HOPS Primitive Equation (PE) model: HOST: maelstrom.harvard.edu (128.103.2.50) TAR FILES: pub/HOPS/PE/pe_9.6.tar.Z (676568:2634240 bytes) pub/HOPS/PE/Ex_pe_9.6.tar.gz (66336311:105523712 bytes) VERSION: 9.6 (August 21, 2001) ORIGIN: Harvard University, Cambridge Massachusetts Harvard Ocean Prediction System (HOPS) DEVELOPERS: Patrick J. Haley Jr. (haley@pacific.harvard.edu) Carlos J. Lozano (lozano@pacific.harvard.edu) LIBRARIES: (1) NetCDF, version 2.3.2 University Corporation for Atmospheric Research/UNIDATA http://www.unidata.ucar.edu/ (2) GNUmake version 3.75 Free Software Foundation http://www.gnu.ai.mit.edu/ (3) PVM, version 3.4.3 Oak Ridge National Laboratory http://www.epm.ornl.gov/pvm/ ============ INTRODUCTION ============ This directory contains HOPS's Primitive Equation (PE) model. This model is used to predict the ocean state. The basic state variables for the HOPS PE model are temperature salinity velocity The velocity is decomposed into an internal mode (zero depth average) and an external transport streamfunction (rigid-lid approximation). The HOPS PE model contains options for: Data Assimilation (via Optimal Interpolation) Surface Forcing Attached Biological Models Nested Sub-Domains Coastal/Land masking ============ Installation ============ This package is available over the INTERNET via anonymous FTP from maelstrom.harvard.edu (128.103.2.50). When connected, you will be in the FTP directory. To obtain this package, go to the directory "pub/HOPS/PE" and get files: Readme.pe This file. pe_9.6.tar.Z Compressed tar file of the PE package. Ex_pe_9.6.tar.gz Compressed tar file of an example using the PE package. To install this package, simply go to the directory in which you want to put the PE package and execute the following commands: zcat pe_9.6.tar.Z | tar -pxvf - gzip -dc Ex_pe_9.6.tar.gz | tar -pxvf - The tar file pe_9.6.tar.Z contains the following files: ocean.F addtide.F all_uc.F anaflds.F aphread.F assiwght.F bdryindx.F bes1d.F bess1d.F bess2d.F bess2d_msk.F bess2d_pmsk.F bioparmAnder.F bioparmDuse.F bioparmFasham.F bioparmMcGillic.F biosourceAnder.F biosourceDuse.F biosourceFasham.F biosourceMcGillic.F blkdat.F boundary.F bracket_z.F caldate.F cdfout.F cdrspv.F cell_ok.F cfl.F check_prf.F chkparm.F clinic.F cnvmix.F day_code.F defbias.F defbparmAnder.F defbparmDuse.F defbparmFasham.F defbparmMcGillic.F defnrg.F defout.F depthslab.F derivs0.F diag.F drftdv.F drifters.F errio.F exitus.F extrap.F extrap2.F file_chk.F flip.F fsigma.F get_date.F get_ewpt.F get_thick.F grad24_p.F gregorian.F headln.F hopsrecv.F host_check.F hvgrid.F ind_bdy.F infld.F init_srch.F inittdpth.F inparm.F int_gradrho.F invtri.F ip2ij.F landsea.F lap_depth.F lap_filt.F lap_lev.F length.F lintrp.F lintslab.F ll2xy.F lnblk.F load_sig.F meanrho.F msk_bdy.F my_handler.F nest_domain.F nest_errchk.F nest_flags.F nest_init.F nest_interior.F nest_rec_bc.F nest_snd_bc.F nest_spawn.F nest_t_align.F nest_test.F no_digit.F odam.F oiassi.F oibndry.F okeep.F osav.F pb0wrtcdf.F ppmix.F press_bias.F press_bias0.F priprod.F putbparmAnder.F putbparmDuse.F putbparmFasham.F putbparmMcGillic.F read_tide.F readgrids.F readprf.F readvbc.F relax.F rem_llist.F reset_t_thickness.F rich_no.F rk40.F rmblklines.FF robc.F rotangle.F rotparm.F rseterr.F scalvcln.F set_brlx.F set_depths.F set_depths_old.F set_edges.F set_pmask.F setvbc.F setvert.F shap_lev.F shap_mean.F sig2z.F sig_search.F sigma2z.F spline.F splineslab.F splint.F splintslab.F state.F step.F tid_indx.F tide_aux.F tide_depth.F tide_val.F tracer.F trackbound.F trackinit.F trackrefresh.F tracksout.F trackstep.F trackup.F trkvscl.F tsource.F upbox.F userdiag.F vavgv.F vbar_test.F vmix_aux.F vntrpv.F writehydro.F wrt_prf.F wrtcdf.F wrtstr.F xtr_psi.F xtr_trc.F xtr_vel.F xtr_vor.F xtract.F xtrsubdom.F xy2ll.F zetabar.F bndata.h bndyrlx.h cbiopnh.h ccfl.h cdefs.h cdiag.h cinpvbc.h cppmix.h ctsrc.h cvbc.h cvmix.h edges.h extra.h fields.h filtdat.h fullwd.h gradp.h gradp2.h gradp4.h gradph2.h gradph4.h hybrid.h hydro.h ioi.h iounits.h moddat.h nest.h oiopts.h onedim.h options.h param.h pconst.h pe_netcdf.h prf.h rhomean.h runid.h scalar.h tidesp.h tracks.h tracktime.h trkfld.h trkscl.h version.h vertical.h vertslabs.h voldat.h workspa.h workspb.h workspr.h xtr_opts.h GNUmakefile.alpha GNUmakefile.cray GNUmakefile.iris GNUmakefile.rs6000 GNUmakefile.sun3 GNUmakefile.sun4 GNUmakefile.sun5 UPDATES VMSmakefile.com aphy.dat bioAnder.in bioAnderCod.in bioDuse.in bioDuseCod.in bioFasham.in bioFashamCod.in bioMcGillic.in bioMcGillicCod.in compile.com extraction.dat lagrange.dat oi.dat pemodel.in sample.dat tidebox.dat tidephase.dat tsource_river.dat ============ The Makefile ============ Currently, there are seven different GNUmakefiles for seven different computer architectures: GNUmakefile.alpha GNUmakefile.cray GNUmakefile.iris GNUmakefile.rs6000 GNUmakefile.sun3 GNUmakefile.sun4 GNUmakefile.sun5 These makefiles are written for GNU Make, version 3.75 Free Software Foundation (617) 876-3296 675 Mass Ave. gnu@prep.ai.mit.edu Cambridge, MA 02139, USA http://www.gnu.ai.mit.edu/ They are NOT compatible with the standard UNIX Make. The GNU Makefiles have been designed to allow the user to compile the PE model source codes in a separate directory from that in which the source codes are located. The makefile searches for the code segments in the following alternate paths: source code: (1) the directory containing the GNUmakefile. (2) the directory specified by the macro SRCDIR include files: (1) the directory containing the GNUmakefile. (2) the directory specified by the macro PARAMDIR (3) the directory specified by the macro SRCDIR (4) the directory specified by the macro NCDIR This provides the user with the flexibility for the following configurations: (1) The user needs only copies of this GNUmakefile, the parameter file "param.h" and a path to the source codes to produce a version of the PE model with the appropriate C-preprocessing and compiler options. (2) The user who is modifying the PE model code, can isolate those routines actually being changed with a copy of this GNUmakefile in a sub-directory. For VAX/VMS systems, two scripts are provided for C-preprocessing and compiling: VMSmakefile.com (driver script) compile.com These are simple scripts which assume everything is in one directory. They have not been tested in years, use with caution. ------------------------------------- GNUmakefile Tunable macro definitions ------------------------------------- The User needs to check and modify the following macro definitions in the appropriate GNUmakefile before compiling and linking the application code: BIN name of the executable code. BINDIR directory path for the executable code. CPPFLAGS C-preprocessing flags and options. FFLAGS flags to the fortran compiler. NCDIR directory path for NetCDF include files PARAMDIR alternate directory path for the include files. SRCDIR directory path for the source code. ----------------------------------- GNUmakefile C-preprocessing Options ----------------------------------- The following are the available C-preprocessing options to use in the macro definition CPPFLAGS: Additional Tracer Sources/Sinks: pttrcsrc specification of point tracer sources rivsrc Specification of river tracer sources by either relaxation or direct specification. Requires the CPP option "pttrcsrc" Analytic Initialization: analytical Analytical initial and boundary fields. (Do not use with both "dblprec" and "forcing" also active) grids Domain configuration from GRIDS NetCDF file Biological Model: bioAnder Anderson expansion of McGillicuddy biological model bioDuse Dusenberry expansion of Anderson biological model bioFasham Fasham et al. (1990) biological model bioMcGillic McGillicuddy et al. (1995) biological model bio_12_A Additional productivity terms (bacterial, zooplankton, etc) bioadjloc Pseudo local biological adjustment. Vertical diffusion is on, but advection is off. bioadjvert Adjustment of biology using vertical dynamics only dusDroop Droop nutrient limitation equations codunlim Append cod model with unlimited response to T & zoo codlim Append cod model with limited response to T & zoo codvadvect Allow cod to be vertically advected. codvmix Allow cod to be vertically mixed. cod_ing Alternative cod model. Requires "codlim" also active. zoo_ing zooplankton following behavior for cod_ing cod_square speed-response is the square functional Coastal/Land masking: coast Coastal boundary conditions coastedge Next to mask, average unmasked values (control noise) islands Islands are present in the model basin Comment Removal: rmcomments Remove all commented lines after C-preprocessing rmdocinc Remove documentation in all include files. Data Assimilation: oias Intermittent OI assimilation option fcsterr Maintain OI forecast errors. (with "oias") wgterr An intuitive form of the OI ramping weight.(with "oias") simpramp Simple ramping scheme. (with "oias" and "fcsterr") Debugging: gendbg Generic Debugging: Preserves intermediate files sunfpe SUN's floating point exception trap Equation of State: leqstate Linear Equation of State unesco Unesco (1980) nonlinear equation of state for seawater Extra Extracted Data: ldrifters Lagrangian Drifters option peprf Extract hydrographic PE profiles usrdiagnostic Report user defined diagnostics. nesttime Report some timing data. (SUN) Requires CPP option "usrdiagnostic". Fictitious Friction: bndy_rlx Boundary relaxation. botfrc Bottom friction. cstfrc Coastal friction. imp_bnd_rlx Use semi-implicit in time scheme for boundary relaxation. Nesting (one-way): extraction Extract initial and boundary data for requested sub-domains Nesting (two-way): nestnultest Create "nested" code without the nesting routines nest2larger Two-way nesting to larger grid via PVM. nest2smaller Two-way nesting to smaller grid via PVM. nest_ext2lrgr Replace fine grid transport streamfunction with coarse nest_ext2smlr Send transport streamfunction to overwrite fine grid Numerics: AsselinFilt Add Asselin filter AsselinFilt_cod Only apply Asselin filter to cod close_tracers Impose closed BCs on tracer N & S boundaries. cyclic Cyclic (west/east) boundary conditions dblprec Double precision floating-point operations and output. (Do not use with both "analytical" and "forcing" also active) explicitvmix Explicit vertical mixing. nowcfl Disable CFL checking in the vertical. sor5pt transport solution via sequential over-relaxation vel_conv Require convergence in velocity when solving PBAR Pressure Gradient Calculation: hpg4 Forth order hydrostatic pressure gradient cubspl Vertical cubic spline interpolation by slabs noxtrp No extrapolation in hydrostatic pressure gradient rmdenbar Remove mean density when computing the pressure gradient vbart Vertical Simpson's integration in pressure gradient Pressure Gradient Bias Removal: pressbias Remove bias from pressure gradient pressinbias Initialize bias file shapmean Remove "mean" tracer field before Shapiro filtering Reduced Physics: frozentrc Initially freeze tracers for specified number of timesteps linear_physics Linear physics: no adv mom, only vert. adv mean tracers nocfl No CFL checking. notadvm Linear Momentum Equation: no horizontal advection notadvt Linear Heat Equation: no horizontal advection Sub-Grid Scale Parameterization: ppvmix Pacanowski and Philander vertical mixing scheme secondmean enforce zero mean internal velocity after Shapiro filter shapiro Shapiro filter for horizontal viscosity bottom Second-order in time bottom stress calculation. shapnocoastflux Revised filter BCs. pindex Revised streamfunction filter indices. Surface Forcing: forcing space/time variable forcing. (Do not use with both "analytical" and "dblprec" also active) resetjulian Start surface forcing clock from supplied value. nkfix Revise protections & input for Niiler-Kraus mixed-layer. System Calls: sunflush regularly flush output buffers in SUN systems. Tides: ext_tide External tidal model. PE model reads tidal fields produced externally and uses them for limited tidal effects. Used to introduce tidal effects into a rigid lid model. advtide Include tidal velocities in tracer advection. Requires CPP option "ext_tide" advtide0 Reduce the size of tidal velocities in tracer advection. Requires CPP options "ext_tide" and "advtide" mixtide Enhance mixing coefficients based on the magnitude of the local tidal velocity. Requires CPP option "ext_tide" tide_zero Include residual tidal stress terms in conservation of momentum equation. Requires CPP option "ext_tide" add_tide Add tidal velocity to total velocity on output. Requires CPP option "ext_tide" posmxtid Enhance mixing coefficients in pre-defined regions with additional pre-defined limitations based on total depth. Primarily used to get minimal tidal representation while tidal fields are being tuned. Superseded by the combination of CPP options "ext_tide" and "mixtide" Time Stamp: aixdate AIX intrinsic date routine (IBM RS6000). craydate CRAY's intrinsic date/time functions decdate DEC's intrinsic date/time functions sundate SUN's intrinsic date/time function Vertical Coordinate System: barotropic barotropic model configuration (one level, KM=1) dblsigma Double "sigma" transformation in the vertical gridold Recover old algorithm for setting vertical coordinates. ------------------------------- GNUmakefile Installation Issues ------------------------------- A number of internal macros are defined for the system commands used by the GNU makefiles. These will generally only have to be defined once, the first time the user installs the PE model on a new system. RMBLKLINES The name given to executable code (provided with this package) to remove blank lines from the pre-processed code. This is provided only to avoid possible conflicts. SHELL The shell to be used by the makefile. RM The remove command. ECHO The echo command. FALSE The false command. Used to set an error condition. LIB The netCDF library CPP The C Pre-Processor. FC The FORTRAN compilier Two-Way Nesting Pointers: To run PVM for the 2-way nesting, you'll have to define some environmental variables in you .cshrc (or equivalent) file. The first is the PVM_ROOT variable. This should point to the base directory where PVM is installed. The system specific libraries should descend from there. Next append the cshrc.stub to your .cshrc file (or their equivalents). This will define some additional environmental variables. Uncomment the appropriate lines so that the PVM commands & directories are added to your path. ===================== Compiling and Linking ===================== Once that the software has been installed and the Makefile has been selected and customized, the User needs to attend the following steps to compile and link the application code: (1) Customize include parameter file "param.h". The User needs to set the following parameters: Parameters Always present: IMT Number of tracer points in the x-direction. JMT Number of tracer points in the y-direction. IJMX Either IMT or JMT, whichever is greater. KM Number of vertical levels. LBC Number of arrays of slab incidental data (usually, LBC=2). LSEG Maximum number of sets of Start and End indices per row or per column. MISLE Maximum number of islands in the model basin. MPROF Maximum number of points in mean TS profile. NT Number of tracer type variables (generally, NT=2 for T & S). Biological Model Parameters: LM Number of intervals in light spectra (for PAR). Only used with CPP option "bioDuse". Coastal/Land Mask Parameters (CPP option "coast"): MCLEN Maximum number of points in a coastal segment. MCSEG Maximum number of coastal segments. Nesting (one-way) Parameters (CPP option "extraction"): MSUBDOM maximum number of subdomains to extract. XIMT maximum number of tracer points in the x-direction to extract. XKM maximum number of vertical levels to extract. Nesting (two-way) Parameters (CPP options "nest2larger" or "nest2smaller"): XMDAT maximum number of points in arrays for passing to external models. A loose upper bound is given by max(nx*ny*nz) XMNDAT maximum number of points in arrays for passing to external models. Loose bound max(nx*ny) for all nested models. Only used with additional CPP options "nest_ext2lrgr" or "nest_ext2smlr". Hydrographic Profile Extraction Parameters (CPP option "peprf"): MHDR Maximum number of lines of text in the file header. MHFLDS Maximum number of field types supported. MHPTS Maximum number of data points per station. MHVAR Maximum number of variables per station. (MHVAR<=MHFLDS) MNBPRF Maximum number of profile per instrument. External Tidal Model Parameters (CPP option "ext_tide"): MAXCOMP Maximum number of tidal components. Geographic Tidal Mixing Parameterization Parameters (CPP option "posmxtid"): TDBOXMX maximum number of tidally active boxes. Not used if both CPP options "ext_tide" and "mixtide" are active. The parameters IMT, JMT, IJMX, KM and NT must be set to the EXACT values for the domain/run of interest. The remaining parameters may be over declared. ================= Input Script File ================= There are several parameters that the User needs to determine and specify before running the application code. These parameters are read from standard input. A sample of the input parameter data is provided in script file "pemodel.in". The input parameters and switches that the User needs to determine are: --------------------------------------------------------------- --- Two-Way Nesting Note: --- --- When creating an input file for a nested sub-domain, --- --- the user should use absolute path-names for any --- --- specified file-name. --- --------------------------------------------------------------- *** CARD 1: Various Initialization 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. (modified 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. 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: Modeling 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 Lagrangian 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 initial/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. =========================== Preparation of input fields =========================== ----------------------------------- Initialization fields [pe_initial] ----------------------------------- The PE model expects a full set of 3D fields, already on the PE model grid, at start-up and in netCDF format unless the CPP option "analytical" is active. The expected fields are: internal mode velocity (3D) transport streamfunction (2D) temperature (3D) salinity (3D) any additional tracers (3D) The necessary boundary condition data is also assumed to be on the PE model grid and in the same netCDF file. The HOPS pe_initial package is used for this purpose. ------------------------------------ Surface forcing fields [pe_forcing] ------------------------------------ The PE model expects a set of 1-2D fields, already on the PE model grid, at start-up and in netCDF format if the CPP option "forcing" is active. The full range of possible surface forcing fields is: wind stress (1-2D) net head flux (1-2D) evaporation - precipitation (1-2D) short wave radiation flux (1-2D) These fields usually have a temporal component. If the model run extends outside the time domain covered by the forcing file, the fields will be linearly extrapolated. One way to avoid this is to bracket the synoptic forcing data with either zero fields or climatological fields. These bracketing time levels should encase the entire run. The HOPS pe_forcing package is used to interpolated the desired fields to the model grid and create the expected netCDF file. --------------------------------- Assimilation fields [pe_initial] --------------------------------- The PE model expects a set of 3D fields, already on the PE model grid, at start-up and in netCDF format if the CPP option "oias" is active. The full range of possible assimilation fields is: internal mode velocity + associated error fields (3D) transport streamfunction + associated error fields (2D) temperature + associated error fields (3D) salinity + associated error fields (3D) any additional tracers + associated error fields (3D) The HOPS pe_initial package is to prepare these fields. In addition, the user must supply an additional (ASCII) file containing instructions to control the assimilation. These instructions determine which fields are assimilated, when they are assimilated and with what strength they are assimilated. Usually, the assimilation fields are "ramped in". That is, they are repeatedly assimilated with increasing strength over the course of a few model days. This is done to avoid shocking the model with the new data. The length of time over which the ramping is done is variable: the model should have enough time to adjust but the data should not come in so early as to be physically unreasonable. An example of this file is included as "oi.dat". The format of this file is: *** CARD 1: NOI, IOBSERR, IOIWRT, COR NOI number of assimilation cycles. IOBSERR switch for type of observation errors: [0] uniform (constant errors per level). [1] nonuniform (variable error everywhere). IOIWRT switch to write detailed assimilation information: [0] no, [1] yes COR correlation between forecast and observation errors. *** CARD 2 to NOI+1: IREAD(n),TOISEC(n),IAP(n),IAUV(n),IATS(n,m) n=1,...,NOI m=1,...,NT IREAD switch to read in a new set of assimilation fields: [0] no, [1] yes TOISEC assimilation times (days) from initial TTSEC. IAP switch to activate assimilation of transport streamfunction: [0] no, [1] yes IAUV switch to activate assimilation of internal velocity: [0] no, [1] yes IATS switch to activate assimilation of NT tracers: (temperature, salinity, etc.; usually NT=2) [0] no, [1] yes *** CARD NOI+2 to NOI+NOI+1: OBSWGT(n,ifield) n=1,...,NOI ifield=1,...,NT+3 OBSWGT weight coefficients (from 0 to 1) needed to compute forecast errors from the provided distribution of observation errors. (u,v,tracers,transport) IFIELD: [1] transport streamfunction. [2] internal mode, u-velocity component. [3] internal mode, v-velocity component. / [4] temperature. NT tracers [5] salinity. \ [6] other tracers, if any. NOTE: there is only one switch to activate the assimilation of internal velocity and there are two values of OBSWGT (one for each component). *** CARD NOI+NOI+2 to ...: If IOBSERR=0, then the normalized uniform (per level) errors are needed. ERRP(n) n=1,...,NOI ERRUV(n,k) n=1,...,NOI k=1,...,km ERRTS(n,k,m) n=1,...,NOI k=1,...,km m=1,...,NT NOTE: these errors are normalized by the field variance, so their values range between 0 and 1. ---------------------------- Lagrangian Drifter Controls ---------------------------- If the CPP option "ldrifters" is active, the PE model will simulate Lagrangian drifters. The user controls the types and initial placement of drifters by specifying instructions in an ASCII file. An example is included as "lagrange.dat". The form of this file is: 1st record: NTRACERS, number of drifters to simulate (free formatted integer) For each drifter, two lines of control data: 1st line: ITYPE, IDENT, drifter type (i4) and drifter identifier (a40) ITYPE = 1 surface drifter ITYPE = 2 density drifter (Swallow Floats) IDENT (01:18) drifter ID (string and/or numbers) IDENT (19:24) starting simulation day (modified Julian day) IDENT (25:29) starting simulation hour (hour/minutes) IDENT (30:35) deployed day (modified Julian day) IDENT (36:40) deployed hour (hour/minutes) 2nd line: LAT, LON, Z, T (free formatted) LAT: drifter latitude at time T (south; negative) LON: drifter longitude at time T (west; negative) Z: drifter depth at time T (meters) T: release time after model initialization (days) ----------------- Nesting (one-way) ----------------- If the CPP option "extraction" is active, the PE model will extract data onto specified sub-domains for one-way nesting. The user controls the sampling frequency and sampling duration by specifying instructions in an ASCII file. An example is included as "extraction.dat". The form of this file is: 1st record: NSUBDOM, number of sub-domains to extract For each domain, two lines of control data: 1st line: TSTR_XTR(n), DT_XTR(n), TEND_XTR(n) TSTR_XTR(n) starting extraction timestep DT_XTR(n) extraction (boundary conditions) sampling rate timestep units TEND_XTR(n) ending extraction timestep 2nd line: XTR_NAME(n) input/output NetCDF filename. Pe_initial file defining the Nth sub-domain. ------------------------------------------------ Pressure Gradient Bias Removal [pe_initial, pe] ------------------------------------------------ If the CPP option "pressbias" is active, the PE model will attempt to remove a bias from the pressure gradient calculation. The PE model expects a file to already exist containing the estimated pressure gradient bias at every model point. This file is expected to be in netCDF format. The creation of this file is a two stage processes. (1) The HOPS pe_initial package is used to create an initialization based on a single TS profile. This initialization depends only upon depth, and hence should have a zero horizontal pressure gradient. (2) A version of the PE model with both of the CPP options "pressbias" and "pressinbias" active is run for one (1) time step. This produces the estimate for the bias in the pressure gradient. This version of the PE model should be thought of as a static version of the PE model to be run. Assimilation and surface forcing should NOT be present. Any other option which can affect the pressure gradient calculation should be the same in both models. Additionally, this same procedure can be used to remove a horizontally uniform field from the tracers before applying the Shapiro filter. To do this, make sure the CPP option "shapmean" is active in both PE models. -------------------------- Attached Biological Models -------------------------- If any of the CPP options "bioAnder", "bioDuse", "bioFasham" or "bioMcGillic" is active, the PE model will run an attached biological model. The user specifies the biological parameters and requests the output in an ASCII file. Four example files ("bioAnder.in", "bioDuse.in", "bioFasham.in" and "bioMcGillic.in") are included, one for each biological model. The forms of the files are: -------- bioAnder -------- *** Card 1: ATTPHY phytoplankton light attenuation scale (liter umole-1 m-1). PARFRAC fraction of shortwave radiation that is photosynthetically active (nondimensional). *** Card 2: PHOTORM maximum photosynthetic rate (1/day). PHOTOR0 initial slope of photosynthesis response to light (cm^2/cal). PHOTOINH photoinhibition parameter (cm^2/cal). *** Card 3: HSNO3 half saturation constant for nitrate uptake (umoles/l). HSNH4 half saturation constant for ammonium uptake (umoles/l). NO3INH strength of ammonium inhibition of nitrate uptake (l/umoles). *** Card 4: PHYLR1 linear phytoplankton mortality rate (1/day). PHYLR2 quadratic phytoplankton mortality rate (1/day l/umoles). *** Card 5: GRAZRM maximum phytoplankton grazing rate (1/day). CIVLEV Ivlev constant for zooplankton grazing of phytoplankton (l/umoles). ZOOEXCN fraction of zooplankton grazing that is excreted as ammonium (nondimensional). ZOOEXCD fraction of zooplankton grazing that is excreted as detritus (nondimensional). *** Card 6: ZOOLR1 linear zooplankton loss rate (1/day). ZOOLR2 quadratic zooplankton loss rate (1/day l/umoles). ZOOLF1 fraction of linear zooplankton loss to detritus (nondimensional). ZOOLF2 fraction of quadratic zooplankton loss to detritus (nondimensional). *** Card 7: WSNKPHY sinking rate for phytoplankton (positive down) (m/day). WSNKDET sinking rate for detritus (positive down) (m/day). FRACRMN fraction of the sinking phytoplankton and detritus flux that reaches the seafloor that remineralizes in the bottom level; the remainder is "buried" (nondimensional). *** Card 8: REMNNH4 ammonium remineralization (nitrification) timescale (1/day). REMNDET detritus remineralization timescale (1/day). *** Card 9: BIOPOS switch to enforce positive biological fields: [0] do not enforce, [1] enforce. *** Card 10: biological model output field switches: Convention: [0] do not write, [1] write. IBIOUT(1) nitrate concentration (millimoles nitrogen meter-3). IBIOUT(2) phytoplankton (millimoles nitrogen meter-3). IBIOUT(3) zooplankton (millimoles nitrogen meter-3). IBIOUT(4) ammonium (millimoles nitrogen meter-3). IBIOUT(5) detritus (millimoles nitrogen meter-3). IBIOUT(6) recycled (NH4) production rate (millimoles nitrogen meter-3 day-1). IBIOUT(7) new (NO3) production rate (millimoles nitrogen meter-3 day-1). IBIOUT(8) zooplankton grazing rate (millimoles nitrogen meter-3 day-1). ------- bioDuse ------- *** Card 1: ATTPHY phytoplankton light attenuation scale (liter umole-1 m-1). PARFRAC fraction of shortwave radiation that is photosynthetically active (nondimensional). *** Card 2: PHOTORM maximum photosynthetic rate (mgC/mgChl/sec). PHOTOR0 initial slope of photosynthesis response to light ((mgC/mgChl/sec)/(umole photons/m2/sec)). PHOTOINH photoinhibition parameter ((mgC/mgChl/sec)/(umole photons/m2/sec)). PHIM maximum quantum yield (mol C/mol photons). *** Card 3: HSNO3 half saturation constant for nitrate uptake (umoles/l). HSNH4 half saturation constant for ammonium uptake (umoles/l). NO3INH strength of ammonium inhibition of nitrate uptake (l/umoles). *** Card 4: NQUOTA minimum nitrogen content for growth (umolesN/ug chl). NO3URM maximum nitrate uptake rate (umoles N/ug chl 1/day). NH4URM maximum ammonia uptake rate (umoles N/ug chl 1/day). *** Card 5: PHYLR1 linear phytoplankton mortality rate (1/day). PHYLR2 quadratic phytoplankton mortality rate (1/day l/umoles). *** Card 6: GRAZRM maximum phytoplankton grazing rate (1/day). CIVLEV Ivlev constant for zooplankton grazing of phytoplankton (l/umoles). ZOOEXCN fraction of zooplankton grazing that is excreted as ammonium (nondimensional). ZOOEXCD fraction of zooplankton grazing that is excreted as detritus (nondimensional). *** Card 7: ZOOLR1 linear zooplankton loss rate (1/day). ZOOLR2 quadratic zooplankton loss rate (1/day l/umoles). ZOOLF1 fraction of linear zooplankton loss to detritus (nondimensional). ZOOLF2 fraction of quadratic zooplankton loss to detritus (nondimensional). *** Card 8: WSNKPHY sinking rate for phytoplankton (positive down) (m/day). WSNKDET sinking rate for detritus (positive down) (m/day). FRACRMN fraction of the sinking phytoplankton and detritus flux that reaches the seafloor that remineralizes in the bottom level; the remainder is "buried" (nondimensional). *** Card 9: REMNNH4 ammonium remineralization (nitrification) timescale (1/day). REMNDET detritus remineralization timescale (1/day). *** Card 10: BIOPOS switch to enforce positive biological fields: [0] do not enforce, [1] enforce. use BIOPOS only for debugging purposes IPMOD switch for productivity model [0] exponential model [1] hyperbolic tangent model [2] not used (to be Kiefer and Mitchel model) [3] smith et al (modified hyperbole) model [4] bidigare et al (spectral - phi based) model *** Card 11: C2N Nitrogen:Carbon ratio of phytoplankton (mol N/mol C). C2CHL Chlorophyll:Carbon ratio (mg Chl/ mg C). CHA2CHB Chl a to Chl b conversion (b:a ratio) (mg/mg). CHA2CHC Chl a to Chl c conversion (c:a ratio) (mg/mg). CHA2PSC Chl a to PS carotenoids (psc:a ratio) (mg/mg). CHA2PPC Chl a to PP carotenoids (ppc:a ratio) (mg/mg). *** Card 12: biological model output field switches: Convention: [0] do not write, [1] write. IBIOUT(1) nitrate concentration (millimoles nitrogen meter-3). IBIOUT(2) phytoplankton nitrogen (nitrate) (millimoles nitrogen meter-3). IBIOUT(3) zooplankton (millimoles nitrogen meter-3). IBIOUT(4) ammonium (millimoles nitrogen meter-3). IBIOUT(5) detritus (millimoles nitrogen meter-3). IBIOUT(6) chlorophyll (milligrams chlorophyll meter-3). IBIOUT(7) phytoplankton nitrogen (ammonia) (millimoles nitrogen meter-3). IBIOUT(8) recycled (NH4) production rate (millimoles nitrogen meter-3 day-1) IBIOUT(9) new (NO3) production rate (millimoles nitrogen meter-3 day-1). IBIOUT(10) zooplankton grazing rate (millimoles nitrogen meter-3 day-1). --------- bioFasham --------- *** Card 1: ATTPHY light attenuation by phytoplankton (liter umole-1 m-1). {"kc" Fasham et al. Model}. PARFRAC fraction of shortwave radiation that is photosynthetically active (nondimensional). {"PAR" Fasham et al. Model}. *** Card 2: PHYGRTH initial slope of P-I curve (Watt-1 m^2 day-1). {"alpha" Fasham et al. Model}. PHYEXUD fraction of primary production exuded as DON (nondimensional). {"gamma1" Fasham et al. Model}. PHYLR1 phytoplankton mortality rate (day-1). {"mu1" Fasham et al. Model}. *** Card 3: GRTHPA temperature-dependent growth rate parameter "a" (day-1). {"a" Fasham et al. Model}. GRTHPB temperature-dependent growth rate parameter "b" (nondimensional). {"b" Fasham et al. Model}. GRTHPC temperature-dependent growth rate parameter "c" (degC-1). {"c" Fasham et al. Model}. *** Card 4: HSNO3 half saturation constant for nitrate uptake (umoles/l). {"K1" Fasham et al. Model}. HSNH4 half saturation constant for ammonium uptake (umoles/l). {"K2" Fasham et al. Model}. NO3INH strength of ammonium inhibition of nitrate uptake (l/umoles). {"Psi" Fasham et al. Model}. *** Card 5: ZGRAZR zooplankton maximum growth rate (day-1). {"g" Fasham et al. Model}. ZGRAZK zooplankton growth half-saturation constant (umoles/l). {"K3" Fasham et al. Model}. ZASSEFF zooplankton assimilation efficiency fraction (nondimensional). {"gamma2" Fasham et al. Model}. *** Card 6: PREFPHY zooplankton grazing preference for phytoplankton (nondimensional). {"rho1" Fasham et al. Model}. PREFBAC zooplankton grazing preference for bacteria (nondimensional). {"rho2" Fasham et al. Model}. PREFPON zooplankton grazing preference for PON (nondimensional). {"rho3" Fasham et al. Model}. *** Card 7: ZEXCRR zooplankton excretion rate (day-1). {"mu2" Fasham et al. Model}. ZEXCNH4 fraction of zooplankton excretion to NH4 (nondimensional). (The remainder goes to DON.) {"gamma3" Fasham et al. Model}. *** Card 8: ZMORTR zooplankton mortality rate (day-1). {"mu5" Fasham et al. Model}. ZMORTEX fraction of zooplankton mortality to export (nondimensional). (The remainder goes to NH4.) {"gamma4" Fasham et al. Model}. *** Card 9: BACGRR bacteria maximum growth rate (day-1). {"VB" Fasham et al. Model}. BACGRK bacteria uptake half-saturation constant (umoles/l). {"K4" Fasham et al. Model}. BACFRAC bacterial ratio of NH4/DON uptake (nondimensional). {"eta" Fasham et al. Model}. BEXCRR bacteria excretion rate to NH4 (day-1). {"mu3" Fasham et al. Model}. *** Card 10: WSNKPON PON sinking velocity (m day-1). {"ws" Fasham et al. Model}. BRKNPON PON breakdown rate to DON (day-1). {"mu4" Fasham et al. Model}. *** Card 11: RMNBIO aphotic zone decay timescale for PHY, ZOO, BAC, DON (day-1). RMNPON1 linear aphotic zone decay timescale for PON (day-1) . RMNPON2 quadratic decay timescale for PON (liter umole-1 day-1). RMNNH4 aphotic zone decay timescale for NH4 (day-1). *** Card 12: SBLDEP euphotic zone depth (m). *** Card 13: BIOPOS switch to enforce positive biological fields: [0] do not enforce, [1] enforce. *** Cards 14-15: biological model output field switches: Convention: [0] do not write, [1] write. IBIOUT(1) nitrate concentration (millimoles nitrogen meter-3). IBIOUT(2) phytoplankton concentration (millimoles nitrogen meter-3). IBIOUT(3) zooplankton concentration (millimoles nitrogen meter-3). IBIOUT(4) ammonium concentration (millimoles nitrogen meter-3). IBIOUT(5) PON concentration (millimoles nitrogen meter-3). IBIOUT(6) DON concentration (millimoles nitrogen meter-3). IBIOUT(7) bacteria concentration (millimoles nitrogen meter-3). IBIOUT(8) recycled (NH4) production rate (millimoles nitrogen meter-3 day-1). IBIOUT(9) new (NO3) production rate (millimoles nitrogen meter-3 day-1). IBIOUT(10) zooplankton grazing rate of phytoplankton (millimoles nitrogen meter-3 day-1). IBIOUT(11) zooplankton grazing rate of bacteria (millimoles nitrogen meter-3 day-1). IBIOUT(12) zooplankton grazing rate of PON (millimoles nitrogen meter-3 day-1). IBIOUT(13) bacteria grazing rate of NH4 (millimoles nitrogen meter-3 day-1). IBIOUT(14) bacteria grazing rate of DON (millimoles nitrogen meter-3 day-1). IBIOUT(15) fast-sinking export flux; note that this is the ZMORTR*ZMORTEX*ZOO term, and does not include the PON sinking flux (micromoles nitrogen meter-2 day-1). ----------- bioMcGillic ----------- *** Card 1: ATTH2O1 light attenuation scale of seawater (m-1). {"kw" from PNH Card 1}. ATTPHY light attenuation scale of phytoplankton (liter umole-1 m-1). {"kc" from PNH Card 1}. *** Card 2: HSNO3 half saturation constant for nitrate uptake (umoles/l). {"ks" from PNH Card 1}. *** Card 3: GRAZRM maximum zooplankton grazing rate (1/s). {"rm" from PNH Card 6}. CIVLEV Ivlev grazing constant (l/umoles). {"civlev" from PNH Card 6}. ZOOLR1 linear zooplankton loss rate (1/s). {"zloss" from PNH Card 6}. ZOOLR2 quadratic zooplankton loss rate (1/s l/umoles). {"zloss2" from PNH Card 6}. ZOOEXC1 zooplankton ammonium excretion fraction (nondimensional). {"fslop" from PNH Card 6}. *** Card 4: PHOTORM maximum photosynthetic rate (1/s). {"pmax" from PNH Card 8}. PHOTOR0 initial slope of photosynthesis response to light (cm^2/cal). {"p1" from PNH Card 8}. PHOTOINH photoinhibition parameter (cm^2/cal). {"p2" from PNH Card 8}. *** Card 5: NO3INH strength of ammonium inhibition on nitrate uptake (l/umoles). {"kn" from PNH Card 9}. HSNH4 half saturation constant for ammonium uptake (umoles/l). {"ks2" from PNH Card 9}. *** Card 6: SINKPHY sinking rate for phytoplankton (positive down) (m/s). {"-wsink(2)" from SBL Card 119}. SINKFAC f-ratio sinking rate factor (m/s). {"-wsinkfac" from PNH Card 27}. *** Card 7: ZOOEXP1 fraction of linear zooplankton loss to export (nondimensional). {"zeff1" from PNH Card 28}. ZOOEXP2 fraction of quadratic zooplankton loss to export (nondimensional). {"zeff2" from PNH Card 28}. *** Card 8: PARFRAC fraction of shortwave radiation that is photosynthetically active (nondimensional). *** Card 9: SBLDEP depth of the "SBL" (m). Used for computing the vertically integrated f-ratio. *** Card 10: BIOPOS switch to enforce positive biological fields: [0] do not enforce, [1] enforce. *** Card 11: biological model output field switches: Convention: [0] do not write, [1] write. IBIOUT(1) nitrate concentration (millimoles nitrogen meter-3). IBIOUT(2) phytoplankton concentration (millimoles nitrogen meter-3). IBIOUT(3) zooplankton concentration (millimoles nitrogen meter-3). IBIOUT(4) ammonium concentration (millimoles nitrogen meter-3). IBIOUT(5) recycled (NH4) production rate (millimoles nitrogen meter-3 day-1). IBIOUT(6) new (NO3) production rate (millimoles nitrogen meter-3 day-1). IBIOUT(7) zooplankton grazing rate (millimoles nitrogen meter-3 day-1). IBIOUT(8) export (permanent zooplankton loss) rate (millimoles nitrogen meter-3 day-1). -------------------------- Attached Fish (Cod) Models -------------------------- If in addition to any of the biological CPP options, one of the CPP options "codunlim", "codlim" or "cod_ing" is active, the PE model will run an attached cod model. The user specifies the cod behavioral response parameters in addition to the biological parameters and requests the output in an ASCII file. Four example files ("bioAnderCod.in", "bioDuseCod.in", "bioFashamCod.in" and "bioMcGillicCod.in") are included, one for each biological model. The only differences between the straight biology input and the biology + fish input are the addition of the cod response parameters and some reordering. The forms of the files are: ----------- bioAnderCod ----------- *** Card 1: ATTPHY phytoplankton light attenuation scale (liter umole-1 m-1). PARFRAC fraction of shortwave radiation that is photosynthetically active (nondimensional). *** Card 2: PHOTORM maximum photosynthetic rate (1/day). PHOTOR0 initial slope of photosynthesis response to light (cm^2/cal). PHOTOINH photoinhibition parameter (cm^2/cal). *** Card 3: HSNO3 half saturation constant for nitrate uptake (umoles/l). HSNH4 half saturation constant for ammonium uptake (umoles/l). NO3INH strength of ammonium inhibition of nitrate uptake (l/umoles). *** Card 4: PHYLR1 linear phytoplankton mortality rate (1/day). PHYLR2 quadratic phytoplankton mortality rate (1/day l/umoles). *** Card 5: GRAZRM maximum phytoplankton grazing rate (1/day). CIVLEV Ivlev constant for zooplankton grazing of phytoplankton (l/umoles). ZOOEXCN fraction of zooplankton grazing that is excreted as ammonium (nondimensional). ZOOEXCD fraction of zooplankton grazing that is excreted as detritus (nondimensional). *** Card 6: ZOOLR1 linear zooplankton loss rate (1/day). ZOOLR2 quadratic zooplankton loss rate (1/day l/umoles). ZOOLF1 fraction of linear zooplankton loss to detritus (nondimensional). ZOOLF2 fraction of quadratic zooplankton loss to detritus (nondimensional). *** Card 7: WSNKPHY sinking rate for phytoplankton (positive down) (m/day). WSNKDET sinking rate for detritus (positive down) (m/day). FRACRMN fraction of the sinking phytoplankton and detritus flux that reaches the seafloor that remineralizes in the bottom level; the remainder is "buried" (nondimensional). *** Card 8: REMNNH4 ammonium remineralization (nitrification) timescale (1/day). REMNDET detritus remineralization timescale (1/day). *** Card 9: BIOPOS switch to enforce positive biological fields: [0] do not enforce, [1] enforce. *** Card 10: (Cod parameters) CDZMIN Cod minimum preferred depth (m) CDZMAX Cod maximum preferred depth (m) CDKZ Cod response to depth coefficient (unlimited response CPP option "codunlim") (1/s) (limited response CPP option "codlim") (1/cm) CDKP Cod response to prey coefficient (unlimited response CPP option "codunlim") [(cm^2 l)/(s umole N)] (limited response CPP option "codlim") [(cm l)/(umole N)] CDTMIN Cod minimum preferred temperature (deg C) CDTMAX Cod maximum preferred temperature (deg C) CDKT Cod response to temperature coefficient (unlimited response CPP option "codunlim") {cm^2/[s (deg C)^2]} (limited response CPP option "codlim") [cm/(deg C)^2] CDSPD Cod maximum cruising speed (cm/s) (only active for limited response, CPP option "codlim") CDWMAX Cod maximum vertical swimming speed (cm/s) (set large to resist all upwelling) *** Card 11: biological model output field switches: Convention: [0] do not write, [1] write. IBIOUT(1) nitrate concentration (millimoles nitrogen meter-3). IBIOUT(2) phytoplankton (millimoles nitrogen meter-3). IBIOUT(3) zooplankton (millimoles nitrogen meter-3). IBIOUT(4) ammonium (millimoles nitrogen meter-3). IBIOUT(5) detritus (millimoles nitrogen meter-3). IBIOUT(6) cod concentration (millimoles nitrogen meter-3). IBIOUT(7) recycled (NH4) production rate (millimoles nitrogen meter-3 day-1). IBIOUT(8) new (NO3) production rate (millimoles nitrogen meter-3 day-1). IBIOUT(9) zooplankton grazing rate (millimoles nitrogen meter-3 day-1). ---------- bioDuseCod ---------- *** Card 1: ATTPHY phytoplankton light attenuation scale (liter umole-1 m-1). PARFRAC fraction of shortwave radiation that is photosynthetically active (nondimensional). *** Card 2: PHOTORM maximum photosynthetic rate (mgC/mgChl/sec). PHOTOR0 initial slope of photosynthesis response to light ((mgC/mgChl/sec)/(umole photons/m2/sec)). PHOTOINH photoinhibition parameter ((mgC/mgChl/sec)/(umole photons/m2/sec)). PHIM maximum quantum yield (mol C/mol photons). *** Card 3: HSNO3 half saturation constant for nitrate uptake (umoles/l). HSNH4 half saturation constant for ammonium uptake (umoles/l). NO3INH strength of ammonium inhibition of nitrate uptake (l/umoles). *** Card 4: NQUOTA minimum nitrogen content for growth (umolesN/ug chl). NO3URM maximum nitrate uptake rate (umoles N/ug chl 1/day). NH4URM maximum ammonia uptake rate (umoles N/ug chl 1/day). *** Card 5: PHYLR1 linear phytoplankton mortality rate (1/day). PHYLR2 quadratic phytoplankton mortality rate (1/day l/umoles). *** Card 6: GRAZRM maximum phytoplankton grazing rate (1/day). CIVLEV Ivlev constant for zooplankton grazing of phytoplankton (l/umoles). ZOOEXCN fraction of zooplankton grazing that is excreted as ammonium (nondimensional). ZOOEXCD fraction of zooplankton grazing that is excreted as detritus (nondimensional). *** Card 7: ZOOLR1 linear zooplankton loss rate (1/day). ZOOLR2 quadratic zooplankton loss rate (1/day l/umoles). ZOOLF1 fraction of linear zooplankton loss to detritus (nondimensional). ZOOLF2 fraction of quadratic zooplankton loss to detritus (nondimensional). *** Card 8: WSNKPHY sinking rate for phytoplankton (positive down) (m/day). WSNKDET sinking rate for detritus (positive down) (m/day). FRACRMN fraction of the sinking phytoplankton and detritus flux that reaches the seafloor that remineralizes in the bottom level; the remainder is "buried" (nondimensional). *** Card 9: REMNNH4 ammonium remineralization (nitrification) timescale (1/day). REMNDET detritus remineralization timescale (1/day). *** Card 10: BIOPOS switch to enforce positive biological fields: [0] do not enforce, [1] enforce. use BIOPOS only for debugging purposes IPMOD switch for productivity model [0] exponential model [1] hyperbolic tangent model [2] not used (to be Kiefer and Mitchel model) [3] smith et al (modified hyperbole) model [4] bidigare et al (spectral - phi based) model *** Card 11: C2N Nitrogen:Carbon ratio of phytoplankton (mol N/mol C). C2CHL Chlorophyll:Carbon ratio (mg Chl/ mg C). CHA2CHB Chl a to Chl b conversion (b:a ratio) (mg/mg). CHA2CHC Chl a to Chl c conversion (c:a ratio) (mg/mg). CHA2PSC Chl a to PS carotenoids (psc:a ratio) (mg/mg). CHA2PPC Chl a to PP carotenoids (ppc:a ratio) (mg/mg). *** Card 12: (Cod parameters) CDZMIN Cod minimum preferred depth (m) CDZMAX Cod maximum preferred depth (m) CDKZ Cod response to depth coefficient (unlimited response CPP option "codunlim") (1/s) (limited response CPP option "codlim") (1/cm) CDKP Cod response to prey coefficient (unlimited response CPP option "codunlim") [(cm^2 l)/(s umole N)] (limited response CPP option "codlim") [(cm l)/(umole N)] CDTMIN Cod minimum preferred temperature (deg C) CDTMAX Cod maximum preferred temperature (deg C) CDKT Cod response to temperature coefficient (unlimited response CPP option "codunlim") {cm^2/[s (deg C)^2]} (limited response CPP option "codlim") [cm/(deg C)^2] CDSPD Cod maximum cruising speed (cm/s) (only active for limited response, CPP option "codlim") CDWMAX Cod maximum vertical swimming speed (cm/s) (set large to resist all upwelling) *** Cards 13-14: biological model output field switches: Convention: [0] do not write, [1] write. IBIOUT(1) nitrate concentration (millimoles nitrogen meter-3). IBIOUT(2) phytoplankton nitrogen (nitrate) (millimoles nitrogen meter-3). IBIOUT(3) zooplankton (millimoles nitrogen meter-3). IBIOUT(4) ammonium (millimoles nitrogen meter-3). IBIOUT(5) detritus (millimoles nitrogen meter-3). IBIOUT(6) chlorophyll (milligrams chlorophyll meter-3). IBIOUT(7) phytoplankton nitrogen (ammonia) (millimoles nitrogen meter-3). IBIOUT(8) cod concentration (millimoles nitrogen meter-3). IBIOUT(9) recycled (NH4) production rate (millimoles nitrogen meter-3 day-1) IBIOUT(10) new (NO3) production rate (millimoles nitrogen meter-3 day-1). IBIOUT(11) zooplankton grazing rate (millimoles nitrogen meter-3 day-1). IBIOUT(12-20) not used ------------ bioFashamCod ------------ *** Card 1: ATTPHY light attenuation by phytoplankton (liter umole-1 m-1). {"kc" Fasham et al. Model}. PARFRAC fraction of shortwave radiation that is photosynthetically active (nondimensional). {"PAR" Fasham et al. Model}. *** Card 2: PHYGRTH initial slope of P-I curve (Watt-1 m^2 day-1). {"alpha" Fasham et al. Model}. PHYEXUD fraction of primary production exuded as DON (nondimensional). {"gamma1" Fasham et al. Model}. PHYLR1 phytoplankton mortality rate (day-1). {"mu1" Fasham et al. Model}. *** Card 3: GRTHPA temperature-dependent growth rate parameter "a" (day-1). {"a" Fasham et al. Model}. GRTHPB temperature-dependent growth rate parameter "b" (nondimensional). {"b" Fasham et al. Model}. GRTHPC temperature-dependent growth rate parameter "c" (degC-1). {"c" Fasham et al. Model}. *** Card 4: HSNO3 half saturation constant for nitrate uptake (umoles/l). {"K1" Fasham et al. Model}. HSNH4 half saturation constant for ammonium uptake (umoles/l). {"K2" Fasham et al. Model}. NO3INH strength of ammonium inhibition of nitrate uptake (l/umoles). {"Psi" Fasham et al. Model}. *** Card 5: ZGRAZR zooplankton maximum growth rate (day-1). {"g" Fasham et al. Model}. ZGRAZK zooplankton growth half-saturation constant (umoles/l). {"K3" Fasham et al. Model}. ZASSEFF zooplankton assimilation efficiency fraction (nondimensional). {"gamma2" Fasham et al. Model}. *** Card 6: PREFPHY zooplankton grazing preference for phytoplankton (nondimensional). {"rho1" Fasham et al. Model}. PREFBAC zooplankton grazing preference for bacteria (nondimensional). {"rho2" Fasham et al. Model}. PREFPON zooplankton grazing preference for PON (nondimensional). {"rho3" Fasham et al. Model}. *** Card 7: ZEXCRR zooplankton excretion rate (day-1). {"mu2" Fasham et al. Model}. ZEXCNH4 fraction of zooplankton excretion to NH4 (nondimensional). (The remainder goes to DON.) {"gamma3" Fasham et al. Model}. *** Card 8: ZMORTR zooplankton mortality rate (day-1). {"mu5" Fasham et al. Model}. ZMORTEX fraction of zooplankton mortality to export (nondimensional). (The remainder goes to NH4.) {"gamma4" Fasham et al. Model}. *** Card 9: BACGRR bacteria maximum growth rate (day-1). {"VB" Fasham et al. Model}. BACGRK bacteria uptake half-saturation constant (umoles/l). {"K4" Fasham et al. Model}. BACFRAC bacterial ratio of NH4/DON uptake (nondimensional). {"eta" Fasham et al. Model}. BEXCRR bacteria excretion rate to NH4 (day-1). {"mu3" Fasham et al. Model}. *** Card 10: WSNKPON PON sinking velocity (m day-1). {"ws" Fasham et al. Model}. BRKNPON PON breakdown rate to DON (day-1). {"mu4" Fasham et al. Model}. *** Card 11: RMNBIO aphotic zone decay timescale for PHY, ZOO, BAC, DON (day-1). RMNPON1 linear aphotic zone decay timescale for PON (day-1) . RMNPON2 quadratic decay timescale for PON (liter umole-1 day-1). RMNNH4 aphotic zone decay timescale for NH4 (day-1). *** Card 12: SBLDEP euphotic zone depth (m). *** Card 13: BIOPOS switch to enforce positive biological fields: [0] do not enforce, [1] enforce. *** Card 14: (Cod parameters) CDZMIN Cod minimum preferred depth (m) CDZMAX Cod maximum preferred depth (m) CDKZ Cod response to depth coefficient (unlimited response CPP option "codunlim") (1/s) (limited response CPP option "codlim") (1/cm) CDKP Cod response to prey coefficient (unlimited response CPP option "codunlim") [(cm^2 l)/(s umole N)] (limited response CPP option "codlim") [(cm l)/(umole N)] CDTMIN Cod minimum preferred temperature (deg C) CDTMAX Cod maximum preferred temperature (deg C) CDKT Cod response to temperature coefficient (unlimited response CPP option "codunlim") {cm^2/[s (deg C)^2]} (limited response CPP option "codlim") [cm/(deg C)^2] CDSPD Cod maximum cruising speed (cm/s) (only active for limited response, CPP option "codlim") CDWMAX Cod maximum vertical swimming speed (cm/s) (set large to resist all upwelling) *** Cards 15-16: biological model output field switches: Convention: [0] do not write, [1] write. IBIOUT(1) nitrate concentration (millimoles nitrogen meter-3). IBIOUT(2) phytoplankton concentration (millimoles nitrogen meter-3). IBIOUT(3) zooplankton concentration (millimoles nitrogen meter-3). IBIOUT(4) ammonium concentration (millimoles nitrogen meter-3). IBIOUT(5) PON concentration (millimoles nitrogen meter-3). IBIOUT(6) DON concentration (millimoles nitrogen meter-3). IBIOUT(7) bacteria concentration (millimoles nitrogen meter-3). IBIOUT(8) cod concentration (millimoles nitrogen meter-3). IBIOUT(9) recycled (NH4) production rate (millimoles nitrogen meter-3 day-1). IBIOUT(10) new (NO3) production rate (millimoles nitrogen meter-3 day-1). IBIOUT(11) zooplankton grazing rate of phytoplankton (millimoles nitrogen meter-3 day-1). IBIOUT(12) zooplankton grazing rate of bacteria (millimoles nitrogen meter-3 day-1). IBIOUT(13) zooplankton grazing rate of PON (millimoles nitrogen meter-3 day-1). IBIOUT(14) bacteria grazing rate of NH4 (millimoles nitrogen meter-3 day-1). IBIOUT(15) bacteria grazing rate of DON (millimoles nitrogen meter-3 day-1). IBIOUT(16) fast-sinking export flux; note that this is the ZMORTR*ZMORTEX*ZOO term, and does not include the PON sinking flux (micromoles nitrogen meter-2 day-1). -------------- bioMcGillicCod -------------- *** Card 1: ATTH2O1 light attenuation scale of seawater (m-1). {"kw" from PNH Card 1}. ATTPHY light attenuation scale of phytoplankton (liter umole-1 m-1). {"kc" from PNH Card 1}. *** Card 2: HSNO3 half saturation constant for nitrate uptake (umoles/l). {"ks" from PNH Card 1}. *** Card 3: GRAZRM maximum zooplankton grazing rate (1/s). {"rm" from PNH Card 6}. CIVLEV Ivlev grazing constant (l/umoles). {"civlev" from PNH Card 6}. ZOOLR1 linear zooplankton loss rate (1/s). {"zloss" from PNH Card 6}. ZOOLR2 quadratic zooplankton loss rate (1/s l/umoles). {"zloss2" from PNH Card 6}. ZOOEXC1 zooplankton ammonium excretion fraction (nondimensional). {"fslop" from PNH Card 6}. *** Card 4: PHOTORM maximum photosynthetic rate (1/s). {"pmax" from PNH Card 8}. PHOTOR0 initial slope of photosynthesis response to light (cm^2/cal). {"p1" from PNH Card 8}. PHOTOINH photoinhibition parameter (cm^2/cal). {"p2" from PNH Card 8}. *** Card 5: NO3INH strength of ammonium inhibition on nitrate uptake (l/umoles). {"kn" from PNH Card 9}. HSNH4 half saturation constant for ammonium uptake (umoles/l). {"ks2" from PNH Card 9}. *** Card 6: SINKPHY sinking rate for phytoplankton (positive down) (m/s). {"-wsink(2)" from SBL Card 119}. SINKFAC f-ratio sinking rate factor (m/s). {"-wsinkfac" from PNH Card 27}. *** Card 7: ZOOEXP1 fraction of linear zooplankton loss to export (nondimensional). {"zeff1" from PNH Card 28}. ZOOEXP2 fraction of quadratic zooplankton loss to export (nondimensional). {"zeff2" from PNH Card 28}. *** Card 8: PARFRAC fraction of shortwave radiation that is photosynthetically active (nondimensional). *** Card 9: SBLDEP depth of the "SBL" (m). Used for computing the vertically integrated f-ratio. *** Card 10: BIOPOS switch to enforce positive biological fields: [0] do not enforce, [1] enforce. *** Card 11: (Cod parameters) CDZMIN Cod minimum preferred depth (m) CDZMAX Cod maximum preferred depth (m) CDKZ Cod response to depth coefficient (unlimited response CPP option "codunlim") (1/s) (limited response CPP option "codlim") (1/cm) CDKP Cod response to prey coefficient (unlimited response CPP option "codunlim") [(cm^2 l)/(s umole N)] (limited response CPP option "codlim") [(cm l)/(umole N)] CDTMIN Cod minimum preferred temperature (deg C) CDTMAX Cod maximum preferred temperature (deg C) CDKT Cod response to temperature coefficient (unlimited response CPP option "codunlim") {cm^2/[s (deg C)^2]} (limited response CPP option "codlim") [cm/(deg C)^2] CDSPD Cod maximum cruising speed (cm/s) (only active for limited response, CPP option "codlim") CDWMAX Cod maximum vertical swimming speed (cm/s) (set large to resist all upwelling) *** Card 12: biological model output field switches: Convention: [0] do not write, [1] write. IBIOUT(1) nitrate concentration (millimoles nitrogen meter-3). IBIOUT(2) phytoplankton concentration (millimoles nitrogen meter-3). IBIOUT(3) zooplankton concentration (millimoles nitrogen meter-3). IBIOUT(4) ammonium concentration (millimoles nitrogen meter-3). IBIOUT(5) cod concentration (millimoles nitrogen meter-3). IBIOUT(6) recycled (NH4) production rate (millimoles nitrogen meter-3 day-1). IBIOUT(7) new (NO3) production rate (millimoles nitrogen meter-3 day-1). IBIOUT(8) zooplankton grazing rate (millimoles nitrogen meter-3 day-1). IBIOUT(9) export (permanent zooplankton loss) rate (millimoles nitrogen meter-3 day-1). -------------------- Point Tracer Sources -------------------- If the CPP option "pttrcsrc" is active, the PE model will apply point sources to the tracers. The current example ("tsource_river.dat") contains the parameters to simulate the effect of river inflow upon tracer fields (CPP option "rivsrc"). This is accomplished by the use of point tracer sources. There are two methods for evaluating the point sources: (1) Bi-modal relaxation. A point forcing is introduced to relax the tracer to a desired value. The "bi-modal" nature means that there are 2 desired values and 2 time scales: a basic value & scale and an initial value & scale, used to quickly adjust the initial fields. (2) Direct insertion. The user directly specifies the time-rate of change forcing for a tracer at a point. The input for the nth tracer source looks like: ITSRC, JTSRC (I,J) location of river for nth source. (integer) MTSRC Tracer index for nth source (integer) TSRCF (variable) Tracer source data. (real) if (FACSRC > 0) TSRCF is the value towards which the tracer is relaxed. (tracer units) if (FACSRC <=0) TSRCF is the time-rate of change of the tracer (tracer units / s) FACSRC Method flag for use of source data. (real) FACSRC > 0 Bi-modal relaxation FACSRC <=0 Direct insertion TAUSRC (s) Relaxation time scale. (real) (only active if FACSRC>0) TSRCD (m) Depth to which source is applied. (real) (only active if FACSRC>0) TSRCI (tracer units) Initial value towards which tracer is relaxed. (real) Only applied out to the time FACSRC*TAUSRCI. (only active if FACSRC>0) TAUSRCI (s) Initial relaxation time scale. (real) Only applied out to the time FACSRC*TAUSRCI. (only active if FACSRC>0) ------------------------------------------ Domain Data for Analytical Initializations ------------------------------------------ If both of the CPP options "analytical" and "grids" are active, the PE model will create initial fields and boundary conditions from a user supplied routine. The topography, land masking and other domain data will be expected to come from a supplied netCDF file. The HOPS GRIDS package is used to create this file. ---------------- Profile Sampling ---------------- If the CPP option "peprf" is active, the PE model will extract hydrographic profiles from the model run. The user specifies the locations and times of sampling in an ASCII file. An example file, "sample.dat", is included. The form of the file is: Lines 1-9: Comment cards describing the file format. Line 10: Title, to be used for the output file. For each sampling instrument: 1st line: HTYPE, NBPRF HTYPE Name of instrument NBPRF Number of profiles to sample with the instrument. next NBPRF lines: I(n), J(n), ITT(n) I(n) I-coordinate for Nth profile J(n) J-coordinate for Nth profile ITT(n) Time step number for Nth profile ========= Executing ========= ------------------- Not Two-Way Nested: ------------------- To execute the PE model package, use the following command UNIX command: pe_model < pe_model.in > & pe_model.log & --------------- Two-Way Nested: --------------- Two-Way nesting uses the PVM (Parallel Virtual Machine) package for message passing. This package employs an intercommunicating set of daemons on multiple machines to create a "virtual machine". The first step is starting the "virtual machine". See the PVM documentation for more details. Once the "virtual machine" is started, simply start the top-most domain by hand as normal: pe_model_biggest < pe_model_biggest.in > & pe_model_biggest.log & The sub-domain models will automatically be started. ======== Examples ======== ----------------- Massachusetts Bay ----------------- The tar file "Ex_pe_9.6.tar.gz" contains an example which illustrates how the PE model package is used. The Example is in Massachusetts Bay (MassBay) and uses data collected by Drs George B. Gardner (University of Massachusetts) and W. Rockwell Geyer (Woods Hole Oceanographic Institution) during a cruise on 24-26 July 1990, funded under the Massachusetts Bays Program. This example is a two stage process. In the first stage, a horizontally uniform initialization is run for one time step to estimate the bias in the pressure gradient calculation. This bias is preserved in a file and used in the second stage to "correct" the pressure gradient calculation. In the second stage, a synoptic initialization based on the 1990 data is run for two weeks with the current (1997) surface forcings applied. These surface forcings were obtained from the Fleet Numerical Meteorology/Oceanography Center (FNMOC) over the period 17 June - 9 July 1997. This method can be used to prepare a synoptic estimate prior to any actual sampling. The initialization fields were created in the PE model initialization and update package. In fact, they're the output from the example in that package. The PE_initial package can be found in "pub/HOPS/PE_initial". The surface forcing fields were created in the PE model forcing processing package. In fact, they're the output from the example in that package. The PE_forcing package can be found in "pub/HOPS/PE_forcing". This example also shows how the plotting package is used to produce horizontal contours and cross-sections. This plotting package can be found in "pub/HOPS/Plot". This example includes the following files: GNUmakefile.sun5 GNUmakefile used to create the executables. param.h PE model main parameter statement. pe_PBI PE model SUN Ultra executable used to estimate the bias in the pressure gradient pe_PBI.in Input script used to estimate the bias in the pressure gradient pi_massbay_setbias.nc Initialization fields used to estimate the bias in the pressure gradient pe_PBI.log Echo file from the run used to estimate the bias in the pressure gradient press_bias.nc Estimate of the bias in the pressure gradient. pe_PB_frc PE model SUN Ultra executable. pe_PB_frc.in input script used to run the PE model. pi_massbay_ini.nc MassBay initialization netCDF file. pe_frc_fnmoc.nc MassBay surface forcing netCDF file. pe_PB_frc.log Echo file from MassBay run. pe_PB_frc_out.nc Output netCDF file containing model fields. pe_PB_frc_nrg.nc Output netCDF file containing model energetics. gmeta.cnt NCAR's plot file of MassBay horizontal contours. gmeta.sec NCAR's plot file of MassBay cross-sections. pe_ccnt.in input script to plotting package CCNT_NCAR. pe_csec.in input script to plotting package CSEC_NCAR. gs1.pal.white color palette used in horizontal contours. gs2.pal.white color palette used in cross-sections. plot_pe.gap.dat plotting package parameters for the MassBay. gulf_cst.dat coastlines/islands data from CIA dataset. sec_line.dat file used to indicate cross-section location on horizontal contour plots. grids_massbay.nc MassBay input GRIDS NetCDF file. Used by CSEC_NCAR. pe_csec.log output of CCNT_NCAR, use to trace version number for plotting package. pe_ccnt.log output of CSEC_NCAR, use to trace version number for plotting package.