Add cutoffs parameter to AllowedStructuresFilter, log_file to ASEGeoOpt

[TobiasDijkhuis]

I was running into an issue where the AllowedStructuresFilter was filtering out molecules that were within the default ASE covalent radii, but upon inspection of the structures it had really not formed these molecules. Adding a cutoffs keyword to the node should hopefully help. Now you can pass a dictionary to it, like cutoffs = {"C": 1, "H": 0.5} sets the cutoff radii of all C atoms to 1 Angstrom and of all H atoms to 0.5 Angstrom. This will result in a more sparsely connected graph.

I got a bit annoyed that ASEGeoOpt was printing the log output, so I added a keyword argument that defaults to opt.log, similar to how molecular dynamics logs default to md.log.

[codecov-commenter]

Codecov Report

❌ Patch coverage is 62.50000% with 9 lines in your changes missing coverage. Please review.
⚠️ Please upload report for BASE (main@3af81bf). Learn more about missing BASE report.
✅ All tests successful. No failed tests found.

Files with missing lines	Patch %	Lines
ipsuite/analysis/bond_stretch.py	0.00%	2 Missing ⚠️
ipsuite/analysis/sensitivity.py	33.33%	2 Missing ⚠️
ipsuite/analysis/md.py	0.00%	1 Missing ⚠️
ipsuite/analysis/molecules.py	50.00%	1 Missing ⚠️
ipsuite/bootstrap/surface_mods.py	0.00%	1 Missing ⚠️
ipsuite/configuration_selection/threshold.py	0.00%	1 Missing ⚠️
ipsuite/geometry/graphs.py	85.71%	1 Missing ⚠️

Additional details and impacted files

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