$InSb_{x}As_{1-x}$ ternary alloy structure generation

[riCatwik]

Dear all Pyiron developers, users and enthusiasts,

I am new here. This is my first problem with Pyiron, but I am stuck at the very beginning.
I would like to generate a ternary $InSb_xAs_{1-x}$ alloy.

Atom positions of primitive zincblende InSb ($a=6.479 \unicode{x212B}$) are:

0.00  0.00  0.00    In
0.25  0.25  0.25    Sb

I want an SQS structure in the following way:

0.00  0.00  0.00    In
0.25  0.25  0.25    Sb=0.25 , As=0.75

Here I would like to

• keep the positions of In atoms at (0 0 0) and its equivalent positions unchanged (or unperturbed - not sure what terminology to use) and
• want only atoms at (0.25 0.25 0.25) and its equivalent positions to be randomized with Sb and As atoms

The general command for SQS generation is "job.input.mole_fractions = {'A': 0.8, 'B':0.2}" but I am unsure how to do it for my specific purpose as I don't want to change the positions of In atoms.

Could someone please help me to solve this?
Looking forward to hearing from you.

Thank you very much.

Regards,
Ritwik

[jan-janssen]

Hi @riCatwik ,

pyiron internally uses https://github.com/dgehringer/sqsgenerator from @dgehringer to generate SQS structures. If I understand your example correctly then you can use the input syntax discussed in:
https://sqsgenerator.readthedocs.io/en/latest/input_parameters.html#composition

But I agree it is not directly clear how to use it in pyiron. @dgehringer can you help us here?

Best,

Jan

[riCatwik]

Thanks for the information.
Yes, I understand how it is done in sqsgenerator, but I still could not figure out how it can be done in Pyiron.

[samwaseda]

I know the answer and I can post it as soon as I can make my atomistics class run again (currently I’m suffering from the fact that my installation is not compatible)

[samwaseda]

I give you the outline here: First you can create a 2-atom structure (here I do it with Fe because I don’t know the base crystal structure of InSbAs):

n_repeat = 3
bcc = pr.create.structure.bulk("Fe", cubic=True)
bcc[1] = "As"
structure = bcc.repeat(n_repeat)

And then you can run the SQS calculation only on the sublattice:

sqs = pr.create.job.SQSJob("sqs_job")
sqs.input.mole_fractions = {"As": 0.75, "Sb": 0.25}
sqs.structure = structure[structure.select_index(“As”)]
sqs.run()

Then you can retrieve the chemical symbols via:

chem_symbols = structure.get_chemical_symbols()
chem_symbols[structure.select_index(“As”)] = sqs[“I_cant_remember_the_tag”]
structure.set_chemical_symbols(chem_symbols)

Something like this should work. As I said I couldn’t test it myself because my installation is not working, but as soon as I manage to run it I will post the final version.

[riCatwik]

@jan-janssen @dgehringer

Thank you very much, @samwaseda, for your answer.

I followed your instruction and did the following:

1. Structure generation

from pyiron import Project
pr = Project(path="sqs")

n_repeat  = 3
structure = pr.create.structure.bulk(name="InSb", 
                                     crystalstructure="zincblende", 
                                     a=6.479, 
                                     cubic=True)
structure = structure.repeat(n_repeat)
len(structure)

2. SQS generation on sublattice

job_sqs = pr.create.job.SQSJob(job_name="sqs_job", 
                               delete_existing_job=True)
job_sqs.input.mole_fractions = {"Sb": 0.5, "As": 0.5}
job_sqs.input.iterations     = 1e6   ##  default:1000000 or 1e6
job_sqs.structure = structure[structure.select_index("Sb")]
job_sqs.run()

Print the first resulting SQS sub-structure

structure_sublattice_sqs = job_sqs.list_structures()[0]
structure_sublattice_sqs

3. Retrieve chemical symbols and merge sublattice with main structure

chem_symbols = structure.get_chemical_symbols()
chem_symbols[structure.select_index("Sb")] = structure_sublattice_sqs.get_chemical_symbols()
print(chem_symbols)

# Set the chemical symbols in the structure
structure_sqs = structure
structure_sqs.set_chemical_symbols(chem_symbols)

# Print the updated structure
structure_sqs

But, unfortunately, SQS structure symbols do not reflects in the main structure.
When I did it with ase and pyiron_atomistics packages, it works. The code is below.

from pyiron_atomistics import ase_to_pyiron
from ase import Atoms

# Define the crystal structure
atoms = Atoms('In2Sb2As2',
              scaled_positions=[(0, 0, 0), (0.5, 0.5, 0), (0.5, 0, 0.5), (0, 0.5, 0.5)],
              cell=[6.479, 6.479, 6.479],
              pbc=True)

# Convert the ase Atoms object to a pyiron Atoms object
structure = ase_to_pyiron(atoms)

# Define the chemical symbols array with a data type of <U3
chem_symbols = np.array(['In', 'Sb', 'As', 'In', 'Sb', 'As'], dtype='<U3')

# Set the chemical symbols in the structure
structure.set_chemical_symbols(chem_symbols)

# Print the updated structure
print(structure)

So, I suppose there is something wrong with this line in step 3.

structure_sqs.set_chemical_symbols(chem_symbols)

I could not catch where it's going wrong. I also checked the data type of chem_symbols (dtype='<U2') length of arrays, which all seems correct to me.

Could you please help me to resolve this?

Thank you very much once again.

Best,
Ritwik

[samwaseda]

Ok I’m not surprised that it didn’t work because I also didn’t know exactly how to change the chemical symbols (which I would have obviously checked if I could have). Let me check what’s wrong in pyiron and I’ll come back to you. For now you can maybe use pyiron_to_ase to change the atom species as it’s done in ASE, I presume, right?