run_tests.py 17.3 KB
Newer Older
1
2
3
4
"""
This is a module for unit testing the CP2K parser. The unit tests are run with
a custom backend that outputs the results directly into native python object for
easier and faster analysis.
5
6
7
8
9
10
11

Each property that has an enumerable list of different possible options is
assigned a new test class, that should ideally test through all the options.

The properties that can have any value imaginable will be tested only for one
specific case inside a test class that is designed for a certain type of run
(MD, optimization, QM/MM, etc.)
12
13
14
15
16
17
18
19
"""
import os
import unittest
import logging
import numpy as np
from cp2kparser import CP2KParser
from nomadcore.unit_conversion.unit_conversion import convert_unit

20
21
22
23
# Setup the logger so that it doesn't spam messages during tests
logger = logging.getLogger("nomad")
logger.setLevel(logging.CRITICAL)

24
25

#===============================================================================
26
def get_results(folder, metainfo_to_keep=None):
27
28
29
30
31
32
    """Get the given result from the calculation in the given folder by using
    the Analyzer in the nomadtoolkit package. Tries to optimize the parsing by
    giving the metainfo_to_keep argument.

    Args:
        folder: The folder relative to the directory of this script where the
33
            parsed calculation resides.
34
35
36
        metaname: The quantity to extract.
    """
    dirname = os.path.dirname(__file__)
37
38
    filename = os.path.join(dirname, folder, "unittest.out")
    parser = CP2KParser(filename, metainfo_to_keep)
39
    results = parser.parse()
40
41
42
43
44
45
    return results


#===============================================================================
def get_result(folder, metaname):
    results = get_results(folder, metaname)
46
    result = results[metaname]
Lauri Himanen's avatar
Lauri Himanen committed
47
    return result
48
49


50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
#===============================================================================
class TestErrors(unittest.TestCase):
    """Test misc. error stuations which may occur during the parsing.
    """
    def test_no_file(self):
        self.assertRaises(IOError, get_result, "errors/no_file", "XC_functional")

    def test_invalid_file(self):
        self.assertRaises(RuntimeError, get_result, "errors/invalid_file", "XC_functional")

    def test_invalid_run_type(self):
        self.assertRaises(KeyError, get_result, "errors/invalid_run_type", "XC_functional")

    def test_unknown_version(self):
        get_result("errors/unknown_version", "XC_functional")


67
68
#===============================================================================
class TestXCFunctional(unittest.TestCase):
69
70
    """Tests that the XC functionals can be properly parsed.
    """
71
72
73

    def test_pade(self):
        xc = get_result("XC_functional/pade", "XC_functional")
74
        self.assertEqual(xc, "1*LDA_XC_TETER93")
75
76
77

    def test_lda(self):
        xc = get_result("XC_functional/lda", "XC_functional")
78
        self.assertEqual(xc, "1*LDA_XC_TETER93")
79
80
81

    def test_blyp(self):
        xc = get_result("XC_functional/blyp", "XC_functional")
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
        self.assertEqual(xc, "1*GGA_C_LYP+1*GGA_X_B88")

    def test_b3lyp(self):
        xc = get_result("XC_functional/b3lyp", "XC_functional")
        self.assertEqual(xc, "1*HYB_GGA_XC_B3LYP")

    def test_olyp(self):
        xc = get_result("XC_functional/olyp", "XC_functional")
        self.assertEqual(xc, "1*GGA_C_LYP+1*GGA_X_OPTX")

    def test_hcth120(self):
        xc = get_result("XC_functional/hcth120", "XC_functional")
        self.assertEqual(xc, "1*GGA_XC_HCTH_120")

    def test_pbe0(self):
        xc = get_result("XC_functional/pbe0", "XC_functional")
        self.assertEqual(xc, "1*HYB_GGA_XC_PBEH")

    def test_pbe(self):
        xc = get_result("XC_functional/pbe", "XC_functional")
        self.assertEqual(xc, "1*GGA_C_PBE+1*GGA_X_PBE")
103
104


105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
#===============================================================================
class TestSCFConvergence(unittest.TestCase):
    """Tests whether the convergence status and number of SCF step can be
    parsed correctly.
    """

    def test_converged(self):
        result = get_result("convergence/converged", "single_configuration_calculation_converged")
        self.assertTrue(result)

    def test_non_converged(self):
        result = get_result("convergence/non_converged", "single_configuration_calculation_converged")
        self.assertFalse(result)


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
#===============================================================================
class TestForceFiles(unittest.TestCase):
    """Tests that different force files that can be output, can actually be
    found and parsed.
    """

    def test_single_point(self):

        # results = get_results("force_file/single_point")
        # print results._results
        result = get_result("force_file/single_point", "atom_forces")
        expected_result = convert_unit(
            np.array([
                [0.00000000, 0.00000000, 0.00000000],
                [0.00000000, 0.00000001, 0.00000001],
                [0.00000001, 0.00000001, 0.00000000],
                [0.00000001, 0.00000000, 0.00000001],
                [-0.00000001, -0.00000001, -0.00000001],
                [-0.00000001, -0.00000001, -0.00000001],
                [-0.00000001, -0.00000001, -0.00000001],
                [-0.00000001, -0.00000001, -0.00000001],
            ]),
            "forceAu"
        )
        self.assertTrue(np.array_equal(result, expected_result))


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
#===============================================================================
class TestSelfInteractionCorrectionMethod(unittest.TestCase):
    """Tests that the self-interaction correction can be properly parsed.
    """

    def test_no(self):
        sic = get_result("sic/no", "self_interaction_correction_method")
        self.assertEqual(sic, "")

    def test_ad(self):
        sic = get_result("sic/ad", "self_interaction_correction_method")
        self.assertEqual(sic, "SIC_AD")

    def test_explicit_orbitals(self):
        sic = get_result("sic/explicit_orbitals", "self_interaction_correction_method")
        self.assertEqual(sic, "SIC_EXPLICIT_ORBITALS")

    def test_mauri_spz(self):
        sic = get_result("sic/mauri_spz", "self_interaction_correction_method")
        self.assertEqual(sic, "SIC_MAURI_SPZ")

    def test_mauri_us(self):
        sic = get_result("sic/mauri_us", "self_interaction_correction_method")
        self.assertEqual(sic, "SIC_MAURI_US")


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
#===============================================================================
class TestStressTensorMethods(unittest.TestCase):
    """Tests that the stress tensor can be properly parsed for different
    calculation methods.
    """
    def test_none(self):
        get_results("stress_tensor/none", "section_stress_tensor")

    def test_analytical(self):
        results = get_results("stress_tensor/analytical", ["stress_tensor_method", "stress_tensor"])
        method = results["stress_tensor_method"]
        results["stress_tensor"]
        self.assertEqual(method, "Analytical")

    def test_numerical(self):
        results = get_results("stress_tensor/numerical", ["stress_tensor_method", "stress_tensor"])
        method = results["stress_tensor_method"]
        results["stress_tensor"]
        self.assertEqual(method, "Numerical")

    def test_diagonal_analytical(self):
        results = get_results("stress_tensor/diagonal_analytical", ["stress_tensor_method", "stress_tensor"])
        method = results["stress_tensor_method"]
        results["stress_tensor"]
        self.assertEqual(method, "Diagonal analytical")

    def test_diagonal_numerical(self):
        results = get_results("stress_tensor/diagonal_numerical", ["stress_tensor_method", "stress_tensor"])
        method = results["stress_tensor_method"]
        results["stress_tensor"]
        self.assertEqual(method, "Diagonal numerical")


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
#===============================================================================
class TestConfigurationPeriodicDimensions(unittest.TestCase):
    """Tests that the self-interaction correction can be properly parsed.
    """

    def test_default(self):
        result = get_result("configuration_periodic_dimensions/default", "configuration_periodic_dimensions")
        self.assertTrue(np.array_equal(result, np.array((True, True, True))))

    def test_none(self):
        result = get_result("configuration_periodic_dimensions/none", "configuration_periodic_dimensions")
        self.assertTrue(np.array_equal(result, np.array((False, False, False))))

    def test_x(self):
        result = get_result("configuration_periodic_dimensions/x", "configuration_periodic_dimensions")
        self.assertTrue(np.array_equal(result, np.array((True, False, False))))

    def test_y(self):
        result = get_result("configuration_periodic_dimensions/y", "configuration_periodic_dimensions")
        self.assertTrue(np.array_equal(result, np.array((False, True, False))))

    def test_z(self):
        result = get_result("configuration_periodic_dimensions/z", "configuration_periodic_dimensions")
        self.assertTrue(np.array_equal(result, np.array((False, False, True))))

    def test_xy(self):
        result = get_result("configuration_periodic_dimensions/xy", "configuration_periodic_dimensions")
        self.assertTrue(np.array_equal(result, np.array((True, True, False))))

    def test_xyz(self):
        result = get_result("configuration_periodic_dimensions/xyz", "configuration_periodic_dimensions")
        self.assertTrue(np.array_equal(result, np.array((True, True, True))))

    def test_xz(self):
        result = get_result("configuration_periodic_dimensions/xz", "configuration_periodic_dimensions")
        self.assertTrue(np.array_equal(result, np.array((True, False, True))))

    def test_yz(self):
        result = get_result("configuration_periodic_dimensions/yz", "configuration_periodic_dimensions")
        self.assertTrue(np.array_equal(result, np.array((False, True, True))))


248
#===============================================================================
249
250
251
class TestEnergyForce(unittest.TestCase):
    """Tests for a CP2K calculation with RUN_TYPE ENERGY_FORCE.
    """
252

253
254
255
    @classmethod
    def setUpClass(cls):
        cls.results = get_results("energy_force", "section_run")
256

257
    def test_energy_total_scf_iteration(self):
Lauri Himanen's avatar
Lauri Himanen committed
258
        energy_total = self.results["energy_total_scf_iteration"]
259
260
261
        expected_result = convert_unit(np.array(-32.2320848878), "hartree")
        self.assertTrue(np.array_equal(energy_total[0], expected_result))

262
263
264
265
266
267
268
269
270
271
    def test_energy_change_scf_iteration(self):
        energy_change = self.results["energy_change_scf_iteration"]
        expected_result = convert_unit(np.array(-3.22E+01), "hartree")
        self.assertTrue(np.array_equal(energy_change[0], expected_result))

    def test_energy_XC_scf_iteration(self):
        result = self.results["energy_XC_scf_iteration"]
        expected_result = convert_unit(np.array(-9.4555961214), "hartree")
        self.assertTrue(np.array_equal(result[0], expected_result))

272
    def test_energy_total(self):
273
        result = self.results["energy_total"]
274
        expected_result = convert_unit(np.array(-31.297885372811063), "hartree")
275
        self.assertTrue(np.array_equal(result, expected_result))
276

277
278
279
280
281
    def test_electronic_kinetic_energy(self):
        result = self.results["electronic_kinetic_energy"]
        expected_result = convert_unit(np.array(13.31525592466418), "hartree")
        self.assertTrue(np.array_equal(result, expected_result))

282
    def test_atom_forces(self):
Lauri Himanen's avatar
Lauri Himanen committed
283
        atomic_forces = self.results["atom_forces"]
284
285
286
287
288
289
290
291
292
293
294
        expected_result = convert_unit(
            np.array([
                [0.00000000, 0.00000000, 0.00000000],
                [0.00000000, 0.00000001, 0.00000001],
                [0.00000001, 0.00000001, 0.00000000],
                [0.00000001, 0.00000000, 0.00000001],
                [-0.00000001, -0.00000001, -0.00000001],
                [-0.00000001, -0.00000001, -0.00000001],
                [-0.00000001, -0.00000001, -0.00000001],
                [-0.00000001, -0.00000001, -0.00000001],
            ]),
295
            "forceAu"
296
297
298
        )
        self.assertTrue(np.array_equal(atomic_forces, expected_result))

299
    def test_atom_label(self):
300
        atom_labels = self.results["atom_labels"]
Lauri Himanen's avatar
Lauri Himanen committed
301
302
303
304
        expected_labels = np.array(8*["Si"])
        self.assertTrue(np.array_equal(atom_labels, expected_labels))

    def test_simulation_cell(self):
Lauri Himanen's avatar
Lauri Himanen committed
305
        cell = self.results["simulation_cell"]
Lauri Himanen's avatar
Lauri Himanen committed
306
307
308
309
310
311
312
313
        n_vectors = cell.shape[0]
        n_dim = cell.shape[1]
        self.assertEqual(n_vectors, 3)
        self.assertEqual(n_dim, 3)
        expected_cell = convert_unit(np.array([[5.431, 0, 0], [0, 5.431, 0], [0, 0, 5.431]]), "angstrom")
        self.assertTrue(np.array_equal(cell, expected_cell))

    def test_number_of_atoms(self):
Lauri Himanen's avatar
Lauri Himanen committed
314
        n_atoms = self.results["number_of_atoms"]
Lauri Himanen's avatar
Lauri Himanen committed
315
316
317
        self.assertEqual(n_atoms, 8)

    def test_atom_position(self):
318
        atom_position = self.results["atom_positions"]
Lauri Himanen's avatar
Lauri Himanen committed
319
320
321
        expected_position = convert_unit(np.array([4.073023, 4.073023, 1.357674]), "angstrom")
        self.assertTrue(np.array_equal(atom_position[-1, :], expected_position))

322
    def test_cp2k_filenames(self):
323
        input_filename = self.results["x_cp2k_input_filename"]
324
325
326
        expected_input = "si_bulk8.inp"
        self.assertTrue(input_filename, expected_input)

327
        bs_filename = self.results["x_cp2k_basis_set_filename"]
328
329
330
        expected_bs = "../BASIS_SET"
        self.assertEqual(bs_filename, expected_bs)

331
        geminal_filename = self.results["x_cp2k_geminal_filename"]
332
333
334
        expected_geminal = "BASIS_GEMINAL"
        self.assertEqual(geminal_filename, expected_geminal)

335
        potential_filename = self.results["x_cp2k_potential_filename"]
336
337
338
        expected_potential = "../GTH_POTENTIALS"
        self.assertEqual(potential_filename, expected_potential)

339
        mm_potential_filename = self.results["x_cp2k_mm_potential_filename"]
340
341
342
        expected_mm_potential = "MM_POTENTIAL"
        self.assertEqual(mm_potential_filename, expected_mm_potential)

343
        coordinate_filename = self.results["x_cp2k_coordinate_filename"]
344
345
        expected_coordinate = "__STD_INPUT__"
        self.assertEqual(coordinate_filename, expected_coordinate)
346

347
    def test_target_multiplicity(self):
348
        multiplicity = self.results["spin_target_multiplicity"]
349
350
351
352
353
354
        self.assertEqual(multiplicity, 1)

    def test_total_charge(self):
        charge = self.results["total_charge"]
        self.assertEqual(charge, 0)

355
356
357
358
359
    def test_single_configuration_calculation_converged(self):
        result = self.results["single_configuration_calculation_converged"]
        self.assertTrue(result)

    def test_scf_dft_number_of_iterations(self):
360
        result = self.results["number_of_scf_iterations"]
361
362
363
364
365
366
367
        self.assertEqual(result, 10)

    def test_single_configuration_to_calculation_method_ref(self):
        result = self.results["single_configuration_to_calculation_method_ref"]
        self.assertEqual(result, 0)

    def test_single_configuration_calculation_to_system_description_ref(self):
368
        result = self.results["single_configuration_calculation_to_system_ref"]
369
370
        self.assertEqual(result, 0)

371
    def test_stress_tensor(self):
372
        result = self.results["stress_tensor"]
373
374
375
376
377
378
379
380
381
382
        expected_result = convert_unit(
            np.array([
                [7.77641684, -0.00000106, -0.00000106],
                [-0.00000106, 7.77641703, -0.00000106],
                [-0.00000106, -0.00000106, 7.77641703],
            ]),
            "GPa"
        )
        self.assertTrue(np.array_equal(result, expected_result))

383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
    def test_stress_tensor_eigenvalues(self):
        result = self.results["x_cp2k_stress_tensor_eigenvalues"]
        expected_result = convert_unit(np.array([7.77641809, 7.77641797, 7.77641485]), "GPa")
        self.assertTrue(np.array_equal(result, expected_result))

    def test_stress_tensor_eigenvectors(self):
        result = self.results["x_cp2k_stress_tensor_eigenvectors"]
        expected_result = np.array([
            [0.00094549, -0.79967815, 0.60042815],
            [-0.70749682, 0.42379757, 0.56554741],
            [0.70671590, 0.42533573, 0.56536905],
        ])
        self.assertTrue(np.array_equal(result, expected_result))

    def test_stress_tensor_determinant(self):
        result = self.results["x_cp2k_stress_tensor_determinant"]
        expected_result = convert_unit(4.70260626E+02, "GPa^3")
        self.assertTrue(np.array_equal(result, expected_result))

    def test_stress_tensor_one_third_of_trace(self):
        result = self.results["x_cp2k_stress_tensor_one_third_of_trace"]
        expected_result = convert_unit(7.77641697E+00, "GPa")
        self.assertTrue(np.array_equal(result, expected_result))

407
408
#===============================================================================
if __name__ == '__main__':
Lauri Himanen's avatar
Lauri Himanen committed
409
    pass
410
411
412
413
    logger = logging.getLogger("cp2kparser")
    logger.setLevel(logging.ERROR)

    suites = []
414
    suites.append(unittest.TestLoader().loadTestsFromTestCase(TestErrors))
Lauri Himanen's avatar
Lauri Himanen committed
415
    suites.append(unittest.TestLoader().loadTestsFromTestCase(TestXCFunctional))
416
    suites.append(unittest.TestLoader().loadTestsFromTestCase(TestEnergyForce))
417
    suites.append(unittest.TestLoader().loadTestsFromTestCase(TestStressTensorMethods))
418
    suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSelfInteractionCorrectionMethod))
419
    suites.append(unittest.TestLoader().loadTestsFromTestCase(TestConfigurationPeriodicDimensions))
420
    suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSCFConvergence))
421
    suites.append(unittest.TestLoader().loadTestsFromTestCase(TestForceFiles))
422
423
    alltests = unittest.TestSuite(suites)
    unittest.TextTestRunner(verbosity=0).run(alltests)