Development of open source software brings amazing new tools in all fields. In hydrogeology and groundwater modeling there is an increasing number of specific open source software and programming packages. We wanted to compile the latest libraries for Python related to hydrogeology, we asked for references and researched over the web to provide you the following list.
Read MoreThis tutorial has a complete case of spatial analysis for the extraction of point data from a raster dataset with Python and its libraries Geopandas and Rasterio. The procedure is entirely geospatial and uses shapefiles and tifs as input data; data calculation was performed on a Jupyter Lab environment.
Read MoreThere are many ways to display spatial data, from the traditional maps, GIS desktop software and most recently on the web. We face certain challenges to display spatial data on the web because we will require certain functionalities that we find on a desktop software and certain spatial analysis tools implemented as buttons. Django is a web framework written in Python that allows to create web applications with moderate simplicity and this framework is capable of displaying vector spatial data using libraries such as Folium.
We have created a tutorial with an applied case of displaying hydrological spatial information on a webapp in Django. The tutorial creates a Django project, creates an app for the spatial data representation, imports the vector data (geojson or shp) and displays spatial data with defined styles.
Read MoreDevelopment of groundwater numerical models on a commercial scale has brought some issues regarding stakeholder participation, prediction quality and indelible price and time.
It might be that the question of how much a model can cost can be resolved as an equilibrium of how much are people willing to pay and how much the consultant is willing to receive. We will discuss some topics of this critical but not well explained topic in this article.
Read MoreModeling the performance and effectiveness of flow barriers or impermeable walls on the groundwater flow regime is a challenge due to the wall geometry / orientation and discretization requirements. The package Horizontal Flow Barrier was designed to simulate barriers of defined thickness and conductances that are located in between flow cells, in this way the flow barrier is independent for the model discretization. This package is not new, it dates back to 1993, and it was implemented on many MODFLOW versions.
Read MoreWe present our own webapp for the representation of the Piper Diagram, Stiff Diagram and Scholler Diagram. The webapp was developed in Python Django and it is entirely free for everyone. The main objective behind this webapp was to develop a user friendly and minimum requirement tool to create these water quality / hidrogeochemical diagrams. The video tutorial shows the complete procedure to update the working file and then generate the diagrams.
Read MoreThere are some shining moments in live where a normal hydrogeologist decide to develop open source software for groundwater modeling and for every great task everyone needs an strategy.
You might need a plan to develop your hydrogeological career but you will certainly need an strategy to develop groundwater modeling software. We have to see a strategy as the optimization of steps towards a goal, from great strategists as Hannibal Barca against the Roman empire, we need to see the whole picture and then decide the best steps to take with the resource available.
Read MoreSoftware is a technology tool, and through the history of mankind, tools are most recent technology have changed our cognitive skills and developed our intelligence. Water resources specialists deal with numerical simulations of surface flow, groundwater flow, interaction with the environment and prediction of future impacts with an extensive use of software and computers. In our point of view, there is a need of professionals that can deal with many types of software and programming codes to develop comprehensive evaluations of the current and future conditions of the water resources.
Read MoreDivide a continuous media as a hydrological / hydrogeological basin into discrete parts is an art. Cell size have to related to hydrological features, cell number have to be optimized to cover areas of interest with an adequate refinement while minimizing the total cell number. The computational process has be fast to allow user run multiple times to achieve a desired mesh.
We have done a tutorial that creates a Voronoi-sh mesh over shapefiles with several options for refinement and polygon relaxation, resulting polygons are clipped to the mesh boundary and exported as shapefile or geojson. The script was done with Python, Scipy, and Geopandas.
Read MoreHEC HMS is a software developed by the US Corps of Engineers that implements a series of hydrological methods to represent different physical process of the water cycle. The tools and options of HEC HMS make it a very versatile and powerful software for the hydrological simulation of different escenarios as extreme events on arid regions, or water balances in wet climates.
This tutorial shows the complete procedure to set up and simulate the hydraulic response of a 8 hour storms over a 20 hour period, model results are intended to show maximum flows and flow development with time. The area of study is a andean basin that was divided on two sub-basins (high and low part), each one has their own storm precipitation data. The model consider the use of hydrological components as subbasin, reaches and sinks.
Read MoreThe following tutorial shows the procedure to run an example model with the simple solver (steady-state for incompressible turbulent flow) from OpenFOAM in Windows 10. The tutorial covers also the steps to install Xming for the direct visualization of the model output with Paraview.
Read MoreA great question came when we deal with numerical modeling in modern times or in the last 5 years, and that question is how much programming skills should a hydrogeologist - numerical modeler have? This question is above this one: Should a hydrogeologist - numerical modeler need to program in any language?
As a part of an socratic method attempt to answer this, we will split the question into some subquestions.
Read MoreModeling groundwater flow on a regional scale has its own challenges because a regional model itself deals with refinement requirements, larger baselines, higher differences in elevations, complex geologies and areas without observation data.
The applied model of this tutorial covers the Angascancha Reservoir basin groundwater flow model in Ayacucho, Peru. This example have been modeled in several courses, tutorials and webinars with Modflow 2005, Flopy and Model Muse, however, this is the first time we port the model (succesfully) to Modflow 6 and Model Muse 4.
Read MoreOpenDroneMap is such a great software for its capabilities to spatially process drone image and create a complete set of outputs as digital elevation model, point clouds, orthophotos and others. For regular users, the installation and the computational resources have allways been a challenge. This time we have develop a succesful procedure to install and run OpenDroneMap in Windows 10 by installing a Ubuntu 18.04 subsystem.
Read MoreGroundwater remediation is a challenge for stakeholders, scientists and population due to the limited baselines, high uncertainty, limited budgets and timeframes, and not so strong modeling capabilities of related professionals on a general scope (don’t take it personal). We might think about the success of groundwater remediation when we achieve a big group - more than a hundred per country - of geoscientists whit high skills on groundwater modeling distributed on the private sector, the regulatory sector and academia.
Read MoreOpenFoam is a great open source software for the numerical simulation of water, air, heat and any other physical fluid. Unfortunately OpenFOAM is Linux native and options to run it on Windows are limited with restrictions on tools, versions and available computational resources. With the latest developments on Windows 10 is is posible to install OpenFoam directly in Windows with something called a Windows Subsystem for Linux (WSL) and installing Ubuntu inside Windows.
This tutorial covers all the step required to install OpenFOAM in Windows 10 and its the base for coming modeling tutorials on OpenFOAM.
Read MoreWhen working with satellite imagery we have to take into account the spatial and temporal scale. The selection and processing of remote sensing data products on a specific area over a certain period of time requires a great amount of time and computational resources. We have explored the web application AppEEARS from the USGS to download land cover images (MCD12Q1v006) over a specific area and time range. The tutorial covers all the steps from creating a polygon in QGIS3 as Geojson, upload into the webapp, the subsequent instructions to download the files, displaying the data in QGIS3 and review the pixel values correspondances.
Read MoreWe have developed an applied groundwater modeling case on the mesoscale that covers the most relevant physical process that affect the underground flow regime. Numerical simulation was constructed on Modflow 6 and Model Muse 4 on steady state conditions with variable hydraulic conductivity with depth to represent interbedded low conductivity layers. The tutorial cover all the steps of model and boundary condition setup, working with spatial data, analysis of water balance and review of water levels on piezometers.
Note: This is a base case for a coming webinar in sensibility analysis with MODFLOW 6, Python and the Flopy and Salib libraries. More information of this event will be posted on our social networks.
Read MoreGreat free and open groundwater flow modeling software are in constant development process, therefore year by year we have newer versions or even new software. This time we have uptated a basic and useful tutorial from 2016 to the new version of Modflow and Model Muse. The tutorial shows the complete procedure to download and install Model Muse 4 and configure Modflow 6.
Read MoreGeopandas is an amazing library for spatial analysis since in combines the spatial tools from Shapely and Fiona with the versatily of Pandas Dataframes. Working with Geopandas in Windows was not exactly easy since there were some incompatibilities with the required packages. Here is a novel procedure to install successfully the Geopandas library when working with Anaconda in Windows.
Read MoreHatarilabs presents its educational program designed for mastering Python in real professional and academic environments. The program has an extensive practical work that goes from the basic concepts of Python, Numpy and Pandas to specific applications in water resources and geosciences coupled with geospatial analysis and machine learning.
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.
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.
ONLINE COURSES:
Phreeqc is a software developed by the USGS written in C++ capable of modeling a variety of aqueous geochemical processes such as mixing of waters, modeling equilibrium between solid and aqueous phase, modeling impact of temperature, calculation of element concentration among others.
Hatarilabs has developed an applied and unique course of Phreeqc integrated with Python undes a class (object type) that can run, parse and provide Phreeqc output as Pandas dataframes and integrate it to plots and further analysis with other Python libraries on a Jupyter notebook.
HEC-RAS is a software designed to perform hydraulic 1D and 2D calculations on river channels either natural or man constructed. It allows steady flow, unsteady flow, sediment transport and water quality modelling. It is developed by the US army corps of engineers, US Department of defence and it is openly available software. The HEC-RAS steady flow is based on one dimensional energy equation, while for the unsteady flow, HEC-RAS uses an implicit, finite difference method to solve the fully dynamic Saint-Venant equations.
The objective of HEC-RAS is to solve river dynamics and river engineering problems. Applications are delimitation of flood areas, embankment and protection work design, river restoration, emergency plans for dam break, optimization of hydraulic work and risk assessment and management.
This course develops the main functions and applications of the latest version of the MODFLOW 6 groundwater modeling code through the ModelMuse interface, both developed by the United States Geological Survey (USGS). This version includes innovative tools for the construction and simulation of hydrogeological models, mainly highlighting the incorporation of the discretization option for discretized by vertices grids.
The development of machine learning and geospatial libraries in Python as Scikit Image, Rasterio and Fiona gave us a new range of tools to analyze vegetation from traditional sources as satellite imagery and new sources as drone orthophotos. The appliance of Python programming for crop identification depends on many factors such as the image resolution, the vegetation stage and even the algorithm setup.
We have developed a course crop identification / delineation with geospatial and machine learning tools of Python, the course is aimed to GIS or related professionals that have basic Python knowledge. The course covers the introductory concepts of the geospatial libraries and a series of machine learning applications for crop indentification in olive trees, palms, agave and corn fields.
Note:
This course is for professionals with previous knowledge of Python. Basic concepts of Python programming will not be covered in the lessons and course material. In case you don’t have any knowledge of Python, we recommend you to take this online course.
The Hydrologic Modeling System (HEC-HMS) is a free program developed by the US Corps of Engineers that implements a series of hydrological methods to represent different physical processes of the water cycle.
HEC-HMS also includes procedures necessary for continuous simulation including evapotranspiration, infiltration, hydrological routing and soil moisture accounting. The tools and options of HEC HMS make it a very versatile and powerful software for the hydrological simulation of different scenarios such as extreme events in arid regions, or water balances in wet climates.
Hatarilabs offers the online course of Hydrological Modeling with HEC-HMS for students and professionals of any country. The course is focused on theory and practical to know the different HEC-HMS tools and its application to the hydrological modeling.
Hatarilabs offers the online course of Hydrological Modeling with QSWAT for students and professionals of any country. The course is focused on the acquisition and preprocessing of data for SWAT+ using QGIS 3.4 for develop hydrological watershed modeling.
This course covers the whole procedure of developing regional groundwater models through the ModelMuse interface, including the model construction, boundary conditions, parameter assignment, model simulation, results analysis and visualization, and model calibration. Flopy is also introduced in the course to import, create, refine and simulate the model as in ModelMuse. Two basins with different aquifer setting and boundary conditions are used as case studies to demonstrate the use of these tools so that the participants learn how to build these models and analyze the results for future decision-making.
Evaluation of long term impacts of the mining activity is a key topic on the public concern and regulatory and sustainability policies. Due to the scale of the mining projects and the different related activities, impacts could be made to several parts of the physical environment. Groundwater modeling is a useful tool for the simulation of mine closure impacts to the groundwater flow system and groundwater quality. Hatarilabs has developed an applied course about the simulation, calibration, representation and impact analysis of a waste dump closure on the environment and water bodies with a long term scope (closure and post closure). The course will be given on Model Muse for flow and contaminant transport modeling and scripts in Flopy for model calibration, water balance analysis and evaluation of remediation techniques performance.
This course is focused on how to use the different packages related to numerical tools, data analysis, representation of graphs, and others. Many of these tools are applicable to the field of Hydrology in the preparation of data for hydrological models, statistical analysis of hydrological parameters and model result representation.
Graphical user interfaces (GUIs) are commonly used to construct and post-process numerical groundwater flow. Flopy is the Python library that builds and executes MODFLOW models; this library has tools and options for the complete geo-referencing of a MODFLOW model.
Python is a simple and powerful programming language; its simplicity is remarkable compared to other programming languages and its power is based on the number of tools available for different areas of study.
Use of Python with the available scientific packages and FloPy, facilitates data exploration, alternative model evaluations and model analyses that can be difficult to perform with GUIs. One advantage of Flopy and Python is that there are many packages available to facilitate the model development process, including packages for plotting, array manipulation, optimization, and data analysis.
This course allows acquired knowledge of the open source programming language to construct model input files, run the model, and read and plot simulation results.
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This guide covers the installation of MF6Voronoi Studio, a Python-based GUI for Modflow 6 Voronoi mesh generation developed by An Ho Taylor. Watch the video below to learn how to download the setup file, manage installation permissions, and launch the application.
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.
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.
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.
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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.