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manual-io.tex
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\chapter{Input / output}\index{I\/O}
In this chapter, the ways to get the internal data in a human readable formats
will be addressed. The models in \akantu handle data associated to the
mesh, but this data can be splitted into several \code{Vectors}. For example, the
data stored per element type in a \code{ByElementTypeVector} is composed by as
many vectors as types in the mesh.
In order to get this data in a visualization software, the models contain a
object to dump \code{VTK} files. These files can be visualized in software such
as \code{ParaView}\cite{paraview}, \code{ViSit}\cite{visit} or \code{Mayavi}\cite{mayavi}.
The internal dumper of the model can be configured to specify which data fields
are to be written. This is done with the
\code{addDumpField}\index{I\/O!addDumpField} method. By default all the files
are generated in a folder called \code{paraview/}
\begin{cpp}
model.setBaseName("output"); // prefix for all generated files
model.addDumpField("displacement");
model.addDumpField("stress");
...
model.dump()
\end{cpp}
The fields are dumped with the number of components of the memory. For example, in 2D, the memory have
the vectors of 2 components, or the $2^{nd}$ order tensors with $2\times2$ components.
This memory can be dealt with \code{addDumpFieldVector}\index{I\/O!addDumpFieldVector} which always dumps
vectors with 3 components or \code{addDumpFieldTensor}\index{I\/O!addDumpFieldTensor} which dumps $2^{nd}$
order tensors with $3\times3$ components respectively.
The fields which are stored by quadrature points are modified to be seen in the
\code{VTK} file as elemental data. To do this, the default is to average the
values of all the quadrature points.
The list of fields depends on the models.
\paragraph{\code{SolidMechanicsModel}:\index{I\/O!SolidMechanicsModel}}\hfill
\vspace*{0.2cm}
\begin{tabular}{llll}
\toprule
key & type & support \\
\midrule
displacement & Vector<Real> & nodes \\
velocity & Vector<Real> & nodes \\
acceleration & Vector<Real> & nodes \\
force & Vector<Real> & nodes \\
residual & Vector<Real> & nodes \\
boundary & Vector<bool> & nodes \\
mass & Vector<Real> & nodes \\
partitions & Real & elements \\
stress & Matrix<Real> & quadrature points \\
strain & Matrix<Real> & quadrature points \\
\textit{material internals} & variable & quadrature points \\
\bottomrule
\end{tabular}
The user can also register external fields which have the same mesh as the mesh from the model as support. To do this an object of type \code{Field} as to be created.\index{I\/O!addDumpFieldExternal}
\begin{itemize}
\item For nodal fields :
\begin{cpp}
Vector<T> vect(nb_nodes, nb_component);
Field field = new DumperIOHelper::NodalField<T>(vect));
model.addDumpFieldExternal("my_field", field);
\end{cpp}
\item For elemental fields :
\begin{cpp}
ByElementTypeVector<T> vect;
Field field = new DumperIOHelper::ElementalField<T>(vect, spatial_displacement));
model.addDumpFieldExternal("my_field", field);
\end{cpp}
\end{itemize}
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