September 29, 2025

7 tutorials for coupling geological information into groundwater flow models build with Model Muse

September 29, 2025/ Saul Montoya

Next challenges on groundwater modeling facing scenarios of climate change and sustainable groundwater management require the implementation of fully coupled geological models into groundwater flow models. Even though we have dealt with this topic, we still have a lot to do in providing applied cases / tutorials for the hydrogeological unit conceptualization based on geological information with open source codes such as MODFLOW.

June 30, 2025

Determination of the Depression Cone from an Open Pit with MODFLOW6, Flopy and mf6Voronoi - Tutorial

June 30, 2025/ Saul Montoya

One of the key objectives from groundwater modeling in mining is the determination of pit inflows and the extension of the depression cone. This tutorial shows an applied case of determination of a depression cone from an open pit model built with MODFLOW6, Flopy and mf6Voronoi. The model has faults and the tutorial covers all steps from model import, data processing and export of geospatial data from the depression cone.

June 11, 2025

Geospatial Crop Recognition from Drone Orthophotos with Python and HatariTools - Tutorial

June 11, 2025/ 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 new Python package called hatariTools that recognizes plants from an orthophoto based on sample points and creates intermediate plots and identifies plants as point shapefiles.

April 30, 2025

How to install Rust in Windows under WSL - Tutorial

April 30, 2025/ Saul Montoya

In this tutorial, we'll walk you through step-by-step how to install Rust inside your WSL environment. Whether you're completely new to WSL, or just want a clean Rust setup, this guide will have you up and running in no time. We'll cover installing WSL, setting up your Linux (Ubuntu) distribution, and installing Rust.

September 04, 2024

Open, modify, run, and read output from HEC-RAS models with Python - Tutorial

September 04, 2024/ Saul Montoya

Python can communicate with other softwares through standards in Windows (COMs) and thus provides a higher level of interoperability for river flow models made in HEC-RAS. The amount of tools provided by HEC-RAS through the COM is huge; in this tutorial we will cover some examples of HEC-RAS model interaction for two applied cases from Python scripts in Jupyter Lab.

August 15, 2024

How to create a Geological Model from a Point Shapefile with Gempy and Aquifer App - Tutorial

August 15, 2024/ Saul Montoya

This is an applied case were we build a geological model only with lithology information stored as a point shapefile. The tutorial covers all steps from raster (array) generation for all surfaces together with the orientation sampling and format of surfaces/orientations as Gempy input files. The generated data was inserted in the Aquifer App that implements an interface to create Gempy models. Finally the lithology and layer surface geometry was exported as Vtk to be represented on Paraview with the initial data to evaluate the accuracy of the simulation.

August 01, 2024

NetCDF for water resources with Python for dummies (CHIRPS dataset) - Tutorial

August 01, 2024/ Saul Montoya

NetCDF has become a popular choice for storing and delivering precipitation and water resources related data. Its capacities to store multiple geospatial raster layers over time allow another level of abstraction on data analysis, however the format is of limited use on normal desktop applications and most times we are required to use a programming language such as Python or R.

May 24, 2024

Introduction to Python and Geopandas for Flooded Area Analysis - Tutorial

May 24, 2024/ Saul Montoya

Geopandas is one of the most advanced geospatial libraries in Python because it combines the spatial tools of Shapely, it can create and read different OGC vector spatial data, it can couple the Pandas tools to manage, filter, and make operations over the columns of the metadata, it has the capability to plot geospatial data on Matplotlib and even to Folium among other features. We have developed a tutorial of Geopandas applied to the analysis of flooded areas over the Boise city for a return period of 200 years; the tutorial covers introductory concepts of Geopandas, it will work with point, line and polygon vector data, create plots, simplify vertices and perform geospatial queries over inundated facilities and highways.

September 02, 2023

Modeling of mixing water / effluent with OpenFoam and HatariUtils - Tutorial

September 02, 2023/ Saul Montoya

Modeling flow on open channels and simulating water mixing to evaluate the final concentrations and mixing area was a hard task with conventional open source software. Based on our research and app development we came up with a process to model flow of water and effluent mixing and then calculate the mass flux with the initial concentration of certain chemical components to have a fully 3d simulation of the concentration development with time and distance from source.

June 02, 2023

Journal of online sensor setup on a Raspberry Pi under the Istsos framework (SOS Standard)

June 02, 2023/ Saul Montoya

We dont call this article a tutorial since not all steps of the sensor settings would be explained. It might be the idea of this article to show the general panorama of the sensor installation on a Raspberry Pi under the Istsos framework that implements the SOS standard.

June 09, 2022

Are hydrogeologists / numerical modelers forbidden from cloud services?

June 09, 2022/ Saul Montoya

In the semantic space the forbidden word is related to refuse to allow, and thus can create a controversy with the freedom of hydrogeologist / numerical modelers to choose whichever tool that can make the work done or the simulation run. However we as specialists in one part of the dynamics of the subsurface are conscious that solutions can not and must not be evaluated by single criteria.

February 09, 2022

Modeling Land Evolution at Basin Scale with Python and Landlab - Tutorial

February 09, 2022/ Saul Montoya

Climate changes, people change and land also changes with time. We can`t believe that the river networks will remain the same over the next 1000 years or that mountains and depressions will have the same elevation in the next 10000 years. But changes are not related to huge time frames, they can occur in decades or years at lower rates as well. In order to evaluate those changes we need some formulation of the key components of land evolution: fluvial, hillslope and uplift. We have developed a tutorial with Python and the Landlab library to simulate the land evolution at basin scale for 100 thousand years; inputs come from geospatial rasters and output data is exported as Ascii raster files.

November 08, 2021

Two open geological modeling softwares that you should know about

November 08, 2021/ Saul Montoya

For geologists, hydrogeologists, geostatistics, petroleum engineers, and other related professionals the choice for 3D geological modeling software was related to expensive and restrictive software that was in fact a “de facto” choice in several companies and institutions.

Although it is a choice of any company or professional to select the software anyone will use to model the geological units, a great gap subsides (using a geological term) on the use of this expensive software. If the software is expensive, how expensive will it be to get trained on this software? If few people have skills with certain software, how easy would it be to change to another software? How people can assess the quality of one software if they have no full capability on managing several softwares. As you have seen, restrictions on the licenses lead to these subsiding gaps, faults on quality, and an intrusion of professional ignorance.

August 16, 2021

Is glTF an alternative to VTK for the representation of voronoi mesh Modflow6 models?

August 16, 2021/ Saul Montoya

Representation of geospatial objects in 2D are well covered by the GIS software and standards where we have powerful tools and interchangeable spatial files, however when we work on 3D objects the universe of software and tools is like a jungle with a wide variety of issues. We will always consider 3D as the ultimate representation of an object using a computer, by sure the holograms and augmented reality can improve the way we interact with a object geometry, but since we are not in the common near future we will give much effort to the representation of these objects in our computer screens, tables and cellphones.

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 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 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.

February 27, 2021

Should groundwater models from environmental evaluations be done in open source software?

February 27, 2021/ Saul Montoya

The topic of open source software and environmental assessments has some interesting associations. For example, if an investment project delivers a groundwater model in Xflow software, the environmental evaluator needs an Xflow license in order to open the model, review the simulations, and report on their observations. But what about civil society? or the communities that have an interest in knowing how the model is built or in the results of the predictive simulations, do these people also need an Xflow license? And what happens if another regulator wants to review the model, can they do so or they can only ask for a technical opinion?

February 17, 2021

How to build a Postgis geodabatase with Python and Geoalchemy (with connection to QGIS3) - Tutorial

February 17, 2021/ Saul Montoya

As a peruvian slang the word “chicha” means mixture, but a mixture of a high level of heterogeneity, something like doing a pizza with all the ingredients from your refrigerator. This time we have developed a tutorial with this “chicha” spirit since it combines a database, sql language, a virtualization engine, Python, a variant of SQL Alchemy, port forwarding and connection to QGIS in Windows. Certainly, we are not code developers by nature, but we are pretty happy to have achieved this level of complexity or mixture.

We have developed an applied tutorial for the implementation of a Postgresql database with Postgis enabled on a Docker image. Information about groundwater well locations have been inserted from a CSV file with Python and Geoalchemy and Docker ports have been forwarded and open to be accessible from QGIS in Windows.

February 11, 2021

How to plot the azimuth and dip from a inclined bedding in QGIS 3 - Tutorial

February 11, 2021/ Saul Montoya

QGIS has a wide range of options for the representation of vector data (point, line and polygon) but specific workflows have to be established to apply QGIS in different fields such as Geology. We found that there were few resources about how to plot geological features as bedding planes, faults, synclines and other and we have decided to do a series of tutorials showing those procedures on applied examples.

This time, we have developed a tutorial with the complete procedure to plot the azimuth and dip of bedding planes with QGIS. The tutorial imports a SVG marker that rotates according to a field value while the dip is presented as a label.

Blog