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@APES_IO_readme.txt
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@APES_IO_readme.txt
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Samuli Launiainen (Luke) 13.1.2016
samuli.launiainen@luke.fi
**************************************************
APES -model input / output class.
All outputs are in Matlab Struct-variables, defined as below
oMeteo =
%above-ground microclimatic profiles
%rows: 1=ground, end=upper boundary
%columns: timesteps
time: [96x4 single] %[YYYY jday hh mm]
U: [200x96 single] %wind speed, m/s
T: [200x96 single] %degC
H2O: [200x96 single] %mol/mol
CO2: [200x96 single] %mol/mol
WatStor: [200x96 single] %stand layer water storage (kg H2O /m2 ground = mm)
df: [200x96 single] %stand layer dry fraction (-)
Trfall: [200x96 single] %Throughfall rate (mm/s) at each stand layer
oRadi = %radiation-related outputs
time: [96x4 single] %[YYYY jday hh mm]
f_sl: [200x96 single] %sunlit fraction of foliage at each stand layer (-)
SWb1: [200x96 single] %direct PAR (Wm-2 ground) at layer
SWd1: [200x96 single] %diffuse PAR
SWu1: [200x96 single] %upward-reflected PAR
SWb2: [200x96 single] %direct NIR (Wm-2 ground) at layer
SWd2: [200x96 single] %diffuse NIR (Wm-2 ground) at layer
SWu2: [200x96 single] %upward-reflected NIR
LWnet: [200x96 single] %net longwave budget (Wm-2 ground at layer)
LWup: [200x96 single] %upward longwave (Wm-2) at layer
LWdn: [200x96 single] %downward -"-
LWleaf: [200x96 single] %net longwave (Wm-2 leaf) at leaf surface in a layer
alb1: [1x96 single] %Stand-level PAR-albedo (-)
alb2: [1x96 single] %Stand-level NIR-albedo (-)
alb_glob: [1x96 single] %Stand-level broadband-albedo (for global radiation, alb1 and alb2 weighted for total incoming PAR & NIR, respectively (-)
q_sl1: [200x96 single] %absorbed PAR at sunlit leaf in a layer (Wm-2 leaf)
q_sh1: [200x96 single] %absorbed PAR at shaded leaf in a layer (Wm-2 leaf)
q_sl2: [200x96 single] %absorbed NIR at sunlit leaf in a layer (Wm-2 leaf)
q_sh2: [200x96 single] %absorbed NIR at shaded leaf in a layer (Wm-2 leaf)
q_floor1: [1x96 single] %absorbed PAR at surface (forest floor + bare ground), (Wm-2 ground)
q_floor2: [1x96 single] %absorbed NIR at surface (forest floor + bare ground), (Wm-2 ground)
oFlux = %flux profiles and sink/source profiles in the canopy air space
%rows: 1=ground, end=top.
%cols: timesteps
time: [96x4 single]
Fc: [200x96 single] %NEE (umol m-2 ground s-1); <0 is net CO2 sink
LE: [200x96 single] %latent heat flux (Wm-2 ground), >0 upwards
E: [200x96 single] %H2O flux (mol m-2 ground s-1)
H: [200x96 single] %sensible heat flux (Wm-2 ground), >0 upwards
G: [1x96 single] %heat conductive flux at soil surface (Wm-2 ground); >0 is towards the soil. If moss layer is included, this is below the moss layer.
Csource: [200x96 single] %CO2 sink/source profile (umol m-3 s-1), <0 is net sink
Esource: [200x96 single] %H2O source/sink profile (mol m-3 s-1)
Hsource: [200x96 single] %Heat source/sink profile (W m-3 = J m-3 s-1)
Rsource: [200x96 double] %Heat source/sink (W m-3) due to 'non-isothermal' component, i.e. radiative conductance term. Relates to linearization of energy balance.
oFloor = %outputs related to weighted fluxes and state variables at forest floor
%cols: timesteps
time: [96x4 single]
T: [1x96 single] %forest floor temperature (deg C)
H: [1x96 single] %sensible heat flux (Wm-2 ground), >0 upward, from the forest floor (weighted based on moss-composition and bare soil)
LE: [1x96 single] %latent heat flux (Wm-2 ground), >0 upward, from the forest floor (weighted based on moss-composition and bare soil)
G: [1x96 double] %heat conductive flux at soil surface (Wm-2 ground); >0 is towards the soil. If moss layer is included, this is below the moss layer.
Fc: [1x96 single] %Forest floor NEE (umol m-2 ground s-1); <0 is net CO2 sink
Rsoil: [1x96 single] %Soil respiration (umol m-2 ground s-1)
Ef: [1x96 single] %Evaporation rate from forest floor (mol m-2 ground s-1), from all mosses & litter), excl. soil evap.
Esoil: [1x96 single] %soil evaporation rate (mol m-2 ground s-1)
Trfall_s: [1x96 single] %throughfall rate (mm/s = kg m-2 ground s-1) that is available for soil infiltration below the moss layer
oBryo = %BryophyteType -specific outputs
%access fields as: oBryo(1).Mdry --> dry mass of Moss_1, oBryo(2).Mdry --> dry mass of Moss_2.
%1st dimension of oBryo refers to BryophyteType -object
time: [96x4 single]
Mdry: [1x96 single] %dry mass (g m-2 ground) of BryophyteType
LAI: [1x96 single] %LAI (m2m-2)
f_cover: [1x96 single] %fractional cover (0...1), (-)
T: [1x96 single] %temperature (degC)
W: [1x96 single] %water content (g H2O / g dry mass)
Theta: [1x96 single] %volumetric water content (m3/m3), water retention curve (pF-curve) gives relationship between Theta and h
h: [1x96 single] %water potential (m). Note -1 m = -10 kPa
GPP: [96x1 single] %gross-primary productivity of specific moss object (umol m-2 ground s-1); i.e. moss phosynthetic rate (umol m-2 ground s-1) * f_cover
Respi: [1x96 single] %autotrophic respiration -"- (umol m-2 ground s-1), i.e. moss respiration rate (umol m-2 ground s-1) * f_cover
Rn: [1x96 single] %net radiation (Wm-2), >0 net gain by moss
LWout: [1x96 single] %upwelling long-wave radiation (Wm-2) from moss
LE: [1x96 single] %latent heat flux (Wm-2) from moss
H: [1x96 single] %sensible heat flux (Wm-2) from moss
G: [1x96 single] %heat conduction between moss and soil (Wm-2), <0 is downwards
dQ: [1x96 single] %change in moss energy storage (Wm-2) during timestep
Fcapi: [1x96 single] %capillary rise from soil to moss object (mm s-1).
oPlant = %PlantType-specific outputs
%1st dimension refers to PlantType -object, i.e. oPlant(1).LAI is LAI of PlantType_1
time: [96x4 single]
LAI: [1x96 single] %leaf-area index (m2m-2) of PlantType, 1-sided (half-total)
WAI: [1x96 single] %woody-area index (m2m-2)
lad: [200x96 single] %leaf-area density (m2m-3)
wad: [200x96 single] %woody-area density (m2m-3)
GPP: [1x96 single] %gross-primary productivity of PlantType (umol m-2 ground s-1);
Respi: [1x96 single] %above-ground autotrophic respiration of PlantType (umol m-2 ground s-1).
Tr: [1x96 single] %Transpiration rate (m s-1); multiply by 1000*dt to get in mm/timestep
RelPhoto_Seasonal: [1x96 single] %Seasonal cycle modifier of photosynthetic capacity (-) ]0, 1]
h_root: [1x96 single] %root-zone effective water potential (m), updated now at midnigt, Note -1 m = -10 kPa
h_leaf: [200x96 single] %leaf water potential (m), assumed to be in hydrostatic equilibrium with h_root as h_leaf=hroot - z, Note -1 m = -10 kPa
RootSink: [33x96 single] %root water sink distibution (s-1). row 1 = uppermost soil layer. sum(Rootsink.*dsz)=Tr
oStand = %outputs related to Stand-object
time: [96x4 single]
LAI: [1x96 single] %total LAI (m2m-2) of all PlantTypes
WAI: [1x96 single] %total WAI (m2m-2) of all PlantTypes
lad: [200x96 single] %total leaf-area density (m2m-3) of all PlantTypes
wad: [200x96 single] %total woody-area density (m2m-3) of all PlantTypes
NrPlantTypes: [1x96 single] %number of active PlantTypes
NrBryoTypes: [1x96 single] % -"- of active BryophyteTypes
f_bryophyte: [1x96 single] % total bryophyte coverage of the soil (-)
f_litter: [1x96 single] % coverage of litter layer
Degree_days: [1x96 single] %degree-day sum (degC)
oSoil = %Soil-related outputs (SoilProfile state and soil fluxes)
%rows: soil layers, 1=uppermost, end =lowest
time: [192x4 single]
h: [33x192 single] %soil water potential (m), -1m = -10kPa
Wliq: [33x192 single] %volumetric liquid water content (m3m-3)
Wice: [33x192 single] %volumetric ice content (m3m-3)
T: [33x192 single] %temperature (degC)
KLh: [33x192 single] %liquid hydraulic conductivity (ms-1)
Ktherm: [33x192 single] %thermal conductivity (Wm-1K-1)
GWL: [1x192 single] %Ground water level (m). if GWL below profile bottom, it is computed from h at lowest node assuming hydrost. equilibrium
Fliq: [33x192 single] %liquid phase vertical water flux (ms-1), <0 downwards
Fvap: [33x192 single] %vapor phase vertical water flux (ms-1), <0 downwards
Fheat: [33x192 single] %heat conduction (Wm-2), >0 downwards
Infil: [1x192 single] %infiltration to soil (mm) during dt
Esoil: [1x192 single] %evaporation from soil (mm) during dt
Drain: [1x192 single] %drainage (mm), to ditch and/or through lower boundary during dt
Roff: [1x192 single] %surface runoff (mm) during dt
h_pond: [1x192 single] %height of ponding water at the surface (m)
RootSink: [33x192 single] %root sink (s-1). Rootsink(1) includes potential capillary rise to mosses. >0 is sink; if <0 then either 'input' or hydraulic lift (depends if included in root uptake model)
HorizFlux: [33x192 single] %horizontal sink/source term (s-1), e.g. due to drainage to ditch.
qtop: [1x192 single] %upper boundary water flux (m s-1), balance of infiltration and evaporation, >0 is upward.
Rsoil: [1x96 single] %soil total respiration rate (umol m-2 s-1)
MBE: [1x192 double] %mass balance error of soil water budget (mm) during dt
%******************OUTPUTS OF LEAF-SCALE FLUXES ETC.******************************
oDLF(1) %dry-leaf fluxes for each PlantType (by LeafModule)
ans =
time: [96x4 single]
sl: [1x1 struct] %sunlit leaves
sh: [1x1 struct] %shaded leaves
oDLF(1).sl %rows: 1=ground, end=uppermost layer. Access fields as oDLF(1).sl.An --> photos. rate of sunlit leaves of PlantType_1
ans =
An: [200x96 single] %photosynthetic rate (umol m-2 leaf s-1)
Rd: [200x96 single] %leaf dark respiration rate (umol m-2 leaf s-1)
E: [200x96 single] %leaf transpiration rate (mol m-2 leaf s-1)
H: [200x96 single] %leaf sensible heat flux (W m-2 leaf s-1)
Tleaf: [200x96 single] %leaf temperature (degC)
Ci: [200x96 single] %CO2 mixing ratio (ppm) inside the leaf (stomatal cavity)
Cs: [200x96 single] %CO2 mixing ratio (ppm) at leaf surface
gsv: [200x96 single] %stomatal conductance (mol m-2 leaf s-1) for H2O
gbv: [200x96 single] %leaf boundary layer conductance (mol m-2 leaf s-1) for H2O
Fr: [200x96 double] %leaf 'radiative heat flux', (W m-2 leaf s-1), related to radiative conductance and linearization of energy balance
oWLF = %fluxes from 'wet' leaves; i.e. values that the leaves would have if they are wet (computed by WetLeafModule)
time: [96x4 single]
Rn: [200x96 single] %leaf isothermal net radiation (Wm-2)
H: [200x96 single] %sensible heat flux rate (W m-2 leaf) from wet leaf
LE: [200x96 single] %latent heat flux rate (W m-2 leaf) from wet leaf
Tleaf: [200x96 single] %wet leaf temperature (degC)
Inter: [200x96 single] %interception at a layer (mm) during dt
Evap: [200x96 single] %evaporation at a condensation (mm) during dt
MBE: [1x96 single] %mass-balance error (mm) during dt (of total water storage in foliage)
Fr: [200x96 double] %leaf 'radiative heat flux', (W m-2 leaf s-1), related to radiative conductance and linearization of energy balance