Presentation by Camille Grimaldi (University of Western Australia, Australia), at the Delft3D User Days, during Delft Software Days - Edition 2022. Monday, 14 November 2022.

1. C. Grimaldi1,2,3, R. Lowe1,2, J. Benthuysen3, M. Cuttler1, R. Green1,2, J. Reyns4,
H. Kernkamp4, J. Gilmour3
Hydrodynamics, connectivity and
thermodynamics of a coral reef atoll
1
3
2
4

2. Reef hydrodynamics
The Guardian
The Guardian
• Circulation patterns regulate
distribution of water and material
(e.g. heat, coral larvae, nutrients)
• Influence on key ecological
processes
Rowley Shoals, Oct. 2018

3. 1. Reef hydrodynamics
2. Reef connectivity
3. Reef thermal variability
Rowley Shoals, WA
Outline

4. Rowley Shoals
Scott Reef
Ashmore Reef
NWS Aus
Mermaid Reef
• Oceanic atoll reef located on
the Northwest Shelf of Aus,
~300 km offshore
• 250 m-wide channel and 15 m
deep central lagoon
• Atoll below mean sea level
Lagoon
Open ocean
Channel
Reef flat Leeward
Windward
2 km
Residual
circulation
MSL
-1.2 m
Channel
Lagoon
Open ocean
Channel
Reef flat Leeward
Windward
2 km
hwest =
-0.7 m

5. 1-year field study (2018)
• Measurements across key reef
locations: reef flat, lagoon, channel
and fore-reef

6. 1-year field study (2018)
• Measurements across key reef
locations: reef flat, lagoon, channel
and fore-reef
• Mean tidal range (TR) = 2.3 m
• Mean significant wave heights (Hs) =
0.9 m, coming from the West
Mermaid reef cross section
Mermaid reef cross section
Water level (m)
Hs (m); Tp (s)
Wave direction (°N)

7. Delft3D FM coupled
wave-flow model
Coupled wave-flow
Flexible Mesh Grid
500-25 m resolution
Bathymetry
LADS (25 m) + Geoscience
Australia (250 m)
Boundary conditions
Tides: TPXO 8.0
Waves and wind: CAWCR (NWW3)
Grimaldi et al., 2022a
(JGR Oceans)
Numerical simulations
DFlow FM
DWaves

8. Windward
Delft3D FM coupled
wave-flow model
Coupled wave-flow
Flexible Mesh Grid
500-25 m resolution
Bathymetry
LADS (25 m) + Geoscience
Australia (250 m)
Boundary conditions
Tides: TPXO 8.0
Waves and wind: CAWCR (NWW3)
Model validation
Lagoon
Channel
Reef
flat
Water levels [m] Tidal velocities [m/s] Subtidal velocities [m/s]
RMSE ~ 0.1 – 0.23 m;
Willmott Skill ~0.98-0.99
RMSE ~ 0.03 – 0.4 m/s;
Willmott Skill ~0.68-0.94
RMSE ~ 0.04 – 0.17 m/s;
Willmott Skill ~0.46-0.81
Grimaldi et al., 2022a
(JGR Oceans)
Numerical simulations

9. Delft3D FM coupled
wave-flow model
Coupled wave-flow
Flexible Mesh Grid
500-25 m resolution
Bathymetry
LADS (25 m) + Geoscience
Australia (250 m)
Boundary conditions
Tides: TPXO 8.0
Waves and wind: CAWCR (NWW3)
Idealized forcing
Grimaldi et al., 2022a
(JGR Oceans)
Numerical simulations
• Wave-only
Hs = 0.5, 1, 1.5, 2, 2.5, 3 m; Dir = 270 ° N
• Tide-only
TR = 0.5, 1 ,1.5, 2, 3, 4 m
• Combined waves and tides

10. Hydrodynamics
Windward
Grimaldi et al., 2022a
(JGR Oceans)
Wave-driven circulation
Residual circulation (over 12.4 hr):
• Waves breaking on the Western Reef flat
• Unidirectional flow to the East
Idealized simulations

11. Windward
Tide-driven circulation
Residual circulation (over 12.4 hr):
• Alternating ebb and flood
• TR = 1 m, residual flow ~0 m2/s
• TR = 3 m, residual flow to the East
Grimaldi et al., 2022a
(JGR Oceans)
• Western reef flat acts as a
physical barrier to flow
Idealized simulations

12. Windward
• 35 idealized simulations
• X: relative importance of hydrodynamic
forcing
• Y: relative importance of nonlinearity
(how net flow from the combined wave
and tide scenarios compares to linear
addition of wave-only and tide-only
conditions)
Grimaldi et al., 2022a
(JGR Oceans)
Idealized simulations

13. TR < 2hwest
(i.e. 1.5 m)
Windward
Wave and tide-driven circulation
• Waves and tide interact nonlinearly
• Western reef flat determines the relative
importance of hydrodynamic forcing
(waves or tides)
1-year field study
• ‘Tide-driven’ for 79% of the time
• ‘Wave-driven’ for the remaining 21%
Grimaldi et al., 2022
(JGR Oceans)
Idealized simulations
TR > 2hwest
(i.e. 1.5 m)

14. 2. Coral reef connectivity

15. Coral reef connectivity
modelling
1. 2D HYDRODYNAMIC MODEL
Wave and tide-driven flows
Down to 30 m resolution
2. PARTICLE TRACKING
~ 9000 ‘virtual larvae’
Released from the reef
+
3. BIOLOGICAL TRAITS
Spawning time, larvae
competency and mortality
+

16. Typical hydrodynamic
conditions during spawning
• When are coral releasing their larvae? 9 nights
after the full moon in March and Oct
• 41 years of waves and tide conditions (1980-2020)
• Stable hydrodynamic conditions apart
from tropical cyclones.
• “Mean release conditions”: starts on neap
tides; constant Hs =1 m

17. Typical hydrodynamic
conditions during spawning
• Connectivity was strongest between
the western to eastern part of the reef
• Maximum of 0.05% on the eastern
reef slope and 0.02% in the lagoon
After 10 days of dispersal

18. Tropical cyclones
• Peak cyclone season during
release
• Tropical cyclones (TC) disturb
“mean” stable conditions
• Generate large wave height
coming from various directions
• 11 cyclones over the 41 years
TC
Vivienne
TC Fay

19. Tropical cyclones
• Change transport pathways within reef (intra-reef connectivity).
• Can also transport larvae further out (inter-reef connectivity).
Probability
difference (%)
TC Fay (1996) TC Vivienne (2004)

20. Importance of fine-
scale processes
30 m, wave and tide-driven flow 5 km, regional currents
• Reef-scale processes act as retention
mechanisms
• Provides an inaccurate description of the
atoll’s connectivity
Imperieuse
Clerke
Mermaid
Imperieuse
Clerke
Mermaid
Spawning
March
2011

21. The Guardian
The Guardian
Coral Reef Watch
Bleached corals (ABC)
3. Reef thermal variability

22. Reef thermal variability
Rowley Shoals, WA
WAVES
TIDES
Atmospheric forcing
Hydrodynamic forcing
Rowley Shoals, WA
𝑑𝑇
𝑑𝑡
=
𝑄𝑁
𝜌 𝑐𝑝ℎ
− 𝑢
𝑑𝑇
𝑑𝑥
𝑻: 𝑇𝑒𝑚𝑝𝑒𝑟𝑎𝑡𝑢𝑟𝑒
𝑸𝑵: 𝑁𝑒𝑡 𝑠𝑜𝑙𝑎𝑟 𝑟𝑎𝑑𝑖𝑎𝑡𝑖𝑜𝑛
𝝆: 𝑤𝑎𝑡𝑒𝑟 𝑑𝑒𝑛𝑠𝑖𝑡𝑦
𝒄𝒑 : 𝑜𝑐𝑒𝑎𝑛 ℎ𝑒𝑎𝑡 𝑐𝑎𝑝𝑎𝑐𝑖𝑡𝑦
𝒉: 𝑤𝑎𝑡𝑒𝑟 𝑙𝑒𝑣𝑒𝑙
𝒖: 𝑣𝑒𝑙𝑜𝑐𝑖𝑡𝑦 𝑖𝑛 𝑡ℎ𝑒 𝑎𝑙𝑜𝑛𝑔𝑠ℎ𝑜𝑟𝑒 𝑑𝑖𝑟𝑒𝑐𝑡𝑖𝑜𝑛
Herdman et al. 2015
Temperature time
rate of change
Air-sea Heat
Fluxes
Advection of
heat
Heat Budget
UK NOC

23. In situ temperature
1-year field study (2018)
SST from GHRSST MUR

24. 𝑑𝑇
𝑑𝑡
=
𝑄𝑁
𝜌 𝑐𝑝ℎ
− 𝑢
𝑑𝑇
𝑑𝑥
Heat Budget
Driver of
temperature varies
between locations
Fore-reef Reef-flat Lagoon
Temperature
time
rate
of
change
Air-sea
Heat
Fluxes
Advective
fluxes
Residual
Channel

25. Relative contribution of the
tide and wave-driven flow
Wave
advection
Tidal
advection
Heat fluxes
Wave-driven
advective flux
𝑑𝑇
𝑑𝑡
=
𝑄𝑁
𝜌 𝑐𝑝ℎ
− 𝑢
𝑑𝑇
𝑑𝑥
𝑑ത
𝑇
𝑑𝑡
=
𝑄𝑁
𝜌 𝑐𝑝ℎ
− ത
𝑢
𝑑ത
𝑇
𝑑𝑥
− 𝑢′
𝑑𝑇′
𝑑𝑥
Tide-driven
advective flux
Fore-reef
Reef-flat
Lagoon
Expect tidal advection to dominate
Rogers et al., 2016

26. SST corrections
• Obtaining in situ temperature
measurements from reefs can be
logistically difficult
• Developing corrections for SST
measurements (e.g., downscaling
methods) is vital
ΔTSST = Tin situ – SSToffshore

27. SST corrections
• Air−sea heat flux term play a key
role in modulating temperature
variability across the reef flat and
lagoon sites
• Does the air−sea heat flux drive the
differences in temperatures between
the reef and offshore waters (ΔTSST)?

28. SST corrections
(R= 0.76) (R= 0.41)
• Air−sea heat flux term play a key
role in modulating temperature
variability across the reef flat and
lagoon sites
• Does the air−sea heat flux drive the
differences in temperatures between
the reef and offshore waters (ΔTSST)?
𝛥𝑇𝑆𝑆𝑇 = 𝑎
𝑄𝑁
ℎ𝜌𝑐𝑝
+ 𝑏

29. Windward
𝑆𝑆𝑇corrected = 𝑆𝑆𝑇𝑜𝑓𝑓𝑠ℎ𝑜𝑟𝑒 + ∆𝑇𝑆𝑆𝑇
• Reef flat:
RMSD= 0.76 → 0.37 °C
• Lagoon:
RMSD= 0.68 → 0.31°C
SST corrections

30. Rowley Shoals, WA
camille.grimaldi@uwa.edu.au
Hydrodynamics, connectivity and
thermodynamics of a coral reef atoll