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https://github.com/driftingtides/hyvr

A package for simulating hydrogeological virtual realities.
https://github.com/driftingtides/hyvr

Last synced: 3 months ago
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A package for simulating hydrogeological virtual realities.

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README 

        
Note: This repository is not actively maintained anymore. A more up-to-date fork is available here: https://github.com/vcantarella/hyvr-no-cython



====================================================================

Introduction

====================================================================



**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 



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.