I have been attempting to optimize the structure of a Si nanowire using SIESTA. The original structure fed into the optimization is as follows.
Once it is optimized, the structure would change to being as given below.
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.
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).
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
10.00 0.00 0.00
0.00 1.00 0.00
0.00 0.00 10.00
%endblock LatticeVectors
AtomCoorFormatOut Ang
AtomicCoordinatesFormat Ang
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%endblock AtomicCoordinatesAndAtomicSpecies
%block kgrid_Monkhorst_Pack
1 0 0 0.0
0 6 0 0.0
0 0 1 0.0
%endblock kgrid_Monkhorst_Pack
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
dm.tolerance
is rather high and yourmeshcutoff
is rather low. I would ensure these are converged with respect to this system before concluding too much. $\endgroup$