add changes page

book/_toc.yml

@@ -4,6 +4,7 @@ root: intro.md
 parts:
   - caption: Getting started with DALES!
     chapters:
+      - file: running/changes.md
       - file: running/settingup.ipynb
       - file: running/compilation.ipynb
   - caption: Running your first case in DALES

book/running/changes.md

@@ -0,0 +1,37 @@
+# Changes between DALES 4.x and 5.0
+
+This page documents the recent changes to DALES, in particular those that require adapting existing cases. For more details, see [CHANGELOG](https://github.com/dalesteam/dales/blob/main/CHANGELOG.md) in the DALES repository.
+
+## Incompatibilities
+
+The following changes require user adaptation, changeing the installation procedure and adapting old case files.
+
+
+### Installation
+
+The installation steps have changed: DALES now uses git submodules, and the options to `cmake` have been modified. See  [](sec:compilation) for the current compilation procedure.
+
+### Scalar variables
+
+Scalar variables are now accessed by name, instead of just index.
+Scalars variables are automatically added as required by the modules that are active.
+
+* nsv in the namelist is now ignored
+* iadv_sv is no longer an array but a single value for all scalars
+* `scalar.inp.NNN` is no longer mandatory. Scalars for which no initial value is provided are initialized to 0. If `scalar.inp.NNN` is provided, it must contain a header line with the names of the scalars in the columns.
+The header must be two lines (as before). The second line must now
+list the scalar names and nothing else (for example an extra `#`, if followed by a space will cause problems).
+This is a valid scalar input file:
+```
+input file Scalar Profiles - RICO Trade Cu Period (12/16-01/08)
+height         nr      qr
+2.0000E+001     0       0
+6.0000E+001     0       0
+1.0000E+002     0       0
+...
+```
+
+## Other major changes
+
+* GPU support with OpenACC (see section [](sec:GPU))
+* Immersed boundary conditions enabling simulation of obstacles e.g. buildings (see section IBM) 

book/running/compilation.ipynb

@@ -4,6 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
+    "(sec:compilation)=",
     "# Compilation of DALES\n",
     "\n",
     "## Generic compilation\n",

book/running/gpu.md

@@ -1,3 +1,4 @@
+(sec:gpu)=
 # Using the GPU
 DALES now has the option to use graphics processing units (GPU's) to accelerate computations.