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Effect of Surface Water Stage Fluctuation on Mixing-Dependent Hyporheic Denitrification in Riverbed Dunes


Authors: Erich Hester Lauren A. Eastes Mark A. Widdowson
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Resource type: Composite Resource
Storage: The size of this resource is 1.7 GB
Created: Jan 13, 2019 at 9:24 p.m.
Last updated: Apr 25, 2019 at 2:30 p.m.
DOI: 10.4211/hs.4a46c1445fb144a8a03b00d2e338bcfd
Citation: See how to cite this resource
Sharing Status: Published
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Abstract

This is the data repository for the journal article entitled "Effect of Surface Water Stage Fluctuation on Mixing-Dependent Hyporheic Denitrification in Riverbed Dunes" published in Water Resources Research in 2019 by Erich T. Hester, Lauren A. Eastes, and Mark A. Widdowson. The data themselves, as well as information about the data, can be found in several locations:

1) Many data are in the journal article or the associated supplementary information, which are available at the journal website or can be requested by emailing Erich Hester at ehester@vt.edu
2) Many data are available in the files associated with this Hydroshare resource, which are described in the readme.txt file
3) Any questions that are not answered by the above methods can be directed to Erich Hester at ehester@vt.edu

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Content

README.txt

This document describes the organization and naming conventions of the files in this dataset and the process we used to produce and utilize the files in this dataset.  

Please contact Erich Hester at ehester@vt.edu with questions.


1.0 File Names

All model runs were completed in Groundwater Modeling System (GMS). GMS software produces 2 folders and 1 .gpr file for each 
run. The general file format of a single run is 

	Folder:   Name_Here_MODFLOW
	Folder:   Name_Here_SEAM3D 
	GPR File: Name_Here.gpr 

To run GMS software, licensing is required, though the mass output files may still be viewed 
without it. There are two specific files found in the SEAM3D folder can be viewed as text files
and are labelled 

	Name_Here.OUT
	smeamass.DAT

The OUT file contains the amount of each solute that entered the system, biodegraded within the 
system, or left the system at timesteps of 0.1 day. The DAT file contains the time series of DOC
biodegraded at each timestep used by SEAM3D during its transport calculations, by both aerobic 
(O2HC1) and anaerobic (NO3HC1) reactions.

If any tracer particles were run, each particle set produces an additional folder with the file 
name format of 

	Name_Here_MODPATH_Particle_Set_Name

Excel files containing mass analyses were converted to .csv and are labelled as
	
	Parameter_tested_mass_analysis.csv

Excel files containing DOC consumption over time were converted to .csv and are labelled as

	Parameter_tested_DOC.csv

Excel files containing the surface water pressure distribution boundary condition were converted to .csv and are labelled as
	
	Parameter_tested_input.csv

In the input.xlsx files, each tab contained the pressure distributions for each node in the model
over time. All of these are from the input.txt file generated by the pressure_dist_input.R code with the
appropriate transient inputs (amplitude, period, etc.). The general layout of the input is this

	Node -->
Timestep
    |
    |
    v

So essentially

	Node 1	Node 2	Node 3	Node 4	Node 5	Node 6	Node 7	Node 8..... Node 20
0 d
0.1 d
0.2 d
0.3 d
0.4 d
0.5 d
0.6 d
0.7 d
...
2.0 d

GMS accepts the surface water inputs as a time series at separate nodes, so to input these, the 
appropriate column may be copied and pasted into the specified transient head boundary condition at 
each node.



2.0 Folder Structure

There are 2 file folders that separate the runs into steady-state and transient runs and results.
Each folder within one of the folders represents a specific test, except those labelled as a
basecase. The files for the runs used in each analysis are located within the appropriate folder 
for that test. Basecase scenarios were used in multiple analyses and are located in the 
designated basecase folder. The contents of each folder can be outlined as
	
	Steady-State
		Benchmark
		Heterogeneous_basecase
		Heterogeneous_VaryCL
		Heterogeneous_VaryVariance
		Homogeneous_VaryHK
		Homogeneous_HK25
	Transient
		Heterogeneous_test
		Homogeneous_Amplitude
		Homogeneous_Period
		Homogeneous_Rate_of_change
		Homogeneous_Transient_basecase

The R_code folder contains the R code used for calculating the pressure distribution across the 
dune surface for a sinusoidal surface water fluctuation and for determining the travel time of 
tracer particles from MODPATH.



3.0 Model Naming Conventions

Given the complexity of the labelling system, the naming convention is broken down by folder for
the sake of clarity. 


3.1 Steady-State folder

3.1.1 Heterogeneous_basecase
A sample label from this folder is

	SS_0.145

where SS refers to the run being steady-state and 0.145 refers to the average surface water depth.


3.1.2 Heterogeneous_VaryCL
A sample label from this folder is

	SS_0.145_0.91CL

where SS refers to the run being steady-state, 0.145 refers to the average surface water depth,
and 0.91CL refers to the horizontal correlation length of the hydraulic conductibity field. All 
runs used a 2 day model run time, and runs from the 9CL field include anadditional "_2d" 
descriptor on the label to indicate this.


3.1.3 Heterogeneous_VaryVariance
A sample label from this folder is

	SS_0.145_0.25StDev

where SS refers to the run being steady-state, 0.145 refers to the average surface water depth,
and 0.25CL refers to the variance of the hydraulic conductivity field.
		
3.1.4 Homogeneous_VaryHK
A sample label from this folder is

	SS_0.145_hom_84.4K

where SS refers to the run being steady-state, 0.145 refers to the average surface water depth,
hom refers to the hydraulic conductivity field being homogeneous, and 84.4K refers to the 
hydraulic conductivity (84.4 m/d).

		
3.1.5 Homogeneous_HK25
A sample label from this folder is

	SS_0.145

where SS refers to the run being steady-state and 0.145 refers to the average surface water depth.



3.2 Transient zip file
		
3.2.1 Heterogeneous_test
The only run in this folder is

	sine_0.145_het_12hr_CorrL9.0

where sine refers to the shape of the surface water fluctuation over time, 0.145 refers to the 
lowest surface water depth reached by the fluctuation, het refers to this being a heterogeneous
hydraulic conductivity field, 12hr refers to the period of the fluctuation, and CorrL9.0 refers
to the correlation length of the hydraulic conductivity field.

		
3.2.2 Homogeneous_Amplitude
A sample label from this folder is

	amp_0.1

where amp refers to this being a test of the amplitude of a surface water fluctuation and 0.1 
refers to the amplitude of the fluctuation in meters.

		
3.2.3 Homogeneous_Period
A sample label from this folder is

	sine_0.145_1.0_48hr

where sine refers to the shape of the surface water fluctuation over time, 0.145 refers to the 
lowest depth reached by the surface water, 1.0 refers to the maximum depth reached by the 
surface water, and 48hr refers to the period of the fluctuation.

		
3.2.4 Homogeneous_Rate_of_change
The only run in this folder is

	instant_0.145_1.0_24hr

where instant refers to this being an instantaneous change in surface water depth, 0.145 is the 
lowest depth reached by the surface water, 1.0 refers to the maximum depth reached by the surface
water, and 24hr refers to the period of the fluctuation.

		
3.2.5 Homogeneous_Transient_basecase
The only run in this folder is

	sine_0.145_1.0_24hr

where sine refers to the shape of the surface water fluctuation over time, 0.145 is the lowest 
depth reached by the surface water, 1.0 refers to the maximum depth reached by the surface water,
and 24hr refers to the period of the fluctuation.

Credits

Funding Agencies

This resource was created using funding from the following sources:
Agency Name Award Title Award Number
National Science Foundation Natural Attenuation of Groundwater Contaminant Plumes in Riverbeds: Control of Hyporheic Zone Mixing 1437021

How to Cite

Hester, E., L. A. Eastes, M. A. Widdowson (2019). Effect of Surface Water Stage Fluctuation on Mixing-Dependent Hyporheic Denitrification in Riverbed Dunes, HydroShare, https://doi.org/10.4211/hs.4a46c1445fb144a8a03b00d2e338bcfd

This resource is shared under the Creative Commons Attribution CC BY.

 http://creativecommons.org/licenses/by/4.0/
CC-BY

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