> Yeah, Usually how to come up with reasonable 'initial guess' of > coordinates > instead of wild guessing? > > For example, carbon tube, I used one ready-made program which generated > coordinates. But it gave me the warning like " WARNING: Atoms >>> 460 641 too close: rij = 0.351881 Ang".
Dear Lily, nobody knows where your atoms 460 and 641 are. But, using any visualization program and looking at generated structure with your problematic atoms will immediately give you a hint whom to blame: the atoms, the ready-made program, or your own typo. Typical errors are wrong length scale (lattice parameter), or wrong translation vectors. Best regards Andrei > > Many thanks > > > Lily > > On Sun, May 15, 2011 at 12:38 AM, sonu kumar <[email protected]> wrote: > >> Hi all Siesta users, >> >> >> >> >> how to fix the question like"siesta: WARNING: Atoms >> >> 460 641 too close: rij = 0.351881 Ang" ? >> >> This warning comes because you have incorrectly specified the >> positions of atoms in your unit cell. >> >> regards, >> >> -- >> Sonu Kumar >> Phd Student >> Physics Department >> Indian Institute of Technology >> Delhi-110016, India >> web:-http://www.iitd.ac.in/ >> >
