[SPH][Sinks] Add option to modify sinks during simulation

[erdruais-spec]

[SPH][Plots] SliceVrPlot
function in VelocityPlots.py to plot a 2D map of radial velocity

[SPH][Example] 0_new_disk.py
take the set up of run_circular_disk_central_pot.py without the analytic potential
star + disk + planet (planet and star are sinks)
the planet can be added progressively (3 different functions)

[github-actions]

Thanks @erdruais-spec for opening this PR!

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[gemini-code-assist]

Code Review

This pull request introduces a new Godunov disc simulation example in Python and adds support for removing and modifying sinks in the SPH model, exposing these methods to Python. The review feedback highlights three key issues: a bug in modify_sink where overwriting the sink object resets its accumulated physical properties; a potential division-by-zero error in the coordinate calculations of the disc example; and a logic error in the simulation loop of the example script that leads to file overwrites and incorrect time labeling.

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[gemini-code-assist]

When modifying an existing sink, assigning a newly constructed temporary object directly to sinks[idx] will reset its accumulated physical properties (such as sph_acceleration, ext_acceleration, and angular_momentum) to zero. This can cause physical inconsistencies and violate conservation laws in the simulation. Instead, only update the specified fields (pos, velocity, mass, and accretion_radius) on the existing sink object to preserve its accumulated state.

            auto &sink = sinks[idx];
            sink.pos = pos;
            sink.velocity = velocity;
            sink.mass = mass;
            sink.accretion_radius = accretion_radius;

[gemini-code-assist]

There is a logic error in the simulation loop and plotting code. The loop runs for i from 0 to 29, evolving the model up to t = 0.29. After the loop, plot(dt * (i + 1), i) is called, which plots the state at t = 0.29 but labels it as t = 0.30 and overwrites the rho_disk_0029.png file. Changing the loop range to range(0, 31) and removing the duplicate final plot call ensures the model is correctly evolved to t = 0.30 and plotted without overwriting files.

Suggested change

	for i in range(0, 30):
	t = dt * i
	model.evolve_until(dt * i)
	d = ctx.collect_data()
	print(
	f"Step {i}, t = {t:0.5f} seconds, min rho = {d['rho'].min():0.5e}, max rho = {d['rho'].max():0.5e}"
	)
	print(
	f"Step {i}, t = {t:0.5f} seconds, min rhoe = {d['rhoetot'].min():0.5e}, max rhov = {d['rhoetot'].max():0.5e}"
	)
	print(
	f"Step {i}, t = {t:0.5f} seconds, min rhov = {d['rhovel'].min():0.5e}, max rhov = {d['rhovel'].max():0.5e}"
	)
	plot(t, i)
	plot(dt * (i + 1), i)
	for i in range(0, 31):
	t = dt * i
	model.evolve_until(dt * i)
	d = ctx.collect_data()
	print(
	f"Step {i}, t = {t:0.5f} seconds, min rho = {d['rho'].min():0.5e}, max rho = {d['rho'].max():0.5e}"
	)
	print(
	f"Step {i}, t = {t:0.5f} seconds, min rhoe = {d['rhoetot'].min():0.5e}, max rhov = {d['rhoetot'].max():0.5e}"
	)
	print(
	f"Step {i}, t = {t:0.5f} seconds, min rhov = {d['rhovel'].min():0.5e}, max rhov = {d['rhovel'].max():0.5e}"
	)
	plot(t, i)

[tdavidcl]

We discussed this PR with @y-lapeyre
I fully agree that this is a cool feature that we'de like to have in the code. However the current API in this PR is a bit cumbersome. The best would be to give a dictionary of sinks to python (like when we do .get_sinks) and simply add a setter (.set_sinks ?). Then you can do any modification that you'd like on the python side