!==============================================================================! ! (1) INPUT FILE TO DETERMINE MODEL STRUCTURE, FUNCTIONS AND PARAMETERS FOR ! ! THE GENERALIZED BIOLOGIAL MODEL. PARAMETER VALUES ARE GIVEN FOLLOWING ! ! THEIR DEFINITION INCLUDING DIMENSION AND UNITS ! ! ! ! (2) 'STRUCTURE' INDICATES MODEL STRUCUTRE FOR WHICH USERS CAN SELECT 'NPZ', ! ! 'NPZD', 'FASHAM', '2NPZD', '2NPZDSB' AND 'NEW'. ! ! ! ! (3) IF 'NEW' IS SELECTED, USERS NEED TO PROVIDE THE TOTAL NUMBER OF STATE ! ! VARIBALES FOR EACH FUNCTIONAL GROUP, FOLLOWED BY THEIR NAME AND UNITS, ! ! WHICH ARE USED FOR NETCDF OUTPUT. FUNCTIONAL GROUPS ARE: ! ! ! ! 'NUTRIENT' 'PHYTOPLANKTON 'ZOOPLANKTON' 'DETRITUS' ! ! 'DOM' 'BACTERIA' 'AUXILIARY' ! ! ! ! FOR EXAMPLE: ! ! 'PHYTOPLANKTON' ! ! 3 ! ! 'Diatom' 'mmole C m-3' ! ! 'Dinoflagellate' 'mmole C m-3' ! ! 'Picophytoplankton' 'mmole C m-3' ! ! ! ! (4) 'L_FUNCTION' INDICATES LIGHT FUNCTION FOR PHYTOPLANKTON GROWTH. 10 LIGHT ! ! FUNCTIONS HAVE BEEN IMPLEMENTED FOR SELECTION. THEY ARE: ! ! ! ! 'EXP_LIGHT' EXPONENTIAL (FRANKS ET AL., 1986) ! ! 'SL62_LIGHT' EXPONEJTIAL (STEELE, 1962) ! ! 'MM_LIGHT' MICHAELIS-MENTEN (CAPERON, 1967) ! ! 'LB_LIGHT' MICHAELIS-MENTEN (BANNISTER, 1979) ! ! 'V65_LIGHT' MICHAELIS-MENTEN (VOLLENWEIDER, 1965) ! ! 'PE78_LIGHT' MICHAELIS-MENTEN (PEETERS & EILERS, 1978) ! ! 'WNS74_LIGHT' EXPONENTIAL (WEBB ET AL., 1974) ! ! 'PGH80_LIGHT' EXPONENTIAL (PLATT ET AL., 1980) ! ! 'JP76_LIGHT' HYPERBOLIC TANGENT (JASSBY & PLATT, 1976) ! ! 'BWDC99_LIGHT' HYPERBOLIC TANGENT (BISSETT ET AL., 1999) ! ! ! ! (5) 'G_FUNCTION' INDICATES ZOOPLANKTON GRAZING FUNCTION. 11 GRAZING ! ! FUNCTIONS HAVE BEEN IMPLEMENTED FOR SELECTION. THEY ARE: ! ! ! ! 'IVLE1_G' IVLEV (IVLEV, 1955) ! ! 'RECTI_G' RECTILINEAR (ARMSTRONG, 1994) ! ! 'CLI_G' IVLEV (LEONARD ET AL., 1999) ! ! 'IVLEV2_G' IVLEV+RECTILINEAR (HOFMANN & AMBER, 1991) ! ! 'MM1_G' MICHAEKIS-MENTEN (MOLONEY & FILED, 1991) ! ! 'MM2_G' MICHAELIS+RECTILINEAR (EVANS, 1988) ! ! 'MM3_G' MICAHELIES-MENTEN (VERITY, 1991) ! ! 'SMM_G' SWITCHING MICAHELIS-MEMTEN (FASHAM ET AL., 1990) ! ! 'GSF1_G' GENERALIZED RECTILINEAR (TANSKY, 1978) ! ! 'GSF2_G' GENERALIZED RECTILINEAR (VANCE, 1978) ! ! 'GSMM_G' GENERALIZED MICHAELIS-MENTEN (GISMERVIK, 1997) ! ! ! ! (6) THE SUM OF CERTAIN PARAMETERS SUCH AS THAT OF GROWTH EFFICIENCY, ACTIVE ! ! RESPIRATION AND FEEDING LOSSES SHOULD EQUAL TO 1. THE MODEL CHECKS THESE ! ! PARAMETERS AND STOPS THE EXECUTION AND PROVIDES A MESSAGE IF THE SUM OF ! ! THOSE PARAMETERS DOES NOT EQUAL TO 1 ! ! ! ! (7) DIMENSION: NNN: THE TOTAL NUMBER OF NUTRIENT. ! ! NNP: THE TOTAL NUMBER OF PHYTOPLANKTON. ! ! NNZ: THE TOTAL NUMBER OF ZOOPLANKTON. ! ! NNB: THE TOTAL NUMBER OF BACTERIA. ! ! NND: THE TOTAL NUMBER OF DETRITUS. ! ! NNM: THE TOTAL NUMBER OF DOM. ! ! NNA: THE TOTAL NUMBER OF AUXILIARY VARIABLES. ! ! ! ! (8) FOR THE INITIALIZATION, EACH BIOLOGICAL STATE VARIABLE HAS AN INDEPENDENT! ! INITIAL CONDITION FILE PLACED IN INPDIR. THEY SHOULD BE NAME AS ! ! "NUTRIENT_INI_1", "NUTRIENT_INI_2","PHYTOPLANKTON_INI_1", "ZOOPLANKTON_ ! ! INI_1", "BACTERIA_INI_1", 'DETRITUS_INI_1", "DOM_INI_1" AND SO FORTH. ! ! THREE TYPES OF INITIAL CONDITIONS WERE IMPLEMENTED: (1) 'CONSTANT': A ! ! SINGLE VALUE; (2) 'LINEAR':WITH AT LEAST TWO PAIRS OF VALUES WITH DEPTH. ! ! VARIABLE VALUES WILL BE LINEARLY INTERPOLATED BETWEEN THE VALUES GIVEN), ! ! (3) "DATA": OBSERVATION DATA SHOULD BE INTERPOLATED ONTO THE GRID POINTS ! ! AT STANDARD LEVELS. VARIABLE VALUES WILL BE INTERPOLATED AT EACH GRID ! ! POINT FROM THE DATA. THE TYPE OF INITIAL CONDITION SHOULD BE PUT ON THE ! ! FIRST LINE OF EACH INITIAL FILE ! !=============================================================================! ! (9) FOLLOWING IS A COMPREHENSIVE LIST OF PARAMETERS. ONLY A SUBSET OF THESE ! ! PARAMETERS IS NEEDED FOR A SPECIFIC MODEL STRUCTURE AND FUNCTION SELEC- ! ! TION. THE MODEL WILL PRINT OUT YOUR SELECTION AND PARAMETER ASSIGNMENT. ! ! PARAMETER ASSIGNMENT FORMAT IS: ! ! ! ! SYMBOL DIMENSION UNIT DEFINITION ! !==============================================================================! !****************** MODEL STRUCUTRE AND FUNCTIONS ******************! 'STRUCTURE' 'NPZD' 'L_FUNCTION' 'SL62_LIGHT' 'MM_LIGHT' !'PGH80_LIGHT' 'G_FUNCTION' 'GSMM_G' !******************************** PHYTOPLANKTON PARAMETERS ****************************! 'ALPHAP' (NNP) mgC/mgCHl/s/W LIGHT FUNCTION COEFFICIENT 0.32e-6 'ALPHA_U' (NNP) dimensionless COEFFICIENT BETWEEN MULTIPLICATION & MINIMUM 0.5 'A_TP' (NNP) (C)-1 EXPONENTIAL FOR T FORCING 0.07 'ATANU_C' SCALAR (mg Chl)-1 m2 ATTENUATION COEFFICIENT OF CHLOROPHYLL 0.03 'ATANU_D' SCALAR (mmole C)-1 m2 ATTENUATION COEFFICIENT OF DETRITUS 0.01 'ATANU_W' SCALAR m-1 ATTENUATION COEFFICIENT OF WATER 0.04 'BETAP' (NNP) mgC (mgCHl s W)-1 PHOTOINHIBITION COEFFICIENT 1.6e-8 'CHL2C' (NNP) mg CHL/mmol C CHLOROPHYLL TO CARBON RATIO IN PHYTO 2.0 'D_DOM' (NNP) dimensionless ACTIVE EXUDATION COEFFICIENT 0.0 !0.1 'DPDOM' (NNP) s-1 PASSIVE PHYTO EXUDATION COEFFICIENT 0.0 !1.74e-7 'I_OPT' (NNP) W OPTIMAL LIGHT FOR PHYTO 100.0 'K_LIGHT' (NNP) W HALF_SATURATION OF LIGHT FUNCTIONS 50 'MPD' (NNP) s-1 PHYTO MORTALITY EOFFICIENT 1.16e-7 'M_P' (NNP) dimensionless PHYTO MORTALITY ORDER 1 'N_P' (NNP) dimensionless POWER OF LIGHT FUNCTIONS 2 'PARFRAC' SCALLAR dimensionless PAR FRACTION OF TOTAL SHORT WAVE RADIATION 0.43 'P_O' (NNP) mmol c m-3 PHYTOPANKTON THRESHOLDS 0.01 'RP_T' SCALAR dimensionless EXPONENTIAL FOR T FORCING ON RESPIRATION 0.0 !0.07 'R_P' (NNP) s-1 PHYTO RESPIRATION COEFFICIENT 1.16e-7 'T_OPTP' (NNP) C OPTIMAL TEMPERATURE FOR PHYTO 20 'UMAX' (NNP) mmol (mgCHL s)-1 PHYTO MAXIMUM GROWTH RATE 0.01 1.6e-5 'W_P' (NNP) m s-1 SINKING VELOCITY OF PHYTO 0.0 !1.16e-5 !******************************** ZOOPLANKTON PARAMETERS **************************! 'ACTIVE_R' (NNZ) dimensionless ACTIVE RESPIRATION COEFFICIENT 0.3 'A_TZ' (NNZ) (C)-1 EXPONENTIAL FOR T FORCING 0.07 'EFFIB' (NNB,NNZ) dimensionless GROWTH EFFICIENCY ON BACTERIA 0.3 'EFFID' (NND,NNZ) dimensionless GROWTH EFFICIENCY ON DETRITUS 0.3 'EFFIP' (NNP,NNZ) dimensionless GROWTH EFFICIENCY ON PHYTO 0.3 'EFFIZ' (NNZ,NNZ) dimensionless GROWTH EFFICIENCY ON ZOOPLANKTON 0.3 'G_MAX' (NNZ) s-1 MAXIMUM GRAZING RATE 1.16e-5 'K_ZG' (NNZ) mmol C m-3 HALF-SATURATION FOR ZOO GRAZING 2 'M_G' (NNZ) dimensionless ZOOPLANKTON GRAZING POWER 1 'MZD' (NNZ) s-1 ZOOPLANKTON MORTALITY COEFFICIENT 2.31e-7 'M_Z' (NNZ) dimensionless ZOOPLANKTON MORTALITY POWER 1.0 'P_C' (NNZ) mmol C m-3 GRAZING THRESHOLD 0.1 'R_RECRUIT' (NNZ) dimensionless RECRUIT COEFFICIENT 0.0 !0.1 'R_Z' (NNZ) s-1 ZOO PASSIVE RESPIRATION COEFFICIENT 5.79e-7 'SIGMA_B' (NNB,NNZ) (mmol C m-3)-1 PREFERENCE ON BACTERIA 1 'SIGMA_D' (NND,NNZ) (mmol C m-3)-1 PREFERENCE ON DETRITUS 0.1 'SIGMA_P' (NNP,NNZ) (mmol C m-3)-1 PREFERENCE ON PHYTO 0.5 'SIGMA_Z' (NNZ,NNZ) (mmol C m-3)-1 PREFERENCE ON ZOOPLANKTON 0.5 'T_OPTZ' (NNZ) C OPTIMAL TEMPERATURE FOR ZOOPLANKTON 20 'Z_0' (NNZ) mmol C m-3 ZOOPLANKTON THRESHOLLD 0.01 !******************************** BACTERIA PARAMETERS ***************************! 'A_TB' (NNB) (C)-1 EXPONENTAIL FOR T FORCING 0.07 'B_0' (NNB) mmol C m-3 BACTERIA THRESHOLLD 0.01 'DELTA_B' (NNB) dimensionless RATIO BETWEEN NH4 AND DON UPTAKE 0.4 'EFFIDOM' (NNM,NNB) dimensionless GROWTH EFFICIENCY ON DOM 0.2 'EFFIN' (NNN,NNB) dimensionless GROWTH EFFICIENCY ON NH4 1.0 'R_B' (NNB) s-1 BACTERIA RESPIRATION COEFFICIENT 4.63e-7 'SIGMA_DOM' (NNM,NNB) (mmol C m-3)-1 PREFERENCE ON DOM 0.1 'SIGMA_N' (NNN,NNB) (mmol n m-3)-1 PREFERENCE ON DON 1.0 'T_OPTB' (NNB) C OPTIMAL T FOR BACTERIA 20.0 'UBMAX' (NNB) s-1 MAXIMUM GROWTH RATE OF BACTERIA !******************************** DETRITUS PARAMETERS ***************************! 'ALPHA_BD' (NND,NNB,NNZ) dimensionless FEEDING LOSS FROM BACTERIA TO DETRITUS 1.0 'ALPHA_DAG' (NND) s-1 AGGREGATION COEFFICIENT 0.0 'ALPHA_DD' (NND,NND,NNZ) dimensionless FEEDING LOSS FROM DETRITUS TO DETRITUS 0.4 'ALPHA_DDG' (NND) s-1 DISAGGREGATION 0.0 'ALPHA_PD' (NND,NNP,NNZ) dimensionless FEEDING LOSS FROM PHYTO TO DETRITUS 0.4 'ALPHA_ZD' (NND,NNZ,NNZ) dimensionless FEEDING LOSS FROM ZOO TO DETRITUS 0.4 'D_D' (NND) s-1 DISSOLUTION COEFFICIENT 0.0 'D_0' (NND) s-1 DETRITUS THRESHOLD 0.0 'D_RN' (NND) s-1 REMINERALIZATION COEFFICIENT 2.31e-7 'D_0' (NND) mmol C m-3 DETRITUS THRESHOLLD 0.01 'EPSILON_PD' (NND,NNP) dimensionless PHYTO MORTALITY TO DETRITUS 1.0 'EPSILON_ZD' (NND,NNZ) dimensionless ZOO MORTALTIY TO DETRITU 1.0 'W_D' (NND) m s-1 DETRITUS SINKING VELOCITY 0.0 !2.31E-4 !******************************** DOM PARAMETERS ****************************! 'ALPHA_DOM' (NNM) s-1 DOM AGEING COEFFICIENT 1.16e-7 'ALPHA_PDOM' (NNM,NNP) dimensionless PHYTO EXUDATION TO DOM 0.0 'ALPHA_DDOM' (NNM,NND) dimensionless DETRITUS DISSOLUTION TO DOM 0.0 'ALPHA_ZPDOM' (NNM,NNP,NNZ) dimensionless FEEDING LOSS FROM PHYTO TO DOM 0.0 'ALPHA_ZDDOM' (NNM,NND,NNZ) dimensionless FEEDING LOSS FROM DETRITUS TO DOM 0.0 'ALPHA_ZZDOM' (NNM,NNZ,NNZ) dimensionless FEEDING LOSS FROM ZOO TO DOM 0.0 'ALPHA_ZBDOM' (NNM,NNB,NNZ) dimensionless FEEDING LOSS FROM BACTERIA TO DOM 0.0 'DOM_0' (NNM) mmol C m-3 DOM THRESHOLLD 0.01 !******************************* NUTRIENT PARAMETERS ****************************! 'KSN' (NNN,NNP) mmol N m-3 HALF-SATURATION OF NUTRIENT 1.0 'N2CB' (NNN,NNB) dimensionless ELEMENT RATIO IN BACTERIA 0.25 'N2CD' (NNN,NND) dimensionless ELEMENT RATIO IN DETRITUS 1.0 !0.15 'N2CP' (NNN,NNP) dimensionless ELEMENT RATIO IN PHYTO 1.0 !0.15 'N2CZ' (NNN,NNZ) dimensionless ELEMENT RATIO IN ZOOPLANKTON 1.0 !0.2 'N2CDOM' (NNN,NNM) dimensionless ELEMENT RATIO IN DOM 0.15 'N_0' (NNN) mmol N m-3 NUTRIENT THRESHOLD 0.1 'R_AN' SCALAR s-1 NITRIFICATION COEFFICIENT 4.63e-7 'END' OF BIOLOGICAL PARAMETERS