I'm working with the Siesta DFT software, and managed to reproduce the band structure of bulk Si without any issues. However, when trying the same with a Si nanowire, the band structure looks nowhere near those published in literature, and there doesn't seem to be any bandgap either. Has anyone had previous experience with a similar situation? Relevant figure from the article

Results from current calculations

SystemName      Si
SystemLabel     Si

NumberOfSpecies         1
NumberOfAtoms           85

%block ChemicalSpeciesLabel
  1  14  Si
%endblock ChemicalSpeciesLabel

LatticeConstant 5.41 Ang
%block LatticeVectors
  16.00  0.00   0.00
   0.00  1.00   0.00
   0.00  0.00  16.00
%endblock LatticeVectors

AtomCoorFormatOut  Ang
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
35.1650000000 0.0000000000 35.1650000000 1
36.5175000000 1.3525000000 36.5175000000 1
51.3950000000 2.7050000000 48.6900000000 1
50.0425000000 1.3525000000 50.0425000000 1
%endblock AtomicCoordinatesAndAtomicSpecies

%block kgrid_Monkhorst_Pack
   1  0   0  0.5
   0  16  0  0.5
   0  0   1  0.5
%endblock kgrid_Monkhorst_Pack

PAO.BasisSize           DZP
XC.functional           LDA      
XC.authors              CA       
SpinPolarized           .false.  
MeshCutoff              300 Ry   
kgrid_cutoff            100.0 Ang

MD.TypeOfRun       CG               
MD.VariableCell    true             
MD.NumCGsteps      50               
MD.MaxCGDispl      0.1 Bohr         
MD.MaxForceTol     0.01 eV/Ang      
MD.MaxStressTol    0.0001 eV/Ang**3 
%block GeometryConstraints          

%endblock GeometryConstraints

MD.UseSaveXV  true
MaxSCFIterations   100
DM.MixingWeight    0.01
DM.NumberPulay     3
DM.Tolerance       1.d-3
ElectronicTemperature  25 meV
SolutionMethod    diagon

BandLinesScale        pi/a
%block BandLines
1  0.0000000000 0.0000000000 0.0000000000 \Gamma
50 0.0000000000 1.0000000000 0.0000000000 Y
%endblock BandLines

%block WaveFuncKPoints
0.000 0.000 0.000 from 1 to 20
%endblock WaveFuncKPoints
  • $\begingroup$ We would need more information, can you show your band structure? I am assuming the ones in the post are from the literature. $\endgroup$ Sep 6, 2021 at 4:46
  • $\begingroup$ Hi @TristanMaxson, I have added the results from my calculations as the second image. The band structure is plotted from Gamma (x=0) to increasing K in the direction of the nanowire length. $\endgroup$
    – PBH
    Sep 6, 2021 at 8:35
  • 1
    $\begingroup$ Is the structure you are using the exact same one as in the reference you are comparing with? The band structures of nanomaterials can vary widely depending on the details of the structure, for example there exist both metallic and insulating carbon nanotubes. $\endgroup$
    – ProfM
    Sep 6, 2021 at 11:21
  • 2
    $\begingroup$ I am not sure what the reason is other than passivating the surface changes the results significantly. Perhaps the dangling bonds without passivation lead to the metallic behavior? Also, I would suggest you write the answer to your own question (allowed) for future reference. $\endgroup$
    – ProfM
    Dec 2, 2021 at 8:08
  • 1
    $\begingroup$ @PBH I think a partial answer would still be useful. My tendency (though you don't necessarily have to do this) is to make answers I'm less confident in or feel are incomplete into Community Wikis, so they can be supplemented if another user comes along that can fill in the gaps. $\endgroup$
    – Tyberius
    Sep 12, 2022 at 17:26

1 Answer 1


This is not a complete answer with complete reasoning behind what had happened. However, I am giving this answer in case someone faces the same situation in the future.

What had happened was, I did not use surface passivated nano-wires. This means that the atoms on the surface of the structure had dangling bonds due to the lack of neighboring atoms. This caused the structures to show surface states of electrons which cause band lines inside the gap of the material. A brief overview of the phenomenon can be found on the Wikipedia page and a better insight can be obtained through this paper.

In order to avoid this complication (for the case of nanostructures), the best way would be to terminate the surface bonds using hydrogen atoms (Sometimes -OH and -NH3 terminations are also used if I remember correctly).

To do this, I tried a lot of software packages such as Pymol and Olex2 etc, but ended up having issues on the resultant structure near the periodic boundaries. Eventually I used my own code to calculate the number of neighbors and added the H atoms based on that. However this wasn't the most convenient or reliable approach since I had to manually verify every structure before the DFT calculations.


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