DanielNScott
commented
8 years ago Hey Lora, I probably can't help much (since I don't use PEcAn), but maybe someone from that group will chime in. In the mean time, can you clarify what you mean when you say: "I have successfully completed runs with the ED.r82 code and am trying to migrate to ED2." ?
Do you mean you can use pecan with r82 and you're trying to update your pecan-associated version? Or roll it back? ED2 is a sort of generic specifier. "Big" releases (as far as I understand it) have been termed ED2.0, ED2.1, or ED2.2 (someone correct me if I'm wrong please). Or are you trying to run and use a clean install of the most recent ED mainline (as featured in this repository)?
robkooper
LMurphy186232
I am running ED2 pulled from the master branch within the PEcAn Ubuntu environment (running it from the command line as though I'm on a Linux machine). I have successfully completed runs with the ED.r82 code and am trying to migrate to ED2.
I have an updated ED2 ED2IN file but when I try to run it, I get a seg fault. gdb tells me the following:
Program received signal SIGSEGV, Segmentation fault. 0x00000000005668f6 in ed_load_work_from_history() at ed_para_init.F90:615 615 if (ied_init_mode /=4 .and. ied_init_mode /= 5 .and. trim(runtype) /= 'HISTORY' then
Any ideas? I am pasting in the ED2IN below.
Thanks for your help, --Lora.
!===========================================================! !==========================================================! ! 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. ! ! ! LEM for ED2 7/21/15 !------------------------------------------------------------------------------------------! $ED_NL
!----- Simulation title (64 characters). -----------------------------------------------! NL%EXPNME = 'Luquillo test 1.0' !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 = 2005 NL%ITIMEA = 0000 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! End of simulation. Information must be given in UTC time. ! !---------------------------------------------------------------------------------------! NL%IMONTHZ = 12 ! Month NL%IDATEZ = 31 ! Day NL%IYEARZ = 2011 ! Year NL%ITIMEZ = 2300 ! UTC !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 = 300 NL%RADFRQ = 300 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 = 0
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 = 18.31 NL%POI_LON = -65.74 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 = 3 NL%IQOUTPUT = 3 NL%IYOUTPUT = 0 NL%ITOUTPUT = 0 NL%ISOUTPUT = 3 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! The following variables control whether site-, patch-, and cohort-level time ! ! means and mean sum of squares should be included in the output files or not. ! ! ! ! Reasons to add them: ! ! a. Sub-polygon variables are more comprehensive. ! ! b. Explore heterogeneity within a polygon and make interesting analysis. ! ! c. More chances to create cool 3-D plots. ! ! ! ! Reasons to NOT add them: ! ! a. Output files will become much larger! ! ! b. In regional/coupled runs, the output files will be ridiculously large. ! ! c. You may fill up the disk. ! ! d. Other people's job may crash due to insufficient disk space. ! ! e. You will gain a bad reputation amongst your colleagues. ! ! f. And it will be entirely your fault. ! ! ! ! Either way, polygon-level averages are always included, and so are the instan- ! ! taneous site-, patch-, and cohort-level variables needed for resuming the run. ! ! ! ! IADD_SITE_MEANS -- Add site-level averages to the output (0 = no; 1 = yes) ! ! IADD_PATCH_MEANS -- Add patch-level averages to the output (0 = no; 1 = yes) ! ! IADD_COHORT_MEANS -- Add cohort-level averages to the output (0 = no; 1 = yes) ! !---------------------------------------------------------------------------------------! NL%IADD_SITE_MEANS = 0 NL%IADD_PATCH_MEANS = 0 NL%IADD_COHORT_MEANS = 0 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 = 1 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 = 2 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 = 0 NL%OUTSTATE = 0 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 = 1800 NL%FRQSTATE = 1 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! FFILOUT -- Path and prefix for analysis files (all but history/restart). ! ! SFILOUT -- Path and prefix for history files. ! !---------------------------------------------------------------------------------------! NL%FFILOUT = '/home/carya/Luquillo/analy/lfdp' NL%SFILOUT = '/home/carya/Luquillo/histo/lfdp' !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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. ! ! ! ! 7. Initialize from a list of both POI and gridded ED2.1 state files, organized ! ! in the same manner as 5. This method overrides the soil database info and ! ! takes the soil texture and soil moisture information from the initializing ! ! ED2.1 state file. It allows for different layering, and assigns via nearest ! ! neighbor. ! ! !---------------------------------------------------------------------------------------! NL%IED_INIT_MODE = 0 ! LEM: For testing !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 = '/home/carya/Luquillo/lfdp' !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 ! UTC NL%IDATEH = 01 ! Day NL%IMONTHH = 08 ! Month NL%IYEARH = 2000 ! Year !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 = 7
NL%NZS = 1
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 = 9 ! Default soil type if ISOILFLG = 2 (choices below:)
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 ! ! their sum doesn't exceed 1. Otherwise standard ED values will be used instead. ! !---------------------------------------------------------------------------------------! NL%SLXCLAY = 0.24 NL%SLXSAND = 0.49 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 = -2.032, -1.778, -0.9144, -0.6858, -0.1778, -0.0762, -0.0254 NL%SLMSTR = 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 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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%VEGDATABASE = '/home/carya/oge2OLD/OGE2'
NL%SOILDATABASE = '/home/carya/faoOLD/FAO' NL%LU_DATABASE = '/home/carya/ed_inputs/glu/' NL%PLANTATION_FILE = '' NL%THSUMS_DATABASE = '/home/carya/ed_inputs/' NL%ED_MET_DRIVER_DB = '/home/carya/Luquillo/LFP/LFP_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. Choose ! ! the option according to the site characteristics. ! ! 0. Flat bedrock. Flux from the bottom of the bottommost layer is zero. ! ! 1. Gravitational flow (free drainage). The flux from the bottom of the ! ! bottommost layer is due to gradient of height only. ! ! 2. Lateral drainage. Similar to free drainage, but the gradient is ! ! reduced by the slope not being completely vertical. The reduction is ! ! controlled by variable SLDRAIN. In the future options 0, 1, and 2 may ! ! be combined into a single option. ! ! 3. Aquifer. Soil moisture of the ficticious layer beneath the bottom is ! ! always at saturation. ! !---------------------------------------------------------------------------------------! NL%ISOILBC = 1 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! SLDRAIN -- This is used only when ISOILBC is set to 2. In this case SLDRAIN is the ! ! equivalent slope that will slow down drainage. If this is set to zero, ! ! then lateral drainage reduces to flat bedrock, and if this is set to 90, ! ! then lateral drainage becomes free drainage. SLDRAIN must be between 0 ! ! and 90. ! !---------------------------------------------------------------------------------------! NL%SLDRAIN = 10. !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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. ! ! ! ! LEM: Copying the example here ! !---------------------------------------------------------------------------------------! NL%RK4_TOLERANCE = 0.001 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 = 0 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 = 0 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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). ! ! 3. Similar to 2, except that tropical leaf biomass is estimated from ! ! Lescure et al. (1983), and PFT differences on bleaf are based on SLA ! ! instead of wood density. Also, the leaf allometry is split into ! ! small classes ("saplings") and large classes ("trees"), like in Cole ! ! and Ewel (2006). ! !---------------------------------------------------------------------------------------! NL%IALLOM = 0 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 = 1 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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. Original 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. ! ! 2. Updated two-stream model (Liou 2002), 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 = 2 NL%LTRANS_VIS = 0.050 NL%LTRANS_NIR = 0.270 NL%LREFLECT_VIS = 0.150 NL%LREFLECT_NIR = 0.540 NL%ORIENT_TREE = 0.100 NL%ORIENT_GRASS = -0.100 NL%CLUMP_TREE = 0.800 NL%CLUMP_GRASS = 1.000 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! DECOMP_SCHEME -- This specifies the dependence of soil decomposition on temperature. ! ! 0. ED-2.1 default, the original exponential (low temperature ! ! limitation only). ! ! 1. Lloyd and Taylor (1994) model ! ! [[option 1 requires parameters to be set in xml]] ! ! 2. Similar to ED-1.0 and CENTURY model, heterotrophic respiration ! ! reaches a maximum at around 38C (using the default parameters), ! ! then quickly falls to zero at around 50C. It applies a similar ! ! function for soil moisture, which allows higher decomposition ! ! rates when it is close to the optimal, plumetting when it is ! ! almost saturated. ! !---------------------------------------------------------------------------------------! 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 = 1 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! IDDMORT_SCHEME -- This flag determines whether storage should be accounted in the ! ! carbon balance. ! ! 0 -- Carbon balance is done in terms of fluxes only. This is the ! ! default in ED-2.1 ! ! 1 -- Carbon balance is offset by the storage pool. Plants will be ! ! in negative carbon balance only when they run out of storage ! ! and are still losing more carbon than gaining. ! ! ! ! CBR_SCHEME -- This flag determines which carbon stress scheme is used: ! ! 0 -- Single stress. CBR = cb/cb_mlmax ! ! cb_mlmax is the carbon balance in full sun and no moisture ! ! limitation ! ! 1 -- Co-limitation from light and moisture ! ! CBR_LIGHT = cb/cb_lightmax and CBR_MOIST = cb/cb_moistmax ! ! CBR_LIGHT and CBR_MOIST are then weighted according to ! ! DDMORT_CONST (below) ! ! 2 -- Leibig Style, i.e. limitation from either light or moisture ! ! depending on which is lower at a given point in time ! ! CBR = cb/max(cb_lightmax, cb_moistmax) ! ! ! ! DDMORT_CONST -- CBR_Scheme = 1 only ! ! This constant (k) determines the relative contribution of light ! ! and soil moisture to the density-dependent mortality rate. Values ! ! range from 0 (soil moisture only) to 1 (light only). ! ! ! ! mort1 ! ! mu_DD = ------------------------- ! ! 1 + exp [ mort2 * CBR ] ! ! ! ! 1 DDMORT_CONST 1 - DDMORT_CONST ! ! ------------ = ------------------ + ------------------ ! ! CBR - CBR_SS CBR_LIGHT - CBR_SS CBR_MOIST - CBR_SS ! ! ! !---------------------------------------------------------------------------------------! NL%IDDMORT_SCHEME = 0 NL%DDMORT_CONST = 0.8 NL%CBR_SCHEME = 0 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 = 1.00 NL%VMFACT_C4 = 1.00 NL%MPHOTO_TRC3 = 9.0 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 = 0.080 NL%ALPHA_C4 = 0.055 NL%KLOWCO2IN = 4000. NL%RRFFACT = 1.000 NL%GROWTHRESP = 0.333 NL%LWIDTH_GRASS = 0.05 NL%LWIDTH_BLTREE = 0.10 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. ! ! 3. Fire will be triggered with enough biomass and accumulated ! ! water deficit exceeds the threshold given by SM_FIRE times. ! ! the total precipitation of the past 12 months. This method ! ! does not directly depend on soil texture. ! ! 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 or 3, and it has different ! ! meanings. The sign here matters. ! ! When INCLUDE_FIRE = 2: ! ! >= 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. ! ! When INCLUDE_FIRE = 3, values between 0 and 2 are allowed. This is ! ! the minimum water deficit relative to the total rainfall, over the ! ! past 12 months, to trigger fires. ! !---------------------------------------------------------------------------------------! NL%INCLUDE_FIRE = 0 NL%FIRE_PARAMETER = 0.5 NL%SM_FIRE = 0.07 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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) and LEAF-3 (Walko et al. 2000). ! ! Roughness and displacement height are found using simple relations ! ! with vegetation height; wind is computed using the similarity theory ! ! for the top cohort, then it is assumed that wind extinguishes follow- ! ! ing an exponential decay with "perceived" cumulative LAI (local LAI ! ! with finite crown area). ! ! 1. The default ED-2.1 scheme, similar to option 0, but the wind profile ! ! is not based on LAI, instead it used the cohort 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 = 1 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 = 0 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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). !
! | 18 - Western Hardwoods ! ! | 19 - Western Pines ! ! | 20 - Firs ! ! | 21 - Dryland C4 grass ! ! | 22 - Dryland C3 grass ! !---------------------------------------------------------------------------------------! NL%INCLUDE_THESE_PFT = 2,3,4 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 = 1 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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. ! ! ! ! IMPORTANT: If MAXPATCH = -1 or 1, then the model will force fusion ! ! until the total number of patches is 1 for each land ! ! use type. ! ! ! ! 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 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 = 10800 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 ! ! ! ! LEM: My choices: ! ! TOTAL_AGB - Polygon Total Above Ground Biomass ([kgC/m2]) ! ! TOTAL_BASAL_AREA - Polygon Total Basal Area ([cm2/m2]) ! ! TOTAL_BASAL_AREA_GROWTH - Polygon basal area gained through growth ([kgC/m2/yr]) ! ! TOTAL_BASAL_AREA_MORT - Polygon basal area lost through growth ([cm2/m2/yr]) ! ! TOTAL_BASAL_AREA_RECRUIT - Polygon basal area gained by recruits ([cm2/m2/yr]) ! ! BSEEDS - Polygon seed biomass ([kgC/m2]) ! ! More to be added, I'm sure, for debugging and diagnostics !---------------------------------------------------------------------------------------! NL%IPRINTPOLYS = 0 NL%NPVARS = 6 NL%PRINTVARS = 'TOTAL_AGB','TOTAL_BASAL_AREA','TOTAL_BASAL_AREA_GROWTH', 'TOTAL_BASAL_AREA_MORT','TOTAL_BASAL_AREA_RECRUIT','BSEEDS' NL%PFMTSTR = 'f10.8','f10.8','f10.8','f10.8','f10.8','f10.8' 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 = 2005 NL%METCYCF = 2011 NL%IMETAVG = 1 NL%IMETRAD = 2 NL%INITIAL_CO2 = 371.0 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 = 2005 NL%IPHENYSF = 2011 NL%IPHENYF1 = 2005 NL%IPHENYFF = 2011 NL%PHENPATH = ''
!---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 = '' NL%EVENT_FILE = '' !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! Census variables. This is going to create unique census statuses to cohorts, to ! ! better compare the model with census observations. In case you don't intend to ! ! compare the model with census data, set up DT_CENSUS to 1., otherwise you may reduce ! ! cohort fusion. ! ! DT_CENSUS -- Time between census, in months. Currently the maximum is 60 ! ! months, to avoid excessive memory allocation. Every time the ! ! simulation reaches the census time step, all census tags will be ! ! reset. ! ! YR1ST_CENSUS -- In which year was the first census conducted? ! ! MON1ST_CENSUS -- In which month was the first census conducted? ! ! MIN_RECRUIT_DBH -- Minimum DBH that is measured in the census, in cm. ! ! ! ! LEM: Not sure what to do with this yet. Our censuses were more than 60 months apart. ! ! Not going to use this for now. ! !---------------------------------------------------------------------------------------! NL%DT_CENSUS = 1 NL%YR1ST_CENSUS = 1901 NL%MON1ST_CENSUS = 7 NL%MIN_RECRUIT_DBH = 10 !---------------------------------------------------------------------------------------!
!---------------------------------------------------------------------------------------! ! 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 = '' !---------------------------------------------------------------------------------------! $END