[ase-users] spacegroup question

[Lars Grabow]

Dear Lasse,

thanks for the reply. If I understand you right, you're suggesting that I should be trying this:

bulk = crystal(['Cu','Au'],[(0,0,0),(0.5,0.5,0.5)], spacegroup=123, cellpar=[a/sqrt(2),a/sqrt(2),c,90,90,90])

where (0,0,0) and (.5,.5,.5) are the Wyckoff positions 1a and 1d of spacegroup 123, respectively. While this makes sense and the values can all be found in this online database http://cst-www.nrl.navy.mil/lattice/struk/l1_0.html it doesn't produce the right output. I get a lattice that resembles a BCC structure and not FCC.

I guess I don't really understand how to use the information from the crystal structure database as input to the ase spacegroup package. A simpler example is the HCP structure for which I find:
http://cst-www.nrl.navy.mil/lattice/struk/a3.html

	• Primitive Vectors:
A1	 = 	½ a X - ½ 31/2 a Y
A2	 = 	½ a X + ½ 31/2 a Y
A3	 = 	c Z
	• Basis Vectors:
B1	 = 	1/3 A1 + 2/3 A2 + ¼ A3	 = 	½ a X + ½ 3-1/2 a Y + ¼ c Z	 (Mg) 	 (2c) 
B2	 = 	2/3 A1 + 1/3 A2 + ¾ A3	 = 	½ a X - ½ 3-1/2 a Y + ¾ c Z	 (Mg) 	 (2c) 

On the ASE spacegroup documentation website there is an example how to make the HCP structure and it is as simple as:

mg = crystal('Mg', [(1./3., 2./3., 3./4.)], spacegroup=194, cellpar=[a, a, c, 90, 90, 120])

How does one relate to the other? Sorry if the answer should be obvious!

Thanks a lot in advance!

Lars

On Sep 7, 2011, at 5:07 PM, Lasse Bjerg wrote:

> Furthermore, the space group no. 123 must refer to the primitive (and also tetragonal) unit cell with a = b = 1./sqrt(2) * old_a, c = old_c; and Au at (0, 0, 0) and Cu at (½, ½, ½).
> 
> On 2011-09-07 17:56, Lasse Bjerg wrote:
>> 
>> Hi Lars
>> 
>> Space group no. 123 does not connect (0,0,0) to (0.5,0.5,0.0), so the two positions are two distinct positions, and both should be given when creating the structure. The connections of space group no. 123 can be seen here:
>> http://img.chem.ucl.ac.uk/sgp/large/123az1.htm
>> Putting an atom on position (x,y,z) will automatically give you atoms on positions 2-16.
>> 
>> Lasse
>> 
>> On 2011-09-07 16:06, Lars Grabow wrote:
>>> 
>>> Hi,
>>> 
>>> I tried to use the ase spacegroup package to make the L_10 bulk structure (http://cst-www.nrl.navy.mil/lattice/struk/l1_0.html)
>>> 
>>> I expected to get the correct results with this command:
>>> 
>>> bulk = crystal(['Cu','Au'],[(0,0,0),(0.5,0.0,0.5)], spacegroup=123, cellpar=[a,a,c,90,90,90])
>>> 
>>> However, when I build this bulk structure, one Cu atom seems to be missing.
>>> The correct structure is obtained when I add an extra Cu atom like this:
>>> 
>>> bulk = crystal(['Cu','Cu','Au'],[(0,0,0),(0.5,0.5,0.0),(0.5,0.0,0.5)], spacegroup=123, cellpar=[a,a,c,90,90,90])
>>> 
>>> Am I using the spacegroup package correctly, or is this possibly a bug?
>>> 
>>> Thanks!
>>> Lars
>>> 
>>> -------------------------------------------------------------------------------------------------------------
>>> Lars C. Grabow
>>> Assistant Professor of Chemical and Biomolecular Engineering
>>> University of Houston
>>> S341 Engineering Building 1
>>> Houston, TX 77204-4004
>>> email: grabow at uh.edu web: http://www.chee.uh.edu/faculty/grabow
>>> phone: (+1) 713-743-9899 fax: (+1) 713-743-4323
>>> 
>>> 
>>> 
>>> 
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>> 
>> -- 
>> Lasse Bjerg
>> Visiting PhD Student
>> Massachusetts Institute of Technology
>> 77 Massachusetts Avenue
>> Room 13-4042
>> Cambridge, MA 02139
>> office (+1) 617-258-0222
>> mobile (+1) 857-272-0769
>> email bjerg at mit.edu
>> 
>> 
>> 
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> 
> -- 
> Lasse Bjerg
> Visiting PhD Student
> Massachusetts Institute of Technology
> 77 Massachusetts Avenue
> Room 13-4042
> Cambridge, MA 02139
> office (+1) 617-258-0222
> mobile (+1) 857-272-0769
> email bjerg at mit.edu
> 
> 
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