Coverage for gpaw/test/big/test_systems/create.py: 0%
181 statements
« prev ^ index » next coverage.py v7.7.1, created at 2025-07-20 00:19 +0000
1from math import sqrt
3import ase.io
4import numpy as np
5from ase import Atoms
6from ase.build import add_adsorbate, fcc100, fcc111, molecule
7from ase.io import read
8from ase.lattice.cubic import FaceCenteredCubic
9from gpaw import FermiDirac
10from gpaw.utilities import h2gpts
13_functions = {}
16def system(func):
17 _functions[func.__name__] = func
18 return func
21def create_test_systems():
22 systems = {}
23 for name, func in _functions.items():
24 atoms, params = func()
25 # Issue #897: add mode='fd' by default
26 if params.get('mode') is None:
27 params = dict(params, mode='fd')
28 systems[name] = (atoms, params)
29 return systems
32@system
33def a5():
34 atoms = ase.io.read('alpra_Mg.CONTCAR')
35 atoms.pbc = True
36 return atoms, dict(xc='vdW-DF',
37 occupations={'name': 'fermi-dirac', 'width': 0.1})
40@system
41def ni100():
42 atoms = fcc100(symbol='Ni', size=(1, 1, 9), a=3.52, vacuum=5.5)
43 atoms.set_initial_magnetic_moments([0.6] * len(atoms))
44 gpts = h2gpts(0.18, atoms.cell, idiv=8)
45 return atoms, dict(gpts=gpts,
46 kpts=(8, 8, 1),
47 xc='PBE')
50@system
51def biimtf():
52 atoms = read('biimtf.xyz')
53 atoms.center(vacuum=5)
54 atoms.set_initial_magnetic_moments([0.5] * len(atoms))
55 return atoms, dict(h=0.16,
56 charge=+1,
57 occupations=FermiDirac(0.05),
58 xc='RPBE')
61@system
62def opt111b():
63 atoms = fcc111('Pt', (2, 2, 6), a=4.00, vacuum=10.0)
64 add_adsorbate(atoms, 'O', 2.0, 'fcc')
65 return atoms, dict(mode='pw',
66 kpts=(8, 8, 1),
67 xc='RPBE')
70@system
71def scsz():
72 # the system losing magnetic moment
73 atoms = read('ScSZ.xyz')
74 atoms.set_cell([[7.307241, 0., 0.],
75 [0., 12.656514, 0.],
76 [0., 0., 19.]],
77 scale_atoms=False)
78 atoms.center(axis=2)
79 magmoms = [0.0 for n in range(len(atoms))]
80 for n, a in enumerate(atoms):
81 if a.symbol == 'Ni':
82 magmoms[n] = 0.6
83 atoms.set_initial_magnetic_moments(magmoms)
85 atoms.pbc = (True, True, False)
87 return atoms, dict(h=0.2,
88 kpts=(2, 1, 1),
89 xc='PBE')
92@system
93def tio2v2o5():
94 atoms = Atoms('(O2Ti4O6)3V2O5',
95 [(8.3411, 1.9309, 9.2647),
96 (3.2338, 0.0854, 9.4461),
97 (1.5783, 0.1417, 8.4327),
98 (6.6126, 2.0588, 8.2126),
99 (9.4072, 2.0891, 7.6857),
100 (4.2748, 0.1256, 7.9470),
101 (9.9477, 0.2283, 7.3281),
102 (4.7391, 2.0618, 7.6111),
103 (7.7533, 2.1354, 6.7529),
104 (2.6347, 0.2585, 6.9403),
105 (6.2080, 0.1462, 8.6280),
106 (0.9517, 1.9798, 8.9832),
107 (8.5835, 6.2280, 9.4350),
108 (3.1930, 3.9040, 9.7886),
109 (1.4899, 4.0967, 8.8898),
110 (6.6167, 5.8865, 8.8463),
111 (9.3207, 5.9258, 7.7482),
112 (4.1984, 3.9386, 8.2442),
113 (9.9075, 3.9778, 7.6337),
114 (4.7626, 5.8322, 8.0051),
115 (7.6143, 5.6963, 7.1276),
116 (2.5760, 3.9661, 7.3115),
117 (6.2303, 3.8223, 8.8067),
118 (1.1298, 5.9913, 8.6968),
119 (8.3845, 9.7338, 9.1214),
120 (3.1730, 7.9593, 9.3632),
121 (1.5914, 7.8120, 8.2310),
122 (6.7003, 9.7064, 8.1528),
123 (9.3943, 9.7202, 7.6037),
124 (4.3168, 7.7857, 7.9666),
125 (9.9045, 7.7968, 7.2716),
126 (4.7772, 9.7015, 7.4648),
127 (7.7314, 9.7221, 6.6253),
128 (2.7673, 7.6929, 6.8222),
129 (6.2358, 7.8628, 8.6557),
130 (1.0528, 9.7017, 8.5919),
131 (8.4820, 5.0952, 11.4981),
132 (9.7787, 2.0447, 11.0800),
133 (6.4427, 5.6315, 10.7415),
134 (10.7389, 0.4065, 11.8697),
135 (8.3109, 3.0048, 12.4083),
136 (10.4702, 4.1612, 10.6543),
137 (8.9827, 6.3884, 13.0109)],
138 cell=[10.152054, 11.430000, 18.295483],
139 pbc=[1, 1, 0])
141 return atoms, dict(h=0.20,
142 kpts=(2, 2, 1),
143 xc='RPBE')
146@system
147def pt_h2o():
148 atoms = read('Pt_H2O.xyz')
149 atoms.set_cell([[8.527708, 0, 0],
150 [0, 4.923474, 0],
151 [0, 0, 16]],
152 scale_atoms=False)
153 atoms.center(axis=2)
155 atoms.pbc = (True, True, False)
157 return atoms, dict(h=0.20,
158 kpts=(2, 4, 1),
159 xc='RPBE',
160 poissonsolver={'dipolelayer': 'xy'},
161 basis='dzp',
162 maxiter=200)
165@system
166def lih():
167 atoms = molecule('LiH')
168 atoms.cell = [12, 12.01, 12.02]
169 atoms.center()
170 return atoms, dict(mode=dict(name='pw', ecut=400),
171 xc='PBE')
174@system
175def gs_small():
176 NBN = 7
177 NGr = 7
178 a = 2.5
179 c = 3.22
181 GR = Atoms(symbols='C2',
182 positions=[(0.5 * a, -sqrt(3) / 6 * a, 0.0),
183 (0.5 * a, +sqrt(3) / 6 * a, 0.0)],
184 cell=[(0.5 * a, -0.5 * 3**0.5 * a, 0),
185 (0.5 * a, +0.5 * 3**0.5 * a, 0), (0.0, 0.0, c * 2.0)])
186 GR.set_pbc((True, True, True))
188 GR2 = GR.copy()
189 cell = GR2.get_cell()
190 uv = cell[0] - cell[1]
191 uv = uv / np.sqrt(np.sum(uv**2.0))
192 dist = np.array([0.5 * a, -sqrt(3) / 6 * a]) - np.array(
193 [0.5 * a, +sqrt(3) / 6 * a])
194 dist = np.sqrt(np.sum(dist**2.0))
195 GR2.translate(uv * dist)
197 BN = Atoms(symbols='BN',
198 positions=[(0.5 * a, -sqrt(3) / 6 * a, 0.0),
199 (0.5 * a, +sqrt(3) / 6 * a, 0.0)],
200 cell=[(0.5 * a, -0.5 * 3**0.5 * a, 0),
201 (0.5 * a, +0.5 * 3**0.5 * a, 0), (0.0, 0.0, c * 2.0)])
202 BN.set_pbc((True, True, True))
204 NB = Atoms(symbols='NB',
205 positions=[(0.5 * a, -sqrt(3) / 6 * a, 0.0),
206 (0.5 * a, +sqrt(3) / 6 * a, 0.0)],
207 cell=[(0.5 * a, -0.5 * 3**0.5 * a, 0),
208 (0.5 * a, +0.5 * 3**0.5 * a, 0), (0.0, 0.0, c * 2.0)])
209 NB.set_pbc((True, True, True))
211 GR2.translate([0, 0, c])
212 NB.translate([0, 0, (NGr + 1.0 * (1 - NGr % 2)) * c] +
213 uv * dist * (NGr % 2))
214 BN.translate([0, 0, (NGr + 1.0 * (NGr % 2)) * c] + uv * dist * (NGr % 2))
216 GRBN = (GR * (1, 1, (NGr % 2 + NGr // 2)) + GR2 * (1, 1, (NGr // 2)) + NB *
217 (1, 1, (NBN // 2 + (NBN % 2) * (NGr % 2))) + BN *
218 (1, 1, (NBN // 2 + (NBN % 2) * (1 - NGr % 2))))
219 BNNB = BN + NB
220 Graphite = GR + GR2
222 Graphite.set_pbc((True, True, True))
223 old_cell = GR.get_cell()
224 old_cell[2, 2] = 2 * c
225 Graphite.set_cell(old_cell)
227 BNNB.set_pbc((True, True, True))
228 old_cell = BN.get_cell()
229 old_cell[2, 2] = 2 * c
230 BNNB.set_cell(old_cell)
231 BNNB.center()
233 GRBN.set_pbc((True, True, True))
234 old_cell = BN.get_cell()
235 old_cell[2, 2] = (NGr + NBN) * c
236 GRBN.set_cell(old_cell)
238 atoms = GRBN
240 return atoms, dict(h=0.18,
241 mode=dict(name='pw', ecut=600),
242 kpts=(29, 29, 1),
243 xc='PBE',
244 occupations=FermiDirac(0.01))
247@system
248def na2():
249 atoms = molecule('Na2')
250 atoms.cell = [12, 12.01, 12.02]
251 atoms.center()
252 return atoms, dict(mode=dict(name='pw', ecut=400),
253 xc='PBE')
256@system
257def opt111():
258 atoms = fcc111('Pt', (2, 2, 6), a=4.00, vacuum=10.0)
259 add_adsorbate(atoms, 'O', 2.5, 'fcc')
260 return atoms, dict(mode='pw',
261 kpts=(8, 8, 1),
262 xc='RPBE')
265@system
266def pt13():
267 element = 'Pt'
268 atoms = FaceCenteredCubic(symbol=element,
269 size=(2, 2, 2),
270 directions=[[1, 1, 0],
271 [-1, 1, 0],
272 [0, 0, 1]])
273 del atoms[4]
274 del atoms[3]
275 del atoms[2]
277 kpts = (8, 8, 4)
278 ecut = 800
279 xc1 = 'PBE'
280 return atoms, dict(mode=dict(name='pw', ecut=ecut),
281 kpts=kpts,
282 xc=xc1)
285@system
286def cuni():
287 atoms = Atoms('CuNi', magmoms=[0, 0.055])
288 atoms.positions[1, 2] = 9.2920211200 - 7.4999788800
289 atoms.center(vacuum=7.5)
290 return atoms, dict(mode=dict(name='pw', ecut=40 * 13.6),
291 xc='PBE',
292 occupations=FermiDirac(width=0.003))
295@system
296def gqd_triangle_o():
297 atoms = Atoms('C22H12O',
298 cell=[27.32059936, 20.76985686, 27.31710493],
299 positions=[[10.73088624, 8.89837485, 12.55791070],
300 [10.05301739, 8.89679181, 13.79134457],
301 [10.75109359, 8.93020267, 14.99413278],
302 [12.87455486, 8.96133088, 11.26154178],
303 [12.15171434, 8.95142166, 12.50351937],
304 [12.88537206, 8.99960120, 13.73593471],
305 [12.18470434, 8.97912415, 15.00615124],
306 [12.93041976, 9.00897627, 16.21171088],
307 [15.00139248, 9.04826138, 9.94920307],
308 [14.26001879, 9.03723869, 11.21347057],
309 [15.00007481, 9.12042787, 12.44746145],
310 [14.31001394, 9.07881510, 13.70577598],
311 [15.05204214, 9.11724418, 14.94015062],
312 [14.35398396, 9.06815937, 16.20191803],
313 [15.12643840, 9.08256916, 17.40641817],
314 [16.34154900, 9.19271021, 9.89960611],
315 [17.21352972, 9.46240940, 11.11599421],
316 [16.43580351, 9.23675012, 12.44682100],
317 [17.15060465, 9.27560508, 13.63423194],
318 [16.48917583, 9.19801051, 14.90782943],
319 [17.19566489, 9.21120025, 16.13019394],
320 [16.51583146, 9.14444384, 17.35895034],
321 [8.95901044, 8.86943060, 13.79990435],
322 [10.22073262, 8.92555557, 15.94924199],
323 [12.40194675, 8.99027108, 17.16999696],
324 [14.60100969, 9.04207920, 18.36575973],
325 [17.08913360, 9.14288668, 18.29186733],
326 [18.28620375, 9.27200790, 16.10970058],
327 [18.23171084, 9.40588926, 13.60237819],
328 [18.05103187, 8.72914292, 11.10056947],
329 [16.84288323, 9.24967730, 8.93522359],
330 [14.39939659, 8.96835388, 9.02869781],
331 [12.30013204, 8.91463681, 10.32539251],
332 [10.17280943, 8.86784643, 11.61496353],
333 [17.66988350, 10.75156430, 11.03936397]])
334 atoms.set_initial_magnetic_moments([0] * 34 + [1])
335 return atoms, {'xc': 'RPBE'}
338@system
339def cofe2o4():
340 atoms = Atoms('CoFe2O4',
341 magmoms=[3, 3, 3, 0, 0, 0, 0],
342 cell=[19.25300000, 20.91400000, 21.31300000],
343 positions=[[9.26470177, 10.75627983, 9.27350608],
344 [10.18629541, 11.21886515, 11.29618968],
345 [9.56307536, 9.00478168, 10.73991807],
346 [8.99650931, 9.87814613, 12.50179659],
347 [9.24889533, 8.89915474, 8.99153197],
348 [10.40644251, 9.61524884, 12.32000271],
349 [9.80651995, 12.33897925, 9.84687046]])
350 return atoms, {'xc': 'RPBE'}
353@system
354def isa():
355 return read('MoC2-graphene-4N-1Co-clean.xyz'), {}
358@system
359def te2fe2():
360 atoms = Atoms('Te2Fe2',
361 pbc=[True, True, False],
362 cell=[3.94202037, 3.94202037, 18.85580293, 90, 90, 120],
363 magmoms=[1, 1, 1, 1],
364 positions=[[0.00063252, 0.00171344, 7.69113746],
365 [-0.00062763, 2.27543515, 11.31172532],
366 [-0.00018445, -0.00014811, 10.16305636],
367 [-0.00016985, 2.27732626, 8.84062204]])
368 return atoms, {}
371@system
372def na2o4():
373 atoms = Atoms('Na2O4',
374 [[-0.005656852113573, -0.009141105365509, 0.000000000000000],
375 [2.161214131892207, 2.794086550115908, 1.740634406465105],
376 [0.521583455087382, 2.355416660497631, -0.000000000000000],
377 [0.506813139423620, 3.231326151362120, 0.000000000000000],
378 [1.633952935614323, 5.158614635891004, 1.740634406465105],
379 [2.662348656820273, 6.034500642267626, 1.740634406465105]],
380 cell=[4.31110615, 5.60646198, 3.48126881],
381 magmoms=[0, 0, 0.5, 0.5, 0.5, 0.5],
382 pbc=True)
383 return atoms, dict(kpts=dict(size=(4, 4, 4), gamma=True),
384 mode='pw',
385 xc='PBE')
388@system
389def c2():
390 atoms = Atoms(symbols='C2',
391 magmoms=[-0.5, 0.5],
392 positions=[
393 [0., 0., -0.62000006],
394 [0., 0., 0.62000006]])
395 atoms.center(vacuum=4.0)
396 return atoms, dict(h=0.18,
397 xc='PBE',
398 basis='dzp',
399 occupations={'name': 'fermi-dirac', 'width': 0.0})
402positions = [
403 (-0.069, 0.824, -1.295), (0.786, 0.943, -0.752), (-0.414, -0.001, -0.865),
404 (-0.282, -0.674, -3.822), (0.018, -0.147, -4.624),
405 (-0.113, -0.080, -3.034),
406 (2.253, 1.261, 0.151), (2.606, 0.638, -0.539), (2.455, 0.790, 1.019),
407 (3.106, -0.276, -1.795), (2.914, 0.459, -2.386), (2.447, -1.053, -1.919),
408 (6.257, -0.625, -0.626), (7.107, -1.002, -0.317), (5.526, -1.129, -0.131),
409 (5.451, -1.261, -2.937), (4.585, -0.957, -2.503), (6.079, -0.919, -2.200),
410 (-0.515, 3.689, 0.482), (-0.218, 3.020, -0.189), (0.046, 3.568, 1.382),
411 (-0.205, 2.640, -3.337), (-1.083, 2.576, -3.771), (-0.213, 1.885, -2.680),
412 (0.132, 6.301, -0.278), (1.104, 6.366, -0.068), (-0.148, 5.363, -0.112),
413 (-0.505, 6.680, -3.285), (-0.674, 7.677, -3.447), (-0.965, 6.278, -2.517),
414 (4.063, 3.342, -0.474), (4.950, 2.912, -0.663), (3.484, 2.619, -0.125),
415 (2.575, 2.404, -3.170), (1.694, 2.841, -3.296), (3.049, 2.956, -2.503),
416 (6.666, 2.030, -0.815), (7.476, 2.277, -0.316), (6.473, 1.064, -0.651),
417 (6.860, 2.591, -3.584), (6.928, 3.530, -3.176), (6.978, 2.097, -2.754),
418 (2.931, 6.022, -0.243), (3.732, 6.562, -0.004), (3.226, 5.115, -0.404),
419 (2.291, 7.140, -2.455), (1.317, 6.937, -2.532), (2.586, 6.574, -1.669),
420 (6.843, 5.460, 1.065), (7.803, 5.290, 0.852), (6.727, 5.424, 2.062),
421 (6.896, 4.784, -2.130), (6.191, 5.238, -2.702), (6.463, 4.665, -1.259),
422 (0.398, 0.691, 4.098), (0.047, 1.567, 3.807), (1.268, 0.490, 3.632),
423 (2.687, 0.272, 2.641), (3.078, 1.126, 3.027), (3.376, -0.501, 2.793),
424 (6.002, -0.525, 4.002), (6.152, 0.405, 3.660), (5.987, -0.447, 4.980),
425 (0.649, 3.541, 2.897), (0.245, 4.301, 3.459), (1.638, 3.457, 3.084),
426 (-0.075, 5.662, 4.233), (-0.182, 6.512, 3.776), (-0.241, 5.961, 5.212),
427 (3.243, 2.585, 3.878), (3.110, 2.343, 4.817), (4.262, 2.718, 3.780),
428 (5.942, 2.582, 3.712), (6.250, 3.500, 3.566), (6.379, 2.564, 4.636),
429 (2.686, 5.638, 5.164), (1.781, 5.472, 4.698), (2.454, 6.286, 5.887),
430 (6.744, 5.276, 3.826), (6.238, 5.608, 4.632), (7.707, 5.258, 4.110),
431 (8.573, 8.472, 0.407), (9.069, 7.656, 0.067), (8.472, 8.425, 1.397),
432 (8.758, 8.245, 2.989), (9.294, 9.091, 3.172), (7.906, 8.527, 3.373),
433 (4.006, 7.734, 3.021), (4.685, 8.238, 3.547), (3.468, 7.158, 3.624),
434 (5.281, 6.089, 6.035), (5.131, 7.033, 6.378), (4.428, 5.704, 5.720),
435 (5.067, 7.323, 0.662), (5.785, 6.667, 0.703), (4.718, 7.252, 1.585)]
438@system
439def water():
440 L = 9.8553729
441 atoms = Atoms('32(OH2)',
442 positions=positions,
443 cell=[L, L, L],
444 pbc=True)
445 atoms = atoms.repeat([1, 1, 2])
446 n = 56
447 es = dict(name='rmm-diis', keep_htpsit=False)
448 return atoms, dict(
449 nbands=132 * 2,
450 gpts=(n, n, 2 * n),
451 occupations={'name': 'fermi-dirac', 'width': 0.01},
452 eigensolver=es)
455if __name__ == '__main__':
456 from ase.db import connect
457 with connect('systems.db', append=False) as db:
458 for name, (atoms, params) in create_test_systems().items():
459 formula = atoms.symbols.formula.format('periodic')
460 print(f'{name:15} {formula:25} {params}')
461 db.write(atoms=atoms, name=name, data={'params': params})