$ set noverify $!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! $! ! $! VAX VMS Script to compile and link the PE MODEL. Use the following ! $! command: ! $! @ VMSmakefile ! $! ! $! Patrick J. Haley Jr. 08/21/2001 ! $! PE model version 9.6 ! $! ! $! C-preprocessing options: ! $! ! $! advtide Add tidal advection to tracer eqns. (only with ext_tide). $! advtide0 Scale down tidal advection. (only with ext_tide & advtide) $! aixdate AIX intrinsic date routine (IBM RS6000). $! analytical Analytical initial and boundary fields. (Do not use $! with both "dblprec" and "forcing" also active) $! barotropic barotropic model configuration (one level, KM=1) $! bioadjvert Adjustment of biology using vertical dynamics only $! bioAnder Anderson expansion of McGillicuddy biological model $! bioDuse Dusenberry bio-optical models. $! bioFasham Fasham et al. (1990) biological model $! bioMcGillic McGillicuddy et al. (1995) biological model $! bndy_rlx Boundary relaxation. $! botfrc Bottom friction. $! close_tracers Impose closed BCs on tracer N & S boundaries. $! coast Coastal boundary conditions $! coastedge Next to mask, average unmasked values (control noise) $! craydate CRAY's intrisic date/time functions $! cstfrc Coastal friction. $! cubspl Vertical cubic spline interpolation by slabs $! cyclic Cyclic (west/east) boundary conditions $! dblprec Double precision floating-point operations and output $! (Do not use with both "analytical" and "forcing" also $! active) $! dblsigma Double "sigma" transformation in the vertical $! decdate DEC's intrisic date/time functions $! dusDroop Droop nutrient limitation equations $! explicitvmix Explicit vertical mixing $! ext_tide Enable tidal forcing, read and manage barotropic tide info. $! extraction Extract initial and boundary data for requested sub-domains $! fcsterr Maintain OI forecast errors. (with "oias") $! forcing space/time variable forcing. (Do not use with both $! "analytical" and "dblprec" also active) $! frozentrc Initially freeze tracers for specified number of timesteps $! gendbg Generic Debugging: Preserves intermediate files $! grids Domain configuration from GRIDS NetCDF file $! hpg4 Forth order hydrostatic pressure gradient $! imp_bnd_rlx Use semi-implicit in time scheme for boundary relaxation. $! islands Islands are present in the model basin $! ldrifters Lagrangian Drifters option $! leqstate Linear Equation of State $! linear_physics Linear physics: no adv mom, only vert. adv mean tracers $! mixtide Add tide/turbulence interactions in vertical mixing $! coefficient. (only with ext_tide) $! nestnultest Create "nested" code without the nesting routines? $! nocfl No CFL checking. $! notadvm Linear Momentum Equation: no horizontal advection $! notadvt Linear Heat Equation: no horizontal advection $! nowcfl Disable CFL checking in the vertical. $! noxtrp No extrapolation in hydrostatic pressure gradient $! oias Intermittent OI assimilation option $! peprf Hydrographic PE profiles $! ppvmix Pacanowski and Philander vertical mixing scheme $! pressbias Remove bias from pressure gradient $! pressinbias Initialize bias file $! pttrcsrc specification of point tracer sources $! resetjulian Start surface forcing clock from supplied value. $! rmcomments Remove all commented lines after C-preprocessing $! rmdenbar Remove mean density when computing the pressure gradient $! rmdocinc Remove documentation in all include files. $! secondmean enforce zero mean internal vel. after Shapiro filter $! shapiro Shapiro filter for horizontal viscosity $! shapmean Remove "mean" tracer field before shapiro filtering $! simpramp Simple ramping scheme. (with "oias" and "fcsterr") $! sor5pt transport solution via sequential over-relaxation $! sundate SUN's intrisic date/time function $! sunflush regularly flush output buffers in SUN systems. $! sunfpe SUN's floating point exception trap $! unesco Unesco (1980) nonlinear equation of state for seawater $! usrdiagnostic Report user defined diagnostics. $! vbart Vertical Simpson's integration in pressure gradient $! vel_conv Require convergence in velocity when solving PBAR $! wgterr An intuitive form of the OI ramping weight. (with "oias") $! $! New/testing $! $! add_tide On output, tidal velocity added to total velocity. $! bio_12_A Additional productivity terms (bacterial, zooplankton, etc) $! bioadjloc pseudo local biological adjustment. Vertical diffusion $! is on, but advection is off. $! bottom Second-order in time bottom stress calculation. $! 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 Enable cod vertical mixing. (only with codunlim or codlim) $! gridold Recover old algorithm for setting vertical coordinates. $! 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 $! nesttime Times various elements of the run. (SUN only) $! nkfix Revise protections & input for Niiler-Kraus mixed-layer. $! pindex Revised streamfunction filter indices. $! posmxtid Sets (tidal) vertical mixing in pre-defined areas and $! over given depth range. $! rivsrc River sources. Use with PTTRCSRC $! shapnocoastflux Revised filter BCs. $! tide_zero Adds tidal Reynolds stresses (zero freq.) to momemtum $! equations. (only with ext_tide) $! $! cod_ing CJL's modified cod model. Requires "codlim" also active. $! zoo_ing zooplankton following behavior for CJL's cod $! cod_square speed-response is the square functional $! AsselinFilt Add Asselin filter $! AsselinFilt_cod Only apply Asselin filter to cod $! ! $!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! $!!!!!!!!!!!!!!!!!!!!!!!! USERS's tunable definitions !!!!!!!!!!!!!!!!!!!!! $!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! $! $! Directory paths: $! $ define/nolog pebin$dir [...bin] $ define/nolog pe$bin pebin$dir:pemodel.exe $! $! $!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! $!!!!!!!!!!!!!!!!!!!!!! End USERS's tunable definitions !!!!!!!!!!!!!!!!!!! $!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! $goto proceed $! $@compile ocean.F $@compile addtide.F $@compile all_uc.F $@compile anaflds.F $@compile aphread.F $@compile assiwght.F $@compile bdryindx.F $@compile bes1d.F $@compile bess1d.F $@compile bess2d.F $@compile bess2d_msk.F $@compile bess2d_pmsk.F $@compile blkdat.F $@compile boundary.F $@compile bracket_z.F $@compile caldate.F $@compile cdfout.F $@compile cdrspv.F $@compile cell_ok.F $@compile cfl.F $@compile check_prf.F $@compile chkparm.F $@compile clinic.F $@compile cnvmix.F $@compile day_code.F $@compile defbias.F $@compile defnrg.F $@compile defout.F $@compile depthlev.F $@compile depthslab.F $@compile derivs0.F $@compile diag.F $@compile drftdv.F $@compile drifters.F $@compile errio.F $@compile exitus.F $@compile extrap.F $@compile extrap2.F $@compile file_chk.F $@compile flip.F $@compile fsigma.F $@compile get_date.F $@compile get_ewpt.F $@compile get_thick.F $@compile grad24_p.F $@compile gregorian.F $@compile headln.F $@compile hopsrecv.F $@compile host_check.F $@compile hvgrid.F $@compile ind_bdy.F $@compile infld.F $@compile init_srch.F $@compile inittdpth.F $@compile inparm.F $@compile int_gradrho.F $@compile invtri.F $@compile ip2ij.F $@compile landsea.F $@compile lap_depth.F $@compile lap_filt.F $@compile lap_lev.F $@compile length.F $@compile lintrp.F $@compile lintslab.F $@compile ll2xy.F $@compile lnblk.F $@compile load_sig.F $@compile meanrho.F $@compile msk_bdy.F $@compile nest_domain.F $@compile nest_errchk.F $@compile nest_flags.F $@compile nest_init.F $@compile nest_interior.F $@compile nest_rec_bc.F $@compile nest_snd_bc.F $@compile nest_spawn.F $@compile nest_t_align.F $@compile nest_test.F $@compile no_digit.F $@compile odam.F $@compile oiassi.F $@compile oibndry.F $@compile okeep.F $@compile osav.F $@compile pb0wrtcdf.F $@compile ppmix.F $@compile press_bias.F $@compile press_bias0.F $@compile priprod.F $@compile read_tide.F $@compile readgrids.F $@compile readprf.F $@compile readvbc.F $@compile relax.F $@compile rem_llist.F $@compile reset_t_thickness.F $@compile rich_no.F $@compile rk40.F $@compile robc.F $@compile rotangle.F $@compile rotparm.F $@compile rseterr.F $@compile scalvcln.F $@compile set_brlx.F $! $! Only want one of the following 2: $! use set_depths.F without CPP option "gridold" $! use set_depths_old.F with CPP option "gridold" $! $@compile set_depths.F $!@compile set_depths_old.F $! $@compile set_edges.F $@compile set_pmask.F $@compile setvbc.F $@compile setvert.F $@compile shap_lev.F $@compile shap_mean.F $@compile sig2z.F $@compile sig_search.F $@compile sigma2z.F $@compile spline.F $@compile splineslab.F $@compile splint.F $@compile splintslab.F $@compile state.F $@compile step.F $@compile tid_indx.F $@compile tide_aux.F $@compile tide_depth.F $@compile tide_val.F $@compile tracer.F $@compile trackbound.F $@compile trackinit.F $@compile trackrefresh.F $@compile tracksout.F $@compile trackstep.F $@compile trackup.F $@compile trkvscl.F $@compile tsource.F $@compile upbox.F $@compile userdiag.F $@compile vavgv.F $@compile vbar_test.F $@compile vmix_aux.F $@compile vntrpv.F $@compile writehydro.F $@compile wrt_prf.F $@compile wrtcdf.F $@compile wrtstr.F $@compile xtr_psi.F $@compile xtr_trc.F $@compile xtr_vel.F $@compile xtr_vor.F $@compile xtract.F $@compile xtrsubdom.F $@compile xy2ll.F $@compile zetabar.F $! $! Pick at most one of the following sets of biological routines $! $!@compile bioparmAnder.F $!@compile biosourceAnder.F $!@compile defbparmAnder.F $!@compile putbparmAnder.F $! $!@compile bioparmDuse.F $!@compile biosourceDuse.F $!@compile defbparmDuse.F $!@compile putbparmDuse.F $! $!@compile bioparmFasham.F $!@compile biosourceFasham.F $!@compile defbparmFasham.F $!@compile putbparmFasham.F $! $!@compile bioparmMcGillic.F $!@compile biosourceMcGillic.F $!@compile defbparmMcGillic.F $!@compile putbparmMcGillic.F $! $proceed: $ set ver $ DEFINE LNK$LIBRARY SYS$LIBRARY:VAXCRTL $ link/executable=PE_MODEL ocean, - addtide, all_uc, anaflds, aphread, - assiwght, bdryindx, bes1d, bess1d, - bess2d, bess2d_msk, bess2d_pmsk, blkdat, - boundary, bracket_z, caldate, cdfout, - cdrspv, cell_ok, cfl, check_prf, - chkparm, clinic, cnvmix, day_code, - defbias, defnrg, defout, depthlev, - depthslab, derivs0, diag, drftdv, - drifters, errio, exitus, extrap, - extrap2, file_chk, flip, fsigma, - get_date, get_ewpt, get_thick, grad24_p, - gregorian, headln, hopsrecv, host_check, - hvgrid, ind_bdy, infld, init_srch, - inittdpth, inparm, int_gradrho, invtri, - ip2ij, landsea, lap_depth, lap_filt, - lap_lev, length, lintrp, lintslab, - ll2xy, lnblk, load_sig, meanrho, - msk_bdy, nest_domain, nest_errchk, nest_flags, - nest_init, nest_interior, nest_rec_bc, nest_snd_bc, - nest_spawn, nest_t_align, nest_test, no_digit, - odam, oiassi, oibndry, okeep, - osav, pb0wrtcdf, ppmix, press_bias, - press_bias0, priprod, read_tide, readgrids, - readprf, readvbc, relax, rem_llist, - reset_t_thickness, rich_no, rk40, robc, - rotangle, rotparm, rseterr, scalvcln, - set_brlx, set_depths, set_edges, set_pmask, - setvbc, setvert, shap_lev, shap_mean, - sig2z, sig_search, sigma2z, spline, - splineslab, splint, splintslab, state, - step, tid_indx, tide_aux, tide_depth, - tide_val, tracer, trackbound, trackinit, - trackrefresh, tracksout, trackstep, trackup, - trkvscl, tsource, upbox, userdiag, - vavgv, vbar_test, vmix_aux, vntrpv, - writehydro, wrt_prf, wrtcdf, wrtstr, - xtr_psi, xtr_trc, xtr_vel, xtr_vor, - xtract, xtrsubdom, xy2ll, zetabar, - SYS$USRROOT2:[GUEST.LIB]NETCDF.OLB/lib $! $ exit