The permafrost module of iLand simulates permafrost and soil-surface organic layer (SOL) dynamics at a fine spatial (1 ha) and temporal (daily) resolution. It efficiently models daily changes in permafrost depth, annual SOL accumulation, and their complex effects on boreal forest structure and functions.

Permafrost Dynamics


The module simulates the annual freeze-thaw cycle of the active layer, driven by heat transfer from the atmosphere and the deeper permafrost layer. Key elements include:

  • Active Layer: The top layer of soil that freezes and thaws annually.
  • Zero Isoline: The depth where the soil temperature is 0°C, separating frozen and thawed soil.
  • Energy Fluxes:
  •  Primary Flux: Heat transfer from the atmosphere to the soil, driving active layer dynamics.
  •  Secondary Flux: Heat transfer from the deeper permafrost layer, influencing the freezing process.
  • Resistances: Thermal resistances of snow, SOL, and mineral soil are considered to affect heat transfer.
  • Snow Depth: Modeled as a function of precipitation and temperature, affecting the insulating properties of the soil

Soil Organic Layer (SOL):

  •  Composition: Includes litter and dead moss.
  •  Dynamics: Depth is modeled based on litter and coarse wood production and decomposition.
  •  Thermal Conductivity: Varies with soil moisture and texture.

SOL and Moss Dynamics


The module also simulates the growth dynamics of the moss layer, which plays a crucial role in insulating the permafrost. Key features include:

  • Moss Growth: Influenced by light availability (affected by canopy cover), temperature, and litter accumulation.
  • Moss Litter: Decomposes and contributes to the SOL, influencing its insulating properties.
  • Effects on Ecosystem:
  • Tree Establishment: Thick SOL layers can hinder tree seedling establishment.
  • Water Cycle: Permafrost and SOL depth affect water availability for trees.
  • Fire Dynamics: The moss layer acts as both fuel and insulation in fire events.

Settings in the project file

The “permafrost” section is a sub-section of “model.settings”. Example with full names: model.settings.permafrost.lambdaSnow, model.settings.permafrost.moss.light_sat. To enable / switch on the module, set model.settings.permafrost.enabled to true.


Key

Datatype

Description

enabled

Boolean

Permafrost sub module switched on when true

onlySimulate

Boolean

if true, permafrost is calculated but has no effect on the water cycle

initialGroundTemperature

numeric

Initial temperature in depth ‘groundBaseDepth’ below the active layer: at depth "groundBaseDepth" the temperature is assumed to remain +- constant within a year and to follow MAT with a 10yr delay. The initial value is given with 'initialGroundTemperature'. and the depth from which thermal energy flows

initialDepthFrozen

Numeric

depth (m) up to which the soil is frozen at the start of the simulation (1st of January). For permanent permafrost the value is capped at 2m.

groundBaseDepth

Numeric

depth (m) of the zone below the active layer from where the secondary heat flux (from below) originates

lambdaOrganicLayer
Numeric
thermal conductivity W/m*K of soil organic layer and moss

organicLayerDensity

Numeric

density (kg/m3) of the soil organic layer (default: 50)

organicLayerDefaultDepth

Numeric

depth of the soil organic layer (m) (only relevant when dynamic carbon cycle is disabled) (default: 0.1)

maxFreezeThawPerDay

Numeric

cap for daily freezing and thawing (mm water column)

Section moss
   

biomass

Numeric

initial life moss kg/ha

bulk_density

Numeric

Density of the moss layer (kg/m3)

light_k

Numeric

Light extinction coefficient used for tree canopy and moss

light_comp

Numeric

light compensation point: light level (proportion of light above canopy) above which photosynthesis is possible

light_sat

Numeric

light saturation point: level of light (relative to light level above canopy) above which an increase in light does not increase GPP

respiration_b

Numeric

Annual loss of moss biomass due to respiration (flux to atmosphere)

respiration_q

numeric

Annual loss of moss biomass due to turnover (flux to litter)

CNRatio

Numeric

CN-ratio of moss litter entering the litter pool of iLand

r_decomp

Numeric

Decomposition rate of moss litter that enters the litter pool of iLand

r_deciduous_inhibition

Numeric

Parameter to calculate inhibition effect of fresh broadleaved litter (default: 0.45)

Related (new) parameters


Key

Datatype

Description

model.settings.snowDensity

Numeric

Density of snow in kg/m³ (default: 300)

model.settings.snowInitialDepth

Numeric

Depth of the snow pack (in m) at the start of the simulation (default: 0)

 

Permafrost visualization

When the permafrost module is enabled, you can visualize certain aspects in iLand. The following layers are available in the 'permafrost' section:


Option

description

maxDepthFrozen

maximum depth of freezing (m). Is 2m for full freeze.

maxDepthThawed

maximum depth of thawing (m). Is 2m for fully thawed soil

deepSoilTemperature

temperature of ground deep below the soil (C)

maxSnowCover

maximum snow height (cm)

SOLDepth

depth of the soil organic layer (litter+dead moss) (cm)

moss

depth of the life moss layer (cm)

Note that you can access / retrieve those grids in Javascript, e.g., to save them as files for external analysis.

 

The (new) species parameter “estSOLthickness” is used to specify the species-specific establishment response to thick soil organic layer (0: no effect).

Water-Output

Columns related to permafrost in the water output (annual timesteps)


Column

description

maxDepthFrozen

Permafrost: maximum depth of freezing (m). The value is 2m when soil is fully frozen in a year."

maxDepthThawed

Permafrost: maximum depth of thawing (m). The value is 2m if soil is fully thawed in a year.

maxSnowCover

Permafrost: maximum snow height (m) in a year.

SOLLayer

Permafrost: total depth of soil organic layer (excl. life moss) (m).

mossLayer

depth of the life moss layer (m).

 

Debug-Output (water)

Daily values for the state of permafrost (per resource unit) are in the water-debug output:


Column

description

pftop

top of frozen layer (m) when thawing (above that soil is thawed)

pfbottom

bottom of the frozen layer (m) (important for seasonal permafrost; soil is frozen *up to* this depth), for permanent permafrost, the bottom is 2m

pffreezeback

depth (m) up to which the soil is frozen again (in autumn)

delta_mm

change of water (mm within iLand water bucket), freezing is negative

delta_soil

change of ice layer (m) (within iLand water bucket), freezing is negative

thermalConductivity

Current conductivity of mineral soil W / m2 / K

soilfrozen

depth of soil (m) that is currently frozen (this is a part of the soil plant accessible soil)

waterfrozen

amount of water (mm) trapped currently in ice

current_capacity

Current field capacity of the (non-frozen) soil bucket (mm)

moss_fLight

Value of the light response for moss growth

moss_fDecid

Value of the limiting factor of deciduous litter

moss_fCanopy

Response value for the drying out  effect due to canopy openness

 

 Creating custom permafrost graphs

 

# R example code
# rids: data.frame with a selection of resource ids
# dbg_wc: file created by debug output
ggplot( rids %>% left_join(dbg_wc) %>% group_by(rid, year) %>% mutate(n=row_number()) %>% ungroup() %>% 
          mutate(   groundice.high = pmax(pftop, pffreezeback), 
                    topice.min = pmin(pftop, pffreezeback)), aes(x=n)) + 
  geom_ribbon( aes( ymax=2, ymin=pfbottom), fill="lightblue" ) + 
  geom_ribbon( aes( ymax=pfbottom, ymin=groundice.high), fill="darkgray" ) + 
  geom_ribbon( aes( ymax=groundice.high, ymin=topice.min), fill="lightblue" ) + 
  geom_ribbon( aes( ymax=topice.min, ymin=0), fill="darkgray" ) + 
  geom_ribbon (aes( ymax= -snow_height/300, ymin=0), fill="lightgray") +
  geom_line (aes(y=-temp/100)) +
  scale_y_reverse() + facet_wrap(~round(tmean,2)) + theme_bw()


Image

The code creates figures such as: