Commit 29d44165 authored by matecellab's avatar matecellab
Browse files

small manual update

parent 9c8e42db
......@@ -154,13 +154,21 @@ E = 15.6\,\text{kPa} = 15600\,{\text{N}}/{\text{m}^2} = 0.0156\,{\text{N}}/{\tex
And when you read the element volume from the Abaqus output, this volume is in mm\ap{3}.\\
\noindent See also section 1.2.2 `Conventions' in the Abaqus Analysis User's Guide of the \adoc .
\noindent See also section `1.2.2 Conventions' in the Abaqus Analysis User's Guide of the \adoc{} and the \href{http://furnace.wfw.wtb.tue.nl:2080/v6.14/books/popups/usb-tbl.html}{Conversion Tables, Constants, and Material Properties} provided by Abaqus.
\section{Large displacements and logarithmic strain}
The FE models are analysed with Abaqus' `Large Displacement' option for geometrically non-linear problems. As a result, Abaqus will output \textsl{logarithmic} strains `LE':
\begin{equation}
\text{LE} = \epsilon^\text{L} = \ln V = \sum_{i=1}^3 \ln \lambda_i \ten{n}_i {\ten{n}_i}^\text{T}
\end{equation}
When you use a hyperelastic material law (such as the Ogden material model that is used in BasilLab), Abaqus will also output the logarithmic strains `LE'. See section `1.2.2 Conventions' in the Abaqus Analysis User's Guide of the \adoc{} .
\section{Directory structure}
BasilLab requires knowledge on two directories: one \texttt{<MRI-root>} where the (raw) MRI-data can be found, and one \texttt{<basilhome>} where the processed MRI-data and model data can be found. Raw MRI-data for each individual experiment/animal should be stored in a unique folder \textsl{inside} \texttt{<MRI-root>}. Processed MRI-data and model data is stored \textsl{inside} a unique folder in \texttt{<basilhome>}.
The link between the unique raw MRI-data folder inside \texttt{<MRI-root>} and the unique folder for model data inside \texttt{<basilhome>} is \textsl{hard-coded} in \texttt{bas\_getMeta.m}. When you add animals/experiments or rename certain directories, you will have to adopt this file.
The link between the unique raw MRI-data folder inside \texttt{<MRI-root>} and the unique folder for model data inside \texttt{<basilhome>} is \textsl{hard-coded} in \texttt{bas\_getMeta.m}. When you add animals/experiments or rename certain directories, you will have to adapt this file.
Each animal/experiment should have unique \textsl{numerical} identifier \texttt{<basilid>}. BasilLab calls \texttt{bas\_ getMeta.m} to find out where the raw MRI-data is stored for \texttt{<basilid>}, and it will look for \texttt{<basilhome>/<basilid>/} to store and read modelling data. Currently, the unique \texttt{<basilid>} is the date of the experiment in \texttt{yymmdd}-format.\\
......@@ -172,7 +180,7 @@ Thus, for the experiment performed on June 11\ap{th} 2015
\item[the link] between `\texttt{<basilid> = 140611}' and `raw MRI-data is stored in \texttt{<MRI-root>/140611.qd1/}' is hard-coded in \texttt{bas\_getMeta.m}
\end{description}
\noindent BasilLab provides \texttt{bas\_setMRIroot.m} to set \texttt{<MRI-root>} and \texttt{bas\_setDataRoot.m} to set \texttt{<basilhome>}.
\noindent BasilLab provides \texttt{bas\_setMRIroot.m} to set \texttt{<MRI-root>}, and \texttt{bas\_setDataRoot.m} to set \texttt{<basilhome>}.
......
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