root / ase / test / geometry.py @ 13
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"Test the ase.utils.geometry module"
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import numpy as np |
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import ase |
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from ase.lattice.spacegroup import crystal |
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from ase.utils.geometry import get_layers, cut, stack |
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np.set_printoptions(suppress=True)
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al = crystal('Al', [(0,0,0)], spacegroup=225, cellpar=4.05) |
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# Cut out slab of 5 Al(001) layers
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al001 = cut(al, nlayers=5)
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correct_pos = np.array([[ 0. , 0. , 0. ], |
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[ 0. , 0.5, 0.2], |
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[ 0.5, 0. , 0.2], |
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[ 0.5, 0.5, 0. ], |
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[ 0. , 0. , 0.4], |
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[ 0. , 0.5, 0.6], |
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[ 0.5, 0. , 0.6], |
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[ 0.5, 0.5, 0.4], |
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[ 0. , 0. , 0.8], |
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[ 0.5, 0.5, 0.8]]) |
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assert np.allclose(correct_pos, al001.get_scaled_positions())
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# Check layers along 001
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tags, levels = get_layers(al001, (0, 0, 1)) |
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assert np.allclose(tags, [0, 1, 1, 0, 2, 3, 3, 2, 4, 4]) |
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assert np.allclose(levels, [ 0., 2.025, 4.05, 6.075, 8.1]) |
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# Check layers along 101
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tags, levels = get_layers(al001, (1, 0, 1)) |
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assert np.allclose(tags, [0, 1, 5, 3, 2, 4, 8, 7, 6, 9]) |
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assert np.allclose(levels, [0.000, 0.752, 1.504, 1.880, 2.256, |
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2.632, 3.008, 3.384, 4.136, 4.888], atol=0.001) |
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# Check layers along 111
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tags, levels = get_layers(al001, (1, 1, 1)) |
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assert np.allclose(tags, [0, 2, 2, 4, 1, 5, 5, 6, 3, 7]) |
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assert np.allclose(levels, [0.000, 1.102, 1.929, 2.205, |
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2.756, 3.031, 3.858, 4.960], atol=0.001) |
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# Cut out slab of three Al(111) layers
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al111 = cut(al, (1,-1,0), (0,1,-1), nlayers=3) |
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correct_pos = np.array([[ 0. , 0.5 , 0. ], |
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[ 0.5 , 0.5 , 0. ], |
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[ 2/3. , 5/6. , 1/3. ], |
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[ 0.5 , 0. , 0. ], |
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[ 0. , 0. , 0. ], |
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[ 1/6. , 1/3. , 1/3. ], |
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[ 2/3. , 1/3. , 1/3. ], |
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[ 1/3. , 1/6. , 2/3. ], |
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[ 5/6. , 1/6. , 2/3. ], |
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[ 5/6. , 2/3. , 2/3. ], |
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[ 1/6. , 5/6. , 1/3. ], |
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[ 1/3. , 2/3. , 2/3. ]]) |
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assert np.allclose(correct_pos, al111.get_scaled_positions())
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# Cut out cell including all corner and edge atoms (non-periodic structure)
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al = cut(al, extend=1.1)
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correct_pos = np.array([[ 0. , 0. , 0. ], |
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[ 0. , 0.5, 0.5], |
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[ 0.5, 0. , 0.5], |
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[ 0.5, 0.5, 0. ], |
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[ 0. , 0. , 0. ], |
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[ 0. , 0.5, 0.5], |
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[ 0. , 0. , 0. ], |
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[ 0.5, 0. , 0.5], |
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[ 0. , 0. , 0. ], |
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[ 0. , 0. , 0. ], |
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[ 0.5, 0.5, 0. ], |
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[ 0. , 0. , 0. ], |
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[ 0. , 0. , 0. ], |
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[ 0. , 0. , 0. ]]) |
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assert np.allclose(correct_pos, al.get_scaled_positions())
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# Create an Ag(111)/Si(111) interface
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ag = crystal(['Ag'], basis=[(0,0,0)], spacegroup=225, cellpar=4.09) |
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si = crystal(['Si'], basis=[(0,0,0)], spacegroup=227, cellpar=5.43) |
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ag111 = cut(ag, a=(4, -4, 0), b=(4, 4, -8), nlayers=5) |
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si111 = cut(si, a=(3, -3, 0), b=(3, 3, -6), nlayers=5) |
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interface = stack(ag111, si111) |
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assert len(interface) == 1000 |
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assert np.allclose(interface.positions[::100], |
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[[ 28.56875 , -2.040625 , -26.528125 ], |
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[ 20.40916667, 6.12479167, -22.44395833], |
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[ 24.49916667, 12.25541667, -20.39458333], |
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[ 24.49041667, -6.11895833, -14.28145833], |
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[ 10.20895833, 10.20895833, -12.23791667], |
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[ 24.49625 , 2.049375 , -14.275625 ], |
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[ 16.33375 , -4.0725 , 0.00875 ], |
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[ 31.30027778, 12.25444444, -17.67472222], |
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[ 25.85861111, 14.97527778, -14.95388889], |
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[ 23.13777778, 4.09194444, -1.34972222]]) |
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