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Copy pathrun.NOx.tests.mam5-chemUCI.mosaic.mam4.chrysalis.amip.2000.2014.t5.5days.sh
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run.NOx.tests.mam5-chemUCI.mosaic.mam4.chrysalis.amip.2000.2014.t5.5days.sh
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#!/bin/bash -fe
# E3SM Water Cycle v2 run_e3sm script template.
#
# Inspired by v1 run_e3sm script as well as SCREAM group simplified run script.
#
# Bash coding style inspired by:
# http://kfirlavi.herokuapp.com/blog/2012/11/14/defensive-bash-programming
# TO DO:
# - custom pelayout
main() {
# For debugging, uncomment libe below
#set -x
# --- Configuration flags ----
# Machine and project
readonly MACHINE=chrysalis
readonly PROJECT="e3sm"
# Simulation
readonly COMPSET="F20TR_chemUCI-Linozv3"
readonly RESOLUTION="ne30pg2_EC30to60E2r2"
readonly CASE_NAME="M4.UCI.M5-UCI-MOSAIC-MZT.NOx.t5.5days"
#readonly CASE_GROUP="v2.LR.chemUCI"
# Code and compilation
readonly CHECKOUT="chemUCI-MOSAIC-MAM5-08162022"
#readonly BRANCH="master" #420e251265928a4122a5eb5d4eab4ae8110f84f2 05/172022
readonly BRANCH="keziming/atm/chemUCI-MOSAIC-MAM5"
#readonly CHERRY=( "7e4d1c9fec40ce1cf2c272d671f5d9111fa4dea7" "a5b1d42d7cd24924d0dbda95e24ad8d4556d93f1" ) # PR4349
readonly DEBUG_COMPILE=false
# Run options
readonly MODEL_START_TYPE="hybrid" # 'initial', 'continue', 'branch', 'hybrid'
readonly START_DATE="2000-01-01"
# Additional options for 'branch' and 'hybrid'
readonly GET_REFCASE=TRUE
readonly RUN_REFDIR="/lcrc/group/e3sm/ac.mwu/archive/20220504.v2.LR.bi-grid.amip.chemMZT.chrysalis/archive/rest/2000-01-01-00000/"
readonly RUN_REFCASE="20220504.v2.LR.bi-grid.amip.chemMZT.chrysalis"
readonly RUN_REFDATE="2000-01-01" # same as MODEL_START_DATE for 'branch', can be different for 'hybrid'
# Set paths
readonly CODE_ROOT="${HOME}/E3SM_models/${CHECKOUT}"
#readonly CODE_ROOT="/qfs/people/tang338/E3SM_code/${CHECKOUT}"
readonly CASE_ROOT="/lcrc/group/e3sm/${USER}/E3SM_simulations/${CASE_NAME}"
# Sub-directories
readonly CASE_BUILD_DIR=${CASE_ROOT}/build
readonly CASE_ARCHIVE_DIR=${CASE_ROOT}/archive
# Define type of run
# short tests: 'XS_2x5_ndays', 'XS_1x10_ndays', 'S_1x10_ndays',
# 'M_1x10_ndays', 'M2_1x10_ndays', 'M80_1x10_ndays', 'L_1x10_ndays'
# or 'production' for full simulation
readonly run='production'
#readonly run='S_1x5_ndays'
if [ "${run}" != "production" ]; then
# Short test simulations
tmp=($(echo $run | tr "_" " "))
layout=${tmp[0]}
units=${tmp[2]}
resubmit=$(( ${tmp[1]%%x*} -1 ))
length=${tmp[1]##*x}
readonly CASE_SCRIPTS_DIR=${CASE_ROOT}/tests/${run}/case_scripts
readonly CASE_RUN_DIR=${CASE_ROOT}/tests/${run}/run
#readonly PELAYOUT=${layout}
readonly PELAYOUT="custom-10"
readonly WALLTIME="00:20:00"
readonly STOP_OPTION=${units}
readonly STOP_N=${length}
readonly REST_OPTION=${STOP_OPTION}
readonly REST_N=${STOP_N}
readonly RESUBMIT=${resubmit}
readonly DO_SHORT_TERM_ARCHIVING=false
else
# Production simulation
readonly CASE_SCRIPTS_DIR=${CASE_ROOT}/case_scripts
readonly CASE_RUN_DIR=${CASE_ROOT}/run
#readonly PELAYOUT="M"
readonly PELAYOUT="custom-30"
readonly WALLTIME="15:00:00"
readonly STOP_OPTION="ndays"
readonly STOP_N="5"
readonly REST_OPTION="ndays"
readonly REST_N="5"
readonly RESUBMIT="0"
readonly DO_SHORT_TERM_ARCHIVING=false
fi
# Coupler histfalse
readonly HIST_OPTION="nyears"
readonly HIST_N="5"
# Leave empty (unless you understand what it does)
readonly OLD_EXECUTABLE=""
# --- Toggle flags for what to do ----
do_fetch_code=false
do_create_newcase=true
do_case_setup=true
do_case_build=true
do_case_submit=true
# --- Now, do the work ---
# Make directories created by this script world-readable
umask 022
# Fetch code from Github
fetch_code
# Create case
create_newcase
# Custom PE layout
custom_pelayout
# Setup
case_setup
# Build
case_build
# Configure runtime options
runtime_options
# Copy script into case_script directory for provenance
copy_script
# Submit
case_submit
# All done
echo $'\n----- All done -----\n'
}
# =======================
# Custom user_nl settings
# =======================
user_nl() {
readonly new_emis_dir="/compyfs/wumi635/inputdata/cam/chem/emis/CMIP6_emissions_1750_2015_2deg_FINAL"
cat << EOF >> user_nl_eam
nhtfrq = 1,1,1,1,1,1,1
mfilt = 48,48,48,48,48,48,48
avgflag_pertape = 'A','I','I','I','I','I','I'
fincl1 = 'E90','N2OLNZ','NOYLNZ','H2OLNZ','CH4LNZ','MASS','AREA','TOZ','TROPC_P','TROPC_T','TROPC_Z','TROPS_P','TROPS_T','TROPS_Z','TROPT_P','TROPT_T','TROPT_Z','TROPW_P','TROPW_T','TROPW_Z','TROPH_P','TROPH_T','TROPH_Z','TROPE_P','TROPE_T','TROPE_Z',"O3","OH","HO2","H2O2","NO","NO2","NO3","N2O5","HNO3","HO2NO2","CO","CH2O","CH3O2","CH3OOH","DMS","SO2","ISOP","H2SO4","SOAG","so4_a1","pom_a1","soa_a1","bc_a1 ","dst_a1","ncl_a1","mom_a1","num_a1","so4_a2","soa_a2","ncl_a2","mom_a2","num_a2","dst_a3","ncl_a3","so4_a3","bc_a3","pom_a3","soa_a3","mom_a3","num_a3","pom_a4","bc_a4","mom_a4","num_a4","M_dens","H2O_vmr","CH4","NO_Lightning","NO_Aircraft","CO_Aircraft","CH4_vmr","prsd_ch4","C2H5OOH","CH3CHO",'LNO_COL_PROD','LNO_PROD','PAN','DV_O3','PS','PSDRY','lch4','r_lch4','M_dens','lco_h','r_lco_h','uci1','r_uci1'
fincl2 = 'E90','N2OLNZ','NOYLNZ','H2OLNZ','CH4LNZ','MASS','AREA','TOZ','TROPC_P','TROPC_T','TROPC_Z','TROPS_P','TROPS_T','TROPS_Z','TROPT_P','TROPT_T','TROPT_Z','TROPW_P','TROPW_T','TROPW_Z','TROPH_P','TROPH_T','TROPH_Z','TROPE_P','TROPE_T','TROPE_Z',"O3","OH","HO2","H2O2","NO","NO2","NO3","N2O5","HNO3","HO2NO2","CO","CH2O","CH3O2","CH3OOH","DMS","SO2","ISOP","H2SO4","SOAG","so4_a1","pom_a1","soa_a1","bc_a1 ","dst_a1","ncl_a1","mom_a1","num_a1","so4_a2","soa_a2","ncl_a2","mom_a2","num_a2","dst_a3","ncl_a3","so4_a3","bc_a3","pom_a3","soa_a3","mom_a3","num_a3","pom_a4","bc_a4","mom_a4","num_a4","M_dens","H2O_vmr","CH4","NO_Lightning","NO_Aircraft","CO_Aircraft","CH4_vmr","prsd_ch4","C2H5OOH","CH3CHO",'LNO_COL_PROD','LNO_PROD','PAN','DV_O3','PS','PSDRY','lch4','r_lch4','M_dens','lco_h','r_lco_h','uci1','r_uci1'
fincl3 = 'PS','T','Z3','M_dens','M_vmr','N2_dens','N2_vmr','O2_dens','O2_vmr','H2O_dens','H2O_vmr','H2_dens','H2_vmr','CH4_dens','CH4_vmr',
'CO',
'C2H6',
'C3H8',
'CH3COCH3',
'E90',
'N2OLNZ',
'NOYLNZ',
'CH4LNZ',
'H2OLNZ',
'DMS',
'SO2',
'H2SO4',
'SOAG',
'so4_a1',
'so4_a2',
'so4_a3',
'pom_a1',
'pom_a3',
'pom_a4',
'soa_a1',
'soa_a2',
'soa_a3',
'bc_a1',
'bc_a3',
'bc_a4',
'dst_a1',
'dst_a3',
'ncl_a1',
'ncl_a2',
'ncl_a3',
'mom_a1',
'mom_a2',
'mom_a3',
'mom_a4',
'num_a1',
'num_a2',
'num_a3',
'num_a4',
'O3',
'OH',
'HO2',
'H2O2',
'CH2O',
'CH3O2',
'CH3OOH',
'NO',
'NO2',
'NO3',
'N2O5',
'HNO3',
'HO2NO2',
'PAN',
'C2H5O2',
'C2H5OOH',
'CH3CHO',
'CH3CO3',
'C2H4',
'ROHO2',
'ISOP',
'ISOPO2',
'MVKMACR',
'MVKO2'
fincl4 = 'PS','H2O_vmr','T',
'uci1', 'uci2', 'uci3', 'lco_h','lco_ho2',
'lh2_ho2','lch4','lc2h6','lc3h8','lc2h4_oh',
'lc2h4_o3', 'lisop_o3','lisop_oh','lch2o','lo3_oh',
'po3_oh','lo3_ho2','lho2_oh','uci4','uci5',
'ph2o2','lh2o2','lo3_no','lno_ho2','lo3_no2',
'lno3_oh','lno3_no','lhno4','lhno3','uci6',
'lno2_oh','HO2NO2f','N2O5f','PANf','uci7',
'uci8', 'uci9','lch3o2_ho2','lch3o2_no','lch3o2',
'lch3ooh', 'lc2h5o2_no','lc2h5o2','lc2h5o2_ch3','lc2h5o2_ho2',
'lc2h5ooh_a', 'lc2h5ooh_b','lch3cho_oh','lch3cho_no3','lch3co3_no',
'lch3co3_ch3', 'lch3co3','lch3coch3_a','lch3coch3_b','lroho2_no',
'lroho2_ho2', 'lroho2_ch3o2','lisopo2_no','lisopo2_ho2','lisopo2_ch3',
'lmvkmacr_o3', 'lmvkmacr_oh','lmvko2_no','lmvko2_ho2','usr_e90',
'ldms_oh','usr_DMS_OH','usr_SO2_OH','ldms_no3'
fincl5 = 'PS','H2O_vmr','T',
'r_uci1', 'r_uci2', 'r_uci3', 'r_lco_h','r_lco_ho2',
'r_lh2_ho2','r_lch4','r_lc2h6','r_lc3h8','r_lc2h4_oh',
'r_lc2h4_o3', 'r_lisop_o3','r_lisop_oh','r_lch2o','r_lo3_oh',
'r_po3_oh','r_lo3_ho2','r_lho2_oh','r_uci4','r_uci5',
'r_ph2o2','r_lh2o2','r_lo3_no','r_lno_ho2','r_lo3_no2',
'r_lno3_oh','r_lno3_no','r_lhno4','r_lhno3','r_uci6',
'r_lno2_oh','r_HO2NO2f','r_N2O5f','r_PANf','r_uci7',
'r_uci8', 'r_uci9','r_lch3o2_ho2','r_lch3o2_no','r_lch3o2',
'r_lch3ooh', 'r_lc2h5o2_no','r_lc2h5o2','r_lc2h5o2_ch3','r_lc2h5o2_ho2',
'r_lc2h5ooh_a', 'r_lc2h5ooh_b','r_lch3cho_oh','r_lch3cho_no3','r_lch3co3_no',
'r_lch3co3_ch3', 'r_lch3co3','r_lch3coch3_a','r_lch3coch3_b','r_lroho2_no',
'r_lroho2_ho2', 'r_lroho2_ch3o2','r_lisopo2_no','r_lisopo2_ho2','r_lisopo2_ch3',
'r_lmvkmacr_o3', 'r_lmvkmacr_oh','r_lmvko2_no','r_lmvko2_ho2','r_e90',
'r_ldms_oh','r_DMS_OH','r_SO2_OH','r_ldms_no3'
fincl6 = 'jo1dU','jo2_b', 'jh2o2', 'jch2o_a', 'jch2o_b',
'jch3ooh', 'jc2h5ooh', 'jno2','jno3_a','jno3_b',
'jn2o5_a','jn2o5_b','jhno3','jho2no2_a','jho2no2_b',
'jch3cho','jpan','jacet','jmvk'
fincl7 = 'r_jo1dU', 'r_jo2_b', 'r_jh2o2', 'r_jch2o_a', 'r_jch2o_b',
'r_jch3ooh', 'r_jc2h5ooh', 'r_jno2', 'r_jno3_a', 'r_jno3_b',
'r_jn2o5_a','r_jn2o5_b','r_jhno3','r_jho2no2_a','r_jho2no2_b',
'r_jch3cho','r_jpan','r_jacet','r_jmvk'
tropopause_e90_thrd = 80.0e-9
!history_gaschmbudget = .true.
history_gaschmbudget_2D = .true.
history_gaschmbudget_2D_levels = .true.
history_UCIgaschmbudget_2D = .true.
history_UCIgaschmbudget_2D_levels = .true.
gaschmbudget_2D_L1_s = 1
gaschmbudget_2D_L1_e = 26
gaschmbudget_2D_L2_s = 27
gaschmbudget_2D_L2_e = 38
gaschmbudget_2D_L3_s = 39
gaschmbudget_2D_L3_e = 58
gaschmbudget_2D_L4_s = 59
gaschmbudget_2D_L4_e = 72
linoz_psc_t = 198.0
rad_climate = 'A:H2OLNZ:H2O', 'N:O2:O2', 'N:CO2:CO2',
'A:O3:O3', 'A:N2OLNZ:N2O', 'A:CH4LNZ:CH4',
'N:CFC11:CFC11', 'N:CFC12:CFC12',
'M:mam4_mode1:/lcrc/group/e3sm/data/inputdata/atm/cam/physprops/mam4_mode1_rrtmg_aeronetdust_c141106.nc',
'M:mam4_mode2:/lcrc/group/e3sm/data/inputdata/atm/cam/physprops/mam4_mode2_rrtmg_c130628.nc',
'M:mam4_mode3:/lcrc/group/e3sm/data/inputdata/atm/cam/physprops/mam4_mode3_rrtmg_aeronetdust_c141106.nc',
'M:mam4_mode4:/lcrc/group/e3sm/data/inputdata/atm/cam/physprops/mam4_mode4_rrtmg_c130628.nc'
sad_file = '/lcrc/group/e3sm/data/inputdata/atm/waccm/sulf/SAD_SULF_1849-2100_1.9x2.5_c090817.nc'
&chem_inparm
airpl_emis_file = ''
chlorine_loading_file = '/lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart/ub/Linoz_Chlorine_Loading_CMIP6_0003-2017_c20171114.nc'
chlorine_loading_type = 'SERIAL'
clim_soilw_file = '/lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart/dvel/clim_soilw.nc'
depvel_file = '/lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart/dvel/depvel_monthly.nc'
depvel_lnd_file = '/lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart/dvel/regrid_vegetation.nc'
drydep_srf_file = '/lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mam/atmsrf_ne30pg2_200129.nc'
exo_coldens_file = '/lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart/phot/exo_coldens.nc'
ext_frc_specifier = 'NO2 -> /lcrc/group/e3sm/ac.zke/Analysis/ncfile_modification/emissions-cmip6_NO2_aircraft_vertical_1750-2015_1.9x2.5_c20170608_1pct_kzm.nc',
'SO2 -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_so2_elev_1850-2014_c180205.nc',
'SOAG -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_soag_elev_1850-2014_c180205.nc',
'bc_a4 -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_bc_a4_elev_1850-2014_c180205.nc',
'num_a1 -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_num_a1_elev_1850-2014_c180205.nc',
'num_a2 -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_num_a2_elev_1850-2014_c180205.nc',
'num_a4 -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_num_a4_elev_1850-2014_c180205.nc',
'pom_a4 -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_pom_a4_elev_1850-2014_c180205.nc',
'so4_a1 -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_so4_a1_elev_1850-2014_c180205.nc',
'so4_a2 -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_so4_a2_elev_1850-2014_c180205.nc'
ext_frc_type = 'INTERP_MISSING_MONTHS'
fstrat_efold_list = 'CH2O', 'CH3O2', 'CH3OOH', 'PAN', 'CO', 'C2H6', 'C3H8', 'C2H4', 'ROHO2', 'CH3COCH3',
'C2H5O2', 'C2H5OOH', 'CH3CHO', 'CH3CO3', 'ISOP', 'ISOPO2', 'MVKMACR', 'MVKO2'
fstrat_file = '/lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart/ub/ubvals_b40.20th.track1_1996-2005_c110315.nc'
fstrat_list = ''
linoz_data_file = 'linv3_1849-2015_2010JPL_cmip6_historical_10deg_58km_c20210625.nc'
linoz_data_path = '/lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart/ub'
linoz_data_type = 'INTERP_MISSING_MONTHS'
o2_xsect_file = '/lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart/phot/o2src.nc'
rsf_file = '/lcrc/group/e3sm/data/inputdata/atm/waccm/phot/RSF_GT200nm_v3.0_c080811.nc'
sad_file = '/lcrc/group/e3sm/data/inputdata/atm/waccm/sulf/SAD_SULF_1849-2100_1.9x2.5_c090817.nc'
sad_type = 'SERIAL'
season_wes_file = '/lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart/dvel/season_wes.nc'
solar_parms_file = '/lcrc/group/e3sm/data/inputdata/atm/waccm/phot/wasolar_ave.nc'
srf_emis_specifier = 'C2H4 -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/chem_gases/2degrees/emissions-cmip6_e3sm_C2H4_surface_1850-2014_1.9x2.5_c20210323.nc',
'C2H6 -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/chem_gases/2degrees/emissions-cmip6_e3sm_C2H6_surface_1850-2014_1.9x2.5_c20210323.nc',
'C3H8 -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/chem_gases/2degrees/emissions-cmip6_e3sm_C3H8_surface_1850-2014_1.9x2.5_c20210323.nc',
'CH2O -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/chem_gases/2degrees/emissions-cmip6_e3sm_CH2O_surface_1850-2014_1.9x2.5_c20210323.nc',
'CH3CHO -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/chem_gases/2degrees/emissions-cmip6_e3sm_CH3CHO_surface_1850-2014_1.9x2.5_c20210323.nc',
'CH3COCH3 -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/chem_gases/2degrees/emissions-cmip6_e3sm_CH3COCH3_surface_1850-2014_1.9x2.5_c20210323.nc',
'CO -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/chem_gases/2degrees/emissions-cmip6_e3sm_CO_surface_1850-2014_1.9x2.5_c20210323.nc',
'DMS -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/DMSflux.1850-2100.1deg_latlon_conserv.POPmonthlyClimFromACES4BGC_c20160727.nc',
'E90 -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/chem_gases/2degrees/emissions_E90_surface_1750-2015_1.9x2.5_c20210408.nc',
'ISOP -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/chem_gases/2degrees/emissions-cmip6_e3sm_ISOP_surface_1850-2014_1.9x2.5_c20210323.nc',
'NO -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/chem_gases/2degrees/emissions-cmip6_e3sm_NO_surface_1850-2014_1.9x2.5_c20220425.nc',
'SO2 -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_so2_surf_1850-2014_c180205.nc',
'bc_a4 -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_bc_a4_surf_1850-2014_c180205.nc',
'num_a1 -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_num_a1_surf_1850-2014_c180205.nc',
'num_a2 -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_num_a2_surf_1850-2014_c180205.nc',
'num_a4 -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_num_a4_surf_1850-2014_c180205.nc',
'pom_a4 -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_pom_a4_surf_1850-2014_c180205.nc',
'so4_a1 -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_so4_a1_surf_1850-2014_c180205.nc',
'so4_a2 -> /lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_so4_a2_surf_1850-2014_c180205.nc'
srf_emis_type = 'INTERP_MISSING_MONTHS'
sulf_file = '/lcrc/group/e3sm/data/inputdata/atm/waccm/sulf/sulfate.ar5_camchem_c130304.nc'
tracer_cnst_cycle_yr = 1995
tracer_cnst_datapath = '/lcrc/group/e3sm/data/inputdata/atm/cam/chem/methane'
tracer_cnst_file = 'ch4_oxid_1.9x2.5_L26_1990-1999clim.c090804.nc'
tracer_cnst_filelist = ''
tracer_cnst_specifier = 'CH4'
tracer_cnst_type = 'CYCLICAL'
tuv_xsect_file = '/lcrc/group/e3sm/data/inputdata/atm/cam/chem/trop_mozart/phot/tuv_xsect.nc'
xactive_prates = .false.
xs_long_file = '/lcrc/group/e3sm/data/inputdata/atm/waccm/phot/temp_prs_GT200nm_JPL10_c130206.nc'
/
EOF
cat << EOF >> user_nl_elm
check_finidat_year_consistency = .false.
check_dynpft_consistency = .false.
fsurdat = "/lcrc/group/e3sm/data/inputdata/lnd/clm2/surfdata_map/surfdata_ne30pg2_simyr1850_c210402.nc"
EOF
}
# =====================================
# Customize MPAS stream files if needed
# =====================================
patch_mpas_streams() {
echo
}
# =====================================================
# Custom PE layout: custom-N where N is number of nodes
# =====================================================
custom_pelayout() {
if [[ ${PELAYOUT} == custom-* ]];
then
echo $'\n CUSTOMIZE PROCESSOR CONFIGURATION:'
# Number of cores per node (machine specific)
if [ "${MACHINE}" == "chrysalis" ]; then
ncore=64
elif [ "${MACHINE}" == "compy" ]; then
ncore=40
else
echo 'ERROR: MACHINE = '${MACHINE}' is not supported for custom PE layout.'
exit 400
fi
# Extract number of nodes
tmp=($(echo ${PELAYOUT} | tr "-" " "))
nnodes=${tmp[1]}
# Customize
pushd ${CASE_SCRIPTS_DIR}
./xmlchange NTASKS=$(( $nnodes * $ncore ))
./xmlchange NTHRDS=1
./xmlchange MAX_MPITASKS_PER_NODE=$ncore
./xmlchange MAX_TASKS_PER_NODE=$ncore
popd
fi
}
######################################################
### Most users won't need to change anything below ###
######################################################
#-----------------------------------------------------
fetch_code() {
if [ "${do_fetch_code,,}" != "true" ]; then
echo $'\n----- Skipping fetch_code -----\n'
return
fi
echo $'\n----- Starting fetch_code -----\n'
local path=${CODE_ROOT}
local repo=e3sm
echo "Cloning $repo repository branch $BRANCH under $path"
if [ -d "${path}" ]; then
echo "ERROR: Directory already exists. Not overwriting"
exit 20
fi
mkdir -p ${path}
pushd ${path}
# This will put repository, with all code
git clone [email protected]:E3SM-Project/${repo}.git .
# Setup git hooks
rm -rf .git/hooks
git clone [email protected]:E3SM-Project/E3SM-Hooks.git .git/hooks
git config commit.template .git/hooks/commit.template
# Bring in all submodule components
git submodule update --init --recursive
# Check out desired branch
git checkout ${BRANCH}
# Custom addition
if [ "${CHERRY}" != "" ]; then
echo ----- WARNING: adding git cherry-pick -----
for commit in "${CHERRY[@]}"
do
echo ${commit}
git cherry-pick ${commit}
done
echo -------------------------------------------
fi
# Bring in all submodule components
git submodule update --init --recursive
popd
}
#-----------------------------------------------------
create_newcase() {
if [ "${do_create_newcase,,}" != "true" ]; then
echo $'\n----- Skipping create_newcase -----\n'
return
fi
echo $'\n----- Starting create_newcase -----\n'
if [[ ${PELAYOUT} == custom-* ]];
then
layout="M" # temporary placeholder for create_newcase
else
layout=${PELAYOUT}
fi
if [[ -z "$CASE_GROUP" ]]; then
${CODE_ROOT}/cime/scripts/create_newcase \
--case ${CASE_NAME} \
--output-root ${CASE_ROOT} \
--script-root ${CASE_SCRIPTS_DIR} \
--handle-preexisting-dirs u \
--compset ${COMPSET} \
--res ${RESOLUTION} \
--machine ${MACHINE} \
--project ${PROJECT} \
--walltime ${WALLTIME} \
--pecount ${PELAYOUT}
else
${CODE_ROOT}/cime/scripts/create_newcase \
--case ${CASE_NAME} \
--case-group ${CASE_GROUP} \
--output-root ${CASE_ROOT} \
--script-root ${CASE_SCRIPTS_DIR} \
--handle-preexisting-dirs u \
--compset ${COMPSET} \
--res ${RESOLUTION} \
--machine ${MACHINE} \
--project ${PROJECT} \
--walltime ${WALLTIME} \
--pecount ${PELAYOUT}
fi
if [ $? != 0 ]; then
echo $'\nNote: if create_newcase failed because sub-directory already exists:'
echo $' * delete old case_script sub-directory'
echo $' * or set do_newcase=false\n'
exit 35
fi
}
#-----------------------------------------------------
case_setup() {
if [ "${do_case_setup,,}" != "true" ]; then
echo $'\n----- Skipping case_setup -----\n'
return
fi
echo $'\n----- Starting case_setup -----\n'
pushd ${CASE_SCRIPTS_DIR}
# Setup some CIME directories
./xmlchange EXEROOT=${CASE_BUILD_DIR}
./xmlchange RUNDIR=${CASE_RUN_DIR}
# Short term archiving
./xmlchange DOUT_S=${DO_SHORT_TERM_ARCHIVING^^}
./xmlchange DOUT_S_ROOT=${CASE_ARCHIVE_DIR}
# QT turn off cosp for testing
## Build with COSP, except for a data atmosphere (datm)
#if [ `./xmlquery --value COMP_ATM` == "datm" ]; then
# echo $'\nThe specified configuration uses a data atmosphere, so cannot activate COSP simulator\n'
#else
# echo $'\nConfiguring E3SM to use the COSP simulator\n'
# ./xmlchange --id CAM_CONFIG_OPTS --append --val='-cosp'
#fi
# Extracts input_data_dir in case it is needed for user edits to the namelist later
local input_data_dir=`./xmlquery DIN_LOC_ROOT --value`
# QT changing chemistry mechanism
#local usr_mech_infile="${CODE_ROOT}/components/eam/chem_proc/inputs/pp_chemUCI_linozv3_mam4_resus_mom_soag_tag.in"
#echo '[QT] Changing chemistry to :'${usr_mech_infile}
#./xmlchange --id CAM_CONFIG_OPTS --append --val='-usr_mech_infile '${usr_mech_infile}
if [ "${run}" != "production" ]; then
local CASE_ROOT_1="/lcrc/group/e3sm/${USER}/E3SM_simulations/${CASE_NAME}/tests/S_1x5_ndays/case_scripts/"
else
local CASE_ROOT_1="$CASE_ROOT/case_scripts/"
fi
echo $CASE_ROOT_1
#local usr_mech_infile="${CODE_ROOT}/components/eam/chem_proc/inputs/pp_chemUCI_linozv3_mam4_resus_mom_soag_tag_n2o5_to_HNO3.in"
#./xmlchange --id CAM_CONFIG_OPTS --append --val='-cosp -chem superfast_mam4_resus_mom_soag -rain_evap_to_coarse_aero -nlev 72 -usr_mech_infile '${usr_mech_infile}
./xmlchange --id CAM_CONFIG_OPTS --append --val='-cosp '
# Custom user_nl
user_nl
./xmlchange --id SSTICE_DATA_FILENAME --val='$DIN_LOC_ROOT/ocn/docn7/SSTDATA/sst_ice_CMIP6_DECK_E3SM_1x1_c20180213.nc'
cp /home/ac.zke/E3SM_codes/uci_nox_test/turn_off_NOYLNZ/lin_strat_chem.F90 ${CASE_SCRIPTS_DIR}/SourceMods/src.eam/
# Finally, run CIME case.setup
./case.setup --reset
popd
}
#-----------------------------------------------------
case_build() {
pushd ${CASE_SCRIPTS_DIR}
# do_case_build = false
if [ "${do_case_build,,}" != "true" ]; then
echo $'\n----- case_build -----\n'
if [ "${OLD_EXECUTABLE}" == "" ]; then
# Ues previously built executable, make sure it exists
if [ -x ${CASE_BUILD_DIR}/e3sm.exe ]; then
echo 'Skipping build because $do_case_build = '${do_case_build}
else
echo 'ERROR: $do_case_build = '${do_case_build}' but no executable exists for this case.'
exit 297
fi
else
# If absolute pathname exists and is executable, reuse pre-exiting executable
if [ -x ${OLD_EXECUTABLE} ]; then
echo 'Using $OLD_EXECUTABLE = '${OLD_EXECUTABLE}
cp -fp ${OLD_EXECUTABLE} ${CASE_BUILD_DIR}/
else
echo 'ERROR: $OLD_EXECUTABLE = '$OLD_EXECUTABLE' does not exist or is not an executable file.'
exit 297
fi
fi
echo 'WARNING: Setting BUILD_COMPLETE = TRUE. This is a little risky, but trusting the user.'
./xmlchange BUILD_COMPLETE=TRUE
# do_case_build = true
else
echo $'\n----- Starting case_build -----\n'
# Turn on debug compilation option if requested
if [ "${DEBUG_COMPILE^^}" == "TRUE" ]; then
./xmlchange DEBUG=${DEBUG_COMPILE^^}
fi
# Run CIME case.build
./case.build
fi
# Some user_nl settings won't be updated to *_in files under the run directory
# Call preview_namelists to make sure *_in and user_nl files are consistent.
echo $'\n----- Preview namelists -----\n'
./preview_namelists
popd
}
#-----------------------------------------------------
runtime_options() {
echo $'\n----- Starting runtime_options -----\n'
pushd ${CASE_SCRIPTS_DIR}
# Set simulation start date
./xmlchange RUN_STARTDATE=${START_DATE}
# Segment length
./xmlchange STOP_OPTION=${STOP_OPTION,,},STOP_N=${STOP_N}
# Restart frequency
./xmlchange REST_OPTION=${REST_OPTION,,},REST_N=${REST_N}
# Coupler history
./xmlchange HIST_OPTION=${HIST_OPTION,,},HIST_N=${HIST_N}
# Coupler budgets (always on)
./xmlchange BUDGETS=TRUE
# Set resubmissions
if (( RESUBMIT > 0 )); then
./xmlchange RESUBMIT=${RESUBMIT}
fi
# Run type
# Start from default of user-specified initial conditions
if [ "${MODEL_START_TYPE,,}" == "initial" ]; then
./xmlchange RUN_TYPE="startup"
./xmlchange CONTINUE_RUN="FALSE"
# Continue existing run
elif [ "${MODEL_START_TYPE,,}" == "continue" ]; then
./xmlchange CONTINUE_RUN="TRUE"
elif [ "${MODEL_START_TYPE,,}" == "branch" ] || [ "${MODEL_START_TYPE,,}" == "hybrid" ]; then
./xmlchange RUN_TYPE=${MODEL_START_TYPE,,}
./xmlchange GET_REFCASE=${GET_REFCASE}
./xmlchange RUN_REFDIR=${RUN_REFDIR}
./xmlchange RUN_REFCASE=${RUN_REFCASE}
./xmlchange RUN_REFDATE=${RUN_REFDATE}
echo 'Warning: $MODEL_START_TYPE = '${MODEL_START_TYPE}
echo '$RUN_REFDIR = '${RUN_REFDIR}
echo '$RUN_REFCASE = '${RUN_REFCASE}
echo '$RUN_REFDATE = '${START_DATE}
else
echo 'ERROR: $MODEL_START_TYPE = '${MODEL_START_TYPE}' is unrecognized. Exiting.'
exit 380
fi
# Patch mpas streams files
patch_mpas_streams
popd
}
#-----------------------------------------------------
case_submit() {
if [ "${do_case_submit,,}" != "true" ]; then
echo $'\n----- Skipping case_submit -----\n'
return
fi
echo $'\n----- Starting case_submit -----\n'
pushd ${CASE_SCRIPTS_DIR}
# Run CIME case.submit
./case.submit
popd
}
#-----------------------------------------------------
copy_script() {
echo $'\n----- Saving run script for provenance -----\n'
local script_provenance_dir=${CASE_SCRIPTS_DIR}/run_script_provenance
mkdir -p ${script_provenance_dir}
local this_script_name=`basename $0`
local script_provenance_name=${this_script_name}.`date +%Y%m%d-%H%M%S`
cp -vp ${this_script_name} ${script_provenance_dir}/${script_provenance_name}
}
#-----------------------------------------------------
# Silent versions of popd and pushd
pushd() {
command pushd "$@" > /dev/null
}
popd() {
command popd "$@" > /dev/null
}
# Now, actually run the script
#-----------------------------------------------------
main