Add mdu keywords (not listed in appendix A of the manual)

[tim-vd-aardweg]

Is your feature request related to a problem? Please describe.
In #571 we have added keywords that were listed in the DHYDRO manual. A lot more keywords were requested to be added. We have decided to create a separate issue for those keywords that are not listed in the manual, since these keywords first have to be verified by the kernel developers.

Describe the solution you'd like

• Determine whether the keywords listed below are correct, have the correct type/default value/description.
• Add these keywords to HYDROLIB-core.

Describe alternatives you've considered
We have considered setting the Extra.allow but decided against this, as this removes some of HYDROLIB-core's features: type safety, validation and user-friendliness.

Keywords to be checked and added

Section	Keyword	Type	Default	Description
general	modelspecific	Optional[str]	None	Optional 'model specific ID', to enable certain custom runtime function calls (instead of via MDU name).
general	inputspecific	bool	False	Use of hardcoded specific inputs, shall not be used by users (0: no, 1: yes).
geometry	toplayminthick	float	1.e-2	Minimum top layer thickness(m), only for Z-layers.
geometry	helmert	boolean	False	Use Helmert (0: no, 1: yes).
geometry	waterdepthini1d	float	-999.0	Initial waterdepth in 1D.
geometry	zlayeratubybob	int	0	Lowest connected cells governed by bob instead of by bL L/R.
geometry	shipdeffile	Optional[DiskOnlyFileModel]	None	File *.shd containing ship definitions.
geometry	stripmesh	bool	False	Strip unused nodes and links from the mesh after clipping (1: strip, 0: do not strip).
geometry	bedwavelength	float	0.0	Bed testcases.
geometry	removesmalllinkstrsh	float	0.1	0-1, 0= no removes.
geometry	createlinks1d2d	bool	False	Ruecksichtslos create links between 1D nodes and 2D cells when initializing model (1: yes, 0: no).
geometry	bedwaveamplitude	float	0.0	Bed testcases.
geometry	uniformhu	float	-999.0	Waterdepth in rigid-lid-like solution.
geometry	tsigma	float	100.0	Sigma Adaptation period for Layertype==4 (s).
geometry	dpuopt	int	1	Bed level interpolation at velocity point in case of tile approach bed level: 1 = max (default); 2 = mean.
geometry	ihuzcsig	int	3	???
geometry	ihuz	int	4	???
geometry	cosphiutrsh	float	0.5	0-1, 1= no bad orthos.
geometry	cutcelllist	Optional[DiskOnlyFileModel]	None	File with names of cutcell polygons, e.g. cutcellpolygons.lst.
geometry	uniformtyp1d	int	3	Uniform type for channel profiles not specified by profloc.
geometry	oned2dinternallinktype	int	1	Link treatment method for type-3 internal links.
geometry	orgfloorlevtoplaydef	bool	False	Keep original definition of Floor level of top layer.
geometry	pipefile	Optional[PolyFile]	None	File *.pliz containing pipe-based 'culverts'.
geometry	groundlayerthickness	float	-999.0	Only in pipes: groundlayer thickness (m).
numerics	faclaxturb	float	0.0	Default: 0=TurKin0 from links, 1.0=from nodes. 0.5=fityfifty.
numerics	jafaclaxturbtyp	int	0	Vertical distr of facLaxturb, 1=: (sigm<0.5=0.0 sigm>0.75=1.0 linear in between), 2:=1.0 for whole column.
numerics	locsaltmin	float	5.0	Minimum salinity for case of lock exchange.
numerics	lincontin	int	0	Default 0; Set to 1 for linearizing d(Hu)/dx; link to AdvecType.
numerics	cfexphormom	float	1.0	Exponent for including (1-CFL) in HO term horizontal mom.
numerics	jbasqbnddownwindhs	int	0	Water depth scheme at discharge boundaries (0: original hu, 1: downwind hs).
numerics	coriohhtrsh	float	0.0	0=default=no safety in hu/hus weightings, only for Newcorio=1.
numerics	limtypw	int	4	Limiter type for wave action transport (0: none, 1: minmod, 2: van Leer, 3: Koren, 4: monotone central).
numerics	huweirregular	float	0.0	For villemonte and Tabellenboek, regular hu below Huweirregular.
numerics	structurelayersactive	int	1	0=structure flow through all layers, 1=structure flow only through open layers.
numerics	corioadamsbashfordfac	float	0.5	0=No, 0.5d0=AdamsBashford, only for Newcorio=1.
numerics	vertadvtypsal	int	6	Vertical advection type for salinity (0: none, 1: upwind explicit, 2: central explicit, 3: upwind implicit, 4: central implicit, 5: central implicit but upwind for neg. stratif., 6: higher order explicit, no Forester).
numerics	baorgfracmin	float	0.0	Cell area = max(orgcellarea*Baorgfracmin, cutcell area)
numerics	epstke	float	1.e-32	TKE=max(TKE, EpsTKE), default=1d-32
numerics	jadrhodz	int	1	1:central org, 2:centralnew, 3:upw cell, 4:most stratf. cell, 5:least stratf. cell.
numerics	logprofkepsbndin	int	0	Inflow: 0=0 keps, 1 = log keps inflow, 2 = log keps in and outflow.
numerics	epshstem	float	1.e-3	Only compute heatflx + evap if depth > epshstem.
numerics	newcorio	bool	True	0=prior to 27-11-2019, 1=no normal forcing on open bnds, plus 12 variants.
numerics	diffusiononbnd	bool	True	On open boundaries, 0 switches off horizontal diffusion Default = 1.
numerics	barrieradvection	int	1	1 = no correction, 2 = advection correction.
numerics	rhointerfaces	int	0	Evaluate rho at interfaces, 0=org at centers, 1=at interfaces.
numerics	logprofatubndin	int	1	ubnds inflow: 0=uniform U1, 1 = log U1, 2 = user3D.
numerics	horadvtypzlayer	int	1	Horizontal advection treatment of z-layers (1: default, 2: sigma-like).
numerics	chkdifd	float	1.e-2	Check diffusion terms if depth < chkdifd, only if jatransportautotimestepdiff==1.
numerics	lateral_fixedweir_umin	float	0.0	Minimal velocity treshold for weir losses in iterative lateral 1d2d weir coupling.
numerics	fixedweirfrictscheme	int	0	Fixed weir friction scheme (0: friction based on hu, 1: friction based on subgrid weir friction scheme).
numerics	icoriolistype	int	5	0=No, 5=default, 3, 4 no weights, 5-10 Kleptsova hu/hs, 25-30 Ham hs/hu, odd: 2D hs/hu, even: hsk/huk.
numerics	zwsbtol	float	0.0	Tolerance for zws(kb-1) at bed.
numerics	cfexphu	float	1.0	Exp for including (1-CFL) in sethu.
numerics	drop3d	float	1.0	Apply droplosses in 3D if z upwind below bob + 2/3 hu*drop3D.
numerics	zlayercenterbedvel	int	1	Reconstruction of center velocity at half closed bedcells (0=no, 1: copy bed link velocities).
numerics	cffacver	float	0.0	Factor for including (1-CFL) in HO term vertical (0d0: no, 1d0: yes).
numerics	eddyviscositybedfacmax	float	0.0	Limit eddy viscosity at bed.
numerics	epseps	float	1.e-32	EPS=max(EPS, EpsEPS), default=1d-32, (or TAU).
numerics	lateral_fixedweir_umin _method	int	0	Method for minimal velocity treshold for weir losses in iterative lateral 1d2d weir coupling.
numerics	lateral_fixedweir _minimal_1d2d_embankment	float	0.0	Minimal crest height of 1D2D SOBEK-DFM embankments.
numerics	testfixedweirs	int	0	Test for fixed weir algoritms (0 = Sieben2010, 1 = Sieben2007 ).
numerics	jposhchk	int	2	Check for positive waterdepth (0: no, 1: 0.7dts, just redo, 2: 1.0dts, close all links, 3: 0.7dts, close all links, 4: 1.0dts, reduce au, 5: 0.7dts, reduce au, 6: 1.0dts, close outflowing links, 7: 0.7*dts, close outflowing link.
numerics	cfconhormom	float	0.0	Constant for including (1-CFL) in HO term horizontal mom.
numerics	cffachormom	float	1.0	Factor for including (1-CFL) in HO term horizontal mom (0d0: no, 1d0: yes).
numerics	trsh_u1lb	float	0.0	2D bedfriction in 3D below this threshold (m).
numerics	corioconstant	int	0	0=default, 1=Coriolis constant in sferic models anyway, 2=beta plane, both in cart. and spher. coord.
numerics	jaupwindsrc	int	1	1st-order upwind advection at sources/sinks (1) or higher-order (0).
numerics	locsaltlev	float	1.0	Salinity level for case of lock exchange.
numerics	subsuplupdates1	bool	False	Update water levels (S1) due to subsidence / uplift.
numerics	linkdriedmx	int	0	Nr of Au reduction steps after having dried.
numerics	maxitpresdens	int	1	Max nr of iterations in pressure-density coupling, only used if idensform > 10.
numerics	lateral_fixedweir_relax	float	0.1	Relaxation factor for iterative lateral 1d2d weir coupling algorithm.
numerics	numlimdt_baorg	int	0	If previous numlimdt > Numlimdt_baorg keep original cell area ba in cutcell.
numerics	locsaltmax	float	10.0	Maximum salinity for case of lock exchange.
numerics	cffachu	float	1.0	Factor for including (1-CFL) in sethu (0d0: no, 1d0: yes).
numerics	jasfer3d	bool	True	Corrections for spherical coordinates.
physics	surftempsmofac	float	0.0	Hor. Smoothing factor for surface water in heatflx comp. (0.0-1.0), 0=no.
physics	selfattractionloading _correct_wl_with_ini	bool	False	Correct water level with initial water level in Self attraction and loading (0=no, 1=yes).
physics	nfentrainmentmomentum	bool	False	1: Switch on momentum transfer in NearField related entrainment.
physics	uniffrictcoef1d2d	float	2.3e-2	Uniform friction coefficient in 1D links (0: no friction).
physics	equili	bool	False	Equilibrium spiral flow intensity (0: no, 1: yes).
physics	allowcoolingbelowzero	bool	False	0 = no, 1 = yes.
physics	soiltempthick	float	0.0	Use soil temperature buffer if > 0
physics	selfattractionloading	int	0	Self attraction and loading (0=no, 1=yes, 2=only self attraction).
sediment	mxgrkrone	int	0	Highest fraction index treated by Krone.
sediment	seddenscoupling	bool	False	Sed rho coupling (0=no, 1=yes).
sediment	implicitfallvelocity	int	1	1=Impl., 0 = Expl.
sediment	nr_of_sedfractions	int	0	Nr of sediment fractions, (specify the next parameters for each fraction).
wind	windhuorzwsbased	int	1	Wind hu or zws based, 0 = hu, 1 = zws.
wind	varyingairdensity	bool	False	Compute air density yes/no (), 1/0, default 0.
waves	waveswartdelwaq	bool	False	If WaveSwartDelwaq == 1 .and. Tiwaq > 0 then increase tauwave to Delwaq with 0.5rhofwuorbuorb.
waves	hwavuni	float	0.0	Root mean square wave height (m).
waves	tifetchcomp	float	0.0	Time interval fetch comp (s) in wavemodel 1, 2.
waves	phiwavuni	float	0.0	Root mean square wave direction, (deg), math convention.
waves	threedwavestreaming	int	0	Influence of wave streaming. 0: no, 1: added to adve.
waves	threedwaveboundarylayer	int	1	Boundary layer formulation. 1: Sana.
waves	twavuni	float	0.0	Root mean square wave period (s).
waves	uorbfac	int	0	Orbital velocities: 0=D3D style; 1=Guza style.
waves	threedstokesprofile	int	1	Stokes profile. 0: no, 1:uniform over depth, 2: 2nd order Stokes theory; 3: 2, with vertical stokes gradient in adve.
waves	jamapsigwav	int	0	1: sign wave height on map output; 0: hrms wave height on map output. Default=0 (legacy behaviour).
waves	hminlw	float	0.2	Cut-off depth for application of wave forces in momentum balance.
waves	jahissigwav	int	1	Sign wave height on his output; 0: hrms wave height on his output. Default=1.
time	timestepanalysis	int	0	0=no, 1=see file *.steps.
time	autotimestepvisc	bool	False	0 = no, 1 = yes (Time limitation based on explicit diffusive term).
time	dtfacmax	float	1.1	Max timestep increase factor ( ).
restart	rstignorebl	bool	False	Flag indicating whether bed level from restart should be ignored (0=no (default), 1=yes).
trachytopes	trtmth	int	1	Area averaging method, (1=Nikuradse k based, 2=Chezy C based (parallel and serial)).
trachytopes	trtmnh	float	0.1	Minimum water depth for roughness computations.
trachytopes	trtcll	Optional[DiskOnlyFileModel]	None	Calibration factor file for roughness from trachytopes (see also [calibration] block).
output	mbalumpsourcesinks	bool	False	Lump MBA source/sink mass balance terms (1: yes, 0: no).
output	wrimap_nearfield	bool	False	Write near field parameters (1: yes, 0: no).
output	velocitymagnitudeclasses	Optional[List[str]]	None	Class map's list of class values for velocity magnitudes.
output	writedfminterpretedvalues	bool	False	Write DFMinterpretedvalues (1: yes, 0: no).
output	deleteobspointsoutsidegrid	bool	False	0 - do not delete, 1 - delete.
output	mbalumpboundaries	bool	False	Lump MBA boundary mass balance terms (1: yes, 0: no).
output	writepart_domain	bool	True	Write partition domain info. for postprocessing.
output	waqhoraggr	Optional[DiskOnlyFileModel]	None	DELWAQ output horizontal aggregation file (*.dwq).
output	writedetailedtimers	bool	False	Write detailed timers output file (1: yes, 0: no).
output	metadatafile	Optional[DiskOnlyFileModel]	None	???
output	mbainterval	float	0.0	Mass balance area output interval (s).
output	velocitydirectionclassesinterval	Optional[int]	None	Class map's step size of class values for velocity direction.
output	wrirst_bnd	bool	True	Write waterlevel
output	generateuuid	bool	True	Generate UUID as unique dataset identifier and include in output NetCDF files.
output	timesplitinterval	str	0 s	Time splitting interval, after which a new output file is started. value+unit, e.g. '1 M', valid units: Y,M,D,h,m,s.
output	rugfile	Optional[PolyFile]	None	Polyline file *_rug.pli defining runup gauges.
output	mbawritecsv	bool	False	Write mass balance area output to a csv-file (1: yes, 0: no).
output	mbalumpfromtomba	bool	False	Lump MBA from/to other areas mass balance terms (1: yes, 0: no).
output	mbalumpprocesses	bool	False	Lump MBA processes mass balance terms (1: yes, 0: no).
output	waqvertaggr	Optional[DiskOnlyFileModel]	None	DELWAQ output vertical aggregation file (*.vag).
processes	substancedensitycoupling	bool	False	Substance rho coupling (0=no, 1=yes).

[tim-vd-aardweg]

Found a couple more keywords that are not yet in HYDROLIB-core:

Keywords to be checked and added

Section	Keyword	Type	Default	Description
Numerics	Vertadvtypmom3onbnd	int	0	vert. adv. u1 bnd UpwimpL: 0=follow javau , 1 = on bnd, 2= on and near bnd.
Physics	PrandtlNumberTemperature	float	0.7	Turbulent Prandtl number for temperature.
Physics	SchmidtNumberSalinity	float	0.7	Turbulent Schmidt number for salinity.
Physics	SchmidtNumberTracer	float	1.0	Turbulent Schmidt number for tracer(s).
Physics	Umodlin	float	0.0	Linear friction umod, for ifrctyp=4,5,6.
Physics	UnifFrictCoef1DgrLay	float	5.d-2	Uniform ground layer friction coefficient for ocean models (m/s) (0: no friction).
Wind	Wind_eachstep	int	0	1=wind (and air pressure) each computational timestep, 0=wind (and air pressure) each usertimestep.
Time	TStartTlfsmo	float	0.0	Start time of smoothing of boundary conditions (Tlfsmo) w.r.t. RefDate (in TUnit).
Geometry	ExtrBl	bool	False	Extrapolation of bed level at boundaries according to the slope: 0 = no extrapolation (default); 1 = extrapolate.
Output	MbaWriteNetCDF	bool	False	Write mass balance area output to a netCDF-file (1: yes, 0: no).
Output	MbaWriteTxt	bool	True	Write mass balance area output to a txt-file (1: yes, 0: no).
Output	NcCompression	bool	False	Whether or not (1/0) to apply compression to NetCDF output files - NOTE: only works when NcFormat = 4.
Output	Wrimap_ice	bool	False	Write output to map file for ice cover, 0=no (default), 1=yes.
Output	Wrimap_trachytopes	bool	True	Write trachytope roughnesses to map file (1: yes, 0: no).