Advanced Use of the GCM - Revision history

Martin.turbet: /* Pre-Tabulated spectra */

2025-10-29T14:07:02Z

‎Pre-Tabulated spectra

Martin.turbet: /* Pre-Tabulated spectra */

2025-10-29T14:05:22Z

‎Pre-Tabulated spectra

Martin.turbet: /* Pre-Tabulated spectra */

2025-10-29T13:53:19Z

‎Pre-Tabulated spectra

Martin.turbet: /* Pre-Tabulated spectra */

2025-10-29T13:52:06Z

‎Pre-Tabulated spectra

Martin.turbet: /* Pre-Tabulated spectra */

2025-10-29T13:51:53Z

‎Pre-Tabulated spectra

Martin.turbet: /* Pre-Tabulated spectra */

2025-10-29T13:50:00Z

‎Pre-Tabulated spectra

Martin.turbet: /* Pre-Tabulated spectra */

2025-10-29T13:41:44Z

‎Pre-Tabulated spectra

Emillour: /* Changing the output temporal resolution and time duration */

2025-04-30T13:30:48Z

‎Changing the output temporal resolution and time duration

Martin.turbet: /* Getting opacity tables for your desired atmospheric composition */

2025-04-30T10:35:54Z

‎Getting opacity tables for your desired atmospheric composition

Martin.turbet: /* How to Add continuum opacities */

2025-04-30T10:35:30Z

‎How to Add continuum opacities

@@ Line 288: / Line 288: @@
 </pre>
-Here we used the stellar spectrum and effective temperature of the Sun, but you can add stellar spectrum from any star, as soon as the stellar spectrum is provided in your /datadir/stellar_spectra repository.
+Here we used the stellar spectrum and effective temperature of the Sun, but you can add any stellar spectrum from any star, as soon as the stellar spectrum is provided in your /datadir/stellar_spectra repository.
 For this, you can first check our database of stellar spectra here: https://web.lmd.jussieu.fr/~lmdz/planets/generic/datagcm/stellar_spectra/
 We provide spectra for reference stars: Sun, Proxima Centauri, TRAPPIST-1, K2-18, WASP43, etc.
-We also provide a grid of stellar spectra based on the BT-Settl database here: https://web.lmd.jussieu.fr/~lmdz/planets/generic/datagcm/stellar_spectra/BT-Settl_stellar_spectra_grid/
+We also provide a grid of stellar spectra based on the BT-Settl database here (stellar effective temperature from 2000 to 7000K): https://web.lmd.jussieu.fr/~lmdz/planets/generic/datagcm/stellar_spectra/BT-Settl_stellar_spectra_grid/
 You can also create your own stellar spectra (2-columns file, first column = wavelength in microns ; second column = stellar flux). The flux needs to be proportional to a flux per units of wavelength, but absolute units is not important. This is because to calculate the true stellar spectrum at the top of the atmosphere, the Generic PCM renormalizes the stellar spectrum by the bolometric flux at 1 Astronomical Unit (AU) provided by the user, which it then converts into the true stellar spectrum by using the star-planet distance. So only relative flux is used by the Generic PCM. This strategy allows to precisely control the total incoming stellar radiation on the planet.

@@ Line 282: / Line 282: @@
 <pre>
 stelbbody = .false.
 stelspec_file = spectrum_Sun_2025.dat
-tstellar = 5780.0
+# effective temperature of the star in Kelvin
 </pre>
 Here we used the stellar spectrum and effective temperature of the Sun, but you can add stellar spectrum from any star, as soon as the stellar spectrum is provided in your /datadir/stellar_spectra repository.
-you also need to make sure the spectra are available in your /datadir/stellar_spectra (or /datagcm/stellar_spectra) directory.
+We provide spectra for reference stars: Sun, Proxima Centauri, TRAPPIST-1, K2-18, WASP43, etc.
+We also provide a grid of stellar spectra based on the BT-Settl database here: https://web.lmd.jussieu.fr/~lmdz/planets/generic/datagcm/stellar_spectra/BT-Settl_stellar_spectra_grid/
 Traditionally, we have used synthetic spectra from the PHOENIX database, that we adapt to the Generic PCM by decreasing the spectral resolution (use 10000 points with a fixed spectral resolution of 0.001 micron) and by adapting the units (in W/m2/micron). This is the option that is generally preferred to better represent the effect of the star (whose real spectrum can strongly deviate from the black body approximation).
-To calculate the true stellar spectrum at the top of the atmosphere, the Generic PCM renormalizes the stellar spectrum by the bolometric flux at 1 Astronomical Unit (AU) provided by the user, which it then converts into the true stellar spectrum by using the star-planet distance.
+You can also create your own stellar spectra (2-columns file, first column = wavelength in microns ; second column = stellar flux). The flux needs to be proportional to a flux per units of wavelength, but absolute units is not important. This is because to calculate the true stellar spectrum at the top of the atmosphere, the Generic PCM renormalizes the stellar spectrum by the bolometric flux at 1 Astronomical Unit (AU) provided by the user, which it then converts into the true stellar spectrum by using the star-planet distance. So only relative flux is used by the Generic PCM. This strategy allows to precisely control the total incoming stellar radiation on the planet.
 To specify the flux at 1 AU, you need to add in the [[The_callphys.def_Input_File | callphys.def]] file, the following line:
 <pre>
-Fat1AU = 1366.0
+Fat1AU = 1366.0 # in W/m2
 </pre>
-(here 1366W/m2 corresponds to the flux at 1AU for the Sun)
+(here 1366W/m2 corresponds to the flux at 1AU for the Sun, i.e. the top-of-atmosphere flux received on Earth)
-NOTE: The Generic PCM eventually has the capability to run without any stellar flux. To do that, you can simply put Fat1AU = 0. (@LUCAS_TEINTURIER, could you check that?)
+NOTE: The Generic PCM eventually has the capability to run without any stellar flux. To do that, you can simply put Fat1AU = 0.
 == How to Change the Opacity Tables ==

@@ Line 276: / Line 276: @@
 * the option 'stelbbody' in the [[The_callphys.def_Input_File | callphys.def]] file is equal to .false. (it not specified, by default stelbbody is assumed to be .false.).
-* to fill the options 'stelspec_file' and 'tstellar' in the [[The_callphys.def_Input_File | callphys.def]] with
+* to fill the options 'stelspec_file' and 'tstellar' in the [[The_callphys.def_Input_File | callphys.def]] with the name of the stellar spectrum and associated effective temperature.
 <pre>

@@ Line 275: / Line 275: @@
 For this, you need to make sure:
-- the option 'stelbbody' in the [[The_callphys.def_Input_File | callphys.def]] file is equal to .false. (it not specified, by default stelbbody is assumed to be .false.).
+* the option 'stelbbody' in the [[The_callphys.def_Input_File | callphys.def]] file is equal to .false. (it not specified, by default stelbbody is assumed to be .false.).
-- to fill the options 'stelspec_file' and 'tstellar' in the [[The_callphys.def_Input_File | callphys.def]] with
+* to fill the options 'stelspec_file' and 'tstellar' in the [[The_callphys.def_Input_File | callphys.def]] with
 <pre>

@@ Line 276: / Line 276: @@
 - the option 'stelbbody' in the [[The_callphys.def_Input_File | callphys.def]] file is equal to .false. (it not specified, by default stelbbody is assumed to be .false.).
-- to fill the options 'stelspec_file' and 'tstellar' in the [[The_callphys.def_Input_File | callphys.def]], as follows:
+- to fill the options 'stelspec_file' and 'tstellar' in the [[The_callphys.def_Input_File | callphys.def]] with
 <pre>
-stelspec_file=spectrum_Sun_2025.dat
+stelbbody = .false.
-tstellar=5780.0
+stelspec_file = spectrum_Sun_2025.dat
 </pre>

@@ Line 271: / Line 271: @@
 === Pre-Tabulated spectra ===
-Second, the model can read a file containing any pre-computed stellar spectrum. Traditionally, we have used synthetic spectra from the PHOENIX database, that we adapt to the Generic PCM by decreasing the spectral resolution (use 10000 points with a fixed spectral resolution of 0.001 micron) and by adapting the units (in W/m2/micron). This is the option that is generally preferred to better represent the effect of the star (whose real spectrum can strongly deviate from the black body approximation).
+Second, the model can read a file containing any pre-computed stellar spectrum.
-For this, you need to make sure the option 'stelbbody' in the [[The_callphys.def_Input_File | callphys.def]] file is equal to .false. (it not specified, by default stelbbody is assumed to be .false.).
+For this, you need to make sure:
-Then you need to add in the [[The_callphys.def_Input_File | callphys.def]] file, the following line:
+- the option 'stelbbody' in the [[The_callphys.def_Input_File | callphys.def]] file is equal to .false. (it not specified, by default stelbbody is assumed to be .false.).
 <pre>
-startype = 1
+stelspec_file=spectrum_Sun_2025.dat
 </pre>
-and change the value of startype depending on the star you want to model. (here 1 means we use the solar spectrum)
+(here we used the stellar spectrum of the Sun)
 To know which stellar spectra are available, you need to open the file LMDZ.GENERIC/libf/phystd/ave_stelspec.F90 and adapt the value of startype accordingly. You also need to make sure the spectra are available in your /datadir/stellar_spectra (or /datagcm/stellar_spectra) directory.

@@ Line 35: / Line 35: @@
 Note: in the example, they are not necessarily 1000 Earth days, because it depends on the definition of the day duration that has been taken in the start files.
-* To change the temporal resolution of the output files, you need to open the [[The_run.def_Input_File | run.def]] file and change the variable 'ecritphy':
+* To change the temporal resolution of the output files, you need to open the [[The_callphys.def_Input_File | callphys.def]] file and change the variable 'diagfi_output_rate':
 <pre>
-ecritphy = 200 # this means the simulation will write variables in the output files every 200 time steps of the simulation.
+diagfi_output_rate = 240 # this means the simulation will write variables in the output files every 240 physics time steps of the simulation.
 </pre>
-Note: The output temporal resolution of the output files then depends also on the number of timestep per day ('day_step' variable in [[The_run.def_Input_File | run.def]] file). In this example:
+Note: The output temporal resolution of the output files then depends also on the number of physics timestep per day (the 'day_step' variable in [[The_run.def_Input_File | run.def]] file is the number of dynamical steps per day but physics are called every 'iphysiq' dynamical time step). In this example:
 <pre>
 nday = 1000
-daystep = 800
+daystep = 480
-ecritphy = 200
+iphysiq= 10
 </pre>
-The output file will provide results every 0.25 days (800/200), and for a total duration of 1000 days (so 4000 time values in total).
+The physics are called every 10 dynamical time step (i.e. the physics are called 48(=daystep/iphysiq=480/10) times per day and the output file will provide results every 0.25 days (=diagfi_output_rate/48), and for a total duration of 1000 days (so 4000 time values in total).
 === Changing the output variable ===

@@ Line 307: / Line 307: @@
 * You can also check databases provided by the community (the format of the opacity tables may have to be changed/adapted though):
 - https://lesia.obspm.fr/exorem/
 - https://petitradtrans.readthedocs.io/en/latest/content/available_opacities.html
 * If your desired atmospheric composition is not available in the directory above, you will have to build a new opacity table. (Spoiler alert: this can be a long and quite tricky process).
 We have created a dedicated page on how to build new opacity tables here: https://lmdz-forge.lmd.jussieu.fr/mediawiki/Planets/index.php/Building_Opacity_Tables
 === Implementing your opacity tables in the Generic PCM ===

@@ Line 324: / Line 324: @@
 == How to Add continuum opacities ==
-In general, opacity tables (above) only include so-called "permitted" absorptions (coming from line centers, computed from line lists).
+In general, opacity tables (above) only include so-called "permitted" absorptions (coming from line centers, computed from line lists). But other sources of absorption -- so-called "continuum absorptions" -- can be important : contribution from line far wings, collision-induced absorptions, and dimer absorption (these two last contributions are known as "forbidden" absorptions). How do we handle these continuum absorptions in the model?
 Historically, we used to compile (unstructured) data from HITRAN and other sources to build the continuum tables in the model.