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Updated fel to triclinic box case

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This commit is contained in:
Sebastian Kloth
2024-02-08 17:24:22 +01:00
parent 37bf496b21
commit b0f29907df
2 changed files with 116 additions and 22 deletions
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18
test/test_free_energy_landscape.py
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@ -39,15 +39,21 @@ def test_get_fel(trajectory):
OW = trajectory.subset(atom_name="OW")
box = np.diag(trajectory[0].box)
box_voxels = (box // [0.05, 0.05, 0.05] + [1, 1, 1]) * [0.05, 0.05, 0.05]
box = trajectory[0].box
box_voxels = (np.diag(box) // [0.05, 0.05, 0.05] + [1, 1, 1]) * [0.05, 0.05, 0.05]
occupation_matrix = fel.occupation_matrix(OW, skip=0, segments=1000)
maxima_matrix = fel.find_maxima(occupation_matrix, box=box_voxels, edge_length=0.05)
maxima_matrix = fel.add_distances(maxima_matrix, "cylindrical", box / 2)
r_bins = np.arange(0, 2, 0.02)
radius_maxima = 0.05 * 3 ** (1 / 2) + 0.05 / 100
maxima_matrix = fel.find_maxima(
occupation_matrix,
box=box_voxels,
radius=radius_maxima,
pore_geometry="cylindrical"
)
maxima_matrix = fel.add_distances(maxima_matrix, "cylindrical", np.diag(box) / 2)
r_bins = np.arange(0, 1, 0.02)
distance_bins = np.arange(0.05, 2.05, 0.1)
energy_df = fel.distance_resolved_energies(
maxima_matrix, distance_bins, r_bins, box, 225
maxima_matrix, distance_bins, r_bins, box, "cylindrical", 225
)
result = fel.find_energy_maxima(energy_df, r_min=0.05, r_max=0.15)