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add readme expert_only and new sites
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| @@ -1 +1,74 @@ | ||
| To be added soon. | ||
| $CTSMROOT/README_fates_emerald_api_expert_only 03/06/2020 | ||
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| ################################################################################# | ||
| # This document explains how to update the model codes and | ||
| # how to create atmospheric forcing and inputdata for new sites | ||
| # (No technical support will be promised, use at your own risk!) | ||
| # See also Yeliz's notes: https://ctsm-docs.readthedocs.io/en/latest/ for additional details | ||
| ################################################################################# | ||
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| ######## Two important things to watch out first!!! | ||
| ######## Two important things to watch out first!!! | ||
| ######## Two important things to watch out first!!! | ||
| (1) Module environment on your supercomputer: DON'T load any module beforehand, except "StdEvn"! | ||
| (2) Git version control: | ||
| CLM-FATES have very complex and sperate repository system: | ||
| -> ctsm: always create your own branch, do not touch master! | ||
| -> cime: remember to create your own branch in cime folder also, to record all the changes you make. | ||
| -> fates: remember to create your own branch in fates folder also, to record all the changes you make. | ||
| If you do not create your own branch for "cime" and "fates", when you run "./manage_externals/checkout_externals", your previous "cime" and "fates" will be overwritten. | ||
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| ######## Download ctsm and update ctsm-fates (Only important steps are illustrated here!!!) | ||
| **** If you are already using fates_emerald_api, skip this! **** | ||
| e.g.: | ||
| git remote add ctsm_ncar https://github.com/ESCOMP/CTSM.git # set a remote name for NCAR CTSM git repository | ||
| git fetch ctsm_ncar # get the most recent updates of CTSM | ||
| git merge ctsm_ncar/master # update your current branch with the newest CTSM version | ||
| git merge ctsm_ncar/fates_next_api # update your current branch with the newest CLM-FATES interface | ||
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| ##To update fates, you need to go to fates folder | ||
| e.g.: | ||
| git remote add NGEET_fates https://github.com/NGEET/fates.git | ||
| git fetch NGEET_fates # get the most recent updates of FATES | ||
| git merge NGEET_fates.git/master # update your current branch with the newest FATES | ||
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| ######## Adapt ctsm/cime to specific machine (e.g., SAGA and FRAM) | ||
| **** If you are already using fates_emerald_api, skip this! **** | ||
| Following file need to be modified | ||
| ..../cime/config/cesm/machines/config_batch.xml | ||
| ..../cime/config/cesm/machines/config_compilers.xml | ||
| ..../cime/config/cesm/machines/config_machines.xml | ||
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| See example here, you need look for the setup | ||
| https://github.com/NordicESMhub/cime/blob/cime5.6.10_noresm2_1_rel_06/config/cesm/machines/config_compilers.xml | ||
| https://github.com/NordicESMhub/cime/blob/cime5.6.10_noresm2_1_rel_06/config/cesm/machines/config_machines.xml | ||
| https://github.com/NordicESMhub/cime/blob/cime5.6.10_noresm2_1_rel_06/config/cesm/machines/config_batch.xml | ||
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| **** If you want to set up new sites, please follow the following steps **** | ||
| ######## Make script grids (see "prepare_inputdata.sh" in ./tools) | ||
| ######## Make domain file (see "prepare_inputdata.sh" in ./tools) | ||
| ######## Make mapping file (see "prepare_inputdata.sh" in ./tools) | ||
| ######## Make surface data file (see "prepare_inputdata.sh" in ./tools) | ||
| ######## Make and modify FATES parameter file: | ||
| ## Use existing tools: | ||
| ./src/fates/tools/FatesPFTIndexSwapper.py # Select PFTs interested. | ||
| ./src/fates/tools/modify_fates_paramfile.py # Modify PFT parameters | ||
| ## To use these tools, netcdf and python modules need to be loaded. | ||
| module load netCDF-Fortran/4.4.4-intel-2018b | ||
| module load Python/3.6.6-intel-2018b | ||
| ./FatesPFTIndexSwapper.py --pft-indices=2,6,9,10 --fin=****.nc --fout=****.nc | ||
| ## The default FATES parameter file is in ./src/fates/parameter_files | ||
| ## To create a netcdf parameter file: ncgen -o ****.nc fates_params_default.cdl | ||
| ######## Make atmospheric forcing for new sites (see "prepare_atm_forcing_****.ncl" in ./tools) | ||
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| ######## Set each sites as a unique grid type. The following file need to be modified: | ||
| ~/ctsm/cime/config/cesm/config_grids.xml | ||
| ~/ctsm/cime/src/components/data_comps/datm/cime_config/namelist_definition_datm.xml | ||
| ~/ctsm/bld/namelist_files/namelist_defaults_clm4_5.xml | ||
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| ######## Set new atmospheric forcing for the sites | ||
| ~/ctsm/cime/src/components/data_comps/datm/cime_config/config_component.xml (for different climate forcing) | ||
| ~/ctsm/cime_config/config_component.xml (for different climate forcing) | ||
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| load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/contributed.ncl" | ||
| load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/popRemap.ncl" | ||
| load "$NCARG_ROOT/lib/ncarg/nclscripts/esmf/ESMF_regridding.ncl" | ||
| load "$NCARG_ROOT/lib/ncarg/nclscripts/contrib/cd_string.ncl" | ||
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| begin | ||
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| ;######### SeedClim Sites | ||
| ; plot_lat=(/61.0243,60.8231,60.8328,60.9335,60.8203,60.8760,61.0866,60.5445,61.0355,60.8803,60.6652,60.6901/) | ||
| ; plot_lon=(/8.12343,7.27596,7.17561,6.41504,8.70466,7.17666,6.63028,6.51468,9.07876,7.16982,6.33738,5.96487/) | ||
| ; plot_name=(/"ALP1","ALP2","ALP3","ALP4","SUB1","SUB2","SUB3","SUB4","BOR1","BOR2","BOR3","BOR4"/) | ||
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| ;######### Landpress Sites | ||
| ; plot_lat=(/60.70084,65.83677,64.779,65.79602/) | ||
| ; plot_lon=(/5.092566,12.224506,11.2193,12.219299/) | ||
| ; plot_name=(/"LYG","BUO","HAV","SKO"/) | ||
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| ;######### Three-D Sites | ||
| plot_lat=(/60.88019,60.86183,60.85994/) | ||
| plot_lon=(/7.16990,7.16800,7.19504/) | ||
| plot_name=(/"VIKE","JOAS","LIAH"/) | ||
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| ;######### Finnmark Site | ||
| ; plot_lat=(/69.341088/) | ||
| ; plot_lon=(/25.293524/) | ||
| ; plot_name=(/"FINN"/) | ||
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| mon = ispan(0,11,1) | ||
| mon@units = "month" | ||
| month =cd_string(mon,"%N") | ||
| print(month) | ||
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| do p=0,2,1 | ||
| clim_output = "/cluster/shared/noresm/inputdata/atm/datm7/fates_platform/"+plot_name(p)+"/" | ||
| clim_input = "/cluster/shared/noresm/inputdata/atm/datm7/atm_forcing.datm7.GSWP3.0.5d.v1.c170516/" | ||
| system("mkdir -p "+ clim_output) | ||
| xfloor=plot_lon(p)-0.005 | ||
| xceil =plot_lon(p)+0.005 | ||
| yfloor=plot_lat(p)-0.005 | ||
| yceil =plot_lat(p)+0.005 | ||
| print(yceil) | ||
| print(xceil) | ||
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| do year=1901,2010,1 | ||
| do m=0,11,1 | ||
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| frsds=addfile(clim_input+"/Solar/clmforc.GSWP3.c2011.0.5x0.5.Solr."+year+"-"+month(m)+".nc","r") | ||
| fprec=addfile(clim_input+"/Precip/clmforc.GSWP3.c2011.0.5x0.5.Prec."+year+"-"+month(m)+".nc","r") | ||
| ftphw=addfile(clim_input+"/TPHWL/clmforc.GSWP3.c2011.0.5x0.5.TPQWL."+year+"-"+month(m)+".nc","r") | ||
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| rsds=frsds->FSDS(:,:,:) | ||
| prec=fprec->PRECTmms(:,:,:) | ||
| psrf=ftphw->PSRF(:,:,:) | ||
| tbot=ftphw->TBOT(:,:,:) | ||
| wind=ftphw->WIND(:,:,:) | ||
| qbot=ftphw->QBOT(:,:,:) | ||
| flds=ftphw->FLDS(:,:,:) | ||
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| lon=frsds->LONGXY(0,:) | ||
| lat=frsds->LATIXY(:,0) | ||
| time=frsds->time(:) | ||
| edgew =frsds->EDGEW | ||
| edgee =frsds->EDGEE | ||
| edges =frsds->EDGES | ||
| edgen =frsds->EDGEN | ||
| longxy =frsds->LONGXY | ||
| latixy =frsds->LATIXY | ||
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| loni=ind_nearest_coord(plot_lon(p), lon, 0) | ||
| latj=ind_nearest_coord(plot_lat(p), lat, 0) | ||
| print(loni) | ||
| print(latj) | ||
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| ;########## Creat forcing in netcdf format | ||
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| system("rm -f "+clim_output+"clm1pt_"+plot_name(p)+"_"+year+"-"+month(m)+".nc") ; remove if exists | ||
| fclim = addfile(clim_output+"clm1pt_"+plot_name(p)+"_"+year+"-"+month(m)+".nc","c") | ||
| ntim = dimsizes(time) ; get dimension sizes | ||
| nlat = 1 | ||
| nlon = 1 | ||
| nscalar = 1 | ||
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| setfileoption(fclim,"DefineMode",True) | ||
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| fAtt = True ; assign file attributes | ||
| fAtt@case_title = "GSWP3v1: norway " | ||
| fAtt@conventions = "CF-1.0" | ||
| fAtt@title = "CLM single point datm input data" | ||
| fAtt@history = "Original data from GSWP3v1 data" | ||
| fAtt@creation_date = systemfunc ("date") | ||
| fileattdef( fclim, fAtt ) ; copy file attributes | ||
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| dimNames = (/"scalar","lon","lat","time"/) | ||
| dimSizes = (/ nscalar, nlon, nlat, -1 /) | ||
| dimUnlim = (/ False, False, False, True/) | ||
| filedimdef(fclim,dimNames,dimSizes,dimUnlim) | ||
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| filevardef(fclim, "EDGEW" ,typeof(edgew),getvardims(edgew)) | ||
| filevardef(fclim, "EDGEE" ,typeof(edgee),getvardims(edgee)) | ||
| filevardef(fclim, "EDGES" ,typeof(edges),getvardims(edges)) | ||
| filevardef(fclim, "EDGEN" ,typeof(edgen),getvardims(edgen)) | ||
| filevardef(fclim, "LONGXY" ,typeof(longxy) ,getvardims(longxy)) | ||
| filevardef(fclim, "LATIXY" ,typeof(latixy) ,getvardims(latixy)) | ||
| filevardef(fclim, "time",typeof(time),getvardims(time)) | ||
| filevardef(fclim, "FSDS",typeof(rsds),getvardims(rsds)) | ||
| filevardef(fclim, "PRECTmms",typeof(prec),getvardims(prec)) | ||
| filevardef(fclim, "TBOT",typeof(tbot),getvardims(tbot)) | ||
| filevardef(fclim, "WIND",typeof(wind),getvardims(wind)) | ||
| filevardef(fclim, "PSRF",typeof(psrf),getvardims(psrf)) | ||
| filevardef(fclim, "QBOT",typeof(qbot),getvardims(qbot)) | ||
| filevardef(fclim, "FLDS",typeof(flds),getvardims(flds)) | ||
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| filevarattdef(fclim,"EDGEW",edgew) | ||
| filevarattdef(fclim,"EDGEE",edgee) | ||
| filevarattdef(fclim,"EDGES",edges) | ||
| filevarattdef(fclim,"EDGEN",edgen) | ||
| filevarattdef(fclim,"LONGXY",longxy) | ||
| filevarattdef(fclim,"LATIXY",latixy) | ||
| filevarattdef(fclim,"time",time) | ||
| filevarattdef(fclim,"FSDS",rsds) | ||
| filevarattdef(fclim,"PRECTmms",prec) | ||
| filevarattdef(fclim,"TBOT",tbot) | ||
| filevarattdef(fclim,"WIND",wind) | ||
| filevarattdef(fclim,"PSRF",psrf) | ||
| filevarattdef(fclim,"QBOT",qbot) | ||
| filevarattdef(fclim,"FLDS",flds) | ||
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| setfileoption(fclim,"DefineMode",False) | ||
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| print(time) | ||
| fclim->time = (/time/) ; "(/", "/)" syntax tells NCL to only output the data values to the predefined locations on the file. | ||
| fclim->EDGEW = (/xfloor/) | ||
| fclim->EDGEE = (/xceil/) | ||
| fclim->EDGES = (/yfloor/) | ||
| fclim->EDGEN = (/yceil/) | ||
| fclim->LONGXY = (/plot_lon(p)/) | ||
| fclim->LATIXY = (/plot_lat(p)/) | ||
| fclim->FSDS = (/rsds(:,latj,loni)/) | ||
| fclim->PRECTmms = (/prec(:,latj,loni)/) ; !!!! time variable can be modified in the attributes of the variable is also copied. make sure to use (/ /) to only copy data. | ||
| fclim->TBOT = (/tbot(:,latj,loni)/) | ||
| fclim->WIND = (/wind(:,latj,loni)/) | ||
| fclim->PSRF = (/psrf(:,latj,loni)/) | ||
| fclim->QBOT = (/qbot(:,latj,loni)/) | ||
| fclim->FLDS = (/flds(:,latj,loni)/) | ||
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| delete(time) | ||
| delete(rsds) | ||
| delete(prec) | ||
| delete(tbot) | ||
| delete(qbot) | ||
| delete(wind) | ||
| delete(psrf) | ||
| delete(flds) | ||
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| end do | ||
| end do | ||
| end do | ||
| end | ||
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