update: expand synchronize operation order to be determined in the or…

…der of the specification

elastica/modules/base_system.py

@@ -5,16 +5,19 @@
 Basic coordinating for multiple, smaller systems that have an independently integrable
 interface (i.e. works with symplectic or explicit routines `timestepper.py`.)
 """
-from typing import Iterable, Callable, AnyStr
+from typing import AnyStr, Iterable
+from elastica.typing import OperatorType, OperatorCallbackType, OpeatorFinalizeType
 
 from collections.abc import MutableSequence
 
 from elastica.rod import RodBase
 from elastica.rigidbody import RigidBodyBase
 from elastica.surface import SurfaceBase
-from elastica.modules.memory_block import construct_memory_block_structures
 from elastica._synchronize_periodic_boundary import _ConstrainPeriodicBoundaries
 
+from .memory_block import construct_memory_block_structures
+from .feature_group import FeatureGroupFIFO
+
 
 class BaseSystemCollection(MutableSequence):
     """
@@ -45,13 +48,11 @@ def __init__(self):
         # Collection of functions. Each group is executed as a collection at the different steps.
         # Each component (Forcing, Connection, etc.) registers the executable (callable) function
         # in the group that that needs to be executed. These should be initialized before mixin.
-        self._feature_group_synchronize: Iterable[Callable[[float], None]] = []
-        self._feature_group_constrain_values: Iterable[Callable[[float], None]] = []
-        self._feature_group_constrain_rates: Iterable[Callable[[float], None]] = []
-        self._feature_group_callback: Iterable[Callable[[float, int, AnyStr], None]] = (
-            []
-        )
-        self._feature_group_finalize: Iterable[Callable] = []
+        self._feature_group_synchronize: Iterable[OperatorType] = FeatureGroupFIFO()
+        self._feature_group_constrain_values: Iterable[OperatorType] = []
+        self._feature_group_constrain_rates: Iterable[OperatorType] = []
+        self._feature_group_callback: Iterable[OperatorCallbackType] = []
+        self._feature_group_finalize: Iterable[OpeatorFinalizeType] = []
         # We need to initialize our mixin classes
         super(BaseSystemCollection, self).__init__()
         # List of system types/bases that are allowed
@@ -169,34 +170,23 @@ def finalize(self):
 
         # Toggle the finalize_flag
         self._finalize_flag = True
-        # sort _feature_group_synchronize so that _call_contacts is at the end
-        _call_contacts_index = []
-        for idx, feature in enumerate(self._feature_group_synchronize):
-            if feature.__name__ == "_call_contacts":
-                _call_contacts_index.append(idx)
-
-        # Move to the _call_contacts to the end of the _feature_group_synchronize list.
-        for index in _call_contacts_index:
-            self._feature_group_synchronize.append(
-                self._feature_group_synchronize.pop(index)
-            )
 
     def synchronize(self, time: float):
         # Collection call _feature_group_synchronize
-        for feature in self._feature_group_synchronize:
-            feature(time)
+        for func in self._feature_group_synchronize:
+            func(time)
 
     def constrain_values(self, time: float):
         # Collection call _feature_group_constrain_values
-        for feature in self._feature_group_constrain_values:
-            feature(time)
+        for func in self._feature_group_constrain_values:
+            func(time)
 
     def constrain_rates(self, time: float):
         # Collection call _feature_group_constrain_rates
-        for feature in self._feature_group_constrain_rates:
-            feature(time)
+        for func in self._feature_group_constrain_rates:
+            func(time)
 
     def apply_callbacks(self, time: float, current_step: int):
         # Collection call _feature_group_callback
-        for feature in self._feature_group_callback:
-            feature(time, current_step)
+        for func in self._feature_group_callback:
+            func(time, current_step)

elastica/modules/connections.py

@@ -5,6 +5,7 @@
 Provides the connections interface to connect entities (rods,
 rigid bodies) using joints (see `joints.py`).
 """
+import functools
 import numpy as np
 from elastica.joint import FreeJoint
 
@@ -24,7 +25,6 @@ class Connections:
     def __init__(self):
         self._connections = []
         super(Connections, self).__init__()
-        self._feature_group_synchronize.append(self._call_connections)
         self._feature_group_finalize.append(self._finalize_connections)
 
     def connect(
@@ -63,6 +63,7 @@ def connect(
         _connector = _Connect(*sys_idx, *sys_dofs)
         _connector.set_index(first_connect_idx, second_connect_idx)
         self._connections.append(_connector)
+        self._feature_group_synchronize.append_id(_connector)
 
         return _connector
 
@@ -71,38 +72,41 @@ def _finalize_connections(self):
 
         # dev : the first indices stores the
         # (first rod index, second_rod_idx, connection_idx_on_first_rod, connection_idx_on_second_rod)
-        # to apply the connections to
-        # Technically we can use another array but it its one more book-keeping
-        # step. Being lazy, I put them both in the same array
-        self._connections[:] = [
-            (*connection.id(), connection()) for connection in self._connections
-        ]
+        # to apply the connections to.
+
+        for connection in self._connections:
+            first_sys_idx, second_sys_idx, first_connect_idx, second_connect_idx = (
+                connection.id()
+            )
+            connect_instance = connection.instantiate()
+
+            # FIXME: lambda t is included because OperatorType takes time as an argument
+            def apply_forces(time):
+                return functools.partial(
+                    connect_instance.apply_forces,
+                    system_one=self._systems[first_sys_idx],
+                    index_one=first_connect_idx,
+                    system_two=self._systems[second_sys_idx],
+                    index_two=second_connect_idx,
+                )
+
+            def apply_torques(time):
+                return functools.partial(
+                    connect_instance.apply_torques,
+                    system_one=self._systems[first_sys_idx],
+                    index_one=first_connect_idx,
+                    system_two=self._systems[second_sys_idx],
+                    index_two=second_connect_idx,
+                )
+
+            self._feature_group_synchronize.add_operators(
+                connection, [apply_forces, apply_torques]
+            )
 
         # Need to finally solve CPP here, if we are doing things properly
         # This is to optimize the call tree for better memory accesses
         # https://brooksandrew.github.io/simpleblog/articles/intro-to-graph-optimization-solving-cpp/
 
-    def _call_connections(self, *args, **kwargs):
-        for (
-            first_sys_idx,
-            second_sys_idx,
-            first_connect_idx,
-            second_connect_idx,
-            connection,
-        ) in self._connections:
-            connection.apply_forces(
-                self._systems[first_sys_idx],
-                first_connect_idx,
-                self._systems[second_sys_idx],
-                second_connect_idx,
-            )
-            connection.apply_torques(
-                self._systems[first_sys_idx],
-                first_connect_idx,
-                self._systems[second_sys_idx],
-                second_connect_idx,
-            )
-
 
 class _Connect:
     """
@@ -265,7 +269,7 @@ def id(self):
             self.second_sys_connection_idx,
         )
 
-    def __call__(self, *args, **kwargs):
+    def instantiate(self):
         if not self._connect_cls:
             raise RuntimeError(
                 "No connections provided to link rod id {0}"

elastica/modules/contact.py

@@ -5,7 +5,7 @@
 Provides the contact interface to apply contact forces between objects
 (rods, rigid bodies, surfaces).
 """
-
+import functools
 from elastica.typing import SystemType, AllowedContactType
 
 
@@ -23,7 +23,6 @@ class Contact:
     def __init__(self):
         self._contacts = []
         super(Contact, self).__init__()
-        self._feature_group_synchronize.append(self._call_contacts)
         self._feature_group_finalize.append(self._finalize_contact)
 
     def detect_contact_between(
@@ -51,6 +50,7 @@ def detect_contact_between(
         # Create _Contact object, cache it and return to user
         _contact = _Contact(*sys_idx)
         self._contacts.append(_contact)
+        self._feature_group_synchronize.append_id(_contact)
 
         return _contact
 
@@ -61,30 +61,24 @@ def _finalize_contact(self) -> None:
         # to apply the contacts to
         # Technically we can use another array but it its one more book-keeping
         # step. Being lazy, I put them both in the same array
-        self._contacts[:] = [(*contact.id(), contact()) for contact in self._contacts]
-
-        # check contact order
-        for (
-            first_sys_idx,
-            second_sys_idx,
-            contact,
-        ) in self._contacts:
-            contact._check_systems_validity(
-                self._systems[first_sys_idx],
-                self._systems[second_sys_idx],
-            )
+        for contact in self._contacts:
+            first_sys_idx, second_sys_idx = contact.id()
+            contact_instance = contact.instantiate()
 
-    def _call_contacts(self, time: float):
-        for (
-            first_sys_idx,
-            second_sys_idx,
-            contact,
-        ) in self._contacts:
-            contact.apply_contact(
+            contact_instance._check_systems_validity(
                 self._systems[first_sys_idx],
                 self._systems[second_sys_idx],
             )
 
+            def apply_contact(time):
+                return functools.partial(
+                    contact_instance.apply_contact,
+                    system_one=self._systems[first_sys_idx],
+                    system_two=self._systems[second_sys_idx],
+                )
+
+            self._feature_group_synchronize.add_operators(contact, [apply_contact])
+
 
 class _Contact:
     """
@@ -153,7 +147,7 @@ def id(self):
             self.second_sys_idx,
         )
 
-    def __call__(self, *args, **kwargs):
+    def instantiate(self, *args, **kwargs):
         if not self._contact_cls:
             raise RuntimeError(
                 "No contacts provided to to establish contact between rod-like object id {0}"

elastica/modules/feature_group.py

@@ -0,0 +1,27 @@
+from typing import Callable
+from elastica.typing import OperatorType
+
+from collection.abc import Iterable
+
+import itertools
+
+
+class FeatureGroupFIFO(Iterable):
+    def __init__(self):
+        self._operator_collection: list[list[OperatorType]] = []
+        self._operator_ids: list[int] = []
+
+    def __iter__(self) -> Callable[[...], None]:
+        if not self._operator_collection:
+            raise RuntimeError("Feature group is not instantiated.")
+        operator_chain = itertools.chain(self._operator_collection)
+        for operator in operator_chain:
+            yield operator
+
+    def append_id(self, feature):
+        self._operator_ids.append(id(feature))
+        self._operator_collection.append([])
+
+    def add_operators(self, feature, operators: list[OperatorType]):
+        idx = self._operator_idx.index(feature)
+        self._operator_collection[idx].extend(operators)

elastica/modules/forcing.py

@@ -5,6 +5,7 @@
 Provides the forcing interface to apply forces and torques to rod-like objects
 (external point force, muscle torques, etc).
 """
+import functools
 from elastica.interaction import AnisotropicFrictionalPlane
 
 
@@ -23,7 +24,6 @@ class Forcing:
     def __init__(self):
         self._ext_forces_torques = []
         super(Forcing, self).__init__()
-        self._feature_group_synchronize.append(self._call_ext_forces_torques)
         self._feature_group_finalize.append(self._finalize_forcing)
 
     def add_forcing_to(self, system):
@@ -46,6 +46,7 @@ def add_forcing_to(self, system):
         # Create _Constraint object, cache it and return to user
         _ext_force_torque = _ExtForceTorque(sys_idx)
         self._ext_forces_torques.append(_ext_force_torque)
+        self._feature_group_synchronize.append_id(_ext_force_torque)
 
         return _ext_force_torque
 
@@ -54,21 +55,23 @@ def _finalize_forcing(self):
         # inplace : https://stackoverflow.com/a/1208792
 
         # dev : the first index stores the rod index to apply the boundary condition
-        # to. Technically we can use another array but it its one more book-keeping
-        # step. Being lazy, I put them both in the same array
-        self._ext_forces_torques[:] = [
-            (ext_force_torque.id(), ext_force_torque())
-            for ext_force_torque in self._ext_forces_torques
-        ]
-
-        # Sort from lowest id to highest id for potentially better memory access
-        # _ext_forces_torques contains list of tuples. First element of tuple is
-        # rod number and following elements are the type of boundary condition such as
-        # [(0, NoForces, GravityForces), (1, UniformTorques), ... ]
-        # Thus using lambda we iterate over the list of tuples and use rod number (x[0])
-        # to sort _ext_forces_torques.
-        self._ext_forces_torques.sort(key=lambda x: x[0])
+        # to.
+        for ext_force_torque in self._ext_forces_torques:
+            sys_id = ext_force_torque.id()
+            forcing_instance = ext_force_torque.instantiate()
 
+            apply_forces = functools.partial(
+                forcing_instance.apply_forces, system=self._systems[sys_id]
+            )
+            apply_torques = functools.partial(
+                forcing_instance.apply_torques, system=self._systems[sys_id]
+            )
+
+            self._feature_group_synchronize.add_operators(
+                ext_force_torque, [apply_forces, apply_torques]
+            )
+
+        # TODO: remove: we decided to let user to fully decide the order of operations
         # Find if there are any friction plane forcing, if add them to the end of the list,
         # since friction planes uses external forces.
         friction_plane_index = []
@@ -80,12 +83,6 @@ def _finalize_forcing(self):
         for index in friction_plane_index:
             self._ext_forces_torques.append(self._ext_forces_torques.pop(index))
 
-    def _call_ext_forces_torques(self, time, *args, **kwargs):
-        for sys_id, ext_force_torque in self._ext_forces_torques:
-            ext_force_torque.apply_forces(self._systems[sys_id], time, *args, **kwargs)
-            ext_force_torque.apply_torques(self._systems[sys_id], time, *args, **kwargs)
-            # TODO Apply torque, see if necessary
-
 
 class _ExtForceTorque:
     """
@@ -146,7 +143,7 @@ def using(self, forcing_cls, *args, **kwargs):
     def id(self):
         return self._sys_idx
 
-    def __call__(self, *args, **kwargs):
+    def instantiate(self):
         """Constructs a constraint after checks
 
         Parameters

elastica/typing.py

@@ -2,8 +2,12 @@
 from elastica.rigidbody import RigidBodyBase
 from elastica.surface import SurfaceBase
 
-from typing import Type, Union
+from typing import Type, Union, TypingAlias, Callable
 
 RodType = Type[RodBase]
 SystemType = Union[RodType, Type[RigidBodyBase]]
 AllowedContactType = Union[SystemType, Type[SurfaceBase]]
+
+OperatorType: TypingAlias = Callable[[float], None]
+OperatorCallbackType: TypingAlias = Callable[[float, int], None]
+OperatorFinalizeType: TypingAlias = Callable