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Fixing #317 Invalid Eigenvalues #318

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Merged
skfegan merged 1 commit into from
Apr 22, 2026
Merged

Fixing #317 Invalid Eigenvalues #318

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7 changes: 4 additions & 3 deletions CodeEntropy/levels/level_dag.py
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Original file line number Diff line number Diff line change
Expand Up @@ -179,6 +179,7 @@ def _run_frame_stage(
Notes:
The task title shows the current frame index being processed.
"""
u = shared_data["reduced_universe"]
n_frames = shared_data["n_frames"]

task: TaskID | None = None
Expand All @@ -196,11 +197,11 @@ def _run_frame_stage(
title="Initializing",
)

for frame_index in range(n_frames):
for ts in u.trajectory:
if progress is not None and task is not None:
progress.update(task, title=f"Frame {frame_index}")
progress.update(task, title=f"Frame {ts.frame}")

frame_out = self._frame_dag.execute_frame(shared_data, frame_index)
frame_out = self._frame_dag.execute_frame(shared_data, ts.frame)
self._reduce_one_frame(shared_data, frame_out)

if progress is not None and task is not None:
Expand Down
2 changes: 1 addition & 1 deletion tests/regression/baselines/benzaldehyde/axes_off.json
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Expand Up @@ -26,7 +26,7 @@
"python": "3.13.5",
"platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39",
"codeentropy_version": "2.1.1",
"git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096"
"git_sha": "f2e0e7c509c6683eea94dd25a25bba2639c0bb96"
},
"groups": {
"0": {
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2 changes: 1 addition & 1 deletion tests/regression/baselines/benzaldehyde/combined_forcetorque_false.json
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Expand Up @@ -26,7 +26,7 @@
"python": "3.13.5",
"platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39",
"codeentropy_version": "2.1.1",
"git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096"
"git_sha": "f2e0e7c509c6683eea94dd25a25bba2639c0bb96"
},
"groups": {
"0": {
Expand Down
2 changes: 1 addition & 1 deletion tests/regression/baselines/benzaldehyde/default.json
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Expand Up @@ -26,7 +26,7 @@
"python": "3.13.5",
"platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39",
"codeentropy_version": "2.1.1",
"git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096"
"git_sha": "f2e0e7c509c6683eea94dd25a25bba2639c0bb96"
},
"groups": {
"0": {
Expand Down
12 changes: 6 additions & 6 deletions tests/regression/baselines/benzaldehyde/frame_window.json
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Expand Up @@ -26,20 +26,20 @@
"python": "3.13.5",
"platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39",
"codeentropy_version": "2.1.1",
"git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096"
"git_sha": "f2e0e7c509c6683eea94dd25a25bba2639c0bb96"
},
"groups": {
"0": {
"components": {
"united_atom:Transvibrational": 0.06976323861519099,
"united_atom:Rovibrational": 43.1148685234083,
"residue:FTmat-Transvibrational": 81.88770108142911,
"residue:FTmat-Rovibrational": 54.95209390854072,
"united_atom:Transvibrational": 40.30267601961045,
"united_atom:Rovibrational": 38.21906858443615,
"residue:FTmat-Transvibrational": 73.41098578352612,
"residue:FTmat-Rovibrational": 57.881504393660364,
"united_atom:Conformational": 0.0,
"residue:Conformational": 0.0,
"residue:Orientational": 20.481571492615355
},
"total": 200.50599824460866
"total": 230.29580627384846
}
}
}
2 changes: 1 addition & 1 deletion tests/regression/baselines/benzaldehyde/grouping_each.json
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Expand Up @@ -26,7 +26,7 @@
"python": "3.13.5",
"platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39",
"codeentropy_version": "2.1.1",
"git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096"
"git_sha": "f2e0e7c509c6683eea94dd25a25bba2639c0bb96"
},
"groups": {
"0": {
Expand Down
2 changes: 1 addition & 1 deletion tests/regression/baselines/benzaldehyde/rad.json
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Expand Up @@ -26,7 +26,7 @@
"python": "3.13.5",
"platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39",
"codeentropy_version": "2.1.1",
"git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096"
"git_sha": "f2e0e7c509c6683eea94dd25a25bba2639c0bb96"
},
"groups": {
"0": {
Expand Down
2 changes: 1 addition & 1 deletion tests/regression/baselines/benzaldehyde/selection_subset.json
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Expand Up @@ -26,7 +26,7 @@
"python": "3.13.5",
"platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39",
"codeentropy_version": "2.1.1",
"git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096"
"git_sha": "f2e0e7c509c6683eea94dd25a25bba2639c0bb96"
},
"groups": {
"0": {
Expand Down
2 changes: 1 addition & 1 deletion tests/regression/baselines/benzene/axes_off.json
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Expand Up @@ -26,7 +26,7 @@
"python": "3.13.5",
"platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39",
"codeentropy_version": "2.1.1",
"git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096"
"git_sha": "f2e0e7c509c6683eea94dd25a25bba2639c0bb96"
},
"groups": {
"0": {
Expand Down
2 changes: 1 addition & 1 deletion tests/regression/baselines/benzene/combined_forcetorque_off.json
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Expand Up @@ -26,7 +26,7 @@
"python": "3.13.5",
"platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39",
"codeentropy_version": "2.1.1",
"git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096"
"git_sha": "f2e0e7c509c6683eea94dd25a25bba2639c0bb96"
},
"groups": {
"0": {
Expand Down
2 changes: 1 addition & 1 deletion tests/regression/baselines/benzene/default.json
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Expand Up @@ -26,7 +26,7 @@
"python": "3.13.5",
"platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39",
"codeentropy_version": "2.1.1",
"git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096"
"git_sha": "f2e0e7c509c6683eea94dd25a25bba2639c0bb96"
},
"groups": {
"0": {
Expand Down
14 changes: 7 additions & 7 deletions tests/regression/baselines/benzene/frame_window.json
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
"bin_width": 30,
"temperature": 298.0,
"verbose": false,
"output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw6/test_regression_matches_baseli0/job001/output_file.json",
"output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw5/test_regression_matches_baseli0/job001/output_file.json",
"force_partitioning": 0.5,
"water_entropy": true,
"grouping": "molecules",
Expand All @@ -26,20 +26,20 @@
"python": "3.13.5",
"platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39",
"codeentropy_version": "2.1.1",
"git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096"
"git_sha": "f2e0e7c509c6683eea94dd25a25bba2639c0bb96"
},
"groups": {
"0": {
"components": {
"united_atom:Transvibrational": 0.19795850062580336,
"united_atom:Rovibrational": 37.022046871408385,
"residue:FTmat-Transvibrational": 89.61712603903918,
"residue:FTmat-Rovibrational": 59.882255851985164,
"united_atom:Transvibrational": 11.46552036084548,
"united_atom:Rovibrational": 34.98492056748493,
"residue:FTmat-Transvibrational": 71.83491878606151,
"residue:FTmat-Rovibrational": 55.6098400281744,
"united_atom:Conformational": 0.0,
"residue:Conformational": 0.0,
"residue:Orientational": 0.0
},
"total": 186.71938726305854
"total": 173.89519974256632
}
}
}
4 changes: 2 additions & 2 deletions tests/regression/baselines/benzene/grouping_each.json
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Expand Up @@ -14,7 +14,7 @@
"bin_width": 30,
"temperature": 298.0,
"verbose": false,
"output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw6/test_regression_matches_baseli1/job001/output_file.json",
"output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw5/test_regression_matches_baseli1/job001/output_file.json",
"force_partitioning": 0.5,
"water_entropy": true,
"grouping": "each",
Expand All @@ -26,7 +26,7 @@
"python": "3.13.5",
"platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39",
"codeentropy_version": "2.1.1",
"git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096"
"git_sha": "f2e0e7c509c6683eea94dd25a25bba2639c0bb96"
},
"groups": {
"0": {
Expand Down
4 changes: 2 additions & 2 deletions tests/regression/baselines/benzene/rad.json
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Expand Up @@ -14,7 +14,7 @@
"bin_width": 30,
"temperature": 298.0,
"verbose": false,
"output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw5/test_regression_matches_baseli0/job001/output_file.json",
"output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw6/test_regression_matches_baseli0/job001/output_file.json",
"force_partitioning": 0.5,
"water_entropy": true,
"grouping": "molecules",
Expand All @@ -26,7 +26,7 @@
"python": "3.13.5",
"platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39",
"codeentropy_version": "2.1.1",
"git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096"
"git_sha": "f2e0e7c509c6683eea94dd25a25bba2639c0bb96"
},
"groups": {
"0": {
Expand Down
4 changes: 2 additions & 2 deletions tests/regression/baselines/benzene/selection_subset.json
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
"bin_width": 30,
"temperature": 298.0,
"verbose": false,
"output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw5/test_regression_matches_baseli1/job001/output_file.json",
"output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw6/test_regression_matches_baseli1/job001/output_file.json",
"force_partitioning": 0.5,
"water_entropy": true,
"grouping": "molecules",
Expand All @@ -26,7 +26,7 @@
"python": "3.13.5",
"platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39",
"codeentropy_version": "2.1.1",
"git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096"
"git_sha": "f2e0e7c509c6683eea94dd25a25bba2639c0bb96"
},
"groups": {
"0": {
Expand Down
2 changes: 1 addition & 1 deletion tests/regression/baselines/cyclohexane/axes_off.json
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Expand Up @@ -26,7 +26,7 @@
"python": "3.13.5",
"platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39",
"codeentropy_version": "2.1.1",
"git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096"
"git_sha": "f2e0e7c509c6683eea94dd25a25bba2639c0bb96"
},
"groups": {
"0": {
Expand Down
2 changes: 1 addition & 1 deletion tests/regression/baselines/cyclohexane/combined_forcetorque_off.json
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Expand Up @@ -26,7 +26,7 @@
"python": "3.13.5",
"platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39",
"codeentropy_version": "2.1.1",
"git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096"
"git_sha": "f2e0e7c509c6683eea94dd25a25bba2639c0bb96"
},
"groups": {
"0": {
Expand Down
2 changes: 1 addition & 1 deletion tests/regression/baselines/cyclohexane/default.json
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Expand Up @@ -26,7 +26,7 @@
"python": "3.13.5",
"platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39",
"codeentropy_version": "2.1.1",
"git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096"
"git_sha": "f2e0e7c509c6683eea94dd25a25bba2639c0bb96"
},
"groups": {
"0": {
Expand Down
12 changes: 6 additions & 6 deletions tests/regression/baselines/cyclohexane/frame_window.json
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Expand Up @@ -26,20 +26,20 @@
"python": "3.13.5",
"platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39",
"codeentropy_version": "2.1.1",
"git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096"
"git_sha": "f2e0e7c509c6683eea94dd25a25bba2639c0bb96"
},
"groups": {
"0": {
"components": {
"united_atom:Transvibrational": 0.9922566704968832,
"united_atom:Rovibrational": 25.157330630108138,
"residue:FTmat-Transvibrational": 88.28792477558463,
"residue:FTmat-Rovibrational": 65.39813357771244,
"united_atom:Transvibrational": 17.398382397359153,
"united_atom:Rovibrational": 73.96792995794405,
"residue:FTmat-Transvibrational": 76.4267996157354,
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},
"total": 179.83564565390208
"total": 231.09780323388605
}
}
}
4 changes: 2 additions & 2 deletions tests/regression/baselines/cyclohexane/grouping_each.json
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Expand Up @@ -14,7 +14,7 @@
"bin_width": 30,
"temperature": 298.0,
"verbose": false,
"output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw10/test_regression_matches_baseli0/job001/output_file.json",
"output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw9/test_regression_matches_baseli0/job001/output_file.json",
"force_partitioning": 0.5,
"water_entropy": true,
"grouping": "each",
Expand All @@ -26,7 +26,7 @@
"python": "3.13.5",
"platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39",
"codeentropy_version": "2.1.1",
"git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096"
"git_sha": "f2e0e7c509c6683eea94dd25a25bba2639c0bb96"
},
"groups": {
"0": {
Expand Down
4 changes: 2 additions & 2 deletions tests/regression/baselines/cyclohexane/rad.json
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Expand Up @@ -14,7 +14,7 @@
"bin_width": 30,
"temperature": 298.0,
"verbose": false,
"output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw10/test_regression_matches_baseli1/job001/output_file.json",
"output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw9/test_regression_matches_baseli1/job001/output_file.json",
"force_partitioning": 0.5,
"water_entropy": true,
"grouping": "molecules",
Expand All @@ -26,7 +26,7 @@
"python": "3.13.5",
"platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39",
"codeentropy_version": "2.1.1",
"git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096"
"git_sha": "f2e0e7c509c6683eea94dd25a25bba2639c0bb96"
},
"groups": {
"0": {
Expand Down
4 changes: 2 additions & 2 deletions tests/regression/baselines/cyclohexane/selection_subset.json
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Expand Up @@ -14,7 +14,7 @@
"bin_width": 30,
"temperature": 298.0,
"verbose": false,
"output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw9/test_regression_matches_baseli0/job001/output_file.json",
"output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw10/test_regression_matches_baseli0/job001/output_file.json",
"force_partitioning": 0.5,
"water_entropy": true,
"grouping": "molecules",
Expand All @@ -26,7 +26,7 @@
"python": "3.13.5",
"platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39",
"codeentropy_version": "2.1.1",
"git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096"
"git_sha": "f2e0e7c509c6683eea94dd25a25bba2639c0bb96"
},
"groups": {
"0": {
Expand Down
20 changes: 10 additions & 10 deletions tests/regression/baselines/dna/axes_off.json
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Expand Up @@ -14,7 +14,7 @@
"bin_width": 30,
"temperature": 298.0,
"verbose": false,
"output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw9/test_regression_matches_baseli1/job001/output_file.json",
"output_file": "/tmp/pytest-of-ogo12949/pytest-3/popen-gw10/test_regression_matches_baseli1/job001/output_file.json",
"force_partitioning": 0.5,
"water_entropy": true,
"grouping": "molecules",
Expand All @@ -26,36 +26,36 @@
"python": "3.13.5",
"platform": "Linux-6.17.0-1017-oem-x86_64-with-glibc2.39",
"codeentropy_version": "2.1.1",
"git_sha": "ac1f2ac999409433f391e45cffd116cdecc46096"
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"total": 97.61010312099201
}
}
}
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