Last Modified 17 December 1999
Example XI showed how to use static to generate the energy of an eight-atom copper cluster as a function of the spacing between that atoms. This example will show how to use the skingen script to construct the SKIN file for this problem.
Briefly, we want to set up a calculation with eight copper atoms, each at the corner of a cube of side a. We do this by specifying a very large simple cubic unit cell, and placing the atoms near the origin, using the Cartesian coordinates option for atomic input. Note that the calculation used Mode = 3 (energy only), with a Fermi Temperature of 5 mRy.
$ skingen Welcome to the NRL SKIN file generatorAs noted above, use Mode 3, with T = 0.005 Ry:
Enter the mode you want to use (1-9, h for help): 3<cr>
Using mode 3
Enter the Fermi temperature for the electron states
(>=0, h==help): .005<cr>
T_{Fermi} = .005
Mode = 3
Hopefully you have a copy of the parameters in this directory:Enter the path to the tight-binding parameterization file: cu_par<cr> Enter the long label for structure 1. The default is ' ': Eight-atom copper cluster<cr> Enter the short (20 character) label (Default ' '): 5.00<cr> (The cube size)Note that any primitive lattice would do, so long as it is large enough. We'll use a very large unit cell, with no strain:
Enter the lattice type (-13,...,13,h=help): 1<cr> Enter the lattice constant a (Default ' '): 100.0<cr> Enter the strain type [0=none, h=help]: 0<cr>Note that we want to shorten the search distance as much as possible:
How far should we search for neighbors along each primitive lattice vector? (default = "4 4 4") 1 1 1<cr>There are eight atoms in the unit cell, each of type 1 (Copper), and we're going to list their positions in Cartesian coordinates:
How many atoms in this structure (Default 1)? 8<cr> Enter atomic positions in (1) lattice (default) or (2) Cartesian coordinates: 2<cr> The atomic positions will be in Cartesian coordinatesNow we have to specify the position of each atom, just as we did in the original example. An easy way of speeding up this process would be appreciated.
Enter the index number of atom 1 (Default 1): <cr>
Enter the atomic position in Cartesian coordinates, separated by spaces (Default:
'0.000 0.000 0.000': 2.5 2.5 2.5<cr>
Enter the index number of atom 2 (Default 1): <cr>
Enter the atomic position in Cartesian coordinates, separated by spaces (Default:
'0.000 0.000 0.000': 2.5 2.5 -2.5<cr>
Enter the index number of atom 3 (Default 1): <cr>
Enter the atomic position in Cartesian coordinates, separated by spaces (Default:
'0.000 0.000 0.000': 2.5 -2.5 2.5<cr>
Enter the index number of atom 4 (Default 1): <cr>
Enter the atomic position in Cartesian coordinates, separated by spaces (Default:
'0.000 0.000 0.000': 2.5 -2.5 -2.5<cr>
Enter the index number of atom 5 (Default 1): <cr>
Enter the atomic position in Cartesian coordinates, separated by spaces (Default:
'0.000 0.000 0.000': -2.5 2.5 2.5<cr>
Enter the index number of atom 6 (Default 1): <cr>
Enter the atomic position in Cartesian coordinates, separated by spaces (Default:
'0.000 0.000 0.000': -2.5 2.5 -2.5<cr>
Enter the index number of atom 7 (Default 1): <cr>
Enter the atomic position in Cartesian coordinates, separated by spaces (Default:
'0.000 0.000 0.000': -2.5 -2.5 2.5<cr>
Enter the index number of atom 8 (Default 1): <cr>
Enter the atomic position in Cartesian coordinates, separated by spaces (Default:
'0.000 0.000 0.000': -2.5 -2.5 -2.5<cr>
Now we could select any space group, but we might as well take
the simplest one, which we call ``general:''
Select a space group: (0=general,1=fcc/bcc/sc/diamond,2=hcp/hexagonal/graphite,3=path,h=help): 0<cr>We only want 1 k-point, located at gamma. Fortunately, this is saved as ``regular.00 in the fcc directory:
Pre-defined k-points are available for (1) fcc/diamond, (2) bcc, (3) sc, (4) hexagonal/hcp lattices. Please pick one: 1<cr> total 118 -r--r--r-- 45 mehl bind 28 Oct 28 1994 regular.00 -r--r--r-- 14 mehl bind 729 May 30 1996 regular.04 -r--r--r-- 12 mehl bind 3532 Sep 24 1996 regular.06 -r--r--r-- 16 mehl bind 3468 Jun 1 1995 regular.08 -r--r--r-- 13 mehl bind 4350 Mar 29 1996 regular.10 -r--r--r-- 14 mehl bind 18090 Jul 2 1996 regular.12 -r--r--r-- 12 mehl bind 26494 Nov 23 1993 regular.14 -r--r--r-- 13 mehl bind 10003 Jul 28 1997 spcgrp.fcc -r--r--r-- 12 mehl bind 314 May 20 1994 special.04 -r--r--r-- 12 mehl bind 2162 Dec 8 1993 special.06 -r--r--r-- 12 mehl bind 2226 Nov 15 1993 special.08 -r--r--r-- 12 mehl bind 2866 Nov 15 1993 special.10 -r--r--r-- 12 mehl bind 14020 Nov 23 1993 special.12 -r--r--r-- 12 mehl bind 21566 Nov 23 1993 special.14 Your choice? regular.00<cr>That is the end of the first structure. Remember that in the next structure we use a separation of 4.80 Bohr, so we adjust everything accordingly:
To add another structure, continue answering questions as before. To exit, hit ^D at the next prompt. Enter the long label for structure 2. The default is 'Eight-atom copper cluster': <cr> Enter the short (20 character) label (Default '5.00'): 4.80<cr>Note that the lattice constant doesn't change:
Enter the lattice constant a
(Default '100.0'): <cr>
Enter the index number of atom 1 (Default 1): <cr>
Enter the atomic position in Cartesian coordinates, separated by spaces (Default:
'2.5 2.5 2.5': 2.4 2.4 2.4<cr>
Enter the index number of atom 2 (Default 1): <cr>
Enter the atomic position in Cartesian coordinates, separated by spaces (Default:
'2.5 2.5 -2.5': 2.4 2.4 -2.4<cr>
Enter the index number of atom 3 (Default 1): <cr>
Enter the atomic position in Cartesian coordinates, separated by spaces (Default:
'2.5 -2.5 2.5': 2.4 -2.4 2.4<cr>
Enter the index number of atom 4 (Default 1): <cr>
Enter the atomic position in Cartesian coordinates, separated by spaces (Default:
'2.5 -2.5 -2.5': 2.4 -2.4 -2.4<cr>
Enter the index number of atom 5 (Default 1): <cr>
Enter the atomic position in Cartesian coordinates, separated by spaces (Default:
'-2.5 2.5 2.5': -2.4 2.4 2.4<cr>
Enter the index number of atom 6 (Default 1): <cr>
Enter the atomic position in Cartesian coordinates, separated by spaces (Default:
'-2.5 2.5 -2.5': -2.4 2.4 -2.4<cr>
Enter the index number of atom 7 (Default 1): <cr>
Enter the atomic position in Cartesian coordinates, separated by spaces (Default:
'-2.5 -2.5 2.5': -2.4 -2.4 2.4<cr>
Enter the index number of atom 8 (Default 1): <cr>
Enter the atomic position in Cartesian coordinates, separated by spaces (Default:
'-2.5 -2.5 -2.5': -2.4 -2.4 -2.4<cr>
To add another structure, continue answering questions as before.
To exit, hit ^D at the next prompt.
Enter the long label for structure 3.
The default is 'Eight-atom copper cluster':
At this point I quit. Some things are easier to do with a text editor and ``search and replace.'' Perhaps someone can come up with a way of altering the script which makes it easy to do small changes in the input.
Or you can continue with the script through the spacings used in
Example 11. If you do, your
final result should look like this new SKIN file.
5.00 ************ .137678958 1.119595488
4.80 ************ .163069552 1.063931226
4.60 ************ .192971858 1.024286948
4.55 ************ .201186773 1.018186262
4.50 ************ .209707198 1.014046539
4.40 ************ .227690265 1.012693070
4.35 ************ .237169258 1.016060544
4.30 ************ .246987253 1.022553977
4.20 ************ .267697037 1.046367643
4.00 ************ .290909611 1.148887375
Return to the skingen page.
Look at other other skingen examples.
Look at other static examples.
Get other parameters from the Tight-binding periodic table.
Return to the static Reference Manual.