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parse the number of valence electrons #575

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merged 2 commits into from Apr 6, 2020
Merged

parse the number of valence electrons #575

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8ff15ef
parse the number of valence electrons
samwaseda Apr 6, 2020
f7a43e1
Jan's request (even though I personally find it ugly...)
samwaseda Apr 6, 2020
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19 changes: 13 additions & 6 deletions pyiron/sphinx/base.py
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Expand Up @@ -1722,15 +1722,21 @@ def check_conv(line):
if not np.any(["Program exited normally." in line for line in log_file]):
self._job.status.aborted = True
warnings.warn("SPHInX parsing failed; most likely SPHInX crashed.")
main_start = np.where(["Enter Main Loop" in line for line in log_file])[0][
0
]
main_start = np.where([
"Enter Main Loop" in line
for line in log_file]
)[0][0]
log_main = log_file[main_start:]

self._parse_dict["n_valence"] = {log_file[ii-1].split()[1]:int(ll.split('=')[-1])
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self._parse_dict["n_valence"] = {
    log_file[ii-1].split()[1]:int(ll.split('=')[-1])
    for ii, ll in enumerate(log_file)
    if ll.startswith('| Z')
}

for ii, ll in enumerate(log_file)
if ll.startswith('| Z')}

def get_partial_log(file_content, start_line, end_line):
start_line = np.where([line == start_line for line in file_content])[0][
0
]
start_line = np.where([
line == start_line
for line in file_content]
)[0][0]
end_line = np.where(
[line == end_line for line in file_content[start_line:]]
)[0][0]
Expand Down Expand Up @@ -1998,6 +2004,7 @@ def to_hdf(self, hdf, force_update=False):
"bands_k_weights",
"bands_eigen_values",
"atom_scf_spins",
"n_valence",
]:
if len(self._parse_dict[k]) > 0:
hdf5_dft[k] = self._parse_dict[k]
Expand Down