addressing PR reviews

examples/cfd/flow_past_sphere_3d.py

@@ -49,9 +49,9 @@ def _setup(self, omega):
 
     def define_boundary_indices(self):
         box = self.grid.bounding_box_indices()
-        box_noedge = self.grid.bounding_box_indices(remove_edges=True)
-        inlet = box_noedge["left"]
-        outlet = box_noedge["right"]
+        box_no_edge = self.grid.bounding_box_indices(remove_edges=True)
+        inlet = box_no_edge["left"]
+        outlet = box_no_edge["right"]
         walls = [box["bottom"][i] + box["top"][i] + box["front"][i] + box["back"][i] for i in range(self.velocity_set.d)]
         walls = np.unique(np.array(walls), axis=-1).tolist()
 
@@ -101,8 +101,6 @@ def run(self, num_steps, post_process_interval=100):
             self.f_0, self.f_1 = self.stepper(self.f_0, self.f_1, self.bc_mask, self.missing_mask, i)
             self.f_0, self.f_1 = self.f_1, self.f_0
 
-            if i == 0:
-                self.check_boundary_mask()
             if i % post_process_interval == 0 or i == num_steps - 1:
                 self.post_process(i)
                 end_time = time.time()
@@ -132,23 +130,6 @@ def post_process(self, i):
 
         # save_fields_vtk(fields, timestep=i)
         save_image(fields["u_magnitude"][:, self.grid_shape[1] // 2, :], timestep=i)
-        return
-
-    def check_boundary_mask(self):
-        # Write the results. We'll use JAX backend for the post-processing
-        if not isinstance(self.f_0, jnp.ndarray):
-            bmask = wp.to_jax(self.bc_mask)[0]
-        else:
-            bmask = self.bc_mask[0]
-
-        # save_fields_vtk(fields, timestep=i)
-        save_image(bmask[0, :, :], prefix="00_left")
-        save_image(bmask[self.grid_shape[0] - 1, :, :], prefix="00_right")
-        save_image(bmask[:, :, self.grid_shape[2] - 1], prefix="00_top")
-        save_image(bmask[:, :, 0], prefix="00_bottom")
-        save_image(bmask[:, 0, :], prefix="00_front")
-        save_image(bmask[:, self.grid_shape[1] - 1, :], prefix="00_back")
-        save_image(bmask[:, self.grid_shape[1] // 2, :], prefix="00_middle")
 
 
 if __name__ == "__main__":

examples/cfd/lid_driven_cavity_2d.py

@@ -41,8 +41,8 @@ def _setup(self, omega):
 
     def define_boundary_indices(self):
         box = self.grid.bounding_box_indices()
-        box_noedge = self.grid.bounding_box_indices(remove_edges=True)
-        lid = box_noedge["top"]
+        box_no_edge = self.grid.bounding_box_indices(remove_edges=True)
+        lid = box_no_edge["top"]
         walls = [box["bottom"][i] + box["left"][i] + box["right"][i] for i in range(self.velocity_set.d)]
         walls = np.unique(np.array(walls), axis=-1).tolist()
         return lid, walls

examples/cfd/windtunnel_3d.py

@@ -68,9 +68,9 @@ def voxelize_stl(self, stl_filename, length_lbm_unit):
 
     def define_boundary_indices(self):
         box = self.grid.bounding_box_indices()
-        box_noedge = self.grid.bounding_box_indices(remove_edges=True)
-        inlet = box_noedge["left"]
-        outlet = box_noedge["right"]
+        box_no_edge = self.grid.bounding_box_indices(remove_edges=True)
+        inlet = box_no_edge["left"]
+        outlet = box_no_edge["right"]
         walls = [box["bottom"][i] + box["top"][i] + box["front"][i] + box["back"][i] for i in range(self.velocity_set.d)]
         walls = np.unique(np.array(walls), axis=-1).tolist()
 

examples/performance/mlups_3d.py

@@ -49,8 +49,8 @@ def create_grid_and_fields(cube_edge):
 
 def define_boundary_indices(grid):
     box = grid.bounding_box_indices()
-    box_noedge = grid.bounding_box_indices(remove_edges=True)
-    lid = box_noedge["top"]
+    box_no_edge = grid.bounding_box_indices(remove_edges=True)
+    lid = box_no_edge["top"]
     walls = [box["bottom"][i] + box["left"][i] + box["right"][i] + box["front"][i] + box["back"][i] for i in range(len(grid.shape))]
     return lid, walls
 

xlb/distribute/__init__.py

@@ -1 +1 @@
-from .distribute import distribute as distribute
+from .distribute import distribute

xlb/experimental/ooc/__init__.py

@@ -1,2 +1,2 @@
-from xlb.experimental.ooc.out_of_core import OOCmap as OOCmap
-from xlb.experimental.ooc.ooc_array import OOCArray as OOCArray
+from xlb.experimental.ooc.out_of_core import OOCmap
+from xlb.experimental.ooc.ooc_array import OOCArray

xlb/helper/__init__.py

@@ -1,3 +1,3 @@
-from xlb.helper.nse_solver import create_nse_fields as create_nse_fields
-from xlb.helper.initializers import initialize_eq as initialize_eq
-from xlb.helper.check_boundary_overlaps import check_bc_overlaps as check_bc_overlaps
+from xlb.helper.nse_solver import create_nse_fields
+from xlb.helper.initializers import initialize_eq
+from xlb.helper.check_boundary_overlaps import check_bc_overlaps

xlb/helper/check_boundary_overlaps.py

@@ -12,6 +12,7 @@ def check_bc_overlaps(bclist, dim, backend):
         if index_arr.shape[-1] != len(bc.indices[0]):
             if backend == ComputeBackend.WARP:
                 raise ValueError(f"Boundary condition {bc.__class__.__name__} has duplicate indices!")
+            print(f"WARNING: there are duplicate indices in {bc.__class__.__name__} and hence the order in bc list matters!")
         for d in range(dim):
             index_list[d] += bc.indices[d]
 
@@ -20,3 +21,4 @@ def check_bc_overlaps(bclist, dim, backend):
     if index_arr.shape[-1] != len(index_list[0]):
         if backend == ComputeBackend.WARP:
             raise ValueError("Boundary condition list containes duplicate indices!")
+        print("WARNING: there are duplicate indices in the boundary condition list and hence the order in this list matters!")

xlb/operator/__init__.py

@@ -1,2 +1,2 @@
-from xlb.operator.operator import Operator as Operator
-from xlb.operator.parallel_operator import ParallelOperator as ParallelOperator
+from xlb.operator.operator import Operator
+from xlb.operator.parallel_operator import ParallelOperator

xlb/operator/boundary_condition/__init__.py

@@ -1,12 +1,10 @@
-from xlb.operator.boundary_condition.boundary_condition import BoundaryCondition as BoundaryCondition
-from xlb.operator.boundary_condition.boundary_condition_registry import (
-    BoundaryConditionRegistry as BoundaryConditionRegistry,
-)
-from xlb.operator.boundary_condition.bc_equilibrium import EquilibriumBC as EquilibriumBC
-from xlb.operator.boundary_condition.bc_do_nothing import DoNothingBC as DoNothingBC
-from xlb.operator.boundary_condition.bc_halfway_bounce_back import HalfwayBounceBackBC as HalfwayBounceBackBC
-from xlb.operator.boundary_condition.bc_fullway_bounce_back import FullwayBounceBackBC as FullwayBounceBackBC
-from xlb.operator.boundary_condition.bc_zouhe import ZouHeBC as ZouHeBC
-from xlb.operator.boundary_condition.bc_regularized import RegularizedBC as RegularizedBC
-from xlb.operator.boundary_condition.bc_extrapolation_outflow import ExtrapolationOutflowBC as ExtrapolationOutflowBC
-from xlb.operator.boundary_condition.bc_grads_approximation import GradsApproximationBC as GradsApproximationBC
+from xlb.operator.boundary_condition.boundary_condition import BoundaryCondition
+from xlb.operator.boundary_condition.boundary_condition_registry import BoundaryConditionRegistry
+from xlb.operator.boundary_condition.bc_equilibrium import EquilibriumBC
+from xlb.operator.boundary_condition.bc_do_nothing import DoNothingBC
+from xlb.operator.boundary_condition.bc_halfway_bounce_back import HalfwayBounceBackBC
+from xlb.operator.boundary_condition.bc_fullway_bounce_back import FullwayBounceBackBC
+from xlb.operator.boundary_condition.bc_zouhe import ZouHeBC
+from xlb.operator.boundary_condition.bc_regularized import RegularizedBC
+from xlb.operator.boundary_condition.bc_extrapolation_outflow import ExtrapolationOutflowBC
+from xlb.operator.boundary_condition.bc_grads_approximation import GradsApproximationBC

xlb/operator/boundary_masker/__init__.py

@@ -1,9 +1,3 @@
-from xlb.operator.boundary_masker.indices_boundary_masker import (
-    IndicesBoundaryMasker as IndicesBoundaryMasker,
-)
-from xlb.operator.boundary_masker.mesh_boundary_masker import (
-    MeshBoundaryMasker as MeshBoundaryMasker,
-)
-from xlb.operator.boundary_masker.mesh_distance_boundary_masker import (
-    MeshDistanceBoundaryMasker as MeshDistanceBoundaryMasker,
-)
+from xlb.operator.boundary_masker.indices_boundary_masker import IndicesBoundaryMasker
+from xlb.operator.boundary_masker.mesh_boundary_masker import MeshBoundaryMasker
+from xlb.operator.boundary_masker.mesh_distance_boundary_masker import MeshDistanceBoundaryMasker

xlb/operator/collision/__init__.py

@@ -1,4 +1,4 @@
-from xlb.operator.collision.collision import Collision as Collision
-from xlb.operator.collision.bgk import BGK as BGK
-from xlb.operator.collision.kbc import KBC as KBC
-from xlb.operator.collision.forced_collision import ForcedCollision as ForcedCollision
+from xlb.operator.collision.collision import Collision
+from xlb.operator.collision.bgk import BGK
+from xlb.operator.collision.kbc import KBC
+from xlb.operator.collision.forced_collision import ForcedCollision

xlb/operator/equilibrium/__init__.py

@@ -1,4 +1 @@
-from xlb.operator.equilibrium.quadratic_equilibrium import (
-    Equilibrium as Equilibrium,
-    QuadraticEquilibrium as QuadraticEquilibrium,
-)
+from xlb.operator.equilibrium.quadratic_equilibrium import Equilibrium, QuadraticEquilibrium

xlb/operator/force/__init__.py

@@ -1,2 +1,2 @@
-from xlb.operator.force.momentum_transfer import MomentumTransfer as MomentumTransfer
-from xlb.operator.force.exact_difference_force import ExactDifference as ExactDifference
+from xlb.operator.force.momentum_transfer import MomentumTransfer
+from xlb.operator.force.exact_difference_force import ExactDifference

xlb/operator/precision_caster/__init__.py

@@ -1 +1 @@
-from xlb.operator.precision_caster.precision_caster import PrecisionCaster as PrecisionCaster
+from xlb.operator.precision_caster.precision_caster import PrecisionCaster

xlb/operator/stepper/__init__.py

@@ -1,2 +1,2 @@
-from xlb.operator.stepper.stepper import Stepper as Stepper
-from xlb.operator.stepper.nse_stepper import IncompressibleNavierStokesStepper as IncompressibleNavierStokesStepper
+from xlb.operator.stepper.stepper import Stepper
+from xlb.operator.stepper.nse_stepper import IncompressibleNavierStokesStepper

xlb/operator/stream/__init__.py

@@ -1 +1 @@
-from xlb.operator.stream.stream import Stream as Stream
+from xlb.operator.stream.stream import Stream

xlb/utils/__init__.py

@@ -1,9 +1,9 @@
 from .utils import (
-    downsample_field as downsample_field,
-    save_image as save_image,
-    save_fields_vtk as save_fields_vtk,
-    save_BCs_vtk as save_BCs_vtk,
-    rotate_geometry as rotate_geometry,
-    voxelize_stl as voxelize_stl,
-    axangle2mat as axangle2mat,
+    downsample_field,
+    save_image,
+    save_fields_vtk,
+    save_BCs_vtk,
+    rotate_geometry,
+    voxelize_stl,
+    axangle2mat,
 )

xlb/velocity_set/__init__.py

@@ -1,4 +1,4 @@
-from xlb.velocity_set.velocity_set import VelocitySet as VelocitySet
-from xlb.velocity_set.d2q9 import D2Q9 as D2Q9
-from xlb.velocity_set.d3q19 import D3Q19 as D3Q19
-from xlb.velocity_set.d3q27 import D3Q27 as D3Q27
+from xlb.velocity_set.velocity_set import VelocitySet
+from xlb.velocity_set.d2q9 import D2Q9
+from xlb.velocity_set.d3q19 import D3Q19
+from xlb.velocity_set.d3q27 import D3Q27