34 singularity
Running a model using singularity.
This is work in progress.
This assumes you have singulariy already installed.
This will work on a Linux machine (x86_64).
First make sure you have all the data files:
bash script to install required files (click to expand)
#!/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
fiNext edit the ED2IN file in testrun.s83
ED2IN file (click to expand)
!==========================================================================================!
!==========================================================================================!
! 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
!==========================================================================================!
!==========================================================================================!Convert the docker image to singularity
singularity pull docker://pecan/model-ed2-gitFinally you can run the singularity image
singularity exec -B ed_inputs:/data/ed_inputs -B faoOLD:/data/faoOLD -B oge2OLD:/data/oge2OLD -B sites:/data/sites -B testrun.s83:/data/testrun.s83 --pwd /data/testrun.s83 ./model-ed2-git.simg ed2.git -sNote that the -B option will mount the folder into the singularity image as the second argument (afther the :)
The ed2.git command is started with the -s which will run it in single mode, and not initialize and use MPI.
Once the model is finished the outputs should be available under testrun.s83.
The example ED2IN file is not 100% correct and will result in the following error:
output of (failed) run (click to expand)
+---------------- MPI parallel info: --------------------+
+ - Machnum = 0
+ - Machsize = 1
+---------------- OMP parallel info: --------------------+
+ - thread use: 1
+ - threads max: 1
+ - cpu use: 1
+ - cpus max: 1
+ Note: Max vals are for node, not sockets.
+--------------------------------------------------------+
Reading namelist information
Copying namelist
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!! WARNING! WARNING! WARNING! WARNING! WARNING! !!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-> Outfast cannot be less than frqfast.
Oufast was redefined to 3600. seconds.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!! WARNING! WARNING! WARNING! WARNING! WARNING! !!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-> Outstate cannot be different than frqstate when
unitstate is set to 3 (years).
Oustate was set to 1. years.
Oustate was redefined to 1. years.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+------------------------------------------------------------+
| Ecosystem Demography Model, version 2.2
+------------------------------------------------------------+
| Input namelist filename is ED2IN
|
| Single process execution on INITIAL run.
+------------------------------------------------------------+
=> Generating the land/sea mask.
/data/oge2OLD/OGE2_HEADER
-> Getting file: /data/oge2OLD/OGE2_30S060W.h5...
+ Work allocation, node 1;
+ Polygon array allocation, node 1;
+ Memory successfully allocated on none 1;
[+] Load_Ed_Ecosystem_Params...
----------------------------------------
Treefall disturbance parameters:
- LAMBDA_REF = 1.40000E-02
- LAMBDA_EFF = 1.40000E-02
- TIME2CANOPY = 0.00000E+00
----------------------------------------
[+] Checking for XML config...
*********************************************
** WARNING! **
** **
** XML file wasn't found. Using default **
** parameters in ED. **
** (You provided config.xml).
** **
*********************************************
[+] Alloc_Soilgrid...
[+] Set_Polygon_Coordinates...
[+] Sfcdata_ED...
[+] Load_Ecosystem_State...
+ Doing sequential initialization over nodes.
+ Initializing from ED restart file. Node: 001
[-] filelist_f: Checking prefix: /data/sites/Santarem_Km83/s83_default.
+ Showing first 10 files:
[-] File #: 1 /data/sites/Santarem_Km83/s83_default.lat-3.018lon-54.971.css
[-] File #: 2 /data/sites/Santarem_Km83/s83_default.lat-3.018lon-54.971.pss
Using patch file: /data/sites/Santarem_Km83/s83_default.lat-3.018lon-54.971.pss
Using cohort file: /data/sites/Santarem_Km83/s83_default.lat-3.018lon-54.971.css
+ Initializing phenology. Node: 001
- Reading thermal sums.
+ Initializing anthropogenic disturbance forcing. Node: 001
--------------------------------------------------------
Soil information:
Polygon name : ts83
Longitude : -54.971
Latitude : -3.018
Prescribed sand and clay : T
# of sites : 1
Site : 1
- Type : 16
- Clay fraction = 5.90000E-01
- Sand fraction = 3.90000E-01
- Silt fraction = 2.00000E-02
- SLBS = 1.22460E+01
- SLPOTS = -1.52090E-01
- SLCONS = 2.30320E-06
- Dry air soil = 2.29248E-01
- Wilting point = 2.43249E-01
- Field capacity = 3.24517E-01
- Saturation = 4.27790E-01
- Heat capacity = 1.30601E+06
--------------------------------------------------------
[+] Init_Met_Drivers...
[+] Read_Met_Drivers_Init...
------------------------------
- METCYC1 = 2000
- METCYCF = 2003
- NYEARS = 2
------------------------------
IYEAR YEAR_USE
1 2001
2 2002
------------------------------
[+] Update_met_drivers...
[+] Ed_Init_Atm...
Total count in node 1 for grid 1 : POLYGONS= 1 SITES= 1 PATCHES= 18 COHORTS= 1753
Grid: 1 Poly: 1 Lon: -54.9710 Lat: -3.0180 Nplants: 0.73 Avg. LAI: 4.45 NPatches: 18 NCohorts: 660
[+] initHydrology...
initHydrology | mynum= 1 ngrids= 1 mpolys= 1 msites= 1
Allocated | mynum= 1 ngrids= 1 mpolys= 1 msites= 1
Updated | mynum= 1 ngrids= 1 mpolys= 1 msites= 1
Deallocated | mynum= 1 ngrids= 1 mpolys= 1 msites= 1
[+] Filltab_Alltypes...
[+] Finding frqsum...
[+] Loading obstime_list
File /nowhere not found!
Specify OBSTIME_DB properly in ED namelist.
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
--------------------------------------------------------------
!!! FATAL ERROR !!!
--------------------------------------------------------------
---> File: ed_init.F90
---> Subroutine: read_obstime
---> Reason: OBSTIME_DB not found!
--------------------------------------------------------------
ED execution halts (see previous error message)...
--------------------------------------------------------------
STOP fatal_error