A few handy jobs for looking aat a few UK MPA regions.

.gitignore

@@ -20,3 +20,4 @@ _sidebar.rst.inc
 local_test/BGC_data/valeriu
 mass_scripts
 CompareReports2
+.idea/workspace.xml

bgcval2/bgcvaltools/makeMask.py

@@ -45,13 +45,13 @@ def makeMask(name, newSlice, xt, xz, xy, xx, xd, debug=False):
 	:param xy: A one-dimensional array of the dataset latitudes.
 	:param xx: A one-dimensional array of the dataset longitudes.
 	:param xd: A one-dimensional array of the data.
-	
+
 	This function produces a mask to hides all points that are not in the requested region.
-	
-	Note that xt,xz,xy,xx,xd should all be the same shape and size. 
-	
+
+	Note that xt,xz,xy,xx,xd should all be the same shape and size.
+
 	This functional can call itself, if two regional masks are needed.
-	
+
 	Please add your own regions, at the bottom of the list, if needed.
 	"""
     if debug:
@@ -270,6 +270,26 @@ def makeMask(name, newSlice, xt, xz, xy, xx, xd, debug=False):
         mx += np.ma.masked_outside(xy, 49., 52.).mask
         return mx
 
+    if newSlice == 'Ascension':
+        mx = np.ma.masked_outside(xx, -17.246, -11.487).mask # longitude
+        mx += np.ma.masked_outside(xy, -10.813, -5.053).mask # Lattitue
+        return mx
+
+    if newSlice == 'TristandaCunha': # MPA covers two islands. This is very approximate
+        # Edinburgh of 7 seas: -37.10646514207477 South,, -12.297874143783694  West
+        # Gough island: -40.322968275628654 South, -9.935193569988446 West
+        mx = np.ma.masked_outside(xx, -12.3 - 3., -9.9 + 3.).mask # longitude # West
+        mx += np.ma.masked_outside(xy, -40.3 -3, -37.1 + 3.).mask # Lattitue  # South
+        return mx
+
+    if newSlice == 'Pitcairn': # MPA covers several islands. This is very approximate
+        # Ducie Island:  24.66 S 124.75 W (Eastern most)
+        # Oeno island: 23.9 S 130.74 W (western most) (Western boundary is not the full EEZ)
+        mx = np.ma.masked_outside(xx, -130.74 - 1.5, 124.75 + 3.).mask # longitude # West
+        mx += np.ma.masked_outside(xy, -24.66 -3, -23.9 + 3.).mask # Lattitue  # South
+        return mx
+
+
     if newSlice == 'WeddelSea':
         mx = np.ma.masked_outside(xx, -60., -20.).mask
         mx += np.ma.masked_outside(xy, -80., -64.).mask
@@ -487,13 +507,13 @@ def makeMask(name, newSlice, xt, xz, xy, xx, xd, debug=False):
                 print("Corner case:", la, lo, bathy[la, lo])
                 nmask[i] = 1
             if newSlice == "maskBelowBathy":
-                if (bathy[la, lo] - 10.) > abs(z): 
+                if (bathy[la, lo] - 10.) > abs(z):
                     nmask[i] = 1
             elif newSlice in ["OnShelf", 'AMM_Shelf']:
-                if bathy[la, lo] >= shelfDepth: 
+                if bathy[la, lo] >= shelfDepth:
                     nmask[i] = 1
             elif newSlice in ["OffShelf", 'AMM_OffShelf']:
-                if bathy[la, lo] < shelfDepth: 
+                if bathy[la, lo] < shelfDepth:
                     nmask[i] = 1
         if i > 0:
             try:

bgcval2/bgcvaltools/pftnames.py

@@ -209,7 +209,7 @@ def makeLongNameDict():
     lnd['Chlorophylla'] = 'Chlorophyll'
     lnd['Chlorophyll_cci'] = "Chlorophyll (CCI)"
     lnd['Chlorophyll_pig'] = "Chlorophyll (Pigments)"
-    lnd['TotalChlorophyll'] = 'Total Chlorophyll' 
+    lnd['TotalChlorophyll'] = 'Total Chlorophyll'
     lnd['CHD'] = "Diatom Chlorophyll"
     lnd['CHN'] = "Non-Diatom Chlorophyll"
     lnd['DiatomChlorophyll'] = "Diatom Chlorophyll"
@@ -247,7 +247,7 @@ def makeLongNameDict():
 
     lnd['VolumeMeanTemperature'] = "Volume-weighted Mean Temperature"
     lnd['GlobalMeanSalinity'] = "Global Volume-weighted Mean Salinity"
-   
+
 
     lnd['TotalHeatFlux'] = "Global Total Heat Flux"
     lnd['HeatFlux'] = "Heat Flux"
@@ -326,7 +326,7 @@ def makeLongNameDict():
     lnd['SSS'] = 'Sea Surface Salinty'
 
     lnd['MA_DraKE'] = 'Drake Passage Current'
-    lnd['MA_AMOC_26N'] = 'AMOC at 26.5N' 
+    lnd['MA_AMOC_26N'] = 'AMOC at 26.5N'
     lnd['MA_ZOS'] = 'Sea Surface Height'
     lnd['MA_MLD'] = 'Mixed Layer Depth'
     lnd['MA_MLD_Sigma'] = 'Mixed Layer Depth (Sigma)'
@@ -400,6 +400,10 @@ def makeLongNameDict():
     lnd['LabradorSea'] = "Labrador Sea"
     lnd['NorwegianSea'] = "Norwegian Sea"
     lnd['Cornwall'] = "Cornwall"
+    lnd['Ascension'] = "Ascension Island"
+    lnd['TristandaCunha'] = "Tristan da Cunha"
+    lnd['Pitcairn'] = "Pitcairn"
+
 
     lnd['100m'] = "100m deep"
     lnd['200m'] = "200m deep"
@@ -732,7 +736,7 @@ def getLongName(text, debug=False):
 
 
 def fancyUnits(units, debug=False):
-    """	
+    """
 	Converts ascii units string into latex style formatting.
 	"""
     units = units.replace('[', '').replace(']', '')

input_yml/TerraFIRMA_overshoot_mpas.yml

@@ -0,0 +1,120 @@
+---
+# GC5 N96 ORCA1 spinup analysis
+name: TerraFIRMA_overshoot_MPAs
+
+# Run the single job analysis
+do_analysis_timeseries: True  
+
+# Download from mass:
+do_mass_download: False
+
+# master analysis suite
+master_suites: kmf mpas # 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 mpas #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 mpas #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 mpas # 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 mpas # 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 mpas # 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 mpas # 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 mpas # 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 mpas # 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 mpas #physics bgc #alkalinity physics
+
+
+
+
+
+
+

key_files/mpa_airseafluxco2.yml

@@ -0,0 +1,13 @@
+---
+name            : AirSeaFluxCO2
+units           : mmolC/m2/d
+model           : MEDUSA
+modelgrid       : eORCA1
+dimensions      : 2
+modelFiles      : $BASEDIR_MODEL/$JOBID/medusa*$JOBIDo_1y_*_diad-T.nc
+model_vars      : CO2FLUX
+model_convert   : NoChange
+layers          : layerless
+regions         : Global Ascension TristandaCunha Pitcairn Cornwall
+
+

key_files/mpa_alkalinity.yml

@@ -0,0 +1,23 @@
+---
+name            : Alkalinity
+units           : meq/m^3
+model           : MEDUSA
+modelgrid       : eORCA1
+dimensions      : 3
+
+# The filenames
+modelFiles      : $BASEDIR_MODEL/$JOBID/medusa*$JOBID*_1y_*_ptrc-T.nc
+modelFile_p2p   : $BASEDIR_MODEL/$JOBID/medusa*$JOBID*_1y_*$YEAR????_ptrc-T.nc
+#dataFile        : $BASEDIR_OBS/Alk.nc
+
+# # Model coordinates/dimension names
+model_vars      : ALK
+model_convert   : NoChange
+
+#data_vars : Alk
+#data_convert:
+#    function: convertmeqm3TOumolkg
+
+layers          : Surface #50m #;100m 200m 500m 1000m 2000m
+regions         : Global Ascension TristandaCunha Pitcairn Cornwall
+

key_files/mpa_chlorophyll.yml

@@ -0,0 +1,20 @@
+---
+name            : Chlorophyll
+units           : mg C/m^3
+model           : MEDUSA
+modelgrid       : eORCA1
+dimensions      : 3
+
+# The filenames
+modelFiles      : $BASEDIR_MODEL/$JOBID/medusa*_1y_*_ptrc-T.nc
+gridFile        : $BASEDIR_MODEL/mesh_mask_eORCA1_wrk.nc
+
+# Model coordinates/dimension names
+model_vars      : CHD CHN
+model_convert   : sum
+
+layers          : Surface
+regions         : Global Ascension TristandaCunha Pitcairn Cornwall
+
+
+

key_files/mpa_dic.yml

@@ -0,0 +1,19 @@
+---
+name            : DIC
+units           : mmol C/m^3
+model           : MEDUSA
+modelgrid       : eORCA1
+dimensions      : 3
+
+# The filenames
+modelFiles      : $BASEDIR_MODEL/$JOBID/medusa*$JOBIDo_1y_*_ptrc-T.nc
+modelFile_p2p   : $BASEDIR_MODEL/$JOBID/medusa*$JOBIDo_1y_*$YEAR????_ptrc-T.nc
+
+# # Model coordinates/dimension names
+model_vars      : DIC
+model_convert   : NoChange
+
+
+layers          : Surface #50m #;100m 200m 500m 1000m 2000m
+regions         : Global Ascension TristandaCunha Pitcairn Cornwall
+

key_files/mpa_iron.yml

@@ -0,0 +1,32 @@
+---
+name            : Iron
+units           : mmol Fe/m^3
+datasource      : Initial Conditions
+model           : MEDUSA
+modelgrid       : eORCA1
+dimensions      : 3
+
+# The filenames
+modelFiles      : $BASEDIR_MODEL/$JOBID/medusa*$JOBIDo_1y_*_ptrc-T.nc
+modelFile_p2p   : $BASEDIR_MODEL/$JOBID/medusa*$JOBDo_1y_*$YEAR????_ptrc-T.nc
+#dataFile        : /data/euryale7/backup/ledm/UKESM/InitialConditions/UKESM_fields_1860_eORCA1_small.nc
+gridFile        : $BASEDIR_MODEL/mesh_mask_eORCA1_wrk.nc
+
+# Model coordinates/dimension names
+model_vars      : FER
+model_convert   : 
+    function: multiplyBy
+    factor : 1000
+
+# Data coordinates names
+#data_vars       : FER
+#data_tdict      : ZeroToZero
+#data_convert    : multiplyBy
+#data_convert_factor : 1000
+
+layers          : Surface #Transect ;CanRusTransect PTransect SOTransect Equator ArcTransect AntTransect ArcTransect AntTransect
+regions         : Global Ascension TristandaCunha Pitcairn Cornwall
+
+
+
+

key_files/mpa_mld.yml

@@ -0,0 +1,35 @@
+---
+name            : MLD
+units           : m
+dimensions      : 2
+model           : NEMO
+datasource      : IFERMER
+
+# 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/IFREMER-MLD/mld_DT02_c1m_reg2.0-annual.nc
+
+# Model coordinates/dimension names
+model_vars      : mlotst
+model_convert   : NoChange
+layers          : layerless
+
+#model_vars      : somxl010 somxzint1
+#model_convert:
+#    path: bgcval2/functions/applyLandMask.py
+#    function: applyLandMask
+#    areafile: $PATHS_GRIDFILE
+#    maskname : tmask
+
+data_vars       : mld
+data_tdict      : ZeroToZero
+data_convert:
+    path: bgcval2/functions/applyLandMask.py
+    function: applyLandMask
+    maskname : mask
+    areafile: $BASEDIR_OBS/IFREMER-MLD/mld_DT02_c1m_reg2.0-annual.nc
+#layers          : Surface
+#regions         : Global ignoreInlandSeas SouthernOcean ArcticOcean Equator10 NorthPacificOcean SouthPacificOcean NorthAtlanticOcean  SouthAtlanticOcean 
+regions         : Global Ascension TristandaCunha Pitcairn Cornwall
+