ArcNLET-Py: A Python Version of ArcGIS-Based Nitrogen Load Estimation Toolbox Developed for ArcGIS Pro

User’s Manual

Manuscript Completed: December 2023

Prepared by

Michael Core(mcore@fsu.edu), Wei Mao (wm23a@fsu.edu), and Ming Ye (mye@fsu.edu)

Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL 32306

Prepared for Florida Department of Environmental Protection Tallahassee, FL

The ArcNLET Assistant is currently in preliminary development and is designed to assist users by answering questions and providing guidance on using ArcNLET. You can access this GPT-powered assistant through the URL provided below. https://chatgpt.com/g/g-K7j2iDlDK-arcnlet-assistant

Introduction

The original ArcNLET (ArcGIS-based Nitrogen Load Estimation Toolbox) was developed using the Visual Basic programming language for ArcMap. Since ESRI stopped supporting Visual Basic programming for ArcGIS and ArcGIS Pro is the current ArcGIS platform, we developed a new version of ArcNLET for ArcGIS Pro. In addition, the new version was written in Python, and the Python source codes are open to the public through GitHub. This new version is referred to as ArcNLET-Py. It has all the features of ArcNLET, with several new features that will be discussed in the manual later on. Since the graphic user interface of ArcNLET-Py is entirely different from ArcNLET, we developed this manual for using ArcNLET-Py. The numerical simulation behind ArcNLET-Py is similar to ArcNLET, and it should be conceptually straightforward for ArcNLET users to use ArcNLET-Py.

ArcNLET-Py simulates the fate and transport of nitrogen (including both ammonium and nitrate) and phosphorus (as phosphate, PO43-) in a surficial groundwater aquifer originating from onsite sewage treatment and disposal systems (OSTDS), a.k.a., septic tanks. ArcNLET-Py produces estimated values of ammonium, nitrate, and phosphate load to specified surface water bodies. The primary functions performed by ArcNLET-Py are to:

  • Aid in preparing data that represents the soil hydraulic properties (e.g., hydraulic conductivity and porosity) within the domain boundary.

  • Evaluate the groundwater flow directions and magnitudes at discrete points (i.e., OSTDS locations) of a domain of interest.

  • Determine the flow paths along which nitrogen travels from an OSTDS to its receiving water body.

  • Simulate reactive transport of ammonium and nitrate in the vertical direction at the distance between an OSTDS drainfield and groundwater table.

  • Simulate reactive transport of phosphorus in the vertical direction from an OSTDS drainfield to the groundwater table and estimate the subsequent phosphate load reaching surface water bodies.

  • Estimate the nitrogen plumes originating from OSTDS and ending at receiving surface water bodies.

  • Calculate nitrate-nitrogen loss due to denitrification during nitrate transport and calculate the final nitrate load to target water bodies.

The impetus behind developing the original ArcNLET and ArcNLET-Py is to have a simplified nitrogen and phosphorus transformation and transport model that is easy to implement, integrated into a geographic information system (GIS) for ease of data management, and uses input data that are available in the public domain. Traditional numerical models for groundwater flow and contaminant transport, such as the Modular Three-Dimensional Finite-Difference Groundwater Flow Model (MODFLOW), Modular Three-Dimensional Particle Tracking Model (MODPATH), and Modular Three-Dimensional Multispecies Transport Model for Simulation (MT3DMS), can simulate nitrogen and phosphorus fate and transport under complicated field conditions and produce simulated results that may agree well with field measurements. Developing these models and generating such agreement requires extensive data collection of the study area and an experienced modeler. An approach involving traditional modeling tools may not be ideal for obtaining quick but realistic estimates of nitrogen and phosphorus loads to surface water bodies since traditional modeling processes can be difficult and time-consuming. Additionally, traditional tools do not integrate well with GIS. As a result, a simplified model is developed to address the concerns with traditional modeling software. An outcome of the simplified model is that it becomes possible to integrate the modeling toolbox effectively within the GIS framework and to use the advanced spatial analysis tools made available by the GIS.

The model is implemented as a Python Toolbox for ArcGIS Pro from the Environmental Systems Research Institute, Inc. (Esri). Integrating this model with ArcGIS Pro makes it easy to incorporate the spatial nature of data, such as the locations of individual OSTDS and spatially variable hydraulic conductivity and porosity. Finally, embedding the model within ArcGIS facilitates data pre- and post-processing and the visualization of results.

  1. Please keep in mind that ArcNLET-Py uses shapefiles stored in folders on your local machine.

  2. ArcNLET-Py is compatible neither with the Esri feature class nor with any of the Esri geodatabases (i.e., file geodatabase, personal geodatabase, or enterprise geodatabase).

The model is controlled via the Geoprocessing Pane and accessed as tools in the content pane or Catalog View of ArcGIS Pro. A point-and-click approach facilitates user interaction, as it is more user-friendly than the input file-oriented interaction used in traditional groundwater modeling software such as MODFLOW and MT3DMS.

This manual describes the practical usage of the toolbox. The underlying model of nitrogen fate and transport and the associated algorithmic implementation are described in detail in the technical manual (Rios et al., 2011). Readers of this manual should be familiar with ArcGIS Pro 3.2.0 and basic scientific and hydrological terminology.

1.1 Organization of the Manual 1.2 Acronyms and Abbreviations

Organization of the Manual

The structure of the manual is as follows: the manual begins with an abbreviated description of the simplified model used in this toolbox, followed by a discussion of the assumptions employed in the model with a detailed description of each module’s data inputs, outputs, and parameters. After a brief overview of the simplified model, the focus turns to installation requirements for the toolbox and instructions for accessing the tools within. After learning to access the tool, there is a detailed breakdown for finding and preparing data inputs for OSTDS locations, groundwater modeling, and particle tracking. Once comfortable with preparing data inputs, the manual explains the theory and practice of sensitivity analysis and model calibration within the toolbox. Finally, an example problem (referred to as Lakeshore example) for preparing the input files and executing each module is provided.

The measurement units used in this manual may vary between metric and imperial units. However, required units are always explicitly stated. For clarification, it is best to use the units of meters and the projection coordinate system of North American Datum (NAD) 1983 Universal Transverse Mercator (UTM) Zone 17 North (N), identified by the European Petroleum Survey Group (EPSG) via the Well-Known ID (WKID) of 26917. To make this manual more straightforward to read, a specific typographic convention has been adopted as follows:

  • Model inputs and parameters are in bold in the document text and are surrounded by [brackets] in the Lakeshore example. Names of attributes (i.e., field names) in attribute tables are always shown in the Courier New font.

Acronyms and Abbreviations

In this manual, abbreviated acronyms or terms are spelled out in full the first time they appear. Table 1 is a list of acronyms and abbreviations used in this manual:

Table 1: Abbreviations

ArcNLET-Py

ArcGIS Pro Nitrogen Loading and Estimation Toolbox for Python

CPU

Central Processing Unit

CSV

Comma-Separated Values text file

DEM

Digital Elevation Model

DTW

Depth to Water Table

Esri

Environmental Systems Research Institute, Inc.

FDEP

Florida Department of Environmental Protection

FID

Feature ID

GIS

Geographic Information System.

GUI

Graphical User Interface

MODFLOW

Modular Three-Dimensional Finite-Difference Groundwater Flow Model

MODPATH

Modular Three-Dimensional Particle Tracking Model

MT3DMS

Modular Three-Dimensional Multispecies Transport Model for Simulation

NED

National Elevation Dataset

NH4

Ammonium

NHD

National Hydrography dataset

NO3

Nitrate

OSTDS

Onsite Sewage Treatment and Disposal System. A septic tank is an example of an OSTDS.

RAM

Randon Access Memory

PO4

Phosphate

SA

Spatial Analyst (extension for ArcGIS)

STU

Soil Treatment Unit

STUMOD

Spreadsheet-Based Analytical Flow and Transport Model

SSURGO

Soil Survey Geographic Database

TNM

USGS The National Map Download v2.0

VZMOD

Vadose Zone Model

See also: - Simplified Model of Nitrogen and Phosphorus Transformation and Transport for details on the simplified model. - Installation and Requirements for installation requirements. - Preparing Input Data for information on preparing input data. - Lakeshore Example for the lakeshore example. - Sensitivity and Calibration for sensitivity analysis and calibration. - References for the references section.