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
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
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).
Once you have activated your virtual environment, you can install HyVR from PyPI using
pip install hyvr
The version on PyPI should always be up to date. If it's not, you can also install HyVR from github:
git clone https://github.com/driftingtides/hyvr.git pip install hyvr
Installation from conda-forge will (hopefully) be coming soon.
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
import hyvr hyvr.run('my_configfile.ini')
Examples can be found in the
testcases directory of the github repository, the general setup and possible
options of the config-file are described in the documentation.
HyVR was developed for use with Python 3.4 or greater. It may be possible to use with earlier versions of Python 3, however this has not been tested.
- scipy = 1.0.0
- pandas = 0.21.0
- numpy <= 1.13.3
- matplotlib <= 2.1.0
- flopy == 3.2.9 (optional for modflow output)
- pyevtk = 1.1.0
- h5py (optional for HDF5 output)
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.
If you find that the documentation is unclear, lacking, or wrong, please contact us.