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poetry update & new version #160

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merged 6 commits into from
Jul 31, 2023
Merged

poetry update & new version #160

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810555e
poetry update & new version
PythonFZ Jul 27, 2023
b988dec
bugfix for new zntrack release
PythonFZ Jul 27, 2023
f8cf05a
fix ApaxJaxMD API update
PythonFZ Jul 27, 2023
d452dca
remove _hash
PythonFZ Jul 27, 2023
9c01e39
apax update
PythonFZ Jul 31, 2023
6d7588e
allow to continue on error
PythonFZ Jul 31, 2023
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14 changes: 12 additions & 2 deletions ipsuite/calculators/apax_jax_md.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,9 @@
import typing

import ase.io
import h5py
import yaml
import znh5md
import zntrack.utils
from zntrack import dvc, zn

Expand Down Expand Up @@ -92,5 +94,13 @@ def run(self):
@functools.cached_property
def atoms(self) -> typing.List[ase.Atoms]:
# filename should be changeable
with self.state.fs.open((self.sim_dir / "md.traj").as_posix()) as f:
return list(ase.io.iread(f))
def file_handle(filename):
file = self.state.fs.open(filename, "rb")
return h5py.File(file)

return znh5md.ASEH5MD(
self.sim_dir / "md.h5",
format_handler=functools.partial(
znh5md.FormatHandler, file_handle=file_handle
),
).get_atoms_list()
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