Stability hotfix

desc/compute/_core.py

@@ -850,6 +850,8 @@ def compute_geometry(
         data["a"] = jnp.sqrt(data["A"] / jnp.pi)
         data["R0/a"] = data["V"] / (2 * jnp.sqrt(jnp.pi * data["A"] ** 3))
     if check_derivs("V_rr(r)", R_transform, Z_transform):
-        data["V_rr(r)"] = surface_integrals(grid, jnp.abs(data["sqrt(g)_r"]))
+        data["V_rr(r)"] = surface_integrals(
+            grid, data["sqrt(g)_r"] * jnp.sign(data["sqrt(g)"])
+        )
 
     return data

desc/compute/_stability.py

@@ -263,19 +263,19 @@ def compute_magnetic_well(
         # Thermal pressure is constant over a rho surface.
         # surface average(pressure) = thermal + surface average(magnetic)
         dp_drho = 2 * mu_0 * data["p_r"]
-        dB2_drho_avg = (
+        dB2_avg_drho = (
             surface_integrals(
                 grid,
-                jnp.abs(data["sqrt(g)_r"]) * data["|B|^2"]
+                data["sqrt(g)_r"] * jnp.sign(data["sqrt(g)"]) * data["|B|^2"]
                 + jnp.abs(data["sqrt(g)"]) * 2 * dot(data["B"], data["B_r"]),
             )
-            - surface_integrals(grid, jnp.abs(data["sqrt(g)_r"])) * B2_avg
+            - data["V_rr(r)"] * B2_avg
         ) / data["V_r(r)"]
         data["magnetic well"] = (
-            data["V(r)"] * (dp_drho + dB2_drho_avg) / (data["V_r(r)"] * B2_avg)
+            data["V(r)"] * (dp_drho + dB2_avg_drho) / (data["V_r(r)"] * B2_avg)
         )
 
         # equivalent method (besides scaling factor) that avoids computing the volume
-        # data["magnetic well"] = data["rho"] * (dp_drho + dB2_drho_avg) / B2_avg
+        # data["magnetic well"] = data["rho"] * (dp_drho + dB2_avg_drho) / B2_avg
 
     return data

desc/equilibrium.py

@@ -374,7 +374,7 @@ def solve(
             print("Start of solver")
             objective.print_value(objective.x(eq))
         for key, value in result["history"].items():
-            # don't set nonexistent profile
+            # don't set nonexistent profile (values are empty ndarrays)
             if not (key == "c_l" or key == "i_l") or value[-1].size:
                 setattr(eq, key, value[-1])
 
@@ -474,7 +474,7 @@ def optimize(
             print("Start of solver")
             objective.print_value(objective.x(eq))
         for key, value in result["history"].items():
-            # don't set nonexistent profile
+            # don't set nonexistent profile (values are empty ndarrays)
             if not (key == "c_l" or key == "i_l") or value[-1].size:
                 setattr(eq, key, value[-1])
         if verbose > 0:

desc/perturbations.py

@@ -308,7 +308,7 @@ def perturb(
             value = put(  # parameter values below threshold are set to 0
                 value, np.where(np.abs(value) < 10 * np.finfo(value.dtype).eps)[0], 0
             )
-            # don't set nonexistent profile
+            # don't set nonexistent profile (values are empty ndarrays)
             if not (key == "c_l" or key == "i_l") or value.size:
                 setattr(eq_new, key, value)
 
@@ -696,7 +696,7 @@ def optimal_perturb(
             value = put(  # parameter values below threshold are set to 0
                 value, np.where(np.abs(value) < 10 * np.finfo(value.dtype).eps)[0], 0
             )
-            # don't set nonexistent profile
+            # don't set nonexistent profile (values are empty ndarrays)
             if not (key == "c_l" or key == "i_l") or value.size:
                 setattr(eq_new, key, value)
 

devtools/README.rst

@@ -2,18 +2,18 @@
 Scripts for Linting with Pylint and Flake8
 ##########################################
 
-Useage
+Usage
 ======
 
 To use, run either the run_pylint_linting.sh or run_flake8_linting.sh scripts
 
 These will generate a pylint.output file, or flake8_errors.ouput and flake8_summary.output files.
 
-Currently, black is still ran through github actions.
+Currently, black is still ran through GitHub actions.
 
-Most formatting-level errors are being supressed; errors that touch the code logic are primarily the ones being raised.
+Most formatting-level errors are being suppressed; errors that touch the code logic are primarily the ones being raised.
 
-Currently, black is still ran through github actions.
+Currently, black is still ran through GitHub actions.
 
 
 
@@ -40,13 +40,13 @@ Configuration
 Flake8
 ------
 
-Currently, error messages about whitespace and indenting that black does not care about have been supressed.  
+Currently, error messages about whitespace and indenting that black does not care about have been suppressed.  
 These will be fixed in a future cleanup branch.
-More errors can be added to the [flake8] section of settings.cfg after "ignore=", seperated by commas.
+More errors can be added to the [flake8] section of settings.cfg after "ignore=", separated by commas.
 
 Pylint:
 -------
-Currently several classes of error are being supressed, mostly to do with preferring encapsulating behavior into simpler classes and modules.
+Currently several classes of error are being suppressed, mostly to do with preferring encapsulating behavior into simpler classes and modules.
 To disable certain classes of error message, go to the [MESSAGES] section of pylinrc, and add the error to "disable=" separated by commas.
-Additionally, several very minor errors are being supressed to be fixed in a future cleanup branch.
+Additionally, several very minor errors are being suppressed to be fixed in a future cleanup branch.
 

devtools/pylintrc

@@ -359,7 +359,7 @@ known-third-party=enchant
 
 # Analyse import fallback blocks. This can be used to support both Python 2 and
 # 3 compatible code, which means that the block might have code that exists
-# only in one or another interpreter, leading to false positives when analysed.
+# only in one or another interpreter, leading to false positives when analyzed.
 analyse-fallback-blocks=no
 
 

tests/conftest.py

@@ -116,7 +116,6 @@ def DSHAPE_current(tmpdir_factory):
     output_dir = tmpdir_factory.mktemp("result")
     desc_h5_path = output_dir.join("DSHAPE_current_out.h5")
     desc_nc_path = output_dir.join("DSHAPE_current_out.nc")
-    # TODO: change these paths too? (note that DSHAPE_current converges to DSHAPE)
     vmec_nc_path = ".//tests//inputs//wout_DSHAPE.nc"
     booz_nc_path = output_dir.join("DSHAPE_bx.nc")