fix: examples for removed internal damping option

ankith26 · May 3, 2023 · 96734a3 · 96734a3
1 parent 826c0ca
commit 96734a3
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Showing 37 changed files with 71 additions and 155 deletions.
diff --git a/examples/AxialStretchingCase/axial_stretching.py b/examples/AxialStretchingCase/axial_stretching.py
@@ -65,8 +65,7 @@ class StretchingBeamSimulator(
     base_length,
     base_radius,
     density,
-    0.0,  # internal damping constant, deprecated in v0.3.0
-    youngs_modulus,
+    youngs_modulus=youngs_modulus,
     shear_modulus=shear_modulus,
 )
 
@@ -83,9 +82,6 @@ class StretchingBeamSimulator(
 
 # add damping
 dl = base_length / n_elem
-# old damping model (deprecated in v0.3.0) values
-# dt = 0.01 * dl
-# damping_constant = 1.0
 dt = 0.1 * dl
 damping_constant = 0.1
 stretch_sim.dampen(stretchable_rod).using(

diff --git a/examples/Binder/1_Timoshenko_Beam.ipynb b/examples/Binder/1_Timoshenko_Beam.ipynb
@@ -162,8 +162,7 @@
     "    base_length,\n",
     "    base_radius,\n",
     "    density,\n",
-    "    0.0,     # internal damping constant, deprecated in v0.3.0\n",
-    "    E,\n",
+    "    youngs_modulus=E,\n",
     "    shear_modulus=shear_modulus,\n",
     ")\n",
     "\n",
@@ -310,8 +309,7 @@
     "    base_length,\n",
     "    base_radius,\n",
     "    density,\n",
-    "    0.0,     # internal damping constant, deprecated in v0.3.0\n",
-    "    E,\n",
+    "    youngs_modulus=E,\n",
     "    # Unshearable rod needs G -> inf, which is achievable with a poisson ratio of -1.0\n",
     "    shear_modulus=E / (-0.85 + 1.0),\n",
     ")\n",
@@ -582,8 +580,7 @@
     "    base_length,\n",
     "    base_radius,\n",
     "    density,\n",
-    "    0.0,     # internal damping constant, deprecated in v0.3.0\n",
-    "    E,\n",
+    "    youngs_modulus=E,\n",
     "    shear_modulus=shear_modulus,\n",
     ")\n",
     "dynamic_update_sim.append(shearable_rod_new)\n",
@@ -607,8 +604,7 @@
     "    base_length,\n",
     "    base_radius,\n",
     "    density,\n",
-    "    0.0,     # internal damping constant, deprecated in v0.3.0\n",
-    "    E,\n",
+    "    youngs_modulus=E,\n",
     "    # Unshearable rod needs G -> inf, which is achievable with a poisson ratio of -1.0\n",
     "    shear_modulus=E / (-0.85 + 1.0),\n",
     ")\n",

diff --git a/examples/Binder/2_Slithering_Snake.ipynb b/examples/Binder/2_Slithering_Snake.ipynb
@@ -100,8 +100,7 @@
     "    base_length,\n",
     "    base_radius,\n",
     "    density,\n",
-    "    0.0,     # internal damping constant, deprecated in v0.3.0\n",
-    "    E,\n",
+    "    youngs_modulus=E,\n",
     "    shear_modulus=shear_modulus,\n",
     ")\n",
     "\n",

diff --git a/examples/BoundaryConditionsCases/general_constraint_allow_yaw.py b/examples/BoundaryConditionsCases/general_constraint_allow_yaw.py
@@ -57,8 +57,7 @@ class GeneralConstraintSimulator(
     base_length,
     base_radius,
     density,
-    0.0,  # internal damping constant, deprecated in v0.3.0
-    E,
+    youngs_modulus=E,
     shear_modulus=shear_modulus,
 )
 general_constraint_sim.append(rod1)

diff --git a/examples/ButterflyCase/butterfly.py b/examples/ButterflyCase/butterfly.py
@@ -68,7 +68,6 @@ class ButterflySimulator(ea.BaseSystemCollection, ea.CallBacks):
     base_length=total_length,
     base_radius=base_radius,
     density=density,
-    nu=0.0,  # internal damping constant, deprecated in v0.3.0
     youngs_modulus=youngs_modulus,
     shear_modulus=shear_modulus,
     position=positions,

diff --git a/examples/ContinuumFlagellaCase/continuum_flagella.py b/examples/ContinuumFlagellaCase/continuum_flagella.py
@@ -43,8 +43,7 @@ def run_flagella(
         base_length,
         base_radius,
         density,
-        0.0,  # internal damping constant, deprecated in v0.3.0
-        E,
+        youngs_modulus=E,
         shear_modulus=shear_modulus,
     )
 
@@ -78,9 +77,6 @@ def run_flagella(
     )
 
     # add damping
-    # old damping model (deprecated in v0.3.0) values
-    # damping_constant = 2.5
-    # dt = 2.5e-5 * period
     damping_constant = 0.625
     dt = 1e-4 * period
     flagella_sim.dampen(shearable_rod).using(

diff --git a/examples/ContinuumSnakeCase/continuum_snake.py b/examples/ContinuumSnakeCase/continuum_snake.py
@@ -48,8 +48,7 @@ def run_snake(
         base_length,
         base_radius,
         density,
-        0.0,  # internal damping constant, deprecated in v0.3.0
-        E,
+        youngs_modulus=E,
         shear_modulus=shear_modulus,
     )
 
@@ -98,9 +97,6 @@ def run_snake(
     )
 
     # add damping
-    # old damping model (deprecated in v0.3.0) values
-    # damping_constant = 2e-3
-    # time_step = 8e-6
     damping_constant = 2e-3
     time_step = 1e-4
     snake_sim.dampen(shearable_rod).using(

diff --git a/examples/DynamicCantileverCase/dynamic_cantilever.py b/examples/DynamicCantileverCase/dynamic_cantilever.py
@@ -68,8 +68,7 @@ class DynamicCantileverSimulator(
         base_length,
         base_radius,
         density,
-        0.0,
-        youngs_modulus,
+        youngs_modulus=youngs_modulus,
     )
 
     # Add constraints

diff --git a/examples/ExperimentalCases/GenericSystemConnectionCases/generic_system_type_fixed_joint.py b/examples/ExperimentalCases/GenericSystemConnectionCases/generic_system_type_fixed_joint.py
@@ -58,8 +58,7 @@ class FixedJointSimulator(
     base_length,
     base_radius,
     density,
-    0.0,  # internal damping constant, deprecated in v0.3.0
-    E,
+    youngs_modulus=E,
     shear_modulus=shear_modulus,
 )
 fixed_joint_sim.append(rod1)
@@ -72,8 +71,7 @@ class FixedJointSimulator(
     base_length,
     base_radius,
     density,
-    0.0,  # internal damping constant, deprecated in v0.3.0
-    E,
+    youngs_modulus=E,
     shear_modulus=shear_modulus,
 )
 fixed_joint_sim.append(rod2)
@@ -125,9 +123,6 @@ class FixedJointSimulator(
 )
 
 # add damping
-# old damping model (deprecated in v0.3.0) values
-# damping_constant = 0.4
-# dt = 1e-5
 damping_constant = 0.4
 fixed_joint_sim.dampen(rod1).using(
     ea.AnalyticalLinearDamper,

diff --git a/...les/ExperimentalCases/GenericSystemConnectionCases/generic_system_type_spherical_joint.py b/...les/ExperimentalCases/GenericSystemConnectionCases/generic_system_type_spherical_joint.py
@@ -59,8 +59,7 @@ class SphericalJointSimulator(
     base_length,
     base_radius,
     density,
-    0.0,  # internal damping constant, deprecated in v0.3.0
-    E,
+    youngs_modulus=E,
     shear_modulus=shear_modulus,
 )
 spherical_joint_sim.append(rod1)
@@ -73,8 +72,7 @@ class SphericalJointSimulator(
     base_length,
     base_radius,
     density,
-    0.0,  # internal damping constant, deprecated in v0.3.0
-    E,
+    youngs_modulus=E,
     shear_modulus=shear_modulus,
 )
 spherical_joint_sim.append(rod2)
@@ -121,9 +119,6 @@ class SphericalJointSimulator(
 )
 
 # add damping
-# old damping model (deprecated in v0.3.0) values
-# damping_constant = 4e-3
-# dt = 1e-5
 damping_constant = 4e-3
 spherical_joint_sim.dampen(rod1).using(
     ea.AnalyticalLinearDamper,

diff --git a/examples/ExperimentalCases/ParallelConnectionExample/parallel_connection_example.py b/examples/ExperimentalCases/ParallelConnectionExample/parallel_connection_example.py
@@ -53,8 +53,7 @@ class ParallelConnection(
     base_length,
     base_radius,
     density,
-    0.0,  # internal damping constant, deprecated in v0.3.0
-    E,
+    youngs_modulus=E,
     shear_modulus=shear_modulus,
 )
 parallel_connection_sim.append(rod_one)
@@ -67,8 +66,7 @@ class ParallelConnection(
     base_length,
     base_radius,
     density,
-    0.0,  # internal damping constant, deprecated in v0.3.0
-    E,
+    youngs_modulus=E,
     shear_modulus=shear_modulus,
 )
 parallel_connection_sim.append(rod_two)
@@ -134,9 +132,6 @@ def apply_forces(self, system, time: np.float64 = 0.0):
 
 
 # add damping
-# old damping model (deprecated in v0.3.0) values
-# damping_constant = 4e-2
-# dt = 1e-5
 damping_constant = 4e-3
 dt = 1e-3
 parallel_connection_sim.dampen(rod_one).using(

diff --git a/examples/FlexibleSwingingPendulumCase/flexible_swinging_pendulum.py b/examples/FlexibleSwingingPendulumCase/flexible_swinging_pendulum.py
@@ -45,8 +45,7 @@ class SwingingFlexiblePendulumSimulator(
     base_length,
     base_radius,
     density,
-    0.0,  # internal damping constant, deprecated in v0.3.0
-    youngs_modulus,
+    youngs_modulus=youngs_modulus,
     shear_modulus=youngs_modulus / (poisson_ratio + 1.0),
 )
 

diff --git a/examples/FrictionValidationCases/axial_friction.py b/examples/FrictionValidationCases/axial_friction.py
@@ -47,8 +47,7 @@ def simulate_axial_friction_with(force=0.0):
         base_length,
         base_radius,
         density,
-        0.0,  # internal damping constant, deprecated in v0.3.0
-        E,
+        youngs_modulus=E,
         shear_modulus=shear_modulus,
     )
 

diff --git a/examples/FrictionValidationCases/rolling_friction_initial_velocity.py b/examples/FrictionValidationCases/rolling_friction_initial_velocity.py
@@ -51,8 +51,7 @@ def simulate_rolling_friction_initial_velocity_with(IFactor=0.0):
         base_length,
         base_radius,
         density,
-        0.0,  # internal damping constant, deprecated in v0.3.0
-        E,
+        youngs_modulus=E,
         shear_modulus=shear_modulus,
     )
 

diff --git a/examples/FrictionValidationCases/rolling_friction_on_inclined_plane.py b/examples/FrictionValidationCases/rolling_friction_on_inclined_plane.py
@@ -50,8 +50,7 @@ def simulate_rolling_friction_on_inclined_plane_with(alpha_s=0.0):
         base_length,
         base_radius,
         density,
-        0.0,  # internal damping constant, deprecated in v0.3.0
-        E,
+        youngs_modulus=E,
         shear_modulus=shear_modulus,
     )
 

diff --git a/examples/FrictionValidationCases/rolling_friction_torque.py b/examples/FrictionValidationCases/rolling_friction_torque.py
@@ -50,8 +50,7 @@ def simulate_rolling_friction_torque_with(C_s=0.0):
         base_length,
         base_radius,
         density,
-        0.0,  # internal damping constant, deprecated in v0.3.0
-        E,
+        youngs_modulus=E,
         shear_modulus=shear_modulus,
     )
 

diff --git a/examples/HelicalBucklingCase/convergence_helicalbuckling.py b/examples/HelicalBucklingCase/convergence_helicalbuckling.py
@@ -43,7 +43,6 @@ def simulate_helicalbucklin_beam_with(
     number_of_rotations = 27
     # For shear modulus of 1e4, nu is 99!
     poisson_ratio = 99
-    shear_modulus = E / (poisson_ratio + 1.0)
     shear_matrix = np.repeat(1e5 * np.identity((3))[:, :, np.newaxis], n_elem, axis=2)
     temp_bend_matrix = np.zeros((3, 3))
     np.fill_diagonal(temp_bend_matrix, [1.345, 1.345, 0.789])
@@ -57,8 +56,7 @@ def simulate_helicalbucklin_beam_with(
         base_length,
         base_radius,
         density,
-        0.0,  # internal damping constant, deprecated in v0.3.0
-        E,
+        youngs_modulus=E,
     )
     # TODO: CosseratRod has to be able to take shear matrix as input, we should change it as done below
 

diff --git a/examples/HelicalBucklingCase/helicalbuckling.py b/examples/HelicalBucklingCase/helicalbuckling.py
@@ -52,8 +52,7 @@ class HelicalBucklingSimulator(
     base_length,
     base_radius,
     density,
-    0.0,  # internal damping constant, deprecated in v0.3.0
-    E,
+    youngs_modulus=E,
     shear_modulus=shear_modulus,
 )
 # TODO: CosseratRod has to be able to take shear matrix as input, we should change it as done below

diff --git a/examples/JointCases/fixed_joint.py b/examples/JointCases/fixed_joint.py
@@ -48,8 +48,7 @@ class FixedJointSimulator(
     base_length,
     base_radius,
     density,
-    0.0,  # internal damping constant, deprecated in v0.3.0
-    E,
+    youngs_modulus=E,
     shear_modulus=shear_modulus,
 )
 fixed_joint_sim.append(rod1)
@@ -62,8 +61,7 @@ class FixedJointSimulator(
     base_length,
     base_radius,
     density,
-    0.0,  # internal damping constant, deprecated in v0.3.0
-    E,
+    youngs_modulus=E,
     shear_modulus=shear_modulus,
 )
 fixed_joint_sim.append(rod2)
@@ -89,9 +87,6 @@ class FixedJointSimulator(
 )
 
 # add damping
-# old damping model (deprecated in v0.3.0) values
-# damping_constant = 0.4
-# dt = 1e-5
 damping_constant = 0.4
 dt = 1e-4
 fixed_joint_sim.dampen(rod1).using(

diff --git a/examples/JointCases/fixed_joint_torsion.py b/examples/JointCases/fixed_joint_torsion.py
@@ -51,8 +51,7 @@ class FixedJointSimulator(
     base_length,
     base_radius,
     density,
-    0.0,  # internal damping constant, deprecated in v0.3.0
-    E,
+    youngs_modulus=E,
     shear_modulus=shear_modulus,
 )
 fixed_joint_sim.append(rod1)
@@ -65,8 +64,7 @@ class FixedJointSimulator(
     base_length,
     base_radius,
     density,
-    0.0,  # internal damping constant, deprecated in v0.3.0
-    E,
+    youngs_modulus=E,
     shear_modulus=shear_modulus,
 )
 fixed_joint_sim.append(rod2)

diff --git a/examples/JointCases/hinge_joint.py b/examples/JointCases/hinge_joint.py
@@ -48,8 +48,7 @@ class HingeJointSimulator(
     base_length,
     base_radius,
     density,
-    0.0,  # internal damping constant, deprecated in v0.3.0
-    E,
+    youngs_modulus=E,
     shear_modulus=shear_modulus,
 )
 hinge_joint_sim.append(rod1)
@@ -62,8 +61,7 @@ class HingeJointSimulator(
     base_length,
     base_radius,
     density,
-    0.0,  # internal damping constant, deprecated in v0.3.0
-    E,
+    youngs_modulus=E,
     shear_modulus=shear_modulus,
 )
 hinge_joint_sim.append(rod2)
@@ -91,9 +89,6 @@ class HingeJointSimulator(
 )
 
 # add damping
-# old damping model (deprecated in v0.3.0) values
-# damping_constant = 4e-3
-# dt = 1e-5
 damping_constant = 4e-3
 dt = 5e-5
 hinge_joint_sim.dampen(rod1).using(