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1. 1 1 The ELCOM model ELCOM Estuary and Lake Computer Model is a numerical modeling tool that applies hydrodynamic and thermodynamic models to simulate the temporal behavior of stratified water bodies with environmental forcing The hydrodynamic simulation method solves the unsteady viscous Navier Stokes equations for incompressible flow using the hydrostatic assumption for pressure Modeled and simulated processes include baroclinic and barotropic responses rotational effects tidal forcing wind stresses surface thermal forcing inflows outflows and transport of salt heat and passive scalars Through coupling with the CAEDYM Computational Aquatic Ecosystem DYnamics Model water quality module ELCOM can be used to simulate three dimensional transport and interactions of flow physics biology and chemistry The hydrodynamic algorithms in ELCOM are based on the Euler Lagrange method for advection of momentum with a conjugate gradient solution for the free surface height Casulli and Cheng 1992 Passive and active scalars i e tracers salinity and temperature are advected using a conservative ULTIMATE QUICKEST discretization Leonard 1991 1 2 Implementation language ELCOM is implemented in Fortran 90 with F95 extensions so that three dimensional space can be mapped into a single vector for fast operation using array processing techniques Only the computational cells that contain water are represented in the single vector so that memory
2. 10 number of datatypes in group TRUE is_interval logical true if time step interval is used for output 5 output interval 0 output start time 0 output end time 0 indicates entire run 0 size of time list non zero only if is interval BEGIN GROUP DESCRIPTION 21 group reference number sheet6 group user label sheet6 unf output filename 20 set reference number 10 number of datatypes in group TRUE is_interval logical true if time step interval is used for output 5 output interval 0 output start time 0 output end time 0 indicates entire run 0 size of time list non zero only if is interval BEGIN GROUP DESCRIPTION 23 group reference number sheet 7 group user label sheet7 unf output filename 22 set reference number 10 number of datatypes in group TRUE is_interval logical true if time step interval is used for output http www cwr uwa edu au blaval manual elcom templates datablock db 2 of 9 31 8 2000 1 14 33 PM http www cwr uwa edu au blaval manual elcom templates datablock db 5 output interval 0 output start time 0 output end time 0 indicates entire run 0 size of time list non zero only if is_interval FALSE BEGIN GROUP_DESCRIPTION 25 group reference number sheet8 group user label sheet8 unf output filename 24 set
3. 6 End time step 1 for end of file 7 Overwriting of nc file replace for overwriting noreplace for no overwriting 8 Output diagnosics to monitor echo to output to monitor noecho to not output to monitor Once the run_db2nc file is correctly configured db2nc can be executed at the command line by typing db2nc run db2nc Notes e f you get the path for the sparsedata unf file wrong in your run db2nc file db2nc will still run through and create a slightly smaller nc file complete with correct scalar data however all spatial information x y z etc will be assigned a value of zero e The run_db2nc can have any file name however the correct file name must be invoked at run time e The run_db2nc can only be configured for one file at a time For batch processing of several unf files it is recommended that a run_db2nc file be created for each unf to converted and db2nc be invoked for each run_db2nc using a batch file 3 9 2 Save and Restart output files Save and Restart output files are Fortran unformatted binary files that contain run configuration information used to allow the user to restart ELCOM runs from a certain point As described in the run_elcom section the kernel name and output frequency of save and restart files are defined in the run_elcom file The save files are created starting at the time step specified by the value assigned to the run_elcom keyword start_output_save and subsquently at intervals defi
4. 16 set reference number BEGIN SET CELL DATA 8 set ference number BEGIN SET CELL DATA 20 set ference number BEGIN SET CELL DATA 22 set ference number BEGIN SET CELL DATA 24 set reference number http www cwr uwa edu au blaval manual elcom templates datablock db 9 of 9 31 8 2000 1 14 33 PM http www cwr uwa edu au blaval manual elcom templates met dat A Very Large Lake Top hat 5m s wind File prepared by I M Underpaid 24 05 00 OO data sets seconds between data 0 0 0 0 0 0 0 1 TIME WIND_SPEED WIND_DIR SOLAR_RAD AIR_TEMP REL HUM CLOUDS 2000001 00 0 050 100 00 20 0 0 94 0 20 2000001 15 0 0 0 100 00 20 0 0 94 0 20 2000001 50 5 0 0 100 00 20 0 0 94 0 20 2000002 00 5 0 0 100 00 20 0 0 94 0 20 2000003 10 5 0 0 100 00 20 0 0 94 0 20 2000003 55 0 0 0 100 00 20 0 0 94 0 20 2000004 00 0 0 0 100 00 20 0 0 94 0 20 2000005 00 0 0 0 100 00 20 0 0 94 0 20 2000006 00 0 0 0 100 00 20 0 0 94 0 20 2000007 00 0 0 0 100 00 20 0 0 94 0 20 2000008 00 0 0 0 100 00 20 0 0 94 0 20 2000009 00 0 0 0 100 00 20 0 0 94 0 20 http www cwr uwa edu au blaval manual elcom templates met dat 31 8 2000 1 15 01 PM http www cwr uwa edu au blaval manual elcom templates run_db2nc Curtain translation curtainl unf infiles sparsedata unf ncfiles curtainl nc 1 a replace echo http www cwr uwa edu au blaval manual elcom templates run_db2nc 31 8 2000 1 15 02 PM Templates A Pre processo
5. 2 3 3 Creating a bathymetry dat file An up to date copy of bathymetry dat can be downloaded from Appendix A This file can be used as a template for creating your own bathymetry dat file The judicious use of extra comment lines and comments after the keywords leads to a file that is much more readable The bathymetry dat file can be renamed but the corresponding name in the run_pre must also be changed The pre processor will run with some items out of order but the GUI will be unable to process the bathymetry file The remainder of this section will detail the use of each keyword in the bathymetry dat file File header keywords FILE VERSION The first two non comment lines of the bathymetry dat file must begin with the keywords FILE and ERSION The data following FILE must be the name of the file The data following VERSION must be 1 1 a the present version of the bathymetry dat file Thus the first two non comment lines must appear as shown lt FILE bathymetry dat ERSION 1 l a Description lines keywords TITLE ANALYST ORGANIZATION COMMENT Several keywords are provided to allow the user to put identifying information at the top of the bathymetry file This information is printed to the standard output at the start of the run to provide identification of the debugging output data The format for the header linesis string keyword where the string must be a non null character array enclosed i
6. DATAOUT_FILE usedata unf E sparsedata unf E LCOM USEDATA FILE LCOM SPARSEDATA FILE permission to overwrite existing files yes overwrite http www cwr uwa edu au blaval manual elcom templates run pre 31 8 2000 1 14 05 PM ELCOM Operation 3 ELCOM Operation 3 1 Introduction Running an ELCOM simulation requires the user to provide several types of data 1 initial conditions 2 temporal boundary conditions 3 configuration parameters and 4 output control ELCOM obtains this data from the user through user prepared input files pre processor prepared input files CWR Modeller prepared input files and user prepared subroutines A separate user guide is provided for the use of CWR Modeller so this aspect of configuring ELCOM will not be covered in detail within this document The following section will describe the types of data that CWR Modeller is used to set the files the user is required to prepare without CWR Modeller and the files that will be produced as ELCOM output 3 2 Files for ELCOM ELCOM is a command line executable that communicates with the user through files To simplify the task of setting up a simulation run CWR Modeller pre processor and makefile have been developed The pre processor creates the files sparsedata unf and usedata unf which provide all the geometrical information for a simulation run The makefile compiles the source code into an executable ELCOM CWR Modeller creates
7. The user is free to choose any suitable z 0 baseline for the bathymetry as long as positive z upward is maintained as the convention for measurement The pre processor will adjust the user defined z 0 baseline to an internal code baseline that is suitable for the ELCOM simulation For the most part the user does not need to know or consider this internal baseline adjustment However some debugging monitoring output is presented in terms of the code coordinate system rather than the user coordinate system so care must be taken in interpreting debugging output that is intended for use by code developers The position of physical space origin x 0 y 0 is set implicitly by the user through the layout of the bathymetry data in the file bathymetry dat This will be covered in more detail below Physical space x and y values may not be negative i e the x y origin must be in a corner of the domain Figure 1 Schematic of coordinate system ELCOM performs its simulation on computational cells of a three dimensional Cartesian mesh The user needs to understand the layout of the mesh so that boundary condition cells can be properly identified In the present version of the code the mesh has uniform spacing in each of the horizontal dimensions x and http www cwr uwa edu au blaval manual elcom elcom_guide pre html 2 of 14 31 8 2000 1 14 00 PM Pre Processor y and allows non uniform spacing in the vertical 2 direction Figure 2 shows a plan
8. blaval manual elcom elcom_guide contents_long html 1 of 2 31 8 2000 1 15 08 PM Contents Full 3 7 1 sparsedata unf and usedata unf 3 7 2 Datablock db 3 7 3 Temporal boundary condition 1D files Non Uniform Initial Conditions elcom_user f90 Output files 3 9 1 Datablock output files 3 9 2 Restart output files 3 9 3 Three dimensional output files 3 9 3 Save output files 3 8 3 9 Appendices http www cwr uwa edu au blaval manual elcom elcom_guide contents_long html 2 of 2 31 8 2000 1 15 08 PM
9. calc 2 dynamic direction 2 dynamic valu 2 ESCRIPTION set reference number user label type of set number of cells in set 1 sheet type sheet calc sheet value dynamic nam dynamic calc 1 dynamic direction 1 dynamic valu 1 dynamic nam 2 dynamic calc 2 dynamic direction 2 dynamic valu 2 _DESCRIPTION set reference number user label type of set number of cells in set sheet type sheet calc http www cwr uwa edu au blaval manual elcom templates datablock db 0 0 sheet value NULL dynamic nam NULL dynamic calc 1 NULL dynamic direction 1 0 0 dynamic valu 1 NULL dynamic nam 2 NULL dynamic calc 2 NULL dynamic direction 2 0 0 dynamic valu 2 BEGIN SET_DESCRIPTION 24 set reference number sheet 8_set user label SHEET_2D type of set 0 number of cells in set FLAT sheet type TOTAL sheet calc 0 0 sheet value NULL dynamic nam NULL dynamic calc 1 NULL dynamic direction 1 0 0 dynamic valu 1 NULL dynamic nam 2 NULL dynamic calc 2
10. cells with i gt 2 Then to get free slip on the y minus and y plus faces at i 2 requires two more definitions These are not inconsistent with the flow_xm definition since they are on different faces of the same cell Thi s file also shows the use of the section_top to segregate the free surface into different sets onto which different wind data can be enforced bc dat file comment lines need thr items flow_xm outflow number 1 2 section_top wind_region_a LO section top wind region b T1 5 21 slip all sides free slip section 3 34 slip ym free slip near infl 2 slip_yp free slip near infl 2 Table Example of boundary cell set file bc dat 2 5 Running the pre processor with run_pre An up to date copy of run_pre can be downloaded from Appendix A The run_pre file is a text file that contains the names and location of user supplied input files and pre processor output files The pre processor requires two user supplied text files bathymetry dat and bc dat The former describes the bathymetry of the lake and grid configuration The latter defines sets of boundary cells The pre processor output consists of two Fortran unformatted binary files sparsedata unf and usedata unf The former contains information on three dimensional space and is used by CWR Modeller and ELCOM The latter is used by ELCOM and contains the one dimensional spatial relationships required for the simulation These files may be renamed but
11. debug_baroclinic_y error trapping on 1 off 0 frequency of outputs 10 iter_out_monitor monitoring output to screen 2000 iter_out_save saving separate restart files 500 iter_out_restart overwriting restart output start of outputs 1 start_output_monitor monitor output to screen 1 start_output_save saved restart files http www cwr uwa edu au blaval manual elcom templates run_elcom 2 of 3 31 8 2000 1 14 31 PM http www cwr uwa edu au blaval manual elcom templates run_elcom time controls LI 2000001 0 start date cwr CWR Julian day 950 del t Time step 100 iter max Number of time steps LI conjugate gradient iteration controls LI 1 e 16 CGM TOL CGM tolerance 30 CGM_MIN minimum iterations of CGM 1000 CGM_MAX maximum iterations of CGM 1 default values superseded by other inputs 1 default_height default_salinity 260 default_temperature 0 default_wind_speed 0 default_wind_direction 3 default_extinction default bc input file names include exact file extension LI sparsedata unf 3D data file usedata unf preprocessor file met dat boundary condition file datablock db datablock_file file directories require quote marks around note that incomplete quotes can cause code to hang infiles infile dir unffiles outfile unf dir txtfiles outfile txt dir output file names do not include
12. end time 0 indicates entire run 0 size of time list non zero only if is interval FALSE BEGIN GROUP DESCRIPTION 7 group reference number all group user label all3d unf output filename 6 set reference number 9 number of datatypes in group TRUE is interval logical true if time step interval is used 5 output interval 0 output start time 0 output end time 0 indicates entire run 0 size of time list non zero only if is interval FALSE BEGIN GROUP DESCRIPTION 9 group reference number general group user label general3d unf output filename 8 set reference number 9 number of datatypes in group TRUE is interval logical true if time step interval is used 5 output interval 0 output start time 0 output end time 0 indicates entire run 0 size of time list non zero only if is interval FALSE BEGIN GROUP DESCRIPTION tt group reference number sheetl group user label sheetl unf output filename 10 set reference number 10 number of datatypes in group TRUE is interval logical true if time step interval is used http www cwr uwa edu au blaval manual elcom templates datablock db 1 of 9 31 8 2000 1 14 33 PM for output for output for output for output for output for output http www cwr uwa edu au blaval manual elcom templates datablock db 5 output interval 0 output start t
13. of 14 31 8 2000 1 14 01 PM Pre Processor land cells The Land boundary condition is the default for all faces of cells identified by the land value in the bathymetry dat file and for all boundary cell faces below the bathymetry data As such the user will rarely need to use a land boundary condition in the bc dat file For a lake without any inflows outflows or special boundary conditions the bc dat file need not be present 2 4 3 Boundary cell set face direction The cell faces of the boundaries are identified by the i j k coordinates of the interior cell and the direction from the cell center to the boundary The conventions used are as follows xp the y z cell face in the positive x direction from the cell center YP the x z cell face in the positive y direction from the cell center xm the y z cell face in the negative x direction from the cell center ym the x z cell face in the negative y direction from the cell center top the x y cell face above the all_sides all possible side boundary faces i e all y z and x z faces a all possible side boundary faces plus the bottom boundary 2 4 4 Boundary cell set keywords The keywords used to identify boundary cell sets are a concatenation of the categories and the face direction The valid keywords are listed below Boundary Cell Set Keywords flow xp lip xp tion xp land xm low xm lip xm n xm land yp flow yp lip yp tion yp land ym low ym lip ym n ym la
14. the executable directing the screen output to a file see section 3 3 11 post process data ELCOM uses and creates a large number of files The following directory structure is suggested to help streamline ELCOM s use http www cwr uwa edu au blaval manual elcom elcom_guide introduction html 1 of 3 31 8 2000 1 13 47 PM Introduction source PRE contains pre processor source code source ELCOM contains ELCOM source code BIN contains ELCOM PRE db2nc executables and must be in the UNIX search path bathymetry contains bathymetry dat and bc dat files for various user simulations runs RUN_A contains run_elcom file for a simulation as well as ELCOM status output files runs RUN_A infiles contains user input files for a simulation ie sparsedata unf usedata unf temporal boundary condition files and datablock db LCOM runs RUN_A unffiles contains ELCOM unf output files to be converted to nc files using db2nc LCOM runs RUN_A txtfile contains output text files from ELCOM The ELCOM BIN directory must be in the UNIX search as defined in your user cshrc file For example the following line should be included in your cshre file setenv PATH S PATH S HOME ELCOM bin 1 4 Conventions and definitions In this document a number of conventions will be used For clarity the computational domain will generally be referred to as a lake However the simu
15. usage is minimized This allows Fortran 90 compiler parallelization and vectorization without platform specific modification of the code A future extension of ELCOM will include dynamic pressure effects to account for nonlinear dynamics of internal waves that may be lost due to the hydrostatic approximation 1 3 Outline of a simulation run ELCOM is designed to be used in conjunction with a graphical user interface GUI called CWR Modeller which supports post processing and analysis of the data However ELCOM is not executed by CWR Modeller but is initiated with simple command line execution statements Setting up and running an ELCOM simulation requires the following steps 1 compile the PRE executable see section 2 2 prepare bathymetry dat file that provides topography and grid information see section 2 3 prepare bc dat file that designates sets of cells for applying boundary conditions see section 2 4 run the pre processor to produce sparsedata unf and usedata unf files section 2 5 compile the ELCOM executable see section 3 3 configure the simulation run_elcom file see section 3 6 specify output in a datablock file db for designating data output operations see section 3 7 2 0 N DOO A OO N prepare temporal boundary condition files dat for data applied to the boundary condition cells see section 3 7 3 9 prepare any user defined subroutines for initial conditions see section 3 8 10 run
16. E I M Underpaid ANALYST Centre for Water Research ORGANIZATION ELCOM guide template COMMENT simulation modules 0 OFF 1 ON 1 iwind wind forcing l stress 0 iheat_input surface thermodynamics 0 iflow inflow outflow 1 itemperature temperature 1 isalinity salinity 1 idensity density baroclinic forcing 0 ntracer number of tracers 0 1CAEDYM water quality module 0 icoriolis turn off on coriolis forcing 0 icurvilinear curvilinear terms l output only 2 use 6 output 2 idatablock datablock version control initialization options 0 irestart start from restart fil 0 user_init_u_vel 1 use stub routine in 0 user init v vel 0 user init w vel 0 user init temperature 0 user init salinity 0 user init tracer 0 user_init_viscosity 0 user_init_height 0 user_init_extinction O user update SURFACE_SLOPE CASE_KEYWORD turbulence modeling O no mixing iclosure bottom drag 1 0e 4 drag btm cd eddy viscosities is_u is_v is_w is x tracer is y tracer is z tracer is x salt is y salt is z salt is x temp is y temp is z temp prandtl q w SSW4 s GS S 4S ss ss ss HOODOO GOOO OW OKO o0o0000000000o0oOo l static stability mixing closure model 6 mixed layer drag coefficient on bottom cells x dir eddy viscosity y dir eddy viscosity z dir vertical viscosity x dir eddy vis for tracer y dir
17. EGIN GROUP_TIME_LIST T group ref nce number BEGIN GROUP_TIME_LIST 9 group ref nce number BEGIN GROUP_TIME_LIST 11 group ref nce number BEGIN GROUP_TIME_LIST 13 group reference number BEGIN GROUP_TIME_LIS 15 group reference number BEGIN GROUP TIME LIST Y group ref nce number BEGIN GROUP TIME LIST 19 group ref nce number BEGIN GROUP TIME LIST 21 group ref nce number BEGIN GROUP TIME LIST http www cwr uwa edu au blaval manual elcom templates datablock db 8 of 9 31 8 2000 1 14 33 PM http www cwr uwa edu au blaval manual elcom templates datablock db 23 group reference number BEGIN GROUP TIME LIST 25 group reference number BEGIN SET CELL DATA 100 GUI set reference number 4300 4 600 4 11 00 BEGIN SET CELL DATA 2 set reference number 3 7 00 47 00 SWA OQ BEGIN SET CELL DATA set reference number DOAOOOQOOQOOMOO OTOOTO GOG O Ps bs BB BRB BRB BW aK Ai RRP0 J0O0d0d DN 00 0 100 1200 BEGIN SET CELL DATA 6 set reference number BEGIN SE CE DATA 8 set reference number 462 46 3 4101 4 10 3 BEGIN SET_CELL_ DATA 10 set ference number BEGIN SET CELL DATA 12 set reference number BEGIN SET CELL DATA 14 set ference number BEGIN SET CELL DATA
18. Initialization and update options irestart use of restart file for initial conditions 0 do not user restart file 1 use restart file specified by restart_in_file user_init_u_vel controls user written subroutine for initializing x velocity 0 ignore subroutine user_u_init 1 execute subroutine user_u_ init with USER_START_U 1 user_init_v_vel controls user written subroutine for initializing y velocity 0 ignore subroutine user_v_init 1 execute subroutine user_v_init with USER_START_V 1 user_init_w_vel controls user written subroutine for initializing y velocity 0 ignore subroutine user_w_init 1 execute subroutine user_w_ init with USER START w 1 user_init_temperature controls user written subroutine for initializing temperature 0 ignore subroutine user_temperature_init 1 execute subroutine user_temperature_init with USER_START_TEMPERATURE 1 user_init_salinity controls user written subroutine for initializing salinity 0 ignore subroutine user_salinity_init 1 execute subroutine user_salinity_init with USER START SALINITY 1 user_init_tracer controls user written subroutine for initializing tracer http www cwr uwa edu au blaval manual elcom elcom_guide elcom_op html 6 of 16 31 8 2000 1 14 11 PM ELCOM Operation 0 ignore subroutine user_tracer_init 1 execute subroutine user_trace_init with USER_START_TRACER 1 user_init_viscosity controls user written subr
19. NULL dynamic direction 2 0 0 dynamic valu 2 BEGIN GROUP_DATA_TYPES 100 GUI group reference number U_VELOCITY V_VELOCITY W_VELOCITY TEMPERATURE DENSITY AUX_1 AUX_2 AUX_3 AUX_4 AUX_5 MIX_ENERGY SHEAR RI_NUM BEGIN GROUP_DATA_TYPES 1 group reference number U VELOCITY V_VELOCITY W_VELOCITY U_VIS BEGIN GROUP_DATA_TYPES 3 group reference number U_VELOCITY V_VELOCITY W_VELOCITY SALINITY EMPERATURE DENSITY TRACER_1 TRACER_2 U_VIS BEGIN GROUP_DATA_TYPES 7 group reference number U VELOCITY V_VELOCITY W_VELOCITY SALINITY TEMPERATURE DENSITY TRACER_1 http www cwr uwa edu au blaval manual elcom templates datablock db 6 of 9 31 8 2000 1 14 33 PM http www cwr uwa edu au blaval manual elcom templates datablock db TRACER_2 U_VIS BEGIN GROUP_DATA_TYPES group reference number ELOCITY ELOCITY VELOCITY SALINITY EMPERATURE DENSITY TRACER 1 TRACER 2 U VIS BEGIN GROUP DATA TYPES LI group reference number U_VELOCITY V_VELOCITY W_VELOCITY SALINITY EMPERATURE DENSITY TRACER_1 TRACER_2 HEIGHT U_VIS BEGIN GROUP_DATA_TYPES 13 group reference number U_VELOCITY V_VELOCITY W_VELOCITY SALINITY EMPERATURE DENSITY TRACER_1 TRACER_2 HEIGHT U_VIS BEGIN GROUP_DATA_TYPES 15 group reference number U VELOCITY V VELOCITY W VELOCITY SALINITY EMPERATURE DENSITY RACER 1 TRACER 2 HEIGHT U VIS BEGIN GROUP DATA TYPES 157 group referen
20. NULL 0 0 BEGIN SE 18 sheet5_set SHEET 2D 0 FLAT T I 0 0 BEGIN SE 20 sheet 6_set SHEET 2D 0 FLAT MIN 0 0 NULL NULL NULL 0 0 NULL N N 0 0 BEGIN SE 22 sheet 7_set SHEET 2D 0 FLAT AVG l l l l T l ULL U T I http www cwr uwa edu au blaval manual elcom templates datablock db 5 of 9 31 8 2000 1 14 33 PM 2D sheet type sheet calc sheet value dynamic nam dynamic calc 1 dynamic direction 1 dynamic valu 1 dynamic nam 2 dynamic calc 2 dynamic direction 2 dynamic valu 2 _DESCRIPTION set reference number user label type of set number of cells in set sheet type sheet calc sheet value dynamic nam dynamic calc 1 dynamic direction 1 dynamic valu 1 dynamic nam 2 dynamic calc 2 dynamic direction 2 dynamic valu 2 _ DESCRIPTION set reference number user label type of set number of cells in set sheet type sheet calc sheet value dynamic nam dynamic calc 1 dynamic direction 1 dynamic valu sl dynamic nam 2 dynamic
21. The CWR Estuary and Lake Computer Model ELCOM User Guide by Bernard Laval and Ben R Hodges Copyright 2000 Centre for Water Research The University of Western Australia code version 1 1 a patch 54 September 1 2000 http www cwr uwa edu au blaval manual elcom elcom_guide title html 31 8 2000 1 13 45 PM Contents ELCOM User Guide Welcome Long Contents 1 Introduction 1 1 The ELCOM model 1 2 Implementation language 1 3 Outline of a simulation run 1 4 Conventions and definitions 2 Pre processor Introduction Compiling bathymetry dat pe dat Running N MN N ND OF WYN FB 3 ELCOM Introduction Files for ELCOM Compiling Simulation modules Configuration controls Configuration Input files Non Uniform Initial Conditions Output files WWWW WWW WwW WwW wont our WN FE Appendices http www cwr uwa edu au blaval manual elcom elcom_guide contents_short html 31 8 2000 1 13 46 PM Welcome Estuary and Lake Computer Model ELCOM User Manual These notes are designed to aid an uninitiated user in performing an ELCOM simulation This document gives a basic description of ELCOM s operation and instructions on how to create the input files required for a standard simulation Continue to the Introduction http www cwr uwa edu au blaval manual elcom elcom_guide welcome html 31 8 2000 1 13 47 PM Introduction 1 Introduction
22. ablock db A datablock db template can be obtained from Appendix A The file datablock db is a text file produced by CWR Modeller and contains the configuration data used to set up the users output The name for this file is specified by the user from CWR Modeller Alternatively the datablock db file may be setup manually using a text editor A datablock db file is structured as a series of blocks of instructions Each block requires an exact number of lines with specific instructions on each line Each line contains a single instruction followed by a comment The comment must begin with a character In manually editing dat ablock db files it is important to keep in mind that while blocks of instructions may be added or removed lines within a block can only be modified but not removed The following will discuss the structure of each block of instructions 3 7 2 1 Datablock Description The first 4 lines of a datablock db are the datablock description In order they are the block descriptor the current datablock version number the number of output groups and the number of output sets Output groups and sets are described below 3 7 2 2 Group Description Following the datablock description are the group description blocks A group represents a group of data to be output A data group is defined as an output filename datatypes to be output ie TEMPERATURE SALINITY etc the location within the simulation domain of the points a
23. algorithm mixes momentum and transported scalars in vertical cells where an unstable gradient of potential density exists i e Ri lt 0 0 For stratified flows driven by surface wind the wind mixed layer closure scheme with energy transport iclosure 6 is recommended This approach computes the turbulent kinetic energy due to wind stirring convective overturns and wind shear then uses this to compute vertical mixing Note that iwind 2 must be used with iclosure 6 3 5 4 Output frequency Outputs of data that are not controlled by the datablock file are set through the iter_out_ and start_output_ keywords The former controls the time step interval for providing output the latter controls the first step on which output will be provided http www cwr uwa edu au blaval manual elcom elcom_guide elcom_op html 4 of 16 31 8 2000 1 14 10 PM ELCOM Operation 3 6 Configuration using file run_elcom A run_elcom template can be obtained from Appendix A ELCOM looks for the file run_elcom in the local directory where the executable reside to set the configuration of the simulation run In future versions the run elcom file will be produced through CWR Modeller The run_elcom configuration file controls execution of optional modules and models within ELCOM allowing the user to set the parameters that govern the physical and numerical simulation The format of the file is flexible in that lines may occur in any order and not all i
24. ce number U VELOCITY V VELOCITY W VELOCITY SALINITY TEMPERATURE DENSITY TRACER_1 TRACER_2 HEIGHT U_VIS BEGIN GROUP_DATA_TYPES 19 group reference number U VELOCITY V VELOCITY W VELOCITY S a lt lt lt http www cwr uwa edu au blaval manual elcom templates datablock db 7 of 9 31 8 2000 1 14 33 PM http www cwr uwa edu au blaval manual elcom templates datablock db SALINITY TEMPERATURE DENSITY TRACER_1 TRACER_2 HEIGHT U_VIS BEGIN GROUP_DATA_TYPES ZIN group reference number U VELOCITY V VELOCITY W VELOCITY SALINITY TEMPERATURE DENSITY TRACER 1 TRACER 2 HEIGH U VIS BEGIN GROUP DATA TYPES 23 group reference number U VELOCITY V VELOCITY W VELOCITY SALINITY TEMPERATURE DENSITY TRACER 1 TRACER 2 HEIGHT U VIS BEGIN GROUP DATA TYPES 25 group reference number U VELOCITY V VELOCITY W VELOCITY SALINITY TEMPERATURE DENSITY TRACER 1 TRACER 2 HEIGH U VIS BEGIN GROUP TIME LIST 100 GUI group reference number BEGIN GROUP TIME LIS 1 group reference number BEGIN GROUP_TIME_LIST 3 group ref nce number B
25. code consists of all the files listed below plus any user prepared files http www cwr uwa edu au blaval manual elcom elcom_guide elcom_op html 1 of 16 31 8 2000 1 14 10 PM ELCOM Operation ELCOM Fortran90 Modules lcom_bc f90 elcom_caedym1 f90 cgm_setup f90 datablock f90 L flowbound 90 globals f90 inputs f 90 lcom_caedym2 90 elco lcom_curvilinear f90 elco lcom errors f90 elco lcom free surface f90 elco lcom heat f90 elco lcom mixing f90 elcom momentum 90 Ilcom no caedymi f90 elcom no caedym2 f90 outputs f90 scalar_solve f90 setup f90 testcase f90 update f90 user_examples f90 m m m m m m m m lcom_openbound f 90 elcom lcom_quick f 90 elcom lcom scalar ultilities f90 elcom lcom solver f90 elcom lcom time step f90 elcom m lcom user f90 elco lcom_utilities f90 elcom_velocities f90 e e e e e e el e e e e e e e e e lcom wind f90 main elcom main o fd no caedym 90 ELCOM is compiled by typing the command make at the command line in the same directory as the source code and the makefile This executes the makefile and produces the executable ELCOM The ELCOM executable file is then installed using the UNIX syntax make install The ELCOM source code directory can then be cleaned up using the following UNIX command make clean ELCOM is executed at the command line by typing ELCOM capital letters are required within
26. e number all_set user label http www cwr uwa edu au blaval manual elcom templates datablock db 3 of 9 31 8 2000 1 14 33 PM http www cwr uwa edu au blaval manual elcom templates datablock db ALL_3D type of set 0 number of cells in set NULL sheet type NULL sheet calc 0 0 sheet value NUL dynamic nam NUL dynamic calc 1 NUL dynamic direction 1 0 0 dynamic valu 1 NUL dynamic nam 2 NUL dynamic calc 2 NULL dynamic direction 2 0 0 dynamic valu 2 BEGIN SET_DESCRIPTION 8 set reference number general_set user label GENERAL_3D type of set 4 number of cells in set NULL sheet type NULL sheet calc 0 0 sheet
27. eddy vis for tracer z dir eddy vis for tracer x dir eddy vis for salt y dir eddy vis for salt z dir eddy vis for salt x dir eddy vis for temperature y dir eddy vis for temperature z dir eddy vis for temperature turbulent Prandtl number http www cwr uwa edu au blaval manual elcom templates run_elcom 1 of 3 31 8 2000 1 14 31 PM http www cwr uwa edu au blaval manual elcom templates run_elcom salt_schmidt turbulent salinity Schmidt number tracer_schmidt tracer Schmidt number model settings and controls model grav damp x damping of gravity for x baroclinic term model grav damp y damping of gravity for y baroclinic term scalar max and min for debugging in temperature 0 ax temperature in salinity 5 ax_salinity in_tracer_1 1 max_tracer_1 in_tracer_2 1 max_tracer_2 in_tracer_3 ax_tracer_3 in_tracer_4 ax_tracer_4 in_tracer_5 ax_tracer_5 in_tracer_6 ax_tracer_6 in_tracer_7 ax_tracer_7 in_tracer_8 ax_tracer_8 in_tracer_9 ax_tracer_9 in_tracer_10 ax_tracer_10 3333333333333 333030_33333 0000000000000 000rPorPO0OoQuyol o special setup see elcom_setup f90 0 itest_case test case number 0 iflow_special special flow setup debug output controls 1 debug_check level of error checking 2 debug_print level of debug printing 0 debug_point sparse data index point for debug output 1 debug_baroclinic_x error trapping on 1 off 0 1
28. elcom file using keywords of the form default_ Any default value entered will be overwritten by the user initialization subroutines when invoked Time step The time step keyword de1_t is the number of seconds that the simulation advances in time for each simulation step Number of steps The total number of time steps to be computed in the present simulation run is set using the keyword iter_max in the run_elcom file Start date The start date is entered in CWR Julian Day format which specifies the year and day using a real number with 7 digits to the left of the decimal place as yyyyddd ddd The first 4 digits are the year and the subsequent 3 digits are the Julian Day Hours minutes seconds are represented as fractions of a day ie 1am on January 1st 2000 is represented as 2000000 041667 3 5 2 CGM tolerance The CGM_TOL is the residual at which iteration of the conjugate gradient method used for the free surface solution is stopped 3 5 3 Turbulence ELCOM solves the unsteady Reynolds averaged Navier Stokes equations RANS with four types of turbulence closure The base closure scheme which is always applied iclosure 0 requires the user to set fixed values for horizontal h_vis and vertical v_vis eddy viscosity The base closure scheme is best applied only in unstratified flows For stratified flow the base closure scheme can be supplemented by unstable mixing iclosure 1 algorithms The unstable mixing
29. ewed with a text processor or spreadsheet The present convention gives the user a What You See Is What You Get view of the bathymetry simply by opening the file with a word processor or importing into a spreadsheet This convention has been found to be intuitive for users who are not graphics experts However caution needs to be taken when converting raw bathymetry data from graphics programs that use a mirror image standard Likewise the direction of the positive u x direction velocity is confusing as it is positive down the page Figure 3 shows the physical space outline of the lake as the border of the shaded area The discrete outline of a lake is shown with a heavy solid line In developing a bathymetry dat file for an ELCOM simulation the user is required to provide bathymetry values i e vertical distance measured from the user s z 0 baseline for each of the cells within the discrete boundary of the lake The region outside the lake boundary is defined as the land region In Figure 3 the cell center dots have been replaced with numbers that represent the distance from the user s z 0 baseline to the bottom of the lake In this case all of the land regions have been given a value of 99 Note that the boundary of the bathymetry data set shown in Figure 3 has land values around the entire boundary In general it is required that either a land cell or open boundary cell is required around the outside of the bathymetry data For the purpo
30. file extension save restart save file restart final restart out file http www cwr uwa edu au blaval manual elcom templates run_elcom 3 of 3 31 8 2000 1 14 31 PM http www cwr uwa edu au blaval manual elcom templates datablock db DATABLOCK DESCRIPTION FILE alia datablock version 13 number of output groups 13 number of output sets BEGIN GROUP_DESCRIPTION 100 GUI group reference number tchain user label tchain unf output filename 100 GUI set reference number 13 number of datatypes in group TRUE is interval logical true if time step interval is used 5 output interval 0 output start time 0 output end time 0 indicates entire run 0 size of time list non zero only if is interval FALSE BEGIN GROUP DESCRIPTION il group reference number curtain_groupl user label curtainl unf output filename 2 set reference number 4 number of datatypes in group TRUE is interval logical true if time step interval is used 5 output interval 0 output start time 0 output end time 0 indicates entire run 0 size of time list non zero only if is interval FALSE BEGIN GROUP DESCRIPTION 3 group reference number curtain group2 user label curtain2 unf output filename 4 set reference number 9 number of datatypes in group TRUE is interval logical true if time step interval is used 5 output interval 0 output start time 0 output
31. group time list 2 group reference number An integer referencing the group number defined in the group description 3 7 2 6 Set Cell Data This block describes the spatial location of each datablock set The locations are described as row column and or layer number EGIN SET_CELL_DATA Begin set cell data 2 set reference number An integer referencing the set number defined in the set description 3 cell locations This input varies for different set types as follows PROFILE Each profile requires a row of input Each row requires 4 integers 1 x row 2 y column 3 0 4 0 CURTAIN_2D Each profile making up the curtain requires a row of input Each row requires 4 integers x row y column 0 0 SHEET_2D No Input ALL_3D No input GENERAL_3D Each point requires a row of input Each row requires 3 integers x row y column z layer 3 7 3 Temporal boundary condition 1D files A temporal boundary condition file template can be obtained from Appendix A The one dimensional temporal boundary condition files keyword boundary_condition_file are set up by the user to provide environmental forcing information that changes as a function of time These files require a format that consists of four header lines followed by columns of data The data supplied are values for particular instants of time that are applied at particular points in space i e over a boundary cell set Each column is data
32. hymetry values 99 land_value 88 open_value geographic position A 4 0 north_x positive x towards bottom of page 2 0 north_y positive y towards right on line 32 0 latitude 0 0 longitude 0 0 altitude grid spacing t a 100 0 x grid size 100 0 y_grid_size dz vector starting from top going down 0 5 dz top 0 5 dz 0 5 dz 0 54 dz 0 58 dz 0 65 dz 0 75 dz 0 90 dz al 3 dz 1 41 dz 1 65 dz 1 88 dz 2 0 dz bottom x in rows increasing down y in columns increasing across BATHYMETRY DATA 99 99 99 99 99 99 99 99 99 99 99 99 991 lt Old Dis 99 99 99 99 99 99 99 99 0 4 I2 Ta 1 1 1 4 2i5 5 Ze s t 3 3 0 7 99 99 1 1 1 6 2 2 S62 3 8 33 3 4 1 Dd Sh 5 2 99 03 0 8 EZ ZisL 22 2 4 Z2 3 3 4 1 5 0 99 99 99 99 99 99 99 99 99 37 id 99 99 99 99 99 99 99 99 99 0 7 0 9 99 99 99 99 99 99 99 99 99 39 99 http www cwr uwa edu au blaval manual elcom templates bathymetry dat 31 8 2000 1 14 04 PM http www cwr uwa edu au blaval manual elcom templates bc dat boundary condition file for A Very Large Lake File prepared by I M Underpaid 24 05 00 http www cwr uwa edu au blaval manual elcom templates bc dat 31 8 2000 1 14 04 PM http www cwr uwa edu au blaval manual elcom templates run_pre l 1 FILE run_pre VERSION l l a input files 1 bathymetry dat BATHYMETRY_FILE bc dat BOUNDARY_CONDITION_FILE output files bathout txt
33. ime 0 output end time 0 indicates entire run 0 size of time list non zero only if is_interval BEGIN GROUP_DESCRIPTION 18 group reference number sheet2 group user label sheet2 unf output filename 12 set reference number 10 number of datatypes in group TRUE is_interval logical true if time step interval is used for output 5 output interval 0 output start time 0 output end time 0 indicates entire run 0 size of time list non zero only if is interval BEGIN GROUP DESCRIPTION 15 group reference number sheet3 group user label sheet3 unf output filename 14 set reference number 10 number of datatypes in group TRUE is_interval logical true if time step interval is used for output 5 output interval 0 output start time 0 output end time 0 indicates entire run 0 size of time list non zero only if is interval BEGIN GROUP DESCRIPTION 17 group reference number sheet4 group user label sheet4 unf output filename 16 set reference number 10 number of datatypes in group TRUE is_interval logical true if time step interval is used for output 5 output interval 0 output start time 0 output end time 0 indicates entire run 0 size of time list non zero only if is interval BEGIN GROUP DESCRIPTION 19 group reference number sheet5 group user label sheet5 unf output filename 18 set reference number
34. imensional data format required for CWR Modeller Configuration for running the pre processor comes from a run_pre file The run_pre file is a text file that contains the names and location of user supplied input files and pre processor output files The pre processor requires two user supplied text files bathymetry dat and bc dat The former describes the bathymetry of the lake and grid configuration The latter defines sets of boundary cells The pre processor output consists of two Fortran unformatted binary files sparsedata unf and usedata unf The former contains information on three dimensional space and is used by CWR Modeller and ELCOM The latter is used by ELCOM and contains the one dimensional spatial relationships required for the simulation These files may be renamed but the user must keep track of which files are sparsedata files and which files are usedata files 2 2 Compiling the pre processor Before compiling the pre processor source code directory should contain the following files e pre_main f90 pre_globals f90 pre process f90 pre bathymetry f90 pre common f90 makefile run pre The 90 files should not need modification by the user However the makefile file will need modification by the user to indicate the path to the bin directory The pre processor is compiled using a make utility and the file makefile Typical UNIX syntax for compiling is simply make This produces an executable file PRE which i
35. in the run elcon file 3 9 Output files 3 9 1 Datablock output files An example of a current run db2nc file can be found in Appendix A The datablock output files are named and configured through the datablock db file which is configured either manually or through CWR modeller ELCOM produces Fortran unformatted binary files as specified by the datablock output configuration In general one datablock output file contains one or more data types e g velocity temperature applied to as set of points chosen through CWR Modeller at a specified time interval These files can be reprocessed into NETCDF files through CWR Modeller or manually using the command line program db2nc The program db2nc is used for converting datablock unformatted by binary files created by ELCOM to NETCDF files which can then be processed and viewed in a program such as Matlab The db2nc executable should be placed either in the working directory or as recommended in the bin directory which is in the operating system s search path db2nc is run through a configuration file called run_db2nc The run_db2nc file contains 8 lines as follows 1 Comment line up to 64 characters 2 unf file name and path 3 sparsedata unf file name and path http www cwr uwa edu au blaval manual elcom elcom_guide elcom_op html 15 of 16 31 8 2000 1 14 14 PM ELCOM Operation 4 nc netcdf output file name and path 5 Start time step 1 for beginning
36. ions Obviously this is inconsistent and the flow simulation cannot enforce both boundary conditions Checking for which combinations of multiple definitions are consistent and which are not is an error capturing routine that is not yet implemented Thus the above boundary cell sets would be processed and provided to ELCOM Within ELCOM only one of the two boundary conditions will actually be enforced but one cannot tell a priori which boundary condition it will be without detailed examination of source code Note that the order the items are defined may affect the operation of an inconsistent definition Thus if the above inconsistent definition were reversed and written as 214 slip_all freeslip_domain 2791 flow ym river inflow S215 The results in ELCOM may be different than the previous implementation they would be wrong in a different manner As a general rule the user should not provide multiple definitions of velocity boundary conditions on a single cell face The land flow and slip keywords all effect the type of velocity boundary condition it is incumbent on the user to be sure that the cell faces defined with these types do not have multiple definitions The following table illustrates a bc dat file with a few subtle uses of the boundary cell set definitions A flow boundary has been declared on the x minus faces of cells with i 2 Thus to get free slip boundary conditions on all the other face we use the keyword slip_all for
37. ip condition applied while the normal component of the velocity is a Dirichlet no flux condition this may be thought of more precisely as normal Dirichlet tangential Neumann or NDTN A Neumann zero gradient condition is imposed on transported scalars flow Cell boundary through which an inflow or outflow will be imposed as a Dirichlet fixed velocity condition This also enforces a Dirichlet condition on transported scalars section Cell boundary which is grouped into a set for application of an environmental forcing or scalar forcing boundary condition but does not change the underlying form of the velocity boundary condition e g the free surface may be divided into sections over which different wind conditions may be enforced the type velocity boundary condition is not changed but its magnitude is adjusted on different open Cell boundary which is open to inflows and outflows from another body of water where the velocity is not fixed a priori i e not a Dirchlet boundary but is a function of the baroclinic and barotropic forcing near the boundary presently not implemented interior An interior cell on which a source or sink of mass or tracer is enforced e g a sewage outfall or drinking water offtake presently not implemented A boundary cell set consists of a collection of cell faces that are the boundaries between interior cells and http www cwr uwa edu au blaval manual elcom elcom_guide pre html 10
38. lation method is designed for applicability to estuaries and coastal ocean environments X y Z Space Full Cartesian space which covers all of the bathymetry i j k space Discrete integer space of computational cells which covers all of the bathymetry land A computational cell that cannot contain water open A cell used for an open boundary condition interior A cell that may contain water X_rows Number of grid cells in the x direction y_columns Number of grid cells in the y direction z_layers Number of grid cells in the vertical z direction land_value Number used in the bathymetry file to represent the land cells open value http www cwr uwa edu au blaval manual elcom elcom_guide introduction html 2 of 3 31 8 2000 1 13 47 PM Introduction Number used in the bathymetry file to represent the open boundary cells dx Uniform grid spacing delta in the x direction in metres dy Uniform grid spacing delta in the y direction in metres dz Grid spacing delta in the z direction may be uniform or non uniform in metres Continue on to Pre processor http www cwr uwa edu au blaval manual elcom elcom_guide introduction html 3 of 3 31 8 2000 1 13 47 PM Pre Processor 2 Pre Processor 2 1 Introduction The ELCOM pre processor is used to convert the user s three dimensional data of lake bathymetry boundary forcing sections and grid structure into one dimensional vectors used by ELCOM and the three d
39. n of points a contiguous series of column of points curtain a horizontal sheet of points or any group of points in the three dimensional domain The valid set types are PROFILE CURTAIN_2D SHEET_2D ALL_3D GENERAL_3D Profiles and curtains require only the x y locations of the base of each column to describe their location Sheets can be referenced to a layer a height above user datum a height above bottom or a height below the free surface ALL_3D simply outputs all points in the domain and GENERAL_3D at points whos coordinates are individually specified A set description block contains 16 lines which are as follows 1 BEGIN SET_DESCRIPTION begin set statement 2 set reference number an integer labelling the set this can have any value 3 user label a name containing no blank spaces labelling the set used by CWR modeller only 4 type of set on of the 5 valid set type names described above 5 number of cells in set for type PROFILE this is the desired number of columns for type CURTAIN2D this is the number of columns making up the desired curtain for type GENERAL_3D this is the desired number of points for types SHEET 2D and ALL_3D this value is 0 6 sheet type for type SHEET_2D this indicates the SHEET datum for all other set types the keyword is NULL Valid sheet type keywords are LAYER horizontal layer referenced as layer number up from bottom as desc
40. n single quotations marks If the string is left blank or not enclosed in quotes the pre processor will crash with a Fortran read error The user must have only one COMMENT line A typical set of header keywords is shown below Nowhere TITLE Underpaid ANALYST Large Company ORGANIZATION run number 1 COMMENT Overwriting files keyword overwrite This command is now superceeded by the run pre file yes overwrite no overwrite Size of input bathymetry data keywords x_rows y_columns z_layers n_max In order to correctly read the bathymetry data from file bathymetry dat the user must tell the pre processor the size of grid to expect The value for x_rows is the number of rows in a two dimensional plan view of the bathymetry e g figure 4 The y_columns is the number of columns in the two dimensional plan view The number of layers in the vertical direction is identified with the keyword z_layers The keyword n max is used to set an estimate of the number of grid cells in the domain that are required for simulation i e interior points plus the land points in one layer surrounding the interior For most simulations n_max can be set to 0 and the code will start with an estimate of x_rows x y_columns x z_layers However in some cases this may create a temporary data array larger than can be processed http www cwr uwa edu au blaval manual elcom elcom_guide pre html 5 of 14 31 8 2000 1 14 01 PM Pre P
41. nd bottom flow bottom lip bottom tion bottom land xp land all sides low all sides slip all sides n all sides land all flow all lip all n all n top interior not implemented open not implemented 2 4 5 Organization of the boundary cell set file bc dat At the top of the boundary cell set file bc dat the user may put any number of comment lines Each comment line must be started with an exclamation point and have at least 3 items on the line i e two words or numbers separated from the exclamation point and each other by a spaces or tabs After the initial comments the boundary cell set file consists of a series of definitions of boundary sets Each set consists of a set identification line followed by one or more lines of cell definitions Each line must have three items on it or the pre processor will crash with a Fortran file read error Blank lines are not allowed in the boundary cell set file http www cwr uwa edu au blaval manual elcom elcom_guide pre html 11 of 14 31 8 2000 1 14 02 PM Pre Processor Each set identification line is of the form integer keyword title The first item integer isa reference number for the boundary cell set that is used in preparing temporal boundary condition data files for the ELCOM simulation run see section 3 5 Each boundary cell set must have a unique integer reference number The keyword is one of the valid ke
42. ned by iter_out_save The file name of the save files begin with the user specified kernel given by restart_save_file appended by atime stamp appended by unf Note that the time stamp does not currently include the simulation year and there exists the possibility that save files will be overwritten after a year of simulation time The restart files are created at intervals defined by iter_out_restart starting from the first time step Subsequent restart files overwrite existing restart files The file name of the restart files begin with the user specified kernel given by restart_out_file appended by unf All start and restart files are written in the outfiles directory specified in the run_elcon file To restart an ELCOM simulation using a save or restart file the user must place a copy of the desired save or restart file in the infiles directory as specified in the run_elcom file In the run elcom file the name of the desired save or restart file must be assigned to the restart_infile keyword and keyword i_restart must be assigned the value 1 Continue on to templates http www cwr uwa edu au blaval manual elcom elcom_guide elcom_op html 16 of 16 31 8 2000 1 14 14 PM http www cwr uwa edu au blaval manual elcom templates run_elcom run_elcom 1 1 a e pese Il 2 momentum special yes 1 no 0 elcom user f90 A Very Large Lake TITL
43. niform initial conditions for certain variables can be set up within the elcom user f90 file As described in the Compiling ELCOM section elcom user 90 is a module of the ELCOM source code Within elcom_user 90 are a number of subroutines which the user can modify to implement initial conditions The elcom user f90 file will contain a number of examples which the user can emulate to create their own initial conditions A list of the initialization subroutines contained within elcom_user 90 is given below User Initialization Subroutines in ELCOM user 90 user_u_init user_v_init user_w_init user temperature init user salinity init user tracer init user extinction init user height init user uvis init user vvis init user wvis init user tracer xvis init user tracer yvis init user tracer zvis init user salt xvis init user salt yvis init user salt zvis init user temp xvis init user temp yvis init user temp zvis init For a particular subroutine to be used the appropriate user_init_ keyword must be set to 1 in the run_elconm file Within each initialization subroutine various possible initial conditions are separated from each other by a series of IF CASE KEYWORD stringl THEN Or ELSEIF CASE_KEYWORD string2 THEN statements A particular initial condition is implemented by setting the CASE WORD equal to the appropriate string variable in the IF logical argument The CASE WORD is assigned
44. nput Therefore with iwind 0 any wind value read in temporal boundary condition files will not provide a wind stress boundary condition but will be used in the surface thermodynamics module for iheat_input gt 0 With iwind 1 or 2 any wind value read in temporal boundary condition files will provide a wind stress boundary condition or a momentum source to the wind mixed layer As well the wind value will be used in the surface thermodynamics module for iheat_input gt 0 If the keywords WIND_SPEED and WIND DIR in the temporal boundary condition files are associated with the boundary cell set 0 the entire free surface then a wind field of uniform speed and direction is applied across the entire free surface Alternatively the user may declare multiple boundary cell sets on the free surface using the keyword section top in the file bc dat for the preprocessor The different sections are given reference numbers in bc dat which are then used in the temporal boundary condition files to identify the WIND_SPEED and WIND DIR for each section 3 4 5 Inflow outflow Inflow and outflow boundaries must be initially declared in the preprocessor bc dat file The user must then ensure that temporal boundary conditions are provided for the flow rate n in the temporal boundary condition files For inflow conditions all transported scalars must also be given boundary values temporal boundary condition files If a transported
45. of a particular type defined by a keyword in the header The first column must be time in CWR format yyyyddd dd Each row is data at a particular time The file may have as many comment lines preceded by at the top of the file as desired Comment lines within the header data must have as many items as there are columns i e if there are 3 columns a valid comment line is No comment lines are allowed within the columns of data The columns must be completely dense with data i e there may not be missing data such that a row has less data than the number of columns The first header line contains one number the number of data sets columns in the boundary condition file not including the time column The second line in the header also contains the number 0 indicating that the CWR time format will be used in the data below and the first column in the data file should be a TIME column Note that the user does not have to supply boundary condition data at the same time interval that the simulation uses as the computational time step de1_t the simulation interpolates linearly between the temporal boundary condition data to find the appropriate data value at an instant in time The third line in the header must have an integer for each column This is the reference number for the applicable set of boundary cell set defined in the file bc dat during the setup of the pre processor that each column of data will be applied to Fo
46. of the domain or an error will occur default_salinity Default salinity in practical salinity units psu which is essentially equivalent to parts per thousand May be over ridden by user prepared subroutine if user_init_salinity default_temperature Default water temperature in Celsius degrees May be over ridden by user prepared subroutine ifuser init temperature 1 default_wind_speed Default wind speed in ms May be over ridden by user prepared input file see following section default_wind_direction Default wind direction in degrees measured counter clockwise from North in direction wind is coming from May be over ridden by user prepared input file see following section de fault_extinction Default light extinction coefficient in Celsius degrees May be over ridden by user prepared subroutine if user_init_extinction 1 default_bc Default boundary conditions 1 no slip all 2 free slip all 3 drag all 4 neumann all 5 free slip sides no slip bottom 6 free slip sides drag bottom 7 free slip sides neumann bottom 8 values defined in mixing_elcom f90 Input file names require exact file name including extension 3D_data_file Name of the file containing the 3D data produced by the pre processor sparsedata unf preprocessor_file Name of the file containing the 1D data maps produced by the pre processor usedata unf boundary_condition_file Name s of the files containing boundar
47. outine for initializing viscosity 0 ignore subroutine user_viscosity_init 1 execute subroutine user_viscosity_init with USER START VIS 1 user_init_height controls user written subroutine for initializing free surface height 0 ignore subroutine user_height_init 1 execute subroutine user height initwith USER_START_HEIGHT 1 user_init_extinction controls user written subroutine for initializing the light extinction or attenuation coefficient 0 ignore subroutine user_extinction_init 1 execute subroutine user_extinction_init with USER_START_EXTINCTION 1 user_update controls user written subroutine for temporal updating of scalars 0 ignore subroutine user_update 1 execute subroutine user_update Turbulence modeling iclosure controls the type of closure scheme used 0 constant eddy viscosity 1 closure model 1 constant eddy viscosity plus mixing of statically unstable stratification 2 disabled 3 disabled 4 disabled 5 disabled 6 wind mixed layer model including mixing energy transport must be used with iwind 2 RECOMMENDED vis_u x dir eddy viscosity metres2 second vis_v y dir eddy viscosity metres2 second vis w z dir eddy viscosity metres second vis_u_tracer x dir eddy viscosity for tracers metres2 second vis_v_tracer y dir eddy viscosity for tracers metres2 second vis_w_tracer z dir eddy viscosity for tracers metres2 second vis_u_salt x dir eddy viscosi
48. parse data index point for debug output debug_baroclinic_x error trapping O off 1 on debug_baroclinic_y error trapping 0 off 1 on Output frequency iter_out_monitor time step interval for ouput of monitoring data iter_out_save time step interval for output of saved full simulation data iter_out_restart time step interval for output of restart data Output start time start_output_monitor time step to start providing monitoring data start_output_save time step to start providing simulation save files Time controls start date CWR start day in CWR Julian Day format yyyyddd real del_t size of time step in seconds iter_max maximum number of time steps in the simulation Iterative Conjugate gradient method solution controls CGM_TOL Tolerance residual for stopping conjugate gradient solution of free surface equation CGM_MIN Minimum number of iterations that must be computed for the conjugate gradient method to solve the free surface over rides the CGM TOL CGM MAX Maximum number of iterations that must be computed for the conjugate gradient method to solve the free surface http www cwr uwa edu au blaval manual elcom elcom_guide elcom_op html 8 of 16 31 8 2000 1 14 12 PM ELCOM Operation Default uniformly distributed values default_height Default water height in metres May be over ridden by user prepared subroutine if user_init_height 1 Note that default height must be lower than the maximum height
49. r to provide more complete graphics Presently they have no effect on the simulation or output and may be safely set to 0 The latitude is used to provide appropriate Coriolis forcing in the ELCOM simulation North latitudes are entered as positive numbers while south latitudes are entered as negative numbers 32 0 latitude 0 0 longitude 0 0 altitude Horizontal grid spacing keywords x grid y_grid The present version of ELCOM uses uniform non stretched grid spacing in the x and y direction Separate grid spacings are implemented in each horizontal dimension so that dx dy is valid However the user should be careful in implementing a solution grid with different dx and dy grid spacings since this can effect the solution accuracy The x and y grid spacings are designated with the key words x_grid and y grid 100 0 x grid 100 0 y_grid Layer thickness keyword dz In the vertical direction ELCOM allows the user to design a structure of horizontal layers whose thickness varies with depth i e dz f z Note that the layer thickness may not vary with x or y coordinates In the bathymetry dat file the successive layer thicknesses in descending order from the top of the domain http www cwr uwa edu au blaval manual elcom elcom_guide pre html 7 of 14 31 8 2000 1 14 01 PM Pre Processor are designated by the keyword dz While the user is free to set the dz values in an arbitrary manner the accuracy and stabili
50. r Templates e bathymetry dat e bc dat e run re ELCOM Templates yo e run elcom e datablock db e temporal boundary conditions e run db2nc http www cwr uwa edu au blaval manual elcom elcom_guide appendix_A html 31 8 2000 1 15 03 PM Contents Full ELCOM User Guide Long Contents 1 Introduction 1 1 The ELCOM model 1 2 Implementation language 1 3 Outline of a simulation run 1 4 Conventions and definitions 2 Pre processor 2 1 Introduction Compiling 2 3 bathymetry dat 2 3 1 Introduction 2 3 2 Physical and computational space coordinates 2 3 3 Creating a bathymetry dat file N N 2 4 bc dat 2 4 1 Introduction 2 4 2 Boundary cell set categori 2 4 3 Boundary cell set face direction 2 4 4 Boundary cell set keywords 2 4 5 Organization of the boundary cell set file bc dat 2 5 Running 3 ELCOM inbroduction Files for ELCOM Compiling and running ELCOM WWW WwW amp WN k Simulation modules 4 Stratification Tracers Surface thermodynamics Wind Inflow outflow User initialization User update 3 5 Configuration controls WWW WWW Ww kb Ha JO 0 ahun 3 5 1 Uniform initial conditions 3 5 2 Time step 3 5 3 Number of steps 3 5 4 Start date 3 5 5 CGM tolerance 3 5 6 Turbulence 3 5 7 Output frequency 3 6 Configuration using file run elcom 3 7 Input files http www cwr uwa edu au
51. r example the example bc dat file shown here example bc dat at bottom of section 2D provides three sets of boundary points with reference numbers 34 75 118 25 26 27 These numbers are used in the third line of the header to identify the points to which a http www cwr uwa edu au blaval manual elcom elcom_guide elcom_op html 13 of 16 31 8 2000 1 14 13 PM ELCOM Operation column of data applies Note that a given reference number may be used for multiple data columns in multiple files so that for example inflow volumes and temperatures for a particular set of boundary points may be supplied in one file while tracer inflow for the same set of points may be supplied in a different file Any temporal data boundary condition applied to the entire free surface which is not required to be defined as a boundary cell set in bc dat is given a reference number of 0 zero The fourth line in the header contains the keyword that describes the data in the column The keywords are limited to a set specifically defined and understood by ELCOM and are listed in the table below The remaining lines in the file contain the data for the specified time or time intervals Temporal Boundary Condition Data types HEIGHT m water height for open boundary condition zwe m3s 1 inflow volume ov TLFOW m3s 1 inflow volume WIND_SPE p ms wind speed WIND_DIR degrees wind direction degrees measured clockwise from north that
52. ratification Density stratification in ELCOM can be through temperature salinity or a combination of the two by using the controls itemperature and isalinity in combination with idensity 1 If the user desires temperature and salinity can be treated as passive tracers i e eliminating the density term from the momentum equation by setting idensity 0 If temperature and or salinity are turned on they must be initialized throughout the simulation domain through the default_ controls or the user_init_ controls and their associated subroutines 3 4 2 Tracers Up to 10 passive tracers may be transported in a simulation They may be initialized in the domain using the user_init_tracer control and subroutine or they may flow into the domain through an inflow boundary cell set using the keywords TRACER_ in a temporal boundary condition file 3 4 3 Surface thermodynamics The surface thermodynamics module controls the heat transfer across the free surface To use this module the user is required to provide the following data in temporal boundary condition files solar radiation wind speed air temperature relative humidity 3 4 4 Wind The wind effects ELCOM simulations in three ways 1 evaporative cooling in the surface thermodynamics module 2 application of a wind stress to the free surface or 3 application of a wind induced momentum source to the wind mixed layer The control iwind only sets the functioning of the wind i
53. rding insufficient input data This is typically because 1 one or more non optional items were omitted from the input file or 2 a data line or comment line has less than two items The file bathymetry dat is organized as a series of text lines of keywords data and comments that follow one of the formats shown below keyword data data keyword Ke comment keyword keyword data j 1 y_columns The keywords are ELCOM defined words that indicate the type of user provided data presented 1 before the keyword 2 after the keyword or 3 on succeeding lines of the file Exclamation points are used to indicate lines with comments For proper functioning with CWR Modeller the bathymetry dat file must be organized with the arguments presented in a fixed order however any number of comment lines may be inserted Additional comments may be provided after the keywords to help the user remember the keyword purpose the code only reads the first two items on a line Detailed information on the keywords and the format of the file are presented in the following sections 2 3 2 Physical and computational space coordinates In the literature bathymetry is generally presented as the vertical distance from some horizontal baseline often a mean water height and may be either positive downward or positive upward The convention used in ELCOM is an x y z space that follows the right hand rule and has z positive in the upward direction Figure 1
54. reference number 10 number of datatypes in group TRUE is interval logical true if time step interval is used for output 5 output interval 0 output start time 0 output end time 0 indicates entire run 0 size of time list non zero only if is_interval FALSE BEGIN SET_DESCRIPTION 100 GUI set reference number tchain user label PROFILE_1D type of set 3 number of cells in set NULL sheet type NULL sheet calc 0 0 sheet value NUL dynamic nam NUL dynamic calc 1 NUL dynamic direction 1 0 0 dynamic valu 1 NUL dynamic nam 2 NUL dynamic calc 2 NULL dynamic direction 2 0 0 dynamic valu 2 BEGIN SET_DESCRIPTION 2 set reference number curtain set user label CURTAIN_2D type of set 3 number of cells in set NULL sheet type NULL sheet calc 0 0 sheet value NULL dynamic nam NULL dynamic calc 1 NULL dynamic direction 1 0 0 dynamic valu 1 NULL dynamic nam 2 NULL dynamic calc 2 NULL dynamic direction 2 0 0 dynamic valu 2 BEGIN SET_DESCRIPTION 4 set reference number curtain set2 user label CURTAIN 2D type of set 11 number of cells in set NULL sheet type NULL sheet calc 0 0 sheet value NULL dynamic nam NUL dynamic calc 1 NUL dynamic direction 1 0 0 dynamic valu 1 NUL dynamic nam 2 NUL dynamic calc 2 NULL dynamic direction 2 0 0 dynamic valu 2 BEGIN SET_DESCRIPTION 6 set referenc
55. ribed in bathymetry dat file HEIGHT horizontal layer referenced as vertical distance in metres up from datum as defined in bathymetry dat file BOTTOM two dimensional surface defined as a vertical distance in metres up from the bottom SURFACE two dimensional surface defined as a vertical distance down from the free surface note the location of this sheet will evolve in time as the free surface evolves FLAT a two dimensional sheet made up of calculated properties in each water column the calculation type is specified below http www cwr uwa edu au blaval manual elcom elcom_guide elcom_op html 11 of 16 31 8 2000 1 14 13 PM ELCOM Operation 7 sheet calc calculation type for SHEET_2D for all other set types the keyword is NULL Valid sheet calcs keywords are NEAREST Assigns each sheet value to the grid value vertically nearest the specified sheet height Required for sheet types LAYER HEIGHT BOTTOM and SURFACE Not used with sheet type FLAT MAX Assigns each sheet value to the maximum value in a column Used only with sheet type FLAT MIN Assigns each sheet value to the minimum value in a column Used only with sheet type FLAT AVG Assigns each sheet value to the average value in a column Used only with sheet type FLAT TOTAL Assigns each sheet value to the integrated value ina column Used only with sheet type FLAT 8 sheet value Layer number for sheet t
56. river_inflow 3 15 2 This would group all the possible y minus cell faces for cells at any k level where j 2 and is bounded by 3 and 15 This generalizes such that a boundary cell set may be written as jou slip all freeslip domain which enforces a free slip boundary condition on all boundary faces sides and bottom of the domain There is no error cross checking within the pre processor for cell faces which have been defined as belonging to more than one boundary cell set In some cases multiple definitions may be desirable For example one might define a river inflow which covers the entire depth of the river for purposes of the velocity boundary condition and then define a separate section at the bottom of the river that is used to place a tracer The bc dat file might then contain 2791 flow_ym river_inflow So 2 73 section_ymtracer_inflow 32515 2 1 55 In other cases multiple set definitions for a particular face can produce unintended results For example if we define an inflow boundary and a global definition of free slip boundaries on all the cells 2791 flow_ym river_inflow FELS 2 214 slip_all freeslip_domain http www cwr uwa edu au blaval manual elcom elcom_guide pre html 12 of 14 31 8 2000 1 14 02 PM Pre Processor We then find that the cells 3 15 2 get defined both with imposed velocity Dirichlet boundary conditions and free slip normal Dirichlet tangential Neumann boundary condit
57. rocessor using the available memory and the pre processor will crash The crash may produce a machine error message Stating out of memory or a more enigmatic segmentation fault If insufficient memory is available the user can estimate the actual number of grid points required for the simulation and rerun the preprocessor 102 x_rows 84 y_columns 22 z_layers 0 n_max Land cells keyword land_value The land region and is designated by a unique bathymetry value defined using the keyword land value that is greater than any value found within the lake The user is free to choose the land value as any convenient number that meets this criterion Thus if the user chooses a z 0 baseline at the very top of the domain the 1and_value may be set to zero and all the bathymetry values should be negative numbers If the user chooses the bottom of the domain as the z 0 baseline then the land value may be any positive number that is greater than the largest number appearing within the lake boundary it is usually convenient to use 9999 In this latter case all the bathymetry values will be positive numbers Note that any cell whose bathymetry is not equal to the land value is considered a cell within the domain thus typographical errors can produce spurious interior cells of the domain The user is not required to have a z 0 baseline within the domain it may be convenient to use an external reference such as sea level This may re
58. s run to generate the pre processor output binary files The PRE executable file is then installed using the UNIX syntax make install The pre processor source code directory can then be cleaned up using the following UNIX command make clean 2 3 Setting up the bathymetry file bathymetry dat An up to date copy of bathymetry dat can be downloaded from Appendix A 2 3 1 Introduction The bathymetry file is designed to allow the user to input the geometry of the simulation domain at the resolution that the simulation will be conducted The format of the bathymetry file is rigid with regards to the amount of data provided and the order in which it is listed Each item in the bathymetry file must be present even if it is not applicable to the present simulation Comment lines may be added into the file at any point before the actual bathymetry values Each line of the bathymetry dat file must have at least two items separated by a space or a tab An item may be an integer a real number or a character string Comment http www cwr uwa edu au blaval manual elcom elcom_guide pre html 1 of 14 31 8 2000 1 14 00 PM Pre Processor lines must also have at least two items the first of which is an exclamation point the Fortran 90 comment symbol The order in which the data is presented is fixed so that CWR Modeller can process the bathymetry dat file2 A common crash of the ELCOM preprocessor produces a Fortran error message rega
59. scalar is not given an inflow value the inflow volume will have a scalar concentration of 0 3 4 6 User initialization The user is provided with the ability to set up complex initial conditions through the adding code to subroutines in the elcom_user 90 file The subroutines in this file are only called if the appropriate user_init_ control in the run elconm file is non zero The stub routines supplied with ELCOM are designed to be executed with the user_init_ controls 1 However this can be modified by the user so that different initializations are performed for different values of user_init_ see section 4 for more detail http www cwr uwa edu au blaval manual elcom elcom_guide elcom_op html 3 of 16 31 8 2000 1 14 10 PM ELCOM Operation 3 4 7 User update The user is provided with the ability to design new subroutines for modifying the velocity or any transported scalars in the simulation These are invoked through the subroutine user_update in the file elcom_user f90 Details of writing code for user developed subroutines is provided in section 5 This code is turned on or off with the control user_update in file run_elcom 3 5 Configuration controls 3 5 1 Uniform initial conditions For simple initial conditions that 1 distribute a scalar temperature or salinity over the entire simulation volume or 2 provide a flat free surface across the entire domain the user can set the desired values through the run
60. ses of the bathymetry dat file the user must provide bathymetry values for all cells in a rectangular array including those cells that only contain land ELCOM will only reserve computational memory for 1 the cells which may contain water and 2 the first layer of land cells surrounding the water cells http www cwr uwa edu au blaval manual elcom elcom_guide pre html 3 of 14 31 8 2000 1 14 00 PM Pre Processor 99 99 09 99 99 99 99 99 99 99 O RN 99 94 99 99 99 99 99 99 99 99 99 99 99 lao L leoso L o bkb gt gt gt 2 gt gt gt 2 doo b o b hk a gt Figure 3 Plan view of bathymetry data Figure 4 shows an elevation view in the x z plane of a lake with a Cartesian overlay A continuous physical space lake bottom is shown as a dashed line with the resulting discrete lake bottom shown in a solid line ELCOM computes the bathymetry on the face of each cell the dashed lines from user supplied bathymetry data at the cell centers on the solid dots In this figure the user z 0 baseline is chosen as the top of the domain so that all the bathymetry values should be negative Note that the k 7 index of i j k space corresponds with the lowermost layer regardless of the user z 0 baseline position IK re a Figure 4 Elevation view of bathymetry data http www cwr uwa edu au blaval manual elcom elcom_guide pre html 4 of 14 31 8 2000 1 14 00 PM Pre Processor
61. sult in the lowest point in the domain having a positive non zero bathymetry value 99 land_value Open boundary cells keyword open_value Open boundary cells are boundaries with tidal forcing from an adjacent body of water that is not in the simulation domain The user defined bathymetry value that indicates an open boundary cell is defined with the keyword open_value 88 open_value North vector keywords north_x north_y The user may create a bathymetry data file with any orientation i e there is no requirement that north be at the top of the page Since wind forcing on the free surface requires a direction the user must designate the north direction The north vector is determined as shown in Figure 5 Note that the north vector is given in terms of a vector in physical x y z space not the discrete i j k space Because the origin is in the upper left corner a standard north up data set has a north vector of 1 0 1 O north x 0 5 north y http www cwr uwa edu au blaval manual elcom elcom_guide pre html 6 of 14 31 8 2000 1 14 01 PM Pre Processor ti 1 81 ro ro orooroorooroorooroo tnt EL Figure 5 Calculation of the north vector Geographic position keywords latitude longitude altitude The user provides the geographic position of the simulation domain using the keywords latitude longitude and altitude Longitude and altitude are provided for future use in expanding CWR Modelle
62. t which data is to be output and the time at which data is to be output If several groups are desired the group descriptions must follow each other without breaks between them A group description block contains 11 lines which are as follows 1 BEGIN GROUP_DESCRIPTION begin block statement 2 group reference number an integer labelling the group this can have any value 3 user label a name containing no blank spaces labelling the group used by CWR modeller only 4 output filename should include unf suffix 5 set reference number an integer corresponding to a description of a set of points at which the data are to be output sets will be described after groups 6 number of datatypes in group an integer indicating the desired number of datatypes to be output ie TEMPERATURE SALINITY etc 7 should read TRUE do not modify http www cwr uwa edu au blaval manual elcom elcom_guide elcom_op html 10 of 16 31 8 2000 1 14 12 PM ELCOM Operation 8 output interval an integer indicating the desired number of timesteps between outputs 9 output start time an integer indicating which time step to begin outputing data 10 output end time an integer indicating which time step to stop outputing data O indicates entire run 11 should read 0 do not modify 3 7 2 3 Set Description A set is a set of points at which data are to be output This can include a vertical colum
63. tems must be present Comment lines preceded by may occur anywhere in the file Blank lines are not allowed in the file the code stops reading at a blank line Each line including comment lines must have at least two items separated by a blank space The comment marker counts as an item so a valid line is or while no space between is not valid The general format for the file is a series of lines with each line listing a user setting then a keyword that defines the parameter A typical run_elcom file can be viewed here The individual keywords and settings are explained briefly below File headers FILE file name for this file must be run_elcom VERSION current version of run elcom file 1 1 a TITLE user title for this run must be inside single quotes ANALYST user name must be inside single quotes ORGANIZATION user company name must be inside single quotes COMMENT user comment only 1 line must be inside single quotes CASE_KEYWORD allows user to add code to be executed for a particular simulaton case Must be a string without blank spaces enclosed in single quotes Simulation module controls iwind controls the wind module 0 no wind 1 wind model 1 wind stress boundary conditions used only with iclosure 0 or 1 2 wind model 2 direct wind momentum input used only with iclosure 6 RECOMMENDED iheat_input controls the s
64. the dat ablock db file that controls simulation output The following table provides a summary of file types whether their presence is required or optional the purpose of the file and responsibility for preparation of the file The file names in the courier bold font without brackets are fixed named files i e the file must be present with exactly this name File names such as data_name unf use square brackets to indicate that various names determined by ELCOM or CWR Modeller may be in the bracketed section these are specified in the following sections of this document File names such as lt datablock gt deb use the lt gt brackets to indicate file names or sections of names which the user can set either through CWR Modeller or by changing the file name at the command line Files for ELCOM File Name Presence usage Preparation m of run_elcom required configuration control user eae AA e cusedata gt unf required geometry data preprocessor 1 lt group_name gt unf output datablock output ELCOM fnolimt Tdata_name unf output 3D data type output ELCOM fnolimt Icime lt save gt unf output simulation space output ELCOM fnolimt es par at ASE fnakefile optional compiling and linking none a ra 90 optional source code OU none makefile 3 3 Compiling and running ELCOM If the ELCOM executable ELCOM is not available one must be created by compiling the source code The source
65. the directory where the run_elcom and all the appropriate input data files are located The monitoring debugging output is sent to the standard output of the computer the display terminal on most UNIX workstations Unless the simulation run is very short it is recommended that the user redirect the output to a file with a UNIX execution redirection such as ELCOM gt run_output 3 4 Simulation modules ELCOM is organized into simulation modules that can be turned off on depending on the type of simulation that is desired A module is turned off on by setting the value of control keywords This is done withing the run_elconm file These controls provide a simple method for modifying the simulation For example a boundary condition file can be set up to include both meterological data and inflow data As a simple test the user decides to turn off the inflow One approach would be to return to the pre processor eliminate the inflow boundary cell set re run the pre processor then modify the temporal boundary condition file to remove the inflow data As a simpler approach the user need only set if Low 0 and the inflow data and boundary cell sets will be ignored This section will give a brief overview of the modules within ELCOM and their corresponding keywords which are set within the run elconm file http www cwr uwa edu au blaval manual elcom elcom_guide elcom_op html 2 of 16 31 8 2000 1 14 10 PM ELCOM Operation 3 4 1 St
66. the user must keep track of which files are sparsedata files and which files are usedata files Once the run pre file is in the http www cwr uwa edu au blaval manual elcom elcom_guide pre html 13 of 14 31 8 2000 1 14 02 PM Pre Processor directory from which you intend to run the pre processor and the paths and names of the two input and two output files are specified in run_pre then the pre processor can be run by invoking the name of the executable namely PRE Notes 1 The pre processor cannot interpolate from a coarse bathymetry to a finer grid or filter from a fine grid to a coarse grid The user must preform this task before setting up the bathymetry file 2 The pre processor will correctly operate on on files with any line order of the data keyword commands however the GUI can only process bathymetry dat file that fit the data order prescribed in this section Continue on to ELCOM http www cwr uwa edu au blaval manual elcom elcom_guide pre html 14 of 14 31 8 2000 1 14 02 PM http www cwr uwa edu au blaval manual elcom templates bathymetry dat FILE bathymetry dat VERSION l l a l headers must be contained in quotes fs a very small lake TITLE I M Underpaid ANALYST Very Large Corporation ORGANIZATION example file COMMENT yes overwrite files number of grid cells ian 8 X rows TS y_columns 14 z_layers 0 n_max land and open boundary bat
67. the wind comes from SOLAR_RA gt Wm2 solar radiation that reaches water surface anupresS arueress Pascals atmopheric pressure CLOUD fractional cloud cover non dimensional number between 0 and 1 inclusive Ret relative humidity non dimensional number between 0 and 1 inclusive is INITY as salinity practical salinity units which can be treated as parts per thousand within the numerical resolution of the model we DENSITY kgm3 density of inflowing water ara TEMP degC air temperature wre TEMP degC water temperature for inflowing water fave ms velocity in x direction NOT_IMPLEMENTED vav ms velocity in y direction NOT_IMPLEMENTED Z ms velocity in z direction NOT_IMPLEMENTED degrees inflow outflow angle degrees measured clockwise from north the water is flowing to rea concentration tracer input rea concentration tracer input rea concentration tracer input rua concentration tracer input rua concentration tracer input rua concentration tracer input http www cwr uwa edu au blaval manual elcom elcom_guide elcom_op html 14 of 16 31 8 2000 1 14 14 PM ELCOM Operation zra concentration tracer input aza concentration tracer input ES concentration tracer input aza o concentration tracer input 3 8 Non Uniform Initial Conditions elcom_user 90 Non u
68. to the bathymetry dat file as shown http www cwr uwa edu au blaval manual elcom elcom_guide pre html 9 of 14 31 8 2000 1 14 01 PM Pre Processor BATHYMETRY DATA 99 99 99 99 99 99 99 99 99 2 4 Setting up the boundary cell set file bc dat An up to date copy of bc dat can be downloaded from Appendix A 2 4 1 Introduction The boundary cell set file designates logical grouping of grid cells over which boundary conditions are enforced in ELCOM One set of points may have a river inflow another set may have a dam offtake another set may represent groundwater inflows etc Each set of boundary points is defined by a unique reference number used also by ELCOM temporal boundary condition files type one of several keywords title user reference only and a series of cell i j k coordinates This file gives the user complete flexibility in the assignment of diverse and complex boundary conditions around a three dimensional topography 2 4 2 Boundary cell set categories The keywords for the boundary cell sets fall into six categories defined asfollows land Cell boundary which is considered to be land on which a Dirichlet no slip condition is imposed on all components of the velocity and a Neumann zero gradient condition is imposed on transported scalars slip Cell boundary which is considered to be land but on which the velocity components tangential to the boundary have a Neumann free sl
69. ty for salt metres2 second vis_v_salt y dir eddy viscosity for salt metres2 second vis w salt w dir eddy viscosity for salt metres second vis_u_temperature x dir eddy viscosity for heat metres2 second vis_v_temperature y dir eddy viscosity for heat metres2 second vis_w_temperature z dir eddy viscosity for heat metres2 second prandt1 turbulent Prandtl number diffusion of heat 8nu r 8kappa r salt_schmidt turbulent Schmidt number diffusion of salinity 8nu r 8kappa r tracer_schmidt turbulent Schmidt number diffusion of tracer 8nu r 8kappa r Model Settings and Controls drag_btm_cd drag coefficient on bottom cells model_grav_damp_x damping of gravity for x baroclinic term http www cwr uwa edu au blaval manual elcom elcom_guide elcom_op html 7 of 16 31 8 2000 1 14 11 PM ELCOM Operation model_grav_damp_y damping of gravity for y baroclinic term Scalar maximum and minimum for debugging min_temperature max_temperature min_salinity max_salinity min_tracerl min_tracer 2 min_tracerl0 max_tracerl max_tracer2 max_tracerl0 Debugging controls debug_check controls level of error checking in code 0 no error checking 1 checking for errors stop on fatal errors 2 highest level of checking for errors stop on fatal errors 3 highest level of checking for errors stop on warning debug_print controls level of debugging printout 0 none 1 minimal 2 moderate 10 extensive debug_point s
70. ty of the simulation method may be effected by the degree of non uniformity of the layers In general the simulation method will perform best i e with greatest accuracy using a grid with uniform dz For non uniform dz the degradation of accuracy is a function of the rate at which the az changes Thus a grid that has a dz that varies slowly will perform very well while a grid with abrupt changes in grid size will be less accurate For example Figure 6 shows two possible configurations which provide vertical resolution of 0 25 metres in the upper portion of a lake and 2 0 metre resolution in the lower portion Both use the same number of grid cells but the dz distribution on the left of Figure 6 will show better performance http www cwr uwa edu au blaval manual elcom elcom_guide pre html 8 of 14 31 8 2000 1 14 01 PM Pre Processor free surface thermocline Figure 6 Vertical grid spacings Bathymetry values keywords BATHYMETRY DATA The bathymetry values must be presented in the file bathymetry dat following a line with the two keywords BATHYMETRY DATA Each line of bathymetry values must contain exactly y_columns of data and there must be exactly x_rows of data lines following BATHYMETRY DATA Each value on the line may be separated from then next by one or more spaces or tabs Thus for a domain with x_rows 8 and y_columns 13 and land_value 99 i e similar to figure 3 the bathymetry values would be entered in
71. urface thermodynamics 0 no surface thermodynamics 1 surface thermodynamics model 1 iflow controls inflow outflow Dirichlet boundaries overrides boundary condition files 0 no inflow outflow 1 inflow outflow model 1 itemperature controls whether temperature is a transported scalar 0 no temperature simulation 1 temperature as transported scalar http www cwr uwa edu au blaval manual elcom elcom_guide elcom_op html 5 of 16 31 8 2000 1 14 11 PM ELCOM Operation isalinity controls whether salinity is a transported scalar 0 no salinity in simulation 1 salinity as a transported scalar idensity controls whether density buoyancy term is included in simulation 0 no buoyancy term 1 density computed from UNESCO equation of state and used for buoyancy term ntracer sets the number of tracers which can be transported in a simulation 0 no tracers 1 to 10 number of tracers initialized in user_init_tracer or supplied through inflows or user_update ICAEDYM controls whether the CAEDYM water quality module is used 0 CAEDYM off 1 CAEDYM on icoriolis controls whether or not the latitude from bathymetry dat is used to compute a Coriolis term 0 Coriolis off 1 Coriolis on idatablock controls which version of datablock db is used 1 version 1 0 2 version 1 1 icurvilinear controls function of curvilinear approximation module 0 curvilinear off 1 output only 2 use curvilinear and output
72. value NUL dynamic nam NUL dynamic calc 1 NUL dynamic direction 1 0 0 dynamic valu 1 NUL dynamic nam 2 NUL dynamic calc 2 NULL dynamic direction 2 0 0 dynamic valu 2 BEGIN SET_DESCRIPTION 10 set reference number sheetl set user label SHEET 2D type of set 0 number of cells in set LAYER sheet type NEAREST sheet calc 3 sheet value NUL dynamic nam NUL dynamic calc 1 NUL dynamic direction 1 0 0 dynamic valu 1 NUL dynamic nam 2 NUL dynamic calc 2 NULL dynamic direction 2 0 0 dynamic valu 2 BEGIN SET_DESCRIPTION 12 set reference number sheet2_set user label SHEET_2D type of set 0 number of cells in set HEIGHT sheet type NEAREST sheet calc 4 5 sheet value NUL dynamic nam NUL dynamic calc 1 NUL dynamic direction 1 0 0 dynamic valu di NUL dynamic nam 2 NUL dynamic calc 2 NULL dynamic direction 2 0 0 dynamic valu 2 BEGIN SET_DESCRIPTION 14 set reference number sheet3_set user label SHEET_2D type of set 0 number of cells in set http www cwr uwa edu au blaval manual elcom templates datablock db 4 of 9 31 8 2000 1 14 33 PM http www cwr uwa edu au blaval manual elcom templates datablock db BOTTOM NEAREST O45 NULL NULL NULL 0 0 NULL N N 0 0 BEGIN SE 16 sheet4_set SHEET 2D 0 SURFACE NEAREST 5 ULL U l l l l T 1
73. view x y plane of a lake with a discrete uniform Cartesian mesh overlay The computational domain is divided into cells whose centers are represented in Figure 2 by solid dots Dashed lines represent the faces between the cells Each cell center has an i j k coordinate that designates its location in discrete computational space The i j k values are the integer indices of a three dimensional array The right hand rule is used with i j k being non zero positive integer values k 1 is associated with the lower most cell layer in the domain The ij pairs of a horizontal plane represent a matrix so that by conventional mathematical notation the 1 1 position is always in the upper left corner The i index is the row index and increases down the page The f index is the column index and increases across the page The i indices for corner cells are shown in Figure 2 For convenience and consistency the origin 0 0 of the x y physical space coordinates is taken to be at the 1 1 location in the computational space i j indices LE RARA Figure 2 Plan view of Cartesian mesh Using the upper left corner as the origin may initially be confusing to users familiar with mirror image storage used by many graphics programs where the lower left corner is stored in position 1 1 The problem with mirror image storage is that a simple printout of bathymetry data always appears as an upside down mirror image of the real world when vi
74. y condition information CAEDYM file Name of the file containing CAEDYM configuration information datablock_file Name of the file containing output datablock configuration produced by GUI File Directories require quote marks around note that incomplete quotes can cause code to hang infile_dir input files directory ie datablock db sparsedata unf usedata unf boundary condition files outfile_txt_dir output unf files directory Unformatted binary output files specified by datablock db file outfile txt dir ELCOM diagnostic ascii format files Output files names do not include extension restart save file kernel of name used for simulation save file time stamp and unf are appended by ELCOM restart_out_file kernel of name used for simulation restart output file unf is appended by ELCOM http www cwr uwa edu au blaval manual elcom elcom_guide elcom_op html 9 of 16 31 8 2000 1 14 12 PM ELCOM Operation 3 7 Input files 3 7 1 sparsedata unf and usedata unf The files sparsedata unf and usedata unf are required files for ELCOM These are the Fortran unformatted binary files produced by the pre processor The user may rename these files but must keep track of which file is the sparsedata file keyword 3D_data_file and which is the usedata file keyword preprocessor_file ELCOM will look for the files specified in the run_elcom file If the incorrect files are used the simulation will crash 3 7 2 Dat
75. ype LAYER Vertical distance in metres for sheet types HEIGHT BOTTOM and SURFACE 0 for sheet type FLAT 9 16 Not implemented do not modify 3 7 2 4 Group data types This block begins with the desired number of data types followed a listing of the desired data types 1 BEGIN GROUP_DATA_TYPES Begin data type description 2 group reference number An integer referencing the group number defined in the group description 3 data types One data type descriptor per line The possible data type descriptors are Output Datatype Keywords U_VELOCITY V_VELOCITY TEMPERATURE SALINITY EXTINCTION_COE FLUC_PRESSURE TRACER 1 RACER 2 TRACER 4 TRACER 5 TRACER 7 TRACER 8 TRACER 10 EIGHT RI NUM HEAR MIX ENERGY UX 1 AUX 2 AUX 3 UX 4 AUX 5 vis v vis W_VIS TRACER XVIS RACER YVIS TRACER ZVIS ALT XVIS SALT YVIS SALT ZVIS TEMP_XVIS TEMP_YVIS TEMP_ZVI LS NORTH lA URVATURE EPSILON LAMBDA RAPH X RAPH Y IND U IND V ADIAL ANGENT RAPH R RAPH S http www cwr uwa edu au blaval manual elcom elcom_guide elcom_op html 12 of 16 31 8 2000 1 14 13 PM ELCOM Operation 3 7 2 5 Group Time List This block is required to initialize a time stamp for each group It requires only two lines as follows EGIN GROUP TIME LIST Begin
76. ywords listed in table 14 The titleisa user designated name for the boundary condition set The t it le may have more than one word although only the first word will be used by the code After the set identification line there will be one or more lines of cell definitions A cell definition consists of three sets of number in the general form i tart iena jstart Jend Kstartikend The i j and k are integer values of the cell positions in space for a rectangular box of cells on which the relevant boundary cell keyword will be applied For example a simple boundary cell set definition might be 107 flow_xp river_inflow 3 10 4 5 10 14 The preprocessor would designate as a single set all positive x boundaries in the range 3 lt lt 10 and 4 lt j lt 5 and 10 lt k lt 14 A boundary cell set may have multiple lines of cell definitions 13 flow_bottom groundwater_inflow 5 10 155 10 14 5 10 7 11 10 14 358 12317 13 5 Note that each number pair in a cell definition must be in increasing order There are two simpler cases for implementing boundary cell sets 1 where i j or kis a single value rather than a range 2 where all possible values in i j or k are to be included In the former case only a single number needs to be provided rather than a pair in the latter case only the colon needs to be listed For example the cell set for an inflow boundary along a flat side where j 2 might be written as 2791 flow_ym

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