solve #380

Author: skim0119

Makefile

@@ -53,11 +53,11 @@ format-codestyle: black autoflake-format
 .PHONY: mypy
 mypy:
 	uv run mypy --config-file pyproject.toml elastica  # Main
-	uv run mypy --config-file pyproject.toml --explicit-package-bases \  # Examples
+	uv run mypy --config-file pyproject.toml --explicit-package-bases \
 		examples/AxialStretchingCase \
 		examples/ButterflyCase \
 		examples/CatenaryCase \
-		examples/KnotCase \your interest in PyElastica.
+		examples/KnotCase \
 		examples/ContinuumSnakeCase
 
 .PHONY: test

elastica/contact_forces.py

@@ -45,7 +45,6 @@ def __init__(self) -> None:
         """
         NoContact class does not need any input parameters.
         """
-        pass
 
     @property
     def _allowed_system_one(self) -> list[Type]:
@@ -77,6 +76,7 @@ def apply_contact(
         self,
         system_one: S1,
         system_two: S2,
+        time: np.float64 = np.float64(0.0),
     ) -> None:
         """
         Apply contact forces and torques between two system object..
@@ -88,7 +88,6 @@ def apply_contact(
         system_one
         system_two
         """
-        pass
 
 
 class RodRodContact(NoContact):
@@ -120,7 +119,12 @@ def __init__(self, k: np.float64, nu: np.float64) -> None:
         self.k = k
         self.nu = nu
 
-    def apply_contact(self, system_one: RodType, system_two: RodType) -> None:
+    def apply_contact(
+        self,
+        system_one: RodType,
+        system_two: RodType,
+        time: np.float64 = np.float64(0.0),
+    ) -> None:
         """
         Apply contact forces and torques between RodType object and RodType object.
 
@@ -226,7 +230,12 @@ def _allowed_system_two(self) -> list[Type]:
         # Modify this list to include the allowed system types for contact
         return [Cylinder]
 
-    def apply_contact(self, system_one: RodType, system_two: Cylinder) -> None:
+    def apply_contact(
+        self,
+        system_one: RodType,
+        system_two: Cylinder,
+        time: np.float64 = np.float64(0.0),
+    ) -> None:
         # First, check for a global AABB bounding box, and see whether that
         # intersects
         if _prune_using_aabbs_rod_cylinder(
@@ -313,7 +322,12 @@ def _check_systems_validity(
         common_check_systems_validity(system_two, self._allowed_system_two)
         common_check_systems_different(system_one, system_two)
 
-    def apply_contact(self, system_one: RodType, system_two: RodType) -> None:
+    def apply_contact(
+        self,
+        system_one: RodType,
+        system_two: RodType,
+        time: np.float64 = np.float64(0.0),
+    ) -> None:
         """
         Apply contact forces and torques between RodType object and itself.
 
@@ -392,7 +406,12 @@ def __init__(
     def _allowed_system_two(self) -> list[Type]:
         return [Sphere]
 
-    def apply_contact(self, system_one: RodType, system_two: Sphere) -> None:
+    def apply_contact(
+        self,
+        system_one: RodType,
+        system_two: Sphere,
+        time: np.float64 = np.float64(0.0),
+    ) -> None:
         """
         Apply contact forces and torques between RodType object and Sphere object.
 
@@ -485,7 +504,12 @@ def __init__(
     def _allowed_system_two(self) -> list[Type]:
         return [SurfaceBase]
 
-    def apply_contact(self, system_one: RodType, system_two: SurfaceType) -> None:
+    def apply_contact(
+        self,
+        system_one: RodType,
+        system_two: SurfaceType,
+        time: np.float64 = np.float64(0.0),
+    ) -> None:
         """
         Apply contact forces and torques between RodType object and Plane object.
 
@@ -577,7 +601,12 @@ def __init__(
     def _allowed_system_two(self) -> list[Type]:
         return [SurfaceBase]
 
-    def apply_contact(self, system_one: RodType, system_two: SurfaceType) -> None:
+    def apply_contact(
+        self,
+        system_one: RodType,
+        system_two: SurfaceType,
+        time: np.float64 = np.float64(0.0),
+    ) -> None:
         """
         Apply contact forces and torques between RodType object and Plane object with anisotropic friction.
 
@@ -659,7 +688,12 @@ def _allowed_system_one(self) -> list[Type]:
     def _allowed_system_two(self) -> list[Type]:
         return [SurfaceBase]
 
-    def apply_contact(self, system_one: Cylinder, system_two: SurfaceType) -> None:
+    def apply_contact(
+        self,
+        system_one: Cylinder,
+        system_two: SurfaceType,
+        time: np.float64 = np.float64(0.0),
+    ) -> None:
         """
         This function computes the plane force response on the cylinder, in the
         case of contact. Contact model given in Eqn 4.8 Gazzola et. al. RSoS 2018 paper

elastica/dissipation.py

@@ -4,7 +4,6 @@
 Built in damper module implementations
 """
 
-import logging
 from abc import ABC, abstractmethod
 from typing import Any, Generic, TypeVar, TypeAlias, Callable
 
@@ -159,10 +158,6 @@ def __init__(self, time_step: np.float64, **kwargs: Any) -> None:
             and (translational_damping_constant is None)
             and (rotational_damping_constant is None)
         ):
-            logging.warning(
-                "Analytical linear damping using generic damping constant "
-                "will be deprecated in 0.4.0"
-            )
             self._dampen_rates_protocol = self._deprecated_damping_protocol(
                 damping_constant=damping_constant, time_step=time_step
             )

elastica/joint.py

@@ -50,6 +50,7 @@ def apply_forces(
         index_one: ConnectionIndex,
         system_two: "RodType | RigidBodyType",
         index_two: ConnectionIndex,
+        time: np.float64 = np.float64(0.0),
     ) -> None:
         """
         Apply joint force to the connected rod objects.
@@ -93,6 +94,7 @@ def apply_torques(
         index_one: ConnectionIndex,
         system_two: "RodType | RigidBodyType",
         index_two: ConnectionIndex,
+        time: np.float64 = np.float64(0.0),
     ) -> None:
         """
         Apply restoring joint torques to the connected rod objects.
@@ -174,6 +176,7 @@ def apply_forces(
         index_one: ConnectionIndex,
         system_two: "RodType | RigidBodyType",
         index_two: ConnectionIndex,
+        time: np.float64 = np.float64(0.0),
     ) -> None:
         return super().apply_forces(system_one, index_one, system_two, index_two)
 
@@ -183,6 +186,7 @@ def apply_torques(
         index_one: ConnectionIndex,
         system_two: "RodType | RigidBodyType",
         index_two: ConnectionIndex,
+        time: np.float64 = np.float64(0.0),
     ) -> None:
         # current tangent direction of the `index_two` element of system two
         system_two_tangent = system_two.director_collection[2, :, index_two]
@@ -281,6 +285,7 @@ def apply_forces(
         index_one: ConnectionIndex,
         system_two: "RodType | RigidBodyType",
         index_two: ConnectionIndex,
+        time: np.float64 = np.float64(0.0),
     ) -> None:
         return super().apply_forces(system_one, index_one, system_two, index_two)
 
@@ -290,6 +295,7 @@ def apply_torques(
         index_one: ConnectionIndex,
         system_two: "RodType | RigidBodyType",
         index_two: ConnectionIndex,
+        time: np.float64 = np.float64(0.0),
     ) -> None:
         # collect directors of systems one and two
         # note that systems can be either rods or rigid bodies

elastica/modules/connections.py

@@ -87,44 +87,30 @@ def _finalize_connections(self: ConnectedSystemCollectionProtocol) -> None:
         # (first rod index, second_rod_idx, connection_idx_on_first_rod, connection_idx_on_second_rod)
         # to apply the connections to.
 
-        def apply_forces_and_torques(
-            time: np.float64,
-            connect_instance: FreeJoint,
-            system_one: "RodType | RigidBodyType",
-            first_connect_idx: ConnectionIndex,
-            system_two: "RodType | RigidBodyType",
-            second_connect_idx: ConnectionIndex,
-        ) -> None:
-            connect_instance.apply_forces(
-                system_one=system_one,
-                index_one=first_connect_idx,
-                system_two=system_two,
-                index_two=second_connect_idx,
-            )
-            connect_instance.apply_torques(
-                system_one=system_one,
-                index_one=first_connect_idx,
-                system_two=system_two,
-                index_two=second_connect_idx,
-            )
-
         for connection in self._connections:
             first_sys_idx, second_sys_idx, first_connect_idx, second_connect_idx = (
                 connection.id()
             )
             connect_instance: FreeJoint = connection.instantiate()
 
-            # FIXME: lambda t is included because OperatorType takes time as an argument
-            func = functools.partial(
-                apply_forces_and_torques,
-                connect_instance=connect_instance,
+            func_force = functools.partial(
+                connect_instance.apply_forces,
                 system_one=self[first_sys_idx],
-                first_connect_idx=first_connect_idx,
+                index_one=first_connect_idx,
                 system_two=self[second_sys_idx],
-                second_connect_idx=second_connect_idx,
+                index_two=second_connect_idx,
+            )
+            func_torque = functools.partial(
+                connect_instance.apply_torques,
+                system_one=self[first_sys_idx],
+                index_one=first_connect_idx,
+                system_two=self[second_sys_idx],
+                index_two=second_connect_idx,
             )
 
-            self._feature_group_synchronize.add_operators(connection, [func])
+            self._feature_group_synchronize.add_operators(
+                connection, [func_force, func_torque]
+            )
 
         self._connections = []
         del self._connections

elastica/modules/contact.py

@@ -7,6 +7,8 @@
 """
 from typing import Type, Any
 from typing_extensions import Self
+
+import functools
 from elastica.typing import (
     SystemIdxType,
     OperatorType,
@@ -86,7 +88,9 @@ def _finalize_contact(self: ContactedSystemCollectionProtocol) -> None:
                 self[first_sys_idx],
                 self[second_sys_idx],
             )
-            func: OperatorType = lambda time: contact_instance.apply_contact(
+
+            func = functools.partial(
+                contact_instance.apply_contact,
                 system_one=self[first_sys_idx],
                 system_two=self[second_sys_idx],
             )

elastica/modules/damping.py

@@ -78,7 +78,9 @@ def _finalize_dampers(self: DampenedSystemCollectionProtocol) -> None:
             sys_id = damping.id()
             damping_instance = damping.instantiate(self[sys_id])
 
-            dampen_rate = functools.partial(damping_instance.dampen_rates, self[sys_id])
+            dampen_rate = functools.partial(
+                damping_instance.dampen_rates, system=self[sys_id]
+            )
             self._feature_group_constrain_rates.add_operators(damping, [dampen_rate])
 
         self._damping_list = []