WQ - function PhytoLightLimitationFactor - WRN01

MOHID Water forum. Questions and discussion around MOHID Water
ruedabayona@gmail.com
MOHID User
Posts: 42
Joined: Thu Jan 01, 1970 00:00

WQ - function PhytoLightLimitationFactor - WRN01

Postby ruedabayona@gmail.com » Wed Mar 23, 2011 15:42

Hi all of MOHID users,

this is my first post, thanks by your atention.

I have a problem when I use de WQ module. When I run the model, It goes ok, but during processing appears a constant message as follows:

Light Limitation Factor negative NaN
Set to zero
Function PhytoLightLimitationFactor - WRN01
Me%PhytoGrossGrowRate set to zero : NaN
Me%TPhytoLimitationFactor : 0.8855870
Me%PhytoNutrientsLimitationFactor : NaN
Me%ExternalVar%Mass (AM,index) : NaN
Me%ExternalVar%Mass (NA,index) : NaN
Me%ExternalVar%Mass (IP,index) : NaN

Afterwards I check the hdf results and unfortunately there are NaN values in WQ parameters.

Thanks a lot !! :D

%%%% water properties file %%

REFERENCE_DENSITY : 1026.72
OUTPUT_TIME : 0 3600.
DT_OUTPUT_TIME : 600.
TIME_SERIE_LOCATION : ..\\..\\GeneralData\\monitoring_stations\\cartag_loca_puntos_registro.dat
<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : No description was given.
IS_COEF : 1
PARTICULATE : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 29.
DEFAULTBOUNDARY : 30.
BOUNDARY_INITIALIZATION : EXTERIOR
BOUNDARY_CONDITION : 2
OLD : 0
ADVECTION_DIFFUSION : 1
DISCHARGES : 1
DISCHARGES_TRACKING : 0
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
MIN_VALUE : 28
MAX_VALUE : 32
<endproperty>

<beginproperty>
NAME : salinity
UNITS : psu
DESCRIPTION : No description was given.
IS_COEF : 1
PARTICULATE : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 32.
DEFAULTBOUNDARY : 34.
BOUNDARY_INITIALIZATION : EXTERIOR
BOUNDARY_CONDITION : 2
OLD : 0
TIME_SERIE : 1
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
STATISTICS : 0
STATISTICS_FILE : ..\\..\\GeneralData\\statistics_salinity.dat
MIN_VALUE : 0
MAX_VALUE : 35
<endproperty>
Last edited by ruedabayona@gmail.com on Sun Jun 26, 2011 06:08, edited 1 time in total.

lilianseiler@yahoo.com.br
MOHID User
Posts: 24
Joined: Thu Jan 01, 1970 00:00

Postby lilianseiler@yahoo.com.br » Thu Mar 24, 2011 21:42

I have the same problem !!!

Lilian

ruedabayona@gmail.com
MOHID User
Posts: 42
Joined: Thu Jan 01, 1970 00:00

solution

Postby ruedabayona@gmail.com » Mon Mar 28, 2011 16:07

Well, taking into account my previous ask, a great friend gave me a hand, therefore I post a solution for my problem:

hydrodinamic file:

BAROCLINIC : 0
CONTINUOUS : 0
TIDE : 1
WATER_DISCHARGES : 1
RESIDUAL : 1
ENERGY : 0
CORIOLIS : 1
TIDEPOTENTIAL : 0
WIND : 1
ATM_PRESSURE : 0
SURFACEWATERFLUX : 1
TIME_SERIE : 1
DT_OUTPUT_TIME : 3600.
OUTPUT_TIME : 0 3600
TIME_SERIE_LOCATION : ..\\..\\GeneralData\\discharges_monitoring_points.dat

water properties fiel:
OUTPUT_TIME : 0 3600.
TIME_SERIE_LOCATION : ..\\..\\GeneralData\\discharges_monitoring_points.dat
! Correlação obtida pelo Poortela para o Tejo
SW_EXTINCTION_TYPE : 3

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : No description was given.
IS_COEF : 1
PARTICULATE : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 29.
DEFAULTBOUNDARY : 29.
BOUNDARY_INITIALIZATION : EXTERIOR
BOUNDARY_CONDITION : 2
OLD : 0
ADVECTION_DIFFUSION : 1
DISCHARGES : 1
DISCHARGES_TRACKING : 1
SURFACE_FLUXES : 1
DATA_ASSIMILATION : 0
ADVECTION_H_IMP_EXP : 0
TIME_SERIE : 1
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
MIN_VALUE : 10
MAX_VALUE : 35

<endproperty>

<beginproperty>
NAME : salinity
UNITS : psu
DESCRIPTION : No description was given.
IS_COEF : 1
PARTICULATE : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 35.
DEFAULTBOUNDARY : 36.
BOUNDARY_INITIALIZATION : EXTERIOR
BOUNDARY_CONDITION : 2
OLD : 0
ADVECTION_DIFFUSION : 1
DISCHARGES : 1
DISCHARGES_TRACKING : 1
DATA_ASSIMILATION : 0
ADVECTION_H_IMP_EXP : 0
TIME_SERIE : 1
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
STATISTICS : 0
STATISTICS_FILE : G:\\Aplica\\Hidrodinamica\\GeneralData\\statistics_salinity.dat
MIN_VALUE : 5
MAX_VALUE : 38
<endproperty>

<beginproperty>
NAME : cohesive sediment
UNITS : mg/l
DESCRIPTION : No description was given.
IS_COEF : .001
PARTICULATE : 1
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 50
DEFAULTBOUNDARY : 15.0
BOUNDARY_INITIALIZATION : EXTERIOR
BOUNDARY_CONDITION : 2
OLD : 0
ADVECTION_DIFFUSION : 1
DISCHARGES : 1
DISCHARGES_TRACKING : 0
VERTICAL_MOVEMENT : 1
BOTTOM_FLUXES : 1
DATA_ASSIMILATION : 0
ADVECTION_H_IMP_EXP : 0
TIME_SERIE : 1
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
STATISTICS : 0
STATISTICS_FILE : G:\\Aplica\\Hidrodinamica\\GeneralData\\statistics_cohesive.dat
MIN_VALUE : 1e-3
<endproperty>


! Optimum light intensity for phytoplankton photosynthesis [W/m2]
PHOTOIN : 100

!1________ABIOTIC____________________________

!1.1_________NITROGEN___________

NITRIREF : 0.18 ! Reference rate of nitrification
TNITCOEF : 1.08 ! Temperature coefficient for nitrification
NITSATCO : 2.0 ! Nitrification half-saturation constant (mgO2/L)
DENITREF : 0.07 ! Reference rate of denitrification Van Gils, Ouboter & Rooij (1993)
TDENCOEF : 1.046 ! Temperature coefficient for denitrification
DENSATCO : 0.1 ! Denitrification half-saturation constant (mgO2/L)
NOPREF : 0.1 ! Reference rate for the dissolution of PON to DONnr (d-1)
NOPCOEF : 1.02 ! PON decomposition temperature coefficient (adim)
NMINR : 0.0 ! Reference rate for the mineralisation of DONre at Tref (d-1)
TMINR : 1.02 ! Temperature coefficient for the mineralization of DONre
NMINENR : 0.1 ! Reference rate for the mineralization of DONnr at Tref (d-1)
TMINNR : 1.02 ! Temperature coefficient for the mineralization of DONnr (adim)
NSATCONS : 0.014 ! Ks for mineralisation (half-saturation constant) mgN/l
PHDECOMP : 0.5 ! Available PON for transformation into ammonia (adim)

!1.2________PHOSPHORUS__________

PPARTMIN : 0.03 ! POP reference decomposition rate (day-1)
TPPARTMINCOEF : 1.08 ! POP decomposition temperature coefficient (adim)
PMINR : 0.0 ! DOPre mineralisation rate at Tref (day-1)
PMINTCOEF : 1.064 ! DOPre mineralisation temperature coefficient (adim)
PMINNR : 0.22 ! DOPnr mineralisation rate at Tref (day-1)
PMINNRCOEF : 1.064 ! DOPnr mineralisation temperature coefficient (adim)
PSATCONS : 0.005 ! Phosphorus half-saturation constant, phosphorus, M/L^3

!1.3________OXYGEN__________

PHOTOSOC : 2.66 ! Photosynthesis oxygen/carbon ratio (2O/1C)= 32/12g/g
PLANK_OC_RAT : 2.66 ! Phytoplankton oxygen/carbon ratio (2O/1C)= 32/12g/g
ZOCRATIO : 2.66 ! Zooplankton oxygen/carbon ratio (2O/1C)= 32/12g/g
NITONRAT : 3.429 ! NO3 Oxy/Nitrogen ratio (3O/1N)=48/14g/g (secondary oxygen production due to nitrate uptake)
PHOSOPRAT : 2.064 ! PO4 Oxy/Phosphorus ratio (4O/1P)=64/31 g/g (secondary oxygen production due to phosphate uptake)
OPMINRATIO : 127.27 ! Mineralisation O/P ratio (oxygen consumed during organic P mineralisation)
ONMINRATIO : 2.285714 ! Mineralisation O/N ratio (oxygen consumed during organic N mineralisation)
BODCOEF : 1.047 ! BOD oxidation coefficient
BODREF : 0.18 ! Reference BOD oxidation, 1/T
BODSSAT : 0.5 ! Oxygen limitation half-saturation constant, 1/T
DENITRON : 2.285714 ! During the Denitrification the organic material is decomposed, we need to convert oxygen mass to Nitrogen mass, (M/L^3)/(M/L^3)


!2________BACTERIA____________________________(see WQM_users_manual.pdf)

BARESPCO : 2.5 ! Excretion rate
NATMORB : 0.1 ! Natural mortality rate
BMAXUPTA : 0.25 ! Maximum specific nutrient uptake rate
BMINUPTA : 0.05 ! Minimum specific nutrient uptake rate
BACNCONS : 8.0E-4 ! Half-saturation constant for nutrient uptake
BACMINSUB : 1.0E-2 ! Bacteria minimum substrate concentration
BRATIONC : 0.2 ! Bacteria N:C ratio (Redfield's ratio) (mgN/mgC)
SRATIONC : 0.252 ! Dissolved org. matter N:C ratio (Redfield's ratio) (mgN/mgC)
BRATIOPC : 0.2 ! Bacteria P:C ratio (Redfield's ratio) (mgP/mgC) (inventado)
SRATIOPC : 0.2 ! Dissolved org. matter P:C ratio (Redfield's ratio) (mgP/mgC) (inventado)
TOPTBMIN : 24.8 ! Minimum Temp for the \"optimal growth interval\"
TOPTBMAX : 25.1 ! Maximum Temp for the \"optimal growth interval\"
TBMIN : 3.5 ! Minimum tolerable temperature
TBMAX : 35.0 ! Maximum tolerable temperature
TBCONST1 : 5.0E-2 ! Constant to control temp. response curve shape
TBCONST2 : 0.98 ! Constant to control temp. response curve shape
TBCONST3 : 0.98 ! Constant to control temp. response curve shape
TBCONST4 : 2.0E-2 ! Constant to control temp. response curve shape

!3________PHYTOPLANKTON_________________________

FRATIONC : 0.18 ! Phytoplankton N:C ratio (Redfield's ratio) (mgN/mgC)
FRATIOPC : 0.024 ! Phytoplankton P:C ratio (Redfield's ratio) (mgP/mgC)
FREGSATC : 1.0 ! Ks(half-saturation constant) of Nutrient Regeneration (mgC/L)
GROWMAXF : 2.2 ! Maximum growth rate
!GROWMAXF : 2.4 ! Maximum growth rate
FMORTCON : 0.3 ! Ks of mortality
FMORTMAX : 0.03 ! Maximum mortality
FENDREPC : 0.0175 ! Endogenous respiration constant (day-1)
PHOTORES : 0.018 ! Photorespiration factor (adim)
EXCRCONS : 0.08 ! Excretion constant (Adim)
PHDECOMP : 0.5 ! Excretion-inorganic soluble fraction
FSOLEXCR : 0.25 ! Excretion-organic particulate fraction(adim)
FDISSDON : 0.4 ! Excretion-organic soluble fraction(adim)
TOPTFMIN : 25.0 ! Minimum Temp for the \"optimal growth interval\"
TOPTFMAX : 26.5 ! Maximum Temp for the \"optimal growth interval\"
TFMIN : 4.0 ! Minimum tolerable temperature
TFMAX : 37.0 ! Maximum tolerable temperature
TFCONST1 : 0.05 ! Constant to control temp. response curve shape
TFCONST2 : 0.98 ! Constant to control temp. response curve shape
TFCONST3 : 0.98 ! Constant to control temp. response curve shape
TFCONST4 : 0.02 ! Constant to control temp. response curve shape

!4________ZOOPLANKTON____________________________

!4.1______MICROZOOPLANKTON (OR CILIATE)_________

CRATIONC : 0.21 ! Microzooplankton N:C ratio (Redfield's ratio) (mgN/mgC)
CRATIOPC : 0.786E-3 ! Microzooplankton P:C ratio (Redfield's ratio) (mgP/mgC)
CILBACASS : 0.5 ! Assimilation coeff. of microzooplankton for bacteria
CINGMAX : 0.25 ! Maximum ingestion rate of bacteria (grazing on bacteria)
EFFCAPBA : 0.2 ! Capture efficiency of bacteria
GRAZBACMIN : 4.5E-2 ! Threshold standing stock of bacteria below predation cease
INGCONSC : 0.85 ! Half saturation constant for grazing
MAXMORTCI : 4.4E-2 ! Mortality rate due to the absent of preys (high)
MINMORTCI : 0.0 ! Minimum mortality rate
MORTCICOEF : 0.0 ! Shape factor for the mortality curve
CEXCFAC : 8.0E-2 ! Excretion rate at 0 degrees
CEXCCONS : 1.0305 ! Shape factor for the excretion curve
CREFRESP : 3.6E-2 ! Respiration rate (respiration assumed constant)
TOPTCMIN : 25.0 ! Minimum Temp for the \"optimal growth interval\"
TOPTCMAX : 26.5 ! Maximum Temp for the \"optimal growth interval\"
TCMIN : 4.0 ! Minimum tolerable temperature
TCMAX : 37.0 ! Maximum tolerable temperature
TCCONST1 : 0.05 ! Constant to control temp. response curve shape
TCCONST2 : 0.98 ! Constant to control temp. response curve shape
TCCONST3 : 0.98 ! Constant to control temp. response curve shape
TCCONST4 : 0.02 ! Constant to control temp. response curve shape

!4.2______MESOZOOPLANKTON__________

ZRATIONC : 0.13 ! Zooplankton N:C ratio (Redfield's ratio) (mgN/mgC)
!ZRATIONC : 0.15 ! Zooplankton N:C ratio (Redfield's ratio) (mgN/mgC)
ZRATIOPC : 0.024 ! Zooplankton P:C ratio (Redfield's ratio) (mgP/mgC)
GROWMAXZ : 0.10 ! Maximum growth rate at reference temperature (day-1)
!GROWMAXZ : 0.16 ! Maximum growth rate at reference temperature (day-1)
IVLEVCON : 13. ! Ivlev grazing constant (L.mgC-1)
GRAZFITOMIN : 0.0045 ! Minimum concentration of phytoplankton for grazing (mgCL-1)
ZREFRESP : 0.036 ! Natural mortality and respiration rate (day-1)
ZPREDMOR : 0.01 ! Predatory mortality rate (predation by higher trophic levels)
ASS_EFIC : 0.6 ! Assimilation efficiency (adim)
ZOOPHYASS : 0.7 ! Assimilation coefficient of phyto by mesozooplankton
ZOOCILASS : 0.5 ! Assimilation coefficient of microzoo by mesozooplankton
PHYRATING : 0.5 ! Proportion of phyto in mesozooplankton ingestion
ZINGMAX : 0.25 ! Maximum ingestion rate
EFFCAPHI : 0.8 ! Capture efficiency of phytoplankton
EFFCAPCIL : 0.2 ! Capture efficiency of microzooplankton
GRAZCILMIN : 4.5E-2 ! Minimum concentration of microzooplankton for grazing
INGCONSZ : 0.85 ! Half saturation constant for microzooplankton ingestion
MAXMORTZ : 4.0E-2 ! Mortality rate due to the absent of preys (high)
MINMORTZ : 0.0 ! Minimum mortality rate
MORTZCOEF : 0.0 ! Shape factor for the mortality curve
ZEXCFAC : 8.55E-2 ! Excretion rate at 0 degrees
ZEXCCONS : 1.0305 ! Shape factor for the excretion curve
ZREFRESP : 0.2 ! Respiration rate (respiration assumed constant)
ZSOLEXCR : 0.25 ! Soluble inorg. fraction of the zooplankton excretions
ZDISSDON : 0.25 ! Dissolved org. fraction of the zooplankton organic excretions
TOPTZMIN : 24.8 ! Minimum Temp for the \"optimal growth interval\"
TOPTZMAX : 25.1 ! Maximum Temp for the \"optimal growth interval\"
TZMIN : 5.0 ! Minimum tolerable temperature MSc Paula
TZMAX : 35.0 ! Maximum tolerable temperature MSc Paula
TZCONST1 : 0.05 ! Constant to control temp. response curve shape
TZCONST2 : 0.98 ! Constant to control temp. response curve shape
TZCONST3 : 0.98 ! Constant to control temp. response curve shape
TZCONST4 : 0.02 ! Constant to control temp. response curve shape
Last edited by ruedabayona@gmail.com on Thu Aug 23, 2012 16:55, edited 2 times in total.

ruedabayona@gmail.com
MOHID User
Posts: 42
Joined: Thu Jan 01, 1970 00:00

continue

Postby ruedabayona@gmail.com » Mon Mar 28, 2011 20:08

end
Last edited by ruedabayona@gmail.com on Thu Aug 23, 2012 16:53, edited 1 time in total.

ruedabayona@gmail.com
MOHID User
Posts: 42
Joined: Thu Jan 01, 1970 00:00

continue

Postby ruedabayona@gmail.com » Mon Mar 28, 2011 20:10

end
Last edited by ruedabayona@gmail.com on Thu Aug 23, 2012 16:54, edited 1 time in total.

ruedabayona@gmail.com
MOHID User
Posts: 42
Joined: Thu Jan 01, 1970 00:00

continue

Postby ruedabayona@gmail.com » Mon Mar 28, 2011 20:11

<beginproperty>
NAME : zooplankton
UNITS : mg/l
DESCRIPTION : zooplankton concentration
IS_COEF : .001
PARTICULATE : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 0.003
DEFAULTBOUNDARY : 0.003
BOUNDARY_INITIALIZATION : EXTERIOR
BOUNDARY_CONDITION : 2
OLD : 0
ADVECTION_DIFFUSION : 1
DISCHARGES : 1
DISCHARGES_TRACKING : 1
ADVECTION_H_IMP_EXP : 0 ! Only for 2D simulations (3D : 1)
VERTICAL_MOVEMENT : 0
SURFACE_FLUXES : 0
BOTTOM_FLUXES : 0
DATA_ASSIMILATION : 0
PARTITION : 0
WATER_QUALITY : 1
TIME_SERIE : 1
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
MIN_VALUE : 1e-5
<endproperty>

free vertical movement:

<beginproperty>
NAME : cohesive sediment
WS_TYPE : 1
SALTINT : 1
SALTINTVALUE : 3
FREEVERT_IMPEXP_ADV : 0
WS_VALUE : 1e-4
DEPOSITION : 1
<endproperty>

<beginproperty>
NAME : particulate organic nitrogen
SALTINT : 1
WS_TYPE : 1
WS_VALUE : 0.00001
FREEVERT_IMPEXP_ADV : 0
<endproperty>

<beginproperty>
NAME : particulate organic phosphorus
SALTINT : 1
WS_TYPE : 1
WS_VALUE : 0.00001
FREEVERT_IMPEXP_ADV : 0
<endproperty>

WQ module:

DTSECONDS : 3600.
NITROGEN : 1
PHOSPHOR : 1
PHYTO : 1
ZOO : 1
OXYGEN : 1
BOD : 0
BACTERIA : 0
CILIATE : 0
EXPLICIT : 1

! Optimum light intensity for phytoplankton photosynthesis [W/m2]
PHOTOIN : 100

!1________ABIOTIC____________________________

!1.1_________NITROGEN___________

NITRIREF : 0.18 ! Reference rate of nitrification
TNITCOEF : 1.08 ! Temperature coefficient for nitrification
NITSATCO : 2.0 ! Nitrification half-saturation constant (mgO2/L)
DENITREF : 0.07 ! Reference rate of denitrification Van Gils, Ouboter & Rooij (1993)
TDENCOEF : 1.046 ! Temperature coefficient for denitrification
DENSATCO : 0.1 ! Denitrification half-saturation constant (mgO2/L)
NOPREF : 0.1 ! Reference rate for the dissolution of PON to DONnr (d-1)
NOPCOEF : 1.02 ! PON decomposition temperature coefficient (adim)
NMINR : 0.0 ! Reference rate for the mineralisation of DONre at Tref (d-1)
TMINR : 1.02 ! Temperature coefficient for the mineralization of DONre
NMINENR : 0.1 ! Reference rate for the mineralization of DONnr at Tref (d-1)
TMINNR : 1.02 ! Temperature coefficient for the mineralization of DONnr (adim)
NSATCONS : 0.014 ! Ks for mineralisation (half-saturation constant) mgN/l
PHDECOMP : 0.5 ! Available PON for transformation into ammonia (adim)

!1.2________PHOSPHORUS__________

PPARTMIN : 0.03 ! POP reference decomposition rate (day-1)
TPPARTMINCOEF : 1.08 ! POP decomposition temperature coefficient (adim)
PMINR : 0.0 ! DOPre mineralisation rate at Tref (day-1)
PMINTCOEF : 1.064 ! DOPre mineralisation temperature coefficient (adim)
PMINNR : 0.22 ! DOPnr mineralisation rate at Tref (day-1)
PMINNRCOEF : 1.064 ! DOPnr mineralisation temperature coefficient (adim)
PSATCONS : 0.005 ! Phosphorus half-saturation constant, phosphorus, M/L^3

!1.3________OXYGEN__________

PHOTOSOC : 2.66 ! Photosynthesis oxygen/carbon ratio (2O/1C)= 32/12g/g
PLANK_OC_RAT : 2.66 ! Phytoplankton oxygen/carbon ratio (2O/1C)= 32/12g/g
ZOCRATIO : 2.66 ! Zooplankton oxygen/carbon ratio (2O/1C)= 32/12g/g
NITONRAT : 3.429 ! NO3 Oxy/Nitrogen ratio (3O/1N)=48/14g/g (secondary oxygen production due to nitrate uptake)
PHOSOPRAT : 2.064 ! PO4 Oxy/Phosphorus ratio (4O/1P)=64/31 g/g (secondary oxygen production due to phosphate uptake)
OPMINRATIO : 127.27 ! Mineralisation O/P ratio (oxygen consumed during organic P mineralisation)
ONMINRATIO : 2.285714 ! Mineralisation O/N ratio (oxygen consumed during organic N mineralisation)
BODCOEF : 1.047 ! BOD oxidation coefficient
BODREF : 0.18 ! Reference BOD oxidation, 1/T
BODSSAT : 0.5 ! Oxygen limitation half-saturation constant, 1/T
DENITRON : 2.285714 ! During the Denitrification the organic material is decomposed, we need to convert oxygen mass to Nitrogen mass, (M/L^3)/(M/L^3)


!2________BACTERIA____________________________(see WQM_users_manual.pdf)

BARESPCO : 2.5 ! Excretion rate
NATMORB : 0.1 ! Natural mortality rate
BMAXUPTA : 0.25 ! Maximum specific nutrient uptake rate
BMINUPTA : 0.05 ! Minimum specific nutrient uptake rate
BACNCONS : 8.0E-4 ! Half-saturation constant for nutrient uptake
BACMINSUB : 1.0E-2 ! Bacteria minimum substrate concentration
BRATIONC : 0.2 ! Bacteria N:C ratio (Redfield's ratio) (mgN/mgC)
SRATIONC : 0.252 ! Dissolved org. matter N:C ratio (Redfield's ratio) (mgN/mgC)
BRATIOPC : 0.2 ! Bacteria P:C ratio (Redfield's ratio) (mgP/mgC) (inventado)
SRATIOPC : 0.2 ! Dissolved org. matter P:C ratio (Redfield's ratio) (mgP/mgC) (inventado)
TOPTBMIN : 24.8 ! Minimum Temp for the \"optimal growth interval\"
TOPTBMAX : 25.1 ! Maximum Temp for the \"optimal growth interval\"
TBMIN : 3.5 ! Minimum tolerable temperature
TBMAX : 35.0 ! Maximum tolerable temperature
TBCONST1 : 5.0E-2 ! Constant to control temp. response curve shape
TBCONST2 : 0.98 ! Constant to control temp. response curve shape
TBCONST3 : 0.98 ! Constant to control temp. response curve shape
TBCONST4 : 2.0E-2 ! Constant to control temp. response curve shape

!3________PHYTOPLANKTON_________________________

FRATIONC : 0.18 ! Phytoplankton N:C ratio (Redfield's ratio) (mgN/mgC)
FRATIOPC : 0.024 ! Phytoplankton P:C ratio (Redfield's ratio) (mgP/mgC)
FREGSATC : 1.0 ! Ks(half-saturation constant) of Nutrient Regeneration (mgC/L)
GROWMAXF : 2.2 ! Maximum growth rate
!GROWMAXF : 2.4 ! Maximum growth rate
FMORTCON : 0.3 ! Ks of mortality
FMORTMAX : 0.03 ! Maximum mortality
FENDREPC : 0.0175 ! Endogenous respiration constant (day-1)
PHOTORES : 0.018 ! Photorespiration factor (adim)
EXCRCONS : 0.08 ! Excretion constant (Adim)
PHDECOMP : 0.5 ! Excretion-inorganic soluble fraction
FSOLEXCR : 0.25 ! Excretion-organic particulate fraction(adim)
FDISSDON : 0.4 ! Excretion-organic soluble fraction(adim)
TOPTFMIN : 25.0 ! Minimum Temp for the \"optimal growth interval\"
TOPTFMAX : 26.5 ! Maximum Temp for the \"optimal growth interval\"
TFMIN : 4.0 ! Minimum tolerable temperature
TFMAX : 37.0 ! Maximum tolerable temperature
TFCONST1 : 0.05 ! Constant to control temp. response curve shape
TFCONST2 : 0.98 ! Constant to control temp. response curve shape
TFCONST3 : 0.98 ! Constant to control temp. response curve shape
TFCONST4 : 0.02 ! Constant to control temp. response curve shape

!4________ZOOPLANKTON____________________________

!4.1______MICROZOOPLANKTON (OR CILIATE)_________

CRATIONC : 0.21 ! Microzooplankton N:C ratio (Redfield's ratio) (mgN/mgC)
CRATIOPC : 0.786E-3 ! Microzooplankton P:C ratio (Redfield's ratio) (mgP/mgC)
CILBACASS : 0.5 ! Assimilation coeff. of microzooplankton for bacteria
CINGMAX : 0.25 ! Maximum ingestion rate of bacteria (grazing on bacteria)
EFFCAPBA : 0.2 ! Capture efficiency of bacteria
GRAZBACMIN : 4.5E-2 ! Threshold standing stock of bacteria below predation cease
INGCONSC : 0.85 ! Half saturation constant for grazing
MAXMORTCI : 4.4E-2 ! Mortality rate due to the absent of preys (high)
MINMORTCI : 0.0 ! Minimum mortality rate
MORTCICOEF : 0.0 ! Shape factor for the mortality curve
CEXCFAC : 8.0E-2 ! Excretion rate at 0 degrees
CEXCCONS : 1.0305 ! Shape factor for the excretion curve
CREFRESP : 3.6E-2 ! Respiration rate (respiration assumed constant)
TOPTCMIN : 25.0 ! Minimum Temp for the \"optimal growth interval\"
TOPTCMAX : 26.5 ! Maximum Temp for the \"optimal growth interval\"
TCMIN : 4.0 ! Minimum tolerable temperature
TCMAX : 37.0 ! Maximum tolerable temperature
TCCONST1 : 0.05 ! Constant to control temp. response curve shape
TCCONST2 : 0.98 ! Constant to control temp. response curve shape
TCCONST3 : 0.98 ! Constant to control temp. response curve shape
TCCONST4 : 0.02 ! Constant to control temp. response curve shape

!4.2______MESOZOOPLANKTON__________

ZRATIONC : 0.13 ! Zooplankton N:C ratio (Redfield's ratio) (mgN/mgC)
!ZRATIONC : 0.15 ! Zooplankton N:C ratio (Redfield's ratio) (mgN/mgC)
ZRATIOPC : 0.024 ! Zooplankton P:C ratio (Redfield's ratio) (mgP/mgC)
GROWMAXZ : 0.10 ! Maximum growth rate at reference temperature (day-1)
!GROWMAXZ : 0.16 ! Maximum growth rate at reference temperature (day-1)
IVLEVCON : 13. ! Ivlev grazing constant (L.mgC-1)
GRAZFITOMIN : 0.0045 ! Minimum concentration of phytoplankton for grazing (mgCL-1)
ZREFRESP : 0.036 ! Natural mortality and respiration rate (day-1)
ZPREDMOR : 0.01 ! Predatory mortality rate (predation by higher trophic levels)
ASS_EFIC : 0.6 ! Assimilation efficiency (adim)
ZOOPHYASS : 0.7 ! Assimilation coefficient of phyto by mesozooplankton
ZOOCILASS : 0.5 ! Assimilation coefficient of microzoo by mesozooplankton
PHYRATING : 0.5 ! Proportion of phyto in mesozooplankton ingestion
ZINGMAX : 0.25 ! Maximum ingestion rate
EFFCAPHI : 0.8 ! Capture efficiency of phytoplankton
EFFCAPCIL : 0.2 ! Capture efficiency of microzooplankton
GRAZCILMIN : 4.5E-2 ! Minimum concentration of microzooplankton for grazing
INGCONSZ : 0.85 ! Half saturation constant for microzooplankton ingestion
MAXMORTZ : 4.0E-2 ! Mortality rate due to the absent of preys (high)
MINMORTZ : 0.0 ! Minimum mortality rate
MORTZCOEF : 0.0 ! Shape factor for the mortality curve
ZEXCFAC : 8.55E-2 ! Excretion rate at 0 degrees
ZEXCCONS : 1.0305 ! Shape factor for the excretion curve
ZREFRESP : 0.2 ! Respiration rate (respiration assumed constant)
ZSOLEXCR : 0.25 ! Soluble inorg. fraction of the zooplankton excretions
ZDISSDON : 0.25 ! Dissolved org. fraction of the zooplankton organic excretions
TOPTZMIN : 24.8 ! Minimum Temp for the \"optimal growth interval\"
TOPTZMAX : 25.1 ! Maximum Temp for the \"optimal growth interval\"
TZMIN : 5.0 ! Minimum tolerable temperature MSc Paula
TZMAX : 35.0 ! Maximum tolerable temperature MSc Paula
TZCONST1 : 0.05 ! Constant to control temp. response curve shape
TZCONST2 : 0.98 ! Constant to control temp. response curve shape
TZCONST3 : 0.98 ! Constant to control temp. response curve shape
TZCONST4 : 0.02 ! Constant to control temp. response curve shape

lilianseiler@yahoo.com.br
MOHID User
Posts: 24
Joined: Thu Jan 01, 1970 00:00

Postby lilianseiler@yahoo.com.br » Fri Apr 01, 2011 15:37

Hello!

Thanks a lot for your files!

Could you please post your InterfaceSedimentWater ?
I want confirm with mine.
At mine i just have the coesive sediment and i dont know if it is correct

Thanks again!

ruedabayona@gmail.com
MOHID User
Posts: 42
Joined: Thu Jan 01, 1970 00:00

of course!!

Postby ruedabayona@gmail.com » Mon Apr 04, 2011 16:48

Hi Lilian,

I'm sending you the file requested to your email,

greetings from Colombia

administrator@.
Site Admin
Posts: 349
Joined: Thu Jan 01, 1970 00:00
Location: Instituto Superior Tecnico - Lisbon - Portugal
Contact:

Postby administrator@. » Mon Apr 25, 2011 08:51

Hi,

Could you post what was the actual solution to the problem? What was wrong with the initial files.

Thanks,
Luis

ruedabayona@gmail.com
MOHID User
Posts: 42
Joined: Thu Jan 01, 1970 00:00

solution

Postby ruedabayona@gmail.com » Thu May 19, 2011 16:44

Hi everyone,

regarding to my previous ask, the solution is sumarized adding the following keyword in the WQ file:

! Optimum light intensity for phytoplankton photosynthesis [W/m2]
PHOTOIN : 100

good luck!

ruedabayona@gmail.com
MOHID User
Posts: 42
Joined: Thu Jan 01, 1970 00:00

Re: WQ - function PhytoLightLimitationFactor - WRN01

Postby ruedabayona@gmail.com » Sun Jun 26, 2011 06:07

[quote="ruedabayona@gmail.com"]Hi all of MOHID users,

this is my first post, thanks by your atention.

I have a problem when I use de WQ module. When I run the model, It goes ok, but during processing appears a constant message as follows:

Light Limitation Factor negative NaN
Set to zero
Function PhytoLightLimitationFactor - WRN01
Me%PhytoGrossGrowRate set to zero : NaN
Me%TPhytoLimitationFactor : 0.8855870
Me%PhytoNutrientsLimitationFactor : NaN
Me%ExternalVar%Mass (AM,index) : NaN
Me%ExternalVar%Mass (NA,index) : NaN
Me%ExternalVar%Mass (IP,index) : NaN

Afterwards I check the hdf results and unfortunately there are NaN values in WQ parameters.

Thanks a lot !! :D

%%%% water properties file %%

REFERENCE_DENSITY : 1026.72
OUTPUT_TIME : 0 3600.
DT_OUTPUT_TIME : 600.
TIME_SERIE_LOCATION : ..\\..\\GeneralData\\monitoring_stations\\cartag_loca_puntos_registro.dat

4

<beginproperty>
NAME : temperature
UNITS : ºC
DESCRIPTION : No description was given.
IS_COEF : 1
PARTICULATE : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 29.
DEFAULTBOUNDARY : 30.
BOUNDARY_INITIALIZATION : EXTERIOR
BOUNDARY_CONDITION : 2
OLD : 0
ADVECTION_DIFFUSION : 1
DISCHARGES : 1
DISCHARGES_TRACKING : 0
TIME_SERIE : 1
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
MIN_VALUE : 28
MAX_VALUE : 32
<endproperty>

<beginproperty>
NAME : salinity
UNITS : psu
DESCRIPTION : No description was given.
IS_COEF : 1
PARTICULATE : 0
INITIALIZATION_METHOD : CONSTANT
DEFAULTVALUE : 32.
DEFAULTBOUNDARY : 34.
BOUNDARY_INITIALIZATION : EXTERIOR
BOUNDARY_CONDITION : 2
TIME_SERIE : 1
BOX_TIME_SERIE : 0
OUTPUT_HDF : 1
STATISTICS : 0
STATISTICS_FILE : ..\\..\\GeneralData\\statistics_salinity.dat
MIN_VALUE : 0
MAX_VALUE : 35
<endproperty>


<


Return to “MOHID Water”

Who is online

Users browsing this forum: No registered users and 3 guests