Difference between revisions of "Other GCM Configurations worth knowing about"

Revision as of 11:34, 28 September 2022

3D lon-lat LMDZ setup

early Mars

It is already described in the Quick Install and Run section.

Earth with slab ocean

TBD by Martin

TRAPPIST-1e with photochemistry

A temperate rocky planet in synchronous rotation around a low mass star

TBD by Yassin

TRAPPIST-1c in Venus-like conditions

A warm rocky planet in synchronous rotation around a low mass star

TBD by Gabriella (waiting for the SVN update by Ehouarn)

mini-Neptune GJ1214b

A warm mini-Neptune

TBD by Benjamin

3D DYNAMICO setup

Due to the rich dynamical activities in their atmospheres (banded zonal jets, eddies, vortices, storms, equatorial oscillations,...) resulting from multi-scale dynamic interactions, the Global Climate Modelling of the giant planet requires to resolve eddies arising from hydrodynamical instabilities to correctly establish the planetary-scaled jets regime. To this purpose, their Rossby radius deformation $$L_D$$, which is the length scale at which rotational effects become as important as buoyancy or gravity wave effects in the evolution of the flow about some disturbance, is calculated to determine the most suitable horizontal grid resolution. At mid-latitude range, for the giant planets, $$L_D$$ is of the same order of magnitude as that of the Earth. As the giant planets have a size of roughly 10 times the Earth size (i.e., Jupiter and Saturn), the modelling grid must be of a horizontal resolution of 0.5$$^{\circ}$$ over longitude and latitude (vs 5$$^{\circ}$$ for the Earth), considering 3 grid points to resolved $$L_D$$. Moreover, to have a chance to model the equatorial oscillation, meridional cell circulations and/or a seasonal inter-hemispheric circulation, a giant planet GCM must also include a high vertical resolution. Indeed, these climate phenomena have been studied for decades for the Earth's atmosphere, and result from small- and large-scale interactions between the troposphere and stratosphere. This implies that the propagation of dynamic instabilities, waves and turbulence should be resolved as far as possible along the vertical. Contrary to horizontal resolution, it doesn't really exist a criterion (similar to $$L_D$$) to determine the most suitable vertical grid resolution and still an adjustable parameter according to the processes to be represented. However, we advise the user to set a vertical resolution of at least 5 grid points per scale height as first stage. Finally, these atmospheres are cold, with long radiative response time which needs radiative transfer computations over decade-long years of Jupiter (given that a Jupiter year $$\approx$$ 12 Earth years), Saturn ( a Saturn year $$\approx$$ 30 Earth years), Uranus (a Uranus year $$\approx$$ 84 earth years) or Neptune (a Neptune year $$\approx$$ 169 Earth years), depending on the chosen planet.

To be able to deal with these three -- and non-exhaustive -- requirements to build a giant planet GCM, we need massive computational ressources. For this, we use a dynamical core suitable and numerical stable for massive parallel ressource computations: DYNAMICO [Dubos et al,. 2015].

In these two following subsections, we purpose an example of installation for Jupiter and a Hot Jupiter. All the install, compiling, setting and parameters files for each giant planets could be found on: https://github.com/aymeric-spiga/dynamico-giant

If you have already downloaded LMDZ.COMMON, LMDZ.GENERIC, IOIPSL, ARCH, you only have to download:

ICOSAGCM: the DYNAMICO dynamical core

git clone https://gitlab.in2p3.fr/ipsl/projets/dynamico/dynamico.git ICOSAGCM
cd ICOSAGCM
git checkout 90f7138a60ebd3644fbbc42bc9dfa22923386385

ICOSA_LMDZ: the interface using to link LMDZ.GENERIC physical packages and ICOSAGCM

svn update -r 2655 -q ICOSA_LMDZ

XIOS (XML Input Output Server): the library to interpolate input/output fields between the icosahedral and longitude/latitude regular grids on fly

svn co -r 2319 -q http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk XIOS

If you haven't already download LMDZ.COMMON, LMDZ.GENERIC, IOIPSL, ARCH, you can use the install.sh script provided by the Github repository.

Jupiter with DYNAMICO

TBD by Deborah

Using a new dynamical core implies new setting files, in addition or as a replacement of those relevant to LMDZ.COMMON dynamical core using. There are two kind of setting files, a first group relevant to DYNAMICO:

- context_dynamico.xml:

- context_input_dynamico.xml:

- file_def_dynamico.xml:

- field_def_dynamico.xml:

- tracer.def:

a second group relevant to LMDZ.GENERIC physical packages:

- context_lmdz_physics.xml:

- field_def_physics.xml:

- callphys.def:

- gases.def:

- jupiter_const.def:

- traceur.def

Two additional files are used to set the running parameter of the simulation itself:

- run.def:

- run_icosa.def: file containing parameters to execute the simulation, use to determine the horizontal and vertical resolutions, the number of processors, the number of subdivisions, the duration of the simulation, etc

Hot Jupiter with DYNAMICO

Modelling the atmosphere of Hot Jupiter is challenging because of the extreme temperature conditions, and the fact that these planets are gas giants. Therefore, using a dynamical core such as Dynamico is strongly recommended. Here, we discuss how to perform a cloudless simulation of the Hot Jupiter WASP-43 b, using Dynamico.

1st step: You need to go to the github mentionned previously for Dynamico: https://github.com/aymeric-spiga/dynamico-giant. Git clone this repo on your favorite cluster, and checkout to the "hot_jupiter" branch.

2nd step: Now, run the install.sh script. This script will install all the required models (LMDZ.COMMON, LMDZ.GENERIC,ICOSA_LMDZ,XIOS,FCM,ICOSAGCM). At this point, you only miss IOIPSL. To install it, go to

 
dynamico-giant/code/LMDZ.COMMON/ioipsl/

There, you will find some examples of installations script. You need to create one that will work on your cluster, with your own arch files. During the installation of IOIPSL, you might be asked for a login/password. Contact TGCC computing center to get access.

3rd step: Great, now we have all we need to get started. Navigate to the hot_jupiter folder. You will find a compile_mesopsl.sh and a compile_occigen.sh script. Use them as examples to create the compile script adapted to your own cluster, then run it. While running, I suggest that you take a look at the log_compile file. The compilation can take a while (~ 10minutes, especially because of XIOS). On quick trick to make sure that everything went right is to check the number of Build command finished messages in log_compile. If everything worked out, there should be 6 of them.

4th step: Okay, the model compiled, good job ! Now we need to create the initial condition for our run. In the hot_jupiter1d folder, you already have a temp_profile.txt computed with the 1D version of the LMDZ.GENERIC (see rcm1d on this page). Thus, no need to recompute a 1D model but it will be needed if you want to model another Hot Jupiter. Navigate to the 'makestart' folder, located at

 
dynamico-giant/hot_jupiter/makestart/

To generate the initial conditions for the 3D run, we're gonna start the model using the temperature profile from the 1D run. to do that, you will find a "job_mpi" script. Open it, and adapt it to your cluster and launch the job. This job is using 20 procs, and it runs 5 days of simulations. If everything goes well, you should see few netcdf files appear. The important ones are start_icosa0.nc, startfi0.nc and Xhistins.nc. If you see these files, you're all set to launch a real simulation !

5th step: Go back to hot_jupiter folder. There are a bunch of script to launch your simulation. Take a look at the astro_fat_mpi script, and adapt it to your cluster. Then you can launch your simulation by doing

 
./run_astro_fat

This will start the simulation, using 90 procs. In the same folder, check if the icosa_lmdz.out file is created. This is the logfile of the simulation, while it is running. You can check there that everything is going well.

Important side note: When using the run_astro_fat script to run a simulation, it will run a chained simulation, restarting the simulation from the previous state after 100 days of simulations and generating Xhistins.nc files. This is your results file, where you will find all the variables that controls your atmosphere (temperature field, wind fields, etc..).

Good luck and enjoy the generic PCM Dynamico for Hot Jupiter !

2nd important side note: These 5 steps are the basic needed steps to run a simulation. If you want to tune simulations to another planet, or change other stuff, you need to take a look at *.def and *.xml files. If you're lost in all of this, take a look at the different pages of this website and/or contact us ! Also, you might want to check the wiki on the Github, that explains a lot of settings for Dynamico

3D LES setup

Proxima b with LES

TBD by Maxence

1D setup

rcm1d test case

Our 1-D forward model

TBD by Gwenael ? (you can have a look at the Generic GCM User Manual for inspiration)

kcm1d test case

Our 1-D inverse model

TBD by Guillaume or Martin