Package: hyvr
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
onlinetechnical 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 availablehere.Installing the HyVR packageInstalling PythonWindowsIf you are using Windows, we recommend installing theAnaconda distributionof Python 3. This distribution has the
majority of dependencies that HyVR requires.It is also a good idea to install the HyVR package into avirtual environment. Do this by
opening a command prompt window and typing the following:conda create --name hyvr_envYou need to then activate this environment:conda activate hyvr_envLinuxDepending 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.apton Ubuntu/Debian).In any way we recommend using a virtual environment. Non-conda users can use for
examplevirtualenvwrapper.Installing HyVROnce you have activated your virtual environment, you can install HyVR from PyPI
usingpip(with Anaconda you might have to install pip first into your
environment usingconda install pip):pip install hyvrIt might be necessary to install numpy separately before installing HyVR.
To check whether installation was successful, you can run:python -m hyvrIf this runs without error (warnings are ok),hyvrshould 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 sourceIf installation viapipfails, 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 havegitinstalled on your machine, you can do:git clone https://github.com/driftingtides/hyvr.git
pip install ./hyvrOtherwise 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 unzippedhyvrdirectory make sure to
use./hyvrinstead ofhyvr, otherwise pip tries to install from PyPI.Dependenciespipshould normally install all required dependencies. Optional dependencies are:Cythonto recreate the C-extensionsh5pyfor HDF5 outputflopyfor output of MODFLOW filespyevtkfor VTR outputUsageTo 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.iniHyVR 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 hyvrIf you want to use HyVR in a script, you can import it and use therunfunction:import hyvr
hyvr.run('my_configfile.ini')Examples can be found in thetests/testcasesdirectory of thegithub
repository, the general setup and
possible options of the config-file are described in the
documentation. Currently onlytests/testcaes/made.iniis ported to version 1.0.0.DevelopmentHyVR 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 byemailor via github.Problems, Bugs, Unclear DocumentationIf you have problems with HyVR have a look at thetroubleshootingsection. 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.