FATES parameters XML schema

bandre-ucar commented 7 years ago

Summary of Issue:

Need to create an XML schema to store FATES parameters.

Requirements and Design considerations:

Want PFT oriented data rather than array oriented.
Should /can the schema be based on the cime 5 generic EntryID or specialized EntryID namelist? Or do we need to create a custom schema?
Metadata support and checking is desired. Possible metadata includes:
- Provenance
- Units
- Nonnegativity
- Nonzero
- Upper and lower bounds of values.

bandre-ucar commented 7 years ago

Straw-man formats from the telecon on 2016-11-01

XML database, array oriented

<fates_pft_parameters>
<leaf_params>
    <SLA>40, 60, 50, 44</SLA>
    <Vcmax>120, 121, 122</Vcmax>
</leaf_params>
<canopy_params>
    <clumping>0.85, 0.75, 0.80</clumping>
</canopy_params>
</fates_pft_parameters>

XML database, pft oriented

<fates_pft_parameters>
<size_class name=’4’>
    <parameter name=’foo’ value=’1.234’/>
</size_class>
<pft name=’1’>
    <group name=’canopy_params’>
        <parameter name=’clumping’ value=’0.85’>
   </group>
   <group name=’leaf_params’>
       <parameter name=’Vcmax’ value=’120’/>
       <parameter name=’SLA’ value=’40’/>
  </group>
</pft>
<pft name=’2’>
    <group name=’canopy_params’>
        <parameter name=’clumping’ value=’0.95’>
   </group>
   <group name=’leaf_params’>
       <parameter name=’Vcmax’ value=’130’/>
       <parameter name=’SLA’ value=’50’/>
  </group>
</pft>
</fates_pft_parameters>

mdietze commented 7 years ago

For reference, this is what ED2's parameter XML files look like

<?xml version="1.0"?>
<!DOCTYPE config SYSTEM "ed.dtd">
<config>
 <pft>
  <num>1</num>
  <is_tropical>0</is_tropical>
  <is_grass>0</is_grass>
  <include_pft>1</include_pft>
  <include_pft_ag>0</include_pft_ag>
  <include_pft_fp>0</include_pft_fp>
  <clumping_factor>0.84</clumping_factor>
  <orient_factor>0</orient_factor>
  <leaf_emiss_tir>0.95</leaf_emiss_tir>
  <wood_emiss_tir>0.9</wood_emiss_tir>
  <leaf_reflect_vis>0.11</leaf_reflect_vis>
  <leaf_reflect_nir>0.11</leaf_reflect_nir>
  <wood_reflect_vis>0.11</wood_reflect_vis>
  <wood_reflect_nir>0.11</wood_reflect_nir>
  <leaf_trans_vis>0.11</leaf_trans_vis>
  <leaf_trans_nir>0.11</leaf_trans_nir>
  <wood_trans_vis>0.11</wood_trans_vis>
  <wood_trans_nir>0.11</wood_trans_nir>
  <leaf_backscatter_vis>0</leaf_backscatter_vis>
  <leaf_backscatter_nir>0</leaf_backscatter_nir>
  <leaf_backscatter_tir>0.625</leaf_backscatter_tir>
  <wood_backscatter_vis>0</wood_backscatter_vis>
  <wood_backscatter_nir>0</wood_backscatter_nir>
  <wood_backscatter_tir>0.625</wood_backscatter_tir>
  <leaf_scatter_vis>0</leaf_scatter_vis>
  <leaf_scatter_nir>0</leaf_scatter_nir>
  <wood_scatter_vis>0</wood_scatter_vis>
  <wood_scatter_nir>0</wood_scatter_nir>
  <phi1>0</phi1>
  <phi2>0</phi2>
  <mu_bar>0</mu_bar>
  <photosyn_pathway>3</photosyn_pathway>
  <quantum_efficiency>0.0573330142402985</quantum_efficiency>
  <Vm0>20.3870754242</Vm0>
  <Vm_low_temp>4.97324470801869</Vm_low_temp>
  <Vm_high_temp>45</Vm_high_temp>
  <Vm_decay_e>0.400000006</Vm_decay_e>
  <Vm_decay_a>220000</Vm_decay_a>
  <Vm_decay_b>690</Vm_decay_b>
  <vm_hor>3000</vm_hor>
  <vm_q10>2.4000000954</vm_q10>
  <dark_respiration_factor>0.0205220375463813</dark_respiration_factor>
  <Rd_low_temp>4.7136998177</Rd_low_temp>
  <Rd_high_temp>45</Rd_high_temp>
  <Rd_decay_e>0.400000006</Rd_decay_e>
  <Rd_hor>3000</Rd_hor>
  <Rd_q10>2.4000000954</Rd_q10>
  <Rd0>0.2956125736</Rd0>
  <D0>0.0160000008</D0>
  <stomatal_slope>6.16141699805087</stomatal_slope>
  <cuticular_cond>10000</cuticular_cond>
  <water_conductance>0.00449237129880371</water_conductance>
  <leaf_width>0.100480603284365</leaf_width>
  <growth_resp_factor>0.35310875899935</growth_resp_factor>
  <leaf_turnover_rate>0</leaf_turnover_rate>
  <root_turnover_rate>1.30227639921882</root_turnover_rate>
  <storage_turnover_rate>0.6243000031</storage_turnover_rate>
  <f_labile>0.49934071486063</f_labile>
  <root_respiration_factor>0.2800000012</root_respiration_factor>
  <rrf_low_temp>4.7136998177</rrf_low_temp>
  <rrf_high_temp>45</rrf_high_temp>
  <rrf_decay_e>0.400000006</rrf_decay_e>
  <rrf_hor>3000</rrf_hor>
  <rrf_q10>2.4000000954</rrf_q10>
  <frost_mort>3</frost_mort>
  <mort0>0</mort0>
  <mort1>1</mort1>
  <mort2>43.4199967054883</mort2>
  <mort3>0.0061440002</mort3>
  <cbr_severe_stress>-0.7971192598</cbr_severe_stress>
  <seedling_mortality>0.953000449763003</seedling_mortality>
  <treefall_s_gt>0</treefall_s_gt>
  <treefall_s_lt>0.1000000015</treefall_s_lt>
  <fire_s_gt>0</fire_s_gt>
  <fire_s_lt>0</fire_s_lt>
  <plant_min_temp>193.1499938965</plant_min_temp>
  <rho>0</rho>
  <SLA>43.0866657730942</SLA>
  <horiz_branch>0.5699999928</horiz_branch>
  <q>1.1274000406</q>
  <sapwood_ratio>3900</sapwood_ratio>
  <qsw>0.0076923077</qsw>
  <init_density>0.1000000015</init_density>
  <b1Ht>22.6798992157</b1Ht>
  <b2Ht>-0.0653399974</b2Ht>
  <hgt_ref>1.2999999523</hgt_ref>
  <hgt_min>1.5</hgt_min>
  <hgt_max>22.6572189331</hgt_max>
  <min_dbh>0.1355601549</min_dbh>
  <dbh_crit>43.4928016663</dbh_crit>
  <dbh_adult>10</dbh_adult>
  <dbh_bigleaf>14.4976005554</dbh_bigleaf>
  <b1Bl_small>0.0129000004</b1Bl_small>
  <b1Bl_large>0.0129000004</b1Bl_large>
  <b2Bl_small>1.747699976</b2Bl_small>
  <b2Bl_large>1.747699976</b2Bl_large>
  <bleaf_adult>0.3607943356</bleaf_adult>
  <b1Bs_small>0.0264800005</b1Bs_small>
  <b1Bs_large>0.0264800005</b1Bs_large>
  <b2Bs_small>2.9595398903</b2Bs_small>
  <b2Bs_large>2.9595398903</b2Bs_large>
  <min_bdead>0.0000357601</min_bdead>
  <bdead_crit>935.0818481445</bdead_crit>
  <b1Ca>2.4901540279</b1Ca>
  <b2Ca>0.8068805933</b2Ca>
  <b1WAI>0.0096000005</b1WAI>
  <b2WAI>2.094700098</b2WAI>
  <brf_wd>0.1599999964</brf_wd>
  <agf_bs>0.6999999881</agf_bs>
  <b1Vol>0.0247086249</b1Vol>
  <b2Vol>2</b2Vol>
  <b1Rd>-1.1140580177</b1Rd>
  <b2Rd>0.4223014116</b2Rd>
  <c2n_leaf>19.6962207498013</c2n_leaf>
  <c2n_recruit>17.8949623108</c2n_recruit>
  <phenology>2</phenology>
  <c_grn_leaf_dry>3218</c_grn_leaf_dry>
  <wat_dry_ratio_grn>2.5</wat_dry_ratio_grn>
  <wat_dry_ratio_ngrn>0.6999999881</wat_dry_ratio_ngrn>
  <c_ngrn_biom_dry>1217.3759765625</c_ngrn_biom_dry>
  <delta_c>-225.1618652344</delta_c>
  <b1Cl>0.3106774986</b1Cl>
  <b2Cl>1.0980000496</b2Cl>
  <r_fract>0.313704346253454</r_fract>
  <st_fract>0</st_fract>
  <nonlocal_dispersal>0.406417639689195</nonlocal_dispersal>
  <repro_min_h>18</repro_min_h>
  <one_plant_c>0.0004555048</one_plant_c>
  <min_recruit_size>0.000004555</min_recruit_size>
  <min_cohort_size>0.0000004555</min_cohort_size>
  <seed_rain>0.0100000007</seed_rain>
  <negligible_nplant>0.00000001</negligible_nplant>
  <veg_hcap_min>0.0895049497</veg_hcap_min>
  <fineroot2leaf>0.635751856504247</fineroot2leaf>
  <root_respiration_rate>2.19115261520877</root_respiration_rate>
  <Vcmax>52.7790070920269</Vcmax>
  <c2n_fineroot>248.944801627658</c2n_fineroot>
 </pft>
 <pft>
  <num>2</num>
  <is_tropical>0</is_tropical>
  <is_grass>0</is_grass>
  <include_pft>1</include_pft>
  <include_pft_ag>0</include_pft_ag>
  <include_pft_fp>0</include_pft_fp>
   ...

ckoven commented 6 years ago

closing this and related issues because the new cdl file scheme takes care of these problems.

NGEET / fates

FATES parameters XML schema #157

Summary of Issue:

Requirements and Design considerations: