Commit cafa53d5 authored by Turnhout, M.C. van's avatar Turnhout, M.C. van
Browse files

contributing & readme

parents f5ac9225 796d855a
......@@ -11,7 +11,6 @@
############
# it's better to unpack these files and commit the raw source
# git has its own built in compression methods
*.rpy*
*.7z
*.dmg
*.gz
......@@ -59,16 +58,20 @@ Thumbs.db
# Simulink Code Generation
slprj/
matlab/Gibbon/
# Abaqus gitignore
*.rpy*
# LaTeX git ignore
*.acn
*.acr
*.alg
*.aux
*.bak
*.bbl
*.blg
*.dvi
*.dep
*.fls
*.fdb_latexmk
*.glg
......@@ -89,6 +92,7 @@ matlab/Gibbon/
*.out
*.pdfsync
*.ps
*.sav
*.snm
*.synctex.gz
*.toc
......@@ -96,3 +100,4 @@ matlab/Gibbon/
*.xdy
*.tdo
# repo specific ignores
......@@ -2,18 +2,18 @@ Contributing
============
Your contributions and thoughts are highly valued.
In order to conribute to the repo, you need to make a GitLab account (http://stbe-nas.wfw.wtb.tue.nl:3000/).
Permissions for the repos can then be requested with the GitLab-admin: m.c.v.turnhout@tue.nl
In order to conribute to the repo, you need to make a BitBucket account (http://bitbucket.org).
Permissions for the repos can then be requested with the BasilLab-admin: m.c.v.turnhout@tue.nl
Note
====
that when you commit code to the STEM repos
- everybody from within the university domain can access the STEM repos and see your commits
that when you commit code to this repo
- everybody can access the repo and see your commits
- your code will be released with a GNU Public License, for all eternity ever
For working on/with a repo
- when in doubt, work in your own branch
- when in doubt, discuss with the FibLab-admin: m.c.v.turnhout@tue.nl
- when in doubt, discuss with the BasiLab-admin: m.c.v.turnhout@tue.nl
Of course:
==========
......
basillab
BasilLab
========
http://stbe-nas.wfw.wtb.tue.nl:3000/STEM/basillab
https://bitbucket.org/matecellab/basillab
FYI (for your inspiration): a toolbox to get from raw MRI data to a
3D Abaqus FE model with as little user interaction as possible.
......@@ -10,7 +10,7 @@ using & downloading
===================
You do not need (to run or use) Git to able to use basillab. You can
download your favourite version from http://stbe-nas.wfw.wtb.tue.nl:3000/STEM/basillab
download your favourite version from https://bitbucket.org/matecellab/basillab
Once downloaded, the code is yours to (ab)use to your liking (as
long as you do not violate the GPL license).
......@@ -25,7 +25,7 @@ compiling documentation from source
The main file to be compiled is BasilLab.tex
In order to compile from source, you may need some custom LaTeX-files
from stexmf: http://stbe-nas.wfw.wtb.tue.nl:3000/STEM/stexmf
from stexmf: http://mategit.wfw.wtb.tue.nl/STEM/stexmf
copyright
=========
......@@ -36,7 +36,7 @@ Technology.
Copyright (C) 2017 Soft Tissue Engineering and Mechanobiology (STEM)
group, Department of Biomedical Engineering, Eindhoven University of
Technology: http://www.stem-research.nl https://www.tue.nl/stem
Technology: https://www.tue.nl/stem
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
......
......@@ -177,7 +177,7 @@ The \texttt{cae}-file can be opened with the Abaqus GUI. When this model is subm
\subsection{Processing \texttt{param} options}
The function \bas{buildFEM} starts with some book-keeping. First the options in the parameter structure \texttt{param} are processed, and defaults substitued for missing values. When all necessary fields of \texttt{param} have been read or set, the first action of \bas{buildFEM} is to write the file \texttt{basil<basilid>\_model\-param.m\index{basil<basilid>\_modelparam.m@\texttt{basil<basilid>\_modelparam.m}}}.
The function \bas{buildFEM} starts with some book-keeping. First the options in the parameter structure \texttt{param} are processed, and defaults substituted for missing values. When all necessary fields of \texttt{param} have been read or set, the first action of \bas{buildFEM} is to write the file \texttt{basil<basilid>\_model\-param.m\index{basil<basilid>\_modelparam.m@\texttt{basil<basilid>\_modelparam.m}}}.
All \texttt{<basilid}$i$\texttt{>} are processed with the same \texttt{param}-options, so this file is equal for each \texttt{<basilid}$i$\texttt{>} (except for the small differences in the \texttt{buildon}-time).
......
......@@ -169,7 +169,7 @@ These Euler angles follow the \gibbon-convention (see \gib{euler2DCM.m}): $\alph
\begin{equation}
\mat{R}_{\alpha\beta\gamma} = \mat{R}_\alpha\cdot\mat{R}_\beta \cdot \mat{R}_\gamma
\end{equation}
This kind of angle multiplication is not commutative. Abaqus uses a different definition for Euler angles. These three Euler angles from \gibbon{} can not be directly used in Abaqus. It will wreak havoc.
This kind of angle multiplication is not commutative. Abaqus uses a different definition for Euler angles. These three Euler angles from \warning\gibbon{} can not be directly used in Abaqus. It will wreak havoc.
The $3\times 3$ matrix (centres of mass, Euler angles) is written to \texttt{Bone\_preload\_loading.txt\index{Bone\_preload\_loading.txt@\texttt{Bone\_preload\_loading.txt}}} or \texttt{Bone\_preload\_postload.txt\index{Bone\_preload\_postload.txt@\texttt{Bone\_preload\_postload.txt}}}, depending on the case, in \basilhome\texttt{/<basilid>/}. To map the tibia movements for \texttt{<basilid> = 140611} and \texttt{<basilid> = 140613} call:
\begin{lstlisting}[numbers=none,language=basillab]
......
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