mrhardman

Adding bpar to stella, explicit and implicit algorithms

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This pull request is intended to deliver a fully functional implementation of the explicit and implicit algorithms using all three fields, phi, apar, and bpar. Starting from the development/apar2 branch...

Numerical instability for very small ky rhoref in electrostatic stella

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In trying to understand a numerical instability in a high fidelity linear simulation, I have discovered a numerical instability that affects electrostatic stella. In the attached .zip file is a...

Numerical instability in nonlinear electrostatic "big box" ETG simulations

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Performing simulations recently on Marconi, I noticed an unusual numerical instability. With commit 8eba66af5ea631d6ee9be4ec13d067afdf04ce47 (close enough to the master of stella to be of interest, I hope), I was testing...

post_processing/stella_data.py: *.out.nc is not a valid NetCDF 3 file

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Executing $ python3 kspectra_plots.py On my favourite stella *.out.nc file leads to the following error Traceback (most recent call last): File "kspectra_plots.py", line 3, in from stella_data import time, ntime,...

This pull request attempts to address the issue highlighted https://github.com/boutproject/xBOUT/issues/311 by introducing the ability to make animations with a plotting function based on polygons, not `pcolormesh()`. This feature is not...

Extend `poloidal_plot` option in `animate_list()` to support polygon plotting.

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Mike Kryjak improved the poloidal plotting in https://github.com/boutproject/xBOUT/pull/280, by introducing a function https://github.com/boutproject/xBOUT/blob/64408ea26de5751f6104fcd8598ab250e237b049/xbout/plotting/plotfuncs.py#L852-L872 , so that unphysical artefacts of plotting do not appear. This feature has not been extended to...

Plotting grids using `open_boutdataset` seems broken

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There is a suggested example for plotting the fields of a `grid.nc` file https://github.com/boutproject/xBOUT/blob/master/examples/plot_grid.py. I have tried to use this code to plot the output from a simple Hyponotoad-generated grid....

`neutral_mixed` docs and spurious (?) mass factor

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In the present docs https://hermes3.readthedocs.io/en/latest/equations.html#d-3d-neutral-mixed we have the following equations.   There are some errors here: - missing factors of mass in the momentum equation breaking dimensional consistency, -...

`neutral_mixed` MMS tests and expanded differential operator MMS tests

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The changes included here aim to significantly expand the tests available in `tests/mms`. The following features are added: - symbolic operators in the `tests/mms/perpendicular_laplacian.py` module covering all of the differential...

Nonorthogonal with minimal differential operators MMS test.

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Fixes to the `Div_a_Grad_perp_nonorthog(a, f)` operator (commit 3d11cb75a90be1125b873b6500d01a1d97aabef6, commit 2e5e82709cfea8af074234df01bf28470c1c487e), merge with master, and new automatic tests integrated with `ctest` showing a correct implementation. Theses tests are `hermes-3/tests/mms/orthogonal_test.py` and `hermes-3/tests/mms/nonorthogonal_test.py`,...