March 22, 2024

Simple example of ion exchange modeling with Phreeqc and Aquifer App - Tutorial

March 22, 2024/ Saul Montoya

An example that demonstrates the Phreeqc and Aquifer App capabilities to model ion exchange. This example uses the cation ion exchange approach where only the EXCHANGE keyword is used because EXCHANGE_MASTER_SPECIES and EXCHANGE_SPECIES are included in phreeqc.dat database. The model output is parsed as charts and tables and the solution composition and description are calculated and compared before and after the exchange.

March 21, 2024

A Python class to export Modflow 2005 model 3D geometry and parameters to Vtk - Tutorial

March 21, 2024/ Saul Montoya

Generating 3D visualizations of groundwater models is essential to analyze the flow regime, perform quality checks and see the interaction of the groundwater body with external factors / boundary conditions. The Flopy library has tools to export the parameters, boundary conditions and results that we have modified and compiled within a Python class. The use of this class allows the generation of Vtk files on a friendly way and in few steps. The tutorial also includes a representation of the parameters generated in ParaView.

March 18, 2024

Simple example of kinetic dissolution of calcite with Phreeqc and Aquifer Lab - Tutorial

March 18, 2024/ Saul Montoya

This is an example of calcite dissolution with kinetics where a simplified rate and initial molality are defined. The tutorial covers creation of an input file for Phreeqc, database selection, Phreeqc simulation in Aquifer App and analysis of processed output data on a Jupyter notebook. Finally the molality of Calcium and pH are plotted with time.

March 14, 2024

Interactive representation of a geospatial raster with Python, Folium and Rasterio - Tutorial

March 14, 2024/ Saul Montoya

Sometimes we want to reproduce or want to get something similar to a desktop GIS environment on a Jupyter notebook with options to show/hide layers and select background maps, but there was a missing part on our effort and it was the raster representation.

We have developed an applied case of single band raster representation on a Jupyter notebook with Rasterio and Folium. The raster has to be in WGS84 and the script can be coupled with more Folium features for the representation of vector data, background maps, menus and popups.

March 12, 2024

Simple example of irreversible reactions in Phreeqc and Aquifer App - Tutorial

March 12, 2024/ Saul Montoya

This is a tutorial of geochemical modeling in Phreeqc and Aquifer App that uses the REACTION keyword for the simulation of irreversible reactions that transfer a certain amount of elements to or from the solution. The selected example deals with the reaction of rainwater with NaCl and Calcite over 4 steps. Phreeqc simulation and model output analysis are performed on the Aquifer App that has great tools for the model setup and the analysis through interactive menus, tables and charts.

March 05, 2024

Simple example of mineral equilibrium in water with Phreeqc and Aquifer App - Tutorial

March 05, 2024/ Saul Montoya

This tutorial cover all the steps to build and run a geochemical model of a water sample in equilibrium with Fluorite and Gypsum. The tutorial explains the parameters to setup a mineral together with and analysis of the element concentrations, the amount of dissolved phases and the final saturation indices.

February 14, 2024

Automatic calibration of transient pumping test with MODFLOW 6, Python, FloPy and Scikit Learn - Tutorial

February 14, 2024/ Saul Montoya

Python has awesome packages for machine learning that can be coupled to groundwater models and perform automatic calibration of hydraulic parameters. This tutorial covers the procedure to implement a neural network based on a set of parameters set with corresponding head values; the study case is on a transient pumping test model with an observation point located around 10 meters away from the pump well. The analysis predicts the calibration parameters from the spatially interpolated observed head values.

February 13, 2024

How to export a MODFLOW 6 model grid to shapefile with Python and Flopy - Tutorial

February 13, 2024/ Saul Montoya

We did this tutorial since the documentation or examples on the topic were not available. Flopy can export the model grid and model attributes to shapefile with a coordinate system of reference for the three types of discretizations of MODFLOW 6. We have done an applied example to export the grid of a discretized by vertices model (DISV) to the ESRI Shapefile model. The tutorial also show options for the final grid representation in geopandas.

February 12, 2024

Seawater speciation modeling on cloud with Aquifer App and Phreeqc - Tutorial

February 12, 2024/ Saul Montoya

No more installations, no more database link up, no more raw text data as model output. Aquifer App now can run Phreeqc with great tools for the geochemical model setup, database selection and tables / graphics for the different simulation components.

This applied example calculates the distribution of aqueous species in seawater and the saturation state of seawater relative to a set of minerals and is based on the Example 1 of the USGS Phreeqc example documentation.

January 24, 2024

Sensibility analysis of transient pumping test with MODFLOW-6, Flopy and SALib - Tutorial

January 24, 2024/ Saul Montoya

This tutorial covers the whole procedure to perform a sensitivity analysis over a 72 hour pumping test plus recovery on the hydraulic response in an observation piezometer located at 11 meters from the well. the Since the study case it’s a transient model the sensitivities will vary over time and stage of pumping/recovery.

January 17, 2024

How to import a Leapfrog geological model to Model Muse with Python - Tutorial

January 17, 2024/ Saul Montoya

Having a geological model can enhance numerical models since it allows to represent higher accuracy the potential distribution of hydraulic parameters in the horizontal and vertical direction. The process to implement/insert a geological model into a Modflow model is a challenge due to restrictions on proprietary software and spatial tools; we have done the whole procedure to insert a geological model into a MODFLOW-NWT groundwater model with scripts in Python, Pyvista and others.

The code extracts the cell centroids of the modflow model and then compares its position with the different geological units exported from Leapfrog to Vtk. Once the corresponding lithology of the cell is identified a hydraulic parameter is assigned. The tutorial works from Vtks of a geological model done in Leapfrog, but it can work with any Vtk.

January 12, 2024

Convert geological units from Leapfrog (*.msh) to VTK using Python and GemGIS - Tutorial

January 12, 2024/ Saul Montoya

This tutorial shows the complete procedure to convert a geological unit as a Leapfrog mesh (*.msh) to the VTK (Visualization Toolkit) format using Python and GemGIS. Follow these steps to seamlessly transfer your geological data for advanced visualization, analysis and comparison with other model results.

January 11, 2024

Geological modeling of sedimentary layers from geospatial rasters with Python and Gempy - Tutorial

January 11, 2024/ Saul Montoya

Based on a coupled workflow on QGIS and Python it is possible to extract the required information for a Gempy model and run it for defined voxel sizes. This tutorial covers the whole procedure of spatial data preparation, data preprocessing in defined formats and geological modeling with Python and Gempy.

January 10, 2024

How to georeference a image/raster with Python and Rasterio - Tutorial

January 10, 2024/ Saul Montoya

Georeferencing in Python has the advantage that it can be performed repeatedly without the need to define control points each time. It also allows you to add/remove control points and observe the impact on the transformation array. This tutorial demonstrates the complete georeferencing process of a national map using 3 points whose pixel coordinates have been extracted from the Paint utility in Windows. The tutorial also exports the raster while assigning a reference system.

January 09, 2024

Groundwater modeling of a pumping test over a confined aquifer with MODFLOW-6 and FloPy - Tutorial

January 09, 2024/ Saul Montoya

We have done an applied groundwater model for a pumping test on a confined aquifer. The wellsite is located on the Clairborne aquifer (Georgia, USA) and has two observations on different layers besides the well itself. The aquifer test has two periods of pumping and recovery that last 3 days each one and the numerical model was constructed with MODFLOW-6 based on a Python script with the FloPy package. Comparison among observed and simulated wells were done with plots in Matplotlib.

December 04, 2023

Lithium speciation calculation on salt lake brines with Phreeqc and Python - Tutorial

December 04, 2023/ Saul Montoya

Lithium interaction with the aqueous phase on brines phase is not well understood or at least not well covered by the scientific publications. To evaluate brine composition, brine dynamics and the interaction of the different components is really a challenge with the available tools for geochemical modeling as Phreeqc since it doesn’t appear in all the databases and in most it is only associated with sulfates.

November 09, 2023

Online tools for groundwater modeling preprocessing with Model Muse - Tutorial

November 09, 2023/ Saul Montoya

If you want to speed up some steps in groundwater modeling you might be interested in the tools presented on this tutorial. We have developed some online tools that replace intense and time consuming tasks on desktop software and web servers and provide vector and raster data on the formats required by Model Muse. The tutorial covers the steps of DEM generation as Surfer Grid File (*.grd) with the definition of watersheds and river network based on two online services provided by Hatarilabs.

October 18, 2023

How to split Modflow 6 groundwater model with Flopy and MF6Splitter - Tutorial

October 18, 2023/ Saul Montoya

Modflow 6 has changed in many ways the traditional concepts of groundwater modeling; now a group of models can run under a "simulation" and these models can interchange flow and transport. Under this structure Flopy has implemented a tool to split a groundwater model into several models where their results can be reconstructed and compared to the original entire models. Capabilities and features like this make Flopy and Modflow 6 a great tool for developing advanced groundwater models that simulate complicated tasks or requirements to the groundwater flow regime.

October 06, 2023

How to reproject, clip and interactively plot HDFs with Python and GDAL - Tutorial

October 06, 2023/ Saul Montoya

Large amount of spatial data is indexed and delivered through files in Hierarchical Data Format (HDF). These files are compatible with desktop GIS software as QGIS but they are not so easy to open/read/process with standard Python libraries as Rasterio, or with dedicated libraries. On our research we found the spatial functionality on the powerful GDAL binaries and library for Python.

September 28, 2023

Online crop counting from drone orthophotos with Hatari Utils - Tutorial

September 28, 2023/ Saul Montoya

Orthophoto from drones provide us aerial imagery with spatial resolution in the scale of centimeters. With this high definition and cheap orthophotos we can interpret, analyze and quantify objects on a horizontal distribution by means of machine learning libraries for image recognition and cluster analysis.

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.

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.

unsteadyTransient2DRiverFlowModelingWithHECRAS_en_12.png

June 30, 2026

Unsteady / transient 2D river flow modeling with HECRAS - Tutorial

This applied example demonstrates the simulation of unsteady flow around a river island, guiding you through the complete numerical modeling workflow. It begins with pre-processing, covering spatial data import, boundary condition definition, and computational mesh generation. Next, the setup details importing hydraulic loading data from DSS files and optimizing the computational time step based on the Courant condition to ensure strict numerical stability and convergence. Finally, the example features a comprehensive post-processing review of the simulation results, analyzing velocity fields, water surface profiles (stages), particle tracking, and immersive 3D visualizations.

April 29, 2026

Automatic calibration of pumping test data with MODFLOW6, Model Muse and Pest - Tutorial

This tutorial walks hydrogeologists through the full workflow of automatic calibration of pumping test data using MODFLOW 6, ModelMuse, and PEST. A real pumping test scenario — comprising a 6-hour pumping phase and an 18-hour recovery phase — is set up in ModelMuse, where the well is conceptualized as a Multinode Aquifer Well (MAW) boundary condition to accurately represent multilayer aquifer interactions. PEST is then implemented to automatically estimate key hydraulic parameters including hydraulic conductivity, specific storage, and specific yield, eliminating tedious manual calibration and delivering reproducible, optimized results. Whether you're new to parameter estimation or looking to streamline your existing workflow, this tutorial offers a practical, hands-on guide to modern groundwater model calibration.

Blog