Re: There is an error in the electron transport calculation ( No.1 ) |
- Date: 2021/07/27 16:43
- Name: Zhipeng Huang <202021001449@smail.xtu.edu.cn>
- Can you please tell me why?
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Re: There is an error in the electron transport calculation ( No.2 ) |
- Date: 2021/07/27 16:48
- Name: Bin <1016081206@qq.com>
- Hello
I have the same problem, does anyone know how to solve it?
Best regards
Bin
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Re: There is an error in the electron transport calculation ( No.3 ) |
- Date: 2021/07/27 18:17
- Name: Naoya Yamaguchi
- Hi,
Have you applied the patch (Ver. 3.9.2)? Ver. 3.9 without patches may fail to calculate the test case of the chain. You can find a number of the installed version at the beginning of the standard output.
Regards, Naoya Yamaguchi
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Re: There is an error in the electron transport calculation ( No.4 ) |
- Date: 2021/07/27 23:35
- Name: Zhipeng Huang <202021001449@smail.xtu.edu.cn>
- Hi,
Thank you for your reply.
I am using version 3.8 without a patch. Version 3.9 was previously installed, but failed when testing the electron transport calculations. I'm also very concerned about the fact that when I calculate the transmission spectrum, I draw a picture that has a lot of spikes or waves rather than terraces.How should I set some parameters of NEGF calculation to adjust.
Regards, Zhipeng Huang
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Re: There is an error in the electron transport calculation ( No.5 ) |
- Date: 2021/07/28 01:56
- Name: Naoya Yamaguchi
- Dear Zhipeng Huang,
I can't say anything unless you provide a case. Generally, you can check the SCF convergence in "Step 1" and "Step 2" in http://www.openmx-square.org/openmx_man3.8/node113.html If the convergence is not obtained enough, spikes or waves may appear.
Regards, Naoya Yamaguchi
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Re: There is an error in the electron transport calculation ( No.6 ) |
- Date: 2021/07/28 22:23
- Name: T. Ozaki
- Hi,
If possible, could you show us your input files of lead and NEGF calculations so that we can trace the calculation?
Regards,
TO
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Re: There is an error in the electron transport calculation ( No.7 ) |
- Date: 2021/11/09 17:03
- Name: Zhipeng Huang <202021001449@smail.xtu.edu.cn>
- Hi
Thank you for your reply. there are my input files # # File Name #
iystem.CurrrentDirectory ./ # default=./ System.Name lead-r-5-0 level.of.stdout 1 # default=1 (1-3) level.of.fileout 0 # default=1 (0-2)
NEGF.output_hks on NEGF.filename.hks lead-r-5-0.hks
# # Definition of Atomic Species # DATA.PATH /public/home/st3/hzp/openmx/DFT_DATA19 Species.Number 1 <Definition.of.Atomic.Species C C6.0-s2p2d1 C_PBE19 Definition.of.Atomic.Species>
# # Atoms #
Atoms.Number 40 Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU <Atoms.SpeciesAndCoordinates 1 C 1.4103360 10.4360311 14.9998800 2.0 2.0 2 C 2.8182931 10.4360311 14.9998800 2.0 2.0 3 C 3.5404531 11.4561513 15.7413200 2.0 2.0 4 C 0.6881760 11.4561513 15.7413200 2.0 2.0 5 C 1.4103360 11.8458041 16.9405600 2.0 2.0 6 C 2.8182931 11.8458041 16.9405600 2.0 2.0 7 C 3.5404531 11.4561513 18.1400800 2.0 2.0 8 C 0.6881760 11.4561513 18.1400800 2.0 2.0 9 C 1.4103360 10.4360311 18.8812400 2.0 2.0 10 C 2.8182931 10.4360311 18.8812400 2.0 2.0 11 C 3.5404531 9.1748968 18.8812400 2.0 2.0 12 C 0.6881760 9.1748968 18.8812400 2.0 2.0 13 C 1.4103360 8.1545771 18.1400800 2.0 2.0 14 C 2.8182931 8.1545771 18.1400800 2.0 2.0 15 C 3.5401133 7.7651238 16.9405600 2.0 2.0 16 C 0.6881760 7.7651238 16.9405600 2.0 2.0 17 C 1.4103360 8.1545771 15.7413200 2.0 2.0 18 C 2.8182931 8.1545771 15.7413200 2.0 2.0 19 C 3.5401133 9.1748968 14.9998800 2.0 2.0 20 C 0.6881760 9.1748968 14.9998800 2.0 2.0 21 C 5.6583360 10.4360311 14.9998800 2.0 2.0 22 C 7.0662931 10.4360311 14.9998800 2.0 2.0 23 C 7.7884531 11.4561513 15.7413200 2.0 2.0 24 C 4.9361760 11.4561513 15.7413200 2.0 2.0 25 C 5.6583360 11.8458041 16.9405600 2.0 2.0 26 C 7.0662931 11.8458041 16.9405600 2.0 2.0 27 C 7.7884531 11.4561513 18.1400800 2.0 2.0 28 C 4.9361760 11.4561513 18.1400800 2.0 2.0 29 C 5.6583360 10.4360311 18.8812400 2.0 2.0 30 C 7.0662931 10.4360311 18.8812400 2.0 2.0 31 C 7.7884531 9.1748968 18.8812400 2.0 2.0 32 C 4.9361760 9.1748968 18.8812400 2.0 2.0 33 C 5.6583360 8.1545771 18.1400800 2.0 2.0 34 C 7.0662931 8.1545771 18.1400800 2.0 2.0 35 C 7.7881133 7.7651238 16.9405600 2.0 2.0 36 C 4.9361760 7.7651238 16.9405600 2.0 2.0 37 C 5.6583360 8.1545771 15.7413200 2.0 2.0 38 C 7.0662931 8.1545771 15.7413200 2.0 2.0 39 C 7.7881133 9.1748968 14.9998800 2.0 2.0 40 C 4.9361760 9.1748968 14.9998800 2.0 2.0 Atoms.SpeciesAndCoordinates> Atoms.UnitVectors.Unit Ang # Ang|AU <Atoms.UnitVectors 8.49600000000000 0.00000000000000 0.00000000000000 0.00000000000000 19.9515000000000 0.00000000000000 0.00000000000000 0.00000000000000 28.000000000000000 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 200.0 # default=150 (Ry) scf.maxIter 300 # 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 40 # default=5 scf.Mixing.StartPulay 7 # default=6 scf.Mixing.EveryPulay 1 # default=6 scf.criterion 1.0e-6 # default=1.0e-6 (Hartree)
# # MD or Geometry Optimization #
MD.Type Nomd # Opt|EF|BFGS|RF|DIIS MD.Opt.DIIS.History 6 # default=3 MD.Opt.StartDIIS 7 # default=5 MD.Opt.EveryDIIS 6 # default=10 MD.maxIter 200 # MD.Opt.criterion 1.0e-4 # default=1.0e-4 (a.u.)
# # Band dispersion #
Band.dispersion off # on|off, default=off # if <Band.KPath.UnitCell does not exist, # the reciprical lattice vector is employed. Band.Nkpath 1 <Band.kpath 20 0.0 0.0 0.0 0.5 0.0 0.0 G X Band.kpath>
# # DOS and PDOS #
Dos.fileout off # on|off, default=off Dos.Erange -15.0 25.0 # default = -20 20 Dos.Kgrid 300 300 1 # default = Kgrid1 Kgrid2 Kgrid3
DosGauss.fileout off DosGauss.Num.Mesh 4000 DosGauss.Width 0.01 #######################################################################################
[st3@admin 5-0x8]$ cat NEGF-5-0.dat # # File Name #
System.CurrrentDirectory ./ # default=./ System.Name negf-5-0 level.of.stdout 1 # default=1 (1-3) level.of.fileout 0 # default=1 (0-2)
NEGF.filename.hks.l lead-l-5-0.hks NEGF.filename.hks.r lead-r-5-0.hks
NEGF.Num.Poles 150 # defalut=150 NEGF.scf.Kgrid 1 1 # defalut=1 1
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 -25.0 25.0 5.0e-3 #default=-10.0 10.0 5.0e-3 (eV) NEGF.Dos.energy.div 200 # default=200 NEGF.Dos.Kgrid 600 1 # default=1 1 NEGF.SCF.Iter.Band 20
# # Transmission & Eigen Channel #
NEGF.tran.Analysis on # default on NEGF.tran.energydiv 200 # default=200 NEGF.tran.energyrange -20.0 20.0 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 # DATA.PATH /public/home/st3/hzp/openmx/DFT_DATA19 Species.Number 1 <Definition.of.Atomic.Species C C6.0-s2p2d1 C_PBE19 Definition.of.Atomic.Species>
# # Atoms #
Atoms.Number 80 Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU <Atoms.SpeciesAndCoordinates 1 C 9.9063360 10.4360311 14.9998800 2.0 2.0 2 C 11.3142931 10.4360311 14.9998800 2.0 2.0 3 C 12.0364531 11.4561513 15.7413200 2.0 2.0 4 C 9.1841760 11.4561513 15.7413200 2.0 2.0 5 C 9.9063360 11.8458041 16.9405600 2.0 2.0 6 C 11.3142931 11.8458041 16.9405600 2.0 2.0 7 C 12.0364531 11.4561513 18.1400800 2.0 2.0 8 C 9.1841760 11.4561513 18.1400800 2.0 2.0 9 C 9.9063360 10.4360311 18.8812400 2.0 2.0 10 C 11.3142931 10.4360311 18.8812400 2.0 2.0 11 C 12.0364531 9.1748968 18.8812400 2.0 2.0 12 C 9.1841760 9.1748968 18.8812400 2.0 2.0 13 C 9.9063360 8.1545771 18.1400800 2.0 2.0 14 C 11.3142931 8.1545771 18.1400800 2.0 2.0 15 C 12.0361133 7.7651238 16.9405600 2.0 2.0 16 C 9.1841760 7.7651238 16.9405600 2.0 2.0 17 C 9.9063360 8.1545771 15.7413200 2.0 2.0 18 C 11.3142931 8.1545771 15.7413200 2.0 2.0 19 C 12.0361133 9.1748968 14.9998800 2.0 2.0 20 C 9.1841760 9.1748968 14.9998800 2.0 2.0 21 C 14.1543360 10.4360311 14.9998800 2.0 2.0 22 C 15.5622931 10.4360311 14.9998800 2.0 2.0 23 C 16.2844531 11.4561513 15.7413200 2.0 2.0 24 C 13.4321760 11.4561513 15.7413200 2.0 2.0 25 C 14.1543360 11.8458041 16.9405600 2.0 2.0 26 C 15.5622931 11.8458041 16.9405600 2.0 2.0 27 C 16.2844531 11.4561513 18.1400800 2.0 2.0 28 C 13.4321760 11.4561513 18.1400800 2.0 2.0 29 C 14.1543360 10.4360311 18.8812400 2.0 2.0 30 C 15.5622931 10.4360311 18.8812400 2.0 2.0 31 C 16.2844531 9.1748968 18.8812400 2.0 2.0 32 C 13.4321760 9.1748968 18.8812400 2.0 2.0 33 C 14.1543360 8.1545771 18.1400800 2.0 2.0 34 C 15.5622931 8.1545771 18.1400800 2.0 2.0 35 C 16.2841133 7.7651238 16.9405600 2.0 2.0 36 C 13.4321760 7.7651238 16.9405600 2.0 2.0 37 C 14.1543360 8.1545771 15.7413200 2.0 2.0 38 C 15.5622931 8.1545771 15.7413200 2.0 2.0 39 C 16.2841133 9.1748968 14.9998800 2.0 2.0 40 C 13.4321760 9.1748968 14.9998800 2.0 2.0 41 C 18.4023360 10.4360311 14.9998800 2.0 2.0 42 C 19.8102931 10.4360311 14.9998800 2.0 2.0 43 C 20.5324531 11.4561513 15.7413200 2.0 2.0 44 C 17.6801760 11.4561513 15.7413200 2.0 2.0 45 C 18.4023360 11.8458041 16.9405600 2.0 2.0 46 C 19.8102931 11.8458041 16.9405600 2.0 2.0 47 C 20.5324531 11.4561513 18.1400800 2.0 2.0 48 C 17.6801760 11.4561513 18.1400800 2.0 2.0 49 C 18.4023360 10.4360311 18.8812400 2.0 2.0 50 C 19.8102931 10.4360311 18.8812400 2.0 2.0 51 C 20.5324531 9.1748968 18.8812400 2.0 2.0 52 C 17.6801760 9.1748968 18.8812400 2.0 2.0 53 C 18.4023360 8.1545771 18.1400800 2.0 2.0 54 C 19.8102931 8.1545771 18.1400800 2.0 2.0 55 C 20.5321133 7.7651238 16.9405600 2.0 2.0 56 C 17.6801760 7.7651238 16.9405600 2.0 2.0 57 C 18.4023360 8.1545771 15.7413200 2.0 2.0 58 C 19.8102931 8.1545771 15.7413200 2.0 2.0 59 C 20.5321133 9.1748968 14.9998800 2.0 2.0 60 C 17.6801760 9.1748968 14.9998800 2.0 2.0 61 C 22.6503360 10.4360311 14.9998800 2.0 2.0 62 C 24.0582931 10.4360311 14.9998800 2.0 2.0 63 C 24.7801133 11.4561513 15.7413200 2.0 2.0 64 C 21.9281760 11.4561513 15.7413200 2.0 2.0 65 C 22.6503360 11.8458041 16.9405600 2.0 2.0 66 C 24.0582931 11.8458041 16.9405600 2.0 2.0 67 C 24.7801133 11.4561513 18.1400800 2.0 2.0 68 C 21.9281760 11.4561513 18.1400800 2.0 2.0 69 C 22.6503360 10.4360311 18.8812400 2.0 2.0 70 C 24.0582931 10.4360311 18.8812400 2.0 2.0 71 C 24.7801133 9.1748968 18.8812400 2.0 2.0 72 C 21.9281760 9.1748968 18.8812400 2.0 2.0 73 C 22.6503360 8.1545771 18.1400800 2.0 2.0 74 C 24.0582931 8.1545771 18.1400800 2.0 2.0 75 C 24.7801133 7.7651238 16.9405600 2.0 2.0 76 C 21.9281760 7.7651238 16.9405600 2.0 2.0 77 C 22.6503360 8.1545771 15.7413200 2.0 2.0 78 C 24.0582931 8.1545771 15.7413200 2.0 2.0 79 C 24.7801133 9.1748968 14.9998800 2.0 2.0 80 C 21.9281760 9.1748968 14.9998800 2.0 2.0 Atoms.SpeciesAndCoordinates>
# # Lead-Left #
LeftLeadAtoms.Number 40 <LeftLeadAtoms.SpeciesAndCoordinates # Unit=Ang. 1 C 1.4103360 10.4360311 14.9998800 2.0 2.0 2 C 2.8182931 10.4360311 14.9998800 2.0 2.0 3 C 3.5404531 11.4561513 15.7413200 2.0 2.0 4 C 0.6881760 11.4561513 15.7413200 2.0 2.0 5 C 1.4103360 11.8458041 16.9405600 2.0 2.0 6 C 2.8182931 11.8458041 16.9405600 2.0 2.0 7 C 3.5404531 11.4561513 18.1400800 2.0 2.0 8 C 0.6881760 11.4561513 18.1400800 2.0 2.0 9 C 1.4103360 10.4360311 18.8812400 2.0 2.0 10 C 2.8182931 10.4360311 18.8812400 2.0 2.0 11 C 3.5404531 9.1748968 18.8812400 2.0 2.0 12 C 0.6881760 9.1748968 18.8812400 2.0 2.0 13 C 1.4103360 8.1545771 18.1400800 2.0 2.0 14 C 2.8182931 8.1545771 18.1400800 2.0 2.0 15 C 3.5401133 7.7651238 16.9405600 2.0 2.0 16 C 0.6881760 7.7651238 16.9405600 2.0 2.0 17 C 1.4103360 8.1545771 15.7413200 2.0 2.0 18 C 2.8182931 8.1545771 15.7413200 2.0 2.0 19 C 3.5401133 9.1748968 14.9998800 2.0 2.0 20 C 0.6881760 9.1748968 14.9998800 2.0 2.0 21 C 5.6583360 10.4360311 14.9998800 2.0 2.0 22 C 7.0662931 10.4360311 14.9998800 2.0 2.0 23 C 7.7884531 11.4561513 15.7413200 2.0 2.0 24 C 4.9361760 11.4561513 15.7413200 2.0 2.0 25 C 5.6583360 11.8458041 16.9405600 2.0 2.0 26 C 7.0662931 11.8458041 16.9405600 2.0 2.0 27 C 7.7884531 11.4561513 18.1400800 2.0 2.0 28 C 4.9361760 11.4561513 18.1400800 2.0 2.0 29 C 5.6583360 10.4360311 18.8812400 2.0 2.0 30 C 7.0662931 10.4360311 18.8812400 2.0 2.0 31 C 7.7884531 9.1748968 18.8812400 2.0 2.0 32 C 4.9361760 9.1748968 18.8812400 2.0 2.0 33 C 5.6583360 8.1545771 18.1400800 2.0 2.0 34 C 7.0662931 8.1545771 18.1400800 2.0 2.0 35 C 7.7881133 7.7651238 16.9405600 2.0 2.0 36 C 4.9361760 7.7651238 16.9405600 2.0 2.0 37 C 5.6583360 8.1545771 15.7413200 2.0 2.0 38 C 7.0662931 8.1545771 15.7413200 2.0 2.0 39 C 7.7881133 9.1748968 14.9998800 2.0 2.0 40 C 4.9361760 9.1748968 14.9998800 2.0 2.0 LeftLeadAtoms.SpeciesAndCoordinates>
# # Lead-Right #
RightLeadAtoms.Number 40 <RightLeadAtoms.SpeciesAndCoordinates # Unit=Ang. 1 C 26.8983360 10.4360311 14.9998800 2.0 2.0 2 C 28.3062931 10.4360311 14.9998800 2.0 2.0 3 C 29.0284531 11.4561513 15.7413200 2.0 2.0 4 C 26.1761760 11.4561513 15.7413200 2.0 2.0 5 C 26.8983360 11.8458041 16.9405600 2.0 2.0 6 C 28.3062931 11.8458041 16.9405600 2.0 2.0 7 C 29.0284531 11.4561513 18.1400800 2.0 2.0 8 C 26.1761760 11.4561513 18.1400800 2.0 2.0 9 C 26.8983360 10.4360311 18.8812400 2.0 2.0 10 C 28.3062931 10.4360311 18.8812400 2.0 2.0 11 C 29.0284531 9.1748968 18.8812400 2.0 2.0 12 C 26.1761760 9.1748968 18.8812400 2.0 2.0 13 C 26.8983360 8.1545771 18.1400800 2.0 2.0 14 C 28.3062931 8.1545771 18.1400800 2.0 2.0 15 C 29.0281133 7.7651238 16.9405600 2.0 2.0 16 C 26.1761760 7.7651238 16.9405600 2.0 2.0 17 C 26.8983360 8.1545771 15.7413200 2.0 2.0 18 C 28.3062931 8.1545771 15.7413200 2.0 2.0 19 C 29.0281133 9.1748968 14.9998800 2.0 2.0 20 C 26.1761760 9.1748968 14.9998800 2.0 2.0 21 C 31.1463360 10.4360311 14.9998800 2.0 2.0 22 C 32.5542931 10.4360311 14.9998800 2.0 2.0 23 C 33.2764531 11.4561513 15.7413200 2.0 2.0 24 C 30.4241760 11.4561513 15.7413200 2.0 2.0 25 C 31.1463360 11.8458041 16.9405600 2.0 2.0 26 C 32.5542931 11.8458041 16.9405600 2.0 2.0 27 C 33.2764531 11.4561513 18.1400800 2.0 2.0 28 C 30.4241760 11.4561513 18.1400800 2.0 2.0 29 C 31.1463360 10.4360311 18.8812400 2.0 2.0 30 C 32.5542931 10.4360311 18.8812400 2.0 2.0 31 C 33.2764531 9.1748968 18.8812400 2.0 2.0 32 C 30.4241760 9.1748968 18.8812400 2.0 2.0 33 C 31.1463360 8.1545771 18.1400800 2.0 2.0 34 C 32.5542931 8.1545771 18.1400800 2.0 2.0 35 C 33.2761133 7.7651238 16.9405600 2.0 2.0 36 C 30.4241760 7.7651238 16.9405600 2.0 2.0 37 C 31.1463360 8.1545771 15.7413200 2.0 2.0 38 C 32.5542931 8.1545771 15.7413200 2.0 2.0 39 C 33.2761133 9.1748968 14.9998800 2.0 2.0 40 C 30.4241760 9.1748968 14.9998800 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 300.0 # default=300 (K) scf.energycutoff 200.0 # default=150 (Ry) scf.maxIter 1000 # 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 0.010 # default=0.30 scf.Min.Mixing.Weight 0.001 # default=0.001 scf.Max.Mixing.Weight 0.100 # default=0.40 scf.Mixing.History 40 # 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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