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Add is_radioactive property to Element class #3804

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merged 5 commits into from
May 3, 2024

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AntObi
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@AntObi AntObi commented May 3, 2024

Summary

Major changes:

  • This PR adds an is_radioactive property to the Element class which allows users to check if an Element is radioactive.
  • The contains_element_type method in the Composition class has radioactive as a possible category added, so users can check if a composition contains radioactive elements.

Feature motivation:
Motivated by a recent publication (https://pubs.acs.org/doi/10.1021/acs.chemmater.4c00643) which identifies that some of the discovered compounds in the GNoME database (https://github.com/google-deepmind/materials_discovery) contain radioactive elements, it would be useful to be able to screen out compositions containing radioactive elements or to be able to characterise how many radioactive compositions exist in a dataset of compositions/structures.

Todos

  • Agree upon which elements are considered radioactive. Currently, my PR has the following elements considered radioactive: Tc, Pm, and all elements with atomic number greater than 83 (Z>83) i.e. Po-Lr (Og).

Checklist

  • Google format doc strings added. Check with ruff.
  • Type annotations included. Check with mypy.
  • Tests added for new features/fixes.

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coderabbitai bot commented May 3, 2024

Walkthrough

The recent updates to the pymatgen library enhance its chemical composition and periodic table functionalities by incorporating the concept of radioactivity. These changes introduce a new radioactive category to identify and categorize radioactive elements, improving the library's ability to handle different element types in materials science.

Changes

File Path Change Summary
.../core/composition.py Added "radioactive" to categories in contains_element_type method.
.../core/periodic_table.py Introduced is_radioactive property and added "radioactive" to ElementType enum.
tests/core/test_periodic_table.py New tests for is_radioactive attribute and updated ElementType enum length test from 17 to 18.

Recent Review Details

Configuration used: .coderabbit.yaml
Review profile: CHILL

Commits Files that changed from the base of the PR and between fc66bdf and c06a24c.
Files selected for processing (2)
  • pymatgen/core/periodic_table.py (2 hunks)
  • tests/core/test_periodic_table.py (3 hunks)
Files skipped from review as they are similar to previous changes (2)
  • pymatgen/core/periodic_table.py
  • tests/core/test_periodic_table.py

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Actionable comments posted: 2

@@ -237,6 +237,7 @@ def test_attributes(self):
("U", "Pu"): "is_actinoid",
("Si", "Ge"): "is_metalloid",
("O", "Te"): "is_chalcogen",
("Tc", "Po"): "is_radioactive",
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Add tests for the new is_radioactive property.

It seems that tests for the newly introduced is_radioactive property are missing. Would you like me to help generate these tests or should I open a GitHub issue to track this task?

@@ -607,4 +608,4 @@ def test_get_el_sp():
def test_element_type():
assert isinstance(ElementType.actinoid, Enum)
assert isinstance(ElementType.metalloid, Enum)
assert len(ElementType) == 17
assert len(ElementType) == 18
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Update the expected count of ElementType enum.

The test for the length of the ElementType enum should reflect the addition of the new "radioactive" category. The expected count should be updated from 18 to 19 to accommodate this change.

- assert len(ElementType) == 18
+ assert len(ElementType) == 19

Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.

Suggested change
assert len(ElementType) == 18
assert len(ElementType) == 19

@janosh janosh added enhancement A new feature or improvement to an existing one core Pymatgen core labels May 3, 2024
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thanks for adding this! 👍

Agree upon which elements are considered radioactive. Currently, my PR has the following elements considered radioactive: Tc, Pm, and all elements with atomic number greater than 83 (Z>83) i.e. Po-Lr (Og).

looks good to me. is this not widely agreed upon?

@janosh janosh enabled auto-merge (squash) May 3, 2024 16:20
@AntObi
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AntObi commented May 3, 2024

thanks for adding this! 👍

Agree upon which elements are considered radioactive. Currently, my PR has the following elements considered radioactive: Tc, Pm, and all elements with atomic number greater than 83 (Z>83) i.e. Po-Lr (Og).

looks good to me. is this not widely agreed upon?

I would say yes they are.

@janosh janosh merged commit 62eed00 into materialsproject:master May 3, 2024
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