Merge branch 'wip/401' into type/instance-check

Makefile

@@ -50,7 +50,6 @@ flake8:
 .PHONY: autoflake-check
 autoflake-check:
 	poetry run autoflake --version
-	poetry run autoflake $(AUTOFLAKE_ARGS) elastica tests examples
 	poetry run autoflake --check $(AUTOFLAKE_ARGS) elastica tests examples
 
 .PHONY: autoflake-format

elastica/__init__.py

@@ -75,12 +75,9 @@
 from elastica.utils import isqrt
 from elastica.timestepper import (
     integrate,
-    PositionVerlet,
-    PEFRL,
-    RungeKutta4,
-    EulerForward,
     extend_stepper_interface,
 )
+from elastica.timestepper.symplectic_steppers import PositionVerlet, PEFRL
 from elastica.memory_block.memory_block_rigid_body import MemoryBlockRigidBody
 from elastica.memory_block.memory_block_rod import MemoryBlockCosseratRod
 from elastica.restart import save_state, load_state

elastica/timestepper/explicit_steppers.py → elastica/experimental/timestepper/explicit_steppers.py

@@ -8,12 +8,15 @@
 from elastica.typing import (
     SystemType,
     SystemCollectionType,
-    OperatorType,
+    StepType,
     SteppersOperatorsType,
     StateType,
 )
-from elastica.systems.protocol import ExplicitSystemProtocol
-from .protocol import ExplicitStepperProtocol, MemoryProtocol
+from elastica.experimental.timestepper.protocol import (
+    ExplicitSystemProtocol,
+    ExplicitStepperProtocol,
+    MemoryProtocol,
+)
 
 
 """
@@ -166,10 +169,10 @@ class EulerForward(ExplicitStepperMixin):
     Classical Euler Forward stepper. Stateless, coordinates operations only.
     """
 
-    def get_stages(self) -> list[OperatorType]:
+    def get_stages(self) -> list[StepType]:
         return [self._first_stage]
 
-    def get_updates(self) -> list[OperatorType]:
+    def get_updates(self) -> list[StepType]:
         return [self._first_update]
 
     def _first_stage(
@@ -198,15 +201,15 @@ class RungeKutta4(ExplicitStepperMixin):
     to be externally managed and allocated.
     """
 
-    def get_stages(self) -> list[OperatorType]:
+    def get_stages(self) -> list[StepType]:
         return [
             self._first_stage,
             self._second_stage,
             self._third_stage,
             self._fourth_stage,
         ]
 
-    def get_updates(self) -> list[OperatorType]:
+    def get_updates(self) -> list[StepType]:
         return [
             self._first_update,
             self._second_update,

elastica/systems/memory.py → elastica/experimental/timestepper/memory.py

@@ -1,6 +1,10 @@
 from typing import Iterator, TypeVar, Generic, Type
-from elastica.timestepper.protocol import ExplicitStepperProtocol
 from elastica.typing import SystemCollectionType
+from elastica.experimental.timestepper.explicit_steppers import (
+    RungeKutta4,
+    EulerForward,
+)
+from elastica.experimental.timestepper.protocol import ExplicitStepperProtocol
 
 from copy import copy
 
@@ -12,11 +16,6 @@ def make_memory_for_explicit_stepper(
 ) -> "MemoryCollection":
     # TODO Automated logic (class creation, memory management logic) agnostic of stepper details (RK, AB etc.)
 
-    from elastica.timestepper.explicit_steppers import (
-        RungeKutta4,
-        EulerForward,
-    )
-
     # is_this_system_a_collection = is_system_a_collection(system)
 
     memory_cls: Type

elastica/experimental/timestepper/protocol.py

@@ -0,0 +1,86 @@
+from typing import Protocol
+
+from elastica.typing import StepType, StateType
+from elastica.systems.protocol import SystemProtocol, SlenderBodyGeometryProtocol
+from elastica.timestepper.protocol import StepperProtocol
+
+import numpy as np
+
+
+class ExplicitSystemProtocol(SystemProtocol, SlenderBodyGeometryProtocol, Protocol):
+    # TODO: Temporarily made to handle explicit stepper.
+    # Need to be refactored as the explicit stepper is further developed.
+    def __call__(self, time: np.float64, dt: np.float64) -> np.float64: ...
+    @property
+    def state(self) -> StateType: ...
+    @state.setter
+    def state(self, state: StateType) -> None: ...
+    @property
+    def n_elems(self) -> int: ...
+
+
+class MemoryProtocol(Protocol):
+    @property
+    def initial_state(self) -> bool: ...
+
+
+class ExplicitStepperProtocol(StepperProtocol, Protocol):
+    """symplectic stepper protocol."""
+
+    def get_stages(self) -> list[StepType]: ...
+
+    def get_updates(self) -> list[StepType]: ...
+
+
+# class _LinearExponentialIntegratorMixin:
+#     """
+#     Linear Exponential integrator mixin wrapper.
+#     """
+#
+#     def __init__(self):
+#         pass
+#
+#     def _do_stage(self, System, Memory, time, dt):
+#         # TODO : Make more general, system should not be calculating what the state
+#         # transition matrix directly is, but rather it should just give
+#         Memory.linear_operator = System.get_linear_state_transition_operator(time, dt)
+#
+#     def _do_update(self, System, Memory, time, dt):
+#         # FIXME What's the right formula when doing update?
+#         # System.linearly_evolving_state = _batch_matmul(
+#         #     System.linearly_evolving_state,
+#         #     Memory.linear_operator
+#         # )
+#         System.linearly_evolving_state = np.einsum(
+#             "ijk,ljk->ilk", System.linearly_evolving_state, Memory.linear_operator
+#         )
+#         return time + dt
+#
+#     def _first_prefactor(self, dt):
+#         """Prefactor call to satisfy interface of SymplecticStepper. Should never
+#         be used in actual code.
+#
+#         Parameters
+#         ----------
+#         dt : the time step of simulation
+#
+#         Raises
+#         ------
+#         RuntimeError
+#         """
+#         raise RuntimeError(
+#             "Symplectic prefactor of LinearExponentialIntegrator should not be called!"
+#         )
+#
+#     # Code repeat!
+#     # Easy to avoid, but keep for performance.
+#     def _do_one_step(self, System, time, prefac):
+#         System.linearly_evolving_state = np.einsum(
+#             "ijk,ljk->ilk",
+#             System.linearly_evolving_state,
+#             System.get_linear_state_transition_operator(time, prefac),
+#         )
+#         return (
+#             time  # TODO fix hack that treats time separately here. Shuold be time + dt
+#         )
+#         # return time + dt

elastica/modules/base_system.py

@@ -27,6 +27,7 @@
 
 from .memory_block import construct_memory_block_structures
 from .operator_group import OperatorGroupFIFO
+from .protocol import ModuleProtocol
 
 
 class BaseSystemCollection(MutableSequence):
@@ -55,10 +56,18 @@ def __init__(self) -> None:
         # 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[OperatorType] = OperatorGroupFIFO()
-        self._feature_group_constrain_values: list[OperatorType] = []
-        self._feature_group_constrain_rates: list[OperatorType] = []
-        self._feature_group_callback: list[OperatorCallbackType] = []
+        self._feature_group_synchronize: OperatorGroupFIFO[
+            OperatorType, ModuleProtocol
+        ] = OperatorGroupFIFO()
+        self._feature_group_constrain_values: OperatorGroupFIFO[
+            OperatorType, ModuleProtocol
+        ] = OperatorGroupFIFO()
+        self._feature_group_constrain_rates: OperatorGroupFIFO[
+            OperatorType, ModuleProtocol
+        ] = OperatorGroupFIFO()
+        self._feature_group_callback: OperatorGroupFIFO[
+            OperatorCallbackType, ModuleProtocol
+        ] = OperatorGroupFIFO()
         self._feature_group_finalize: list[OperatorFinalizeType] = []
         # We need to initialize our mixin classes
         super().__init__()

elastica/modules/callbacks.py

@@ -9,6 +9,8 @@
 from elastica.typing import SystemType, SystemIdxType, OperatorFinalizeType
 from .protocol import ModuleProtocol
 
+import functools
+
 import numpy as np
 
 from elastica.callback_functions import CallBackBaseClass
@@ -29,9 +31,7 @@ class CallBacks:
 
     def __init__(self: SystemCollectionWithCallbackProtocol) -> None:
         self._callback_list: list[ModuleProtocol] = []
-        self._callback_operators: list[tuple[int, CallBackBaseClass]] = []
         super(CallBacks, self).__init__()
-        self._feature_group_callback.append(self._callback_execution)
         self._feature_group_finalize.append(self._finalize_callback)
 
     def collect_diagnostics(
@@ -54,31 +54,26 @@ def collect_diagnostics(
         sys_idx: SystemIdxType = self.get_system_index(system)
 
         # Create _Constraint object, cache it and return to user
-        _callbacks: ModuleProtocol = _CallBack(sys_idx)
-        self._callback_list.append(_callbacks)
+        _callback: ModuleProtocol = _CallBack(sys_idx)
+        self._callback_list.append(_callback)
+        self._feature_group_callback.append_id(_callback)
 
-        return _callbacks
+        return _callback
 
     def _finalize_callback(self: SystemCollectionWithCallbackProtocol) -> None:
         # dev : the first index stores the rod index to collect data.
-        self._callback_operators = [
-            (callback.id(), callback.instantiate()) for callback in self._callback_list
-        ]
+        for callback in self._callback_list:
+            sys_id = callback.id()
+            callback_instance = callback.instantiate()
+
+            callback_operator = functools.partial(
+                callback_instance.make_callback, system=self[sys_id]
+            )
+            self._feature_group_callback.add_operators(callback, [callback_operator])
+
         self._callback_list.clear()
         del self._callback_list
 
-        # First callback execution
-        time = np.float64(0.0)
-        self._callback_execution(time=time, current_step=0)
-
-    def _callback_execution(
-        self: SystemCollectionProtocol,
-        time: np.float64,
-        current_step: int,
-    ) -> None:
-        for sys_id, callback in self._callback_operators:
-            callback.make_callback(self[sys_id], time, current_step)
-
 
 class _CallBack:
     """

elastica/modules/constraints.py

@@ -7,6 +7,8 @@
 from typing import Any, Type, cast
 from typing_extensions import Self
 
+import functools
+
 import numpy as np
 
 from elastica.boundary_conditions import ConstraintBase
@@ -36,8 +38,6 @@ class Constraints:
     def __init__(self: ConstrainedSystemCollectionProtocol) -> None:
         self._constraints_list: list[ModuleProtocol] = []
         super(Constraints, self).__init__()
-        self._feature_group_constrain_values.append(self._constrain_values)
-        self._feature_group_constrain_rates.append(self._constrain_rates)
         self._feature_group_finalize.append(self._finalize_constraints)
 
     def constrain(
@@ -62,6 +62,8 @@ def constrain(
         # Create _Constraint object, cache it and return to user
         _constraint: ModuleProtocol = _Constraint(sys_idx)
         self._constraints_list.append(_constraint)
+        self._feature_group_constrain_values.append_id(_constraint)
+        self._feature_group_constrain_rates.append_id(_constraint)
 
         return _constraint
 
@@ -71,11 +73,14 @@ def _finalize_constraints(self: ConstrainedSystemCollectionProtocol) -> None:
         periodic boundaries, a new constrain for memory block rod added called as _ConstrainPeriodicBoundaries. This
         constrain will synchronize the only periodic boundaries of position, director, velocity and omega variables.
         """
-        from elastica._synchronize_periodic_boundary import _ConstrainPeriodicBoundaries
 
         for block in self.block_systems():
             # append the memory block to the simulation as a system. Memory block is the final system in the simulation.
             if hasattr(block, "ring_rod_flag"):
+                from elastica._synchronize_periodic_boundary import (
+                    _ConstrainPeriodicBoundaries,
+                )
+
                 # Apply the constrain to synchronize the periodic boundaries of the memory rod. Find the memory block
                 # sys idx among other systems added and then apply boundary conditions.
                 memory_block_idx = self.get_system_index(block)
@@ -89,31 +94,38 @@ def _finalize_constraints(self: ConstrainedSystemCollectionProtocol) -> None:
 
         # dev : the first index stores the rod index to apply the boundary condition
         # to.
-        self._constraints_operators = [
-            (constraint.id(), constraint.instantiate(self[constraint.id()]))
-            for constraint in self._constraints_list
-        ]
-
         # Sort from lowest id to highest id for potentially better memory access
         # _constraints contains list of tuples. First element of tuple is rod number and
         # following elements are the type of boundary condition such as
         # [(0, ConstraintBase, OneEndFixedBC), (1, HelicalBucklingBC), ... ]
         # Thus using lambda we iterate over the list of tuples and use rod number (x[0])
         # to sort constraints.
-        self._constraints_operators.sort(key=lambda x: x[0])
+        self._constraints_list.sort(key=lambda x: x.id())
+        for constraint in self._constraints_list:
+            sys_id = constraint.id()
+            constraint_instance = constraint.instantiate(self[sys_id])
+
+            constrain_values = functools.partial(
+                constraint_instance.constrain_values, system=self[sys_id]
+            )
+            constrain_rates = functools.partial(
+                constraint_instance.constrain_rates, system=self[sys_id]
+            )
+
+            self._feature_group_constrain_values.add_operators(
+                constraint, [constrain_values]
+            )
+            self._feature_group_constrain_rates.add_operators(
+                constraint, [constrain_rates]
+            )
 
         # At t=0.0, constrain all the boundary conditions (for compatability with
         # initial conditions)
-        self._constrain_values(time=np.float64(0.0))
-        self._constrain_rates(time=np.float64(0.0))
-
-    def _constrain_values(self: SystemCollectionProtocol, time: np.float64) -> None:
-        for sys_id, constraint in self._constraints_operators:
-            constraint.constrain_values(self[sys_id], time)
+        self.constrain_values(time=np.float64(0.0))
+        self.constrain_rates(time=np.float64(0.0))
 
-    def _constrain_rates(self: SystemCollectionProtocol, time: np.float64) -> None:
-        for sys_id, constraint in self._constraints_operators:
-            constraint.constrain_rates(self[sys_id], time)
+        self._constraints_list = []
+        del self._constraints_list
 
 
 class _Constraint: