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Iss25 mmrt function #37

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3467c50
Update enzyme.py mmrt params
jgwalkup Jun 13, 2025
643c981
Update enzyme.py
jgwalkup Jun 13, 2025
2195999
upload enzyme_S.csv file
jgwalkup Jun 13, 2025
ce80797
Update parameters.csv
jgwalkup Jun 13, 2025
c850c83
Merge branch 'main' into iss25-mmrt-function
jgwalkup Aug 20, 2026
6993589
Fix indentation for enzyme_ST0 method
jgwalkup Aug 20, 2026
4b8c611
ruff formatting in enzyme.py
jgwalkup Aug 20, 2026
47be696
Add files via upload
jgwalkup Aug 20, 2026
bafd8da
Add files via upload
jgwalkup Aug 20, 2026
8a0c7b6
Add additional parameters to parameters.csv
jgwalkup Aug 20, 2026
bf89a78
Add new parameters to parameters.csv
jgwalkup Aug 20, 2026
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13 changes: 13 additions & 0 deletions grassland/enzyme_S.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
,S_min,S_max
DeadMic,-135,-135
DeadEnz,-131,-131
Cellulose,-133,-133
Hemicellulose,-131,-131
Starch,-131,-131
Chitin,-135,-135
Lignin,-140,-140
Protein1,-131,-131
Protein2,-131,-131
Protein3,-131,-131
OrgP1,-133,-133
OrgP2,-129,-129
48 changes: 48 additions & 0 deletions grassland/parameters.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -54,5 +54,53 @@ Uptake_Vmax_Km,0.2
Uptake_Vmax_Km_int,0
Km_error,0
Specif_factor,1
AE_max,0.7
AE_min,0.4
Avg_extra_req_enz,0
Cell_maint_C_cost,0.000001
Enz_Cp_max,-3000
Enz_Cp_min,-3001
Enz_H_S_error,0
Enz_H_S_int,0
Enz_H_S_slope,0
Enz_HT0_max,23501
Enz_HT0_min,23500
Enz_Km_temp_sens,0
Enz_max,0
Enz_min,0
Enzymes_per_sub,1
Init_NH4,0
Init_PO4,0
Input_NH4,0
Input_PO4,0
Km_Tref,15
Min_Resp_Temp_Adj,1
mmrt_Km_error,0
mmrt_Vmax_Km_int,0
mmrt_Vmax_Km_slope,1.5
Monomer_Substrate_Ratio,0.0001
NormalizeProd,1
NormalizeUptake,1
Osmolyte_maint_C_cost,0.05
TR_Cp_H_intercept,22375
TR_Cp_H_slope,-0.563
TR_Cp_S_intercept,-169.27
TR_Cp_S_slope,-0.00213
TR_mag_Cp_intercept,-3000
TR_mag_Cp_slope,0
Tref,293
Uptake_Cp_max,-3000
Uptake_Cp_min,-3001
Uptake_H_S_error,0
Uptake_H_S_int,0
Uptake_H_S_slope,0
Uptake_HT0_max,23501
Uptake_HT0_min,23500
Uptake_Km_temp_sens,0
Uptake_mmrt_Vmax_Km_int,0
Uptake_mmrt_Vmax_Km_slope,0.15
Uptake_per_monomer,1
Uptake_ST0_max,-131.9
Uptake_ST0_min,-132
R_moist_decay,0.05
R_moist_uptake,0.1
13 changes: 13 additions & 0 deletions grassland/scrubland/enzyme_S.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
,S_min,S_max
DeadMic,-135,-135
DeadEnz,-131,-131
Cellulose,-133,-133
Hemicellulose,-131,-131
Starch,-131,-131
Chitin,-135,-135
Lignin,-140,-140
Protein1,-131,-131
Protein2,-131,-131
Protein3,-131,-131
OrgP1,-133,-133
OrgP2,-129,-129
48 changes: 48 additions & 0 deletions grassland/scrubland/parameters.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -54,5 +54,53 @@ Uptake_Vmax_Km,0.2
Uptake_Vmax_Km_int,0
Km_error,0
Specif_factor,1
AE_max,0.7
AE_min,0.4
Avg_extra_req_enz,0
Cell_maint_C_cost,0.000001
Enz_Cp_max,-3000
Enz_Cp_min,-3001
Enz_H_S_error,0
Enz_H_S_int,0
Enz_H_S_slope,0
Enz_HT0_max,23501
Enz_HT0_min,23500
Enz_Km_temp_sens,0
Enz_max,0
Enz_min,0
Enzymes_per_sub,1
Init_NH4,0
Init_PO4,0
Input_NH4,0
Input_PO4,0
Km_Tref,15
Min_Resp_Temp_Adj,1
mmrt_Km_error,0
mmrt_Vmax_Km_int,0
mmrt_Vmax_Km_slope,1.5
Monomer_Substrate_Ratio,0.0001
NormalizeProd,1
NormalizeUptake,1
Osmolyte_maint_C_cost,0.05
TR_Cp_H_intercept,22375
TR_Cp_H_slope,-0.563
TR_Cp_S_intercept,-169.27
TR_Cp_S_slope,-0.00213
TR_mag_Cp_intercept,-3000
TR_mag_Cp_slope,0
Tref,293
Uptake_Cp_max,-3000
Uptake_Cp_min,-3001
Uptake_H_S_error,0
Uptake_H_S_int,0
Uptake_H_S_slope,0
Uptake_HT0_max,23501
Uptake_HT0_min,23500
Uptake_Km_temp_sens,0
Uptake_mmrt_Vmax_Km_int,0
Uptake_mmrt_Vmax_Km_slope,0.15
Uptake_per_monomer,1
Uptake_ST0_max,-131.9
Uptake_ST0_min,-132
R_moist_decay,0.05
R_moist_uptake,0.1
13 changes: 13 additions & 0 deletions input/enzyme_S.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
,S_min,S_max
DeadMic,-135,-135
DeadEnz,-131,-131
Cellulose,-133,-133
Hemicellulose,-131,-131
Starch,-131,-131
Chitin,-135,-135
Lignin,-140,-140
Protein1,-131,-131
Protein2,-131,-131
Protein3,-131,-131
OrgP1,-133,-133
OrgP2,-129,-129
48 changes: 48 additions & 0 deletions input/parameters.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -54,5 +54,53 @@ Uptake_Vmax_Km,0.2
Uptake_Vmax_Km_int,0
Km_error,0
Specif_factor,1
AE_max,0.7
AE_min,0.4
Avg_extra_req_enz,0
Cell_maint_C_cost,0.000001
Enz_Cp_max,-3000
Enz_Cp_min,-3001
Enz_H_S_error,0
Enz_H_S_int,0
Enz_H_S_slope,0
Enz_HT0_max,23501
Enz_HT0_min,23500
Enz_Km_temp_sens,0
Enz_max,0
Enz_min,0
Enzymes_per_sub,1
Init_NH4,0
Init_PO4,0
Input_NH4,0
Input_PO4,0
Km_Tref,15
Min_Resp_Temp_Adj,1
mmrt_Km_error,0
mmrt_Vmax_Km_int,0
mmrt_Vmax_Km_slope,1.5
Monomer_Substrate_Ratio,0.0001
NormalizeProd,1
NormalizeUptake,1
Osmolyte_maint_C_cost,0.05
TR_Cp_H_intercept,22375
TR_Cp_H_slope,-0.563
TR_Cp_S_intercept,-169.27
TR_Cp_S_slope,-0.00213
TR_mag_Cp_intercept,-3000
TR_mag_Cp_slope,0
Tref,293
Uptake_Cp_max,-3000
Uptake_Cp_min,-3001
Uptake_H_S_error,0
Uptake_H_S_int,0
Uptake_H_S_slope,0
Uptake_HT0_max,23501
Uptake_HT0_min,23500
Uptake_Km_temp_sens,0
Uptake_mmrt_Vmax_Km_int,0
Uptake_mmrt_Vmax_Km_slope,0.15
Uptake_per_monomer,1
Uptake_ST0_max,-131.9
Uptake_ST0_min,-132
R_moist_decay,0.05
R_moist_uptake,0.1
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