To use time-average mode for GC outputs

src/components/inversion_component/inversion.sh

@@ -29,7 +29,6 @@ setup_inversion() {
     cp ${InversionPath}/src/inversion_scripts/jacobian.py inversion/
     cp ${InversionPath}/src/inversion_scripts/operators/*.py inversion/operators/
     cp ${InversionPath}/src/inversion_scripts/make_gridded_posterior.py inversion/
-    cp ${InversionPath}/src/inversion_scripts/postproc_diags.py inversion/
     cp ${InversionPath}/src/inversion_scripts/setup_gc_cache.py inversion/
     cp ${InversionPath}/src/inversion_scripts/utils.py inversion/
     cp ${InversionPath}/src/inversion_scripts/merge_partial_k.py inversion/
@@ -84,11 +83,12 @@ run_inversion() {
     InvMem="${InversionMemory:-$RequestedMemory}"
     InvCPU="${InversionCPUs:-$RequestedCPUs}"
     InvTime="${InversionTime:-$RequestedTime}"
+    InvPartition="${InvSchedulerPartition:-$SchedulerPartition}"
     # Execute inversion driver script
     sbatch --mem $InvMem \
         -c $InvCPU \
         -t $InvTime \
-        -p $SchedulerPartition \
+        -p $InvPartition \
         -W run_inversion.sh $FirstSimSwitch
     wait
 

src/components/jacobian_component/jacobian.sh

@@ -171,7 +171,7 @@ create_simulation_dir() {
                 -e 's/#'\''LevelEdgeDiags/'\''LevelEdgeDiags/g' \
                 -e 's/LevelEdgeDiags.frequency:   00000100 000000/LevelEdgeDiags.frequency:   00000000 010000/g' \
                 -e 's/LevelEdgeDiags.duration:    00000100 000000/LevelEdgeDiags.duration:    00000001 000000/g' \
-                -e 's/LevelEdgeDiags.mode:        '\''time-averaged/LevelEdgeDiags.mode:        '\''instantaneous/g' HISTORY.rc
+                HISTORY.rc
         fi
     # For all other runs, just disable Restarts
     else

src/components/kalman_component/kalman.sh

@@ -151,12 +151,6 @@ run_period() {
 
     run_posterior
 
-    # Make a copy of the posterior output/diags files for postproc_diags.py
-    copydir="${PosteriorRunDir}/OutputDir"
-    cp ${copydir}/GEOSChem.SpeciesConc.${EndDate_i}_0000z.nc4 ${copydir}/GEOSChem.SpeciesConc.Copy.${EndDate_i}_0000z.nc4
-    cp ${copydir}/GEOSChem.LevelEdgeDiags.${EndDate_i}_0000z.nc4 ${copydir}/GEOSChem.LevelEdgeDiags.Copy.${EndDate_i}_0000z.nc4
-    echo "Made a copy of the final posterior SpeciesConc and LevelEdgeDiags files"
-
     # Make link to restart file from posterior run directory in prior, OH, and background simulation
     # and link to 1ppb restart file for perturbations
     python ${InversionPath}/src/components/jacobian_component/make_jacobian_icbc.py ${PosteriorRunDir}/Restarts/GEOSChem.Restart.${EndDate_i}_0000z.nc4 ${RunDirs}/jacobian_1ppb_ics_bcs/Restarts $EndDate_i

src/components/posterior_component/posterior.sh

@@ -70,7 +70,6 @@ setup_posterior() {
         sed -i -e 's/#'\''LevelEdgeDiags/'\''LevelEdgeDiags/g' \
             -e 's/LevelEdgeDiags.frequency:   00000100 000000/LevelEdgeDiags.frequency:   00000000 010000/g' \
             -e 's/LevelEdgeDiags.duration:    00000100 000000/LevelEdgeDiags.duration:    00000001 000000/g' \
-            -e 's/LevelEdgeDiags.mode:        '\''time-averaged/LevelEdgeDiags.mode:        '\''instantaneous/g' \
             -e 's/Restart.frequency:          '\''End'\''/Restart.frequency:          00000001 000000/g' \
             -e 's/Restart.duration:           '\''End'\''/Restart.duration:           00000001 000000/g' HISTORY.rc
     fi
@@ -186,25 +185,13 @@ run_posterior() {
     printf "\n=== DONE POSTERIOR SIMULATION ===\n"
     if "$KalmanMode"; then
         cd ${RunDirs}/kf_inversions/period${period_i}
-        if ((period_i == 1)); then
-            PrevDir="${RunDirs}/spinup_run"
-        else
-            PrevDir="${RunDirs}/posterior_run"
-        fi
     else
         StartDate_i=$StartDate
         EndDate_i=$EndDate
         cd ${RunDirs}/inversion
-        PrevDir="${RunDirs}/spinup_run"
     fi
 
-    # Fill missing data (first hour of simulation) in posterior output
     PosteriorRunDir="${RunDirs}/posterior_run"
-    printf "\n=== Calling postproc_diags.py for posterior ===\n"
-    python ${InversionPath}/src/inversion_scripts/postproc_diags.py $RunName $PosteriorRunDir $PrevDir $StartDate_i $Res
-    wait
-    printf "\n=== DONE -- postproc_diags.py ===\n"
-
     # Build directory for hourly posterior GEOS-Chem output data
     mkdir -p data_converted_posterior
     mkdir -p data_visualization_posterior

src/components/spinup_component/spinup.sh

@@ -44,13 +44,10 @@ setup_spinup() {
     sed -i -e "s|${StartDate}|${SpinupStart}|g" \
         -e "s|${EndDate}|${SpinupEnd}|g" geoschem_config.yml
 
-    # Turn on LevelEdgeDiags output
-    if "$HourlyCH4"; then
-        sed -i -e 's/#'\''LevelEdgeDiags/'\''LevelEdgeDiags/g' \
-            -e 's/LevelEdgeDiags.frequency:   00000100 000000/LevelEdgeDiags.frequency:   00000000 010000/g' \
-            -e 's/LevelEdgeDiags.duration:    00000100 000000/LevelEdgeDiags.duration:    00000001 000000/g' \
-            -e 's/LevelEdgeDiags.mode:        '\''time-averaged/LevelEdgeDiags.mode:        '\''instantaneous/g' HISTORY.rc
-    fi
+    # Disable diagnostic outputs from spinup (we only need restart file from spin up)
+    sed -i -e 's/'\''LevelEdgeDiags/#'\''LevelEdgeDiags/g' \
+        -e 's/'\''SpeciesConc/#'\''SpeciesConc/g' \
+        HISTORY.rc
 
     # Create run script from template
     sed -e "s:namename:${SpinupName}:g" \

src/components/template_component/template.sh

@@ -150,7 +150,7 @@ setup_template() {
     if "$HourlyCH4"; then
         sed -i -e 's/SpeciesConc.frequency:      00000100 000000/SpeciesConc.frequency:      00000000 010000/g' \
             -e 's/SpeciesConc.duration:       00000100 000000/SpeciesConc.duration:       00000001 000000/g' \
-            -e 's/SpeciesConc.mode:           '\''time-averaged/SpeciesConc.mode:           '\''instantaneous/g' HISTORY.rc
+            HISTORY.rc
     fi
 
     # Remove sample restart file

src/inversion_scripts/run_inversion.sh

@@ -47,7 +47,6 @@ nElements={STATE_VECTOR_ELEMENTS}
 nTracers={NUM_JACOBIAN_TRACERS}
 OutputPath={OUTPUT_PATH}
 Res={RES}
-SpinupDir="${OutputPath}/${RunName}/spinup_run"
 JacobianRunsDir="${OutputPath}/${RunName}/jacobian_runs"
 PriorRunDir="${JacobianRunsDir}/${RunName}_0000"
 BackgroundRunDir="${JacobianRunsDir}/${RunName}_background"
@@ -80,42 +79,6 @@ if [[ ! -f ${StateVectorFile} ]]; then
     exit 1
 fi
 
-#=======================================================================
-# Postprocess the SpeciesConc and LevelEdgeDiags files from GEOS-Chem
-#=======================================================================
-
-printf "Calling postproc_diags.py, FSS=$FirstSimSwitch\n"
-if "$FirstSimSwitch"; then
-    if [[ ! -d ${SpinupDir} ]]; then
-	printf "${SpinupDir} does not exist. Please fix SpinupDir or set FirstSimSwitch to False in run_inversion.sh.\n"
-	exit 1
-    fi
-    PrevDir=$SpinupDir
-else
-    PrevDir=$PosteriorRunDir
-    if [[ ! -d ${PosteriorRunDir} ]]; then
-	printf "${PosteriorRunDir} does not exist. Please fix PosteriorRunDir in run_inversion.sh.\n"
-	exit 1
-    fi
-fi
-printf "  - Hour 0 for ${StartDate} will be obtained from ${PrevDir}\n"
-
-if ! "$PrecomputedJacobian"; then
-
-    # Postprocess all the Jacobian simulations
-    python postproc_diags.py $RunName $JacobianRunsDir $PrevDir $StartDate $Res; wait
-
-else
-
-    # Only postprocess the Prior simulation
-    python postproc_diags.py $RunName $PriorRunDir $PrevDir $StartDate $Res; wait
-    if "$LognormalErrors"; then
-        # for lognormal errors we need to postprocess the background run too
-        python postproc_diags.py $RunName $BackgroundRunDir $PrevDir $StartDate $Res; wait
-    fi
-fi
-printf "DONE -- postproc_diags.py\n\n"
-
 #=======================================================================
 # Setup GC data directory in workdir
 #=======================================================================