Merge pull request #84 from bhosale2/update-0.2.3

Blacken example files (#83)

Makefile

@@ -1,6 +1,6 @@
 black:
 	@black --version
-	@black --required-version 21.12b0 elastica tests
+	@black --required-version 21.12b0 elastica tests examples
 
 
 black_check:

examples/ExperimentalCases/ParallelConnectionExample/parallel_connection_example.py

@@ -6,7 +6,10 @@
 # FIXME without appending sys.path make it more generic
 sys.path.append("../../../../")
 from elastica import *
-from elastica.experimental.connection_contact_joint.parallel_connection import get_connection_vector_straight_straight_rod, SurfaceJointSideBySide
+from elastica.experimental.connection_contact_joint.parallel_connection import (
+    get_connection_vector_straight_straight_rod,
+    SurfaceJointSideBySide,
+)
 from elastica._calculus import difference_kernel
 from examples.JointCases.joint_cases_postprocessing import (
     plot_position,
@@ -82,34 +85,54 @@ class ParallelConnection(
 
 # Apply a contraction force on rod one.
 class ContractionForce(NoForces):
-    def __init__(self, ramp, force_mag, ):
+    def __init__(
+        self,
+        ramp,
+        force_mag,
+    ):
         self.ramp = ramp
         self.force_mag = force_mag
 
     def apply_forces(self, system, time: np.float64 = 0.0):
         # Ramp the force
         factor = min(1.0, time / self.ramp)
 
-        system.external_forces[:] -= factor * difference_kernel(self.force_mag * system.tangents)
+        system.external_forces[:] -= factor * difference_kernel(
+            self.force_mag * system.tangents
+        )
+
 
-parallel_connection_sim.add_forcing_to(rod_one).using(ContractionForce, ramp=0.5, force_mag=1. )
+parallel_connection_sim.add_forcing_to(rod_one).using(
+    ContractionForce, ramp=0.5, force_mag=1.0
+)
 
 # Connect rod 1 and rod 2
 (
     rod_one_direction_vec_in_material_frame,
     rod_two_direction_vec_in_material_frame,
     offset_btw_rods,
-) = get_connection_vector_straight_straight_rod(rod_one, rod_two, (0, n_elem), (0, n_elem))
+) = get_connection_vector_straight_straight_rod(
+    rod_one, rod_two, (0, n_elem), (0, n_elem)
+)
 
 for i in range(n_elem):
     parallel_connection_sim.connect(
         first_rod=rod_one, second_rod=rod_two, first_connect_idx=i, second_connect_idx=i
     ).using(
-        SurfaceJointSideBySide, k=1E2, nu=1E-5, k_repulsive = 1E3, rod_one_direction_vec_in_material_frame=rod_one_direction_vec_in_material_frame[:,i],
-        rod_two_direction_vec_in_material_frame = rod_two_direction_vec_in_material_frame[:,i],
-        offset_btw_rods = offset_btw_rods[i]
+        SurfaceJointSideBySide,
+        k=1e2,
+        nu=1e-5,
+        k_repulsive=1e3,
+        rod_one_direction_vec_in_material_frame=rod_one_direction_vec_in_material_frame[
+            :, i
+        ],
+        rod_two_direction_vec_in_material_frame=rod_two_direction_vec_in_material_frame[
+            :, i
+        ],
+        offset_btw_rods=offset_btw_rods[i],
     )  # k=kg/s2 nu=kg/s 1e-2
 
+
 class ParallelConnecitonCallback(CallBackBaseClass):
     """
     Call back function for parallel connection

examples/MuscularSnake/muscle_forces.py

@@ -37,7 +37,7 @@ def __init__(
         side_of_body,
         muscle_start_end_index,
         step,
-            post_processing,
+        post_processing,
     ):
         """
 
@@ -76,7 +76,7 @@ def __init__(
 
         self.post_processing = post_processing
         self.step = step
-        self.counter=0
+        self.counter = 0
 
     def apply_forces(self, system, time: np.float = 0.0):
         forces = self._apply_forces(
@@ -90,15 +90,16 @@ def apply_forces(self, system, time: np.float = 0.0):
             system.external_forces,
         )
 
-        if self.counter % self.step ==0:
+        if self.counter % self.step == 0:
             self.post_processing["time"].append(time)
             self.post_processing["step"].append(self.counter)
             self.post_processing["external_forces"].append(forces.copy())
-            self.post_processing["element_position"].append(np.cumsum(system.lengths).copy())
+            self.post_processing["element_position"].append(
+                np.cumsum(system.lengths).copy()
+            )
 
         self.counter += 1
 
-
     @staticmethod
     @njit(cache=True)
     def _apply_forces(
@@ -130,4 +131,4 @@ def _apply_forces(
         ] += difference_kernel(muscle_forces)
 
         external_forces += forces
-        return forces
+        return forces

examples/MuscularSnake/muscular_snake.py

@@ -260,8 +260,8 @@ class MuscularSnakeSimulator(
     ) = get_connection_vector_straight_straight_rod(
         rod_one,
         rod_two,
-        (muscle_start_connection_index[idx],muscle_end_connection_index[idx]),
-        (0, rod_two.n_elems)
+        (muscle_start_connection_index[idx], muscle_end_connection_index[idx]),
+        (0, rod_two.n_elems),
     )
     straight_straight_rod_connection_list.append(
         [

examples/MuscularSnake/post_processing.py

@@ -12,16 +12,16 @@
 
 
 def plot_video_with_surface(
-        rods_history: Sequence[Dict],
-        video_name="video.mp4",
-        fps=60,
-        step=1,
-        vis2D=True,
-        **kwargs,
+    rods_history: Sequence[Dict],
+    video_name="video.mp4",
+    fps=60,
+    step=1,
+    vis2D=True,
+    **kwargs,
 ):
     plt.rcParams.update({"font.size": 22})
 
-    folder_name = kwargs.get("folder_name","")
+    folder_name = kwargs.get("folder_name", "")
 
     # 2d case <always 2d case for now>
     import matplotlib.animation as animation
@@ -115,7 +115,7 @@ def plot_video_with_surface(
                 ax.add_artist(sphere_artists[sphere_idx])
 
         # ax.set_aspect("equal")
-        video_name_3D = folder_name+"3D_" + video_name
+        video_name_3D = folder_name + "3D_" + video_name
 
         with writer.saving(fig, video_name_3D, dpi):
             with plt.style.context("seaborn-whitegrid"):
@@ -127,7 +127,7 @@ def plot_video_with_surface(
                         )
                         if not inst_position.shape[1] == inst_radius.shape[0]:
                             inst_position = 0.5 * (
-                                    inst_position[..., 1:] + inst_position[..., :-1]
+                                inst_position[..., 1:] + inst_position[..., :-1]
                             )
 
                         rod_scatters[rod_idx]._offsets3d = (
@@ -206,7 +206,7 @@ def plot_video_with_surface(
                 ax.add_artist(sphere_artists[sphere_idx])
 
         ax.set_aspect("equal")
-        video_name_2D = folder_name+"2D_xy_" + video_name
+        video_name_2D = folder_name + "2D_xy_" + video_name
 
         with writer.saving(fig, video_name_2D, dpi):
             with plt.style.context("seaborn-whitegrid"):
@@ -218,7 +218,7 @@ def plot_video_with_surface(
                         )
                         if not inst_position.shape[1] == inst_radius.shape[0]:
                             inst_position = 0.5 * (
-                                    inst_position[..., 1:] + inst_position[..., :-1]
+                                inst_position[..., 1:] + inst_position[..., :-1]
                             )
 
                         rod_lines[rod_idx].set_xdata(inst_position[0])
@@ -297,7 +297,7 @@ def plot_video_with_surface(
                 ax.add_artist(sphere_artists[sphere_idx])
 
         ax.set_aspect("equal")
-        video_name_2D = folder_name+"2D_zy_" + video_name
+        video_name_2D = folder_name + "2D_zy_" + video_name
 
         with writer.saving(fig, video_name_2D, dpi):
             with plt.style.context("seaborn-whitegrid"):
@@ -309,7 +309,7 @@ def plot_video_with_surface(
                         )
                         if not inst_position.shape[1] == inst_radius.shape[0]:
                             inst_position = 0.5 * (
-                                    inst_position[..., 1:] + inst_position[..., :-1]
+                                inst_position[..., 1:] + inst_position[..., :-1]
                             )
 
                         rod_lines[rod_idx].set_xdata(inst_position[2])
@@ -390,7 +390,7 @@ def plot_video_with_surface(
                 ax.add_artist(sphere_artists[sphere_idx])
 
         ax.set_aspect("equal")
-        video_name_2D = folder_name+"2D_xz_" + video_name
+        video_name_2D = folder_name + "2D_xz_" + video_name
 
         with writer.saving(fig, video_name_2D, dpi):
             with plt.style.context("seaborn-whitegrid"):
@@ -402,7 +402,7 @@ def plot_video_with_surface(
                         )
                         if not inst_position.shape[1] == inst_radius.shape[0]:
                             inst_position = 0.5 * (
-                                    inst_position[..., 1:] + inst_position[..., :-1]
+                                inst_position[..., 1:] + inst_position[..., :-1]
                             )
 
                         rod_lines[rod_idx].set_xdata(inst_position[0])
@@ -437,10 +437,11 @@ def plot_video_with_surface(
         # See https://github.com/matplotlib/matplotlib/issues/8560/
         plt.close(plt.gcf())
 
+
 def plot_snake_velocity(
-        plot_params: dict,
-        period,
-        filename="slithering_snake_velocity.png",
+    plot_params: dict,
+    period,
+    filename="slithering_snake_velocity.png",
 ):
     time_per_period = np.array(plot_params["time"]) / period
     avg_velocity = np.array(plot_params["avg_velocity"])
@@ -469,6 +470,7 @@ def plot_snake_velocity(
     fig.legend(prop={"size": 20})
     fig.savefig(filename)
 
+
 def compute_projected_velocity(plot_params: dict, period):
 
     time_per_period = np.array(plot_params["time"]) / period
@@ -494,7 +496,7 @@ def compute_projected_velocity(plot_params: dict, period):
             center_of_mass[(i + 1) * period_step : (i + 2) * period_step]
             - center_of_mass[(i + 0) * period_step : (i + 1) * period_step],
             axis=0,
-            )
+        )
 
     # Average the rod directions over multiple periods and get the direction of the rod.
     direction_of_rod = np.mean(center_of_mass_averaged_over_one_period, axis=0)
@@ -526,4 +528,3 @@ def compute_projected_velocity(plot_params: dict, period):
         average_velocity_over_simulation[0],
         average_velocity_over_simulation[1],
     )
-

examples/RestartExample/restart_example.py

@@ -3,9 +3,11 @@
 """
 
 import sys
+
 sys.path.append("../../")
 from elastica import *
 
+
 class RestartExampleSimulator(BaseSystemCollection, Constraints, Forcing, CallBacks):
     pass
 
@@ -62,7 +64,7 @@ class RestartExampleSimulator(BaseSystemCollection, Constraints, Forcing, CallBa
 
 # After finalize you can load restart file. This step is important for current implementation of restart functions,
 # it is required to load restart files after the finalize step.
-LOAD_FROM_RESTART = False 
+LOAD_FROM_RESTART = False
 SAVE_DATA_RESTART = True
 restart_file_location = "data/"
 
@@ -76,11 +78,16 @@ class RestartExampleSimulator(BaseSystemCollection, Constraints, Forcing, CallBa
 dt = 0.01 * dl
 total_steps = int(final_time / dt)
 
-time = integrate(timestepper, restart_example_simulator, final_time, total_steps, restart_time=restart_time)
+time = integrate(
+    timestepper,
+    restart_example_simulator,
+    final_time,
+    total_steps,
+    restart_time=restart_time,
+)
 
 # Save all the systems appended on the simulator class. Since in this example have only one system, under the
 # `restart_file_location` directory there is one file called system_0.npz . For each system appended on the simulator
 # separate system_#.npz file will be created.
 if SAVE_DATA_RESTART:
     save_state(restart_example_simulator, restart_file_location, time, True)
-

examples/RodContactCase/RodRodContact/rod_rod_contact_inclined_validation.py

@@ -35,7 +35,9 @@ class InclinedRodRodContact(
 shear_modulus = E / (poisson_ratio + 1.0)
 
 # Rod orientations
-start = np.zeros(3,)
+start = np.zeros(
+    3,
+)
 inclination = np.deg2rad(30)
 direction = np.array([0.0, np.cos(inclination), np.sin(inclination)])
 normal = np.array([0.0, -np.sin(inclination), np.cos(inclination)])
@@ -56,7 +58,7 @@ class InclinedRodRodContact(
     nu,
     E,
     poisson_ratio,
-    shear_modulus = shear_modulus,
+    shear_modulus=shear_modulus,
 )
 
 rod_one.velocity_collection[:] += 0.05 * -normal.reshape(3, 1)
@@ -94,9 +96,7 @@ class InclinedRodRodContact(
 
 # Add call backs
 class RodCallBack(CallBackBaseClass):
-    """
-
-    """
+    """ """
 
     def __init__(self, step_skip: int, callback_params: dict):
         CallBackBaseClass.__init__(self)
@@ -130,15 +130,19 @@ def make_callback(self, system, time, current_step: int):
 )  # list which collected data will be append
 # set the diagnostics for rod and collect data
 inclined_rod_rod_contact_sim.collect_diagnostics(rod_one).using(
-    RodCallBack, step_skip=step_skip, callback_params=post_processing_dict_rod1,
+    RodCallBack,
+    step_skip=step_skip,
+    callback_params=post_processing_dict_rod1,
 )
 
 post_processing_dict_rod2 = defaultdict(
     list
 )  # list which collected data will be append
 # set the diagnostics for rod and collect data
 inclined_rod_rod_contact_sim.collect_diagnostics(rod_two).using(
-    RodCallBack, step_skip=step_skip, callback_params=post_processing_dict_rod2,
+    RodCallBack,
+    step_skip=step_skip,
+    callback_params=post_processing_dict_rod2,
 )
 
 inclined_rod_rod_contact_sim.finalize()