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 Korea