root / ase / test / geometry.py @ 1
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| 1 | 1 | tkerber | "Test the ase.utils.geometry module"
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| 2 | 1 | tkerber | |
| 3 | 1 | tkerber | import numpy as np |
| 4 | 1 | tkerber | |
| 5 | 1 | tkerber | import ase |
| 6 | 1 | tkerber | from ase.lattice.spacegroup import crystal |
| 7 | 1 | tkerber | from ase.utils.geometry import get_layers, cut, stack |
| 8 | 1 | tkerber | |
| 9 | 1 | tkerber | np.set_printoptions(suppress=True)
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| 10 | 1 | tkerber | |
| 11 | 1 | tkerber | al = crystal('Al', [(0,0,0)], spacegroup=225, cellpar=4.05) |
| 12 | 1 | tkerber | |
| 13 | 1 | tkerber | |
| 14 | 1 | tkerber | # Cut out slab of 5 Al(001) layers
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| 15 | 1 | tkerber | al001 = cut(al, nlayers=5)
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| 16 | 1 | tkerber | correct_pos = np.array([[ 0. , 0. , 0. ], |
| 17 | 1 | tkerber | [ 0. , 0.5, 0.2], |
| 18 | 1 | tkerber | [ 0.5, 0. , 0.2], |
| 19 | 1 | tkerber | [ 0.5, 0.5, 0. ], |
| 20 | 1 | tkerber | [ 0. , 0. , 0.4], |
| 21 | 1 | tkerber | [ 0. , 0.5, 0.6], |
| 22 | 1 | tkerber | [ 0.5, 0. , 0.6], |
| 23 | 1 | tkerber | [ 0.5, 0.5, 0.4], |
| 24 | 1 | tkerber | [ 0. , 0. , 0.8], |
| 25 | 1 | tkerber | [ 0.5, 0.5, 0.8]]) |
| 26 | 1 | tkerber | assert np.allclose(correct_pos, al001.get_scaled_positions())
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| 27 | 1 | tkerber | |
| 28 | 1 | tkerber | # Check layers along 001
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| 29 | 1 | tkerber | tags, levels = get_layers(al001, (0, 0, 1)) |
| 30 | 1 | tkerber | assert np.allclose(tags, [0, 1, 1, 0, 2, 3, 3, 2, 4, 4]) |
| 31 | 1 | tkerber | assert np.allclose(levels, [ 0., 2.025, 4.05, 6.075, 8.1]) |
| 32 | 1 | tkerber | |
| 33 | 1 | tkerber | # Check layers along 101
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| 34 | 1 | tkerber | tags, levels = get_layers(al001, (1, 0, 1)) |
| 35 | 1 | tkerber | assert np.allclose(tags, [0, 1, 5, 3, 2, 4, 8, 7, 6, 9]) |
| 36 | 1 | tkerber | assert np.allclose(levels, [0.000, 0.752, 1.504, 1.880, 2.256, |
| 37 | 1 | tkerber | 2.632, 3.008, 3.384, 4.136, 4.888], atol=0.001) |
| 38 | 1 | tkerber | |
| 39 | 1 | tkerber | # Check layers along 111
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| 40 | 1 | tkerber | tags, levels = get_layers(al001, (1, 1, 1)) |
| 41 | 1 | tkerber | assert np.allclose(tags, [0, 2, 2, 4, 1, 5, 5, 6, 3, 7]) |
| 42 | 1 | tkerber | assert np.allclose(levels, [0.000, 1.102, 1.929, 2.205, |
| 43 | 1 | tkerber | 2.756, 3.031, 3.858, 4.960], atol=0.001) |
| 44 | 1 | tkerber | |
| 45 | 1 | tkerber | |
| 46 | 1 | tkerber | # Cut out slab of three Al(111) layers
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| 47 | 1 | tkerber | al111 = cut(al, (1,-1,0), (0,1,-1), nlayers=3) |
| 48 | 1 | tkerber | correct_pos = np.array([[ 0. , 0.5 , 0. ], |
| 49 | 1 | tkerber | [ 0.5 , 0.5 , 0. ], |
| 50 | 1 | tkerber | [ 2/3. , 5/6. , 1/3. ], |
| 51 | 1 | tkerber | [ 0.5 , 0. , 0. ], |
| 52 | 1 | tkerber | [ 0. , 0. , 0. ], |
| 53 | 1 | tkerber | [ 1/6. , 1/3. , 1/3. ], |
| 54 | 1 | tkerber | [ 2/3. , 1/3. , 1/3. ], |
| 55 | 1 | tkerber | [ 1/3. , 1/6. , 2/3. ], |
| 56 | 1 | tkerber | [ 5/6. , 1/6. , 2/3. ], |
| 57 | 1 | tkerber | [ 5/6. , 2/3. , 2/3. ], |
| 58 | 1 | tkerber | [ 1/6. , 5/6. , 1/3. ], |
| 59 | 1 | tkerber | [ 1/3. , 2/3. , 2/3. ]]) |
| 60 | 1 | tkerber | assert np.allclose(correct_pos, al111.get_scaled_positions())
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| 61 | 1 | tkerber | |
| 62 | 1 | tkerber | |
| 63 | 1 | tkerber | # Cut out cell including all corner and edge atoms (non-periodic structure)
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| 64 | 1 | tkerber | al = cut(al, extend=1.1)
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| 65 | 1 | tkerber | correct_pos = np.array([[ 0. , 0. , 0. ], |
| 66 | 1 | tkerber | [ 0. , 0.5, 0.5], |
| 67 | 1 | tkerber | [ 0.5, 0. , 0.5], |
| 68 | 1 | tkerber | [ 0.5, 0.5, 0. ], |
| 69 | 1 | tkerber | [ 0. , 0. , 0. ], |
| 70 | 1 | tkerber | [ 0. , 0.5, 0.5], |
| 71 | 1 | tkerber | [ 0. , 0. , 0. ], |
| 72 | 1 | tkerber | [ 0.5, 0. , 0.5], |
| 73 | 1 | tkerber | [ 0. , 0. , 0. ], |
| 74 | 1 | tkerber | [ 0. , 0. , 0. ], |
| 75 | 1 | tkerber | [ 0.5, 0.5, 0. ], |
| 76 | 1 | tkerber | [ 0. , 0. , 0. ], |
| 77 | 1 | tkerber | [ 0. , 0. , 0. ], |
| 78 | 1 | tkerber | [ 0. , 0. , 0. ]]) |
| 79 | 1 | tkerber | assert np.allclose(correct_pos, al.get_scaled_positions())
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| 80 | 1 | tkerber | |
| 81 | 1 | tkerber | |
| 82 | 1 | tkerber | # Create an Ag(111)/Si(111) interface
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| 83 | 1 | tkerber | ag = crystal(['Ag'], basis=[(0,0,0)], spacegroup=225, cellpar=4.09) |
| 84 | 1 | tkerber | si = crystal(['Si'], basis=[(0,0,0)], spacegroup=227, cellpar=5.43) |
| 85 | 1 | tkerber | |
| 86 | 1 | tkerber | ag111 = cut(ag, a=(4, -4, 0), b=(4, 4, -8), nlayers=5) |
| 87 | 1 | tkerber | si111 = cut(si, a=(3, -3, 0), b=(3, 3, -6), nlayers=5) |
| 88 | 1 | tkerber | |
| 89 | 1 | tkerber | interface = stack(ag111, si111) |
| 90 | 1 | tkerber | assert len(interface) == 1000 |
| 91 | 1 | tkerber | assert np.allclose(interface.positions[::100], |
| 92 | 1 | tkerber | [[ 28.56875 , -2.040625 , -26.528125 ], |
| 93 | 1 | tkerber | [ 20.40916667, 6.12479167, -22.44395833], |
| 94 | 1 | tkerber | [ 24.49916667, 12.25541667, -20.39458333], |
| 95 | 1 | tkerber | [ 24.49041667, -6.11895833, -14.28145833], |
| 96 | 1 | tkerber | [ 10.20895833, 10.20895833, -12.23791667], |
| 97 | 1 | tkerber | [ 24.49625 , 2.049375 , -14.275625 ], |
| 98 | 1 | tkerber | [ 16.33375 , -4.0725 , 0.00875 ], |
| 99 | 1 | tkerber | [ 31.30027778, 12.25444444, -17.67472222], |
| 100 | 1 | tkerber | [ 25.85861111, 14.97527778, -14.95388889], |
| 101 | 1 | tkerber | [ 23.13777778, 4.09194444, -1.34972222]]) |