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clears output for restarted jobs #1549

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merged 8 commits into from
Aug 28, 2024
Merged

clears output for restarted jobs #1549

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2110301
clears output for restarted jobs
skatnagallu Aug 28, 2024
f7309df
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 28, 2024
02b2842
output init calls the clear_output_for_restart
skatnagallu Aug 28, 2024
0c8da16
Update pyiron_atomistics/sphinx/base.py
skatnagallu Aug 28, 2024
46186d1
Update pyiron_atomistics/sphinx/base.py
skatnagallu Aug 28, 2024
4f35bdc
Update pyiron_atomistics/sphinx/base.py
skatnagallu Aug 28, 2024
ffc1aef
changed the function name to clear
skatnagallu Aug 28, 2024
9ee71e7
Update comment to reflect changed method name
pmrv Aug 28, 2024
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20 changes: 16 additions & 4 deletions pyiron_atomistics/sphinx/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -836,6 +836,8 @@ def restart(
)
if recreate_guess:
new_job.load_guess_group()

new_job.output.clear() # temporary fix for clearing output for restarted jobs (restarted jobs copy output of parent job)
return new_job

def relocate_hdf5(self, h5_path=None):
Expand Down Expand Up @@ -1888,10 +1890,11 @@ class Output:

def __init__(self, job):
self._job = job
self.generic = DataContainer(table_name="output/generic")
self.charge_density = SphinxVolumetricData()
self.electrostatic_potential = SphinxVolumetricData()
self.generic.create_group("dft")
# --- define internal variables (overwritten in clear()) as None to silence code linters
self.generic = None
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self.charge_density = None
self.electrostatic_potential = None
self.clear()
self.old_version = False

def collect_spins_dat(self, file_name="spins.dat", cwd=None):
Expand Down Expand Up @@ -2151,6 +2154,15 @@ def from_hdf(self, hdf):
self.old_version = True
pass

def clear(self):
"""(Re)set to a clean state."""
# This function is part of a temporary fix for restart jobs (see SphinxBase.restart).
# It could also be used when existing jobs should be reparsed (e.g. after code fixes, updates, etc.)
self.generic = DataContainer(table_name="output/generic")
self.charge_density = SphinxVolumetricData()
self.electrostatic_potential = SphinxVolumetricData()
self.generic.create_group("dft")


def _update_datacontainer(job):
job.output.generic.create_group("dft")
Expand Down
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