Bug Report

When running a calculation with the current version of CodeEntropy on main, a lot of invalid eigenvalues are identified. This was not the case with an earlier version of CodeEntropy 2.1.1.

To Reproduce

YAML configuration

│ top_traj_file │ ['ramp2.prmtop', 'ramp2_1_500fr_imaged.nc']
│ force_file │ None │
│ file_format │ None │
│ kcal_force_units │ False │
│ selection_string │ all │
│ start │ 0 │
│ end │ -1 │
│ step │ 1 │
│ bin_width │ 30 │
│ temperature │ 298.0 │
│ verbose │ False │
│ grouping │ molecules │
│ combined_forcetorque │ False │
│ customised_axes │ False │
│ search_type │ RAD |

CLI command used

CodeEntropy --top_traj_file ramp2.prmtop ramp2_1_500fr_imaged.nc --combined_forcetorque False --customised_axes False --end -1

Actual output

program_output.txt

Expected output

Output was expected to be similar to that from a previous version, such as the one below.
program_output_prev.txt

Environment and Versions

• Operating System: Ubuntu 24.04.1
• CodeEntropy Version: 2.1.1
• Python Version: 3.12.0
• Package list: (https://github.com/user-attachments/files/26925992/packages.txt)

Additional Context

Issue appears with flag --customised_axes set either True or False.