CESM2.1.3 CLM Namelist Definitions

Multiplier for nitrate concentration for max denitrification rates
(ONLY used if use_nitrif_denitrif is enabled)

Exponent power for nitrate concentrationfor max denitrification rates
(ONLY used if use_nitrif_denitrif is enabled)

Multiplier for heterotrophic respiration for max denitrification rates
(ONLY used if use_nitrif_denitrif is enabled)

Exponent power for heterotrophic respiration for max denitrification rates
(ONLY used if use_nitrif_denitrif is enabled)

Maximum nitrification rate constant (1/s)
(ONLY used if use_nitrif_denitrif is enabled)

Use parameters for decomposition from the CENTURY Carbon model
Requires the CN or FATES model to work (either CN or CNDV).

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')

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.

Nitrification/denitrification splits the prognostic mineral N pool into two 
   mineral N pools: NO3 and NH4, and includes the transformations between them.
Requires the CN model to work (either CN or CNDV).

Turn on vertical soil carbon.
Requires the CN or FATES model to work (either CN or CNDV).

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)

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 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 and NOT tested)

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 and NOT tested)

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 and NOT tested)

If TRUE, apply a limitation to methane production based on the soil pH dataset.

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 and NOT tested)

Evergreen phenology option for CNPhenology
(EXPERIMENTAL and NOT tested)

Partition option for flexible-CN
   CN_partition_opt = 1
(EXPERIMENTAL and NOT tested)

Residual option for flexible-CN
(EXPERIMENTAL and NOT tested)

   Flexible CN ratio used for Phenology
(EXPERIMENTAL and NOT tested)

   GPP downregulation for use_flexibleCN option
(EXPERIMENTAL and NOT tested)

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

   Michaelis Menten nitrogen limitation for use_flexibleCN option
(EXPERIMENTAL and NOT tested)

   Plant nitrogen demand for use_flexibleCN option
(EXPERIMENTAL and NOT tested)

   Reduce day length factor
(NOT implemented)

   Michaelis Menten substrate limitation for use_flexibleCN option
(EXPERIMENTAL and NOT tested)

   Michaelis Menten temperature limitation for use_flexibleCN option
(EXPERIMENTAL and NOT tested)

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 NOT TESTED!)
    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 and NOT tested)

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 and NOT tested)

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.

Scalar multiplier for base flow rate
(ONLY used if lower_boundary_condition is not aquifer or table)

boreal peat fires (/hr)

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 litter and CWD[Course Woody Debris]) (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

Scalar for cropfire (/hr)

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

Time step (seconds)

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

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

Intercept of free living Nitrogen fixation with zero annual ET

Slope of free living Nitrogen fixation with annual ET

maximum warm (at freezing) fresh snow effective radius [microns]

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)
Behavior of 'virtual' is required in the region where we have an ice sheet model

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.
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
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, you cannot use this behavior where GLC is
operating.
Regions with the 'replaced_by_ice' behavior also compute SMB for the
vegetated column.

When rain-snow repartitioning / downscaling results in rain being converted to
snow, the behavior of the resulting additional snow.
First item corresponds to GLACIER_REGION with ID 0 in the surface dataset,
second to GLACIER_REGION with ID 1, etc.
Allowed values are:
'converted_to_snow': rain is converted to snow, with a corresponding sensible
   heat flux correction
'runs_off': rather than being converted to snow, the excess rain runs off
   immediately
IMPORTANT NOTE: Unlike other glacier_region*behavior namelist options, this
option applies to all landunit types in the given regions.
Only applies when repartition_rain_snow is .true.

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 glc_mec 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.

Initial stocks of Carbon to use in soil organic matter pools for CENTURY decomposition

Soil depth to place initial stocks of Carbon in soil organic matter pools for CENTURY decomposition

Limit applied to integrated snowfall when determining changes in snow-covered fraction during melt
(mm H2O)

Fraction of intercepted precipitation

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.

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.

baseline proportion of nitrogen allocated for electron transport (J)

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. 

Maximum fraction of leaf that may be wet prior to drip occuring

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.)

Minimum wind speed tht results in compaction (m/s)

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.

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)

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

Use old snow cover fraction from Niu et al. 2007
(deprecated -- will be removed)

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)

Use original CLM4 soil hydraulic properties
(deprecated -- will be removed)

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

Perturbation limit when doing error growth test

Potential human ignition counts (/person/month)

Temperature above which all precipitation falls as rain, for glacier columns (deg C)
Only relevant if repartition_rain_snow is .true.

Temperature below which all precipitation falls as snow, for glacier columns (deg C)
Only relevant if repartition_rain_snow is .true.

Temperature above which all precipitation falls as rain, for non-glacier columns (deg C)
Only relevant if repartition_rain_snow is .true.

Temperature below which all precipitation falls as snow, for non-glacier columns (deg C)
Only relevant if repartition_rain_snow is .true.

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).

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.

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

Turn vegetation snow canopy ON, OFF, or ON with albedo influence (ON_RAD)

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

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

Subgrid fluxes for snow

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.

Upper Limit on Destructive Metamorphism Compaction [kg/m3]

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 use clm5 equation for fraction of intercepted precipitation

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

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

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

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)

Override the start type from the driver: it can only be
set to 3 meaning branch.

If FALSE, don't write any restart files.

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

If TRUE, weight calculation of oxygen limitation by the inundated fraction and diagnostic saturated column gas
concentration profile calculated in the CH4 submodel. Only applies if anoxia = TRUE.
(EXPERIMENTAL AND NOT FUNCTIONAL!)
(deprecated -- will be removed)

E-folding depth over which decomposition is slowed with depth in all soils.

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 and NOT tested)

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).

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.

Full pathname to the inventory initialization control file.
(Required, if use_fates_inventory_init=T)

Full pathname datafile with fates parameters

Full pathname of land fraction data file.

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

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

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

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.

If FALSE (which is the default): If an output type cannot be found in the input for initInterp,
code aborts
If TRUE: If an 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.)

Mapping method from LAI input file to the model resolution
    bilinear = bilinear interpolation
    nn       = nearest neighbor
    nnoni    = nearest neighbor on the "i" (longitude) axis
    nnonj    = nearest neighbor on the "j" (latitude) axis
    spval    = set to special value
    copy     = copy using the same indices

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
    nnoni    = nearest neighbor on the "i" (longitude) axis
    nnonj    = nearest neighbor on the "j" (latitude) axis
    spval    = set to special value
    copy     = copy using the same indices

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
    nnoni    = nearest neighbor on the "i" (longitude) axis
    nnonj    = nearest neighbor on the "j" (latitude) axis
    spval    = set to special value
    copy     = copy using the same indices

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
    nnoni    = nearest neighbor on the "i" (longitude) axis
    nnonj    = nearest neighbor on the "j" (latitude) axis
    spval    = set to special value
    copy     = copy using the same indices

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 finundated inversion of observed (from Prigent dataset) 
to hydrologic variables (either TWS or ZWT)

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 prescribed soil moisture streams data

Filename of input stream data for urban time varying

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 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
    nnoni    = nearest neighbor on the "i" (longitude) axis
    nnonj    = nearest neighbor on the "j" (latitude) axis
    spval    = set to special value
    copy     = copy using the same indices

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
   cn  = Carbon Nitrogen model
   bgc = CLM4.5 BGC model with: 
        CENTURY model pools 
        Nitrification/De-nitrification
        Methane model
        Vertically resolved Carbon
   fates = FATES/ED 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.
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)

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 fire model
(only applies when CN and the CN fire model are 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.

Land mask description

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

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

Horizontal resolutions
Note: 0.1x0.1, 0.25x0.25, 0.5x0.5, 5x5min, 10x10min, 3x3min, 1km-merge-10min and 0.33x0.33 are only used for CLM tools

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)

Per file averaging flag.
    'A' (average over history period)
    'I' (instantaneous)
    'X' (maximum over history period)
    'M' (minimum over history period)

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_fincl* to set the exact output fields to use)..

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.

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

If TRUE, write diagnostic of global radiative temperature written to CLM log file.

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)

SCRIP format grid data file

Flag to pass to the ESMF mapping utility, telling it what kind of large
file support is needed for an output file generated with this grid as
either the source or destination ('none', '64bit_offset' or 'netcdf4'). 

For UGRID files, flag to pass to the ESMF mapping utility, telling it the
name of the dummy variable that has all of the topology information stored
in its attributes. (Only used if scripgriddata_src_type = UGRID.)

Flag to pass to the ESMF mapping utility, telling it what kind of grid
file this is (SCRIP or UGRID).

If TRUE, ignore other files, and set the output percentage to 100% urban and
zero for other land-use types.

Output of "git describe" to give the tag/commit the version being used corresponds to

Horizontal grid resolutions for mksurfdata input files

Land mask description for mksurfdata input files

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

Agricultural burning dominant month dataset for mksurfdata

Inversion-derived CH4 parameters dataset for mksurfdata

Text file with filepaths (or list of XML elements) for vegetation fractions
and harvesting for each year to run over for mksurfdata to be able to model
transient land-use change

High resolution land mask/fraction dataset for mksurfdata
(used for glacier_mec land-units)

GDP dataset for mksurfdata

Dataset for percent glacier land-unit for mksurfdata

Dataset for glacier region ID for mksurfdata

Grid file at the output resolution for mksurfdata

Harvest dataset for mksurfdata

Filename for mksurfdata_map to remap raw data into the output surface dataset

Irrigation dataset for mksurfdata

Leaf Area Index dataset for mksurfdata

Lake water dataset for mksurfdata

Soil max fraction dataset for mksurfdata

Organic soil dataset for mksurfdata

Peat dataset for mksurfdata

Soil color dataset for mksurfdata

Soil depth dataset for mksurfdata

Soil texture dataset for mksurfdata

High resolution topography dataset for mksurfdata
(used for glacier_mec land-units)

Topography statistics dataset for mksurfdata

Urban dataset for mksurfdata

Dataset for topography used to define urban threshold

Plant Function Type dataset for mksurfdata

VIC parameters dataset for mksurfdata

Biogenic Volatile Organic Compounds (VOC) emissions dataset for mksurfdata

Wetland dataset for mksurfdata

Type of grid to create for mksurfdata

If TRUE, set wetland to 0% over land (renormalizing other landcover types as needed);
wetland will only be used for ocean points.

Number of Plant Functional Types (excluding bare-soil)

If TRUE, output variables in double precision for mksurfdata

Plant Function Type fraction to override global file with for mksurfdata

Plant Function Type index to override global file with for mksurfdata

Soil percent clay to override global file with for mksurfdata

Soil color index to override global file with for mksurfdata

Soil maximum fraction to override global file with for mksurfdata

Soil percent sand to override global file with for mksurfdata

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 

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

Switch deciding which nutrient model to use in FATES.

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!

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

Max number of plant functional types in naturally vegetated landunit.

Toggle to turn on the prognostic crop model

Toggle to turn on the dynamic root model

Toggle to use 25 lake layers instead of 10
(extralaklayers=".true." is EXPERIMENTAL NOT SUPPORTED! Nor is it Tested!)

Toggle to turn on the FATES model
(use_fates= '.true.' is EXPERIMENTAL NOT SUPPORTED!)

Toggle to turn on prescribed physiology (only relevant if FATES is being used).

Toggle to turn on Static Stand Structure Mode (only relevant if FATES is being used).
(use_fates_ed_st3=".true." is EXPERIMENTAL NOT SUPPORTED! Nor is it Tested!)

Toggle to turn on inventory initialization to startup FATES (only relevant if FATES is being used).
(use_fates_inventory_init=".true." is EXPERIMENTAL NOT SUPPORTED! Nor is it Tested!)

Toggle to turn on the logging module (only relevant if FATES is being used).

Toggle to turn on plant hydraulics (only relevant if FATES is on).
(use_fates_planthydro=".true." is EXPERIMENTAL NOT SUPPORTED! Nor is it Tested!)

Toggle to turn on spitfire module for modeling fire (only relevant if FATES is being used).

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 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.
(EXPERIMENTAL and NOT tested)

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.

Toggle to turn on ozone stress

Toggle to turn on calculation of SNow and Ice Aerosol Radiation model (SNICAR) radiative forcing
(snicar_frc=".true." is EXPERIMENTAL NOT SUPPORTED!)

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 NOT SUPPORTED!)

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