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input files for periodic system under zero bias Date: 2018/06/29 02:10 Name: Frank Hi everyone, I noticed that for the transport calculation, there is a mode namely 'periodic system under zero bias' in the manual. As the manual says, only step1 and step3 are needed. My question is the following: 1. As we know, for the biased calculation, the input file for step1 is for the band calculation of the lead. What about the input file for step1 of the periodic zero bias calculation? Is it still only for the lead? Or it should also include the central scattering region, since step2 is skipped. 2. As the manual says, for step1, a keyword 'NEGF.Output.for.TranMain' should be added. I am wondering if the other keywords should be modified. For example, since step2 is skipped, I think there is no need to generate the .hks file. Am I right? 3. The input file for step3 is used to calculate the transmission, eigenchannel and so on. Are the keywords like 'NEGF.filename.hks.l', 'NEGF.scf.Kgrid', etc.,and atomic coordinates necessary? I would really appreciate if anyone can provide me examples of the input files for this 'periodic system under zero bias' mode. Thank you very much. Best, Frank

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Re: input files for periodic system under zero bias ( No.1 ) Date: 2018/06/29 02:26 Name: Frank I am sorry I forgot one more question. Does the keyword 'NEGF.tran.SCF.skip' really work in the version 3.8.5? It seems it does not work. Looking forward to your reply. Thank you very much. Best, Frank Re: input files for periodic system under zero bias ( No.2 ) Date: 2018/07/12 01:21 Name: Mitsuaki Kawamura  <mkawamura@issp.u-tokyo.ac.jp> Dear Frank Hello, 1, In this case, L0+C+R0 in Fig. 31 of http://www.openmx-square.org/openmx_man3.8/node114.html should be specified. 2, *.hks is still needed. 3, NEGF.filename.hks.l(r) is nessesary, but NEGF.scf.Kgrid is not. 4, I found 'NEGF.tran.SCF.skip' works in the version 3.8.5. I attached the input files for this function. for step 1 ######################################################################## System.CurrrentDirectory ./ # default=./ System.Name lead-chain level.of.stdout 1 # default=1 (1-3) level.of.fileout 0 # default=1 (0-2) NEGF.output_hks on NEGF.filename.hks lead-chain.hks NEGF.Output.for.TranMain on # # Definition of Atomic Species # Species.Number 1 <Definition.of.Atomic.Species C C5.0-s2p2d1 C_CA13 Definition.of.Atomic.Species> # # Atoms # Atoms.Number 9 Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU <Atoms.SpeciesAndCoordinates 1 C -1.500 0.000 0.000 2.0 2.0 2 C 0.000 0.000 0.000 2.0 2.0 3 C 1.500 0.000 0.000 2.0 2.0 4 C 3.000 0.000 0.000 2.0 2.0 5 C 4.500 0.000 0.000 2.0 2.0 6 C 6.000 0.000 0.000 2.0 2.0 7 C 7.500 0.000 0.000 2.0 2.0 8 C 9.000 0.000 0.000 2.0 2.0 9 C 10.500 0.000 0.000 2.0 2.0 Atoms.SpeciesAndCoordinates> Atoms.UnitVectors.Unit Ang # Ang|AU <Atoms.UnitVectors 13.5 0.0 0.0 0.0 10.0 0.0 0.0 0.0 10.0 Atoms.UnitVectors> # # SCF or Electronic System # scf.XcType LDA # LDA|LSDA-CA|LSDA-PW|GGA-PBE scf.SpinPolarization off # On|Off|NC scf.ElectronicTemperature 600.0 # default=300 (K) scf.energycutoff 180.0 # default=150 (Ry) scf.maxIter 100 # default=40 scf.EigenvalueSolver Band # DC|GDC|Cluster|Band scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr scf.Kgrid 200 1 1 # means n1 x n2 x n3 scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk scf.Init.Mixing.Weight 0.010 # default=0.30 scf.Min.Mixing.Weight 0.001 # default=0.001 scf.Max.Mixing.Weight 0.020 # default=0.40 scf.Mixing.History 20 # default=5 scf.Mixing.StartPulay 7 # default=6 scf.criterion 1.0e-10 # default=1.0e-6 (Hartree) ################################################################################ for step 3 ################################################################ System.CurrrentDirectory ./ # default=./ System.Name lead-chain level.of.stdout 1 # default=1 (1-3) level.of.fileout 0 # default=1 (0-2) NEGF.filename.hks.l lead-chain.hks NEGF.filename.hks.r lead-chain.hks NEGF.Num.Poles 100 # default=150 NEGF.scf.Kgrid 1 1 # default=1 1 NEGF.SCF.Iter.Band 50 NEGF.bias.voltage 0.1 # default=0.0 (eV) NEGF.bias.neq.im.energy 0.01 # default=0.01 (eV) NEGF.bias.neq.energy.step 0.02 # default=0.02 (eV) Dos.fileout off # on|off, default=off NEGF.Dos.energyrange -15.0 25.0 5.0e-3 #default=-10.0 10.0 5.0e-3 (eV) NEGF.Dos.energy.div 200 # default=200 NEGF.Dos.Kgrid 1 1 # default=1 1 # # Transmission & Eigen Channel # NEGF.tran.Analysis on # default on NEGF.tran.energydiv 200 # default=200 NEGF.tran.energyrange -10 10 1.0e-3 # default=-10.0 10.0 1.0e-3 (eV) NEGF.tran.Kgrid 1 1 # default= 1 1 NEGF.tran.Channel on # default on NEGF.Channel.Nkpoint 1 # default=1 <NEGF.Channel.kpoint 0.0 0.0 NEGF.Channel.kpoint> # default 0.0 0.0 NEGF.Channel.Nenergy 1 # default=1 <NEGF.Channel.energy 0.0 NEGF.Channel.energy> # default 0.0 NEGF.Channel.Num 5 # defualt=5(for collinear), 10(for Non-collinear) # # Definition of Atomic Species # Species.Number 1 <Definition.of.Atomic.Species C C5.0-s2p2d1 C_CA13 Definition.of.Atomic.Species> # # Atoms # Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU Atoms.Number 3 <Atoms.SpeciesAndCoordinates 1 C 3.000 0.000 0.000 2.0 2.0 2 C 4.500 0.000 0.000 2.0 2.0 3 C 6.000 0.000 0.000 2.0 2.0 Atoms.SpeciesAndCoordinates> # # Lead-Left # LeftLeadAtoms.Number 3 <LeftLeadAtoms.SpeciesAndCoordinates # Unit=Ang. 1 C -1.500 0.000 0.000 2.0 2.0 2 C 0.000 0.000 0.000 2.0 2.0 3 C 1.500 0.000 0.000 2.0 2.0 LeftLeadAtoms.SpeciesAndCoordinates> # # Lead-Right # RightLeadAtoms.Number 3 <RightLeadAtoms.SpeciesAndCoordinates # Unit=Ang. 1 C 7.500 0.000 0.000 2.0 2.0 2 C 9.000 0.000 0.000 2.0 2.0 3 C 10.500 0.000 0.000 2.0 2.0 RightLeadAtoms.SpeciesAndCoordinates> # # SCF or Electronic System # scf.XcType LDA # LDA|LSDA-CA|LSDA-PW|GGA-PBE scf.SpinPolarization off # On|Off|NC scf.ElectronicTemperature 600.0 # default=300 (K) scf.energycutoff 180.0 # default=150 (Ry) scf.maxIter 500 # default=40 scf.EigenvalueSolver NEGF # DC|GDC|Cluster|Band #scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr scf.Kgrid 1 1 1 # means n1 x n2 x n3 scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk scf.Init.Mixing.Weight 0.020 # default=0.30 scf.Min.Mixing.Weight 0.020 # default=0.001 scf.Max.Mixing.Weight 0.050 # default=0.40 scf.Mixing.History 100 # default=5 scf.Mixing.StartPulay 20 # default=6 scf.criterion 1.0e-7 # default=1.0e-6 (Hartree) scf.Kerker.factor 30.0 # default=1 NEGF.Poisson.Solver FFT NEGF.tran.SCF.skip on ############################################################ Best regards, Mitsuaki Kawamura Re: input files for periodic system under zero bias ( No.3 ) Date: 2018/07/15 12:00 Name: Frank Dear Mitsuaki, Thanks for your reply. You have totally solved my problem and gave a very helpful example. Best regards, Frank

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