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Description of debug outputs

Debug Outputs

Debug outputs

The so called debug outputs are - besides the database oriented Outputs and the direct visualization - the third type of data outputs available in iLand. Debug outputs are usually on a very detailed level and are typically used during development and for debugging purposes (hence the name). In addition, debug output data is available within the iLand viewer application and is linked to iLand objects (e.g., trees or resource units). Outputs are enabled/disabled from the Debug Data menu of the GUI or via the project file and the keys system.settings.debugOutput and system.settings.debugOutputAutoSave. If debugOutputAutoSave is true, the debug data is written to the temp directory as CSV files (;-separated). The behavior is modified by the model.parameter.debug_clear switch: if true the debug output will be written every year (if auto-save is enabled) and then deleted from the memory. This limits the additional memory footprint of debug outputs (which can be quite high for larger simulations).

Note that these codes can also be combined, i.e. "12" will trigger the two debug outputs "tree growth" and "standlevel NPP".

Debug outputs based on individual trees (Tree NPP, Tree partition, Tree growth) produce potentially huge amounts of data and are therefore filtered by default. Only trees that satisfy the condition provided by the setting debug_tree (see project file ) are allowed producing debug output data.

The following codes trigger the respective debug outputs:

Tree NPP (1)

This output details the calculation of a tree's gross and net primary production (GPP, NPP) for the year. It shows how the available resources and the tree's state translate into potential growth.

NameDescription
Idunique tree Id (numeric)
Species4-character species code (e.g. 'psme')
Dbhdiamter at breast height (cm)
Heighttree height (m)
xx-coordinate of the tree (index of the pixel on the 2m grid)
yy-coordinate of the tree (index of the pixel on the 2m grid)
ru_indexindex of the resource unit that hosts the tree
LRIlight-resource-index of the tree
mStemMassbiomass (kg) of the stem (biomass states before growth)
mCoarseRootMassbiomass (kg) of the coarse roots
mFoliageMassbiomass (kg) of the foliage
mLeafArealeaf area (m2) of the tree
LRI_modifiedThe Light Resource Index after being modified by the resource unit's modifier (e.g., from water stress).
light_responseThe tree's physiological response (0-1) to the modified LRI.
effective_areaThe effective light-intercepting area of the tree (m2), considering its leaf area and light response.
raw_gppThe raw Gross Primary Production (kg biomass) for the tree before accounting for age-related decline.
gppThe final GPP (kg biomass) for the tree after applying the species-specific aging factor.
nppThe Net Primary Production (kg biomass), calculated as GPP reduced by autotrophic respiration losses.
aging_factorThe aging factor (0-1) applied to the tree, which reduces GPP based on its age and height.

Tree partition (2)

The output focuses on how NPP is split between the tree compartments.
Biomass pools are given after growth (at the end of the year).

NameDescription
Idunique tree Id (numeric)
Species4-character species code (e.g. 'psme')
Dbhdiamter at breast height (cm)
Heighttree height (m)
xx-coordinate of the tree (index of the pixel on the 2m grid)
yy-coordinate of the tree (index of the pixel on the 2m grid)
ru_indexindex of the resource unit that hosts the tree
LRIlight-resource-index of the tree
mWoodybiomass (kg) of the stem (biomass states after growth)
mRootbiomass (kg) of the coarse roots
mFoliagebiomass (kg) of the foliage
LAleaf area (m2) of the tree
mFinerootbiomass (kg) of fine roots
mBranchbiomass (kg) of the branches
npp_kgNPP (kg biomass) produced by the tree in this year (note that the state of the reserve pool is added interally for distribution, and that the reserve pool (with increased size) is substracted again)
apct_foliageallocation (0..1) to the foliage compartment
apct_woodfraction of NPP that goes into woody organs (this is: stem, branches, reserve)
apct_rootfraction of NPP that is routed to the roots (coarse + fine roots)
delta_foliagenet increment of foliage biomass (kg)
delta_woodynet increment of woody compartments (stem and branches, flow to reserve already subtracted).
delta_rootnet increment (kg) of roots (fine + coarse)
biomass_lossbiomass (kg) that is lost due to senescene (fine roots, foliage) and coarse root turnover
mNPPReserveamount of the NPP reserve at the end of the year (kg)
netStemIncbiomass increment (kg) of the stem (branch increment: delta_woody - netStemInc)
stress_index Carbon balance based stress index (see base mortality )

Tree growth (4)

This output details the calculation of the stem diameter and height increment based on the net stem NPP allocated for the year.

NameDescription
Idunique tree Id (numeric)
Species4-character species code (e.g. 'psme')
Dbhdiamter at breast height (cm)
Heighttree height (m)
xx-coordinate of the tree (index of the pixel on the 2m grid)
yy-coordinate of the tree (index of the pixel on the 2m grid)
ru_indexindex of the resource unit that hosts the tree
LRIlight-resource-index of the tree
mStemMassbiomass (kg) of the stem (biomass states before growth)
mCoarseRootMassbiomass (kg) of the coarse roots
mFoliageMassbiomass (kg) of the foliage
mLeafArealeaf area (m2) of the tree
net_stem_nppThe portion of NPP (kg biomass) allocated to stem growth for the year.
stem_mass_beforeThe tree's stem mass (kg) at the beginning of the year, before the current increment is added.
hd_growth_ratioThe relative height-to-diameter growth ratio for the year, determined by the tree's light environment (LRI).
factor_diameterA calculated conversion factor representing the diameter increment per kg of stem NPP.
dbh_inc_estimate_cmAn initial estimate of the diameter increment (cm) for the year.
dbh_inc_final_cmThe final calculated diameter increment (cm) for the year after iterative correction.

Standlevel GPP (8)

The output gives raw values for GPP productivity on resource unit x species level.

NameDescription
speciesshort name of the species
RU_index0-based index of resource unit
ridID of the resource unit (0 if no IDs are provided)
laileaf area index (m2/m2) for trees >4m height of the species
gpp_kg_m2 GPP production (yearly) (kg Biomass) per m2 (stocked area)
gpp_kgTotal GPP (kg Biomass) of the species on the whole resource unit (i.e., gpp_kg_m2 * stocked_area_m2)
avg_agingAverage aging factor (0..1) of the species' trees on the resource unit.
f_env_yrAggregated environmental factor 0..1 for the year, used for sapling growth calculations. See sapling growth and competition for details on on $f_{env,yr}$

Water Cycle (16)

This output details the daily calculations of the water balance for a resource unit. The permafrost-related columns are only populated with meaningful values if the permafrost module is enabled in the project file; otherwise, they will be zero.

NameDescription
dateDate of the day (yyyymmdd) from the climate record.
ruindexIndex of the RU (0-based).
ridID of the resource unit.
tempAverage day temp (°C).
vpdVapour pressure deficit of the day (kPa).
precPrecipitation of the day (mm).
radGlobal radiation (MJ/m2).
combined_responseCombined daily response modifier (0-1) of all species on the RU, representing the minimum of the water and VPD responses.
after_interceptPrecipitation that reaches the ground after canopy interception (mm).
after_snowWater input to the soil after accounting for the snow pack (i.e., snowmelt or rain passing through) (mm).
et_canopyEvapotranspiration of the day from the canopy (mm).
evapo_interceptedEvaporation from intercepted water on the canopy (mm).
contentCurrent soil water content at the end of the day, after evapotranspiration (mm).
psi_kpaSoil water potential (kPa) at the beginning of the day, before evapotranspiration.
excess_mmWater that leaves the soil profile as runoff or deep percolation (mm).
snow_heightCurrent snow height (mm).
lai_effectiveEffective leaf area index (m2/m2), i.e. the sum of LAI of adult trees, saplings, and ground vegetation.
pf_topDepth of the top of the frozen soil layer (m). During summer thaw, this value increases from zero.
pf_bottomDepth of the bottom of the frozen soil layer (m).
pf_freezebackDepth of the soil layer that is freezing from the surface downwards during autumn (m).
pf_delta_water_mmDaily change (mm) in the liquid water pool due to thawing (+) or freezing (-) of soil water.
pf_delta_soil_mDaily change in the depth of the unfrozen soil column (m).
pf_k_unfrozenThermal conductivity of the unfrozen soil (W/m/K).
pf_soil_frozen_mTotal current depth of frozen soil (m).
pf_water_frozen_mmTotal water currently held in the frozen soil layer (mm).
pf_unfrozen_fc_mmThe current field capacity (mm) of the unfrozen portion of the soil.
moss_f_lightLight limitation factor (0-1) for moss growth on the current day.
moss_f_deciduousDeciduous litter inhibition factor (0-1) for moss growth on the current day.

Daily responses (32)

This output provides a detailed look at the monthly response functions for each species on a resource unit. These response functions are modifiers (typically 0-1) that represent limitations on growth due to various environmental factors. The final utilizableRadiation is the culmination of these factors applied to the absorbed radiation. Note that while the output is logged daily, the response values themselves are calculated and reported as monthly averages or sums.

NameDescription
day_idUnique identifier for the day of the year (yyyymmdd).
ru_index0-based index of the resource unit.
ru_idUser-defined ID of the resource unit.
species4-character species code.
tempAverage daily temperature (°C).
vpdVapour Pressure Deficit of the day (kPa).
radGlobal radiation of the day (MJ/m2).
resp_soilMonthly average of the daily soil water response modifier (0-1). A value of 1 indicates no water limitation.
resp_vpdMonthly average of the daily Vapour Pressure Deficit (VPD) response modifier (0-1). A value of 1 indicates no limitation from atmospheric drought.
resp_tempMonthly average of the daily temperature response modifier (0-1). A value of 1 indicates optimal temperature for growth.
resp_meteoThe monthly meteorological response, calculated as the monthly average of the daily minimum of soil water, VPD, and temperature responses.
resp_phenoMonthly phenology response (0 or 1), indicating if the species is photosynthetically active during the month.
resp_co2The CO2 fertilization effect modifier for the month, based on atmospheric CO2 concentration.
apar_mj_m2The total absorbed photosynthetically active radiation (APAR) for the month (MJ/m2).
resp_daylengthMonthly average of the daily daylength response modifier (0-1).
utilizable_radThe utilizable radiation for the month (MJ/m2). This is the APAR value after being reduced by all preceding response modifiers (meteo, pheno, co2, daylength).

Establishment (64)

Note: The debug output is only created if seeds of the species are present on the resource unit.

NameDescription
speciesshort name of the species
RU_index0-based index of resource unit
ridID of the resource unit (0 if no IDs are provided)
avgSeedDensityAverage seed density of the species on the resource unit.
TACAminTempBoolean switch (true/false). Is false if the daily minimum temperature drops below the species-specific threshold. If false, establishment is not possible.
TACAchillBoolean switch (true/false). Is true if the species' chilling requirement is met. If false, establishment is not possible.
TACAfrostFreeBoolean switch (true/false). Is true if the number of frost-free days exceeds the species-specific threshold. If false, establishment is not possible.
TACAgddBoolean switch (true/false). Is true if the calculated growing degree days (GDD) are within the species-specific min/max thresholds. If false, establishment is not possible.
frostDaysAfterBudburstThe number of frost days (Tmin <= 0°C) that occur after bud burst. This value is used to calculate a frost damage effect.
waterLimitationA value from 0 to 1 indicating the limitation on establishment due to soil water availability. A value of 1 means no limitation.
GDDThe calculated growing degree days for the year.
pAbioticThe final probability (0-1) for establishment based on the abiotic environment. It is a multiplicative combination of the effects of frost after bud burst, water limitation, and limitations by the soil organic layer depth. It is only > 0 if all TACA-requirements (TACAminTemp, TACAchill, TACAfrostFree, TACAgdd) are met.
fEnvYrThe aggregated environmental factor 0..1 from the 3PG production model for the resource unit and year.
newSaplingsThe number of new saplings of the species established on the resource unit in the current year.


Sapling Growth (128)

This output provides detailed statistics on the population dynamics of saplings (trees < 4m height) for each species on a resource unit. It is only created if there are living saplings of a species on the resource unit.

NameDescription
speciesShort name of the species.
RU_index0-based index of the resource unit.
ridUser-defined ID of the resource unit.
Living_cohortsNumber of living sapling cohorts for the species on the resource unit at the end of the year.
averageHeightAverage height (m) of all surviving sapling cohorts.
averageAgeAverage age (years) of all surviving sapling cohorts.
avgDeltaHPotAverage potential height increment (m) for the year, before considering competition effects.
avgDeltaHRealizedAverage realized height increment (m) for the year, after accounting for competition and environmental factors.
addedNumber of new sapling cohorts established from seed in the current year.
addedVegetativeNumber of new sapling cohorts created by vegetative sprouting in the current year.
diedNumber of sapling cohorts that died due to environmental stress in the current year.
recruitedNumber of sapling cohorts that grew taller than the 4m threshold and were recruited as adult trees into the main model.
refRatioThe species-specific reference ratio parameter, used for scaling sapling growth responses. See sapling growth and competition.
carbonLivingTotal carbon (kg) stored in the biomass of all living saplings at the end of the year.
carbonGainNet carbon gain (kg) of the sapling pool during the current year.

Carbon Cycle (256)

This output details the state of various carbon and nitrogen pools and their fluxes for each resource unit. Note that values for snags (standing and downed dead wood) are for the stockable area of the resource unit, while the soil values (from the ICBM/2N model) are scaled to a full hectare.

NameDescription
SnagState_cTotal carbon content in all snag pools (standing dead wood, coarse roots, branches) (kg/ha).
TotalC_inTotal carbon input into all snag pools from tree mortality (kg/ha).
TotalC_toAtmTotal carbon flux to the atmosphere from the decay of all snag pools (kg/ha).
SWDtoDWD_c,SWDtoDWD_nCarbon and Nitrogen flux from standing dead wood (SWD) to downed dead wood (DWD) (kg/ha).
toLabile_c, toLabile_nTotal C and N flux into the labile soil pool from litterfall and fine root turnover (kg/ha).
toRefr_c, to_Refr_nTotal C and N flux into the refractory soil pool from the decay of coarse woody debris (kg/ha).
for each class X=1..3
swdX_c, swdX_nCarbon and Nitrogen content in standing woody debris (SWD) class X (kg/ha).
swdX_countNumber of individual snags in SWD class X.
swdX_tsdAverage time since death (years) for snags in SWD class X.
dbhXAverage DBH (cm) of snags in SWD class X.
heightXAverage height (m) of snags in SWD class X.
volumeXAverage volume (m³) of snags in SWD class X.
toSwdX_c, toSwdX_nInput flux of Carbon and Nitrogen into SWD class X from tree mortality (kg/ha).
other wood classes: X: 1..5
otherWoodX_c, otherWoodX_nCarbon and Nitrogen content of other woody debris classes (e.g., branches, coarse roots) (kg/ha).
Soil (ICBM/2N)
iLabC, iLabNCarbon and Nitrogen input to the soil's labile pool (t/ha).
iKylDecomposition rate of the labile input pool.
iRefC, iRefNCarbon and Nitrogen input to the soil's refractory pool (t/ha).
iKyrDecomposition rate of the refractory input pool.
reClimate modifier for decomposition, based on temperature and moisture.
kyl, kyrCurrent annual decomposition rates for the labile and refractory pools, respectively.
ylC, yLNState of the young labile matter pool (C, N) in t/ha.
yrC, yrNState of the young refractory matter pool (C, N) in t/ha.
somC, somNState of the old soil organic matter pool (C, N) in t/ha.
NAvailableTotal calculated plant-available nitrogen for the year (kg/ha).
NAVLabPlant-available nitrogen mineralized from the labile pool (kg/ha/yr).
NAVRefPlant-available nitrogen mineralized from the refractory pool (kg/ha/yr).
NAVSomPlant-available nitrogen mineralized from the old SOM pool, also including atmospheric N deposition (kg/ha/yr).

Performance (512)

This output provides a summary of key model performance metrics for each simulation year, including counts of simulated entities and execution times for major model processes. The time values are reported in milliseconds (ms).

NameDescription
yearYear of the simulation.
treeCountTotal number of individual trees (> 4m height) in the simulation.
saplingCountTotal number of sapling cohorts (< 4m height) in the simulation.
newSaplingsNumber of sapling cohorts newly established in the current year.
managementExecution time spent in the management module (ms).
applyPatternExecution time for applying the Light Influence Patterns (LIP) of all trees to the light grid (ms).
readPatternExecution time for reading the light grid and calculating the Light Resource Index (LRI) for all trees (ms).
treeGrowthExecution time spent in the individual tree growth, partitioning, and mortality routines (ms).
seedDistributionExecution time for the seed dispersal module (ms).
establishmentExecution time for the sapling establishment routine (ms).
saplingGrowthExecution time for the growth of all sapling cohorts (ms).
carbonCycleExecution time for the carbon cycle module, including snag and soil dynamics (ms).
writeOutputTime spent writing the standard database outputs (ms).
totalYearTotal execution time for the entire year's simulation loop (ms).

Dynamic Output

The dynamic output produces statistics for all trees in the simulation. The "dynamic" output is configured in the project file section "output" (output.dynamic) and switched on/off there. In addition, the dynamic debug output can be switched on/off using the Globals Javascript function Globals.startOutput("debug_dynamic") and stopOutput().
The defintion of columns is similar to the dynamic stand output.

Example for the section in the project file:

<dynamic> <!-- clipboard -->
      <!-- free defined output that uses expressions/filter on all trees of the simulation -->
      <enabled>false</enabled>
      <columns>dbh.mean, dbh.max, dbh.min, dbh.p5, dbh.p25, dbh.p75, dbh.p95,
	  height.mean, height.max, height.min, height.p5,height.p95, height.p25,height.p75,
	  stress.mean, stress.max, if(stress>0,1,0).sum, if(stress>0,stress,0).sum, if(dbh>0,1,0).sum,
	  leafarea.sum,woodymass.sum,rootmass.sum,foliagemass.sum
      </columns>
    </dynamic>


Created by werner. Last Modification: Friday 06 of June, 2025 07:50:38 GMT by werner.