Revision history
Contents
1. 2 Alternative cloud cover algorithms added but Reid 1977 is still used 3 dtime function modified to account for time zone Latest Revision Dec 18 2011 Revision 1957 December 18 2011 Revision 1935 1957 Included crash recovery Section 6 4 User s Manual Included exclusion of cells for sediments BGC waves and tracerstats Section 4 4 User s Manual November 28 2011 Revision 1913 1932 Added mean offset Section 4 30 2 User s Manual Added standard deviation for regions Section 4 30 15 User s Manual Added default timescale for local flux adjustment Section 4 10 7 User s Manual Added raw data dump when computing tracer scaling Added multifiles for scaling data Section 4 9 4 User s Manual Made meteorological variables airtemp wetbulb cloud precip multi files September 21 2011 Revision 1855 1902 Included a bottom stress diagnostic Section 4 30 11 User s Manual Included option to explicitly set bottom drag Section 4 19 User s Manual Bugfixes for inter tidal wetting and drying Bugfixes for alert diagnostics on multiple windows Bugfix for mean region mass on multiple windows Bugfix for tangential radiation stress transfers on multiple windows Improved transport fill algoritms June 7th 2011 Revision 1828 1848 Numerous bugfixes to regional budgets Section 4 30 15 User s Manual Added volume error to transport output using semi Lagrange Section 9 User s Manual Added add2. 851 Fixed running without wave library UR Oct 26 2007 Revision 821 841 Added improved filling method for the transport mode to ensure a monotonic solution Section 4 21 User s Manual This method is the default Added fill method options for the transport mode Section 4 21 User s Manual Added OBC phase speed diagnostic for elevation Section 4 31 11 User s Manual Added temporal phase speed smoothing for elevation Section 4 11 9 User s Manual Added increments for velocity for data assimilation This functionality is currently commented out Bugfix for Kondo Bulk fluxes using MESOLAPS met data Oct 10 2007 Revision 807 819 Added UPSTRM OBC for use with LAGRANGE e g in transport mode Bugfix for source sinks source sink input depth range now correctly tracks sea level variations Buxfix for WINDOWS gt 1 amp HEATFLUX ADVANCED density is transferred to the master Horizontal diffusion operational for transport model as long as stability is satisfied Added wave enhanced vertical mixing WAVES VERT_MIX Section 4 21 User s Manual Included Craig and Banner 1994 wave enhanced vertical mixing for k e Section 4 22 6 User s Manual Oct 2 2007 Revision 797 803 The pre version 794 formulation of horizontal momentum mixing has been retained see entry below for an explanation of differences This is invoked using VISC_METHOD PRE_V794 Sep 27 2007 Revision 738 794 Included wav
3. transport mode Bugfix for Schumann Gerz stability function Numerous bugfixes for multiple windows IMPORTANT these fixes render multiple windows non backwards compatible The changes are 1 Grid metrics e g botzgrid are now correctly set at ghost cells 2 Cell thickness at cell faces dzu1 and dzu2 are transferred correctly These are used in tracer horizontal diffusion 3 Surface boundary condition for vertical velocity wtop is set correctly at window boundaries 4 Vertical gradients of velocity in MY2 0 and k e are set correctly by looping over cell centres Some auxiliary cells were not captured when looping over cell faces with multiple windows 5 cells to process vectors include open boundary cells based on global rather than window open boundary structures 6 Thin layer adjustment occurrs over all cells used from other windows not just E W N or S directional cells i e diagonals are included IMPORTANT Several general bugs have also been identified and corrected 1 A surface u2 velocity was used in the u1 bottom stress used in vertical diffusion This has been changed to the bottom u2 velocity note this is included in a sum of 4 velocities the remaining 3 were correctly specified 2 Wet cells with land to the west amp east or north amp south are now correctly contained in the cells to process vector These locations are required to compute the horizontal viscosity 3 Ghost cells at the backw
4. 25 User s Manual Check for eta NaNs on input and replace with nearest non NaN Remove wet holes on input Read in 2D TRANS_VARS in transport mode e g wave variables AVHRR accepts the file list as input ETA_RELAX included in default RAMPVARS Chenged coordinate attribute for vertical velocity to z_centre so that coordinates can be inferred on input Bugfixes for ROAM multiple windows Bugfix for read write of window maps Bugfix to check for lost particles vertically Included additional checks for valid thin layers February 1 2010 Revisions 1412 1417 FR Added capability to specify plain ascii files for tracer data field Must have at least lon lat and tracer value but may contain other columns for convenience New iterp_type field this can be linear default cubic nn_sibson Or nn_non_sibson Any grid points that are outside the interpolation field of influence are padded with the 111_value Note there is no 3D support at the moment all wc and sed layers are indentically distributed horizontally Also fixed the bug that was causing the 2D and sediment variable s data and data_sed respectively field not to be honoured December 7 2009 Revision 1398 1399 FR Added timing for transport mode December 7 2009 Revision 1395 1397 FR Added option to log timing statistics use the enable do timing configure option and then build as per usual Model runs using this version of
5. 4347 4375 Added reference depth for sourcesinks Section 4 22 User s Manual Allow standard files to dump modulo formats Section 4 20 6 User s Manual Added extended types to tracers Section 4 9 7 User s Manual Added tracer exposure and rmse tracerstat Section 13 User s Manual April 12 2013 Revisions 4308 4320 Included auto mode for RECOM Use rg option with ROAMv 5 April 3 2013 Revisions 4282 4301 Added mean volume flux Section 4 29 2 User s Manual Included Flux Form Semi Lagrange FFSL write read option in transport mode Allow auto tracer attributes to be re read by tracer name Bugfix on auto tracer indexing Bugfix on crash recovery for multiple windows March 20 2013 Revisions 4261 4282 Added GLOBAL transport mode Section 9 User s Manual Added dual flux adjustment time scales Section 4 10 7 User s Manual Added Flather radiation standard conditions Section 4 10 27 User s Manual Added geostrophic velocity initial condition Section 4 11 User s Manual Prevent window transitions occurring along OBC boundaries October 8 2012 Revision 4167 4181 Added sediment and BGC automation framework Tracer scaling can be handled via tracer tag attribute Section 4 9 5 User s Manual Added general tracer surface flux specification Section 4 9 6 User s Manual September 20 2012 Revision 4166 Fixed Ecology seg fault in previous revision September 10 2012 Revision 4155 4165 Include
6. SHOC will log timings for various stages in the file timing txt December 2 2009 Revision 1385 1394 Added a more efficient method to set thin layers for multiple windows November 27 2009 Revision 1349 1371 Bugfix for multiple windows Smagorinsky k e k and MY2 5 Added additional attributes to particle output file November 19 2009 Revision 1343 1349 Bugfix set h1au1 and h2au2 where undefined for Smagorinsky calculation November 18 2009 Revision 1337 1343 Changed attribute organisation in particle output file Bugfixes on thin layer merging masks November 17 2009 Revision 1331 1337 Added more attributes in particle tracking output file Added more checks for multifile wave and pressure forcing November 17 2009 Revision 1331 1337 Added more attributes in particle tracking output file Added more checks for multifile wave and pressure forcing November 16 2009 Revision 1283 1331 Added HEATFLUX_RAMP Section 4 18 Users Manual Added WATER_TYPE for shortwave penetration Section 4 18 Users Manual Added eta scaling for open boundaries additive only Section 4 11 24 Users Manual Sonic depth sound channed added to SOUND diagnostic Section 4 31 11 Users Manual Multifile input available for wave variables and atmospheric pressure ADVANCED heatflux renamed to BULK Backwards compatibility is maintained Bugfix on transport mode Added heatflux ramp and explicit mappings to
7. angle and cloud amount if 1 lt albedo lt 0 Section 4 18 User s Manual April 13 2010 Revisions 1525 1538 Added MONTHLY SEASONAL and YEARLY dump intervals Section 4 32 6 User s Manual Added MONTHLY and SEASONAL increments for MEANS Section 4 31 1 User s Manual Made all MEANS into rolling means April 7 2010 Revisions 1498 1523 Added temporal percentile computations ps mode Section 10 User s Manual Reworked particle settling and added swimming mortality Section 4 29 User s Manual Added Sigma_t in NUMBERS Section 4 31 11 User s Manual Allowed window maps to be created using the p mode Section 4 2 User s Manual Added scaling to the eta relaxation data in OBC local flux adjustments and changed the relaxation ramp Section 4 11 7 User s Manual Added particle concentration as an auto tracer A no gradient condition above the surface is set for tracers after the sed eco step if sediments or ecology is invoked April 7 2010 Revisions 1487 1498 Added sonic depth variable Bugfixes to global filling algorithm Improved the mapping function for multi grid transport March 18 2010 Revisions 1417 1487 Added code to set up INEXACT multi grids for transport Section 9 1 User s Manual Added T S NaN fatality checks Section 4 4 User s Manual Added instability de bugging diagnostics Section 4 33 User s Manual Added ability to dump boundary location information Section 4 11
8. facility and cf file format introduced by Jason Waring Aug 11 2006 Revision 504 Optimized LAGRANGE scheme for transport and added global tracer fill to conserve mass during advection July 31 2006 Revision 491 Tracer percentile diagnostic included see Section 4 30 12 of User s Manual Tracer fluxes have been changed to text based tracer name specification in the input file rather than the tracer number Section 4 30 1 User s Manual Flushing tracer is changed to a boolean input with an auto tracer flush generated for FLUSHING_TR YES Section 4 30 4 User s Manual IMPORTANT The boolean FLUSHING_TR and CALC_FLUXES fields are no longer backwards compatible and prm files must be changed to CALC_FLUXES NONE FLUSHING_TR NO Sparse formatted output files can have the modulo attribute Section 4 31 6 User s Manual Transport mode now accepts input files with modulo specified July 27 2006 Revision 472 Bugfixes on transport mode July 25 2006 Revision 470 Previously caused disruptions on 64 bit machines running multiple partitions in threaded mode have lead to make the asynchronious dumping of output optional The flag to be set to enable is SCHED_MODE pthread if the entry is missing or different threading will not be used for the dumping of output UR July 21 2006 Revision 467 Transport mode is now functional refer to Transport mode Chapter 8 in the Users Manual Sparse format files can be gen
9. 2 User s Manual Included run regulation Section 4 31 1 User s Manual Included more standard OBCs Section 4 10 27 User s Manual Included multi dumpfiles Section 4 30 7 User s Manual Bugfix for density with layerfaces gt 0 Allow open boundaries in the domain interior i e doesn t need to be adjacent to OUTSIDE cells April 13 2012 Revision 3985 3991 Various bugfixes for TRCONC April 11 2012 Revision 3980 3985 Added RIVER boundary specification Section 4 10 6 User s Manual Allow multi files for data using NEST1WAY amp RIVER boundary specification Bugfix for dew point multifiles April 5 2012 Revision 3963 3975 Added compatible V1957 this creates makes without the open boundary ghost cells Use with pre V1957 window map files Added mean runtime ratio to diag txt Bugfixes for sediment ecology process exclusion and OBC ghost initialisation March 27 2012 Revision 3963 Note svn repository has moved to https svnserv csiro au svn EMS src main This has resulted in the leap in version numbers Added TRCONC and TRFLUX boundary conditions Section 4 10 6 User s Manual Added standard NEST1WAY boundary condition Section 4 10 7 User s Manual Added 2 way nesting capability February 14 2012 Revision 1958 Changes to calculation of shortwave radiation in heatflux c 1 Maximum irradiance se calculated using a cosine function instead of piecewise linear interpolation in time
10. CT is included for NSPONGE_HORZ Section 4 11 14 Users Manual Wave enhanced vertical mixing improved for k e and k w schemes Section 4 22 10 User Manual 6 10 Science Manual Choice of stability functions for turbulence closure Section 4 22 9 User Manual 6 10 Science Manual Wilcox 1988 closure scheme added Section 4 22 8 User Manual 6 9 Science Manual OUTSIDE ZONE added to fill OUTSIDE cells adjacent to open boundaries 4 11 Streamlined tracer relaxation for a option Section 4 10 1 Users Manual INVERSE BAROMETER is switched off if no PRESSUE file is supplied Bugfix for Orlanski radiation when relaxed to data backward time step used rather than current time step IMPORTANT this will be non backwards compatibe when BCOND_ETA FILEIN ORLANS or FILEIN CAMOBR Bugfix for eta landfills Bugfix in fcw function for k w February 11 2009 Revision 1076 1130 Improved MONOTONIC global filling for the transport mode Added conservation option for non Lagrange transport mode Section 9 User s Manual Added option to ignore leap years for the transport mode e g when using MOM4 input Section 9 User s Manual Added momentum sources for sourcesinks Section 4 24 User s Manual Added option to horizontally smooth Vz and Kz with Shuman filter Section 4 22 3 User s Manual Added heatflux components from MOM4 input Section 4 18 User s Manual Added time step and boundary volume fluxes for TOTA
11. DY Section 4 6 4 User s Manual Added river salinity tracer Section 4 10 6 User s Manual Included river length for salt balance Section 4 10 6 User s Manual Set monotonicity constraint for FFSL cross terms Refinement of mempack file generation December 12 2014 Revisions 5008 5016 Added vector attributes to tracers for simple output Bugfixes to salt balance in OP_NOSALT OBC options Bugfixes on Stokes velocity implementation November 13 2014 Revisions 4964 4985 Added TRATIO lt 1 for FFSL Section 4 11 User s Manual Added age tracer Section 4 30 5 User s Manual Added expanded CFL diagnostic Section 4 30 9 User s Manual Allow sourcesinks to be specified using region files Section 4 23 User s Manual Added unit tracer Section 4 30 13 User s Manual Added spatially variable tracer decay rate Section 4 9 User s Manual Added regions to compute partcle age within Section 4 28 3 User s Manual Region residence times computed using mean flow Section 4 30 17 User s Manual Reset OBC CLAMPD default to tracer fill value Added light to default timeseries output TRCONF scaled for inflow only September 16 2014 Revisions 4905 4917 Added option to override pss volume fluxes for ffsl Added scaling factors for point sourcesinks Section 4 22 User s Manual Reformulated density scaling OBC Section 4 10 18 User s Manual Reformulated density scaling initial conditions Section 4 9 User s Manu
12. LS Section 4 31 14 User s Manual Shortened INVERSE_BAROMETER tag Section 4 11 15 User s Manual Added OutputPath for alerts totals and flushing Changed interpolation at NaN cells to cascade searches for MOM4 conversions Changed loop for wave routines to be over wet points only Bugfix to include OBC cells for multiple windows using bcond_ele NOTHIN Bugfix for cascade searches December 15 2008 Revision 1036 1075 Modified transport model to allow different source and target grids Added STREAMLINE option for transport model i e streamline origin saved and read from file Added source sinks for momentum Section 4 24 User s Manual Added current speed squared diagnostic Section 4 31 11 User s Manual Added run number sequence diagnostic Section 4 4 User s Manual Added OutputPath to set path for netCDF and timeseries output Section 4 32 6 User s Manual Various bugfixes sourcesink for multiple windows CUSTOM velocity BCOND_TAN forcing cyclic offsets for MOM conversions zoneshift for TIDALC August 14 2008 Revision 1006 1025 Included explicit maps in bathymetry smoothing Allow a name and path for restart files Local OBC solutions added and available for use with FLATHR Section 4 11 5 User s Manual Bugfix for TIDALC to allow for local timezones i e TIDALC constituents must be relative to the local timezone Bugfixes for Smagorinsky mixing with sponges u1 PRESS_BC tendency T S rela
13. al Added regional initial conditions Section 4 9 User s Manual Bugfixes for regions non transport mode August 27 2014 Revisions 4880 4883 Added multiple blocks for bathy modification Section 4 8 User s Manual Added default for window sizes Section 4 2 User s Manual Added tracer initialisation using inverse density profile Section 4 9 User s Manual August 8 2014 Revisions 4850 4854 Bugfixes for pointsourcesinks with flow in transport mode using FFSL August 6 2014 Revisions 4828 4844 Added depth based relaxation for sea level Section 4 11 1 User s Manual Added TRCONF boundary condition Section 4 10 17 User s Manual Added UPSTRM open boundary condition for FFSL Added conservation options for FFSL June 20 2014 Revisions 4793 4811 Allow forcing of conservation for eta or w in transport Section 9 User s Manual Include Stokes drift velocity Section 4 19 User s Manual Include cosine exponential depth relaxation Section 4 9 2 User s Manual Bugfixes to FFSL June 20 2014 Revisions 4768 4782 Bugfixes on dumps read for non cell centered variables Bugfixes to FFSL Allow OBCs to overwrite velocity if specified Allow transport fill MONOTONIC NONE to operate with PSS_INPUT IMPLICIT June 10 2014 Revisions 4751 4757 Bugfixes to adaptive relaxation Added relaxation time constant tracer for adaptive relaxation June 10 2014 Revisions 4729 4734 Added file in
14. ard time step are correctly set using the lateral boundary conditions These are not set correctly in the Asselin time filtering since velocities at the forward timestep are not computed in ghost cells This affects the stress tensors for horizontal viscosity 4 Newly wetted cells are set before the lateral boundary conditions are computed so these locations are correctly set at land water boundaries 5 Backward velocites subjected to thin layer merging are restored to original values in the vertical diffusion scheme If the bottom lies in the layer below the surface the u1 backward velocities are used in u2 vertical diffusion to compute the bottom stress and the un merged velocities are required to be used here IMPORTANT these changes render the code non backwards compatible for 1 or multiple windows Backward compatiblity for points 2 and 3 above can be established for one window even though solutions are subject to the above bugs by setting the flag COMPATIBLE V1283 September 11 2009 Revision 1256 1283 Included SP_CHECK to check sparse files generated for the transport mode Section 9 Users Manual Added vertical mixing to the transport mode Added new boundary conditions for tracers TRCONC amp TRFLUX Section 4 11 16 Users Manual Added open boundary condition on vertical velocity BCOND_W Changed global cells to process vector to exclude e1 e2 open boundary cells Added COMPATIBLE flag to invoke backwa
15. ards compatible with older parameter files To revert to the pre v794 formulation for backward compatibility reasons set VISC_METHOD PRE_V794 Improvements to MOM conversions OBC s inside domains OBC list in grid_spec nc scaling in df_mom c July 9 2007 726 Revision 723 Fixed error when number of output files exceeds limit increased number of output files limit to 300 UR July 3 2007 Revision 723 RANGE specification for OBC lists Section 4 11 User s Manual SMOOTH_VARS and SCALE_VARS specification Section 4 4 User s Manual Allow dewpoint input for ADVANCED heattflux Section 4 18 User s Manual Heatflux now works with MESOLAPS products SPEED 2D and SPEED_ 3D included in NUMBERS Section 4 31 11 User s Manual Wave interactions cleaned up Radiation stresses included Section 4 21 User s Manual IMPORTANT WAVE_ENHANCED_BOTTOM_FRICTION is superseded by WAVES and is no longer functional Dumpfiles in sigma mode are mapped to the vertical layers specified in the parameter file Time series master slave transfers included and optimised master filling for output dumps Wanings for TINY violations disabled TINY now set to 1e 20 June 28 2007 Revision 685 fixed memory bug in preprocessor UR May 2 2007 Revision 642 673 Included scaling options for horizontal diffusion see Section 4 22 User s Manual Added a variety of fill_rules Section 4 31 6 User s Manual Atmospheric variables wind p
16. d ecology autotracers Included OBCs in sediment and ecology autotracers August 31 2012 Revision 4138 4150 Included sediment transport automation Section 15 User s Manual August 21 2012 Revision 4127 4137 Added automatically generated sediment tracers August 16 2012 Revision 4115 4127 Allowed a transport output DT to be specified for TRANS_FILES Section 9 User s Manual Allow all variable initialisation 2D 3D sed using TRACER_DATA Section 4 9 1 User s Manual Streamlined tracer initialisation added 2D and sediment tracer initialisation at runtime Allow sediment layers to be read from parameter file if not specified in input file August 7 2012 Revision 4111 Added ability to output netcdf dumps in DAILY MONTHLY or YEARLY chunks Section 4 30 6 User s Manual Included auto sediment tracer attributes Included library error handling for sediments July 23 2012 Revision 4035 4083 Run regulation for time series point source sinks Section 4 31 1 User s Manual Added tracer tendencies Section 4 29 10 User s Manual Allow multiplicative boundary scaling Section 4 10 25 User s Manual Added netCDF file initialisation for new tracers Section 4 9 1 User s Manual Added parameter file revision number Added library error handling Added means debugging auto transport file output to transport model May 7 2012 Revision 3991 4024 Included window partitioning methods Section 4
17. e library Section 4 21 User s Manual IMPORTANT wave routines now reside in model lib waves Added additional tracers for TOTALS Section 4 31 14 User s Manual Added OBC eta relaxation zone Section 4 11 8 User s Manual Added OBC 2D velocity forcing 2D point array output and OBC flux adjustment on velocity forcing Section 4 11 6 User s Manual Added state variable increments for data assimilation Section 4 10 3 User s Manual Added wind drag diagnostic in NUMBERS Section 4 31 11 User s Manual Added Kondo 1975 bulk wind drag Section 4 14 User s Manual Added wave enhanced vertical mixing after Craig amp Banner 1994 Moved all horizontal momentum mixing to separate module and made invoke mixing via function pointers Bugfixes on stress tensors IMPORTANT The stress tensors for the horizontal momentum formulation has been altered and is no longer backwards compatible Blumberg and Herring 1987 multiply the first term in t11 t22 by h2 h1 This seems to be in error as for uniform h1 amp h2 the units of the mixing term don t equate to ms 2 Also Apel 1987 derives the mixing tensors in Cartesian coordinates and multiplies the first term in the t11 t12 stress tensor by 2 rather than h2 h1 This latter formulation is now considered correct and modifications to the code have been made to reflect this The corrected formulation may need tuning of U1VH and U2VH to attain stability i e current code may not be backw
18. erated as output Refer to Section 4 31 6 in the Users Manual These files are accepted as input into PLUM Sparse format files are accepted as input for tracer resets
19. flux adjustment Bugfixes to uv_to_ulav uv_to_u2av hdstd_to_u1 and hdstd_to_u2 OBC custom routines Created separate module inputs readparam_r c for ROAM configuration Added VELOCITY initialisation from a 3D horizontal velocity field e g VELOCITY velocity_file nc Added a ramp period for OBC inverse barometer effect e g RAMPVARS INV_BARO Added eta relaxation during the ramp period e g RAMPVARS ETA_RELAX Added velocity data input for roam e g VELOCITY_DATA velocity_file nc Added local OBC velocity approximations e g bcond_nor LOCALN bcond_tan LOCALT Added hdstd_to_utav and hdstd_to_u2av custom OBC routines Added phase speed smoothing to FLATHR e g bcond_ele FLATHR FILEIN ORLANS SMOOTH_PHASE 0 7 Apr 08 2008 Revision 888 918 Added ability for outside or inside open boundary staggers Section 4 11 2 User s Manual Fixed bugs on FLATHR passive radiation using inside staggers Modified active FLATHR to use linear local solution Section 4 11 5 User s Manual Added ability to change a zone of wet cells to OUTSIDE cells adjacent to an open boundary Section 4 11 User s Manual Added checks for NaNs on tracer initial conditions Modified ROBUST 6 for ROAM constant VH Smagorinsky KH Added cyclic compatibility for MOM gridspec conversions Added the ability to create shorter input files for use with extremely large grids usage shoc g in prm in_short nc Oct 26 2007 Revision 848
20. itional level of transport checking TR_CHECK Section 9 User s Manual May 13th 2011 Revision 1799 1828 Added mass budgets for regions Section 4 30 15 User s Manual Added semi Lagrange advection scheme for momentum Section 4 11 User s Manual Added percentile sub sampling of input file Section 10 User s Manual Addressed numerous bugs identified by Mark Szyszka MetOcean Engineers Mar 25th 2011 Revision 1748 1788 Added velocity relaxation Section 4 12 1 User s Manual Added adaptive relaxation Section 4 12 1 User s Manual Added tidal removal method for eta relaxation Section 4 12 1 User s Manual Added open boundary data path Section 4 10 3 User s Manual Added more debugging functionality Section 4 32 User s Manual Added memory packet IO in library functions Mar 3rd 2011 Revision 1748 FR Added OpenMP support openmp is now an option for DP_MODE This yields somewhat better performance than pthreads and will make it easier to parallelise other code plus it is more robust and offers more flexibility than pthreads It also paves the way for MPI support coming soon We will soon have the ability to run SHOC in hybrid MPI OpenMP mode This will now run the g option in parallel as well To use run configure with the enable omp option and then specify openmp for the DP_MODE parameter Feb 2nd 2011 Revision 1724 1745 Added maximum momentum tendencies diagnostic Section 4 30 9 User
21. nydia Latest Revision October 19 2015 Revision 5238 October 19 2015 Revisions 5233 5238 Included neighbourhood techniques for time series output Section 4 31 5 User s Manual August 20 2015 Revisions 5188 5199 Include spatial decorrelation length scale diagnostic Section 4 30 17 User s Manual August 11 2015 Revisions 5171 5175 Added tracer filling and filtering options Section 4 9 8 User s Manual August 6 2015 Revisions 5148 5163 Added merged fluxes option for FFSL Section 9 4 User s Manual Added STOKES to ramp Section 4 3 User s Manual Added Stokes momentum tendencies Section 4 30 10 User s Manual Added MacCready river mouth salinity approximation Section 4 10 6 User s Manual Added Stokes vortex force Section 4 20 User s Manual Added mean temperature and salinity Section 4 30 2 User s Manual June 4 2015 Revisions 5113 5123 ROBUST flags re configured for RECOM Include EXCLUDE_BGCSED for process exclusion Section 4 4 User s Manual April 10 2015 Revisions 5096 5102 Added NOGRAD option for FFSL Section 9 4 User s Manual Recast roammode flags Section 7 User s Manual April 10 2015 Revisions 5063 5084 No overwrite of timeseries file using g option Totals for 2D tracers is the areal mean Section 4 30 16 User s Manual Allow clamped nesting standard OBC NEST_CPD Section 4 10 27 User s Manual Allow false pole to be specified for grids using DX and
22. om the 2D mode in vel_w_bounds Section 4 4 User s Manual Added 2nd order upwind advection scheme for tracers stable for Courant lt 2 Section 4 11 User s Manual Added NUMBERS SLOPE SURF_LAYER amp DUMMIES Section 4 31 15 User s Manual Added FILTERING option Only 1st order Shapiro filtering of momentum tendencies is currently supported Section 4 11 4 4 User s Manual Moved momentum advection code from momentum vel3d c to momentum advect c Bugfix for sediment TOTALS June 10 2010 Revisions 1584 1598 Added mechanical energy diagnostic Section 4 31 11 User s Manual Added wet cell diagnostic Section 4 31 11 User s Manual Source terms for short wave radiation penetration added implicitly in vertical diffusion Bugfix on ETAMAX specification Bugfix on monotonic global filling for the transport mode May 28 2010 Revisions 1562 1581 Made short wave radiation attenuation transmission and bottom absorption 2D auto tracers Short wave contribution to the water column included as a source term in vertical diffusion Added FLUX_ADJUST for OBCs as a RAMP variable By default it is turned off DEBUG_LOC can be invoked using the auto a mode April 21 2010 Revisions 1539 1562 Bugfixes for MONTHLY SEASONAL means Included a timeseries type Section 4 32 5 User s Manual Included a RIVER specification for a and g modes Section 5 User s Manual Allow albedo to be computed from hour
23. ple cells e g the sum of inputs total flow Modified DEBUG info to include 3D velocity and utinter u2inter values Included data assimilation scheduling Dec 13th 2010 Revision 1669 1670 FR e Added multi ts file support for point source sinks Multiple timeseries files can now be listed in the prm file and they are considered as if everything was in the one file e Added new use_eqn custom boundary condition This calls the new equation parser routines in the EMS library and allow boundary conditions to be a combination of tracers Section 4 10 8 User s Manual e Modified LIGHT to be read from a tracer instead of file August 20 2010 Revisions 1641 1652 Added quadratic cubic and quartic interpolation for the semi Lagrange advection scheme Section 9 User s Manual Added code to stop streamline intrusions into land for the semi Lagrange scheme Bugfix to total mechanical energy diagnostic using ALERTS Bugfix to sediment ghost cell maps only affects semi Lagrange scheme July 27 2010 Revisions 1612 1632 Transport mode added local fill and implicit pss input Use 4th order approximations and detadt from the 3D mode in vel_w_bounds Section 4 11 User s Manual Zero velocity used above the surface for horizontal momentum advection and no gradient for vertical advection Section 4 11 User s Manual Added V1598 no gradient on velocity above the surface for momentum advection Low order approximations and detadt fr
24. put for surface and bottom DESCAL amp dens_scale options Sections 4 9 amp 4 10 18 User s Manual Added depth dependent tracer relaxation Section 4 9 2 User s Manual June 5 2014 Revisions 4718 4727 Included density scaled initial condition for tracers Section 4 9 User s Manual Included density scaled OBCs for tracers Section 4 10 18 User s Manual May 15 2014 Revisions 4701 4715 Included isotropic mixing in sponges Section 4 10 15 User s Manual Added averaging for tracers amp w for CORNER_MEANS Hard relaxation for velocity using CORNER_MEANS Transport file dumps with FFSL only dump waterss if npss gt 0 Read in eta_t for GLOBAL mode in transport model Include 2D mean velocity in transport mode May 15 2014 Revisions 4670 4693 Included additional wave enhanced mixing methods Section 4 19 User s Manual Reset defaults for dynamic river method Section 4 10 6 User s Manual Included option to average across OBC overlap Section 4 10 7 User s Manual Included river input salinity diagnostic for TRCONC Apr 8 9 2014 Revisions 4628 4646 Added block reads for BATHY_MASK Included NLAND set blocks to land Section 4 8 User s Manual Added ROBUST 0 option optimized Improved ramping of geostrophically initialised velocities on boundaries Section 7 User s Manual Allowed for rivers with multiple cells Streamlined dynamic riverflow options Changed ROAMv 5 ROBUST 4 to hard relaxa
25. rds compatibility Currently e V1246 will include e1 e2 open boundary cells in global cells to process vector e V794 will use VISC_METHOD PRE_V794 for horizontal viscosity Improved performance of streamline origin computation in the transport mode for thin layers Bugfix on MONOTONIC global filling for the transport mode Bugfix on WIMPLICIT IMPORTANT previously horizontal advective tendencies were zero Bugfix on v1256 bugfix for mean velocities August 13 2009 Revision 1256 Bugfix for Mean velocities This is really an artifact of fixing the model time to keep in sync of the 3d timesteps Also added support for dumping out the stack trace on a segmentation fault July 13 2009 Revision 1228 1246 Added near real time operation mode nrt Section 6 User s Manual Added run identifier tag Section 4 4 User s Manual June 30 2009 Revision 1208 1222 Added implicit vertical advection Section 4 12 Users Manual Section 5 1 8 Science Manual Added read write of window map to netCDF file Section 4 2 User s Manual Added bathymetry smoothing of selected cells Section 4 9 User s Manual May 13 2009 Revision 1148 1190 Improved global filling algorithm for the transport mode Volume error diagnostics and time series of residual mass and scaling factors now available SWR_BOT_ABSORB may be input via netCDF file as a 2D spatially varying field Section 4 18 User s Manual A scaling factor SPONGE_FA
26. ressure are also filled Added ability to explicitly change SURFACE e g for tsunami modelling Section 4 13 User s Manual IMPORTANT Feedback of waves to hydro is formally included by setting WAVE_ENHANCED_BOTTOM_FRICTION YES The default or if absent is NO Note that an ORBITAL_VEL file must be present to invoke wave friction Bottom roughness is modified in the sediment code if ORBITAL_VEL is present regardless of the status of WAVE_ENHANCED_BOTTOM_FRICTION See Section 4 20 User s Manual OBC s for tracers may be set using tracer names e g BOUNDARY0 BCOND_ temp see Section 4 11 User s Manual A warning is issued if variables become less than TINY 1e 100 if linked to ecology All heatflux components are included in output using COMP_HEAT Mar 6 2007 Revision 630 641 Included layer thickness diagnostic for sigma SHOW_LAYERS YES Minor bigfixes for sigma Included FILEINIJNOTHIN OBC NOTHIN is relaxed to FILEIN on the RELAX_TIME scale Included zero_fill and no_fill fill rules for output Feb 22 2007 Revision 628 629 Changed the MEAN_DT default for ROAM to account for negative START_TIME Feb 13 2007 Revision 621 627 Bug fixes on sigma layer computation and particle tracking cleanup Feb 09 2007 Revision 600 620 Added AVHRR heatflux to relax temp surface to AVHRR sst data Added custom tide specification where tidal amplitude and phase constituents are read from file Section 4 11 15 user
27. s Manual Added memory packet output not documented yet Added OutputPath to TRANS_OUTPUT files Added time increment input for FILEIN OBC input Added check for Nan on tracer input amp replace with nearest non NaN Bugfixes for velocity initialisation using multiple windows Bugfix for GEOGRAPHIC_RECTANGULAR false pole grid specification Fixes for ROAM with improved OBC flux adhuxtment algorithm Feb 2nd 2011 Revision 1705 1724 Added automated transport output file dumps Section 9 User s Manual Changed OBC flux adjustment to read eta using FILEIN rather than eta_relaxation The previous input method can be invoked using COMPATIBLE V1670 Section 4 10 7 User s Manual Bugfix on anisotropic grid refinement Jan 21st 2011 Revision 1670 1705 Allow prescribed tracer to set the density Section 4 4 User s Manual WRITE_BDRY invoked on p and g modes Section 4 10 25 User s Manual Kinetic energy added to NUMBERS Section 4 30 11 User s Manual Allow reinitialisation or no initialisation for CONSERVE in transport mode Section 9 User s Manual Write a transport file in g or p mode Section 9 User s Manual Grid refinement allows different factors in x and y directions and grid refinments reverts a PRECONDITIONED refined grid to a uniform grid Section 4 29 User s Manual Isotropic grid refinement maps used with COMPATIBLE V1652 Grid blending added Section 4 29 User s Manual Allow river input over multi
28. s Manual Modified Smagorinsky smoothing using ROBUST parameter diffusion is smoothed ROBUST 1 times and has an upper limit of U1KH U1VH etc Jan 18 2007 Revision 583 593 Added land maps for dump cascade fills to speed up land filling Added post processing on AVHRR images to remove land cloud contaminated pixels and smooth image Bugfix on global filling in transport mode Jan 8 2007 Revision 580 Added Executable name to setup log UR Nov 22 2006 Revision 565 567 Enabled wildcards for variable definitions under the file identifier i e file vars Phy will include all variables starting with Phy Enabled provision of external files instead of providing data in parameter file for file points gt file pointfile BATHY gt BAHYFILE X amp YCOORDS gt COORDFILE NTRACERS TRACERFILE TSPOINTS gt TSFILE npointss gt pointssfile Note that the old original identifier will always overwrite the file directive UR Nov 17 2006 Revision 558 Added relaxation times for ingoing and outgoing OBC radiation conditions Added NONE mode for transport model i e run transport with no advection IO only Included MOM4 gridspec generation and file output in MOM4 format Nov 9 2006 Revision 530 Increased the number of allowable tracers to 300 Sep 18 2006 Revision 523 Added the ability to read in extra tracers for the transport mode see Section 8 User s Manual Sep 2006 Revision 512 restart
29. tion over spinup Section 7 User s Manual Added temporal linear relaxation for tracers eta Section 4 9 2 4 11 1 User s Manual Mar 5 2013 Revisions 4553 4564 Included residence time in regions Section 4 29 16 User s Manual Included point source sink input on at multiple horizontal locations Section 4 23 User s Manual Feb 18 2013 Revisions 4516 4537 Included scale_factor for exposure maps output units Section 13 User s Manual Include boundary bathymetry smoothing Section 4 10 24 User s Manual Reference dynamic river input pycnocline depth to the free surface Section 4 10 6 User s Manual Included porus plate code experimental Include bathymetry RESET using p mode experimental Dec 16 2013 Revisions 4498 4507 Included bathymetry statistics Section 4 8 User s Manual Added Smagorinsky to transport mode Nov 25 2013 Revisions 4460 4484 Include DYNAMIC river input method Section 4 10 6 User s Manual Added Smagorinsky smoothing parameter Section 4 21 User s Manual Added restart options for particles Section 4 27 User s Manual Added open boundary OPTIONS Section 4 10 6 User s Manual Write setup txt to output directory Section 4 31 User s Manual Print computational sequence in DEBUG_LOC Section 4 31 User s Manual Added a modified ROAM auto parameterisation roammode 5 Added ROMS grid generation Section 4 4 User s Manual Added RECOM roammodes6 May 17 2013 Revisions
30. xation and OBC energy flux diagnostic July 11 2008 Revision 1000 1002 Bugfixes to tracerstats July 9 2008 Revision 979 999 Temperature and salinity relaxation now performed every timestep rather than input_dt Temperature salinity and elevation relaxation time constant can be read from file with temporal and spatial variation May 20 2008 Revision 968 975 Bugfix for VELOCITY initialisation Bugfix for re setting maps in tracers reset_map_t IMPORTANT This may alter vertical velocity and vertical advective u1 and u2 fluxes across eastern and northern open boundaries respectively hence affect backwards compatibility May 16 2008 Revision 966 967 Bugfix for OBC stagger in ROAM configuration May 15 2008 Revision 955 964 Added tracer missing value and missing_value_sed to be maintained in model UR Missing value landfill function available fill_rule missing_value Speed of sound routines now in lib math underwater c Default SOUND calculation is unesco_speed_of_sound May 13 2008 Revision 947 955 Added OFAM velocity as auto tracers ovelu ovelv ROAM defaults changed ROAMv4 SPEED 5 ROBUST 6 Inverse_barometer and VELOCITY initialisation on May 08 2008 Revision 922 944 Tracer checks for NaNs give a warning only Bugfixes and inprovements to inner stagger OBCs Bugfixes to OBC flux adjustment Added tide e g bcond_ele NOTHIN TIDALH and inverse barometer effects to
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