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e67b827 change scaffold term to biodegradable part for #1

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mbarzegary committed Apr 11, 2022
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10 changes: 5 additions & 5 deletions manual/intro.tex
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\biodeg{} is an open-source software written in FreeFEM (a domain-specific language for finite element programming), C++, and Python for modeling the degradation of metallic biomaterials and simulating the biodegradation behavior of medical devices, implants, and scaffolds in corrosion experiments. It can handle any geometry of desire and supports parallel computing to simulate large-scale models.
\biodeg{} is an open-source software written in FreeFEM (a domain-specific language for finite element programming), C++, and Python for modeling the degradation of metallic biomaterials and simulating the biodegradation behavior of medical devices and implants in corrosion experiments. It can handle any geometry of desire and supports parallel computing to simulate large-scale models.

\subsection{Authors}
\label{sec:authors}
\biodeg{} is developed by the \href{http://www.biomech.ulg.ac.be/}{Biomechanics Research group at KU Leuven and University of Liege}. The code is currently maintained by its principal developer,
who manages the development of the mathematical models and the core functionalities.
\biodeg{} is developed by the \href{http://www.biomech.ulg.ac.be/}{Biomechanics Research group at KU Leuven and University of Liege}. The code is currently maintained by its principal developer,
who manages the development of the mathematical models and the core functionalities.

\paragraph*{Principal developer}
\begin{itemize}
Expand Down Expand Up @@ -34,5 +34,5 @@ \subsection{Acknowledgments}

\subsection{Referencing \biodeg{}}

Please refer to \href{https://github.com/mbarzegary/BioDeg}{\biodeg{} repository}, section "Publications and referencing" to properly cite the use of
\biodeg{} in your scientific work.
Please refer to \href{https://github.com/mbarzegary/BioDeg}{\biodeg{} repository}, section "Publications and referencing" to properly cite the use of
\biodeg{} in your scientific work.
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38 changes: 19 additions & 19 deletions manual/parameters.tex
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Expand Up @@ -12,7 +12,7 @@ \subsection{Geometry and mesh parameters}

{\it Default:} true (1)

{\it Description:} [Standard] Boolean parameter specifying whether an external mesh file is imported or a container box, as well as a cubic scaffold, would be created on the fly for simulation.
{\it Description:} [Standard] Boolean parameter specifying whether an external mesh file is imported or a container box, as well as a cubic biodegradable part, would be created on the fly for simulation.

{\it Possible values:} A boolean value (1 or 0)

Expand All @@ -27,7 +27,7 @@ \subsection{Geometry and mesh parameters}

{\it Description:} [Standard] Path to the input mesh file (in MEDIT {\tt .mesh} format), which can be either absolute or relative. Is relevant only if parameter {\tt import\_mesh} is set to TRUE.

{\it Possible values:} Any string value
{\it Possible values:} Any string value


\item {\it Parameter name:} {\tt label\_scaffold}
Expand All @@ -39,9 +39,9 @@ \subsection{Geometry and mesh parameters}

{\it Default:} 1

{\it Description:} [Standard] The label of the (volume) region which is supposed to be scaffold in the input mesh (can be viewed in programs like GMSH before importing into \biodeg{}).
{\it Description:} [Standard] The label of the (volume) region which is supposed to be the biodegradable part in the input mesh (can be viewed in programs like GMSH before importing into \biodeg{}).

{\it Possible values:} Any positive integer value
{\it Possible values:} Any positive integer value


\item {\it Parameter name:} {\tt label\_medium}
Expand All @@ -51,11 +51,11 @@ \subsection{Geometry and mesh parameters}
\index[prmindex]{label\_medium}
\index[prmindexfull]{Geometry and mesh!label medium}

{\it Default:} 2
{\it Default:} 2

{\it Description:} [Standard] The label of the (volume) region which is supposed to be the medium (electrolyte) in the input mesh.

{\it Possible values:} Any positive integer value
{\it Possible values:} Any positive integer value


\item {\it Parameter name:} {\tt label\_wall}
Expand All @@ -69,7 +69,7 @@ \subsection{Geometry and mesh parameters}

{\it Description:} [Advanced] The label of the surface in the input mesh to be assigned as wall (no-slip boundary condition) in the fluid flow simulations.

{\it Possible values:} Any positive integer value
{\it Possible values:} Any positive integer value


\item {\it Parameter name:} {\tt label\_inlet}
Expand All @@ -83,7 +83,7 @@ \subsection{Geometry and mesh parameters}

{\it Description:} [Advanced] The label of the surface in the input mesh to be assigned as flow inlet (constant velocity boundary condition) in the fluid flow simulations.

{\it Possible values:} Any positive integer value
{\it Possible values:} Any positive integer value


\item {\it Parameter name:} {\tt label\_outlet}
Expand All @@ -97,7 +97,7 @@ \subsection{Geometry and mesh parameters}

{\it Description:} [Advanced] The label of the surface in the input mesh to be assigned as flow outlet (zero pressure boundary condition) in the fluid flow simulations.

{\it Possible values:} Any positive integer value
{\it Possible values:} Any positive integer value


\item {\it Parameter name:} {\tt box\_length}
Expand All @@ -111,7 +111,7 @@ \subsection{Geometry and mesh parameters}

{\it Description:} [Standard] In case of {\tt import\_mesh} being FALSE, specifies the length of the container box (for the electrolyte) in mm.

{\it Possible values:} Any positive floating-point number
{\it Possible values:} Any positive floating-point number


\item {\it Parameter name:} {\tt cube\_size\_x}
Expand All @@ -123,9 +123,9 @@ \subsection{Geometry and mesh parameters}

{\it Default:} 13.0

{\it Description:} [Standard] In case of {\tt import\_mesh} being FALSE, specifies the length of the scaffold cuboid along the x axis in mm.
{\it Description:} [Standard] In case of {\tt import\_mesh} being FALSE, specifies the length of the biodegradable cuboid along the x axis in mm.

{\it Possible values:} Any positive floating-point number
{\it Possible values:} Any positive floating-point number


\item {\it Parameter name:} {\tt cube\_size\_y}
Expand All @@ -137,9 +137,9 @@ \subsection{Geometry and mesh parameters}

{\it Default:} 13.0

{\it Description:} [Standard] In case of {\tt import\_mesh} being FALSE, specifies the length of the scaffold cuboid along the y axis in mm.
{\it Description:} [Standard] In case of {\tt import\_mesh} being FALSE, specifies the length of the biodegradable cuboid along the y axis in mm.

{\it Possible values:} Any positive floating-point number
{\it Possible values:} Any positive floating-point number


\item {\it Parameter name:} {\tt cube\_size\_z}
Expand All @@ -151,10 +151,10 @@ \subsection{Geometry and mesh parameters}

{\it Default:} 4.0

{\it Description:} [Standard] In case of {\tt import\_mesh} being FALSE, specifies the length of the scaffold cuboid along the z axis in mm.
{\it Description:} [Standard] In case of {\tt import\_mesh} being FALSE, specifies the length of the biodegradable cuboid along the z axis in mm.


{\it Possible values:} Any positive floating-point number
{\it Possible values:} Any positive floating-point number


\item {\it Parameter name:} {\tt mesh\_size}
Expand All @@ -168,7 +168,7 @@ \subsection{Geometry and mesh parameters}

{\it Description:} [Standard] Number of elements on each edge of the container box, so a higher number means a finer mesh. The mesh size of the cuboid will be adjusted accordingly or can be adaptively refined by setting parameter {\tt refine\_initial\_mesh} to TRUE.

{\it Possible values:} Any positive integer number
{\it Possible values:} Any positive integer number


\item {\it Parameter name:} {\tt refine\_initial\_mesh}
Expand Down Expand Up @@ -313,7 +313,7 @@ \subsection{Materials and boundary conditions parameters}

{\it Default:} 0.05

{\it Description:} [Standard]
{\it Description:} [Standard]

{\it Possible values:} The diffusion coefficient of the metallic ions transport. This parameter is one of the most effective ones on the rate of degradation.

Expand Down Expand Up @@ -705,7 +705,7 @@ \subsection{Output parameters}

{\it Default:} 0.25

{\it Description:} [Standard] The interval of saving results, text and VTK (if selected), to disk.
{\it Description:} [Standard] The interval of saving results, text and VTK (if selected), to disk.

{\it Possible values:} Any floating-point number

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