Merge pull request #318 from CCPBioSim/317-bug-invalid-eigenvalues

Fixing #317 Invalid Eigenvalues

Author: skfegan

CodeEntropy/levels/level_dag.py

@@ -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
@@ -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:

tests/regression/baselines/benzaldehyde/axes_off.json

@@ -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": {

tests/regression/baselines/benzaldehyde/combined_forcetorque_false.json

@@ -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": {

tests/regression/baselines/benzaldehyde/default.json

@@ -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": {

tests/regression/baselines/benzaldehyde/frame_window.json

@@ -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
     }
   }
 }

tests/regression/baselines/benzaldehyde/grouping_each.json

@@ -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": {

tests/regression/baselines/benzaldehyde/rad.json

@@ -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": {

tests/regression/baselines/benzaldehyde/selection_subset.json

@@ -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": {

tests/regression/baselines/benzene/axes_off.json

@@ -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": {

tests/regression/baselines/benzene/combined_forcetorque_off.json

@@ -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": {