Changes between Version 36 and Version 37 of Documentation/UserGuide/CheckList


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Timestamp:
2020-06-03T17:35:56+02:00 (4 years ago)
Author:
luyssaert
Comment:

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  • Documentation/UserGuide/CheckList

    v36 v37  
    8181- OOL_SEC_STO_FG3, for a run without spin-up (default restart state) under the WFDEI_GPCC atmospheric forcing 
    8282- OOL_SEC_STO_FG3nd, for a run like FG3 but with the [wiki:Documentation/Forcings#a0.Generalinformation new driver] developped by Jan Polcher (this configuration is available starting at tag2.1) 
    83 - OOL_SEC_STO_FG4 and OOL_SEC_STO_FG5 to use age classes, species-level PFTs, diameter classes, forest management, litter raking, species changes, management changes, etc  
    84 - [browser:tags/ORCHIDEE_2_0/ORCHIDEE_OL/OOL_SEC OOL_SEC], without STOMATE (no dynamic phenology nor nutrient cycles). 
     83- OOL_SEC_STO_FG4 and OOL_SEC_STO_FG5 (available since r6616) to use age classes, species-level PFTs, diameter classes, forest management, litter raking, species changes, management changes, etc  
     84- OOL_SEC, without STOMATE (no dynamic phenology nor nutrient cycles). 
    8585 
    86 In the above names, "OOL" in a directory title refers to "ORCHIDEE offline", "SEC" refers to the SEChiba module in charge of the water and energy cycles, and "STO" refers to the STOmate model controlling vegetation and nutrient cycles.  OOL_SEC_STO, therefore, means the configuration is designed to use meteorological forcing files to drive the water, energy, and nutrient cycles.   
     86In the above names, "OOL" in a directory title refers to "ORCHIDEE offline", "SEC" refers to the SEChiba module in charge of the water and energy cycles, and "STO" refers to the STOmate model controlling vegetation and nutrient cycles. OOL_SEC_STO, therefore, means the configuration is designed to use meteorological forcing files to drive the water, energy, and nutrient cycles.   
    8787 
    8888'''4b) To create your own configuration,''' the simplest way is to modify an existing configuration: copy the corresponding directory with a new name in your modipsl/config/ORCHIDEE_OL/ and change what you want: 
    8989 
    90 - [browser:tags/ORCHIDEE_2_0/ORCHIDEE_OL/OOL_SEC_STO_FG3/config.card config.card]=> to choose the name, length, restart of your simulation ([https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/Doc/Setup#config.card more details]) 
    91 - [browser:tags/ORCHIDEE_2_0/ORCHIDEE_OL/OOL_SEC_STO_FG3/PARAM/run.def PARAM/run.def] => to choose the options of your simulation, via the "keywords". These keywords can be flag (y or n to activate them or not) or they can be parameters values that you can change without recompiling the model. The number of these keywords is huge, and it has a large effect on the outcome of your simulation. The default values depend on the revision (see 2). More details on [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/Doc/Setup#PARAMdirectory run.def] and see 4c for a list of keywords. 
    92 - [browser:tags/ORCHIDEE_2_0/ORCHIDEE_OL/OOL_SEC_STO_FG3/COMP/orchidee_ol.card COMP/orchidee_ol.card] => defines the meteorological forcing files and xml files (the latter of which are only used with XIOS; ORCHIDEE can also be run [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/DeactivateXIOS without XIOS], though it is not recommended). The list of available atmospheric forcing datasets is regularly updated [wiki:Documentation/Forcings here].  
    93 - [browser:tags/ORCHIDEE_2_0/ORCHIDEE_OL/OOL_SEC_STO_FG3/COMP/sechiba.card COMP/sechiba.card] => defines the other input files ([https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/Ancillary list of available datasets]), and some important user option for sechiba: 
     90- config.card => to choose the name, length, restart of your simulation ([https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/Doc/Setup#config.card more details]) 
     91- PARAM/run.def, PARAM/orchidee.def and PARAM/orchidee_pft.def => Prior to r6616 the information contained in these three files was combined in a single file called PARAM/run.def. Since r6616 three different files have been defined to better match what is being done in LMDzOR. The concept and many details on these three files can be found  [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/TrunkFunctionality4#Parameterfilesr6614 here]. The basic idea is that those files enable the users to choose the options of their simulation, via "keywords". These keywords can be a flag (y or n to activate them or not) or they can be parameters values that you can change without recompiling the model. The number of these keywords is huge, and it has a large effect on the outcome of your simulation. The default values depend on the revision (see 2). More details on [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/Doc/Setup#PARAMdirectory run.def] and see 4c for a list of keywords. 
     92- COMP/orchidee_ol.card => defines the meteorological forcing files and xml files (the latter of which are only used with XIOS; ORCHIDEE can also be run [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/DeactivateXIOS without XIOS], though it is not recommended). The list of available atmospheric forcing datasets is regularly updated [wiki:Documentation/Forcings here].  
     93- COMP/sechiba.card => defines the other input files ([https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/Ancillary list of available datasets]), and some important user option for sechiba: 
    9494    * do we change the vegetation map every year of not (VEGET_UPDATE)? 
    9595    * frequency of the output and name of the corresponding output files 
    9696    * the last part of the file is about [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/Doc/Running#Simulation-Postprocessing post-processing]  
    97 - [browser:tags/ORCHIDEE_2_0/ORCHIDEE_OL/OOL_SEC_STO_FG3/COMP/stomate.card COMP/stomate.card] => defines some important user option for stomate: 
     97- COMP/stomate.card => defines some important user option for stomate: 
    9898    * do we use the analytical spinup? (SPINUP_ANALYTIC, see wiki:Documentation/UserGuide/SpinUpCarbon) 
    9999    * frequency of the output and name of the corresponding output files 
    … …  
    105105'''4c) More on keywords''' 
    106106 
    107 The externalized parameters are parameters or flags that are not hard-coded and can be changed via an input file, namely PARAM/run.def. The advantage is that you can test various sets of parameters with the same executable and without recompiling. It can be particularly useful for parameter calibration. 
     107The externalized parameters are parameters or flags that are not hard-coded and can be changed via input files, namely PARAM/run.def, PARAM/orchidee.def and PARAM/orchidee_pft.def (prior to r6616 these files were combined in a single files called PARAM/run.def). The advantage is that you can test various sets of parameters with the same executable and without recompiling. It can be particularly useful for parameter calibration. 
    108108 
    109109These parameters are linked to "keywords", which appear in the code in capital letter and are fed with the parameter values by a "getin" call.  
    … …  
    111111The list of the keywords related externalized parameters is different for different versions of the code: 
    112112- trunk up to v2.2 : [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/OrchideeParameters list of parameters] and [https://docs.google.com/spreadsheets/d/1DYVvvqxVoXFAqA_M_hvkd-Ooru6ZQ32Lz2oa8oKKA5E/edit#gid=1984497631 recommended range of values] 
    113 - trunk after v4.0 : [http://forge.ipsl.jussieu.fr/orchidee/browser/trunk/ORCHIDEE/orchidee.default list of parameters] 
     113- trunk v4.0 (since r6616): [http://forge.ipsl.jussieu.fr/orchidee/browser/trunk/ORCHIDEE/orchidee.default list of parameters] 
    114114 
    115115WARNING:  some options or parameters depend on other options. It's important to test the configuration you select. [wiki:Documentation/UserGuide/UserDefinedSoilParameters Example]. 
    … …  
    119119'''4d) Spinup and initialization''' 
    120120 
    121 A simulation requires initial conditions, which are defined by section #D-- Restarts - in [browser:tags/ORCHIDEE_2_0/ORCHIDEE_OL/OOL_SEC_STO_FG2/config.card config.card].  
     121A simulation requires initial conditions, which are defined by section #D-- Restarts - in the config.card.  
    122122 
    123 There are two options: Restart = n ("from scratch" with arbitrary initial values) vs. Restart = y (we use state variables from a pre-existing simulation as initial conditions; only works if the two simulations have the same horizontal and vertical resolution, and the same processes thus state variables). In both cases, we usually need some warmup or spinup, unless we are just pursuing a simulation.  
    124  
    125 Read more on the ways to set up your spinup on [wiki:Documentation/UserGuide/SpinUpCarbon Spinup : why, how and how long? The answer depends on the ORCHIDEE component].  It is also possible to do an [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/SpinupInJobBasic analytical spinup] that is faster. 
     123There are two options: Restart = n ("from scratch" with arbitrary initial values) vs. Restart = y (we use state variables from a pre-existing simulation as initial conditions; only works if the two simulations have the same horizontal and vertical resolution, and the same processes thus state variables). In both cases, we usually need some spinup, unless we are just pursuing a simulation. Read more on the ways to set up your spinup on [wiki:Documentation/UserGuide/SpinUpCarbon Spinup : why, how and how long? The answer depends on the ORCHIDEE component].  It is also possible to do an [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/SpinupInJobBasic analytical spinup] that is faster. 
    126124 
    127125'''4e) Output''' 
    128126 
    129 ORCHIDEE output is controlled by separate modules, referred to as XIOS ([[https://forge.ipsl.jussieu.fr/orchidee/wiki/DevelopmentActivities/ORCHIDEE-CNP here] PDF] and [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/XIOSinConfig webpage]) and IOIPSL.  These modules greatly improve reading and writing data for large simulations, although the benefits may not be seen for single pixel, single CPU runs. 
     127ORCHIDEE output is controlled by separate modules, referred to as XIOS ([[https://forge.ipsl.jussieu.fr/orchidee/wiki/DevelopmentActivities/ORCHIDEE-CNP here] PDF] and [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/XIOSinConfig webpage]) and IOIPSL.  These modules greatly improve reading and writing data for large simulations, although the benefits may not be seen for single pixel and thus a single CPU run. 
    130128 
    131129If you want to change the variables that are output by your simulation, read the dedicated section [wiki:Documentation/UserGuide#Historyoutputfiles History/output files].