diff --git a/octopusparser/aseoct.py b/octopusparser/aseoct.py
index cebb6035d535a77da935ccf97aa6cd6cee801e52..e3aa10fc7c4ddf08b453569b014221a1e551ac83 100644
--- a/octopusparser/aseoct.py
+++ b/octopusparser/aseoct.py
@@ -310,8 +310,14 @@ 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):
- #import os # tmk
+#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`
+ fd: file descriptor
+ energy_unit: string
+ Returns: dictionary
+ '''
values_sknx = {}
nbands = 0
@@ -321,14 +327,11 @@ def read_static_info_eigenvalues(fd, energy_unit):
if line.startswith('#'):
continue
if line.startswith('Fermi'): # tmk
- pass # print(line)
+ # print(line, '##') # OK!
+ tokens = line.split()
+ unit = {'eV': eV, 'H': Hartree}[tokens[-1]]
+ eFermi = float(tokens[-2]) * unit
if not line[:1].isdigit():
- # print('hithere', line)
- # I SHOULD JUMP BACK ONE LINE RIGTH HERE
- # fd.seek(-len(line))
- # I TRIED THIS:
- # fd.seek(fd.tell() - len(line))
- # -> "OSError: telling position disabled by next() call"
break
tokens = line.split()
@@ -351,11 +354,13 @@ def read_static_info_eigenvalues(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)
+ occupations=occ_skn,
+ efermi=eFermi)
def read_static_info_energy(fd, energy_unit):
@@ -367,34 +372,22 @@ def read_static_info_energy(fd, energy_unit):
def read_static_info(fd):
+ # fd: file descriptor
results = {}
- # print('?????????????????????', type(fd)) # tmk
- # print('read_static_info()@aseoct.py') # tmk
def get_energy_unit(line): # Convert "title [unit]": ---> unit
return {'[eV]': eV, '[H]': Hartree}[line.split()[1].rstrip(':')]
for line in fd:
- # print('line::', line.strip())
- if line.startswith('Fermi'):
- #print('EUREKA:', line)
if line.strip('*').strip().startswith('Brillouin zone'):
- #print('X1', line)
results.update(read_static_info_kpoints(fd))
elif line.startswith('Eigenvalues ['):
- #print('X2', line)
unit = get_energy_unit(line)
- results.update(read_static_info_eigenvalues(fd, unit))
- fd.seek(0, 0) # TMK:
- elif line.startswith('Fermi'):
- #print('X2b1') # TMK:
- fd.seek(-1, 1) # TMK:
- #print('X2b2', line)
+ results.update(read_static_info_eigenvalues_efermi(fd, unit))
+ ## print('I found:', results['efermi'])
elif line.startswith('Energy ['):
- #print('\nX3', line)
unit = get_energy_unit(line)
results.update(read_static_info_energy(fd, unit))
elif line.startswith('Total Magnetic Moment'):
- #print('X4', line)
if 0:
line = next(fd)
values = line.split()
@@ -415,12 +408,10 @@ def read_static_info(fd):
results['magmoms'] = np.array(mag_moment)
elif line.startswith('Dipole'):
- #print('X5', line)
assert line.split()[-1] == '[Debye]'
dipole = [float(next(fd).split()[-1]) for i in range(3)]
results['dipole'] = np.array(dipole) * Debye
elif line.startswith('Forces'):
- #print('X6', line)
forceunitspec = line.split()[-1]
forceunit = {'[eV/A]': eV / Angstrom,
'[H/b]': Hartree / Bohr}[forceunitspec]
@@ -434,22 +425,16 @@ def read_static_info(fd):
forces.append([float(f) for f in tokens])
results['forces'] = np.array(forces) * forceunit
elif line.startswith('Fermi'):
- #print('X7', line)
- tokens = line.split()
- unit = {'eV': eV, 'H': Hartree}[tokens[-1]]
- eFermi = float(tokens[-2]) * unit
- results['efermi'] = eFermi
- #print('####1', line)
-
- # TMK: MARKUS:the last `elif` should be simply `if`
- # otherwise when the head `if` is True
- # then all other `elif`s wont be evaluated
- if 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('####2', line)
+ # print("helloo, eFermi:", eFermi, unit)
+ # print('####1', line)
if 'ibz_k_points' not in results:
@@ -467,8 +452,9 @@ def read_static_info(fd):
break
eFermi = all_energies[arg]
results['efermi'] = eFermi
- print('eFermi NOW', eFermi) # this produces bad estimate
-
+ # print('eFermi estimate', eFermi) # this produces bad estimate
+ # ----
+ #print('finish', results['efermi'])
return results
diff --git a/octopusparser/parser_octopus.py b/octopusparser/parser_octopus.py
index 0283e89788da37379725ee5a87665d370f48b6f7..a05cdf26fbd0e033bf7bfec2b3f241584cf0cd50 100644
--- a/octopusparser/parser_octopus.py
+++ b/octopusparser/parser_octopus.py
@@ -110,13 +110,13 @@ def parse_infofile(meta_info_env, pew, fname):
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):
+ '''Parse the mainfile'''
maxlines = 100
with open(fname) as fd:
for i, line in enumerate(fd):
@@ -131,6 +131,9 @@ def parse_logfile(meta_info_env, pew, fname):
def parse_gridinfo(metaInfoEnv, pew, fname):
+ '''
+ fname: main filename
+ '''
results = {}
with open(fname) as fd:
@@ -541,7 +544,7 @@ 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)
+ logging.debug('Parse info file %s' % fname) # mainfile
parse_infofile(metaInfoEnv, pew, fname)
with open_section('section_method') as method_gid: