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
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
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.
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 : 2 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 : 2 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 HAS_LEAVES : 1 FEDDES_H1 : -0.1 FEDDES_H2 : -0.25 FEDDES_H3 : -2.0 FEDDES_H4 : -80.0 <endvegetationtype> !Floresta <beginvegetationtype> ID : 2 NAME : Forest HAS_LEAVES : 1 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.
TRANSPIRATION_METHOD : 1 LIMIT_TRANSP_WATER_VEL : 0 ROOT_PROFILE : 2 WATER_UPTAKE_STRESS_METHOD : 1
TEMPERATURE_STRESS : 1
GRAZING : 0 MANAGEMENT : 1 DORMANCY : 0
CHANGE_LAI_SENESCENCE : 0 CHANGE_CANOPY_HEIGHT : 0
POTENTIALHUTOTAL : 5475. POTENTIALHUBASE : 0.00 ISPLANTGROWING : FALSE !NITROGENINSOIL : 1.0 !PHOSPHORUSINSOIL : 0.1
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 : 1000. 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 : 50.
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 : 1. 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 : 200. 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 : 1. 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 !FILENAME : ..\..\GeneralData\LAI-2001-2007-RZWQM.dat !DATA_COLUMN : 2 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
FEDDES_H1 : -0.1
FEDDES_H2 : -0.25
FEDDES_H3 : -2.0
FEDDES_H4 : -80.0
<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
FEDDES_H1 : -0.1
FEDDES_H2 : -0.25
FEDDES_H3 : -6.0
FEDDES_H4 : -30.0
<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>
Some keywords/properties od the input file vegetation_x.dat are:
<beginvegetationtype>
ID : 1 NAME : Sample vegetation type
<<begin_property>> !total leaf are / projected crown area PROPERTY_NAME : leaf area index IS_CONSTANT : 1 CONSTANT_VALUE : 0 <<end_property>>
<<begin_property>> !the depth of water that can be retained by leaves of a particular species per unit leaf area PROPERTY_NAME : specific leaf storage IS_CONSTANT : 1 CONSTANT_VALUE : 0 <<end_property>>
<<begin_property>> !factor for lowering evapotranspiration due to the crop type based on a reference evapotranspiration PROPERTY_NAME : evtp crop coefficient IS_CONSTANT : 1 CONSTANT_VALUE : 1 <<end_property>>
<<begin_property>> !self declaring... PROPERTY_NAME : root depth IS_CONSTANT : 1 CONSTANT_VALUE : 0 <<end_property>>
<<begin_property>> !Parameter of the root water uptake model after FEDDES (1978): 'Simulation of field water use and crop yield' PROPERTY_NAME : feddes h1 IS_CONSTANT : 1 CONSTANT_VALUE : -0.1 <<end_property>>
<<begin_property>> !Parameter of the root water uptake model after FEDDES (1978): 'Simulation of field water use and crop yield' PROPERTY_NAME : feddes h2 IS_CONSTANT : 1 CONSTANT_VALUE : -0.25 <<end_property>>
<<begin_property>> !Parameter of the root water uptake model after FEDDES (1978): 'Simulation of field water use and crop yield' PROPERTY_NAME : feddes h3 IS_CONSTANT : 1 CONSTANT_VALUE : -5.0 <<end_property>>
<<begin_property>> !Parameter of the root water uptake model after FEDDES (1978): 'Simulation of field water use and crop yield' !Wilting point PROPERTY_NAME : feddes h4 IS_CONSTANT : 1 CONSTANT_VALUE : -80.0 <<end_property>>
<<begin_property>> !self declaring... PROPERTY_NAME : permeable fraction IS_CONSTANT : 1 CONSTANT_VALUE : 1.0 <<end_property>>
<endvegetationtype>
