r2ogs6
r2ogs6 is an R-API to the multiphysics simulator OpenGeoSys 6.
r2ogs6 allows pre-processing (preparing input files), executing simulation runs, retrieving, post-processing and visualizing output data in R.
Furthermore, the package comes with functionality to define ensemble runs.
Setup
Preparing your environment
Before you install and load r2ogs6, there are two prerequisites that need to be met so you can use r2ogs6 to its full extent later.
The most important one is having OpenGeoSys 6 installed on your system. You can download the current version of OpenGeoSys 6 from here.
Secondly, to read in the .vtu and .pvd files produced by OpenGeoSys 6, you need a Python installation including the libraries numpy and vtk. If you have an Anaconda installation on your system, setting up a Python environment with numpy and vtk will work. r2ogs6 was tested with the following environment:
$ conda create -n r2ogs6 python=3.7
$ conda install -c anaconda numpy, vtk==8.2.0
If you don't have any Python installation on your system, you can download the latest release of Python from here. Instructions on how to install numpy and vtk can be found here and here.
Installation
First, open a terminal and clone the r2ogs6 repository to your local machine.
$ git clone https://gitlab.opengeosys.org/ogs/tools/r2ogs6.git
After that, open R from your local (anaconda) environment.
To install r2ogs6, you first need the R-package devtools.
# Install devtools
install.packages("devtools")With devtools, you can now install r2ogs6.
# Install r2ogs6. Change the path to that of the cloned repository!
devtools::install("path/to/r2ogs6")
# Alternatively, install directly from the Gitlab repo:
devtools::install_git("https://gitlab.opengeosys.org/ogs/tools/r2ogs6")This will install all necessary R dependencies except rhdf5.
This package is needed to handle hdf5 output files and can be installed via:
install.packages("BiocManager") # install BiocManager from CRAN
BiocManager::install("rhdf5") # install rhdf5 from bioconductor.orgIf r2ogs6 is installed or loaded via library()in interactive sessions e.g. in RStudio, the package will check if rhdf5 is available in the library and if not, ask the user to install it automatically. If installing r2ogs6 in a script e.g. via R -e devtools::install_git("https://gitlab.opengeosys.org/ogs/tools/r2ogs6") make sure to include the manual installation of rhdf5 as above in your script.
Usage
For tutorials on how to use the r2ogs6 package, have a look at its vignettes:
Corresponding HTML versions can be found here.