Thank you very much, Guangping, got it!
Lily On Thu, Jul 28, 2011 at 11:28 AM, Guangping Zhang <[email protected]> wrote: > ** > ** > Dear Lily, > > Please remember the first line in which contains the number of the atoms in > the system. And the scond line can be a blank line or you can leave some > comments in it. From the third line, the xyz coordinates for each atom in > the system should be given following its element name. > > Best > > Guangping > > 2011-07-29 > ------------------------------ > Guangping Zhang > ------------------------------ > 发件人: lily zheng <[email protected]> > 发送时间: 2011-07-29 00:23 > 主 题: Re: [SIESTA-L] quick questions about XYZ file > 收件人: [email protected] > > > Thanks Roland, > > But when there is no such line , Molekel could not open it up to see the > structure for CH4 which has not the first two lines. Like the first one > for (3,3) tube, there is such lines, Molekel can open it up and show the > structure. what's wrong? > > thanks > Lily > > On Thu, Jul 28, 2011 at 11:15 AM, Roland Gillen > <[email protected]>wrote: > >> ** >> Dear Lily, >> >> the second line is for comments, such as the name or the system. In your >> case of the (3,3)-CNT, the comment consists of the lattice constant and the >> C-C bond length. It is, however, just a comment, it could be pretty much >> anything. Most molecular viewer programs will simply ignore the line. >> >> Roland >> >> >> Dear all, >> >> >> In XYZ file, for instance, Nanotube(3.3) It is like: >> >> 12 *How many atoms in the system* >> 2.45778 *Lattice constant* 1.41900 *what >> this one stands for?* >> C 2.03256769511475710033 0.00000000000000000000 >> 0.00000000000000000000 >> C 1.55703715080933680071 1.30650937471709660542 >> -0.00000000000000005254 >> C 1.01628384755737877221 1.76025525888096323612 >> 1.22889004797011835990 >> C -0.35295173338285917852 2.00168841459557622642 >> 1.22889004797011835990 >> C -1.01628384755737810607 1.76025525888096345817 >> 0.00000010049879950458 >> C -1.90998888419219636781 0.69517903987847973202 >> 0.00000010049879945204 >> C -2.03256769511475710033 0.00000000000000024891 >> 1.22889014846891786448 >> C -1.55703715080933746684 -1.30650937471709593929 >> 1.22889014846891786448 >> C -1.01628384755737943834 -1.76025525888096279203 >> 0.00000020099759900916 >> C 0.35295173338285806830 -2.00168841459557622642 >> 0.00000020099759895662 >> C 1.01628384755737721790 -1.76025525888096412430 >> 1.22889024896771736906 >> C 1.90998888419219636781 -0.69517903987847995406 >> 1.22889024896771736906 >> >> When we write XYZ file for CH4: >> >> >> 5 *Atom number in systems* >> >> * how to write down the other two parameters? >> * >> ** >> >> * *C 0.000 0.000 0.000 * * >> H 1.219 -0.284 -0.377 >> H -0.284 1.219 -0.377 >> H -0.140 -0.140 1.219 >> H -0.833 -0.833 -0.503 >> >> >> >> >> Any hints would be much much appreciated! >> >> >> Lily >> >> > ** >
