Commit 3d1f063a authored by phit0's avatar phit0
Browse files

[doc] vignette paragraph for hdf5 files

parent 65b5c763
Pipeline #7368 passed with stage
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---
title: "r2ogs6 User Guide"
author: "Ruben Heinrich"
output: html_document
#output: rmarkdown::html_vignette
#vignette: >
# %\VignetteIndexEntry{r2ogs6 User Guide}
# %\VignetteEngine{knitr::rmarkdown}
# %\VignetteEncoding{UTF-8}
#output: html_document
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{r2ogs6 User Guide}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r, include = FALSE}
knitr::opts_chunk$set(
eval = nzchar(Sys.getenv("r2ogs6_ensemble_guide_eval")),
#eval = nzchar(Sys.getenv("r2ogs6_ensemble_guide_eval")),
eval = TRUE,
collapse = TRUE,
comment = "#>"
)
options("r2ogs6.default_ogs6_bin_path" = "/usr/local/bin/ogs6.4.1.sif")
# the python library vtk needs an explicit import statement for knitting
vtk <- reticulate::import("vtk")
dsa <- reticulate::import("vtk.numpy_interface.dataset_adapter")
......@@ -135,7 +136,8 @@ Since I already read in a `.prj` file earlier, I won't run the above snippet. If
As soon as we've added all necessary parameters, we can try starting our simulation. This will run a few additional checks and then start OpenGeoSys 6. If `write_logfile` is set to `FALSE`, the output from OpenGeoSys 6 will be shown on the console.
```{r results='hide'}
ogs6_run_simulation(ogs6_obj, write_logfile = TRUE)
ogs6_run_simulation(ogs6_obj)
```
## Retrieve the results
......@@ -163,6 +165,32 @@ ggplot(result_df,
theme_bw()
```
```{r, echo=FALSE, results='hide'}
ogs6_obj$h5s <- list(OGS6_h5$new(system.file("/extdata/benchmarks/EllipticPETSc",
"cube_1e3_np3.h5",
package = "r2ogs6")))
```
Similar to the idea with `.pvd` output, `hdf5` files are automatically referenced under `$h5s` if returned by the simulation. Here, we have added a file artificially from the benchmark library for demonstration.
```{r}
ogs6_obj$h5s
```
As can be seen, hdf5 files have a very particular structure. To work with the data, a simple method `get_h5()` allows to access the different data elements as a very raw starting point for post processing the data.
```{r}
h5_list <- ogs6_obj$h5s[[1]]$get_h5("/")
```
If the file has a reasonably "clean" structure, a more convenient way of importing the data is using the method `get_df` that returns a *tibble* table.
```{r}
df <- ogs6_obj$h5s[[1]]$get_df(group = "/t_0", names = "pressure")
df
```
## Running multiple simulations
......
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