference,theusermanualforQuantumEspressoandlistofcommandsforPWscfcanbefoundonline: http://www.quantumespresso.org/user_guide.pdf http://www.quantumespresso.org/inputsyntax/INPUT_PW.html Wewillberunningourcalculationsonthesameclusteraslasttime: mrprhpcm1.hosts.jhmi.edu Onceyoulogin,youshouldbeabletoviewinputfilesforthislabbytyping cd510.633 cdlab2 cdinputs ls Asalways,considereveryparameterinyourinputfilebeforeyoustartarun,andexplainyourdecisions andallthestepsinyourcalculationswhenyouturninyoursolutions.

Problem1(25points)
Enterthedirectorycontainingthesampleinputfilesforproblem1bytyping cdproblem1 Therearefourfilesinthisdirectory.Thefirst,condor_script,resemblesthesamescriptweusedlast time.ThefileSi.GGAPBEpaw.UPFcontainsdataforusingtheprojectoraugmentedwave(PAW) methodforSi,calibratedforthePBEexchangecorrelationfunctional.QuantumEspressowilllookat thepseudopotential(orPAW)filesbeingusedtodeterminetheappropriateexchangecorrelation functionaltouse. Theinput.static.qefileistheinputfileforaPWscfrunthatisstatic,i.e.thenucleidontmove.The differentparametersofthisfileareshownbelow:

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 Torunacalculationwiththisfile,firstcopyittoafilenamedinput.qe cpinput.static.qeinput.qe Thensubmityourcondorjobasbefore: condor_submitcondor_script Youshouldseeafilenamedoutput.qeappear.ThisistheoutputfilefortheQuantumEspresso calculation.Attheendoftheselfconsistencyloop,thefinalenergyisprintedoutinalinethatlooks somethinglikethis: !totalenergy=xxxxxxxxxRy Theexclamationpointatthebeginningofthelinemarksitasthelaststepintheselfconsistencyloop. Theexclamationpointmakesiteasytoextractthetotalenergyfromthefilebytyping: grep!totalenergyoutput.qe ComputationalMaterialsDesign(510.633) JohnsHopkinsWhitingSchoolofEngineering

Makesureyouhavethepropernumberofspacesaftertheexclamationpoint(4). Theotherinputfile,input.relax.qe,istheinputfileforarelaxationrun,inwhichtheforcesare calculatedaftereachselfconsistencyloop,andtheionsandlatticevectorsarerelaxedinthedirection oftheforces.Thisfilecanbeusedtorelaxthestructuretoalocalminimumenergy.Ifyoutype diffinput.static.qeinput.relax.qe Youcanseethedifferencesbetweenthetwofiles.Thecalculationtypeisnowvcrelax,meaning variablecellrelax.Thismeanswewillrelaxbothlatticevectorsandatomicpositions.Wehavealso changedtheoccupationsparameter.Thetetrahedronmethoddoesnotworkwellforrelaxations,sowe switchtoMarzariVanderbiltsmearingforBrillouinzoneintegration.Theparameterdegaussgivesthe widthofthesmearingdistribution.Thelargerthisparameter,thelessaccurateyourcalculationwillbe, butthefewerkpointsyouwillneedforconvergence. Usingtheprovidedfiles,calculatetheenergyperatomofsilicon.Youwillneedtocheckforkpoint convergence,planewavecutoffconvergence,andanythingelseyouthinkmightberelevanttothe qualityofyourresult.Trytoconvergeyourresulttowithin104Rydberg/atom. Hint:Sometimesitisfastertodoaninitialrelaxationwithasetofparametersthatarenotfully convergedandusetheresultsfromtheinitialrelaxationtostartrunswithafullyconvergedsetof parameters. Hint:Whenthelatticeparameterschange,errorcanbeintroducedintoyourcalculationsbecausethe planewavebasisdoesnotchangewiththelatticeparameters.Toaccountforthis,PWscfwill automaticallydoaseparaterun,withanewplanewavebasisgeneratedfortherelaxedlattice parameters,attheendoftherelaxation.Youcanfindthefinalcoordinatesintheoutputfileafterthe line: Beginfinalcoordinates Thelatticevectorsprovidedintheoutputfileneedtobemultipliedbyalattocreatetheinputlattice vectorsforanotherrun. HowdoeskpointconvergencechangewhenyouuseaMonkhorstPackgrid(offsetfromtheGamma pointinallthreedimensions)insteadofagammacenteredgrid?

Problem2(25points)
Inthisproblemwewillcalculatethepropertiesofgraphite.Graphiteconsistsofseveralplanesof hexagonalringsofcarbonstackeduponeachother:

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 Byconvention,thethirdlatticevectorrepresentsthedirectionnormaltotheplane. Therearetwonewpseudopotentialfiles.ThefileC.pberrkjus.UPFrepresentsanultrasoft pseudopotentialforcarbon,calibratedforusewiththePBEexchangecorrelationfunctional.(Iwas unabletofindaPAWpotentialforcarbonIliked).ThefileC.pzrrkjus.UPFrepresentsanultrasoft pseudopotential,calibratedforusewiththePerdewZungerparameterizationofanLDAexchange correlationfunctional. UsingboththeLDAandtheGGApseudopotentials,findthegroundstatestructureforgraphite.Tosave youthetroubleofhavingtodeterminethesizeofthebasissettouse,youcanjustuseacutoffenergy of50Rydberg. Afterfindingthegroundstatestructures,freezethelatticevectorsparalleltothegraphiteplanesand plottheenergyofgraphiteasafunctionofthelengthofthethirdlatticevector.Howdotheresults differbetweenGGAandLDA?Howdotheydifferfromexperiment?Doyougetthesamelattice parameteryougotduringtherelaxationrun?Foreachofthesequestions,explainwhyyouthinkyou gottheresultyoudid.

Problem3(25points)
Wewillnowlookattheoxygenmolecule.Thegroundstateofoxygenisspinpolarized,meaningthat therearemoreelectronswithupspinthandownspin.Forthisreason,wewillrunaspinpolarized calculation.Thiscanbedonebyaddingtwolinestotheinputfile: nspin=2, starting_magnetization(1)=0.7, ThefirstofthesetwolinestellsPWscfthatwearerunningaspinpolarizedcalculation,sotheupand downspinsaretobetreatedindependently.Thesecondlinegivesastartingmagnetization.Thiswill ComputationalMaterialsDesign(510.633) JohnsHopkinsWhitingSchoolofEngineering

changeoverthecourseoftherun,butitisusuallyagoodideatosetittosomethingnonzerotobreak symmetry. BecausePWscfisaperiodiccode,wecannotjusttreatanisolatedoxygenmolecule.Insteadweneedto puttheoxygenmoleculeatthecenterofalarge,mostlyemptyperiodiccell.Forexample,thegiven inputfileputsoxygeninthecenterofacubiccellthatis10Bohrradiilongineachdirection.Thismeans thatwearereallycalculatingtheenergyofalatticeofoxygenmolecule,each10Bohrradiiapart.Aswe increasethespacingbetweentheoxygenmolecules,theenergypercellshouldconvergetotheenergy ofanisolatedmolecule. Calculatetheconvergedenergyofanoxygenmolecule.Whatsizekpointgriddoyouneedtouse? Why?Canyouusethetetrahedronmethodwiththiscalculation?Why? Hint:Todoacalculationinwhichthenuclearpositionscanrelax,butthelatticevectorsdonot,youcan set calculation='relax'

Problem4(25points)
TheinputfilesforthisproblemgiveyoutheexperimentalstructuresofSiCandSiO2.Calculatethe convergedenergiesforeachofthesestructuresusingthepseudopotential/PAWfilesfromtheearlier problems. Whatcutoffenergydidyouuse?Couldyouhavearrivedatthisvalue,oroneclosetoit,withouttesting differentcutoffenergiesonthesestructures? Whatistheformationenergyofeachofthesecompounds?TheenthalpyofformationforSiCunder standardconditionsis71.55kJ/mol.ForSiO2itis910.86kJ/mol,andat0Kitis905.87kJ/mol. Howdoyourcalculatedvaluescomparetothesevalues?Whatmightbethereasonsforany discrepancies?

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