Changes between Version 10 and Version 11 of DevelopmentActivities/ORCHIDEE-CNP


Ignore:
Timestamp:
2016-02-03T08:37:10+01:00 (8 years ago)
Author:
dgoll
Comment:

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  • DevelopmentActivities/ORCHIDEE-CNP

    v10 v11  
    11 
    2 = ORCHIDEE-CNP = 
     2= ORCHIDEE-CN-P (former branch ORCHIDEE-CNP) = 
    33 
    44This page describes the work done to include the phosphorus cycle into ORCHIDEE. It is based on MERGE-OCN, which was extended and corrected as described here: https://forge.ipsl.jussieu.fr/orchidee/wiki/Branches/MergeOCN/Goll as well as a recruitment routine by S. Peng (ask him if you need infos) 
    … …  
    1818  
    1919 
    20  
    2120[[PageOutline(2,SECTIONS,outline)]] 
    2221 
    23 == Soil type problem == 
     22== Soil type inconsistency in ORCHIDEE-CN-P == 
    2423The phosphorus model needs soil type specific parameters. Therefore, a new input routine is going to be written which reads in USDA soil orders. According to the soil order the parameter values are set for each grid box. 
    2524 
    2625The problem is that ORCHIDEE already reads in fields of soil texture classes which were originally derived from soil orders. According to the soil texture classes, parameter related to soil hydrology are set. As the original data cannot be found anymore, ORCHIDEE will run with two independent sets of soil order specific parameters. Thereby inconsistencies between the phosphorus related parameters and the the hydrology related parameters can be introduced. The practice of reading in soil texture classes instead of soil orders is also problematic in respect of future developments and I suggest to change that. 
    2726 
    28 == Work for Albert == 
    29 We need a routine which reads the soil orders (n=12) from this file: /home/users/dgoll/ORC_data/USDA_soilorders/USDA_SoilSuborder.nc .The file itself does not respect the netCDF standards, you would need to fix this. Also delete non necessary variables. 
     27== HOWTO install/compile/run ORCHIDEE-CN-P for offline use with libIGCM on obelix. == 
     28This howto is based on the information which can be found in the ORCHIDEE wiki regarding the trunk version of ORCHIDEE. 
     29Please check the wiki for information regarding the respective commands listed here.  
    3030 
    31 Currently, all input reading routines are located in src_stomate/stomate_io.f90; for example the routines to read ref_temp, deposition and the lithological fractions. 
    32 There is quite some doubling of code which could be minimized by re-writting the routines, for example outsourcing the remap procedure in a own subroutine/function. 
     31=== 1. install libIGCM === 
     32{{{ 
     33svn co http://forge.ipsl.jussieu.fr/igcmg/svn/modipsl/trunk modipsl 
     34cd modipsl/util 
     35./model ORCHIDEE_trunk 
     36}}} 
    3337 
    34 The soil orders as read in from the file should be assigned to a new variable of your choice (following the texture classes or lithological fractions).  
    35 I handle the rest. 
     38=== 2. Exchange the trunk ORCHIDEE with ORCHIDEE-CN-P === 
     39{{{ 
     40cd ../modeles 
     41rm -fr ORCHIDEE 
     42svn co svn://forge.ipsl.jussieu.fr/orchidee/branches/ORCHIDEE-CN-P ORCHIDEE 
     43cd ../util ; ./ins_make 
     44}}} 
    3645 
    37 You find the deposition input file here: 
    38 /home/scratch01/dgoll/ORCHIDEE/ORC-CNP/simulations/simple_forcing_DSG/deposition.nc 
     46=== 3. Compile ORCHIDEE (obelix) ==== 
     47{{{ 
     48cd ../modeles/ORCHIDEE ; ./makeorchidee_fcm -driver -arch ifort_LSCE -noxios 
     49}}} 
    3950 
     51=== 4. Run ORCHIDEE (obelix) === 
     52==== 4.1 SPINUP_ANALYTIC ==== 
     53===== 4.1.1 create new experiment folder ===== 
     54{{{ 
     55cd ../../config/ORCHIDEE_OL/ 
     56cp -fr SPINUP_ANALYTIC/ MY_SPINUP_ANALYTIC/ 
     57cd MY_SPINUP_ANALYTIC/ 
     58}}} 
     59===== 4.1.2 tell libIGCM about the new input files ===== 
     60modify the variable "ListNonDel" in COMP/stomate.card: 
     61{{{ 
     62ListNonDel= (${R_IN}/SRF/reftemp.nc, .) \         
     63(/home/scratch01/dgoll/ORCHIDEE/ORC-CNP/simulations/simple_forcing_DSG/USDA_SoilSuborder.nc, .), \ 
     64(/home/scratch01/dgoll/ORCHIDEE/ORC-CNP/simulations/simple_forcing_DSG/lithology.nc, .), \ 
     65(/home/scratch01/dgoll/ORCHIDEE/ORC-CNP/simulations/simple_forcing_DSG/deposition.nc, .) 
     66}}} 
     67WARNING: the deposition file is a static field at the moment. 
    4068 
     69tell that we use the new “soil_param.nc”; in COMP/sechiba.card: 
     70{{{ 
     71(/home/scratch01/dgoll/ORCHIDEE/ORC-CNP/simulations/simple_foring_DSG/soils_param.nc, .), \ 
     72}}} 
     73===== 4.1.3 adjust the libIGCM to a site scale simulation (like in wiki) ===== 
     74modify config.card as usual (see wiki) 
    4175 
     76add the new flags for the nutrient cycles: 
     77{{{ 
     78# to activate P cycle set =y 
     79STOMATE_OK_PCYCLE=y 
     80# to activate N cycle set =y 
     81STOMATE_OK_NCYCLE=y 
     82# make sure we don't fake 
     83LD_FAKE_HEIGHT=n 
     84# you can enable mass conservation and stoichiometry checks by =y 
     85STOMATE_MASS_CONSERVATION=y 
     86STOMATE_DSG_DEBUG=y 
     87}}} 
     88in addition you should  add all the PFT and soil parameter values as set in  
     89~/ORCHIDEE/DEFS_n_CARDS/run.def 
    4290 
     91if you want to archive, for example in the IMBALANCE-P storage; add to config.card: 
     92{{{ 
     93ARCHIVE=/home/surface3/dgoll  
     94}}}  
    4395 
    44   
     96===== 4.1.4 create job ===== 
     97{{{ 
     98../../../libIGCM/ins_job 
     99}}} 
    45100 
    46   
     101===== 4.1.5 adjust job_file (optional) ===== 
    47102 
     103Header to run a site scale simulation on obelix 
     104{{{ 
     105###################### 
     106        ## OBELIX      LSCE ## 
     107        ###################### 
     108        #PBS -N test 
     109        #PBS -m a 
     110        #PBS -j oe 
     111        #PBS -q short 
     112        #PBS -o Script_Output_test.000001 
     113        #PBS -S /bin/ksh 
     114        #PBS -v BATCH_NUM_PROC_TOT=1 
     115        #PBS -l nodes=1:ppn=1 
     116}}} 
     117 
     118to automatically have existing files deleted, set JobType=DEV 
     119{{{ 
     120        #D- Experience type : DEB(ug), DEV(elopment), RUN (default) 
     121        JobType=DEV  
     122}}} 
     123to avoid queuing take full advantage of your job time; the value depends on #PBS -q short and computation time of orchidee 
     124{{{ 
     125#D- Number of execution in one job 
     126        PeriodNb=60 
     127}}} 
     128 
     129         
     130to have a temp directory you can access on obelix; exchange dgoll with your ID 
     131{{{ 
     132#D- Define running directory 
     133#D- Default=${TMPDIR} ie temporary batch directory 
     134#D- 
     135#RUN_DIR_PATH=/workdir/or/scratchdir/of/this/machine 
     136RUN_DIR_PATH=/home/scratch01/dgoll/RUN_DIR 
     137}}}