1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368
|
# fmt: off
from collections import OrderedDict
from typing import Any, List, Tuple
import numpy as np
import pytest
from ase.spectrum.dosdata import DOSData, GridDOSData, RawDOSData
class MinimalDOSData(DOSData):
"""Inherit from ABC to test its features"""
def get_energies(self):
return NotImplementedError()
def get_weights(self):
return NotImplementedError()
def copy(self):
return NotImplementedError()
class TestDosData:
"""Test the abstract base class for DOS data"""
sample_info: List[Tuple[Any, Any]] = [
(None, {}),
({}, {}),
({'symbol': 'C', 'index': '2', 'strangekey': 'isallowed'},
{'symbol': 'C', 'index': '2', 'strangekey': 'isallowed'}),
('notadict', TypeError),
(False, TypeError)]
@pytest.mark.parametrize('info, expected', sample_info)
def test_dosdata_init_info(self, info, expected):
"""Check 'info' parameter is handled properly"""
if isinstance(expected, type) and isinstance(expected(), Exception):
with pytest.raises(expected):
dos_data = MinimalDOSData(info=info)
else:
dos_data = MinimalDOSData(info=info)
assert dos_data.info == expected
@pytest.mark.parametrize('info, expected',
[({}, ''),
({'key1': 'value1'}, 'key1: value1'),
(OrderedDict([('key1', 'value1'),
('key2', 'value2')]),
'key1: value1; key2: value2'),
({'key1': 'value1', 'label': 'xyz'}, 'xyz'),
({'label': 'xyz'}, 'xyz')])
def test_label_from_info(self, info, expected):
assert DOSData.label_from_info(info) == expected
class TestRawDosData:
"""Test the raw DOS data container"""
@pytest.fixture()
def sparse_dos(self):
return RawDOSData([1.2, 3.4, 5.], [3., 2.1, 0.],
info={'symbol': 'H', 'number': '1', 'food': 'egg'})
@pytest.fixture()
def another_sparse_dos(self):
return RawDOSData([8., 2., 2., 5.], [1., 1., 1., 1.],
info={'symbol': 'H', 'number': '2'})
def test_init(self):
with pytest.raises(ValueError):
RawDOSData([1, 2, 3], [4, 5], info={'symbol': 'H'})
def test_access(self, sparse_dos):
assert sparse_dos.info == {'symbol': 'H', 'number': '1', 'food': 'egg'}
assert np.allclose(sparse_dos.get_energies(), [1.2, 3.4, 5.])
assert np.allclose(sparse_dos.get_weights(), [3., 2.1, 0.])
def test_copy(self, sparse_dos):
copy_dos = sparse_dos.copy()
assert copy_dos.info == sparse_dos.info
sparse_dos.info['symbol'] = 'X'
assert sparse_dos.info['symbol'] == 'X'
assert copy_dos.info['symbol'] == 'H'
@pytest.mark.parametrize('other', [True, 1, 0.5, 'string'])
def test_equality_wrongtype(self, sparse_dos, other):
assert not sparse_dos._almost_equals(other)
equality_data = [(((1., 2.), (3., 4.), {'symbol': 'H'}),
((1., 2.), (3., 4.), {'symbol': 'H'}),
True),
(((1., 3.), (3., 4.), {'symbol': 'H'}),
((1., 2.), (3., 4.), {'symbol': 'H'}),
False),
(((1., 2.), (3., 5.), {'symbol': 'H'}),
((1., 2.), (3., 4.), {'symbol': 'H'}),
False),
(((1., 3.), (3., 5.), {'symbol': 'H'}),
((1., 2.), (3., 4.), {'symbol': 'H'}),
False),
(((1., 2.), (3., 4.), {'symbol': 'H'}),
((1., 2.), (3., 4.), {'symbol': 'He'}),
False),
(((1., 3.), (3., 4.), {'symbol': 'H'}),
((1., 2.), (3., 4.), {'symbol': 'He'}),
False)]
@pytest.mark.parametrize('data_1, data_2, isequal', equality_data)
def test_equality(self, data_1, data_2, isequal):
assert (RawDOSData(*data_1[:2], info=data_1[2])
._almost_equals(RawDOSData(*data_2[:2], info=data_2[2]))
) == isequal
def test_addition(self, sparse_dos, another_sparse_dos):
summed_dos = sparse_dos + another_sparse_dos
assert summed_dos.info == {'symbol': 'H'}
assert np.allclose(summed_dos.get_energies(),
[1.2, 3.4, 5., 8., 2., 2., 5.])
assert np.allclose(summed_dos.get_weights(),
[3., 2.1, 0., 1., 1., 1., 1.])
sampling_data_args_results = [
# Special case: peak max at width 1
([[0.], [1.]],
[[0.], {'width': 1}],
[1. / (np.sqrt(2. * np.pi))]),
# Peak max with different width, position
([[1.], [2.]],
[[1.], {'width': 0.5}],
[2. / (np.sqrt(2. * np.pi) * 0.5)]),
# Peak max for two simultaneous deltas
([[1., 1.], [2., 1.]],
[[1.], {'width': 1}],
[3. / (np.sqrt(2. * np.pi))]),
# Compare with theoretical half-maximum
([[0.], [1.]],
[[np.sqrt(2 * np.log(2)) * 3],
{'width': 3}],
[0.5 / (np.sqrt(2 * np.pi) * 3)]),
# And a case with multiple values, generated
# using the ASE code (not benchmarked)
([[1.2, 3.4, 5], [3., 2.1, 0.]],
[[1., 1.5, 2., 2.4], {'width': 2}],
[0.79932418, 0.85848101, 0.88027184, 0.8695055])]
@pytest.mark.parametrize('data, args, result',
sampling_data_args_results)
def test_sampling(self, data, args, result):
dos = RawDOSData(data[0], data[1])
weights = dos._sample(*args[:-1], **args[-1])
assert np.allclose(weights, result)
with pytest.raises(ValueError):
dos._sample([1], smearing="Gauss's spherical cousin")
def test_sampling_error(self, sparse_dos):
with pytest.raises(ValueError):
sparse_dos._sample([1, 2, 3], width=0.)
with pytest.raises(ValueError):
sparse_dos._sample([1, 2, 3], width=-1)
def test_sample_grid(self, sparse_dos):
min_dos = sparse_dos.sample_grid(10, xmax=5, padding=3, width=0.1)
assert min_dos.get_energies()[0] == pytest.approx(1.2 - 3 * 0.1)
max_dos = sparse_dos.sample_grid(10, xmin=0, padding=2, width=0.2)
assert max_dos.get_energies()[-1] == pytest.approx(5 + 2 * 0.2)
default_dos = sparse_dos.sample_grid(10)
assert np.allclose(default_dos.get_energies(),
np.linspace(0.9, 5.3, 10))
dos0 = sparse_dos._sample(np.linspace(0.9, 5.3, 10))
assert np.allclose(default_dos.get_weights(),
dos0)
# Comparing plot outputs is hard, so we
# - inspect the line values
# - check that a line styling parameter is correctly passed through mplargs
# - set a kwarg from self.sample() to check broadening args are recognised
linewidths = [1, 5, None]
@pytest.mark.usefixtures("figure")
@pytest.mark.parametrize('linewidth', linewidths)
def test_plot(self, sparse_dos, figure, linewidth):
if linewidth is None:
mplargs = None
else:
mplargs = {'linewidth': linewidth}
ax = figure.add_subplot(111)
ax_out = sparse_dos.plot(npts=5, ax=ax, mplargs=mplargs,
smearing='Gauss')
assert ax_out == ax
line_data = ax.lines[0].get_data()
assert np.allclose(line_data[0], np.linspace(0.9, 5.3, 5))
assert np.allclose(line_data[1],
[1.32955452e-01, 1.51568133e-13,
9.30688167e-02, 1.06097693e-13, 3.41173568e-78])
@pytest.mark.usefixtures("figure")
@pytest.mark.parametrize('linewidth', linewidths)
def test_plot_deltas(self, sparse_dos, figure, linewidth):
if linewidth is None:
mplargs = None
else:
mplargs = {'linewidth': linewidth}
ax = figure.add_subplot(111)
ax_out = sparse_dos.plot_deltas(ax=ax, mplargs=mplargs)
assert ax_out == ax
assert np.allclose(list(map(lambda x: x.vertices,
ax.get_children()[0].get_paths())),
[[[1.2, 0.], [1.2, 3.]],
[[3.4, 0.], [3.4, 2.1]],
[[5., 0.], [5., 0.]]])
class TestGridDosData:
"""Test the grid DOS data container"""
def test_init(self):
# energies and weights must be equal lengths
with pytest.raises(ValueError):
GridDOSData(np.linspace(0, 10, 11), np.zeros(10))
# energies must be evenly spaced
with pytest.raises(ValueError):
GridDOSData(np.linspace(0, 10, 11)**2, np.zeros(11))
@pytest.fixture()
def dense_dos(self):
x = np.linspace(0., 10., 11)
y = np.sin(x / 10)
return GridDOSData(x, y, info={'symbol': 'C', 'orbital': '2s',
'day': 'Tue'})
@pytest.fixture()
def denser_dos(self):
x = np.linspace(0., 10., 21)
y = np.sin(x / 10)
return GridDOSData(x, y)
@pytest.fixture()
def another_dense_dos(self):
x = np.linspace(0., 10., 11)
y = np.sin(x / 10) * 2
return GridDOSData(x, y, info={'symbol': 'C', 'orbital': '2p',
'month': 'Feb'})
def test_access(self, dense_dos):
assert dense_dos.info == {'symbol': 'C', 'orbital': '2s', 'day': 'Tue'}
assert len(dense_dos.get_energies()) == 11
assert dense_dos.get_energies()[-2] == pytest.approx(9.)
assert dense_dos.get_weights()[-1] == pytest.approx(np.sin(1))
def test_copy(self, dense_dos):
copy_dos = dense_dos.copy()
assert copy_dos.info == dense_dos.info
dense_dos.info['symbol'] = 'X'
assert dense_dos.info['symbol'] == 'X'
assert copy_dos.info['symbol'] == 'C'
def test_addition(self, dense_dos, another_dense_dos):
sum_dos = dense_dos + another_dense_dos
assert np.allclose(sum_dos.get_energies(), dense_dos.get_energies())
assert np.allclose(sum_dos.get_weights(), dense_dos.get_weights() * 3)
assert sum_dos.info == {'symbol': 'C'}
with pytest.raises(ValueError):
dense_dos + GridDOSData(dense_dos.get_energies() + 1.,
dense_dos.get_weights())
with pytest.raises(ValueError):
dense_dos + GridDOSData(dense_dos.get_energies()[1:],
dense_dos.get_weights()[1:])
def test_check_spacing(self, dense_dos):
"""Check a warning is logged when width < 2 * grid spacing"""
# In the sample data, grid spacing is 1.0
dense_dos._sample([1], width=2.1)
with pytest.warns(UserWarning, match="The broadening width is small"):
dense_dos._sample([1], width=1.9)
def test_resampling_consistency(self, dense_dos, denser_dos):
"""Check that resampled spectra are independent of the original density
Compare resampling of sample function on two different grids to the
same new grid with broadening. We accept a 5% difference because the
initial shape is slightly different; what we are checking for is a
factor 2 difference from "double-counting" the extra data points.
"""
sampling_params = dict(npts=500, xmin=0, xmax=10, width=4)
from_dense = dense_dos.sample_grid(**sampling_params)
from_denser = denser_dos.sample_grid(**sampling_params)
assert np.allclose(from_dense.get_energies(),
from_denser.get_energies())
assert np.allclose(from_dense.get_weights(),
from_denser.get_weights(),
rtol=0.05, atol=0.01)
linewidths = [1, 5, None]
@pytest.mark.usefixtures("figure")
@pytest.mark.parametrize('linewidth', linewidths)
def test_plot(self, dense_dos, figure, linewidth):
if linewidth is None:
mplargs = None
else:
mplargs = {'linewidth': linewidth}
ax = figure.add_subplot(111)
ax_out = dense_dos.plot(ax=ax, mplargs=mplargs,
smearing='Gauss')
assert ax_out == ax
line_data = ax.lines[0].get_data()
# With default settings, plot data should be unchanged from input data;
# this is a special feature of "grid" data to avoid repeated broadening
assert np.allclose(line_data[0], np.linspace(0., 10., 11))
assert np.allclose(line_data[1], np.sin(np.linspace(0., 1., 11)))
@pytest.mark.usefixtures("figure")
def test_plot_broad_dos(self, dense_dos, figure):
# Check that setting a grid/broadening does not blow up and reproduces
# previous results; this result has not been rigorously checked but at
# least it should not _change_ unexpectedly
ax = figure.add_subplot(111)
_ = dense_dos.plot(ax=ax, npts=10, xmin=0, xmax=9,
width=4, smearing='Gauss')
line_data = ax.lines[0].get_data()
assert np.allclose(line_data[0], range(10))
assert np.allclose(line_data[1],
[0.14659725, 0.19285644, 0.24345501, 0.29505574,
0.34335948, 0.38356488, 0.41104823, 0.42216901,
0.41503382, 0.39000808])
smearing_args = [(dict(npts=0, width=None), (0, None)),
(dict(npts=10, width=None, default_width=5.), (10, 5.)),
(dict(npts=0, width=0.5, default_npts=100), (100, 0.5)),
(dict(npts=10, width=0.5), (10, 0.5))]
@pytest.mark.parametrize('inputs, expected', smearing_args)
def test_smearing_args_interpreter(self, inputs, expected):
assert GridDOSData._interpret_smearing_args(**inputs) == expected
class TestMultiDosData:
"""Test interaction between DOS data objects"""
@pytest.fixture()
def sparse_dos(self):
return RawDOSData([1.2, 3.4, 5.], [3., 2.1, 0.],
info={'symbol': 'H', 'number': '1', 'food': 'egg'})
@pytest.fixture()
def dense_dos(self):
x = np.linspace(0., 10., 11)
y = np.sin(x / 10)
return GridDOSData(x, y, info={'symbol': 'C', 'orbital': '2s',
'day': 'Tue'})
def test_addition(self, sparse_dos, dense_dos):
with pytest.raises(TypeError):
sparse_dos + dense_dos
with pytest.raises(TypeError):
dense_dos + sparse_dos
|