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WIP: Consistent handling of COCOS conventions #181

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@bendudson bendudson commented Aug 22, 2024

Tools to convert GEQDSK files using different COCOS conventions.
Internally Hypnotoad will use COCOS-1.

  • Closes #xxxx
  • Tests added
  • Udated manual
  • Updated doc/whats-new.md with a summary of the changes

HarukiST added 30 commits August 1, 2024 11:32
@HarukiST
fix fprime for the negative Bp case
6f6e546
@HarukiST
define increasing radial label xcoord
731a330
@HarukiST
pressure extrapolation fix
107c5db
@HarukiST
pressure and pprime has been added in __init__
0c6a084
@HarukiST
slight modification on f_psi_sign
aecafcb
@HarukiST
fprime and pprime have been added in read_geqdsk
16c5697
@HarukiST
extrapolation rule for fprime/pprime should be ext=1 for consistency …
2816d33 
…with f_pol and pressure with ext=3
@HarukiST
function pprime has been added
6f38a09
@HarukiST
add pprime and ffprime in doc of read
4c1fb53
@HarukiST
fix interpolation for negative Bp case
44c2778
@HarukiST
cocos=+1 convention fix in find_critical
f3a364c
@HarukiST
fix xrd in _geqdsk.py
9c86ab1
@HarukiST
fix xrd in _geqdsk.py
58489ae
@HarukiST
fix pprime in _geqdsk.py
59dabca
@HarukiST
flake8 fix in tokamak.py
4b26b80
@HarukiST
flake8 fix in _geqdsk.py
93bdecf
@HarukiST
flake8 fix in _geqdsk.py
0bf561f
@HarukiST
flake8 fix in _geqdsk.py
efbd961
@HarukiST
flake8 fix in tokamak.py
be66d65
@HarukiST
flake8 fix in tokamak.py
0d3ae26
@HarukiST
black fix in tokamak.py
e806fb4
@HarukiST
black fixs in _geqdsk.py
8f5b7c6
@HarukiST
cocos class has been added
bf27fa4
@HarukiST
flake8 and black fixes
ac8593d
@HarukiST
add signed Bp function in module equilibrium
c6bf6dd
@HarukiST
use signed Bp in zShift calculation
8458d98
@HarukiST
black reformatting forsigned Bp
de512ca
@HarukiST
f_psi_sign has been added for signed Bp
7d849d3
@HarukiST
f_psi_sign has been added in torpex.py for signed Bp
f7e7882
@HarukiST
f_psi_sign has been added for matfile in torpex.py for signed Bp
7653245
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ZedThree commented Sep 20, 2024

Worth looking at pyloidal, which does COCOS conversions

@HarukiST
add dummy sinty for backward compatibility
7705e2c
@HarukiST
add dummy sinty for backward compatibility (black)
ed2c33c
@HarukiST
fix bxcvx in bxkappae
f5b8f87
@HarukiST
fix curvature terms in bxkappae
de25952
@HarukiST
fix curvature terms in bxkappae
aeaddb9
@HarukiST
add in bxkappa2 and bxkappa3
2617c5d
@HarukiST
re-define BOUT-3 style curvature with pre-cancellation as bxkappa
36fb632
@HarukiST
dx should be always positive definie
b5331ed
@HarukiST
comment fix
ffb98cd
@HarukiST
add netcdf3_64bit for BOUTv3.1
37f12e3
@HarukiST
black fix
0dcac98
@HarukiST
black fix
d7af073
@HarukiST
delete useless duplication of hthe and hy
598fd8e
@HarukiST
set dx at separatrix without pf regions
4a5dde0
@HarukiST
set minimum grid width around sepatatrix
4ebd334
@HarukiST
clean pressure and Jpar
218c501
@HarukiST
add dummy data for kinetic profiles
80b01e5
@HarukiST
add user option of kinetic profiles
756be55
@HarukiST
name of option of kinetic profiles has been changed
30ee20a
@HarukiST
delete options for kinetic profiles
edbe03e
@HarukiST
delete options for kinetic profiles
8574183
@HarukiST
formatted with black
06a8fca
@HarukiST
formatted with black
2707fb6
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4 participants

@bendudson @ZedThree @HarukiST