documentation for IBM

book/_toc.yml

@@ -17,16 +17,14 @@ parts:
   - caption:  Advanced DALES options
     chapters:
       - file: running/tracers.ipynb
+      - file: running/ibm.ipynb
       # - file: running/chemistry.ipynb
       # - file: running/ibm.ipynb
       # - file: running/openbcs.ipynb
       - file: running/gpu.md
-  - caption:  Options outside main branch (for now)
-    chapters:
-      - file: running/ibm.ipynb
   - caption:  Recent publications using DALES
     chapters:
       - file: running/papers.ipynb
-  - caption: Contributing
+  - caption: Contributing to the documentation
     chapters:
       - file: developers/usermanual.md

book/developers/usermanual.md

@@ -1,6 +1,6 @@
 # User Manual
 
-The DALES user manual is built using [Jupyter Book](https://jupyterbook.org/en/stable/intro.html). In short, Jupyter Book allows you to easily build a website from Markdown files and/or Jupyter Notebooks. This page will explain the very basics of adding new content to the user manual.
+The DALES documentation is built using [Jupyter Book](https://jupyterbook.org/en/stable/intro.html). In short, Jupyter Book allows you to easily build a website from Markdown files and/or Jupyter Notebooks. This page will explain the very basics of adding new content to the documentation.
 
 ## Prerequisites
 

book/intro.md

@@ -9,7 +9,7 @@ This documentation is a work-in-progress and for a future release of DALES.
 The aim of this manual is to provide an up-to-date starting point for new users, explaining how to compile, setup and run the Dutch Atmospheric Large-Eddy Simulation. The manual will cover, among other things, general settings, and options (for example, statistics output), and instructions how to make more advanced cases (for example, simulations with tracers). The principles of the DALES model are described in [Heus et al., 2010](https://doi.org/10.5194/gmd-3-415-2010).
 
 ```{note}
-This manual is written for the main-branch (v. X.Y) in mind. Other branches may contain new features that are not necessarily described in this manual.
+This manual is written for the main-branch (v5.0) in mind. Other branches may contain new features that are not necessarily described in this manual.
 ```
 
 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.

book/running/compilation.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "(sec:compilation)=",
+    "(sec:compilation)=\n",
     "# Compilation of DALES\n",
     "\n",
     "## Generic compilation\n",
@@ -34,11 +34,11 @@
     "\n",
     "| Option | Description | Allowed values | Default |\n",
     "| ------ | ----------- | -------------- | ------- |\n",
-    "| `-DENABLE_FFTW` | Build with FFTW | On/Off | On |\n",
-    "| `-DENABLE_HYPRE` | Build with HYPRE | On/Off | Off |\n",
-    "| `-DENABLE_FP32_FIELDS` | Use single precision floating-point numbers for prognostic fields (momentum, temperature, et cetera) | On/Off | Off |\n",
-    "| `-DENABLE_FP32_POIS` | Use single precision floating-point numbers for the Poisson solver | On/Off | Off |\n",
-    "| `-DENABLE_ACC` | Build with GPU support through OpenACC | On/Off | Off |\n",
+    "| `-DENABLE_FFTW` | Build with FFTW | True/False | True |\n",
+    "| `-DENABLE_HYPRE` | Build with HYPRE | True/False | False |\n",
+    "| `-DENABLE_FP32_FIELDS` | Use single precision floating-point numbers for prognostic fields (momentum, temperature, etc.) | True/False | False |\n",
+    "| `-DENABLE_FP32_POIS` | Use single precision floating-point numbers for the Poisson solver | True/False | False |\n",
+    "| `-DENABLE_ACC` | Build with GPU support through OpenACC | True/False | False |\n",
     "\n",
     "```{caution}\n",
     "To use HYPRE or FFTW, the library needs to both be enabled at compilation and selected at runtime by setting the &SOLVER section of the namoptions input file. `FIX LINK: See Alternative Poisson solvers`.\n",

book/running/papers.ipynb

@@ -7,10 +7,16 @@
     "## List of publications using DALES\n",
     "The following contains a _non-exhaustive_ list of publications in which DALES was used.\n",
     "\n",
+    "### 2025\n",
+    "- Janssens, M., Jansson, F., Alinaghi, P., Glassmeier, F., and Siebesma, A. P. (2025). _Symmetry in mesoscale circulations explains weak impact of trade cumulus self‐organization on the radiation budget in large‐eddy simulations._ Geophysical Research Letters, **52**, e2024GL112288. https://doi.org/10.1029/2024GL112288\n",
+    "- Alinaghi, P., Siebesma, A. P., Jansson, F., Janssens, M., and Glassmeier, F. (2025). _External drivers and mesoscale self‐organization of shallow cold pools in the trade‐wind regime._ Journal of Advances in Modeling Earth Systems, **17**, e2024MS004540. https://doi.org/10.1029/2024MS004540\n",
+    "\n",
     "### 2024\n",
     "- Liqui Lung, F., Jakob, C., Siebesma, A. P. and Jansson, F. (2024). _Open boundary conditions for atmospheric large-eddy simulations and their implementation in DALES4.4_. Geoscientific Model Development, **17(9)**, 4053--4076, https://doi.org/10.5194/gmd-17-4053-2024\n",
+    "\n",
     "### 2023\n",
     "-  Jansson, F., Janssens, M., Grönqvist, J. H., Siebesma, A. P., Glassmeier, F., Attema, J., et al. (2023). _Cloud Botany: Shallow cumulus clouds in an ensemble of idealized large-domain large-eddy simulations of the trades_. Journal of Advances in Modeling Earth Systems, **15**, e2023MS003796. https://doi.org/10.1029/2023MS003796 \n",
+    "\n",
     "### 2022\n",
     "\n",
     "### 2021\n",

book/running/settingup.ipynb

@@ -85,7 +85,7 @@
     "...\n",
     "```\n",
     "\n",
-    "Checking out a specific branch (e.g., the `ruisdael` bracnh) is done via\n",
+    "Checking out a specific branch (e.g., the `ruisdael` branch) is done via\n",
     "```{code} shell\n",
     "git checkout -b <newname> remotes/origin/ruisdael\n",
     "```"