Changes between Version 22 and Version 23 of Documentation/UserGuide/CheckList


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Timestamp:
2020-05-31T23:08:58+02:00 (4 years ago)
Author:
aducharne
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  • Documentation/UserGuide/CheckList

    v22 v23  
    4949- allow vegetation to burn in fires (FIRE_DISABLE in PARAM/run.def) 
    5050- dynamic nitrogen cycle, where nitrogen scarcity can limit vegetation growth (STOMATE_IMPOSE_CN in PARAM/run.def) 
    51 - activate soil_freezing, etc... *** complete the list, give the keywords 
     51- activate soil_freezing, etc... (more details on flags and keywords in 4c).  
    5252 
    5353NOTE:  not all of these components can be activated at the same time and still give reliable results.  It's important to test the configuration you select. 
    … …  
    5555== 3) Installation and compilation 
    5656 
    57 Read here about to download ORCHIDEE for offline (i.e., driven by separate meteorological forcing files) use: [wiki:Documentation/UserGuide/InstallingORCHIDEEBasic] 
     57Read here about to download ORCHIDEE for offline (i.e., driven by separate meteorological forcing files) use: [wiki:Documentation/UserGuide/InstallingORCHIDEEBasic]. Information for downloading the [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/ORCHIDEEDOFOCOInstall CAN] and [https://forge.ipsl.jussieu.fr/orchidee/wiki/DevelopmentActivities/ORCHIDEE-CNP CNP] branches of ORCHIDEE also exists and can likely be adapted for any branch, but note that permission to access branches is generally restricted. 
    5858 
    59 The same method is used for offline and coupled configurations, where "coupled" typically refers to coupling ORCHIDEE to an atmospheric model that generates meteorological data at every time step. Find the full documentation about installation and using of IPSL-cmc coupled models [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/Doc here]. 
     59The same method is used for offline and coupled configurations, where "coupled" typically refers to coupling ORCHIDEE to an atmospheric model that generates meteorological data at every time step. Find the full documentation about installation and using of IPSL-cmc coupled models [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/Doc here], or go directly to a brief description of the [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/DocHconfigBlmdzorv6 LMDZOR_v6 configuration] (LMDZ coupled to ORCHIDEE).  
    6060 
    61 or go directly to a brief description of the [https://forge.ipsl.jussieu.fr/igcmg_doc/wiki/DocHconfigBlmdzorv6 LMDZOR_v6 configuration] (LMDZ coupled to ORCHIDEE).  
    62  
    63 Always recompile your code if you make changes in the fortran code. Further information on compiling ORCHIDEE can be found [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/CompileMethods here].  Information for downloading the [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/ORCHIDEEDOFOCOInstall CAN] and [https://forge.ipsl.jussieu.fr/orchidee/wiki/DevelopmentActivities/ORCHIDEE-CNP CNP] branches of ORCHIDEE also exists and can likely be modified for any branch, but note that permission to access branches is generally restricted. 
     61Always recompile your code if you make changes in the fortran code. Further information on compiling ORCHIDEE can be found [https://forge.ipsl.jussieu.fr/orchidee/wiki/Documentation/UserGuide/CompileMethods here].   
    6462 
    6563== 4) Configuration of your simulation 
    66 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. 
    6764 
    68 In the configuration directory, "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.  OOL_SEC, on the other hand, does not include dynamic vegetation or nutrient cycles. 
    6965 
    7066'''4a) The simplest option if you use libIGCM is to use a predefined configuration''' 
    … …  
    7470- SPINUP_ANALYTIC_FG1, OOL_SEC_STO_FG1trans, OOL_SEC_STO_FG2, which are designed to be used one after the other to run a simulation with CRU-NCEP atmospheric forcing and the long spinup required for the carbon cycle ([wiki:Documentation/UserGuide/SpinUpCarbon#StandardprotocolforCarbon-relatedvariables more details])  
    7571- [browser:tags/ORCHIDEE_2_0/ORCHIDEE_OL/OOL_SEC_STO_FG3 OOL_SEC_STO_FG3], for a run without spin-up (default restart state) under the WFDEI_GPCC atmospheric forcing 
     72- [browser:tags/ORCHIDEE_2_0/ORCHIDEE_OL/OOL_SEC OOL_SEC], without STOMATE (no dynamic phenology nor nutrient cycles). 
     73 
     74In 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.   
    7675 
    7776Each of the submission directory contains the required elements to run a particular offline simulation:  
    … …  
    9594'''4c) More on keywords''' 
    9695 
    97 Give definition (externalized parameters), and explain the ones to be careful with after the merge to CN. *** Explain more, links 
     96The 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. 
    9897 
     98These parameters are linked to "keywords", which appear in the code in capital letter and are fed with the parameter values by a "getin" call.  
    9999 
     100The list of the keywords related externalized parameters is different for different versions of the code: 
     101- 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] 
     102- trunk after v4.0 : [http://forge.ipsl.jussieu.fr/orchidee/browser/trunk/ORCHIDEE/orchidee.default list of parameters] 
     103 
     104USEFUL TIP: after your simulation has run, you have a summary of externalized parameters and options in your output directory: SRF/Debug/xxx_used_ref.def  
    100105 
    101106'''4d) Spinup and initialization''' 
    … …  
    106111 
    107112Read 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. 
     113 
     114'''4e) Output''' 
     115 
     116ORCHIDEE 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. 
    108117 
    109118== 5) Run your simulation