[ENH] Update parameters in geology vector model

The borehole radius and units limit for thresholding were adjusted in the structural modeling scripts for improved accuracy. The element dictionary was also updated by commenting out two elements. The initialization API now retrieves bottom coordinates for each lithification instead of top coordinates, and the methods get_top_coords_for_each_lith() and get_bottom_coords_for_each_lith() were added to the Borehole class for more flexibility when analysing geological data.

Author: Leguark

gempy/API/initialization_API.py

@@ -98,7 +98,7 @@ def structural_elements_from_borehole_set(
     borehole_set: ss.core.geological_formats.BoreholeSet
 
     elements = []
-    component_lith: dict[Hashable, np.ndarray] = borehole_set.get_top_coords_for_each_lith()
+    component_lith: dict[Hashable, np.ndarray] = borehole_set.get_bottom_coords_for_each_lith()
 
     for name, properties in elements_dict.items():
         top_coordinates = component_lith.get(properties['id'])