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Files *.bulk.xyz Date: 2014/04/25 00:35 Name: Leone   <leoqmc@gmail.com> Hello users of OpenMX. I am calculating electronic transport properties of the a molecular junction: ....-Au-Au-Au-[Au-B-Au]-Au-Au-Au-..... Among the files generated are the *.bulk.xyz. We notice that the same contains replicas of the molecular junction: ...Au-Au-[Au-B-Au]-Au-Au-Au-...-Au-Au-Au-[Au-B-Au]-Au-Au-Au-...-Au-Au-[Au-B-Au]-Au-... I expected something like: ...-Au-Au-Au-[Au-B-Au]-Au-Au-Au-... Only with electrodes extending semi-infinitely. Did I do something wrong? I appreciate any help. Leone

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Re: Files *.bulk.xyz ( No.1 ) Date: 2014/04/29 19:20 Name: Artem  <artem.pulkin@epfl.ch> I do not think so. These files have nothing to do with NEGF calculation, as far as I understand. But you may provide an input file for your scattering region for a more precise answer. Re: Files *.bulk.xyz ( No.2 ) Date: 2014/05/03 01:33 Name: Leone  <leoqmc@gmail.com> Artem, I'm grateful for your help. Here are the three input files: the left lead, NEGF and Transport. I thank you. best regards Leone Left Lead: # # File Name # DATA.PATH /nfs-share/software/openmx/openmx3.7/DFT_DATA13 System.CurrrentDirectory ./ # default=./ System.Name teste_lead level.of.stdout 1 # default=1 (1-3) level.of.fileout 0 # default=1 (0-2) NEGF.output_hks on NEGF.filename.hks teste_lead.hks NEGF.Output.for.TranMain off # # Definition of Atomic Species # Species.Number 1 <Definition.of.Atomic.Species Au Au7.0-s2p2d2f1 Au_PBE13 Definition.of.Atomic.Species> Atoms.Number 27 Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU <Atoms.SpeciesAndCoordinates 1 Au -3.605235000 7.074898000 1.177289000 8.5 8.5 2 Au 2.162282000 7.074898000 1.177289000 8.5 8.5 3 Au -0.721476300 7.074898000 1.177289000 8.5 8.5 4 Au 3.604161000 4.577490000 1.177289000 8.5 8.5 5 Au -2.163355000 4.577490000 1.177289000 8.5 8.5 6 Au 0.720402800 4.577490000 1.177289000 8.5 8.5 7 Au -0.721476300 2.080082000 1.177289000 8.5 8.5 8 Au 2.162282000 2.080082000 1.177289000 8.5 8.5 9 Au 5.046040000 2.080082000 1.177289000 8.5 8.5 10 Au 0.720402800 2.912551000 3.531868000 8.5 8.5 11 Au -0.721476300 5.409959000 3.531868000 8.5 8.5 12 Au 5.046040000 5.409959000 3.531868000 8.5 8.5 13 Au 3.604161000 2.912551000 3.531868000 8.5 8.5 14 Au 2.162282000 5.409959000 3.531868000 8.5 8.5 15 Au 6.487919000 2.912551000 3.531868000 8.5 8.5 16 Au 5.046040000 0.415143300 3.531868000 8.5 8.5 17 Au 2.162282000 0.415143300 3.531868000 8.5 8.5 18 Au 7.929798000 0.415143300 3.531868000 8.5 8.5 19 Au 3.604161000 6.242428000 5.886447000 8.5 8.5 20 Au 5.046040000 3.745021000 5.886447000 8.5 8.5 21 Au 0.720402800 1.247613000 5.886447000 8.5 8.5 22 Au -0.721476300 3.745021000 5.886447000 8.5 8.5 23 Au 0.720402800 6.242428000 5.886447000 8.5 8.5 24 Au 2.162282000 3.745021000 5.886447000 8.5 8.5 25 Au 3.604161000 1.247613000 5.886447000 8.5 8.5 26 Au -2.163355000 6.242428000 5.886447000 8.5 8.5 27 Au 6.487919000 1.247613000 5.886447000 8.5 8.5 Atoms.SpeciesAndCoordinates> # # Atoms # <Atoms.UnitVectors 0.0 0.0 7.0518 21.684611 0.0 0.0 0.0 15.489008 0.0 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 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 0.010 # 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) NEGF: # # File Name # DATA.PATH /nfs-share/software/openmx/openmx3.7/DFT_DATA13 System.CurrrentDirectory ./ # default=./ System.Name teste_negf level.of.stdout 1 # default=1 (1-3) level.of.fileout 0 # default=1 (0-2) NEGF.filename.hks.l teste_lead.hks NEGF.filename.hks.r teste_lead_direita.hks NEGF.Num.Poles 150 # default=150 NEGF.scf.Kgrid 1 1 # default=1 1 NEGF.SCF.Iter.Band 10 NEGF.bias.voltage 0.0 # 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 #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 Species.Number 4 <Definition.of.Atomic.Species C C5.0-s2p2d1 C_PBE13 N N5.0-s2p2d1 N_PBE13 H H5.0-s2p2 H_PBE13 Au Au7.0-s2p2d2f1 Au_PBE13 Definition.of.Atomic.Species> # # Atoms # Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU Atoms.Number 14 <Atoms.SpeciesAndCoordinates 1 C 2.162619000 3.744360000 9.285241000 2.0 2.0 2 C 2.162885000 3.744965000 10.688600000 2.0 2.0 3 C 2.153515000 4.968598000 11.390390000 2.0 2.0 4 C 2.172322000 2.522356000 11.392200000 2.0 2.0 5 C 2.153252000 4.969770000 12.766700000 2.0 2.0 6 C 2.172100000 2.523514000 12.768540000 2.0 2.0 7 C 2.162413000 3.747170000 13.470340000 2.0 2.0 8 C 2.162051000 3.748203000 14.873680000 2.0 2.0 9 H 2.146578000 5.914887000 10.828690000 0.5 0.5 10 H 2.179692000 1.574925000 10.832380000 0.5 0.5 11 H 2.145983000 5.917256000 13.326420000 0.5 0.5 12 H 2.179292000 1.577155000 13.330130000 0.5 0.5 13 N 2.162130000 3.744245000 8.115006000 2.5 2.5 14 N 2.161714000 3.749023000 16.043960000 2.5 2.5 Atoms.SpeciesAndCoordinates> # # Lead-Left # LeftLeadAtoms.Number 27 <LeftLeadAtoms.SpeciesAndCoordinates # Unit=Ang. 1 Au -3.605235000 7.074898000 1.177289000 8.5 8.5 2 Au 2.162282000 7.074898000 1.177289000 8.5 8.5 3 Au -0.721476300 7.074898000 1.177289000 8.5 8.5 4 Au 3.604161000 4.577490000 1.177289000 8.5 8.5 5 Au -2.163355000 4.577490000 1.177289000 8.5 8.5 6 Au 0.720402800 4.577490000 1.177289000 8.5 8.5 7 Au -0.721476300 2.080082000 1.177289000 8.5 8.5 8 Au 2.162282000 2.080082000 1.177289000 8.5 8.5 9 Au 5.046040000 2.080082000 1.177289000 8.5 8.5 10 Au 0.720402800 2.912551000 3.531868000 8.5 8.5 11 Au -0.721476300 5.409959000 3.531868000 8.5 8.5 12 Au 5.046040000 5.409959000 3.531868000 8.5 8.5 13 Au 3.604161000 2.912551000 3.531868000 8.5 8.5 14 Au 2.162282000 5.409959000 3.531868000 8.5 8.5 15 Au 6.487919000 2.912551000 3.531868000 8.5 8.5 16 Au 5.046040000 0.415143300 3.531868000 8.5 8.5 17 Au 2.162282000 0.415143300 3.531868000 8.5 8.5 18 Au 7.929798000 0.415143300 3.531868000 8.5 8.5 19 Au 3.604161000 6.242428000 5.886447000 8.5 8.5 20 Au 5.046040000 3.745021000 5.886447000 8.5 8.5 21 Au 0.720402800 1.247613000 5.886447000 8.5 8.5 22 Au -0.721476300 3.745021000 5.886447000 8.5 8.5 23 Au 0.720402800 6.242428000 5.886447000 8.5 8.5 24 Au 2.162282000 3.745021000 5.886447000 8.5 8.5 25 Au 3.604161000 1.247613000 5.886447000 8.5 8.5 26 Au -2.163355000 6.242428000 5.886447000 8.5 8.5 27 Au 6.487919000 1.247613000 5.886447000 8.5 8.5 LeftLeadAtoms.SpeciesAndCoordinates> # # Lead-Right RightLeadAtoms.Number 27 <RightLeadAtoms.SpeciesAndCoordinates # Unit=Ang. 1 Au -2.163751000 6.245988000 18.272900000 8.5 8.5 2 Au 6.487524000 1.251172000 18.272900000 8.5 8.5 3 Au 5.045645000 3.748580000 18.272900000 8.5 8.5 4 Au 0.720007400 1.251172000 18.272900000 8.5 8.5 5 Au 3.603766000 6.245988000 18.272900000 8.5 8.5 6 Au 0.720007400 6.245988000 18.272900000 8.5 8.5 7 Au 3.603766000 1.251172000 18.272900000 8.5 8.5 8 Au -0.721871800 3.748580000 18.272900000 8.5 8.5 9 Au 2.161886000 3.748580000 18.272900000 8.5 8.5 10 Au 3.603766000 4.581049000 20.627480000 8.5 8.5 11 Au 2.161886000 7.078457000 20.627480000 8.5 8.5 12 Au -0.721871800 2.083641000 20.627480000 8.5 8.5 13 Au 5.045645000 2.083641000 20.627480000 8.5 8.5 14 Au -0.721871800 7.078457000 20.627480000 8.5 8.5 15 Au 0.720007400 4.581049000 20.627480000 8.5 8.5 16 Au 2.161886000 2.083641000 20.627480000 8.5 8.5 17 Au -3.605630000 7.078457000 20.627480000 8.5 8.5 18 Au -2.163751000 4.581049000 20.627480000 8.5 8.5 19 Au 6.487524000 2.916110000 22.982060000 8.5 8.5 20 Au 5.045645000 5.413518000 22.982060000 8.5 8.5 21 Au 2.161886000 0.418702600 22.982060000 8.5 8.5 22 Au 2.161886000 5.413518000 22.982060000 8.5 8.5 23 Au 3.603766000 2.916110000 22.982060000 8.5 8.5 24 Au -0.721871800 5.413518000 22.982060000 8.5 8.5 25 Au 0.720007400 2.916110000 22.982060000 8.5 8.5 26 Au 5.045645000 0.418702600 22.982060000 8.5 8.5 27 Au 7.929403000 0.418702600 22.982060000 8.5 8.5 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 100 # 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 0.100 # default=0.40 scf.Mixing.History 20 # default=5 scf.Mixing.StartPulay 10 # default=6 scf.Kerker.factor 1.0 # default=1.0 scf.criterion 1.0e-7 # default=1.0e-6 (Hartree) TRANSPORT # # File Name # DATA.PATH /nfs-share/software/openmx/openmx3.7/DFT_DATA13 System.CurrrentDirectory ./ # default=./ System.Name teste_negf level.of.stdout 1 # default=1 (1-3) level.of.fileout 0 # default=1 (0-2) NEGF.filename.hks.l teste_lead.hks NEGF.filename.hks.r teste_lead_direita.hks NEGF.Num.Poles 150 # default=150 NEGF.scf.Kgrid 1 1 # default=1 1 NEGF.SCF.Iter.Band 10 NEGF.bias.voltage 0.0 # 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 NEGF.tran.energydiv 200 # default=200 NEGF.tran.energyrange -5 5 1.0e-3 # default=-10.0 10.0 1.0e-3 (eV) NEGF.tran.Kgrid 1 1 # default= 1 1 Species.Number 4 <Definition.of.Atomic.Species C C5.0-s2p2d1 C_PBE13 N N5.0-s2p2d1 N_PBE13 H H5.0-s2p2 H_PBE13 Au Au7.0-s2p2d2f1 Au_PBE13 Definition.of.Atomic.Species> # # Atoms # Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU Atoms.Number 14 <Atoms.SpeciesAndCoordinates 1 C 2.162619000 3.744360000 9.285241000 2.0 2.0 2 C 2.162885000 3.744965000 10.688600000 2.0 2.0 3 C 2.153515000 4.968598000 11.390390000 2.0 2.0 4 C 2.172322000 2.522356000 11.392200000 2.0 2.0 5 C 2.153252000 4.969770000 12.766700000 2.0 2.0 6 C 2.172100000 2.523514000 12.768540000 2.0 2.0 7 C 2.162413000 3.747170000 13.470340000 2.0 2.0 8 C 2.162051000 3.748203000 14.873680000 2.0 2.0 9 H 2.146578000 5.914887000 10.828690000 0.5 0.5 10 H 2.179692000 1.574925000 10.832380000 0.5 0.5 11 H 2.145983000 5.917256000 13.326420000 0.5 0.5 12 H 2.179292000 1.577155000 13.330130000 0.5 0.5 13 N 2.162130000 3.744245000 8.115006000 2.5 2.5 14 N 2.161714000 3.749023000 16.043960000 2.5 2.5 Atoms.SpeciesAndCoordinates> # # Lead-Left # LeftLeadAtoms.Number 27 <LeftLeadAtoms.SpeciesAndCoordinates # Unit=Ang. 1 Au -3.605235000 7.074898000 1.177289000 8.5 8.5 2 Au 2.162282000 7.074898000 1.177289000 8.5 8.5 3 Au -0.721476300 7.074898000 1.177289000 8.5 8.5 4 Au 3.604161000 4.577490000 1.177289000 8.5 8.5 5 Au -2.163355000 4.577490000 1.177289000 8.5 8.5 6 Au 0.720402800 4.577490000 1.177289000 8.5 8.5 7 Au -0.721476300 2.080082000 1.177289000 8.5 8.5 8 Au 2.162282000 2.080082000 1.177289000 8.5 8.5 9 Au 5.046040000 2.080082000 1.177289000 8.5 8.5 10 Au 0.720402800 2.912551000 3.531868000 8.5 8.5 11 Au -0.721476300 5.409959000 3.531868000 8.5 8.5 12 Au 5.046040000 5.409959000 3.531868000 8.5 8.5 13 Au 3.604161000 2.912551000 3.531868000 8.5 8.5 14 Au 2.162282000 5.409959000 3.531868000 8.5 8.5 15 Au 6.487919000 2.912551000 3.531868000 8.5 8.5 16 Au 5.046040000 0.415143300 3.531868000 8.5 8.5 17 Au 2.162282000 0.415143300 3.531868000 8.5 8.5 18 Au 7.929798000 0.415143300 3.531868000 8.5 8.5 19 Au 3.604161000 6.242428000 5.886447000 8.5 8.5 20 Au 5.046040000 3.745021000 5.886447000 8.5 8.5 21 Au 0.720402800 1.247613000 5.886447000 8.5 8.5 22 Au -0.721476300 3.745021000 5.886447000 8.5 8.5 23 Au 0.720402800 6.242428000 5.886447000 8.5 8.5 24 Au 2.162282000 3.745021000 5.886447000 8.5 8.5 25 Au 3.604161000 1.247613000 5.886447000 8.5 8.5 26 Au -2.163355000 6.242428000 5.886447000 8.5 8.5 27 Au 6.487919000 1.247613000 5.886447000 8.5 8.5 LeftLeadAtoms.SpeciesAndCoordinates> # # Lead-Right RightLeadAtoms.Number 27 <RightLeadAtoms.SpeciesAndCoordinates # Unit=Ang. 1 Au -2.163751000 6.245988000 18.272900000 8.5 8.5 2 Au 6.487524000 1.251172000 18.272900000 8.5 8.5 3 Au 5.045645000 3.748580000 18.272900000 8.5 8.5 4 Au 0.720007400 1.251172000 18.272900000 8.5 8.5 5 Au 3.603766000 6.245988000 18.272900000 8.5 8.5 6 Au 0.720007400 6.245988000 18.272900000 8.5 8.5 7 Au 3.603766000 1.251172000 18.272900000 8.5 8.5 8 Au -0.721871800 3.748580000 18.272900000 8.5 8.5 9 Au 2.161886000 3.748580000 18.272900000 8.5 8.5 10 Au 3.603766000 4.581049000 20.627480000 8.5 8.5 11 Au 2.161886000 7.078457000 20.627480000 8.5 8.5 12 Au -0.721871800 2.083641000 20.627480000 8.5 8.5 13 Au 5.045645000 2.083641000 20.627480000 8.5 8.5 14 Au -0.721871800 7.078457000 20.627480000 8.5 8.5 15 Au 0.720007400 4.581049000 20.627480000 8.5 8.5 16 Au 2.161886000 2.083641000 20.627480000 8.5 8.5 17 Au -3.605630000 7.078457000 20.627480000 8.5 8.5 18 Au -2.163751000 4.581049000 20.627480000 8.5 8.5 19 Au 6.487524000 2.916110000 22.982060000 8.5 8.5 20 Au 5.045645000 5.413518000 22.982060000 8.5 8.5 21 Au 2.161886000 0.418702600 22.982060000 8.5 8.5 22 Au 2.161886000 5.413518000 22.982060000 8.5 8.5 23 Au 3.603766000 2.916110000 22.982060000 8.5 8.5 24 Au -0.721871800 5.413518000 22.982060000 8.5 8.5 25 Au 0.720007400 2.916110000 22.982060000 8.5 8.5 26 Au 5.045645000 0.418702600 22.982060000 8.5 8.5 27 Au 7.929403000 0.418702600 22.982060000 8.5 8.5 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 100 # 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 0.100 # default=0.40 scf.Mixing.History 20 # default=5 scf.Mixing.StartPulay 10 # default=6 scf.Kerker.factor 1.0 # default=1.0 scf.criterion 1.0e-7 # default=1.0e-6 (Hartree)

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