add function to overwrite several mdu keywords with coastal 2D/3D values

[veenstrajelmer]

Workflow was:

• improve mdu keywords (email FZ/SR 27-6-2024)
• resulted in jupyter notebook code
• manually edited in mdu file later on

Todo:

• discuss values for all settings to be changed from their defaults (two blocks and bullet list below)
• add keywords from 2D block below to modelbuilder notebook
• also temporarily use stretchtype=-1 for 3D models until there is a new hydrolib-core release containing mdu stretchtype should be -1 or 0 instead of 1 HYDROLIB-core#691 (and minimal version is updated in the dfm_tools pyproject.toml)
• consider adding nchisdataprecision and ncmapdataprecision and others, but this will fail for old software versions >> no
• consider adding computedAirdensity, but this will fail for old software versions >> no
• create function to overwrite 3D-specific settings? >> added to notebook instead

The defaults that were changed independent of whether the model is 2D/3D:

mdu.geometry.openboundarytolerance = 0.1
mdu.geometry.bedlevuni = 5
mdu.geometry.dxwuimin2d = 0.1 # improved stability in triangular network cells

mdu.numerics.izbndpos = 1 # boundary points are on network boundary
# mdu.numerics.tlfsmo = 86400. # smoothing can improve stability
mdu.numerics.mintimestepbreak = 0.1 # causes instable model to crash
mdu.numerics.keepstbndonoutflow = 1 # s/t on outflow boundaries, should be new default
mdu.numerics.barocponbnd = 1 # enable baroclinic pressure gradient on open boundaries, should be new default

mdu.physics.rhomean = 1023. # for coastal models
# mdu.physics.tidalforcing = 1 # gravitational tide, for large models
# mdu.physics.itcap = 1 # IT capping, not generic

mdu.wind.icdtyp = 4 # Charnock in case of ERA5
mdu.wind.cdbreakpoints = [0.025] # important if icdtyp=4, but 0.018 or 0.041 might be better. Value is overwritten by spacevarying charnock from ERA5.
mdu.wind.pavbnd = 101330 # for inverse barometer correction, important in case of CMEMS boundary conditions
# mdu.wind.relativewind = 0.5 # use default
# mdu.wind.rhoair = 1.2265 # not generic

The 3D-specific settings are the following:

# z-sigma layer setup
mdu.geometry.kmx = 20
mdu.geometry.layertype = 2 # z-layers
mdu.geometry.numtopsig = 20
mdu.geometry.numtopsiguniform = 1
mdu.geometry.sigmagrowthfactor = 1.19
mdu.geometry.dztop = 5.0
mdu.geometry.floorlevtoplay = -5.0
mdu.geometry.dztopuniabovez = -100.0
mdu.geometry.keepzlayeringatbed = 2

>> instead
mdu.geometry.kmx = 10
mdu.geometry.layertype = 1 # sigma-layers, is default

mdu.numerics.vertadvtypsal = 4 # should be new default (default is 6)
mdu.numerics.vertadvtyptem = 4 # should be new default (default is 6)

# mdu.physics.vicoww = 0.0001 # generic? (default is 1e-6)
# mdu.physics.dicoww = 0.00001 # generic? (default is 1e-6)
# support for initial sal/tem fields via iniwithnudge, this requires 3D model
mdu.physics.iniwithnudge = 2
mdu.physics.salinity = 1
mdu.physics.temperature = 5
mdu.physics.initialsalinity = 30 # generic (default is 0)
# mdu.physics.backgroundsalinity = 30 # generic? (default is 30) >> comment
# mdu.physics.initialtemperature = 5.5 # generic? (default is 6) >> comment
# mdu.physics.backgroundwatertemperature = 20. # generic? (default is 20) >> comment
# mdu.physics.tempmin = -999 >> not generic, comment
# mdu.physics.tempmax = 50. >> not generic, comment
mdu.physics.heat_eachstep = 1
mdu.physics.rhoairrhowater = 1

Some 2D keywords were already updated in #1068.