update: moduli assignment for Cosserat Rod

The logging level of some messages are lowered (warning->info) in order
to avoid unnecessary logging.

elastica/rod/factory_function.py

@@ -1,6 +1,9 @@
 __doc__ = """ Factory function to allocate variables for Cosserat Rod"""
 __all__ = ["allocate"]
+import typing
+from typing import Optional
 import warnings
+import logging
 import numpy as np
 from numpy.testing import assert_allclose
 from elastica.utils import MaxDimension, Tolerance
@@ -16,8 +19,9 @@ def allocate(
     base_radius,
     density,
     nu,
-    youngs_modulus,
-    # poisson_ratio,
+    youngs_modulus:float,
+    poisson_ratio:Optional[float]=None,
+    shear_modulus:Optional[float]=None,
     # alpha_c=0.964,
     *args,
     **kwargs
@@ -215,7 +219,7 @@ def allocate(
         )
 
     # Shear/Stretch matrix
-    shear_modulus = get_shear_modulus(youngs_modulus, kwargs)
+    shear_modulus = get_shear_modulus(youngs_modulus, poisson_ratio, shear_modulus)
 
     # Value taken based on best correlation for Poisson ratio = 0.5, from
     # "On Timoshenko's correction for shear in vibrating beams" by Kaneko, 1975
@@ -398,31 +402,34 @@ def allocate(
     )
 
 
-def get_shear_modulus(youngs_modulus, kwargs):
+def get_shear_modulus(youngs_modulus:float, poisson_ratio:Optional[float], shear_modulus:Optional[float]):
     """
-    From the kwargs get shear modulus, or compute it. This function contains warnining messages.
+    From the kwargs get shear modulus, or compute it. This function contains logging messages.
 
     Parameters
     ----------
     youngs_modulus : float
-
-    kwargs
+    poisson_ratio: Optional[float]
+    shear_modulus: Optional[float]
 
     Returns
     -------
+    shear_modulus: float
 
     """
+
+    log = logging.getLogger("rod constructor: get_shear_modulus")
+
     # Shear/Stretch matrix
-    if kwargs.__contains__("shear_modulus"):
+    if shear_modulus and not poisson_ratio:
         # User set shear modulus use that.
-        shear_modulus = kwargs.get("shear_modulus")
+        pass
 
-    if kwargs.__contains__("shear_modulus") and kwargs.__contains__("poisson_ratio"):
+    if shear_modulus and poisson_ratio:
         # User set shear modulus and also a poisson ratio. Do not use poisson ratio and raise warning.
-        shear_modulus = kwargs.get("shear_modulus")
-        poisson_ratio = kwargs.get("poisson_ratio")
         message = (
             "Both a Poisson ratio and a shear modulus are provided. "
+            "In such case, we prioritize the shear modulus."
             "The Poisson ratio is only used to compute a shear modulus "
             "so the provided Poisson ratio of ( "
             + str(poisson_ratio)
@@ -432,12 +439,8 @@ def get_shear_modulus(youngs_modulus, kwargs):
         )
         warnings.warn(message, category=UserWarning)
 
-    if kwargs.__contains__("poisson_ratio") and (
-        not kwargs.__contains__("shear_modulus")
-    ):
-        # User set poisson ratio but not the shear modulus. Then use poisson ratio to compute shear modulus, and
-        # raise a warning.
-        poisson_ratio = kwargs.get("poisson_ratio")
+    if poisson_ratio and not shear_modulus:
+        # Use poisson ratio to compute shear modulus
         shear_modulus = youngs_modulus / (poisson_ratio + 1.0)
 
         message = (
@@ -450,14 +453,11 @@ def get_shear_modulus(youngs_modulus, kwargs):
             "Use of a Poisson ratio will be depreciated in a future release. "
             "It is encouraged that you discontinue using a Poisson ratio and instead directly provide the shear_modulus. \n"
         )
-        warnings.warn(message, category=UserWarning)
+        log.info(message)
 
-    if not (
-        kwargs.__contains__("poisson_ratio") or kwargs.__contains__("shear_modulus")
-    ):
+    if not poisson_ratio and not shear_modulus:
         # If user does not set poisson ratio or shear modulus, then take poisson ratio as 0.5 and raise warning.
         poisson_ratio = 0.5
-
         shear_modulus = youngs_modulus / (poisson_ratio + 1.0)
 
         message = (
@@ -469,7 +469,6 @@ def get_shear_modulus(youngs_modulus, kwargs):
             + ", "
             "using the equation: shear_modulus = youngs_modulus / (poisson_ratio + 1.0)."
         )
-
-        warnings.warn(message, category=UserWarning)
+        log.info(message)
 
     return shear_modulus