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Merge pull request #31 from rgknox/parameter-switch-migration
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add leaf biophysics parameters
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@glemieux
glemieux authored Jan 17, 2025
2 parents a265f96 + 01e418c commit 9cb1611
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64 changes: 63 additions & 1 deletion parameter_files/archive/api37.0.0_121024_patch_params.xml
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Expand Up @@ -18,7 +18,7 @@

<base_file>archive/api37.0.0_121024_params_default.cdl</base_file>
<new_file>fates_params_default.cdl</new_file>
<pft_list> 1,2,3,4,5,6,7,8,9,10,11,12 </pft_list>
<pft_list> 1,2,3,4,5,6,7,8,9,10,11,12,13,14 </pft_list>
<mods>
<mod type="variable_del">
<na> fates_daylength_factor_switch </na>
Expand Down Expand Up @@ -47,5 +47,67 @@
<mod type="variable_del">
<na> fates_regeneration_model </na>
</mod>
<mod type="variable_add">
<na> fates_leaf_stomatal_btran_model </na>
<di> fates_pft </di>
<un> index </un>
<ln> model switch for how btran reduces conductance. See LeafBiophysicsMod.F90, integer constants: btran_on_ </ln>
<val> 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 </val>
</mod>
<mod type="variable_add">
<na> fates_leaf_agross_btran_model </na>
<di> fates_pft </di>
<un> index </un>
<ln> model switch for how btran reduces gross assimilation. See LeafBiophysicsMod.F90, integer constants: btran_on_ </ln>
<val> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 </val>
</mod>
<mod type="variable_change" name="fates_leaf_theta_cj_c3">
<ln> SOON TO BE DEPRECATED, DO NOT USE </ln>
</mod>
<mod type="variable_change" name="fates_leaf_theta_cj_c4">
<ln> SOON TO BE DEPRECATED, DO NOT USE </ln>
</mod>
<mod type="variable_add">
<na> fates_landuse_grazing_palatability </na>
<di> fates_pft </di>
<un> unitless 0-1 </un>
<ln> Relative intensity of leaf grazing/browsing per PFT </ln>
<val> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1 </val>
</mod>
<mod type="variable_add">
<na> fates_landuse_grazing_rate </na>
<di> fates_landuseclass </di>
<un> 1/day </un>
<ln> fraction of leaf biomass consumed by grazers per day </ln>
<val> 0.0, 0.0, 0.0, 0.0, 0.0 </val>
</mod>
<mod type="variable_add">
<na> fates_landuse_grazing_carbon_use_eff </na>
<di>scalar</di>
<un> unitless </un>
<ln> carbon use efficiency of material eaten by grazers/browsers (i.e. amount in manure / amount consumed) </ln>
<val> 0.0 </val>
</mod>
<mod type="variable_add">
<na> fates_landuse_grazing_maxheight </na>
<di>scalar</di>
<un> m </un>
<ln> maximum height that grazers (browsers, actually) can reach </ln>
<val> 1 </val>
</mod>
<mod type="variable_add">
<na> fates_landuse_grazing_nitrogen_use_eff </na>
<di>scalar</di>
<un> unitless </un>
<ln> nitrogen use efficiency of material eaten by grazers/browsers (i.e. amount in manure / amount consumed) </ln>
<val> 0.25 </val>
</mod>
<mod type="variable_add">
<na> fates_landuse_grazing_phosphorus_use_eff </na>
<di>scalar</di>
<un> unitless </un>
<ln> phosphorus use efficiency of material eaten by grazers/browsers (i.e. amount in manure / amount consumed) </ln>
<val> 0.5 </val>
</mod>
</mods>
</all>
46 changes: 43 additions & 3 deletions parameter_files/fates_params_default.cdl
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@@ -1,4 +1,4 @@
netcdf fates_params_default {
netcdf tmp {
dimensions:
fates_NCWD = 4 ;
fates_history_age_bins = 7 ;
Expand Down Expand Up @@ -348,6 +348,9 @@ variables:
double fates_hydro_vg_n_node(fates_hydr_organs, fates_pft) ;
fates_hydro_vg_n_node:units = "unitless" ;
fates_hydro_vg_n_node:long_name = "(used if hydr_htftype_node = 2),n in van Genuchten 1980 model, pore size distribution parameter" ;
double fates_landuse_grazing_palatability(fates_pft) ;
fates_landuse_grazing_palatability:units = "unitless 0-1" ;
fates_landuse_grazing_palatability:long_name = "Relative intensity of leaf grazing/browsing per PFT" ;
double fates_landuse_harvest_pprod10(fates_pft) ;
fates_landuse_harvest_pprod10:units = "fraction" ;
fates_landuse_harvest_pprod10:long_name = "fraction of harvest wood product that goes to 10-year product pool (remainder goes to 100-year pool)" ;
Expand All @@ -360,6 +363,9 @@ variables:
double fates_landuse_luc_pprod10(fates_pft) ;
fates_landuse_luc_pprod10:units = "fraction" ;
fates_landuse_luc_pprod10:long_name = "fraction of land use change wood product that goes to 10-year product pool (remainder goes to 100-year pool)" ;
double fates_leaf_agross_btran_model(fates_pft) ;
fates_leaf_agross_btran_model:units = "index" ;
fates_leaf_agross_btran_model:long_name = "model switch for how btran reduces gross assimilation. See LeafBiophysicsMod.F90, integer constants: btran_on_" ;
double fates_leaf_c3psn(fates_pft) ;
fates_leaf_c3psn:units = "flag" ;
fates_leaf_c3psn:long_name = "Photosynthetic pathway (1=c3, 0=c4)" ;
Expand All @@ -378,6 +384,9 @@ variables:
double fates_leaf_slatop(fates_pft) ;
fates_leaf_slatop:units = "m^2/gC" ;
fates_leaf_slatop:long_name = "Specific Leaf Area (SLA) at top of canopy, projected area basis" ;
double fates_leaf_stomatal_btran_model(fates_pft) ;
fates_leaf_stomatal_btran_model:units = "index" ;
fates_leaf_stomatal_btran_model:long_name = "model switch for how btran reduces conductance. See LeafBiophysicsMod.F90, integer constants: btran_on_" ;
double fates_leaf_stomatal_intercept(fates_pft) ;
fates_leaf_stomatal_intercept:units = "umol H2O/m**2/s" ;
fates_leaf_stomatal_intercept:long_name = "Minimum unstressed stomatal conductance for Ball-Berry model and Medlyn model" ;
Expand Down Expand Up @@ -708,6 +717,9 @@ variables:
double fates_landuse_crop_lu_pft_vector(fates_landuseclass) ;
fates_landuse_crop_lu_pft_vector:units = "NA" ;
fates_landuse_crop_lu_pft_vector:long_name = "the FATES PFT index to use on a given crop land-use type (dummy value of -999 for non-crop types)" ;
double fates_landuse_grazing_rate(fates_landuseclass) ;
fates_landuse_grazing_rate:units = "1/day" ;
fates_landuse_grazing_rate:long_name = "fraction of leaf biomass consumed by grazers per day" ;
double fates_max_nocomp_pfts_by_landuse(fates_landuseclass) ;
fates_max_nocomp_pfts_by_landuse:units = "count" ;
fates_max_nocomp_pfts_by_landuse:long_name = "maximum number of nocomp PFTs on each land use type (only used in nocomp mode)" ;
Expand Down Expand Up @@ -792,6 +804,18 @@ variables:
double fates_hydro_psicap ;
fates_hydro_psicap:units = "MPa" ;
fates_hydro_psicap:long_name = "sapwood water potential at which capillary reserves exhausted" ;
double fates_landuse_grazing_carbon_use_eff ;
fates_landuse_grazing_carbon_use_eff:units = "unitless" ;
fates_landuse_grazing_carbon_use_eff:long_name = "carbon use efficiency of material eaten by grazers/browsers (i.e. amount in manure / amount consumed)" ;
double fates_landuse_grazing_maxheight ;
fates_landuse_grazing_maxheight:units = "m" ;
fates_landuse_grazing_maxheight:long_name = "maximum height that grazers (browsers, actually) can reach" ;
double fates_landuse_grazing_nitrogen_use_eff ;
fates_landuse_grazing_nitrogen_use_eff:units = "unitless" ;
fates_landuse_grazing_nitrogen_use_eff:long_name = "nitrogen use efficiency of material eaten by grazers/browsers (i.e. amount in manure / amount consumed)" ;
double fates_landuse_grazing_phosphorus_use_eff ;
fates_landuse_grazing_phosphorus_use_eff:units = "unitless" ;
fates_landuse_grazing_phosphorus_use_eff:long_name = "phosphorus use efficiency of material eaten by grazers/browsers (i.e. amount in manure / amount consumed)" ;
double fates_landuse_logging_coll_under_frac ;
fates_landuse_logging_coll_under_frac:units = "fraction" ;
fates_landuse_logging_coll_under_frac:long_name = "Fraction of stems killed in the understory when logging generates disturbance" ;
Expand Down Expand Up @@ -827,10 +851,10 @@ variables:
fates_leaf_photo_temp_acclim_timescale:long_name = "Length of the window for the exponential moving average (ema) of vegetation temperature used in photosynthesis temperature acclimation (used if fates_maintresp_leaf_model=2 or fates_leaf_photo_tempsens_model = 2)" ;
double fates_leaf_theta_cj_c3 ;
fates_leaf_theta_cj_c3:units = "unitless" ;
fates_leaf_theta_cj_c3:long_name = "Empirical curvature parameter for ac, aj photosynthesis co-limitation in c3 plants" ;
fates_leaf_theta_cj_c3:long_name = "SOON TO BE DEPRECATED, DO NOT USE" ;
double fates_leaf_theta_cj_c4 ;
fates_leaf_theta_cj_c4:units = "unitless" ;
fates_leaf_theta_cj_c4:long_name = "Empirical curvature parameter for ac, aj photosynthesis co-limitation in c4 plants" ;
fates_leaf_theta_cj_c4:long_name = "SOON TO BE DEPRECATED, DO NOT USE" ;
double fates_maintresp_nonleaf_baserate ;
fates_maintresp_nonleaf_baserate:units = "gC/gN/s" ;
fates_maintresp_nonleaf_baserate:long_name = "Base maintenance respiration rate for plant tissues, using Ryan 1991" ;
Expand Down Expand Up @@ -1309,6 +1333,8 @@ data:
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 ;

fates_landuse_grazing_palatability = 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1 ;

fates_landuse_harvest_pprod10 = 1, 0.75, 0.75, 0.75, 1, 0.75, 1, 1, 1, 1, 1,
1, 1, 1 ;

Expand All @@ -1321,6 +1347,8 @@ data:
fates_landuse_luc_pprod10 = 1, 0.75, 0.75, 0.75, 1, 0.75, 1, 1, 1, 1, 1, 1,
1, 1 ;

fates_leaf_agross_btran_model = 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ;

fates_leaf_c3psn = 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0 ;

fates_leaf_jmaxha = 43540, 43540, 43540, 43540, 43540, 43540, 43540, 43540,
Expand All @@ -1338,6 +1366,8 @@ data:
fates_leaf_slatop = 0.012, 0.005, 0.024, 0.009, 0.03, 0.03, 0.012, 0.03,
0.03, 0.01, 0.032, 0.027, 0.05, 0.05 ;

fates_leaf_stomatal_btran_model = 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 ;

fates_leaf_stomatal_intercept = 10000, 10000, 10000, 10000, 10000, 10000,
10000, 10000, 10000, 10000, 10000, 10000, 10000, 40000 ;

Expand Down Expand Up @@ -1682,6 +1712,8 @@ data:

fates_landuse_crop_lu_pft_vector = -999, -999, -999, -999, 11 ;

fates_landuse_grazing_rate = 0, 0, 0, 0, 0 ;

fates_max_nocomp_pfts_by_landuse = 4, 4, 1, 1, 1 ;

fates_maxpatches_by_landuse = 9, 4, 1, 1, 1 ;
Expand Down Expand Up @@ -1738,6 +1770,14 @@ data:

fates_hydro_psicap = -0.6 ;

fates_landuse_grazing_carbon_use_eff = 0 ;

fates_landuse_grazing_maxheight = 1 ;

fates_landuse_grazing_nitrogen_use_eff = 0.25 ;

fates_landuse_grazing_phosphorus_use_eff = 0.5 ;

fates_landuse_logging_coll_under_frac = 0.55983 ;

fates_landuse_logging_collateral_frac = 0.05 ;
Expand Down

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