CESM3.0a CTSM5.4 Namelist Definitions

Multiplier for heterotrophic respiration for max denitrification rates

Exponent power for heterotrophic respiration for max denitrification rates

Turn on extra output for the matrix solution

The restart file will be based on the average of all analytic solutions within the iloop_avg^th loop.
eg. if nyr_forcing = 20, iloop_avg = 8, the restart file in yr 160 will be based on analytic solutions from yr 141 to 160.
The number of the analytic solutions within one loop depends on ratio between nyr_forcing and nyr_SASU.
eg. if nyr_forcing = 20, nyr_SASU = 5, number of analytic solutions is 20/5=4

Maximum nitrification rate constant (1/s)

Number of years to average the storage capacitance over for the soil Matrix solution during semi-analytic spinup (spinup_matrixcn=T)
Normally should be the same as the number of years the atmospheric forcing is run over

length of each semi-analytic solution. eg. nyr_SASU=5, analytic solutions will be calculated every five years.
nyr_SASU=1: the fastest SASU, but inaccurate; nyr_SASU=nyr_forcing(eg. 20): the lowest SASU but accurate

Turn on semi-analytic spinup solution for the CN/Soil matrix, requires soil matrix to be on
This will drive the solution to equilibrium

CLM Biogeochemistry mode : Carbon Nitrogen model (CN)
(or CLM45BGC if phys=clm4_5, vsoilc_centbgc='on', and clm4me='on')

CLM Biogeochemistry mode : Carbon Nitrogen with Dynamic Global Vegetation Model (CNDV)
(or CLM45BGCDV if phys=clm4_5, vsoilc_centbgc='on', and clm4me='on')
(deprecated -- will be removed)

Turn the Fixation and Uptate of Nitrogen model version 2 (FUN2.0)
Requires the CN model to work (either CN or CNDV).

Turn on methane model. Standard part of CLM45BGC model.

Turn on the Matrix solution for above ground biogeochemistry, requires CN to be on

Nitrification/denitrification splits the prognostic mineral N pool into two
   mineral N pools: NO3 and NH4, and includes the transformations between them.
Turned on for BGC
FATES currently allows it to be true or false, but will be hardwired to true later

   use_nvmovement = true use soil nitrogen vertical movement
   use_nvmovement = false do not use soil nitrogen vertical movement
   use_nvmovement cannot be true while use_nitrif_denitrif is false

Turn on the Matrix solution for soil biogeochemistry

Filename with time series of atmospheric Delta C13 data, which use CMIP6 format.  variables in file are "time" and "delta13co2_in_air".  time variable is in format: years since 1850-01-01 0:0:0.0. units are permil.

Filename with time series of atmospheric Delta C14 data.  variables in file are "time" and "Delta14co2_in_air". time variable is in format: years since 1850-01-01 0:0:0.0  units are permil.

There is a bug that causes incorrect values for C isotopes if running
init_interp from a case without C isotopes to a case with C isotopes
(https://github.com/ESCOMP/ctsm/issues/67). Normally, an error-check
prevents you from doing this interpolation (until we have fixed that
bug). However, we sometimes want to bypass this error-check in system
tests. This namelist flag bypasses this error-check.

Enable C13 model

Flag to use the atmospheric time series of C13 concentrations from natural abundance and the Seuss Effect, rather than static values.

Enable C14 model

Flag to use the atmospheric time series of C14 concentrations from bomb fallout and Seuss effect, rather than natural abundance C14 (nominally set as 10^-12 mol C14 / mol C)

Minimum lake depth to increase non-molecular thermal diffusivities by the factor deepmixing_mixfact.

Factor to increase non-molecular thermal diffusivities for lakes deeper than deepmixing_depthcrit
to account for unresolved 3D processes.
Set to 1 to

Visible and Near-infrared albedo values for melting lakes. Albedo will relax to these values as temperature
reaches melting when ice is present with no snow layers. Represents puddling, ice disintegration, and white ice.
Set to alblak values (0.6, 0.4) to keep albedo constant for ice-covered lakes without snow layers.

If TRUE, turn on methane biogeochemistry model for lake columns, using a simplified version of the CH4 submodel.
(EXPERIMENTAL, UNSUPPORTED!)

If TRUE, run the methane submodel decoupled from the atmosphere. The atmospheric methane concentration is prescribed by
atmch4, the methane flux is not passed to the atmosphere, and the CO2 flux to the atmosphere is not adjusted for
net methane production. NOTE: Currently this must be TRUE.
(EXPERIMENTAL, UNSUPPORTED, and NOT functional!)

Inundated fraction method type to use for the CH4 submodel (possibly affecting soil
heterotrophic respiration and denitrification depending on the configuration),

h2osfc ----------- Use prognostic saturated fraction h2osfc value calculated in Soil Hydrology
ZWT_inversion ---- Use inversion of Prigent Satellite data to model ZWT
TWS_inversion ---- Use inversion of Prigent Satellite data to model TWS

Inversion options require additional data on fsurdat or use of stream_fldfilename_ch4finundated files.
(h2osfc option is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)

If TRUE, maintain constant soil carbon under lakes, and use the methane submodel simply to predict the net conversion of
CO2 (via biological assimilation, decomposition, and methanogenesis) to CH4. If FALSE, transiently decompose initial
soil carbon stock based on soil carbon dataset.  NOTE: if FALSE, a new transient source of C is added to the climate system,
so the coupled system will NOT conserve carbon in this mode if the methane model is coupled to the atmosphere.
(EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)

Allows user to tune the value of aereoxid.  If set to FALSE, then use the value of aereoxid from
the parameter file (set to 0.0, but may be tuned with values in the range {0.0,1.0}.  If set to TRUE,
then don't fix aere (see ch4Mod.F90).

If TRUE, use the fine root carbon predicted by CN when calculating the aerenchyma area, rather than the parametrization
based on annual NPP, aboveground NPP fraction, and LAI.
(EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)

If TRUE, apply a limitation to methane production based on the soil pH dataset.
(EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)

Michaelis-Mentin maximum methane oxidation rate (mol/m^3-water/s), in the unsaturated zone.

Carbon respiration option to burn off carbon when CN ratio is too high (do NOT use when FUN is on)
(EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)

Evergreen phenology option for CNPhenology
(EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)

   Flexible CN ratio used for Phenology
(EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)

How much Carbon to initialize vegetation pools (leafc/frootc and storage) to when -- Michaelis Menten nitrogen uptake kinetics is on

How LUNA and Photosynthesis (if needed) will get Leaf nitrogen content
   lnc_opt = true  get from leaf N from CN model
   lnc_opt = false get based on LAI and fixed CN ratio from parameter file

   Michaelis Menten nitrogen uptake kinetics

   Reduce day length factor
(NOT implemented)

Allow the CN ratio to flexibly change with the simulation, rather than being fixed

Vcmax calculation for Photosynthesis
    vcmax_opt = 4 As for vcmax_opt=0, but using leafN, and exponential if tree (EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)
    vcmax_opt = 3 Based on leafN and VCAD (used with Luna for crop and C4 vegetation)
    vcmax_opt = 0 Based on canopy top and foilage Nitrogen limitation factor from params file (clm4.5)

Clumps per processor.

number of segments per clump for decomposition

If TRUE, weight btran (vegetation soil moisture availability) by unfrozen layers only, assuming that vegetation
will allocate roots preferentially to the active layer.
(EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)

If TRUE, weight btran (vegetation soil moisture availability) by the active layer, as defined by the greatest thaw depth over the current and prior years.
(EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)

Visible and Near-infrared albedo's for glacier ice

If TRUE, make ALL pfts, columns and landunits active, even those with 0 weight.
This means that computations will be run even over these 0-weight points.

THIS IS ONLY FOR TESTING PURPOSES - IT HAS NOT BEEN CHECKED FOR SCIENTIFIC VALIDITY.

boreal peat fires (/hr)

Denominator of exponential in soil moisture term of equation relating that and temperature to boreal peat fire (unitless). Eq. 10 in Li et al. (2013, doi:10.5194/bg-10-2293-2013).

CN Maintenence Respiration base rate for roots
(if NOT set, use the value for br_mr on the params file)

Saturation BTRAN for ignition (0-1)

Critical BTRAN for ignition (0-1)

0 = simpler method (clm4_5)
1 = prognostic calculation of interior building temp (clm5_0)

Human heat stress indices:
    ALL  = All indices will be calculated
    FAST = A subset of indices will be calculated (will not include the computationally
           expensive wet bulb calculation and associated indices)
    NONE = No indices will be calculated

Critical threshold for truncation of Carbon (truncate Carbon states to zero below this value)

Global constant for deforestation fires (/day)

Combustion completeness factor for CWD[Course Woody Debris] (unitless)

Combustion completeness factor for litter (unitless)

Critical threshold of negative Carbon to die (abort when Carbon states are below this value)

Atmospheric CO2 molar ratio (by volume) only used when co2_type==constant (umol/mol)
(Set by CCSM_CO2_PPMV)

Type of CO2 feedback.
    constant   = use the input co2_ppmv value
    prognostic = use the prognostic value sent from the atmosphere
    diagnostic = use the diagnostic value sent from the atmosphere

If TRUE use additional stress deciduous onset trigger

If TRUE, separate the vegetated landunit into a crop landunit and a natural vegetation landunit

If TRUE, fsat will be set to zero for crop columns.

Scalar for cropfire (/hr)

Value (mm/d) above which running mean daily precipitation (10 or 60 days) does not allow deforestation fire for a column with broadleaf deciduous tropical trees but no broadleaf evergreen tropical trees. "PFT-dependent thresholds of P60d and P10d" in Li et al. (2013, doi:10.5194/bg-10-2293-2013).

Value (mm/d) above which running mean daily precipitation (10 or 60 days) does not allow deforestation fire for a column with broadleaf evergreen tropical trees but no broadleaf deciduous tropical trees. "PFT-dependent thresholds of P60d and P10d" in Li et al. (2013, doi:10.5194/bg-10-2293-2013).

option to activate organic carbon (OC) in SNICAR snow albedo calculation
(do_sno_oc='.true.' is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)

Harvest the XSMR pool at crop harvest time to the atmosphere slowly at an exponential rate

minimum time step length (seconds) for adaptive time stepping in richards equation

If .true., run with water isotopes

If .true., add water tracers needed to perform water tracer consistency checks.

These consistency checks ensure that all water tracers are updated to remain in-sync with
the related bulk quantities.

Soil depth below which initial excess ice concentration will be applied during a run starting with coldstart (m). Value only applys if use_excess_ice is true.
If this is set below depth of the soil depth, only the last soil layer will get excess ice.

Initial soil temperature to use for gridcells with excess ice present during a run starting with coldstart (deg C). Value only applys if use_excess_ice is true.

The method type to use for CNFire

nofire:        Turn fire effects off
li2014qianfrc: Reference paper Li, et. al.(2014) tuned with QIAN atmospheric forcing
li2016crufrc:  Reference paper Li, et. al.(2016) tuned with CRU-NCEP atmospheric forcing
li2021gswpfrc: No reference paper yet, tuned with GSWP3 atmospheric forcing
li2024gswpfrc: No reference paper yet, tuned with GSWP3 atmospheric forcing
li2024crujra:  No reference paper yet, tuned with CRU-JRA forcing (CRUJRA2024)

Intercept of free living Nitrogen fixation with zero annual ET

Slope of free living Nitrogen fixation with annual ET

Behavior of each glacier region (GLACIER_REGION in surface dataset).
First item corresponds to GLACIER_REGION with ID 0 in the surface dataset,
second to GLACIER_REGION with ID 1, etc.
Allowed values are:
'multiple': grid cells can potentially have multiple glacier elevation classes,
   but no virtual columns
'virtual': grid cells have virtual columns: values are computed for every glacier
   elevation class, even those with 0 area (in order to provide surface mass
   balance for every glacier elevation class).
'single_at_atm_topo': glacier landunits in these grid cells have a single column,
   whose elevation matches the atmosphere's topographic height (so that there is no
   adjustment due to downscaling)
'UNSET': place-holder for non-existent regions
Most (if not all) of the region where there is an ice sheet model should have a behavior
of 'virtual': This behavior is needed to compute surface mass balance (SMB) in all
elevation classes for the sake of vertical downscaling, and is needed to allow two-way
feedbacks of glacier areas. You are allowed to have gridcells with non-virtual behavior in
this domain, but this should be minimized: SMB cannot be computed there, and CLM subgrid
areas will not remain in sync with the GLC model. (Within the icemask - i.e., the active
glc domain - you are NOT allowed to have gridcells with non-virtual behavior that also
have glacier_region_melt_behavior='replaced_by_ice': within the icemask, you're only
allowed to have non-virtual behavior in places where you are not computing SMB).

Treatment of ice runoff for each glacier region (GLACIER_REGION in surface dataset).
First item corresponds to GLACIER_REGION with ID 0 in the surface dataset,
second to GLACIER_REGION with ID 1, etc.
Allowed values are:
'remains_ice': ice runoff is sent to the river model as ice; this is a crude parameterization
   of iceberg calving, and so is appropriate in regions where there is substantial iceberg calving
   in reality
'melted': ice runoff generated by the CLM physics (primarily due to snow capping) is melted
   (generating a negative sensible heat flux) and runs off as liquid; this is appropriate in
   regions that have little iceberg calving in reality. This can be important to avoid unrealistic
   cooling of the ocean and consequent runaway sea ice growth. This option cannot be
   combined with glacier_region_melt_behavior='replaced_by_ice': While there is nothing
   fundamentally wrong with this combination, it can result in problematic, non-physical
   fluxes (particularly, a large positive sensible heat flux during glacial melt in
   regions where the ice sheet is not fully dynamic and two-way-coupled; see
   https://github.com/ESCOMP/ctsm/issues/423 for details).
'UNSET': place-holder for non-existent regions
Only applies when melt_non_icesheet_ice_runoff is .true.

Treatment of ice melt for each glacier region (GLACIER_REGION in surface dataset).
First item corresponds to GLACIER_REGION with ID 0 in the surface dataset,
second to GLACIER_REGION with ID 1, etc.
Allowed values are:
'replaced_by_ice': any melted ice runs off and is immediately replaced by solid ice;
   this results in positive liquid runoff and negative ice runoff
'remains_in_place': any melted ice remains in place as liquid until it refreezes;
   thus, ice melt does not result in any runoff
'UNSET': place-holder for non-existent regions
IMPORTANT NOTE: Regions with the 'remains_in_place' behavior also do not compute SMB
(because negative SMB would be pretty much meaningless in those regions). Thus, most (if
not all) of the region where there is an ice sheet model should have the 'replaced_by_ice'
behavior; the SMB sent to the GLC model will be 0 in any gridcells with the
'remains_in_place' behavior.
Regions with the 'replaced_by_ice' behavior also compute SMB for the vegetated column.

If TRUE, dynamically change areas and topographic heights over glacier points.
Only works when running with a non-stub glacier model.

Number of days before one considers the perennially snow-covered point 'land ice'
(and thus capable of generating a positive surface mass balance for the glacier model).
This is meant to compensate for the fact that, with small values of h2osno_max,
the onset of a snow-capped state (and thus conversion to land ice) can occur in an
unrealistically short amount of time.
Thus, in general, large values of h2osno_max should have glc_snow_persistence_max_days = 0;
small values of h2osno_max should have glc_snow_persistence_max_days > 0.

If TRUE, downscale longwave radiation over glacier landunits.
This downscaling is conservative.

If surface water is active or not
(deprecated -- will be removed)

Maximum snow depth in mm H2O equivalent. Additional mass gains will be capped when this depth
is exceeded.
Changes in this value should possibly be accompanied by changes in:
- nlevsno: larger values of h2osno_max should be accompanied by increases in nlevsno
- glc_snow_persistence_max_days: large values of h2osno_max should generally have
  glc_snow_persistence_max_days = 0; small values of h2osno_max should generally have
  glc_snow_persistence_max_days > 0.

Limit applied to integrated snowfall when determining changes in snow-covered fraction during melt
(mm H2O)
Only applies when using the SwensonLawrence2012 snow cover fraction method

Soil depth to which we measure for irrigation (m)

Desired amount of time to irrigate per day (sec).
Actual time may differ if this is not a multiple of dtime.

Irrigation method used if not specified on surface dataset

Minimum leaf area index for irrigation to occur

Threshold for river water volume below which irrigation is shut off (as a fraction of available river water), if limit_irrigation_if_rof_enabled is .true.
A threshold of 0 means allow all river water to be used;
a threshold of 0.1 means allow 90% of the river volume to be used; etc.

Time of day to check whether we need irrigation, seconds (0 = midnight).
We start applying the irrigation in the time step FOLLOWING this time.

Target soil matric potential for irrigation (mm).
When we irrigate, we aim to bring the total soil moisture in the top (irrig_depth) m of soil up to this level.

Determines soil moisture threshold at which we irrigate.
If h2osoi_liq_wilting_point is the soil moisture level at wilting point and
h2osoi_liq_target is the soil moisture level at the target irrigation level
(given by irrig_target_smp), then the threshold at which we irrigate is
    h2osoi_liq_wilting_point +
         irrig_threshold_fraction*(h2osoi_liq_target - h2osoi_liq_wilting_point)
A value of 1 means that we irrigate whenever soil moisture falls below the target.
A value of 0 means that we only irrigate when soil moisture falls below the wilting point.

If TRUE, irrigation will be active.

Max number of iterations used in subr. CanopyFluxes. For many years, 40 was the hardwired default value.

Surface temperature lapse rate (K m-1)
A positive value means a decrease in temperature with increasing height

Longwave radiation lapse rate (W m-2 m-1)
A positive value means a decrease in LW radiation with increasing height
Only relevant if glcmec_downscale_longwave is .true.

Scalar of leaf respiration to vcmax

Leaf maintencence respiration for canopy top at 25C method to use

    0  Scaled by vcmax25top
    1  Ryan 1991
    2  Atkin 2015

Lower threshold for fuel mass needed for ignition

Switch to inihibit photosynthesis in daytime
Lloyd et al. 2010, & Metcalfe et al. 2012

If TRUE, limit irrigation when river storage drops below a threshold.
Only applies if using an active runoff (ROF) model; otherwise, river storage-based limitation
is turned off regardless of the setting of this namelist variable.

Relative limit for how much longwave downscaling can be done (unitless)
The pre-normalized, downscaled longwave is restricted to be in the range
[lwrad*(1-longwave_downscaling_limit), lwrad*(1+longwave_downscaling_limit)]
This parameter must be in the range [0,1]
Only relevant if glcmec_downscale_longwave is .true.

Snow density method to use for low temperatures (below -15C)
TruncatedAnderson1976 -- Truncate the Anderson-1976 equation at the value for -15C
Slater2017 ------------- Use equation from Slater that increases snow density for very cold temperatures  (Arctic, Antarctic)

Index of lower boundary condition for Richards equation.

lower_boundary_condition = 1 : flux lower boundary condition                                     (use with soilwater_movement_method=adaptive time stepping)
lower_boundary_condition = 2 : zero-flux lower boundary condition                                (use with soilwater_movement_method=adaptive time stepping)
lower_boundary_condition = 3 : water table head-based lower boundary condition w/ aquifer layer. (use with soilwater_movement_method=adaptive time stepping)
lower_boundary_condition = 4 : 11-layer solution w/ aquifer layer                                (only used with soilwater_movement_method=Zeng&Decker 2009)

TODO(bja, 2015-09) these should be strings so they have meaningful names instead of ints.

Value above which 30-day running relative humidity has no effect on fuel combustibility

Number of  multiple elevation classes over glacier points.

If TRUE, ice runoff generated from non-glacier columns and glacier columns outside icesheet regions
is converted to liquid, with an appropriate sensible heat flux.
That is, the atmosphere (rather than the ocean) melts the ice.
(Exception: ice runoff generated to ensure conservation with dynamic landunits remains as ice.)

Modify photosynthesis and leaf maintence respiration for crop

SCA shape parameter for glc_mec (glacier multiple elevation class) columns
For most columns, n_melt is based on the standard deviation of 1km topography in the grid cell;
but glc_mec columns already account for subgrid topographic variability through their use of
multiple elevation classes; thus, to avoid double-accounting for topographic variability
in these columns, we use a fixed value of n_melt.
Only applies when using the SwensonLawrence2012 snow cover fraction method

Critical threshold for truncation of Nitrogen (truncate Nitrogen states to zero below this value)

Number of snow layers.
Values less than 5 are mainly useful for testing, and should not be used for science.

Critical threshold of negative Nitrogen to die (abort when Nitrogen states are below this value)

non-boreal peat fires (/hr)

Denominator of precipitation in equation relating that to non-boreal peat fire (unitless). Eq. 9 in Li et al. (2013, doi:10.5194/bg-10-2293-2013).

Fire occurance for high GDP areas that are tree dominated (fraction)

If TRUE, square the organic fraction when it's used (as was done in CLM4.5)
Otherwise use the fraction straight up              (the default for CLM5.0)

Snow compaction overburden exponential factor (1/K)
Not used for snow_overburden_compaction_method=Vionnet2012

Perturbation limit when doing error growth test
(EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)
(deprecated -- will be removed)

Potential human ignition counts (/person/month)

If TRUE, repartition rain/snow from atmosphere based on temperature.

Flag to reseed any dead plants on startup from reading the initial conditions file

If set to .true., then reset the snow pack over non-glacier columns to a small value.
This is useful when transitioning from a spinup under one set of atmospheric forcings
to a run under a different set of atmospheric forcings: By resetting too-large snow packs,
we make it more likely that points will remain only seasonally snow-covered under the new
atmospheric forcings. (This is particularly true in a coupled run, where starting with a
too-large snow pack can cool the atmosphere, thus maintaining the too-large snow pack.)

WARNING: Setting this to .true. will break water conservation for approximately the first
day of the new run. This is by design: The excess snow is completely removed from the system.

If set to .true., then reset the snow pack over glacier columns to a small value.
This is useful when transitioning from a spinup under one set of atmospheric forcings
to a run under a different set of atmospheric forcings: By resetting too-large snow packs,
we make it more likely that points will remain only seasonally snow-covered under the new
atmospheric forcings. (This is particularly true in a coupled run, where starting with a
too-large snow pack can cool the atmosphere, thus maintaining the too-large snow pack.)

See also reset_snow_glc_ela, which controls the elevation below which
glacier columns are reset.

WARNING: Setting this to .true. will break water conservation for approximately the first
day of the new run. This is by design: The excess snow is completely removed from the system.

WARNING: This variable is intended for short test runs, and generally
should not be used for scientific production runs. By resetting snow
below a given elevation, you risk forcing the system to evolve
differently in areas below and above reset_snow_glc_ela.

Only relevant if reset_snow_glc is .true.

When resetting snow pack over glacier columns, one can choose to do this over all glacier
columns, or only those below a certain elevation. A typical use case is to reset only those
columns that have a seasonal snow pack in the real world, i.e. SMB less than 0, also known as
the equilibrium line altitude (ELA). This parameter sets a single global ELA value. By
setting this parameter to a large value (i.e. 10000 m), all glacier columns will be reset.

WARNING: This variable is intended for short test runs, and generally
should not be used for scientific production runs. By resetting snow
below a given elevation, you risk forcing the system to evolve
differently in areas below and above reset_snow_glc_ela.

Saturation RH for ignition (0-100)

Critical RH for ignition (0-100)

Index of rooting profile for carbon

Changes rooting profile from Zeng 2001 double exponential (0) to
Jackson 1996 single exponential (1) to Koven uniform exponential (2).

Index of rooting profile for carbon

Changes rooting profile from Zeng 2001 double exponential (0) to
Jackson 1996 single exponential (1) to Koven uniform exponential (2).

Index of rooting profile for soil carbon

Changes rooting profile from Zeng 2001 double exponential (0) to
Jackson 1996 single exponential (1) to Koven uniform exponential (2).
(REMOVE, NOT in the CODE)

Index of rooting profile for water

Changes rooting profile from Zeng 2001 double exponential (0) to
Jackson 1996 single exponential (1) to Koven uniform exponential (2).

Variant index of rooting profile for carbon and soil carbon
(Currently only used for Jackson 1996 method)

Variant index of rooting profile for water
(Currently only used for Jackson 1996 method)

Switch to turn on root and stem respiratory acclimation
Atkin, Fisher et al. (2008) and Lombardozzi et al. (2015)

If TRUE, run all urban landunits everywhere where we have valid urban data.
This forces memory to be allocated and calculations to be run even for 0-weight urban points.
This has a substantial impact on memory use and performance, and should only be used
if you're interested in potential urban behavior globally.

dust optics type for SNICAR snow albedo calculation
(snicar_dust_optics='sahara' is the only supported option; others are EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)

number of wavelength bands used in SNICAR snow albedo calculation
(snicar_numrad_snw=5 is the only supported option; others are EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)

option to activate BC-snow internal mixing in SNICAR snow albedo calculation
(snicar_snobc_intmix='.true.' is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)

option to activate dust-snow internal mixing in SNICAR snow albedo calculation
(snicar_snodst_intmix='.true.' is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)

snow grain shape used in SNICAR snow albedo calculation
(snicar_snw_shape='sphere' is supported in pre-ctsm5.1 model versions and 'hexagonal place' is supported in newer versions; others are EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)

type of downward solar radiation spectrum for SNICAR snow albedo calculation
(snicar_solarspec='mid_latitude_winter' is the only supported option; others are EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)

Toggle to turn on/off aerosol deposition flux in snow in SNICAR
(snicar_use_aerosol='.false.' is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)

Parameterization to use for snow cover fraction
NiuYang2007: Niu and Yang 2007
SwensonLawrence2012: Swenson and Lawrence 2012

Max snow thickness of layer 1 (top snow layer) when no layers beneath; values other than the default 0.03 have not been tested as of Sep 6, 2019

Max snow thickness of layer 2 when no layers beneath; values other than the default 0.07 have not been tested as of Sep 6, 2019; snow_dzmax_l of remaining layers is generated with the following recursive formula: dzmax_l(j) = dzmax_u(j) + dzmax_l(j-1)

Max snow thickness of layer 1 (top snow layer) when layers beneath; values other than the default 0.02 have not been tested as of Sep 6, 2019

Max snow thickness of layer 2 when layers beneath; values other than the default 0.05 have not been tested as of Sep 6, 2019; snow_dzmax_u of remaining layers is generated with the following recursive formula: dzmax_u(j) = 2._r8 * dzmax_u(j-1) + 0.01_r8

Min snow thickness of layer 1 (top snow layer); values other than the default 0.01 have not been tested as of Sep 6, 2019

Min snow thickness of layer 2; values other than the default 0.015 have not been tested as of Sep 6, 2019; snow_dzmin of remaining layers is generated with the following recursive formula: dzmin(j) = dzmax_u(j-1) * 0.5_r8

Method used to compute snow overburden compaction
Anderson1976 -- older method, default in CLM45
Vionnet2012 --- newer method, default in CLM50

Parameterization to use for snow thermal conductivity over glacier land units

Parameterization to use for snow thermal conductivity over lake land units

Parameterization to use for snow thermal conductivity

Whether snow on the vegetation canopy affects the radiation/albedo calculations

Soil decomposition method
  None --  No soil decomposition is done
  CENTURYKoven2013 -- CENTURY model in CTSM from Koven et. al. 2013
  MIMICSWieder2015 -- MIMICS model in CTSM from Wieder et. al. 2015

An active soil decomposition method requires the BGC or FATES model to work
And both BGC and FATES models require an active soil decomposition model

10SL_3.5m    = standard CLM4 and CLM4.5 version
23SL_3.5m    = more vertical layers for permafrost simulations
49SL_10m     = 49 layer soil column, 10m of soil, 5 bedrock layers
20SL_8.5m    = 20 layer soil column, 8m of soil, 5 bedrock layers
4SL_2m       = 4 layer soil column, 2m of soil, 0 bedrock layers

User-defined vector of dzsoi. The length of this vector determines nlevgrnd. When the user sets this vector, they have to set soil_layerstruct_userdefined_nlevsoi in the namelist, too; soil_layerstruct_userdefined_nlevsoi must be less than nlevgrnd in this version of the model, even though ideally soil_layerstruct_userdefined_nlevsoi could also equal nlevgrnd.

User-defined number of soil layers required to be set in the namelist when the user sets soil_layerstruct_userdefined in the namelist.

Index of evaporative resistance method.

Changes soil evaporative resistance method from Sakaguchi and Zeng
2009 Beta function (0) to Swenson and Lawrence 2014 dry surface layer
formulation (1).

Index of solution method of Richards equation.

Change method for richards equation solution and boundary
conditions.

CLM 4.5 - soilwater_movement_method = 0 (Zeng and Decker, 2009, method).
CLM 5.0 - soilwater_movement_method = 1 (adaptive time stepping moisture form from Martyn Clark).

1 (adaptive time stepping moisture form

Stomatal conductance model method to use

    Ball-Berry1987 --- Ball Berry 1987 methodology
    Medlyn2011 ------- Medlyn 2011 methodology

Supplemental Nitrogen mode and for what type of vegetation it's turned on for.
In this mode Nitrogen is unlimited rather than prognosed and in general vegetation is
over-productive.
    NONE           = No vegetation types get supplemental Nitrogen
    ALL            = Supplemental Nitrogen is active for all vegetation types

Upper threshold for fuel mass needed for ignition

Index of upper boundary condition for Richards equation.

If TRUE, use explicit, time-varying AC adoption rate for air-conditioning flux and interior building temperature calculations.

Turn urban air conditioning/heating ON or OFF and add wasteheat:
    OFF          = Air conditioning/heating is OFF in buildings, internal temperature allowed to float freely
    ON           = Air conditioning/heating is ON in buildings, internal temperature constrained
    ON_WASTEHEAT = Air conditioning/heating is ON and waste-heat sent to urban canyon

If TRUE, urban traffic flux will be activated
(Currently NOT implemented).

If TRUE, use variable soil depth.

If present on surface dataset, use depth to bedrock information to
specify spatially variable soil thickness. If not present, use bottom
of soil column (nlevsoi).

If TRUE, include biomass heat storage in canopy energy balance.

If TRUE use clm5 equation for fraction of intercepted precipitation

If TRUE turn on the excess ice physics, (Lee et al., 2014; Cai et al., 2020)

If TRUE and use_excess_ice is TRUE, use the excess ice stream to determine the initial values of the excess ice field
if FALSE and use_excess_ice is TRUE, expect excess ice to come from the initial conditions or restart file
Expect to be FALSE is use_excess_ice is FALSE

If TRUE, supply irrigation from groundwater (in addition to surface water).

Can only be set if limit_irrigation_if_rof_enabled is true (otherwise
groundwater extraction is never invoked).

Cannot be combined with lower_boundary_condition = 3 or 4

Apply the guardrail for leaf-Nitrogen that ensures it doesn't go negative or too small

If TRUE use the Prigent roughness dataset

Whether to use subgrid fluxes for snow

If TRUE use the undercanopy stability term used with CLM4.5 (Sakaguchi&Zeng, 2008)

If FALSE use constant snow z0m
If TRUE use parameterization of snow z0m as a function of accumulated
snow melt of Brock et al. (2006)

a very small number: used to check for sub step completion for adaptive time stepping in richards equation

If TRUE, the density of new snow depends on wind speed, and there is also
wind-dependent snow compaction.

tolerance to double length of substep for adaptive time stepping in richards equation

tolerance to halve length of substep for adaptive time stepping in richards equation

Parameterization/parameters to use for surface roughness
ZengWang2007: Zeng and Wang 2007
Meier2022: Meier et al. in prep. 2022

The maximum value to use for zeta under stable conditions

If TRUE (which is the default), check consistency between pct_pft on the finidat file
and pct_pft read from the surface dataset. This check is only done for a NON-transient run.

If TRUE (which is the default), check consistency between year on the finidat file
and the current model year. This check is only done for a transient run.

Full pathname of master restart file for a branch run. (only used if RUN_TYPE=branch)
(Set with RUN_REFCASE and RUN_REFDATE)

If FALSE, don't write any restart files.

If TRUE, reduce heterotrophic respiration according to available oxygen predicted by CH4 submodel.

separate q10 for frozen soil respiration rates.  default to same as above zero rates

Maximum depth to mix soils to by croturbation, in permafrost soils.

Number of days over which to use exponential relaxation of NPP in N fixation calculation

If true, no denitrification or nitrification in frozen soil layers.
(EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)

Flag for overriding the crash that should occur if user tries to start the model from a restart file made with a different version of the soil decomposition structure than is currently being used.

Base advective flux (downwards) for SOM.

Flag for setting the state of the Accelerated decomposition spinup state for the BGC model.
   0 = normal model behavior;
   1 = AD spinup (standard)
   2 = AD spinup (accelerated spinup from Ricciuto, doesn't work for CNDV and not implemented for CN soil decomposition)
Entering and exiting spinup mode occurs automatically by comparing the namelist and restart file values for this variable.
NOTE: THIS CAN ONLY BE SET TO NON-ZERO WHEN BGC_MODE IS NOT SATELITE PHENOLOGY!

Profile over which to distribute C and N coming from surface pools (leaves, stem, grain).

Choice of Nitrogen Fixation parameterization

By default, a value in stream_fldFileName_gdd20_season_start or _end outside the range [1, 365] (or 366 in leap years) will cause the run to fail. Set this to .true. to instead have such cells fall back to the hard-coded hemisphere-specific "warm seasons."

By default, a value in stream_fldFileName_swindow_start or _end outside the range [1, 365] (or 366 in leap years) will cause the run to fail. Set this to .true. to instead fall back on the paramfile sowing windows.

If TRUE (which is the default), check consistency between pct_nat_pft on the flanduse_timeseries file
and pct_nat_pft read from the surface dataset.

Component name to use in history and restart files

Flag to enable prescribed crop calendars (sowing window dates and maturity requirement)

Flag to enable prescribed crop calendars (sowing window dates and maturity requirement), with maturity requirement adaptive based on recent climate

Full pathname to the inventory initialization control file.
(Required, if use_fates_inventory_init=T)
(Only relevant if FATES is on).

Full pathname datafile with fates parameters
(Only relevant if FATES is on).

Full pathname of land fraction data file.

Full pathname of initial conditions file. If blank CLM will startup from
arbitrary initial conditions.

Full pathname of time varying landuse data file. This causes the land-use types of
the initial surface dataset to vary over time.

Full pathname of fates landuse x pft association static data map.
The file associates land use types with pfts across a static global map.
This file is necessary for running FATES with use_fates_luh,
use_fates_nocomp, and use_fates_fixedbiogeo engaged (note that use_fates_lupft
is provided as a namelist option to engage all necessary options).  The file is output
by the FATES land use data tool (https://github.com/NGEET/tools-fates-landusedata)
which processes the raw land use data from the THEMIS tool data sets
(https://doi.org/10.5065/29s7-7b41)

Full pathname of unified land use harmonization (LUH) data file. This causes the land-use
types to vary over time.
(Required, if use_fates_luh=T)
(Only relevant if FATES is on).

Set this to true to flush the accumulated GDD20 variables as soon as possible.

SNICAR (SNow, ICe, and Aerosol Radiative model) snow aging data file name

SNICAR (SNow, ICe, and Aerosol Radiative model) optical data file name

Full pathname of surface data file.

Full pathname of hillslope data file.

If FALSE (which is the default): If an urban output type cannot be found in the input for initInterp,
code aborts
If TRUE: If an urban output type cannot be found in the input, fill with closest urban high density
(HD) landunit

If FALSE (which is the default): If an output type cannot be found in the input for initInterp,
code aborts
If TRUE: If a non-urban output type cannot be found in the input, fill with closest natural veg column
(using bare soil for patch-level variables)

NOTE: Natural vegetation and crop landunits always behave as if this were true. e.g., if
we can't find a column with the same type as a given crop column in the output, then we
always fill with the closest natural veg patch / column, regardless of the value of this
flag. So interpolation from non-crop to crop cases can be done without setting this flag.

Method to use for init_interp. Only applies when use_init_interp = .true.

'general': The general-purpose method that can be used when changing
grids, configurations, etc. This starts off with subgrid areas taken
from the surface dataset.

'use_finidat_areas': This starts off with subgrid areas taken from the
input finidat file. This is needed to achieve bit-for-bit results in a
coupled case (where areas in initialization impact initial fields sent
to the atmosphere) (but using the 'general' method will typically have
only a very minor impact on results in this case). For this method to
work, the input finidat file needs to be at the same resolution as the
current configuration. So this is a less general form of
init_interp. However, it can be used in cases where the only difference
is in internal memory allocation. In order to catch possible problems,
this uses a different algorithm for finding the input point for each
output point, which ensures that each active output point is associated
with exactly one input point with the same latitude, longitude and
type. This method requires (a) the same grid for input and output,
within roundoff; (b) any non-zero-weight point in the input must have
memory allocated for it in this grid cell in the output (this will be
satisfied if the point is non-zero-weight on the surface dataset or if
it's a point for which we allocate memory even for zero-weight points);
(c) any active point in the output (based on the surface dataset and
rules for determining active points) must have a matching point in this
grid cell in the input. (Note that this generally can NOT be used when
transitioning from a spinup run to a transient run, because spinup runs
typically have irrigation off and transient runs have irrigation on, and
the presence/absence of irrigation affects the subgrid structure; if it
weren't for that difference, then this option would be useful for this
use case.)

dtlimit (ratio of max/min stream delta times) for LAI streams, which allows for cycling over a year of data

Mapping method from LAI input file to the model resolution
    bilinear = bilinear interpolation
    nn       = nearest neighbor
    redist   = Redistributes data from source mesh to destination mesh
    consd    = First-order conservative interpolation
    consf    = Same as consd with fraction area normalization
    none     = no interpolation

Time interpolation method to use with LAI streams

Time interpolation method to use with Lightning streams

Mapping method from Lightning input file to the model resolution
    bilinear = bilinear interpolation
    nn       = nearest neighbor
    redist   = Redistributes data from source mesh to destination mesh
    consd    = First-order conservative interpolation
    consf    = Same as consd with fraction area normalization
    none     = no interpolation

Simulation year that aligns with stream_year_first_cropcal_cultivar_gdds value

Simulation year that aligns with stream_year_first_cropcal_swindows value

Simulation year that aligns with stream_year_first_lai value

Simulation year that aligns with stream_year_first_lightng value

Simulation year that aligns with stream_year_first_ndep value

Simulation year that aligns with stream_year_first_popdens value

Simulation year that aligns with stream_year_first_soilm value

Simulation year that aligns with stream_year_first_urbantv value

Time interpolation mode to determine how to handle data before and after the times in the file
    cycle   = Always cycle over the data
    extend  = Use the first time before the available data, and use the last time after the available data
    limit   = Only use the data within the times available -- abort if the model tries to go outside it

Time interpolation method to use for Nitrogen Deposition

Colon delimited list of variables to read from the streams file for nitrogen deposition
(Normally just read the single variable NDEP_year or NDEP_month)

Mapping method from Nitrogen deposition input file to the model resolution
    bilinear = bilinear interpolation
    nn       = nearest neighbor
    redist   = Redistributes data from source mesh to destination mesh
    consd    = First-order conservative interpolation
    consf    = Same as consd with fraction area normalization
    none     = no interpolation

Full pathname datafile with plant function type (PFT) constants combined with
constants for biogeochem modules

Time interpolation method to use with human population density streams

Mapping method from human population density input file to the model resolution
    bilinear = bilinear interpolation
    nn       = nearest neighbor
    redist   = Redistributes data from source mesh to destination mesh
    consd    = First-order conservative interpolation
    consf    = Same as consd with fraction area normalization
    none     = no interpolation

If false will abort if using soil moisture streams and find a point where the model shows H2OSOI_VOL
should be set because it's vegetated, but the input soilm streams dataset shows that point is missing.
If true, will ignore the prescribed soilm data for that point and let the model run for that point without
prescribed data.

Offset in time coordinate for soil moisture streams (sec)

Time interpolation method to use for prescribed soil moisture streams data

Filename of input stream data for atmospheric C13 isotope delta data

Filename of input stream data for atmospheric C14 isotope delta data

Filename of input stream data for finundated inversion of observed (from Prigent dataset)
to hydrologic variables (either TWS or ZWT)

Filename of input stream data for cultivar growing degree-day targets

Filename of input stream data for excess ice data

Filename of input stream data for baseline GDD20 values

Filename of input stream data for date (day of year) of end of gdd20 accumulation season.

Filename of input stream data for date (day of year) of start of gdd20 accumulation season.

Filename of input stream data for LAI

Filename of input stream data for Lightning

Filename of input stream data for Nitrogen Deposition

Filename of input stream data for human population density

Filename of input stream data for aeolian roughness length (from Prigent's roughness dataset)

Filename of input stream data for prescribed soil moisture streams data

Filename of input stream data for date (day of year) of end of sowing window. Cells with the same sowing window start and end date are always planted on that date, regardless of climatic conditions/history.

Filename of input stream data for date (day of year) of start of sowing window. Cells with the same sowing window start and end date are always planted on that date, regardless of climatic conditions/history.

Filename of input stream data for urban time varying

Filename of input stream data for Zender's soil erodibility source function
(only used when dust_emis_method is Zender_2003, and zender_soil_erod_source is lnd)

Set this to true to read gdd20 accumulation season start and end dates from stream files, rather than using hard-coded hemisphere-specific "warm seasons."

Mapping method from excess ice input stream data to the model resolution
    bilinear = bilinear interpolation
    nn       = nearest neighbor
    redist   = Redistributes data from source mesh to destination mesh
    consd    = First-order conservative interpolation
    consf    = Same as consd with fraction area normalization
    none     = no interpolation

Filename of input stream mesh for atmospheric C14 isotope delta data

mesh filename of input stream data for finundated inversion of observed (from Prigent dataset)
to hydrologic variables (either TWS or ZWT)

Filename of input stream data for crop calendar inputs

mesh filename of input stream data for excess ice

Filename of input stream data for LAI

Stream meshfile for Nitrogen Deposition data

Stream meshfile for Nitrogen Deposition data

mesh file for input stream data for human population density

mesh filename of input stream data for aeolian roughness length (from Prigent's roughness dataset)

mesh filename of input stream data for urban time varying

mesh filename of input stream data for Zender's soil erodibility source function
(only used when dust_emis_method is Zender_2003, and zender_soil_erod_source is lnd)

Simulation year that aligns with stream_year_first_atm_c13 value

Simulation year that aligns with stream_year_first_atm_c14 value

Time interpolation mode for atmospheric C13 delta data to determine how to handle data before and after the times in the file
    cycle   = Always cycle over the data
    extend  = Use the first time before the available data, and use the last time after the available data
    limit   = Only use the data within the times available -- abort if the model tries to go outside it

Time interpolation mode for atmospheric C14 delta data to determine how to handle data before and after the times in the file
    cycle   = Always cycle over the data
    extend  = Use the first time before the available data, and use the last time after the available data
    limit   = Only use the data within the times available -- abort if the model tries to go outside it

Time interpolation method to use for atmospheric C13 delta data

Time interpolation method to use for atmospheric C14 delta data

First year to loop over for atmospheric C13 isotope delta data

First year to loop over for atmospheric C14 isotope delta data

First year to loop over for crop maturity requirements

First year to loop over for crop sowing windows

First year to loop over for LAI data

First year to loop over for Lightning data

First year to loop over for Nitrogen Deposition data

First year to loop over for human population density data

First year to loop over for prescribed soil moisture streams data

First year to loop over for urban time varying data

Last year to loop over for data atmospheric C13 isotope delta data

Last year to loop over for atmospheric C14 isotope delta data

Last year to loop over for crop maturity requirements

Last year to loop over for crop sowing windows

Last year to loop over for LAI data

Last year to loop over for Lightning data

Last year to loop over for Nitrogen Deposition data

Last year to loop over for human population density data

Last year to loop over for prescribed soil moisture streams data

Last year to loop over for urban time varying data

Time interpolation method to use with urban time varying streams

Mapping method from urban time varying input file to the model resolution
    bilinear = bilinear interpolation
    nn       = nearest neighbor
    redist   = Redistributes data from source mesh to destination mesh
    consd    = First-order conservative interpolation
    consf    = Same as consd with fraction area normalization
    none     = no interpolation

If set to .true., interpinic will be called to interpolate the file given by finidat,
creating the output file specified by finidat_interp_dest.

This requires that finidat be non-blank.

datm input directory

datm output directory

Datm logfile name

Command line arguement for biogeochemistry mode for CLM4.5
   sp  = Satellitte Phenology
   bgc = CLM4.5 BGC model with:
        CENTURY model pools
        Nitrification/De-nitrification
        Methane model
        Vertically resolved Carbon
   fates = FATES Functionally Assembled Terrestrial Ecosystem Simulator (ecosystem demography model with below ground BGC):

Check that the resolution and land-mask is valid before continuing.

Command line argument for setting up your simulation in a mode for faster
throughput. By default turns off some options, and sets up for a lower level
of output. When bgc_mode is some level of prognostic BGC (so NOT Satellite Phenology)
it also sets up for accelerated decomposition. The "sasu" mode sets up
for using the CN-matrix mode with Semi-Analytic Spin Up.
NOTE: THIS CORRESPONDS DIRECTLY TO THE env_run.xml VARIABLE OF THE SAME NAME.
      Set the env_run variable, rather than setting this directly.

Namelist entries to demand be provided on the namelist.

CLM run type.
    'default' use the default type of clm_start type for this configuration
    'cold' is a run from arbitrary initial conditions
    'arb_ic' is a run using initial conditions if provided, OR arbitrary initial conditions if no files can be found
    'startup' is an initial run with initial conditions provided.
    'continue' is a restart run.
    'branch' is a restart run in which properties of the output history files may be changed.

Resolution of finundated inversion streams dataset (stream_fldfilename_ch4finundated)
to use for methane model
(only applies when CN and methane model are turned on)

If true, do NOT use grain C/N to replenish the crop seed deficits. This
is needed when doing software testing to verify that we can get
bit-for-bit identical answers when using a reproductive structure pool
as when using a grain pool (in conjunction with
for_testing_use_repr_structure_pool). We do this testing to have some
tests of the infrastructure to support the AgSys crop model integration.
This option can be dropped if/when we stop doing this software testing,
e.g., because we have integrated AgSys and have tests of it that make
these software infrastructure tests obsolete.

Whether to run some tests of ncdio_pio as part of the model run. This is
typically only used in automated tests.

If true, allocate memory for two crop reproductive structure pools and
send all reproductive C and N to the second reproductive structure pool
instead of the grain pool. This is meant only for software testing of
infrastructure to support the AgSys crop model integration. This option
can be dropped once AgSys is integrated and we have tests of it.

If true, allocate memory for and use a second crop grain pool. This is
meant only for software testing of infrastructure to support the AgSys
crop model integration. This option can be dropped once AgSys is
integrated and we have tests of it.

Attributes to use when looking for an initial condition file (finidat) if interpolation is turned on (use_init_interp is .true.)

How close in years to use when looking for an initial condition file (finidat) if interpolation is turned on (use_init_interp is .true.)

Simulation years you can look for in initial condition files (finidat) if interpolation is turned on (use_init_interp is .true.)

Resolution of Lightning dataset to use for CN or FATES fire model
(only applies when CN or FATES and the fire model is turned on)

General configuration of model version and atmospheric forcing to tune the model to run under.
This sets the model to run with constants and initial conditions that were set to run well under
the configuration of model version and atmospheric forcing. To run well constants would need to be changed
to run with a different type of atmospheric forcing.
(Some options for the newest physics will be based on previous tuning, and buildnml will let you know about this)

Land mask description

If 1, turn on the MEGAN model for BVOC's (Biogenic Volatile Organic Compounds)

Add a note to the output namelist about the options given to build-namelist

Year to simulate and to provide datasets for (such as surface datasets, initial conditions, aerosol-deposition, Nitrogen deposition rates etc.)
A sim_year of 1000 corresponds to data used for testing only, NOT corresponding to any real datasets.
A sim_year greater than 2015 corresponds to ssp_rcp scenario data
A sim_year of PtVg refers to the Potential Vegetation dataset, that doesn't include human influences
Most years are only used for clm_tools and there aren't CLM datasets that correspond to them.
CLM datasets exist for years: 1000 (for testing), 1850, and 2000

Range of years to simulate transitory datasets for (such as dynamic: land-use datasets, aerosol-deposition, Nitrogen deposition rates etc.)
Constant means simulation will be held at a constant year given in sim_year.
A sim_year_range of 1000-1002 or 1000-1004 corresponds to data used for testing only, NOT corresponding to any real datasets.
A sim_year_range that goes beyond 2005 corresponds to historical data until 2005 and then scenario data beyond that point.

Shared Socioeconomic Pathway (SSP) and Representative Concentration Pathway (RCP) combination for future scenarios
The form is SSPn-m.m Where n is the SSP number and m.m is RCP radiative forcing at peak or 2100 in W/m^2
n is just the whole number of the specific SSP scenario. The lower numbers have higher mitigation
- the higher numbers less mitigation, more than one SSP can result in the same RCP forcing
hist means do NOT use a future scenario, just use historical data.

Description of the use case selected.

Toggle to turn all history output completely OFF (possibly used for testing)

If TRUE (which is the default), send the expcrt state for the nuopc driver to the ATM even if running with a data ATM

If TRUE, indicates output ALL history fields on the primary tape.

Per file averaging flag.
    'A' (average over history period)
    'I' (instantaneous)
    'X' (maximum over history period)
    'M' (minimum over history period)
    'LXXXXX' (local solar time at XXXXX seconds of day)

If TRUE, implies output data on a 2D latitude/longitude grid. False means
output in 1D vector format.  One setting per history tape series.

If TRUE, indicates do NOT output any default history fields (requires you to use
hist_fincl1 to set the exact output fields to use). Note only the
primary tape has default history fields.

Fields to exclude from history tape series 1.

Fields to exclude from history tape series 10.

Fields to exclude from history tape series  2.

Fields to exclude from history tape series  3.

Fields to exclude from history tape series  4.

Fields to exclude from history tape series  5.

Fields to exclude from history tape series  6.

Fields to exclude from history tape series  7.

Fields to exclude from history tape series  8.

Fields to exclude from history tape series  9.

If TRUE, write list of all output fields to separate file for documentation purposes

Fields to add to history tape series  1.

Fields to add to history tape series 10.

Fields to add to history tape series  2.

Fields to add to history tape series  3.

Fields to add to history tape series  4.

Fields to add to history tape series  5.

Fields to add to history tape series  6.

Fields to add to history tape series  7.

Fields to add to history tape series  8.

Fields to add to history tape series  9.

Per tape series  maximum number of time samples.

Per tape series  history file density (i.e. output precision)
    1=double precision
    2=single precision

Per tape series history write frequency.
    positive means in time steps
    0=monthly
    negative means hours
(i.e. 5 means every 24 time-steps and -24 means every day

Averaging type of output for 1D vector output (when hist_dov2xy is false).
    GRID means average all land-units up to the grid-point level
    LAND means average all columns up to the land-unit level
    COLS means average all PFT's up to the column level
    PFTS means report everything on native PFT level

If TRUE, add extra diagnostics for methane model to the history files

Minimum activity factor for soil moisture for MEGAN isoprene emissions.

If TRUE, use activity factor for soil moisture for MEGAN isoprene emissions.

Eastern edge of the regional grid

Northern edge of the regional grid

Southern edge of the regional grid

Western edge of the regional grid

CAM file

CAM topography file

CESM domain file

CLM grid file

Orography file with surface heights and land area fraction

Raw topography file

Number of latitudes to use for a regional grid (for single-point set to 1)

Number of longitudes to use for a regional grid (for single-point set to 1)

Land mask description for mksurfdata input files

Mapping file to go from one resolution/land-mask to another resolution/land-mask

Only used when baset_mapping == varytropicsbylat
Intercept at zero latitude to add to baset from the PFT parameter file

Only used when baset_mapping == varytropicsbylat
Slope with latitude in degrees to vary tropical baset by

Type of mapping to use for base temperature for prognostic crop model
constant = Just use baset from the PFT parameter file
varytropicsbylat = Vary the tropics by latitude

Mapping method for the finundated inversion input file to the model resolution
(Only used when use_ch4 is TRUE)
    bilinear = bilinear interpolation
    nn       = nearest neighbor
    redist   = Redistributes data from source mesh to destination mesh
    consd    = First-order conservative interpolation
    consf    = Same as consd with fraction area normalization
    none     = no interpolation

If true, this directs the model to collapse the urban landunits to the dominant urban landunit. Selecting .false. means DO NOTHING, ie all urban landunits found in the input data are active.

If true, any ocean (i.e., wetland) points on the surface dataset are
converted to bare ground (or whatever vegetation is given in that grid
cell - but typically this will be bare ground due to lack of vegetation
in grid cells with 100% ocean).

Fraction of post-harvest crop residues (leaf and stem) to move to
1-year product pool instead of letting them fall as litter.

If TRUE, apply gross unrepresented landuse/land-cover change from flanduse_timeseries file.
(Only valid for transient runs, where there is a flanduse_timeseries file.)
(Also, only valid for use_cn = true.)

If TRUE, apply harvest from flanduse_timeseries file.
(Only valid for transient runs, where there is a flanduse_timeseries file.)
(Also, only valid for use_cn = true.)

If TRUE, apply transient crops from flanduse_timeseries file.
(Only valid for transient runs, where there is a flanduse_timeseries file.)

If TRUE, apply transient lakes from flanduse_timeseries file.
(Only valid for transient runs, where there is a flanduse_timeseries file.)

If TRUE, apply transient natural PFTs from flanduse_timeseries file.
(Only valid for transient runs, where there is a flanduse_timeseries file.)

If TRUE, apply transient urban from flanduse_timeseries file.
(Only valid for transient runs, where there is a flanduse_timeseries file.)

Toggle to turn on meteorological downscaling in hillslope model

Set the FATES carbon starvation model

Set the FATES electron transport model to either Johnson-Berry 2021 or
  Farquhar von Caemmerer and Berry 1980 (FvCB1980).

Set FATES harvesting mode by setting fates_harvest_mode to a valid string option.
Allowed values are:
 no_harvest: no fates harvesting of any kind
 event_code: fates logging via fates logging event codes (see fates parameter file) only
 landuse_timeseries: fates harvest driven by CLM flanduse_timeseries file (dynHarvestMod)**
 luhdata_area: fates harvest driven by LUH2 raw harvest data, area-based (dynFATESLandUseChangeMod)
 luhdata_mass: fates harvest driven by LUH2 raw harvest data, mass-based (dynFATESLandUseChangeMod)
**Note that the landuse_timeseries option is not the same as the FATES fluh_timeseries data file.
This option is older than the luhdata options and may be depricated at some point in the future.

  Setting for what types of FATES history to be allocate and
  calculated at the dynamics timestep (1st integer) and the
  model timestep (2nd integer). This must be consistent with
  hist_fincl*, ie output variables must not be listed if the
  output level is not enabled.
  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
  (Only relevant if FATES is on)

Set the FATES hydro solver method

Set the FATES leaf maintenance respiration model

Select the logic for land use class transitions.
Allowed values are 1-9. See the Land Use subsection of the Namelist Options section 
of the FATES user guide for an explanation of the options.
(Only relevant if FATES with land use is on)

Switch deciding which nutrient model to use in FATES.
(Only relevant if FATES is on)
(fates_parteh_mode='carbon_nitrogen' is EXPERIMENTAL and UNSUPPORTED)

Set the FATES photosynthesis temperature acclimation model.
(Only relevant if FATES is on)

Set the FATES radiation model

Set the FATES seed regeneration model
Valid values:
  default: default scheme
  trs: Tree Recruitment Scheme (Hanbury-Brown et al., 2022)
  trs_no_seed_dyn: Tree Recruitment Scheme (Hanbury-Brown et al., 2022) without seed dynamics

Switch defining the cadence at which seeds are dispersed across
gridcells.  Setting the switch value to zero turns off dispersal.
Setting the switch to 1, 2, or 3 sets the dispersal cadence to
daily, monthly or yearly.  The daily cadence is primarily
recommended for test and debug only. Note that turning this
feature on will result in more memory usage.
(Only relevant if FATES is on)

Turn on spitfire module to simulate fire by setting fates_spitfire_mode > 0.
Allowed values are:
 0 : Simulations of fire are off
 1 : use a global constant lightning rate found in fates_params.
 2 : use an external lightning dataset.
 3 : use an external confirmed ignitions dataset (not available through standard CSEM dataset collection).
 4 : use external lightning and population datasets to simulate both natural and anthropogenic
 5 : use gross domestic production and population datasets to simulate anthropogenic fire supression
ignitions.
(Only relevant if FATES is on)

Set net or gross asslimiation for the FATES stomatal model

Set the FATES stomatal conductance model

If TRUE, allow area changes at times other than the year boundary. This should
only arise in some test configurations where we artifically create changes more
frequently so that we can run short tests. This flag is only used for
error-checking, not controlling any model behavior. Do not set this in a
production (non-test) run unless you know what you're doing!

If TRUE, set the dynbal water and energy fluxes to zero. This should typically
only be done for testing: This is needed in some tests where we have daily
rather than annual glacier dynamics: if we allow the true dynbal adjustment
fluxes in those tests, we end up with sensible heat fluxes of thousands of W m-2
or more, which causes CAM to blow up. However, note that setting it to true will
break water and energy conservation!

Set to .true. in order to override crop harvesting logic and to instead harvest the day before the next sowing date. Used to generate growing-degree day outputs that can be used with an external script to generate new GDD requirement ("cultivar") files.

If true, set fsat to zero for hillslope columns

Method for calculating hillslope saturated head gradient

Method for distributing pfts across hillslope columns

Method for distributing soil thickness across hillslope columns

Method for calculating transmissivity of hillslope columns

Initial seed Carbon to use at planting
(only used when CN is on as well as crop)

Maximum depth to till soil (m). Default 0.26; original (Graham et al., 2021) value was unintentionally 0.32.

Method for determining what the minimum critical day length for seasonal decidious leaf offset depends on
Constant ----------- constant value of crit_dayl from parameter file (value from White 2001)
DependsOnLat ------- Higher values at high latitudes down to value from parameter file for temperate and equatorial regions
                     (L. Birch et. al, GMD 2021)
DependsOnVeg ------- Arctic vegetation with higher value and temperate vegetation with crit_dayl from parameter file
DependsOnLatAndVeg - Arctic vegetation depends on latitude as above, but temperate vegetation fixed at crit_dayl value from parameter file
(only used when CN is on)

Number of dominant landunits, so this determines the number of active landunits. Selecting the value 0 means DO NOTHING, ie all landunits in the input data are active.

Number of dominant pfts, so this determines the number of active pfts. Selecting the value 0 means DO NOTHING, ie all pfts in the input data are active.

       Parameter to set the type of ozone vegetation stress method
       unset                  = (default) ozone stress vegetation method is off
       stress_lombardozzi2015 = ozone stress vegetation functions from Danica Lombardozzi 2015
       stress_falk            = ozone stress vegetation functions from Stefanie Falk (issue #1224)

Phenology onset depends on the vegetation type
(only used when CN is on)

Mapping method for the Prigent roughness input file to the model resolution
(Only used when use_prigent_roughness is TRUE and normally only needed with the Leung_2023 dust emission method)
    bilinear = bilinear interpolation
    nn       = nearest neighbor
    redist   = Redistributes data from source mesh to destination mesh
    consd    = First-order conservative interpolation
    consf    = Same as consd with fraction area normalization
    none     = no interpolation

If TRUE, reset baseline values of total column water and energy in the
first step of the run. This should typically be set when transitioning
from an offline spinup to a coupled run with transient glaciers, and
*possibly* when transitioning from the spinup to the transient portion
of a coupled run with transient glaciers; it should typically remain
unset at other times.

These baseline values are computed only for particular columns
(currently, only for glacier columns). They provide values that are
subtracted from the current state when counting total column water and
energy. For glacier columns, these discount the water and energy
contents in the "virtual" glacier ice, while adding representative
amounts of water and energy in the non-explicitly-modeled soil beneath
the ice. Subtracting these baselines reduces the fictitious dynbal
fluxes generated when total grid cell water and energy changes as a
result of dynamic column/landunit areas.

These baseline values are initially computed based on cold start
states. If this flag remains unset (.false.), these baseline values will
remain fixed at their cold start values. This will conserve mass and
energy, but may result in larger-than-desired dynbal energy fluxes (and,
in principle, also larger dynbal water fluxes; but currently, the mass
of glacier ice remains fixed over time, so dynbal water fluxes are
fairly small regardless of whether this flag is ever set). To further
reduce these dynbal fluxes, you can set this flag to .true. when
starting a startup or hybrid run from a partially or entirely spun-up
state. This will reset the baseline values based on the state at the
start of this run.

Note that setting this flag can break water and energy conservation!
Specifically, any water and energy that has previously been added to or
removed from states that contribute to these baselines (currently, (a)
glacier ice and (b) soil water and energy in the vegetated landunit in
the same grid cell as glaciers) will effectively be ignored when
computing conservation corrections due to land cover change. Instead,
only the change in states from this point forward will be
considered. So, for example, this flag should NOT be set when
transitioning from a historical run to a future scenario.

This setting only impacts startup and hybrid runs; it has no effect in a
continue run; it is an error for this to be set in a branch
run. Furthermore, this setting has no effect in a cold start run.

If set to .true., suppress the warning message when a prescribed cultivar GDD requirement is below the minimum allowed value and is replaced with min_gddmaturity. Useful when using prescribed crop calendars with intentionally low GDD requirements.

Whether to till crop soil, and if so, with what intensity.

Percentage threshold above which the model keeps the crop landunit. Selecting the value 0 means DO NOTHING.

Percentage threshold above which the model keeps the glacier landunit. Selecting the value 0 means DO NOTHING.

Percentage threshold above which the model keeps the lake landunit. Selecting the value 0 means DO NOTHING.

Percentage threshold above which the model keeps the soil landunit. Selecting the value 0 means DO NOTHING.

Percentage threshold above which the model keeps the urban landunits. Selecting the value 0 means DO NOTHING. If collapse_urban = .false., the same threshold will apply to all three urban landunits if they are present. If collapse_urban = .true., this threshold will apply to the single collapsed urban landunit if presnet.

Percentage threshold above which the model keeps the wetland landunit. Selecting the value 0 means DO NOTHING.

Toggle to turn on the prognostic crop model

Toggle to use 25 lake layers instead of 10
(extralaklayers=".true." is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)

Toggle to turn on the FATES model
Functionally Assembled Terrestrial Ecosystem Simulator (FATES)

Toggle to turn on cohort age tracking (by default FATES only tracks age of patches)
(Only relevant if FATES is on).

If TRUE, enable FATES to utilize the day length factor from the host land model.
(Only relevant if FATES is on)

Initialize cohorts at coldstart with diameter at breast height instead of density
(Applies only if use_fates_nocomp=.true.)
(Only relevant if FATES is on).

Toggle to turn on prescribed physiology
(Only relevant if FATES is on).

Toggle to turn on Static Stand Structure Mode (only relevant if FATES is being used).
(Only relevant if FATES is on).

Toggle to turn on fixed biogeography mode
(Only relevant if FATES is on)

Toggle to turn on inventory initialization to startup FATES
(Only relevant if FATES is on).

If TRUE, enable use of land use harmonization (LUH) state and transition data from luh_timeseries file.
This is enabled by default if fates_harvest_mode is set to use the raw LUH2 harvest data
(Also, only valid for use_fates = true and is incompatible with transient runs currently.)

If TRUE, enable use of FATES land use with no competition and fixed biogeography.  This mode
requires the use of the land use x pft association static data map file.  See the
flandusepftdat definition entry in this file for more information.
(Only valid for use_fates = true and is incompatible with transient runs currently.)

Enable FATES managed fire mode.  Requires that fates_spitfire_mode is on (in any mode).
This mode allows the FATES model to conduct fuel-load reduction through managed burns.
The boundary conditions in which a managed fire is allowed is set via the FATES parameter
file.  The burned area fraction of a managed burn is defined through the FATES parameter
file as well.  This mode works in conjunction with the SPITFIRE module to determine
whether a wildfire or managed fire takes place on a given patch.
(Only relevant if FATES is on)

Toggle to turn on no competition mode (only relevant if FATES is being used).

Toggle to turn on plant hydraulics
(Only relevant if FATES is on)

If TRUE, ignore the land-use state vector and transitions, and assert that all lands
are primary, and that there is no harvest.  This mode is only relevant for FATES
spin-up workflows that are intending to use the spin-up restart output to start a
FATES land use transient case using the use_fates_lupft namelist option.  The option
should be set to true for the spin-up case and false for the transient case.

Toggle to turn on FATES satellite phenology mode (only relevant if FATES is being used).

Toggle to turn on the tree damage module in FATES
(Only relevant if FATES is on)

Toggle to turn on the prognostic fertilizer for crop model

Toggle to turn on the 1-year grain product pool in the crop model

Toggle to turn on the hillslope model

Toggle to turn on surface water routing in the hillslope hydrology model

Toggle to turn on the plant hydraulic stress model

Toggle to turn on use of LAI streams in place of the LAI on the surface dataset when using Satellite Phenology mode.

Toggle to turn on the LUNA model, to effect Photosynthesis by leaf Nitrogen
LUNA operates on C3 and non-crop vegetation (see vcmax_opt for how other veg is handled)
LUNA: Leaf Utilization of Nitrogen for Assimilation

Toggle for mexico city specific logic.

Set to .false. in order to ignore crop PFT parameter for maximum growing season length (mxmat). Must be set to .false. when generate_crop_gdds is .true.

Toggle to use original (Graham et al. 2021) tillage logic, with bug for seasons crossing into a new calendar year

Toggle to turn on calculation of SNow and Ice Aerosol Radiation model (SNICAR) albedo forcing diagnostics for each aerosol species

Toggle to turn on use of input prescribed soil moisture streams rather than have CLM prognose it (EXPERIMENTAL)

Toggle to turn on on diagnostic Snow Radiative Effect

Toggle for vancouver specific logic.

Toggle to turn on the VIC hydrologic parameterizations
(vichydro=".true." is EXPERIMENTAL, UNSUPPORTED!)
(deprecated -- will be removed)

A TRUE setting adds the time dimension to all 1dwt variables that appear in
files generated as a result of hist_dov2xy = .false. (e.g. pfts1d_wtcol).
Transient simulations (run_has_transient_landcover = .true.) have the same
outcome as vars_1dwt_w_time = .true..
Use this flag if you wish to change FALSE to TRUE when run_has_transient_landcover = .false..

Option only applying for the Zender_2003 method for whether the soil erodibility file is handled
here in CTSM, or in the ATM model.
(only used when dust_emis_method is Zender_2003)
    bilinear = bilinear interpolation
    nn       = nearest neighbor
    redist   = Redistributes data from source mesh to destination mesh
    consd    = First-order conservative interpolation
    consf    = Same as consd with fraction area normalization
    none     = no interpolation

Type of domain file to create (ocean or atmosphere) (only used for mkdatadomain)

Full pathname of output domain dataset (only used for mkdatadomain).

Full pathname of CLM fraction dataset (only used for mkdatadomain).

Full pathname of CLM grid dataset (only used for mkdatadomain).

Aerosol deposition file name (only used for aerdepregrid.ncl)

Historical greenhouse gas concentrations from CAM, only used
by getco2_historical.ncl