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Band unfolding of heterojunction Date: 2022/11/06 18:44 Name: Xinliang Huang   <xilhuang@foxmail.com> Dear Developers, Recently, I was calculating the relevant electronic structure of MoS2(4*4 supercell)/Graphene(5*5 supercell) heterojunction, and I used OpenMX to perform band unfolding calculation. I input the "Unfolding. ReferenceVectors" of graphene to get the correct band unfolding, but the "Unfolding. ReferenceVectors" of MoS2 reported an error as follows: ******************************************************* Unfolding of Bands ******************************************************* Cannot assign atoms in the reference cell properly! Could be due to more than one same atom in the reference cell! Check the input file, maybe the structure is highly disordered or you need to set the reference origin by yourself! Cannot assign atoms in the reference cell properly! Could be due to more than one same atom in the reference cell! Check the input file, maybe the structure is highly disordered or you need to set the reference origin by yourself! I tried to change the "Unfolding. ReferenceOrigin" and still reported an error as above. The complete calculation input file is as follows: # # File Name # System.CurrrentDirectory ./ # default=./ System.Name mos2_graphene level.of.stdout 1 # default=1 (1-3) level.of.fileout 1 # default=1 (0-2) DATA.PATH /job/huangxl_job/software/openmx3.9/DFT_DATA19 # # Definition of Atomic Species # Species.Number 3 <Definition.of.Atomic.Species Mo Mo7.0-s3p2d1 Mo_PBE19 S S7.0-s2p2d1 S_PBE19 C C6.0-s2p2 C_PBE19 Definition.of.Atomic.Species> # # Atoms # Atoms.Number 98 Atoms.SpeciesAndCoordinates.Unit FRAC # Ang|AU <Atoms.SpeciesAndCoordinates 1 Mo 0.0011500000000026 0.9953000000000003 0.4303699999999964 7 7 2 Mo 0.2511500000000026 0.9953000000000003 0.4303699999999964 7 7 3 Mo 0.5011500000000026 0.9953000000000003 0.4303699999999964 7 7 4 Mo 0.7511500000000026 0.9953000000000003 0.4303699999999964 7 7 5 Mo 0.0011500000000026 0.2453000000000003 0.4303699999999964 7 7 6 Mo 0.2511500000000026 0.2453000000000003 0.4303699999999964 7 7 7 Mo 0.5011500000000026 0.2453000000000003 0.4303699999999964 7 7 8 Mo 0.7511500000000026 0.2453000000000003 0.4303699999999964 7 7 9 Mo 0.0011500000000026 0.4953000000000003 0.4303699999999964 7 7 10 Mo 0.2511500000000026 0.4953000000000003 0.4303699999999964 7 7 11 Mo 0.5011500000000026 0.4953000000000003 0.4303699999999964 7 7 12 Mo 0.7511500000000026 0.4953000000000003 0.4303699999999964 7 7 13 Mo 0.0011500000000026 0.7453000000000003 0.4303699999999964 7 7 14 Mo 0.2511500000000026 0.7453000000000003 0.4303699999999964 7 7 15 Mo 0.5011500000000026 0.7453000000000003 0.4303699999999964 7 7 16 Mo 0.7511500000000026 0.7453000000000003 0.4303699999999964 7 7 17 S 0.0844799999999992 0.1619699999999966 0.4906500000000023 3 3 18 S 0.0844799999999992 0.1619699999999966 0.3700800000000015 3 3 19 S 0.3344799999999992 0.1619699999999966 0.4906500000000023 3 3 20 S 0.3344799999999992 0.1619699999999966 0.3700800000000015 3 3 21 S 0.5844799999999992 0.1619699999999966 0.4906500000000023 3 3 22 S 0.5844799999999992 0.1619699999999966 0.3700800000000015 3 3 23 S 0.8344799999999992 0.1619699999999966 0.4906500000000023 3 3 24 S 0.8344799999999992 0.1619699999999966 0.3700800000000015 3 3 25 S 0.0844799999999992 0.4119699999999966 0.4906500000000023 3 3 26 S 0.0844799999999992 0.4119699999999966 0.3700800000000015 3 3 27 S 0.3344799999999992 0.4119699999999966 0.4906500000000023 3 3 28 S 0.3344799999999992 0.4119699999999966 0.3700800000000015 3 3 29 S 0.5844799999999992 0.4119699999999966 0.4906500000000023 3 3 30 S 0.5844799999999992 0.4119699999999966 0.3700800000000015 3 3 31 S 0.8344799999999992 0.4119699999999966 0.4906500000000023 3 3 32 S 0.8344799999999992 0.4119699999999966 0.3700800000000015 3 3 33 S 0.0844799999999992 0.6619699999999966 0.4906500000000023 3 3 34 S 0.0844799999999992 0.6619699999999966 0.3700800000000015 3 3 35 S 0.3344799999999992 0.6619699999999966 0.4906500000000023 3 3 36 S 0.3344799999999992 0.6619699999999966 0.3700800000000015 3 3 37 S 0.5844799999999992 0.6619699999999966 0.4906500000000023 3 3 38 S 0.5844799999999992 0.6619699999999966 0.3700800000000015 3 3 39 S 0.8344799999999992 0.6619699999999966 0.4906500000000023 3 3 40 S 0.8344799999999992 0.6619699999999966 0.3700800000000015 3 3 41 S 0.0844799999999992 0.9119699999999966 0.4906500000000023 3 3 42 S 0.0844799999999992 0.9119699999999966 0.3700800000000015 3 3 43 S 0.3344799999999992 0.9119699999999966 0.4906500000000023 3 3 44 S 0.3344799999999992 0.9119699999999966 0.3700800000000015 3 3 45 S 0.5844799999999992 0.9119699999999966 0.4906500000000023 3 3 46 S 0.5844799999999992 0.9119699999999966 0.3700800000000015 3 3 47 S 0.8344799999999992 0.9119699999999966 0.4906500000000023 3 3 48 S 0.8344799999999992 0.9119699999999966 0.3700800000000015 3 3 49 C 0.0006038681495290 0.9950551891565307 0.6127862932133835 2 2 50 C 0.0672064194743607 0.1283624558127175 0.6126217650989774 2 2 51 C 0.2005951201490047 0.9950678210743900 0.6124290440047375 2 2 52 C 0.2672198978150110 0.1283901116158321 0.6126931607793378 2 2 53 C 0.4006624844382395 0.9951635798946884 0.6118181346651469 2 2 54 C 0.4672575048288349 0.1284672935111524 0.6127736955654519 2 2 55 C 0.6006908086092336 0.9951671386781147 0.6118233432024457 2 2 56 C 0.6672673948074581 0.1284703927127194 0.6127714619612405 2 2 57 C 0.8006371000187754 0.9950882265102631 0.6124362162954451 2 2 58 C 0.8672228825412747 0.1284219634404318 0.6126904299000636 2 2 59 C 0.0005483838053764 0.1950125923327483 0.6124260213830381 2 2 60 C 0.0672059658801566 0.3283290651616275 0.6116817678278095 2 2 61 C 0.2005868875146735 0.1950302404643399 0.6124311071885001 2 2 62 C 0.2672771944332936 0.3283193832436961 0.6116951233283853 2 2 63 C 0.4006340517589177 0.1950799229667323 0.6129110478331428 2 2 64 C 0.4672664794526883 0.3283722726627952 0.6127799998238553 2 2 65 C 0.6006303360479384 0.1951204230178217 0.6131786154154425 2 2 66 C 0.6672263989123173 0.3283954955673475 0.6134291464896389 2 2 67 C 0.8005965399661296 0.1950959598487301 0.6129008636598243 2 2 68 C 0.8671854731713424 0.3283737288365083 0.6127563132257597 2 2 69 C 0.0005528376452663 0.3950254130685134 0.6118028716114031 2 2 70 C 0.0671602710402467 0.5283404884616456 0.6110549740433606 2 2 71 C 0.2005786795208163 0.3949833026040794 0.6109641491170856 2 2 72 C 0.2672707403693292 0.5283617276530569 0.6099960547262362 2 2 73 C 0.4006530402575393 0.3950321366733042 0.6118305870526627 2 2 74 C 0.4673528549703985 0.5283696920193156 0.6110880157126416 2 2 75 C 0.6006306186725695 0.3950491161755890 0.6131822155949102 2 2 76 C 0.6672724136261990 0.5283735348784825 0.6127777216101421 2 2 77 C 0.8005862069089323 0.3950682997948425 0.6131668994935398 2 2 78 C 0.8671839108290054 0.5283781004135583 0.6127559598769514 2 2 79 C 0.0005506936428063 0.5950338920410984 0.6118022339159664 2 2 80 C 0.0672189513320832 0.7284220705822380 0.6116755386317907 2 2 81 C 0.2005659082512466 0.5950421924268569 0.6100000963140119 2 2 82 C 0.2672763846416040 0.7284759277471449 0.6099935557971631 2 2 83 C 0.4006465245941532 0.5950357641414717 0.6100154797791192 2 2 84 C 0.4674000049465997 0.7284912913332153 0.6100100252499941 2 2 85 C 0.6006685782191569 0.5950397265811033 0.6118367408700863 2 2 86 C 0.6673730373516714 0.7284332383587152 0.6117056629572442 2 2 87 C 0.8005963459242124 0.5950249771041654 0.6129006779161122 2 2 88 C 0.8672421150142332 0.7284085412939878 0.6126927677550730 2 2 89 C 0.0005688734539525 0.7950264546683805 0.6124235650302252 2 2 90 C 0.0672144064540950 0.9284066716395893 0.6126203567876000 2 2 91 C 0.2005943748600479 0.7951014748705384 0.6109555039845096 2 2 92 C 0.2672943542657629 0.9284926778633517 0.6116852833308196 2 2 93 C 0.4006667936201436 0.7951672701259643 0.6100104541566080 2 2 94 C 0.4673647679384312 0.9285380335806422 0.6110739889809966 2 2 95 C 0.6007005273624184 0.7951072291662394 0.6109781405148756 2 2 96 C 0.6673656940296485 0.9284887336662457 0.6116996095406795 2 2 97 C 0.8006286614924846 0.7950564199717590 0.6124386475098543 2 2 98 C 0.8672723920733404 0.9284226199382870 0.6126270506791696 2 2 Atoms.SpeciesAndCoordinates> Atoms.UnitVectors.Unit Ang <Atoms.UnitVectors 12.5378000000000007 0.0000000000000000 0.0000000000000000 -6.2689000000000004 10.8580533100000007 0.0000000000000000 0.0000000000000000 0.0000000000000000 26.7220000000000013 Atoms.UnitVectors> # # SCF or Electronic System # scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW|GGA-PBE scf.SpinPolarization on # On|Off|NC scf.ElectronicTemperature 300.0 # default=300 (K) scf.energycutoff 200.0 # default=150 (Ry) scf.maxIter 100 # default=40 scf.EigenvalueSolver band # DC|GDC|Cluster|Band scf.Kgrid 2 2 1 # means n1 x n2 x n3 scf.ProExpn.VNA off # default=on scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk scf.Init.Mixing.Weight 0.10 # default=0.30 scf.Min.Mixing.Weight 0.001 # default=0.001 scf.Max.Mixing.Weight 0.300 # default=0.40 scf.Mixing.History 10 # default=5 scf.Mixing.StartPulay 5 # default=6 scf.Mixing.EveryPulay 1 # default=5 scf.criterion 1.0e-9 # default=1.0e-6 (Hartree) # # Unfolding of bands # Unfolding.Electronic.Band on # on|off, default=off <Unfolding.ReferenceVectors 3.1828769430842301 0.0000000000000033 0.0000000000000000 -1.5914384715420247 2.7564522898337636 0.0000000000000000 -0.0000000000000000 0.0000000000000000 16.5313622491351140 Unfolding.ReferenceVectors> Unfolding.LowerBound -8.0 Unfolding.UpperBound 8.0 <Unfolding.Map 1 1 2 1 3 1 4 1 5 1 6 1 7 1 8 1 9 1 10 1 11 1 12 1 13 1 14 1 15 1 16 1 17 3 18 2 19 3 20 2 21 3 22 2 23 3 24 2 25 3 26 2 27 3 28 2 29 3 30 2 31 3 32 2 33 3 34 2 35 3 36 2 37 3 38 2 39 3 40 2 41 3 42 2 43 3 44 2 45 3 46 2 47 3 48 2 49 4 50 5 51 4 52 5 53 4 54 5 55 4 56 5 57 4 58 5 59 4 60 5 61 4 62 5 63 4 64 5 65 4 66 5 67 4 68 5 69 4 70 5 71 4 72 5 73 4 74 5 75 4 76 5 77 4 78 5 79 4 80 5 81 4 82 5 83 4 84 5 85 4 86 5 87 4 88 5 89 4 90 5 91 4 92 5 93 4 94 5 95 4 96 5 97 4 98 5 Unfolding.Map> Unfolding.desired_totalnkpt 100 Unfolding.Nkpoint 4 <Unfolding.kpoint G 0.0000 0.0000 0.0000 M 0.5000 0.0000 0.0000 K 0.3333 0.3333 0.0000 G 0.0000 0.0000 0.0000 Unfolding.kpoint> scf.restart on <Unfolding.ReferenceOrigin -3.09057 5.37799 11.5003 Unfolding.ReferenceOrigin> How should OpenMX calculate the band unfolding of heterostructures? The result I want is to band unfolding the band of the heterojunction to MoS2 and graphene respectively, but there is an error in band unfolding of MoS2. What should I do? primitive cell of graphene: 1.2344083195740001 -2.1380573715510001 0.0000000000000000 1.2344083195740001 2.1380573715510001 0.0000000000000000 0.0000000000000000 0.0000000000000000 12.0000000000000000 primitive cell of MoS2: 3.1828769430842301 0.0000000000000033 0.0000000000000000 -1.5914384715420247 2.7564522898337636 0.0000000000000000 -0.0000000000000000 0.0000000000000000 16.5313622491351140 Thanks in advance.

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Re: Band unfolding of heterojunction ( No.1 ) Date: 2022/11/08 13:25 Name: Chi-Cheng Lee Hi Xinliang, My quick suggestions for the problem are the following. 1. The c axis in Unfolding.ReferenceVectors can be set to 26.722. 2. Unfolding.ReferenceOrigin can be set to 0 0 0. 3. To use the primitive cell of graphene, MoS2, or others for the a and b axes in Unfolding.ReferenceVectors actually depends on your purpose. If you want to treat graphene as the defect, you should set all the graphene labels differently in Unfolding.Map and use MoS2 primitive lattice constants for the a and b axes. The integer atomic labels for MoS2 should be similar to what you set before. If you want to treat MoS2 as the defect, you should set all the atomic integer labels for MoS2 differently and use the a and b axes of graphene for the a and b axes in Unfolding.ReferenceVectors. The integer atomic labels for graphene should be similar to what you set before. If you want to compare with experiments, you can find a much smaller commensurate reference unit cell to perform the unfolding. In this case, there should be only several integers to be set for the atoms of graphene and MoS2. Hope the above suggestions help. Cheers, Chi-Cheng

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