Merge pull request #86 from mehdiataei/profile_inlet

Added abstraction layer for boundary condition application and stepper initialization, and the capability to add profiles to boundary conditions

CHANGELOG.md

@@ -18,3 +18,5 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - XLB is now installable via pip
 - Complete rewrite of the codebase for better modularity and extensibility based on "Operators" design pattern
 - Added NVIDIA's Warp backend for state-of-the-art performance
+- Added abstraction layer for boundary condition efficient encoding/decoding of auxiliary data
+- Added the capability to add profiles to boundary conditions

examples/cfd/flow_past_sphere_3d.py

@@ -1,20 +1,16 @@
 import xlb
 from xlb.compute_backend import ComputeBackend
 from xlb.precision_policy import PrecisionPolicy
-from xlb.helper import create_nse_fields, initialize_eq, check_bc_overlaps
+from xlb.grid import grid_factory
 from xlb.operator.stepper import IncompressibleNavierStokesStepper
 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
+from xlb.utils import save_image
 import warp as wp
 import numpy as np
 import jax.numpy as jnp
@@ -34,18 +30,19 @@ 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.bc_mask = create_nse_fields(grid_shape)
-        self.stepper = None
+        self.omega = omega
         self.boundary_conditions = []
+        self.u_max = 0.04
 
-        # Setup the simulation BC, its initial conditions, and the stepper
-        self._setup(omega)
+        # Create grid using factory
+        self.grid = grid_factory(grid_shape, compute_backend=backend)
 
-    def _setup(self, omega):
+        # Setup the simulation BC and stepper
+        self._setup()
+
+    def _setup(self):
         self.setup_boundary_conditions()
-        self.setup_boundary_masker()
-        self.initialize_fields()
-        self.setup_stepper(omega)
+        self.setup_stepper()
 
     def define_boundary_indices(self):
         box = self.grid.bounding_box_indices()
@@ -69,31 +66,63 @@ def define_boundary_indices(self):
 
     def setup_boundary_conditions(self):
         inlet, outlet, walls, sphere = self.define_boundary_indices()
-        bc_left = RegularizedBC("velocity", (0.04, 0.0, 0.0), indices=inlet)
-        # bc_left = EquilibriumBC(rho = 1, u=(0.04, 0.0, 0.0), indices=inlet)
+        bc_left = RegularizedBC("velocity", profile=self.bc_profile(), indices=inlet)
+        # bc_left = RegularizedBC("velocity", prescribed_value=(self.u_max, 0.0, 0.0), indices=inlet)
         bc_walls = FullwayBounceBackBC(indices=walls)
-        # bc_outlet = RegularizedBC("pressure", 1.0, indices=outlet)
-        # bc_outlet = DoNothingBC(indices=outlet)
         bc_outlet = ExtrapolationOutflowBC(indices=outlet)
         bc_sphere = HalfwayBounceBackBC(indices=sphere)
         self.boundary_conditions = [bc_walls, bc_left, bc_outlet, bc_sphere]
 
-    def setup_boundary_masker(self):
-        # check boundary condition list for duplicate indices before creating bc mask
-        check_bc_overlaps(self.boundary_conditions, self.velocity_set.d, self.backend)
-
-        indices_boundary_masker = IndicesBoundaryMasker(
-            velocity_set=self.velocity_set,
-            precision_policy=self.precision_policy,
-            compute_backend=self.backend,
+    def setup_stepper(self):
+        self.stepper = IncompressibleNavierStokesStepper(
+            omega=self.omega,
+            grid=self.grid,
+            boundary_conditions=self.boundary_conditions,
+            collision_type="BGK",
         )
-        self.bc_mask, self.missing_mask = indices_boundary_masker(self.boundary_conditions, self.bc_mask, self.missing_mask, (0, 0, 0))
-
-    def initialize_fields(self):
-        self.f_0 = initialize_eq(self.f_0, self.grid, self.velocity_set, self.precision_policy, self.backend)
-
-    def setup_stepper(self, omega):
-        self.stepper = IncompressibleNavierStokesStepper(omega, boundary_conditions=self.boundary_conditions, collision_type="BGK")
+        self.f_0, self.f_1, self.bc_mask, self.missing_mask = self.stepper.prepare_fields()
+
+    def bc_profile(self):
+        u_max = self.u_max  # u_max = 0.04
+        # Get the grid dimensions for the y and z directions
+        H_y = float(self.grid_shape[1] - 1)  # Height in y direction
+        H_z = float(self.grid_shape[2] - 1)  # Height in z direction
+
+        @wp.func
+        def bc_profile_warp(index: wp.vec3i):
+            # Poiseuille flow profile: parabolic velocity distribution
+            y = self.precision_policy.store_precision.wp_dtype(index[1])
+            z = self.precision_policy.store_precision.wp_dtype(index[2])
+
+            # Calculate normalized distance from center
+            y_center = y - (H_y / 2.0)
+            z_center = z - (H_z / 2.0)
+            r_squared = (2.0 * y_center / H_y) ** 2.0 + (2.0 * z_center / H_z) ** 2.0
+
+            # Parabolic profile: u = u_max * (1 - r²)
+            return wp.vec(u_max * wp.max(0.0, 1.0 - r_squared), length=1)
+
+        def bc_profile_jax():
+            y = jnp.arange(self.grid_shape[1])
+            z = jnp.arange(self.grid_shape[2])
+            Y, Z = jnp.meshgrid(y, z, indexing="ij")
+
+            # Calculate normalized distance from center
+            y_center = Y - (H_y / 2.0)
+            z_center = Z - (H_z / 2.0)
+            r_squared = (2.0 * y_center / H_y) ** 2.0 + (2.0 * z_center / H_z) ** 2.0
+
+            # Parabolic profile for x velocity, zero for y and z
+            u_x = u_max * jnp.maximum(0.0, 1.0 - r_squared)
+            u_y = jnp.zeros_like(u_x)
+            u_z = jnp.zeros_like(u_x)
+
+            return jnp.stack([u_x, u_y, u_z])
+
+        if self.backend == ComputeBackend.JAX:
+            return bc_profile_jax
+        elif self.backend == ComputeBackend.WARP:
+            return bc_profile_warp
 
     def run(self, num_steps, post_process_interval=100):
         start_time = time.time()

examples/cfd/lid_driven_cavity_2d.py

@@ -1,8 +1,7 @@
 import xlb
 from xlb.compute_backend import ComputeBackend
 from xlb.precision_policy import PrecisionPolicy
-from xlb.helper import create_nse_fields, initialize_eq, check_bc_overlaps
-from xlb.operator.boundary_masker import IndicesBoundaryMasker
+from xlb.grid import grid_factory
 from xlb.operator.stepper import IncompressibleNavierStokesStepper
 from xlb.operator.boundary_condition import HalfwayBounceBackBC, EquilibriumBC
 from xlb.operator.macroscopic import Macroscopic
@@ -26,19 +25,21 @@ def __init__(self, omega, prescribed_vel, grid_shape, velocity_set, backend, pre
         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.bc_mask = create_nse_fields(grid_shape)
-        self.stepper = None
+        self.omega = omega
         self.boundary_conditions = []
         self.prescribed_vel = prescribed_vel
 
-        # Setup the simulation BC, its initial conditions, and the stepper
-        self._setup(omega)
+        # Create grid using factory
+        self.grid = grid_factory(grid_shape, compute_backend=backend)
 
-    def _setup(self, omega):
+        # Setup the simulation BC and stepper
+        self._setup()
+
+    def _setup(self):
         self.setup_boundary_conditions()
-        self.setup_boundary_masker()
-        self.initialize_fields()
-        self.setup_stepper(omega)
+        self.setup_stepper()
+        # Initialize fields using the stepper
+        self.f_0, self.f_1, self.bc_mask, self.missing_mask = self.stepper.prepare_fields()
 
     def define_boundary_indices(self):
         box = self.grid.bounding_box_indices()
@@ -54,21 +55,13 @@ def setup_boundary_conditions(self):
         bc_walls = HalfwayBounceBackBC(indices=walls)
         self.boundary_conditions = [bc_walls, bc_top]
 
-    def setup_boundary_masker(self):
-        # check boundary condition list for duplicate indices before creating bc mask
-        check_bc_overlaps(self.boundary_conditions, self.velocity_set.d, self.backend)
-        indices_boundary_masker = IndicesBoundaryMasker(
-            velocity_set=self.velocity_set,
-            precision_policy=self.precision_policy,
-            compute_backend=self.backend,
+    def setup_stepper(self):
+        self.stepper = IncompressibleNavierStokesStepper(
+            omega=self.omega,
+            grid=self.grid,
+            boundary_conditions=self.boundary_conditions,
+            collision_type="BGK",
         )
-        self.bc_mask, self.missing_mask = indices_boundary_masker(self.boundary_conditions, self.bc_mask, self.missing_mask)
-
-    def initialize_fields(self):
-        self.f_0 = initialize_eq(self.f_0, self.grid, self.velocity_set, self.precision_policy, self.backend)
-
-    def setup_stepper(self, omega):
-        self.stepper = IncompressibleNavierStokesStepper(omega, boundary_conditions=self.boundary_conditions)
 
     def run(self, num_steps, post_process_interval=100):
         for i in range(num_steps):

examples/cfd/lid_driven_cavity_2d_distributed.py

@@ -10,15 +10,21 @@ class LidDrivenCavity2D_distributed(LidDrivenCavity2D):
     def __init__(self, omega, prescribed_vel, grid_shape, velocity_set, backend, precision_policy):
         super().__init__(omega, prescribed_vel, grid_shape, velocity_set, backend, precision_policy)
 
-    def setup_stepper(self, omega):
-        stepper = IncompressibleNavierStokesStepper(omega, boundary_conditions=self.boundary_conditions)
-        distributed_stepper = distribute(
+    def setup_stepper(self):
+        # Create the base stepper
+        stepper = IncompressibleNavierStokesStepper(
+            omega=self.omega,
+            grid=self.grid,
+            boundary_conditions=self.boundary_conditions,
+            collision_type="BGK",
+        )
+
+        # Distribute the stepper
+        self.stepper = distribute(
             stepper,
             self.grid,
             self.velocity_set,
         )
-        self.stepper = distributed_stepper
-        return
 
 
 if __name__ == "__main__":

examples/cfd/turbulent_channel_3d.py

@@ -2,12 +2,12 @@
 import time
 from xlb.compute_backend import ComputeBackend
 from xlb.precision_policy import PrecisionPolicy
-from xlb.helper import create_nse_fields, initialize_eq
+from xlb.grid import grid_factory
 from xlb.operator.stepper import IncompressibleNavierStokesStepper
 from xlb.operator.boundary_condition import RegularizedBC
 from xlb.operator.macroscopic import Macroscopic
-from xlb.operator.boundary_masker import IndicesBoundaryMasker
 from xlb.utils import save_fields_vtk, save_image
+from xlb.helper import initialize_eq
 import warp as wp
 import numpy as np
 import jax.numpy as jnp
@@ -48,18 +48,16 @@ def __init__(self, channel_half_width, Re_tau, u_tau, grid_shape, velocity_set,
         self.u_tau = u_tau
         self.visc = u_tau * channel_half_width / Re_tau
         self.omega = 1.0 / (3.0 * self.visc + 0.5)
-        # DeltaPlus = Re_tau / channel_half_width
-        # DeltaPlus = u_tau / nu * Delta where u_tau / nu = Re_tau / channel_half_width
-
         self.grid_shape = grid_shape
         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.bc_mask = create_nse_fields(grid_shape)
-        self.stepper = None
         self.boundary_conditions = []
 
-        # Setup the simulation BC, its initial conditions, and the stepper
+        # Create grid using factory
+        self.grid = grid_factory(grid_shape, compute_backend=backend)
+
+        # Setup the simulation BC and stepper
         self._setup()
 
     def get_force(self):
@@ -71,9 +69,10 @@ def get_force(self):
 
     def _setup(self):
         self.setup_boundary_conditions()
-        self.setup_boundary_masker()
-        self.initialize_fields()
         self.setup_stepper()
+        # Initialize fields using the stepper
+        self.f_0, self.f_1, self.bc_mask, self.missing_mask = self.stepper.prepare_fields()
+        self.initialize_fields()
 
     def define_boundary_indices(self):
         # top and bottom sides of the channel are no-slip and the other directions are periodic
@@ -83,19 +82,12 @@ def define_boundary_indices(self):
 
     def setup_boundary_conditions(self):
         walls = self.define_boundary_indices()
-        bc_walls = RegularizedBC("velocity", (0.0, 0.0, 0.0), indices=walls)
+        bc_walls = RegularizedBC("velocity", prescribed_value=(0.0, 0.0, 0.0), indices=walls)
         self.boundary_conditions = [bc_walls]
 
-    def setup_boundary_masker(self):
-        indices_boundary_masker = IndicesBoundaryMasker(
-            velocity_set=self.velocity_set,
-            precision_policy=self.precision_policy,
-            compute_backend=self.backend,
-        )
-        self.bc_mask, self.missing_mask = indices_boundary_masker(self.boundary_conditions, self.bc_mask, self.missing_mask)
-
     def initialize_fields(self):
-        shape = (self.velocity_set.d,) + (self.grid_shape)
+        # Initialize with random velocity field
+        shape = (self.velocity_set.d,) + self.grid_shape
         np.random.seed(0)
         u_init = np.random.random(shape)
         if self.backend == ComputeBackend.JAX:
@@ -105,9 +97,12 @@ def initialize_fields(self):
         self.f_0 = initialize_eq(self.f_0, self.grid, self.velocity_set, self.precision_policy, self.backend, u=u_init)
 
     def setup_stepper(self):
-        force = self.get_force()
         self.stepper = IncompressibleNavierStokesStepper(
-            self.omega, boundary_conditions=self.boundary_conditions, collision_type="KBC", forcing_scheme="exact_difference", force_vector=force
+            omega=self.omega,
+            grid=self.grid,
+            boundary_conditions=self.boundary_conditions,
+            collision_type="KBC",
+            force_vector=self.get_force(),
         )
 
     def run(self, num_steps, print_interval, post_process_interval=100):
@@ -142,14 +137,12 @@ def post_process(self, i):
         u_magnitude = (u[0] ** 2 + u[1] ** 2 + u[2] ** 2) ** 0.5
         fields = {"rho": rho[0], "u_x": u[0], "u_y": u[1], "u_z": u[2], "u_magnitude": u_magnitude}
         save_fields_vtk(fields, timestep=i)
-        save_image(fields["u_magnitude"][:, grid_size_y // 2, :], timestep=i)
+        save_image(fields["u_magnitude"][:, self.grid_shape[1] // 2, :], timestep=i)
 
         # Save monitor plot
         self.plot_uplus(u, i)
-        return
 
     def plot_uplus(self, u, timestep):
-        # Compute moving average of drag coefficient, 100, 1000, 10000
         # mean streamwise velocity in wall units u^+(z)
         # Wall distance in wall units to be used inside output_data
         zz = np.arange(self.grid_shape[-1])
@@ -165,6 +158,7 @@ def plot_uplus(self, u, timestep):
         ax.set_ylim([0, 20])
         fname = "uplus_" + str(timestep // 10000).zfill(5) + ".png"
         plt.savefig(fname, format="png")
+        plt.close()
 
 
 if __name__ == "__main__":