src/mdevaluate/coordinates.py

@@ -218,7 +218,7 @@ class Coordinates:
             self.get_frame.clear_cache()
 
     def __iter__(self):
-        for i in range(len(self.frames))[self._slice]:
+        for i in range(len(self)):
             yield self[i]
 
     @singledispatchmethod

test/test_free_energy_landscape.py

@@ -15,34 +15,46 @@ def trajectory(request):
 def test_get_fel(trajectory):
     test_array = np.array(
         [
-            184.4909136,
-            233.79320471,
-            223.12003988,
-            228.49746397,
-            200.5626769,
-            212.82484221,
-            165.10818396,
-            170.74123681,
-            175.86672931,
+            174.46253634,
+            174.60905476,
+            178.57658092,
+            182.43001192,
+            180.57916378,
+            176.49886217,
+            178.96018547,
+            181.13561782,
+            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")
+
     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=10)
+    occupation_matrix = fel.occupation_matrix(OW, skip=0, segments=1000)
     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",
+        pore_geometry="cylindrical"
     )
     maxima_matrix = fel.add_distances(maxima_matrix, "cylindrical", np.diag(box) / 2)
-    r_bins = np.arange(0, 0.5, 0.02)
-    distance_bins = np.arange(1.8, 1.9, 0.01)
+    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, "cylindrical", 225
     )
     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()