From 339d3b13b44465499d114f44aca7a9b17258c81c Mon Sep 17 00:00:00 2001
From: minghangli-uni <24727729+minghangli-uni@users.noreply.github.com>
Date: Mon, 22 Sep 2025 09:06:34 +1000
Subject: [PATCH 1/3] Add a payu init script to auto-generate updated
 diag_table after payu setup / payu run

---
 .../init_scripts/run_make_diag_table.sh       | 55 +++++++++++++++++++
 1 file changed, 55 insertions(+)
 create mode 100755 payu_config/init_scripts/run_make_diag_table.sh

diff --git a/payu_config/init_scripts/run_make_diag_table.sh b/payu_config/init_scripts/run_make_diag_table.sh
new file mode 100755
index 0000000..a487aea
--- /dev/null
+++ b/payu_config/init_scripts/run_make_diag_table.sh
@@ -0,0 +1,55 @@
+#!/usr/bin/env bash
+set -e  # exit on error
+
+source /etc/profile.d/modules.sh
+module use /g/data/vk83/prerelease/modules && module load payu/dev
+
+# detect model
+if [ ! -f "config.yaml" ]; then
+    echo "Error: config.yaml not found!"
+    exit 1
+fi
+MODEL=$(grep '^model:' config.yaml | awk '{print $2}')
+echo "-- Detected model: $MODEL"
+
+case $MODEL in
+    access-om3)
+        DEST="diagnostic_profiles/source_yaml_files/make_diag_table"
+        ;;
+    access-om2)
+        DEST="tools/make_diag_table"
+        ;;
+    access | access-esm1.6)
+        DEST="ocean/diagnostic_profiles/source_yaml_files/make_diag_table"
+        ;;
+    *)
+        echo "Error: Unknown model '$MODEL' (expected access-om3 | access-om2 | access-esm1.6 | access)" >&2
+        exit 1
+        ;;
+esac
+
+BASE=$(dirname $DEST)
+
+mkdir -p $BASE
+
+if [ -d "$DEST" ]; then
+    echo "Directory $DEST already exists!" >&2
+
+else
+    git clone https://github.com/COSIMA/make_diag_table $DEST
+    scp $DEST/make_diag_table.py $BASE/
+
+    cd $BASE
+    echo "-- Cloned make_diag_table repo to $DEST"
+
+    if [ $MODEL = "access-om2" ]; then
+    python3 make_diag_table.py
+    else
+    cp -f diag_table_standard_source.yaml diag_table_source.yaml
+    echo "-- Copied diag_table_standard_source.yaml to diag_table_source.yaml"
+    python3 make_diag_table.py
+    cp -f diag_table ../diag_table_standard
+    fi
+
+    echo "-- diag_table is ready for use! (model: $MODEL)"
+fi
\ No newline at end of file

From 1c96cd19b82d60cd514bedaae0eef17a3e839fc9 Mon Sep 17 00:00:00 2001
From: minghangli-uni <24727729+minghangli-uni@users.noreply.github.com>
Date: Fri, 27 Feb 2026 11:23:45 +1100
Subject: [PATCH 2/3] Fix dest path for om3

---
 payu_config/init_scripts/run_make_diag_table.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/payu_config/init_scripts/run_make_diag_table.sh b/payu_config/init_scripts/run_make_diag_table.sh
index a487aea..c720250 100755
--- a/payu_config/init_scripts/run_make_diag_table.sh
+++ b/payu_config/init_scripts/run_make_diag_table.sh
@@ -14,7 +14,7 @@ echo "-- Detected model: $MODEL"
 
 case $MODEL in
     access-om3)
-        DEST="diagnostic_profiles/source_yaml_files/make_diag_table"
+        DEST="make_diag_table"
         ;;
     access-om2)
         DEST="tools/make_diag_table"
@@ -52,4 +52,4 @@ else
     fi
 
     echo "-- diag_table is ready for use! (model: $MODEL)"
-fi
\ No newline at end of file
+fi

From b2c9bb10a3f67cf19a9df70e1df79e8f9842947e Mon Sep 17 00:00:00 2001
From: minghangli-uni <24727729+minghangli-uni@users.noreply.github.com>
Date: Fri, 27 Feb 2026 11:25:36 +1100
Subject: [PATCH 3/3] Add  MODEL == 'access-om3' in addition to access-om2

---
 payu_config/init_scripts/run_make_diag_table.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/payu_config/init_scripts/run_make_diag_table.sh b/payu_config/init_scripts/run_make_diag_table.sh
index c720250..2bd7359 100755
--- a/payu_config/init_scripts/run_make_diag_table.sh
+++ b/payu_config/init_scripts/run_make_diag_table.sh
@@ -42,7 +42,7 @@ else
     cd $BASE
     echo "-- Cloned make_diag_table repo to $DEST"
 
-    if [ $MODEL = "access-om2" ]; then
+    if [[ $MODEL == "access-om2" || $MODEL == "access-om3" ]]; then
     python3 make_diag_table.py
     else
     cp -f diag_table_standard_source.yaml diag_table_source.yaml