How to specify sites with "enumerate_strucutures"

icet
1

Hi, I’m annoying with “icet.tools.enumerate_structures”

How can I specify separate crystal sites?

I’d like to make cluster with three atomic sites like ABOx.
In the official examples, GaAs clusters are produced with two distinct sites, but I failed to make clusters from primitive structure which is made by ase.spacegroup.crystal which has 3 sites.

I did some testings with “icet.tools.enumerate_structures”.
When I set up the chemical_symbols like this ,the below error occurs.
chemical_symbols=[[‘A’],[‘B’, ‘C’],[‘O’]]
Exception: chemical_symbols needs to be a list of strings or a list of list of strings.

When I set up the chemical_symbols like this, the kernel can run but there is no meaning.
chemical_symbols=[[‘A’, ‘B’, ‘O’]]

I’m a beginner on ase and icet.

Thank you．

2

I dont understand what problem/error you are running into.
Can you post a script/snippet including any other files that fully reproduces your error?

3

Thank you for your reply.
Sorry, I wasn’t able to explain my problem fully.

I think “crystal” is same as ''bulk(tutorial)", however “crystal” doesn’t work.The below error happens.
“Exception: chemical_symbols needs to be a list of strings or a list of list of strings.”
I want to know my code is wrong or icet doesn’t have a function to generate clusters from “crystal”.

from ase.spacegroup import crystal
#crystal(I tried)
a = 5.65  
prim = crystal(['Ga', 'As'], basis=[(0,0,0), (0.25,0.25,0.25)], spacegroup=216, cellpar=[a, a, a, 90, 90, 90])

for structure in enumerate_structures(structure=prim,
                                      sizes=range(1, 9),
                                      chemical_symbols=[['Ga', 'Al'], ['As']]):
    pass # Do something with the structure

#bulk(tutorial)
prim = bulk('GaAs', crystalstructure='zincblende', a=5.65)
for structure in enumerate_structures(structure=prim,
                                      sizes=range(1, 9),
                                      chemical_symbols=[['Ga', 'Al'], ['As']]):
    pass # Do something with the structure
4

The chemical symbols list needs to be as long as the primitive structure. When you use crystal you create a cubic 8-atom cell. Also you need to check the ordering of atoms (sites) in the primitive structure so that it matches with your chemical-symbols. E.g. for you crystal snippet I think you would need [['Ga', 'Al'], ['Ga', 'Al'], ['Ga', 'Al'], ['Ga', 'Al'], ['As'], ['As'], ['As'], ['As']] .

Note that typically when doing enumeration you want to use the smallest possible primitive, but of course it depends on what you actually want to do with the enumerated structures.

5

Hi

I’m grateful for your advice.
I had missed that perspective. I was able to solve my issue.

Thank you.