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Simulating vegetation effects on flows in 3D using an unstructured grid model: model development and validation

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Abstract

Prevalence of vegetation (either submerged or emergent) in shallow water significantly affects the flow and turbulence structure in this environment. In this paper, we develop a new 3D unstructured grid hydrostatic model that accounts for the 3D effects of vegetation on flows. The model uses a semi-implicit time stepping method and treats the new vegetation-related terms implicitly to enhance numerical stability, so the time step does not need to be reduced as compared with the no-vegetation cases. The stability is also independent of the vegetation parameters, so as to efficiently account for large shear that can occur around the canopy. We validate the model using lab data before applying it to a field study in San Francisco Bay-Delta to illustrate the influence of the vegetation on the flow structure as well as tidal energetics. The efficiency of the model enabled by the implicit method allows, for the first time, the simulation of the vegetation effects during multi-year evolution of vegetation in full three dimensions at large spatial scales.

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References

  • Ateljevich E, Nam K, Zhang Y, Wang R, Shu Q (2014) “Bay-Delta SELFE calibration overview.” In: Methodology for flow and salinity estimates in the Sacramento-San Joaquin delta and Suisun Marsh. 35th Annual Progress Report to the State Water Resources Control Board. Chapter 7. Sacramento (CA): Bay-Delta Office. Delta Modeling Section. California Department of Water Resources

  • Azevedo A, Oliveira A, Fortunato AB, Zhang Y, Baptista AM (2014) A cross-scale numerical modeling system for management support of oil spill accidents. Mar Pollut Bull 80:132–147

    Article  Google Scholar 

  • Bennett S, Pirim T, Barkdoll B (2002) Using simulated emergent vegetation to alter stream flow direction within a straight experimental channel. Geomorphology 44:115–126

    Article  Google Scholar 

  • Bertin X, Bruneau N, Breilh J-F, Fortunato AB, Karpytchev M (2012) Importance of wave age and resonance in storm surges: the case Xynthia, Bay of Biscay. Ocean Model 42:16–30

    Article  Google Scholar 

  • Beudin A, Kalra TS, Ganju NK, Warner JC (2017a) Development of a coupled wave-flow-vegetation interaction model. Comput Geosci 100:76–86. https://doi.org/10.1016/j.cageo.2016.12.010

    Article  Google Scholar 

  • Beudin A, Ganju NK, Defne Z, Aretxabaleta AL (2017b) Physical response of a back-barrier estuary to a post-tropical cyclone. J Geophys Res Oceans 122:5888–5904. https://doi.org/10.1002/2016JC012344

    Article  Google Scholar 

  • Brookes A, Shields FD (1996) River channel restoration: guiding principles for sustainable projects. Wiley, Chichester

    Google Scholar 

  • Brovchenko I, Maderich V, Terletska K (2011) Numerical simulations of 3D structure of currents in the region of deep canyons on the east coast of the Black Sea. Int J Comput Civ Struct Eng 7(2):47–53

    Google Scholar 

  • Burla M, Baptista AM, Zhang Y, Frolov S (2010) Seasonal and interannual variability of the Columbia River plume: a perspective enabled by multiyear simulation databases. J Geophys Res 115:C00B16

    Article  Google Scholar 

  • Cai X (2018) Impact of submerged aquatic vegetation on water quality in cache slough complex, Sacramento-San Joaquin delta: a numerical modeling study. MSc Thesis, Virginia Institute of Marine Science

  • Camporeale C, Perucca E, Ridolfi L, Gurnell AM (2013) Modeling the interactions between river morphodynamics and riparian vegetation. Rev Geophys 51:379–414. https://doi.org/10.1002/rog.20014

    Article  Google Scholar 

  • Castagno KA, Jiménez-Robles AM, Donnelly JP, Wiberg PL, Fenster MS, Fagherazzi S (2018) Intense storms increase the stability of tidal bays. Geophys Res Lett:1–10. https://doi.org/10.1029/2018GL078208

    Article  Google Scholar 

  • Casulli V, Cattani E (1994) Stability, accuracy and efficiency of a semiimplicit method for 3D shallow water flow. Comput Math Appl 27:99–112

    Article  Google Scholar 

  • Cho HJ, Kirui P, Natarajan H (2008) Test of multi-spectral vegetation index for floating and canopy-forming submerged vegetation. Int. J. Environ. Res. Public Health 5:477–483

    Google Scholar 

  • D’Alpaos A, Lanzoni S, Marani M, Rinaldo A (2007) Landscape evolution in tidal embayments: modeling the interplay of erosion, sedimentation, and vegetation dynamics. J Geophys Res 112. https://doi.org/10.1029/2006JF000537

  • Da Paz A, Villanueva A, Schettini E (2005) The influence of spatial vegetation distribution on Taim Wetland hydrodynamics. Dyn Biogeochem River Corridors Wetland, IAHS-AISH Publication, 78–85

  • Deleersnijder E, Campin JM, Delhez EJM (2001) The concept of age in marine modeling, I. Theory and preliminary model results. J Mar Syst 28:229e267

    Article  Google Scholar 

  • Dijkstra JT, Uittenbogaard RE (2010) Modeling the interaction between flow and highly flexible aquatic vegetation. Water Resour Res 46:1–14. https://doi.org/10.1029/2010WR009246

    Article  Google Scholar 

  • Fischer-Antze T, Stoesser T, Bates P, Olsen NRB (2001) 3D numerical modelling of open-channel flow with submerged vegetation. J Hydraul Res 39:303–310. https://doi.org/10.1080/00221680109499833

    Article  Google Scholar 

  • Gandhi GM, Parthiban S, Thummalu N, Christy A (2015) NDVI: vegetation change detection using remote sensing and Gis – a case study of Vellore District. Proc Comput Sci 57:1199–1210. https://doi.org/10.1016/j.procs.2015.07.415

    Article  Google Scholar 

  • Gaylord B, Denny M, Koehl M (2003) Modulation of wave forces on kelp canopies by alongshore currents. Limnol Oceanogr 48:860–871

    Article  Google Scholar 

  • Gaylord B, Denny M, Koehl M (2008) Flow forces on seaweeds: field evidence for roles of wave impingement and organism inertia. Biol Bull 215:295–308

    Article  Google Scholar 

  • Gedan KB, Kirwan M, Wolanski E, Barbier EB, Silliman BR (2011) The present and future role of coastal wetland vegetation in protecting shorelines: answering recent challenges to the paradigm. Climate Change 106:7–29

    Article  Google Scholar 

  • Ghisalberti M, Nepf HM (2002) Mixing layers and coherent structures in vegetated aquatic flows. J Geophys Res 107(C2). https://doi.org/10.1029/2001JC000871

  • Hestir EL, Khanna S, Andrew ME, Santos MJ, Viers JH, Greenberg JA, Rajapakse SS, Ustin SL (2008) Identification of invasive vegetation using hyperspectral remote sensing in the California Delta ecosystem. Remote Sens Environ 112:4034–4047

    Article  Google Scholar 

  • Horstman E, Dohmen-Janssen C, Narra P, van den Berg N, Siemerink M, Hulscher S (2014) Wave attenuation in mangroves: a quantitative approach to field observations. Coast Eng 94:47–62

    Article  Google Scholar 

  • Jin KR, Ji Z, Thomas JR (2007) Three-dimensional water quality and SAV modeling of a large shallow lake. J Great Lakes Res 33:28–45

    Article  Google Scholar 

  • Khanna S, Santos MJ, Ustin SL, Haverkamp PJ (2011) An integrated approach to a biophysiologically based classification of floating aquatic macrophytes. Int J Remote Sens 32:1067–1094

    Article  Google Scholar 

  • Kiss M, Jozsa J (2014) Measurement-based hydrodynamic characterisation of reed – open water interface zones in shallow lake environment. Per Pol Civil Eng 58:229–241

    Article  Google Scholar 

  • Knutson PL, Brochu RA, Seelig WN, Inskeep MR (1982) Wave damping in Spartina alterniflora marshes. Wetlands 2(1):87–104

    Article  Google Scholar 

  • Kombiadou K, Ganthy F, Verney R, Plus M, Sottolichio A (2014) Modelling the effects of Zostera noltei meadows on sediment dynamics: application to the Arcachon lagoon. Ocean Dyn 64(10):1499–1516

    Article  Google Scholar 

  • Lapetina A, Sheng YP (2014) Three-dimensional modeling of storm surge and inundation including the effects of coastal vegetation. Estuar Coasts 37:1028–1040

    Article  Google Scholar 

  • Lera S, Nardin W, Sanford L, Palinkas C, Guercio R (2019) The impact of submersed aquatic vegetation on the development of river mouth bars. Earth Surf Process Landf 44:1494–1506. https://doi.org/10.1002/esp.4585

    Article  Google Scholar 

  • Li CW, Xie JF (2011) Numerical modeling of free surface flow over submerged and highly flexible vegetation. Adv. Water Resource 34:468–477. https://doi.org/10.1016/j.advwatres.2011.01.002

    Article  Google Scholar 

  • Li CW, Yan K (2007) Numerical investigation of wave–current–vegetation interaction. J Hydraul Eng 133:794–803. https://doi.org/10.1061/(ASCE)0733-9429(2007)133:7(794)

    Article  Google Scholar 

  • Lopez F, García M (2001) Mean flow and turbulence structure of open-channel flow through non-emergent vegetation. J Hydraul Eng:392–402

    Article  Google Scholar 

  • Lowe RJ, Koseff JR, Monismith SG (2005) Oscillatory flow through submerged canopies: 1. Velocity structure J Geophys Res 110:C10016. https://doi.org/10.1029/2004JC002788

    Article  Google Scholar 

  • Lucas LV, Stewart AR (2005) Transport, transformation and effects of selenium and carbon in the delta of the Sacramento-San Joaquin Rivers: implications for ecosystem restoration. Final Reprt. Project No. ERP-01-C07. California Bay Delta Authority, Sacramento

    Google Scholar 

  • Luhar M, Nepf HM (2011) Flow induced reconfiguration of buoyant and flexible aquatic vegetation. Limnol Oceanogr 56. https://doi.org/10.4319/lo.2011.56.6.2003

    Article  Google Scholar 

  • Mendez F, Losada IJ (2004) An empirical model to estimate the propagation of random breaking and nonbreaking waves over vegetation fields. Coast Eng 51:103–118. https://doi.org/10.1016/j.coastaleng.2003.11.003

    Article  Google Scholar 

  • Möller I, Kudella M, Rupprecht F, Spencer T, Paul M, van Wesenbeeck BK et al (2014) Wave attenuation over coastal salt marshes under storm surge conditions. Nat Geosci 7(10):727–731. https://doi.org/10.1038/ngeo2251

    Article  Google Scholar 

  • Nardin W, Larsen L, Fagherazzi S, Wiberg P (2018) Tradeoffs among hydrodynamics, sediment fluxes and vegetation community in the Virginia Coast Reserve, USA. Estuar Coast Shelf Sci 210:98–108

    Article  Google Scholar 

  • Nepf HM (1999) Drag, turbulence, and diffusion in flow through emergent vegetation. Water Resour Res 35:479–489

    Article  Google Scholar 

  • Nepf HM, Vivoni ER (2000) Flow structure in depth-limited, vegetated flow. J Geophys Res 105:28547. https://doi.org/10.1029/2000JC900145

    Article  Google Scholar 

  • Pinto L, Fortunato AB, Zhang Y, Oliveira A, Sancho FEP (2012) Development and validation of a three-dimensional morphodynamic modelling system. Ocean Model 57-58:1–14

    Article  Google Scholar 

  • Rodrigues M, Oliveira A, Queiroga H, Fortunato AB, Zhang MY (2009) Three-dimensional modeling of the lower trophic levels in the Ria de Aveiro (Portugal). Ecol Model 220(9–10):1274–1290

    Article  Google Scholar 

  • Roland A, Zhang Y, Wang HV, Meng Y, Teng Y, Maderich V, Brovchenko I, Dutour-Sikiric M, Zanke U (2012) A fully coupled wave-current model on unstructured grids. J Geophys Res-Ocean 117:C00J33. https://doi.org/10.1029/2012JC007952

    Article  Google Scholar 

  • Shimizu Y, Tsujimoto T (1994) Numerical analysis of turbulent open-channel flow over a vegetation layer using a k-e turbulence model. J Hydrosci Hydraul Eng 11:57–67

    Google Scholar 

  • Soliveres S, Maestre FT (2014) Plant–plant interactions, environmental gradients and plant diversity: a global synthesis of community-level studies. Perspect Plant Ecol Evol Syst 16(4):154–163

    Article  Google Scholar 

  • Statzner B, Lamouroux N, Nikora V, Sagnes P (2006) The debate about drag and reconfiguration of freshwater macrophytes: comparing results obtained by three recently discussed approaches. Freshw Biol 51:2173–2183. https://doi.org/10.1111/j.1365-2427.2006.01636.x

    Article  Google Scholar 

  • Su, X. and Li, C.W. (2002), Large eddy simulation of free surface turbulent flow in partly vegetated open channels. Int. J. Numer. Meth. Fluids, 39: 919-937. https://doi.org/10.1002/fld.352

    Article  Google Scholar 

  • Sutton-Grier AE, Wowk K, Bamford H (2015) Future of our coasts: the potential for natural or hybrid infrastructure to enhance the resilience of our coastal communities, economies, and ecosystems. Environ Sci Pol 51:137–148

    Article  Google Scholar 

  • Swann L (2008) The use of living shorelines to mitigate the effects of storm events on Dauphin Island, Alabama, USA. American Fisheries Society Symposium, paper # 64, 11 pp.

  • Tanino Y, Nepf HM (2008) Laboratory investigation of mean drag in a random array of rigid, emergent cylinders. J Hydraul Eng 134:34–41

    Article  Google Scholar 

  • Temmerman S, Bouma TJ, Govers G, Wang ZB, De Vries MB, Herman PMJ (2005) Impact of vegetation on flow routing and sedimentation patterns: three-dimensional modeling for a tidal marsh. J Geophys Res 110:F04019. https://doi.org/10.1029/2005JF000301

    Article  Google Scholar 

  • Tsujimoto T, Kitamura T (1992) Experimental study on open-channel flow with vegetated zone along side wall. KHL Progressive Report, Hydrology Laboratory, Kanazawa University, Japan, 1992; 21–35

  • Umlauf L, Burchard H (2003) A generic length-scale equation for geophysical turbulence models. J Mar Res 61:235–265

    Article  Google Scholar 

  • W. Kimmerer, F. Wilkerson, B. Downing, R. Dugdale, E.S. Gross (RMA), K. Kayfetz, S. Khanna, A.E. Parker, J. Thompson. (2019). “Effects of Drought and the Emergency Drought Barrier on the Ecosystem of the California Delta”, San Francisco Estuary and Watershed Science, 17(3).

  • Wu C, Yuan H, Young C (2007) Non-hydrostatic modeling of vegetation effects on wave and flow motions, 10th International Conference on Estuarine and Coastal Modeling, 304–321

  • Ye F, Chen Q, Blanckaert K, Ma J (2013) Riparian vegetation dynamics: insight provided by a process-based model, a statistical model and field data. Ecohydrology 6:567–585. https://doi.org/10.1002/eco.1348

    Article  Google Scholar 

  • Zhang Y, Baptista AM (2008) SELFE: a semi-implicit Eulerian–Lagrangian finite-element model for cross-scale ocean circulation. Ocean Model 21:71–96

    Article  Google Scholar 

  • Zhang Y, Witter RC, Priest GR (2011) Tsunami–tide interaction in 1964 Prince William Sound tsunami. Ocean Model 40(3–4):246–259

    Article  Google Scholar 

  • Zhang Y, Ateljevich E, Yu H-C, Wu CH, Yu JCS (2015) A new vertical coordinate system for a 3D unstructured-grid model. Ocean Model 85:16–31

    Article  Google Scholar 

  • Zhang Y, Ye F, Stanev EV, Grashorn S (2016) Seamless cross-scale modelling with SCHISM. Ocean Model 102:64–81

    Article  Google Scholar 

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Funding

This research is funded by the California Department of Water Resources. Simulations presented in this paper were conducted using the following computational facilities: (1) Sciclone at the College of William and Mary which were provided with the assistance of the National Science Foundation, the Virginia Port Authority, and Virginia’s Commonwealth Technology Research Fund; (2) the Extreme Science and Engineering Discovery Environment (XSEDE; Grant TG-OCE130032), which is supported by National Science Foundation grant number OCI-1053575; (3) NASA’s Pleiades.

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Authors and Affiliations

  1. Virginia Institute of Marine Science, College of William & Mary, 1375 Greate Road, Gloucester Point, VA, 23062, USA

    Yinglong J. Zhang

  2. Innovyze, Broomfield, CO, USA

    Nathan Gerdts

  3. California Department of Water Resources, Sacramento, CA, USA

    Eli Ateljevich & Kijin Nam

Authors
  1. Yinglong J. Zhang
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  2. Nathan Gerdts
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  3. Eli Ateljevich
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  4. Kijin Nam
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Correspondence to Yinglong J. Zhang.

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Zhang, Y.J., Gerdts, N., Ateljevich, E. et al. Simulating vegetation effects on flows in 3D using an unstructured grid model: model development and validation. Ocean Dynamics 70, 213–230 (2020). https://doi.org/10.1007/s10236-019-01333-8

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