Uvic ice dev

resolute/fabm.yaml

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+# jpnote: variable values from mortenson fabm.nml 
+require_initialization: true
+instances:  
+  uvic_eco:  # University of Victoria Ecosystem model
+    use: true 
+    model: uvic/uvic_eco
+    parameters:
+      use_icealgae: true                   # if true use vars from icealgae model  #jpnote
+      ac : 0.03                            # light attenuation coefficient [m-1]
+      f_seed: 0.1                          # fraction of ice algal fux as ph2 seeding [-]
+      w1    : -1    #L09                   # de1 sinking rate [m/d]
+      w2    : -50   #L09 6Steiner 2006     # de2 sinking rate [m/d]
+      mu1   : 0.5   #de:0.5 #0.341 Paranjape 1987   # ph1 maximum growth rate [1/d]
+      mu2   : 2.0   #de:2.0 #steiner061.5dupont (eppley at 10deg.~1.6) #0.567 #Fig.3: Suzuki and Takahashi 1995  #ph2 maximum growth rate [1/d]
+      kn    : 1     #L09                    # no3 & nh4 half saturation constant [umol/L]
+      ## al1  :                             # initial slope of P-I curve [m2/W/time] ([time] is same unit as pmax)
+      ## al2  :                             # initial slope of P-I curve [m2/W/time] ([time] is same unit as pmax)
+      rpp1  : 0.3 #0.07125 Cota & Smith 1991   # maximum photosynthetic rate [1/time] ([time] is same unit as alpha)
+      rpp2  : 0.3 #0.045 Lavoie 2009       # maximum photosynthetic rate [1/time] ([time] is same unit as alpha)
+      mp1   : 0.03 # L09                   # ph1 excretion rate [1/d]
+      mp2   : 0.03 # L09                   # ph2 excretion rate [1/d]
+      mz1   : 0.03 #0.377 #Forest 2011     # zo1 excretion rate [1/d]
+      mz2   : 0.03 #L09                    # zo2 excretion rate [1/d]
+      gz1   : 1   #1.3#steiner06 #paranjape 1987     # zo1 maximum grazing rate [1/d]
+      gz2   : 1   #0.8#steiner06 #0.5 L09  # zo2 maximum grazing rate [1/d]
+      kz1   : 1   #0.6#1 #same as below    # zo1 grazing half saturation constant [umol/L]
+      kz2   : 1   #0.75#1 #L09             # zo2 grazing half saturation constant [umol/L]
+      az1   : 0.7 #L09                     # zo1 assimilation fraction [-]
+      az2   : 0.7 #same as above           # zo2 assimilation fraction [-]
+      rc    : 0.1                          # closure mortality rate [1/d]
+     ## #htlnh4  :                         # closure loss fraction to nh4 [-]
+     ## #htldet  :                         # closure loss fraction to det [-]
+      pp1   : 1                            # ph1 fraction as food for zo1 [-]
+      pp2   : 1                            # ph2 fraction as food for zo2 [-]
+      pd1   : 0.5                          # de1 fraction as food for zo1 [-]
+      pd2   : 0.5 #L09                     # de2 fraction as food for zo2 [-]
+      pz1   : 0.5                          # zo1 fraction as food for zo2 [-]
+      rd1   : 0.03                         # de1 remineralization rate [1/d]
+      rd2   : 0.3 #L09                     # de2 remineralization rate [1/d]
+      rd3   : 0.01                         # bsi remineralization rate [1/d]
+      rpf   : 0.2 #steiner06               # scale factor for nitrogen preference function [-]
+      rn0   : 0.03 #0.01 steiner06 0.03 Kawamiya     # nitrification rate at 0 deg.C [1/d]
+      knt   : 0.0693 #Kawamiya             # nitrification temperature coefficient [1/deg.C]
+      qp    : 1.55   # Table 2 Suzuki and Takahashi 1995       #ph1 & ph2 Q10 factor [-]
+      qz    : 2.14 #PISCES                 # zo1 & zo2 Q10 factor [-]
+      qb    : 1.9 #PISCES                  # bacteria Q10 factor [-]
+      agg   : 0.05   #steiner06            # ph2 aggregation rate [1/d]
+      rsin  : 1.7 # L09                    # ph2 Si:N ratio [mol-Si/mol-N]
+      ks    : 4 #L09                       # si half saturation constant [umol/L]
+      pmin  : 0.01 #def:0.01               # background plankton concentration [umol-N/L]
+# ice algae vars that need to be read in in the eco model #jpnote
+      zia      : 0.03                      # ice algal layer thickness [m]
+      ac_ia    : 0.017  #mcdonald2015      # specific light attenuation coefficient for ice algae
+    initialization: 
+      ph1 : 0.01 #de:0.01                  # ph1 initial value [umol/L]
+      ph2 : 0.01 #de:0.01                  # ph2 initial value [umol/L]
+      zo1 : 0.01                           # zo1 initial value [umol/L]
+      zo2 : 0.01                           # zo2 initial value [umol/L]
+      no3 : 7.2                            # no3 initial value [umol/L]
+      nh4 : 0.01                           # nh4 initial value [umol/L]
+      de1 : 0.01                           # de1 initial value [umol/L]
+      de2 : 0.01                           # de2 initial value [umol/L]
+      bsi : 0.01                           # bsi initial value [umol/L]
+      sil : 14.7                           # sil initial value [umol/L]
+
+  uvic_icealgae: #University of Victoria Ice Algae model
+    use: true
+    model: uvic/uvic_icealgae
+    parameters:
+      r_pond   : 0.0175                 # melt pond drainage rate [m d-1] 
+      fmethod  : 0                      # method for ice-ocean flux (0 for diffusion; 1 for ice growth/melting; 2 for both diffusion and growth/melting) 
+      fflush   : 0                      # method for flushing (0 for no flushing; 1 for surface flushing; 2 for surface+internal flushing)                                               
+      drag     : 0.0054                   # drag coefficient at the ice-water interface [-]
+      f_graze  : 0.0 #L2005               # fraction of ice algal growth lost due to grazing [-]
+      zia      : 0.03                     # ice algal layer thickness [m]
+      ac_ia    : 0.017  #mcdonald2015     # specific light attenuation coefficient for ice algae
+      rnit     : 0.01                     # nitrification rate [per day]
+      ia_b     : 1.0 #1.0#0.03-0.16 based on Michel's reply.   #ia background value [mmol-N/m3]
+      ks_no3   : 1.0                      # no3 half-saturation value [mmol/m3]
+      ks_sil   : 4.0                      # sil half-saturation value [mmol/m3]
+      maxg     : 0.85                     # maximum specific growth rate [d-1]
+      mort     : 0.03                     # linear mortality rate [d-1]
+      mort2    : 0.00015                  # quadratic mortality rate [d-1]
+      crit_melt: 0.015                    # critical melt rate [m d-1]
+      lcompp   : 0.0 # 1.0 #mock&gradinger99   # compensation intensity [umol m-2 s-1]
+      rpp      : 2.0                      # ratio of photosynthetic parameters (alpha and pbm) [W m-2]-1
+      ## rpi       :                      # ratio of photoinhibition parameters (beta and pbm)
+      t_sens   : 0.0633                   # temperature sensitivity [deg.C-1]
+      nu       : 1.85e-6                  # kinematic viscosity?
+      md_no3   : 0.47e-9                  # molecular diffusion coefficient for nitrate
+      md_sil   : 0.47e-9                  # molecular diffusion coefficient for dissolved silica
+      chl2n    : 3.533  #Lavoie 2.80134   # chl to nitrogen ratio
+      sil2n    : 1.7                      # silicon to nitrogen ratio                  
+    initialization:
+      no3  : 7.2                          # no3 initial value [mmol/m3]
+      sil  : 14.7                         # sil initial value [mmol/m3]
+      ia  : 1.0 #1.0#321.0 # ca. 900 mg-chl m-3    # ia initial value [mmol-N/m3]
+      nh4 : 0.01                          # nh4 initial value [mmol/m3]
+
+  uvic_dic: #University of Victoria Ice DIC model
+    use: false
+    model: uvic/uvic_dic
+    parameters:  
+      dic_0: 2200.0 # default: 2200.0,
+      # dic0 SA range: +50, +10, +5, SR, -5, -10, -50 !BUT can also be manipulated in profile.dat read by fabm_input.nml
+      alk_0: 2285.0 # default: 2285.0, 
+          #ta0 SA range: +50, +10, +5, SR, -5, -10, -50   (2365.0, 2325.0, SR, 2305.0, 2265.0)                                
+      dic_sw: 2100.0 # def = 2100.0  
+      alk_sw: 2200.0 # def = 2200.0 
+      dic_ice: 400.0 #def = 400.0, !NEW range: -50, +450 
+      alk_ice: 500.0 #def = 500.0  !NEW range: -50, +450
+      ik_diff: 50.0  #def = 50.0,  !NEW range: -40 +450 (0, 500) 
+      # difference (in melting ice) in [DIC] and 2*[TA] for ice with ikaite precipitaion
+      ik_on: 1.0   #turn on/off ikaite precipitation pump
+      ice_on: 1.0   #turn on/off ice pump
+      IA_on: 1.0   #turn on/off ice algae pump
+      tplv: 30.0  #def = 30.0   !top of brine-associated DIC depth (m)
+      btlv: 40.0  #def = 40.0   !bot of brine-associated DIC depth (m)
+      prop2sw: 0.99  #def=0.99
+
+  uvic_dms:  # University of Victoria DMS(P) model
+    use: true
+    model: uvic/uvic_dms
+    parameters:
+      use_icedms: true         #use icealgae vars #jpnote 
+      f_ow: 0.0                #fraction of open water during ice melting (e.g. leads)
+   # #  dms_0    : 0.1               
+   # #  dmspd_0  : 0.1               
+      q1: 100 #0.15, !Stefels 2007   #S:N ratio for ph1 [mol-S:mol-N]
+      q2: 9.5  #6 !0.015 Galindo 2014   #S:N ratio for ph2 [mol-S:mol-N]
+      yield: 0.20 #Galindo 2015  #bacterial lyase rate constant [per day]
+               #f_slop1 :    #fraction
+               #f_slop2 :
+      k_ly1: 0.03               #
+      k_ly2: 0.03               #
+      f_sl1: 0.3                #
+      f_sl2: 0.3                #
+      f_ex1: 0.05               #
+      f_ex2: 0.05               #
+      k_enz: 0.02               # rate constant for enzymatic cleavage (free lyase) [d-1]
+      k_in1: 0                  #
+      k_in2: 0                  #
+      h_dmspd: 0                # half-saturation constant for bacterial dmspd uptake
+      h_dms: 0                  # half-saturation constant for bacterial dms uptake
+      k_dmspd: 5                #
+      k_dms: 0.5                #
+      k_pho: 0.1                #
+      flux: 0                   # air-sea gas transfer velocity parameterization (0=Nightingale et al, 2000; 1=Liss and Merlivat, 1986+bubble from Woolf 1997)
+      zia: 0.03  
+    initialization: 
+      dms    : 0.1              # dms initial value [nmol/L]
+      dmspd  : 0.1              # dmspd initial value [nmol/L]
+
+      ##  s_dmspd :             # dmspd sloppy fraction [-]
+      ## e_dmspd :              # dmspd excrete fraction [-]
+      ## y_dms   :              # bacterial dms yield [-]
+      ## b_dmspd :              # bacterial dmspd consumption rate [1/d]
+      ## l_dmspd :              # dmspd lysis rate [1/d]
+      ## s_dms   :              # dms sloppy fraction [-]
+      ## e_dms   :              # dms excrete fraction [-]
+      ## b_dms   :              # bacterial dms consumption rate [1/d]
+      ## ddp     :              # photolysis rate [1/d]
+  uvic_icedms:
+    use: true
+    model: uvic/uvic_icedms
+    parameters: 
+      qi: 9.5       #Galindo 2014
+      h_dmspdi: 0
+      h_dmsi: 0
+      k_dmspdi: 1   #Galindo 2015
+      k_dmsi: 0.2
+      yieldi: 0.2   #Galindo 2015
+      f_exi: 0.05
+      k_lyi: 0.03
+      k_exi: 0.02
+      k_ini: 0
+      k_phoi: 0.1 # Taalba 2012 
+      zia: 0.03                   # ice algal layer thickness [m]
+    initialization:
+      dms   : 0.1           
+      dmspd : 0.1 
+