Presentation by Ingrid Holzwarth (BAW) at the Delft3D User Days, during Delft Software Days 2016. Thursday 3 November 2016, Delft.

1. Delft3D User Meeting
Delft, 03 November 2016
Ingrid Holzwarth
Levin Nickelsen
Untrim2 and D-Water Quality for estuarine
biogeochemical modeling
An example from the Elbe (Germany)
Image: Extract of nautical chart ‘Nordsee‘ (2011)
Bundesamt für Seeschifffahrt und Hydrographie
Delft

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Motivation: estuarine management
06-09-2016
Untrim2 and D-Water Quality| Ingrid Holzwarth & Levin Nickelsen| D3D User Meeting 03-Nov-2016
Page 2
YearYear
mio m3
Development of the amount of maintenance dredging in the Elbe Estuary
Diagram: Water and Shipping Administration (WSV), modified. Download https://www.portaltideelbe.de
2010 2011
End of winter
Early May
Late June
Early August
Begin of winter
Measurements from FGG Elbe (www.fgg-elbe.de, download on
30/11/2013)
Interdependencies
and
Restrictions
?

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Mid-term:
 Integration of ecological restrictions on sediment management and
estuarine development
Long-term
 Feedback between abiotic and biotic processes for a more realistic
simulation of estuarine sediment transport
Motivation for model development
06-09-2016
Untrim2 and D-Water Quality| Ingrid Holzwarth & Levin Nickelsen| D3D User Meeting 03-Nov-2016
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Untrim2
… produces input files for D-Water Quality
06-09-2016
Untrim2 and D-Water Quality| Ingrid Holzwarth & Levin Nickelsen| D3D User Meeting 03-Nov-2016
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Untrim2 (CASULLI & STELLING)
computational grid with subgrid bathymetry
Hydrodynamics
Conservative transport
(salt, water temperature, SPMi)
D-WAQ input files
WAQ.utromp2009.vol
WAQ.utromp2009.dat
WAQ.utromp2009.hyd
WAQ.utromp2009.are
WAQ.utromp2009.flo
WAQ.utromp2009.poi
WAQ.utromp2009.srf
WAQ.utromp2009.are
WAQ.utromp2009.vdf
WAQ.utromp2009.atr
WAQ.utromp2009.nc
WAQ.utromp2009.sal
WAQ.utromp2009.tem
WAQ.utromp2009.ssc
Casulli, V. and Stelling, G. S. (2010) Semi-implicit subgrid modelling of three-dimensional free-surface flows,
Int. J. Numer. Meth. Fluids, 67

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Untrim2 and D-Water Quality
06-09-2016
Untrim2 and D-Water Quality| Ingrid Holzwarth & Levin Nickelsen| D3D User Meeting 03-Nov-2016
Page 5
Source: BAW 2016, file Untrim_DWAQ_dataflow.png

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Uniform post-processing
based on UGRID CF NetCDF files
06-09-2016
Untrim2 and D-Water Quality| Ingrid Holzwarth & Levin Nickelsen| D3D User Meeting 03-Nov-2016
Page 6
Source:GüntherLang(2016)Uniformpost-processingofcomputationalresultsbased
onUGRIDCFNetCDFfiles.
Downloadhttps://www.researchgate.net/publication/303822983_Uniform_post-
processing_of_computational_results_based_on_UGRID_CF_NetCDF_files
DOI:10.13140/RG.2.1.5059.8000

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Uniformly post-processed files
06-09-2016
Untrim2 and D-Water Quality| Ingrid Holzwarth & Levin Nickelsen| D3D User Meeting 03-Nov-2016
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Hydrodynamic key figure:
mean tidal range [m]
Period of high oxygen concentration [d]
WQ key figure:
Time period exceeding an O2-threshold [d]

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Basic study on relevant estuarine processes
Idealized estuary geometry: funnel shape with 1D-x resolution.
Background: topography of the Elbe estuary (as used in: Sehili, A., Lang, G., and Lippert, C. (2014): High-resolution
subgrid models: background, grid generation, and implementation, Ocean Dynamics, 64, 519–535, doi:10.1007/s10236-014-0693-x)
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Untrim2 and D-Water Quality| Ingrid Holzwarth & Levin Nickelsen| D3D User Meeting 03-Nov-2016
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D-Water Quality
Biogeochemical configuration
06-09-2016
Untrim2 and D-Water Quality| Ingrid Holzwarth & Levin Nickelsen| D3D User Meeting 03-Nov-2016
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Model skill:
Dissolved oxygen concentrations at specific positions
S1 (Bunthaus):
directly upstream of
the Port of Hamburg
S2 (Seemannshöft):
in the Port area
Measurements provided by: Institut
fuer Hygiene und Umwelt; licence:
dl-de/by-2-0 (www.govdata.de/dl-
de/by-2-0);
www.wgmn.hamburg.de
06-09-2016
Untrim2 and D-Water Quality| Ingrid Holzwarth & Levin Nickelsen| D3D User Meeting 03-Nov-2016
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Model skill:
Longitudinal (helicopter) transects
06-09-2016
Untrim2 and D-Water Quality| Ingrid Holzwarth & Levin Nickelsen| D3D User Meeting 03-Nov-2016
Page 11
Measurements
from FGG Elbe
(www.fgg-elbe.de,
download on
30/11/2013)
Profiling on 06 Aug 2013
Picture: Ingrid Holzwarth

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Model skill:
Longitudinal (helicopter) transects
06-09-2016
Untrim2 and D-Water Quality| Ingrid Holzwarth & Levin Nickelsen| D3D User Meeting 03-Nov-2016
Page 12
Measurements
from FGG Elbe
(www.fgg-elbe.de,
download on
30/11/2013)

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Sensitivity study
06-09-2016
Untrim2 and D-Water Quality| Ingrid Holzwarth & Levin Nickelsen| D3D User Meeting 03-Nov-2016
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max growth rate (d-1) mortality (d-1)
nitrification (mmol m-3 d-1) mineralization POC1 (d-1) mineralization DOC (d-1)
Dependency of
the absolute DO
minimum on
several model
parameters.
Grey area
indicates
common range
found in
literature.
our value

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Sensitivity study
06-09-2016
Untrim2 and D-Water Quality| Ingrid Holzwarth & Levin Nickelsen| D3D User Meeting 03-Nov-2016
Page 14
max growth rate (d-1) mortality (d-1)
nitrification (mmol m-3 d-1) mineralization POC1 (d-1) mineralization DOC (d-1)
Dependency of
the absolute DO
minimum on
several model
parameters.
Grey area
indicates
common range
found in
literature.
our value

15. www.baw.de
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Mass balance output: DO fluxes per process
06-09-2016
Untrim2 and D-Water Quality| Ingrid Holzwarth & Levin Nickelsen| D3D User Meeting 03-Nov-2016
Page 15
2011 Primary
production
Mineralization Nitrification Reaeration Sum of all
Jan/Feb 0.1 -5.8 -0.2 40.0 48.5
Mar/Apr 5.7 -24.3 -4.0 0.7 -11.2
May/Jun 16.7 -66.3 -15.4 25.7 -34.1
Jul/Aug 9.5 -67.1 -10.7 28.4 -35.7
Sep/Oct 1.6 -40.4 -6.3 25.9 -18.3
Nov/Dec 0.1 -11.7 -2.6 8.0 -2.7
Table: Mean volumetric DO fluxes in the freshwater zone between km-0 and km-120 in mmol m-3 d-1.
Sum of all contains all process fluxes and transport-related DO exchanges.

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Longitudinal development of DO fluxes
06-09-2016
Untrim2 and D-Water Quality| Ingrid Holzwarth & Levin Nickelsen| D3D User Meeting 03-Nov-2016
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Daily oxygen fluxes
per surface area.
’Sum of all’ also
includes advection
fluxes which are not
depicted in the plots.

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Summary
06-09-2016
Untrim2 and D-Water Quality| Ingrid Holzwarth & Levin Nickelsen| D3D User Meeting 03-Nov-2016
Page 17
Technical environment
 Flexible model combination Untrim2 and D-Water Quality
 Uniform post-processing based on UGRID CF NetCDF
Large-scale situation
 Dominance of heterotrophic processes in the Elbe Estuary
 Riverine load controls the estuarine freshwater system
Upcoming work
 Transfer to realistic 3D model
 Integration of salt sensitivity and (bottom) sediment processes

18. Ingrid.Holzwarth@baw.de
Bundesanstalt für Wasserbau
22559 Hamburg, Germany
www.baw.de
Thank you for your attention

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Additional material
Temporal aggregation for D-WAQ output
06-09-2016
Untrim2 and D-Water Quality| Ingrid Holzwarth & Levin Nickelsen| D3D User Meeting 03-Nov-2016
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WQ integration time step mΔt
n
N+1
n+m
N
UnTRIM2 time step Δtn+1
V
n
V
n+m
Qh
n+θ
Qh
n+1+θ
…
… Qh
n+m-1+θ





1
0
WQ
QQ
m
l
ln
hh t 
Modified from: Günther Lang, UUM 2012, p.12, “Horizontal and Vertical Fluxes from UnTRIM2 Results”