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ParamDescription.txt
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ParamDescription.txt
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Parameter Descriptionend_time Number of iterations through the gridpulses Number of pulses of litter to simulaten_enzymes Number of enzyme genes in communityn_substrates Number of chemical polymersn_uptake Number of uptake genes in community (do not change)n_taxa Number of taxa in communityEnzyme_Loss_Rate Rate constant for enzyme loss per iterationDeath_Rate Rate constant for microbial death per iterationDeath_Ratio Fraction of death rate that applies to fungiset.seed whether seed should be fixed (1) or not (0)seed Seed value for random number generationTol_CUE Coefficient for effect of stress tolerance investment on CUETol_min Minimum stress tolerance investmentTol_max Maximium stress tolerance investmentVmax_Km slope relating Km to Vmax0 in the Vmax-Km tradeoff (set to zero for no tradeoff)Vmax_Km_int Km-intercept for Vmax-Km tradeoffUptake_Vmax_Km slope relating uptake Km to Uptake_Vmax0 in the Vmax-Km tradeoff (set to zero for no tradeoff)Uptake_Vmax_Km_int Km-intercept for uptake Vmax-Km tradeoffKm_error factor to multiply by SD to calculate error term in Vmax-Km tradeoff (also used for uptake)Specif_factor "factor by which enzyme efficiency declines with increasing number of substrates targeted (0 for no decline, 1 to divide by total substrates targeted)"uptake_prob Probability that a taxon possesses the uptake gene for a monomer targeted by an enzyme it has (1-uptake_prob is the probability of having an uptake gene for a monomer it does not produce)CUE_ref Carbon use efficiency at the reference temperatureCUE_temp CUE change per degree temp increaseCUE_enz CUE change per (normalized enzymes per taxon)CUE_uptake CUE change per (normalized uptake genes per taxon)Vmax0_min Vmax0_max Uptake_Vmax0_min Uptake_Vmax0_max Uptake_Ea_min Ea for uptakeUptake_Ea_max Km_Ea Ea for Km (enzymes and uptake)Km_min "min Km for enzymes- sets a minimum value if calculation based on Vmax correlation is not realistic, i.e. zero or negative"Uptake_Km_min "min Km for uptake- sets a minimum value if calculation based on uptake Vmax correlation is not realistic, i.e. zero or negative"LCI_slope slope for cellulose decay dependence on LCINormalizeProd "Normalize enzyme production for the number of enzyme genes (0 for no, 1 for yes)"NormalizeUptake "Normalize uptake investment for the number of uptake genes (0 for no, 1 for yes)"Enzymes_per_sub Number of enzymes that degrade each substrate; needs to be at least 1Avg_extra_req_enz Average number of additional enzymes required for substrate degradationUptake_per_monomer Number of uptake enzymes that take up each monomer; must be at least 1Enz_per_taxon_min Min/Max possible number of enzyme genes each taxon may possessEnz_per_taxon_max Cfrac_b C fraction of bacterial biomassNfrac_b Pfrac_b Cfrac_f C fraction of fungal biomassNfrac_f Pfrac_f Crange Range (+/-) for biomass CNrange Prange Enz_Prod_min Enzyme C production as a fraction of microbial uptake per iteration- keep well below CUE/n_enzymes to avoid microbial crashEnz_Prod_max Constit_Prod_min Enzyme C production as a fraction of microbial biomass per iteration- keep well below CUE/n_enzymes to avoid microbial crashConstit_Prod_max Enz_C_cost multiplier on enzyme productionEnz_N_cost multiplier on enzyme costEnz_P_cost multiplier on enzyme costEnz_Maint_cost multiplier on enzyme costUptake_C_cost_min Uptake C cost as a fraction of microbial biomass (stays internal)Uptake_C_cost_max Uptake_Maint_cost multiplier on uptake costMonomer_Substrate_Ratio Amount of initial monomer relative to substrate per grid boxInit_NH4 amount per grid boxInit_PO4 amount per grid boxInput_NH4 Input_PO4 Leaching leaching rate as a fraction of the pool per iterationEnz_min Initial enzyme presentEnz_max x Grid lengthy Grid widthtaxa_per_box Initial probability of each bacterial taxon occupying a boxdist Max dispersal distance in grid boxesmax_size_b C quota threshold for bacterial cell divisionmax_size_f C quota threshold for fungal cell divisionC_min minimum C quotaN_min minimum N quotaP_min minimum P quotafb initial biomass fraction of fungidirect probability of fungi moving in a given directionbeta.bac drought sensitivity of bacterial mortality (1 minus per MPa multiplier on Psi)beta.fungi drought sensitivity of fungal mortality (1 minus per MPa multiplier on Psi)Psi.slope.leach drought sensitivity of leaching (exponential decay constant multiplied by Psi)Psi.slope.Vmax drought sensitivity of enzyme Vmax (exponential decay constant multiplied by Psi)Psi.slope.uptake drought sensitivity of uptake Vmax (exponential decay constant multiplied by Psi)output.mid "output grid at time of max enzyme (1 for yes, 0 for end)"print.grid print grid every print.grid timesteps