37 lines
1.2 KiB
Python
37 lines
1.2 KiB
Python
import os
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import pytest
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import numpy as np
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import mdevaluate
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import mdevaluate.extra.free_energy_landscape as fel
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@pytest.fixture
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def trajectory(request):
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return mdevaluate.open(os.path.join(os.path.dirname(__file__), "data/pore"))
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def test_get_fel(trajectory):
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test_array = np.array([210., 214., 209., 192., 200., 193., 230., 218., 266.])
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OW = trajectory.subset(atom_name="OW")
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box = trajectory[0].box
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box_voxels = (np.diag(box) // [0.05, 0.05, 0.05] + [1, 1, 1]) * [0.05, 0.05, 0.05]
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occupation_matrix = fel.occupation_matrix(OW, skip=0, segments=10)
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radius_maxima = 0.05 * 3 ** (1 / 2) + 0.05 / 100
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maxima_matrix = fel.find_maxima(
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occupation_matrix,
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box=box_voxels,
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radius=radius_maxima,
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pore_geometry="cylindrical",
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)
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maxima_matrix = fel.add_distances(maxima_matrix, "cylindrical", np.diag(box) / 2)
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r_bins = np.arange(0, 0.5, 0.02)
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distance_bins = np.arange(1.8, 1.9, 0.01)
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energy_df = fel.distance_resolved_energies(
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maxima_matrix, distance_bins, r_bins, box, "cylindrical", 225
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)
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result = fel.find_energy_maxima(energy_df, r_min=0.05, r_max=0.15)
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assert (np.round(np.array(result["energy"])) == np.round(test_array)).all()
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