DOI: 10.5281/zenodo.14592955
title: Research data related to the article "Reactive transport modeling to reveal the impacts of beach morphodynamics, storm floods and seasonal groundwater recharge on the biogeochemistry of sandy subterranean estuaries"

description: Research Data related to the article "Reactive transport modeling to reveal the impacts of beach morphodynamics, storm floods and seasonal groundwater recharge on the biogeochemistry of sandy subterranean estuaries" by Seibert et al. (2024) published in Advances in Water Resources (https://doi.org/10.1016/j.advwatres.2024.104884)

 

Dear reader,

 

reasearch data are provided for the research article "Reactive transport modeling to reveal the impacts of beach morphodynamics, storm floods and seasonal groundwater recharge on the biogeochemistry of sandy subterranean estuaries" by Seibert et al. (2024) published in Advances in Water Resources (https://doi.org/10.1016/j.advwatres.2024.104884). 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 'dynamic_RTM_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).

Base data files, e.g., phase-averaged heads and measured beach topographies, are stored in './model_data/flopy_scripts/base_data/'.



SEAWAT/PHT3D input files



Original SEAWAT and PHT3D input files, which were created with the corresponding model scripts previously (see step before), 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 Python scripts.



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_v012.py' was used to generate the output files.

2-D species concentration arrays for the final four years of the simulation period are stored in the subfolder './model_data/model_files/vXYZ/npy_arrays/species_last_year/', where 'XYZ' is a wildcard for the model number.

Species min./max. concentration arrays for the entire simulation period 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 (GHB, RCH, WEL boundaries) for the final four years of the simulation period are stored in the subfolder './model_data/model_files/vXYZ/npy_arrays/budgets_last_year/', 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'.

Videos illustrating the species and mineral evolution over the entire simulation period are stored in the subfolder './videos/' as 'Video_01.mp4' and 'Video_02.mp4', respectively.





 

Numbering of the model variants is as follows:

 

v601 --> TOPOv602 --> TERR-GWv603 --> STORMv604 --> DYNAMICv605 --> CONSTANT

 

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

 

Contact one of the authors if you have further questions: Stephan L. Seibert (stephan.seibert@uol.de), Janek Greskowiak (janek.greskowiak@uol.de), Vincent E.A. Post (vincent@edinsi.nl), Rena Meyer (rena.meyer@uol.de) or Gudrun Massmann (gudrun.massmann@uol.de)