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import numpy as np |
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2
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import pytest |
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3
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import amd |
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4
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5
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6
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def test_AMD(reference_data): |
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7
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for name in reference_data: |
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8
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for s in reference_data[name]: |
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9
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calc_amd = amd.AMD(s["PeriodicSet"], 100) |
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10
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11
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if not np.allclose(calc_amd, s["AMD100"]): |
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12
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n = s["PeriodicSet"].name |
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ref_amd = str(s["AMD100"]) |
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14
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15
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pytest.fail( |
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16
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f"AMD of structure {n} disagrees with reference. " |
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f"reference: {ref_amd}, calculated: {calc_amd}" |
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) |
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19
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20
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21
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def test_PDD(reference_data): |
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22
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for name in reference_data: |
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23
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for s in reference_data[name]: |
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24
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calc_pdd = amd.PDD(s["PeriodicSet"], 100, lexsort=False) |
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25
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26
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# Not ideal, but it seems different Python versions can make |
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# floating point changes that reorders the rows of the PDD. |
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28
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if not np.allclose(calc_pdd, s["PDD100"]): |
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29
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# if not amd.EMD(s["PDD100"], calc_pdd) < 1e-14: |
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30
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abs_diffs = np.abs(calc_pdd - s["PDD100"]) |
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31
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diffs = str(np.sort(abs_diffs.flatten())[::-1][:10]) |
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32
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n = s["PeriodicSet"].name |
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ref_pdd = str(s["PDD100"]) |
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34
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35
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pytest.fail( |
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36
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f"PDD of structure {n} disagrees with reference; " |
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f"reference: {ref_pdd}, calculated: {calc_pdd}; " |
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f"Largest elementwise diff between PDDs: {diffs}; " |
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f"PDD EMD: {amd.EMD(s['PDD100'], calc_pdd)}" |
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40
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) |
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41
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42
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43
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def test_PDD_to_AMD(reference_data): |
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for name in reference_data: |
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for s in reference_data[name]: |
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calc_pdd = amd.PDD(s["PeriodicSet"], 100, lexsort=False) |
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calc_amd = amd.AMD(s["PeriodicSet"], 100) |
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48
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amd_from_pdd = amd.PDD_to_AMD(calc_pdd) |
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49
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50
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if not np.allclose(calc_amd, amd_from_pdd): |
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n = s["PeriodicSet"].name |
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pytest.fail( |
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f"Directly calculated AMD of structure {n} disagrees " |
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54
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"with AMD calculated from PDD." |
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55
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) |
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56
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57
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58
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def test_AMD_finite(): |
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59
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trapezium = np.array([[0, 0], [1, 1], [3, 1], [4, 0]]) |
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60
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kite = np.array([[0, 0], [1, 1], [1, -1], [4, 0]]) |
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61
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trap_amd = amd.AMD_finite(trapezium) |
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kite_amd = amd.AMD_finite(kite) |
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63
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dist = np.linalg.norm(trap_amd - kite_amd) |
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64
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65
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if not abs(dist - 0.6180339887498952) < 1e-16: |
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66
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pytest.fail( |
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67
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"AMDs of finite sets trapezium and kite are different than expected." |
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68
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) |
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69
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70
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71
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def test_PDD_finite(): |
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72
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trapezium = np.array([[0, 0], [1, 1], [3, 1], [4, 0]]) |
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kite = np.array([[0, 0], [1, 1], [1, -1], [4, 0]]) |
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trap_pdd = amd.PDD_finite(trapezium) |
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kite_pdd = amd.PDD_finite(kite) |
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76
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dist = amd.EMD(trap_pdd, kite_pdd) |
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77
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78
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if not abs(dist - 0.874032045) < 1e-8: |
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79
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pytest.fail( |
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80
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"PDDs of finite sets trapezium and kite are different than " "expected." |
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81
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) |
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82
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dwiddo /
average-minimum-distance
