Fermi energy: fixed bug on unopened section_single_configuration_calculation

octopusparser/aseoct.py

@@ -310,7 +310,6 @@ def read_static_info_kpoints(fd):
     return dict(ibz_k_points=ibz_k_points, k_point_weights=k_point_weights)
 
 
-#def read_static_info_eigenvalues(fd, energy_unit):
 def read_static_info_eigenvalues_efermi(fd, energy_unit):
     '''
     Parse eigenvalues and Fermi Energy from `static/info`
@@ -318,6 +317,13 @@ def read_static_info_eigenvalues_efermi(fd, energy_unit):
     energy_unit: string
     Returns: dictionary
     '''
+
+    # we had to allow this function to handle both
+    # eigenvalues and Fermi energies because the later
+    # comes in the output file immediately after the last
+    # eigenvalue, hence the "fermi line" is consumed by the
+    # line checkers that look for eigenvalues.
+
     values_sknx = {}
 
     nbands = 0
@@ -383,7 +389,6 @@ def read_static_info(fd):
         elif line.startswith('Eigenvalues ['):
             unit = get_energy_unit(line)
             results.update(read_static_info_eigenvalues_efermi(fd, unit))
-            ## print('I found:', results['efermi'])
         elif line.startswith('Energy ['):
             unit = get_energy_unit(line)
             results.update(read_static_info_energy(fd, unit))
@@ -424,18 +429,6 @@ def read_static_info(fd):
                 tokens = line.split()[-3:]
                 forces.append([float(f) for f in tokens])
             results['forces'] = np.array(forces) * forceunit
-        elif line.startswith('Fermi'):
-            # this check is 'one line too late'
-            # hence we capture Fermi energy from
-            # `read_static_info_eigenvalues()`
-            # print('Point 1', line)
-            tokens = line.split()
-            unit = {'eV': eV, 'H': Hartree}[tokens[-1]]
-            eFermi = float(tokens[-2]) * unit
-            results['efermi'] = eFermi
-            # print("helloo, eFermi:", eFermi, unit)
-            # print('####1', line)
-
 
     if 'ibz_k_points' not in results:
         results['ibz_k_points'] = np.zeros((1, 3))
@@ -454,7 +447,6 @@ def read_static_info(fd):
         results['efermi'] = eFermi
         # print('eFermi estimate', eFermi) # this produces bad estimate
         # ----
-    #print('finish', results['efermi'])
     return results
 
 
@@ -490,6 +482,9 @@ class Octopus(FileIOCalculator):
     def get_fermi_level(self):
         return self.results['efermi']
 
+    def get_fermi_energy(self):
+        return self.results['efermi']
+
     def get_dipole_moment(self, atoms=None):
         if 'dipole' not in self.results:
             msg = ('Dipole moment not calculated.\n'

octopusparser/parser_octopus.py

@@ -67,20 +67,6 @@ def parse_infofile(meta_info_env, pew, fname):
                 iterations = int(line.split()[-2])
                 pew.addValue('x_octopus_info_scf_converged_iterations',
                              iterations)
-            # - - - -
-            if  line.startswith('Fermi'):
-                # print('\tLINE:', line)
-                #pew.addValue('energy_reference_fermi', fermiref)
-                break
-        # ############
-        # CHAT WITH MARKUS
-        for line in fd:  # Jump down to Fermi FIXME as in FIRST BLOCK
-            # beware of units
-            # 'Fermi energy': 'energy_reference_fermi'
-            if line.startswith('Fermi'):
-                #octunit = line.strip().split()[-1].strip('[]:')
-                #nomadunit = {'eV': 'eV', 'H': 'hartree'}[octunit] # keep it
-                break
 
         for line in fd:  # Jump down to energies:
             if line.startswith('Energy ['):
@@ -109,10 +95,6 @@ def parse_infofile(meta_info_env, pew, fname):
             if tokens[0] in names:
                 pew.addValue(names[tokens[0]],
                              convert_unit(float(tokens[2]), nomadunit))
-            if tokens[0] == 'Fermi energy':
-                pass
-                # print(tokens)
-            # print('#', line)
 
 
 def parse_logfile(meta_info_env, pew, fname):
@@ -451,6 +433,10 @@ 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])
+
         if logfile is None:
             # print('No stdout logfile found', file=fd)
             logging.debug('No stdout logfile found')
@@ -541,6 +527,9 @@ def parse_without_class(fname, backend, parser_info):
             #                   np.array(atoms.pbc))
 
         with open_section('section_single_configuration_calculation'):
+            fermi_energy = calc.get_fermi_level()
+            pew.addArrayValues('energy_reference_fermi', [fermi_energy, fermi_energy])
+
             pew.addValue('single_configuration_calculation_to_system_ref',
                          system_gid)
             # print('Parse info file %s' % fname) #, file=fd)