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A python package for simulating hydrogeological virtual realities

Project description

HyVR: Turning your geofantasy into reality!

The Hydrogeological Virtual Reality simulation package (HyVR) is a Python module that helps researchers and practitioners generate subsurface models with multiple scales of heterogeneity that are based on geological concepts. The simulation outputs can then be used to explore groundwater flow and solute transport behaviour. This is facilitated by HyVR outputs in common flow simulation packages’ input formats. As each site is unique, HyVR has been designed that users can take the code and extend it to suit their particular simulation needs.

The original motivation for HyVR was the lack of tools for modelling sedimentary deposits that include bedding structure model outputs (i.e., dip and azimuth). Such bedding parameters were required to approximate full hydraulic-conductivity tensors for groundwater flow modelling. HyVR is able to simulate these bedding parameters and generate spatially distributed parameter fields, including full hydraulic-conductivity tensors. More information about HyVR is available in the online technical documentation.

I hope you enjoy using HyVR much more than I enjoyed putting it together! I look forward to seeing what kind of funky fields you created in the course of your work.

HyVR can be attributed by citing the following journal article: Bennett, J. P., Haslauer, C. P., Ross, M., & Cirpka, O. A. (2018). An open, object-based framework for generating anisotropy in sedimentary subsurface models. Groundwater. DOI: 10.1111/gwat.12803. A preprint version of the article is available here.

Installing the HyVR package

Installing Python

Windows

If you are using Windows, we recommend installing the Anaconda distribution of Python 3. This distribution has the majority of dependencies that HyVR requires.

It is also a good idea to install the HyVR package into a virtual environment. Do this by opening a command prompt window and typing the following:

conda create --name hyvr_env

You need to then activate this environment:

conda activate hyvr_env

Linux

Depending on your preferences you can either use the Anaconda/Miniconda distribution of python, or the version of your package manager. If you choose the former, follow the same steps as for Windows.

If you choose the latter, you probably already have Python 3 installed. If not, you can install it using your package manager (e.g. apt on Ubuntu/Debian).

In any way we recommend using a virtual environment. Non-conda users can use for example virtualenvwrapper.

Installing HyVR

Once you have activated your virtual environment, you can install HyVR from PyPI using pip (with Anaconda you might have to install pip first into your environment using conda install pip):

pip install hyvr

It might be necessary to install numpy separately before installing HyVR. To check whether installation was successful, you can run:

python -m hyvr

If this runs without error (warnings are ok), hyvr should be successfully installed.

If installing from PyPI doesn’t work for you, please let us know (see below). You might want to try installing from source instead.

Installation from conda-forge will (hopefully) be coming soon.

Installing from source

If installation via pip fails, you can try to install from source by cloning or downloading the github repository. To install from source you need a C/C++ compiler. On Windows you can get one by installing “Build Tools for Visual Studio”. If you have git installed on your machine, you can do:

git clone https://github.com/driftingtides/hyvr.git
pip install ./hyvr

Otherwise you can download the code as a zip file, unzip it, and then install it via:

pip install <path/to/unzipped/hyvr>

If you are in the same directory as the unzipped hyvr directory make sure to use ./hyvr instead of hyvr, otherwise pip tries to install from PyPI.

Dependencies

pip should normally install all required dependencies. Optional dependencies are:

  • Cython to recreate the C-extensions
  • h5py for HDF5 output
  • flopy for output of MODFLOW files
  • pyevtk for VTR output

Usage

To use HyVR you have to create a configuration file with your settings. You can then run HyVR the following way:

(hyvr_env) $ python -m hyvr my_configfile.ini

HyVR will then run and store all results in a subdirectory. If no configfile is given, it will run a test case instead:

(hyvr_env) $ python -m hyvr

If you want to use HyVR in a script, you can import it and use the run function:

import hyvr
hyvr.run('my_configfile.ini')

Examples can be found in the tests/testcases directory of the github repository, the general setup and possible options of the config-file are described in the documentation. Currently only tests/testcaes/made.ini is ported to version 1.0.0.

Development

HyVR has been developed by Jeremy Bennett (website) as part of his doctoral research at the University of Tübingen and by Samuel Scherrer as a student assistant.

You can contact the developer(s) of HyVR by email or via github.

Problems, Bugs, Unclear Documentation

If you have problems with HyVR have a look at the troubleshooting section. If this doesn’t help, don’t hesitate to contact us via email or at github.

If you find that the documentation is unclear, lacking, or wrong, please also contact us.

Project details


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