From 101808d274ae41e32ab30d266918000488e0af50 Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Wed, 22 Nov 2023 15:58:48 +0000
Subject: [PATCH 01/13] Added TF ymls

---
 .../TerraFIRMA_overshoot_historical_debug.yml |  28 +++
 ...TerraFIRMA_overshoot_pi_stablilisation.yml |  90 ++++++++
 ...vershoot_pi_stablilisation_report_only.yml |  89 ++++++++
 input_yml/TerraFIRMA_overshoot_runs.yml       | 194 ++++++++++++++++++
 input_yml/TerraFIRMA_overshoot_runs_debug.yml |  67 ++++++
 .../TerraFIRMA_overshoot_runs_minimal.yml     | 120 +++++++++++
 6 files changed, 588 insertions(+)
 create mode 100644 input_yml/TerraFIRMA_overshoot_historical_debug.yml
 create mode 100644 input_yml/TerraFIRMA_overshoot_pi_stablilisation.yml
 create mode 100644 input_yml/TerraFIRMA_overshoot_pi_stablilisation_report_only.yml
 create mode 100644 input_yml/TerraFIRMA_overshoot_runs.yml
 create mode 100644 input_yml/TerraFIRMA_overshoot_runs_debug.yml
 create mode 100644 input_yml/TerraFIRMA_overshoot_runs_minimal.yml

diff --git a/input_yml/TerraFIRMA_overshoot_historical_debug.yml b/input_yml/TerraFIRMA_overshoot_historical_debug.yml
new file mode 100644
index 00000000..7822d563
--- /dev/null
+++ b/input_yml/TerraFIRMA_overshoot_historical_debug.yml
@@ -0,0 +1,28 @@
+---
+# GC5 N96 ORCA1 spinup analysis
+name: TerraFIRMA_overshoot_historical_debug
+
+# Run the single job analysis
+do_analysis_timeseries: True 
+
+# Download from mass:
+do_mass_download: False
+
+# master analysis suite
+master_suites: physics bgc #alkalinity physics kmf1
+
+clean: True
+
+jobs:
+    u-cy693:
+       description: ' static ice sheets, started from picontrol yr 2317'
+       colour: goldenrod
+       thickness: 1.7
+       linestyle: '-'
+       shifttime: 0.
+       suite: kmf physics bgc #alkalinity physics kmf
+
+
+
+
+
diff --git a/input_yml/TerraFIRMA_overshoot_pi_stablilisation.yml b/input_yml/TerraFIRMA_overshoot_pi_stablilisation.yml
new file mode 100644
index 00000000..99adfae3
--- /dev/null
+++ b/input_yml/TerraFIRMA_overshoot_pi_stablilisation.yml
@@ -0,0 +1,90 @@
+---
+# GC5 N96 ORCA1 spinup analysis
+name: TerraFIRMA_overshoot_pi_stabilization_2023
+
+# Run the single job analysis
+do_analysis_timeseries: True 
+
+# Download from mass:
+do_mass_download: False
+
+# master analysis suite
+master_suites: physics #bgc #alkalinity physics kmf1
+
+clean: True
+
+#           u-cp530: CO2 conc mode, interactive ice but fixed ice geometry (red)
+#           u-cs495: CO2 emission mode, interactive ice but fixed ice geometry (green) 
+#           u-cp345: CO2 conc mode, interactive ice and interactive (variable) ice geometry (blue)
+
+# Job ID's suites as named by Rose/Cylc
+# •     u-co094 - no alk added
+# •     u-cp800 - alk add at surface
+# •     u-cp799 - alk added at bathy - or 100m (if bathy deeper)
+# •     u-cn857 - alk added at bathy - or 200m (if bathy deeper)
+#
+jobs:
+#    u-by230:
+#       description: 'UKESM1.1 piControl (abridged)'
+#       colour: 'black'
+#       thickness: 0.6
+#       linestyle: '-'
+#       shifttime: -1000.
+#       timerange: [1900, 2000]
+#       suite: physics bgc #alkalinity physics
+
+#    u-cs568:
+#       description: 'TF overshoot piControl variant #1'
+#       colour: red  
+#       thickness: 1.7
+#       linestyle: '-'
+#       shifttime: 0.
+#       suite: physics bgc #alkalinity physics
+
+#    u-cp530: 
+#       description: 'TF overshoot piControl variant #4 conc mode, interactive ice but fixed ice geometry'
+#       colour: purple
+#       thickness: 1.7
+#       linestyle: '-'
+#       shifttime: 0.
+#       suite: physics bgc #alkalinity physics
+
+
+
+#   u-cp345:
+#      description: 'TF overshoot piControl variant #2 CO2 conc mode, interactive ice and interactive (variable) ice geometry'
+#      colour: blue
+#      thickness: 1.7
+#      linestyle: '-'
+#      shifttime: 0.
+#      suite: physics bgc #alkalinity physics
+
+
+    u-cs495:
+       description: 'TF overshoot piControl variant #3 CO2 emission mode, interactive ice but fixed ice geometry'
+       colour: green
+       thickness: 1.7
+       linestyle: '-'
+       shifttime: 0.
+       suite: physics  bgc #alkalinity physics kmf
+
+    u-cs772:
+       description: 'TF overshoot ramp-up +10GtC/yr'
+       colour: blue 
+       thickness: 1.7
+       linestyle: '-'
+       shifttime: 0.
+       suite: physics  #bgc #alkalinity physics kmf
+
+    u-cv996:
+       description: 'TF overshoot 2C stabilization'
+       colour: purple
+       thickness: 1.7
+       linestyle: '-'
+       shifttime: 0.
+       suite: physics  #bgc #alkalinity physics kmf
+
+
+
+
+
diff --git a/input_yml/TerraFIRMA_overshoot_pi_stablilisation_report_only.yml b/input_yml/TerraFIRMA_overshoot_pi_stablilisation_report_only.yml
new file mode 100644
index 00000000..8e63d822
--- /dev/null
+++ b/input_yml/TerraFIRMA_overshoot_pi_stablilisation_report_only.yml
@@ -0,0 +1,89 @@
+---
+# GC5 N96 ORCA1 spinup analysis
+name: TerraFIRMA_overshoot_pi_stabilization_2023
+
+# Run the single job analysis
+do_analysis_timeseries: False
+
+# Download from mass:
+do_mass_download: False
+
+# master analysis suite
+master_suites: physics #bgc #alkalinity physics kmf1
+
+clean: True
+
+#           u-cp530: CO2 conc mode, interactive ice but fixed ice geometry (red)
+#           u-cs495: CO2 emission mode, interactive ice but fixed ice geometry (green) 
+#           u-cp345: CO2 conc mode, interactive ice and interactive (variable) ice geometry (blue)
+
+# Job ID's suites as named by Rose/Cylc
+# •     u-co094 - no alk added
+# •     u-cp800 - alk add at surface
+# •     u-cp799 - alk added at bathy - or 100m (if bathy deeper)
+# •     u-cn857 - alk added at bathy - or 200m (if bathy deeper)
+#
+jobs:
+#    u-by230:
+#       description: 'UKESM1.1 piControl (abridged)'
+#       colour: 'black'
+#       thickness: 0.6
+#       linestyle: '-'
+#       shifttime: -1000.
+#       timerange: [1900, 2000]
+#       suite: physics bgc #alkalinity physics
+
+#    u-cs568:
+#       description: 'TF overshoot piControl variant #1'
+#       colour: red  
+#       thickness: 1.7
+#       linestyle: '-'
+#       shifttime: 0.
+#       suite: physics bgc #alkalinity physics
+
+#    u-cp530: 
+#       description: 'TF overshoot piControl variant #4 conc mode, interactive ice but fixed ice geometry'
+#       colour: purple
+#       thickness: 1.7
+#       linestyle: '-'
+#       shifttime: 0.
+#       suite: physics bgc #alkalinity physics
+
+
+
+#   u-cp345:
+#      description: 'TF overshoot piControl variant #2 CO2 conc mode, interactive ice and interactive (variable) ice geometry'
+#      colour: blue
+#      thickness: 1.7
+#      linestyle: '-'
+#      shifttime: 0.
+#      suite: physics bgc #alkalinity physics
+
+    u-cs495:
+       description: 'TF overshoot piControl variant #3 CO2 emission mode, interactive ice but fixed ice geometry'
+       colour: green
+       thickness: 1.7
+       linestyle: '-'
+       shifttime: 0.
+       suite: physics  bgc #alkalinity physics kmf
+
+    u-cs772:
+       description: 'TF overshoot piControl variant #?'
+       colour: blue 
+       thickness: 1.7
+       linestyle: '-'
+       shifttime: 0.
+       suite: physics  #bgc #alkalinity physics kmf
+
+    u-cv996:
+       description: 'TF overshoot piControl variant #?'
+       colour: purple
+       thickness: 1.7
+       linestyle: '-'
+       shifttime: 0.
+       suite: physics  #bgc #alkalinity physics kmf
+
+
+
+
+
diff --git a/input_yml/TerraFIRMA_overshoot_runs.yml b/input_yml/TerraFIRMA_overshoot_runs.yml
new file mode 100644
index 00000000..ca5154d5
--- /dev/null
+++ b/input_yml/TerraFIRMA_overshoot_runs.yml
@@ -0,0 +1,194 @@
+---
+# GC5 N96 ORCA1 spinup analysis
+name: TerraFIRMA_overshoot_runs
+
+# Run the single job analysis
+do_analysis_timeseries: True  
+
+# Download from mass:
+do_mass_download: False
+
+# master analysis suite
+master_suites: physics bgc kmf #alkalinity physics kmf1
+
+# Run without strick check (if True, breaks if job has no years.)
+strict_file_check: False
+
+clean: True
+
+jobs:
+    u-cs495:
+       description: 'PI-Control'
+       label: 'PIcontrol'
+       colour: 'blue' 
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: -100.
+       timerange: [1850, 2300]
+       suite: kmf physics bgc #alkalinity physics
+         
+ 
+    u-cx209:
+       description: 'E-mode free ice RAMP UP 8GtC/yr #1'
+       label: 'Ramp-up #1'
+       colour: 'black'
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+
+    u-cw988:
+       description: 'E-mode free ice RAMP UP 8GtC/yr #2'
+       label: 'Ramp-up #2'
+       colour: 'black'
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+           
+    u-cw989:
+       description: 'E-mode free ice RAMP UP 8GtC/yr #3'
+       label: 'Ramp-up #3'
+       colour: 'black'
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+
+    u-cw990:
+       description: 'E-mode free ice RAMP UP 8GtC/yr #4'
+       label: 'Ramp-up #4'
+       colour: 'black'
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+
+    # 1.5k Stabilisation
+    u-cy837:
+       description: '1.5K Stabilisation from u-cx209 (#1)'
+       label: '1.5K Stable #1'
+       colour: 'lawngreen'
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics   
+    u-cz834:
+       description: '1.5K Stabilisation from u-cw988 (#2)'
+       label: '1.5K Stable #2'
+       colour: 'lawngreen'
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+    u-da087:
+       description: '1.5K Stabilisation from u-cw989 (#3)'
+       label: '1.5K Stable #3'
+       colour: 'lawngreen' 
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+           
+    # 2k Stabilisation
+    u-cy838:
+       description: '2.0K Stabilisation from u-cx209 (#1)'
+       label: '2K Stable #1'
+       colour: 'goldenrod'
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics   
+
+    u-cz855:
+       description: '2.0K Stabilisation from cw988 (#2)'
+       label: '2K Stable #2'
+       colour: 'goldenrod'
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+
+           
+    # 2.5k Stabilisation
+    u-cz374:
+       description: '2.5K Stabilisation from u-cx209 (#1)'
+       label: '2.5K Stable #1'
+       colour: 'orange'
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics   
+    u-cz859:
+       description: '2.5K Stabilisation from cw988 (#2)'
+       label: '2.5K Stable #2'
+       colour: 'orange' 
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+
+
+    # other Stabilisations
+    u-cz375:
+       description: '3.0K Stabilisation from u-cx209 (#1)'
+       label: '3K Stable #1'
+       colour: 'red'     #
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics          
+    u-cz376:
+       description: '4.0K Stabilisation from u-cx209 (#1)'
+       label: '4K Stable #1'
+       colour: 'sienna'
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics  
+    u-cz377:
+       description: '5.0K Stabilisation from u-cx209 (#1)'
+       label: '5K Stable #1'
+       colour: 'maroon'
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics 
+           
+    # Ramp downs
+    u-cz944:
+       description: 'Ramp down from cy838 (- 2.0K Stabilisation from u-cx209) (#1)'
+       label: '2K Rampdown #1'
+       colour: 'goldenrod'
+       thickness: 1.2
+       linestyle: ':' 
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics   
+
+    u-da697:
+       description: '1.5K Rampdown from u-cx209 (#1)'
+       label: '1.5K Rampdown #1'
+       colour: 'lawngreen'
+       thickness: 1.2
+       linestyle: ':'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+
+
+
diff --git a/input_yml/TerraFIRMA_overshoot_runs_debug.yml b/input_yml/TerraFIRMA_overshoot_runs_debug.yml
new file mode 100644
index 00000000..68afbd06
--- /dev/null
+++ b/input_yml/TerraFIRMA_overshoot_runs_debug.yml
@@ -0,0 +1,67 @@
+---
+# GC5 N96 ORCA1 spinup analysis
+name: TerraFIRMA_overshoot_runs
+
+# Run the single job analysis
+do_analysis_timeseries: False 
+
+# Download from mass:
+do_mass_download: False
+
+# master analysis suite
+master_suites: physics bgc #alkalinity physics kmf1
+
+# Run without strick check (if True, breaks if job has no years.)
+strict_file_check: False
+
+clean: True
+
+jobs:
+    u-cx209:
+       description: 'E-mode free ice RAMP UP 8GtC/yr #1'
+       colour: 'red'
+       thickness: 0.6
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+
+    u-cw988:
+       description: 'E-mode free ice RAMP UP 8GtC/yr #2'
+       colour: '#0000FF'
+       thickness: 0.6
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+           
+    u-cw989:
+       description: 'E-mode free ice RAMP UP 8GtC/yr #3'
+       colour: 'orange'
+       thickness: 0.6
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+
+    u-cw990:
+       description: 'E-mode free ice RAMP UP 8GtC/yr #4'
+       colour: 'goldenrod'
+       thickness: 0.6
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+
+    # 1.5k Stabilisation
+    u-cy837:
+       description: '1.5K Stabilisation from u-cx209 (#1)'
+       colour: 'darkred'
+       thickness: 0.6
+       linestyle: ':'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics   
+
+
+
diff --git a/input_yml/TerraFIRMA_overshoot_runs_minimal.yml b/input_yml/TerraFIRMA_overshoot_runs_minimal.yml
new file mode 100644
index 00000000..cfa54aac
--- /dev/null
+++ b/input_yml/TerraFIRMA_overshoot_runs_minimal.yml
@@ -0,0 +1,120 @@
+---
+# GC5 N96 ORCA1 spinup analysis
+name: TerraFIRMA_overshoot_runs_minimal
+
+# Run the single job analysis
+do_analysis_timeseries: True  
+
+# Download from mass:
+do_mass_download: False
+
+# master analysis suite
+master_suites: kmf # physics bgc #alkalinity physics kmf1
+
+# Run without strick check (if True, breaks if job has no years.)
+strict_file_check: False
+
+clean: True
+
+jobs:
+    u-cs495:
+       description: 'PI-Control'
+       label: 'Pi-Control'
+       colour: 'blue' 
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: -100.
+       timerange: [1850, 2200]
+       suite: kmf #physics bgc #alkalinity physics
+         
+ 
+    u-cx209:
+       description: 'E-mode free ice RAMP UP 8GtC/yr #1'
+       label: 'Ramp-up'
+       colour: 'black'
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf #physics bgc #alkalinity physics
+
+    # 1.5k Stabilisation
+    u-cy837:
+       description: '1.5K Stabilisation from u-cx209 (#1)'
+       label: '1.5K Stable'
+       colour: 'lawngreen'
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf # physics bgc #alkalinity physics
+    
+
+    # 2k Stabilisation
+    u-cy838:
+       description: '2.0K Stabilisation from u-cx209 (#1)'
+       label: '2K Stable'
+       colour: 'goldenrod'
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf # physics bgc #alkalinity physics
+
+
+    # other Stabilisations
+    u-cz375:
+       description: '3.0K Stabilisation from u-cx209 (#1)'
+       label: '3K Stable'
+       colour: 'red'     #
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf # physics bgc #alkalinity physics
+    u-cz376:
+       description: '4.0K Stabilisation from u-cx209 (#1)'
+       label: '4K Stable'
+       colour: 'sienna'
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf # physics bgc #alkalinity physics
+    u-cz377:
+       description: '5.0K Stabilisation from u-cx209 (#1)'
+       label: '5K Stable'
+       colour: 'maroon'
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf # physics bgc #alkalinity physics
+
+    # Ramp downs
+    u-da697:
+       description: '1.5K Rampdown from u-cx209 (#1)'
+       label: '1.5K Rampdown'
+       colour: 'lawngreen'
+       thickness: 1.2
+       linestyle: ':'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf # physics bgc #alkalinity physics
+
+    u-cz944:
+       description: 'Ramp down from cy838 (- 2.0K Stabilisation from u-cx209) (#1)'
+       label: '2K Rampdown' 
+       colour: 'goldenrod'
+       thickness: 1.2
+       linestyle: 'dashed'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+
+
+
+
+
+
+

From 195870eab8b140f767c99ddd8654c80c638c7041 Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Mon, 27 Nov 2023 15:08:00 +0000
Subject: [PATCH 02/13] added additional runs

---
 input_yml/TerraFIRMA_overshoot_runs.yml | 34 ++++++++++++++++++++++++-
 1 file changed, 33 insertions(+), 1 deletion(-)

diff --git a/input_yml/TerraFIRMA_overshoot_runs.yml b/input_yml/TerraFIRMA_overshoot_runs.yml
index ca5154d5..b9478b6e 100644
--- a/input_yml/TerraFIRMA_overshoot_runs.yml
+++ b/input_yml/TerraFIRMA_overshoot_runs.yml
@@ -118,6 +118,16 @@ jobs:
        #timerange: [1800, 2050]
        suite: kmf physics bgc #alkalinity physics
 
+    u-da266:
+       description: '2.0K Stabilisation from cw988 (#3)'
+       label: '2K Stable #3'
+       colour: 'goldenrod'
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+       #
            
     # 2.5k Stabilisation
     u-cz374:
@@ -140,7 +150,7 @@ jobs:
        suite: kmf physics bgc #alkalinity physics
 
 
-    # other Stabilisations
+    # 3.0K Stabilisations
     u-cz375:
        description: '3.0K Stabilisation from u-cx209 (#1)'
        label: '3K Stable #1'
@@ -150,6 +160,28 @@ jobs:
        shifttime: 0.
        #timerange: [1800, 2050]
        suite: kmf physics bgc #alkalinity physics          
+
+    u-db587:
+       description: '3.0K Stabilisation from u-cx209 (#2)'
+       label: '3K Stable #2'
+       colour: 'red'     #
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics  
+
+    u-db597:
+       description: '3.0K Stabilisation from u-cx209 (#3)'
+       label: '3K Stable #3'
+       colour: 'red'     #
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics         #       
+
+    # other Stabilisations
     u-cz376:
        description: '4.0K Stabilisation from u-cx209 (#1)'
        label: '4K Stable #1'

From 009d6f378bbdf13a65e878223775c455859f91ae Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Thu, 14 Dec 2023 13:21:42 +0000
Subject: [PATCH 03/13] working here

---
 bgcval2/analysis_compare.py             |  1 +
 input_yml/TerraFIRMA_overshoot_runs.yml | 30 +++++++++++++++++++++----
 key_lists/kmf.yml                       |  1 +
 3 files changed, 28 insertions(+), 4 deletions(-)

diff --git a/bgcval2/analysis_compare.py b/bgcval2/analysis_compare.py
index f1d6b833..f8805486 100755
--- a/bgcval2/analysis_compare.py
+++ b/bgcval2/analysis_compare.py
@@ -503,6 +503,7 @@ def load_comparison_yml(master_compare_yml_fn):
     details['do_analysis_timeseries'] = input_yml_dict.get('do_analysis_timeseries', False)
     details['do_mass_download'] = input_yml_dict.get('do_mass_download', False)
     details['master_suites'] = input_yml_dict.get('master_suites', [])
+    details['strictFileCheck'] = input_yml_dict.get('strict_file_check', True)
 
     # auto download, can differ for each job.
     auto_download = input_yml_dict.get('auto_download', True)
diff --git a/input_yml/TerraFIRMA_overshoot_runs.yml b/input_yml/TerraFIRMA_overshoot_runs.yml
index 9f4b975f..49395f03 100644
--- a/input_yml/TerraFIRMA_overshoot_runs.yml
+++ b/input_yml/TerraFIRMA_overshoot_runs.yml
@@ -118,7 +118,6 @@ jobs:
        #timerange: [1800, 2050]
        suite: kmf physics bgc #alkalinity physics
 
-<<<<<<< HEAD
     u-da266:
        description: '2.0K Stabilisation from cw988 (#3)'
        label: '2K Stable #3'
@@ -128,9 +127,6 @@ jobs:
        shifttime: 0.
        #timerange: [1800, 2050]
        suite: kmf physics bgc #alkalinity physics
-       #
-=======
->>>>>>> origin/dev_parrallel_ts
            
     # 2.5k Stabilisation
     u-cz374:
@@ -214,6 +210,15 @@ jobs:
        shifttime: 0.
        #timerange: [1800, 2050]
        suite: kmf physics bgc #alkalinity physics   
+    u-da800:
+       description: 'Ramp down from cy838 (- 2.0K Stabilisation from u-cx209) (#1)'
+       label: '2K Rampdown #1'
+       colour: 'goldenrod'
+       thickness: 1.2
+       linestyle: ':'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics   
 
     u-da697:
        description: '1.5K Rampdown from u-cx209 (#1)'
@@ -225,5 +230,22 @@ jobs:
        #timerange: [1800, 2050]
        suite: kmf physics bgc #alkalinity physics
 
+    u-da892:
+       description: '4.K Rampdown (#1)'
+       label: '4.K Rampdown #1'
+       colour: 'sienna'
+       thickness: 1.2
+       linestyle: ':'
+       shifttime: 0.
+       suite: kmf physics bgc #alkalinity physics
+
+    u-db223:
+       description: '3.K Rampdown (#1)'
+       label: '3.K Rampdown #1'
+       colour: 'red'
+       thickness: 1.2
+       linestyle: ':'
+       shifttime: 0.
+       suite: kmf physics bgc #alkalinity physics
 
 
diff --git a/key_lists/kmf.yml b/key_lists/kmf.yml
index 14f5895b..08525c8f 100644
--- a/key_lists/kmf.yml
+++ b/key_lists/kmf.yml
@@ -4,6 +4,7 @@
 # of how a model is working.
 keys:
     GlobalMeanTemperature: True
+    SST: True
     DrakePassageTransport: True
     AMOC_26N: True
     TotalAirSeaFluxCO2: True

From d9215f423d01077fcf22bad578766a1f35edb9b7 Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Wed, 31 Jan 2024 09:43:11 +0000
Subject: [PATCH 04/13] recent small changes

---
 input_yml/TerraFIRMA_overshoot_runs.yml | 28 +++++++++++++++++++++++++
 scripts/shared_mass_cron.sh             |  2 +-
 2 files changed, 29 insertions(+), 1 deletion(-)

diff --git a/input_yml/TerraFIRMA_overshoot_runs.yml b/input_yml/TerraFIRMA_overshoot_runs.yml
index 49395f03..d91dd936 100644
--- a/input_yml/TerraFIRMA_overshoot_runs.yml
+++ b/input_yml/TerraFIRMA_overshoot_runs.yml
@@ -248,4 +248,32 @@ jobs:
        shifttime: 0.
        suite: kmf physics bgc #alkalinity physics
 
+    u-dc032:
+       description: 'ramp-down from yr 50 of 3.0 stab #1, free ice, -4GtC/yr (#1)'
+       label: '3K Rampdown #1'
+       colour: 'red'
+       thickness: 1.2
+       linestyle: ':'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+    u-dc123:
+       description: 'ramp-down from yr 50 of 4.0 stab #1, free ice, -4GtC/yr (#1)'
+       label: '4K Rampdown #1'
+       colour: 'sienna'
+       thickness: 1.2
+       linestyle: ':'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+    u-dc130:
+       description: 'ramp-down from yr 50 of 5.0 stab #1, free ice, -4GtC/yr (#1)'
+       label: '5K Rampdown #1'
+       colour: 'maroon'
+       thickness: 1.2
+       linestyle: ':'
+       shifttime: 0.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+
 
diff --git a/scripts/shared_mass_cron.sh b/scripts/shared_mass_cron.sh
index 6db7007d..5a24636a 100755
--- a/scripts/shared_mass_cron.sh
+++ b/scripts/shared_mass_cron.sh
@@ -15,7 +15,7 @@
 
 
 # delete files older than 2 weeks
-find /gws/nopw/j04/esmeval/bgcval2/shared_mass_scripts -mindepth 1 -mtime +15 -print -delete
+find /gws/nopw/j04/esmeval/bgcval2/shared_mass_scripts -mindepth 1 -mtime +15 -print -delete -name 'u-*.sh'
 
 # run all files:
 find /gws/nopw/j04/esmeval/bgcval2/shared_mass_scripts/*.sh -exec bash {} \;

From 3724c0e60b47fd719cc2bb33cca790b0ab9d0b89 Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Mon, 26 Feb 2024 16:09:42 +0000
Subject: [PATCH 05/13] working on TF runs.

---
 input_yml/TerraFIRMA_en1_reversible.yml     |  80 ++++++
 input_yml/TerraFIRMA_overshoot_recovery.yml | 282 ++++++++++++++++++++
 input_yml/proto_ukesm2_v2.yml               |  36 +++
 key_files/sst.yml                           |  29 ++
 key_files/temperature_ukesm1.yml            |  28 ++
 key_lists/ukesm1.yml                        |  98 +++++++
 6 files changed, 553 insertions(+)
 create mode 100644 input_yml/TerraFIRMA_en1_reversible.yml
 create mode 100644 input_yml/TerraFIRMA_overshoot_recovery.yml
 create mode 100644 input_yml/proto_ukesm2_v2.yml
 create mode 100644 key_files/sst.yml
 create mode 100644 key_files/temperature_ukesm1.yml
 create mode 100644 key_lists/ukesm1.yml

diff --git a/input_yml/TerraFIRMA_en1_reversible.yml b/input_yml/TerraFIRMA_en1_reversible.yml
new file mode 100644
index 00000000..314f57aa
--- /dev/null
+++ b/input_yml/TerraFIRMA_en1_reversible.yml
@@ -0,0 +1,80 @@
+---
+# GC5 N96 ORCA1 spinup analysis
+name: TerraFIRMA_en1_reversible
+
+# Run the single job analysis
+do_analysis_timeseries: True 
+
+# Download from mass:
+do_mass_download: False
+
+# master analysis suite
+master_suites: physics
+
+clean: True
+
+jobs:
+    u-cy837:
+       description: '1.5C branch'
+       colour: purple  
+       thickness: 1.7
+       linestyle: '-'
+       shifttime: 0.
+       suite: kmf physics
+
+    u-cy838: 
+       description: '2.0C branch'
+       colour: violet
+       thickness: 1.7
+       linestyle: '-'
+       shifttime: 0.
+       suite: kmf physics
+
+    u-cz374:
+       description: '2.5C branch'
+       colour: blue
+       thickness: 1.7
+       linestyle: '-'
+       shifttime: 0.
+       suite: kmf physics
+
+    u-cz375:
+       description: '3.0C branch'
+       colour: cyan
+       thickness: 1.7
+       linestyle: '-'
+       shifttime: 0.
+       suite: kmf physics
+
+    u-cz376:
+       description: '4.0C branch'
+       colour: green
+       thickness: 1.7
+       linestyle: '-'
+       shifttime: 0.
+       suite: kmf physics
+
+    u-cz377:
+       description: '5.0C branch'
+       colour: goldenrod
+       thickness: 1.7
+       linestyle: '-'
+       shifttime: 0.
+       suite: kmf physics
+
+    u-cx209:
+       description: 'Ramp up'
+       colour: 'red'
+       thickness: 0.6
+       linestyle: '-'
+       shifttime: 0.
+       suite: kmf physics
+
+    u-cs495:
+       description: 'piControl'
+       colour: 'black'
+       thickness: 0.6
+       linestyle: '-'
+       shifttime: -100.
+       suite: kmf physics
+
diff --git a/input_yml/TerraFIRMA_overshoot_recovery.yml b/input_yml/TerraFIRMA_overshoot_recovery.yml
new file mode 100644
index 00000000..7961d266
--- /dev/null
+++ b/input_yml/TerraFIRMA_overshoot_recovery.yml
@@ -0,0 +1,282 @@
+---
+# GC5 N96 ORCA1 spinup analysis
+name: TerraFIRMA_overshoot_recovery
+
+# Run the single job analysis
+do_analysis_timeseries: True  
+
+# Download from mass:
+do_mass_download: False
+
+# master analysis suite
+master_suites: physics bgc kmf #alkalinity physics kmf1
+
+# Run without strick check (if True, breaks if job has no years.)
+strict_file_check: False
+
+clean: True
+
+jobs:
+    u-cs495:
+       description: 'PI-Control'
+       label: 'PIcontrol'
+       colour: 'blue' 
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: -2094
+       timerange: [-50., 100.]
+       suite: kmf physics bgc #alkalinity physics
+         
+ 
+#    u-cx209:
+#       description: 'E-mode free ice RAMP UP 8GtC/yr #1'
+#       label: 'Ramp-up #1'
+#       colour: 'black'
+#       thickness: 1.2
+#       linestyle: '-'
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics
+#
+#    u-cw988:
+#       description: 'E-mode free ice RAMP UP 8GtC/yr #2'
+#       label: 'Ramp-up #2'
+#       colour: 'black'
+#       thickness: 1.2
+#       linestyle: '-'
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics
+#           
+#    u-cw989:
+#       description: 'E-mode free ice RAMP UP 8GtC/yr #3'
+#       label: 'Ramp-up #3'
+#       colour: 'black'
+#       thickness: 1.2
+#       linestyle: '-'
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics
+#
+#    u-cw990:
+#       description: 'E-mode free ice RAMP UP 8GtC/yr #4'
+#       label: 'Ramp-up #4'
+#       colour: 'black'
+#       thickness: 1.2
+#       linestyle: '-'
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics
+
+    # 1.5k Stabilisation
+#    u-cy837:
+#       description: '1.5K Stabilisation from u-cx209 (#1)'
+#       label: '1.5K Stable #1'
+#       colour: 'lawngreen'
+#       thickness: 1.2
+#       linestyle: '-'
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics   
+#    u-cz834:
+#       description: '1.5K Stabilisation from u-cw988 (#2)'
+#       label: '1.5K Stable #2'
+#       colour: 'lawngreen'
+#       thickness: 1.2
+#       linestyle: '-'
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics
+#    u-da087:
+#       description: '1.5K Stabilisation from u-cw989 (#3)'
+#       label: '1.5K Stable #3'
+#       colour: 'lawngreen' 
+#       thickness: 1.2
+#       linestyle: '-'
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics
+#           
+#    # 2k Stabilisation
+#    u-cy838:
+#       description: '2.0K Stabilisation from u-cx209 (#1)'
+#       label: '2K Stable #1'
+#       colour: 'goldenrod'
+#       thickness: 1.2
+#       linestyle: '-'
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics   
+#
+#    u-cz855:
+#       description: '2.0K Stabilisation from cw988 (#2)'
+#       label: '2K Stable #2'
+#       colour: 'goldenrod'
+#       thickness: 1.2
+#       linestyle: '-'
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics
+
+#    u-da266:
+#       description: '2.0K Stabilisation from cw988 (#3)'
+#       label: '2K Stable #3'
+#       colour: 'goldenrod'
+#       thickness: 1.2
+#       linestyle: '-'
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics
+#           
+#    # 2.5k Stabilisation
+#    u-cz374:
+#       description: '2.5K Stabilisation from u-cx209 (#1)'
+#       label: '2.5K Stable #1'
+#       colour: 'orange'
+#       thickness: 1.2
+#       linestyle: '-'
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics   
+#    u-cz859:
+#       description: '2.5K Stabilisation from cw988 (#2)'
+#       label: '2.5K Stable #2'
+#       colour: 'orange' 
+#       thickness: 1.2
+#       linestyle: '-'
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics
+
+
+#    # 3.0K Stabilisations
+#    u-cz375:
+#       description: '3.0K Stabilisation from u-cx209 (#1)'
+#       label: '3K Stable #1'
+#       colour: 'red'     #
+#       thickness: 1.2
+#       linestyle: '-'
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics          
+#
+#    u-db587:
+#       description: '3.0K Stabilisation from u-cx209 (#2)'
+#       label: '3K Stable #2'
+#       colour: 'red'     #
+#       thickness: 1.2
+#       linestyle: '-'
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics  
+#
+#    u-db597:
+#       description: '3.0K Stabilisation from u-cx209 (#3)'
+#       label: '3K Stable #3'
+#       colour: 'red'     #
+#       thickness: 1.2
+#       linestyle: '-'
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics         #       
+#
+#    # other Stabilisations
+#    u-cz376:
+#       description: '4.0K Stabilisation from u-cx209 (#1)'
+#       label: '4K Stable #1'
+#       colour: 'sienna'
+#       thickness: 1.2
+#       linestyle: '-'
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics  
+#    u-cz377:
+#       description: '5.0K Stabilisation from u-cx209 (#1)'
+#       label: '5K Stable #1'
+#       colour: 'maroon'
+#       thickness: 1.2
+#       linestyle: '-'
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics 
+           
+    # Ramp downs
+    u-cz944:
+       description: 'Ramp down from cy838 (- 2.0K Stabilisation from u-cx209) (#1)'
+       label: '2K Rampdown #1'
+       colour: 'goldenrod'
+       thickness: 1.2
+       linestyle: ':' 
+       shifttime: -1994.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics   
+
+    u-da800:
+       description: 'Ramp down from cy838 (- 2.0K Stabilisation from u-cx209) (#1)'
+       label: '2K Rampdown #1'
+       colour: 'goldenrod'
+       thickness: 1.2
+       linestyle: ':'
+       shifttime: -2144.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics   
+
+    u-da697:
+       description: '1.5K Rampdown from u-cx209 (#1)'
+       label: '1.5K Rampdown #1'
+       colour: 'lawngreen'
+       thickness: 1.2
+       linestyle: ':'
+       shifttime: -1969.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+
+    u-da892:
+       description: '4.K Rampdown (#1)'
+       label: '4.K Rampdown #1'
+       colour: 'sienna'
+       thickness: 1.2
+       linestyle: ':'
+       shifttime: -2094.
+       suite: kmf physics bgc #alkalinity physics
+
+    u-db223:
+       description: '3.K Rampdown (#1)'
+       label: '3.K Rampdown #1'
+       colour: 'red'
+       thickness: 1.2
+       linestyle: ':'
+       shifttime: -2032.
+       suite: kmf physics bgc #alkalinity physics
+
+    u-dc032:
+       description: 'ramp-down from yr 50 of 3.0 stab #1, free ice, -4GtC/yr (#1)'
+       label: '3K Rampdown #1'
+       colour: 'red'
+       thickness: 1.2
+       linestyle: ':'
+       shifttime: -2023.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+
+    u-dc123:
+       description: 'ramp-down from yr 50 of 4.0 stab #1, free ice, -4GtC/yr (#1)'
+       label: '4K Rampdown #1'
+       colour: 'sienna'
+       thickness: 1.2
+       linestyle: ':'
+       shifttime: -2096.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+
+    u-dc130:
+       description: 'ramp-down from yr 50 of 5.0 stab #1, free ice, -4GtC/yr (#1)'
+       label: '5K Rampdown #1'
+       colour: 'maroon'
+       thickness: 1.2
+       linestyle: ':'
+       shifttime: -2133.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+
+
diff --git a/input_yml/proto_ukesm2_v2.yml b/input_yml/proto_ukesm2_v2.yml
new file mode 100644
index 00000000..9019170e
--- /dev/null
+++ b/input_yml/proto_ukesm2_v2.yml
@@ -0,0 +1,36 @@
+---
+# GC5 N96 ORCA1 spinup analysis
+name: proto_ukesm2_v2
+
+# Run the single job analysis
+do_analysis_timeseries: True 
+# Download from mass:
+do_mass_download: False
+
+# master analysis suite
+master_suites: kmf_phys physics_no_mld
+
+clean: True
+
+# Job ID's suites as named by Rose/Cylc
+# •     u-ct200 - GC5
+# •     u-ct739 - GC5-ESMproto
+#
+jobs:
+#
+    u-ct200:
+       description: 'GC5'
+       colour: red 
+       thickness: 2.0
+       linestyle: '-'
+       shifttime: 0.
+       suite: kmf_phys physics_no_mld
+#
+    u-ct739:
+       description: 'GC5-ESM-proto'
+       colour: blue
+       thickness: 2.0
+       linestyle: '-'
+       shifttime: 0.
+       suite: kmf_phys physics_no_mld
+#
diff --git a/key_files/sst.yml b/key_files/sst.yml
new file mode 100644
index 00000000..ae779eda
--- /dev/null
+++ b/key_files/sst.yml
@@ -0,0 +1,29 @@
+---
+name            : Temperature
+units           : degrees C
+dimensions      : 3
+model           : NEMO
+datasource      : WOA
+# The filenames
+modelFiles      : $BASEDIR_MODEL/$JOBID/nemo_$JOBIDo_1y_*_grid-T.nc
+modelFile_p2p   : $BASEDIR_MODEL/$JOBID/nemo*$JOBIDo_1y_*$YEAR????_grid-T.nc
+dataFile        : $BASEDIR_OBS/WOA/annual/woa13_decav_t00_01v2.nc
+gridFile        : $PATHS_GRIDFILE
+
+# Model coordinates/dimension names
+model_vars      : thetao_con thetao
+model_convert   : choose_best_var
+
+
+# Data coordinates names
+data_vars       : t_an
+data_convert    : NoChange
+data_tdict      : ZeroToZero
+
+layers          : Surface
+regions         : Global 
+smoothings      : DataOnly 5and30 
+
+
+
+
diff --git a/key_files/temperature_ukesm1.yml b/key_files/temperature_ukesm1.yml
new file mode 100644
index 00000000..1c989e6c
--- /dev/null
+++ b/key_files/temperature_ukesm1.yml
@@ -0,0 +1,28 @@
+---
+name            : Temperature
+units           : degrees C
+dimensions      : 3
+model           : NEMO
+datasource      : WOA
+# The filenames
+modelFiles      : $BASEDIR_MODEL/$JOBID/nemo_$JOBIDo_1y_*_grid-T.nc
+modelFile_p2p   : $BASEDIR_MODEL/$JOBID/nemo*$JOBIDo_1y_*$YEAR????_grid-T.nc
+dataFile        : $BASEDIR_OBS/WOA/annual/woa13_decav_t00_01v2.nc
+gridFile        : $PATHS_GRIDFILE
+
+# Model coordinates/dimension names
+model_vars      : thetao_con thetao
+model_convert   : choose_best_var
+
+
+# Data coordinates names
+data_vars       : t_an
+data_convert    : NoChange
+data_tdict      : ZeroToZero
+
+layers          : Surface
+regions         : Global  #ignoreInlandSeas SouthernOcean ArcticOcean Equator10 Remainder NorthernSubpolarAtlantic NorthernSubpolarPacific
+
+
+
+
diff --git a/key_lists/ukesm1.yml b/key_lists/ukesm1.yml
new file mode 100644
index 00000000..1d5c7837
--- /dev/null
+++ b/key_lists/ukesm1.yml
@@ -0,0 +1,98 @@
+---
+# Level 1 analysis
+# A full list of both BGC and Physical keys
+keys:
+    # Nutrients
+    Nitrate: True                          # WOA Nitrate
+    Silicate: True                         # WOA Siliate
+    Iron: True                       # Iron
+
+    # Chlorophyll, Production, Export and DMS
+    Chlorophyll: True                        # Total Chlorophyll
+    TotalIntPP: True                 # Global Total Integrated Primary Production
+    # CHD: True                      # Diatom Chlorophyll
+    # CHN: True                      # Non-diatom Chlorophyll
+    #   DiaFrac: True                  # Diatom Fraction
+#    IntPP_OSU: True                  # OSU Integrated primpary production
+#    PP_OSU: True                     # OSU Integrated primpary production
+    #   LocalExportRatio: True         # Export ratio
+    #   GlobalExportRatio: True        # Export ratio
+    # DMS_ARAN: True
+    # DMS: True
+    # DTC: True                      # Detrital carbon
+
+    # Carbonate system:
+    Alkalinity: True                        # Glodap Alkalinity
+    pH: True
+    DIC: True                        # Globap dissolved inorganic carbon
+    AirSeaFluxCO2: True              # Air Sea Flux of CO2
+    TotalAirSeaFluxCO2: True         # Total global air sea flux
+
+    # Oxygen:
+    Oxygen: True                         # WOA Oxygen
+#    TotalOMZVolume: True             # Total Oxygen Minimum zone Volume
+    #   OMZThickness: True             # Oxygen Minimum Zone Thickness
+    #   OMZMeanDepth: True             # Oxygen Minimum Zone mean depth
+#    VolumeMeanOxygen: True           # Volune Mean regional oxygen concentation
+    #   AOU: True                      # Apparent Oxygen Usage
+
+    # Misc.
+    Dust: True  # Dust
+    TotalDust: True                # Total Dust
+
+    # Physics:
+    # Temperature keys:
+    Temperature: True  # WOA Temperature
+#    GlobalMeanTemperature: True  # Global Mean Temperature
+#    GlobalMeanTemperature_700: True
+#    GlobalMeanTemperature_2000: True
+#    VolumeMeanTemperature: True  # Global Mean Temperature
+    #VolWeightedT: True			# Volume weighted WOA Temperature
+    #	IcelessMeanSST: True    		# Global Mean Surface Temperature with no ice
+#    thetaoga: True
+
+    # Salinity keys:
+    GlobalMeanSalinity: True  # Global Mean Salinity
+    Salinity: True  # WOA Salinity
+
+    # Mixed layer depth keys:
+    MLD: True  # iFERMER Mixed Layer Depth
+    # MaxMonthlyMLD: True               # MLD Monthly max
+    # MinMonthlyMLD: True               # MLD Monthly min
+
+    # Ice keys:
+    #	TotalIceArea: True			# work in progress
+    #	NorthernTotalIceArea: True		# work in progress
+    #	SouthernTotalIceArea: True		# work in progress
+    #	WeddelTotalIceArea: True
+    TotalIceExtent: True  # work in progress
+    NorthernTotalIceExtent: True  # work in progress
+    SouthernTotalIceExtent: True  # work in progress
+    # WeddelIceExent: True       # work in progress
+    # NorthernMIZArea: True
+    # SouthernMIZArea: True
+    # TotalMIZArea: True
+    # NorthernMIZfraction: True
+    # SouthernMIZfraction: True
+    # TotalMIZfraction: True
+
+    # Circulation keys:
+    DrakePassageTransport: True  # DrakePassageTransport
+    #	AMOC_32S: True                 	# AMOC 32S
+    AMOC_26N: True  # AMOC 26N
+    # AMOC_26N_nomexico: True            # AMOC 26N
+    #	ADRC_26N: True                 	# ADRC 26N
+    #	ZonalCurrent: True             	# Zonal Veloctity
+    #	MeridionalCurrent: True        	# Meridional Veloctity
+    #	VerticalCurrent: True          	# Vertical Veloctity
+
+    # Misc fluxes:
+    #FreshwaterFlux: True  # Freshwater flux
+    #sowaflup: True  # Net Upward Water Flux
+    #	soicecov: True			# Ice fraction
+    # HeatFlux: True
+    # WindStress: True                   # Wind Stress
+    # sohefldo: True                     # Net downward Water Flux
+    # sofmflup: True                     # Water flux due to freezing/melting
+    # sosfldow: True                     # Downward salt flux
+    # sossheig: True                 # Sea surface height

From 2a620da4b1e42864e26160aa85727a791465d765 Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Tue, 27 Feb 2024 10:41:35 +0000
Subject: [PATCH 06/13] Update TerraFIRMA_overshoot_recovery.yml

new jobs
---
 input_yml/TerraFIRMA_overshoot_recovery.yml | 58 +++++++++++++++++++++
 1 file changed, 58 insertions(+)

diff --git a/input_yml/TerraFIRMA_overshoot_recovery.yml b/input_yml/TerraFIRMA_overshoot_recovery.yml
index 7961d266..4e014767 100644
--- a/input_yml/TerraFIRMA_overshoot_recovery.yml
+++ b/input_yml/TerraFIRMA_overshoot_recovery.yml
@@ -249,6 +249,64 @@ jobs:
        shifttime: -2032.
        suite: kmf physics bgc #alkalinity physics
 
+
+
+    u-dc051:
+       description: 'Rampdown from yr 50 of 1.5 stab #1, -4GtC/yr (#1)'
+       label: '1.5K Rampdown #1'
+       colour: 'lawngreen'
+       thickness: 1.2
+       linestyle: ':'
+       shifttime: -1995.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics  
+
+    u-dc052:
+       description: 'Rampdown from yr 200 of 1.5deg, -4GtC/yr (#1)'
+       label: '1.5K Rampdown #1'
+       colour: 'lawngreen'
+       thickness: 1.2
+       linestyle: ':'
+       shifttime: -1969
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics  
+
+    u-dc248:
+       description: '1.5K Rampdown -4GtC/yr, (#1)'
+       label: '1.5K Rampdown #1'
+       colour: 'lawngreen'
+       thickness: 1.2
+       linestyle: ':'
+       shifttime: -2119.
+       suite: kmf physics bgc #alkalinity physics
+
+    u-dc249:
+       description: '3.K Rampdown -4GtC/yr, 200 years, (#1)'
+       label: '3.K Rampdown #1'
+       colour: 'red'
+       thickness: 1.2
+       linestyle: ':'
+       shifttime: -2182.
+       suite: kmf physics bgc #alkalinity physics
+
+    u-dc251:
+       description: '5K Rampdown -8GtC/yr, 50 years, (#1)'
+       label: '5K Rampdown #1'
+       colour: 'maroon'
+       thickness: 1.2
+       linestyle: ':'
+       shifttime: -2132.
+       suite: kmf physics bgc #alkalinity physics
+
+    u-db956:
+       description: '1.5K Rampdown -8GtC/yr, 0 years, (#1)'
+       label: '1.5K Rampdown #1'
+       colour: 'lawngreen'
+       thickness: 1.2
+       linestyle: ':'
+       shifttime: -1919.
+       suite: kmf physics bgc #alkalinity physics
+       
     u-dc032:
        description: 'ramp-down from yr 50 of 3.0 stab #1, free ice, -4GtC/yr (#1)'
        label: '3K Rampdown #1'

From 8b76bdff2696c75d06b9b3c9fb0fe033e99bef9e Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Tue, 27 Feb 2024 11:34:20 +0000
Subject: [PATCH 07/13] added other jobs and changed tabs

---
 input_yml/TerraFIRMA_overshoot_runs.yml | 604 ++++++++++++++----------
 1 file changed, 366 insertions(+), 238 deletions(-)

diff --git a/input_yml/TerraFIRMA_overshoot_runs.yml b/input_yml/TerraFIRMA_overshoot_runs.yml
index d91dd936..747b3c21 100644
--- a/input_yml/TerraFIRMA_overshoot_runs.yml
+++ b/input_yml/TerraFIRMA_overshoot_runs.yml
@@ -16,264 +16,392 @@ strict_file_check: False
 
 clean: True
 
+
+
 jobs:
-    u-cs495:
-       description: 'PI-Control'
-       label: 'PIcontrol'
-       colour: 'blue' 
-       thickness: 1.2
-       linestyle: '-'
-       shifttime: -100.
-       timerange: [1850, 2300]
-       suite: kmf physics bgc #alkalinity physics
+   u-cs495:
+      description: 'PI-Control'
+      label: 'PIcontrol'
+      colour: 'blue' 
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: -100.
+      timerange: [1850, 2300]
+      suite: kmf physics bgc #alkalinity physics
          
  
-    u-cx209:
-       description: 'E-mode free ice RAMP UP 8GtC/yr #1'
-       label: 'Ramp-up #1'
-       colour: 'black'
-       thickness: 1.2
-       linestyle: '-'
-       shifttime: 0.
-       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics
+   u-cx209:
+      description: 'E-mode free ice RAMP UP 8GtC/yr #1'
+      label: 'Ramp-up #1'
+      colour: 'black'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics
 
-    u-cw988:
-       description: 'E-mode free ice RAMP UP 8GtC/yr #2'
-       label: 'Ramp-up #2'
-       colour: 'black'
-       thickness: 1.2
-       linestyle: '-'
-       shifttime: 0.
-       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics
+   u-cw988:
+      description: 'E-mode free ice RAMP UP 8GtC/yr #2'
+      label: 'Ramp-up #2'
+      colour: 'black'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics
            
-    u-cw989:
-       description: 'E-mode free ice RAMP UP 8GtC/yr #3'
-       label: 'Ramp-up #3'
-       colour: 'black'
-       thickness: 1.2
-       linestyle: '-'
-       shifttime: 0.
-       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics
+   u-cw989:
+      description: 'E-mode free ice RAMP UP 8GtC/yr #3'
+      label: 'Ramp-up #3'
+      colour: 'black'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics
 
-    u-cw990:
-       description: 'E-mode free ice RAMP UP 8GtC/yr #4'
-       label: 'Ramp-up #4'
-       colour: 'black'
-       thickness: 1.2
-       linestyle: '-'
-       shifttime: 0.
-       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics
+   u-cw990:
+      description: 'E-mode free ice RAMP UP 8GtC/yr #4'
+      label: 'Ramp-up #4'
+      colour: 'black'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics
+
+   u-cz826:
+      description: 'like cx209 but static ice sheet geometry 8GtC/yr #5'
+      label: 'Ramp-up #5'
+      colour: 'black'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics
 
     # 1.5k Stabilisation
-    u-cy837:
-       description: '1.5K Stabilisation from u-cx209 (#1)'
-       label: '1.5K Stable #1'
-       colour: 'lawngreen'
-       thickness: 1.2
-       linestyle: '-'
-       shifttime: 0.
-       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics   
-    u-cz834:
-       description: '1.5K Stabilisation from u-cw988 (#2)'
-       label: '1.5K Stable #2'
-       colour: 'lawngreen'
-       thickness: 1.2
-       linestyle: '-'
-       shifttime: 0.
-       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics
-    u-da087:
-       description: '1.5K Stabilisation from u-cw989 (#3)'
-       label: '1.5K Stable #3'
-       colour: 'lawngreen' 
-       thickness: 1.2
-       linestyle: '-'
-       shifttime: 0.
-       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics
+   u-cy837:
+      description: '1.5K Stabilisation from u-cx209 (#1)'
+      label: '1.5K Stable #1'
+      colour: 'lawngreen'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics   
+   u-cz834:
+      description: '1.5K Stabilisation from u-cw988 (#2)'
+      label: '1.5K Stable #2'
+      colour: 'lawngreen'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics
+   u-da087:
+      description: '1.5K Stabilisation from u-cw989 (#3)'
+      label: '1.5K Stable #3'
+      colour: 'lawngreen' 
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics
            
     # 2k Stabilisation
-    u-cy838:
-       description: '2.0K Stabilisation from u-cx209 (#1)'
-       label: '2K Stable #1'
-       colour: 'goldenrod'
-       thickness: 1.2
-       linestyle: '-'
-       shifttime: 0.
-       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics   
-
-    u-cz855:
-       description: '2.0K Stabilisation from cw988 (#2)'
-       label: '2K Stable #2'
-       colour: 'goldenrod'
-       thickness: 1.2
-       linestyle: '-'
-       shifttime: 0.
-       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics
+   u-cy838:
+      description: '2.0K Stabilisation from u-cx209 (#1)'
+      label: '2K Stable #1'
+      colour: 'goldenrod'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics   
 
-    u-da266:
-       description: '2.0K Stabilisation from cw988 (#3)'
-       label: '2K Stable #3'
-       colour: 'goldenrod'
-       thickness: 1.2
-       linestyle: '-'
-       shifttime: 0.
-       #timerange: [1800, 2050]
+   u-cz855:
+      description: '2.0K Stabilisation from cw988 (#2)'
+      label: '2K Stable #2'
+      colour: 'goldenrod'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
        suite: kmf physics bgc #alkalinity physics
+
+   u-da266:
+      description: '2.0K Stabilisation from cw988 (#3)'
+      label: '2K Stable #3'
+      colour: 'goldenrod'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics
            
     # 2.5k Stabilisation
-    u-cz374:
-       description: '2.5K Stabilisation from u-cx209 (#1)'
-       label: '2.5K Stable #1'
-       colour: 'orange'
-       thickness: 1.2
-       linestyle: '-'
-       shifttime: 0.
-       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics   
-    u-cz859:
-       description: '2.5K Stabilisation from cw988 (#2)'
-       label: '2.5K Stable #2'
-       colour: 'orange' 
-       thickness: 1.2
-       linestyle: '-'
-       shifttime: 0.
-       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics
+   u-cz374:
+      description: '2.5K Stabilisation from u-cx209 (#1)'
+      label: '2.5K Stable #1'
+      colour: 'orange'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics   
+   u-cz859:
+      description: '2.5K Stabilisation from cw988 (#2)'
+      label: '2.5K Stable #2'
+      colour: 'orange' 
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics
 
 
     # 3.0K Stabilisations
-    u-cz375:
-       description: '3.0K Stabilisation from u-cx209 (#1)'
-       label: '3K Stable #1'
-       colour: 'red'     #
-       thickness: 1.2
-       linestyle: '-'
-       shifttime: 0.
-       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics          
-
-    u-db587:
-       description: '3.0K Stabilisation from u-cx209 (#2)'
-       label: '3K Stable #2'
-       colour: 'red'     #
-       thickness: 1.2
-       linestyle: '-'
-       shifttime: 0.
-       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics  
-
-    u-db597:
-       description: '3.0K Stabilisation from u-cx209 (#3)'
-       label: '3K Stable #3'
-       colour: 'red'     #
-       thickness: 1.2
-       linestyle: '-'
-       shifttime: 0.
-       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics         #       
-
-    # other Stabilisations
-    u-cz376:
-       description: '4.0K Stabilisation from u-cx209 (#1)'
-       label: '4K Stable #1'
-       colour: 'sienna'
-       thickness: 1.2
-       linestyle: '-'
-       shifttime: 0.
-       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics  
-    u-cz377:
-       description: '5.0K Stabilisation from u-cx209 (#1)'
-       label: '5K Stable #1'
-       colour: 'maroon'
-       thickness: 1.2
-       linestyle: '-'
-       shifttime: 0.
-       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics 
-           
+   u-cz375:
+      description: '3.0K Stabilisation from u-cx209 (#1)'
+      label: '3K Stable #1'
+      colour: 'red'     #
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics          
+
+   u-db587:
+      description: '3.0K Stabilisation from u-cx209 (#2)'
+      label: '3K Stable #2'
+      colour: 'red'     #
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics  
+
+   u-db597:
+      description: '3.0K Stabilisation from u-cx209 (#3)'
+      label: '3K Stable #3'
+      colour: 'red'     #
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics         #       
+
+    # 4k  Stabilisations
+   u-cz376:
+      description: '4.0K Stabilisation from u-cx209 (#1)'
+      label: '4K Stable #1'
+      colour: 'sienna'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics  
+   u-db723:
+      description: '4.0K Stabilisation from u-cw988 (#2)'
+      label: '4K Stable #2'
+      colour: 'sienna'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics      
+   u-db733:
+      description: '4.0K Stabilisation from u-cw989 (#3)'
+      label: '4K Stable #3'
+      colour: 'sienna'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics      
+
+    # 5k & 6K  Stabilisations
+   u-cz377:
+      description: '5.0K Stabilisation from u-cx209 (#1)'
+      label: '5K Stable #1'
+      colour: 'maroon'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics 
+   u-db731:
+      description: '5.0K Stabilisation from u-cw988 (#2)'
+      label: '5K Stable #2'
+      colour: 'maroon'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics 
+   u-dc324:
+      description: '5.0K Stabilisation from u-cw989 (#3)'
+      label: '5K Stable #3'
+      colour: 'maroon'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics 
+
+   u-cz378:
+      description: '6.0K Stabilisation from u-cx209 (#1)'
+      label: '6K Stable #1'
+      colour: 'darkbrown'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics 
+								
     # Ramp downs
-    u-cz944:
-       description: 'Ramp down from cy838 (- 2.0K Stabilisation from u-cx209) (#1)'
-       label: '2K Rampdown #1'
-       colour: 'goldenrod'
-       thickness: 1.2
-       linestyle: ':' 
-       shifttime: 0.
-       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics   
-    u-da800:
-       description: 'Ramp down from cy838 (- 2.0K Stabilisation from u-cx209) (#1)'
-       label: '2K Rampdown #1'
-       colour: 'goldenrod'
-       thickness: 1.2
-       linestyle: ':'
-       shifttime: 0.
-       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics   
-
-    u-da697:
-       description: '1.5K Rampdown from u-cx209 (#1)'
-       label: '1.5K Rampdown #1'
-       colour: 'lawngreen'
-       thickness: 1.2
-       linestyle: ':'
-       shifttime: 0.
-       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics
+   u-cz944:
+      description: 'Ramp down from cy838 (- 2.0K Stabilisation from u-cx209) (#1)'
+      label: '2K Rampdown #1'
+      colour: 'goldenrod'
+      thickness: 1.2
+      linestyle: ':' 
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics   
+   u-da800:
+      description: 'Ramp down from cy838 (- 2.0K Stabilisation from u-cx209) (#1)'
+      label: '2K Rampdown #1'
+      colour: 'goldenrod'
+      thickness: 1.2
+      linestyle: ':'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics   
 
-    u-da892:
-       description: '4.K Rampdown (#1)'
-       label: '4.K Rampdown #1'
-       colour: 'sienna'
-       thickness: 1.2
-       linestyle: ':'
-       shifttime: 0.
-       suite: kmf physics bgc #alkalinity physics
+   u-da697:
+      description: '1.5K Rampdown from u-cx209 (#1)'
+      label: '1.5K Rampdown #1'
+      colour: 'lawngreen'
+      thickness: 1.2
+      linestyle: ':'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics
 
-    u-db223:
-       description: '3.K Rampdown (#1)'
-       label: '3.K Rampdown #1'
-       colour: 'red'
-       thickness: 1.2
-       linestyle: ':'
-       shifttime: 0.
-       suite: kmf physics bgc #alkalinity physics
+   u-da892:
+      description: '4.K Rampdown (#1)'
+      label: '4.K Rampdown #1'
+      colour: 'sienna'
+      thickness: 1.2
+      linestyle: ':'
+      shifttime: 0.
+      suite: kmf physics bgc #alkalinity physics
+
+   u-db223:
+      description: '3.K Rampdown (#1)'
+      label: '3.K Rampdown #1'
+      colour: 'red'
+      thickness: 1.2
+      linestyle: ':'
+      shifttime: 0.
+      suite: kmf physics bgc #alkalinity physics
+
+
+
+   u-dc051:
+      description: 'Rampdown from yr 50 of 1.5 stab #1, -4GtC/yr (#1)'
+      label: '1.5K Rampdown #1'
+      colour: 'lawngreen'
+      thickness: 1.2
+      linestyle: ':'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics  
+
+   u-dc052:
+      description: 'Rampdown from yr 200 of 1.5deg, -4GtC/yr (#1)'
+      label: '1.5K Rampdown #1'
+      colour: 'lawngreen'
+      thickness: 1.2
+      linestyle: ':'
+      shifttime: 0
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics  
+
+   u-dc248:
+      description: '1.5K Rampdown -4GtC/yr, (#1)'
+      label: '1.5K Rampdown #1'
+      colour: 'lawngreen'
+      thickness: 1.2
+      linestyle: ':'
+      shifttime: 0.
+      suite: kmf physics bgc #alkalinity physics
+
+   u-dc249:
+      description: '3.K Rampdown -4GtC/yr, 200 years, (#1)'
+      label: '3.K Rampdown #1'
+      colour: 'red'
+      thickness: 1.2
+      linestyle: ':'
+      shifttime: 0.
+      suite: kmf physics bgc #alkalinity physics
+
+   u-dc251:
+      description: '5K Rampdown -8GtC/yr, 50 years, (#1)'
+      label: '5K Rampdown #1'
+      colour: 'maroon'
+      thickness: 1.2
+      linestyle: ':'
+      shifttime: 0.
+      suite: kmf physics bgc #alkalinity physics
+
+   u-db956:
+      description: '1.5K Rampdown -8GtC/yr, 0 years, (#1)'
+      label: '1.5K Rampdown #1'
+      colour: 'lawngreen'
+      thickness: 1.2
+      linestyle: ':'
+      shifttime: 0.
+      suite: kmf physics bgc #alkalinity physics
+
+   u-dc032:
+      description: 'ramp-down from yr 50 of 3.0 stab #1, free ice, -4GtC/yr (#1)'
+      label: '3K Rampdown #1'
+      colour: 'red'
+      thickness: 1.2
+      linestyle: ':'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics
+   u-dc123:
+      description: 'ramp-down from yr 50 of 4.0 stab #1, free ice, -4GtC/yr (#1)'
+      label: '4K Rampdown #1'
+      colour: 'sienna'
+      thickness: 1.2
+      linestyle: ':'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics
+   u-dc130:
+      description: 'ramp-down from yr 50 of 5.0 stab #1, free ice, -4GtC/yr (#1)'
+      label: '5K Rampdown #1'
+      colour: 'maroon'
+      thickness: 1.2
+      linestyle: ':'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics
 
-    u-dc032:
-       description: 'ramp-down from yr 50 of 3.0 stab #1, free ice, -4GtC/yr (#1)'
-       label: '3K Rampdown #1'
-       colour: 'red'
-       thickness: 1.2
-       linestyle: ':'
-       shifttime: 0.
-       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics
-    u-dc123:
-       description: 'ramp-down from yr 50 of 4.0 stab #1, free ice, -4GtC/yr (#1)'
-       label: '4K Rampdown #1'
-       colour: 'sienna'
-       thickness: 1.2
-       linestyle: ':'
-       shifttime: 0.
-       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics
-    u-dc130:
-       description: 'ramp-down from yr 50 of 5.0 stab #1, free ice, -4GtC/yr (#1)'
-       label: '5K Rampdown #1'
-       colour: 'maroon'
-       thickness: 1.2
-       linestyle: ':'
-       shifttime: 0.
-       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics
 
+   u-dc163:
+      description: 'Stable post ramp-down (#1)'
+      label: 'Stab Rampdown #1'
+      colour: 'lawngreen'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics      
 

From 25eaec62a8ccc04bcb7e6317c0786f3320e8d01d Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Tue, 27 Feb 2024 11:41:00 +0000
Subject: [PATCH 08/13] added new stable plots and comments

---
 input_yml/TerraFIRMA_overshoot_runs.yml    |   6 +-
 input_yml/TerraFIRMA_overshoot_stables.yml | 406 +++++++++++++++++++++
 2 files changed, 409 insertions(+), 3 deletions(-)
 create mode 100644 input_yml/TerraFIRMA_overshoot_stables.yml

diff --git a/input_yml/TerraFIRMA_overshoot_runs.yml b/input_yml/TerraFIRMA_overshoot_runs.yml
index 747b3c21..608749d3 100644
--- a/input_yml/TerraFIRMA_overshoot_runs.yml
+++ b/input_yml/TerraFIRMA_overshoot_runs.yml
@@ -17,8 +17,8 @@ strict_file_check: False
 clean: True
 
 
-
 jobs:
+   # PI CONTROL
    u-cs495:
       description: 'PI-Control'
       label: 'PIcontrol'
@@ -29,7 +29,7 @@ jobs:
       timerange: [1850, 2300]
       suite: kmf physics bgc #alkalinity physics
          
- 
+   # ramp up
    u-cx209:
       description: 'E-mode free ice RAMP UP 8GtC/yr #1'
       label: 'Ramp-up #1'
@@ -394,7 +394,7 @@ jobs:
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics
 
-
+   # Ramp down stables.
    u-dc163:
       description: 'Stable post ramp-down (#1)'
       label: 'Stab Rampdown #1'
diff --git a/input_yml/TerraFIRMA_overshoot_stables.yml b/input_yml/TerraFIRMA_overshoot_stables.yml
new file mode 100644
index 00000000..8fcb7cff
--- /dev/null
+++ b/input_yml/TerraFIRMA_overshoot_stables.yml
@@ -0,0 +1,406 @@
+---
+# GC5 N96 ORCA1 spinup analysis
+name: TerraFIRMA_overshoot_runs
+
+# Run the single job analysis
+do_analysis_timeseries: True  
+
+# Download from mass:
+do_mass_download: False
+
+# master analysis suite
+master_suites: physics bgc kmf #alkalinity physics kmf1
+
+# Run without strick check (if True, breaks if job has no years.)
+strict_file_check: False
+
+clean: True
+
+
+
+jobs:
+   # PI CONTROL
+   # u-cs495:
+   #    description: 'PI-Control'
+   #    label: 'PIcontrol'
+   #    colour: 'blue' 
+   #    thickness: 1.2
+   #    linestyle: '-'
+   #    shifttime: -100.
+   #    timerange: [1850, 2300]
+   #    suite: kmf physics bgc #alkalinity physics
+         
+   # # ramp ups
+   # u-cx209:
+   #    description: 'E-mode free ice RAMP UP 8GtC/yr #1'
+   #    label: 'Ramp-up #1'
+   #    colour: 'black'
+   #    thickness: 1.2
+   #    linestyle: '-'
+   #    shifttime: 0.
+   #    #timerange: [1800, 2050]
+   #    suite: kmf physics bgc #alkalinity physics
+
+   # u-cw988:
+   #    description: 'E-mode free ice RAMP UP 8GtC/yr #2'
+   #    label: 'Ramp-up #2'
+   #    colour: 'black'
+   #    thickness: 1.2
+   #    linestyle: '-'
+   #    shifttime: 0.
+   #    #timerange: [1800, 2050]
+   #    suite: kmf physics bgc #alkalinity physics
+           
+   # u-cw989:
+   #    description: 'E-mode free ice RAMP UP 8GtC/yr #3'
+   #    label: 'Ramp-up #3'
+   #    colour: 'black'
+   #    thickness: 1.2
+   #    linestyle: '-'
+   #    shifttime: 0.
+   #    #timerange: [1800, 2050]
+   #    suite: kmf physics bgc #alkalinity physics
+
+   # u-cw990:
+   #    description: 'E-mode free ice RAMP UP 8GtC/yr #4'
+   #    label: 'Ramp-up #4'
+   #    colour: 'black'
+   #    thickness: 1.2
+   #    linestyle: '-'
+   #    shifttime: 0.
+   #    #timerange: [1800, 2050]
+   #    suite: kmf physics bgc #alkalinity physics
+
+   # u-cz826:
+   #    description: 'like cx209 but static ice sheet geometry 8GtC/yr #5'
+   #    label: 'Ramp-up #5'
+   #    colour: 'black'
+   #    thickness: 1.2
+   #    linestyle: '-'
+   #    shifttime: 0.
+   #    #timerange: [1800, 2050]
+   #    suite: kmf physics bgc #alkalinity physics
+
+   # 1.5k Stabilisation
+   u-cy837:
+      description: '1.5K Stabilisation from u-cx209 (#1)'
+      label: '1.5K Stable #1'
+      colour: 'lawngreen'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics   
+   u-cz834:
+      description: '1.5K Stabilisation from u-cw988 (#2)'
+      label: '1.5K Stable #2'
+      colour: 'lawngreen'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics
+   u-da087:
+      description: '1.5K Stabilisation from u-cw989 (#3)'
+      label: '1.5K Stable #3'
+      colour: 'lawngreen' 
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics
+           
+    # 2k Stabilisation
+   u-cy838:
+      description: '2.0K Stabilisation from u-cx209 (#1)'
+      label: '2K Stable #1'
+      colour: 'goldenrod'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics   
+
+   u-cz855:
+      description: '2.0K Stabilisation from cw988 (#2)'
+      label: '2K Stable #2'
+      colour: 'goldenrod'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+
+   u-da266:
+      description: '2.0K Stabilisation from cw988 (#3)'
+      label: '2K Stable #3'
+      colour: 'goldenrod'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics
+           
+    # 2.5k Stabilisation
+   u-cz374:
+      description: '2.5K Stabilisation from u-cx209 (#1)'
+      label: '2.5K Stable #1'
+      colour: 'orange'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics   
+   u-cz859:
+      description: '2.5K Stabilisation from cw988 (#2)'
+      label: '2.5K Stable #2'
+      colour: 'orange' 
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics
+
+
+    # 3.0K Stabilisations
+   u-cz375:
+      description: '3.0K Stabilisation from u-cx209 (#1)'
+      label: '3K Stable #1'
+      colour: 'red'     #
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics          
+
+   u-db587:
+      description: '3.0K Stabilisation from u-cx209 (#2)'
+      label: '3K Stable #2'
+      colour: 'red'     #
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics  
+
+   u-db597:
+      description: '3.0K Stabilisation from u-cx209 (#3)'
+      label: '3K Stable #3'
+      colour: 'red'     #
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics         #       
+
+    # 4k  Stabilisations
+   u-cz376:
+      description: '4.0K Stabilisation from u-cx209 (#1)'
+      label: '4K Stable #1'
+      colour: 'sienna'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics  
+   u-db723:
+      description: '4.0K Stabilisation from u-cw988 (#2)'
+      label: '4K Stable #2'
+      colour: 'sienna'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics      
+   u-db733:
+      description: '4.0K Stabilisation from u-cw989 (#3)'
+      label: '4K Stable #3'
+      colour: 'sienna'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics      
+
+    # 5k & 6K  Stabilisations
+   u-cz377:
+      description: '5.0K Stabilisation from u-cx209 (#1)'
+      label: '5K Stable #1'
+      colour: 'maroon'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics 
+   u-db731:
+      description: '5.0K Stabilisation from u-cw988 (#2)'
+      label: '5K Stable #2'
+      colour: 'maroon'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics 
+   u-dc324:
+      description: '5.0K Stabilisation from u-cw989 (#3)'
+      label: '5K Stable #3'
+      colour: 'maroon'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics 
+
+   u-cz378:
+      description: '6.0K Stabilisation from u-cx209 (#1)'
+      label: '6K Stable #1'
+      colour: 'darkbrown'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics 
+								
+   #  # Ramp downs
+   # u-cz944:
+   #    description: 'Ramp down from cy838 (- 2.0K Stabilisation from u-cx209) (#1)'
+   #    label: '2K Rampdown #1'
+   #    colour: 'goldenrod'
+   #    thickness: 1.2
+   #    linestyle: ':' 
+   #    shifttime: 0.
+   #    #timerange: [1800, 2050]
+   #    suite: kmf physics bgc #alkalinity physics   
+   # u-da800:
+   #    description: 'Ramp down from cy838 (- 2.0K Stabilisation from u-cx209) (#1)'
+   #    label: '2K Rampdown #1'
+   #    colour: 'goldenrod'
+   #    thickness: 1.2
+   #    linestyle: ':'
+   #    shifttime: 0.
+   #    #timerange: [1800, 2050]
+   #    suite: kmf physics bgc #alkalinity physics   
+
+   # u-da697:
+   #    description: '1.5K Rampdown from u-cx209 (#1)'
+   #    label: '1.5K Rampdown #1'
+   #    colour: 'lawngreen'
+   #    thickness: 1.2
+   #    linestyle: ':'
+   #    shifttime: 0.
+   #    #timerange: [1800, 2050]
+   #    suite: kmf physics bgc #alkalinity physics
+
+   # u-da892:
+   #    description: '4.K Rampdown (#1)'
+   #    label: '4.K Rampdown #1'
+   #    colour: 'sienna'
+   #    thickness: 1.2
+   #    linestyle: ':'
+   #    shifttime: 0.
+   #    suite: kmf physics bgc #alkalinity physics
+
+   # u-db223:
+   #    description: '3.K Rampdown (#1)'
+   #    label: '3.K Rampdown #1'
+   #    colour: 'red'
+   #    thickness: 1.2
+   #    linestyle: ':'
+   #    shifttime: 0.
+   #    suite: kmf physics bgc #alkalinity physics
+
+   # u-dc051:
+   #    description: 'Rampdown from yr 50 of 1.5 stab #1, -4GtC/yr (#1)'
+   #    label: '1.5K Rampdown #1'
+   #    colour: 'lawngreen'
+   #    thickness: 1.2
+   #    linestyle: ':'
+   #    shifttime: 0.
+   #    #timerange: [1800, 2050]
+   #    suite: kmf physics bgc #alkalinity physics  
+
+   # u-dc052:
+   #    description: 'Rampdown from yr 200 of 1.5deg, -4GtC/yr (#1)'
+   #    label: '1.5K Rampdown #1'
+   #    colour: 'lawngreen'
+   #    thickness: 1.2
+   #    linestyle: ':'
+   #    shifttime: 0
+   #    #timerange: [1800, 2050]
+   #    suite: kmf physics bgc #alkalinity physics  
+
+   # u-dc248:
+   #    description: '1.5K Rampdown -4GtC/yr, (#1)'
+   #    label: '1.5K Rampdown #1'
+   #    colour: 'lawngreen'
+   #    thickness: 1.2
+   #    linestyle: ':'
+   #    shifttime: 0.
+   #    suite: kmf physics bgc #alkalinity physics
+
+   # u-dc249:
+   #    description: '3.K Rampdown -4GtC/yr, 200 years, (#1)'
+   #    label: '3.K Rampdown #1'
+   #    colour: 'red'
+   #    thickness: 1.2
+   #    linestyle: ':'
+   #    shifttime: 0.
+   #    suite: kmf physics bgc #alkalinity physics
+
+   # u-dc251:
+   #    description: '5K Rampdown -8GtC/yr, 50 years, (#1)'
+   #    label: '5K Rampdown #1'
+   #    colour: 'maroon'
+   #    thickness: 1.2
+   #    linestyle: ':'
+   #    shifttime: 0.
+   #    suite: kmf physics bgc #alkalinity physics
+
+   # u-db956:
+   #    description: '1.5K Rampdown -8GtC/yr, 0 years, (#1)'
+   #    label: '1.5K Rampdown #1'
+   #    colour: 'lawngreen'
+   #    thickness: 1.2
+   #    linestyle: ':'
+   #    shifttime: 0.
+   #    suite: kmf physics bgc #alkalinity physics
+
+   # u-dc032:
+   #    description: 'ramp-down from yr 50 of 3.0 stab #1, free ice, -4GtC/yr (#1)'
+   #    label: '3K Rampdown #1'
+   #    colour: 'red'
+   #    thickness: 1.2
+   #    linestyle: ':'
+   #    shifttime: 0.
+   #    #timerange: [1800, 2050]
+   #    suite: kmf physics bgc #alkalinity physics
+   # u-dc123:
+   #    description: 'ramp-down from yr 50 of 4.0 stab #1, free ice, -4GtC/yr (#1)'
+   #    label: '4K Rampdown #1'
+   #    colour: 'sienna'
+   #    thickness: 1.2
+   #    linestyle: ':'
+   #    shifttime: 0.
+   #    #timerange: [1800, 2050]
+   #    suite: kmf physics bgc #alkalinity physics
+   # u-dc130:
+   #    description: 'ramp-down from yr 50 of 5.0 stab #1, free ice, -4GtC/yr (#1)'
+   #    label: '5K Rampdown #1'
+   #    colour: 'maroon'
+   #    thickness: 1.2
+   #    linestyle: ':'
+   #    shifttime: 0.
+   #    #timerange: [1800, 2050]
+   #    suite: kmf physics bgc #alkalinity physics
+
+   # Ramp down stables.
+   u-dc163:
+      description: 'Stable post ramp-down (#1)'
+      label: 'Stab Rampdown #1'
+      colour: 'lawngreen'
+      thickness: 1.2
+      linestyle: '-'
+      shifttime: 0.
+      #timerange: [1800, 2050]
+      suite: kmf physics bgc #alkalinity physics      
+

From f06ea8a5391aa30e45550d9f674314e4332f2d01 Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Wed, 28 Feb 2024 17:26:29 +0000
Subject: [PATCH 09/13] added new suites.

---
 input_yml/TerraFIRMA_overshoot_recovery.yml   | 18 +++----
 input_yml/TerraFIRMA_overshoot_runs.yml       | 51 +++++++++++--------
 .../TerraFIRMA_overshoot_runs_minimal.yml     |  2 +-
 input_yml/TerraFIRMA_overshoot_stables.yml    | 26 +++++-----
 4 files changed, 52 insertions(+), 45 deletions(-)

diff --git a/input_yml/TerraFIRMA_overshoot_recovery.yml b/input_yml/TerraFIRMA_overshoot_recovery.yml
index 4e014767..6bd94f08 100644
--- a/input_yml/TerraFIRMA_overshoot_recovery.yml
+++ b/input_yml/TerraFIRMA_overshoot_recovery.yml
@@ -24,7 +24,7 @@ jobs:
        thickness: 1.2
        linestyle: '-'
        shifttime: -2094
-       timerange: [-50., 100.]
+       timerange: [-50., 200.]
        suite: kmf physics bgc #alkalinity physics
          
  
@@ -298,14 +298,14 @@ jobs:
        shifttime: -2132.
        suite: kmf physics bgc #alkalinity physics
 
-    u-db956:
-       description: '1.5K Rampdown -8GtC/yr, 0 years, (#1)'
-       label: '1.5K Rampdown #1'
-       colour: 'lawngreen'
-       thickness: 1.2
-       linestyle: ':'
-       shifttime: -1919.
-       suite: kmf physics bgc #alkalinity physics
+#    u-db956:
+#       description: '1.5K Rampdown -8GtC/yr, 0 years, (#1)'
+#       label: '1.5K Rampdown #1'
+#       colour: 'lawngreen'
+#       thickness: 1.2
+#       linestyle: ':'
+#       shifttime: -1919.
+#       suite: kmf physics bgc #alkalinity physics
        
     u-dc032:
        description: 'ramp-down from yr 50 of 3.0 stab #1, free ice, -4GtC/yr (#1)'
diff --git a/input_yml/TerraFIRMA_overshoot_runs.yml b/input_yml/TerraFIRMA_overshoot_runs.yml
index 608749d3..a4b2d9e0 100644
--- a/input_yml/TerraFIRMA_overshoot_runs.yml
+++ b/input_yml/TerraFIRMA_overshoot_runs.yml
@@ -26,7 +26,7 @@ jobs:
       thickness: 1.2
       linestyle: '-'
       shifttime: -100.
-      timerange: [1850, 2300]
+      timerange: [1850, 2400]
       suite: kmf physics bgc #alkalinity physics
          
    # ramp up
@@ -80,7 +80,7 @@ jobs:
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics
 
-    # 1.5k Stabilisation
+   # 1.5k Stabilisation
    u-cy837:
       description: '1.5K Stabilisation from u-cx209 (#1)'
       label: '1.5K Stable #1'
@@ -89,7 +89,8 @@ jobs:
       linestyle: '-'
       shifttime: 0.
       #timerange: [1800, 2050]
-      suite: kmf physics bgc #alkalinity physics   
+      suite: kmf physics bgc #alkalinity physics  
+ 
    u-cz834:
       description: '1.5K Stabilisation from u-cw988 (#2)'
       label: '1.5K Stable #2'
@@ -99,6 +100,7 @@ jobs:
       shifttime: 0.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics
+
    u-da087:
       description: '1.5K Stabilisation from u-cw989 (#3)'
       label: '1.5K Stable #3'
@@ -109,7 +111,7 @@ jobs:
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics
            
-    # 2k Stabilisation
+   # 2k Stabilisation
    u-cy838:
       description: '2.0K Stabilisation from u-cx209 (#1)'
       label: '2K Stable #1'
@@ -128,7 +130,7 @@ jobs:
       linestyle: '-'
       shifttime: 0.
       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics
+      suite: kmf physics bgc #alkalinity physics
 
    u-da266:
       description: '2.0K Stabilisation from cw988 (#3)'
@@ -140,7 +142,7 @@ jobs:
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics
            
-    # 2.5k Stabilisation
+   # 2.5k Stabilisation
    u-cz374:
       description: '2.5K Stabilisation from u-cx209 (#1)'
       label: '2.5K Stable #1'
@@ -161,7 +163,7 @@ jobs:
       suite: kmf physics bgc #alkalinity physics
 
 
-    # 3.0K Stabilisations
+   # 3.0K Stabilisations
    u-cz375:
       description: '3.0K Stabilisation from u-cx209 (#1)'
       label: '3K Stable #1'
@@ -192,7 +194,7 @@ jobs:
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics         #       
 
-    # 4k  Stabilisations
+   # 4k  Stabilisations
    u-cz376:
       description: '4.0K Stabilisation from u-cx209 (#1)'
       label: '4K Stable #1'
@@ -202,6 +204,7 @@ jobs:
       shifttime: 0.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics  
+
    u-db723:
       description: '4.0K Stabilisation from u-cw988 (#2)'
       label: '4K Stable #2'
@@ -211,6 +214,7 @@ jobs:
       shifttime: 0.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics      
+
    u-db733:
       description: '4.0K Stabilisation from u-cw989 (#3)'
       label: '4K Stable #3'
@@ -221,7 +225,7 @@ jobs:
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics      
 
-    # 5k & 6K  Stabilisations
+   # 5k & 6K  Stabilisations
    u-cz377:
       description: '5.0K Stabilisation from u-cx209 (#1)'
       label: '5K Stable #1'
@@ -231,6 +235,7 @@ jobs:
       shifttime: 0.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics 
+
    u-db731:
       description: '5.0K Stabilisation from u-cw988 (#2)'
       label: '5K Stable #2'
@@ -240,6 +245,7 @@ jobs:
       shifttime: 0.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics 
+
    u-dc324:
       description: '5.0K Stabilisation from u-cw989 (#3)'
       label: '5K Stable #3'
@@ -253,14 +259,14 @@ jobs:
    u-cz378:
       description: '6.0K Stabilisation from u-cx209 (#1)'
       label: '6K Stable #1'
-      colour: 'darkbrown'
+      colour: 'indigo'
       thickness: 1.2
       linestyle: '-'
       shifttime: 0.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics 
-								
-    # Ramp downs
+
+   # Ramp downs
    u-cz944:
       description: 'Ramp down from cy838 (- 2.0K Stabilisation from u-cx209) (#1)'
       label: '2K Rampdown #1'
@@ -270,6 +276,7 @@ jobs:
       shifttime: 0.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics   
+
    u-da800:
       description: 'Ramp down from cy838 (- 2.0K Stabilisation from u-cx209) (#1)'
       label: '2K Rampdown #1'
@@ -308,8 +315,6 @@ jobs:
       shifttime: 0.
       suite: kmf physics bgc #alkalinity physics
 
-
-
    u-dc051:
       description: 'Rampdown from yr 50 of 1.5 stab #1, -4GtC/yr (#1)'
       label: '1.5K Rampdown #1'
@@ -357,14 +362,14 @@ jobs:
       shifttime: 0.
       suite: kmf physics bgc #alkalinity physics
 
-   u-db956:
-      description: '1.5K Rampdown -8GtC/yr, 0 years, (#1)'
-      label: '1.5K Rampdown #1'
-      colour: 'lawngreen'
-      thickness: 1.2
-      linestyle: ':'
-      shifttime: 0.
-      suite: kmf physics bgc #alkalinity physics
+#   u-db956:
+#      description: '1.5K Rampdown -8GtC/yr, 0 years, (#1)'
+#      label: '1.5K Rampdown #1'
+#      colour: 'lawngreen'
+#      thickness: 1.2
+#      linestyle: ':'
+#      shifttime: 0.
+#      suite: kmf physics bgc #alkalinity physics
 
    u-dc032:
       description: 'ramp-down from yr 50 of 3.0 stab #1, free ice, -4GtC/yr (#1)'
@@ -375,6 +380,7 @@ jobs:
       shifttime: 0.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics
+
    u-dc123:
       description: 'ramp-down from yr 50 of 4.0 stab #1, free ice, -4GtC/yr (#1)'
       label: '4K Rampdown #1'
@@ -384,6 +390,7 @@ jobs:
       shifttime: 0.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics
+
    u-dc130:
       description: 'ramp-down from yr 50 of 5.0 stab #1, free ice, -4GtC/yr (#1)'
       label: '5K Rampdown #1'
diff --git a/input_yml/TerraFIRMA_overshoot_runs_minimal.yml b/input_yml/TerraFIRMA_overshoot_runs_minimal.yml
index f0e778ba..1f675bd9 100644
--- a/input_yml/TerraFIRMA_overshoot_runs_minimal.yml
+++ b/input_yml/TerraFIRMA_overshoot_runs_minimal.yml
@@ -27,7 +27,7 @@ jobs:
        thickness: 1.2
        linestyle: '-'
        shifttime: -100.
-       timerange: [1850, 2200]
+       timerange: [1850, 2400]
        suite: kmf #physics bgc #alkalinity physics
          
  
diff --git a/input_yml/TerraFIRMA_overshoot_stables.yml b/input_yml/TerraFIRMA_overshoot_stables.yml
index 8fcb7cff..104d8d2a 100644
--- a/input_yml/TerraFIRMA_overshoot_stables.yml
+++ b/input_yml/TerraFIRMA_overshoot_stables.yml
@@ -1,6 +1,6 @@
 ---
 # GC5 N96 ORCA1 spinup analysis
-name: TerraFIRMA_overshoot_runs
+name: TerraFIRMA_overshoot_stables
 
 # Run the single job analysis
 do_analysis_timeseries: True  
@@ -20,15 +20,15 @@ clean: True
 
 jobs:
    # PI CONTROL
-   # u-cs495:
-   #    description: 'PI-Control'
-   #    label: 'PIcontrol'
-   #    colour: 'blue' 
-   #    thickness: 1.2
-   #    linestyle: '-'
-   #    shifttime: -100.
-   #    timerange: [1850, 2300]
-   #    suite: kmf physics bgc #alkalinity physics
+   u-cs495:
+       description: 'PI-Control'
+       label: 'PIcontrol'
+       colour: 'blue'
+       thickness: 1.2
+       linestyle: '-'
+       shifttime: -2094
+       timerange: [-50., 200.]
+       suite: kmf physics bgc #alkalinity physics
          
    # # ramp ups
    # u-cx209:
@@ -129,7 +129,7 @@ jobs:
       linestyle: '-'
       shifttime: 0.
       #timerange: [1800, 2050]
-       suite: kmf physics bgc #alkalinity physics
+      suite: kmf physics bgc #alkalinity physics
 
    u-da266:
       description: '2.0K Stabilisation from cw988 (#3)'
@@ -254,13 +254,13 @@ jobs:
    u-cz378:
       description: '6.0K Stabilisation from u-cx209 (#1)'
       label: '6K Stable #1'
-      colour: 'darkbrown'
+      colour: 'indigo'
       thickness: 1.2
       linestyle: '-'
       shifttime: 0.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics 
-								
+
    #  # Ramp downs
    # u-cz944:
    #    description: 'Ramp down from cy838 (- 2.0K Stabilisation from u-cx209) (#1)'

From af2988c47eb7914e274aadd3417e948411c30071 Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Wed, 28 Feb 2024 17:33:03 +0000
Subject: [PATCH 10/13] added zero to years.

---
 input_yml/TerraFIRMA_overshoot_stables.yml | 38 +++++++++++-----------
 1 file changed, 19 insertions(+), 19 deletions(-)

diff --git a/input_yml/TerraFIRMA_overshoot_stables.yml b/input_yml/TerraFIRMA_overshoot_stables.yml
index 104d8d2a..b5ca893c 100644
--- a/input_yml/TerraFIRMA_overshoot_stables.yml
+++ b/input_yml/TerraFIRMA_overshoot_stables.yml
@@ -88,7 +88,7 @@ jobs:
       colour: 'lawngreen'
       thickness: 1.2
       linestyle: '-'
-      shifttime: 0.
+      shifttime: -1919.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics   
    u-cz834:
@@ -97,7 +97,7 @@ jobs:
       colour: 'lawngreen'
       thickness: 1.2
       linestyle: '-'
-      shifttime: 0.
+      shifttime: -1931.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics
    u-da087:
@@ -106,7 +106,7 @@ jobs:
       colour: 'lawngreen' 
       thickness: 1.2
       linestyle: '-'
-      shifttime: 0.
+      shifttime: -1922.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics
            
@@ -117,7 +117,7 @@ jobs:
       colour: 'goldenrod'
       thickness: 1.2
       linestyle: '-'
-      shifttime: 0.
+      shifttime: -1944.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics   
 
@@ -127,7 +127,7 @@ jobs:
       colour: 'goldenrod'
       thickness: 1.2
       linestyle: '-'
-      shifttime: 0.
+      shifttime: -1956.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics
 
@@ -137,7 +137,7 @@ jobs:
       colour: 'goldenrod'
       thickness: 1.2
       linestyle: '-'
-      shifttime: 0.
+      shifttime: -1947
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics
            
@@ -148,7 +148,7 @@ jobs:
       colour: 'orange'
       thickness: 1.2
       linestyle: '-'
-      shifttime: 0.
+      shifttime: -1970.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics   
    u-cz859:
@@ -157,7 +157,7 @@ jobs:
       colour: 'orange' 
       thickness: 1.2
       linestyle: '-'
-      shifttime: 0.
+      shifttime: -1979.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics
 
@@ -169,7 +169,7 @@ jobs:
       colour: 'red'     #
       thickness: 1.2
       linestyle: '-'
-      shifttime: 0.
+      shifttime: -1992.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics          
 
@@ -179,7 +179,7 @@ jobs:
       colour: 'red'     #
       thickness: 1.2
       linestyle: '-'
-      shifttime: 0.
+      shifttime: -2004.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics  
 
@@ -189,7 +189,7 @@ jobs:
       colour: 'red'     #
       thickness: 1.2
       linestyle: '-'
-      shifttime: 0.
+      shifttime: -1994.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics         #       
 
@@ -200,7 +200,7 @@ jobs:
       colour: 'sienna'
       thickness: 1.2
       linestyle: '-'
-      shifttime: 0.
+      shifttime: -2044.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics  
    u-db723:
@@ -209,7 +209,7 @@ jobs:
       colour: 'sienna'
       thickness: 1.2
       linestyle: '-'
-      shifttime: 0.
+      shifttime: -2049.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics      
    u-db733:
@@ -218,7 +218,7 @@ jobs:
       colour: 'sienna'
       thickness: 1.2
       linestyle: '-'
-      shifttime: 0.
+      shifttime: -2036.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics      
 
@@ -229,7 +229,7 @@ jobs:
       colour: 'maroon'
       thickness: 1.2
       linestyle: '-'
-      shifttime: 0.
+      shifttime: -2082.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics 
    u-db731:
@@ -238,7 +238,7 @@ jobs:
       colour: 'maroon'
       thickness: 1.2
       linestyle: '-'
-      shifttime: 0.
+      shifttime: -2095.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics 
    u-dc324:
@@ -247,7 +247,7 @@ jobs:
       colour: 'maroon'
       thickness: 1.2
       linestyle: '-'
-      shifttime: 0.
+      shifttime: -2084.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics 
 
@@ -257,7 +257,7 @@ jobs:
       colour: 'indigo'
       thickness: 1.2
       linestyle: '-'
-      shifttime: 0.
+      shifttime: -2137.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics 
 
@@ -400,7 +400,7 @@ jobs:
       colour: 'lawngreen'
       thickness: 1.2
       linestyle: '-'
-      shifttime: 0.
+      shifttime: -2019.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics      
 

From 6d962c70aeb5b89208f073a144c54d900f20c1be Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Thu, 29 Feb 2024 11:09:33 +0000
Subject: [PATCH 11/13] dashed dotted drawdown lines

---
 input_yml/TerraFIRMA_overshoot_recovery.yml | 59 +++++++++++----------
 1 file changed, 31 insertions(+), 28 deletions(-)

diff --git a/input_yml/TerraFIRMA_overshoot_recovery.yml b/input_yml/TerraFIRMA_overshoot_recovery.yml
index 6bd94f08..ec93407d 100644
--- a/input_yml/TerraFIRMA_overshoot_recovery.yml
+++ b/input_yml/TerraFIRMA_overshoot_recovery.yml
@@ -201,12 +201,15 @@ jobs:
 #       suite: kmf physics bgc #alkalinity physics 
            
     # Ramp downs
+    # -8: dotted
+    # -4: dashed
+    # -2 dashdot
     u-cz944:
        description: 'Ramp down from cy838 (- 2.0K Stabilisation from u-cx209) (#1)'
        label: '2K Rampdown #1'
        colour: 'goldenrod'
-       thickness: 1.2
-       linestyle: ':' 
+       thickness: 1.7
+       linestyle: 'dotted' 
        shifttime: -1994.
        #timerange: [1800, 2050]
        suite: kmf physics bgc #alkalinity physics   
@@ -215,8 +218,8 @@ jobs:
        description: 'Ramp down from cy838 (- 2.0K Stabilisation from u-cx209) (#1)'
        label: '2K Rampdown #1'
        colour: 'goldenrod'
-       thickness: 1.2
-       linestyle: ':'
+       thickness: 1.7
+       linestyle: 'dotted'
        shifttime: -2144.
        #timerange: [1800, 2050]
        suite: kmf physics bgc #alkalinity physics   
@@ -225,8 +228,8 @@ jobs:
        description: '1.5K Rampdown from u-cx209 (#1)'
        label: '1.5K Rampdown #1'
        colour: 'lawngreen'
-       thickness: 1.2
-       linestyle: ':'
+       thickness: 1.7
+       linestyle: 'dotted'
        shifttime: -1969.
        #timerange: [1800, 2050]
        suite: kmf physics bgc #alkalinity physics
@@ -235,8 +238,8 @@ jobs:
        description: '4.K Rampdown (#1)'
        label: '4.K Rampdown #1'
        colour: 'sienna'
-       thickness: 1.2
-       linestyle: ':'
+       thickness: 1.7
+       linestyle: 'dotted'
        shifttime: -2094.
        suite: kmf physics bgc #alkalinity physics
 
@@ -244,8 +247,8 @@ jobs:
        description: '3.K Rampdown (#1)'
        label: '3.K Rampdown #1'
        colour: 'red'
-       thickness: 1.2
-       linestyle: ':'
+       thickness: 1.7
+       linestyle: 'dotted'
        shifttime: -2032.
        suite: kmf physics bgc #alkalinity physics
 
@@ -255,8 +258,8 @@ jobs:
        description: 'Rampdown from yr 50 of 1.5 stab #1, -4GtC/yr (#1)'
        label: '1.5K Rampdown #1'
        colour: 'lawngreen'
-       thickness: 1.2
-       linestyle: ':'
+       thickness: 1.7
+       linestyle: 'dashed'
        shifttime: -1995.
        #timerange: [1800, 2050]
        suite: kmf physics bgc #alkalinity physics  
@@ -265,8 +268,8 @@ jobs:
        description: 'Rampdown from yr 200 of 1.5deg, -4GtC/yr (#1)'
        label: '1.5K Rampdown #1'
        colour: 'lawngreen'
-       thickness: 1.2
-       linestyle: ':'
+       thickness: 1.7
+       linestyle: 'dashed'
        shifttime: -1969
        #timerange: [1800, 2050]
        suite: kmf physics bgc #alkalinity physics  
@@ -275,8 +278,8 @@ jobs:
        description: '1.5K Rampdown -4GtC/yr, (#1)'
        label: '1.5K Rampdown #1'
        colour: 'lawngreen'
-       thickness: 1.2
-       linestyle: ':'
+       thickness: 1.7
+       linestyle: 'dashed'
        shifttime: -2119.
        suite: kmf physics bgc #alkalinity physics
 
@@ -284,8 +287,8 @@ jobs:
        description: '3.K Rampdown -4GtC/yr, 200 years, (#1)'
        label: '3.K Rampdown #1'
        colour: 'red'
-       thickness: 1.2
-       linestyle: ':'
+       thickness: 1.7
+       linestyle: 'dashed'
        shifttime: -2182.
        suite: kmf physics bgc #alkalinity physics
 
@@ -293,8 +296,8 @@ jobs:
        description: '5K Rampdown -8GtC/yr, 50 years, (#1)'
        label: '5K Rampdown #1'
        colour: 'maroon'
-       thickness: 1.2
-       linestyle: ':'
+       thickness: 1.7
+       linestyle: 'dotted'
        shifttime: -2132.
        suite: kmf physics bgc #alkalinity physics
 
@@ -302,8 +305,8 @@ jobs:
 #       description: '1.5K Rampdown -8GtC/yr, 0 years, (#1)'
 #       label: '1.5K Rampdown #1'
 #       colour: 'lawngreen'
-#       thickness: 1.2
-#       linestyle: ':'
+#       thickness: 1.7
+#       linestyle: '-'
 #       shifttime: -1919.
 #       suite: kmf physics bgc #alkalinity physics
        
@@ -311,8 +314,8 @@ jobs:
        description: 'ramp-down from yr 50 of 3.0 stab #1, free ice, -4GtC/yr (#1)'
        label: '3K Rampdown #1'
        colour: 'red'
-       thickness: 1.2
-       linestyle: ':'
+       thickness: 1.7
+       linestyle: 'dashed'
        shifttime: -2023.
        #timerange: [1800, 2050]
        suite: kmf physics bgc #alkalinity physics
@@ -321,8 +324,8 @@ jobs:
        description: 'ramp-down from yr 50 of 4.0 stab #1, free ice, -4GtC/yr (#1)'
        label: '4K Rampdown #1'
        colour: 'sienna'
-       thickness: 1.2
-       linestyle: ':'
+       thickness: 1.7
+       linestyle: 'dashed'
        shifttime: -2096.
        #timerange: [1800, 2050]
        suite: kmf physics bgc #alkalinity physics
@@ -331,8 +334,8 @@ jobs:
        description: 'ramp-down from yr 50 of 5.0 stab #1, free ice, -4GtC/yr (#1)'
        label: '5K Rampdown #1'
        colour: 'maroon'
-       thickness: 1.2
-       linestyle: ':'
+       thickness: 1.7
+       linestyle: 'dashed'
        shifttime: -2133.
        #timerange: [1800, 2050]
        suite: kmf physics bgc #alkalinity physics

From 05873dccba437f966fcb24141d5de2103310a4dd Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Thu, 29 Feb 2024 11:12:15 +0000
Subject: [PATCH 12/13] Update TerraFIRMA_overshoot_runs.yml

---
 input_yml/TerraFIRMA_overshoot_runs.yml | 362 +++++++++++++++++-------
 1 file changed, 252 insertions(+), 110 deletions(-)

diff --git a/input_yml/TerraFIRMA_overshoot_runs.yml b/input_yml/TerraFIRMA_overshoot_runs.yml
index a4b2d9e0..64c7465d 100644
--- a/input_yml/TerraFIRMA_overshoot_runs.yml
+++ b/input_yml/TerraFIRMA_overshoot_runs.yml
@@ -265,141 +265,283 @@ jobs:
       shifttime: 0.
       #timerange: [1800, 2050]
       suite: kmf physics bgc #alkalinity physics 
-
+          
    # Ramp downs
+   # -8: dotted
+   # -4: dashed
+   # -2 dashdot
    u-cz944:
-      description: 'Ramp down from cy838 (- 2.0K Stabilisation from u-cx209) (#1)'
-      label: '2K Rampdown #1'
-      colour: 'goldenrod'
-      thickness: 1.2
-      linestyle: ':' 
-      shifttime: 0.
-      #timerange: [1800, 2050]
-      suite: kmf physics bgc #alkalinity physics   
+       description: 'Ramp down from cy838 (- 2.0K Stabilisation from u-cx209) (#1)'
+       label: '2K Rampdown #1'
+       colour: 'goldenrod'
+       thickness: 1.7
+       linestyle: 'dotted' 
+       #shifttime: -1994.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics   
 
    u-da800:
-      description: 'Ramp down from cy838 (- 2.0K Stabilisation from u-cx209) (#1)'
-      label: '2K Rampdown #1'
-      colour: 'goldenrod'
-      thickness: 1.2
-      linestyle: ':'
-      shifttime: 0.
-      #timerange: [1800, 2050]
-      suite: kmf physics bgc #alkalinity physics   
+       description: 'Ramp down from cy838 (- 2.0K Stabilisation from u-cx209) (#1)'
+       label: '2K Rampdown #1'
+       colour: 'goldenrod'
+       thickness: 1.7
+       linestyle: 'dotted'
+       #shifttime: -2144.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics   
 
    u-da697:
-      description: '1.5K Rampdown from u-cx209 (#1)'
-      label: '1.5K Rampdown #1'
-      colour: 'lawngreen'
-      thickness: 1.2
-      linestyle: ':'
-      shifttime: 0.
-      #timerange: [1800, 2050]
-      suite: kmf physics bgc #alkalinity physics
+       description: '1.5K Rampdown from u-cx209 (#1)'
+       label: '1.5K Rampdown #1'
+       colour: 'lawngreen'
+       thickness: 1.7
+       linestyle: 'dotted'
+       #shifttime: -1969.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
 
    u-da892:
-      description: '4.K Rampdown (#1)'
-      label: '4.K Rampdown #1'
-      colour: 'sienna'
-      thickness: 1.2
-      linestyle: ':'
-      shifttime: 0.
-      suite: kmf physics bgc #alkalinity physics
+       description: '4.K Rampdown (#1)'
+       label: '4.K Rampdown #1'
+       colour: 'sienna'
+       thickness: 1.7
+       linestyle: 'dotted'
+       #shifttime: -2094.
+       suite: kmf physics bgc #alkalinity physics
 
    u-db223:
-      description: '3.K Rampdown (#1)'
-      label: '3.K Rampdown #1'
-      colour: 'red'
-      thickness: 1.2
-      linestyle: ':'
-      shifttime: 0.
-      suite: kmf physics bgc #alkalinity physics
+       description: '3.K Rampdown (#1)'
+       label: '3.K Rampdown #1'
+       colour: 'red'
+       thickness: 1.7
+       linestyle: 'dotted'
+       #shifttime: -2032.
+       suite: kmf physics bgc #alkalinity physics
+
+
 
    u-dc051:
-      description: 'Rampdown from yr 50 of 1.5 stab #1, -4GtC/yr (#1)'
-      label: '1.5K Rampdown #1'
-      colour: 'lawngreen'
-      thickness: 1.2
-      linestyle: ':'
-      shifttime: 0.
-      #timerange: [1800, 2050]
-      suite: kmf physics bgc #alkalinity physics  
+       description: 'Rampdown from yr 50 of 1.5 stab #1, -4GtC/yr (#1)'
+       label: '1.5K Rampdown #1'
+       colour: 'lawngreen'
+       thickness: 1.7
+       linestyle: 'dashed'
+      # shifttime: -1995.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics  
 
    u-dc052:
-      description: 'Rampdown from yr 200 of 1.5deg, -4GtC/yr (#1)'
-      label: '1.5K Rampdown #1'
-      colour: 'lawngreen'
-      thickness: 1.2
-      linestyle: ':'
-      shifttime: 0
-      #timerange: [1800, 2050]
-      suite: kmf physics bgc #alkalinity physics  
+       description: 'Rampdown from yr 200 of 1.5deg, -4GtC/yr (#1)'
+       label: '1.5K Rampdown #1'
+       colour: 'lawngreen'
+       thickness: 1.7
+       linestyle: 'dashed'
+       #shifttime: -1969
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics  
 
    u-dc248:
-      description: '1.5K Rampdown -4GtC/yr, (#1)'
-      label: '1.5K Rampdown #1'
-      colour: 'lawngreen'
-      thickness: 1.2
-      linestyle: ':'
-      shifttime: 0.
-      suite: kmf physics bgc #alkalinity physics
+       description: '1.5K Rampdown -4GtC/yr, (#1)'
+       label: '1.5K Rampdown #1'
+       colour: 'lawngreen'
+       thickness: 1.7
+       linestyle: 'dashed'
+       #shifttime: -2119.
+       suite: kmf physics bgc #alkalinity physics
 
    u-dc249:
-      description: '3.K Rampdown -4GtC/yr, 200 years, (#1)'
-      label: '3.K Rampdown #1'
-      colour: 'red'
-      thickness: 1.2
-      linestyle: ':'
-      shifttime: 0.
-      suite: kmf physics bgc #alkalinity physics
+       description: '3.K Rampdown -4GtC/yr, 200 years, (#1)'
+       label: '3.K Rampdown #1'
+       colour: 'red'
+       thickness: 1.7
+       linestyle: 'dashed'
+       #shifttime: -2182.
+       suite: kmf physics bgc #alkalinity physics
 
    u-dc251:
-      description: '5K Rampdown -8GtC/yr, 50 years, (#1)'
-      label: '5K Rampdown #1'
-      colour: 'maroon'
-      thickness: 1.2
-      linestyle: ':'
-      shifttime: 0.
-      suite: kmf physics bgc #alkalinity physics
-
-#   u-db956:
-#      description: '1.5K Rampdown -8GtC/yr, 0 years, (#1)'
-#      label: '1.5K Rampdown #1'
-#      colour: 'lawngreen'
-#      thickness: 1.2
-#      linestyle: ':'
-#      shifttime: 0.
-#      suite: kmf physics bgc #alkalinity physics
-
+       description: '5K Rampdown -8GtC/yr, 50 years, (#1)'
+       label: '5K Rampdown #1'
+       colour: 'maroon'
+       thickness: 1.7
+       linestyle: 'dotted'
+       #shifttime: -2132.
+       suite: kmf physics bgc #alkalinity physics
+
+#    u-db956:
+#       description: '1.5K Rampdown -8GtC/yr, 0 years, (#1)'
+#       label: '1.5K Rampdown #1'
+#       colour: 'lawngreen'
+#       thickness: 1.7
+#       linestyle: '-'
+#       shifttime: -1919.
+#       suite: kmf physics bgc #alkalinity physics
+       
    u-dc032:
-      description: 'ramp-down from yr 50 of 3.0 stab #1, free ice, -4GtC/yr (#1)'
-      label: '3K Rampdown #1'
-      colour: 'red'
-      thickness: 1.2
-      linestyle: ':'
-      shifttime: 0.
-      #timerange: [1800, 2050]
-      suite: kmf physics bgc #alkalinity physics
+       description: 'ramp-down from yr 50 of 3.0 stab #1, free ice, -4GtC/yr (#1)'
+       label: '3K Rampdown #1'
+       colour: 'red'
+       thickness: 1.7
+       linestyle: 'dashed'
+      # shifttime: -2023.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
 
    u-dc123:
-      description: 'ramp-down from yr 50 of 4.0 stab #1, free ice, -4GtC/yr (#1)'
-      label: '4K Rampdown #1'
-      colour: 'sienna'
-      thickness: 1.2
-      linestyle: ':'
-      shifttime: 0.
-      #timerange: [1800, 2050]
-      suite: kmf physics bgc #alkalinity physics
+       description: 'ramp-down from yr 50 of 4.0 stab #1, free ice, -4GtC/yr (#1)'
+       label: '4K Rampdown #1'
+       colour: 'sienna'
+       thickness: 1.7
+       linestyle: 'dashed'
+      # shifttime: -2096.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
 
    u-dc130:
-      description: 'ramp-down from yr 50 of 5.0 stab #1, free ice, -4GtC/yr (#1)'
-      label: '5K Rampdown #1'
-      colour: 'maroon'
-      thickness: 1.2
-      linestyle: ':'
-      shifttime: 0.
-      #timerange: [1800, 2050]
-      suite: kmf physics bgc #alkalinity physics
+       description: 'ramp-down from yr 50 of 5.0 stab #1, free ice, -4GtC/yr (#1)'
+       label: '5K Rampdown #1'
+       colour: 'maroon'
+       thickness: 1.7
+       linestyle: 'dashed'
+      # shifttime: -2133.
+       #timerange: [1800, 2050]
+       suite: kmf physics bgc #alkalinity physics
+
+
+
+#    # Ramp downs
+#    u-cz944:
+#       description: 'Ramp down from cy838 (- 2.0K Stabilisation from u-cx209) (#1)'
+#       label: '2K Rampdown #1'
+#       colour: 'goldenrod'
+#       thickness: 1.2
+#       linestyle: ':' 
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics   
+
+#    u-da800:
+#       description: 'Ramp down from cy838 (- 2.0K Stabilisation from u-cx209) (#1)'
+#       label: '2K Rampdown #1'
+#       colour: 'goldenrod'
+#       thickness: 1.2
+#       linestyle: ':'
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics   
+
+#    u-da697:
+#       description: '1.5K Rampdown from u-cx209 (#1)'
+#       label: '1.5K Rampdown #1'
+#       colour: 'lawngreen'
+#       thickness: 1.2
+#       linestyle: ':'
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics
+
+#    u-da892:
+#       description: '4.K Rampdown (#1)'
+#       label: '4.K Rampdown #1'
+#       colour: 'sienna'
+#       thickness: 1.2
+#       linestyle: ':'
+#       shifttime: 0.
+#       suite: kmf physics bgc #alkalinity physics
+
+#    u-db223:
+#       description: '3.K Rampdown (#1)'
+#       label: '3.K Rampdown #1'
+#       colour: 'red'
+#       thickness: 1.2
+#       linestyle: ':'
+#       shifttime: 0.
+#       suite: kmf physics bgc #alkalinity physics
+
+#    u-dc051:
+#       description: 'Rampdown from yr 50 of 1.5 stab #1, -4GtC/yr (#1)'
+#       label: '1.5K Rampdown #1'
+#       colour: 'lawngreen'
+#       thickness: 1.2
+#       linestyle: ':'
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics  
+
+#    u-dc052:
+#       description: 'Rampdown from yr 200 of 1.5deg, -4GtC/yr (#1)'
+#       label: '1.5K Rampdown #1'
+#       colour: 'lawngreen'
+#       thickness: 1.2
+#       linestyle: ':'
+#       shifttime: 0
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics  
+
+#    u-dc248:
+#       description: '1.5K Rampdown -4GtC/yr, (#1)'
+#       label: '1.5K Rampdown #1'
+#       colour: 'lawngreen'
+#       thickness: 1.2
+#       linestyle: ':'
+#       shifttime: 0.
+#       suite: kmf physics bgc #alkalinity physics
+
+#    u-dc249:
+#       description: '3.K Rampdown -4GtC/yr, 200 years, (#1)'
+#       label: '3.K Rampdown #1'
+#       colour: 'red'
+#       thickness: 1.2
+#       linestyle: ':'
+#       shifttime: 0.
+#       suite: kmf physics bgc #alkalinity physics
+
+#    u-dc251:
+#       description: '5K Rampdown -8GtC/yr, 50 years, (#1)'
+#       label: '5K Rampdown #1'
+#       colour: 'maroon'
+#       thickness: 1.2
+#       linestyle: ':'
+#       shifttime: 0.
+#       suite: kmf physics bgc #alkalinity physics
+
+# #   u-db956:
+# #      description: '1.5K Rampdown -8GtC/yr, 0 years, (#1)'
+# #      label: '1.5K Rampdown #1'
+# #      colour: 'lawngreen'
+# #      thickness: 1.2
+# #      linestyle: ':'
+# #      shifttime: 0.
+# #      suite: kmf physics bgc #alkalinity physics
+
+#    u-dc032:
+#       description: 'ramp-down from yr 50 of 3.0 stab #1, free ice, -4GtC/yr (#1)'
+#       label: '3K Rampdown #1'
+#       colour: 'red'
+#       thickness: 1.2
+#       linestyle: ':'
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics
+
+#    u-dc123:
+#       description: 'ramp-down from yr 50 of 4.0 stab #1, free ice, -4GtC/yr (#1)'
+#       label: '4K Rampdown #1'
+#       colour: 'sienna'
+#       thickness: 1.2
+#       linestyle: ':'
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics
+
+#    u-dc130:
+#       description: 'ramp-down from yr 50 of 5.0 stab #1, free ice, -4GtC/yr (#1)'
+#       label: '5K Rampdown #1'
+#       colour: 'maroon'
+#       thickness: 1.2
+#       linestyle: ':'
+#       shifttime: 0.
+#       #timerange: [1800, 2050]
+#       suite: kmf physics bgc #alkalinity physics
 
    # Ramp down stables.
    u-dc163:

From 3407f9f64ade3ed216e58176d6ab41e95656f353 Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Wed, 20 Mar 2024 10:46:59 +0000
Subject: [PATCH 13/13] Added recent changes

---
 bgcval2/download_from_mass.py              | 2 ++
 input_yml/TerraFIRMA_overshoot_stables.yml | 2 +-
 key_files/totalintpp.yml                   | 2 +-
 3 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/bgcval2/download_from_mass.py b/bgcval2/download_from_mass.py
index 1270c1de..139c67c6 100755
--- a/bgcval2/download_from_mass.py
+++ b/bgcval2/download_from_mass.py
@@ -442,6 +442,8 @@ def download_from_mass(
     header_lines.append(''.join(['# run script with:\n# source ', os.path.abspath(download_script_path),'\n']))
     header_lines.append('# moo passwd -r # if mass password is expired\n')
     header_lines.append('source /etc/bashrc\n') # make sure script can access moo tools.
+    header_lines.append('echo "\n\nDownloading '+jobID+' on mass-cli1"\n') # make sure script can access moo tools.
+
     download_script_txt = ''.join(header_lines)
 
     # moo ls:
diff --git a/input_yml/TerraFIRMA_overshoot_stables.yml b/input_yml/TerraFIRMA_overshoot_stables.yml
index b5ca893c..25a66994 100644
--- a/input_yml/TerraFIRMA_overshoot_stables.yml
+++ b/input_yml/TerraFIRMA_overshoot_stables.yml
@@ -27,7 +27,7 @@ jobs:
        thickness: 1.2
        linestyle: '-'
        shifttime: -2094
-       timerange: [-50., 200.]
+       timerange: [-50., 400.]
        suite: kmf physics bgc #alkalinity physics
          
    # # ramp ups
diff --git a/key_files/totalintpp.yml b/key_files/totalintpp.yml
index 3553d94c..773c89be 100644
--- a/key_files/totalintpp.yml
+++ b/key_files/totalintpp.yml
@@ -12,4 +12,4 @@ model_convert   :
     areafile: $PATHS_GRIDFILE
 layers          : layerless
 regions         : regionless
-
+smoothings      : DataOnly both5 both30 movingav30years 5and30 30and100