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Update commensurability warning #37

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merged 6 commits into from
Oct 27, 2023
Merged

Update commensurability warning #37

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fd31dd2
Update commensurability warning
kavanase Oct 25, 2023
92d17f1
Fix earlier errors in commensurability check (revealed by testing wit…
kavanase Oct 27, 2023
158b0e7
Make incommensurate warnings more verbose in case of drastic mismatch…
kavanase Oct 27, 2023
3e219bb
Update `--matrix` help message so users know what form it should be in
kavanase Oct 27, 2023
1acf74d
Add test for matrix handling with Sabrine data
kavanase Oct 27, 2023
d13ee17
Add Sabrine test data
kavanase Oct 27, 2023
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38 changes: 31 additions & 7 deletions easyunfold/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,11 @@ def easyunfold():
type=click.Choice(SUPPORTED_DFT_CODES),
show_default=True,
)
@click.option('--matrix', '-m', help='Transformation matrix')
@click.option('--matrix',
'-m',
help='Transformation matrix, in the form "x y z" for a diagonal matrix, '
'or "x1 y1 z1, x2 y2 z2, x3 y3 z3" for a 3x3 matrix. Automatically guessed if not '
'provided.')
@click.option('--symprec', help='Tolerance for determining the symmetry', type=float, default=1e-5, show_default=True)
@click.option('--out-file', '-o', default='easyunfold.json', help='Name of the output file')
@click.option('--no-expand', help='Do not expand the kpoints by symmetry', default=False, is_flag=True)
Expand Down Expand Up @@ -80,18 +84,38 @@ def generate(pc_file, code, sc_file, matrix, kpoints, time_reversal, out_file, n

primitive = read(pc_file)
supercell = read(sc_file)
_quantitative_inaccuracy_warning = (
'Warning: There is a lattice parameter mismatch in the range 2-5% between the primitive (multiplied by the '
'transformation matrix) and the supercell. This will lead to some quantitative inaccuracies in the Brillouin '
'Zone spacing (and thus effective masses) of the unfolded band structures.')
_incommensurate_warning = (
'Warning: the super cell and the primitive cell are not commensurate (lattice parameter difference >5%). This '
'will likely lead to severe inaccuracies in the results! You should double check the correct transformation '
'matrix, primitive and super cells have been provided.')

if matrix:
transform_matrix = matrix_from_string(matrix)
if not np.allclose(primitive.cell @ transform_matrix, supercell.cell):
click.echo('Warning: the super cell and the the primitive cell are not commensure.')
click.echo('Proceed with the assumed tranform matrix')
if not np.allclose(transform_matrix @ primitive.cell, supercell.cell, rtol=2e-2): # 2% mismatch tolerance
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if np.allclose(transform_matrix @ primitive.cell, supercell.cell, rtol=5e-2): # 2-5% mismatch
click.echo(_quantitative_inaccuracy_warning)
else:
click.echo(_incommensurate_warning)
click.echo(f'Transform matrix x primitive cell:\n{transform_matrix @ primitive.cell}')
click.echo(f'Supercell cell:\n{supercell.cell}')
click.echo('Proceeding with the assumed transformation matrix.')
click.echo(f'Transform matrix:\n{transform_matrix.tolist()}')
else:
tmp = supercell.cell @ np.linalg.inv(primitive.cell)
transform_matrix = np.rint(tmp)
if not np.allclose(tmp, transform_matrix):
click.echo('The super cell and the the primitive cell are not commensure.')
raise click.Abort()
if not np.allclose(tmp, transform_matrix, rtol=2e-2): # 2% mismatch tolerance
if np.allclose(transform_matrix @ primitive.cell, supercell.cell, rtol=5e-2): # 2-5% mismatch
click.echo(_quantitative_inaccuracy_warning)
else:
click.echo(_incommensurate_warning)
click.echo(f'(Guessed) Transform matrix:\n{transform_matrix.tolist()}')
click.echo(f'Transform matrix x primitive cell:\n{transform_matrix @ primitive.cell}')
click.echo(f'Supercell cell:\n{supercell.cell}')
raise click.Abort()

click.echo(f'(Guessed) Transform matrix:\n{transform_matrix.tolist()}')

Expand Down
11 changes: 11 additions & 0 deletions tests/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,17 @@ def _inner(tag=''):
return _inner


@pytest.fixture
def agsbte2_project_dir(datapath, tmp_path):
"""Create a temporary directory containing AgSbTe2 inputs for testing"""

def _inner(tag=''):
shutil.copytree(datapath('AgSbTe2'), tmp_path / 'AgSbTe2')
return tmp_path / 'AgSbTe2'

return _inner


@pytest.fixture
def mgo_project_dir(datapath, tmp_path):
shutil.copy2(datapath('mgo.json'), tmp_path / 'mgo.json')
Expand Down
60 changes: 60 additions & 0 deletions tests/test_cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,66 @@ def test_generate(si_project_dir):
assert len(kpts) == 96 + kpts_expected


def test_generate_agsbte2(agsbte2_project_dir):
"""
Test the generate function
"""
runner = CliRunner()

tmp_dir = agsbte2_project_dir(None)
os.chdir(tmp_dir)

output = runner.invoke(
easyunfold, # ~2.5% lattice mismatch in this case, print warning but continue fine
['generate', 'POSCAR_prim', 'SQS_POSCAR', 'KPOINTS_band', '--out-file', 'test'])
assert output.exit_code == 0

assert ('Warning: There is a lattice parameter mismatch in the range 2-5% between the primitive (multiplied by the '
'transformation matrix) and the supercell. This will lead to some quantitative inaccuracies in the '
'Brillouin Zone spacing (and thus effective masses) of the unfolded band structures.' in output.output)
assert '(Guessed) Transform matrix:\n[[1.0, -0.0, 0.0], [1.0, -3.0, 1.0], [1.0, 1.0, -3.0]]' in output.output
assert '194 kpoints specified along the path' in output.output
for i in [
'Supercell cell information:', 'Space group number: 6', 'International symbol: Pm', 'Point group: m',
'Primitive cell information:', 'Space group number: 225', 'International symbol: Fm-3m', 'Point group: m-3m'
]:
assert i in output.output
assert 'Supercell kpoints written to KPOINTS_test' in output.output
assert 'Unfolding settings written to test' in output.output

kpts = read_kpoints('KPOINTS_test')[0]
kpts_expected = 1023
assert len(kpts) == kpts_expected

# test with also specifying transformation matrix:
os.remove('KPOINTS_test')
os.remove('test')
output = runner.invoke(
easyunfold, # ~2.5% lattice mismatch in this case, print warning but continue fine
['generate', 'POSCAR_prim', 'SQS_POSCAR', 'KPOINTS_band', '--out-file', 'test', '-m', '1 0 0 1 -3 1 1 1 -3'])
print(output.output)
print(output.stdout)
assert output.exit_code == 0

assert ('Warning: There is a lattice parameter mismatch in the range 2-5% between the primitive (multiplied by the '
'transformation matrix) and the supercell. This will lead to some quantitative inaccuracies in the '
'Brillouin Zone spacing (and thus effective masses) of the unfolded band structures.' in output.output)
assert 'Proceeding with the assumed transformation matrix.' in output.output
assert 'Transform matrix:\n[[1.0, 0.0, 0.0], [1.0, -3.0, 1.0], [1.0, 1.0, -3.0]]' in output.output
assert '194 kpoints specified along the path' in output.output
for i in [
'Supercell cell information:', 'Space group number: 6', 'International symbol: Pm', 'Point group: m',
'Primitive cell information:', 'Space group number: 225', 'International symbol: Fm-3m', 'Point group: m-3m'
]:
assert i in output.output
assert 'Supercell kpoints written to KPOINTS_test' in output.output
assert 'Unfolding settings written to test' in output.output

kpts = read_kpoints('KPOINTS_test')[0]
kpts_expected = 1023
assert len(kpts) == kpts_expected


@pytest.mark.parametrize('tag', ['', '_spin', '_soc'])
def test_unfold(si_project_dir, tag):
"""
Expand Down
197 changes: 197 additions & 0 deletions tests/test_data/AgSbTe2/KPOINTS_band
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Original file line number Diff line number Diff line change
@@ -0,0 +1,197 @@
\Gamma -> L -> W -> X -> \Gamma
194
Reciprocal
0.0 0.0 0.0 1 \Gamma
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0.3703703703703703 0.3703703703703703 0.3703703703703703 1
0.37962962962962965 0.37962962962962965 0.37962962962962965 1
0.3888888888888889 0.3888888888888889 0.3888888888888889 1
0.3981481481481481 0.39814814814814814 0.39814814814814814 1
0.40740740740740733 0.40740740740740733 0.40740740740740733 1
0.4166666666666667 0.4166666666666667 0.4166666666666667 1
0.42592592592592593 0.42592592592592593 0.42592592592592593 1
0.4351851851851851 0.4351851851851852 0.4351851851851852 1
0.44444444444444436 0.44444444444444436 0.44444444444444436 1
0.4537037037037037 0.4537037037037037 0.4537037037037037 1
0.4629629629629629 0.46296296296296297 0.46296296296296297 1
0.47222222222222215 0.47222222222222215 0.47222222222222215 1
0.4814814814814814 0.4814814814814814 0.4814814814814814 1
0.49074074074074076 0.49074074074074076 0.49074074074074076 1
0.49999999999999994 0.5 0.5 1 L
0.5 0.4943181818181818 0.5056818181818181 1
0.5 0.48863636363636365 0.5113636363636364 1
0.49999999999999994 0.4829545454545454 0.5170454545454546 1
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0.49999999999999994 0.47159090909090906 0.5284090909090909 1
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0.5 0.44886363636363635 0.5511363636363636 1
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0.007936507936507943 0.0 0.007936507936507943 1
0.0 0.0 0.0 1 \Gamma
10 changes: 10 additions & 0 deletions tests/test_data/AgSbTe2/POSCAR_prim
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Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
Ag1 Te1
1.0
0.0000000000000000 3.0399999999999991 3.0399999999999991
3.0399999999999991 0.0000000000000000 3.0399999999999991
3.0399999999999991 3.0399999999999991 0.0000000000000000
Ag Te
1 1
direct
0.0000000000000000 0.0000000000000000 0.0000000000000000 Ag
-0.5000000000000000 0.5000000000000000 0.5000000000000000 Te
41 changes: 41 additions & 0 deletions tests/test_data/AgSbTe2/SQS_POSCAR
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Original file line number Diff line number Diff line change
@@ -0,0 +1,41 @@
Ag4 Sb4 Te8
1.0000000000000000
0.0000000000000000 3.0153641666817892 3.0153641666817892
-6.3146236125343318 5.8489685063819117 -5.8489685063819117
-6.3469556992336607 -5.8654942008784907 5.8654942008784907
Ag Sb Te
4 4 8
Direct
0.0000000000000000 0.7527020370361285 0.2759265817118562
-0.0000000000000000 0.4935370195973322 0.5138950873723097
-0.0000000000000000 0.2587596038798642 0.7615285940182124
0.5000000000000000 0.8768400938939700 0.6165996651820500
-0.0000000000000000 0.9953006355473802 0.0085537967871281
0.5000000000000000 0.3842174318681571 0.1227410907740850
0.5000000000000000 0.1219783801937458 0.3760017615926263
0.5000000000000000 0.6300065004980725 0.8574337035506276
0.0000000000000000 0.7715898516865103 0.7457215845430222
-0.0000000000000000 0.5064226597851310 0.9851925528078957
0.0000000000000000 0.2494475112407989 0.2374070649248258
0.5000000000000000 0.1226897397507456 0.8663781307658880
0.0000000000000000 0.0119377410978760 0.5023102979327116
0.5000000000000000 0.8567663249734002 0.1320448189015473
0.5000000000000000 0.6033195325030615 0.3724492380933057
0.5000000000000000 0.3644849364479630 0.6258160310418472

0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
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