Merge pull request #105 from SophT-Team/54_eulerian_grid_field_io

(#54) Eulerian grid field IO
SophT-Team · Jan 18, 2023 · e7d24c7 · e7d24c7
2 parents a42e862 + 3ba4327
commit e7d24c7
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Showing 13 changed files with 191 additions and 158 deletions.
diff --git a/examples/2d_examples/FlowPastRodCase/flow_past_rod.py b/examples/2d_examples/FlowPastRodCase/flow_past_rod.py
@@ -131,20 +131,13 @@ class FlowPastRodSimulator(
     )
     # ==================FLOW-ROD COMMUNICATOR SETUP END======
     if save_flow_data:
-        # setup IO
-        # TODO internalise this in flow simulator as dump_fields
-        io_origin = np.array(
-            [
-                flow_sim.position_field[y_axis_idx].min(),
-                flow_sim.position_field[x_axis_idx].min(),
-            ]
-        )
-        io_dx = flow_sim.dx * np.ones(grid_dim)
-        io_grid_size = np.array(grid_size)
-        io = spu.IO(dim=grid_dim, real_dtype=real_t)
-        io.define_eulerian_grid(origin=io_origin, dx=io_dx, grid_size=io_grid_size)
-        io.add_as_eulerian_fields_for_io(
-            vorticity=flow_sim.vorticity_field, velocity=flow_sim.velocity_field
+        # setup flow IO
+        io = spu.EulerianFieldIO(
+            position_field=flow_sim.position_field,
+            eulerian_fields_dict={
+                "vorticity": flow_sim.vorticity_field,
+                "velocity": flow_sim.velocity_field,
+            },
         )
         # Initialize rod IO
         rod_io = spu.CosseratRodIO(

diff --git a/examples/2d_examples/VortexInducedFlagFlappingCase/turek_and_hron_benchmark.py b/examples/2d_examples/VortexInducedFlagFlappingCase/turek_and_hron_benchmark.py
@@ -238,20 +238,13 @@ class FlowPastRodSimulator(ea.BaseSystemCollection, ea.Constraints, ea.Forcing):
     # ==================FLOW-ROD COMMUNICATOR SETUP END======
     # =================FLOW H5 DUMPING====================
     if save_flow_data:
-        # setup IO
-        # TODO internalise this in flow simulator as dump_fields
-        io_origin = np.array(
-            [
-                flow_sim.position_field[y_axis_idx].min(),
-                flow_sim.position_field[x_axis_idx].min(),
-            ]
-        )
-        io_dx = flow_sim.dx * np.ones(grid_dim)
-        io_grid_size = np.array(grid_size)
-        io = spu.IO(dim=grid_dim, real_dtype=real_t)
-        io.define_eulerian_grid(origin=io_origin, dx=io_dx, grid_size=io_grid_size)
-        io.add_as_eulerian_fields_for_io(
-            vorticity=flow_sim.vorticity_field, velocity=flow_sim.velocity_field
+        # setup flow IO
+        io = spu.EulerianFieldIO(
+            position_field=flow_sim.position_field,
+            eulerian_fields_dict={
+                "vorticity": flow_sim.vorticity_field,
+                "velocity": flow_sim.velocity_field,
+            },
         )
         # Initialize rod IO
         rod_io = spu.CosseratRodIO(

diff --git a/examples/3d_examples/ElasticNetCase/immersed_elastic_net.py b/examples/3d_examples/ElasticNetCase/immersed_elastic_net.py
@@ -21,7 +21,6 @@ def immersed_elastic_net_case(
     grid_dim = 3
     real_t = spu.get_real_t(precision)
     x_axis_idx = spu.VectorField.x_axis_idx()
-    y_axis_idx = spu.VectorField.y_axis_idx()
     z_axis_idx = spu.VectorField.z_axis_idx()
     z_range, y_range, x_range = domain_range
     grid_size_y = round(y_range / x_range * grid_size_x)
@@ -72,21 +71,13 @@ def immersed_elastic_net_case(
         )
     # ==================FLOW-ROD COMMUNICATOR SETUP END======
     if save_flow_data:
-        # setup IO
-        # TODO internalise this in flow simulator as dump_fields
-        io_origin = np.array(
-            [
-                flow_sim.position_field[z_axis_idx].min(),
-                flow_sim.position_field[y_axis_idx].min(),
-                flow_sim.position_field[x_axis_idx].min(),
-            ]
-        )
-        io_dx = flow_sim.dx * np.ones(grid_dim)
-        io_grid_size = np.array(grid_size)
-        io = spu.IO(dim=grid_dim, real_dtype=real_t)
-        io.define_eulerian_grid(origin=io_origin, dx=io_dx, grid_size=io_grid_size)
-        io.add_as_eulerian_fields_for_io(
-            vorticity=flow_sim.vorticity_field, velocity=flow_sim.velocity_field
+        # setup flow IO
+        io = spu.EulerianFieldIO(
+            position_field=flow_sim.position_field,
+            eulerian_fields_dict={
+                "vorticity": flow_sim.vorticity_field,
+                "velocity": flow_sim.velocity_field,
+            },
         )
         # Initialize carpet IO
         elastic_net_io = spu.IO(dim=grid_dim, real_dtype=real_t)

diff --git a/examples/3d_examples/FlowPastRodCase/flow_past_rod_case.py b/examples/3d_examples/FlowPastRodCase/flow_past_rod_case.py
@@ -28,7 +28,6 @@ def flow_past_rod_case(
     grid_size_z, grid_size_y, grid_size_x = grid_size
     real_t = spu.get_real_t(precision)
     x_axis_idx = spu.VectorField.x_axis_idx()
-    y_axis_idx = spu.VectorField.y_axis_idx()
     z_axis_idx = spu.VectorField.z_axis_idx()
     rho_f = 1.0
     U_free_stream = 1.0
@@ -139,21 +138,13 @@ class FlowPastRodSimulator(
     )
 
     if save_data:
-        # setup IO
-        # TODO internalise this in flow simulator as dump_fields
-        io_origin = np.array(
-            [
-                flow_sim.position_field[z_axis_idx].min(),
-                flow_sim.position_field[y_axis_idx].min(),
-                flow_sim.position_field[x_axis_idx].min(),
-            ]
-        )
-        io_dx = flow_sim.dx * np.ones(grid_dim)
-        io_grid_size = np.array(grid_size)
-        io = spu.IO(dim=grid_dim, real_dtype=real_t)
-        io.define_eulerian_grid(origin=io_origin, dx=io_dx, grid_size=io_grid_size)
-        io.add_as_eulerian_fields_for_io(
-            vorticity=flow_sim.vorticity_field, velocity=flow_sim.velocity_field
+        # setup flow IO
+        io = spu.EulerianFieldIO(
+            position_field=flow_sim.position_field,
+            eulerian_fields_dict={
+                "vorticity": flow_sim.vorticity_field,
+                "velocity": flow_sim.velocity_field,
+            },
         )
         # Initialize sphere IO
         rod_io = spu.CosseratRodIO(

diff --git a/examples/3d_examples/FlowPastSphereCase/flow_past_sphere_case.py b/examples/3d_examples/FlowPastSphereCase/flow_past_sphere_case.py
@@ -22,7 +22,6 @@ def flow_past_sphere_case(
     grid_size_z, grid_size_y, grid_size_x = grid_size
     real_t = spu.get_real_t(precision)
     x_axis_idx: int = spu.VectorField.x_axis_idx()
-    y_axis_idx = spu.VectorField.y_axis_idx()
     z_axis_idx = spu.VectorField.z_axis_idx()
     x_range = 1.0
     far_field_velocity = 1.0
@@ -79,21 +78,13 @@ def flow_past_sphere_case(
     # ==================FLOW-BODY COMMUNICATOR SETUP END======
 
     if save_flow_data:
-        # setup IO
-        # TODO internalise this in flow simulator as dump_fields
-        io_origin = np.array(
-            [
-                flow_sim.position_field[z_axis_idx].min(),
-                flow_sim.position_field[y_axis_idx].min(),
-                flow_sim.position_field[x_axis_idx].min(),
-            ]
-        )
-        io_dx = flow_sim.dx * np.ones(grid_dim)
-        io_grid_size = np.array(grid_size)
-        io = spu.IO(dim=grid_dim, real_dtype=real_t)
-        io.define_eulerian_grid(origin=io_origin, dx=io_dx, grid_size=io_grid_size)
-        io.add_as_eulerian_fields_for_io(
-            vorticity=flow_sim.vorticity_field, velocity=flow_sim.velocity_field
+        # setup flow IO
+        io = spu.EulerianFieldIO(
+            position_field=flow_sim.position_field,
+            eulerian_fields_dict={
+                "vorticity": flow_sim.vorticity_field,
+                "velocity": flow_sim.velocity_field,
+            },
         )
         # Initialize sphere IO
         sphere_io = spu.IO(dim=grid_dim, real_dtype=real_t)

diff --git a/examples/3d_examples/FlowThroughPipeCase/flow_through_circular_pipe_case.py b/examples/3d_examples/FlowThroughPipeCase/flow_through_circular_pipe_case.py
@@ -26,7 +26,6 @@ def flow_through_circular_pipe_case(
     real_t = spu.get_real_t(precision)
     x_axis_idx = spu.VectorField.x_axis_idx()
     y_axis_idx = spu.VectorField.y_axis_idx()
-    z_axis_idx = spu.VectorField.z_axis_idx()
     x_range = 1.0
     nu = 1e-2
     flow_sim = sps.UnboundedNavierStokesFlowSimulator3D(
@@ -72,21 +71,13 @@ def flow_through_circular_pipe_case(
     # ==================FLOW-BODY COMMUNICATOR SETUP END======
 
     if save_data:
-        # setup IO
-        # TODO internalise this in flow simulator as dump_fields
-        io_origin = np.array(
-            [
-                flow_sim.position_field[z_axis_idx].min(),
-                flow_sim.position_field[y_axis_idx].min(),
-                flow_sim.position_field[x_axis_idx].min(),
-            ]
-        )
-        io_dx = flow_sim.dx * np.ones(grid_dim)
-        io_grid_size = np.array(grid_size)
-        io = spu.IO(dim=grid_dim, real_dtype=real_t)
-        io.define_eulerian_grid(origin=io_origin, dx=io_dx, grid_size=io_grid_size)
-        io.add_as_eulerian_fields_for_io(
-            vorticity=flow_sim.vorticity_field, velocity=flow_sim.velocity_field
+        # setup flow IO
+        io = spu.EulerianFieldIO(
+            position_field=flow_sim.position_field,
+            eulerian_fields_dict={
+                "vorticity": flow_sim.vorticity_field,
+                "velocity": flow_sim.velocity_field,
+            },
         )
 
     t_end = 1.0

diff --git a/examples/3d_examples/HillSphericalVortexCase/hill_sphere_vortex_case.py b/examples/3d_examples/HillSphericalVortexCase/hill_sphere_vortex_case.py
@@ -15,7 +15,6 @@ def hill_sphere_vortex_case(
     the velocity recovery and vortex stretching steps, for the solver,
     by comparing against analytical expressions.
     """
-    grid_dim = 3
     grid_size_z, grid_size_y, grid_size_x = grid_size
     real_t = spu.get_real_t(precision)
     x_axis_idx = spu.VectorField.x_axis_idx()
@@ -116,23 +115,14 @@ def hill_sphere_vortex_case(
     fig2.savefig("midplane_radial_velocity.png")
 
     if save_data:
-        # setup IO
-        # TODO internalise this in flow simulator as dump_fields
-        io_origin = np.array(
-            [
-                flow_sim.position_field[z_axis_idx].min(),
-                flow_sim.position_field[y_axis_idx].min(),
-                flow_sim.position_field[x_axis_idx].min(),
-            ]
-        )
-        io_dx = flow_sim.dx * np.ones(grid_dim)
-        io_grid_size = np.array(grid_size)
-        io = spu.IO(dim=grid_dim, real_dtype=real_t)
-        io.define_eulerian_grid(origin=io_origin, dx=io_dx, grid_size=io_grid_size)
-        io.add_as_eulerian_fields_for_io(
-            vorticity=flow_sim.vorticity_field,
-            stream_func=flow_sim.stream_func_field,
-            velocity=flow_sim.velocity_field,
+        # setup flow IO
+        io = spu.EulerianFieldIO(
+            position_field=flow_sim.position_field,
+            eulerian_fields_dict={
+                "vorticity": flow_sim.vorticity_field,
+                "stream_func": flow_sim.stream_func_field,
+                "velocity": flow_sim.velocity_field,
+            },
         )
         io.save(h5_file_name="sopht.h5")
 

diff --git a/examples/3d_examples/MagneticCiliaCarpetCase/immersed_magnetic_cilia_carpet.py b/examples/3d_examples/MagneticCiliaCarpetCase/immersed_magnetic_cilia_carpet.py
@@ -19,7 +19,6 @@ def immersed_magnetic_cilia_carpet_case(
     grid_dim = 3
     real_t = spu.get_real_t(precision)
     x_axis_idx = spu.VectorField.x_axis_idx()
-    y_axis_idx = spu.VectorField.y_axis_idx()
     z_axis_idx = spu.VectorField.z_axis_idx()
     z_range, y_range, x_range = domain_range
     grid_size_y = round(y_range / x_range * grid_size_x)
@@ -65,21 +64,13 @@ def immersed_magnetic_cilia_carpet_case(
         )
     # ==================FLOW-ROD COMMUNICATOR SETUP END======
     if save_data:
-        # setup IO
-        # TODO internalise this in flow simulator as dump_fields
-        io_origin = np.array(
-            [
-                flow_sim.position_field[z_axis_idx].min(),
-                flow_sim.position_field[y_axis_idx].min(),
-                flow_sim.position_field[x_axis_idx].min(),
-            ]
-        )
-        io_dx = flow_sim.dx * np.ones(grid_dim)
-        io_grid_size = np.array(grid_size)
-        io = spu.IO(dim=grid_dim, real_dtype=real_t)
-        io.define_eulerian_grid(origin=io_origin, dx=io_dx, grid_size=io_grid_size)
-        io.add_as_eulerian_fields_for_io(
-            vorticity=flow_sim.vorticity_field, velocity=flow_sim.velocity_field
+        # setup flow IO
+        io = spu.EulerianFieldIO(
+            position_field=flow_sim.position_field,
+            eulerian_fields_dict={
+                "vorticity": flow_sim.vorticity_field,
+                "velocity": flow_sim.velocity_field,
+            },
         )
         # Initialize carpet IO
         carpet_io = spu.IO(dim=grid_dim, real_dtype=real_t)

diff --git a/examples/3d_examples/OctopusArmCase3D/run_tapered_arm_and_sphere_with_flow.py b/examples/3d_examples/OctopusArmCase3D/run_tapered_arm_and_sphere_with_flow.py
@@ -183,22 +183,13 @@ def tapered_arm_and_cylinder_flow_coupling(
     # ==================FLOW-ROD COMMUNICATOR SETUP END======
 
     if save_data:
-        # setup IO
-        # TODO internalise this in flow simulator as dump_fields
-        io_origin = np.array(
-            [
-                flow_sim.position_field[z_axis_idx].min(),
-                flow_sim.position_field[y_axis_idx].min(),
-                flow_sim.position_field[x_axis_idx].min(),
-            ]
-        )
-        io_dx = flow_sim.dx * np.ones(grid_dim)
-        io_grid_size = np.array(grid_size)
-        # Initialize flow eulerian grid IO
-        io = spu.IO(dim=grid_dim, real_dtype=real_t)
-        io.define_eulerian_grid(origin=io_origin, dx=io_dx, grid_size=io_grid_size)
-        io.add_as_eulerian_fields_for_io(
-            vorticity=flow_sim.vorticity_field, velocity=flow_sim.velocity_field
+        # setup flow IO
+        io = spu.EulerianFieldIO(
+            position_field=flow_sim.position_field,
+            eulerian_fields_dict={
+                "vorticity": flow_sim.vorticity_field,
+                "velocity": flow_sim.velocity_field,
+            },
         )
         # Initialize rod io
         rod_io = spu.CosseratRodIO(

diff --git a/examples/3d_examples/PointSourceAdvectAndDiffuseCase/point_source_advection_diffusion.py b/examples/3d_examples/PointSourceAdvectAndDiffuseCase/point_source_advection_diffusion.py
@@ -15,7 +15,6 @@ def point_source_advection_diffusion_case(
     constant velocity in 3D, while it diffuses in time.
     """
     grid_dim = 3
-    grid_size_z, grid_size_y, grid_size_x = grid_size
     real_t = spu.get_real_t(precision)
     x_axis_idx = spu.VectorField.x_axis_idx()
     y_axis_idx = spu.VectorField.y_axis_idx()
@@ -62,20 +61,13 @@ def point_source_advection_diffusion_case(
     flow_sim.velocity_field[...] = velocity_free_stream
 
     if save_data:
-        # setup IO
-        # TODO internalise this in flow simulator as dump_fields
-        io_origin = np.array(
-            [
-                flow_sim.position_field[z_axis_idx].min(),
-                flow_sim.position_field[y_axis_idx].min(),
-                flow_sim.position_field[x_axis_idx].min(),
-            ]
+        # setup flow IO
+        io = spu.EulerianFieldIO(
+            position_field=flow_sim.position_field,
+            eulerian_fields_dict={
+                "vorticity": vorticity_field,
+            },
         )
-        io_dx = flow_sim.dx * np.ones(grid_dim)
-        io_grid_size = np.array([grid_size_z, grid_size_y, grid_size_x])
-        io = spu.IO(dim=grid_dim, real_dtype=real_t)
-        io.define_eulerian_grid(origin=io_origin, dx=io_dx, grid_size=io_grid_size)
-        io.add_as_eulerian_fields_for_io(vorticity=vorticity_field)
 
     foto_timer = 0.0
     foto_timer_limit = (t_end - t_start) / 20

diff --git a/sopht/utils/__init__.py b/sopht/utils/__init__.py
@@ -2,7 +2,7 @@
 from .plot_field import create_figure_and_axes, save_and_clear_fig
 from .post_process import make_video_from_image_series, make_dir_and_transfer_h5_data
 from .field import VectorField
-from .io import IO, CosseratRodIO
+from .io import IO, CosseratRodIO, EulerianFieldIO
 from .rod_viz import plot_video_of_rod_surface
 from .precision import get_real_t, get_test_tol
 from .pyst_kernel_config import get_pyst_dtype, get_pyst_kernel_config