1 NFIRST NLAST D0START NNERGY NTSOUT NTSI NMIX NCON NTDGN 1 400 11659.5 50 50 1 10 0 0 2 DTTS DTUV DTSF (seconds) 216 216 216 3 MIXVEL MIXTRC MIXZTD (mixing scheme: momentum, tracers and vorticity) 1 1 1 4 NORD NTIM NFRQ (momentum, tracers, vorticity, and transport) 4 1 1 4 1 1 4 1 1 4 1 1 5 AM AH 1.E9 2.E7 6 AIDIF FKPM VVCLIM WVMIX FRICMX FKPH VDCLIM WDMIX 1.0 0.1 50.0 50.0 50.0 0.01 50.0 50.0 7 MLDOPT MLDVAL MLDMIN MLDMAX EKFAC MCOEF NCOEF WSDFAC 1 1.0E+4 175.0 4.2E+3 0.144 0.3507 -9.578 0.0004 8 MXSCAN SOR CRIT ACOR 300 1.0 1.0E-4 0.5 9 CDBOT 2.5E-3 10 CDTID MTDDPTH TDMXFRC TDMXFAC SADV 2.592E-4 36.0 0.0625 200.0 0.2 11 DVBRLX TVBRLX DTBRLX TTBRLX DCSFRC TCSFRC DBTFRC TBTFRC -1.0 -1.0 -1.0 -1.0 0.5 7200.0 4.0 3600.0 12 (1) (2) (3) (4) (5) (6) (7) (8) (9) (10) IOPT(I) 1 1 1 1 0 9 0 2 2 9 13 (PSI) (Vt) (Vi) (Vb) (Vg) (W@V) (W@T) (w@V) (w@T) (KE) (VOR) IOUT(01-11) 1 1 1 0 0 1 1 1 1 0 1 14 (T) (S) (RHO) (Buoy) (MLD) (Vtide) (Stide) (Ttide) (TrcBal) (Err) IOUT(12-21) 1 1 0 0 1 0 0 0 0 0 15 NLEV LEV(nlev) in ascending numerical order 30 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 16 TITLRUN (a80): Application title. MREA-04: Alliance Initialization Survey (run 64) 17 OUTNAME (a80): output PE fields NetCDF file name. pe_ms_out.nc 18 NRGNAME (a80): output PE energy and diagnostics NetCDF file name. pe_ms_nrg.nc 19 TRKNAME (a80): output Langrangian trajectories NetCDF file name, if any. /dev/null 20 INPNAME (a80): input inital/boundary conditions NetCDF file name, if any. /data2/AOSN2/MREA04/PE_initial/2004/Apr06/PJH11/pi_ms_ini.nc 21 FRCNAME (a80): input forcing fields NetCDF file name, if any. /data2/AOSN2/MREA04/PE_forcing/2004/Apr06/PJH01/pe_frc_minXS.nc 22 ASSNAME (a80): input assimilation fields NetCDF file name, if any. /dev/null 23 APARNAM (a80): input assimilation parameters ASCII file name, if any. /dev/null 24 DPOSNAM (a80): input drifter's initial positions ASCII file name, if any. /dev/null 25 XPARNAM (a80): input domain extraction parameters ASCII file name, if any. /dev/null 26 SMLTNM (a80): Name of executable for smaller domain, if any. /dev/null 27 SMLHNM (a80): Name of host on which to run smaller domain, if any. /dev/null 28 SMLINM (a80): Name of parameter input file for smaller domain, if any. /dev/null 29 SMLONM (a80): Name of output log file for smaller domain, if any. /dev/null 30 PBISNAM (a80): name of pressure bias netCDF file, if any. /data2/AOSN2/MREA04/PE/2004/Apr06/PJH10/press_bias.nc 31 BPARNAM (a80): input biological model parameters ASCII file name, if any. /dev/null 32 TSRCNAM (a80): input tracer point sources ASCII file name, if any. /dev/null 33 GRDNAME (a80): input GRIDS NetCDF file name, if applicable. /dev/null 34 USRNAME (a80): input User's generic file name, if applicable. /dev/null 35 SAMPIN (a80): input hydrographic sampling parameters, if applicable. /dev/null 36 SAMPOUT (a80): output ASCII hydrographic profiles, if applicable. /dev/null 37 TIDEDAT (a80): input NetCDF external tide data file, if applicable. /dev/null 38 TDPHDAT (a80): input ASCII file containing tide phase data, if applicable. /dev/null 39 TIDEBOX (a80): input ASCII file defining tidal regions, if applicable. /dev/null 99 END of input data GLOSSARY -------- *** CARD 1: Various Intialization parameters: NFIRST [1] to start from scratch, [0] to start using re-start file. NLAST abs(NLAST) is the number of timesteps to compute. If negative, write re-start file at this timestep (used with NFIRST=0 later on) D0START Starting time. (modfied Julian date) Only active if CPP option "resetjulian" is active. Note: There are up to 3 different initial times associated with the elapsed model time of the PE model. (1) The "clock" associated with the Initial and Boundary conditions starts with the initial time in the IC/BC netCDF file (card 20) at the start of the model run. (2) The "clock" associated with the assimilation cycles starts at zero at model initialization. This clock is just the elapsed model time since the beginning of the run. See card 23 (3) The "clock" associated with surface forcing, tidal forcing and the output time of extracted profiles has 2 possible initial values. If the CPP option "resetjulian" is active, this clock is initialized with D0START, otherwise it is identical to clock (1). NNERGY number of timesteps between energy diagnostics output. NTSOUT number of timesteps between output of data. NTSI number of timesteps between print of single line of information. NMIX number of timesteps between mixing timesteps or if used with the C-preprocessing option "Asselinfilt" then there are no mixing steps and the Asselin time filtering is active with a factor _NU=0.001*NMIX. NCON maximum number of passes through convection loop (if explicit mixing) NTDGN number of initial timesteps with frozen tracers [Used only with C-preprocessing option "frozentrc"]. After NTDGN steps the tracers are calculated. *** CARD 2: Time-Stepping Parameters: DTTS timestep size for the temperature and salinity (seconds). DTUV timestep size for the internal mode velocity (seconds). DTSF timestep size for the transport function (seconds). *** CARD 3: Horizontal Mixing Scheme Switches: MIXVEL momentum equation horizontal mixing scheme: [1] Shapiro filter. [2] Laplacian at constant depths. [3] Laplacian along terrain following levels. MIXTRC tracers horizontal mixing scheme: [1] Shapiro filter. [2] Laplacian at constant depths. [3] Laplacian along terrain following levels. MIXZTD mixing scheme for the rate of change vorticity (ZTD): [1] Shapiro filter. [2] Laplacian. *** CARD 4: Shapiro Filter parameters for momentum, tracers, vorticity, and transport (if applicable): NORD order of the Shapiro filter. NTIM number of times to apply the Shapiro filter. NFRQ number of timesteps between filter applications. *** CARD 5: Laplacian horizontal mixing parameters (cm^2/s): AM coefficient for horizontal mixing, momentum equation. AH coefficient for horizontal mixing, tracers. *** CARD 6: Vertical mixing parameters AIDIF coefficient for implicit time differencing for vertical diffusion in the range [0,1.0]. If AIDIF=1.0 => fully implicit case AIDIF=0.0 => fully explicit case FKPM background vertical eddy viscosity coefficient (cm^2/s), momentum. VVCLIM vertical eddy viscosity coefficient (cm^2/s) for momentum used when the water column is gravitationally unstable. WVMIX vertical eddy viscosity coefficient (cm^2/s) for momentum used in the wind-mixed "surface layer" (see MLDOPT). FRICMX only used if Pacanowski and Philander (-Dppvmix) vertical mixing scheme is used: vertical eddy viscosity coefficient (cm^2/s) used (for momentum) when the Richardson Number is zero; i.e. the maximum value used in the stable regime, before transition to the unstable regime. This parameter thus controls the dependency of the viscosity and diffusion coefficients on Richardson Number in the -Dppvmix option. (FRICMX is "nu0" in Pacanowski & Philander (1981) notation, who suggest a value of ~ 50 cm^2/s for the upper Equatorial Pacific). FKPH background vertical eddy diffusion coefficient (cm^2/s), for tracers. (including salt, heat, and biological tracers). VDCLIM vertical eddy diffusion coefficient (cm^2/s) used (for tracers) when the water column is gravitationally unstable. WDMIX vertical eddy diffusion coefficient (cm^2/s) used (for tracers) in the wind-mixed "surface layer" (see MLDOPT). *** CARD 7: Mixed Layer Depth parameters: MLDOPT Surface layer mixing option: if MLDOPT=0, WVMIX and WDMIX are applied to a prescribed "mixed-layer depth", MLDMIN or MLDMAX. if MLDOPT=1, WVMIX and WDMIX are applied to an "Ekman depth" as determined by the wind stress forcing. if MLDOPT=2, WVMIX and WDMIX are applied to a "mixed-layer depth" determined by the wind stress and buoyancy forcing. The use of the remaining parameters in this card depends on the value of MLDOPT. The table below indicates which parameters are potentially active for each value of MLDOPT. See the descriptions below for more details. +--------+-----------------------------------------------------------+ | | Activity | | MLDOPT | MLDVAL | MLDMIN | MLDMAX | EKFAC | MCOEF | NCOEF | WSDFAC | +--------+--------+--------+--------+-------+-------+-------+--------+ | 0 | | X | X | | | | | +--------+--------+--------+--------+-------+-------+-------+--------+ | 1 | | X | X | X | | | | +--------+--------+--------+--------+-------+-------+-------+--------+ | 2 | X | X | X | | X | X | X | +--------+--------+--------+--------+-------+-------+-------+--------+ MLDVAL If MLDOPT=2 and CPP option "nkfix" is on: default mixed layer depth (cm). Used when Niiler-Kraus would give indeterminate results. else not used MLDMIN If MLDOPT=0: "mixed-layer depth" for tracers (in centimeters). if MLDOPT is 1 or 2: minimum allowable mixed-layer depth estimate (in centimeters). MLDMAX If MLDOPT=0: "mixed-layer depth" for velocity (in centimeters). if MLDOPT is 1 or 2: maximum allowable mixed-layer depth estimate (in centimeters). Note: MLDMIN and MLDMAX are *not* used to constrain the mixed- ---- layer depth, but only used to constrain the depth to which WVMIX and WDMIX are applied! EKFAC Factor in the Ekman depth Equation (Large et al., 1994; eq.29): Ekman depth = EKFAC * USTAR / F where USTAR = sqrt ( windstress / density ) F = Coriolis parameter Large et al. suggest EKFAC=0.7; however, the derivation of the above equation indicates the value is somewhat arbitrary; therefore we allow the freedom to increase or decrease this value, if the Ekman depth estimate appears too shallow or too deep, respectively. MCOEF Wind stress coefficient for estimating mixed-layer depth. It is the "m" parameter from Eq. 10.30 in Niiler and Kraus (1977; in: Modelling and Prediction of the Upper Layers of the Ocean, Ed by E.B. Kraus, p 143-172). The larger MCOEF, the larger the influence of wind stress on mixed-layer depth (relative to buoyancy). It is generally observed that MCOEF=1.25, although it can be > 8 during storm events (ibid.). Actually, MCOEF is not constant but increases as the Richardson Number decreases (ibid). Presuming storm events of MCOEF=8 to occur 1/7 or 1/30 of the time would suggest a time-mean MCOEF of 2.21 or 1.48, respectively. Thus, generally use 1.25 =< MCOEF =< 2.21. NCOEF Buoyancy coefficient for estimating mixed-layer depth. It is the "n" parameter from Eq. 10.30 in Niiler and Kraus (1977). It is a weight for the effects of positive buoyancy; 0 =< NCOEF =< 1: NCOEF=0 all convectively produced energy is dissipated i.e. a positive buoyancy flux (surface cooling) does not influence MLD. NCOEF=1 convectively-produced eddies are not dissipated i.e. positive buoyancy influences mixed-layer depth in an equal and opposite manner as negative buoyancy). Observations suggest 0.0 MXSCAN or RES < CRIT * RMS of the Initial Transport streamfunction ACOR coefficient for implicit treatment of Coriolis term in the range [0,1.0]. ACOR=0.0 => fully explicit case. ACOR=0.5 => centers the weight equally at N. ACOR=1.0 => fully implicit case. *** CARD 9: Bottom Mixed Layer. CDBOT bottom drag coefficient. (nondimensional) *** CARD 10: Tidal mixing. CDTID Tidal friction coefficient. (s) This multiplies the square of the tidal velocity to create a mixing coefficient. Ex: CDTID=0.08 and a tidal velocity of 50 cm/s results in a tidal mixing coefficient of 200 cm^2/s. MTDDPTH Maximum water depth over which to apply tidal enhancing to vertical mixing. (m) TDMXFRC Tidal mixing limit. (cm^2/s) TDMXFAC Constant tidal mixing coefficient. (cm^2/s) SADV Scaling factor for tidal advection. (nondimensional) The first three parameters are active if both CPP options "ext_tide" and "mixtide" are enabled. Otherwise, if the CPP option "posmxtid" is enabled the fourth parameter is active. The final parameter (SADV) doesn't actually deal with tidal mixing, but with the advection of tracers by tidal velocities. If the CPP options "ext_tide", "advtide" and "advtide0" are all active, then the tidal velocity fields are added to the subtidal velocity fields for tracer advection, but the strength of the tidal velocity fields are scaled by the factor SADV. *** CARD 11: Boundary Relaxation parameters. DVBRLX Velocity grid spatial e-folding distance (grid points). TVBRLX Velocity grid temporal e-folding distance (seconds). DTBRLX Tracer grid spatial e-folding distance (grid points). TTBRLX Tracer grid temporal e-folding distance (seconds). DCSFRC Coastal friction spatial e-folding distance (grid points). TCSFRC Coastal friction temporal e-folding distance (seconds). DBTFRC Bottom friction spatial e-folding distance (grid points). TBTFRC Bottom friction temporal e-folding distance (seconds). Note: If any of these parameters are less than or equal to zero, the boundary relaxation is shut off for that grid. (i.e. DVBRLX<=0 shuts off boundary relaxation on the velocity grid, but allows boundary relaxation on the tracer grid.) *** CARD 12: PE model various switches (ten elements integer vector): IOPT(1) type of boundary conditions on tracers. IOPT(2) type of boundary conditions on velocity. IOPT(3) type of boundary conditions on transport streamfunction. IOPT(4) type of boundary conditions on vorticity. Boundary condition types are: [0] closed boundary conditions. [1] provided values in boundary data. [2] Spall and Robinson boundary conditions (CFvN like). [3] Orlanski radiation (implicit). [4] modified Orlanski radiation (implicit). [5] one time level, spatial extrapolation. [6] reduced physics. +-------------------------------+---------------------------+ | | Valid Boundary Condition | | Field | | | | 0 | 1 | 2 | 3 | 4 | 5 | 6 | +-------------------------------+---+---+---+---+---+---+---+ | Tracers | X | X | X | X | X | X | | +-------------------------------+---+---+---+---+---+---+---+ | Velocity | X | X | X | X | X | X | | +-------------------------------+---+---+---+---+---+---+---+ | Transport Streamfunction | X | X | X | X | X | | | +-------------------------------+---+---+---+---+---+---+---+ | Barotropic Vorticity Tendency | | X | X | X | | X | X | +-------------------------------+---+---+---+---+---+---+---+ IOPT(5) amount of "diagnostic" information printed to log file. [0] terse [1] verbose IOPT(6) not used. IOPT(7) Representation of Coriolis term: [0] full curvature, [1] f-plane, [2] beta-plane IOPT(8) Number of tracers exchanged with larger domain. (CPP: nest2larger) IOPT(9) Number of tracers exchanged with smaller domain. (CPP: nest2smaller) IOPT(10) not used. *** CARD 13: PE model output field switches (1-10 elements of an integer (vector): Convention: [0] do not write, [1] write IOUT(1) transport streamfunction (cm^3/s). IOUT(2) total (internal+external) velocity Ut,Vt (cm/s). IOUT(3) internal component velocity Ui,Vi (cm/s). IOUT(4) barotropic component velocity Ub,Vb (cm/s) IOUT(5) internal mode, geostrophic shear Ug,Vg (cm/s). IOUT(6) omega vertical velocity at velocity points (cm/s). IOUT(7) omega vertical velocity at tracer points (cm/s). IOUT(8) vertical velocity at velocity points (cm/s). IOUT(9) vertical velocity at tracer points (cm/s). IOUT(10) kinetic energy (petaJoules): IOUT(10)=1 total kinetic energy. IOUT(10)=2 rate of change of kinetic energy components. IOUT(10)=3 both total kinetic energy and rate of change of kinetic energy components. WARNING: The kinetic energy here is volume data and the rate of change by components involves up to 12 volume data terms. IOUT(11) rate of change of barotropic vorticity (s-2) *** CARD 14: PE model output field switches (11-20 elements of an integer (vector) continued: IOUT(12) temperature (deg C). IOUT(13) salinity (PSU). IOUT(14) density anomaly (sigma-1000) kg/m^3. IOUT(15) buoyancy work (gigaWatts). IOUT(16) mixed-layer depth (meters); written if MLDOPT>0. IOUT(17) tidal velocity Utide,Vtide (cm/s). IOUT(18) tidal surface elevation (m). IOUT(19) residual tidal stress tensor (cm/s^2). IOUT(20) point by point tracer balance terms. WARNING: The tracer balance terms are volume data and the rate of change by components involves up to 9xNT volume data terms. IOUT(21) forecast errors; written if IOBSERR~=0 and CPP option combinations ( OIAS and FCSTERR ) are defined. *** CARD 15: Number and Levels to output: NLEV number of levels at which to write out information. LEV levels to write out information (ascending order). Requested values greater than KM to activate interpolation to a flat level; in this case LEV is the depth in meters. *** CARD 16: string with a maximum of eighty characters. TITLE Title of model run. *** CARD 17: string with a maximum of eighty characters. OUTNAME Output PE fields NetCDF file name. *** CARD 18: string with a maximum of eighty characters. NRGNAME Output PE energy and diagnostics NetCDF file name. *** CARD 19: string with a maximum of eighty characters. TRKNAME Output Langrangian trajectories NetCDF file name. This file is written if the C-preprocessing option "ldrifters" is activated. *** CARD 20: string with a maximum of eighty characters. INPNAME Input inital/boundary conditions NetCDF file name. This file is read always, except when the C-preprocessing option "analytical" is activated. *** CARD 21: string with a maximum of eighty characters. FRCNAME Input forcing fields NetCDF file name. This file is read if the C-preprocessing option "forcing" is activated. *** CARD 22: string with a maximum of eighty characters. ASSNAME Input assimilation fields NetCDF file name. This file is read if the C-preprocessing option "oias" is activated. *** CARD 23: string with a maximum of eighty characters. APARNAM Input assimilation parameters ASCII file name. This file is read if the C-preprocessing option "oias" is activated. *** CARD 24: string with a maximum of eighty characters. DPOSNAM Input drifter's initial positions ASCII file name. This file is read if the C-preprocessing option "ldrifters" is activated. *** CARD 25: string with a maximum of eighty characters. XPARNAM Input domain extraction parameters ASCII file name. This file is read if the C-preprocessing option "extraction" is activated. *** CARD 26: string with a maximum of eighty characters. SMLTNM Name of executable for smaller domain. This program is used if the C-preprocessing option "nest2smaller" is activated. *** CARD 27: string with a maximum of eighty characters. SMLHNM Name of host on which to run smaller domain. This machine is used if the C-preprocessing option "nest2smaller" is activated. To let PVM decide which host to use, enter the string /dev/null *** CARD 28: string with a maximum of eighty characters. SMLINM Name of parameter input file for smaller domain. The name should be an absolute path, to ensure the proper file is used. Within this file, all filenames should also be absolute paths. This file is used if the C-preprocessing option "nest2smaller" is activated. *** CARD 29: string with a maximum of eighty characters. SMLONM Name of output log file for smaller domain. The name should be an absolute path, to ensure the proper file is used. This file is used if the C-preprocessing option "nest2smaller" is activated. *** CARD 30: string with a maximum of eighty characters. PBISNAM Input/Output name for "pressure gradient bias" netCDF file. This file is used if the C-preprocessing option "pressbias" is activated. *** CARD 31: string with a maximum of eighty characters. BPARNAM Input biological model parameters ASCII file name. This file is read if either of the C-preprocessing options "bioAnder", "bioFasham", or "bioMcGillic" is activated. *** CARD 32: string with a maximum of eighty characters. TSRCNAM Input tracer point sources ASCII file name. This file is read if the C-preprocessing option "pttrcsrc" is activated. This file contains point data sources, for example, river sources. *** CARD 33: string with a maximum of eighty characters. GRDNAME Input GRIDS NetCDF file name. If applicable, this file can be read when the C-preprocessing option "analytical" is activated. If that it the case, use this file to read the bottom topography at tracer points, masking data, and other domain parameters. *** CARD 34: string with a maximum of eighty characters. USRNAME Input User's generic file name, if applicable. *** CARD 35: string with a maximum of eighty characters. SAMPIN Input hydrographic sampling parameters. An ASCII file containing grid positions and time steps at which to sample profiles from the PE model work space. Only active if the CPP option "peprf" is selected. *** CARD 36: string with a maximum of eighty characters. SAMPOUT Output ASCII hydrographic profiles. A MODS formatted file containing the sampled profiles. Only active if the CPP option "peprf" is selected. *** CARD 37: string with a maximum of eighty characters. TIDEDAT Input NetCDF external tide data file. Contains tidal amplitudes and phases on the model horizontal grid. Only active if the CPP option "ext_tide" is selected. *** CARD 38: string with a maximum of eighty characters. TDPHDAT Input ASCII file containing tide phase data. For each component of the external tide model, this file supplies the tidal phase at a specific time. Only active if the CPP option "ext_tide" is selected. *** CARD 39: string with a maximum of eighty characters. TIDEBOX Input ASCII file defining tidal regions. Starting & ending indices for tidally active regions along with maximal depth restrictions for those regions. Only active if the CPP option "posmxtid" is selected and the CPP option "mixtide" is NOT selected.