orex / supercell

The program allows you to create regular structure supercell from cif file with partial occupancy and/or substitutions.
GNU General Public License v2.0
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unexpected output when there are only two atoms in the unit cell #51

Closed Satinelamp closed 1 year ago

Satinelamp commented 2 years ago

I create a cif file that only contains two atoms:

Zn15-T1      0.5   0   0   0.5
Cd15-T1     0.5   0  0   0.5

I expect supercell would output 2 configurations, which contain one type of atom in the unit cell, respectively, but there is only one output configuration, here is the output:

Chemical formula of the supercell: Cd1 Zn0
Total charge of supercell: 0

----------------------------------------------------
 Identification of groups of crystallographic sites
----------------------------------------------------

 Group 1 (1 atomic positions in supercell):
   Site #1: Zn15-T1 (occ. 0.5) -> FIXED with occupancy 0.000.
   Site #2: Cd15-T1 (occ. 0.5) -> FIXED with occupancy 1.000.

Minimal distance between atoms of two distinct groups: -1 A.

-------------------------------------------------
The total number of combinations is 1

Here are the detailed log and cif files I use. cif.zip

output.txt

orex commented 2 years ago

Supercell is not working in such way. The output configurations have fixed composition. Composition you can vary by yourself, using, for example, -p parameter. See tutorial https://orex.github.io/supercell/docs/tutorial/ and supercell paper https://jcheminf.biomedcentral.com/articles/10.1186/s13321-016-0129-3

Satinelamp commented 2 years ago

In my case, why does supercell program choose Cd elecment instead of Zn?

orex commented 2 years ago

Let's say that this is a random choice.