Merge branch 'master' into yge/print

desc/grid.py

@@ -216,7 +216,7 @@ def is_meshgrid(self):
         Let the tuple (r, p, t) ∈ R³ denote a radial, poloidal, and toroidal
         coordinate value. The is_meshgrid flag denotes whether any coordinate
         can be iterated over along the relevant axis of the reshaped grid:
-        nodes.reshape(num_radial, num_poloidal, num_toroidal, 3).
+        nodes.reshape((num_poloidal, num_radial, num_toroidal, 3), order="F").
         """
         return self.__dict__.setdefault("_is_meshgrid", False)
 
@@ -598,6 +598,52 @@ def replace_at_axis(self, x, y, copy=False, **kwargs):
             )
         return x
 
+    def meshgrid_reshape(self, x, order):
+        """Reshape data to match grid coordinates.
+
+        Given flattened data on a tensor product grid, reshape the data such that
+        the axes of the array correspond to coordinate values on the grid.
+
+        Parameters
+        ----------
+        x : ndarray, shape(N,) or shape(N,3)
+            Data to reshape.
+        order : str
+            Desired order of axes for returned data. Should be a permutation of
+            ``grid.coordinates``, eg ``order="rtz"`` has the first axis of the returned
+            data correspond to different rho coordinates, the second axis to different
+            theta, etc.  ``order="trz"`` would have the first axis correspond to theta,
+            and so on.
+
+        Returns
+        -------
+        x : ndarray
+            Data reshaped to align with grid nodes.
+        """
+        errorif(
+            not self.is_meshgrid,
+            ValueError,
+            "grid is not a tensor product grid, so meshgrid_reshape doesn't "
+            "make any sense",
+        )
+        errorif(
+            sorted(order) != sorted(self.coordinates),
+            ValueError,
+            f"order should be a permutation of {self.coordinates}, got {order}",
+        )
+        shape = (self.num_poloidal, self.num_rho, self.num_zeta)
+        vec = False
+        if x.ndim > 1:
+            vec = True
+            shape += (-1,)
+        x = x.reshape(shape, order="F")
+        x = jnp.moveaxis(x, 1, 0)  # now shape rtz/raz etc
+        newax = tuple(self.coordinates.index(c) for c in order)
+        if vec:
+            newax += (3,)
+        x = jnp.transpose(x, newax)
+        return x
+
 
 class Grid(_Grid):
     """Collocation grid with custom node placement.
@@ -632,7 +678,7 @@ class Grid(_Grid):
         Let the tuple (r, p, t) ∈ R³ denote a radial, poloidal, and toroidal
         coordinate value. The is_meshgrid flag denotes whether any coordinate
         can be iterated over along the relevant axis of the reshaped grid:
-        nodes.reshape(num_radial, num_poloidal, num_toroidal, 3).
+        nodes.reshape((num_poloidal, num_radial, num_toroidal, 3), order="F").
     jitable : bool
         Whether to skip certain checks and conditionals that don't work under jit.
         Allows grid to be created on the fly with custom nodes, but weights, symmetry
@@ -762,11 +808,16 @@ def create_meshgrid(
             dc = _periodic_spacing(c, period[2])[1] * NFP
         else:
             da, db, dc = spacing
+
+        bb, aa, cc = jnp.meshgrid(b, a, c, indexing="ij")
+
         nodes = jnp.column_stack(
-            list(map(jnp.ravel, jnp.meshgrid(a, b, c, indexing="ij")))
+            [aa.flatten(order="F"), bb.flatten(order="F"), cc.flatten(order="F")]
         )
+        bb, aa, cc = jnp.meshgrid(db, da, dc, indexing="ij")
+
         spacing = jnp.column_stack(
-            list(map(jnp.ravel, jnp.meshgrid(da, db, dc, indexing="ij")))
+            [aa.flatten(order="F"), bb.flatten(order="F"), cc.flatten(order="F")]
         )
         weights = (
             spacing.prod(axis=1)
@@ -776,19 +827,18 @@ def create_meshgrid(
             else None
         )
 
-        unique_a_idx = jnp.arange(a.size) * b.size * c.size
-        unique_b_idx = jnp.arange(b.size) * c.size
-        unique_c_idx = jnp.arange(c.size)
-        inverse_a_idx = repeat(
-            unique_a_idx // (b.size * c.size),
-            b.size * c.size,
-            total_repeat_length=a.size * b.size * c.size,
+        unique_a_idx = jnp.arange(a.size) * b.size
+        unique_b_idx = jnp.arange(b.size)
+        unique_c_idx = jnp.arange(c.size) * a.size * b.size
+        inverse_a_idx = jnp.tile(
+            repeat(unique_a_idx // b.size, b.size, total_repeat_length=a.size * b.size),
+            c.size,
         )
         inverse_b_idx = jnp.tile(
-            repeat(unique_b_idx // c.size, c.size, total_repeat_length=b.size * c.size),
-            a.size,
+            unique_b_idx,
+            a.size * c.size,
         )
-        inverse_c_idx = jnp.tile(unique_c_idx, a.size * b.size)
+        inverse_c_idx = repeat(unique_c_idx // (a.size * b.size), (a.size * b.size))
         return Grid(
             nodes=nodes,
             spacing=spacing,
@@ -908,6 +958,7 @@ def __init__(
         self._toroidal_endpoint = False
         self._node_pattern = "linear"
         self._coordinates = "rtz"
+        self._is_meshgrid = True
         self._period = (np.inf, 2 * np.pi, 2 * np.pi / self._NFP)
         self._nodes, self._spacing = self._create_nodes(
             L=L,
@@ -1200,6 +1251,7 @@ def __init__(self, L, M, N, NFP=1):
         self._sym = False
         self._node_pattern = "quad"
         self._coordinates = "rtz"
+        self._is_meshgrid = True
         self._period = (np.inf, 2 * np.pi, 2 * np.pi / self._NFP)
         self._nodes, self._spacing = self._create_nodes(L=L, M=M, N=N, NFP=NFP)
         # symmetry is never enforced for Quadrature Grid
@@ -1341,6 +1393,7 @@ def __init__(self, L, M, N, NFP=1, sym=False, axis=False, node_pattern="jacobi")
         self._sym = sym
         self._node_pattern = node_pattern
         self._coordinates = "rtz"
+        self._is_meshgrid = False
         self._period = (np.inf, 2 * np.pi, 2 * np.pi / self._NFP)
         self._nodes, self._spacing = self._create_nodes(
             L=L, M=M, N=N, NFP=NFP, axis=axis, node_pattern=node_pattern

tests/test_grid.py

@@ -738,20 +738,81 @@ def test_meshgrid(self):
         """Test meshgrid constructor."""
         R = np.linspace(0, 1, 4)
         A = np.linspace(0, 2 * np.pi, 2)
-        Z = np.linspace(0, 10 * np.pi, 3)
+        Z = np.linspace(0, 2 * np.pi, 3)
         grid = Grid.create_meshgrid(
-            [R, A, Z], coordinates="raz", period=(np.inf, 2 * np.pi, np.inf)
+            [R, A, Z], coordinates="raz", period=(np.inf, 2 * np.pi, 2 * np.pi)
         )
+        # treating theta == alpha just for grid construction
+        grid1 = LinearGrid(rho=R, theta=A, zeta=Z)
+        # atol=1e-12 bc Grid by default shifts points away from the axis a tiny bit
+        np.testing.assert_allclose(grid1.nodes, grid.nodes, atol=1e-12)
+        # want radial/poloidal/toroidal nodes sorted in the same order for both
+        np.testing.assert_allclose(grid1.unique_rho_idx, grid.unique_rho_idx)
+        np.testing.assert_allclose(grid1.unique_theta_idx, grid.unique_alpha_idx)
+        np.testing.assert_allclose(grid1.unique_zeta_idx, grid.unique_zeta_idx)
+        np.testing.assert_allclose(grid1.inverse_rho_idx, grid.inverse_rho_idx)
+        np.testing.assert_allclose(grid1.inverse_theta_idx, grid.inverse_alpha_idx)
+        np.testing.assert_allclose(grid1.inverse_zeta_idx, grid.inverse_zeta_idx)
+
+    @pytest.mark.unit
+    def test_meshgrid_reshape(self):
+        """Test that reshaping meshgrids works correctly."""
+        grid = LinearGrid(2, 3, 4)
+
+        r = grid.nodes[grid.unique_rho_idx, 0]
+        t = grid.nodes[grid.unique_theta_idx, 1]
+        z = grid.nodes[grid.unique_zeta_idx, 2]
+
+        # user regular allclose for broadcasting to work correctly
+        # reshaping rtz should have rho along first axis
+        assert np.allclose(
+            grid.meshgrid_reshape(grid.nodes[:, 0], "rtz"), r[:, None, None]
+        )
+        # reshaping rzt should have theta along last axis
+        assert np.allclose(
+            grid.meshgrid_reshape(grid.nodes[:, 1], "rzt"), t[None, None, :]
+        )
+        # reshaping tzr should have zeta along 2nd axis
+        assert np.allclose(
+            grid.meshgrid_reshape(grid.nodes, "tzr")[:, :, :, 2], z[None, :, None]
+        )
+
+        # coordinates are rtz, not raz
+        with pytest.raises(ValueError):
+            grid.meshgrid_reshape(grid.nodes[:, 0], "raz")
+
+        # not a meshgrid
+        grid = ConcentricGrid(2, 3, 4)
+        with pytest.raises(ValueError):
+            grid.meshgrid_reshape(grid.nodes[:, 0], "rtz")
+
+        rho = np.linspace(0, 1, 3)
+        alpha = np.linspace(0, 2 * np.pi, 4)
+        zeta = np.linspace(0, 6 * np.pi, 5)
+        grid = Grid.create_meshgrid([rho, alpha, zeta], coordinates="raz")
         r, a, z = grid.nodes.T
-        _, unique, inverse = np.unique(r, return_index=True, return_inverse=True)
-        np.testing.assert_allclose(grid.unique_rho_idx, unique)
-        np.testing.assert_allclose(grid.inverse_rho_idx, inverse)
-        _, unique, inverse = np.unique(a, return_index=True, return_inverse=True)
-        np.testing.assert_allclose(grid.unique_alpha_idx, unique)
-        np.testing.assert_allclose(grid.inverse_alpha_idx, inverse)
-        _, unique, inverse = np.unique(z, return_index=True, return_inverse=True)
-        np.testing.assert_allclose(grid.unique_zeta_idx, unique)
-        np.testing.assert_allclose(grid.inverse_zeta_idx, inverse)
+        r = grid.meshgrid_reshape(r, "raz")
+        a = grid.meshgrid_reshape(a, "raz")
+        z = grid.meshgrid_reshape(z, "raz")
+        # functions of zeta should separate along first two axes
+        # since those are contiguous, this should work
+        f = z.reshape(-1, zeta.size)
+        for i in range(1, f.shape[0]):
+            np.testing.assert_allclose(f[i - 1], f[i])
+        # likewise for rho
+        f = r.reshape(rho.size, -1)
+        for i in range(1, f.shape[-1]):
+            np.testing.assert_allclose(f[:, i - 1], f[:, i])
+        # test reshaping result won't mix data
+        f = (a**2 + z).reshape(rho.size, alpha.size, zeta.size)
+        for i in range(1, f.shape[0]):
+            np.testing.assert_allclose(f[i - 1], f[i])
+        f = (r**2 + z).reshape(rho.size, alpha.size, zeta.size)
+        for i in range(1, f.shape[1]):
+            np.testing.assert_allclose(f[:, i - 1], f[:, i])
+        f = (r**2 + a).reshape(rho.size, alpha.size, zeta.size)
+        for i in range(1, f.shape[-1]):
+            np.testing.assert_allclose(f[..., i - 1], f[..., i])
 
 
 @pytest.mark.unit