From 4f05b3771ce6daa2a7a0cebaf364515aba21c498 Mon Sep 17 00:00:00 2001 From: Dario Panici Date: Wed, 11 Dec 2024 14:18:25 -0500 Subject: [PATCH 1/2] upload failing test that needs fix to pass --- tests/test_objective_funs.py | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/tests/test_objective_funs.py b/tests/test_objective_funs.py index 4ebcece58..f7954c689 100644 --- a/tests/test_objective_funs.py +++ b/tests/test_objective_funs.py @@ -3024,6 +3024,27 @@ def test_objective_no_nangrad_boundary_error(self): g = obj.grad(obj.x(eq, ext_field)) assert not np.any(np.isnan(g)), "boundary error" + @pytest.mark.unit + def test_objective_no_nangrad_boundary_error_with_coil(self): + """BoundaryError.""" + ext_field = FourierPlanarCoil(center=[0, 0, 10], normal=[0, 0, 1]) + + pres = PowerSeriesProfile([1.25e-1, 0, -1.25e-1]) + iota = PowerSeriesProfile([-4.9e-1, 0, 3.0e-1]) + surf = FourierRZToroidalSurface( + R_lmn=[4.0, 1.0], + modes_R=[[0, 0], [1, 0]], + Z_lmn=[-1.0], + modes_Z=[[-1, 0]], + NFP=1, + ) + + eq = Equilibrium(M=6, N=0, Psi=1.0, surface=surf, pressure=pres, iota=iota) + obj = ObjectiveFunction(BoundaryError(eq, ext_field), use_jit=False) + obj.build() + g = obj.grad(obj.x(eq, ext_field)) + assert not np.any(np.isnan(g)), "boundary error" + @pytest.mark.unit def test_objective_no_nangrad_vacuum_boundary_error(self): """VacuumBoundaryError.""" From e8726dbdc66cfc633e11881975fd23f3c01cb740 Mon Sep 17 00:00:00 2001 From: Dario Panici Date: Wed, 11 Dec 2024 16:29:34 -0500 Subject: [PATCH 2/2] add vector-vector based rotation matrix to correct reverse mode bug --- desc/compute/_curve.py | 26 ++++++++++----------- desc/compute/geom_utils.py | 45 +++++++++++++++++++++++++++++++++++- tests/test_curves.py | 6 ++--- tests/test_geometry.py | 4 ++++ tests/test_objective_funs.py | 23 +----------------- 5 files changed, 64 insertions(+), 40 deletions(-) diff --git a/desc/compute/_curve.py b/desc/compute/_curve.py index 1be68dfe5..0db4e07a1 100644 --- a/desc/compute/_curve.py +++ b/desc/compute/_curve.py @@ -2,9 +2,15 @@ from desc.backend import jnp, sign -from ..utils import cross, dot, safenormalize +from ..utils import cross, dot from .data_index import register_compute_fun -from .geom_utils import rotation_matrix, rpz2xyz, rpz2xyz_vec, xyz2rpz, xyz2rpz_vec +from .geom_utils import ( + rotation_matrix_vector_vector, + rpz2xyz, + rpz2xyz_vec, + xyz2rpz, + xyz2rpz_vec, +) @register_compute_fun( @@ -208,9 +214,7 @@ def _x_FourierPlanarCurve(params, transforms, profiles, data, **kwargs): coords = jnp.array([X, Y, Z]).T # rotate into place Zaxis = jnp.array([0.0, 0.0, 1.0]) # 2D curve in X-Y plane has normal = +Z axis - axis = cross(Zaxis, normal) - angle = jnp.arccos(dot(Zaxis, safenormalize(normal))) - A = rotation_matrix(axis=axis, angle=angle) + A = rotation_matrix_vector_vector(Zaxis, normal) coords = jnp.matmul(coords, A.T) + center coords = jnp.matmul(coords, params["rotmat"].reshape((3, 3)).T) + params["shift"] # convert back to rpz @@ -248,9 +252,7 @@ def _x_s_FourierPlanarCurve(params, transforms, profiles, data, **kwargs): coords = jnp.array([dX, dY, dZ]).T # rotate into place Zaxis = jnp.array([0.0, 0.0, 1.0]) # 2D curve in X-Y plane has normal = +Z axis - axis = cross(Zaxis, normal) - angle = jnp.arccos(dot(Zaxis, safenormalize(normal))) - A = rotation_matrix(axis=axis, angle=angle) + A = rotation_matrix_vector_vector(Zaxis, normal) coords = jnp.matmul(coords, A.T) coords = jnp.matmul(coords, params["rotmat"].reshape((3, 3)).T) # convert back to rpz @@ -293,9 +295,7 @@ def _x_ss_FourierPlanarCurve(params, transforms, profiles, data, **kwargs): coords = jnp.array([d2X, d2Y, d2Z]).T # rotate into place Zaxis = jnp.array([0.0, 0.0, 1.0]) # 2D curve in X-Y plane has normal = +Z axis - axis = cross(Zaxis, normal) - angle = jnp.arccos(dot(Zaxis, safenormalize(normal))) - A = rotation_matrix(axis=axis, angle=angle) + A = rotation_matrix_vector_vector(Zaxis, normal) coords = jnp.matmul(coords, A.T) coords = jnp.matmul(coords, params["rotmat"].reshape((3, 3)).T) # convert back to rpz @@ -345,9 +345,7 @@ def _x_sss_FourierPlanarCurve(params, transforms, profiles, data, **kwargs): coords = jnp.array([d3X, d3Y, d3Z]).T # rotate into place Zaxis = jnp.array([0.0, 0.0, 1.0]) # 2D curve in X-Y plane has normal = +Z axis - axis = cross(Zaxis, normal) - angle = jnp.arccos(dot(Zaxis, safenormalize(normal))) - A = rotation_matrix(axis=axis, angle=angle) + A = rotation_matrix_vector_vector(Zaxis, normal) coords = jnp.matmul(coords, A.T) coords = jnp.matmul(coords, params["rotmat"].reshape((3, 3)).T) # convert back to rpz diff --git a/desc/compute/geom_utils.py b/desc/compute/geom_utils.py index eeda658b6..a51b88e41 100644 --- a/desc/compute/geom_utils.py +++ b/desc/compute/geom_utils.py @@ -4,7 +4,7 @@ from desc.backend import jnp -from ..utils import safenorm, safenormalize +from ..utils import cross, dot, safediv, safenorm, safenormalize def reflection_matrix(normal): @@ -28,6 +28,10 @@ def reflection_matrix(normal): def rotation_matrix(axis, angle=None): """Matrix to rotate points about axis by given angle. + NOTE: not correct if a and b are antiparallel, will + simply return identity when in reality negative identity + is correct. + Parameters ---------- axis : array-like, shape(3,) @@ -53,6 +57,45 @@ def rotation_matrix(axis, angle=None): return jnp.where(norm < eps, jnp.eye(3), R1 + R2 + R3) # if axis=0, no rotation +def _skew_matrix(a): + return jnp.array([[0, -a[2], a[1]], [a[2], 0, -a[0]], [-a[1], a[0], 0]]) + + +def rotation_matrix_vector_vector(a, b): + """Matrix to rotate vector a onto b. + + NOTE: not correct if a and b are antiparallel, will + simply return identity when in reality negative identity + is correct. + + Parameters + ---------- + a,b : array-like, shape(3,) + Vectors, in cartesian (X,Y,Z) coordinates + Matrix will correspond to rotating a onto b + + + Returns + ------- + rotmat : ndarray, shape(3,3) + Matrix to rotate points in cartesian (X,Y,Z) coordinates. + + """ + a = jnp.asarray(a) + b = jnp.asarray(b) + a = safenormalize(a) + b = safenormalize(b) + axis = cross(a, b) + norm = safenorm(axis) + axis = safenormalize(axis) + eps = 1e2 * jnp.finfo(axis.dtype).eps + skew = _skew_matrix(axis) + R1 = jnp.eye(3) + R2 = skew + R3 = (skew @ skew) * safediv(1, 1 + dot(a, b)) + return jnp.where(norm < eps, jnp.eye(3), R1 + R2 + R3) # if axis=0, no rotation + + def xyz2rpz(pts): """Transform points from cartesian (X,Y,Z) to polar (R,phi,Z) form. diff --git a/tests/test_curves.py b/tests/test_curves.py index 0b1af1d63..f56f816a2 100644 --- a/tests/test_curves.py +++ b/tests/test_curves.py @@ -615,15 +615,15 @@ def test_basis(self): xs_xyz = cxyz.compute("x_s")["x_s"] xs_rpz = crpz.compute("x_s")["x_s"] - np.testing.assert_allclose(xs_xyz, xs_rpz, atol=2e-15) + np.testing.assert_allclose(xs_xyz, xs_rpz, atol=3e-15) xss_xyz = cxyz.compute("x_ss")["x_ss"] xss_rpz = crpz.compute("x_ss")["x_ss"] - np.testing.assert_allclose(xss_xyz, xss_rpz, atol=2e-15) + np.testing.assert_allclose(xss_xyz, xss_rpz, atol=3e-15) xsss_xyz = cxyz.compute("x_sss")["x_sss"] xsss_rpz = crpz.compute("x_sss")["x_sss"] - np.testing.assert_allclose(xsss_xyz, xsss_rpz, atol=2e-15) + np.testing.assert_allclose(xsss_xyz, xsss_rpz, atol=3e-15) @pytest.mark.unit def test_misc(self): diff --git a/tests/test_geometry.py b/tests/test_geometry.py index f95cd9b23..a5bbbd243 100644 --- a/tests/test_geometry.py +++ b/tests/test_geometry.py @@ -5,6 +5,7 @@ from desc.compute.geom_utils import ( rotation_matrix, + rotation_matrix_vector_vector, rpz2xyz, rpz2xyz_vec, xyz2rpz, @@ -19,6 +20,9 @@ def test_rotation_matrix(): At = np.array([[0, -1, 0], [1, 0, 0], [0, 0, 1]]) np.testing.assert_allclose(A, At, atol=1e-10) + A = rotation_matrix_vector_vector([1, 0, 0], [0, 1, 0]) + np.testing.assert_allclose(A, At, atol=1e-10) + @pytest.mark.unit def test_xyz2rpz(): diff --git a/tests/test_objective_funs.py b/tests/test_objective_funs.py index f7954c689..447dad846 100644 --- a/tests/test_objective_funs.py +++ b/tests/test_objective_funs.py @@ -3024,27 +3024,6 @@ def test_objective_no_nangrad_boundary_error(self): g = obj.grad(obj.x(eq, ext_field)) assert not np.any(np.isnan(g)), "boundary error" - @pytest.mark.unit - def test_objective_no_nangrad_boundary_error_with_coil(self): - """BoundaryError.""" - ext_field = FourierPlanarCoil(center=[0, 0, 10], normal=[0, 0, 1]) - - pres = PowerSeriesProfile([1.25e-1, 0, -1.25e-1]) - iota = PowerSeriesProfile([-4.9e-1, 0, 3.0e-1]) - surf = FourierRZToroidalSurface( - R_lmn=[4.0, 1.0], - modes_R=[[0, 0], [1, 0]], - Z_lmn=[-1.0], - modes_Z=[[-1, 0]], - NFP=1, - ) - - eq = Equilibrium(M=6, N=0, Psi=1.0, surface=surf, pressure=pres, iota=iota) - obj = ObjectiveFunction(BoundaryError(eq, ext_field), use_jit=False) - obj.build() - g = obj.grad(obj.x(eq, ext_field)) - assert not np.any(np.isnan(g)), "boundary error" - @pytest.mark.unit def test_objective_no_nangrad_vacuum_boundary_error(self): """VacuumBoundaryError.""" @@ -3097,7 +3076,7 @@ def test_objective_no_nangrad_quadratic_flux(self): @pytest.mark.unit def test_objective_no_nangrad_quadratic_flux_minimizing(self): """SurfaceQuadraticFlux.""" - ext_field = ToroidalMagneticField(1.0, 1.0) + ext_field = FourierPlanarCoil(normal=[0, 0, 1]) surf = FourierRZToroidalSurface( R_lmn=[4.0, 1.0],