Thank you Marcos, I'll definitely try what you suggested, but I have 2 more questions:
1)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)? 2) 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 2010/10/14 Marcos Veríssimo Alves <[email protected]> > Artem, > > On Thu, Oct 14, 2010 at 6:06 PM, Artem Baskin <[email protected]> wrote: > > Dear Siesta 3.0 beta users! Thank you for you time. > > I have three simple (hope that) questions about processing SIESTA. > > > > 1) how to fix the coordinates of atoms that I choose relaxing the rest > > part of my system? > > > > I used > > %block GeometryConstraints > > position # of atom which position I want to be fixed > > %endblock GeometryConstraints > > to control coordinates of atoms to be fixed. BUT AT THE END OF > RELAXATION > > PROCEDURE final coordinates ARE CHANGED. Why? How to overcome this > > > > problem? > > In principle it should work well. However, try > > %block GeometryConstraints > position 10 11 12 1.0 0.0 0.0 > position 10 11 12 0.0 1.0 0.0 > position 10 11 12 0.0 0.0 1.0 > %endblock GeometryConstraints > > as a radical measure. Check the manual for the meaning. > > > > > 2)I run SIESTA jobs at remote cluster with limited time of each job. If > > the granted time elapsed before the calculations are finished how can I > > restart the same job (using something like check file in Gaussian) > without > > > > running it from the very begging? Is there any specific file containing > > that information, and how to restart it (I mean, the particular command > > etc.)? > > > > http://www.icmab.es/siesta/manuales/manual-3.0-b/node119.html and > check the entry "reading saved data" > > > 3)I want to study interaction between neutral lattice and ions. Is there > > > > any way (besides that mentioned in manual) to do that associating the > > charge with ions (but not with the whole system)? If not, how to > interpret > > the results? If I have, for example, Na(+) should I look for a specific > > > > pseudopotential for that particle or pseudopotential for neutral Na is > > enough? > > Sorry I can't help you with that. > > Cheers, > > Marcos > > > > > Any help will be appreciated, > > Thank you in advance > > > > Artem Baskin, > > PhD student, > > University of Illinois at Chicago > > >
