November 10, 2021

Data extraction and spatial / 3D representation from BGS borehole data in AGS format with Python

November 10, 2021/ Saul Montoya

Open lithology datasets are scarce and most times they come in certain exchange formats that can´t be easily coupled with other softwares. Python has the tools to read and extract data from those files and provide them in more friendly formats as csv or xlsx. With the use of spatial libraries as Fiona or 3D visualization libraries as Pyvistas we can go one step further and process our data as shapefiles or vtks.

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.

November 03, 2021

The best Youtube channels in QGIS (and open source GIS tools)

November 03, 2021/ Saul Montoya

Education is aimed to acquire knowledge and it's based on the learning process and as any process has some steps and means that have to be analyzed. Traditionally, if you want to get knowledge you can go to a university, get a degree, visit a library, but why don’t you just check a Youtube channel; will you get the same knowledge? Will you do better research with what you learned on video? Those are excellent questions to pose in these times where we need knowledge that shapes our future in the context of climate change.

October 25, 2021

How long does it take to develop a groundwater model for my research project / master thesis?

October 25, 2021/ Saul Montoya

Developing a hydrogeological research project that considers groundwater modeling for a bachelor thesis or a master thesis requires you to take into consideration several topics, such as input data, hydrogeological knowledge and time to learn the software in order to provide a numerical simulation that reaches the objectives of your research project.

Learning a software for groundwater modeling should be easy as developing some tutorials and playing around with your own data; however it is not that easy since it involves the review of lots of documentation, have strong knowledge in hydrogeology and numerical modeling and deal with uncertainties and numerical unconvergences.

October 21, 2021

Fill Missing Precipitation Data with Machine Learning in Python and Scikit-Learn - Tutorial

October 21, 2021/ Saul Montoya

Evaluation of hydrological processes as evapotranspiration, runoff, routing and infiltration require data as precipitation, flow, temperature and radiation on a daily basis. Required data for hydrological modeling need to be accurate and must be completed over the study period. It is common that historical data from hydrological stations are incomplete and has many gaps that can be filled by the use of machine learning algorithms like Scikit-Learn in Python3. This tutorial shows a applied procedure to run a complete script for the filling of missing precipitation in one station by the use of data from 2 nearby stations. The script will be run on Python 3.9 on a Anaconda Prompt environment.

October 04, 2021

New website! MODFLOW Questions and Answers: ask anything on groundwater modeling

October 04, 2021/ Saul Montoya

Until now we had limited options to provide specific support in groundwater modeling. We know that modeling requires the review of extensive documentation and practical work with the software and sometimes or most times we don't have the time to sort things out.

September 17, 2021

The Groundwater Project as a source of free books in basic and applied hydrogeology

September 17, 2021/ Saul Montoya

We usually received some emails and messages regarding basic or reference books and publications in Hydrogeology and we didn't have any reference of free and high quality material until we knew about the Groundwater Project. It´s true that we found the project website some months ago, but it was at the latest IAH conference where we had a presentation with a complete overview of the program.

September 15, 2021

Example of Seawater Intrusion Modeling with Modflow 6, Model Muse and Flopy - Tutorial

September 15, 2021/ Saul Montoya

MODFLOW 6 implements the Buoyancy package for the simulation of variable density and seawater intrusion cases. The tools are implemented in the Python package Flopy, however the workflow has changed substantially from the previous models of flow and transport. We have developed an applied case seawater intrusion model on a regular geometry model constructed with Model Muse for flow and Flopy for transport.

August 23, 2021

What to do when your MODFLOW MT3D contaminant plume doesn’t migrate?

August 23, 2021/ Saul Montoya

This is a problem that every hydrogeologist - numerical modeler has faced many times over his/her professional career independently from the theoretical background and skills with the code, graphical user interface or Python library.

We don’t know why groundwater “flows” and a contaminant plume “migrates” when both move on the aquifer system. After you construct you model geometry, setup the flow boundary condition, specify your transport package, define your contaminant sources, run your MODFLOW flow model and then run your MT3D model (or even your MT3DMS model) you will find that there is no plume, none, nada, nichts.

August 18, 2021

Open source groundwater software besides MODFLOW - Updated July 2023

August 18, 2021/ Saul Montoya

A special concern arises from the gap between the stage of development of open source groundwater software and the actual capabilities of the common groundwater modelers (we mean, the main group of modelers). Even though we are passionate about software we don’t find the time or the right momentum to have a real experience with those codes.

From our research, we have listed the top open source groundwater software with a brief summary of the capabilities and useful links. We have to mention that there are some packages that can simulate groundwater flow in software like OpenFoam; however, those variants are not listed here.

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.

August 10, 2021

How to reproject single and multiple rasters with Python and Rasterio - Tutorial

August 10, 2021/ Saul Montoya

Raster reprojection is a common task on GIS analysis however to do it with only Python commands has some challenges. We have done an applied example of raster reprojection for single and multiple rasters from WGS 84 UTM to WGS 84 Geographic. The codes work on monoband and multiband rasters and can reproject from to any projection by specifiyin it EPSG code.

The tutorial is done on a conda enviroment that has the geospatial libraries installed. You can set up the environment by following this tutorial:

https://hatarilabs.com/ih-en/how-to-install-python-geospatial-libraries-gdal-fiona-rasterio-etc-under-a-conda-env-in-windows

August 02, 2021

Tutorial to do a tutorial in open source software for water resources

August 02, 2021/ Saul Montoya

Let's have a look at the tutorial concept in its real dimension. A tutorial is a period of instruction that provides practical information about a specific topic. The tutorial can be given by an individual or institution and has a goal to teach you something or master you in something you didn't know before.

However in water resources software, we don’t see the tutorial as a part of the documentation or a key part of the learning experience. The tutorial is in fact an essential part needed to understand the whole capabilities of the software in practical exercises. It´s true that most software delivery exercises of different applied cases, but we can’t say they are tutorial in fact because those exercises lack a perspective of guided work.

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.

Blog