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Merge pull request #1 from AquaticEcoDynamics/master
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rqthomas committed Apr 11, 2022
2 parents 7748cea + f24fa6a commit bdcd3ca
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6 changes: 3 additions & 3 deletions Makefile
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# #
# http:https://aquatic.science.uwa.edu.au/ #
# #
# Copyright 2013 - 2021 - The University of Western Australia #
# Copyright 2013 - 2022 - The University of Western Australia #
# #
# GLM is free software: you can redistribute it and/or modify #
# AED is free software: you can redistribute it and/or modify #
# it under the terms of the GNU General Public License as published by #
# the Free Software Foundation, either version 3 of the License, or #
# (at your option) any later version. #
# #
# GLM is distributed in the hope that it will be useful, #
# AED is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
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41 changes: 41 additions & 0 deletions examples/aed_pathogen_pars.csv
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p_name, 'crypto', 'ecoli', 'totalcoli',[COMMENT],string, pathogen name
coef_grwth_uMAX, 0, 3, 2.4,[COMMENT],real, Max growth rate at 20C
coef_grwth_Tmin, 4, 4, 4,[COMMENT],real, Tmin and Tmax, f(T)
coef_grwth_Tmax, 35, 35, 35,[COMMENT],real, Tmin and Tmax, f(T)
coef_grwth_T1, 0.008, 0.008, 0.008,[COMMENT],real, coef_grwth_T1 and coef_grwth_T2
coef_grwth_T2, 0.1, 0.1, 0.1,[COMMENT],real, coef_grwth_T1 and coef_grwth_T2
coef_grwth_Kdoc, 0, 0.3, 0.3,[COMMENT],real, Half-saturation for growth, coef_grwth_Kdoc
coef_grwth_ic, 1.0E-9, 1.0E-9, 1.0E-9,[COMMENT],real, coef_grwth_ic
coef_mort_kd20, 0.03, 0.48, 0.34,[COMMENT],real, Mortality rate (Dark death rate) @ 20C and 0 psu
coef_mort_theta, 1.08, 1.08, 1.11,[COMMENT],real, Temperature multiplier for mortality: coef_mort_theta
coef_mort_c_SM, 0, 2.0E-10, 2.0E-7,[COMMENT],real, Salinity effect on mortality
coef_mort_alpha, 0, 6.1, 4.2,[COMMENT],real, Salinity effect on mortality
coef_mort_beta, 0, 0.25, 0.25,[COMMENT],real, Salinity effect on mortality
coef_mort_c_PHM, 0, 50, 50,[COMMENT],real, pH effect on mortality
coef_mort_K_PHM, 0, 6, 6,[COMMENT],real, pH effect on mortality
coef_mort_delta_M, 0, 4, 4,[COMMENT],real, pH effect on mortality
coef_mort_fdoc, 0, 0.5, 0.5,[COMMENT],real, Fraction of mortality back to doc
coef_light_kb_vis, 0, 0.097, 0.097,[COMMENT],real, Light inactivation
coef_light_kb_uva, 0, 1.16, 1.16,[COMMENT],real, Light inactivation
coef_light_kb_uvb, 0, 36.4, 36.4,[COMMENT],real, Light inactivation
coef_light_cSb_vis, 0.0067, 0.0067, 0.0067,[COMMENT],real, Salinity effect on light inactivation
coef_light_cSb_uva, 0.0067, 0.0067, 0.0067,[COMMENT],real, Salinity effect on light inactivation
coef_light_cSb_uvb, 0.0067, 0.0067, 0.0067,[COMMENT],real, Salinity effect on light inactivation
coef_light_kDOb_vis, 0.5, 0.5, 0.5,[COMMENT],real, DO effect on light
coef_light_kDOb_uva, 0.5, 0.5, 0.5,[COMMENT],real, DO effect on light
coef_light_kDOb_uvb, 0.5, 0.5, 0.5,[COMMENT],real, DO effect on light
coef_light_cpHb_vis, 10, 10, 10,[COMMENT],real, pH effect on light inactivation
coef_light_cpHb_uva, 10, 10, 10,[COMMENT],real, pH effect on light inactivation
coef_light_cpHb_uvb, 10, 10, 10,[COMMENT],real, pH effect on light inactivation
coef_light_KpHb_vis, 5, 5, 5,[COMMENT],real, pH effect on light inactivation
coef_light_KpHb_uva, 5, 5, 5,[COMMENT],real, pH effect on light inactivation
coef_light_KpHb_uvb, 5, 5, 5,[COMMENT],real, pH effect on light inactivation
coef_light_delb_vis, 3, 3, 3,[COMMENT],real, exponent for pH effect on light inactivation
coef_light_delb_uva, 3, 3, 3,[COMMENT],real, exponent for pH effect on light inactivation
coef_light_delb_uvb, 3, 3, 3,[COMMENT],real, exponent for pH effect on light inactivation
coef_pred_kp20, 0, 0.2, 0.2,[COMMENT],real, Loss rate due to predation and temp multiplier
coef_pred_theta_P, 1, 1.04, 1.04,[COMMENT],real, Loss rate due to predation and temp multiplier
coef_sett_fa, 0, 0.94, 0.81,[COMMENT],real, Attached fraction in water column
coef_sett_w_path, -2.5E-6, -5.0E-7, -5.0E-7,[COMMENT],real, Sedimentation velocity (m/d) at 20C (-ve means down) for NON-ATTACHED orgs
coef_resus_epsilonP, 0.01, 0.01, 0.01,[COMMENT],real, Pathogen resuspension rate
coef_resus_tauP_0, 0.01, 0.01, 0.01,[COMMENT],real, Critical shear stress for organism resuspension
56 changes: 56 additions & 0 deletions examples/aed_phyto_pars-bak.csv
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[COMMENT],!-- GENERAL parameters
p_name, 'Peridinium', 'cyano', 'green', 'karlodinium', 'phy05', 'phy06', 'diatom', 'crypto', 'cryptophyte', 'chlorophyte', 'synechococcus', 'MICROCYSTIS', 'Cyanobacteria', 'Cyanobacteria', 'n_spumigena', 'Peridinium', 'Microcystis', 'Microcystis(1)', 'Aphanizomenon', 'Nanoplankton', 'Cayelan_Test',[COMMENT],string, Name of phytoplankton group
p_initial, 1, 10, 0.04, 10, 10, 10, 10, 8.4, 2.4, 10, 10, 10, 200, 10, 10, 2.81, 102, 2.81, 2.81, 2.81, 2.81,[COMMENT],real, Initial concentration of phytoplankton (mmol C/m3)
p0, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 5, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03,[COMMENT],real, Minimum concentration of phytoplankton (mmol C/m3)
w_p, 0, 0, -0.01, 0, 0, 0, -0.104, -0.104, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,[COMMENT],real, sedimentation rate (m/d)
Xcc, 50, 50, 40, 50, 50, 50, 40, 40, 40, 50, 50, 50, 40, 40, 50, 55, 50, 92, 77, 80, 77,[COMMENT],real, carbon to chlorophyll ratio (mg C/mg chla)
[COMMENT],!-- GROWTH parameters
R_growth, 1.1, 1.1, 0.7, 1.1, 1.1, 1.1, 2.8, 1.1, 0.7, 1.1, 1.1, 1.1, 0.53, 1.1, 1.1, 0.35, 1.1, 0.7, 0.41, 2.7, 0.41,[COMMENT],real, Phyto max growth rate @20C (/day)
fT_Method, 1, 1, 0, 1, 1, 1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1,[COMMENT],integer, Specifies temperature limitation function of growth (-); 0 = no temperature limitation 1= CAEDYM style
theta_growth, 1.06, 1.06, 1.08, 1.06, 1.06, 1.06, 1.06, 1.06, 1.06, 1.06, 1.06, 1.06, 1.08, 1.06, 1.06, 1.07, 1.06, 1.07, 1.1, 1.07, 1.1,[COMMENT],real, Arrenhius temperature scaling for growth function (-)
T_std, 20, 20, 20, 20, 20, 20, 15, 15, 20, 20, 20, 20, 20, 20, 20, 19, 20, 19, 24, 20, 24,[COMMENT],real, Standard temperature (deg C)
T_opt, 28, 28, 27, 28, 28, 28, 20, 20, 28, 28, 28, 28, 28.7, 28, 28, 24, 28, 26, 29, 27, 29,[COMMENT],real, Optimum temperature (deg C)
T_max, 35, 35, 33, 35, 35, 35, 32, 32, 34, 35, 35, 35, 35, 35, 35, 32, 35, 35, 34, 35, 34,[COMMENT],real, Maximum temperature (deg C)
[COMMENT],!-- LIGHT parameters
lightModel, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,[COMMENT],integer, Type of light response function [0 = no photoinhibition; 1 = photoinhibition]
I_K, 25, 25, 25, 25, 25, 25, 10, 10, 25, 25, 25, 25, 228, 25, 25, 17.5, 25, 17.5, 17.5, 17.5, 17.5,[COMMENT],real, Half saturation constant for light limitation of growth (microE/m^2/s) used if lightModel=0
I_S, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 230, 100, 100, 600, 100, 150, 80, 400, 80,[COMMENT],real, saturating light intensity (microE/m^2/s) used if lightModel=1
KePHY, 0.005, 0.005, 0.005, 0.005, 0.005, 0.005, 0.001, 0.001, 0.005, 0.005, 0.005, 0.005, 0, 0.005, 0.005, 0.00012, 0.005, 0.00012, 0.00012, 0.00012, 0.00012,[COMMENT],real, Specific attenuation coefficient ((mmol C m^3^-1)^1 m^-1)
[COMMENT],!-- RESPIRATION parameters
f_pr, 0.005, 0.005, 0.005, 0.005, 0.005, 0.005, 0.002, 0.002, 0.005, 0.005, 0.005, 0.005, 0.005, 0.005, 0.005, 0.004, 0.005, 0.004, 0.004, 0.004, 0.004,[COMMENT],real, Fraction of primary production lost to exudation (-)
R_resp, 0.08, 0.08, 0.012, 0.08, 0.08, 0.08, 0.12, 0.12, 0.012, 0.08, 0.08, 0.08, 0.08, 0.08, 0.08, 0.066, 0.08, 0.066, 0.066, 0.066, 0.066,[COMMENT],real, Phytoplankton respiration/metabolic loss rate @ 20 (degC)
theta_resp, 1.05, 1.05, 1.06, 1.05, 1.05, 1.05, 1.07, 1.07, 1.05, 1.05, 1.05, 1.05, 1.05, 1.05, 1.05, 1.05, 1.05, 1.05, 1.05, 1.05, 1.05,[COMMENT],real, Arrhenius temperature scaling factor for respiration (-)
k_fres, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.6, 0.25, 0.6, 0.25, 0.25, 0.25, 0.25,[COMMENT],real, Fraction of metabolic loss that is true respiration (-)
k_fdom, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.2, 0.05, 0.2, 0.2, 0.2, 0.2,[COMMENT],real, Fraction of metabolic loss that is DOM (-)
[COMMENT],!-- SALINITY parameters
salTol, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,[COMMENT],integer, Type of salinity limitation function (-)
S_bep, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,[COMMENT],real, Salinity limitation value at maximum salinity S_maxsp (-)
S_maxsp, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35,[COMMENT],real, Maximum salinity (g/kg)
S_opt, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,[COMMENT],real, Optimal salinity (g/kg)
[COMMENT],!-- NITROGEN parameters
simDINUptake, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,[COMMENT],integer, Simulate DIN uptake (0 = false, 1 = true)
simDONUptake, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,[COMMENT],integer, Simulate DON uptake (0 = false, 1 = true)
simNFixation, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,[COMMENT],integer, Simulate N fixation (0 = false, 1 = true)
simINDynamics, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,[COMMENT],integer, Simulate internal N (0 = assumed fixed C:N, 2 = dynamic C:N)
N_o, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25, 0.25,[COMMENT],real, Nitrogen concentraion below which uptake is 0 (mmol N/m^3)
K_N, 4, 4, 3.21, 4, 4, 4, 3.57, 3.57, 3.21, 4, 4, 4, 4, 4, 4, 3.39, 4, 3.39, 3.39, 3.39, 3.39,[COMMENT],real, Half-saturation concentration of nitrogen (mmol N/m^3)
X_ncon, 232342, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035,[COMMENT],real, Constant internal nitrogen concentration (mmol N/ mmol C) used if simINDynamics = 0 or 1
X_nmin, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.003, 0.02, 0.002, 0.017, 0.007, 0.017,[COMMENT],real, minimum internal nitrogen concentration (mmol N/ mmol C) used if simINDynamics = 2
X_nmax, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.07, 0.006, 0.07, 0.005, 0.009, 0.028, 0.009,[COMMENT],real, maximum internal nitrogen concentration (mmol N/ mmol C) used if simINDynamics = 2
R_nuptake, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02,[COMMENT],real, maximum nitrogen uptake rate(mmol N/m^3/d) used if simINDynamics = 2
k_nfix, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7,[COMMENT],real, growth rate reduction under maximum nitrogen fixation (/day) used if simNFixation >0
R_nfix, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0.035, 0, 0.035, 0, 0.012, 0, 0.012,[COMMENT],real, nitrogen fixation rate (mmol N/mmol C/day)
[COMMENT],!-- PHOSPHORUS parameters
simDIPUptake, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,[COMMENT],integer, Simulate DIP uptake (0 = false, 1 = true)
simIPDynamics, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,[COMMENT],integer, Simulate internal phosphorus dynamics (0 = assumed fixed C:P, 2 = dynamic C:P)
P_0, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03,[COMMENT],real, Phosphorus concentraion below which uptake is 0 (mmol P/m^3)
K_P, 0.15, 0.15, 0.16, 0.15, 0.15, 0.15, 0.16, 0.16, 0.16, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15, 7.74E-5, 0.15, 5.8E-5, 3.87E-5, 4.51E-5, 3.87E-5,[COMMENT],real, Half-saturation concentration of phosphorus (mmol P/m^3)
X_pcon, 0.0015, 0.0015, 0.0015, 0.0015, 0.0015, 0.0015, 0.0015, 0.0015, 0.0015, 0.0015, 0.0015, 0.0015, 0.0015, 0.0015, 0.0015, 0.0015, 0.0015, 0.0015, 0.0015, 0.0015, 0.0015,[COMMENT],real, Constant internal phosphorus concentration (mmol P/ mmol C) used if simIPDynamics = 0 or 1
X_pmin, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0.0005, 0, 0.0005, 0.003, 0.006, 0.003, 0.006,[COMMENT],real, Minimum internal phosphorus concentration (mmol P/mmol C) used if simIPDynamics = 2
X_pmax, 0.005, 0.005, 0.005, 0.005, 0.005, 0.005, 0.005, 0.005, 0.005, 0.005, 0.005, 0.005, 0.005, 0.005, 0.005, 0.001, 0.005, 0.019, 0.502, 0.012, 0.502,[COMMENT],real, Maximum internal phosphorus concentration (mmol P/mmol C) used if simIPDynamics = 2
R_puptake, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001,[COMMENT],real, Maximum phosphorus uptake rate(mmol P/m^3/d) used if simIPDynamics = 2
[COMMENT],!-- SILICA parameter
simSiUptake, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,[COMMENT],integer, Simulate Si uptake (0 = false, 1 = true)
Si_0, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3,[COMMENT],real, Silica concentraion below which uptake is 0 (mmol Si/m^3)
K_Si, 2.5, 2.5, 2.5, 2.5, 2.5, 2.5, 2.5, 2.5, 2.5, 2.5, 2.5, 2.5, 2.5, 2.5, 2.5, 2.5, 2.5, 2.5, 2.5, 2.5, 2.5,[COMMENT],real, Half-saturation concentration of silica (mmol Si /m3)
X_sicon, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4,[COMMENT],real, Constant interal silica concentration (mmol Si/mmol C)
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