Research data related to the article "Impact of mineral reactions and surface complexation on the transport of dissolved species in a subterranean estuary: Application of a comprehensive reactive transport modeling approach"

Research Data related to the article "Impact of mineral reactions and surface complexation on the transport of dissolved species in a subterranean estuary: Application of a comprehensive reactive transport modeling approach" by Seibert et al. (2024) published in Advances in Water Resources Dear reader, reasearch data are provided for the research article "Impact of mineral reactions and surface complexation on the transport of dissolved species in a subterranean estuary: Application of a comprehensive reactive transport modeling approach" by Seibert et al. (2024) published in Advances in Water Resources (https://doi.org/10.1016/j.advwatres.2024.104763). The authors hope that the research data allows for a better understanding of the modeling workflow. The research data covers the following files: Python scripts to create the models Model scripts using FloPy (Bakker et al., 2016) are stored as .py files in './model_data/flopy_scripts/', named 'model_variant_vXYZ.py', where 'XYZ' is a wildcard for the model number. --> Note that model numbers correspond to the different model variants as referred to in the article, see overview below. The model scripts require postfix files, stored in './model_data/flopy_scripts/postfix/', a PHREEQC database file, stored in './model_data/flopy_scripts/template_database/', as well as spreadsheets that contain the initial concentrations as well as reaction rate parameters needed by PHT3D, stored as .xlsx files in './model_data/flopy_scripts/', to create the models. Note that the .xlsx files are used by PHT3D-FSP in the model scripts to generate relevant PHT3D input files (compare https://doi.org/10.5281/zenodo.7559750 for more details). SEAWAT/PHT3D input files Original SEAWAT and PHT3D input files, which were created with the corresponding model scripts previously (see step before). Input files are stored in './model_data/model_files/vXYZ/model_files/' for each model variant, where 'XYZ' is a wildcard for the model number. SEAWAT/PHT3D executables can directly run the model files files. Thus, the files don't need to be re-created via the previous step. Model outputs Model output data is stored as NumPy arrays in './model_data/model_files/vXYZ/npy_arrays/', where 'XYZ' is a wildcard for the model number. The script './model_data/flopy_scripts/template_output/pht3d_output_hpc_v006.py' was used to generate the output files. 2-D species concentration arrays are stored in the subfolder './model_data/model_files/vXYZ/npy_arrays/species/', where 'XYZ' is a wildcard for the model number. Species min./max. concentration arrays are stored in the subfolder './model_data/model_files/vXYZ/npy_arrays/min_max/', where 'XYZ' is a wildcard for the model number. 2-D water budget arrays (CH & WEL boundaries) are stored in the subfolder './model_data/model_files/vXYZ/npy_arrays/budgets/', where 'XYZ' is a wildcard for the model number. Model discretization information (ncol, nrow, nlay etc.) are stored in the subfolder './model_data/model_files/vXYZ/npy_arrays/discretization/', where 'XYZ' is a wildcard for the model number. Figure files Original figure files as well as the corresponding Python scripts to create the figures are stored in the subfolder'./figures'. Numbering of the model variants is as follows:v401 --> VAR-conservativev402 --> VAR-OMv403 --> VAR-C/Iv404 --> VAR-C/I/Sv405 --> VAR-C/I/Pv406 --> VAR-C/I/P/Hv407 --> VAR-C/I/P/Vv408 --> VAR-C/I/P-Cov409 --> VAR-allv410 --> VAR-all (no C) Literature: Bakker, M., Post, V., Langevin, C.D., Hughes, J.D., White, J.T., Starn, J.J. and Fienen, M.N., 2016. Scripting MODFLOW model development using Python and FloPy. Groundwater, 54(5), pp.733-739. https://doi.org/10.1111/gwat.12413 Seibert, S.L., Massmann, G., Meyer, R., Post, V.E.A., Greskowiak, J., 2024. Impact of mineral reactions and surface complexation on the transport of dissolved species in a subterranean estuary: Application of a comprehensive reactive transport modeling approach. Advances in Water Resources. https://doi.org/10.1016/j.advwatres.2024.104763 Contact one of the authors if you have further questions: Stephan L. Seibert ([e-mail]), Janek Greskowiak ([e-mail]), Vincent E.A. Post ([e-mail]), Rena Meyer ([e-mail]) or Gudrun Massmann ([e-mail])本数据集对应发表于《Advances in Water Resources》（《水资源进展》）、Seibert等人（2024年）的论文《矿物反应与表面络合（surface complexation）对地下河口（subterranean estuary）溶解溶质运移的影响：综合反应溶质运移模拟（reactive transport modeling）方法的应用》相关研究数据。 尊敬的读者： 本研究数据对应Seibert等人（2024年）发表于《Advances in Water Resources》（https://doi.org/10.1016/j.advwatres.2024.104763）的上述论文。作者希望本研究数据可帮助读者更好地理解模型构建流程。本数据集包含以下文件： ### 用于构建模型的Python脚本 使用FloPy（Bakker等，2016）的模型脚本以.py格式存储于`./model_data/flopy_scripts/`路径下，文件命名为`model_variant_vXYZ.py`，其中`XYZ`为模型编号通配符。请注意，模型编号与论文中提及的不同模型变体一一对应，详见下文概述。 上述模型脚本运行需依赖以下文件：存储于`./model_data/flopy_scripts/postfix/`的后缀文件、存储于`./model_data/flopy_scripts/template_database/`的PHREEQC数据库文件，以及存储于`./model_data/flopy_scripts/`的.xlsx格式电子表格——该表格包含PHT3D所需的初始浓度与反应速率参数，用于完成模型构建。 请注意，模型脚本中PHT3D-FSP将利用上述.xlsx文件生成对应的PHT3D输入文件（详细信息可参考https://doi.org/10.5281/zenodo.7559750）。 ### SEAWAT/PHT3D输入文件 原始SEAWAT与PHT3D输入文件由前文所述的对应模型脚本生成。所有模型变体的输入文件均存储于`./model_data/model_files/vXYZ/model_files/`路径下，其中`XYZ`为模型编号通配符。SEAWAT/PHT3D可执行文件可直接运行该输入文件，无需通过前文步骤重新生成。 ### 模型输出数据 模型输出数据以NumPy数组格式存储于`./model_data/model_files/vXYZ/npy_arrays/`路径下，其中`XYZ`为模型编号通配符。输出文件由脚本`./model_data/flopy_scripts/template_output/pht3d_output_hpc_v006.py`生成。 - 二维溶质浓度数组存储于子文件夹`./model_data/model_files/vXYZ/npy_arrays/species/`； - 溶质最小/最大浓度数组存储于子文件夹`./model_data/model_files/vXYZ/npy_arrays/min_max/`； - 二维水收支数组（恒定水头CH与井WEL边界）存储于子文件夹`./model_data/model_files/vXYZ/npy_arrays/budgets/`； - 模型离散化信息（列数、行数、层数等）存储于子文件夹`./model_data/model_files/vXYZ/npy_arrays/discretization/`。 ### 图表文件 原始图表文件及对应的图表生成Python脚本均存储于`./figures`子文件夹中。 ### 模型变体编号规则 v401 → VAR-保守溶质运移模型（VAR-conservative） v402 → VAR-有机质模型（VAR-OM） v403 → VAR-碳/离子模型（VAR-C/I） v404 → VAR-碳/离子/硫模型（VAR-C/I/S） v405 → VAR-碳/离子/磷模型（VAR-C/I/P） v406 → VAR-碳/离子/磷/氢模型（VAR-C/I/P/H） v407 → VAR-碳/离子/磷/钒模型（VAR-C/I/P/V） v408 → VAR-碳/离子/磷/钴模型（VAR-C/I/P-Co） v409 → VAR-全组分模型（VAR-all） v410 → VAR-全组分（不含碳）模型（VAR-all (no C)） ### 参考文献 [1] Bakker M, Post V, Langevin C D, et al., 2016. 基于Python与FloPy的MODFLOW模型开发脚本编写. 地下水, 54(5): 733-739. https://doi.org/10.1111/gwat.12413 [2] Seibert S L, Massmann G, Meyer R, et al., 2024. 矿物反应与表面络合对地下河口溶解溶质运移的影响：综合反应溶质运移模拟方法的应用. 水资源进展, https://doi.org/10.1016/j.advwatres.2024.104763 ### 联系方式 如有进一步疑问，请联系以下作者之一：Stephan L. Seibert（[e-mail]）、Janek Greskowiak（[e-mail]）、Vincent E.A. Post（[e-mail]）、Rena Meyer（[e-mail]）或Gudrun Massmann（[e-mail]）