enh: enabled tolerance for Shapes as argument

Signed-off-by: Nick Papior <[email protected]>

Author: zerothi

sisl/shape/base.py

@@ -83,7 +83,7 @@ def toCuboid(self):
         """ Create a cuboid which is surely encompassing the *full* shape """
         return self.toEllipsoid().toCuboid()
 
-    def within(self, other):
+    def within(self, other, *args, **kwargs):
         """ Return ``True`` if `other` is fully within `self`
 
         If `other` is an array, an array will be returned for each of these.
@@ -92,20 +92,24 @@ def within(self, other):
         ----------
         other : array_like
            the array/object that is checked for containment
+        *args :
+           passed directly to `within_index`
+        **kwargs :
+           passed directly to `within_index`
         """
         other = _a.asarrayd(other)
         ndim = other.ndim
         other.shape = (-1, 3)
 
-        idx = self.within_index(other)
+        idx = self.within_index(other, *args, **kwargs)
         # Initialize a boolean array with all false
         within = np.zeros(len(other), dtype=bool)
         within[idx] = True
         if ndim == 1 and other.size == 3:
             return within[0]
         return within
 
-    def within_index(self, other):
+    def within_index(self, other, *args, **kwargs):
         """ Return indices of the elements of `other` that are within the shape """
         raise NotImplementedError('within_index has not been implemented in: '+self.__class__.__name__)
 
@@ -303,7 +307,7 @@ def __init__(self, *args, **kwargs):
         M = np.finfo(np.float64).max / 100
         self._center = np.array([M, M, M], np.float64)
 
-    def within_index(self, other):
+    def within_index(self, other), *args, **kwargs:
         """ Always returns a zero length array """
         return np.empty(0, dtype=np.int32)
 

sisl/shape/ellipsoid.py

@@ -123,14 +123,21 @@ def set_center(self, center):
         """ Change the center of the object """
         super().__init__(center)
 
-    def within_index(self, other):
-        """ Return indices of the points that are within the shape """
+    def within_index(self, other, tol=1.e-12):
+        r""" Return indices of the points that are within the shape
+
+        Parameters
+        ----------
+        other : array_like
+           the object that is checked for containment
+        tol : float, optional
+           absolute tolerance for boundaries
+        """
         other = _a.asarrayd(other)
         other.shape = (-1, 3)
 
         # First check
         tmp = dot(other - self.center[None, :], self._iv)
-        tol = 1.e-12
 
         # Get indices where we should do the more
         # expensive exact check of being inside shape

sisl/shape/prism4.py

@@ -115,19 +115,20 @@ def toCuboid(self):
         """ Return a copy of itself """
         return self.copy()
 
-    def within_index(self, other):
+    def within_index(self, other, tol=1.e-12):
         """ Return indices of the `other` object which are contained in the shape
 
         Parameters
         ----------
         other : array_like
            the object that is checked for containment
+        tol : float, optional
+           absolute tolerance for boundaries
         """
         other = _a.asarrayd(other).reshape(-1, 3)
 
         # Offset origo
         tmp = dot(other - self.origo[None, :], self._iv)
-        tol = 1.e-12
 
         # First reject those that are definitely not inside
         # The proximity is 1e-12 of the inverse cell.