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- .gitattributes +1 -0
- evalkit_internvl/lib/libcrypto.so.3 +3 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/__pycache__/__init__.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/__pycache__/hydrogen.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/__pycache__/matrices.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/__pycache__/paulialgebra.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/__pycache__/pring.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/__pycache__/qho_1d.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/__pycache__/secondquant.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/__pycache__/sho.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/__pycache__/wigner.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/__init__.py +53 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/__pycache__/__init__.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/__pycache__/_mixin.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/__pycache__/activation.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/__pycache__/curve.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/__pycache__/musculotendon.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/_mixin.py +53 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/activation.py +869 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/curve.py +1763 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/musculotendon.py +1424 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/tests/__init__.py +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/tests/__pycache__/__init__.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/tests/__pycache__/test_activation.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/tests/__pycache__/test_curve.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/tests/__pycache__/test_mixin.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/tests/__pycache__/test_musculotendon.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/tests/test_activation.py +348 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/tests/test_curve.py +1784 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/tests/test_mixin.py +48 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/tests/test_musculotendon.py +837 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/continuum_mechanics/__pycache__/__init__.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/continuum_mechanics/__pycache__/cable.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/continuum_mechanics/tests/__pycache__/__init__.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/continuum_mechanics/tests/__pycache__/test_beam.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/control/__init__.py +16 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/control/control_plots.py +978 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/control/lti.py +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/control/tests/__init__.py +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/control/tests/test_control_plots.py +299 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/hep/__init__.py +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/hep/__pycache__/__init__.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/hep/__pycache__/gamma_matrices.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/hep/gamma_matrices.py +716 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/hep/tests/__init__.py +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/hep/tests/__pycache__/__init__.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/hep/tests/__pycache__/test_gamma_matrices.cpython-310.pyc +0 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/hep/tests/test_gamma_matrices.py +427 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/optics/__init__.py +38 -0
- evalkit_internvl/lib/python3.10/site-packages/sympy/physics/optics/__pycache__/__init__.cpython-310.pyc +0 -0
.gitattributes
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evalkit_internvl/lib/python3.10/site-packages/safetensors/_safetensors_rust.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
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evalkit_internvl/lib/python3.10/site-packages/transformers/__pycache__/trainer.cpython-310.pyc filter=lfs diff=lfs merge=lfs -text
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evalkit_internvl/lib/python3.10/site-packages/safetensors/_safetensors_rust.cpython-310-x86_64-linux-gnu.so filter=lfs diff=lfs merge=lfs -text
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evalkit_internvl/lib/libcrypto.so.3 filter=lfs diff=lfs merge=lfs -text
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version https://git-lfs.github.com/spec/v1
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size 5172040
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evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/__init__.py
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"""Biomechanics extension for SymPy.
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+
Includes biomechanics-related constructs which allows users to extend multibody
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| 4 |
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models created using `sympy.physics.mechanics` into biomechanical or
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musculoskeletal models involding musculotendons and activation dynamics.
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"""
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from .activation import (
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ActivationBase,
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FirstOrderActivationDeGroote2016,
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ZerothOrderActivation,
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)
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from .curve import (
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CharacteristicCurveCollection,
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CharacteristicCurveFunction,
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FiberForceLengthActiveDeGroote2016,
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FiberForceLengthPassiveDeGroote2016,
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FiberForceLengthPassiveInverseDeGroote2016,
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FiberForceVelocityDeGroote2016,
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| 21 |
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FiberForceVelocityInverseDeGroote2016,
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TendonForceLengthDeGroote2016,
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TendonForceLengthInverseDeGroote2016,
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)
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from .musculotendon import (
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MusculotendonBase,
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MusculotendonDeGroote2016,
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MusculotendonFormulation,
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)
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| 31 |
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__all__ = [
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| 33 |
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# Musculotendon characteristic curve functions
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| 34 |
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'CharacteristicCurveCollection',
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| 35 |
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'CharacteristicCurveFunction',
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| 36 |
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'FiberForceLengthActiveDeGroote2016',
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| 37 |
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'FiberForceLengthPassiveDeGroote2016',
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| 38 |
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'FiberForceLengthPassiveInverseDeGroote2016',
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| 39 |
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'FiberForceVelocityDeGroote2016',
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| 40 |
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'FiberForceVelocityInverseDeGroote2016',
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| 41 |
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'TendonForceLengthDeGroote2016',
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| 42 |
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'TendonForceLengthInverseDeGroote2016',
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| 43 |
+
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| 44 |
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# Activation dynamics classes
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| 45 |
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'ActivationBase',
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| 46 |
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'FirstOrderActivationDeGroote2016',
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| 47 |
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'ZerothOrderActivation',
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| 48 |
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| 49 |
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# Musculotendon classes
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| 50 |
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'MusculotendonBase',
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| 51 |
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'MusculotendonDeGroote2016',
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| 52 |
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'MusculotendonFormulation',
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| 53 |
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]
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evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/_mixin.py
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| 1 |
+
"""Mixin classes for sharing functionality between unrelated classes.
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| 2 |
+
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| 3 |
+
This module is named with a leading underscore to signify to users that it's
|
| 4 |
+
"private" and only intended for internal use by the biomechanics module.
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| 5 |
+
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| 6 |
+
"""
|
| 7 |
+
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| 8 |
+
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| 9 |
+
__all__ = ['_NamedMixin']
|
| 10 |
+
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| 11 |
+
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| 12 |
+
class _NamedMixin:
|
| 13 |
+
"""Mixin class for adding `name` properties.
|
| 14 |
+
|
| 15 |
+
Valid names, as will typically be used by subclasses as a suffix when
|
| 16 |
+
naming automatically-instantiated symbol attributes, must be nonzero length
|
| 17 |
+
strings.
|
| 18 |
+
|
| 19 |
+
Attributes
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| 20 |
+
==========
|
| 21 |
+
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| 22 |
+
name : str
|
| 23 |
+
The name identifier associated with the instance. Must be a string of
|
| 24 |
+
length at least 1.
|
| 25 |
+
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| 26 |
+
"""
|
| 27 |
+
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| 28 |
+
@property
|
| 29 |
+
def name(self) -> str:
|
| 30 |
+
"""The name associated with the class instance."""
|
| 31 |
+
return self._name
|
| 32 |
+
|
| 33 |
+
@name.setter
|
| 34 |
+
def name(self, name: str) -> None:
|
| 35 |
+
if hasattr(self, '_name'):
|
| 36 |
+
msg = (
|
| 37 |
+
f'Can\'t set attribute `name` to {repr(name)} as it is '
|
| 38 |
+
f'immutable.'
|
| 39 |
+
)
|
| 40 |
+
raise AttributeError(msg)
|
| 41 |
+
if not isinstance(name, str):
|
| 42 |
+
msg = (
|
| 43 |
+
f'Name {repr(name)} passed to `name` was of type '
|
| 44 |
+
f'{type(name)}, must be {str}.'
|
| 45 |
+
)
|
| 46 |
+
raise TypeError(msg)
|
| 47 |
+
if name in {''}:
|
| 48 |
+
msg = (
|
| 49 |
+
f'Name {repr(name)} is invalid, must be a nonzero length '
|
| 50 |
+
f'{type(str)}.'
|
| 51 |
+
)
|
| 52 |
+
raise ValueError(msg)
|
| 53 |
+
self._name = name
|
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|
| 1 |
+
r"""Activation dynamics for musclotendon models.
|
| 2 |
+
|
| 3 |
+
Musculotendon models are able to produce active force when they are activated,
|
| 4 |
+
which is when a chemical process has taken place within the muscle fibers
|
| 5 |
+
causing them to voluntarily contract. Biologically this chemical process (the
|
| 6 |
+
diffusion of :math:`\textrm{Ca}^{2+}` ions) is not the input in the system,
|
| 7 |
+
electrical signals from the nervous system are. These are termed excitations.
|
| 8 |
+
Activation dynamics, which relates the normalized excitation level to the
|
| 9 |
+
normalized activation level, can be modeled by the models present in this
|
| 10 |
+
module.
|
| 11 |
+
|
| 12 |
+
"""
|
| 13 |
+
|
| 14 |
+
from abc import ABC, abstractmethod
|
| 15 |
+
from functools import cached_property
|
| 16 |
+
|
| 17 |
+
from sympy.core.symbol import Symbol
|
| 18 |
+
from sympy.core.numbers import Float, Integer, Rational
|
| 19 |
+
from sympy.functions.elementary.hyperbolic import tanh
|
| 20 |
+
from sympy.matrices.dense import MutableDenseMatrix as Matrix, zeros
|
| 21 |
+
from sympy.physics.biomechanics._mixin import _NamedMixin
|
| 22 |
+
from sympy.physics.mechanics import dynamicsymbols
|
| 23 |
+
|
| 24 |
+
|
| 25 |
+
__all__ = [
|
| 26 |
+
'ActivationBase',
|
| 27 |
+
'FirstOrderActivationDeGroote2016',
|
| 28 |
+
'ZerothOrderActivation',
|
| 29 |
+
]
|
| 30 |
+
|
| 31 |
+
|
| 32 |
+
class ActivationBase(ABC, _NamedMixin):
|
| 33 |
+
"""Abstract base class for all activation dynamics classes to inherit from.
|
| 34 |
+
|
| 35 |
+
Notes
|
| 36 |
+
=====
|
| 37 |
+
|
| 38 |
+
Instances of this class cannot be directly instantiated by users. However,
|
| 39 |
+
it can be used to created custom activation dynamics types through
|
| 40 |
+
subclassing.
|
| 41 |
+
|
| 42 |
+
"""
|
| 43 |
+
|
| 44 |
+
def __init__(self, name):
|
| 45 |
+
"""Initializer for ``ActivationBase``."""
|
| 46 |
+
self.name = str(name)
|
| 47 |
+
|
| 48 |
+
# Symbols
|
| 49 |
+
self._e = dynamicsymbols(f"e_{name}")
|
| 50 |
+
self._a = dynamicsymbols(f"a_{name}")
|
| 51 |
+
|
| 52 |
+
@classmethod
|
| 53 |
+
@abstractmethod
|
| 54 |
+
def with_defaults(cls, name):
|
| 55 |
+
"""Alternate constructor that provides recommended defaults for
|
| 56 |
+
constants."""
|
| 57 |
+
pass
|
| 58 |
+
|
| 59 |
+
@property
|
| 60 |
+
def excitation(self):
|
| 61 |
+
"""Dynamic symbol representing excitation.
|
| 62 |
+
|
| 63 |
+
Explanation
|
| 64 |
+
===========
|
| 65 |
+
|
| 66 |
+
The alias ``e`` can also be used to access the same attribute.
|
| 67 |
+
|
| 68 |
+
"""
|
| 69 |
+
return self._e
|
| 70 |
+
|
| 71 |
+
@property
|
| 72 |
+
def e(self):
|
| 73 |
+
"""Dynamic symbol representing excitation.
|
| 74 |
+
|
| 75 |
+
Explanation
|
| 76 |
+
===========
|
| 77 |
+
|
| 78 |
+
The alias ``excitation`` can also be used to access the same attribute.
|
| 79 |
+
|
| 80 |
+
"""
|
| 81 |
+
return self._e
|
| 82 |
+
|
| 83 |
+
@property
|
| 84 |
+
def activation(self):
|
| 85 |
+
"""Dynamic symbol representing activation.
|
| 86 |
+
|
| 87 |
+
Explanation
|
| 88 |
+
===========
|
| 89 |
+
|
| 90 |
+
The alias ``a`` can also be used to access the same attribute.
|
| 91 |
+
|
| 92 |
+
"""
|
| 93 |
+
return self._a
|
| 94 |
+
|
| 95 |
+
@property
|
| 96 |
+
def a(self):
|
| 97 |
+
"""Dynamic symbol representing activation.
|
| 98 |
+
|
| 99 |
+
Explanation
|
| 100 |
+
===========
|
| 101 |
+
|
| 102 |
+
The alias ``activation`` can also be used to access the same attribute.
|
| 103 |
+
|
| 104 |
+
"""
|
| 105 |
+
return self._a
|
| 106 |
+
|
| 107 |
+
@property
|
| 108 |
+
@abstractmethod
|
| 109 |
+
def order(self):
|
| 110 |
+
"""Order of the (differential) equation governing activation."""
|
| 111 |
+
pass
|
| 112 |
+
|
| 113 |
+
@property
|
| 114 |
+
@abstractmethod
|
| 115 |
+
def state_vars(self):
|
| 116 |
+
"""Ordered column matrix of functions of time that represent the state
|
| 117 |
+
variables.
|
| 118 |
+
|
| 119 |
+
Explanation
|
| 120 |
+
===========
|
| 121 |
+
|
| 122 |
+
The alias ``x`` can also be used to access the same attribute.
|
| 123 |
+
|
| 124 |
+
"""
|
| 125 |
+
pass
|
| 126 |
+
|
| 127 |
+
@property
|
| 128 |
+
@abstractmethod
|
| 129 |
+
def x(self):
|
| 130 |
+
"""Ordered column matrix of functions of time that represent the state
|
| 131 |
+
variables.
|
| 132 |
+
|
| 133 |
+
Explanation
|
| 134 |
+
===========
|
| 135 |
+
|
| 136 |
+
The alias ``state_vars`` can also be used to access the same attribute.
|
| 137 |
+
|
| 138 |
+
"""
|
| 139 |
+
pass
|
| 140 |
+
|
| 141 |
+
@property
|
| 142 |
+
@abstractmethod
|
| 143 |
+
def input_vars(self):
|
| 144 |
+
"""Ordered column matrix of functions of time that represent the input
|
| 145 |
+
variables.
|
| 146 |
+
|
| 147 |
+
Explanation
|
| 148 |
+
===========
|
| 149 |
+
|
| 150 |
+
The alias ``r`` can also be used to access the same attribute.
|
| 151 |
+
|
| 152 |
+
"""
|
| 153 |
+
pass
|
| 154 |
+
|
| 155 |
+
@property
|
| 156 |
+
@abstractmethod
|
| 157 |
+
def r(self):
|
| 158 |
+
"""Ordered column matrix of functions of time that represent the input
|
| 159 |
+
variables.
|
| 160 |
+
|
| 161 |
+
Explanation
|
| 162 |
+
===========
|
| 163 |
+
|
| 164 |
+
The alias ``input_vars`` can also be used to access the same attribute.
|
| 165 |
+
|
| 166 |
+
"""
|
| 167 |
+
pass
|
| 168 |
+
|
| 169 |
+
@property
|
| 170 |
+
@abstractmethod
|
| 171 |
+
def constants(self):
|
| 172 |
+
"""Ordered column matrix of non-time varying symbols present in ``M``
|
| 173 |
+
and ``F``.
|
| 174 |
+
|
| 175 |
+
Only symbolic constants are returned. If a numeric type (e.g. ``Float``)
|
| 176 |
+
has been used instead of ``Symbol`` for a constant then that attribute
|
| 177 |
+
will not be included in the matrix returned by this property. This is
|
| 178 |
+
because the primary use of this property attribute is to provide an
|
| 179 |
+
ordered sequence of the still-free symbols that require numeric values
|
| 180 |
+
during code generation.
|
| 181 |
+
|
| 182 |
+
Explanation
|
| 183 |
+
===========
|
| 184 |
+
|
| 185 |
+
The alias ``p`` can also be used to access the same attribute.
|
| 186 |
+
|
| 187 |
+
"""
|
| 188 |
+
pass
|
| 189 |
+
|
| 190 |
+
@property
|
| 191 |
+
@abstractmethod
|
| 192 |
+
def p(self):
|
| 193 |
+
"""Ordered column matrix of non-time varying symbols present in ``M``
|
| 194 |
+
and ``F``.
|
| 195 |
+
|
| 196 |
+
Only symbolic constants are returned. If a numeric type (e.g. ``Float``)
|
| 197 |
+
has been used instead of ``Symbol`` for a constant then that attribute
|
| 198 |
+
will not be included in the matrix returned by this property. This is
|
| 199 |
+
because the primary use of this property attribute is to provide an
|
| 200 |
+
ordered sequence of the still-free symbols that require numeric values
|
| 201 |
+
during code generation.
|
| 202 |
+
|
| 203 |
+
Explanation
|
| 204 |
+
===========
|
| 205 |
+
|
| 206 |
+
The alias ``constants`` can also be used to access the same attribute.
|
| 207 |
+
|
| 208 |
+
"""
|
| 209 |
+
pass
|
| 210 |
+
|
| 211 |
+
@property
|
| 212 |
+
@abstractmethod
|
| 213 |
+
def M(self):
|
| 214 |
+
"""Ordered square matrix of coefficients on the LHS of ``M x' = F``.
|
| 215 |
+
|
| 216 |
+
Explanation
|
| 217 |
+
===========
|
| 218 |
+
|
| 219 |
+
The square matrix that forms part of the LHS of the linear system of
|
| 220 |
+
ordinary differential equations governing the activation dynamics:
|
| 221 |
+
|
| 222 |
+
``M(x, r, t, p) x' = F(x, r, t, p)``.
|
| 223 |
+
|
| 224 |
+
"""
|
| 225 |
+
pass
|
| 226 |
+
|
| 227 |
+
@property
|
| 228 |
+
@abstractmethod
|
| 229 |
+
def F(self):
|
| 230 |
+
"""Ordered column matrix of equations on the RHS of ``M x' = F``.
|
| 231 |
+
|
| 232 |
+
Explanation
|
| 233 |
+
===========
|
| 234 |
+
|
| 235 |
+
The column matrix that forms the RHS of the linear system of ordinary
|
| 236 |
+
differential equations governing the activation dynamics:
|
| 237 |
+
|
| 238 |
+
``M(x, r, t, p) x' = F(x, r, t, p)``.
|
| 239 |
+
|
| 240 |
+
"""
|
| 241 |
+
pass
|
| 242 |
+
|
| 243 |
+
@abstractmethod
|
| 244 |
+
def rhs(self):
|
| 245 |
+
"""
|
| 246 |
+
|
| 247 |
+
Explanation
|
| 248 |
+
===========
|
| 249 |
+
|
| 250 |
+
The solution to the linear system of ordinary differential equations
|
| 251 |
+
governing the activation dynamics:
|
| 252 |
+
|
| 253 |
+
``M(x, r, t, p) x' = F(x, r, t, p)``.
|
| 254 |
+
|
| 255 |
+
"""
|
| 256 |
+
pass
|
| 257 |
+
|
| 258 |
+
def __eq__(self, other):
|
| 259 |
+
"""Equality check for activation dynamics."""
|
| 260 |
+
if type(self) != type(other):
|
| 261 |
+
return False
|
| 262 |
+
if self.name != other.name:
|
| 263 |
+
return False
|
| 264 |
+
return True
|
| 265 |
+
|
| 266 |
+
def __repr__(self):
|
| 267 |
+
"""Default representation of activation dynamics."""
|
| 268 |
+
return f'{self.__class__.__name__}({self.name!r})'
|
| 269 |
+
|
| 270 |
+
|
| 271 |
+
class ZerothOrderActivation(ActivationBase):
|
| 272 |
+
"""Simple zeroth-order activation dynamics mapping excitation to
|
| 273 |
+
activation.
|
| 274 |
+
|
| 275 |
+
Explanation
|
| 276 |
+
===========
|
| 277 |
+
|
| 278 |
+
Zeroth-order activation dynamics are useful in instances where you want to
|
| 279 |
+
reduce the complexity of your musculotendon dynamics as they simple map
|
| 280 |
+
exictation to activation. As a result, no additional state equations are
|
| 281 |
+
introduced to your system. They also remove a potential source of delay
|
| 282 |
+
between the input and dynamics of your system as no (ordinary) differential
|
| 283 |
+
equations are involed.
|
| 284 |
+
|
| 285 |
+
"""
|
| 286 |
+
|
| 287 |
+
def __init__(self, name):
|
| 288 |
+
"""Initializer for ``ZerothOrderActivation``.
|
| 289 |
+
|
| 290 |
+
Parameters
|
| 291 |
+
==========
|
| 292 |
+
|
| 293 |
+
name : str
|
| 294 |
+
The name identifier associated with the instance. Must be a string
|
| 295 |
+
of length at least 1.
|
| 296 |
+
|
| 297 |
+
"""
|
| 298 |
+
super().__init__(name)
|
| 299 |
+
|
| 300 |
+
# Zeroth-order activation dynamics has activation equal excitation so
|
| 301 |
+
# overwrite the symbol for activation with the excitation symbol.
|
| 302 |
+
self._a = self._e
|
| 303 |
+
|
| 304 |
+
@classmethod
|
| 305 |
+
def with_defaults(cls, name):
|
| 306 |
+
"""Alternate constructor that provides recommended defaults for
|
| 307 |
+
constants.
|
| 308 |
+
|
| 309 |
+
Explanation
|
| 310 |
+
===========
|
| 311 |
+
|
| 312 |
+
As this concrete class doesn't implement any constants associated with
|
| 313 |
+
its dynamics, this ``classmethod`` simply creates a standard instance
|
| 314 |
+
of ``ZerothOrderActivation``. An implementation is provided to ensure
|
| 315 |
+
a consistent interface between all ``ActivationBase`` concrete classes.
|
| 316 |
+
|
| 317 |
+
"""
|
| 318 |
+
return cls(name)
|
| 319 |
+
|
| 320 |
+
@property
|
| 321 |
+
def order(self):
|
| 322 |
+
"""Order of the (differential) equation governing activation."""
|
| 323 |
+
return 0
|
| 324 |
+
|
| 325 |
+
@property
|
| 326 |
+
def state_vars(self):
|
| 327 |
+
"""Ordered column matrix of functions of time that represent the state
|
| 328 |
+
variables.
|
| 329 |
+
|
| 330 |
+
Explanation
|
| 331 |
+
===========
|
| 332 |
+
|
| 333 |
+
As zeroth-order activation dynamics simply maps excitation to
|
| 334 |
+
activation, this class has no associated state variables and so this
|
| 335 |
+
property return an empty column ``Matrix`` with shape (0, 1).
|
| 336 |
+
|
| 337 |
+
The alias ``x`` can also be used to access the same attribute.
|
| 338 |
+
|
| 339 |
+
"""
|
| 340 |
+
return zeros(0, 1)
|
| 341 |
+
|
| 342 |
+
@property
|
| 343 |
+
def x(self):
|
| 344 |
+
"""Ordered column matrix of functions of time that represent the state
|
| 345 |
+
variables.
|
| 346 |
+
|
| 347 |
+
Explanation
|
| 348 |
+
===========
|
| 349 |
+
|
| 350 |
+
As zeroth-order activation dynamics simply maps excitation to
|
| 351 |
+
activation, this class has no associated state variables and so this
|
| 352 |
+
property return an empty column ``Matrix`` with shape (0, 1).
|
| 353 |
+
|
| 354 |
+
The alias ``state_vars`` can also be used to access the same attribute.
|
| 355 |
+
|
| 356 |
+
"""
|
| 357 |
+
return zeros(0, 1)
|
| 358 |
+
|
| 359 |
+
@property
|
| 360 |
+
def input_vars(self):
|
| 361 |
+
"""Ordered column matrix of functions of time that represent the input
|
| 362 |
+
variables.
|
| 363 |
+
|
| 364 |
+
Explanation
|
| 365 |
+
===========
|
| 366 |
+
|
| 367 |
+
Excitation is the only input in zeroth-order activation dynamics and so
|
| 368 |
+
this property returns a column ``Matrix`` with one entry, ``e``, and
|
| 369 |
+
shape (1, 1).
|
| 370 |
+
|
| 371 |
+
The alias ``r`` can also be used to access the same attribute.
|
| 372 |
+
|
| 373 |
+
"""
|
| 374 |
+
return Matrix([self._e])
|
| 375 |
+
|
| 376 |
+
@property
|
| 377 |
+
def r(self):
|
| 378 |
+
"""Ordered column matrix of functions of time that represent the input
|
| 379 |
+
variables.
|
| 380 |
+
|
| 381 |
+
Explanation
|
| 382 |
+
===========
|
| 383 |
+
|
| 384 |
+
Excitation is the only input in zeroth-order activation dynamics and so
|
| 385 |
+
this property returns a column ``Matrix`` with one entry, ``e``, and
|
| 386 |
+
shape (1, 1).
|
| 387 |
+
|
| 388 |
+
The alias ``input_vars`` can also be used to access the same attribute.
|
| 389 |
+
|
| 390 |
+
"""
|
| 391 |
+
return Matrix([self._e])
|
| 392 |
+
|
| 393 |
+
@property
|
| 394 |
+
def constants(self):
|
| 395 |
+
"""Ordered column matrix of non-time varying symbols present in ``M``
|
| 396 |
+
and ``F``.
|
| 397 |
+
|
| 398 |
+
Only symbolic constants are returned. If a numeric type (e.g. ``Float``)
|
| 399 |
+
has been used instead of ``Symbol`` for a constant then that attribute
|
| 400 |
+
will not be included in the matrix returned by this property. This is
|
| 401 |
+
because the primary use of this property attribute is to provide an
|
| 402 |
+
ordered sequence of the still-free symbols that require numeric values
|
| 403 |
+
during code generation.
|
| 404 |
+
|
| 405 |
+
Explanation
|
| 406 |
+
===========
|
| 407 |
+
|
| 408 |
+
As zeroth-order activation dynamics simply maps excitation to
|
| 409 |
+
activation, this class has no associated constants and so this property
|
| 410 |
+
return an empty column ``Matrix`` with shape (0, 1).
|
| 411 |
+
|
| 412 |
+
The alias ``p`` can also be used to access the same attribute.
|
| 413 |
+
|
| 414 |
+
"""
|
| 415 |
+
return zeros(0, 1)
|
| 416 |
+
|
| 417 |
+
@property
|
| 418 |
+
def p(self):
|
| 419 |
+
"""Ordered column matrix of non-time varying symbols present in ``M``
|
| 420 |
+
and ``F``.
|
| 421 |
+
|
| 422 |
+
Only symbolic constants are returned. If a numeric type (e.g. ``Float``)
|
| 423 |
+
has been used instead of ``Symbol`` for a constant then that attribute
|
| 424 |
+
will not be included in the matrix returned by this property. This is
|
| 425 |
+
because the primary use of this property attribute is to provide an
|
| 426 |
+
ordered sequence of the still-free symbols that require numeric values
|
| 427 |
+
during code generation.
|
| 428 |
+
|
| 429 |
+
Explanation
|
| 430 |
+
===========
|
| 431 |
+
|
| 432 |
+
As zeroth-order activation dynamics simply maps excitation to
|
| 433 |
+
activation, this class has no associated constants and so this property
|
| 434 |
+
return an empty column ``Matrix`` with shape (0, 1).
|
| 435 |
+
|
| 436 |
+
The alias ``constants`` can also be used to access the same attribute.
|
| 437 |
+
|
| 438 |
+
"""
|
| 439 |
+
return zeros(0, 1)
|
| 440 |
+
|
| 441 |
+
@property
|
| 442 |
+
def M(self):
|
| 443 |
+
"""Ordered square matrix of coefficients on the LHS of ``M x' = F``.
|
| 444 |
+
|
| 445 |
+
Explanation
|
| 446 |
+
===========
|
| 447 |
+
|
| 448 |
+
The square matrix that forms part of the LHS of the linear system of
|
| 449 |
+
ordinary differential equations governing the activation dynamics:
|
| 450 |
+
|
| 451 |
+
``M(x, r, t, p) x' = F(x, r, t, p)``.
|
| 452 |
+
|
| 453 |
+
As zeroth-order activation dynamics have no state variables, this
|
| 454 |
+
linear system has dimension 0 and therefore ``M`` is an empty square
|
| 455 |
+
``Matrix`` with shape (0, 0).
|
| 456 |
+
|
| 457 |
+
"""
|
| 458 |
+
return Matrix([])
|
| 459 |
+
|
| 460 |
+
@property
|
| 461 |
+
def F(self):
|
| 462 |
+
"""Ordered column matrix of equations on the RHS of ``M x' = F``.
|
| 463 |
+
|
| 464 |
+
Explanation
|
| 465 |
+
===========
|
| 466 |
+
|
| 467 |
+
The column matrix that forms the RHS of the linear system of ordinary
|
| 468 |
+
differential equations governing the activation dynamics:
|
| 469 |
+
|
| 470 |
+
``M(x, r, t, p) x' = F(x, r, t, p)``.
|
| 471 |
+
|
| 472 |
+
As zeroth-order activation dynamics have no state variables, this
|
| 473 |
+
linear system has dimension 0 and therefore ``F`` is an empty column
|
| 474 |
+
``Matrix`` with shape (0, 1).
|
| 475 |
+
|
| 476 |
+
"""
|
| 477 |
+
return zeros(0, 1)
|
| 478 |
+
|
| 479 |
+
def rhs(self):
|
| 480 |
+
"""Ordered column matrix of equations for the solution of ``M x' = F``.
|
| 481 |
+
|
| 482 |
+
Explanation
|
| 483 |
+
===========
|
| 484 |
+
|
| 485 |
+
The solution to the linear system of ordinary differential equations
|
| 486 |
+
governing the activation dynamics:
|
| 487 |
+
|
| 488 |
+
``M(x, r, t, p) x' = F(x, r, t, p)``.
|
| 489 |
+
|
| 490 |
+
As zeroth-order activation dynamics have no state variables, this
|
| 491 |
+
linear has dimension 0 and therefore this method returns an empty
|
| 492 |
+
column ``Matrix`` with shape (0, 1).
|
| 493 |
+
|
| 494 |
+
"""
|
| 495 |
+
return zeros(0, 1)
|
| 496 |
+
|
| 497 |
+
|
| 498 |
+
class FirstOrderActivationDeGroote2016(ActivationBase):
|
| 499 |
+
r"""First-order activation dynamics based on De Groote et al., 2016 [1]_.
|
| 500 |
+
|
| 501 |
+
Explanation
|
| 502 |
+
===========
|
| 503 |
+
|
| 504 |
+
Gives the first-order activation dynamics equation for the rate of change
|
| 505 |
+
of activation with respect to time as a function of excitation and
|
| 506 |
+
activation.
|
| 507 |
+
|
| 508 |
+
The function is defined by the equation:
|
| 509 |
+
|
| 510 |
+
.. math::
|
| 511 |
+
|
| 512 |
+
\frac{da}{dt} = \left(\frac{\frac{1}{2} + a0}{\tau_a \left(\frac{1}{2}
|
| 513 |
+
+ \frac{3a}{2}\right)} + \frac{\left(\frac{1}{2}
|
| 514 |
+
+ \frac{3a}{2}\right) \left(\frac{1}{2} - a0\right)}{\tau_d}\right)
|
| 515 |
+
\left(e - a\right)
|
| 516 |
+
|
| 517 |
+
where
|
| 518 |
+
|
| 519 |
+
.. math::
|
| 520 |
+
|
| 521 |
+
a0 = \frac{\tanh{\left(b \left(e - a\right) \right)}}{2}
|
| 522 |
+
|
| 523 |
+
with constant values of :math:`tau_a = 0.015`, :math:`tau_d = 0.060`, and
|
| 524 |
+
:math:`b = 10`.
|
| 525 |
+
|
| 526 |
+
References
|
| 527 |
+
==========
|
| 528 |
+
|
| 529 |
+
.. [1] De Groote, F., Kinney, A. L., Rao, A. V., & Fregly, B. J., Evaluation
|
| 530 |
+
of direct collocation optimal control problem formulations for
|
| 531 |
+
solving the muscle redundancy problem, Annals of biomedical
|
| 532 |
+
engineering, 44(10), (2016) pp. 2922-2936
|
| 533 |
+
|
| 534 |
+
"""
|
| 535 |
+
|
| 536 |
+
def __init__(self,
|
| 537 |
+
name,
|
| 538 |
+
activation_time_constant=None,
|
| 539 |
+
deactivation_time_constant=None,
|
| 540 |
+
smoothing_rate=None,
|
| 541 |
+
):
|
| 542 |
+
"""Initializer for ``FirstOrderActivationDeGroote2016``.
|
| 543 |
+
|
| 544 |
+
Parameters
|
| 545 |
+
==========
|
| 546 |
+
activation time constant : Symbol | Number | None
|
| 547 |
+
The value of the activation time constant governing the delay
|
| 548 |
+
between excitation and activation when excitation exceeds
|
| 549 |
+
activation.
|
| 550 |
+
deactivation time constant : Symbol | Number | None
|
| 551 |
+
The value of the deactivation time constant governing the delay
|
| 552 |
+
between excitation and activation when activation exceeds
|
| 553 |
+
excitation.
|
| 554 |
+
smoothing_rate : Symbol | Number | None
|
| 555 |
+
The slope of the hyperbolic tangent function used to smooth between
|
| 556 |
+
the switching of the equations where excitation exceed activation
|
| 557 |
+
and where activation exceeds excitation. The recommended value to
|
| 558 |
+
use is ``10``, but values between ``0.1`` and ``100`` can be used.
|
| 559 |
+
|
| 560 |
+
"""
|
| 561 |
+
super().__init__(name)
|
| 562 |
+
|
| 563 |
+
# Symbols
|
| 564 |
+
self.activation_time_constant = activation_time_constant
|
| 565 |
+
self.deactivation_time_constant = deactivation_time_constant
|
| 566 |
+
self.smoothing_rate = smoothing_rate
|
| 567 |
+
|
| 568 |
+
@classmethod
|
| 569 |
+
def with_defaults(cls, name):
|
| 570 |
+
r"""Alternate constructor that will use the published constants.
|
| 571 |
+
|
| 572 |
+
Explanation
|
| 573 |
+
===========
|
| 574 |
+
|
| 575 |
+
Returns an instance of ``FirstOrderActivationDeGroote2016`` using the
|
| 576 |
+
three constant values specified in the original publication.
|
| 577 |
+
|
| 578 |
+
These have the values:
|
| 579 |
+
|
| 580 |
+
:math:`tau_a = 0.015`
|
| 581 |
+
:math:`tau_d = 0.060`
|
| 582 |
+
:math:`b = 10`
|
| 583 |
+
|
| 584 |
+
"""
|
| 585 |
+
tau_a = Float('0.015')
|
| 586 |
+
tau_d = Float('0.060')
|
| 587 |
+
b = Float('10.0')
|
| 588 |
+
return cls(name, tau_a, tau_d, b)
|
| 589 |
+
|
| 590 |
+
@property
|
| 591 |
+
def activation_time_constant(self):
|
| 592 |
+
"""Delay constant for activation.
|
| 593 |
+
|
| 594 |
+
Explanation
|
| 595 |
+
===========
|
| 596 |
+
|
| 597 |
+
The alias ```tau_a`` can also be used to access the same attribute.
|
| 598 |
+
|
| 599 |
+
"""
|
| 600 |
+
return self._tau_a
|
| 601 |
+
|
| 602 |
+
@activation_time_constant.setter
|
| 603 |
+
def activation_time_constant(self, tau_a):
|
| 604 |
+
if hasattr(self, '_tau_a'):
|
| 605 |
+
msg = (
|
| 606 |
+
f'Can\'t set attribute `activation_time_constant` to '
|
| 607 |
+
f'{repr(tau_a)} as it is immutable and already has value '
|
| 608 |
+
f'{self._tau_a}.'
|
| 609 |
+
)
|
| 610 |
+
raise AttributeError(msg)
|
| 611 |
+
self._tau_a = Symbol(f'tau_a_{self.name}') if tau_a is None else tau_a
|
| 612 |
+
|
| 613 |
+
@property
|
| 614 |
+
def tau_a(self):
|
| 615 |
+
"""Delay constant for activation.
|
| 616 |
+
|
| 617 |
+
Explanation
|
| 618 |
+
===========
|
| 619 |
+
|
| 620 |
+
The alias ``activation_time_constant`` can also be used to access the
|
| 621 |
+
same attribute.
|
| 622 |
+
|
| 623 |
+
"""
|
| 624 |
+
return self._tau_a
|
| 625 |
+
|
| 626 |
+
@property
|
| 627 |
+
def deactivation_time_constant(self):
|
| 628 |
+
"""Delay constant for deactivation.
|
| 629 |
+
|
| 630 |
+
Explanation
|
| 631 |
+
===========
|
| 632 |
+
|
| 633 |
+
The alias ``tau_d`` can also be used to access the same attribute.
|
| 634 |
+
|
| 635 |
+
"""
|
| 636 |
+
return self._tau_d
|
| 637 |
+
|
| 638 |
+
@deactivation_time_constant.setter
|
| 639 |
+
def deactivation_time_constant(self, tau_d):
|
| 640 |
+
if hasattr(self, '_tau_d'):
|
| 641 |
+
msg = (
|
| 642 |
+
f'Can\'t set attribute `deactivation_time_constant` to '
|
| 643 |
+
f'{repr(tau_d)} as it is immutable and already has value '
|
| 644 |
+
f'{self._tau_d}.'
|
| 645 |
+
)
|
| 646 |
+
raise AttributeError(msg)
|
| 647 |
+
self._tau_d = Symbol(f'tau_d_{self.name}') if tau_d is None else tau_d
|
| 648 |
+
|
| 649 |
+
@property
|
| 650 |
+
def tau_d(self):
|
| 651 |
+
"""Delay constant for deactivation.
|
| 652 |
+
|
| 653 |
+
Explanation
|
| 654 |
+
===========
|
| 655 |
+
|
| 656 |
+
The alias ``deactivation_time_constant`` can also be used to access the
|
| 657 |
+
same attribute.
|
| 658 |
+
|
| 659 |
+
"""
|
| 660 |
+
return self._tau_d
|
| 661 |
+
|
| 662 |
+
@property
|
| 663 |
+
def smoothing_rate(self):
|
| 664 |
+
"""Smoothing constant for the hyperbolic tangent term.
|
| 665 |
+
|
| 666 |
+
Explanation
|
| 667 |
+
===========
|
| 668 |
+
|
| 669 |
+
The alias ``b`` can also be used to access the same attribute.
|
| 670 |
+
|
| 671 |
+
"""
|
| 672 |
+
return self._b
|
| 673 |
+
|
| 674 |
+
@smoothing_rate.setter
|
| 675 |
+
def smoothing_rate(self, b):
|
| 676 |
+
if hasattr(self, '_b'):
|
| 677 |
+
msg = (
|
| 678 |
+
f'Can\'t set attribute `smoothing_rate` to {b!r} as it is '
|
| 679 |
+
f'immutable and already has value {self._b!r}.'
|
| 680 |
+
)
|
| 681 |
+
raise AttributeError(msg)
|
| 682 |
+
self._b = Symbol(f'b_{self.name}') if b is None else b
|
| 683 |
+
|
| 684 |
+
@property
|
| 685 |
+
def b(self):
|
| 686 |
+
"""Smoothing constant for the hyperbolic tangent term.
|
| 687 |
+
|
| 688 |
+
Explanation
|
| 689 |
+
===========
|
| 690 |
+
|
| 691 |
+
The alias ``smoothing_rate`` can also be used to access the same
|
| 692 |
+
attribute.
|
| 693 |
+
|
| 694 |
+
"""
|
| 695 |
+
return self._b
|
| 696 |
+
|
| 697 |
+
@property
|
| 698 |
+
def order(self):
|
| 699 |
+
"""Order of the (differential) equation governing activation."""
|
| 700 |
+
return 1
|
| 701 |
+
|
| 702 |
+
@property
|
| 703 |
+
def state_vars(self):
|
| 704 |
+
"""Ordered column matrix of functions of time that represent the state
|
| 705 |
+
variables.
|
| 706 |
+
|
| 707 |
+
Explanation
|
| 708 |
+
===========
|
| 709 |
+
|
| 710 |
+
The alias ``x`` can also be used to access the same attribute.
|
| 711 |
+
|
| 712 |
+
"""
|
| 713 |
+
return Matrix([self._a])
|
| 714 |
+
|
| 715 |
+
@property
|
| 716 |
+
def x(self):
|
| 717 |
+
"""Ordered column matrix of functions of time that represent the state
|
| 718 |
+
variables.
|
| 719 |
+
|
| 720 |
+
Explanation
|
| 721 |
+
===========
|
| 722 |
+
|
| 723 |
+
The alias ``state_vars`` can also be used to access the same attribute.
|
| 724 |
+
|
| 725 |
+
"""
|
| 726 |
+
return Matrix([self._a])
|
| 727 |
+
|
| 728 |
+
@property
|
| 729 |
+
def input_vars(self):
|
| 730 |
+
"""Ordered column matrix of functions of time that represent the input
|
| 731 |
+
variables.
|
| 732 |
+
|
| 733 |
+
Explanation
|
| 734 |
+
===========
|
| 735 |
+
|
| 736 |
+
The alias ``r`` can also be used to access the same attribute.
|
| 737 |
+
|
| 738 |
+
"""
|
| 739 |
+
return Matrix([self._e])
|
| 740 |
+
|
| 741 |
+
@property
|
| 742 |
+
def r(self):
|
| 743 |
+
"""Ordered column matrix of functions of time that represent the input
|
| 744 |
+
variables.
|
| 745 |
+
|
| 746 |
+
Explanation
|
| 747 |
+
===========
|
| 748 |
+
|
| 749 |
+
The alias ``input_vars`` can also be used to access the same attribute.
|
| 750 |
+
|
| 751 |
+
"""
|
| 752 |
+
return Matrix([self._e])
|
| 753 |
+
|
| 754 |
+
@property
|
| 755 |
+
def constants(self):
|
| 756 |
+
"""Ordered column matrix of non-time varying symbols present in ``M``
|
| 757 |
+
and ``F``.
|
| 758 |
+
|
| 759 |
+
Only symbolic constants are returned. If a numeric type (e.g. ``Float``)
|
| 760 |
+
has been used instead of ``Symbol`` for a constant then that attribute
|
| 761 |
+
will not be included in the matrix returned by this property. This is
|
| 762 |
+
because the primary use of this property attribute is to provide an
|
| 763 |
+
ordered sequence of the still-free symbols that require numeric values
|
| 764 |
+
during code generation.
|
| 765 |
+
|
| 766 |
+
Explanation
|
| 767 |
+
===========
|
| 768 |
+
|
| 769 |
+
The alias ``p`` can also be used to access the same attribute.
|
| 770 |
+
|
| 771 |
+
"""
|
| 772 |
+
constants = [self._tau_a, self._tau_d, self._b]
|
| 773 |
+
symbolic_constants = [c for c in constants if not c.is_number]
|
| 774 |
+
return Matrix(symbolic_constants) if symbolic_constants else zeros(0, 1)
|
| 775 |
+
|
| 776 |
+
@property
|
| 777 |
+
def p(self):
|
| 778 |
+
"""Ordered column matrix of non-time varying symbols present in ``M``
|
| 779 |
+
and ``F``.
|
| 780 |
+
|
| 781 |
+
Explanation
|
| 782 |
+
===========
|
| 783 |
+
|
| 784 |
+
Only symbolic constants are returned. If a numeric type (e.g. ``Float``)
|
| 785 |
+
has been used instead of ``Symbol`` for a constant then that attribute
|
| 786 |
+
will not be included in the matrix returned by this property. This is
|
| 787 |
+
because the primary use of this property attribute is to provide an
|
| 788 |
+
ordered sequence of the still-free symbols that require numeric values
|
| 789 |
+
during code generation.
|
| 790 |
+
|
| 791 |
+
The alias ``constants`` can also be used to access the same attribute.
|
| 792 |
+
|
| 793 |
+
"""
|
| 794 |
+
constants = [self._tau_a, self._tau_d, self._b]
|
| 795 |
+
symbolic_constants = [c for c in constants if not c.is_number]
|
| 796 |
+
return Matrix(symbolic_constants) if symbolic_constants else zeros(0, 1)
|
| 797 |
+
|
| 798 |
+
@property
|
| 799 |
+
def M(self):
|
| 800 |
+
"""Ordered square matrix of coefficients on the LHS of ``M x' = F``.
|
| 801 |
+
|
| 802 |
+
Explanation
|
| 803 |
+
===========
|
| 804 |
+
|
| 805 |
+
The square matrix that forms part of the LHS of the linear system of
|
| 806 |
+
ordinary differential equations governing the activation dynamics:
|
| 807 |
+
|
| 808 |
+
``M(x, r, t, p) x' = F(x, r, t, p)``.
|
| 809 |
+
|
| 810 |
+
"""
|
| 811 |
+
return Matrix([Integer(1)])
|
| 812 |
+
|
| 813 |
+
@property
|
| 814 |
+
def F(self):
|
| 815 |
+
"""Ordered column matrix of equations on the RHS of ``M x' = F``.
|
| 816 |
+
|
| 817 |
+
Explanation
|
| 818 |
+
===========
|
| 819 |
+
|
| 820 |
+
The column matrix that forms the RHS of the linear system of ordinary
|
| 821 |
+
differential equations governing the activation dynamics:
|
| 822 |
+
|
| 823 |
+
``M(x, r, t, p) x' = F(x, r, t, p)``.
|
| 824 |
+
|
| 825 |
+
"""
|
| 826 |
+
return Matrix([self._da_eqn])
|
| 827 |
+
|
| 828 |
+
def rhs(self):
|
| 829 |
+
"""Ordered column matrix of equations for the solution of ``M x' = F``.
|
| 830 |
+
|
| 831 |
+
Explanation
|
| 832 |
+
===========
|
| 833 |
+
|
| 834 |
+
The solution to the linear system of ordinary differential equations
|
| 835 |
+
governing the activation dynamics:
|
| 836 |
+
|
| 837 |
+
``M(x, r, t, p) x' = F(x, r, t, p)``.
|
| 838 |
+
|
| 839 |
+
"""
|
| 840 |
+
return Matrix([self._da_eqn])
|
| 841 |
+
|
| 842 |
+
@cached_property
|
| 843 |
+
def _da_eqn(self):
|
| 844 |
+
HALF = Rational(1, 2)
|
| 845 |
+
a0 = HALF * tanh(self._b * (self._e - self._a))
|
| 846 |
+
a1 = (HALF + Rational(3, 2) * self._a)
|
| 847 |
+
a2 = (HALF + a0) / (self._tau_a * a1)
|
| 848 |
+
a3 = a1 * (HALF - a0) / self._tau_d
|
| 849 |
+
activation_dynamics_equation = (a2 + a3) * (self._e - self._a)
|
| 850 |
+
return activation_dynamics_equation
|
| 851 |
+
|
| 852 |
+
def __eq__(self, other):
|
| 853 |
+
"""Equality check for ``FirstOrderActivationDeGroote2016``."""
|
| 854 |
+
if type(self) != type(other):
|
| 855 |
+
return False
|
| 856 |
+
self_attrs = (self.name, self.tau_a, self.tau_d, self.b)
|
| 857 |
+
other_attrs = (other.name, other.tau_a, other.tau_d, other.b)
|
| 858 |
+
if self_attrs == other_attrs:
|
| 859 |
+
return True
|
| 860 |
+
return False
|
| 861 |
+
|
| 862 |
+
def __repr__(self):
|
| 863 |
+
"""Representation of ``FirstOrderActivationDeGroote2016``."""
|
| 864 |
+
return (
|
| 865 |
+
f'{self.__class__.__name__}({self.name!r}, '
|
| 866 |
+
f'activation_time_constant={self.tau_a!r}, '
|
| 867 |
+
f'deactivation_time_constant={self.tau_d!r}, '
|
| 868 |
+
f'smoothing_rate={self.b!r})'
|
| 869 |
+
)
|
evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/curve.py
ADDED
|
@@ -0,0 +1,1763 @@
|
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|
| 1 |
+
"""Implementations of characteristic curves for musculotendon models."""
|
| 2 |
+
|
| 3 |
+
from dataclasses import dataclass
|
| 4 |
+
|
| 5 |
+
from sympy.core.expr import UnevaluatedExpr
|
| 6 |
+
from sympy.core.function import ArgumentIndexError, Function
|
| 7 |
+
from sympy.core.numbers import Float, Integer
|
| 8 |
+
from sympy.functions.elementary.exponential import exp, log
|
| 9 |
+
from sympy.functions.elementary.hyperbolic import cosh, sinh
|
| 10 |
+
from sympy.functions.elementary.miscellaneous import sqrt
|
| 11 |
+
from sympy.printing.precedence import PRECEDENCE
|
| 12 |
+
|
| 13 |
+
|
| 14 |
+
__all__ = [
|
| 15 |
+
'CharacteristicCurveCollection',
|
| 16 |
+
'CharacteristicCurveFunction',
|
| 17 |
+
'FiberForceLengthActiveDeGroote2016',
|
| 18 |
+
'FiberForceLengthPassiveDeGroote2016',
|
| 19 |
+
'FiberForceLengthPassiveInverseDeGroote2016',
|
| 20 |
+
'FiberForceVelocityDeGroote2016',
|
| 21 |
+
'FiberForceVelocityInverseDeGroote2016',
|
| 22 |
+
'TendonForceLengthDeGroote2016',
|
| 23 |
+
'TendonForceLengthInverseDeGroote2016',
|
| 24 |
+
]
|
| 25 |
+
|
| 26 |
+
|
| 27 |
+
class CharacteristicCurveFunction(Function):
|
| 28 |
+
"""Base class for all musculotendon characteristic curve functions."""
|
| 29 |
+
|
| 30 |
+
@classmethod
|
| 31 |
+
def eval(cls):
|
| 32 |
+
msg = (
|
| 33 |
+
f'Cannot directly instantiate {cls.__name__!r}, instances of '
|
| 34 |
+
f'characteristic curves must be of a concrete subclass.'
|
| 35 |
+
|
| 36 |
+
)
|
| 37 |
+
raise TypeError(msg)
|
| 38 |
+
|
| 39 |
+
def _print_code(self, printer):
|
| 40 |
+
"""Print code for the function defining the curve using a printer.
|
| 41 |
+
|
| 42 |
+
Explanation
|
| 43 |
+
===========
|
| 44 |
+
|
| 45 |
+
The order of operations may need to be controlled as constant folding
|
| 46 |
+
the numeric terms within the equations of a musculotendon
|
| 47 |
+
characteristic curve can sometimes results in a numerically-unstable
|
| 48 |
+
expression.
|
| 49 |
+
|
| 50 |
+
Parameters
|
| 51 |
+
==========
|
| 52 |
+
|
| 53 |
+
printer : Printer
|
| 54 |
+
The printer to be used to print a string representation of the
|
| 55 |
+
characteristic curve as valid code in the target language.
|
| 56 |
+
|
| 57 |
+
"""
|
| 58 |
+
return printer._print(printer.parenthesize(
|
| 59 |
+
self.doit(deep=False, evaluate=False), PRECEDENCE['Atom'],
|
| 60 |
+
))
|
| 61 |
+
|
| 62 |
+
_ccode = _print_code
|
| 63 |
+
_cupycode = _print_code
|
| 64 |
+
_cxxcode = _print_code
|
| 65 |
+
_fcode = _print_code
|
| 66 |
+
_jaxcode = _print_code
|
| 67 |
+
_lambdacode = _print_code
|
| 68 |
+
_mpmathcode = _print_code
|
| 69 |
+
_octave = _print_code
|
| 70 |
+
_pythoncode = _print_code
|
| 71 |
+
_numpycode = _print_code
|
| 72 |
+
_scipycode = _print_code
|
| 73 |
+
|
| 74 |
+
|
| 75 |
+
class TendonForceLengthDeGroote2016(CharacteristicCurveFunction):
|
| 76 |
+
r"""Tendon force-length curve based on De Groote et al., 2016 [1]_.
|
| 77 |
+
|
| 78 |
+
Explanation
|
| 79 |
+
===========
|
| 80 |
+
|
| 81 |
+
Gives the normalized tendon force produced as a function of normalized
|
| 82 |
+
tendon length.
|
| 83 |
+
|
| 84 |
+
The function is defined by the equation:
|
| 85 |
+
|
| 86 |
+
$fl^T = c_0 \exp{c_3 \left( \tilde{l}^T - c_1 \right)} - c_2$
|
| 87 |
+
|
| 88 |
+
with constant values of $c_0 = 0.2$, $c_1 = 0.995$, $c_2 = 0.25$, and
|
| 89 |
+
$c_3 = 33.93669377311689$.
|
| 90 |
+
|
| 91 |
+
While it is possible to change the constant values, these were carefully
|
| 92 |
+
selected in the original publication to give the characteristic curve
|
| 93 |
+
specific and required properties. For example, the function produces no
|
| 94 |
+
force when the tendon is in an unstrained state. It also produces a force
|
| 95 |
+
of 1 normalized unit when the tendon is under a 5% strain.
|
| 96 |
+
|
| 97 |
+
Examples
|
| 98 |
+
========
|
| 99 |
+
|
| 100 |
+
The preferred way to instantiate :class:`TendonForceLengthDeGroote2016` is using
|
| 101 |
+
the :meth:`~.with_defaults` constructor because this will automatically
|
| 102 |
+
populate the constants within the characteristic curve equation with the
|
| 103 |
+
floating point values from the original publication. This constructor takes
|
| 104 |
+
a single argument corresponding to normalized tendon length. We'll create a
|
| 105 |
+
:class:`~.Symbol` called ``l_T_tilde`` to represent this.
|
| 106 |
+
|
| 107 |
+
>>> from sympy import Symbol
|
| 108 |
+
>>> from sympy.physics.biomechanics import TendonForceLengthDeGroote2016
|
| 109 |
+
>>> l_T_tilde = Symbol('l_T_tilde')
|
| 110 |
+
>>> fl_T = TendonForceLengthDeGroote2016.with_defaults(l_T_tilde)
|
| 111 |
+
>>> fl_T
|
| 112 |
+
TendonForceLengthDeGroote2016(l_T_tilde, 0.2, 0.995, 0.25,
|
| 113 |
+
33.93669377311689)
|
| 114 |
+
|
| 115 |
+
It's also possible to populate the four constants with your own values too.
|
| 116 |
+
|
| 117 |
+
>>> from sympy import symbols
|
| 118 |
+
>>> c0, c1, c2, c3 = symbols('c0 c1 c2 c3')
|
| 119 |
+
>>> fl_T = TendonForceLengthDeGroote2016(l_T_tilde, c0, c1, c2, c3)
|
| 120 |
+
>>> fl_T
|
| 121 |
+
TendonForceLengthDeGroote2016(l_T_tilde, c0, c1, c2, c3)
|
| 122 |
+
|
| 123 |
+
You don't just have to use symbols as the arguments, it's also possible to
|
| 124 |
+
use expressions. Let's create a new pair of symbols, ``l_T`` and
|
| 125 |
+
``l_T_slack``, representing tendon length and tendon slack length
|
| 126 |
+
respectively. We can then represent ``l_T_tilde`` as an expression, the
|
| 127 |
+
ratio of these.
|
| 128 |
+
|
| 129 |
+
>>> l_T, l_T_slack = symbols('l_T l_T_slack')
|
| 130 |
+
>>> l_T_tilde = l_T/l_T_slack
|
| 131 |
+
>>> fl_T = TendonForceLengthDeGroote2016.with_defaults(l_T_tilde)
|
| 132 |
+
>>> fl_T
|
| 133 |
+
TendonForceLengthDeGroote2016(l_T/l_T_slack, 0.2, 0.995, 0.25,
|
| 134 |
+
33.93669377311689)
|
| 135 |
+
|
| 136 |
+
To inspect the actual symbolic expression that this function represents,
|
| 137 |
+
we can call the :meth:`~.doit` method on an instance. We'll use the keyword
|
| 138 |
+
argument ``evaluate=False`` as this will keep the expression in its
|
| 139 |
+
canonical form and won't simplify any constants.
|
| 140 |
+
|
| 141 |
+
>>> fl_T.doit(evaluate=False)
|
| 142 |
+
-0.25 + 0.2*exp(33.93669377311689*(l_T/l_T_slack - 0.995))
|
| 143 |
+
|
| 144 |
+
The function can also be differentiated. We'll differentiate with respect
|
| 145 |
+
to l_T using the ``diff`` method on an instance with the single positional
|
| 146 |
+
argument ``l_T``.
|
| 147 |
+
|
| 148 |
+
>>> fl_T.diff(l_T)
|
| 149 |
+
6.787338754623378*exp(33.93669377311689*(l_T/l_T_slack - 0.995))/l_T_slack
|
| 150 |
+
|
| 151 |
+
References
|
| 152 |
+
==========
|
| 153 |
+
|
| 154 |
+
.. [1] De Groote, F., Kinney, A. L., Rao, A. V., & Fregly, B. J., Evaluation
|
| 155 |
+
of direct collocation optimal control problem formulations for
|
| 156 |
+
solving the muscle redundancy problem, Annals of biomedical
|
| 157 |
+
engineering, 44(10), (2016) pp. 2922-2936
|
| 158 |
+
|
| 159 |
+
"""
|
| 160 |
+
|
| 161 |
+
@classmethod
|
| 162 |
+
def with_defaults(cls, l_T_tilde):
|
| 163 |
+
r"""Recommended constructor that will use the published constants.
|
| 164 |
+
|
| 165 |
+
Explanation
|
| 166 |
+
===========
|
| 167 |
+
|
| 168 |
+
Returns a new instance of the tendon force-length function using the
|
| 169 |
+
four constant values specified in the original publication.
|
| 170 |
+
|
| 171 |
+
These have the values:
|
| 172 |
+
|
| 173 |
+
$c_0 = 0.2$
|
| 174 |
+
$c_1 = 0.995$
|
| 175 |
+
$c_2 = 0.25$
|
| 176 |
+
$c_3 = 33.93669377311689$
|
| 177 |
+
|
| 178 |
+
Parameters
|
| 179 |
+
==========
|
| 180 |
+
|
| 181 |
+
l_T_tilde : Any (sympifiable)
|
| 182 |
+
Normalized tendon length.
|
| 183 |
+
|
| 184 |
+
"""
|
| 185 |
+
c0 = Float('0.2')
|
| 186 |
+
c1 = Float('0.995')
|
| 187 |
+
c2 = Float('0.25')
|
| 188 |
+
c3 = Float('33.93669377311689')
|
| 189 |
+
return cls(l_T_tilde, c0, c1, c2, c3)
|
| 190 |
+
|
| 191 |
+
@classmethod
|
| 192 |
+
def eval(cls, l_T_tilde, c0, c1, c2, c3):
|
| 193 |
+
"""Evaluation of basic inputs.
|
| 194 |
+
|
| 195 |
+
Parameters
|
| 196 |
+
==========
|
| 197 |
+
|
| 198 |
+
l_T_tilde : Any (sympifiable)
|
| 199 |
+
Normalized tendon length.
|
| 200 |
+
c0 : Any (sympifiable)
|
| 201 |
+
The first constant in the characteristic equation. The published
|
| 202 |
+
value is ``0.2``.
|
| 203 |
+
c1 : Any (sympifiable)
|
| 204 |
+
The second constant in the characteristic equation. The published
|
| 205 |
+
value is ``0.995``.
|
| 206 |
+
c2 : Any (sympifiable)
|
| 207 |
+
The third constant in the characteristic equation. The published
|
| 208 |
+
value is ``0.25``.
|
| 209 |
+
c3 : Any (sympifiable)
|
| 210 |
+
The fourth constant in the characteristic equation. The published
|
| 211 |
+
value is ``33.93669377311689``.
|
| 212 |
+
|
| 213 |
+
"""
|
| 214 |
+
pass
|
| 215 |
+
|
| 216 |
+
def _eval_evalf(self, prec):
|
| 217 |
+
"""Evaluate the expression numerically using ``evalf``."""
|
| 218 |
+
return self.doit(deep=False, evaluate=False)._eval_evalf(prec)
|
| 219 |
+
|
| 220 |
+
def doit(self, deep=True, evaluate=True, **hints):
|
| 221 |
+
"""Evaluate the expression defining the function.
|
| 222 |
+
|
| 223 |
+
Parameters
|
| 224 |
+
==========
|
| 225 |
+
|
| 226 |
+
deep : bool
|
| 227 |
+
Whether ``doit`` should be recursively called. Default is ``True``.
|
| 228 |
+
evaluate : bool.
|
| 229 |
+
Whether the SymPy expression should be evaluated as it is
|
| 230 |
+
constructed. If ``False``, then no constant folding will be
|
| 231 |
+
conducted which will leave the expression in a more numerically-
|
| 232 |
+
stable for values of ``l_T_tilde`` that correspond to a sensible
|
| 233 |
+
operating range for a musculotendon. Default is ``True``.
|
| 234 |
+
**kwargs : dict[str, Any]
|
| 235 |
+
Additional keyword argument pairs to be recursively passed to
|
| 236 |
+
``doit``.
|
| 237 |
+
|
| 238 |
+
"""
|
| 239 |
+
l_T_tilde, *constants = self.args
|
| 240 |
+
if deep:
|
| 241 |
+
hints['evaluate'] = evaluate
|
| 242 |
+
l_T_tilde = l_T_tilde.doit(deep=deep, **hints)
|
| 243 |
+
c0, c1, c2, c3 = [c.doit(deep=deep, **hints) for c in constants]
|
| 244 |
+
else:
|
| 245 |
+
c0, c1, c2, c3 = constants
|
| 246 |
+
|
| 247 |
+
if evaluate:
|
| 248 |
+
return c0*exp(c3*(l_T_tilde - c1)) - c2
|
| 249 |
+
|
| 250 |
+
return c0*exp(c3*UnevaluatedExpr(l_T_tilde - c1)) - c2
|
| 251 |
+
|
| 252 |
+
def fdiff(self, argindex=1):
|
| 253 |
+
"""Derivative of the function with respect to a single argument.
|
| 254 |
+
|
| 255 |
+
Parameters
|
| 256 |
+
==========
|
| 257 |
+
|
| 258 |
+
argindex : int
|
| 259 |
+
The index of the function's arguments with respect to which the
|
| 260 |
+
derivative should be taken. Argument indexes start at ``1``.
|
| 261 |
+
Default is ``1``.
|
| 262 |
+
|
| 263 |
+
"""
|
| 264 |
+
l_T_tilde, c0, c1, c2, c3 = self.args
|
| 265 |
+
if argindex == 1:
|
| 266 |
+
return c0*c3*exp(c3*UnevaluatedExpr(l_T_tilde - c1))
|
| 267 |
+
elif argindex == 2:
|
| 268 |
+
return exp(c3*UnevaluatedExpr(l_T_tilde - c1))
|
| 269 |
+
elif argindex == 3:
|
| 270 |
+
return -c0*c3*exp(c3*UnevaluatedExpr(l_T_tilde - c1))
|
| 271 |
+
elif argindex == 4:
|
| 272 |
+
return Integer(-1)
|
| 273 |
+
elif argindex == 5:
|
| 274 |
+
return c0*(l_T_tilde - c1)*exp(c3*UnevaluatedExpr(l_T_tilde - c1))
|
| 275 |
+
|
| 276 |
+
raise ArgumentIndexError(self, argindex)
|
| 277 |
+
|
| 278 |
+
def inverse(self, argindex=1):
|
| 279 |
+
"""Inverse function.
|
| 280 |
+
|
| 281 |
+
Parameters
|
| 282 |
+
==========
|
| 283 |
+
|
| 284 |
+
argindex : int
|
| 285 |
+
Value to start indexing the arguments at. Default is ``1``.
|
| 286 |
+
|
| 287 |
+
"""
|
| 288 |
+
return TendonForceLengthInverseDeGroote2016
|
| 289 |
+
|
| 290 |
+
def _latex(self, printer):
|
| 291 |
+
"""Print a LaTeX representation of the function defining the curve.
|
| 292 |
+
|
| 293 |
+
Parameters
|
| 294 |
+
==========
|
| 295 |
+
|
| 296 |
+
printer : Printer
|
| 297 |
+
The printer to be used to print the LaTeX string representation.
|
| 298 |
+
|
| 299 |
+
"""
|
| 300 |
+
l_T_tilde = self.args[0]
|
| 301 |
+
_l_T_tilde = printer._print(l_T_tilde)
|
| 302 |
+
return r'\operatorname{fl}^T \left( %s \right)' % _l_T_tilde
|
| 303 |
+
|
| 304 |
+
|
| 305 |
+
class TendonForceLengthInverseDeGroote2016(CharacteristicCurveFunction):
|
| 306 |
+
r"""Inverse tendon force-length curve based on De Groote et al., 2016 [1]_.
|
| 307 |
+
|
| 308 |
+
Explanation
|
| 309 |
+
===========
|
| 310 |
+
|
| 311 |
+
Gives the normalized tendon length that produces a specific normalized
|
| 312 |
+
tendon force.
|
| 313 |
+
|
| 314 |
+
The function is defined by the equation:
|
| 315 |
+
|
| 316 |
+
${fl^T}^{-1} = frac{\log{\frac{fl^T + c_2}{c_0}}}{c_3} + c_1$
|
| 317 |
+
|
| 318 |
+
with constant values of $c_0 = 0.2$, $c_1 = 0.995$, $c_2 = 0.25$, and
|
| 319 |
+
$c_3 = 33.93669377311689$. This function is the exact analytical inverse
|
| 320 |
+
of the related tendon force-length curve ``TendonForceLengthDeGroote2016``.
|
| 321 |
+
|
| 322 |
+
While it is possible to change the constant values, these were carefully
|
| 323 |
+
selected in the original publication to give the characteristic curve
|
| 324 |
+
specific and required properties. For example, the function produces no
|
| 325 |
+
force when the tendon is in an unstrained state. It also produces a force
|
| 326 |
+
of 1 normalized unit when the tendon is under a 5% strain.
|
| 327 |
+
|
| 328 |
+
Examples
|
| 329 |
+
========
|
| 330 |
+
|
| 331 |
+
The preferred way to instantiate :class:`TendonForceLengthInverseDeGroote2016` is
|
| 332 |
+
using the :meth:`~.with_defaults` constructor because this will automatically
|
| 333 |
+
populate the constants within the characteristic curve equation with the
|
| 334 |
+
floating point values from the original publication. This constructor takes
|
| 335 |
+
a single argument corresponding to normalized tendon force-length, which is
|
| 336 |
+
equal to the tendon force. We'll create a :class:`~.Symbol` called ``fl_T`` to
|
| 337 |
+
represent this.
|
| 338 |
+
|
| 339 |
+
>>> from sympy import Symbol
|
| 340 |
+
>>> from sympy.physics.biomechanics import TendonForceLengthInverseDeGroote2016
|
| 341 |
+
>>> fl_T = Symbol('fl_T')
|
| 342 |
+
>>> l_T_tilde = TendonForceLengthInverseDeGroote2016.with_defaults(fl_T)
|
| 343 |
+
>>> l_T_tilde
|
| 344 |
+
TendonForceLengthInverseDeGroote2016(fl_T, 0.2, 0.995, 0.25,
|
| 345 |
+
33.93669377311689)
|
| 346 |
+
|
| 347 |
+
It's also possible to populate the four constants with your own values too.
|
| 348 |
+
|
| 349 |
+
>>> from sympy import symbols
|
| 350 |
+
>>> c0, c1, c2, c3 = symbols('c0 c1 c2 c3')
|
| 351 |
+
>>> l_T_tilde = TendonForceLengthInverseDeGroote2016(fl_T, c0, c1, c2, c3)
|
| 352 |
+
>>> l_T_tilde
|
| 353 |
+
TendonForceLengthInverseDeGroote2016(fl_T, c0, c1, c2, c3)
|
| 354 |
+
|
| 355 |
+
To inspect the actual symbolic expression that this function represents,
|
| 356 |
+
we can call the :meth:`~.doit` method on an instance. We'll use the keyword
|
| 357 |
+
argument ``evaluate=False`` as this will keep the expression in its
|
| 358 |
+
canonical form and won't simplify any constants.
|
| 359 |
+
|
| 360 |
+
>>> l_T_tilde.doit(evaluate=False)
|
| 361 |
+
c1 + log((c2 + fl_T)/c0)/c3
|
| 362 |
+
|
| 363 |
+
The function can also be differentiated. We'll differentiate with respect
|
| 364 |
+
to l_T using the ``diff`` method on an instance with the single positional
|
| 365 |
+
argument ``l_T``.
|
| 366 |
+
|
| 367 |
+
>>> l_T_tilde.diff(fl_T)
|
| 368 |
+
1/(c3*(c2 + fl_T))
|
| 369 |
+
|
| 370 |
+
References
|
| 371 |
+
==========
|
| 372 |
+
|
| 373 |
+
.. [1] De Groote, F., Kinney, A. L., Rao, A. V., & Fregly, B. J., Evaluation
|
| 374 |
+
of direct collocation optimal control problem formulations for
|
| 375 |
+
solving the muscle redundancy problem, Annals of biomedical
|
| 376 |
+
engineering, 44(10), (2016) pp. 2922-2936
|
| 377 |
+
|
| 378 |
+
"""
|
| 379 |
+
|
| 380 |
+
@classmethod
|
| 381 |
+
def with_defaults(cls, fl_T):
|
| 382 |
+
r"""Recommended constructor that will use the published constants.
|
| 383 |
+
|
| 384 |
+
Explanation
|
| 385 |
+
===========
|
| 386 |
+
|
| 387 |
+
Returns a new instance of the inverse tendon force-length function
|
| 388 |
+
using the four constant values specified in the original publication.
|
| 389 |
+
|
| 390 |
+
These have the values:
|
| 391 |
+
|
| 392 |
+
$c_0 = 0.2$
|
| 393 |
+
$c_1 = 0.995$
|
| 394 |
+
$c_2 = 0.25$
|
| 395 |
+
$c_3 = 33.93669377311689$
|
| 396 |
+
|
| 397 |
+
Parameters
|
| 398 |
+
==========
|
| 399 |
+
|
| 400 |
+
fl_T : Any (sympifiable)
|
| 401 |
+
Normalized tendon force as a function of tendon length.
|
| 402 |
+
|
| 403 |
+
"""
|
| 404 |
+
c0 = Float('0.2')
|
| 405 |
+
c1 = Float('0.995')
|
| 406 |
+
c2 = Float('0.25')
|
| 407 |
+
c3 = Float('33.93669377311689')
|
| 408 |
+
return cls(fl_T, c0, c1, c2, c3)
|
| 409 |
+
|
| 410 |
+
@classmethod
|
| 411 |
+
def eval(cls, fl_T, c0, c1, c2, c3):
|
| 412 |
+
"""Evaluation of basic inputs.
|
| 413 |
+
|
| 414 |
+
Parameters
|
| 415 |
+
==========
|
| 416 |
+
|
| 417 |
+
fl_T : Any (sympifiable)
|
| 418 |
+
Normalized tendon force as a function of tendon length.
|
| 419 |
+
c0 : Any (sympifiable)
|
| 420 |
+
The first constant in the characteristic equation. The published
|
| 421 |
+
value is ``0.2``.
|
| 422 |
+
c1 : Any (sympifiable)
|
| 423 |
+
The second constant in the characteristic equation. The published
|
| 424 |
+
value is ``0.995``.
|
| 425 |
+
c2 : Any (sympifiable)
|
| 426 |
+
The third constant in the characteristic equation. The published
|
| 427 |
+
value is ``0.25``.
|
| 428 |
+
c3 : Any (sympifiable)
|
| 429 |
+
The fourth constant in the characteristic equation. The published
|
| 430 |
+
value is ``33.93669377311689``.
|
| 431 |
+
|
| 432 |
+
"""
|
| 433 |
+
pass
|
| 434 |
+
|
| 435 |
+
def _eval_evalf(self, prec):
|
| 436 |
+
"""Evaluate the expression numerically using ``evalf``."""
|
| 437 |
+
return self.doit(deep=False, evaluate=False)._eval_evalf(prec)
|
| 438 |
+
|
| 439 |
+
def doit(self, deep=True, evaluate=True, **hints):
|
| 440 |
+
"""Evaluate the expression defining the function.
|
| 441 |
+
|
| 442 |
+
Parameters
|
| 443 |
+
==========
|
| 444 |
+
|
| 445 |
+
deep : bool
|
| 446 |
+
Whether ``doit`` should be recursively called. Default is ``True``.
|
| 447 |
+
evaluate : bool.
|
| 448 |
+
Whether the SymPy expression should be evaluated as it is
|
| 449 |
+
constructed. If ``False``, then no constant folding will be
|
| 450 |
+
conducted which will leave the expression in a more numerically-
|
| 451 |
+
stable for values of ``l_T_tilde`` that correspond to a sensible
|
| 452 |
+
operating range for a musculotendon. Default is ``True``.
|
| 453 |
+
**kwargs : dict[str, Any]
|
| 454 |
+
Additional keyword argument pairs to be recursively passed to
|
| 455 |
+
``doit``.
|
| 456 |
+
|
| 457 |
+
"""
|
| 458 |
+
fl_T, *constants = self.args
|
| 459 |
+
if deep:
|
| 460 |
+
hints['evaluate'] = evaluate
|
| 461 |
+
fl_T = fl_T.doit(deep=deep, **hints)
|
| 462 |
+
c0, c1, c2, c3 = [c.doit(deep=deep, **hints) for c in constants]
|
| 463 |
+
else:
|
| 464 |
+
c0, c1, c2, c3 = constants
|
| 465 |
+
|
| 466 |
+
if evaluate:
|
| 467 |
+
return log((fl_T + c2)/c0)/c3 + c1
|
| 468 |
+
|
| 469 |
+
return log(UnevaluatedExpr((fl_T + c2)/c0))/c3 + c1
|
| 470 |
+
|
| 471 |
+
def fdiff(self, argindex=1):
|
| 472 |
+
"""Derivative of the function with respect to a single argument.
|
| 473 |
+
|
| 474 |
+
Parameters
|
| 475 |
+
==========
|
| 476 |
+
|
| 477 |
+
argindex : int
|
| 478 |
+
The index of the function's arguments with respect to which the
|
| 479 |
+
derivative should be taken. Argument indexes start at ``1``.
|
| 480 |
+
Default is ``1``.
|
| 481 |
+
|
| 482 |
+
"""
|
| 483 |
+
fl_T, c0, c1, c2, c3 = self.args
|
| 484 |
+
if argindex == 1:
|
| 485 |
+
return 1/(c3*(fl_T + c2))
|
| 486 |
+
elif argindex == 2:
|
| 487 |
+
return -1/(c0*c3)
|
| 488 |
+
elif argindex == 3:
|
| 489 |
+
return Integer(1)
|
| 490 |
+
elif argindex == 4:
|
| 491 |
+
return 1/(c3*(fl_T + c2))
|
| 492 |
+
elif argindex == 5:
|
| 493 |
+
return -log(UnevaluatedExpr((fl_T + c2)/c0))/c3**2
|
| 494 |
+
|
| 495 |
+
raise ArgumentIndexError(self, argindex)
|
| 496 |
+
|
| 497 |
+
def inverse(self, argindex=1):
|
| 498 |
+
"""Inverse function.
|
| 499 |
+
|
| 500 |
+
Parameters
|
| 501 |
+
==========
|
| 502 |
+
|
| 503 |
+
argindex : int
|
| 504 |
+
Value to start indexing the arguments at. Default is ``1``.
|
| 505 |
+
|
| 506 |
+
"""
|
| 507 |
+
return TendonForceLengthDeGroote2016
|
| 508 |
+
|
| 509 |
+
def _latex(self, printer):
|
| 510 |
+
"""Print a LaTeX representation of the function defining the curve.
|
| 511 |
+
|
| 512 |
+
Parameters
|
| 513 |
+
==========
|
| 514 |
+
|
| 515 |
+
printer : Printer
|
| 516 |
+
The printer to be used to print the LaTeX string representation.
|
| 517 |
+
|
| 518 |
+
"""
|
| 519 |
+
fl_T = self.args[0]
|
| 520 |
+
_fl_T = printer._print(fl_T)
|
| 521 |
+
return r'\left( \operatorname{fl}^T \right)^{-1} \left( %s \right)' % _fl_T
|
| 522 |
+
|
| 523 |
+
|
| 524 |
+
class FiberForceLengthPassiveDeGroote2016(CharacteristicCurveFunction):
|
| 525 |
+
r"""Passive muscle fiber force-length curve based on De Groote et al., 2016
|
| 526 |
+
[1]_.
|
| 527 |
+
|
| 528 |
+
Explanation
|
| 529 |
+
===========
|
| 530 |
+
|
| 531 |
+
The function is defined by the equation:
|
| 532 |
+
|
| 533 |
+
$fl^M_{pas} = \frac{\frac{\exp{c_1 \left(\tilde{l^M} - 1\right)}}{c_0} - 1}{\exp{c_1} - 1}$
|
| 534 |
+
|
| 535 |
+
with constant values of $c_0 = 0.6$ and $c_1 = 4.0$.
|
| 536 |
+
|
| 537 |
+
While it is possible to change the constant values, these were carefully
|
| 538 |
+
selected in the original publication to give the characteristic curve
|
| 539 |
+
specific and required properties. For example, the function produces a
|
| 540 |
+
passive fiber force very close to 0 for all normalized fiber lengths
|
| 541 |
+
between 0 and 1.
|
| 542 |
+
|
| 543 |
+
Examples
|
| 544 |
+
========
|
| 545 |
+
|
| 546 |
+
The preferred way to instantiate :class:`FiberForceLengthPassiveDeGroote2016` is
|
| 547 |
+
using the :meth:`~.with_defaults` constructor because this will automatically
|
| 548 |
+
populate the constants within the characteristic curve equation with the
|
| 549 |
+
floating point values from the original publication. This constructor takes
|
| 550 |
+
a single argument corresponding to normalized muscle fiber length. We'll
|
| 551 |
+
create a :class:`~.Symbol` called ``l_M_tilde`` to represent this.
|
| 552 |
+
|
| 553 |
+
>>> from sympy import Symbol
|
| 554 |
+
>>> from sympy.physics.biomechanics import FiberForceLengthPassiveDeGroote2016
|
| 555 |
+
>>> l_M_tilde = Symbol('l_M_tilde')
|
| 556 |
+
>>> fl_M = FiberForceLengthPassiveDeGroote2016.with_defaults(l_M_tilde)
|
| 557 |
+
>>> fl_M
|
| 558 |
+
FiberForceLengthPassiveDeGroote2016(l_M_tilde, 0.6, 4.0)
|
| 559 |
+
|
| 560 |
+
It's also possible to populate the two constants with your own values too.
|
| 561 |
+
|
| 562 |
+
>>> from sympy import symbols
|
| 563 |
+
>>> c0, c1 = symbols('c0 c1')
|
| 564 |
+
>>> fl_M = FiberForceLengthPassiveDeGroote2016(l_M_tilde, c0, c1)
|
| 565 |
+
>>> fl_M
|
| 566 |
+
FiberForceLengthPassiveDeGroote2016(l_M_tilde, c0, c1)
|
| 567 |
+
|
| 568 |
+
You don't just have to use symbols as the arguments, it's also possible to
|
| 569 |
+
use expressions. Let's create a new pair of symbols, ``l_M`` and
|
| 570 |
+
``l_M_opt``, representing muscle fiber length and optimal muscle fiber
|
| 571 |
+
length respectively. We can then represent ``l_M_tilde`` as an expression,
|
| 572 |
+
the ratio of these.
|
| 573 |
+
|
| 574 |
+
>>> l_M, l_M_opt = symbols('l_M l_M_opt')
|
| 575 |
+
>>> l_M_tilde = l_M/l_M_opt
|
| 576 |
+
>>> fl_M = FiberForceLengthPassiveDeGroote2016.with_defaults(l_M_tilde)
|
| 577 |
+
>>> fl_M
|
| 578 |
+
FiberForceLengthPassiveDeGroote2016(l_M/l_M_opt, 0.6, 4.0)
|
| 579 |
+
|
| 580 |
+
To inspect the actual symbolic expression that this function represents,
|
| 581 |
+
we can call the :meth:`~.doit` method on an instance. We'll use the keyword
|
| 582 |
+
argument ``evaluate=False`` as this will keep the expression in its
|
| 583 |
+
canonical form and won't simplify any constants.
|
| 584 |
+
|
| 585 |
+
>>> fl_M.doit(evaluate=False)
|
| 586 |
+
0.0186573603637741*(-1 + exp(6.66666666666667*(l_M/l_M_opt - 1)))
|
| 587 |
+
|
| 588 |
+
The function can also be differentiated. We'll differentiate with respect
|
| 589 |
+
to l_M using the ``diff`` method on an instance with the single positional
|
| 590 |
+
argument ``l_M``.
|
| 591 |
+
|
| 592 |
+
>>> fl_M.diff(l_M)
|
| 593 |
+
0.12438240242516*exp(6.66666666666667*(l_M/l_M_opt - 1))/l_M_opt
|
| 594 |
+
|
| 595 |
+
References
|
| 596 |
+
==========
|
| 597 |
+
|
| 598 |
+
.. [1] De Groote, F., Kinney, A. L., Rao, A. V., & Fregly, B. J., Evaluation
|
| 599 |
+
of direct collocation optimal control problem formulations for
|
| 600 |
+
solving the muscle redundancy problem, Annals of biomedical
|
| 601 |
+
engineering, 44(10), (2016) pp. 2922-2936
|
| 602 |
+
|
| 603 |
+
"""
|
| 604 |
+
|
| 605 |
+
@classmethod
|
| 606 |
+
def with_defaults(cls, l_M_tilde):
|
| 607 |
+
r"""Recommended constructor that will use the published constants.
|
| 608 |
+
|
| 609 |
+
Explanation
|
| 610 |
+
===========
|
| 611 |
+
|
| 612 |
+
Returns a new instance of the muscle fiber passive force-length
|
| 613 |
+
function using the four constant values specified in the original
|
| 614 |
+
publication.
|
| 615 |
+
|
| 616 |
+
These have the values:
|
| 617 |
+
|
| 618 |
+
$c_0 = 0.6$
|
| 619 |
+
$c_1 = 4.0$
|
| 620 |
+
|
| 621 |
+
Parameters
|
| 622 |
+
==========
|
| 623 |
+
|
| 624 |
+
l_M_tilde : Any (sympifiable)
|
| 625 |
+
Normalized muscle fiber length.
|
| 626 |
+
|
| 627 |
+
"""
|
| 628 |
+
c0 = Float('0.6')
|
| 629 |
+
c1 = Float('4.0')
|
| 630 |
+
return cls(l_M_tilde, c0, c1)
|
| 631 |
+
|
| 632 |
+
@classmethod
|
| 633 |
+
def eval(cls, l_M_tilde, c0, c1):
|
| 634 |
+
"""Evaluation of basic inputs.
|
| 635 |
+
|
| 636 |
+
Parameters
|
| 637 |
+
==========
|
| 638 |
+
|
| 639 |
+
l_M_tilde : Any (sympifiable)
|
| 640 |
+
Normalized muscle fiber length.
|
| 641 |
+
c0 : Any (sympifiable)
|
| 642 |
+
The first constant in the characteristic equation. The published
|
| 643 |
+
value is ``0.6``.
|
| 644 |
+
c1 : Any (sympifiable)
|
| 645 |
+
The second constant in the characteristic equation. The published
|
| 646 |
+
value is ``4.0``.
|
| 647 |
+
|
| 648 |
+
"""
|
| 649 |
+
pass
|
| 650 |
+
|
| 651 |
+
def _eval_evalf(self, prec):
|
| 652 |
+
"""Evaluate the expression numerically using ``evalf``."""
|
| 653 |
+
return self.doit(deep=False, evaluate=False)._eval_evalf(prec)
|
| 654 |
+
|
| 655 |
+
def doit(self, deep=True, evaluate=True, **hints):
|
| 656 |
+
"""Evaluate the expression defining the function.
|
| 657 |
+
|
| 658 |
+
Parameters
|
| 659 |
+
==========
|
| 660 |
+
|
| 661 |
+
deep : bool
|
| 662 |
+
Whether ``doit`` should be recursively called. Default is ``True``.
|
| 663 |
+
evaluate : bool.
|
| 664 |
+
Whether the SymPy expression should be evaluated as it is
|
| 665 |
+
constructed. If ``False``, then no constant folding will be
|
| 666 |
+
conducted which will leave the expression in a more numerically-
|
| 667 |
+
stable for values of ``l_T_tilde`` that correspond to a sensible
|
| 668 |
+
operating range for a musculotendon. Default is ``True``.
|
| 669 |
+
**kwargs : dict[str, Any]
|
| 670 |
+
Additional keyword argument pairs to be recursively passed to
|
| 671 |
+
``doit``.
|
| 672 |
+
|
| 673 |
+
"""
|
| 674 |
+
l_M_tilde, *constants = self.args
|
| 675 |
+
if deep:
|
| 676 |
+
hints['evaluate'] = evaluate
|
| 677 |
+
l_M_tilde = l_M_tilde.doit(deep=deep, **hints)
|
| 678 |
+
c0, c1 = [c.doit(deep=deep, **hints) for c in constants]
|
| 679 |
+
else:
|
| 680 |
+
c0, c1 = constants
|
| 681 |
+
|
| 682 |
+
if evaluate:
|
| 683 |
+
return (exp((c1*(l_M_tilde - 1))/c0) - 1)/(exp(c1) - 1)
|
| 684 |
+
|
| 685 |
+
return (exp((c1*UnevaluatedExpr(l_M_tilde - 1))/c0) - 1)/(exp(c1) - 1)
|
| 686 |
+
|
| 687 |
+
def fdiff(self, argindex=1):
|
| 688 |
+
"""Derivative of the function with respect to a single argument.
|
| 689 |
+
|
| 690 |
+
Parameters
|
| 691 |
+
==========
|
| 692 |
+
|
| 693 |
+
argindex : int
|
| 694 |
+
The index of the function's arguments with respect to which the
|
| 695 |
+
derivative should be taken. Argument indexes start at ``1``.
|
| 696 |
+
Default is ``1``.
|
| 697 |
+
|
| 698 |
+
"""
|
| 699 |
+
l_M_tilde, c0, c1 = self.args
|
| 700 |
+
if argindex == 1:
|
| 701 |
+
return c1*exp(c1*UnevaluatedExpr(l_M_tilde - 1)/c0)/(c0*(exp(c1) - 1))
|
| 702 |
+
elif argindex == 2:
|
| 703 |
+
return (
|
| 704 |
+
-c1*exp(c1*UnevaluatedExpr(l_M_tilde - 1)/c0)
|
| 705 |
+
*UnevaluatedExpr(l_M_tilde - 1)/(c0**2*(exp(c1) - 1))
|
| 706 |
+
)
|
| 707 |
+
elif argindex == 3:
|
| 708 |
+
return (
|
| 709 |
+
-exp(c1)*(-1 + exp(c1*UnevaluatedExpr(l_M_tilde - 1)/c0))/(exp(c1) - 1)**2
|
| 710 |
+
+ exp(c1*UnevaluatedExpr(l_M_tilde - 1)/c0)*(l_M_tilde - 1)/(c0*(exp(c1) - 1))
|
| 711 |
+
)
|
| 712 |
+
|
| 713 |
+
raise ArgumentIndexError(self, argindex)
|
| 714 |
+
|
| 715 |
+
def inverse(self, argindex=1):
|
| 716 |
+
"""Inverse function.
|
| 717 |
+
|
| 718 |
+
Parameters
|
| 719 |
+
==========
|
| 720 |
+
|
| 721 |
+
argindex : int
|
| 722 |
+
Value to start indexing the arguments at. Default is ``1``.
|
| 723 |
+
|
| 724 |
+
"""
|
| 725 |
+
return FiberForceLengthPassiveInverseDeGroote2016
|
| 726 |
+
|
| 727 |
+
def _latex(self, printer):
|
| 728 |
+
"""Print a LaTeX representation of the function defining the curve.
|
| 729 |
+
|
| 730 |
+
Parameters
|
| 731 |
+
==========
|
| 732 |
+
|
| 733 |
+
printer : Printer
|
| 734 |
+
The printer to be used to print the LaTeX string representation.
|
| 735 |
+
|
| 736 |
+
"""
|
| 737 |
+
l_M_tilde = self.args[0]
|
| 738 |
+
_l_M_tilde = printer._print(l_M_tilde)
|
| 739 |
+
return r'\operatorname{fl}^M_{pas} \left( %s \right)' % _l_M_tilde
|
| 740 |
+
|
| 741 |
+
|
| 742 |
+
class FiberForceLengthPassiveInverseDeGroote2016(CharacteristicCurveFunction):
|
| 743 |
+
r"""Inverse passive muscle fiber force-length curve based on De Groote et
|
| 744 |
+
al., 2016 [1]_.
|
| 745 |
+
|
| 746 |
+
Explanation
|
| 747 |
+
===========
|
| 748 |
+
|
| 749 |
+
Gives the normalized muscle fiber length that produces a specific normalized
|
| 750 |
+
passive muscle fiber force.
|
| 751 |
+
|
| 752 |
+
The function is defined by the equation:
|
| 753 |
+
|
| 754 |
+
${fl^M_{pas}}^{-1} = \frac{c_0 \log{\left(\exp{c_1} - 1\right)fl^M_pas + 1}}{c_1} + 1$
|
| 755 |
+
|
| 756 |
+
with constant values of $c_0 = 0.6$ and $c_1 = 4.0$. This function is the
|
| 757 |
+
exact analytical inverse of the related tendon force-length curve
|
| 758 |
+
``FiberForceLengthPassiveDeGroote2016``.
|
| 759 |
+
|
| 760 |
+
While it is possible to change the constant values, these were carefully
|
| 761 |
+
selected in the original publication to give the characteristic curve
|
| 762 |
+
specific and required properties. For example, the function produces a
|
| 763 |
+
passive fiber force very close to 0 for all normalized fiber lengths
|
| 764 |
+
between 0 and 1.
|
| 765 |
+
|
| 766 |
+
Examples
|
| 767 |
+
========
|
| 768 |
+
|
| 769 |
+
The preferred way to instantiate
|
| 770 |
+
:class:`FiberForceLengthPassiveInverseDeGroote2016` is using the
|
| 771 |
+
:meth:`~.with_defaults` constructor because this will automatically populate the
|
| 772 |
+
constants within the characteristic curve equation with the floating point
|
| 773 |
+
values from the original publication. This constructor takes a single
|
| 774 |
+
argument corresponding to the normalized passive muscle fiber length-force
|
| 775 |
+
component of the muscle fiber force. We'll create a :class:`~.Symbol` called
|
| 776 |
+
``fl_M_pas`` to represent this.
|
| 777 |
+
|
| 778 |
+
>>> from sympy import Symbol
|
| 779 |
+
>>> from sympy.physics.biomechanics import FiberForceLengthPassiveInverseDeGroote2016
|
| 780 |
+
>>> fl_M_pas = Symbol('fl_M_pas')
|
| 781 |
+
>>> l_M_tilde = FiberForceLengthPassiveInverseDeGroote2016.with_defaults(fl_M_pas)
|
| 782 |
+
>>> l_M_tilde
|
| 783 |
+
FiberForceLengthPassiveInverseDeGroote2016(fl_M_pas, 0.6, 4.0)
|
| 784 |
+
|
| 785 |
+
It's also possible to populate the two constants with your own values too.
|
| 786 |
+
|
| 787 |
+
>>> from sympy import symbols
|
| 788 |
+
>>> c0, c1 = symbols('c0 c1')
|
| 789 |
+
>>> l_M_tilde = FiberForceLengthPassiveInverseDeGroote2016(fl_M_pas, c0, c1)
|
| 790 |
+
>>> l_M_tilde
|
| 791 |
+
FiberForceLengthPassiveInverseDeGroote2016(fl_M_pas, c0, c1)
|
| 792 |
+
|
| 793 |
+
To inspect the actual symbolic expression that this function represents,
|
| 794 |
+
we can call the :meth:`~.doit` method on an instance. We'll use the keyword
|
| 795 |
+
argument ``evaluate=False`` as this will keep the expression in its
|
| 796 |
+
canonical form and won't simplify any constants.
|
| 797 |
+
|
| 798 |
+
>>> l_M_tilde.doit(evaluate=False)
|
| 799 |
+
c0*log(1 + fl_M_pas*(exp(c1) - 1))/c1 + 1
|
| 800 |
+
|
| 801 |
+
The function can also be differentiated. We'll differentiate with respect
|
| 802 |
+
to fl_M_pas using the ``diff`` method on an instance with the single positional
|
| 803 |
+
argument ``fl_M_pas``.
|
| 804 |
+
|
| 805 |
+
>>> l_M_tilde.diff(fl_M_pas)
|
| 806 |
+
c0*(exp(c1) - 1)/(c1*(fl_M_pas*(exp(c1) - 1) + 1))
|
| 807 |
+
|
| 808 |
+
References
|
| 809 |
+
==========
|
| 810 |
+
|
| 811 |
+
.. [1] De Groote, F., Kinney, A. L., Rao, A. V., & Fregly, B. J., Evaluation
|
| 812 |
+
of direct collocation optimal control problem formulations for
|
| 813 |
+
solving the muscle redundancy problem, Annals of biomedical
|
| 814 |
+
engineering, 44(10), (2016) pp. 2922-2936
|
| 815 |
+
|
| 816 |
+
"""
|
| 817 |
+
|
| 818 |
+
@classmethod
|
| 819 |
+
def with_defaults(cls, fl_M_pas):
|
| 820 |
+
r"""Recommended constructor that will use the published constants.
|
| 821 |
+
|
| 822 |
+
Explanation
|
| 823 |
+
===========
|
| 824 |
+
|
| 825 |
+
Returns a new instance of the inverse muscle fiber passive force-length
|
| 826 |
+
function using the four constant values specified in the original
|
| 827 |
+
publication.
|
| 828 |
+
|
| 829 |
+
These have the values:
|
| 830 |
+
|
| 831 |
+
$c_0 = 0.6$
|
| 832 |
+
$c_1 = 4.0$
|
| 833 |
+
|
| 834 |
+
Parameters
|
| 835 |
+
==========
|
| 836 |
+
|
| 837 |
+
fl_M_pas : Any (sympifiable)
|
| 838 |
+
Normalized passive muscle fiber force as a function of muscle fiber
|
| 839 |
+
length.
|
| 840 |
+
|
| 841 |
+
"""
|
| 842 |
+
c0 = Float('0.6')
|
| 843 |
+
c1 = Float('4.0')
|
| 844 |
+
return cls(fl_M_pas, c0, c1)
|
| 845 |
+
|
| 846 |
+
@classmethod
|
| 847 |
+
def eval(cls, fl_M_pas, c0, c1):
|
| 848 |
+
"""Evaluation of basic inputs.
|
| 849 |
+
|
| 850 |
+
Parameters
|
| 851 |
+
==========
|
| 852 |
+
|
| 853 |
+
fl_M_pas : Any (sympifiable)
|
| 854 |
+
Normalized passive muscle fiber force.
|
| 855 |
+
c0 : Any (sympifiable)
|
| 856 |
+
The first constant in the characteristic equation. The published
|
| 857 |
+
value is ``0.6``.
|
| 858 |
+
c1 : Any (sympifiable)
|
| 859 |
+
The second constant in the characteristic equation. The published
|
| 860 |
+
value is ``4.0``.
|
| 861 |
+
|
| 862 |
+
"""
|
| 863 |
+
pass
|
| 864 |
+
|
| 865 |
+
def _eval_evalf(self, prec):
|
| 866 |
+
"""Evaluate the expression numerically using ``evalf``."""
|
| 867 |
+
return self.doit(deep=False, evaluate=False)._eval_evalf(prec)
|
| 868 |
+
|
| 869 |
+
def doit(self, deep=True, evaluate=True, **hints):
|
| 870 |
+
"""Evaluate the expression defining the function.
|
| 871 |
+
|
| 872 |
+
Parameters
|
| 873 |
+
==========
|
| 874 |
+
|
| 875 |
+
deep : bool
|
| 876 |
+
Whether ``doit`` should be recursively called. Default is ``True``.
|
| 877 |
+
evaluate : bool.
|
| 878 |
+
Whether the SymPy expression should be evaluated as it is
|
| 879 |
+
constructed. If ``False``, then no constant folding will be
|
| 880 |
+
conducted which will leave the expression in a more numerically-
|
| 881 |
+
stable for values of ``l_T_tilde`` that correspond to a sensible
|
| 882 |
+
operating range for a musculotendon. Default is ``True``.
|
| 883 |
+
**kwargs : dict[str, Any]
|
| 884 |
+
Additional keyword argument pairs to be recursively passed to
|
| 885 |
+
``doit``.
|
| 886 |
+
|
| 887 |
+
"""
|
| 888 |
+
fl_M_pas, *constants = self.args
|
| 889 |
+
if deep:
|
| 890 |
+
hints['evaluate'] = evaluate
|
| 891 |
+
fl_M_pas = fl_M_pas.doit(deep=deep, **hints)
|
| 892 |
+
c0, c1 = [c.doit(deep=deep, **hints) for c in constants]
|
| 893 |
+
else:
|
| 894 |
+
c0, c1 = constants
|
| 895 |
+
|
| 896 |
+
if evaluate:
|
| 897 |
+
return c0*log(fl_M_pas*(exp(c1) - 1) + 1)/c1 + 1
|
| 898 |
+
|
| 899 |
+
return c0*log(UnevaluatedExpr(fl_M_pas*(exp(c1) - 1)) + 1)/c1 + 1
|
| 900 |
+
|
| 901 |
+
def fdiff(self, argindex=1):
|
| 902 |
+
"""Derivative of the function with respect to a single argument.
|
| 903 |
+
|
| 904 |
+
Parameters
|
| 905 |
+
==========
|
| 906 |
+
|
| 907 |
+
argindex : int
|
| 908 |
+
The index of the function's arguments with respect to which the
|
| 909 |
+
derivative should be taken. Argument indexes start at ``1``.
|
| 910 |
+
Default is ``1``.
|
| 911 |
+
|
| 912 |
+
"""
|
| 913 |
+
fl_M_pas, c0, c1 = self.args
|
| 914 |
+
if argindex == 1:
|
| 915 |
+
return c0*(exp(c1) - 1)/(c1*(fl_M_pas*(exp(c1) - 1) + 1))
|
| 916 |
+
elif argindex == 2:
|
| 917 |
+
return log(fl_M_pas*(exp(c1) - 1) + 1)/c1
|
| 918 |
+
elif argindex == 3:
|
| 919 |
+
return (
|
| 920 |
+
c0*fl_M_pas*exp(c1)/(c1*(fl_M_pas*(exp(c1) - 1) + 1))
|
| 921 |
+
- c0*log(fl_M_pas*(exp(c1) - 1) + 1)/c1**2
|
| 922 |
+
)
|
| 923 |
+
|
| 924 |
+
raise ArgumentIndexError(self, argindex)
|
| 925 |
+
|
| 926 |
+
def inverse(self, argindex=1):
|
| 927 |
+
"""Inverse function.
|
| 928 |
+
|
| 929 |
+
Parameters
|
| 930 |
+
==========
|
| 931 |
+
|
| 932 |
+
argindex : int
|
| 933 |
+
Value to start indexing the arguments at. Default is ``1``.
|
| 934 |
+
|
| 935 |
+
"""
|
| 936 |
+
return FiberForceLengthPassiveDeGroote2016
|
| 937 |
+
|
| 938 |
+
def _latex(self, printer):
|
| 939 |
+
"""Print a LaTeX representation of the function defining the curve.
|
| 940 |
+
|
| 941 |
+
Parameters
|
| 942 |
+
==========
|
| 943 |
+
|
| 944 |
+
printer : Printer
|
| 945 |
+
The printer to be used to print the LaTeX string representation.
|
| 946 |
+
|
| 947 |
+
"""
|
| 948 |
+
fl_M_pas = self.args[0]
|
| 949 |
+
_fl_M_pas = printer._print(fl_M_pas)
|
| 950 |
+
return r'\left( \operatorname{fl}^M_{pas} \right)^{-1} \left( %s \right)' % _fl_M_pas
|
| 951 |
+
|
| 952 |
+
|
| 953 |
+
class FiberForceLengthActiveDeGroote2016(CharacteristicCurveFunction):
|
| 954 |
+
r"""Active muscle fiber force-length curve based on De Groote et al., 2016
|
| 955 |
+
[1]_.
|
| 956 |
+
|
| 957 |
+
Explanation
|
| 958 |
+
===========
|
| 959 |
+
|
| 960 |
+
The function is defined by the equation:
|
| 961 |
+
|
| 962 |
+
$fl_{\text{act}}^M = c_0 \exp\left(-\frac{1}{2}\left(\frac{\tilde{l}^M - c_1}{c_2 + c_3 \tilde{l}^M}\right)^2\right)
|
| 963 |
+
+ c_4 \exp\left(-\frac{1}{2}\left(\frac{\tilde{l}^M - c_5}{c_6 + c_7 \tilde{l}^M}\right)^2\right)
|
| 964 |
+
+ c_8 \exp\left(-\frac{1}{2}\left(\frac{\tilde{l}^M - c_9}{c_{10} + c_{11} \tilde{l}^M}\right)^2\right)$
|
| 965 |
+
|
| 966 |
+
with constant values of $c0 = 0.814$, $c1 = 1.06$, $c2 = 0.162$,
|
| 967 |
+
$c3 = 0.0633$, $c4 = 0.433$, $c5 = 0.717$, $c6 = -0.0299$, $c7 = 0.2$,
|
| 968 |
+
$c8 = 0.1$, $c9 = 1.0$, $c10 = 0.354$, and $c11 = 0.0$.
|
| 969 |
+
|
| 970 |
+
While it is possible to change the constant values, these were carefully
|
| 971 |
+
selected in the original publication to give the characteristic curve
|
| 972 |
+
specific and required properties. For example, the function produces a
|
| 973 |
+
active fiber force of 1 at a normalized fiber length of 1, and an active
|
| 974 |
+
fiber force of 0 at normalized fiber lengths of 0 and 2.
|
| 975 |
+
|
| 976 |
+
Examples
|
| 977 |
+
========
|
| 978 |
+
|
| 979 |
+
The preferred way to instantiate :class:`FiberForceLengthActiveDeGroote2016` is
|
| 980 |
+
using the :meth:`~.with_defaults` constructor because this will automatically
|
| 981 |
+
populate the constants within the characteristic curve equation with the
|
| 982 |
+
floating point values from the original publication. This constructor takes
|
| 983 |
+
a single argument corresponding to normalized muscle fiber length. We'll
|
| 984 |
+
create a :class:`~.Symbol` called ``l_M_tilde`` to represent this.
|
| 985 |
+
|
| 986 |
+
>>> from sympy import Symbol
|
| 987 |
+
>>> from sympy.physics.biomechanics import FiberForceLengthActiveDeGroote2016
|
| 988 |
+
>>> l_M_tilde = Symbol('l_M_tilde')
|
| 989 |
+
>>> fl_M = FiberForceLengthActiveDeGroote2016.with_defaults(l_M_tilde)
|
| 990 |
+
>>> fl_M
|
| 991 |
+
FiberForceLengthActiveDeGroote2016(l_M_tilde, 0.814, 1.06, 0.162, 0.0633,
|
| 992 |
+
0.433, 0.717, -0.0299, 0.2, 0.1, 1.0, 0.354, 0.0)
|
| 993 |
+
|
| 994 |
+
It's also possible to populate the two constants with your own values too.
|
| 995 |
+
|
| 996 |
+
>>> from sympy import symbols
|
| 997 |
+
>>> c0, c1, c2, c3, c4, c5, c6, c7, c8, c9, c10, c11 = symbols('c0:12')
|
| 998 |
+
>>> fl_M = FiberForceLengthActiveDeGroote2016(l_M_tilde, c0, c1, c2, c3,
|
| 999 |
+
... c4, c5, c6, c7, c8, c9, c10, c11)
|
| 1000 |
+
>>> fl_M
|
| 1001 |
+
FiberForceLengthActiveDeGroote2016(l_M_tilde, c0, c1, c2, c3, c4, c5, c6,
|
| 1002 |
+
c7, c8, c9, c10, c11)
|
| 1003 |
+
|
| 1004 |
+
You don't just have to use symbols as the arguments, it's also possible to
|
| 1005 |
+
use expressions. Let's create a new pair of symbols, ``l_M`` and
|
| 1006 |
+
``l_M_opt``, representing muscle fiber length and optimal muscle fiber
|
| 1007 |
+
length respectively. We can then represent ``l_M_tilde`` as an expression,
|
| 1008 |
+
the ratio of these.
|
| 1009 |
+
|
| 1010 |
+
>>> l_M, l_M_opt = symbols('l_M l_M_opt')
|
| 1011 |
+
>>> l_M_tilde = l_M/l_M_opt
|
| 1012 |
+
>>> fl_M = FiberForceLengthActiveDeGroote2016.with_defaults(l_M_tilde)
|
| 1013 |
+
>>> fl_M
|
| 1014 |
+
FiberForceLengthActiveDeGroote2016(l_M/l_M_opt, 0.814, 1.06, 0.162, 0.0633,
|
| 1015 |
+
0.433, 0.717, -0.0299, 0.2, 0.1, 1.0, 0.354, 0.0)
|
| 1016 |
+
|
| 1017 |
+
To inspect the actual symbolic expression that this function represents,
|
| 1018 |
+
we can call the :meth:`~.doit` method on an instance. We'll use the keyword
|
| 1019 |
+
argument ``evaluate=False`` as this will keep the expression in its
|
| 1020 |
+
canonical form and won't simplify any constants.
|
| 1021 |
+
|
| 1022 |
+
>>> fl_M.doit(evaluate=False)
|
| 1023 |
+
0.814*exp(-19.0519737844841*(l_M/l_M_opt
|
| 1024 |
+
- 1.06)**2/(0.390740740740741*l_M/l_M_opt + 1)**2)
|
| 1025 |
+
+ 0.433*exp(-12.5*(l_M/l_M_opt - 0.717)**2/(l_M/l_M_opt - 0.1495)**2)
|
| 1026 |
+
+ 0.1*exp(-3.98991349867535*(l_M/l_M_opt - 1.0)**2)
|
| 1027 |
+
|
| 1028 |
+
The function can also be differentiated. We'll differentiate with respect
|
| 1029 |
+
to l_M using the ``diff`` method on an instance with the single positional
|
| 1030 |
+
argument ``l_M``.
|
| 1031 |
+
|
| 1032 |
+
>>> fl_M.diff(l_M)
|
| 1033 |
+
((-0.79798269973507*l_M/l_M_opt
|
| 1034 |
+
+ 0.79798269973507)*exp(-3.98991349867535*(l_M/l_M_opt - 1.0)**2)
|
| 1035 |
+
+ (10.825*(-l_M/l_M_opt + 0.717)/(l_M/l_M_opt - 0.1495)**2
|
| 1036 |
+
+ 10.825*(l_M/l_M_opt - 0.717)**2/(l_M/l_M_opt
|
| 1037 |
+
- 0.1495)**3)*exp(-12.5*(l_M/l_M_opt - 0.717)**2/(l_M/l_M_opt - 0.1495)**2)
|
| 1038 |
+
+ (31.0166133211401*(-l_M/l_M_opt + 1.06)/(0.390740740740741*l_M/l_M_opt
|
| 1039 |
+
+ 1)**2 + 13.6174190361677*(0.943396226415094*l_M/l_M_opt
|
| 1040 |
+
- 1)**2/(0.390740740740741*l_M/l_M_opt
|
| 1041 |
+
+ 1)**3)*exp(-21.4067977442463*(0.943396226415094*l_M/l_M_opt
|
| 1042 |
+
- 1)**2/(0.390740740740741*l_M/l_M_opt + 1)**2))/l_M_opt
|
| 1043 |
+
|
| 1044 |
+
References
|
| 1045 |
+
==========
|
| 1046 |
+
|
| 1047 |
+
.. [1] De Groote, F., Kinney, A. L., Rao, A. V., & Fregly, B. J., Evaluation
|
| 1048 |
+
of direct collocation optimal control problem formulations for
|
| 1049 |
+
solving the muscle redundancy problem, Annals of biomedical
|
| 1050 |
+
engineering, 44(10), (2016) pp. 2922-2936
|
| 1051 |
+
|
| 1052 |
+
"""
|
| 1053 |
+
|
| 1054 |
+
@classmethod
|
| 1055 |
+
def with_defaults(cls, l_M_tilde):
|
| 1056 |
+
r"""Recommended constructor that will use the published constants.
|
| 1057 |
+
|
| 1058 |
+
Explanation
|
| 1059 |
+
===========
|
| 1060 |
+
|
| 1061 |
+
Returns a new instance of the inverse muscle fiber act force-length
|
| 1062 |
+
function using the four constant values specified in the original
|
| 1063 |
+
publication.
|
| 1064 |
+
|
| 1065 |
+
These have the values:
|
| 1066 |
+
|
| 1067 |
+
$c0 = 0.814$
|
| 1068 |
+
$c1 = 1.06$
|
| 1069 |
+
$c2 = 0.162$
|
| 1070 |
+
$c3 = 0.0633$
|
| 1071 |
+
$c4 = 0.433$
|
| 1072 |
+
$c5 = 0.717$
|
| 1073 |
+
$c6 = -0.0299$
|
| 1074 |
+
$c7 = 0.2$
|
| 1075 |
+
$c8 = 0.1$
|
| 1076 |
+
$c9 = 1.0$
|
| 1077 |
+
$c10 = 0.354$
|
| 1078 |
+
$c11 = 0.0$
|
| 1079 |
+
|
| 1080 |
+
Parameters
|
| 1081 |
+
==========
|
| 1082 |
+
|
| 1083 |
+
fl_M_act : Any (sympifiable)
|
| 1084 |
+
Normalized passive muscle fiber force as a function of muscle fiber
|
| 1085 |
+
length.
|
| 1086 |
+
|
| 1087 |
+
"""
|
| 1088 |
+
c0 = Float('0.814')
|
| 1089 |
+
c1 = Float('1.06')
|
| 1090 |
+
c2 = Float('0.162')
|
| 1091 |
+
c3 = Float('0.0633')
|
| 1092 |
+
c4 = Float('0.433')
|
| 1093 |
+
c5 = Float('0.717')
|
| 1094 |
+
c6 = Float('-0.0299')
|
| 1095 |
+
c7 = Float('0.2')
|
| 1096 |
+
c8 = Float('0.1')
|
| 1097 |
+
c9 = Float('1.0')
|
| 1098 |
+
c10 = Float('0.354')
|
| 1099 |
+
c11 = Float('0.0')
|
| 1100 |
+
return cls(l_M_tilde, c0, c1, c2, c3, c4, c5, c6, c7, c8, c9, c10, c11)
|
| 1101 |
+
|
| 1102 |
+
@classmethod
|
| 1103 |
+
def eval(cls, l_M_tilde, c0, c1, c2, c3, c4, c5, c6, c7, c8, c9, c10, c11):
|
| 1104 |
+
"""Evaluation of basic inputs.
|
| 1105 |
+
|
| 1106 |
+
Parameters
|
| 1107 |
+
==========
|
| 1108 |
+
|
| 1109 |
+
l_M_tilde : Any (sympifiable)
|
| 1110 |
+
Normalized muscle fiber length.
|
| 1111 |
+
c0 : Any (sympifiable)
|
| 1112 |
+
The first constant in the characteristic equation. The published
|
| 1113 |
+
value is ``0.814``.
|
| 1114 |
+
c1 : Any (sympifiable)
|
| 1115 |
+
The second constant in the characteristic equation. The published
|
| 1116 |
+
value is ``1.06``.
|
| 1117 |
+
c2 : Any (sympifiable)
|
| 1118 |
+
The third constant in the characteristic equation. The published
|
| 1119 |
+
value is ``0.162``.
|
| 1120 |
+
c3 : Any (sympifiable)
|
| 1121 |
+
The fourth constant in the characteristic equation. The published
|
| 1122 |
+
value is ``0.0633``.
|
| 1123 |
+
c4 : Any (sympifiable)
|
| 1124 |
+
The fifth constant in the characteristic equation. The published
|
| 1125 |
+
value is ``0.433``.
|
| 1126 |
+
c5 : Any (sympifiable)
|
| 1127 |
+
The sixth constant in the characteristic equation. The published
|
| 1128 |
+
value is ``0.717``.
|
| 1129 |
+
c6 : Any (sympifiable)
|
| 1130 |
+
The seventh constant in the characteristic equation. The published
|
| 1131 |
+
value is ``-0.0299``.
|
| 1132 |
+
c7 : Any (sympifiable)
|
| 1133 |
+
The eighth constant in the characteristic equation. The published
|
| 1134 |
+
value is ``0.2``.
|
| 1135 |
+
c8 : Any (sympifiable)
|
| 1136 |
+
The ninth constant in the characteristic equation. The published
|
| 1137 |
+
value is ``0.1``.
|
| 1138 |
+
c9 : Any (sympifiable)
|
| 1139 |
+
The tenth constant in the characteristic equation. The published
|
| 1140 |
+
value is ``1.0``.
|
| 1141 |
+
c10 : Any (sympifiable)
|
| 1142 |
+
The eleventh constant in the characteristic equation. The published
|
| 1143 |
+
value is ``0.354``.
|
| 1144 |
+
c11 : Any (sympifiable)
|
| 1145 |
+
The tweflth constant in the characteristic equation. The published
|
| 1146 |
+
value is ``0.0``.
|
| 1147 |
+
|
| 1148 |
+
"""
|
| 1149 |
+
pass
|
| 1150 |
+
|
| 1151 |
+
def _eval_evalf(self, prec):
|
| 1152 |
+
"""Evaluate the expression numerically using ``evalf``."""
|
| 1153 |
+
return self.doit(deep=False, evaluate=False)._eval_evalf(prec)
|
| 1154 |
+
|
| 1155 |
+
def doit(self, deep=True, evaluate=True, **hints):
|
| 1156 |
+
"""Evaluate the expression defining the function.
|
| 1157 |
+
|
| 1158 |
+
Parameters
|
| 1159 |
+
==========
|
| 1160 |
+
|
| 1161 |
+
deep : bool
|
| 1162 |
+
Whether ``doit`` should be recursively called. Default is ``True``.
|
| 1163 |
+
evaluate : bool.
|
| 1164 |
+
Whether the SymPy expression should be evaluated as it is
|
| 1165 |
+
constructed. If ``False``, then no constant folding will be
|
| 1166 |
+
conducted which will leave the expression in a more numerically-
|
| 1167 |
+
stable for values of ``l_M_tilde`` that correspond to a sensible
|
| 1168 |
+
operating range for a musculotendon. Default is ``True``.
|
| 1169 |
+
**kwargs : dict[str, Any]
|
| 1170 |
+
Additional keyword argument pairs to be recursively passed to
|
| 1171 |
+
``doit``.
|
| 1172 |
+
|
| 1173 |
+
"""
|
| 1174 |
+
l_M_tilde, *constants = self.args
|
| 1175 |
+
if deep:
|
| 1176 |
+
hints['evaluate'] = evaluate
|
| 1177 |
+
l_M_tilde = l_M_tilde.doit(deep=deep, **hints)
|
| 1178 |
+
constants = [c.doit(deep=deep, **hints) for c in constants]
|
| 1179 |
+
c0, c1, c2, c3, c4, c5, c6, c7, c8, c9, c10, c11 = constants
|
| 1180 |
+
|
| 1181 |
+
if evaluate:
|
| 1182 |
+
return (
|
| 1183 |
+
c0*exp(-(((l_M_tilde - c1)/(c2 + c3*l_M_tilde))**2)/2)
|
| 1184 |
+
+ c4*exp(-(((l_M_tilde - c5)/(c6 + c7*l_M_tilde))**2)/2)
|
| 1185 |
+
+ c8*exp(-(((l_M_tilde - c9)/(c10 + c11*l_M_tilde))**2)/2)
|
| 1186 |
+
)
|
| 1187 |
+
|
| 1188 |
+
return (
|
| 1189 |
+
c0*exp(-((UnevaluatedExpr(l_M_tilde - c1)/(c2 + c3*l_M_tilde))**2)/2)
|
| 1190 |
+
+ c4*exp(-((UnevaluatedExpr(l_M_tilde - c5)/(c6 + c7*l_M_tilde))**2)/2)
|
| 1191 |
+
+ c8*exp(-((UnevaluatedExpr(l_M_tilde - c9)/(c10 + c11*l_M_tilde))**2)/2)
|
| 1192 |
+
)
|
| 1193 |
+
|
| 1194 |
+
def fdiff(self, argindex=1):
|
| 1195 |
+
"""Derivative of the function with respect to a single argument.
|
| 1196 |
+
|
| 1197 |
+
Parameters
|
| 1198 |
+
==========
|
| 1199 |
+
|
| 1200 |
+
argindex : int
|
| 1201 |
+
The index of the function's arguments with respect to which the
|
| 1202 |
+
derivative should be taken. Argument indexes start at ``1``.
|
| 1203 |
+
Default is ``1``.
|
| 1204 |
+
|
| 1205 |
+
"""
|
| 1206 |
+
l_M_tilde, c0, c1, c2, c3, c4, c5, c6, c7, c8, c9, c10, c11 = self.args
|
| 1207 |
+
if argindex == 1:
|
| 1208 |
+
return (
|
| 1209 |
+
c0*(
|
| 1210 |
+
c3*(l_M_tilde - c1)**2/(c2 + c3*l_M_tilde)**3
|
| 1211 |
+
+ (c1 - l_M_tilde)/((c2 + c3*l_M_tilde)**2)
|
| 1212 |
+
)*exp(-(l_M_tilde - c1)**2/(2*(c2 + c3*l_M_tilde)**2))
|
| 1213 |
+
+ c4*(
|
| 1214 |
+
c7*(l_M_tilde - c5)**2/(c6 + c7*l_M_tilde)**3
|
| 1215 |
+
+ (c5 - l_M_tilde)/((c6 + c7*l_M_tilde)**2)
|
| 1216 |
+
)*exp(-(l_M_tilde - c5)**2/(2*(c6 + c7*l_M_tilde)**2))
|
| 1217 |
+
+ c8*(
|
| 1218 |
+
c11*(l_M_tilde - c9)**2/(c10 + c11*l_M_tilde)**3
|
| 1219 |
+
+ (c9 - l_M_tilde)/((c10 + c11*l_M_tilde)**2)
|
| 1220 |
+
)*exp(-(l_M_tilde - c9)**2/(2*(c10 + c11*l_M_tilde)**2))
|
| 1221 |
+
)
|
| 1222 |
+
elif argindex == 2:
|
| 1223 |
+
return exp(-(l_M_tilde - c1)**2/(2*(c2 + c3*l_M_tilde)**2))
|
| 1224 |
+
elif argindex == 3:
|
| 1225 |
+
return (
|
| 1226 |
+
c0*(l_M_tilde - c1)/(c2 + c3*l_M_tilde)**2
|
| 1227 |
+
*exp(-(l_M_tilde - c1)**2 /(2*(c2 + c3*l_M_tilde)**2))
|
| 1228 |
+
)
|
| 1229 |
+
elif argindex == 4:
|
| 1230 |
+
return (
|
| 1231 |
+
c0*(l_M_tilde - c1)**2/(c2 + c3*l_M_tilde)**3
|
| 1232 |
+
*exp(-(l_M_tilde - c1)**2/(2*(c2 + c3*l_M_tilde)**2))
|
| 1233 |
+
)
|
| 1234 |
+
elif argindex == 5:
|
| 1235 |
+
return (
|
| 1236 |
+
c0*l_M_tilde*(l_M_tilde - c1)**2/(c2 + c3*l_M_tilde)**3
|
| 1237 |
+
*exp(-(l_M_tilde - c1)**2/(2*(c2 + c3*l_M_tilde)**2))
|
| 1238 |
+
)
|
| 1239 |
+
elif argindex == 6:
|
| 1240 |
+
return exp(-(l_M_tilde - c5)**2/(2*(c6 + c7*l_M_tilde)**2))
|
| 1241 |
+
elif argindex == 7:
|
| 1242 |
+
return (
|
| 1243 |
+
c4*(l_M_tilde - c5)/(c6 + c7*l_M_tilde)**2
|
| 1244 |
+
*exp(-(l_M_tilde - c5)**2 /(2*(c6 + c7*l_M_tilde)**2))
|
| 1245 |
+
)
|
| 1246 |
+
elif argindex == 8:
|
| 1247 |
+
return (
|
| 1248 |
+
c4*(l_M_tilde - c5)**2/(c6 + c7*l_M_tilde)**3
|
| 1249 |
+
*exp(-(l_M_tilde - c5)**2/(2*(c6 + c7*l_M_tilde)**2))
|
| 1250 |
+
)
|
| 1251 |
+
elif argindex == 9:
|
| 1252 |
+
return (
|
| 1253 |
+
c4*l_M_tilde*(l_M_tilde - c5)**2/(c6 + c7*l_M_tilde)**3
|
| 1254 |
+
*exp(-(l_M_tilde - c5)**2/(2*(c6 + c7*l_M_tilde)**2))
|
| 1255 |
+
)
|
| 1256 |
+
elif argindex == 10:
|
| 1257 |
+
return exp(-(l_M_tilde - c9)**2/(2*(c10 + c11*l_M_tilde)**2))
|
| 1258 |
+
elif argindex == 11:
|
| 1259 |
+
return (
|
| 1260 |
+
c8*(l_M_tilde - c9)/(c10 + c11*l_M_tilde)**2
|
| 1261 |
+
*exp(-(l_M_tilde - c9)**2 /(2*(c10 + c11*l_M_tilde)**2))
|
| 1262 |
+
)
|
| 1263 |
+
elif argindex == 12:
|
| 1264 |
+
return (
|
| 1265 |
+
c8*(l_M_tilde - c9)**2/(c10 + c11*l_M_tilde)**3
|
| 1266 |
+
*exp(-(l_M_tilde - c9)**2/(2*(c10 + c11*l_M_tilde)**2))
|
| 1267 |
+
)
|
| 1268 |
+
elif argindex == 13:
|
| 1269 |
+
return (
|
| 1270 |
+
c8*l_M_tilde*(l_M_tilde - c9)**2/(c10 + c11*l_M_tilde)**3
|
| 1271 |
+
*exp(-(l_M_tilde - c9)**2/(2*(c10 + c11*l_M_tilde)**2))
|
| 1272 |
+
)
|
| 1273 |
+
|
| 1274 |
+
raise ArgumentIndexError(self, argindex)
|
| 1275 |
+
|
| 1276 |
+
def _latex(self, printer):
|
| 1277 |
+
"""Print a LaTeX representation of the function defining the curve.
|
| 1278 |
+
|
| 1279 |
+
Parameters
|
| 1280 |
+
==========
|
| 1281 |
+
|
| 1282 |
+
printer : Printer
|
| 1283 |
+
The printer to be used to print the LaTeX string representation.
|
| 1284 |
+
|
| 1285 |
+
"""
|
| 1286 |
+
l_M_tilde = self.args[0]
|
| 1287 |
+
_l_M_tilde = printer._print(l_M_tilde)
|
| 1288 |
+
return r'\operatorname{fl}^M_{act} \left( %s \right)' % _l_M_tilde
|
| 1289 |
+
|
| 1290 |
+
|
| 1291 |
+
class FiberForceVelocityDeGroote2016(CharacteristicCurveFunction):
|
| 1292 |
+
r"""Muscle fiber force-velocity curve based on De Groote et al., 2016 [1]_.
|
| 1293 |
+
|
| 1294 |
+
Explanation
|
| 1295 |
+
===========
|
| 1296 |
+
|
| 1297 |
+
Gives the normalized muscle fiber force produced as a function of
|
| 1298 |
+
normalized tendon velocity.
|
| 1299 |
+
|
| 1300 |
+
The function is defined by the equation:
|
| 1301 |
+
|
| 1302 |
+
$fv^M = c_0 \log{\left(c_1 \tilde{v}_m + c_2\right) + \sqrt{\left(c_1 \tilde{v}_m + c_2\right)^2 + 1}} + c_3$
|
| 1303 |
+
|
| 1304 |
+
with constant values of $c_0 = -0.318$, $c_1 = -8.149$, $c_2 = -0.374$, and
|
| 1305 |
+
$c_3 = 0.886$.
|
| 1306 |
+
|
| 1307 |
+
While it is possible to change the constant values, these were carefully
|
| 1308 |
+
selected in the original publication to give the characteristic curve
|
| 1309 |
+
specific and required properties. For example, the function produces a
|
| 1310 |
+
normalized muscle fiber force of 1 when the muscle fibers are contracting
|
| 1311 |
+
isometrically (they have an extension rate of 0).
|
| 1312 |
+
|
| 1313 |
+
Examples
|
| 1314 |
+
========
|
| 1315 |
+
|
| 1316 |
+
The preferred way to instantiate :class:`FiberForceVelocityDeGroote2016` is using
|
| 1317 |
+
the :meth:`~.with_defaults` constructor because this will automatically populate
|
| 1318 |
+
the constants within the characteristic curve equation with the floating
|
| 1319 |
+
point values from the original publication. This constructor takes a single
|
| 1320 |
+
argument corresponding to normalized muscle fiber extension velocity. We'll
|
| 1321 |
+
create a :class:`~.Symbol` called ``v_M_tilde`` to represent this.
|
| 1322 |
+
|
| 1323 |
+
>>> from sympy import Symbol
|
| 1324 |
+
>>> from sympy.physics.biomechanics import FiberForceVelocityDeGroote2016
|
| 1325 |
+
>>> v_M_tilde = Symbol('v_M_tilde')
|
| 1326 |
+
>>> fv_M = FiberForceVelocityDeGroote2016.with_defaults(v_M_tilde)
|
| 1327 |
+
>>> fv_M
|
| 1328 |
+
FiberForceVelocityDeGroote2016(v_M_tilde, -0.318, -8.149, -0.374, 0.886)
|
| 1329 |
+
|
| 1330 |
+
It's also possible to populate the four constants with your own values too.
|
| 1331 |
+
|
| 1332 |
+
>>> from sympy import symbols
|
| 1333 |
+
>>> c0, c1, c2, c3 = symbols('c0 c1 c2 c3')
|
| 1334 |
+
>>> fv_M = FiberForceVelocityDeGroote2016(v_M_tilde, c0, c1, c2, c3)
|
| 1335 |
+
>>> fv_M
|
| 1336 |
+
FiberForceVelocityDeGroote2016(v_M_tilde, c0, c1, c2, c3)
|
| 1337 |
+
|
| 1338 |
+
You don't just have to use symbols as the arguments, it's also possible to
|
| 1339 |
+
use expressions. Let's create a new pair of symbols, ``v_M`` and
|
| 1340 |
+
``v_M_max``, representing muscle fiber extension velocity and maximum
|
| 1341 |
+
muscle fiber extension velocity respectively. We can then represent
|
| 1342 |
+
``v_M_tilde`` as an expression, the ratio of these.
|
| 1343 |
+
|
| 1344 |
+
>>> v_M, v_M_max = symbols('v_M v_M_max')
|
| 1345 |
+
>>> v_M_tilde = v_M/v_M_max
|
| 1346 |
+
>>> fv_M = FiberForceVelocityDeGroote2016.with_defaults(v_M_tilde)
|
| 1347 |
+
>>> fv_M
|
| 1348 |
+
FiberForceVelocityDeGroote2016(v_M/v_M_max, -0.318, -8.149, -0.374, 0.886)
|
| 1349 |
+
|
| 1350 |
+
To inspect the actual symbolic expression that this function represents,
|
| 1351 |
+
we can call the :meth:`~.doit` method on an instance. We'll use the keyword
|
| 1352 |
+
argument ``evaluate=False`` as this will keep the expression in its
|
| 1353 |
+
canonical form and won't simplify any constants.
|
| 1354 |
+
|
| 1355 |
+
>>> fv_M.doit(evaluate=False)
|
| 1356 |
+
0.886 - 0.318*log(-8.149*v_M/v_M_max - 0.374 + sqrt(1 + (-8.149*v_M/v_M_max
|
| 1357 |
+
- 0.374)**2))
|
| 1358 |
+
|
| 1359 |
+
The function can also be differentiated. We'll differentiate with respect
|
| 1360 |
+
to v_M using the ``diff`` method on an instance with the single positional
|
| 1361 |
+
argument ``v_M``.
|
| 1362 |
+
|
| 1363 |
+
>>> fv_M.diff(v_M)
|
| 1364 |
+
2.591382*(1 + (-8.149*v_M/v_M_max - 0.374)**2)**(-1/2)/v_M_max
|
| 1365 |
+
|
| 1366 |
+
References
|
| 1367 |
+
==========
|
| 1368 |
+
|
| 1369 |
+
.. [1] De Groote, F., Kinney, A. L., Rao, A. V., & Fregly, B. J., Evaluation
|
| 1370 |
+
of direct collocation optimal control problem formulations for
|
| 1371 |
+
solving the muscle redundancy problem, Annals of biomedical
|
| 1372 |
+
engineering, 44(10), (2016) pp. 2922-2936
|
| 1373 |
+
|
| 1374 |
+
"""
|
| 1375 |
+
|
| 1376 |
+
@classmethod
|
| 1377 |
+
def with_defaults(cls, v_M_tilde):
|
| 1378 |
+
r"""Recommended constructor that will use the published constants.
|
| 1379 |
+
|
| 1380 |
+
Explanation
|
| 1381 |
+
===========
|
| 1382 |
+
|
| 1383 |
+
Returns a new instance of the muscle fiber force-velocity function
|
| 1384 |
+
using the four constant values specified in the original publication.
|
| 1385 |
+
|
| 1386 |
+
These have the values:
|
| 1387 |
+
|
| 1388 |
+
$c_0 = -0.318$
|
| 1389 |
+
$c_1 = -8.149$
|
| 1390 |
+
$c_2 = -0.374$
|
| 1391 |
+
$c_3 = 0.886$
|
| 1392 |
+
|
| 1393 |
+
Parameters
|
| 1394 |
+
==========
|
| 1395 |
+
|
| 1396 |
+
v_M_tilde : Any (sympifiable)
|
| 1397 |
+
Normalized muscle fiber extension velocity.
|
| 1398 |
+
|
| 1399 |
+
"""
|
| 1400 |
+
c0 = Float('-0.318')
|
| 1401 |
+
c1 = Float('-8.149')
|
| 1402 |
+
c2 = Float('-0.374')
|
| 1403 |
+
c3 = Float('0.886')
|
| 1404 |
+
return cls(v_M_tilde, c0, c1, c2, c3)
|
| 1405 |
+
|
| 1406 |
+
@classmethod
|
| 1407 |
+
def eval(cls, v_M_tilde, c0, c1, c2, c3):
|
| 1408 |
+
"""Evaluation of basic inputs.
|
| 1409 |
+
|
| 1410 |
+
Parameters
|
| 1411 |
+
==========
|
| 1412 |
+
|
| 1413 |
+
v_M_tilde : Any (sympifiable)
|
| 1414 |
+
Normalized muscle fiber extension velocity.
|
| 1415 |
+
c0 : Any (sympifiable)
|
| 1416 |
+
The first constant in the characteristic equation. The published
|
| 1417 |
+
value is ``-0.318``.
|
| 1418 |
+
c1 : Any (sympifiable)
|
| 1419 |
+
The second constant in the characteristic equation. The published
|
| 1420 |
+
value is ``-8.149``.
|
| 1421 |
+
c2 : Any (sympifiable)
|
| 1422 |
+
The third constant in the characteristic equation. The published
|
| 1423 |
+
value is ``-0.374``.
|
| 1424 |
+
c3 : Any (sympifiable)
|
| 1425 |
+
The fourth constant in the characteristic equation. The published
|
| 1426 |
+
value is ``0.886``.
|
| 1427 |
+
|
| 1428 |
+
"""
|
| 1429 |
+
pass
|
| 1430 |
+
|
| 1431 |
+
def _eval_evalf(self, prec):
|
| 1432 |
+
"""Evaluate the expression numerically using ``evalf``."""
|
| 1433 |
+
return self.doit(deep=False, evaluate=False)._eval_evalf(prec)
|
| 1434 |
+
|
| 1435 |
+
def doit(self, deep=True, evaluate=True, **hints):
|
| 1436 |
+
"""Evaluate the expression defining the function.
|
| 1437 |
+
|
| 1438 |
+
Parameters
|
| 1439 |
+
==========
|
| 1440 |
+
|
| 1441 |
+
deep : bool
|
| 1442 |
+
Whether ``doit`` should be recursively called. Default is ``True``.
|
| 1443 |
+
evaluate : bool.
|
| 1444 |
+
Whether the SymPy expression should be evaluated as it is
|
| 1445 |
+
constructed. If ``False``, then no constant folding will be
|
| 1446 |
+
conducted which will leave the expression in a more numerically-
|
| 1447 |
+
stable for values of ``v_M_tilde`` that correspond to a sensible
|
| 1448 |
+
operating range for a musculotendon. Default is ``True``.
|
| 1449 |
+
**kwargs : dict[str, Any]
|
| 1450 |
+
Additional keyword argument pairs to be recursively passed to
|
| 1451 |
+
``doit``.
|
| 1452 |
+
|
| 1453 |
+
"""
|
| 1454 |
+
v_M_tilde, *constants = self.args
|
| 1455 |
+
if deep:
|
| 1456 |
+
hints['evaluate'] = evaluate
|
| 1457 |
+
v_M_tilde = v_M_tilde.doit(deep=deep, **hints)
|
| 1458 |
+
c0, c1, c2, c3 = [c.doit(deep=deep, **hints) for c in constants]
|
| 1459 |
+
else:
|
| 1460 |
+
c0, c1, c2, c3 = constants
|
| 1461 |
+
|
| 1462 |
+
if evaluate:
|
| 1463 |
+
return c0*log(c1*v_M_tilde + c2 + sqrt((c1*v_M_tilde + c2)**2 + 1)) + c3
|
| 1464 |
+
|
| 1465 |
+
return c0*log(c1*v_M_tilde + c2 + sqrt(UnevaluatedExpr(c1*v_M_tilde + c2)**2 + 1)) + c3
|
| 1466 |
+
|
| 1467 |
+
def fdiff(self, argindex=1):
|
| 1468 |
+
"""Derivative of the function with respect to a single argument.
|
| 1469 |
+
|
| 1470 |
+
Parameters
|
| 1471 |
+
==========
|
| 1472 |
+
|
| 1473 |
+
argindex : int
|
| 1474 |
+
The index of the function's arguments with respect to which the
|
| 1475 |
+
derivative should be taken. Argument indexes start at ``1``.
|
| 1476 |
+
Default is ``1``.
|
| 1477 |
+
|
| 1478 |
+
"""
|
| 1479 |
+
v_M_tilde, c0, c1, c2, c3 = self.args
|
| 1480 |
+
if argindex == 1:
|
| 1481 |
+
return c0*c1/sqrt(UnevaluatedExpr(c1*v_M_tilde + c2)**2 + 1)
|
| 1482 |
+
elif argindex == 2:
|
| 1483 |
+
return log(
|
| 1484 |
+
c1*v_M_tilde + c2
|
| 1485 |
+
+ sqrt(UnevaluatedExpr(c1*v_M_tilde + c2)**2 + 1)
|
| 1486 |
+
)
|
| 1487 |
+
elif argindex == 3:
|
| 1488 |
+
return c0*v_M_tilde/sqrt(UnevaluatedExpr(c1*v_M_tilde + c2)**2 + 1)
|
| 1489 |
+
elif argindex == 4:
|
| 1490 |
+
return c0/sqrt(UnevaluatedExpr(c1*v_M_tilde + c2)**2 + 1)
|
| 1491 |
+
elif argindex == 5:
|
| 1492 |
+
return Integer(1)
|
| 1493 |
+
|
| 1494 |
+
raise ArgumentIndexError(self, argindex)
|
| 1495 |
+
|
| 1496 |
+
def inverse(self, argindex=1):
|
| 1497 |
+
"""Inverse function.
|
| 1498 |
+
|
| 1499 |
+
Parameters
|
| 1500 |
+
==========
|
| 1501 |
+
|
| 1502 |
+
argindex : int
|
| 1503 |
+
Value to start indexing the arguments at. Default is ``1``.
|
| 1504 |
+
|
| 1505 |
+
"""
|
| 1506 |
+
return FiberForceVelocityInverseDeGroote2016
|
| 1507 |
+
|
| 1508 |
+
def _latex(self, printer):
|
| 1509 |
+
"""Print a LaTeX representation of the function defining the curve.
|
| 1510 |
+
|
| 1511 |
+
Parameters
|
| 1512 |
+
==========
|
| 1513 |
+
|
| 1514 |
+
printer : Printer
|
| 1515 |
+
The printer to be used to print the LaTeX string representation.
|
| 1516 |
+
|
| 1517 |
+
"""
|
| 1518 |
+
v_M_tilde = self.args[0]
|
| 1519 |
+
_v_M_tilde = printer._print(v_M_tilde)
|
| 1520 |
+
return r'\operatorname{fv}^M \left( %s \right)' % _v_M_tilde
|
| 1521 |
+
|
| 1522 |
+
|
| 1523 |
+
class FiberForceVelocityInverseDeGroote2016(CharacteristicCurveFunction):
|
| 1524 |
+
r"""Inverse muscle fiber force-velocity curve based on De Groote et al.,
|
| 1525 |
+
2016 [1]_.
|
| 1526 |
+
|
| 1527 |
+
Explanation
|
| 1528 |
+
===========
|
| 1529 |
+
|
| 1530 |
+
Gives the normalized muscle fiber velocity that produces a specific
|
| 1531 |
+
normalized muscle fiber force.
|
| 1532 |
+
|
| 1533 |
+
The function is defined by the equation:
|
| 1534 |
+
|
| 1535 |
+
${fv^M}^{-1} = \frac{\sinh{\frac{fv^M - c_3}{c_0}} - c_2}{c_1}$
|
| 1536 |
+
|
| 1537 |
+
with constant values of $c_0 = -0.318$, $c_1 = -8.149$, $c_2 = -0.374$, and
|
| 1538 |
+
$c_3 = 0.886$. This function is the exact analytical inverse of the related
|
| 1539 |
+
muscle fiber force-velocity curve ``FiberForceVelocityDeGroote2016``.
|
| 1540 |
+
|
| 1541 |
+
While it is possible to change the constant values, these were carefully
|
| 1542 |
+
selected in the original publication to give the characteristic curve
|
| 1543 |
+
specific and required properties. For example, the function produces a
|
| 1544 |
+
normalized muscle fiber force of 1 when the muscle fibers are contracting
|
| 1545 |
+
isometrically (they have an extension rate of 0).
|
| 1546 |
+
|
| 1547 |
+
Examples
|
| 1548 |
+
========
|
| 1549 |
+
|
| 1550 |
+
The preferred way to instantiate :class:`FiberForceVelocityInverseDeGroote2016`
|
| 1551 |
+
is using the :meth:`~.with_defaults` constructor because this will automatically
|
| 1552 |
+
populate the constants within the characteristic curve equation with the
|
| 1553 |
+
floating point values from the original publication. This constructor takes
|
| 1554 |
+
a single argument corresponding to normalized muscle fiber force-velocity
|
| 1555 |
+
component of the muscle fiber force. We'll create a :class:`~.Symbol` called
|
| 1556 |
+
``fv_M`` to represent this.
|
| 1557 |
+
|
| 1558 |
+
>>> from sympy import Symbol
|
| 1559 |
+
>>> from sympy.physics.biomechanics import FiberForceVelocityInverseDeGroote2016
|
| 1560 |
+
>>> fv_M = Symbol('fv_M')
|
| 1561 |
+
>>> v_M_tilde = FiberForceVelocityInverseDeGroote2016.with_defaults(fv_M)
|
| 1562 |
+
>>> v_M_tilde
|
| 1563 |
+
FiberForceVelocityInverseDeGroote2016(fv_M, -0.318, -8.149, -0.374, 0.886)
|
| 1564 |
+
|
| 1565 |
+
It's also possible to populate the four constants with your own values too.
|
| 1566 |
+
|
| 1567 |
+
>>> from sympy import symbols
|
| 1568 |
+
>>> c0, c1, c2, c3 = symbols('c0 c1 c2 c3')
|
| 1569 |
+
>>> v_M_tilde = FiberForceVelocityInverseDeGroote2016(fv_M, c0, c1, c2, c3)
|
| 1570 |
+
>>> v_M_tilde
|
| 1571 |
+
FiberForceVelocityInverseDeGroote2016(fv_M, c0, c1, c2, c3)
|
| 1572 |
+
|
| 1573 |
+
To inspect the actual symbolic expression that this function represents,
|
| 1574 |
+
we can call the :meth:`~.doit` method on an instance. We'll use the keyword
|
| 1575 |
+
argument ``evaluate=False`` as this will keep the expression in its
|
| 1576 |
+
canonical form and won't simplify any constants.
|
| 1577 |
+
|
| 1578 |
+
>>> v_M_tilde.doit(evaluate=False)
|
| 1579 |
+
(-c2 + sinh((-c3 + fv_M)/c0))/c1
|
| 1580 |
+
|
| 1581 |
+
The function can also be differentiated. We'll differentiate with respect
|
| 1582 |
+
to fv_M using the ``diff`` method on an instance with the single positional
|
| 1583 |
+
argument ``fv_M``.
|
| 1584 |
+
|
| 1585 |
+
>>> v_M_tilde.diff(fv_M)
|
| 1586 |
+
cosh((-c3 + fv_M)/c0)/(c0*c1)
|
| 1587 |
+
|
| 1588 |
+
References
|
| 1589 |
+
==========
|
| 1590 |
+
|
| 1591 |
+
.. [1] De Groote, F., Kinney, A. L., Rao, A. V., & Fregly, B. J., Evaluation
|
| 1592 |
+
of direct collocation optimal control problem formulations for
|
| 1593 |
+
solving the muscle redundancy problem, Annals of biomedical
|
| 1594 |
+
engineering, 44(10), (2016) pp. 2922-2936
|
| 1595 |
+
|
| 1596 |
+
"""
|
| 1597 |
+
|
| 1598 |
+
@classmethod
|
| 1599 |
+
def with_defaults(cls, fv_M):
|
| 1600 |
+
r"""Recommended constructor that will use the published constants.
|
| 1601 |
+
|
| 1602 |
+
Explanation
|
| 1603 |
+
===========
|
| 1604 |
+
|
| 1605 |
+
Returns a new instance of the inverse muscle fiber force-velocity
|
| 1606 |
+
function using the four constant values specified in the original
|
| 1607 |
+
publication.
|
| 1608 |
+
|
| 1609 |
+
These have the values:
|
| 1610 |
+
|
| 1611 |
+
$c_0 = -0.318$
|
| 1612 |
+
$c_1 = -8.149$
|
| 1613 |
+
$c_2 = -0.374$
|
| 1614 |
+
$c_3 = 0.886$
|
| 1615 |
+
|
| 1616 |
+
Parameters
|
| 1617 |
+
==========
|
| 1618 |
+
|
| 1619 |
+
fv_M : Any (sympifiable)
|
| 1620 |
+
Normalized muscle fiber extension velocity.
|
| 1621 |
+
|
| 1622 |
+
"""
|
| 1623 |
+
c0 = Float('-0.318')
|
| 1624 |
+
c1 = Float('-8.149')
|
| 1625 |
+
c2 = Float('-0.374')
|
| 1626 |
+
c3 = Float('0.886')
|
| 1627 |
+
return cls(fv_M, c0, c1, c2, c3)
|
| 1628 |
+
|
| 1629 |
+
@classmethod
|
| 1630 |
+
def eval(cls, fv_M, c0, c1, c2, c3):
|
| 1631 |
+
"""Evaluation of basic inputs.
|
| 1632 |
+
|
| 1633 |
+
Parameters
|
| 1634 |
+
==========
|
| 1635 |
+
|
| 1636 |
+
fv_M : Any (sympifiable)
|
| 1637 |
+
Normalized muscle fiber force as a function of muscle fiber
|
| 1638 |
+
extension velocity.
|
| 1639 |
+
c0 : Any (sympifiable)
|
| 1640 |
+
The first constant in the characteristic equation. The published
|
| 1641 |
+
value is ``-0.318``.
|
| 1642 |
+
c1 : Any (sympifiable)
|
| 1643 |
+
The second constant in the characteristic equation. The published
|
| 1644 |
+
value is ``-8.149``.
|
| 1645 |
+
c2 : Any (sympifiable)
|
| 1646 |
+
The third constant in the characteristic equation. The published
|
| 1647 |
+
value is ``-0.374``.
|
| 1648 |
+
c3 : Any (sympifiable)
|
| 1649 |
+
The fourth constant in the characteristic equation. The published
|
| 1650 |
+
value is ``0.886``.
|
| 1651 |
+
|
| 1652 |
+
"""
|
| 1653 |
+
pass
|
| 1654 |
+
|
| 1655 |
+
def _eval_evalf(self, prec):
|
| 1656 |
+
"""Evaluate the expression numerically using ``evalf``."""
|
| 1657 |
+
return self.doit(deep=False, evaluate=False)._eval_evalf(prec)
|
| 1658 |
+
|
| 1659 |
+
def doit(self, deep=True, evaluate=True, **hints):
|
| 1660 |
+
"""Evaluate the expression defining the function.
|
| 1661 |
+
|
| 1662 |
+
Parameters
|
| 1663 |
+
==========
|
| 1664 |
+
|
| 1665 |
+
deep : bool
|
| 1666 |
+
Whether ``doit`` should be recursively called. Default is ``True``.
|
| 1667 |
+
evaluate : bool.
|
| 1668 |
+
Whether the SymPy expression should be evaluated as it is
|
| 1669 |
+
constructed. If ``False``, then no constant folding will be
|
| 1670 |
+
conducted which will leave the expression in a more numerically-
|
| 1671 |
+
stable for values of ``fv_M`` that correspond to a sensible
|
| 1672 |
+
operating range for a musculotendon. Default is ``True``.
|
| 1673 |
+
**kwargs : dict[str, Any]
|
| 1674 |
+
Additional keyword argument pairs to be recursively passed to
|
| 1675 |
+
``doit``.
|
| 1676 |
+
|
| 1677 |
+
"""
|
| 1678 |
+
fv_M, *constants = self.args
|
| 1679 |
+
if deep:
|
| 1680 |
+
hints['evaluate'] = evaluate
|
| 1681 |
+
fv_M = fv_M.doit(deep=deep, **hints)
|
| 1682 |
+
c0, c1, c2, c3 = [c.doit(deep=deep, **hints) for c in constants]
|
| 1683 |
+
else:
|
| 1684 |
+
c0, c1, c2, c3 = constants
|
| 1685 |
+
|
| 1686 |
+
if evaluate:
|
| 1687 |
+
return (sinh((fv_M - c3)/c0) - c2)/c1
|
| 1688 |
+
|
| 1689 |
+
return (sinh(UnevaluatedExpr(fv_M - c3)/c0) - c2)/c1
|
| 1690 |
+
|
| 1691 |
+
def fdiff(self, argindex=1):
|
| 1692 |
+
"""Derivative of the function with respect to a single argument.
|
| 1693 |
+
|
| 1694 |
+
Parameters
|
| 1695 |
+
==========
|
| 1696 |
+
|
| 1697 |
+
argindex : int
|
| 1698 |
+
The index of the function's arguments with respect to which the
|
| 1699 |
+
derivative should be taken. Argument indexes start at ``1``.
|
| 1700 |
+
Default is ``1``.
|
| 1701 |
+
|
| 1702 |
+
"""
|
| 1703 |
+
fv_M, c0, c1, c2, c3 = self.args
|
| 1704 |
+
if argindex == 1:
|
| 1705 |
+
return cosh((fv_M - c3)/c0)/(c0*c1)
|
| 1706 |
+
elif argindex == 2:
|
| 1707 |
+
return (c3 - fv_M)*cosh((fv_M - c3)/c0)/(c0**2*c1)
|
| 1708 |
+
elif argindex == 3:
|
| 1709 |
+
return (c2 - sinh((fv_M - c3)/c0))/c1**2
|
| 1710 |
+
elif argindex == 4:
|
| 1711 |
+
return -1/c1
|
| 1712 |
+
elif argindex == 5:
|
| 1713 |
+
return -cosh((fv_M - c3)/c0)/(c0*c1)
|
| 1714 |
+
|
| 1715 |
+
raise ArgumentIndexError(self, argindex)
|
| 1716 |
+
|
| 1717 |
+
def inverse(self, argindex=1):
|
| 1718 |
+
"""Inverse function.
|
| 1719 |
+
|
| 1720 |
+
Parameters
|
| 1721 |
+
==========
|
| 1722 |
+
|
| 1723 |
+
argindex : int
|
| 1724 |
+
Value to start indexing the arguments at. Default is ``1``.
|
| 1725 |
+
|
| 1726 |
+
"""
|
| 1727 |
+
return FiberForceVelocityDeGroote2016
|
| 1728 |
+
|
| 1729 |
+
def _latex(self, printer):
|
| 1730 |
+
"""Print a LaTeX representation of the function defining the curve.
|
| 1731 |
+
|
| 1732 |
+
Parameters
|
| 1733 |
+
==========
|
| 1734 |
+
|
| 1735 |
+
printer : Printer
|
| 1736 |
+
The printer to be used to print the LaTeX string representation.
|
| 1737 |
+
|
| 1738 |
+
"""
|
| 1739 |
+
fv_M = self.args[0]
|
| 1740 |
+
_fv_M = printer._print(fv_M)
|
| 1741 |
+
return r'\left( \operatorname{fv}^M \right)^{-1} \left( %s \right)' % _fv_M
|
| 1742 |
+
|
| 1743 |
+
|
| 1744 |
+
@dataclass(frozen=True)
|
| 1745 |
+
class CharacteristicCurveCollection:
|
| 1746 |
+
"""Simple data container to group together related characteristic curves."""
|
| 1747 |
+
tendon_force_length: CharacteristicCurveFunction
|
| 1748 |
+
tendon_force_length_inverse: CharacteristicCurveFunction
|
| 1749 |
+
fiber_force_length_passive: CharacteristicCurveFunction
|
| 1750 |
+
fiber_force_length_passive_inverse: CharacteristicCurveFunction
|
| 1751 |
+
fiber_force_length_active: CharacteristicCurveFunction
|
| 1752 |
+
fiber_force_velocity: CharacteristicCurveFunction
|
| 1753 |
+
fiber_force_velocity_inverse: CharacteristicCurveFunction
|
| 1754 |
+
|
| 1755 |
+
def __iter__(self):
|
| 1756 |
+
"""Iterator support for ``CharacteristicCurveCollection``."""
|
| 1757 |
+
yield self.tendon_force_length
|
| 1758 |
+
yield self.tendon_force_length_inverse
|
| 1759 |
+
yield self.fiber_force_length_passive
|
| 1760 |
+
yield self.fiber_force_length_passive_inverse
|
| 1761 |
+
yield self.fiber_force_length_active
|
| 1762 |
+
yield self.fiber_force_velocity
|
| 1763 |
+
yield self.fiber_force_velocity_inverse
|
evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/musculotendon.py
ADDED
|
@@ -0,0 +1,1424 @@
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|
| 1 |
+
"""Implementations of musculotendon models.
|
| 2 |
+
|
| 3 |
+
Musculotendon models are a critical component of biomechanical models, one that
|
| 4 |
+
differentiates them from pure multibody systems. Musculotendon models produce a
|
| 5 |
+
force dependent on their level of activation, their length, and their
|
| 6 |
+
extension velocity. Length- and extension velocity-dependent force production
|
| 7 |
+
are governed by force-length and force-velocity characteristics.
|
| 8 |
+
These are normalized functions that are dependent on the musculotendon's state
|
| 9 |
+
and are specific to a given musculotendon model.
|
| 10 |
+
|
| 11 |
+
"""
|
| 12 |
+
|
| 13 |
+
from abc import abstractmethod
|
| 14 |
+
from enum import IntEnum, unique
|
| 15 |
+
|
| 16 |
+
from sympy.core.numbers import Float, Integer
|
| 17 |
+
from sympy.core.symbol import Symbol, symbols
|
| 18 |
+
from sympy.functions.elementary.miscellaneous import sqrt
|
| 19 |
+
from sympy.functions.elementary.trigonometric import cos, sin
|
| 20 |
+
from sympy.matrices.dense import MutableDenseMatrix as Matrix, diag, eye, zeros
|
| 21 |
+
from sympy.physics.biomechanics.activation import ActivationBase
|
| 22 |
+
from sympy.physics.biomechanics.curve import (
|
| 23 |
+
CharacteristicCurveCollection,
|
| 24 |
+
FiberForceLengthActiveDeGroote2016,
|
| 25 |
+
FiberForceLengthPassiveDeGroote2016,
|
| 26 |
+
FiberForceLengthPassiveInverseDeGroote2016,
|
| 27 |
+
FiberForceVelocityDeGroote2016,
|
| 28 |
+
FiberForceVelocityInverseDeGroote2016,
|
| 29 |
+
TendonForceLengthDeGroote2016,
|
| 30 |
+
TendonForceLengthInverseDeGroote2016,
|
| 31 |
+
)
|
| 32 |
+
from sympy.physics.biomechanics._mixin import _NamedMixin
|
| 33 |
+
from sympy.physics.mechanics.actuator import ForceActuator
|
| 34 |
+
from sympy.physics.vector.functions import dynamicsymbols
|
| 35 |
+
|
| 36 |
+
|
| 37 |
+
__all__ = [
|
| 38 |
+
'MusculotendonBase',
|
| 39 |
+
'MusculotendonDeGroote2016',
|
| 40 |
+
'MusculotendonFormulation',
|
| 41 |
+
]
|
| 42 |
+
|
| 43 |
+
|
| 44 |
+
@unique
|
| 45 |
+
class MusculotendonFormulation(IntEnum):
|
| 46 |
+
"""Enumeration of types of musculotendon dynamics formulations.
|
| 47 |
+
|
| 48 |
+
Explanation
|
| 49 |
+
===========
|
| 50 |
+
|
| 51 |
+
An (integer) enumeration is used as it allows for clearer selection of the
|
| 52 |
+
different formulations of musculotendon dynamics.
|
| 53 |
+
|
| 54 |
+
Members
|
| 55 |
+
=======
|
| 56 |
+
|
| 57 |
+
RIGID_TENDON : 0
|
| 58 |
+
A rigid tendon model.
|
| 59 |
+
FIBER_LENGTH_EXPLICIT : 1
|
| 60 |
+
An explicit elastic tendon model with the muscle fiber length (l_M) as
|
| 61 |
+
the state variable.
|
| 62 |
+
TENDON_FORCE_EXPLICIT : 2
|
| 63 |
+
An explicit elastic tendon model with the tendon force (F_T) as the
|
| 64 |
+
state variable.
|
| 65 |
+
FIBER_LENGTH_IMPLICIT : 3
|
| 66 |
+
An implicit elastic tendon model with the muscle fiber length (l_M) as
|
| 67 |
+
the state variable and the muscle fiber velocity as an additional input
|
| 68 |
+
variable.
|
| 69 |
+
TENDON_FORCE_IMPLICIT : 4
|
| 70 |
+
An implicit elastic tendon model with the tendon force (F_T) as the
|
| 71 |
+
state variable as the muscle fiber velocity as an additional input
|
| 72 |
+
variable.
|
| 73 |
+
|
| 74 |
+
"""
|
| 75 |
+
|
| 76 |
+
RIGID_TENDON = 0
|
| 77 |
+
FIBER_LENGTH_EXPLICIT = 1
|
| 78 |
+
TENDON_FORCE_EXPLICIT = 2
|
| 79 |
+
FIBER_LENGTH_IMPLICIT = 3
|
| 80 |
+
TENDON_FORCE_IMPLICIT = 4
|
| 81 |
+
|
| 82 |
+
def __str__(self):
|
| 83 |
+
"""Returns a string representation of the enumeration value.
|
| 84 |
+
|
| 85 |
+
Notes
|
| 86 |
+
=====
|
| 87 |
+
|
| 88 |
+
This hard coding is required due to an incompatibility between the
|
| 89 |
+
``IntEnum`` implementations in Python 3.10 and Python 3.11
|
| 90 |
+
(https://github.com/python/cpython/issues/84247). From Python 3.11
|
| 91 |
+
onwards, the ``__str__`` method uses ``int.__str__``, whereas prior it
|
| 92 |
+
used ``Enum.__str__``. Once Python 3.11 becomes the minimum version
|
| 93 |
+
supported by SymPy, this method override can be removed.
|
| 94 |
+
|
| 95 |
+
"""
|
| 96 |
+
return str(self.value)
|
| 97 |
+
|
| 98 |
+
|
| 99 |
+
_DEFAULT_MUSCULOTENDON_FORMULATION = MusculotendonFormulation.RIGID_TENDON
|
| 100 |
+
|
| 101 |
+
|
| 102 |
+
class MusculotendonBase(ForceActuator, _NamedMixin):
|
| 103 |
+
r"""Abstract base class for all musculotendon classes to inherit from.
|
| 104 |
+
|
| 105 |
+
Explanation
|
| 106 |
+
===========
|
| 107 |
+
|
| 108 |
+
A musculotendon generates a contractile force based on its activation,
|
| 109 |
+
length, and shortening velocity. This abstract base class is to be inherited
|
| 110 |
+
by all musculotendon subclasses that implement different characteristic
|
| 111 |
+
musculotendon curves. Characteristic musculotendon curves are required for
|
| 112 |
+
the tendon force-length, passive fiber force-length, active fiber force-
|
| 113 |
+
length, and fiber force-velocity relationships.
|
| 114 |
+
|
| 115 |
+
Parameters
|
| 116 |
+
==========
|
| 117 |
+
|
| 118 |
+
name : str
|
| 119 |
+
The name identifier associated with the musculotendon. This name is used
|
| 120 |
+
as a suffix when automatically generated symbols are instantiated. It
|
| 121 |
+
must be a string of nonzero length.
|
| 122 |
+
pathway : PathwayBase
|
| 123 |
+
The pathway that the actuator follows. This must be an instance of a
|
| 124 |
+
concrete subclass of ``PathwayBase``, e.g. ``LinearPathway``.
|
| 125 |
+
activation_dynamics : ActivationBase
|
| 126 |
+
The activation dynamics that will be modeled within the musculotendon.
|
| 127 |
+
This must be an instance of a concrete subclass of ``ActivationBase``,
|
| 128 |
+
e.g. ``FirstOrderActivationDeGroote2016``.
|
| 129 |
+
musculotendon_dynamics : MusculotendonFormulation | int
|
| 130 |
+
The formulation of musculotendon dynamics that should be used
|
| 131 |
+
internally, i.e. rigid or elastic tendon model, the choice of
|
| 132 |
+
musculotendon state etc. This must be a member of the integer
|
| 133 |
+
enumeration ``MusculotendonFormulation`` or an integer that can be cast
|
| 134 |
+
to a member. To use a rigid tendon formulation, set this to
|
| 135 |
+
``MusculotendonFormulation.RIGID_TENDON`` (or the integer value ``0``,
|
| 136 |
+
which will be cast to the enumeration member). There are four possible
|
| 137 |
+
formulations for an elastic tendon model. To use an explicit formulation
|
| 138 |
+
with the fiber length as the state, set this to
|
| 139 |
+
``MusculotendonFormulation.FIBER_LENGTH_EXPLICIT`` (or the integer value
|
| 140 |
+
``1``). To use an explicit formulation with the tendon force as the
|
| 141 |
+
state, set this to ``MusculotendonFormulation.TENDON_FORCE_EXPLICIT``
|
| 142 |
+
(or the integer value ``2``). To use an implicit formulation with the
|
| 143 |
+
fiber length as the state, set this to
|
| 144 |
+
``MusculotendonFormulation.FIBER_LENGTH_IMPLICIT`` (or the integer value
|
| 145 |
+
``3``). To use an implicit formulation with the tendon force as the
|
| 146 |
+
state, set this to ``MusculotendonFormulation.TENDON_FORCE_IMPLICIT``
|
| 147 |
+
(or the integer value ``4``). The default is
|
| 148 |
+
``MusculotendonFormulation.RIGID_TENDON``, which corresponds to a rigid
|
| 149 |
+
tendon formulation.
|
| 150 |
+
tendon_slack_length : Expr | None
|
| 151 |
+
The length of the tendon when the musculotendon is in its unloaded
|
| 152 |
+
state. In a rigid tendon model the tendon length is the tendon slack
|
| 153 |
+
length. In all musculotendon models, tendon slack length is used to
|
| 154 |
+
normalize tendon length to give
|
| 155 |
+
:math:`\tilde{l}^T = \frac{l^T}{l^T_{slack}}`.
|
| 156 |
+
peak_isometric_force : Expr | None
|
| 157 |
+
The maximum force that the muscle fiber can produce when it is
|
| 158 |
+
undergoing an isometric contraction (no lengthening velocity). In all
|
| 159 |
+
musculotendon models, peak isometric force is used to normalized tendon
|
| 160 |
+
and muscle fiber force to give
|
| 161 |
+
:math:`\tilde{F}^T = \frac{F^T}{F^M_{max}}`.
|
| 162 |
+
optimal_fiber_length : Expr | None
|
| 163 |
+
The muscle fiber length at which the muscle fibers produce no passive
|
| 164 |
+
force and their maximum active force. In all musculotendon models,
|
| 165 |
+
optimal fiber length is used to normalize muscle fiber length to give
|
| 166 |
+
:math:`\tilde{l}^M = \frac{l^M}{l^M_{opt}}`.
|
| 167 |
+
maximal_fiber_velocity : Expr | None
|
| 168 |
+
The fiber velocity at which, during muscle fiber shortening, the muscle
|
| 169 |
+
fibers are unable to produce any active force. In all musculotendon
|
| 170 |
+
models, maximal fiber velocity is used to normalize muscle fiber
|
| 171 |
+
extension velocity to give :math:`\tilde{v}^M = \frac{v^M}{v^M_{max}}`.
|
| 172 |
+
optimal_pennation_angle : Expr | None
|
| 173 |
+
The pennation angle when muscle fiber length equals the optimal fiber
|
| 174 |
+
length.
|
| 175 |
+
fiber_damping_coefficient : Expr | None
|
| 176 |
+
The coefficient of damping to be used in the damping element in the
|
| 177 |
+
muscle fiber model.
|
| 178 |
+
with_defaults : bool
|
| 179 |
+
Whether ``with_defaults`` alternate constructors should be used when
|
| 180 |
+
automatically constructing child classes. Default is ``False``.
|
| 181 |
+
|
| 182 |
+
"""
|
| 183 |
+
|
| 184 |
+
def __init__(
|
| 185 |
+
self,
|
| 186 |
+
name,
|
| 187 |
+
pathway,
|
| 188 |
+
activation_dynamics,
|
| 189 |
+
*,
|
| 190 |
+
musculotendon_dynamics=_DEFAULT_MUSCULOTENDON_FORMULATION,
|
| 191 |
+
tendon_slack_length=None,
|
| 192 |
+
peak_isometric_force=None,
|
| 193 |
+
optimal_fiber_length=None,
|
| 194 |
+
maximal_fiber_velocity=None,
|
| 195 |
+
optimal_pennation_angle=None,
|
| 196 |
+
fiber_damping_coefficient=None,
|
| 197 |
+
with_defaults=False,
|
| 198 |
+
):
|
| 199 |
+
self.name = name
|
| 200 |
+
|
| 201 |
+
# Supply a placeholder force to the super initializer, this will be
|
| 202 |
+
# replaced later
|
| 203 |
+
super().__init__(Symbol('F'), pathway)
|
| 204 |
+
|
| 205 |
+
# Activation dynamics
|
| 206 |
+
if not isinstance(activation_dynamics, ActivationBase):
|
| 207 |
+
msg = (
|
| 208 |
+
f'Can\'t set attribute `activation_dynamics` to '
|
| 209 |
+
f'{activation_dynamics} as it must be of type '
|
| 210 |
+
f'`ActivationBase`, not {type(activation_dynamics)}.'
|
| 211 |
+
)
|
| 212 |
+
raise TypeError(msg)
|
| 213 |
+
self._activation_dynamics = activation_dynamics
|
| 214 |
+
self._child_objects = (self._activation_dynamics, )
|
| 215 |
+
|
| 216 |
+
# Constants
|
| 217 |
+
if tendon_slack_length is not None:
|
| 218 |
+
self._l_T_slack = tendon_slack_length
|
| 219 |
+
else:
|
| 220 |
+
self._l_T_slack = Symbol(f'l_T_slack_{self.name}')
|
| 221 |
+
if peak_isometric_force is not None:
|
| 222 |
+
self._F_M_max = peak_isometric_force
|
| 223 |
+
else:
|
| 224 |
+
self._F_M_max = Symbol(f'F_M_max_{self.name}')
|
| 225 |
+
if optimal_fiber_length is not None:
|
| 226 |
+
self._l_M_opt = optimal_fiber_length
|
| 227 |
+
else:
|
| 228 |
+
self._l_M_opt = Symbol(f'l_M_opt_{self.name}')
|
| 229 |
+
if maximal_fiber_velocity is not None:
|
| 230 |
+
self._v_M_max = maximal_fiber_velocity
|
| 231 |
+
else:
|
| 232 |
+
self._v_M_max = Symbol(f'v_M_max_{self.name}')
|
| 233 |
+
if optimal_pennation_angle is not None:
|
| 234 |
+
self._alpha_opt = optimal_pennation_angle
|
| 235 |
+
else:
|
| 236 |
+
self._alpha_opt = Symbol(f'alpha_opt_{self.name}')
|
| 237 |
+
if fiber_damping_coefficient is not None:
|
| 238 |
+
self._beta = fiber_damping_coefficient
|
| 239 |
+
else:
|
| 240 |
+
self._beta = Symbol(f'beta_{self.name}')
|
| 241 |
+
|
| 242 |
+
# Musculotendon dynamics
|
| 243 |
+
self._with_defaults = with_defaults
|
| 244 |
+
if musculotendon_dynamics == MusculotendonFormulation.RIGID_TENDON:
|
| 245 |
+
self._rigid_tendon_musculotendon_dynamics()
|
| 246 |
+
elif musculotendon_dynamics == MusculotendonFormulation.FIBER_LENGTH_EXPLICIT:
|
| 247 |
+
self._fiber_length_explicit_musculotendon_dynamics()
|
| 248 |
+
elif musculotendon_dynamics == MusculotendonFormulation.TENDON_FORCE_EXPLICIT:
|
| 249 |
+
self._tendon_force_explicit_musculotendon_dynamics()
|
| 250 |
+
elif musculotendon_dynamics == MusculotendonFormulation.FIBER_LENGTH_IMPLICIT:
|
| 251 |
+
self._fiber_length_implicit_musculotendon_dynamics()
|
| 252 |
+
elif musculotendon_dynamics == MusculotendonFormulation.TENDON_FORCE_IMPLICIT:
|
| 253 |
+
self._tendon_force_implicit_musculotendon_dynamics()
|
| 254 |
+
else:
|
| 255 |
+
msg = (
|
| 256 |
+
f'Musculotendon dynamics {repr(musculotendon_dynamics)} '
|
| 257 |
+
f'passed to `musculotendon_dynamics` was of type '
|
| 258 |
+
f'{type(musculotendon_dynamics)}, must be '
|
| 259 |
+
f'{MusculotendonFormulation}.'
|
| 260 |
+
)
|
| 261 |
+
raise TypeError(msg)
|
| 262 |
+
self._musculotendon_dynamics = musculotendon_dynamics
|
| 263 |
+
|
| 264 |
+
# Must override the placeholder value in `self._force` now that the
|
| 265 |
+
# actual force has been calculated by
|
| 266 |
+
# `self._<MUSCULOTENDON FORMULATION>_musculotendon_dynamics`.
|
| 267 |
+
# Note that `self._force` assumes forces are expansile, musculotendon
|
| 268 |
+
# forces are contractile hence the minus sign preceeding `self._F_T`
|
| 269 |
+
# (the tendon force).
|
| 270 |
+
self._force = -self._F_T
|
| 271 |
+
|
| 272 |
+
@classmethod
|
| 273 |
+
def with_defaults(
|
| 274 |
+
cls,
|
| 275 |
+
name,
|
| 276 |
+
pathway,
|
| 277 |
+
activation_dynamics,
|
| 278 |
+
*,
|
| 279 |
+
musculotendon_dynamics=_DEFAULT_MUSCULOTENDON_FORMULATION,
|
| 280 |
+
tendon_slack_length=None,
|
| 281 |
+
peak_isometric_force=None,
|
| 282 |
+
optimal_fiber_length=None,
|
| 283 |
+
maximal_fiber_velocity=Float('10.0'),
|
| 284 |
+
optimal_pennation_angle=Float('0.0'),
|
| 285 |
+
fiber_damping_coefficient=Float('0.1'),
|
| 286 |
+
):
|
| 287 |
+
r"""Recommended constructor that will use the published constants.
|
| 288 |
+
|
| 289 |
+
Explanation
|
| 290 |
+
===========
|
| 291 |
+
|
| 292 |
+
Returns a new instance of the musculotendon class using recommended
|
| 293 |
+
values for ``v_M_max``, ``alpha_opt``, and ``beta``. The values are:
|
| 294 |
+
|
| 295 |
+
:math:`v^M_{max} = 10`
|
| 296 |
+
:math:`\alpha_{opt} = 0`
|
| 297 |
+
:math:`\beta = \frac{1}{10}`
|
| 298 |
+
|
| 299 |
+
The musculotendon curves are also instantiated using the constants from
|
| 300 |
+
the original publication.
|
| 301 |
+
|
| 302 |
+
Parameters
|
| 303 |
+
==========
|
| 304 |
+
|
| 305 |
+
name : str
|
| 306 |
+
The name identifier associated with the musculotendon. This name is
|
| 307 |
+
used as a suffix when automatically generated symbols are
|
| 308 |
+
instantiated. It must be a string of nonzero length.
|
| 309 |
+
pathway : PathwayBase
|
| 310 |
+
The pathway that the actuator follows. This must be an instance of a
|
| 311 |
+
concrete subclass of ``PathwayBase``, e.g. ``LinearPathway``.
|
| 312 |
+
activation_dynamics : ActivationBase
|
| 313 |
+
The activation dynamics that will be modeled within the
|
| 314 |
+
musculotendon. This must be an instance of a concrete subclass of
|
| 315 |
+
``ActivationBase``, e.g. ``FirstOrderActivationDeGroote2016``.
|
| 316 |
+
musculotendon_dynamics : MusculotendonFormulation | int
|
| 317 |
+
The formulation of musculotendon dynamics that should be used
|
| 318 |
+
internally, i.e. rigid or elastic tendon model, the choice of
|
| 319 |
+
musculotendon state etc. This must be a member of the integer
|
| 320 |
+
enumeration ``MusculotendonFormulation`` or an integer that can be
|
| 321 |
+
cast to a member. To use a rigid tendon formulation, set this to
|
| 322 |
+
``MusculotendonFormulation.RIGID_TENDON`` (or the integer value
|
| 323 |
+
``0``, which will be cast to the enumeration member). There are four
|
| 324 |
+
possible formulations for an elastic tendon model. To use an
|
| 325 |
+
explicit formulation with the fiber length as the state, set this to
|
| 326 |
+
``MusculotendonFormulation.FIBER_LENGTH_EXPLICIT`` (or the integer
|
| 327 |
+
value ``1``). To use an explicit formulation with the tendon force
|
| 328 |
+
as the state, set this to
|
| 329 |
+
``MusculotendonFormulation.TENDON_FORCE_EXPLICIT`` (or the integer
|
| 330 |
+
value ``2``). To use an implicit formulation with the fiber length
|
| 331 |
+
as the state, set this to
|
| 332 |
+
``MusculotendonFormulation.FIBER_LENGTH_IMPLICIT`` (or the integer
|
| 333 |
+
value ``3``). To use an implicit formulation with the tendon force
|
| 334 |
+
as the state, set this to
|
| 335 |
+
``MusculotendonFormulation.TENDON_FORCE_IMPLICIT`` (or the integer
|
| 336 |
+
value ``4``). The default is
|
| 337 |
+
``MusculotendonFormulation.RIGID_TENDON``, which corresponds to a
|
| 338 |
+
rigid tendon formulation.
|
| 339 |
+
tendon_slack_length : Expr | None
|
| 340 |
+
The length of the tendon when the musculotendon is in its unloaded
|
| 341 |
+
state. In a rigid tendon model the tendon length is the tendon slack
|
| 342 |
+
length. In all musculotendon models, tendon slack length is used to
|
| 343 |
+
normalize tendon length to give
|
| 344 |
+
:math:`\tilde{l}^T = \frac{l^T}{l^T_{slack}}`.
|
| 345 |
+
peak_isometric_force : Expr | None
|
| 346 |
+
The maximum force that the muscle fiber can produce when it is
|
| 347 |
+
undergoing an isometric contraction (no lengthening velocity). In
|
| 348 |
+
all musculotendon models, peak isometric force is used to normalized
|
| 349 |
+
tendon and muscle fiber force to give
|
| 350 |
+
:math:`\tilde{F}^T = \frac{F^T}{F^M_{max}}`.
|
| 351 |
+
optimal_fiber_length : Expr | None
|
| 352 |
+
The muscle fiber length at which the muscle fibers produce no
|
| 353 |
+
passive force and their maximum active force. In all musculotendon
|
| 354 |
+
models, optimal fiber length is used to normalize muscle fiber
|
| 355 |
+
length to give :math:`\tilde{l}^M = \frac{l^M}{l^M_{opt}}`.
|
| 356 |
+
maximal_fiber_velocity : Expr | None
|
| 357 |
+
The fiber velocity at which, during muscle fiber shortening, the
|
| 358 |
+
muscle fibers are unable to produce any active force. In all
|
| 359 |
+
musculotendon models, maximal fiber velocity is used to normalize
|
| 360 |
+
muscle fiber extension velocity to give
|
| 361 |
+
:math:`\tilde{v}^M = \frac{v^M}{v^M_{max}}`.
|
| 362 |
+
optimal_pennation_angle : Expr | None
|
| 363 |
+
The pennation angle when muscle fiber length equals the optimal
|
| 364 |
+
fiber length.
|
| 365 |
+
fiber_damping_coefficient : Expr | None
|
| 366 |
+
The coefficient of damping to be used in the damping element in the
|
| 367 |
+
muscle fiber model.
|
| 368 |
+
|
| 369 |
+
"""
|
| 370 |
+
return cls(
|
| 371 |
+
name,
|
| 372 |
+
pathway,
|
| 373 |
+
activation_dynamics=activation_dynamics,
|
| 374 |
+
musculotendon_dynamics=musculotendon_dynamics,
|
| 375 |
+
tendon_slack_length=tendon_slack_length,
|
| 376 |
+
peak_isometric_force=peak_isometric_force,
|
| 377 |
+
optimal_fiber_length=optimal_fiber_length,
|
| 378 |
+
maximal_fiber_velocity=maximal_fiber_velocity,
|
| 379 |
+
optimal_pennation_angle=optimal_pennation_angle,
|
| 380 |
+
fiber_damping_coefficient=fiber_damping_coefficient,
|
| 381 |
+
with_defaults=True,
|
| 382 |
+
)
|
| 383 |
+
|
| 384 |
+
@abstractmethod
|
| 385 |
+
def curves(cls):
|
| 386 |
+
"""Return a ``CharacteristicCurveCollection`` of the curves related to
|
| 387 |
+
the specific model."""
|
| 388 |
+
pass
|
| 389 |
+
|
| 390 |
+
@property
|
| 391 |
+
def tendon_slack_length(self):
|
| 392 |
+
r"""Symbol or value corresponding to the tendon slack length constant.
|
| 393 |
+
|
| 394 |
+
Explanation
|
| 395 |
+
===========
|
| 396 |
+
|
| 397 |
+
The length of the tendon when the musculotendon is in its unloaded
|
| 398 |
+
state. In a rigid tendon model the tendon length is the tendon slack
|
| 399 |
+
length. In all musculotendon models, tendon slack length is used to
|
| 400 |
+
normalize tendon length to give
|
| 401 |
+
:math:`\tilde{l}^T = \frac{l^T}{l^T_{slack}}`.
|
| 402 |
+
|
| 403 |
+
The alias ``l_T_slack`` can also be used to access the same attribute.
|
| 404 |
+
|
| 405 |
+
"""
|
| 406 |
+
return self._l_T_slack
|
| 407 |
+
|
| 408 |
+
@property
|
| 409 |
+
def l_T_slack(self):
|
| 410 |
+
r"""Symbol or value corresponding to the tendon slack length constant.
|
| 411 |
+
|
| 412 |
+
Explanation
|
| 413 |
+
===========
|
| 414 |
+
|
| 415 |
+
The length of the tendon when the musculotendon is in its unloaded
|
| 416 |
+
state. In a rigid tendon model the tendon length is the tendon slack
|
| 417 |
+
length. In all musculotendon models, tendon slack length is used to
|
| 418 |
+
normalize tendon length to give
|
| 419 |
+
:math:`\tilde{l}^T = \frac{l^T}{l^T_{slack}}`.
|
| 420 |
+
|
| 421 |
+
The alias ``tendon_slack_length`` can also be used to access the same
|
| 422 |
+
attribute.
|
| 423 |
+
|
| 424 |
+
"""
|
| 425 |
+
return self._l_T_slack
|
| 426 |
+
|
| 427 |
+
@property
|
| 428 |
+
def peak_isometric_force(self):
|
| 429 |
+
r"""Symbol or value corresponding to the peak isometric force constant.
|
| 430 |
+
|
| 431 |
+
Explanation
|
| 432 |
+
===========
|
| 433 |
+
|
| 434 |
+
The maximum force that the muscle fiber can produce when it is
|
| 435 |
+
undergoing an isometric contraction (no lengthening velocity). In all
|
| 436 |
+
musculotendon models, peak isometric force is used to normalized tendon
|
| 437 |
+
and muscle fiber force to give
|
| 438 |
+
:math:`\tilde{F}^T = \frac{F^T}{F^M_{max}}`.
|
| 439 |
+
|
| 440 |
+
The alias ``F_M_max`` can also be used to access the same attribute.
|
| 441 |
+
|
| 442 |
+
"""
|
| 443 |
+
return self._F_M_max
|
| 444 |
+
|
| 445 |
+
@property
|
| 446 |
+
def F_M_max(self):
|
| 447 |
+
r"""Symbol or value corresponding to the peak isometric force constant.
|
| 448 |
+
|
| 449 |
+
Explanation
|
| 450 |
+
===========
|
| 451 |
+
|
| 452 |
+
The maximum force that the muscle fiber can produce when it is
|
| 453 |
+
undergoing an isometric contraction (no lengthening velocity). In all
|
| 454 |
+
musculotendon models, peak isometric force is used to normalized tendon
|
| 455 |
+
and muscle fiber force to give
|
| 456 |
+
:math:`\tilde{F}^T = \frac{F^T}{F^M_{max}}`.
|
| 457 |
+
|
| 458 |
+
The alias ``peak_isometric_force`` can also be used to access the same
|
| 459 |
+
attribute.
|
| 460 |
+
|
| 461 |
+
"""
|
| 462 |
+
return self._F_M_max
|
| 463 |
+
|
| 464 |
+
@property
|
| 465 |
+
def optimal_fiber_length(self):
|
| 466 |
+
r"""Symbol or value corresponding to the optimal fiber length constant.
|
| 467 |
+
|
| 468 |
+
Explanation
|
| 469 |
+
===========
|
| 470 |
+
|
| 471 |
+
The muscle fiber length at which the muscle fibers produce no passive
|
| 472 |
+
force and their maximum active force. In all musculotendon models,
|
| 473 |
+
optimal fiber length is used to normalize muscle fiber length to give
|
| 474 |
+
:math:`\tilde{l}^M = \frac{l^M}{l^M_{opt}}`.
|
| 475 |
+
|
| 476 |
+
The alias ``l_M_opt`` can also be used to access the same attribute.
|
| 477 |
+
|
| 478 |
+
"""
|
| 479 |
+
return self._l_M_opt
|
| 480 |
+
|
| 481 |
+
@property
|
| 482 |
+
def l_M_opt(self):
|
| 483 |
+
r"""Symbol or value corresponding to the optimal fiber length constant.
|
| 484 |
+
|
| 485 |
+
Explanation
|
| 486 |
+
===========
|
| 487 |
+
|
| 488 |
+
The muscle fiber length at which the muscle fibers produce no passive
|
| 489 |
+
force and their maximum active force. In all musculotendon models,
|
| 490 |
+
optimal fiber length is used to normalize muscle fiber length to give
|
| 491 |
+
:math:`\tilde{l}^M = \frac{l^M}{l^M_{opt}}`.
|
| 492 |
+
|
| 493 |
+
The alias ``optimal_fiber_length`` can also be used to access the same
|
| 494 |
+
attribute.
|
| 495 |
+
|
| 496 |
+
"""
|
| 497 |
+
return self._l_M_opt
|
| 498 |
+
|
| 499 |
+
@property
|
| 500 |
+
def maximal_fiber_velocity(self):
|
| 501 |
+
r"""Symbol or value corresponding to the maximal fiber velocity constant.
|
| 502 |
+
|
| 503 |
+
Explanation
|
| 504 |
+
===========
|
| 505 |
+
|
| 506 |
+
The fiber velocity at which, during muscle fiber shortening, the muscle
|
| 507 |
+
fibers are unable to produce any active force. In all musculotendon
|
| 508 |
+
models, maximal fiber velocity is used to normalize muscle fiber
|
| 509 |
+
extension velocity to give :math:`\tilde{v}^M = \frac{v^M}{v^M_{max}}`.
|
| 510 |
+
|
| 511 |
+
The alias ``v_M_max`` can also be used to access the same attribute.
|
| 512 |
+
|
| 513 |
+
"""
|
| 514 |
+
return self._v_M_max
|
| 515 |
+
|
| 516 |
+
@property
|
| 517 |
+
def v_M_max(self):
|
| 518 |
+
r"""Symbol or value corresponding to the maximal fiber velocity constant.
|
| 519 |
+
|
| 520 |
+
Explanation
|
| 521 |
+
===========
|
| 522 |
+
|
| 523 |
+
The fiber velocity at which, during muscle fiber shortening, the muscle
|
| 524 |
+
fibers are unable to produce any active force. In all musculotendon
|
| 525 |
+
models, maximal fiber velocity is used to normalize muscle fiber
|
| 526 |
+
extension velocity to give :math:`\tilde{v}^M = \frac{v^M}{v^M_{max}}`.
|
| 527 |
+
|
| 528 |
+
The alias ``maximal_fiber_velocity`` can also be used to access the same
|
| 529 |
+
attribute.
|
| 530 |
+
|
| 531 |
+
"""
|
| 532 |
+
return self._v_M_max
|
| 533 |
+
|
| 534 |
+
@property
|
| 535 |
+
def optimal_pennation_angle(self):
|
| 536 |
+
"""Symbol or value corresponding to the optimal pennation angle
|
| 537 |
+
constant.
|
| 538 |
+
|
| 539 |
+
Explanation
|
| 540 |
+
===========
|
| 541 |
+
|
| 542 |
+
The pennation angle when muscle fiber length equals the optimal fiber
|
| 543 |
+
length.
|
| 544 |
+
|
| 545 |
+
The alias ``alpha_opt`` can also be used to access the same attribute.
|
| 546 |
+
|
| 547 |
+
"""
|
| 548 |
+
return self._alpha_opt
|
| 549 |
+
|
| 550 |
+
@property
|
| 551 |
+
def alpha_opt(self):
|
| 552 |
+
"""Symbol or value corresponding to the optimal pennation angle
|
| 553 |
+
constant.
|
| 554 |
+
|
| 555 |
+
Explanation
|
| 556 |
+
===========
|
| 557 |
+
|
| 558 |
+
The pennation angle when muscle fiber length equals the optimal fiber
|
| 559 |
+
length.
|
| 560 |
+
|
| 561 |
+
The alias ``optimal_pennation_angle`` can also be used to access the
|
| 562 |
+
same attribute.
|
| 563 |
+
|
| 564 |
+
"""
|
| 565 |
+
return self._alpha_opt
|
| 566 |
+
|
| 567 |
+
@property
|
| 568 |
+
def fiber_damping_coefficient(self):
|
| 569 |
+
"""Symbol or value corresponding to the fiber damping coefficient
|
| 570 |
+
constant.
|
| 571 |
+
|
| 572 |
+
Explanation
|
| 573 |
+
===========
|
| 574 |
+
|
| 575 |
+
The coefficient of damping to be used in the damping element in the
|
| 576 |
+
muscle fiber model.
|
| 577 |
+
|
| 578 |
+
The alias ``beta`` can also be used to access the same attribute.
|
| 579 |
+
|
| 580 |
+
"""
|
| 581 |
+
return self._beta
|
| 582 |
+
|
| 583 |
+
@property
|
| 584 |
+
def beta(self):
|
| 585 |
+
"""Symbol or value corresponding to the fiber damping coefficient
|
| 586 |
+
constant.
|
| 587 |
+
|
| 588 |
+
Explanation
|
| 589 |
+
===========
|
| 590 |
+
|
| 591 |
+
The coefficient of damping to be used in the damping element in the
|
| 592 |
+
muscle fiber model.
|
| 593 |
+
|
| 594 |
+
The alias ``fiber_damping_coefficient`` can also be used to access the
|
| 595 |
+
same attribute.
|
| 596 |
+
|
| 597 |
+
"""
|
| 598 |
+
return self._beta
|
| 599 |
+
|
| 600 |
+
@property
|
| 601 |
+
def activation_dynamics(self):
|
| 602 |
+
"""Activation dynamics model governing this musculotendon's activation.
|
| 603 |
+
|
| 604 |
+
Explanation
|
| 605 |
+
===========
|
| 606 |
+
|
| 607 |
+
Returns the instance of a subclass of ``ActivationBase`` that governs
|
| 608 |
+
the relationship between excitation and activation that is used to
|
| 609 |
+
represent the activation dynamics of this musculotendon.
|
| 610 |
+
|
| 611 |
+
"""
|
| 612 |
+
return self._activation_dynamics
|
| 613 |
+
|
| 614 |
+
@property
|
| 615 |
+
def excitation(self):
|
| 616 |
+
"""Dynamic symbol representing excitation.
|
| 617 |
+
|
| 618 |
+
Explanation
|
| 619 |
+
===========
|
| 620 |
+
|
| 621 |
+
The alias ``e`` can also be used to access the same attribute.
|
| 622 |
+
|
| 623 |
+
"""
|
| 624 |
+
return self._activation_dynamics._e
|
| 625 |
+
|
| 626 |
+
@property
|
| 627 |
+
def e(self):
|
| 628 |
+
"""Dynamic symbol representing excitation.
|
| 629 |
+
|
| 630 |
+
Explanation
|
| 631 |
+
===========
|
| 632 |
+
|
| 633 |
+
The alias ``excitation`` can also be used to access the same attribute.
|
| 634 |
+
|
| 635 |
+
"""
|
| 636 |
+
return self._activation_dynamics._e
|
| 637 |
+
|
| 638 |
+
@property
|
| 639 |
+
def activation(self):
|
| 640 |
+
"""Dynamic symbol representing activation.
|
| 641 |
+
|
| 642 |
+
Explanation
|
| 643 |
+
===========
|
| 644 |
+
|
| 645 |
+
The alias ``a`` can also be used to access the same attribute.
|
| 646 |
+
|
| 647 |
+
"""
|
| 648 |
+
return self._activation_dynamics._a
|
| 649 |
+
|
| 650 |
+
@property
|
| 651 |
+
def a(self):
|
| 652 |
+
"""Dynamic symbol representing activation.
|
| 653 |
+
|
| 654 |
+
Explanation
|
| 655 |
+
===========
|
| 656 |
+
|
| 657 |
+
The alias ``activation`` can also be used to access the same attribute.
|
| 658 |
+
|
| 659 |
+
"""
|
| 660 |
+
return self._activation_dynamics._a
|
| 661 |
+
|
| 662 |
+
@property
|
| 663 |
+
def musculotendon_dynamics(self):
|
| 664 |
+
"""The choice of rigid or type of elastic tendon musculotendon dynamics.
|
| 665 |
+
|
| 666 |
+
Explanation
|
| 667 |
+
===========
|
| 668 |
+
|
| 669 |
+
The formulation of musculotendon dynamics that should be used
|
| 670 |
+
internally, i.e. rigid or elastic tendon model, the choice of
|
| 671 |
+
musculotendon state etc. This must be a member of the integer
|
| 672 |
+
enumeration ``MusculotendonFormulation`` or an integer that can be cast
|
| 673 |
+
to a member. To use a rigid tendon formulation, set this to
|
| 674 |
+
``MusculotendonFormulation.RIGID_TENDON`` (or the integer value ``0``,
|
| 675 |
+
which will be cast to the enumeration member). There are four possible
|
| 676 |
+
formulations for an elastic tendon model. To use an explicit formulation
|
| 677 |
+
with the fiber length as the state, set this to
|
| 678 |
+
``MusculotendonFormulation.FIBER_LENGTH_EXPLICIT`` (or the integer value
|
| 679 |
+
``1``). To use an explicit formulation with the tendon force as the
|
| 680 |
+
state, set this to ``MusculotendonFormulation.TENDON_FORCE_EXPLICIT``
|
| 681 |
+
(or the integer value ``2``). To use an implicit formulation with the
|
| 682 |
+
fiber length as the state, set this to
|
| 683 |
+
``MusculotendonFormulation.FIBER_LENGTH_IMPLICIT`` (or the integer value
|
| 684 |
+
``3``). To use an implicit formulation with the tendon force as the
|
| 685 |
+
state, set this to ``MusculotendonFormulation.TENDON_FORCE_IMPLICIT``
|
| 686 |
+
(or the integer value ``4``). The default is
|
| 687 |
+
``MusculotendonFormulation.RIGID_TENDON``, which corresponds to a rigid
|
| 688 |
+
tendon formulation.
|
| 689 |
+
|
| 690 |
+
"""
|
| 691 |
+
return self._musculotendon_dynamics
|
| 692 |
+
|
| 693 |
+
def _rigid_tendon_musculotendon_dynamics(self):
|
| 694 |
+
"""Rigid tendon musculotendon."""
|
| 695 |
+
self._l_MT = self.pathway.length
|
| 696 |
+
self._v_MT = self.pathway.extension_velocity
|
| 697 |
+
self._l_T = self._l_T_slack
|
| 698 |
+
self._l_T_tilde = Integer(1)
|
| 699 |
+
self._l_M = sqrt((self._l_MT - self._l_T)**2 + (self._l_M_opt*sin(self._alpha_opt))**2)
|
| 700 |
+
self._l_M_tilde = self._l_M/self._l_M_opt
|
| 701 |
+
self._v_M = self._v_MT*(self._l_MT - self._l_T_slack)/self._l_M
|
| 702 |
+
self._v_M_tilde = self._v_M/self._v_M_max
|
| 703 |
+
if self._with_defaults:
|
| 704 |
+
self._fl_T = self.curves.tendon_force_length.with_defaults(self._l_T_tilde)
|
| 705 |
+
self._fl_M_pas = self.curves.fiber_force_length_passive.with_defaults(self._l_M_tilde)
|
| 706 |
+
self._fl_M_act = self.curves.fiber_force_length_active.with_defaults(self._l_M_tilde)
|
| 707 |
+
self._fv_M = self.curves.fiber_force_velocity.with_defaults(self._v_M_tilde)
|
| 708 |
+
else:
|
| 709 |
+
fl_T_constants = symbols(f'c_0:4_fl_T_{self.name}')
|
| 710 |
+
self._fl_T = self.curves.tendon_force_length(self._l_T_tilde, *fl_T_constants)
|
| 711 |
+
fl_M_pas_constants = symbols(f'c_0:2_fl_M_pas_{self.name}')
|
| 712 |
+
self._fl_M_pas = self.curves.fiber_force_length_passive(self._l_M_tilde, *fl_M_pas_constants)
|
| 713 |
+
fl_M_act_constants = symbols(f'c_0:12_fl_M_act_{self.name}')
|
| 714 |
+
self._fl_M_act = self.curves.fiber_force_length_active(self._l_M_tilde, *fl_M_act_constants)
|
| 715 |
+
fv_M_constants = symbols(f'c_0:4_fv_M_{self.name}')
|
| 716 |
+
self._fv_M = self.curves.fiber_force_velocity(self._v_M_tilde, *fv_M_constants)
|
| 717 |
+
self._F_M_tilde = self.a*self._fl_M_act*self._fv_M + self._fl_M_pas + self._beta*self._v_M_tilde
|
| 718 |
+
self._F_T_tilde = self._F_M_tilde
|
| 719 |
+
self._F_M = self._F_M_tilde*self._F_M_max
|
| 720 |
+
self._cos_alpha = cos(self._alpha_opt)
|
| 721 |
+
self._F_T = self._F_M*self._cos_alpha
|
| 722 |
+
|
| 723 |
+
# Containers
|
| 724 |
+
self._state_vars = zeros(0, 1)
|
| 725 |
+
self._input_vars = zeros(0, 1)
|
| 726 |
+
self._state_eqns = zeros(0, 1)
|
| 727 |
+
self._curve_constants = Matrix(
|
| 728 |
+
fl_T_constants
|
| 729 |
+
+ fl_M_pas_constants
|
| 730 |
+
+ fl_M_act_constants
|
| 731 |
+
+ fv_M_constants
|
| 732 |
+
) if not self._with_defaults else zeros(0, 1)
|
| 733 |
+
|
| 734 |
+
def _fiber_length_explicit_musculotendon_dynamics(self):
|
| 735 |
+
"""Elastic tendon musculotendon using `l_M_tilde` as a state."""
|
| 736 |
+
self._l_M_tilde = dynamicsymbols(f'l_M_tilde_{self.name}')
|
| 737 |
+
self._l_MT = self.pathway.length
|
| 738 |
+
self._v_MT = self.pathway.extension_velocity
|
| 739 |
+
self._l_M = self._l_M_tilde*self._l_M_opt
|
| 740 |
+
self._l_T = self._l_MT - sqrt(self._l_M**2 - (self._l_M_opt*sin(self._alpha_opt))**2)
|
| 741 |
+
self._l_T_tilde = self._l_T/self._l_T_slack
|
| 742 |
+
self._cos_alpha = (self._l_MT - self._l_T)/self._l_M
|
| 743 |
+
if self._with_defaults:
|
| 744 |
+
self._fl_T = self.curves.tendon_force_length.with_defaults(self._l_T_tilde)
|
| 745 |
+
self._fl_M_pas = self.curves.fiber_force_length_passive.with_defaults(self._l_M_tilde)
|
| 746 |
+
self._fl_M_act = self.curves.fiber_force_length_active.with_defaults(self._l_M_tilde)
|
| 747 |
+
else:
|
| 748 |
+
fl_T_constants = symbols(f'c_0:4_fl_T_{self.name}')
|
| 749 |
+
self._fl_T = self.curves.tendon_force_length(self._l_T_tilde, *fl_T_constants)
|
| 750 |
+
fl_M_pas_constants = symbols(f'c_0:2_fl_M_pas_{self.name}')
|
| 751 |
+
self._fl_M_pas = self.curves.fiber_force_length_passive(self._l_M_tilde, *fl_M_pas_constants)
|
| 752 |
+
fl_M_act_constants = symbols(f'c_0:12_fl_M_act_{self.name}')
|
| 753 |
+
self._fl_M_act = self.curves.fiber_force_length_active(self._l_M_tilde, *fl_M_act_constants)
|
| 754 |
+
self._F_T_tilde = self._fl_T
|
| 755 |
+
self._F_T = self._F_T_tilde*self._F_M_max
|
| 756 |
+
self._F_M = self._F_T/self._cos_alpha
|
| 757 |
+
self._F_M_tilde = self._F_M/self._F_M_max
|
| 758 |
+
self._fv_M = (self._F_M_tilde - self._fl_M_pas)/(self.a*self._fl_M_act)
|
| 759 |
+
if self._with_defaults:
|
| 760 |
+
self._v_M_tilde = self.curves.fiber_force_velocity_inverse.with_defaults(self._fv_M)
|
| 761 |
+
else:
|
| 762 |
+
fv_M_constants = symbols(f'c_0:4_fv_M_{self.name}')
|
| 763 |
+
self._v_M_tilde = self.curves.fiber_force_velocity_inverse(self._fv_M, *fv_M_constants)
|
| 764 |
+
self._dl_M_tilde_dt = (self._v_M_max/self._l_M_opt)*self._v_M_tilde
|
| 765 |
+
|
| 766 |
+
self._state_vars = Matrix([self._l_M_tilde])
|
| 767 |
+
self._input_vars = zeros(0, 1)
|
| 768 |
+
self._state_eqns = Matrix([self._dl_M_tilde_dt])
|
| 769 |
+
self._curve_constants = Matrix(
|
| 770 |
+
fl_T_constants
|
| 771 |
+
+ fl_M_pas_constants
|
| 772 |
+
+ fl_M_act_constants
|
| 773 |
+
+ fv_M_constants
|
| 774 |
+
) if not self._with_defaults else zeros(0, 1)
|
| 775 |
+
|
| 776 |
+
def _tendon_force_explicit_musculotendon_dynamics(self):
|
| 777 |
+
"""Elastic tendon musculotendon using `F_T_tilde` as a state."""
|
| 778 |
+
self._F_T_tilde = dynamicsymbols(f'F_T_tilde_{self.name}')
|
| 779 |
+
self._l_MT = self.pathway.length
|
| 780 |
+
self._v_MT = self.pathway.extension_velocity
|
| 781 |
+
self._fl_T = self._F_T_tilde
|
| 782 |
+
if self._with_defaults:
|
| 783 |
+
self._fl_T_inv = self.curves.tendon_force_length_inverse.with_defaults(self._fl_T)
|
| 784 |
+
else:
|
| 785 |
+
fl_T_constants = symbols(f'c_0:4_fl_T_{self.name}')
|
| 786 |
+
self._fl_T_inv = self.curves.tendon_force_length_inverse(self._fl_T, *fl_T_constants)
|
| 787 |
+
self._l_T_tilde = self._fl_T_inv
|
| 788 |
+
self._l_T = self._l_T_tilde*self._l_T_slack
|
| 789 |
+
self._l_M = sqrt((self._l_MT - self._l_T)**2 + (self._l_M_opt*sin(self._alpha_opt))**2)
|
| 790 |
+
self._l_M_tilde = self._l_M/self._l_M_opt
|
| 791 |
+
if self._with_defaults:
|
| 792 |
+
self._fl_M_pas = self.curves.fiber_force_length_passive.with_defaults(self._l_M_tilde)
|
| 793 |
+
self._fl_M_act = self.curves.fiber_force_length_active.with_defaults(self._l_M_tilde)
|
| 794 |
+
else:
|
| 795 |
+
fl_M_pas_constants = symbols(f'c_0:2_fl_M_pas_{self.name}')
|
| 796 |
+
self._fl_M_pas = self.curves.fiber_force_length_passive(self._l_M_tilde, *fl_M_pas_constants)
|
| 797 |
+
fl_M_act_constants = symbols(f'c_0:12_fl_M_act_{self.name}')
|
| 798 |
+
self._fl_M_act = self.curves.fiber_force_length_active(self._l_M_tilde, *fl_M_act_constants)
|
| 799 |
+
self._cos_alpha = (self._l_MT - self._l_T)/self._l_M
|
| 800 |
+
self._F_T = self._F_T_tilde*self._F_M_max
|
| 801 |
+
self._F_M = self._F_T/self._cos_alpha
|
| 802 |
+
self._F_M_tilde = self._F_M/self._F_M_max
|
| 803 |
+
self._fv_M = (self._F_M_tilde - self._fl_M_pas)/(self.a*self._fl_M_act)
|
| 804 |
+
if self._with_defaults:
|
| 805 |
+
self._fv_M_inv = self.curves.fiber_force_velocity_inverse.with_defaults(self._fv_M)
|
| 806 |
+
else:
|
| 807 |
+
fv_M_constants = symbols(f'c_0:4_fv_M_{self.name}')
|
| 808 |
+
self._fv_M_inv = self.curves.fiber_force_velocity_inverse(self._fv_M, *fv_M_constants)
|
| 809 |
+
self._v_M_tilde = self._fv_M_inv
|
| 810 |
+
self._v_M = self._v_M_tilde*self._v_M_max
|
| 811 |
+
self._v_T = self._v_MT - (self._v_M/self._cos_alpha)
|
| 812 |
+
self._v_T_tilde = self._v_T/self._l_T_slack
|
| 813 |
+
if self._with_defaults:
|
| 814 |
+
self._fl_T = self.curves.tendon_force_length.with_defaults(self._l_T_tilde)
|
| 815 |
+
else:
|
| 816 |
+
self._fl_T = self.curves.tendon_force_length(self._l_T_tilde, *fl_T_constants)
|
| 817 |
+
self._dF_T_tilde_dt = self._fl_T.diff(dynamicsymbols._t).subs({self._l_T_tilde.diff(dynamicsymbols._t): self._v_T_tilde})
|
| 818 |
+
|
| 819 |
+
self._state_vars = Matrix([self._F_T_tilde])
|
| 820 |
+
self._input_vars = zeros(0, 1)
|
| 821 |
+
self._state_eqns = Matrix([self._dF_T_tilde_dt])
|
| 822 |
+
self._curve_constants = Matrix(
|
| 823 |
+
fl_T_constants
|
| 824 |
+
+ fl_M_pas_constants
|
| 825 |
+
+ fl_M_act_constants
|
| 826 |
+
+ fv_M_constants
|
| 827 |
+
) if not self._with_defaults else zeros(0, 1)
|
| 828 |
+
|
| 829 |
+
def _fiber_length_implicit_musculotendon_dynamics(self):
|
| 830 |
+
raise NotImplementedError
|
| 831 |
+
|
| 832 |
+
def _tendon_force_implicit_musculotendon_dynamics(self):
|
| 833 |
+
raise NotImplementedError
|
| 834 |
+
|
| 835 |
+
@property
|
| 836 |
+
def state_vars(self):
|
| 837 |
+
"""Ordered column matrix of functions of time that represent the state
|
| 838 |
+
variables.
|
| 839 |
+
|
| 840 |
+
Explanation
|
| 841 |
+
===========
|
| 842 |
+
|
| 843 |
+
The alias ``x`` can also be used to access the same attribute.
|
| 844 |
+
|
| 845 |
+
"""
|
| 846 |
+
state_vars = [self._state_vars]
|
| 847 |
+
for child in self._child_objects:
|
| 848 |
+
state_vars.append(child.state_vars)
|
| 849 |
+
return Matrix.vstack(*state_vars)
|
| 850 |
+
|
| 851 |
+
@property
|
| 852 |
+
def x(self):
|
| 853 |
+
"""Ordered column matrix of functions of time that represent the state
|
| 854 |
+
variables.
|
| 855 |
+
|
| 856 |
+
Explanation
|
| 857 |
+
===========
|
| 858 |
+
|
| 859 |
+
The alias ``state_vars`` can also be used to access the same attribute.
|
| 860 |
+
|
| 861 |
+
"""
|
| 862 |
+
state_vars = [self._state_vars]
|
| 863 |
+
for child in self._child_objects:
|
| 864 |
+
state_vars.append(child.state_vars)
|
| 865 |
+
return Matrix.vstack(*state_vars)
|
| 866 |
+
|
| 867 |
+
@property
|
| 868 |
+
def input_vars(self):
|
| 869 |
+
"""Ordered column matrix of functions of time that represent the input
|
| 870 |
+
variables.
|
| 871 |
+
|
| 872 |
+
Explanation
|
| 873 |
+
===========
|
| 874 |
+
|
| 875 |
+
The alias ``r`` can also be used to access the same attribute.
|
| 876 |
+
|
| 877 |
+
"""
|
| 878 |
+
input_vars = [self._input_vars]
|
| 879 |
+
for child in self._child_objects:
|
| 880 |
+
input_vars.append(child.input_vars)
|
| 881 |
+
return Matrix.vstack(*input_vars)
|
| 882 |
+
|
| 883 |
+
@property
|
| 884 |
+
def r(self):
|
| 885 |
+
"""Ordered column matrix of functions of time that represent the input
|
| 886 |
+
variables.
|
| 887 |
+
|
| 888 |
+
Explanation
|
| 889 |
+
===========
|
| 890 |
+
|
| 891 |
+
The alias ``input_vars`` can also be used to access the same attribute.
|
| 892 |
+
|
| 893 |
+
"""
|
| 894 |
+
input_vars = [self._input_vars]
|
| 895 |
+
for child in self._child_objects:
|
| 896 |
+
input_vars.append(child.input_vars)
|
| 897 |
+
return Matrix.vstack(*input_vars)
|
| 898 |
+
|
| 899 |
+
@property
|
| 900 |
+
def constants(self):
|
| 901 |
+
"""Ordered column matrix of non-time varying symbols present in ``M``
|
| 902 |
+
and ``F``.
|
| 903 |
+
|
| 904 |
+
Explanation
|
| 905 |
+
===========
|
| 906 |
+
|
| 907 |
+
Only symbolic constants are returned. If a numeric type (e.g. ``Float``)
|
| 908 |
+
has been used instead of ``Symbol`` for a constant then that attribute
|
| 909 |
+
will not be included in the matrix returned by this property. This is
|
| 910 |
+
because the primary use of this property attribute is to provide an
|
| 911 |
+
ordered sequence of the still-free symbols that require numeric values
|
| 912 |
+
during code generation.
|
| 913 |
+
|
| 914 |
+
The alias ``p`` can also be used to access the same attribute.
|
| 915 |
+
|
| 916 |
+
"""
|
| 917 |
+
musculotendon_constants = [
|
| 918 |
+
self._l_T_slack,
|
| 919 |
+
self._F_M_max,
|
| 920 |
+
self._l_M_opt,
|
| 921 |
+
self._v_M_max,
|
| 922 |
+
self._alpha_opt,
|
| 923 |
+
self._beta,
|
| 924 |
+
]
|
| 925 |
+
musculotendon_constants = [
|
| 926 |
+
c for c in musculotendon_constants if not c.is_number
|
| 927 |
+
]
|
| 928 |
+
constants = [
|
| 929 |
+
Matrix(musculotendon_constants)
|
| 930 |
+
if musculotendon_constants
|
| 931 |
+
else zeros(0, 1)
|
| 932 |
+
]
|
| 933 |
+
for child in self._child_objects:
|
| 934 |
+
constants.append(child.constants)
|
| 935 |
+
constants.append(self._curve_constants)
|
| 936 |
+
return Matrix.vstack(*constants)
|
| 937 |
+
|
| 938 |
+
@property
|
| 939 |
+
def p(self):
|
| 940 |
+
"""Ordered column matrix of non-time varying symbols present in ``M``
|
| 941 |
+
and ``F``.
|
| 942 |
+
|
| 943 |
+
Explanation
|
| 944 |
+
===========
|
| 945 |
+
|
| 946 |
+
Only symbolic constants are returned. If a numeric type (e.g. ``Float``)
|
| 947 |
+
has been used instead of ``Symbol`` for a constant then that attribute
|
| 948 |
+
will not be included in the matrix returned by this property. This is
|
| 949 |
+
because the primary use of this property attribute is to provide an
|
| 950 |
+
ordered sequence of the still-free symbols that require numeric values
|
| 951 |
+
during code generation.
|
| 952 |
+
|
| 953 |
+
The alias ``constants`` can also be used to access the same attribute.
|
| 954 |
+
|
| 955 |
+
"""
|
| 956 |
+
musculotendon_constants = [
|
| 957 |
+
self._l_T_slack,
|
| 958 |
+
self._F_M_max,
|
| 959 |
+
self._l_M_opt,
|
| 960 |
+
self._v_M_max,
|
| 961 |
+
self._alpha_opt,
|
| 962 |
+
self._beta,
|
| 963 |
+
]
|
| 964 |
+
musculotendon_constants = [
|
| 965 |
+
c for c in musculotendon_constants if not c.is_number
|
| 966 |
+
]
|
| 967 |
+
constants = [
|
| 968 |
+
Matrix(musculotendon_constants)
|
| 969 |
+
if musculotendon_constants
|
| 970 |
+
else zeros(0, 1)
|
| 971 |
+
]
|
| 972 |
+
for child in self._child_objects:
|
| 973 |
+
constants.append(child.constants)
|
| 974 |
+
constants.append(self._curve_constants)
|
| 975 |
+
return Matrix.vstack(*constants)
|
| 976 |
+
|
| 977 |
+
@property
|
| 978 |
+
def M(self):
|
| 979 |
+
"""Ordered square matrix of coefficients on the LHS of ``M x' = F``.
|
| 980 |
+
|
| 981 |
+
Explanation
|
| 982 |
+
===========
|
| 983 |
+
|
| 984 |
+
The square matrix that forms part of the LHS of the linear system of
|
| 985 |
+
ordinary differential equations governing the activation dynamics:
|
| 986 |
+
|
| 987 |
+
``M(x, r, t, p) x' = F(x, r, t, p)``.
|
| 988 |
+
|
| 989 |
+
As zeroth-order activation dynamics have no state variables, this
|
| 990 |
+
linear system has dimension 0 and therefore ``M`` is an empty square
|
| 991 |
+
``Matrix`` with shape (0, 0).
|
| 992 |
+
|
| 993 |
+
"""
|
| 994 |
+
M = [eye(len(self._state_vars))]
|
| 995 |
+
for child in self._child_objects:
|
| 996 |
+
M.append(child.M)
|
| 997 |
+
return diag(*M)
|
| 998 |
+
|
| 999 |
+
@property
|
| 1000 |
+
def F(self):
|
| 1001 |
+
"""Ordered column matrix of equations on the RHS of ``M x' = F``.
|
| 1002 |
+
|
| 1003 |
+
Explanation
|
| 1004 |
+
===========
|
| 1005 |
+
|
| 1006 |
+
The column matrix that forms the RHS of the linear system of ordinary
|
| 1007 |
+
differential equations governing the activation dynamics:
|
| 1008 |
+
|
| 1009 |
+
``M(x, r, t, p) x' = F(x, r, t, p)``.
|
| 1010 |
+
|
| 1011 |
+
As zeroth-order activation dynamics have no state variables, this
|
| 1012 |
+
linear system has dimension 0 and therefore ``F`` is an empty column
|
| 1013 |
+
``Matrix`` with shape (0, 1).
|
| 1014 |
+
|
| 1015 |
+
"""
|
| 1016 |
+
F = [self._state_eqns]
|
| 1017 |
+
for child in self._child_objects:
|
| 1018 |
+
F.append(child.F)
|
| 1019 |
+
return Matrix.vstack(*F)
|
| 1020 |
+
|
| 1021 |
+
def rhs(self):
|
| 1022 |
+
"""Ordered column matrix of equations for the solution of ``M x' = F``.
|
| 1023 |
+
|
| 1024 |
+
Explanation
|
| 1025 |
+
===========
|
| 1026 |
+
|
| 1027 |
+
The solution to the linear system of ordinary differential equations
|
| 1028 |
+
governing the activation dynamics:
|
| 1029 |
+
|
| 1030 |
+
``M(x, r, t, p) x' = F(x, r, t, p)``.
|
| 1031 |
+
|
| 1032 |
+
As zeroth-order activation dynamics have no state variables, this
|
| 1033 |
+
linear has dimension 0 and therefore this method returns an empty
|
| 1034 |
+
column ``Matrix`` with shape (0, 1).
|
| 1035 |
+
|
| 1036 |
+
"""
|
| 1037 |
+
is_explicit = (
|
| 1038 |
+
MusculotendonFormulation.FIBER_LENGTH_EXPLICIT,
|
| 1039 |
+
MusculotendonFormulation.TENDON_FORCE_EXPLICIT,
|
| 1040 |
+
)
|
| 1041 |
+
if self.musculotendon_dynamics is MusculotendonFormulation.RIGID_TENDON:
|
| 1042 |
+
child_rhs = [child.rhs() for child in self._child_objects]
|
| 1043 |
+
return Matrix.vstack(*child_rhs)
|
| 1044 |
+
elif self.musculotendon_dynamics in is_explicit:
|
| 1045 |
+
rhs = self._state_eqns
|
| 1046 |
+
child_rhs = [child.rhs() for child in self._child_objects]
|
| 1047 |
+
return Matrix.vstack(rhs, *child_rhs)
|
| 1048 |
+
return self.M.solve(self.F)
|
| 1049 |
+
|
| 1050 |
+
def __repr__(self):
|
| 1051 |
+
"""Returns a string representation to reinstantiate the model."""
|
| 1052 |
+
return (
|
| 1053 |
+
f'{self.__class__.__name__}({self.name!r}, '
|
| 1054 |
+
f'pathway={self.pathway!r}, '
|
| 1055 |
+
f'activation_dynamics={self.activation_dynamics!r}, '
|
| 1056 |
+
f'musculotendon_dynamics={self.musculotendon_dynamics}, '
|
| 1057 |
+
f'tendon_slack_length={self._l_T_slack!r}, '
|
| 1058 |
+
f'peak_isometric_force={self._F_M_max!r}, '
|
| 1059 |
+
f'optimal_fiber_length={self._l_M_opt!r}, '
|
| 1060 |
+
f'maximal_fiber_velocity={self._v_M_max!r}, '
|
| 1061 |
+
f'optimal_pennation_angle={self._alpha_opt!r}, '
|
| 1062 |
+
f'fiber_damping_coefficient={self._beta!r})'
|
| 1063 |
+
)
|
| 1064 |
+
|
| 1065 |
+
def __str__(self):
|
| 1066 |
+
"""Returns a string representation of the expression for musculotendon
|
| 1067 |
+
force."""
|
| 1068 |
+
return str(self.force)
|
| 1069 |
+
|
| 1070 |
+
|
| 1071 |
+
class MusculotendonDeGroote2016(MusculotendonBase):
|
| 1072 |
+
r"""Musculotendon model using the curves of De Groote et al., 2016 [1]_.
|
| 1073 |
+
|
| 1074 |
+
Examples
|
| 1075 |
+
========
|
| 1076 |
+
|
| 1077 |
+
This class models the musculotendon actuator parametrized by the
|
| 1078 |
+
characteristic curves described in De Groote et al., 2016 [1]_. Like all
|
| 1079 |
+
musculotendon models in SymPy's biomechanics module, it requires a pathway
|
| 1080 |
+
to define its line of action. We'll begin by creating a simple
|
| 1081 |
+
``LinearPathway`` between two points that our musculotendon will follow.
|
| 1082 |
+
We'll create a point ``O`` to represent the musculotendon's origin and
|
| 1083 |
+
another ``I`` to represent its insertion.
|
| 1084 |
+
|
| 1085 |
+
>>> from sympy import symbols
|
| 1086 |
+
>>> from sympy.physics.mechanics import (LinearPathway, Point,
|
| 1087 |
+
... ReferenceFrame, dynamicsymbols)
|
| 1088 |
+
|
| 1089 |
+
>>> N = ReferenceFrame('N')
|
| 1090 |
+
>>> O, I = O, P = symbols('O, I', cls=Point)
|
| 1091 |
+
>>> q, u = dynamicsymbols('q, u', real=True)
|
| 1092 |
+
>>> I.set_pos(O, q*N.x)
|
| 1093 |
+
>>> O.set_vel(N, 0)
|
| 1094 |
+
>>> I.set_vel(N, u*N.x)
|
| 1095 |
+
>>> pathway = LinearPathway(O, I)
|
| 1096 |
+
>>> pathway.attachments
|
| 1097 |
+
(O, I)
|
| 1098 |
+
>>> pathway.length
|
| 1099 |
+
Abs(q(t))
|
| 1100 |
+
>>> pathway.extension_velocity
|
| 1101 |
+
sign(q(t))*Derivative(q(t), t)
|
| 1102 |
+
|
| 1103 |
+
A musculotendon also takes an instance of an activation dynamics model as
|
| 1104 |
+
this will be used to provide symbols for the activation in the formulation
|
| 1105 |
+
of the musculotendon dynamics. We'll use an instance of
|
| 1106 |
+
``FirstOrderActivationDeGroote2016`` to represent first-order activation
|
| 1107 |
+
dynamics. Note that a single name argument needs to be provided as SymPy
|
| 1108 |
+
will use this as a suffix.
|
| 1109 |
+
|
| 1110 |
+
>>> from sympy.physics.biomechanics import FirstOrderActivationDeGroote2016
|
| 1111 |
+
|
| 1112 |
+
>>> activation = FirstOrderActivationDeGroote2016('muscle')
|
| 1113 |
+
>>> activation.x
|
| 1114 |
+
Matrix([[a_muscle(t)]])
|
| 1115 |
+
>>> activation.r
|
| 1116 |
+
Matrix([[e_muscle(t)]])
|
| 1117 |
+
>>> activation.p
|
| 1118 |
+
Matrix([
|
| 1119 |
+
[tau_a_muscle],
|
| 1120 |
+
[tau_d_muscle],
|
| 1121 |
+
[ b_muscle]])
|
| 1122 |
+
>>> activation.rhs()
|
| 1123 |
+
Matrix([[((1/2 - tanh(b_muscle*(-a_muscle(t) + e_muscle(t)))/2)*(3*...]])
|
| 1124 |
+
|
| 1125 |
+
The musculotendon class requires symbols or values to be passed to represent
|
| 1126 |
+
the constants in the musculotendon dynamics. We'll use SymPy's ``symbols``
|
| 1127 |
+
function to create symbols for the maximum isometric force ``F_M_max``,
|
| 1128 |
+
optimal fiber length ``l_M_opt``, tendon slack length ``l_T_slack``, maximum
|
| 1129 |
+
fiber velocity ``v_M_max``, optimal pennation angle ``alpha_opt, and fiber
|
| 1130 |
+
damping coefficient ``beta``.
|
| 1131 |
+
|
| 1132 |
+
>>> F_M_max = symbols('F_M_max', real=True)
|
| 1133 |
+
>>> l_M_opt = symbols('l_M_opt', real=True)
|
| 1134 |
+
>>> l_T_slack = symbols('l_T_slack', real=True)
|
| 1135 |
+
>>> v_M_max = symbols('v_M_max', real=True)
|
| 1136 |
+
>>> alpha_opt = symbols('alpha_opt', real=True)
|
| 1137 |
+
>>> beta = symbols('beta', real=True)
|
| 1138 |
+
|
| 1139 |
+
We can then import the class ``MusculotendonDeGroote2016`` from the
|
| 1140 |
+
biomechanics module and create an instance by passing in the various objects
|
| 1141 |
+
we have previously instantiated. By default, a musculotendon model with
|
| 1142 |
+
rigid tendon musculotendon dynamics will be created.
|
| 1143 |
+
|
| 1144 |
+
>>> from sympy.physics.biomechanics import MusculotendonDeGroote2016
|
| 1145 |
+
|
| 1146 |
+
>>> rigid_tendon_muscle = MusculotendonDeGroote2016(
|
| 1147 |
+
... 'muscle',
|
| 1148 |
+
... pathway,
|
| 1149 |
+
... activation,
|
| 1150 |
+
... tendon_slack_length=l_T_slack,
|
| 1151 |
+
... peak_isometric_force=F_M_max,
|
| 1152 |
+
... optimal_fiber_length=l_M_opt,
|
| 1153 |
+
... maximal_fiber_velocity=v_M_max,
|
| 1154 |
+
... optimal_pennation_angle=alpha_opt,
|
| 1155 |
+
... fiber_damping_coefficient=beta,
|
| 1156 |
+
... )
|
| 1157 |
+
|
| 1158 |
+
We can inspect the various properties of the musculotendon, including
|
| 1159 |
+
getting the symbolic expression describing the force it produces using its
|
| 1160 |
+
``force`` attribute.
|
| 1161 |
+
|
| 1162 |
+
>>> rigid_tendon_muscle.force
|
| 1163 |
+
-F_M_max*(beta*(-l_T_slack + Abs(q(t)))*sign(q(t))*Derivative(q(t), t)...
|
| 1164 |
+
|
| 1165 |
+
When we created the musculotendon object, we passed in an instance of an
|
| 1166 |
+
activation dynamics object that governs the activation within the
|
| 1167 |
+
musculotendon. SymPy makes a design choice here that the activation dynamics
|
| 1168 |
+
instance will be treated as a child object of the musculotendon dynamics.
|
| 1169 |
+
Therefore, if we want to inspect the state and input variables associated
|
| 1170 |
+
with the musculotendon model, we will also be returned the state and input
|
| 1171 |
+
variables associated with the child object, or the activation dynamics in
|
| 1172 |
+
this case. As the musculotendon model that we created here uses rigid tendon
|
| 1173 |
+
dynamics, no additional states or inputs relating to the musculotendon are
|
| 1174 |
+
introduces. Consequently, the model has a single state associated with it,
|
| 1175 |
+
the activation, and a single input associated with it, the excitation. The
|
| 1176 |
+
states and inputs can be inspected using the ``x`` and ``r`` attributes
|
| 1177 |
+
respectively. Note that both ``x`` and ``r`` have the alias attributes of
|
| 1178 |
+
``state_vars`` and ``input_vars``.
|
| 1179 |
+
|
| 1180 |
+
>>> rigid_tendon_muscle.x
|
| 1181 |
+
Matrix([[a_muscle(t)]])
|
| 1182 |
+
>>> rigid_tendon_muscle.r
|
| 1183 |
+
Matrix([[e_muscle(t)]])
|
| 1184 |
+
|
| 1185 |
+
To see which constants are symbolic in the musculotendon model, we can use
|
| 1186 |
+
the ``p`` or ``constants`` attribute. This returns a ``Matrix`` populated
|
| 1187 |
+
by the constants that are represented by a ``Symbol`` rather than a numeric
|
| 1188 |
+
value.
|
| 1189 |
+
|
| 1190 |
+
>>> rigid_tendon_muscle.p
|
| 1191 |
+
Matrix([
|
| 1192 |
+
[ l_T_slack],
|
| 1193 |
+
[ F_M_max],
|
| 1194 |
+
[ l_M_opt],
|
| 1195 |
+
[ v_M_max],
|
| 1196 |
+
[ alpha_opt],
|
| 1197 |
+
[ beta],
|
| 1198 |
+
[ tau_a_muscle],
|
| 1199 |
+
[ tau_d_muscle],
|
| 1200 |
+
[ b_muscle],
|
| 1201 |
+
[ c_0_fl_T_muscle],
|
| 1202 |
+
[ c_1_fl_T_muscle],
|
| 1203 |
+
[ c_2_fl_T_muscle],
|
| 1204 |
+
[ c_3_fl_T_muscle],
|
| 1205 |
+
[ c_0_fl_M_pas_muscle],
|
| 1206 |
+
[ c_1_fl_M_pas_muscle],
|
| 1207 |
+
[ c_0_fl_M_act_muscle],
|
| 1208 |
+
[ c_1_fl_M_act_muscle],
|
| 1209 |
+
[ c_2_fl_M_act_muscle],
|
| 1210 |
+
[ c_3_fl_M_act_muscle],
|
| 1211 |
+
[ c_4_fl_M_act_muscle],
|
| 1212 |
+
[ c_5_fl_M_act_muscle],
|
| 1213 |
+
[ c_6_fl_M_act_muscle],
|
| 1214 |
+
[ c_7_fl_M_act_muscle],
|
| 1215 |
+
[ c_8_fl_M_act_muscle],
|
| 1216 |
+
[ c_9_fl_M_act_muscle],
|
| 1217 |
+
[c_10_fl_M_act_muscle],
|
| 1218 |
+
[c_11_fl_M_act_muscle],
|
| 1219 |
+
[ c_0_fv_M_muscle],
|
| 1220 |
+
[ c_1_fv_M_muscle],
|
| 1221 |
+
[ c_2_fv_M_muscle],
|
| 1222 |
+
[ c_3_fv_M_muscle]])
|
| 1223 |
+
|
| 1224 |
+
Finally, we can call the ``rhs`` method to return a ``Matrix`` that
|
| 1225 |
+
contains as its elements the righthand side of the ordinary differential
|
| 1226 |
+
equations corresponding to each of the musculotendon's states. Like the
|
| 1227 |
+
method with the same name on the ``Method`` classes in SymPy's mechanics
|
| 1228 |
+
module, this returns a column vector where the number of rows corresponds to
|
| 1229 |
+
the number of states. For our example here, we have a single state, the
|
| 1230 |
+
dynamic symbol ``a_muscle(t)``, so the returned value is a 1-by-1
|
| 1231 |
+
``Matrix``.
|
| 1232 |
+
|
| 1233 |
+
>>> rigid_tendon_muscle.rhs()
|
| 1234 |
+
Matrix([[((1/2 - tanh(b_muscle*(-a_muscle(t) + e_muscle(t)))/2)*(3*...]])
|
| 1235 |
+
|
| 1236 |
+
The musculotendon class supports elastic tendon musculotendon models in
|
| 1237 |
+
addition to rigid tendon ones. You can choose to either use the fiber length
|
| 1238 |
+
or tendon force as an additional state. You can also specify whether an
|
| 1239 |
+
explicit or implicit formulation should be used. To select a formulation,
|
| 1240 |
+
pass a member of the ``MusculotendonFormulation`` enumeration to the
|
| 1241 |
+
``musculotendon_dynamics`` parameter when calling the constructor. This
|
| 1242 |
+
enumeration is an ``IntEnum``, so you can also pass an integer, however it
|
| 1243 |
+
is recommended to use the enumeration as it is clearer which formulation you
|
| 1244 |
+
are actually selecting. Below, we'll use the ``FIBER_LENGTH_EXPLICIT``
|
| 1245 |
+
member to create a musculotendon with an elastic tendon that will use the
|
| 1246 |
+
(normalized) muscle fiber length as an additional state and will produce
|
| 1247 |
+
the governing ordinary differential equation in explicit form.
|
| 1248 |
+
|
| 1249 |
+
>>> from sympy.physics.biomechanics import MusculotendonFormulation
|
| 1250 |
+
|
| 1251 |
+
>>> elastic_tendon_muscle = MusculotendonDeGroote2016(
|
| 1252 |
+
... 'muscle',
|
| 1253 |
+
... pathway,
|
| 1254 |
+
... activation,
|
| 1255 |
+
... musculotendon_dynamics=MusculotendonFormulation.FIBER_LENGTH_EXPLICIT,
|
| 1256 |
+
... tendon_slack_length=l_T_slack,
|
| 1257 |
+
... peak_isometric_force=F_M_max,
|
| 1258 |
+
... optimal_fiber_length=l_M_opt,
|
| 1259 |
+
... maximal_fiber_velocity=v_M_max,
|
| 1260 |
+
... optimal_pennation_angle=alpha_opt,
|
| 1261 |
+
... fiber_damping_coefficient=beta,
|
| 1262 |
+
... )
|
| 1263 |
+
|
| 1264 |
+
>>> elastic_tendon_muscle.force
|
| 1265 |
+
-F_M_max*TendonForceLengthDeGroote2016((-sqrt(l_M_opt**2*...
|
| 1266 |
+
>>> elastic_tendon_muscle.x
|
| 1267 |
+
Matrix([
|
| 1268 |
+
[l_M_tilde_muscle(t)],
|
| 1269 |
+
[ a_muscle(t)]])
|
| 1270 |
+
>>> elastic_tendon_muscle.r
|
| 1271 |
+
Matrix([[e_muscle(t)]])
|
| 1272 |
+
>>> elastic_tendon_muscle.p
|
| 1273 |
+
Matrix([
|
| 1274 |
+
[ l_T_slack],
|
| 1275 |
+
[ F_M_max],
|
| 1276 |
+
[ l_M_opt],
|
| 1277 |
+
[ v_M_max],
|
| 1278 |
+
[ alpha_opt],
|
| 1279 |
+
[ beta],
|
| 1280 |
+
[ tau_a_muscle],
|
| 1281 |
+
[ tau_d_muscle],
|
| 1282 |
+
[ b_muscle],
|
| 1283 |
+
[ c_0_fl_T_muscle],
|
| 1284 |
+
[ c_1_fl_T_muscle],
|
| 1285 |
+
[ c_2_fl_T_muscle],
|
| 1286 |
+
[ c_3_fl_T_muscle],
|
| 1287 |
+
[ c_0_fl_M_pas_muscle],
|
| 1288 |
+
[ c_1_fl_M_pas_muscle],
|
| 1289 |
+
[ c_0_fl_M_act_muscle],
|
| 1290 |
+
[ c_1_fl_M_act_muscle],
|
| 1291 |
+
[ c_2_fl_M_act_muscle],
|
| 1292 |
+
[ c_3_fl_M_act_muscle],
|
| 1293 |
+
[ c_4_fl_M_act_muscle],
|
| 1294 |
+
[ c_5_fl_M_act_muscle],
|
| 1295 |
+
[ c_6_fl_M_act_muscle],
|
| 1296 |
+
[ c_7_fl_M_act_muscle],
|
| 1297 |
+
[ c_8_fl_M_act_muscle],
|
| 1298 |
+
[ c_9_fl_M_act_muscle],
|
| 1299 |
+
[c_10_fl_M_act_muscle],
|
| 1300 |
+
[c_11_fl_M_act_muscle],
|
| 1301 |
+
[ c_0_fv_M_muscle],
|
| 1302 |
+
[ c_1_fv_M_muscle],
|
| 1303 |
+
[ c_2_fv_M_muscle],
|
| 1304 |
+
[ c_3_fv_M_muscle]])
|
| 1305 |
+
>>> elastic_tendon_muscle.rhs()
|
| 1306 |
+
Matrix([
|
| 1307 |
+
[v_M_max*FiberForceVelocityInverseDeGroote2016((l_M_opt*...],
|
| 1308 |
+
[ ((1/2 - tanh(b_muscle*(-a_muscle(t) + e_muscle(t)))/2)*(3*...]])
|
| 1309 |
+
|
| 1310 |
+
It is strongly recommended to use the alternate ``with_defaults``
|
| 1311 |
+
constructor when creating an instance because this will ensure that the
|
| 1312 |
+
published constants are used in the musculotendon characteristic curves.
|
| 1313 |
+
|
| 1314 |
+
>>> elastic_tendon_muscle = MusculotendonDeGroote2016.with_defaults(
|
| 1315 |
+
... 'muscle',
|
| 1316 |
+
... pathway,
|
| 1317 |
+
... activation,
|
| 1318 |
+
... musculotendon_dynamics=MusculotendonFormulation.FIBER_LENGTH_EXPLICIT,
|
| 1319 |
+
... tendon_slack_length=l_T_slack,
|
| 1320 |
+
... peak_isometric_force=F_M_max,
|
| 1321 |
+
... optimal_fiber_length=l_M_opt,
|
| 1322 |
+
... )
|
| 1323 |
+
|
| 1324 |
+
>>> elastic_tendon_muscle.x
|
| 1325 |
+
Matrix([
|
| 1326 |
+
[l_M_tilde_muscle(t)],
|
| 1327 |
+
[ a_muscle(t)]])
|
| 1328 |
+
>>> elastic_tendon_muscle.r
|
| 1329 |
+
Matrix([[e_muscle(t)]])
|
| 1330 |
+
>>> elastic_tendon_muscle.p
|
| 1331 |
+
Matrix([
|
| 1332 |
+
[ l_T_slack],
|
| 1333 |
+
[ F_M_max],
|
| 1334 |
+
[ l_M_opt],
|
| 1335 |
+
[tau_a_muscle],
|
| 1336 |
+
[tau_d_muscle],
|
| 1337 |
+
[ b_muscle]])
|
| 1338 |
+
|
| 1339 |
+
Parameters
|
| 1340 |
+
==========
|
| 1341 |
+
|
| 1342 |
+
name : str
|
| 1343 |
+
The name identifier associated with the musculotendon. This name is used
|
| 1344 |
+
as a suffix when automatically generated symbols are instantiated. It
|
| 1345 |
+
must be a string of nonzero length.
|
| 1346 |
+
pathway : PathwayBase
|
| 1347 |
+
The pathway that the actuator follows. This must be an instance of a
|
| 1348 |
+
concrete subclass of ``PathwayBase``, e.g. ``LinearPathway``.
|
| 1349 |
+
activation_dynamics : ActivationBase
|
| 1350 |
+
The activation dynamics that will be modeled within the musculotendon.
|
| 1351 |
+
This must be an instance of a concrete subclass of ``ActivationBase``,
|
| 1352 |
+
e.g. ``FirstOrderActivationDeGroote2016``.
|
| 1353 |
+
musculotendon_dynamics : MusculotendonFormulation | int
|
| 1354 |
+
The formulation of musculotendon dynamics that should be used
|
| 1355 |
+
internally, i.e. rigid or elastic tendon model, the choice of
|
| 1356 |
+
musculotendon state etc. This must be a member of the integer
|
| 1357 |
+
enumeration ``MusculotendonFormulation`` or an integer that can be cast
|
| 1358 |
+
to a member. To use a rigid tendon formulation, set this to
|
| 1359 |
+
``MusculotendonFormulation.RIGID_TENDON`` (or the integer value ``0``,
|
| 1360 |
+
which will be cast to the enumeration member). There are four possible
|
| 1361 |
+
formulations for an elastic tendon model. To use an explicit formulation
|
| 1362 |
+
with the fiber length as the state, set this to
|
| 1363 |
+
``MusculotendonFormulation.FIBER_LENGTH_EXPLICIT`` (or the integer value
|
| 1364 |
+
``1``). To use an explicit formulation with the tendon force as the
|
| 1365 |
+
state, set this to ``MusculotendonFormulation.TENDON_FORCE_EXPLICIT``
|
| 1366 |
+
(or the integer value ``2``). To use an implicit formulation with the
|
| 1367 |
+
fiber length as the state, set this to
|
| 1368 |
+
``MusculotendonFormulation.FIBER_LENGTH_IMPLICIT`` (or the integer value
|
| 1369 |
+
``3``). To use an implicit formulation with the tendon force as the
|
| 1370 |
+
state, set this to ``MusculotendonFormulation.TENDON_FORCE_IMPLICIT``
|
| 1371 |
+
(or the integer value ``4``). The default is
|
| 1372 |
+
``MusculotendonFormulation.RIGID_TENDON``, which corresponds to a rigid
|
| 1373 |
+
tendon formulation.
|
| 1374 |
+
tendon_slack_length : Expr | None
|
| 1375 |
+
The length of the tendon when the musculotendon is in its unloaded
|
| 1376 |
+
state. In a rigid tendon model the tendon length is the tendon slack
|
| 1377 |
+
length. In all musculotendon models, tendon slack length is used to
|
| 1378 |
+
normalize tendon length to give
|
| 1379 |
+
:math:`\tilde{l}^T = \frac{l^T}{l^T_{slack}}`.
|
| 1380 |
+
peak_isometric_force : Expr | None
|
| 1381 |
+
The maximum force that the muscle fiber can produce when it is
|
| 1382 |
+
undergoing an isometric contraction (no lengthening velocity). In all
|
| 1383 |
+
musculotendon models, peak isometric force is used to normalized tendon
|
| 1384 |
+
and muscle fiber force to give
|
| 1385 |
+
:math:`\tilde{F}^T = \frac{F^T}{F^M_{max}}`.
|
| 1386 |
+
optimal_fiber_length : Expr | None
|
| 1387 |
+
The muscle fiber length at which the muscle fibers produce no passive
|
| 1388 |
+
force and their maximum active force. In all musculotendon models,
|
| 1389 |
+
optimal fiber length is used to normalize muscle fiber length to give
|
| 1390 |
+
:math:`\tilde{l}^M = \frac{l^M}{l^M_{opt}}`.
|
| 1391 |
+
maximal_fiber_velocity : Expr | None
|
| 1392 |
+
The fiber velocity at which, during muscle fiber shortening, the muscle
|
| 1393 |
+
fibers are unable to produce any active force. In all musculotendon
|
| 1394 |
+
models, maximal fiber velocity is used to normalize muscle fiber
|
| 1395 |
+
extension velocity to give :math:`\tilde{v}^M = \frac{v^M}{v^M_{max}}`.
|
| 1396 |
+
optimal_pennation_angle : Expr | None
|
| 1397 |
+
The pennation angle when muscle fiber length equals the optimal fiber
|
| 1398 |
+
length.
|
| 1399 |
+
fiber_damping_coefficient : Expr | None
|
| 1400 |
+
The coefficient of damping to be used in the damping element in the
|
| 1401 |
+
muscle fiber model.
|
| 1402 |
+
with_defaults : bool
|
| 1403 |
+
Whether ``with_defaults`` alternate constructors should be used when
|
| 1404 |
+
automatically constructing child classes. Default is ``False``.
|
| 1405 |
+
|
| 1406 |
+
References
|
| 1407 |
+
==========
|
| 1408 |
+
|
| 1409 |
+
.. [1] De Groote, F., Kinney, A. L., Rao, A. V., & Fregly, B. J., Evaluation
|
| 1410 |
+
of direct collocation optimal control problem formulations for
|
| 1411 |
+
solving the muscle redundancy problem, Annals of biomedical
|
| 1412 |
+
engineering, 44(10), (2016) pp. 2922-2936
|
| 1413 |
+
|
| 1414 |
+
"""
|
| 1415 |
+
|
| 1416 |
+
curves = CharacteristicCurveCollection(
|
| 1417 |
+
tendon_force_length=TendonForceLengthDeGroote2016,
|
| 1418 |
+
tendon_force_length_inverse=TendonForceLengthInverseDeGroote2016,
|
| 1419 |
+
fiber_force_length_passive=FiberForceLengthPassiveDeGroote2016,
|
| 1420 |
+
fiber_force_length_passive_inverse=FiberForceLengthPassiveInverseDeGroote2016,
|
| 1421 |
+
fiber_force_length_active=FiberForceLengthActiveDeGroote2016,
|
| 1422 |
+
fiber_force_velocity=FiberForceVelocityDeGroote2016,
|
| 1423 |
+
fiber_force_velocity_inverse=FiberForceVelocityInverseDeGroote2016,
|
| 1424 |
+
)
|
evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/tests/__init__.py
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|
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evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/tests/test_activation.py
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|
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|
|
| 1 |
+
"""Tests for the ``sympy.physics.biomechanics.activation.py`` module."""
|
| 2 |
+
|
| 3 |
+
import pytest
|
| 4 |
+
|
| 5 |
+
from sympy import Symbol
|
| 6 |
+
from sympy.core.numbers import Float, Integer, Rational
|
| 7 |
+
from sympy.functions.elementary.hyperbolic import tanh
|
| 8 |
+
from sympy.matrices import Matrix
|
| 9 |
+
from sympy.matrices.dense import zeros
|
| 10 |
+
from sympy.physics.mechanics import dynamicsymbols
|
| 11 |
+
from sympy.physics.biomechanics import (
|
| 12 |
+
ActivationBase,
|
| 13 |
+
FirstOrderActivationDeGroote2016,
|
| 14 |
+
ZerothOrderActivation,
|
| 15 |
+
)
|
| 16 |
+
from sympy.physics.biomechanics._mixin import _NamedMixin
|
| 17 |
+
from sympy.simplify.simplify import simplify
|
| 18 |
+
|
| 19 |
+
|
| 20 |
+
class TestZerothOrderActivation:
|
| 21 |
+
|
| 22 |
+
@staticmethod
|
| 23 |
+
def test_class():
|
| 24 |
+
assert issubclass(ZerothOrderActivation, ActivationBase)
|
| 25 |
+
assert issubclass(ZerothOrderActivation, _NamedMixin)
|
| 26 |
+
assert ZerothOrderActivation.__name__ == 'ZerothOrderActivation'
|
| 27 |
+
|
| 28 |
+
@pytest.fixture(autouse=True)
|
| 29 |
+
def _zeroth_order_activation_fixture(self):
|
| 30 |
+
self.name = 'name'
|
| 31 |
+
self.e = dynamicsymbols('e_name')
|
| 32 |
+
self.instance = ZerothOrderActivation(self.name)
|
| 33 |
+
|
| 34 |
+
def test_instance(self):
|
| 35 |
+
instance = ZerothOrderActivation(self.name)
|
| 36 |
+
assert isinstance(instance, ZerothOrderActivation)
|
| 37 |
+
|
| 38 |
+
def test_with_defaults(self):
|
| 39 |
+
instance = ZerothOrderActivation.with_defaults(self.name)
|
| 40 |
+
assert isinstance(instance, ZerothOrderActivation)
|
| 41 |
+
assert instance == ZerothOrderActivation(self.name)
|
| 42 |
+
|
| 43 |
+
def test_name(self):
|
| 44 |
+
assert hasattr(self.instance, 'name')
|
| 45 |
+
assert self.instance.name == self.name
|
| 46 |
+
|
| 47 |
+
def test_order(self):
|
| 48 |
+
assert hasattr(self.instance, 'order')
|
| 49 |
+
assert self.instance.order == 0
|
| 50 |
+
|
| 51 |
+
def test_excitation_attribute(self):
|
| 52 |
+
assert hasattr(self.instance, 'e')
|
| 53 |
+
assert hasattr(self.instance, 'excitation')
|
| 54 |
+
e_expected = dynamicsymbols('e_name')
|
| 55 |
+
assert self.instance.e == e_expected
|
| 56 |
+
assert self.instance.excitation == e_expected
|
| 57 |
+
assert self.instance.e is self.instance.excitation
|
| 58 |
+
|
| 59 |
+
def test_activation_attribute(self):
|
| 60 |
+
assert hasattr(self.instance, 'a')
|
| 61 |
+
assert hasattr(self.instance, 'activation')
|
| 62 |
+
a_expected = dynamicsymbols('e_name')
|
| 63 |
+
assert self.instance.a == a_expected
|
| 64 |
+
assert self.instance.activation == a_expected
|
| 65 |
+
assert self.instance.a is self.instance.activation is self.instance.e
|
| 66 |
+
|
| 67 |
+
def test_state_vars_attribute(self):
|
| 68 |
+
assert hasattr(self.instance, 'x')
|
| 69 |
+
assert hasattr(self.instance, 'state_vars')
|
| 70 |
+
assert self.instance.x == self.instance.state_vars
|
| 71 |
+
x_expected = zeros(0, 1)
|
| 72 |
+
assert self.instance.x == x_expected
|
| 73 |
+
assert self.instance.state_vars == x_expected
|
| 74 |
+
assert isinstance(self.instance.x, Matrix)
|
| 75 |
+
assert isinstance(self.instance.state_vars, Matrix)
|
| 76 |
+
assert self.instance.x.shape == (0, 1)
|
| 77 |
+
assert self.instance.state_vars.shape == (0, 1)
|
| 78 |
+
|
| 79 |
+
def test_input_vars_attribute(self):
|
| 80 |
+
assert hasattr(self.instance, 'r')
|
| 81 |
+
assert hasattr(self.instance, 'input_vars')
|
| 82 |
+
assert self.instance.r == self.instance.input_vars
|
| 83 |
+
r_expected = Matrix([self.e])
|
| 84 |
+
assert self.instance.r == r_expected
|
| 85 |
+
assert self.instance.input_vars == r_expected
|
| 86 |
+
assert isinstance(self.instance.r, Matrix)
|
| 87 |
+
assert isinstance(self.instance.input_vars, Matrix)
|
| 88 |
+
assert self.instance.r.shape == (1, 1)
|
| 89 |
+
assert self.instance.input_vars.shape == (1, 1)
|
| 90 |
+
|
| 91 |
+
def test_constants_attribute(self):
|
| 92 |
+
assert hasattr(self.instance, 'p')
|
| 93 |
+
assert hasattr(self.instance, 'constants')
|
| 94 |
+
assert self.instance.p == self.instance.constants
|
| 95 |
+
p_expected = zeros(0, 1)
|
| 96 |
+
assert self.instance.p == p_expected
|
| 97 |
+
assert self.instance.constants == p_expected
|
| 98 |
+
assert isinstance(self.instance.p, Matrix)
|
| 99 |
+
assert isinstance(self.instance.constants, Matrix)
|
| 100 |
+
assert self.instance.p.shape == (0, 1)
|
| 101 |
+
assert self.instance.constants.shape == (0, 1)
|
| 102 |
+
|
| 103 |
+
def test_M_attribute(self):
|
| 104 |
+
assert hasattr(self.instance, 'M')
|
| 105 |
+
M_expected = Matrix([])
|
| 106 |
+
assert self.instance.M == M_expected
|
| 107 |
+
assert isinstance(self.instance.M, Matrix)
|
| 108 |
+
assert self.instance.M.shape == (0, 0)
|
| 109 |
+
|
| 110 |
+
def test_F(self):
|
| 111 |
+
assert hasattr(self.instance, 'F')
|
| 112 |
+
F_expected = zeros(0, 1)
|
| 113 |
+
assert self.instance.F == F_expected
|
| 114 |
+
assert isinstance(self.instance.F, Matrix)
|
| 115 |
+
assert self.instance.F.shape == (0, 1)
|
| 116 |
+
|
| 117 |
+
def test_rhs(self):
|
| 118 |
+
assert hasattr(self.instance, 'rhs')
|
| 119 |
+
rhs_expected = zeros(0, 1)
|
| 120 |
+
rhs = self.instance.rhs()
|
| 121 |
+
assert rhs == rhs_expected
|
| 122 |
+
assert isinstance(rhs, Matrix)
|
| 123 |
+
assert rhs.shape == (0, 1)
|
| 124 |
+
|
| 125 |
+
def test_repr(self):
|
| 126 |
+
expected = 'ZerothOrderActivation(\'name\')'
|
| 127 |
+
assert repr(self.instance) == expected
|
| 128 |
+
|
| 129 |
+
|
| 130 |
+
class TestFirstOrderActivationDeGroote2016:
|
| 131 |
+
|
| 132 |
+
@staticmethod
|
| 133 |
+
def test_class():
|
| 134 |
+
assert issubclass(FirstOrderActivationDeGroote2016, ActivationBase)
|
| 135 |
+
assert issubclass(FirstOrderActivationDeGroote2016, _NamedMixin)
|
| 136 |
+
assert FirstOrderActivationDeGroote2016.__name__ == 'FirstOrderActivationDeGroote2016'
|
| 137 |
+
|
| 138 |
+
@pytest.fixture(autouse=True)
|
| 139 |
+
def _first_order_activation_de_groote_2016_fixture(self):
|
| 140 |
+
self.name = 'name'
|
| 141 |
+
self.e = dynamicsymbols('e_name')
|
| 142 |
+
self.a = dynamicsymbols('a_name')
|
| 143 |
+
self.tau_a = Symbol('tau_a')
|
| 144 |
+
self.tau_d = Symbol('tau_d')
|
| 145 |
+
self.b = Symbol('b')
|
| 146 |
+
self.instance = FirstOrderActivationDeGroote2016(
|
| 147 |
+
self.name,
|
| 148 |
+
self.tau_a,
|
| 149 |
+
self.tau_d,
|
| 150 |
+
self.b,
|
| 151 |
+
)
|
| 152 |
+
|
| 153 |
+
def test_instance(self):
|
| 154 |
+
instance = FirstOrderActivationDeGroote2016(self.name)
|
| 155 |
+
assert isinstance(instance, FirstOrderActivationDeGroote2016)
|
| 156 |
+
|
| 157 |
+
def test_with_defaults(self):
|
| 158 |
+
instance = FirstOrderActivationDeGroote2016.with_defaults(self.name)
|
| 159 |
+
assert isinstance(instance, FirstOrderActivationDeGroote2016)
|
| 160 |
+
assert instance.tau_a == Float('0.015')
|
| 161 |
+
assert instance.activation_time_constant == Float('0.015')
|
| 162 |
+
assert instance.tau_d == Float('0.060')
|
| 163 |
+
assert instance.deactivation_time_constant == Float('0.060')
|
| 164 |
+
assert instance.b == Float('10.0')
|
| 165 |
+
assert instance.smoothing_rate == Float('10.0')
|
| 166 |
+
|
| 167 |
+
def test_name(self):
|
| 168 |
+
assert hasattr(self.instance, 'name')
|
| 169 |
+
assert self.instance.name == self.name
|
| 170 |
+
|
| 171 |
+
def test_order(self):
|
| 172 |
+
assert hasattr(self.instance, 'order')
|
| 173 |
+
assert self.instance.order == 1
|
| 174 |
+
|
| 175 |
+
def test_excitation(self):
|
| 176 |
+
assert hasattr(self.instance, 'e')
|
| 177 |
+
assert hasattr(self.instance, 'excitation')
|
| 178 |
+
e_expected = dynamicsymbols('e_name')
|
| 179 |
+
assert self.instance.e == e_expected
|
| 180 |
+
assert self.instance.excitation == e_expected
|
| 181 |
+
assert self.instance.e is self.instance.excitation
|
| 182 |
+
|
| 183 |
+
def test_excitation_is_immutable(self):
|
| 184 |
+
with pytest.raises(AttributeError):
|
| 185 |
+
self.instance.e = None
|
| 186 |
+
with pytest.raises(AttributeError):
|
| 187 |
+
self.instance.excitation = None
|
| 188 |
+
|
| 189 |
+
def test_activation(self):
|
| 190 |
+
assert hasattr(self.instance, 'a')
|
| 191 |
+
assert hasattr(self.instance, 'activation')
|
| 192 |
+
a_expected = dynamicsymbols('a_name')
|
| 193 |
+
assert self.instance.a == a_expected
|
| 194 |
+
assert self.instance.activation == a_expected
|
| 195 |
+
|
| 196 |
+
def test_activation_is_immutable(self):
|
| 197 |
+
with pytest.raises(AttributeError):
|
| 198 |
+
self.instance.a = None
|
| 199 |
+
with pytest.raises(AttributeError):
|
| 200 |
+
self.instance.activation = None
|
| 201 |
+
|
| 202 |
+
@pytest.mark.parametrize(
|
| 203 |
+
'tau_a, expected',
|
| 204 |
+
[
|
| 205 |
+
(None, Symbol('tau_a_name')),
|
| 206 |
+
(Symbol('tau_a'), Symbol('tau_a')),
|
| 207 |
+
(Float('0.015'), Float('0.015')),
|
| 208 |
+
]
|
| 209 |
+
)
|
| 210 |
+
def test_activation_time_constant(self, tau_a, expected):
|
| 211 |
+
instance = FirstOrderActivationDeGroote2016(
|
| 212 |
+
'name', activation_time_constant=tau_a,
|
| 213 |
+
)
|
| 214 |
+
assert instance.tau_a == expected
|
| 215 |
+
assert instance.activation_time_constant == expected
|
| 216 |
+
assert instance.tau_a is instance.activation_time_constant
|
| 217 |
+
|
| 218 |
+
def test_activation_time_constant_is_immutable(self):
|
| 219 |
+
with pytest.raises(AttributeError):
|
| 220 |
+
self.instance.tau_a = None
|
| 221 |
+
with pytest.raises(AttributeError):
|
| 222 |
+
self.instance.activation_time_constant = None
|
| 223 |
+
|
| 224 |
+
@pytest.mark.parametrize(
|
| 225 |
+
'tau_d, expected',
|
| 226 |
+
[
|
| 227 |
+
(None, Symbol('tau_d_name')),
|
| 228 |
+
(Symbol('tau_d'), Symbol('tau_d')),
|
| 229 |
+
(Float('0.060'), Float('0.060')),
|
| 230 |
+
]
|
| 231 |
+
)
|
| 232 |
+
def test_deactivation_time_constant(self, tau_d, expected):
|
| 233 |
+
instance = FirstOrderActivationDeGroote2016(
|
| 234 |
+
'name', deactivation_time_constant=tau_d,
|
| 235 |
+
)
|
| 236 |
+
assert instance.tau_d == expected
|
| 237 |
+
assert instance.deactivation_time_constant == expected
|
| 238 |
+
assert instance.tau_d is instance.deactivation_time_constant
|
| 239 |
+
|
| 240 |
+
def test_deactivation_time_constant_is_immutable(self):
|
| 241 |
+
with pytest.raises(AttributeError):
|
| 242 |
+
self.instance.tau_d = None
|
| 243 |
+
with pytest.raises(AttributeError):
|
| 244 |
+
self.instance.deactivation_time_constant = None
|
| 245 |
+
|
| 246 |
+
@pytest.mark.parametrize(
|
| 247 |
+
'b, expected',
|
| 248 |
+
[
|
| 249 |
+
(None, Symbol('b_name')),
|
| 250 |
+
(Symbol('b'), Symbol('b')),
|
| 251 |
+
(Integer('10'), Integer('10')),
|
| 252 |
+
]
|
| 253 |
+
)
|
| 254 |
+
def test_smoothing_rate(self, b, expected):
|
| 255 |
+
instance = FirstOrderActivationDeGroote2016(
|
| 256 |
+
'name', smoothing_rate=b,
|
| 257 |
+
)
|
| 258 |
+
assert instance.b == expected
|
| 259 |
+
assert instance.smoothing_rate == expected
|
| 260 |
+
assert instance.b is instance.smoothing_rate
|
| 261 |
+
|
| 262 |
+
def test_smoothing_rate_is_immutable(self):
|
| 263 |
+
with pytest.raises(AttributeError):
|
| 264 |
+
self.instance.b = None
|
| 265 |
+
with pytest.raises(AttributeError):
|
| 266 |
+
self.instance.smoothing_rate = None
|
| 267 |
+
|
| 268 |
+
def test_state_vars(self):
|
| 269 |
+
assert hasattr(self.instance, 'x')
|
| 270 |
+
assert hasattr(self.instance, 'state_vars')
|
| 271 |
+
assert self.instance.x == self.instance.state_vars
|
| 272 |
+
x_expected = Matrix([self.a])
|
| 273 |
+
assert self.instance.x == x_expected
|
| 274 |
+
assert self.instance.state_vars == x_expected
|
| 275 |
+
assert isinstance(self.instance.x, Matrix)
|
| 276 |
+
assert isinstance(self.instance.state_vars, Matrix)
|
| 277 |
+
assert self.instance.x.shape == (1, 1)
|
| 278 |
+
assert self.instance.state_vars.shape == (1, 1)
|
| 279 |
+
|
| 280 |
+
def test_input_vars(self):
|
| 281 |
+
assert hasattr(self.instance, 'r')
|
| 282 |
+
assert hasattr(self.instance, 'input_vars')
|
| 283 |
+
assert self.instance.r == self.instance.input_vars
|
| 284 |
+
r_expected = Matrix([self.e])
|
| 285 |
+
assert self.instance.r == r_expected
|
| 286 |
+
assert self.instance.input_vars == r_expected
|
| 287 |
+
assert isinstance(self.instance.r, Matrix)
|
| 288 |
+
assert isinstance(self.instance.input_vars, Matrix)
|
| 289 |
+
assert self.instance.r.shape == (1, 1)
|
| 290 |
+
assert self.instance.input_vars.shape == (1, 1)
|
| 291 |
+
|
| 292 |
+
def test_constants(self):
|
| 293 |
+
assert hasattr(self.instance, 'p')
|
| 294 |
+
assert hasattr(self.instance, 'constants')
|
| 295 |
+
assert self.instance.p == self.instance.constants
|
| 296 |
+
p_expected = Matrix([self.tau_a, self.tau_d, self.b])
|
| 297 |
+
assert self.instance.p == p_expected
|
| 298 |
+
assert self.instance.constants == p_expected
|
| 299 |
+
assert isinstance(self.instance.p, Matrix)
|
| 300 |
+
assert isinstance(self.instance.constants, Matrix)
|
| 301 |
+
assert self.instance.p.shape == (3, 1)
|
| 302 |
+
assert self.instance.constants.shape == (3, 1)
|
| 303 |
+
|
| 304 |
+
def test_M(self):
|
| 305 |
+
assert hasattr(self.instance, 'M')
|
| 306 |
+
M_expected = Matrix([1])
|
| 307 |
+
assert self.instance.M == M_expected
|
| 308 |
+
assert isinstance(self.instance.M, Matrix)
|
| 309 |
+
assert self.instance.M.shape == (1, 1)
|
| 310 |
+
|
| 311 |
+
def test_F(self):
|
| 312 |
+
assert hasattr(self.instance, 'F')
|
| 313 |
+
da_expr = (
|
| 314 |
+
((1/(self.tau_a*(Rational(1, 2) + Rational(3, 2)*self.a)))
|
| 315 |
+
*(Rational(1, 2) + Rational(1, 2)*tanh(self.b*(self.e - self.a)))
|
| 316 |
+
+ ((Rational(1, 2) + Rational(3, 2)*self.a)/self.tau_d)
|
| 317 |
+
*(Rational(1, 2) - Rational(1, 2)*tanh(self.b*(self.e - self.a))))
|
| 318 |
+
*(self.e - self.a)
|
| 319 |
+
)
|
| 320 |
+
F_expected = Matrix([da_expr])
|
| 321 |
+
assert self.instance.F == F_expected
|
| 322 |
+
assert isinstance(self.instance.F, Matrix)
|
| 323 |
+
assert self.instance.F.shape == (1, 1)
|
| 324 |
+
|
| 325 |
+
def test_rhs(self):
|
| 326 |
+
assert hasattr(self.instance, 'rhs')
|
| 327 |
+
da_expr = (
|
| 328 |
+
((1/(self.tau_a*(Rational(1, 2) + Rational(3, 2)*self.a)))
|
| 329 |
+
*(Rational(1, 2) + Rational(1, 2)*tanh(self.b*(self.e - self.a)))
|
| 330 |
+
+ ((Rational(1, 2) + Rational(3, 2)*self.a)/self.tau_d)
|
| 331 |
+
*(Rational(1, 2) - Rational(1, 2)*tanh(self.b*(self.e - self.a))))
|
| 332 |
+
*(self.e - self.a)
|
| 333 |
+
)
|
| 334 |
+
rhs_expected = Matrix([da_expr])
|
| 335 |
+
rhs = self.instance.rhs()
|
| 336 |
+
assert rhs == rhs_expected
|
| 337 |
+
assert isinstance(rhs, Matrix)
|
| 338 |
+
assert rhs.shape == (1, 1)
|
| 339 |
+
assert simplify(self.instance.M.solve(self.instance.F) - rhs) == zeros(1)
|
| 340 |
+
|
| 341 |
+
def test_repr(self):
|
| 342 |
+
expected = (
|
| 343 |
+
'FirstOrderActivationDeGroote2016(\'name\', '
|
| 344 |
+
'activation_time_constant=tau_a, '
|
| 345 |
+
'deactivation_time_constant=tau_d, '
|
| 346 |
+
'smoothing_rate=b)'
|
| 347 |
+
)
|
| 348 |
+
assert repr(self.instance) == expected
|
evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/tests/test_curve.py
ADDED
|
@@ -0,0 +1,1784 @@
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|
| 1 |
+
"""Tests for the ``sympy.physics.biomechanics.characteristic.py`` module."""
|
| 2 |
+
|
| 3 |
+
import pytest
|
| 4 |
+
|
| 5 |
+
from sympy.core.expr import UnevaluatedExpr
|
| 6 |
+
from sympy.core.function import Function
|
| 7 |
+
from sympy.core.numbers import Float, Integer
|
| 8 |
+
from sympy.core.symbol import Symbol, symbols
|
| 9 |
+
from sympy.external.importtools import import_module
|
| 10 |
+
from sympy.functions.elementary.exponential import exp, log
|
| 11 |
+
from sympy.functions.elementary.hyperbolic import cosh, sinh
|
| 12 |
+
from sympy.functions.elementary.miscellaneous import sqrt
|
| 13 |
+
from sympy.physics.biomechanics.curve import (
|
| 14 |
+
CharacteristicCurveCollection,
|
| 15 |
+
CharacteristicCurveFunction,
|
| 16 |
+
FiberForceLengthActiveDeGroote2016,
|
| 17 |
+
FiberForceLengthPassiveDeGroote2016,
|
| 18 |
+
FiberForceLengthPassiveInverseDeGroote2016,
|
| 19 |
+
FiberForceVelocityDeGroote2016,
|
| 20 |
+
FiberForceVelocityInverseDeGroote2016,
|
| 21 |
+
TendonForceLengthDeGroote2016,
|
| 22 |
+
TendonForceLengthInverseDeGroote2016,
|
| 23 |
+
)
|
| 24 |
+
from sympy.printing.c import C89CodePrinter, C99CodePrinter, C11CodePrinter
|
| 25 |
+
from sympy.printing.cxx import (
|
| 26 |
+
CXX98CodePrinter,
|
| 27 |
+
CXX11CodePrinter,
|
| 28 |
+
CXX17CodePrinter,
|
| 29 |
+
)
|
| 30 |
+
from sympy.printing.fortran import FCodePrinter
|
| 31 |
+
from sympy.printing.lambdarepr import LambdaPrinter
|
| 32 |
+
from sympy.printing.latex import LatexPrinter
|
| 33 |
+
from sympy.printing.octave import OctaveCodePrinter
|
| 34 |
+
from sympy.printing.numpy import (
|
| 35 |
+
CuPyPrinter,
|
| 36 |
+
JaxPrinter,
|
| 37 |
+
NumPyPrinter,
|
| 38 |
+
SciPyPrinter,
|
| 39 |
+
)
|
| 40 |
+
from sympy.printing.pycode import MpmathPrinter, PythonCodePrinter
|
| 41 |
+
from sympy.utilities.lambdify import lambdify
|
| 42 |
+
|
| 43 |
+
jax = import_module('jax')
|
| 44 |
+
numpy = import_module('numpy')
|
| 45 |
+
|
| 46 |
+
if jax:
|
| 47 |
+
jax.config.update('jax_enable_x64', True)
|
| 48 |
+
|
| 49 |
+
|
| 50 |
+
class TestCharacteristicCurveFunction:
|
| 51 |
+
|
| 52 |
+
@staticmethod
|
| 53 |
+
@pytest.mark.parametrize(
|
| 54 |
+
'code_printer, expected',
|
| 55 |
+
[
|
| 56 |
+
(C89CodePrinter, '(a + b)*(c + d)*(e + f)'),
|
| 57 |
+
(C99CodePrinter, '(a + b)*(c + d)*(e + f)'),
|
| 58 |
+
(C11CodePrinter, '(a + b)*(c + d)*(e + f)'),
|
| 59 |
+
(CXX98CodePrinter, '(a + b)*(c + d)*(e + f)'),
|
| 60 |
+
(CXX11CodePrinter, '(a + b)*(c + d)*(e + f)'),
|
| 61 |
+
(CXX17CodePrinter, '(a + b)*(c + d)*(e + f)'),
|
| 62 |
+
(FCodePrinter, ' (a + b)*(c + d)*(e + f)'),
|
| 63 |
+
(OctaveCodePrinter, '(a + b).*(c + d).*(e + f)'),
|
| 64 |
+
(PythonCodePrinter, '(a + b)*(c + d)*(e + f)'),
|
| 65 |
+
(NumPyPrinter, '(a + b)*(c + d)*(e + f)'),
|
| 66 |
+
(SciPyPrinter, '(a + b)*(c + d)*(e + f)'),
|
| 67 |
+
(CuPyPrinter, '(a + b)*(c + d)*(e + f)'),
|
| 68 |
+
(JaxPrinter, '(a + b)*(c + d)*(e + f)'),
|
| 69 |
+
(MpmathPrinter, '(a + b)*(c + d)*(e + f)'),
|
| 70 |
+
(LambdaPrinter, '(a + b)*(c + d)*(e + f)'),
|
| 71 |
+
]
|
| 72 |
+
)
|
| 73 |
+
def test_print_code_parenthesize(code_printer, expected):
|
| 74 |
+
|
| 75 |
+
class ExampleFunction(CharacteristicCurveFunction):
|
| 76 |
+
|
| 77 |
+
@classmethod
|
| 78 |
+
def eval(cls, a, b):
|
| 79 |
+
pass
|
| 80 |
+
|
| 81 |
+
def doit(self, **kwargs):
|
| 82 |
+
a, b = self.args
|
| 83 |
+
return a + b
|
| 84 |
+
|
| 85 |
+
a, b, c, d, e, f = symbols('a, b, c, d, e, f')
|
| 86 |
+
f1 = ExampleFunction(a, b)
|
| 87 |
+
f2 = ExampleFunction(c, d)
|
| 88 |
+
f3 = ExampleFunction(e, f)
|
| 89 |
+
assert code_printer().doprint(f1*f2*f3) == expected
|
| 90 |
+
|
| 91 |
+
|
| 92 |
+
class TestTendonForceLengthDeGroote2016:
|
| 93 |
+
|
| 94 |
+
@pytest.fixture(autouse=True)
|
| 95 |
+
def _tendon_force_length_arguments_fixture(self):
|
| 96 |
+
self.l_T_tilde = Symbol('l_T_tilde')
|
| 97 |
+
self.c0 = Symbol('c_0')
|
| 98 |
+
self.c1 = Symbol('c_1')
|
| 99 |
+
self.c2 = Symbol('c_2')
|
| 100 |
+
self.c3 = Symbol('c_3')
|
| 101 |
+
self.constants = (self.c0, self.c1, self.c2, self.c3)
|
| 102 |
+
|
| 103 |
+
@staticmethod
|
| 104 |
+
def test_class():
|
| 105 |
+
assert issubclass(TendonForceLengthDeGroote2016, Function)
|
| 106 |
+
assert issubclass(TendonForceLengthDeGroote2016, CharacteristicCurveFunction)
|
| 107 |
+
assert TendonForceLengthDeGroote2016.__name__ == 'TendonForceLengthDeGroote2016'
|
| 108 |
+
|
| 109 |
+
def test_instance(self):
|
| 110 |
+
fl_T = TendonForceLengthDeGroote2016(self.l_T_tilde, *self.constants)
|
| 111 |
+
assert isinstance(fl_T, TendonForceLengthDeGroote2016)
|
| 112 |
+
assert str(fl_T) == 'TendonForceLengthDeGroote2016(l_T_tilde, c_0, c_1, c_2, c_3)'
|
| 113 |
+
|
| 114 |
+
def test_doit(self):
|
| 115 |
+
fl_T = TendonForceLengthDeGroote2016(self.l_T_tilde, *self.constants).doit()
|
| 116 |
+
assert fl_T == self.c0*exp(self.c3*(self.l_T_tilde - self.c1)) - self.c2
|
| 117 |
+
|
| 118 |
+
def test_doit_evaluate_false(self):
|
| 119 |
+
fl_T = TendonForceLengthDeGroote2016(self.l_T_tilde, *self.constants).doit(evaluate=False)
|
| 120 |
+
assert fl_T == self.c0*exp(self.c3*UnevaluatedExpr(self.l_T_tilde - self.c1)) - self.c2
|
| 121 |
+
|
| 122 |
+
def test_with_defaults(self):
|
| 123 |
+
constants = (
|
| 124 |
+
Float('0.2'),
|
| 125 |
+
Float('0.995'),
|
| 126 |
+
Float('0.25'),
|
| 127 |
+
Float('33.93669377311689'),
|
| 128 |
+
)
|
| 129 |
+
fl_T_manual = TendonForceLengthDeGroote2016(self.l_T_tilde, *constants)
|
| 130 |
+
fl_T_constants = TendonForceLengthDeGroote2016.with_defaults(self.l_T_tilde)
|
| 131 |
+
assert fl_T_manual == fl_T_constants
|
| 132 |
+
|
| 133 |
+
def test_differentiate_wrt_l_T_tilde(self):
|
| 134 |
+
fl_T = TendonForceLengthDeGroote2016(self.l_T_tilde, *self.constants)
|
| 135 |
+
expected = self.c0*self.c3*exp(self.c3*UnevaluatedExpr(-self.c1 + self.l_T_tilde))
|
| 136 |
+
assert fl_T.diff(self.l_T_tilde) == expected
|
| 137 |
+
|
| 138 |
+
def test_differentiate_wrt_c0(self):
|
| 139 |
+
fl_T = TendonForceLengthDeGroote2016(self.l_T_tilde, *self.constants)
|
| 140 |
+
expected = exp(self.c3*UnevaluatedExpr(-self.c1 + self.l_T_tilde))
|
| 141 |
+
assert fl_T.diff(self.c0) == expected
|
| 142 |
+
|
| 143 |
+
def test_differentiate_wrt_c1(self):
|
| 144 |
+
fl_T = TendonForceLengthDeGroote2016(self.l_T_tilde, *self.constants)
|
| 145 |
+
expected = -self.c0*self.c3*exp(self.c3*UnevaluatedExpr(self.l_T_tilde - self.c1))
|
| 146 |
+
assert fl_T.diff(self.c1) == expected
|
| 147 |
+
|
| 148 |
+
def test_differentiate_wrt_c2(self):
|
| 149 |
+
fl_T = TendonForceLengthDeGroote2016(self.l_T_tilde, *self.constants)
|
| 150 |
+
expected = Integer(-1)
|
| 151 |
+
assert fl_T.diff(self.c2) == expected
|
| 152 |
+
|
| 153 |
+
def test_differentiate_wrt_c3(self):
|
| 154 |
+
fl_T = TendonForceLengthDeGroote2016(self.l_T_tilde, *self.constants)
|
| 155 |
+
expected = self.c0*(self.l_T_tilde - self.c1)*exp(self.c3*UnevaluatedExpr(self.l_T_tilde - self.c1))
|
| 156 |
+
assert fl_T.diff(self.c3) == expected
|
| 157 |
+
|
| 158 |
+
def test_inverse(self):
|
| 159 |
+
fl_T = TendonForceLengthDeGroote2016(self.l_T_tilde, *self.constants)
|
| 160 |
+
assert fl_T.inverse() is TendonForceLengthInverseDeGroote2016
|
| 161 |
+
|
| 162 |
+
def test_function_print_latex(self):
|
| 163 |
+
fl_T = TendonForceLengthDeGroote2016(self.l_T_tilde, *self.constants)
|
| 164 |
+
expected = r'\operatorname{fl}^T \left( l_{T tilde} \right)'
|
| 165 |
+
assert LatexPrinter().doprint(fl_T) == expected
|
| 166 |
+
|
| 167 |
+
def test_expression_print_latex(self):
|
| 168 |
+
fl_T = TendonForceLengthDeGroote2016(self.l_T_tilde, *self.constants)
|
| 169 |
+
expected = r'c_{0} e^{c_{3} \left(- c_{1} + l_{T tilde}\right)} - c_{2}'
|
| 170 |
+
assert LatexPrinter().doprint(fl_T.doit()) == expected
|
| 171 |
+
|
| 172 |
+
@pytest.mark.parametrize(
|
| 173 |
+
'code_printer, expected',
|
| 174 |
+
[
|
| 175 |
+
(
|
| 176 |
+
C89CodePrinter,
|
| 177 |
+
'(-0.25 + 0.20000000000000001*exp(33.93669377311689*(l_T_tilde - 0.995)))',
|
| 178 |
+
),
|
| 179 |
+
(
|
| 180 |
+
C99CodePrinter,
|
| 181 |
+
'(-0.25 + 0.20000000000000001*exp(33.93669377311689*(l_T_tilde - 0.995)))',
|
| 182 |
+
),
|
| 183 |
+
(
|
| 184 |
+
C11CodePrinter,
|
| 185 |
+
'(-0.25 + 0.20000000000000001*exp(33.93669377311689*(l_T_tilde - 0.995)))',
|
| 186 |
+
),
|
| 187 |
+
(
|
| 188 |
+
CXX98CodePrinter,
|
| 189 |
+
'(-0.25 + 0.20000000000000001*exp(33.93669377311689*(l_T_tilde - 0.995)))',
|
| 190 |
+
),
|
| 191 |
+
(
|
| 192 |
+
CXX11CodePrinter,
|
| 193 |
+
'(-0.25 + 0.20000000000000001*std::exp(33.93669377311689*(l_T_tilde - 0.995)))',
|
| 194 |
+
),
|
| 195 |
+
(
|
| 196 |
+
CXX17CodePrinter,
|
| 197 |
+
'(-0.25 + 0.20000000000000001*std::exp(33.93669377311689*(l_T_tilde - 0.995)))',
|
| 198 |
+
),
|
| 199 |
+
(
|
| 200 |
+
FCodePrinter,
|
| 201 |
+
' (-0.25d0 + 0.2d0*exp(33.93669377311689d0*(l_T_tilde - 0.995d0)))',
|
| 202 |
+
),
|
| 203 |
+
(
|
| 204 |
+
OctaveCodePrinter,
|
| 205 |
+
'(-0.25 + 0.2*exp(33.93669377311689*(l_T_tilde - 0.995)))',
|
| 206 |
+
),
|
| 207 |
+
(
|
| 208 |
+
PythonCodePrinter,
|
| 209 |
+
'(-0.25 + 0.2*math.exp(33.93669377311689*(l_T_tilde - 0.995)))',
|
| 210 |
+
),
|
| 211 |
+
(
|
| 212 |
+
NumPyPrinter,
|
| 213 |
+
'(-0.25 + 0.2*numpy.exp(33.93669377311689*(l_T_tilde - 0.995)))',
|
| 214 |
+
),
|
| 215 |
+
(
|
| 216 |
+
SciPyPrinter,
|
| 217 |
+
'(-0.25 + 0.2*numpy.exp(33.93669377311689*(l_T_tilde - 0.995)))',
|
| 218 |
+
),
|
| 219 |
+
(
|
| 220 |
+
CuPyPrinter,
|
| 221 |
+
'(-0.25 + 0.2*cupy.exp(33.93669377311689*(l_T_tilde - 0.995)))',
|
| 222 |
+
),
|
| 223 |
+
(
|
| 224 |
+
JaxPrinter,
|
| 225 |
+
'(-0.25 + 0.2*jax.numpy.exp(33.93669377311689*(l_T_tilde - 0.995)))',
|
| 226 |
+
),
|
| 227 |
+
(
|
| 228 |
+
MpmathPrinter,
|
| 229 |
+
'(mpmath.mpf((1, 1, -2, 1)) + mpmath.mpf((0, 3602879701896397, -54, 52))'
|
| 230 |
+
'*mpmath.exp(mpmath.mpf((0, 9552330089424741, -48, 54))*(l_T_tilde + '
|
| 231 |
+
'mpmath.mpf((1, 8962163258467287, -53, 53)))))',
|
| 232 |
+
),
|
| 233 |
+
(
|
| 234 |
+
LambdaPrinter,
|
| 235 |
+
'(-0.25 + 0.2*math.exp(33.93669377311689*(l_T_tilde - 0.995)))',
|
| 236 |
+
),
|
| 237 |
+
]
|
| 238 |
+
)
|
| 239 |
+
def test_print_code(self, code_printer, expected):
|
| 240 |
+
fl_T = TendonForceLengthDeGroote2016.with_defaults(self.l_T_tilde)
|
| 241 |
+
assert code_printer().doprint(fl_T) == expected
|
| 242 |
+
|
| 243 |
+
def test_derivative_print_code(self):
|
| 244 |
+
fl_T = TendonForceLengthDeGroote2016.with_defaults(self.l_T_tilde)
|
| 245 |
+
dfl_T_dl_T_tilde = fl_T.diff(self.l_T_tilde)
|
| 246 |
+
expected = '6.787338754623378*math.exp(33.93669377311689*(l_T_tilde - 0.995))'
|
| 247 |
+
assert PythonCodePrinter().doprint(dfl_T_dl_T_tilde) == expected
|
| 248 |
+
|
| 249 |
+
def test_lambdify(self):
|
| 250 |
+
fl_T = TendonForceLengthDeGroote2016.with_defaults(self.l_T_tilde)
|
| 251 |
+
fl_T_callable = lambdify(self.l_T_tilde, fl_T)
|
| 252 |
+
assert fl_T_callable(1.0) == pytest.approx(-0.013014055039221595)
|
| 253 |
+
|
| 254 |
+
@pytest.mark.skipif(numpy is None, reason='NumPy not installed')
|
| 255 |
+
def test_lambdify_numpy(self):
|
| 256 |
+
fl_T = TendonForceLengthDeGroote2016.with_defaults(self.l_T_tilde)
|
| 257 |
+
fl_T_callable = lambdify(self.l_T_tilde, fl_T, 'numpy')
|
| 258 |
+
l_T_tilde = numpy.array([0.95, 1.0, 1.01, 1.05])
|
| 259 |
+
expected = numpy.array([
|
| 260 |
+
-0.2065693181344816,
|
| 261 |
+
-0.0130140550392216,
|
| 262 |
+
0.0827421191989246,
|
| 263 |
+
1.04314889144172,
|
| 264 |
+
])
|
| 265 |
+
numpy.testing.assert_allclose(fl_T_callable(l_T_tilde), expected)
|
| 266 |
+
|
| 267 |
+
@pytest.mark.skipif(jax is None, reason='JAX not installed')
|
| 268 |
+
def test_lambdify_jax(self):
|
| 269 |
+
fl_T = TendonForceLengthDeGroote2016.with_defaults(self.l_T_tilde)
|
| 270 |
+
fl_T_callable = jax.jit(lambdify(self.l_T_tilde, fl_T, 'jax'))
|
| 271 |
+
l_T_tilde = jax.numpy.array([0.95, 1.0, 1.01, 1.05])
|
| 272 |
+
expected = jax.numpy.array([
|
| 273 |
+
-0.2065693181344816,
|
| 274 |
+
-0.0130140550392216,
|
| 275 |
+
0.0827421191989246,
|
| 276 |
+
1.04314889144172,
|
| 277 |
+
])
|
| 278 |
+
numpy.testing.assert_allclose(fl_T_callable(l_T_tilde), expected)
|
| 279 |
+
|
| 280 |
+
|
| 281 |
+
class TestTendonForceLengthInverseDeGroote2016:
|
| 282 |
+
|
| 283 |
+
@pytest.fixture(autouse=True)
|
| 284 |
+
def _tendon_force_length_inverse_arguments_fixture(self):
|
| 285 |
+
self.fl_T = Symbol('fl_T')
|
| 286 |
+
self.c0 = Symbol('c_0')
|
| 287 |
+
self.c1 = Symbol('c_1')
|
| 288 |
+
self.c2 = Symbol('c_2')
|
| 289 |
+
self.c3 = Symbol('c_3')
|
| 290 |
+
self.constants = (self.c0, self.c1, self.c2, self.c3)
|
| 291 |
+
|
| 292 |
+
@staticmethod
|
| 293 |
+
def test_class():
|
| 294 |
+
assert issubclass(TendonForceLengthInverseDeGroote2016, Function)
|
| 295 |
+
assert issubclass(TendonForceLengthInverseDeGroote2016, CharacteristicCurveFunction)
|
| 296 |
+
assert TendonForceLengthInverseDeGroote2016.__name__ == 'TendonForceLengthInverseDeGroote2016'
|
| 297 |
+
|
| 298 |
+
def test_instance(self):
|
| 299 |
+
fl_T_inv = TendonForceLengthInverseDeGroote2016(self.fl_T, *self.constants)
|
| 300 |
+
assert isinstance(fl_T_inv, TendonForceLengthInverseDeGroote2016)
|
| 301 |
+
assert str(fl_T_inv) == 'TendonForceLengthInverseDeGroote2016(fl_T, c_0, c_1, c_2, c_3)'
|
| 302 |
+
|
| 303 |
+
def test_doit(self):
|
| 304 |
+
fl_T_inv = TendonForceLengthInverseDeGroote2016(self.fl_T, *self.constants).doit()
|
| 305 |
+
assert fl_T_inv == log((self.fl_T + self.c2)/self.c0)/self.c3 + self.c1
|
| 306 |
+
|
| 307 |
+
def test_doit_evaluate_false(self):
|
| 308 |
+
fl_T_inv = TendonForceLengthInverseDeGroote2016(self.fl_T, *self.constants).doit(evaluate=False)
|
| 309 |
+
assert fl_T_inv == log(UnevaluatedExpr((self.fl_T + self.c2)/self.c0))/self.c3 + self.c1
|
| 310 |
+
|
| 311 |
+
def test_with_defaults(self):
|
| 312 |
+
constants = (
|
| 313 |
+
Float('0.2'),
|
| 314 |
+
Float('0.995'),
|
| 315 |
+
Float('0.25'),
|
| 316 |
+
Float('33.93669377311689'),
|
| 317 |
+
)
|
| 318 |
+
fl_T_inv_manual = TendonForceLengthInverseDeGroote2016(self.fl_T, *constants)
|
| 319 |
+
fl_T_inv_constants = TendonForceLengthInverseDeGroote2016.with_defaults(self.fl_T)
|
| 320 |
+
assert fl_T_inv_manual == fl_T_inv_constants
|
| 321 |
+
|
| 322 |
+
def test_differentiate_wrt_fl_T(self):
|
| 323 |
+
fl_T_inv = TendonForceLengthInverseDeGroote2016(self.fl_T, *self.constants)
|
| 324 |
+
expected = 1/(self.c3*(self.fl_T + self.c2))
|
| 325 |
+
assert fl_T_inv.diff(self.fl_T) == expected
|
| 326 |
+
|
| 327 |
+
def test_differentiate_wrt_c0(self):
|
| 328 |
+
fl_T_inv = TendonForceLengthInverseDeGroote2016(self.fl_T, *self.constants)
|
| 329 |
+
expected = -1/(self.c0*self.c3)
|
| 330 |
+
assert fl_T_inv.diff(self.c0) == expected
|
| 331 |
+
|
| 332 |
+
def test_differentiate_wrt_c1(self):
|
| 333 |
+
fl_T_inv = TendonForceLengthInverseDeGroote2016(self.fl_T, *self.constants)
|
| 334 |
+
expected = Integer(1)
|
| 335 |
+
assert fl_T_inv.diff(self.c1) == expected
|
| 336 |
+
|
| 337 |
+
def test_differentiate_wrt_c2(self):
|
| 338 |
+
fl_T_inv = TendonForceLengthInverseDeGroote2016(self.fl_T, *self.constants)
|
| 339 |
+
expected = 1/(self.c3*(self.fl_T + self.c2))
|
| 340 |
+
assert fl_T_inv.diff(self.c2) == expected
|
| 341 |
+
|
| 342 |
+
def test_differentiate_wrt_c3(self):
|
| 343 |
+
fl_T_inv = TendonForceLengthInverseDeGroote2016(self.fl_T, *self.constants)
|
| 344 |
+
expected = -log(UnevaluatedExpr((self.fl_T + self.c2)/self.c0))/self.c3**2
|
| 345 |
+
assert fl_T_inv.diff(self.c3) == expected
|
| 346 |
+
|
| 347 |
+
def test_inverse(self):
|
| 348 |
+
fl_T_inv = TendonForceLengthInverseDeGroote2016(self.fl_T, *self.constants)
|
| 349 |
+
assert fl_T_inv.inverse() is TendonForceLengthDeGroote2016
|
| 350 |
+
|
| 351 |
+
def test_function_print_latex(self):
|
| 352 |
+
fl_T_inv = TendonForceLengthInverseDeGroote2016(self.fl_T, *self.constants)
|
| 353 |
+
expected = r'\left( \operatorname{fl}^T \right)^{-1} \left( fl_{T} \right)'
|
| 354 |
+
assert LatexPrinter().doprint(fl_T_inv) == expected
|
| 355 |
+
|
| 356 |
+
def test_expression_print_latex(self):
|
| 357 |
+
fl_T = TendonForceLengthInverseDeGroote2016(self.fl_T, *self.constants)
|
| 358 |
+
expected = r'c_{1} + \frac{\log{\left(\frac{c_{2} + fl_{T}}{c_{0}} \right)}}{c_{3}}'
|
| 359 |
+
assert LatexPrinter().doprint(fl_T.doit()) == expected
|
| 360 |
+
|
| 361 |
+
@pytest.mark.parametrize(
|
| 362 |
+
'code_printer, expected',
|
| 363 |
+
[
|
| 364 |
+
(
|
| 365 |
+
C89CodePrinter,
|
| 366 |
+
'(0.995 + 0.029466630034306838*log(5.0*fl_T + 1.25))',
|
| 367 |
+
),
|
| 368 |
+
(
|
| 369 |
+
C99CodePrinter,
|
| 370 |
+
'(0.995 + 0.029466630034306838*log(5.0*fl_T + 1.25))',
|
| 371 |
+
),
|
| 372 |
+
(
|
| 373 |
+
C11CodePrinter,
|
| 374 |
+
'(0.995 + 0.029466630034306838*log(5.0*fl_T + 1.25))',
|
| 375 |
+
),
|
| 376 |
+
(
|
| 377 |
+
CXX98CodePrinter,
|
| 378 |
+
'(0.995 + 0.029466630034306838*log(5.0*fl_T + 1.25))',
|
| 379 |
+
),
|
| 380 |
+
(
|
| 381 |
+
CXX11CodePrinter,
|
| 382 |
+
'(0.995 + 0.029466630034306838*std::log(5.0*fl_T + 1.25))',
|
| 383 |
+
),
|
| 384 |
+
(
|
| 385 |
+
CXX17CodePrinter,
|
| 386 |
+
'(0.995 + 0.029466630034306838*std::log(5.0*fl_T + 1.25))',
|
| 387 |
+
),
|
| 388 |
+
(
|
| 389 |
+
FCodePrinter,
|
| 390 |
+
' (0.995d0 + 0.02946663003430684d0*log(5.0d0*fl_T + 1.25d0))',
|
| 391 |
+
),
|
| 392 |
+
(
|
| 393 |
+
OctaveCodePrinter,
|
| 394 |
+
'(0.995 + 0.02946663003430684*log(5.0*fl_T + 1.25))',
|
| 395 |
+
),
|
| 396 |
+
(
|
| 397 |
+
PythonCodePrinter,
|
| 398 |
+
'(0.995 + 0.02946663003430684*math.log(5.0*fl_T + 1.25))',
|
| 399 |
+
),
|
| 400 |
+
(
|
| 401 |
+
NumPyPrinter,
|
| 402 |
+
'(0.995 + 0.02946663003430684*numpy.log(5.0*fl_T + 1.25))',
|
| 403 |
+
),
|
| 404 |
+
(
|
| 405 |
+
SciPyPrinter,
|
| 406 |
+
'(0.995 + 0.02946663003430684*numpy.log(5.0*fl_T + 1.25))',
|
| 407 |
+
),
|
| 408 |
+
(
|
| 409 |
+
CuPyPrinter,
|
| 410 |
+
'(0.995 + 0.02946663003430684*cupy.log(5.0*fl_T + 1.25))',
|
| 411 |
+
),
|
| 412 |
+
(
|
| 413 |
+
JaxPrinter,
|
| 414 |
+
'(0.995 + 0.02946663003430684*jax.numpy.log(5.0*fl_T + 1.25))',
|
| 415 |
+
),
|
| 416 |
+
(
|
| 417 |
+
MpmathPrinter,
|
| 418 |
+
'(mpmath.mpf((0, 8962163258467287, -53, 53))'
|
| 419 |
+
' + mpmath.mpf((0, 33972711434846347, -60, 55))'
|
| 420 |
+
'*mpmath.log(mpmath.mpf((0, 5, 0, 3))*fl_T + mpmath.mpf((0, 5, -2, 3))))',
|
| 421 |
+
),
|
| 422 |
+
(
|
| 423 |
+
LambdaPrinter,
|
| 424 |
+
'(0.995 + 0.02946663003430684*math.log(5.0*fl_T + 1.25))',
|
| 425 |
+
),
|
| 426 |
+
]
|
| 427 |
+
)
|
| 428 |
+
def test_print_code(self, code_printer, expected):
|
| 429 |
+
fl_T_inv = TendonForceLengthInverseDeGroote2016.with_defaults(self.fl_T)
|
| 430 |
+
assert code_printer().doprint(fl_T_inv) == expected
|
| 431 |
+
|
| 432 |
+
def test_derivative_print_code(self):
|
| 433 |
+
fl_T_inv = TendonForceLengthInverseDeGroote2016.with_defaults(self.fl_T)
|
| 434 |
+
dfl_T_inv_dfl_T = fl_T_inv.diff(self.fl_T)
|
| 435 |
+
expected = '1/(33.93669377311689*fl_T + 8.484173443279222)'
|
| 436 |
+
assert PythonCodePrinter().doprint(dfl_T_inv_dfl_T) == expected
|
| 437 |
+
|
| 438 |
+
def test_lambdify(self):
|
| 439 |
+
fl_T_inv = TendonForceLengthInverseDeGroote2016.with_defaults(self.fl_T)
|
| 440 |
+
fl_T_inv_callable = lambdify(self.fl_T, fl_T_inv)
|
| 441 |
+
assert fl_T_inv_callable(0.0) == pytest.approx(1.0015752885)
|
| 442 |
+
|
| 443 |
+
@pytest.mark.skipif(numpy is None, reason='NumPy not installed')
|
| 444 |
+
def test_lambdify_numpy(self):
|
| 445 |
+
fl_T_inv = TendonForceLengthInverseDeGroote2016.with_defaults(self.fl_T)
|
| 446 |
+
fl_T_inv_callable = lambdify(self.fl_T, fl_T_inv, 'numpy')
|
| 447 |
+
fl_T = numpy.array([-0.2, -0.01, 0.0, 1.01, 1.02, 1.05])
|
| 448 |
+
expected = numpy.array([
|
| 449 |
+
0.9541505769,
|
| 450 |
+
1.0003724019,
|
| 451 |
+
1.0015752885,
|
| 452 |
+
1.0492347951,
|
| 453 |
+
1.0494677341,
|
| 454 |
+
1.0501557022,
|
| 455 |
+
])
|
| 456 |
+
numpy.testing.assert_allclose(fl_T_inv_callable(fl_T), expected)
|
| 457 |
+
|
| 458 |
+
@pytest.mark.skipif(jax is None, reason='JAX not installed')
|
| 459 |
+
def test_lambdify_jax(self):
|
| 460 |
+
fl_T_inv = TendonForceLengthInverseDeGroote2016.with_defaults(self.fl_T)
|
| 461 |
+
fl_T_inv_callable = jax.jit(lambdify(self.fl_T, fl_T_inv, 'jax'))
|
| 462 |
+
fl_T = jax.numpy.array([-0.2, -0.01, 0.0, 1.01, 1.02, 1.05])
|
| 463 |
+
expected = jax.numpy.array([
|
| 464 |
+
0.9541505769,
|
| 465 |
+
1.0003724019,
|
| 466 |
+
1.0015752885,
|
| 467 |
+
1.0492347951,
|
| 468 |
+
1.0494677341,
|
| 469 |
+
1.0501557022,
|
| 470 |
+
])
|
| 471 |
+
numpy.testing.assert_allclose(fl_T_inv_callable(fl_T), expected)
|
| 472 |
+
|
| 473 |
+
|
| 474 |
+
class TestFiberForceLengthPassiveDeGroote2016:
|
| 475 |
+
|
| 476 |
+
@pytest.fixture(autouse=True)
|
| 477 |
+
def _fiber_force_length_passive_arguments_fixture(self):
|
| 478 |
+
self.l_M_tilde = Symbol('l_M_tilde')
|
| 479 |
+
self.c0 = Symbol('c_0')
|
| 480 |
+
self.c1 = Symbol('c_1')
|
| 481 |
+
self.constants = (self.c0, self.c1)
|
| 482 |
+
|
| 483 |
+
@staticmethod
|
| 484 |
+
def test_class():
|
| 485 |
+
assert issubclass(FiberForceLengthPassiveDeGroote2016, Function)
|
| 486 |
+
assert issubclass(FiberForceLengthPassiveDeGroote2016, CharacteristicCurveFunction)
|
| 487 |
+
assert FiberForceLengthPassiveDeGroote2016.__name__ == 'FiberForceLengthPassiveDeGroote2016'
|
| 488 |
+
|
| 489 |
+
def test_instance(self):
|
| 490 |
+
fl_M_pas = FiberForceLengthPassiveDeGroote2016(self.l_M_tilde, *self.constants)
|
| 491 |
+
assert isinstance(fl_M_pas, FiberForceLengthPassiveDeGroote2016)
|
| 492 |
+
assert str(fl_M_pas) == 'FiberForceLengthPassiveDeGroote2016(l_M_tilde, c_0, c_1)'
|
| 493 |
+
|
| 494 |
+
def test_doit(self):
|
| 495 |
+
fl_M_pas = FiberForceLengthPassiveDeGroote2016(self.l_M_tilde, *self.constants).doit()
|
| 496 |
+
assert fl_M_pas == (exp((self.c1*(self.l_M_tilde - 1))/self.c0) - 1)/(exp(self.c1) - 1)
|
| 497 |
+
|
| 498 |
+
def test_doit_evaluate_false(self):
|
| 499 |
+
fl_M_pas = FiberForceLengthPassiveDeGroote2016(self.l_M_tilde, *self.constants).doit(evaluate=False)
|
| 500 |
+
assert fl_M_pas == (exp((self.c1*UnevaluatedExpr(self.l_M_tilde - 1))/self.c0) - 1)/(exp(self.c1) - 1)
|
| 501 |
+
|
| 502 |
+
def test_with_defaults(self):
|
| 503 |
+
constants = (
|
| 504 |
+
Float('0.6'),
|
| 505 |
+
Float('4.0'),
|
| 506 |
+
)
|
| 507 |
+
fl_M_pas_manual = FiberForceLengthPassiveDeGroote2016(self.l_M_tilde, *constants)
|
| 508 |
+
fl_M_pas_constants = FiberForceLengthPassiveDeGroote2016.with_defaults(self.l_M_tilde)
|
| 509 |
+
assert fl_M_pas_manual == fl_M_pas_constants
|
| 510 |
+
|
| 511 |
+
def test_differentiate_wrt_l_M_tilde(self):
|
| 512 |
+
fl_M_pas = FiberForceLengthPassiveDeGroote2016(self.l_M_tilde, *self.constants)
|
| 513 |
+
expected = self.c1*exp(self.c1*UnevaluatedExpr(self.l_M_tilde - 1)/self.c0)/(self.c0*(exp(self.c1) - 1))
|
| 514 |
+
assert fl_M_pas.diff(self.l_M_tilde) == expected
|
| 515 |
+
|
| 516 |
+
def test_differentiate_wrt_c0(self):
|
| 517 |
+
fl_M_pas = FiberForceLengthPassiveDeGroote2016(self.l_M_tilde, *self.constants)
|
| 518 |
+
expected = (
|
| 519 |
+
-self.c1*exp(self.c1*UnevaluatedExpr(self.l_M_tilde - 1)/self.c0)
|
| 520 |
+
*UnevaluatedExpr(self.l_M_tilde - 1)/(self.c0**2*(exp(self.c1) - 1))
|
| 521 |
+
)
|
| 522 |
+
assert fl_M_pas.diff(self.c0) == expected
|
| 523 |
+
|
| 524 |
+
def test_differentiate_wrt_c1(self):
|
| 525 |
+
fl_M_pas = FiberForceLengthPassiveDeGroote2016(self.l_M_tilde, *self.constants)
|
| 526 |
+
expected = (
|
| 527 |
+
-exp(self.c1)*(-1 + exp(self.c1*UnevaluatedExpr(self.l_M_tilde - 1)/self.c0))/(exp(self.c1) - 1)**2
|
| 528 |
+
+ exp(self.c1*UnevaluatedExpr(self.l_M_tilde - 1)/self.c0)*(self.l_M_tilde - 1)/(self.c0*(exp(self.c1) - 1))
|
| 529 |
+
)
|
| 530 |
+
assert fl_M_pas.diff(self.c1) == expected
|
| 531 |
+
|
| 532 |
+
def test_inverse(self):
|
| 533 |
+
fl_M_pas = FiberForceLengthPassiveDeGroote2016(self.l_M_tilde, *self.constants)
|
| 534 |
+
assert fl_M_pas.inverse() is FiberForceLengthPassiveInverseDeGroote2016
|
| 535 |
+
|
| 536 |
+
def test_function_print_latex(self):
|
| 537 |
+
fl_M_pas = FiberForceLengthPassiveDeGroote2016(self.l_M_tilde, *self.constants)
|
| 538 |
+
expected = r'\operatorname{fl}^M_{pas} \left( l_{M tilde} \right)'
|
| 539 |
+
assert LatexPrinter().doprint(fl_M_pas) == expected
|
| 540 |
+
|
| 541 |
+
def test_expression_print_latex(self):
|
| 542 |
+
fl_M_pas = FiberForceLengthPassiveDeGroote2016(self.l_M_tilde, *self.constants)
|
| 543 |
+
expected = r'\frac{e^{\frac{c_{1} \left(l_{M tilde} - 1\right)}{c_{0}}} - 1}{e^{c_{1}} - 1}'
|
| 544 |
+
assert LatexPrinter().doprint(fl_M_pas.doit()) == expected
|
| 545 |
+
|
| 546 |
+
@pytest.mark.parametrize(
|
| 547 |
+
'code_printer, expected',
|
| 548 |
+
[
|
| 549 |
+
(
|
| 550 |
+
C89CodePrinter,
|
| 551 |
+
'(0.01865736036377405*(-1 + exp(6.666666666666667*(l_M_tilde - 1))))',
|
| 552 |
+
),
|
| 553 |
+
(
|
| 554 |
+
C99CodePrinter,
|
| 555 |
+
'(0.01865736036377405*(-1 + exp(6.666666666666667*(l_M_tilde - 1))))',
|
| 556 |
+
),
|
| 557 |
+
(
|
| 558 |
+
C11CodePrinter,
|
| 559 |
+
'(0.01865736036377405*(-1 + exp(6.666666666666667*(l_M_tilde - 1))))',
|
| 560 |
+
),
|
| 561 |
+
(
|
| 562 |
+
CXX98CodePrinter,
|
| 563 |
+
'(0.01865736036377405*(-1 + exp(6.666666666666667*(l_M_tilde - 1))))',
|
| 564 |
+
),
|
| 565 |
+
(
|
| 566 |
+
CXX11CodePrinter,
|
| 567 |
+
'(0.01865736036377405*(-1 + std::exp(6.666666666666667*(l_M_tilde - 1))))',
|
| 568 |
+
),
|
| 569 |
+
(
|
| 570 |
+
CXX17CodePrinter,
|
| 571 |
+
'(0.01865736036377405*(-1 + std::exp(6.666666666666667*(l_M_tilde - 1))))',
|
| 572 |
+
),
|
| 573 |
+
(
|
| 574 |
+
FCodePrinter,
|
| 575 |
+
' (0.0186573603637741d0*(-1 + exp(6.666666666666667d0*(l_M_tilde - 1\n'
|
| 576 |
+
' @ ))))',
|
| 577 |
+
),
|
| 578 |
+
(
|
| 579 |
+
OctaveCodePrinter,
|
| 580 |
+
'(0.0186573603637741*(-1 + exp(6.66666666666667*(l_M_tilde - 1))))',
|
| 581 |
+
),
|
| 582 |
+
(
|
| 583 |
+
PythonCodePrinter,
|
| 584 |
+
'(0.0186573603637741*(-1 + math.exp(6.66666666666667*(l_M_tilde - 1))))',
|
| 585 |
+
),
|
| 586 |
+
(
|
| 587 |
+
NumPyPrinter,
|
| 588 |
+
'(0.0186573603637741*(-1 + numpy.exp(6.66666666666667*(l_M_tilde - 1))))',
|
| 589 |
+
),
|
| 590 |
+
(
|
| 591 |
+
SciPyPrinter,
|
| 592 |
+
'(0.0186573603637741*(-1 + numpy.exp(6.66666666666667*(l_M_tilde - 1))))',
|
| 593 |
+
),
|
| 594 |
+
(
|
| 595 |
+
CuPyPrinter,
|
| 596 |
+
'(0.0186573603637741*(-1 + cupy.exp(6.66666666666667*(l_M_tilde - 1))))',
|
| 597 |
+
),
|
| 598 |
+
(
|
| 599 |
+
JaxPrinter,
|
| 600 |
+
'(0.0186573603637741*(-1 + jax.numpy.exp(6.66666666666667*(l_M_tilde - 1))))',
|
| 601 |
+
),
|
| 602 |
+
(
|
| 603 |
+
MpmathPrinter,
|
| 604 |
+
'(mpmath.mpf((0, 672202249456079, -55, 50))*(-1 + mpmath.exp('
|
| 605 |
+
'mpmath.mpf((0, 7505999378950827, -50, 53))*(l_M_tilde - 1))))',
|
| 606 |
+
),
|
| 607 |
+
(
|
| 608 |
+
LambdaPrinter,
|
| 609 |
+
'(0.0186573603637741*(-1 + math.exp(6.66666666666667*(l_M_tilde - 1))))',
|
| 610 |
+
),
|
| 611 |
+
]
|
| 612 |
+
)
|
| 613 |
+
def test_print_code(self, code_printer, expected):
|
| 614 |
+
fl_M_pas = FiberForceLengthPassiveDeGroote2016.with_defaults(self.l_M_tilde)
|
| 615 |
+
assert code_printer().doprint(fl_M_pas) == expected
|
| 616 |
+
|
| 617 |
+
def test_derivative_print_code(self):
|
| 618 |
+
fl_M_pas = FiberForceLengthPassiveDeGroote2016.with_defaults(self.l_M_tilde)
|
| 619 |
+
fl_M_pas_dl_M_tilde = fl_M_pas.diff(self.l_M_tilde)
|
| 620 |
+
expected = '0.12438240242516*math.exp(6.66666666666667*(l_M_tilde - 1))'
|
| 621 |
+
assert PythonCodePrinter().doprint(fl_M_pas_dl_M_tilde) == expected
|
| 622 |
+
|
| 623 |
+
def test_lambdify(self):
|
| 624 |
+
fl_M_pas = FiberForceLengthPassiveDeGroote2016.with_defaults(self.l_M_tilde)
|
| 625 |
+
fl_M_pas_callable = lambdify(self.l_M_tilde, fl_M_pas)
|
| 626 |
+
assert fl_M_pas_callable(1.0) == pytest.approx(0.0)
|
| 627 |
+
|
| 628 |
+
@pytest.mark.skipif(numpy is None, reason='NumPy not installed')
|
| 629 |
+
def test_lambdify_numpy(self):
|
| 630 |
+
fl_M_pas = FiberForceLengthPassiveDeGroote2016.with_defaults(self.l_M_tilde)
|
| 631 |
+
fl_M_pas_callable = lambdify(self.l_M_tilde, fl_M_pas, 'numpy')
|
| 632 |
+
l_M_tilde = numpy.array([0.5, 0.8, 0.9, 1.0, 1.1, 1.2, 1.5])
|
| 633 |
+
expected = numpy.array([
|
| 634 |
+
-0.0179917778,
|
| 635 |
+
-0.0137393336,
|
| 636 |
+
-0.0090783522,
|
| 637 |
+
0.0,
|
| 638 |
+
0.0176822155,
|
| 639 |
+
0.0521224686,
|
| 640 |
+
0.5043387669,
|
| 641 |
+
])
|
| 642 |
+
numpy.testing.assert_allclose(fl_M_pas_callable(l_M_tilde), expected)
|
| 643 |
+
|
| 644 |
+
@pytest.mark.skipif(jax is None, reason='JAX not installed')
|
| 645 |
+
def test_lambdify_jax(self):
|
| 646 |
+
fl_M_pas = FiberForceLengthPassiveDeGroote2016.with_defaults(self.l_M_tilde)
|
| 647 |
+
fl_M_pas_callable = jax.jit(lambdify(self.l_M_tilde, fl_M_pas, 'jax'))
|
| 648 |
+
l_M_tilde = jax.numpy.array([0.5, 0.8, 0.9, 1.0, 1.1, 1.2, 1.5])
|
| 649 |
+
expected = jax.numpy.array([
|
| 650 |
+
-0.0179917778,
|
| 651 |
+
-0.0137393336,
|
| 652 |
+
-0.0090783522,
|
| 653 |
+
0.0,
|
| 654 |
+
0.0176822155,
|
| 655 |
+
0.0521224686,
|
| 656 |
+
0.5043387669,
|
| 657 |
+
])
|
| 658 |
+
numpy.testing.assert_allclose(fl_M_pas_callable(l_M_tilde), expected)
|
| 659 |
+
|
| 660 |
+
|
| 661 |
+
class TestFiberForceLengthPassiveInverseDeGroote2016:
|
| 662 |
+
|
| 663 |
+
@pytest.fixture(autouse=True)
|
| 664 |
+
def _fiber_force_length_passive_arguments_fixture(self):
|
| 665 |
+
self.fl_M_pas = Symbol('fl_M_pas')
|
| 666 |
+
self.c0 = Symbol('c_0')
|
| 667 |
+
self.c1 = Symbol('c_1')
|
| 668 |
+
self.constants = (self.c0, self.c1)
|
| 669 |
+
|
| 670 |
+
@staticmethod
|
| 671 |
+
def test_class():
|
| 672 |
+
assert issubclass(FiberForceLengthPassiveInverseDeGroote2016, Function)
|
| 673 |
+
assert issubclass(FiberForceLengthPassiveInverseDeGroote2016, CharacteristicCurveFunction)
|
| 674 |
+
assert FiberForceLengthPassiveInverseDeGroote2016.__name__ == 'FiberForceLengthPassiveInverseDeGroote2016'
|
| 675 |
+
|
| 676 |
+
def test_instance(self):
|
| 677 |
+
fl_M_pas_inv = FiberForceLengthPassiveInverseDeGroote2016(self.fl_M_pas, *self.constants)
|
| 678 |
+
assert isinstance(fl_M_pas_inv, FiberForceLengthPassiveInverseDeGroote2016)
|
| 679 |
+
assert str(fl_M_pas_inv) == 'FiberForceLengthPassiveInverseDeGroote2016(fl_M_pas, c_0, c_1)'
|
| 680 |
+
|
| 681 |
+
def test_doit(self):
|
| 682 |
+
fl_M_pas_inv = FiberForceLengthPassiveInverseDeGroote2016(self.fl_M_pas, *self.constants).doit()
|
| 683 |
+
assert fl_M_pas_inv == self.c0*log(self.fl_M_pas*(exp(self.c1) - 1) + 1)/self.c1 + 1
|
| 684 |
+
|
| 685 |
+
def test_doit_evaluate_false(self):
|
| 686 |
+
fl_M_pas_inv = FiberForceLengthPassiveInverseDeGroote2016(self.fl_M_pas, *self.constants).doit(evaluate=False)
|
| 687 |
+
assert fl_M_pas_inv == self.c0*log(UnevaluatedExpr(self.fl_M_pas*(exp(self.c1) - 1)) + 1)/self.c1 + 1
|
| 688 |
+
|
| 689 |
+
def test_with_defaults(self):
|
| 690 |
+
constants = (
|
| 691 |
+
Float('0.6'),
|
| 692 |
+
Float('4.0'),
|
| 693 |
+
)
|
| 694 |
+
fl_M_pas_inv_manual = FiberForceLengthPassiveInverseDeGroote2016(self.fl_M_pas, *constants)
|
| 695 |
+
fl_M_pas_inv_constants = FiberForceLengthPassiveInverseDeGroote2016.with_defaults(self.fl_M_pas)
|
| 696 |
+
assert fl_M_pas_inv_manual == fl_M_pas_inv_constants
|
| 697 |
+
|
| 698 |
+
def test_differentiate_wrt_fl_T(self):
|
| 699 |
+
fl_M_pas_inv = FiberForceLengthPassiveInverseDeGroote2016(self.fl_M_pas, *self.constants)
|
| 700 |
+
expected = self.c0*(exp(self.c1) - 1)/(self.c1*(self.fl_M_pas*(exp(self.c1) - 1) + 1))
|
| 701 |
+
assert fl_M_pas_inv.diff(self.fl_M_pas) == expected
|
| 702 |
+
|
| 703 |
+
def test_differentiate_wrt_c0(self):
|
| 704 |
+
fl_M_pas_inv = FiberForceLengthPassiveInverseDeGroote2016(self.fl_M_pas, *self.constants)
|
| 705 |
+
expected = log(self.fl_M_pas*(exp(self.c1) - 1) + 1)/self.c1
|
| 706 |
+
assert fl_M_pas_inv.diff(self.c0) == expected
|
| 707 |
+
|
| 708 |
+
def test_differentiate_wrt_c1(self):
|
| 709 |
+
fl_M_pas_inv = FiberForceLengthPassiveInverseDeGroote2016(self.fl_M_pas, *self.constants)
|
| 710 |
+
expected = (
|
| 711 |
+
self.c0*self.fl_M_pas*exp(self.c1)/(self.c1*(self.fl_M_pas*(exp(self.c1) - 1) + 1))
|
| 712 |
+
- self.c0*log(self.fl_M_pas*(exp(self.c1) - 1) + 1)/self.c1**2
|
| 713 |
+
)
|
| 714 |
+
assert fl_M_pas_inv.diff(self.c1) == expected
|
| 715 |
+
|
| 716 |
+
def test_inverse(self):
|
| 717 |
+
fl_M_pas_inv = FiberForceLengthPassiveInverseDeGroote2016(self.fl_M_pas, *self.constants)
|
| 718 |
+
assert fl_M_pas_inv.inverse() is FiberForceLengthPassiveDeGroote2016
|
| 719 |
+
|
| 720 |
+
def test_function_print_latex(self):
|
| 721 |
+
fl_M_pas_inv = FiberForceLengthPassiveInverseDeGroote2016(self.fl_M_pas, *self.constants)
|
| 722 |
+
expected = r'\left( \operatorname{fl}^M_{pas} \right)^{-1} \left( fl_{M pas} \right)'
|
| 723 |
+
assert LatexPrinter().doprint(fl_M_pas_inv) == expected
|
| 724 |
+
|
| 725 |
+
def test_expression_print_latex(self):
|
| 726 |
+
fl_T = FiberForceLengthPassiveInverseDeGroote2016(self.fl_M_pas, *self.constants)
|
| 727 |
+
expected = r'\frac{c_{0} \log{\left(fl_{M pas} \left(e^{c_{1}} - 1\right) + 1 \right)}}{c_{1}} + 1'
|
| 728 |
+
assert LatexPrinter().doprint(fl_T.doit()) == expected
|
| 729 |
+
|
| 730 |
+
@pytest.mark.parametrize(
|
| 731 |
+
'code_printer, expected',
|
| 732 |
+
[
|
| 733 |
+
(
|
| 734 |
+
C89CodePrinter,
|
| 735 |
+
'(1 + 0.14999999999999999*log(1 + 53.598150033144236*fl_M_pas))',
|
| 736 |
+
),
|
| 737 |
+
(
|
| 738 |
+
C99CodePrinter,
|
| 739 |
+
'(1 + 0.14999999999999999*log(1 + 53.598150033144236*fl_M_pas))',
|
| 740 |
+
),
|
| 741 |
+
(
|
| 742 |
+
C11CodePrinter,
|
| 743 |
+
'(1 + 0.14999999999999999*log(1 + 53.598150033144236*fl_M_pas))',
|
| 744 |
+
),
|
| 745 |
+
(
|
| 746 |
+
CXX98CodePrinter,
|
| 747 |
+
'(1 + 0.14999999999999999*log(1 + 53.598150033144236*fl_M_pas))',
|
| 748 |
+
),
|
| 749 |
+
(
|
| 750 |
+
CXX11CodePrinter,
|
| 751 |
+
'(1 + 0.14999999999999999*std::log(1 + 53.598150033144236*fl_M_pas))',
|
| 752 |
+
),
|
| 753 |
+
(
|
| 754 |
+
CXX17CodePrinter,
|
| 755 |
+
'(1 + 0.14999999999999999*std::log(1 + 53.598150033144236*fl_M_pas))',
|
| 756 |
+
),
|
| 757 |
+
(
|
| 758 |
+
FCodePrinter,
|
| 759 |
+
' (1 + 0.15d0*log(1.0d0 + 53.5981500331442d0*fl_M_pas))',
|
| 760 |
+
),
|
| 761 |
+
(
|
| 762 |
+
OctaveCodePrinter,
|
| 763 |
+
'(1 + 0.15*log(1 + 53.5981500331442*fl_M_pas))',
|
| 764 |
+
),
|
| 765 |
+
(
|
| 766 |
+
PythonCodePrinter,
|
| 767 |
+
'(1 + 0.15*math.log(1 + 53.5981500331442*fl_M_pas))',
|
| 768 |
+
),
|
| 769 |
+
(
|
| 770 |
+
NumPyPrinter,
|
| 771 |
+
'(1 + 0.15*numpy.log(1 + 53.5981500331442*fl_M_pas))',
|
| 772 |
+
),
|
| 773 |
+
(
|
| 774 |
+
SciPyPrinter,
|
| 775 |
+
'(1 + 0.15*numpy.log(1 + 53.5981500331442*fl_M_pas))',
|
| 776 |
+
),
|
| 777 |
+
(
|
| 778 |
+
CuPyPrinter,
|
| 779 |
+
'(1 + 0.15*cupy.log(1 + 53.5981500331442*fl_M_pas))',
|
| 780 |
+
),
|
| 781 |
+
(
|
| 782 |
+
JaxPrinter,
|
| 783 |
+
'(1 + 0.15*jax.numpy.log(1 + 53.5981500331442*fl_M_pas))',
|
| 784 |
+
),
|
| 785 |
+
(
|
| 786 |
+
MpmathPrinter,
|
| 787 |
+
'(1 + mpmath.mpf((0, 5404319552844595, -55, 53))*mpmath.log(1 '
|
| 788 |
+
'+ mpmath.mpf((0, 942908627019595, -44, 50))*fl_M_pas))',
|
| 789 |
+
),
|
| 790 |
+
(
|
| 791 |
+
LambdaPrinter,
|
| 792 |
+
'(1 + 0.15*math.log(1 + 53.5981500331442*fl_M_pas))',
|
| 793 |
+
),
|
| 794 |
+
]
|
| 795 |
+
)
|
| 796 |
+
def test_print_code(self, code_printer, expected):
|
| 797 |
+
fl_M_pas_inv = FiberForceLengthPassiveInverseDeGroote2016.with_defaults(self.fl_M_pas)
|
| 798 |
+
assert code_printer().doprint(fl_M_pas_inv) == expected
|
| 799 |
+
|
| 800 |
+
def test_derivative_print_code(self):
|
| 801 |
+
fl_M_pas_inv = FiberForceLengthPassiveInverseDeGroote2016.with_defaults(self.fl_M_pas)
|
| 802 |
+
dfl_M_pas_inv_dfl_T = fl_M_pas_inv.diff(self.fl_M_pas)
|
| 803 |
+
expected = '32.1588900198865/(214.392600132577*fl_M_pas + 4.0)'
|
| 804 |
+
assert PythonCodePrinter().doprint(dfl_M_pas_inv_dfl_T) == expected
|
| 805 |
+
|
| 806 |
+
def test_lambdify(self):
|
| 807 |
+
fl_M_pas_inv = FiberForceLengthPassiveInverseDeGroote2016.with_defaults(self.fl_M_pas)
|
| 808 |
+
fl_M_pas_inv_callable = lambdify(self.fl_M_pas, fl_M_pas_inv)
|
| 809 |
+
assert fl_M_pas_inv_callable(0.0) == pytest.approx(1.0)
|
| 810 |
+
|
| 811 |
+
@pytest.mark.skipif(numpy is None, reason='NumPy not installed')
|
| 812 |
+
def test_lambdify_numpy(self):
|
| 813 |
+
fl_M_pas_inv = FiberForceLengthPassiveInverseDeGroote2016.with_defaults(self.fl_M_pas)
|
| 814 |
+
fl_M_pas_inv_callable = lambdify(self.fl_M_pas, fl_M_pas_inv, 'numpy')
|
| 815 |
+
fl_M_pas = numpy.array([-0.01, 0.0, 0.01, 0.02, 0.05, 0.1])
|
| 816 |
+
expected = numpy.array([
|
| 817 |
+
0.8848253714,
|
| 818 |
+
1.0,
|
| 819 |
+
1.0643754386,
|
| 820 |
+
1.1092744701,
|
| 821 |
+
1.1954331425,
|
| 822 |
+
1.2774998934,
|
| 823 |
+
])
|
| 824 |
+
numpy.testing.assert_allclose(fl_M_pas_inv_callable(fl_M_pas), expected)
|
| 825 |
+
|
| 826 |
+
@pytest.mark.skipif(jax is None, reason='JAX not installed')
|
| 827 |
+
def test_lambdify_jax(self):
|
| 828 |
+
fl_M_pas_inv = FiberForceLengthPassiveInverseDeGroote2016.with_defaults(self.fl_M_pas)
|
| 829 |
+
fl_M_pas_inv_callable = jax.jit(lambdify(self.fl_M_pas, fl_M_pas_inv, 'jax'))
|
| 830 |
+
fl_M_pas = jax.numpy.array([-0.01, 0.0, 0.01, 0.02, 0.05, 0.1])
|
| 831 |
+
expected = jax.numpy.array([
|
| 832 |
+
0.8848253714,
|
| 833 |
+
1.0,
|
| 834 |
+
1.0643754386,
|
| 835 |
+
1.1092744701,
|
| 836 |
+
1.1954331425,
|
| 837 |
+
1.2774998934,
|
| 838 |
+
])
|
| 839 |
+
numpy.testing.assert_allclose(fl_M_pas_inv_callable(fl_M_pas), expected)
|
| 840 |
+
|
| 841 |
+
|
| 842 |
+
class TestFiberForceLengthActiveDeGroote2016:
|
| 843 |
+
|
| 844 |
+
@pytest.fixture(autouse=True)
|
| 845 |
+
def _fiber_force_length_active_arguments_fixture(self):
|
| 846 |
+
self.l_M_tilde = Symbol('l_M_tilde')
|
| 847 |
+
self.c0 = Symbol('c_0')
|
| 848 |
+
self.c1 = Symbol('c_1')
|
| 849 |
+
self.c2 = Symbol('c_2')
|
| 850 |
+
self.c3 = Symbol('c_3')
|
| 851 |
+
self.c4 = Symbol('c_4')
|
| 852 |
+
self.c5 = Symbol('c_5')
|
| 853 |
+
self.c6 = Symbol('c_6')
|
| 854 |
+
self.c7 = Symbol('c_7')
|
| 855 |
+
self.c8 = Symbol('c_8')
|
| 856 |
+
self.c9 = Symbol('c_9')
|
| 857 |
+
self.c10 = Symbol('c_10')
|
| 858 |
+
self.c11 = Symbol('c_11')
|
| 859 |
+
self.constants = (
|
| 860 |
+
self.c0, self.c1, self.c2, self.c3, self.c4, self.c5,
|
| 861 |
+
self.c6, self.c7, self.c8, self.c9, self.c10, self.c11,
|
| 862 |
+
)
|
| 863 |
+
|
| 864 |
+
@staticmethod
|
| 865 |
+
def test_class():
|
| 866 |
+
assert issubclass(FiberForceLengthActiveDeGroote2016, Function)
|
| 867 |
+
assert issubclass(FiberForceLengthActiveDeGroote2016, CharacteristicCurveFunction)
|
| 868 |
+
assert FiberForceLengthActiveDeGroote2016.__name__ == 'FiberForceLengthActiveDeGroote2016'
|
| 869 |
+
|
| 870 |
+
def test_instance(self):
|
| 871 |
+
fl_M_act = FiberForceLengthActiveDeGroote2016(self.l_M_tilde, *self.constants)
|
| 872 |
+
assert isinstance(fl_M_act, FiberForceLengthActiveDeGroote2016)
|
| 873 |
+
assert str(fl_M_act) == (
|
| 874 |
+
'FiberForceLengthActiveDeGroote2016(l_M_tilde, c_0, c_1, c_2, c_3, '
|
| 875 |
+
'c_4, c_5, c_6, c_7, c_8, c_9, c_10, c_11)'
|
| 876 |
+
)
|
| 877 |
+
|
| 878 |
+
def test_doit(self):
|
| 879 |
+
fl_M_act = FiberForceLengthActiveDeGroote2016(self.l_M_tilde, *self.constants).doit()
|
| 880 |
+
assert fl_M_act == (
|
| 881 |
+
self.c0*exp(-(((self.l_M_tilde - self.c1)/(self.c2 + self.c3*self.l_M_tilde))**2)/2)
|
| 882 |
+
+ self.c4*exp(-(((self.l_M_tilde - self.c5)/(self.c6 + self.c7*self.l_M_tilde))**2)/2)
|
| 883 |
+
+ self.c8*exp(-(((self.l_M_tilde - self.c9)/(self.c10 + self.c11*self.l_M_tilde))**2)/2)
|
| 884 |
+
)
|
| 885 |
+
|
| 886 |
+
def test_doit_evaluate_false(self):
|
| 887 |
+
fl_M_act = FiberForceLengthActiveDeGroote2016(self.l_M_tilde, *self.constants).doit(evaluate=False)
|
| 888 |
+
assert fl_M_act == (
|
| 889 |
+
self.c0*exp(-((UnevaluatedExpr(self.l_M_tilde - self.c1)/(self.c2 + self.c3*self.l_M_tilde))**2)/2)
|
| 890 |
+
+ self.c4*exp(-((UnevaluatedExpr(self.l_M_tilde - self.c5)/(self.c6 + self.c7*self.l_M_tilde))**2)/2)
|
| 891 |
+
+ self.c8*exp(-((UnevaluatedExpr(self.l_M_tilde - self.c9)/(self.c10 + self.c11*self.l_M_tilde))**2)/2)
|
| 892 |
+
)
|
| 893 |
+
|
| 894 |
+
def test_with_defaults(self):
|
| 895 |
+
constants = (
|
| 896 |
+
Float('0.814'),
|
| 897 |
+
Float('1.06'),
|
| 898 |
+
Float('0.162'),
|
| 899 |
+
Float('0.0633'),
|
| 900 |
+
Float('0.433'),
|
| 901 |
+
Float('0.717'),
|
| 902 |
+
Float('-0.0299'),
|
| 903 |
+
Float('0.2'),
|
| 904 |
+
Float('0.1'),
|
| 905 |
+
Float('1.0'),
|
| 906 |
+
Float('0.354'),
|
| 907 |
+
Float('0.0'),
|
| 908 |
+
)
|
| 909 |
+
fl_M_act_manual = FiberForceLengthActiveDeGroote2016(self.l_M_tilde, *constants)
|
| 910 |
+
fl_M_act_constants = FiberForceLengthActiveDeGroote2016.with_defaults(self.l_M_tilde)
|
| 911 |
+
assert fl_M_act_manual == fl_M_act_constants
|
| 912 |
+
|
| 913 |
+
def test_differentiate_wrt_l_M_tilde(self):
|
| 914 |
+
fl_M_act = FiberForceLengthActiveDeGroote2016(self.l_M_tilde, *self.constants)
|
| 915 |
+
expected = (
|
| 916 |
+
self.c0*(
|
| 917 |
+
self.c3*(self.l_M_tilde - self.c1)**2/(self.c2 + self.c3*self.l_M_tilde)**3
|
| 918 |
+
+ (self.c1 - self.l_M_tilde)/((self.c2 + self.c3*self.l_M_tilde)**2)
|
| 919 |
+
)*exp(-(self.l_M_tilde - self.c1)**2/(2*(self.c2 + self.c3*self.l_M_tilde)**2))
|
| 920 |
+
+ self.c4*(
|
| 921 |
+
self.c7*(self.l_M_tilde - self.c5)**2/(self.c6 + self.c7*self.l_M_tilde)**3
|
| 922 |
+
+ (self.c5 - self.l_M_tilde)/((self.c6 + self.c7*self.l_M_tilde)**2)
|
| 923 |
+
)*exp(-(self.l_M_tilde - self.c5)**2/(2*(self.c6 + self.c7*self.l_M_tilde)**2))
|
| 924 |
+
+ self.c8*(
|
| 925 |
+
self.c11*(self.l_M_tilde - self.c9)**2/(self.c10 + self.c11*self.l_M_tilde)**3
|
| 926 |
+
+ (self.c9 - self.l_M_tilde)/((self.c10 + self.c11*self.l_M_tilde)**2)
|
| 927 |
+
)*exp(-(self.l_M_tilde - self.c9)**2/(2*(self.c10 + self.c11*self.l_M_tilde)**2))
|
| 928 |
+
)
|
| 929 |
+
assert fl_M_act.diff(self.l_M_tilde) == expected
|
| 930 |
+
|
| 931 |
+
def test_differentiate_wrt_c0(self):
|
| 932 |
+
fl_M_act = FiberForceLengthActiveDeGroote2016(self.l_M_tilde, *self.constants)
|
| 933 |
+
expected = exp(-(self.l_M_tilde - self.c1)**2/(2*(self.c2 + self.c3*self.l_M_tilde)**2))
|
| 934 |
+
assert fl_M_act.doit().diff(self.c0) == expected
|
| 935 |
+
|
| 936 |
+
def test_differentiate_wrt_c1(self):
|
| 937 |
+
fl_M_act = FiberForceLengthActiveDeGroote2016(self.l_M_tilde, *self.constants)
|
| 938 |
+
expected = (
|
| 939 |
+
self.c0*(self.l_M_tilde - self.c1)/(self.c2 + self.c3*self.l_M_tilde)**2
|
| 940 |
+
*exp(-(self.l_M_tilde - self.c1)**2/(2*(self.c2 + self.c3*self.l_M_tilde)**2))
|
| 941 |
+
)
|
| 942 |
+
assert fl_M_act.diff(self.c1) == expected
|
| 943 |
+
|
| 944 |
+
def test_differentiate_wrt_c2(self):
|
| 945 |
+
fl_M_act = FiberForceLengthActiveDeGroote2016(self.l_M_tilde, *self.constants)
|
| 946 |
+
expected = (
|
| 947 |
+
self.c0*(self.l_M_tilde - self.c1)**2/(self.c2 + self.c3*self.l_M_tilde)**3
|
| 948 |
+
*exp(-(self.l_M_tilde - self.c1)**2/(2*(self.c2 + self.c3*self.l_M_tilde)**2))
|
| 949 |
+
)
|
| 950 |
+
assert fl_M_act.diff(self.c2) == expected
|
| 951 |
+
|
| 952 |
+
def test_differentiate_wrt_c3(self):
|
| 953 |
+
fl_M_act = FiberForceLengthActiveDeGroote2016(self.l_M_tilde, *self.constants)
|
| 954 |
+
expected = (
|
| 955 |
+
self.c0*self.l_M_tilde*(self.l_M_tilde - self.c1)**2/(self.c2 + self.c3*self.l_M_tilde)**3
|
| 956 |
+
*exp(-(self.l_M_tilde - self.c1)**2/(2*(self.c2 + self.c3*self.l_M_tilde)**2))
|
| 957 |
+
)
|
| 958 |
+
assert fl_M_act.diff(self.c3) == expected
|
| 959 |
+
|
| 960 |
+
def test_differentiate_wrt_c4(self):
|
| 961 |
+
fl_M_act = FiberForceLengthActiveDeGroote2016(self.l_M_tilde, *self.constants)
|
| 962 |
+
expected = exp(-(self.l_M_tilde - self.c5)**2/(2*(self.c6 + self.c7*self.l_M_tilde)**2))
|
| 963 |
+
assert fl_M_act.diff(self.c4) == expected
|
| 964 |
+
|
| 965 |
+
def test_differentiate_wrt_c5(self):
|
| 966 |
+
fl_M_act = FiberForceLengthActiveDeGroote2016(self.l_M_tilde, *self.constants)
|
| 967 |
+
expected = (
|
| 968 |
+
self.c4*(self.l_M_tilde - self.c5)/(self.c6 + self.c7*self.l_M_tilde)**2
|
| 969 |
+
*exp(-(self.l_M_tilde - self.c5)**2/(2*(self.c6 + self.c7*self.l_M_tilde)**2))
|
| 970 |
+
)
|
| 971 |
+
assert fl_M_act.diff(self.c5) == expected
|
| 972 |
+
|
| 973 |
+
def test_differentiate_wrt_c6(self):
|
| 974 |
+
fl_M_act = FiberForceLengthActiveDeGroote2016(self.l_M_tilde, *self.constants)
|
| 975 |
+
expected = (
|
| 976 |
+
self.c4*(self.l_M_tilde - self.c5)**2/(self.c6 + self.c7*self.l_M_tilde)**3
|
| 977 |
+
*exp(-(self.l_M_tilde - self.c5)**2/(2*(self.c6 + self.c7*self.l_M_tilde)**2))
|
| 978 |
+
)
|
| 979 |
+
assert fl_M_act.diff(self.c6) == expected
|
| 980 |
+
|
| 981 |
+
def test_differentiate_wrt_c7(self):
|
| 982 |
+
fl_M_act = FiberForceLengthActiveDeGroote2016(self.l_M_tilde, *self.constants)
|
| 983 |
+
expected = (
|
| 984 |
+
self.c4*self.l_M_tilde*(self.l_M_tilde - self.c5)**2/(self.c6 + self.c7*self.l_M_tilde)**3
|
| 985 |
+
*exp(-(self.l_M_tilde - self.c5)**2/(2*(self.c6 + self.c7*self.l_M_tilde)**2))
|
| 986 |
+
)
|
| 987 |
+
assert fl_M_act.diff(self.c7) == expected
|
| 988 |
+
|
| 989 |
+
def test_differentiate_wrt_c8(self):
|
| 990 |
+
fl_M_act = FiberForceLengthActiveDeGroote2016(self.l_M_tilde, *self.constants)
|
| 991 |
+
expected = exp(-(self.l_M_tilde - self.c9)**2/(2*(self.c10 + self.c11*self.l_M_tilde)**2))
|
| 992 |
+
assert fl_M_act.diff(self.c8) == expected
|
| 993 |
+
|
| 994 |
+
def test_differentiate_wrt_c9(self):
|
| 995 |
+
fl_M_act = FiberForceLengthActiveDeGroote2016(self.l_M_tilde, *self.constants)
|
| 996 |
+
expected = (
|
| 997 |
+
self.c8*(self.l_M_tilde - self.c9)/(self.c10 + self.c11*self.l_M_tilde)**2
|
| 998 |
+
*exp(-(self.l_M_tilde - self.c9)**2/(2*(self.c10 + self.c11*self.l_M_tilde)**2))
|
| 999 |
+
)
|
| 1000 |
+
assert fl_M_act.diff(self.c9) == expected
|
| 1001 |
+
|
| 1002 |
+
def test_differentiate_wrt_c10(self):
|
| 1003 |
+
fl_M_act = FiberForceLengthActiveDeGroote2016(self.l_M_tilde, *self.constants)
|
| 1004 |
+
expected = (
|
| 1005 |
+
self.c8*(self.l_M_tilde - self.c9)**2/(self.c10 + self.c11*self.l_M_tilde)**3
|
| 1006 |
+
*exp(-(self.l_M_tilde - self.c9)**2/(2*(self.c10 + self.c11*self.l_M_tilde)**2))
|
| 1007 |
+
)
|
| 1008 |
+
assert fl_M_act.diff(self.c10) == expected
|
| 1009 |
+
|
| 1010 |
+
def test_differentiate_wrt_c11(self):
|
| 1011 |
+
fl_M_act = FiberForceLengthActiveDeGroote2016(self.l_M_tilde, *self.constants)
|
| 1012 |
+
expected = (
|
| 1013 |
+
self.c8*self.l_M_tilde*(self.l_M_tilde - self.c9)**2/(self.c10 + self.c11*self.l_M_tilde)**3
|
| 1014 |
+
*exp(-(self.l_M_tilde - self.c9)**2/(2*(self.c10 + self.c11*self.l_M_tilde)**2))
|
| 1015 |
+
)
|
| 1016 |
+
assert fl_M_act.diff(self.c11) == expected
|
| 1017 |
+
|
| 1018 |
+
def test_function_print_latex(self):
|
| 1019 |
+
fl_M_act = FiberForceLengthActiveDeGroote2016(self.l_M_tilde, *self.constants)
|
| 1020 |
+
expected = r'\operatorname{fl}^M_{act} \left( l_{M tilde} \right)'
|
| 1021 |
+
assert LatexPrinter().doprint(fl_M_act) == expected
|
| 1022 |
+
|
| 1023 |
+
def test_expression_print_latex(self):
|
| 1024 |
+
fl_M_act = FiberForceLengthActiveDeGroote2016(self.l_M_tilde, *self.constants)
|
| 1025 |
+
expected = (
|
| 1026 |
+
r'c_{0} e^{- \frac{\left(- c_{1} + l_{M tilde}\right)^{2}}{2 \left(c_{2} + c_{3} l_{M tilde}\right)^{2}}} '
|
| 1027 |
+
r'+ c_{4} e^{- \frac{\left(- c_{5} + l_{M tilde}\right)^{2}}{2 \left(c_{6} + c_{7} l_{M tilde}\right)^{2}}} '
|
| 1028 |
+
r'+ c_{8} e^{- \frac{\left(- c_{9} + l_{M tilde}\right)^{2}}{2 \left(c_{10} + c_{11} l_{M tilde}\right)^{2}}}'
|
| 1029 |
+
)
|
| 1030 |
+
assert LatexPrinter().doprint(fl_M_act.doit()) == expected
|
| 1031 |
+
|
| 1032 |
+
@pytest.mark.parametrize(
|
| 1033 |
+
'code_printer, expected',
|
| 1034 |
+
[
|
| 1035 |
+
(
|
| 1036 |
+
C89CodePrinter,
|
| 1037 |
+
(
|
| 1038 |
+
'(0.81399999999999995*exp(-19.051973784484073'
|
| 1039 |
+
'*pow(l_M_tilde - 1.0600000000000001, 2)'
|
| 1040 |
+
'/pow(0.39074074074074072*l_M_tilde + 1, 2)) '
|
| 1041 |
+
'+ 0.433*exp(-12.499999999999998'
|
| 1042 |
+
'*pow(l_M_tilde - 0.71699999999999997, 2)'
|
| 1043 |
+
'/pow(l_M_tilde - 0.14949999999999999, 2)) '
|
| 1044 |
+
'+ 0.10000000000000001*exp(-3.9899134986753491'
|
| 1045 |
+
'*pow(l_M_tilde - 1.0, 2)))'
|
| 1046 |
+
),
|
| 1047 |
+
),
|
| 1048 |
+
(
|
| 1049 |
+
C99CodePrinter,
|
| 1050 |
+
(
|
| 1051 |
+
'(0.81399999999999995*exp(-19.051973784484073'
|
| 1052 |
+
'*pow(l_M_tilde - 1.0600000000000001, 2)'
|
| 1053 |
+
'/pow(0.39074074074074072*l_M_tilde + 1, 2)) '
|
| 1054 |
+
'+ 0.433*exp(-12.499999999999998'
|
| 1055 |
+
'*pow(l_M_tilde - 0.71699999999999997, 2)'
|
| 1056 |
+
'/pow(l_M_tilde - 0.14949999999999999, 2)) '
|
| 1057 |
+
'+ 0.10000000000000001*exp(-3.9899134986753491'
|
| 1058 |
+
'*pow(l_M_tilde - 1.0, 2)))'
|
| 1059 |
+
),
|
| 1060 |
+
),
|
| 1061 |
+
(
|
| 1062 |
+
C11CodePrinter,
|
| 1063 |
+
(
|
| 1064 |
+
'(0.81399999999999995*exp(-19.051973784484073'
|
| 1065 |
+
'*pow(l_M_tilde - 1.0600000000000001, 2)'
|
| 1066 |
+
'/pow(0.39074074074074072*l_M_tilde + 1, 2)) '
|
| 1067 |
+
'+ 0.433*exp(-12.499999999999998'
|
| 1068 |
+
'*pow(l_M_tilde - 0.71699999999999997, 2)'
|
| 1069 |
+
'/pow(l_M_tilde - 0.14949999999999999, 2)) '
|
| 1070 |
+
'+ 0.10000000000000001*exp(-3.9899134986753491'
|
| 1071 |
+
'*pow(l_M_tilde - 1.0, 2)))'
|
| 1072 |
+
),
|
| 1073 |
+
),
|
| 1074 |
+
(
|
| 1075 |
+
CXX98CodePrinter,
|
| 1076 |
+
(
|
| 1077 |
+
'(0.81399999999999995*exp(-19.051973784484073'
|
| 1078 |
+
'*std::pow(l_M_tilde - 1.0600000000000001, 2)'
|
| 1079 |
+
'/std::pow(0.39074074074074072*l_M_tilde + 1, 2)) '
|
| 1080 |
+
'+ 0.433*exp(-12.499999999999998'
|
| 1081 |
+
'*std::pow(l_M_tilde - 0.71699999999999997, 2)'
|
| 1082 |
+
'/std::pow(l_M_tilde - 0.14949999999999999, 2)) '
|
| 1083 |
+
'+ 0.10000000000000001*exp(-3.9899134986753491'
|
| 1084 |
+
'*std::pow(l_M_tilde - 1.0, 2)))'
|
| 1085 |
+
),
|
| 1086 |
+
),
|
| 1087 |
+
(
|
| 1088 |
+
CXX11CodePrinter,
|
| 1089 |
+
(
|
| 1090 |
+
'(0.81399999999999995*std::exp(-19.051973784484073'
|
| 1091 |
+
'*std::pow(l_M_tilde - 1.0600000000000001, 2)'
|
| 1092 |
+
'/std::pow(0.39074074074074072*l_M_tilde + 1, 2)) '
|
| 1093 |
+
'+ 0.433*std::exp(-12.499999999999998'
|
| 1094 |
+
'*std::pow(l_M_tilde - 0.71699999999999997, 2)'
|
| 1095 |
+
'/std::pow(l_M_tilde - 0.14949999999999999, 2)) '
|
| 1096 |
+
'+ 0.10000000000000001*std::exp(-3.9899134986753491'
|
| 1097 |
+
'*std::pow(l_M_tilde - 1.0, 2)))'
|
| 1098 |
+
),
|
| 1099 |
+
),
|
| 1100 |
+
(
|
| 1101 |
+
CXX17CodePrinter,
|
| 1102 |
+
(
|
| 1103 |
+
'(0.81399999999999995*std::exp(-19.051973784484073'
|
| 1104 |
+
'*std::pow(l_M_tilde - 1.0600000000000001, 2)'
|
| 1105 |
+
'/std::pow(0.39074074074074072*l_M_tilde + 1, 2)) '
|
| 1106 |
+
'+ 0.433*std::exp(-12.499999999999998'
|
| 1107 |
+
'*std::pow(l_M_tilde - 0.71699999999999997, 2)'
|
| 1108 |
+
'/std::pow(l_M_tilde - 0.14949999999999999, 2)) '
|
| 1109 |
+
'+ 0.10000000000000001*std::exp(-3.9899134986753491'
|
| 1110 |
+
'*std::pow(l_M_tilde - 1.0, 2)))'
|
| 1111 |
+
),
|
| 1112 |
+
),
|
| 1113 |
+
(
|
| 1114 |
+
FCodePrinter,
|
| 1115 |
+
(
|
| 1116 |
+
' (0.814d0*exp(-19.051973784484073d0*(l_M_tilde - 1.06d0)**2/(\n'
|
| 1117 |
+
' @ 0.39074074074074072d0*l_M_tilde + 1.0d0)**2) + 0.433d0*exp(\n'
|
| 1118 |
+
' @ -12.499999999999998d0*(l_M_tilde - 0.717d0)**2/(l_M_tilde -\n'
|
| 1119 |
+
' @ 0.14949999999999999d0)**2) + 0.1d0*exp(-3.9899134986753491d0*(\n'
|
| 1120 |
+
' @ l_M_tilde - 1.0d0)**2))'
|
| 1121 |
+
),
|
| 1122 |
+
),
|
| 1123 |
+
(
|
| 1124 |
+
OctaveCodePrinter,
|
| 1125 |
+
(
|
| 1126 |
+
'(0.814*exp(-19.0519737844841*(l_M_tilde - 1.06).^2'
|
| 1127 |
+
'./(0.390740740740741*l_M_tilde + 1).^2) '
|
| 1128 |
+
'+ 0.433*exp(-12.5*(l_M_tilde - 0.717).^2'
|
| 1129 |
+
'./(l_M_tilde - 0.1495).^2) '
|
| 1130 |
+
'+ 0.1*exp(-3.98991349867535*(l_M_tilde - 1.0).^2))'
|
| 1131 |
+
),
|
| 1132 |
+
),
|
| 1133 |
+
(
|
| 1134 |
+
PythonCodePrinter,
|
| 1135 |
+
(
|
| 1136 |
+
'(0.814*math.exp(-19.0519737844841*(l_M_tilde - 1.06)**2'
|
| 1137 |
+
'/(0.390740740740741*l_M_tilde + 1)**2) '
|
| 1138 |
+
'+ 0.433*math.exp(-12.5*(l_M_tilde - 0.717)**2'
|
| 1139 |
+
'/(l_M_tilde - 0.1495)**2) '
|
| 1140 |
+
'+ 0.1*math.exp(-3.98991349867535*(l_M_tilde - 1.0)**2))'
|
| 1141 |
+
),
|
| 1142 |
+
),
|
| 1143 |
+
(
|
| 1144 |
+
NumPyPrinter,
|
| 1145 |
+
(
|
| 1146 |
+
'(0.814*numpy.exp(-19.0519737844841*(l_M_tilde - 1.06)**2'
|
| 1147 |
+
'/(0.390740740740741*l_M_tilde + 1)**2) '
|
| 1148 |
+
'+ 0.433*numpy.exp(-12.5*(l_M_tilde - 0.717)**2'
|
| 1149 |
+
'/(l_M_tilde - 0.1495)**2) '
|
| 1150 |
+
'+ 0.1*numpy.exp(-3.98991349867535*(l_M_tilde - 1.0)**2))'
|
| 1151 |
+
),
|
| 1152 |
+
),
|
| 1153 |
+
(
|
| 1154 |
+
SciPyPrinter,
|
| 1155 |
+
(
|
| 1156 |
+
'(0.814*numpy.exp(-19.0519737844841*(l_M_tilde - 1.06)**2'
|
| 1157 |
+
'/(0.390740740740741*l_M_tilde + 1)**2) '
|
| 1158 |
+
'+ 0.433*numpy.exp(-12.5*(l_M_tilde - 0.717)**2'
|
| 1159 |
+
'/(l_M_tilde - 0.1495)**2) '
|
| 1160 |
+
'+ 0.1*numpy.exp(-3.98991349867535*(l_M_tilde - 1.0)**2))'
|
| 1161 |
+
),
|
| 1162 |
+
),
|
| 1163 |
+
(
|
| 1164 |
+
CuPyPrinter,
|
| 1165 |
+
(
|
| 1166 |
+
'(0.814*cupy.exp(-19.0519737844841*(l_M_tilde - 1.06)**2'
|
| 1167 |
+
'/(0.390740740740741*l_M_tilde + 1)**2) '
|
| 1168 |
+
'+ 0.433*cupy.exp(-12.5*(l_M_tilde - 0.717)**2'
|
| 1169 |
+
'/(l_M_tilde - 0.1495)**2) '
|
| 1170 |
+
'+ 0.1*cupy.exp(-3.98991349867535*(l_M_tilde - 1.0)**2))'
|
| 1171 |
+
),
|
| 1172 |
+
),
|
| 1173 |
+
(
|
| 1174 |
+
JaxPrinter,
|
| 1175 |
+
(
|
| 1176 |
+
'(0.814*jax.numpy.exp(-19.0519737844841*(l_M_tilde - 1.06)**2'
|
| 1177 |
+
'/(0.390740740740741*l_M_tilde + 1)**2) '
|
| 1178 |
+
'+ 0.433*jax.numpy.exp(-12.5*(l_M_tilde - 0.717)**2'
|
| 1179 |
+
'/(l_M_tilde - 0.1495)**2) '
|
| 1180 |
+
'+ 0.1*jax.numpy.exp(-3.98991349867535*(l_M_tilde - 1.0)**2))'
|
| 1181 |
+
),
|
| 1182 |
+
),
|
| 1183 |
+
(
|
| 1184 |
+
MpmathPrinter,
|
| 1185 |
+
(
|
| 1186 |
+
'(mpmath.mpf((0, 7331860193359167, -53, 53))'
|
| 1187 |
+
'*mpmath.exp(-mpmath.mpf((0, 5362653877279683, -48, 53))'
|
| 1188 |
+
'*(l_M_tilde + mpmath.mpf((1, 2386907802506363, -51, 52)))**2'
|
| 1189 |
+
'/(mpmath.mpf((0, 3519479708796943, -53, 52))*l_M_tilde + 1)**2) '
|
| 1190 |
+
'+ mpmath.mpf((0, 7800234554605699, -54, 53))'
|
| 1191 |
+
'*mpmath.exp(-mpmath.mpf((0, 7036874417766399, -49, 53))'
|
| 1192 |
+
'*(l_M_tilde + mpmath.mpf((1, 6458161865649291, -53, 53)))**2'
|
| 1193 |
+
'/(l_M_tilde + mpmath.mpf((1, 5386305154335113, -55, 53)))**2) '
|
| 1194 |
+
'+ mpmath.mpf((0, 3602879701896397, -55, 52))'
|
| 1195 |
+
'*mpmath.exp(-mpmath.mpf((0, 8984486472937407, -51, 53))'
|
| 1196 |
+
'*(l_M_tilde + mpmath.mpf((1, 1, 0, 1)))**2))'
|
| 1197 |
+
),
|
| 1198 |
+
),
|
| 1199 |
+
(
|
| 1200 |
+
LambdaPrinter,
|
| 1201 |
+
(
|
| 1202 |
+
'(0.814*math.exp(-19.0519737844841*(l_M_tilde - 1.06)**2'
|
| 1203 |
+
'/(0.390740740740741*l_M_tilde + 1)**2) '
|
| 1204 |
+
'+ 0.433*math.exp(-12.5*(l_M_tilde - 0.717)**2'
|
| 1205 |
+
'/(l_M_tilde - 0.1495)**2) '
|
| 1206 |
+
'+ 0.1*math.exp(-3.98991349867535*(l_M_tilde - 1.0)**2))'
|
| 1207 |
+
),
|
| 1208 |
+
),
|
| 1209 |
+
]
|
| 1210 |
+
)
|
| 1211 |
+
def test_print_code(self, code_printer, expected):
|
| 1212 |
+
fl_M_act = FiberForceLengthActiveDeGroote2016.with_defaults(self.l_M_tilde)
|
| 1213 |
+
assert code_printer().doprint(fl_M_act) == expected
|
| 1214 |
+
|
| 1215 |
+
def test_derivative_print_code(self):
|
| 1216 |
+
fl_M_act = FiberForceLengthActiveDeGroote2016.with_defaults(self.l_M_tilde)
|
| 1217 |
+
fl_M_act_dl_M_tilde = fl_M_act.diff(self.l_M_tilde)
|
| 1218 |
+
expected = (
|
| 1219 |
+
'(0.79798269973507 - 0.79798269973507*l_M_tilde)'
|
| 1220 |
+
'*math.exp(-3.98991349867535*(l_M_tilde - 1.0)**2) '
|
| 1221 |
+
'+ (10.825*(0.717 - l_M_tilde)/(l_M_tilde - 0.1495)**2 '
|
| 1222 |
+
'+ 10.825*(l_M_tilde - 0.717)**2/(l_M_tilde - 0.1495)**3)'
|
| 1223 |
+
'*math.exp(-12.5*(l_M_tilde - 0.717)**2/(l_M_tilde - 0.1495)**2) '
|
| 1224 |
+
'+ (31.0166133211401*(1.06 - l_M_tilde)/(0.390740740740741*l_M_tilde + 1)**2 '
|
| 1225 |
+
'+ 13.6174190361677*(0.943396226415094*l_M_tilde - 1)**2'
|
| 1226 |
+
'/(0.390740740740741*l_M_tilde + 1)**3)'
|
| 1227 |
+
'*math.exp(-21.4067977442463*(0.943396226415094*l_M_tilde - 1)**2'
|
| 1228 |
+
'/(0.390740740740741*l_M_tilde + 1)**2)'
|
| 1229 |
+
)
|
| 1230 |
+
assert PythonCodePrinter().doprint(fl_M_act_dl_M_tilde) == expected
|
| 1231 |
+
|
| 1232 |
+
def test_lambdify(self):
|
| 1233 |
+
fl_M_act = FiberForceLengthActiveDeGroote2016.with_defaults(self.l_M_tilde)
|
| 1234 |
+
fl_M_act_callable = lambdify(self.l_M_tilde, fl_M_act)
|
| 1235 |
+
assert fl_M_act_callable(1.0) == pytest.approx(0.9941398866)
|
| 1236 |
+
|
| 1237 |
+
@pytest.mark.skipif(numpy is None, reason='NumPy not installed')
|
| 1238 |
+
def test_lambdify_numpy(self):
|
| 1239 |
+
fl_M_act = FiberForceLengthActiveDeGroote2016.with_defaults(self.l_M_tilde)
|
| 1240 |
+
fl_M_act_callable = lambdify(self.l_M_tilde, fl_M_act, 'numpy')
|
| 1241 |
+
l_M_tilde = numpy.array([0.0, 0.5, 1.0, 1.5, 2.0])
|
| 1242 |
+
expected = numpy.array([
|
| 1243 |
+
0.0018501319,
|
| 1244 |
+
0.0529122812,
|
| 1245 |
+
0.9941398866,
|
| 1246 |
+
0.2312431531,
|
| 1247 |
+
0.0069595432,
|
| 1248 |
+
])
|
| 1249 |
+
numpy.testing.assert_allclose(fl_M_act_callable(l_M_tilde), expected)
|
| 1250 |
+
|
| 1251 |
+
@pytest.mark.skipif(jax is None, reason='JAX not installed')
|
| 1252 |
+
def test_lambdify_jax(self):
|
| 1253 |
+
fl_M_act = FiberForceLengthActiveDeGroote2016.with_defaults(self.l_M_tilde)
|
| 1254 |
+
fl_M_act_callable = jax.jit(lambdify(self.l_M_tilde, fl_M_act, 'jax'))
|
| 1255 |
+
l_M_tilde = jax.numpy.array([0.0, 0.5, 1.0, 1.5, 2.0])
|
| 1256 |
+
expected = jax.numpy.array([
|
| 1257 |
+
0.0018501319,
|
| 1258 |
+
0.0529122812,
|
| 1259 |
+
0.9941398866,
|
| 1260 |
+
0.2312431531,
|
| 1261 |
+
0.0069595432,
|
| 1262 |
+
])
|
| 1263 |
+
numpy.testing.assert_allclose(fl_M_act_callable(l_M_tilde), expected)
|
| 1264 |
+
|
| 1265 |
+
|
| 1266 |
+
class TestFiberForceVelocityDeGroote2016:
|
| 1267 |
+
|
| 1268 |
+
@pytest.fixture(autouse=True)
|
| 1269 |
+
def _muscle_fiber_force_velocity_arguments_fixture(self):
|
| 1270 |
+
self.v_M_tilde = Symbol('v_M_tilde')
|
| 1271 |
+
self.c0 = Symbol('c_0')
|
| 1272 |
+
self.c1 = Symbol('c_1')
|
| 1273 |
+
self.c2 = Symbol('c_2')
|
| 1274 |
+
self.c3 = Symbol('c_3')
|
| 1275 |
+
self.constants = (self.c0, self.c1, self.c2, self.c3)
|
| 1276 |
+
|
| 1277 |
+
@staticmethod
|
| 1278 |
+
def test_class():
|
| 1279 |
+
assert issubclass(FiberForceVelocityDeGroote2016, Function)
|
| 1280 |
+
assert issubclass(FiberForceVelocityDeGroote2016, CharacteristicCurveFunction)
|
| 1281 |
+
assert FiberForceVelocityDeGroote2016.__name__ == 'FiberForceVelocityDeGroote2016'
|
| 1282 |
+
|
| 1283 |
+
def test_instance(self):
|
| 1284 |
+
fv_M = FiberForceVelocityDeGroote2016(self.v_M_tilde, *self.constants)
|
| 1285 |
+
assert isinstance(fv_M, FiberForceVelocityDeGroote2016)
|
| 1286 |
+
assert str(fv_M) == 'FiberForceVelocityDeGroote2016(v_M_tilde, c_0, c_1, c_2, c_3)'
|
| 1287 |
+
|
| 1288 |
+
def test_doit(self):
|
| 1289 |
+
fv_M = FiberForceVelocityDeGroote2016(self.v_M_tilde, *self.constants).doit()
|
| 1290 |
+
expected = (
|
| 1291 |
+
self.c0 * log((self.c1 * self.v_M_tilde + self.c2)
|
| 1292 |
+
+ sqrt((self.c1 * self.v_M_tilde + self.c2)**2 + 1)) + self.c3
|
| 1293 |
+
)
|
| 1294 |
+
assert fv_M == expected
|
| 1295 |
+
|
| 1296 |
+
def test_doit_evaluate_false(self):
|
| 1297 |
+
fv_M = FiberForceVelocityDeGroote2016(self.v_M_tilde, *self.constants).doit(evaluate=False)
|
| 1298 |
+
expected = (
|
| 1299 |
+
self.c0 * log((self.c1 * self.v_M_tilde + self.c2)
|
| 1300 |
+
+ sqrt(UnevaluatedExpr(self.c1 * self.v_M_tilde + self.c2)**2 + 1)) + self.c3
|
| 1301 |
+
)
|
| 1302 |
+
assert fv_M == expected
|
| 1303 |
+
|
| 1304 |
+
def test_with_defaults(self):
|
| 1305 |
+
constants = (
|
| 1306 |
+
Float('-0.318'),
|
| 1307 |
+
Float('-8.149'),
|
| 1308 |
+
Float('-0.374'),
|
| 1309 |
+
Float('0.886'),
|
| 1310 |
+
)
|
| 1311 |
+
fv_M_manual = FiberForceVelocityDeGroote2016(self.v_M_tilde, *constants)
|
| 1312 |
+
fv_M_constants = FiberForceVelocityDeGroote2016.with_defaults(self.v_M_tilde)
|
| 1313 |
+
assert fv_M_manual == fv_M_constants
|
| 1314 |
+
|
| 1315 |
+
def test_differentiate_wrt_v_M_tilde(self):
|
| 1316 |
+
fv_M = FiberForceVelocityDeGroote2016(self.v_M_tilde, *self.constants)
|
| 1317 |
+
expected = (
|
| 1318 |
+
self.c0*self.c1
|
| 1319 |
+
/sqrt(UnevaluatedExpr(self.c1*self.v_M_tilde + self.c2)**2 + 1)
|
| 1320 |
+
)
|
| 1321 |
+
assert fv_M.diff(self.v_M_tilde) == expected
|
| 1322 |
+
|
| 1323 |
+
def test_differentiate_wrt_c0(self):
|
| 1324 |
+
fv_M = FiberForceVelocityDeGroote2016(self.v_M_tilde, *self.constants)
|
| 1325 |
+
expected = log(
|
| 1326 |
+
self.c1*self.v_M_tilde + self.c2
|
| 1327 |
+
+ sqrt(UnevaluatedExpr(self.c1*self.v_M_tilde + self.c2)**2 + 1)
|
| 1328 |
+
)
|
| 1329 |
+
assert fv_M.diff(self.c0) == expected
|
| 1330 |
+
|
| 1331 |
+
def test_differentiate_wrt_c1(self):
|
| 1332 |
+
fv_M = FiberForceVelocityDeGroote2016(self.v_M_tilde, *self.constants)
|
| 1333 |
+
expected = (
|
| 1334 |
+
self.c0*self.v_M_tilde
|
| 1335 |
+
/sqrt(UnevaluatedExpr(self.c1*self.v_M_tilde + self.c2)**2 + 1)
|
| 1336 |
+
)
|
| 1337 |
+
assert fv_M.diff(self.c1) == expected
|
| 1338 |
+
|
| 1339 |
+
def test_differentiate_wrt_c2(self):
|
| 1340 |
+
fv_M = FiberForceVelocityDeGroote2016(self.v_M_tilde, *self.constants)
|
| 1341 |
+
expected = (
|
| 1342 |
+
self.c0
|
| 1343 |
+
/sqrt(UnevaluatedExpr(self.c1*self.v_M_tilde + self.c2)**2 + 1)
|
| 1344 |
+
)
|
| 1345 |
+
assert fv_M.diff(self.c2) == expected
|
| 1346 |
+
|
| 1347 |
+
def test_differentiate_wrt_c3(self):
|
| 1348 |
+
fv_M = FiberForceVelocityDeGroote2016(self.v_M_tilde, *self.constants)
|
| 1349 |
+
expected = Integer(1)
|
| 1350 |
+
assert fv_M.diff(self.c3) == expected
|
| 1351 |
+
|
| 1352 |
+
def test_inverse(self):
|
| 1353 |
+
fv_M = FiberForceVelocityDeGroote2016(self.v_M_tilde, *self.constants)
|
| 1354 |
+
assert fv_M.inverse() is FiberForceVelocityInverseDeGroote2016
|
| 1355 |
+
|
| 1356 |
+
def test_function_print_latex(self):
|
| 1357 |
+
fv_M = FiberForceVelocityDeGroote2016(self.v_M_tilde, *self.constants)
|
| 1358 |
+
expected = r'\operatorname{fv}^M \left( v_{M tilde} \right)'
|
| 1359 |
+
assert LatexPrinter().doprint(fv_M) == expected
|
| 1360 |
+
|
| 1361 |
+
def test_expression_print_latex(self):
|
| 1362 |
+
fv_M = FiberForceVelocityDeGroote2016(self.v_M_tilde, *self.constants)
|
| 1363 |
+
expected = (
|
| 1364 |
+
r'c_{0} \log{\left(c_{1} v_{M tilde} + c_{2} + \sqrt{\left(c_{1} '
|
| 1365 |
+
r'v_{M tilde} + c_{2}\right)^{2} + 1} \right)} + c_{3}'
|
| 1366 |
+
)
|
| 1367 |
+
assert LatexPrinter().doprint(fv_M.doit()) == expected
|
| 1368 |
+
|
| 1369 |
+
@pytest.mark.parametrize(
|
| 1370 |
+
'code_printer, expected',
|
| 1371 |
+
[
|
| 1372 |
+
(
|
| 1373 |
+
C89CodePrinter,
|
| 1374 |
+
'(0.88600000000000001 - 0.318*log(-8.1489999999999991*v_M_tilde '
|
| 1375 |
+
'- 0.374 + sqrt(1 + pow(-8.1489999999999991*v_M_tilde - 0.374, 2))))',
|
| 1376 |
+
),
|
| 1377 |
+
(
|
| 1378 |
+
C99CodePrinter,
|
| 1379 |
+
'(0.88600000000000001 - 0.318*log(-8.1489999999999991*v_M_tilde '
|
| 1380 |
+
'- 0.374 + sqrt(1 + pow(-8.1489999999999991*v_M_tilde - 0.374, 2))))',
|
| 1381 |
+
),
|
| 1382 |
+
(
|
| 1383 |
+
C11CodePrinter,
|
| 1384 |
+
'(0.88600000000000001 - 0.318*log(-8.1489999999999991*v_M_tilde '
|
| 1385 |
+
'- 0.374 + sqrt(1 + pow(-8.1489999999999991*v_M_tilde - 0.374, 2))))',
|
| 1386 |
+
),
|
| 1387 |
+
(
|
| 1388 |
+
CXX98CodePrinter,
|
| 1389 |
+
'(0.88600000000000001 - 0.318*log(-8.1489999999999991*v_M_tilde '
|
| 1390 |
+
'- 0.374 + std::sqrt(1 + std::pow(-8.1489999999999991*v_M_tilde - 0.374, 2))))',
|
| 1391 |
+
),
|
| 1392 |
+
(
|
| 1393 |
+
CXX11CodePrinter,
|
| 1394 |
+
'(0.88600000000000001 - 0.318*std::log(-8.1489999999999991*v_M_tilde '
|
| 1395 |
+
'- 0.374 + std::sqrt(1 + std::pow(-8.1489999999999991*v_M_tilde - 0.374, 2))))',
|
| 1396 |
+
),
|
| 1397 |
+
(
|
| 1398 |
+
CXX17CodePrinter,
|
| 1399 |
+
'(0.88600000000000001 - 0.318*std::log(-8.1489999999999991*v_M_tilde '
|
| 1400 |
+
'- 0.374 + std::sqrt(1 + std::pow(-8.1489999999999991*v_M_tilde - 0.374, 2))))',
|
| 1401 |
+
),
|
| 1402 |
+
(
|
| 1403 |
+
FCodePrinter,
|
| 1404 |
+
' (0.886d0 - 0.318d0*log(-8.1489999999999991d0*v_M_tilde - 0.374d0 +\n'
|
| 1405 |
+
' @ sqrt(1.0d0 + (-8.149d0*v_M_tilde - 0.374d0)**2)))',
|
| 1406 |
+
),
|
| 1407 |
+
(
|
| 1408 |
+
OctaveCodePrinter,
|
| 1409 |
+
'(0.886 - 0.318*log(-8.149*v_M_tilde - 0.374 '
|
| 1410 |
+
'+ sqrt(1 + (-8.149*v_M_tilde - 0.374).^2)))',
|
| 1411 |
+
),
|
| 1412 |
+
(
|
| 1413 |
+
PythonCodePrinter,
|
| 1414 |
+
'(0.886 - 0.318*math.log(-8.149*v_M_tilde - 0.374 '
|
| 1415 |
+
'+ math.sqrt(1 + (-8.149*v_M_tilde - 0.374)**2)))',
|
| 1416 |
+
),
|
| 1417 |
+
(
|
| 1418 |
+
NumPyPrinter,
|
| 1419 |
+
'(0.886 - 0.318*numpy.log(-8.149*v_M_tilde - 0.374 '
|
| 1420 |
+
'+ numpy.sqrt(1 + (-8.149*v_M_tilde - 0.374)**2)))',
|
| 1421 |
+
),
|
| 1422 |
+
(
|
| 1423 |
+
SciPyPrinter,
|
| 1424 |
+
'(0.886 - 0.318*numpy.log(-8.149*v_M_tilde - 0.374 '
|
| 1425 |
+
'+ numpy.sqrt(1 + (-8.149*v_M_tilde - 0.374)**2)))',
|
| 1426 |
+
),
|
| 1427 |
+
(
|
| 1428 |
+
CuPyPrinter,
|
| 1429 |
+
'(0.886 - 0.318*cupy.log(-8.149*v_M_tilde - 0.374 '
|
| 1430 |
+
'+ cupy.sqrt(1 + (-8.149*v_M_tilde - 0.374)**2)))',
|
| 1431 |
+
),
|
| 1432 |
+
(
|
| 1433 |
+
JaxPrinter,
|
| 1434 |
+
'(0.886 - 0.318*jax.numpy.log(-8.149*v_M_tilde - 0.374 '
|
| 1435 |
+
'+ jax.numpy.sqrt(1 + (-8.149*v_M_tilde - 0.374)**2)))',
|
| 1436 |
+
),
|
| 1437 |
+
(
|
| 1438 |
+
MpmathPrinter,
|
| 1439 |
+
'(mpmath.mpf((0, 7980378539700519, -53, 53)) '
|
| 1440 |
+
'- mpmath.mpf((0, 5728578726015271, -54, 53))'
|
| 1441 |
+
'*mpmath.log(-mpmath.mpf((0, 4587479170430271, -49, 53))*v_M_tilde '
|
| 1442 |
+
'+ mpmath.mpf((1, 3368692521273131, -53, 52)) '
|
| 1443 |
+
'+ mpmath.sqrt(1 + (-mpmath.mpf((0, 4587479170430271, -49, 53))*v_M_tilde '
|
| 1444 |
+
'+ mpmath.mpf((1, 3368692521273131, -53, 52)))**2)))',
|
| 1445 |
+
),
|
| 1446 |
+
(
|
| 1447 |
+
LambdaPrinter,
|
| 1448 |
+
'(0.886 - 0.318*math.log(-8.149*v_M_tilde - 0.374 '
|
| 1449 |
+
'+ sqrt(1 + (-8.149*v_M_tilde - 0.374)**2)))',
|
| 1450 |
+
),
|
| 1451 |
+
]
|
| 1452 |
+
)
|
| 1453 |
+
def test_print_code(self, code_printer, expected):
|
| 1454 |
+
fv_M = FiberForceVelocityDeGroote2016.with_defaults(self.v_M_tilde)
|
| 1455 |
+
assert code_printer().doprint(fv_M) == expected
|
| 1456 |
+
|
| 1457 |
+
def test_derivative_print_code(self):
|
| 1458 |
+
fv_M = FiberForceVelocityDeGroote2016.with_defaults(self.v_M_tilde)
|
| 1459 |
+
dfv_M_dv_M_tilde = fv_M.diff(self.v_M_tilde)
|
| 1460 |
+
expected = '2.591382*(1 + (-8.149*v_M_tilde - 0.374)**2)**(-1/2)'
|
| 1461 |
+
assert PythonCodePrinter().doprint(dfv_M_dv_M_tilde) == expected
|
| 1462 |
+
|
| 1463 |
+
def test_lambdify(self):
|
| 1464 |
+
fv_M = FiberForceVelocityDeGroote2016.with_defaults(self.v_M_tilde)
|
| 1465 |
+
fv_M_callable = lambdify(self.v_M_tilde, fv_M)
|
| 1466 |
+
assert fv_M_callable(0.0) == pytest.approx(1.002320622548512)
|
| 1467 |
+
|
| 1468 |
+
@pytest.mark.skipif(numpy is None, reason='NumPy not installed')
|
| 1469 |
+
def test_lambdify_numpy(self):
|
| 1470 |
+
fv_M = FiberForceVelocityDeGroote2016.with_defaults(self.v_M_tilde)
|
| 1471 |
+
fv_M_callable = lambdify(self.v_M_tilde, fv_M, 'numpy')
|
| 1472 |
+
v_M_tilde = numpy.array([-1.0, -0.5, 0.0, 0.5])
|
| 1473 |
+
expected = numpy.array([
|
| 1474 |
+
0.0120816781,
|
| 1475 |
+
0.2438336294,
|
| 1476 |
+
1.0023206225,
|
| 1477 |
+
1.5850003903,
|
| 1478 |
+
])
|
| 1479 |
+
numpy.testing.assert_allclose(fv_M_callable(v_M_tilde), expected)
|
| 1480 |
+
|
| 1481 |
+
@pytest.mark.skipif(jax is None, reason='JAX not installed')
|
| 1482 |
+
def test_lambdify_jax(self):
|
| 1483 |
+
fv_M = FiberForceVelocityDeGroote2016.with_defaults(self.v_M_tilde)
|
| 1484 |
+
fv_M_callable = jax.jit(lambdify(self.v_M_tilde, fv_M, 'jax'))
|
| 1485 |
+
v_M_tilde = jax.numpy.array([-1.0, -0.5, 0.0, 0.5])
|
| 1486 |
+
expected = jax.numpy.array([
|
| 1487 |
+
0.0120816781,
|
| 1488 |
+
0.2438336294,
|
| 1489 |
+
1.0023206225,
|
| 1490 |
+
1.5850003903,
|
| 1491 |
+
])
|
| 1492 |
+
numpy.testing.assert_allclose(fv_M_callable(v_M_tilde), expected)
|
| 1493 |
+
|
| 1494 |
+
|
| 1495 |
+
class TestFiberForceVelocityInverseDeGroote2016:
|
| 1496 |
+
|
| 1497 |
+
@pytest.fixture(autouse=True)
|
| 1498 |
+
def _tendon_force_length_inverse_arguments_fixture(self):
|
| 1499 |
+
self.fv_M = Symbol('fv_M')
|
| 1500 |
+
self.c0 = Symbol('c_0')
|
| 1501 |
+
self.c1 = Symbol('c_1')
|
| 1502 |
+
self.c2 = Symbol('c_2')
|
| 1503 |
+
self.c3 = Symbol('c_3')
|
| 1504 |
+
self.constants = (self.c0, self.c1, self.c2, self.c3)
|
| 1505 |
+
|
| 1506 |
+
@staticmethod
|
| 1507 |
+
def test_class():
|
| 1508 |
+
assert issubclass(FiberForceVelocityInverseDeGroote2016, Function)
|
| 1509 |
+
assert issubclass(FiberForceVelocityInverseDeGroote2016, CharacteristicCurveFunction)
|
| 1510 |
+
assert FiberForceVelocityInverseDeGroote2016.__name__ == 'FiberForceVelocityInverseDeGroote2016'
|
| 1511 |
+
|
| 1512 |
+
def test_instance(self):
|
| 1513 |
+
fv_M_inv = FiberForceVelocityInverseDeGroote2016(self.fv_M, *self.constants)
|
| 1514 |
+
assert isinstance(fv_M_inv, FiberForceVelocityInverseDeGroote2016)
|
| 1515 |
+
assert str(fv_M_inv) == 'FiberForceVelocityInverseDeGroote2016(fv_M, c_0, c_1, c_2, c_3)'
|
| 1516 |
+
|
| 1517 |
+
def test_doit(self):
|
| 1518 |
+
fv_M_inv = FiberForceVelocityInverseDeGroote2016(self.fv_M, *self.constants).doit()
|
| 1519 |
+
assert fv_M_inv == (sinh((self.fv_M - self.c3)/self.c0) - self.c2)/self.c1
|
| 1520 |
+
|
| 1521 |
+
def test_doit_evaluate_false(self):
|
| 1522 |
+
fv_M_inv = FiberForceVelocityInverseDeGroote2016(self.fv_M, *self.constants).doit(evaluate=False)
|
| 1523 |
+
assert fv_M_inv == (sinh(UnevaluatedExpr(self.fv_M - self.c3)/self.c0) - self.c2)/self.c1
|
| 1524 |
+
|
| 1525 |
+
def test_with_defaults(self):
|
| 1526 |
+
constants = (
|
| 1527 |
+
Float('-0.318'),
|
| 1528 |
+
Float('-8.149'),
|
| 1529 |
+
Float('-0.374'),
|
| 1530 |
+
Float('0.886'),
|
| 1531 |
+
)
|
| 1532 |
+
fv_M_inv_manual = FiberForceVelocityInverseDeGroote2016(self.fv_M, *constants)
|
| 1533 |
+
fv_M_inv_constants = FiberForceVelocityInverseDeGroote2016.with_defaults(self.fv_M)
|
| 1534 |
+
assert fv_M_inv_manual == fv_M_inv_constants
|
| 1535 |
+
|
| 1536 |
+
def test_differentiate_wrt_fv_M(self):
|
| 1537 |
+
fv_M_inv = FiberForceVelocityInverseDeGroote2016(self.fv_M, *self.constants)
|
| 1538 |
+
expected = cosh((self.fv_M - self.c3)/self.c0)/(self.c0*self.c1)
|
| 1539 |
+
assert fv_M_inv.diff(self.fv_M) == expected
|
| 1540 |
+
|
| 1541 |
+
def test_differentiate_wrt_c0(self):
|
| 1542 |
+
fv_M_inv = FiberForceVelocityInverseDeGroote2016(self.fv_M, *self.constants)
|
| 1543 |
+
expected = (self.c3 - self.fv_M)*cosh((self.fv_M - self.c3)/self.c0)/(self.c0**2*self.c1)
|
| 1544 |
+
assert fv_M_inv.diff(self.c0) == expected
|
| 1545 |
+
|
| 1546 |
+
def test_differentiate_wrt_c1(self):
|
| 1547 |
+
fv_M_inv = FiberForceVelocityInverseDeGroote2016(self.fv_M, *self.constants)
|
| 1548 |
+
expected = (self.c2 - sinh((self.fv_M - self.c3)/self.c0))/self.c1**2
|
| 1549 |
+
assert fv_M_inv.diff(self.c1) == expected
|
| 1550 |
+
|
| 1551 |
+
def test_differentiate_wrt_c2(self):
|
| 1552 |
+
fv_M_inv = FiberForceVelocityInverseDeGroote2016(self.fv_M, *self.constants)
|
| 1553 |
+
expected = -1/self.c1
|
| 1554 |
+
assert fv_M_inv.diff(self.c2) == expected
|
| 1555 |
+
|
| 1556 |
+
def test_differentiate_wrt_c3(self):
|
| 1557 |
+
fv_M_inv = FiberForceVelocityInverseDeGroote2016(self.fv_M, *self.constants)
|
| 1558 |
+
expected = -cosh((self.fv_M - self.c3)/self.c0)/(self.c0*self.c1)
|
| 1559 |
+
assert fv_M_inv.diff(self.c3) == expected
|
| 1560 |
+
|
| 1561 |
+
def test_inverse(self):
|
| 1562 |
+
fv_M_inv = FiberForceVelocityInverseDeGroote2016(self.fv_M, *self.constants)
|
| 1563 |
+
assert fv_M_inv.inverse() is FiberForceVelocityDeGroote2016
|
| 1564 |
+
|
| 1565 |
+
def test_function_print_latex(self):
|
| 1566 |
+
fv_M_inv = FiberForceVelocityInverseDeGroote2016(self.fv_M, *self.constants)
|
| 1567 |
+
expected = r'\left( \operatorname{fv}^M \right)^{-1} \left( fv_{M} \right)'
|
| 1568 |
+
assert LatexPrinter().doprint(fv_M_inv) == expected
|
| 1569 |
+
|
| 1570 |
+
def test_expression_print_latex(self):
|
| 1571 |
+
fv_M = FiberForceVelocityInverseDeGroote2016(self.fv_M, *self.constants)
|
| 1572 |
+
expected = r'\frac{- c_{2} + \sinh{\left(\frac{- c_{3} + fv_{M}}{c_{0}} \right)}}{c_{1}}'
|
| 1573 |
+
assert LatexPrinter().doprint(fv_M.doit()) == expected
|
| 1574 |
+
|
| 1575 |
+
@pytest.mark.parametrize(
|
| 1576 |
+
'code_printer, expected',
|
| 1577 |
+
[
|
| 1578 |
+
(
|
| 1579 |
+
C89CodePrinter,
|
| 1580 |
+
'(-0.12271444348999878*(0.374 - sinh(3.1446540880503142*(fv_M '
|
| 1581 |
+
'- 0.88600000000000001))))',
|
| 1582 |
+
),
|
| 1583 |
+
(
|
| 1584 |
+
C99CodePrinter,
|
| 1585 |
+
'(-0.12271444348999878*(0.374 - sinh(3.1446540880503142*(fv_M '
|
| 1586 |
+
'- 0.88600000000000001))))',
|
| 1587 |
+
),
|
| 1588 |
+
(
|
| 1589 |
+
C11CodePrinter,
|
| 1590 |
+
'(-0.12271444348999878*(0.374 - sinh(3.1446540880503142*(fv_M '
|
| 1591 |
+
'- 0.88600000000000001))))',
|
| 1592 |
+
),
|
| 1593 |
+
(
|
| 1594 |
+
CXX98CodePrinter,
|
| 1595 |
+
'(-0.12271444348999878*(0.374 - sinh(3.1446540880503142*(fv_M '
|
| 1596 |
+
'- 0.88600000000000001))))',
|
| 1597 |
+
),
|
| 1598 |
+
(
|
| 1599 |
+
CXX11CodePrinter,
|
| 1600 |
+
'(-0.12271444348999878*(0.374 - std::sinh(3.1446540880503142'
|
| 1601 |
+
'*(fv_M - 0.88600000000000001))))',
|
| 1602 |
+
),
|
| 1603 |
+
(
|
| 1604 |
+
CXX17CodePrinter,
|
| 1605 |
+
'(-0.12271444348999878*(0.374 - std::sinh(3.1446540880503142'
|
| 1606 |
+
'*(fv_M - 0.88600000000000001))))',
|
| 1607 |
+
),
|
| 1608 |
+
(
|
| 1609 |
+
FCodePrinter,
|
| 1610 |
+
' (-0.122714443489999d0*(0.374d0 - sinh(3.1446540880503142d0*(fv_M -\n'
|
| 1611 |
+
' @ 0.886d0))))',
|
| 1612 |
+
),
|
| 1613 |
+
(
|
| 1614 |
+
OctaveCodePrinter,
|
| 1615 |
+
'(-0.122714443489999*(0.374 - sinh(3.14465408805031*(fv_M '
|
| 1616 |
+
'- 0.886))))',
|
| 1617 |
+
),
|
| 1618 |
+
(
|
| 1619 |
+
PythonCodePrinter,
|
| 1620 |
+
'(-0.122714443489999*(0.374 - math.sinh(3.14465408805031*(fv_M '
|
| 1621 |
+
'- 0.886))))',
|
| 1622 |
+
),
|
| 1623 |
+
(
|
| 1624 |
+
NumPyPrinter,
|
| 1625 |
+
'(-0.122714443489999*(0.374 - numpy.sinh(3.14465408805031'
|
| 1626 |
+
'*(fv_M - 0.886))))',
|
| 1627 |
+
),
|
| 1628 |
+
(
|
| 1629 |
+
SciPyPrinter,
|
| 1630 |
+
'(-0.122714443489999*(0.374 - numpy.sinh(3.14465408805031'
|
| 1631 |
+
'*(fv_M - 0.886))))',
|
| 1632 |
+
),
|
| 1633 |
+
(
|
| 1634 |
+
CuPyPrinter,
|
| 1635 |
+
'(-0.122714443489999*(0.374 - cupy.sinh(3.14465408805031*(fv_M '
|
| 1636 |
+
'- 0.886))))',
|
| 1637 |
+
),
|
| 1638 |
+
(
|
| 1639 |
+
JaxPrinter,
|
| 1640 |
+
'(-0.122714443489999*(0.374 - jax.numpy.sinh(3.14465408805031'
|
| 1641 |
+
'*(fv_M - 0.886))))',
|
| 1642 |
+
),
|
| 1643 |
+
(
|
| 1644 |
+
MpmathPrinter,
|
| 1645 |
+
'(-mpmath.mpf((0, 8842507551592581, -56, 53))*(mpmath.mpf((0, '
|
| 1646 |
+
'3368692521273131, -53, 52)) - mpmath.sinh(mpmath.mpf((0, '
|
| 1647 |
+
'7081131489576251, -51, 53))*(fv_M + mpmath.mpf((1, '
|
| 1648 |
+
'7980378539700519, -53, 53))))))',
|
| 1649 |
+
),
|
| 1650 |
+
(
|
| 1651 |
+
LambdaPrinter,
|
| 1652 |
+
'(-0.122714443489999*(0.374 - math.sinh(3.14465408805031*(fv_M '
|
| 1653 |
+
'- 0.886))))',
|
| 1654 |
+
),
|
| 1655 |
+
]
|
| 1656 |
+
)
|
| 1657 |
+
def test_print_code(self, code_printer, expected):
|
| 1658 |
+
fv_M_inv = FiberForceVelocityInverseDeGroote2016.with_defaults(self.fv_M)
|
| 1659 |
+
assert code_printer().doprint(fv_M_inv) == expected
|
| 1660 |
+
|
| 1661 |
+
def test_derivative_print_code(self):
|
| 1662 |
+
fv_M_inv = FiberForceVelocityInverseDeGroote2016.with_defaults(self.fv_M)
|
| 1663 |
+
dfv_M_inv_dfv_M = fv_M_inv.diff(self.fv_M)
|
| 1664 |
+
expected = (
|
| 1665 |
+
'0.385894476383644*math.cosh(3.14465408805031*fv_M '
|
| 1666 |
+
'- 2.78616352201258)'
|
| 1667 |
+
)
|
| 1668 |
+
assert PythonCodePrinter().doprint(dfv_M_inv_dfv_M) == expected
|
| 1669 |
+
|
| 1670 |
+
def test_lambdify(self):
|
| 1671 |
+
fv_M_inv = FiberForceVelocityInverseDeGroote2016.with_defaults(self.fv_M)
|
| 1672 |
+
fv_M_inv_callable = lambdify(self.fv_M, fv_M_inv)
|
| 1673 |
+
assert fv_M_inv_callable(1.0) == pytest.approx(-0.0009548832444487479)
|
| 1674 |
+
|
| 1675 |
+
@pytest.mark.skipif(numpy is None, reason='NumPy not installed')
|
| 1676 |
+
def test_lambdify_numpy(self):
|
| 1677 |
+
fv_M_inv = FiberForceVelocityInverseDeGroote2016.with_defaults(self.fv_M)
|
| 1678 |
+
fv_M_inv_callable = lambdify(self.fv_M, fv_M_inv, 'numpy')
|
| 1679 |
+
fv_M = numpy.array([0.8, 0.9, 1.0, 1.1, 1.2])
|
| 1680 |
+
expected = numpy.array([
|
| 1681 |
+
-0.0794881459,
|
| 1682 |
+
-0.0404909338,
|
| 1683 |
+
-0.0009548832,
|
| 1684 |
+
0.043061991,
|
| 1685 |
+
0.0959484397,
|
| 1686 |
+
])
|
| 1687 |
+
numpy.testing.assert_allclose(fv_M_inv_callable(fv_M), expected)
|
| 1688 |
+
|
| 1689 |
+
@pytest.mark.skipif(jax is None, reason='JAX not installed')
|
| 1690 |
+
def test_lambdify_jax(self):
|
| 1691 |
+
fv_M_inv = FiberForceVelocityInverseDeGroote2016.with_defaults(self.fv_M)
|
| 1692 |
+
fv_M_inv_callable = jax.jit(lambdify(self.fv_M, fv_M_inv, 'jax'))
|
| 1693 |
+
fv_M = jax.numpy.array([0.8, 0.9, 1.0, 1.1, 1.2])
|
| 1694 |
+
expected = jax.numpy.array([
|
| 1695 |
+
-0.0794881459,
|
| 1696 |
+
-0.0404909338,
|
| 1697 |
+
-0.0009548832,
|
| 1698 |
+
0.043061991,
|
| 1699 |
+
0.0959484397,
|
| 1700 |
+
])
|
| 1701 |
+
numpy.testing.assert_allclose(fv_M_inv_callable(fv_M), expected)
|
| 1702 |
+
|
| 1703 |
+
|
| 1704 |
+
class TestCharacteristicCurveCollection:
|
| 1705 |
+
|
| 1706 |
+
@staticmethod
|
| 1707 |
+
def test_valid_constructor():
|
| 1708 |
+
curves = CharacteristicCurveCollection(
|
| 1709 |
+
tendon_force_length=TendonForceLengthDeGroote2016,
|
| 1710 |
+
tendon_force_length_inverse=TendonForceLengthInverseDeGroote2016,
|
| 1711 |
+
fiber_force_length_passive=FiberForceLengthPassiveDeGroote2016,
|
| 1712 |
+
fiber_force_length_passive_inverse=FiberForceLengthPassiveInverseDeGroote2016,
|
| 1713 |
+
fiber_force_length_active=FiberForceLengthActiveDeGroote2016,
|
| 1714 |
+
fiber_force_velocity=FiberForceVelocityDeGroote2016,
|
| 1715 |
+
fiber_force_velocity_inverse=FiberForceVelocityInverseDeGroote2016,
|
| 1716 |
+
)
|
| 1717 |
+
assert curves.tendon_force_length is TendonForceLengthDeGroote2016
|
| 1718 |
+
assert curves.tendon_force_length_inverse is TendonForceLengthInverseDeGroote2016
|
| 1719 |
+
assert curves.fiber_force_length_passive is FiberForceLengthPassiveDeGroote2016
|
| 1720 |
+
assert curves.fiber_force_length_passive_inverse is FiberForceLengthPassiveInverseDeGroote2016
|
| 1721 |
+
assert curves.fiber_force_length_active is FiberForceLengthActiveDeGroote2016
|
| 1722 |
+
assert curves.fiber_force_velocity is FiberForceVelocityDeGroote2016
|
| 1723 |
+
assert curves.fiber_force_velocity_inverse is FiberForceVelocityInverseDeGroote2016
|
| 1724 |
+
|
| 1725 |
+
@staticmethod
|
| 1726 |
+
@pytest.mark.skip(reason='kw_only dataclasses only valid in Python >3.10')
|
| 1727 |
+
def test_invalid_constructor_keyword_only():
|
| 1728 |
+
with pytest.raises(TypeError):
|
| 1729 |
+
_ = CharacteristicCurveCollection(
|
| 1730 |
+
TendonForceLengthDeGroote2016,
|
| 1731 |
+
TendonForceLengthInverseDeGroote2016,
|
| 1732 |
+
FiberForceLengthPassiveDeGroote2016,
|
| 1733 |
+
FiberForceLengthPassiveInverseDeGroote2016,
|
| 1734 |
+
FiberForceLengthActiveDeGroote2016,
|
| 1735 |
+
FiberForceVelocityDeGroote2016,
|
| 1736 |
+
FiberForceVelocityInverseDeGroote2016,
|
| 1737 |
+
)
|
| 1738 |
+
|
| 1739 |
+
@staticmethod
|
| 1740 |
+
@pytest.mark.parametrize(
|
| 1741 |
+
'kwargs',
|
| 1742 |
+
[
|
| 1743 |
+
{'tendon_force_length': TendonForceLengthDeGroote2016},
|
| 1744 |
+
{
|
| 1745 |
+
'tendon_force_length': TendonForceLengthDeGroote2016,
|
| 1746 |
+
'tendon_force_length_inverse': TendonForceLengthInverseDeGroote2016,
|
| 1747 |
+
'fiber_force_length_passive': FiberForceLengthPassiveDeGroote2016,
|
| 1748 |
+
'fiber_force_length_passive_inverse': FiberForceLengthPassiveInverseDeGroote2016,
|
| 1749 |
+
'fiber_force_length_active': FiberForceLengthActiveDeGroote2016,
|
| 1750 |
+
'fiber_force_velocity': FiberForceVelocityDeGroote2016,
|
| 1751 |
+
'fiber_force_velocity_inverse': FiberForceVelocityInverseDeGroote2016,
|
| 1752 |
+
'extra_kwarg': None,
|
| 1753 |
+
},
|
| 1754 |
+
]
|
| 1755 |
+
)
|
| 1756 |
+
def test_invalid_constructor_wrong_number_args(kwargs):
|
| 1757 |
+
with pytest.raises(TypeError):
|
| 1758 |
+
_ = CharacteristicCurveCollection(**kwargs)
|
| 1759 |
+
|
| 1760 |
+
@staticmethod
|
| 1761 |
+
def test_instance_is_immutable():
|
| 1762 |
+
curves = CharacteristicCurveCollection(
|
| 1763 |
+
tendon_force_length=TendonForceLengthDeGroote2016,
|
| 1764 |
+
tendon_force_length_inverse=TendonForceLengthInverseDeGroote2016,
|
| 1765 |
+
fiber_force_length_passive=FiberForceLengthPassiveDeGroote2016,
|
| 1766 |
+
fiber_force_length_passive_inverse=FiberForceLengthPassiveInverseDeGroote2016,
|
| 1767 |
+
fiber_force_length_active=FiberForceLengthActiveDeGroote2016,
|
| 1768 |
+
fiber_force_velocity=FiberForceVelocityDeGroote2016,
|
| 1769 |
+
fiber_force_velocity_inverse=FiberForceVelocityInverseDeGroote2016,
|
| 1770 |
+
)
|
| 1771 |
+
with pytest.raises(AttributeError):
|
| 1772 |
+
curves.tendon_force_length = None
|
| 1773 |
+
with pytest.raises(AttributeError):
|
| 1774 |
+
curves.tendon_force_length_inverse = None
|
| 1775 |
+
with pytest.raises(AttributeError):
|
| 1776 |
+
curves.fiber_force_length_passive = None
|
| 1777 |
+
with pytest.raises(AttributeError):
|
| 1778 |
+
curves.fiber_force_length_passive_inverse = None
|
| 1779 |
+
with pytest.raises(AttributeError):
|
| 1780 |
+
curves.fiber_force_length_active = None
|
| 1781 |
+
with pytest.raises(AttributeError):
|
| 1782 |
+
curves.fiber_force_velocity = None
|
| 1783 |
+
with pytest.raises(AttributeError):
|
| 1784 |
+
curves.fiber_force_velocity_inverse = None
|
evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/tests/test_mixin.py
ADDED
|
@@ -0,0 +1,48 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
"""Tests for the ``sympy.physics.biomechanics._mixin.py`` module."""
|
| 2 |
+
|
| 3 |
+
import pytest
|
| 4 |
+
|
| 5 |
+
from sympy.physics.biomechanics._mixin import _NamedMixin
|
| 6 |
+
|
| 7 |
+
|
| 8 |
+
class TestNamedMixin:
|
| 9 |
+
|
| 10 |
+
@staticmethod
|
| 11 |
+
def test_subclass():
|
| 12 |
+
|
| 13 |
+
class Subclass(_NamedMixin):
|
| 14 |
+
|
| 15 |
+
def __init__(self, name):
|
| 16 |
+
self.name = name
|
| 17 |
+
|
| 18 |
+
instance = Subclass('name')
|
| 19 |
+
assert instance.name == 'name'
|
| 20 |
+
|
| 21 |
+
@pytest.fixture(autouse=True)
|
| 22 |
+
def _named_mixin_fixture(self):
|
| 23 |
+
|
| 24 |
+
class Subclass(_NamedMixin):
|
| 25 |
+
|
| 26 |
+
def __init__(self, name):
|
| 27 |
+
self.name = name
|
| 28 |
+
|
| 29 |
+
self.Subclass = Subclass
|
| 30 |
+
|
| 31 |
+
@pytest.mark.parametrize('name', ['a', 'name', 'long_name'])
|
| 32 |
+
def test_valid_name_argument(self, name):
|
| 33 |
+
instance = self.Subclass(name)
|
| 34 |
+
assert instance.name == name
|
| 35 |
+
|
| 36 |
+
@pytest.mark.parametrize('invalid_name', [0, 0.0, None, False])
|
| 37 |
+
def test_invalid_name_argument_not_str(self, invalid_name):
|
| 38 |
+
with pytest.raises(TypeError):
|
| 39 |
+
_ = self.Subclass(invalid_name)
|
| 40 |
+
|
| 41 |
+
def test_invalid_name_argument_zero_length_str(self):
|
| 42 |
+
with pytest.raises(ValueError):
|
| 43 |
+
_ = self.Subclass('')
|
| 44 |
+
|
| 45 |
+
def test_name_attribute_is_immutable(self):
|
| 46 |
+
instance = self.Subclass('name')
|
| 47 |
+
with pytest.raises(AttributeError):
|
| 48 |
+
instance.name = 'new_name'
|
evalkit_internvl/lib/python3.10/site-packages/sympy/physics/biomechanics/tests/test_musculotendon.py
ADDED
|
@@ -0,0 +1,837 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
| 1 |
+
"""Tests for the ``sympy.physics.biomechanics.musculotendon.py`` module."""
|
| 2 |
+
|
| 3 |
+
import abc
|
| 4 |
+
|
| 5 |
+
import pytest
|
| 6 |
+
|
| 7 |
+
from sympy.core.expr import UnevaluatedExpr
|
| 8 |
+
from sympy.core.numbers import Float, Integer, Rational
|
| 9 |
+
from sympy.core.symbol import Symbol
|
| 10 |
+
from sympy.functions.elementary.exponential import exp
|
| 11 |
+
from sympy.functions.elementary.hyperbolic import tanh
|
| 12 |
+
from sympy.functions.elementary.miscellaneous import sqrt
|
| 13 |
+
from sympy.functions.elementary.trigonometric import sin
|
| 14 |
+
from sympy.matrices.dense import MutableDenseMatrix as Matrix, eye, zeros
|
| 15 |
+
from sympy.physics.biomechanics.activation import (
|
| 16 |
+
FirstOrderActivationDeGroote2016
|
| 17 |
+
)
|
| 18 |
+
from sympy.physics.biomechanics.curve import (
|
| 19 |
+
CharacteristicCurveCollection,
|
| 20 |
+
FiberForceLengthActiveDeGroote2016,
|
| 21 |
+
FiberForceLengthPassiveDeGroote2016,
|
| 22 |
+
FiberForceLengthPassiveInverseDeGroote2016,
|
| 23 |
+
FiberForceVelocityDeGroote2016,
|
| 24 |
+
FiberForceVelocityInverseDeGroote2016,
|
| 25 |
+
TendonForceLengthDeGroote2016,
|
| 26 |
+
TendonForceLengthInverseDeGroote2016,
|
| 27 |
+
)
|
| 28 |
+
from sympy.physics.biomechanics.musculotendon import (
|
| 29 |
+
MusculotendonBase,
|
| 30 |
+
MusculotendonDeGroote2016,
|
| 31 |
+
MusculotendonFormulation,
|
| 32 |
+
)
|
| 33 |
+
from sympy.physics.biomechanics._mixin import _NamedMixin
|
| 34 |
+
from sympy.physics.mechanics.actuator import ForceActuator
|
| 35 |
+
from sympy.physics.mechanics.pathway import LinearPathway
|
| 36 |
+
from sympy.physics.vector.frame import ReferenceFrame
|
| 37 |
+
from sympy.physics.vector.functions import dynamicsymbols
|
| 38 |
+
from sympy.physics.vector.point import Point
|
| 39 |
+
from sympy.simplify.simplify import simplify
|
| 40 |
+
|
| 41 |
+
|
| 42 |
+
class TestMusculotendonFormulation:
|
| 43 |
+
@staticmethod
|
| 44 |
+
def test_rigid_tendon_member():
|
| 45 |
+
assert MusculotendonFormulation(0) == 0
|
| 46 |
+
assert MusculotendonFormulation.RIGID_TENDON == 0
|
| 47 |
+
|
| 48 |
+
@staticmethod
|
| 49 |
+
def test_fiber_length_explicit_member():
|
| 50 |
+
assert MusculotendonFormulation(1) == 1
|
| 51 |
+
assert MusculotendonFormulation.FIBER_LENGTH_EXPLICIT == 1
|
| 52 |
+
|
| 53 |
+
@staticmethod
|
| 54 |
+
def test_tendon_force_explicit_member():
|
| 55 |
+
assert MusculotendonFormulation(2) == 2
|
| 56 |
+
assert MusculotendonFormulation.TENDON_FORCE_EXPLICIT == 2
|
| 57 |
+
|
| 58 |
+
@staticmethod
|
| 59 |
+
def test_fiber_length_implicit_member():
|
| 60 |
+
assert MusculotendonFormulation(3) == 3
|
| 61 |
+
assert MusculotendonFormulation.FIBER_LENGTH_IMPLICIT == 3
|
| 62 |
+
|
| 63 |
+
@staticmethod
|
| 64 |
+
def test_tendon_force_implicit_member():
|
| 65 |
+
assert MusculotendonFormulation(4) == 4
|
| 66 |
+
assert MusculotendonFormulation.TENDON_FORCE_IMPLICIT == 4
|
| 67 |
+
|
| 68 |
+
|
| 69 |
+
class TestMusculotendonBase:
|
| 70 |
+
|
| 71 |
+
@staticmethod
|
| 72 |
+
def test_is_abstract_base_class():
|
| 73 |
+
assert issubclass(MusculotendonBase, abc.ABC)
|
| 74 |
+
|
| 75 |
+
@staticmethod
|
| 76 |
+
def test_class():
|
| 77 |
+
assert issubclass(MusculotendonBase, ForceActuator)
|
| 78 |
+
assert issubclass(MusculotendonBase, _NamedMixin)
|
| 79 |
+
assert MusculotendonBase.__name__ == 'MusculotendonBase'
|
| 80 |
+
|
| 81 |
+
@staticmethod
|
| 82 |
+
def test_cannot_instantiate_directly():
|
| 83 |
+
with pytest.raises(TypeError):
|
| 84 |
+
_ = MusculotendonBase()
|
| 85 |
+
|
| 86 |
+
|
| 87 |
+
@pytest.mark.parametrize('musculotendon_concrete', [MusculotendonDeGroote2016])
|
| 88 |
+
class TestMusculotendonRigidTendon:
|
| 89 |
+
|
| 90 |
+
@pytest.fixture(autouse=True)
|
| 91 |
+
def _musculotendon_rigid_tendon_fixture(self, musculotendon_concrete):
|
| 92 |
+
self.name = 'name'
|
| 93 |
+
self.N = ReferenceFrame('N')
|
| 94 |
+
self.q = dynamicsymbols('q')
|
| 95 |
+
self.origin = Point('pO')
|
| 96 |
+
self.insertion = Point('pI')
|
| 97 |
+
self.insertion.set_pos(self.origin, self.q*self.N.x)
|
| 98 |
+
self.pathway = LinearPathway(self.origin, self.insertion)
|
| 99 |
+
self.activation = FirstOrderActivationDeGroote2016(self.name)
|
| 100 |
+
self.e = self.activation.excitation
|
| 101 |
+
self.a = self.activation.activation
|
| 102 |
+
self.tau_a = self.activation.activation_time_constant
|
| 103 |
+
self.tau_d = self.activation.deactivation_time_constant
|
| 104 |
+
self.b = self.activation.smoothing_rate
|
| 105 |
+
self.formulation = MusculotendonFormulation.RIGID_TENDON
|
| 106 |
+
self.l_T_slack = Symbol('l_T_slack')
|
| 107 |
+
self.F_M_max = Symbol('F_M_max')
|
| 108 |
+
self.l_M_opt = Symbol('l_M_opt')
|
| 109 |
+
self.v_M_max = Symbol('v_M_max')
|
| 110 |
+
self.alpha_opt = Symbol('alpha_opt')
|
| 111 |
+
self.beta = Symbol('beta')
|
| 112 |
+
self.instance = musculotendon_concrete(
|
| 113 |
+
self.name,
|
| 114 |
+
self.pathway,
|
| 115 |
+
self.activation,
|
| 116 |
+
musculotendon_dynamics=self.formulation,
|
| 117 |
+
tendon_slack_length=self.l_T_slack,
|
| 118 |
+
peak_isometric_force=self.F_M_max,
|
| 119 |
+
optimal_fiber_length=self.l_M_opt,
|
| 120 |
+
maximal_fiber_velocity=self.v_M_max,
|
| 121 |
+
optimal_pennation_angle=self.alpha_opt,
|
| 122 |
+
fiber_damping_coefficient=self.beta,
|
| 123 |
+
)
|
| 124 |
+
self.da_expr = (
|
| 125 |
+
(1/(self.tau_a*(Rational(1, 2) + Rational(3, 2)*self.a)))
|
| 126 |
+
*(Rational(1, 2) + Rational(1, 2)*tanh(self.b*(self.e - self.a)))
|
| 127 |
+
+ ((Rational(1, 2) + Rational(3, 2)*self.a)/self.tau_d)
|
| 128 |
+
*(Rational(1, 2) - Rational(1, 2)*tanh(self.b*(self.e - self.a)))
|
| 129 |
+
)*(self.e - self.a)
|
| 130 |
+
|
| 131 |
+
def test_state_vars(self):
|
| 132 |
+
assert hasattr(self.instance, 'x')
|
| 133 |
+
assert hasattr(self.instance, 'state_vars')
|
| 134 |
+
assert self.instance.x == self.instance.state_vars
|
| 135 |
+
x_expected = Matrix([self.a])
|
| 136 |
+
assert self.instance.x == x_expected
|
| 137 |
+
assert self.instance.state_vars == x_expected
|
| 138 |
+
assert isinstance(self.instance.x, Matrix)
|
| 139 |
+
assert isinstance(self.instance.state_vars, Matrix)
|
| 140 |
+
assert self.instance.x.shape == (1, 1)
|
| 141 |
+
assert self.instance.state_vars.shape == (1, 1)
|
| 142 |
+
|
| 143 |
+
def test_input_vars(self):
|
| 144 |
+
assert hasattr(self.instance, 'r')
|
| 145 |
+
assert hasattr(self.instance, 'input_vars')
|
| 146 |
+
assert self.instance.r == self.instance.input_vars
|
| 147 |
+
r_expected = Matrix([self.e])
|
| 148 |
+
assert self.instance.r == r_expected
|
| 149 |
+
assert self.instance.input_vars == r_expected
|
| 150 |
+
assert isinstance(self.instance.r, Matrix)
|
| 151 |
+
assert isinstance(self.instance.input_vars, Matrix)
|
| 152 |
+
assert self.instance.r.shape == (1, 1)
|
| 153 |
+
assert self.instance.input_vars.shape == (1, 1)
|
| 154 |
+
|
| 155 |
+
def test_constants(self):
|
| 156 |
+
assert hasattr(self.instance, 'p')
|
| 157 |
+
assert hasattr(self.instance, 'constants')
|
| 158 |
+
assert self.instance.p == self.instance.constants
|
| 159 |
+
p_expected = Matrix(
|
| 160 |
+
[
|
| 161 |
+
self.l_T_slack,
|
| 162 |
+
self.F_M_max,
|
| 163 |
+
self.l_M_opt,
|
| 164 |
+
self.v_M_max,
|
| 165 |
+
self.alpha_opt,
|
| 166 |
+
self.beta,
|
| 167 |
+
self.tau_a,
|
| 168 |
+
self.tau_d,
|
| 169 |
+
self.b,
|
| 170 |
+
Symbol('c_0_fl_T_name'),
|
| 171 |
+
Symbol('c_1_fl_T_name'),
|
| 172 |
+
Symbol('c_2_fl_T_name'),
|
| 173 |
+
Symbol('c_3_fl_T_name'),
|
| 174 |
+
Symbol('c_0_fl_M_pas_name'),
|
| 175 |
+
Symbol('c_1_fl_M_pas_name'),
|
| 176 |
+
Symbol('c_0_fl_M_act_name'),
|
| 177 |
+
Symbol('c_1_fl_M_act_name'),
|
| 178 |
+
Symbol('c_2_fl_M_act_name'),
|
| 179 |
+
Symbol('c_3_fl_M_act_name'),
|
| 180 |
+
Symbol('c_4_fl_M_act_name'),
|
| 181 |
+
Symbol('c_5_fl_M_act_name'),
|
| 182 |
+
Symbol('c_6_fl_M_act_name'),
|
| 183 |
+
Symbol('c_7_fl_M_act_name'),
|
| 184 |
+
Symbol('c_8_fl_M_act_name'),
|
| 185 |
+
Symbol('c_9_fl_M_act_name'),
|
| 186 |
+
Symbol('c_10_fl_M_act_name'),
|
| 187 |
+
Symbol('c_11_fl_M_act_name'),
|
| 188 |
+
Symbol('c_0_fv_M_name'),
|
| 189 |
+
Symbol('c_1_fv_M_name'),
|
| 190 |
+
Symbol('c_2_fv_M_name'),
|
| 191 |
+
Symbol('c_3_fv_M_name'),
|
| 192 |
+
]
|
| 193 |
+
)
|
| 194 |
+
assert self.instance.p == p_expected
|
| 195 |
+
assert self.instance.constants == p_expected
|
| 196 |
+
assert isinstance(self.instance.p, Matrix)
|
| 197 |
+
assert isinstance(self.instance.constants, Matrix)
|
| 198 |
+
assert self.instance.p.shape == (31, 1)
|
| 199 |
+
assert self.instance.constants.shape == (31, 1)
|
| 200 |
+
|
| 201 |
+
def test_M(self):
|
| 202 |
+
assert hasattr(self.instance, 'M')
|
| 203 |
+
M_expected = Matrix([1])
|
| 204 |
+
assert self.instance.M == M_expected
|
| 205 |
+
assert isinstance(self.instance.M, Matrix)
|
| 206 |
+
assert self.instance.M.shape == (1, 1)
|
| 207 |
+
|
| 208 |
+
def test_F(self):
|
| 209 |
+
assert hasattr(self.instance, 'F')
|
| 210 |
+
F_expected = Matrix([self.da_expr])
|
| 211 |
+
assert self.instance.F == F_expected
|
| 212 |
+
assert isinstance(self.instance.F, Matrix)
|
| 213 |
+
assert self.instance.F.shape == (1, 1)
|
| 214 |
+
|
| 215 |
+
def test_rhs(self):
|
| 216 |
+
assert hasattr(self.instance, 'rhs')
|
| 217 |
+
rhs_expected = Matrix([self.da_expr])
|
| 218 |
+
rhs = self.instance.rhs()
|
| 219 |
+
assert isinstance(rhs, Matrix)
|
| 220 |
+
assert rhs.shape == (1, 1)
|
| 221 |
+
assert simplify(rhs - rhs_expected) == zeros(1)
|
| 222 |
+
|
| 223 |
+
|
| 224 |
+
@pytest.mark.parametrize(
|
| 225 |
+
'musculotendon_concrete, curve',
|
| 226 |
+
[
|
| 227 |
+
(
|
| 228 |
+
MusculotendonDeGroote2016,
|
| 229 |
+
CharacteristicCurveCollection(
|
| 230 |
+
tendon_force_length=TendonForceLengthDeGroote2016,
|
| 231 |
+
tendon_force_length_inverse=TendonForceLengthInverseDeGroote2016,
|
| 232 |
+
fiber_force_length_passive=FiberForceLengthPassiveDeGroote2016,
|
| 233 |
+
fiber_force_length_passive_inverse=FiberForceLengthPassiveInverseDeGroote2016,
|
| 234 |
+
fiber_force_length_active=FiberForceLengthActiveDeGroote2016,
|
| 235 |
+
fiber_force_velocity=FiberForceVelocityDeGroote2016,
|
| 236 |
+
fiber_force_velocity_inverse=FiberForceVelocityInverseDeGroote2016,
|
| 237 |
+
),
|
| 238 |
+
)
|
| 239 |
+
],
|
| 240 |
+
)
|
| 241 |
+
class TestFiberLengthExplicit:
|
| 242 |
+
|
| 243 |
+
@pytest.fixture(autouse=True)
|
| 244 |
+
def _musculotendon_fiber_length_explicit_fixture(
|
| 245 |
+
self,
|
| 246 |
+
musculotendon_concrete,
|
| 247 |
+
curve,
|
| 248 |
+
):
|
| 249 |
+
self.name = 'name'
|
| 250 |
+
self.N = ReferenceFrame('N')
|
| 251 |
+
self.q = dynamicsymbols('q')
|
| 252 |
+
self.origin = Point('pO')
|
| 253 |
+
self.insertion = Point('pI')
|
| 254 |
+
self.insertion.set_pos(self.origin, self.q*self.N.x)
|
| 255 |
+
self.pathway = LinearPathway(self.origin, self.insertion)
|
| 256 |
+
self.activation = FirstOrderActivationDeGroote2016(self.name)
|
| 257 |
+
self.e = self.activation.excitation
|
| 258 |
+
self.a = self.activation.activation
|
| 259 |
+
self.tau_a = self.activation.activation_time_constant
|
| 260 |
+
self.tau_d = self.activation.deactivation_time_constant
|
| 261 |
+
self.b = self.activation.smoothing_rate
|
| 262 |
+
self.formulation = MusculotendonFormulation.FIBER_LENGTH_EXPLICIT
|
| 263 |
+
self.l_T_slack = Symbol('l_T_slack')
|
| 264 |
+
self.F_M_max = Symbol('F_M_max')
|
| 265 |
+
self.l_M_opt = Symbol('l_M_opt')
|
| 266 |
+
self.v_M_max = Symbol('v_M_max')
|
| 267 |
+
self.alpha_opt = Symbol('alpha_opt')
|
| 268 |
+
self.beta = Symbol('beta')
|
| 269 |
+
self.instance = musculotendon_concrete(
|
| 270 |
+
self.name,
|
| 271 |
+
self.pathway,
|
| 272 |
+
self.activation,
|
| 273 |
+
musculotendon_dynamics=self.formulation,
|
| 274 |
+
tendon_slack_length=self.l_T_slack,
|
| 275 |
+
peak_isometric_force=self.F_M_max,
|
| 276 |
+
optimal_fiber_length=self.l_M_opt,
|
| 277 |
+
maximal_fiber_velocity=self.v_M_max,
|
| 278 |
+
optimal_pennation_angle=self.alpha_opt,
|
| 279 |
+
fiber_damping_coefficient=self.beta,
|
| 280 |
+
with_defaults=True,
|
| 281 |
+
)
|
| 282 |
+
self.l_M_tilde = dynamicsymbols('l_M_tilde_name')
|
| 283 |
+
l_MT = self.pathway.length
|
| 284 |
+
l_M = self.l_M_tilde*self.l_M_opt
|
| 285 |
+
l_T = l_MT - sqrt(l_M**2 - (self.l_M_opt*sin(self.alpha_opt))**2)
|
| 286 |
+
fl_T = curve.tendon_force_length.with_defaults(l_T/self.l_T_slack)
|
| 287 |
+
fl_M_pas = curve.fiber_force_length_passive.with_defaults(self.l_M_tilde)
|
| 288 |
+
fl_M_act = curve.fiber_force_length_active.with_defaults(self.l_M_tilde)
|
| 289 |
+
v_M_tilde = curve.fiber_force_velocity_inverse.with_defaults(
|
| 290 |
+
((((fl_T*self.F_M_max)/((l_MT - l_T)/l_M))/self.F_M_max) - fl_M_pas)
|
| 291 |
+
/(self.a*fl_M_act)
|
| 292 |
+
)
|
| 293 |
+
self.dl_M_tilde_expr = (self.v_M_max/self.l_M_opt)*v_M_tilde
|
| 294 |
+
self.da_expr = (
|
| 295 |
+
(1/(self.tau_a*(Rational(1, 2) + Rational(3, 2)*self.a)))
|
| 296 |
+
*(Rational(1, 2) + Rational(1, 2)*tanh(self.b*(self.e - self.a)))
|
| 297 |
+
+ ((Rational(1, 2) + Rational(3, 2)*self.a)/self.tau_d)
|
| 298 |
+
*(Rational(1, 2) - Rational(1, 2)*tanh(self.b*(self.e - self.a)))
|
| 299 |
+
)*(self.e - self.a)
|
| 300 |
+
|
| 301 |
+
def test_state_vars(self):
|
| 302 |
+
assert hasattr(self.instance, 'x')
|
| 303 |
+
assert hasattr(self.instance, 'state_vars')
|
| 304 |
+
assert self.instance.x == self.instance.state_vars
|
| 305 |
+
x_expected = Matrix([self.l_M_tilde, self.a])
|
| 306 |
+
assert self.instance.x == x_expected
|
| 307 |
+
assert self.instance.state_vars == x_expected
|
| 308 |
+
assert isinstance(self.instance.x, Matrix)
|
| 309 |
+
assert isinstance(self.instance.state_vars, Matrix)
|
| 310 |
+
assert self.instance.x.shape == (2, 1)
|
| 311 |
+
assert self.instance.state_vars.shape == (2, 1)
|
| 312 |
+
|
| 313 |
+
def test_input_vars(self):
|
| 314 |
+
assert hasattr(self.instance, 'r')
|
| 315 |
+
assert hasattr(self.instance, 'input_vars')
|
| 316 |
+
assert self.instance.r == self.instance.input_vars
|
| 317 |
+
r_expected = Matrix([self.e])
|
| 318 |
+
assert self.instance.r == r_expected
|
| 319 |
+
assert self.instance.input_vars == r_expected
|
| 320 |
+
assert isinstance(self.instance.r, Matrix)
|
| 321 |
+
assert isinstance(self.instance.input_vars, Matrix)
|
| 322 |
+
assert self.instance.r.shape == (1, 1)
|
| 323 |
+
assert self.instance.input_vars.shape == (1, 1)
|
| 324 |
+
|
| 325 |
+
def test_constants(self):
|
| 326 |
+
assert hasattr(self.instance, 'p')
|
| 327 |
+
assert hasattr(self.instance, 'constants')
|
| 328 |
+
assert self.instance.p == self.instance.constants
|
| 329 |
+
p_expected = Matrix(
|
| 330 |
+
[
|
| 331 |
+
self.l_T_slack,
|
| 332 |
+
self.F_M_max,
|
| 333 |
+
self.l_M_opt,
|
| 334 |
+
self.v_M_max,
|
| 335 |
+
self.alpha_opt,
|
| 336 |
+
self.beta,
|
| 337 |
+
self.tau_a,
|
| 338 |
+
self.tau_d,
|
| 339 |
+
self.b,
|
| 340 |
+
]
|
| 341 |
+
)
|
| 342 |
+
assert self.instance.p == p_expected
|
| 343 |
+
assert self.instance.constants == p_expected
|
| 344 |
+
assert isinstance(self.instance.p, Matrix)
|
| 345 |
+
assert isinstance(self.instance.constants, Matrix)
|
| 346 |
+
assert self.instance.p.shape == (9, 1)
|
| 347 |
+
assert self.instance.constants.shape == (9, 1)
|
| 348 |
+
|
| 349 |
+
def test_M(self):
|
| 350 |
+
assert hasattr(self.instance, 'M')
|
| 351 |
+
M_expected = eye(2)
|
| 352 |
+
assert self.instance.M == M_expected
|
| 353 |
+
assert isinstance(self.instance.M, Matrix)
|
| 354 |
+
assert self.instance.M.shape == (2, 2)
|
| 355 |
+
|
| 356 |
+
def test_F(self):
|
| 357 |
+
assert hasattr(self.instance, 'F')
|
| 358 |
+
F_expected = Matrix([self.dl_M_tilde_expr, self.da_expr])
|
| 359 |
+
assert self.instance.F == F_expected
|
| 360 |
+
assert isinstance(self.instance.F, Matrix)
|
| 361 |
+
assert self.instance.F.shape == (2, 1)
|
| 362 |
+
|
| 363 |
+
def test_rhs(self):
|
| 364 |
+
assert hasattr(self.instance, 'rhs')
|
| 365 |
+
rhs_expected = Matrix([self.dl_M_tilde_expr, self.da_expr])
|
| 366 |
+
rhs = self.instance.rhs()
|
| 367 |
+
assert isinstance(rhs, Matrix)
|
| 368 |
+
assert rhs.shape == (2, 1)
|
| 369 |
+
assert simplify(rhs - rhs_expected) == zeros(2, 1)
|
| 370 |
+
|
| 371 |
+
|
| 372 |
+
@pytest.mark.parametrize(
|
| 373 |
+
'musculotendon_concrete, curve',
|
| 374 |
+
[
|
| 375 |
+
(
|
| 376 |
+
MusculotendonDeGroote2016,
|
| 377 |
+
CharacteristicCurveCollection(
|
| 378 |
+
tendon_force_length=TendonForceLengthDeGroote2016,
|
| 379 |
+
tendon_force_length_inverse=TendonForceLengthInverseDeGroote2016,
|
| 380 |
+
fiber_force_length_passive=FiberForceLengthPassiveDeGroote2016,
|
| 381 |
+
fiber_force_length_passive_inverse=FiberForceLengthPassiveInverseDeGroote2016,
|
| 382 |
+
fiber_force_length_active=FiberForceLengthActiveDeGroote2016,
|
| 383 |
+
fiber_force_velocity=FiberForceVelocityDeGroote2016,
|
| 384 |
+
fiber_force_velocity_inverse=FiberForceVelocityInverseDeGroote2016,
|
| 385 |
+
),
|
| 386 |
+
)
|
| 387 |
+
],
|
| 388 |
+
)
|
| 389 |
+
class TestTendonForceExplicit:
|
| 390 |
+
|
| 391 |
+
@pytest.fixture(autouse=True)
|
| 392 |
+
def _musculotendon_tendon_force_explicit_fixture(
|
| 393 |
+
self,
|
| 394 |
+
musculotendon_concrete,
|
| 395 |
+
curve,
|
| 396 |
+
):
|
| 397 |
+
self.name = 'name'
|
| 398 |
+
self.N = ReferenceFrame('N')
|
| 399 |
+
self.q = dynamicsymbols('q')
|
| 400 |
+
self.origin = Point('pO')
|
| 401 |
+
self.insertion = Point('pI')
|
| 402 |
+
self.insertion.set_pos(self.origin, self.q*self.N.x)
|
| 403 |
+
self.pathway = LinearPathway(self.origin, self.insertion)
|
| 404 |
+
self.activation = FirstOrderActivationDeGroote2016(self.name)
|
| 405 |
+
self.e = self.activation.excitation
|
| 406 |
+
self.a = self.activation.activation
|
| 407 |
+
self.tau_a = self.activation.activation_time_constant
|
| 408 |
+
self.tau_d = self.activation.deactivation_time_constant
|
| 409 |
+
self.b = self.activation.smoothing_rate
|
| 410 |
+
self.formulation = MusculotendonFormulation.TENDON_FORCE_EXPLICIT
|
| 411 |
+
self.l_T_slack = Symbol('l_T_slack')
|
| 412 |
+
self.F_M_max = Symbol('F_M_max')
|
| 413 |
+
self.l_M_opt = Symbol('l_M_opt')
|
| 414 |
+
self.v_M_max = Symbol('v_M_max')
|
| 415 |
+
self.alpha_opt = Symbol('alpha_opt')
|
| 416 |
+
self.beta = Symbol('beta')
|
| 417 |
+
self.instance = musculotendon_concrete(
|
| 418 |
+
self.name,
|
| 419 |
+
self.pathway,
|
| 420 |
+
self.activation,
|
| 421 |
+
musculotendon_dynamics=self.formulation,
|
| 422 |
+
tendon_slack_length=self.l_T_slack,
|
| 423 |
+
peak_isometric_force=self.F_M_max,
|
| 424 |
+
optimal_fiber_length=self.l_M_opt,
|
| 425 |
+
maximal_fiber_velocity=self.v_M_max,
|
| 426 |
+
optimal_pennation_angle=self.alpha_opt,
|
| 427 |
+
fiber_damping_coefficient=self.beta,
|
| 428 |
+
with_defaults=True,
|
| 429 |
+
)
|
| 430 |
+
self.F_T_tilde = dynamicsymbols('F_T_tilde_name')
|
| 431 |
+
l_T_tilde = curve.tendon_force_length_inverse.with_defaults(self.F_T_tilde)
|
| 432 |
+
l_MT = self.pathway.length
|
| 433 |
+
v_MT = self.pathway.extension_velocity
|
| 434 |
+
l_T = l_T_tilde*self.l_T_slack
|
| 435 |
+
l_M = sqrt((l_MT - l_T)**2 + (self.l_M_opt*sin(self.alpha_opt))**2)
|
| 436 |
+
l_M_tilde = l_M/self.l_M_opt
|
| 437 |
+
cos_alpha = (l_MT - l_T)/l_M
|
| 438 |
+
F_T = self.F_T_tilde*self.F_M_max
|
| 439 |
+
F_M = F_T/cos_alpha
|
| 440 |
+
F_M_tilde = F_M/self.F_M_max
|
| 441 |
+
fl_M_pas = curve.fiber_force_length_passive.with_defaults(l_M_tilde)
|
| 442 |
+
fl_M_act = curve.fiber_force_length_active.with_defaults(l_M_tilde)
|
| 443 |
+
fv_M = (F_M_tilde - fl_M_pas)/(self.a*fl_M_act)
|
| 444 |
+
v_M_tilde = curve.fiber_force_velocity_inverse.with_defaults(fv_M)
|
| 445 |
+
v_M = v_M_tilde*self.v_M_max
|
| 446 |
+
v_T = v_MT - v_M/cos_alpha
|
| 447 |
+
v_T_tilde = v_T/self.l_T_slack
|
| 448 |
+
self.dF_T_tilde_expr = (
|
| 449 |
+
Float('0.2')*Float('33.93669377311689')*exp(
|
| 450 |
+
Float('33.93669377311689')*UnevaluatedExpr(l_T_tilde - Float('0.995'))
|
| 451 |
+
)*v_T_tilde
|
| 452 |
+
)
|
| 453 |
+
self.da_expr = (
|
| 454 |
+
(1/(self.tau_a*(Rational(1, 2) + Rational(3, 2)*self.a)))
|
| 455 |
+
*(Rational(1, 2) + Rational(1, 2)*tanh(self.b*(self.e - self.a)))
|
| 456 |
+
+ ((Rational(1, 2) + Rational(3, 2)*self.a)/self.tau_d)
|
| 457 |
+
*(Rational(1, 2) - Rational(1, 2)*tanh(self.b*(self.e - self.a)))
|
| 458 |
+
)*(self.e - self.a)
|
| 459 |
+
|
| 460 |
+
def test_state_vars(self):
|
| 461 |
+
assert hasattr(self.instance, 'x')
|
| 462 |
+
assert hasattr(self.instance, 'state_vars')
|
| 463 |
+
assert self.instance.x == self.instance.state_vars
|
| 464 |
+
x_expected = Matrix([self.F_T_tilde, self.a])
|
| 465 |
+
assert self.instance.x == x_expected
|
| 466 |
+
assert self.instance.state_vars == x_expected
|
| 467 |
+
assert isinstance(self.instance.x, Matrix)
|
| 468 |
+
assert isinstance(self.instance.state_vars, Matrix)
|
| 469 |
+
assert self.instance.x.shape == (2, 1)
|
| 470 |
+
assert self.instance.state_vars.shape == (2, 1)
|
| 471 |
+
|
| 472 |
+
def test_input_vars(self):
|
| 473 |
+
assert hasattr(self.instance, 'r')
|
| 474 |
+
assert hasattr(self.instance, 'input_vars')
|
| 475 |
+
assert self.instance.r == self.instance.input_vars
|
| 476 |
+
r_expected = Matrix([self.e])
|
| 477 |
+
assert self.instance.r == r_expected
|
| 478 |
+
assert self.instance.input_vars == r_expected
|
| 479 |
+
assert isinstance(self.instance.r, Matrix)
|
| 480 |
+
assert isinstance(self.instance.input_vars, Matrix)
|
| 481 |
+
assert self.instance.r.shape == (1, 1)
|
| 482 |
+
assert self.instance.input_vars.shape == (1, 1)
|
| 483 |
+
|
| 484 |
+
def test_constants(self):
|
| 485 |
+
assert hasattr(self.instance, 'p')
|
| 486 |
+
assert hasattr(self.instance, 'constants')
|
| 487 |
+
assert self.instance.p == self.instance.constants
|
| 488 |
+
p_expected = Matrix(
|
| 489 |
+
[
|
| 490 |
+
self.l_T_slack,
|
| 491 |
+
self.F_M_max,
|
| 492 |
+
self.l_M_opt,
|
| 493 |
+
self.v_M_max,
|
| 494 |
+
self.alpha_opt,
|
| 495 |
+
self.beta,
|
| 496 |
+
self.tau_a,
|
| 497 |
+
self.tau_d,
|
| 498 |
+
self.b,
|
| 499 |
+
]
|
| 500 |
+
)
|
| 501 |
+
assert self.instance.p == p_expected
|
| 502 |
+
assert self.instance.constants == p_expected
|
| 503 |
+
assert isinstance(self.instance.p, Matrix)
|
| 504 |
+
assert isinstance(self.instance.constants, Matrix)
|
| 505 |
+
assert self.instance.p.shape == (9, 1)
|
| 506 |
+
assert self.instance.constants.shape == (9, 1)
|
| 507 |
+
|
| 508 |
+
def test_M(self):
|
| 509 |
+
assert hasattr(self.instance, 'M')
|
| 510 |
+
M_expected = eye(2)
|
| 511 |
+
assert self.instance.M == M_expected
|
| 512 |
+
assert isinstance(self.instance.M, Matrix)
|
| 513 |
+
assert self.instance.M.shape == (2, 2)
|
| 514 |
+
|
| 515 |
+
def test_F(self):
|
| 516 |
+
assert hasattr(self.instance, 'F')
|
| 517 |
+
F_expected = Matrix([self.dF_T_tilde_expr, self.da_expr])
|
| 518 |
+
assert self.instance.F == F_expected
|
| 519 |
+
assert isinstance(self.instance.F, Matrix)
|
| 520 |
+
assert self.instance.F.shape == (2, 1)
|
| 521 |
+
|
| 522 |
+
def test_rhs(self):
|
| 523 |
+
assert hasattr(self.instance, 'rhs')
|
| 524 |
+
rhs_expected = Matrix([self.dF_T_tilde_expr, self.da_expr])
|
| 525 |
+
rhs = self.instance.rhs()
|
| 526 |
+
assert isinstance(rhs, Matrix)
|
| 527 |
+
assert rhs.shape == (2, 1)
|
| 528 |
+
assert simplify(rhs - rhs_expected) == zeros(2, 1)
|
| 529 |
+
|
| 530 |
+
|
| 531 |
+
class TestMusculotendonDeGroote2016:
|
| 532 |
+
|
| 533 |
+
@staticmethod
|
| 534 |
+
def test_class():
|
| 535 |
+
assert issubclass(MusculotendonDeGroote2016, ForceActuator)
|
| 536 |
+
assert issubclass(MusculotendonDeGroote2016, _NamedMixin)
|
| 537 |
+
assert MusculotendonDeGroote2016.__name__ == 'MusculotendonDeGroote2016'
|
| 538 |
+
|
| 539 |
+
@staticmethod
|
| 540 |
+
def test_instance():
|
| 541 |
+
origin = Point('pO')
|
| 542 |
+
insertion = Point('pI')
|
| 543 |
+
insertion.set_pos(origin, dynamicsymbols('q')*ReferenceFrame('N').x)
|
| 544 |
+
pathway = LinearPathway(origin, insertion)
|
| 545 |
+
activation = FirstOrderActivationDeGroote2016('name')
|
| 546 |
+
l_T_slack = Symbol('l_T_slack')
|
| 547 |
+
F_M_max = Symbol('F_M_max')
|
| 548 |
+
l_M_opt = Symbol('l_M_opt')
|
| 549 |
+
v_M_max = Symbol('v_M_max')
|
| 550 |
+
alpha_opt = Symbol('alpha_opt')
|
| 551 |
+
beta = Symbol('beta')
|
| 552 |
+
instance = MusculotendonDeGroote2016(
|
| 553 |
+
'name',
|
| 554 |
+
pathway,
|
| 555 |
+
activation,
|
| 556 |
+
musculotendon_dynamics=MusculotendonFormulation.RIGID_TENDON,
|
| 557 |
+
tendon_slack_length=l_T_slack,
|
| 558 |
+
peak_isometric_force=F_M_max,
|
| 559 |
+
optimal_fiber_length=l_M_opt,
|
| 560 |
+
maximal_fiber_velocity=v_M_max,
|
| 561 |
+
optimal_pennation_angle=alpha_opt,
|
| 562 |
+
fiber_damping_coefficient=beta,
|
| 563 |
+
)
|
| 564 |
+
assert isinstance(instance, MusculotendonDeGroote2016)
|
| 565 |
+
|
| 566 |
+
@pytest.fixture(autouse=True)
|
| 567 |
+
def _musculotendon_fixture(self):
|
| 568 |
+
self.name = 'name'
|
| 569 |
+
self.N = ReferenceFrame('N')
|
| 570 |
+
self.q = dynamicsymbols('q')
|
| 571 |
+
self.origin = Point('pO')
|
| 572 |
+
self.insertion = Point('pI')
|
| 573 |
+
self.insertion.set_pos(self.origin, self.q*self.N.x)
|
| 574 |
+
self.pathway = LinearPathway(self.origin, self.insertion)
|
| 575 |
+
self.activation = FirstOrderActivationDeGroote2016(self.name)
|
| 576 |
+
self.l_T_slack = Symbol('l_T_slack')
|
| 577 |
+
self.F_M_max = Symbol('F_M_max')
|
| 578 |
+
self.l_M_opt = Symbol('l_M_opt')
|
| 579 |
+
self.v_M_max = Symbol('v_M_max')
|
| 580 |
+
self.alpha_opt = Symbol('alpha_opt')
|
| 581 |
+
self.beta = Symbol('beta')
|
| 582 |
+
|
| 583 |
+
def test_with_defaults(self):
|
| 584 |
+
origin = Point('pO')
|
| 585 |
+
insertion = Point('pI')
|
| 586 |
+
insertion.set_pos(origin, dynamicsymbols('q')*ReferenceFrame('N').x)
|
| 587 |
+
pathway = LinearPathway(origin, insertion)
|
| 588 |
+
activation = FirstOrderActivationDeGroote2016('name')
|
| 589 |
+
l_T_slack = Symbol('l_T_slack')
|
| 590 |
+
F_M_max = Symbol('F_M_max')
|
| 591 |
+
l_M_opt = Symbol('l_M_opt')
|
| 592 |
+
v_M_max = Float('10.0')
|
| 593 |
+
alpha_opt = Float('0.0')
|
| 594 |
+
beta = Float('0.1')
|
| 595 |
+
instance = MusculotendonDeGroote2016.with_defaults(
|
| 596 |
+
'name',
|
| 597 |
+
pathway,
|
| 598 |
+
activation,
|
| 599 |
+
musculotendon_dynamics=MusculotendonFormulation.RIGID_TENDON,
|
| 600 |
+
tendon_slack_length=l_T_slack,
|
| 601 |
+
peak_isometric_force=F_M_max,
|
| 602 |
+
optimal_fiber_length=l_M_opt,
|
| 603 |
+
)
|
| 604 |
+
assert instance.tendon_slack_length == l_T_slack
|
| 605 |
+
assert instance.peak_isometric_force == F_M_max
|
| 606 |
+
assert instance.optimal_fiber_length == l_M_opt
|
| 607 |
+
assert instance.maximal_fiber_velocity == v_M_max
|
| 608 |
+
assert instance.optimal_pennation_angle == alpha_opt
|
| 609 |
+
assert instance.fiber_damping_coefficient == beta
|
| 610 |
+
|
| 611 |
+
@pytest.mark.parametrize(
|
| 612 |
+
'l_T_slack, expected',
|
| 613 |
+
[
|
| 614 |
+
(None, Symbol('l_T_slack_name')),
|
| 615 |
+
(Symbol('l_T_slack'), Symbol('l_T_slack')),
|
| 616 |
+
(Rational(1, 2), Rational(1, 2)),
|
| 617 |
+
(Float('0.5'), Float('0.5')),
|
| 618 |
+
],
|
| 619 |
+
)
|
| 620 |
+
def test_tendon_slack_length(self, l_T_slack, expected):
|
| 621 |
+
instance = MusculotendonDeGroote2016(
|
| 622 |
+
self.name,
|
| 623 |
+
self.pathway,
|
| 624 |
+
self.activation,
|
| 625 |
+
musculotendon_dynamics=MusculotendonFormulation.RIGID_TENDON,
|
| 626 |
+
tendon_slack_length=l_T_slack,
|
| 627 |
+
peak_isometric_force=self.F_M_max,
|
| 628 |
+
optimal_fiber_length=self.l_M_opt,
|
| 629 |
+
maximal_fiber_velocity=self.v_M_max,
|
| 630 |
+
optimal_pennation_angle=self.alpha_opt,
|
| 631 |
+
fiber_damping_coefficient=self.beta,
|
| 632 |
+
)
|
| 633 |
+
assert instance.l_T_slack == expected
|
| 634 |
+
assert instance.tendon_slack_length == expected
|
| 635 |
+
|
| 636 |
+
@pytest.mark.parametrize(
|
| 637 |
+
'F_M_max, expected',
|
| 638 |
+
[
|
| 639 |
+
(None, Symbol('F_M_max_name')),
|
| 640 |
+
(Symbol('F_M_max'), Symbol('F_M_max')),
|
| 641 |
+
(Integer(1000), Integer(1000)),
|
| 642 |
+
(Float('1000.0'), Float('1000.0')),
|
| 643 |
+
],
|
| 644 |
+
)
|
| 645 |
+
def test_peak_isometric_force(self, F_M_max, expected):
|
| 646 |
+
instance = MusculotendonDeGroote2016(
|
| 647 |
+
self.name,
|
| 648 |
+
self.pathway,
|
| 649 |
+
self.activation,
|
| 650 |
+
musculotendon_dynamics=MusculotendonFormulation.RIGID_TENDON,
|
| 651 |
+
tendon_slack_length=self.l_T_slack,
|
| 652 |
+
peak_isometric_force=F_M_max,
|
| 653 |
+
optimal_fiber_length=self.l_M_opt,
|
| 654 |
+
maximal_fiber_velocity=self.v_M_max,
|
| 655 |
+
optimal_pennation_angle=self.alpha_opt,
|
| 656 |
+
fiber_damping_coefficient=self.beta,
|
| 657 |
+
)
|
| 658 |
+
assert instance.F_M_max == expected
|
| 659 |
+
assert instance.peak_isometric_force == expected
|
| 660 |
+
|
| 661 |
+
@pytest.mark.parametrize(
|
| 662 |
+
'l_M_opt, expected',
|
| 663 |
+
[
|
| 664 |
+
(None, Symbol('l_M_opt_name')),
|
| 665 |
+
(Symbol('l_M_opt'), Symbol('l_M_opt')),
|
| 666 |
+
(Rational(1, 2), Rational(1, 2)),
|
| 667 |
+
(Float('0.5'), Float('0.5')),
|
| 668 |
+
],
|
| 669 |
+
)
|
| 670 |
+
def test_optimal_fiber_length(self, l_M_opt, expected):
|
| 671 |
+
instance = MusculotendonDeGroote2016(
|
| 672 |
+
self.name,
|
| 673 |
+
self.pathway,
|
| 674 |
+
self.activation,
|
| 675 |
+
musculotendon_dynamics=MusculotendonFormulation.RIGID_TENDON,
|
| 676 |
+
tendon_slack_length=self.l_T_slack,
|
| 677 |
+
peak_isometric_force=self.F_M_max,
|
| 678 |
+
optimal_fiber_length=l_M_opt,
|
| 679 |
+
maximal_fiber_velocity=self.v_M_max,
|
| 680 |
+
optimal_pennation_angle=self.alpha_opt,
|
| 681 |
+
fiber_damping_coefficient=self.beta,
|
| 682 |
+
)
|
| 683 |
+
assert instance.l_M_opt == expected
|
| 684 |
+
assert instance.optimal_fiber_length == expected
|
| 685 |
+
|
| 686 |
+
@pytest.mark.parametrize(
|
| 687 |
+
'v_M_max, expected',
|
| 688 |
+
[
|
| 689 |
+
(None, Symbol('v_M_max_name')),
|
| 690 |
+
(Symbol('v_M_max'), Symbol('v_M_max')),
|
| 691 |
+
(Integer(10), Integer(10)),
|
| 692 |
+
(Float('10.0'), Float('10.0')),
|
| 693 |
+
],
|
| 694 |
+
)
|
| 695 |
+
def test_maximal_fiber_velocity(self, v_M_max, expected):
|
| 696 |
+
instance = MusculotendonDeGroote2016(
|
| 697 |
+
self.name,
|
| 698 |
+
self.pathway,
|
| 699 |
+
self.activation,
|
| 700 |
+
musculotendon_dynamics=MusculotendonFormulation.RIGID_TENDON,
|
| 701 |
+
tendon_slack_length=self.l_T_slack,
|
| 702 |
+
peak_isometric_force=self.F_M_max,
|
| 703 |
+
optimal_fiber_length=self.l_M_opt,
|
| 704 |
+
maximal_fiber_velocity=v_M_max,
|
| 705 |
+
optimal_pennation_angle=self.alpha_opt,
|
| 706 |
+
fiber_damping_coefficient=self.beta,
|
| 707 |
+
)
|
| 708 |
+
assert instance.v_M_max == expected
|
| 709 |
+
assert instance.maximal_fiber_velocity == expected
|
| 710 |
+
|
| 711 |
+
@pytest.mark.parametrize(
|
| 712 |
+
'alpha_opt, expected',
|
| 713 |
+
[
|
| 714 |
+
(None, Symbol('alpha_opt_name')),
|
| 715 |
+
(Symbol('alpha_opt'), Symbol('alpha_opt')),
|
| 716 |
+
(Integer(0), Integer(0)),
|
| 717 |
+
(Float('0.1'), Float('0.1')),
|
| 718 |
+
],
|
| 719 |
+
)
|
| 720 |
+
def test_optimal_pennation_angle(self, alpha_opt, expected):
|
| 721 |
+
instance = MusculotendonDeGroote2016(
|
| 722 |
+
self.name,
|
| 723 |
+
self.pathway,
|
| 724 |
+
self.activation,
|
| 725 |
+
musculotendon_dynamics=MusculotendonFormulation.RIGID_TENDON,
|
| 726 |
+
tendon_slack_length=self.l_T_slack,
|
| 727 |
+
peak_isometric_force=self.F_M_max,
|
| 728 |
+
optimal_fiber_length=self.l_M_opt,
|
| 729 |
+
maximal_fiber_velocity=self.v_M_max,
|
| 730 |
+
optimal_pennation_angle=alpha_opt,
|
| 731 |
+
fiber_damping_coefficient=self.beta,
|
| 732 |
+
)
|
| 733 |
+
assert instance.alpha_opt == expected
|
| 734 |
+
assert instance.optimal_pennation_angle == expected
|
| 735 |
+
|
| 736 |
+
@pytest.mark.parametrize(
|
| 737 |
+
'beta, expected',
|
| 738 |
+
[
|
| 739 |
+
(None, Symbol('beta_name')),
|
| 740 |
+
(Symbol('beta'), Symbol('beta')),
|
| 741 |
+
(Integer(0), Integer(0)),
|
| 742 |
+
(Rational(1, 10), Rational(1, 10)),
|
| 743 |
+
(Float('0.1'), Float('0.1')),
|
| 744 |
+
],
|
| 745 |
+
)
|
| 746 |
+
def test_fiber_damping_coefficient(self, beta, expected):
|
| 747 |
+
instance = MusculotendonDeGroote2016(
|
| 748 |
+
self.name,
|
| 749 |
+
self.pathway,
|
| 750 |
+
self.activation,
|
| 751 |
+
musculotendon_dynamics=MusculotendonFormulation.RIGID_TENDON,
|
| 752 |
+
tendon_slack_length=self.l_T_slack,
|
| 753 |
+
peak_isometric_force=self.F_M_max,
|
| 754 |
+
optimal_fiber_length=self.l_M_opt,
|
| 755 |
+
maximal_fiber_velocity=self.v_M_max,
|
| 756 |
+
optimal_pennation_angle=self.alpha_opt,
|
| 757 |
+
fiber_damping_coefficient=beta,
|
| 758 |
+
)
|
| 759 |
+
assert instance.beta == expected
|
| 760 |
+
assert instance.fiber_damping_coefficient == expected
|
| 761 |
+
|
| 762 |
+
def test_excitation(self):
|
| 763 |
+
instance = MusculotendonDeGroote2016(
|
| 764 |
+
self.name,
|
| 765 |
+
self.pathway,
|
| 766 |
+
self.activation,
|
| 767 |
+
)
|
| 768 |
+
assert hasattr(instance, 'e')
|
| 769 |
+
assert hasattr(instance, 'excitation')
|
| 770 |
+
e_expected = dynamicsymbols('e_name')
|
| 771 |
+
assert instance.e == e_expected
|
| 772 |
+
assert instance.excitation == e_expected
|
| 773 |
+
assert instance.e is instance.excitation
|
| 774 |
+
|
| 775 |
+
def test_excitation_is_immutable(self):
|
| 776 |
+
instance = MusculotendonDeGroote2016(
|
| 777 |
+
self.name,
|
| 778 |
+
self.pathway,
|
| 779 |
+
self.activation,
|
| 780 |
+
)
|
| 781 |
+
with pytest.raises(AttributeError):
|
| 782 |
+
instance.e = None
|
| 783 |
+
with pytest.raises(AttributeError):
|
| 784 |
+
instance.excitation = None
|
| 785 |
+
|
| 786 |
+
def test_activation(self):
|
| 787 |
+
instance = MusculotendonDeGroote2016(
|
| 788 |
+
self.name,
|
| 789 |
+
self.pathway,
|
| 790 |
+
self.activation,
|
| 791 |
+
)
|
| 792 |
+
assert hasattr(instance, 'a')
|
| 793 |
+
assert hasattr(instance, 'activation')
|
| 794 |
+
a_expected = dynamicsymbols('a_name')
|
| 795 |
+
assert instance.a == a_expected
|
| 796 |
+
assert instance.activation == a_expected
|
| 797 |
+
|
| 798 |
+
def test_activation_is_immutable(self):
|
| 799 |
+
instance = MusculotendonDeGroote2016(
|
| 800 |
+
self.name,
|
| 801 |
+
self.pathway,
|
| 802 |
+
self.activation,
|
| 803 |
+
)
|
| 804 |
+
with pytest.raises(AttributeError):
|
| 805 |
+
instance.a = None
|
| 806 |
+
with pytest.raises(AttributeError):
|
| 807 |
+
instance.activation = None
|
| 808 |
+
|
| 809 |
+
def test_repr(self):
|
| 810 |
+
instance = MusculotendonDeGroote2016(
|
| 811 |
+
self.name,
|
| 812 |
+
self.pathway,
|
| 813 |
+
self.activation,
|
| 814 |
+
musculotendon_dynamics=MusculotendonFormulation.RIGID_TENDON,
|
| 815 |
+
tendon_slack_length=self.l_T_slack,
|
| 816 |
+
peak_isometric_force=self.F_M_max,
|
| 817 |
+
optimal_fiber_length=self.l_M_opt,
|
| 818 |
+
maximal_fiber_velocity=self.v_M_max,
|
| 819 |
+
optimal_pennation_angle=self.alpha_opt,
|
| 820 |
+
fiber_damping_coefficient=self.beta,
|
| 821 |
+
)
|
| 822 |
+
expected = (
|
| 823 |
+
'MusculotendonDeGroote2016(\'name\', '
|
| 824 |
+
'pathway=LinearPathway(pO, pI), '
|
| 825 |
+
'activation_dynamics=FirstOrderActivationDeGroote2016(\'name\', '
|
| 826 |
+
'activation_time_constant=tau_a_name, '
|
| 827 |
+
'deactivation_time_constant=tau_d_name, '
|
| 828 |
+
'smoothing_rate=b_name), '
|
| 829 |
+
'musculotendon_dynamics=0, '
|
| 830 |
+
'tendon_slack_length=l_T_slack, '
|
| 831 |
+
'peak_isometric_force=F_M_max, '
|
| 832 |
+
'optimal_fiber_length=l_M_opt, '
|
| 833 |
+
'maximal_fiber_velocity=v_M_max, '
|
| 834 |
+
'optimal_pennation_angle=alpha_opt, '
|
| 835 |
+
'fiber_damping_coefficient=beta)'
|
| 836 |
+
)
|
| 837 |
+
assert repr(instance) == expected
|
evalkit_internvl/lib/python3.10/site-packages/sympy/physics/continuum_mechanics/__pycache__/__init__.cpython-310.pyc
ADDED
|
Binary file (334 Bytes). View file
|
|
|
evalkit_internvl/lib/python3.10/site-packages/sympy/physics/continuum_mechanics/__pycache__/cable.cpython-310.pyc
ADDED
|
Binary file (16.6 kB). View file
|
|
|
evalkit_internvl/lib/python3.10/site-packages/sympy/physics/continuum_mechanics/tests/__pycache__/__init__.cpython-310.pyc
ADDED
|
Binary file (201 Bytes). View file
|
|
|
evalkit_internvl/lib/python3.10/site-packages/sympy/physics/continuum_mechanics/tests/__pycache__/test_beam.cpython-310.pyc
ADDED
|
Binary file (21.6 kB). View file
|
|
|
evalkit_internvl/lib/python3.10/site-packages/sympy/physics/control/__init__.py
ADDED
|
@@ -0,0 +1,16 @@
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|
| 1 |
+
from .lti import (TransferFunction, Series, MIMOSeries, Parallel, MIMOParallel,
|
| 2 |
+
Feedback, MIMOFeedback, TransferFunctionMatrix, StateSpace, gbt, bilinear, forward_diff,
|
| 3 |
+
backward_diff, phase_margin, gain_margin)
|
| 4 |
+
from .control_plots import (pole_zero_numerical_data, pole_zero_plot, step_response_numerical_data,
|
| 5 |
+
step_response_plot, impulse_response_numerical_data, impulse_response_plot, ramp_response_numerical_data,
|
| 6 |
+
ramp_response_plot, bode_magnitude_numerical_data, bode_phase_numerical_data, bode_magnitude_plot,
|
| 7 |
+
bode_phase_plot, bode_plot)
|
| 8 |
+
|
| 9 |
+
__all__ = ['TransferFunction', 'Series', 'MIMOSeries', 'Parallel',
|
| 10 |
+
'MIMOParallel', 'Feedback', 'MIMOFeedback', 'TransferFunctionMatrix', 'StateSpace',
|
| 11 |
+
'gbt', 'bilinear', 'forward_diff', 'backward_diff', 'phase_margin', 'gain_margin',
|
| 12 |
+
'pole_zero_numerical_data', 'pole_zero_plot', 'step_response_numerical_data',
|
| 13 |
+
'step_response_plot', 'impulse_response_numerical_data', 'impulse_response_plot',
|
| 14 |
+
'ramp_response_numerical_data', 'ramp_response_plot',
|
| 15 |
+
'bode_magnitude_numerical_data', 'bode_phase_numerical_data',
|
| 16 |
+
'bode_magnitude_plot', 'bode_phase_plot', 'bode_plot']
|
evalkit_internvl/lib/python3.10/site-packages/sympy/physics/control/control_plots.py
ADDED
|
@@ -0,0 +1,978 @@
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|
| 1 |
+
from sympy.core.numbers import I, pi
|
| 2 |
+
from sympy.functions.elementary.exponential import (exp, log)
|
| 3 |
+
from sympy.polys.partfrac import apart
|
| 4 |
+
from sympy.core.symbol import Dummy
|
| 5 |
+
from sympy.external import import_module
|
| 6 |
+
from sympy.functions import arg, Abs
|
| 7 |
+
from sympy.integrals.laplace import _fast_inverse_laplace
|
| 8 |
+
from sympy.physics.control.lti import SISOLinearTimeInvariant
|
| 9 |
+
from sympy.plotting.series import LineOver1DRangeSeries
|
| 10 |
+
from sympy.polys.polytools import Poly
|
| 11 |
+
from sympy.printing.latex import latex
|
| 12 |
+
|
| 13 |
+
__all__ = ['pole_zero_numerical_data', 'pole_zero_plot',
|
| 14 |
+
'step_response_numerical_data', 'step_response_plot',
|
| 15 |
+
'impulse_response_numerical_data', 'impulse_response_plot',
|
| 16 |
+
'ramp_response_numerical_data', 'ramp_response_plot',
|
| 17 |
+
'bode_magnitude_numerical_data', 'bode_phase_numerical_data',
|
| 18 |
+
'bode_magnitude_plot', 'bode_phase_plot', 'bode_plot']
|
| 19 |
+
|
| 20 |
+
matplotlib = import_module(
|
| 21 |
+
'matplotlib', import_kwargs={'fromlist': ['pyplot']},
|
| 22 |
+
catch=(RuntimeError,))
|
| 23 |
+
|
| 24 |
+
numpy = import_module('numpy')
|
| 25 |
+
|
| 26 |
+
if matplotlib:
|
| 27 |
+
plt = matplotlib.pyplot
|
| 28 |
+
|
| 29 |
+
if numpy:
|
| 30 |
+
np = numpy # Matplotlib already has numpy as a compulsory dependency. No need to install it separately.
|
| 31 |
+
|
| 32 |
+
|
| 33 |
+
def _check_system(system):
|
| 34 |
+
"""Function to check whether the dynamical system passed for plots is
|
| 35 |
+
compatible or not."""
|
| 36 |
+
if not isinstance(system, SISOLinearTimeInvariant):
|
| 37 |
+
raise NotImplementedError("Only SISO LTI systems are currently supported.")
|
| 38 |
+
sys = system.to_expr()
|
| 39 |
+
len_free_symbols = len(sys.free_symbols)
|
| 40 |
+
if len_free_symbols > 1:
|
| 41 |
+
raise ValueError("Extra degree of freedom found. Make sure"
|
| 42 |
+
" that there are no free symbols in the dynamical system other"
|
| 43 |
+
" than the variable of Laplace transform.")
|
| 44 |
+
if sys.has(exp):
|
| 45 |
+
# Should test that exp is not part of a constant, in which case
|
| 46 |
+
# no exception is required, compare exp(s) with s*exp(1)
|
| 47 |
+
raise NotImplementedError("Time delay terms are not supported.")
|
| 48 |
+
|
| 49 |
+
|
| 50 |
+
def pole_zero_numerical_data(system):
|
| 51 |
+
"""
|
| 52 |
+
Returns the numerical data of poles and zeros of the system.
|
| 53 |
+
It is internally used by ``pole_zero_plot`` to get the data
|
| 54 |
+
for plotting poles and zeros. Users can use this data to further
|
| 55 |
+
analyse the dynamics of the system or plot using a different
|
| 56 |
+
backend/plotting-module.
|
| 57 |
+
|
| 58 |
+
Parameters
|
| 59 |
+
==========
|
| 60 |
+
|
| 61 |
+
system : SISOLinearTimeInvariant
|
| 62 |
+
The system for which the pole-zero data is to be computed.
|
| 63 |
+
|
| 64 |
+
Returns
|
| 65 |
+
=======
|
| 66 |
+
|
| 67 |
+
tuple : (zeros, poles)
|
| 68 |
+
zeros = Zeros of the system. NumPy array of complex numbers.
|
| 69 |
+
poles = Poles of the system. NumPy array of complex numbers.
|
| 70 |
+
|
| 71 |
+
Raises
|
| 72 |
+
======
|
| 73 |
+
|
| 74 |
+
NotImplementedError
|
| 75 |
+
When a SISO LTI system is not passed.
|
| 76 |
+
|
| 77 |
+
When time delay terms are present in the system.
|
| 78 |
+
|
| 79 |
+
ValueError
|
| 80 |
+
When more than one free symbol is present in the system.
|
| 81 |
+
The only variable in the transfer function should be
|
| 82 |
+
the variable of the Laplace transform.
|
| 83 |
+
|
| 84 |
+
Examples
|
| 85 |
+
========
|
| 86 |
+
|
| 87 |
+
>>> from sympy.abc import s
|
| 88 |
+
>>> from sympy.physics.control.lti import TransferFunction
|
| 89 |
+
>>> from sympy.physics.control.control_plots import pole_zero_numerical_data
|
| 90 |
+
>>> tf1 = TransferFunction(s**2 + 1, s**4 + 4*s**3 + 6*s**2 + 5*s + 2, s)
|
| 91 |
+
>>> pole_zero_numerical_data(tf1) # doctest: +SKIP
|
| 92 |
+
([-0.+1.j 0.-1.j], [-2. +0.j -0.5+0.8660254j -0.5-0.8660254j -1. +0.j ])
|
| 93 |
+
|
| 94 |
+
See Also
|
| 95 |
+
========
|
| 96 |
+
|
| 97 |
+
pole_zero_plot
|
| 98 |
+
|
| 99 |
+
"""
|
| 100 |
+
_check_system(system)
|
| 101 |
+
system = system.doit() # Get the equivalent TransferFunction object.
|
| 102 |
+
|
| 103 |
+
num_poly = Poly(system.num, system.var).all_coeffs()
|
| 104 |
+
den_poly = Poly(system.den, system.var).all_coeffs()
|
| 105 |
+
|
| 106 |
+
num_poly = np.array(num_poly, dtype=np.complex128)
|
| 107 |
+
den_poly = np.array(den_poly, dtype=np.complex128)
|
| 108 |
+
|
| 109 |
+
zeros = np.roots(num_poly)
|
| 110 |
+
poles = np.roots(den_poly)
|
| 111 |
+
|
| 112 |
+
return zeros, poles
|
| 113 |
+
|
| 114 |
+
|
| 115 |
+
def pole_zero_plot(system, pole_color='blue', pole_markersize=10,
|
| 116 |
+
zero_color='orange', zero_markersize=7, grid=True, show_axes=True,
|
| 117 |
+
show=True, **kwargs):
|
| 118 |
+
r"""
|
| 119 |
+
Returns the Pole-Zero plot (also known as PZ Plot or PZ Map) of a system.
|
| 120 |
+
|
| 121 |
+
A Pole-Zero plot is a graphical representation of a system's poles and
|
| 122 |
+
zeros. It is plotted on a complex plane, with circular markers representing
|
| 123 |
+
the system's zeros and 'x' shaped markers representing the system's poles.
|
| 124 |
+
|
| 125 |
+
Parameters
|
| 126 |
+
==========
|
| 127 |
+
|
| 128 |
+
system : SISOLinearTimeInvariant type systems
|
| 129 |
+
The system for which the pole-zero plot is to be computed.
|
| 130 |
+
pole_color : str, tuple, optional
|
| 131 |
+
The color of the pole points on the plot. Default color
|
| 132 |
+
is blue. The color can be provided as a matplotlib color string,
|
| 133 |
+
or a 3-tuple of floats each in the 0-1 range.
|
| 134 |
+
pole_markersize : Number, optional
|
| 135 |
+
The size of the markers used to mark the poles in the plot.
|
| 136 |
+
Default pole markersize is 10.
|
| 137 |
+
zero_color : str, tuple, optional
|
| 138 |
+
The color of the zero points on the plot. Default color
|
| 139 |
+
is orange. The color can be provided as a matplotlib color string,
|
| 140 |
+
or a 3-tuple of floats each in the 0-1 range.
|
| 141 |
+
zero_markersize : Number, optional
|
| 142 |
+
The size of the markers used to mark the zeros in the plot.
|
| 143 |
+
Default zero markersize is 7.
|
| 144 |
+
grid : boolean, optional
|
| 145 |
+
If ``True``, the plot will have a grid. Defaults to True.
|
| 146 |
+
show_axes : boolean, optional
|
| 147 |
+
If ``True``, the coordinate axes will be shown. Defaults to False.
|
| 148 |
+
show : boolean, optional
|
| 149 |
+
If ``True``, the plot will be displayed otherwise
|
| 150 |
+
the equivalent matplotlib ``plot`` object will be returned.
|
| 151 |
+
Defaults to True.
|
| 152 |
+
|
| 153 |
+
Examples
|
| 154 |
+
========
|
| 155 |
+
|
| 156 |
+
.. plot::
|
| 157 |
+
:context: close-figs
|
| 158 |
+
:format: doctest
|
| 159 |
+
:include-source: True
|
| 160 |
+
|
| 161 |
+
>>> from sympy.abc import s
|
| 162 |
+
>>> from sympy.physics.control.lti import TransferFunction
|
| 163 |
+
>>> from sympy.physics.control.control_plots import pole_zero_plot
|
| 164 |
+
>>> tf1 = TransferFunction(s**2 + 1, s**4 + 4*s**3 + 6*s**2 + 5*s + 2, s)
|
| 165 |
+
>>> pole_zero_plot(tf1) # doctest: +SKIP
|
| 166 |
+
|
| 167 |
+
See Also
|
| 168 |
+
========
|
| 169 |
+
|
| 170 |
+
pole_zero_numerical_data
|
| 171 |
+
|
| 172 |
+
References
|
| 173 |
+
==========
|
| 174 |
+
|
| 175 |
+
.. [1] https://en.wikipedia.org/wiki/Pole%E2%80%93zero_plot
|
| 176 |
+
|
| 177 |
+
"""
|
| 178 |
+
zeros, poles = pole_zero_numerical_data(system)
|
| 179 |
+
|
| 180 |
+
zero_real = np.real(zeros)
|
| 181 |
+
zero_imag = np.imag(zeros)
|
| 182 |
+
|
| 183 |
+
pole_real = np.real(poles)
|
| 184 |
+
pole_imag = np.imag(poles)
|
| 185 |
+
|
| 186 |
+
plt.plot(pole_real, pole_imag, 'x', mfc='none',
|
| 187 |
+
markersize=pole_markersize, color=pole_color)
|
| 188 |
+
plt.plot(zero_real, zero_imag, 'o', markersize=zero_markersize,
|
| 189 |
+
color=zero_color)
|
| 190 |
+
plt.xlabel('Real Axis')
|
| 191 |
+
plt.ylabel('Imaginary Axis')
|
| 192 |
+
plt.title(f'Poles and Zeros of ${latex(system)}$', pad=20)
|
| 193 |
+
|
| 194 |
+
if grid:
|
| 195 |
+
plt.grid()
|
| 196 |
+
if show_axes:
|
| 197 |
+
plt.axhline(0, color='black')
|
| 198 |
+
plt.axvline(0, color='black')
|
| 199 |
+
if show:
|
| 200 |
+
plt.show()
|
| 201 |
+
return
|
| 202 |
+
|
| 203 |
+
return plt
|
| 204 |
+
|
| 205 |
+
|
| 206 |
+
def step_response_numerical_data(system, prec=8, lower_limit=0,
|
| 207 |
+
upper_limit=10, **kwargs):
|
| 208 |
+
"""
|
| 209 |
+
Returns the numerical values of the points in the step response plot
|
| 210 |
+
of a SISO continuous-time system. By default, adaptive sampling
|
| 211 |
+
is used. If the user wants to instead get an uniformly
|
| 212 |
+
sampled response, then ``adaptive`` kwarg should be passed ``False``
|
| 213 |
+
and ``n`` must be passed as additional kwargs.
|
| 214 |
+
Refer to the parameters of class :class:`sympy.plotting.series.LineOver1DRangeSeries`
|
| 215 |
+
for more details.
|
| 216 |
+
|
| 217 |
+
Parameters
|
| 218 |
+
==========
|
| 219 |
+
|
| 220 |
+
system : SISOLinearTimeInvariant
|
| 221 |
+
The system for which the unit step response data is to be computed.
|
| 222 |
+
prec : int, optional
|
| 223 |
+
The decimal point precision for the point coordinate values.
|
| 224 |
+
Defaults to 8.
|
| 225 |
+
lower_limit : Number, optional
|
| 226 |
+
The lower limit of the plot range. Defaults to 0.
|
| 227 |
+
upper_limit : Number, optional
|
| 228 |
+
The upper limit of the plot range. Defaults to 10.
|
| 229 |
+
kwargs :
|
| 230 |
+
Additional keyword arguments are passed to the underlying
|
| 231 |
+
:class:`sympy.plotting.series.LineOver1DRangeSeries` class.
|
| 232 |
+
|
| 233 |
+
Returns
|
| 234 |
+
=======
|
| 235 |
+
|
| 236 |
+
tuple : (x, y)
|
| 237 |
+
x = Time-axis values of the points in the step response. NumPy array.
|
| 238 |
+
y = Amplitude-axis values of the points in the step response. NumPy array.
|
| 239 |
+
|
| 240 |
+
Raises
|
| 241 |
+
======
|
| 242 |
+
|
| 243 |
+
NotImplementedError
|
| 244 |
+
When a SISO LTI system is not passed.
|
| 245 |
+
|
| 246 |
+
When time delay terms are present in the system.
|
| 247 |
+
|
| 248 |
+
ValueError
|
| 249 |
+
When more than one free symbol is present in the system.
|
| 250 |
+
The only variable in the transfer function should be
|
| 251 |
+
the variable of the Laplace transform.
|
| 252 |
+
|
| 253 |
+
When ``lower_limit`` parameter is less than 0.
|
| 254 |
+
|
| 255 |
+
Examples
|
| 256 |
+
========
|
| 257 |
+
|
| 258 |
+
>>> from sympy.abc import s
|
| 259 |
+
>>> from sympy.physics.control.lti import TransferFunction
|
| 260 |
+
>>> from sympy.physics.control.control_plots import step_response_numerical_data
|
| 261 |
+
>>> tf1 = TransferFunction(s, s**2 + 5*s + 8, s)
|
| 262 |
+
>>> step_response_numerical_data(tf1) # doctest: +SKIP
|
| 263 |
+
([0.0, 0.025413462339411542, 0.0484508722725343, ... , 9.670250533855183, 9.844291913708725, 10.0],
|
| 264 |
+
[0.0, 0.023844582399907256, 0.042894276802320226, ..., 6.828770759094287e-12, 6.456457160755703e-12])
|
| 265 |
+
|
| 266 |
+
See Also
|
| 267 |
+
========
|
| 268 |
+
|
| 269 |
+
step_response_plot
|
| 270 |
+
|
| 271 |
+
"""
|
| 272 |
+
if lower_limit < 0:
|
| 273 |
+
raise ValueError("Lower limit of time must be greater "
|
| 274 |
+
"than or equal to zero.")
|
| 275 |
+
_check_system(system)
|
| 276 |
+
_x = Dummy("x")
|
| 277 |
+
expr = system.to_expr()/(system.var)
|
| 278 |
+
expr = apart(expr, system.var, full=True)
|
| 279 |
+
_y = _fast_inverse_laplace(expr, system.var, _x).evalf(prec)
|
| 280 |
+
return LineOver1DRangeSeries(_y, (_x, lower_limit, upper_limit),
|
| 281 |
+
**kwargs).get_points()
|
| 282 |
+
|
| 283 |
+
|
| 284 |
+
def step_response_plot(system, color='b', prec=8, lower_limit=0,
|
| 285 |
+
upper_limit=10, show_axes=False, grid=True, show=True, **kwargs):
|
| 286 |
+
r"""
|
| 287 |
+
Returns the unit step response of a continuous-time system. It is
|
| 288 |
+
the response of the system when the input signal is a step function.
|
| 289 |
+
|
| 290 |
+
Parameters
|
| 291 |
+
==========
|
| 292 |
+
|
| 293 |
+
system : SISOLinearTimeInvariant type
|
| 294 |
+
The LTI SISO system for which the Step Response is to be computed.
|
| 295 |
+
color : str, tuple, optional
|
| 296 |
+
The color of the line. Default is Blue.
|
| 297 |
+
show : boolean, optional
|
| 298 |
+
If ``True``, the plot will be displayed otherwise
|
| 299 |
+
the equivalent matplotlib ``plot`` object will be returned.
|
| 300 |
+
Defaults to True.
|
| 301 |
+
lower_limit : Number, optional
|
| 302 |
+
The lower limit of the plot range. Defaults to 0.
|
| 303 |
+
upper_limit : Number, optional
|
| 304 |
+
The upper limit of the plot range. Defaults to 10.
|
| 305 |
+
prec : int, optional
|
| 306 |
+
The decimal point precision for the point coordinate values.
|
| 307 |
+
Defaults to 8.
|
| 308 |
+
show_axes : boolean, optional
|
| 309 |
+
If ``True``, the coordinate axes will be shown. Defaults to False.
|
| 310 |
+
grid : boolean, optional
|
| 311 |
+
If ``True``, the plot will have a grid. Defaults to True.
|
| 312 |
+
|
| 313 |
+
Examples
|
| 314 |
+
========
|
| 315 |
+
|
| 316 |
+
.. plot::
|
| 317 |
+
:context: close-figs
|
| 318 |
+
:format: doctest
|
| 319 |
+
:include-source: True
|
| 320 |
+
|
| 321 |
+
>>> from sympy.abc import s
|
| 322 |
+
>>> from sympy.physics.control.lti import TransferFunction
|
| 323 |
+
>>> from sympy.physics.control.control_plots import step_response_plot
|
| 324 |
+
>>> tf1 = TransferFunction(8*s**2 + 18*s + 32, s**3 + 6*s**2 + 14*s + 24, s)
|
| 325 |
+
>>> step_response_plot(tf1) # doctest: +SKIP
|
| 326 |
+
|
| 327 |
+
See Also
|
| 328 |
+
========
|
| 329 |
+
|
| 330 |
+
impulse_response_plot, ramp_response_plot
|
| 331 |
+
|
| 332 |
+
References
|
| 333 |
+
==========
|
| 334 |
+
|
| 335 |
+
.. [1] https://www.mathworks.com/help/control/ref/lti.step.html
|
| 336 |
+
|
| 337 |
+
"""
|
| 338 |
+
x, y = step_response_numerical_data(system, prec=prec,
|
| 339 |
+
lower_limit=lower_limit, upper_limit=upper_limit, **kwargs)
|
| 340 |
+
plt.plot(x, y, color=color)
|
| 341 |
+
plt.xlabel('Time (s)')
|
| 342 |
+
plt.ylabel('Amplitude')
|
| 343 |
+
plt.title(f'Unit Step Response of ${latex(system)}$', pad=20)
|
| 344 |
+
|
| 345 |
+
if grid:
|
| 346 |
+
plt.grid()
|
| 347 |
+
if show_axes:
|
| 348 |
+
plt.axhline(0, color='black')
|
| 349 |
+
plt.axvline(0, color='black')
|
| 350 |
+
if show:
|
| 351 |
+
plt.show()
|
| 352 |
+
return
|
| 353 |
+
|
| 354 |
+
return plt
|
| 355 |
+
|
| 356 |
+
|
| 357 |
+
def impulse_response_numerical_data(system, prec=8, lower_limit=0,
|
| 358 |
+
upper_limit=10, **kwargs):
|
| 359 |
+
"""
|
| 360 |
+
Returns the numerical values of the points in the impulse response plot
|
| 361 |
+
of a SISO continuous-time system. By default, adaptive sampling
|
| 362 |
+
is used. If the user wants to instead get an uniformly
|
| 363 |
+
sampled response, then ``adaptive`` kwarg should be passed ``False``
|
| 364 |
+
and ``n`` must be passed as additional kwargs.
|
| 365 |
+
Refer to the parameters of class :class:`sympy.plotting.series.LineOver1DRangeSeries`
|
| 366 |
+
for more details.
|
| 367 |
+
|
| 368 |
+
Parameters
|
| 369 |
+
==========
|
| 370 |
+
|
| 371 |
+
system : SISOLinearTimeInvariant
|
| 372 |
+
The system for which the impulse response data is to be computed.
|
| 373 |
+
prec : int, optional
|
| 374 |
+
The decimal point precision for the point coordinate values.
|
| 375 |
+
Defaults to 8.
|
| 376 |
+
lower_limit : Number, optional
|
| 377 |
+
The lower limit of the plot range. Defaults to 0.
|
| 378 |
+
upper_limit : Number, optional
|
| 379 |
+
The upper limit of the plot range. Defaults to 10.
|
| 380 |
+
kwargs :
|
| 381 |
+
Additional keyword arguments are passed to the underlying
|
| 382 |
+
:class:`sympy.plotting.series.LineOver1DRangeSeries` class.
|
| 383 |
+
|
| 384 |
+
Returns
|
| 385 |
+
=======
|
| 386 |
+
|
| 387 |
+
tuple : (x, y)
|
| 388 |
+
x = Time-axis values of the points in the impulse response. NumPy array.
|
| 389 |
+
y = Amplitude-axis values of the points in the impulse response. NumPy array.
|
| 390 |
+
|
| 391 |
+
Raises
|
| 392 |
+
======
|
| 393 |
+
|
| 394 |
+
NotImplementedError
|
| 395 |
+
When a SISO LTI system is not passed.
|
| 396 |
+
|
| 397 |
+
When time delay terms are present in the system.
|
| 398 |
+
|
| 399 |
+
ValueError
|
| 400 |
+
When more than one free symbol is present in the system.
|
| 401 |
+
The only variable in the transfer function should be
|
| 402 |
+
the variable of the Laplace transform.
|
| 403 |
+
|
| 404 |
+
When ``lower_limit`` parameter is less than 0.
|
| 405 |
+
|
| 406 |
+
Examples
|
| 407 |
+
========
|
| 408 |
+
|
| 409 |
+
>>> from sympy.abc import s
|
| 410 |
+
>>> from sympy.physics.control.lti import TransferFunction
|
| 411 |
+
>>> from sympy.physics.control.control_plots import impulse_response_numerical_data
|
| 412 |
+
>>> tf1 = TransferFunction(s, s**2 + 5*s + 8, s)
|
| 413 |
+
>>> impulse_response_numerical_data(tf1) # doctest: +SKIP
|
| 414 |
+
([0.0, 0.06616480200395854,... , 9.854500743565858, 10.0],
|
| 415 |
+
[0.9999999799999999, 0.7042848373025861,...,7.170748906965121e-13, -5.1901263495547205e-12])
|
| 416 |
+
|
| 417 |
+
See Also
|
| 418 |
+
========
|
| 419 |
+
|
| 420 |
+
impulse_response_plot
|
| 421 |
+
|
| 422 |
+
"""
|
| 423 |
+
if lower_limit < 0:
|
| 424 |
+
raise ValueError("Lower limit of time must be greater "
|
| 425 |
+
"than or equal to zero.")
|
| 426 |
+
_check_system(system)
|
| 427 |
+
_x = Dummy("x")
|
| 428 |
+
expr = system.to_expr()
|
| 429 |
+
expr = apart(expr, system.var, full=True)
|
| 430 |
+
_y = _fast_inverse_laplace(expr, system.var, _x).evalf(prec)
|
| 431 |
+
return LineOver1DRangeSeries(_y, (_x, lower_limit, upper_limit),
|
| 432 |
+
**kwargs).get_points()
|
| 433 |
+
|
| 434 |
+
|
| 435 |
+
def impulse_response_plot(system, color='b', prec=8, lower_limit=0,
|
| 436 |
+
upper_limit=10, show_axes=False, grid=True, show=True, **kwargs):
|
| 437 |
+
r"""
|
| 438 |
+
Returns the unit impulse response (Input is the Dirac-Delta Function) of a
|
| 439 |
+
continuous-time system.
|
| 440 |
+
|
| 441 |
+
Parameters
|
| 442 |
+
==========
|
| 443 |
+
|
| 444 |
+
system : SISOLinearTimeInvariant type
|
| 445 |
+
The LTI SISO system for which the Impulse Response is to be computed.
|
| 446 |
+
color : str, tuple, optional
|
| 447 |
+
The color of the line. Default is Blue.
|
| 448 |
+
show : boolean, optional
|
| 449 |
+
If ``True``, the plot will be displayed otherwise
|
| 450 |
+
the equivalent matplotlib ``plot`` object will be returned.
|
| 451 |
+
Defaults to True.
|
| 452 |
+
lower_limit : Number, optional
|
| 453 |
+
The lower limit of the plot range. Defaults to 0.
|
| 454 |
+
upper_limit : Number, optional
|
| 455 |
+
The upper limit of the plot range. Defaults to 10.
|
| 456 |
+
prec : int, optional
|
| 457 |
+
The decimal point precision for the point coordinate values.
|
| 458 |
+
Defaults to 8.
|
| 459 |
+
show_axes : boolean, optional
|
| 460 |
+
If ``True``, the coordinate axes will be shown. Defaults to False.
|
| 461 |
+
grid : boolean, optional
|
| 462 |
+
If ``True``, the plot will have a grid. Defaults to True.
|
| 463 |
+
|
| 464 |
+
Examples
|
| 465 |
+
========
|
| 466 |
+
|
| 467 |
+
.. plot::
|
| 468 |
+
:context: close-figs
|
| 469 |
+
:format: doctest
|
| 470 |
+
:include-source: True
|
| 471 |
+
|
| 472 |
+
>>> from sympy.abc import s
|
| 473 |
+
>>> from sympy.physics.control.lti import TransferFunction
|
| 474 |
+
>>> from sympy.physics.control.control_plots import impulse_response_plot
|
| 475 |
+
>>> tf1 = TransferFunction(8*s**2 + 18*s + 32, s**3 + 6*s**2 + 14*s + 24, s)
|
| 476 |
+
>>> impulse_response_plot(tf1) # doctest: +SKIP
|
| 477 |
+
|
| 478 |
+
See Also
|
| 479 |
+
========
|
| 480 |
+
|
| 481 |
+
step_response_plot, ramp_response_plot
|
| 482 |
+
|
| 483 |
+
References
|
| 484 |
+
==========
|
| 485 |
+
|
| 486 |
+
.. [1] https://www.mathworks.com/help/control/ref/dynamicsystem.impulse.html
|
| 487 |
+
|
| 488 |
+
"""
|
| 489 |
+
x, y = impulse_response_numerical_data(system, prec=prec,
|
| 490 |
+
lower_limit=lower_limit, upper_limit=upper_limit, **kwargs)
|
| 491 |
+
plt.plot(x, y, color=color)
|
| 492 |
+
plt.xlabel('Time (s)')
|
| 493 |
+
plt.ylabel('Amplitude')
|
| 494 |
+
plt.title(f'Impulse Response of ${latex(system)}$', pad=20)
|
| 495 |
+
|
| 496 |
+
if grid:
|
| 497 |
+
plt.grid()
|
| 498 |
+
if show_axes:
|
| 499 |
+
plt.axhline(0, color='black')
|
| 500 |
+
plt.axvline(0, color='black')
|
| 501 |
+
if show:
|
| 502 |
+
plt.show()
|
| 503 |
+
return
|
| 504 |
+
|
| 505 |
+
return plt
|
| 506 |
+
|
| 507 |
+
|
| 508 |
+
def ramp_response_numerical_data(system, slope=1, prec=8,
|
| 509 |
+
lower_limit=0, upper_limit=10, **kwargs):
|
| 510 |
+
"""
|
| 511 |
+
Returns the numerical values of the points in the ramp response plot
|
| 512 |
+
of a SISO continuous-time system. By default, adaptive sampling
|
| 513 |
+
is used. If the user wants to instead get an uniformly
|
| 514 |
+
sampled response, then ``adaptive`` kwarg should be passed ``False``
|
| 515 |
+
and ``n`` must be passed as additional kwargs.
|
| 516 |
+
Refer to the parameters of class :class:`sympy.plotting.series.LineOver1DRangeSeries`
|
| 517 |
+
for more details.
|
| 518 |
+
|
| 519 |
+
Parameters
|
| 520 |
+
==========
|
| 521 |
+
|
| 522 |
+
system : SISOLinearTimeInvariant
|
| 523 |
+
The system for which the ramp response data is to be computed.
|
| 524 |
+
slope : Number, optional
|
| 525 |
+
The slope of the input ramp function. Defaults to 1.
|
| 526 |
+
prec : int, optional
|
| 527 |
+
The decimal point precision for the point coordinate values.
|
| 528 |
+
Defaults to 8.
|
| 529 |
+
lower_limit : Number, optional
|
| 530 |
+
The lower limit of the plot range. Defaults to 0.
|
| 531 |
+
upper_limit : Number, optional
|
| 532 |
+
The upper limit of the plot range. Defaults to 10.
|
| 533 |
+
kwargs :
|
| 534 |
+
Additional keyword arguments are passed to the underlying
|
| 535 |
+
:class:`sympy.plotting.series.LineOver1DRangeSeries` class.
|
| 536 |
+
|
| 537 |
+
Returns
|
| 538 |
+
=======
|
| 539 |
+
|
| 540 |
+
tuple : (x, y)
|
| 541 |
+
x = Time-axis values of the points in the ramp response plot. NumPy array.
|
| 542 |
+
y = Amplitude-axis values of the points in the ramp response plot. NumPy array.
|
| 543 |
+
|
| 544 |
+
Raises
|
| 545 |
+
======
|
| 546 |
+
|
| 547 |
+
NotImplementedError
|
| 548 |
+
When a SISO LTI system is not passed.
|
| 549 |
+
|
| 550 |
+
When time delay terms are present in the system.
|
| 551 |
+
|
| 552 |
+
ValueError
|
| 553 |
+
When more than one free symbol is present in the system.
|
| 554 |
+
The only variable in the transfer function should be
|
| 555 |
+
the variable of the Laplace transform.
|
| 556 |
+
|
| 557 |
+
When ``lower_limit`` parameter is less than 0.
|
| 558 |
+
|
| 559 |
+
When ``slope`` is negative.
|
| 560 |
+
|
| 561 |
+
Examples
|
| 562 |
+
========
|
| 563 |
+
|
| 564 |
+
>>> from sympy.abc import s
|
| 565 |
+
>>> from sympy.physics.control.lti import TransferFunction
|
| 566 |
+
>>> from sympy.physics.control.control_plots import ramp_response_numerical_data
|
| 567 |
+
>>> tf1 = TransferFunction(s, s**2 + 5*s + 8, s)
|
| 568 |
+
>>> ramp_response_numerical_data(tf1) # doctest: +SKIP
|
| 569 |
+
(([0.0, 0.12166980856813935,..., 9.861246379582118, 10.0],
|
| 570 |
+
[1.4504508011325967e-09, 0.006046440489058766,..., 0.12499999999568202, 0.12499999999661349]))
|
| 571 |
+
|
| 572 |
+
See Also
|
| 573 |
+
========
|
| 574 |
+
|
| 575 |
+
ramp_response_plot
|
| 576 |
+
|
| 577 |
+
"""
|
| 578 |
+
if slope < 0:
|
| 579 |
+
raise ValueError("Slope must be greater than or equal"
|
| 580 |
+
" to zero.")
|
| 581 |
+
if lower_limit < 0:
|
| 582 |
+
raise ValueError("Lower limit of time must be greater "
|
| 583 |
+
"than or equal to zero.")
|
| 584 |
+
_check_system(system)
|
| 585 |
+
_x = Dummy("x")
|
| 586 |
+
expr = (slope*system.to_expr())/((system.var)**2)
|
| 587 |
+
expr = apart(expr, system.var, full=True)
|
| 588 |
+
_y = _fast_inverse_laplace(expr, system.var, _x).evalf(prec)
|
| 589 |
+
return LineOver1DRangeSeries(_y, (_x, lower_limit, upper_limit),
|
| 590 |
+
**kwargs).get_points()
|
| 591 |
+
|
| 592 |
+
|
| 593 |
+
def ramp_response_plot(system, slope=1, color='b', prec=8, lower_limit=0,
|
| 594 |
+
upper_limit=10, show_axes=False, grid=True, show=True, **kwargs):
|
| 595 |
+
r"""
|
| 596 |
+
Returns the ramp response of a continuous-time system.
|
| 597 |
+
|
| 598 |
+
Ramp function is defined as the straight line
|
| 599 |
+
passing through origin ($f(x) = mx$). The slope of
|
| 600 |
+
the ramp function can be varied by the user and
|
| 601 |
+
the default value is 1.
|
| 602 |
+
|
| 603 |
+
Parameters
|
| 604 |
+
==========
|
| 605 |
+
|
| 606 |
+
system : SISOLinearTimeInvariant type
|
| 607 |
+
The LTI SISO system for which the Ramp Response is to be computed.
|
| 608 |
+
slope : Number, optional
|
| 609 |
+
The slope of the input ramp function. Defaults to 1.
|
| 610 |
+
color : str, tuple, optional
|
| 611 |
+
The color of the line. Default is Blue.
|
| 612 |
+
show : boolean, optional
|
| 613 |
+
If ``True``, the plot will be displayed otherwise
|
| 614 |
+
the equivalent matplotlib ``plot`` object will be returned.
|
| 615 |
+
Defaults to True.
|
| 616 |
+
lower_limit : Number, optional
|
| 617 |
+
The lower limit of the plot range. Defaults to 0.
|
| 618 |
+
upper_limit : Number, optional
|
| 619 |
+
The upper limit of the plot range. Defaults to 10.
|
| 620 |
+
prec : int, optional
|
| 621 |
+
The decimal point precision for the point coordinate values.
|
| 622 |
+
Defaults to 8.
|
| 623 |
+
show_axes : boolean, optional
|
| 624 |
+
If ``True``, the coordinate axes will be shown. Defaults to False.
|
| 625 |
+
grid : boolean, optional
|
| 626 |
+
If ``True``, the plot will have a grid. Defaults to True.
|
| 627 |
+
|
| 628 |
+
Examples
|
| 629 |
+
========
|
| 630 |
+
|
| 631 |
+
.. plot::
|
| 632 |
+
:context: close-figs
|
| 633 |
+
:format: doctest
|
| 634 |
+
:include-source: True
|
| 635 |
+
|
| 636 |
+
>>> from sympy.abc import s
|
| 637 |
+
>>> from sympy.physics.control.lti import TransferFunction
|
| 638 |
+
>>> from sympy.physics.control.control_plots import ramp_response_plot
|
| 639 |
+
>>> tf1 = TransferFunction(s, (s+4)*(s+8), s)
|
| 640 |
+
>>> ramp_response_plot(tf1, upper_limit=2) # doctest: +SKIP
|
| 641 |
+
|
| 642 |
+
See Also
|
| 643 |
+
========
|
| 644 |
+
|
| 645 |
+
step_response_plot, impulse_response_plot
|
| 646 |
+
|
| 647 |
+
References
|
| 648 |
+
==========
|
| 649 |
+
|
| 650 |
+
.. [1] https://en.wikipedia.org/wiki/Ramp_function
|
| 651 |
+
|
| 652 |
+
"""
|
| 653 |
+
x, y = ramp_response_numerical_data(system, slope=slope, prec=prec,
|
| 654 |
+
lower_limit=lower_limit, upper_limit=upper_limit, **kwargs)
|
| 655 |
+
plt.plot(x, y, color=color)
|
| 656 |
+
plt.xlabel('Time (s)')
|
| 657 |
+
plt.ylabel('Amplitude')
|
| 658 |
+
plt.title(f'Ramp Response of ${latex(system)}$ [Slope = {slope}]', pad=20)
|
| 659 |
+
|
| 660 |
+
if grid:
|
| 661 |
+
plt.grid()
|
| 662 |
+
if show_axes:
|
| 663 |
+
plt.axhline(0, color='black')
|
| 664 |
+
plt.axvline(0, color='black')
|
| 665 |
+
if show:
|
| 666 |
+
plt.show()
|
| 667 |
+
return
|
| 668 |
+
|
| 669 |
+
return plt
|
| 670 |
+
|
| 671 |
+
|
| 672 |
+
def bode_magnitude_numerical_data(system, initial_exp=-5, final_exp=5, freq_unit='rad/sec', **kwargs):
|
| 673 |
+
"""
|
| 674 |
+
Returns the numerical data of the Bode magnitude plot of the system.
|
| 675 |
+
It is internally used by ``bode_magnitude_plot`` to get the data
|
| 676 |
+
for plotting Bode magnitude plot. Users can use this data to further
|
| 677 |
+
analyse the dynamics of the system or plot using a different
|
| 678 |
+
backend/plotting-module.
|
| 679 |
+
|
| 680 |
+
Parameters
|
| 681 |
+
==========
|
| 682 |
+
|
| 683 |
+
system : SISOLinearTimeInvariant
|
| 684 |
+
The system for which the data is to be computed.
|
| 685 |
+
initial_exp : Number, optional
|
| 686 |
+
The initial exponent of 10 of the semilog plot. Defaults to -5.
|
| 687 |
+
final_exp : Number, optional
|
| 688 |
+
The final exponent of 10 of the semilog plot. Defaults to 5.
|
| 689 |
+
freq_unit : string, optional
|
| 690 |
+
User can choose between ``'rad/sec'`` (radians/second) and ``'Hz'`` (Hertz) as frequency units.
|
| 691 |
+
|
| 692 |
+
Returns
|
| 693 |
+
=======
|
| 694 |
+
|
| 695 |
+
tuple : (x, y)
|
| 696 |
+
x = x-axis values of the Bode magnitude plot.
|
| 697 |
+
y = y-axis values of the Bode magnitude plot.
|
| 698 |
+
|
| 699 |
+
Raises
|
| 700 |
+
======
|
| 701 |
+
|
| 702 |
+
NotImplementedError
|
| 703 |
+
When a SISO LTI system is not passed.
|
| 704 |
+
|
| 705 |
+
When time delay terms are present in the system.
|
| 706 |
+
|
| 707 |
+
ValueError
|
| 708 |
+
When more than one free symbol is present in the system.
|
| 709 |
+
The only variable in the transfer function should be
|
| 710 |
+
the variable of the Laplace transform.
|
| 711 |
+
|
| 712 |
+
When incorrect frequency units are given as input.
|
| 713 |
+
|
| 714 |
+
Examples
|
| 715 |
+
========
|
| 716 |
+
|
| 717 |
+
>>> from sympy.abc import s
|
| 718 |
+
>>> from sympy.physics.control.lti import TransferFunction
|
| 719 |
+
>>> from sympy.physics.control.control_plots import bode_magnitude_numerical_data
|
| 720 |
+
>>> tf1 = TransferFunction(s**2 + 1, s**4 + 4*s**3 + 6*s**2 + 5*s + 2, s)
|
| 721 |
+
>>> bode_magnitude_numerical_data(tf1) # doctest: +SKIP
|
| 722 |
+
([1e-05, 1.5148378120533502e-05,..., 68437.36188804005, 100000.0],
|
| 723 |
+
[-6.020599914256786, -6.0205999155219505,..., -193.4117304087953, -200.00000000260573])
|
| 724 |
+
|
| 725 |
+
See Also
|
| 726 |
+
========
|
| 727 |
+
|
| 728 |
+
bode_magnitude_plot, bode_phase_numerical_data
|
| 729 |
+
|
| 730 |
+
"""
|
| 731 |
+
_check_system(system)
|
| 732 |
+
expr = system.to_expr()
|
| 733 |
+
freq_units = ('rad/sec', 'Hz')
|
| 734 |
+
if freq_unit not in freq_units:
|
| 735 |
+
raise ValueError('Only "rad/sec" and "Hz" are accepted frequency units.')
|
| 736 |
+
|
| 737 |
+
_w = Dummy("w", real=True)
|
| 738 |
+
if freq_unit == 'Hz':
|
| 739 |
+
repl = I*_w*2*pi
|
| 740 |
+
else:
|
| 741 |
+
repl = I*_w
|
| 742 |
+
w_expr = expr.subs({system.var: repl})
|
| 743 |
+
|
| 744 |
+
mag = 20*log(Abs(w_expr), 10)
|
| 745 |
+
|
| 746 |
+
x, y = LineOver1DRangeSeries(mag,
|
| 747 |
+
(_w, 10**initial_exp, 10**final_exp), xscale='log', **kwargs).get_points()
|
| 748 |
+
|
| 749 |
+
return x, y
|
| 750 |
+
|
| 751 |
+
|
| 752 |
+
def bode_magnitude_plot(system, initial_exp=-5, final_exp=5,
|
| 753 |
+
color='b', show_axes=False, grid=True, show=True, freq_unit='rad/sec', **kwargs):
|
| 754 |
+
r"""
|
| 755 |
+
Returns the Bode magnitude plot of a continuous-time system.
|
| 756 |
+
|
| 757 |
+
See ``bode_plot`` for all the parameters.
|
| 758 |
+
"""
|
| 759 |
+
x, y = bode_magnitude_numerical_data(system, initial_exp=initial_exp,
|
| 760 |
+
final_exp=final_exp, freq_unit=freq_unit)
|
| 761 |
+
plt.plot(x, y, color=color, **kwargs)
|
| 762 |
+
plt.xscale('log')
|
| 763 |
+
|
| 764 |
+
|
| 765 |
+
plt.xlabel('Frequency (%s) [Log Scale]' % freq_unit)
|
| 766 |
+
plt.ylabel('Magnitude (dB)')
|
| 767 |
+
plt.title(f'Bode Plot (Magnitude) of ${latex(system)}$', pad=20)
|
| 768 |
+
|
| 769 |
+
if grid:
|
| 770 |
+
plt.grid(True)
|
| 771 |
+
if show_axes:
|
| 772 |
+
plt.axhline(0, color='black')
|
| 773 |
+
plt.axvline(0, color='black')
|
| 774 |
+
if show:
|
| 775 |
+
plt.show()
|
| 776 |
+
return
|
| 777 |
+
|
| 778 |
+
return plt
|
| 779 |
+
|
| 780 |
+
|
| 781 |
+
def bode_phase_numerical_data(system, initial_exp=-5, final_exp=5, freq_unit='rad/sec', phase_unit='rad', phase_unwrap = True, **kwargs):
|
| 782 |
+
"""
|
| 783 |
+
Returns the numerical data of the Bode phase plot of the system.
|
| 784 |
+
It is internally used by ``bode_phase_plot`` to get the data
|
| 785 |
+
for plotting Bode phase plot. Users can use this data to further
|
| 786 |
+
analyse the dynamics of the system or plot using a different
|
| 787 |
+
backend/plotting-module.
|
| 788 |
+
|
| 789 |
+
Parameters
|
| 790 |
+
==========
|
| 791 |
+
|
| 792 |
+
system : SISOLinearTimeInvariant
|
| 793 |
+
The system for which the Bode phase plot data is to be computed.
|
| 794 |
+
initial_exp : Number, optional
|
| 795 |
+
The initial exponent of 10 of the semilog plot. Defaults to -5.
|
| 796 |
+
final_exp : Number, optional
|
| 797 |
+
The final exponent of 10 of the semilog plot. Defaults to 5.
|
| 798 |
+
freq_unit : string, optional
|
| 799 |
+
User can choose between ``'rad/sec'`` (radians/second) and '``'Hz'`` (Hertz) as frequency units.
|
| 800 |
+
phase_unit : string, optional
|
| 801 |
+
User can choose between ``'rad'`` (radians) and ``'deg'`` (degree) as phase units.
|
| 802 |
+
phase_unwrap : bool, optional
|
| 803 |
+
Set to ``True`` by default.
|
| 804 |
+
|
| 805 |
+
Returns
|
| 806 |
+
=======
|
| 807 |
+
|
| 808 |
+
tuple : (x, y)
|
| 809 |
+
x = x-axis values of the Bode phase plot.
|
| 810 |
+
y = y-axis values of the Bode phase plot.
|
| 811 |
+
|
| 812 |
+
Raises
|
| 813 |
+
======
|
| 814 |
+
|
| 815 |
+
NotImplementedError
|
| 816 |
+
When a SISO LTI system is not passed.
|
| 817 |
+
|
| 818 |
+
When time delay terms are present in the system.
|
| 819 |
+
|
| 820 |
+
ValueError
|
| 821 |
+
When more than one free symbol is present in the system.
|
| 822 |
+
The only variable in the transfer function should be
|
| 823 |
+
the variable of the Laplace transform.
|
| 824 |
+
|
| 825 |
+
When incorrect frequency or phase units are given as input.
|
| 826 |
+
|
| 827 |
+
Examples
|
| 828 |
+
========
|
| 829 |
+
|
| 830 |
+
>>> from sympy.abc import s
|
| 831 |
+
>>> from sympy.physics.control.lti import TransferFunction
|
| 832 |
+
>>> from sympy.physics.control.control_plots import bode_phase_numerical_data
|
| 833 |
+
>>> tf1 = TransferFunction(s**2 + 1, s**4 + 4*s**3 + 6*s**2 + 5*s + 2, s)
|
| 834 |
+
>>> bode_phase_numerical_data(tf1) # doctest: +SKIP
|
| 835 |
+
([1e-05, 1.4472354033813751e-05, 2.035581932165858e-05,..., 47577.3248186011, 67884.09326036123, 100000.0],
|
| 836 |
+
[-2.5000000000291665e-05, -3.6180885085e-05, -5.08895483066e-05,...,-3.1415085799262523, -3.14155265358979])
|
| 837 |
+
|
| 838 |
+
See Also
|
| 839 |
+
========
|
| 840 |
+
|
| 841 |
+
bode_magnitude_plot, bode_phase_numerical_data
|
| 842 |
+
|
| 843 |
+
"""
|
| 844 |
+
_check_system(system)
|
| 845 |
+
expr = system.to_expr()
|
| 846 |
+
freq_units = ('rad/sec', 'Hz')
|
| 847 |
+
phase_units = ('rad', 'deg')
|
| 848 |
+
if freq_unit not in freq_units:
|
| 849 |
+
raise ValueError('Only "rad/sec" and "Hz" are accepted frequency units.')
|
| 850 |
+
if phase_unit not in phase_units:
|
| 851 |
+
raise ValueError('Only "rad" and "deg" are accepted phase units.')
|
| 852 |
+
|
| 853 |
+
_w = Dummy("w", real=True)
|
| 854 |
+
if freq_unit == 'Hz':
|
| 855 |
+
repl = I*_w*2*pi
|
| 856 |
+
else:
|
| 857 |
+
repl = I*_w
|
| 858 |
+
w_expr = expr.subs({system.var: repl})
|
| 859 |
+
|
| 860 |
+
if phase_unit == 'deg':
|
| 861 |
+
phase = arg(w_expr)*180/pi
|
| 862 |
+
else:
|
| 863 |
+
phase = arg(w_expr)
|
| 864 |
+
|
| 865 |
+
x, y = LineOver1DRangeSeries(phase,
|
| 866 |
+
(_w, 10**initial_exp, 10**final_exp), xscale='log', **kwargs).get_points()
|
| 867 |
+
|
| 868 |
+
half = None
|
| 869 |
+
if phase_unwrap:
|
| 870 |
+
if(phase_unit == 'rad'):
|
| 871 |
+
half = pi
|
| 872 |
+
elif(phase_unit == 'deg'):
|
| 873 |
+
half = 180
|
| 874 |
+
if half:
|
| 875 |
+
unit = 2*half
|
| 876 |
+
for i in range(1, len(y)):
|
| 877 |
+
diff = y[i] - y[i - 1]
|
| 878 |
+
if diff > half: # Jump from -half to half
|
| 879 |
+
y[i] = (y[i] - unit)
|
| 880 |
+
elif diff < -half: # Jump from half to -half
|
| 881 |
+
y[i] = (y[i] + unit)
|
| 882 |
+
|
| 883 |
+
return x, y
|
| 884 |
+
|
| 885 |
+
|
| 886 |
+
def bode_phase_plot(system, initial_exp=-5, final_exp=5,
|
| 887 |
+
color='b', show_axes=False, grid=True, show=True, freq_unit='rad/sec', phase_unit='rad', phase_unwrap=True, **kwargs):
|
| 888 |
+
r"""
|
| 889 |
+
Returns the Bode phase plot of a continuous-time system.
|
| 890 |
+
|
| 891 |
+
See ``bode_plot`` for all the parameters.
|
| 892 |
+
"""
|
| 893 |
+
x, y = bode_phase_numerical_data(system, initial_exp=initial_exp,
|
| 894 |
+
final_exp=final_exp, freq_unit=freq_unit, phase_unit=phase_unit, phase_unwrap=phase_unwrap)
|
| 895 |
+
plt.plot(x, y, color=color, **kwargs)
|
| 896 |
+
plt.xscale('log')
|
| 897 |
+
|
| 898 |
+
plt.xlabel('Frequency (%s) [Log Scale]' % freq_unit)
|
| 899 |
+
plt.ylabel('Phase (%s)' % phase_unit)
|
| 900 |
+
plt.title(f'Bode Plot (Phase) of ${latex(system)}$', pad=20)
|
| 901 |
+
|
| 902 |
+
if grid:
|
| 903 |
+
plt.grid(True)
|
| 904 |
+
if show_axes:
|
| 905 |
+
plt.axhline(0, color='black')
|
| 906 |
+
plt.axvline(0, color='black')
|
| 907 |
+
if show:
|
| 908 |
+
plt.show()
|
| 909 |
+
return
|
| 910 |
+
|
| 911 |
+
return plt
|
| 912 |
+
|
| 913 |
+
|
| 914 |
+
def bode_plot(system, initial_exp=-5, final_exp=5,
|
| 915 |
+
grid=True, show_axes=False, show=True, freq_unit='rad/sec', phase_unit='rad', phase_unwrap=True, **kwargs):
|
| 916 |
+
r"""
|
| 917 |
+
Returns the Bode phase and magnitude plots of a continuous-time system.
|
| 918 |
+
|
| 919 |
+
Parameters
|
| 920 |
+
==========
|
| 921 |
+
|
| 922 |
+
system : SISOLinearTimeInvariant type
|
| 923 |
+
The LTI SISO system for which the Bode Plot is to be computed.
|
| 924 |
+
initial_exp : Number, optional
|
| 925 |
+
The initial exponent of 10 of the semilog plot. Defaults to -5.
|
| 926 |
+
final_exp : Number, optional
|
| 927 |
+
The final exponent of 10 of the semilog plot. Defaults to 5.
|
| 928 |
+
show : boolean, optional
|
| 929 |
+
If ``True``, the plot will be displayed otherwise
|
| 930 |
+
the equivalent matplotlib ``plot`` object will be returned.
|
| 931 |
+
Defaults to True.
|
| 932 |
+
prec : int, optional
|
| 933 |
+
The decimal point precision for the point coordinate values.
|
| 934 |
+
Defaults to 8.
|
| 935 |
+
grid : boolean, optional
|
| 936 |
+
If ``True``, the plot will have a grid. Defaults to True.
|
| 937 |
+
show_axes : boolean, optional
|
| 938 |
+
If ``True``, the coordinate axes will be shown. Defaults to False.
|
| 939 |
+
freq_unit : string, optional
|
| 940 |
+
User can choose between ``'rad/sec'`` (radians/second) and ``'Hz'`` (Hertz) as frequency units.
|
| 941 |
+
phase_unit : string, optional
|
| 942 |
+
User can choose between ``'rad'`` (radians) and ``'deg'`` (degree) as phase units.
|
| 943 |
+
|
| 944 |
+
Examples
|
| 945 |
+
========
|
| 946 |
+
|
| 947 |
+
.. plot::
|
| 948 |
+
:context: close-figs
|
| 949 |
+
:format: doctest
|
| 950 |
+
:include-source: True
|
| 951 |
+
|
| 952 |
+
>>> from sympy.abc import s
|
| 953 |
+
>>> from sympy.physics.control.lti import TransferFunction
|
| 954 |
+
>>> from sympy.physics.control.control_plots import bode_plot
|
| 955 |
+
>>> tf1 = TransferFunction(1*s**2 + 0.1*s + 7.5, 1*s**4 + 0.12*s**3 + 9*s**2, s)
|
| 956 |
+
>>> bode_plot(tf1, initial_exp=0.2, final_exp=0.7) # doctest: +SKIP
|
| 957 |
+
|
| 958 |
+
See Also
|
| 959 |
+
========
|
| 960 |
+
|
| 961 |
+
bode_magnitude_plot, bode_phase_plot
|
| 962 |
+
|
| 963 |
+
"""
|
| 964 |
+
plt.subplot(211)
|
| 965 |
+
mag = bode_magnitude_plot(system, initial_exp=initial_exp, final_exp=final_exp,
|
| 966 |
+
show=False, grid=grid, show_axes=show_axes,
|
| 967 |
+
freq_unit=freq_unit, **kwargs)
|
| 968 |
+
mag.title(f'Bode Plot of ${latex(system)}$', pad=20)
|
| 969 |
+
mag.xlabel(None)
|
| 970 |
+
plt.subplot(212)
|
| 971 |
+
bode_phase_plot(system, initial_exp=initial_exp, final_exp=final_exp,
|
| 972 |
+
show=False, grid=grid, show_axes=show_axes, freq_unit=freq_unit, phase_unit=phase_unit, phase_unwrap=phase_unwrap, **kwargs).title(None)
|
| 973 |
+
|
| 974 |
+
if show:
|
| 975 |
+
plt.show()
|
| 976 |
+
return
|
| 977 |
+
|
| 978 |
+
return plt
|
evalkit_internvl/lib/python3.10/site-packages/sympy/physics/control/lti.py
ADDED
|
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evalkit_internvl/lib/python3.10/site-packages/sympy/physics/control/tests/__init__.py
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evalkit_internvl/lib/python3.10/site-packages/sympy/physics/control/tests/test_control_plots.py
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|
| 1 |
+
from math import isclose
|
| 2 |
+
from sympy.core.numbers import I
|
| 3 |
+
from sympy.core.symbol import Dummy
|
| 4 |
+
from sympy.functions.elementary.complexes import (Abs, arg)
|
| 5 |
+
from sympy.functions.elementary.exponential import log
|
| 6 |
+
from sympy.abc import s, p, a
|
| 7 |
+
from sympy.external import import_module
|
| 8 |
+
from sympy.physics.control.control_plots import \
|
| 9 |
+
(pole_zero_numerical_data, pole_zero_plot, step_response_numerical_data,
|
| 10 |
+
step_response_plot, impulse_response_numerical_data,
|
| 11 |
+
impulse_response_plot, ramp_response_numerical_data,
|
| 12 |
+
ramp_response_plot, bode_magnitude_numerical_data,
|
| 13 |
+
bode_phase_numerical_data, bode_plot)
|
| 14 |
+
from sympy.physics.control.lti import (TransferFunction,
|
| 15 |
+
Series, Parallel, TransferFunctionMatrix)
|
| 16 |
+
from sympy.testing.pytest import raises, skip
|
| 17 |
+
|
| 18 |
+
matplotlib = import_module(
|
| 19 |
+
'matplotlib', import_kwargs={'fromlist': ['pyplot']},
|
| 20 |
+
catch=(RuntimeError,))
|
| 21 |
+
|
| 22 |
+
numpy = import_module('numpy')
|
| 23 |
+
|
| 24 |
+
tf1 = TransferFunction(1, p**2 + 0.5*p + 2, p)
|
| 25 |
+
tf2 = TransferFunction(p, 6*p**2 + 3*p + 1, p)
|
| 26 |
+
tf3 = TransferFunction(p, p**3 - 1, p)
|
| 27 |
+
tf4 = TransferFunction(10, p**3, p)
|
| 28 |
+
tf5 = TransferFunction(5, s**2 + 2*s + 10, s)
|
| 29 |
+
tf6 = TransferFunction(1, 1, s)
|
| 30 |
+
tf7 = TransferFunction(4*s*3 + 9*s**2 + 0.1*s + 11, 8*s**6 + 9*s**4 + 11, s)
|
| 31 |
+
tf8 = TransferFunction(5, s**2 + (2+I)*s + 10, s)
|
| 32 |
+
|
| 33 |
+
ser1 = Series(tf4, TransferFunction(1, p - 5, p))
|
| 34 |
+
ser2 = Series(tf3, TransferFunction(p, p + 2, p))
|
| 35 |
+
|
| 36 |
+
par1 = Parallel(tf1, tf2)
|
| 37 |
+
|
| 38 |
+
|
| 39 |
+
def _to_tuple(a, b):
|
| 40 |
+
return tuple(a), tuple(b)
|
| 41 |
+
|
| 42 |
+
def _trim_tuple(a, b):
|
| 43 |
+
a, b = _to_tuple(a, b)
|
| 44 |
+
return tuple(a[0: 2] + a[len(a)//2 : len(a)//2 + 1] + a[-2:]), \
|
| 45 |
+
tuple(b[0: 2] + b[len(b)//2 : len(b)//2 + 1] + b[-2:])
|
| 46 |
+
|
| 47 |
+
def y_coordinate_equality(plot_data_func, evalf_func, system):
|
| 48 |
+
"""Checks whether the y-coordinate value of the plotted
|
| 49 |
+
data point is equal to the value of the function at a
|
| 50 |
+
particular x."""
|
| 51 |
+
x, y = plot_data_func(system)
|
| 52 |
+
x, y = _trim_tuple(x, y)
|
| 53 |
+
y_exp = tuple(evalf_func(system, x_i) for x_i in x)
|
| 54 |
+
return all(Abs(y_exp_i - y_i) < 1e-8 for y_exp_i, y_i in zip(y_exp, y))
|
| 55 |
+
|
| 56 |
+
|
| 57 |
+
def test_errors():
|
| 58 |
+
if not matplotlib:
|
| 59 |
+
skip("Matplotlib not the default backend")
|
| 60 |
+
|
| 61 |
+
# Invalid `system` check
|
| 62 |
+
tfm = TransferFunctionMatrix([[tf6, tf5], [tf5, tf6]])
|
| 63 |
+
expr = 1/(s**2 - 1)
|
| 64 |
+
raises(NotImplementedError, lambda: pole_zero_plot(tfm))
|
| 65 |
+
raises(NotImplementedError, lambda: pole_zero_numerical_data(expr))
|
| 66 |
+
raises(NotImplementedError, lambda: impulse_response_plot(expr))
|
| 67 |
+
raises(NotImplementedError, lambda: impulse_response_numerical_data(tfm))
|
| 68 |
+
raises(NotImplementedError, lambda: step_response_plot(tfm))
|
| 69 |
+
raises(NotImplementedError, lambda: step_response_numerical_data(expr))
|
| 70 |
+
raises(NotImplementedError, lambda: ramp_response_plot(expr))
|
| 71 |
+
raises(NotImplementedError, lambda: ramp_response_numerical_data(tfm))
|
| 72 |
+
raises(NotImplementedError, lambda: bode_plot(tfm))
|
| 73 |
+
|
| 74 |
+
# More than 1 variables
|
| 75 |
+
tf_a = TransferFunction(a, s + 1, s)
|
| 76 |
+
raises(ValueError, lambda: pole_zero_plot(tf_a))
|
| 77 |
+
raises(ValueError, lambda: pole_zero_numerical_data(tf_a))
|
| 78 |
+
raises(ValueError, lambda: impulse_response_plot(tf_a))
|
| 79 |
+
raises(ValueError, lambda: impulse_response_numerical_data(tf_a))
|
| 80 |
+
raises(ValueError, lambda: step_response_plot(tf_a))
|
| 81 |
+
raises(ValueError, lambda: step_response_numerical_data(tf_a))
|
| 82 |
+
raises(ValueError, lambda: ramp_response_plot(tf_a))
|
| 83 |
+
raises(ValueError, lambda: ramp_response_numerical_data(tf_a))
|
| 84 |
+
raises(ValueError, lambda: bode_plot(tf_a))
|
| 85 |
+
|
| 86 |
+
# lower_limit > 0 for response plots
|
| 87 |
+
raises(ValueError, lambda: impulse_response_plot(tf1, lower_limit=-1))
|
| 88 |
+
raises(ValueError, lambda: step_response_plot(tf1, lower_limit=-0.1))
|
| 89 |
+
raises(ValueError, lambda: ramp_response_plot(tf1, lower_limit=-4/3))
|
| 90 |
+
|
| 91 |
+
# slope in ramp_response_plot() is negative
|
| 92 |
+
raises(ValueError, lambda: ramp_response_plot(tf1, slope=-0.1))
|
| 93 |
+
|
| 94 |
+
# incorrect frequency or phase unit
|
| 95 |
+
raises(ValueError, lambda: bode_plot(tf1,freq_unit = 'hz'))
|
| 96 |
+
raises(ValueError, lambda: bode_plot(tf1,phase_unit = 'degree'))
|
| 97 |
+
|
| 98 |
+
|
| 99 |
+
def test_pole_zero():
|
| 100 |
+
if not numpy:
|
| 101 |
+
skip("NumPy is required for this test")
|
| 102 |
+
|
| 103 |
+
def pz_tester(sys, expected_value):
|
| 104 |
+
z, p = pole_zero_numerical_data(sys)
|
| 105 |
+
z_check = numpy.allclose(z, expected_value[0])
|
| 106 |
+
p_check = numpy.allclose(p, expected_value[1])
|
| 107 |
+
return p_check and z_check
|
| 108 |
+
|
| 109 |
+
exp1 = [[], [-0.24999999999999994+1.3919410907075054j, -0.24999999999999994-1.3919410907075054j]]
|
| 110 |
+
exp2 = [[0.0], [-0.25+0.3227486121839514j, -0.25-0.3227486121839514j]]
|
| 111 |
+
exp3 = [[0.0], [-0.5000000000000004+0.8660254037844395j,
|
| 112 |
+
-0.5000000000000004-0.8660254037844395j, 0.9999999999999998+0j]]
|
| 113 |
+
exp4 = [[], [5.0, 0.0, 0.0, 0.0]]
|
| 114 |
+
exp5 = [[-5.645751311064592, -0.5000000000000008, -0.3542486889354093],
|
| 115 |
+
[-0.24999999999999986+1.3919410907075052j,
|
| 116 |
+
-0.24999999999999986-1.3919410907075052j, -0.2499999999999998+0.32274861218395134j,
|
| 117 |
+
-0.2499999999999998-0.32274861218395134j]]
|
| 118 |
+
exp6 = [[], [-1.1641600331447917-3.545808351896439j,
|
| 119 |
+
-0.8358399668552097+2.5458083518964383j]]
|
| 120 |
+
|
| 121 |
+
assert pz_tester(tf1, exp1)
|
| 122 |
+
assert pz_tester(tf2, exp2)
|
| 123 |
+
assert pz_tester(tf3, exp3)
|
| 124 |
+
assert pz_tester(ser1, exp4)
|
| 125 |
+
assert pz_tester(par1, exp5)
|
| 126 |
+
assert pz_tester(tf8, exp6)
|
| 127 |
+
|
| 128 |
+
|
| 129 |
+
def test_bode():
|
| 130 |
+
if not numpy:
|
| 131 |
+
skip("NumPy is required for this test")
|
| 132 |
+
|
| 133 |
+
def bode_phase_evalf(system, point):
|
| 134 |
+
expr = system.to_expr()
|
| 135 |
+
_w = Dummy("w", real=True)
|
| 136 |
+
w_expr = expr.subs({system.var: I*_w})
|
| 137 |
+
return arg(w_expr).subs({_w: point}).evalf()
|
| 138 |
+
|
| 139 |
+
def bode_mag_evalf(system, point):
|
| 140 |
+
expr = system.to_expr()
|
| 141 |
+
_w = Dummy("w", real=True)
|
| 142 |
+
w_expr = expr.subs({system.var: I*_w})
|
| 143 |
+
return 20*log(Abs(w_expr), 10).subs({_w: point}).evalf()
|
| 144 |
+
|
| 145 |
+
def test_bode_data(sys):
|
| 146 |
+
return y_coordinate_equality(bode_magnitude_numerical_data, bode_mag_evalf, sys) \
|
| 147 |
+
and y_coordinate_equality(bode_phase_numerical_data, bode_phase_evalf, sys)
|
| 148 |
+
|
| 149 |
+
assert test_bode_data(tf1)
|
| 150 |
+
assert test_bode_data(tf2)
|
| 151 |
+
assert test_bode_data(tf3)
|
| 152 |
+
assert test_bode_data(tf4)
|
| 153 |
+
assert test_bode_data(tf5)
|
| 154 |
+
|
| 155 |
+
|
| 156 |
+
def check_point_accuracy(a, b):
|
| 157 |
+
return all(isclose(*_, rel_tol=1e-1, abs_tol=1e-6
|
| 158 |
+
) for _ in zip(a, b))
|
| 159 |
+
|
| 160 |
+
|
| 161 |
+
def test_impulse_response():
|
| 162 |
+
if not numpy:
|
| 163 |
+
skip("NumPy is required for this test")
|
| 164 |
+
|
| 165 |
+
def impulse_res_tester(sys, expected_value):
|
| 166 |
+
x, y = _to_tuple(*impulse_response_numerical_data(sys,
|
| 167 |
+
adaptive=False, n=10))
|
| 168 |
+
x_check = check_point_accuracy(x, expected_value[0])
|
| 169 |
+
y_check = check_point_accuracy(y, expected_value[1])
|
| 170 |
+
return x_check and y_check
|
| 171 |
+
|
| 172 |
+
exp1 = ((0.0, 1.1111111111111112, 2.2222222222222223, 3.3333333333333335, 4.444444444444445,
|
| 173 |
+
5.555555555555555, 6.666666666666667, 7.777777777777779, 8.88888888888889, 10.0),
|
| 174 |
+
(0.0, 0.544019738507865, 0.01993849743234938, -0.31140243360893216, -0.022852779906491996, 0.1778306498155759,
|
| 175 |
+
0.01962941084328499, -0.1013115194573652, -0.014975541213105696, 0.0575789724730714))
|
| 176 |
+
exp2 = ((0.0, 1.1111111111111112, 2.2222222222222223, 3.3333333333333335, 4.444444444444445, 5.555555555555555,
|
| 177 |
+
6.666666666666667, 7.777777777777779, 8.88888888888889, 10.0), (0.1666666675, 0.08389223412935855,
|
| 178 |
+
0.02338051973475047, -0.014966807776379383, -0.034645954223054234, -0.040560075735512804,
|
| 179 |
+
-0.037658628907103885, -0.030149507719590022, -0.021162090730736834, -0.012721292737437523))
|
| 180 |
+
exp3 = ((0.0, 1.1111111111111112, 2.2222222222222223, 3.3333333333333335, 4.444444444444445, 5.555555555555555,
|
| 181 |
+
6.666666666666667, 7.777777777777779, 8.88888888888889, 10.0), (4.369893391586999e-09, 1.1750333000630964,
|
| 182 |
+
3.2922404058312473, 9.432290008148343, 28.37098083007151, 86.18577464367974, 261.90356653762115,
|
| 183 |
+
795.6538758627842, 2416.9920942096983, 7342.159505206647))
|
| 184 |
+
exp4 = ((0.0, 1.1111111111111112, 2.2222222222222223, 3.3333333333333335, 4.444444444444445, 5.555555555555555,
|
| 185 |
+
6.666666666666667, 7.777777777777779, 8.88888888888889, 10.0), (0.0, 6.17283950617284, 24.69135802469136,
|
| 186 |
+
55.555555555555564, 98.76543209876544, 154.320987654321, 222.22222222222226, 302.46913580246917,
|
| 187 |
+
395.0617283950618, 500.0))
|
| 188 |
+
exp5 = ((0.0, 1.1111111111111112, 2.2222222222222223, 3.3333333333333335, 4.444444444444445, 5.555555555555555,
|
| 189 |
+
6.666666666666667, 7.777777777777779, 8.88888888888889, 10.0), (0.0, -0.10455606138085417,
|
| 190 |
+
0.06757671513476461, -0.03234567568833768, 0.013582514927757873, -0.005273419510705473,
|
| 191 |
+
0.0019364083003354075, -0.000680070134067832, 0.00022969845960406913, -7.476094359583917e-05))
|
| 192 |
+
exp6 = ((0.0, 1.1111111111111112, 2.2222222222222223, 3.3333333333333335, 4.444444444444445,
|
| 193 |
+
5.555555555555555, 6.666666666666667, 7.777777777777779, 8.88888888888889, 10.0),
|
| 194 |
+
(-6.016699583000218e-09, 0.35039802056107394, 3.3728423827689884, 12.119846079276684,
|
| 195 |
+
25.86101014293389, 29.352480635282088, -30.49475907497664, -273.8717189554019, -863.2381702029659,
|
| 196 |
+
-1747.0262164682233))
|
| 197 |
+
exp7 = ((0.0, 1.1111111111111112, 2.2222222222222223, 3.3333333333333335,
|
| 198 |
+
4.444444444444445, 5.555555555555555, 6.666666666666667, 7.777777777777779,
|
| 199 |
+
8.88888888888889, 10.0), (0.0, 18.934638095560974, 5346.93244680907, 1384609.8718249386,
|
| 200 |
+
358161126.65801865, 92645770015.70108, 23964739753087.42, 6198974342083139.0, 1.603492601616059e+18,
|
| 201 |
+
4.147764422869658e+20))
|
| 202 |
+
|
| 203 |
+
assert impulse_res_tester(tf1, exp1)
|
| 204 |
+
assert impulse_res_tester(tf2, exp2)
|
| 205 |
+
assert impulse_res_tester(tf3, exp3)
|
| 206 |
+
assert impulse_res_tester(tf4, exp4)
|
| 207 |
+
assert impulse_res_tester(tf5, exp5)
|
| 208 |
+
assert impulse_res_tester(tf7, exp6)
|
| 209 |
+
assert impulse_res_tester(ser1, exp7)
|
| 210 |
+
|
| 211 |
+
|
| 212 |
+
def test_step_response():
|
| 213 |
+
if not numpy:
|
| 214 |
+
skip("NumPy is required for this test")
|
| 215 |
+
|
| 216 |
+
def step_res_tester(sys, expected_value):
|
| 217 |
+
x, y = _to_tuple(*step_response_numerical_data(sys,
|
| 218 |
+
adaptive=False, n=10))
|
| 219 |
+
x_check = check_point_accuracy(x, expected_value[0])
|
| 220 |
+
y_check = check_point_accuracy(y, expected_value[1])
|
| 221 |
+
return x_check and y_check
|
| 222 |
+
|
| 223 |
+
exp1 = ((0.0, 1.1111111111111112, 2.2222222222222223, 3.3333333333333335, 4.444444444444445,
|
| 224 |
+
5.555555555555555, 6.666666666666667, 7.777777777777779, 8.88888888888889, 10.0),
|
| 225 |
+
(-1.9193285738516863e-08, 0.42283495488246126, 0.7840485977945262, 0.5546841805655717,
|
| 226 |
+
0.33903033806932087, 0.4627251747410237, 0.5909907598988051, 0.5247213989553071,
|
| 227 |
+
0.4486997874319281, 0.4839358435839171))
|
| 228 |
+
exp2 = ((0.0, 1.1111111111111112, 2.2222222222222223, 3.3333333333333335, 4.444444444444445,
|
| 229 |
+
5.555555555555555, 6.666666666666667, 7.777777777777779, 8.88888888888889, 10.0),
|
| 230 |
+
(0.0, 0.13728409095645816, 0.19474559355325086, 0.1974909129243011, 0.16841657696573073,
|
| 231 |
+
0.12559777736159378, 0.08153828016664713, 0.04360471317348958, 0.015072994568868221,
|
| 232 |
+
-0.003636420058445484))
|
| 233 |
+
exp3 = ((0.0, 1.1111111111111112, 2.2222222222222223, 3.3333333333333335, 4.444444444444445,
|
| 234 |
+
5.555555555555555, 6.666666666666667, 7.777777777777779, 8.88888888888889, 10.0),
|
| 235 |
+
(0.0, 0.6314542141914303, 2.9356520038101035, 9.37731009663807, 28.452300356688376,
|
| 236 |
+
86.25721933273988, 261.9236645044672, 795.6435410577224, 2416.9786984578764, 7342.154119725917))
|
| 237 |
+
exp4 = ((0.0, 1.1111111111111112, 2.2222222222222223, 3.3333333333333335, 4.444444444444445,
|
| 238 |
+
5.555555555555555, 6.666666666666667, 7.777777777777779, 8.88888888888889, 10.0),
|
| 239 |
+
(0.0, 2.286236899862826, 18.28989519890261, 61.72839629629631, 146.31916159122088, 285.7796124828532,
|
| 240 |
+
493.8271703703705, 784.1792566529494, 1170.553292729767, 1666.6667))
|
| 241 |
+
exp5 = ((0.0, 1.1111111111111112, 2.2222222222222223, 3.3333333333333335, 4.444444444444445,
|
| 242 |
+
5.555555555555555, 6.666666666666667, 7.777777777777779, 8.88888888888889, 10.0),
|
| 243 |
+
(-3.999999997894577e-09, 0.6720357068882895, 0.4429938256137113, 0.5182010838004518,
|
| 244 |
+
0.4944139147159695, 0.5016379853883338, 0.4995466896527733, 0.5001154784851325,
|
| 245 |
+
0.49997448824584123, 0.5000039745919259))
|
| 246 |
+
exp6 = ((0.0, 1.1111111111111112, 2.2222222222222223, 3.3333333333333335, 4.444444444444445,
|
| 247 |
+
5.555555555555555, 6.666666666666667, 7.777777777777779, 8.88888888888889, 10.0),
|
| 248 |
+
(-1.5433688493882158e-09, 0.3428705539937336, 1.1253619102202777, 3.1849962651016517,
|
| 249 |
+
9.47532757182671, 28.727231099148135, 87.29426924860557, 265.2138681048606, 805.6636260007757,
|
| 250 |
+
2447.387582370878))
|
| 251 |
+
|
| 252 |
+
assert step_res_tester(tf1, exp1)
|
| 253 |
+
assert step_res_tester(tf2, exp2)
|
| 254 |
+
assert step_res_tester(tf3, exp3)
|
| 255 |
+
assert step_res_tester(tf4, exp4)
|
| 256 |
+
assert step_res_tester(tf5, exp5)
|
| 257 |
+
assert step_res_tester(ser2, exp6)
|
| 258 |
+
|
| 259 |
+
|
| 260 |
+
def test_ramp_response():
|
| 261 |
+
if not numpy:
|
| 262 |
+
skip("NumPy is required for this test")
|
| 263 |
+
|
| 264 |
+
def ramp_res_tester(sys, num_points, expected_value, slope=1):
|
| 265 |
+
x, y = _to_tuple(*ramp_response_numerical_data(sys,
|
| 266 |
+
slope=slope, adaptive=False, n=num_points))
|
| 267 |
+
x_check = check_point_accuracy(x, expected_value[0])
|
| 268 |
+
y_check = check_point_accuracy(y, expected_value[1])
|
| 269 |
+
return x_check and y_check
|
| 270 |
+
|
| 271 |
+
exp1 = ((0.0, 2.0, 4.0, 6.0, 8.0, 10.0), (0.0, 0.7324667795033895, 1.9909720978650398,
|
| 272 |
+
2.7956587704217783, 3.9224897567931514, 4.85022655284895))
|
| 273 |
+
exp2 = ((0.0, 1.1111111111111112, 2.2222222222222223, 3.3333333333333335, 4.444444444444445,
|
| 274 |
+
5.555555555555555, 6.666666666666667, 7.777777777777779, 8.88888888888889, 10.0),
|
| 275 |
+
(2.4360213402019326e-08, 0.10175320182493253, 0.33057612497658406, 0.5967937263298935,
|
| 276 |
+
0.8431511866718248, 1.0398805391471613, 1.1776043125035738, 1.2600994825747305, 1.2981042689274653,
|
| 277 |
+
1.304684417610106))
|
| 278 |
+
exp3 = ((0.0, 1.1111111111111112, 2.2222222222222223, 3.3333333333333335, 4.444444444444445, 5.555555555555555,
|
| 279 |
+
6.666666666666667, 7.777777777777779, 8.88888888888889, 10.0), (-3.9329040468771836e-08,
|
| 280 |
+
0.34686634635794555, 2.9998828170537903, 12.33303690737476, 40.993913948137795, 127.84145222317912,
|
| 281 |
+
391.41713691996, 1192.0006858708389, 3623.9808672503405, 11011.728034546572))
|
| 282 |
+
exp4 = ((0.0, 1.1111111111111112, 2.2222222222222223, 3.3333333333333335, 4.444444444444445, 5.555555555555555,
|
| 283 |
+
6.666666666666667, 7.777777777777779, 8.88888888888889, 10.0), (0.0, 1.9051973784484078, 30.483158055174524,
|
| 284 |
+
154.32098765432104, 487.7305288827924, 1190.7483615302544, 2469.1358024691367, 4574.3789056546275,
|
| 285 |
+
7803.688462124678, 12500.0))
|
| 286 |
+
exp5 = ((0.0, 1.1111111111111112, 2.2222222222222223, 3.3333333333333335, 4.444444444444445, 5.555555555555555,
|
| 287 |
+
6.666666666666667, 7.777777777777779, 8.88888888888889, 10.0), (0.0, 3.8844361856975635, 9.141792069209865,
|
| 288 |
+
14.096349157657231, 19.09783068994694, 24.10179770390321, 29.09907319114121, 34.10040420185154,
|
| 289 |
+
39.09983919254265, 44.10006013058409))
|
| 290 |
+
exp6 = ((0.0, 1.1111111111111112, 2.2222222222222223, 3.3333333333333335, 4.444444444444445, 5.555555555555555,
|
| 291 |
+
6.666666666666667, 7.777777777777779, 8.88888888888889, 10.0), (0.0, 1.1111111111111112, 2.2222222222222223,
|
| 292 |
+
3.3333333333333335, 4.444444444444445, 5.555555555555555, 6.666666666666667, 7.777777777777779, 8.88888888888889, 10.0))
|
| 293 |
+
|
| 294 |
+
assert ramp_res_tester(tf1, 6, exp1)
|
| 295 |
+
assert ramp_res_tester(tf2, 10, exp2, 1.2)
|
| 296 |
+
assert ramp_res_tester(tf3, 10, exp3, 1.5)
|
| 297 |
+
assert ramp_res_tester(tf4, 10, exp4, 3)
|
| 298 |
+
assert ramp_res_tester(tf5, 10, exp5, 9)
|
| 299 |
+
assert ramp_res_tester(tf6, 10, exp6)
|
evalkit_internvl/lib/python3.10/site-packages/sympy/physics/hep/__init__.py
ADDED
|
File without changes
|
evalkit_internvl/lib/python3.10/site-packages/sympy/physics/hep/__pycache__/__init__.cpython-310.pyc
ADDED
|
Binary file (179 Bytes). View file
|
|
|
evalkit_internvl/lib/python3.10/site-packages/sympy/physics/hep/__pycache__/gamma_matrices.cpython-310.pyc
ADDED
|
Binary file (14 kB). View file
|
|
|
evalkit_internvl/lib/python3.10/site-packages/sympy/physics/hep/gamma_matrices.py
ADDED
|
@@ -0,0 +1,716 @@
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|
| 1 |
+
"""
|
| 2 |
+
Module to handle gamma matrices expressed as tensor objects.
|
| 3 |
+
|
| 4 |
+
Examples
|
| 5 |
+
========
|
| 6 |
+
|
| 7 |
+
>>> from sympy.physics.hep.gamma_matrices import GammaMatrix as G, LorentzIndex
|
| 8 |
+
>>> from sympy.tensor.tensor import tensor_indices
|
| 9 |
+
>>> i = tensor_indices('i', LorentzIndex)
|
| 10 |
+
>>> G(i)
|
| 11 |
+
GammaMatrix(i)
|
| 12 |
+
|
| 13 |
+
Note that there is already an instance of GammaMatrixHead in four dimensions:
|
| 14 |
+
GammaMatrix, which is simply declare as
|
| 15 |
+
|
| 16 |
+
>>> from sympy.physics.hep.gamma_matrices import GammaMatrix
|
| 17 |
+
>>> from sympy.tensor.tensor import tensor_indices
|
| 18 |
+
>>> i = tensor_indices('i', LorentzIndex)
|
| 19 |
+
>>> GammaMatrix(i)
|
| 20 |
+
GammaMatrix(i)
|
| 21 |
+
|
| 22 |
+
To access the metric tensor
|
| 23 |
+
|
| 24 |
+
>>> LorentzIndex.metric
|
| 25 |
+
metric(LorentzIndex,LorentzIndex)
|
| 26 |
+
|
| 27 |
+
"""
|
| 28 |
+
from sympy.core.mul import Mul
|
| 29 |
+
from sympy.core.singleton import S
|
| 30 |
+
from sympy.matrices.dense import eye
|
| 31 |
+
from sympy.matrices.expressions.trace import trace
|
| 32 |
+
from sympy.tensor.tensor import TensorIndexType, TensorIndex,\
|
| 33 |
+
TensMul, TensAdd, tensor_mul, Tensor, TensorHead, TensorSymmetry
|
| 34 |
+
|
| 35 |
+
|
| 36 |
+
# DiracSpinorIndex = TensorIndexType('DiracSpinorIndex', dim=4, dummy_name="S")
|
| 37 |
+
|
| 38 |
+
|
| 39 |
+
LorentzIndex = TensorIndexType('LorentzIndex', dim=4, dummy_name="L")
|
| 40 |
+
|
| 41 |
+
|
| 42 |
+
GammaMatrix = TensorHead("GammaMatrix", [LorentzIndex],
|
| 43 |
+
TensorSymmetry.no_symmetry(1), comm=None)
|
| 44 |
+
|
| 45 |
+
|
| 46 |
+
def extract_type_tens(expression, component):
|
| 47 |
+
"""
|
| 48 |
+
Extract from a ``TensExpr`` all tensors with `component`.
|
| 49 |
+
|
| 50 |
+
Returns two tensor expressions:
|
| 51 |
+
|
| 52 |
+
* the first contains all ``Tensor`` of having `component`.
|
| 53 |
+
* the second contains all remaining.
|
| 54 |
+
|
| 55 |
+
|
| 56 |
+
"""
|
| 57 |
+
if isinstance(expression, Tensor):
|
| 58 |
+
sp = [expression]
|
| 59 |
+
elif isinstance(expression, TensMul):
|
| 60 |
+
sp = expression.args
|
| 61 |
+
else:
|
| 62 |
+
raise ValueError('wrong type')
|
| 63 |
+
|
| 64 |
+
# Collect all gamma matrices of the same dimension
|
| 65 |
+
new_expr = S.One
|
| 66 |
+
residual_expr = S.One
|
| 67 |
+
for i in sp:
|
| 68 |
+
if isinstance(i, Tensor) and i.component == component:
|
| 69 |
+
new_expr *= i
|
| 70 |
+
else:
|
| 71 |
+
residual_expr *= i
|
| 72 |
+
return new_expr, residual_expr
|
| 73 |
+
|
| 74 |
+
|
| 75 |
+
def simplify_gamma_expression(expression):
|
| 76 |
+
extracted_expr, residual_expr = extract_type_tens(expression, GammaMatrix)
|
| 77 |
+
res_expr = _simplify_single_line(extracted_expr)
|
| 78 |
+
return res_expr * residual_expr
|
| 79 |
+
|
| 80 |
+
|
| 81 |
+
def simplify_gpgp(ex, sort=True):
|
| 82 |
+
"""
|
| 83 |
+
simplify products ``G(i)*p(-i)*G(j)*p(-j) -> p(i)*p(-i)``
|
| 84 |
+
|
| 85 |
+
Examples
|
| 86 |
+
========
|
| 87 |
+
|
| 88 |
+
>>> from sympy.physics.hep.gamma_matrices import GammaMatrix as G, \
|
| 89 |
+
LorentzIndex, simplify_gpgp
|
| 90 |
+
>>> from sympy.tensor.tensor import tensor_indices, tensor_heads
|
| 91 |
+
>>> p, q = tensor_heads('p, q', [LorentzIndex])
|
| 92 |
+
>>> i0,i1,i2,i3,i4,i5 = tensor_indices('i0:6', LorentzIndex)
|
| 93 |
+
>>> ps = p(i0)*G(-i0)
|
| 94 |
+
>>> qs = q(i0)*G(-i0)
|
| 95 |
+
>>> simplify_gpgp(ps*qs*qs)
|
| 96 |
+
GammaMatrix(-L_0)*p(L_0)*q(L_1)*q(-L_1)
|
| 97 |
+
"""
|
| 98 |
+
def _simplify_gpgp(ex):
|
| 99 |
+
components = ex.components
|
| 100 |
+
a = []
|
| 101 |
+
comp_map = []
|
| 102 |
+
for i, comp in enumerate(components):
|
| 103 |
+
comp_map.extend([i]*comp.rank)
|
| 104 |
+
dum = [(i[0], i[1], comp_map[i[0]], comp_map[i[1]]) for i in ex.dum]
|
| 105 |
+
for i in range(len(components)):
|
| 106 |
+
if components[i] != GammaMatrix:
|
| 107 |
+
continue
|
| 108 |
+
for dx in dum:
|
| 109 |
+
if dx[2] == i:
|
| 110 |
+
p_pos1 = dx[3]
|
| 111 |
+
elif dx[3] == i:
|
| 112 |
+
p_pos1 = dx[2]
|
| 113 |
+
else:
|
| 114 |
+
continue
|
| 115 |
+
comp1 = components[p_pos1]
|
| 116 |
+
if comp1.comm == 0 and comp1.rank == 1:
|
| 117 |
+
a.append((i, p_pos1))
|
| 118 |
+
if not a:
|
| 119 |
+
return ex
|
| 120 |
+
elim = set()
|
| 121 |
+
tv = []
|
| 122 |
+
hit = True
|
| 123 |
+
coeff = S.One
|
| 124 |
+
ta = None
|
| 125 |
+
while hit:
|
| 126 |
+
hit = False
|
| 127 |
+
for i, ai in enumerate(a[:-1]):
|
| 128 |
+
if ai[0] in elim:
|
| 129 |
+
continue
|
| 130 |
+
if ai[0] != a[i + 1][0] - 1:
|
| 131 |
+
continue
|
| 132 |
+
if components[ai[1]] != components[a[i + 1][1]]:
|
| 133 |
+
continue
|
| 134 |
+
elim.add(ai[0])
|
| 135 |
+
elim.add(ai[1])
|
| 136 |
+
elim.add(a[i + 1][0])
|
| 137 |
+
elim.add(a[i + 1][1])
|
| 138 |
+
if not ta:
|
| 139 |
+
ta = ex.split()
|
| 140 |
+
mu = TensorIndex('mu', LorentzIndex)
|
| 141 |
+
hit = True
|
| 142 |
+
if i == 0:
|
| 143 |
+
coeff = ex.coeff
|
| 144 |
+
tx = components[ai[1]](mu)*components[ai[1]](-mu)
|
| 145 |
+
if len(a) == 2:
|
| 146 |
+
tx *= 4 # eye(4)
|
| 147 |
+
tv.append(tx)
|
| 148 |
+
break
|
| 149 |
+
|
| 150 |
+
if tv:
|
| 151 |
+
a = [x for j, x in enumerate(ta) if j not in elim]
|
| 152 |
+
a.extend(tv)
|
| 153 |
+
t = tensor_mul(*a)*coeff
|
| 154 |
+
# t = t.replace(lambda x: x.is_Matrix, lambda x: 1)
|
| 155 |
+
return t
|
| 156 |
+
else:
|
| 157 |
+
return ex
|
| 158 |
+
|
| 159 |
+
if sort:
|
| 160 |
+
ex = ex.sorted_components()
|
| 161 |
+
# this would be better off with pattern matching
|
| 162 |
+
while 1:
|
| 163 |
+
t = _simplify_gpgp(ex)
|
| 164 |
+
if t != ex:
|
| 165 |
+
ex = t
|
| 166 |
+
else:
|
| 167 |
+
return t
|
| 168 |
+
|
| 169 |
+
|
| 170 |
+
def gamma_trace(t):
|
| 171 |
+
"""
|
| 172 |
+
trace of a single line of gamma matrices
|
| 173 |
+
|
| 174 |
+
Examples
|
| 175 |
+
========
|
| 176 |
+
|
| 177 |
+
>>> from sympy.physics.hep.gamma_matrices import GammaMatrix as G, \
|
| 178 |
+
gamma_trace, LorentzIndex
|
| 179 |
+
>>> from sympy.tensor.tensor import tensor_indices, tensor_heads
|
| 180 |
+
>>> p, q = tensor_heads('p, q', [LorentzIndex])
|
| 181 |
+
>>> i0,i1,i2,i3,i4,i5 = tensor_indices('i0:6', LorentzIndex)
|
| 182 |
+
>>> ps = p(i0)*G(-i0)
|
| 183 |
+
>>> qs = q(i0)*G(-i0)
|
| 184 |
+
>>> gamma_trace(G(i0)*G(i1))
|
| 185 |
+
4*metric(i0, i1)
|
| 186 |
+
>>> gamma_trace(ps*ps) - 4*p(i0)*p(-i0)
|
| 187 |
+
0
|
| 188 |
+
>>> gamma_trace(ps*qs + ps*ps) - 4*p(i0)*p(-i0) - 4*p(i0)*q(-i0)
|
| 189 |
+
0
|
| 190 |
+
|
| 191 |
+
"""
|
| 192 |
+
if isinstance(t, TensAdd):
|
| 193 |
+
res = TensAdd(*[gamma_trace(x) for x in t.args])
|
| 194 |
+
return res
|
| 195 |
+
t = _simplify_single_line(t)
|
| 196 |
+
res = _trace_single_line(t)
|
| 197 |
+
return res
|
| 198 |
+
|
| 199 |
+
|
| 200 |
+
def _simplify_single_line(expression):
|
| 201 |
+
"""
|
| 202 |
+
Simplify single-line product of gamma matrices.
|
| 203 |
+
|
| 204 |
+
Examples
|
| 205 |
+
========
|
| 206 |
+
|
| 207 |
+
>>> from sympy.physics.hep.gamma_matrices import GammaMatrix as G, \
|
| 208 |
+
LorentzIndex, _simplify_single_line
|
| 209 |
+
>>> from sympy.tensor.tensor import tensor_indices, TensorHead
|
| 210 |
+
>>> p = TensorHead('p', [LorentzIndex])
|
| 211 |
+
>>> i0,i1 = tensor_indices('i0:2', LorentzIndex)
|
| 212 |
+
>>> _simplify_single_line(G(i0)*G(i1)*p(-i1)*G(-i0)) + 2*G(i0)*p(-i0)
|
| 213 |
+
0
|
| 214 |
+
|
| 215 |
+
"""
|
| 216 |
+
t1, t2 = extract_type_tens(expression, GammaMatrix)
|
| 217 |
+
if t1 != 1:
|
| 218 |
+
t1 = kahane_simplify(t1)
|
| 219 |
+
res = t1*t2
|
| 220 |
+
return res
|
| 221 |
+
|
| 222 |
+
|
| 223 |
+
def _trace_single_line(t):
|
| 224 |
+
"""
|
| 225 |
+
Evaluate the trace of a single gamma matrix line inside a ``TensExpr``.
|
| 226 |
+
|
| 227 |
+
Notes
|
| 228 |
+
=====
|
| 229 |
+
|
| 230 |
+
If there are ``DiracSpinorIndex.auto_left`` and ``DiracSpinorIndex.auto_right``
|
| 231 |
+
indices trace over them; otherwise traces are not implied (explain)
|
| 232 |
+
|
| 233 |
+
|
| 234 |
+
Examples
|
| 235 |
+
========
|
| 236 |
+
|
| 237 |
+
>>> from sympy.physics.hep.gamma_matrices import GammaMatrix as G, \
|
| 238 |
+
LorentzIndex, _trace_single_line
|
| 239 |
+
>>> from sympy.tensor.tensor import tensor_indices, TensorHead
|
| 240 |
+
>>> p = TensorHead('p', [LorentzIndex])
|
| 241 |
+
>>> i0,i1,i2,i3,i4,i5 = tensor_indices('i0:6', LorentzIndex)
|
| 242 |
+
>>> _trace_single_line(G(i0)*G(i1))
|
| 243 |
+
4*metric(i0, i1)
|
| 244 |
+
>>> _trace_single_line(G(i0)*p(-i0)*G(i1)*p(-i1)) - 4*p(i0)*p(-i0)
|
| 245 |
+
0
|
| 246 |
+
|
| 247 |
+
"""
|
| 248 |
+
def _trace_single_line1(t):
|
| 249 |
+
t = t.sorted_components()
|
| 250 |
+
components = t.components
|
| 251 |
+
ncomps = len(components)
|
| 252 |
+
g = LorentzIndex.metric
|
| 253 |
+
# gamma matirices are in a[i:j]
|
| 254 |
+
hit = 0
|
| 255 |
+
for i in range(ncomps):
|
| 256 |
+
if components[i] == GammaMatrix:
|
| 257 |
+
hit = 1
|
| 258 |
+
break
|
| 259 |
+
|
| 260 |
+
for j in range(i + hit, ncomps):
|
| 261 |
+
if components[j] != GammaMatrix:
|
| 262 |
+
break
|
| 263 |
+
else:
|
| 264 |
+
j = ncomps
|
| 265 |
+
numG = j - i
|
| 266 |
+
if numG == 0:
|
| 267 |
+
tcoeff = t.coeff
|
| 268 |
+
return t.nocoeff if tcoeff else t
|
| 269 |
+
if numG % 2 == 1:
|
| 270 |
+
return TensMul.from_data(S.Zero, [], [], [])
|
| 271 |
+
elif numG > 4:
|
| 272 |
+
# find the open matrix indices and connect them:
|
| 273 |
+
a = t.split()
|
| 274 |
+
ind1 = a[i].get_indices()[0]
|
| 275 |
+
ind2 = a[i + 1].get_indices()[0]
|
| 276 |
+
aa = a[:i] + a[i + 2:]
|
| 277 |
+
t1 = tensor_mul(*aa)*g(ind1, ind2)
|
| 278 |
+
t1 = t1.contract_metric(g)
|
| 279 |
+
args = [t1]
|
| 280 |
+
sign = 1
|
| 281 |
+
for k in range(i + 2, j):
|
| 282 |
+
sign = -sign
|
| 283 |
+
ind2 = a[k].get_indices()[0]
|
| 284 |
+
aa = a[:i] + a[i + 1:k] + a[k + 1:]
|
| 285 |
+
t2 = sign*tensor_mul(*aa)*g(ind1, ind2)
|
| 286 |
+
t2 = t2.contract_metric(g)
|
| 287 |
+
t2 = simplify_gpgp(t2, False)
|
| 288 |
+
args.append(t2)
|
| 289 |
+
t3 = TensAdd(*args)
|
| 290 |
+
t3 = _trace_single_line(t3)
|
| 291 |
+
return t3
|
| 292 |
+
else:
|
| 293 |
+
a = t.split()
|
| 294 |
+
t1 = _gamma_trace1(*a[i:j])
|
| 295 |
+
a2 = a[:i] + a[j:]
|
| 296 |
+
t2 = tensor_mul(*a2)
|
| 297 |
+
t3 = t1*t2
|
| 298 |
+
if not t3:
|
| 299 |
+
return t3
|
| 300 |
+
t3 = t3.contract_metric(g)
|
| 301 |
+
return t3
|
| 302 |
+
|
| 303 |
+
t = t.expand()
|
| 304 |
+
if isinstance(t, TensAdd):
|
| 305 |
+
a = [_trace_single_line1(x)*x.coeff for x in t.args]
|
| 306 |
+
return TensAdd(*a)
|
| 307 |
+
elif isinstance(t, (Tensor, TensMul)):
|
| 308 |
+
r = t.coeff*_trace_single_line1(t)
|
| 309 |
+
return r
|
| 310 |
+
else:
|
| 311 |
+
return trace(t)
|
| 312 |
+
|
| 313 |
+
|
| 314 |
+
def _gamma_trace1(*a):
|
| 315 |
+
gctr = 4 # FIXME specific for d=4
|
| 316 |
+
g = LorentzIndex.metric
|
| 317 |
+
if not a:
|
| 318 |
+
return gctr
|
| 319 |
+
n = len(a)
|
| 320 |
+
if n%2 == 1:
|
| 321 |
+
#return TensMul.from_data(S.Zero, [], [], [])
|
| 322 |
+
return S.Zero
|
| 323 |
+
if n == 2:
|
| 324 |
+
ind0 = a[0].get_indices()[0]
|
| 325 |
+
ind1 = a[1].get_indices()[0]
|
| 326 |
+
return gctr*g(ind0, ind1)
|
| 327 |
+
if n == 4:
|
| 328 |
+
ind0 = a[0].get_indices()[0]
|
| 329 |
+
ind1 = a[1].get_indices()[0]
|
| 330 |
+
ind2 = a[2].get_indices()[0]
|
| 331 |
+
ind3 = a[3].get_indices()[0]
|
| 332 |
+
|
| 333 |
+
return gctr*(g(ind0, ind1)*g(ind2, ind3) - \
|
| 334 |
+
g(ind0, ind2)*g(ind1, ind3) + g(ind0, ind3)*g(ind1, ind2))
|
| 335 |
+
|
| 336 |
+
|
| 337 |
+
def kahane_simplify(expression):
|
| 338 |
+
r"""
|
| 339 |
+
This function cancels contracted elements in a product of four
|
| 340 |
+
dimensional gamma matrices, resulting in an expression equal to the given
|
| 341 |
+
one, without the contracted gamma matrices.
|
| 342 |
+
|
| 343 |
+
Parameters
|
| 344 |
+
==========
|
| 345 |
+
|
| 346 |
+
`expression` the tensor expression containing the gamma matrices to simplify.
|
| 347 |
+
|
| 348 |
+
Notes
|
| 349 |
+
=====
|
| 350 |
+
|
| 351 |
+
If spinor indices are given, the matrices must be given in
|
| 352 |
+
the order given in the product.
|
| 353 |
+
|
| 354 |
+
Algorithm
|
| 355 |
+
=========
|
| 356 |
+
|
| 357 |
+
The idea behind the algorithm is to use some well-known identities,
|
| 358 |
+
i.e., for contractions enclosing an even number of `\gamma` matrices
|
| 359 |
+
|
| 360 |
+
`\gamma^\mu \gamma_{a_1} \cdots \gamma_{a_{2N}} \gamma_\mu = 2 (\gamma_{a_{2N}} \gamma_{a_1} \cdots \gamma_{a_{2N-1}} + \gamma_{a_{2N-1}} \cdots \gamma_{a_1} \gamma_{a_{2N}} )`
|
| 361 |
+
|
| 362 |
+
for an odd number of `\gamma` matrices
|
| 363 |
+
|
| 364 |
+
`\gamma^\mu \gamma_{a_1} \cdots \gamma_{a_{2N+1}} \gamma_\mu = -2 \gamma_{a_{2N+1}} \gamma_{a_{2N}} \cdots \gamma_{a_{1}}`
|
| 365 |
+
|
| 366 |
+
Instead of repeatedly applying these identities to cancel out all contracted indices,
|
| 367 |
+
it is possible to recognize the links that would result from such an operation,
|
| 368 |
+
the problem is thus reduced to a simple rearrangement of free gamma matrices.
|
| 369 |
+
|
| 370 |
+
Examples
|
| 371 |
+
========
|
| 372 |
+
|
| 373 |
+
When using, always remember that the original expression coefficient
|
| 374 |
+
has to be handled separately
|
| 375 |
+
|
| 376 |
+
>>> from sympy.physics.hep.gamma_matrices import GammaMatrix as G, LorentzIndex
|
| 377 |
+
>>> from sympy.physics.hep.gamma_matrices import kahane_simplify
|
| 378 |
+
>>> from sympy.tensor.tensor import tensor_indices
|
| 379 |
+
>>> i0, i1, i2 = tensor_indices('i0:3', LorentzIndex)
|
| 380 |
+
>>> ta = G(i0)*G(-i0)
|
| 381 |
+
>>> kahane_simplify(ta)
|
| 382 |
+
Matrix([
|
| 383 |
+
[4, 0, 0, 0],
|
| 384 |
+
[0, 4, 0, 0],
|
| 385 |
+
[0, 0, 4, 0],
|
| 386 |
+
[0, 0, 0, 4]])
|
| 387 |
+
>>> tb = G(i0)*G(i1)*G(-i0)
|
| 388 |
+
>>> kahane_simplify(tb)
|
| 389 |
+
-2*GammaMatrix(i1)
|
| 390 |
+
>>> t = G(i0)*G(-i0)
|
| 391 |
+
>>> kahane_simplify(t)
|
| 392 |
+
Matrix([
|
| 393 |
+
[4, 0, 0, 0],
|
| 394 |
+
[0, 4, 0, 0],
|
| 395 |
+
[0, 0, 4, 0],
|
| 396 |
+
[0, 0, 0, 4]])
|
| 397 |
+
>>> t = G(i0)*G(-i0)
|
| 398 |
+
>>> kahane_simplify(t)
|
| 399 |
+
Matrix([
|
| 400 |
+
[4, 0, 0, 0],
|
| 401 |
+
[0, 4, 0, 0],
|
| 402 |
+
[0, 0, 4, 0],
|
| 403 |
+
[0, 0, 0, 4]])
|
| 404 |
+
|
| 405 |
+
If there are no contractions, the same expression is returned
|
| 406 |
+
|
| 407 |
+
>>> tc = G(i0)*G(i1)
|
| 408 |
+
>>> kahane_simplify(tc)
|
| 409 |
+
GammaMatrix(i0)*GammaMatrix(i1)
|
| 410 |
+
|
| 411 |
+
References
|
| 412 |
+
==========
|
| 413 |
+
|
| 414 |
+
[1] Algorithm for Reducing Contracted Products of gamma Matrices,
|
| 415 |
+
Joseph Kahane, Journal of Mathematical Physics, Vol. 9, No. 10, October 1968.
|
| 416 |
+
"""
|
| 417 |
+
|
| 418 |
+
if isinstance(expression, Mul):
|
| 419 |
+
return expression
|
| 420 |
+
if isinstance(expression, TensAdd):
|
| 421 |
+
return TensAdd(*[kahane_simplify(arg) for arg in expression.args])
|
| 422 |
+
|
| 423 |
+
if isinstance(expression, Tensor):
|
| 424 |
+
return expression
|
| 425 |
+
|
| 426 |
+
assert isinstance(expression, TensMul)
|
| 427 |
+
|
| 428 |
+
gammas = expression.args
|
| 429 |
+
|
| 430 |
+
for gamma in gammas:
|
| 431 |
+
assert gamma.component == GammaMatrix
|
| 432 |
+
|
| 433 |
+
free = expression.free
|
| 434 |
+
# spinor_free = [_ for _ in expression.free_in_args if _[1] != 0]
|
| 435 |
+
|
| 436 |
+
# if len(spinor_free) == 2:
|
| 437 |
+
# spinor_free.sort(key=lambda x: x[2])
|
| 438 |
+
# assert spinor_free[0][1] == 1 and spinor_free[-1][1] == 2
|
| 439 |
+
# assert spinor_free[0][2] == 0
|
| 440 |
+
# elif spinor_free:
|
| 441 |
+
# raise ValueError('spinor indices do not match')
|
| 442 |
+
|
| 443 |
+
dum = []
|
| 444 |
+
for dum_pair in expression.dum:
|
| 445 |
+
if expression.index_types[dum_pair[0]] == LorentzIndex:
|
| 446 |
+
dum.append((dum_pair[0], dum_pair[1]))
|
| 447 |
+
|
| 448 |
+
dum = sorted(dum)
|
| 449 |
+
|
| 450 |
+
if len(dum) == 0: # or GammaMatrixHead:
|
| 451 |
+
# no contractions in `expression`, just return it.
|
| 452 |
+
return expression
|
| 453 |
+
|
| 454 |
+
# find the `first_dum_pos`, i.e. the position of the first contracted
|
| 455 |
+
# gamma matrix, Kahane's algorithm as described in his paper requires the
|
| 456 |
+
# gamma matrix expression to start with a contracted gamma matrix, this is
|
| 457 |
+
# a workaround which ignores possible initial free indices, and re-adds
|
| 458 |
+
# them later.
|
| 459 |
+
|
| 460 |
+
first_dum_pos = min(map(min, dum))
|
| 461 |
+
|
| 462 |
+
# for p1, p2, a1, a2 in expression.dum_in_args:
|
| 463 |
+
# if p1 != 0 or p2 != 0:
|
| 464 |
+
# # only Lorentz indices, skip Dirac indices:
|
| 465 |
+
# continue
|
| 466 |
+
# first_dum_pos = min(p1, p2)
|
| 467 |
+
# break
|
| 468 |
+
|
| 469 |
+
total_number = len(free) + len(dum)*2
|
| 470 |
+
number_of_contractions = len(dum)
|
| 471 |
+
|
| 472 |
+
free_pos = [None]*total_number
|
| 473 |
+
for i in free:
|
| 474 |
+
free_pos[i[1]] = i[0]
|
| 475 |
+
|
| 476 |
+
# `index_is_free` is a list of booleans, to identify index position
|
| 477 |
+
# and whether that index is free or dummy.
|
| 478 |
+
index_is_free = [False]*total_number
|
| 479 |
+
|
| 480 |
+
for i, indx in enumerate(free):
|
| 481 |
+
index_is_free[indx[1]] = True
|
| 482 |
+
|
| 483 |
+
# `links` is a dictionary containing the graph described in Kahane's paper,
|
| 484 |
+
# to every key correspond one or two values, representing the linked indices.
|
| 485 |
+
# All values in `links` are integers, negative numbers are used in the case
|
| 486 |
+
# where it is necessary to insert gamma matrices between free indices, in
|
| 487 |
+
# order to make Kahane's algorithm work (see paper).
|
| 488 |
+
links = {i: [] for i in range(first_dum_pos, total_number)}
|
| 489 |
+
|
| 490 |
+
# `cum_sign` is a step variable to mark the sign of every index, see paper.
|
| 491 |
+
cum_sign = -1
|
| 492 |
+
# `cum_sign_list` keeps storage for all `cum_sign` (every index).
|
| 493 |
+
cum_sign_list = [None]*total_number
|
| 494 |
+
block_free_count = 0
|
| 495 |
+
|
| 496 |
+
# multiply `resulting_coeff` by the coefficient parameter, the rest
|
| 497 |
+
# of the algorithm ignores a scalar coefficient.
|
| 498 |
+
resulting_coeff = S.One
|
| 499 |
+
|
| 500 |
+
# initialize a list of lists of indices. The outer list will contain all
|
| 501 |
+
# additive tensor expressions, while the inner list will contain the
|
| 502 |
+
# free indices (rearranged according to the algorithm).
|
| 503 |
+
resulting_indices = [[]]
|
| 504 |
+
|
| 505 |
+
# start to count the `connected_components`, which together with the number
|
| 506 |
+
# of contractions, determines a -1 or +1 factor to be multiplied.
|
| 507 |
+
connected_components = 1
|
| 508 |
+
|
| 509 |
+
# First loop: here we fill `cum_sign_list`, and draw the links
|
| 510 |
+
# among consecutive indices (they are stored in `links`). Links among
|
| 511 |
+
# non-consecutive indices will be drawn later.
|
| 512 |
+
for i, is_free in enumerate(index_is_free):
|
| 513 |
+
# if `expression` starts with free indices, they are ignored here;
|
| 514 |
+
# they are later added as they are to the beginning of all
|
| 515 |
+
# `resulting_indices` list of lists of indices.
|
| 516 |
+
if i < first_dum_pos:
|
| 517 |
+
continue
|
| 518 |
+
|
| 519 |
+
if is_free:
|
| 520 |
+
block_free_count += 1
|
| 521 |
+
# if previous index was free as well, draw an arch in `links`.
|
| 522 |
+
if block_free_count > 1:
|
| 523 |
+
links[i - 1].append(i)
|
| 524 |
+
links[i].append(i - 1)
|
| 525 |
+
else:
|
| 526 |
+
# Change the sign of the index (`cum_sign`) if the number of free
|
| 527 |
+
# indices preceding it is even.
|
| 528 |
+
cum_sign *= 1 if (block_free_count % 2) else -1
|
| 529 |
+
if block_free_count == 0 and i != first_dum_pos:
|
| 530 |
+
# check if there are two consecutive dummy indices:
|
| 531 |
+
# in this case create virtual indices with negative position,
|
| 532 |
+
# these "virtual" indices represent the insertion of two
|
| 533 |
+
# gamma^0 matrices to separate consecutive dummy indices, as
|
| 534 |
+
# Kahane's algorithm requires dummy indices to be separated by
|
| 535 |
+
# free indices. The product of two gamma^0 matrices is unity,
|
| 536 |
+
# so the new expression being examined is the same as the
|
| 537 |
+
# original one.
|
| 538 |
+
if cum_sign == -1:
|
| 539 |
+
links[-1-i] = [-1-i+1]
|
| 540 |
+
links[-1-i+1] = [-1-i]
|
| 541 |
+
if (i - cum_sign) in links:
|
| 542 |
+
if i != first_dum_pos:
|
| 543 |
+
links[i].append(i - cum_sign)
|
| 544 |
+
if block_free_count != 0:
|
| 545 |
+
if i - cum_sign < len(index_is_free):
|
| 546 |
+
if index_is_free[i - cum_sign]:
|
| 547 |
+
links[i - cum_sign].append(i)
|
| 548 |
+
block_free_count = 0
|
| 549 |
+
|
| 550 |
+
cum_sign_list[i] = cum_sign
|
| 551 |
+
|
| 552 |
+
# The previous loop has only created links between consecutive free indices,
|
| 553 |
+
# it is necessary to properly create links among dummy (contracted) indices,
|
| 554 |
+
# according to the rules described in Kahane's paper. There is only one exception
|
| 555 |
+
# to Kahane's rules: the negative indices, which handle the case of some
|
| 556 |
+
# consecutive free indices (Kahane's paper just describes dummy indices
|
| 557 |
+
# separated by free indices, hinting that free indices can be added without
|
| 558 |
+
# altering the expression result).
|
| 559 |
+
for i in dum:
|
| 560 |
+
# get the positions of the two contracted indices:
|
| 561 |
+
pos1 = i[0]
|
| 562 |
+
pos2 = i[1]
|
| 563 |
+
|
| 564 |
+
# create Kahane's upper links, i.e. the upper arcs between dummy
|
| 565 |
+
# (i.e. contracted) indices:
|
| 566 |
+
links[pos1].append(pos2)
|
| 567 |
+
links[pos2].append(pos1)
|
| 568 |
+
|
| 569 |
+
# create Kahane's lower links, this corresponds to the arcs below
|
| 570 |
+
# the line described in the paper:
|
| 571 |
+
|
| 572 |
+
# first we move `pos1` and `pos2` according to the sign of the indices:
|
| 573 |
+
linkpos1 = pos1 + cum_sign_list[pos1]
|
| 574 |
+
linkpos2 = pos2 + cum_sign_list[pos2]
|
| 575 |
+
|
| 576 |
+
# otherwise, perform some checks before creating the lower arcs:
|
| 577 |
+
|
| 578 |
+
# make sure we are not exceeding the total number of indices:
|
| 579 |
+
if linkpos1 >= total_number:
|
| 580 |
+
continue
|
| 581 |
+
if linkpos2 >= total_number:
|
| 582 |
+
continue
|
| 583 |
+
|
| 584 |
+
# make sure we are not below the first dummy index in `expression`:
|
| 585 |
+
if linkpos1 < first_dum_pos:
|
| 586 |
+
continue
|
| 587 |
+
if linkpos2 < first_dum_pos:
|
| 588 |
+
continue
|
| 589 |
+
|
| 590 |
+
# check if the previous loop created "virtual" indices between dummy
|
| 591 |
+
# indices, in such a case relink `linkpos1` and `linkpos2`:
|
| 592 |
+
if (-1-linkpos1) in links:
|
| 593 |
+
linkpos1 = -1-linkpos1
|
| 594 |
+
if (-1-linkpos2) in links:
|
| 595 |
+
linkpos2 = -1-linkpos2
|
| 596 |
+
|
| 597 |
+
# move only if not next to free index:
|
| 598 |
+
if linkpos1 >= 0 and not index_is_free[linkpos1]:
|
| 599 |
+
linkpos1 = pos1
|
| 600 |
+
|
| 601 |
+
if linkpos2 >=0 and not index_is_free[linkpos2]:
|
| 602 |
+
linkpos2 = pos2
|
| 603 |
+
|
| 604 |
+
# create the lower arcs:
|
| 605 |
+
if linkpos2 not in links[linkpos1]:
|
| 606 |
+
links[linkpos1].append(linkpos2)
|
| 607 |
+
if linkpos1 not in links[linkpos2]:
|
| 608 |
+
links[linkpos2].append(linkpos1)
|
| 609 |
+
|
| 610 |
+
# This loop starts from the `first_dum_pos` index (first dummy index)
|
| 611 |
+
# walks through the graph deleting the visited indices from `links`,
|
| 612 |
+
# it adds a gamma matrix for every free index in encounters, while it
|
| 613 |
+
# completely ignores dummy indices and virtual indices.
|
| 614 |
+
pointer = first_dum_pos
|
| 615 |
+
previous_pointer = 0
|
| 616 |
+
while True:
|
| 617 |
+
if pointer in links:
|
| 618 |
+
next_ones = links.pop(pointer)
|
| 619 |
+
else:
|
| 620 |
+
break
|
| 621 |
+
|
| 622 |
+
if previous_pointer in next_ones:
|
| 623 |
+
next_ones.remove(previous_pointer)
|
| 624 |
+
|
| 625 |
+
previous_pointer = pointer
|
| 626 |
+
|
| 627 |
+
if next_ones:
|
| 628 |
+
pointer = next_ones[0]
|
| 629 |
+
else:
|
| 630 |
+
break
|
| 631 |
+
|
| 632 |
+
if pointer == previous_pointer:
|
| 633 |
+
break
|
| 634 |
+
if pointer >=0 and free_pos[pointer] is not None:
|
| 635 |
+
for ri in resulting_indices:
|
| 636 |
+
ri.append(free_pos[pointer])
|
| 637 |
+
|
| 638 |
+
# The following loop removes the remaining connected components in `links`.
|
| 639 |
+
# If there are free indices inside a connected component, it gives a
|
| 640 |
+
# contribution to the resulting expression given by the factor
|
| 641 |
+
# `gamma_a gamma_b ... gamma_z + gamma_z ... gamma_b gamma_a`, in Kahanes's
|
| 642 |
+
# paper represented as {gamma_a, gamma_b, ... , gamma_z},
|
| 643 |
+
# virtual indices are ignored. The variable `connected_components` is
|
| 644 |
+
# increased by one for every connected component this loop encounters.
|
| 645 |
+
|
| 646 |
+
# If the connected component has virtual and dummy indices only
|
| 647 |
+
# (no free indices), it contributes to `resulting_indices` by a factor of two.
|
| 648 |
+
# The multiplication by two is a result of the
|
| 649 |
+
# factor {gamma^0, gamma^0} = 2 I, as it appears in Kahane's paper.
|
| 650 |
+
# Note: curly brackets are meant as in the paper, as a generalized
|
| 651 |
+
# multi-element anticommutator!
|
| 652 |
+
|
| 653 |
+
while links:
|
| 654 |
+
connected_components += 1
|
| 655 |
+
pointer = min(links.keys())
|
| 656 |
+
previous_pointer = pointer
|
| 657 |
+
# the inner loop erases the visited indices from `links`, and it adds
|
| 658 |
+
# all free indices to `prepend_indices` list, virtual indices are
|
| 659 |
+
# ignored.
|
| 660 |
+
prepend_indices = []
|
| 661 |
+
while True:
|
| 662 |
+
if pointer in links:
|
| 663 |
+
next_ones = links.pop(pointer)
|
| 664 |
+
else:
|
| 665 |
+
break
|
| 666 |
+
|
| 667 |
+
if previous_pointer in next_ones:
|
| 668 |
+
if len(next_ones) > 1:
|
| 669 |
+
next_ones.remove(previous_pointer)
|
| 670 |
+
|
| 671 |
+
previous_pointer = pointer
|
| 672 |
+
|
| 673 |
+
if next_ones:
|
| 674 |
+
pointer = next_ones[0]
|
| 675 |
+
|
| 676 |
+
if pointer >= first_dum_pos and free_pos[pointer] is not None:
|
| 677 |
+
prepend_indices.insert(0, free_pos[pointer])
|
| 678 |
+
# if `prepend_indices` is void, it means there are no free indices
|
| 679 |
+
# in the loop (and it can be shown that there must be a virtual index),
|
| 680 |
+
# loops of virtual indices only contribute by a factor of two:
|
| 681 |
+
if len(prepend_indices) == 0:
|
| 682 |
+
resulting_coeff *= 2
|
| 683 |
+
# otherwise, add the free indices in `prepend_indices` to
|
| 684 |
+
# the `resulting_indices`:
|
| 685 |
+
else:
|
| 686 |
+
expr1 = prepend_indices
|
| 687 |
+
expr2 = list(reversed(prepend_indices))
|
| 688 |
+
resulting_indices = [expri + ri for ri in resulting_indices for expri in (expr1, expr2)]
|
| 689 |
+
|
| 690 |
+
# sign correction, as described in Kahane's paper:
|
| 691 |
+
resulting_coeff *= -1 if (number_of_contractions - connected_components + 1) % 2 else 1
|
| 692 |
+
# power of two factor, as described in Kahane's paper:
|
| 693 |
+
resulting_coeff *= 2**(number_of_contractions)
|
| 694 |
+
|
| 695 |
+
# If `first_dum_pos` is not zero, it means that there are trailing free gamma
|
| 696 |
+
# matrices in front of `expression`, so multiply by them:
|
| 697 |
+
resulting_indices = [ free_pos[0:first_dum_pos] + ri for ri in resulting_indices ]
|
| 698 |
+
|
| 699 |
+
resulting_expr = S.Zero
|
| 700 |
+
for i in resulting_indices:
|
| 701 |
+
temp_expr = S.One
|
| 702 |
+
for j in i:
|
| 703 |
+
temp_expr *= GammaMatrix(j)
|
| 704 |
+
resulting_expr += temp_expr
|
| 705 |
+
|
| 706 |
+
t = resulting_coeff * resulting_expr
|
| 707 |
+
t1 = None
|
| 708 |
+
if isinstance(t, TensAdd):
|
| 709 |
+
t1 = t.args[0]
|
| 710 |
+
elif isinstance(t, TensMul):
|
| 711 |
+
t1 = t
|
| 712 |
+
if t1:
|
| 713 |
+
pass
|
| 714 |
+
else:
|
| 715 |
+
t = eye(4)*t
|
| 716 |
+
return t
|
evalkit_internvl/lib/python3.10/site-packages/sympy/physics/hep/tests/__init__.py
ADDED
|
File without changes
|
evalkit_internvl/lib/python3.10/site-packages/sympy/physics/hep/tests/__pycache__/__init__.cpython-310.pyc
ADDED
|
Binary file (185 Bytes). View file
|
|
|
evalkit_internvl/lib/python3.10/site-packages/sympy/physics/hep/tests/__pycache__/test_gamma_matrices.cpython-310.pyc
ADDED
|
Binary file (13.2 kB). View file
|
|
|
evalkit_internvl/lib/python3.10/site-packages/sympy/physics/hep/tests/test_gamma_matrices.py
ADDED
|
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|
|
|
|
|
|
|
|
|
|
| 1 |
+
from sympy.matrices.dense import eye, Matrix
|
| 2 |
+
from sympy.tensor.tensor import tensor_indices, TensorHead, tensor_heads, \
|
| 3 |
+
TensExpr, canon_bp
|
| 4 |
+
from sympy.physics.hep.gamma_matrices import GammaMatrix as G, LorentzIndex, \
|
| 5 |
+
kahane_simplify, gamma_trace, _simplify_single_line, simplify_gamma_expression
|
| 6 |
+
from sympy import Symbol
|
| 7 |
+
|
| 8 |
+
|
| 9 |
+
def _is_tensor_eq(arg1, arg2):
|
| 10 |
+
arg1 = canon_bp(arg1)
|
| 11 |
+
arg2 = canon_bp(arg2)
|
| 12 |
+
if isinstance(arg1, TensExpr):
|
| 13 |
+
return arg1.equals(arg2)
|
| 14 |
+
elif isinstance(arg2, TensExpr):
|
| 15 |
+
return arg2.equals(arg1)
|
| 16 |
+
return arg1 == arg2
|
| 17 |
+
|
| 18 |
+
def execute_gamma_simplify_tests_for_function(tfunc, D):
|
| 19 |
+
"""
|
| 20 |
+
Perform tests to check if sfunc is able to simplify gamma matrix expressions.
|
| 21 |
+
|
| 22 |
+
Parameters
|
| 23 |
+
==========
|
| 24 |
+
|
| 25 |
+
`sfunc` a function to simplify a `TIDS`, shall return the simplified `TIDS`.
|
| 26 |
+
`D` the number of dimension (in most cases `D=4`).
|
| 27 |
+
|
| 28 |
+
"""
|
| 29 |
+
|
| 30 |
+
mu, nu, rho, sigma = tensor_indices("mu, nu, rho, sigma", LorentzIndex)
|
| 31 |
+
a1, a2, a3, a4, a5, a6 = tensor_indices("a1:7", LorentzIndex)
|
| 32 |
+
mu11, mu12, mu21, mu31, mu32, mu41, mu51, mu52 = tensor_indices("mu11, mu12, mu21, mu31, mu32, mu41, mu51, mu52", LorentzIndex)
|
| 33 |
+
mu61, mu71, mu72 = tensor_indices("mu61, mu71, mu72", LorentzIndex)
|
| 34 |
+
m0, m1, m2, m3, m4, m5, m6 = tensor_indices("m0:7", LorentzIndex)
|
| 35 |
+
|
| 36 |
+
def g(xx, yy):
|
| 37 |
+
return (G(xx)*G(yy) + G(yy)*G(xx))/2
|
| 38 |
+
|
| 39 |
+
# Some examples taken from Kahane's paper, 4 dim only:
|
| 40 |
+
if D == 4:
|
| 41 |
+
t = (G(a1)*G(mu11)*G(a2)*G(mu21)*G(-a1)*G(mu31)*G(-a2))
|
| 42 |
+
assert _is_tensor_eq(tfunc(t), -4*G(mu11)*G(mu31)*G(mu21) - 4*G(mu31)*G(mu11)*G(mu21))
|
| 43 |
+
|
| 44 |
+
t = (G(a1)*G(mu11)*G(mu12)*\
|
| 45 |
+
G(a2)*G(mu21)*\
|
| 46 |
+
G(a3)*G(mu31)*G(mu32)*\
|
| 47 |
+
G(a4)*G(mu41)*\
|
| 48 |
+
G(-a2)*G(mu51)*G(mu52)*\
|
| 49 |
+
G(-a1)*G(mu61)*\
|
| 50 |
+
G(-a3)*G(mu71)*G(mu72)*\
|
| 51 |
+
G(-a4))
|
| 52 |
+
assert _is_tensor_eq(tfunc(t), \
|
| 53 |
+
16*G(mu31)*G(mu32)*G(mu72)*G(mu71)*G(mu11)*G(mu52)*G(mu51)*G(mu12)*G(mu61)*G(mu21)*G(mu41) + 16*G(mu31)*G(mu32)*G(mu72)*G(mu71)*G(mu12)*G(mu51)*G(mu52)*G(mu11)*G(mu61)*G(mu21)*G(mu41) + 16*G(mu71)*G(mu72)*G(mu32)*G(mu31)*G(mu11)*G(mu52)*G(mu51)*G(mu12)*G(mu61)*G(mu21)*G(mu41) + 16*G(mu71)*G(mu72)*G(mu32)*G(mu31)*G(mu12)*G(mu51)*G(mu52)*G(mu11)*G(mu61)*G(mu21)*G(mu41))
|
| 54 |
+
|
| 55 |
+
# Fully Lorentz-contracted expressions, these return scalars:
|
| 56 |
+
|
| 57 |
+
def add_delta(ne):
|
| 58 |
+
return ne * eye(4) # DiracSpinorIndex.delta(DiracSpinorIndex.auto_left, -DiracSpinorIndex.auto_right)
|
| 59 |
+
|
| 60 |
+
t = (G(mu)*G(-mu))
|
| 61 |
+
ts = add_delta(D)
|
| 62 |
+
assert _is_tensor_eq(tfunc(t), ts)
|
| 63 |
+
|
| 64 |
+
t = (G(mu)*G(nu)*G(-mu)*G(-nu))
|
| 65 |
+
ts = add_delta(2*D - D**2) # -8
|
| 66 |
+
assert _is_tensor_eq(tfunc(t), ts)
|
| 67 |
+
|
| 68 |
+
t = (G(mu)*G(nu)*G(-nu)*G(-mu))
|
| 69 |
+
ts = add_delta(D**2) # 16
|
| 70 |
+
assert _is_tensor_eq(tfunc(t), ts)
|
| 71 |
+
|
| 72 |
+
t = (G(mu)*G(nu)*G(-rho)*G(-nu)*G(-mu)*G(rho))
|
| 73 |
+
ts = add_delta(4*D - 4*D**2 + D**3) # 16
|
| 74 |
+
assert _is_tensor_eq(tfunc(t), ts)
|
| 75 |
+
|
| 76 |
+
t = (G(mu)*G(nu)*G(rho)*G(-rho)*G(-nu)*G(-mu))
|
| 77 |
+
ts = add_delta(D**3) # 64
|
| 78 |
+
assert _is_tensor_eq(tfunc(t), ts)
|
| 79 |
+
|
| 80 |
+
t = (G(a1)*G(a2)*G(a3)*G(a4)*G(-a3)*G(-a1)*G(-a2)*G(-a4))
|
| 81 |
+
ts = add_delta(-8*D + 16*D**2 - 8*D**3 + D**4) # -32
|
| 82 |
+
assert _is_tensor_eq(tfunc(t), ts)
|
| 83 |
+
|
| 84 |
+
t = (G(-mu)*G(-nu)*G(-rho)*G(-sigma)*G(nu)*G(mu)*G(sigma)*G(rho))
|
| 85 |
+
ts = add_delta(-16*D + 24*D**2 - 8*D**3 + D**4) # 64
|
| 86 |
+
assert _is_tensor_eq(tfunc(t), ts)
|
| 87 |
+
|
| 88 |
+
t = (G(-mu)*G(nu)*G(-rho)*G(sigma)*G(rho)*G(-nu)*G(mu)*G(-sigma))
|
| 89 |
+
ts = add_delta(8*D - 12*D**2 + 6*D**3 - D**4) # -32
|
| 90 |
+
assert _is_tensor_eq(tfunc(t), ts)
|
| 91 |
+
|
| 92 |
+
t = (G(a1)*G(a2)*G(a3)*G(a4)*G(a5)*G(-a3)*G(-a2)*G(-a1)*G(-a5)*G(-a4))
|
| 93 |
+
ts = add_delta(64*D - 112*D**2 + 60*D**3 - 12*D**4 + D**5) # 256
|
| 94 |
+
assert _is_tensor_eq(tfunc(t), ts)
|
| 95 |
+
|
| 96 |
+
t = (G(a1)*G(a2)*G(a3)*G(a4)*G(a5)*G(-a3)*G(-a1)*G(-a2)*G(-a4)*G(-a5))
|
| 97 |
+
ts = add_delta(64*D - 120*D**2 + 72*D**3 - 16*D**4 + D**5) # -128
|
| 98 |
+
assert _is_tensor_eq(tfunc(t), ts)
|
| 99 |
+
|
| 100 |
+
t = (G(a1)*G(a2)*G(a3)*G(a4)*G(a5)*G(a6)*G(-a3)*G(-a2)*G(-a1)*G(-a6)*G(-a5)*G(-a4))
|
| 101 |
+
ts = add_delta(416*D - 816*D**2 + 528*D**3 - 144*D**4 + 18*D**5 - D**6) # -128
|
| 102 |
+
assert _is_tensor_eq(tfunc(t), ts)
|
| 103 |
+
|
| 104 |
+
t = (G(a1)*G(a2)*G(a3)*G(a4)*G(a5)*G(a6)*G(-a2)*G(-a3)*G(-a1)*G(-a6)*G(-a4)*G(-a5))
|
| 105 |
+
ts = add_delta(416*D - 848*D**2 + 584*D**3 - 172*D**4 + 22*D**5 - D**6) # -128
|
| 106 |
+
assert _is_tensor_eq(tfunc(t), ts)
|
| 107 |
+
|
| 108 |
+
# Expressions with free indices:
|
| 109 |
+
|
| 110 |
+
t = (G(mu)*G(nu)*G(rho)*G(sigma)*G(-mu))
|
| 111 |
+
assert _is_tensor_eq(tfunc(t), (-2*G(sigma)*G(rho)*G(nu) + (4-D)*G(nu)*G(rho)*G(sigma)))
|
| 112 |
+
|
| 113 |
+
t = (G(mu)*G(nu)*G(-mu))
|
| 114 |
+
assert _is_tensor_eq(tfunc(t), (2-D)*G(nu))
|
| 115 |
+
|
| 116 |
+
t = (G(mu)*G(nu)*G(rho)*G(-mu))
|
| 117 |
+
assert _is_tensor_eq(tfunc(t), 2*G(nu)*G(rho) + 2*G(rho)*G(nu) - (4-D)*G(nu)*G(rho))
|
| 118 |
+
|
| 119 |
+
t = 2*G(m2)*G(m0)*G(m1)*G(-m0)*G(-m1)
|
| 120 |
+
st = tfunc(t)
|
| 121 |
+
assert _is_tensor_eq(st, (D*(-2*D + 4))*G(m2))
|
| 122 |
+
|
| 123 |
+
t = G(m2)*G(m0)*G(m1)*G(-m0)*G(-m2)
|
| 124 |
+
st = tfunc(t)
|
| 125 |
+
assert _is_tensor_eq(st, ((-D + 2)**2)*G(m1))
|
| 126 |
+
|
| 127 |
+
t = G(m0)*G(m1)*G(m2)*G(m3)*G(-m1)
|
| 128 |
+
st = tfunc(t)
|
| 129 |
+
assert _is_tensor_eq(st, (D - 4)*G(m0)*G(m2)*G(m3) + 4*G(m0)*g(m2, m3))
|
| 130 |
+
|
| 131 |
+
t = G(m0)*G(m1)*G(m2)*G(m3)*G(-m1)*G(-m0)
|
| 132 |
+
st = tfunc(t)
|
| 133 |
+
assert _is_tensor_eq(st, ((D - 4)**2)*G(m2)*G(m3) + (8*D - 16)*g(m2, m3))
|
| 134 |
+
|
| 135 |
+
t = G(m2)*G(m0)*G(m1)*G(-m2)*G(-m0)
|
| 136 |
+
st = tfunc(t)
|
| 137 |
+
assert _is_tensor_eq(st, ((-D + 2)*(D - 4) + 4)*G(m1))
|
| 138 |
+
|
| 139 |
+
t = G(m3)*G(m1)*G(m0)*G(m2)*G(-m3)*G(-m0)*G(-m2)
|
| 140 |
+
st = tfunc(t)
|
| 141 |
+
assert _is_tensor_eq(st, (-4*D + (-D + 2)**2*(D - 4) + 8)*G(m1))
|
| 142 |
+
|
| 143 |
+
t = 2*G(m0)*G(m1)*G(m2)*G(m3)*G(-m0)
|
| 144 |
+
st = tfunc(t)
|
| 145 |
+
assert _is_tensor_eq(st, ((-2*D + 8)*G(m1)*G(m2)*G(m3) - 4*G(m3)*G(m2)*G(m1)))
|
| 146 |
+
|
| 147 |
+
t = G(m5)*G(m0)*G(m1)*G(m4)*G(m2)*G(-m4)*G(m3)*G(-m0)
|
| 148 |
+
st = tfunc(t)
|
| 149 |
+
assert _is_tensor_eq(st, (((-D + 2)*(-D + 4))*G(m5)*G(m1)*G(m2)*G(m3) + (2*D - 4)*G(m5)*G(m3)*G(m2)*G(m1)))
|
| 150 |
+
|
| 151 |
+
t = -G(m0)*G(m1)*G(m2)*G(m3)*G(-m0)*G(m4)
|
| 152 |
+
st = tfunc(t)
|
| 153 |
+
assert _is_tensor_eq(st, ((D - 4)*G(m1)*G(m2)*G(m3)*G(m4) + 2*G(m3)*G(m2)*G(m1)*G(m4)))
|
| 154 |
+
|
| 155 |
+
t = G(-m5)*G(m0)*G(m1)*G(m2)*G(m3)*G(m4)*G(-m0)*G(m5)
|
| 156 |
+
st = tfunc(t)
|
| 157 |
+
|
| 158 |
+
result1 = ((-D + 4)**2 + 4)*G(m1)*G(m2)*G(m3)*G(m4) +\
|
| 159 |
+
(4*D - 16)*G(m3)*G(m2)*G(m1)*G(m4) + (4*D - 16)*G(m4)*G(m1)*G(m2)*G(m3)\
|
| 160 |
+
+ 4*G(m2)*G(m1)*G(m4)*G(m3) + 4*G(m3)*G(m4)*G(m1)*G(m2) +\
|
| 161 |
+
4*G(m4)*G(m3)*G(m2)*G(m1)
|
| 162 |
+
|
| 163 |
+
# Kahane's algorithm yields this result, which is equivalent to `result1`
|
| 164 |
+
# in four dimensions, but is not automatically recognized as equal:
|
| 165 |
+
result2 = 8*G(m1)*G(m2)*G(m3)*G(m4) + 8*G(m4)*G(m3)*G(m2)*G(m1)
|
| 166 |
+
|
| 167 |
+
if D == 4:
|
| 168 |
+
assert _is_tensor_eq(st, (result1)) or _is_tensor_eq(st, (result2))
|
| 169 |
+
else:
|
| 170 |
+
assert _is_tensor_eq(st, (result1))
|
| 171 |
+
|
| 172 |
+
# and a few very simple cases, with no contracted indices:
|
| 173 |
+
|
| 174 |
+
t = G(m0)
|
| 175 |
+
st = tfunc(t)
|
| 176 |
+
assert _is_tensor_eq(st, t)
|
| 177 |
+
|
| 178 |
+
t = -7*G(m0)
|
| 179 |
+
st = tfunc(t)
|
| 180 |
+
assert _is_tensor_eq(st, t)
|
| 181 |
+
|
| 182 |
+
t = 224*G(m0)*G(m1)*G(-m2)*G(m3)
|
| 183 |
+
st = tfunc(t)
|
| 184 |
+
assert _is_tensor_eq(st, t)
|
| 185 |
+
|
| 186 |
+
|
| 187 |
+
def test_kahane_algorithm():
|
| 188 |
+
# Wrap this function to convert to and from TIDS:
|
| 189 |
+
|
| 190 |
+
def tfunc(e):
|
| 191 |
+
return _simplify_single_line(e)
|
| 192 |
+
|
| 193 |
+
execute_gamma_simplify_tests_for_function(tfunc, D=4)
|
| 194 |
+
|
| 195 |
+
|
| 196 |
+
def test_kahane_simplify1():
|
| 197 |
+
i0,i1,i2,i3,i4,i5,i6,i7,i8,i9,i10,i11,i12,i13,i14,i15 = tensor_indices('i0:16', LorentzIndex)
|
| 198 |
+
mu, nu, rho, sigma = tensor_indices("mu, nu, rho, sigma", LorentzIndex)
|
| 199 |
+
D = 4
|
| 200 |
+
t = G(i0)*G(i1)
|
| 201 |
+
r = kahane_simplify(t)
|
| 202 |
+
assert r.equals(t)
|
| 203 |
+
|
| 204 |
+
t = G(i0)*G(i1)*G(-i0)
|
| 205 |
+
r = kahane_simplify(t)
|
| 206 |
+
assert r.equals(-2*G(i1))
|
| 207 |
+
t = G(i0)*G(i1)*G(-i0)
|
| 208 |
+
r = kahane_simplify(t)
|
| 209 |
+
assert r.equals(-2*G(i1))
|
| 210 |
+
|
| 211 |
+
t = G(i0)*G(i1)
|
| 212 |
+
r = kahane_simplify(t)
|
| 213 |
+
assert r.equals(t)
|
| 214 |
+
t = G(i0)*G(i1)
|
| 215 |
+
r = kahane_simplify(t)
|
| 216 |
+
assert r.equals(t)
|
| 217 |
+
t = G(i0)*G(-i0)
|
| 218 |
+
r = kahane_simplify(t)
|
| 219 |
+
assert r.equals(4*eye(4))
|
| 220 |
+
t = G(i0)*G(-i0)
|
| 221 |
+
r = kahane_simplify(t)
|
| 222 |
+
assert r.equals(4*eye(4))
|
| 223 |
+
t = G(i0)*G(-i0)
|
| 224 |
+
r = kahane_simplify(t)
|
| 225 |
+
assert r.equals(4*eye(4))
|
| 226 |
+
t = G(i0)*G(i1)*G(-i0)
|
| 227 |
+
r = kahane_simplify(t)
|
| 228 |
+
assert r.equals(-2*G(i1))
|
| 229 |
+
t = G(i0)*G(i1)*G(-i0)*G(-i1)
|
| 230 |
+
r = kahane_simplify(t)
|
| 231 |
+
assert r.equals((2*D - D**2)*eye(4))
|
| 232 |
+
t = G(i0)*G(i1)*G(-i0)*G(-i1)
|
| 233 |
+
r = kahane_simplify(t)
|
| 234 |
+
assert r.equals((2*D - D**2)*eye(4))
|
| 235 |
+
t = G(i0)*G(-i0)*G(i1)*G(-i1)
|
| 236 |
+
r = kahane_simplify(t)
|
| 237 |
+
assert r.equals(16*eye(4))
|
| 238 |
+
t = (G(mu)*G(nu)*G(-nu)*G(-mu))
|
| 239 |
+
r = kahane_simplify(t)
|
| 240 |
+
assert r.equals(D**2*eye(4))
|
| 241 |
+
t = (G(mu)*G(nu)*G(-nu)*G(-mu))
|
| 242 |
+
r = kahane_simplify(t)
|
| 243 |
+
assert r.equals(D**2*eye(4))
|
| 244 |
+
t = (G(mu)*G(nu)*G(-nu)*G(-mu))
|
| 245 |
+
r = kahane_simplify(t)
|
| 246 |
+
assert r.equals(D**2*eye(4))
|
| 247 |
+
t = (G(mu)*G(nu)*G(-rho)*G(-nu)*G(-mu)*G(rho))
|
| 248 |
+
r = kahane_simplify(t)
|
| 249 |
+
assert r.equals((4*D - 4*D**2 + D**3)*eye(4))
|
| 250 |
+
t = (G(-mu)*G(-nu)*G(-rho)*G(-sigma)*G(nu)*G(mu)*G(sigma)*G(rho))
|
| 251 |
+
r = kahane_simplify(t)
|
| 252 |
+
assert r.equals((-16*D + 24*D**2 - 8*D**3 + D**4)*eye(4))
|
| 253 |
+
t = (G(-mu)*G(nu)*G(-rho)*G(sigma)*G(rho)*G(-nu)*G(mu)*G(-sigma))
|
| 254 |
+
r = kahane_simplify(t)
|
| 255 |
+
assert r.equals((8*D - 12*D**2 + 6*D**3 - D**4)*eye(4))
|
| 256 |
+
|
| 257 |
+
# Expressions with free indices:
|
| 258 |
+
t = (G(mu)*G(nu)*G(rho)*G(sigma)*G(-mu))
|
| 259 |
+
r = kahane_simplify(t)
|
| 260 |
+
assert r.equals(-2*G(sigma)*G(rho)*G(nu))
|
| 261 |
+
t = (G(mu)*G(-mu)*G(rho)*G(sigma))
|
| 262 |
+
r = kahane_simplify(t)
|
| 263 |
+
assert r.equals(4*G(rho)*G(sigma))
|
| 264 |
+
t = (G(rho)*G(sigma)*G(mu)*G(-mu))
|
| 265 |
+
r = kahane_simplify(t)
|
| 266 |
+
assert r.equals(4*G(rho)*G(sigma))
|
| 267 |
+
|
| 268 |
+
def test_gamma_matrix_class():
|
| 269 |
+
i, j, k = tensor_indices('i,j,k', LorentzIndex)
|
| 270 |
+
|
| 271 |
+
# define another type of TensorHead to see if exprs are correctly handled:
|
| 272 |
+
A = TensorHead('A', [LorentzIndex])
|
| 273 |
+
|
| 274 |
+
t = A(k)*G(i)*G(-i)
|
| 275 |
+
ts = simplify_gamma_expression(t)
|
| 276 |
+
assert _is_tensor_eq(ts, Matrix([
|
| 277 |
+
[4, 0, 0, 0],
|
| 278 |
+
[0, 4, 0, 0],
|
| 279 |
+
[0, 0, 4, 0],
|
| 280 |
+
[0, 0, 0, 4]])*A(k))
|
| 281 |
+
|
| 282 |
+
t = G(i)*A(k)*G(j)
|
| 283 |
+
ts = simplify_gamma_expression(t)
|
| 284 |
+
assert _is_tensor_eq(ts, A(k)*G(i)*G(j))
|
| 285 |
+
|
| 286 |
+
execute_gamma_simplify_tests_for_function(simplify_gamma_expression, D=4)
|
| 287 |
+
|
| 288 |
+
|
| 289 |
+
def test_gamma_matrix_trace():
|
| 290 |
+
g = LorentzIndex.metric
|
| 291 |
+
|
| 292 |
+
m0, m1, m2, m3, m4, m5, m6 = tensor_indices('m0:7', LorentzIndex)
|
| 293 |
+
n0, n1, n2, n3, n4, n5 = tensor_indices('n0:6', LorentzIndex)
|
| 294 |
+
|
| 295 |
+
# working in D=4 dimensions
|
| 296 |
+
D = 4
|
| 297 |
+
|
| 298 |
+
# traces of odd number of gamma matrices are zero:
|
| 299 |
+
t = G(m0)
|
| 300 |
+
t1 = gamma_trace(t)
|
| 301 |
+
assert t1.equals(0)
|
| 302 |
+
|
| 303 |
+
t = G(m0)*G(m1)*G(m2)
|
| 304 |
+
t1 = gamma_trace(t)
|
| 305 |
+
assert t1.equals(0)
|
| 306 |
+
|
| 307 |
+
t = G(m0)*G(m1)*G(-m0)
|
| 308 |
+
t1 = gamma_trace(t)
|
| 309 |
+
assert t1.equals(0)
|
| 310 |
+
|
| 311 |
+
t = G(m0)*G(m1)*G(m2)*G(m3)*G(m4)
|
| 312 |
+
t1 = gamma_trace(t)
|
| 313 |
+
assert t1.equals(0)
|
| 314 |
+
|
| 315 |
+
# traces without internal contractions:
|
| 316 |
+
t = G(m0)*G(m1)
|
| 317 |
+
t1 = gamma_trace(t)
|
| 318 |
+
assert _is_tensor_eq(t1, 4*g(m0, m1))
|
| 319 |
+
|
| 320 |
+
t = G(m0)*G(m1)*G(m2)*G(m3)
|
| 321 |
+
t1 = gamma_trace(t)
|
| 322 |
+
t2 = -4*g(m0, m2)*g(m1, m3) + 4*g(m0, m1)*g(m2, m3) + 4*g(m0, m3)*g(m1, m2)
|
| 323 |
+
assert _is_tensor_eq(t1, t2)
|
| 324 |
+
|
| 325 |
+
t = G(m0)*G(m1)*G(m2)*G(m3)*G(m4)*G(m5)
|
| 326 |
+
t1 = gamma_trace(t)
|
| 327 |
+
t2 = t1*g(-m0, -m5)
|
| 328 |
+
t2 = t2.contract_metric(g)
|
| 329 |
+
assert _is_tensor_eq(t2, D*gamma_trace(G(m1)*G(m2)*G(m3)*G(m4)))
|
| 330 |
+
|
| 331 |
+
# traces of expressions with internal contractions:
|
| 332 |
+
t = G(m0)*G(-m0)
|
| 333 |
+
t1 = gamma_trace(t)
|
| 334 |
+
assert t1.equals(4*D)
|
| 335 |
+
|
| 336 |
+
t = G(m0)*G(m1)*G(-m0)*G(-m1)
|
| 337 |
+
t1 = gamma_trace(t)
|
| 338 |
+
assert t1.equals(8*D - 4*D**2)
|
| 339 |
+
|
| 340 |
+
t = G(m0)*G(m1)*G(m2)*G(m3)*G(m4)*G(-m0)
|
| 341 |
+
t1 = gamma_trace(t)
|
| 342 |
+
t2 = (-4*D)*g(m1, m3)*g(m2, m4) + (4*D)*g(m1, m2)*g(m3, m4) + \
|
| 343 |
+
(4*D)*g(m1, m4)*g(m2, m3)
|
| 344 |
+
assert _is_tensor_eq(t1, t2)
|
| 345 |
+
|
| 346 |
+
t = G(-m5)*G(m0)*G(m1)*G(m2)*G(m3)*G(m4)*G(-m0)*G(m5)
|
| 347 |
+
t1 = gamma_trace(t)
|
| 348 |
+
t2 = (32*D + 4*(-D + 4)**2 - 64)*(g(m1, m2)*g(m3, m4) - \
|
| 349 |
+
g(m1, m3)*g(m2, m4) + g(m1, m4)*g(m2, m3))
|
| 350 |
+
assert _is_tensor_eq(t1, t2)
|
| 351 |
+
|
| 352 |
+
t = G(m0)*G(m1)*G(-m0)*G(m3)
|
| 353 |
+
t1 = gamma_trace(t)
|
| 354 |
+
assert t1.equals((-4*D + 8)*g(m1, m3))
|
| 355 |
+
|
| 356 |
+
# p, q = S1('p,q')
|
| 357 |
+
# ps = p(m0)*G(-m0)
|
| 358 |
+
# qs = q(m0)*G(-m0)
|
| 359 |
+
# t = ps*qs*ps*qs
|
| 360 |
+
# t1 = gamma_trace(t)
|
| 361 |
+
# assert t1 == 8*p(m0)*q(-m0)*p(m1)*q(-m1) - 4*p(m0)*p(-m0)*q(m1)*q(-m1)
|
| 362 |
+
|
| 363 |
+
t = G(m0)*G(m1)*G(m2)*G(m3)*G(m4)*G(m5)*G(-m0)*G(-m1)*G(-m2)*G(-m3)*G(-m4)*G(-m5)
|
| 364 |
+
t1 = gamma_trace(t)
|
| 365 |
+
assert t1.equals(-4*D**6 + 120*D**5 - 1040*D**4 + 3360*D**3 - 4480*D**2 + 2048*D)
|
| 366 |
+
|
| 367 |
+
t = G(m0)*G(m1)*G(n1)*G(m2)*G(n2)*G(m3)*G(m4)*G(-n2)*G(-n1)*G(-m0)*G(-m1)*G(-m2)*G(-m3)*G(-m4)
|
| 368 |
+
t1 = gamma_trace(t)
|
| 369 |
+
tresu = -7168*D + 16768*D**2 - 14400*D**3 + 5920*D**4 - 1232*D**5 + 120*D**6 - 4*D**7
|
| 370 |
+
assert t1.equals(tresu)
|
| 371 |
+
|
| 372 |
+
# checked with Mathematica
|
| 373 |
+
# In[1]:= <<Tracer.m
|
| 374 |
+
# In[2]:= Spur[l];
|
| 375 |
+
# In[3]:= GammaTrace[l, {m0},{m1},{n1},{m2},{n2},{m3},{m4},{n3},{n4},{m0},{m1},{m2},{m3},{m4}]
|
| 376 |
+
t = G(m0)*G(m1)*G(n1)*G(m2)*G(n2)*G(m3)*G(m4)*G(n3)*G(n4)*G(-m0)*G(-m1)*G(-m2)*G(-m3)*G(-m4)
|
| 377 |
+
t1 = gamma_trace(t)
|
| 378 |
+
# t1 = t1.expand_coeff()
|
| 379 |
+
c1 = -4*D**5 + 120*D**4 - 1200*D**3 + 5280*D**2 - 10560*D + 7808
|
| 380 |
+
c2 = -4*D**5 + 88*D**4 - 560*D**3 + 1440*D**2 - 1600*D + 640
|
| 381 |
+
assert _is_tensor_eq(t1, c1*g(n1, n4)*g(n2, n3) + c2*g(n1, n2)*g(n3, n4) + \
|
| 382 |
+
(-c1)*g(n1, n3)*g(n2, n4))
|
| 383 |
+
|
| 384 |
+
p, q = tensor_heads('p,q', [LorentzIndex])
|
| 385 |
+
ps = p(m0)*G(-m0)
|
| 386 |
+
qs = q(m0)*G(-m0)
|
| 387 |
+
p2 = p(m0)*p(-m0)
|
| 388 |
+
q2 = q(m0)*q(-m0)
|
| 389 |
+
pq = p(m0)*q(-m0)
|
| 390 |
+
t = ps*qs*ps*qs
|
| 391 |
+
r = gamma_trace(t)
|
| 392 |
+
assert _is_tensor_eq(r, 8*pq*pq - 4*p2*q2)
|
| 393 |
+
t = ps*qs*ps*qs*ps*qs
|
| 394 |
+
r = gamma_trace(t)
|
| 395 |
+
assert _is_tensor_eq(r, -12*p2*pq*q2 + 16*pq*pq*pq)
|
| 396 |
+
t = ps*qs*ps*qs*ps*qs*ps*qs
|
| 397 |
+
r = gamma_trace(t)
|
| 398 |
+
assert _is_tensor_eq(r, -32*pq*pq*p2*q2 + 32*pq*pq*pq*pq + 4*p2*p2*q2*q2)
|
| 399 |
+
|
| 400 |
+
t = 4*p(m1)*p(m0)*p(-m0)*q(-m1)*q(m2)*q(-m2)
|
| 401 |
+
assert _is_tensor_eq(gamma_trace(t), t)
|
| 402 |
+
t = ps*ps*ps*ps*ps*ps*ps*ps
|
| 403 |
+
r = gamma_trace(t)
|
| 404 |
+
assert r.equals(4*p2*p2*p2*p2)
|
| 405 |
+
|
| 406 |
+
|
| 407 |
+
def test_bug_13636():
|
| 408 |
+
"""Test issue 13636 regarding handling traces of sums of products
|
| 409 |
+
of GammaMatrix mixed with other factors."""
|
| 410 |
+
pi, ki, pf = tensor_heads("pi, ki, pf", [LorentzIndex])
|
| 411 |
+
i0, i1, i2, i3, i4 = tensor_indices("i0:5", LorentzIndex)
|
| 412 |
+
x = Symbol("x")
|
| 413 |
+
pis = pi(i2) * G(-i2)
|
| 414 |
+
kis = ki(i3) * G(-i3)
|
| 415 |
+
pfs = pf(i4) * G(-i4)
|
| 416 |
+
|
| 417 |
+
a = pfs * G(i0) * kis * G(i1) * pis * G(-i1) * kis * G(-i0)
|
| 418 |
+
b = pfs * G(i0) * kis * G(i1) * pis * x * G(-i0) * pi(-i1)
|
| 419 |
+
ta = gamma_trace(a)
|
| 420 |
+
tb = gamma_trace(b)
|
| 421 |
+
t_a_plus_b = gamma_trace(a + b)
|
| 422 |
+
assert ta == 4 * (
|
| 423 |
+
-4 * ki(i0) * ki(-i0) * pf(i1) * pi(-i1)
|
| 424 |
+
+ 8 * ki(i0) * ki(i1) * pf(-i0) * pi(-i1)
|
| 425 |
+
)
|
| 426 |
+
assert tb == -8 * x * ki(i0) * pf(-i0) * pi(i1) * pi(-i1)
|
| 427 |
+
assert t_a_plus_b == ta + tb
|
evalkit_internvl/lib/python3.10/site-packages/sympy/physics/optics/__init__.py
ADDED
|
@@ -0,0 +1,38 @@
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|
| 1 |
+
__all__ = [
|
| 2 |
+
'TWave',
|
| 3 |
+
|
| 4 |
+
'RayTransferMatrix', 'FreeSpace', 'FlatRefraction', 'CurvedRefraction',
|
| 5 |
+
'FlatMirror', 'CurvedMirror', 'ThinLens', 'GeometricRay', 'BeamParameter',
|
| 6 |
+
'waist2rayleigh', 'rayleigh2waist', 'geometric_conj_ab',
|
| 7 |
+
'geometric_conj_af', 'geometric_conj_bf', 'gaussian_conj',
|
| 8 |
+
'conjugate_gauss_beams',
|
| 9 |
+
|
| 10 |
+
'Medium',
|
| 11 |
+
|
| 12 |
+
'refraction_angle', 'deviation', 'fresnel_coefficients', 'brewster_angle',
|
| 13 |
+
'critical_angle', 'lens_makers_formula', 'mirror_formula', 'lens_formula',
|
| 14 |
+
'hyperfocal_distance', 'transverse_magnification',
|
| 15 |
+
|
| 16 |
+
'jones_vector', 'stokes_vector', 'jones_2_stokes', 'linear_polarizer',
|
| 17 |
+
'phase_retarder', 'half_wave_retarder', 'quarter_wave_retarder',
|
| 18 |
+
'transmissive_filter', 'reflective_filter', 'mueller_matrix',
|
| 19 |
+
'polarizing_beam_splitter',
|
| 20 |
+
]
|
| 21 |
+
from .waves import TWave
|
| 22 |
+
|
| 23 |
+
from .gaussopt import (RayTransferMatrix, FreeSpace, FlatRefraction,
|
| 24 |
+
CurvedRefraction, FlatMirror, CurvedMirror, ThinLens, GeometricRay,
|
| 25 |
+
BeamParameter, waist2rayleigh, rayleigh2waist, geometric_conj_ab,
|
| 26 |
+
geometric_conj_af, geometric_conj_bf, gaussian_conj,
|
| 27 |
+
conjugate_gauss_beams)
|
| 28 |
+
|
| 29 |
+
from .medium import Medium
|
| 30 |
+
|
| 31 |
+
from .utils import (refraction_angle, deviation, fresnel_coefficients,
|
| 32 |
+
brewster_angle, critical_angle, lens_makers_formula, mirror_formula,
|
| 33 |
+
lens_formula, hyperfocal_distance, transverse_magnification)
|
| 34 |
+
|
| 35 |
+
from .polarization import (jones_vector, stokes_vector, jones_2_stokes,
|
| 36 |
+
linear_polarizer, phase_retarder, half_wave_retarder,
|
| 37 |
+
quarter_wave_retarder, transmissive_filter, reflective_filter,
|
| 38 |
+
mueller_matrix, polarizing_beam_splitter)
|
evalkit_internvl/lib/python3.10/site-packages/sympy/physics/optics/__pycache__/__init__.cpython-310.pyc
ADDED
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Binary file (1.51 kB). View file
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