Dear Siesta 3.0 beta users! Thank you for you time. I calculate the band structure for different types of graphene based ribbons and I encountered with the following problems:
1) To calculate the BS for pristine NR I used the relaxation part MD.TypeOfRun CG MD.VariableCell .true. MD.NumCGsteps 40 MD.MaxStressTol 0.1 GPa and I got more or less reasonable results. But now I want to take into account the dependence of the band gap on the z-coordinate of molecule/atom which is above the ribbon. In order to do that I used %block GeometryConstraints position # of atom which position I want to be fixed %endblock GeometryConstraints I expected that at the end of relaxation procedure the position of chosen atom remains the same BUT IT IS CHANGED quite strongly (sometimes, depending on the initial position, more than 50% of initial coordinate). So my question is how to fix the distance (z-coordinate) between ribbon and the molecule/atom? Does the option (MD.VariableCell .true. ) contradict to freezing of the coordinates of some atoms? 2) To calculate the energy (binding energy) between nanoribbon and a molecule (above the ribbon) I used the value of TOTAL energy in block siesta: Final energy (eV): siesta: Kinetic = 7168.537907 siesta: Hartree = 83393.002729 siesta: Ext. field = 0.000000 siesta: Exch.-corr. = -3071.032309 siesta: Ion-electron = -173190.442014 siesta: Ion-ion = 75708.722958 siesta: Ekinion = 0.000000 siesta: Total = -9991.210729 of output file. Am I right doing like this (providing that all thermodynamic parameters are by default)? 3) And finally I have the general question about the meaning of relaxation procedure and its connection to the convergence. Trying to calculate the BS for armchair nanoribbon without relaxation part I got absolutely wrong BS, an spurious dipole moment and other weird things. As I understood, the problem is that my initial geometry was not appropriate and needed to be corrected. Moreover, I could not get the convergence within 100 SCF steps (there were oscillations of dDmax level). But it seems to be strange. If I want to calculate the electronic energy of a system with the particular geometry (like in Gaussian) I expect to have that energy but not the energy corresponding to optimized geometry. So far I do not know how to calculate the BS, electronic energy and so on of non-relaxed geometry. Any help will be appreciated, Thank you in advance Artem Baskin, PhD student, University of Illinois at Chicago
