Merge pull request #34 from molsturm/dev-mfh

Extend Structure object to allow for empty structures

README.md

@@ -90,5 +90,6 @@ Further external dependencies required by `libcint`:
 - BLAS
 
 ### Sturmians: sturmint
-Sturmint is currently not released (but this is planned for the near future).
+[`sturmint`](https://molsturm.org/sturmint)
+is currently not released (but this is planned for the near future).
 It can be enabled using the option `-DGINT_ENABLE_STURMINT=ON`.

src/interface/python/gint/Structure.py

@@ -26,23 +26,22 @@
 
 
 class Structure:
-    def __init__(self, atoms, coords=None):
-        """Setup a structure object.
+    def __init__(self, atoms=[], coords=[]):
+        """Setup a structure object representing the structure of a chemical system.
 
         atoms:   List of all atoms of the structure. Either symbol or atomic numbers
-                 or names are accepted.
+                 or names of the elements are accepted.
         coords:  List of the coordinates of the involved atoms.
 
         If there is only a single atom, then coords may be absent and atoms may be just
         a single atom number or atom name/symbol.
         """
-        if not isinstance(atoms, (list, tuple, np.ndarray)):
-            if coords is None:
-                atoms = [atoms]
-            else:
-                raise TypeError("atoms needs to be a list or tuple")
+        if isinstance(atoms, (int, str)):
+            atoms = [atoms]
+        elif not isinstance(atoms, (list, tuple, np.ndarray)):
+            raise TypeError("atoms needs to be a list or tuple")
 
-        if coords is None:
+        if atoms and not coords:
             if len(atoms) == 1:
                 coords = [[0, 0, 0]]
             else:
@@ -54,7 +53,8 @@ def __init__(self, atoms, coords=None):
 
         self.atom_numbers = np.array(element.to_atom_numbers(atoms))
         self.coords = np.array(coords)
-        if self.coords.shape[1] != 3:
+
+        if coords and self.coords.shape[1] != 3:
             raise ValueError("The coords list needs to have exactly 3 items per "
                              "coordinate.")
 
@@ -70,4 +70,8 @@ def n_atoms(self):
     @property
     def total_charge(self):
         """Compute the total charge of the atoms in the structure"""
-        return sum(self.atom_numbers)
+        return self.atom_numbers.sum()
+
+    @property
+    def empty(self):
+        return self.n_atoms == 0

src/interface/python/gint/gaussian/_gaussian_shells.py

@@ -122,7 +122,7 @@ def cartesian_shell(x, y, z, l, centre, coefficient, zeta, ordering):
   # _shell_expressions.py
   norm = expr.normalisation_cartesian_gaussians(l, zeta)
 
-  if np.all(centre != np.zeros(3)):
+  if np.any(centre != np.zeros(3)):
     xs = x - centre[0]
     ys = y - centre[1]
     zs = z - centre[2]
@@ -194,7 +194,7 @@ def pure_shell(x, y, z, l, centre, coefficient, zeta):
   if np.min(zeta) <= 0:
     raise ValueError("All exponents (zeta) need to be larger than zero")
 
-  if np.all(centre != np.zeros(3)):
+  if np.any(centre != np.zeros(3)):
     xs = x - centre[0]
     ys = y - centre[1]
     zs = z - centre[2]