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Implement start of musculotendon model in sympy.physics._biomechanics #25567

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merged 8 commits into from
Aug 22, 2023

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@brocksam brocksam commented Aug 21, 2023

This PR follows directly on from #25553 and should not be merged until #25553 has been merged.

References to other Issues or PRs

Forms part of the CZI biomechanics work program described in #24240. Follows on from #25553.

Brief description of what is fixed or changed

Introduces a new class, MusculotendonDeGroote2016, which implements musculotendon dynamics as a subclass of sympy.physics.mechanics.actuator.ForceActuator.

This PR introduces two formulations for musculotendon dynamics:
0. Rigid tendon.

  1. Explicit elastic tendon (using muscle fiber length as the state variable).

Boilerplate is also added to support other musculotendon dynamics formulations in the future:
2. Explicit elastic tendon (using tendon force as the state variable).
3. Implicit elastic tendon (using muscle fiber length as the state variable and muscle fiber velocity as the additional input variable).
4. Implicit elastic tendon (using tendon force as the state variable and muscle fiber velocity as the additional input variable).

Other comments

This PR is pretty rough and ready as is mean to just get some form of musculotendon dynamics into the WIP sympy.physics_biomechanics module. Other PRs this month will add additional tests, complete docstrings etc.

Release Notes

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**_This PR follows directly on from #25553 and should not be merged until #25553 has been merged._**

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#### References to other Issues or PRs
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Forms part of the CZI biomechanics work program described in https://github.com/sympy/sympy/issues/24240. Follows on from #25553.

#### Brief description of what is fixed or changed

Introduces a new class, `MusculotendonDeGroote2016`, which implements musculotendon dynamics as a subclass of `sympy.physics.mechanics.actuator.ForceActuator`.

This PR introduces two formulations for musculotendon dynamics:
0. Rigid tendon.
1. Explicit elastic tendon (using muscle fiber length as the state variable).

Boilerplate is also added to support other musculotendon dynamics formulations in the future:
2. Explicit elastic tendon (using tendon force as the state variable).
3. Implicit elastic tendon (using muscle fiber length as the state variable and muscle fiber velocity as the additional input variable).
4. Implicit elastic tendon (using tendon force as the state variable and muscle fiber velocity as the additional input variable).

#### Other comments

This PR is pretty rough and ready as is mean to just get some form of musculotendon dynamics into the WIP `sympy.physics_biomechanics` module. Other PRs this month will add additional tests, complete docstrings etc.

#### Release Notes

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  * Added a new solver for logarithmic equations.

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  * Fixed a bug with log of integers. Formerly, `log(-x)` incorrectly gave `-log(x)`.

* physics.units
  * Corrected a semantical error in the conversion between volt and statvolt which
    reported the volt as being larger than the statvolt.

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sympy-bot commented Aug 21, 2023

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Hi, I am the SymPy bot. I've noticed that some of your commits add or delete files. Since this is sometimes done unintentionally, I wanted to alert you about it.

This is an experimental feature of SymPy Bot. If you have any feedback on it, please comment at sympy/sympy-bot#75.

The following commits add new files:

  • 312f91f:
    • sympy/physics/_biomechanics/tests/test_musculotendon.py
  • ee8c45d:
    • sympy/physics/_biomechanics/musculotendon.py

If these files were added/deleted on purpose, you can ignore this message.

@brocksam brocksam added CZI: Codegen/Biomech Sam Brockie's CZI-funded postdoc work on codegen and biomechanics physics.biomechanics labels Aug 21, 2023
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LGTM, merging as private so we can get the full examples working. Will review in detail as we build out the examples and before we make _biomechanics public.

@moorepants moorepants merged commit 351cc00 into sympy:master Aug 22, 2023
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3 participants