No complete grid file created with the tokamak example

[carlito1720]

Hi. I have been trying to create a grid using the tokamak example provided. I can get the visual representation of the grid but the file created seems to be incomplete as I get the following error

DataFile: None passed as data to write. Ignoring
DataFile: None passed as data to write. Ignoring

I have tried to use the incomplete file in a simulation, and that also comes up with errors

Is there any way of using the tokamak example script to create a usable grid file?

[johnomotani]

I don't see any errors running that script. Could you post the exact command you ran, and the full output please?

[carlito1720]

It's not a direct error, the created file just does not contain all the grid points.

The output when running 'python tokamak_example.py' in terminal is:

UserWarning: At least one element of rtol is too small. Setting rtol = np.maximum(rtol, 2.220446049250313e-14).
warn("At least one element of rtol is too small. "
Generating a lower single null

Options

Name | Value

N_norm_prefactor | 1.0 (default)
cap_Bp_ylow_xpoint | False (default)
curvature_smoothing | None (default)
curvature_type | curl(b/B) (default)
finecontour_Nfine | 100 (default)
finecontour_atol | 1e-12 (default)
finecontour_diagnose | False (default)
finecontour_extend_prefactor | 2.0 (default)
finecontour_maxits | 200 (default)
finecontour_overdamping_factor | 0.8 (default)
follow_perpendicular_atol | 1e-08 (default)
follow_perpendicular_rtol | 2e-08 (default)
geometry_rtol | 1e-10 (default)
number_of_processors | 1 (default)
orthogonal | True (default)
poloidal_spacing_delta_psi | None (default)
poloidal_spacing_method | sqrt (default)
poloidalfunction_diagnose | False (default)
psi_interpolation_method | spline (default)
psi_spacing_separatrix_multiplier | 0.5
refine_atol | 2e-08 (default)
refine_methods | ['integrate+newton', 'integrate'] (default)
refine_timeout | 10.0 (default)
refine_width | 1e-05 (default)
sfunc_checktol | 1e-13 (default)
shiftedmetric | True (default)
target_all_poloidal_spacing_length | 0.3
target_inner_lower_poloidal_spacing_length | 0.3 (default)
target_inner_upper_poloidal_spacing_length | 0.3 (default)
target_outer_lower_poloidal_spacing_length | 0.3 (default)
target_outer_upper_poloidal_spacing_length | 0.3 (default)
wall_point_exclude_radius | 0.001 (default)
xpoint_poloidal_spacing_length | 0.05
y_boundary_guards | 2

creating region 0 - inner_lower_divertor(0)
creating region 1 - inner_lower_divertor(1)
creating region 2 - core(0)
creating region 3 - core(1)
creating region 4 - outer_lower_divertor(0)
creating region 5 - outer_lower_divertor(1)
Get RZ valuespendicular: 13
Calculate geometry
Distances inner_lower_divertor(0)
Distances inner_lower_divertor(1)
Distances core(0)ur distances: 11
Distances core(1)ur distances: 11
Distances outer_lower_divertor(0)
Distances outer_lower_divertor(1)
1 inner_lower_divertor(0)nces: 11
Poloidal field is in opposite direction to Grad(theta) -> Bp negative
1 inner_lower_divertor(1)
Poloidal field is in opposite direction to Grad(theta) -> Bp negative
1 core(0)
Poloidal field is in opposite direction to Grad(theta) -> Bp negative
1 core(1)
Poloidal field is in opposite direction to Grad(theta) -> Bp negative
1 outer_lower_divertor(0)
Poloidal field is in opposite direction to Grad(theta) -> Bp negative
1 outer_lower_divertor(1)
Poloidal field is in opposite direction to Grad(theta) -> Bp negative
Calculate zShiftrtor(1) calcHy 10 / 11
Calculate Metricrtor(1)divertor(1)
/Users/carlamiquel-davidson/.local/lib/python3.9/site-packages/hypnotoad/core/mesh.py:1709: RuntimeWarning: invalid value encountered in divide
result.xlow[1:-1, :] = (f.centre[1:, :] - f.centre[:-1, :]) / self.dx.xlow[
/Users/carlamiquel-davidson/.local/lib/python3.9/site-packages/hypnotoad/core/mesh.py:1716: RuntimeWarning: invalid value encountered in divide
result.xlow[0, :] = (f.centre[0, :] - f.xlow[0, :]) / (
/Users/carlamiquel-davidson/.local/lib/python3.9/site-packages/hypnotoad/core/mesh.py:1721: RuntimeWarning: invalid value encountered in divide
result.xlow[-1, :] = (f_outer - f.centre[-1, :]) / self.dx.xlow[-1, :]
/Users/carlamiquel-davidson/.local/lib/python3.9/site-packages/hypnotoad/core/mesh.py:1732: RuntimeWarning: invalid value encountered in divide
result.corners[1:-1, :] = (
/Users/carlamiquel-davidson/.local/lib/python3.9/site-packages/hypnotoad/core/mesh.py:1739: RuntimeWarning: invalid value encountered in divide
result.corners[0, :] = (f.ylow[0, :] - f.corners[0, :]) / (
/Users/carlamiquel-davidson/.local/lib/python3.9/site-packages/hypnotoad/core/mesh.py:1744: RuntimeWarning: invalid value encountered in divide
result.corners[-1, :] = (f_outer - f.ylow[-1, :]) / self.dx.corners[
/Users/carlamiquel-davidson/.local/lib/python3.9/site-packages/hypnotoad/core/mesh.py:1714: RuntimeWarning: invalid value encountered in divide
result.xlow[0, :] = (f.centre[0, :] - f_inner) / self.dx.xlow[0, :]
/Users/carlamiquel-davidson/.local/lib/python3.9/site-packages/hypnotoad/core/mesh.py:1723: RuntimeWarning: invalid value encountered in divide
result.xlow[-1, :] = (f.xlow[-1, :] - f.centre[-1, :]) / (
/Users/carlamiquel-davidson/.local/lib/python3.9/site-packages/hypnotoad/core/mesh.py:1737: RuntimeWarning: invalid value encountered in divide
result.corners[0, :] = (f.ylow[0, :] - f_inner) / self.dx.corners[0, :]
/Users/carlamiquel-davidson/.local/lib/python3.9/site-packages/hypnotoad/core/mesh.py:1748: RuntimeWarning: invalid value encountered in divide
result.corners[-1, :] = (f.corners[-1, :] - f.ylow[-1, :]) / (
DataFile: None passed as data to write. Ignoring
DataFile: None passed as data to write. Ignoring
/Users/carlamiquel-davidson/.local/lib/python3.9/site-packages/hypnotoad/core/multilocationarray.py:116: RuntimeWarning: invalid value encountered in divide
this_result = getattr(ufunc, method)(*this_inputs, **kwargs)
/Users/carlamiquel-davidson/.local/lib/python3.9/site-packages/hypnotoad/core/mesh.py:3596: RuntimeWarning: invalid value encountered in divide
chi.ylow = 2.0 * numpy.pi * self.zShift.ylow / self.ShiftAngle.centre

There is also two plot of the grid that show up with no visible issue.

[johnomotani]

Ah, OK. I was looking in the wrong place. I see the DataFile: None passed as data to write. Ignoring error in my output now. Not sure where that's coming from...