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.

Name	Description
Id	unique tree Id (numeric)
Species	4-character species code (e.g. 'psme')
Dbh	diamter at breast height (cm)
Height	tree height (m)
x	x-coordinate of the tree (index of the pixel on the 2m grid)
y	y-coordinate of the tree (index of the pixel on the 2m grid)
ru_index	index of the resource unit that hosts the tree
LRI	light-resource-index of the tree
mStemMass	biomass (kg) of the stem (biomass states before growth)
mCoarseRootMass	biomass (kg) of the coarse roots
mFoliageMass	biomass (kg) of the foliage
mLeafArea	leaf area (m2) of the tree
LRI_modified	The Light Resource Index after being modified by the resource unit's modifier (e.g., from water stress).
light_response	The tree's physiological response (0-1) to the modified LRI.
effective_area	The effective light-intercepting area of the tree (m2), considering its leaf area and light response.
raw_gpp	The raw Gross Primary Production (kg biomass) for the tree before accounting for age-related decline.
gpp	The final GPP (kg biomass) for the tree after applying the species-specific aging factor.
npp	The Net Primary Production (kg biomass), calculated as GPP reduced by autotrophic respiration losses.
aging_factor	The 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).

Name	Description
Id	unique tree Id (numeric)
Species	4-character species code (e.g. 'psme')
Dbh	diamter at breast height (cm)
Height	tree height (m)
x	x-coordinate of the tree (index of the pixel on the 2m grid)
y	y-coordinate of the tree (index of the pixel on the 2m grid)
ru_index	index of the resource unit that hosts the tree
LRI	light-resource-index of the tree
mWoody	biomass (kg) of the stem (biomass states after growth)
mRoot	biomass (kg) of the coarse roots
mFoliage	biomass (kg) of the foliage
LA	leaf area (m2) of the tree
mFineroot	biomass (kg) of fine roots
mBranch	biomass (kg) of the branches
npp_kg	NPP (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_foliage	allocation (0..1) to the foliage compartment
apct_wood	fraction of NPP that goes into woody organs (this is: stem, branches, reserve)
apct_root	fraction of NPP that is routed to the roots (coarse + fine roots)
delta_foliage	net increment of foliage biomass (kg)
delta_woody	net increment of woody compartments (stem and branches, flow to reserve already subtracted).
delta_root	net increment (kg) of roots (fine + coarse)
biomass_loss	biomass (kg) that is lost due to senescene (fine roots, foliage) and coarse root turnover
mNPPReserve	amount of the NPP reserve at the end of the year (kg)
netStemInc	biomass 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.

Name	Description
Id	unique tree Id (numeric)
Species	4-character species code (e.g. 'psme')
Dbh	diamter at breast height (cm)
Height	tree height (m)
x	x-coordinate of the tree (index of the pixel on the 2m grid)
y	y-coordinate of the tree (index of the pixel on the 2m grid)
ru_index	index of the resource unit that hosts the tree
LRI	light-resource-index of the tree
mStemMass	biomass (kg) of the stem (biomass states before growth)
mCoarseRootMass	biomass (kg) of the coarse roots
mFoliageMass	biomass (kg) of the foliage
mLeafArea	leaf area (m2) of the tree
net_stem_npp	The portion of NPP (kg biomass) allocated to stem growth for the year.
stem_mass_before	The tree's stem mass (kg) at the beginning of the year, before the current increment is added.
hd_growth_ratio	The relative height-to-diameter growth ratio for the year, determined by the tree's light environment (LRI).
factor_diameter	A calculated conversion factor representing the diameter increment per kg of stem NPP.
dbh_inc_estimate_cm	An initial estimate of the diameter increment (cm) for the year.
dbh_inc_final_cm	The 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.

Name	Description
species	short name of the species
RU_index	0-based index of resource unit
rid	ID of the resource unit (0 if no IDs are provided)
lai	leaf area index (m2/m2) for trees >4m height of the species
gpp_kg_m2	GPP production (yearly) (kg Biomass) per m2 (stocked area)
gpp_kg	Total GPP (kg Biomass) of the species on the whole resource unit (i.e., gpp_kg_m2 * stocked_area_m2)
avg_aging	Average aging factor (0..1) of the species' trees on the resource unit.
f_env_yr	Aggregated 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.

Name	Description
date	Date of the day (yyyymmdd) from the climate record.
ruindex	Index of the RU (0-based).
rid	ID of the resource unit.
temp	Average day temp (°C).
vpd	Vapour pressure deficit of the day (kPa).
prec	Precipitation of the day (mm).
rad	Global radiation (MJ/m2).
combined_response	Combined daily response modifier (0-1) of all species on the RU, representing the minimum of the water and VPD responses.
after_intercept	Precipitation that reaches the ground after canopy interception (mm).
after_snow	Water input to the soil after accounting for the snow pack (i.e., snowmelt or rain passing through) (mm).
et_canopy	Evapotranspiration of the day from the canopy (mm).
evapo_intercepted	Evaporation from intercepted water on the canopy (mm).
content	Current soil water content at the end of the day, after evapotranspiration (mm).
psi_kpa	Soil water potential (kPa) at the beginning of the day, before evapotranspiration.
excess_mm	Water that leaves the soil profile as runoff or deep percolation (mm).
snow_height	Current snow height (mm).
lai_effective	Effective leaf area index (m2/m2), i.e. the sum of LAI of adult trees, saplings, and ground vegetation.
pf_top	Depth of the top of the frozen soil layer (m). During summer thaw, this value increases from zero.
pf_bottom	Depth of the bottom of the frozen soil layer (m).
pf_freezeback	Depth of the soil layer that is freezing from the surface downwards during autumn (m).
pf_delta_water_mm	Daily change (mm) in the liquid water pool due to thawing (+) or freezing (-) of soil water.
pf_delta_soil_m	Daily change in the depth of the unfrozen soil column (m).
pf_k_unfrozen	Thermal conductivity of the unfrozen soil (W/m/K).
pf_soil_frozen_m	Total current depth of frozen soil (m).
pf_water_frozen_mm	Total water currently held in the frozen soil layer (mm).
pf_unfrozen_fc_mm	The current field capacity (mm) of the unfrozen portion of the soil.
moss_f_light	Light limitation factor (0-1) for moss growth on the current day.
moss_f_deciduous	Deciduous 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.

Name	Description
day_id	Unique identifier for the day of the year (yyyymmdd).
ru_index	0-based index of the resource unit.
ru_id	User-defined ID of the resource unit.
species	4-character species code.
temp	Average daily temperature (°C).
vpd	Vapour Pressure Deficit of the day (kPa).
rad	Global radiation of the day (MJ/m2).
resp_soil	Monthly average of the daily soil water response modifier (0-1). A value of 1 indicates no water limitation.
resp_vpd	Monthly average of the daily Vapour Pressure Deficit (VPD) response modifier (0-1). A value of 1 indicates no limitation from atmospheric drought.
resp_temp	Monthly average of the daily temperature response modifier (0-1). A value of 1 indicates optimal temperature for growth.
resp_meteo	The monthly meteorological response, calculated as the monthly average of the daily minimum of soil water, VPD, and temperature responses.
resp_pheno	Monthly phenology response (0 or 1), indicating if the species is photosynthetically active during the month.
resp_co2	The CO2 fertilization effect modifier for the month, based on atmospheric CO2 concentration.
apar_mj_m2	The total absorbed photosynthetically active radiation (APAR) for the month (MJ/m2).
resp_daylength	Monthly average of the daily daylength response modifier (0-1).
utilizable_rad	The 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.

Name	Description
species	short name of the species
RU_index	0-based index of resource unit
rid	ID of the resource unit (0 if no IDs are provided)
avgSeedDensity	Average seed density of the species on the resource unit.
TACAminTemp	Boolean switch (true/false). Is false if the daily minimum temperature drops below the species-specific threshold. If false, establishment is not possible.
TACAchill	Boolean switch (true/false). Is true if the species' chilling requirement is met. If false, establishment is not possible.
TACAfrostFree	Boolean switch (true/false). Is true if the number of frost-free days exceeds the species-specific threshold. If false, establishment is not possible.
TACAgdd	Boolean 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.
frostDaysAfterBudburst	The number of frost days (Tmin <= 0°C) that occur after bud burst. This value is used to calculate a frost damage effect.
waterLimitation	A value from 0 to 1 indicating the limitation on establishment due to soil water availability. A value of 1 means no limitation.
GDD	The calculated growing degree days for the year.
pAbiotic	The 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.
fEnvYr	The aggregated environmental factor 0..1 from the 3PG production model for the resource unit and year.
newSaplings	The 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.

Name	Description
species	Short name of the species.
RU_index	0-based index of the resource unit.
rid	User-defined ID of the resource unit.
Living_cohorts	Number of living sapling cohorts for the species on the resource unit at the end of the year.
averageHeight	Average height (m) of all surviving sapling cohorts.
averageAge	Average age (years) of all surviving sapling cohorts.
avgDeltaHPot	Average potential height increment (m) for the year, before considering competition effects.
avgDeltaHRealized	Average realized height increment (m) for the year, after accounting for competition and environmental factors.
added	Number of new sapling cohorts established from seed in the current year.
addedVegetative	Number of new sapling cohorts created by vegetative sprouting in the current year.
died	Number of sapling cohorts that died due to environmental stress in the current year.
recruited	Number of sapling cohorts that grew taller than the 4m threshold and were recruited as adult trees into the main model.
refRatio	The species-specific reference ratio parameter, used for scaling sapling growth responses. See sapling growth and competition.
carbonLiving	Total carbon (kg) stored in the biomass of all living saplings at the end of the year.
carbonGain	Net 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.

Name	Description
SnagState_c	Total carbon content in all snag pools (standing dead wood, coarse roots, branches) (kg/ha).
TotalC_in	Total carbon input into all snag pools from tree mortality (kg/ha).
TotalC_toAtm	Total carbon flux to the atmosphere from the decay of all snag pools (kg/ha).
SWDtoDWD_c,SWDtoDWD_n	Carbon and Nitrogen flux from standing dead wood (SWD) to downed dead wood (DWD) (kg/ha).
toLabile_c, toLabile_n	Total C and N flux into the labile soil pool from litterfall and fine root turnover (kg/ha).
toRefr_c, to_Refr_n	Total 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_n	Carbon and Nitrogen content in standing woody debris (SWD) class X (kg/ha).
swdX_count	Number of individual snags in SWD class X.
swdX_tsd	Average time since death (years) for snags in SWD class X.
dbhX	Average DBH (cm) of snags in SWD class X.
heightX	Average height (m) of snags in SWD class X.
volumeX	Average volume (m³) of snags in SWD class X.
toSwdX_c, toSwdX_n	Input flux of Carbon and Nitrogen into SWD class X from tree mortality (kg/ha).
other wood classes: X: 1..5
otherWoodX_c, otherWoodX_n	Carbon and Nitrogen content of other woody debris classes (e.g., branches, coarse roots) (kg/ha).
Soil (ICBM/2N)
iLabC, iLabN	Carbon and Nitrogen input to the soil's labile pool (t/ha).
iKyl	Decomposition rate of the labile input pool.
iRefC, iRefN	Carbon and Nitrogen input to the soil's refractory pool (t/ha).
iKyr	Decomposition rate of the refractory input pool.
re	Climate modifier for decomposition, based on temperature and moisture.
kyl, kyr	Current annual decomposition rates for the labile and refractory pools, respectively.
ylC, yLN	State of the young labile matter pool (C, N) in t/ha.
yrC, yrN	State of the young refractory matter pool (C, N) in t/ha.
somC, somN	State of the old soil organic matter pool (C, N) in t/ha.
NAvailable	Total calculated plant-available nitrogen for the year (kg/ha).
NAVLab	Plant-available nitrogen mineralized from the labile pool (kg/ha/yr).
NAVRef	Plant-available nitrogen mineralized from the refractory pool (kg/ha/yr).
NAVSom	Plant-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).

Name	Description
year	Year of the simulation.
treeCount	Total number of individual trees (> 4m height) in the simulation.
saplingCount	Total number of sapling cohorts (< 4m height) in the simulation.
newSaplings	Number of sapling cohorts newly established in the current year.
management	Execution time spent in the management module (ms).
applyPattern	Execution time for applying the Light Influence Patterns (LIP) of all trees to the light grid (ms).
readPattern	Execution time for reading the light grid and calculating the Light Resource Index (LRI) for all trees (ms).
treeGrowth	Execution time spent in the individual tree growth, partitioning, and mortality routines (ms).
seedDistribution	Execution time for the seed dispersal module (ms).
establishment	Execution time for the sapling establishment routine (ms).
saplingGrowth	Execution time for the growth of all sapling cohorts (ms).
carbonCycle	Execution time for the carbon cycle module, including snag and soil dynamics (ms).
writeOutput	Time spent writing the standard database outputs (ms).
totalYear	Total 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>