Commit 5ff9419e authored by Jorn Bruggeman's avatar Jorn Bruggeman
Browse files

replaced gotm/ergom nml with yaml

parent 4d0d90bb
!-------------------------------------------------------------------------------
!fabm.nml
!-------------------------------------------------------------------------------
&fabm_nml
models = 'gotm_ergom'
/
!-------------------------------------------------------------------------------
! IOW biological model according to Neumann et al. 2002 and Burchard et al. 2005!-------------------------------------------------------------------------------!
! p1_initial -> initial diatoms concentration [mmol n/m3]
! p2_initial -> initial flagellates concentration [mmol n/m3]
! p3_initial -> initial cyanobacterias concentration [mmol n/m3]
! zo_initial -> initial zooplankton concentration [mmol n/m3]
! de_initial -> initial detritus concentration [mmol n/m3]
! am_initial -> initial ammonium concentration [mmol n/m3]
! ni_initial -> initial nitrate concentration [mmol n/m3]
! po_initial -> initial phosphate concentration [mmol p/m3]
! o2_initial -> initial oxygen concentration [mmol n/m3]
! sfl_po -> constant surface phosphate flux [mmol n/m2/d]
! sfl_am -> constant surface ammonium flux [mmol n/m2/d]
! sfl_ni -> constant surface nitrate flux [mmol n/m2/d]
! fluff -> .true.: caluclate fluff layer
! fl_initial -> initial fluff concentration [mmol n/m2]
! p10= -> minimum diatoms concentration [mmol n/m3]
! p20= -> minimum flagellates concentration [mmol n/m3]
! p30= -> minimum cyanobacterias concentration [mmol n/m3]
! zo0= -> minimum zooplankton concentration [mmol n/m3]
! w_p1= -> sinking speed diatom [m/d]
! w_p2= -> sinking speed flagellates [m/d]
! w_p3= -> sinking speed cyanobacteria [m/d]
! w_de= -> sinking speed detritus [m/d]
! kc= -> attenuation constant for the self shading effect [m2/mmol N]
! i_min= -> minimum photosynthetically active radiation (PAR) [W/m2]
! r1max= -> maximum growth rate diatoms [1/d]
! r2max= -> maximum growth rate flagellates [1/d]
! r3max= -> maximum growth rate cyanobacteria [1/d]
! alpha1= -> half saturation diatoms [mmol n/m3]
! alpha2= -> half saturation flagellates [mmol n/m3]
! alpha3= -> half saturation cyanobacteria [mmol n/m3]
! lpa= -> p --> a rate (p respiration) [1/d]
! lpd= -> p --> d rate (p mortality) [1/d]
! tf= -> temperature control flagellates [deg C]
! tbg= -> temperature control cyanos [deg C]
! beta_bg= -> temperature control cyanos [1/deg C]
! g1max= -> maximum grazing rate on diatoms [1/d]
! g2max= -> maximum grazing rate on flagellates [1/d]
! g3max= -> maximum grazing rate on cyanos [1/d]
! lza= -> z --> a rate (z exkudation) [m3/d/mmol n]
! lzd= -> z --> d rate (z mortality) [m3/d/mmol n]
! iv= -> Ivlev constant [1/(mmol n/m3)3]
! topt= -> optimum temperature [deg C]
! lan= -> nitrification constant [1/d]
! oan= -> oxygen parameter [ - ]
! beta_an= -> temperature control [1/deg C]
! lda= -> detritus mineralisation constant [1/d]
! tda= -> temperature control [deg C]
! beta_da= -> temperature control [1/deg C]
! pvel= -> piston velocity [m/d]
! sr= -> redfield ratio(p/n) [ - ]
! s1= -> reduced nitrate/oxidized detritus [ - ]
! s2= -> oxygen produktion/recycled nitrogen [ - ]
! s3= -> oyxgen produktion related to n [ - ]
! s4= -> nitrification [ - ]
! a0= -> osat Parameter [mmol/m**3]
! a1= -> osat Parameter [ - ]
! a2= -> osat Parameter [1/ deg C]
! lds= -> rate of detritus sinking into sediment [m/d]
! lsd= -> rate of sediment resuspension [1/d]
! tau_crit= -> critical bottom stress [N/m2]
! lsa= -> rate of sediment mineralisation [1/d]
! bsa= -> temperature control of sediment mineralisation [1/deg C]
! ph1= -> release of phosphate [ - ]
! ph2= -> release of phosphate [ - ]
!-------------------------------------------------------------------------------
&gotm_ergom
p1_initial= 0.1
p2_initial= 0.1
p3_initial= 0.1
zo_initial= 0.1
de_initial= 5.0
am_initial= 0.1
ni_initial= 5.0
po_initial= 0.6
o2_initial= 85.0
sfl_po= 0.055
sfl_am= 0.36
sfl_ni= 0.45
fluff= .true.
fl_initial= 0.0
p10= 0.0045
p20= 0.0045
p30= 0.0045
zo0= 0.0045
w_p1= -0.5
w_p2= 0.
w_p3= 0.1
w_de= -3.
kc= 0.03
i_min= 25.
r1max= 2.0
r2max= 0.7
r3max= 0.5
alpha1= 1.35
alpha2= 0.675
alpha3= 0.5
lpa= 0.01
lpd= 0.02
tf= 10.
tbg= 14.
beta_bg= 1.
g1max= 0.5
g2max= 0.5
g3max= 0.25
lza= 0.0666666666
lzd= 0.1333333333
iv= 0.24444444
topt= 20.
lan= 0.1
oan= 0.01
beta_an= 0.11
lda= 0.003
tda= 13.
beta_da= 20.
pvel= 5.
sr= 0.0625
s1= 5.3
s2= 6.625
s3= 8.625
s4= 2.
a0= 31.25
a1= 14.603
a2= 0.4025
lds= 3.5
lsd= 25.
tau_crit= 0.07
lsa= 0.001
bsa= 0.15
ph1= 0.15
ph2= 0.1
/
instances:
ergom:
model: gotm/ergom
parameters:
sfl_po: 0.055 # surface phosphate flux (mmol P/m2/d), default = 0.0015
sfl_ni: 0.45 # surface nitrate flux (mmol N/m2/d), default = 0.09
sfl_am: 0.36 # surface ammonium flux (mmol N/m2/d), default = 0.07
fluff: true # use fluff, default = false
p10: 0.0045 # background concentration of diatoms (mmol N/m3), default = 0.0225
p20: 0.0045 # background concentration of flagellates (mmol N/m3), default = 0.0225
p30: 0.0045 # background concentration of cyanobacteria (mmol N/m3), default = 0.0225
zo0: 0.0045 # background concentration of zooplankton (mmol N/m3), default = 0.0225
kc: 0.03 # specific light attenuation of phytoplankton and detritus (m2/mmol N), default = 0.03
i_min: 25.0 # minimum optimal photosynthetically active radiation (W/m2), default = 25.0
r1max: 2.0 # maximum growth rate of diatoms (1/d), default = 2.0
r2max: 0.7 # maximum growth rate of flagellates (1/d), default = 0.7
r3max: 0.5 # maximum growth rate of cyanobacteria (1/d), default = 0.5
alpha1: 1.35 # half-saturation nutrient concentration for diatoms (mmol N/m3), default = 1.35
alpha2: 0.675 # half-saturation nutrient concentration for flagellates (mmol N/m3), default = 0.675
alpha3: 0.5 # half-saturation nutrient concentration for cyanobacteria (mmol N/m3), default = 0.5
lpa: 0.01 # phytoplankton exudation (1/d), default = 0.01
lpd: 0.02 # phytoplankton mortality (1/d), default = 0.02
tf: 10.0 # half-saturation temperature for flagellates (deg C), default = 10.0
tbg: 14.0 # reference temperature for cyanobacteria (deg C), default = 14.0
beta_bg: 1.0 # temperature sensitivity for cyanobacteria (1/deg C), default = 1.0
g1max: 0.5 # maximum grazing rate on diatoms (1/d), default = 0.5
g2max: 0.5 # maximum grazing rate on flagellates (1/d), default = 0.5
g3max: 0.25 # maximum grazing rate on cyanobacteria (1/d), default = 0.25
lza: 0.0666666666 # quadratic zooplankton loss to dissolved matter (m3/mmol N/d), default = 0.0666666666
lzd: 0.1333333333 # quadratic zooplankton loss to detritus (m3/mmol N/d), default = 0.1333333333
iv: 0.24444444 # Ivlev constant for grazing (m3/mmol N), default = 0.24444444
topt: 20.0 # optimum temperature for grazing (deg C), default = 20.0
lan: 0.1 # maximum nitrification rate (1/d), default = 0.1
oan: 0.01 # half-saturation oxygen concentration for nitrification (mmol o2/m3), default = 0.01
beta_an: 0.11 # temperature sensitivity of nitrification (1/deg C), default = 0.11
lda: 0.003 # remineralisation rate (1/d), default = 0.003
tda: 13.0 # half-saturation temperature for remineralisation (deg C), default = 13.0
beta_da: 20.0 # temperature sensitivity of remineralisation (-), default = 20.0
pvel: 5.0 # piston velocity (m/d), default = 5.0
sr: 0.0625 # phosphorus to nitrogen ratio (mol P/mol N), default = 0.0625
s1: 5.3 # reduced nitrate : oxidized detritus for denitrification (-), default = 5.3
s2: 6.625 # oxygen : nitrogen ratio for ammonium-based biomass synthesis and remineralisation (mol O2/mol N), default = 6.625
s3: 8.625 # oxygen : nitrogen ratio for nitrate-based biomass synthesis (mol O2/mol N), default = 8.625
s4: 2.0 # oxygen : nitrogen ratio for nitrification (mol O2/mol N), default = 2.0
a0: 31.25 # mmol O2 per gram (mmol O2/g), default = 31.25
a1: 14.603 # saturation mass concentration of oxygen at 0 deg C (g/m3), default = 14.603
a2: 0.4025 # decrease in saturation mass concentration of oxygen per deg C (g/m3/deg C), default = 0.4025
lds: 3.5 # sedimentation rate of detritus (m/d), default = 3.5
lsd: 25.0 # resuspension rate of fluff (1/d), default = 25.0
tau_crit: 0.07 # N/m2 (critical bottom stress), default = 0.07
lsa: 0.001 # fluff mineralisation rate (1/d), default = 0.001
bsa: 0.15 # temperature sensitivity of fluff mineralisation (1/deg C), default = 0.15
ph1: 0.15 # inhibition of phosphate release during fluff mineralisation (-), default = 0.15
ph2: 0.1 # half-saturation oxygen concentration for inhibition of phosphate release (mmol O2/m3), default = 0.1
w_p1: -0.5 # m/d (vertical velocity of diatoms (< for sinking)), default = -1.0
w_p2: 0.0 # m/d (vertical velocity of flagellates (< for sinking)), default = -5.0
w_p3: 0.1 # m/d (vertical velocity of cyanobacteria (< for sinking)), default = -5.0
w_de: -3.0 # m/d (vertical velocity of detritus (< for sinking)), default = -3.0
initialization:
dia: 0.1 # diatoms (mmol N/m3)
fla: 0.1 # flagellates (mmol N/m3)
cya: 0.1 # cyanobacteria (mmol N/m3)
zoo: 0.1 # zooplankton (mmol N/m3)
det: 5.0 # detritus (mmol N/m3)
amm: 0.1 # ammonium (mmol N/m3)
nit: 5.0 # nitrate (mmol N/m3)
pho: 0.6 # phosphate (mmol P/m3)
oxy: 85.0 # oxygen (mmol O2/m3)
flf: 0.0 # fluff (mmol N/m2)
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