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COS frozen atoms sanity check #326

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COS frozen atoms sanity check #326

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14 changes: 14 additions & 0 deletions pysisyphus/cos/ChainOfStates.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,20 @@ def __init__(
):
assert len(images) >= 2, "Need at least 2 images!"
self.images = list(images)

if len(self.images[0].freeze_atoms) > 0:
# Check coherence of frozen positions
ref_coords = self.images[0].coords3d[self.images[0].freeze_atoms]
for image in self.images[1:]:
other_coords = image.coords3d[image.freeze_atoms]
diff = ref_coords - other_coords

# All frozen positions should be mappable to each other with a translation,
# so the 3D cartesian position differences should be identical.
ref = diff[0, :]
for pos in diff[1:, :]:
assert np.allclose(ref, pos), "Frozen positions are not consistent between images!"

self.fix_first = fix_first
self.fix_last = fix_last
self.align_fixed = align_fixed
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