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

Revision as of 17:53, 12 October 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 numerically 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.

Once each part of the GCM is downloaded, you are able to compile it. Firstly, you have to define your target architecture file (hereafter named YOUR_ARCH_FILE) where you will fill in all the necessary information about the local environment, where libraries are located, which compiler, and compiler options will be used, etc. Some architecture files related to specific machines are provided in the ARCH directory.

The main specificity of DYNAMICO-giant is that every main parts of the model (ICOSAGCM, LMDZ.COMMON and LMDZ.GENERIC) are compiled as libraries, and settings and running configuration are managed by the ICOSA_LMDZ interface.

First, you have to compile IOIPSL,

cd ../IOIPSL                                                                                                             
    ./makeioipsl_fcm -prod -parallel -arch YOUR_ARCH_FILE -arch_path ../ARCH -j 8 -full
cd -

then XIOS library,

cd ../XIOS                                                                                                               
    ./make_xios --prod --arch YOUR_ARCH_FILE --arch_path ../ARCH --job 8 --full
cd -

the physics packaging,

cd ../LMDZ.COMMON                                                                                                        
    ./makelmdz_fcm -p std -p_opt "-b 20x25 -s 2" -prod -parallel mpi -libphy -io xios -arch YOUR_ARCH_FILE -arch_path ../ARCH -j 8 -full
cd -

the dynamical core DYNAMICO (located in ICOSAGCM directory, named from the icosahedral shape of the horizontal mesh),

cd ../ICOSAGCM
    ./make_icosa -prod -parallel mpi -external_ioipsl -with_xios -arch YOUR_ARCH_FILE -arch_path ../ARCH -job 8 -full
cd -

and finally the ICOSA_LMDZ interface

cd ../ICOSA_LMDZ
    ./build --job 8 --full

and your executable programs should appeared in ICOSA_LMDZ/bin subdirectory, as: icosa_lmdz.exe and xios_server.exe

All these compiling steps are summed up in make_isoca_lmdz program that should be adapted to your own computational settings.

./make_icosa_lmdz -p std -p_opt "-b 20x25 -s 2" -parallel mpi -arch YOUR_ARCH_FILE -arch_path ../ARCH -job 8 -full

Now you can move your two executable files to your working directory and start to run your own simulation of Jupiter or a Hot Jupiter, as what follows.

Note: If you are using the GitHub file architecture (https://github.com/aymeric-spiga/dynamico-giant), you should be able to compile the model directly from your working directory (for instance Jupiter) by using the compile_occigen.sh program, which has to be adapted to your machine/cluster.

Jupiter with DYNAMICO

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: Configuration file for DYNAMICO for reading and writing files using XIOS, mainly used when you want to check the installation of ICOSAGCM with an Held and Suarez test case. When your installation, compilation and run environment is fully functional, the dynamic core output files will not (necessarily) be useful and you can disable their writing.

- context_input_dynamico.xml:

- file_def_dynamico.xml: Definition of output diagnostic files which will be written into the output files only related to ICOSAGCM.

- field_def_dynamico.xml: Definition of all existing variables that can be output from DYNAMICO.

- tracer.def: Definition of the name and physico-chemical properties of the tracers which will be advected by the dynamical core. For now, there is two files related to tracers, we are working to harmonise it.

A second group relevant to LMDZ.GENERIC physical packages:

- context_lmdz_physics.xml: File in which are defined the horizontal grid, vertical coordinate, output file(s) definition, with the setting of frequency output writing, time unit, geophysical variables to be written, etc. Each new geophysical variables added here have to be defined in the field_def_physics.xml file.

- field_def_physics.xml: Definition of all existing variables that can be output from the physical packages interfaced with DYNAMICO. This is where you will add each geophysical fields that you want to appear in the Xhistins.nc output files. For instance, related to the thermal plume scheme using for Jupiter's tropospheric dynamics, we have added the following variables:

 1              <field id="h2o_vap" 
 2                    long_name="Vapor mass mixing ratio" 
 3                    unit="kg/kg" />
 4             <field id="h2o_ice" 
 5                    long_name="Vapor mass mixing ratio" 
 6                    unit="kg/kg" />
 7             <field id="detr" 
 8                    long_name="Detrainment" 
 9                    unit="kg/m2/s" />
10             <field id="entr" 
11                    long_name="Entrainment" 
12                    unit="kg/m2/s" />
13             <field id="w_plm" 
14                    long_name="Plume vertical velocity" 
15                    unit="m/s" />

- callphys.def: This setting file is used either with DYNAMICO or LMDZ.COMMON and allows the user to choose the physical parametrisation schemes and their appropriate main parameter values relevant to the planet being simulated. In our case of Jupiter, there are some specific parametrisations that should be added or modified from the example given as link at the beginning of this line:

  1 # Diurnal cycle ?  if diurnal=false, diurnally averaged solar heating
  2 diurnal      = .false. #.true.
  3 # Seasonal cycle ? if season=false, Ls stays constant, to value set in "start"
  4 season       = .true. 
  5 # Tidally resonant orbit ? must have diurnal=false, correct rotation rate in newstart
  6 tlocked      = .false.
  7 # Tidal resonance ratio ? ratio T_orbit to T_rotation
  8 nres         = 1
  9 # Planet with rings?
 10 rings_shadow = .false.
 11 # Compute latitude-dependent gravity field??
 12 oblate       = .true.
 13 # Include non-zero flattening (a-b)/a?
 14 flatten      = 0.06487
 15 # Needed if oblate=.true.: J2
 16 J2           = 0.01470
 17 # Needed if oblate=.true.: Planet mean radius (m)
 18 Rmean        = 69911000.
 19 # Needed if oblate=.true.: Mass of the planet (*1e24 kg)
 20 MassPlanet   = 1898.3
 21 # use (read/write) a startfi.nc file? (default=.true.)
 22 startphy_file = .false.
 23 # constant value for surface albedo (if startphy_file = .false.)
 24 surfalbedo   = 0.0
 25 # constant value for surface emissivity (if startphy_file = .false.)
 26 surfemis     = 1.0
 27 
 28 # the rad. transfer is computed every "iradia" physical timestep
 29 iradia           = 160
 30 # folder in which correlated-k data is stored ?
 31 corrkdir         = Jupiter_HITRAN2012_REY_ISO_NoKarko_T460K_article2019_gauss8p8_095
 32 # Uniform absorption coefficient in radiative transfer?
 33 graybody         = .false.
 34 # Characteristic planetary equilibrium (black body) temperature
 35 # This is used only in the aerosol radiative transfer setup. (see aerave.F)
 36 tplanet          = 100.
 37 # Output global radiative balance in file 'rad_bal.out' - slow for 1D!!
 38 meanOLR          = .false.
 39 # Variable gas species: Radiatively active ?
 40 varactive        = .false.
 41 # Computes atmospheric specific heat capacity and
 42 # could calculated by the dynamics, set in callphys.def or calculeted from gases.def.
 43 # You have to choose: 0 for dynamics (3d), 1 for forced in callfis (1d) or 2: computed from gases.def (1d)
 44 # Force_cpp and check_cpp_match are now deprecated.  
 45 cpp_mugaz_mode = 0
 46 # Specific heat capacity in J K-1 kg-1 [only used if cpp_mugaz_mode = 1]
 47 cpp              = 11500.
 48 # Molecular mass in g mol-1 [only used if cpp_mugaz_mode = 1]
 49 mugaz            = 2.30
 50 ### DEBUG
 51 # To not call abort when temperature is outside boundaries:
 52 strictboundcorrk = .false.
 53 # To not stop run when temperature is greater than 400 K for H2-H2 CIA dataset:   
 54 strictboundcia = .false.
 55 # Add temperature sponge effect after radiative transfer?
 56 callradsponge    = .false.
 57 
 58 Fat1AU = 1366.0
 59 
 60 ## Other physics options
 61 ## ~~~~~~~~~~~~~~~~~~~~~
 62 # call turbulent vertical diffusion ?
 63 calldifv    = .false.
 64 # use turbdiff instead of vdifc ?
 65 UseTurbDiff = .true.
 66 # call convective adjustment ?
 67 calladj     = .true.
 68 # call thermal plume model ?
 69 calltherm   = .true.
 70 # call thermal conduction in the soil ?
 71 callsoil    = .false.
 72 # Internal heat flux (matters only if callsoil=F)
 73 intheat     = 7.48
 74 # Remove lower boundary (e.g. for gas giant sims)
 75 nosurf      = .true.
 76 #########################################################################
 77 ## extra non-standard definitions for Earth
 78 #########################################################################
 79 
 80 ## Thermal plume model options
 81 ## ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 82 dvimpl               = .true.
 83 r_aspect_thermals    = 2.0
 84 tau_thermals         = 0.0
 85 betalpha             = 0.9
 86 afact                = 0.7
 87 fact_epsilon         = 2.e-4
 88 alpha_max            = 0.7
 89 fomass_max           = 0.5
 90 pres_limit           = 2.e5
 91 
 92 ## Tracer and aerosol options
 93 ## ~~~~~~~~~~~~~~~~~~~~~~~~~~
 94 # Ammonia cloud (Saturn/Jupiter)?
 95 aeronh3             = .true.
 96 size_nh3_cloud      = 10.D-6
 97 pres_nh3_cloud      = 1.1D5                        # old: 9.D4
 98 tau_nh3_cloud       = 10.                          # old: 15.
 99 # Radiatively active aerosol (Saturn/Jupiter)?
100 aeroback2lay         = .true.
101 optprop_back2lay_vis = optprop_jupiter_vis_n20.dat
102 optprop_back2lay_ir  = optprop_jupiter_ir_n20.dat
103 obs_tau_col_tropo    = 4.0
104 size_tropo           = 5.e-7
105 pres_bottom_tropo    = 8.0D4
106 pres_top_tropo       = 1.8D4
107 obs_tau_col_strato   = 0.1D0
108 # Auroral aerosols (Saturn/Jupiter)?
109 aeroaurora         = .false.
110 size_aurora        = 3.e-7
111 obs_tau_col_aurora = 2.0
112 
113 # Radiatively active CO2 aerosol?
114 aeroco2            = .false.
115 # Fixed CO2 aerosol distribution?
116 aerofixco2     = .false.
117 # Radiatively active water aerosol?
118 aeroh2o        = .false.
119 # Fixed water aerosol distribution?
120 aerofixh2o     = .false.
121 # basic dust opacity
122 dusttau        = 0.0
123 # Varying H2O cloud fraction?
124 CLFvarying     = .false.
125 # H2O cloud fraction if fixed?
126 CLFfixval      = 0.0
127 # fixed radii for cloud particles?
128 radfixed       = .false.
129 # number mixing ratio of CO2 ice particles
130 Nmix_co2       = 100000.
131 # number mixing ratio of water particles (for rafixed=.false.)
132 Nmix_h2o       = 1.e7
133 # number mixing ratio of water ice particles (for rafixed=.false.)
134 Nmix_h2o_ice   = 5.e5
135 # radius of H2O water particles (for rafixed=.true.):
136 rad_h2o        = 10.e-6
137 # radius of H2O ice particles (for rafixed=.true.):
138 rad_h2o_ice    = 35.e-6
139 # atm mass update due to tracer evaporation/condensation?
140 mass_redistrib = .false.
141 
142 ## Water options 
143 ## ~~~~~~~~~~~~~
144 # Model water cycle
145 water         = .true.
146 # Model water cloud formation
147 watercond     = .true.
148 # Model water precipitation (including coagulation etc.)
149 waterrain     = .true.
150 # Use simple precipitation scheme?
151 precip_scheme = 1
152 # Evaporate precipitation?
153 evap_prec     = .true.
154 # multiplicative constant in Boucher 95 precip scheme
155 Cboucher      = 1.
156 # Include hydrology ?
157 hydrology     = .false.
158 # H2O snow (and ice) albedo ?
159 albedosnow    = 0.6
160 # Maximum sea ice thickness ?
161 maxicethick   = 10.
162 # Freezing point of seawater (degrees C) ?
163 Tsaldiff      = 0.0
164 # Evolve surface water sources ?
165 sourceevol    = .false.
166 
167 ## CO2 options 
168 ## ~~~~~~~~~~~
169 # call CO2 condensation ?
170 co2cond       = .false.
171 # Set initial temperature profile to 1 K above CO2 condensation everywhere?
172 nearco2cond   = .false.

- gases.def: File containing the gas composition of the atmosphere you want to model, with their molar mixing ratios.

 1 # gases
 2 5
 3 H2_
 4 He_
 5 CH4
 6 C2H2
 7 C2H6
 8 0.863
 9 0.134
10 0.0018
11 1.e-7
12 1.e-5
13 # First line is number of gases
14 # Followed by gas names (always 3 characters)
15 # and then molar mixing ratios.
16 # mixing ratio -1 means the gas is variable.

- jupiter_const.def: Files that gather all orbital and physical parameters of Jupiter.

- traceur.def: At this time, only two tracers are used for modelling Jupiter atmosphere, so the traceur.def file is summed up as follow

1 2
2 h2o_vap
3 h2o_ice

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

- run_icosa.def: file containing parameters for ICOSAGCM 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.

- run.def: file which brings together all the setting files and will be reading by the interface ICOSA_LMDZ to link each part of the model (ICOSAGCM, LMDZ.GENERIC) with its particular setting file(s) when the library XIOS does not take action (through the .xml files).

 1 ###########################################################################
 2 ### INCLUDE OTHER DEF FILES (physics, specific settings, etc...)
 3 ###########################################################################
 4 INCLUDEDEF=run_icosa.def
 5 
 6 INCLUDEDEF=jupiter_const.def
 7 
 8 INCLUDEDEF=callphys.def
 9 
10 
11 prt_level=0
12 
13 ## iphysiq must be same as itau_physics
14 iphysiq=40

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