OCEAN Tutorial, Session 1monalisa.phys.washington.edu/OCEAN/workshops/2019/Hands... · 2019. 5....

OCEANTutorial,Session1

Getting started with OCEAN �  RunningonBNLcluster

�  Running�  StagesofOCEAN�  Firstresults�  ConvergingtheDFTstage�  Inputfile(s)�  ConvergingOCEAN

What is OCEAN? � OCEANisaperlscript:ocean.pl

�  Parsestheinputfile�  Bunchoffilemanagementthroughout�  RunssomeDFTcalculations�  Calculatesthescreenedcore-holepotential�  RunsanumberofBethe-Salpeterequation(BSE)calculations

� OCEANisacompiledexecutable:ocean.x�  CalculatestheBSE�  Alsoindependentparticle,RPA*,adiabaticTDLDA*

Simulating materials with OCEAN �  Everythingisperiodic!

�  Crystallinesystemsuseunitcell�  Liquids,surfaces,andmoleculesalsopossible

�  Cellneedstobe“bigenough”�  Capturethedisorder�  Avoidspuriousinteractions

�  Structureistheonlyfreeparameter�  Choosesystemandx-ray�  Otherparametersareforconvergence

�  BestBSEanswer,notnecessarilybestagreement

Brief aside on using UNIX variants � Notalwaysintuitive� Askifyouaren’tsure!

�  Tostopthecomputerfromdoingthings�  Qquitsmanyprograms�  Control+Ckillsthings(^C)

Detour for the workshop � We’llberunningonBNLlocalcluster� Openupaterminal&connect

�  Replace“jtv3”withyourusername1.  >ssh–Y–[email protected].  >ssh–Y–Ajtv3@icsubmit01

Detour for the workshop � We’llberunningonBNLlocalcluster� Openupaterminal&connect

�  Replace“jtv3”withyourusername1.  >ssh–Y–[email protected].  >ssh–Y–Ajtv3@icsubmit01

� Makesureplottingworks1.  >gnuplot2.  >plotx

� Windowsusers:checkoutmobaxterm,MacusersmightneedtoinstallX11

Running OCEAN >/path/to/ocean/ocean.plinputFile

Running OCEAN: important etymology >pwd

Prompt

Running OCEAN: important etymology >pwd/current/path

Running OCEAN: important etymology >pwd/current/path>/path/to/ocean/ocean.plinputFile

Running OCEAN: important etymology >pwd/current/path>/path/to/ocean/ocean.plinputFile

RunDirectory•  WhereyouranOCEANfrom•  Alloutputisrelativetohere

Detour for this workshop � OCEANisbuiltandinstalled

�  /hpcgpfs01/work/workshop/ocean_tutorial/bin� Wewanttorunonthescratchfilesystem!

1.  >cd/hpcgpfs01/scratch

changedirectory



1.  >cd/hpcgpfs01/scratch2.  >mkdir[yourusername]

Makeanewdirectory



1.  >cd/hpcgpfs01/scratch2.  >mkdir[yourusername]3.  >cd[yourusername]



1.  >cd/hpcgpfs01/scratch2.  >mkdir[yourusername]3.  >cd[yourusername]4.  >pwd

Detour for this workshop � Wewanttorunonthescratchfilesystem!

1.  >cd/hpcgpfs01/scratch2.  >mkdir[yourusername]3.  >cd[yourusername]4.  >pwd

�  Copythetutorialfilesover1.  >cp–r/hpcgpfs01/work/workshop/ocean_tutorial/session1.2.  >cdsession13.  >pwd

Detour for this workshop �  Lookatthefilerunit

�  ls(lowercaseL)showsthefilesinthecurrentdirectory

�  >lessrunit�  Gettingaroundinless

�  Up/downarrow�  Gjumpstobottom�  Flockstobottomandrefreshes

�  Control+c(^c)tostopthis�  qquits

Detour for this workshop �  Lookatthefilerunit

�  ls(lowercaseL)showsthefilesinthecurrentdirectory

�  >lessrunit�  Cluster-dependent

�  Queueinformation�  Loaduplibraries

�  RunOCEAN�  Onyourowncomputeryou

wouldjusttypethisline

Detour for this workshop �  Tosubmitourjobtothequeue

�  >sbatchrunit�  Submittedbatchjob369632

�  OCEANwritesstufftotheterminalwhileitruns�  Withthequeuethisgoesinto

afile“slurm-369632.out”

Detour for this workshop �  OCEANwritesstufftotheterminalwhileitruns

�  Withthequeuethisgoesintoafile�  “slurm-369632.out”�  >lessslurm-369632.out

Detour for this workshop �  OCEANwritesstufftotheterminalwhileitruns

�  Withthequeuethisgoesintoafile�  “slurm-369632.out”�  >lessslurm-369632.out�  Whenfinishedyou’llget“Oceanisdone”

First Run: LiF

Whilethatruns…

Stages of OCEAN 1)  Parsing(Common)2)  Atomic(OPF)3)  DFT4)  PREP5)  SCREEN6)  BSE(CNBSE/NBSE)

Parsing �  Inputfileread�  LotsoflittlefilescreatedinCommon/

Atomic � OCEANusespseudopotentials

�  Replacenuclei’sCoulombpotentialZ/r�  Nocoreelectrons

�  X-rayspectroscopyinvolvesthecoreelectrons

� Obviouslythereisaproblemhere

Atomic �  Carryouttwoatomiccalculations

�  All-electron�  Pseudo-ized

� Outsideofcutoffrcorbitalsarethesame

All-electron Pseudo-ized

Atomic �  Carryouttwoatomiccalculations

�  All-electron�  Pseudo-ized

� Outsideofcutoffrcorbitalsarethesame� OptimalProjectorFunctions(OPFs)

�  BasisfunctionstospanAE/PS�  Limitedradius(~2Bohr)�  Limitedenergyrange(100eV)

�  PAW-likemethod�  P.E.BlöchlPRB50,17953(1994)�  E.L.ShirleyJ.Elect.Spect.Relat.Phenom.110-111,305(2000)

AE PS

Density Functional Theory (DFT) � OCEANseekstobeDFTcodeagnostic

�  QuantumESPRESSO(4.3-6.1,6.2-6.3*)�  www.quantum-espresso.org�  6.2-6.3:add“-D__OLDXML”tomake.inc

�  ABINIT5.x?-8.10�  www.abinit.org

�  Todaywe’reusingQE

Density Functional Theory (DFT) � WhatdoweneedDFTfor?

Density Functional Theory (DFT) Threesteps:1)  Self-ConsistentField(SCF)

�  DFTmeansHisH[n]�  Convergedensityiteratively�  Onlyoccupiedstates

2)  Non-SCFforBSEorbitals�  Densek-pointmesh

3)  Non-SCFforscreening�  Fewk-points,butmanybands

Density Functional Theory (DFT) Logfiles:1)  Self-ConsistentField(SCF)

�  DFT/scf.out2)  Non-SCFforBSEorbitals

�  DFT/XXXYYYZZZ/nscf.out�  Directorydeterminedbyk-pointgrid(e.g.,008008008)

3)  Non-SCFforscreening�  DFT/SCREEN/nscf.out

PREP �  Filemanagement

�  HidesdifferencesbetweenABINIT&QE�  NewDFTinterfacesgohere

SCREENing �  Electron-holeattractionisscreenedintheBSE� UseRPAscreening

�  �  Eachatomicsitewillhaveauniqueresponse

� Wewillcomebacktothis

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BSE �  CNBSE(NBSEforvalence)�  Collectinfofromothersections�  Calculatematrixelements

�  <a|d|v>�  RunBSEcodeocean.x

LiF �  Shouldbefinishedbynow�  Theoutputshouldendwith“OCEANisdone”�  FinalspectraareinCNBSE

�  absspct_F_.0001_1s_01

� Opengnuplot�  plot“CNBSE/absspct_F_.0001_1s_01”wlp�  replot“Results/absspct.1.01”wl

Outline �  Running�  StagesofOCEAN�  Firstresults�  ConvergingtheDFTstage�  Inputfile(s)�  ConvergingOCEAN

DFT � Hamiltoniandependsonelectrondensity�  ElectrondensityfromsolvingHamiltonian

�  SCF:Self-consistentfield�  Repeatuntildensitydoesn’tchange�  DFTcodehandlesthis

SCF convergence � Needcorrectstructure,spinordering,etc.

1.  ecut:Energycut-off�  Discretizecalculationusingplanewaves�  Highestenergyplanewavesetbyecut=½G2

�  Larger=moreaccurate,butmoreexpensive2.  ngkpt:K-pointsamplingfortheSCFrun

�  IntegralsoverBrillouinzonereplacedbysums�  Larger=moreaccurate,butmoreexpensive

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SCF convergence �  CheckthetotalenergyoftheSCFcalculation

�  Ifecut→∞andngkpt→∞doestheresultchange?�  0.01eV/atom

�  >lessDFT/scf.outandscrolldown(hit‘G’thenuse‘b’tojumpup)

�  >grep‘!’DFT/scf.out

SCF convergence �  ecut:Setbypseudopotential

� Mostrestrictivepseudoinyourstructure�  Notbyelement!

�  Changingpseudoforsameelementcanchangecutoff

�  ngkpt:unitcelldependent�  Higherforsmallerbandgaps�  Higherforsmallerunitcells

SCF convergence �  Startconvergencescriptthenexamineit

�  >sbatchrunConvergence�  >lessrunConvergence

�  Firstloopisforngkpt�  23–83

SCF convergence �  Startconvergencescriptthenexamineit

�  >sbatchrunConvergence�  >lessrunConvergence

�  Firstloopisforngkpt�  Secondisforecut

�  40Ry–120Ry

SCF convergence �  Startwithngkpt

�  >gnuplot�  >p‘CONV/k.txt’wlp

�  Thisisngkpt�  {222}–{888}�  33isconverged

-667.884

-667.883

-667.882

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-667.88

-667.879

-667.878

2 3 4 5 6 7 8

Tota

l Ene

rgy

(eV)

ngkpt grid

’CONV/k.txt’

SCF convergence � Nowecut

�  >p‘CONV/e.txt’wlp

�  Plane-waveenergycutoff�  40Ry–120Ry�  80Rylooksgood�  Zoomin,100Ryisbetter

-668

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-664

-662

-660

-658

-656

40 50 60 70 80 90 100 110 120

Tota

l Ene

rgy

(eV)

Ecut Energy (Ry)

’CONV/e.txt’

SCF convergence �  Importanttocheck

�  SCFisthefoundation�  DFT/scf.outhasimportantinfo

�  Forcesonatoms�  Magnetizationinfowhenrelevant

�  SettingsinLiF.inarealreadygood!

Outline �  Running�  StagesofOCEAN�  Firstresults�  ConvergingtheDFTstage�  Inputfile(s)

�  Photonfiles� Maininput�  Pseudopotentials�  fill&opts

�  Convergence

Spectra files: absspct_F_.0001_1s_01 �  absspct–absorption

�  xesspctisemission�  rxsspctisRIXS

�  F_–fluoreneatom�  “_”forsingleletterelements�  O_,N_,V_,…�  Si,Ti,Cu,…

�  1s–theKedge

�  0001–atomindex�  Firstfluoreneininput�  ConsideramorphousSiO2

�  64formulaunits�  Si–0001–0064�  O–0001–0128

�  01–photonfileindex�  Polarizations� Momentumdirection&transfer(NRIXS)

Photon files �  photon1–photon99

�  Automaticdetectioninrundirectory�  Completelyspecifiestheelectron-photonoperator

Photon files: LiF/photon1 dipolecartesian001endcartesian010end696

�  Electron-photonoperator�  Polarizationdirection

� Momentumdirection*

�  Photonenergy*

*Notusedfordipole

Photon files: LiF/photon2 quadcartesian001endcartesian010end696

�  Electron-photonoperator�  Polarizationdirection

� Momentumdirection

�  Photonenergy*

*Determinesmomentummagnitude

X-ray absorption operator � 

�  (Simplified)dipoleselectionrules:�  Δl=±1,0�  Nos→s

� Quadrupole�  Requireslargeq–higherenergy�  Pre-edgefeatures,e.g.,3dtransitionmetalKedges�  Averagingoverdirectionsismorecomplicated

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LiF: No quadrupole contribution �  Gnuplot(again)

�  plot“CNBSE/absspct_F_.0001_1s_01”wlp�  replot“CNBSE/absspct_F_.0001_1s_02”wl

Photon files: qRaman Non-resonantInelasticX-rayScattering(NRIXS)

orX-rayRamanScattering(XRS)�  Energyandmomentumdecoupled

Largemomentumtransfer

Smallmomentumtransfer

NRIXS operator � Non-resonantInelasticX-rayScattering(X-rayRamanScattering)� Decouplestransferredmomentumandenergy

�  Highmomentumatlowenergyedges

�  �  Forsmallqthisisdipolelike�  Largeqallowsnon-dipoletransitions

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Photon files: LiF/photon3 qRamancartesian001endcartesian010length3.55inverseangstromend696

�  Electron-photonoperator�  Polarizationdirection*

� Momentumdirection� Momentumtransferred

�  Photonenergy**NotusedforqRaman

LiF: q-dependence �  plot“CNBSE/absspct_F_.0001_1s_01”wl,

“CNBSE/absspct_F_.0001_1s_03”wl�  replot“CNBSE/absspct_F_.0001_1s_04”

u1:($2*3)wl

LiF: q-dependence �  Pre-edgeshowsstrongmomentumdependence

� s-typeexcitonislowestenergyexcitation

� 1s→3sisdipoleforbidden

Outline �  Running�  StagesofOCEAN�  Firstresults�  ConvergingtheDFTstage�  Inputfile(s)


�  Convergence

Main input: grammar �  #commentoutallfollowingtextonaline

� Multi-wordinputsrequire{}�  “nkpt{888}” not “nkpt888”�  “ecut100” or “ecut{100}”

�  Separateinputsmustbeseparatedbyanewline

Outline � Maininput

�  Control�  Structure�  Pseudopotentials�  Edgeinformation

Main input: Control �  dftqe

�  SelectDFTcode�  qe(QuantumESPRESSO)orabi(ABINIT)

�  para_prefix{srun-n16}�  Paralleljoblaunch�  Common

�  mpirun�  mpiexec

�  Numberofprocessorsshouldbefirstnumber�  WRONG:mpirun--nper-node8-n16

Main input: structure �  Latticevectors,dielectricconstant,elements,andatomicpositions� AdoptedthestylefromABINIT

Main input: structure �  acell{ABC}�  rprim{ a1a2a3

b1b2b3 c1c2c3}

�  Latticevectorsare(A*a1,A*a2,A*a3),etc� UnitsareinBohr

Main input: structure �  diemac1.92

� Dielectricconstant(epsiloninfinity)� ABINITusesitasapreconditioner(minor)� NeededforSCREENing(session2)

Main input: structure Atomsandlocations:�  znucl{39}

�  Uniqueatomicnumbersincell�  (trickierformagneticsystems)

�  typat{12}�  Listofatoms,numberedbyznucl�  1→Z=3�  2→Z=9

�  xred{0.50.50.50.00.00.0}

�  Reducedcoordinatesofatoms�  Atom1:

�  Locatedat½½½�  typat=1→Z=3→Li

�  Atom2:�  Locatedat000�  typat=2→Z=9→F

Outline � Maininput

�  Control�  Structure�  Pseudopotentials�  Edgeinformation

Main input: pseudopotentials �  pp_list{

03-li.lda.fhi09-f.lda.fhi}

�  Inthesameorderasznucl� WARNING:codeisn’tsmartenoughtosaveyou�  Bydefault,pseudosareintherundirectory

�  ecut100�  Planewaveenergycut-offinRydberg�  Necessarycut-offdependsonyourpseudopotentials

Main input: edge information �  Eachedgeselectionrequires3integers:ANL�  Twomethodsofselectingedges

1)  {-910}–RuneveryZ=9atominthecell2)  {210}–Runthe2ndatominthecell

�  edges{-910}�  A=-9:runeveryFatom(identicalto{210})�  N=1,L=0:1s

Main input: edge information �  edges{-910}�  opf.fill{9f.fill}�  opf.opts{9f.opts}

�  Z filename�  Needfillandoptsfilesforelementbeinginvestigated

�  cnbse.broaden0.4�  BroadeningappliedtofinalspectraineV�  Finitecoreholelifetime

Outline �  Running�  StagesofOCEAN�  Inputfile(s)


�  Convergence

Pseudopotentials �  Coreelectrons

�  Don’tparticipateinbonding�  Don’tchangewithchemicalenvironment�  Requirelargenumbersofplane-waves

�  Removethem,modifyatomicpotential�  Valenceelectronsnowthemost-boundallowedstates�  e.g.Si1s22s22p63s23p2becomesSi*3s23p2

�  Only4electrons�  3s/3porbitalshaveNOnodes

Pseudopotentials � Needapseudopotentialforeachelement�  Compatibleformats:

�  fhi�  oncv

� Usefultools:�  opium�  oncv�  fhi2upf.x(QEdistribution)

opts & fill files � Auxiliaryfilesfortargetelement

�  Fluorene1sneedsf.opts&f.fill�  Titanium1sand2pusesameti.opts&ti.fill

�  Setonceperpseudopotential

opts �  009�  1000�  scalarrel�  lda�  2.04.50.250.0�  2.04.50.250.0

�  Z� Occ.ofcoreshells:spdf�  Treatmentofrelativity�  LDAorHartree-Fock� Occ.ofvalenceshells:spdf

fill �  2�  0.203.000.0001

�  3.0�  0.0520.

�  npower�  Energywindow

MinstartsbelowlowestoccupiedMax(bothinHartree)Precision

�  Cut-offradius�  Besseltransformcontrols

fill �  EnergyWindow: 0.203.000.0001

�  SolveDFTatom�  EachangularmomentumhasalowestvalenceenergyE�  Energywindowfrom0.20belowEto3.00Ha.�  OPFschosentospanthiswindow

�  Cut-offradius: 3.0Bohr�  DefinesspaceforOPFs� Mustbelargerthanthepseudopotentialcutoff

Outline �  Running�  StagesofOCEAN�  Firstresults�  ConvergingtheDFTstage�  Inputfile(s)�  Convergence

�  Backtomaininputfile

Main input: convergence 1)  Bands2)  K-points3)  X-points

Main input: converging bands Sothatwearen’twaiting!First,keepacopyofCNBSE�  >mvCNBSECNBSE.1EditLiF.in�  #dft_energy_range50�  nbands24Re-runOCEAN�  >sbatchrunit

Main input: converging bands Specifyoneof:�  nbands�  dft_energy_range

ScrollbackthroughtheOCEANoutputtonearthebeginning“ Defaultrequestedfornbands.Energyrangeis50eV.

Defaultchosenfornbands:18”

Main input: converging bands �  Gnuplot!

�  plot“CNBSE.1/absspct_F_.0001_1s_01”wl�  replot“CNBSE/absspct_F_.0001_1s_01”wl

Main input: converging bands � Morebands→Higherenergy�  Bandsarefromground-state

�  NotbasisstatesoftheBSE�  Evenhigh-energybandscancontributeattheexciton

�  nbandsincludesoccupied�  (mightchangeinv3)

Main input: converging bands �  Changenbandsto40�  Re-run

�  >mvCNBSECNBSE.2�  >sbatchrunit

� Whendone�  >mvCNBSECNBSE.3

� Goodtimeforquestions

Main input: converging k-points �  First:editLiF.in&re-runOCEAN

�  nbands24�  nkpt{101010}

� Meanwhile:Whatdoesk-pointsamplingdo?1)  Capturesbanddispersion

Main input: converging k-points � Whatdoesk-pointsamplingdo?

1)  Capturesbanddispersion2)  Definesasupercell

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Main input: converging k-points �  83(CNBSE.2)vs.103(CNBSE)

Main input: converging x-points LookatthetopofthelastOCEANlog(slurm.??????)“ Defaultsrequestedforxmesh.ipt

Defaultschosenforxmesh.ipt:444”KeepCNBSE�  >mvCNBSECNBSE.4EditLiF.in,�  cnbse.xmesh{666}Re-runOCEAN�  >sbatchrunit

Main input: converging x-points �  X-pointsarewithintheunitcell

�  DFTcodestendtouseG–theFourierpairtox� Morex/GpointsneededforDFTthanforBSE

� OCEANhastworeal-spacerepresentations1)  X-pointsarearegulargrid(alonglatticevectors)2)  OPFsprovidealocalbasisaroundabsorbingatom

� Numberx-points>numberofbands

Main input: converging x-points �  43vs.63�  LiFhasasmallunitcell�  1-2x-points/Bohr

Convergence; final thoughts �  Bothx-pointandk-pointsareFFTgridsinternally

�  Choosesmallprimefactors:2,3,5� Onlyconvergewhatexperimentsees

�  Limitedenergyrange�  Core-holelifetimebroadening

� Numberofx-pointsgrowwithcellsize�  1-2x-points/Bohr

� Numberofk-pointsshrinkwithcellsize� Metalsrequiremorethaninsulators

OCEAN Tutorial, Session 1monalisa.phys.washington.edu/OCEAN/workshops/2019/Hands... · 2019. 5....

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Transcript of OCEAN Tutorial, Session 1monalisa.phys.washington.edu/OCEAN/workshops/2019/Hands... · 2019. 5....