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post_process uses full correlation, fix filter_atoms #284

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merged 4 commits into from
Aug 23, 2024
Merged

post_process uses full correlation, fix filter_atoms #284

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c258ff5
post_process uses full correlation mode
harveydevereux Aug 16, 2024
70932fe
Update janus_core/helpers/post_process.py
harveydevereux Aug 21, 2024
478ab9d
Use optional
harveydevereux Aug 21, 2024
f14575e
Test vaf value and writing
harveydevereux Aug 22, 2024
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12 changes: 6 additions & 6 deletions janus_core/helpers/post_process.py
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Original file line number Diff line number Diff line change
Expand Up @@ -189,7 +189,7 @@ def compute_vaf(
use_velocities: bool = False,
fft: bool = False,
index: SliceLike = (0, None, 1),
filter_atoms: MaybeSequence[MaybeSequence[int]] = ((),),
filter_atoms: MaybeSequence[MaybeSequence[None | int]] = ((None),),
) -> NDArray[float64]:
"""
Compute the velocity autocorrelation function (VAF) of `data`.
Expand Down Expand Up @@ -238,9 +238,7 @@ def compute_vaf(
data = data[slice(*index)]

if use_velocities:
momenta = np.asarray(
[datum.get_momenta() / datum.get_masses() for datum in data]
)
momenta = np.asarray([datum.get_velocities() for datum in data])
else:
momenta = np.asarray([datum.get_momenta() for datum in data])

Expand All @@ -249,7 +247,7 @@ def compute_vaf(

# If filter_atoms not specified use all atoms
filter_atoms = [
atom if atom and atom[0] else range(n_atoms) for atom in filter_atoms
atom if atom[0] is not None else range(n_atoms) for atom in filter_atoms
]

used_atoms = {atom for atoms in filter_atoms for atom in atoms}
Expand All @@ -259,7 +257,9 @@ def compute_vaf(
np.asarray(
[
[
np.correlate(momenta[:, j, i], momenta[:, j, i], "same")
np.correlate(momenta[:, j, i], momenta[:, j, i], "full")[
n_steps - 1 :
]
for i in range(3)
]
for j in used_atoms
Expand Down
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