Dear Siesta users and experts

I have a phosphorene nanoribbon and I remove on P atom from the scattering
region and want to relax this structure but after running this RUN.fdf with
including the STRUCT.fdf, there is no change in the scattering region. I
check the bond distance to the first and second neighbor atoms before and
after it is the same. I tried many methods like by moving one of the P atom
(first neighbor) to the vacancy but still after relaxation no change
neither with nor without moving the neighbor P atom. Although after
relaxation I saw in the output file that “outcoor: Relaxed atomic
coordinates (Ang):” My RUN.fdf file is given below.

SystemName     SV-H1

SystemLabel     P

PAO.BasisSize   DZP

PAO.BasisType   split

PAO.EnergyShift  0.01 Ry

XC.functional GGA

XC.authors    PBE

%block kgrid_Monkhorst_Pack

   1   0   0    0.0

   0   1   0    0.0

   0   0   5    0.0

%endblock Kgrid_Monkhorst_Pack

maxSCFIterations        300

MeshCutoff     300.0 Ry

MD.TypeOfRun    CG

MD.NumCGSteps     300                   #<---Relaxe

MD.MaxForceTol  0.05 eV/Ang

MD.MaxCGDispl   0.04 Ang

MD.UseSaveCG   .true.

DM.Require.Energy.Convergence   .true.

DM.Energy.Tolerance  0.1E-03 eV

DM.MixingWeight      0.03

DM.NumberPulay       5

DM.UseSaveDM .true.

DM.Tolerance         1.d-4

SpinPolarized .false.

WriteCoorXmol   .true.

SolutionMethod       diagon

%block GeometryConstraints

position from 1 to 56          #<---Fix the left lead

position from 167 to 222   #<---Fix the right lead

%endblock GeometryConstraints

%include STRUCT.fdf

End of File

Can anyone suggest me what is wrong in this input file?

Thanks in advance

Fazle Subhan
PhD Student

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