Module Vegetation
From MohidWiki
Overview
Vegetation Model handles information about vegetation cover and interacts with atmosphere and soil properties. Vegetation dynamics can be handled by the model in two different manners: i) reading from file (time serie, hdf, grid); ii) using a vegetation growth model. The first option is the previous formulation where LAI and root depth properties are provided by user and water uptake is simulated. The second option uses a SWAT based vegetation growth model and plant biomass, LAI, nutrient content and nutrient uptake are explicitly simulated.
SWAT vegetation growth model uses the concepts from EPIC crop model (Izaurralde et al., 2006) of radiation-use efficiency by which a fraction of daily photosynthetically active radiation is intercepted by the plant canopy and converted into plant biomass. Gains in plant biomass are affected by vapor pressure deficits and atmospheric CO2 concentration. Stress indices for water, temperature, nitrogen, phosphorus and aeration are calculated using the value of the most severe of these stresses to reduce potential plant growth and crop yield. Nutrient uptake is done based on plant target (optimal content) and availability in soil.
Concepts
Property
Vegetation model was redesigned to be structured in properties instead of vegetation types. The advantage of this structure is that in the input file the number of properties is fixed (no matter the complexity of the vegetation cover) and input can be preprocessed for the entire grid (see How to pre-process vegetation). In the previous structure, applications with several vegetation covers could rapidly increase input file lines and input errors. More over as they are not graphed in time serie or hdf the visual inspection could take longer.
See the list of allowed properties names
How to Pre-Process Vegetation
Fill Matrix was updated to fill grids without interpolation. Instead of space stations (X,Y coordinate) user has to provide a vegetation grid with ID's and the values assigned to each ID (time serie or single value). Fill Matrix reads ID in the grid and searches for the value to fill the cell. If cells are not filled error message is sent. See FillMatrix for more details
Main processes
If Vegetation is readed from file
If the user chooses the option to simulate vegetation giving properties evolution from file (hdf5, grid), than leaf area index and root depth properties must be given. This option correspond to the old formulation and, yet, only water uptake is simulated.
Water Uptake
This process corresponds to plant transpiration taking water from soil. The user may want to compute a global evapotranspiration or separate transpiration (in plants along the root depth) and evaporation (on soil surface) based on leaf area index. This option is defined in Basin module with the keyword:
EVPOTRANSPIRATION_METHOD: 1/2 (1-Global Evapotranspiration; 2-Transpiration and Evaporation)
Water Uptake in this old formulation is done with Feddes formulation. This means that plant has soil pressure heads tresholds where uptake is optimum and soil heads (under field capacity and below wilting point) where no uptake occurs.
Soil pressure heads tresholds must be provided for each vegetation type in the vegetation file (example below):
!Arable Land - Trigo <beginvegetationtype> ID : 1 NAME : Agriculture FEDDES_H1 : -0.1 FEDDES_H2 : -0.25 FEDDES_H3 : -2.0 FEDDES_H4 : -80.0 <endvegetationtype> !Forest <beginvegetationtype> ID : 2 NAME : Forest FEDDES_H1 : -0.1 FEDDES_H2 : -0.25 FEDDES_H3 : -6.0 FEDDES_H4 : -30.0 <endvegetationtype>
If Vegetation is explicitly simulated - Growth Model
If the user chooses the option to simulate explicitly vegetation, than plant biomass, root biomass, LAI, canopy height and nutrient content, are simulated.
Water Uptake
total plant biomass
total plant nitrogen
total plant phosphorus
root biomass
root depth
canopy height
Other Features
Outputs
Time series
To write time series results define keyword:
TIME_SERIE : 1
in each property that you wish to write results.
Box integration
Maps (HDF5 format)
To write 3D results use keyword OUTPUT_TIME and define keyword:
OUTPUT_HDF : 1
in each property that you wish to write results.
Statistics
References
Izaurralde, R.C.; Williams, J.R. ; McGill, W.B.; Rosenberg, N.J.; Quiroga Jakas, M.C. (2006) - Simulating soil C dynamics with EPIC: Model description and testing against long‐term data. Ecol. Model. 192(3‐4): 362‐384.
Data File
Keywords
[Keyword] [Format] [Units] [Default] [Short Description]
VEGETATION_ID_FILE : string - [-] !Vegetation distribution grid path
VEGETATION_DT : real s [ModelDT] !Vegetation DT
INTEGRATION_DT : real s [ModelDT] !DT to integrate external variables
until vegetation is called
(vegetation DT)
TRANSPIRATION_METHOD : integer - [1] !Plant transpiration method: 1-MOHID
(previous approach); 2- SWAT based
ROOT_PROFILE : integer - [1] !Read if TRANSPIRATION_METHOD == 1:
!1-Triangular / 2-Constant /
3-Exponential(SWAT like)
WATER_UPTAKE_STRESS_METHOD : integer - [1] !Read if TRANSPIRATION_METHOD == 1:
1-Feddes; 2-VanGenuchten
<beginproperty>
See module fillmatrix
EVOLUTION : integer - - !Property evolution: 1-Read from file
!2-vegetation growth model
<endproperty>
!Vegetation growth parameters
TEMPERATURE_STRESS : 0/1 - [1] !Connects/disconnects temperature
stress on vegetation growth
GRAZING : 0/1 - [0] !Connects/disconnects grazing
MANAGEMENT : 0/1 - [0] !Connects/disconnects management
DORMANCY : 0/1 - [0] !Connects/disconnects dormancy
<beginvegetationtype>
ID
NAME
HAS_LEAVES
FEDDES_H1
FEDDES_H2
FEDDES_H3
FEDDES_H4
<begintimingdatabase>
MATURITY_HU : 1700.
PLANTING_JULIANDAY : -99.
PLANTING_HUBASE : 0.15
<endgtimingdatabase>
<begingrowthdatabase>
PLANT_TYPE : 5
OPTIMAL_NITROGENFRACTION_N1 : 0.0663
OPTIMAL_NITROGENFRACTION_N2 : 0.0255
OPTIMAL_NITROGENFRACTION_N3 : 0.0148
OPTIMAL_PHOSPHORUSFRACTION_P1 : 0.0053
OPTIMAL_PHOSPHORUSFRACTION_P2 : 0.0020
OPTIMAL_PHOSPHORUSFRACTION_P3 : 0.0012
BASE_TEMPERATURE : 0.
OPTIMAL_TEMPERATURE : 18.0
RADIATION_EXTINCTION_COEF : 0.65
BIOMASS_ENERGY_RATIO : 30.0
CO2_HIGH : 660.0
BIOMASS_ENERGY_RATIO_HIGH : 39.0
RUE_DECLINE_RATE : 6.0
LAI_MAX : 4.0
OPTIMAL_LAIMAXFRACTION_1 : 0.05
OPTIMAL_LAIMAXFRACTION_2 : 0.95
GROWFRACTION_1 : 0.05
GROWFRACTION_2 : 0.45
GROWFRACTION_LAIDECLINE : 0.50
ROOT_DEPTH_MAX : 1.30
CANOPY_HEIGHT_MAX : 0.9
OPTIMAL_HARVEST_INDEX : 0.4
MINIMUM_HARVEST_INDEX : 0.2
YELD_NITROGENFRACTION : 0.0250
YELD_PHOSPHORUSFRACTION : 0.0022
<endgrowthdatabase>
<beginmanagementandgrazedatabase>
GRAZING_START_JULIANDAY : -99.
GRAZING_START_PLANTHU : 0.5
GRAZING_DAYS : 10
MINIMUM_BIOMASS_FOR_GRAZING : 10.
GRAZING_BIOMASS : 70.
TRAMPLING_BIOMASS : 30.
HARVESTKILL_JULIANDAY : -99.
HARVESTKILL_PLANTHU : 1.2
HARVEST_JULIANDAY : -99.
HARVEST_PLANTHU : -99.
HARVEST_EFFICIENCY : 1.0
KILL_JULIANDAY : -99.
KILL_PLANTHU : -99.
<endmanagementandgrazedatabase>
<endvegetationtype>
Sample
If vegetation is readed from file
TRANSPIRATION_METHOD : 1 ROOT_PROFILE : 1 WATER_UPTAKE_STRESS_METHOD : 1 TIME_SERIE_LOCATION : ..\..\GeneralData\TimeSeriesLocation.dat VEGETATION_ID_FILE : ..\..\GeneralData\vegetation.dat OUTPUT_TIME : 0. 86400. <beginproperty> NAME : root depth UNITS : m DESCRIPTION : plant root depth EVOLUTION : 1 OLD : 0 FILE_IN_TIME : HDF FILENAME : ..\..\GeneralData\Trancao\Vegetation\RootDepth.hdf5 DEFAULTVALUE : 0.0 REMAIN_CONSTANT : 0 OUTPUT_HDF : 1 TIME_SERIE : 1 BOX_TIME_SERIE : 0 <endproperty> <beginproperty> NAME : leaf area index UNITS : m2/m2 DESCRIPTION : plant leaf area index EVOLUTION : 1 OLD : 0 FILE_IN_TIME : HDF FILENAME : ..\..\GeneralData\Trancao\Vegetation\LAI.hdf5 DEFAULTVALUE : 0. REMAIN_CONSTANT : 0 OUTPUT_HDF : 1 TIME_SERIE : 1 BOX_TIME_SERIE : 0 <endproperty> <beginproperty> NAME : specific leaf storage UNITS : m3/m2 DESCRIPTION : plant specific leaf storage EVOLUTION : 1 OLD : 0 FILE_IN_TIME : HDF FILENAME : ..\..\GeneralData\Trancao\Vegetation\SpecificLeafStorage.hdf5 DEFAULTVALUE : 0.0001 REMAIN_CONSTANT : 0 OUTPUT_HDF : 0 TIME_SERIE : 1 BOX_TIME_SERIE : 0 <endproperty> <beginproperty> NAME : crop coefficient UNITS : - DESCRIPTION : plant transpiration coefficient EVOLUTION : 1 OLD : 0 FILE_IN_TIME : HDF FILENAME : ..\..\GeneralData\Trancao\Vegetation\CropCoefficient.hdf5 DEFAULTVALUE : 1. REMAIN_CONSTANT : 0 OUTPUT_HDF : 0 TIME_SERIE : 1 BOX_TIME_SERIE : 0 <endproperty> !Arable Land - Trigo <beginvegetationtype> ID : 1 NAME : Agriculture FEDDES_H1 : -0.1 FEDDES_H2 : -0.25 FEDDES_H3 : -2.0 FEDDES_H4 : -80.0 <endvegetationtype> !Floresta <beginvegetationtype> ID : 2 NAME : Forest FEDDES_H1 : -0.1 FEDDES_H2 : -0.25 FEDDES_H3 : -6.0 FEDDES_H4 : -30.0 <endvegetationtype>
If vegetation growth model is used
VEGETATION_DT : 86400. INTEGRATION_DT : 3600. TRANSPIRATION_METHOD : 2 !begin Vegetation growth keywords TEMPERATURE_STRESS : 1 GRAZING : 0 MANAGEMENT : 1 DORMANCY : 0 POTENTIALHUTOTAL : 5475. POTENTIALHUBASE : 0.00 ISPLANTGROWING : FALSE !end Vegetation growth keywords TIME_SERIE_LOCATION : ..\..\GeneralData\TimeSeriesLocation2D_2.dat VEGETATION_ID_FILE : ..\..\GeneralData\vegetation_2cells.dat OUTPUT_TIME : 0. 86400. <beginproperty> NAME : total plant biomass UNITS : kg/ha DESCRIPTION : plant biomass EVOLUTION : 2 OLD : 0 DEFAULTVALUE : 0. REMAIN_CONSTANT : 0 OUTPUT_HDF : 1 TIME_SERIE : 1 BOX_TIME_SERIE : 0 <endproperty> <beginproperty> NAME : total plant nitrogen UNITS : kg/ha DESCRIPTION : plant nitrogen content EVOLUTION : 2 OLD : 0 DEFAULTVALUE : 0. REMAIN_CONSTANT : 0 OUTPUT_HDF : 1 TIME_SERIE : 1 BOX_TIME_SERIE : 0 <endproperty> <beginproperty> NAME : total plant phosphorus UNITS : kg/ha DESCRIPTION : plant phosphorus content EVOLUTION : 2 OLD : 0 FILE_IN_TIME : NONE INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 0. REMAIN_CONSTANT : 0 OUTPUT_HDF : 1 TIME_SERIE : 1 BOX_TIME_SERIE : 0 <endproperty> <beginproperty> NAME : root biomass UNITS : kg/ha DESCRIPTION : plant root biomass EVOLUTION : 2 OLD : 0 FILE_IN_TIME : NONE INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 0. REMAIN_CONSTANT : 0 OUTPUT_HDF : 1 TIME_SERIE : 1 BOX_TIME_SERIE : 0 <endproperty> <beginproperty> NAME : root depth UNITS : m DESCRIPTION : plant root depth EVOLUTION : 2 OLD : 0 FILE_IN_TIME : NONE INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 0.0 REMAIN_CONSTANT : 0 OUTPUT_HDF : 1 TIME_SERIE : 1 BOX_TIME_SERIE : 0 <endproperty> <beginproperty> NAME : leaf area index UNITS : m2/m2 DESCRIPTION : plant leaf area index EVOLUTION : 2 OLD : 0 FILE_IN_TIME : NONE DEFAULTVALUE : 0. REMAIN_CONSTANT : 0 OUTPUT_HDF : 1 TIME_SERIE : 1 BOX_TIME_SERIE : 0 <endproperty> <beginproperty> NAME : canopy height UNITS : m DESCRIPTION : plant canopy height EVOLUTION : 2 OLD : 0 FILE_IN_TIME : NONE INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 0. REMAIN_CONSTANT : 0 OUTPUT_HDF : 1 TIME_SERIE : 1 BOX_TIME_SERIE : 0 <endproperty> <beginproperty> NAME : specific leaf storage UNITS : m3/m2 DESCRIPTION : plant specific leaf storage EVOLUTION : 1 OLD : 0 FILE_IN_TIME : NONE INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 0.0001 REMAIN_CONSTANT : 1 OUTPUT_HDF : 0 TIME_SERIE : 1 BOX_TIME_SERIE : 0 <endproperty> <beginproperty> NAME : crop coefficient UNITS : - DESCRIPTION : plant transpiration coefficient EVOLUTION : 1 OLD : 0 FILE_IN_TIME : NONE INITIALIZATION_METHOD : CONSTANT DEFAULTVALUE : 1. REMAIN_CONSTANT : 1 OUTPUT_HDF : 0 TIME_SERIE : 1 BOX_TIME_SERIE : 0 <endproperty> !Arable Land - Trigo <beginvegetationtype> ID : 1 NAME : Agriculture HAS_LEAVES : 1 <begintimingdatabase> PLANTING_JULIANDAY : -99. PLANTING_HUBASE : 0.95 MATURITY_HU : 1700. <endtimingdatabase> <begingrowthdatabase> PLANT_TYPE : 5 OPTIMAL_NITROGENFRACTION_N1 : 0.0663 OPTIMAL_NITROGENFRACTION_N2 : 0.0255 OPTIMAL_NITROGENFRACTION_N3 : 0.0148 OPTIMAL_PHOSPHORUSFRACTION_P1 : 0.0053 OPTIMAL_PHOSPHORUSFRACTION_P2 : 0.0020 OPTIMAL_PHOSPHORUSFRACTION_P3 : 0.0012 BASE_TEMPERATURE : 0. OPTIMAL_TEMPERATURE : 18.0 RADIATION_EXTINCTION_COEF : 0.65 BIOMASS_ENERGY_RATIO : 30.0 CO2_HIGH : 660.0 BIOMASS_ENERGY_RATIO_HIGH : 39.0 RUE_DECLINE_RATE : 6.0 LAI_MAX : 4.0 OPTIMAL_LAIMAXFRACTION_1 : 0.05 OPTIMAL_LAIMAXFRACTION_2 : 0.95 GROWFRACTION_1 : 0.05 GROWFRACTION_2 : 0.45 GROWFRACTION_LAIDECLINE : 0.50 ROOT_DEPTH_MAX : 1.30 CANOPY_HEIGHT_MAX : 0.9 OPTIMAL_HARVEST_INDEX : 0.4 MINIMUM_HARVEST_INDEX : 0.2 YELD_NITROGENFRACTION : 0.0250 YELD_PHOSPHORUSFRACTION : 0.0022 <endgrowthdatabase> <beginmanagementandgrazedatabase> GRAZING_START_JULIANDAY : -99. GRAZING_START_PLANTHU : 0.5 GRAZING_DAYS : 10 MINIMUM_BIOMASS_FOR_GRAZING : 10. GRAZING_BIOMASS : 70. TRAMPLING_BIOMASS : 30. HARVESTKILL_JULIANDAY : -99. HARVESTKILL_PLANTHU : 1.2 HARVEST_JULIANDAY : -99. HARVEST_PLANTHU : -99. HARVEST_EFFICIENCY : 1.0 KILL_JULIANDAY : -99. KILL_PLANTHU : -99. <endmanagementandgrazedatabase> <endvegetationtype> !Floresta <beginvegetationtype> ID : 2 NAME : Forest HAS_LEAVES : 1 <begintimingdatabase> PLANTING_JULIANDAY : -99. PLANTING_HUBASE : 0.95 MATURITY_HU : 1700. <endtimingdatabase> <begingrowthdatabase> PLANT_TYPE : 7 OPTIMAL_NITROGENFRACTION_N1 : 0.0060 OPTIMAL_NITROGENFRACTION_N2 : 0.0020 OPTIMAL_NITROGENFRACTION_N3 : 0.0015 OPTIMAL_PHOSPHORUSFRACTION_P1 : 0.0007 OPTIMAL_PHOSPHORUSFRACTION_P2 : 0.0004 OPTIMAL_PHOSPHORUSFRACTION_P3 : 0.0003 BASE_TEMPERATURE : 10. OPTIMAL_TEMPERATURE : 30.0 RADIATION_EXTINCTION_COEF : 0.65 BIOMASS_ENERGY_RATIO : 15.0 CO2_HIGH : 660.0 BIOMASS_ENERGY_RATIO_HIGH : 16.0 RUE_DECLINE_RATE : 8.0 LAI_MAX : 5.0 OPTIMAL_LAIMAXFRACTION_1 : 0.05 OPTIMAL_LAIMAXFRACTION_2 : 0.95 GROWFRACTION_1 : 0.05 GROWFRACTION_2 : 0.40 GROWFRACTION_LAIDECLINE : 0.99 ROOT_DEPTH_MAX : 3.50 CANOPY_HEIGHT_MAX : 6.0 OPTIMAL_HARVEST_INDEX : 0.76 MINIMUM_HARVEST_INDEX : 0.010 YELD_NITROGENFRACTION : 0.0015 YELD_PHOSPHORUSFRACTION : 0.0003 TREE_YEARSTOMATURITY : -99. TREE_MAXIMUMBIOMASS : -99. <endgrowthdatabase> <beginmanagementandgrazedatabase> GRAZING_START_JULIANDAY : -99. GRAZING_START_PLANTHU : -99. GRAZING_DAYS : 0. MINIMUM_BIOMASS_FOR_GRAZING : 0. GRAZING_BIOMASS : 0. TRAMPLING_BIOMASS : 0. HARVESTKILL_JULIANDAY : -99. HARVESTKILL_PLANTHU : -99. HARVEST_JULIANDAY : -99. HARVEST_PLANTHU : -99. HARVEST_EFFICIENCY : 1.0 KILL_JULIANDAY : -99. KILL_PLANTHU : -99. <endmanagementandgrazedatabase> <endvegetationtype>
