run_e3sm_scm_DYNAMO_revelle.csh

#!/bin/csh

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#######  Script to run E3SM in SCM for
#######  DYNAMO_revelle 
#######  Dynamics of the Madden Julian Oscillation Revelle
#######  
#######  Script Author: P. Bogenschutz (bogenschutz1@llnl.gov)
#######  Forcing provided by: Shuaiqi Tang and Shaocheng Xie

#######################################################
#######  BEGIN USER DEFINED SETTINGS

  # Set the name of your case here
  setenv casename run_e3sm_scm_DYNAMO_revelle

  # 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 E3SM_codetag   
                                                         
  # Name of machine you are running on (i.e. cori, anvil, etc)                                                    
  setenv machine mach_name
  
  # Name of project to run on, if submitting to queue
  setenv projectname proj_name  

  # 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
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# Case specific information kept here
  set lat = 3.0 # latitude  
  set lon = 76.5 # 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 = .false. # Turn off precipitation
  set micro_nccons_val = 100.0D6 # cons_droplet value for liquid
  set micro_nicons_val = 0.0001D6 # cons_droplet value for ice
  set startdate = 2011-10-02 # Start date in IOP file
  set start_in_sec = 0 # start time in seconds in IOP file
  set stop_option = ndays 
  set stop_n = 90
  set iop_file = DYNAMO_revelle_iopfile_4scam.nc #IOP file name
# End Case specific stuff here

  # 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_gamma_coef = 0.32
 clubb_gamma_coefb = 0.32
 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
 clubb_C1 = 1.335
 raytau0 = 5.0D0
 prc_coef1 = 30500.0D0
 prc_exp = 3.19D0 
 prc_exp1 = -1.2D0
 se_ftype = 2
 clubb_C14 = 1.3D0
 relvar_fix = .true. 
 mg_prc_coeff_fix = .true.
 rrtmg_temp_fix = .true.
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