From 5877fe2e0eae3c43cbacc0031f553d4ce6935e37 Mon Sep 17 00:00:00 2001
From: temok-mx <temok.mx@gmail.com>
Date: Wed, 19 Aug 2020 15:05:33 -0500
Subject: [PATCH] Fermi energy: fixed bug on unopened
section_single_configuration_calculation
---
octopusparser/aseoct.py | 25 ++++++++++---------------
octopusparser/parser_octopus.py | 25 +++++++------------------
2 files changed, 17 insertions(+), 33 deletions(-)
diff --git a/octopusparser/aseoct.py b/octopusparser/aseoct.py
index e3aa10f..02904d8 100644
--- a/octopusparser/aseoct.py
+++ b/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'
diff --git a/octopusparser/parser_octopus.py b/octopusparser/parser_octopus.py
index a05cdf2..f0f5966 100644
--- a/octopusparser/parser_octopus.py
+++ b/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)
--
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