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Merge branch 'new-arctic-shrubPFT' into api36.1.0-merge
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@glemieux
glemieux committed Oct 2, 2024
2 parents 651a732 + ba7ea1a commit 309075c
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161 changes: 161 additions & 0 deletions parameter_files/archive/new_shrubPFT_patch_params.xml
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<?xml version="1.0"?>
<all>
<!-- This parameter patch file updates the parameter file with the changes -->
<!-- Introduces two new arctic shrub PFTs, first by duplicating the default -->
<!-- #7 broadleaf_avergreen_extratrop_shrub, and the -->
<!-- #9 broadleaf_colddecid_extratrop_shrub, then updating the parameters -->
<!-- based on Yanlan Liu's 2024 publication in Earth's Future. -->

<!-- ORGINIAL PFT KEY -->
<!-- 1 broadleaf_evergreen_tropical_tree -->
<!-- 2 needleleaf_evergreen_extratrop_tree -->
<!-- 3 needleleaf_colddecid_extratrop_tree -->
<!-- 4 broadleaf_evergreen_extratrop_tree -->
<!-- 5 broadleaf_hydrodecid_tropical_tree -->
<!-- 6 broadleaf_colddecid_extratrop_tree -->
<!-- 7 broadleaf_evergreen_extratrop_shrub -->
<!-- 8 broadleaf_hydrodecid_extratrop_shrub -->
<!-- 9 broadleaf_colddecid_extratrop_shrub -->
<!-- 10 arctic_c3_grass -->
<!-- 11 cool_c3_grass -->
<!-- 12 c4_grass -->


<!-- NEW PFT KEY -->
<!-- 1 broadleaf_evergreen_tropical_tree -->
<!-- 2 needleleaf_evergreen_extratrop_tree -->
<!-- 3 needleleaf_colddecid_extratrop_tree -->
<!-- 4 broadleaf_evergreen_extratrop_tree -->
<!-- 5 broadleaf_hydrodecid_tropical_tree -->
<!-- 6 broadleaf_colddecid_extratrop_tree -->
<!-- 7 broadleaf_evergreen_extratrop_shrub -->
<!-- 8 broadleaf_hydrodecid_extratrop_shrub -->
<!-- 9 broadleaf_colddecid_extratrop_shrub -->
<!-- 10 broadleaf_evergreen_arctic_shrub -->
<!-- 11 broadleaf_colddecid_arctic_shrub -->
<!-- 12 arctic_c3_grass -->
<!-- 13 cool_c3_grass -->
<!-- 14 c4_grass -->

<base_file>archive/api36.1.0_params_default.cdl</base_file>
<new_file>fates_params_default.cdl</new_file>
<pft_trim_list>1,2,3,4,5,6,7,8,9,7,9,10,11,12</pft_trim_list>
<parameters>

<!-- Naming conventions: date stamp and the last tag it was valid through -->
<!-- api36.0.0_051724 -->

<!-- Override values for the new evergreen arctic PFT, this is now PFT 10 -->
<!-- which duplicated the orginial 7th PFT -->
<pft_group ids="10">
<fates_allom_d2bl1> 0.0481934 </fates_allom_d2bl1>
<fates_allom_d2bl2> 1.0600586 </fates_allom_d2bl2>
<fates_allom_agb2> 0.5289883 </fates_allom_agb2>
<fates_allom_agb3> 2.1010352 </fates_allom_agb3>
<fates_allom_d2h1> 0.8165625 </fates_allom_d2h1>
<fates_allom_d2h2> 0.2316113 </fates_allom_d2h2>
<fates_recruit_height_min> 0.8 </fates_recruit_height_min>
<fates_allom_dbh_maxheight> 2.4 </fates_allom_dbh_maxheight>
<fates_recruit_seed_dbh_repro_threshold> 2.4 </fates_recruit_seed_dbh_repro_threshold>
<fates_allom_d2ca_coefficient_min> 0.4363427 </fates_allom_d2ca_coefficient_min>
<fates_allom_d2ca_coefficient_max> 0.4363427 </fates_allom_d2ca_coefficient_max>
<fates_alloc_store_priority_frac> 0.7 </fates_alloc_store_priority_frac>
<fates_alloc_storage_cushion> 1.5 </fates_alloc_storage_cushion>
<fates_leaf_slatop> 0.010 </fates_leaf_slatop>
<fates_leaf_vcmax25top> 38 </fates_leaf_vcmax25top>
<fates_grperc> 0.12 </fates_grperc>
<fates_mort_bmort> 0.016 </fates_mort_bmort>
<fates_mort_freezetol> -71 </fates_mort_freezetol>
<fates_frag_seed_decay_rate> 0.74 </fates_frag_seed_decay_rate>
<fates_recruit_seed_alloc> 0.07 </fates_recruit_seed_alloc>
<fates_recruit_seed_germination_rate> 0.40 </fates_recruit_seed_germination_rate>
<fates_recruit_init_density> 0.16 </fates_recruit_init_density>
</pft_group>


<!-- Override values for the new colddecid arctic PFT, this is now PFT 11 -->
<!-- which duplicated the orginial 9th PFT -->
<pft_group ids="11">
<fates_allom_d2bl1> 0.0481934 </fates_allom_d2bl1>
<fates_allom_d2bl2> 1.7176758 </fates_allom_d2bl2>
<fates_allom_agb2> 0.6853945 </fates_allom_agb2>
<fates_allom_agb3> 1.7628613 </fates_allom_agb3>
<fates_allom_d2h1> 0.7781250 </fates_allom_d2h1>
<fates_allom_d2h2> 0.4027002 </fates_allom_d2h2>
<fates_recruit_height_min> 0.8 </fates_recruit_height_min>
<fates_allom_dbh_maxheight> 1.9 </fates_allom_dbh_maxheight>
<fates_recruit_seed_dbh_repro_threshold> 1.9 </fates_recruit_seed_dbh_repro_threshold>
<fates_allom_d2ca_coefficient_min> 0.3166497 </fates_allom_d2ca_coefficient_min>
<fates_allom_d2ca_coefficient_max> 0.3166497 </fates_allom_d2ca_coefficient_max>
<fates_alloc_store_priority_frac> 0.6 </fates_alloc_store_priority_frac>
<fates_alloc_storage_cushion> 1.4 </fates_alloc_storage_cushion>
<fates_leaf_slatop> 0.032 </fates_leaf_slatop>
<fates_leaf_slamax> 0.032 </fates_leaf_slamax>
<fates_leaf_vcmax25top> 54 </fates_leaf_vcmax25top>
<fates_mort_scalar_hydrfailure> 0.8 </fates_mort_scalar_hydrfailure>
<fates_mort_scalar_cstarvation> 0.57 </fates_mort_scalar_cstarvation>
<fates_mort_scalar_coldstress> 3.5 </fates_mort_scalar_coldstress>
<fates_mort_bmort> 0.010 </fates_mort_bmort>
<fates_mort_freezetol> -95 </fates_mort_freezetol>
<fates_frag_seed_decay_rate> 0.46 </fates_frag_seed_decay_rate>
<fates_recruit_seed_germination_rate> 0.49 </fates_recruit_seed_germination_rate>
</pft_group>

<!-- Updating parameters for c3_arctic grass based on Yanlan's work. Now PFT 12 -->
<pft_group ids="12">
<fates_recruit_height_min> 0.11 </fates_recruit_height_min>
<fates_alloc_store_priority_frac> 0.6 </fates_alloc_store_priority_frac>
<fates_leaf_slatop> 0.027 </fates_leaf_slatop>
<fates_leaf_vcmax25top> 86 </fates_leaf_vcmax25top>
<fates_grperc> 0.16 </fates_grperc>
<fates_mort_scalar_coldstress> 2.3 </fates_mort_scalar_coldstress>
<fates_mort_freezetol> -89 </fates_mort_freezetol>
<fates_frag_seed_decay_rate> 0.35 </fates_frag_seed_decay_rate>
<fates_recruit_seed_germination_rate> 0.29 </fates_recruit_seed_germination_rate>
</pft_group>

<!-- Update the HLM-PFT map since PFTs 9, 10, 11 now share area -->
<!-- Splits the HLM deciduous boreal shrub (which must sum to 1.0) -->
<!-- into 0.1 for the evergreen arctic, and 0.8 for cold-decid arctic -->
<!-- and leaves 0.1 in the orginial non-arctic extratrop cold-decid shrub -->
<pft_group ids="9" >
<fates_hlm_pft_map> 0, 0, 0, 0, 0, 0, 0, 0, 0, 1.0, 0.1, 0, 0, 0 </fates_hlm_pft_map>
</pft_group>

<pft_group ids="10">
<fates_hlm_pft_map> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.0, 0.1, 0, 0, 0 </fates_hlm_pft_map>
</pft_group>

<pft_group ids="11">
<fates_hlm_pft_map> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.0, 0.8, 0.0, 0, 0 </fates_hlm_pft_map>
</pft_group>
<non_pft_group></non_pft_group>


<!-- Creates a new 10th and 11th column, for the two new arctic shrub PFTs -->
<!-- then splits the HLM deciduous boreal shrub (which must sum to 1.0) -->
<!-- into 0.1 for the evergreen arctic, and 0.8 for cold-decid arctic -->
<!-- and leaves 0.1 in the orginial non-arctic extratrop cold-decid shrub -->
<!--<mods>
<mod type="variable_change" name="fates_hlm_pft_map">
<di> fates_hlm_pftno, fates_pft </di>
<val> 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0.1, 0.1, 0.8, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1 ;
</val>
</mod>
</mods> -->

</parameters>
</all>
8 changes: 4 additions & 4 deletions tools/modify_fates_paramfile.py
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Original file line number Diff line number Diff line change
Expand Up @@ -75,13 +75,13 @@ def main():
else:

try:
outputval = float(args.val)
outputval = np.float64(args.val)
if args.changeshape:
raise Exception
except:
try:
#print('output variable not interpretable as real. trying array')
outputval = np.fromstring(args.val, sep=',', dtype=np.float32)
print('output variable not interpretable as real. trying array')
outputval = np.fromstring(args.val, sep=',', dtype=np.float64)
if len(outputval) == 0:
raise RuntimeError('output variable needs to have size greater than zero')
except:
Expand Down Expand Up @@ -240,7 +240,7 @@ def main():
' New length is shorter than old, so its been truncated.')
x[0:length_specified,:] = variable[0:length_specified,:]
else:
x.assignValue(float(variable.data))
x.assignValue(np.float64(variable.data))
#
var = ncfile.variables[args.varname]
else:
Expand Down

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