Property:Extended model description
From CSDMS
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Mrip consists of a matrix representing the sea floor (25x25 m at this time). Blocks in the matrix are picked up (or deposited) according to transport rules or equations (users choice) and moved with the flow. The user-determined flow is altered, depending on the height and slope of the bed, thus creating feedback. +
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NEMO is a state-of-the-art modelling framework. It is used for research activities and forecasting services in ocean and climate sciences. NEMO is developed by a European consortium with the objective of ensuring long term reliability and sustainability. NEMO includes three major components; the blue ocean (dynamics), the white ocean (sea-ice), the green ocean (ocean biogeochemistry). It also allows coupling through interfaces with atmosphere (through OASIS software), waves, ice-shelves, so as nesting through the adaptive mesh refinement software AGRIF. +
NearCoM predicts waves, currents, sediment transport and bathymetric change in the nearshore ocean, between the shoreline and about 10 m water depth. The model consists of a "backbone", i.e., the master program, handling data input and output as well as internal storage, together with a suite of "modules": wave module, circulation module and sediment transport module. +
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Network-based modeling framework of Czuba and Foufoula-Georgiou as applied to bed-material sediment transport.
This code is capable of reproducing the results (with some work by the end user) described in the following publications:
Czuba, J.A., and E. Foufoula-Georgiou (2014), A network-based framework for identifying potential synchronizations and amplifications of sediment delivery in river basins, Water Resources Research, 50(5), 3826–3851, doi:10.1002/2013WR014227.
Czuba, J.A., and E. Foufoula-Georgiou (2015), Dynamic connectivity in a fluvial network for identifying hotspots of geomorphic change, Water Resources Research, 51(3), 1401-1421, doi:10.1002/2014WR016139.
Gran, K.B., and J.A. Czuba, (2017), Sediment pulse evolution and the role of network structure,
Geomorphology, 277, 17-30, doi:10.1016/j.geomorph.2015.12.015.
Czuba, J.A., E. Foufoula-Georgiou, K.B. Gran, P. Belmont, and P.R. Wilcock (2017), Interplay between spatially-explicit sediment sourcing, hierarchical river-network structure, and in-channel bed-material sediment transport and storage dynamics, Journal of Geophysical Research - Earth Surface, 122(5), 1090-1120, doi:10.1002/2016JF003965.
As of 20 March 2019, additional model codes were added to the repository in the folder "Gravel_Bed_Dynamics" that extend the model to gravel bed dynamics. The new methods for gravel bed dynamics are described in:
Czuba, J.A. (2018), A Lagrangian framework for exploring complexities of mixed-size sediment transport in gravel-bedded river networks, Geomorphology, 321, 146-152, doi:10.1016/j.geomorph.2018.08.031.
And an application to Clear Creek/Tushar Mountains in Utah is described in:
Murphy, B.P., J.A. Czuba, and P. Belmont (2019), Post-wildfire sediment cascades: a modeling framework linking debris flow generation and network-scale sediment routing, Earth Surface Processes and Landforms, 44(11), 2126-2140, doi:10.1002/esp.4635.
Note: the application code and data files for Murphy et al., 2019 are included in the repository as example files.
As of 24 September 2020, this code has largely been converted to Python and has been incorporated into Landlab version 2.2 as the NetworkSedimentTransporter. See:
Pfeiffer, A.M., K.R. Barnhart, J.A. Czuba, and E.W.H. Hutton (2020), NetworkSedimentTransporter: A Landlab component for bed material transport through river networks, Journal of Open Source Software, 5(53), 2341, doi:10.21105/joss.02341.
This initial release is the core code, but development is ongoing to make the data preprocessing, model interface, and exploration of model results more user friendly. All future developments will be in the Landlab/Python version of the code instead of this Matlab version.
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Network-based modeling framework of Czuba and Foufoula-Georgiou as applied to nitrate and organic carbon on a wetland-river network.
This code is capable of reproducing the results (with some work of commenting/uncommenting code by the end user) described in the following publication:
Czuba, J.A., A.T. Hansen, E. Foufoula-Georgiou, and J.C. Finlay (2018), Contextualizing wetlands within a river network to assess nitrate removal and inform watershed management, Water Resources Research, 54(2), 1312-1337, doi:10.1002/2017WR021859. +
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Nonlinear three dimensional simulations of miscible Hele-Shaw flows using DNS of incompressible Navier-Stokes and transport equations. +
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Oceananigans.jl is designed for high-resolution simulations in idealized geometries and supports direct numerical simulation, large eddy simulation, arbitrary numbers of active and passive tracers, and linear and nonlinear equations of state for seawater. +
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One dimensional model for the coupled long-term evolution of salt marshes and tidal flats. The model framework includes tidal currents, wind waves, sediment erosion and deposition, as well as the effect of vegetation on sediment dynamics. The model is used to explore the evolution of the marsh boundary under different scenarios of sediment supply and sea level rise. Time resolution 30 min, simulation length about 100 years. +
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One-Dimensional Transport with Equilibrium Chemistry (OTEQ):
A Reactive Transport Model for Streams and Rivers
OTEQ is a mathematical simulation model used to characterize the fate and transport of waterborne solutes in streams and rivers. The model is formed by coupling a solute transport model with a chemical equilibrium submodel. The solute transport model is based on OTIS, a model that considers the physical processes of advection, dispersion, lateral inflow, and transient storage. The equilibrium submodel is based on MINTEQ, a model that considers the speciation and complexation of aqueous species, acid-base reactions, precipitation/dissolution, and sorption.
Within OTEQ, reactions in the water column may result in the formation of solid phases (precipitates and sorbed species) that are subject to downstream transport and settling processes. Solid phases on the streambed may also interact with the water column through dissolution and sorption/desorption reactions. Consideration of both mobile (waterborne) and immobile (streambed) solid phases requires a unique set of governing differential equations and solution techniques that are developed herein. The partial differential equations describing physical transport and the algebraic equations describing chemical equilibria are coupled using the sequential iteration approach. The model's ability to simulate pH, precipitation/dissolution, and pH-dependent sorption provides a means of evaluating the complex interactions between instream chemistry and hydrologic transport at the field scale.
OTEQ is generally applicable to solutes which undergo reactions that are sufficiently fast relative to hydrologic processes ("Local Equilibrium"). Although the definition of "sufficiently fast" is highly solute and application dependent, many reactions involving inorganic solutes quickly reach a state of chemical equilibrium. Given a state of chemical equilibrium, inorganic solutes may be modeled using OTEQ's equilibrium approach. This equilibrium approach is facilitated through the use of an existing database that describes chemical equilibria for a wide range of inorganic solutes. In addition, solute reactions not included in the existing database may be added by defining the appropriate mass-action equations and the associated equilibrium constants. As such, OTEQ provides a general framework for the modeling of solutes under the assumption of chemical equilibrium. Despite this generality, most OTEQ applications to date have focused on the transport of metals in streams and small rivers. The OTEQ documentation is therefore focused on metal transport. Potential model users should note, however, that additional applications are possible.
One-Dimensional Transport with Inflow and Storage (OTIS): A Solute Transport Model for Streams and Rivers
OTIS is a mathematical simulation model used to characterize the fate and transport of water-borne solutes in streams and rivers. The governing equation underlying the model is the advection-dispersion equation with additional terms to account for transient storage, lateral inflow, first-order decay, and sorption. This equation and the associated equations describing transient storage and sorption are solved using a Crank-Nicolson finite-difference solution.
OTIS may be used in conjunction with data from field-scale tracer experiments to quantify the hydrologic parameters affecting solute transport. This application typically involves a trial-and-error approach wherein parameter estimates are adjusted to obtain an acceptable match between simulated and observed tracer concentrations. Additional applications include analyses of nonconservative solutes that are subject to sorption processes or first-order decay. OTIS-P, a modified version of OTIS, couples the solution of the governing equation with a nonlinear regression package. OTIS-P determines an optimal set of parameter estimates that minimize the squared differences between the simulated and observed concentrations, thereby automating the parameter estimation process. +
OpenFOAM (Open Field Operation and Manipulation) is a toolbox for the development of customized numerical solvers, and pre-/post-processing utilities for the solution of continuum mechanics problems, including computational fluid dynamics. +
Optimization Technique in Transient Evolution of Rivers (OTTER). This models a 1D river profile while incorporating a algorithm for dynamic channel width. The channel width algorithm dynamically adjusts channel geometry in response to values of water discharge, rock-uplift/erosion, and sediment supply. It operates by calculating the current shear stress (no wide channel assumption), the shear stress if channel width is slightly larger, and shear stress for a slightly narrower channel. Using these values, erosion potential is calculated for all three scenarios (no change in width, slightly wider, slightly narrower) and the one that generates the maximum erosion rate dictates the direction of channel change. See Yanites, 2018 JGR for further information. +
OrderID is a method that takes thickness and facies data from a vertical succession of strata and tests for the presence of order in the strata +
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Originally developed for modeling tsunami generation, propagation, and inundation. Also used for storm surge modeling and overland flooding (e.g. dam break problems). Uses adaptive mesh refinement to allow much greater spatial resolutions in some regions than others, and to automatically follow dynamic evolution of waves or floods. Uses high-resolution finite volume methods that robustly handle wetting and drying. The package also includes tools for working with geophysical data including topography DEMs, earthquake source models for tsunami generation, and observed gauge data. The simulation code is in Fortran with OpenMP for shared memory parallelization, and Python for the user interface, visualization, and data tools. +
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PCR-GLOBWB 2 has been fully rewritten in Python and PCRaster Python and has a modular structure, allowing easier replacement, maintenance, and development of model components. PCR-GLOBWB 2 has been implemented at 5 arcmin resolution, but a version parameterized at 30 arcmin resolution is also available. +
PHREEQC implements several types of aqueous models: two ion-association aqueous models (the Lawrence Livermore National Laboratory model and WATEQ4F), a Pitzer specific-ion-interaction aqueous model, and the SIT (Specific ion Interaction Theory) aqueous model. Using any of these aqueous models, PHREEQC has capabilities for (1) speciation and saturation-index calculations; (2) batch-reaction and one-dimensional (1D) transport calculations with reversible and irreversible reactions, which include aqueous, mineral, gas, solid-solution, surface-complexation, and ion-exchange equilibria, and specified mole transfers of reactants, kinetically controlled reactions, mixing of solutions, and pressure and temperature changes; and (3) inverse modeling, which finds sets of mineral and gas mole transfers that account for differences in composition between waters within specified compositional uncertainty limits. +
PIHM is a multiprocess, multi-scale hydrologic model where the major hydrological processes are fully coupled using the semi-discrete finite volume method. PIHM is a physical model for surface and groundwater, “tightly-coupled” to a GIS interface. PIHMgis which is open source, platform independent and extensible. The tight coupling between GIS and the model is achieved by developing a shared data-model and hydrologic-model data structure. +
PISM is a hybrid shallow ice, shallow shelf model. PISM is designed to scale with increasing problem size
by harnessing the computational power of supercomputing systems and by leveraging the scalable software libraries that have been developed by the high-performance computing research community. The model combines two shallow (small depth-to-width ratio) stress balances, namely the shallow-ice approximation (SIA) and the shallow-shelf approximation (SSA), which are computationally efficient schemes to simulate ice flow by internal deformation and ice-stream flow, respectively. In PISM, deformational velocities from the SIA and sliding velocities from the SSA are weighted and averaged to achieve a smooth transition from shearing flow to sliding flow. +
