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Created February 11, 2020 20:34
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Example of running ED container in singularity.
Raw
ED2IN
!==========================================================================================!
!==========================================================================================!
! ED2IN . !
! !
! This is the file that contains the variables that define how ED is to be run. There !
! is some brief information about the variables here. !
!------------------------------------------------------------------------------------------!
$ED_NL
!----- Simulation title (64 characters). -----------------------------------------------!
NL%EXPNME = 'ED version 2.1 test'
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! Type of run: !
! INITIAL -- Starts a new run, that can be based on a previous run (restart/history), !
! but then it will use only the biomass and soil carbon information. !
! HISTORY -- Resumes a simulation from the last history. This is different from !
! initial in the sense that exactly the same information written in the !
! history will be used here. !
!---------------------------------------------------------------------------------------!
NL%RUNTYPE = 'INITIAL'
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! Start of simulation. Information must be given in UTC time. !
!---------------------------------------------------------------------------------------!
NL%IMONTHA = 01
NL%IDATEA = 01
NL%IYEARA = 2001
NL%ITIMEA = 0000
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! End of simulation. Information must be given in UTC time. !
!---------------------------------------------------------------------------------------!
NL%IMONTHZ = 01
NL%IDATEZ = 01
NL%IYEARZ = 2002
NL%ITIMEZ = 0000
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! DTLSM -- Time step to integrate photosynthesis, and the maximum time step for !
! integration of energy and water budgets (units: seconds). Notice that the !
! model will take steps shorter than this if this is too coarse and could !
! lead to loss of accuracy or unrealistic results in the biophysics. !
! Recommended values are < 60 seconds if INTEGRATION_SCHEME is 0, and 240-900 !
! seconds otherwise. !
! RADFRQ -- Time step to integrate radiation, in seconds. This must be an integer !
! multiple of DTLSM, and we recommend it to be exactly the same as DTLSM. !
!---------------------------------------------------------------------------------------!
NL%DTLSM = 600.
NL%RADFRQ = 600.
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! The following variables are used in case the user wants to run a regional run. !
! !
! N_ED_REGION -- number of regions for which you want to run ED. This can be set to !
! zero provided that N_POI is not... !
! GRID_TYPE -- which kind of grid to run: !
! 0. Longitude/latitude grid !
! 1. Polar-stereographic !
!---------------------------------------------------------------------------------------!
NL%N_ED_REGION = 0
NL%GRID_TYPE = 1
!------------------------------------------------------------------------------------!
! The following variables are used only when GRID_TYPE is set to 0. You must !
! provide one value for each grid, except otherwise noted. !
! !
! GRID_RES -- Grid resolution, in degrees (first grid only, the other grids !
! resolution will be defined by NSTRATX/NSTRATY). !
! ED_REG_LATMIN -- Southernmost point of each region. !
! ED_REG_LATMAX -- Northernmost point of each region. !
! ED_REG_LONMIN -- Westernmost point of each region. !
! ED_REG_LONMAX -- Easternmost point of each region. !
!------------------------------------------------------------------------------------!
NL%GRID_RES = 1.0
NL%ED_REG_LATMIN = -12.0, -7.5, 10.0, -6.0
NL%ED_REG_LATMAX = 1.0, -3.5, 15.0, -1.0
NL%ED_REG_LONMIN = -66.0,-58.5, 70.0, -63.0
NL%ED_REG_LONMAX = -49.0,-54.5, 35.0, -53.0
!------------------------------------------------------------------------------------!
!------------------------------------------------------------------------------------!
! The following variables are used only when GRID_TYPE is set to 1. !
! !
! NNXP -- number of points in the X direction. One value for each grid. !
! NNYP -- number of points in the Y direction. One value for each grid. !
! DELTAX -- grid resolution in the X direction, near the grid pole. Units: [ m]. !
! this value is used to define the first grid only, other grids are !
! defined using NNSTRATX. !
! DELTAY -- grid resolution in the Y direction, near the grid pole. Units: [ m]. !
! this value is used to define the first grid only, other grids are !
! defined using NNSTRATX. Unless you are running some specific tests, !
! both DELTAX and DELTAY should be the same. !
! POLELAT -- Latitude of the pole point. Set this close to CENTLAT for a more !
! traditional "square" domain. One value for all grids. !
! POLELON -- Longitude of the pole point. Set this close to CENTLON for a more !
! traditional "square" domain. One value for all grids. !
! CENTLAT -- Latitude of the central point. One value for each grid. !
! CENTLON -- Longitude of the central point. One value for each grid. !
!------------------------------------------------------------------------------------!
NL%NNXP = 110
NL%NNYP = 70
NL%DELTAX = 60000.
NL%DELTAY = 60000.
NL%POLELAT = -2.609075
NL%POLELON = -60.2093
NL%CENTLAT = -2.609075
NL%CENTLON = -60.2093
!------------------------------------------------------------------------------------!
!------------------------------------------------------------------------------------!
! Nest ratios. These values are used by both GRID_TYPE=0 and GRID_TYPE=1. !
! NSTRATX -- this is will divide the values given by DELTAX or GRID_RES for the !
! nested grids. The first value should be always one. !
! NSTRATY -- this is will divide the values given by DELTAY or GRID_RES for the !
! nested grids. The first value should be always one, and this must !
! be always the same as NSTRATX when GRID_TYPE = 0, and this is also !
! strongly recommended for when GRID_TYPE = 1. !
!------------------------------------------------------------------------------------!
NL%NSTRATX = 1,4
NL%NSTRATY = 1,4
!------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! The following variables are used to define single polygon of interest runs, and !
! they are ignored when N_ED_REGION = 0. !
! !
! N_POI -- number of polygons of interest (POIs). This can be zero as long as !
! N_ED_REGION is not. !
! POI_LAT -- list of latitudes of each POI. !
! POI_LON -- list of longitudes of each POI. !
! POI_RES -- grid resolution of each POI (degrees). This is used only to define the !
! soil types !
!---------------------------------------------------------------------------------------!
NL%N_POI = 1
NL%POI_LAT = -3.018
NL%POI_LON = -54.971
NL%POI_RES = 1.00
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! LOADMETH -- Load balancing method. This is used only in regional runs run in !
! parallel. !
! 0. Let ED decide the best way of splitting the polygons. Commonest !
! option and default. !
! 1. One of the methods to split polygons based on their previous !
! work load. Developpers only. !
! 2. Try to load an equal number of SITES per node. Useful for when !
! total number of polygon is the same as the total number of cores. !
! 3. Another method to split polygons based on their previous work load. !
! Developpers only. !
!---------------------------------------------------------------------------------------!
NL%LOADMETH = 0
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! ED2 File output. For all the variables 0 means no output and 3 means HDF5 output. !
! !
! IFOUTPUT -- Fast analysis. These are mostly polygon-level averages, and the time !
! interval between files is determined by FRQANL !
! IDOUTPUT -- Daily means (one file per day) !
! IMOUTPUT -- Monthly means (one file per month) !
! IQOUTPUT -- Monthly means of the diurnal cycle (one file per month). The number !
! of points for the diurnal cycle is 86400 / FRQANL !
! IYOUTPUT -- Annual output. !
! ITOUTPUT -- Instantaneous fluxes, mostly polygon-level variables, one file per year. !
! ISOUTPUT -- restart file, for HISTORY runs. The time interval between files is !
! determined by FRQHIS !
!---------------------------------------------------------------------------------------!
NL%IFOUTPUT = 0
NL%IDOUTPUT = 0
NL%IMOUTPUT = 0
NL%IQOUTPUT = 3
NL%IYOUTPUT = 0
NL%ITOUTPUT = 0
NL%ISOUTPUT = 3
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! ATTACH_METADATA -- Flag for attaching metadata to HDF datasets. Attaching metadata !
! will aid new users in quickly identifying dataset descriptions but !
! will compromise I/O performance significantly. !
! 0 = no metadata, 1 = attach metadata !
!---------------------------------------------------------------------------------------!
NL%ATTACH_METADATA = 0
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! UNITFAST -- The following variables control the units for FRQFAST/OUTFAST, and !
! UNITSTATE FRQSTATE/OUTSTATE, respectively. Possible values are: !
! 0. Seconds; !
! 1. Days; !
! 2. Calendar months (variable) !
! 3. Calendar years (variable) !
! !
! N.B.: 1. In case OUTFAST/OUTSTATE are set to special flags (-1 or -2) !
! UNITFAST/UNITSTATE will be ignored for them. !
! 2. In case IQOUTPUT is set to 3, then UNITFAST has to be 0. !
! !
!---------------------------------------------------------------------------------------!
NL%UNITFAST = 0
NL%UNITSTATE = 3
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! OUTFAST/OUTSTATE -- these control the number of times per file. !
! 0. Each time gets its own file !
! -1. One file per day !
! -2. One file per month !
! > 0. Multiple timepoints can be recorded to a single file reducing !
! the number of files and i/o time in post-processing. !
! Multiple timepoints should not be used in the history files !
! if you intend to use these for HISTORY runs. !
!---------------------------------------------------------------------------------------!
NL%OUTFAST = 1.
NL%OUTSTATE = 1.
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! ICLOBBER -- What to do in case the model finds a file that it was supposed the !
! written? 0 = stop the run, 1 = overwrite without warning. !
! FRQFAST -- time interval between analysis files, units defined by UNITFAST. !
! FRQSTATE -- time interval between history files, units defined by UNITSTATE. !
!---------------------------------------------------------------------------------------!
NL%ICLOBBER = 1
NL%FRQFAST = 3600.
NL%FRQSTATE = 1.
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! FFILOUT -- Path and prefix for analysis files (all but history/restart). !
! SFILOUT -- Path and prefix for history files. !
!---------------------------------------------------------------------------------------!
NL%FFILOUT = '/data/testrun.s83/analy/ts83'
NL%SFILOUT = '/data/testrun.s83/histo/ts83'
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! IED_INIT_MODE -- This controls how the plant community and soil carbon pools are !
! initialised. !
! !
! -1. Start from a true bare ground run, or an absolute desert run. This will !
! never grow any plant. !
! 0. Start from near-bare ground (only a few seedlings from each PFT to be included !
! in this run). !
! 1. This will use history files written by ED-1.0. It will grab the ecosystem !
! state (like biomass, LAI, plant density, etc.), but it will start the !
! thermodynamic state as a new simulation. !
! 2. Same as 1, but it uses history files from ED-2.0 without multiple sites, and !
! with the old PFT numbers. !
! 3. Same as 1, but using history files from ED-2.0 with multiple sites and !
! TOPMODEL hydrology. !
! 4. Same as 1, but using ED2.1 H5 history/state files that take the form: !
! 'dir/prefix-gxx.h5' !
! Initialization files MUST end with -gxx.h5 where xx is a two digit integer !
! grid number. Each grid has its own initialization file. As an example, if a !
! user has two files to initialize their grids with: !
! example_file_init-g01.h5 and example_file_init-g02.h5 !
! NL%SFILIN = 'example_file_init' !
! !
! 5. This is similar to option 4, except that you may provide several files !
! (including a mix of regional and POI runs, each file ending at a different !
! date). This will not check date nor grid structure, it will simply read all !
! polygons and match the nearest neighbour to each polygon of your run. SFILIN !
! must have the directory common to all history files that are sought to be used,!
! up to the last character the files have in common. For example if your files !
! are !
! /mypath/P0001-S-2000-01-01-000000-g01.h5, !
! /mypath/P0002-S-1966-01-01-000000-g02.h5, !
! ... !
! /mypath/P1000-S-1687-01-01-000000-g01.h5: !
! NL%SFILIN = '/mypath/P' !
! !
! 6 - Initialize with ED-2 style files without multiple sites, exactly like option !
! 2, except that the PFT types are preserved. !
!---------------------------------------------------------------------------------------!
NL%IED_INIT_MODE = 6
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! EDRES -- Expected input resolution for ED2.0 files. This is not used unless !
! IED_INIT_MODE = 3. !
!---------------------------------------------------------------------------------------!
NL%EDRES = 1.0
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! SFILIN -- The meaning and the size of this variable depends on the type of run, set !
! at variable NL%RUNTYPE. !
! !
! 1. INITIAL. Then this is the path+prefix of the previous ecosystem state. This has !
! dimension of the number of grids so you can initialize each grid with a !
! different dataset. In case only one path+prefix is given, the same will !
! be used for every grid. Only some ecosystem variables will be set up !
! here, and the initial condition will be in thermodynamic equilibrium. !
! !
! 2. HISTORY. This is the path+prefix of the history file that will be used. Only the !
! path+prefix will be used, as the history for every grid must have come !
! from the same simulation. !
!---------------------------------------------------------------------------------------!
NL%SFILIN = '/data/sites/Santarem_Km83/s83_default.'
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! History file information. These variables are used to continue a simulation from !
! a point other than the beginning. Time must be in UTC. !
! !
! IMONTHH -- the time of the history file. This is the only place you need to change !
! IDATEH dates for a HISTORY run. You may change IMONTHZ and related in case you !
! IYEARH want to extend the run, but yo should NOT change IMONTHA and related. !
! ITIMEH !
!---------------------------------------------------------------------------------------!
NL%ITIMEH = 0000
NL%IDATEH = 01
NL%IMONTHH = 05
NL%IYEARH = 2001
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! NZG - number of soil layers. One value for all grids. !
! NZS - maximum number of snow/water pounding layers. This is used only for !
! snow, if only liquid water is standing, the water will be all collapsed !
! into a single layer, so if you are running for places where it doesn't snow !
! a lot, leave this set to 1. One value for all grids. !
!---------------------------------------------------------------------------------------!
NL%NZG = 16
NL%NZS = 4
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! ISOILFLG -- this controls which soil type input you want to use. !
! 1. Read in from a dataset I will provide in the SOIL_DATABASE variable a !
! few lines below. !
! below. !
! 2. No data available, I will use constant values I will provide in !
! NSLCON or by prescribing the fraction of sand and clay (see SLXSAND !
! and SLXCLAY). !
!---------------------------------------------------------------------------------------!
NL%ISOILFLG = 2
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! NSLCON -- ED-2 Soil classes that the model will use when ISOILFLG is set to 2. !
! Possible values are: !
!---------------------------------------------------------------------------------------!
! 1 -- sand | 7 -- silty clay loam | 13 -- bedrock !
! 2 -- loamy sand | 8 -- clayey loam | 14 -- silt !
! 3 -- sandy loam | 9 -- sandy clay | 15 -- heavy clay !
! 4 -- silt loam | 10 -- silty clay | 16 -- clayey sand !
! 5 -- loam | 11 -- clay | 17 -- clayey silt !
! 6 -- sandy clay loam | 12 -- peat !
!---------------------------------------------------------------------------------------!
NL%NSLCON = 11
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! ISOILCOL -- LEAF-3 and ED-2 soil colour classes that the model will use when ISOILFLG !
! is set to 2. Soil classes are from 1 to 20 (1 = lightest; 20 = darkest). !
! The values are the same as CLM-4.0. The table is the albedo for visible !
! and near infra-red. !
!---------------------------------------------------------------------------------------!
! !
! |-----------------------------------------------------------------------| !
! | | Dry soil | Saturated | | Dry soil | Saturated | !
! | Class |-------------+-------------| Class +-------------+-------------| !
! | | VIS | NIR | VIS | NIR | | VIS | NIR | VIS | NIR | !
! |-------+------+------+------+------+-------+------+------+------+------| !
! | 1 | 0.36 | 0.61 | 0.25 | 0.50 | 11 | 0.24 | 0.37 | 0.13 | 0.26 | !
! | 2 | 0.34 | 0.57 | 0.23 | 0.46 | 12 | 0.23 | 0.35 | 0.12 | 0.24 | !
! | 3 | 0.32 | 0.53 | 0.21 | 0.42 | 13 | 0.22 | 0.33 | 0.11 | 0.22 | !
! | 4 | 0.31 | 0.51 | 0.20 | 0.40 | 14 | 0.20 | 0.31 | 0.10 | 0.20 | !
! | 5 | 0.30 | 0.49 | 0.19 | 0.38 | 15 | 0.18 | 0.29 | 0.09 | 0.18 | !
! | 6 | 0.29 | 0.48 | 0.18 | 0.36 | 16 | 0.16 | 0.27 | 0.08 | 0.16 | !
! | 7 | 0.28 | 0.45 | 0.17 | 0.34 | 17 | 0.14 | 0.25 | 0.07 | 0.14 | !
! | 8 | 0.27 | 0.43 | 0.16 | 0.32 | 18 | 0.12 | 0.23 | 0.06 | 0.12 | !
! | 9 | 0.26 | 0.41 | 0.15 | 0.30 | 19 | 0.10 | 0.21 | 0.05 | 0.10 | !
! | 10 | 0.25 | 0.39 | 0.14 | 0.28 | 20 | 0.08 | 0.16 | 0.04 | 0.08 | !
! |-----------------------------------------------------------------------| !
! !
! Soil type 21 is a special case in which we use the albedo method that used to be !
! the default in ED-2.1. !
!---------------------------------------------------------------------------------------!
NL%ISOILCOL = 21
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! These variables are used to define the soil properties when you don't want to use !
! the standard soil classes. !
! !
! SLXCLAY -- Prescribed fraction of clay [0-1] !
! SLXSAND -- Prescribed fraction of sand [0-1]. !
! !
! They are used only when ISOILFLG is 2, both values are between 0. and 1., and !
! theira sum doesn't exceed 1. Otherwise standard ED values will be used instead. !
!---------------------------------------------------------------------------------------!
NL%SLXCLAY = 0.59
NL%SLXSAND = 0.39
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! Soil grid and initial conditions if no file is provided: !
! !
! SLZ - soil depth in m. Values must be negative and go from the deepest layer to !
! the top. !
! SLMSTR - this is the initial soil moisture, now given as the soil moisture index. !
! Values can be fraction, in which case they will be linearly interpolated !
! between the special points (e.g. 0.5 will put soil moisture half way !
! between the wilting point and field capacity). !
! -1 = dry air soil moisture !
! 0 = wilting point !
! 1 = field capacity !
! 2 = porosity (saturation) !
! STGOFF - initial temperature offset (soil temperature = air temperature + offset) !
!---------------------------------------------------------------------------------------!
NL%SLZ = -8.000, -6.959, -5.995, -5.108, -4.296, -3.560, -2.897, -2.307,
-1.789, -1.340, -0.961, -0.648, -0.400, -0.215, -0.089, -0.020
NL%SLMSTR = 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00,
1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00
NL%STGOFF = 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00,
0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! Input databases !
! VEG_DATABASE -- vegetation database, used only to determine the land/water mask. !
! Fill with the path and the prefix. !
! SOIL_DATABASE -- soil database, used to determine the soil type. Fill with the !
! path and the prefix. !
! LU_DATABASE -- land-use change disturbance rates database, used only when !
! IANTH_DISTURB is set to 1. Fill with the path and the prefix. !
! PLANTATION_FILE -- plantation fraction file. In case you don't have such a file or !
! you do not want to use it, you must leave this variable empty: !
! (NL%PLANTATION_FILE = '' !
! THSUMS_DATABASE -- input directory with dataset to initialise chilling degrees and !
! growing degree days, which is used to drive the cold-deciduous !
! phenology (you must always provide this, even when your PFTs are !
! not cold deciduous). !
! ED_MET_DRIVER_DB -- File containing information for meteorological driver !
! instructions (the "header" file). !
! SOILSTATE_DB -- Dataset in case you want to provide the initial conditions of !
! soil temperature and moisture. !
! SOILDEPTH_DB -- Dataset in case you want to read in soil depth information. !
!---------------------------------------------------------------------------------------!
NL%VEG_DATABASE = '/data/oge2OLD/OGE2_'
NL%SOIL_DATABASE = '/data/faoOLD/FAO_'
NL%LU_DATABASE = '/data/ed_inputs/glu/'
NL%PLANTATION_FILE = ''
NL%THSUMS_DATABASE = '/data/ed_inputs/'
NL%ED_MET_DRIVER_DB = '/data/sites/Santarem_Km83/ED_MET_DRIVER_HEADER'
NL%SOILSTATE_DB = ''
NL%SOILDEPTH_DB = ''
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! ISOILSTATEINIT -- Variable controlling how to initialise the soil temperature and !
! moisture !
! 0. Use SLMSTR and STGOFF. !
! 1. Read from SOILSTATE_DB. !
! ISOILDEPTHFLG -- Variable controlling how to initialise soil depth !
! 0. Constant, always defined by the first SLZ layer. !
! 1. Read from SOILDEPTH_DB. !
!---------------------------------------------------------------------------------------!
NL%ISOILSTATEINIT = 0
NL%ISOILDEPTHFLG = 0
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! ISOILBC -- This controls the soil moisture boundary condition at the bottom. If !
! unsure, use 0 for short-term simulations (couple of days), and 1 for long- !
! -term simulations (months to years). !
! 0. Bedrock. Flux from the bottom of the bottommost layer is set to 0. !
! 1. Gravitational flow. The flux from the bottom of the bottommost layer !
! is due to gradient of height only. !
! 2. Super drainage. Soil moisture of the ficticious layer beneath the !
! bottom is always at dry air soil moisture. !
! 3. Half-way. Assume that the fictious layer beneath the bottom is always !
! at field capacity. !
! 4. Aquifer. Soil moisture of the ficticious layer beneath the bottom is !
! always at saturation. !
!---------------------------------------------------------------------------------------!
NL%ISOILBC = 1
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! IVEGT_DYNAMICS -- The vegetation dynamics scheme. !
! 0. No vegetation dynamics, the initial state will be preserved, !
! even though the model will compute the potential values. This !
! option is useful for theoretical simulations only. !
! 1. Normal ED vegetation dynamics (Moorcroft et al 2001). !
! The normal option for almost any simulation. !
!---------------------------------------------------------------------------------------!
NL%IVEGT_DYNAMICS = 1
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! IBIGLEAF -- Do you want to run ED as a 'big leaf' model? !
! 0. No, use the standard size- and age-structure (Moorcroft et al. 2001) !
! This is the recommended method for most applications. !
! 1. 'big leaf' ED: this will have no horizontal or vertical hetero- !
! geneities; 1 patch per PFT and 1 cohort per patch; no vertical !
! growth, recruits will 'appear' instantaneously at maximum height. !
! !
! N.B. if you set IBIGLEAF to 1, you MUST turn off the crown model (CROWN_MOD = 0) !
!---------------------------------------------------------------------------------------!
NL%IBIGLEAF = 0
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! INTEGRATION_SCHEME -- The biophysics integration scheme. !
! 0. Euler step. The fastest, but it doesn't estimate !
! errors. !
! 1. Fourth-order Runge-Kutta method. ED-2.1 default method !
! 2. Heun's method (a second-order Runge-Kutta). !
! 3. Hybrid Stepping (BDF2 implicit step for the canopy air and !
! leaf temp, forward Euler for else, under development). !
!---------------------------------------------------------------------------------------!
NL%INTEGRATION_SCHEME = 1
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! RK4_TOLERANCE -- This is the relative tolerance for Runge-Kutta or Heun's !
! integration. Larger numbers will make runs go faster, at the !
! expense of being less accurate. Currently the valid range is !
! between 1.e-7 and 1.e-1, but recommended values are between 1.e-4 !
! and 1.e-2. !
!---------------------------------------------------------------------------------------!
NL%RK4_TOLERANCE = 0.01
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! IBRANCH_THERMO -- This determines whether branches should be included in the !
! vegetation thermodynamics and radiation or not. !
! 0. No branches in energy/radiation (ED-2.1 default); !
! 1. Branches are accounted in the energy and radiation. Branchwood !
! and leaf are treated separately in the canopy radiation scheme, !
! but solved as a single pool in the biophysics integration. !
! 2. Similar to 1, but branches are treated as separate pools in the !
! biophysics (thus doubling the number of prognostic variables). !
!---------------------------------------------------------------------------------------!
NL%IBRANCH_THERMO = 1
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! IPHYSIOL -- This variable will determine the functional form that will control how !
! the various parameters will vary with temperature, and how the CO2 !
! compensation point for gross photosynthesis (Gamma*) will be found. !
! Options are: !
! !
! 0 -- Original ED-2.1, we use the "Arrhenius" function as in Foley et al. (1996) and !
! Moorcroft et al. (2001). Gamma* is found using the parameters for tau as in !
! Foley et al. (1996). !
! 1 -- Modified ED-2.1. In this case Gamma* is found using the Michaelis-Mentel !
! coefficients for CO2 and O2, as in Farquhar et al. (1980) and in CLM. !
! 2 -- Collatz et al. (1991). We use the power (Q10) equations, with Collatz et al. !
! parameters for compensation point, and the Michaelis-Mentel coefficients. The !
! correction for high and low temperatures are the same as in Moorcroft et al. !
! (2001). !
! 3 -- Same as 2, except that we find Gamma* as in Farquhar et al. (1980) and in CLM. !
!---------------------------------------------------------------------------------------!
NL%IPHYSIOL = 2
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! IALLOM -- Which allometry to use (this mostly affects tropical PFTs. Temperate PFTs !
! will use the new root allometry and the maximum crown area if IALLOM is set !
! to 1 or 2). !
! 0. Original ED-2.1 !
! 1. a. The coefficients for structural biomass are set so the total AGB !
! is similar to Baker et al. (2004), equation 2. Balive is the !
! default ED-2.1; !
! b. Experimental root depth that makes canopy trees to have root depths !
! of 5m and grasses/seedlings at 0.5 to have root depth of 0.5 m. !
! c. Crown area defined as in Poorter et al. (2006), imposing maximum !
! crown area !
! 2. Similar to 1, but with a few extra changes. !
! a. Height -> DBH allometry as in Poorter et al. (2006) !
! b. Balive is retuned, using a few leaf biomass allometric equations for !
! a few genuses in Costa Rica. References: !
! Cole and Ewel (2006), and Calvo Alvarado et al. (2008). !
!---------------------------------------------------------------------------------------!
NL%IALLOM = 2
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! IGRASS -- This controls the dynamics and growth calculation for grasses. A new !
! grass scheme is now available where bdead = 0, height is a function of bleaf!
! and growth happens daily. ALS (3/3/12) !
! 0: grasses behave like trees as in ED2.1 (old scheme) !
! !
! 1: new grass scheme as described above !
!---------------------------------------------------------------------------------------!
NL%IGRASS = 0
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! IPHEN_SCHEME -- It controls the phenology scheme. Even within each scheme, the !
! actual phenology will be different depending on the PFT. !
! !
! -1: grasses - evergreen; !
! tropical - evergreen; !
! conifers - evergreen; !
! hardwoods - cold-deciduous (Botta et al.); !
! !
! 0: grasses - drought-deciduous (old scheme); !
! tropical - drought-deciduous (old scheme); !
! conifers - evergreen; !
! hardwoods - cold-deciduous; !
! !
! 1: prescribed phenology !
! !
! 2: grasses - drought-deciduous (new scheme); !
! tropical - drought-deciduous (new scheme); !
! conifers - evergreen; !
! hardwoods - cold-deciduous; !
! !
! 3: grasses - drought-deciduous (new scheme); !
! tropical - drought-deciduous (light phenology); !
! conifers - evergreen; !
! hardwoods - cold-deciduous; !
! !
! Old scheme: plants shed their leaves once instantaneous amount of available water !
! becomes less than a critical value. !
! New scheme: plants shed their leaves once a 10-day running average of available !
! water becomes less than a critical value. !
!---------------------------------------------------------------------------------------!
NL%IPHEN_SCHEME = 2
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! Parameters that control the phenology response to radiation, used only when !
! IPHEN_SCHEME = 3. !
! !
! RADINT -- Intercept !
! RADSLP -- Slope. !
!---------------------------------------------------------------------------------------!
NL%RADINT = -11.3868
NL%RADSLP = 0.0824
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! REPRO_SCHEME -- This controls plant reproduction and dispersal. !
! 0. Reproduction off. Useful for very short runs only. !
! 1. Original reproduction scheme. Seeds are exchanged between !
! patches belonging to the same site, but they can't go outside !
! their original site. !
! 2. Similar to 1, but seeds are exchanged between patches belonging !
! to the same polygon, even if they are in different sites. They !
! can't go outside their original polygon, though. This is the !
! same as option 1 if there is only one site per polygon. !
! 3. Similar to 2, but recruits will only be formed if their phenology !
! status would be "leaves fully flushed". This only matters for !
! drought deciduous plants. This option is for testing purposes !
! only, think 50 times before using it... !
!---------------------------------------------------------------------------------------!
NL%REPRO_SCHEME = 2
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! LAPSE_SCHEME -- This specifies the met lapse rate scheme: !
! 0. No lapse rates !
! 1. phenomenological, global !
! 2. phenomenological, local (not yet implemented) !
! 3. mechanistic(not yet implemented) !
!---------------------------------------------------------------------------------------!
NL%LAPSE_SCHEME = 0
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! CROWN_MOD -- Specifies how tree crowns are represent in the canopy radiation model, !
! and in the turbulence scheme depending on ICANTURB. !
! 0. ED1 default, crowns are evenly spread throughout the patch area, and !
! cohorts are stacked on the top of each other. !
! 1. Dietze (2008) model. Cohorts have a finite radius, and cohorts are !
! stacked on the top of each other. !
!---------------------------------------------------------------------------------------!
NL%CROWN_MOD = 0
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! The following variables control the canopy radiation solver. !
! !
! ICANRAD -- Specifies how canopy radiation is solved. This variable sets both !
! shortwave and longwave. !
! 0. Two-stream model (Medvigy 2006), with the possibility to apply !
! finite crown area to direct shortwave radiation. !
! 1. Multiple-scattering model (Zhao and Qualls 2005,2006), with the !
! possibility to apply finite crown area to all radiation fluxes. !
! LTRANS_VIS -- Leaf transmittance for tropical plants - Visible/PAR !
! LTRANS_NIR -- Leaf transmittance for tropical plants - Near Infrared !
! LREFLECT_VIS -- Leaf reflectance for tropical plants - Visible/PAR !
! LREFLECT_NIR -- Leaf reflectance for tropical plants - Near Infrared !
! ORIENT_TREE -- Leaf orientation factor for tropical trees. Extremes are: !
! -1. All leaves are oriented in the vertical !
! 0. Leaf orientation is perfectly random !
! 1. All leaves are oriented in the horizontal !
! In practice, acceptable values range from -0.4 and 0.6 !
! ORIENT_GRASS -- Leaf orientation factor for tropical grasses. Extremes are: !
! -1. All leaves are oriented in the vertical !
! 0. Leaf orientation is perfectly random !
! 1. All leaves are oriented in the horizontal !
! In practice, acceptable values range from -0.4 and 0.6 !
! CLUMP_TREE -- Clumping factor for tropical trees. Extremes are: !
! lim -> 0. Black hole (0 itself is unacceptable) !
! 1. Homogeneously spread over the layer (i.e., no clumping) !
! CLUMP_GRASS -- Clumping factor for tropical grasses. Extremes are: !
! lim -> 0. Black hole (0 itself is unacceptable) !
! 1. Homogeneously spread over the layer (i.e., no clumping) !
!---------------------------------------------------------------------------------------!
NL%ICANRAD = 0
NL%LTRANS_VIS = 0.050
NL%LTRANS_NIR = 0.230
NL%LREFLECT_VIS = 0.100
NL%LREFLECT_NIR = 0.460
NL%ORIENT_TREE = 0.100
NL%ORIENT_GRASS = 0.000
NL%CLUMP_TREE = 0.800
NL%CLUMP_GRASS = 1.000
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! DECOMP_SCHEME -- This specifies the dependence of soil decomposition on temperature. !
! 0. ED-2.0 default, the original exponential !
! 1. Lloyd and Taylor (1994) model !
! [[option 1 requires parameters to be set in xml]] !
!---------------------------------------------------------------------------------------!
NL%DECOMP_SCHEME = 0
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! H2O_PLANT_LIM -- this determines whether plant photosynthesis can be limited by !
! soil moisture, the FSW, defined as FSW = Supply / (Demand + Supply). !
! !
! Demand is always the transpiration rates in case soil moisture is !
! not limiting (the psi_0 term times LAI). The supply is determined !
! by Kw * nplant * Broot * Available_Water, and the definition of !
! available water changes depending on H2O_PLANT_LIM: !
! 0. Force FSW = 1 (effectively available water is infinity). !
! 1. Available water is the total soil water above wilting point, !
! integrated across all layers within the rooting zone. !
! 2. Available water is the soil water at field capacity minus !
! wilting point, scaled by the so-called wilting factor: !
! (psi(k) - (H - z(k)) - psi_wp) / (psi_fc - psi_wp) !
! where psi is the matric potentital at layer k, z is the layer !
! depth, H it the crown height and psi_fc and psi_wp are the !
! matric potentials at wilting point and field capacity. !
!---------------------------------------------------------------------------------------!
NL%H2O_PLANT_LIM = 2
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! The following variables are factors that control photosynthesis and respiration. !
! Notice that some of them are relative values whereas others are absolute. !
! !
! VMFACT_C3 -- Factor multiplying the default Vm0 for C3 plants (1.0 = default). !
! VMFACT_C4 -- Factor multiplying the default Vm0 for C4 plants (1.0 = default). !
! MPHOTO_TRC3 -- Stomatal slope (M) for tropical C3 plants !
! MPHOTO_TEC3 -- Stomatal slope (M) for conifers and temperate C3 plants !
! MPHOTO_C4 -- Stomatal slope (M) for C4 plants. !
! BPHOTO_BLC3 -- cuticular conductance for broadleaf C3 plants [umol/m2/s] !
! BPHOTO_NLC3 -- cuticular conductance for needleleaf C3 plants [umol/m2/s] !
! BPHOTO_C4 -- cuticular conductance for C4 plants [umol/m2/s] !
! KW_GRASS -- Water conductance for trees, in m2/yr/kgC_root. This is used only !
! when H2O_PLANT_LIM is not 0. !
! KW_TREE -- Water conductance for grasses, in m2/yr/kgC_root. This is used only !
! when H2O_PLANT_LIM is not 0. !
! GAMMA_C3 -- The dark respiration factor (gamma) for C3 plants. Subtropical !
! conifers will be scaled by GAMMA_C3 * 0.028 / 0.02 !
! GAMMA_C4 -- The dark respiration factor (gamma) for C4 plants. !
! D0_GRASS -- The transpiration control in gsw (D0) for ALL grasses. !
! D0_TREE -- The transpiration control in gsw (D0) for ALL trees. !
! ALPHA_C3 -- Quantum yield of ALL C3 plants. This is only applied when !
! QUANTUM_EFFICIENCY_T = 0. !
! ALPHA_C4 -- Quantum yield of C4 plants. This is always applied. !
! KLOWCO2IN -- The coefficient that controls the PEP carboxylase limited rate of !
! carboxylation for C4 plants. !
! RRFFACT -- Factor multiplying the root respiration factor for ALL PFTs. !
! (1.0 = default). !
! GROWTHRESP -- The actual growth respiration factor (C3/C4 tropical PFTs only). !
! (1.0 = default). !
! LWIDTH_GRASS -- Leaf width for grasses, in metres. This controls the leaf boundary !
! layer conductance (gbh and gbw). !
! LWIDTH_BLTREE -- Leaf width for trees, in metres. This controls the leaf boundary !
! layer conductance (gbh and gbw). This is applied to broadleaf trees !
! only. !
! LWIDTH_NLTREE -- Leaf width for trees, in metres. This controls the leaf boundary !
! layer conductance (gbh and gbw). This is applied to conifer trees !
! only. !
! Q10_C3 -- Q10 factor for C3 plants (used only if IPHYSIOL is set to 2 or 3). !
! Q10_C4 -- Q10 factor for C4 plants (used only if IPHYSIOL is set to 2 or 3). !
!---------------------------------------------------------------------------------------!
NL%VMFACT_C3 = 1
NL%VMFACT_C4 = 1
NL%MPHOTO_TRC3 = 9
NL%MPHOTO_TEC3 = 7.2
NL%MPHOTO_C4 = 5.2
NL%BPHOTO_BLC3 = 10000
NL%BPHOTO_NLC3 = 1000
NL%BPHOTO_C4 = 10000
NL%KW_GRASS = 900
NL%KW_TREE = 600
NL%GAMMA_C3 = 0.0145
NL%GAMMA_C4 = 0.035
NL%D0_GRASS = 0.016
NL%D0_TREE = 0.016
NL%ALPHA_C3 = 0.08
NL%ALPHA_C4 = 0.055
NL%KLOWCO2IN = 4000
NL%RRFFACT = 1
NL%GROWTHRESP = 0.333
NL%LWIDTH_GRASS = 0.05
NL%LWIDTH_BLTREE = 0.1
NL%LWIDTH_NLTREE = 0.05
NL%Q10_C3 = 2.4
NL%Q10_C4 = 2.4
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! THETACRIT -- Leaf drought phenology threshold. The sign matters here: !
! >= 0. -- This is the relative soil moisture above the wilting point !
! below which the drought-deciduous plants will start shedding !
! their leaves !
! < 0. -- This is the soil potential in MPa below which the drought- !
! -deciduous plants will start shedding their leaves. The wilt- !
! ing point is by definition -1.5MPa, so make sure that the value !
! is above -1.5. !
!---------------------------------------------------------------------------------------!
NL%THETACRIT = -1.20
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! QUANTUM_EFFICIENCY_T -- Which quantum yield model should to use for C3 plants !
! 0. Original ED-2.1, quantum efficiency is constant. !
! 1. Quantum efficiency varies with temperature following !
! Ehleringer (1978) polynomial fit. !
!---------------------------------------------------------------------------------------!
NL%QUANTUM_EFFICIENCY_T = 0
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! N_PLANT_LIM -- This controls whether plant photosynthesis can be limited by nitrogen. !
! 0. No limitation !
! 1. ED-2.1 nitrogen limitation model. !
!---------------------------------------------------------------------------------------!
NL%N_PLANT_LIM = 0
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! N_DECOMP_LIM -- This controls whether decomposition can be limited by nitrogen. !
! 0. No limitation !
! 1. ED-2.1 nitrogen limitation model. !
!---------------------------------------------------------------------------------------!
NL%N_DECOMP_LIM = 0
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! The following parameters adjust the fire disturbance in the model. !
! INCLUDE_FIRE -- Which threshold to use for fires. !
! 0. No fires; !
! 1. (deprecated) Fire will be triggered with enough biomass and !
! integrated ground water depth less than a threshold. Based on !
! ED-1, the threshold assumes that the soil is 1 m, so deeper !
! soils will need to be much drier to allow fires to happen and !
! often will never allow fires. !
! 2. Fire will be triggered with enough biomass and the total soil !
! water at the top 75 cm falls below a threshold. !
! FIRE_PARAMETER -- If fire happens, this will control the intensity of the disturbance !
! given the amount of fuel (currently the total above-ground !
! biomass). !
! SM_FIRE -- This is used only when INCLUDE_FIRE = 2. The sign here matters. !
! >= 0. - Minimum relative soil moisture above dry air of the top 1m !
! that will prevent fires to happen. !
! < 0. - Minimum mean soil moisture potential in MPa of the top 1m !
! that will prevent fires to happen. The dry air soil !
! potential is defined as -3.1 MPa, so make sure SM_FIRE is !
! greater than this value. !
!---------------------------------------------------------------------------------------!
NL%INCLUDE_FIRE = 0
NL%FIRE_PARAMETER = 0.5
NL%SM_FIRE = -1.40
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! IANTH_DISTURB -- This flag controls whether to include anthropogenic disturbances !
! such as land clearing, abandonment, and logging. !
! 0. no anthropogenic disturbance. !
! 1. use anthropogenic disturbance dataset. !
!---------------------------------------------------------------------------------------!
NL%IANTH_DISTURB = 0
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! ICANTURB -- This flag controls the canopy roughness. !
! 0. Based on Leuning et al. (1995), wind is computed using the similarity !
! theory for the top cohort, and they are extinguished with cumulative !
! LAI. If using CROWN_MOD 1 or 2, this will use local LAI and average !
! by crown area. !
! 1. The default ED-2.1 scheme, except that it uses the zero-plane !
! displacement height. !
! 2. This uses the method of Massman (1997) using constant drag and no !
! sheltering factor. !
! 3. This is also based on Massman (1997), but with the option of varying !
! the drag and sheltering within the canopy. !
! 4. Same as 0, but if finds the ground conductance following CLM !
! technical note (equations 5.98-5.100). !
!---------------------------------------------------------------------------------------!
NL%ICANTURB = 2
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! ISFCLYRM -- Similarity theory model. The model that computes u*, T*, etc... !
! 1. BRAMS default, based on Louis (1979). It uses empirical relations to !
! estimate the flux based on the bulk Richardson number !
! !
! All models below use an interative method to find z/L, and the only change !
! is the functional form of the psi functions. !
! !
! 2. Oncley and Dudhia (1995) model, based on MM5. !
! 3. Beljaars and Holtslag (1991) model. Similar to 2, but it uses an alternative !
! method for the stable case that mixes more than the OD95. !
! 4. CLM (2004). Similar to 2 and 3, but they have special functions to deal with !
! very stable and very stable cases. !
!---------------------------------------------------------------------------------------!
NL%ISFCLYRM = 3
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! IED_GRNDVAP -- Methods to find the ground -> canopy conductance. !
! 0. Modified Lee Pielke (1992), adding field capacity, but using beta factor !
! without the square, like in Noilhan and Planton (1989). This is the closest !
! to the original ED-2.0 and LEAF-3, and it is also the recommended one. !
! 1. Test # 1 of Mahfouf and Noilhan (1991) !
! 2. Test # 2 of Mahfouf and Noilhan (1991) !
! 3. Test # 3 of Mahfouf and Noilhan (1991) !
! 4. Test # 4 of Mahfouf and Noilhan (1991) !
! 5. Combination of test #1 (alpha) and test #2 (soil resistance). !
! In all cases the beta term is modified so it approaches zero as soil moisture goes !
! to dry air soil. !
!---------------------------------------------------------------------------------------!
NL%IED_GRNDVAP = 0
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! The following variables are used to control the similarity theory model. For the !
! meaning of these parameters, check Beljaars and Holtslag (1991). !
! GAMM -- gamma coefficient for momentum, unstable case (dimensionless) !
! Ignored when ISTAR = 1 !
! GAMH -- gamma coefficient for heat, unstable case (dimensionless) !
! Ignored when ISTAR = 1 !
! TPRANDTL -- Turbulent Prandtl number !
! Ignored when ISTAR = 1 !
! RIBMAX -- maximum bulk Richardson number. !
! LEAF_MAXWHC -- Maximum water that can be intercepted by leaves, in kg/m2leaf. !
!---------------------------------------------------------------------------------------!
NL%GAMM = 13.0
NL%GAMH = 13.0
NL%TPRANDTL = 0.74
NL%RIBMAX = 0.50
NL%LEAF_MAXWHC = 0.11
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! IPERCOL -- This controls percolation and infiltration. !
! 0. Default method. Assumes soil conductivity constant and for the !
! temporary surface water, it sheds liquid in excess of a 1:9 liquid- !
! -to-ice ratio through percolation. Temporary surface water exists !
! only if the top soil layer is at saturation. !
! 1. Constant soil conductivity, and it uses the percolation model as in !
! Anderson (1976) NOAA technical report NWS 19. Temporary surface !
! water may exist after a heavy rain event, even if the soil doesn't !
! saturate. Recommended value. !
! 2. Soil conductivity decreases with depth even for constant soil moisture !
! , otherwise it is the same as 1. !
!---------------------------------------------------------------------------------------!
NL%IPERCOL = 1
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! The following variables control the plant functional types (PFTs) that will be !
! used in this simulation. !
! !
! INCLUDE_THESE_PFT -- a list containing all the PFTs you want to include in this run !
! AGRI_STOCK -- which PFT should be used for agriculture !
! (used only when IANTH_DISTURB = 1) !
! PLANTATION_STOCK -- which PFT should be used for plantation !
! (used only when IANTH_DISTURB = 1) !
! !
! PFT table !
!---------------------------------------------------------------------------------------!
! 1 - C4 grass | 9 - early temperate deciduous !
! 2 - early tropical | 10 - mid temperate deciduous !
! 3 - mid tropical | 11 - late temperate deciduous !
! 4 - late tropical | 12:15 - agricultural PFTs !
! 5 - temperate C3 grass | 16 - Subtropical C3 grass !
! 6 - northern pines | (C4 grass with C3 photo). !
! 7 - southern pines | 17 - "Araucaria" (non-optimised !
! 8 - late conifers | Southern Pines). !
!---------------------------------------------------------------------------------------!
NL%INCLUDE_THESE_PFT = 1,2,3,4,16
NL%AGRI_STOCK = 1
NL%PLANTATION_STOCK = 3
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! PFT_1ST_CHECK -- What to do if the initialisation file has a PFT that is not listed !
! in INCLUDE_THESE_PFT (ignored if IED_INIT_MODE is -1 or 0) !
! 0. Stop the run !
! 1. Add the PFT in the INCLUDE_THESE_PFT list !
! 2. Ignore the cohort !
!---------------------------------------------------------------------------------------!
NL%PFT_1ST_CHECK = 0
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! The following variables control the size of sub-polygon structures in ED-2. !
! MAXSITE -- This is the strict maximum number of sites that each polygon can !
! contain. Currently this is used only when the user wants to run !
! the same polygon with multiple soil types. If there aren't that !
! many different soil types with a minimum area (check MIN_SITE_AREA !
! below), then the model will allocate just the amount needed. !
! MAXPATCH -- If number of patches in a given site exceeds MAXPATCH, force patch !
! fusion. If MAXPATCH is 0, then fusion will never happen. If !
! MAXPATCH is negative, then the absolute value is used only during !
! the initialization, and fusion will never happen again. Notice !
! that if the patches are too different, then the actual number of !
! patches in a site may exceed MAXPATCH. !
! MAXCOHORT -- If number of cohorts in a given patch exceeds MAXCOHORT, force !
! cohort fusion. If MAXCOHORT is 0, then fusion will never happen. !
! If MAXCOHORT is negative, then the absolute value is used only !
! during the initialization, and fusion will never happen again. !
! Notice that if the cohorts are too different, then the actual !
! number of cohorts in a patch may exceed MAXCOHORT. !
! MIN_SITE_AREA -- This is the minimum fraction area of a given soil type that allows !
! a site to be created (ignored if IED_INIT_MODE is set to 3). !
! MIN_PATCH_AREA -- This is the minimum fraction area of a given soil type that allows !
! a site to be created (ignored if IED_INIT_MODE is set to 3). !
!---------------------------------------------------------------------------------------!
NL%MAXSITE = 1
NL%MAXPATCH = 10
NL%MAXCOHORT = 40
NL%MIN_SITE_AREA = 0.005
NL%MIN_PATCH_AREA = 0.005
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! ZROUGH -- constant roughness, in metres, if for all domain !
!---------------------------------------------------------------------------------------!
NL%ZROUGH = 0.1
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! Treefall disturbance parameters. !
! TREEFALL_DISTURBANCE_RATE -- Sign-dependent treefall disturbance rate: !
! > 0. usual disturbance rate, in 1/years; !
! = 0. No treefall disturbance; !
! < 0. Treefall will be added as a mortality rate (it !
! will kill plants, but it won't create a new patch). !
! TIME2CANOPY -- Minimum patch age for treefall disturbance to happen. !
! If TREEFALL_DISTURBANCE_RATE = 0., this value will be !
! ignored. If this value is different than zero, then !
! TREEFALL_DISTURBANCE_RATE is internally adjusted so the !
! average patch age is still 1/TREEFALL_DISTURBANCE_RATE !
!---------------------------------------------------------------------------------------!
NL%TREEFALL_DISTURBANCE_RATE = 0.014
NL%TIME2CANOPY = 0.0
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! RUNOFF_TIME -- In case a temporary surface water (TSW) is created, this is the "e- !
! -folding lifetime" of the TSW in seconds due to runoff. If you don't !
! want runoff to happen, set this to 0. !
!---------------------------------------------------------------------------------------!
NL%RUNOFF_TIME = 3600.0
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! The following variables control the minimum values of various velocities in the !
! canopy. This is needed to avoid the air to be extremely still, or to avoid singular- !
! ities. When defining the values, keep in mind that UBMIN >= UGBMIN >= USTMIN. !
! !
! UBMIN -- minimum wind speed at the top of the canopy air space [ m/s] !
! UGBMIN -- minimum wind speed at the leaf level [ m/s] !
! USTMIN -- minimum friction velocity, u*, in m/s. [ m/s] !
!---------------------------------------------------------------------------------------!
NL%UBMIN = 0.65
NL%UGBMIN = 0.25
NL%USTMIN = 0.05
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! Control parameters for printing to standard output. Any variable can be printed !
! to standard output as long as it is one dimensional. Polygon variables have been !
! tested, no gaurtantees for other hierarchical levels. Choose any variables that are !
! defined in the variable table fill routine in ed_state_vars.f90. Choose the start !
! and end index of the polygon,site,patch or cohort. It should work in parallel. The !
! indices are global indices of the entire domain. The are printed out in rows of 10 !
! columns each. !
! !
! IPRINTPOLYS -- 0. Do not print information to screen !
! 1. Print polygon arrays to screen, use variables described below to !
! determine which ones and how !
! NPVARS -- Number of variables to be printed !
! PRINTVARS -- List of variables to be printed !
! PFMTSTR -- The standard fortran format for the prints. One format per variable !
! IPMIN -- First polygon (absolute index) to be print !
! IPMAX -- Last polygon (absolute index) to print !
!---------------------------------------------------------------------------------------!
NL%IPRINTPOLYS = 0
NL%NPVARS = 1
NL%PRINTVARS = 'AVG_PCPG','AVG_CAN_TEMP','AVG_VAPOR_AC','AVG_CAN_SHV'
NL%PFMTSTR = 'f10.8','f5.1','f7.2','f9.5'
NL%IPMIN = 1
NL%IPMAX = 60
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! Variables that control the meteorological forcing. !
! !
! IMETTYPE -- Format of the meteorological dataset !
! 0. ASCII (deprecated) !
! 1. HDF5 !
! ISHUFFLE -- How to choose an year outside the meterorological data range (see !
! METCYC1 and METCYCF). !
! 0. Sequentially cycle over years !
! 1. Randomly pick the years, using the same sequence. This has worked !
! with gfortran running in Mac OS X system, but it acts like option 2 !
! when running ifort. !
! 2. Randomly pick the years, choosing a different sequence each time !
! the model is run. !
! IMETCYC1 -- First year with meteorological information !
! IMETCYCF -- Last year with meteorological information !
! IMETAVG -- How the input radiation was originally averaged. You must tell this !
! because ED-2.1 can make a interpolation accounting for the cosine of !
! zenith angle. !
! -1. I don't know, use linear interpolation. !
! 0. No average, the values are instantaneous !
! 1. Averages ending at the reference time !
! 2. Averages beginning at the reference time !
! 3. Averages centred at the reference time !
! IMETRAD -- What should the model do with the input short wave radiation? !
! 0. Nothing, use it as is. !
! 1. Add them together, then use the SiB method to break radiation down !
! into the four components (PAR direct, PAR diffuse, NIR direct, !
! NIR diffuse). !
! 2. Add then together, then use the method by Weiss and Norman (1985) !
! to break radiation down to the four components. !
! 3. Gloomy -- All radiation goes to diffuse. !
! 4. Sesame street -- all radiation goes to direct, except at night. !
! INITIAL_CO2 -- Initial value for CO2 in case no CO2 is provided at the meteorological !
! driver dataset [Units: µmol/mol] !
!---------------------------------------------------------------------------------------!
NL%IMETTYPE = 1
NL%ISHUFFLE = 0
NL%METCYC1 = 2000
NL%METCYCF = 2003
NL%IMETAVG = 1
NL%IMETRAD = 2
NL%INITIAL_CO2 = 378.0
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! The following variables control the phenology prescribed from observations: !
! !
! IPHENYS1 -- First year for spring phenology !
! IPHENYSF -- Final year for spring phenology !
! IPHENYF1 -- First year for fall/autumn phenology !
! IPHENYFF -- Final year for fall/autumn phenology !
! PHENPATH -- path and prefix of the prescribed phenology data. !
! !
! If the years don't cover the entire simulation period, they will be recycled. !
!---------------------------------------------------------------------------------------!
NL%IPHENYS1 = 1992
NL%IPHENYSF = 2003
NL%IPHENYF1 = 1992
NL%IPHENYFF = 2003
NL%PHENPATH = '/n/moorcroft_data/data/ed2_data/phenology/phenology'
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! These are some additional configuration files. !
! IEDCNFGF -- XML file containing additional parameter settings. If you don't have !
! one, leave it empty !
! EVENT_FILE -- file containing specific events that must be incorporated into the !
! simulation. !
! PHENPATH -- path and prefix of the prescribed phenology data. !
!---------------------------------------------------------------------------------------!
NL%IEDCNFGF = 'config.xml'
NL%EVENT_FILE = 'myevents.xml'
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! The following variables are used to control the detailed output for debugging !
! purposes. !
! !
! IDETAILED -- This flag controls the possible detailed outputs, mostly used for !
! debugging purposes. Notice that this doesn't replace the normal debug- !
! ger options, the idea is to provide detailed output to check bad !
! assumptions. The options are additive, and the indices below represent !
! the different types of output: !
! !
! 1 -- Detailed budget (every DTLSM) !
! 2 -- Detailed photosynthesis (every DTLSM) !
! 4 -- Detailed output from the integrator (every HDID) !
! 8 -- Thermodynamic bounds for sanity check (every DTLSM) !
! 16 -- Daily error stats (which variable caused the time step to shrink) !
! 32 -- Allometry parameters, and minimum and maximum sizes !
! (two files, only at the beginning) !
! !
! In case you don't want any detailed output (likely for most runs), set !
! IDETAILED to zero. In case you want to generate multiple outputs, add !
! the number of the sought options: for example, if you want detailed !
! photosynthesis and detailed output from the integrator, set IDETAILED !
! to 6 (2 + 4). Any combination of the above outputs is acceptable, al- !
! though all but the last produce a sheer amount of txt files, in which !
! case you may want to look at variable PATCH_KEEP. It is also a good !
! idea to set IVEGT_DYNAMICS to 0 when using the first five outputs. !
! !
! !
! PATCH_KEEP -- This option will eliminate all patches except one from the initial- !
! isation. This is only used when one of the first five types of !
! detailed output is active, otherwise it will be ignored. Options are: !
! -2. Keep only the patch with the lowest potential LAI !
! -1. Keep only the patch with the highest potential LAI !
! 0. Keep all patches. !
! > 0. Keep the patch with the provided index. In case the index is !
! not valid, the model will crash. !
!---------------------------------------------------------------------------------------!
NL%IDETAILED = 0
NL%PATCH_KEEP = 0
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------!
! IOPTINPT -- Optimization configuration. (Currently not used) !
!---------------------------------------------------------------------------------------!
!NL%IOPTINPT = ''
!---------------------------------------------------------------------------------------!
NL%IOOUTPUT = 3
NL%IADD_SITE_MEANS = 0
NL%IADD_PATCH_MEANS = 0
NL%IADD_COHORT_MEANS = 0
NL%GROWTH_RESP_SCHEME = 0
NL%STORAGE_RESP_SCHEME = 0
NL%PLANT_HYDRO_SCHEME = 0
NL%ISTOMATA_SCHEME = 0
NL%ISTRUCT_GROWTH_SCHEME = 0
NL%TRAIT_PLASTICITY_SCHEME = 0
NL%IDDMORT_SCHEME = 0
NL%CBR_SCHEME = 0
NL%DDMORT_CONST = 0
NL%ICANRAD = 1
NL%DT_CENSUS = 60
NL%YR1ST_CENSUS = 2000
NL%MON1ST_CENSUS = 6
NL%MIN_RECRUIT_DBH = 50
$END
!==========================================================================================!
!==========================================================================================!
Raw
install.sh
#!/bin/bash
if [ ! -e sites ]; then
curl -s -o sites.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/sites.tgz
tar zxf sites.tgz
sed -i -e "s#/home/kooper/Projects/EBI#/data/sites#" sites/*/ED_MET_DRIVER_HEADER
rm sites.tgz
fi
if [ ! -e inputs ]; then
curl -s -o inputs.tgz http://isda.ncsa.illinois.edu/~kooper/EBI/inputs.tgz
tar zxf inputs.tgz
rm inputs.tgz
fi
if [ ! -e testrun.s83 ]; then
curl -s -o testrun.s83.zip http://isda.ncsa.illinois.edu/~kooper/EBI/testrun.s83.zip
unzip -q testrun.s83.zip
sed -i -e "s#/home/pecan#/data#" testrun.s83/ED2IN
rm testrun.s83.zip
fi
if [ ! -e ${HOME}/sites/Santarem_Km83 ]; then
curl -s -o Santarem_Km83.zip http://isda.ncsa.illinois.edu/~kooper/EBI/Santarem_Km83.zip
unzip -q -d sites Santarem_Km83.zip
sed -i -e "s#/home/pecan#/data#" sites/Santarem_Km83/ED_MET_DRIVER_HEADER
rm Santarem_Km83.zip
fi
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