November 25, 2019

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

November 25, 2019/ Saul Montoya

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.

November 18, 2019

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

November 18, 2019/ Saul Montoya

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.

November 06, 2019

Geochemical Speciation Modeling and Analysis with Phreeqc and Julia - Tutorial

November 06, 2019/ Saul Montoya

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.

October 25, 2019

Websites where you can download complete groundwater flow models in MODFLOW

October 25, 2019/ Saul Montoya

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.

October 18, 2019

Introducing Hataripy, the unofficial Flopy version that creates awesome VTKs

October 18, 2019/ Saul Montoya

A new unofficial version of the Flopy is available as Hataripy. This “fork” has tools for the representation of many features, boundary conditions and output with options for grid smoothing. Documentation for this library is on progress as we expect to introduce other features and identify some bugs.

Currently the library can:

Create the model mesh on the active zone with point and cell values
Create a shell of the water table
Create the geometry of any boundary condition

October 02, 2019

Unofficial MODFLOW flow and transport executables for Linux (Ubuntu tested)

October 02, 2019/ Saul Montoya

It might be that you are a talented groundwater modeler and very proficient with Python and Flopy that you start to realize that you don´t need to work in Windows anymore and want to migrate your favorite groundwater modeling code to other nice, soft, and warm Linux-based operating systems. Or, it might be the case that you want to configure and run MODFLOW models as a part of a webapp or in a web server. For the reasons mentioned before and other reasons that modern world could bring to us, a compiled version of MODFLOW in Linux is needed.

September 02, 2019

How to fill missing Elevations to empty Contour Lines with PyQGIS

September 02, 2019/ Saul Montoya

Elevation contour lines without the elevation attribute is common when we import contour lines from Autocad DXF files, but it has also happened that contour data was stored on a hard disk drive without elevation attribute and years later data is found and there is no one to ask to restore the missing information. This tutorial shows a practical procedure to fill missing elevations on contour lines with the use of PyQGIS on QGIS 3. The procedure uses an intersection line that crosses the contour lines where the base elevation and interval is known. There are some specific instructions to run the script that are well described on the video.

August 13, 2019

Temporal discretization impact on MODFLOW Model Heads and Water Budget

August 13, 2019/ Saul Montoya

For a transient model, a modeler needs to conceptualize a coherent and feasible time discretization approach, nevertheless searching for temporal discretization guidelines the Internet gives you digital noise: nothing relevant, nothing precise, nothing useful. These is the type of situation where you ask yourself: how many stress periods do I need, how many time steps do I require, which should be an appropriate size of the model output, or more important, will the size and number of stress periods and time steps have an effect on the model output?

August 08, 2019

How to Convert a PDF to ESRI Shapefile with Python, Geopandas and Inkscape - Tutorial

August 08, 2019/ Saul Montoya

In order to use the spatial data provided on a report we need procedures to extract the data on effective way. The amount of tools and techniques are quite advanced, and requires several open source software for specific procedures. We have done a complete tutorial with all the step required to extract the vector spatial data of a map reported as PDF into a ESRI shapefile. For this tutorial we have used Inkscape for the conversion of the PDF to DXF, QGIS to extract some information of the DXF, Python and Geopandas on a Jupyter Lab session for spatial translation and scaling.

July 24, 2019

The dark side of Python for Hydrology / Hydrogeology and the nightmare of unmet dependencies

July 24, 2019/ Saul Montoya

The near future of data processing for Hydrology / Hydrogeology is written in Python 3, and many universities and institutions are shifting from teaching C++, Matlab or Fortran to Python. It is surprising the amount of tools, packages, codes and Ipython notebooks available for the data processing and data analysis of water related data, even with high success in data analysis reproducibility.

However, there is not always a sunshine on working with Python, especially if you are working on Windows. After you have done your first steps in hydrological series plotting, statistical analysis or even run a neural network, you might want to do more with Python and there is when the situation can become unbearable.

July 15, 2019

How to do more Groundwater Modeling (or any modeling) in less amount of time

July 15, 2019/ Saul Montoya

Because time matters and everybody wants results and solutions now, groundwater modelers (or any water resources modeler) have to think how they can do more with the limited time available. This is a restructuration, a reengineering, a new conceptualization of not only what we do, but how we do, and if in the end we are happy with the main results, and secondary results we get from our modeling work.

Groundwater modelers are water resources specialists with high skills in computing, coding, maths and groundwater flow regime comprehension. The type of work, the complexity of the given areas of study, the limited observation data, the limited budget, the short completion times and the overall low perception and low understanding of groundwater flow and groundwater quality makes the modeling work somehow particular where we have to adopt special techniques to deliver good work while preserving the modeler integrity and wellness.

July 09, 2019

The soft and hard courses every Applied Hydrogeology Master Program should have

July 09, 2019/ Saul Montoya

There isn’t as well a clear definition of applied hydrogeology, that following the literal meaning should be the hydrogeology in practice. We like the definition of applied hydrogeology as the real world hydrogeology, as the hydrogeology of non-homogeneous, non-infinite, non-isotropic and even non-porous media; applied hydrogeology is the hydrogeology that goes behind the book, far away from the “aquifer, aquitard, aquiclude” classification. Applied hydrogeology is the part of hydrogeology that solve problems, the science that tells us if the groundwater remediation will work, if a industrial complex will have water on the coming decade, or when the salinitization from the pumping well will overcome the reverse osmosis plant capacity.

July 08, 2019

6 aquifers that every hydrogeologist should visit on a lifetime

July 08, 2019/ Saul Montoya

Perception and interest on the groundwater resources are of high initial interest but long term low popularity, that is why normal and plain hydrogeologist need to promote an innovative perspective of the relation from human society with the groundwater resources as a strong part for every environmental protection plan and sustainable management policy elaboration.

This article has a list of aquifers around the globe, with special characteristics where a normal audience can see how water can exist below surface, how people have interacted with the aquifer

July 04, 2019

How to work with Transmissivities in MODFLOW with Model Muse - Tutorial

July 04, 2019/ Saul Montoya

Hydraulic parameters for an aquifer flow can be expressed on different terms like Hydraulic Conductivity (K) or Transmissivity (T). On the default setup of MODFLOW 2005 with Model Muse there is no option to use directly Transmissivity unless a manual conversion is done to transform into K, this is because the selected flow package is Layer Property Flow (LPF).

When the flow package changes to Block Centered Flow (BCF6) it is possible to insert Transmissivities directly as datasets or as a object property. The BCF package also has more options for the layer type, with unconfined and partial confined aquifer options.

July 03, 2019

Performance analysis of Open Drone Map to process hundreds of drone images

July 03, 2019/ Saul Montoya

So far, OpenDroneMap is a strong open source alternative for the processing of drone imagery. We have done a recursive analysis over a set of aerial photos on a standard desktop computer to have a panorama of the rates and trends from OpenDroneMap in the computation of different amount of images. Although the rates and trends apply only for a specific dataset and computer configuration, this study can to be taken as a reference for the computational time and as a perspective of how the software works with great amount of data.

June 30, 2019

Tutorial of Unstructured Grid Groundwater Model with MODFLOW 6 and Model Muse 4

June 30, 2019/ Saul Montoya

Of the latest devopments in groundwater modeling there are two softwares: Modflow 6 and Model Muse 4. both developed by the USGS. The first software is the latest version of MODFLOW that allows triangular and unstructured grids, and the second is the latest version (from June 23) of the graphical user interface Model Muse that supports Modflow 6.

Unstructured grid it a type of discretization that allows us to have small cells at certain parts of the model while the rest of the model has bigger cells. This optimization of the model grid and cell number decrease the computing time, the size of the output files and the speed of the visualization tools. With unstructured grids we can model a great extension while preserving the right accuracy of the points of interest, we can even insert regional faulting or complex geological setups.

This tutorial shows the complete procedure to create a geospatial model of a alluvial aquifer with the interaction of regional flow, river and wells. The tutorial creates the unstructured grid, boundary conditions, model geometry, simulate flow with MODFLOW 6 and represent results in Model Muse 4.

June 24, 2019

Basic Example of Land Subsidence Modeling with MODFLOW SUB and Model Muse 4

June 24, 2019/ Saul Montoya

Cities under high exploitation of groundwater resources face severe problems of land subsidence due to pumping. This complex problem was addressed from earlier versions of MODFLOW as MODFLOW 2000 and has two packages: MODFLOW SUB and for its simulation with different options for the conceptualization and numerical modeling of normal aquifers and low conductivity interbeds.

Scientific research and professional consulting on the field of land subsidence modeling is limited; this scarcity might be because the coupled complexity of the appliance of numerical groundwater modeling and consolidation theory.

June 18, 2019

How to convert an ArcGIS Style to QGIS 3 - Tutorial

June 18, 2019/ Saul Montoya

Spatial data created / processed by commercial or open source software follows standards by institutions like the Open Geospatial Consortium; this standards allow the interoperability of the vector or raster data among different software however standards apply to the position but not the style. Styles from ArcGIS were not easy to convert to formats compatible with QGIS, specially if you don’t have the commercial software.

Governmental offices release spatial data as land use, land cover, infraestructures, and sometimes release styles in ArcGIS formats posing a great obstacle for the QGIS users. This tutorial shows the complete procedure to convert ArcGIS Style to QGIS as *.xml format with a case study of land cover from Costa Rica. The tutorial is developed in Windows, if you are a Linux and Mac users its necessary to install Mdbtools on your own operating system.

June 10, 2019

How to create a fully Geospatial Groundwater Model with MODFLOW and Flopy - Tutorial

June 10, 2019/ Saul Montoya

Nature is geospatial, and every physical process related to the groundwater flow and transport regime is spatially located or spatially distributed. Groundwater models are based on a grid structure and models are discretized on cells located on arrangements of rows and columns; is that level of disconnexion of the spatial position of a piece of porous media and the corresponding cell row and column that creates some challenges for the sustainable management of groundwater resources.

We have to create or re-create the duality in between the geospatial and the model grid, that would be similar to duality of a vector GIS object and its metadata on its essence but more difficult to manage. Affortunately Flopy, the Python library to build and simulate MODFLOW models, has tools to georeference the model grid even with rotation options. The workflow is kind of explicit, meaning that the modeler need a medium knowledge of Python and Flopy tools. This tutorial shows the whole procedure to create a fully geospatial groundwater with MODFLOW and Flopy.

June 04, 2019

Which is the most critical hydrogeological data needed for a numerical model?

June 04, 2019/ Saul Montoya

From a conversation with a specialist in soil subsidence we came to the conclusion about which was the most critical hydrogeological data needed for a numerical model. There is a proposed list of required data on this link, but when we plan a hydrogeological study which is critical? Data about the groundwater flow regime and the hydrogeological environment is always scarce. And there are even more complications on the data gathering because these data depend on a number of institutions and shareholders that could not be willing to share it because there is a mainstream idea

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.

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October 1, 2026

Smart analysis of online temperature sensor data with SensorThingsAPI and Python - Tutorial

This tutorial demonstrates how to connect to a SensorThings API FROST server using Python to retrieve, inspect, and visualize IoT sensor datastreams. After setting up the server connection and querying datastream details such as units and observation counts, the notebook extracts time-series observations using paginated REST requests and loads them into a Pandas DataFrame. Following the data preparation phase, the script produces a series of continuous time-series line charts using Matplotlib and Seaborn, displaying the chronological trend of air temperature measurements recorded over time.

riverAquiferGeospatialGroundwaterModelmfVoronoiStudio_en_12.png

September 30, 2026

River Aquifer Groundwater Flow Model with mf6Voronoi Studio and Model Muse - Tutorial

This tutorial demonstrates how to build and simulate a groundwater model focused on river-aquifer interactions using open-source software. The workflow begins in mf6Voronoi Studio, where a Voronoi grid mesh is generated to capture complex spatial geometries efficiently. The mesh is then imported into ModelMuse, where key aquifer properties and essential boundary conditions—including general head, river, well, recharge, and evapotranspiration—are configured. After running the model, the simulated results are evaluated through an analysis of the water balance and head distribution.

September 29, 2026

Mesh Generation of Regional MODFLOW 6 Groundwater Flow Models with mf6Voronoi - Tutorial

In this tutorial we introduce mf6Voronoi, a specialized tool for generating optimized Voronoi meshes for regional groundwater models capable of spanning thousand of square kilometers. The video demonstrates how to set up and run a Python script using Anaconda Prompt, leveraging Dask parallel processing to refine mesh resolution along key rivers and riparian ecosystems while maintaining a coarse discretization elsewhere. By utilizing multi-core computing, the workflow reduces total mesh generation time by approximately 40–45%, delivering a high-resolution, multi-scale MODFLOW 6 mesh consisting of over 150,000 cells in just a few minutes.

September 28, 2026

Introduction to Online Sensor Analysis with SensorThings API and Python - Tutorial

In this Hatarilabs tutorial, viewers learn how to access and query live environmental sensor data using Python and the OGC SensorThings API standard. The video walks through setting up a Jupyter Notebook environment to interact with a FROST-Server, explaining key SensorThings API concepts—including Things, Sensors, Observed Properties, and DataStreams. Using packages such as requests, pandas, and datetime, the session demonstrates how to apply API parameters like $top, $skip, $orderby, and $expand to efficiently filter and retrieve time-series observations, culminating in a data frame visualization of temperature readings from a live outdoor sensor.

September 22, 2026

Regional groundwater flow modeling with mf6Voronoi Studio and Model Muse - Tutorial

In this tutorial, we demonstrate how to build a regional groundwater flow model of an Andean basin using MF6Voronoi Studio and ModelMuse.

Generating flexible, non-rectangular meshes has historically been one of the most challenging steps in Modflow 6 modeling. MF6Voronoi Studio addresses this by providing a graphical interface for Python-based Voronoi mesh generation (DISV), allowing high-resolution cell refinement along river networks while maintaining a coarse mesh across the broader basin.

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