Momchil/nonuniform

.pylintrc

@@ -1,6 +1,6 @@
 [MASTER]
 extension-pkg-allow-list=pydantic
-good-names=ax, im, Lx, Ly, Lz, x0, y0, z0, x, y, z, u, v, w, f, t, y1, y2, x1, x2, x3, x4, y3, y4, xs, ys, zs, Ax, Ay, Az, Nx, Ny, Nz, N, dl, rr, E, H, xx, yy, zz, dx, dy, Jx, Jy, Jz, Ex, Ey, Ez, Mx, My, Mz, Hx, Hy, Hz, dz, e, fp, dt, a, c, kx, ky, kz, k0, Jx_k, Jy_k, My_k, Mx_k, N_theta, N_phi, L_theta, L_phi, ux, uy, uz, nk, i, j, k, J, M, _N_th, _N_ph, _L_th, _L_ph, r, Et_array, Ep_array, Er_array, Ht_array, Hp_array, Hr_array, Et, Ep, Er, Ht, Hp, Hr, Ex_data, Ey_data, Ez_data, Hx_data, Hy_data, Hz_data, Ar, Atheta, Aphi, mu
+good-names=ax, im, Lx, Ly, Lz, x0, y0, z0, x, y, z, u, v, w, f, t, y1, y2, x1, x2, x3, x4, y3, y4, xs, ys, zs, Ax, Ay, Az, Nx, Ny, Nz, N, dl, rr, E, H, xx, yy, zz, dx, dy, Jx, Jy, Jz, Ex, Ey, Ez, Mx, My, Mz, Hx, Hy, Hz, dz, e, fp, dt, a, c, kx, ky, kz, k0, Jx_k, Jy_k, My_k, Mx_k, N_theta, N_phi, L_theta, L_phi, ux, uy, uz, nk, i, j, k, J, M, _N_th, _N_ph, _L_th, _L_ph, r, Et_array, Ep_array, Er_array, Ht_array, Hp_array, Hr_array, Et, Ep, Er, Ht, Hp, Hr, Ex_data, Ey_data, Ez_data, Hx_data, Hy_data, Hz_data, Ar, Atheta, Aphi, mu, n, k
 
 [BASIC]
 

CHANGELOG.md

@@ -7,7 +7,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- New `grid_spec` Field in `Simulation` that allows more flexibility in defining the mesh.
+- `GridSpec1d` class defining how the meshing along each dimension should be done, with sublcasses `UniformGrid` and `CustomGrid` that cover the functionality 
+  previously offered by supplying a float or a list of floats to `Simulation.grid_size`. New functionality offered by `AutoGrid` subclass, with the 
+  mesh automatically generated based on the minimum required steps per wavelength.
+
 ### Changed
+- `Simulation.grid_spec` uses the default `GridSpec`, which has `AutoGrid(min_steps_per_wvl=10)` in each direction. To initialize a `Simulation` then it is no 
+  longer needed to provide grid information, if sources are added to the simulation. Otherwise an error will be raised to provide a wavelength for the auto mesh.
+
+### Removed
+- `Simulation.grid_size` is now deprecated in favor of `Simulation.grid_spec`.
 
 ## [1.2.2] - 2022-4-16
 

requirements/core.txt

@@ -6,7 +6,7 @@ h5py>=3.0.0
 rich
 nlopt
 matplotlib
-shapely>=1.8.1
+shapely<=1.8.0,>=1.7.0
 descartes
 pydantic>=1.9.0
 PyYAML

test_local.sh

@@ -1,4 +1,5 @@
 #!/bin/bash
+set -e
 
 black .
 python lint.py
@@ -8,5 +9,6 @@ pytest -ra tests/test_IO.py
 pytest -ra tests/test_material_library.py
 pytest -ra tests/test_plugins.py
 pytest -ra tests/test_sidewall.py
+pytest -ra tests/test_meshgenerate.py
 
 pytest --doctest-modules tidy3d/components --ignore=tidy3d/components/base.py

tests/test_IO.py

@@ -24,7 +24,6 @@ def test_simulation_preserve_types():
 
     sim_all = Simulation(
         size=(10.0, 10.0, 10.0),
-        grid_size=(1, 1, 1),
         structures=[
             Structure(geometry=Box(size=(1, 1, 1)), medium=Medium()),
             Structure(geometry=Sphere(radius=1), medium=PoleResidue(eps_inf=1, poles=[])),

tests/test_components.py

@@ -13,7 +13,6 @@ def test_sim():
 
     sim = Simulation(
         size=(2.0, 2.0, 2.0),
-        grid_size=(0.01, 0.01, 0.01),
         run_time=1e-12,
         structures=[
             Structure(
@@ -71,7 +70,6 @@ def _test_version():
 
     sim = Simulation(
         size=(1, 1, 1),
-        grid_size=(0.1, 0.1, 0.1),
         run_time=1e-12,
     )
     path = "tests/tmp/simulation.json"
@@ -94,7 +92,7 @@ def place_box(center_offset):
         sim = Simulation(
             size=(1, 1, 1),
             center=CENTER_SHIFT,
-            grid_size=(0.1, 0.1, 0.1),
+            grid_spec=GridSpec(wavelength=1.0),
             run_time=1e-12,
             structures=[
                 Structure(geometry=Box(size=(1, 1, 1), center=shifted_center), medium=Medium())
@@ -123,20 +121,17 @@ def place_box(center_offset):
                 place_box(tuple(center))
 
 
-def test_sim_grid_size():
-
-    size = (1, 1, 1)
-    _ = Simulation(size=size, grid_size=(1.0, 1.0, 1.0), run_time=1e-12)
+def test_sim_size():
 
-
-def _test_sim_size():
+    mesh1d = UniformGrid(dl=1e-5)
+    grid_spec = GridSpec(grid_x=mesh1d, grid_y=mesh1d, grid_z=mesh1d)
 
     with pytest.raises(SetupError):
-        s = Simulation(size=(1, 1, 1), grid_size=(1e-5, 1e-5, 1e-5), run_time=1e-12)
+        s = Simulation(size=(1, 1, 1), grid_spec=grid_spec, run_time=1e-12)
         s._validate_size()
 
     with pytest.raises(SetupError):
-        s = Simulation(size=(1, 1, 1), grid_size=(0.1, 0.1, 0.1), run_time=1e-7)
+        s = Simulation(size=(1, 1, 1), run_time=1e-7)
         s._validate_size()
 
 
@@ -145,16 +140,13 @@ def _test_monitor_size():
     with pytest.raises(SetupError):
         s = Simulation(
             size=(1, 1, 1),
-            grid_size=(1e-3, 1e-3, 1e-3),
+            grid_spec=GridSpec.uniform(1e-3),
             monitors=[
-                FieldMonitor(
-                    size=(inf, inf, inf), freqs=np.linspace(0, 200e12, 10000001), name="test"
-                )
+                FieldMonitor(size=(inf, inf, inf), freqs=np.linspace(0, 200e12, 10001), name="test")
             ],
             run_time=1e-12,
         )
-
-        s.validate_contents()
+        s.validate_pre_upload()
 
 
 @pytest.mark.parametrize("freq, log_level", [(1.5, 30), (2.5, None), (3.5, 30)])
@@ -172,7 +164,6 @@ def test_monitor_medium_frequency_range(caplog, freq, log_level):
     )
     sim = Simulation(
         size=(1, 1, 1),
-        grid_size=(0.1, 0.1, 0.1),
         structures=[box],
         monitors=[mnt],
         sources=[src],
@@ -192,26 +183,23 @@ def test_monitor_simulation_frequency_range(caplog, fwidth, log_level):
         polarization="Ex",
     )
     mnt = FieldMonitor(size=(0, 0, 0), name="freq", freqs=[1.5])
-    sim = Simulation(
-        size=(1, 1, 1), grid_size=(0.1, 0.1, 0.1), monitors=[mnt], sources=[src], run_time=1e-12
-    )
+    sim = Simulation(size=(1, 1, 1), monitors=[mnt], sources=[src], run_time=1e-12)
     assert_log_level(caplog, log_level)
 
 
 @pytest.mark.parametrize("grid_size,log_level", [(0.001, None), (3, 30)])
-def test_sim_grid_size(caplog, grid_size, log_level):
+def test_large_grid_size(caplog, grid_size, log_level):
     # small fwidth should be inside range, large one should throw warning
 
     medium = Medium(permittivity=2, frequency_range=(2e14, 3e14))
     box = Structure(geometry=Box(size=(0.1, 0.1, 0.1)), medium=medium)
-    src = UniformCurrentSource(
+    src = PointDipole(
         source_time=GaussianPulse(freq0=2.5e14, fwidth=1e12),
-        size=(0, 0, 0),
         polarization="Ex",
     )
     _ = Simulation(
         size=(1, 1, 1),
-        grid_size=(0.01, 0.01, grid_size),
+        grid_spec=GridSpec.uniform(dl=grid_size),
         structures=[box],
         sources=[src],
         run_time=1e-12,
@@ -232,7 +220,6 @@ def test_sim_structure_gap(caplog, box_size, log_level):
     )
     sim = Simulation(
         size=(10, 10, 10),
-        grid_size=(0.1, 0.1, 0.1),
         structures=[box],
         sources=[src],
         pml_layers=[PML(num_layers=5), PML(num_layers=5), PML(num_layers=5)],
@@ -262,7 +249,6 @@ def test_sim_plane_wave_error():
     # with transparent box continue
     _ = Simulation(
         size=(1, 1, 1),
-        grid_size=(0.1, 0.1, 0.1),
         medium=medium_bg,
         structures=[box_transparent],
         sources=[src],
@@ -273,7 +259,6 @@ def test_sim_plane_wave_error():
     with pytest.raises(SetupError):
         _ = Simulation(
             size=(1, 1, 1),
-            grid_size=(0.1, 0.1, 0.1),
             medium=medium_bg,
             structures=[box_transparent, box],
             sources=[src],
@@ -293,9 +278,7 @@ def test_sim_structure_extent(caplog, box_size, log_level):
         polarization="Ex",
     )
     box = Structure(geometry=Box(size=box_size), medium=Medium(permittivity=2))
-    sim = Simulation(
-        size=(1, 1, 1), grid_size=(0.1, 0.1, 0.1), structures=[box], sources=[src], run_time=1e-12
-    )
+    sim = Simulation(size=(1, 1, 1), structures=[box], sources=[src], run_time=1e-12)
 
     assert_log_level(caplog, log_level)
 
@@ -304,21 +287,18 @@ def test_num_mediums():
     """Make sure we error if too many mediums supplied."""
 
     structures = []
+    grid_spec = GridSpec.auto(wavelength=1.0)
     for i in range(200):
         structures.append(
             Structure(geometry=Box(size=(1, 1, 1)), medium=Medium(permittivity=i + 1))
         )
-    sim = Simulation(
-        size=(1, 1, 1), grid_size=(0.1, 0.1, 0.1), structures=structures, run_time=1e-12
-    )
+    sim = Simulation(size=(1, 1, 1), grid_spec=grid_spec, structures=structures, run_time=1e-12)
 
     with pytest.raises(SetupError):
         structures.append(
             Structure(geometry=Box(size=(1, 1, 1)), medium=Medium(permittivity=i + 2))
         )
-        sim = Simulation(
-            size=(1, 1, 1), grid_size=(0.1, 0.1, 0.1), structures=structures, run_time=1e-12
-        )
+        sim = Simulation(size=(1, 1, 1), grid_spec=grid_spec, structures=structures, run_time=1e-12)
 
 
 """ geometry """
@@ -359,13 +339,11 @@ def test_geometry_sizes():
         with pytest.raises(pydantic.ValidationError) as e_info:
             a = Box(size=size, center=(0, 0, 0))
         with pytest.raises(pydantic.ValidationError) as e_info:
-            s = Simulation(size=size, grid_size=(1.0, 1.0, 1.0), run_time=1e-12)
-        with pytest.raises(pydantic.ValidationError) as e_info:
-            s = Simulation(size=(1, 1, 1), grid_size=size, run_time=1e-12)
+            s = Simulation(size=size, run_time=1e-12, grid_spec=GridSpec(wavelength=1.0))
 
     # negative grid sizes error?
     with pytest.raises(pydantic.ValidationError) as e_info:
-        s = Simulation(size=(1, 1, 1), grid_size=-1.0, run_time=1e-12)
+        s = Simulation(size=(1, 1, 1), grid_spec=GridSpec.uniform(dl=-1.0), run_time=1e-12)
 
 
 def test_pop_axis():
@@ -577,7 +555,6 @@ def _test_names_default():
 
     sim = Simulation(
         size=(2.0, 2.0, 2.0),
-        grid_size=(0.01, 0.01, 0.01),
         run_time=1e-12,
         structures=[
             Structure(
@@ -633,7 +610,6 @@ def test_names_unique():
     with pytest.raises(SetupError) as e:
         sim = Simulation(
             size=(2.0, 2.0, 2.0),
-            grid_size=(0.01, 0.01, 0.01),
             run_time=1e-12,
             structures=[
                 Structure(
@@ -652,7 +628,6 @@ def test_names_unique():
     with pytest.raises(SetupError) as e:
         sim = Simulation(
             size=(2.0, 2.0, 2.0),
-            grid_size=(0.01, 0.01, 0.01),
             run_time=1e-12,
             sources=[
                 UniformCurrentSource(
@@ -675,7 +650,6 @@ def test_names_unique():
     with pytest.raises(SetupError) as e:
         sim = Simulation(
             size=(2.0, 2.0, 2.0),
-            grid_size=(0.01, 0.01, 0.01),
             run_time=1e-12,
             monitors=[
                 FluxMonitor(size=(1, 1, 0), center=(0, -0.5, 0), freqs=[1], name="mon1"),
@@ -822,7 +796,7 @@ def test_mode_object_syms():
         sim = Simulation(
             center=(1.0, -1.0, 0.5),
             size=(2.0, 2.0, 2.0),
-            grid_size=(0.01, 0.01, 0.01),
+            grid_spec=GridSpec.auto(wavelength=C_0 / 1.0),
             run_time=1e-12,
             symmetry=(1, -1, 0),
             sources=[ModeSource(size=(2, 2, 0), direction="+", source_time=g)],
@@ -833,7 +807,7 @@ def test_mode_object_syms():
         sim = Simulation(
             center=(1.0, -1.0, 0.5),
             size=(2.0, 2.0, 2.0),
-            grid_size=(0.01, 0.01, 0.01),
+            grid_spec=GridSpec.auto(wavelength=C_0 / 1.0),
             run_time=1e-12,
             symmetry=(1, -1, 0),
             monitors=[ModeMonitor(size=(2, 2, 0), name="mnt", freqs=[2], mode_spec=ModeSpec())],
@@ -843,7 +817,7 @@ def test_mode_object_syms():
     sim = Simulation(
         center=(1.0, -1.0, 0.5),
         size=(2.0, 2.0, 2.0),
-        grid_size=(0.01, 0.01, 0.01),
+        grid_spec=GridSpec.auto(wavelength=C_0 / 1.0),
         run_time=1e-12,
         symmetry=(1, -1, 0),
         sources=[ModeSource(center=(1, -1, 1), size=(2, 2, 0), direction="+", source_time=g)],
@@ -853,7 +827,7 @@ def test_mode_object_syms():
     sim = Simulation(
         center=(1.0, -1.0, 0.5),
         size=(2.0, 2.0, 2.0),
-        grid_size=(0.01, 0.01, 0.01),
+        grid_spec=GridSpec.auto(wavelength=C_0 / 1.0),
         run_time=1e-12,
         symmetry=(1, -1, 0),
         monitors=[