Planets - User contributions [en]

WRF dynamical core for LES/mesoscale simulations

2026-01-14T11:15:27Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and the two others are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).
<syntaxhighlight lang="text">
git clone git@gitlab.in2p3.fr:aymeric.spiga/les_mars_project.git
</syntaxhighlight>
NB: The old name of 'LES_planet_workflow' is 'les_mars_project', the original address can not be modified.

NB2: You may need to ask for access to Aymeric's repository before.

NB3: Cloning with 'ssh' is better than cloning with 'https' (for later commits)

Set this repo on the branch "wrfv4".
<syntaxhighlight lang="text">
git checkout wrfv4
</syntaxhighlight>

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='/absolute_path_to_your_LES_planet_workflow/code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=/absolute_path_to_your_LES_planet_workflow/code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download child repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

<syntaxhighlight lang="text">
archname="ADASTRA-ifort" # (or other cluster)
</syntaxhighlight>

Modify the 0_defining.sh file to have the right physics compiling options, for example:

<syntaxhighlight lang="text">
add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)
</syntaxhighlight>

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

<syntaxhighlight lang="text">
source mesoscale.env
</syntaxhighlight>

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

<syntaxhighlight lang="text">
echo 15 > configure_inputs
echo 1 >> configure_inputs
</syntaxhighlight>

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

First, "source mesoscale.env"

And then execute, one by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====
<syntaxhighlight lang="text">
gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)
</syntaxhighlight>

For example, for Neptune:

<syntaxhighlight lang="text">
11.15
10200.
2.3
175.
10.e5
24622.0e3
</syntaxhighlight>

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

<syntaxhighlight lang="text">
#! /bin/bash
#SBATCH --job-name=batch_adastra
#SBATCH --account=cin0391
#SBATCH --constraint=GENOA
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --threads-per-core=1 # --hint=nomultithread
#SBATCH --cpus-per-task=1
#SBATCH --output=batch_adastra.out
#SBATCH --time=06:00:00

source ../mesoscale.env

srun --cpu-bind=threads --label ideal.exe
srun --cpu-bind=threads --label wrf.exe

mkdir wrfout_results_$SLURM_JOB_ID
mv wrfout_d01* wrfout_results_$SLURM_JOB_ID
mv wrfrst* wrfout_results_$SLURM_JOB_ID

cp -rf namelist.input wrfout_results_$SLURM_JOB_ID/used_namelist.input
cp -rf callphys.def wrfout_results_$SLURM_JOB_ID/used_callphys.def
cp input_sounding wrfout_results_$SLURM_JOB_ID/used_input_sounding

mkdir wrfout_results_$SLURM_JOB_ID/messages_simulations
mv batch_adastra.out wrfout_results_$SLURM_JOB_ID/messages_simulations
mv rsl.* wrfout_results_$SLURM_JOB_ID/messages_simulations
</syntaxhighlight>

==== Files in the folder ====

To launch the simulation:
<ul>
<li> batch_adastra </li>
</ul>
WRF specific:
<ul>
<li> planet_constant </li>
<li> input_sounding </li>
<li> input_coord </li>
<li> namelist.input </li>
</ul>
Generic PCM specific:
<ul>
<li> run.def </li>
<li> callphys.def </li>
<li> gases.def </li>
<li> traceur.def </li>
</ul>
Executables:
<ul>
<li> ideal.exe </li>
<li> wrf.exe </li>
</ul>

The run.def file is required even if unused (no need to change it).

Optional for additional outputs
<ul>
<li> my_iofields_list.txt </li>
</ul>

which can be like:

<syntaxhighlight lang="text">
+:h:0:DQVAP,DQICE,WW,TT
-:h:0:QH2O
</syntaxhighlight>

and you need to put an additional line in ''namelist.input
with for example
<syntaxhighlight lang="text">
iofields_filename = "my_iofields_list.txt"
</syntaxhighlight>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2026-01-14T11:09:28Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and the two others are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Set this repo on the branch "wrfv4".
<syntaxhighlight lang="text">
git checkout wrfv4
</syntaxhighlight>

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='/absolute_path_to_your_LES_planet_workflow/code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=/absolute_path_to_your_LES_planet_workflow/code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download child repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

<syntaxhighlight lang="text">
archname="ADASTRA-ifort" # (or other cluster)
</syntaxhighlight>

Modify the 0_defining.sh file to have the right physics compiling options, for example:

<syntaxhighlight lang="text">
add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)
</syntaxhighlight>

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

<syntaxhighlight lang="text">
source mesoscale.env
</syntaxhighlight>

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

<syntaxhighlight lang="text">
echo 15 > configure_inputs
echo 1 >> configure_inputs
</syntaxhighlight>

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

First, "source mesoscale.env"

And then execute, one by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====
<syntaxhighlight lang="text">
gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)
</syntaxhighlight>

For example, for Neptune:

<syntaxhighlight lang="text">
11.15
10200.
2.3
175.
10.e5
24622.0e3
</syntaxhighlight>

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

<syntaxhighlight lang="text">
#! /bin/bash
#SBATCH --job-name=batch_adastra
#SBATCH --account=cin0391
#SBATCH --constraint=GENOA
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --threads-per-core=1 # --hint=nomultithread
#SBATCH --cpus-per-task=1
#SBATCH --output=batch_adastra.out
#SBATCH --time=06:00:00

source ../mesoscale.env

srun --cpu-bind=threads --label ideal.exe
srun --cpu-bind=threads --label wrf.exe

mkdir wrfout_results_$SLURM_JOB_ID
mv wrfout_d01* wrfout_results_$SLURM_JOB_ID
mv wrfrst* wrfout_results_$SLURM_JOB_ID

cp -rf namelist.input wrfout_results_$SLURM_JOB_ID/used_namelist.input
cp -rf callphys.def wrfout_results_$SLURM_JOB_ID/used_callphys.def
cp input_sounding wrfout_results_$SLURM_JOB_ID/used_input_sounding

mkdir wrfout_results_$SLURM_JOB_ID/messages_simulations
mv batch_adastra.out wrfout_results_$SLURM_JOB_ID/messages_simulations
mv rsl.* wrfout_results_$SLURM_JOB_ID/messages_simulations
</syntaxhighlight>

==== Files in the folder ====

To launch the simulation:
<ul>
<li> batch_adastra </li>
</ul>
WRF specific:
<ul>
<li> planet_constant </li>
<li> input_sounding </li>
<li> input_coord </li>
<li> namelist.input </li>
</ul>
Generic PCM specific:
<ul>
<li> run.def </li>
<li> callphys.def </li>
<li> gases.def </li>
<li> traceur.def </li>
</ul>
Executables:
<ul>
<li> ideal.exe </li>
<li> wrf.exe </li>
</ul>

The run.def file is required even if unused (no need to change it).

Optional for additional outputs
<ul>
<li> my_iofields_list.txt </li>
</ul>

which can be like:

<syntaxhighlight lang="text">
+:h:0:DQVAP,DQICE,WW,TT
-:h:0:QH2O
</syntaxhighlight>

and you need to put an additional line in ''namelist.input
with for example
<syntaxhighlight lang="text">
iofields_filename = "my_iofields_list.txt"
</syntaxhighlight>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2026-01-14T11:01:45Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and the two others are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Set this repo on the branch "wrfv4". "git checkout wrfv4"

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='/absolute_path_to_your_LES_planet_workflow/code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=/absolute_path_to_your_LES_planet_workflow/code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download child repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

<syntaxhighlight lang="text">
archname="ADASTRA-ifort" # (or other cluster)
</syntaxhighlight>

Modify the 0_defining.sh file to have the right physics compiling options, for example:

<syntaxhighlight lang="text">
add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)
</syntaxhighlight>

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

<syntaxhighlight lang="text">
source mesoscale.env
</syntaxhighlight>

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

<syntaxhighlight lang="text">
echo 15 > configure_inputs
echo 1 >> configure_inputs
</syntaxhighlight>

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

First, "source mesoscale.env"

And then execute, one by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====
<syntaxhighlight lang="text">
gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)
</syntaxhighlight>

For example, for Neptune:

<syntaxhighlight lang="text">
11.15
10200.
2.3
175.
10.e5
24622.0e3
</syntaxhighlight>

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

<syntaxhighlight lang="text">
#! /bin/bash
#SBATCH --job-name=batch_adastra
#SBATCH --account=cin0391
#SBATCH --constraint=GENOA
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --threads-per-core=1 # --hint=nomultithread
#SBATCH --cpus-per-task=1
#SBATCH --output=batch_adastra.out
#SBATCH --time=06:00:00

source ../mesoscale.env

srun --cpu-bind=threads --label ideal.exe
srun --cpu-bind=threads --label wrf.exe

mkdir wrfout_results_$SLURM_JOB_ID
mv wrfout_d01* wrfout_results_$SLURM_JOB_ID
mv wrfrst* wrfout_results_$SLURM_JOB_ID

cp -rf namelist.input wrfout_results_$SLURM_JOB_ID/used_namelist.input
cp -rf callphys.def wrfout_results_$SLURM_JOB_ID/used_callphys.def
cp input_sounding wrfout_results_$SLURM_JOB_ID/used_input_sounding

mkdir wrfout_results_$SLURM_JOB_ID/messages_simulations
mv batch_adastra.out wrfout_results_$SLURM_JOB_ID/messages_simulations
mv rsl.* wrfout_results_$SLURM_JOB_ID/messages_simulations
</syntaxhighlight>

==== Files in the folder ====

To launch the simulation:
<ul>
<li> batch_adastra </li>
</ul>
WRF specific:
<ul>
<li> planet_constant </li>
<li> input_sounding </li>
<li> input_coord </li>
<li> namelist.input </li>
</ul>
Generic PCM specific:
<ul>
<li> run.def </li>
<li> callphys.def </li>
<li> gases.def </li>
<li> traceur.def </li>
</ul>
Executables:
<ul>
<li> ideal.exe </li>
<li> wrf.exe </li>
</ul>

The run.def file is required even if unused (no need to change it).

Optional for additional outputs
<ul>
<li> my_iofields_list.txt </li>
</ul>

which can be like:

<syntaxhighlight lang="text">
+:h:0:DQVAP,DQICE,WW,TT
-:h:0:QH2O
</syntaxhighlight>

and you need to put an additional line in ''namelist.input
with for example
<syntaxhighlight lang="text">
iofields_filename = "my_iofields_list.txt"
</syntaxhighlight>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2026-01-14T10:58:17Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and the two others are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Set this repo on the branch "wrfv4". "git checkout wrfv4"

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=/absolute_path_to_your_LES_planet_workflow/code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download child repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

<syntaxhighlight lang="text">
archname="ADASTRA-ifort" # (or other cluster)
</syntaxhighlight>

Modify the 0_defining.sh file to have the right physics compiling options, for example:

<syntaxhighlight lang="text">
add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)
</syntaxhighlight>

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

<syntaxhighlight lang="text">
source mesoscale.env
</syntaxhighlight>

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

<syntaxhighlight lang="text">
echo 15 > configure_inputs
echo 1 >> configure_inputs
</syntaxhighlight>

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

First, "source mesoscale.env"

And then execute, one by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====
<syntaxhighlight lang="text">
gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)
</syntaxhighlight>

For example, for Neptune:

<syntaxhighlight lang="text">
11.15
10200.
2.3
175.
10.e5
24622.0e3
</syntaxhighlight>

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

<syntaxhighlight lang="text">
#! /bin/bash
#SBATCH --job-name=batch_adastra
#SBATCH --account=cin0391
#SBATCH --constraint=GENOA
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --threads-per-core=1 # --hint=nomultithread
#SBATCH --cpus-per-task=1
#SBATCH --output=batch_adastra.out
#SBATCH --time=06:00:00

source ../mesoscale.env

srun --cpu-bind=threads --label ideal.exe
srun --cpu-bind=threads --label wrf.exe

mkdir wrfout_results_$SLURM_JOB_ID
mv wrfout_d01* wrfout_results_$SLURM_JOB_ID
mv wrfrst* wrfout_results_$SLURM_JOB_ID

cp -rf namelist.input wrfout_results_$SLURM_JOB_ID/used_namelist.input
cp -rf callphys.def wrfout_results_$SLURM_JOB_ID/used_callphys.def
cp input_sounding wrfout_results_$SLURM_JOB_ID/used_input_sounding

mkdir wrfout_results_$SLURM_JOB_ID/messages_simulations
mv batch_adastra.out wrfout_results_$SLURM_JOB_ID/messages_simulations
mv rsl.* wrfout_results_$SLURM_JOB_ID/messages_simulations
</syntaxhighlight>

==== Files in the folder ====

To launch the simulation:
<ul>
<li> batch_adastra </li>
</ul>
WRF specific:
<ul>
<li> planet_constant </li>
<li> input_sounding </li>
<li> input_coord </li>
<li> namelist.input </li>
</ul>
Generic PCM specific:
<ul>
<li> run.def </li>
<li> callphys.def </li>
<li> gases.def </li>
<li> traceur.def </li>
</ul>
Executables:
<ul>
<li> ideal.exe </li>
<li> wrf.exe </li>
</ul>

The run.def file is required even if unused (no need to change it).

Optional for additional outputs
<ul>
<li> my_iofields_list.txt </li>
</ul>

which can be like:

<syntaxhighlight lang="text">
+:h:0:DQVAP,DQICE,WW,TT
-:h:0:QH2O
</syntaxhighlight>

and you need to put an additional line in ''namelist.input
with for example
<syntaxhighlight lang="text">
iofields_filename = "my_iofields_list.txt"
</syntaxhighlight>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2026-01-13T15:19:17Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and the two others are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Set this repo on the branch "wrfv4". "git checkout wrfv4"

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download child repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

<syntaxhighlight lang="text">
archname="ADASTRA-ifort" # (or other cluster)
</syntaxhighlight>

Modify the 0_defining.sh file to have the right physics compiling options, for example:

<syntaxhighlight lang="text">
add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)
</syntaxhighlight>

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

<syntaxhighlight lang="text">
source mesoscale.env
</syntaxhighlight>

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

<syntaxhighlight lang="text">
echo 15 > configure_inputs
echo 1 >> configure_inputs
</syntaxhighlight>

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

First, "source mesoscale.env"

And then execute, one by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====
<syntaxhighlight lang="text">
gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)
</syntaxhighlight>

For example, for Neptune:

<syntaxhighlight lang="text">
11.15
10200.
2.3
175.
10.e5
24622.0e3
</syntaxhighlight>

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

<syntaxhighlight lang="text">
#! /bin/bash
#SBATCH --job-name=batch_adastra
#SBATCH --account=cin0391
#SBATCH --constraint=GENOA
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --threads-per-core=1 # --hint=nomultithread
#SBATCH --cpus-per-task=1
#SBATCH --output=batch_adastra.out
#SBATCH --time=06:00:00

source ../mesoscale.env

srun --cpu-bind=threads --label ideal.exe
srun --cpu-bind=threads --label wrf.exe

mkdir wrfout_results_$SLURM_JOB_ID
mv wrfout_d01* wrfout_results_$SLURM_JOB_ID
mv wrfrst* wrfout_results_$SLURM_JOB_ID

cp -rf namelist.input wrfout_results_$SLURM_JOB_ID/used_namelist.input
cp -rf callphys.def wrfout_results_$SLURM_JOB_ID/used_callphys.def
cp input_sounding wrfout_results_$SLURM_JOB_ID/used_input_sounding

mkdir wrfout_results_$SLURM_JOB_ID/messages_simulations
mv batch_adastra.out wrfout_results_$SLURM_JOB_ID/messages_simulations
mv rsl.* wrfout_results_$SLURM_JOB_ID/messages_simulations
</syntaxhighlight>

==== Files in the folder ====

To launch the simulation:
<ul>
<li> batch_adastra </li>
</ul>
WRF specific:
<ul>
<li> planet_constant </li>
<li> input_sounding </li>
<li> input_coord </li>
<li> namelist.input </li>
</ul>
Generic PCM specific:
<ul>
<li> run.def </li>
<li> callphys.def </li>
<li> gases.def </li>
<li> traceur.def </li>
</ul>
Executables:
<ul>
<li> ideal.exe </li>
<li> wrf.exe </li>
</ul>

The run.def file is required even if unused (no need to change it).

Optional for additional outputs
<ul>
<li> my_iofields_list.txt </li>
</ul>

which can be like:

<syntaxhighlight lang="text">
+:h:0:DQVAP,DQICE,WW,TT
-:h:0:QH2O
</syntaxhighlight>

and you need to put an additional line in ''namelist.input
with for example
<syntaxhighlight lang="text">
iofields_filename = "my_iofields_list.txt"
</syntaxhighlight>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2026-01-09T15:18:54Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and the two others are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Set this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download child repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

<syntaxhighlight lang="text">
archname="ADASTRA-ifort" # (or other cluster)
</syntaxhighlight>

Modify the 0_defining.sh file to have the right physics compiling options, for example:

<syntaxhighlight lang="text">
add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)
</syntaxhighlight>

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

<syntaxhighlight lang="text">
source mesoscale.env
</syntaxhighlight>

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

<syntaxhighlight lang="text">
echo 15 > configure_inputs
echo 1 >> configure_inputs
</syntaxhighlight>

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

First, "source mesoscale.env"

And then execute, one by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====
<syntaxhighlight lang="text">
gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)
</syntaxhighlight>

For example, for Neptune:

<syntaxhighlight lang="text">
11.15
10200.
2.3
175.
10.e5
24622.0e3
</syntaxhighlight>

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

<syntaxhighlight lang="text">
#! /bin/bash
#SBATCH --job-name=batch_adastra
#SBATCH --account=cin0391
#SBATCH --constraint=GENOA
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --threads-per-core=1 # --hint=nomultithread
#SBATCH --cpus-per-task=1
#SBATCH --output=batch_adastra.out
#SBATCH --time=06:00:00

source ../mesoscale.env

srun --cpu-bind=threads --label ideal.exe
srun --cpu-bind=threads --label wrf.exe

mkdir wrfout_results_$SLURM_JOB_ID
mv wrfout_d01* wrfout_results_$SLURM_JOB_ID
mv wrfrst* wrfout_results_$SLURM_JOB_ID

cp -rf namelist.input wrfout_results_$SLURM_JOB_ID/used_namelist.input
cp -rf callphys.def wrfout_results_$SLURM_JOB_ID/used_callphys.def
cp input_sounding wrfout_results_$SLURM_JOB_ID/used_input_sounding

mkdir wrfout_results_$SLURM_JOB_ID/messages_simulations
mv batch_adastra.out wrfout_results_$SLURM_JOB_ID/messages_simulations
mv rsl.* wrfout_results_$SLURM_JOB_ID/messages_simulations
</syntaxhighlight>

==== Files in the folder ====

To launch the simulation:
<ul>
<li> batch_adastra </li>
</ul>
WRF specific:
<ul>
<li> planet_constant </li>
<li> input_sounding </li>
<li> input_coord </li>
<li> namelist.input </li>
</ul>
Generic PCM specific:
<ul>
<li> run.def </li>
<li> callphys.def </li>
<li> gases.def </li>
<li> traceur.def </li>
</ul>
Executables:
<ul>
<li> ideal.exe </li>
<li> wrf.exe </li>
</ul>

The run.def file is required even if unused (no need to change it).

Optional for additional outputs
<ul>
<li> my_iofields_list.txt </li>
</ul>

which can be like:

<syntaxhighlight lang="text">
+:h:0:DQVAP,DQICE,WW,TT
-:h:0:QH2O
</syntaxhighlight>

and you need to put an additional line in ''namelist.input
with for example
<syntaxhighlight lang="text">
iofields_filename = "my_iofields_list.txt"
</syntaxhighlight>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2026-01-08T13:50:48Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and the two others are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Set this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download child repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

<syntaxhighlight lang="text">
archname="ADASTRA-ifort" # (or other cluster)
</syntaxhighlight>

Modify the 0_defining.sh file to have the right physics compiling options, for example:

<syntaxhighlight lang="text">
add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)
</syntaxhighlight>

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

<syntaxhighlight lang="text">
source mesoscale.env
</syntaxhighlight>

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

<syntaxhighlight lang="text">
echo 15 > configure_inputs
echo 1 >> configure_inputs
</syntaxhighlight>

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

First, "source mesoscale.env"

And then execute, one by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====
<syntaxhighlight lang="text">
gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)
</syntaxhighlight>

For example, for Neptune:

<syntaxhighlight lang="text">
11.15
10200.
2.3
175.
10.e5
24622.0e3
</syntaxhighlight>

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

<syntaxhighlight lang="text">
#! /bin/bash
#SBATCH --job-name=batch_adastra
#SBATCH --account=cin0391
#SBATCH --constraint=GENOA
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --threads-per-core=1 # --hint=nomultithread
#SBATCH --output=batch_adastra.out
#SBATCH --time=06:00:00

source ../mesoscale.env

srun --cpu-bind=threads --label ideal.exe
srun --cpu-bind=threads --label wrf.exe

mkdir wrfout_results_$SLURM_JOB_ID
mv wrfout_d01* wrfout_results_$SLURM_JOB_ID
mv wrfrst* wrfout_results_$SLURM_JOB_ID

cp -rf namelist.input wrfout_results_$SLURM_JOB_ID/used_namelist.input
cp -rf callphys.def wrfout_results_$SLURM_JOB_ID/used_callphys.def
cp input_sounding wrfout_results_$SLURM_JOB_ID/used_input_sounding

mkdir wrfout_results_$SLURM_JOB_ID/messages_simulations
mv batch_adastra.out wrfout_results_$SLURM_JOB_ID/messages_simulations
mv rsl.* wrfout_results_$SLURM_JOB_ID/messages_simulations
</syntaxhighlight>

==== Files in the folder ====

To launch the simulation:
<ul>
<li> batch_adastra </li>
</ul>
WRF specific:
<ul>
<li> planet_constant </li>
<li> input_sounding </li>
<li> input_coord </li>
<li> namelist.input </li>
</ul>
Generic PCM specific:
<ul>
<li> run.def </li>
<li> callphys.def </li>
<li> gases.def </li>
<li> traceur.def </li>
</ul>
Executables:
<ul>
<li> ideal.exe </li>
<li> wrf.exe </li>
</ul>

The run.def file is required even if unused (no need to change it).

Optional for additional outputs
<ul>
<li> my_iofields_list.txt </li>
</ul>

which can be like:

<syntaxhighlight lang="text">
+:h:0:DQVAP,DQICE,WW,TT
-:h:0:QH2O
</syntaxhighlight>

and you need to put an additional line in ''namelist.input
with for example
<syntaxhighlight lang="text">
iofields_filename = "my_iofields_list.txt"
</syntaxhighlight>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2026-01-08T13:42:24Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and the two others are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Set this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download child repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

<syntaxhighlight lang="text">
archname="ADASTRA-ifort" # (or other cluster)
</syntaxhighlight>

Modify the 0_defining.sh file to have the right physics compiling options, for example:

<syntaxhighlight lang="text">
add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)
</syntaxhighlight>

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

<syntaxhighlight lang="text">
source mesoscale.env
</syntaxhighlight>

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

<syntaxhighlight lang="text">
echo 15 > configure_inputs
echo 1 >> configure_inputs
</syntaxhighlight>

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====
<syntaxhighlight lang="text">
gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)
</syntaxhighlight>

For example, for Neptune:

<syntaxhighlight lang="text">
11.15
10200.
2.3
175.
10.e5
24622.0e3
</syntaxhighlight>

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

<syntaxhighlight lang="text">
#! /bin/bash
#SBATCH --job-name=batch_adastra
#SBATCH --account=cin0391
#SBATCH --constraint=GENOA
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --threads-per-core=1 # --hint=nomultithread
#SBATCH --output=batch_adastra.out
#SBATCH --time=06:00:00

source ../mesoscale.env

srun --cpu-bind=threads --label ideal.exe
srun --cpu-bind=threads --label wrf.exe

mkdir wrfout_results_$SLURM_JOB_ID
mv wrfout_d01* wrfout_results_$SLURM_JOB_ID
mv wrfrst* wrfout_results_$SLURM_JOB_ID

cp -rf namelist.input wrfout_results_$SLURM_JOB_ID/used_namelist.input
cp -rf callphys.def wrfout_results_$SLURM_JOB_ID/used_callphys.def
cp input_sounding wrfout_results_$SLURM_JOB_ID/used_input_sounding

mkdir wrfout_results_$SLURM_JOB_ID/messages_simulations
mv batch_adastra.out wrfout_results_$SLURM_JOB_ID/messages_simulations
mv rsl.* wrfout_results_$SLURM_JOB_ID/messages_simulations
</syntaxhighlight>

==== Files in the folder ====

To launch the simulation:
<ul>
<li> batch_adastra </li>
</ul>
WRF specific:
<ul>
<li> planet_constant </li>
<li> input_sounding </li>
<li> input_coord </li>
<li> namelist.input </li>
</ul>
Generic PCM specific:
<ul>
<li> run.def </li>
<li> callphys.def </li>
<li> gases.def </li>
<li> traceur.def </li>
</ul>
Executables:
<ul>
<li> ideal.exe </li>
<li> wrf.exe </li>
</ul>

The run.def file is required even if unused (no need to change it).

Optional for additional outputs
<ul>
<li> my_iofields_list.txt </li>
</ul>

which can be like:

<syntaxhighlight lang="text">
+:h:0:DQVAP,DQICE,WW,TT
-:h:0:QH2O
</syntaxhighlight>

and you need to put an additional line in ''namelist.input
with for example
<syntaxhighlight lang="text">
iofields_filename = "my_iofields_list.txt"
</syntaxhighlight>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T15:14:07Z

Noe clement: /* Terrestrial WRF */

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Set this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download child repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

<syntaxhighlight lang="text">
archname="ADASTRA-ifort" # (or other cluster)
</syntaxhighlight>

Modify the 0_defining.sh file to have the right physics compiling options, for example:

<syntaxhighlight lang="text">
add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)
</syntaxhighlight>

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

<syntaxhighlight lang="text">
source mesoscale.env
</syntaxhighlight>

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

<syntaxhighlight lang="text">
echo 15 > configure_inputs
echo 1 >> configure_inputs
</syntaxhighlight>

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====
<syntaxhighlight lang="text">
gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)
</syntaxhighlight>

For example, for Neptune:

<syntaxhighlight lang="text">
11.15
10200.
2.3
175.
10.e5
24622.0e3
</syntaxhighlight>

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

<syntaxhighlight lang="text">
#! /bin/bash
#SBATCH --job-name=batch_adastra
#SBATCH --account=cin0391
#SBATCH --constraint=GENOA
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --threads-per-core=1 # --hint=nomultithread
#SBATCH --output=batch_adastra.out
#SBATCH --time=06:00:00

source ../mesoscale.env

srun --cpu-bind=threads --label ideal.exe
srun --cpu-bind=threads --label wrf.exe

mkdir wrfout_results_$SLURM_JOB_ID
mv wrfout_d01* wrfout_results_$SLURM_JOB_ID
mv wrfrst* wrfout_results_$SLURM_JOB_ID

cp -rf namelist.input wrfout_results_$SLURM_JOB_ID/used_namelist.input
cp -rf callphys.def wrfout_results_$SLURM_JOB_ID/used_callphys.def
cp input_sounding wrfout_results_$SLURM_JOB_ID/used_input_sounding

mkdir wrfout_results_$SLURM_JOB_ID/messages_simulations
mv batch_adastra.out wrfout_results_$SLURM_JOB_ID/messages_simulations
mv rsl.* wrfout_results_$SLURM_JOB_ID/messages_simulations
</syntaxhighlight>

==== Files in the folder ====

To launch the simulation:
<ul>
<li> batch_adastra </li>
</ul>
WRF specific:
<ul>
<li> planet_constant </li>
<li> input_sounding </li>
<li> input_coord </li>
<li> namelist.input </li>
</ul>
Generic PCM specific:
<ul>
<li> run.def </li>
<li> callphys.def </li>
<li> gases.def </li>
<li> traceur.def </li>
</ul>
Executables:
<ul>
<li> ideal.exe </li>
<li> wrf.exe </li>
</ul>

The run.def file is required even if unused (no need to change it).

Optional for additional outputs
<ul>
<li> my_iofields_list.txt </li>
</ul>

which can be like:

<syntaxhighlight lang="text">
+:h:0:DQVAP,DQICE,WW,TT
-:h:0:QH2O
</syntaxhighlight>

and you need to put an additional line in ''namelist.input
with for example
<syntaxhighlight lang="text">
iofields_filename = "my_iofields_list.txt"
</syntaxhighlight>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T15:13:17Z

Noe clement: /* Modify options to fit your compiling environment & your modelled planetary atmosphere */

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Set this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download child repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

<syntaxhighlight lang="text">
archname="ADASTRA-ifort" # (or other cluster)
</syntaxhighlight>

Modify the 0_defining.sh file to have the right physics compiling options, for example:

<syntaxhighlight lang="text">
add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)
</syntaxhighlight>

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

<syntaxhighlight lang="text">
source mesoscale.env
</syntaxhighlight>

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====
<syntaxhighlight lang="text">
gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)
</syntaxhighlight>

For example, for Neptune:

<syntaxhighlight lang="text">
11.15
10200.
2.3
175.
10.e5
24622.0e3
</syntaxhighlight>

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

<syntaxhighlight lang="text">
#! /bin/bash
#SBATCH --job-name=batch_adastra
#SBATCH --account=cin0391
#SBATCH --constraint=GENOA
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --threads-per-core=1 # --hint=nomultithread
#SBATCH --output=batch_adastra.out
#SBATCH --time=06:00:00

source ../mesoscale.env

srun --cpu-bind=threads --label ideal.exe
srun --cpu-bind=threads --label wrf.exe

mkdir wrfout_results_$SLURM_JOB_ID
mv wrfout_d01* wrfout_results_$SLURM_JOB_ID
mv wrfrst* wrfout_results_$SLURM_JOB_ID

cp -rf namelist.input wrfout_results_$SLURM_JOB_ID/used_namelist.input
cp -rf callphys.def wrfout_results_$SLURM_JOB_ID/used_callphys.def
cp input_sounding wrfout_results_$SLURM_JOB_ID/used_input_sounding

mkdir wrfout_results_$SLURM_JOB_ID/messages_simulations
mv batch_adastra.out wrfout_results_$SLURM_JOB_ID/messages_simulations
mv rsl.* wrfout_results_$SLURM_JOB_ID/messages_simulations
</syntaxhighlight>

==== Files in the folder ====

To launch the simulation:
<ul>
<li> batch_adastra </li>
</ul>
WRF specific:
<ul>
<li> planet_constant </li>
<li> input_sounding </li>
<li> input_coord </li>
<li> namelist.input </li>
</ul>
Generic PCM specific:
<ul>
<li> run.def </li>
<li> callphys.def </li>
<li> gases.def </li>
<li> traceur.def </li>
</ul>
Executables:
<ul>
<li> ideal.exe </li>
<li> wrf.exe </li>
</ul>

The run.def file is required even if unused (no need to change it).

Optional for additional outputs
<ul>
<li> my_iofields_list.txt </li>
</ul>

which can be like:

<syntaxhighlight lang="text">
+:h:0:DQVAP,DQICE,WW,TT
-:h:0:QH2O
</syntaxhighlight>

and you need to put an additional line in ''namelist.input
with for example
<syntaxhighlight lang="text">
iofields_filename = "my_iofields_list.txt"
</syntaxhighlight>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T15:11:30Z

Noe clement: /* Installing & Compiling the Generic PCM + WRF */

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Set this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download child repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

<syntaxhighlight lang="text"></syntaxhighlight>
archname="ADASTRA-ifort" # (or other cluster)
</syntaxhighlight>

Modify the 0_defining.sh file to have the right physics compiling options, for example:

<syntaxhighlight lang="text">
add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)
</syntaxhighlight>

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

<syntaxhighlight lang="text">
source mesoscale.env
</syntaxhighlight>

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====
<syntaxhighlight lang="text">
gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)
</syntaxhighlight>

For example, for Neptune:

<syntaxhighlight lang="text">
11.15
10200.
2.3
175.
10.e5
24622.0e3
</syntaxhighlight>

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

<syntaxhighlight lang="text">
#! /bin/bash
#SBATCH --job-name=batch_adastra
#SBATCH --account=cin0391
#SBATCH --constraint=GENOA
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --threads-per-core=1 # --hint=nomultithread
#SBATCH --output=batch_adastra.out
#SBATCH --time=06:00:00

source ../mesoscale.env

srun --cpu-bind=threads --label ideal.exe
srun --cpu-bind=threads --label wrf.exe

mkdir wrfout_results_$SLURM_JOB_ID
mv wrfout_d01* wrfout_results_$SLURM_JOB_ID
mv wrfrst* wrfout_results_$SLURM_JOB_ID

cp -rf namelist.input wrfout_results_$SLURM_JOB_ID/used_namelist.input
cp -rf callphys.def wrfout_results_$SLURM_JOB_ID/used_callphys.def
cp input_sounding wrfout_results_$SLURM_JOB_ID/used_input_sounding

mkdir wrfout_results_$SLURM_JOB_ID/messages_simulations
mv batch_adastra.out wrfout_results_$SLURM_JOB_ID/messages_simulations
mv rsl.* wrfout_results_$SLURM_JOB_ID/messages_simulations
</syntaxhighlight>

==== Files in the folder ====

To launch the simulation:
<ul>
<li> batch_adastra </li>
</ul>
WRF specific:
<ul>
<li> planet_constant </li>
<li> input_sounding </li>
<li> input_coord </li>
<li> namelist.input </li>
</ul>
Generic PCM specific:
<ul>
<li> run.def </li>
<li> callphys.def </li>
<li> gases.def </li>
<li> traceur.def </li>
</ul>
Executables:
<ul>
<li> ideal.exe </li>
<li> wrf.exe </li>
</ul>

The run.def file is required even if unused (no need to change it).

Optional for additional outputs
<ul>
<li> my_iofields_list.txt </li>
</ul>

which can be like:

<syntaxhighlight lang="text">
+:h:0:DQVAP,DQICE,WW,TT
-:h:0:QH2O
</syntaxhighlight>

and you need to put an additional line in ''namelist.input
with for example
<syntaxhighlight lang="text">
iofields_filename = "my_iofields_list.txt"
</syntaxhighlight>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T15:08:38Z

Noe clement: /* Downloading/Cloning the parent repository */

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Set this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download child repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====
<syntaxhighlight lang="text">
gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)
</syntaxhighlight>

For example, for Neptune:

<syntaxhighlight lang="text">
11.15
10200.
2.3
175.
10.e5
24622.0e3
</syntaxhighlight>

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

<syntaxhighlight lang="text">
#! /bin/bash
#SBATCH --job-name=batch_adastra
#SBATCH --account=cin0391
#SBATCH --constraint=GENOA
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --threads-per-core=1 # --hint=nomultithread
#SBATCH --output=batch_adastra.out
#SBATCH --time=06:00:00

source ../mesoscale.env

srun --cpu-bind=threads --label ideal.exe
srun --cpu-bind=threads --label wrf.exe

mkdir wrfout_results_$SLURM_JOB_ID
mv wrfout_d01* wrfout_results_$SLURM_JOB_ID
mv wrfrst* wrfout_results_$SLURM_JOB_ID

cp -rf namelist.input wrfout_results_$SLURM_JOB_ID/used_namelist.input
cp -rf callphys.def wrfout_results_$SLURM_JOB_ID/used_callphys.def
cp input_sounding wrfout_results_$SLURM_JOB_ID/used_input_sounding

mkdir wrfout_results_$SLURM_JOB_ID/messages_simulations
mv batch_adastra.out wrfout_results_$SLURM_JOB_ID/messages_simulations
mv rsl.* wrfout_results_$SLURM_JOB_ID/messages_simulations
</syntaxhighlight>

==== Files in the folder ====

To launch the simulation:
<ul>
<li> batch_adastra </li>
</ul>
WRF specific:
<ul>
<li> planet_constant </li>
<li> input_sounding </li>
<li> input_coord </li>
<li> namelist.input </li>
</ul>
Generic PCM specific:
<ul>
<li> run.def </li>
<li> callphys.def </li>
<li> gases.def </li>
<li> traceur.def </li>
</ul>
Executables:
<ul>
<li> ideal.exe </li>
<li> wrf.exe </li>
</ul>

The run.def file is required even if unused (no need to change it).

Optional for additional outputs
<ul>
<li> my_iofields_list.txt </li>
</ul>

which can be like:

<syntaxhighlight lang="text">
+:h:0:DQVAP,DQICE,WW,TT
-:h:0:QH2O
</syntaxhighlight>

and you need to put an additional line in ''namelist.input
with for example
<syntaxhighlight lang="text">
iofields_filename = "my_iofields_list.txt"
</syntaxhighlight>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T14:34:05Z

Noe clement: /* Files in the folder */

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download child repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====
<syntaxhighlight lang="text">
gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)
</syntaxhighlight>

For example, for Neptune:

<syntaxhighlight lang="text">
11.15
10200.
2.3
175.
10.e5
24622.0e3
</syntaxhighlight>

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

<syntaxhighlight lang="text">
#! /bin/bash
#SBATCH --job-name=batch_adastra
#SBATCH --account=cin0391
#SBATCH --constraint=GENOA
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --threads-per-core=1 # --hint=nomultithread
#SBATCH --output=batch_adastra.out
#SBATCH --time=06:00:00

source ../mesoscale.env

srun --cpu-bind=threads --label ideal.exe
srun --cpu-bind=threads --label wrf.exe

mkdir wrfout_results_$SLURM_JOB_ID
mv wrfout_d01* wrfout_results_$SLURM_JOB_ID
mv wrfrst* wrfout_results_$SLURM_JOB_ID

cp -rf namelist.input wrfout_results_$SLURM_JOB_ID/used_namelist.input
cp -rf callphys.def wrfout_results_$SLURM_JOB_ID/used_callphys.def
cp input_sounding wrfout_results_$SLURM_JOB_ID/used_input_sounding

mkdir wrfout_results_$SLURM_JOB_ID/messages_simulations
mv batch_adastra.out wrfout_results_$SLURM_JOB_ID/messages_simulations
mv rsl.* wrfout_results_$SLURM_JOB_ID/messages_simulations
</syntaxhighlight>

==== Files in the folder ====

To launch the simulation:
<ul>
<li> batch_adastra </li>
</ul>
WRF specific:
<ul>
<li> planet_constant </li>
<li> input_sounding </li>
<li> input_coord </li>
<li> namelist.input </li>
</ul>
Generic PCM specific:
<ul>
<li> run.def </li>
<li> callphys.def </li>
<li> gases.def </li>
<li> traceur.def </li>
</ul>
Executables:
<ul>
<li> ideal.exe </li>
<li> wrf.exe </li>
</ul>

The run.def file is required even if unused (no need to change it).

Optional for additional outputs
<ul>
<li> my_iofields_list.txt </li>
</ul>

which can be like:

<syntaxhighlight lang="text">
+:h:0:DQVAP,DQICE,WW,TT
-:h:0:QH2O
</syntaxhighlight>

and you need to put an additional line in ''namelist.input
with for example
<syntaxhighlight lang="text">
iofields_filename = "my_iofields_list.txt"
</syntaxhighlight>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T14:33:20Z

Noe clement: /* Files in the folder */

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download child repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====
<syntaxhighlight lang="text">
gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)
</syntaxhighlight>

For example, for Neptune:

<syntaxhighlight lang="text">
11.15
10200.
2.3
175.
10.e5
24622.0e3
</syntaxhighlight>

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

<syntaxhighlight lang="text">
#! /bin/bash
#SBATCH --job-name=batch_adastra
#SBATCH --account=cin0391
#SBATCH --constraint=GENOA
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --threads-per-core=1 # --hint=nomultithread
#SBATCH --output=batch_adastra.out
#SBATCH --time=06:00:00

source ../mesoscale.env

srun --cpu-bind=threads --label ideal.exe
srun --cpu-bind=threads --label wrf.exe

mkdir wrfout_results_$SLURM_JOB_ID
mv wrfout_d01* wrfout_results_$SLURM_JOB_ID
mv wrfrst* wrfout_results_$SLURM_JOB_ID

cp -rf namelist.input wrfout_results_$SLURM_JOB_ID/used_namelist.input
cp -rf callphys.def wrfout_results_$SLURM_JOB_ID/used_callphys.def
cp input_sounding wrfout_results_$SLURM_JOB_ID/used_input_sounding

mkdir wrfout_results_$SLURM_JOB_ID/messages_simulations
mv batch_adastra.out wrfout_results_$SLURM_JOB_ID/messages_simulations
mv rsl.* wrfout_results_$SLURM_JOB_ID/messages_simulations
</syntaxhighlight>

==== Files in the folder ====

To launch the simulation:
<ul>
<li> batch_adastra </li>
</ul>
WRF specific:
<ul>
<li> planet_constant </li>
<li> input_sounding </li>
<li> input_coord </li>
<li> namelist.input </li>
</ul>
Generic PCM specific:
<ul>
<li> run.def </li>
<li> callphys.def </li>
<li> gases.def </li>
<li> traceur.def </li>
</ul>
Executables:
<ul>
<li> ideal.exe </li>
<li> wrf.exe </li>
</ul>

The run.def file is required even if unused (no need to change it).

Optional for additional outputs
<ul>
<li> my_iofields_list.txt </li>
</ul>

<syntaxhighlight lang="text">
+:h:0:DQVAP,DQICE,WW,TT
-:h:0:QH2O
</syntaxhighlight>

and you need to put an additional line in ''namelist.input
with for example
<syntaxhighlight lang="text">
iofields_filename = "my_iofields_list.txt"
</syntaxhighlight>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T14:31:19Z

Noe clement: /* Files in the folder */

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download child repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====
<syntaxhighlight lang="text">
gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)
</syntaxhighlight>

For example, for Neptune:

<syntaxhighlight lang="text">
11.15
10200.
2.3
175.
10.e5
24622.0e3
</syntaxhighlight>

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

<syntaxhighlight lang="text">
#! /bin/bash
#SBATCH --job-name=batch_adastra
#SBATCH --account=cin0391
#SBATCH --constraint=GENOA
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --threads-per-core=1 # --hint=nomultithread
#SBATCH --output=batch_adastra.out
#SBATCH --time=06:00:00

source ../mesoscale.env

srun --cpu-bind=threads --label ideal.exe
srun --cpu-bind=threads --label wrf.exe

mkdir wrfout_results_$SLURM_JOB_ID
mv wrfout_d01* wrfout_results_$SLURM_JOB_ID
mv wrfrst* wrfout_results_$SLURM_JOB_ID

cp -rf namelist.input wrfout_results_$SLURM_JOB_ID/used_namelist.input
cp -rf callphys.def wrfout_results_$SLURM_JOB_ID/used_callphys.def
cp input_sounding wrfout_results_$SLURM_JOB_ID/used_input_sounding

mkdir wrfout_results_$SLURM_JOB_ID/messages_simulations
mv batch_adastra.out wrfout_results_$SLURM_JOB_ID/messages_simulations
mv rsl.* wrfout_results_$SLURM_JOB_ID/messages_simulations
</syntaxhighlight>

==== Files in the folder ====

To launch the simulation:
<ul>
<li> batch_adastra </li>
</ul>
WRF specific:
<ul>
<li> planet_constant </li>
<li> input_sounding </li>
<li> input_coord </li>
<li> namelist.input </li>
</ul>
Generic PCM specific:
<ul>
<li> run.def </li>
<li> callphys.def </li>
<li> gases.def </li>
<li> traceur.def </li>
</ul>
Executables:
<ul>
<li> ideal.exe </li>
<li> wrf.exe </li>
</ul>

The run.def file is required even if unused (no need to change it).

Optional for additional outputs
<ul>
<li> my_iofields_list.txt </li>
</ul>

with an additional line in ''namelist.input
<syntaxhighlight lang="text">
iofields_filename = "my_iofields_list.txt"
</syntaxhighlight>

<syntaxhighlight lang="text">
+:h:0:DQVAP,DQICE,WW,TT
-:h:0:QH2O
</syntaxhighlight>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T14:29:27Z

Noe clement: /* Files in the folder */

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download child repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====
<syntaxhighlight lang="text">
gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)
</syntaxhighlight>

For example, for Neptune:

<syntaxhighlight lang="text">
11.15
10200.
2.3
175.
10.e5
24622.0e3
</syntaxhighlight>

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

<syntaxhighlight lang="text">
#! /bin/bash
#SBATCH --job-name=batch_adastra
#SBATCH --account=cin0391
#SBATCH --constraint=GENOA
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --threads-per-core=1 # --hint=nomultithread
#SBATCH --output=batch_adastra.out
#SBATCH --time=06:00:00

source ../mesoscale.env

srun --cpu-bind=threads --label ideal.exe
srun --cpu-bind=threads --label wrf.exe

mkdir wrfout_results_$SLURM_JOB_ID
mv wrfout_d01* wrfout_results_$SLURM_JOB_ID
mv wrfrst* wrfout_results_$SLURM_JOB_ID

cp -rf namelist.input wrfout_results_$SLURM_JOB_ID/used_namelist.input
cp -rf callphys.def wrfout_results_$SLURM_JOB_ID/used_callphys.def
cp input_sounding wrfout_results_$SLURM_JOB_ID/used_input_sounding

mkdir wrfout_results_$SLURM_JOB_ID/messages_simulations
mv batch_adastra.out wrfout_results_$SLURM_JOB_ID/messages_simulations
mv rsl.* wrfout_results_$SLURM_JOB_ID/messages_simulations
</syntaxhighlight>

==== Files in the folder ====

To launch the simulation:
<ul>
<li> batch_adastra </li>
</ul>
WRF specific:
<ul>
<li> planet_constant </li>
<li> input_sounding </li>
<li> input_coord </li>
<li> namelist.input </li>
</ul>
Generic PCM specific:
<ul>
<li> run.def </li>
<li> callphys.def </li>
<li> gases.def </li>
<li> traceur.def </li>
</ul>
Executables:
<ul>
<li> ideal.exe </li>
<li> wrf.exe </li>
</ul>

The run.def file is required even if unused (no need to change it).

Optional for additional outputs
<ul>
<li> my_iofields_list.txt </li>
</ul>
with an additional line in namelist.input

iofields_filename = "my_iofields_list.txt"

+:h:0:DQVAP,DQICE,WW,TT
-:h:0:QH2O

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T14:27:48Z

Noe clement: /* Files in the folder */

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download child repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====
<syntaxhighlight lang="text">
gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)
</syntaxhighlight>

For example, for Neptune:

<syntaxhighlight lang="text">
11.15
10200.
2.3
175.
10.e5
24622.0e3
</syntaxhighlight>

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

<syntaxhighlight lang="text">
#! /bin/bash
#SBATCH --job-name=batch_adastra
#SBATCH --account=cin0391
#SBATCH --constraint=GENOA
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --threads-per-core=1 # --hint=nomultithread
#SBATCH --output=batch_adastra.out
#SBATCH --time=06:00:00

source ../mesoscale.env

srun --cpu-bind=threads --label ideal.exe
srun --cpu-bind=threads --label wrf.exe

mkdir wrfout_results_$SLURM_JOB_ID
mv wrfout_d01* wrfout_results_$SLURM_JOB_ID
mv wrfrst* wrfout_results_$SLURM_JOB_ID

cp -rf namelist.input wrfout_results_$SLURM_JOB_ID/used_namelist.input
cp -rf callphys.def wrfout_results_$SLURM_JOB_ID/used_callphys.def
cp input_sounding wrfout_results_$SLURM_JOB_ID/used_input_sounding

mkdir wrfout_results_$SLURM_JOB_ID/messages_simulations
mv batch_adastra.out wrfout_results_$SLURM_JOB_ID/messages_simulations
mv rsl.* wrfout_results_$SLURM_JOB_ID/messages_simulations
</syntaxhighlight>

==== Files in the folder ====

List of needed .def files:

To launch the simulation:
<ul>
<li> batch_adastra </li>
</ul>
WRF specific:
<ul>
<li> planet_constant </li>
<li> input_sounding </li>
<li> input_coord </li>
<li> namelist.input </li>
</ul>
Generic PCM specific:
<ul>
<li> run.def </li>
<li> callphys.def </li>
<li> gases.def </li>
<li> traceur.def </li>
</ul>
Executables:
<ul>
<li> ideal.exe </li>
<li> wrf.exe </li>
</ul>

The run.def file is required even if unused (no need to change it).

Optional:
<ul>
<li> my_iofields_list.txt # for additional outputs with an additional line in namelist.input </li>
</ul>

iofields_filename = "my_iofields_list.txt"

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T14:25:50Z

Noe clement: /* Files in the folder */

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download child repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====
<syntaxhighlight lang="text">
gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)
</syntaxhighlight>

For example, for Neptune:

<syntaxhighlight lang="text">
11.15
10200.
2.3
175.
10.e5
24622.0e3
</syntaxhighlight>

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

<syntaxhighlight lang="text">
#! /bin/bash
#SBATCH --job-name=batch_adastra
#SBATCH --account=cin0391
#SBATCH --constraint=GENOA
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --threads-per-core=1 # --hint=nomultithread
#SBATCH --output=batch_adastra.out
#SBATCH --time=06:00:00

source ../mesoscale.env

srun --cpu-bind=threads --label ideal.exe
srun --cpu-bind=threads --label wrf.exe

mkdir wrfout_results_$SLURM_JOB_ID
mv wrfout_d01* wrfout_results_$SLURM_JOB_ID
mv wrfrst* wrfout_results_$SLURM_JOB_ID

cp -rf namelist.input wrfout_results_$SLURM_JOB_ID/used_namelist.input
cp -rf callphys.def wrfout_results_$SLURM_JOB_ID/used_callphys.def
cp input_sounding wrfout_results_$SLURM_JOB_ID/used_input_sounding

mkdir wrfout_results_$SLURM_JOB_ID/messages_simulations
mv batch_adastra.out wrfout_results_$SLURM_JOB_ID/messages_simulations
mv rsl.* wrfout_results_$SLURM_JOB_ID/messages_simulations
</syntaxhighlight>

==== Files in the folder ====

List of needed .def files:
<ul>
<li> batch_adastra # to launch the simulation! </li>
</ul>
WRF specific:
<ul>
<li> planet_constant </li>
<li> input_sounding </li>
<li> input_coord </li>
<li> namelist.input </li>
</ul>
Generic PCM specific:
<ul>
<li> run.def </li>
<li> callphys.def </li>
<li> gases.def </li>
<li> traceur.def </li>
</ul>
Executables:
<ul>
<li> ideal.exe </li>
<li> wrf.exe </li>
</ul>
Optional:
<ul>
<li> my_iofields_list.txt # for additional outputs with an additional line '' in namelist.input </li>
</ul>

The run.def file is required even if unused (no need to change it).

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T14:23:29Z

Noe clement: /* Files in the folder */

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download child repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====
<syntaxhighlight lang="text">
gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)
</syntaxhighlight>

For example, for Neptune:

<syntaxhighlight lang="text">
11.15
10200.
2.3
175.
10.e5
24622.0e3
</syntaxhighlight>

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

<syntaxhighlight lang="text">
#! /bin/bash
#SBATCH --job-name=batch_adastra
#SBATCH --account=cin0391
#SBATCH --constraint=GENOA
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --threads-per-core=1 # --hint=nomultithread
#SBATCH --output=batch_adastra.out
#SBATCH --time=06:00:00

source ../mesoscale.env

srun --cpu-bind=threads --label ideal.exe
srun --cpu-bind=threads --label wrf.exe

mkdir wrfout_results_$SLURM_JOB_ID
mv wrfout_d01* wrfout_results_$SLURM_JOB_ID
mv wrfrst* wrfout_results_$SLURM_JOB_ID

cp -rf namelist.input wrfout_results_$SLURM_JOB_ID/used_namelist.input
cp -rf callphys.def wrfout_results_$SLURM_JOB_ID/used_callphys.def
cp input_sounding wrfout_results_$SLURM_JOB_ID/used_input_sounding

mkdir wrfout_results_$SLURM_JOB_ID/messages_simulations
mv batch_adastra.out wrfout_results_$SLURM_JOB_ID/messages_simulations
mv rsl.* wrfout_results_$SLURM_JOB_ID/messages_simulations
</syntaxhighlight>

==== Files in the folder ====

List of needed .def files:
<ul>
<li> batch_adastra # to launch the simulation! </li>
### WRF specific
<li> planet_constant </li>
<li> input_sounding </li>
<li> input_coord </li>
<li> namelist.input </li>
### Generic PCM specific
<li> run.def </li>
<li> callphys.def </li>
<li> gases.def </li>
<li> traceur.def </li>
### Executables
<li> ideal.exe </li>
<li> wrf.exe </li>
### Optional
<li> my_iofields_list.txt # for additional outputs </li>
</ul>

The run.def file is required even if unused (no need to change it).

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T14:22:54Z

Noe clement: /* Files in the folder */

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download child repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====
<syntaxhighlight lang="text">
gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)
</syntaxhighlight>

For example, for Neptune:

<syntaxhighlight lang="text">
11.15
10200.
2.3
175.
10.e5
24622.0e3
</syntaxhighlight>

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

<syntaxhighlight lang="text">
#! /bin/bash
#SBATCH --job-name=batch_adastra
#SBATCH --account=cin0391
#SBATCH --constraint=GENOA
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --threads-per-core=1 # --hint=nomultithread
#SBATCH --output=batch_adastra.out
#SBATCH --time=06:00:00

source ../mesoscale.env

srun --cpu-bind=threads --label ideal.exe
srun --cpu-bind=threads --label wrf.exe

mkdir wrfout_results_$SLURM_JOB_ID
mv wrfout_d01* wrfout_results_$SLURM_JOB_ID
mv wrfrst* wrfout_results_$SLURM_JOB_ID

cp -rf namelist.input wrfout_results_$SLURM_JOB_ID/used_namelist.input
cp -rf callphys.def wrfout_results_$SLURM_JOB_ID/used_callphys.def
cp input_sounding wrfout_results_$SLURM_JOB_ID/used_input_sounding

mkdir wrfout_results_$SLURM_JOB_ID/messages_simulations
mv batch_adastra.out wrfout_results_$SLURM_JOB_ID/messages_simulations
mv rsl.* wrfout_results_$SLURM_JOB_ID/messages_simulations
</syntaxhighlight>

==== Files in the folder ====

List of needed .def files:
<ul>
<li> batch_adastra # to launch the simulation! </li>
### WRF specific
<li> planet_constant </li>
<li> input_sounding </li>
<li> input_coord </li>
<li> namelist.input </li>
### Generic PCM specific
<li> run.def </li>
<li> callphys.def </li>
<li> gases.def </li>
<li> traceur.def </li>
### Executables
<li> ideal.exe </li>
<li> wrf.exe </li>
### Optional
<li> my_iofields_list.txt # for additional outputs </li>
</ul>

The run.def file is required even if unused (no need to change it).

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T14:04:46Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download child repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====
<syntaxhighlight lang="text">
gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)
</syntaxhighlight>

For example, for Neptune:

<syntaxhighlight lang="text">
11.15
10200.
2.3
175.
10.e5
24622.0e3
</syntaxhighlight>

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

<syntaxhighlight lang="text">
#! /bin/bash
#SBATCH --job-name=batch_adastra
#SBATCH --account=cin0391
#SBATCH --constraint=GENOA
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --threads-per-core=1 # --hint=nomultithread
#SBATCH --output=batch_adastra.out
#SBATCH --time=06:00:00

source ../mesoscale.env

srun --cpu-bind=threads --label ideal.exe
srun --cpu-bind=threads --label wrf.exe

mkdir wrfout_results_$SLURM_JOB_ID
mv wrfout_d01* wrfout_results_$SLURM_JOB_ID
mv wrfrst* wrfout_results_$SLURM_JOB_ID

cp -rf namelist.input wrfout_results_$SLURM_JOB_ID/used_namelist.input
cp -rf callphys.def wrfout_results_$SLURM_JOB_ID/used_callphys.def
cp input_sounding wrfout_results_$SLURM_JOB_ID/used_input_sounding

mkdir wrfout_results_$SLURM_JOB_ID/messages_simulations
mv batch_adastra.out wrfout_results_$SLURM_JOB_ID/messages_simulations
mv rsl.* wrfout_results_$SLURM_JOB_ID/messages_simulations
</syntaxhighlight>

==== Files in the folder ====

batch_adastra # to launch the simulation!
### WRF specific
planet_constant
input_sounding
input_coord
namelist.input
### Generic PCM specific
run.def
callphys.def
gases.def
traceur.def
### Executables
ideal.exe
wrf.exe
### Optional
my_iofields_list.txt # for additional outputs

The run.def file is required even if unused (no need to change it).

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T14:03:38Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download child repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====

gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)

For example, for Neptune:

11.15
10200.
2.3
175.
10.e5
24622.0e3

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

<syntaxhighlight lang="text">
#! /bin/bash
#SBATCH --job-name=batch_adastra
#SBATCH --account=cin0391
#SBATCH --constraint=GENOA
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --threads-per-core=1 # --hint=nomultithread
#SBATCH --output=batch_adastra.out
#SBATCH --time=06:00:00

source ../mesoscale.env

srun --cpu-bind=threads --label ideal.exe
srun --cpu-bind=threads --label wrf.exe

mkdir wrfout_results_$SLURM_JOB_ID
mv wrfout_d01* wrfout_results_$SLURM_JOB_ID
mv wrfrst* wrfout_results_$SLURM_JOB_ID

cp -rf namelist.input wrfout_results_$SLURM_JOB_ID/used_namelist.input
cp -rf callphys.def wrfout_results_$SLURM_JOB_ID/used_callphys.def
cp input_sounding wrfout_results_$SLURM_JOB_ID/used_input_sounding

mkdir wrfout_results_$SLURM_JOB_ID/messages_simulations
mv batch_adastra.out wrfout_results_$SLURM_JOB_ID/messages_simulations
mv rsl.* wrfout_results_$SLURM_JOB_ID/messages_simulations
</syntaxhighlight>

==== Files in the folder ====

batch_adastra # to launch the simulation!
### WRF specific
planet_constant
input_sounding
input_coord
namelist.input
### Generic PCM specific
run.def
callphys.def
gases.def
traceur.def
### Executables
ideal.exe
wrf.exe
### Optional
my_iofields_list.txt # for additional outputs

The run.def file is required even if unused (no need to change it).

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T13:43:41Z

Noe clement: /* Download repositories */

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download child repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====

gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)

For example, for Neptune:

11.15
10200.
2.3
175.
10.e5
24622.0e3

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

==== Files in the folder ====

batch_adastra # to launch the simulation!
### WRF specific
planet_constant
input_sounding
input_coord
namelist.input
### Generic PCM specific
run.def
callphys.def
gases.def
traceur.def
### Executables
ideal.exe
wrf.exe
### Optional
my_iofields_list.txt # for additional outputs

The run.def file is required even if unused (no need to change it).

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T13:40:32Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====

gravity (m/s2)
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature (K)
bottom pressure (Pa)
radius (m)

For example, for Neptune:

11.15
10200.
2.3
175.
10.e5
24622.0e3

==== 'input_coord' file ====

==== WRF Settings: 'namelist.input' file ====

'namelist.input' file

==== batch file for slurm ====

==== Files in the folder ====

batch_adastra # to launch the simulation!
### WRF specific
planet_constant
input_sounding
input_coord
namelist.input
### Generic PCM specific
run.def
callphys.def
gases.def
traceur.def
### Executables
ideal.exe
wrf.exe
### Optional
my_iofields_list.txt # for additional outputs

The run.def file is required even if unused (no need to change it).

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T13:37:42Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====

gravity
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature
bottom pressure
radius

For example, for Neptune:

11.15
10200.
2.3
175.
10.e5
24622.0e3

==== 'input_coord' file ====

==== Files in the folder ====

batch_adastra # to launche the simulation

# WRF specific
planet_constant
input_sounding
input_coord
namelist.input
# Generic PCM specific
run.def
callphys.def
gases.def
traceur.def
# Executables
ideal.exe
wrf.exe
# Optional
my_iofields_list.txt # for additional outputs

The run.def file is required even if unused (no need to change it).

=== WRF Settings: 'namelist.input' file ===

'namelist.input' file

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T13:35:22Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' file ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====
gravity
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature
bottom pressure
radius

For example, for Neptune:
11.15
10200.
2.3
175.
10.e5
24622.0e3

==== 'input_coord' file ====

==== Files in the folder ====

batch_adastra # to launche the simulation

* WRF specific

planet_constant

input_sounding

input_coord

namelist.input

* Generic PCM specific

run.def

callphys.def

gases.def

traceur.def

* Executables

ideal.exe

wrf.exe

* Optional

my_iofields_list.txt # for additional outputs

The run.def file is required even if unused (no need to change it).

=== WRF Settings: 'namelist.input' file ===

'namelist.input' file

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T13:30:52Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

==== 'input_sounding' ====
This file has a header with 3 parameters, followed by 5 columns

The header contains: the bottom pressure (in mbar), the bottom temperature (K), and "0.0"
For example, for Neptune: 10000.0 166.6004857302868 0.0

5 columns are profiles for: equivalent altitude, potential temperature, vapor, ice, and X (?)

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding
[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

==== 'planet_constant' file ====
gravity
heat capacity (J/kg/K)
molar mass (g/mol)
reference temperature
bottom pressure
radius

For example, for Neptune:
11.15
10200.
2.3
175.
10.e5
24622.0e3

==== Files in the folder ====

batch_adastra
# WRF specific
planet_constant
input_sounding
input_coord
namelist.input
# Generic PCM specific
run.def
callphys.def
gases.def
traceur.def
# Executables
ideal.exe
wrf.exe

# Optional:
my_iofields_list.txt # for additional outputs

The run.def file is required even if unused (no need to change it).

=== WRF Settings ===

'namelist.input' file

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T13:10:20Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

Building the 'input_sounding' file.
This file has a header with 3 parameters, followed by 5 columns

The header contains

[https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html exo_k] will help you!

You need to run a 1D simulation and use the diagfi.nc file to initialize fields for the input_sounding

=== Settings ===

'namelist.input' file

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T13:06:04Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Running a simulation ==

=== Initializing a simulation ===

Building the 'input_sounding' file.

exo_k can help you!

=== Settings ===

'namelist.input' file

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T13:01:58Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (which will be named 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T10:54:34Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download repositories ===

In 'LES_planet_workflow', execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (it takes the name 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

In 'LES_planet_workflow', modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T10:52:05Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put this repo on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one above by inserting it in the LES_planet_workflow, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download repositories ===

Execute the 1_downloading.sh file to download (i.e. clone) the 'git-trunk' repository (it takes the name 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

Modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T10:49:56Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put it on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one below by inserting it in the LES_planet_workflow, for example, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download repositories ===

Execute the 1_downloading.sh to download (i.e. clone) the 'git-trunk' repository (it takes the name 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

Modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks if it does not work ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T10:48:20Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing & Compiling the Generic PCM + WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put it on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one below by inserting it in the LES_planet_workflow, for example, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Download repositories ===

Execute the 1_downloading.sh to download (i.e. clone) the 'git-trunk' repository (it takes the name 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

Modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T10:47:34Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing the Generic PCM+WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put it on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one below by inserting it in the LES_planet_workflow, for example, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Compiling the Generic PCM +WRF ===

=== Download repositories ===

Execute the 1_downloading.sh to download (i.e. clone) the 'git-trunk' repository (it takes the name 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

=== Modify options to fit your compiling environment & your modelled planetary atmosphere ===

Modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

=== Put the 3 repositories on the right branch/commit ===

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

=== Execute installing and compiling files ===

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T10:45:26Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing the Generic PCM+WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put it on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one below by inserting it in the LES_planet_workflow, for example, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Compiling the Generic PCM +WRF ===

==== Download repositories ====

Execute the 1_downloading.sh to download (i.e. clone) the 'git-trunk' repository (it takes the name 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

==== Modify options to fit your compiling environment & your modelled planetary atmosphere ====

Modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

==== Terrestrial WRF ====

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

==== Put the 3 repositories on the right branch/commit ====

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model. (!!! For developers, this has to be corrected and put in the master branch !!!)

- On branch "generic" for WRFV4 workflow

==== Execute installing and compiling files ====

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T10:42:47Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing the Generic PCM+WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put it on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one below by inserting it in the LES_planet_workflow, for example, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Compiling the Generic PCM +WRF ===

==== Download repositories ====

Execute the 1_downloading.sh to download (i.e. clone) the 'git-trunk' repository (it takes the name 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

==== Modify options to fit your compiling environment & your modelled planetary atmosphere ====

Modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

==== Terrestrial WRF ====

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the 0_defining.sh file at lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

Replace 15 & 1 with the numbers/options you selected.

==== Put the 3 repositories on the right branch/commit ====

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

!!! This has to be corrected !!!
See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model

- On branch "generic" for WRFV4 workflow

==== Execute installing and compiling files ====

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T10:40:35Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing the Generic PCM+WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put it on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

If you work on Adastra, you can directly use the one below by inserting it in the LES_planet_workflow, for example, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

=== Compiling the Generic PCM +WRF ===

==== Download repositories ====

Execute the 1_downloading.sh to download (i.e. clone) the 'git-trunk' repository (it takes the name 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

==== Modify options to fit your compiling environment & your modelled planetary atmosphere ====

Modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

replace 15 & 1 with the options you selected.

==== Terrestrial WRF ====

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source the "mesoscale.env" file:

source mesoscale.env

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

==== Put the 3 repositories on the right branch/commit ====

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

!!! This has to be corrected !!!
See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model

- On branch "generic" for WRFV4 workflow

==== Execute installing and compiling files ====

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T10:35:19Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing the Generic PCM+WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).

Put it on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA, the following one works:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

=== Compiling the Generic PCM +WRF ===

==== Modify options to fit your compiling environment & your modelled planetary atmosphere ====

Modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

replace 15 & 1 with the options you selected.

==== Download repositories ====

Execute the 1_downloading.sh to download (i.e. clone) the 'git-trunk' repository (it takes the name 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

==== Terrestrial WRF ====

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source a ".env" file, just like the ones above. If you work on Adastra, you can directly use the one below by inserting it in your home directory (or in the LES_planet_workflow), for example, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

==== Put the 3 repositories on the right branch/commit ====

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

!!! This has to be corrected !!!
See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model

- On branch "generic" for WRFV4 workflow

==== Execute installing and compiling files ====

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T10:32:15Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing the Generic PCM+WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading (i.e. cloning) the parent repository 'LES_planet_workflow' from Aymeric Spiga's git (you will download the other two later).
Put it on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source a ".env" file, just like the ones above. If you work on Adastra, you can directly use the one below by inserting it in your home directory (or in the LES_planet_workflow), for example, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

=== Compiling the Generic PCM +WRF ===

==== Modify options to fit your compiling environment & your modelled planetary atmosphere ====

Modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

replace 15 & 1 with the options you selected.

==== Download repositories ====

Execute the 1_downloading.sh to download (i.e. clone) the 'git-trunk' repository (it takes the name 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

==== Put the 3 repositories on the right branch/commit ====

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

!!! This has to be corrected !!!
See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model

- On branch "generic" for WRFV4 workflow

==== Execute installing and compiling files ====

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T10:30:33Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing the Generic PCM+WRF ==

=== 3 git repositories to handle ===

==== Review of the repositories ====

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics)

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

==== Downloading/Cloning the parent repository ====

The first step is downloading the parent repository 'LES_planet_workflow' (you will download the other two later).
Put it on the branch "wrfv4".

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source a ".env" file, just like the ones above. If you work on Adastra, you can directly use the one below by inserting it in your home directory (or in the LES_planet_workflow), for example, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

=== Compiling the Generic PCM +WRF ===

==== Modify options to fit your compiling environment & your modelled planetary atmosphere ====

Modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

replace 15 & 1 with the options you selected.

==== Download repositories ====

Execute the 1_downloading.sh to download (i.e. clone) the 'git-trunk' repository (it takes the name 'code').

Download (i.e. clone) the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory (keep the name "WRFV4")

Now you have the 3 repositories!

==== Put the 3 repositories on the right branch/commit ====

- On branch "wrfv4" for LES_planet_workflow repo (already done normally)

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

!!! This has to be corrected !!!
See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model

- On branch "generic" for WRFV4 workflow

==== Execute installing and compiling files ====

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T10:26:24Z

Noe clement:

== Introduction ==

WRF is a mesoscale numerical weather prediction system designed for both atmospheric research and operational forecasting applications over the Earth's atmosphere: see [https://www.mmm.ucar.edu/models/wrf WRF presentation].

In the PCM, we take advantage of the dynamical core of the WRF model to run LES (large-eddy simulations) or mesoscale simulations.

To do so, we take the WRF model, remove all its physical packages related to the Earth's atmosphere, and plug in the physical package from the PCM (either Venus, Mars, Titan, or Generic).

A description of the various equations solved by WRF can be found here: [https://opensky.ucar.edu/islandora/object/technotes%3A588 Skamarock et al. (2019, 2021)].

== Studies with PCM+WRF ==

Descriptions of the application of WRF dynamical core with the PCM can be found in:

- [https://theses.hal.science/tel-04861192 Noé CLEMENT's PhD thesis] (chapter 3) for the Generic PCM.

- [https://theses.hal.science/tel-02924996 Maxence Lefevre's PhD thesis] for the Venus PCM.

- [https://theses.hal.science/tel-00347021 Aymeric Spiga's PhD thesis] for the Mars PCM

Studies with the PCM coupled to the WRF dynamical core have been done using WRF V2, WRF V3, WRF V4.

Our aim is now to use WRF V4 as much as possible, which offers significant improvements in terms of numerical schemes in particular.

Here is a list of studies using the PCM coupled to the WRF dynamical core:

<table border="1">
<tr>
<th>Planet</th>
<th>Reference</th>
<th>Physical package</th>
<th>Dynamical core</th>
</tr>
<tr>
<td>Mars</td>
<td>[https://doi.org/10.1029/2008JE003242 Spiga and Forget (2009)]</td>
<td>Mars PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Mars</td>
<td>[https://rmets.onlinelibrary.wiley.com/doi/10.1002/qj.563 Spiga et al. (2010)]</td>
<td>Mars PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JE005679 Lefèvre et al. (2018)]</td>
<td>Venus PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Venus</td>
<td>[https://www.sciencedirect.com/science/article/pii/S0019103519301216?via%3Dihub Lefèvre et al. (2020)]</td>
<td>Venus PCM</td>
<td>WRF V2</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://iopscience.iop.org/article/10.3847/1538-4357/abf2c1 Lefèvre et al. (2021)]</td>
<td>Generic PCM</td>
<td>WRF V3</td>
</tr>
<tr>
<td>Exoplanets</td>
<td>[https://doi.org/10.1051/0004-6361/202348928 Leconte et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
<tr>
<td>Uranus, Neptune</td>
<td>[https://doi.org/10.1051/0004-6361/202348936 Clément et al. (2024)]</td>
<td>Generic PCM</td>
<td>WRF V4</td>
</tr>
</table>

== Remarks ==

For advanced users:

When compiling the model, the flags:

<syntaxhighlight lang="text">
#ifndef MESOSCALE
use ...
#else
use ...
</syntaxhighlight>

select lines compiled depending on the configuration.

== WRF equations ==

Below is a synthesis of equations solved by WRF.

[[File:WRF_dynamical_core.png]]

== Installing the Generic PCM+WRF ==

=== 3 git repositories to handle ===

- LES_planet_workflow

- git-trunk (physics & GCM dynamical core), which takes the name "code" when being cloned

- WRFV4 (dynamics), for now to be manually installed by cloning it (keep the name "WRFV4) in the "code/WRF.COMMON" directory

The first is hosted on [https://gitlab.in2p3.fr/aymeric.spiga/les_mars_project Aymeric Spiga's git], and will download (git clone) the two others, which are part of [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires La communauté des modèles atmosphériques planétaires] repositories.

The 3 repositories are managed by git. You will need to do a little juggling between these repositories to be sure they are on the right branches for your project (see later).

The first step is downloading the first repository (you will download the other two later).

=== .env file ===

!!! For now, only the Intel compiler has been tested and works. !!!

On any cluster, one has to build a file "mesoscale.env" which should look more or less like:

<syntaxhighlight lang="text">
# mesoscale.env file

source YOUR_ifort_ENV

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# PCM/WRFV4 interface
declare -x LMDZ_LIBO='code/LMDZ.COMMON/libo/YOUR_ARCH_NAME'
</syntaxhighlight>

On ADASTRA:

<syntaxhighlight lang="text">
# mesoscale.env file

source code/LMDZ.COMMON/arch/arch-ADASTRA-ifort.env

# for WRFV4
declare -x WRFIO_NCD_LARGE_FILE_SUPPORT=1

declare -x NETCDF=$NETCDF_DIR
# alternatively: declare -x NETCDF=`nf-config --prefix`
declare -x NCDFLIB=$NETCDF/lib
declare -x NCDFINC=$NETCDF/include

# specific to ADASTRA
declare -x NETCDF_classic=1

# fix for "undefined symbol: __libm_feature_flag" errors at runtime:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib

# PCM/WRFV4 interface
declare -x LMDZ_LIBO=code/LMDZ.COMMON/libo/ADASTRA-ifort
</syntaxhighlight>

This file should be sourced before performing compilation steps. Ideally, it will be integrated automatically (no need to source manually).
It should also be sourced before executing the compiled files to run simulations.

=== Terrestrial WRF ===

Compiling terrestrial [https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php WRF] is a good first step to check if the environment is working.

Somewhere else in your work directory, do:

"git clone --recurse-submodules https://github.com/wrf-model/WRF"

Before executing the following commands, you have to source a ".env" file, just like the ones above. If you work on Adastra, you can directly use the one below by inserting it in your home directory (or in the LES_planet_workflow), for example, and calling it "mesoscale.env". It will work for both the WRF terrestrial and the Generic PCM+WRF

Commands:
<syntaxhighlight lang="text">
./configure
</syntaxhighlight>

During the configure step, you will be asked about the compiler, choose "INTEL (ifort/icc) dmpar" (probably number 15), and then about nesting, choose "basic" (=1).

then

<syntaxhighlight lang="text">
./compile em_les
</syntaxhighlight>

WRF compilation can take some time. Consider doing:

<syntaxhighlight lang="text">
nohup ./compile em_les &
</syntaxhighlight>

Final built executables are: "ideal.exe" and "wrf.exe" (in the WRF/main directory).

=== Compiling the Generic PCM +WRF ===

==== Modify options to fit your compiling environment & your modelled planetary atmosphere ====

Modify the 0_defining.sh file to fit your Intel environment

archname="ADASTRA-ifort" # (or other cluster)

Modify the 0_defining.sh file to have the right physics compiling options, for example:

add="-t 1 -b 20x34 -d 25" # Uranus & Neptune with CH4 visible bands (compilation options are maybe depreciated)

When compiling terrestrial WRF, if you indeed selected 15 and 1, you do not have to modify the following. Otherwise, in the lines:

echo 15 > configure_inputs
echo 1 >> configure_inputs

replace 15 & 1 with the options you selected.

==== Download repositories ====

Execute the 1_downloading.sh to download the 'git-trunk' repository (it takes the name 'code').

Download the WRFV4 repository in the 'LES_planet_workflow/code/WRF.COMMON' directory

Now you have the 3 repositories!

==== Put the 3 repositories on the right branch/commit ====

- On branch "wrfv4" for LES_planet_workflow repo

- On a branch that matches your physics developments on the git-trunk (=code) repo.

The branch "hackathon_wrfv4" works for Uranus/Neptune test cases.

This [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/0c1280715875b36669271e59655ab4d306296217 commit] shows you what to modify if you want to work with another tracer than water (e.g., CH4).

!!! This has to be corrected !!!
See this [https://gitlab.in2p3.fr/la-communaut-des-mod-les-atmosph-riques-plan-taires/git-trunk/-/commit/78c8eedabbad4db120ef6fda3bd912687d412ec0 commit] to fix a little bug with the slab ocean model

- On branch "generic" for WRFV4 workflow

==== Execute installing and compiling files ====

One by one:

- 2_preparing.sh

- 3_compiling_physics.sh

- 4_compiling_dynamics.sh

Good luck!

=== Executables ===

If you succeed in compiling the model, executables should be in the 'LES_planet_workflow/code/WRF.COMMON/WRFV4/main' directory.
Executables of the Generic PCM+WRF have the same name as terrestrial WRF.

"ideal.exe" prepares the domain. "wrf.exe" runs the simulation.

The modifications we make in these files during compilation aim to incorporate the Physics of the PCM as a library, as well as the interface between WRF and the PCM.

=== Some tricks ===

In case of a failed compilation, the command

<syntaxhighlight lang="text">
./clean -a
</syntaxhighlight>

in the WRFV4 directory allows you to remove intermediate compiled files and properly restart the compilation.

[[Category:Generic-Model]]
[[Category:Mars-Model]]
[[Category:Venus-Model]]
[[Category:Titan-Model]]

WRF dynamical core for LES/mesoscale simulations

2025-09-17T10:12:52Z

Noe clement:

WRF dynamical core for LES/mesoscale simulations

2025-09-17T10:11:52Z

Noe clement:

WRF dynamical core for LES/mesoscale simulations

2025-09-17T10:11:02Z

Noe clement:

WRF dynamical core for LES/mesoscale simulations

2025-09-17T10:10:00Z

Noe clement:

WRF dynamical core for LES/mesoscale simulations

2025-09-17T10:06:52Z

Noe clement:

WRF dynamical core for LES/mesoscale simulations

2025-09-17T10:00:03Z

Noe clement:

WRF dynamical core for LES/mesoscale simulations

2025-09-17T09:59:16Z

Noe clement:

WRF dynamical core for LES/mesoscale simulations

2025-09-17T09:57:40Z

Noe clement: