Easier plotting of real space densities (#204)

The purpose of this PR is to simplify calling `write_xsf` as a standalone routine (to plot the real space densities, e.g. for debugging). For this purpose
1. an additional flag was added to `read_xml_array`, to be able to return the array obtained from the xml file in the correct format that is required for the xsf-format (where the last element is equal to the first element in each dimension)
2. a small bug in `read_xml_array` was fixed (missing `" \n"`)

src/koopmans/utils/_xml.py

@@ -35,9 +35,20 @@ def read_xml_nr(xml_file: Path, string: str = 'EFFECTIVE-POTENTIAL') -> List[int
     return _get_nr(branch)
 
 
-def read_xml_array(xml_file: Path, norm_const: float, string: str = 'EFFECTIVE-POTENTIAL') -> np.ndarray:
+def read_xml_array(
+    xml_file: Path, norm_const: float, string: str = 'EFFECTIVE-POTENTIAL', retain_final_element: bool=False
+    ) -> np.ndarray:
     """
-    Loads an array from an xml file
+    Loads an array from an xml file.
+    
+    :param xml_file: The xml file to read from
+    :param norm_const: The normalization constant to multiply the array with (in our case 1/((Bohr radii)^3)
+    :param string: The name of the field in the xml file that contains the array, in our case either 
+    'EFFECTIVE-POTENTIAL' or 'CHARGE-DENSITY'
+    :param retain_final_element: If True, the array is returned in with periodic boundary conditions, i.e. the last 
+    element in each dimension is equal to the first element in each dimension. This is required for the xsf format.
+    
+    :return: The array
     """
 
     # Load the branch of the xml tree
@@ -60,4 +71,8 @@ def read_xml_array(xml_file: Path, norm_const: float, string: str = 'EFFECTIVE-P
                 array_xml[k, j, i] = rho_tmp[(j % (nr_xml[1]-1))*(nr_xml[0]-1)+(i % (nr_xml[0]-1))]
     array_xml *= norm_const
 
-    return array_xml[:-1, :-1, :-1]
+    if retain_final_element: 
+        # the xsf format requires an array where the last element is equal to the first element in each dimension
+        return array_xml
+    else:
+        return array_xml[:-1, :-1, :-1]

src/koopmans/utils/_xsf.py

@@ -28,7 +28,7 @@ def write_xsf(filename: Path, atoms: Atoms, arrays: List[np.ndarray], nr_xml: Tu
         out.write('CRYSTAL\n\n')
         out.write('PRIMVEC\n\n')
         for vec in cell_parameters:
-            out.write("\t" + " ".join([f"{x:13.10f}" for x in vec]))
+            out.write("\t" + " ".join([f"{x:13.10f}" for x in vec])+ " \n")
         out.write('PRIMCOORD\n')
         out.write(f"\t{len(symbols)}\t1\n")
         for symbol, pos in zip(symbols, positions):