Namelist Option Summary Tables

The namelist options are governed by the Host Land Model (HLM) that drives FATES. Efforts are made to keep these options consistent in the different driving models (e.g. E3SM/CSTM/etc).

For more information on how to set and use these modes, click on the links in the table where available.

Basic Usage Options

The following table discusses the basic usage options and settings to enable FATES in the Host Land Model. Note that compsets with FATES in the name, for example _ELMXX%FATES_, will set use_fates to true to automatically turn on FATES. Also note that each HLM provides a default fates parameter file that is stored on the public input data servers. See the page discussing the Parameter File for more information on modifying the default parameter file that is provided within the FATES source code.

Option	Type	Default	Options	Description
use_fates	Boolean	.true.	.true. .false.	Turns on/off fates!
fates_paramfile	String	default file	-	path to an alternative netcdf fates parameter file

Control of History Complexity

All FATES history output variables are categorized as either a complex variable (having more than time x space dimensions), or a simple variable (just time and space). They are also broken up by being calculated at the dynamics timescale (daily) or at the high-frequency timescale (half-hourly). Users may wish to either competely deactivate all variables at one of these timescales. Or, perhaps they want just the simple variables. Or, perhaps they want everything, even if it slows the simulation down a little bit. This is controlled by “fates_history_dimlevel”, and its slightly different in E3SM compared to CTSM. In both cases, the high-frequency timescale variables are the first index:

E3SM Option	Type	Default	Options	Description
fates_history_dimlevel(1)	Integer	2	0 1 2	high-frequency: 0 = no fates history variables are calculated or allocated, 1 = only time x space (3d) fates history variables allowed, 2 = multiplexed dimensioned fates history is also allowed
fates_history_dimlevel(2)	Integer	2	0 1 2	daily frequency: …

CTSM Option	Type	Default	Options	Description
fates_history_dimlevel	Integer list	2,2	0 1 2	high-frequency, daily-frequency: 0 = no fates history variables are calculated or allocated, 1 = only time x space (3d) fates history variables allowed, 2 = multiplexed dimensioned fates history is also allowed

Reduced Complexity Modes

The full FATES model has a high degree of complexity. In order to isolate different processes to allow for cleaner experimental design and facilitate calibration and testing of different model components, FATES includes a number of reduced-complexity configurations. A summary of these configurations is shown in table FATES reduced complexity modes table below:

Option	Type	Default	Options	Description
use_fates_ed_prescribed_phys	Boolean	.false.	.true. .false.	Turns on/off Prescribed Physiology mode
use_fates_ed_st3	Boolean	.false.	.true. .false.	Turns on/off Static Stand Structure mode
use_fates_fixed_biogeog	Boolean	.false.	.true. .false.	Turns on/off fixed biogeography mode
use_fates_nocomp	Boolean	.false.	.true. .false.	Turns on/off no-competition mode
use_fates_sp	Boolean	.false.	.true. .false.	Turns on/off satellite phenology mode

For the nocomp and fixed biogeography, there are logical interactions between them, so what happens is related to the values of both switches. This logic looks like:

	use_fixed_biogeog = .true.	use_fixed_biogeog = .false.
use_fates_nocomp = .true.	Every PFT is given its own patch and the patch area for each PFT corresponds to the observed map	Every PFT is given its own patch and every PFT is given the same amount of patch area everywhere
use_fates_nocomp = .false.	Competition happens, but only between the PFTs that are allowed on a given gridcell	Competition occurs and governs the distribution of PFTs

For namelist entries that control the soil properties, or biogeochemical cycling, please refer to the host land-model documentation. Also, compare the desired namelist entries with the defaults generated by a FATES compset. Please create issues with questions regarding incompatibilities until more comprehensive documentation becomes available.

Model Components

The namelist options for the various model components of FATES are presented in the subsections below.

Damage and Mortality

Option	Type	Default	Options	Description
use_fates_cohort_age_tracking	Boolean	.false.	.true. .false.	Turns on/off Cohort age tracking mode
use_fates_tree_damage	Boolean	.false.	.true. .false.	Turns on/of tree crown damage
fates_cstarvation_model	String	'linear'	'linear' 'exponential'	Sets the FATES carbon starvation model

Fire

Option	Type	Default	Options	Description
fates_spitfire_mode	Integer	0	0 1 2 3 4	SPITFIRE Namelist Options

Hydraulics

Option	Type	Default	Options	Description
use_fates_planthydro	Boolean	.false.	.true. .false.	Turns on/off the plant hydrodynamics module
fates_hydro_solver	String	'1D_Taylor'	'1D_Taylor' '2D_Picard' '2D_Newton'	Sets the FATES hydro solver method

Inventory

Option	Type	Default	Options	Description
fates_inventory_ctrl_filename	String	empty	-	When inventory initialization true, points to control file
use_fates_inventory_init	Boolean	.false.	.true. .false.	Turns on/off initialization from plant inventory data

Land Use and Harvest

Option	Type	Default	Options	Description
use_fates_luh	Boolean	.false.	.true. .false.	Turns on/off land use.
use_fates_lupft	Boolean	.false.	.true. .false.	If true, enables the use of fates land use x pft mapping data file.
use_fates_potentialveg	Boolean	.false.	.true. .false.	If true, assert that all lands are primary and that there is no harvest.
fluh_timeseries	String	empty	-	Full pathname of unified land use harmonization data file.
flandusepftdat	String	empty	-	Full pathname of FATES landuse x pft data map.
fates_harvest_mode	String	'no_harvest'	'no_harvest' 'event_code' 'landuse_timeseries' 'luhdata_area' 'luhdata_mass'	See Land use namelist options
fates_lu_transition_logic	Integer	4	1,2,3,4,5,6,7,8,9	Selects the landuse clearing matrix. See Land use namelist options

Nutrients

Option	Type	Default	Options	Description
fates_parteh_mode	Integer	1	1 2	Specifies which plant allocation model to use

Photosynthesis

Option	Type	Default	Options	Description
use_fates_daylength_factor	Boolean	.true.	.true. .false.	Switch to enable FATES to use the day length factor from the host land model
fates_electron_transport_model	String	'FvCB1980'	.true. .false.	Selects the type of electron transport model
fates_photosynth_acclimation	String	'nonacclimating'	'nonacclimating' 'kumarathunge2019'	Set the FATES photosynthesis temperature acclimation model
fates_stomatal_assimilation	String	'net'	'net' 'gross'	Set net or gross asslimiation for the FATES stomatal model
fates_stomatal_model	String	'ballberry1987'	'ballberry1987' 'medlyn2011'	Set the FATES stomatal conductance model
fates_radiation_model	String	'norman'	'norman' 'twostream'	Sets the FATES radiation model

Respiration

Option	Type	Default	Options	Description
fates_leafresp_model	String	'ryan1991'	'ryan1991' 'atkin2017'	Sets the FATES leaf maintenance respiration model

Seeds

Option	Type	Default w/FATES compset	Options	Description
fates_regeneration_model	String	'default'	'default' 'trs' 'trs_no_seed_dyn'	Sets the FATES seed regeneration model
fates_seeddisp_cadence	Integer	1	0 1 2 3	Switch defining the cadence at which seeds are dispersed across gridcells, 0 = no seed dispersal, 1 = daily, 2 = monthly, 3 = yearly.

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How to modify namelist options

Both E3SM and CTSM (as of Jan 2018) use the file “user_nl_clm” as the means of modifying the namelist entries from the default values generated by different compsets. In this file, append a line for each option, with syntax “<option_name> = <option_value>”. Each line should be appended to the end of the file, usually just below the comments at the header of the file.

Example:

> use_fates_planthydro = .true.

This user control file will be interpreted when the script “./case.build” is called. It will then use this information to generate the “lnd_in” file located in the run directory.”