Namelists ^{β}
The MOM code uses fortran namelists as a configuration mechanism.
This page provides documentation on the available namelist values for each module.
The contents of this page are derived directly from the model source code. If you find an error, or would like to make any improvements then you can either lodge a bug report or make the changes directly via github.
Warning
This page is currently in beta. The contents and formatting may change without notice. All namelist items used should be checked against the source code of your deployed model before being used.
src/mom5/ocean_bgc
Filename: src/mom5/ocean_bgc/ocean_ibgc.F90
Namelist: ocean_ibgc_nml
Name 
 Description  

do_ideal 
 If true, then do ideal_n and suntan. This does not require any other part of the model.  
do_po4 
 If true, then do the nonFelimited P cycle, iPO4 and iDOP. If either this or do_po4f is true, PO4_pre and chl will be calculated as well. If both do_po4 and do_po4f are true, po4 will be the master variable, unless bgc_felim is true.  
do_gasses 
 If true, then do the gases Dissolved Inorganic Carbon (iDIC) and oxygen (iO2). Requires that do_po4 and/or do_po4f be true.  
do_carbon_comp 
 If true, then do the dissolved inorganic carbon component tracers, Saturation DIC (iDIC_sat) and preformed DIC (iDIC_pre). Requires that do_po4 and/or do_po4f be true, and that do_gasses be true.  
do_radiocarbon 
 If true, then do the radiocarbon tracers (iDI14C and iDO14C). Requires that do_po4 and/or do_po4f be true, and that do_gasses be true.  
do_bgc_felim 
 If true, then use PO4f as the master variable for biogeochemical calculations (gases, PO4_pre, chl, isotopes). Requires that do_PO4f be true.  
do_po4f 
 If true, then do the Felimited P cycle, with iFe, iPO4f and DOP. If either this or do_po4 is true, PO4_pre and chl will be calculated as well. If both do_po4 and do_po4f are true, po4 will be the master variable, unless do_bgc_felim is true.  
do_isio4 
 If true, then do silica cycle and silicon isotopes, iSiO4 and i30SiO4.  
do_no3_iso 
 If true, then do NO3 isotopes, i15NO3, iN18O3 and iDO15N. Requires that do_po4 and/or do_po4f be true. 
src/mom5/ocean_blobs
Filename: src/mom5/ocean_blobs/ocean_blob.F90
Namelist: ocean_blob_nml
Name 
 Description  

debug_this_module 
 Writes additional diagnostic data to fms.out. This also controls debug output for the other related blob modules. Default is debug_this_module=.false.  
really_debug 
 Be careful what you wish for, this outputs A LOT of diagnostics to standard out Default is debug_this_module=.false.  
do_bitwise_exact_sum 
 When global sum outputs are done there is additional computational expense to ensure that they are bitwise the same across an arbitrary number of processors. However, for debugging purposes, it can be useful for global sums to be the same. Note, that this differs from bitwise_reproduction in that it do_bitwise_exact_sum only applies to the mpp_global_sum diagnostic. Note that this flag controls the output for all associated blob modules. Default is do_bitwise_exact_sum=.false.  
bitwise_reproduction 
 There is additional cost involved in ensuring that results are reproducable across an arbitrary number of processors and across restarts. Bitwise reproduction is a very memory intensive operation and should only be used for debugging. For bitwise_reproduction=.true. We need to process blobs and their histories in the same relative order regardless of domain decomposition and restarts. To do so, we save the "history" of each blob subcycle is saved to a number of arrays (which can be a very memory intensive process) and process them in order. Note that this flag controls reproducability for all associated blob modules. Bitwise reproducibility is only possible with the appropriate compiler flags AND when the simulation is run on hardware that is capable of producing bitwise reproduction. Default is bitwise_reproduction=.false.  
blob_small_mass 
 Will delete blobs of mass less than blob_small_mass. Note that this variable is for all associated blob modules. The deletion of blobs is a conservative action, any mass/tracer fields that are nonzero have the remaining properties transferred back to the Eulerian system. So, in principle, blob_small_mass can actually be a relatively large number, and the model will remain conservative. It has been found in certain test cases (with very low tracer values) that setting blob_small_mass to be very small (i.e. <1e2) that roundoff error can cause nontrivial errors. So, it is recommended that blob_small_mass be no smaller than than 1e3 kg (which is approximately 1.0m**3  a very small blob Default is blob_small_mass=1.e3  
max_prop_thickness 

Filename: src/mom5/ocean_blobs/ocean_blob_diag.F90
Namelist: ocean_blob_diag_nml
Name 
 Description  

blob_diagnostics 
 Logical as to whether diagnostics should be saved or not. Default is .false.  
diag_table 
 Name of file to look for blob diagnostic information. Default is "blob_diag_table"  
dump_num 
 The number of entried to keep in memory before writing them to file. The higher the number, the more memory that the module will take up, but, it should lower the frequency of IO operations. Default is 2000000  
frequency 
 The frequency (in number of E system time steps) that blob diagnostics should be saved. Default is 1 
Filename: src/mom5/ocean_blobs/ocean_blob_dynamic_bottom.F90
Namelist: ocean_blob_dynamic_bottom_nml
Name 
 Description  

use_this_module 
 Must be true to use this module. Default is use_this_module=.false.  
update_method 
 
blob_overflow_mu 
 Frictional dissipation rate used for calculating initial properties of bottom blobs. Corresponds to mu in Campin and Goosse (1999). Units are 1/s. Default is blob_overflow_mu=1.0e4  
blob_overflow_delta 
 Fraction of a grid cell participating in an overflow event. Corresponds to delta in Campin and Goosse (1999). Dimensionless. Default is blob_overflow_mu=1.0e4  
drag 
 Coefficient of drag used for bottom stress drag. Corresponds to Cd in Price and Baringer (1994). Dimensionless. Default is drag=3.0e3  
enforce_big_blobs 
 
det_param 
 The detrainment parameter (kg m^2/s). Corresponds to Gamma in the notes. Default is det_param=5.0e8  
max_detrainment 
 The Maximum allowable detrainment velocity (m/s). Default is max_detrainment=1.0e3  
rel_error 
 Relative error for the RK scheme (dimensionless). A smaller number is more accurate, but, is more computationally expensive. Corresponds to zeta* in the notes. Must be 0<rel_error<=1.0 Default is rel_error=0.01  
safety_factor 
 Safety factor for the RK scheme (dimensionless). A smaller number should reduce the number of rejected steps, but, decreases the locally extrapolated step. Corresponds to varrho in the notes. Must be 0<safety_factor<=1.0 Default is safety_factor=0.8  
minstep 
 Minimum step size (in seconds) for a blob. Default is minstep=9.0  
first_step 
 
elastic 
 The elasticity of a blob's collision with the topography. Corresponds to epsilon in the notes. Should have values 0<=elastic<=1.0 Values greater than 1 would be superelastic, and values less than 0 would send the blob in the opposite direction than it should be going in. Default is elastic=1.0  
min_do_levels 
 Minimum number of deep ocean levels for overflows to be considered. That is, how many k levels lower should the deep ocean water column be than the shelf/shallow ocean column. Value must be greater than 0. Default is min_do_levels=1  
rho_threshold 
 The density difference required before a blob is formed. rho_threshold must be greater than zero. Default is rho_threshold=0.01  
accept_free_blobs 
 
large_speed 
 A value for error checking. If the speed of a blob exceeds large_speed in any of x,y,z then a warning flag is raised. Default is large_speed=10.0  
no_rotation 
 Sets the coriolis parameter to zero regardless of latitude Default is no_rotation=.false.  
critical_richardson 
 The critical Richardson number for the entrainment velocity. Default is based on Price and Baringer (1994). Default is critical_richardson=0.8  
blob_height 

Filename: src/mom5/ocean_blobs/ocean_blob_dynamic_free.F90
Namelist: ocean_blob_dynamic_free_nml
Name 
 Description  

use_this_module 
 Must be true to use this module. Default is use_this_module=.false.  
rayleigh_drag_new 
 Rayleigh drag coefficient (1/s) for new blobs that are formed due to the vertical instability criterion. Corresponds to alpha in the notes. Default is rayleigh_drag_new=1.0e5  
rayleigh_drag_bot 
 Rayleigh drag coefficient (1/s) for bottom blobs that become free blobs. Corresponds to alpha in the notes. Default is rayleigh_drag_bot=1.0e7  
update_method 
 Decide which method to use to integrate the blobs. Choices are 'BS_RK3(2)' or 'CK_RK5(4)' for the BogakiShampine or CashKarp methods respectively. Default is update_method='CK_RK5(4)  
rel_error 
 Relative error for the RK scheme (dimensionless). A smaller number is more accurate, but, is more computationally expensive. Corresponds to zeta* in the notes. Must be 0<rel_error<=1.0 Default is rel_error=0.01  
safety_factor 
 Safety factor for the RK scheme (dimensionless). A smaller number should reduce the number of rejected steps, but, decreases the locally extrapolated step. Corresponds to varrho in the notes. Must be 0<safety_factor<=1.0 Default is safety_factor=0.8  
minstep 
 Minimum step size (in seconds) for a blob. Default is minstep=9.0  
first_step 
 
size_fact 
 An Adjustment for blob size, 0<size_fact<=1.0 Corresponds to Lambda in the notes. Default is size_fact=1.0  
det_param 
 The detrainment parameter (kg m^2/s). Corresponds to Gamma in the notes. Default is det_param=5.0e8  
max_detrainment 
 The Maximum allowable detrainment velocity (m/s). Default is max_detrainment=1.0e3  
bv_freq_threshold 
 The buoyancy frequency threshold at which the scheme will start to create blobs, i.e. blobs will be formed when N^2<bv_freq_threshold Default is bv_freq_threshold=1.0e15  
full_N2 
 Whether to use the buoyancy frequency calculated from the combined E and L system (true) or, from the E system only (false). Default is full_N2=.true.  
large_speed 
 A value for error checking. If the speed of a blob exceeds large_speed in any of x,y,z then a warning flag is raised. Default is large_speed=10.0 
Filename: src/mom5/ocean_blobs/ocean_blob_static_bottom.F90
Namelist: ocean_blob_static_bottom_nml
Name 
 Description  

use_this_module 
 
overflow_no_return 
 When .false. creates return blobs to replicate the original Campin and Goosse scheme. When .true. only creates blobs that sink. See further overflow_one_return  
overflow_one_return 
 Creates a single return blob when .true. Cannot be .true. when overflow_no_return is also .true.  
blob_overflow_mu 
 Frictional dissipation used in blob_overflow scheme Default is blob_overflow_mu=1.0e4  
blob_overflow_delta 
 Fraction of grid cell participating in overflow Valid values are 0<=delta<=1 Default is blob_overflow_delta=1/3  
blob_overflow_umax 
 Maximum downslope speed allowed for overflow Default is blob_overflow_umax=0.01 
Filename: src/mom5/ocean_blobs/ocean_blob_static_free.F90
Namelist: ocean_blob_static_free_nml
Name 
 Description  

use_this_module 
 
blob_ncon_like 
 If true, will use NConlike formulation. Default blob_ncon_like = .true.  
blob_diff_like 
 If true, will use the diffusionlike formulation. Default is "blob_diff_like=.false.  
blob_swap_like 
 If true, will use the swaplike formulation. Default is blob_switch_like=.false.  
ncon_blob 
 The number of times that the water column is checked and adjusted for instability. 
src/mom5/ocean_core
Filename: src/mom5/ocean_core/ocean_advection_velocity.F90
Namelist: ocean_advection_velocity_nml
Name 
 Description  

max_advection_velocity 
 This is a check value used to determine if the time steps will result in linearly stable advection. If set to a number < 0, then model will estimate the value as a function of maximum grid size. Note that this time step check is not rigorous, and it depends on the details of the advection scheme. Nonetheless, it provides some useful warning for setting the time steps in the model.  
debug_this_module 
 For debugging.  
inflow_nboundary 
 For adding an inflow velocity from the northern boundary. Default is inflow_nboundary=.false.  
read_advection_velocity 
 For reading in a file with specified zonal, meridional, and vertical components to the advective velocity. The file should have velocity at the east face of Tcell, north face, and bottom, just as on a Cgrid. The units should be m/s for each component. MOM then multiplies but the appropriate thickness and density factors to generate transport for use in the model. Default read_advection_velocity=.false.  
read_advection_transport 
 For reading in a file with specified zonal, meridional, and vertical components to the advection transport. The file should have transport at the east face of Tcell, north face, and bottom, just as on a Cgrid. The units should be (kg/m^3)(m^2/sec) for horz components, and (kg/m^3)(m/sec) for vertical component. MOM then uses these fields directly to initialize uhrho_et, vhrho_nt, and wrho_bt. Default read_advection_transport=.false.  
constant_advection_velocity 
 When reading in the advection velocity components, we may choose to keep them constant in time. This facilitates idealized tests of tracer advection. Default constant_advection_velocity=.false. 
Filename: src/mom5/ocean_core/ocean_barotropic.F90
Namelist: ocean_barotropic_nml
Name 
 Description  

zero_tendency 
 If true, will not integrate the barotropic fields.  
zero_eta_ic 
 To initialize eta_t to zero.  
zero_eta_tendency 
 To maintain deta_dt at zero. For debugging. Default zero_eta_t=.false.  
zero_eta_t 
 To maintain eta_t at zero, but to allow other fields to evolve. For debugging. Default zero_eta_t=.false.  
zero_eta_u 
 To maintain eta_u at zero, but to allow other fields to evolve. For debugging. Default zero_eta_u=.false.  
zero_forcing_bt 
 Will set to zero all of the terms forcing the barotropic velocity.  
zero_nonlinear_forcing_bt 
 Will set to zero the nonlinear forcing terms, leaving only the smf and bmf terms to force the barotropic velocity.  
zero_coriolis_bt 
 Will set to zero the Coriolis parameter for purpooses of computing the barotropic momentum equation. This option is for testing alone. Default zero_coriolis_bt = .false.  
ideal_initial_eta 
 To initialize eta_t to an ideal profile. This option overrides all other initialization that may have occurred. Default=.false.  
ideal_initial_eta_amplitude 
 Amplitude for initializing eta with an ideal profile. Default ideal_initial_eta_amplitude = 5.0  
ideal_initial_eta_xwidth 
 Width in xdirection for sinewave profile. Default xwidth=100e3  
ideal_initial_eta_ywidth 
 Width in ydirection for sinewave profile. Default ywidth=100e3  
truncate_eta 
 To truncate the surface height so to ensure positive thickness within the top cell. This method will not conserve volume or tracer. It is coded for cases when conservation is not critical but wish to run GEOPOTENTIAL models w/ large free surface height deviations, such as when running with tides and very fine vertical resolution. The preferred approach is to use zstar or pstart vertical coordinates. Default truncate_eta = .false..  
verbose_truncate 
 For verbose printout on truncate_eta  
frac_crit_cell_height 
 When use GEOPOTENTIAL vertical coordinate, the top model tracer grid cell has thickness dzt(i,j,1) = dzt(1) + eta_t(i,j). 0 < frac_crit_cell_height <= 1 sets the fraction of dzt(1) that is allowed prior to bringing the model down due to overly small dzt(i,j,1). Default frac_crit_cell_height=0.20.  
eta_max 
 The maximum positive eta_t allowed when truncate_eta is true. Default eta_max = 5.0.  
debug_this_module 
 Print out lots of diagnostics of use for debugging. Default debug_this_module=.false.  
verbose_init 
 For brief or full printout on initialization Default verbose_init=.true.  
diag_step 
 Frequency for output of ascii barotropic diagnostics. Setting diag_step=1 will compute diagnostics each time step and print to stdout. This setting is useful when developing a model in order to examine various budgets and stability issues. But when running production, one should set diag_step to a mucch larger number in order to reduce i/o and model cost. Default diag_step=1, which means will not compute any of the online diagnostics.  
tidal_forcing_m2 
 Forces from lunar M2 tidal constituent. Default tidal_forcing_m2=.false.  
tidal_forcing_8 
 Forces from 8 lunar and solar tidal constituents. Default tidal_forcing_8=.false.  
tidal_forcing_ideal 
 For ideal tidal forcing, which has a bump configuration. Default tidal_forcing_ideal=.false.  
geoid_forcing 
 For modifying the geoid, implemented as a time independent tidal forcing. Need to read in a file to obtain the offset geoid profile. Default geoid_forcing=.false.  
do_bitwise_exact_sum 
 Set true to do bitwise exact global sum. When it is false, the global sum will be nonbitwise_exact, but will significantly increase efficiency. Default do_bitwise_exact_sum=.false.  
smooth_eta_t_bt_laplacian 
 For spatially smoothing the eta_t field at each barotropic time step using a Laplacian operator. This option may not be necessary when pred_corr_gamma > 0.0, since the predictorcorrector approach has dissipation from pred_corr_gamma > 0.0. Also, smoothing is not needed in general for Cgrid MOM, since the gravity wave null mode only appears for the Bgrid. This option is only applicable for DEPTH_BASED vertical coordinates. Default smooth_eta_t_bt_laplacian=.false.  
smooth_eta_t_bt_biharmonic 
 For spatially smoothing the eta_t field at each barotropic time step using a biharmonic operator. May not be necessary when pred_corr_gamma > 0.0, since predictorcorrector has dissipation from pred_corr_gamma > 0.0. Also, smoothing is not needed in general for Cgrid MOM, since the gravity wave null mode only appears for the Bgrid. Applicable just for DEPTH_BASED vertical coordinates. WARNING: this operator is NOT positive definite, and so can produce spurious extrema. It is not generally recommended just for this reason. Default smooth_eta_t_bt_laplacian=.false.  
smooth_eta_t_laplacian 
 For spatially smoothing the eta_t field on the big time step by using a laplacian operator. For compatibility and global conservation, must also introduce a mixing to the thickness weighted tracer concentration in the k=1 cell. Applicable just for DEPTH_BASED vertical coordinates. Also, smoothing is not needed in general for Cgrid MOM, since the gravity wave null mode only appears for the Bgrid. Default mooth_eta_t_laplacian=.true.  
smooth_eta_t_biharmonic 
 For spatially smoothing the eta_t field on the big time step by using a biharmonic operator. For compatibility and global conservation, must also introduce a mixing to the thickness weighted tracer concentration in the k=1 cell. Applicable just for DEPTH_BASED vertical coordinates. Also, smoothing is not needed in general for Cgrid MOM, since the gravity wave null mode only appears for the Bgrid. WARNING: This operator is NOT positive definite, and so can produce spurious extrema. It is not recommended just for this reason. Default smooth_eta_t_biharmonic=.false.  
smooth_eta_diag_laplacian 
 For spatially smoothing the diagnosed eta_t field using a laplacian operator. This option is used for PRESSURE_BASED vertical coordinates, in which case the free surface is diagnosed rather than prognosed. Also, smoothing is not needed in general for Cgrid MOM, since the gravity wave null mode only appears for the Bgrid. Default smooth_eta_diag_laplacian=.true.  
smooth_eta_diag_biharmonic 
 For spatially smoothing the diagnosed eta_t field using a biharmonic operator. This option is used for PRESSURE_BASED vertical coordinates, in which case the free surface is diagnosed rather than prognosed. Also, smoothing is not needed in general for Cgrid MOM, since the gravity wave null mode only appears for the Bgrid. Default smooth_eta_diag_biharmonic=.false.  
smooth_anompb_bt_laplacian 
 For spatially smoothing anomalous pbot_t at each barotropic time step using a Laplacian operator. May not be necessary when pred_corr_gamma > 0.0, since predictorcorrector has dissipation from pred_corr_gamma > 0.0. This option is applicable just for PRESSURE_BASED vertical coordinates. Also, smoothing is not needed in general for Cgrid MOM, since the gravity wave null mode only appears for the Bgrid. Default smooth_anompb_bt_laplacian=.false.  
smooth_anompb_bt_biharmonic 
 For spatially smoothing the anomalous pbot_t field at each barotropic time step using a biharmonic operator. May not be necessary when when pred_corr_gamma > 0.0, since predictorcorrector has dissipation from pred_corr_gamma > 0.0. This option is applicable just for PRESSURE_BASED vertical coordinates. Also, smoothing is not needed in general for Cgrid MOM, since the gravity wave null mode only appears for the Bgrid. WARNING: This operator is NOT positive definite, and so can produce spurious extrema. It is not recommended just for this reason. Default smooth_anompb_bt_biharmonic=.false.  
smooth_pbot_t_laplacian 
 For spatially smoothing pbot_tpbot0 on the big time step using a laplacian operator. For compatibility and global conservation, must also introduce a mixing to the thickness weighted tracer concentration in the k=kbot cell. Applicable just for PRESSURE_BASED vertical coordinates. Also, smoothing is not needed in general for Cgrid MOM, since the gravity wave null mode only appears for the Bgrid. Default smooth_pbot_t_laplacian=.true.  
smooth_pbot_t_biharmonic 
 For spatially smoothing pbot_tpbot0 on the big time step by using a biharmonic operator. For compatibility and global conservation, must also introduce a mixing to the thickness weighted tracer concentration in the k=kbot cell. Applicable just for PRESSURE_BASED vertical coordinates. Also, smoothing is not needed in general for Cgrid MOM, since the gravity wave null mode only appears for the Bgrid. WARNING: This operator is NOT positive definite, and so can produce spurious extrema. It is not recommended just for this reason. Default smooth_pbot_t_biharmonic=.false.  
smooth_pbot_t_biharmonic_legacy 
 For using an older version of the smooth_pbot_t_biharmonic scheme. The smooth_pbot_t_biharmonic_legacy option has a minor bug, but it is maintained in order to allow for backward compatible legacy simulations. It is not recommended for new simulations. To use it requires also setting smooth_pbot_t_biharmonic=.true. Default smooth_pbot_t_biharmonic_legacy=.false.  
vel_micom_lap 
 Velocity scale that is used for computing the MICOM Laplacian mixing coefficient used in the Laplacian smoothing of surface height or anomalous bottom pressure. Default vel_micom_lap=0.05.  
vel_micom_lap_diag 
 Velocity scale that is used for computing the MICOM Laplacian mixing coefficient used in the Laplacian smoothing of diagnosed surface height. Default vel_micom_lap_diag=0.2.  
vel_micom_bih 
 Velocity scale that is used for computing the MICOM biharmonic mixing coefficient used in the biharmonic smoothing of surface height or anomalous bottom pressure. Default vel_micom_bih=0.01.  
vel_micom_bih_diag 
 Velocity scale that is used for computing the MICOM biharmonic mixing coefficient used in the biharmonic smoothing of diagnosed surface height. Default vel_micom_bih_diag=0.1.  
eta_offset 
 Uniform offset for use in determining the filter acting on tracer when smoothing the surface height. Default eta_offset=1e12.  
pbot_offset 
 Uniform offset for use in determining the filter acting on tracer when smoothing the bottom pressure anomaly. Default pbot_offset=1e12.  
udrho_lap_vel_micom 
 Velocity scale that is used for computing the MICOM Laplacian mixing coefficient used in the Laplacian smoothing of udrho. This options will soon be removed from MOM. Default udrho_lap_vel_micom=.05  
udrho_bih_vel_micom 
 Velocity scale that is used for computing the MICOM biharmonic mixing coefficient used in the biharmonic smoothing of udrho. This options will soon be removed from MOM. Default udrho_bih_vel_micom=.01  
udrho_bt_lap 
 The vertically integrated horizontal momentum can be noisy on the Bgrid. It is therefore sometimes useful to add a smoothing operator to the barotropic time stepping. Here, we apply the laplacian friction as coded in the friction module using the vertically averaged isotropic viscosity as well as a background, and we do so on each barotropic time step. It is an expensive option. It is an option rarely used GFDL. This options will soon be removed from MOM. Default udrho_bt_lap=.false.  
udrho_bt_bih 
 The vertically integrated horizontal momentum on the Bgrid can be noisy. It is therefore sometimes useful to add a smoothing operator. Here, we apply the biharmonic friction as coded in the friction module using the vertically averaged isotropic viscosity as well as a background. Do so on each barotropic time step, which makes it an expensive option. This option is rarely used GFDL. Default udrho_bt_bih=.false. This options will soon be removed from MOM.  
udrho_lap 
 The vertically integrated horizontal momentum on the Bgrid can be noisy. It is therefore sometimes useful to add a smoothing operator. Here, we apply the laplacian friction as coded in the friction module using the vertically averaged isotropic viscosity as well as a background. Do so just on the baroclinic time step, so the option is less expensive than udrho_bt_lap. This options will soon be removed from MOM. Default udrho_lap=.false.  
udrho_bih 
 The vertically integrated horizontal momentum on the Bgrid can be noisy. It is therefore sometimes useful to add a smoothing operator. Here, we apply the biharmonic friction as coded in the friction module using the vertically averaged isotropic viscosity as well as a background. Do so just on the baroclinic time step, so the option is less expensive than udrho_bt_lap. This options will soon be removed from MOM. Default udrho_bih=.false.  
barotropic_time_stepping_A 
 Use the general approach from MOM4.0, in which the eta_t and pbot_t fields are updated with a big time step. This is the recommended approach for most applications that do not employ and open boundary condition. Default barotropic_time_stepping_A=.false.  
barotropic_time_stepping_B 
 Use the alternative approach in which we assume the barotropic scheme is a predictorcorrector, which is now the default in MOM. We use this assumption so that the eta_t and pbot_t fields are updated with a time average. This approach is used for open boundary condition applications. Default barotropic_time_stepping_B=.false.  
initsum_with_bar_mom4p0 
 
initsum_with_bar_mom4p1 
 
pred_corr_gamma 
 Dimensionless dissipation parameter for the preditorcorrector scheme. Setting pred_corr_gamma=0.0 reduces the scheme to a forwardbackward, but it has been found to be unstable. So pred_corr_gamma > 0.0 is recommended. Note that pred_corr_gamma > 0.25 may be overdissipated and so may go unstable. Default pred_corr_gamma=0.2.  
write_a_restart 
 Set true to write a restart. False setting only for rare cases where wish to benchmark model without measuring the cost of writing restarts and associated chksums. Default is write_a_restart=.true.  
barotropic_halo 
 Set barotropic_halo > 1 to use wide halo in the barotropic time step to improve the performance. In barotropic time step, most time is spent on mpp_update_domains. Use wide halo to decrease the number of mpp_update_domain calls and hence improve the performance. The default value is barotropic_halo=1, which is the older approach (nonwide halo). Users are encouraged to experiment with larger halos, as the model speedup can be tremendous.  
use_legacy_barotropic_halos 
 
alphat 
 Dimensionless selfattraction and loading term. Used only when tidal_forcing=.true. Default alphat=0.948. 
Filename: src/mom5/ocean_core/ocean_bbc.F90
Namelist: ocean_bbc_nml
Name 
 Description  

bmf_implicit 
 For incorporating the bottom momentum drag implicitly in time. Default is bmf_implicit=.false.  
debug_this_module 
 For debugging purposes.  
cdbot_law_of_wall 
 For determining bottom drag coefficient using a constant roughness length. Will take maximum between cdbot and the computed value using law of wall logprofile. This option of use when have very very refined vertical resolution (say on order of meters) near the bottom. Terrain following coordinates should use this option since they generally have very refined vertical grid spacing on topography. Default is cdbot_law_of_wall=.false.  
cdbot_roughness_length 
 For determining bottom drag coefficient using a map of the roughness length. This approach is more relevant for coarse models than the constant roughness length used in the cdbot_law_of_wall option. Default is cdbot_roughness_length=.false.  
cdbot_wave 
 For determining bottom drag coefficient using a map of the roughness length and the surface wind wave field. The modified drag coefficient is calculated following Grant and Mattsen. Likewise this method can be improved using more sophisticated wave models including swell. Default is cdbot_wave=.false.  
cdbot_roughness_uamp 
 For determining bottom drag coefficient using a map of the roughness length and tidal velocity amplitude. This approach is more relevant for coarse models than the constant roughness length used in the cdbot_law_of_wall option. cdbot_lo <= cdbot(i,j) <= cdbot_hi. Default is cdbot_roughness_length=.false.  
use_geothermal_heating 
 
convert_geothermal 
 
law_of_wall_rough_length 
 Bottom roughness length. Default is law_of_wall_rough_length=0.01m, following the default used in the Princeton Ocean Model (POM). This value corresponds to "Law of Wall" physics.  
cdbot 
 Dimensionless coefficient for quadratic bottom drag.  
uresidual 
 Residual bottom velocity due to unresolved fluctuations (e.g., waves and tides) that contribute to bottom dissipation. Should be set to zero when running with explicit representation of tidal forcing and when waves are well resolved. Default is uresidual=.05.  
cdbot_hi 
 
cdbot_lo 
 
cdbot_gamma 
 
uvmag_max 
 Maximum magnitude of the bottom velocity used to compute the bottom momentum drag. Default is uvmag_max=10.0.  
bmf_max 
 Maximum magnitude of the bottom momentum drag. Default is bmf_max=1.0.  
cdbot_HH 
 H0 in a parameterization of cdbot_roughness_uamp. Default is cdbot_HH=1100.0.  
cdbot_UU 
 U0 in a parameterization of cdbot_roughness_uamp. Default is cdbot_UU=1.0. 
Filename: src/mom5/ocean_core/ocean_coriolis.F90
Namelist: ocean_coriolis_nml
Name 
 Description  

debug_this_module 
 For debugging.  
use_this_module 
 Must be true to add contributions from Coriolis force.  
acor 
 acor=0.0 means explicit Coriolis force. 0.5 < = acor < 1.0 means semiimplicit, and acor = 1.0 is implicit. This option is only relevant for the Bgrid, since the Cgrid compute Coriolis using 3rd order AdamsBashforth scheme. For the Bgrid, the semiimplicit method removes dtuv time step constraint associated with inertial oscillations, but it leads to Coriolis force affecting energy balances. If use twolevel tendency discretization, then acor=0 is NOT allowed since the model will be linearly unstable with growth rate going as f*(delta time). 
Filename: src/mom5/ocean_core/ocean_density.F90
Namelist: ocean_density_nml
Name 
 Description  

eos_linear 
 Set to true to use an idealized linear equation of state, which has no pressure dependence, and is a linear function of salinity and temperature. Default eos_linear=.false.  
alpha_linear_eos 
 Constant "thermal expansion coefficient" for linear EOS rho = rho0  alpha_linear_eostheta + beta_linear_eossalinity  
beta_linear_eos 
 Constant "saline contraction coefficient" for linear EOS rho = rho0  alpha_linear_eostheta + beta_linear_eossalinity  
eos_preteos10 
 Set to true to use preTEOS10 equation of state, which is a function of potential temperature and practical salinity, or conservative temperature and practical salinity. Default eos_preteos10=.false.  
eos_teos10 
 Set to true to use TEOS10 equation of state, which is a function of conservative temperature and absolute salinity. Default eos_teos10=.false.  
s_test 
 Salinity for testing the EOS.  
t_test 
 Conservative temperature or potential temperature for testing the EOS.  
p_test 
 Sea pressure for testing the EOS.  
sn_test 
 Salinity the equation for neutral density.  
tn_test 
 Conservative temperature or potential temperature for testing the equation for neutral density.  
layer_nk 
 Number of classes used to partition vertical according to potential density, conservative temperature, or potential temperature. Used for diagnostics.  
potrho_press 
 Reference sea pressure for computing diagnostic potential density of use for computing diagnostics with potential density. Default potrho_press=2000.0  
potrho_min 
 Minimum potential density used to partition vertical according to potential density.  
potrho_max 
 Maximum potential density used to partition vertical according to potential density.  
neutral_density_omega 
 Set to true to compute the neutral density according to the omega method based on Klocker and McDougall. This approach has not yet been coded. Presently as a placeholder we use potential density referenced to 2000dbar. Default neutral_density_omega=.false.  
neutral_density_potrho 
 Set to true to compute the neutral density as just a selected potential density, set according to potrho_press. Since the neutral_density_omega approach has yet to be coded, we only have the neutral_density_potrho option to choose from at this time. Default neutral_density_potrho=.true.  
neutralrho_min 
 Minimum neutral density used to partition vertical according to rational polynomial approximation to neutral density.  
neutralrho_max 
 Maximum neutral density used to partition vertical according to rational polynomial approximation to neutral density.  
theta_min 
 Minimum conservative temperature or potential temperature used to partition vertical according to temperature.  
theta_max 
 Maximum conservative temperature or potential temperature used to partition vertical according to temperature.  
press_standard 
 Standard atmospheric pressure (dbar). The realistic EOS used in MOM requires "sea pressure" as an argument rather than absolute pressure. Sea pressure is absolute pressure minus a standard atmospheric pressure of 10.1325dbar. For models that do have a realistic atmospheric loading, then it is appropriate to remove 10.1325dbar prior to computing the EOS. For those cases with zero atmospheric pressure, then it is not necessary to remove the standard atmosphere. The default for the press_standard is 0.0dbar.  
buoyfreq_smooth_vert 
 To smooth the vertical temp and salt derivative for diagnosing the buoyancy frequency. Default buoyfreq_smooth_vert=.true.  
num_121_passes 
 
epsln_drhodz 
 To normalize the inverse vertical derivative of neutral density for computing the buoyancy frequency. Default epsln_drhodz=1e10.  
drhodz_diag_stable 
 When computing drhodz_diag, we can enforce that it is negative, thus reflecting a stable stratification. The field drhodz_diag is used for many water mass transformation diagnostics, such as wdian_rho. Allowing for unstable profiles can bias the wdian_rho calculation in an improper way, since the magnitude of drhodz_diag is very small when it is positive, whereas it is larger magnitude when negative. Default drhodz_diag_stable=.true.  
epsln_drhodz_diag 
 To normalize the inverse vertical derivative of neutral density for computing neutral_rho and wdian diagnostics. Default epsln_drhodz_diag=1e10.  
grad_nrho_lrpotrho_compute 
 To perform the diagnostic calculation of grad_nrho_lrpotrho for analysis diagnostics. This factor is not well constrained, and can be problematic in certain regions. So presently we do not recommend computing it, so that the default is grad_nrho_lrpotrho_compute=.false.  
grad_nrho_lrpotrho_max 
 Maximum value used for grad_nrho_lrpotrho. Default grad_nrho_lrpotrho_max=10.  
grad_nrho_lrpotrho_min 
 Minimum value used for grad_nrho_lrpotrho. Default grad_nrho_lrpotrho_min=1.  
smooth_stratification_factor 
 For doing an S2D smoothing of the stratification factor used for diagnostic purposes. Requires an extra call to mpp update. Default smooth_stratification_factor=.false. since the smoothing incurs a cost that should be borne only when desired.  
smax_min_in_column 
 To compute the diagnostic maximum neutral slope within a column as the minimum vertical to horizontal grid aspect ratio. This method ensures that the slope is adequately "resolved" by the grid, and that all depths use the same definition of "resolved", even if presumably thicker grid cells can "resolve" larger neutral slopes. This approach is not very useful generally, so it is retained only for testing purposes. Default smax_min_in_column=.false.  
smax_diag 
 A diagnostic maximum neutral slope for use in computing which direction is deemed the most stratified. For use in computing the stratification_factor which is then used to diagnose the dianeutral mass transport. smax_diag should corresond to the choice used in neutral diffusion scheme. Should have 0 <= smax_diag <= 1.0. Default smax_diag=1.0, in which case we compute the smax according to the vertical to horizontal grid aspect ratio. This method ensures that the slope is adequately "resolved" by the grid.  
update_diagnostic_factors 
 To update the watermass_factor and stratification_factor for use in the water mass transformation diagnostics. Default update_diagnostic_factors=.false.  
mask_domain_restart 
 For cases where use the domain masking, it is necessary to initialize the field denominator_r to nonzero in order to avoid NaNs in the case when change processor layout in between restarts. Note that when use solid wall boundary conditions, this logical should remain false in order to bitwise reproduce across restarts. Default mask_domain_restart=.false.  
debug_this_module 
 For debugging nonlinear equation of state  
rho0_density 
 For debugging, it is often useful to have rho=rho0 uniform.  
density_equal_potrho 
 For idealized tests, set the in situ density equal to the potential density referenced to potrho_press. All density derivatives will also be computed with respect to constant potrho_press pressure. Default density_equal_potrho=.false.  
write_a_restart 
 Set true to write a restart. False setting only for rare cases where wish to benchmark model without measuring the cost of writing restarts and associated chksums. Default is write_a_restart=.true.  
do_bitwise_exact_sum 
 Set true to do bitwise exact global sum. When it is false, the global sum will be nonbitwise_exact, but will significantly increase efficiency. default: do_bitwise_exact_sum=.false. 
Filename: src/mom5/ocean_core/ocean_domains.F90
Namelist: ocean_domains_nml
Name 
 Description  

halo 
 For specifying the halo size by hand.  
max_tracers 
 temporary  need to call domains_init before tracer_init Used for computing mpp_stack_size.  
x_cyclic_offset 
 offset to be applied on xdirection boundary condition. Its value could be positive or negative and the default value is 0. When the ydirection boundary condition is foldednorth(tripolar grid), x_cyclic_offset must be 0. For torus (cyclic in x and ydirection), at least one of x_cyclic_offset and y_cyclic_offset must be 0.  
y_cyclic_offset 
 offset to be applied on ydirection boundary condition. Its value could be positive or negative and the default value is 0. For torus (cyclic in x and ydirection), at least one of x_cyclic_offset and y_cyclic_offset must be 0. 
Filename: src/mom5/ocean_core/ocean_grids.F90
Namelist: ocean_grids_nml
Name 
 Description  

do_bitwise_exact_sum 
 Set true to do bitwise exact global sum. When it is false, the global sum will be nonbitwise_exact, but will significantly increase efficiency. The default value is do_bitwise_exact_sum=.false.  
debug_this_module 
 For debugging. Note that most of the debugging stuff has been removed, but keep flag around in case need in future.  
verbose_init 
 Prints out lots of initial checksums. Useful to have on, so defaulted to true.  
read_rho0_profile 
 To read in an initial rho0(k) profile to assist in defining the initial settings for the pressure increments dst, for use in setting the pressurebased vertical coordinate grids. Ideally, this profile is determined by the level averaged density in the initial conditions. Note that it is essential to have rho0_profile have a sensible value at all depths even if there is no water there, since there are places where we divide by rho0_profile in rock. Also, be mindful that with denser water at depth, the pressure levels will be coarser at depth than if using the trivial density profile rho0(k)=rho0. This option is experimental, so it is recommended that user maintain the default read_rho0_profile=.false.  
write_grid 

Filename: src/mom5/ocean_core/ocean_model.F90
Namelist: ocean_model_nml
Name 
 Description  

impose_init_from_restart 
 Consider the following situation: We have run the model for many years and generated restarts. Time%init is then .false. Then, we wish to start a series of perturbation experiments from this restart file. The generic situation is for Time%init to then be .true. However, we need it to be .false. in MOM in order to have a proper reading of the full restart information. Setting impose_init_from_restart=.true. will facilitate this setup. The default is impose_init_from_restart=.false., in which case the model will run through its normal start/stop segments using restarts.  
reinitialize_thickness 
 When initialized with a nontrivial eta field, it is necessary to reinitialize the thickness arrays.  
baroclinic_split 
 baroclinic_split = dtts/dtuv = (tracer time step)/(baroclinic time step) = (ocean model time step)/(baroclinic time step) Transients corrupted if baroclinic_split > 1, so it is recommended to use baroclinic_split=1.  
surface_height_split 
 Ratio surface_height_split = dtts/dteta = (tracer time step)/(surface height time step) = (tracer time step)/(bottom pressure time step) Typically this split is set to unity for models where baroclinic_split=1, but something larger when baroclinic_split is order 10. dteta is the time step used for update of eta_t or pbot_t. If surface_height_split is not equal to unity, then tracer conservation properties are compromised.  
barotropic_split 
 Ratio barotropic_split = dtuv/dtbt = (baroclinic time step)/(barotropic time step). Must be large enough to resolve the barotropic gravity waves captured by the barotropic part of the model. Barotropic waves are dissipated when this splitting is greater than unity. Model algorithm is not fully implemented when barotropic_split=1, so user beware if wishing to run an unsplit model simulation.  
time_tendency 
 Possible time stepping schemes are the following. 1. "threelevel" has the following characteristics leapfrog for the time tendency which means the inviscid/nondissipative processes are at time tau. forward for lateral mixing processes (dissipation at taum1) implicit for vertical dissipative (with aidif = 1.0) semiimplicit for Coriolis (with acor>0) Because of the need to apply time filters to suppress leapfrog splitting, the threelevel time stepping scheme does not conserve total tracer content in the model. 2. "twolevel" has the following characteristics: staggered 2nd order forward time tendency, which means that tracer advection, lateral tracer and velocity mixing, are at time tau. Pressure gradients are at taup1. AdamsBashforth (either 2nd or 3rd order) for velocity advection Third order is default as it is more stable. implicit vertical mixing (with aidif = 1.0) semiimplicit for Coriolis (with acor > 0) This scheme conserves total volume and tracer in the ocean model.  
vertical_coordinate 
 This string determines the vertical coordinate used in MOM. There are 3 + 3 options in MOM: Depthbased Boussinesq are 'geopotential', 'zstar', 'zsigma', Pressurebased nonBoussinesq are 'pressure', 'pstar', and 'psigma'. The two terrainfollowing sigma options are not well tested in MOM, whereas the other options are standard. The recommended Boussinesq vertical coordinate is zstar, and the recommended nonBoussineq coordinate is pstar. The default is vertical_coordinate='zstar'.  
horizontal_grid 
 This string determines the arrangement of variables on the discrete horizontal grid. The standard case is horizontal_grid='bgrid'. However, the Cgrid is being developed in MOM. It is not yet supported for general use. Default horizontal_grid='bgrid'.  
layout 
 Processor domain layout for ocean model.  
io_layout 
 Processor IO domain layout for ocean model. The default value is (0,0). If either io_layout(1) or (2) is 0, it will default to the number of processors in the computational layout, except restart file will default to single file if fms_io_nml fileset_write is set to 'single'. When both entry of io_layout is positive, io_domain will be defined(a pointer in domain2d) and number of distributed files will be layout(1)*layout(2). For example, assume the restart file is ocean_velocity.res.nc and the diagnostics file is ocean_daily.nc, if the layout = (1,2), the restart files will be ocean_velocity.res.nc.0000 and ocean_veloicity.res.nc.0001, the diagnostics files will be ocean_daily.res.nc.0000 and ocean_daily.res.nc.0001. When the io_domain is defined, restart file and diagnostics file name will be controlled by the io_domain (ignoring fms_io_nml fileset_write).  
debug 
 For overall model debugging. Set true to print cksums at each timestep for debugging purposes.  
mask_table 
 A text file to specify n_mask, layout and mask_list. This table aims to reduce the number of processors that are cycling over pure land regions. These processors will be masked out of regions that which contain all land points. The default file name of mask_table is "INPUT/ocean_mask_table". Please note that the file name must begin with "INPUT/". The first line of mask_table is the number of region to be masked out. The second line is the layout of the model. User need to set ocean_model_nml variable layout to be the same as the second line of the mask table. The following n_mask line will be the position of the processor to be masked out. The mask_table could be created by tools check_mask. For example the mask_table will be as following if n_mask=2, layout=4,6 and the processor (1,2) and (3,6) are to be masked out. 2 4,6 1,2 3,6  
cmip_units 
 For CMIP output, we need to have temperature in deg K and mass transport in kg/s. The flag cmip_units=.true. will diagnose CMIP5related fields with the CMIP units for sending to the diagnostic manager. Default cmip_units=.false.  
use_blobs 
 For using Lagrangian blobs. Default use_blobs=.false.  
introduce_blobs 
 For the Lagrangian blobs after a model has already been running. Default introduce_blobs=.false.  
use_velocity_override 
 For overriding the velocity field with values from a file. Note that we need separate files for (u,v) read into ocean_velocity.F90, as well as (udrho,vdrho) read into ocean_barotropic.F90. Default use_velocity_override=.false.  
dt_ocean 
 Ocean model time step in seconds. 
Filename: src/mom5/ocean_core/ocean_obc.F90
Namelist: ocean_obc_nml
Name 
 Description  

direction 
 open boundary direction. Each element value should be west, east, south or north.  
name 
 type of open bounday.  
ctrop_max 
 Maximum value to clip diagnosed barotropic phase speed in terms of sqrt(gH). Should be about 1.  
ctrop_min 
 Minimum value to diagnosed barotropic phase speed in terms of sqrt(gH). Should be about 0. Default is 0.1.  
ctrop_inc 
 value to be set for barotropic phase speed if incoming waves are diagnosed. (in terms of sqrt(gH)) Should be about 0. Default is 0.  
ctrop_smooth 
 
enh_pnts 
 Enhance viscosity and mixing at a stripe of enh_pnts decreasing with the distance from the boundary. Default = 1.  
enh_fac_v 
 'Safety factor' applied to maximum stable viscosity at the boundary. Default = 0.9  
enh_fac_d 
 Factor applied to enhance mixing at the boundary. Default = 1.  
obc_enhance_visc_back 
 logical variable that decide whether to enhance viscosity at the boundary. Default value is .false.  
obc_enhance_diff_back 
 logical variable that decide whether to enhance mixing at the boundary. Default value is .false.  
obc_consider_convu 
 logical variable that decide whether to account for one component of convu within the boundary. The appropriate behavior depends on the model configuration. Default value is .false.  
obc_vert_advel_t 
 logical variable that decide whether to account for vertical advection of tracers at the boundary. The appropriate behavior depends on the model configuration. Default value is .false. (Currently inactive)  
obc_vert_advel_u 
 logical variable that decide whether to account for vertical advection of momentum at the boundary. The appropriate behavior depends on the model configuration. Default value is .false.  
obc_adjust_forcing_bt 
 
obc_damp_newton 
 
damp_factor 
 
nobc 
 number of open boundary condition. Its value should be less than max_obc. Increase max_obc if needed.  
is 
 
ie 
 
js 
 
je 
 
iers 
 
iere 
 
jers 
 
jere 
 
itrs 
 
itre 
 
jtrs 
 
jtre 
 
obc_nor 
 Normal velocity OBC  
obc_tan 
 Tangential velocity OBC  
obc_eta 
 Surface elevation OBC  
obc_ud 
 
obc_mix 
 Vertical mixing coefficient OBC  
obc_tra 
 Tracers OBC  
rel_coef_eta_in 
 Relaxation coefficient to be used for incoming wave situation.  
rel_coef_eta_out 
 Relaxation coefficient to be used for outgoing wave situation. Should be smaller then or equal to rel_coef_eta_in.  
rel_eta_pnts 
 Relax sea level at a stripe of rel_eta_pnts. Default = 1.  
filename_eta 
 Filename to read sea level data.  
fieldname_eta 
 Fieldname to read sea level data.  
filename_ud 
 
fieldname_ud 
 
obc_relax_tracer 
 logical variable that decide whether relax tracer or not. Default value is .false.  
obc_flow_relax 
 Integer variable specifying the flow relaxation zone (flow realxation of Martinsen and Engedahl (1987). Default value is 1.  
obc_consider_sources 
 Logical variable specifying if source and SGS terms of the normal tracer scheme are valid. Default value is .false..  
obc_tracer_no_inflow 
 logical variable that decide whether apply orlanski obc on tracer or not. Default value is .false.  
rel_clin_pnts 
 Relax a tracer at a stripe of rel_clin_pnts. Default = 1.  
rel_coef_tracer_in 
 Relaxation coefficient to be used for inflow situation.  
rel_coef_tracer_out 
 Relaxation coefficient to be used for outflow situation. Should be smaller then or equal to rel_coef_tracer_in.  
fieldname_tracer 
 Fieldname of a tracer.  
filename_tracer 
 Filename to read a tracer. It is allowed to put all data for a boundary in one file.  
debug_this_module 
 For debugging.  
debug_phase_speed 
 Includes the phase speed into the model output. 
Filename: src/mom5/ocean_core/ocean_operators.F90
Namelist: ocean_operators_nml
Name 
 Description  

use_legacy_DIV_UD 
 Set use_legacy_DIV_UD=.true. to reproduce Riga results for DIV_UD on Bgrid. For the case that the model grid is tripolar grid, when barotropic_halo > 1 in ocean_barotropic.F90, then we must set use_legacy_DIV_UD=.false., since will not reproduce between different number of processors if set use_legacy_DIV_UD=.true. Tests indicate that with wider barotropic halos, there are some performance enhancements for use_legacy_DIV_UD=.false. Hence, the default is use_legacy_DIV_UD=.false. For the case that the model grid is regular latlon grid, use_legacy_DIV_UD could be set to .true. or .false. for any positive value of barotropic_halo. Note that the only difference between the new and old DIV_UD is order of operations induced by parentheses, which occurs in the tripolar fold region in the Arctic: old: DIV_UD(i,j) = (uh_bay  uhim_bay + vh_bax  vhjm_bax)datr_bt(i,j) new: DIV_UD(i,j) = ((uh_bay  uhim_bay) + (vh_bax  vhjm_bax))datr_bt(i,j) 
Filename: src/mom5/ocean_core/ocean_parameters.F90
Namelist: ocean_parameters_nml
Name 
 Description  

grav 
 Gravitational acceleration at earth surface. Assumed to be constant throughout the ocean domain. Default grav=9.8 corresponds to the "grav" parameter from shared/constants.F90.  
cp_ocean 
 Specific heat capacity J/(kg degC) for liquid seawater. Values are taken from from Jackett etal (2006) for preTEOS10 and from TEOS10 manual for TEOS10 value. The default values differ from that in shared/constants since the MOM defaults are more updated. Note that there is a check inside of ocean_tempsalt.F90 to ensure that cp_ocean=cp_ocean_teos10 if using the teos10 recommendations, and cp_ocean=cp_ocean_preteos10 for cases not using teos10.  
cp_solid_runoff 
 Specific heat capacity J/(kg degC) for solid water runoff via calving land ice. Default cp_solid_runoff = 2106.0 is consistent with that used in the GFDL land model.  
cp_liquid_runoff 
 Specific heat capacity J/(kg degC) for liquid water runoff from land. Default cp_liquid_runoff = 4218.0 is consistent with that used in the GFDL land model.  
rho0 
 Boussinesq reference density. Default rho0=1035.0 corresponds to the value in Gill (page 47), where he notes that the ocean density typically deviates less than 2 per cent from this value. But if using the Boussinesq approximation for other water bodies, such as the Baltic, then may wish to change rho0 to a more appropriate value.  
tfreeze 
 freezing point of fresh water at standard atmos pressure. Default tfreeze=273.15  
omega_earth 
 rotation of earth in radians per second Default omega_earth= 7.2921e5, as per equation (4.1) in Griffies (2004). 
Filename: src/mom5/ocean_core/ocean_pressure.F90
Namelist: ocean_pressure_nml
Name 
 Description  

debug_this_module 
 For debugging.  
zero_pressure_force 
 For debugging it is often useful to zero the pressure force to zero.  
zero_correction_term_grad 
 For debugging it is often useful to zero the contribution to the pressure gradient that arises from the "correction" term. Implemented only for depth based vertical coordinate models.  
zero_diagonal_press_grad 
 For debugging it is often useful to zero the contribution to the pressure gradient that arises from the along klevel gradient. Implemented only for depth based vertical coordinate models.  
zero_eta_over_h_zstar_pressure 
 For debugging zstar, we drop any eta/H contribution to the hydrostatic pressure. This is wrong physically, but useful for certain tests. 
Filename: src/mom5/ocean_core/ocean_sbc.F90
Namelist: ocean_sbc_nml
Name 
 Description  

use_waterflux 
 Set to true when wish to use real fresh water flux as opposed to virtual salt fluxes. This is the recommended method. The alternative virtual tracer flux method (use_waterflux=.false.) is not routinely used at GFDL, so it may suffer from poor testing. Default use_waterflux=.true.  
waterflux_tavg 
 Set to true when aiming to suppress the leapfrog computational mode by setting pme and river equal to a time averaged value over the present and previous time step. This method requires an extra field in the restart file. This method is not needed when using the TWO_LEVEL time tendency. It remains for those who wish to use the leapfrog THREE_LEVEL time stepping scheme. Note that it does not lead to simple checks of conservation across model components, since there is a time averaging performed for the water flux added to the ocean model. It is generally NOT recommended. Default waterflux_tavg=.false.  
use_waterflux_override_calving 
 Set to true will allow for model to incorporate the latent heating from a calving field that comes in through coupled model instantaneous interactions, but later will override the mass flux from calving with a dataset that is read in from a climatology or observations. The idea is to only modify the mass contribution from calving through the override, and leave the latent heat contribution untouched. Default use_waterflux_override_calving=.false.  
use_waterflux_override_fprec 
 Set to true will allow for model to incorporate the latent heating from a fprec field that comes in through coupled model instantaneous interactions, but later will override the mass flux from fprec with a dataset that is read in from a climatology or observations. The idea is to only modify the mass contribution from fprec through the override, and leave the latent heat contribution untouched. Default use_waterflux_override_fprec=.false.  
use_waterflux_override_evap 
 Set to true will allow for model to incorporate the latent heating from an evap field that comes in through coupled model instantaneous interactions, but later will override the mass flux from evap with a dataset that is read in from a climatology or observations. The idea is to only modify the mass contribution from evap through the override, and leave the latent heat contribution untouched. Default use_waterflux_override_evap=.false.  
rotate_winds 
 Set to true when need to rotate the winds onto the ocean model grid. This is needed for cases where the winds are on a spherical grid and the ocean model uses tripolar=.true. If generate the wind data on the ocean model grid, then do not need to rotate, since the rotation has already been done.  
runoffspread 
 Set to true if wish to use the spread_river_horz algorithm to spread the river runoff flux horizontally over an area into the ocean wider than set by the coupler. This option requires the setup of a table for determining the points over which we spread. Default runoffspread=.false.  
calvingspread 
 Set to true if wish to use the spread_river_horz algorithm to spread the calving flux horizontally over an area into the ocean wider than set by the coupler. This option requires the setup of a table for determining the points over which we spread. Default calvingspread=.false.  
salt_restore_under_ice 
 Logical indicating whether to restore salinity under sea ice or not. When .false. then will not restore salinity in regions where we use a "frazil" condition as a proxy for where seaice is present. Do not use sea ice extent from a sea ice model since we generally do not pass information regarding ice extent between the sea ice model and the ocean model.  
salt_restore_as_salt_flux 
 When running a use_waterflux=.true. model, we may choose to add the salinity from a restoring condition as a salt flux or convert to a fresh water flux. The addition of salt does not alter the sea level nor does it alter the concentration of other tracers, whereas converting to an implied water flux will alter sea level and other concentrations. So we generally recommend the default salt_restore_as_salt_flux=.true.  
zero_net_salt_restore 
 Logical indicating whether to remove the area mean of the salinity restore flux so there is a net zero input of salt to the ocean associated with restoring.  
zero_net_salt_correction 
 Logical indicating whether to remove the area mean of the salinity correction flux so there is a net zero input of salt to the ocean associated with salt correction.  
zero_net_water_restore 
 Logical indicating whether to remove the area mean of the water restore flux so there is a net zero input of water to the ocean associated with restoring.  
zero_net_water_correction 
 Logical indicating whether to remove the area mean of the water correction flux so there is a net zero input of water to the ocean associated with water correction.  
zero_net_water_coupler 
 Logical indicating whether to remove the area mean of the water passed through the coupler so there is a net zero input of fresh water to the ocean associated with pe+r. Do so by removing area mean from pmekeep river values unchanged. Note that a choice must be made whether to remove the area mean from rivers or pme. We choose pme since it is more evenly distributed than rivers. Also note that we DO NOT include the ice melt in this normalization. The reason is that we only wish to ensure the ocean+ice system has a zero net water. When melt or form sea ice, this only transfers water between liquid ocean and solid sea ice, and no normalization is appropriate for this case. It is only the water exchanged with the land and atmosphere that is normalized.  
zero_net_water_couple_restore 
 This logical keeps the total water forcing on the ocean+ice system to a global mean of zero at each time step. We DO NOT include the ice melt in this normalization. Setting zero_net_water_couple_restore to true may be appropriate when running an iceocean model using a bulk formulae to compute evaporation (e.g., CORE) and when only providing a weak (or zero) salinity restoring. It is not appropriate when running a coupled oceanatmosphere model, where the moisture budget should be conserved without an artificial removal of the global mean.  
zero_net_pme_eta_restore 
 
debug_water_fluxes 
 Logical for debugging water fluxes. Must be true for any of the options zero_water_fluxes, zero_calving_fluxes, zero_pme_fluxes or zero_runoff_fluxes to be enabled. Default debug_water_fluxes=.false.  
zero_water_fluxes 
 Logical for debugging to zero the pme, river, and pme_taum1 into ocean, overriding any input from Ice_ocean_boundary. Default zero_water_fluxes=.false.  
zero_pme_fluxes 
 Logical for debugging to zero the pme flux passed into the ocean. Default zero_pme_fluxes=.false.  
zero_calving_fluxes 
 Logical for debugging to zero the calving flux passed into the ocean. Default zero_calving_fluxes=.false.  
zero_runoff_fluxes 
 Logical for debugging to zero the runoff flux passed into the ocean. Default zero_runoff_fluxes=.false.  
zero_river_fluxes 
 Logical for debugging to zero the river (calving+runoff) flux passed into the ocean. Default zero_river_fluxes=.false.  
convert_river_to_pme 
 Logical for debugging. Here we add the river water input (calving+runoff) to pme, then set river=calving=runoff=0.0. Default convert_river_to_pme=.false.  
zero_heat_fluxes 
 Logical for debugging to set all heat fluxes into the ocean to zero, overriding any input from Ice_ocean_boundary. Default is .false.  
zero_surface_stress 
 Logical for debugging to zero all surface stress applied to the ocean, overriding any input from Ice_ocean_boundary. Default is .false.  
read_restore_mask 
 For reading in a mask that selects regions of the domain that are restored (mask=1) or not restored (mask=0). Default read_restore_mask=.false., whereby restore_mask is set to tmask(k=1).  
restore_mask_gfdl 
 For modifying the restore mask based on reading in the GFDL regional mask. Default restore_mask_gfdl=.false.  
land_model_heat_fluxes 
 For the case where land model passes through the coupler the heat flux associated with the liquid runoff and calving land ice fields. This heat flux is computed relative to 0C, and takes the form heat flux = mass flux of water temp of water heat capacity, where the water can be either liquid or solid. For many coupled models, the water temperature is assumed to be that of the SST. But more complete land models now carry the heat of its water relative to 0C, in which case the ocean model does not need to assume anything about the heat content of the land water. Default land_model_heat_fluxes=.false.  
do_flux_correction 
 For applying surface flux correction to to a tracer or wind stress field. This code is used at GFDL for idealized perturbation experiments, such as when one wishes to artificially enhance the wind stress to test model sensitivity. It is also appropriate for coupled models that may require a modification to the fluxes arrising from a coupled model, via reading in information from a predefined data file, Default do_flux_correction=.false.  
sbc_heat_fluxes_const 
 Logical for setting the surface heat flux from the coupler to a global constant. Default is sbc_heat_fluxes_const=.false.  
sbc_heat_fluxes_const_seasonal 
 Logical for setting the surface heat flux from the coupler to a global constant, and giving it a seasonally varying amplitude. Default is sbc_heat_fluxes_const_seasonal=.false.  
use_constant_sss_for_restore 
 To override the sfc_restore.nc value for salinity restoring. use_constant_sss_for_restore=.false.  
use_constant_sst_for_restore 
 To override the sfc_restore.nc value for temp restoring. use_constant_sst_for_restore=.false.  
use_ideal_runoff 
 To add an idealized liquid runoff read from a file. This runoff is assumed to enter the ocean with the same temperature as SST, and to be liquid. It is an additional runoff, so that any other runoff remains unaltered. The runoff coming from idealized runoff is NOT subject to the global normalization realized from zero_net_water_coupler=.true. Default use_ideal_runoff=.false.  
use_ideal_calving 
 To add an idealized solid runoff or calving read from a file. This calving runoff is assumed to require melting, so it extracts latent heat of fusion from the liquid ocean The runoff coming from idealized cavling is NOT subject to the global normalization realized from zero_net_water_coupler=.true. Default use_ideal_calving=.false.  
read_stokes_drift 
 This option is to be used when coupling to a surface wave model such as Wavewatch III that provides both the Stokes drift (m/s) velocity at the ocean surface, and a decay scale for projecting the Stokes drift into the interior. Default read_stokes_drift = .false.  
constant_sss_for_restore 
 The SSS value used if use_constant_sss_for_restore=.true. Default constant_sss_for_restore=35.0  
constant_sst_for_restore 
 The SST value used if use_constant_sst_for_restore=.true. Default constant_sst_for_restore=12.0  
sbc_heat_fluxes_const_value 
 Value for the constant heat flux when using sbc_heat_fluxes_const=.true. Default sbc_heat_fluxes_const_value=0.0.  
ice_salt_concentration 
 The salt concentration of sea ice. This is taken as a bulk value, and should be the same as that used by the ice model. Default is ice_salt_concentration=0.005, as that is the value used in the GFDL coupled climate model.  
runoff_salinity 
 The salinity of river runoff water. Default is runoff_salinity=0.0.  
runoff_temp_min 
 The minimum temperature that river runoff into the ocean is assigned. Default runoff_temp_min=0.0.  
temp_restore_tscale 
 Time scale in days for restoring temperature within the top model grid cell.  
salt_restore_tscale 
 Time scale in days for restoring salinity within the top model grid cell.  
eta_restore_tscale 
 Time scale in days for restoring surface height to produce a modification to surface water flux. This option is only available when run with use_waterflux=.true.  
max_ice_thickness 
 When coupling MOM to an ice model, the sea ice thickness may need to be restricted to prevent vanishing toplevel in MOM. Set max_ice_thickness (meters) < dzt(k=1) to restrict. This truncation avoids the numerical problem but we loose mass conservation in the coupled sea ice and ocean system. We also alter the pressure felt on the ocean as applied by the sea ice. Different vertical coordinates are needed to do the problem more realistically. Note that the problem of vanishing top layer is removed when use either ZSTAR or PSTAR as vertical coordinate.  
salinity_ref 
 Reference salinity used for converting fresh water flux to salt flux.  
max_delta_salinity_restore 
 When computing the restoring flux for salinity, we can define a maximum absolute value for the difference between salinity(k=1) and the restoring salinity from a dataset. This approach is useful especially in NAtl western boundary, where poor Gulf Stream separation can lead to large salinity biases. If restore too much the salinity field, we can spuriously transport large amounts of fresh water to the subpoloar gyre, thus impacting the overturning circulation too much. If max_delta_salinity_restore < 0.0, then will NOT provide a max to the delta salinity; will instead compute an unbounded restoring flux. Default max_delta_salinity_restore=0.50.  
temp_correction_scale 
 A scale multiplying the flux correction for temperature. Default temp_correction_scale=0.0.  
salt_correction_scale 
 A scale multiplying the flux correction for salinity. Default salt_correction_scale=0.0.  
tau_x_correction_scale 
 A scale multiplying the flux correction for tau_x. Default tau_x_correction_scale=0.0.  
tau_y_correction_scale 
 A scale multiplying the flux correction for tau_y. Default tau_y_correction_scale=0.0.  
constant_hlf 
 Treat latent heat of fusion as a constant. Otherwise, use the TEOS10 approach in which hlf is function of surface salinity. Note, TEOS10 approach is only valid using Absolute Salinity and conservative temperature as the prognostic fields. Default constant_hlf = .true., which is the case for preTEOS10 methods.  
constant_hlv 
 Treat latent heat of vaporization as a constant. Otherwise, use the TEOS10 approach in which hlf is function of surface salinity. Note, TEOS10 approach is only valid using Absolute Salinity and conservative temperature as the prognostic fields. Default constant_hlv = .true., which is the case for preTEOS10 methods.  
avg_sfc_velocity 
 If set to true, the u and v fields passed up to the sea ice are averaged over a coupling interval. TRUE by default.  
avg_sfc_temp_salt_eta 
 If set to true, the t, s and sea_level fields passed up to the sea ice are averaged over a coupling interval. TRUE by default.  
use_full_patm_for_sea_level 
 The option use_full_patm_for_sea_level allows for the passing of the sea level including the full weight of sea ice back to the ice model. This approach maintains the max weight on the liquid ocean according to the nml variable max_ice_thickness. But it does allow the sea ice to know when there is actually more sea ice than that set by max_ice_thickness. This option then provides for a negative feedback on the runaway growth of sea ice, since the full pressure acting to make the ice flow will be correctly felt. This is a new option, and is not fully tested, So the default is use_full_patm_for_sea_level=.false  
do_bitwise_exact_sum 
 Set true to do bitwise exact global sum. When it is false, the global sum will be nonbitwise_exact, but will significantly increase efficiency. The default value is do_bitwise_exact_sum=.true. in order to ensure answers do not change when alter processors. But if wish to enhance the efficiency of coupled oceanice models that use one of the global normalization options zero_net_salt_restore =.true. zero_net_salt_correction =.true. zero_net_water_restore =.true. zero_net_water_correction =.true. zero_net_water_coupler =.true. zero_net_water_couple_restore=.true. then one may wish to consider setting do_bitwise_exact_sum=.false. 
Filename: src/mom5/ocean_core/ocean_thickness.F90
Namelist: ocean_thickness_nml
Name 
 Description  

rescale_mass_to_get_ht_mod 
 Expedient to allow for the computation of ht_mod. in the case when initialize_zero_eta=.true. Here, we run the pressure based model with a rescaled mass that is sufficient to maintain nonnegative dzt, at least for a short period. This allows for one to run a day integration to produce ht_mod. rescale_mass_to_get_ht_mod=.true. will produce spurious results in general due to problems with the pressure gradient computation. So it is not recommended for more than initial day or so. Default rescale_mass_to_get_ht_mod=.false.  
thickness_method 
 To determine whether use energetic method or finite volume method to compute the thickness of a grid cell. Options are thickness_method=energetic or thickness_method=finitevolume. There is little overall difference in results for pbot and eta. However, it has been found that for realistic bottom topography simulations, the vertical velocity component is very noisy with the finitevolume approach. So this approach is considered experimental. The default is thickness_method='energetic'.  
linear_free_surface 
 For debugging, set the thickness of top cell in geopotential model to time independent values. This option is needed if use the kappa_sort diagnostic. Default linear_free_surface=.false.  
full_step_topography 
 For case where with to only have the dzt be determined by the full step bottom topography. This nml option is provided only for backwards compatibility with older mom experiments using the full step topog.  
enforce_positive_dzt 
 For cases where wish to run model even with negative thickness. Default enforce_positive_dzt=.false.  
debug_this_module 
 For debugging.  
debug_this_module_detail 
 For debugging pressure coordinate models. Lots of grid information printed.  
write_a_restart 
 Set true to write a restart. False setting only for rare cases where wish to benchmark model without measuring the cost of writing restarts and associated chksums. Default is write_a_restart=.true.  
read_rho0_profile 
 To read in an initial rho0(z) profile to assist in defining the initial settings for the pressure increments dst, for use in setting the pressurebased vertical coordinate grids. Ideally, this profile is determined by the level averaged density in the initial conditions. Note that it is essential to have rho0_profile have a sensible value at all depths even if there is no water there, since there are places where we divide by rho0_profile in rock. Also, be mindful that with denser water at depth, the pressure levels will be coarser at depth than if using the trivial density profile rho0(k)=rho0. This option is experimental, so it is recommended that user maintain the default read_rho0_profile=.false.  
pbot0_simple 
 For testing purposes, have this option compute pbot0=grho0ht with rho0= constant. Default pbot0_simple=.false.  
initialize_zero_eta 
 For pressurebased models, we can (with some work) initialize the model to have a zero surface height. The recomended approach is to allow the surface height to be whatever it wants to be, and let adjustments smooth it over time. Default initialize_zero_eta=.false.  
read_rescale_rho0_mask 
 For reading in a basin mask of use to redefine rho0 in isolated regions such as the Black Sea. This is used for modifying the definition of the pressure or pstar levels during the initialization of the thicknesses dst. This approach is appropriate in general, but has only been tested when modify the pressure levels within a fully enclosed basin. Default read_rescale_rho0_mask=.false.  
rescale_rho0_mask_gfdl 
 For specifying the rescale_rho0_mask based on reading in the GFDL regional mask. Default rescale_rho0_mask_gfdl=.false.  
update_dzwu_k0 
 A bug in certain versions of MOM4p1 was present, whereby Thickness%dzwu(i,j,k=0) was never updated, except for GEOPOTENTIAL vertical coordinates. This logical, whose default is update_dzwu_k0=.true., is provided for legacy purposes. To test the older results, have update_dzwu_k0=.false.  
max_num_bad_print 
 Maximum bad grid cells printout for identifying problematic simulations. Default max_num_bad_print=25.  
rescale_rho0_value 
 Fractional value for rescaling rho0 in the a region. Default rescale_rho0_value=1.0.  
rescale_rho0_basin_label 
 For rescaling rho0 in a basin with a number rescale_rho0_basin_label. For the Black Sea using GFDL basin masks in OM3, rescale_rho0_basin_label=7.0. Default rescale_rho0_basin_label=1.0  
thickness_dzt_min_init 
 For determining a modified bottom depth array that is required to ensure pressure model, based on initial insitu density, retains a nontrivial bottom cell thickness in the case when initialize_zero_eta=0.0 Default thickness_dzt_min_init=5.0.  
thickness_dzt_min 
 Minimum dzt set when enforce_positive_dzt set true. Default thickness_dzt_min=1.0.  
depth_min_for_sigma 
 For sigma coordinates, have minimum depth so that have layers defined globally. Masks will zero out results over land, but for numerics it is useful to compute everywhere. Default depth_min_for_sigma=0.01.  
epsilon_init_thickness 
 For determining how strict we are to check for the thickness of a column when initializing pressure based vertical coordinate models. 
Filename: src/mom5/ocean_core/ocean_topog.F90
Namelist: ocean_topog_nml
Name 
 Description  

flat_bottom 
 For debugging, it is often useful to override the grid spec file and simply make the domain flat bottom.  
flat_bottom_kmt 
 Number of depth levels to use for the flat_bottom option.  
flat_bottom_ht 
 Depth to make the flat_bottom.  
min_thickness 
 min_thickness is only used for Mosaic grid. Since there is no kmt available in mosaic grid, need to set min_thickness to configure kmt based on ht and zw. Default min_thickness=1.0 metre.  
kmt_recompute_offset 
 To recompute the kmt array based on min_thickness, with an offset determined by kmt_recompute_offset. Default kmt_recompute_offset=0.  
kmt_recompute 
 To recompute the kmt array based on min_thickness. This step is not recommended in general, since it can modify the kmt array which may be in the grid spec file. But it may be of use for specialized situations, such as when you wish to use the same topography file with a refined vertical resolution.  
write_topog 
 
debug_this_module 
 For debugging. 
Filename: src/mom5/ocean_core/ocean_velocity.F90
Namelist: ocean_velocity_nml
Name 
 Description  

adams_bashforth_third 
 For a third order treatment of the velocity advection. This is stable and so needs no temporal dissipation (Section 2.3.6 of Durran). This is the model default.  
adams_bashforth_epsilon 
 Dimensionless parameter for 2nd order AdamsBashforth implementation of velocity advection. Values between 0.5 and 1.0 are recommended. Value of 0.5 leads to second order accurate, but it is formally weakly unstable (Durran, Section 2.3.4).  
update_velocity_via_uprime 
 When updating the velocity, this method first computes uprime as the updated velocity minus the barotropic pressure gradient. This approach is motivated from the rigid lid approach, in which the surface pressure was never used to update the barotropic fields. With the explicit free surface, we have the choice to update the full velocity field, with the barotropic contributions to the pressure field resulting from a time average in the external mode algorithm. This approach is for testing only, and it has been found to be unstable for many cases. update_velocity_via_uprime=.true. uses the older aproach, in which the udrho,vdrho fields are taken from the external mode module. update_velocity_via_uprime=.false. only takes the time averaged pressure from the external mode, and thus updates the full velocity and so recomputes the udrho,vdrho fields. Default update_velocity_via_uprime=.true. The case of update_velocity_via_uprime=.false. is for testing only. It is not supported for general use.  
zero_tendency 
 For debugging. Will freeze the baroclinic velocity fields.  
zero_tendency_explicit_a 
 For debugging. Will not use explicita part of the tendency.  
zero_tendency_explicit_b 
 For debugging. Will not use explicitb part of the tendency.  
zero_tendency_implicit 
 For debugging. Will not use implicit part of the tendency.  
truncate_velocity 
 Truncate the baroclinic velocity to a maximum value. Useful for cases where the initial spinup initiates spuriously large model velocities that would otherwise cause the model to blowup. Also can be used as a very simple "polar filter" in cases where have spherical coordinates and wish to avoid using the traditional polar filters.  
truncate_verbose 
 For verbose printout  
truncate_velocity_lat 
 Latitude poleward of which we truncate the velocity. Useful in cases when wish to truncate the velocity only in polar regions. Default is 0.0  
truncate_velocity_value 
 Speed above which will truncate the baroclinic velocity  
use_constant_velocity 
 For running with time independent constant velocity. For use with idealized cases. Default=.false.  
constant_u 
 For running with use_constant_velocity. Set the ivelocity component to this value. Default constant_u=0.0  
constant_v 
 For running with use_constant_velocity. Set the jvelocity component to this value. Default constant_v=0.0  
max_cgint 
 Maximum internal gravity wave speedused for diagnosing conservative estimate of stable time steps.  
debug_this_module 
 For debugging.  
write_a_restart 
 Set true to write a restart. False setting only for rare cases where wish to benchmark model without measuring the cost of writing restarts and associated chksums. Default is write_a_restart=.true. 
Filename: src/mom5/ocean_core/ocean_velocity_advect.F90
Namelist: ocean_velocity_advect_nml
Name 
 Description  

debug_this_module 
 For debugging  
zero_velocity_advect_horz 
 For debugging, it is often useful to remove horizontal advection of velocity.  
zero_velocity_advect_vert 
 For debugging, it is often useful to remove vertical advection of velocity.  
velocity_advect_centered 
 For using the standard second order centered method for computing the advection of linear momentum. This is the default: velocity_advect_centered=.true.  
velocity_advect_upwind 
 For using the first order upwind method for computing the advection of linear momentum. Default: velocity_advect_upwind=.false. 
Filename: src/mom5/ocean_core/oda_driver.F90
Namelist: oda_nml
Name 
 Description  

max_profiles 
 Size of allocation for profile data  
max_sfc_obs 
 Size of allocation for surface observations  
assim_method 
 Options are: Var2d, EAKF and NO_ASSIM  
do_iau 
 Incremental analysis update (evenly distribute increments between calls to ODA.)  
do_convect_adjust 
 Adjust for gravitational instability in model after applying increments.  
save_omf_snaps 
 
save_oma_snaps 
 
nk_asm 
 Bottom model level for data mask  
assim_start_lat 
 Southern data mask boundary  
assim_end_lat 
 Northern data mask boundary  
assim_interval 
 Time between calls to oda (hours)  
assim_layout 
 
use_this_module 

src/mom5/ocean_diag
Filename: src/mom5/ocean_diag/ocean_adv_vel_diag.F90
Namelist: ocean_adv_vel_diag_nml
Name 
 Description  

diag_step 
 Number of time steps between which compute the diagnostics.  
max_cfl_value 
 Critical value for Courant number, above which the model will be brought down.  
large_cfl_value 
 Large value for Courant number, above which will write some diagnostics.  
verbose_cfl 
 For printing out lots of information about regions of large Courant numbers. 
Filename: src/mom5/ocean_diag/ocean_drifters.F90
Namelist: ocean_drifters_nml
Name 
 Description  

use_this_module 
 Must be true to run this module. Default use_this_module=.false.  
output_interval 
 Interval in timesteps between drifter writes 
Filename: src/mom5/ocean_diag/ocean_tracer_diag.F90
Namelist: ocean_tracer_diag_nml
Name 
 Description  

tracer_conserve_days 
 Number of days between which compute the tracer conservation diagnostics.  
debug_diagnose_mixingA 
 Set true for help with debugging the diagnostic for mixing.  
debug_diagnose_mixingB 
 Set true for more help with debugging the diagnostic for mixing. Lots of output.  
debug_diagnose_mixingC 
 Set true for more help with debugging the diagnostic for mixing. Lots of output.  
debug_diagnose_mixingD 
 Set true for more help with debugging the diagnostic for mixing. Lots of output.  
rho_grad_max 
 max vertical density gradient (kg/m^3/m) used in computing kappa sorted  
rho_grad_min 
 min vertical density gradient (kg/m^3/m) used in computing kappa sorted in the diagnostic mixing sorted.  
smooth_kappa_sort 
 Number of 121 smooths applied to kappa_sort  
diag_step 
 Number of time steps between which compute the diagnostics.  
buoyancy_crit 
 Critical buoyancy difference relative to surface for computing mixed layer depth. Default buoyancy_crit=0.0003.  
dtheta_crit 
 Critical temperature difference relative to surface for computing mixed_layer_depth_dtheta . Default dtheta_crit=2.0.  
psu2ppt 
 The preTEOS10 EOS used in MOM requires salinity to use the Practical Salinity Scale (pss). This scale is also known as the Practical Salinity Unit (psu). However, salinity as an absolute concentration in parts per thousand is more convenient to use when performing budget analyses such as in this module. Conversion between pss and ppt depends on the precise ratio of ions in the seawater. Hence, the conversion is not constant. However, it is close to a constant, as reported in Jackett etal (2004). For purposes of budgets, we take this conversion as a constant. The conversion is s(ppt) = psu2ppt s(psu) where again s(psu) is what MOM carries as its prognostic salinity field when preTEOS10 EOS is used. Jackett etal (2004), correcting a type in equation (53) of Feistel (2003), report that s(ppt) = 1.004867 s(psu)  
do_bitwise_exact_sum 
 Set true to do bitwise exact global sum. When it is false, the global sum will be nonbitwise_exact, but will significantly increase efficiency. The default value is false.  
frazil_factor 
 
smooth_mld 
 Smooth the diagnosed mixed layer depth. Default smooth_mld=.false.  
smooth_mld_for_subduction 
 Smooth the diagnosed mixed layer depth to be used for subduction diagnostics. Default smooth_mld_for_subduction=.true. 
Filename: src/mom5/ocean_diag/ocean_tracer_util.F90
Namelist: ocean_tracer_util_nml
Name 
 Description  

rebin_onto_rho_all_values 
 Set true to if wish to bin all values into density classes, even those cells whose density is outside the max and min range of the density bins. The default is rebin_onto_rho_all_values=.true., which means those cells with extreme density values will be included. This default is consistent with the default computation of transport_on_nrho.  
debug_diagnose_mass_of_layer 
 To help debug the algorithm to diagnose mass of fluid within a neutral density layer. Default: debug_diagnose_mass_of_layer=.false.  
epsln_diagnose_mass_of_layer 
 Relative mass difference allowable between layer and level total mass. Default: epsln_diagnose_mass_of_layer=1e4. 
Filename: src/mom5/ocean_diag/ocean_velocity_diag.F90
Namelist: ocean_velocity_diag_nml
Name 
 Description  

diag_step 
 Number of time steps between which compute the diagnostics.  
energy_diag_step 
 Perform energy analysis every n timesteps (1==every time step). This diagnostic is expensive, so should be used sparingly during production runs.  
land_cell_num_max 
 Maximum number of land cells where will printout nonzero velocity points. Default land_cell_num_max=100.  
max_cfl_value 
 Critical value for Courant number, above which the model will be brought down.  
large_cfl_value 
 Large value for Courant number, above which will write some diagnostics.  
verbose_cfl 
 For printing out lots of information about regions of large Courant numbers.  
do_bitwise_exact_sum 
 Set true to do bitwise exact global sum. When it is false, the global sum will be nonbitwise_exact, but will significantly increase efficiency. The default value is false.  
debug_this_module 
 For some debugging purposes 
src/mom5/ocean_param/gotm4.0/turbulence
Filename: src/mom5/ocean_param/gotm4.0/turbulence/kpp.F90
Namelist: kpp
Name 
 Description  

Ric 
 
kpp_interior 
 
clip_mld 

Filename: src/mom5/ocean_param/gotm4.0/turbulence/turbulence.F90
Namelist: scnd
Name 
 Description  

scnd_method 
 
kb_method 
 
epsb_method 
 
scnd_coeff 
 
cc1 

Filename: src/mom5/ocean_param/gotm4.0/turbulence/turbulence.F90
Namelist: keps
Name 
 Description  

ce1 
 
ce2 
 
ce3minus 
 
ce3plus 
 
sig_k 
 
sig_e 
 
sig_peps 

Filename: src/mom5/ocean_param/gotm4.0/turbulence/turbulence.F90
Namelist: turb_param
Name 
 Description  

cm0_fix 
 
Prandtl0_fix 
 
cw 
 
compute_kappa 
 
kappa 
 
compute_c3 
 
ri_st 
 
length_lim 
 
galp 
 
const_num 
 
const_nuh 
 
k_min 
 
eps_min 
 
kb_min 
 
epsb_min 

Filename: src/mom5/ocean_param/gotm4.0/turbulence/turbulence.F90
Namelist: bc
Name 
 Description  

k_ubc 
 
k_lbc 
 
kb_ubc 
 
kb_lbc 
 
psi_ubc 
 
psi_lbc 
 
ubc_type 
 
lbc_type 

Filename: src/mom5/ocean_param/gotm4.0/turbulence/turbulence.F90
Namelist: generic
Name 
 Description  

compute_param 
 
gen_m 
 
gen_n 
 
gen_p 
 
cpsi1 
 
cpsi2 
 
cpsi3minus 
 
cpsi3plus 
 
sig_kpsi 
 
sig_psi 
 
gen_d 
 
gen_alpha 
 
gen_l 

Filename: src/mom5/ocean_param/gotm4.0/turbulence/turbulence.F90
Namelist: iw
Name 
 Description  

iw_model 
 
alpha 
 
klimiw 
 
rich_cr 
 
numiw 
 
nuhiw 
 
numshear 

Filename: src/mom5/ocean_param/gotm4.0/turbulence/turbulence.F90
Namelist: turbulence
Name 
 Description  

turb_method 
 
tke_method 
 
len_scale_method 
 
stab_method 

Filename: src/mom5/ocean_param/gotm4.0/turbulence/turbulence.F90
Namelist: my
Name 
 Description  

e1 
 
e2 
 
e3 
 
sq 
 
sl 
 
my_length 
 
new_constr 

src/mom5/ocean_param/lateral
Filename: src/mom5/ocean_param/lateral/ocean_bih_friction.F90
Namelist: ocean_bih_friction_nml
Name 
 Description  

bih_friction_scheme 
 To determine the biharmonic friction scheme: "const" or "general"  
debug_this_module 
 For debugging.  
write_a_restart 
 Set true to write a restart. False setting only for rare cases where wish to benchmark model without measuring the cost of writing restarts and associated chksums. Default is write_a_restart=.true. 
Filename: src/mom5/ocean_param/lateral/ocean_bih_tracer.F90
Namelist: ocean_bih_tracer_nml
Name 
 Description  

abih 
 This is the value for the spacetime constant biharmonic diffusivity.  
vel_micom 
 Velocity scale that is used for computing the MICOM diffusivity.  
tracer_mix_micom 
 If .true., then the diffusivity is set according to a velocity scale times the cube of the grid spacing. It is based on an approach recommended by Eric Chassignet that is used in the Miami Isopycnal Model.  
use_this_module 
 Must be true to use this module  
horz_z_diffuse 
 To compute fluxes along surfaces of constant depth. This operation must necessarily be approximate for the two cases (i) nongeopotential vertical coordinates, (2) next to partial bottom step topography. There are cases where use of this operator can lead to spurious creation of extrema due to truncation errors associated with the "slope" term. The option to use horz_z_diffuse=.true. is maintained for legacy purposes alone.  
horz_s_diffuse 
 To compute diffusion along surfaces of constant vertical scoordinate.  
read_diffusivity_mask 
 Allows for reading of a mask that to apply diffusivity only in selected regions. Default read_diffusivity_mask=.false. 
Filename: src/mom5/ocean_param/lateral/ocean_bihcgrid_friction.F90
Namelist: ocean_bihcgrid_friction_nml
Name 
 Description  

k_smag_iso 
 This is the dimensionless Smagorinsky coefficient used to set the scale of the Smagorinsky isotropic viscosity.  
k_smag_aniso 
 This is the dimensionless Smagorinsky coefficient used to set the scale of the Smagorinsky anisotropic viscosity.  
vel_micom_iso 
 Velocity scale that is used for computing the MICOM isotropic viscosity.  
vel_micom_aniso 
 Velocity scale that is used for computing the MICOM anisotropic viscosity.  
eq_vel_micom_iso 
 Velocity scale that is used for computing the MICOM isotropic viscosity within a user specified equatorial band.  
eq_vel_micom_aniso 
 Velocity scale that is used for computing the MICOM anisotropic viscosity within a user specified equatorial band.  
eq_lat_micom 
 Equatorial latitude band (degrees) within which the MICOM viscosity is set according to eq_vel_micom_iso and eq_vel_micom_aniso.  
equatorial_zonal_lat 
 Latitudinal band to use the zonal friction orientation.  
equatorial_zonal 
 Orient the anisotropic friction within a latitudinal band according to zonal direction.  
ncar_boundary_scaling 
 
ncar_boundary_scaling_read 
 
ncar_vconst_4 
 
ncar_vconst_5 
 
ncar_rescale_power 
 
neptune 
 Set to true for computing friction relative to Neptune barotropic velocity. Default neptune=.false.  
neptune_smooth 
 For doing a horizontal 121 smoothing on the diagnosed neptune velocity scale. Default neptune_smooth=.true.  
neptune_smooth_num 
 Number of smoothing passes for neptune velocity. Default neptune_smooth_num=1.  
neptune_length_eq 
 Length scale used to compute Neptune velocity at equator.  
neptune_length_pole 
 Length scale used to compute Neptune velocity at pole.  
neptune_depth_min 
 Minimum depth scale used for computing Neptune velocity. Default neptune_depth_min=100.0  
use_side_drag_friction 
 For converting friction at Ucells next to walls into a drag law, as per Deremble et al. Use cdbot_array from ocean_core/ocean_bbc.F90 to compute drag force. Default use_side_drag_friction=.false.  
side_drag_friction_scaling 
 Dimensionless scaling used for cdbot_array when setting side drag friction. So the effective side dragy coefficient is side_drag_friction_scaling*cdbot_array. Default side_drag_friction_scaling=1.0.  
side_drag_friction_max 
 Maximum magnitude of the side drag induced friction. This parameter can be useful especially for pressure models where the bottom cells can be quite thin and subject to sporadic large magnitudes. We do the same thing with bottom drag calculations in ocean_bbc. Default side_drag_friction_max=1.0.  
side_drag_friction_uvmag_max 
 Maximum magnitude of horizontal velocity used to compute the side drag friction. This parameter can be useful especially for pressure models where the bottom cells can be quite thin and subject to sporadic large magnitudes. We do the same thing with bottom drag calculations. Default side_drag_friction_uvmag_max=10.0.  
use_this_module 
 Must be true to use this module. Default is false.  
debug_this_module 
 For debugging by printing checksums. 
Filename: src/mom5/ocean_param/lateral/ocean_bihcst_friction.F90
Namelist: ocean_bihcst_friction_nml
Name 
 Description  

use_this_module 
 Must be true to use this module. Default is false.  
debug_this_module 
 For debugging by printing checksums.  
abih 
 This is the value for the spacetime constant biharmonic viscosity.  
vel_micom 
 Velocity scale that is used for computing the MICOM viscosity.  
eq_vel_micom 
 Velocity scale that is used for computing the MICOM viscosity within a latitude band surrounding the equator. This is useful for some models of enhanced equatorial resolution that can maintain numerical integrity in this region with less friction than outside the tropical band.  
eq_lat_micom 
 Equatorial latitude band (degrees) within which the MICOM viscosity is set according to eq_vel_micom.  
velocity_mix_micom 
 If .true., then the viscosity is set according to a velocity scale times the cube of the grid spacing. It is based on an approach recommended by Eric Chassignet that is used in the Miami Isopycnal Model. 
Filename: src/mom5/ocean_param/lateral/ocean_bihgen_friction.F90
Namelist: ocean_bihgen_friction_nml
Name 
 Description  

k_smag_iso 
 This is the dimensionless Smagorinsky coefficient used to set the scale of the Smagorinsky isotropic viscosity.  
k_smag_aniso 
 This is the dimensionless Smagorinsky coefficient used to set the scale of the Smagorinsky anisotropic viscosity.  
vel_micom_iso 
 Velocity scale that is used for computing the MICOM isotropic viscosity.  
vel_micom_aniso 
 Velocity scale that is used for computing the MICOM anisotropic viscosity.  
eq_vel_micom_iso 
 Velocity scale that is used for computing the MICOM isotropic viscosity within a user specified equatorial band.  
eq_vel_micom_aniso 
 Velocity scale that is used for computing the MICOM anisotropic viscosity within a user specified equatorial band.  
eq_lat_micom 
 Equatorial latitude band (degrees) within which the MICOM viscosity is set according to eq_vel_micom_iso and eq_vel_micom_aniso.  
vel_micom_bottom 
 Velocity scale that is used for computing the MICOM viscosity for 5point Laplacian at the bottom.  
equatorial_zonal_lat 
 Latitudinal band to use the zonal friction orientation.  
visc_crit_scale 
 Scaling factor used to determine the critical viscosity, above which the viscosity is not allowed to reach. Use visc_crit_scale < 1.0 for cases where the visc_crit from linear stability allows for still too large of a viscosity. Use visc_crit_scale>1.0 when wish to allow for larger viscosity. Default is visc_crit_scale=1.0.  
equatorial_zonal 
 Orient the anisotropic friction within a latitudinal band according to zonal direction.  
bottom_5point 
 To alleviate problems with small partial cells, it is often necessary to reduce the operator to the traditional 5point Laplacian at the ocean bottom. This logical implements this mixing. Default bottom_5point=.false.  
ncar_boundary_scaling 
 To enhance the velocity scale used in western boundaries for the isotropic and anisotropic background viscosities, we compute a scaling using the algorithm from the laplacian NCAR anisotropic scheme. Default ncar_boundary_scaling=.false.  
ncar_boundary_scaling_read 
 To read in the ncar boundary scaling field rather than generating it during initialization. Generating during initialization can be a bottleneck on fine resolution models since there are some global 2d fields needed. So if the rescaling is produced once and then saved, it can be read in during subsequent runs without incurring the slowdown of regenerating the scalings. Default ncar_boundary_scaling_read=.false.  
ncar_vconst_4 
 Inverse damping length for exponential falloff of the velocity scale as move eastward away from western boundary. Default ncar_vconst_4=2.e8.  
ncar_vconst_5 
 For determining number of grid points in boundary calculation. Default ncar_vconst_5=3.  
ncar_rescale_power 
 For determining rescaling of the viscosity so to enhance the friction near the western boundaries. Default ncar_rescale_power=1.  
neptune 
 Set to true for computing friction relative to Neptune barotropic velocity. Default neptune=.false.  
neptune_smooth 
 For doing a horizontal 121 smoothing on the diagnosed neptune velocity scale. Default neptune_smooth=.true.  
neptune_smooth_num 
 Number of smoothing passes for neptune velocity. Default neptune_smooth_num=1.  
neptune_length_eq 
 Length scale used to compute Neptune velocity at equator. Default neptune_length_eq= 4.2e3 from Maltrud and Holloway.  
neptune_length_pole 
 Length scale used to compute Neptune velocity at pole. Default neptune_length_pole= 17.0e3 from Maltrud and Holloway.  
neptune_depth_min 
 Minimum depth scale used for computing Neptune velocity. Default neptune_depth_min=100.0 from Maltrud and Holloway.  
neptune_scaling 
 Overall scaling parameter to help tune neptune. Default neptune_scaling=1.0  
visc_diverge_scaling 
 Dimensionless scaling used for divergence based viscosity. Default visc_diverge_scaling=0.0 turns off the scheme. visc_diverge_scaling=10.0 produces sensible viscosities for 1degree model. May need tuning for different resolutions.  
use_side_drag_friction 
 For converting friction at Ucells next to walls into a drag law, as per Deremble et al. Use cdbot_array from ocean_core/ocean_bbc.F90 to compute drag force. Default use_side_drag_friction=.false.  
side_drag_friction_scaling 
 Dimensionless scaling used for cdbot_array when setting side drag friction. So the effective side dragy coefficient is side_drag_friction_scaling*cdbot_array. Default side_drag_friction_scaling=1.0.  
side_drag_friction_max 
 Maximum magnitude of the side drag induced friction. This parameter can be useful especially for pressure models where the bottom cells can be quite thin and subject to sporadic large magnitudes. We do the same thing with bottom drag calculations. Default side_drag_friction_max=1.0.  
side_drag_friction_uvmag_max 
 Maximum magnitude of horizontal velocity used to compute the side drag friction. This parameter can be useful especially for pressure models where the bottom cells can be quite thin and subject to sporadic large magnitudes. We do the same thing with bottom drag calculations. Default side_drag_friction_uvmag_max=10.0.  
use_this_module 
 Must be true to use this module. Default is false.  
debug_this_module 
 For debugging by printing checksums.  
read_aiso_bih_back 

Filename: src/mom5/ocean_param/lateral/ocean_lap_friction.F90
Namelist: ocean_lap_friction_nml
Name 
 Description  

lap_friction_scheme 
 To determine the laplacian friction scheme: "const" or "general"  
debug_this_module 
 For debugging.  
write_a_restart 
 Set true to write a restart. False setting only for rare cases where wish to benchmark model without measuring the cost of writing restarts and associated chksums. Default is write_a_restart=.true. 
Filename: src/mom5/ocean_param/lateral/ocean_lap_tracer.F90
Namelist: ocean_lap_tracer_nml
Name 
 Description  

alap 
 This is the value for the spacetime constant Laplacian diffusivity.  
vel_micom 
 Velocity scale that is used for computing the MICOM diffusivity.  
tracer_mix_micom 
 If .true., then the diffusivity is set according to a velocity scale times the grid spacing. It is based on an approach recommended by Eric Chassignet that is used in the Miami Isopycnal Model (MICOM).  
verbose_init 
 For verbose writes during initialization  
use_this_module 
 Must be true to use this module. Default is false.  
horz_z_diffuse 
 To compute diffusion along surfaces of constant depth. This operation must necessarily be approximate for the two cases (i) nongeopotential vertical coordinates, (2) next to partial bottom step topography. There are cases where use of this operator can lead to spurious creation of extrema due to truncation errors associated with the "slope" term. For most cases where lateral diffusion is required, we will want it to be "diffusive" in the sense that no extrema are created. So the default is horz_z_diffuse=.false. The option to use horz_z_diffuse=.true. is maintained for legacy purposes alone.  
horz_s_diffuse 
 To compute diffusion along surfaces of constant vertical scoordinate. This operation is ensured of obtaining a smoothing operator that does not create extrema. It is the default for this reason.  
read_diffusivity_mask 
 Allows for reading of a mask that to apply diffusivity only in selected regions. Default read_diffusivity_mask=.false. 
Filename: src/mom5/ocean_param/lateral/ocean_lapcgrid_friction.F90
Namelist: ocean_lapcgrid_friction_nml
Name 
 Description  

k_smag_iso 
 This is the dimensionless Smagorinsky coefficient used to set the scale of the Smagorinsky isotropic viscosity.  
k_smag_aniso 
 This is the dimensionless Smagorinsky coefficient used to set the scale of the Smagorinsky anisotropic viscosity.  
vel_micom_iso 
 Velocity scale that is used for computing the MICOM isotropic viscosity.  
vel_micom_aniso 
 Velocity scale that is used for computing the MICOM anisotropic viscosity.  
eq_vel_micom_iso 
 Velocity scale that is used for computing the MICOM isotropic viscosity within a user specified equatorial band.  
eq_vel_micom_aniso 
 Velocity scale that is used for computing the MICOM anisotropic viscosity within a user specified equatorial band.  
eq_lat_micom 
 Equatorial latitude band (degrees) within which the MICOM viscosity is set according to eq_vel_micom_iso and eq_vel_micom_aniso.  
equatorial_zonal_lat 
 Latitudinal band to use the zonal friction orientation.  
equatorial_zonal 
 Orient the anisotropic friction within a latitudinal band according to zonal direction.  
equatorial_no_smag 
 Turn smag off within equatorial_zonal_lat region.  
viscosity_scale_by_rossby 
 To scale down the laplacian viscosity according to the relative scale of the horizontal grid and the first baroclinic Rossby radius. This is a useful scheme for models that resolve the Rossby radius in the lower latitudes, and so presumably do not wish to have much laplacian friction, whereas the higher latitudes need more friction. Default viscosity_scale_by_rossby=.false.  
viscosity_scale_by_rossby_power 
 The power used to determine the viscosity scaling function. Default viscosity_scale_by_rossby_power=2.0.  
restrict_polar_visc 
 For restricting the background viscosity poleward of a latitude. This method may be useful for coupling to an ice model in which case the horizontal viscosity may need to be a bit smaller to maintain time step constraints. This is because the effective friction is larger than that just within the ocean.  
restrict_polar_visc_lat 
 Latitude poleward of which we restrict the viscosity.  
restrict_polar_visc_ratio 
 Ratio of the normal critical value that we limit the viscosity to be no greater than. If restrict_polar_visc_ratio=1.0 then there is no special limitation of the viscosity beyond that of the onedimensional stability constraint.  
divergence_damp 
 To damp the divergence field.  
divergence_damp_vel_micom 
 Velocity scale to set the viscosity used with divergence damping.  
neptune 
 Set to true for computing friction relative to Neptune barotropic velocity. Default neptune=.false.  
neptune_smooth 
 For doing a horizontal 121 smoothing on the diagnosed neptune velocity scale. Default neptune_smooth=.true.  
neptune_smooth_num 
 Number of smoothing passes for neptune velocity. Default neptune_smooth_num=1.  
neptune_length_eq 
 Length scale used to compute Neptune velocity at equator.  
neptune_length_pole 
 Length scale used to compute Neptune velocity at pole.  
neptune_depth_min 
 Minimum depth scale used for computing Neptune velocity. Default neptune_depth_min=100.0  
use_side_drag_friction 
 For converting friction at Ucells next to walls into a drag law, as per Deremble et al. Use cdbot_array from ocean_core/ocean_bbc.F90 to compute drag force. Default use_side_drag_friction=.false.  
side_drag_friction_scaling 
 Dimensionless scaling used for cdbot_array when setting side drag friction. So the effective side dragy coefficient is side_drag_friction_scaling*cdbot_array. Default side_drag_friction_scaling=1.0.  
side_drag_friction_max 
 Maximum magnitude of the side drag induced friction. This parameter can be useful especially for pressure models where the bottom cells can be quite thin and subject to sporadic large magnitudes. We do the same thing with bottom drag calculations in ocean_bbc. Default side_drag_friction_max=1.0.  
side_drag_friction_uvmag_max 
 Maximum magnitude of horizontal velocity used to compute the side drag friction. This parameter can be useful especially for pressure models where the bottom cells can be quite thin and subject to sporadic large magnitudes. We do the same thing with bottom drag calculations. Default side_drag_friction_uvmag_max=10.0.  
use_this_module 
 Must be true to use this module. Default is false.  
debug_this_module 
 For debugging by printing checksums. 
Filename: src/mom5/ocean_param/lateral/ocean_lapcst_friction.F90
Namelist: ocean_lapcst_friction_nml
Name 
 Description  

alap 
 This is the value for the spacetime constant Laplacian viscosity.  
vel_micom 
 Velocity scale that is used for computing the MICOM viscosity.  
alap_taper_start_lat 
 
alap_taper_end_lat 
 
alap_taper_min_fac 
 
alap_taper_hi_lats 
 
velocity_mix_micom 
 If .true., then the viscosity is set according to a velocity scale times the cube of the grid spacing. It is based on an approach recommended by Eric Chassignet that is used in the Miami Isopycnal Model.  
use_this_module 
 Must be true to use this module. Default is false.  
debug_this_module 
 For debugging by printing checksums.  
read_alap 

Filename: src/mom5/ocean_param/lateral/ocean_lapgen_friction.F90
Namelist: ocean_lapgen_friction_nml
Name 
 Description  

k_smag_iso 
 This is the dimensionless Smagorinsky coefficient used to set the scale of the Smagorinsky isotropic viscosity.  
k_smag_aniso 
 This is the dimensionless Smagorinsky coefficient used to set the scale of the Smagorinsky anisotropic viscosity.  
vel_micom_iso 
 Velocity scale that is used for computing the MICOM isotropic viscosity.  
vel_micom_aniso 
 Velocity scale that is used for computing the MICOM anisotropic viscosity.  
eq_vel_micom_iso 
 Velocity scale that is used for computing the MICOM isotropic viscosity within a user specified equatorial band.  
eq_vel_micom_aniso 
 Velocity scale that is used for computing the MICOM anisotropic viscosity within a user specified equatorial band.  
eq_lat_micom 
 Equatorial latitude band (degrees) within which the MICOM viscosity is set according to eq_vel_micom_iso and eq_vel_micom_aniso.  
equatorial_zonal_lat 
 Latitudinal band to use the zonal friction orientation.  
equatorial_zonal 
 Orient the anisotropic friction within a latitudinal band according to zonal direction.  
equatorial_no_smag 
 Turn smag off within equatorial_zonal_lat region.  
bottom_5point 
 To alleviate problems with small partial cells, it is often necessary to reduce the operator to the traditional 5point Laplacian at the ocean bottom. This logical implements this mixing. Default bottom_5point=.false.  
viscosity_scale_by_rossby 
 To scale down the laplacian viscosity according to the relative scale of the horizontal grid and the first baroclinic Rossby radius. This is a useful scheme for models that resolve the Rossby radius in the lower latitudes, and so presumably do not wish to have much laplacian friction, whereas the higher latitudes need more friction. Default viscosity_scale_by_rossby=.false.  
viscosity_scale_by_rossby_power 
 The power used to determine the viscosity scaling function. Default viscosity_scale_by_rossby_power=2.0.  
restrict_polar_visc 
 For restricting the background viscosity poleward of a latitude. This method may be useful for coupling to an ice model in which case the horizontal viscosity may need to be a bit smaller to maintain time step constraints. This is because the effective friction is larger than that just within the ocean.  
restrict_polar_visc_lat 
 Latitude poleward of which we restrict the viscosity.  
restrict_polar_visc_ratio 
 Ratio of the normal critical value that we limit the viscosity to be no greater than. If restrict_polar_visc_ratio=1.0 then there is no special limitation of the viscosity beyond that of the onedimensional stability constraint.  
divergence_damp 
 To damp the divergence field.  
divergence_damp_vel_micom 
 Velocity scale to set the viscosity used with divergence damping.  
vconst_1 
 Background viscosity for NCAR algorithm.  
vconst_2 
 For NCAR viscosity algorithm.  
vconst_3 
 For NCAR viscosity algorithm.  
vconst_4 
 For NCAR viscosity algorithm.  
vconst_5 
 For NCAR viscosity algorithm.  
vconst_6 
 For NCAR viscosity algorithm.  
vconst_7 
 For NCAR viscosity algorithm.  
vconst_8 
 For NCAR viscosity algorithm.  
visc_vel_scale_length 
 For NCAR viscosity algorithm: efolding depth for depth dependent background viscosity. Default visc_vel_scale_length=1500.e2 cm  
viscosity_ncar 
 Anisotropic background viscosities used by NCAR.  
viscosity_ncar_2000 
 Anisotropic background viscosities used by NCAR, using the formulation as of 2000. Default viscosity_ncar_2000=.true.  
viscosity_ncar_2007 
 Anisotropic background viscosities used by NCAR, using the formulation as of 2007. Default viscosity_ncar_2007=.false.  
debug_ncar_A 
 Sets f_perp=f_para for debugging purposes with the NCAR scheme.  
debug_ncar_B 
 Sets f_para=f_perp for debugging purposes with the NCAR scheme.  
ncar_isotropic_off_equator 
 Polewards of equatorial_zonal_lat, revert NCAR scheme to isotropic  
ncar_only_equatorial 
 
ncar_isotropic_at_depth 
 Sets the NCAR scheme to be isotropic beneath a chosen depth.  
ncar_isotropic_depth 
 Sets the NCAR scheme to be isotropic beneath this chosen depth.  
ncar_isotropic_at_depth_visc 
 Sets the NCAR scheme to be isotropic beneath this chosen depth, with minimum viscosity set according to this value.  
neptune 
 Set to true for computing friction relative to Neptune barotropic velocity. Default neptune=.false.  
neptune_smooth 
 For doing a horizontal 121 smoothing on the diagnosed neptune velocity scale. Default neptune_smooth=.true.  
neptune_smooth_num 
 Number of smoothing passes for neptune velocity. Default neptune_smooth_num=1.  
neptune_length_eq 
 Length scale used to compute Neptune velocity at equator.  
neptune_length_pole 
 Length scale used to compute Neptune velocity at pole.  
neptune_depth_min 
 Minimum depth scale used for computing Neptune velocity. Default neptune_depth_min=100.0  
use_side_drag_friction 
 For converting friction at Ucells next to walls into a drag law, as per Deremble et al. Use cdbot_array from ocean_core/ocean_bbc.F90 to compute drag force. Default use_side_drag_friction=.false.  
side_drag_friction_scaling 
 Dimensionless scaling used for cdbot_array when setting side drag friction. So the effective side dragy coefficient is side_drag_friction_scaling*cdbot_array. Default side_drag_friction_scaling=1.0.  
side_drag_friction_max 
 Maximum magnitude of the side drag induced friction. This parameter can be useful especially for pressure models where the bottom cells can be quite thin and subject to sporadic large magnitudes. We do the same thing with bottom drag calculations. Default side_drag_friction_max=1.0.  
side_drag_friction_uvmag_max 
 Maximum magnitude of horizontal velocity used to compute the side drag friction. This parameter can be useful especially for pressure models where the bottom cells can be quite thin and subject to sporadic large magnitudes. We do the same thing with bottom drag calculations. Default side_drag_friction_uvmag_max=10.0.  
use_this_module 
 Must be true to use this module. Default is false.  
debug_this_module 
 For debugging by printing checksums.  
async_domain_update 
 
blocksize 

Filename: src/mom5/ocean_param/lateral/ocean_mixdownslope.F90
Namelist: ocean_mixdownslope_nml
Name 
 Description  

use_this_module 
 For using this module. Default use_this_module=.false.  
debug_this_module 
 For debugging  
do_bitwise_exact_sum 
 Set true to do bitwise exact global sum. When it is false, the global sum will be nonbitwise_exact, but will significantly increase efficiency. The default value is false.  
mixdownslope_weight_far 
 To place more weight on points further from central point. This may be done to enhance properties getting downslope. Default is mixdownslope_weight_far=.false.  
read_mixdownslope_mask 
 For reading in a mask that selects regions of the domain where mixdownslope is allowed to function (mask=1) or not to function (mask=0). Default read_mixdownslope_mask=.false., whereby mixdownslope_mask is set to tmask(k=1).  
mixdownslope_mask_gfdl 
 For modifying the mixdownslope mask based on reading in the GFDL regional mask. Default mixdownslope_mask_gfdl=.false.  
mixdownslope_npts 
 Number of horizontally distant points used in search downslope. Note: it is not possible to have mixdownslope_npts greater than or equal to the computational domain extents, as this would require updates across multiple processors. Default mixdownslope_npts=1.  
mixdownslope_width 
 Width of the reweighting function used to emphasize points further along in the search for exchange points. Default mixdownslope_width=1.  
mixdownslope_frac_central 
 Fraction of the central cell that participates in downslope mixing in any particular direction. Default mixdownslope_frac_central=0.25 
Filename: src/mom5/ocean_param/lateral/ocean_sigma_transport.F90
Namelist: ocean_sigma_transport_nml
Name 
 Description  

tmask_sigma_on 
 IF .true. then masks out fluxes passing into the sigma layer, except those associated with sigma transport. Typically set to .false.  
use_this_module 
 Must be true to use this module. Default is false.  
debug_this_module 
 For debugging.  
verbose_init 
 
sigma_diffusion_on 
 For using sigma diffusion. Default is true.  
sigma_advection_on 
 For using sigma advection. Default is false.  
sigma_advection_sgs_only 
 In many cases, adding the resolved transport to the sigmaadvective transport produces a tremendous level of noise at the bottom. The problem is that there are gridscale features that may cause large jumps in whether the velocity should be added or not, depending on the logic of the scheme. For this reason, it may be prudent to remove the resolved velocity from that contributing to the sigma transport scheme. Note that its removal from sigma transport does not remove the contributions of the resolved velocity from the resolved advective transport arising from ocean_tracer_advect_mod. It simply removes it from the added transport arising in the sigma transport module. Default is sigma_advection_sgs_only=.true.  
sigma_advection_check 
 If true, then will only include the resolved advection velocity in the sigmalayer if the direction of transport is downslope favorable for enhancing deep density. IF false, then will include the velocity regardless. This option aims to reduce the large divergences that occur for the case when only include the velocity if it is favorable for deep water getting more dense. Default is sigma_advection_check=.true.  
sigma_diffusivity 
 Sigma tracer diffusivity for use if not using micom diffusivity.  
sigma_diffusivity_ratio 
 When flow along sigma surface is stable (i.e., heavy parcels are below lighter parcels) then sigma diffusivity is reduced by sigma_diffusivity_ratio from the case where heavy parcels are above lighter parcels.  
thickness_sigma_max 
 Maximum thickness of the bottom sigma layer.  
thickness_sigma_min 
 Minimum thickness of the bottom sigma layer.  
thickness_sigma_layer 
 Initial thickness of the bottom sigma layer.  
vel_micom 
 Velocity scale that is used for computing the MICOM diffusivity.  
campingoose_mu 
 Dissipation rate for the bottom friction. Campin and Goosse suggest campingoose_mu=10^4  
campingoose_delta 
 Fraction of a grid cell participating in the overflow process. Campin and Goosse suggest campingoose_delta=1/3.  
sigma_umax 
 Maximum downslope speed allowed in sigma layer. In some cases, the model will be unstable if sigma_umax is too large.  
tracer_mix_micom 
 If .true., then the sigma diffusivity is set according to a velocity scale times the grid spacing.  
sigma_just_in_bottom_cell 
 For just having sigma layer in the bottom cell, as in mom4p0. This option must be .false. in order to use sigma_advection_on=.true. Default sigma_just_in_bottom_cell=.true.  
write_a_restart 
 
smooth_sigma_thickness 
 To smooth the sigma thickness. This may be needed especially for case with sigma advection, in which case the thickness can become noisy. Default is smooth_sigma_thickness=.true.  
smooth_sigma_velocity 
 To smooth the sigma advective transport velocity. Default is smooth_sigma_velocity=.true.  
smooth_velmicom 

Filename: src/mom5/ocean_param/lateral/ocean_submesoscale.F90
Namelist: ocean_submesoscale_nml
Name 
 Description  

use_this_module 
 
debug_this_module 
 For debugging purposes.  
submeso_skew_flux 
 For computing the tendency as convergence of skew flux. This is the recommended method. Default submeso_skew_flux=.true.  
submeso_advect_flux 
 For computing the tendency as convergence of advective flux. This approach uses either a flux limited sweby advection or first order upwind, both of which ensure that the resulting tendency will not create extrema in the tracer field. Default submeso_advect_flux=.false.  
submeso_advect_upwind 
 For computing the tendency as convergence of a first order advective flux. Default submeso_advect_upwind=.true.  
submeso_advect_sweby 
 For computing the tendency as convergence of a sweby advective flux. This routine is incomplete and has a bug. Default submeso_advect_sweby=.false.  
submeso_advect_limit 
 For limiting the value of the horizontal transports to be less than a velocity scale set by limit_psi_velocity_scale. This option is not needed if limit_psi=.true. Default submeso_advect_limit=.false.  
submeso_advect_zero_bdy 
 For removing the advective transport next to boundaries. This is useful since computation of the advective transport velocity components can be problematic next to boundaries. Default submeso_advect_zero_bdy=.false.  
submeso_limit_flux 
 For limiting the fluxes arising from submeso scheme, according to tmask_limit. When reach a point where tmask_limit=1.0, then set the submeso flux for this cell to zero. Default submeso_limit_flux=.true.  
use_hblt_constant 
 For running with a constant boundary layer depth. This for the case when not using a realistic mixed layer scheme. Default use_hblt_constant=.false.  
use_hblt_equal_mld 
 For using the diagnosed mld as the hblt for submeso. This is useful for those test models that do not have a mixed layer scheme enabled, such as KPP, where the mixed layer scheme provides a boundary layer depth. In this case, it is sensible to employ the diagnosed mixed layer depth for the submeso scheme. Additionally, in general it is more physical to use the mld than the KPP hblt as the depth over which the submesoscale eddies act. Hence, default use_hblt_equal_mld=.true.  
smooth_hblt 
 For smoothing on the submeso bldepth field. This is useful since the bldepth obtained from KPP or diagnosed mld can have some grid noise. Default smooth_hblt=.false. since this agrees with legacy. Note that this scheme fails to reproduce across processor layout, so it remains broken.  
smooth_psi 
 For doing a horizontal 121 smoothing on the psix_horz and psiy_horz fields. Default smooth_psi=.true.  
smooth_advect_transport 
 For doing a horizontal 121 smoothing on the diagnosed uhrho_et_submeso and vhrho_nt_submeso fields. Default smooth_advect_transport=.true.  
front_length_deform_radius 
 To compute the front length using the mixed layer deformation radius. Default front_length_deform_radius=.true. Note, will have a floor on the variable front length set by the nml setting for front_length_const.  
limit_psi 
 For limiting the magnitude of psi in order to reduce possibility of model crashes. Rescales the full psi to maintain vertical structure but to keep overall magnitude within bounds. Default limit_psi=.false.  
use_psi_legacy 
 For computing psi using older legacy methods. These methods are not ideal, and can be problematic depending on nml settings for the limiters and smoothers. This option is retained only for legacy purposes. Default use_psi_legacy=.false.  
submeso_diffusion 
 For computing a horizontal diffusive flux in the boundary layer as determined by the strength of the vector streamfunction. Default submeso_diffusion=.false.  
submeso_diffusion_biharmonic 
 The default submeso diffusion is Laplacian. However, one may wish to use a biharmonic mixing operator instead. Default submeso_diffusion_biharmonic=.false.  
limit_psi_velocity_scale 
 Velocity scale used to limit the value of psi when limit_psi=.true. Default limit_psi_velocity_scale=5.0  
coefficient_ce 
 The dimensionless coefficient from the FoxKemper etal scheme. They recommend setting coefficient_ce between 0.06 and 0.08. Default coefficient_ce=0.07.  
time_constant 
 Timescale to mix momentum across the mixed layer. Default time_constant=86400.0 = 1day.  
front_length_const 
 Take constant horizontal length scale of submesoscale front. Default front_length_const=5e3.  
constant_hblt 
 The boundary layer depth for the case when use_hblt_constant=.true. Default constant_hblt=100.0.  
minimum_hblt 
 For setting a floor to the hblt used for submesoscale scheme. Default minimum_hblt=0.0.  
submeso_diffusion_scale 
 A dimensionless scaling to be used for scaling up or down the effects from horizontal diffusion in the boundary layer. Default submeso_diffusion_scale=1.0.  
min_kblt 
 The minimum number of vertical cells in the surface boundary layer that are required in order to compute the submesoscale streamfunction. Default min_kblt=4. Need at least three to fit a parabola with zero streamfunction at the top and bottom of the boundary layer.  
diag_step 
 Number of time steps between computing max bottom value for wrho_bt_submeso. Default diag_step=1200.  
smooth_psi_num 
 Number of iterations for the smooothing of psi. Default smooth_psi_num=2.  
smooth_advect_transport_num 
 Number of iterations for the smooothing of horizontal transport. Default smooth_advect_transport_num=2.  
smooth_hblt_num 
 Number of iterations for the smooothing of bldepth. Default smooth_hblt_num=1. 
src/mom5/ocean_param/neutral
Filename: src/mom5/ocean_param/neutral/ocean_nphysics.F90
Namelist: ocean_nphysics_nml
Name 
 Description  

use_nphysicsA 
 For using the nphysicsA method of neutral physics, based on that developed in MOM4.0. This scheme is more robust and recommended for general use. Default use_nphysicsA=.true.  
use_nphysicsB 
 For using the nphysicsB method of neutral physics. This method is experimental, and is not recommended for general use. Default use_nphysicsB=.false.  
use_nphysicsC 
 For using the nphysicsC method of neutral physics. This method is experimental, and is not recommended for general use. Default use_nphysicsC=.false.  
use_this_module 
 Must be true to use this module. Default use_this_module=.false.  
debug_this_module 
 For printing starting and ending checksums for restarts Default debug_this_module=.false.  
write_a_restart 
 Set true to write a restart. False setting only for rare cases where wish to benchmark model without measuring the cost of writing restarts and associated chksums. Default is write_a_restart=.true. 
Filename: src/mom5/ocean_param/neutral/ocean_nphysics_diff.F90
Namelist: ocean_nphysics_diff_nml
Name 
 Description  

agm_const 
 
agm 
 
agm_closure_micom 
 
agm_micom_vel 
 
agm_lat_bands 
 
agm_lat_bands_boundary 
 
agm_lat_bands_ratio 
 
agm_closure 
 
agm_max 
 
agm_min 
 
agm_scaling 
 
agm_closure_rate_len2 
 
agm_grid_scaling 
 
agm_grid_scaling_power 
 
agm_smooth_space 
 
agm_smooth_time 
 
agm_damping_time 
 
agm_closure_n2_scale 
 
agm_n2_scale_coeff 
 
agm_n2_scale_nref_cst 
 
agm_n2_scale_buoy_freq 
 
agm_rate_upper_depth 
 
agm_rate_lower_depth 
 
agm_rate_eady 
 
agm_rate_baroclinic 
 
agm_rate_baro_buoy_freq 
 
agm_rate_smooth_vert 
 
agm_rate_smooth_horiz 
 
agm_rate_cap 
 
agm_rate_cap_scale 
 
agm_rate_ave_mixed 
 
agm_rate_zave 
 
agm_rate_eden_greatbatch 
 
agm_rate_eg_alpha 
 
agm_length_eden_greatbatch 
 
agm_length_cap 
 
agm_length_max 
 
agm_length_fixed 
 
agm_length 
 
agm_length_rossby 
 
agm_length_bczone 
 
agm_bczone_max_pts 
 
agm_bczone_crit_rate 
 
aredi_equal_agm 
 
aredi 
 
aredi_fixed 
 
aredi_grid_scaling 
 
aredi_grid_scaling_power 
 
neutral_horiz_mix_bdy 
 
ah_micom 
 
ah_micom_vel 
 
ah_const 
 
ah 

Filename: src/mom5/ocean_param/neutral/ocean_nphysics_flux.F90
Namelist: ocean_nphysics_flux_nml
Name 
 Description  

diffusion_all_explicit 
 To compute K33 explicitly in time. This setting is meant only for debugging tests, since in general the simulation will go unstable. Default diffusion_all_explicit=.false.  
neutral_physics_limit 
 Revert to horizontal diffusion when tracer falls outside specified range. Default neutral_physics_limit=.true., so to keep tracers from going too far outside of physical range. 
Filename: src/mom5/ocean_param/neutral/ocean_nphysics_new.F90
Namelist: ocean_nphysics_new_nml
Name 
 Description  

use_this_module 
 Must be set .true. to use this module. Default use_this_module = .false.  
smax 
 Slope maximum parameter for setting behaviour of neutral physics. Default smax=0.01.  
drhodz_smooth_vert 
 For smoothing vertical density gradient before computing neutral slope. Exercise caution if using this option. Default drhodz_smooth_vert=.false.  
drhodz_smooth_horz 
 For smoothing vertical density gradient before computing neutral slope. Exercise caution if using this option. Default drhodz_smooth_horz=.false.  
vel_micom_smooth 
 For horizontal smoothing of drhodz before computing neutral slopes. Default vel_micom_smooth=0.2. 
Filename: src/mom5/ocean_param/neutral/ocean_nphysics_skew.F90
Namelist: ocean_nphysics_skew_nml
Name 
 Description  

gm_transport 
 To compute tendency from GM skewsion. Default gm_transport=.false.  
bc_modes_transport 
 To compute tendency from GM skewsion using streamfunction established by baroclinic modes. Default bc_modes_transport=.false.  
number_bc_modes 
 The number of baroclinic modes used to construct the eddy induced streamfunction when bc_modes_transport. Default number_bc_modes=1.  
regularize_transport 
 To reduce the magnitude of psi in regions of weak stratification, using the slope = smax_psi to set the overall scale of the max allowed for psi. Default regularize_transport=.true.  
smax_psi 
 Maximum slope used for setting the overall scale of a modal contribution to the parameterized transport. Default smax_psi=0.1.  
bvp_transport 
 To compute tendency from GM skewsion using streamfunction established by a boundary value problem. Default bvp_transport=.false.  
bvp_constant_speed 
 For taking a constant speed to be used for the calculation of the BVP streamfunction. Default bvp_constant_speed=.false.  
bvp_speed 
 For setting the speed weighting the second order derivative operator in the BVP streamfunction method: c^2 = max[bvp_min_speed, (bvp_speedc_mode)^2]. If bvp_constant_speed, then c^2 = bvp_speed^2. Default bvp_speed=0.0, in which case c^2 = c_mode^2.  
bvp_bc_mode 
 The particular baroclinic mode used to construct the BVP streamfunction. If bvp_bc_mode=0, then will set bc_speed=0 when computing the BVP streamfunction. Default bvp_bc_mode=1.  
bvp_min_speed 
 For setting a minimum speed for use with the calculation of the BVP streamfunction. We need bvp_min_speed>0 to ensure that the second order derivative operator contributes to the calculation of the streamfunction. Default bvp_min_speed=0.1.  
smooth_transport 
 For doing a horizontal 121 smoothing on the psix and psiy fields. This is useful to reduce noise. Default smooth_psi=.true. 
Filename: src/mom5/ocean_param/neutral/ocean_nphysics_tensor.F90
Namelist: ocean_nphysics_tensor_nml
Name 
 Description  

neutral_sine_taper 
 
turb_blayer_min 
 
rossby_radius_max 
 
rossby_radius_min 
 
dm_taper 
 
swidth 
 
neutral_taper_diagonal 
 
tmask_neutral_on 

Filename: src/mom5/ocean_param/neutral/ocean_nphysics_util.F90
Namelist: ocean_nphysics_util_nml
Name 
 Description  

drhodz_mom4p1 
 For computing the vertical deriviative of locally referenced potrho as in the preferred MOM algorithm rather than the earlier mom4p0 approach. Default drhodz_mom4p1=.true.  
drhodz_smooth_horz 
 For horizontal laplacian smoothing the vertical derivative of density prior to its use in computing the neutral slopes. This smoothing helps to produce regularized slopes. Note that this option breaks the integrity of the triads and is thus NOT generally recommended. Default drhodz_smooth_horz=.false.  
drhodz_smooth_vert 
 For vertical 121 smoothing the vertical derivative of density prior to its use in computing the neutral slopes. This smoothing helps to produce regularized slopes. Note that this option breaks the integrity of the triads and is thus NOT generally recommended. Default drhodz_smooth_vert=.false.  
num_121_passes 
 For number of 121 passes through to smooth drhodz or eady_rate in vertical. Default num_121_passes=1.  
vel_micom_smooth 
 Velocity scale that is used for computing the MICOM Laplacian mixing coefficient used in smoothing of drhodzb. Default vel_micom_smooth=0.2.  
epsln_drhodz 
 For computing drhodz used in slope calculation. We must keep drhodz < 0 in order to maintain integrity of the quasiStokes streamfunction as well as computation of buoyancy frequency. Default epsln_drhodz=1e30.  
aredi 
 Neutral diffusivity used for experiments using a constant diffusivity.  
agm 
 GMskew diffusivity used for experiments using a constant diffusivity.  
aredi_equal_agm 
 Will set aredi_array=agm_array, overriding any other specification of aredi_array. Default aredi_equal_agm=.true.  
smax 
 Value of the maximum neutral direction slope above which the neutral fluxes are either tapered to zero or saturated. Typical value is smax=0.01 or smaller.  
swidth 
 Width in slope over which use tanh with dm_taper scheme to taper fluxes in steep sloped regions. Typical value swidth=0.1*smax  
neutral_horz_mix_bdy 
 If .true., then use a horizontal diffusivity in the neutral boundary layer.  
vel_micom_bdy 
 Velocity scale that is used for computing the MICOM horizontal diffusivity within the neutral boundary layer.  
ah_bdy 
 Constant horizontal diffusivity for the boundary layer. Default ah_bdy=0.0.  
bryan_lewis_aredi 
 Set bryan_lewis_aredi=.true. when want to have aredi a function of depth according to the Bryan and Lewis (1979) profile. Maintained for legacy purposes, and not recommended for new models.  
ahs 
 ahs = adjustable parameter at the surface for bryan_lewis_aredi  
ahb 
 ahb = adjustable parameter at the bottom for bryan_lewis_aredi  
agm_lat_bands 
 
agm_lat_bands_boundary 
 
agm_lat_bands_ratio 
 
tracer_mix_micom 
 If .true., then the GMskew diffusivity is set according to a velocity scale times the grid spacing.  
vel_micom 
 Velocity scale that is used for computing the MICOM diffusivity.  
agm_read_restart 
 For those cases with agm_closure=.false. where we wish to read in the agm_array from restart files and keep the value from the restart. This approach allows us to read in a spatially dependent agm_array that may have been computed from another integration, but to leave the coefficient static in time. Default agm_read_restart=.false.  
agm_closure 
 If .true. then will compute the GMskew diffusivity as a function of the flow. The length scale is determined by the Rossby radius and the time scale is determined by the Eady growth rate. Diffusivities are depth independent.  
agm_closure_scaling 
 Dimensionless tuning parameter for computing flow dependent diffusivities.  
agm_closure_max 
 Maximum GM diffusivity allowed when using agm_closure=.true.  
agm_closure_min 
 Minimum GM diffusivity allowed when using agm_closure=.true.  
agm_closure_length_fixed 
 Use fixed length scale for computing agm_closure diffusivity  
agm_closure_length 
 Fixed length scale for use with agm_closure_fixed_length  
agm_closure_length_rossby 
 For computing the agm_closure length scale according to Rossby radius.  
rossby_radius_max 
 Maximum Rossby radius used for agm_closure_length_rossby and the neutral_sine_taper. Default = 100e3 m.  
rossby_radius_min 
 Minimum Rossby Radius used for agm_closure_length_rossby and the neutral_sine_taper. Default = 15e3 m.  
agm_closure_length_bczone 
 For computing the agm_closure length scale according to radius of baroclinic zone.  
bczone_max_pts 
 Max number of horizontal grid points for use in computing the baroclinic zone radius.  
agm_closure_bczone_crit_rate 
 Critical growth rate for determining width of the baroclinic zone.  
agm_closure_length_cap 
 For setting a maximum length scale for the agm_closure calculation. Default agm_closure_length_cap=.false.  
agm_closure_length_max 
 Maximum length scale used for computing agm_closure. Default agm_closure_length_max=50e3.  
agm_closure_n2_scale 
 For computing the agm coefficient using a 3dimensional scaling by (N/Nref)^2, with N=buoyancy frequency and Nref the buoyancy frequency at the base of the neutral blayer. Default agm_closure_n2_scale=.false.  
agm_closure_n2_scale_nref_cst 
 For taking the reference buoyancy frequency as agm_closure_buoy_freq for the (N/Nref)^2 scaling. Default agm_closure_n2_scale_nref_cst=.false.  
agm_closure_n2_scale_coeff 
 Coefficient setting the scale for the diffusivity computed from agm_closure_n2_scale. Default agm_closure_n2_scale_coeff=1e3.  
agm_closure_eden_greatbatch 
 For computing the agm_closure length scale according to minimum of the Rhines scale and the Rossby radius, and using 3d Eady growth rate.  
agm_closure_eden_length_const 
 To set the length scale for agm_closure_eden_greatbatch to constant. Default agm_closure_eden_length_const=.false.  
agm_closure_eden_gamma 
 For use in regularizing the growth rate used in the eden/greatbatch approach. Default agm_closure_eden_gamma=200. Setting to zero removes the regularization.  
agm_closure_eden_length 
 Length scale for use with agm_closure_eden_length_const=.true. Default agm_closure_eden_length=10e3.  
agm_closure_baroclinic 
 For computing the agm coefficient using only the vertically averaged magnitude of the horizontal density gradient (i.e., the "baroclinicity").  
agm_closure_buoy_freq 
 For computing the agm coefficient using only the vertically averaged horizontal density gradient, we need to specify a buoyancy frequency, which is taken to be fixed over all spacetime.  
agm_closure_upper_depth 
 Upper depth where start the depth integration to compute the Eady growth rate and/or baroclinicity.  
agm_closure_lower_depth 
 Deeper depth where finish the depth integration to compute the Eady growth rate and/or baroclinicity.  
agm_closure_eady_smooth_vert 
 For vertical 121 smoothing the eady_rate Default agm_closure_eady_smooth=.false.  
agm_closure_eady_smooth_horz 
 For horizontal Laplacian smoothing of eady growth rate. Default agm_closure_eady_smooth_horz=.false.  
agm_closure_eady_cap 
 For capping the eady growth rate to avoid huge values. Default agm_closure_eady_cap=.false.  
agm_closure_eady_ave_mixed 
 To set the Eady growth rate to its average within mixed layer region. This is used to avoid spuriously large values which often appear just in the upper regions of the ocean mixed layer. Default agm_closure_eady_ave_mixed=.false.  
agm_closure_growth_scale 
 Dimensionless scaling used to set a maximum for agm_growth.  
agm_smooth_space 
 For smoothing the agm diffusivity in space when nonconstant diffusivity used. Default is agm_smooth_space=.false.  
agm_smooth_time 
 For smoothing the agm diffusivity in time when nonconstant diffusivity used. Default is agm_smooth_time=.false.  
agm_damping_time 
 The damping time used for time smoothing agm_array. Default agm_damping_time=10days.  
agm_closure_grid_scaling 
 For an overall scaling of the agm coefficient, according to the relative resolution of the grid and deformation radius. Default is agm_closure_grid_scaling=.false.  
agm_closure_grid_scaling_power 
 Power used to scale the agm_closure diffusivity. Default is agm_closure_grid_scaling_power=2.0  
aredi_diffusivity_grid_scaling 
 For an overall scaling of the aredi coefficient, according to the relative resolution of the grid and deformation radius. This option is used only when aredi_equal_agm=.false. Default is aredi_diffusivity_grid_scaling=.false.  
nphysics_util_zero_init 
 For Time%init=.true. and wishing to ensure starting with a clean suite of nphysics_util fields, even if ocean_neutral.res.nc exists.  
wdianeutral_smooth 
 For smoothing the diagnosed dianeutral velocity component using a horizontal 121 smoother. Default is wdianeutral_smooth=.true.  
epsln_drhodz_diagnostics 
 For drhodz used in calculation of dianeutral velocity component from cabbeling and thermobaricity. Default epsln_drhodz_diagnostics=1e7.  
smax_grad_gamma_scalar 
 For calculation of gradients of scalars along a neutral direction, then when abs(slope) > smax_grad_gamma_scalar, will compute the gradient using only the vertical scalar gradient, since the slopes are so large they are effectively infinite. Default smax_grad_gamma_scalar=.01  
smooth_eta_tend_gm90 
 For smoothing the diagnosed contribution to steric sea level time tendency associated with the GM90 scheme. Default is smooth_eta_tend_gm90=.false.  
debug_this_module 
 For printing starting and ending checksums for restarts 
Filename: src/mom5/ocean_param/neutral/ocean_nphysics_util_new.F90
Namelist: ocean_nphysics_util_new_nml
Name 
 Description  

num_121_passes 
 For number of 121 passes through to smooth drhodz or eady_rate in vertical. Default num_121_passes=1. 
Filename: src/mom5/ocean_param/neutral/ocean_nphysicsA.F90
Namelist: ocean_nphysicsA_nml
Name 
 Description  

use_gm_skew 
 Must be true to use GM skewsion. Set to false if wish to incorporate the "GMeffect" through form drag, as in ocean_form_drag module. Default use_gm_skew=.true.  
dm_taper 
 Set to true to use the tanh tapering scheme of Danabasoglu and McWilliams. Default is true.  
gkw_taper 
 Set to true to use the quadradic tapering scheme of Gerdes, Koberle, and Willebrand. Default is false.  
neutral_physics_simple 
 If .true. then must have aredi_equal_agm=.true.. The horizontal fluxes are then computed as horizontal downgradient diffusive fluxes regardless the neutral slope. This approach precluds one from being able to have the GMskew fluxes remain active in the steep sloped regions, thus shutting off their effects to reduce the slopes of isopycnals in convective and mixed layer regimes. It is for this reason that neutral_physics_simple=.false. is the recommended default in MOM.  
turb_blayer_min 
 Minimum depth of a surface turbulent boundary layer used in the transition of the neutral physics fluxes to the surface. Note that in MOM4.0, turb_blayer_min was always set to zero.  
neutral_blayer_diagnose 
 Diagnose properties of the neutral physics boundary layer, whether have neutral_linear_gm_taper or neutral_sine_taper true or not.  
neutral_linear_gm_taper 
 If .true. then with neutral_physics_simple=.false., will linearly taper GM skew fluxes towards the surface within regions of steep neutral slopes. This approach leads to a constant horizontal eddyinduced velocity in the steeply sloping regions and is recommended for realistic simulations.  
neutral_sine_taper 
 If .true. then with neutral_physics_simple=.false., will apply a sinetaper to GM and neutral diffusive fluxes in regions where the penetration depth of eddies is deeper than the grid point. This method is essential for fine vertical resolution grids.  
neutral_taper_diagonal 
 For cases with neutral_physics_simple=.false., then neutral_taper_diagonal=.true. will taper the diagonal pieces of the horizontal flux components when neutral slopes are steep. With neutral_taper_diagonal=.false., then the horizontal flux components will remain enabled for all slopes, thus producing horizontal downgradient diffusion in regions of vertical neutral directions.  
tmask_neutral_on 
 If .true. then this logical reduces the neutral fluxes to horizontal/vertical diffusion next to boundaries. This approach has been found to reduce spurious extrema resulting from truncation of triads used to compute a neutral flux component. Default tmask_neutral_on=.false.  
diffusion_all_explicit 
 To compute all contributions from neutral diffusion explicitly in time, including the K33 diagonal piece. This approach is available only when have small time steps and/or running with just a single tracer. It is for testing purposes.  
neutral_physics_limit 
 When tracer falls outside a specified range, revert to horizontal diffusive fluxes at this cell. This is an ad hoc and incomplete attempt to maintain monotonicity with the neutral physics scheme. Default neutral_physics_limit=.true.  
use_this_module 
 Must be true to use this module. Default is false.  
debug_this_module 
 For printing starting and ending checksums for restarts 
Filename: src/mom5/ocean_param/neutral/ocean_nphysicsB.F90
Namelist: ocean_nphysicsB_nml
Name 
 Description  

use_gm_skew 
 Must be true to use GM skewsion. Set to false if wish to incorporate the "GMeffect" through form drag, as in ocean_form_drag module. Default use_gm_skew=.true.  
neutral_damping_time 
 The damping time used for determining the effective surface boundary layer thickness from other portions of the model. Default neutral_damping_time=10days.  
nblayer_smooth 
 For smoothing the neutral blayer fields. This is useful when aiming to produce a smooth quasistokes streamfunction within the boundary layers. Default is nblayer_smooth=.true.  
vel_micom_smooth 
 Velocity scale that is used for computing the MICOM Laplacian mixing coefficient used in the Laplacian smoothing of neutral blayer fields.  
dm_taper 
 
gkw_taper 
 
surf_turb_thick_min_k 
 Minimum number of klevels in surface turbulent boundary layer used in the transition of the neutral physics fluxes to the surface. Default surf_turb_thick_min_k = 2.  
surf_turb_thick_min 
 Minimum thickness of surface turbulent boundary layer used in the transition of the neutral physics fluxes to the surface. Default surf_turb_thick_min=20m.  
diffusion_all_explicit 
 To compute all contributions from neutral diffusion explicitly in time, including the K33 diagonal piece. This approach is available only when have small time steps and/or running with just a single tracer. It is for testing purposes.  
neutral_physics_limit 
 When tracer falls outside a specified range, revert to horizontal diffusive fluxes at this cell. This is an ad hoc and incomplete attempt to maintain monotonicity with the neutral physics scheme. Default neutral_physics_limit=.true.  
tmask_neutral_on 
 If .true. then this logical reduces the neutral fluxes to horizontal/vertical diffusion next to boundaries. This approach has been found to reduce spurious extrema resulting from truncation of triads used to compute a neutral flux component. Default tmask_neutral_on=.false.  
use_this_module 
 Must be true to use this module. Default is false.  
debug_this_module 
 For printing starting and ending checksums for restarts 
Filename: src/mom5/ocean_param/neutral/ocean_nphysicsC.F90
Namelist: ocean_nphysicsC_nml
Name 
 Description  

smooth_advect_transport 
 For doing a horizontal 121 smoothing on the diagnosed uhrho_et_gm and vhrho_nt_gm fields. Default smooth_advect_transport=.true.  
smooth_advect_transport_num 
 Number of iterations for the smooothing of horizontal transport. Default smooth_advect_transport_num=2.  
do_neutral_diffusion 
 To compute tendency from neutral diffusion. Default do_neutral_diffusion=.true.  
do_gm_skewsion 
 To compute tendency from GM skewsion. Default do_gm_skewsion=.true.  
gm_skewsion_modes 
 To compute tendency from GM skewsion using streamfunction established by baroclinic modes. Default gm_skewsion_modes=.false.  
gm_skewsion_bvproblem 
 To compute tendency from GM skewsion using streamfunction established by a boundary value problem. Default gm_skewsion_bvproblem=.true.  
number_bc_modes 
 The number of baroclinic modes used to construct the eddy induced streamfunction. Default number_bc_modes=1.  
bvp_bc_mode 
 The particular baroclinic mode used to construct the BVP streamfunction. If bvp_bc_mode=0, then will set bc_speed=0 when computing the BVP streamfunction. Default bvp_bc_mode=1.  
bvp_constant_speed 
 For taking a constant speed to be used for the calculation of the BVP streamfunction. Default bvp_constant_speed=.false.  
bvp_speed 
 For setting the speed weighting the second order derivative operator in the BVP streamfunction method: c^2 = max[bvp_min_speed, (bvp_speedc_mode)^2]. If bvp_constant_speed, then c^2 = bvp_speed^2. Default bvp_speed=0.0, in which case c^2 = c_mode^2.  
bvp_min_speed 
 For setting a minimum speed for use with the calculation of the BVP streamfunction. We need bvp_min_speed>0 to ensure that the second order derivative operator contributes to the calculation of the streamfunction. Default bvp_min_speed=0.1.  
regularize_psi 
 To reduce the magnitude of psi in regions of weak stratification, using the slope = smax_psi to set the overall scale of the max allowed for psi. Default regularize_psi=.true.  
smax_psi 
 
epsln_bv_freq 
 Minimum buoyancy frequency accepted for the computation of baroclinic modes. Default epsln_bv_freq=1e10. Note there is also a minimum drhodz set in ocean_density.F90 via the nml epsln_drhodz in that module. We provide yet another minimum here in case we need an extra regularization for the amplitude of the baroclinic modes.  
min_bc_speed 
 The minimum speed used for computing the baroclinic modes. Default min_bc_speed=1e6  
smooth_psi 
 For doing a horizontal 121 smoothing on the psix and psiy fields. This is useful to reduce noise. Default smooth_psi=.true.  
smooth_bc_modes 
 For doing a vertical 121 smoothing on the baroclinic modes prior to normalization. This is useful to reduce noise. Default smooth_bc_modes=.false.  
bv_freq_smooth_vert 
 To smooth the buoyancy frequency for use in computing the baroclinic modes. Generally this field has already been smooted in ocean_density_mod, but we maintain the possibility of further smoothing here. Default bv_freq_smooth_vert=.false.  
num_121_passes 
 The number of 121 passes used to smooth buoyancy frequency when bv_freq_smooth_vert=.true. Default num_121_passes=1.  
dm_taper 
 Set to true to use the tanh tapering scheme of Danabasoglu and McWilliams. Default is true.  
gkw_taper 
 Set to true to use the quadradic tapering scheme of Gerdes, Koberle, and Willebrand. Default is false.  
turb_blayer_min 
 Minimum depth of a surface turbulent boundary layer used in the transition of the neutral diffusion fluxes to the surface. Note that in mom4p0, turb_blayer_min was always set to zero.  
neutral_eddy_depth 
 Compute eddy_depth according to depth over which eddies feel the ocean surface. Default neutral_eddy_depth=.true.  
tmask_neutral_on 
 If .true. then this logical reduces the neutral diffusive fluxes to horizontal/vertical diffusion next to boundaries. This approach has been found to reduce spurious extrema resulting from truncation of triads used to compute a neutral flux component. Default tmask_neutral_on=.false.  
diffusion_all_explicit 
 To compute all contributions from neutral diffusion explicitly in time, including the K33 diagonal piece. This approach is available only when have small time steps and/or running with just a single tracer. It is for testing purposes.  
neutral_physics_limit 
 When tracer falls outside a specified range, revert to horizontal diffusive fluxes at this cell. This is an ad hoc and incomplete attempt to maintain monotonicity with the neutral physics scheme. Default neutral_physics_limit=.true.  
use_neutral_slopes_potrho 
 To compute the neutral slopes based on globally referenced potential density rather than locally referenced potential density. This approach is meant solely for sensitivity studies; it is not meant for realistic simulations. Default use_neutral_slopes_potrho=.false.  
neutral_slopes_potrho_press 
 The reference pressure used to compute neutral slopes when setting use_neutral_slopes_potrho=.true. Default neutral_slopes_potrho_press=2000.0  
use_this_module 
 Must be true to use this module. Default is false.  
debug_this_module 
 For printing starting and ending checksums for restarts 
src/mom5/ocean_param/sources
Filename: src/mom5/ocean_param/sources/ocean_increment_eta.F90
Namelist: ocean_increment_eta_nml
Name 
 Description  

use_this_module 
 For using this module. Default use_this_module=.false.  
fraction_increment 
 For prescribing the fraction of the increment. applied to the restoring period. Default fraction_increment=1.0  
days_to_increment 
 For specifying the amount of days to restore. Default days_to_increment=1  
secs_to_increment 
 For specifying the amount of seconds to restore. Default secs_to_increment=0 
Filename: src/mom5/ocean_param/sources/ocean_increment_tracer.F90
Namelist: ocean_increment_tracer_nml
Name 
 Description  

use_this_module 
 For using this module. Default use_this_module=.false.  
fraction_increment 
 For prescribing the fraction of the increment. applied to the restoring period. Default fraction_increment=1.0  
days_to_increment 
 For specifying the amount of days to restore. Default days_to_increment=1  
secs_to_increment 
 For specifying the amount of seconds to restore. Default secs_to_increment=0 
Filename: src/mom5/ocean_param/sources/ocean_increment_velocity.F90
Namelist: ocean_increment_velocity_nml
Name 
 Description  

use_this_module 
 For using this module. Default use_this_module=.false.  
fraction_increment 
 For prescribing the fraction of the increment. applied to the restoring period. Default fraction_increment=1.0  
days_to_increment 
 For specifying the amount of days to restore. Default days_to_increment=1  
secs_to_increment 
 For specifying the amount of seconds to restore. Default secs_to_increment=0 
Filename: src/mom5/ocean_param/sources/ocean_momentum_source.F90
Namelist: ocean_momentum_source_nml
Name 
 Description  

use_rayleigh_damp_table 
 For reading in Rayleigh damping times from a table.  
rayleigh_damp_exp_from_bottom 
 For computing a Rayleigh damping time with largest at bottom and decaying towards surface.  
rayleigh_damp_exp_scale 
 Exponential decay scale from bottom upwards for computing the Rayleigh damping time.  
rayleigh_damp_exp_time 
 
verbose_init 
 For verbose initialization information.  
use_this_module 
 Needs to be true in order to use this scheme. Default is false.  
debug_this_module 
 For debugging. 
Filename: src/mom5/ocean_param/sources/ocean_overexchange.F90
Namelist: ocean_overexchange_nml
Name 
 Description  

use_this_module 
 For using this module. Default use_this_module=.false.  
debug_this_module 
 For debugging  
do_bitwise_exact_sum 
 Set true to do bitwise exact global sum. When it is false, the global sum will be nonbitwise_exact, but will significantly increase efficiency. The default value is false.  
overexch_weight_far 
 To place more weight on points further from central point. This may be done to enhance properties getting downslope. Default is overexch_weight_far=.false.  
overexch_check_extrema 
 Check to be sure there are no global tracer extrema formed due to the overexch process. Note that this approach DOES NOT conserve tracer, so it is not generally recommended. Default overexch_check_extrema=.false.  
overexch_npts 
 Number of points used in search for the exchange method. Default overexch_npts=1. Note: it is not possible to have overexch_npts greater than or equal to the computational domain extents, as this would require updates across multiple processors. Default overexch_npts=1.  
overexch_width 
 Width of the reweighting function used to emphasize the points further along in the search for exchange points. Default overexch_width=1.  
overflow_mu 
 Dissipation rate for the bottom friction. Campin and Goosse suggest overflow_mu=10^4  
overflow_delta 
 Fraction of a grid cell participating in the overflow process. Campin and Goosse suggest overflow_delta=1/3.  
overflow_umax 
 Maximum downslope speed used for determining the exchange rate. Default overflow_umax=1.0.  
overexch_stability 
 Stability factor for determining the maximum overexch_flux. Default overexch_stability=0.25  
overexch_min_thickness 
 Minimum bottom cell thickness allowed for use of this scheme. Have found that with very thin cells, the model can become very unstable. Default overexch_min_thickness=4.0 
Filename: src/mom5/ocean_param/sources/ocean_overflow.F90
Namelist: ocean_overflow_nml
Name 
 Description  

transport_units 
 
use_this_module 
 For using this module. Default is false.  
debug_this_module 
 For debugging  
do_bitwise_exact_sum 
 Set true to do bitwise exact global sum. When it is false, the global sum will be nonbitwise_exact, but will significantly increase efficiency. The default value is false.  
no_return_flow 
 Set true to remove the Campin and Goose return flow "piping". Default no_return_flow=.false. to recover the standard approach from Campin and Goose.  
overflow_mu 
 Dissipation rate for the bottom friction. Campin and Goosse suggest overflow_mu=10^4  
overflow_delta 
 Fraction of a grid cell participating in the overflow process. Campin and Goosse suggest overflow_delta=1/3.  
overflow_umax 
 Maximum downslope speed. 
Filename: src/mom5/ocean_param/sources/ocean_overflow_OFP.F90
Namelist: ocean_overflow_OFP_nml
Name 
 Description  

use_this_module 
 For using this module. Default use_this_module=.false.  
debug_this_module 
 For debugging. Default is false.  
crit_Fr_geo_ofp 
 Maximum overflow speed at the source region Default is 3.0 m/s  
frac_exchange_src 
 Areal fraction of the overflow exchange at the source region Default is 1.0  
max_ofp_speed 
 Maximum overflow speed [m^/s] Default is 2.0  
do_mass_ofp 
 Considering the mass source in the overflow process Default is .true.  
diag_step 
 Diagnostic time step for OFP. Default is diag_step = 1 The diagnostic output is saved in the ascii directory as the ascii format.  
do_entrainment_para_ofp 
 Considering the parameterization of entrainment process in the overflow process Default is .true. 
Filename: src/mom5/ocean_param/sources/ocean_rivermix.F90
Namelist: ocean_rivermix_nml
Name 
 Description  

river_insertion_thickness 
 Thickness of the column over which to insert tracers from rivers. Default river_insertion_thickness=0.0 (all in top).  
runoff_insertion_thickness 
 Thickness of the column over which to insert tracers carried by liquid runoff. Default runoff_insertion_thickness=0.0 (all in top).  
calving_insertion_thickness 
 Thickness of the column over which to insert tracers carried by solid runoff. Default calving_insertion_thickness=0.0 (all in top).  
river_diffusion_thickness 
 Thickness of the column over which to diffuse tracers from rivers.  
river_diffusivity 
 Vertical diffusivity enhancement at river mouths which is applied to a depth of river_diffusion_thickness, with linear tapering to zero enhancement from the ocean surface to river_diffusion_thickness.  
river_diffuse_temp 
 Logical to determine if enhance vertical diffusion of temp at river mouths  
river_diffuse_salt 
 Logical to determine if enhance vertical diffusion of salt and all other passive tracers at river mouths  
discharge_combine_runoff_calve 
 Set discharge_combine_runoff_calve=.true. to discharge combined tracer carried by liquid and solid runoff. This approach is sensible when ocean assigns a tracer content to the liquid and solid runoff fields. The alternative is to have a land model that provides information about the tracer coming into the ocean from land water, in which case it is preferable to set discharge_combine_runoff_calve=.false., so to do the runoff and calving separately. Default discharge_combine_runoff_calve=.true.  
do_bitwise_exact_sum 
 Set true to do bitwise exact global sum. When it is false, the global sum will be nonbitwise_exact, but will significantly increase efficiency. The default value is do_bitwise_exact_sum=.false.  
debug_this_module 
 For debugging  
debug_all_in_top_cell 
 For debugging, by placing all in top cell, regardless value of river_insertion_thickness.  
debug_this_module_heat 
 For debugging, print global sum of heating rate by river water.  
use_this_module 
 Must be true to enable this module. Default=.true., since this is the only way that tracer in river water enters the ocean. 
Filename: src/mom5/ocean_param/sources/ocean_riverspread.F90
Namelist: ocean_riverspread_nml
Name 
 Description  

use_this_module 
 Must be true to enable this module. Default=.false.  
debug_this_module 
 For debugging. Default=.false.  
riverspread_diffusion 
 For spreading river water via a Laplacian diffusion operation. Default=.false.  
riverspread_diffusion_passes 
 Number of diffusion passes applied to the runoff/calving array. Default riverspread_diffusion_passes = 0.  
vel_micom_smooth 
 Velocity scale that is used for computing the MICOM Laplacian mixing coefficient used in the Laplacian smoothing of river water. Default vel_micom_smooth=0.2. 
Filename: src/mom5/ocean_param/sources/ocean_shortwave.F90
Namelist: ocean_shortwave_nml
Name 
 Description  

use_this_module 
 
use_shortwave_gfdl 
 
use_shortwave_csiro 
 
use_shortwave_jerlov 
 
use_shortwave_ext 

Filename: src/mom5/ocean_param/sources/ocean_shortwave_csiro.F90
Namelist: ocean_shortwave_csiro_nml
Name 
 Description  

use_this_module 
 
read_depth 
 If .true. then read in e folding depth for radiation attenuation.  
debug_this_module 
 For debugging purposes.  
enforce_sw_frac 
 To ensure the shortwave fraction is monotonically decreasing with depth.  
sw_pen_fixed_depths 
 To compute penetration assuming fixed depths via Grd%zw(k) depths. This is strictly incorrect when have undulating free surface or generatlized vertical coordinates. This option is here for purposes of legacy, as this was done in MOM4.0 versions. The default is .false.  
depth_default 
 Default efolding depth = 20m.  
zmax_pen 
 Maximum depth of penetration of shortwave radiation. Below this depth, shortwave penetration is exponentially small and so is ignored.  
sw_frac_top 
 The fraction of shortwave radiation that should be incorporated into the sw_source array at k=1. The generic treatment in MOM is to assume that shortwave radiation is already contained inside the T_prog(index_temp)%stf field. Hence, to avoid double counting, sw_frac(k=0)=sw_frac_top should=0.0. If one removes shortwave from stf, then set sw_frac_top=1.0. 
Filename: src/mom5/ocean_param/sources/ocean_shortwave_gfdl.F90
Namelist: ocean_shortwave_gfdl_nml
Name 
 Description  

use_this_module 
 Must be .true. to run with module. Default is false.  
read_chl 
 If .true. then read in climatological data of chlorophylla.  
optics_morel_antoine 
 For using the Morel and Antoine optics. This was the default in MOM4.0 for use with chlorophyll data. This scheme is NOT available in MOM4p1 for use with the prognostic biology models, since it has been improved by the Manizza scheme. Default optics_morel_antoine=.false.  
optics_manizza 
 For using the Manizza optics with chlorophyll data. Note that when running with a prognostic biology model, GFDL scientists use the Manizza optics. Default optics_manizza=.false.  
debug_this_module 
 For debugging purposes.  
enforce_sw_frac 
 To ensure the shortwave fraction is monotonically decreasing with depth. Applied only if optics_morel=.true. Default enforce_sw_frac=.true.  
override_f_vis 
 To fix the fraction of incoming shortwave assigned to the visible at 0.57.  
sw_morel_fixed_depths 
 To compute penetration assuming fixed depths via Grd%zw(k) depths. This is strictly incorrect when have undulating free surface and/or generatlized vertical coordinates. This option is here for purposes of legacy, as this was done in MOM4.0 versions. The default is sw_morel_fixed_depths=.false.  
optics_for_uniform_chl 
 To set the coefficients for optical model assuming the chlorophyll has a uniform distribution. Default optics_for_uniform_chl=.false.  
chl_default 
 Default concentration chl_default=0.08 roughly yields Jerlov Type 1A optics.  
zmax_pen 
 Maximum depth of penetration of shortwave radiation. Below this depth, shortwave penetration is exponentially small and so is ignored. This option formerly was useful, since computation of exponentials expensive. But with more modern computers, exponentials are cheap, so the default has been changed from 200 to 1e6, making this option irrelevant. But the option remains both for legacy purposes, and for those computers where exponentials are not cheap. Default zmax_pen=1e6.  
sw_frac_top 
 The fraction of shortwave radiation that should be incorporated into the sw_source array at k=1. The generic treatment in MOM is to assume that shortwave radiation is already contained inside the T_prog(index_temp)%stf field. Hence, to avoid double counting, sw_frac(k=0)=sw_frac_top should=0.0. If one removes shortwave from stf, then set sw_frac_top=1.0. 
Filename: src/mom5/ocean_param/sources/ocean_shortwave_jerlov.F90
Namelist: ocean_shortwave_jerlov_nml
Name 
 Description  

f_vis_in 
 F_vis is the amount of light in the shortwave versus the long wave. F_vis=0.54 on sunny days and F_vis=0.60 on cloudy days. With override_f_vis = .true. F_vis is defined from f_vis_in. We believe, that this effect is in the first exponential in Paulson and Simpson (1977). The default is f_vis_in=1., instead of .57 but it is still possible to define this quantity.  
use_this_module 
 
debug_this_module 
 For debugging purposes.  
enforce_sw_frac 
 To ensure the shortwave fraction is monotonically decreasing with depth.  
override_f_vis 
 With override_f_vis = .true. F_vis is defined from f_vis_in, otherwise it is the shortwave versus the long wave amount of light. The default is .true.  
override_coeff 
 With override_coeff = .true. rpart_in, coef1_in, coef2_in specify the parameters for the double exponential. The default is .false..  
sw_pen_fixed_depths 
 To compute penetration assuming fixed depths via Grd%zw(k) depths. This is strictly incorrect when have undulating free surface or generatlized vertical coordinates. This option is here for purposes of legacy, as this was done in MOM4.0 versions. It saves some compute time if the surface elevation is small compared with the upper cells' thickness. The default is .false.  
jerlov_1 
 
jerlov_2 
 
jerlov_3 
 
jerlov_1a 
 
jerlov_1b 
 
baltic_optics 
 
rpart_in 
 rpart_in = (0..1)  
coef1_in 
 
coef2_in 
 
zmax_pen 
 Maximum depth of penetration of shortwave radiation. Below this depth, shortwave penetration is exponentially small and so is ignored.  
sw_frac_top 
 The fraction of shortwave radiation that should be incorporated into the sw_source array at k=1. The generic treatment in MOM is to assume that shortwave radiation is already contained inside the T_prog(index_temp)%stf field. Hence, to avoid double counting, sw_frac(k=0)=sw_frac_top should=0.0. If one removes shortwave from stf, then set sw_frac_top=1.0. 
Filename: src/mom5/ocean_param/sources/ocean_sponges_eta.F90
Namelist: ocean_sponges_eta_nml
Name 
 Description  

use_this_module 
 For using this module. Default use_this_module=.false. 
Filename: src/mom5/ocean_param/sources/ocean_sponges_tracer.F90
Namelist: ocean_sponges_tracer_nml
Name 
 Description  

damp_coeff_3d 
 For case when damping coefficients are full 3d field of values. Default damp_coeff_3d=.false., which means damping coeffs are 2d horizontal array.  
use_this_module 
 For using this module. Default use_this_module=.false. 
Filename: src/mom5/ocean_param/sources/ocean_sponges_velocity.F90
Namelist: ocean_sponges_velocity_nml
Name 
 Description  

damp_coeff_3d 
 For case when damping coefficients are full 3d field of values. Default damp_coeff_3d=.false., which means damping coeffs are 2d horizontal array.  
use_this_module 
 For using this module. Default use_this_module=.false. 
Filename: src/mom5/ocean_param/sources/ocean_xlandinsert.F90
Namelist: ocean_xlandinsert_nml
Name 
 Description  

verbose_init 
 For verbose initialization information.  
use_this_module 
 Needs to be true in order to use this scheme. Default is false.  
debug_this_module 
 For debugging. 
Filename: src/mom5/ocean_param/sources/ocean_xlandmix.F90
Namelist: ocean_xlandmix_nml
Name 
 Description  

verbose_init 
 For verbose initialization information.  
use_this_module 
 Needs to be true in order to use this scheme. Default is false.  
xlandmix_kmt 
 To allow xlandmixing to occur at k=kmt cell. Default is xlandmix_kmt=.false. 
src/mom5/ocean_param/vertical
Filename: src/mom5/ocean_param/vertical/ocean_convect.F90
Namelist: ocean_convect_nml
Name 
 Description  

use_this_module 
 Must be true to use this module. Default is false.  
convect_ncon 
 If true, will use the old NCON convection scheme from Cox. Retained only for legacy purposes to reproduce very old results.  
convect_full_scalar 
 If true, will use the full convection scheme as implemented at GFDL for scalar machines.  
convect_full_vector 
 If true, will use the full convection scheme as optimized for vector machines by russell.fiedler@csiro.au.  
ncon 
 Number of passes through the NCONscheme. 
Filename: src/mom5/ocean_param/vertical/ocean_form_drag.F90
Namelist: ocean_form_drag_nml
Name 
 Description  

use_form_drag_aiki 
 For using the Aiki form drag approach.  
form_drag_aiki_bottom_layer 
 For implementing the Aiki form drag just in a selected number of bottom layers. Will still insist that the scheme conserves momentum, as a form drag scheme should do. Default form_drag_aiki_bottom_layer=.false.  
form_drag_aiki_scale_by_gradH 
 For scaling the coefficient used by the form drag scheme with the bottom slope.  
form_drag_aiki_gradH_max 
 For scaling setting the maximum of the bottom slope for use with scaling the form drag coefficient. Default form_drag_aiki_gradH_max=.05  
form_drag_aiki_gradH_power 
 For scaling the coefficient used by the form drag scheme with the bottom slope raised to the power "form_drag_aiki_gradH_power".  
form_drag_aiki_bottom_klevels 
 Number of klevels above the bottom that we choose to close the Aiki form drag scheme. Default form_drag_aiki_bottom_klevels=3. This should ideally be less than the minimum number of klevels in the model.  
cprime_aiki 
 Dimensionless parameters from the Aiki etal scheme. Default cprime_aiki=0.3.  
use_form_drag_gbatch 
 For using the Greatbatch form drag approach, which places the contributions from "GM" into the momentum equation. use_form_drag_gbatch, is the traditional transformed Eulerian mean approach as per Greatbatch and Lamb (1990) and Greatbatch (1998). In this approach, we modify visc_cbu so that the the "GMeffects" occur through vertical viscosity. Since thise scheme is experimental, it is not recommended for general use, so we set default use_form_drag_gbatch=.false.  
form_drag_gbatch_surf_layer 
 Logical to enable the use of a diabatic layer over which the eddyinduce velocity is assumed to be constant with depth. Default form_drag_gbatch_surf_layer=.false.  
form_drag_gbatch_alpha_f2 
 For use of a vertical viscosity with the form_drag_gbatch that is equal to visc = form_drag_gbatch_alpha * f^2. This form of the vertical viscosity is used by Ferreira and Marshall, 2006. Default form_drag_gbatch_alpha_f2=.false.  
form_drag_gbatch_f2overN2 
 To compute vertical viscosity according to visc=kappa(f/N)*2 with kappa=gmdiffusivity, f=Coriolis, and N=buoyancy frequency. This is the form suggested by Greatbatch and Lamb (1990). Default form_drag_gbatch_f2overN2=.false.  
form_drag_gbatch_f2overNb2 
 To compute vertical viscosity according to visc=kappa(f/Nb)*2 with kappa=gmdiffusivity, f=Coriolis, and Nb=buoyancy frequency just below the diabatic mixed layer. This is the form suggested by Danabasoglu and Marshall (2007). Default form_drag_gbatch_f2overNb2=.false.  
form_drag_gbatch_f2overNo2 
 To compute vertical viscosity according to visc=kappa(f/No)*2 with kappa=gmdiffusivity, f=Coriolis, and No=constant buoyancy frequency set via namelist. Default form_drag_gbatch_f2overNo2=.false.  
form_drag_gbatch_smooth_N2 
 For vertically smoothing the squared buoyancy frequency for use in computing the vertical viscosity in the form drag approach. Default form_drag_gbatch_smooth_N2=.false.  
form_drag_aiki_scale_by_gm 
 Compute a dimensionless scale function proportional to the GMdiffusivity, for use with the Aiki etal form drag scheme. Default form_drag_aiki_scale_by_gm=.false.  
num_121_passes 
 Number of 121 passes for vertically smoothing the squared buoyancy frequency. Default num_121_passes=1.  
ksurf_blayer_min 
 Minimum number of vertical grid points in the surface turbulent boundary layer for use with form_drag_gbatch_surf_layer=.true. Default ksurf_blayer_min=3.  
form_drag_gbatch_alpha 
 For use of a vertical viscosity with the form_drag_gbatch that is equal to visc = form_drag_gbatch_alpha * f^2. Default form_drag_gbatch_alpha=3e8  
form_drag_gbatch_No 
 To compute vertical viscosity according to visc=kappa(f/No)*2 with kappa=gmdiffusivity, f=Coriolis, and No=constant buoyancy frequency. Default form_drag_gbatch_No=5e3  
visc_cbu_form_drag_max 
 Maximum vertical viscosity used for the form drag contribution to vertical friction from the Greatbatch TEM approach. Default visc_cbu_form_drag_max=1m^2/sec.  
vel_form_drag_max 
 For diagnostic purpuses, maximum form drag eddy induced velocity. Default vel_form_drag_max=1m/sec.  
N_squared_min 
 Minimum sequared buoyancy frequency (N^2) for use in computing the vertical viscosity from the Greatbatch form drag scheme. Default N_squared_min=1e10.  
agm_form_drag 
 
verbose_init 
 For verbose initialization information.  
use_this_module 
 Needs to be true in order to use this scheme. Default is false.  
debug_this_module 
 For debugging. 
Filename: src/mom5/ocean_param/vertical/ocean_vert_chen.F90
Namelist: ocean_vert_chen_nml
Name 
 Description  

visc_cbu_limit 
 Enhanced vertical viscosity due to shear instability  
diff_cbt_limit 
 Enhanced vertical diffusivity due to shear instability  
visc_con_limit 
 
diff_con_limit 
 
visc_cbu_iw 
 Background vertical viscosity  
diff_cbt_iw 
 Background vertical diffusivity. Note that if using BryanLewis as a background diffusivity, then should set diff_cbt_iw=0.0.  
bulk_tm 
 Bulk turblence parameter m_0  
bulk_tn 
 Bulk turblence parameter n_0  
hbl_growth_max 
 Maximum growth rate of kraus mixed layer  
use_this_module 
 Must be true to use this module. Default is false.  
debug_this_module 
 For debugging. Default debug_this_module=.false. 
Filename: src/mom5/ocean_param/vertical/ocean_vert_const.F90
Namelist: ocean_vert_const_nml
Name 
 Description  

use_this_module 
 Must be true to use this module. Default is false.  
kappa_h 
 The constant vertical diffusivity. Used for cases when wanting a spacetime independent diffusivity. The "h" is historical and stands for "heat".  
kappa_m 
 The constant vertical viscosity. Used for cases when wanting a spacetime independent viscosity.  
diff_cbt_limit 
 The largest allowable vertical diffusivity. Of use for cases where vertically unstable columns are stabilized with a large vertical diffusivity. 
Filename: src/mom5/ocean_param/vertical/ocean_vert_gotm.F90
Namelist: ocean_vert_gotm_nml
Name 
 Description  

advect_gotm_method 
 For choosing how to advect the GOTM scalar fields tke and diss. Options are advect_gotm_method='upwind' (the default) advect_gotm_method='sweby'  
use_this_module 
 Must be true to use this module. Default is .false.  
debug_this_module 
 For debugging. Default is .false.  
do_turbulence_gotm 
 For debugging. If do_turbulence_gotm=.false., then will not invoke the GOTM scheme. Will only advect tke and diss using 3d advection scheme. Default is .true., so that will invoke GOTM scheme.  
do_advection_gotm 
 For debugging. If do_advection_gotm=.false., then will not invoke the advection of tke and diss. Default is .true., so that will 3d advect tke and diss.  
write_a_restart 
 Set true to write a restart. False setting only for rare cases where wish to benchmark model without measuring the cost of writing restarts and associated chksums. Default is write_a_restart=.true.  
map_velocity_gotm 
 
map_production_gotm 
 
correct_adv_errors 
 
diff_cbt_min 
 Background diffusivity. Default is 1.0e5.  
visc_cbu_min 
 Background viscosity. Default is 1.0e5.  
z0s 
 Surface roughness length. Default is 1m.  
z0b 
 Bottom roughness length. Default is .002m.  
min_tke 
 Minimum turbulent kinetic energy. Default=1.0e6.  
min_diss 
 Minimum energy dissipation. Default=1.0e10. 
Filename: src/mom5/ocean_param/vertical/ocean_vert_kpp_mom4p0.F90
Namelist: ocean_vert_kpp_mom4p0_nml
Name 
 Description  

Ricr 
 Critical bulk Richardson number. Default from NCAR is 0.3, though this number has a large uncertainty and some find that 1.0 can be of use.  
visc_cbu_limit 
 Enhanced vertical viscosity due to shear instability  
diff_cbt_limit 
 Enhanced vertical diffusivity due to shear instability  
visc_con_limit 
 Enhanced vertical viscosity in regions of convection  
diff_con_limit 
 Enhanced vertical diffusivity in regions of convection  
visc_cbu_iw 
 Background vertical viscosity  
diff_cbt_iw 
 Background vertical diffusivity. Note that if using BryanLewis as a background diffusivity, then should set diff_cbt_iw=0.0.  
concv 
 constant for pure convection (eqn. 23 of Large etal)  
use_this_module 
 Logical switch to enable kpp diffusion. Default is false.  
shear_instability 
 logical switch for shear instability mixing. Default shear_instability=.true.  
double_diffusion 
 Logical switch for doublediffusive mixing. Default double_diffusion=.true.  
wsfc_combine_runoff_calve 
 For computing wsfc as in the mom4p0d code, where we combine the runoff+calving into a single field called river. The alternative keeps the fields separate, as would be appropriate for a land model that separately tracks the tracer content in the calving and runoff. Default wsfc_combine_runoff_calve=.true., as this will recover the previous behaviour, to the bit.  
non_local_kpp 
 logical switch for enabling the nonlocal mixing aspect of kpp. Default is .true. as this is what the original KPP scheme suggests.  
smooth_blmc 
 Smooth boundary layer diffusitivies to remove grid scale noise. Such noise is apparent in the diagnosed mixed layer depth as well as the SST, especially when running coupled models where forcing has high temporal frequency.  
coastal_tidal_mix 
 For adding an extra vertical shear associated with tidal mixing. This method has found to be of use for mixing near shelves.  
sigma_tide 
 The sigma constant in the MunkAnderson scheme Default sigma_tide=3.0  
p_tide 
 The p constant in the MunkAnderson scheme Default p_tide=0.25  
int_tidal_mix 
 For adding an internal tidal mixing over rough topography. This method has found to be of use for mixing in the rough topography in open ocean. Default int_tidal_mix=.false.  
int_tide_zeta1 
 Shallow depth for computation of internal tide. Default int_tide_zeta1=300.0  
int_tide_zeta2 
 Deeper depth for computation of internal tide. Default int_tide_zeta2=1800.0  
int_tide_min_depth 
 Minimum depth for internal tide mixing to be computed. Default int_tide_min_depth=100.0  
int_tide_q 
 Fraction of internal tide energy locally dissipated. Default int_tide_q=.33333  
int_tide_gamma 
 Dimensionless efficiency for converting energy dissipation to diffusivity. Default int_tide_gamma=0.2 
Filename: src/mom5/ocean_param/vertical/ocean_vert_kpp_mom4p1.F90
Namelist: ocean_vert_kpp_mom4p1_nml
Name 
 Description  

Ricr 
 Critical bulk Richardson number. Default from NCAR is 0.3, though this number has a large uncertainty and some find that 1.0 can be of use.  
visc_cbu_limit 
 Enhanced vertical viscosity due to shear instability  
diff_cbt_limit 
 Enhanced vertical diffusivity due to shear instability  
visc_con_limit 
 Enhanced vertical viscosity in regions of convection  
diff_con_limit 
 Enhanced vertical diffusivity in regions of convection  
visc_cbu_iw 
 Background vertical viscosity  
diff_cbt_iw 
 Background vertical diffusivity. Note that if using BryanLewis as a background diffusivity, then should set diff_cbt_iw=0.0.  
concv 
 constant for pure convection (eqn. 23 of Large etal)  
kl_min 
 Lower loop index for finding new kbl. Needed for use with certain tests of OBC, where kl_min=1 needed, whereas default in original implementation has kl_min=2. Default in MOM is kl_min=2.  
kbl_standard_method 
 For computing kbl as in the MOM4p0d code, which is taken from the original NCAR scheme. If false, then will slightly modify the logic. The modified logic has been found necessary when running with as few as two grid cells in the vertical. Default kbl_standard_method=.true.  
use_this_module 
 Logical switch to enable kpp diffusion. Default is false.  
shear_instability 
 logical switch for shear instability mixing. Default shear_instability=.true.  
double_diffusion 
 Logical switch for doublediffusive mixing. Default double_diffusion=.true.  
limit_ghats 
 Limits the nonlocal vertical tracer flux to the value of the tracer surface flux. Default limit_ghats=.false.  
limit_with_hekman 
 Limiting the boundary layer depth with the Ekman depth may result in a shallow boundary layer. In this case the internal values of the vertical mixing and viscosity coefficients may be large. This results in unrealistically large nonlocal vertical mixing Default limit_with_hekman=.true.  
radiation_large 
 Remove the shortwave radiation leaving the boundary layer to the ocean interior (hence, not absorbed in the boundary layer) from nonlocal vertical heat flux Default radiation_large=.false.  
radiation_zero 
 Remove the all shortwave radiation from nonlocal vertical heat flux. Default radiation_zero=.false.  
radiation_iow 
 Keep only the shortwave radiation absorbed between the surface and a certain level in nonlocal vertical heat flux through this level. Default radiation_iow=.false.  
hbl_with_rit 
 The default method for determination of the boundary layer depth may fail if the water column is instable (negative Richardson number) below or above the layer that contains the diagnosed hbl. With hbl_with_rit=.true. the search for the boundary layer depth is continued downward in this case even if the bulk Richardson number exceeds the critical value. This removes a lot of noise from the boundary layer depth. Default hbl_with_rit=.false.  
use_sbl_bottom_flux 
 
wsfc_combine_runoff_calve 
 For computing wsfc as in the MOM4p0d code, where we combine the runoff+calving into a single field called river. The alternative keeps the fields separate, as would be appropriate for a land model that separately tracks the tracer content in the calving and runoff. Default wsfc_combine_runoff_calve=.true., as this will recover the previous behaviour, to the bit.  
bvf_from_below 
 Use BVfreq. at the cell bottom instead of the cell top as in Danabasoglu et al. (2006). Default bvf_from_below=.false., as this will recover older behaviour.  
variable_vtc 
 Make vtc dependent on BVfreq. as in Danabasoglu et al. (2006). Default variable_vtc=.false., as this will recover older behaviour.  
use_max_shear 
 Use maximum shear instead of 4point average (as in Danabasoglu et al. (2006)). Default use_max_shear=.false., as this will recover older behaviour.  
linear_hbl 
 Use linear interpolation to find the position of hbl. If set to false, then use the quadratic interpolation as in Danabasoglu et al. (2006). The quadratic approach generally yields a slightly deeper surface boundary layer. Default linear_hbl=.true., as this will recover older behaviour.  
calc_visc_on_cgrid 
 
smooth_ri_kmax_eq_kmu 
 When smoothing the Richardson number, we do so over a vertical column with max klevels set by either kmt or kmu. The proper approach is kmu, since we are smoothing riu. But for backwards compatibility, we default to smooth_ri_kmax_eq_kmu=.false.  
non_local_kpp 
 logical switch for enabling the nonlocal mixing aspect of kpp. Default is .true. as this is what the original KPP scheme suggests.  
smooth_blmc 
 Smooth boundary layer diffusitivies to remove grid scale noise. Such noise is apparent in the diagnosed mixed layer depth as well as the SST, especially when running coupled models where forcing has high temporal frequency. Default smooth_blmc=.false. Warning: This smoother can cause some problems with ghat in regions of zero surface forcing. To understand details, one needs the paper of Large et al. Vertical diffusion has the general form wx = K(x_z  ghats) In the surface layer a vertical scale function ws is estimated. We have K ~ ws and ghats ~1/ws. If wind stress is zero the vertical scale ws becomes zero too. Hence, ghats is very large (something finite, since it is divided by ws+epsln). Now it may happen, that the bouyancy flux becomes negative (~ 1030). This enables the nonlocal scheme. Because the mixing coefficient in the surface boundary layer scales with ws the corresponding time tendency should be of the order (1/ws * ws = finite). However, if smooth_blmc is enabled, it may happen, that from neighbouring points with different mixing depth a finite value for the mixing coefficient leaks in. In this case the tracer time tendency from the nonlocal scheme becomes huge and the model fails. The smoother destroys the consistency between ghats and diff_cbt. In most cases this should not matter, but the example shows, that sudden model failure is possible under otherwise stable and smooth conditions.  
debug_this_module 
 Logical switch for debugging. Default debug_this_module=.false. 
Filename: src/mom5/ocean_param/vertical/ocean_vert_kpp_test.F90
Namelist: ocean_vert_kpp_test_nml
Name 
 Description  

Ricr 
 Critical bulk Richardson number. Default from NCAR is 0.3, though this number has a large uncertainty and some find that 1.0 can be of use.  
visc_cbu_limit 
 Enhanced vertical viscosity due to shear instability  
diff_cbt_limit 
 Enhanced vertical diffusivity due to shear instability  
visc_con_limit 
 Enhanced vertical viscosity in regions of convection  
diff_con_limit 
 Enhanced vertical diffusivity in regions of convection  
visc_cbu_iw 
 Background vertical viscosity  
diff_cbt_iw 
 Background vertical diffusivity. Note that if using BryanLewis as a background diffusivity, then should set diff_cbt_iw=0.0.  
concv 
 constant for pure convection (eqn. 23 of Large etal)  
kl_min 
 Lower loop index for finding new kbl. Needed for use with certain tests of OBC, where kl_min=1 needed, whereas default in original implementation has kl_min=2. Default in MOM is kl_min=2.  
kbl_standard_method 
 For computing kbl as in the MOM4p0d code, which is taken from the original NCAR scheme. If false, then will slightly modify the logic. The modified logic has been found necessary when running with as few as two grid cells in the vertical. Default kbl_standard_method=.true.  
use_this_module 
 Logical switch to enable kpp diffusion. Default is false.  
shear_instability 
 logical switch for shear instability mixing. Default shear_instability=.true.  
double_diffusion 
 Logical switch for doublediffusive mixing. Default double_diffusion=.true.  
limit_ghats 
 Limits the nonlocal vertical tracer flux to the value of the tracer surface flux. Default limit_ghats=.false.  
limit_with_hekman 
 Limiting the boundary layer depth with the Ekman depth may result in a shallow boundary layer. In this case the internal values of the vertical mixing and viscosity coefficients may be large. This results in unrealistically large nonlocal vertical mixing Default limit_with_hekman=.true.  
radiation_large 
 Remove the shortwave radiation leaving the boundary layer to the ocean interior (hence, not absorbed in the boundary layer) from nonlocal vertical heat flux Default radiation_large=.false.  
radiation_zero 
 Remove the all shortwave radiation from nonlocal vertical heat flux. Default radiation_zero=.false.  
radiation_iow 
 Keep only the shortwave radiation absorbed between the surface and a certain level in nonlocal vertical heat flux through this level. Default radiation_iow=.false.  
hbl_with_rit 
 The default method for determination of the boundary layer depth may fail if the water column is instable (negative Richardson number) below or above the layer that contains the diagnosed hbl. With hbl_with_rit=.true. the search for the boundary layer depth is continued downward in this case even if the bulk Richardson number exceeds the critical value. This removes a lot of noise from the boundary layer depth. Default hbl_with_rit=.false.  
use_sbl_bottom_flux 
 
wsfc_combine_runoff_calve 
 For computing wsfc as in the MOM4p0d code, where we combine the runoff+calving into a single field called river. The alternative keeps the fields separate, as would be appropriate for a land model that separately tracks the tracer content in the calving and runoff. Default wsfc_combine_runoff_calve=.true., as this will recover the previous behaviour, to the bit.  
bvf_from_below 
 Use BVfreq. at the cell bottom instead of the cell top as in Danabasoglu et al. (2006). Default bvf_from_below=.false., as this will recover older behaviour.  
variable_vtc 
 Make vtc dependent on BVfreq. as in Danabasoglu et al. (2006). Default variable_vtc=.false., as this will recover older behaviour.  
use_max_shear 
 Use maximum shear instead of 4point average (as in Danabasoglu et al. (2006)). Default use_max_shear=.false., as this will recover legacy behaviour.  
linear_hbl 
 Use linear interpolation to find the position of hbl. If set to false, then use the quadratic interpolation as in Danabasoglu et al. (2006). The quadratic approach generally yields a slightly deeper surface boundary layer. Default linear_hbl=.true., as this will recover older behaviour.  
smooth_ri_kmax_eq_kmu 
 When smoothing the Richardson number, we do so over a vertical column with max klevels set by either kmt or kmu. The proper approach is kmu, since we are smoothing riu. But for backwards compatibility, we default to smooth_ri_kmax_eq_kmu=.false.  
non_local_kpp 
 logical switch for enabling the nonlocal mixing aspect of kpp. Default is .true. as this is what the original KPP scheme suggests.  
smooth_blmc 
 Smooth boundary layer diffusitivies to remove grid scale noise. Such noise is apparent in the diagnosed mixed layer depth as well as the SST, especially when running coupled models where forcing has high temporal frequency. Default smooth_blmc=.false. Warning: This smoother can cause some problems with ghat in regions of zero surface forcing. To understand details, one needs the paper of Large et al. Vertical diffusion has the general form wx = K(x_z  ghats) In the surface layer a vertical scale function ws is estimated. We have K ~ ws and ghats ~1/ws. If wind stress is zero the vertical scale ws becomes zero too. Hence, ghats is very large (something finite, since it is divided by ws+epsln). Now it may happen, that the bouyancy flux becomes negative (~ 1030). This enables the nonlocal scheme. Because the mixing coefficient in the surface boundary layer scales with ws the corresponding time tendency should be of the order (1/ws * ws = finite). However, if smooth_blmc is enabled, it may happen, that from neighbouring points with different mixing depth a finite value for the mixing coefficient leaks in. In this case the tracer time tendency from the nonlocal scheme becomes huge and the model fails. The smoother destroys the consistency between ghats and diff_cbt. In most cases this should not matter, but the example shows, that sudden model failure is possible under otherwise stable and smooth conditions.  
debug_this_module 
 Logical switch for debugging. Default debug_this_module=.false. 
Filename: src/mom5/ocean_param/vertical/ocean_vert_mix.F90
Namelist: ocean_vert_mix_nml
Name 
 Description  

vert_mix_scheme 
 To determine the vertical mixing scheme: "const", "kpp", "kpp_mom4p0","kpp_mom4p1", "chen", "pp", or "gotm".  
aidif 
 aidif=1 for implicit in time solution of the vertical mixing equation. aidif=0 for explicit in time solution of the vertical mixing equation. semiimplicit method with 0 < aidif < 1 is not fully supported in MOM.  
vert_diff_back_via_max 
 If .true. then include a static background diffusivity via the max function, as used in mom4p0d. The alternative is via simply adding the background to the diffusivity obtained via other approaches. This option remains for legacy. Default is vert_diff_back_via_max=.true.  
use_explicit_vert_diffuse 
 Must be true to use timeexplicit vertical tracer diffusion.  
bryan_lewis_diffusivity 
 If .true. then add a BryanLewis background to the diffusivity. This background is a timeindependent function of depth. This diffusivity is NOT used when have use_pp_vert_mix_coeff=.true. This scheme should NOT be used if HWF is used.  
bryan_lewis_lat_depend 
 If .true. then allow for BryanLewis background to be different outside of a tropical band than inside the band.  
bryan_lewis_lat_transition 
 North/South latitude where transition from BryanLewis values in the tropic to those in the higher latitudes.  
vert_visc_back 
 If .true. then include a static depth dependent vertical viscosity which is used only if running w/ constant vertical viscosity scheme. Standard application is when have a model with fine vertical resolution, yet no mixed layer scheme. Wind stress must be spread deeper than the top cell, or the model may go unstable, or at the least it will produce spuriously large vertical shears.  
visc_cbu_back_max 
 For use in setting background vertical viscosity.  
visc_cbu_back_min 
 For use in setting background vertical viscosity.  
visc_cbu_back_zmid 
 Midpoint of tanh function used to define background vertical viscosity.  
visc_cbu_back_zwid 
 Width of tanh function used to define background vertical viscosity.  
diff_cbt_tanh 
 For enabling tanh background vertical diffusivity profile. Default diff_cbt_tanh=.false.  
diff_cbt_tanh_max 
 For use in setting background vertical diffusivity. Default diff_cbt_tanh_max=1e3.  
diff_cbt_tanh_min 
 For use in setting background vertical diffusivity. Default diff_cbt_tanh_min=2e5.  
diff_cbt_tanh_zmid 
 Midpoint of tanh function used to define background vertical diffusivity. Default diff_cbt_tanh_zmid=150.0.  
diff_cbt_tanh_zwid 
 Width of tanh function used to define background vertical diffusivity. Default diff_cbt_tanh_zwid=30.0.  
use_diff_cbt_table 
 If .true., then read in a table that specifies (i,j,ktop>kbottom) and the diffusivity. This method is useful when aiming to mix vertically at points where do crossland insertion or where may wish to enhance mixing at river mouths.  
linear_taper_diff_cbt_table 
 If .true., then linear taper the diff_cbt_table value from so that it gets smaller with depth.  
hwf_diffusivity 
 3D background diffusivity which gets smaller in equatorial region. Based on the work of Henyey etal (1986). This scheme should NOT be used if BryanLewis is used. Default hwf_diffusivity=.false.  
hwf_diffusivity_3d 
 3D background diffusivity which gets smaller in equatorial region. Based on the work of Henyey etal (1986). This form has not been used much at GFDL, with preference given to a simpler twodimensional (depth independent) form assessed with the default hwf_diffusivity_3d=.false.  
hwf_depth_transition 
 Depth of transition for hwf scheme. The HWF method actually has no depth dependence. But we include the atan depth dependency from BryanLewis, for those cases where we wish to replace BryanLewis with the HWF scheme. To get the usual BryanLewis transition, set hwf_depth_transition=2500.0. However, since we often use hwf in the presence of tide mixing, we do not wish to have any depth dependence, in which case the default is hwf_depth_transition=2500.0e4.  
hwf_min_diffusivity 
 Minimum diffusivity for the HWF scheme. Default hwf_min_diffusivity=2e6.  
hwf_30_diffusivity 
 Diffusivity at 30deg latitude for the HWF scheme. Default hwf_30_diffusivity=2e5.  
hwf_N0_2Omega 
 Ratio of the typical Buoyancy frequency to twice the earth's rotation period. Default hwf_N0_2Omega=20.0.  
vmix_rescale_nonbouss 
 To rescale the vertical mixing coefficients by rho0/rho in order to bring the effects from vertical diffusion in a nonBoussinesq model more in line with that from a Boussinesq model. Default vmix_rescale_nonbouss=.false.  
vmix_set_min_dissipation 
 To set a minimum dissipation rate. This scheme will compute the dissipation from the full diffusivity. If the resulting dissipation is smaller than a specified dissipation, then the diffusivity will be locally increased so that the min dissipation is maintained. Default vmix_set_min_dissipation=.false.  
vmix_min_diss_const 
 Minimum dissipation rate as a constant. Default vmix_min_diss_const=1e7.  
vmix_min_diss_bvfreq_scale 
 Scaling use to set the minimum dissipation rate as determined by the local stratification. Default vmix_min_diss_bvfreq_scale=6e4.  
vmix_min_diss_flux_ri_max 
 Maximum flux Richardson number for computation of diffusivity from dissipation. Default vmix_min_diss_flux_ri_max=0.2.  
smooth_rho_N2 
 
num_121_passes 
 
debug_this_module 
 For debugging purposes.  
verbose_init 
 For verbose writes during initialization.  
quebec_2009_10_bug 

Filename: src/mom5/ocean_param/vertical/ocean_vert_pp.F90
Namelist: ocean_vert_pp_nml
Name 
 Description  

use_this_module 
 Must be true to use this module. Default is false.  
fricmx 
 Maximum mixing  
wndmix 
 Minimum viscosity at bottom of 1st level to simulate missing high frequency windstress components.  
diff_cbt_back_pp 
 Spacetime independent background vertical diffusivity thought to be that arising from internal waves. Note that if using BryanLewis background diffusivity, then should set diff_cbt_back_pp=0.0.  
visc_cbu_back_pp 
 Background vertical viscosity  
visc_cbu_limit 
 
diff_cbt_limit 

Filename: src/mom5/ocean_param/vertical/ocean_vert_tidal.F90
Namelist: ocean_vert_tidal_nml
Name 
 Description  

use_this_module 
 
use_legacy_methods 
 To compute all mixing coefficients using legacy methods. There are good reasons to prefer the newer approaches, which motivates setting the default use_legacy_methods=.false.  
debug_this_module 
 For debugging purposes.  
use_wave_dissipation 
 
use_drag_dissipation 
 
use_leewave_dissipation 
 
read_roughness 
 If .true. then read in bottom roughness amplitude h, where roughness_length = kappa*h^2, with kappa a representative roughness wavelength and h a representative topographic amplitude. This information is used for the Simmons etal wave dissipation parameterization.  
read_wave_dissipation 
 If .true. then read in wave dissipation computed from Jayne and St.Laurent (2001) tide model (or another model). Default read_wave_dissipation=.false.  
read_leewave_dissipation 
 If .true. then read in leewave dissipation from a file. Default read_leewave_dissipation=.false.  
reading_roughness_amp 
 If .true., then the field in the roughness file is roughness_amp=h, where roughness_length=kappa*h^2. This information is used for the Simmons etal wave dissipation parameterization. Default reading_roughness_amp=.false.  
reading_roughness_length 
 If .true., then the field in the roughness file is roughness_length = kappa*h^2, with kappa a representative roughness wavelength and h a representative topographic amplitude. This information is used for the Simmons etal wave dissipation parameterization. Default reading_roughness_length=.false.  
read_tide_speed 
 If .true. then read in tidal speed (m/s) from a tidal model. This information is used for the computing the energy dissipation from tides. scheme.  
wave_diffusivity_monotonic 
 Enforce a monotonic decay of the wave dissipation diffusivity, with largest values near bottom and smaller as move to shallower water. This behaviour is not guaranteed in general, since the division by the buoyancy frequency can give nonmonotone diffusivities. Default wave_diffusivity_monotonic=.true.  
tide_speed_data_on_t_grid 
 To set the input tide speed data on Tgrid, set to true. Otherwise, set to false. Default tide_speed_data_on_t_grid=.true.  
fixed_wave_dissipation 
 If .true. then fix the wave dissipation from that read in by the tide model, such as Jayne and St.Laurent (2001). This power dissipation will be employed for computing wave induced mixing. Default fixed_wave_dissipation=.false.  
mixing_efficiency_n2depend 
 Allow for mixing efficiency to be a function of N^2/(N^2+Omega^2), which is close to unity except in regions where N is very small. Default mixing_efficiency_n2depend=.false.  
drag_dissipation_efold 
 For setting an efolding whereby the drag dissipation diffusivity exponentially decreases as move upward in the water column. There are good reasons to set this logical to true, as the scheme can produce unreasonably large diffusivities far from the bottom, if there are tides in the deep ocean. Default drag_dissipation_efold=.true.  
smooth_bvfreq_bottom 
 For smoothing the buoyancy frequency at the bottom. Default smooth_bvfreq_bottom=.true.  
drag_mask_deep 
 For masking out the deep ocean regions for the drag dissipation scheme. This scheme is meant to apply only in shallow shelves, so it is physically relevant to mask it out. We apply a mask as determined by the ratio of the frictional tide depth scale and the total ocean depth. Default drag_mask_deep=.true.  
smooth_rho_N2 
 For smoothing the rho_N2 field via a 121 filter in vertical. This is useful to produce smoother diffusivities. Default is smooth_rho_N2=.true.  
num_121_passes 
 Number of passes of 121 filter in vertical for smoothing the rho_N2 field. Default num_121_passes=1.  
drag_mask_deep_ratio 
 For determining the drag dissipation mask. The mask = 0 in regions where tide_depth/total_depth < drag_mask_deep_ratio Default drag_mask_deep_ratio=0.1  
roughness_scale 
 Scale for the roughness that characterizes the roughness affecting the tidal dissipation process. Used for setting roughness_length via roughness_length = kappa*h^2, with kappa = 2pi/(roughness_scale) and h=topography amplitude. Default roughness_scale=1e4 as in Jayne and St. Laurent (2001)  
default_roughness_length 
 Default value for kappa*h^2 = roughness length for use in the absence of a roughness length dataset. MOM default is default_roughness_length=25.0m.  
default_tide_speed 
 Default value for tidal speed for use in the absence of a value from a tidal model.  
shelf_depth_cutoff 
 For use in defining a mask for the Simmons scheme, with depths shallower than shelf_depth_cutoff removed from the scheme. shelf_depth_cutoff=1000m in Simmons etal. Default shelf_depth_cutoff=1000m so there is no cutoff.  
decay_scale 
 In the Simmons etal vertical profile function, the exponential decay scale is determined by this parameter. Default = 500m as in Simmons etal (2004). This vertical profile determines how to deposit the internal wave energy within a vertical column.  
tidal_diss_efficiency 
 Fraction of barotropic tidal energy that is dissipated locally, as opposed to that which propagates away. Default=1/3 as in Simmons etal (2004).  
mixing_efficiency 
 Fraction of energy that is dissipated which is converted into dianeutral diffusion of tracer. Default=0.2 based on Osborn (1980).  
munk_anderson_p 
 The p constant in the MunkAnderson scheme employed by Lee etal. This parameter is minus the "p_tide" parameter in the KPP schemes. Default munk_anderson_p=0.25  
munk_anderson_sigma 
 The sigma constant in the MunkAnderson scheme employed by Lee etal. This parameter is called "sigma_tide" in the KPP schemes. Default munk_anderson_sigma=3.0  
bottom_drag_cd 
 Bottom drag coefficient from Lee etal. Default bottom_drag_cd=2.4e3  
background_diffusivity 
 Background vertical diffusivity not accounted for by the tidal schemes nor any other scheme such as KPP. Default=0.1e4.  
background_viscosity 
 Background vertical viscosity not accounted for by the tidal schemes nor any other scheme such as KPP. Default=0.1e4.  
max_wave_diffusivity 
 Maximum tracer diffusivity deduced from the wave dissipation scheme from Simmons etal. Default = 5.e3 m^2/sec.  
max_drag_diffusivity 
 Maximum tracer diffusivity deduced from the drag dissipation scheme from Lee etal. Default = 5.e3 m^2/sec.  
drhodz_min 
 Minimum absolute value for the drhodz used to compute N^2 and rhoN2. This value is needed in order to regularize the diffusivity computed from the tide mixing schemes. Default is drhodz_min=1e10, which is much smaller than the (N^2)min = 10^8 sec^2 used by Simmons etal. There is some sensitivity to the choice of drhodz_min, with larger values leading to reduced deep diffusivities, due to the N^2 dependence in the diffusivity calculation.  
speed_min 
 For the drag scheme, we set the diffusivity as well as the Richardson number to zero if the tide speed is less than speed_min. This serves two purposes: 1/ to reduce overflows in some of the diagnostics; 2/ to set the drag induced diffusivity to zero in regions where the tide speed is small. Default speed_min=5e3m/s.  
wave_energy_flux_max 
 The maximum mechanical energy from internal tides that is provided for mixing. Default wave_energy_flux_max=0.1Watt/m^2.  
drag_dissipation_tide_period 
 Characteristic tide period for use in computing efolding depth for the tide drag scheme. Default = 126060 = 12hours for semidiurnal tide.  
vel_micom_smooth 
 Velocity scale that is used for computing the MICOM Laplacian mixing coefficient used in the Laplacian smoothing of diffusivities. Default vel_micom_smooth=0.2.  
drag_dissipation_use_cdbot 
 For using the cdbot_array computed from ocean_bbc.F90 module. Default drag_dissipation_use_cdbot=.false., as this is consistent with earlier simulations. 
Filename: src/mom5/ocean_param/vertical/ocean_vert_util.F90
Namelist: ocean_vert_util_nml
Name 
 Description  

smooth_n2 
 For vertical smoothing the N2 calculation for Richardson number. Default smooth_n2 = .true.  
smooth_ri_number 
 For vertical smoothing richardson number. Default smooth_ri_number = .true.  
num_n2_smooth 
 For vertical smoothing N2 for Richardson number. Default num_n2_smooth = 1.  
num_ri_smooth 
 For vertical smoothing richardson number. Default num_ri_smooth = 1.  
debug_this_module 
 For debugging purposes. 
src/mom5/ocean_tracers
Filename: src/mom5/ocean_tracers/ocean_frazil.F90
Namelist: ocean_frazil_nml
Name 
 Description  

use_this_module 
 If true, then compute frazil heating.  
debug_this_module 
 For debugging this module  
freezing_temp_simple 
 To use the simplified freezing point temperature of seawater, as used in MOM4.0.  
freezing_temp_preteos10 
 
freezing_temp_teos10 
 
air_saturated_water 
 
frazil_only_in_surface 
 For typical case where compute frazil heating only in the surface grid cell. Will assume the gauge pressure is zero in this case when computing freezing temperature.  
frazil_factor 
 This factor accounts for possibly different time stepping used in the sea ice model relative to the ocean model. If seaice and ocean use same time stepping schemes, then frazil_factor=1.0. If seaice uses a twolevel scheme and ocean a threelevel leapfrog, then frazil_factor=0.5. Default is 1.0 since the GFDL sea ice model SIS uses a twolevel time stepping scheme and MOM defaults to a staggered twolevel scheme. 
Filename: src/mom5/ocean_tracers/ocean_passive.F90
Namelist: ocean_passive_nml
Name 
 Description  

debug_this_module 
 For debugging the module.  
common_init_condition 
 Default for the tracer initial conditions. Options are the following: commoninit_condition='level' common_init_condition='wall' common_init_condition='patch' common_init_condition='patch'klevel, with "klevel" an integer for the klevel that will place the patch. common_init_condition='exponential' common_init_condition='shelfbowl' common_init_condition='rho_surface' common_init_condition='temp_sq_init' common_init_condition='salt_sq_init' Default=common_init_condition='patch'  
layer_value 
 Value of tracer concentration within the layer. Default=1.0.  
layer_ztop 
 Depth at the top of the tracer layer.  
layer_zbot 
 Depth at the bottom of the tracer layer.  
wall_value 
 Value of tracer concentration within the wall. Default=1.0.  
wall_ratio_south 
 Ratio of the full jrange, northward of which we place the wall.  
wall_ratio_north 
 Ratio of the full jrange, southward of which we place the wall.  
patch_value 
 Value of the tracer concentration within a patch. Default=1.0.  
patch_ztop 
 Depth at the top of the tracer patch.  
patch_zbot 
 Depth at the bottom of the tracer patch.  
patch_ratio1 
 For setting position of tracer patch.  
patch_ratio2 
 For setting position of tracer patch.  
patch_init_klevel_gaussian 
 To initialize on the klevel with a gaussian region. Default=patch_init_klevel_gaussian=.false.  
shelfbowl_north 
 
shelf_value 
 
efold_depth 
 The efolding depth used for exponential tracer profile. Default=1000.0.  
exponential_value 
 The tracer value at zero depth when choosing the exponential profile. Default=1.0. 
Filename: src/mom5/ocean_tracers/ocean_tempsalt.F90
Namelist: ocean_tempsalt_nml
Name 
 Description  

reinit_ts_with_ideal 
 For setting up an ideal temperature and salinity profile that is generated in the model. This profile can be generated after the model has already been running, hence the name "reinit" for "reinitialize."  
reinit_ts_with_ideal_efold 
 For setting efolding of reinitialized temp and salinity profile. Default reinit_ts_with_ideal_efold=1000.  
reinit_ts_with_ideal_tvalue 
 For setting the reinitialized temperature value using the ideal profile. Default reinit_ts_with_ideal_tvalue = 10.0  
reinit_ts_with_ideal_svalue 
 For setting the reinitialized temperature value using the ideal profile. Default reinit_ts_with_ideal_svalue = 30.0  
t_min 
 Minimum potential/conservative temperature below which we gracefully bring down the model.  
t_max 
 Maximum potential/conservative temperature above which we gracefully bring down the model.  
s_min 
 Minimum salinity below which we gracefully bring down the model.  
s_max 
 Maximum salinity below which we gracefully bring down the model.  
t_min_limit 
 Minimum potential/conservative temperature below which will employ upwind advection instead of quicker, and horizontal diffusion instead of neutral physics.  
t_max_limit 
 Maximum potential/conservative temperature above which will employ upwind advection instead of quicker, and horizontal diffusion instead of neutral physics.  
s_min_limit 
 Minimum salinity below which will employ upwind advection instead of quicker, and horizontal diffusion instead of neutral physics.  
s_max_limit 
 Maximum salinity below which will employ upwind advection instead of quicker, and horizontal diffusion instead of neutral physics.  
debug_this_module 
 For debugging the module.  
pottemp_2nd_iteration 
 For taking extra iteration in computation of potential temperature from conservative temperature and salinity. Default is true.  
pottemp_equal_contemp 
 For certain idealized cases where the difference between potential temperature and conservative temperature is irrelevant. Default=.false.  
teos10 
 For choosing whether to use the TEOS10 equation of state. This usage requires conservative temperature as the temperature variable, and two salinity variables: Preformed Salinity and Absolute Salinity anomaly. Default teos10=.false.  
temperature_variable 
 For choosing the temperature variable used in the model. Choices are 'conservative_temp' and 'potential_temp'. Since conservative temperature is more accurate, it is the default. 
Filename: src/mom5/ocean_tracers/ocean_tracer.F90
Namelist: ocean_tracer_nml
Name 
 Description  

zero_tendency 
 If true, then will freeze the tracer fields.  
zero_tracer_source 
 To remove the T_prog%source contribution to tracer evolution. For debugging purposes. Default zero_tracer_source=.false.  
debug_this_module 
 For debugging the tracer module  
tmask_limit_ts_same 
 tmask_limit is derived separately for the tracers. However, it may be appropriate to have the mask be the same for temp and salinity, in which case the neutral physics fluxes are selfconsistent. But for some cases, such as when running with linear eos, may not wish to have the temp and salinity coupled when computing the mask.  
write_a_restart 
 Set true to write a restart. False setting only for rare cases where wish to benchmark model without measuring the cost of writing restarts and associated chksums. Default is write_a_restart=.true.  
remap_depth_to_s_init 
 For remapping initial tracer distributions, generally determined according to depth vertical coordinates using the mom preprocessing schemes, onto scoordinates. This method is of use for initializing terrain following coordinate simulations with mom.  
inflow_nboundary 
 For adding an inflow transport from the northern boundary which brings in temp and salinity according to inflow data files. Default is inflow_nboundary=.false.  
interpolate_tprog_to_pbott 
 To linear interpolate the initial conditions for prognostic tracers to the partial bottom cells. Default interpolate_tprog_to_pbott=.true.  
interpolate_tdiag_to_pbott 
 To linear interpolate the initial conditions for diagnostic tracers to the partial bottom cells. Default interpolate_tdiag_to_pbott=.false.  
limit_age_tracer 
 Limit the values of age tracer to be less than total run time and greater than zero. Default limit_age_tracer=.false.  
frazil_heating_before_vphysics 
 For computing frazil heating before the implicit vertical physics (which includes boundary fluxes), and before vertical convection. This is the order that CM2.0 and CM2.1 performed their calculations of frazil. It is arguable that one should NOT do frazil until the end of a time step, after vertical physics and after surface boundary fluxes. Default frazil_heating_before_vphysics=.false.  
frazil_heating_after_vphysics 
 For computing frazil heating after the implicit vertical physics (which includes boundary fluxes), and after vertical convection. This is the recommended method. Default frazil_heating_after_vphysics=.false.  
compute_tmask_limit_on 
 For updating the tmaks_limit array. This calculation is recommended for the following physics and advection schemes: 1/ quicker advection 2/ neutral physics 3/ submesoscale closure. The default is compute_tmask_limit_on=.true., but if none of the above schemes is used, then some time savings can be realized by setting compute_tmask_limit_on=.false.  
use_tempsalt_check_range 
 To call a check to see that temperature and salinity are within their preselected range. Default use_tempsalt_check_range=.false. since this check may incur some cost that users should be aware of.  
age_tracer_max_init 
 Initial maximum age tracer. This nml provides the ability to start an integration with an age tracer that is not initialized to zero, say if we took an age tracer from another spinup. Default age_tracer_max_init=0.0.  
ocean_tpm_debug 
 For debugging ocean tracer package manager. 
Filename: src/mom5/ocean_tracers/ocean_tracer_advect.F90
Namelist: ocean_tracer_advect_nml
Name 
 Description  

read_basin_mask 
 For reading in a mask that selects regions of the domain for performing gyre and overturning diagnostics. The basinmask convention used at GFDL has Southern=1.0,Atlantic=2.0,Pacific=3.0,Arctic=4.0,Indian=5.0 Default read_basin_mask=.false., whereby basin_mask is set to tmask(k=1).  
limit_with_upwind 
 If true, will compute tracer fluxes entering a cell using upwind if the tracer value is outside a specified range. Implemented only for quick at this time. This is an ad hoc and incomplete attempt to maintain monotonicity with the quicker scheme.  
debug_this_module 
 For debugging  
advect_sweby_all 
 For running all tracers with sweby, thereby utilizing a bitwise same routine that reorganizes loops and can be faster for certain configurations. Default advect_sweby_all=.false.  
zero_tracer_advect_horz 
 For debugging. Set to .true. to turn off horizontal advection.  
zero_tracer_advect_vert 
 For debugging. Set to .true. to turn off vertical advection.  
write_a_restart 
 Set true to write a restart. False setting only for rare cases where wish to benchmark model without measuring the cost of writing restarts and associated chksums. Default is write_a_restart=.true.  
psom_limit_prather 
 For running with the original Prather limiter for the PSOM scheme. The limiter is positive definite, but not monotonic. This limiter is NOT recommended for most applications. The default is psom_limit_prather=.false., since we prefer to use the limiter from Merryfield and Holloway (2003).  
async_domain_update 

src/mom5/ocean_wave
Filename: src/mom5/ocean_wave/ocean_wave.F90
Namelist: ocean_wave_nml
Name 
 Description  

wavedamp 
 
damp_where_ice 
 
filter_wave_mom 
 
write_a_restart 
 
use_this_module 
 
use_TMA 
