[Bug]: Investigate calculations that hang or run unexpectedly slowly

[harryswift01]

Bug Report

Some SIST calculations appear to stop making progress or take much longer than expected.

There is currently not enough timing or progress information to distinguish a genuine hang from an expensive calculation.

To Reproduce

Add known slow or hanging cases.

YAML configuration

# Add the configuration here.

CLI command used

# Add the command here.

Actual output

Terminal output may stop for a long period, memory may continue to grow, or the calculation may never complete.

Expected output

SIST should complete, report meaningful progress, or stop with a useful diagnostic.

Proposed Work

• Collect reproducible slow or hanging cases.
• Add timing around the main calculation stages.
• Profile CPU and memory use.
• Review chunking and repeated work.
• Investigate possible race conditions.
• Add progress reporting.
• Add convergence or iteration safeguards where needed.
• Create performance benchmarks.
• Add regression tests for corrected cases.

Done When

• Known cases are reproduced or sufficiently characterised.
• The responsible calculation stages are identified.
• CPU and memory behaviour are understood.
• Confirmed hangs are corrected or stop safely.
• Long calculations show meaningful progress.
• Corrective changes preserve validated scientific results.