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compare: IPKM:b5395098ced4fd37870d799d72c361fe7464eb2a
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2 changed files with 26 additions and 14 deletions
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src/mdevaluate/coordinates.py
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@ -218,7 +218,7 @@ class Coordinates:
self.get_frame.clear_cache() self.get_frame.clear_cache()
def __iter__(self): def __iter__(self):
for i in range(len(self.frames))[self._slice]: for i in range(len(self)):
yield self[i] yield self[i]
@singledispatchmethod @singledispatchmethod

38
test/test_free_energy_landscape.py
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@ -15,34 +15,46 @@ def trajectory(request):
def test_get_fel(trajectory): def test_get_fel(trajectory):
test_array = np.array( test_array = np.array(
[ [
184.4909136, 174.46253634,
233.79320471, 174.60905476,
223.12003988, 178.57658092,
228.49746397, 182.43001192,
200.5626769, 180.57916378,
212.82484221, 176.49886217,
165.10818396, 178.96018547,
170.74123681, 181.13561782,
175.86672931, 178.31026314,
176.08903996,
180.71215345,
181.59703135,
180.34329368,
187.02474488,
197.99167477,
214.05788031,
245.58571282,
287.52457507,
331.53492965,
] ]
) )
OW = trajectory.subset(atom_name="OW") OW = trajectory.subset(atom_name="OW")
box = trajectory[0].box box = trajectory[0].box
box_voxels = (np.diag(box) // [0.05, 0.05, 0.05] + [1, 1, 1]) * [0.05, 0.05, 0.05] 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=10) occupation_matrix = fel.occupation_matrix(OW, skip=0, segments=1000)
radius_maxima = 0.05 * 3 ** (1 / 2) + 0.05 / 100 radius_maxima = 0.05 * 3 ** (1 / 2) + 0.05 / 100
maxima_matrix = fel.find_maxima( maxima_matrix = fel.find_maxima(
occupation_matrix, occupation_matrix,
box=box_voxels, box=box_voxels,
radius=radius_maxima, radius=radius_maxima,
pore_geometry="cylindrical", pore_geometry="cylindrical"
) )
maxima_matrix = fel.add_distances(maxima_matrix, "cylindrical", np.diag(box) / 2) maxima_matrix = fel.add_distances(maxima_matrix, "cylindrical", np.diag(box) / 2)
r_bins = np.arange(0, 0.5, 0.02) r_bins = np.arange(0, 1, 0.02)
distance_bins = np.arange(1.8, 1.9, 0.01) distance_bins = np.arange(0.05, 2.05, 0.1)
energy_df = fel.distance_resolved_energies( energy_df = fel.distance_resolved_energies(
maxima_matrix, distance_bins, r_bins, box, "cylindrical", 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) result = fel.find_energy_maxima(energy_df, r_min=0.05, r_max=0.15)
assert (np.round(np.array(result["energy"])) == np.round(test_array)).all() assert (np.round(np.array(result["energy"])) == np.round(test_array)).all()