Custom states

[AntObi]

Custom oxidation states call

Description

• Enable users to load in their oxidation states text file
• Allow smact_filter to use a custom oxidation state list
• Fixed line-length to 80 in pre-commit-config.yaml for isort and black

Fixes #164

Type of change

• New feature (non-breaking change which adds functionality)
• This change requires a documentation update

How Has This Been Tested?

• Verified smact_filter works by passing an oxidation states text file to the oxidation_states_set argument

Test Configuration:

• Python version: 3.9
• Operating System: WSL2(Ubuntu)

Reviewers

@keeeto I've added the feature you've requested. I want to check if you're happy with the implementation before I merge it into the master branch

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published in downstream modules
• I have checked my code and corrected any misspellings

[codecov]

Codecov Report

Merging #165 (aea3937) into master (6ae0c2e) will increase coverage by 0.08%.
The diff coverage is 81.81%.

@@            Coverage Diff             @@
##           master     #165      +/-   ##
==========================================
+ Coverage   72.71%   72.80%   +0.08%     
==========================================
  Files          24       24              
  Lines        1913     1945      +32     
==========================================
+ Hits         1391     1416      +25     
- Misses        522      529       +7     

Files	Coverage Δ
smact/screening.py	89.34% <100.00%> (+0.36%)	⬆️
smact/structure_prediction/database.py	86.84% <100.00%> (ø)
smact/structure_prediction/mutation.py	81.50% <ø> (ø)
smact/structure_prediction/prediction.py	44.18% <ø> (ø)
smact/structure_prediction/structure.py	70.14% <ø> (ø)
smact/tests/test_core.py	100.00% <100.00%> (ø)
smact/tests/test_structure.py	92.36% <100.00%> (ø)
smact/__init__.py	85.27% <80.00%> (-1.17%)	⬇️
smact/data_loader.py	74.00% <68.75%> (-0.34%)	⬇️

[mdi-group]

Hi @AntObi - I am just curious, where would one set the list of oxidation states to be used in a typical workflow?
For example in the SolarOxides example where would I tell it to use a different set of oxidation states?

[AntObi]

Hi @AntObi - I am just curious, where would one set the list of oxidation states to be used in a typical workflow? For example in the SolarOxides example where would I tell it to use a different set of oxidation states?

Currently to use the other built-in oxidation states list, we can modify that example as follows:

Original oxidation states call:

    # For each set of species (in oxidation states) apply both SMACT tests
    for ox_a, ox_b, ox_c in product(
        els[0].oxidation_states,
        els[1].oxidation_states,
        els[2].oxidation_states,
    ):

To use the built in icsd oxidation states:

    # For each set of species (in oxidation states) apply both SMACT tests
    for ox_a, ox_b, ox_c in product(
        els[0].oxidation_states_icsd,
        els[1].oxidation_states_icsd,
        els[2].oxidation_states_icsd,
    ):

Using the pymatgen structure prediction oxidation states in this example:

    # For each set of species (in oxidation states) apply both SMACT tests
    for ox_a, ox_b, ox_c in product(
        els[0].oxidation_states_sp,
        els[1].oxidation_states_sp,
        els[2].oxidation_states_sp,
    ):

I've originally made this pull request with the built-in smact_filter in mind, and a custom oxidation states file could be supplied to the oxidation_states_set argument.

If we want to have a similar API for making these calls, then I could make a new attribute for the Element class:
Element.oxidation_states_custom. For the examples above, we would access the attribute el.oxidation_states_custom. To implement this, the Element class can take an optional argument, let's call it oxi_states_custom_filepath, which will then set the property oxidation_states_custom to the oxidation states for that particular element based on the supplied file.

[mdi-group]

Thanks @AntObi - that is very clear. I understand now. I was struggling to see how this would be accessed. But I think that implementing in the smact_filter in the first instance is a sound decision. Code looks good and tests are passing. I think we can merge!

[keeeto]

Hi @AntObi sorry I just realised I was commenting from the wrong account! Anyway, there appears to be one conflict to resolve then it can be merged.

[AntObi]

Hi @keeeto, I've made some more changes:

The Element class now takes an optional argument of oxi_states_custom_filepath which allows a user to supply a text file containing oxidation states. Then the oxidation states can be accessed through the attribute oxidation_states_custom.

Example:

import smact

Fe = smact.Element("Fe", oxi_states_custom_filepath = "/path/to/oxidation_states.txt")

print(Fe.oxidation_states_custom)

I've also updated the element_dictionary function to take the optional argument of oxi_states_custom_filepath. This should allow users to quickly create a list of Element objects which have access to the custom oxidation states.

So for the solar oxides example, you would apply the following changes:

Instead of

all_el = smact.element_dictionary()

You would create the dictionary of all elements with a supplied oxidation states text file:

all_el = smact.element_dictionary(oxi_states_custom_filepath = "/path/to/oxidation_states.txt")

Then the oxidation states call in the smact_filter function defined in that particular example becomes:

 # For each set of species (in oxidation states) apply both SMACT tests
    for ox_a, ox_b, ox_c in product(
        els[0].oxidation_states.custom,
        els[1].oxidation_states.custom,
        els[2].oxidation_states.custom,
    ):

[keeeto]

All looks good to me!