Merge pull request #61 from hsalehipour/dev

Added boundary force computation and more

examples/cfd/flow_past_sphere_3d.py

@@ -3,13 +3,22 @@
 from xlb.precision_policy import PrecisionPolicy
 from xlb.helper import create_nse_fields, initialize_eq
 from xlb.operator.stepper import IncompressibleNavierStokesStepper
-from xlb.operator.boundary_condition import FullwayBounceBackBC, ZouHeBC, RegularizedBC, EquilibriumBC, DoNothingBC, ExtrapolationOutflowBC
+from xlb.operator.boundary_condition import (
+    FullwayBounceBackBC,
+    HalfwayBounceBackBC,
+    ZouHeBC,
+    RegularizedBC,
+    EquilibriumBC,
+    DoNothingBC,
+    ExtrapolationOutflowBC,
+)
 from xlb.operator.macroscopic import Macroscopic
 from xlb.operator.boundary_masker import IndicesBoundaryMasker
 from xlb.utils import save_fields_vtk, save_image
 import warp as wp
 import numpy as np
 import jax.numpy as jnp
+import time
 
 
 class FlowOverSphere:
@@ -25,7 +34,7 @@ def __init__(self, omega, grid_shape, velocity_set, backend, precision_policy):
         self.velocity_set = velocity_set
         self.backend = backend
         self.precision_policy = precision_policy
-        self.grid, self.f_0, self.f_1, self.missing_mask, self.boundary_mask = create_nse_fields(grid_shape)
+        self.grid, self.f_0, self.f_1, self.missing_mask, self.boundary_map = create_nse_fields(grid_shape)
         self.stepper = None
         self.boundary_conditions = []
 
@@ -34,7 +43,7 @@ def __init__(self, omega, grid_shape, velocity_set, backend, precision_policy):
 
     def _setup(self, omega):
         self.setup_boundary_conditions()
-        self.setup_boundary_masks()
+        self.setup_boundary_masker()
         self.initialize_fields()
         self.setup_stepper(omega)
 
@@ -69,19 +78,20 @@ def setup_boundary_conditions(self):
         # bc_outlet = RegularizedBC("pressure", 1.0, indices=outlet)
         # bc_outlet = DoNothingBC(indices=outlet)
         bc_outlet = ExtrapolationOutflowBC(indices=outlet)
-        bc_sphere = FullwayBounceBackBC(indices=sphere)
+        bc_sphere = HalfwayBounceBackBC(indices=sphere)
+
         self.boundary_conditions = [bc_left, bc_outlet, bc_sphere, bc_walls]
         # Note: it is important to add bc_walls to be after bc_outlet/bc_inlet because
         # of the corner nodes. This way the corners are treated as wall and not inlet/outlet.
         # TODO: how to ensure about this behind in the src code?
 
-    def setup_boundary_masks(self):
+    def setup_boundary_masker(self):
         indices_boundary_masker = IndicesBoundaryMasker(
             velocity_set=self.velocity_set,
             precision_policy=self.precision_policy,
             compute_backend=self.backend,
         )
-        self.boundary_mask, self.missing_mask = indices_boundary_masker(self.boundary_conditions, self.boundary_mask, self.missing_mask, (0, 0, 0))
+        self.boundary_map, self.missing_mask = indices_boundary_masker(self.boundary_conditions, self.boundary_map, self.missing_mask, (0, 0, 0))
 
     def initialize_fields(self):
         self.f_0 = initialize_eq(self.f_0, self.grid, self.velocity_set, self.backend)
@@ -90,12 +100,16 @@ def setup_stepper(self, omega):
         self.stepper = IncompressibleNavierStokesStepper(omega, boundary_conditions=self.boundary_conditions, collision_type="BGK")
 
     def run(self, num_steps, post_process_interval=100):
+        start_time = time.time()
         for i in range(num_steps):
-            self.f_1 = self.stepper(self.f_0, self.f_1, self.boundary_mask, self.missing_mask, i)
+            self.f_1 = self.stepper(self.f_0, self.f_1, self.boundary_map, self.missing_mask, i)
             self.f_0, self.f_1 = self.f_1, self.f_0
 
             if i % post_process_interval == 0 or i == num_steps - 1:
                 self.post_process(i)
+                end_time = time.time()
+                print(f"Completing {i} iterations. Time elapsed for 1000 LBM steps in {end_time - start_time:.6f} seconds.")
+                start_time = time.time()
 
     def post_process(self, i):
         # Write the results. We'll use JAX backend for the post-processing
@@ -114,7 +128,7 @@ def post_process(self, i):
 
         fields = {"u_magnitude": u_magnitude, "u_x": u[0], "u_y": u[1], "u_z": u[2], "rho": rho[0]}
 
-        save_fields_vtk(fields, timestep=i)
+        # save_fields_vtk(fields, timestep=i)
         save_image(fields["u_magnitude"][:, self.grid_shape[1] // 2, :], timestep=i)
 
 

examples/cfd/lid_driven_cavity_2d.py

@@ -24,7 +24,7 @@ def __init__(self, omega, grid_shape, velocity_set, backend, precision_policy):
         self.velocity_set = velocity_set
         self.backend = backend
         self.precision_policy = precision_policy
-        self.grid, self.f_0, self.f_1, self.missing_mask, self.boundary_mask = create_nse_fields(grid_shape)
+        self.grid, self.f_0, self.f_1, self.missing_mask, self.boundary_map = create_nse_fields(grid_shape)
         self.stepper = None
         self.boundary_conditions = []
 
@@ -33,7 +33,7 @@ def __init__(self, omega, grid_shape, velocity_set, backend, precision_policy):
 
     def _setup(self, omega):
         self.setup_boundary_conditions()
-        self.setup_boundary_masks()
+        self.setup_boundary_masker()
         self.initialize_fields()
         self.setup_stepper(omega)
 
@@ -51,13 +51,13 @@ def setup_boundary_conditions(self):
         bc_walls = HalfwayBounceBackBC(indices=walls)
         self.boundary_conditions = [bc_top, bc_walls]
 
-    def setup_boundary_masks(self):
+    def setup_boundary_masker(self):
         indices_boundary_masker = IndicesBoundaryMasker(
             velocity_set=self.velocity_set,
             precision_policy=self.precision_policy,
             compute_backend=self.backend,
         )
-        self.boundary_mask, self.missing_mask = indices_boundary_masker(self.boundary_conditions, self.boundary_mask, self.missing_mask)
+        self.boundary_map, self.missing_mask = indices_boundary_masker(self.boundary_conditions, self.boundary_map, self.missing_mask)
 
     def initialize_fields(self):
         self.f_0 = initialize_eq(self.f_0, self.grid, self.velocity_set, self.backend)
@@ -67,7 +67,7 @@ def setup_stepper(self, omega):
 
     def run(self, num_steps, post_process_interval=100):
         for i in range(num_steps):
-            self.f_1 = self.stepper(self.f_0, self.f_1, self.boundary_mask, self.missing_mask, i)
+            self.f_1 = self.stepper(self.f_0, self.f_1, self.boundary_map, self.missing_mask, i)
             self.f_0, self.f_1 = self.f_1, self.f_0
 
             if i % post_process_interval == 0 or i == num_steps - 1:

examples/cfd/windtunnel_3d.py

@@ -9,14 +9,18 @@
     FullwayBounceBackBC,
     EquilibriumBC,
     DoNothingBC,
+    RegularizedBC,
+    HalfwayBounceBackBC,
     ExtrapolationOutflowBC,
 )
+from xlb.operator.force.momentum_transfer import MomentumTransfer
 from xlb.operator.macroscopic import Macroscopic
-from xlb.operator.boundary_masker import IndicesBoundaryMasker
+from xlb.operator.boundary_masker import IndicesBoundaryMasker, MeshBoundaryMasker
 from xlb.utils import save_fields_vtk, save_image
 import warp as wp
 import numpy as np
 import jax.numpy as jnp
+import matplotlib.pyplot as plt
 
 
 class WindTunnel3D:
@@ -32,18 +36,25 @@ def __init__(self, omega, wind_speed, grid_shape, velocity_set, backend, precisi
         self.velocity_set = velocity_set
         self.backend = backend
         self.precision_policy = precision_policy
-        self.grid, self.f_0, self.f_1, self.missing_mask, self.boundary_mask = create_nse_fields(grid_shape)
+        self.grid, self.f_0, self.f_1, self.missing_mask, self.boundary_map = create_nse_fields(grid_shape)
         self.stepper = None
         self.boundary_conditions = []
 
         # Setup the simulation BC, its initial conditions, and the stepper
-        self._setup(omega, wind_speed)
-
-    def _setup(self, omega, wind_speed):
-        self.setup_boundary_conditions(wind_speed)
-        self.setup_boundary_masks()
+        self.wind_speed = wind_speed
+        self.omega = omega
+        self._setup()
+
+        # Make list to store drag coefficients
+        self.time_steps = []
+        self.drag_coefficients = []
+        self.lift_coefficients = []
+
+    def _setup(self):
+        self.setup_boundary_conditions()
+        self.setup_boundary_masker()
         self.initialize_fields()
-        self.setup_stepper(omega)
+        self.setup_stepper()
 
     def voxelize_stl(self, stl_filename, length_lbm_unit):
         mesh = trimesh.load_mesh(stl_filename, process=False)
@@ -64,46 +75,66 @@ def define_boundary_indices(self):
             for i in range(self.velocity_set.d)
         ]
 
+        # Load the mesh
         stl_filename = "examples/cfd/stl-files/DrivAer-Notchback.stl"
-        grid_size_x = self.grid_shape[0]
-        car_length_lbm_unit = grid_size_x / 4
-        car_voxelized, pitch = self.voxelize_stl(stl_filename, car_length_lbm_unit)
-
-        # car_area = np.prod(car_voxelized.shape[1:])
-        tx, ty, _ = np.array([grid_size_x, grid_size_y, grid_size_z]) - car_voxelized.shape
-        shift = [tx // 4, ty // 2, 0]
-        car = np.argwhere(car_voxelized) + shift
-        car = np.array(car).T
-        car = [tuple(car[i]) for i in range(self.velocity_set.d)]
+        mesh = trimesh.load_mesh(stl_filename, process=False)
+        mesh_vertices = mesh.vertices
+
+        # Transform the mesh points to be located in the right position in the wind tunnel
+        mesh_vertices -= mesh_vertices.min(axis=0)
+        mesh_extents = mesh_vertices.max(axis=0)
+        length_phys_unit = mesh_extents.max()
+        length_lbm_unit = self.grid_shape[0] / 4
+        dx = length_phys_unit / length_lbm_unit
+        shift = np.array([self.grid_shape[0] * dx / 4, (self.grid_shape[1] * dx - mesh_extents[1]) / 2, 0.0])
+        car = mesh_vertices + shift
+        self.grid_spacing = dx
+        self.car_cross_section = np.prod(mesh_extents[1:]) / dx**2
 
         return inlet, outlet, walls, car
 
-    def setup_boundary_conditions(self, wind_speed):
+    def setup_boundary_conditions(self):
         inlet, outlet, walls, car = self.define_boundary_indices()
-        bc_left = EquilibriumBC(rho=1.0, u=(wind_speed, 0.0, 0.0), indices=inlet)
+        bc_left = EquilibriumBC(rho=1.0, u=(self.wind_speed, 0.0, 0.0), indices=inlet)
+        # bc_left = RegularizedBC('velocity', (self.wind_speed, 0.0, 0.0), indices=inlet)
         bc_walls = FullwayBounceBackBC(indices=walls)
         bc_do_nothing = ExtrapolationOutflowBC(indices=outlet)
-        bc_car = FullwayBounceBackBC(indices=car)
+        bc_car = HalfwayBounceBackBC(mesh_vertices=car)
+        # bc_car = FullwayBounceBackBC(mesh_vertices=car)
         self.boundary_conditions = [bc_left, bc_do_nothing, bc_walls, bc_car]
 
-    def setup_boundary_masks(self):
+    def setup_boundary_masker(self):
         indices_boundary_masker = IndicesBoundaryMasker(
             velocity_set=self.velocity_set,
             precision_policy=self.precision_policy,
             compute_backend=self.backend,
         )
-        self.boundary_mask, self.missing_mask = indices_boundary_masker(self.boundary_conditions, self.boundary_mask, self.missing_mask, (0, 0, 0))
+        mesh_boundary_masker = MeshBoundaryMasker(
+            velocity_set=self.velocity_set,
+            precision_policy=self.precision_policy,
+            compute_backend=self.backend,
+        )
+        bclist_other = self.boundary_conditions[:-1]
+        bc_mesh = self.boundary_conditions[-1]
+        dx = self.grid_spacing
+        origin, spacing = (0, 0, 0), (dx, dx, dx)
+        self.boundary_map, self.missing_mask = indices_boundary_masker(bclist_other, self.boundary_map, self.missing_mask)
+        self.boundary_map, self.missing_mask = mesh_boundary_masker(bc_mesh, origin, spacing, self.boundary_map, self.missing_mask)
 
     def initialize_fields(self):
         self.f_0 = initialize_eq(self.f_0, self.grid, self.velocity_set, self.backend)
 
-    def setup_stepper(self, omega):
-        self.stepper = IncompressibleNavierStokesStepper(omega, boundary_conditions=self.boundary_conditions, collision_type="KBC")
+    def setup_stepper(self):
+        self.stepper = IncompressibleNavierStokesStepper(self.omega, boundary_conditions=self.boundary_conditions, collision_type="KBC")
 
     def run(self, num_steps, print_interval, post_process_interval=100):
+        # Setup the operator for computing surface forces at the interface of the specified BC
+        bc_car = self.boundary_conditions[-1]
+        self.momentum_transfer = MomentumTransfer(bc_car)
+
         start_time = time.time()
         for i in range(num_steps):
-            self.f_1 = self.stepper(self.f_0, self.f_1, self.boundary_mask, self.missing_mask, i)
+            self.f_1 = self.stepper(self.f_0, self.f_1, self.boundary_map, self.missing_mask, i)
             self.f_0, self.f_1 = self.f_1, self.f_0
 
             if (i + 1) % print_interval == 0:
@@ -133,6 +164,49 @@ def post_process(self, i):
         save_fields_vtk(fields, timestep=i)
         save_image(fields["u_magnitude"][:, grid_size_y // 2, :], timestep=i)
 
+        # Compute lift and drag
+        boundary_force = self.momentum_transfer(self.f_0, self.boundary_map, self.missing_mask)
+        drag = np.sqrt(boundary_force[0] ** 2 + boundary_force[1] ** 2)  # xy-plane
+        lift = boundary_force[2]
+        c_d = 2.0 * drag / (self.wind_speed**2 * self.car_cross_section)
+        c_l = 2.0 * lift / (self.wind_speed**2 * self.car_cross_section)
+        self.drag_coefficients.append(c_d)
+        self.lift_coefficients.append(c_l)
+        self.time_steps.append(i)
+
+        # Save monitor plot
+        self.plot_drag_coefficient()
+        return
+
+    def plot_drag_coefficient(self):
+        # Compute moving average of drag coefficient, 100, 1000, 10000
+        drag_coefficients = np.array(self.drag_coefficients)
+        self.drag_coefficients_ma_10 = np.convolve(drag_coefficients, np.ones(10) / 10, mode="valid")
+        self.drag_coefficients_ma_100 = np.convolve(drag_coefficients, np.ones(100) / 100, mode="valid")
+        self.drag_coefficients_ma_1000 = np.convolve(drag_coefficients, np.ones(1000) / 1000, mode="valid")
+        self.drag_coefficients_ma_10000 = np.convolve(drag_coefficients, np.ones(10000) / 10000, mode="valid")
+        self.drag_coefficients_ma_100000 = np.convolve(drag_coefficients, np.ones(100000) / 100000, mode="valid")
+
+        # Plot drag coefficient
+        plt.plot(self.time_steps, drag_coefficients, label="Raw")
+        if len(self.time_steps) > 10:
+            plt.plot(self.time_steps[9:], self.drag_coefficients_ma_10, label="MA 10")
+        if len(self.time_steps) > 100:
+            plt.plot(self.time_steps[99:], self.drag_coefficients_ma_100, label="MA 100")
+        if len(self.time_steps) > 1000:
+            plt.plot(self.time_steps[999:], self.drag_coefficients_ma_1000, label="MA 1,000")
+        if len(self.time_steps) > 10000:
+            plt.plot(self.time_steps[9999:], self.drag_coefficients_ma_10000, label="MA 10,000")
+        if len(self.time_steps) > 100000:
+            plt.plot(self.time_steps[99999:], self.drag_coefficients_ma_100000, label="MA 100,000")
+
+        plt.ylim(-1.0, 1.0)
+        plt.legend()
+        plt.xlabel("Time step")
+        plt.ylabel("Drag coefficient")
+        plt.savefig("drag_coefficient_ma.png")
+        plt.close()
+
 
 if __name__ == "__main__":
     # Grid parameters

examples/cfd_old_to_be_migrated/flow_past_sphere.py

@@ -75,7 +75,7 @@ def warp_implementation(self, rho, u, vel):
     u = grid.create_field(cardinality=velocity_set.d, dtype=wp.float32)
     f0 = grid.create_field(cardinality=velocity_set.q, dtype=wp.float32)
     f1 = grid.create_field(cardinality=velocity_set.q, dtype=wp.float32)
-    boundary_mask = grid.create_field(cardinality=1, dtype=wp.uint8)
+    boundary_map = grid.create_field(cardinality=1, dtype=wp.uint8)
     missing_mask = grid.create_field(cardinality=velocity_set.q, dtype=wp.bool)
 
     # Make operators
@@ -154,23 +154,19 @@ def warp_implementation(self, rho, u, vel):
     indices = wp.from_numpy(indices, dtype=wp.int32)
 
     # Set boundary conditions on the indices
-    boundary_mask, missing_mask = indices_boundary_masker(indices, half_way_bc.id, boundary_mask, missing_mask, (0, 0, 0))
+    boundary_map, missing_mask = indices_boundary_masker(indices, half_way_bc.id, boundary_map, missing_mask, (0, 0, 0))
 
     # Set inlet bc
     lower_bound = (0, 0, 0)
     upper_bound = (0, nr, nr)
     direction = (1, 0, 0)
-    boundary_mask, missing_mask = planar_boundary_masker(
-        lower_bound, upper_bound, direction, equilibrium_bc.id, boundary_mask, missing_mask, (0, 0, 0)
-    )
+    boundary_map, missing_mask = planar_boundary_masker(lower_bound, upper_bound, direction, equilibrium_bc.id, boundary_map, missing_mask, (0, 0, 0))
 
     # Set outlet bc
     lower_bound = (nr - 1, 0, 0)
     upper_bound = (nr - 1, nr, nr)
     direction = (-1, 0, 0)
-    boundary_mask, missing_mask = planar_boundary_masker(
-        lower_bound, upper_bound, direction, do_nothing_bc.id, boundary_mask, missing_mask, (0, 0, 0)
-    )
+    boundary_map, missing_mask = planar_boundary_masker(lower_bound, upper_bound, direction, do_nothing_bc.id, boundary_map, missing_mask, (0, 0, 0))
 
     # Set initial conditions
     rho, u = initializer(rho, u, vel)
@@ -185,7 +181,7 @@ def warp_implementation(self, rho, u, vel):
     num_steps = 1024 * 8
     start = time.time()
     for _ in tqdm(range(num_steps)):
-        f1 = stepper(f0, f1, boundary_mask, missing_mask, _)
+        f1 = stepper(f0, f1, boundary_map, missing_mask, _)
         f1, f0 = f0, f1
         if (_ % plot_freq == 0) and (not compute_mlup):
             rho, u = macroscopic(f0, rho, u)
@@ -195,7 +191,7 @@ def warp_implementation(self, rho, u, vel):
             plt.imshow(u[0, :, nr // 2, :].numpy())
             plt.colorbar()
             plt.subplot(1, 2, 2)
-            plt.imshow(boundary_mask[0, :, nr // 2, :].numpy())
+            plt.imshow(boundary_map[0, :, nr // 2, :].numpy())
             plt.colorbar()
             plt.savefig(f"{save_dir}/{str(_).zfill(6)}.png")
             plt.close()

examples/cfd_old_to_be_migrated/taylor_green.py

@@ -113,7 +113,7 @@ def run_taylor_green(backend, compute_mlup=True):
     u = grid.create_field(cardinality=velocity_set.d, precision=xlb.Precision.FP32)
     f0 = grid.create_field(cardinality=velocity_set.q, precision=xlb.Precision.FP32)
     f1 = grid.create_field(cardinality=velocity_set.q, precision=xlb.Precision.FP32)
-    boundary_mask = grid.create_field(cardinality=1, precision=xlb.Precision.UINT8)
+    boundary_map = grid.create_field(cardinality=1, precision=xlb.Precision.UINT8)
     missing_mask = grid.create_field(cardinality=velocity_set.q, precision=xlb.Precision.BOOL)
 
     # Make operators
@@ -149,10 +149,10 @@ def run_taylor_green(backend, compute_mlup=True):
     for _ in tqdm(range(num_steps)):
         # Time step
         if backend == "warp":
-            f1 = stepper(f0, f1, boundary_mask, missing_mask, _)
+            f1 = stepper(f0, f1, boundary_map, missing_mask, _)
             f1, f0 = f0, f1
         elif backend == "jax":
-            f0 = stepper(f0, boundary_mask, missing_mask, _)
+            f0 = stepper(f0, boundary_map, missing_mask, _)
 
         # Plot if needed
         if (_ % plot_freq == 0) and (not compute_mlup):