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Add NEB [WIP] #393

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Add NEB [WIP] #393

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7cc995c
Refactor setting minimize_kwargs
ElliottKasoar Jan 28, 2025
540ab96
Add NEB calculation
ElliottKasoar Jan 28, 2025
2f8aede
Add interpolation options
ElliottKasoar Jan 30, 2025
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11 changes: 4 additions & 7 deletions janus_core/calculations/eos.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@
PathLike,
)
from janus_core.helpers.struct_io import output_structs
from janus_core.helpers.utils import none_to_dict
from janus_core.helpers.utils import none_to_dict, set_minimize_logging


class EoS(BaseCalculation):
Expand Down Expand Up @@ -257,12 +257,9 @@ def __init__(
raise ValueError("Please attach a calculator to `struct`.")

if self.minimize and self.logger:
self.minimize_kwargs["log_kwargs"] = {
"filename": self.log_kwargs["filename"],
"name": self.logger.name,
"filemode": "a",
}
self.minimize_kwargs["track_carbon"] = self.track_carbon
set_minimize_logging(
self.logger, self.minimize_kwargs, self.log_kwargs, track_carbon
)

# Set output files
self.write_kwargs.setdefault("filename", None)
Expand Down
12 changes: 4 additions & 8 deletions janus_core/calculations/md.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@
PostProcessKwargs,
)
from janus_core.helpers.struct_io import input_structs, output_structs
from janus_core.helpers.utils import none_to_dict, write_table
from janus_core.helpers.utils import none_to_dict, set_minimize_logging, write_table
from janus_core.processing.correlator import Correlation
from janus_core.processing.post_process import compute_rdf, compute_vaf

Expand Down Expand Up @@ -492,13 +492,9 @@ def __init__(
self.minimize_kwargs["write_kwargs"] = {"filename": opt_file}

# Use MD logger for geometry optimization
if self.logger:
self.minimize_kwargs["log_kwargs"] = {
"filename": self.log_kwargs["filename"],
"name": self.logger.name,
"filemode": "a",
}
self.minimize_kwargs["track_carbon"] = self.track_carbon
set_minimize_logging(
self.logger, self.minimize_kwargs, self.log_kwargs, track_carbon
)

self.dyn: Langevin | VelocityVerlet | ASE_NPT
self.n_atoms = len(self.struct)
Expand Down
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