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.

本数据集采用通过Alquimia接口耦合PFLOTRAN反应性输运模型的E3SM陆面模型（E3SM Land Model, ELM）开展模拟实验。模拟区域设置在美国马萨诸塞州罗利附近的普拉姆岛生态系统长期生态研究站（Plum Island Ecosystems LTER）的潮汐盐沼。模拟驱动数据采用站点专属的潮汐周期与盐度数据，所使用的生物地球化学反应网络涵盖好氧分解、硫酸盐还原、铁还原与产甲烷作用。模型输出结果包括模拟碳储量、二氧化碳与甲烷通量，以及与硫、铁、碳循环相关的关键溶质孔隙水浓度。本次模拟包含三类设置：其一为盐度驱动模拟（输入潮汐携带的硫酸盐），其二为淡水驱动模拟（盐度与硫酸盐输入量均较低），其三为降低植被生产力的盐度驱动模拟，用以表征盐度对植被的影响。开展上述模拟旨在验证两个核心目标：一是将地下氧化还原与生物地球化学交互作用集成至陆面模型的新型模型框架，能够复现潮汐盐沼生态系统中实测的地表温室气体通量与生物地球化学动态；二是检验在陆面模型中纳入氧化还原交互作用后，是否可以区分咸水与淡水湿地间的生物地球化学循环与温室气体产生差异。本数据包包含三类模型配置的模型输出结果的gzip压缩tar归档文件（可通过标准tar与gzip工具解压），三类配置分别为：盐度驱动且植被生产力因盐度降低的场景、盐度驱动但植被生产力未降低的场景、淡水驱动场景。数据包还包含经gzip压缩的tar格式的修改版E3SM模型代码、Alquimia接口代码与PFLOTRAN反应性输运模拟器代码；纯文本格式的参数与配置文件；用于可视化模型输出、定义模型配置的Python代码文件；以及netCDF格式的模型输出、潮汐与盐度驱动数据及配置文件。有关数据包内所有文件的详细说明，请参阅数据包中的README.md文件。所有文件格式包括netCDF（.nc）、gzip压缩tar归档（.tar.gz或.tgz），其余文件为纯文本格式。更新日期：2024年5月13日。本次更新对模型输出、E3SM代码、PFLOTRAN输入文件与结果可视化Python代码进行了修订，以适配稿件修改要求。更新后的归档文件包含最终录用稿件对应的代码与模型输出结果，修订内容包括：更新了反应参数以体现更优化的参数化方案，新增了与野外实测数据的对比分析；E3SM代码的更新内容包括对多网格单元的更好支持，以及改进的水流与输运参数化方案。