[Feature] Blood, vessels and heart simulations

[lhemerly]

Introduce multiphase support for SPH-based particle entities to enable realistic blood simulations. This enhancement lays the groundwork for future developments in blood, vessel, and heart simulations.

Implements #373

[lhemerly]

Thanks for the hint on creating a Solver, it makes more sense now that I understand better the codebase.

This is a first draft to align how we would be making it. I did not write tests neither tested in the viewer yet.

A few things to think about:
1 - Should the solver be a general multiphase solver with blood being inherited from that general multiphase solver as an specialized solver?
2 - How do we integrate it with the coupler? Would we need a specialized solver for FSI with multiphase?
3 - Is the file structure fine? Maybe a baseline of solvers with some kind of "plugin" folder for specific implementations?

There's still several TODOs for a full implementation:

1 - Review of the current implementation (baseline for multiphase/blood)
2 - Coupler FSI integration with multiphase SPH, shear rates, yield and mainly with the blood constituents changing shape and biochemical
3 - Pulsatile flow emitter implementation

It's worth nothing that there could be severeal different implementations of this with different levels of accuracy and compute cost. We could also implement a simplified version.

[duburcqa]

@lhemerly Are you still interested in getting this feature merged? If so, I will reopen and discuss with you how to proceed. I suggest to implement this as part of some additional optional plugins, since it is quite niche compared to what Genesis is focusing on.

[lemonlimelim]

@duburcqa
Hi! I am a medical student researching on stroke simulations. I have been eyeing on this page but haven't had the chance to comment until starting my research year this summer. I believe the framework suggested previously here could be very effectively adapted for brain-specific vascular simulations—particularly for modeling the Circle of Willis.

I’m currently working with a real-world dataset that includes detailed blood flow measurements across cerebral vessels. Having a multiphase SPH-based foundation like the one introduced here would be highly valuable for simulating cerebrovascular dynamics and pathological conditions such as aneurysms or vasospasm.

The structure proposed by @lhemerly (e.g., plugin-style solver, modular coupling with FSI) seems well-suited to my needs, and I’d be happy to contribute to reimplementing it in a way that aligns with Genesis’s long-term goals. Would it be possible to reopen or revive this PR as a plugin track focused on neurovascular modeling?

[duburcqa]

Would it be possible to reopen or revive this PR as a plugin track focused on neurovascular modeling?

if you can do it, certainly, but I'm afraid no internal resources can be allocated to this task at the moment.

[lhemerly]

Dear all, I'm sorry it took me long to answer. I was expecting some guidelines on how to implement this keeping consistency with the rest of the library but I see that it is too niche and probably out of scope for Genesis. I will leave the draft PR here that may serve as baseline for others and could help anyone interested into creating an implementation of this in Genesis or somewhere else. Best!

[lemonlimelim]

No worries thank you everyone for the support and the replies! I am very excited to pick where this has been left off! Will keep this updated.

[lemonlimelim]

@duburcqa No worries regarding internal resources! I will need some time to get up to speed anyways. I would really appreciate if you could keep the discussion open! I plan on merging some real life doppler data to simulate patient specific dataset for cerebrovascular aneurysm models. Would love to get some feedback down the road when you guys have more bandwidth @duburcqa

[duburcqa]

@YilingQiao It would be great if you could have a look at some point!

[lemonlimelim]

@duburcqa Hi! I just talked to my PI, and we would love to integrate the neuro & cardio vascular features int eh genesis AI. Would you be able to open this pull request again? I wouldn't mind contributing and maintaining it etc.! I will need time to get up to speed with things anyways, so I won't require much resources for the time being!

[YilingQiao]

yeah, sure, we can reopen it

[lemonlimelim]

Thank you for reopening!

Just a quick progress update--will get to the codes to review them. I am currently working on implementing doppler flow data to input in the real life patient aneurysm models for genesis ai to do some iterative modeling based on different parameters. We are currently working on automating extraction of the doppler data for automation. Will review the codes after figuring out data abstraction.