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I have been attempting to optimize the structure of a Si nanowire using SIESTA. The original structure fed into the optimization is as follows.

Original structure

Once it is optimized, the structure would change to being as given below. Optimized structure

In this, there appears to be several atoms moving away from cubic diamond lattice structure (white atoms) as the structure gets optimized (which is something that I expected). However, if I deleted these (white) atoms, the overall structure appears to be much cleaner and nicer as below. New structure: with atoms deleted manually Legend

Now with all these changes in the structure, I am seeing several band lines pass through the Fermi level in the optimized structure (shown in image 2). Band Structure

Does this (lack of band-gap) occur because of the atoms deviating from the cubic diamond crystal arrangement? Is this acceptable to occur in a structure (since the original cross section was manually set by carving out a cylindrical region from a bulk block of Si)? Or could it be some error caused by me during the calculation?

My fdf script is attached as well

SystemName       Si
SystemLabel      Si

NumberOfSpecies    1
NumberOfAtoms      185

%block ChemicalSpeciesLabel
 1 14 Si
%endblock ChemicalSpeciesLabel

LatticeConstant 5.41 Ang
%block LatticeVectors 
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  0.00  1.00   0.00
  0.00  0.00  10.00
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AtomicCoordinatesFormat     Ang
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  1  0  0  0.0
  0  6  0  0.0
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PAO.BasisSize           DZP
XC.functional           LDA 
XC.authors              CA 
SpinPolarized           .false. 
MeshCutoff              150 Ry  
kgrid_cutoff            100.0 Ang

MD.TypeOfRun            CG 
MD.VariableCell         true 
MD.NumCGsteps           500 
MD.MaxCGDispl           0.1 Bohr 
MD.MaxForceTol          0.04 eV/Ang  
MD.MaxStressTol         0.0001 eV/Ang**3 

MD.UseSaveCG            true
MD.UseSaveXV            true
MaxSCFIterations        500
DM.MixingWeight         0.01
DM.NumberPulay          3
DM.Tolerance            1.d-3
#ElectronicTemperature   25 meV
SolutionMethod          diagon

BandLinesScale ReciprocalLatticeVectors
%block BandLines
1   0.0000000000 0.0000000000 0.0000000000 \Gamma
100 0.0000000000 0.5000000000 0.0000000000 y
%endblock BandLines

%block WaveFuncKPoints
0.000 0.000 0.000 from 1 to 100
%endblock WaveFuncKPoints
Improve this question
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  • 3
    $\begingroup$ Two comments, your dm.tolerance is rather high and your meshcutoff is rather low. I would ensure these are converged with respect to this system before concluding too much. $\endgroup$
    – nickpapior
    Oct 12, 2021 at 8:01
  • $\begingroup$ @zeroth thanks for the comment. I shall start working on that as well. $\endgroup$
    – PBH
    Oct 12, 2021 at 8:53
  • 4
    $\begingroup$ Briefly speaking, what you observe during the geometry optimization is the surface restructuring of the Si surface, and the vanishing band gap is due to surface states. Do you really want to calculate a Si nanowire with a clean surface? Real-world Si surfaces are seldom clean, but are usually either terminated by hydrogen atoms or by hydroxyl groups. I don't know if the surfaces of Si nanowires are generally clean, but I guess this is not the case. $\endgroup$
    – wzkchem5
    Oct 12, 2021 at 11:56
  • 2
    $\begingroup$ @wzkchem5 thanks for the reply. The thing is I am studying the thermal transport in pristine Si nanowires using molecular dynamics simulations. This is why I did not try to terminate the surface using 'H' or 'OH' groups. Now that this problem has risen, I think that it is best to terminate the surface as mentioned. Also, is there a way to define these terminations? I know that Avogadro can do this, but the final structure usually consists of excess H atoms. $\endgroup$
    – PBH
    Oct 12, 2021 at 12:42
  • 1
    $\begingroup$ @CarlosAndrésdelValle what do you mean by that? I am aware that DFT cannot produce the accurate band gap of a material and so on. However when experimental investigations are not feasible, how exactly does one compare (band structure and other electronic properties) several nanostructures with one another? Are you saying that there are alternate and significantly more accurate methods? $\endgroup$
    – PBH
    Dec 31, 2021 at 5:25

1 Answer 1

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$\begingroup$

I believe that after taking into consideration what the comments have pointed out you should also look into the fact that as your geometry has changed somewhat considerably after the optimization. This change in geometry would cause a breaking in the symmetry and thus when the BS is being calculated, as you go through your Brillouin zone you are not going to "see" the same states you saw before. Have you looked into this ? Hope this makes sense.

Here is reference on what I am trying to convey:

G. Vasseur, et al. Effect of Symmetry Breaking on Electronic Band Structure: Gap Opening at the High Symmetry Points Symmetry 2013, 5(4), 344-354; https://doi.org/10.3390/sym5040344

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  • 1
    $\begingroup$ No I have not looked into this. I decided to look at structures with H terminations to remove the surface states and managed to get a decent band structure. $\endgroup$
    – PBH
    Nov 16, 2021 at 17:03

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