From 77ce83b2236568f7d9801d119372d85ee46acdf1 Mon Sep 17 00:00:00 2001
From: Benjamin Hillman <bhillma@sandia.gov>
Date: Fri, 31 Oct 2025 08:54:25 -0700
Subject: [PATCH 1/3] Add draft ecomip run script and output yaml

---
 run_scripts/ecomip/eamxx_ecomip_output.yaml |  42 ++++++++
 run_scripts/ecomip/run.ecomip.sh            | 109 ++++++++++++++++++++
 2 files changed, 151 insertions(+)
 create mode 100644 run_scripts/ecomip/eamxx_ecomip_output.yaml
 create mode 100755 run_scripts/ecomip/run.ecomip.sh

diff --git a/run_scripts/ecomip/eamxx_ecomip_output.yaml b/run_scripts/ecomip/eamxx_ecomip_output.yaml
new file mode 100644
index 0000000..c4e12b2
--- /dev/null
+++ b/run_scripts/ecomip/eamxx_ecomip_output.yaml
@@ -0,0 +1,42 @@
+%YAML 1.2
+---
+averaging_type: average
+fields:
+  physics_pg2:
+    field_names:
+    # For Earthcare simulators
+    - z_mid
+    - p_int
+    - p_mid
+    - T_mid
+    - horiz_winds
+    - tracers
+    - cldfrac_tot
+    - precip_total_surf_mass_flux
+    - precip_liq_surf_mass_flux
+    - precip_ice_surf_mass_flux
+    - omega
+#   - convective_mass_flux # Conditional diagnostic
+    - surf_radiative_T #skin_temperature
+    - wind_speed_10m
+    - sea_level_pressure
+    - U_at_10m
+    - V_at_10m
+    - pseudo_density
+    # For diagnosis
+    - sw_flux_up_at_model_top
+    - sw_flux_dn_at_model_top
+    - lw_flux_up_at_model_top
+    - lw_flux_dn_at_model_top
+    - sw_clrsky_flux_up_at_model_top
+    - lw_clrsky_flux_up_at_model_top
+    - IceWaterPath
+    - LiqWaterPath
+    - VapWaterPath
+    #- precip_accumulated_over_30min
+filename_prefix: ecomip.eamxx.h
+output_control:
+  frequency: 1 #${HIST_N}
+  frequency_units: nhours #${HIST_OPTION}
+  skip_t0_output: 'false'
+...
diff --git a/run_scripts/ecomip/run.ecomip.sh b/run_scripts/ecomip/run.ecomip.sh
new file mode 100755
index 0000000..535b100
--- /dev/null
+++ b/run_scripts/ecomip/run.ecomip.sh
@@ -0,0 +1,109 @@
+#!/bin/bash
+set -e
+umask 022
+
+script_root=${PWD}
+branch="brhillman" #"decadal-production-run4" #"fix-nanobug-in-horiz-remap" #"decadal-production-run4" #"scorpio-update"
+code_root=${HOME}/codes/e3sm/branches/${branch}
+res=ne4pg2_ne4pg2 #ne1024pg2_ne1024pg2  #ne1024pg2_ne1024pg2 #ne1024pg2_ne1024pg2 #ne30pg2_EC30to60E2r2
+compset=F2010-SCREAMv1
+machine="pm-gpu" #chrysalis
+compiler="gnugpu" #intel
+project="e3sm"
+walltime="00:10:00"
+datestring="20250929"
+casename=${branch}.${res}.${compset}.${datestring}
+caseroot=${SCRATCH}/e3sm/cases/${casename}
+pecount=32x1
+
+mkdir -p `dirname ${caseroot}`
+${code_root}/cime/scripts/create_newcase \
+    --case=${caseroot} \
+    --res=${res} \
+    --compset=${compset} \
+    --machine=${machine} \
+    --compiler=${compiler} \
+    --pecount=${pecount} \
+    --project=${project} \
+    --walltime=${walltime}
+
+cd ${caseroot}
+
+# Extract input_data_dir for user edits to the namelist
+DIN_LOC_ROOT=`./xmlquery DIN_LOC_ROOT --value`
+
+# Change run length
+./xmlchange STOP_OPTION=ndays,STOP_N=3
+./xmlchange REST_OPTION=ndays,REST_N=3
+./xmlchange RESUBMIT=0
+./xmlchange RUN_STARTDATE="2024-08-01"
+
+# Run setup before configuring components
+./case.setup
+
+# Namelist options for EAMxx
+if [ "${res}" == "ne1024pg2_ne1024pg2" ]; then
+    ./atmchange initial_conditions::Filename="${DIN_LOC_ROOT}/atm/scream/init/screami_ne1024np4L128_era5-19941001-topoadjx6t_20240214.nc"
+elif [ "${res}" == "ne256pg2_ne256pg2" ]; then
+    ./atmchange initial_conditions::Filename="${DIN_LOC_ROOT}/atm/scream/init/screami_ne256np4L128_era5-19941001-topoadjx6t_20240123.nc"
+fi
+
+# Turn on cosp and set frequency
+./atmchange physics::atm_procs_list="mac_aero_mic,rrtmgp,cosp"
+./atmchange physics::cosp::cosp_frequency_units="hours"
+./atmchange physics::cosp::cosp_frequency=1
+
+output_yaml_files=(`ls ${script_root}/*.yaml`)
+for file in ${output_yaml_files[@]}; do
+    cp -v ${file} ./
+    ./atmchange output_yaml_files+=${file}
+done
+
+# Namelist options for ELM
+# Specify land initial condition and surface datasets
+if [ "${res}" == "ne1024pg2_ne1024pg2" ]; then
+cat << EOF >> user_nl_elm
+  ! Set input data paths
+  finidat = "${DIN_LOC_ROOT}/lnd/clm2/initdata/20231226.I2010CRUELM.ne1024pg2_ICOS10.elm.r.1994-10-01-00000.nc"
+EOF
+elif [ "${res}" == "ne256pg2_ne256pg2" ]; then
+cat << EOF >> user_nl_elm
+  ! Set input data paths
+  finidat = "${DIN_LOC_ROOT}/lnd/clm2/initdata/20240104.I2010CRUELM.ne256pg2.elm.r.1994-10-01-00000.nc"
+EOF
+elif [ "${res}" == "ne30pg2_EC30to60E2r2" ]; then
+cat << EOF >> user_nl_elm
+  finidat = "$DIN_LOC_ROOT/lnd/clm2/initdata/20210802.ICRUELM-1950.ne30pg2_EC30to60E2r2.elm.r.0051-01-01-00000.nc"
+EOF
+fi
+
+# Set MOSART initial condition
+if [ "${res}" == "ne1024pg2_ne1024pg2" ]; then
+cat << EOF >> user_nl_mosart
+  finidat_rtm = "${DIN_LOC_ROOT}/rof/mosart/initdata/20231226.I2010CRUELM.ne1024pg2_ICOS10.mosart.r.1994-10-01-00000.nc"
+EOF
+elif [ "${res}" == "ne256pg2_ne256pg2" ]; then
+cat << EOF >> user_nl_mosart
+  finidat_rtm = "${DIN_LOC_ROOT}/rof/mosart/initdata/20240104.I2010CRUELM.ne256pg2.mosart.r.1994-10-01-00000.nc"
+EOF
+fi
+
+# Point to new SST forcing
+# TODO: need new SST data for 2024
+#./xmlchange --file env_run.xml --id SSTICE_DATA_FILENAME --val "${DIN_LOC_ROOT}/atm/cam/sst/sst_ostia_3600x7200_19940930_20151231_c20240125.nc"
+#./xmlchange --file env_run.xml --id SSTICE_GRID_FILENAME --val "${DIN_LOC_ROOT}/ocn/docn7/domain.ocn.3600x7200.230522.nc"
+#./xmlchange --file env_run.xml --id SSTICE_YEAR_ALIGN --val 1994
+#./xmlchange --file env_run.xml --id SSTICE_YEAR_START --val 1994
+#./xmlchange --file env_run.xml --id SSTICE_YEAR_END --val 2015
+
+# Link to rundir
+ln -s `./xmlquery --value RUNDIR` run
+
+# Copy runscript to case dir
+cp ${script_root}/`basename $0` ./
+
+# Setup, build, run
+./case.setup
+./case.build
+./case.submit -a="--job-name=${casename} -t ${walltime} --mail-type=ALL --mail-user=bhillma@sandia.gov"
+echo "caseroot = ${caseroot}"

From bb054ea08f734b9418efa669e9ccb7be4c72111c Mon Sep 17 00:00:00 2001
From: Benjamin Hillman <bhillma@sandia.gov>
Date: Tue, 11 Nov 2025 15:30:54 -0800
Subject: [PATCH 2/3] Edits to ecomip script for ne1024

---
 run_scripts/ecomip/run.ecomip.sh | 25 ++++++++++++-------------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/run_scripts/ecomip/run.ecomip.sh b/run_scripts/ecomip/run.ecomip.sh
index 535b100..05f5b53 100755
--- a/run_scripts/ecomip/run.ecomip.sh
+++ b/run_scripts/ecomip/run.ecomip.sh
@@ -3,18 +3,18 @@ set -e
 umask 022
 
 script_root=${PWD}
-branch="brhillman" #"decadal-production-run4" #"fix-nanobug-in-horiz-remap" #"decadal-production-run4" #"scorpio-update"
+branch="master" #"decadal-production-run4" #"fix-nanobug-in-horiz-remap" #"decadal-production-run4" #"scorpio-update"
 code_root=${HOME}/codes/e3sm/branches/${branch}
-res=ne4pg2_ne4pg2 #ne1024pg2_ne1024pg2  #ne1024pg2_ne1024pg2 #ne1024pg2_ne1024pg2 #ne30pg2_EC30to60E2r2
+res=ne1024pg2_ne1024pg2 #ne30pg2_ne30pg2 #ne1024pg2_ne1024pg2  #ne1024pg2_ne1024pg2 #ne1024pg2_ne1024pg2 #ne30pg2_EC30to60E2r2
 compset=F2010-SCREAMv1
 machine="pm-gpu" #chrysalis
 compiler="gnugpu" #intel
 project="e3sm"
-walltime="00:10:00"
-datestring="20250929"
-casename=${branch}.${res}.${compset}.${datestring}
+walltime="01:00:00"
+datestring=20251111 #`date +'%Y%m%d'` #"20251031"
+casename=ecomip.${res}.${compset}.${datestring}
 caseroot=${SCRATCH}/e3sm/cases/${casename}
-pecount=32x1
+#pecount=32x1
 
 mkdir -p `dirname ${caseroot}`
 ${code_root}/cime/scripts/create_newcase \
@@ -23,7 +23,6 @@ ${code_root}/cime/scripts/create_newcase \
     --compset=${compset} \
     --machine=${machine} \
     --compiler=${compiler} \
-    --pecount=${pecount} \
     --project=${project} \
     --walltime=${walltime}
 
@@ -33,19 +32,19 @@ cd ${caseroot}
 DIN_LOC_ROOT=`./xmlquery DIN_LOC_ROOT --value`
 
 # Change run length
-./xmlchange STOP_OPTION=ndays,STOP_N=3
-./xmlchange REST_OPTION=ndays,REST_N=3
+./xmlchange STOP_OPTION=ndays,STOP_N=2
+./xmlchange REST_OPTION=ndays,REST_N=2
 ./xmlchange RESUBMIT=0
-./xmlchange RUN_STARTDATE="2024-08-01"
+./xmlchange RUN_STARTDATE="2024-09-02"
+#./xmlchange ATM_NCPL=48
 
 # Run setup before configuring components
 ./case.setup
 
 # Namelist options for EAMxx
 if [ "${res}" == "ne1024pg2_ne1024pg2" ]; then
-    ./atmchange initial_conditions::Filename="${DIN_LOC_ROOT}/atm/scream/init/screami_ne1024np4L128_era5-19941001-topoadjx6t_20240214.nc"
-elif [ "${res}" == "ne256pg2_ne256pg2" ]; then
-    ./atmchange initial_conditions::Filename="${DIN_LOC_ROOT}/atm/scream/init/screami_ne256np4L128_era5-19941001-topoadjx6t_20240123.nc"
+    #./atmchange initial_conditions::filename="${DIN_LOC_ROOT}/atm/scream/init/screami_ne1024np4L128_era5-19941001-topoadjx6t_20240214.nc"
+    ./atmchange initial_conditions::filename="/global/cfs/cdirs/e3sm/bhillma/ecomip/ecomip_ifs_od-0001_analysis20240902T0000Z_0.05deg_ml.ne1024np4.surface_adjusted.L128.temperature_adjusted.nc"
 fi
 
 # Turn on cosp and set frequency

From 302081f2fa80ad2f0e98249b1ca03a1103e3d528 Mon Sep 17 00:00:00 2001
From: Benjamin Hillman <bhillma@sandia.gov>
Date: Tue, 11 Nov 2025 15:31:38 -0800
Subject: [PATCH 3/3] Edits to ecomip yaml

---
 run_scripts/ecomip/eamxx_ecomip_output.yaml | 38 ++++++++++++++-------
 1 file changed, 25 insertions(+), 13 deletions(-)

diff --git a/run_scripts/ecomip/eamxx_ecomip_output.yaml b/run_scripts/ecomip/eamxx_ecomip_output.yaml
index c4e12b2..15ae907 100644
--- a/run_scripts/ecomip/eamxx_ecomip_output.yaml
+++ b/run_scripts/ecomip/eamxx_ecomip_output.yaml
@@ -1,42 +1,54 @@
 %YAML 1.2
 ---
-averaging_type: average
+averaging_type: instant
 fields:
   physics_pg2:
     field_names:
     # For Earthcare simulators
+    - ps  # For computing pressure from hybrid levels
     - z_mid
     - p_int
     - p_mid
     - T_mid
     - horiz_winds
     - tracers
+    - qv
+    - qc
+    - qi
+    - qr
+    - qm
+    - nc
+    - ni
+    - nr
+    - bm
     - cldfrac_tot
     - precip_total_surf_mass_flux
     - precip_liq_surf_mass_flux
     - precip_ice_surf_mass_flux
     - omega
-#   - convective_mass_flux # Conditional diagnostic
+    #- convective_mass_flux # Conditional diagnostic
     - surf_radiative_T #skin_temperature
     - wind_speed_10m
-    - sea_level_pressure
-    - U_at_10m
-    - V_at_10m
+    #- U_at_10m
+    #- V_at_10m
+    - SeaLevelPressure
+    - phis
     - pseudo_density
     # For diagnosis
-    - sw_flux_up_at_model_top
-    - sw_flux_dn_at_model_top
-    - lw_flux_up_at_model_top
-    - lw_flux_dn_at_model_top
-    - sw_clrsky_flux_up_at_model_top
-    - lw_clrsky_flux_up_at_model_top
+    - SW_flux_up_at_model_top
+    - SW_flux_dn_at_model_top
+    - LW_flux_up_at_model_top
+    - LW_flux_dn_at_model_top
+    - SW_clrsky_flux_up_at_model_top
+    - LW_clrsky_flux_up_at_model_top
     - IceWaterPath
     - LiqWaterPath
     - VapWaterPath
     #- precip_accumulated_over_30min
+    - diag_equiv_reflectivity
 filename_prefix: ecomip.eamxx.h
 output_control:
-  frequency: 1 #${HIST_N}
-  frequency_units: nhours #${HIST_OPTION}
+  frequency: 30 #${HIST_N}
+  frequency_units: nminutes #${HIST_OPTION}
   skip_t0_output: 'false'
 ...