pyiron / pyiron/atomistics

Symmetry analyser in elastic module (probably) does not work

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Description

I tested the list of strains from the magnesium structure, once with the default ASE structure, once by changing the axis from x to y. I got exactly the same list of strains. That's not so surprising given the fact that the internal algorithm seems to check only the symmetry group and not how the structure is oriented.

import numpy as np
from ase.build import bulk
from atomistics.workflows.elastic import helper

F_list = []
for rotate in [True, False]:
    structure = bulk("Mg", orthorhombic=True)
    if rotate:
        rot = np.array([[0, -1, 0], [1, 0, 0], [0, 0, 1]])
        structure.set_cell(rot.T @ structure.cell @ rot)
        structure.set_positions(structure.positions @ rot)    
    data_dict = helper.get_tasks_for_elastic_matrix(structure, 0.01, 3)
    F_list.append([struct.cell.diagonal() / structure.cell.diagonal() for struct in data_dict[0]["calc_energy"].values()])
print(np.allclose(F_list[0], F_list[1]))

output: True

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Research direction

Start by running the provided Python reproducer and read the atomistics.workflows.elastic.helper.get_tasks_for_elastic_matrix entry point. Compare the generated strain lists for the original and rotated magnesium structures, then verify that the result reflects the structure orientation rather than only its symmetry group.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
48/100

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