> 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". > > Many thanks > > Lily
Dear Lily, try any visualization code to have a look at your generated structure (e.g., use xv2xsf from my Sies2xsf tools, then XCrySDen) and at the problem atoms, then you'll have a better idea what's going on. Typical sources of problem: wrong length unit (lattice constant), wrong translation vectors (the atoms are translated across the box boundary where they are not supposed to be), or human typo. Best regards Andrei > > 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/ >> >
