Groundwater modeling tutorial in MODFLOW 6 with regional flow, lakes, rives and piezometers

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We have developed an applied groundwater modeling case on the mesoscale that covers the most relevant physical process that affect the underground flow regime. Numerical simulation was constructed on Modflow 6 and Model Muse 4 on steady state conditions with variable hydraulic conductivity with depth to represent interbedded low conductivity layers. The tutorial cover all the steps of model and boundary condition setup, working with spatial data, analysis of water balance and review of water levels on piezometers.

Note: This is a base case for a coming webinar in sensibility analysis with MODFLOW 6, Python and the Flopy and Salib libraries. More information of this event will be posted on our social networks.

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How to install Modflow 6 on Model Muse 4 - Tutorial

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Great free and open groundwater flow modeling software are in constant development process, therefore year by year we have newer versions or even new software. This time we have uptated a basic and useful tutorial from 2016 to the new version of Modflow and Model Muse. The tutorial shows the complete procedure to download and install Model Muse 4 and configure Modflow 6.

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How to install Python - Geopandas on Anaconda in Windows - Tutorial

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Geopandas is an amazing library for spatial analysis since in combines the spatial tools from Shapely and Fiona with the versatily of Pandas Dataframes. Working with Geopandas in Windows was not exactly easy since there were some incompatibilities with the required packages. Here is a novel procedure to install successfully the Geopandas library when working with Anaconda in Windows.

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How to record GPS position on a Postgresql database using a Raspberry Pi - Tutorial

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Nowadays we can track GPS position with several devices as smartphones, wearables and handheld devices, but how can we store massive GPS positions on a effective way for later postprocessing, analysis and comparison with another device information. We have created a whole procedure enable the a GPS module as a serial device on a Raspberry Pi, then read the GPS information and sent it to a Postgresql database. The tutorial have several steps from the software installation, scripting to monitoring stored data.

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How to insert Piezometers (HOB) into a Regional Modflow 6 Model and plot Observed - Calculated Heads

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This tutorial has the complete process to insert piezometers as a HOB package into a regional groundwater flow in Modflow6. Original location, surface elevation and screen elevation are in csv format that was converted to shapefile in order to be imported by Model Muse 4. The tutorial also covers a Python script to represent the plot of calculated-observed heads with the NRMSE value as a header.

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Tutorial of Regional Groundwater Modeling with Local Refinement using MODFLOW 6 - DISV and Model Muse 4

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We have explored the new (or not so new) options of Modflow 6 and Model Muse 4 to create local refinements on a regional scale based on hydraulic features. So far, we came up with a decent example of regional groundwater modeling on a andean basin with three boundary conditions and decreasing hydraulic conductivity with depth. The tutorial also explores the complexities to model basins with high difference on elevation and the use of text defined parameters to implement the Newton formulation in Modflow 6.

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Basic Example of Particle Tracking Modeling with Modpath 7 on MODFLOW6 - DISV

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We have developed a tutorial on particle tracking with Modpath7 on grid with local refinement made by the Discretized by Vertices (DISV) option of Modflow6. Model constrution, boundary condition setup, groundwater flow simulation and particle tracking simulation was done on Model Muse 4. Groundwater flow conditions were conceptualized as steady state, and the particle tracking was simulated on forward and backwards tracking direction.

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Web 3D Representation of a MODFLOW Model with Hataripy, Paraview and Steno3D

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Groundwater can’t be seen (because its on the ground, obviously) and groundwater flow is extremely hard to understand unless we have a bigger scope of the theory and main features of the hydrogeological flow regime. One of the limitations for the understanding is the lack of interactive tools that provides user friendly environments for the representation of recharge zones, discharge zones, wells, wetlands, and other hydrogeological features.

We have developed a tutorial for the web representation of a MODFLOW model main features and head results in a combined process with the use of the Hataripy library, Paraview, Python and Steno3D.

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How to insert a 3D Geology into a MODFLOW Model with Python and Flopy - Tutorial

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Finite difference method as well as any other discretization method allows the conceptualization of a geological media into cells or other volumes. Geological models come in diverse formats in binary or text format and need to be “translated” to the cell extension of a groundwater model.

This tutorial has a applied example of the implementation of a 3D geological model from a neural network into a groundwater model with determined horizontal discretization and layer thickness. The tutorial covers all the steps for model construction and hydrogeological unit determination with scripts in Python with Flopy and other libraries. Comparisons of the original and translated geological model were done as Matplotlib plots and Vtk files in Paraview.

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3D Geological Models using Neural Networks with Python Scikit Learn and Vtk - Tutorial

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We have done tutorial in Python and recent and powerful libraries as Scikit Learn to create a geological model based on lithology from drillings on the Treasure Valley (Idaho, USA). The tutorial generates a point cloud of drillings lithologies that are transformed and scaled for the neural network. The selected neural network classifier is Multi-layer Perceptron classifier implemented on the Scikit Learn library as sklearn.neural_network.MLPClassifier. An analysis of the confusion from the neural network is performed. The tutorial also includes a georeferenced 3D visualization from well lithology and interpolated geology as Vtk format in Paraview.

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3D Visualization of Well Lithology with Python, Pyvista and VTK - Tutorial

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There are standards for the lithology descriptions, but there are no standards about how to store lithological information and relate it to the drilling position. This disorder leads to the use of many formats and data files related to open and proprietary software.

In the search of “one tool that manages all tools”, as a similar concept of the “one ring that rule them all” from the Lord of the Rings (J.R.R Tolkien), we found that Python and its libraries: Pandas, Pyvista and VTK can do a decent job on the compilation, geotransformation, spatial location, and 3d geometry generation.

This tutorial deals with the 3D visualization as Vtk files on Paraview of the lithological information from hundreds of wells located on the Snake River - Idaho. The tutorial covers all steps from the download of the raw information processing to the list and arrays generation for the vtk file. The scripting work was done on a Jupyter Nobebook and the output 3D files were plotted on Paraview.

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How to translate Coordinate Systems for XY Point Data tables with Python Pandas and Pyproj

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Spatial information is linked to the position and a system of reference. There are many coordinate systems worldwide with different length units, projections and origins. Somehow, spatial analysis is always linked to information stored on different coordinate systems and we have to provide effective ways to translate them to a specific CRS (coordinate reference system).

We have developed a tutorial for the coordinate system translation of XY point location stored in tables. The tutorial shows the procedure to change coordinate systems from geographic and planar coordinates using the Pyproj library over a Pandas dataframe on a Jupyter notebook.

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How to smooth a Aster DEM elevation raster with QGIS 3 - Tutorial

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In developed parts of the world there are online elevation repositories with current and historical elevation data from field surveys, lidar, etc. However, for the rest of the world, the availability of online resources for elevation with adequate resolution are scarce. The ASTER Global Digital Elevation Model 1 arc second (ASTGTM v003) is one of the most reliable sources for elevation worldwide with a cell resolution of 30m and interpreted from "recent" images (from 2000 to 2013). In flat or vegetated areas the procedure to interpreted elevations face some complexities and the Aster DEM images show some bumps or high elevation spots that are not coherent when contrasting the elevation model with satellite panchromatic images. This tutorial shows a procedure to smooth the Aster elevation models with standard QGIS 3 tools on a practical exercise over a study area. The procedure can be applied to Alos Palsar images or any other noisy elevation raster.

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Fault Zone Groundwater Flow Modeling with MODFLOW6 DISV and Model Muse -Tutorial

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Conceptualization and simulation of groundwater flow in the area of influence of geological faults is really a challenge for numerical modelers. Besides the complexities and variety of faults there were some limitations of the numerical codes to simulate the mixed behaviour of faults and altered zones. We have developed an example tutorial to represent the main characteristics of groundwater flow in the fault zone for an applied case. The tutorial is developed in Model Muse with the MODFLOW DISV option for unstructured grid generation. Groundwater flow was analyzed on the water balance and a particle tracking simulation was done with MODPATH 7.

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How to create an Elevation Raster from Contour Lines with Python, Geopandas, Numpy and Gdal - Tutorial

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Spatial analysis is such an interesting discipline because it allows the evaluation of every phenomena related to their location. However, for some parts of the data processing the workflow on a GIS Graphical Computer Interface (GUI) can be repetitive and time consuming. Researchers need better and more efficient tools to process more amount of data in less amount of time and even with less quantity of software tools.

We have create a innovative script to generate an elevation raster file from a contour line with several steps of data processing. The script recognizes invalid geometries, simplify the polylines and extract vertices while creates a point geodataframe that is interpolated and geotransformed as a geospatial raster in .tiff format.

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How to define cell / layer confinement in MODFLOW 6 with Model Muse

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The process and options to define the cell / layer confinement has changed in MODFLOW 6 with respect to MODFLOW 2005. We have done an explanatory video about the process to setup the confinement for cells in MODFLOW 6 with Model Muse. There is also a discussion on the influence of the confined / convertible option on the aquifer response on an example model.

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Produced Water Chemistry and Isotope Analysis with Python and Pandas - Tutorial

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On hydrocarbon extraction, water is a byproduct that comes from the geologic formations that have also oil and gas. Produced water can be defined as fossil water, or water with a high residence time on the earth, with a particular water chemistry that is important to analyze when we deal with the treatment methods, disposal techniques or safety to drinking water sources. The USGS has developed a produced water geochemical database with more than 100K points that includes spatial information, well description, rock properties, water chemistry and isotopes.

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Basic Example of Stream Flow Routing (SFR) Package with MODFLOW and Model Muse

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The disconnexion of surface groundwater flow it is fact very common on highly exploited aquifers or under impacts from climate change. Many rivers are disconnected from the groundwater flow regime decreasing their flow amount due to infiltration losses. For the simulation of this surface flow, unsaturated flow and groundwater flow phenomena the MODFLOW package Streamflow Routing (SFR) was developed.

This tutorial develops an numerical model of disconnected surface groundwater flow with MODFLOW SFR and Model Muse. The study case has regional flow and a river network with monthly flow on transient conditions over 2 years.

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Geochemical Speciation Modeling and Analysis with Phreeqc and Julia - Tutorial

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The speciation modeling allows to calculate the distribution of aqueous species in a solution. Phreeqc is capable to simulate this speciation calculation and we are going to demonstrate this capability on a study case of aqueous species in seawater. Modeling was done with a Phreeqc executable and results were analysed on a interactive Julia script. Both parts were done on a Jupyter Lab session.

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Websites where you can download complete groundwater flow models in MODFLOW

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Learning groundwater modeling is a challenge for the complexities of the codes, the lack or scarce piezometric and water quality data, the heterogeneity of the porous media and the few resources to explore complete and applied groundwater models with different boundary conditions and predictive scenarios.

Just few websites had uploaded complete groundwater flow models in MODFLOW and are accessible to the general public. We have to admit that most of the websites come from public institutions in the US. We hope that in a near future we can have more resources to get model reports and the complete MODFLOW model.

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