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Data id in atoms #269

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Data id in atoms #269

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0ba2a9a
add support for `data_id` for `ProcessAtoms`
PythonFZ Apr 18, 2024
665cee0
new zntrack attributes
PythonFZ Apr 18, 2024
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32 changes: 22 additions & 10 deletions ipsuite/base/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,8 @@ class ProcessAtoms(IPSNode):
"""

data: list[ase.Atoms] = zntrack.deps()
data_file: str = zntrack.dvc.deps(None)
data_file: str = zntrack.deps_path(None)
data_id: typing.Optional[int] = None # zntrack.params(None)
atoms: list[ase.Atoms] = fields.Atoms()

def _post_init_(self):
Expand All @@ -50,17 +51,22 @@ def update_data(self):
def get_data(self) -> list[ase.Atoms]:
"""Get the atoms data to process."""
if self.data is not None:
return self.data
data = self.data
elif self.data_file is not None:
try:
with self.state.fs.open(pathlib.Path(self.data_file).as_posix()) as f:
return list(ase.io.iread(f))
data = list(ase.io.iread(f))
except FileNotFoundError:
# File can not be opened with DVCFileSystem, try normal open
return list(ase.io.iread(self.data_file))
data = list(ase.io.iread(self.data_file))
else:
raise ValueError("No data given.")

if self.data_id is not None:
return [data[self.data_id]]
else:
return data


class ProcessSingleAtom(IPSNode):
"""Protocol for objects that process a single atom.
Expand Down Expand Up @@ -88,8 +94,8 @@ class ProcessSingleAtom(IPSNode):
"""

data: typing.Union[ase.Atoms, typing.List[ase.Atoms]] = zntrack.deps()
data_file: str = zntrack.dvc.deps(None)
data_id: typing.Optional[int] = zntrack.zn.params(0)
data_file: str = zntrack.deps_path(None)
data_id: typing.Optional[int] = zntrack.params(0)

atoms: typing.List[ase.Atoms] = fields.Atoms()

Expand Down Expand Up @@ -134,10 +140,16 @@ class AnalyseProcessAtoms(IPSNode):
"""Analyse the output of a ProcessAtoms Node."""

data: ProcessAtoms = zntrack.deps()
reference: ProcessAtoms = zntrack.deps(None)

def get_data(self) -> typing.Tuple[list[ase.Atoms], list[ase.Atoms]]:
self.data.update_data() # otherwise, data might not be available
return self.data.data, self.data.atoms

if self.reference is None:
self.data.update_data() # otherwise, data might not be available
return self.data.data, self.data.atoms
else:
# TODO: support both, Nodes and Connections
return self.reference, self.data


class Mapping(ProcessAtoms):
Expand All @@ -160,8 +172,8 @@ class Mapping(ProcessAtoms):
The indices of the molecules will be frozen for all configurations.
"""

molecules: list[ase.Atoms] = zntrack.zn.outs()
frozen: bool = zntrack.zn.params(False)
molecules: list[ase.Atoms] = zntrack.outs()
frozen: bool = zntrack.params(False)

# TODO, should we allow to transfer the frozen mapping to another node?
# mapping = Mapping(frozen=True, reference=mapping)
Expand Down