diff --git a/tests/calculation/test_partial_charge.py b/tests/calculation/test_partial_charge.py index f9d4a2d5..53009a3f 100644 --- a/tests/calculation/test_partial_charge.py +++ b/tests/calculation/test_partial_charge.py @@ -103,7 +103,7 @@ def make_reference_partial_charge(raw_data, selection): return parchg -def test_read(PartialCharge, Assert): +def test_read(PartialCharge, Assert, not_core): actual = PartialCharge.read() expected = PartialCharge.ref Assert.allclose(actual["bands"], expected.bands) @@ -114,31 +114,31 @@ def test_read(PartialCharge, Assert): Assert.same_structure(actual["structure"], expected.structure.read()) -def test_topology(PartialCharge): +def test_topology(PartialCharge, not_core): actual = PartialCharge._topology() expected = str(PartialCharge.ref.structure._topology()) assert actual == expected -def test_bands(PartialCharge, Assert): +def test_bands(PartialCharge, Assert, not_core): actual = PartialCharge.bands() expected = PartialCharge.ref.bands Assert.allclose(actual, expected) -def test_kpoints(PartialCharge, Assert): +def test_kpoints(PartialCharge, Assert, not_core): actual = PartialCharge.kpoints() expected = PartialCharge.ref.kpoints Assert.allclose(actual, expected) -def test_grid(PartialCharge, Assert): +def test_grid(PartialCharge, Assert, not_core): actual = PartialCharge.grid() expected = PartialCharge.ref.grid Assert.allclose(actual, expected) -def test_non_split_to_numpy(PolarizedNonSplitPartialCharge, Assert): +def test_non_split_to_numpy(PolarizedNonSplitPartialCharge, Assert, not_core): actual = PolarizedNonSplitPartialCharge.to_numpy("total") expected = PolarizedNonSplitPartialCharge.ref.partial_charge Assert.allclose(actual, expected[0, 0, 0].T) @@ -150,7 +150,7 @@ def test_non_split_to_numpy(PolarizedNonSplitPartialCharge, Assert): Assert.allclose(actual, 0.5 * (expected[0, 0, 0].T - expected[0, 0, 1].T)) -def test_split_to_numpy(PolarizedAllSplitPartialCharge, Assert): +def test_split_to_numpy(PolarizedAllSplitPartialCharge, Assert, not_core): bands = PolarizedAllSplitPartialCharge.ref.bands kpoints = PolarizedAllSplitPartialCharge.ref.kpoints for band_index, band in enumerate(bands): @@ -176,13 +176,15 @@ def test_split_to_numpy(PolarizedAllSplitPartialCharge, Assert): assert msg in str(excinfo.value) -def test_non_polarized_to_numpy(NonSplitPartialCharge, spin, Assert): +def test_non_polarized_to_numpy(NonSplitPartialCharge, spin, Assert, not_core): actual = NonSplitPartialCharge.to_numpy(selection=spin) expected = NonSplitPartialCharge.ref.partial_charge Assert.allclose(actual, np.asarray(expected).T[:, :, :, 0, 0, 0]) -def test_split_bands_to_numpy(NonPolarizedBandSplitPartialCharge, spin, Assert): +def test_split_bands_to_numpy( + NonPolarizedBandSplitPartialCharge, spin, Assert, not_core +): bands = NonPolarizedBandSplitPartialCharge.ref.bands for band_index, band in enumerate(bands): actual = NonPolarizedBandSplitPartialCharge.to_numpy(spin, band=band) @@ -190,14 +192,14 @@ def test_split_bands_to_numpy(NonPolarizedBandSplitPartialCharge, spin, Assert): Assert.allclose(actual, np.asarray(expected).T[:, :, :, 0, band_index, 0]) -def test_to_stm_split(PolarizedAllSplitPartialCharge): +def test_to_stm_split(PolarizedAllSplitPartialCharge, not_core): msg = "set LSEPK and LSEPB to .FALSE. in the INCAR file." with pytest.raises(NotImplemented) as excinfo: PolarizedAllSplitPartialCharge.to_stm(selection="constant_current") assert msg in str(excinfo.value) -def test_to_stm_nonsplit_tip_to_high(NonSplitPartialCharge): +def test_to_stm_nonsplit_tip_to_high(NonSplitPartialCharge, not_core): actual = NonSplitPartialCharge tip_height = 8.4 error = f"""The tip position at {tip_height:.2f} is above half of the @@ -209,6 +211,7 @@ def test_to_stm_nonsplit_tip_to_high(NonSplitPartialCharge): def test_to_stm_nonsplit_not_orthogonal_no_vacuum( PolarizedNonSplitPartialChargeSr2TiO4, + not_core, ): msg = "The vacuum region in your cell is too small for STM simulations." with pytest.raises(IncorrectUsage) as excinfo: @@ -216,20 +219,20 @@ def test_to_stm_nonsplit_not_orthogonal_no_vacuum( assert msg in str(excinfo.value) -def test_to_stm_wrong_spin_nonsplit(PolarizedNonSplitPartialCharge): +def test_to_stm_wrong_spin_nonsplit(PolarizedNonSplitPartialCharge, not_core): msg = "'up', 'down', or 'total'" with pytest.raises(IncorrectUsage) as excinfo: PolarizedNonSplitPartialCharge.to_stm(selection="all") assert msg in str(excinfo.value) -def test_to_stm_wrong_mode(PolarizedNonSplitPartialCharge): +def test_to_stm_wrong_mode(PolarizedNonSplitPartialCharge, not_core): with pytest.raises(IncorrectUsage) as excinfo: PolarizedNonSplitPartialCharge.to_stm(selection="stm") assert "STM mode" in str(excinfo.value) -def test_wrong_vacuum_direction(NonSplitPartialChargeNi_100): +def test_wrong_vacuum_direction(NonSplitPartialChargeNi_100, not_core): msg = """The vacuum region in your cell is not located along the third lattice vector.""" with pytest.raises(NotImplemented) as excinfo: @@ -312,7 +315,7 @@ def test_to_stm_nonsplit_constant_current_non_ortho( assert f"{current:.2f}" in actual.title -def test_stm_settings(PolarizedNonSplitPartialCharge): +def test_stm_settings(PolarizedNonSplitPartialCharge, not_core): actual = dataclasses.asdict(PolarizedNonSplitPartialCharge.stm_settings) defaults = { "sigma_xy": 4.0, @@ -333,7 +336,7 @@ def test_stm_settings(PolarizedNonSplitPartialCharge): assert graph.series.settings == modified -def test_smoothening_change(PolarizedNonSplitPartialCharge): +def test_smoothening_change(PolarizedNonSplitPartialCharge, not_core): mod_settings = STM_settings(sigma_xy=2.0, sigma_z=2.0, truncate=1.0) data = PolarizedNonSplitPartialCharge.to_numpy("total", band=0, kpoint=0) default_smoothed_density = PolarizedNonSplitPartialCharge._smooth_stm_data( @@ -345,7 +348,7 @@ def test_smoothening_change(PolarizedNonSplitPartialCharge): assert not np.allclose(default_smoothed_density, new_smoothed_density) -def test_enhancement_setting_change(PolarizedNonSplitPartialCharge, Assert): +def test_enhancement_setting_change(PolarizedNonSplitPartialCharge, Assert, not_core): enhance_settings = STM_settings( enhancement_factor=STM_settings().enhancement_factor / 2.0 ) @@ -356,7 +359,7 @@ def test_enhancement_setting_change(PolarizedNonSplitPartialCharge, Assert): Assert.allclose(graph_def.series.data, graph_less_enhanced.series.data * 2) -def test_interpolation_setting_change(PolarizedNonSplitPartialCharge): +def test_interpolation_setting_change(PolarizedNonSplitPartialCharge, not_core): interp_settings = STM_settings( interpolation_factor=STM_settings().interpolation_factor / 4.0 ) diff --git a/tests/conftest.py b/tests/conftest.py index 6a2be952..a996a4a8 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -7,9 +7,11 @@ import numpy as np import pytest from numpy.testing import assert_array_almost_equal_nulp -from scipy.stats import multivariate_normal from py4vasp import exception, raw +from py4vasp._util import import_ + +stats = import_.optional("scipy.stats") number_steps = 4 number_atoms = 7 @@ -717,7 +719,7 @@ def _partial_charge(selection): for gy in range(grid_dim[1]): for gx in range(grid_dim[2]): m = int(grid_dim[0] / 2) + gy / 10 + gx / 10 - val = multivariate_normal(mean=m, cov=cov).pdf(z) + val = stats.multivariate_normal(mean=m, cov=cov).pdf(z) # Fill the gaussian_charge array gaussian_charge[:, :, :, :, gy, gx] = val gaussian_charge = raw.VaspData(gaussian_charge)