Commit 0ec83b6587945f5cc08fa6b5f2ef3d01947d054c

Authored by Dany Dumont
1 parent da3f2822
Exists in master and in 1 other branch snow

Ajout du modele nocera dans test_cases

test_cases/nocera/airsea.nml 0 → 100644
... ... @@ -0,0 +1,98 @@
  1 +!$Id: airsea.proto,v 1.1.1.1 2003/03/11 13:38:58 kbk Exp $
  2 +!-------------------------------------------------------------------------------
  3 +!
  4 +!-------------------------------------------------------------------------------
  5 +! air-sea interaction (heat, momentum and freshwater fluxes and solar radiation)
  6 +!
  7 +! calc_fluxes -> surface fluxes calculated by means of bulk formulae
  8 +! (.true./.false.). Solar radiation is calculated from
  9 +! time, latitude, longitude and clouds. If (.true.),
  10 +! meteo_file must be given and wet_mode must be specified.
  11 +! If (.false.), surface fluxes and solar radiation are
  12 +! prescribed.
  13 +!
  14 +! meteo_file -> file with meteo data (for calc_fluxes=.true.) with
  15 +! - date (yyyy-mm-dd hh:mm:ss)
  16 +! - x-comp. of wind (10 m) in m/s
  17 +! - y-comp. of wind (10 m) in m/s
  18 +! - air pressure ( 2 m) in hectopascal
  19 +! - dry air temp. ( 2 m) in Celsius
  20 +! - relative humidity in % or wet bulb temperature in C
  21 +! or dew point temperature in C (depending on wet_mode)
  22 +! - cloud cover in 1/10
  23 +!
  24 +! wet_mode -> decides what is given in 7. column in meteo_file
  25 +! 1: relative humidity
  26 +! 2: wet bulb temperature
  27 +! 3: dew point temperature
  28 +!
  29 +! heat_method -> method to provide short wave radiation (swr) and
  30 +! surface heat flux (qh)
  31 +! (only for calc_fluxes=.false.)
  32 +! 0: heat flux not prescribed
  33 +! 1: constant "const_swr" and "const_qh" given (see below)
  34 +! 2: swr and qh are read from heatflux_file
  35 +
  36 +! const_swr -> constant value of incoming short wave radiation in W/m^2
  37 +! (always positive)
  38 +!
  39 +! const_qh -> constant value of surface heat flux in W/m^2
  40 +! (negative for heat loss)
  41 +!
  42 +! heatflux_file -> file with qin and qout given in W/m^2
  43 +! (negative for net outgoing)
  44 +!
  45 +! momentum_method -> method how momentum fluxes are given
  46 +! (only for calc_fluxes=.false.)
  47 +! 0: momentum flux not prescribed
  48 +! 1: constant surface momentum fluxes given
  49 +! 2: surface momentum fluxes given from file momentumflux_file
  50 +!
  51 +! const_tx -> x-component of surface momentum flux in N/m^2
  52 +! const_ty -> y-component of surface momentum flux in N/m^2
  53 +!
  54 +! momentumflux_file-> file with tx and ty given in N/m^2
  55 +!
  56 +! p_e_method -> method how fresh water fluxes (P-E) are given
  57 +! 0: P-E not used
  58 +! 1: constant value for P-E (in m/s) used
  59 +! (P-E = precipitation-evaporation)
  60 +! 2: values for P-E read from file
  61 +!
  62 +! const_p_e -> constant value for P-E in m/s (positive for P>E)
  63 +!
  64 +! p_e_flux_file -> file with value for P-E (positive for P>E)
  65 +! used if p_e_method=2
  66 +!
  67 +! sst_method -> method how sea surface temperature (SST) is given
  68 +! 0: no independent SST observation is read from file
  69 +! 2: independent SST observation is read from file,
  70 +! only for output
  71 +!
  72 +! sst_file -> file with independent SST observation
  73 +!
  74 +! sss_method -> method how sea surface salinity (SSS) is given
  75 +! 0: no independent SSS observation is read from file
  76 +! 2: independent SSS observation is read from file,
  77 +! only for output
  78 +!-------------------------------------------------------------------------------
  79 + &airsea
  80 + calc_fluxes= .true.
  81 + meteo_file= 'meteo.dat'
  82 + wet_mode= 1
  83 + heat_method= 0
  84 + const_swr= 200.0
  85 + const_heat= 0.0
  86 + heatflux_file= 'heatflux.dat'
  87 + momentum_method= 1
  88 + const_tx= 0.1
  89 + const_ty= 0.0
  90 + momentumflux_file='momentumflux.dat'
  91 + p_e_method= 0
  92 + const_p_e= 0.
  93 + p_e_flux_file= 'p_e.dat'
  94 + sst_method= 0
  95 + sst_file= 'sst.dat'
  96 + sss_method= 0
  97 + sss_file= 'sss.dat'
  98 + /
... ...
test_cases/nocera/bio.nml 0 → 100644
... ... @@ -0,0 +1,58 @@
  1 +!$Id$
  2 +!-------------------------------------------------------------------------------
  3 +! Basic settings for biogeochemical model
  4 +!
  5 +! bio_calc -> calculation of the bio model 'bio_model' (.true./.false.)
  6 +! bio_model -> choice of the bio model:
  7 +! 1: NPZD (4 variables)
  8 +! 2: IOW-ERGOM (9 variables)
  9 +! 3: Suspended matter only (1 variable)
  10 +! 4: Fasham et al. 1990 (7 variables)
  11 +! 5: IOW-ERGOM MaBenE version (9 variables)
  12 +! 6: ISMER model (9 variables)
  13 +!
  14 +! bio_eulerian -> state variables are Eulerian (.true./.false.)
  15 +!
  16 +! cnpar -> Cranck-Nicolson parameter for vertical diffusion
  17 +!
  18 +! w_adv_discr -> advection scheme for vertical motion
  19 +! 1: first order upstream
  20 +! 2: not coded yet
  21 +! 3: third-order polynomial
  22 +! 4: TVD with Superbee limiter
  23 +! 5: TVD with MUSCL limiter
  24 +! 6: TVD with ULTIMATE QUICKEST
  25 +!
  26 +! ode_method -> ODE scheme for source and sink dynamics
  27 +! 1: first-order explicit (not positive)
  28 +! 2: second order explicit Runge-Kutta (not positive)
  29 +! 3: fourth-order explicit Runge-Kutta (not positive)
  30 +! 4: Patankar (first order, not conservative)
  31 +! 5: Patankar-RK (second order, not conservative)
  32 +! 6: Patankar-RK (does not work, not conservative)
  33 +! 7: Modified Patankar (1. order, conservat., posit.)
  34 +! 8: Modified Patankar-RK (2. order, conservat., posit.)
  35 +! 9: Modified Patankar-RK (does not work, conservat., posit.)
  36 +! 10: Ext. Modified Patankar (1. order, conservat., posit.)
  37 +! 11: Ext. Modified Patankar-RK (2. order, conservat., posit.)
  38 +!
  39 +! split_factor -> number of biogeochemical time steps per physical time step
  40 +!
  41 +! bioshade_feedback -> feedback of bio-turbidity to temp. eq. (.true./.false.)
  42 +!
  43 +! bio_lagrange_mean -> averaging Lagrangian conc. on output (.true./.false.)
  44 +!
  45 +! bio_npar -> total number of Lagrangian particles
  46 +!-------------------------------------------------------------------------------
  47 +&bio_nml
  48 + bio_calc= .true.
  49 + bio_model= 8
  50 + bio_eulerian= .true.
  51 + cnpar= 1.0
  52 + w_adv_discr= 4
  53 + ode_method= 11
  54 + split_factor= 1
  55 + bioshade_feedback= .true.
  56 + bio_lagrange_mean= .true.
  57 + bio_npar= 10000
  58 + /
... ...
test_cases/nocera/bio_fasham.nml 0 → 100644
... ... @@ -0,0 +1,87 @@
  1 +#$Id$
  2 +!-------------------------------------------------------------------------------
  3 +! Fasham et al. biological model with modifications by Kuehn and Radach
  4 +!
  5 +! numc= number of compartments for geobiochemical model
  6 +!
  7 +! p_initial= initial phytoplankton concentration [mmol n/m3]
  8 +! z_initial= initial zooplakton concentration [mmol n/m3]
  9 +! b_initial= initial bacteria concentration [mmol n/m3]
  10 +! d_initial= initial detritus concentration [mmol n/m3]
  11 +! n_initial= initial nitrate concentration [mmol n/m3]
  12 +! a_initial= initial ammonium concentration [mmol n/m3]
  13 +! l_initial= initial LDON concentration [mmol n/m3]
  14 +! p0 = minimum phytoplankton concentration [mmol n/m3]
  15 +! z0 = minimum zooplakton concentration [mmol n/m3]
  16 +! b0 = minimum bacteria concentration [mmol n/m3]
  17 +! vp = maximum phytoplankton uptake rate [1/day]
  18 +! alpha = slope of the PI-curvea [m2/(W day)]
  19 +! k1 = half saturation constant nitrate uptake [mmol n/m3]
  20 +! k2 = half saturation constant ammonium uptake [mmol n/m3]
  21 +! mu1 = phytoplankton mortality rate [1/day]
  22 +! k5 = half saturation constant phytoplankton mortality [mmol n/m3]
  23 +! gamma = exudation fraction [-]
  24 +! w_p = phytoplankton settling velocity [m/day]
  25 +! gmax = maximum ingestion rate [1/day]
  26 +! k3 = half saturation constant ingestion [mmol n/m3]
  27 +! beta = grazing efficiency [-]
  28 +! mu2 = maximum zooplankton loss rate [1/day]
  29 +! k6 = half saturation zooplankton loss [mmol n/m3]
  30 +! delta = fractional zooplankton loss to LDON [-]
  31 +! epsi = fractional zooplankton loss to ammonium [-]
  32 +! r1 = grazing preference phytoplankton [-]
  33 +! r2 = grazing preference bacteria [-]
  34 +! r3 = grazing preference detritus [-]
  35 +! vb = maximum bacterial uptake rate [1/day]
  36 +! k4 = half saturation bacterial uptake [mmol n/m3]
  37 +! mu3 = bacteria excretion rate [1/day]
  38 +! eta = uptake ratio ammonium:LDON [-]
  39 +! mu4 = detritus breakdown rate [1/day]
  40 +! w_d = detritus settling velocity [m/day]
  41 +! kc = attenuation constant for the self shading effect [m**2/mmol N]
  42 +! I_min = minimum photosynthetically active radiation (PAR) [W/m**2]
  43 +! I_opt = optimal photosynthetically active radiation (PAR) [W/m**2] !CHG1
  44 +! inib = inhibition slope of the PI-curve (positive) [m2/(W day)] !CHG1
  45 +! theta = phytoplancton buoyancy parameter [m3 day/(mmol N)] !CHG2
  46 +!-------------------------------------------------------------------------------
  47 + &bio_fasham_nml
  48 + numc= 7
  49 + p_initial= 0.0001
  50 + z_initial= 0.0001
  51 + b_initial= 0.0001
  52 + d_initial= 0.001
  53 + l_initial= 0.001
  54 + p0= 0.00001
  55 + z0= 0.00001
  56 + b0= 0.00001
  57 + vp= 1.5
  58 + alpha= 0.45
  59 + inib= 0.001
  60 + I_opt= 5.0
  61 + k1= 1.5
  62 + k2= 1.5
  63 + mu1= 0.05
  64 + k5= 0.3
  65 + gamma= 0.05
  66 + w_p= -0.38
  67 + theta= 0.0
  68 + w_pmin= -0.06
  69 + w_pmax= -0.38
  70 + gmax= 1.0
  71 + k3= 1.0
  72 + beta= 0.625
  73 + mu2= 0.3
  74 + k6= 0.2
  75 + delta= 0.1
  76 + epsi= 0.70
  77 + r1= 0.55
  78 + r2= 0.3
  79 + r3= 0.15
  80 + vb= 0.24
  81 + k4= 0.5
  82 + mu3= 0.03
  83 + eta= 0.0
  84 + mu4= 0.02
  85 + w_d= -5.0
  86 + kc= 0.03
  87 + /
... ...
test_cases/nocera/bio_gsj.nml 0 → 100644
... ... @@ -0,0 +1,134 @@
  1 +#$Id$
  2 +!-------------------------------------------------------------------------------
  3 +! Fasham et al. biological model with modifications by Kuehn and Radach
  4 +!
  5 +! numc= number of compartments for geobiochemical model
  6 +!
  7 +! p1_init = initial flagellate concentration [mmol n/m3]
  8 +! p2_init = initial diatom concentration [mmol n/m3]
  9 +! z1_init = initial micro-zooplakton concentration [mmol n/m3]
  10 +! z2_init = initial meso-zooplakton concentration [mmol n/m3]
  11 +! b_init = initial bacteria concentration [mmol n/m3]
  12 +! d_init = initial detritus concentration [mmol n/m3]
  13 +! l_init = initial LDON concentration [mmol n/m3]
  14 +! p0 = minimum phytoplankton concentration [mmol n/m3]
  15 +! z0 = minimum zooplakton concentration [mmol n/m3]
  16 +! b0 = minimum bacteria concentration [mmol n/m3]
  17 +! mte = if .true. use temperature-dependent metabolic rates
  18 +! ca1 = temp-dependence coeff for p1
  19 +! ca2 = temp-dependence coeff for p2
  20 +! ch1 = temp-dependence coeff for z1
  21 +! ch2 = temp-dependence coeff for z2
  22 +! amratio = Mass ratio between p2 and p1
  23 +! hmratio = Mass ratio between z2 and z1
  24 +! vp1 = maximum flagellate uptake rate by flagellates [1/day]
  25 +! vp2 = maximum diatom uptake rate by diatoms [1/day]
  26 +! alpha1 = slope of the flagellate PI-curve [m2/(W day)]
  27 +! alpha2 = slope of the diatom PI-curve [m2/(W day)]
  28 +! inib1 = inhibition slope of the flagellate PI-curve (pos.) [m2/(W day)]
  29 +! inib2 = inhibition slope of the PI-curve (pos.) [m2/(W day)]
  30 +! kn1 = half sat. constant nitrate uptake by p1 [mmol n/m3]
  31 +! ka1 = half sat. constant ammonium uptake by p1 [mmol n/m3]
  32 +! kn2 = half sat. constant nitrate uptake by p2 [mmol n/m3]
  33 +! ka2 = half sat. constant ammonium uptake by p2 [mmol n/m3]
  34 +! mu11 = mortality rate for p1 [1/day]
  35 +! mu12 = mortality rate for p2 [1/day]
  36 +! k5 = half sat. constant phy. mortality [mmol n/m3]
  37 +! gamma = exudation fraction [-]
  38 +! w_p1 = settling velocity for p1 [m/day]
  39 +! w_p2 = settling velocity for p2 [m/day]
  40 +! theta = phytoplancton buoyancy parameter [m3 day/(mmol N)]
  41 +! g1max = maximum ingestion rate for z1 [1/day]
  42 +! g2max = maximum ingestion rate for z2 [1/day]
  43 +! k3 = half saturation constant ingestion [mmol n/m3]
  44 +! beta = grazing efficiency [-]
  45 +! k6 = half saturation zooplankton loss (z1 & z2) [mmol n/m3]
  46 +! mu21 = maximum loss rate for z1 [1/day]
  47 +! mu22 = maximum loss rate for z2 [1/day]
  48 +! delta = fractional zooplankton loss to LDON (z1 & z2) [-]
  49 +! epsi = fractional zooplankton loss to ammonium (z1 & z2) [-]
  50 +! r11 = z1 grazing preference on p1 [-]
  51 +! r12 = z1 grazing preference on p2 [-]
  52 +! r13 = z1 grazing preference on bacteria [-]
  53 +! r14 = z1 grazing preference on detritus [-]
  54 +! r21 = z2 grazing preference on p1 [-]
  55 +! r22 = z2 grazing preference on p2 [-]
  56 +! r23 = z2 grazing preference on detritus [-]
  57 +! r24 = z2 grazing preference on z1 [-]
  58 +! vb = maximum bacterial uptake rate [1/day]
  59 +! k4 = half saturation bacterial uptake [mmol n/m3]
  60 +! mu3 = bacteria excretion rate [1/day]
  61 +! eta = uptake ratio ammonium:LDON [-]
  62 +! mu4 = detritus breakdown rate [1/day]
  63 +! mu5 = nitrification rate [1/day]
  64 +! w_d = detritus settling velocity [m/day]
  65 +! kc = attenuation constant for the self shading effect [m**2/mmol N]
  66 +!-------------------------------------------------------------------------------
  67 + &bio_gsj_nml
  68 + numc = 11
  69 + p1_init = 0.012
  70 + p2_init = 0.012
  71 + z1_init = 0.012
  72 + z2_init = 0.012
  73 + b_init = 0.001
  74 + d_init = 0.01
  75 + l_init = 0.1
  76 + p0 = 0.0001
  77 + z0 = 0.0001
  78 + b0 = 0.0001
  79 + mte = .true.
  80 + ca1 = 3.61
  81 + ca2 = 14.58
  82 + ch1 = 3.265
  83 + ch2 = 24.923
  84 + amratio = 200
  85 + hmratio = 1000
  86 + vp1 = 0.02
  87 + vp2 = 0.8
  88 + alpha1 = 0.02
  89 + alpha2 = 0.04
  90 + inib1 = 0.0
  91 + inib2 = 0.006
  92 + kn1 = 1.0
  93 + ka1 = 0.8
  94 + kn2 = 1.0
  95 + ka2 = 0.8
  96 + mu11 = 0.05
  97 + mu12 = 0.05
  98 + k5 = 0.2
  99 + gamma = 0.05
  100 + w_p1 =-0.38
  101 + w_p2 =-0.00
  102 + theta = 0.0
  103 + w_p1min =-0.01
  104 + w_p1max =-0.10
  105 + w_p2min =-0.05
  106 + w_p2max =-0.38
  107 + g1max = 1.0
  108 + g2max = 1.0
  109 + k3 = 1.0
  110 + beta = 0.625
  111 + mu21 = 0.3
  112 + mu22 = 0.3
  113 + k6 = 0.2
  114 + delta = 0.1
  115 + epsi = 0.70
  116 + r11 = 0.55
  117 + r12 = 0.30
  118 + r13 = 0.05
  119 + r14 = 0.10
  120 + r21 = 0.50
  121 + r22 = 0.30
  122 + r23 = 0.05
  123 + r24 = 0.15
  124 + vb = 0.24
  125 + k4 = 0.5
  126 + k10 = 0.5
  127 + w_h = 10.0
  128 + mu3 = 0.03
  129 + eta = 0.0
  130 + mu4 = 0.02
  131 + mu5 = 0.00
  132 + w_d = -5.0
  133 + kc = 0.03
  134 + /
... ...
test_cases/nocera/bio_iow.nml 0 → 100644
... ... @@ -0,0 +1,143 @@
  1 +#$Id$
  2 +!-------------------------------------------------------------------------------
  3 +! IOW biological model according to Neumann et al. 2002 and Burchard et al. 2005
  4 +!
  5 +! numc -> number of compartments for geobiochemical model
  6 +! p1_initial -> initial diatoms concentration [mmol n/m3]
  7 +! p2_initial -> initial flagellates concentration [mmol n/m3]
  8 +! p3_initial -> initial cyanobacterias concentration [mmol n/m3]
  9 +! zo_initial -> initial zooplankton concentration [mmol n/m3]
  10 +! de_initial -> initial detritus concentration [mmol n/m3]
  11 +! am_initial -> initial ammonium concentration [mmol n/m3]
  12 +! ni_initial -> initial nitrate concentration [mmol n/m3]
  13 +! po_initial -> initial phosphate concentration [mmol p/m3]
  14 +! o2_initial -> initial oxygen concentration [mmol n/m3]
  15 +! sfl_po -> constant surface phosphate flux [mmol n/m2/d]
  16 +! sfl_am -> constant surface ammonium flux [mmol n/m2/d]
  17 +! sfl_ni -> constant surface nitrate flux [mmol n/m2/d]
  18 +! surface_flux_method -> 0: constant; 2: from file 'bio_fluxes.dat'
  19 +! fluff -> .true.: caluclate fluff layer
  20 +! fl_initial -> initial fluff concentration [mmol n/m2]
  21 +! p10= -> minimum diatoms concentration [mmol n/m3]
  22 +! p20= -> minimum flagellates concentration [mmol n/m3]
  23 +! p30= -> minimum cyanobacterias concentration [mmol n/m3]
  24 +! zo0= -> minimum zooplankton concentration [mmol n/m3]
  25 +! w_p1= -> sinking speed diatom [m/d]
  26 +! w_p2= -> sinking speed flagellates [m/d]
  27 +! w_p3= -> sinking speed cyanobacteria [m/d]
  28 +! w_de= -> sinking speed detritus [m/d]
  29 +! kc= -> attenuation constant for the self shading effect [m2/mmol N]
  30 +! i_min= -> minimum photosynthetically active radiation (PAR) [W/m2]
  31 +! r1max= -> maximum growth rate diatoms [1/d]
  32 +! r2max= -> maximum growth rate flagellates [1/d]
  33 +! r3max= -> maximum growth rate cyanobacteria [1/d]
  34 +! alpha1= -> half saturation diatoms [mmol n/m3]
  35 +! alpha2= -> half saturation flagellates [mmol n/m3]
  36 +! alpha3= -> half saturation cyanobacteria [mmol n/m3]
  37 +! lpa= -> p --> a rate (p respiration) [1/d]
  38 +! lpd= -> p --> d rate (p mortality) [1/d]
  39 +! tf= -> temperature control flagellates [deg C]
  40 +! tbg= -> temperature control cyanos [deg C]
  41 +! beta_bg= -> temperature control cyanos [1/deg C]
  42 +! g1max= -> maximum grazing rate on diatoms [1/d]
  43 +! g2max= -> maximum grazing rate on flagellates [1/d]
  44 +! g3max= -> maximum grazing rate on cyanos [1/d]
  45 +! lza= -> z --> a rate (z exkudation) [m3/d/mmol n]
  46 +! lzd= -> z --> d rate (z mortality) [m3/d/mmol n]
  47 +! iv= -> Ivlev constant [1/(mmol n/m3)3]
  48 +! topt= -> optimum temperature [deg C]
  49 +!
  50 +! lan= -> nitrification constant [1/d]
  51 +! oan= -> oxygen parameter [ - ]
  52 +! beta_an= -> temperature control [1/deg C]
  53 +!
  54 +! lda= -> detritus mineralisation constant [1/d]
  55 +! tda= -> temperature control [deg C]
  56 +! lds= -> rate of detritus sinking into sediment [m/d]
  57 +! lsa= -> rate of sediment mineralisation [1/d]
  58 +! bsa= -> temperature control of sediment mineralisation [1/deg C]
  59 +! ph1= -> release of phosphate [ - ]
  60 +! ph2= -> release of phosphate [ - ]
  61 +! pvel= -> piston velocity [m/d]
  62 +!
  63 +! sr= -> redfield ratio(p/n) [ - ]
  64 +! s1= -> reduced nitrate/oxidized detritus [ - ]
  65 +! s2= -> oxygen produktion/recycled nitrogen [ - ]
  66 +! s3= -> oyxgen produktion related to n [ - ]
  67 +! s4= -> nitrification [ - ]
  68 +!
  69 +! a0= -> osat Parameter [mmol/m**3]
  70 +! a1= -> osat Parameter [ - ]
  71 +! a2= -> osat Parameter [1/ deg C]
  72 +!
  73 +! aa -> weighting factor for visible light fraction [-]
  74 +! g2 -> attenuation length for visible light [m]
  75 +!-------------------------------------------------------------------------------
  76 + &bio_iow_nml
  77 + numc= 9
  78 + p1_initial= 0.1
  79 + p2_initial= 0.1
  80 + p3_initial= 0.1
  81 + zo_initial= 0.1
  82 + de_initial= 5.0
  83 + am_initial= 0.1
  84 + ni_initial= 5.0
  85 + po_initial= 0.6
  86 + o2_initial= 85.0
  87 + sfl_po= -0.055
  88 + sfl_am= -0.36
  89 + sfl_ni= -0.45
  90 + surface_flux_method= 0
  91 + fluff= .true.
  92 + fl_initial= 0.0
  93 + p10= 0.0045
  94 + p20= 0.0045
  95 + p30= 0.0045
  96 + zo0= 0.0045
  97 + w_p1= -0.5
  98 + w_p2= 0.
  99 + w_p3= 0.1
  100 + w_de= -3.
  101 + kc= 0.03
  102 + i_min= 25.
  103 + r1max= 2.0
  104 + r2max= 0.7
  105 + r3max= 0.5
  106 + alpha1= 1.35
  107 + alpha2= 0.675
  108 + alpha3= 0.5
  109 + lpa= 0.01
  110 + lpd= 0.02
  111 + tf= 10.
  112 + tbg= 14.
  113 + beta_bg= 1.
  114 + g1max= 0.5
  115 + g2max= 0.5
  116 + g3max= 0.25
  117 + lza= 0.0666666666
  118 + lzd= 0.1333333333
  119 + iv= 0.24444444
  120 + topt= 20.
  121 + lan= 0.1
  122 + oan= 0.01
  123 + beta_an= 0.11
  124 + lda= 0.003
  125 + tda= 13.
  126 + beta_da= 20.
  127 + lds= 3.5
  128 + lsa= 0.001
  129 + bsa= 0.15
  130 + ph1= 0.15
  131 + ph2= 0.1
  132 + pvel= 5.
  133 + sr= 0.0625
  134 + s1= 5.3
  135 + s2= 6.625
  136 + s3= 8.125
  137 + s4= 0.6666666666666
  138 + a0= 31.25
  139 + a1= 14.603
  140 + a2= 0.4025
  141 + aa= 0.78
  142 + g2= 7.9
  143 + /
... ...
test_cases/nocera/bio_ismer.nml 0 → 100644
... ... @@ -0,0 +1,118 @@
  1 +#$Id$
  2 +!-------------------------------------------------------------------------------
  3 +! Fasham et al. biological model with modifications by Kuehn and Radach
  4 +!
  5 +! numc= number of compartments for geobiochemical model
  6 +!
  7 +! p1_init = initial flagellate concentration [mmol n/m3]
  8 +! p2_init = initial diatom concentration [mmol n/m3]
  9 +! z1_init = initial micro-zooplakton concentration [mmol n/m3]
  10 +! z2_init = initial meso-zooplakton concentration [mmol n/m3]
  11 +! b_init = initial bacteria concentration [mmol n/m3]
  12 +! d_init = initial detritus concentration [mmol n/m3]
  13 +! n_init = *** see obs.nml *** [mmol n/m3]
  14 +! a_init = *** see obs.nml *** [mmol n/m3]
  15 +! l_init = initial LDON concentration [mmol n/m3]
  16 +! p0 = minimum phytoplankton concentration [mmol n/m3]
  17 +! z0 = minimum zooplakton concentration [mmol n/m3]
  18 +! b0 = minimum bacteria concentration [mmol n/m3]
  19 +! theta = phytoplancton buoyancy parameter [m3 day/(mmol N)] !CHG2
  20 +! vp1 = maximum flagellate uptake rate by flagellates [1/day]
  21 +! vp2 = maximum diatom uptake rate by diatoms [1/day]
  22 +! alpha1 = slope of the flagellate PI-curve [m2/(W day)]
  23 +! alpha2 = slope of the diatom PI-curve [m2/(W day)]
  24 +! inib1 = inhibition slope of the flagellate PI-curve (pos.) [m2/(W day)] !CHG1
  25 +! inib2 = inhibition slope of the PI-curve (pos.) [m2/(W day)] !CHG1
  26 +! kn1 = half sat. constant nitrate uptake by fla [mmol n/m3]
  27 +! ka1 = half sat. constant ammonium uptake by fla [mmol n/m3]
  28 +! kn2 = half sat. constant nitrate uptake by diatoms [mmol n/m3]
  29 +! ka2 = half sat. constant ammonium uptake by diatoms [mmol n/m3]
  30 +! mu11 = pico-phytoplankton mortality rate [1/day]
  31 +! mu12 = nano-phytoplankton mortality rate [1/day]
  32 +! k5 = half sat. constant phy. mortality [mmol n/m3]
  33 +! gamma = exudation fraction [-]
  34 +! w_p1 = flagellate settling velocity [m/day]
  35 +! w_p2 = diatom settling velocity [m/day]
  36 +! g1max = maximum microzooplankton ingestion rate [1/day]
  37 +! g2max = maximum mesozooplankton ingestion rate [1/day]
  38 +! k3 = half saturation constant ingestion [mmol n/m3]
  39 +! beta = grazing efficiency [-]
  40 +! k6 = half saturation zooplankton loss (mcz & msz) [mmol n/m3]
  41 +! mu21 = maximum micro-zooplankton loss rate [1/day]
  42 +! mu22 = maximum meso-zooplankton loss rate [1/day]
  43 +! delta = fractional zooplankton loss to LDON (mcz & msz) [-]
  44 +! epsi = fractional zooplankton loss to ammonium (mcz & msz) [-]
  45 +! r11 = mcz grazing preference on flagellates [-]
  46 +! r12 = mcz grazing preference on bacteria [-]
  47 +! r13 = mcz grazing preference on detritus [-]
  48 +! r21 = msz grazing preference on flagellates [-]
  49 +! r22 = msz grazing preference on diatoms [-]
  50 +! r23 = msz grazing preference on detritus [-]
  51 +! r24 = msz grazing preference on mcz [-]
  52 +! vb = maximum bacterial uptake rate [1/day]
  53 +! k4 = half saturation bacterial uptake [mmol n/m3]
  54 +! mu3 = bacteria excretion rate [1/day]
  55 +! eta = uptake ratio ammonium:LDON [-]
  56 +! mu4 = detritus breakdown rate [1/day]
  57 +! mu5 = nitrification rate [1/day]
  58 +! w_d = detritus settling velocity [m/day]
  59 +! kc = attenuation constant for the self shading effect [m**2/mmol N]
  60 +!-------------------------------------------------------------------------------
  61 + &bio_ismer_nml
  62 + numc = 9
  63 + p1_init = 0.012
  64 + p2_init = 0.012
  65 + z1_init = 0.012
  66 + z2_init = 0.012
  67 + b_init = 0.001
  68 + d_init = 0.01
  69 + l_init = 0.1
  70 + p0 = 0.0001
  71 + z0 = 0.0001
  72 + b0 = 0.0001
  73 + vp1 = 1.0
  74 + vp2 = 0.8
  75 + alpha1 = 0.04
  76 + alpha2 = 0.04
  77 + inib1 = 0.006
  78 + inib2 = 0.006
  79 + kn1 = 1.0
  80 + ka1 = 0.8
  81 + kn2 = 1.0
  82 + ka2 = 0.8
  83 + mu11 = 0.05
  84 + mu12 = 0.05
  85 + k5 = 0.2
  86 + gamma = 0.05
  87 + w_p1 =-0.05
  88 + w_p2 =-0.20
  89 + theta = 0.0
  90 + w_p1min =-0.01
  91 + w_p1max =-0.10
  92 + w_p2min =-0.05
  93 + w_p2max =-0.38
  94 + g1max = 1.0
  95 + g2max = 1.0
  96 + k3 = 1.0
  97 + beta = 0.625
  98 + mu21 = 0.3
  99 + mu22 = 0.3
  100 + k6 = 0.2
  101 + delta = 0.1
  102 + epsi = 0.70
  103 + r11 = 0.55
  104 + r12 = 0.40
  105 + r13 = 0.05
  106 + r21 = 0.50
  107 + r22 = 0.30
  108 + r23 = 0.05
  109 + r24 = 0.15
  110 + vb = 0.24
  111 + k4 = 0.5
  112 + mu3 = 0.03
  113 + eta = 0.0
  114 + mu4 = 0.02
  115 + mu5 = 0.00
  116 + w_d = -5.0
  117 + kc = 0.03
  118 + /
... ...
test_cases/nocera/bio_nocera.nml 0 → 100644
... ... @@ -0,0 +1,87 @@
  1 +#$Id$
  2 +!-------------------------------------------------------------------------------
  3 +! Fasham et al. biological model with modifications by Kuehn and Radach
  4 +!
  5 +! numc= number of compartments for geobiochemical model
  6 +!
  7 +! p_initial= initial phytoplankton concentration [mmol n/m3]
  8 +! z_initial= initial zooplakton concentration [mmol n/m3]
  9 +! b_initial= initial bacteria concentration [mmol n/m3]
  10 +! d_initial= initial detritus concentration [mmol n/m3]
  11 +! n_initial= *** see obs.nml *** [mmol n/m3]
  12 +! a_initial= *** see obs.nml *** [mmol n/m3]
  13 +! l_initial= initial LDON concentration [mmol n/m3]
  14 +! p0 = minimum phytoplankton concentration [mmol n/m3]
  15 +! z0 = minimum zooplakton concentration [mmol n/m3]
  16 +! b0 = minimum bacteria concentration [mmol n/m3]
  17 +! vp = maximum phytoplankton uptake rate [1/day]
  18 +! alpha = slope of the PI-curvea [m2/(W day)]
  19 +! k1 = half saturation constant nitrate uptake [mmol n/m3]
  20 +! k2 = half saturation constant ammonium uptake [mmol n/m3]
  21 +! mu1 = phytoplankton mortality rate [1/day]
  22 +! k5 = half saturation constant phytoplankton mortality [mmol n/m3]
  23 +! gamma = exudation fraction [-]
  24 +! w_p = phytoplankton settling velocity [m/day]
  25 +! gmax = maximum ingestion rate [1/day]
  26 +! k3 = half saturation constant ingestion [mmol n/m3]
  27 +! beta = grazing efficiency [-]
  28 +! mu2 = maximum zooplankton loss rate [1/day]
  29 +! k6 = half saturation zooplankton loss [mmol n/m3]
  30 +! delta = fractional zooplankton loss to LDON [-]
  31 +! epsi = fractional zooplankton loss to ammonium [-]
  32 +! r1 = grazing preference phytoplankton [-]
  33 +! r2 = grazing preference bacteria [-]
  34 +! r3 = grazing preference detritus [-]
  35 +! vb = maximum bacterial uptake rate [1/day]
  36 +! k4 = half saturation bacterial uptake [mmol n/m3]
  37 +! mu3 = bacteria excretion rate [1/day]
  38 +! eta = uptake ratio ammonium:LDON [-]
  39 +! mu4 = detritus breakdown rate [1/day]
  40 +! w_d = detritus settling velocity [m/day]
  41 +! kc = attenuation constant for the self shading effect [m**2/mmol N]
  42 +! I_min = minimum photosynthetically active radiation (PAR) [W/m**2]
  43 +! I_opt = optimal photosynthetically active radiation (PAR) [W/m**2] !CHG1
  44 +! inib = inhibition slope of the PI-curve (positive) [m2/(W day)] !CHG1
  45 +! theta = phytoplancton buoyancy parameter [m3 day/(mmol N)] !CHG2
  46 +!-------------------------------------------------------------------------------
  47 + &bio_nocera_nml
  48 + numc= 7
  49 + p_initial= 0.012
  50 + z_initial= 0.012
  51 + b_initial= 0.001
  52 + d_initial= 0.01
  53 + l_initial= 0.1
  54 + p0= 0.0001
  55 + z0= 0.0001
  56 + b0= 0.0001
  57 + vp= 0.3
  58 + alpha= 0.04
  59 + inib= 0.06
  60 + I_opt= 20.0
  61 + k1= 1.0
  62 + k2= 0.8
  63 + mu1= 0.05
  64 + k5= 0.2
  65 + gamma= 0.05
  66 + w_p= -0.38
  67 + theta= 0.0
  68 + w_pmin= -0.06
  69 + w_pmax= -0.38
  70 + gmax= 1.0
  71 + k3= 1.0
  72 + beta= 0.625
  73 + mu2= 0.3
  74 + k6= 0.2
  75 + delta= 0.1
  76 + epsi= 0.70
  77 + r1= 0.55
  78 + r2= 0.4
  79 + r3= 0.05
  80 + vb= 0.24
  81 + k4= 0.5
  82 + mu3= 0.03
  83 + eta= 0.0
  84 + mu4= 0.02
  85 + w_d= -5.0
  86 + kc= 0.03
  87 + /
... ...
test_cases/nocera/bio_npzd.nml 0 → 100644
... ... @@ -0,0 +1,50 @@
  1 +!-------------------------------------------------------------------------------
  2 +! NPZD biological model
  3 +!
  4 +! numc= number of compartments for geobiochemical model
  5 +! n_initial= initial nutrient concentration [mmol N/m**3]
  6 +! p_initial= initial phytoplankton concentration [mmol N/m**3]
  7 +! z_initial= initial zooplankton concentration [mmol N/m**3]
  8 +! d_initial= initial detritus concentration [mmol N/m**3]
  9 +! p0= minimum phytoplankton concentration (to be added to p) [ " ]
  10 +! z0= minimum zooplankton concentration (to be added to z) [ " ]
  11 +! w_p= settling velocity of phytoplankton [m/d]
  12 +! w_d= settling velocity of zooplankton [m/d]
  13 +! kc= attenuation constant for the self shading effect [m**2/mmol N]
  14 +! I_min= minimum photosynthetically active radiation (PAR) [W/m**2]
  15 +! rmax= maximum nutrient uptake rate [1/d]
  16 +! gmax= maximum grazing rate [1/d]
  17 +! Iv= Ivlev constant [ - ]
  18 +! alpha= half saturation [mmol N/m**3]
  19 +! rpn= p --> n rate (p metabolism) [1/d]
  20 +! rzn= z --> n rate (z metabolism) [1/d]
  21 +! rdn= d --> n rate (remineralisation) [1/d]
  22 +! rpdu= p --> d rate (p mortality), in euphotic zone [1/d]
  23 +! rpdl= p --> d rate (p mortality), below euphotic zone [1/d]
  24 +! rzd= z --> d rate (z mortality) [1/d]
  25 +!-------------------------------------------------------------------------------
  26 +&bio_npzd_nml
  27 + numc= 4
  28 + n_initial= 4.5
  29 + p_initial= 1.e-15
  30 + z_initial= 1.e-15
  31 + d_initial= 4.5
  32 + p0= 0.0225
  33 + z0= 0.0225
  34 + w_p= -0.5
  35 + w_d= -5.
  36 + kc= 0.03
  37 + i_min= 25.
  38 + rmax= 1.
  39 + gmax= 0.2
  40 + Iv= 1.1
  41 + alpha= 0.4
  42 + inib= 0.04
  43 + k1= 0.5
  44 + rpn= 0.01
  45 + rzn= 0.01
  46 + rdn= 0.003
  47 + rpdu= 0.02
  48 + rpdl= 0.1
  49 + rzd= 0.02
  50 + /
... ...
test_cases/nocera/bio_sed.nml 0 → 100644
... ... @@ -0,0 +1,13 @@
  1 +#$Id$
  2 +!-------------------------------------------------------------------------------
  3 +! SEDIMENTATION biological model
  4 +!
  5 +! numc= number of compartments for geobiochemical model
  6 +! C_initial= initial nutrient concentration [mmol N/m**3]
  7 +! w_C= settling velocity of phytoplankton [m/d]
  8 +!-------------------------------------------------------------------------------
  9 +&bio_sed_nml
  10 + numc= 1
  11 + C_initial= 1.0
  12 + w_C= 0.0
  13 + /
... ...
test_cases/nocera/gotm_prod_GFORTRAN 0 → 120000
... ... @@ -0,0 +1 @@
  1 +/home/dumoda01/git/gotm_ismer/src/gotm_prod_GFORTRAN
0 2 \ No newline at end of file
... ...
test_cases/nocera/gotmmean.nml 0 → 100644
... ... @@ -0,0 +1,49 @@
  1 +!$Id: gotmmean.proto,v 1.1.1.1 2003/03/11 13:38:58 kbk Exp $
  2 +!-------------------------------------------------------------------------------
  3 +! The namelists 'meanflow' is read in meanflow.F90.
  4 +!-------------------------------------------------------------------------------
  5 +
  6 +!-------------------------------------------------------------------------------
  7 +! Specify variables related to the 1D meanflow model.
  8 +!
  9 +! h0b= bottom roughness - Note: z0b=0.03*h0b+0.1*nu/ustar [m]
  10 +! z0s_min= minimum value of z0s, default value if charnock=.false. [m]
  11 +! charnock= .true.: adaptation of Charnok 1955 formula used
  12 +! .false.: constant surface roughness length z0s_min used
  13 +! charnock_val= emp. constant in Charnok 1955 formula (default = 1400.)
  14 +! ddu= grid zooming (surface), 0: no zooming; > 3 strong zooming
  15 +! ddl= grid zooming (bottom), 0: no zooming; > 3 strong zooming
  16 +! grid_method= 0: zooming of grid with ddl, ddu >= 0
  17 +! 1: sigma grid (relative depth fractions) read from file
  18 +! 2: cartesian grid (fixed layer height in m) read from file
  19 +!
  20 +! grid_file= file for sigma or cartesian grid. the first line gives the
  21 +! number of layers, the following lines give fractions or
  22 +! layer heights in m from the surface down to the bottom.
  23 +! gravity= gravitational acceleration [m/s^2]
  24 +! rho_0= Reference density [kg/m^3].
  25 +! cp= Specific heat of sea water [J/kg/K].
  26 +! avmolu= molecular viscosity for momentum [m^2/s].
  27 +! avmolt= molecular diffusity for temperature [m^2/s].
  28 +! avmols= molecular diffusity for salinity [m^2/s].
  29 +! MaxItz0b= max # of iterations for z0b as function of u_taub.
  30 +! no_shear= .true.: shear production term P is set to zero
  31 +!-------------------------------------------------------------------------------
  32 + &meanflow
  33 + h0b= 0.05
  34 + z0s_min= 0.02
  35 + charnock= .false.
  36 + charnock_val= 1400.
  37 + ddu= 0.
  38 + ddl= 0.
  39 + grid_method= 0
  40 + grid_file= 'grid.dat'
  41 + gravity= 9.81
  42 + rho_0= 1027.
  43 + cp= 3985.
  44 + avmolu= 1.3e-6
  45 + avmolt= 1.4e-7
  46 + avmols= 1.1e-9
  47 + MaxItz0b= 1
  48 + no_shear= .false.
  49 + /
... ...
test_cases/nocera/gotmrun.nml 0 → 100644
... ... @@ -0,0 +1,136 @@
  1 +
  2 +!
  3 +!-------------------------------------------------------------------------------
  4 +! general model setup
  5 +!
  6 +! title -> title of simulation
  7 +! nlev -> number of levels
  8 +! dt -> time step in seconds
  9 +! cnpar -> parameter for "explicitness" of numerical scheme
  10 +! (between 0.0 and 1.0)
  11 +! buoy_method -> method to compute mean buoyancy
  12 +! 1: from equation of state
  13 +! (i.e. from potential temperature and salinity)
  14 +! 2: from prognostic equation
  15 +!
  16 +!-------------------------------------------------------------------------------
  17 + &model_setup
  18 + title= "TP3"
  19 + nlev= 50
  20 + dt= 120.
  21 + cnpar= 1.0
  22 + buoy_method= 1
  23 + /
  24 +
  25 +!-------------------------------------------------------------------------------
  26 +! geographic location
  27 +!
  28 +! name -> name of the station
  29 +! latitude -> latitude in degree (north is positive)
  30 +! longitude -> longitude in degree (east is positive)
  31 +! depth -> water depth in meters
  32 +!
  33 +!-------------------------------------------------------------------------------
  34 + &station
  35 + name= "Name"
  36 + latitude= -45.0
  37 + longitude= -30.0
  38 + depth= 100.
  39 +/
  40 +
  41 +!-------------------------------------------------------------------------------
  42 +! duration of run
  43 +!
  44 +! timefmt -> method to specify start and duration of model run
  45 +! 1: duration computed from number of time steps, MaxN
  46 +! (bogus start date used)
  47 +! 2: duration computed from given start and stop dates
  48 +! (number of time steps MaxN computed)
  49 +! 3: duration computed from number of time steps, MaxN
  50 +! (start date as specified, stop date computed)
  51 +!
  52 +! MaxN -> nominal number of time steps (see "timefmt")
  53 +! start -> nominal start date: YYYY/MM/DD HH:MM:SS (see "timefmt")
  54 +! stop -> nominal stop date: YYYY/MM/DD HH:MM:SS (see "timefmt")
  55 +!
  56 +!-------------------------------------------------------------------------------
  57 + &time
  58 + timefmt= 2
  59 + MaxN= 10
  60 + start= '2008-01-01 00:00:00'
  61 + stop= '2008-06-28 00:00:00'
  62 + /
  63 +!-------------------------------------------------------------------------------
  64 +! format for output and filename(s).
  65 +!
  66 +! out_fmt -> format for GOTM output
  67 +! 1: ASCII
  68 +! 2: NetCDF
  69 +! 3: GrADS
  70 +!
  71 +! out_dir -> path to output directory (set permissions)
  72 +! out_fn -> output string used to generate output file names
  73 +! nsave -> save results every 'nsave' timesteps
  74 +! diagnostics -> diagnostics are written to output (if .true.)
  75 +!
  76 +! mld_method -> how to diagnose mixed layer depth
  77 +! 1: mixed layer depth computed from TKE threshold
  78 +! 2: mixed layer depth from Ri threshold
  79 +! diff_k -> TKE threshold [m^2/s^2] for mixed layer depth
  80 +! ri_crit -> Ri threshold for mixed layer depth
  81 +!
  82 +! rad_corr -> correct surface buoyancy flux for solar radiation
  83 +! for output (if true)
  84 +!
  85 +!-------------------------------------------------------------------------------
  86 + &output
  87 + out_fmt= 2
  88 + out_dir= "./"
  89 + out_fn= "out"
  90 + nsave= 10
  91 + diagnostics= .false.
  92 + mld_method= 2
  93 + diff_k= 1.e-5
  94 + Ri_crit= 0.5
  95 + rad_corr= .true.
  96 + /
  97 +
  98 +!-------------------------------------------------------------------------------
  99 +! Specify variables related to the equation of state.
  100 +!
  101 +! eq_state_mode -> choice for empirical formula for equation of state
  102 +! 1: UNESCO equation of state by Fofonoff and Millard (1983)
  103 +! 2: equation of state according Jackett et al. (2005)
  104 +!
  105 +! eq_state_method -> method to compute density and buoyancy from salinity,
  106 +! potential temperature and pressure
  107 +! 1: full equation of state (i.e. with the LOCAL
  108 +! pressure). This implies that T is NOT treated as
  109 +! the potential temperature but rather as the in-situ
  110 +! temperature!
  111 +! 2: equation of state with pressure evaluated at the surface.
  112 +! This implies that T is treated as the potential
  113 +! temperature and thus rho as the potential density.
  114 +! 3: linearized equation of state at T0,S0,p0
  115 +! (again, use p0=p_surf to work with potential
  116 +! temperature and density.)
  117 +! 4: linear equation of state with T0,S0,dtr0,dsr0
  118 +!
  119 +! For the precise definition of the following quantities, see
  120 +! GOTM documentation:
  121 +!
  122 +! T0 -> reference temperature (deg C) for linear equation of state
  123 +! S0 -> reference salinity (psu) for linear equation of state
  124 +! p0 -> reference pressure (bar) for linear equation of state
  125 +! dtr0 -> thermal expansion coefficient for linear equation of state
  126 +! dsr0 -> saline expansion coefficient for linear equation of state
  127 +!-------------------------------------------------------------------------------
  128 + &eqstate