From fe77d532e554922929a4ace517d4e6ebcc3f7d45 Mon Sep 17 00:00:00 2001
From: Teagan King <98482480+TeaganKing@users.noreply.github.com>
Date: Wed, 22 Jan 2025 11:05:01 -0700
Subject: [PATCH 1/2] Update template.cupid to include ilamb

---
 machines/template.cupid | 22 ++++++++++++++++++++--
 1 file changed, 20 insertions(+), 2 deletions(-)

diff --git a/machines/template.cupid b/machines/template.cupid
index 8b1b94e2fd..9776bcb414 100755
--- a/machines/template.cupid
+++ b/machines/template.cupid
@@ -18,6 +18,7 @@ conda activate cupid-infrastructure
 CUPID_EXAMPLE=key_metrics
 RUN_CUPID_ANALYSIS=TRUE
 RUN_CUPID_TIMESERIES=TRUE
+LAND_CASE_TYPE=BGC
 
 if [ "${RUN_CUPID_ANALYSIS}" == "TRUE" ]; then
   # 1. Generate CUPiD config file
@@ -31,15 +32,32 @@ if [ "${RUN_CUPID_ANALYSIS}" == "TRUE" ]; then
       --adf-template {{ SRCROOT }}/tools/CUPiD/externals/ADF/config_amwg_default_plots.yaml \
       --out-file adf_config.yml
 
-  # 3. Generate timeseries files and run ADF
+  # 3. Generate ILAMB config files
+  {{ srcroot }}/tools/CUPiD/helper_scripts/generate_ilamb_config_files.py \
+      --cesm-root {{ SRCROOT }} \
+      --cupid-config-loc ${PWD} \
+      --run-type ${LAND_CASE_TYPE}
+
+  # 4. Generate timeseries files
   if [ "${RUN_CUPID_TIMESERIES}" == "TRUE" ]; then
     {{ srcroot }}/tools/CUPiD/cupid/run_timeseries.py
   fi
+
+  # 5. Do any necessary regridding
+
+  # 6. Run ADF & ILAMB
   conda deactivate
   conda activate cupid-analysis
   {{ SRCROOT }}/tools/CUPiD/externals/ADF/run_adf_diag adf_config.yml
+  ilamb-run --config  {{ srcroot }}/tools/CUPiD/helper_scripts/ilamb_aux/ilamb_nohoff_final_CLM_BGC.cfg \
+      --build_dir {{ srcroot }}/tools/CUPiD/examples/external_diag_packages//ILAMB_output/ \
+      --df_errs {{ srcroot }}/tools/CUPiD/ilamb_aux/quantiles_Whittaker_cmip5v6.parquet \
+      --define_regions {{ srcroot }}/tools/CUPiD/ilamb_aux/DATA/regions/LandRegions.nc \
+      {{ srcroot }}/tools/CUPiD/ilamb_aux/DATA/regions/Whittaker.nc \
+      --regions global --model_setup {{ srcroot }}/tools/CUPiD/helper_scripts/model_setup.txt \
+      --filter .clm2.h0.
 
-  # 4. Run CUPiD and build webpage
+  # 7. Run CUPiD and build webpage
   conda deactivate
   conda activate cupid-infrastructure
   {{ srcroot }}/tools/CUPiD/cupid/run_diagnostics.py

From d1dff1a4c83d2aef1590da740708892d59eb49ab Mon Sep 17 00:00:00 2001
From: Teagan King <98482480+TeaganKing@users.noreply.github.com>
Date: Wed, 22 Jan 2025 11:11:01 -0700
Subject: [PATCH 2/2] Update template.cupid

---
 machines/template.cupid | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/machines/template.cupid b/machines/template.cupid
index 9776bcb414..76b2b9e290 100755
--- a/machines/template.cupid
+++ b/machines/template.cupid
@@ -49,7 +49,7 @@ if [ "${RUN_CUPID_ANALYSIS}" == "TRUE" ]; then
   conda deactivate
   conda activate cupid-analysis
   {{ SRCROOT }}/tools/CUPiD/externals/ADF/run_adf_diag adf_config.yml
-  ilamb-run --config  {{ srcroot }}/tools/CUPiD/helper_scripts/ilamb_aux/ilamb_nohoff_final_CLM_BGC.cfg \
+  ilamb-run --config  {{ srcroot }}/tools/CUPiD/helper_scripts/ilamb_aux/ilamb_nohoff_final_CLM_${LAND_CASE_TYPE}.cfg \
       --build_dir {{ srcroot }}/tools/CUPiD/examples/external_diag_packages//ILAMB_output/ \
       --df_errs {{ srcroot }}/tools/CUPiD/ilamb_aux/quantiles_Whittaker_cmip5v6.parquet \
       --define_regions {{ srcroot }}/tools/CUPiD/ilamb_aux/DATA/regions/LandRegions.nc \