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DOE OSTI2025

Alquimia v1.0: a generic interface to biogeochemical codes – a tool for interoperable development, prototyping and benchmarking for multiphysics simulators

Alquimia v1.0 is a generic interface to geochemical solvers that facilitates development of multiphysics simulators by enabling code coupling, prototyping and benchmarking. The interface enforces the function arguments and their types for setting up, solving, serving up output data and carrying out other common auxiliary tasks while providing a set of structures for data transfer between the multiphysics code driving the simulation and the geochemical solver. Alquimia relies on a single-cell approach that permits operator splitting coupling and parallel computation. We describe the implementation in Alquimia of two widely used open-source codes that perform geochemical calculations: PFLOTRAN and CrunchFlow. We then exemplify its use for the implementation and simulation of reactive transport in porous media by two open-source flow and transport simulators: Amanzi and ParFlow. We also demonstrate its use for the simulation of coupled processes in novel multiphysics applications including the effect of multiphase flow on reaction rates at the pore scale with OpenFOAM, the role of complex biogeochemical processes in land surface models such as the E3SM Land Model (ELM) and the impact of surface–subsurface hydrological interactions on hydrogeochemical export from watersheds with the Advanced Terrestrial Simulator (ATS). These applications make it apparent that the availability of a well-defined yet flexible interface has the potential to improve the software development workflow, freeing up resources to focus on advances in process models and mechanistic understanding of coupled problems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Model simulations of Plum Island Ecosystems LTER low marsh site using ELM-PFLOTRAN

Model simulations using the E3SM Land Model (ELM) coupled to the PFLOTRAN reactive transport model via the Alquimia interface. The simulations were conducted for a tidal salt marsh at the Plum Island Ecosystems LTER near Rowley, Massachusetts, USA. Model simulations were forced using site-specific tidal cycles and salinity, and the simulations used a biogeochemical reaction network including aerobic decomposition, sulfate reduction, iron reduction, and methanogenesis. Model outputs include simulated carbon stocks, carbon dioxide and methane fluxes, and porewater concentrations of key solutes related to sulfur, iron, and carbon cycling. The model simulations included a saline simulation (with tidal sulfate inputs), a fresh simulation (with low salinity and low sulfate inputs), and a saline simulation with lower vegetation productivity to represent the effect of salinity on vegetation. These simulations were conducted to demonstrate that a new model framework incorporating subsurface redox and biogeochemical interactions into a land surface model could reproduce measured surface greenhouse gas fluxes and biogeochemical dynamics in tidal marsh ecosystems, and to test whether including redox interactions in a land surface model would allow the model to resolve contrasts in biogeochemical cycling and greenhouse gas production between saline and freshwater wetlands.The data package includes gzipped tar archives (which can be expanded using standard tar and gzip utilities) of model outputs from three model configurations: saline subsurface and reduced vegetation productivity related to salinity; saline subsurface with vegetation productivity not reduced; and freshwater. Also included are code for the modified E3SM model, Alquimia interface, and PFLOTRAN reactive transport simulator in gzipped tar format; plain text parameter and configuration files; python code files for visualizing model output and defining model configurations; and model output, tide and salinity forcing, and configuration files in netCDF format. See the README.md file in the data package for a detailed description of all files contained in the package. All files are in netCDF (.nc), gzipped tar archive (.tar.gz or .tgz), or text (all other files).Updated: May 13, 2024. Model output, E3SM code, PFLOTRAN input files, and python codes for visualizing results were updated to reflect changes made for the manuscript revision. The updated archive reflects the code and model output from the final accepted manuscript. Changes included updated reaction parameters reflecting improved parameterization and additional comparisons with field measurements. E3SM code changes included better support for multiple grid cells and improved flow and transport parameterization.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Simulated hydrological dynamics and coupled iron redox cycling impact methane production in an Arctic soil: Modeling Archive

This Modeling Archive is in support of an NGEE Arctic publication "Simulated hydrological dynamics and coupled iron redox cycling impact methane production in an Arctic soil" in the Journal of Geophysical Research-Biogeosciences. We simulated biogeochemical cycling in arctic soils using the PFLOTRAN geochemical model combined with measurements from previous NGEE Arctic incubations of polygonal permafrost soils in northern Alaska (Zheng et al., 2018). Simulated iron cycling, carbon dioxide production, and methane production were compared with incubation measurements and the parameterized model was then used to simulate coupled iron and carbon cycling over repeated oxic-anoxic cycles at different levels of carbon substrate availability and pH. The most recent data version (2.0) in the archive incorporates changes to the model and simulations as suggested by reviewers during the manuscript review process. These changes include an updated parameterization of the model; a new set of simulations omitting the iron cycle for direct evaluation of how iron cycle processes affect modeled outcomes; and a set of simulations testing different scenarios of carbon substrate availability in addition to scenarios of initial soil pH. This archive contains simulation code, model output, and analysis code for PFLOTRAN simulations. All scripts are python except the batch script for submitting multiprocessor jobs. Note that the model also requires compiled versions of the Alquimia interface and the NGEE Arctic fork of the PFLOTRAN geochemical simulator (see the README_INSTALL document for basic instructions). The Output directory contains eight data files in netCDF format generated by the model. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a 10-year research effort (2012-2022) to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗