Merge pull request #34 from molssi-seamm/dev

Making the Fermi level a scalar to avoid problems.

HISTORY.rst

@@ -1,6 +1,12 @@
 =======
 History
 =======
+2023.11.8 -- Bugfix: Fermi level being an array caused problems
+ * The Fermi level in DFTB+ is a vector with 1 or 2 elements, depending whether the
+ calculation is spin-polarized. DFTB+ can handle different Fermi levels, but it is
+ not clear how useful this is, so for the time being not allowing such calculations
+ and treating the Fermi level as a scalar.
+
 2023.11.7 -- Added structure to orbital and density plots
  * The Dashboard expects 'structure.sdf' in order to display the structure with the
  orbital or debsity plots from CUBE files.

dftbplus_step/base.py

@@ -616,7 +616,12 @@ def parse_results(self, lines):
  if _type == "real":
  values = [float(x) for x in values]
 
- property_data[key] = redimension(values, dims)
+ if key == "fermi_level":
+ # The Fermi level has one or two values if spin-polarized, but
+ # normally they are the same, so turn into a scalar.
+ property_data[key] = values[0]
+ else:
+ property_data[key] = redimension(values, dims)
  if key not in properties:
  self.logger.warning("Property '{}' not recognized.".format(key))
  if key in properties and "units" in properties[key]:

dftbplus_step/energy.py

@@ -618,7 +618,8 @@ def analyze(self, indent="", data={}, out=[]):
 
  # Prepare the DOS graph(s)
  if "fermi_level" in data:
- Efermi = list(Q_(data["fermi_level"], "hartree").to("eV").magnitude)
+ # Efermi = list(Q_(data["fermi_level"], "hartree").to("eV").magnitude)
+ Efermi = [Q_(data["fermi_level"], "hartree").to("eV").magnitude]
  else:
  Efermi = [0.0]
  wd = Path(self.directory)

dftbplus_step/metadata.py

@@ -46,7 +46,7 @@
  "optimization",
  ],
  "description": "The Fermi level",
- "dimensionality": [2],
+ "dimensionality": "scalar",
  "property": "Fermi level#DFTB+#{model}",
  "type": "float",
  "units": "E_h",