Hi,
I’m attempting to run nemo-pisces with 2way sediments in a regional Baltic- North Sea setup. The model runs fine without sediments as well as with one way sediments. When trying out the 2 way coupling the model freezes after about two model days with no error or indication of what’s wrong. I’ve tried decreasing the time-step, removing all output, different order of rosenbrock method, different error tolerance, different number of vertical layers and with and without bioirrigation but all with the same result.
Is this something that anyone else has seen? I would really appreciate any ideas on how to proceed!
What do you mean by “freeze”, is there any indication in ocean.output or error file ? Usually when this happens it can because there is CFL violation within the barotropic loop.
Hello Jenny
I got similar problems while developing the model. An error that may occur can be caused by the formulation of advection/dissolution of the solid phases. This part of the code is quite a pain.
Could you post your sediment.output file ? Otherwise, did you try to restart the sediment component from an offline run ? Did you look at the output (both in the water column and sediments) before the model crashes (you may need to increase the output frequency to generate output over the few days before crashing) ?
Olivier
Thanks for you advice. I will try adding hourly output. Here’s my sediment.output (time stepping goes on in the same manner until ts 2075 where it stops with no additional info).
PISCES framework
SEDIMENT model
version 3.0 (2018)
sed_ini : Initialization of sediment module
sed_ini_nam : Read namelists
number of seconds in one year : ryear = 31536000.0000000
sed_ini_nam : read SEDIMENT namelist
~~~~~~~~~~~~~~
namelist nam_run
2-way coupling between PISCES and Sed ln_sed_2way = T
Order of the Rosenbrock method (2,3,4) = 3
Tolerance for absolute error = 1.000000000000000E-003
Tolerance for relative order = 1.000000000000000E-003
namelist nam_geom
Number of vertical layers jpksed = 18
Minimum vertical spacing sedzmin = 0.500000000000000
Maximum depth of the sediment sedhmax = 30.0000000000000
Default parameter sedkth = 9.00000000000000
Default parameter sedacr = 2.00000000000000
Sediment porosity at the surface porsurf = 0.900000000000000
Sediment porosity at infinite depth porinf = 0.750000000000000
Length scale of porosity variation rhox = 0.250000000000000
namelist nam_trased
name of 3d output sediment field number : 1 : SedFeO
long name Fe(OH)3 Concentration
in unit = %
name of 3d output sediment field number : 2 : SedFeS
long name FeS Concentration
in unit = %
name of 3d output sediment field number : 3 : SedPOC
long name POC Concentration
in unit = %
name of 3d output sediment field number : 4 : SedPOS
long name Semi-ref POC Concentration
in unit = %
name of 3d output sediment field number : 5 : SedPOR
long name Refractory POC Concentration
in unit = %
name of 3d output sediment field number : 6 : SedCaCO3
long name Calcite Concentration
in unit = %
name of 3d output sediment field number : 7 : SedBSi
long name Biogenic Silicate Concentration
in unit = %
name of 3d output sediment field number : 8 : SedClay
long name Clay Concentration
in unit = %
name of 3d output sediment field number : 9 : SedO2
long name Dissolved Oxygen Concentration
in unit = mol/L
name of 3d output sediment field number : 10 : SedNO3
long name Nitrates Concentration
in unit = mol/L
name of 3d output sediment field number : 11 : SedPO4
long name Phosphate Concentration
in unit = mol/L
name of 3d output sediment field number : 12 : SedNH4
long name Total Ammonium Concentration
in unit = mol/L
name of 3d output sediment field number : 13 : SedH2S
long name Total H2S Concentration
in unit = mol/L
name of 3d output sediment field number : 14 : SedSO4
long name Total SO4 Concentration
in unit = mol/L
name of 3d output sediment field number : 15 : SedFe2
long name Total Fe2+ Concentration
in unit = mol/L
name of 3d output sediment field number : 16 : SedAlkalini
long name Total Alkalinity Concentration
in unit = eq/L
name of 3d output sediment field number : 17 : Sedligand
long name Total ligand Concentration
in unit = mol/L
name of 3d output sediment field number : 18 : SedDIC
long name Dissolved inorganic Concentration
in unit = mol/L
name of 3d output sediment field number : 19 : SedSil
long name Silicate Concentration
in unit = mol/L
namelist nam_diased
name of 3D output diag number : 1 : SedpH
long name pH
in unit = -
name of 3D output diag number : 2 : SedCO3por
long name Dissolved CO3 concentration
in unit = mol/L
name of 3D output diag number : 3 : SaturCO3
long name CO3 saturation
in unit = -
name of 2D output diag number : 1 : FlxO2
long name Dissolved Oxygen Flux
in unit = mol/L
name of 2D output diag number : 2 : FlxNO3
long name Nitrates flux
in unit = mol/cm2/s
name of 2D output diag number : 3 : FlxPO4
long name Phosphate flux
in unit = mol/cm2/s
name of 2D output diag number : 4 : FlxNH4
long name Total Ammonium flux
in unit = mol/cm2/s
name of 2D output diag number : 5 : FlxH2S
long name Total H2S flux
in unit = mol/cm2/s
name of 2D output diag number : 6 : FlxSO4
long name Total SO4 flux
in unit = mol/cm2/s
name of 2D output diag number : 7 : FlxFe2
long name Total Fe2+ flux
in unit = mol/cm2/s
name of 2D output diag number : 8 : FlxAlkalini
long name Total Alkalinity flux
in unit = mol/cm2/s
name of 2D output diag number : 9 : FlxLig
long name Total Ligand flux
in unit = mol/cm2/s
name of 2D output diag number : 10 : FlxDIC
long name Dissolved inorganic carbon flux
in unit = mol/cm2/s
name of 2D output diag number : 11 : FlxSi
long name Silicate flux
in unit = mol/cm2/s
name of 2D output diag number : 12 : FlxFeO
long name FeO burial flux
in unit = mol/cm2/s
name of 2D output diag number : 13 : FlxFeS
long name FeS burial flux
in unit = mol/cm2/s
name of 2D output diag number : 14 : FlxPOC
long name POC burial flux
in unit = mol/cm2/s
name of 2D output diag number : 15 : FlxPOS
long name POS burial flux
in unit = mol/cm2/s
name of 2D output diag number : 16 : FlxPOR
long name POR burial flux
in unit = mol/cm2/s
name of 2D output diag number : 17 : FlxCaCO3
long name Calcite burial flux
in unit = mol/cm2/s
name of 2D output diag number : 18 : FlxBSi
long name BSi burial flux
in unit = mol/cm2/s
name of 2D output diag number : 19 : FlxClay
long name Clay burial flux
in unit = mol/cm2/s
name of 2D output diag number : 20 : Flxtot
long name Total burial flux
in unit = mol/cm2/s
name of 2D output diag number : 21 : dzdep
long name Sedimentation rate
in unit = cm/s
name of 2D output diag number : 22 : Rstepros
long name Number of iterations
in unit = -
namelist nam_inorg
reactivity for Si rcopal = 1.25000000000000
reactivity for calcite rccal = 0.100000000000000
L/C ratio in POC ratligc = 1.000000000000000E-004
reactivity for ligands rcligc = 0.100000000000000
namelist nam_poc
Redfield coef for oxy redO2 = 138.000000000000
Redfield coef for no3 redNo3 = 16.0000000000000
Redfield coef for po4 redPo4 = 1.00000000000000
Redfield coef for carbon redC = 117.000000000000
Ration for iron bound P redfep = 5.000000000000000E-002
reactivity for labile POC rcorgl = 10.0000000000000
reactivity for semi-refract. POC rcorgs = 0.100000000000000
reactivity for refractory POC rcorgr = 1.000000000000000E-004
reactivity for NH4 rcnh4 = 10000000.0000000
reactivity for H2S rch2s = 100000000.000000
reactivity for Fe2+ rcfe2 = 500000000.000000
reactivity for FeOH/H2S rcfeh2s = 10000.0000000000
reactivity for FeS/O2 rcfeso = 2000000.00000000
Precipitation of FeS rcfesp = 1.000000000000000E-004
Dissolution of FeS rcfesd = 1.000000000000000E-003
Half-sat. cste for oxic remin xksedo2 = 1.000000000000000E-006
Half-sat. cste for denit. xksedno3 = 5.000000000000000E-006
Half-sat. cste for iron remin xksedfeo = 6.000000000000000E-003
Half-sat. cste for SO4 remin xksedso4 = 5.000000000000000E-004
namelist nam_btb
coefficient for bioturbation dbiot = 8.00000000000000
Depth varying bioturbation ln_btbz = T
coefficient for btb attenuation dbtbzsc = 5.00000000000000
Adsorption coefficient of NH4 adsnh4 = 4.16000000000000
Adsorption coefficient of Fe2 adsfe2 = 697.000000000000
Bioirrigation in sediment ln_irrig = T
coefficient for irrig attenuation xirrzsc = 2.00000000000000
namelist nam_rst
boolean term for restart (T or F) ln_rst_sed = F
sed_ini_geom : Initialization of sediment geometry
total number of ocean points jpoce = 67
sed_initrc : Initialization of sediment concentration
Initilization of default values of sediment components
sed_dta : Bottom layer fields
~~~~~~
Data from SMS model
sed_dta : Sediment fields
sed_dta : Bottom layer fields at time kt = 1
Getting Chemical constants from tracer model at time kt = 1
sed_co3 : carbonate ion and proton concentration calculation
======== Write summary of sediment char. ============
-------------------------------------------------------------------
Initial Conditions
-------------------------------------------------------------------
dzm = dzkbot minimum to calculate 0.000000000000000E+000
Local zone : jpi, jpj, jpksed : 12 17 18
jpoce = 67 nbtot pts = 204 nb earth pts = 137
sublayer thickness dz(1) [cm] : 0.100000000000000
Vertical domain of the sediment
-------------------------------
Indice, profsed, dz
2 0.250119164490545 0.500575407365835
3 0.751586974824761 0.502937560396287
4 1.25694347558398 0.509333102275183
5 1.77280166724157 0.526532257110151
6 2.31670800802939 0.571957784893590
7 2.93337190749323 0.686468525671767
8 3.72545782447399 0.944621449295281
9 4.87644770560986 1.40729921036285
10 6.57087576930540 1.98155691702823
11 8.80874201556061 2.44423467809580
12 11.4055122259709 2.70238760171931
13 14.1777044538982 2.81689834249749
14 17.0226542405014 2.86232387028093
15 19.8956521762349 2.87952302511589
16 22.7791518028668 2.88591856699480
17 25.6665401199236 2.88828072002524
18 28.5553624613437 2.88915098087136
nb solid comp : 8
(1=opal,2=clay,3=POC,4=CaCO3), 5=POS, 6=POR, 7=FEO, 8=FeS
weight mol 1,2,3,4,5,6,7
67.20 430.51 33.62 100.00 33.62 33.62 106.00 87.00
nb dissolved comp 11
1=silicic acid,,2=O2,3=DIC,4=NO3,5=PO4,6=Alk,7=NH4,8=ODU
redfield coef C,O,N P Dit
117.00 138.00 16.00 1.00 110.40
End Of Initialization
sed_sol : Organic/inorganic degradation related reactions and diffusion
sed_btb : bioturbation of solid and adsorbed species
sed_inorg : Dissolution of CaCO3 and BSi
sed_co3 : carbonate ion and proton concentration calculation
sed_org : solute species which do not experience redox reactions
sed_adv : vertical sediment advection
sed_co3 : carbonate ion and proton concentration calculation
sed_wri kt = 1
sed_dta : Bottom layer fields
~~~~~~
Data from SMS model
sed_dta : Bottom layer fields at time kt = 2
Getting Chemical constants from tracer model at time kt = 2
sed_wri kt = 2
A few model hours before the freeze, water column nitrate and phosphate above deep water sediments starts to grow and becomes extremely large, ~1e19 mmolm-3 right before the crash. The same can be seen in corresponding sediment vars (~1e13 mmolm-3) at the upper sediment layers in deep water areas.
Have you seen this before? Any idea what to do about it?
