Add structure

book/intro.md

@@ -13,3 +13,75 @@ This manual is written for the main-branch (v. X.Y) in mind. Other branches may
 ```
 
 At a later stage, this manual may be extended with in-depth information on code structure, variable naming schemes, and implementation details, better enabling people to become _new contributors_ to DALES.
+
+
+## The structure of this manual
+
+This manual is structured as follows. The items without link are not yet available as they are under construction.
+
+Getting started with DALES!
+- [Setting up your system](https://dalesteam.github.io/dalesdocs/running/settingup.html)
+  - [Requirements](https://dalesteam.github.io/dalesdocs/running/settingup.html#requirements)
+  - [Optional libraries/packages](https://dalesteam.github.io/dalesdocs/running/settingup.html#optional-libraries-packages)
+  - [Downloading the code](https://dalesteam.github.io/dalesdocs/running/settingup.html#downloading-the-code)
+- [Compilation of DALES](https://dalesteam.github.io/dalesdocs/running/compilation.html)
+  - [Generic compilation](https://dalesteam.github.io/dalesdocs/running/compilation.html#generic-compilation)
+  - [Compilation options](https://dalesteam.github.io/dalesdocs/running/compilation.html#compilation-options)
+  - [Compilation on specific clusters](https://dalesteam.github.io/dalesdocs/running/compilation.html#compilation-on-specific-clusters)
+
+The physics
+- The governing equations
+  - Anelastic assumption
+- Subfilter-scale model
+- Discretization and Numerical Scheme
+- Condensation Scheme
+- The pressure solver
+- Cloud microphysics
+- Radiation schemes
+
+Running your first case in DALES
+- Test case
+- RICO example
+
+Setting up your own case
+- Input files
+  - Run script
+  - Warm start
+- Output files
+  - Merge output files
+  - Statistics
+- Basic Namoptions
+- All Namoptions
+
+Advanced DALES options
+- Advection schemes
+- Boundary conditions
+  - The surface model
+  - The sides and top
+- Conditional sampling
+- Dispersion and chemically reacting flows
+- [Running a case with tracers](https://dalesteam.github.io/dalesdocs/running/tracers.html)
+  - [Preparing the NetCDF file](https://dalesteam.github.io/dalesdocs/running/tracers.html#preparing-the-netcdf-file)
+  - [Adding a tracer](https://dalesteam.github.io/dalesdocs/running/tracers.html#adding-a-tracer)
+  - [Tracer attributes](https://dalesteam.github.io/dalesdocs/running/tracers.html#tracer-attributes)
+- [Using the GPU](https://dalesteam.github.io/dalesdocs/running/gpu.html)
+  -  [Compiling](https://dalesteam.github.io/dalesdocs/running/gpu.html#compiling)
+  -  [Problems with NetCDF-Fortran](https://dalesteam.github.io/dalesdocs/running/gpu.html#problems-with-netcdf-fortran)
+  -  [Running](https://dalesteam.github.io/dalesdocs/running/gpu.html#running)
+
+Options outside main branch
+- Immersed Boundary Method (IBM)
+- Sampling tendencies
+
+Applications and literature
+- Example cases
+  - RICO
+  - ...
+- [List of publications using DALES](https://dalesteam.github.io/dalesdocs/running/papers.html)
+
+Contributing
+- [User Manual](https://dalesteam.github.io/dalesdocs/developers/usermanual.html)
+  - [Prerequisites](https://dalesteam.github.io/dalesdocs/developers/usermanual.html#prerequisites)
+  - [Writing content](https://dalesteam.github.io/dalesdocs/developers/usermanual.html#writing-content)
+  - [Building the documentation](https://dalesteam.github.io/dalesdocs/developers/usermanual.html#building-the-documentation)
+- The code