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2. Using CCM3.6

2.5 Model Output Datasets

CCM3 produces a series of binary history files containing the atmospheric gridpoint data generated during the course of a run and a series of restart files necessary to continue the run.  These will be described below.
 

2.5.1 Model History Files

History files contain model data values written at specified times during a run. The user can specify the frequency at which the data are written. Options are also available to record averaged, instantaneous, maximum, or minimum field values.  Namelist options to control the frequency and type of output apply to all fields on a history file.  They will all be output at the same frequency (i.e. daily) and will be of the same type (i.e. averaged; except for PHIS and ORO which are always instantaneous).  If the user wishes to see a field written at different time frequencies (e.g. daily, hourly) additional history files must be declared.

Two kinds of history files can be output, "primary" or "auxiliary". A primary history file is always output, whereas auxiliary files are optional. The exact contents of the primary file may be customized using namelist variables PRIMARY and EXCLUDE. Auxiliary history files are created only if requested by the user via namelist variable AUXF. Up to five auxiliary history files can be declared if namelist variable INITHIST is set to 'NONE' and four otherwise.

History files may be examined by various postprocessors. One example is the CCM Modular Processor, which still exists but is no longer maintained.  Alternatively, "ccm2nc", a tool to convert ccm-history files to netCDF format, is now supported. This allows a user to employ any of a number of available tools (both commercial and share-ware) to visualize or otherwise analyze their output history files. Examples include the "CSM Processor" NCAR Graphics package, FERRET, ncview, MATLAB, AVS, IDL, and Yorick. For a list of software tools for interacting with netCDF files view the UNIDATA netCDF web-site: http://www.unidata.ucar.edu/packages/netcdf/software.html.

Values recorded for fields on a history file can be represented in one of four different ways.  Data may be time averaged since the last write to the history file, instantaneous, or point-by-point maximum or minimum over the time interval.  Namelist variable NINAVG(i) controls this function (index "i" here refers to the file index, 1 means the primary file, 2 means 1st auxiliary, etc.). Possible values are 'A' - time averaged, 'I' - instantaneous, 'M' - point minimum, 'X' - point maximum, and 'Q' - monthly averaged ('Q' is allowed only to apply to the primary history file). The default value for each history file is 'A'. Fields in a history file are each of the type indicated by NINAVG(i), except ORO and PHIS which are always instantaneous.

The time frequency at which data are written to the history file is specified by NHTFRQ(i). As an example, consider the namelist input shown in Example 5. Here, NHTFRQ(1)=72 and NINAVG is set to 'A'. Every 72 timesteps a time sample of data is written to the primary history file, with each field being time averaged over the previous 72 timesteps.

The number of time samples written to a single history file, primary or auxiliary, is set via namelist variable  MFILT(i).  The packing density of fields in each history file is set with namelist variable NDENS(i) (only available on an NCAR Cray).  This namelist variable should only be 1, 2, or 4.  A packing density of 4 to 1 (NDENS(i)=4) could result in significant loss of precision.

Refer to Table 2.5 and Table 2.6 in Sec. 2.2  for a complete description of all history file namelist variables.
 

2.5.1.1 Primary History File

The following table contains a list of fields, referred to as the "Master Field List", that can currently be written to the primary or auxiliary history files. The first column indicates whether the field will automatically be included on the primary history file. Fields not on the default primary history file may be included via namelist variable PRIMARY (see "Example 6 -- Initial Run, with additional fields " ).  Conversely, any fields included by default may be removed using namelist variable EXCLUDE  (refer to "Example 5 -- Branch Run" ).  Some field names appearing in the second column contain two upper case letters followed by two lower case x's (e.g. TRxx, DCxx, etc.). These fields correspond to passive tracer constituents that may be transported. In the history file, the two x's will be replaced by a two-digit tracer number (refer to "Adding New Constituents). The third column, associates the history file field name with its mathematical symbol as given in Description of the NCAR Community Climate Model (CCM3) (Kiehl et al., 1996). The fourth column provides a brief description of the field. In the column labeled "NL" a "1" indicates a single-level field and an "N" indicates a multilevel field (on plev vertical levels). The last column in the table shows the physical units associated with each field.
 

Table 2.13: Master Field List

 
Default File?
Field Name
Symbol
Field Description
NL
Units
Basic State variables
yes Q  q specific humidity N  Kg/Kgair
yes TRxx q advected tracers other than specific humidity N  Kg/Kgair
yes NAxx q non-advected tracers N  Kg/Kgair
yes  T T Temperature N K 
yes  U u zonal wind component  N m/s
yes  V v meridional wind component  N m/s 
yes  PS Ps surface pressure 1 Pa 
yes  TS T surface temperature N K
yes  TS1 Ts ice temperature (level 1) 1  K
yes  TS2 T2 ice temperature (level 2)  1  K
yes  TS3 T3 ice temperature (level 3) 1  K
yes  TS4 T4 ice temperature (level 4) 1  K
yes  PHIS surface geopotential 1 m2/s2
yes  ETADOT Vertical motion on half levels N 1/s
Derived variables
no  VT vT Meridional heat transport N K * m/s
no  VZ vz Meridional transport of gravitational potential energy N m3/s3
no  VQ vq Meridional water transport N m/s
no  VVPUU v2+u2 Kinetic energy N m2/s2
no  RELHUM RH Relative humidity N fraction
no  Z3 z Geopotential height (above sea level) N m
no  MQ Water mass N Kg/m2
no  PSL Psl Sea level pressure 1 Pa
yes OMEGA vertical pressure velocity N  Pa/s
yes  LWSH   Liquid water scale height 1 m
Tracers
yes  DCxx tracer tendency from adjustment physics N (Kg/Kgair)/s
yes  TAxx total advection tendency of tracer N (Kg/Kgair)/s
yes  VDxx   vertical diffusion tendency of tracer N (Kg/Kgair)/s
no  HAxx   horizontal advection tendency of tracer N (Kg/Kgair)/s
no  VAxx   vertical advection tendency of tracer N (Kg/Kgair)/s
no  O3VMR   O3 Volume mixing ratio N fraction
no  DFxx   SLT fixer tendency of tracer N (Kg/Kgair)/s
no  TExx   time tendency of tracer N (Kg/Kgair)/s
no  SSxx   tracer source/sinks (pcnst-1 values) N (Kg/Kgair)/s
no  SFxx   tracer surface fluxes (pcnst-1 values) N (Kg/m2)/s
Horizontal Diffusion
no  DUH   u horizontal diffusive heating rate N K/s
no  DVH   v horizontal diffusive heating rate N K/s
yes  DTH T horizontal diffusion N K/s
Precipitation
yes  PRECL Ps large-scale stable precipitation 1 m/s
yes  PRECC P convective precipitation 1 m/s
no  PRECSL   large-scale stable snowfall 1 m/s
no  PRECSC   convective snowfall 1 m/s
no  CMFDQR   rainout (condensation) N (Kg/Kgair)/s
no  DQP Rcs+Rls q tendency from rainout  N  (Kg/Kgair)/s
Surface variables
yes  ORO   surface type flag: 
= 0 for ocean 
= 1 for land 
= 2 for sea ice		 1 flag
yes  SNOWH Sn water equivalent snow depth 1 m
yes  TREFHT   Surface dependent reference height temperature  1 K
yes  SHFLX surface sensible heat flux  1 W/m2
yes  LHFLX surface latent heat flux  1 W/m2
yes  QFLX surface water flux 1 (Kg/m2)/s
no  SICTHK   sea-ice thickness; on default file if using the SOM 1 m
yes  SGH   standard deviation of orography 1 m
Planetary Boundary Layer
yes  PBLH   height of planetary boundary layer 1 m
yes USTAR u* surface friction velocity 1  m/s
no  CGH   pbl nonlocal transport, heat N K/m
no  CGQ   pbl nonlocal transport, humidity N 1/m
yes  CGS   Counter-gradient coefficient on surface kinematic fluxes N s/m2
yes TPERT pbl plume temperature perturbation 1  K
yes QPERT pbl plume moisture perturbation 1  Kg/Kg
yes KVH Kθ diffusivity for heat N m2/s
no  KVM Km diffusivity for momentum N m2/s
no  DUV   u vertical diffusion N m/s2
no  DVV   v vertical diffusion N m/s2
yes DTV   T vertical diffusion tendency  N  K/s
Convection
yes ZMDQ   Q tendency - Zhang moist convection 1  (Kg/Kgair)/s
yes ZMDT   T tendency - Zhang moist convection 1  (Kg/Kgair)/s
yes CMFDT T tendency from moist convection N  K/s
yes CMFDQ q tendency from moist convection  N  (Kg/Kgair)/s
yes CMFMC Mc total convective mass flux  N  (Kg/Kgair)/s
no  CMFSL Fs-Ll convective liquid water static energy flux N  W/m2
no  CMFLQ Fq+l convective total water flux  N  W/m2
yes CNVCLD Acc convective cloud fraction 1  fraction
Radiation
yes FSNS FSN(Ps) net downward solar flux at surface 1  W/m2
yes FLNS FLN(Ps) net upward longwave flux at surface 1  W/m2
yes FLNT FSN(PT) net upward longwave flux at top of model 1  W/m2
yes FSDS   Flux Shortwave Downwelling at Surface 1  W/m2
yes FSNIRT   near-IR shortwave flux absorbed at TOA 1 W/m2
yes FSNRTC   clear-sky near-IR shortwave flux absorbed at TOA 1 W/m2
yes FSNIRTSQ   near-IR Shortwave flux absorbed at TOA >= 0.7 microns 1 W/m2
yes FSNT   net downward solar flux at top of model 1  W/m2
yes FLNTC FLN(PT)clr net clearsky upward longwave flux at top 1  W/m2
yes FSNTC FSN(PT)clr net clearsky downward solar flux at top 1  W/m2
yes FLNSC FLN(PS)clr net clearsky upward longwave flux at surface 1  W/m2
yes FSNSC FSN(PS)clr net clearsky downward solar flux at surface 1  W/m2
no HR   Heating rate. N K/s
yes SRFRAD radiative flux absorbed at the surface 1  W/m2
yes QRS Qs solar heating rate N  K/s
yes QRL Qlw longwave heating rate N  K/s
yes SOLIN SI solar insolation  1  W/m2
yes SOLL   downward near IR direct solar to surface. 1 W/m2
yes SOLS   downward visible direct solar to surface. 1 W/m2
yes SOLLD   downward near IR diffuse solar to surface. 1 W/m2
yes SOLSD   downward visible diffuse solar to surface. 1 W/m2
Clouds
yes CLDTOT ATc random overlap total cloud cover 1  fraction
yes CLDLOW ALc random overlap low cloud cover (lower than 700 mbar) 1  fraction
yes CLDMED AMc random overlap medium cloud cover (700 to 400 mbar) 1  fraction
yes CLDHGH AHc random overlap high cloud cover (400 to 50 mbar) 1  fraction
no  TOTLWP   total liquid water path 1 fraction
yes CLOUD Ac cloud fraction N  fraction
no  SETLWP   prescribed liquid water path N g/m2
no  CLDLWP   cloud-weighted liquid water path N g/m2
yes  EFFCLD effective cloud fraction N  fraction
Tendencies
no  UTEND   u tendency N m/s2
no  VTEND   v tendency N m/s2
no  TTEND   T tendency N K/s
no  LPSTEN   surface pressure tendency 1 Pa/s
Surface Stress
yes TAUX zonal surface stress 1  N/m2
yes TAUY meridional surface stress 1  N/m2
yes UTGW gravity wave drag u tendency  N  m/s2
yes VTGW gravity wave drag v tendency  N  m/s2
yes TAUGWX gravity wave drag zonal surface stress 1  N/m2
yes TAUGWY gravity wave drag meridional surface stress 1  N/m2
yes DTCOND T tendency from adjustment physics N  K/s
 
Fields are written to the history buffer with a call to subroutine outfld (see Sec. 3.5 and Sec. 4.2 for more details). Due to efficiency considerations, calls to outfld for most "inactive" fields (i.e. those not on the default primary history file) are commented out in the code. In order to activate an inactive field either to the primary history file via PRIMARY, or to an auxiliary history file via AUXF, the user must remove the C from column one of the corresponding call to outfld for the particular field. The order in which fields are written to the history file is determined at run time via a hashing algorithm. Hence, the order in which the default fields appear in Table 2.13 does not necessarily reflect the actual storage order of fields in the file.

A namelist option is available to produce a monthly-averaged primary history file. By setting NINAVG(1)='Q', the fields on the primary history file (excluding PHIS and ORO which are always instantaneous) will be averaged over the period beginning from the first timestep of the current month up to and including the last timestep of that month. Each monthly averaged history file will contain exactly one time slice of data, regardless of the values of MFILT(1) and NHTFRQ. In addition to those fields shown as "on" by default in the Master Field List, a monthly-averaged primary history file includes 14 other fields by default. These fields are shown in Table 2.14.  Due to these additional fields, the history buffer will require additional memory whether stored in-core, or out-of-core on the SSD.  For a standard T42 resolution, the memory request should be increased by 1Mw for a monthly averaged run over what would be required if the run were not  monthly averaged. See "Creating and Running the Executable" for information about specifying memory. As with any field on the history file, the additional fields may be excluded from the primary file using the EXCLUDE namelist variable.
 

Table 2.14: Additional Fields on a Monthly-Averaged Primary History File
Field Name
Symbol
Field Description
NL
Units
VT vT Meridional heat transport N K*m/s
VZ vz Meridional transport of gravitational potential energy N m3/s3
VQ vq Meridional water transport N m/s
VVPUU v2+u2 Kinetic energy N m2/s2
RELHUM RH Relative humidity N fraction
Z3 z Geopotential height (above sea level) N m
MQ Water mass N Kg/m2
PSL Psl Sea level pressure 1 Pa
OMEGAUP Average of omega when vertical motion is up N Pa/s
NUMOMGUP Percentage of time vertical motion is up N fraction
CLOUDUP Average of cloud when vertical motion is up N fraction
DPSLON Longitudinal derivative of surface pressure N m/s2
DPSLAT Latitudinal derivative of surface pressure N m/s2
 

2.5.1.2 Auxiliary History Files

CCM3.6 has the capability to write multiple history files simultaneously. All fields that are declared "active" (default) in the Master Field List appear on the primary history file. The user may declare additional files, known as "auxiliary" history files, via namelist variable AUXF. The capability to write auxiliary history files provides the user flexibility in the frequency at which various history data are written. Auxiliary files may contain the same or different fields as compared with the primary history file.  These fields may be written on different timesteps (and therefore have different averaging periods), with different packing densities, different averaging type (A, I, M, or X), and with a different number of time samples per file. A user may specify up to four auxiliary history files if INITHIST is set to MONTHLY or YEARLY and up to five auxiliary history files otherwise.

Why would a user want to write an auxiliary history file? Perhaps there are additional fields resulting from a new parameterization which should be reported more frequently than the primary history file fields. The auxiliary file provides a means of doing this while avoiding the waste of resources required to write the primary file more frequently. The use of namelist variable AUXF in declaring two auxiliary history files is demonstrated in "Example 5 -- Branch Run" . An auxiliary file may contain any number of fields up to the number of fields on the Master Field List. Fields may be removed from the primary file and placed on an auxiliary file for the added convenience of smaller

2.5.1.3 Model generated initial condition dataset files

During a model simulation, initial condition datasets are generated periodically by default. These are simply auxiliary history files containing instantaneous values for only those fields needed to start an initial run. The naming convention for these files (which is different for the other auxiliary files) is ccmi_yyyymmdd_sssss, where yyyy is the year, mm is the month, dd is the day and sssss is the seconds. The output frequency of the files is controlled by namelist variable INITHIST and is independent of the output frequency of other auxiliary files. Note that these datasets must be converted to netCDF format before they can be used as input by the model.

2.5.1.4 Naming the Primary and Auxiliary History Files

Primary history volumes which are not monthly averaged will be named with an "h" followed by a four-digit number. For example, on a typical initial run, the first primary history file written is named "h0001". Once this first disk file has been filled with MFILT(1) time samples, it is closed and new primary history file is opened. This new file, the second in the series, is named h0002. Subsequent primary history files will be named h0003, h0004, etc. There are two exceptions to this naming rule. First, if namelist variable STFNUM is set, naming will begin with this number. For instance, if STFNUM=123, then the first primary history file will be named h0123. Second, if the primary history file is monthly averaged, then the filename will be composed of the year and month of the model date. For instance, if the primary history file is being written at the end of the ninth month of year 26, the file name would be 0026-09 (see "Example 8 -- Generate a Monthly-Averaged History File" ).

Naming of the auxiliary history files is very similar to the primary history file. The first auxiliary file is named with an "ha" followed by a four-digit number. The second auxiliary history file is named with an "hb" followed by a four-digit number, etc. Thus, files named ha0001, ha0002,...  will be generated for the first auxiliary history file, and hb0001, hb0002,...  for the second auxiliary history file, etc.

Sub Sections

    2.5.1 Model History Files
    2.5.2 Restart Datasets
    2.5.3. Mass Store Archiving.

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