Commit b999e637 authored by Thomas Purcell's avatar Thomas Purcell
Browse files

Merge branch 'elena/patch-fix-symmetry' into 'master' 

Bug fix: update constraint optimisation path to use the correct FixSymmetry.

See merge request !120
parents ae53cefd a12d1f94

docs/Documentation/relaxation.md

+1 −1
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@@ -58,7 +58,7 @@ Currently only [BFGS](https://wiki.fysik.dtu.dk/ase/ase/optimize.html#bfgs) is s 


#### `fix_symmetry`



`True/False`: keep the spacegroup of the system fixed using [`ase.constraints.FixSymmetry`](https://wiki.fysik.dtu.dk/ase/dev/ase/constraints.html?highlight=fixsymmetry#ase.spacegroup.symmetrize.FixSymmetry)

`True/False`: keep the spacegroup of the system fixed using [`ase.constraints.FixSymmetry`](https://wiki.fysik.dtu.dk/ase/dev/ase/constraints.html?highlight=fixsymmetry#ase.constraints.FixSymmetry)



#### `hydrostatic_strain`

pyproject.toml

+1 −0
Original line number Diff line number Diff line
@@ -130,6 +130,7 @@ lint.ignore = [ 
    "C416",

    "C901",    # function too complex

    "COM812",  # trailing comma missing

    "CPY001",

    "D100",

    "D101",

    "D102",

tests/md/test_md.py

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@@ -17,7 +17,7 @@ settings = Settings(settings_file=parent / "md.in") 
calculator = EMT()



np.random.seed(4)

MaxwellBoltzmannDistribution(atoms, 300 * u.kB)

MaxwellBoltzmannDistribution(atoms, temperature_K=300)





def test_run(tmp_path):

tests/workflows/test_workflow_relaxation.py

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@@ -42,5 +42,27 @@ def test_relaxation(workdir=workdir): 
            assert np.allclose(pos, refpos)





def test_relaxation_fix_symmetry(workdir=workdir):

    with cwd(parent):

        settings = Settings(settings_file=settings_file)



        if workdir.exists():

            shutil.rmtree(workdir)



        ctx = RelaxationContext(settings, workdir=workdir)

        ctx.kw["fix_symmetry"] = True  # exercise the `from ase.constraints` path

        ctx.atoms.rattle(0.01, seed=4)

        ctx.calculator = EMT()



        # runs without FixSymmetry import error

        ctx.run()



        # constraints have been applies

        from ase.constraints import FixSymmetry

        _ = ctx.opt_atoms

        assert any(isinstance(c, FixSymmetry) for c in ctx.atoms.constraints)





if __name__ == "__main__":

    test_relaxation()

    test_relaxation_fix_symmetry()

vibes/cli/scripts/create_samples.py

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@@ -85,7 +85,7 @@ def generate_samples( 
        info_str += ["created from force constants", f"T = {temp} K"]

        talk(f"Random seed: {seed}")

    else:

        mb_args = {"temp": temp * u.kB, "rng": rng}

        mb_args = {"temperature_K": temp, "rng": rng}

        info_str += ["created from MB distribution", f"T = {temperature} K"]

        talk("Use Maxwell Boltzamnn to set up samples")