July 22, 2021

Effective stress calculation from MODFLOW Groundwater Flow Model with Model Muse & Flopy - Tutorial

July 22, 2021/ Saul Montoya

Effective stress theory was developed by Terzaghi in the 1920s. Based on our modeling experience we wanted to calculate the effective stress based on the results from a MODFLOW groundwater model. Finally, after 6 years from the first thought about it we came with a full deduction of the effective stress calculation based on the model geometry and an applied example for the effective stress calculation on a hillslope groundwater flow model.

The example model was developed in Modflow-Nwt and Model Muse, whereas the effective stress determination was done with scripts in Python and Hataripy (our fork of Flopy). The scripts can also generate 3D objects as VTK files of the model results, geometry and stresses that can be visualized in Paraview.

July 19, 2021

How to change your career to hydrogeology… with appropriate success

July 19, 2021/ Saul Montoya

We are not a talent agency, we are not even a job portal;however, as other topics on this blog, we post based on requests from our followers. We don’t want to conceptualize the definition of a job or a career, but let’s have a common agreement that a successful career in geosciences is an occupation that provides a level of satisfaction, covers some basic necessities and keeps you motivated to know more.

If your idea of success is to manage a big group of people, we might suggest you evaluate the construction or the retail industry; if you want approval and being recognized for your work you can start your own blog or become a Youtuber.

July 16, 2021

Which are the limitations of online learning for hydroinformatics?

July 16, 2021/ Saul Montoya

Based on our experience in online learning for water resources based on open source that dates way before the Covid pandemia, we have seen some limitations of elearning as a framework to teach software for water resources.

Even though we can conceptualize elearning as something new, it is in fact a poor performance copy of the classroom environment on the computer. We simulate the whiteboard (we prefer chalkboard, less allergic), the teacher, the interventions, the assignments, the exams and everything else that is related to the normal classroom, even breaks and graduations. But this “Second Life” version of education has its limitations that have to be well assessed in order to define strategies to achieve the objective of education: bring new and better capabilities to water resources professionals.

July 07, 2021

How to manage psychological stress of hydrogeologists / numerical modelers?

July 07, 2021/ Saul Montoya

Over the time, we have seen numerical modeling as a great tool for the evaluation of the groundwater flow regime and we might have seen numerical modelers as high level professionals with strong analytical capabilities that can provide all the answers we need to proof that a project is sustainable or the accuracy of a predictive simulation. On a broad perspective we might have overestimated the numerical modeling exercise and sometimes deified numerical modelers, but by sure we haven’t seen them as humans.

July 02, 2021

How to insert and read Observation Points (OBS6) in Modflow 6 with Model Muse and Flopy - Tutorial

July 02, 2021/ Saul Montoya

Modflow 6 has a new approach in setting up observation points and it's essentially different to the previous versions. The OBS6 package works not only with heads and drawdowns but also with flows, so it's also possible to calibrate the model against baseflow or any other recorded flow from a boundary condition directly. We have created an applied case of the implementation of piezometers in a hillslope groundwater flow model in Modflow 6 and Model Muse. The tutorial covers all the steps related to the implementation of the observed points in Model Muse as well as the comparison among simulated and observed heads through scripts in Flopy.

June 24, 2021

How to install the Python geological modeling library Gempy in Windows with Debian and WSL

June 24, 2021/ Saul Montoya

Gempy is an open-source library for modeling geology written in Python. The library is capable of creating complex 3D geological models including structures, fault networks, and unconformities and it can be coupled with uncertainty analysis.

Due to the required packages and specific configuration the installation of Gempy is a challenge on Windows, we have developed an alternative installation process by the use of a Debian kernel under a Windows Subsystem for Linux. This tutorial shows the complete procedure to install Gempy from the Debian kernel setup to the review of the Gempy in Python.

June 21, 2021

How to create a point/line/polygon shapefile with Python and Fiona - Tutorial

June 21, 2021/ Saul Montoya

Storage, management and analysis of geospatial vector data as an ESRI shapefile is a common procedure of GIS and related professionals. The generation of these spatial files can be done not only on a desktop software but also by Python commands. We have created an applied example that shows the procedure in Python to create point, line, and polygon shapefiles from a csv file by the use of the Fiona library.

June 18, 2021

How to install Python geospatial libraries (Gdal, Fiona, Rasterio, etc) under a Conda Env in Windows

June 18, 2021/ Saul Montoya

Python is a great tool for spatial analysis and geomachine learning, however sometimes the Windows operating system presents some difficulties to install and run the bunch of Python libraries such as Gdal, Fiona, Geopandas, Rasterio. We are aware that most geoscientists, water resources specialists and related professionals work on Windows, therefore we are always in the search of new ways to get Python working with all its geospatial capabilities in every computer. We have created a tutorial that shows the installation process of the Python geospatial libraries in Windows by the use of a Conda environment; the process is simple on its steps, however the sequence and factors related to the package compatibility are important on the installation.

June 15, 2021

A place to find MODFLOW executables for any operating system: Windows, Mac or Linux

June 15, 2021/ Saul Montoya

A normal distribution of the core versions of MODFLOW as well as its variants, and Modflow-Based particle tracking and solute transport models includes not only the executables for Windows, but also the documentation, source code, test problems and other utility programs. Working with the multiple tools of Modflow implies a huge collection of files that aren’t useful for the simulation itself if you are working on Windows. Modelers working on Mac or Linux had to compile our executable by themselves.

June 03, 2021

How to extract centroid coordinates in QGIS with Field Calculator - Tutorial

June 03, 2021/ Saul Montoya

We did a simple procedure in QGIS but unknown to us that extracts the centroids of lines and polygons with Field Calculator commands inside the attribute table. The procedure is straightforward and does not involve the use of any intermediate layer.

June 02, 2021

How to install Postgresql and Postgis in Windows 10 with WSL and Debian - Tutorial

June 02, 2021/ Saul Montoya

The normal method to install Postgresql and Postgis requires the set up of several binaries and the workflow is usually on graphical user interfaces (GUI). We wanted to come with a way to install Postgresql and Postgis in Windows 10 while keeping the shell experience from Linux. This tutorial shows the procedure to install the database inside a Debian application (it could be Ubuntu as well) in Windows 10 that can actually be accessible from QGIS.

June 01, 2021

What we dont see in the development of open source software for groundwater modeling

June 01, 2021/ Saul Montoya

Usually we dedicate much time to developing tutorials and sometimes, just a few times, we actually write an article on this blog. Lately, our aim to discover and code is much greater than our impulse to give our opinion. This post is a special case where we write something without knowing if it is written because we are motivated or because there is something that needs to be written. In any case, writing this post doesn’t make us more free or happy... “Es macht uns nicht mehr zufrieden”... because we don´t know much about some things related to human nature.

May 28, 2021

5 tutorials for crop detection and vegetation delineation with Python and QGIS

May 28, 2021/ Saul Montoya

Over the last months we have researched the different tools in Python and QGIS available to recognize crops and vegetation as geospatial vector files. We have used a variety of techniques that range from machine learning algorithms with Scikit Learn and Scikit Image to just more innovative band combinations and reclassifications in QGIS. This article shows the summary of the tutorials produced so far that we are sure will be very helpful for GIS professionals and geoscientists.

May 26, 2021

Mixing groundwater and seawater geochemical modeling with Phreeqc and Python - Tutorial

May 26, 2021/ Saul Montoya

Phreeqc can solve geochemical simulations for a specific solution and simulations relying on previous results. We have developed a tutorial that goes through the Example 3 from the Phreeqc documentation in a stepwise approach to simulate groundwater, seawater, the mixing from both and cases regarding the equilibrium with calcite and dolomite. There is a Python class capable of running the input files and parse results incluided on the scripting part of the input files.

May 21, 2021

A geospatial Python class for crop recognition over drone orthophoto - Tutorial

May 21, 2021/ Saul Montoya

Spatial analysis and machine learning sometimes require massive coding in order to achieve decent results such as identifying plants from a drone orthophoto. We wanted to create a simple workflow for beginner and intermediate Python users to work with these libraries without much pain or frustration. This tutorial has the complete procedure to use a Python class that recognizes plants from an orthophoto based on sample points and creates intermediate plots and identifies plants as point shapefiles.

May 18, 2021

How to delineate crops from Drone Orthophotos with QGIS - Tutorial

May 18, 2021/ Saul Montoya

While doing research on machine learning algorithms for drone orthophotos we found that crops can be delineated with just standard QGIS with excellent performance. Based on the addition of the blue and red band divided by the green band we can have a new vegetation index where the most healthy crops have low index values (0-1.5) and the dry crops / barren soil have high values (more than 1.9). This tutorial shows the complete procedure on QGIS to perform the delineation from bean plants on a drone orthophoto with a resolution of 5cm.

May 14, 2021

How to make a geological map with QGIS - Tutorial

May 14, 2021/ Saul Montoya

This tutorial deals with the representation of geological information at regional scale from the Central Beaverhead Mountains, Idaho, US and creates a geological map through a series of processing and representation steps as:

Applying styles to geological units
Representation of contacts and normal / thrust faults

May 08, 2021

How to interpolate geospatial points to contours with Python and GDAL - Tutorial

May 08, 2021/ Saul Montoya

We have developed an alternative to a common procedure in GIS that is to create contours from a point shapefile but just with Python commands. By the use of Python and the GDAL library we can store this process into a function and perform contours from several point sets or different point queries.

May 05, 2021

How to download well info and groundwater levels from the NWIS server with Python - Tutorial

May 05, 2021/ Saul Montoya

We have developed an applied example to download information and groundwater levels for one well and multiple wells with Python and the dataretrieval package. The tutorial stores information and levels on a csv file an can be easily applied for streamflow and water quality data stored on the NWIS.

May 03, 2021

How to make a lake/reservoir volume-elevation curve with Python - Tutorial

May 03, 2021/ Saul Montoya

Python is a programming language capable of performing calculations for hydrological studies and water resources evaluations. We have done a tutorial for the volume-elevation curve determination of the lake Patillas in Puerto Rico with Python and numerical / spatial libraries as Numpy and Rasterio. Finally, results were compared to the volume-elevation curve form a USGS survey. The procedure was done this time for a lake, but can be easily applied to any reservoir or water body when the bottom elevation is available as a raster file.

May 9, 2024

Diploma in Groundwater Modeling with Python and FloPy - Asynchronous

FloPy is the Python library that builds and executes MODFLOW models; this library has been enhanced to provide full support of MODFLOW 6 with most of its recent development is related to functionality for MODFLOW 6, tools to use vector and raster spatial data and common plotting and export functionality.

May 8, 2024

25% Off: Diploma in Applied Groundwater Modeling with MODFLOW and Model Muse - Asynchronous

We have designed a complete program on MODFLOW with Model Muse that ranges from the essential topics in flow and transport modeling to applied cases of regional modeling, infrastructure projects, and seawater intrusion. MODFLOW with Model Muse is a recent open-source software that provides various tools for simulating the groundwater flow regime in different environments.

30% Off: Program in Hydrological Modeling with SWAT+ and QGIS - Asynchronous

This program is designed to provide systematical learning from the most basic and general topics to intermediate and advanced topics, allowing the student to understand the various steps in developing hydrological models using the SWAT+ interface for QGIS. This program has a series of theoretical and practical concepts that allow the student to process spatial data, manage meteorological databases, build hydrological models, develop sensitivity analyses, and perform manual and automatic calibrations using versatile tools such as SWAT+ Toolbox, SQLite, and Python.

September 9, 2026

Benchmarking mf6Voronoi v0.0.38: Parallel Performance, Scaling Limits, and Mesh Refinement Dynamics

With the upcoming release of mf6Voronoi v0.0.38, optimizing mesh generation workflows remains a top priority. Constructing complex unstructured Voronoi grids for MODFLOW 6 can become computationally intensive as spatial resolution increases. To address this challenge, parallel execution capabilities were introduced into mf6Voronoi leveraging dask-geopandas.

August 20, 2026

Geopandas tools for the representation and analysis of water chemistry data - Tutorial

This tutorial explores a powerful interactive GeoPandas tool that facilitates the visual analysis and representation of water chemistry data. Through this Python workflow, you can display sampling points over satellite imagery and various basemaps, map concentrations using automatic color scales, and adjust marker sizes based on analyzed parameters. This direct integration allows you to customize the variables displayed on hover, streamlining data evaluation for baseline studies or water pollution diagnostics.

July 23, 2026

How to Interpolate Over 2 Million Points Quickly and Without Freezing - Tutorial

Interpolating large volumes of spatial data through the QGIS graphical interface is often a headache: the process takes too long or, even worse, the program freezes while consuming all system resources. In this tutorial, we will show you how to interpolate nearly 2 million points in less than two minutes using the OSGeo4W Shell and GDAL commands with the IDW method. By creating a virtual layer file (.vrt), you will learn a highly efficient, reliable, and lightweight workflow that enables you to work with millions of data points without being constrained by the limits of the GUI.

July 17, 2026

Plotting Water Surface Elevation from a 2D HEC-RAS Model using Python - Tutorial

This tutorial demonstrates how to accurately and efficiently extract the water surface elevation at a specific point from a HEC-RAS 2D unsteady flow model using Python in Jupyter Lab. Since water levels vary across the mesh and native software tools can limit automation, the author teaches how to open HDF5 output files (.hdf), load a point shapefile using GeoPandas, and apply a geospatial index K-d tree to locate the nearest computational cell. Finally, the time series data is processed to generate a water level hydrograph, which is essential for hydrogeological model calibration.

July 2, 2026

Advanced Crop Water Demand Modeling: Simulating ETo, ETc, and ETa with Python and pyfao56 - Tutorial

estimations of crop water requirements. This applied case offers a deep dive into modeling crop evapotranspiration using the standardized FAO-56 Dual Crop Coefficient methodology, implemented programmatically through Python.

Using a real-world case study of olive cultivation (Olea europaea) in the hyper-arid coastal desert of Bella Unión (Arequipa, Peru), we will demonstrate how to build an end-to-end hydrological data pipeline. Participants will learn how to integrate spatial data, process satellite-derived and weather station climate parameters, define soil-water-crop constraints, and simulate complex deficit drip-irrigation schedules.

Blog