push changes into run in 1d branch #158
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Drafted first in python. This code makes plots & is adjustable. I commented everything so it's hopefully understandable... Reach out with questions. Similar to SAMI2/3 grid. It's B_par & B_perp aligned, made in dipole (p,q) coords, and specified w/ (nf, nz). Code hands back (r,lat) though, not (q,p) or anything like that... Code needs to be able to be modified for tilted, offset dipole so I left all the for-loops and didn't spend any time optimizing.
…lizing mag grid Paper on this from 2006: <https://arxiv.org/pdf/physics/0606044>
…lizing mag grid Paper on this from 2006: <https://arxiv.org/pdf/physics/0606044>
Working. Need to port to init_mag_grid.cpp
Code can run in 1D (alt)
Couple issues remain: - Longitudes are sometimes nan in output files? - nLats needs to be even. And it's not checked. - Ghost cells probably not implemented correctly.
Netcdf files can't be ready by xarray (python) when a dimension has the same name as a variable. This is a problem for "z". Renames all `(x,y,z,time)` -> `(n_x, n_y, n_z, n_time)` > there are two output_netcdf files. I dont think the other is used?
clean out old comments, improve comments that are gonna be left, refactor a bit. - Some nan's in lon are removed by changing the transform.cpp. It's not a bug so I included it in this commit. - Style in transform.coo too.
- not all ionGrid options are used for sphere/dipole grid. I'll add a doc page on this in the next commit...
! I removed the section about passing btwn N/S hemispheres, since that's undecided.
> Probably won't work. But a decent starting point, I hope. Feel free to revert this commit if it's broken.
Though I could do something clever. It's wasn't. Glad I caught this, geez
## Documentation changes: - Update description of geographic & dipole grids - Rearrange `.md` files, complete docs might be easier to generate with this ## test passing - I found an issue that caused tests to fail. this was a quick fix to the input files. ## DIPOLE GRID > big one here - I rewrote the magnetic grid to be in dipole coordinates. *should* be field-aligned. - Very similar to SAMI2/3 grid - Changed inputs, docs, etc. to support this.
[FEAT]: Dipole grid and 1D improvements
- Grid spacing was not exponential, as expected. The issue was with using nZ vs nAlts & is fixed.
unused funcs rm'ed from in init_mag_grid file for debugging removed from edu/examples/dipole/
- I can't test in 1D since things break in the geographic grid. If the dipole grid is broken in 1D, let me know! The altitude (along-field-line) ghost cells are treated as standard grid points. - At low altitudes, points are close enough this is OK. - At high altitudes, it's going to be hard to get ghost cells. - For example, if they extend along the field line, there will be points at +25 Re (L-shell of max_lat) - If they are scaled to lower radius, or just not as far along the field line, they will not be perpendicular to B anymore! > Maybe specify where field lines should be separated btwn open/closed? Then closed field lines will overlap across equator, and open field lines will not be perpendicular to B in the ghost cells? IDK yet! ---- Ghost cells in latitude currently go over the poles. Discussion is happening on whether this is a good idea or not. ---
[BUG]: Fix altitude spacing error in dipole grid
Advection v2
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lots of NaNs, but that is why I am merging! |
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Description
We need to be able to run in 1D, so this will allow a testing place for that.