!==============================================================================! ! (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 ! ! 'N2P2Z2D2B' Chen et al., 2002 ! ! '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' ! ! ! ! NUTRIENT options: PO4 SiO3 NO3 NH4 ! ! PHYTOPLANKTON options: Phytoplankton Small_phyto Large_phyto ! ! ZOOPLANKTON options: Zooplankton Microzooplankton Mesozooplankton ! ! DETRITUS options: Detritus Detritus_N Detritus_Si ! ! DOM options: DOM ! ! BACTERIA options: Bacteria ! ! ! ! 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) ! ! 'SH92_LIGHT' EXPONEJTIAL (STEEL & Henderson, 1992) ! ! ! ! (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 = NPZD NUTRIENT_NUM = 3 NUTRIENT_NAME = NH4 NO3 SiO3 NUTRIENT_UNIT = 'mmol N m-3' 'mmol N m-3' 'mmol Si m-3' PHYTOPLANKTON_NUM = 2 PHYTOPLANKTON_NAME = Small_P Large_P PHYTOPLANKTON_UNIT = 'mmol C m-3' 'mmol C m-3' ZOOPLANKTON_NUM = 2 ZOOPLANKTON_NAME = Microzooplankton Mesozooplankton ZOOPLANKTON_UNIT = 'mmol C m-3' 'mmol C m-3' DOM_NUM = 1 DOM_NAME = DOM DOM_UNIT = 'mmol C m-3' BACTERIA_NUM = 1 BACTERIA_NAME = Bac BACTERIA_UNIT = 'mmol C m-3' DETRITUS_NUM = 2 DETRITUS_NAME = Detritus_N Detritus_Si DETRITUS_UNIT = 'mmol C m-3' 'mmol Si m-1' AUXILIARY_NUM = 0 AUXILIARY_NAME = '' AUXILIARY_UNIT = '' L_FUNCTION = PGH80_LIGHT G_FUNCTION = GSMM_G !**********************************************************************************! !*****SIMBOL DIMENSION UNIT MODEL DEFINITION *******************! ! ! !******************************* NUTRIENT PARAMETERS ***********************************! ! 'KSN' (NNN,NNP) mmol N m-3 ALL HALF-SATURATION OF NUTRIENT ! 'N2CB' (NNN,NNB) dimensionless N2P2Z2D2SB ELEMENT RATIO IN BACTERIA ! 'N2CD' (NNN,NND) dimensionless ALL-NPZ ELEMENT RATIO IN DETRITUS ! 'N2CP' (NNN,NNP) dimensionless ALL ELEMENT RATIO IN PHYTO ! 'N2CZ' (NNN,NNZ) dimensionless ALL ELEMENT RATIO IN ZOOPLANKTON ! 'N2CDOM' (NNN,NNM) dimensionless N2P2Z2D2SB ELEMENT RATIO IN DOM ! 'N_0' (NNN) mmol N m-3 OPTIONAL NUTRIENT THRESHOLD ! 'R_AN' SCALAR s-1 N2P2Z2D2SB NITRIFICATION COEFFICIENT !********************************************************************************************! KSN = 0.5 0.0001 0.8 2.0 2.0 !P & Si Half_saturation for Ps & Pl N2CB = 1.0 0.0 0.0 N2CD = 1.0 0.151 0.0 0.0 0.0 0.0 1.0 !P:C & Si:C in SP and LP N2CP = 1.0 0.151 0.0 0.0 0.151 0.0 0.26 !P:C & Si:C in Ps and Pl N2CZ = 1.0 0.151 0.0 0.0 0.151 0.0 0.0 !P:C & Si:C in MesoZ and MicroZ N2CDOM = 1.0 0.151 0.0 0.0 N_0 = 0.00 0.01 0.01 R_AN = 0.0 !******************************** PHYTOPLANKTON PARAMETERS ****************************! ! 'ALPHAP' (NNP) mgC/mgCHl/s/W L-OPTION LIGHT FUNCTION COEFFICIENT ! 'ALPHA_U' (NNP) dimensionless L-OPTION !COEFF BETWEEN MULTIPLICATION & MINIMUM ! 'A_TP' (NNP) (C)-1 OPTIONAL EXPONENTIAL FOR T FORCING ! 'ATANU_C' SCALAR (mg Chl)-1 m2 ALL ATTENUATION COEFFICIENT OF CHLOROPHYLL ! 'ATANU_D' SCALAR (mmole C)-1 m2 ALL-NPZ ATTENUATION COEFFICIENT OF DETRITUS ! 'ATANU_W' SCALAR m-1 ALL ATTENUATION COEFFICIENT OF WATER ! 'BETAP' (NNP) mgC (mgCHl s W)-1 L-OPTION PHOTOINHIBITION COEFFICIENT ! 'CHL2C' (NNP) mg CHL/mmol C ALL CHLOROPHYLL TO CARBON RATIO IN PHYTO ! 'D_DOM' (NNP) dimensionless N2P2Z2D2SB ACTIVE EXUDATION COEFFICIENT ! 'DPDOM' (NNP) s-1 N2P2Z2D2SB PASSIVE PHYTO EXUDATION COEFFICIENT ! 'I_OPT' (NNP) W L-OPTION OPTIMAL LIGHT FOR PHYTO ! 'K_LIGHT' (NNP) W L-OPTION HALF_SATURATION OF LIGHT FUNCTIONS ! 'MPD' (NNP) s-1 ALL-NPZ PHYTO MORTALITY EOFFICIENT ! 'M_P' (NNP) dimensionless ALL-NPZ PHYTO MORTALITY ORDER ! 'N_P' (NNP) dimensionless L-OPTION POWER OF LIGHT FUNCTIONS ! 'PARFRAC' SCALLAR dimensionless ALL PAR FRACTION OF TOTAL SHORT WAVE RADIATION ! 'P_0' (NNP) mmol c m-3 OPTIONAL PHYTOPANKTON THRESHOLDS ! 'RP_T' SCALAR dimensionless OPTIONAL EXPONENTIAL FOR T FORCING ON RESPIRATION ! 'R_P' (NNP) s-1 ALL PHYTO RESPIRATION COEFFICIENT ! 'T_OPTP' (NNP) C OPTIONAL OPTIMAL TEMPERATURE FOR PHYTO ! 'UMAX' (NNP) mmol C (mgCHL s)-1 ALL PHYTO MAXIMUM GROWTH RATE ! 'W_P' (NNP) m s-1 ALL SINKING VELOCITY OF PHYTO !********************************************************************************************! ALPHAP = 1.62e-6 ALPHA_U = 1.0 !MULTIPLICATION EFFECTOD A_TP = 0.07 2.0 0.0 ATANU_C = 0.06 ATANU_D = 0.01 ATANU_W = 0.08 BETAP = 3.24e-8 !Ji's value 0.001*umax CHL2C = 1.0 ! Here not used to confirm Ji's `!equivalent 50:1 and 60:1 in C:Chl D_DOM = 0.0 DPDOM = 0.0 I_OPT = 10.0 10.0 !NOT USED K_LIGHT = 5.0 5.0 !NOT USED MPD = 1.047e-6 !2.31e-6 ! doubled Ji's !1.74e-6 !1.157e-6 M_P = 2.0 N_P = 1.0 PARFRAC = 0.45 P_0 = 0.0 RP_T = 0.07 2.0 R_P = 0.0 0.0 T_OPTP = 20. 10. UMAX = 3.24E-5 !With T function, this is the same to Ji. at 5degree. Max double W_P = 1.157e-5 !******************************** ZOOPLANKTON PARAMETERS **************************! ! 'ACTIVE_R' (NNZ) dimensionless ALL ACTIVE RESPIRATION COEFFICIENT ! 'A_TZ' (NNZ) (C)-1 OPTIONAL EXPONENTIAL FOR T FORCING ! 'EFFIB' (NNB,NNZ) dimensionless N2P2Z2D2SB GROWTH EFFICIENCY ON BACTERIA ! 'EFFID' (NND,NNZ) dimensionless ALL-NPZ GROWTH EFFICIENCY ON DETRITUS ! 'EFFIP' (NNP,NNZ) dimensionless ALL GROWTH EFFICIENCY ON PHYTO ! 'EFFIZ' (NNZ,NNZ) dimensionless 2-ZOO GROWTH EFFICIENCY ON ZOOPLANKTON ! 'G_MAX' (NNZ) s-1 ALL MAXIMUM GRAZING RATE ! 'K_ZG' (NNZ) mmol C m-3 G-OPTION HALF-SATURATION FOR ZOO GRAZING ! 'M_G' (NNZ) dimensionless G-OPTION ZOOPLANKTON GRAZING POWER ! 'MZD' (NNZ) s-1 ALL ZOOPLANKTON MORTALITY COEFFICIENT ! 'M_Z' (NNZ) dimensionless OPTIONAL ZOOPLANKTON MORTALITY POWER ! 'P_C' (NNZ) mmol C m-3 G-OPTION GRAZING THRESHOLD ! 'R_RECRUIT' (NNZ) dimensionless 2-ZOO RECRUIT COEFFICIENT ! 'R_Z' (NNZ) s-1 ALL ZOO PASSIVE RESPIRATION COEFFICIENT ! 'SIGMA_B' (NNB,NNZ) (mmol C m-3)-1 N2P2Z2D2SB PREFERENCE ON BACTERIA ! 'SIGMA_D' (NND,NNZ) (mmol C m-3)-1 G-OPTION PREFERENCE ON DETRITUS ! 'SIGMA_P' (NNP,NNZ) (mmol C m-3)-1 G-OPTION PREFERENCE ON PHYTO ! 'SIGMA_Z' (NNZ,NNZ) (mmol C m-3)-1 2-ZOO PREFERENCE ON ZOOPLANKTON ! 'T_OPTZ' (NNZ) C OPTIONAL OPTIMAL TEMPERATURE FOR ZOOPLANKTON ! 'Z_0' (NNZ) mmol C m-3 OPTIONAL ZOOPLANKTON THRESHOLLD !******************************************************************************************! ACTIVE_R = 0.3 A_TZ = 0.09 !2.5 EFFIB = 0.3 EFFID = 0.3 0.3 0.3 0.3 EFFIP = 0.3 0.3 0.3 0.3 EFFIZ = 0.3 0.3 0.3 0.3 G_MAX = 0.694e-5 6.68e-6 ! 3.472e-6 K_ZG = 0.5 M_G = 2.0 MZD = 1.157e-6 !2.315e-6 M_Z = 2.0 P_C = 0.00 R_RECRUIT = 0.0 0.0 R_Z = 0.0 SIGMA_B = 0.0 SIGMA_D = 0.0 SIGMA_P = 4.0 0.0 0.0 0.3 SIGMA_Z = 0.0 0.0 0.2 0.0 T_OPTZ = 20.0 !10 Z_0 = 0.0 !******************************** DETRITUS PARAMETERS ***************************! ! 'ALPHA_BD' (NND,NNB,NNZ) dimensionless N2P2Z2D2SB FEEDING LOSS FROM BACTERIA TO DETRITUS ! 'ALPHA_DAG' (NND) s-1 OPTIONAL AGGREGATION COEFFICIENT ! 'ALPHA_DD' (NND,NND,NNZ) dimensionless ALL-NPZ FEEDING LOSS FROM DETRITUS TO DETRITUS ! 'ALPHA_DDG' (NND) s-1 OPTIONAL DISAGGREGATION ! 'ALPHA_PD' (NND,NNP,NNZ) dimensionless ALL-NPZ FEEDING LOSS FROM PHYTO TO DETRITUS ! 'ALPHA_ZD' (NND,NNZ,NNZ) dimensionless ALL-NPZ FEEDING LOSS FROM ZOO TO DETRITUS ! 'D_D' (NND) s-1 ALL-NPZ DISSOLUTION COEFFICIENT ! 'D_0' (NND) mmol C m-3 OPTIONAL DETRITUS THRESHOLD ! 'D_RN' (NND) s-1 ALL-NPZ REMINERALIZATION COEFFICIENT ! 'EPSILON_PD' (NND,NNP) dimensionless ALL-NPZ PHYTO MORTALITY TO DETRITUS ! 'EPSILON_ZD' (NND,NNZ) dimensionless ALL-NPZ ZOO MORTALTIY TO DETRITUS ! 'W_D' (NND) m s-1 ALL-NPZ DETRITUS SINKING VELOCITY !******************************************************************************************! ALPHA_BD = 0.0 ALPHA_DAG = 0.0 0.0 ALPHA_DD = 0.2 0.0 0.2 0.2 0.2 0.0 0.2 0.2 !NO FEEDING ALPHA_DDG = 0.0 0.0 ALPHA_PD = 0.4 !Pl HAS Si ALPHA_ZD = 0.2 !NO Si D_D = 0.0 0.0 D_0 = 0.00 0.01 D_RN = 2.31e-7 !6.94e-7 EPSILON_PD = 1.0 0.0 1.0 0.26 ! Pl HAS Si EPSILON_ZD = 0.7 ! 30% goes to high trophic level NO Si in ZOO W_D = 0.578e-5 !1.157e-4 !2.315e-5 !1.157e-4 !******************************** BACTERIA PARAMETERS ***************************! ! 'A_TB' (NNB) (C)-1 N2P2Z2D2SB EXPONENTAIL FOR T FORCING ! 'B_0' (NNB) mmol C m-3 OPTIONAL BACTERIA THRESHOLLD ! 'DELTA_B' (NNB) dimensionless N2P2Z2D2SB RATIO BETWEEN NH4 AND DON UPTAKE ! 'EFFIBD' (NND,NNB) dimensionless N2P2Z2D2SB GROWTH EFFICIENCY ON DETRITUS ! 'EFFIDOM' (NNM,NNB) dimensionless N2P2Z2D2SB GROWTH EFFICIENCY ON DOM ! 'EFFIN' (NNN,NNB) dimensionless N2P2Z2D2SB GROWTH EFFICIENCY ON NH4 ! 'R_B' (NNB) s-1 N2P2Z2D2SB BACTERIA RESPIRATION COEFFICIENT ! 'SIGMA_BD' (NND,NNB) (mmol C m-3)-1 N2P2Z2D2SB PREFERENCE ON DETRITUS ! 'SIGMA_DOM' (NNM,NNB) (mmol C m-3)-1 N2P2Z2D2SB PREFERENCE ON DOM ! 'SIGMA_N' (NNN,NNB) (mmol n m-3)-1 N2P2Z2D2SB PREFERENCE ON NUTRIENT ! 'T_OPTB' (NNB) C N2P2Z2D2SB OPTIMAL T FOR BACTERIA ! 'UBMAX' (NNB) s-1 N2P2Z2D2SB MAXIMUM GROWTH RATE OF BACTERIA !*******************************************************************************************! A_TB = 0.18 B_0 = 0.1 DELTA_B = 0.0 !NOT USED EFFIBD = 1.0 1.0 EFFIDOM = 0.3 EFFIN = 1.0 1.0 1.0 R_B = 0.174e-6 SIGMA_BD = 0.0 0.0 ! 1/0.1*0.02 SIGMA_DOM = 0.2 SIGMA_N = 0.1 0.0 0.0 ! B preference on P & Si 0.01*1/0.2 T_OPTB = 10.0 UBMAX = 0.0 !******************************** DOM PARAMETERS ****************************! ! 'ALPHA_DOM' (NNM) s-1 N2P2Z2D2SB DOM AGEING COEFFICIENT ! 'ALPHA_PDOM' (NNM,NNP) dimensionless N2P2Z2D2SB PHYTO EXUDATION TO DOM ! 'ALPHA_DDOM' (NNM,NND) dimensionless N2P2Z2D2SB DETRITUS DISSOLUTION TO DOM ! 'ALPHA_ZPDOM' (NNM,NNP,NNZ) dimensionless N2P2Z2D2SB FEEDING LOSS FROM PHYTO TO DOM ! 'ALPHA_ZDDOM' (NNM,NND,NNZ) dimensionless N2P2Z2D2SB FEEDING LOSS FROM DETRITUS TO DOM ! 'ALPHA_ZZDOM' (NNM,NNZ,NNZ) dimensionless N2P2Z2D2SB FEEDING LOSS FROM ZOO TO DOM ! 'ALPHA_ZBDOM' (NNM,NNB,NNZ) dimensionless N2P2Z2D2SB FEEDING LOSS FROM BACTERIA TO DOM ! 'DOM_0' (NNM) mmol C m-3 OPTIONAL DOM THRESHOLLD !*******************************************************************************************! ALPHA_DOM = 0.0 ALPHA_PDOM = 0.0 ALPHA_DDOM = 0.0 0.0 ALPHA_ZPDOM = 0.0 0.2 0.2 0.2 ALPHA_ZDDOM = 0.0 0.2 0.2 0.2 ALPHA_ZZDOM = 0.0 0.2 0.2 0.2 ALPHA_ZBDOM = 0.0 0.2 DOM_0 = 40.0