Add clone method for beams and elements

[Hespe]

Description

There is currently no reliable way to obtain copies of Beam or Element. This has lead to copy.deepcopy being used in some places which is troublesome in some instances (see the issues linked below).

Motivation and Context

• I have raised an issue to propose this changs
  • Deepcopy in BPM prevents gradient calculation #225
  • plot_reference_particle_traces crashes for non-leaf tensors #285

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• Documentation (update in the documentation)

Checklist

• I have updated the changelog accordingly (required).
• My change requires a change to the documentation.
• I have updated the tests accordingly (required for a bug fix or a new feature).
• I have updated the documentation accordingly.
• I have reformatted the code and checked that formatting passes (required).
• I have have fixed all issues found by flake8 (required).
• I have ensured that all pytest tests pass (required).
• I have run pytest on a machine with a CUDA GPU and made sure all tests pass (required).
• I have checked that the documentation builds (required).

Note: We are using a maximum length of 88 characters per line.

[Hespe]

Would be wise to merge this PR after #284 such that Beam.clone() can be marked abstract.

[Hespe]

Looks like the TransverseDeflectingCavity is broken if its used within a Segment and not on its own. The problem seems to be that Segment.track() calls super.track(), that is Element.track(), if the Segment is skippable. However, Element.track() falls back to the transfer map, which is not implemented for the cavity.

[Hespe]

The second test failure should be fixed once #288 is merged.

[Hespe]

@jank324 There are some lines in the plotting tests that change context beyond their own scope:

cheetah/tests/test_plotting.py

Lines 16 to 20 in 01dbf8e

	ares.areamqzm1.k1 = 5.0
	ares.areamqzm2.k1 = -5.0
	ares.areamcvm1.k1 = 1e-3
	ares.areamqzm3.k1 = 5.0
	ares.areamchm1.k1 = -2e-3

Not sure if we should adjust that somehow or if its fine in this case.

[Hespe]

Looks like the TransverseDeflectingCavity is broken if its used within a Segment and not on its own. The problem seems to be that Segment.track() calls super.track(), that is Element.track(), if the Segment is skippable. However, Element.track() falls back to the transfer map, which is not implemented for the cavity.

Raised this issue in #290

[jank324]

#288 is merged now.

[Hespe]

The plotting related failure is now fixed. This leaves only #290 as a blocker for this PR.

[jank324]

@cr-xu Does this PR now also fix #298?

[jank324]

@Hespe I can't officially request a review, so here is an unofficial request.

[cr-xu]

@cr-xu Does this PR now also fix #298?

Feature / method-wise yes.
I think we should make it clear in the documentation how these values are handled, but this can be done afterwards.

[Hespe]

Looks good to me except for these two comments about potentially missing features in the clone implementation.

[cr-xu]

Apart from that, it's good to go from my side.