fully working vesrion in prep for nemo 4.2

Author: ledm

bgcval2/bgcvaltools/generic_map_legend.py

@@ -210,6 +210,11 @@ def make_figure(region, orcaGridfn=None):
     #cbar = pyplot.colorbar(ax=ax_pc, cax=im3)
 
     pyplot.suptitle(region+': '+getLongName(region))
+
+    area = calc_area(region, orcaGridfn=orcaGridfn)
+    fig.text(
+        0.5, 0.9, 'Area: '+str(f"{int(area):,d}")+' m$^2$', ha='center', va='center')
+
     print('saving:', fig_fn)
     pyplot.savefig(fig_fn,dpi=300.)
     pyplot.savefig(fig_fn.replace('.png', '_trans.png'), transparent=True)
@@ -251,14 +256,15 @@ def calc_area(region, orcaGridfn = None):
 
     new_area = np.ma.masked_where(region_mask + old_mask_flat, flat_area)
     total_area=new_area.sum() 
-    print('region:', total_area)
+    print(region, ' Area:', total_area, 'm2')
 
 
     out_fn = bvt.folder('region_areas')+region+'.txt'
     txt = ''.join([region, ', ', str(int(total_area)), '\n'])
     fn = open(out_fn, 'w')
     fn.write(txt)
     fn.close()
+    return total_area
 
 
 
@@ -274,19 +280,18 @@ def main():
 
 
     regions = [
-#                'LIseas',
-#                'LIGINseas',
+
 #                'GLINseas',
 #                'Ascension',
 #              'ITCZ',
 #               'TristandaCunha',
 #               'Pitcairn',
 #                'Cornwall',
-                'BritishIsles',
+                # 'BritishIsles',
 #                'SubtropicNorthAtlantic',
 #                'SPNA',
 #                'STNA',        
-#                'SouthernOcean',
+               'SouthernOcean',
 #                'subpolar',
 #                'NorthEastAtlantic',
 #                'ArcticOcean',
@@ -298,15 +303,17 @@ def main():
 #                'SouthPacificOcean',
 #                'NorthAtlanticOcean',
 #                'SouthAtlanticOcean',
-#                'GINseas',
-#                'LabradorSea',
-#                'IrmingerSea',
+            #    'GINseas',
+            #    'LabradorSea',
+            #    'IrmingerSea',
+            #    'LIseas',
+               'LIGINseas',               
 #                'EquatorialAtlanticOcean',
 #                'Global',
 #                'ignoreInlandSeas',
     ]
     for region in regions[:]:
-        calc_area(region, orcaGridfn=orcaGridfn)
+        area = calc_area(region, orcaGridfn=orcaGridfn)
         make_figure(region, orcaGridfn=orcaGridfn) 
 
 if __name__ == "__main__":

bgcval2/bgcvaltools/pftnames.py

@@ -324,6 +324,7 @@ def makeLongNameDict():
     lnd['sossheig'] = "Sea Surface Height"
     lnd['FreshwaterFlux'] = "Freshwater Flux"
     lnd['hfbasinatlantic'] = 'Northward Atlantic heat transport'
+    lnd['sltbasinatlantic'] = 'Northward Atlantic salt transport'
     lnd['exportRatio'] = "Export Ratio"
     lnd['LocalExportRatio'] = "Export Ratio"
     lnd['OCN_RHOSW'] = 'Density'
@@ -461,10 +462,14 @@ def makeLongNameDict():
     lnd['MaxMonthlyMLD'] = 'Annual Maximum Mixed Layer Depth'
     lnd['MinMonthlyMLD'] = 'Annual Minimum Mixed Layer Depth'
 
-    lnd['mld_DT02'] = 'MLD:Fixed Threshold Temperature '
+    lnd['mld_DT02'] = 'MLD:Fixed Threshold Temperature'
     lnd['mld_DR003'] = 'MLD:Fixed Threshold Density'
     lnd['mld_DReqDTm02'] = 'MLD:Variable Threshold Density'
 
+    lnd['tnpeo'] = 'Tendency of ocean potential energy content'
+    lnd['mldzintt0_2'] = 'MLD - mldzintt0_2' #  mldr0_3 T based, what was o
+    lnd['mldr0_3'] = 'MLD mldr0_3' #: rho-based, surface reference, output in u-dv346
+
     #####
     # Depth layers/transects.
     lnd['AtlanticTransect'] = "Atlantic Transect"

bgcval2/functions/circulation.py

@@ -325,7 +325,7 @@ def drakePassage(nc, keys, **kwargs):
         assert 0
     print('drakePassage:', grid, 'LON', LON, 'LAT0',LAT0, 'LAT1', LAT1)
 
-    all_e3u_keys = ['thkcello', 'e3u']
+    all_e3u_keys = ['thkcello', 'thkcelluo', 'e3u']
     e3u_keys = find_keys_in_nc(nc, all_e3u_keys)
     e3u = nc.variables[e3u_keys[0]][0, :, LAT0:LAT1, LON]
 
@@ -371,7 +371,15 @@ def davisstraightflux(nc, keys, straight='Davis', **kwargs):
         print('These needs to be multiplied by the thkcello.')
         assert 0
 
-    thkcello = nc.variables['thkcello'][0, :, LAT0:LAT1, LON]
+  
+    if 'thkcello' in nc.variables.keys():
+        thkcello = nc.variables['thkcello'][0, :, LAT0:LAT1, LON]
+    elif 'thkcelluo' in nc.variables.keys():
+        thkcello = nc.variables['thkcelluo'][0, :, LAT0:LAT1, LON]
+    elif 'thkcellvo' in nc.variables.keys():
+        thkcello = nc.variables['thkcellvo'][0, :, LAT0:LAT1, LON]
+    else: assert 0
+    #thkcello = nc.variables['thkcello'][0, :, LAT0:LAT1, LON]
 
     print('Davis straight:', grid, 'LON', LON, 'LAT0',LAT0, 'LAT1', LAT1)
 
@@ -503,11 +511,19 @@ def TwentySixNorth(nc, keys, lat='26N', return_max_depth=False, **kwargs):
 
     atlmoc = np.array(np.zeros_like(zv[0, :, :, 0]))
 
+    # if 'thkcello' in nc.variables.keys():
+    #     thkcello = nc.variables['thkcello'][0, :, latslice, :]
+
     if 'thkcello' in nc.variables.keys():
         thkcello = nc.variables['thkcello'][0, :, latslice, :]
-        thkcello = np.ma.masked_where(thkcello.mask + zv[0].mask, thkcello)
+    elif 'thkcelluo' in nc.variables.keys():
+        thkcello = nc.variables['thkcelluo'][0, :, latslice, :]
+    elif 'thkcellvo' in nc.variables.keys():
+        thkcello = nc.variables['thkcellvo'][0, :, latslice, :]
     else:
         thkcello = e3v_AMOC[:]
+    thkcello = np.ma.array(thkcello)
+    thkcello = np.ma.masked_where(thkcello.mask + zv[0].mask, thkcello)
 
     depths = np.ma.abs(np.cumsum(thkcello, axis=0))
 
@@ -635,9 +651,16 @@ def gulfstream_depth(nc, keys, **kwargs):
     print(lats, lons)
 
     vo = nc.variables[keys[0]][0, :, latslice26Nnm, lonslice_70W].squeeze() # m/s
-    thickness = nc.variables['thkcello'][0,:,latslice26Nnm, lonslice_70W].squeeze()
+    # thickness = nc.variables['thkcello'][0,:,latslice26Nnm, lonslice_70W].squeeze()
     depth = np.abs(np.cumsum(thickness, axis=0))# depth array
 
+    if 'thkcello' in nc.variables.keys():
+        thickness = nc.variables['thkcello'][0,:,latslice26Nnm, lonslice_70W].squeeze()
+    elif 'thkcelluo' in nc.variables.keys():
+        thickness = nc.variables['thkcelluo'][0,:,latslice26Nnm, lonslice_70W].squeeze()
+    elif 'thkcellvo' in nc.variables.keys():
+        thickness = nc.variables['thkcellvo'][0,:,latslice26Nnm, lonslice_70W].squeeze()
+
     vo = np.ma.masked_where(vo.mask + (vo == 0.), vo)
 
 
@@ -726,8 +749,14 @@ def gulfstream(nc, keys, **kwargs):
     lons = nc.variables['nav_lon'][latslice26Nnm, lonslice_70W]
     vo = np.ma.array(nc.variables[keys[0]][0, :, latslice26Nnm, lonslice_70W]) # m/s
     vo = np.ma.masked_where(vo.mask + (vo <= 0.), vo) 
+    
+    if 'thkcello' in nc.variables.keys():
+        thickness = nc.variables['thkcello'][0,:,latslice26Nnm, lonslice_70W] 
+    elif 'thkcelluo' in nc.variables.keys():
+          thickness = nc.variables['thkcelluo'][0,:,latslice26Nnm, lonslice_70W]
+    elif 'thkcellvo' in nc.variables.keys():
+          thickness = nc.variables['thkcellvo'][0,:,latslice26Nnm, lonslice_70W]
 
-    thickness = nc.variables['thkcello'][0,:,latslice26Nnm, lonslice_70W] 
     depth = np.abs(np.cumsum(thickness, axis=0))# depth array
     #print(vo.shape, thickness.shape, e1v_AMOC26N.shape)
     gs = 0.
@@ -767,7 +796,16 @@ def twentysixnorth025(nc, keys, **kwargs):
     latslice26N = eORCA025_latslice26Nnm
     lonslice26N = eORCA025_lonslice26Nnm
     vo =  np.ma.array(nc.variables[keys[0]][..., latslice26N, lonslice26N]) # #vo in m/s
-    thkcello = np.ma.array(nc.variables['thkcello'][..., latslice26N, lonslice26N]) # #thickness
+#   thkcello = np.ma.array(nc.variables['thkcello'][..., latslice26N, lonslice26N]) # #thickness
+
+    if 'thkcello' in nc.variables.keys():
+        thkcello = nc.variables['thkcello'][..., latslice26N, lonslice26N] # #thickness
+    elif 'thkcelluo' in nc.variables.keys():
+        thkcello = nc.variables['thkcelluo'][..., latslice26N, lonslice26N] # #thickness
+    elif 'thkcellvo' in nc.variables.keys():
+        thkcello = nc.variables['thkcellvo'][..., latslice26N, lonslice26N] # #thickness
+    thkcello = np.ma.array(thkcello)
+
     depths = np.ma.cumsum(thkcello, axis=1)
 
     depths = np.ma.masked_where(thkcello.mask + np.abs(depths)<500., depths) # masked above 500m depth.

bgcval2/functions/standard_functions.py

@@ -145,17 +145,40 @@ def maskzeroes(nc, keys):
     print('maskzeroes:', arr.min(), '->', arr.max(), arr.dtype, arr.mean())
     return arr
 
+# def chose_best_mask_zeroes(nc, keys):
+#     """
+#     Chooses the best variable from keys, then masks all instances of exactly zero. 
+#     """
+#     var0 = find_best_var(nc, keys)
+#     arr = np.ma.array(nc.variables[var0][:]) #, dtype=np.float64)
+#     arr = np.ma.masked_where(arr == 0. + arr.mask, arr)
+#     print('chose_best_mask_zeroes:', arr.min(), '->', arr.max(), arr.dtype, arr.mean())
+#     return arr
+
 def sums(nc,keys):
     """
     Loads Key[0] from the netcdf, then sums the other keys.
     """
     a = nc.variables[keys[0]][:]
+    
     for k in keys[1:]:
         a += nc.variables[k]
     a = np.ma.masked_where(a == 0. + a.mask, a)
     return a
 
 
+#def area_sum(nc, keys):
+#    """
+#    Loads Key[0] from the netcdf, then calculates the sum over the area.
+#    """
+#    a = nc.variables[keys[0]][:]
+#    for k in keys[1:]:
+#        a += nc.variables[k]
+#    a = np.ma.masked_where(a == 0. + a.mask, a)
+#    return a
+
+
+
 def oxconvert(nc,keys):
     """
     Loads keys[0] from the netcdf, but multiplies by 44.771 (to convert oxygen units ).

key_files/hfy.yml

@@ -22,7 +22,7 @@ modelFiles      : $BASEDIR_MODEL/$JOBID/nemo_$JOBIDo_1y_*_grid-V.nc
 gridFile        : $PATHS_GRIDFILE
 
 # Model coordinates/dimension names
-model_vars      : hfy
+model_vars      : hfy hfyint 
 model_convert   : maskzeroes
 
 metrics         : mean

key_files/sowaflup.yml

@@ -22,7 +22,7 @@ modelFile_p2p   : $BASEDIR_MODEL/$JOBID/nemo*$JOBIDo_1y_*$YEAR????_grid-T.nc
 gridFile        : $PATHS_GRIDFILE
 
 # Model coordinates/dimension names
-model_vars      : sowaflup
+model_vars      : sowaflup empmr
 model_convert   : choose_best_var
 
 layers          : layerless

key_lists/debug.yml

@@ -19,6 +19,7 @@ keys:
 #   DavisStraightMassFlux: True
 #   NorwegianSeaMassFlux: True
 
+    sltbasinatlantic: True
 #   pbsi3: True
 #    agessc: True
 #   int_pn: True
@@ -47,7 +48,7 @@ keys:
 #    SouthernTotalIceArea: True
 
     #ZOS: True
-    sowindsp: True
+#    sowindsp: True
     #sowflisf: True
     #evs: True
     #precip: True

key_lists/kmf.yml

@@ -13,7 +13,7 @@ keys:
     # NoCaspianAirSeaFluxCO2: True
     # IntPP_OSU: True
     # GlobalExportRatio: True
-    TotalIceExtent: True
+#    TotalIceExtent: True
     # NorthernTotalIceExtent: True
     # SouthernTotalIceExtent: True
     # GlobalMeanSalinity: True

key_lists/physics.yml

@@ -26,14 +26,14 @@ keys:
     # MinMonthlyMLD: True               # MLD Monthly min
 
     # Ice keys:
-    TotalIceArea: True # work in progress
-    NorthernTotalIceArea: True  # work in progress
-    SouthernTotalIceArea: True  # work in progress
+#    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
+#    TotalIceExtent: True  # work in progress
+#    NorthernTotalIceExtent: True  # work in progress
+#    SouthernTotalIceExtent: True  # work in progress
     # WeddelIceExent: True       # work in progress
     # NorthernMIZArea: True
     # SouthernMIZArea: True
@@ -52,16 +52,16 @@ keys:
     #	MeridionalCurrent: True        	# Meridional Veloctity
     #	VerticalCurrent: True          	# Vertical Veloctity
     GulfStream: True
-    GulfStream_depth: True
+#    GulfStream_depth: True
 
 
-    somesatr: True # salt flow # Work in progress in debug
+#    somesatr: True # salt flow # Work in progress in debug
 
     ZOS: True # Sea Surface Height
-    sowindsp: True # Wind speed
+#    sowindsp: True # Wind speed
 #    sowflisf: True # Ice flux
     evs: True # Evaporation
-    precip: True # Precipitation
+#    precip: True # Precipitation
 #    fov: True # Fov (Total salt flux in the Atlantic)
 
 

key_lists/tfamoc.yml

@@ -15,6 +15,10 @@ keys:
     AtlanticSubtropicSalinity: True
     GINSalinity: True
     MLD: True
+    somxzint1: True
+    sltbasinatlantic: True
+
+
     TotalAirSeaFluxCO2: True
     # NoCaspianAirSeaFluxCO2: True
     # IntPP_OSU: True
@@ -29,9 +33,9 @@ keys:
     hfds: True
     hfy: True
     sosafldo: True
-    somesatr: True
-    hfbasinatlantic: True
-    sowindsp: True
+#    somesatr: True
+#    hfbasinatlantic: True
+#    sowindsp: True
     friver: True
     soicecov: True
     agessc: True