POLCOMS User Guide
Contents
1. In each case data 1s provided as one file per variable Logical units are at 20 pr 17 rh 19 we 18 wn 24 cl 21 ep 15 Note in this case rh is specific humidity rather than relative humidity this 15 accounted for in heatin F by the directive SHUMID The mesoscale data uses unformatted files and has nx x ny 218x136 starting at 13E 48 39N and a resolution of 0 11 The global data sub set uses formatted files and has nx x ny 42x47 starting at 20 4166E 39 7233N and a resolution of 0 833 lon and 0 5555 lat Open boundary forcing Open boundary forcing consists of elevations and barotropic currents tidal and residual or combined and temperature and salinity A depth varying component of current can also be included in an advective scalar boundary condition Apart from the radiation component of the barotropic forcing these are all active boundary conditions in that they require the specification of external values for the variables This 1s appropriate for nesting in tidally active flows but more work on the passive boundary conditions e g implementing an Orlanski condition 1s required When a model domain is run three files are produced which list the required location of open boundary conditions These are openbclist z elevation points on the boundary openbclist u velocity points outside the boundary openbclist b elevation points outside the boundary Each has the format nzbc Number of points nzbc nzbc nbbc ipt2. then ipexu 1 if no surrounding ipexb 0 At coastal grid points ipexub 1 and ipexu 0 Hence all masks are derived from the bathymetry no extra mask file is required and this significantly simplifies model setup This case allows wetting and drying to be implemented but the need for a horizontal velocity boundary condition is not desirable for coarser resolution simulations CGase ll boundaries A 2 2 pexb ipz1 mex uli eo Debat LU pexub i p 1 inch i p0 peut ID ar i prz 1 lucoastfi jel B 9 j 13 pexb i i 1 pexulij l paxbblipa pexubli rs indo lp inculi p 1 ar i j i ilaceob 2 i i21 Bosob 4 1 1 1 C i29 214 pexb i pz pasul ija Debat Liz pexubii 1 inc 1 0 incufi pr arfi j 1 D 3 8 1 Debt pl pauli pexbb ijiz1 pasubii rs indo fi pel inculi peo ar i rz 1 lucoastfi lr ifaceobil Liltz Figure 2 Case II coastal boundaries coastal points lie alone u points and open boundary lies along b points Open boundaries Open boundaries always lie along b points with either case I or case II coastal boundaries but any point within the domain can be an open boundary point Open boundary b points are indicated by the incb array and the array ifaceob stores which faces of an open boundary point are open i e receive fluxes from outside the model domain By default any point with ipexb i j 1 at icg 1 icg l jcg 1 jcg m is an open boundary point this means with cas
3. ie not stable COEF NSP Interpolate latitude dependent heat flux parameters TOA communication routines o sea points compress Use compressibility term in equation of state for HPG CONST TS BC const ts bc Boundary temperature and salinity values are held constant values read in from file CONST HORIZ DIF Constant diffusivity in o coordinate horizontal POLCOMS user guide doc TEA Smagorinsky CONVECTU convect_u Convective adjustment MERE for u v temperature and salinity not advisable CTDTRACK Output T S and SPM profiles according to a list of time long and lats Output a range of information and specific values of variables at the debuging point For use in debugging plus extra debugging information on DEBUG MODEL physics model DEBUG ADV advection DEBUG B3DRUN main program control DEBUG BAROC baroclinic integration DEBUG BAROT barotropic integration DEBUG CONVECT convective adjustment DEBUG DIFFUSEB scalar diffusion DEBUG DIFFUSEU velocity diffusion DEBUG HORIZUV Horizontal diff u v DEBUG HORIZTS Horizontal diff T amp S DEBUG PGRAD Pressure gradient DEBUG LAGRANGE Particle tracking DEBUG EXCHANGE Halo exchange DEBUG COMMS Communications DEBUG GLOBCOM Global communications DEBUG LAGRANGE Partical tracking DEBUG STRSET Met Data input DIA F dia f Output flux data for T and S budget DIA T dia t Output temperature diagnostics at specified points and in 3
4. 2 1x 13 idriv nr name icriv nr jcriv nr The format for the river data 1s one row per day and one column per river The number of rivers in the database i e number of columns is set in parameters dat and which of these is in the domain is given by the array idriv 5 Compilation Compilation is carried out using an application specific script make polcoms from the application directory e g pol3db setups plume For example bin csh f set OPTS DFLAT DNOTIDE DRIVERS DNO SCOORD DADV BC set OPTS SOPTS DNOCOMPRESS DANALYTICINIT DANALYTIC DEPTH DANALYTIC INIT DRIVERFIX set MACHINE shelf ibmcluster POLCOMS user guide doc 18 set POLDIR J v6 3 set MAKEDIR cwd set EXE NAME shelf copy application specific files cp boundarycon h POLDIR cp data out F POLDIR cp tmpfield F POLDIR cp set_bathymetry F POLDIR cp set_mask F POLDIR enter source directory cd POLDIR compile make clean make SMACHINE OPTIONS OPTS MAKE TARGET polcoms cd MAKEDIR return to application directory and copy in executable cp POLDIR EXE_NAME exit 0 In this example the OPTS variable sets a list of complier directives see appendix A to define the model problem use MACHINE to choose one of the computer dependent make targets in machine_list and the MAKE_TARGET variable choose which selection of models is to be compiled The makefile currently includes the following
5. S2 14 K2 15 M4 mcon 1 or 0 depending on whether each of the ncond constituents is to be used This information 1s used to apply nodal factors and date corrects to give the correct tidal phase for the specified date The assumption being the data is provided in date independent form if this 1s not the case set nfac 0 The format for the tidal data depends on the whether the LONGBCFORM 1s used The file unit 14 starts with the tidal frequencies sigma 1 frequency of 1 constituent in degrees hour sigma ncond frequency of ncond constituent in degrees hour then the default 1s to read do i 1 ncond read itide 8 10 6 z1 j 1 j 1 nzbc read itide 8 10 6 z2 j 1 j 1 nzbc POLCOMS user guide doc 15 read itide 8f10 6 u1 1 j 1 nubc read itide 8f10 6 u2 3 1 1 nubc read itide 8f10 6 v1 j 1 j 1 nubc read itide 8f10 6 v2 j 1 j 1 nubc enddo from unit itide 14 z1 and z2 are the cosine and sine components of the elevation of each constituent similarly for velocity u and v If LONGBCFORM is used data is read according to do i 1 ncond read itide 8f10 6 z1 j 1 j 1 nobdZ read itide 8f10 6 z2 j 1 j 1 nobdZ read itide f10 6 u1 3 1 J 1 nobdUV read itide 8f10 6 u2 3 1 J 1 nobdUV read itide S 10 6 v1 j 1 j 1 nobdUV read itide S 10 6 v2 j 1 j 1 nobdUV enddo where nobdZ 21 2m nobdUV 2 1 1 2 m 1 and the data is ord
6. a subdirectory of the POLCOMS source code directory An objects list file is provided in the POLCOMS directory and included by the makefile The POLCOMS makefile is then used for the additional model including the machine_list options and all object files created are linked to produce the executable If there are connections between modules then these need to specified in the makefile with a I option Note the dependencies of additional models are not explicitly specified This means for example if a POLCOMS module that the ERSEM model uses 1s changed make clean should be used for both POLCOMS and ERSEM codes and the compilation started from scratch An exception to this procedure is GOTM which is installed as a library and then linked in 6 Execution The mode of execution depends on particular computer used its job submission system and whether the code is run in batch or interactive mode Apart from the simplest single processor execution on a stand alone workstation a batch processing script is required to request resources and control the multi processor execution POLCOMS user guide doc 21 Runtime arguments The follow command line options are available except when the NOGUI directive 1s used Model command line options help Print this usage information quiet Suppress stdout monitor verbose Adds debugging info to monitor tdur Run length hours nstep Run length timesteps mnth
7. boundaries lie along b points Figure 1 and the primary definition of the land sea grid is by the u points ipexu which are either wholly land or sea In the latter case each u point 1s surrounded by four sea b points some of which may be fractional This configuration implies a free slip horizontal boundary condition which 1s appropriate to all but fine resolution simulations Most calculations occur at the coastal b points ipexb i j 1 here but the point is surrounded by a fractional grid box ar i j 0 5 or 0 25 The grid is defined in boset by reading in ipexu from an ASCII file in a similar POLCOMS user guide doc fashion to hs then by setting ipexb 1 at all b points surrounding a u point where ipexu 1 There is a test that the depth hs is non zero at points with non zero ipexb This configuration allows small islands and peninsulas to be included and gives a subgrid scale representation of the coastline but wetting and drying 1s not available because of issues of volume conservation that would arise with fractional grid boxes Model grid setups should use a procedure such as 1 Define mask at u points ipexu using the coastline e g use GMT s command grdlandmask 2 Calculate mask at b points ipexb 3 Find bathymetry at sea b points Matlab or similar is useful for this and sometimes iteration from 3 to 1 is needed 1f the available bathymetry 1s not completely consistent with the available coastline Case bound
8. example parameters dat file from the MRCS domain 251 206 m Model grid dimensions 20 n 10 0d0 hsmin Minimum water depth 53f6 2 bathf Format for bathymetry 5012 maskf Format for mask data 2018 4 ts form Format for initial temperature amp salinity 41 1x f3 0 format for cloud data 5018 4 bounts form boundary T S format only use for unf POLCOMS user guide doc 40 2018 4 bounzuv form boundary U V zeta format only use f 10 0d0 daldi Inverse longitude resolution degrees 15 0d0 dbedi Inverse latitude resolution degrees 11 9875d0 along Western limit of domain B point 1 1 48 00833d0 alatl Southern limit of domain B point 1 0 0d0 st Start time 20 0d0 dit Barotropic time step 15 mt Time step ratio 4 mts Number of fast baroclinic steps 744 0 tdur Run Length 1 0d 5 avmin Minimum Diffusivity 1 0d 15 dbdzmin Minimum buoyancy gradient in TKE equations 1 0d 6 q2min Minimum turbulent energy 200 0d0 ahm Coefficent for Killworth Filter 0 2 ahc Coefficient for Smag or constant h diff 1 0 prt Turbulent Prandlt number 0 005d0 cbf Constant or min coeff of bottom friction 3 0d 3 z0 Bottom roughness length 10000 0d0 conv lim Maximum depth for convective adjustment 0 0d0 land value for dry land in bathymetry data 6 0d0 rstress 24 0d0 rcloud Frequency of forcing hours 24 0d0 rsalt 6 ntypes Number of met data variables 24 000 bounfreq TS Frequency of T and S boundary data hours 1 0d0 bounfreq ZET Fre
9. jpt Global index of each open boundary point POLCOMS user guide doc 14 ipt jpt npts This then defines the data and order of the data required 1n the open boundary forcing files The files can be produced by executing the model but without running any time steps lt exename gt tdur 0 and then used to generate boundary condition data for the first model run Tidal forcing Barotropic tidal elevation and currents are forced using a flux radiation scheme with READ TIDECON Tidal velocities are used to calculate a volume flux into out of each boundary elevation point which is used in the standard model equations in barot The elevation at these grid points 1s also relaxed towards the imposed tidal elevation at a rate proportional to the long wave phase speed Veh a Flather radiation condition Tidal data 1s provided to the model either according to the lists described above or across the whole of the four boundaries of a rectangular model domain Information about the tidal constituents to be used 1s defined in a tidal definition file unit 43 This has the format ncond number of constituents nfac flag gt 0 to use date information idate hours day month year gt corresponding to the start of the model run or series of runs start time usually t 0s indx which of a standard list of 15 each of 1 ncond tidal constituents refers to 1 Q1 2 O1 3 P1 4 S1 5 K1 6 2N2 7 MU2 8 N2 9 NU2 10 M2 11 L2 12 T2 13
10. of Marine Systems 57 167 188 Holt J T and I D James 1999 A simulation of the Southern North Sea in comparison with measurements from the North Sea Project Part 1 Temperature Continental Shelf Research 19 1087 1112 Holt J T and I D James 1999b A simulation of the Southern North Sea in comparison with measurements from the North Sea Project Part 2 Suspended Particulate Matter Continental Shelf Research 19 1617 1642 POLCOMS user guide doc 43 Holt J T and I D James 2001 An s coordinate density evolving model of the North West European Continental Shelf Part 1 Model description and density structure Journal of Geophysical Research 106 C7 14015 14034 Holt J T and I D James 2006 An assessment of the fine scale eddies in a high resolution model of the shelf seas west of Great Britain Ocean Modelling 13 271 291 Holt J T I D James and J E Jones 2001 An s coordinate density evolving model of the North West European Continental Shelf Part 2 Seasonal currents and tides Journal of Geophysical Research 106 C7 14035 14053 Holt J T and R Proctor 2003 The role of advection in determining the temperature structure of the Irish Sea Journal of Physical Oceanography 33 2288 2306 Holt J T R Proctor J C Blackford J I Allen and M Ashworth 2004 Advective controls on primary production in the stratified western Irish Sea an eddy resolving model study Jou
11. pointing restarting For example cp filenames jan01 filenames dat shelf tdur 744 tchk 744 cp filenames feb01 filenames dat shelf tdur 672 tchk 672 restart will run shelf for two legs January 2001 and February 2001 check pointing at the end of the first then restarting at the start of the second This allows a long simulation to be broken down into manageable sections e g to fit in the constraints of a batch queuing system Parallel Execution In a normal parallel execution environment in which the number of processors is specified as part of the batch job script or interactive options POLCOMS picks up the number of processors automatically from the size of the MPI Comm World communicator If necessary the number of processors can be set using the nprocs command line option By default POLCOMS automatically partitions the grid in the two horizontal dimensions using a recursive partitioning algorithm This balances the number of sea points across the processors in order to obtain the optimum run time load balance Usually the default settings are those which will work best and give the best performance The number of processors is factored in two dimensions as near square as possible e g on 8 processors then nprocx 4 and nprocy 2 If a different factorization is required this can be specified using the nprocx and nprocy options The simple option disables the recursive partitioning in favour of a scheme which div
12. relaxation zone POLCOMS user guide doc 35 VECTOR Use code optimized for vector machine i e not cache optimized Verbose Write time steps to screen Use WAM wave model WETDRY Wetdry Use wetting drying code WINDFLUC Windfluc Add a fluctuation component read in from file to the wind field ZBAR Lzbar Include the equilibrium tide in barotropic calculation ZERO PG BC zero pg bc In the pressure gradient calculation use zero pressure gradient near bed boundary condition default is zero density gradient ZVARYBC Zvarybc use depth varying currents in T and S advective boundary condition Appendix B Principle Model variables Variables defined in module b3d F Three dimensional arrays e real 8 dimension n 1 mhalo iesub mhalo 1 mhalo jesub mhalo File changed in aa VerL viscosity ms ms X turulenceF horizdiffuse F ak Vert diffusivity m s turbulnceF Gal dl a a S baroclinic step al Mixing length mO b A Buoyancy Jm bealc F bsal Boundary sal psu boundaryTS F fu Volume flux u ms barotF POLCOMS user guide doc 36 fv Volume flux v m s barotF 333 Al oc slow baroclinic step A mero slow baroclinic step asa EE fms tubuleneF m ee e Bee diffuse F temperature diffuse F A O MO UI a ee advect_vel F advect_vel F KE time step time step velocity u S P
13. velocity v de da ms ms I ms ms Mixing length profile Level width Level spacing to surface and sea bed Level width at u points Level spacing at u points A tll variables b point MN variable u point A cole variable b point HM A variable u point Turbulence F sigmaset F scoordset F sigmaset F scoordset F sigmaset F scoordset F scoordset F POLCOMS user guide doc 37 25 hours means sal tidemeanout F tmp spmstorl spmstor2 tuflx tvflx suflx sal flux u p s u tidemeanout F mod svflx sal flux b tidemeanout F 2 4 ms rowbar compressibility calc NEED advection routines ln jadvcw F advpbiv F ode advpbiv FE o aedvpbhv F o adypbiuw F aedvpbiuv FE gt advpbiu F jadvcb w FE diffusivity at u point ms turbulenceF Dissipation ms turbulenceF Two dimensional arrays at 3 time levels e real 8 dimension 1 mhalo iesub mhalo 1 mhalo jesub mhalo 3 Variable File changed in Elevation m _ JbarotF Depth mean current ms u Depth mean current V Two dimensional arrays e real 8 dimension 1 mhalo iesub mhalo 1 mhalo jesub mhalo File changed in POLCOMS user guide d
14. winds temperature relative humidity and cloud cover poems 2 for horizontal coordinates PROGDENS progdens Set buoyancy temperature 1 e equivalent to linear equation of state PVM Use PVM for message passing not recently tested Use lengthscale equation in MY turbulence closure not tested from zero at start of run i MN read initial ts Read initial temperature and salinity fields from file READOPENBCPOINTS readopenbcpoints Read additional open boundary locations from file from file READ ZETUB read zetub Read from file boundary elevations and currents at frequency set in parameters dat READ ZET read zet Read boundary elevations only boundary condition paga HONDA for time seriesoutput reset Timeandcurrents reset to POLCOMS user guide doc 33 zero allows spin up of T and S resetweekmeans Weekly means are initialized at the start of this run RILIMIT rilimit Option on limiting the mixing length in turbulence routines RIMIX rimix Use the Richardson number dependent boundary layer mixing scheme RIVERFIX Elevation is modified by river inflow at a river grid box during baroclinic rather than barotropic time step from rivers start_time rather than time from resart file calculations precipitation data ncc MN EVEN scoord even s levels are equally spaced in the vertical same as levels irrespective of the water depth SCOORD Use horizontally varying vertical coo
15. www gotm net and is then used as a library 2 Defining the problem Unlike a global model a regional ocean model is defined for a limited area and as such can take on a wide range of configurations and domains each approaching the solution of the equations in a different fashion and being subject to different forcing This requirement for flexibility 1s controlled in three ways in POLCOMS POLCOMS user guide doc e cpp compiler directives are used to select portions of the code or exclude others e g DNOSCOORD selects o coordinates instead of s coordinates Many of these in fact set logical variables in parm_defaults F Compiler directives are most conveniently set in a compilation script specific for the application e g make polcoms e All logical variables defined in the main module b3d F can be set in a name list file logicalvariables inp This overrides the logical variables set by compiler directives e Anumber of run time command line arguments are available to set properties such as length of model run check pointing type of domain decomposition Current compiler directives are described in appendix A and options required for several example applications are listed described in appendix D Control files POLCOMS used a number of control files to set basic model parameters and define input output files These can be used in combination with the model described above to define the model application e parameters dat defi
16. CLD FLIP PRCP ZBAR HORIZTS HORIZDIF READ ZETUB VARY REALAX FLIPBATHY LONGBCFORM FOAM BNDUADV Plume BNDUADV RIVERS ANALYTIC INIT ANALYTIC DEPTH FLAT NO SCOORD NOCOMPRESS Appendix E Logical units for input data interp interp 89 interp_ nterp nterp B POLCOMS user guide doc 42 fwin LO Bibliography Allen J L J Blackford J T Holt R Proctor M Ashworth and J Siddorn 2001 A highly spatially resolved ecosystem model for the North West European continental shelf SARSIA 86 423 440 Ashworth M J T Holt and R Proctor 2004 Optimization of the POLCOMS Hydrodynamic Code for Terascale High Performance Computers in Proceedings of the 18th International Parallel amp Distributed Processing Symposium 26th 30th April 2004 edited Santa Fe New Mexico Ashworth M R Proctor J T Holt J I Allen and J C Blackford 2001 Coupled Marine Ecosystem Modelling on High Performance Computers in Developments in Teracomputing edited by W Z a N Kreitz pp 150 163 Cooper W C Hinton N Ashton A Saulter C Morgan R Proctor C Bell J Holt E Y oung and Q Huggett 2006 UK Marine Renewable Energy Atlas ICE Journal of Maritime Engineering In Press Holt J T J L Allen R Procter and F Gilbert 2005 Error quantification of a high resolution coupled hydrodynamic ecosystem coastal ocean model part 1 model overview and assessment of the hydrodynamics Journal
17. D DSSRDATA Use downward SW radiation forcing rather than astronomical calculation corrected for clouds Requires albedo ee oto a radiation forcing POLCOMS user guide doc 28 documentation ERSEM PSS Use ERSEM CC data for additional rivers Fix for missing FOAM b c data FORCEafterDIFF Moving surface forcing to occur after vertical diffusion FOAM FLAT Flat Use Cartesian coordinates daldi and dbedi in parameters dat represent dx and dy in metres FLIPBATHY flipbathy Bathymetry file is read in by row from north to south default 1s south to north FLIPCLD flipcld Cloud data 1s read 1n by row from south to north default is north to south FLIP PRCP flip prcp Precipitation data 1s read in by row from south to north default 1s north to south FLIP RAD flip rad SW radiation data 1s read in by row from south to north default 1s north to south GLOBMET elobmet Use Met Office s Global NWP data GOTM Use the General Ocean Turbulence Model to calculate vertical diffusivities HARM ANA Do harmonic analysis and output harmonic constants to file Include the vertical velocity in the harmonic analysis calculations requires HARM ANA too HARMW HORIZDIF Horizdif i Add horizontal diffusion to currents on Z levels HORIZTS Do horizontal diffusion of POLCOMS user guide doc requires HORIZDIF too to currents on o levels Do horizontal diffusion of temperature and salinity HORIZ
18. Month number for input particles Enable particle tracking indir Directory for input data files flipcld flips cloud data from north south to south north Restart checkpointing warm start Start from restart file restart Start from restart file reset Resets time u v zet restm Resets time on restart to start time tchk Checkpoint interval hours nchk Checkpoint interval timesteps tcmin Time of first checkpoint hours ncmin Timestep of first checkpoint hours tfwnd Forward wind input data hours Parallel processing nproc nprocs nprocx nprocy nens asynch immed promis nocomms noimmed nosndrcv simple sndrcv synch partrk map Number of processes not usually required Number of processes Re Number of processes in x Number of processes in y Number of ensemble members Use asynchronous comms Use non blocking comms Use promiscuous receives Disable boundary exchange Use blocking comms Do not use send receive mode Use simple partitioning Use send receive mode Use synchronous comms Use RK partitioning Print partitioning map to file Client Server operation SCIVCT start POLCOMS as server POLCOMS user guide doc 22 Debugging idbg Debugging point x coordinate jdbg Debugging point y coordinate kdbg Debugging point z coordinate An important feature available from these run time options is check
19. POLCOMS User Guide V6 4 Jason Holt March 2008 CO ec e e FT TF NA OOM DD NUT OIC O E Back oro Undead l The cope ol POLCON Stata US E lan The CIA nara Denam Tbe proble Control A 2 D fmime a POLCOMS prid ria Horizontal dscretnzapnon sa 3 case I boundaries c ccccccccccceccccccecececcccccuceccceccuceseseccucucesecsceusecesuccucesesecesceseseseccesess case II boundaries cccccccccccccecccccccceccccccuceccccccucecseccucucesececceseceseccecesseceseeseseseccecess Ier E Vertical discretization corno noo aaa se asaan Lem Initial conditions cccccccceccsccecececceccececceccecccscceceecscceceececesccececcscescecscescescscescascesenees CY CY CY Mm Met Oee tm TAM a ANA AA Aa AA AA OPA DONNA OT oe Denning forcing tor TEE RE Ee A A 4 Residual CortbIDie TOCINO errado 15 Temperature Ee 16 A E RR ee ee meee 17 2v COMP HAO aaa nnn UNIO eater PA te Dn ERE RIOR AEA iio 17 Compilation Options ia 19 Compiling Additional Models ei eis 20 Or Dr 1610 18 01 EDI 20 SEENEN 21 Parallel e e EE 27 Oe ensemble mode eoo o ER t PEE PEE pd 22 Te OTid cT 23 a VT EE 23 Phy SC ble ecclesi O MES teuer tai metes iot tad eria Sade en oben act 24 Appendix A Model control CPP directives and logical variables 25 Appendix B Principle Model varables aa 35 TEAM arrays outer de panic diu ttai alo
20. _DIF_SIG HORIZ_DIF_SIG_TS requires HORIZ DIF SIG too hor_press_grad Switch on off hpg IBM Machine dependent option for IBM systems e g HPCx INVERSE_B inverse_b Apply inverse barometer correction at the boundary used when boundary data elevations do not include the effects of atmospheric pressure but either BULKMET or POINTMET is used Use irregular shaped relaxation zone T amp S b c s Filter assimilation Use ensemble optimal interpolation assimilation Perturb cloud cover in ensemble Kalman filter A p EE pa intervals tchk ce tl Ifwnd Forward wind forcing data by time tfwnd O Inoout Suppress output looping AA LOCOMS LONGBCFORM longbcform Run Low resolution POLCOMS user guide doc IRREG BC irreg bc key EnKF Key EnOI key ENSEMBLEOUT key clderr Coastal Ocean Model 1n addition to POLCOMS use long format boundary conditions south north West east 30 warm Readin full restart data a passing oe em Eg speed EON NWP data ico NNNM my25cbf Set a spatially varying coefficient of bottom friction otherwise constant NOCOMPRESS Omit the pressure term from the calculation of potential buoyancy Required if not using s coordinates OLD UR VR Use original calculation of depth varying component of volume fluxes in scalar advection NO CONVADJ Do not do a convective adjustment default with GOTM on NCEP to replace ERA40 diffusion a Switch off h
21. aries A E2 ee pexb ipz1 pexufi 10 pexbb iji 1 pexubli 0 Inch i N0 peut peo ar 1 0 25 B oi Debt pal pexu 101 paxbbl ipis pexub i 1 indo i 1 inzufi pr 1 ar i rz 1 ilaceob 2 i i2 1 Ceci C i29 14 pexbi i nz ex ut Ur pexbb ipzl pexublfi 1 inch fi PHO incufi ar i rz 1 D i Fi pexb i Ir pexufi jea pexbb ijz1 pexub i It indo fi pel inculi peo ar 1 0 5 eecht i 1 Figure 1 Case I boundaries coastal and open boundary lies along b points A simpler definition of case I boundaries 1s available 1f sub grid scale coastline representation 1s not required In this case compiler directive SIMPLECASEI only a bathymetry file is used no mask file which defines ipexb ipexu 1 is then defined when all four surrounding b points have ipexb 1 An alternative method of defining the grid water depth 1s provided by the logical options analytic depth In this case FORTRAN files called set bathymetry F and POLCOMS user guide doc set_maks F are included These adjust set the global arrays depth and mask respectively case ll boundaries In this case land boundaries lie along u points Figure 2 Calculations do not occur at the boundary points but rather a lateral boundary condition is used either non slip default or slip zero horizontal gradients are imposed with compiler directive UBC In this configuration the bathymetry is used to set ipexb where hs gt land
22. code These are usually set in data_out F for output see appendix E for input data units 3 Defining a POLCOMS grid As a finite difference model the spatial discretization on which the equations are solved is especially important In POLCOMS this is a B grid on either spherical polar coordinates or Cartesian coordinates in the horizontal and terrain following coordinates in the vertical Horizontal discretization In the horizontal POLCOMS uses a B grid discretisation so both components of velocity u v are defined at u points half a grid box to the southwest of points where elevations and other scalar variables are defined b points see Figure 1 The domain size 1s icg 1 l jeg 1 m with 1 1 being the southwest corner All horizontal arrays have a halo of at least 1 point i e array size is at least 0 1 1 0 m 1 to facilitate message passing and open boundary data Figure 1 shows the arrangement of grid points The grid resolution rdal rdbe is set in parameters dat either as an inverse angular resolution in degrees or in metres for Cartesian coordinates with directive FLAT The coordinates lat lon or Cartesian of the southwest bottom left elevation points alon0 alat0 at icg 1 jcg 1 are also set in parameters dat IMPORTANT Because the model is coded for multiprocessor systems almost all the horizontal indices in the model code apart from 1 0 refer to the LOCAL arrays i e POLCOMS user guide doc those on a
23. d how these are represented numerically and coded While this document describes many of the options available nothing beats looking in the code to see what they do Throughout this guide the following typographic conventions are used POLCOMS user guide doc Variables in equations in italics e g T Variables names and code in bold e g tmp cpp compiler directives in bold capital e g NOSCOORD Subroutine module names in bold italics e g b3drun Filenames in bold Arial e g b3drun F The code POLCOMS is available under license to collaborators of the Proudman Oceanographic Laboratory The model release un tars into the following directory structure pol3db v6 3 The source code PMLersemv2 0 CICE Additional model codes available from the WAM originators setups Application specific subdirectories plume MRCS IRS The source code consists of e E FORTRAN 90 fixed format source with cpp directives the main body of code e c C source files used for command line arguments and GUI e h include files e makefile for compilation control e objects lists of source object files for POLCOMS and subsidiary models e machine list machine dependent options e dependencies pol3db code inter dependencies Generally one set of source code is used for all applications but there is the option of including application specific code e g for different forms of data output The GOTM model should be installed as per instructions on
24. e I boundaries there can not be a coast line along these rows columns since ipexb 1 on the coast the model domain must be extended to POLCOMS user guide doc 10 accommodate this In addition to these default points a list of points can be read in of which faces around any model points are open boundaries if the directive READOPENBCPOINTS is set This reads the ASCII file openbcpoints dat which has the format npts icg jcg iface 1 icg jcg iface npts where npts is the number of additional open faces and the columns list the position of these icg jcg and which face is open iface 1 south iface 2 north iface 3 west iface 4 east This allows any shaped open boundary to be defined Vertical discretization The model uses a staggered vertical grid Figure 3 with state variables defined 1 2 a grid box above and below the sea surface and bed and flux variables defined at the surface and sea bed Vertical indexing for the state variables is k 2 n 1 k 1 and k n are used for boundary conditions and for flux variables is k 1 n 1 from the sea bed to the surface The model vertical coordinate is written in coordinates but there are two choices of how the model levels are discretized in e space e S coordinates The level spacing in space can vary in the horizontal vertical coordinate variables ds dsu sig sigo have 3 indices and separate variables are defined at u points dsv dsu sig sigo e o coordina
25. earch centre programme Oceans 2025 and the National Centre for Ocean Forecasting The scope of POLCOMS POLCOMS 1s a three dimensional baroclinic B grid model designed for the study of shelf sea processes and ocean shelf interaction Recent work has taken it into estuarine environments The model solves the momentum and scalar transport equations for oceanographic applications with realistic topography bathymetry and forcing The underlying hydrodynamics in POLCOMS are the shallow water equations with the hydrostatic and Boussinesq approximations This limits models applicability to flows where the vertical acceleration is small and in practice this imposes a minimum horizontal resolution simulation can be made at resolutions finer than this but at no benefit to the solution As a rough guide this can be taken as half the maximum water depth Using this guide This guide is aimed at providing a new user with a basic introduction to POLCOMS and to act as a reference for setting up new model domains It lacks much of the details of the solution techniques the most up to date reference for this is Holt and James 2001 a full technical manual is in preparation POLCOMS 1s a complex model system and a large code currently standing at around 95 000 lines of code particularly resulting from the range of options and the parallel message passing code To use it effectively requires an understanding of the model equations and boundary conditions an
26. emp3d 1 m n real 16 ts_form temp3d POLCOMS user guide doc 12 Alternatively if the ANALYTIC_INIT directive is set a FORTRAN file called tmpfield F is included This should set the values of tmp and sal at all local b points This is useful for defining idealised problems test cases 4 Defining forcing for POLCOMS In all but the most idealised cases external forcing provides an important control on a coastal ocean simulation POLCOMS includes a wide range of provisions for surface metrological open boundary lateral and riverine land forcing Surface forcing Complete POLCOMS simulations require surface fluxes of heat hfl in hfl_out momentum fs gs and freshwater ep and also surface pressure pr Apart from pressure which is used directly these are usually defined via bulk formulae from atmospheric data the alternative approach to use fluxes directly from an NWP model e g the Met Office applications of POLCOMS is not described here The model then requires the following variables as local arrays note units at air temperature degrees C we wn wind speed eastwards and northwards m s rh relative humidity 96 cl cloud cover 96 pr atmospheric pressure mb pn precipitation ms The data are read in in metset F which is currently hard wired to a number of fixed data types The data is read in on the native grid and frequency of the atmospheric model data set e g as provided by BADC a copy
27. ered east to west and north to south along the southern northern eastern then western boundaries irrespective of whether points are land or sea The boundary tidal currents are then calculated from these constituents at each barotropic time step If directive ZBAR is used the equilibrium tide is also used Residual combined forcing As well as tidal forcing time series of barotropic elevation and current can be applied around the model boundaries These either represent the residual in which case they are additive with the tidal component or they can be used to provide the full forcing The Data are read from unit nrm 77 at a format default is boundzuv_form unf for unformatted and frequency in hours set in parameters dat less than hour currently causes an error At each time data is read in using read nrm z1 j j 1 nzbc read nrm ul j j 1 nubc read nrm v1 j j 1 nubc and similarly for the unformatted case z1 ul v1 are boundary currents and elevations These are ramped linearly in time between concurrent values and applied as boundary conditions as described above A LONGBCFORM is also available in a similar format to the tidal constituents If only elevations are available these can be imposed using a relaxation condition set using READ ZET this has not been extensively tested POLCOMS user guide doc 16 Temperature and salinity Two options are provided for scalar boundary conditions an up w
28. es netcdf netcdf 3 5 1 lib Inetcdf LIBS S LIBS The POL IBM cluster using MPI shelf ibmcluster mpi MAKE MAKE TARGET OPTIONS OPTIONS OPTIONS OPTIONS DEBUG DEBUG V EXE EXE SIZE S SIZE ENV MPI CPP lib cpp CPPFLAGS P traditional CPPMACH DLINUX V I usr local mpichgm include V CCzmpicc CFLAGS Ktrap fp D FILE OFFSET BITS 64 A FCzmpif90 FFLAGS r8 O2 Mlfs Ktrap fp Mprof byteswapio OFLAGS GFLAGS PFLAGS LOPTS Mprof POLCOMS user guide doc 20 LIBS LIBS The HPCx IBM Power 5 shelf regatta mpi PMAKE S MAKE_TARGED OBJECTS OBJECTS DEPENDS DEPENDS V NPES NPES 1 OPTIONS S OPTIONS DEBUG DEBUG PROGRAM PROGRAM ENV MPI CPP lib cpp CPPFLAGS P CPPMACH I usr lpp ppe poe include thread64 DIBM CC2cc CFLAGS q64 V FCzmpxlf90 r OFLAGS O2 qarch pwr4 qtune pwr4 qhot qsuppress 1500 036 V GFLAGS PFLAGS FFLAGS q64 F77FLAGS qfixed F90FLAGS qsuffix f f90 LFLAGS L usr local lib V LIBS S LIBS For each new computer POLCOMS is compiled run on a new target 1s required in machine_list following this template Compiling Additional Models POLCOMS has been coupled to a range of different modelling systems notably ERSEM ecosystem model GOTM turbulence model CICE sea 1ce model and WAM wave model Generally the additional model code is placed in
29. ides the domain without any regard to the distribution of sea points The map option may be used to write a map of the portioned domain to a file in PPM format The netpbm package http netpbm sourceforge net may be used to convert this file to an image e g using the ppmtogif command Options asynch and synch switch between asynchronous and synchronous communications 1 e normal MPI sends and synchronous MPI sends Options immed and noimmed switch between normal MPI sends and immediate MPI sends The option nocomms may be used to disable all nearest neighbour boundary exchange Whereas this invalidates the results of the code it is useful to compare timings with and without communications Running in ensemble mode It is possible to run POLCOMS in ensemble mode where a number of independent model runs are combined in a single job To enable this specify the command line option nens e g nens 16 For example when running on 64 processors this will execute 16 POLCOMS user guide doc 23 independent model runs with 4 processors each except see later In order to specify different parameters for each ensemble member POLCOMS looks for individual copies of the files parameters dat and filenames dat of the form parameters_001 dat parameters 002 dat etc and filenames_001 dat and filenames_002 dat etc If these files are not found then each ensemble member runs with the same standard parameters dat and filenames dat files In this
30. ind advective scheme and a relaxation scheme Currently the list data format is only available for the advective scheme the relaxation scheme 1s limited to the longer format and hence only rectangular domains The type of T and S boundary condition data is controlled by the file boundarycon h c Zdefine TS boundary condition bost c define TS boundary condition boundaryTS Zdefine TS boundary condition boundaryTS longform c define TS boundary condition bfix c define TS boundary condition no bc The appropriate sub routine is un commented For advective boundary conditions data 1s provided one grid cell outside the model domain and the boundary condition currents used to advect it into the domain on inflow Data frequency is set in parameters dat and at each time data is read from unit nrmt 78 by do j 1 nbbe read nrmt Iin Jin btmpl k j k 1 n 2 enddo do j 1 nbbe read nrmt Iin Jin bsall k j k 1 n 2 enddo unless bounts_form unf in which case do j 1 nbbe read nrmt btmp1 k j k 1 n 2 enddo do j 1 nbbc read nrmt bsall k j k 1 n 2 enddo is used Data 1s ramped linearly in time at each time step For relaxation conditions the width of the relaxation zone niw is set in parameters dat The relaxation coefficient is set to vary linearly from 1 clapped at the open boundary to zero at niw 1 points in side the model Data 1s read uses read nrmt btmp1 k j k 1 n 2 j 1 nobw read nrmt bsal1 k
31. is passed to each processor and is then interpolated 1n spaced onto the model grid this 1s efficient for coarse resolution atmospheric data but could be improved with parallel input for large data sets Note no distinction between u points and b points 1s made in the interpolation both use b point value with the same index Input infrequency 1s set by the istress icloud isalt variables defined in parameters dat The model includes code for reading met data on the Northwest European shelf from two sources Work in the GCOMS project will generalise this to any region around the globe ECMWF data This 1s the default and refers to either reanalysis ERA40 or operational products Data is read from 3 files From unit 17 we wn pr at rh from unit 21 cl from unit 89 pn Optionally solar radiation sr is read from unit 87 In each case the data is on a grid of size nx x ny 41x26 staring at 25E 40N and read from an ASCII file read 17 10f8 2 modata1 j k j 1 nx k 1 ny y POLCOMS user guide doc 13 In a number of cases the daily accumulation files cloud cover precipitation and solar radiation are provided in a north to south format The directives FLIPCLD and FLIP PRCP accommodate this This data are converted from day to s Met Office data There are two sources here differing in resolution the mesoscale model 12km directive MESOMET and a sub set of the global model data 1 directive GLOBMET
32. ive Logical variable METOFFICE Needed 1f using met office heat fluxes and system OOOO GULF A Meet Office domain AMM A Meet Office domain IRSH A Meet Office domain MRCO S A Meet Office domain advection momentum ADV BC adv bc Used advective boundary conditions otherwise relaxation ANALYTIC DEPTH analytic depth Set bathymetry to idealised values defined in set bathymetry F ANALYTIC INIT analytic init set an analytic buoyancy temperature field defined in tmpfield F ATTEN Use IOP derived attenuation coefficients for heating and ecosystem model inflow BIHARM Biharmonic rather than Laplacian in sigma coordinate horizontal diffusivity NOT TESTED POLCOMS user guide doc 26 BIO_LAMDA bio_lambda Use transmissivity from the ERSEM model in the heatflux calculation BNDUADV Include boundary points in velocity advection acts as Sommerfeld type passive boundary condition BULKMET bulk_met Read met data from files s pressure winds temperature relative humidity and cloud cover flux BULK um NN Use Goldsmith and Bunker Heat bulk heat flux CEH eh UseCEHUK river data ac cice Use the Los Alamos CICE sea ice model a cloudpoint a single value of cloud data is read to represent the cloud over the whole domain at each time use with BULKMET COARSEGRID Setup a coarse resolution grid to run alongside standard model
33. j k 1 n 2 j 1 nobw POLCOMS user guide doc 17 where nobw 21 2m unless VARY RELAX is set In this case the imposed data can vary across the relaxation zone and nobwz2 niw l4 2 niw m Data is ordered east to west and north to south along the southern northern eastern then western boundaries irrespective of whether points are land or sea If VARY_RELAX is set this 1s repeated for kk 1 to niw points inside the model domain using the provided data otherwise the data at the boundary is used across the relaxation zone note side length does not decrease as kk increases A number of FORTRAN program are available to extract boundary condition data from POLCOMS output for use as forcing for a smaller and usually finer resolution domain River inputs A simple approach for applying river forcing 1s used this is to increase the sea surface elevation according to the volume flux with a corresponding adjustment to the salinity through the water column The river locations are provided by an index file unit 29 that lists the model grid points The file starts with nofriv number of rivers 1n the domain then the locations are given in a range of formats Default 36 NW shelf rivers read 29 i2 1x a14 2 1x 13 idriv nr name icriv nr jcriv nr If NORIVTMP is set 40 years NW shelf database of 300 rivers read 29 13 2 14 1x a20 idriv nr icriv nr jcriv nr name If CEH set 40 year data base of UK rivers read 29 13 1x a19
34. nes the grid size resolution and a number of model parameters For the current format see the example in appendix C e Scoord params dat defines parameters for the s coordinate transform if used An example 1s 150 0d0 hc 1 0d0 CC S coordinate parameters 5 0d0 theta 0 25d0 bb for an explanation of these see Holt and James 2001 e logicalvariables inp A nameslist file setting the logical variables in b3d F see appendix A e filenames dat sets the names of input and output files The format is INPUT input files directory Path to directory of input files lt numnames gt Number of input files lt input file 17 logical unit gt lt type gt filename logical unit for filename lt input file numnames gt OUTPUT POLCOMS user guide doc lt numnames gt Number of output file names lt Idname gt Run identifier lt output file 17 lt logical unit gt lt type gt lt filename gt logical unit for filename lt output file numnames gt Data Types are 1 formatted 2 unformatted 3 unformatted without input directory path When the model 1s run it opens all input files in the given path with the given name at the given unit and all output files with the suffix Idname to identify the run output Output files are by default written to the directory the model is run in Note the logical units read in here are only used for the purpose of opening the files they must match those used in the
35. oc UI QO Afnlb Depth mean of non linear buoyancy terms u Fraction area of grid cell Air temperature C Depth mean of non S b3dgrid F gt et e Bfnlb linear buoyancy terms u cdb Bottom friction coefficient Csq old bottom friction term Dzdt E Precipitation minus ms evaporation hl Es ms Flxu m s tidemeanout F Flxv tidemeanout F m s depth m m Un PIP Advect_sca F 2 fm _ Advect_sca F hfl out depth depth u points hul Intermediate water m Advect_vel F depth mg N b3dgrid F SR A Fi u Advect vel F hu22 PERENNE Advect vel F Relfac Relaxation zone factor POLCOMS user guide doc 39 We si Eastwardwind Jm metset F Northward wind ms metsetF CC Equilibrium tide tidbndrp2 F Zetbc Elevation boundary m tidbndrp2 F condition boundaryUVZ F bcbr F ume in elevation Neri very shallow water Two dimensional integer arrays e integer dimension n 1 mhalo iesub mhalo mhalo jesub4 mhalo Tapy JadvsetF Tapu l JadvsetF Tapuy JadvetF boundary open boundary Ipexb_________ Calculation mask b boset F pexu calculation mask u bosetF b j bosetF boset F land sea mask b irel relaxation zone points from boundary 3dgrid F Appendix C Model parameters This is an
36. options polcoms polcoms gotm polcoms gotm ersem polcoms ersem polcoms wam Each also requires the corresponding cpp directives to be set DERSEM DGOTM DWAM The optional make clean statement will remove all object files and f files so compilation will start from scratch usually not necessary Compilation proceeds in two stages Each FORTRAN source file F 1s compiled in turn by make first compiler directives are resolved to give a f file then these are compiled with the FORTRAN compiler e g POLCOMS user guide doc 19 cpp D b3drun F b3drun f The resulting f files should not be edited f90 8 c b3drun F o b3drun o Then all object files o files are linked to create the executable The default executable name is Shelf Compilation Options The make targets in machine_list provide the compilation options required for each different computer compiler They are also used for different compilation and linking options e g for debugging and profiling and to set paths to libraries Three examples are shown A linux workstation with debugging on shelf linux pg g MAKE 0 MAKE TARGET OPTIONS OPTIONS OPTIONS OPTIONS DEBUG DEBUG V PROGRAM PROGRAM SIZE SIZE ENV SERIAL CPP cpp CPPFLAGS P traditional CPPMACH DLINUX CC pgf90 CFLAGS Ktrap fp g 1 FC pgf90 FFLAGS g r8 Ktrap fp Mprof Mextend A OFLAGS GFLAGS PFLAGS V LOPTS L packag
37. orizontal pressure gradient calculation NOCLI Make b3drun F the main program needed for error trapping with Portland Compilers but disables command line arguments deis calculations NO PGRAD Calculate the horizontal pressure gradientalong o levels po 1g e advection LERNEN LU wind forcing NORIVERSKIP Read in river data from POLCOMS user guide doc 31 es skipping nday 1 records Do not read in river temperatures force 1s zero A Hn integration NOSCAADV Turn off scalar advection NO_SCOORD scoord Use o rather than s coordinates mm ear SPM wan RE ween rivers of SPM NOSLIP O O NOSTEEP Turn off steepening during calculation of horizontal advection NOSTEEPZ Turn off steepening during calculation of vertical advection A re reo spaced redundant residual forcing eS a integration NEED nell advection EM E advection class inco O outscoord Output 3d array of s coordinates run will stop as soon as file 1s written PARALLEL STATS TTT ri Output parallel statistics model a Ipgrad Calculate the horizontal pressure gradient by interpolating onto POLCOMS user guide doc NORIVTMP 32 horizontal plane default linear interpolation Default true PGRAD_SPLINE Ipgrad_spline Calculate the horizontal pressure by spline interpolation onto horizontal PGRAD TEST Po c pee Execute the PAA model Kees point_met Use single point met data pressure
38. particular processor and range from i 1 iesub and jJ 1 jesub The relation between LOCAL 1 3 and GLOBAL icg jcg indices is icg i ielb 1 jcg jtjelb 1 The model is designed to be highly flexible in its definition of coastal and open boundaries Hence there are 7 masks used to define these ipexu 1 at u point where calculations are conducted ipexb 1 at b point where calculations are conducted ipexub 1 at a sea u point including coastal points ipexbb 1 at a sea b point iucoast 1 where u point is coastal and velocities are evaluated by the lateral boundary condition case II boundaries only see below incb 1 at an open boundary points always on b points incu 1 at sea u points next to open boundaries The distinction between ipexb and ipexbb arises because there can be points across boundaries that are sea points but where model calculations are not conducted Other more specialized masks e g in the advection routines are described in the subroutine documentation The bathymetry hs is read in at the b points as an ASCII file by the subroutine hset real 8 depth 1 m If leader then read 13 depth j i 1 D j 1 m endif call dist leadid depth hs 1 If the flipbathy logical variable 1s set then the array 1s read from north to south rather than south to north the defualt There are two configurations available as to where the sea land boundary lies on this grid case l boundaries In this case land
39. pt points and for each of this open a file physseries lt i gt RUNID to unit 200 1 each call to outseries e g call outseries wcol 200 10utpt writes depth profiles of u v tmp aa ak qsq al and spm if used Variables are converted to integer unless REALSERIES is defined MATLAB code to read these files is like load physseries ni np length physseries ni i 1 np t 1 24 k 2 n 1 ii ni 1 eval clear aa RunID Id J eval clear ak RunID Id eval clear qsq RunID Id eval clear al RunID Id eval time RunID Id zphysseries ni i ii 1 eval u RunID Id physseries ni i 11 k 1000 1i 11 1 eval v RunID Id Zphysseries ni i ii k 1000 1i ii 1 eval tmp RunID Id physseries ni i 11 k 1000 1 11 1 eval sal RunID Id physseries ni i 11 k 1000 1 11 1 eval aa RunID Id 2 n 1 physseries ni i 11 k 100000 1 1 1 eval ak RunID Id 2 n 1 physseries ni 1 i1 k 100000 ii ii 1 eval qsq RunID Id 2 n 1 physseries ni i 11 k 100000 1 11 1 POLCOMS user guide doc 25 eval al RunID Id 2 n 1 physseries ni i 11 k 1000 1 11 1 Work is in progress to replace these files with NetCDF http www unidata ucar edu software netcdf Appendix A Model control CPP directives and logical variables Unless otherwise specified the default value of logical variables is false Compiler direct
40. quency of U V ZET boundary data hours 171 ig 184 jg Debugging co ordinates 2 kg 8 0d0 tmp init Initial temperature 35 1d0 sal init Initial salinity 38 noriv Number of rivers in data base 0 01 ddry wetting drying depth at which points are dry 0 5 zwet change in elevation to next grid point forwetting niw Numer of points in relaxation zone Appendix D Example compiler directive lists MRCS full model SPM MY25CBF READOPENBCPOINTS RIVERFIX BULKMET INVERSE B RIVERS TIMING READ TIDECON READ INITIAL TS BALTIC ADV BC CLOUDPOINT NOSTEEP ONESPMADV BNDUADV SCINTERP REALSERIES NOCOMPRESS PGRAD SPLINE VARY LAMBDA COMPOUT CTDTRACK POLCOMS user guide doc 41 MRCS tide only MY25CBF READOPENBCPOINTS NO_TMP NO_SAL TIMING READ_TIDECON NOSTEEP BNDUADV SCINTERP NOCOMPRESS NOHPG COMPOUT HARM_ANA HRCS Full Model COMPOUT MY25CBF BULKMET NOSTEEP UCOAST BALTIC BNDUADV VARY LAMBDA READOPENBCPOINTS FLIPCLD HORIZ DIF SIG HORIZ DIF SIG TS ADV BC NOCOMPRESS RIVERS READ ZETUB TIMING RIVERS RIVERFIX READ INITIAL TS NORIVTMP ZVARYBC TRACER TRACERSTART BNDUADV DIA F SCINTERP LB TVD wetting drying READ TIDECON NO SCOORD FLIPBATHY MY25CBF NOCOMPRESS UCOAST WETDRY TVD RIVERS NO TMP NO PGRAD S12 full model MY2SCBF RIVERFIX BULKMET INVERSE B RIVERS READ TIDECON READ INITIAL TS BALTIC NOSTEEP SALTFLUX SALFLUX PGRAD SPLINE NOTMPRIV COMPOUT TIMING FLIP
41. rdinate default true SCINTERP Use original calculation of s coordinates at u points pom eer machine LL cm e server Use Cray SHMEM library for message passing in addition to MPI PVM not recently tested SM lpm UsctheSPM submodel POLCOMS user guide doc UI Advect SPM SSRDATA ssrdata Use net SW radiation forcing rather than astronomical calculation corrected for clouds stdout on this processor TIMING Timing Output timing EE information for various stages of the model run TIMING ADV Include detailed timing for advection routines TIMING BAROC Include detailed timing for baroclinic integration TIMING BAROT Include detailed timing for barotropic integration fluxes drying with WETDRY TRACER Advection and diffusion of a passive tracer UBC Use non zero tangential velocities at coastal boundaries for use with case II boundaries UBC CALC MEM Calculate velocities at TVD coastal points with UCOAST Not fully tested UCOAST ucoast Use case II boundaries land boundaries lie along u points default 1s case I UNFORMMET unformmet Use unformatted meteorological data files specific implementation VAMPIR Usevampireprofiler VARY LAMBDA vary lambda Use a water depth dependent transmissivity in the SW downwelling calculation VARY REALAX vary_realax Use a relaxation boundary condition for temperature and salinity with forcing values changing across the
42. rnal of Geophysical Research 109 doi 10 1029 2003JC001951 Lewis K J I Allen A Richardson J and J T Holt 2006 Error quantification of a high resolution coupled hydrodynamic ecosystem coastal ocean model part3 Validation with Continuous Plankton Recorder data Journal of Marine Systems 63 209 224 Proctor R J T Holt J I Allen and J C Blackford 2003 Nutrient fluxes and budgets for the North West European Shelf from a three dimensional model Science of the Total Environment 313 316 769 785 Proctor R J T Holt T R Anderson B A Kelly Gerreyn J Blackford and F Gilbert 2002 Towards 3 D ecosystem modelling of the Irish Sea paper presented at Estuarine and Coastal Modeling Proceedings of the 7th International Conference American Society of Civil Engineers 5 7 November 2001 St Petersburg Florida Siddorn J R J I Allen J C Blackford F J Gilbert J T Holt M W Holt J P Osborne R Procter and D K Mills 2007 Modelling the hydrodynamics and ecosystem of the North West European continental shelf for operational oceanography Journal of Marine Systems 65 417 429 Young E F and J T Holt 2007 Prediction and analysis of long term variability of temperature and salinity in the Irish Sea Journal of Geophysical Research 112 doi 10 1029 2005JC 003386 002007 POLCOMS user guide doc
43. t tu euo 35 Two dimensional arrays at 3 time levels a 37 TWO IAEA brad qose AA decis Veolia dct anan 37 Two dimensionalantes er arrays oae ote n RR I DR UO AKA aea t n d tle LE 39 Appendix C Model Parameter S icem intet iion eese EEEE Retro av o Renee tis 39 Appendix D Example compiler directive jete 40 IVER CSU ned T 40 MECSC IOS OBL oie be AA 4 Fe SE Modelado as 4 LB TVD wetting ENEE siii Ee ae e notte EE 4 A T 4 PUMO eicit mca Ra ee t LE 4 Appendix E Logical units for input data 4 BIDHO TAPD NR ETHER 42 POLCOMS user guide doc 1 Introduction Background The origins of the Proudman Oceanographic Laboratory Coastal Ocean Modelling System POLCOMS lie with studies of frontal dynamics in the North sea for the UK NERC s North Sea Project Since then it has been extensively developed both as a hydrodynamic and a multi disciplinary model including use of its sediment transport module coupling to the European Regional Seas Ecosystem model and the Los Alamos Sea Ice model Coupling to the GOTM model lends it a range of improved turbulence models It has been used extensively in POL and PML s core research programme and in on going research contracts with the UK Met Office and a wide range of NERC and EU funded research project and programmes notably MERSEA CASIX MARPROD LOIS RAPID ODON It currently provides the work horse shelf sea model for the UK marine res
44. tes The level spacing in 7 space is fixed in the horizontal POLCOMS user guide doc 11 x ubij g amp gin lj BEUBPACE C0 Aj sigo n l 0 0 X Utr 1 Lj gig n 2 X ch X X uS sig 2 T OQ gea x ui giel SS e LIX sigo 1 1 0 SUIS II ip SS sig 0 Figure 3 Vertical discretization Hence in s coordinates state variables on b points e g tmp k i j are defined at sig k 1 1 j are separated by dsu k 1 1 j and are associated with a depth ds k 1 1 j Note the difference in indexing of 1 from state variables is a historical anomaly which will be corrected in a future version Initial conditions POLCOMS simulations generally start from rest with a level sea surface u v C 0 currently there are no provisions to initialise the model currents elevations except with a re start files The scalar fields on the other hand are either initialised to a constant value the default read in from a file or specified from an included piece of FORTRAN code With no options the initial T and S are set to the values given in parameters dat With directive READ_INITIAL_TS set they are read from unit 16 according to the format specified by ts form in parameters dat If ts formz unf they are read from an unformatted file otherwise as an ASCII formatted file Either way they are read as global 3D arrays temperature then salinity real 8 temp3d 1 m n read 16 temp3d or real 8 t
45. tten first containing the size of the grid and the location of the sea b points This 1s repeated for u points Then the 3D model fields are output daily FORTRAN code to read these files is like real 4 allocatable dimension tmp sal u v integer allocatable dimension isea jsea iusea jusea read 1 I m n npsea if not allocated isea allocate isea npsea jsea npsea read 1 isea read 1 jsea read 1 l m n npusea if not allocated iusea allocate iusea npusea jusea npusea read 1 iusea read 1 jusea POLCOMS user guide doc 24 if not allocated tmp then allocate tmp 1 m n 2 allocate sal 1 m n 2 allocate u l m n 2 allocate v l m n 2 endif do it 1 ntimes read 1 itimt read 1 u iusea 1 jusea 1 k k 1 n 2 i 1 npusea read 1 v iusea i jusea i k k 1 n 2 i 1 npusea read 1 tmp isea i jsea i k k 1 n 2 1 1 npsea read 1 sal isea 1 3sea 1 k k 1 n 2 1 1 npsea Note the binary format of the input and output system must match As most systems now use IEEE floating point format this is not usually a problem though there can be an issue with file record structures and big endian versus little endian POLCOMS 1s generally set up to use UNIX rather than PC LINUX style binaries Physseries This outputs data at a list of grid points typically every hour The files are opened with e g call initseries 200 physseries This will read from unit 88 a list of 10ut
46. way every aspect of the forcing initial data and output files for the ensemble members may be customized If different bathymetry files are specified for each ensemble member then POLCOMS reads these first before assigning processors and the number of processors per ensemble member 1s balanced according to the number of sea points The standard output from each ensemble member is reassigned to a file named output_001 output_002 etc 7 Output POLCOMS has a range of output options controlled by the subroutine data_out This is an application specific code that is copied into the source directory at compile time it calls generic output routines contained in out F and tidemeanout F The general procedure for spatial arrays 1s to copy data to the leader processor using standard communications routines and output from here For output at a specific grid cell a test 1s required that that cell is on a particular processor if ielb le icg and icg le ieub and jelb le jcg and jcg le jeub then The logical units set by filenames dat need to be consistent with those used in data_out F Typically a model run uses unformatted compressed binary output for high volume data e g 3D fields and formatted output for others Two examples are described here dailymeanUVT These files are used to output 25 hour means of tmp sal u and v and also spm if used It can use a compressed format to only output at sea points In which case a header is wri
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