updating to v.1.1.10

CFM_main/RCMpkl_to_spin.py

@@ -169,7 +169,10 @@ def makeSpinFiles(CLIM_name,timeres='1D',Tinterp='mean',spin_date_st = 1980.0, s
 
     stepsperyear = 1/(df_CLIM_re.decdate.diff().mean())
 
-    BDOT_mean_IE = ((df_CLIM_re['BDOT']+df_CLIM_re['SUBLIM'])*stepsperyear/917).mean()
+    if 'SUBLIM' in df_CLIM_re:
+        BDOT_mean_IE = ((df_CLIM_re['BDOT']+df_CLIM_re['SUBLIM'])*stepsperyear/917).mean()
+    else:
+        BDOT_mean_IE = ((df_CLIM_re['BDOT'])*stepsperyear/917).mean()
     T_mean = (df_TS_re['TSKIN']).mean()
     print(BDOT_mean_IE)
     print(T_mean)
@@ -186,7 +189,7 @@ def makeSpinFiles(CLIM_name,timeres='1D',Tinterp='mean',spin_date_st = 1980.0, s
         depth_S2 = desired_depth * 0.75
     #### Make spin up series ###
     RCI_length = spin_date_end-spin_date_st+1
-    num_reps = int(np.round(desired_depth/BDOT_mean_IE/RCI_length))
+    num_reps = int(np.round(desired_depth/BDOT_mean_IE/RCI_length)) 
     years = num_reps*RCI_length
     sub = np.arange(-1*years,0,RCI_length)
     startyear = int(df_CLIM_re.index[0].year + sub[0])

CFM_main/firn_density_nospin.py

@@ -445,13 +445,13 @@ def __init__(self, configName, climateTS = None, NewSpin = False):
                 self.iceout = self.c['iceout']
                 print('Ensure that your iceout value has units m ice eq. per year!')
             else:
-                self.iceout = np.mean(self.bdot) # this is the rate of ice flow advecting out of the column, units m I.E. per year.
+                self.iceout = np.mean(self.bdot+self.sublim) # this is the rate of ice flow advecting out of the column, units m I.E. per year.
 
         except Exception:
             print('add field "manual_iceout" to .json file to set iceout value manually')
             self.iceout = np.mean(self.bdot) # this is the rate of ice flow advecting out of the column, units m I.E. per year.
 
-        self.w_firn         = np.mean(self.bdot) * RHO_I / self.rho 
+        self.w_firn         = np.mean(self.bdot+self.sublim) * RHO_I / self.rho 
 
         if (np.any(self.bdotSec<0.0) and self.c['bdot_type']=='instant'):
             print('ERROR: bdot_type set to "instant" in .json and input')
@@ -570,14 +570,14 @@ def __init__(self, configName, climateTS = None, NewSpin = False):
             self.Trunoff         = np.array([0.]) #total runoff, single value for the whole firn column
             self.refrozen       = np.zeros_like(self.dz) #vrefreezing in every layer, array of size of our grid
             self.totalrunoff    = np.array([0.]) # Might be useful to have a total final value without having to write every time step
-            self.totalrefrozen  = np.zeros_like(self.dz) # Might be useful to have a total final value without having to write every time step
-            self.totwatersublim = 0. #VV Total amount of liquid water that get sublimated
+            self.totalrefrozen  = np.zeros_like(self.dz) # Might be useful to have a total final value without having to write every time step         
             self.lwcerror       = 0. #VV
             self.totallwcerror  = 0. #
             #VV update (23/03/2021)
             self.refreeze = np.array([0.]) #total liquid water refreezing at each time step [m we]
             self.runoff     = np.array([0.]) #total liquid water runoff at each time step [m we]
             self.meltvol    = np.array([0.]) #total melt volume
+        self.totwatersublim = 0. #VV Total amount of liquid water that get sublimated
 
         ### Strain modules
         self.c = check_strain_settings(self)
@@ -822,7 +822,7 @@ def time_evolve(self):
         print('modeltime',self.modeltime[0],self.modeltime[-1])
         for iii in range(self.stp):
             mtime = self.modeltime[iii]
-            self.D_surf[iii] = iii
+            self.D_surf[iii] = iii # This gives each layer a tracking number that is just iteration number.
             if iii==1000:
                 if ((self.MELT) and (self.c['liquid']=='darcy')):
                     pass

CFM_main/main.py

@@ -22,7 +22,7 @@
 
 __author__ = "C. Max Stevens, Vincent Verjans, Brita Horlings, Annika Horlings, Jessica Lundin"
 __license__ = "MIT"
-__version__ = "1.1.8"
+__version__ = "1.1.10"
 __maintainer__ = "Max Stevens"
 __email__ = "[email protected]"
 __status__ = "Production"

CFM_main/strain.py

@@ -28,6 +28,7 @@ def check_strain_settings(self):
     # Check for deprecated config keys.
     if 'strain' in self.c:
         self.c['horizontal_divergence'] = self.c['strain']
+    if 'InputFileNamedudx' in self.c:
         self.c['InputFileNameStrain'] = self.c['InputFileNamedudx']
 
     # Check if strain settings are set in the config. Otherwise deactivate.

changelog.md

@@ -3,8 +3,16 @@ All notable changes to the Community Firn Model should be documented in this fil
 
 TL;DR: Write down the changes that you made to the the model in this document and update the version number here and in main.py, then update master on github.
 
+To run the update:
+git commit -a -m "updating to vX.Y.Z. Details in changelog."
+git push
+git tag -a vX.Y.Z -m "CFM version vX.Y.Z"
+git push origin vX.Y.Z
+
+Then, on github do a release, which will trigger an updated DOI. 
+
 ## Current Version
-1.1.9
+1.1.10
 
 ## Full Documentation
 
@@ -23,6 +31,11 @@ https://communityfirnmodel.readthedocs.io/en/latest/
 	- Goujon physics work, but could possibly be implemented more elegantly (it would be nice to avoid globals)
 	- Not exactly in progress, but at some point adding a log file that gets saved in the results folder would be a good idea.
 
+## [1.1.10]
+### Notes
+- Version 1.1.10 is a minor update to fix an issue with the strain softening routine introduced in v1.1.9. (The code would throw an error if InputFileNamedudx was not in the .json).
+- There is a small update to the documentation regarding BCO outputs.
+
 ## [1.1.9]
 ### Notes
 - Version 1.1.9 is an update to add strain softening as described by Oraschewski and Grinsted (2021; https://doi.org/10.5194/tc-2021-240) 

docs/running/outputs.rst

@@ -45,11 +45,18 @@ Firn air to a horizon (7) is there because due to the model's lagrangian format,
 
 (I'd advise using caution if you use the modeled elevation change fields - we have made changes to the code to merge deeper nodes together to save computing time, but in doing so that can make the model-outputed dH have blips in it. If you want to work with this field let me know and I can do a bit of testing. I'd recommend structuring your analyses around the FAC variable.)
 
-BCO: bubble close-off properties. 10 columns: time, Martinerie close-off age, Marinerie close-off depth, age of 830 kg m-3 density horizon, depth of 830 kg m-3 density horizon, Martinerie lock-in age, Marinerie lock-in depth, age of 815 kg m-3 density horizon, depth of 815 kg m-3 density horizon, depth of zero porosity.
+BCO: bubble close-off properties. 10 columns: time, Martinerie close-off age, Martinerie close-off depth, age of 830 kg m-3 density horizon, depth of 830 kg m-3 density horizon, Martinerie lock-in age, Martinerie lock-in depth, age of 815 kg m-3 density horizon, depth of 815 kg m-3 density horizon, depth of zero closed porosity. The Martinerie fields refer to paramaterizations for close-off properties published by Patricia Martinerie in the early 1990s. See references below. 
 
 meltvol: two columnes: decimal time, total melt volume at that time step [m w.e.]
 
 refreeze: two columns: decimal time, total liquid water refreezing at that time step [m w.e.]
 
 runoff: two columns: decimal time, total liquid water runoff at that time step [m w.e.]
 
+**References**
+*Goujon, C., Barnola, J.-M., and Ritz, C. (2003), Modeling the densification of polar firn including heat diffusion: Application to close-off characteristics and gas isotopic fractionation for Antarctica and Greenland sites, J. Geophys. Res., 108, 4792, doi:10.1029/2002JD003319, D24.*
+
+*Martinerie, P., Lipenkov, V. Y., Raynaud, D., Chappellaz, J., Barkov, N. I., and Lorius, C. (1994), Air content paleo record in the Vostok ice core (Antarctica): A mixed record of climatic and glaciological parameters, J. Geophys. Res., 99( D5), 10565– 10576, doi:10.1029/93JD03223.*
+
+*Martinerie, P., Raynaud, D., Etheridge, D. M., Barnola, J.-M., & Mazaudier, D. (1992, August). Physical and climatic parameters which influence the air content in polar ice. Earth and Planetary Science Letters. Elsevier BV. https://doi.org/10.1016/0012-821x(92)90002-d*
+