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.

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 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.

January 02, 2024

Export MODFLOW6 3D model geometry (as Vtk) with Python - Tutorial

January 02, 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.

December 12, 2023

Docker image containing the parallel version of MODFLOW 6 with application examples

December 12, 2023/ Saul Montoya

Modflow on parallel processing seemed to lie in the far-off future, but now it’s possible to take advantage of most of your cores to run parallelized versions of MODFLOW 6. Since most MODFLOW modelers work on Windows we wanted to bring something more than a “packed” solution; our goal was to bring an enriched “packed” experience.

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 12, 2023

How to direct download / clip elevations and import them to Model Muse with Python - Tutorial

October 12, 2023/ Saul Montoya

If you work often with numerical models this process will save you much time. The traditional method of downloading elevation models (Aster DEM) from websites, and reprojecting / clipping them with GIS software can be time consuming and pulls you out of other critical tasks on model conceptualization and calibrations. We have done a complete process in Python under WSL that runs Ubuntu in Windows, this platform was chosen due to the complexities of installing GDAL in Windows.

There are two scripts, one to download the images and the second to translate and clip the image. Finally the elevation are imported as a Surfer Grid File (*.grd) into a model in Model Muse.

August 11, 2023

3d visualization of Modflow 6 models with Model Viewer - Tutorial

August 11, 2023/ Saul Montoya

Model Viewer is an excellent option for the visualization and even the animation of MODFLOW models. There is a version of Model Viewer for Modflow 6 models and another for the rest of MODFLOW versions. This tutorial deals with the whole procedure of 3d model visualization that covers the model import, setting up the vertical exaggeration, making isosurfaces, show flow direction arrows, plotting boundary conditions among other features of Model Viewer.

July 31, 2023

Spatial data processing for groundwater modeling in Model Muse - Tutorial

July 31, 2023/ Saul Montoya

Groundwater model creation requires a complete set of spatial data for the different hydraulic parameters, boundary conditions and other model items. Vector and raster data need to be preprocessed, converted, reprojected to fit the requirements of Model Muse.

This tutorial covers an applied case of raster and vector data processing for a groundwater model over the Oahu island (Hawaii, USA). The tutorial covers the steps to download the data, extract the river network and import the spatial data into Model Muse.

April 27, 2023

Seawater intrusion modeling with Flopy and Modflow Buy over a Tupac Cloud project - Tutorial

April 27, 2023/ Saul Montoya

Finally, a complete alternative for the simulation of seawater intrusion on fully geospatial groundwater flow models of coastal aquifers based on open source software. The groundwater flow model was constructed on the Tupac Cloud platform with two stress periods and a total simulation time of 40 years.

The Tupac project is downloaded and run locally on Anaconda where the Buy package for variable density flow together with the transport model are implemented on a Flopy script. A graphical representation of the grid, boundary conditions and results from the flow and transport models are developed as well on the Jupyter notebook.

April 17, 2023

Tupac Cloud T.8: Coastal aquifer simulation with wells and rivers on steady and transient states

April 17, 2023/ Saul Montoya

Applied case of regional groundwater modeling for a coastal aquifer with Modflow 6 using Voronoi meshes on Tupac Cloud. The aquifer has two stress periods (steady state and transient state) of 20 years each that simulate two phases of low/high aquifer exploitation. The model is constructed entirely from zipped shapefiles and rasters on the online platform. Results from the simulation are discussed on the water balances, water table distribution and cross section for all stress periods.

March 16, 2023

Tupac Cloud T.7: How to download your Tupac Cloud project and run it locally with Python and Flopy

March 16, 2023/ Saul Montoya

Tupac Cloud is based on Python and Flopy and every project can be downloaded to your machine for special analysis, furter Modflow 6 feature implementation, machine learning based calibration, or just because a local backup copy is required. This tutorial shows the complete procedure to download a Tupac Cloud project, the executable implementation, the scripts to run the flopy code and well as a description of the different files and folders from a model project.

March 14, 2023

Tupac Cloud T.6: Transient simulation of tunnel interaction with the groundwater flow regime

March 14, 2023/ Saul Montoya

This is an applied example of the impact trough time of a tunnel over the regional groundwater flow regime. The model has 5 stress periods with two variants of the drain (DRN) package implemented in Tupac Cloud. The tutorial covers all steps from model construction, boundary condition setup, model run and output data analysis.

March 08, 2023

Tupac Cloud T.5: Groundwater modeling of a construction site dewatering with well and trenches

March 08, 2023/ Saul Montoya

Applied case for the evaluation of a drainage schema on a construction site with Tupac Cloud. The model has three stress periods where the drainage schema starts with well pumping for 10 days and trench drainage with pumping for another 10 days. Results from the water balance were analyzed as well as the final distribution of head on the proposed construction site.

February 22, 2023

Tupac Cloud T.4: Transient simulation of the trench excavation impact on a coastal aquifer

February 22, 2023/ Saul Montoya

Local scale modeling of a 4 stage trench excavation on a coastal aquifer. The main objective of this modeling work is assessing the impact of the excavation on the nearby groundwater flow regime. The modeling work was done entirely with the tools, charts and tables from Tupac Cloud.

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