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Check SPHInX output class #534

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merged 3 commits into from Feb 16, 2022
Merged

Check SPHInX output class #534

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289dbf0
add HasGroups
samwaseda Feb 11, 2022
f981fd6
append some unrelated small changes XD
samwaseda Feb 15, 2022
f7e3563
Format black
pyiron-runner Feb 15, 2022
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7 changes: 5 additions & 2 deletions pyiron_atomistics/sphinx/base.py
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Expand Up @@ -30,6 +30,7 @@
)
from pyiron_atomistics.sphinx.volumetric_data import SphinxVolumetricData
from pyiron_base import state, DataContainer, job_status_successful_lst, deprecate
from pyiron_base.interfaces.has_groups import HasGroups

__author__ = "Osamu Waseda, Jan Janssen"
__copyright__ = (
Expand Down Expand Up @@ -2030,7 +2031,7 @@ def _rec_cell(self):
return (
np.array([ll.split()[1:4] for ll in log_extract]).astype(float)
/ BOHR_TO_ANGSTROM
)
)[:3]

def get_kpoints_cartesian(self):
return np.einsum("ni,ij->nj", self.k_points, self._rec_cell)
Expand Down Expand Up @@ -2278,7 +2279,9 @@ def collect_energy_struct(self, file_name="energy-structOpt.dat", cwd=None):
"""
file_name = posixpath.join(cwd, file_name)
if os.path.isfile(file_name):
self.generic.dft.energy_free = np.loadtxt(file_name)[:, 1] * HARTREE_TO_EV
self.generic.dft.energy_free = (
np.loadtxt(file_name).reshape(-1, 2)[:, 1] * HARTREE_TO_EV
)

def collect_sphinx_log(
self, file_name="sphinx.log", cwd=None, check_consistency=True
Expand Down