Software Ecosystem

IDEAS-Watersheds integrates standalone siloed codes into an interoperable software ecosystem using common computational libraries and frameworks to share capabilities and advance computational watershed science.

Code Descriptions

Alquimia (Github)
A biogeochemistry Application Program Interface and wrapper library that provides unified access to biogeochemistry capabilities from mature geochemical codes, allowing any subsurface flow and transport simulator to access a range of functionality. Alquimia is not an implementation of a biogeochemistry reaction library and does not do any geochemical calculations. Currently, Alquimia provides access to the geochemical codes PFLOTRAN and CrunchFlow and can be used for the simulation of aqueous complexation reactions, radioactive decay, ion exchange, surface complexation, and mineral dissolution-precipitation. Github repo admin: Sergi Molins

Amanzi (Github)
A flexible and extensible flow and reactive transport simulation capability for environmental applications.  It includes general polyhedral mesh infrastructure, provides advanced nonlinear solvers, such as Nonlinear Krylov Acceleration (NKA) and Anderson Acceleration, and leverages Trilinos-ML and Hypre Algebraic Multigrid for scalable solvers.  The multiphysics framework, Arcos, provides a flexibility for hierarchical weak and strong coupling of processes with subcycling.  Geochemistry support is provided through the Alquimia interface library and can use the geochemistry engine from PFLOTRAN or CrunchFlow. The code is parallel and  leverages Trilinos and PETSc.   Amanzi is used to model contaminant migration at various DOE waste sites (e.g., Hanford, and Savannah River), and is generally applicable to groundwater contaminant migration under partially saturated, nonisothermal conditions and its interaction with surface water.   Amanzi is jointly developed by LANL, LBNL, and PNNL, and ORNL as an open source project under the three-clause BSD license

Advanced Terrestrial Simulator (ATS) (Github)
A code for solving ecosystem-based, integrated, distributed hydrology.  It builds on the multi-physics framework and toolsets (mesh infrastructure, discretizations, solvers) provided by Amanzi and is a key driver of development of the flexible multiphysics framework Acros. Capabilities are largely based on solving various forms of Richards equation coupled to a surface flow equation, along with the needed sources and sinks for ecosystem and climate models.  This can (but need not) include thermal processes (especially ice for frozen soils), evapo-transpiration, albedo-driven surface energy balances, snow, biogeochemistry, plant dynamics, deformation, transport, and much more. It is unique in its thermal integrated hydrology capabilities, which includes thermal energy with freeze/thaw processes in both the surface and subsurface water, and its reactive transport capabilities, which are also coupled in both surface and subsurface water.  ATS is jointly developed by LANL, LBNL, and ORNL as an open source project under the three-clause BSD license.

CrunchFlow (Bitbucket)
An open-source software package for simulating reactive flow and transport applied to a variety of problems in the Earth and environmental sciences that can include an arbitrary number of reactions, including mineral dissolution/precipitation, ion exchange, surface complexation, and microbially mediated reactions (Steefel et al, 2015). Two approaches are available at runtime for coupling reactions and transport: (1) a global-implicit approach that solves transport and reactions simultaneously, and (2) an operator-splitting approach based on a sequential non-iterative solve.

EcoSLIM (Github)
A Lagrangian particle-tracking model designed to operate with integrated hydrologic models.(Reed M. Maxwell et al., 2018) Particles are initialized in the subsurface or added at the surface via precipitation fluxes. Spatially gridded velocity, pressure, and saturation fields are used to move particles through the domain and particles can exit via overland flow or evapotranspiration. In addition to steady-state simulations, EcoSLIM can also use transient model outputs to develop time-varying residence-time distributions. The incorporation of precipitation sources from the land-surface model also allows for the direct evaluation of source water contribution (e.g., rain versus snow). EcoSLIM has been demonstrated using outputs from the ParFlow-CLM hydrologic model; however, the model can easily be combined with other hydrologic tools that generate similar gridded outputs. In proof-of-concept simulations, EcoSLIM has been used to explore spatial variability in plant water sources (i.e., old vs. young water), connections between plan rooting depth and ET residence-time distributions, and seasonal variability in residence-time distributions and source water partitioning.(Reed M. Maxwell et al., 2018)

LaGriT (Github)
A software tool for generating, editing and optimizing multi-material unstructured finite element grids; it also maintains the geometric integrity of complex input volumes, surfaces, and geologic data and produces an optimal grid (Delaunay, Voronoi) elements. The data structures used in the code are compact and powerful and expandable to include hybrid meshes (tet, hex, prism, pyramid, quadrilateral, triangle, line), however the main algorithms are for triangle and tetrahedral meshes. The LaGriT tools are used in many projects including ASCEM meshing for Amanzi, Discrete Fracture Networks (DFN), Arctic Permafrost, and Subsurface Flow and Transport models using FEHM and PFLOTRAN. PyLaGriT provides a python interface to LaGriT capabilities, making it easier to incorporate mesh generation in modeling workflows.

Open source Computational Fluid Dynamics (CFD) software. It has an extensive range of capabilities to solve complex fluid flows involving turbulence, heat transfer and chemical reactions. It has established a large user community across most areas of engineering and Science.

ParFlow (URL, Github)
The integrated watershed model, solves saturated and variably saturated flow in three dimensions using either an orthogonal (Jones & Woodward, 2001; Kollet & Maxwell, 2006) or a terrain-following, semi-structured mesh that enables fine vertical resolution near the land surface and deep (~1 km) confined and unconfined aquifers. ParFlow models dynamic surface and subsurface flow solving the simplified shallow water equations implicitly coupled to Richards’ equation; this allows for two-way exchanges and intermittency in stream and river flow (Kollet & Maxwell, 2006). ParFlow uses robust linear (Ashby & Falgout, 1996) and nonlinear (Jones & Woodward, 2001; Osei-Kuffuor et al., 2014) solution techniques and exhibits efficient parallel scaling to large processor counts, more than 450K cores (Kollet et al., 2010), enabling very large-extent simulations with fine spatial resolution.

ParFlow coupled to the land-surface model CLM (Ferguson et al., 2016; Jefferson & Maxwell, 2015; Jefferson et al., 2017; Reed M. Maxwell & Miller, 2005), provides a comprehensive representation of vegetation, snow, and land-atmosphere water and energy fluxes.  CLM is unique in the land surface modeling community because it is a module that is called from within ParFlow.  This modeling framework has been shown to represent the observed range of temporal scales and non-stationary behavior (R. M. Maxwell et al., 2015) making it appropriate for the proposed work. A 1 km lateral resolution ParFlow-CLM model of CONUS has been developed and used to evaluate large-scale controls on groundwater configuration and connections between lateral groundwater flow and land-surface partitioning (Laura E. Condon & Maxwell, 2015; L. E. Condon & Maxwell, 2017; Reed M. Maxwell & Condon, 2016; R. M. Maxwell et al., 2015). ParFlow-CLM is currently distributed with ParFlow through the GitHub repo. In the IDEAS project the CLM land model interface will be generalized and also be made available as a separate library that other codes in the eco-system can connect use still within the ParFlow GitHub repo.

PFLOTRAN (URL, Bitbucket)
An open-source, state-of-the-art massively parallel subsurface flow and reactive transport code. PFLOTRAN solves a system of generally nonlinear partial differential equations describing multiphase, multicomponent, and multiscale reactive flow and transport in porous materials. The code is designed to run on massively parallel computing architectures as well as workstations and laptops. PFLOTRAN is written in object-oriented, free-formatted FORTRAN 2003. The reactive transport equations can be solved using either a fully implicit Newton-Raphson algorithm or the less robust operator-splitting method. Geochemical capabilities include aqueous complexation, sorption, mineral precipitation and dissolution, and microbially mediated reactions.

Soil & Water Assessment Tool (SWAT) (URL)
A watershed model developed for the USDA Agricultural Research Service. SWAT can be used to predict the impact of land management practices on water, sediment and agricultural chemical yields in large complex watersheds. It can deal with varying soils, land use and management conditions over long periods of time.