Merge pull request #124 from boutproject/example-tokamak-include-boundary-points

Minor improvements to tokamak example (include boundary points)

Author: johnomotani

.github/workflows/pythonpackage.yml

@@ -18,7 +18,7 @@ jobs:
     if: always()
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.8, 3.9, '3.10']
       fail-fast: false
 
     steps:
@@ -40,11 +40,11 @@ jobs:
   integrated-tests:
 
     runs-on: ubuntu-latest
-    timeout-minutes: 10
+    timeout-minutes: 15
     if: always()
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.8, 3.9, '3.10']
       fail-fast: false
 
     steps:
@@ -69,7 +69,7 @@ jobs:
   examples:
 
     runs-on: ubuntu-latest
-    timeout-minutes: 10
+    timeout-minutes: 30
     if: always()
     strategy:
       fail-fast: false

.github/workflows/pythonpublish.yml

@@ -15,7 +15,7 @@ jobs:
     timeout-minutes: 30
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.8, 3.9, '3.10']
 
     steps:
     - uses: actions/checkout@v2

examples/tokamak/README.md

@@ -1,3 +1,6 @@
+> **Warning:** This example does not use/generate a geqdsk file, so does not
+support the 'standard' workflow with `hypnotoad-gui` or `hypnotoad_geqdsk`.
+
 To generate a tokamak grid for a simple poloidal flux, psi, given by an
 analytic function:
 

examples/tokamak/connected-double-null.yaml

@@ -28,5 +28,7 @@ psi_spacing_separatrix_multiplier: 0.5   # Smaller -> pack near separatrix
 
 # Poloidal grid spacing
 
-target_all_poloidal_spacing_length: 0.05   # Smaller -> pack near targets
+target_all_poloidal_spacing_length: 0.3   # Smaller -> pack near targets
 xpoint_poloidal_spacing_length: 0.05   # Smaller -> pack near X-points
+
+y_boundary_guards: 2

examples/tokamak/disconnected-double-null.yaml

@@ -29,5 +29,7 @@ psi_spacing_separatrix_multiplier: 0.5   # Smaller -> pack near separatrix
 
 # Poloidal grid spacing
 
-target_all_poloidal_spacing_length: 0.05   # Smaller -> pack near targets
+target_all_poloidal_spacing_length: 0.3   # Smaller -> pack near targets
 xpoint_poloidal_spacing_length: 0.05   # Smaller -> pack near X-points
+
+y_boundary_guards: 2

examples/tokamak/single-null.yaml

@@ -25,5 +25,7 @@ psi_spacing_separatrix_multiplier: 0.5   # Smaller -> pack near separatrix
 
 # Poloidal grid spacing
 
-target_all_poloidal_spacing_length: 0.05   # Smaller -> pack near targets
+target_all_poloidal_spacing_length: 0.3   # Smaller -> pack near targets
 xpoint_poloidal_spacing_length: 0.05   # Smaller -> pack near X-points
+
+y_boundary_guards: 2

examples/tokamak/tokamak_example.py

@@ -23,8 +23,8 @@ def create_tokamak(geometry="lsn", nx=65, ny=65):
     psi2d[nx,ny]  2D array of poloidal flux [Wb]
     """
 
-    r1d = np.linspace(1.2, 1.8, nx)
-    z1d = np.linspace(-0.5, 0.5, ny)
+    r1d = np.linspace(1.0, 2.0, nx)
+    z1d = np.linspace(-0.7, 0.7, ny)
     r2d, z2d = np.meshgrid(r1d, z1d, indexing="ij")
 
     r0 = 1.5
@@ -115,23 +115,39 @@ def create_tokamak(geometry="lsn", nx=65, ny=65):
 
     from hypnotoad import tokamak
 
+    # Put wall inside grid, so that we can have boundary points outside with wall wthout
+    # hitting extrapolated psi.
+    wall_extra = 0.2
+    rmin = min(r1d) + wall_extra
+    rmax = max(r1d) - wall_extra
+    zmin = min(z1d) + wall_extra
+    zmax = max(z1d) - wall_extra
     eq = tokamak.TokamakEquilibrium(
-        r1d, z1d, psi2d, psi1d, [], settings=options  # psi1d, fpol
+        r1d,
+        z1d,
+        psi2d,
+        psi1d,
+        fpol1D=[],
+        settings=options,
+        wall=[(rmin, zmin), (rmin, zmax), (rmax, zmax), (rmax, zmin)],
     )
 
     from hypnotoad.core.mesh import BoutMesh
 
     mesh = BoutMesh(eq, options)
     mesh.geometry()
+    mesh.writeGridfile("bout.grd.nc")
 
     if not args.no_plot:
         import matplotlib.pyplot as plt
 
         eq.plotPotential(ncontours=40)
+        eq.plotWall()
 
         plt.plot(*eq.x_points[0], "rx")
 
         mesh.plotPoints(xlow=True, ylow=True, corners=True)
+        eq.plotWall()
 
         plt.show()
 

hypnotoad/test_suite/test_fileutils.py

@@ -19,5 +19,5 @@ def test_ChunkOutput():
     assert (
         output.getvalue()
         == """ 1.000000000E+00-3.200000000E+00 6.200000000E+05 8.765400000E-12 4.200000000E+01
-   -76"""
+   -76"""  # noqa: E501
     )

integrated_tests/connected_doublenull_nonorthogonal/runtest.py

@@ -5,7 +5,9 @@
 import sys
 import xarray.testing as xrt
 
-from integrated_tests.utils import run_case
+# Put the integrated_tests directory into sys.path so we can import from it
+sys.path.append(str(Path(__file__).joinpath("..", "..", "..").resolve()))
+from integrated_tests.utils import run_case  # noqa: E402
 
 diagnose = False
 

integrated_tests/connected_doublenull_orthogonal/runtest.py

@@ -5,7 +5,9 @@
 import sys
 import xarray.testing as xrt
 
-from integrated_tests.utils import run_case
+# Put the integrated_tests directory into sys.path so we can import from it
+sys.path.append(str(Path(__file__).joinpath("..", "..", "..").resolve()))
+from integrated_tests.utils import run_case  # noqa: E402
 
 diagnose = False