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* add example script * clean up * consolidate paths * fix more paths * add some docs for input files * update * Update scripts/example_end-to-end_script.sh Co-authored-by: Xylar Asay-Davis <xylarstorm@gmail.com> * Update scripts/example_end-to-end_script.sh Co-authored-by: Xylar Asay-Davis <xylarstorm@gmail.com> * Update scripts/example_end-to-end_script.sh Co-authored-by: Xylar Asay-Davis <xylarstorm@gmail.com> * Update scripts/example_end-to-end_script.sh Co-authored-by: Xylar Asay-Davis <xylarstorm@gmail.com> Co-authored-by: Xylar Asay-Davis <xylarstorm@gmail.com>
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| #!/bin/bash | ||
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| #source /usr/local/e3sm_unified/envs/load_latest_e3sm_unified_acme1.sh | ||
| #conda activate e2c_nco511_13 | ||
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| #historical | ||
| exp=historical | ||
| #expshort=hist-nat | ||
| #exp=hist-all-xGHG-xaer | ||
| caseid=v2.LR.${exp}_0101 | ||
| start=1850 | ||
| end=1850 | ||
| ypf=1 | ||
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| e2c_path=/p/user_pub/e3sm/zhang40/e3sm_to_cmip_data | ||
| model_data=$e2c_path/model-output | ||
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| result_dir=${e2c_path}/reference | ||
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| rgr_dir=${result_dir}/rgr | ||
| rgr_dir_vert=${result_dir}/rgr_vert | ||
| rgr_dir_vert_plev=${result_dir}/rgr_vert_plev | ||
| native_dir=${result_dir}/native | ||
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| map_file=${e2c_path}/maps/map_ne30pg2_to_cmip6_180x360_aave.20200201.nc | ||
| tables_path=${e2c_path}/cmor/cmip6-cmor-tables/Tables/ | ||
| metadata_path=${e2c_path}/user_metadata.json | ||
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| # note: space is not accepted in nco var list | ||
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| ## atm monthly h0 | ||
| input_path=${model_data}/v2.eam_input | ||
| flags='-7 --dfl_lvl=1 --no_cll_msr' | ||
| raw_var_list="ICEFRAC,OCNFRAC,LANDFRAC,PHIS,hyam,hybm,hyai,hybi,TREFHT,TS,PSL,PS,U10,QREFHT,PRECC,PRECL,PRECSC,PRECSL,QFLX,TAUX,TAUY,LHFLX,CLDTOT,FLDS,FLNS,FSDS,FSNS,SHFLX,CLOUD,CLDICE,TGCLDIWP,CLDLIQ,TGCLDCWP,TMQ,FLNSC,FSNTOA,FSNT,FLNT,FLUTC,FSDSC,SOLIN,FSNSC,FSUTOA,FSUTOAC,AODABS,AODVIS,AREL,TREFMNAV,TREFMXAV,FISCCP1_COSP,CLDTOT_ISCCP,MEANCLDALB_ISCCP,MEANPTOP_ISCCP,CLD_CAL,CLDTOT_CAL,CLDLOW_CAL,CLDMED_CAL,CLDHGH_CAL" | ||
| # atm 2D variables | ||
| cmip_var_list="pfull, phalf, tas, ts, psl, ps, sfcWind, huss, pr, prc, prsn, evspsbl, tauu, tauv, hfls, clt, rlds, rlus, rsds, rsus, hfss, cl, clw, cli, clivi, clwvi, prw, rldscs, rlut, rlutcs, rsdt, rsuscs, rsut, rsutcs, rtmt, abs550aer, od550aer, rsdscs, tasmax, tasmin, clisccp, cltisccp, albisccp, pctisccp, clcalipso, cltcalipso, cllcalipso, clmcalipso, clhcalipso" | ||
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| ncclimo -P eam -j 1 --map=${map_file} --start=$start --end=$end --ypf=$ypf --split -c $caseid -o ${native_dir} -O ${rgr_dir} -v ${raw_var_list} -i ${input_path} ${flags} | ||
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| # CMORIZE Atmosphere monthly variables: 2D and model level 3D variables (CLOUD,CLDICE,CLDLIQ) | ||
| e3sm_to_cmip -i ${rgr_dir} -o $result_dir -v ${cmip_var_list} -t $tables_path -u ${metadata_path} | ||
| # | ||
| # atm fixed variables | ||
| raw_var_list="area,PHIS,LANDFRAC" | ||
| cmip_var_list="area, sftlf, orog" | ||
| ncremap --map=${map_file} -v area,PHIS,LANDFRAC -I ${input_path} -O ${rgr_dir}/fixed_vars | ||
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| # CMORIZE Atmosphere fx variables | ||
| e3sm_to_cmip --realm fx -i ${rgr_dir}/fixed_vars -o $result_dir -v areacella, sftlf, orog -t ${tables_path} -u ${metadata_path} | ||
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| # atm 3D variables | ||
| flags='-7 --dfl_lvl=1 --no_cll_msr' | ||
| raw_var_list="Q,O3,T,U,V,Z3,RELHUM,OMEGA" | ||
| cmip_var_list="hur, hus, ta, ua, va, wap, zg, o3" | ||
| ncclimo -P eam -j 1 --map=${map_file} --start=$start --end=$end --ypf=$ypf --split -c $caseid -o ${native_dir} -O ${rgr_dir_vert} -v ${raw_var_list} -i ${input_path} ${flags} | ||
| for file in `ls ${rgr_dir_vert}` | ||
| do | ||
| ncks --rgr xtr_mth=mss_val --vrt_fl=${e2c_path}/grids/vrt_remap_plev19.nc ${rgr_dir_vert}/$file ${rgr_dir}/$file | ||
| done | ||
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| # Note --start=$start --end=$end would not work with ncremap | ||
| #ncremap -P eam -j 1 --xtr_mth=mss_val --vrt_fl=${e2c_path}/grids/vrt_remap_plev19.nc -O ${rgr_dir} -v ${raw_var_list} -I ${rgr_dir_vert} ${flags} | ||
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| # CMORIZE Atmosphere monthly plev variables | ||
| e3sm_to_cmip -i ${rgr_dir} -o $result_dir -v ${cmip_var_list} -t ${tables_path} -u ${metadata_path} | ||
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| # | ||
| # atm high freq daily h1+ | ||
| input_path=${model_data}/v2.eam.h1_input | ||
| flags='-7 --dfl_lvl=1 --no_cll_msr --clm_md=hfs' | ||
| raw_var_list="TREFHTMN,TREFHTMX,PRECT,TREFHT,FLUT,QREFHT" | ||
| cmip_var_list="tasmin, tasmax, tas, huss, rlut, pr" | ||
| rgr_dir=${result_dir}/rgr_day | ||
| native_dir=${result_dir}/native_day | ||
| ncclimo -P eam -j 1 --map=${map_file} --start=$start --end=$end --ypf=$ypf --split -c $caseid -o ${native_dir} -O ${rgr_dir} -v ${raw_var_list} -i ${input_path} ${flags} | ||
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| # CMORIZE Atmosphere daily variables | ||
| e3sm_to_cmip --freq day -i ${rgr_dir} -o $result_dir -v ${cmip_var_list} -t ${tables_path} -u ${metadata_path} | ||
| # | ||
| # atm high freq 3hrly h1+ | ||
| input_path=${model_data}/v2.eam.h4_input | ||
| flags='-7 --dfl_lvl=1 --no_cll_msr --clm_md=hfs' | ||
| raw_var_list="PRECT" | ||
| rgr_dir=${result_dir}/rgr_3hr | ||
| native_dir=${result_dir}/native_3hr | ||
| cmip_var_list="pr" | ||
| ncclimo -P eam -j 1 --map=${map_file} --start=$start --end=$end --ypf=$ypf --split -c $caseid -o ${native_dir} -O ${rgr_dir} -v ${raw_var_list} -i ${input_path} ${flags} | ||
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| # CMORIZE Atmosphere 3hrly variables | ||
| e3sm_to_cmip --freq 3hr -i ${rgr_dir} -o $result_dir -v ${cmip_var_list} -t --tables-path ${e2c_path}/cmor/cmip6-cmor-tables/Tables -u ${metadata_path} | ||
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| ## land monthly h0 | ||
| input_path=${model_data}/v2.elm_input/ | ||
| flags='-7 --dfl_lvl=1 --no_cll_msr' | ||
| raw_var_list="LAISHA,LAISUN,QINTR,QOVER,QRUNOFF,QSOIL,QVEGE,QVEGT,SOILICE,SOILLIQ,SOILWATER_10CM,TSA,TSOI,H2OSNO" | ||
| cmip_var_list="mrsos, mrso, mrfso, mrros, mrro, prveg, evspsblveg, evspsblsoi, tran, tsl, lai" | ||
| rgr_dir=${result_dir}/rgr_lnd | ||
| native_dir=${result_dir}/native_lnd | ||
| # Note either include the extra variable landfrac or specify the file that has landfrac for subgrid scale mode to work. | ||
| ncclimo -P elm -j 1 --var_xtr=landfrac --map=${map_file} --start=$start --end=$end --ypf=$ypf --split -c $caseid -o ${native_dir} -O ${rgr_dir} -v ${raw_var_list} -i ${input_path} ${flags} | ||
| # Alternative ncclimo invocation | ||
| #ncclimo -P elm -j 1 --map=${map_file} --start=$start --end=$end --ypf=$ypf --split -c $caseid -o ${native_dir} -O ${rgr_dir} -v ${raw_var_list} -i ${input_path} ${flags} --sgs_frc=${input_path}/v2.LR.historical_0101.elm.h0.1850-01.nc/landfrac | ||
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| #raw_var_list_elm_bgc="TOTLITC,CWDC,TOTPRODC,SOIL1C,SOIL2C,SOIL3C,^SOIL4C$,COL_FIRE_CLOSS,WOOD_HARVESTC,TOTVEGC,NBP,GPP,AR,HR" | ||
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| # CMORIZE Land Monthly variables | ||
| e3sm_to_cmip -i ${rgr_dir} -o $result_dir -v ${cmip_var_list} -t --tables-path ${e2c_path}/cmor/cmip6-cmor-tables/Tables -u ${metadata_path} | ||
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| # CMORIZE Sea-ice Monthly variables | ||
| # Note the input folder for mpas sea ice files requires: | ||
| # 1. Monthly mean history files: e.g.,v2.LR.historical_0101.mpassi.hist.am.timeSeriesStatsMonthly.1850-01-01.nc | ||
| # 2. A restart file for meshes: can use the mpaso restart e.g., v2.LR.historical_0101.mpaso.rst.1855-01-01_00000.nc | ||
| e3sm_to_cmip -s --realm SImon --var-list siconc, sitemptop, sisnmass, sitimefrac, siu, siv, sithick, sisnthick, simass --map ${e2c_path}/maps/map_EC30to60E2r2_to_cmip6_180x360_aave.20220301.nc --input-path ${model_data}/v2.mpassi_input/ --output-path ${result_dir} --user-metadata ${metadata_path} --tables-path ${e2c_path}/cmor/cmip6-cmor-tables/Tables | ||
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| # CMORIZE Ocean Monthly variables | ||
| # Note the input folder for mpas ocean files requires: | ||
| # 1. History files: e.g.,v2.LR.historical_0101.mpaso.hist.am.timeSeriesStatsMonthly.1850-01-01.nc | ||
| # 2. The namelist file for constants: mpaso_in | ||
| # masso, masscello, msftmz, pbo, and pso require 'config_density0' | ||
| # hfsifrazil requires 'config_density0' and 'config_frazil_heat_of_fusion' | ||
| # 3. A restart file for mesh: e.g., v2.LR.historical_0101.mpaso.rst.1855-01-01_00000.nc | ||
| # 4. A region masks file for MOC regions: EC30to60E2r2_mocBasinsAndTransects20210623.nc (Needed for variable msftmz: Ocean Meridional Overturning Mass Streamfunction) | ||
| e3sm_to_cmip -s --realm Omon --var-list areacello, fsitherm, hfds, masso, mlotst, sfdsi, sob, soga, sos, sosga, tauuo, tauvo, thetaoga, tob, tos, tosga, volo, wfo, zos, thetaoga, hfsifrazil, masscello, so, thetao, thkcello, uo, vo, volcello, wo zhalfo --map ${e2c_path}/maps/map_EC30to60E2r2_to_cmip6_180x360_aave.20220301.nc --input-path ${model_data}/v2.mpaso_input/ --output-path ${result_dir} --user-metadata ${metadata_path} --tables-path ${e2c_path}/cmor/cmip6-cmor-tables/Tables | ||
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| exit | ||
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