CEM_SWAN_manual
Contents
1. Model steps and main function calls as executed by the RUN file Each step below is labeled and annotated within the RUN file Reading this section with the RUN file at hand is recommended Step 1 FindWaveAngle FILE PROGRAM NAME FindWaveAngle an executable file created by compiling FindWaveAngle c INPUTS None OUTPUTS e AngleDegrees txt a text file containing a deep water wave angle in azimuthal degrees to be used by SWAN and CEM PURPOSE Extracted from the original CEM this stand alone function creates a PDF of waves based on wave asymmetry A and highness U proportion of waves that are gt 42 From this PDF CEM picks randomly each model day a deep water wave to drive the daily model simulation The PDF function is made external to CEM because SWAN needs to know the deep water wave angle to generate a wave field before CEM is called The output a text file contains the generated wave angle The RUN file reads the text file and the wave angle is assigned to a variable called temp The variable temp is then used to call the corresponding SWAN coarse grid file Step 2 Run SWAN coarse grid gt FILE PROGRAM NAME temp swn INPUTS e Depth_main bot OUTPUTS 17 e Boundary conditions for nested SWAN run This will also output grid plots of wave height and angle for the coarse grid if you like This is useful for debugging PURPOSE To generate boundary co2. or equal to Xmax 12 Alongshore domain size Must be equal to 2 Ymax and set up according to Figure 2 and the periodic boundary conditions see following section IN Run file Time steps Stored in variable t this controls the number of times the main time loop iterates Internal time steps To speed up the simulation the same SWAN output can be used for multiple CEM iterations By doing this SWAN does not regenerate a wave field every time step The number of times to internally loop CEM with the same wave conditions is stored in the variable ti The underlying assumption is that shoreline position does not change appreciably over one time step so the same waves can be used multiple times this assumption breaks down when ti gt 5 If you do not want to engage the internal loop Le you want SWAN to generate new waves every time step set ti 1 Working directory name and location Make sure the working directory location is correct Your working directory name must be the same as your output directory name How many files you wish to save during the simulation Use the variable cull for this For example if you want to save model output every 100 time steps set cull 100 Making your bathymetry setting up your computational CEM domain and dealing with periodic boundary conditions Orienting your SWAN and CEM computational domains appropriately is the most critical step in coupling the models
3. be 0 5 of the alongshore extent of your nest SWAN grid NOTE when entering grid dimensions to your swn files SWAN requires them to be number of meshes rather than number of grid cells The number of meshes is the number of grid cells minus one So if your bathymetry grid size is 100 cross shore cells by 100 alongshore cells in CEM you would enter 100 x 100 however in the swn files you would enter 99 x 99 10 Shoreface depth Called DepthShoreface in CEM Typical values range from 10 20 m It is the depth over which sediment is evenly distributed as it is transported alongshore If the shoreline moves landward a ravinement surface is left behind corresponding to the shoreface depth see Ashton and Murray 2006a If the shoreface and shelf bathymetry are not merging smoothly in the SaveSWANToFile function in CEM shoreface depth can be adjusted to improve the fit Note however that adjusting the shoreface depth affects the timescales for shoreline adjustment Ashton and Murray 2006a Shoreface slope Called ShorefaceSlope in CEM Typical values range from 0 005 to 0 05 If the shoreface and shelf bathymetry are not merging smoothly in the SaveSWANToFile function in CEM shoreface slope can be adjusted to improve the fit Wave breaking threshold Called WaveBreakDepth in CEM Typical values range from 0 8 to 0 3 The lower the number the farther offshore CEM will look to find a breaking wave The SWAN generate
4. directory 22 cd scratch Ifs username workingdirectory 11 Now you must compile the FindWaveAngle c and CEM_swan c files For the FindWaveAngle c file enter the command gcc o FindWaveAngle FindWaveAngle c Jm gcc calls the compiler o is an option that allows you to specify the name of the executable that is generated by the compiler FindWaveAngle is the name of the executable that is called by the RUN file FindWaveAngle c is the program to be compiled and Im tells the compiler to add the necessary math libraries Note that you must name the executable FindWaveAngle because it is called by the RUN file using the same name After you compile FindWaveAngle c the executable file will appear in your working directory Double check make sure the executable is called FindWaveAngle Do the same thing for the CEM_swan c file gcc o cem CEM_swan c lm This compiles the CEM and the executable must be named cem so that it can be called correctly by the RUN file After you compile the executable file will appear in your working directory Check that it is called cem all in lower case letters Part 3 Submitting your job 12 In your terminal window navigate to your home directory cd home username 23 13 Before submitting your job you must convert the RUN file to UNIX format Type the command dos2unix RUN_file where RUN_file is the name of your Run fil
5. len 220 BLOCK compgrid NOHEADER Hsig HSIGN BLOCK compgrid NOHEADER Dir DIR G COMPUTE STOP 1009 swn Run Clock 22 Feb 2013 13 55 33 conditions 1m 8 s deg 10 deg spread l SET LEVEL 0 NAUTical E 36 0 05 1 XC 99999 MODE STATIONARY TWODimensional gt CGRID REGular o 210 INPgrid BOTtom REGular bot 3 0 FREE Se EEN pa ab ab BOU pec S I 68 CONS PAR OFF BREAKI GRO kaud ae NGR i 0 OUTPUT OPTIONS BLOCK ndec 2 len 22 BLOCK compgrid NOHEADER Hsig_main HSIGN NESTout cem_s cem_f COMPUTE COORDinates C se E 21 6 READinp BOTtom 1 Depth_ OFF QUAD abad 32040 PF QUANTI SIGN DIR excv BLOCK compgrid NOHEA Dir_main DIR STOP cem SWAN c CAPERIFFIC PWL s and a k include include include include include include 7 Run changes to this program for SWAN integration are initialed PWL with the date searchable tag SWAN lt stdlib h gt THIS PROGRAM GONNA MAKE CAPES SANDWAVES lt stdio h gt lt math h gt lt time h gt lt unistd h gt lt ncurses h gt Control Parameters x int SWANflag 1 startflag 0 Are we starting a run from a previous run int re Wave define define define define directio define needed define define steps File int int int int int char int domain char char SWAN char PWL CEM in Are w
6. User Guide to Coupling SWAN and CEM Boundary conditions wave height 2 m wave direction 0 period 12 s Coarse grid Nested orid ater depth m Wave height Table of Contents INTRODUCTION Basic model structure Pre simulation set up Directory Structure Necessary files and scripts E In your home directory Ki In your working directory V7 In your local directory Parameters to adjust and know before starting your simulation Making your bathymetry setting up your computational CEM domain and dealing with periodic boundary conditions Model steps and main function calls as executed by the RUN file Step 1 FindWaveAngle Step 2 Run SWAN coarse grid Step 3 Run SWAN nested grid Step 4 Run CEM Step 5 Save files to output folder Post processing Known issues and limitations Step by step instructions using the sample files Part 1 Setting up the directory structure and uploading necessary files Part 2 Compiling the c files to make executables Part 3 Submitting your job Part 4 Using Matlab to view the model output References Appendix YD 0 0 NNN WW m S 13 17 17 17 18 18 19 20 20 22 22 22 23 24 26 27 INTRODUCTION The Coastline Evolution Model CEM simulates large scale coastline behavior caused by gradients in alongshore sediment flux Ashton et al 2001 Ashton and Murray 2006a 2006b The wave climate or the angle and direction of incoming waves re
7. Your bathymetry and shoreline domains must be set up as in Figure 2 Incorrect grid sizes locations and cell sizes are the most common causes of model crashes or faults All computational domains for SWAN and CEM bathymetry for SWAN shoreline position for CEM must be oriented with the offshore direction facing up or north 13 Figure 2 shows how the bathymetry must be set up for the SWAN runs and how it relates to the CEM computational domain Variables listed above e g Ymax Xmax are also shown in Figure 2 SWAN bathymetry can be set up as it would for any usual nested SWAN run but you must make certain that the nested grid is located correctly within the coordinate space of the coarse main grid and the cell size of the nested grid is the same as the cell size of the CEM domain The boundary conditions in CEM are periodic meaning that 1 sediment is conserved 2 sediment that fluxes out of the right boundary comes back through the left boundary and vice versa and 3 the shoreline domain is therefore effectively repeated to infinity alongshore To impose periodic boundary conditions CEM s main computational domain defined by Ymax and Xmax is split down the middle The right half is placed adjacent to the left boundary and the left half is placed adjacent to the right boundary see Figure 2 Thus CEM effectively operates on an alongshore distance of 2 Ymax The nested SWAN grid over which the wave field is computed must
8. be set up the same way with a central domain defined by Ymax and Xmax that is split into two halves that are placed on either boundary This ensures that CEM will have a smooth and continuous wave field to read when it applies periodic boundary conditions The practical effects on SWAN of imposing periodic boundary conditions in CEM are summarized as follows The nested bathymetry grid must be of alongshore size 2 Ymax and cross shore size Xmax The central grid that corresponds to the CEM domain is of size Ymax by Xmax and is defined on the left by Ymax 2 and on the right by 3 Ymax 2 see Figure 2 The cross shore shoreline position on the left and right edges of the central domain defined on the left by Ymax 2 and on the right by 3 Ymax 2 must be equal This applies to both SWAN and CEM see below Otherwise there will be a discontinuity when CEM applies periodic boundary conditions 14 Wave direction or angle conventions are different between SWAN and CEM in SWAN wave direction is azimuthal where 0 360 is shore normal 270 is directed left and 90 is directed right in CEM 0 is also shore normal but 90 is directed left and 90 is directed right see Figure 2 Once your SWAN bathymetry grids are complete the initial conditions for CEM the file is called 0 in the file list above can be extracted from the nest grid Cells in the CEM domain all contain values between or equal to 0 and 1 t
9. d wave heights and angles are most accurate at least a couple cells seaward of the shoreline cell so using a lower number works best 0 3 0 5 See List and Ashton 2007 for a discussion of this In order to spatially resolve the wave breaking threshold a cell size less than 500 m for your simulation is suggested If the cell size is too big the wave breaking threshold will be exceeded for every nearshore cell and faulty wave characteristics will be retrieved IN coarse grid swn files Wave height Wave height is specified within the swn files that control your coarse grid SWAN runs It must be the same in all 181 files Rather than edit each file individually when wave height and or period need to be changed use the current version of Xcode 5 0 1 to find and replace text within your workspace i e it will change the wave conditions for all 181 files at once see specific instructions below Wave period Wave period is specified within the swn files that control your coarse grid SWAN runs It must be the same in all 181 files 11 Cell size of coarse SWAN grid Cell size can be whatever you wish The cell size of the nested grid however must match the cell size of CEM Domain size coarse SWAN grid Size can be whatever you wish although it is beneficial for the coarse grid alongshore length to be at least 5 times the length of the nested domain with the nest in the center to avoid edge boundary effects In the cross sh
10. dates the shoreline position and updates the shoreface bathymetry extended seaward from the new shoreline position The new shoreface bathymetry is merged with the SWAN nest bathymetry Depth bot and in the next model iteration SWAN uses the new bathymetry to generate a new wave field Step 5 Save files to output folder FILE PROGRAM NAME No program or file just a sequence of UNIX commands issued by the RUN file INPUTS The variable cull assigned at the top of the RUN file OUTPUTS Model outputs that are moved and saved include the coarse grid wave field Hsig_main and Dir_main the nest grid wave field Hsig and Dir CEM shoreline domain named after the timestep and the nested bathymetry Depth bot PURPOSE The UNIX commands move model outputs results at specified intervals set using cull to your output folder Files that are not moved are overwritten to reduce the size and clutter in your working directory 19 Post processing After your model run is complete download your output to a local directory Executing the Matlab script postprocess m will load the saved model output from your output folder into Matlab for viewing plotting etc The file is annotated thoroughly The postprocess m script calls a second script animateoutput m that will 1 animate your loaded output files and 2 save them to a movie avi file In order to run postprocess m a
11. e whatever that may be 14 Now you are ready to submit your job by entering qsub RUN_file where RUN file is the given name of your RUN file While your job is running you can check its status by typing qstat u username or delete your job by typing qdel jobID The jobID is shown when you submit your job and can be found by using the qstat command As your job runs files will accumulate in your output directory Part 4 Using Matlab to view the model output 15 Open Matlab Set your Matlab working directory to your output directory and make sure that directory has the sort_nat m script in it 16 Using the FTP program download your model output to a local directory 24 17 Open postprocess m and make sure that the variables Ymax Xmax and cell size are set the same as in CEM 18 Run postprocess m It will load all of your model output and animateoutput m will show you a movie 25 References Ashton A A B Murray and O Arnoult 2001 Formation of coastline features by large scale instabilities induced by high angle waves Nature 414 296 300 Ashton A D and A B Murray 2006 High angle wave instability and emergent shoreline shapes 1 Modeling of sand waves flying spits and capes J Geophys Res 111 F04011 doi 10 1029 2005JF000422 Ashton A D and A B Murray 2006 High angle wave instability and emergent shoreline shapes 2 Wave climate analysis and com
12. e using SWAN to do wave shoaling climate and timing DO NOT TOUCH L TimeStep 1 0 Of fShoreWvHt 1 days reflects rate of sediment transport per time step wave height meters Not needed with SWAN x Period 10 seconds Not needed with SWAN Asym 0 6 fractional portion of waves coming from positive left n not needed with FSWAN x Highness 0 7 ALL New 5 even dist gt 5 high angle domination Not with ASWAN x Duration 1 Number of time steps calculations loop at same wave angle StopAfter 1 duration of model run stop after what number of time gt Must equal 1 with SWAN x saving S seed 44 random seed control value 1 StartSavingAt 1 time step to begin saving files SaveSpacing 1 space between saved files SaveLineSpacing 100 space between saved line files SaveFile 1 save full file i e the whole 2D domain x savefilename 24 x PWL 10 16 13 leave blank for SWAN coupling SaveLine 0 Save line i e just the shoreline shape not the whole savelinename 24 lineout x StartFromFile y start from saved file If using SWAN must always be y readfilename 24 dfdf 0 x 10 16 13 Must read in the S e file name for SWAN coupling It is tracked outside the PBS script loop SWAN char readfilename 24 char savefilename 24 int t FILE fp FILE xbathyfile FILE Di rfile FILE Hs
13. er Instead the models communicate through a UNIX shell script called a RUN file The RUN file acts as a translator between the models by executing SWAN and CEM sequentially and mediating the exchange of information input output between SWAN and CEM The RUN file can be set to perform as many model iterations as necessary To couple SWAN and CEM no changes have been made to the SWAN program it is run as it would without CEM There are however some critical SWAN parameters that must be set correctly to ensure successful input output between SWAN and CEM see the Pre simulation set up section below Several major changes have been made to CEM in order to couple it with SWAN All changes are flagged with the hashtag SWAN within the CEM_SWAN c file so they are easily searchable The most noteworthy changes to CEM are B The main time loop that sets the number of model iterations in a given simulation has been made external to CEM itis now implemented in the RUN file CEM is set to run for only ONE time step each time it is called by the RUN file and it loads the shoreline position from the previous model iteration to use as initial conditions B The basic wave shoaling routine no longer exists within CEM as it is replaced by SWAN The FindWaveAngle routine that selects a random deep water wave angle before each model iteration has been made external to CEM It is now a stand alone executable pro
14. gram called by the RUN file because it must inform SWAN rather than CEM of wave boundary conditions A new function called LoadSWAN was added that inputs SWAN s output grids wave height angle as well as bathymetry B A new function called ParseSWAN was added that finds breaking wave height and angle from the SWAN grids loaded in the function LoadSWAN For each model shoreline cell the routine searches seaward until a breaking wave threshold wave height divided by water depth is found Then the wave height and angle are stored and used later to calculate alongshore sediment flux with the CERC equation B A new function called SaveSWANToFile was added This function completes two key tasks after CEM has calculated alongshore sediment flux gradients and updated shoreline position First using the updated shoreline position it linearly interpolates the shoreface bathymetry seaward from each model shoreline cell using the user inputted shoreface depth and slope Then using the bathymetry from the earlier SWAN simulation the new shoreface bathymetry is merged with the shelf bathymetry Second the updated shoreface shelf bathymetry grid is written to file so that SWAN can input it during the next model iteration to calculate a new set of wave heights and angles A new function called ConvertAngle was added that converts the angle convention used by SWAN azimuth 0 or 360 is shore nor
15. hat specify how full the cell is with sediment Ashton and Murray 2006a Thus cells can either be land cell is full or equal to 1 water cell is empty or equal to zero or shoreline cell has a fractional value between zero and one Thus in the nest bathymetry grid values greater than and equal to sea level zero elevation are assigned a value of 1 values less than sea level are assigned a value of zero and the seaward most cells greater than or equal to sea level are assigned a fractional number e g 0 5 These fractional cells are the shoreline A Matlab script called makeinitconds m is supplied that will convert your nest bathymetry grid to CEM initial conditions and produce a text file called 0 15 O dl OJaz sI pus K wkyzeq UL IS ISO JO VISIO Plus ureuwr osqeoo NVMS pus AewuAduyeg 9197 Pardde are SUOTITPUOD SABM PIIS UTBUI 9SIBOD JO TISUST SIOUSSUOTE TOL Doaisa JO ULC UISIIO SU O ANLJ J Saal ul BU e SI pluS UIBuu as Ieo ay jo PIS sou NVMS UTeULOP WHO OTPorIe g gbuno Figure 2 Schematic of the computational domains and how they are spatially related The variables Xmax and Ymax are the cross shore and alongshore lengths respectively of the CEM domain Conventions used to define wave direction or angle are shown by the gray circles The procedure for imposing periodic boundary conditions is shown on the bottom right and is explained in the text 16
16. hing to watch out for Adjusting the shoreface depth and slope within CEM can help troubleshoot the problem 21 Step by step instructions using the sample files Part 1 Setting up the directory structure and uploading necessary files 1 Open FileZilla CyberDuck or other FTP program Log in to your HPC account using SSH file transfer protocol and entering the address submit hpc ufl edu 2 Use the FTP program to upload the folder SWAN4091 to your home directory home username 3 Use the FTP program to upload the RUN file RUN_swan_CEM to your home directory 4 In your home directory home username create a directory called output 5 Within the new output directory create a subdirectory named testrun This is where the testrun model output will be stored 6 Now navigate to your scratch directory scratch lfs username 7 Create a working directory there called testrun This directory must have the same name as your testrun output directory 8 Using the FTP program put the required files in your working directory finegrid swn 0 Depth bot Depth_main bot FindWaveAngle c CEM_swan c and the 181 swn files that control the coarse grid SWAN runs Part 2 Compiling the c files to make executables 9 Open a terminal window Log in to your HPC account by typing ssh submit hpc ufl edu You will be prompted for your user name and password 10 Navigate to your working
17. igfile int Waveln Input Wave Distribution file Can input specific wave climate from a wave buoy But it must be formatted correctly See example in the model folder x char readwavename 24 ebropp_30 dat Initial Condition Info A int PWidth 50 int PHeight 75 float MaxOver 0 01 Maximum overwash step size enforced at backbarrier Aspect Parameters define CellWidth 320 size of cells meters Should match SWAN SWAN x define CritBWidth 350 0 width barrier maintains due to overwash m important scaling param x define Xmax 103 number of cells in x cross shore direction Should match SWAN SWAN ES define Ymax 110 number of cells in y longshore direction Should match SWAN SWAN define MaxBeachLength 8 Ymax maximum length of arrays that contain beach data at each time step x define ShelfSlope 0 001 Slope of continental shelf define ShorefaceSlope o QE a linear slope of shoreface define DepthShoreface 8 0 x depth of shoreface due to wave action meters x define InitBeach 10 cell where initial conditions changes from beach to ocean define InitialDepth 5 0 theoretical depth in meters of continental shelf at x InitBeach define LandHeight 1 0 elevation of land above MHW define InitCType 0 type of initial conds 0 sandy 1 barrier define InitBWidth 4 Za initial minimum width of barrier Cells x define OWTy
18. in SWAN run that supplies boundary conditions for the nested run B CEM_SWAN c CEM model that must be compiled to an executable file B FindWaveAngle c Generates a new random deep water wave angle from a probability distribution function each time step Must be compiled to an executable file B finegrid swn SWAN file corresponding to your nested SWAN run B In addition to the above files you must have 181 main SWAN files in your working directory Each file has a unique integer deep water wave angle as a boundary condition and controls the coarse grid SWAN runs that supply boundary conditions for the nested runs They must be named sequentially 1000 swn 1090 swn and 1270 swn 1360 swn The last 3 numbers in the file names correspond to the deep water wave angle in azimuthal degrees relative to the coast that is indicated within the file The angle is selected each time step by the FindWaveAngle function For example if the FindWaveAngle function selects a wave angle of 43 degrees the SWAN file 1043 swn will be called and will execute a coarse grid SWAN run based on that angle 7 In your local directory makeinitconds m This script will create the initial shoreline conditions file called 0 see above from your nested SWAN bathymetry grid postprocess m Main script for viewing and plotting model output Execute the script on your local directory containing model output and it wil
19. l load the whatever output you tell it to wave height wave angle bathymetry etc animateoutput m Animates output files through time and compiles them into movie avi files B sort_nat m Sorting routine must be present with your model output i e in the same folder when running postprocess m Parameters to adjust and know before starting your simulation Below is a list of all parameters that need to set before starting your model run Use the CEM SWAN Reference Guide to see where these variables are located within each file IN CEM_swan c Cell size This must be set exactly the same as the cell size in the nested SWAN run Generally CEM works best when cell size is 100 m or greater so use that as a guide to set your nest grid cell size In order to spatially resolve the wave breaking threshold see below a cell size less than 500 m for your simulation is suggested Cross shore domain size Called Xmax in CEM Should be exactly the same as the cross shore extent of your nest SWAN grid NOTE when entering grid dimensions to your swn files SWAN requires them to be number of meshes rather than number of grid cells The number of meshes is the number of grid cells minus one So if your bathymetry grid size is 100 cross shore cells by 100 alongshore cells in CEM you would enter 100 x 100 however in the swn files you would enter 99 x 99 Alongshore domain size Called Ymax in CEM Should
20. lative to the local coastline orientation is the forcing mechanism and determines the resultant long term coastline morphology e capes spits migrating sandwaves Operating alone CEM transforms waves in the most basic way by assuming shore parallel bathymetry contours that extend seaward only to the depth of the shoreface 10 20 m This simplification inherently excludes alongshore wave energy convergence divergence wave transformation over the shelf and coastlines where bathymetry is complex e g nearshore or cape associated shoals van den Berg et al 2012 Kaergaard and Fredsoe 2013a 2013b 2013c By replacing CEM s basic wave shoaling routine with a more complex spectral wave transformation model Simulating WAves Nearshore or SWAN Booij et al 1999 Ris et al 1999 CEM can simulate a broader array of coastline behaviors especially those influenced by nearshore shoals or irregular bathymetry This manual details how the coupling between CEM and SWAN was accomplished and how to couple CEM and SWAN on the UF High Performance Computing Cluster Basic model structure Before proceeding you need a scripting oriented text editor For Mac Xcode free version 5 or greater is highly recommended Aquamacs or TextWrangler will also work CEM and SWAN are two separate standalone models written in C and Fortran respectively Because they speak different languages CEM and SWAN do not communicate directly with each oth
21. mal to the convention used by CEM 90 lt wave angle lt 90 where negative angles come from the left and positive from the right The SWAN CEM coupled model is executed using the RUN file that is submitted as a job to the HPC cluster Figure 1 is a flow chart showing the order of operations dictated by the RUN file The following sections explain each colored boxes in Figure 1 in detail including the inputs and outputs in each step START Submit RUN file to HPC begin loop Step Step 2 Step 4 Step 3 iteration timestep Figure 1 Flow chart of the coupled SWAN and CEM model Each colored box or step is explained in the manual Pre simulation set up Setting up your CEM SWAN simulation is generally the same as setting up a nested SWAN run with a few added steps this manual assumes the reader knows how to set up a SWAN run on the HPC cluster and has a basic understanding of the shell script Directory Structure On the HPC cluster the RUN file will be stored in your Home directory home username from where it will be submitted as a job Within your home directory the model saves files as the model runs in an output subdirectory home username output The computation does not take place in your home directory This happens in your working directory on the HPC s scratch drive scratch lfs username To summarize the RUN file is stored and submitted as a job from your ho
22. me directory the RUN file sequentially calls executables CEM SWAN etc located in your working directory and as the model runs files you wish to save are moved automatically to your output directory On your local hard drive you will need a directory to store your output downloaded from the HPC where Matlab scripts described below are executed to parse and display model output Necessary files and scripts Before running SWAN CEM the following files must be placed in the correct directories and must be named as specified below unless indicated otherwise Each file is explained in detail below Note that you do not need to put any files in your output directory 7 In your home directory mg RUN file can be named whatever you like mg SWAN4091 the folder containing the SWAN program and executable 17 In your working directory Files that are updated changed during the model run B Depth bot bathymetry input file for nested SWAN run that is updated each timestep by CEM as the shoreline position changes Values below sea level are positive and subaerial values are negative 2 0 initial shoreline conditions for CEM The name corresponds to the timestep and each time the shoreline is updated CEM exports a new shoreline file named after the current timestep Files that are NOT updated changed during the model run Depth_main bot bathymetry for the coarse grid or ma
23. nd animateoutput m you must have the complementary Matlab script called sort_nat m in your output directory Postprocess m calls sort_nat m you do not need to manually execute sort_nat m or alter it in any way it just needs to be present in your folder to efficiently sort the output data before loading into Matlab To understand how they work these Matlab scripts are included with sample model output Known issues and limitations 1 Running the model takes a long time Using the variable ti in the RUN file which uses the same SWAN output for multiple CEM iterations can speed up the process significantly However it can still take several days to complete a simulation There are probably several other ways unexplored here to speed up the simulations 2 Currently the model can deal only with low curvature shorelines This means no spits or overhanging recurving capes or any shoreline that has multiple cross shore shoreline coordinates for a given alongshore coordinate The 20 3 reason for this is that the shoreface interpolation routine within CEM is designed to interpolate the shoreface bathymetry very simply It can be updated to deal with high curvature shorelines fairly easily though Merging the shoreface bathymetry and the shelf bathymetry is sometimes not completed smoothly meaning there is an elevation discontinuity between the shoreface and shelf that affects the SWAN generated wave field This is somet
24. nditions for the nested SWAN run Step 3 Run SWAN nested grid FILE PROGRAM NAME finegrid swn INPUTS e Boundary conditions from coarse grid SWAN run e Depth bot from CEM OUTPUTS e Hsig a text file containing a Ymax by Xmax matrix of significant wave heights to be used by CEM e Dir a text file containing a Ymax by Xmax matrix of wave directions to be used by CEM PURPOSE The nested SWAN run creates the nearshore wave conditions stored in the Hsig and Dir text files used to calculate alongshore sediment transport in CEM If results from a non nested SWAN run are used as input for CEM i e wave conditions are generated from a single SWAN run then the calculated wave field will have edge effects see SWAN user manual and will not be usable by CEM Step 4 Run CEM FILE PROGRAM NAME cem and executable file created by compiling CEM_SWAN c INPUTS e Hsig from SWAN e Dir from SWAN e Depth bot from previous CEM iteration 18 e coastline domain with the same name as the previous time step from previous CEM iteration e AngleDegrees txt from FindWaveAngle e TimeStep txt see below OUTPUTS e Depth bot to be used by SWAN in next iteration e updated coastline domain to be used CEM in the next iteration PURPOSE CEM reads in the wave conditions produced by the nested SWAN run calculates alongshore sediment flux distributes sediment up
25. ore direction the grid should extend to true deep water depth gt 0 5 wavelength Where to apply boundary conditions wave height angle period Wave conditions are applied by the user at the top or seaward boundary of the coarse grid only The nested SWAN run automatically receives boundary conditions from the coarse grid SWAN run IN FindWaveAngle c Wave climate asymmetry Assigned using the variable asym It must range from 0 1 with a value of 0 5 meaning an equal number of waves come from the left and right directions Wave asymmetry is a property that can be found for a given coastline using wave buoy data see Ashton and Murray 2006a 2006b Proportion of high angle waves Assigned using the variable highness It must range from 0 1 with a value of 0 meaning all deep water waves are lt 45 degrees low angle This is a property that can be found for a given coastline using wave buoy data see Ashton and Murray 2006a 2006b IN nest grid swn file Cell size of nested SWAN grid This must be set exactly the same as the cell size in CEM Generally CEM works best when cell size is 100 m or greater so use that as a guide to set your minimum nest grid cell size To set the maximum cell size consider that the wave breaking threshold wave height divided by depth must be spatially resolved Because of this a cell size less than 500 m is optimal Cross shore domain size Must be the same as in CEM
26. parisons to nature J Geophys Res 111 F04012 doi 10 1029 2005JF000423 Kaergaard K and J Fredsoe 2013a Numerical modeling of shoreline undulations Part 1 Constant wave climate Coastal Engineering 75 64 76 Kaergaard K and J Fredsoe 2013b Numerical modeling of shoreline undulations Part 2 Varying wave climate and comparison to observations Coastal Engineering 75 77 90 Kaergaard K and J Fredsoe 2013c A numerical shoreline model for shorelines with large curvature Coastal Engineering 74 19 32 van den Berg N A Falqu s and F Ribas 2012 Modeling large scale shoreline sand waves under oblique wave incidence J Geophys Res 117 F03019 doi 10 1029 2011JF002177 26 Appendix Below are commented copies of the files needed to run the SWAN CEM model They are intended as a reference that is complementary to the manual so that the user can see where the parameters and variables discussed in the manual are actually located in each model file 27 finegrid swn Run 1D Number 20130222cpcnv1 Run Clock 22 Feb 2013 13 55 33 I SET LEVEL 0 NAUTical MODE STATIONARY TWODimensional C inates CART 322 IR LE 36 0 05 1 00 88 XC 99999 C REGular 70 IN id BOTtom REGular 7 READinp BOTtom 1 Dept t 3 0 e E BOUNd SHAPespec JONswap 3 3 PEAK DSPR DEGR BOUNdnest1 NEST cem_f CLOSed OFF QUAD OFF BRE G GROUP c mpgrid Se 0 219 F102 QUANTITY HSIGN OUTPUT OPTIONS BLOCK SR 2
27. pe 1 Q use depth array 1 use geometric rule define OWMinDepth 1 0 littlest overwash of all define FindCellError 5 if we run off of array how far over do we try again float SedTansLimit 90 beyond what absolute slope don t do sed trans degrees x float OverwashLimit 60 beyond what angle don t do overwash New SWAN stuff SWAN x define WaveBreakDepth 0 3 Define wave breaking threshold H d float WvHeight Breaking wave height found from SWAN run float Angle Breaking wave angle found from SWAN run float BreakDepth Breaking wave depth found from SWAN run FindWaveAngle c N FindWaveAngle c x Created by plimber on 11 18 13 Extracted from the original CEM this function creates a PDF of waves based on wave asymmetry and highness proportion of waves that are gt 42 From this PDF CEM picks randomly each model day a deep water wave to drive the daily model simulation The PDF function is made external to CEM because SWAN needs to know the deep water wave angle to generate a wave field before CEM is called x include lt stdlib h gt include lt stdio h gt include lt math h gt include lt time h gt x Wave characteristics adjust these two variables ONLY define Highness 0 2 proportion of high angle waves define Asym 0 5 x proportion of waves coming from positive left direction
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