Tweaks to docs

docs/source/simsopt.geo.rst

@@ -60,6 +60,14 @@ simsopt.geo.curverzfourier module
    :undoc-members:
    :show-inheritance:
 
+simsopt.geo.curveplanarfourier module
+-------------------------------------
+
+.. automodule:: simsopt.geo.curveplanarfourier
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 simsopt.geo.curvexyzfourier module
 ----------------------------------
 

examples/2_Intermediate/stage_two_optimization_planar_coils.py

@@ -1,5 +1,10 @@
 #!/usr/bin/env python
 r"""
+This coil optimization script is similar to stage_two_optimization.py. However
+in this version, the coils are constrained to be planar, by using the curve type
+CurvePlanarFourier. Also the LinkingNumber objective is used to prevent coils
+from becoming topologically linked with each other.
+
 In this example we solve a FOCUS like Stage II coil optimisation problem: the
 goal is to find coils that generate a specific target normal field on a given
 surface.  In this particular case we consider a vacuum field, so the target is
@@ -12,6 +17,7 @@
         + DISTANCE_WEIGHT * MininumDistancePenalty(DISTANCE_THRESHOLD)
         + CURVATURE_WEIGHT * CurvaturePenalty(CURVATURE_THRESHOLD)
         + MSC_WEIGHT * MeanSquaredCurvaturePenalty(MSC_THRESHOLD)
+        + LinkingNumber
 
 if any of the weights are increased, or the thresholds are tightened, the coils
 are more regular and better separated, but the target normal field may not be
@@ -25,15 +31,14 @@
 from pathlib import Path
 import numpy as np
 from scipy.optimize import minimize
-from simsopt.objectives import Weight
-from simsopt.geo import SurfaceRZFourier
-from simsopt.objectives import SquaredFlux
-from simsopt.objectives import QuadraticPenalty
-from simsopt.geo import curves_to_vtk, create_equally_spaced_planar_curves
-from simsopt.field import BiotSavart
-from simsopt.field import Current, coils_via_symmetries
-from simsopt.geo import CurveLength, CurveCurveDistance, \
-    MeanSquaredCurvature, LpCurveCurvature, CurveSurfaceDistance, LinkingNumber
+from simsopt.field import BiotSavart, Current, coils_via_symmetries
+from simsopt.geo import (
+    CurveLength, CurveCurveDistance,
+    MeanSquaredCurvature, LpCurveCurvature, CurveSurfaceDistance, LinkingNumber,
+    SurfaceRZFourier, curves_to_vtk, create_equally_spaced_planar_curves,
+)
+from simsopt.objectives import Weight, SquaredFlux, QuadraticPenalty
+from simsopt.util import in_github_actions
 
 # Number of unique coil shapes, i.e. the number of coils per half field period:
 # (Since the configuration has nfp = 2, multiply by 4 to get the total number of coils.)
@@ -70,8 +75,7 @@
 MSC_WEIGHT = 1e-6
 
 # Number of iterations to perform:
-ci = "CI" in os.environ and os.environ['CI'].lower() in ['1', 'true']
-MAXITER = 50 if ci else 400
+MAXITER = 50 if in_github_actions else 400
 
 # File for the desired boundary magnetic surface:
 TEST_DIR = (Path(__file__).parent / ".." / ".." / "tests" / "test_files").resolve()

examples/run_serial_examples

@@ -16,6 +16,7 @@ set -ex
 ./2_Intermediate/QSC.py
 ./2_Intermediate/boozer.py
 ./2_Intermediate/stage_two_optimization.py
+./2_Intermediate/stage_two_optimization_planar.py
 ./2_Intermediate/stage_two_optimization_stochastic.py
 ./2_Intermediate/stage_two_optimization_finite_beta.py
 ./2_Intermediate/strain_optimization.py

src/simsopt/geo/__init__.py

@@ -8,6 +8,7 @@
 from .curvexyzfourier import *
 from .curveperturbed import *
 from .curveobjectives import *
+from .curveplanarfourier import *
 from .framedcurve import *
 from .finitebuild import *
 from .plotting import *
@@ -28,6 +29,7 @@
 __all__ = (curve.__all__ + curvehelical.__all__ +
            curverzfourier.__all__ + curvexyzfourier.__all__ +
            curveperturbed.__all__ + curveobjectives.__all__ +
+           curveplanarfourier.__all__ +
            finitebuild.__all__ + plotting.__all__ +
            boozersurface.__all__ + qfmsurface.__all__ +
            surface.__all__ +

src/simsopt/geo/curveplanarfourier.py

@@ -9,15 +9,27 @@
 
 class CurvePlanarFourier(sopp.CurvePlanarFourier, Curve):
     r"""
-    ``CurvePlanarFourier`` is a curve that is represented by a polar coordinate fourier serires, a rotation quaternion, and a center point following the form:
+    ``CurvePlanarFourier`` is a curve that is represented by a polar coordinate
+    Fourier serires, a rotation quaternion, and a center point following the
+    form:
+
     .. math::
-       r(\phi) &= \sum_{m=0}^{\text{order}} r_{c,m}\cos(n_{\text{fp}} m \phi) + \sum_{m=1}^{\text{order}} r_{s,m}\sin(n_{\text{fp}} m \phi)
-       \bf{q} &= [q_0,q_i,q_j,q_k] &= [\cos(\theta / 2), \hat{x}\sin(\theta / 2), \hat{y}\sin(\theta / 2), \hat{z}\sin(\theta / 2)]
-    where :math:'\theta' is the counterclockwise rotation about a unit axis :math:'(\hat{x},\hat{y},\hat{z})'.
 
-    The quaternion is normalized for calculations to prevent scaling. The dofs themselves are not normalized. This results in a redundancy in the optimization,
-    where several different sets of dofs may correspond to the same normalized quaternion. 
-    Normalizing the dofs directly would create a dependence between the quaternion dofs, which may cause issues during optimization.
+       r(\phi) &= \sum_{m=0}^{\text{order}} r_{c,m}\cos(m \phi) + \sum_{m=1}^{\text{order}} r_{s,m}\sin(m \phi)
+
+       \bf{q} &= [q_0,q_i,q_j,q_k]
+
+       &= [\cos(\theta / 2), \hat{x}\sin(\theta / 2), \hat{y}\sin(\theta / 2), \hat{z}\sin(\theta / 2)]
+
+    where :math:`\theta` is the counterclockwise rotation about a unit axis
+    :math:`(\hat{x},\hat{y},\hat{z})`.
+
+    The quaternion is normalized for calculations to prevent scaling. The dofs
+    themselves are not normalized. This results in a redundancy in the
+    optimization, where several different sets of dofs may correspond to the
+    same normalized quaternion. Normalizing the dofs directly would create a
+    dependence between the quaternion dofs, which may cause issues during
+    optimization.
 
     The dofs are stored in the order