Merge pull request #143 from valeriupredoi/dev_new_jasmin_disk

Changes needed to migrate to jasmin's new disk

Author: ledm

README.md

@@ -430,7 +430,7 @@ The `analysis_compare` tool creates a script in the `mass_scripts` directory.
 This script is copied to a shared directory in the shared ukesm/terrafirma diskspace:
 
 ```
-/gws/nopw/j04/esmeval/bgcval2/shared_mass_scripts
+/gws/ssde/j25a/esmeval/bgcval2/shared_mass_scripts
 ```
 
 A crontab job is set up to execute these scripts overnight on mass-cli1,
@@ -440,14 +440,14 @@ Very old scripts are automatically deleted.
 The crontab script is:
 
 ```
-/gws/nopw/j04/esmeval/bgcval2/shared_mass_cron.sh
+/gws/ssde/j25a/esmeval/bgcval2/shared_mass_cron.sh
 ```
 
 Note that cron executes this script with the `ldemora` username, so permissions may need to be changed
 in some cases. The output log for this script is sent to the file:
 
 ```
-/gws/nopw/j04/esmeval/bgcval2/shared_mass_cron.out
+/gws/ssde/j25a/esmeval/bgcval2/shared_mass_cron.out
 ```
 
 In the case that data is needed immediately, it's posiible to download manually as well.
@@ -642,7 +642,7 @@ input yamls. If you want to "clear the cache", these images need to be deleted.
 The key place to clear is set by default on jasmin to be:
 
 ```
-/gws/nopw/j04/ukesm/BGC_data/$USER/bgcval2/images/TimeseriesCompare/$NAME
+/gws/ssde/j25a/ukesm/BGC_data/$USER/bgcval2/images/TimeseriesCompare/$NAME
 ```
 
 where `$USER` is your jasmin user name and `$NAME` is the name given to this analysis 
@@ -660,7 +660,7 @@ This is where the report is generated.
 The third place that these plots are kept is on the public facing jasmin directory:
 
 ```
-/gws/nopw/j04/esmeval/public/CompareReports/bgcval2/$USER/$NAME
+/gws/ssde/j25a/esmeval/public/CompareReports/bgcval2/$USER/$NAME
 ```
 
 This is where the report is hosted.

bgcval2/RemoteScripts/downloadOnMassCli.sh

@@ -24,7 +24,7 @@ python /home/users/ldemora/workspace/ukesm-validation/RemoteScripts/hello.py $jo
 
 ssh -X -A mass-cli.jasmin.ac.uk "python /home/users/ldemora/workspace/ukesm-validation/download_from_mass.py $jobid"
 #ssh -X -A mass-cli.jasmin.ac.uk "mkdir -p gws/nopw/j04/ukesm/BGC_data/u/group_workspaces/jasmin2/ukesm/BGC_data/$jobid/1y; ln -s  /group_workspaces/jasmin2/ukesm/BGC_data/$jobid/*1y*grid_[UVWT]*.nc /group_workspaces/jasmin2/ukesm/BGC_data/$jobid/1y/.; ls -lhrt /group_workspaces/jasmin2/ukesm/BGC_data/$jobid"
-ssh -X -A mass-cli.jasmin.ac.uk "mkdir -p /gws/nopw/j04/ukesm/BGC_data/$jobid/1y; ln -s  /gws/nopw/j04/ukesm/BGC_data/$jobid/*1y*grid_[UVWT]*.nc /gws/nopw/j04/ukesm/BGC_data/$jobid/1y/.; ls -lhrt /gws/nopw/j04/ukesm/BGC_data/$jobid"
+ssh -X -A mass-cli.jasmin.ac.uk "mkdir -p /gws/ssde/j25a/ukesm/BGC_data/$jobid/1y; ln -s  /gws/ssde/j25a/ukesm/BGC_data/$jobid/*1y*grid_[UVWT]*.nc /gws/ssde/j25a/ukesm/BGC_data/$jobid/1y/.; ls -lhrt /gws/ssde/j25a/ukesm/BGC_data/$jobid"
 
 #####
 # MLD:

bgcval2/bgcvaltools/generic_map_legend.py

@@ -274,35 +274,36 @@ def main():
 
 
     regions = [
-                'LIseas',
-                'LIGINseas',
-                'GLINseas',
-                'Ascension',
+#                'LIseas',
+#                'LIGINseas',
+#                'GLINseas',
+#                'Ascension',
 #              'ITCZ',
 #               'TristandaCunha',
 #               'Pitcairn',
-                'Cornwall',
-                'SubtropicNorthAtlantic',
-                'SPNA',
-                'STNA',        
-                'SouthernOcean',
-                'subpolar',
-                'NorthEastAtlantic',
-                'ArcticOcean',
-                'Equator10',
-                'NorthPacificOcean',
-                'SouthAtlanticOcean',
-                'NorthernSubpolarPacific',
-                'NorthernSubpolarAtlantic',
-                'SouthPacificOcean',
-                'NorthAtlanticOcean',
-                'SouthAtlanticOcean',
-                'GINseas',
-                'LabradorSea',
-                'IrmingerSea',
-                'EquatorialAtlanticOcean',
-                'Global',
-                'ignoreInlandSeas',
+#                'Cornwall',
+                'BritishIsles',
+#                'SubtropicNorthAtlantic',
+#                'SPNA',
+#                'STNA',        
+#                'SouthernOcean',
+#                'subpolar',
+#                'NorthEastAtlantic',
+#                'ArcticOcean',
+#                'Equator10',
+#                'NorthPacificOcean',
+#                'SouthAtlanticOcean',
+#                'NorthernSubpolarPacific',
+#                'NorthernSubpolarAtlantic',
+#                'SouthPacificOcean',
+#                'NorthAtlanticOcean',
+#                'SouthAtlanticOcean',
+#                'GINseas',
+#                'LabradorSea',
+#                'IrmingerSea',
+#                'EquatorialAtlanticOcean',
+#                'Global',
+#                'ignoreInlandSeas',
     ]
     for region in regions[:]:
         calc_area(region, orcaGridfn=orcaGridfn)

bgcval2/bgcvaltools/makeMask.py

@@ -354,7 +354,10 @@ def makeMask(name, newSlice, xt, xz, xy, xx, xd, debug=False):
         return mx
         #65-75:20W-15E
 
-   
+    if newSlice == 'BritishIsles':
+        mx = np.ma.masked_outside(xx, -11., 2.).mask
+        mx += np.ma.masked_outside(xy, 48., 61.).mask
+        return mx
 
     if newSlice == 'Cornwall':
         mx = np.ma.masked_outside(xx, -8., -4.).mask

bgcval2/bgcvaltools/pftnames.py

@@ -211,6 +211,7 @@ def makeLongNameDict():
     lnd['INT_PN'] = 'Int. Non-Diatoms'
 
     lnd['PRN'] = 'Non-Diatom Production'
+    lnd['PPRN'] = 'Non-Diatom Production'
     lnd['PRD'] = 'Diatom Production'
     lnd['ZI_GROW'] = 'Microzooplankton Growth'
     lnd['ZE_GROW'] = 'Mesozooplankton Growth'
@@ -224,6 +225,7 @@ def makeLongNameDict():
     lnd['PD_NLIM'] = 'Diatom N limitation'
     lnd['PD_JLIM'] = 'Diatom Light Limitation'
     lnd['PD_SILIM'] = 'Diatom Si limitation'
+    lnd['PBSI3'] = 'Biogenic Silica Production'
 
     lnd['epN100'] = "Downward Flux of Particulate Nitrogen"
     lnd['O2min'] = 'Oxygen Minimum Concentration'
@@ -285,6 +287,10 @@ def makeLongNameDict():
     lnd['SubtropicNorthAtlantic'] = 'Subtropic North Atlantic'
     lnd['GINSalinity'] = 'GIN Salinity 0-800m'
 
+    lnd['volSalinity'] = 'Salinity 0-1200m'
+    lnd['volTemperature'] = 'Temperature 0-1200m'
+
+
     lnd['Surfaceto100m'] = 'Surface-to-100m'
     lnd['Surfaceto200m'] = 'Surface-to-200m'
     lnd['Surfaceto300m'] = 'Surface-to-300m'
@@ -293,6 +299,8 @@ def makeLongNameDict():
     lnd['Surfaceto600m'] = 'Surface-to-600m'
     lnd['Surfaceto700m'] = 'Surface-to-700m'
     lnd['Surfaceto800m'] = 'Surface-to-800m'
+    lnd['Surfaceto1200m'] = 'Surface-to-1200m'
+
     lnd['Surfaceto2000m'] = 'Surface-to-2000m'
 
     lnd['TotalHeatFlux'] = "Global Total Heat Flux"
@@ -312,11 +320,13 @@ def makeLongNameDict():
     lnd['sofmflup'] = "Water flux due to freezing/melting"
     lnd['sosfldow'] = "Downward salt flux"
     lnd['soicecov'] = "Ice Fraction"
+    lnd['agessc'] = 'Water age'
     lnd['sossheig'] = "Sea Surface Height"
     lnd['FreshwaterFlux'] = "Freshwater Flux"
     lnd['hfbasinatlantic'] = 'Northward Atlantic heat transport'
     lnd['exportRatio'] = "Export Ratio"
     lnd['LocalExportRatio'] = "Export Ratio"
+    lnd['OCN_RHOSW'] = 'Density'
 
     lnd['PCO2_SW'] = 'pCO2'
     lnd['pCO2'] = 'pCO2'
@@ -349,6 +359,13 @@ def makeLongNameDict():
     lnd['DrakePassageTransport'] = 'Drake Passage Transport'
     lnd['DPT'] = 'Drake Passage Transport'
 
+    lnd['DavisStraightSaltFlux'] = 'Davis Straight Salt Flux'
+    lnd['DavisStraightMassFlux'] = 'Davis Straight Mass Flux'
+    lnd['DavisStraightHeatFlux'] = 'Davis Straight Heat Flux'
+    lnd['NorwegianSeaSaltFlux'] = 'Norwegian Sea Salt Flux'    
+    lnd['NorwegianSeaMassFlux'] = 'Norwegian Sea Mass Flux'    
+    lnd['NorwegianSeaHeatFlux'] = 'Norwegian Sea Heat Flux'
+
     lnd['t_mn'] = 'Mean Temperature'
     lnd['t_an'] = 'Temperature'
     lnd['s_mn'] = 'Mean Salinity'
@@ -467,6 +484,7 @@ def makeLongNameDict():
     lnd['NorthEastAtlantic'] = "North East Atlantic"
     lnd['NorwegianSea'] = "Norwegian Sea"
     lnd['Cornwall'] = "Cornwall"
+    lnd['BritishIsles'] = 'British Isles'
     lnd['Ascension'] = "Ascension Island"
     lnd['TristandaCunha'] = "Tristan da Cunha"
     lnd['Pitcairn'] = "Pitcairn"

bgcval2/default-bgcval2-config.yml

@@ -7,7 +7,7 @@ standard-paths:
   jasmin:
     general:
       machinelocation: "JASMIN"
-      root_dir: "/gws/nopw/j04/ukesm"
+      root_dir: "/gws/ssde/j25a/ukesm"
       shelvedir: "bgcval2/shelves"
       p2p_ppDir: "bgcval2/ukesm_postProcessed"
       imagedir: "bgcval2/images"

bgcval2/functions/circulation.py

@@ -44,6 +44,18 @@
 eORCA1_drake_LAT0=79
 eORCA1_drake_LAT1=109
 
+
+eORCA1_davis_LON=289
+eORCA1_davis_LAT0=232
+eORCA1_davis_LAT1=244
+
+# From Greenland to Norway via Iceland
+eORCA1_norway_LON = 281
+eORCA1_norway_LAT0 = 245
+eORCA1_norway_LAT1 = 294
+
+
+
 eORCA025_drake_LON=875
 eORCA025_drake_LAT0=317
 eORCA025_drake_LAT1=436 
@@ -86,6 +98,9 @@
 e1v_AMOC26N = 0
 e1v_AMOC40N = 0
 e1v_AMOC55N = 0
+e1v_davis = 0
+e1v_norway = 0
+
 tmask_AMOC26N = 0
 tmask_AMOC40N = 0
 tmask_AMOC55N = 0
@@ -136,6 +151,8 @@ def loadDataMask(gridfn, maskname, grid):
     global e3v_AMOC26N
     global e3v_AMOC40N
     global e3v_AMOC55N
+    global e1v_davis   
+    global e1v_norway 
     global e1v_AMOC26N    
     global e1v_AMOC40N    
     global e1v_AMOC55N
@@ -183,6 +200,11 @@ def loadDataMask(gridfn, maskname, grid):
         e1v_AMOC55N = nc.variables['e1v'][..., latslice55Nnm, lonslice55N]     #
         tmask_AMOC55N = nc.variables['tmask'][..., latslice55Nnm, lonslice55N]
 
+        e1v_davis = nc.variables['e1v'][eORCA1_davis_LON, eORCA1_davis_LAT0:eORCA1_davis_LAT1]  
+        e1v_norway = nc.variables['e1v'][eORCA1_norway_LON, eORCA1_norway_LAT0:eORCA1_norway_LAT1]  
+
+        
+
     else:
         e3v_AMOC26N = nc.variables['e3v'][..., latslice26Nnm, :]   # z level height 3D
         e1v_AMOC26N = nc.variables['e1v'][..., latslice26Nnm, :]     #
@@ -196,6 +218,9 @@ def loadDataMask(gridfn, maskname, grid):
         e1v_AMOC55N = nc.variables['e1v'][..., latslice55N, :]     #
         tmask_AMOC55N = nc.variables['tmask'][..., latslice55N, :]
 
+        e1v_davis = nc.variables['e1v'][eORCA1_davis_LON, eORCA1_davis_LAT0:eORCA1_davis_LAT1]
+        e1v_norway = nc.variables['e1v'][eORCA1_norway_LON, eORCA1_norway_LAT0:eORCA1_norway_LAT1]  
+
     #print('e3v_AMOC26N: loaded')#e3v_AMOC26N, latslice26Nnm, e3v_AMOC26N.shape)
     nc.close()
     loadedArea = True
@@ -313,6 +338,110 @@ def drakePassage(nc, keys, **kwargs):
     return drake
 
 
+def davisstraightflux(nc, keys, straight='Davis', **kwargs):
+    """
+    This function calculates the salt flux through the davis straight in eORCA1. 
+    
+    nc: a netcdf openned as a dataset.
+    keys: a list of keys to use in this function.
+    
+    """
+    areafile = get_kwarg_file(kwargs, 'areafile')
+    maskname = kwargs.get('maskname', 'tmask')
+    grid = kwargs.get('grid', 'eORCA1')
+
+    if not loadedArea:
+        loadDataMask(areafile, maskname, grid)
+
+    if grid == 'eORCA1' and straight=='Davis':    
+        LON = eORCA1_davis_LON
+        LAT0 = eORCA1_davis_LAT0
+        LAT1 = eORCA1_davis_LAT1
+        e1v = e1v_davis
+    elif grid == 'eORCA1' and straight=='Norway':    
+        LON = eORCA1_norway_LON
+        LAT0 = eORCA1_norway_LAT0
+        LAT1 = eORCA1_norway_LAT1 
+        e1v = e1v_norway
+
+    else:
+        assert 0
+
+    if keys[0] in ['vo', 'uo']:
+        print('These needs to be multiplied by the thkcello.')
+        assert 0
+
+    thkcello = nc.variables['thkcello'][0, :, LAT0:LAT1, LON]
+
+    print('Davis straight:', grid, 'LON', LON, 'LAT0',LAT0, 'LAT1', LAT1)
+
+    ndim = nc.variables[keys[0]].ndim
+    if ndim == 4: # vso, vmo
+        flux = nc.variables[keys[0]][0, :, LAT0:LAT1, LON]
+        e1v_4d = np.broadcast_to(e1v[np.newaxis, :], thkcello.shape[:])
+
+    if ndim == 3: #hfy
+        flux = nc.variables[keys[0]][0, LAT0:LAT1, LON]
+        e1v_4d = e1v
+        thkcello = thkcello.sum(0)
+
+    flux = np.ma.masked_where(flux==0., flux)
+    if keys[0] in ['vo', 'uo']:
+        flux = np.ma.sum(flux * e1v_4d * thkcello) 
+    else:
+        # sum already calculated.
+        flux = np.ma.sum(flux)
+
+    return flux
+
+
+def norwegianpassage(nc, keys, **kwargs):
+    """
+    This function calculates the salt flux through the Norwegian Sea in eORCA1. 
+    
+    nc: a netcdf openned as a dataset.
+    keys: a list of keys to use in this function.
+    
+    """
+    return davisstraightflux(nc, keys, straight='Norway', **kwargs)
+
+    # areafile = get_kwarg_file(kwargs, 'areafile')
+    # maskname = kwargs.get('maskname', 'tmask')
+    # grid = kwargs.get('grid', 'eORCA1')
+
+    # if not loadedArea:
+    #     loadDataMask(areafile, maskname, grid)
+
+    # if grid == 'eORCA1':    
+    #     LON = eORCA1_norway_LON
+    #     LAT0 = eORCA1_norway_LAT0
+    #     LAT1 = eORCA1_norway_LAT1
+    # else:
+    #     assert 0
+    
+    # if keys[0] in ['vo', 'uo']:
+    #     print('These needs to be multiplied by the thkcello.')
+    #     assert 0
+    # print('Norwegian flux:', grid, 'LON', LON, 'LAT0',LAT0, 'LAT1', LAT1)
+
+
+    # ndim = nc.variables[keys[0]].ndim
+
+
+    # if ndim == 4: # vso, vmo
+    #     flux = nc.variables[keys[0]][0, :, LAT0:LAT1, LON]
+
+    # if ndim == 3: #hfy
+    #     flux = nc.variables[keys[0]][0, LAT0:LAT1, LON]
+
+    # flux = np.ma.masked_where(flux==0., flux)
+
+    # print('Norway:', flux.shape, thkcello.shape, e1v_4d.shape)
+    # Norway = np.ma.sum(flux)  
+
+    # return Norway
+
+
 def TwentySixNorth(nc, keys, lat='26N', return_max_depth=False, **kwargs):
     """
     This function loads the AMOC/ADRC array that is used for eORCA