public release 3.0.0 - see README and CHANGES for details

pmsco/elements/bindingenergy.py

@@ -10,6 +10,8 @@ the binding energies are compiled from Gwyn Williams' web page
 (https://userweb.jlab.org/~gwyn/ebindene.html).
 please refer to the original web page or the x-ray data booklet
 for original sources, definitions and remarks.
+binding energies of gases are replaced by respective values of a common compound
+from the 'handbook of x-ray photoelectron spectroscopy' (physical electronics, inc., 1995).
 
 usage
 -----
@@ -52,15 +54,47 @@ from pmsco.compat import open
 index_energy = np.zeros(0)
 index_number = np.zeros(0)
 index_term = []
+default_data_path = os.path.join(os.path.dirname(__file__), "bindingenergy.json")
 
 
-def load_data():
-    data_path = os.path.join(os.path.dirname(__file__), "bindingenergy.json")
+def load_data(data_path=None):
+    """
+    load binding energy data from json file
+
+    the data file must be in the same format as generated by save_data.
+
+    @param file path of the data file. default: "bindingenergy.json" next to this module file
+
+    @return dictionary
+    """
+    if data_path is None:
+        data_path = default_data_path
     with open(data_path) as fp:
         data = json.load(fp)
     return data
 
 
+def save_data(data_path=None):
+    """
+    save binding energy data to json file
+
+    @param file path of the data file. default: "bindingenergy.json" next to this module file
+
+    @return None
+    """
+    if data_path is None:
+        data_path = default_data_path
+    data = {}
+    for element in pt.elements:
+        element_data = {}
+        for term, energy in element.binding_energy.items():
+            element_data[term] = energy
+        if element_data:
+            data[element.number] = element_data
+    with open(data_path, 'w', 'utf8') as fp:
+        json.dump(data, fp, sort_keys=True, indent='\t')
+
+
 def init(table, reload=False):
     if 'binding_energy' in table.properties and not reload:
         return
@@ -142,6 +176,9 @@ def export_flat_text(f):
     """
     export the binding energies to a flat general text file.
 
+    the file has four space-separated columns `number`, `symbol`, `term`, `energy`.
+    column names are included in the first row.
+
     @param f: file path or open file object
     @return: None
     """
@@ -153,3 +190,23 @@ def export_flat_text(f):
     else:
         with open(f, "w") as fi:
             export_flat_text(fi)
+
+
+def import_flat_text(f):
+    """
+    import binding energies from a flat general text file.
+
+    data is in space-separated columns.
+    the first row contains column names.
+    at least the columns `number`, `term`, `energy` must be present.
+
+    the function updates existing entries and appends entries of non-existing terms.
+    existing terms that are not listed in the file remain unchanged.
+
+    @param f: file path or open file object
+
+    @return: None
+    """
+    data = np.atleast_1d(np.genfromtxt(f, names=True, dtype=None, encoding="utf8"))
+    for d in data:
+        pt.elements[d['number']].binding_energy[d['term']] = d['energy']

pmsco/elements/spectrum.py

@@ -92,6 +92,8 @@ def get_cross_section(photon_energy, element, nlj):
     @return: (float) cross section in Mb.
     """
     nl = nlj[0:2]
+    if not hasattr(element, "photoionization"):
+        element = get_element(element)
     try:
         pet, cst = element.photoionization.cross_section[nl]
     except KeyError:
@@ -196,3 +198,11 @@ def plot_spectrum(photon_energy, elements, binding_energy=False, work_function=4
     ax.set_ylabel('intensity')
     ax.set_title(elements)
     return fig, ax
+
+
+def plot_cross_section(el, nlj):
+    energy = np.arange(100, 1500, 140)
+    cs = get_cross_section(energy, el, nlj)
+    fig, ax = plt.subplots()
+    ax.set_yscale("log")
+    ax.plot(energy, cs)