[Smeagol-discuss] Why no transmission data generated?

[Ivan Rungger]

Hello 徐卓,

 your calculation is converged to an unphysical solution, since the energy
is positive. This indicates most likely some problem in the input file. From
the part of the input file you have added it is not possible to say what
might be the problem. If you send me the input files for leads and
scattering region, I might be able to see what is the problem.

Cheers,

 Ivan

2010/2/24 徐卓 <xuzhuo06 at mails.gucas.ac.cn>

> Hi, I am a  beginner of Smeagol. I could run the example of Au atom wires
> with no problem at all.
>
> After calculating the Au leads, I try to calculate zero bias conductance
> and I-V characteristics of a one dimensional nanostructure of two periods,
> which contains about 100-150 atoms, between Au leads.
>
> The iteration of 0 V (the initial bias) of Smeagol converges to a
> positive energy value, while the scf calculation of the same nanostructure
> by Siesta will converge to a negative energy value, is there anything wrong
> of Smeagol or not?
>
> Moreover, after the convergence of the initial bias, the calculation stops
> automatically. There are files of  .alloc, .CHR, .DM, .fdf (input), .KP, and
> .out (output) only, no transmission data (.CUR, .TRC, .LGF etc.) at all.
> What's wrong with it?
>
> The parameters of my input file are as follows:
>
> %block PAO.BasisSizes
> (...)  SZP
> %endblock PAO.BasisSizes
>
> %block kgrid_Monkhorst_Pack
>   2   0   0    0.0
>   0   2   0    0.0
>   0   0  15    0.0
> %endblock kgrid_Monkhorst_Pack
>
> xc.functional   LDA
> xc.authors     CA
> SpinPolarized   F
> FixSpin                         F
> TotalSpin                       0.0
> NonCollinearSpin  F
> MeshCutoff     180. Ry
> MaxSCFIterations  500
>
> DM.MixingWeight   0.6
> DM.NumberPulay   10
>
> DM.PulayOnFile   F
> DM.Tolerance    5.0E-4
> NeglNonOverlapInt  T
>
> SolutionMethod   diagon
> ElectronicTemperature  300 K
>
> DM.UseSaveDM    T
>
> SaveElectrostaticPotential T
> WriteCoorXmol   T
> SaveHS    F
> SaveRho   T
> SaveDeltaRho   F
> WriteDenchar   F
> WriteEigenvalues  F
> WriteDMT                   T
>
> EMTransport              T
> NEnergReal               0
> NEnergImCircle           15
> NEnergImLine             20
> NPoles                   4
> VInitial                 0.d0 eV
> VFinal                   0.d0 eV
> NIVPoints                0
> Delta                    1.d-4
> EnergLowestBound        -5.0d0 Ry
> SpinConfLeads            0
> NSlices                  1
> TrCoefficients   T
> AtomLeftVCte             (...)
> AtomRightVCte            (...)
> NTransmPoints            100
> InitTransmRange          -10.0d0 eV
> FinalTransmRange         0.d0 eV
>
> %block SaveBiasSteps
>  0
> %endblock SaveBiasSteps
> SaveMemTranspK   F
> PeriodicTransp   T
> TransmissionOverk         F
>
> #ParallelOverK   T
> #Diag.ParallelOverK         T
>
> HartreeLeadsBottom      (...) eV
> HartreeLeadsLeft          0. Ang
> HartreeLeadsRight       (...) Ang
>
> The output file ends as follows:
>
> siesta:                 ===============================
> SMEAGOL                 Bias step =    0, V =  0.000 Ry
>                             Begin CG move =      0
>                         ===============================
>
> iodm: Reading Density Matrix from files
>
> InitMesh: MESH =   192 x   192 x   144 =     5308416
> InitMesh: Mesh cutoff (required, used) =   180.000   191.452 Ry
>
> * Maximum dynamic memory allocated =   416 MB
> WARNING: There are k-points along z
>
> ......
>
> siesta: iscf   Eharris(eV)      E_KS(eV)   FreeEng(eV)   dDmax  Ef(eV)
> siesta:    1   (...)
> timer: Routine,Calls,Time,% = IterSCF        1   14868.199  99.99
> ......
>
> siesta:    (XX)   (...) [reaches the convergence criteria]
>
> [the output file just stops here]
>
> If I set kgrid_Monkhorst_Pack to 1 1 1, it says Segmentation Fault and
> stops at once. I have ever read the Dr. Rocha's research of a DNA molecule
> between Au leads, which even large than my one dimensional nanostructure.
> What's wrong of my case? Could anybody suggest any hint for me please?
>
> Thank you very much.
>
> XU Zhuo
>
> PhD. student from Graduate School of Chinese Academy of Science
>
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