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Community Sea Ice Model (CSIM) User`s Guide Version 5.0

1. The atmospheric forcing datasets for uncoupled CSIM5 are available at the same URL but are not necessary to get the model set up and running For both coupled and uncoupled models the source code should be extracted from the tar file in a small permanent disk such as your home directory or a cross mounted file system If possible the data input files should also be extracted on a large permanent cross mounted disk These files are copied to the temporary disk during the build stage 2 3 Running CSIM Coupled The scripts for running CSIM coupled are documented in the CCSM3 User s Guide http www ccsm ucar edu models ccsm3 0 ccsm There are several configurations that may be of interest to ice modelers The B configuration is the fully coupled model with active atmosphere ice land and ocean components communicating through the flux coupler This configuration will result in the most realistic ice simulations The D configuration consists of CSIM coupled to the data atmosphere datm6 http www ccsm ucar edu models ccsm3 0 datm6 data ocean docn6 http www ccsm ucar edu models ccsm3 0 docn6 and data land dlnd6 http www ccsm ucar edu models ccsm3 0 d1nd6 components This configuration runs quickly and is used for testing the software engineering aspects of the model This configuration will not result in the best sea ice simulation since docn6 does not allow ice growth in open ocean regions or leads and the data read in by datm
2. and E C Hunke 2004 Modeling sea ice transport using incremental remapping Mon Wea Rev in press Rothrock D A 1975 The energetics of the plastic deformation of pack ice by ridging J Geophys Res 80 4514 4519 Thorndike A S D S Rothrock G A Maykut and R Colony 1975 The thickness distribution of sea ice J Geophys Res 80 4501 4513 32
3. false Snow_into_ocn true advection remap grid_type displaced_pole grid_file data domain grid kmt_file data domain kmt incond_dir INIDIR incond_file CASE csim i restart_dir RSTDIR dump_file CASE csim r history_dir HSTDIR history_file CASE csim h pointer_file CSIMDIR rpointer ice oceanmixed_ice OCEANMIXED_ICE oceanmixed_ice_file gt oceanmixed_ice nc oceanmixed_ice_sst_init OML_ICE_SST_INIT prntdiag_oceanmixed false 4 8 4 Example 4 Uncoupled Ice Model with Atmospheric Forcing To run the uncoupled ice model with atmospheric forcing the following options should be added to the above namelist gt ycycle 1 year_init 1997 fyear_init 1997 atm_data_dir ptmp LOGNAME csim_forcing atm gx3v5 20 4 8 5 Example 5 History File Namelist The second namelist controls what variables are written to the history file By default all files are written to the history file Variables that are not output are set in the namelist icefields_nml Some of the following fields are not written to the history file since they can be retrieved from the ocean history files The melt and freeze onset fields are not used since the information they contain may not be correct if the model is restarted mid year The ice areas and volumes for categories six through ten are not used since the defa
4. NLON number of longitudes in grid resolution OML_ICE_SST_INIT logical variable if true initialize ocean mixed layer temperature from within ice model RESTART logical variable used to initialize model from a restart file RSTFILE name of restart file 10 the namelist will be updated even if the ice model is not recompiled One namelist is called icefields_nml and is defined in ice_history F It contains a list of logical variables that correspond to ice fields that will be written to the history file By default all these variables are set to true so leaving the namelist blank will result in all fields being written to the history file The available fields are listed in Table 11 Changing the content of the history files via the namelist is discussed in section 8 3 3 The other namelist is called ice _nml and is defined in ice_init F It contains variables that control the physics used in the model They are listed in Tables 3 8 Some of the variables in the namelist are determined from environment variables set in the scripts Variables that are commonly changed directly in the namelist are the timestep dt the length of the model run npt and the number of subcycles per timestep in the ice dynamics ndte 3 4 The Build Environment The coupled and uncoupled ice models use the same Makefile and make environment These files are located in the ccsm3 models bld directory for the coupled model and in ccsm3 models ice csim4 src bld for the u
5. Run 2 2 0 2 0 e 4 2 Changing the timestep lt 1 ou i aca nee ee ee AA A a an e a lll Gd de eae He Ald Writing Outputss ia ee e 4 4 4 a AM Ane ee eee ay FBR dad eid d 4 4 Model Physics Aae A So dd ra a a ae dd tai na ALS Haile Names vi53 4 et et A et BS ys BBO eM I A RAL MN ok ee ok 4 6 Ocean Mixed Layer Model ee ee Arte Atmospheric Horcing sa a a oA RA A U SS OEE Eee eee Ee amp 4 8 Example Nam lists n s o a Ga eo a ee Eek AR a 4 8 1 Example 1 CCSM Fully Coupled 20 0 0 00 00 0000 4 8 2 Example 2 Coupled Ice Only Model 0 00 02 0000 00 4 8 3 Example 3 Uncoupled Ice Model 0 200 000 0000002 2 4 8 4 Example 4 Uncoupled Ice Model with Atmospheric Forcing 4 8 5 Example 5 History File Namelist o o e e Model Input Datasets bl Atmospheric Forcing oc dd AAA AAA ee eS ae Run Types 61 Startup RUDS dd a A dd A ae des id E et 6 2 NEON RUS e tad e ee A ada pa Gon er oe de Changing the Number of Ice Thickness Categories Output Data o o os we Qa ie ee SS Oe ee be Ee ee ee Ee aaa 8 2 Restart Eil s ssu eu SoG cop dete de der db a a a Se GE gi aad ood 83 History Piles ove gag a eG en ke ee ewe A guerre BS AA AA 8 3 1 Caveats Regarding Averaged Fields 0 o e e eee 8 3 2 Changing Frequency and Averaging 0 0 0 e eee ee ee eee 22 22 23 23 8 3 3 Changing Cont
6. a supported option The value of snow_into_ocean determines what happens to the snow on ice that is ridged The default value is true so the snow cover on ice that undergoes ridging is put into the ocean If this variable is false the snow on ice undergoing ridging remains on the ice advection determines the horizontal transport scheme used The default scheme is the incremental remapping method Lipscomb and Hunke 2004 This method is less diffusive and is computationally efficient for large numbers of categories or tracers The MPDATA scheme is also available It is second order accurate and more computationally expensive than remapping The upwind scheme is only first order accurate For coupled runs both supported grids gx3v5 and gxlv3 are displaced_pole The rectangular option for a regular grid with constant latitude and longitude spacing is not supported The values of the snow and ice albedos are now set in the namelist The ice albedos are those for ice thicker than ahmax which is currently set at 0 5 m This thickness is a parameter that can be changed in ice_albedo F The snow albedos are for cold snow no_ice_ic provides an option to initialize the ice model with no ice cover 4 5 File Names The namelist parameters listed in Table 7 are for initial condition restart and history file and direc tory information During execution the ice model reads grid and land mask information from the files grid_file and k
7. sea ice model that can be run coupled in a global climate model or uncoupled as a stand alone ice model It has been released as the sea ice component of the Community Climate System Model CCSM a fully coupled global climate model that provides simulations of the earths past present and future climate states CSIM5 is supported on high and low resolution Greenland Pole grids which are identical to those used by the Parallel Ocean Program POP ocean model The high resolution version is best suited for simulating present day and future climate scenarios while the low resolution option is used for paleoclimate simulations and debugging An uncoupled version of CSIM is now available It provides a means of running the sea ice model independent of the other CCSM components It reads in atmospheric and ocean forcing which eliminates the need for the flux coupler and the atmosphere land and ocean data models It can be run on a reduced number of processors or without MPI Message Passing Interface for researchers without access to these computer resources The physics in the uncoupled ice model are identical to those in the ice model used in the fully coupled system CSIM is a dynamic thermodynamic model that includes a subgrid scale ice thickness distribution Bitz et al 2001 Lipscomb 2001 It uses the energy conserving thermodynamics of Bitz and Lipscomb 1999 has multiple layers in each thickness category and accounts for the influences of
8. 6 is from previous atmospheric model simulations The M configuration will result more realistic sea ice simulations than the D configuration This setup re places datm6 in the D congifuration with the latm6 http www ccsm ucar edu models ccsm3 0 latm6 data atmosphere model and the ocean mixed layer model within the ice model The ocean mixed layer is a simple slab model which computes an ocean surface temperature and allows for ice formation due to ocean supercooling More information on the formulation of this model can be found in the Scientific Document latm6 runs on the T62 grid and one year of NCEP forcing is included with this release 2 4 Running CSIM Uncoupled It is assumed that the user has downloaded the source code and input data from the web page described in Section 2 2 This section is intended to get uncoupled CSIM running out of the box with a minimal amount of information More information on modifying the scripts is given in Section 3 1 The default configuration is a 10 day startup run on the gx3v5 grid using 8 processors and the message passing interface MPI The debugging option is turned on history files are written out daily and restart files are written out every 5 days The debugging option should be turned off and the output frequency should be decreased before starting any production runs If your system does not have 8 available processors or MPI see Section 2 4 3 on how to run the model on a single proce
9. 9 Namelist Variables for Atmospheric Forcing Varible Name Type Default Value Description atm_data_dir Path Directory for atmospheric forcing data fyear_init Integer First year of atmo spheric forcing data ocn_data_dir Path Directory for oceanic forcing data ycycle Integer Number of years in forcing data cy cle year_init Integer 1 Initial year if not using restart file from the POP forcing file For continuation runs the value of 0ML_ICE_SST_INIT should be set to false and sea surface temperature and the freeze melt potential will be read from a restart file This variable will be automatically set in the scripts depending on the run type When the slab ocean mixed layer within the ice model is used the data that is received from the coupler from the ocean component docn or POP is overwritten by the values calculated by the ocean mixed layer Therefore it is not appropriate to use the ocean mixed layer option coupled to an active ocean model Also using the ice model with the slab ocean mixed layer turned on coupled to an active atmosphere and a data ocean model will require changes to the coupler since the ocean values calculated in the ice model will not be sent to the coupler and received by the atmosphere component 4 7 Atmospheric Forcing CSIM5 can be run uncoupled using atmospheric data from 1997 available from http www ccsm ucar edu models ice cs These data files are on the low resolution grid and were cr
10. Community Climate System Model National Center for Atmospheric Research Boulder CO http www ccsm ucar edu models CVS tag Name Build date July 12 2004 Community Sea Ice Model CSIM User s Guide Version 5 0 Released with CCSM3 0 Julie Schramm Cecilia Bitz Bruce Briegleb Marika Holland Elizabeth Hunke Bill Lipscomb Dick Moritz Contents 1 Introduction 11 Whats new in GSIM 5 cada ok we A E e gece gaa ee EEE A es Quick Start Guide 2 1 What is needed to run OSIMP 0 0 02 ee ee 2 2 Downloading Source Code and Input Datasets o o e 2 3 Running CSIM Coupled 0 2 20 000 0000 0000 eee 24 Running CSIM Uncoupled pe atocar e ere ean ai a a we 2 4 1 Multiple Processors with MPI aoaaa aaa e 2 4 2 Single Processor with MPI 2 4 3 Single Processor without MPI 0 0002000200000 The CSIM Scripts 3 1 Coupled Model Scripts ee 3 2 Uncoupled Run Script essendi ld be a A Ad e Pee 3 2 1 Using the Ocean Mixed Layer Model within CSIM o o 3 2 2 Changing Grid Resolution o ee 3 2 3 Changing the Number of Processors o a 3 3 Uncoupled Setup Script 0 0 0 4040 8 64 a a ee e ee ee 3 4 The Build Environment 3 4 1 CSIM Preprocessor Flags ee 374 2 SIM Compilers Options estocada A ae Se ee ER goles ea Namelist Variables 4 1 Changing the Length of the Model
11. DF command ncdump h filename nc Variables containing grid information are written to every file and are listed in Table 10 In addition to the history files a netCDF file containing a snapshot of the initial ice state is created at the start of each run The file name is SCASE csim i yyyy mm dd sssss nc and is written to init in the executable directory 8 3 1 Caveats Regarding Averaged Fields In computing the monthly averages for output to the history files most arrays are zeroed out before being filled with data These zeros are included in the monthly averages where there is no ice For some fileds this is not a problem for example ice thickness and ice area For other fields this will result in values that are not representative of the field when ice is present Some of the fields affected are e Flat Fsens latent and sensible heat fluxes e albsni snow ice broadband albedo e evap evaporative water flux e Fhnet ice ocn net heat flux e Fswabs snow ice ocn absorbed solar flux e strairx strairy zonal and meridional atm ice stress e strcorx strcory zonal and meridional coriolis stress 25 For some fields a non zero value is set where there is no ice For example Tsfc has the freezing point averaged in and Flwout has oT averaged in At lower latitudes these values can be erroneous To aid in the interpretation of the fields a field called ice_present is written to the history file It contains information on t
12. N U grid center longitude degrees ULAT U grid center latitude degrees tmask ocean grid mask 0 land 1 ocean tarea T grid cell area m uarea U grid cell area m dxt T cell width through middle m dyt T cell height through middle m dxu U cell width through middle m dyu U cell height through middle m HTN T cell width North side m HTE T cell width East side m ANGLET angle grid makes with latitude line on T grid radians ANGLE angle grid makes with latitude line on U grid radians ice_present fraction of time averaging interval that any ice is present Logical Variable Description Units f hi grid box mean ice thickness m f hs grid box mean snow thickness m f_Tsfc snow ice surface temperature C f_aice ice concentration aggregate f_aicel ice concentration category 1 f_aice2 ice concentration category 2 f aice3 ice concentration category 3 f_aice4 ice concentration category 4 f_aiced ice concentration category 5 f_aice6 ice concentration category 6 f_aice7 ice concentration category 7 f_aice8 ice concentration category 8 f_aice9 ice concentration category 9 f aice10 ice concentration category 10 f vicel ice volume category 1 m vice2 ice volume category 2 m f vice3 ice volume category 3 m f_vice4 ice volume category 4 m viceb ice volume category 5 m vice6 ice volume category 6 m f_vice7 ice volume category 7 m f_vice8 ice volume category 8 m f_vice9 ice vol
13. TR is a longer string that describes a model case RUNTYPE is a character string that specifies the state in which the model is to begin a run startup and continue are the supported run types startup run can be initialized by reading input from a file or from initial conditions set within the ice model This option is controlled by the environment variable RESTART in the setup script see Section 6 1 Continue runs are described in Section 6 2 NCAT is an integer that sets the number of ice thickness categories The default value is 5 categories If you are considering changing NCAT to values other than 3 or 10 read Section 7 This is an involved process that deserves its own section 3 2 1 Using the Ocean Mixed Layer Model within CSIM OCEANMIXED_ICE is a logical variable if true is used to implement the slab ocean mixed layer model in the ice model It is a simple model that is forced using output from a POP ocean simulation More details on the physics of the ocean mixed layer model can be found in the Physics Documentation It can be run with the gx3v5 or the gx1v3 grid To use the mixed layer model set setenv O0CEANMIXED _ICE true in csim_run 3 2 2 Changing Grid Resolution GRID is a character string used to specify the horizontal grid Presently two resolutions are supported for the ice model gx3v5 and gx1v3 In both of these grids the North Pole has been displaced into Greenland gx3v5 is the coarser grid with
14. been added that contain code for aborting the model and globally accessible work arrays The gx3v4 grid had been replaced by a new gx3v5 grid The coupled model produced a poor meridional overturning circulation MOC with the gx3v4 grid The new grid has points in different locations and has higher resolution in the North Atlantic than gx3v4 The simulation with gx3v5 gives a better ice thickness distribution and produces a better MOC e The prescribed ice model is not supported in this release e Most CSIM and CICE modules are very similar except for the mechanical redistribution modules The CSIM source code is based on the LOS Alamos sea ice model CICE model After a code merger with CICE was carried out to take advantage of the vector friendly code the models are very similar If there are some topics that are not covered in the CSIM documentation users are encouraged to look at the CICE documentation Hunke and Lipscomb 2004 It is available at http climate lanl gov Models CICE index htm 2 Quick Start Guide 2 1 What is needed to run CSIM A number of target architectures are supported for CCSM including IBM SP SGI Origin SGI Altix Linux NEC Earth Simulator Cray X1 and Compaq ES The resources required to run CSIM coupled in CCSM are listed in the CCSM3 User s Guide at http www ccsm ucar edu models ccsm3 0 ccsm Two target architectures are supported for uncoupled CSIM IBM and SGI Below is a list of what is required
15. brine pockets within the ice cover The ice dynamics utilizes the elastic viscous plastic EVP rheology of Hunke and Dukowicz 1997 Sea ice ridging follows Rothrock 1975 and Thorndike et al 1975 A slab ocean mixed layer model is included A Scientific Reference is available that contains more detailed information on the model physics An attempt has been made throughout this document to provide the following text convention Variable names used in the code are typewritten Subroutine names are given in italic and file names are in boldface 1 1 What s new in CSIM5 CSIM5 is an upgraded version of CSIM4 which was released in October 2002 The model physics are similar to that of CSIM4 but a majority of the code has been rewritten for vectorization and to make the CSIM code similar to that of CICE the LANL sea ice model The major changes are e A module for a new incremental remapping transport scheme was added called ice_transport_remap F The MPDATA transport scheme formerly in ice_transport F was moved to ice_transport_mpdata F Open water advection was added to the incremental remapping e A bug in ice_albedo F was fixed to avoid negative albedos for thin bare melting ice e A bug in ice_ocean F was fixed to include fswthru in the calculation of sea surface temperature e A salt flux calculation was added so the ice reference salinity could be changed to a non zero value e The sea ice momentum equation modified for the free dr
16. ce growth snow ice formation basal ice melt surface ice melt lateral ice melt ice ocn fresh water flux sent to coupler ice ocn fresh water flux ice to ocn salt flux sent to coupler ice to ocn salt flux ice ocn net heat flux sent to coupler ice ocn net heat flux SW transmitted through ice to ocean sent to coupler SW transmitted through ice to ocean zonal atm ice stress meridional atm ice stress zonal sea surface tilt meridional sea surface tilt zonal coriolis stress meridional coriolis stress zonal ocean ice stress cms W m W m cm day cm day cm day cm day cms cms I 1 f 1 continued on next page 28 9 9 1 continued from previous page f_strocny meridional ocean ice stress Nm f strintx zonal internal ice stress N m f_strinty meridional internal ice stress Nm f strength compressive ice strength Nm f_divu velocity divergence day f_shear strain rate day f_ opening lead opening rate day f sigl normalized principal stress component f_sig2 normalized principal stress component f_daidtt area tendency due to thermodynamics day f daidtd area tendency due to dynamics day f_dvidtt ice volume tendency due to thermo cm day f_dvidtd ice volume tendency due to dynamics cm day melt onset date freeze onset date f_mlt_onset f_frz_onset Troubleshooting Code does not Compile or Run Check the ice log file in the executable di
17. d there is a flag called Dfcd_coupled that will keep the fluxes from being divided by the ice area In coupled runs the CCSM coupler multiplies the fluxes by the ice area so they are divided by the ice area in CSIM to get the correct fluxes The options DNPROC_X NX and DNPROC_Y NY set the number of processors used in each grid direction These values are set automatically in the scripts for the coupled model and in csim_run by the user for uncoupled runs NX and NY must divide evenly into the grid and are used only for MPI grid decomposition If NX or NY do not divide evenly into the grid the model setup will exit from the setup script and print an error message to the ice log standard out file The flag D_MPI sets up the message passing interface This must be set for runs using a parallel environment To get a better idea of what code is included or excluded at compile time grep for ifdef and ifndef in the source code or look at the f files in the obj directory 11 3 4 2 CSIM Compiler Options The name of the Fortran compiler is set by the variable FC in the Macros lt OS gt files The default name of the compiler is 90 on the SGI and mpx1f90_r on the IBM SP CSIM uses the following compiler options on the SGI platform FFLAGS c 64 mips4 02 r8 i4 show extend_source On the IBM the following compiler options are set in Macros AIX FFLAGS c 02 qstrict Q qmaxmem 1 qrealsize 8 qarch auto qtune aut
18. de is built here NOTE Files exist only for certain numbers of ice thickness categories 1 3 5 and 10 If you need a number of categories other than these the model will not run as is See Section 7 for information on how to change the number of ice thickness categories The variable 0ML_ICE_SST_INIT is used if 0CEANMIXED_ICE is set to true in the run script and determines the initial sea surface temperature If the run is a startup run this variable is set to true in the ice setup script and the January 1 value of the sea surface temperature is read from the POP forcing file Thereafter the value of 0ML_ICE_SST_INIT is set to false and sea surface temperature and the freeze melt potential is read from a restart file The ice model contains two namelists The variables for both lists are set in csim setup csh and are written to the file ice_in in EXEROOT when the setup script is executed Changes to the namelists must be made in the run or setup script not in the ice_in file The ice model reads his file at runtime Therefore Table 2 Environment Variables Set in the Ice Setup Script Symbol Description HSTDIR directory where history files are written RSTDIR directory where restart files are written INIDIR directory where initial condition files are written ICESRC directory where ice model input templates are located RES grid dimensions used to select model resolution NLAT number of latitudes in grid resolution
19. dt is the timestep in seconds for the ice model thermodynamics The thermodynamics component is stable but not necessarily accurate for any value of the timestep The value chosen for dt depends on the stability of the transport and the grid resolution A conservative estimate of dt for the transport using the MPDATA advection scheme is min Ax Ay 4magz u v At lt 1 Maximum values for dt for the two standard CCSM POP grids assuming maz u v 0 5m s are shown in Table 4 The default timestep for CSIM is one hour The calculation of the ice velocities is subcycled ndte times per timestep so that the elastic waves are damped before the next timestep The subcycling timestep is calculated as dte dt ndte and must be sufficiently smaller than the damping timescale T which needs to be sufficiently shorter than dt dte lt T lt dt 2 This relationship is discussed in Hunke 2001 also see Hunke and Lipscomb 2002 section 4 4 The best ratio for dte T dt is 1 40 120 Typical combinations of dt and ndte are 3600 120 7200 240 10800 120 Occasionally ice velocities are calculated that are larger than what is assumed when the model timestep is chosen This causes a CFL violation in the transport scheme A namelist option was added ndyn dt to subcycle the dynamics to get through these instabilities that arise during long integrations The default value for this variable is one and is typically increased to two w
20. e log file ERROR NX must divide evenly into grid 100 8 The number of MPI processors used by the ice model must divide evenly into the grid dimensions For example running the ice model with 8 tasks on the gx3v5 grid will result in an error since 8 does not divide evenly into the 100 longitude points To fix this error change the value of NTASKS for the uncoupled ice model in the main script In this case a value of 4 would work and the task geometry would also have to be changed 9 6 Enabling the Debugger This section explains how to set some compiler options for debugging For the coupled model set DEBUG to TRUE in the env_run script For the uncoupled ice model set setenv DEBUG TRUE in csim setup csh Before running the model be sure to delete the object files so that the source code will be recompiled If a core file is created it will be in the executable directory Use dbx to look at the core file Useful information may also appear in the standard error and output files 30 9 7 Unit 50 Error Unit 50 is the restart file If the path or file name in the rpointer ice file is incorrect or the restart file does not exist in the rest directory below the executable directory the model will stop with this message 8 1525 014 The 1 0 operation on unit 50 cannot be completed because an errno value of 2 A file or directory in the path name does not exist was received while opening the file The program will stop Verify
21. e CCSM filenaming convention so the default values listed in Table 7 are not the same as those shown in the namelist in Section 4 8 1 See sections 8 2 and 8 3 for an explanation of how the rest of the filename is created 4 6 Ocean Mixed Layer Model An ocean mixed layer model has been incorporated into the ice model since the CCSM data ocean component does not allow frazil ice growth to occur This is due to the minimum ocean mixed layer temperature being fixed at the freezing point It is a simple slab ocean mixed layer model that is forced using output from a POP ocean simulation More details on the physics of the ocean mixed layer model can be found in the Physics Documentation This option can be run with the gx3v5 or the gx1v3 grid The namelist variables for the ocean mixed layer model within the ice model are shown in Table 8 To use the slab ocean model 0CEANMIXED_ICE must be set to true in the namelist There are commands in the scripts that will copy the grid dependent forcing file from the input data directory to the executable directory and rename it oceanmixed_ice nc This is generally not the best ocean forcing but can be used as a template for creating an ocean forcing file appropriate for the application The variable 0ML_ICE_SST_INIT determines the initial sea surface temperature For an initial or startup run this variable should be set to true and the January 1 value of the sea surface temperature will be read 17 Table
22. e default and approximates the thickness distribution in each category as a linear function Lipscomb 2001 The delta function method represents g h in each category as a delta function Bitz et al 2001 This method can leave some categories mostly empty at any given time and cause jumps in the properties of g h kdyn determines the ice dynamics used in the model The default is the elastic viscous plastic EVP dynamics Hunke and Dukowicz 1997 If kdyn is set to 0 the ice dynamics is inactive In this case ice velocities are not computed and ice is not transported Since the initial ice velocities are read in from the restart file the maximum and minimum velocities written to the log file will be non zero in this case but they are not used in any calculations The value of kstrength determines which formulation is used to calculate the strength of the pack ice The Hibler 1979 calculation depends on mean ice thickness and open water fraction The calculation of Rothrock 1975 is based on energetics and should not be used if the ice that participates in ridging is not well resolved evp_damping is used to control the damping of elastic waves in the ice dynamics It is typically set to true for high resolution simulations where the elastic waves are not sufficiently damped out in a small timestep without a significant amount of subcycling This procedure works by reducing the effective ice strength that s used by the dynamics and is not
23. e run types and 13 Table 5 Namelist Variables for Writing Output Varible Type Default Description diagfreq Integer 24 Frequency of diagnostics written min max hemispheric sums to standard output 24 gt writes once every 24 timesteps 1 gt diagnostics written each timestep 0 gt no diagnostics written histfreq Character mM Frequency of output written to history file D or d writes daily data W or w writes weekly data M or m writes monthly data Y or y writes yearly data 1 writes every timestep 0 no history data is written hist_avg Logical true If true averaged history information is written out at a frequency determined by histfreq If false instantaneous val ues rather than time averages are writ ten dumpfreq Character y Frequency restart data is written to file DD or d writes restart every dumpfreq_n days MM or m writes restart every dumpfreq_n months Y or y writes restart every dumpfreq_n years 0 no restart data is written dumpfreqn Integer 1 Frequency restart data is written to file print_points Logical false print diagnostic data for two grid points 14 Table 6 Namelist Variables for Model Physics Varible Name Type Default Value Description restart Logical false If true model is initialized using a restart file if false model is initialized using initial conditions in ice_init F kcolumn Integer 0 Column mod
24. eated for testing the ice model They will not produce the best sea ice simulation Module ce_flux_in F can be modified to change the forcing data Namelist options for using the atmospheric forcing data are shown in Table 9 atm_data_dir is the root directory where the forcing resides fyear_init and year_init should be set to 1997 and ycycle should be set to 1 for the forcing provided ocn_data_dir should not be set since no ocean forcing is provided Subroutines in ce_flux_in F are available for reading in ocean sea surface temperature and salinity data and may be used for initializing and or restoring the mixed layer properties these subroutines currently are commented out in ice_fluz_in F A sample namelist using these options is shown in section 4 8 4 A brief discussion of the atmospheric forcing files is given in section 5 1 as well as changes that should be made to ice F to use this forcing 4 8 Example Namelists This section shows several examples of namelists from the coupled and uncoupled ice models These examples are taken directly from csim buildnml_prestage csh for the coupled model and from csim setup csh for the uncoupled model Most of the variables in the namelist are determined from environment variables set elsewhere in the scripts Since the namelists from the coupled model are resolved by the scripts meaning that the values of most of the shell script variables are put directly into the namelist examples are shown for
25. ed in netCDF global attributes runtype Character unknown runtype Determines if BASEDATE is received from coupler or restart file istep0 Integer 0 Step counter number of steps taken in pre vious integration npt Integer 99999 Total number of timesteps in a model run model stops when istep exceeds npt not used in coupled runs dt Double 3600 Timestep in seconds ndyn_dt Integer 1 Times to loop through ice dynamics ndte Integer 120 Number of subcycles per timestep in ice dynamics The time management namelist options are shown in Table 3 runid is a character string that contains descriptive information gathered from the run script This information is written to the global attributes in the history files runtype is determined from the value of RUNTYPE set in the run script The options for this are discussed in section 6 istepO is the number of steps taken in a previous integration and is written to the restart file 4 1 Changing the Length of the Model Run The length of an uncoupled model run is controlled by the variable npt It is the total number of time steps taken in an integration The value of npt is not used in a coupled run since the point at which integration 12 Table 4 Maximum values for ice model timestep dt Grid min Az Ay maxAt gx3v5 28845 9 m 4 0 hr gxlv3 8558 2 m 1 2 hr is stopped is determined by the coupler The length of a coupled run should be set in the 4 2 Changing the timestep
26. el flag 0 off 1 column model not tested or sup ported kitd Integer 1 Determines ITD conversion 0 delta scheme 1 linear remapping kdyn Integer 1 Determines ice dynamics 0 No ice dynamics 1 Elastic viscous plastic dynamics kstrength Integer 1 Determines pressure formulation 0 Hibler 1979 parameterization 1 Rothrock 1975 parameterization evp_damping Logical false If true use damping procedure in evp dy namics not supported snow_into_ocn Logical true If true snow on ridged ice falls into ocean advection Character remap Determines horizontal advection scheme remap incremental remapping mpdata2 second order advection upwind first order advection grid_type Character displaced_pole Determines grid type displaced_pole or rectangular not sup ported albicev Double 0 73 Visible ice albedo albicei Double 0 33 Near infrared ice albedo albsnowv Double 0 96 Visible snow albedo albsnowi Double 0 68 Near infrared snow albedo no_ice_ic Logical false Initializes ice model with no ice 15 about using restart files and internally generated model data as initial conditions kcolumn is a flag that will run the model as a single column if is set to 1 This option has not been thoroughly tested and is not supported kitd determines the scheme used to redistribute sea ice within the ice thickness distribution ITD as the ice grows and melts The linear remapping scheme is th
27. ent the precipitation rate on the ice cover 8 3 2 Changing Frequency and Averaging The frequency at which data are written to a history file as well as the interval over which the time average is to be performed is controlled by the namelist variable histfreq Data averaging is invoked by the namelist variable hist_avg The averages are constructed by accumulating the running sums of all variables in memory at each timestep The options for both of these variables are described in Table 5 If hist_avg is true and histfreq is set to monthly for example monthly averaged data is written out on the last day of the month 8 3 3 Changing Content The second namelist in the setup script controls what variables are written to the history file To remove a field from this list add the name of the logical variable associated with that field to the amp icefields_nm1 namelist in csim buildnml prestage csh coupled or csim setup csh uncoupled and assign it a value of false For example to remove ice thickness and snow cover from the history file add amp icefields_nml f_hi false f_hs false to the namelist Table 11 Standard Fields Available for Output to History File 26 Table 10 Time and Grid Information Written to History File Field Description Units time model time days time_bounds boundaries for time averaging interval days TLON T grid center longitude degrees TLAT T grid center latitude degrees ULO
28. ents 3 4 0 cca eee RAE OR ERR SAS Gear 6 os 26 9 Troubleshooting 29 9 1 Code does not Compile or Run 2 29 9 2 Negative Ice Area in Horizontal Remapping 0 0000 ee eee eee 29 93 Conservation Prror bo at ae ae Se AAA ASE Pe ee a a G 30 9 4 MPDATA transport unstable 000 0 30 9 5 NX does not divide evenly into grid o 0 0 0 0 00000000000 30 9 6 Enabling the Debugger n ey 40 60 4245 bo POR pew ee ar ae ee 30 9 Unit DO Error s s ae ee ao ae ee A E es Bike de de en Ae te ee 31 1 Introduction This User s Guide accompanies the CCSM3 User s Guide and is intended for those who would like to run CSIM coupled or uncoupled on a supported platform and out of the box Users running CSIM fully coupled should first look at the CCSM3 User s Guide It includes a quick start guide for downloading the CCSM3 source code and input datasets and information on how to configure build and run the model The supported configurations and scripts for building the fully coupled model are also described in the CCSM3 User s Guide The CSIM User s Guide is intended for users interested in making modifications to the ice model scripts or namelists or running the uncoupled ice model Users interested in modifying the source code should see the CSIM Code Reference Developer s Guide CSIM5 is the latest version of the NCAR Community Sea Ice Model It is the result of a community effort to develop a portable efficient
29. file are created from an equilibrium solution and provide more realistic information that is necessary if coupling to an active ocean model The frequency at which restart files are created is controlled by the namelist parameter dumpfreq The names of these files are proceeded by the namelist parameter dump_file and by default are written out yearly to the rest directory under the executable directory To change the directory where these files are located modify the variable RSTDIR at the top of the setup script The names of the restart files follow the CCSM Output Filename Requirements The form of the restart file names are as follows CASE csim r yyyy mm dd sssss 24 For example the file CASE csim r 0002 01 01 00000 would be written out at the end of year 1 month 12 A file containing the name of a restart file is called a restart pointer file This filename information allows the model simulation to continue from the correct point in time and hence the correct restart file Restart Pointer Files A pointer file is an ascii file named rpointer ice that contains the path and filename of the latest restart file The model uses this information to find a restart file from which initialization data is read The pointer files are written to and then read from the executable directory For startup runs a pointer is created by the ice setup script Whenever a restart file is written the existing restart pointer file is overwritten The namel
30. he fraction of the time averaging interval when any ice was present in the grid cell during the time averaging interval in the history file This will give an idea of how many zeros were included in the average The second caveat results from the coupler multiplying fluxes it receives from the ice model by the ice area Before sending fluxes to the coupler they are divided by the ice area in the ice model These are the fluxes that are written to the history files they are not what affects the ice ocean or atmosphere nor are they useful for calculating budgets The division by the ice area also creates large values of the fluxes at the ice edge The affected fields are e Flat Fsens latent and sensible heat fluxes e Flwout outgoing longwave e evap evaporative water flux Fresh ice ocn fresh water flux Fhnet ice ocn net heat flux e Fswabs snow ice ocn absorbed solar flux When applicable two of the above fields will be written to the history file the value of the field that is sent to the coupler divided by ice area and a value of the flux that has been multiplied by ice area what affects the ice Fluxes multiplied by ice area will have the suffix aice appended to the variable names in the history files Fluxes sent to the coupler will have sent to coupler appended to the long_name Fields of rainfall and snowfall multiplied by ice area are written to the history file since the values are valid everywhere and repres
31. hen the ice model reaches an instability The value in the namelist should be returned to one by the user when the model integrates past that point 4 3 Writing Output The namelist variables that control the frequency of the model diagnostics netCDF history files and binary restart files are shown in Table 5 By default diagnostics are written out once every 24 timesteps to the ascii file ice log LID see section 8 1 LID is a time stamp that is set in the main script histfreq controls the output frequency of the netCDF history files writing monthly averages is the default The content of the history files is described in section 8 3 The value of hist_avg determines if instantaneous or averaged variables are written at the frequency set by histfreq If histfreq is set to 1 for instantaneous output hist_avg is set to false within the source code to avoid conflicts dumpfreq and dumpfreq_n control the output frequency of the binary restart files writing one restart file per year is the default If print_points is true diagnostic data is printed out for two grid points one near the north pole and one near the Weddell Sea The points are set at the top of ice_diagnostics F This option can be helpful for debugging 4 4 Model Physics The namelist variables for the ice model physics are listed in Table 6 restart is almost always true since most run types begin by reading in a binary restart file See section 6 for a description of th
32. ift regime The dynamics scheme treats areas with lower ice concentrations more accurately See Hunke and Dukowicz 2003 e ice_coupling F has been rewritten to be compatible with the latest version of the CCSM coupler e An additional field Qref is calculated in atmo_boundary_layer and passed to the coupler Each ice thickness category has 4 thickness layers Previously the two thinnest categories had two layers e A sub cycling timestep ndyn_dt was added to the dynamics to get around a model instability that would manifest itself in MPDATA e The snow and ice albedos used for coupled model tuning were moved to the namelist to make modi fication easier e It is now possible to run CSIM as an uncoupled model The module ice_flux_in F has been added to read in forcing data Most modules have been modified to run efficiently on vector platforms Grid indices i j are no longer passed into subroutines Shorter loops over ice categories and vertical layers have been moved outside the longer loops over i and j Directives have been placed before certain loops to enforce vectorization e The thermodynamics modules from CSIM4 ice_tstm F ice_vthermo F ice_therm_driver F and ice_dh F have been replaced by two new modules ice_therm_vertical F and ice therm _itd F The caclulations in ice_therm_vertical F are done before the to_coupler call and those in ice_therm_itd F are done after this call e New modules ice_exit F and ice_work F have
33. ipts will generate a set of resolved scripts for a specific configuration determined by the user The configuration includes components resolution run type and machine The run and setup scripts that were previously in the scripts directory for CCSM2 are now generated au tomatically See the CCSM3 User s Guide for information on how to use the new scripts The file that contains the ice model namelist is now located in ccsm3 scripts CASE Buildnml Prestage The script containing the environment variables used for building the executable file for the ice model is in ccsm3 scripts CASE Buildexe The contents of the ice model namelist are described in section 4 3 2 Uncoupled Run Script The run script for the uncoupled model is called csim_run and is located in ccsm3 models ice csim4 src Its purpose is to coordinate setting the batch system options the environment variables executing the CSIM setup script setting up the stdout file and submitting the model to run At the top of the run script the settings for the IBM SP and the SGI Origin 2000 batch queue environ ments are set These commands are machine and site dependent Following this the variables for the run environment are defined These variables are listed in Table 1 CASE is a character string that identifies a particular model run It can be up to 16 characters long but it is best kept short since it is used as part of the restart history and initial filenames CASES
34. ist variable pointer_file contains the name of the pointer file Pointer files seldom need editing The contents are usually maintained by the setup script and the component model 8 3 History Files History files contain gridded data values written at specified times during a model run By default the history files will be written to the directory history_dir defined in the namelist The netCDF file names are prepended by the character string given by history_file in the ice _nml namelist This character string has been set according to CCSM Output Filename Requirements If history_file is not set in the namelist the default character string iceh is used The user can specify the frequency at which the data are written Options are also available to record averaged or instantaneous data The form of the history file names are as follows Yearly averaged CASE csim h yyyy nc Monthly averaged CASE csim h yyyy mm nc Weekly averaged CASE csim hw yyyy mm dd sssss nc Daily averaged CASE csim h yyyy mm dd nc Instantaneous histfreq y m w or d CASE csim h yyyy mm dd sssss nc Instantaneous written every dt histfreq 1 CASE csim h yyyy mm dd sssss nc CASE is set in the main setup script All history files are written to hist in the executable directory Changes to the frequency and averaging will affect all output fields The best description of the history data comes from the file itself using the netC
35. l be copied into the directory where the ice model is being built and renamed ice_model size F Files exist for the following configurations CSIMDIR input_templates ice_model size F 100x116x1 CSIMDIR input_templates ice_model size F 100x116x3 CSIMDIR input_templates ice_model_size F 100x116x5 CSIMDIR input_templates ice_model_size F 100x116x10 CSIMDIR input_templates ice_model_size F 320x384x1 CSIMDIR input_templates ice_model_size F 320x384x3 CSIMDIR input_templates ice_model_size F 320x384x5 CSIMDIR input_templates ice_ model_size F 320x384x10 Table 1 Environment Variables Set in the Run Script csim_run Variable Description CASE case name CASESTR short descriptive text string used in history files OCEANMIXED_ICE logical variable used to implement ocean mixed layer model ICE_GRID ice model grid gx3v5 or gx1v3 RUNTYPE run type startup or continue NCAT number of thickness categories in the ice thickness distri bution NX number of processors assigned in the x direction used for MPI grid decomposition NY number of processors assigned in the y direction used for MPI grid decomposition BINTYPE Set to MPI for internal parallelization set to single for non MPI runs CSIMDIR source code base directory SHRCODE share code directory CSIMDATA input data base directory CBLD makefile and Macros directory EXEROOT Run model mv data output put here LID timestamp for file ID string OBJDIR ice model co
36. les ice model _size F RESx8NCAT in CSIMDIR input_templates e The initial condition restart file in the input file directory The number of ice thickness categories is set in cesm3 scripts CASE Buildexe csim buildexe csh coupled or csim_run uncoupled using the variable called NCAT The default value is 5 categories NCAT is used to determine which module ice_model_size F SRESx NCAT is copied to obj before compilation where it is renamed ice_model size F RES is the resolution of the grid 100x116 gx3v5 and 320x384 gx1v3 for low and high resolution grids respectively The input templates are located in CSIMDIR input_templates for 1 3 5 and 10 thickness categories on the default grid sizes of 100x116 and 320x384 NOTE To use one ice thickness category the following changes will need to be made in the namelist kitd 0 kstrength 0 With these settings the model will use the delta scheme instead of linear remapping and a strength parameterization based on open water area and mean ice thickness To create an input template with a number of categories other than the above values copy an existing template that has the desired grid Change ncat to the appropriate number of categories The information in the initial restart file is dependent on the number of ice thickness categories and the total number of layers in the ice distribution An initial condition file exists only for the default case of 5 ice thickness categories
37. lines request a total of eight MPI processes on one 8 way node For the NCAR SGI the default setting is QSUB 1 mpp_p 8 request 8 processors and for other SGI s it may be BSUB n 8 3 3 Uncoupled Setup Script The purpose of the setup script csim setup csh is to build an executable version of the ice model document what source code and data files are being used in the ice log LID file and gather or create any necessary input data files LID is a time stamp set in the run script The environment variables set locally in the ice setup script are listed in Table 2 NOTE The variables shown in Table 2 will rarely have to be modified by the user since they depend on variables set in the run script The most common changes made in the script file will be to the namelist discussed in Section 4 HSTDIR RSTDIR and INIDIR are the directories in EXEROOT where the history restart and initial condition files are output respectively The ice model input templates are located in ICESRC These tem plates are fortran modules that contain information on grid dimensions number of ice thickness categories and vertical resolution in the ice categories The grid is determined in the run script and the resolu tion RES is set in csim setup csh 100x116 for the gx3v5 grid and 320x384 for gxlv3 Depending on RES and the number of ice thickness categories NCAT set in csim_run the appropriate input template ice_model_size RES x NCAT wil
38. longitudinal resolution of 3 6 degrees The latitudinal resolution varies with a resolution of approximately 0 9 degrees near the equator gxlv3 is the finer resolution grid with a longitudinal resolution of approximately one degree Its latitudinal resolution is also variable with a resolution of approximately 0 3 degrees near the equator 3 2 3 Changing the Number of Processors NX and NY are the number of processors used by the ice model for internal parallelization Currently NX and NY MUST divide evenly into the grid dimensions There are checks for this in the setup script and in the ice source code the model will stop if these criteria are not met NLAT and NLON are used for this purpose For load balancing purposes NY should be lt 2 If it is greater than this the processors assigned subdomains near the equator will not be doing much work For the gx3v5 grid the ice model is typically run on 8 tasks with NX 4 NY 2 Running the ice model with NX 8 and NY 1 tasks on the gx3v5 grid wil result in an error since 8 does not divide evenly into the 100 longitude points When this happens the model will stop with an error message written to the log file If you are submitting the model to a batch queue with the number of processors modified from the default you will also have to modify the batch queue environment information at the top of the script The default setting for the IBM is total_tasks 8 node 1 These two
39. ls 21 An additional data file is necessary to use the ocean mixed layer within the ice model depending on the specified grid e pop_frc_gx1v3_010815 nc contains monthly averaged ocean forcing from POP output e pop_frc_gx3v5_040212 nc same as above but for the gx3v5 grid This file is renamed oceanmixed_ice nc when it is copied into the executable directory 5 1 Atmospheric Forcing The uncoupled ice model will run without atmospheric forcing It will use the fluxes set in subroutine init_fluz For atmospheric forcing the following datasets are available on the gx3v5 grid and can be read in using the module ice _flux_in F The directory where the data is located will have to be set in this module and not in the scripts The files are as follows wherever you put it atm gx3v5 ISCCPM MONTHLY RADFLX cldf 1997 dat wherever you put it atm gx3v5 ISCCPM MONTHLY RADFLX swdn 1997 dat wherever you put it atm gx3v5 MXA MONTHLY PRECIP prec 1997 dat wherever you put it atm gx3v5 NCEP 4XDAILY STATES dn10 1997 dat wherever you put it atm gx3v5 NCEP 4XDAILY STATES q 10 1997 dat wherever you put it atm gx3v5 NCEP 4XDAILY STATES t_10 1997 dat wherever you put it atm gx3v5 NCEP 4XDAILY STATES u_10 1997 dat wherever you put it atm gx3v5 NCEP 4XDAILY STATES v_10 1997 dat These files are in direct access binary files and the source is evident from the path names cldf 1997 dat and swdn 1997 dat contain the monthly averaged cloud fracti
40. mt_file that should be located in the executable directory There are commands in the scripts that copy these files from the input data directory rename them from global_ ICE_GRID grid and global ICE_GRID kmt to the default filenames shown in Table 7 The namelist variable pointer_file is set to the name of the pointer file containing the restart file name that will be read when model execution begins The pointer file resides in the scripts directory and is created initially by the ice setup script but is overwritten every time a new restart file is created It will contain the name of the latest restart file The default filename ice restart_file shown in Table 7 will not work unless some modifications are made to the ice setup script and a file is created with this name and contains the name of a valid restart file this variable must be set in the namelist More information on restart pointer files can be found in section 8 2 incond_dir restart_dir and history_dir are the directories where the initial condition file the restart files and the history files will be written respectively These values are set at the top of the setup script and have been modified from the default values to meet the requirements of the CCSM filenaming convention 16 Table 7 Namelist Variables for File Names Varible Type Default Value Description grid_file Character data domain grid Input filename containing grid informa tion kmt_file Character da
41. n as a log file is created for each run that contains information about how the run was set up and how it progressed A series of binary restart files necessary to continue the run are created A series of netCDF history files containing gridded instantaneous or time averaged output are also generated during a run These are described below 8 1 Stdout Output Diagnostics from the ice model are written to an ASCII file that contains information from the compilation a record of the input parameters and how hemispherically averaged maximum and minimum values are evolving with the integration Certain error conditions detected within the ice setup script or the ice model will also appear in this file Upon the completion of the simulation some timing information will appear at the bottom of the file The file name is of the form ice log LID where LID is a timestamp for the file ID It resides in the executable directory The frequency of the diagnostics is determined by the namelist parameter diagfreq 8 2 Restart Files Restart files contain all of the initial condition information necessary to restart from a previous simulation These files are in a standard IEEE 64 bit binary format A restart file is not necessary for an initial run but is highly recommended The initial conditions that are internal to the ice model produce an unrealistic ice cover that an uncoupled ice model will correct in several years The initial conditions from a restart
42. ncoupled model These directories contain the following files e Macros AIX contains build settings specific to ATX IBM SP3 e Macros IRIX64 contains build settings specific to IRIX64 SGI Origin e makdep c evaluates the code dependencies for the source code e Makefile is a generic gnumakefile There is a Macros lt OS gt file for each supported platform These files contain machine dependent preprocessor compiler and library information for building the model The Macros lt OS gt files for the uncoupled model have been simplified since most of the libraries used by the coupled model are not used by the uncoupled ice model If you are running the model on a platform other than those tested you will need to create a new Macros lt OS gt file and modify the paths and settings for your system In some cases CSIM has a set of options that are different from the default values at the top of the file These are after the line ifeq MODEL csim in the Macros lt OS gt files and are described below 3 4 1 CSIM Preprocessor Flags Preprocessor flags are activated in the form Doption in the Macros lt OS gt files The flags specific to the ice model are CPPDEFS CPPDEFS Dcoupled DNPROC_X NX DNPROC_Y NY D_MPI The option Dcoupled is set to activate the coupling interface This will include the source code in ice_coupling F for example For uncoupled runs it has been removed If a coupler other than the CCSM coupler is use
43. nmixed_ice_file gt oceanmixed_ice nc oceanmixed_ice_sst_init prntdiag_oceanmixed pointer_file rpointer ice false false 4 8 2 Example 2 Coupled Ice Only Model This example is the M configuration It is CSIM with the latm data atmosphere model data land model and the ocean mixed layer model within the ice model all communicating through the coupler The following modifications will be made to the namelist when the resolved scrips are created for the M configuration See the CCSM3 User s Guide http www ccsm ucar edu models ccsm3 0 ccsm on how to create scripts for the M configuration runid TER O01a T62_gx1v3 M bluesky 095234 oceanmixed_ice true oceanmixed_ice_sst_init oml_ice_sst_init 19 4 8 3 Example 3 Uncoupled Ice Model This example is the namelist from the uncoupled ice model that resides in the file csim setup csh npt has been modified since it determines the length of the uncoupled run The snow and ice albedos used by CCSM are not set in the name list The default values set in ice_init F are used cat lt lt EOF gt ice_in amp ice_nml runid CASE CASESTR runtype RUNTYPE gt istep0 0 dt 3600 0 gt ndyn_dt 1 ndte 120 npt 240 diagfreq 24 histfreq m dumpfreq d dump req n 5 gt hist_avg true restart RESTART print_points false kitd 1 gt kdyn 1 kstrength 1 evp_damping
44. o 4 Namelist Variables CSIM uses the same namelists for both the coupled and uncoupled models This section describes the namelist variables in the namelist ice_nml which determine time management output frequency model physics filenames and options for the mixed layer ocean model The ice namelists for the coupled model are now located in ccsm3 scripts CASE Buildnml_Prestage Modifications to the uncoupled namelist can be made in ccsm3 models ice csim4 src csim setup csh A script reads the input namelist at runtime and writes the namelist information to the file ice_in in the directory where the model executable is located Therefore the namelist will be updated even if the ice model is not recompiled The default values of ice_nml are set in ice_init F If they are not set in the namelist in the script they will assume the default values listed in Tables 3 8 which list all available namelist parameters The default values shown here are for the coupled model which is set up for a production run Several of the varialbes have different values for the uncoupeld which is set up for a 10 day test run with more frequent output Only a few of these variables are required to be set in the namelist these values are noted in the paragraphs below An example of the default namelist is shown in Section 4 8 1 Table 3 Namelist Variables for Time Management Varible Type Default Value Description runid Character unknown_runid Text us
45. on and downwelling shortwave prec 1997 dat is the monthly averaged precipitation in mm month The remaining files are the atmospheric density spe cific humidity air temperature and wind fields Note that these datasets are meant for testing the model and are not the best observational data for research Users are advised not to publish results based on these datasets To use this forcing the following lines in ice F need to be uncommented call init_getflux call getflux 6 Run Types The run types available for the coupled model are described in the CCSM User s Guide There are two run types available for the uncoupled ice model and are described in this section 6 1 Startup Runs If RUNTYPE is set to startup the model will read in the restart file that resides in CSIMDATA called iced 0001 01 01 8ICE_GRID 20lay The conditions in this file are for the gx1v3 grid and are from an equilibrium run using modified NCEP forcing The setup script will create a pointer file named rpointer ice with the name of the initial restart file in it Startup runs can also be initialized using data created within the ice model as described in the next section Using Initial Conditions from within CSIM Initial conditions can be calculated within the ice model in a subroutine called init_state in ice_init F Here the ocean surface is initialized at the freezing point everywhere north of 40 degrees and south of 40 degrees latitude allowing ice to form every
46. re equal to within a small value The output looks like Conservation error vice add_new_ice 11 14 185 Initial value 1362442 600400560 Final value 1362442 600400561 Difference 2 328306436538696D 10 shr_sys_abort ERROR ice Conservation error shr_sys_abort WARNING calling shr_mpi_abort and stopping shr_mpi_abort ice Conservation error 0 Non conservation can ocur if the ice model is receiving very bad forcing and is not able to deal with it This has occurred after a CFL violation in the ocean The timestep in the ocean may be decreased to get around the problem 9 4 MPDATA transport unstable The ice model dynamics is subcycled ndte times per timestep so that the elastic waves are damped before the next timestep When the value of ndte is too small an instability occurs the model execution stops and an error message similar to this example is written out to the log file mpdata phi 0 122707896960329384E 05 n 5 shr_sys_abort ERROR mpdata transport unstable shr_sys_abort WARNING calling mpi_abort and stopping To get around this problem increase the value of ndte in the namelist Reasonable values of this parameter are discussed in section 4 2 The model run can be restarted from the last set of restart files that were written before the execution halted 9 5 NX does not divide evenly into grid If you modify the number of tasks used by the ice model the model may stop with this error written to th
47. rectory or the standard output and error files for information Also 9 2 This try the following Delete the executable directory and rebuild the model Make sure that there is a Macros lt OS gt file for your platform Modify the directory paths for the libraries Make sure all paths and file names are set correctly in the scripts If changes were made to the ice_model_size F file in the source code directory they will be overwritten by the file in input_templates Negative Ice Area in Horizontal Remapping error is written from ice_transport_remap F when the ice model is checking for negative ice areas If it happens well into a model integration it can be indicative of a CFL violation The output looks like 60 60 60 60 60 60 60 60 New area lt 0 istep 119588 my_task i j n 4 21 380 1 Old area 0 960675000975677174E 05 New area 0 161808948357841311E 06 Net 0 976855895811461324E 05 shr_sys_abort ERROR remap transport negative area shr_sys_abort WARNING calling shr_mpi_abort and stopping shr_mpi_abort remap transport negative area 0 flux The dynamics timestep should be reduced to integrate past this problem Set gt ndyn_dt 2 in the namelist and restart the model When the job completes set the value back to 1 29 9 3 Conservation Error This error is written from ice_itd F when the ice model is checking that initial and final values of a conserved field a
48. s due to changes in the order of operations in calculating the global sums 2 4 3 Single Processor without MPI In the run script csim_run change NX and NY to 1 and BINTYPE to single or anything except MPI This value of BINTYPE will automatically change the preprocessor flags and the compiler name where necessary in the Macros lt OS gt file The model can be run interactively by typing csim_run 3 The CSIM Scripts The scripts for building the coupled and the uncoupled ice models are in separate directories The setup scripts for the coupled model are located in ccsm3 scripts The setup scripts for the uncoupled model are located in ccsm3 models ice csim4 src The directory structure of CSIM5 within CCSM is shown below ccsm3 main directory models EE RA scripts ok ok k ok k k ok ox blds Fns ice build scripts for coupled model Makefile KOK kx OK ok ox ok ok ok ok macros csim4 active ice component docs ss s a Se se src CSIM documentation OK OK OK ok ok OK kk bid input_templates source build scriptsr l for uncoupled Makefile macros resolution dependent F90 source ice model for uncoupled input files code ok k ok k OK Ok kk ice model 3 1 Coupled Model Scripts The CCSM3 scripts have been significantly upgraded from CCSM2 and are based on a completely differ ent design philosophy The new scr
49. ssor without MPI Running this configuration will verify that the library and compiler options are properly set in the Macros lt OS gt file all the input data is in the correct place and the environment variables are set correctly before any further changes are made to the scripts or the source code This will also provide benchmark output NOTE If you are running this model a machine other than an IBM running AIX or an SGI running IRIX you may need to make an equivalent Macros lt OS gt file with the paths and settings modified for your system Before you start modifications will be needed in the run script csim_run to set the directories for the source code input data and executables The following is a list of the environment variables that will need to be changed by the user setenv CSIMDIR home LOGNAME csim5 directory of scripts setenv CSIMDATA fs cgd csm inputdata ice csim4 dir for input data setenv CASE test me Case name setenv EXEROOT ptmp LOGNAME CASE setenv SHRCODE CSIMDIR run model here dir for share code CSIMDIR is the top directory of the source code where the scripts are located CSIMDATA is the directory where the input data sets are located CASE is a string with a case name for the model run and should be kept short since it is used in path and file names EXEROOT is typically a large temporary disk where the executable files and input data sets will reside during execution Information output b
50. ta domain kmt Input filename containing land mask in formation pointer_file Character ice restart_file Pointer file that contains the name of the restart file incond dir Character ed Directory where netCDF initial condi tion file is output restart_dir Character ps Directory where restart files are output history_dir Character oY Directory where history files are output incond_file Character incond Root name of netCDF output initial condition file dump_file Character iced Prefix for output file containing restart information history_file Character iceh Root name of history files Table 8 Namelist Variables for Ocean Mixed Layer Model Varible Name Type Default Value Description oceanmixed_ice Logical false If true run model with ocean mixed layer model oceanmixed_ice_file Character oceanmixed_ice nc Name of file with ocean mixed layer data oceanmixed_ice_sst_init Logical false If true Jan 1 sst is read from forcing file prntdiag_oceanmixed Logical false If true print ocean mixed layer di agnostics This allows each type of output file to be written to a separate directory If the default values are used all of the output files will be written to the executable directory incond_file dump_file and history_file are the root filenames for the initial condition file the restart files and the history files respectively These strings have been determined by the requirements of th
51. that the path and file name in the rpointer are correct and that the restart file exists in the correct location 31 References Bitz C M M Holland M Eby and A J Weaver 2001 Simulating the ice thickness distribution in a coupled climate model J Geophys Res 106 2441 2463 Bitz C M and W H Lipscomb 1999 An energy conserving thermodynamic model of sea ice J Geophys Res 104 15 669 15 677 Hibler W D 1979 A dynamic thermodynamic sea ice model J Phys Oceanogr 9 815 846 Hunke E C 2001 Viscous plastic sea ice dynamics with the evp model Linearization issues J Comp Phys 170 18 38 Hunke E C and J K Dukowicz 1997 An elastic viscous plastic model for sea ice dynamics J Phys Oceanogr 27 1849 1867 Hunke E C and J K Dukowicz 2003 The sea ice momentum equation in the free drift regime Los Alamos National Laboratory Tech Rep LA UR 03 2219 Hunke E C and W H Lipscomb 2002 CICE the Los Alamos sea ice model documentation and software User s Manual T 3 Fluid Dynamics Group Los Alamos National Laboratory Tech Rep LACC 98 16 v 3 Hunke E C and W H Lipscomb 2004 CICE the Los Alamos Sea Ice Model Documentation and Software User s Manual T 3 Fluid Dynamics Group Los Alamos National Laboratory Tech Rep LA CC 98 16 v 3 1 Lipscomb W H 2001 Remapping the thickness distribution in sea ice models J Geophys Res 106 13 989 14 000 Lipscomb W H
52. the most commonly used configurations Variables that are commonly changed directly in the namelist are the timestep dt and the number of subcycles per timestep in the ice dynamics ndte 4 8 1 Example 1 CCSM Fully Coupled The following example is the namelist used for CCSM fully coupled or the B configuration The variables that are still set to shell script variables have been set at the top of csim buildnml_prestage csh or in other scripts A completely resolved version of the namelist will be written to ice_in in the executable directory 18 cat lt lt EOF gt ice_in amp ice_nml runid TER O1a T85_gx1v3 B bluesky 105608 runtype runtype istep0 0 dt 3600 0 ndte 120 gt ndyn_dt 1 gt npt 99999 diagfreq 24 gt histfreq m dumpfreq Sys dumpfreq_n 1 gt hist_avg true restart restart print_points false kitd 1 gt kdyn 1 gt kstrength 1 evp_damping false Snow_into_ocn true advection remap gt grid_type displaced_pole grid_file data domain grid kmt_file data domain kmt incond_dir runinidir incond_file CASE csim i restart_dir runrstdir dump_file CASE csim r history_dir runhstdir history_file CASE csim h albicev 0 73 albicei 0 33 albsnowv 0 96 albsnowi 0 68 no_ice_ic no_ice_ic oceanmixed_ice false ocea
53. to run CSIM uncoupled e Operating System IBM AIX or SGI IRIX64 e Tools gunzip gnumake e Compilers Fortran90 C e Permanent disk space e Temporary disk space Libraries MPI netCDF Input Data 10 86 MB for gx3v5 grid e CSIM source code 0 83 MB Atmospheric Forcing Data 2 7 GB for gx3v5 grid 2 2 Downloading Source Code and Input Datasets The source code to run CSIM fully coupled or uncoupled and the required datasets can be obtained via a web download The source code input datasets and documentation for CCSM are available via the web at http www ccsm ucar edu models ccsm3 0 Instructions for downloading and untarring the CCSM3 0 distribution are in the CCSM3 User s Guide If you have the source code for CCSM you also have all the source code to run CSIM uncoupled If you only need the source code and input files for the uncoupled model it is available at http www ccsm ucar edu models ice csim5 distribution The source code input data and atmospheric forcing for the uncoupled ice model come in the following form e csim5_code tar gz e csim5_inputdata_gx3v5 tar gz for the low resolution grid e csim5_inputdata_gx1v3 tar gz for the high resolution grid e csim5_atmforcing_gx3v5 tar gz To uncompress and untar these files use the following Unix gunzip and tar commands gunzip c csimb_code tar gz tar xf gunzip c csim5_inputdata_gx3v5 tar gz tar xf gunzip c csim5_atmforcing gx3v5 tar gz tar xf
54. ult thickness distribution consists of five ice categories gicefields_nml f_sst false f_sss false f_uocn false f_vocn false f_frzmlt false gt f_strtltx false gt f_strtlty false f_mlt_onset false f_frz_onset false f_aice6 false f_aice7 false f_aice8 false f_aice9 false gt f_aicel0 false f_vicel false f_vice2 false f_vice3 false f_vice4 false f_viced false f_vice6 false f_vice7 false f_vice8 false f_vice9 false f_vice10 false 5 Model Input Datasets Both the coupled and uncoupled CSIM require a minimum of three files to run e global ICE_GRID grid is a binary file containing grid information and is renamed data domain grid when it is copied to the executable directory e global_ ICE_GRID kmt is a binary file containing land mask information and is renamed data domain kmt e iced 0001 01 01 ICE_GRID 20lay or iced 0001 01 01 gx3v5 040213 are binary files contain ing initial condition information for the gx1v3 and gx3v5 grids respectively The thickness distribution in this restart file contains 5 categories each with 4 layers Depending on the grid selected in the scripts the appropriate global and iced files will be copied and renamed in the executable directory Currently only gx3v5 and gxlv3 grids are supported for the ice and ocean mode
55. ume category 9 m f vicel0 ice volume category 10 m f uvel zonal ice velocity cms continued on next page 27 continued from previous page f_vvel f_fswdn f_flwdn f_snow f_snow_ai f_rain f_rain ai f_sst f_sss f_uocn f_vocn f_frzmlt f_fswabs f_fswabs_ai f albsni f_aldvr f_aldvi f_flat f_flat_ai f_fsens f_fsens_ai f_flwout f_flwout_ai f_evap f_evap_ai f_Tref f_Qref f_congel f_frazil f_snoice f_meltb f_meltt f meltl f_fresh f_fresh ai f_fsalt f_fsalt_ai f_fhnet f_fhnet_ai f_fswthru f_fswthru_ai f_strairx f_strairy f_strtltx f_strtlty f_strcorx f_strcory f_strocnx meridional ice velocity downwelling solar flux downwelling longwave flux snow fall rate received from coupler snow fall rate on ice cover rain fall rate received from coupler rain fall rate on ice cover sea surface temperature sea surface salinity zonal ocean current meridional ocean current freeze melt potential absorbed solar flux sent to coupler absorbed solar flux in snow ocn ice snow ice broad band albedo visible direct albedo near infrared direct albedo latent heat flux sent to coupler ice atm latent heat flux sensible heat flux sent to coupler ice atm sensible heat flux outgoing longwave flux sent to coupler ice atm outgoing longwave flux evaporative water flux sent to coupler ice atm evaporative water flux 2 m reference temperature 2 m reference specific humidity basal ice growth frazil i
56. where in these regions While running the ice model with a data ocean will melt any extra ice during the first year of integration is not recommended that these initial conditions be used when running the ice model coupled to an active ocean model The advantage of using this input is that it is not grid or land mask dependent To use these initial conditions set RESTART in csim setup csh 22 set RESTART false Initializing the model using a restart file from an equilibrium run will result in a more physically reasonable scenario than the initial conditions set within CSIM The drawbacks are that the data is binary difficult to edit and is date and grid dependent A restart file will be used as initial conditions if set RESTART true in csim setup csh 6 2 Continue Runs A continue run is an exact continuation of a previous run This means that the run will produce a bit for bit answer as if the existing run had not stopped The input data file is determined by the filename set in the restart pointer file see section 8 2 It is assumed that CASE has not changed For a continue run the only change required in the run script is to set RUNTYPE continue The date will continue from the previous run since it is read in from the restart file 7 Changing the Number of Ice Thickness Categories The number of ice thickness categories affects ice model input files in three places e NCAT in the run script e The input template fi
57. with four layers in each category To create an initial condition file for a different number of categories or layers these steps should be followed e Set NCAT to the desired number of categories in csim_run uncoupled or ccsm3 scripts CASE Buildexe csim buildexe csh coupled 23 e Set the namelist variable dumpfreq m in csim setup csh uncoupled or ccsm3 scripts CASE Buildnml Prestage csim buildnml prestage csh coupled to print out restart files monthly e Set the namelist variable restart false in csim setup csh uncoupled or ccsm3 scripts CASE Buildnml Prestage csim buildnml_prestage csh coupled to use the initial conditions within the ice model e Create an input template or use an existing one with the desired number of categories e Run the model to equilibrium e The last restart file can be used as an initial condition file e Change the name of the last restart file to iced 0001 01 01 GRID e Copy the file into the input data directory or directly into the rest directory under the executable directory Note that the date printed inside the binary restart file will not be the same as 0001 01 01 For coupled runs BASEDATE will be the starting date and the date inside the file will not be used For uncoupled runs the starting date may have to be set in the code or changed in the restart file 8 Output Data The ice model produces three types of output data A file containing ASCIT text also know
58. y the model will also be written to EXEROOT The location of SHRCODE will depend on where the source code was downloaded If it was obtained with CCSM3 0 distribution the SHRCODE directory will be under ccsm3 models csm_share If you only have the source code for CSIM the share code will be in the same directory as the rest of the ice model source code 2 4 1 Multiple Processors with MPI The default setting will use eight processors two nodes with four processors each and the Message Passing Interface MPI so simply submit the job To submit a run to the batch queue on the IBM type 11submit csim_run To submit the job to the batch queue on an SGI type qsub lt csim_run bsub lt csim_run or the appropriate command depending on your batch queueing system On some systems it is possible to run multiple processor jobs interactively 2 4 2 Single Processor with MPI In the run script csim_run change NX and NY to 1 If you are submitting to a batch queue the number of processors you are requesting will also need to be modified in the batch queue environment information at the top of the script For example for the IBM the following two lines should be modified to total_tasks 1 node 1 The model can also be run interactively by typing csim_run NOTE When you change the number of processors the output you get in the log file will be slightly different from that calculated with a different number of processors This i

Community Sea Ice Model (CSIM) User`s Guide Version 5.0

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