Fixed undefined eFermi variable and lint issues

octopusparser/aseoct.py

@@ -63,7 +63,6 @@ def read_eigenvalues_file(fd):
             eigs[-1].setdefault(spin, []).append(float(eig))
             occs[-1].setdefault(spin, []).append(float(occ))
 
-
     nkpts = len(kpts)
     nspins = len(eigs[0])
     nbands = len(eigs[0][spin])
@@ -180,6 +179,7 @@ def block2list(namespace, lines, header=None):
         block.append(tokens)
     return name, block
 
+
 class OctNamespace:
     def __init__(self):
         self.names = {}
@@ -326,13 +326,13 @@ def read_static_info_eigenvalues_efermi(fd, energy_unit):
 
     values_sknx = {}
 
+    eFermi = None
     nbands = 0
     for line in fd:
         line = line.strip()
-        #print('\t\t' , line)
         if line.startswith('#'):
             continue
-        if line.startswith('Fermi'): # tmk
+        if line.startswith('Fermi'):  # tmk
             # print(line, '##') #  OK!
             tokens = line.split()
             unit = {'eV': eV, 'H': Hartree}[tokens[-1]]
@@ -360,13 +360,16 @@ def read_static_info_eigenvalues_efermi(fd, energy_unit):
     eps_skn = eps_skn.transpose(1, 0, 2).copy()
     occ_skn = occ_skn.transpose(1, 0, 2).copy()
     assert eps_skn.flags.contiguous
-    #print('save to dictionary: ', nspins, nkpts, nbands, eps_skn, occ_skn, eFermi)
-    return dict(nspins=nspins,
-                nkpts=nkpts,
-                nbands=nbands,
-                eigenvalues=eps_skn,
-                occupations=occ_skn,
-                efermi=eFermi)
+    # print('save to dictionary: ', nspins, nkpts, nbands, eps_skn, occ_skn, eFermi)
+    info_dict = dict(nspins=nspins,
+                     nkpts=nkpts,
+                     nbands=nbands,
+                     eigenvalues=eps_skn,
+                     occupations=occ_skn)
+    if eFermi is not None:
+        # not all Octopus' output might report the Fermi energy
+        info_dict['efermi'] = eFermi
+    return info_dict
 
 
 def read_static_info_energy(fd, energy_unit):
@@ -617,7 +620,7 @@ class Octopus(FileIOCalculator):
             return False
         elif sc == 'spin_polarized' or sc == 'polarized':
             return True
-        #else:
+        # else:
         #    raise NotImplementedError('SpinComponents keyword %s' % sc)
 
     def get_ibz_k_points(self):
@@ -687,7 +690,7 @@ class Octopus(FileIOCalculator):
         fd = open(inp_path)
         kwargs = parse_input_file(fd)
 
-        #self.atoms, kwargs = kwargs2atoms(kwargs)
+        # self.atoms, kwargs = kwargs2atoms(kwargs)
         self.kwargs.update(kwargs)
 
         fd.close()

octopusparser/parser_octopus.py

@@ -57,6 +57,7 @@ is largely irrelevant.
 
 metaInfoEnv = None
 
+
 def parse_infofile(meta_info_env, pew, fname):
     # print('\n\n### parse_infofile()')
     # print('\tPROBLEM: {}\n\t{} ' .format(fname, 'should be static/info!!'))
@@ -237,15 +238,17 @@ def parse_coordinates_from_parserlog(fname):
 def normalize_names(names):
     return [name.lower() for name in names]
 
+
 # Dictionary of all meta info:
 normalized2real = None
 
 
 parser_info = {
-  "name": "parser_octopus",
-  "version": "1.0"
+    "name": "parser_octopus",
+    "version": "1.0"
 }
 
+
 def read_parser_log(path):
     exec_kwargs = {}
     # print("\n\nPATH: ", path) # 'exec/parser.log'
@@ -257,7 +260,7 @@ def read_parser_log(path):
             try:
                 name, value = tokens
             except ValueError:
-                continue # Not an assignment
+                continue  # Not an assignment
             name = name.strip().lower()
             value = value.strip()
 
@@ -303,7 +306,7 @@ def override_keywords(kwargs, parser_log_kwargs):
     # exec/parser.log but most will just be verbatim from the
     # input file whether they can be parsed or not.
     exec_override_keywords = set(['radius',
-                                  #'lsize',
+                                  # 'lsize',
                                   'spacing'])
 
     outkwargs = kwargs.copy()
@@ -326,8 +329,9 @@ def override_keywords(kwargs, parser_log_kwargs):
             #       '%s obtained from parser log'
             #       % (name, kwargs[name], parser_log_kwargs[name]),
             #       file=fd)
-            logging.debug('Keyword %s with value %s overridden by value '
-                '%s obtained from parser log'
+            logging.debug(
+                ('Keyword %s with value %s overridden by value '
+                 '%s obtained from parser log')
                 % (name, kwargs[name], parser_log_kwargs[name]))
 
             outkwargs[name] = parser_log_kwargs[name]
@@ -433,9 +437,9 @@ def parse_without_class(fname, backend, parser_info):
         nspins = calc.get_number_of_spins()
         nkpts = len(calc.get_k_point_weights())
 
-        #fermi_energy = calc.get_fermi_level()
-        #print('I can see: ', fermi_energy)
-        #pew.addArrayValues('energy_reference_fermi', [fermi_energy, fermi_energy])
+        # fermi_energy = calc.get_fermi_level()
+        # print('I can see: ', fermi_energy)
+        # pew.addArrayValues('energy_reference_fermi', [fermi_energy, fermi_energy])
 
         if logfile is None:
             # print('No stdout logfile found', file=fd)
@@ -519,11 +523,11 @@ def parse_without_class(fname, backend, parser_info):
             pew.addArrayValues('atom_positions', convert_unit(coords, 'bohr'))
 
             # XXX FIXME atoms can be labeled in ways not compatible with ASE.
-            #pew.addArrayValues('atom_labels',
+            # pew.addArrayValues('atom_labels',
             #                   np.array(atoms.get_chemical_symbols()))
-            #pew.addArrayValues('atom_positions',
+            # pew.addArrayValues('atom_positions',
             #                   convert_unit(atoms.get_positions(), 'angstrom'))
-            #pew.addArrayValues('configuration_periodic_dimensions',
+            # pew.addArrayValues('configuration_periodic_dimensions',
             #                   np.array(atoms.pbc))
 
         with open_section('section_single_configuration_calculation'):
@@ -533,7 +537,7 @@ def parse_without_class(fname, backend, parser_info):
             pew.addValue('single_configuration_calculation_to_system_ref',
                          system_gid)
             # print('Parse info file %s' % fname) #, file=fd)
-            logging.debug('Parse info file %s' % fname) # mainfile
+            logging.debug('Parse info file %s' % fname)  # mainfile
             parse_infofile(metaInfoEnv, pew, fname)
 
             with open_section('section_method') as method_gid:
@@ -542,8 +546,8 @@ def parse_without_class(fname, backend, parser_info):
                         pew.addValue('method_basis_set_kind', basis_set_kind)
                         pew.addValue('mapping_section_method_basis_set_cell_associated',
                                      basis_set_cell_dependent_gid)
-                #smearing_width = float(kwargs.get('smearing', 0.0))
-                #pew.addValue('smearing_width',
+                # smearing_width = float(kwargs.get('smearing', 0.0))
+                # pew.addValue('smearing_width',
                 #             convert_unit(smearing_width, ENERGY_UNIT))
                 # XXX remember to get smearing width somehow
                 smearing_func = kwargs.get('smearingfunction',
@@ -556,7 +560,7 @@ def parse_without_class(fname, backend, parser_info):
                                   'fermi_dirac': 'fermi',
                                   'cold_smearing': 'marzari-vanderbilt',
                                   'methfessel_paxton': 'methfessel-paxton'}
-                                  #'': 'tetrahedra',
+                                  # '': 'tetrahedra',
 
                 pew.addValue('smearing_kind',
                              smearing_kinds[smearing_func])