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run_e3sm_scm_ARM_shallow.csh
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#!/bin/csh
#######################################################################
#######################################################################
####### Script to run E3SM in SCM for
####### ARM_shallow
####### ARM GCSS shallow convection
#######
####### Script Author: P. Bogenschutz ([email protected])
#######################################################
####### BEGIN USER DEFINED SETTINGS
# Set the name of your case here
setenv casename run_e3sm_scm_ARM_shallow
# Set the case directory here
setenv casedirectory $CSCRATCH/SCM_runs
# Directory where code lives
setenv code_dir $HOME/E3SM_code
# Code tag name
setenv code_tag zhun
# Name of machine you are running on (i.e. cori, anvil, etc)
setenv machine cori-knl
# Name of project to run on, if submitting to queue
setenv projectname m2136
# Aerosol specification
# Options include:
# 1) cons_droplet (sets cloud liquid and ice concentration
# to a constant)
# 2) prescribed (uses climatologically prescribed aerosol
# concentration)
setenv init_aero_type prescribed
# Set the dynamical core
# 1) Select "Eulerian" IF you are running E3SMv1 release code
#
# 2) Select "SE" IF you are running code from E3SM master branch that
# is AFTER March 10,2019
setenv dycore SE
# WARNING: EULERIAN DYCORE SCM IS NO LONGER SUPPORTED. You are only safe
# to use Eulerian dycore SCM if you are using E3SMv1 release code. Else,
# user be(very)ware
# User enter any needed modules to load or use below
# EXAMPLE:
module load python#/2.7.5
####### END USER DEFINED SETTINGS
####### Likely POSSIBLE EXCEPTION (not limited to):
####### - If the user wants to add addition output, for example, the CAM
####### namelist (user_nl_cam) should be modified below to accomodate for this
###########################################################################
###########################################################################
###########################################################################
# Case specific information kept here
set lat = 36.6 # latitude
set lon = 262.5 # longitude
set do_iop_srf_prop = .true. # Use surface fluxes in IOP file?
set do_scm_relaxation = .false. # Relax case to observations?
set do_turnoff_swrad = .false. # Turn off SW calculation
set do_turnoff_lwrad = .false. # Turn off LW calculation
set do_turnoff_precip = .true. # Turn off precipitation
set micro_nccons_val = 50.0D6 # cons_droplet value for liquid
set micro_nicons_val = 0.0001D6 # cons_droplet value for ice
set startdate = 1997-06-21 # Start date in IOP file
set start_in_sec = 0 # start time in seconds in IOP file
set stop_option = nhours
set stop_n = 14
set iop_file = ARM_shallow_iopfile_4scam.nc #IOP file name
# End Case specific stuff here
set clubb_vars_zt_list = "'thlm', 'thvm', 'rtm', 'rcm', 'rvm', 'um', 'vm', 'um_ref','vm_ref','ug', 'vg', 'cloud_frac', 'cloud_cover', 'rcm_in_layer', 'rcm_in_cloud', 'p_in_Pa', 'exner', 'rho_ds_zt', 'thv_ds_zt', 'Lscale', 'Lscale_pert_1', 'Lscale_pert_2', 'T_in_K', 'rel_humidity', 'wp3', 'wpthlp2', 'wp2thlp', 'wprtp2', 'wp2rtp', 'Lscale_up', 'Lscale_down', 'tau_zt', 'Kh_zt', 'wp2thvp', 'wp2rcp', 'wprtpthlp', 'sigma_sqd_w_zt', 'rho', 'radht', 'radht_LW', 'radht_SW', 'Ncm', 'Nc_in_cloud', 'Nc_activated', 'snowslope', 'sed_rcm', 'rsat', 'rsati', 'diam', 'mass_ice_cryst', 'rcm_icedfs', 'u_T_cm', 'rtm_bt', 'rtm_ma', 'rtm_ta', 'rtm_mfl', 'rtm_tacl', 'rtm_cl', 'rtm_forcing', 'rtm_sdmp','rtm_mc', 'rtm_pd', 'rvm_mc', 'rcm_mc', 'rcm_sd_mg_morr', 'thlm_bt', 'thlm_ma', 'thlm_ta', 'thlm_mfl', 'thlm_tacl', 'thlm_cl', 'thlm_forcing', 'thlm_sdmp','thlm_mc', 'thlm_old', 'thlm_without_ta', 'thlm_mfl_min', 'thlm_mfl_max', 'thlm_enter_mfl', 'thlm_exit_mfl', 'rtm_old', 'rtm_without_ta', 'rtm_mfl_min', 'rtm_mfl_max', 'rtm_enter_mfl', 'rtm_exit_mfl', 'um_bt', 'um_ma', 'um_gf', 'um_cf', 'um_ta', 'um_f', 'um_sdmp', 'um_ndg', 'vm_bt', 'vm_ma', 'vm_gf', 'vm_cf', 'vm_ta', 'vm_f', 'vm_sdmp', 'vm_ndg', 'wp3_bt', 'wp3_ma', 'wp3_ta', 'wp3_tp', 'wp3_ac', 'wp3_bp1', 'wp3_bp2', 'wp3_pr1', 'wp3_pr2', 'wp3_dp1', 'wp3_cl', 'mixt_frac', 'w_1', 'w_2', 'varnce_w_1', 'varnce_w_2', 'thl_1', 'thl_2', 'varnce_thl_1', 'varnce_thl_2', 'rt_1', 'rt_2', 'varnce_rt_1', 'varnce_rt_2', 'rc_1', 'rc_2', 'rsatl_1', 'rsatl_2', 'cloud_frac_1', 'cloud_frac_2', 'a3_coef_zt', 'wp3_on_wp2_zt', 'chi_1', 'chi_2', 'stdev_chi_1', 'stdev_chi_2', 'stdev_eta_1', 'stdev_eta_2', 'covar_chi_eta_1', 'covar_chi_eta_2', 'corr_chi_eta_1', 'corr_chi_eta_2', 'corr_rt_thl_1', 'crt_1', 'crt_2', 'cthl_1', 'cthl_2', 'precip_frac', 'precip_frac_1', 'precip_frac_2', 'Ncnm', 'wp2_zt', 'thlp2_zt', 'wpthlp_zt', 'wprtp_zt', 'rtp2_zt', 'rtpthlp_zt', 'up2_zt', 'vp2_zt', 'upwp_zt', 'vpwp_zt', 'C11_Skw_fnc'"
set clubb_vars_zm_list = "'wp2', 'rtp2', 'thlp2', 'rtpthlp', 'wprtp', 'wpthlp', 'wp4', 'up2', 'vp2', 'wpthvp', 'rtpthvp', 'thlpthvp', 'tau_zm', 'Kh_zm', 'wprcp', 'wm_zm', 'thlprcp', 'rtprcp', 'rcp2', 'upwp', 'vpwp', 'rho_zm', 'sigma_sqd_w', 'Skw_velocity', 'gamma_Skw_fnc', 'C6rt_Skw_fnc', 'C6thl_Skw_fnc', 'C7_Skw_fnc', 'C1_Skw_fnc', 'a3_coef', 'wp3_on_wp2', 'rcm_zm', 'rtm_zm', 'thlm_zm', 'cloud_frac_zm', 'rho_ds_zm', 'thv_ds_zm', 'em', 'mean_w_up', 'mean_w_down', 'shear', 'wp3_zm', 'Frad', 'Frad_LW', 'Frad_SW', 'Frad_LW_up', 'Frad_SW_up', 'Frad_LW_down', 'Frad_SW_down', 'Fprec', 'Fcsed', 'wp2_bt', 'wp2_ma', 'wp2_ta', 'wp2_ac', 'wp2_bp', 'wp2_pr1', 'wp2_pr2', 'wp2_pr3', 'wp2_dp1', 'wp2_dp2', 'wp2_cl', 'wp2_pd', 'wp2_sf', 'vp2_bt', 'vp2_ma', 'vp2_ta', 'vp2_tp', 'vp2_dp1', 'vp2_dp2', 'vp2_pr1', 'vp2_pr2', 'vp2_cl', 'vp2_pd', 'vp2_sf', 'up2_bt', 'up2_ma', 'up2_ta', 'up2_tp', 'up2_dp1', 'up2_dp2', 'up2_pr1', 'up2_pr2', 'up2_cl', 'up2_pd', 'up2_sf', 'wprtp_bt', 'wprtp_ma', 'wprtp_ta', 'wprtp_tp', 'wprtp_ac', 'wprtp_bp', 'wprtp_pr1', 'wprtp_pr2', 'wprtp_pr3', 'wprtp_dp1', 'wprtp_mfl', 'wprtp_cl', 'wprtp_sicl', 'wprtp_pd', 'wprtp_forcing', 'wprtp_mc', 'wpthlp_bt', 'wpthlp_ma', 'wpthlp_ta', 'wpthlp_tp', 'wpthlp_ac', 'wpthlp_bp', 'wpthlp_pr1', 'wpthlp_pr2', 'wpthlp_pr3', 'wpthlp_dp1', 'wpthlp_mfl', 'wpthlp_cl', 'wpthlp_sicl', 'wpthlp_forcing', 'wpthlp_mc', 'rtp2_bt', 'rtp2_ma', 'rtp2_ta', 'rtp2_tp', 'rtp2_dp1', 'rtp2_dp2', 'rtp2_cl', 'rtp2_pd', 'rtp2_sf', 'rtp2_forcing', 'rtp2_mc', 'thlp2_bt', 'thlp2_ma', 'thlp2_ta', 'thlp2_tp', 'thlp2_dp1', 'thlp2_dp2', 'thlp2_cl', 'thlp2_pd', 'thlp2_sf', 'thlp2_forcing', 'thlp2_mc', 'rtpthlp_bt', 'rtpthlp_ma', 'rtpthlp_ta', 'rtpthlp_tp1', 'rtpthlp_tp2', 'rtpthlp_dp1', 'rtpthlp_dp2', 'rtpthlp_cl', 'rtpthlp_sf', 'rtpthlp_forcing', 'rtpthlp_mc', 'wpthlp_entermfl', 'wpthlp_exit_mfl', 'wprtp_enter_mfl', 'wprtp_exit_mfl', 'wpthlp_mfl_min', 'wpthlp_mfl_max', 'wprtp_mfl_min', 'wprtp_mfl_max', 'Richardson_num', 'shear_sqd'"
# Location of IOP file
set iop_path = atm/cam/scam/iop
# Prescribed aerosol file path and name
set presc_aero_path = atm/cam/chem/trop_mam/aero
set presc_aero_file = mam4_0.9x1.2_L72_2000clim_c170323.nc
set PROJECT=$projectname
set E3SMROOT=${code_dir}/${code_tag}
cd $E3SMROOT/cime/scripts
set compset=F_SCAM5
if ($dycore == Eulerian) then
set grid=T42_T42
endif
if ($dycore == SE) then
set grid=ne4_ne4
endif
set CASEID=$casename
set CASEDIR=${casedirectory}/$CASEID
set run_root_dir = $CASEDIR
set temp_case_scripts_dir = $run_root_dir/case_scripts
set case_scripts_dir = $run_root_dir/case_scripts
set case_build_dir = $run_root_dir/build
set case_run_dir = $run_root_dir/run
set walltime = '00:10:00'
# COSP, set to false unless user really wants it
setenv do_cosp false
# Create new case
./create_newcase -case $temp_case_scripts_dir -mach $machine -project $PROJECT -compset $compset -res $grid --walltime $walltime
cd $temp_case_scripts_dir
# SCM must run in serial mode
if ($dycore == Eulerian) then
./xmlchange --id MPILIB --val mpi-serial
endif
# Define executable and run directories
./xmlchange --id EXEROOT --val "${case_build_dir}"
./xmlchange --id RUNDIR --val "${case_run_dir}"
# Set to debug, only on certain machines
if ($machine =~ 'cori*') then
./xmlchange --id JOB_QUEUE --val 'debug'
endif
if ($machine == 'quartz' || $machine == 'syrah') then
./xmlchange --id JOB_QUEUE --val 'pdebug'
endif
# Get local input data directory path
set input_data_dir = `./xmlquery DIN_LOC_ROOT -value`
# need to use single thread
set npes = 1
foreach component ( ATM LND ICE OCN CPL GLC ROF WAV )
./xmlchange NTASKS_$component=$npes,NTHRDS_$component=1
end
# CAM configure options. By default set up with settings the same as E3SMv1
set CAM_CONFIG_OPTS="-phys cam5 -scam -nlev 72 -clubb_sgs"
if ($dycore == Eulerian) then
set CAM_CONFIG_OPTS="$CAM_CONFIG_OPTS -nospmd -nosmp"
endif
if ( $do_cosp == true ) then
set CAM_CONFIG_OPTS="$CAM_CONFIG_OPTS -cosp -verbose"
endif
# CAM configure options dependant on what aerosol specification is used
if ($init_aero_type == cons_droplet || $init_aero_type == none) then
set CAM_CONFIG_OPTS="$CAM_CONFIG_OPTS -chem linoz_mam4_resus_mom_soag -rain_evap_to_coarse_aero -bc_dep_to_snow_updates"
endif
if ($init_aero_type == prescribed || $init_aero_type == observed) then
set CAM_CONFIG_OPTS="$CAM_CONFIG_OPTS -chem none"
endif
./xmlchange CAM_CONFIG_OPTS="$CAM_CONFIG_OPTS"
set clubb_micro_steps = 8
# If SE dycore is used then we need to change the timestep
# to be consistent with ne30 timestep. Also change the
# cld_macmic_num_steps to be consistent
if ($dycore == SE) then
./xmlchange ATM_NCPL='48'
set clubb_micro_steps = 6
endif
# User enter CAM namelist options
# Add additional output here for example
cat <<EOF >> user_nl_cam
cld_macmic_num_steps = $clubb_micro_steps
cosp_lite = .true.
use_gw_front = .true.
iopfile = '$input_data_dir/$iop_path/$iop_file'
mfilt = 10000
nhtfrq = 1
scm_iop_srf_prop = $do_iop_srf_prop
scm_relaxation = $do_scm_relaxation
iradlw = 1
iradsw = 1
swrad_off = $do_turnoff_swrad
lwrad_off = $do_turnoff_lwrad
precip_off = $do_turnoff_precip
scmlat = $lat
scmlon = $lon
EOF
# CAM namelist options to match E3SMv1 settings
# Future implementations this block will not be needed
# Match settings in compset 2000_cam5_av1c-04p2
cat <<EOF >> user_nl_cam
use_hetfrz_classnuc = .true.
micro_mg_dcs_tdep = .true.
microp_aero_wsub_scheme = 1
sscav_tuning = .true.
convproc_do_aer = .true.
demott_ice_nuc = .true.
liqcf_fix = .true.
regen_fix = .true.
resus_fix = .false.
mam_amicphys_optaa = 1
fix_g1_err_ndrop = .true.
ssalt_tuning = .true.
use_rad_dt_cosz = .true.
ice_sed_ai = 500.0
cldfrc_dp1 = 0.045D0
clubb_ice_deep = 16.e-6
clubb_ice_sh = 50.e-6
clubb_liq_deep = 8.e-6
clubb_liq_sh = 10.e-6
clubb_C2rt = 1.75D0
zmconv_c0_lnd = 0.007
zmconv_c0_ocn = 0.007
zmconv_dmpdz = -0.7e-3
zmconv_ke = 1.5E-6
effgw_oro = 0.25
seasalt_emis_scale = 0.85
dust_emis_fact = 2.05D0
clubb_c1b = 1.335
clubb_C8 = 4.3
cldfrc2m_rhmaxi = 1.05D0
clubb_c_K10 = 0.3
effgw_beres = 0.4
do_tms = .false.
so4_sz_thresh_icenuc = 0.075e-6
n_so4_monolayers_pcage = 8.0D0
micro_mg_accre_enhan_fac = 1.5D0
zmconv_tiedke_add = 0.8D0
zmconv_cape_cin = 1
zmconv_mx_bot_lyr_adj = 2
taubgnd = 2.5D-3
raytau0 = 5.0D0
prc_coef1 = 30500.0D0
prc_exp = 3.19D0
prc_exp1 = -1.2D0
se_ftype = 2
relvar_fix = .true.
mg_prc_coeff_fix = .true.
rrtmg_temp_fix = .true.
! clubb_timestep = 150
clubb_C1 = 1.0D0
clubb_C1b = 1.0D0
clubb_C2rt = 2.0D0
clubb_C2thl = 2.0D0
clubb_C2rtthl = 2.0D0
clubb_C4 = 2.0D0
clubb_C5 = 0.3D0
clubb_C6rt = 2.0D0
clubb_C6rtb = 2.0D0
clubb_C6thlb = 2.0D0
clubb_beta = 1.0D0
clubb_gamma_coef = 0.25D0
clubb_gamma_coefb = 0.25D0
clubb_c_K2 = 0.025D0
clubb_nu2 = 1.0D0
clubb_C14 = 1.0D0
clubb_C15 = 0.0D0
clubb_C8 = 0.5D0
clubb_C11 = 0.4D0
clubb_C11b = 0.4D0
clubb_C_invrs_tau_bkgnd = 1.1
clubb_C_invrs_tau_sfc = 0.1
clubb_C_invrs_tau_shear = 0.02
clubb_C_invrs_tau_N2 = 0.4
clubb_C_invrs_tau_N2_wp2 = 0.1
clubb_C_invrs_tau_N2_xp2 = 0.05
clubb_C_invrs_tau_N2_wpxp= 0.0
clubb_C_invrs_tau_N2_clear_wp3 = 1.0
clubb_history = .true.
clubb_rad_history = .false.
history_budget = .true.
!clubb_do_icesuper = .true.
macrop_scheme = 'CLUBB_SGS'
eddy_scheme = 'CLUBB_SGS'
shallow_scheme = 'CLUBB_SGS'
!deep_scheme = 'off'
!subcol_scheme = 'SILHS'
!use_subcol_microp = .true.
!microp_uniform = .true.
history_amwg = .true.
clubb_do_adv = .false.
clubb_expldiff = .false.
clubb_rainevap_turb = .false.
clubb_cloudtop_cooling = .false.
clubb_vars_zt = $clubb_vars_zt_list
clubb_vars_zm = $clubb_vars_zm_list
fincl1 = $clubb_vars_zt_list,$clubb_vars_zm_list
relvar_fix = .true.
mg_prc_coeff_fix = .true.
rrtmg_temp_fix = .true.
microp_scheme = 'MG'
micro_mg_version = 2
micro_mg_sub_version = 0
micro_mg_num_steps = 1
micro_mg_dcs = 390e-6
micro_mg_berg_eff_factor = 1.0
cldfrc2m_rhmini = 0.8
cldfrc2m_rhmaxi = 1.05
EOF
# if constant droplet was selected then modify name list to reflect this
if ($init_aero_type == cons_droplet) then
cat <<EOF >> user_nl_cam
micro_do_nccons = .true.
micro_do_nicons = .true.
micro_nccons = $micro_nccons_val
micro_nicons = $micro_nicons_val
EOF
endif
# if prescribed or observed aerosols set then need to put in settings for prescribed aerosol model
if ($init_aero_type == prescribed ||$init_aero_type == observed) then
cat <<EOF >> user_nl_cam
use_hetfrz_classnuc = .false.
aerodep_flx_type = 'CYCLICAL'
aerodep_flx_datapath = '$input_data_dir/$presc_aero_path'
aerodep_flx_file = '$presc_aero_file'
aerodep_flx_cycle_yr = 01
prescribed_aero_type = 'CYCLICAL'
prescribed_aero_datapath='$input_data_dir/$presc_aero_path'
prescribed_aero_file='$presc_aero_file'
prescribed_aero_cycle_yr = 01
EOF
endif
# if observed aerosols then set flag
if ($init_aero_type == observed) then
cat <<EOF >> user_nl_cam
scm_observed_aero = .true.
EOF
endif
# avoid the monthly cice file from writing as this
# appears to be currently broken for SCM
cat <<EOF >> user_nl_cice
histfreq='y','x','x','x','x'
EOF
# Use CLM4.5. Currently need to point to the correct file for Eulerian
# dy-core (this will be fixed in upcoming PR)
set CLM_CONFIG_OPTS="-phys clm4_5"
./xmlchange CLM_CONFIG_OPTS="$CLM_CONFIG_OPTS"
# Modify the run start and duration parameters for the desired case
./xmlchange RUN_STARTDATE="$startdate",START_TOD="$start_in_sec",STOP_OPTION="$stop_option",STOP_N="$stop_n"
# Modify the latitude and longitude for the particular case
./xmlchange PTS_MODE="TRUE",PTS_LAT="$lat",PTS_LON="$lon"
./xmlchange MASK_GRID="USGS"
./case.setup
# Don't want to write restarts as this appears to be broken for
# CICE model in SCM. For now set this to a high value to avoid
./xmlchange PIO_TYPENAME="netcdf"
./xmlchange REST_N=30000
# Modify some parameters for CICE to make it SCM compatible
./xmlchange CICE_AUTO_DECOMP="FALSE"
./xmlchange CICE_DECOMPTYPE="blkrobin"
./xmlchange --id CICE_BLCKX --val 1
./xmlchange --id CICE_BLCKY --val 1
./xmlchange --id CICE_MXBLCKS --val 1
./xmlchange CICE_CONFIG_OPTS="-nodecomp -maxblocks 1 -nx 1 -ny 1"
# Build the case
./case.build
./case.submit
exit