!==============================================================================! ! (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' DESINGATES MODEL STRUCTURE FOR WHICH THE FOLLOWING ! ! OPTIONS CAN BE SELCTED: ! ! 'NPZ', Frank et al, 1986; Frank & Chen 1996 ! ! 'NPZD', Anderson et al., 2000 ! ! 'FASHAM', Fasham et al., 1990) ! ! 'N2P2Z2D2', Chen et al., 2003 ! ! 'N2P2Z2D2SB' Tian et al., 2000 ! ! 'NEW" New model built by users ! ! ! ! (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) 'PROFILE':WITH AT LEAST TWO PAIRS OF VALUES WITH DEPTH.! ! VARIABLE VALUES WILL BE LINEARLY INTERPOLATED BETWEEN THE VALUES GIVEN), ! ! (3) "3D FIELD": 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' 'NEW' 'NUTRIENT' 3 'NH4' 'mmol N m-3' 'NO3' 'mmol N m-3' 'SiO3' 'mmol Si m-3' 'PHYTOPLANKTON' 2 'Small_P' 'mmol C m-3' 'Large_P' 'mmol C m-3' 'ZOOPLANKTON' 2 'Microzooplankton' 'mmol C m-3' 'Mesozooplankton' 'mmol C m-3' 'DOM' 1 'DOM' 'mmol C m-3' 'BACTERIA' 1 'Bac' 'mmol C m-3' 'DETRITUS' 2 'Detritus_N' 'mmol C m-3' 'Detritus_Si' 'mmol Si m-1' 'L_FUNCTION' 'PGH80_LIGHT' 'EXP_LIGHT' 'G_FUNCTION' 'GSMM_G' 'IVLE1_G' 'GSMM_G' !*****SIMBOL DIMENSION UNIT MODEL DEFINITION *************************! !******************************* NUTRIENT *******************************************! 'KSN' (NNN,NNP) mmol N m-3 ALL HALF-SATURATION OF NUTRIENT 0.1 0.5 0.0001 0.8 2.0 2.0 !P & Si Half_saturation for Ps & Pl 'N2CB' (NNN,NNB) dimensionless N2P2Z2D2SB ELEMENT RATIO IN BACTERIA 0.151 0.0 0.0 'N2CD' (NNN,NND) dimensionless ALL-NPZ ELEMENT RATIO IN DETRITUS 0.151 0.0 0.0 0.0 0.0 1.0 !P:C & Si:C in SP and LP 'N2CP' (NNN,NNP) dimensionless ALL ELEMENT RATIO IN PHYTO 0.151 0.0 0.0 0.151 0.0 0.26 !P:C & Si:C in Ps and Pl 'N2CZ' (NNN,NNZ) dimensionless ALL ELEMENT RATIO IN ZOOPLANKTON 0.151 0.0 0.0 0.151 0.0 0.0 !P:C & Si:C in MesoZ and MicroZ 'N2CDOM' (NNN,NNM) dimensionless N2P2Z2D2SB ELEMENT RATIO IN DOM 0.151 0.0 0.0 'N_0' (NNN) mmol N m-3 OPTIONAL NUTRIENT THRESHOLD 0.01 0.01 0.01 'R_AN' SCALAR s-1 N2P2Z2D2SB NITRIFICATION COEFFICIENT 3.47e-7 !******************************** PHYTOPLANKTON PARAMETERS ****************************! 'ALPHAP' (NNP) mgC/mgCHl/s/W L-OPTION LIGHT FUNCTION COEFFICIENT 14.88e-7 10.85e-7 'ALPHA_U' (NNP) dimensionless L-OPTION !COEFF BETWEEN MULTIPLICATION & MINIMUM 0.5 0.5 'A_TP' (NNP) (C)-1 OPTIONAL EXPONENTIAL FOR T FORCING 0.0 0.0 'ATANU_C' SCALAR (mg Chl)-1 m2 ALL ATTENUATION COEFFICIENT OF CHLOROPHYLL 0.04 0.04 'ATANU_D' SCALAR (mmole C)-1 m2 ALL-NPZ ATTENUATION COEFFICIENT OF DETRITUS 0.02 0.02 'ATANU_W' SCALAR m-1 ALL ATTENUATION COEFFICIENT OF WATER 0.08 'BETAP' (NNP) mgC (mgCHl s W)-1 L-OPTION PHOTOINHIBITION COEFFICIENT 4.25e-8 3.1e-8 'CHL2C' (NNP) mg CHL/mmol C ALL CHLOROPHYLL TO CARBON RATIO IN PHYTO 0.2 0.48 !equivalent 25:1 and 60:1 in C:Chl 'D_DOM' (NNP) dimensionless N2P2Z2D2SB ACTIVE EXUDATION COEFFICIENT 0.1 0.1 'DPDOM' (NNP) s-1 N2P2Z2D2SB PASSIVE PHYTO EXUDATION COEFFICIENT 0.0 1.74e-7 1.16e-7 'I_OPT' (NNP) W L-OPTION OPTIMAL LIGHT FOR PHYTO 100.0 100.0 !NOT USED 'K_LIGHT' (NNP) W L-OPTION HALF_SATURATION OF LIGHT FUNCTIONS 50.0 50.0 !NOT USED 'MPD' (NNP) s-1 ALL-NPZ PHYTO MORTALITY EOFFICIENT 0.58e-7 0.58e-7 'M_P' (NNP) dimensionless ALL-NPZ PHYTO MORTALITY ORDER 2.0 2.0 'N_P' (NNP) dimensionless L-OPTION POWER OF LIGHT FUNCTIONS 1.0 1.0 'PARFRAC' SCALLAR dimensionless ALL PAR FRACTION OF TOTAL SHORT WAVE RADIATION 0.43 'P_0' (NNP) mmol c m-3 OPTIONAL PHYTOPANKTON THRESHOLDS 0.1 0.1 'RP_T' SCALAR dimensionless OPTIONAL EXPONENTIAL FOR T FORCING ON RESPIRATION 0.0 'R_P' (NNP) s-1 ALL PHYTO RESPIRATION COEFFICIENT 0.0 0.0 'T_OPTP' (NNP) C OPTIONAL OPTIMAL TEMPERATURE FOR PHYTO 20. 20. 'UMAX' (NNP) mmol C (mgCHL s)-1 ALL PHYTO MAXIMUM GROWTH RATE 4.25e-5 3.1e-5 'W_P' (NNP) m s-1 ALL SINKING VELOCITY OF PHYTO 0.0 1.16e-5 !******************************** ZOOPLANKTON PARAMETERS **************************! 'ACTIVE_R' (NNZ) dimensionless ALL ACTIVE RESPIRATION COEFFICIENT 0.3 0.3 'A_TZ' (NNZ) (C)-1 OPTIONAL EXPONENTIAL FOR T FORCING 0.069 0.069 'EFFIB' (NNB,NNZ) dimensionless N2P2Z2D2SB GROWTH EFFICIENCY ON BACTERIA 0.3 0.3 'EFFID' (NND,NNZ) dimensionless ALL-NPZ GROWTH EFFICIENCY ON DETRITUS 0.3 0.3 0.3 0.3 'EFFIP' (NNP,NNZ) dimensionless ALL GROWTH EFFICIENCY ON PHYTO 0.3 0.3 0.3 0.3 'EFFIZ' (NNZ,NNZ) dimensionless 2-ZOO GROWTH EFFICIENCY ON ZOOPLANKTON 0.3 0.3 0.3 0.3 'G_MAX' (NNZ) s-1 ALL MAXIMUM GRAZING RATE 1.16e-5 0.58e-5 'K_ZG' (NNZ) mmol C m-3 G-OPTION HALF-SATURATION FOR ZOO GRAZING 1.0 1.0 !NOT USED 'M_G' (NNZ) dimensionless G-OPTION ZOOPLANKTON GRAZING POWER 1.0 1.0 'MZD' (NNZ) s-1 ALL ZOOPLANKTON MORTALITY COEFFICIENT 1.16e-7 1.16e-7 'M_Z' (NNZ) dimensionless OPTIONAL ZOOPLANKTON MORTALITY POWER 2.0 2.0 'P_C' (NNZ) mmol C m-3 G-OPTION GRAZING THRESHOLD 0.01 0.01 'R_RECRUIT' (NNZ) dimensionless 2-ZOO RECRUIT COEFFICIENT 0.0 0.0 'R_Z' (NNZ) s-1 ALL ZOO PASSIVE RESPIRATION COEFFICIENT 2.31e-7 1.74e-7 'SIGMA_B' (NNB,NNZ) (mmol C m-3)-1 N2P2Z2D2SB PREFERENCE ON BACTERIA 0.1 0.0 'SIGMA_D' (NND,NNZ) (mmol C m-3)-1 G-OPTION PREFERENCE ON DETRITUS 0.0 0.0 0.1 0.0 'SIGMA_P' (NNP,NNZ) (mmol C m-3)-1 G-OPTION PREFERENCE ON PHYTO 0.2 0.0 0.0 0.3 'SIGMA_Z' (NNZ,NNZ) (mmol C m-3)-1 2-ZOO PREFERENCE ON ZOOPLANKTON 0.0 0.0 0.2 0.0 'T_OPTZ' (NNZ) C OPTIONAL OPTIMAL TEMPERATURE FOR ZOOPLANKTON 20.0 20.0 'Z_0' (NNZ) mmol C m-3 OPTIONAL ZOOPLANKTON THRESHOLLD 0.1 0.1 !******************************** DETRITUS PARAMETERS ***************************! 'ALPHA_BD' (NND,NNB,NNZ) dimensionless N2P2Z2D2SB FEEDING LOSS FROM BACTERIA TO DETRITUS 0.2 0.0 0.2 0.0 'ALPHA_DAG' (NND) s-1 OPTIONAL AGGREGATION COEFFICIENT 0.0 0.0 'ALPHA_DD' (NND,NND,NNZ) dimensionless ALL-NPZ FEEDING LOSS FROM DETRITUS TO DETRITUS 0.2 0.0 0.2 0.2 0.2 0.0 0.2 0.2 !NO FEEDING 'ALPHA_DDG' (NND) s-1 OPTIONAL DISAGGREGATION 0.0 0.0 'ALPHA_PD' (NND,NNP,NNZ) dimensionless ALL-NPZ FEEDING LOSS FROM PHYTO TO DETRITUS 0.2 0.0 0.2 0.26 0.2 0.0 0.2 0.26 !Pl HAS Si 'ALPHA_ZD' (NND,NNZ,NNZ) dimensionless ALL-NPZ FEEDING LOSS FROM ZOO TO DETRITUS 0.2 0.0 0.2 0.0 0.2 0.0 0.2 0.0 NO Si 'D_D' (NND) s-1 ALL-NPZ DISSOLUTION COEFFICIENT 0.0 0.0 'D_0' (NND) mmol C m-3 OPTIONAL DETRITUS THRESHOLD 0.01 0.01 'D_RN' (NND) s-1 ALL-NPZ REMINERALIZATION COEFFICIENT 6.93e-7 3.47e-7 'EPSILON_PD' (NND,NNP) dimensionless ALL-NPZ PHYTO MORTALITY TO DETRITUS 1.0 0.0 1.0 0.26 Pl HAS Si 'EPSILON_ZD' (NND,NNZ) dimensionless ALL-NPZ ZOO MORTALTIY TO DETRITUS 1.0 0.0 1.0 0.0 NO Si in ZOO 'W_D' (NND) m s-1 ALL-NPZ DETRITUS SINKING VELOCITY 5.76e-5 5.76e-5 !******************************** BACTERIA PARAMETERS ***************************! 'A_TB' (NNB) (C)-1 N2P2Z2D2SB EXPONENTAIL FOR T FORCING 0.18 'B_0' (NNB) mmol C m-3 OPTIONAL BACTERIA THRESHOLLD 0.1 'DELTA_B' (NNB) dimensionless N2P2Z2D2SB RATIO BETWEEN NH4 AND DON UPTAKE 0.0 !NOT USED 'EFFIBD' (NND,NNB) dimensionless N2P2Z2D2SB GROWTH EFFICIENCY ON DETRITUS 1.0 1.0 'EFFIDOM' (NNM,NNB) dimensionless N2P2Z2D2SB GROWTH EFFICIENCY ON DOM 0.3 'EFFIN' (NNN,NNB) dimensionless N2P2Z2D2SB GROWTH EFFICIENCY ON NH4 1.0 1.0 1.0 'R_B' (NNB) s-1 N2P2Z2D2SB BACTERIA RESPIRATION COEFFICIENT 0.174e-6 'SIGMA_BD' (NND,NNB) (mmol C m-3)-1 N2P2Z2D2SB PREFERENCE ON DETRITUS 0.0 0.0 1/0.1*0.02 'SIGMA_DOM' (NNM,NNB) (mmol C m-3)-1 N2P2Z2D2SB PREFERENCE ON DOM 0.2 'SIGMA_N' (NNN,NNB) (mmol n m-3)-1 N2P2Z2D2SB PREFERENCE ON NUTRIENT 0.1 0.0 0.0 !B preference on P & Si 0.01*1/0.2 'T_OPTB' (NNB) C N2P2Z2D2SB OPTIMAL T FOR BACTERIA 20.0 'UBMAX' (NNB) s-1 N2P2Z2D2SB MAXIMUM GROWTH RATE OF BACTERIA 4.5e-5 !******************************** DOM PARAMETERS ****************************! 'ALPHA_DOM' (NNM) s-1 N2P2Z2D2SB DOM AGEING COEFFICIENT 0.0 'ALPHA_PDOM' (NNM,NNP) dimensionless N2P2Z2D2SB PHYTO EXUDATION TO DOM 1.0 1.0 'ALPHA_DDOM' (NNM,NND) dimensionless N2P2Z2D2SB DETRITUS DISSOLUTION TO DOM 0.0 0.0 'ALPHA_ZPDOM' (NNM,NNP,NNZ) dimensionless N2P2Z2D2SB FEEDING LOSS FROM PHYTO TO DOM 0.2 0.2 0.2 0.2 'ALPHA_ZDDOM' (NNM,NND,NNZ) dimensionless N2P2Z2D2SB FEEDING LOSS FROM DETRITUS TO DOM 0.2 0.2 0.2 0.2 'ALPHA_ZZDOM' (NNM,NNZ,NNZ) dimensionless N2P2Z2D2SB FEEDING LOSS FROM ZOO TO DOM 0.2 0.2 0.2 0.2 'ALPHA_ZBDOM' (NNM,NNB,NNZ) dimensionless N2P2Z2D2SB FEEDING LOSS FROM BACTERIA TO DOM 0.2 0.2 'DOM_0' (NNM) mmol C m-3 OPTIONAL DOM THRESHOLLD 40.0 'END' OF BIOLOGICAL PARAMETERS