COAWST Modeling System建模系統(tǒng)概述

1、PAGE PAGE 41COAWSTUsers ManualVersion 3.0/operations/modeling/COAWST/index.htmlJohn C. WarnerUSGSBrandy ArmstrongUSGSRuoying HeNCSUJoseph ZambonNCSUMaitane OlabarrietaUSGS(THIS DOCUMENT is under development)July 12, 2011Table of Contents.1. Introduction2. Obtaining Code3. Installation4. Setting up a

2、nd running applications5. Examples5a) JOE_TCs = WRF-ROMS-SWAN all 3 on same grid.5b) JOE_TCd = WRF-ROMS-SWAN with ROMS and SWAN on the same grid, WRF on a different grid.5c) INLET_TEST/Coupled = ROMS+SWAN same grid5d) INLET_TEST/DiffGrid = ROMS+SWAN different grids5e) INLET_TEST/Refined = ROMS+SWAN

3、same grid + grid refinement in each.6. running COAWST7. Visualization Tools.8. How to set up a WRF application.9. How to get boundary, init, and climatology data for ROMS grids.10. How to get wind, boundary, and init files for SWAN.11. m files.12. Change log.13. Distribution text and user list.14. L

4、ist of references using COAWST.COAWST Users Manual1. IntroductionThe Coupled-Ocean-Atmosphere-Wave-Sediment Transport (COAWST) Modeling System is an agglomeration of open-source modeling components that has been tailored to investigate coastal processes of the atmosphere, ocean, waves, and coastal e

5、nvironment. The modeling system is currently comprised of:Coupler: Model Coupling Toolkit (MCT) v 2.6.0Ocean:Regional Ocean Modeling System (ROMS) svn 455Atmosphere:Weather Research and Forecasting Model (WRF) v 3.2.1Wave(s):Simulating Waves Nearshore (SWAN) v 40.81Refraction Diffraction (RefDif)Sed

6、iment Transport:Community Sediment Transport Modeling Systems (CSTMS)Here are some model specific user forums that can provide useful information:ROMS/forum/index.phpWRF/SWANhttp:/vlm089.citg.tudelft.nl/swan/forum/default.aspSWAN has been preprocessed with options: swch = -unix -impi -mpi -f95 -cdat

7、e14MCT/research/projects/mct/The main reference is:Warner, J.C., Armstrong, B., He, R., and Zambon, J.B., 2010, Development of a Coupled Ocean-Atmosphere-Wave-Sediment Transport (COAWST) modeling system: Ocean Modeling, v. 35, no. 3, p. 230-244.The main website is: HYPERLINK /operations/modeling/COA

8、WST/index.html /operations/modeling/COAWST/index.html2. Obtaining CodeThe code is maintained in a svn repository and is distributed thru subversion checkout. Please contact John Warner for code access at HYPERLINK mailto:jcwarner jcwarner 3. Installation3.1 Obtain the source code via the svn reposit

9、ory. You should get an email with your username and password. To check out the code I suggest you make a directory called COAWST, cd to that dir, and use:svn -checkout -username myusrname HYPERLINK /coawst/COAWST /coawst/COAWST .Notice the “.” at the end of the command to place the code in that loca

10、tion. Alternatively you can not use the “.” and instead put the path of where you want it to go.3.2 Install required librariesThe following libraries are required to run the coupled modeling system. These are:NetcdfFortran CompilerMPIMCTSCRIPThese libraries/programs (SCRIP is a program, others are l

11、ibs) only need to be installed once, typically by an administrator, and set to be available for all users. The Netcdf, Fortran compiler, and MPI are required to be obtained by the users. Currently the system uses netcdf v3.x. It has been tested with ifort and pgi Fortran compilers. For MPI, we have

12、used mvapich, openmpi, and MPICH2. Set your environment variables, such as by using a script hpc_jcw_env.sh# % script hpc_jcw_env.sh %#! /bin/csh#source pgi64_mx-6new.csh#add intel64_mxsetenv MCT_INCDIR /he_data/he/jbzambon/MCT/mctsetenv MCT_LIBDIR /he_data/he/jbzambon/MCT/mctsetenv NETCDF_INCDIR /u

13、sr/local/apps/netcdf-3.6.1/pgi/6.0/x86_64/includesetenv NETCDF_LIBDIR /usr/local/apps/netcdf-3.6.1/pgi/6.0/x86_64/libsetenv NETCDF /usr/local/apps/netcdf-3.6.1/pgi/6.0/x86_64/lib# % end of script hpc_jcw_env.sh %The four settings of MCT and NETCDF _INCDIR and _LIBDIR are for roms. The setting of NET

14、CDF is for WRF.The MCT and SCRIP packages are distributed with the COAWST package because I modified a few parts of these codes to make them compatible with the systems we have tested. The MCT and SCRIP installs are described below.3.2.1 MCT installation1) Copy the MCT package from COAWST/Lib/MCT an

15、d place into a folder that can be shared to all users. It is recommended to only install this once, and just let all users link to this for all their compilations. 2) ./configureThis will create a file Makfile.conf. You should edit this file and see if the paths etc are correct. I included the file

16、Makefile.conf_jcw as an example of how my setup was on a Windows machine.3) makeThis will build the package in both the mct and mpeu directories. I modified the Makefiles in both of those directories so that they can also work in a Windows world. The Windows compilers typically build *.obj files, in

17、stead of just *.o files. So I modified the mct/Makefile and mpeu/Makefile for the $(F90RULECPP). You can edit those files and see the changes.4) make installThis will place the MCT libs and inc files into the /usr/lib and /usr/include folders. The location can be modified, look at the MCT/README fil

18、e.5) Set your environment variables of setenv MCT_INCDIR COAWST/Lib/MCT/includesetenv MCT_LIBDIR COAWST/Lib/MCT/lib(or where ever you installed them)3.2.2 SCRIP InstallationThe SCRIP package is used to create interpolation weights between two separate grids.1) Create some working folder for the SCRI

19、P package. This can be done by the administrator to do this only once. Lets call the location /usr/SCRIP.2) Copy the code into that folder and go to the source dir.cp r COAWST/Libs/SCRIP/ /usr/SCRIPcd /usr/SCRIP/source3) Edit the build script for your particular environment.edit makefileSet FLAGS, L

20、IB, and INLCUDE for the build. These are set for USGS. Values for the HPC are in the makefile but need to be uncommented.4) makeType make to build the executable. The executable scrip is made in the next level up (one up from source, i.e. /usr/SCRIP). It also makes scrip_test, you can try that if yo

21、u want.3.3 Configuring the system for your applicationUsers may need to initialize environmental settings.4. Setting up and running applicationsTo run the COAWST system, users should set up a folder to hold all your project files. In that folder, there will be files for ROMS, SWAN, WRF, and general

22、control files. One of the control files will be your project header file, lets call it project.h. The project.h file will list cpp (c pre-processor) options that get used to compile the code. These options are listed in section 4.1. Section 4.2 describes a control file needed to compile the model.4.

23、1 cpp options for COAWSTHere is a list of cpp options that should be used/required with COAWST. These options would be listed in your project.h file (described below in the test examples section).4.1.1) One set of options is to allow the user to activate a single model or multiple models. To make us

24、e of this concept, you need to specify which model(s) you want to use. (REQUIRED -) To do this you need to activate one or more of these:#define ROMS_MODEL /* if you want to use the ROMS model */#define SWAN_MODEL /* if you also want to use the SWAN model */#define WRF_MODEL /* if you also want to u

25、se the WRF model */Previously, the system was set to work such that you had to run ROMS and then choose if you want to also run WRF or also run SWAN. A new feature, as of svn version 469 (June 2, 2011), I have the system so that you can run only ROMS, only WRF, ROMS+WRF, ROMS+WRF+SWAN, or just ROMS+

26、SWAN.In the very near future, I will have the system to work with each model completely separately so that users can have the added options of just SWAN, or SWAN+WRF. These last 2 capabilities I am working on now. 4.1.2) To activate model coupling:#define MCT_LIB /* if you have more than one model s

27、elected and you want to couple them.*/The following cpp options are activated internally. The user should NOT list these in their project.h file.ROMS_COUPLING means that roms is being used and is coupled to another model.SWAN_COUPLING means that swan is being used and is coupled to another model.WRF

28、_COUPLING means that wrf is being used and is coupled to another model.AIR_OCEAN means that wrf and roms are active (other models could also be active).WAVES_OCEAN means that swan and roms are active (other models could also be active).AIR_WAVES means that swan and wrf are active (other models could

29、 also be active).4.1.3) Some new cpp options that are available for the coupling include:#define UV_KIRBY /* compute depth-avg current based on Hwave that will be sent from the ocn to the wav model for coupling*/#define UV_CONST /* send vel = 0 from the ocn to wave model */#define ZETA_CONST /* send

30、 zeta = 0 from the ocn to wave model */4.1.4) A new option for atmosphere coupling is#define ATM2OCN_FLUXESThis option specifies that the heat and momentum fluxes as computed by the atmosphere model will be used in the ocean model. This will allow both models to be using the identically same fluxes

31、at the interface. When using this option, you should also use#undef BULK_FLUXESbecause the fluxes will be computed by wrf depending on the surface scheme you select. 4.1.5) Methods for grid interpolation.#define MCT_INTERP_WV2AT /* this allows grid interpolation between the wave and atmosphere model

32、s */#define MCT_INTERP_OC2AT /* this allows grid interpolation between the ocean and atmosphere models */#define MCT_INTERP_OC2WV /* this allows grid interpolation between the ocean and wave models */If you use different grids for the ocean, atmosphere, or wave models, then you need to activate the

33、appropriate option above so that the data fields are interpolated between grids. We have updated the method for the grid interpolation to use flux conservative weights. So now the user can have the same fluxes for both atm and ocn models and the fluxes are transferred between models using a flux con

34、servative approach. An example of this is shown below for the SCRIP interpolation in the JOE_TCd (d=different) test case.4.1.6) Methods for grid refinement.#define REFINED_GRID /* this allows grid refinement in roms or in swan.*/- ROMS has two-way and SWAN has one-way grid refinement. For now, if yo

35、u are running a simulation with both roms and swan, we require that ROMS and SWAN have the same number of grids. The test case INLET_TEST_REFINED (explained below) is an example where both roms and swan are coupled, with grid refinement, and coupling on the refined grids. The grids for ROMS and SWAN

36、 can be different sizes, and then the user needs to provide interpolation weights for those grid combinations. These number of grids is set in the coawst.bash file as NestedGrids.- WRF is two-way (from the WRF developers).- If you are running a simulation using WRF + either ROMS or SWAN, then you ne

37、ed to set which WRF grid will be coupled to the ROMS+SWAN grids. This feature is set in the coupling.in file using the parameter WRF_CPL_GRID. The default is 1, to couple with the WRF parent grid. In the future, we will have more options to couple various levels of R/S grids to various WRF grids. Bu

38、t we need to start somewhere, and for now you can only choose 1 WRF grid.4.1.7) SWAN wave interactions to ROMS or to WRF:The following 3 options are available to allow exchange of wave data to ROMS for use in bulk_fluxes for computation of ocean surface stress, and to allow exchange of wave data to

39、WRF for use in MYJSFC and MYNN surface layer schemes to allow increased bottom roughness of the atmosphere over the ocean:#define COARE_TAYLOR_YELLAND Taylor, P. K., and M. A. Yelland, 2001: The dependence of sea surface roughness on the height and steepness of the waves. J. Phys. Oceanogr., 31, 572

40、-590.#define COARE_OOSTOost, W. A., G. J. Komen, C. M. J. Jacobs, and C. van Oort, 2002:New evidence for a relation between wind stress and wave age from measurements during ASGAMAGE. Bound.-Layer Meteor., 103, 409-438.#define DRENNANDrennan, W.M., P.K. Taylor and M.J. Yelland, 2005: Parameterizing

41、the sea surface roughness. J. Phys. Oceanogr. 35, 835-848. 4.1.8) Implementation of new wave-current interaction formulation.We added a new method based on the vortex force approach. The method is described in detail Kumar et al (2012, in press). The new cpp options for this are:#define WEC_MELLOR r

42、adiation stress terms from Mellor 08#define WEC_VF wave-current stresses from Uchiyama et al. #define WDISS_THORGUZA wave dissipation from Thorton/Guza#define WDISS_CHURTHOR wave dissipation from Church/Thorton#define WDISS_WAVEMOD wave dissipation from a wave model#define WDISS_INWAVE wave dissipat

43、ion from a InWave model#define ROLLER_SVENDSEN wave roller based on Svendsen#define ROLLER_MONO wave roller for monchromatic waves#define ROLLER_RENIERS wave roller based on Reniers#define BOTTOM_STREAMING wave enhanced bottom streaming#define SURFACE_STREAMING wave enhanced surface streamingAdditio

44、nal information is to be added soon. Interested users should read the Kumar et al paper.4.1.9) Other model options.The options above work for the coupled system.- For the ROMS model, all other cpp options are listed in:ROMS/Include/cppdefs.hUser should scan this list of options for activating ocean

45、physics and ocean boundary conditions. - For the WRF model, these options are set in the namelist.input.- For the SWAN model, these options are set in the INPUT file.4.2 To compile the modelTo compile the model, you need to use the coawst.bash file. If this does not work then contact me and I will g

46、et a build script for you. You need to edit the coawst.bash. Some important parts are:export ROMS_APPLICATION=JOE_TCFor now, the application you set will be called ROMS_APPLICATION”. This is because the *.bash file is distributed from roms. I will modify this in the future to be more general, rather

47、 than specific to roms. But for now, set this as the name of your application. Use capital letters. This is the name of your project.h file that contains all your cpp options.export NestedGrids=1This is the number of grids for roms or for swan. The number of grids for WRF is set in the namelist.inpu

48、t file.export MY_ROOT_DIR=/raid1/jcwarner/Models/COAWSTexport MY_PROJECT_DIR=$MY_ROOT_DIRThe rootdir is the location of the source code. You can have a project dir that you work in. I typically make a new copy of the code each time in case I change something and this means I have multiple rootdirs.

49、Then I can always go back and see exactly the version of code that was used for a particular run. Therefore I set the project dir as the same location as the rootdir.export MY_ROMS_SRC=$MY_ROOT_DIR/Keep this the same as listed here.export USE_MPI=onexport USE_MPIF90=onexport FORT=pgiThe COAWST syste

50、m works with mpi. It has been tested with ifort and pgi.export MY_HEADER_DIR=$MY_PROJECT_DIR/Projects/JOE_TCsexport MY_ANALYTICAL_DIR=$MY_PROJECT_DIR/Projects/JOE_TCsUse these to set the locations for you application. Header dir is where your project.h file is located.This means to (re)build everyth

51、ing./coawst.bashThis command will just rebuild any changes to roms or swan, and will rebuild all of wrf:./coawst.bash nocleanThis command will rebuild all of roms and swan and just the changes that have been made to wrf:./coawst.bash nocleanwrfThis will only rebuild roms or swan or wrf files that ha

52、ve been changed./coawst.bash noclean nocleanwrfIf you need to make modifications to the WRF configuration file, here are some tips. you could do this:cd WRF./clean -a./configurethen select the options that you want. It will create the configure.wrf file and you can edit that file. then cd . (to the

53、root dir) and use./coawst.bash -nocleanwrfThis way it will not re-create the configure.wrf file and it will build all of the system.Another handy tool is the script command HYPERLINK /skim/cs1901/script.html /skim/cs1901/script.htmlYou could use:script coawst.log./coawst.bashexitand then save that c

54、oawst.log file to see how the system was built.4.3 Some general helpful tips and a few new functionalities in v) ROMS is now very sensitive to the vertical coordinate system. The user needs to make sure that the values set in the roms init file are the same as the values set in the ocean.in file. Fo

55、r example the following values are checked for consistency:Vtransform=1;Vstretching=1;theta_s=5.0;theta_b=0.4;Tcline=50.0;N=16;User should check that these values are the same in their netcdf files as the *.in file. More info is provided at: /wiki/index.php/Vertical_S-coordinate.4.3.2) ROMS grid fil

56、es should not have fill values for mask arrays. A command to remove these are:ncatted -O -a _FillValue,mask_rho,d, -a _FillValue,mask_u,d, -a _FillValue,mask_v,d, -a _FillValue,mask_psi,d, USeast_grd17.nc4.3.3) This version you only need one project.h file. In previous version we had to modify a wrf

57、.h and a swan.h file. You do not need to modify those files anymore. Just modify your project.h file.4.3.4) For SWAN, you do not need to specify any OUTPUT commands for the coupling. The coupling and OUTPUT are now completely separate.4.3.5) For WRF, you can have a 2-way nest in WRF, and have this c

58、oupled to roms and /or swan. For a moving nest in wrf, WRF requires that it be built without fastsse. For a non-moving nest, it can be built with the standard options.5. ExamplesWe will use the JOE_TC and the Inlet_test cases as examples of how to set up different configurations. The JOE_TC applicat

59、ion is a tropical cyclone that travels west from a deep ocean basin onto a shelf that slopes landward to the west. The JOE_TCs (same grid) and JOE_TCd (different grids) are good examples for a coupled WRF-ROMS-SWAN application. The Inlet_test case is for an idealized inlet with wave and tidal driven

60、 flows and has three cases: Coupled is the standard case with the same grid for each roms and swan; DiffGrid has different size grids for roms and swan; Refined has the same parent grids for roms and swan and the same child grids for roms and swan.5a) JOE_TCs = WRF-ROMS-SWAN all 3 on same grid.5b) J