Development and technical paper 02 Nov 2020
Development and technical paper | 02 Nov 2020
Development of a submerged aquatic vegetation growth model in the Coupled Ocean–Atmosphere–Wave–Sediment Transport (COAWST v3.4) model
Tarandeep S. Kalra et al.
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Tarandeep S. Kalra, Alfredo Aretxabaleta, Pranay Seshadri, Neil K. Ganju, and Alexis Beudin
Geosci. Model Dev., 10, 4511–4523, https://doi.org/10.5194/gmd-10-4511-2017, https://doi.org/10.5194/gmd-10-4511-2017, 2017
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The paper details the sensitivity of vegetation properties that are input to a 3-D submerged aquatic vegetation model within a coupled hydrodynamics and wave model. It describes a novel strategy to perform sensitivity analysis efficiently by using a combination of the Effective Quadratures method and Sobol' indices. This method reduces the number of simulations to understand the sensitivity patterns and also quantifies the amount of sensitivity.
Neil K. Ganju, Jeremy M. Testa, Steven E. Suttles, and Alfredo L. Aretxabaleta
Ocean Sci., 16, 593–614, https://doi.org/10.5194/os-16-593-2020, https://doi.org/10.5194/os-16-593-2020, 2020
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Seagrasses, as plants, need light for photosynthesis and production. This study measured the changes in productivity and light in a back-barrier estuary and connected those changes with the type of seabed within the estuary. We found that the locations with seagrass on the seabed had more light getting through the water and higher productivity because of the way seagrass keeps sediment on the seabed during wave events. When sediment stays on the bed, it cannot reduce the light in the water.
Alfredo L. Aretxabaleta, Neil K. Ganju, Zafer Defne, and Richard P. Signell
Nat. Hazards Earth Syst. Sci., 19, 1823–1838, https://doi.org/10.5194/nhess-19-1823-2019, https://doi.org/10.5194/nhess-19-1823-2019, 2019
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Water levels in bays are affected by open-ocean changes and wind. Tides are more dampened in the bays than storm surges and sea level rise. We compare observed and modeled levels with ocean conditions and combine them with analytical models. We consider the local setup, caused by wind along the bay. Expansion using the ADCIRC tidal database will allow coverage of other bay systems on the United States East Coast. Spatial estimates of water level can inform decisions about bay flooding hazards.
Neil K. Ganju, Jeremy M. Testa, Steven E. Suttles, and Alfredo L. Aretxabaleta
Biogeosciences Discuss., https://doi.org/10.5194/bg-2018-335, https://doi.org/10.5194/bg-2018-335, 2018
Revised manuscript not accepted
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Estuaries are productive ecosystems that provide habitat for flora and fauna. We measured changes in light and oxygen, along with variables such as tides and waves, to understand how productivity in the estuary changed over daily and seasonal time periods. We found large differences in productivity between channels and seagrass beds, as well as a link between light climate and productivity. This study will help us understand how estuaries will respond to future changes in conditions.
Tarandeep S. Kalra, Alfredo Aretxabaleta, Pranay Seshadri, Neil K. Ganju, and Alexis Beudin
Geosci. Model Dev., 10, 4511–4523, https://doi.org/10.5194/gmd-10-4511-2017, https://doi.org/10.5194/gmd-10-4511-2017, 2017
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The paper details the sensitivity of vegetation properties that are input to a 3-D submerged aquatic vegetation model within a coupled hydrodynamics and wave model. It describes a novel strategy to perform sensitivity analysis efficiently by using a combination of the Effective Quadratures method and Sobol' indices. This method reduces the number of simulations to understand the sensitivity patterns and also quantifies the amount of sensitivity.
Isaac D. Irby, Marjorie A. M. Friedrichs, Carl T. Friedrichs, Aaron J. Bever, Raleigh R. Hood, Lyon W. J. Lanerolle, Ming Li, Lewis Linker, Malcolm E. Scully, Kevin Sellner, Jian Shen, Jeremy Testa, Hao Wang, Ping Wang, and Meng Xia
Biogeosciences, 13, 2011–2028, https://doi.org/10.5194/bg-13-2011-2016, https://doi.org/10.5194/bg-13-2011-2016, 2016
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A comparison of eight hydrodynamic-oxygen models revealed that while models have difficulty resolving key drivers of dissolved oxygen (DO) variability, all models exhibit skill in reproducing the variability of DO itself. Further, simple oxygen models and complex biogeochemical models reproduced observed DO variability similarly well. Future advances in hypoxia simulations will depend more on the ability to reproduce the depth of the mixed layer than the degree of the vertical density gradient.
W. K. Oestreich, N. K. Ganju, J. W. Pohlman, and S. E. Suttles
Biogeosciences, 13, 583–595, https://doi.org/10.5194/bg-13-583-2016, https://doi.org/10.5194/bg-13-583-2016, 2016
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Colored dissolved organic matter (CDOM) is a factor in determining penetration of light in estuaries. Important plant species growing in the beds of estuaries depend on such light penetration for survival. Previous studies have used CDOM fluorescence to approximate light absorption by CDOM but have found variable relationships between fluorescence and absorbance. This paper describes this variability in three east coast estuaries, and shows that this conversion is dependent on CDOM source.
N. K. Ganju, J. L. Miselis, and A. L. Aretxabaleta
Biogeosciences, 11, 7193–7205, https://doi.org/10.5194/bg-11-7193-2014, https://doi.org/10.5194/bg-11-7193-2014, 2014
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Light availability to seagrass is an important factor in their success. We deployed instrumentation to measure light in Barnegat Bay, New Jersey, and found lower availability in the southern bay due to high turbidity (suspended sediment), while the northern bay has higher availability. In the northern bay, dissolved organic material and chlorophyll are most responsible for blocking light to the seagrass canopy. We also found that boat wakes do not have a large effect on sediment resuspension.
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Geosci. Model Dev., 12, 879–892, https://doi.org/10.5194/gmd-12-879-2019, https://doi.org/10.5194/gmd-12-879-2019, 2019
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Geosci. Model Dev., 12, 651–676, https://doi.org/10.5194/gmd-12-651-2019, https://doi.org/10.5194/gmd-12-651-2019, 2019
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We present a novel finite-volume dynamical core formulation considered for future numerical weather prediction at ECMWF. We demonstrate that this formulation can be competitive in terms of solution quality and computational efficiency to the proven spectral-transform dynamical core formulation currently operational at ECMWF, while providing a local, more scalable discretization, conservative and monotone advective transport, and flexible meshes.
Ramadan Abdelaziz, Broder J. Merkel, Mauricio Zambrano-Bigiarini, and Sreejesh Nair
Geosci. Model Dev., 12, 167–177, https://doi.org/10.5194/gmd-12-167-2019, https://doi.org/10.5194/gmd-12-167-2019, 2019
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The paper presents a robust tool to estimate the thermodynamic surface complexation parameter for the sorption of uranium(VI) onto quartz surfaces. The optimization package hydroPSO R is coupled with the geochemical speciation code PHREEQC. hydroPSO used the m parameter estimation tool for geochemical modeling with PHREEQC. Coupled hydroPSO with PHREEQC proved to be a robust tool to estimate surface complexation constants for uranium(VI) species on quartz.
Miguel de la Varga, Alexander Schaaf, and Florian Wellmann
Geosci. Model Dev., 12, 1–32, https://doi.org/10.5194/gmd-12-1-2019, https://doi.org/10.5194/gmd-12-1-2019, 2019
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GemPy is an open-source Python-based 3-D structural geological modeling software, which allows the implicit (i.e. automatic) creation of complex geological models from interface and orientation data. GemPy is implemented in the programming language Python, making use of a highly efficient underlying library, Theano, for efficient code generation that performs automatic differentiation. This enables the link to probabilistic machine-learning and Bayesian inference frameworks.
Tianfeng Chai, Ariel Stein, and Fong Ngan
Geosci. Model Dev., 11, 5135–5148, https://doi.org/10.5194/gmd-11-5135-2018, https://doi.org/10.5194/gmd-11-5135-2018, 2018
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While model predictions depend on release parameters, model uncertainties in inverse modeling should also vary with the source terms. In this paper, model uncertainties that will change with the source terms are introduced in a weak-constraint inverse modeling system. Tests using HYSPLIT model and CAPTEX observations show that adding such model uncertainty terms improves release rate estimates. A cost function normalization scheme introduced to avoid spurious solutions proves to be effective.
Christopher J. Skinner, Tom J. Coulthard, Wolfgang Schwanghart, Marco J. Van De Wiel, and Greg Hancock
Geosci. Model Dev., 11, 4873–4888, https://doi.org/10.5194/gmd-11-4873-2018, https://doi.org/10.5194/gmd-11-4873-2018, 2018
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Landscape evolution models are computer models used to understand how the Earth’s surface changes over time. Although designed to look at broad changes over very long time periods, they could potentially be used to predict smaller changes over shorter periods. However, to do this we need to better understand how the models respond to changes in their set-up – i.e. their behaviour. This work presents a method which can be applied to these models in order to better understand their behaviour.
Gary L. Russell, David H. Rind, and Jeffrey Jonas
Geosci. Model Dev., 11, 4637–4656, https://doi.org/10.5194/gmd-11-4637-2018, https://doi.org/10.5194/gmd-11-4637-2018, 2018
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This paper presents the Fortran 90 source code for one-layer model GISS:IB on an icosahedral grid. The model solves the shallow water equations on the sphere using three symmetric horizontal components of angular momentum instead of velocity. One-layer shallow water models are a basic building block used in complex global weather and climate models.
Istvan Z. Reguly, Daniel Giles, Devaraj Gopinathan, Laure Quivy, Joakim H. Beck, Michael B. Giles, Serge Guillas, and Frederic Dias
Geosci. Model Dev., 11, 4621–4635, https://doi.org/10.5194/gmd-11-4621-2018, https://doi.org/10.5194/gmd-11-4621-2018, 2018
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We present the VOLNA-OP2 tsunami simulation code, built on the OP2 library. It is unique among such solvers in its support for several high-performance computing platforms: CPUs, the Intel Xeon Phi, and GPUs. This is achieved in a way that the scientific code is kept separate from various parallel implementations, enabling easy maintainability. Scalability and efficiency are demonstrated on three supercomputers built with CPUs, Xeon Phi's, and GPUs.
Joakim Beck, Sören Wolfers, and Gerald P. Roberts
Geosci. Model Dev., 11, 4383–4397, https://doi.org/10.5194/gmd-11-4383-2018, https://doi.org/10.5194/gmd-11-4383-2018, 2018
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Seismic hazard assessment requires records of earthquake recurrence with many slip events. Current data from paleoseismology on individual faults are sparse and do not provide stable estimates of earthquake recurrence. We propose a statistical model-based method to study timings of earthquakes over the past few millennia. The results agree with historical earthquakes for faults in the Italian Apennines, and can aid future studies of fault interactions over multiple earthquake cycles.
Peter D. Dueben and Peter Bauer
Geosci. Model Dev., 11, 3999–4009, https://doi.org/10.5194/gmd-11-3999-2018, https://doi.org/10.5194/gmd-11-3999-2018, 2018
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We discuss the question of whether weather forecast models that are based on deep learning and trained on atmospheric data can compete with conventional weather and climate models that are based on physical principles and the basic equations of motion. We discuss the question in the context of global weather forecasts. A toy model for global weather predictions will be presented and used to identify challenges and fundamental design choices for a forecast system based on neural networks.
Anthony P. Walker, Ming Ye, Dan Lu, Martin G. De Kauwe, Lianhong Gu, Belinda E. Medlyn, Alistair Rogers, and Shawn P. Serbin
Geosci. Model Dev., 11, 3159–3185, https://doi.org/10.5194/gmd-11-3159-2018, https://doi.org/10.5194/gmd-11-3159-2018, 2018
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Large uncertainty is inherent in model predictions due to imperfect knowledge of how to describe the processes that a model is intended to represent. Yet methods to quantify and evaluate this model hypothesis uncertainty are limited. To address this, the multi-assumption architecture and testbed (MAAT) automates the generation of all possible models by combining multiple representations of multiple processes. MAAT provides a formal framework for quantification of model hypothesis uncertainty.
Matthias Rauter, Andreas Kofler, Andreas Huber, and Wolfgang Fellin
Geosci. Model Dev., 11, 2923–2939, https://doi.org/10.5194/gmd-11-2923-2018, https://doi.org/10.5194/gmd-11-2923-2018, 2018
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We present a physical model for the simulation of dense snow avalanches and other gravitational mass flows. The model is solved with OpenFOAM, a popular open-source toolkit for the numerical solution of partial differential equations. The solver has a modular design and is easy to extend. Therefore, it represents an ideal platform for implementing and testing new model approaches.
Zhixuan Cao, Abani Patra, Marcus Bursik, E. Bruce Pitman, and Matthew Jones
Geosci. Model Dev., 11, 2691–2715, https://doi.org/10.5194/gmd-11-2691-2018, https://doi.org/10.5194/gmd-11-2691-2018, 2018
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Plume-SPH provides the first particle-based simulation of volcanic plumes. Smooth particle hydrodynamics used here has several advantages over mesh-based methods for multiphase free boundary flows like volcanic plumes. This tool will provide more accurate eruption source terms to users of volcanic ash transport and dispersion models, greatly improving volcanic ash forecasts. The Plume-SPH code incorporates several newly developed techniques in SPH-needed multiphase compressible turbulent flow.
Sabine Hittmeir, Anne Philipp, and Petra Seibert
Geosci. Model Dev., 11, 2503–2523, https://doi.org/10.5194/gmd-11-2503-2018, https://doi.org/10.5194/gmd-11-2503-2018, 2018
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Model output of quantities such as precipitation usually represents integrals, for example sums over 3 h. It is not trivial to interpolate a time series of such integral values to instantaneous precipitation rates conserving the integral values. A piecewise linear reconstruction is presented which fulfils the conservation, is non-negative, and is continuous at interval boundaries. It will be used in the FLEXPART Lagrangian dispersion model but has many other possible applications.
Richard M. Gorman and Hilary J. Oliver
Geosci. Model Dev., 11, 2153–2173, https://doi.org/10.5194/gmd-11-2153-2018, https://doi.org/10.5194/gmd-11-2153-2018, 2018
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We describe an optimisation suite ("Cyclops") that can be used to apply a selection of nonlinear optimisation algorithms to "tune" the parameters of a geophysical model. Based on the Cylc workflow engine, Cyclops can be used to calibrate any modelling system that has itself been implemented as a (separate) Cylc model suite, provided it includes computation and output of the desired scalar cost function.
David J. Gardner, Jorge E. Guerra, François P. Hamon, Daniel R. Reynolds, Paul A. Ullrich, and Carol S. Woodward
Geosci. Model Dev., 11, 1497–1515, https://doi.org/10.5194/gmd-11-1497-2018, https://doi.org/10.5194/gmd-11-1497-2018, 2018
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As the computational power of supercomputing systems increases, and models for simulating the fluid flow of the Earth's atmosphere operate at higher resolutions, new approaches for advancing these models in time will be necessary. In order to produce the best possible result in the least amount of time, we evaluate a number of splittings, methods, and solvers on two test cases. Based on these results, we identify the most accurate and efficient approaches for consideration in production models.
Philippe Delandmeter, Jonathan Lambrechts, Vincent Legat, Valentin Vallaeys, Jaya Naithani, Wim Thiery, Jean-François Remacle, and Eric Deleersnijder
Geosci. Model Dev., 11, 1161–1179, https://doi.org/10.5194/gmd-11-1161-2018, https://doi.org/10.5194/gmd-11-1161-2018, 2018
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The discontinuous Galerkin (DG) finite element method is well suited for the modelling of three-dimensional flows exhibiting strong density gradients. Here, a vertical adaptive mesh method is developed for DG finite element methods and implemented into SLIM 3D. This technique increases drastically the accuracy of simulations including strong stratification, without affecting the simulation cost. SLIM 3D is then used to simulate the thermocline oscillations of Lake Tanganyika.
Thomas Rößler, Olaf Stein, Yi Heng, Paul Baumeister, and Lars Hoffmann
Geosci. Model Dev., 11, 575–592, https://doi.org/10.5194/gmd-11-575-2018, https://doi.org/10.5194/gmd-11-575-2018, 2018
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In this study, we performed an assessment of truncation errors and computational efficiency of trajectory calculations using six popular numerical integration schemes of the Runge–Kutta family. More than 5000 transport simulations for different seasons and regions of the free troposphere and stratosphere were conducted, driven by the latest version of ECMWF operational analyses and forecasts. The study provides guidelines to achieve the most accurate and efficient trajectory calculations.
Koen Hilgersom, Marcel Zijlema, and Nick van de Giesen
Geosci. Model Dev., 11, 521–540, https://doi.org/10.5194/gmd-11-521-2018, https://doi.org/10.5194/gmd-11-521-2018, 2018
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This study models the local inflow of groundwater at the bottom of a stream with large density gradients between the groundwater and surface water. Modelling salt and heat transport in a water body is very challenging, as it requires large computation times. Due to the circular local groundwater inflow and a negligible stream discharge, we assume axisymmetry around the inflow, which is easily implemented in an existing model, largely reduces the computation times, and still performs accurately.
Tarandeep S. Kalra, Alfredo Aretxabaleta, Pranay Seshadri, Neil K. Ganju, and Alexis Beudin
Geosci. Model Dev., 10, 4511–4523, https://doi.org/10.5194/gmd-10-4511-2017, https://doi.org/10.5194/gmd-10-4511-2017, 2017
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The paper details the sensitivity of vegetation properties that are input to a 3-D submerged aquatic vegetation model within a coupled hydrodynamics and wave model. It describes a novel strategy to perform sensitivity analysis efficiently by using a combination of the Effective Quadratures method and Sobol' indices. This method reduces the number of simulations to understand the sensitivity patterns and also quantifies the amount of sensitivity.
Yanan Fan, Roman Olson, and Jason P. Evans
Geosci. Model Dev., 10, 2321–2332, https://doi.org/10.5194/gmd-10-2321-2017, https://doi.org/10.5194/gmd-10-2321-2017, 2017
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We develop a novel and principled Bayesian statistical approach to computing model weights in climate change projection ensembles of regional climate models. The approach accounts for uncertainty in model bias, trend and internal variability. The weights are easily interpretable and the ensemble weighted models are shown to provide the correct coverage and improve upon existing methods in terms of providing narrower confidence intervals for climate change projections.
Darren Engwirda
Geosci. Model Dev., 10, 2117–2140, https://doi.org/10.5194/gmd-10-2117-2017, https://doi.org/10.5194/gmd-10-2117-2017, 2017
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A new algorithm for the generation of very high-quality staggered unstructured grids for multi-resolution ocean and atmospheric modelling is described. Through use of unstructured triangulation and grid-optimisation techniques, it is shown that meshes satisfying a number of important a priori grid-quality constraints can be constructed. This new algorithm is expected to be of interest to both developers and users of unstructured general circulation models.
Kristofer Döös, Bror Jönsson, and Joakim Kjellsson
Geosci. Model Dev., 10, 1733–1749, https://doi.org/10.5194/gmd-10-1733-2017, https://doi.org/10.5194/gmd-10-1733-2017, 2017
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The TRACMASS trajectory code with corresponding schemes has been improved and become more accurate and user friendly over the years. An outcome of the present study is that we strongly recommend the use of the
time-dependentTRACMASS scheme. We would also like to dissuade the use of the more primitive
stepwise-stationaryscheme, since the velocity fields remain stationary for longer periods, creating abrupt discontinuities in the velocity fields and yielding inaccurate solutions.
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Short summary
The paper covers the description of a 3-D open-source model that dynamically couples the biophysical interactions between submerged aquatic vegetation (SAV), hydrodynamics (currents, waves), sediment dynamics, and nutrient loading. Based on SAV growth model, SAV can use growth or dieback while contributing and sequestering nutrients from the water column (modifying the biological environment) and subsequently affect the hydrodynamics and sediment transport (modifying the physical environment).
The paper covers the description of a 3-D open-source model that dynamically couples the...