reordered folding and shifting coordinates. fixes #65

amep/pbc.py

@@ -635,20 +635,19 @@ def kdtree(
         # get center of the simulation box
         center = np.mean(box_boundary, axis=1)
 
-        # fold coords back into box (to avoid errors)
-        coords = fold(coords, box_boundary)
-
         # shift all coordinates to be within [0,L_i), i=x,y,z
         # (this is required by the KDTree algorithm)
         coords = coords + box/2. - center
 
+        # fold coords back into box (to avoid errors)
+        coords = fold(coords, box_boundary)
+
         # shift particles at the right border to the left border
         # to avoid errors occuring if a particle is placed at L_i
         coords[coords[:,0]==box[0],0]=0
         coords[coords[:,1]==box[1],1]=0
         coords[coords[:,2]==box[2],2]=0
-        # print(box_boundary, box)
-        # print(np.max(coords, axis=0))
+
     return KDTree(coords, boxsize=box)
 
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