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Model parameters and xml parameter files
Michael Dietze edited this page Jan 6, 2014
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6 revisions
Settings in the ED2 setting file correspond to variables defined in the “ed_data” object. These variables have been lumped into a number of groupings related to their role in the model and the common block memory they are assigned to:
| Misc. Settings | <misc></misc> |
| <ed_misc></ed_misc> | |
| Plant Functional Types | <pft></pft> |
| PFT constants | <pftconst></pftconst> |
| Hydrology | <hydro></hydro> |
| Lapse Rates | <lapse></lapse> |
| Solar Radiation/Light Interception | <light></light> |
| Soils | <soil></soil> |
| Decomposition | <decomposition></decomposition> |
| Patch/Cohort Fusion/Fission | <fusefiss></fusefiss> |
| Disturbance | <disturbance></disturbance> |
| Phenology | <phenology></phenology> |
| Physiology | <physiology></physiology> |
| Additional XML files | <extern></extern> |
Configuration files are encoded in XML format using the above tags. The parser doesn't care about the order or number of tags in the config file. In fact, one must specify one <pft></pft> section per plant functional type. Currently there are a large number of defaults built into the model. The config file is read AFTER all the defaults have been set, so any values not set in the config stay at their default. Within a section, as few or as many values can be set as the user desires. An example of a config file might be:
<?xml version=”1.0”>
<config> <ed_misc> <restart_target_year>1993</restart_target_year> </ed_misc> <pft> <num>5</num> <name>SouthernPine</name> <SLA>10</sla> </pft> </config>
Since XML can be easily read/written by a large number of programs/languages, the use of XML config files makes it easy to generate “batch jobs” or “ensembles” of runs where parameters can be sampled from. The use of this functionality for this purpose, as well as for optimization and Bayesian forecasting, is discussed in the STATISTICS section. A set of R functions exist for writing config files that are bundled in a R package called ed2, which is also described in the STATISTICS section .
Allows the user to reset some of the ED2IN values necessary to do batch jobs.
<caption><misc></misc></caption>| TAG | Values | Description |
|---|---|---|
| restart_mode | Integer | IED_INIT_MODE |
| output_filepath | file path and prefix | AFILOUT |
| input_filepath | file path and prefix | ED_INPUTS_DIR |
| history_filepath | file path and prefix | HFILIN |
| integration_scheme | int | integration_scheme |
| TAG | Values | Description |
|---|---|---|
| restart_target_year | Year | If reading a vegetation “restart” file that included multiple years worth of data, which year should be read (if not set, all years are read) |
| burnin | years | number of years vegetation is held constant while other pools burnin (default = off) |
| outputMonth | integer month | month to do annual output (default = 6) |
Defines a plant functional type. Generally there a multiple repeats of pft with different numbers.
| TAG | Values | Description |
|---|---|---|
| Num | integer | PFT number (REQUIRED) |
| name | string | PFT name |
| include_pft | 0/1 | Whether to use the pft |
| include_pft_ag | 0/1 | Whether to initiate on agricultural patches |
| lifeform | 0-2 | 0=tree, 1=grass/forb, 2=shrub |
| phenology | {0,1,2,3,4} | {evergreen, drought deciduous, cold deciduous, ?, ?} |
| photosyn_pathway | 3,4 | C3 (3) or C4 (4) |
| quantum_efficiency | (mol CO2)/(mol photons) | parameter in the Farqhuar model. With the exception of shade tolerant plants, this is almost always around 0.08. |
| Vm0 = Vcmax, T=15 C | umol CO2/m^2/s^1 |
Carboxylase rate constant (Wilson et al 2000). High variability. May be determined through any of the following in literature:
|
| Vm_low_temp | ºC | Photosynthesis begins to rapidly decline below this temperature. |
| Jm0 = Jmax, T=15 C | umol/m^2/s^1 | Maximum electron transport rate |
| dark_respiration_factor | dimensionless | coefficent for leaf respiration |
| cuticular_cond | umol/m^2/s^1 | leaf conductance when stomata fully closed non-standard units |
| stomatal_slope | dimensionless | slope of the relation between stomatal conductance and A [Leuning]. Related to the Ball-Berry parameter in literature. |
| SLA | m2leaf kg-1C | Specific leaf area. High sensitivity. Inverse of leaf mass per area (LMA), in literature. |
| leaf_width | m | Mean leaf width. Used only to calculate boundary layer conductance. Low sensitivity. |
| c2n_leaf | (kgC)/(kgN) | C:N ratio in leaves. Most often derived from N%, in literature. |
| c2n_root | (kgC)/(kgN) | C:N ratio in fine roots. Most often derived from N%, in literature. |
| c2n_stem | (kgC)/(kgN) | C:N stem wood |
| c2n_storage | (kgC)/(kgN) | C:N ratio of the storage pool. Most often derived from N%, in literature. |
| c2n_recruit | (kgC/kgN) | C:N ratio in recruits. Derived from tissue C:N's, allometries, and hgt_min. |
| f_labile | dimensionless; ranges between 0-1 | fraction of litter that is goes into the labile (fast) carbon pool |
| b1Bl | (kg leaf biomass)/plant/(cm^b2Bl) | Leaf biomass allometry coefficient |
| b2Bl | dimensionless | Leaf biomass allometry coefficient |
| b1Bs | (kg stem biomass)/plant/(cm^b2Bs) | Stem biomass allometry coefficient |
| b2Bs | dimensionless | Stem biomass allometry coefficient |
| b1Ht | m | Height allometry coefficient |
| b2Ht | 1/cm | Height allometry coefficient |
| max_dbh | cm | DBH at which trees stop gaining height |
| rho | kg/m3 | wood density (note, if > 0 code will use tropical allometries by default) |
| q | (kg fine roots)/(kg leaves) | ratio of fine root to leaf biomass. Derived from individual root and leaf biomass estimates, in literature. In woody plants, fine roots are defined as any root under 2mm in diameter. In grasses, find root biomass is treated as equivalent to total root biomass. |
| qsw | (kg sapwood)/(kg leaf)/meter | sapwood allocation |
| {r,c}_fract | dimensionless | Fraction of storage to {seed,clonal} reproduction {note: clonal is not currently implemented.} |
| nonlocal_dispersal | dimensionless; ranges between 0-1 | Proportion of dispersal that is global |
| seed_rain | 1/m2 | Background seed rain |
| hgt_min | m | The minimum height of plants represented by ED. Conceptually, the minimum height needed to begin photosynthesis. |
| repro_min_h | m | Mimimum height for reproduction. Low sensitivity, with the exception of grasses. Defaults to 5m in trees and 1m in grasses. |
| leaf_turnover_rate | 1/yr | rate of leaf loss (temperature dependent, check growth_balive.f90 for details) |
| root_turnover_rate | 1/yr | rate of fine root loss (temperature dependent, check growth_balive.f90 for details) |
| storage_turnover_rate | 1/yr | rate of storage pool loss (not temperature dependent) |
| root_respiration_factor | umolCO2 (kg fine roots)-1 s-1 | rate of fine root respiration at reference soil temperature |
| growth_resp_factor | 0-1 | Proportion of daily carbon gain lost to growth respiration |
| mort1 | 1/year | Time scale at which low-carbon balance plants die |
| mort2 | dimensionless | Carbon balance ratio for which mortality rapidly increases |
| mort3 | 1/year | Density independent (background) mortality |
| plant_min_temp | ºC | Freezing mortality |
| seedling_mortality | dimensionless; ranges from 0-1 | proportion of seed that dies and goes to litter pool. |
| treefall_{gt,lt} | m | Survival rate when {above,below} treefall_hite_threshold during treefall disturbance |
| water_conductance | m-2 a-1 (kgC root)-1 | "Water availability factor" Sets a plant's supply of water |
| clumping | dimensionless; range is between 0-1. | Radiative transfer clumping factor |
| leaf_scatter_vis | dimensionless | scattering coefficient for visible radiation |
| diffuse_backscatter_vis | dimensionless | backscatter fraction of diffuse radiation |
| emis_v | dimensionless | leaf emissivity |
Parameters that apply to all PFT's equally
| Variable | Units | Description |
|---|---|---|
| c2n_slow | (kgC)/(kgN) | C:N soil slow carbon pool |
| c2n_structural | (kgC)/(kgN) | C:N soil structural carbon pool |
| l2n_stem | (kgC)/(kgN) | Lignin:N stem wood |
| C2B | (kg carbon)/(kg biomass) | Carbon to Biomass ratio in wood |
| agf_bs | dimensionless; allowed range is 0-1. | Above-ground fraction of the structural stem |
| frost_mort | 1/years | frost mortality rate |
Parameters controlling TOPMODEL lateral soil moisture flow and surface runoff model.
| Variable | Units | Description |
|---|---|---|
| useTOPMODEL | boolean | Use the among site TOPMODEL subsurface hydrology routine |
| useRUNOFF | boolean | Use the among site surface runoff routine |
| outputPeriod | integer | How often hydrology status is written to file |
| MoistRateTuning | Constant multiplier to soil conductivity decay (f) | |
| MoistSatThresh | ||
| MoistdWT | Maximum rate of change in water table | |
| FracLiqRunoff | Threshold fraction of frozen surface water for runoff to occur | |
| runoff_vmax | maximum runoff velocity | |
| GrassLAImax | Grass LAI at which maximum surface resistance to runoff occurs |
Rate of change in meteorological variables with change in elevation
| Variable | Units | Description |
|---|---|---|
| geoht | m/m | Change in geopotential height with elevation |
| vels | m/s/m | Change in wind velocity with elevation |
| atm_temp | C/m | Change in air temperature with elevation |
| rv | (kg H2O)/(kg air)/m | Change in humidity with elevation |
| prss | Pa/m | Change in pressure with elevation |
| pcpg | mm/m | Change in precipitation with elevation |
| atm_co2 | ppm/m | Change in CO2 with elevation |
| rlong | (W/m2)/m | Change in long-wave radiation with elevation |
| par_diffuse | (W/m2)/m | Change in diffuse PAR with elevation |
| par_beam | (W/m2)/m | Change in direct beam PAR with elevation |
| nir_diffuse | (W/m2)/m | Change in diffuse near IR with elevation |
| nir_beam | (W/m2)/m | Change in direct beam near IR with elevation |
| Variable | Units | Description |
|---|---|---|
| mubar | dimensionless | Parameter derived from the distribution of leaf orientation angles. Currently, we assume that leaf angles are distributed isotropically. |
| lai_min | (m2 leaf)/(m2 ground) | Integrator will ignore cohorts with LAI below this threshold |
| visible_fraction | dimensionless | If given total solar radiation, this is the fraction assumed to lie in the visible. |
| visible_fraction_dir | dimensionless | If given direct beam solar radiation, this is the fraction assumed to lie in the visible. |
| visible_fraction_dif | dimensionless | If given diffuse solar radiation, this is the fraction assumed to lie in the visible. |
| leaf_scatter_vis | dimensionless | scattering parameter for visible |
| leaf_scatter_nir | dimensionless | scattering parameter for near infrared |
| leaf_reflect_vis | dimensionless | reflectivity for visible |
| leaf_reflect_nir | dimensionless | reflectivity for near infrared |
| leaf_trans_vis | dimensionless | transmittivity for visible |
| leaf_trans_nir | dimensionless | transmittivity for near infrared |
| diffuse_backscatter_vis | dimensionless | backscatter fraction for visible |
| diffuse_backscatter_nir | dimensionless | backscatter fraction for near infrared |
| Variable | Units | Description |
|---|---|---|
| water_stab_thresh | kg/m2 | Threshold beyond which a temporary water layer is considered stable and is thus treated independently in the integrator |
| infiltration_method | flag specifying infiltration scheme. | For now, the only available option is scheme 0. |
| dewmax | kg/m2/s | maximum rate of dew formation |
| vegetation_database | character string | location of the OGE database. We use this to determine the land-sea mask. |
| soil_database | character string | Location of the FAO soil database. We use this to determine soil textural class. |
| soilstate_db | character string | Location of the file containing the initial conditions for soil temperature and soil water. For more information on the file itself, see documentation on the Soil State File. |
| soildepth_db | character string | Location of the file containing soil depth information. For more information on the file itself, see documentation on the Soil Depth File. |
| isoilstateinit | Flag (0/1) | Set this to 0 for uniform soil water and soil temperature initialization based on namelist values. Set this to 1 to initialize soils according to soilstate_db. |
| isoildepthflg | Flag (0/1) | Set this to 0 for uniform soil depths based on namelist values. Set this to 1 to set soil depths according to soildepth_db. |
| runoff_time | sec | rate of decay in surface moisture to runoff (used if hydro:useRUNOFF = 0) |
| Variable | Units | Description |
|---|---|---|
| cwd_fract | dimensionless | Ratio of CWD:(CWD + Soil Carbon) |
| resp_opt_water | dimensionless; range is between 0-1. | Optimal soil water for heterotrophic respiration as a fraction of the maximum possible soil water. |
| resp_water_below | dimensionless | Determines the rate at which heterotrophic respiration decays as soil water falls below resp_opt_water. |
| resp_water_above | dimensionless | Determines the rate at which heterotrophic respiration decays as soil water increases above resp_opt_water. |
| resp_temperature_increase | 1/K | Determines how rapidly heterotrophic respiration increases with increasing temperature. |
| N_immobil_supply_scale | 1/day | Supply coefficient for nitrogen immobilization. |
| r_fsc | Dimensionless; ranges between 0-1. | Fraction of the fast soil carbon pool going to heterotrophic respiration. |
| r_stsc | Dimensionless; ranges between 0-1. | Fraction of the structural soil carbon pool going to heterotrophic respiration (instead of to the slow pool). |
| r_ssc | Dimensionless; ranges between 0-1. | Fraction of the slow soil carbon pool going to heterotrophic respiration. |
| K1 | 1/day | structural soil carbon decomposition rate |
| K2 | 1/day | fast soil carbon decomposition rate |
| K3 | 1/day | slow soil carbon decomposition rate |
| N_decomp_lim | flag equal to 0 or 1. | Set to 1 if you want decomposition to be limited by nitrogen. |
Parameters controlling the fusion and fission of patches and cohorts due to disturbance, recruitment, aging, etc.
<caption><fusefiss></fusefiss></caption>| Variable | Units | Description |
|---|---|---|
| min_recruitment_size | kgC/m2 | threshold for recruit formation. |
| min_dbh_class | cm | Minimum dbh class in patch profiling |
| min_hgt_class | m | Minimum height class for patch profiling |
| maxdbh | cm | Maximum dbh class in patch profiling |
| fusetol | cm | Cohort fusion tolerance (DBH) |
| fusetol_h | m | Cohort fusion tolerance (HEIGHT) |
| lai_fuse_tol | (m2 leaf) / (m2 ground) | Cohort fusion tolerance (LAI) |
| lai_tol | (m2 leaf) / (m2 ground) | Cohort splitting tolerance (LAI) |
| ntol | (#/m2) | Min plant density for height bin to be usind in height profile comparisons |
| profile_tol | dimensionless | Fractional tolerance for patch pft height comparisons |
| max_patch_age | years | Maximum patch age for fusion |
| Variable | Units | Description |
|---|---|---|
| patch_dynamics | Bool | Specifies if we include disturbance |
| min_new_patch_area | Proportion | Minimum area required to make a new patch |
| include_fire | 0/1 | set this to 1 to turn on internally-calculated fire dynamics |
| ianth_disturb | 0/1 | set this to 1 to include anthropogenic disturbance |
| treefall_disturbance_rate | 1/years | Treefall disturbance rate |
| treefall_hite_threshold | Meters | Cohorts above vs below this height are treated differently during treefall |
| treefall_age_threshold | years | Patches below this age do not suffer treefall disturbance |
| plantation-year | Minimum year for which plantations occur. | |
| plantation_rotation | Number of years that plantations require to reach maturity. | |
| mature_harvest_age | Number of years that non-plantation forest requires to reach maturity. | |
| forestry_on | 0/1 | Set to 1 to turn on forest harvesting. |
| agriculture_on | 0/1 | Set to 1 to turn on agriculture. |
| fire_dryness_threshold | meters | fire may occur if the amount of (soil+surface) water falls below this depth. |
| fire_parameter | dimensionless | controls speed of fire spread. |
| Variable | Units | Description |
|---|---|---|
| istoma_scheme | 0/1 | Set to 0 to solve the full stomatal conductance-photosynthesis equations. Set to 1 to use an approximate but faster form of the equations. |
| n_plant_lim | 0/1 | If this is set to 1, nitrogen limitation will applied to plants. In this case, you will also need to be sure to initialize nitrogen correctly. |
| Variable | Units | Description |
|---|---|---|
| retained_carbon_fraction | fraction ranging from 0-1. | Fraction of carbon translocated from leaf to storage before leaf scenecence |
| theta_crit | fraction ranging from 0-1. | This is a soil water threshold. When soil water (as a fraction of saturation) sinks below this threshold, drought deciduous plants drop their leaves. When soil water (as a fraction of saturation) rises above this threshold, drought deciduous plants flush their leaves. |
| dl_tr | minutes | daylength threshold used in Botta et al. phenology scheme |
| st_tr1 | K | soil temperature threshold used in Botta et al. phenology scheme |
| st_tr2 | K | soil temperature threshold used in Botta et al. phenology scheme |
| phen_a | days | parameter used to determine timing of leaf flush in Botta et al. phenology scheme. |
| phen_b | days | parameter used to determine timing of leaf flush in Botta et al. phenology scheme. |
| phen_c | 1/days | parameter used to determine timing of leaf flush in Botta et al. phenology scheme. |
| iphen_scheme | categorical | Flag specifying which phenology scheme to use. 0 - Botta et al. for cold deciduous. Simple theta_crit threshold for drought deciduous. 1 - Prescribed phenology. 2 - Botta et al. for cold deciduous. Kim et al. for drought deciduous. 3 - Botta et al. for cold deciduous. Kim et al. for drought deciduous and light phenology (not tested). |
| iphenys1 | (year) | If using a prescribed phenology scheme, this is the earliest year for which spring phenology data exists. |
| iphenysf | (year) | If using a prescribed phenology scheme, this is the latest year for which spring phenology data exists. |
| iphenyf1 | (year) | If using a prescribed phenology scheme, this is the earliest year for which fall phenology data exists. |
| iphenyff | (year) | If using a prescribed phenology scheme, this is the latest year for which fall phenology data exists. |
In addition to parameters that apply to the model as a whole, there are parameters that vary in space. Foremost among these are the parameters for soil physics. The soil physics for a polygon are set using two databases. First, the soils are set using a global dataset from the UN Food and Agriculture Organization (FAO) at a 1x1 degree resolution that has been converted to a HDF5 file. Second, soil physics is updated, where available, from the ~1x1 km USGS STATSGO soils database. The directory and prefix for these soil texture files are set by ISOILFN. The STATSGO soils are stored in ASCII files in 5x5 degree tiles that are generated using the program “rextract” which reads the data from the binary file “layertext.bsq”. This database has not yet been ported to v2.1 using HDF5. Data in each file is stored in a 2 character field (no delimiter) and takes on the following values:
| 1 | sand | 6 | Sandy clay loam | 11 | clay |
| 2 | Loamy sand | 7 | Silty clay loam | 12 | peat |
| 3 | Sandy loam | 8 | Clay loam | 13 | Bedrock |
| 4 | Silt loam | 9 | Sandy clay | ||
| 5 | loam | 10 | Silty clay |
Soil physical parameters are then assigned based on a table. The format of the file is with longitude as the outer loop, latitude the middle loop, and soil depth the inner loop. The code assumes 11 soil layers with pre-defined depths (centers = 0.025,0.075,0.15,0.25,0.35,0.5,0.7,0.9,1.25,1.75,2.25m) and that the lat/lon grid is 600x600 cells (i.e. the soils are actually stored on a 30 x 30 second grid). Currently the modal soil type (i.e. The type with the highest frequency) is assigned to the whole polygon, however the soil types for individual types can be specified in the site file, as described in Initial Conditions.