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
