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Adding two new arctic shrub PFTs, and some arctic grass parameter updates #1236

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merged 7 commits into from
Oct 4, 2024
Merged

Adding two new arctic shrub PFTs, and some arctic grass parameter updates #1236

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9b881e0
made new shrubPFT patch file and starting to add in new PFT
jenniferholm Jun 29, 2024
1b5e290
updating parameter batch file
jenniferholm Jul 17, 2024
6c94e74
updating parameter batch file, again
jenniferholm Aug 16, 2024
2f0b323
pftmap bug fix on xml file, made new params cdl file
jenniferholm Aug 16, 2024
068c7a1
adding back the mapping between elm/fates pft 10 & 9 respectively.
rgknox Aug 27, 2024
a43a72c
changed modparam tool to use float64
rgknox Aug 27, 2024
ba7ea1a
update arctic shrub patch file to use archived param file
glemieux Sep 26, 2024
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161 changes: 161 additions & 0 deletions parameter_files/archive/new_shrubPFT_patch_params.xml
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Original file line number Diff line number Diff line change
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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