Repository: gazzolalab/pyelastica
Issue: Possible Bug: Test restart functionality and applying constrains 

We should test the below line in the restart code. We suspect it creates incorrect results, when we load and time-step.

https://github.com/GazzolaLab/PyElastica/blob/7b3fe2d0204a175c9e5e64265c70b9577b4ca8c9/elastica/restart.py#L92-L93

Changed files:
elastica/restart.py, elastica/__init__.py, tests/test_restart.py

diff --git a/elastica/__init__.py b/elastica/__init__.py
index 7622bf2..f60bc90 100644
--- a/elastica/__init__.py
+++ b/elastica/__init__.py
@@ -71,3 +71,4 @@ from elastica.timestepper import (
 )
 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
diff --git a/elastica/restart.py b/elastica/restart.py
index 7e97cb8..1b5fab2 100644
--- a/elastica/restart.py
+++ b/elastica/restart.py
@@ -3,6 +3,7 @@ __doc__ = """Generate or load restart file implementations."""
 import numpy as np
 import os
 from itertools import groupby
+from .memory_block import MemoryBlockCosseratRod, MemoryBlockRigidBody
 
 
 def all_equal(iterable):
@@ -41,6 +42,10 @@ def save_state(simulator, directory: str = "", time=0.0, verbose: bool = False):
     """
     os.makedirs(directory, exist_ok=True)
     for idx, rod in enumerate(simulator):
+        if isinstance(rod, MemoryBlockCosseratRod) or isinstance(
+            rod, MemoryBlockRigidBody
+        ):
+            continue
         path = os.path.join(directory, "system_{}.npz".format(idx))
         np.savez(path, time=time, **rod.__dict__)
 
@@ -69,6 +74,10 @@ def load_state(simulator, directory: str = "", verbose: bool = False):
     """
     time_list = []  # Simulation time of rods when they are saved.
     for idx, rod in enumerate(simulator):
+        if isinstance(rod, MemoryBlockCosseratRod) or isinstance(
+            rod, MemoryBlockRigidBody
+        ):
+            continue
         path = os.path.join(directory, "system_{}.npz".format(idx))
         data = np.load(path, allow_pickle=True)
         for key, value in data.items():
@@ -88,10 +97,6 @@ def load_state(simulator, directory: str = "", verbose: bool = False):
             "Restart time of loaded rods are different, check your inputs!"
         )
 
-    # Apply boundary conditions, after loading the systems.
-    simulator.constrain_values(0.0)
-    simulator.constrain_rates(0.0)
-
     if verbose:
         print("Load complete: {}".format(directory))
 
diff --git a/tests/test_restart.py b/tests/test_restart.py
index 0ba52df..0f814b2 100644
--- a/tests/test_restart.py
+++ b/tests/test_restart.py
@@ -12,6 +12,7 @@ from elastica.modules import (
     CallBacks,
 )
 from elastica.restart import save_state, load_state
+import elastica as ea
 
 
 class GenericSimulatorClass(
@@ -78,6 +79,98 @@ class TestRestartFunctionsWithFeaturesUsingCosseratRod:
 
                 assert_allclose(test_value, correct_value)
 
+    def run_sim(self, final_time, load_from_restart, save_data_restart):
+        class BaseSimulatorClass(
+            BaseSystemCollection, Constraints, Forcing, Connections, CallBacks
+        ):
+            pass
+
+        simulator_class = BaseSimulatorClass()
+
+        rod_list = []
+        for _ in range(5):
+            rod = ea.CosseratRod.straight_rod(
+                n_elements=10,
+                start=np.zeros((3)),
+                direction=np.array([0, 1, 0.0]),
+                normal=np.array([1, 0, 0.0]),
+                base_length=1,
+                base_radius=1,
+                density=1,
+                youngs_modulus=1,
+            )
+            # Bypass check, but its fine for testing
+            simulator_class._systems.append(rod)
+
+            # Also add rods to a separate list
+            rod_list.append(rod)
+
+        for rod in rod_list:
+            simulator_class.add_forcing_to(rod).using(
+                ea.EndpointForces,
+                start_force=np.zeros(
+                    3,
+                ),
+                end_force=np.array([0, 0.1, 0]),
+                ramp_up_time=0.1,
+            )
+
+        # Finalize simulator
+        simulator_class.finalize()
+
+        directory = "restart_test_data/"
+
+        time_step = 1e-4
+        total_steps = int(final_time / time_step)
+
+        if load_from_restart:
+            restart_time = ea.load_state(simulator_class, directory, True)
+
+        else:
+            restart_time = np.float64(0.0)
+
+        timestepper = ea.PositionVerlet()
+        time = ea.integrate(
+            timestepper,
+            simulator_class,
+            final_time,
+            total_steps,
+            restart_time=restart_time,
+        )
+
+        if save_data_restart:
+            ea.save_state(simulator_class, directory, time, True)
+
+        # Compute final time accelerations
+        recorded_list = np.zeros((len(rod_list), rod_list[0].n_elems + 1))
+        for i, rod in enumerate(rod_list):
+            recorded_list[i, :] = rod.acceleration_collection[1, :]
+
+        return recorded_list
+
+    @pytest.mark.parametrize("final_time", [0.2, 1.0])
+    def test_save_restart_run_sim(self, final_time):
+
+        # First half of simulation
+        _ = self.run_sim(
+            final_time / 2, load_from_restart=False, save_data_restart=True
+        )
+
+        # Second half of simulation
+        recorded_list = self.run_sim(
+            final_time / 2, load_from_restart=True, save_data_restart=False
+        )
+        recorded_list_second_half = recorded_list.copy()
+
+        # Full simulation
+        recorded_list = self.run_sim(
+            final_time, load_from_restart=False, save_data_restart=False
+        )
+        recorded_list_full_sim = recorded_list.copy()
+
+        # Compare final accelerations of rods
+        assert_allclose(recorded_list_second_half, recorded_list_full_sim)
+
 
 class TestRestartFunctionsWithFeaturesUsingRigidBodies:
     @pytest.fixture(scope="function")