From cc535fcde1c9d86a6a33f94d27da93eb6334a8a4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?David=20Hrb=C3=A1=C4=8D?= <david@hrbac.cz>
Date: Fri, 8 Sep 2017 13:52:53 +0200
Subject: [PATCH] Correctionsm, added LMG90 to menu
---
docs.it4i/salomon/software/phys/LMGC90.md | 35 ++++++++++++++++-------
mkdocs.yml | 8 ++++--
2 files changed, 29 insertions(+), 14 deletions(-)
diff --git a/docs.it4i/salomon/software/phys/LMGC90.md b/docs.it4i/salomon/software/phys/LMGC90.md
index dc53fc69d..1b5a0244c 100644
--- a/docs.it4i/salomon/software/phys/LMGC90.md
+++ b/docs.it4i/salomon/software/phys/LMGC90.md
@@ -7,17 +7,30 @@ More details on the capabilities of LMGC90 are available [here][Welcome].
## Modules
-The LMGC90, version 2017.rc1 is available on Salomon via module LMGC90:
+The LMGC90, version 2017.rc1 is available on Salomon via module `LMGC90`:
```sh
$ ml LMGC90
```
-The module sets up environment variables and loads some other modules, required for running LMGC90 python scripts. This particular command loads the default module, which is LMGC90/2017.rc1-GCC-6.3.0-2.27, and modules: GCCcore/6.3.0, binutils/2.27-GCCcore-6.3.0, GCC/6.3.0-2.27, bzip2/1.0.6, zlib/1.2.8, ncurses/6.0, libreadline/6.3, Tcl/8.6.3, SQLite/3.8.8.1, Python/2.7.9.
+The module sets up environment variables and loads some other modules, required for running LMGC90 python scripts. This particular command loads the default module, which is `LMGC90/2017.rc1-GCC-6.3.0-2.27`, and modules:
+
+```console
+GCCcore/6.3.0
+binutils/2.27-GCCcore-6.3.0
+GCC/6.3.0-2.27
+bzip2/1.0.6
+zlib/1.2.8
+ncurses/6.0
+libreadline/6.3
+Tcl/8.6.3
+SQLite/3.8.8.1
+Python/2.7.9
+```
## Running generic example
-LMGC90 software main API is a Python module. It comes with a pre-processor written in Python. There are several examples that you can copy from the *examples* directory which is in */apps/all/LMGC90/2017.rc1-GCC-6.3.0-2.27* folder. Follow the next steps to run one of them.
+LMGC90 software main API is a Python module. It comes with a pre-processor written in Python. There are several examples that you can copy from the `examples` directory which is in `/apps/all/LMGC90/2017.rc1-GCC-6.3.0-2.27` folder. Follow the next steps to run one of them.
First choose an example and open a terminal in the directory of the copied example.
@@ -25,29 +38,29 @@ First choose an example and open a terminal in the directory of the copied examp
To have more information on the pre-processor open in a web navigator the file [docs/pre_lmgc/index.html][pre_lmgc].
-To run an example, if there is no *DATBOX* directory or it is empty, run the Python generation script which is mostly called *gen_sample.py* with the command:
+To run an example, if there is no `DATBOX` directory or it is empty, run the Python generation script which is mostly called `gen_sample.py` with the command:
-```sh
+```console
$ python gen_sample.py
```
-You should now have a *DATBOX* directory containing all needed *.DAT* and *.INI* files.
+You should now have a `DATBOX` directory containing all needed `.DAT` and `.INI` files.
### Computation
-Now run the command script usually called *command.py*:
+Now run the command script usually called `command.py`:
-```sh
+```console
$ python command.py
```
To get more information on the structure on command scripts read the documentation opening the file [docs/chipy/index.html][chipy] in a web browser.
-Once the computation is done, you should get the directory *OUTBOX* containing ASCII output files, and a *DISPLAY* directory with output file readable by paraview.
+Once the computation is done, you should get the directory `OUTBOX` containing ASCII output files, and a `DISPLAY` directory with output file readable by paraview.
### Postprocessing and Visualization
-The ASCII files in *POSTPRO* directory result from the commands in the *DATBOX/POSTPRO.DAT* file. To have more information on how to use these features read the documents [manuals/LMGC90_Postpro.pdf][LMGC90_Postpro.pdf].
-The files inside the *DISPLAY* directory can be visualized with paraview. It is advised to read the *.pvd* files which ensure time consistency. The different output files are:
+The ASCII files in `POSTPRO` directory result from the commands in the `DATBOX/POSTPRO.DAT` file. To have more information on how to use these features read the documents [manuals/LMGC90_Postpro.pdf][LMGC90_Postpro.pdf].
+The files inside the `DISPLAY` directory can be visualized with paraview. It is advised to read the `.pvd` files which ensure time consistency. The different output files are:
- tacts: contactors of rigid objects
- rigids: center of mass of rigid objects
diff --git a/mkdocs.yml b/mkdocs.yml
index 365a41c97..e409349ad 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -3,7 +3,7 @@ theme_dir: 'material'
docs_dir: docs.it4i
site_favicon: img/favicon.ico
-extra_css:
+extra_css:
- src/css.css
# Repository
@@ -61,7 +61,7 @@ pages:
- 'Software':
- Lmod Environment: software/lmod.md
- Modules Matrix: modules-matrix.md
- - Singularity Container: software/singularity.md
+ - Singularity Container: software/singularity.md
- EasyBuild: software/easybuild.md
- Spack: software/spack.md
- Salomon Software:
@@ -119,10 +119,12 @@ pages:
- Introduction: salomon/software/numerical-languages/introduction.md
- Matlab: salomon/software/numerical-languages/matlab.md
- Octave: salomon/software/numerical-languages/octave.md
- - R: salomon/software/numerical-languages/r.md
+ - R: salomon/software/numerical-languages/r.md
- OpenCoarrays: salomon/software/numerical-languages/opencoarrays.md
- Operating System: salomon/software/operating-system.md
- ParaView: salomon/software/paraview.md
+ - 'Phys':
+ - LMGC90: salomon/software/phys/LMGC90.md
- Anselm Software:
- Available Modules: modules-anselm.md
- 'Machine learning':
--
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