CMOR user input

{
           "_control_vocabulary_file": "CMIP6_CV.json",
           "_cmip6_option":           "CMIP6",

           "tracking_prefix":        "hdl:21.14100",
           "activity_id":            "ISMIP6",

           "branch_method":          "standard",
           "branch_time_in_child":   "365.0",

           "#output":                "Output Path where files are written",
           "outpath":                "CMIP6",

           "#experiment_id":         "CMIP6 valid experiment_ids are found in CMIP6_CV.json",
           "experiment_id":          "piControl-withism",
           "sub_experiment_id":      "none",
           "sub_experiment":         "none",

           "source_type":            "AOGCM ISM AER",
           "parent_mip_era":         "N/A",
           "mip_era":                "CMIP6",
           "calendar":               "360_day",
           "branch_time":            "1.34",

           "realization_index":      "11",
           "initialization_index":   "1",
           "physics_index":          "1",
           "forcing_index":          "1",

           "#contact ":              "Not required",
           "contact ":              "Python Coder (coder@a.b.c.com)",

           "#history":               "not required, supplemented by CMOR",
           "history":                "Output from archivcl_A1.nce/giccm_03_std_2xCO2_2256.",

           "#comment":               "Not required",
           "comment":                "Equilibrium reached after 30-year spin-up after which data were output starting with nominal date of January 2030",

           "#references":            "Not required",
           "references":             "Model described by Koder and Tolkien (J. Geophys. Res., 2001, 576-591).  Also see http://www.GICC.su/giccm/doc/index.html  2XCO2 simulation described in Dorkey et al. '(Clim. Dyn., 2003, 323-357.)'",

           "grid":                   "gs1x1",
           "grid_label":             "gr",
           "nominal_resolution":     "5 km",

           "institution_id":         "PCMDI",

           "parent_activity_id":     "CMIP",
           "parent_experiment_id":   "histALL",
           "parent_source_id":       "GFDL-CM2-1",
           "parent_variant_label":   "r1i1p1f3",


           "#run_variant":           "Description of run variant (Recommended).",
           "run_variant":            "forcing: black carbon aerosol only",

           "#source_id":              "Model Source",
           "source_id":               "PCMDI-test-1-0",

           "#source":                "source title, first part is source_id",
           "source":                 "PCMDI-test 1.0",


           "#output_path_template":   "Template for output path directory using tables keys or global attributes",
           "output_path_template":    "<activity_id><institution_id><source_id><experiment_id><variant_label><table><variable_id><grid_label><version>",
           "output_file_template":    "<variable_id><table><experiment_id><source_id><variant_label><grid_label>",

           "license":                  "CMIP6 model data produced by PCMDI is licensed under a Creative Commons Attribution \"Share Alike\" 4.0 International License (http://creativecommons.org/licenses/by/4.0/). Use of the data should be acknowledged following guidelines found at https://pcmdi.llnl.gov/home/CMIP6/citation.html. [Permissions beyond the scope of this license may be available at http://pcmdi.llnl.gov.] Further information about this data, including some limitations, can be found via the further_info_url (recorded as a global attribute in data files). The data producers and data providers make no warranty, either express or implied, including, but not limited to, warranties of merchantability and fitness for a particular purpose. All liabilities arising from the supply of the information (including any liability arising in negligence) are excluded to the fullest extent permitted by law."

}

Fortran source code

!!$pgf90 -I/work/NetCDF/5.1/include -L/work/NetCDF/5.1/lib -l netcdf -L. -l cmor Test/test_dimensionless.f90 -IModules -o cmor_test
!!$pgf90 -g -I/pcmdi/charles_work/NetCDF/include -L/pcmdi/charles_work/NetCDF/lib -lnetcdf -module Modules -IModules -L. -lcmor -I/pcmdi/charles_work/Unidata/include -L/pcmdi/charles_work/Unidata/lib -ludunits Test/test_dimensionless.f90 -o cmor_test

MODULE local_subs

  USE cmor_users_functions
  PRIVATE
  PUBLIC read_coords, read_time, read_3d_input_files, read_2d_input_files
CONTAINS
  
  SUBROUTINE read_coords(alats, alons, plevs, bnds_lat, bnds_lon)

    IMPLICIT NONE
    
    DOUBLE PRECISION, INTENT(OUT), DIMENSION(:) :: alats
    DOUBLE PRECISION, INTENT(OUT), DIMENSION(:) :: alons
    DOUBLE PRECISION, INTENT(OUT), DIMENSION(:) :: plevs
    DOUBLE PRECISION, INTENT(OUT), DIMENSION(:,:) :: bnds_lat
    DOUBLE PRECISION, INTENT(OUT), DIMENSION(:,:) :: bnds_lon
    
    INTEGER :: i
    
    DO i = 1, SIZE(alons)
       alons(i) = (i-1)*360./SIZE(alons)
       bnds_lon(1,i) = (i - 1.5)*360./SIZE(alons)
       bnds_lon(2,i) = (i - 0.5)*360./SIZE(alons)
    END DO
    
    DO i = 1, SIZE(alats)
       alats(i) = (size(alats)+1-i)*10
       bnds_lat(1,i) = (size(alats)+1-i)*10 + 5.
       bnds_lat(2,i) = (size(alats)+1-i)*10 - 5.
    END DO
  
    DO i = 1, SIZE(plevs)
       plevs(i) = i*1.0e4
    END DO
      plevs = (/100000., 92500., 85000., 70000.,&
       60000., 50000., 40000., 30000., 25000., 20000.,&
       15000., 10000., 7000., 5000., 3000., 2000., 1000., 500., 100./)
    
    RETURN
  END SUBROUTINE read_coords

  SUBROUTINE read_time(it, time, time_bnds)
    
    IMPLICIT NONE
    
    INTEGER, INTENT(IN) :: it
    DOUBLE PRECISION, INTENT(OUT) :: time
    DOUBLE PRECISION, INTENT(OUT), DIMENSION(2,1) :: time_bnds
    
    time = (it-0.5)*30.
    time_bnds(1,1) = (it-1)*30.
    time_bnds(2,1) = it*30.
    
    RETURN
  END SUBROUTINE read_time
  
INCLUDE "reader_2D_3D.f90"

END MODULE local_subs


PROGRAM ipcc_test_code
!
!   Purpose:   To serve as a generic example of an application that
!       uses the "Climate Model Output Rewriter" (CMOR)

!    CMOR writes CF-compliant netCDF files.
!    Its use is strongly encouraged by the IPCC and is intended for use 
!       by those participating in many community-coordinated standard 
!       climate model experiments (e.g., AMIP, CMIP, CFMIP, PMIP, APE,
!       etc.)
!
!   Background information for this sample code:
!
!      Atmospheric standard output requested by IPCC are listed in 
!   tables available on the web.  Monthly mean output is found in
!   tables A1a and A1c.  This sample code processes only two 3-d 
!   variables listed in table A1c ("monthly mean atmosphere 3-D data" 
!   and only four 2-d variables listed in table A1a ("monthly mean 
!   atmosphere + land surface 2-D (latitude, longitude) data").  The 
!   extension to many more fields is trivial.
!
!      For this example, the user must fill in the sections of code that 
!   extract the 3-d and 2-d fields from his monthly mean "history" 
!   files (which usually contain many variables but only a single time 
!   slice).  The CMOR code will write each field in a separate file, but 
!   many monthly mean time-samples will be stored together.  These 
!   constraints partially determine the structure of the code.
!
!
!   Record of revisions:

!       Date        Programmer(s)           Description of change
!       ====        ==========              =====================
!      10/22/03     Rusty Koder              Original code
!       1/28/04     Les R. Koder             Revised to be consistent
!                                            with evolving code design

! include module that contains the user-accessible cmor functions.
  USE cmor_users_functions
  USE local_subs

  IMPLICIT NONE

  !   dimension parameters:
  ! ---------------------------------
  INTEGER, PARAMETER :: ntimes = 2    ! number of time samples to process
  INTEGER, PARAMETER :: lon = 4       ! number of longitude grid cells  
  INTEGER, PARAMETER :: lat = 3       ! number of latitude grid cells
  INTEGER, PARAMETER :: lev = 5       ! number of standard pressure levels
  INTEGER, PARAMETER :: lev2 = 19       ! number of standard pressure levels
  INTEGER, PARAMETER :: n2d = 4       ! number of IPCC Table A1a fields to be
                                      !     output.
  INTEGER, PARAMETER :: n3d = 3       ! number of IPCC Table A1c fields to 
                                      !     be output.  

  !   Tables associating the user's variables with IPCC standard output 
  !   variables.  The user may choose to make this association in a 
  !   different way (e.g., by defining values of pointers that allow him 
  !   to directly retrieve data from a data record containing many 
  !   different variables), but in some way the user will need to map his 
  !   model output onto the Tables specifying the MIP standard output.

  ! ----------------------------------

                                ! My variable names for IPCC Table A1c fields
  CHARACTER (LEN=5), DIMENSION(n3d) :: &
                                 varin3d=(/'CLOUD', 'U    ', 'T    '/)

                                ! Units appropriate to my data
  CHARACTER (LEN=5), DIMENSION(n3d) :: &
                                  units3d=(/ '%    ', 'm s-1',   'K    '  /)

                     ! Corresponding IPCC Table A1c entry (variable name) 
  CHARACTER (LEN=2), DIMENSION(n3d) :: entry3d = (/ 'cl', 'ua', 'ta' /)

                                ! My variable names for IPCC Table A1a fields
  CHARACTER (LEN=8), DIMENSION(n2d) :: &
                  varin2d=(/ 'LATENT  ', 'TSURF   ', 'SOIL_WET', 'PSURF   ' /)

                                ! Units appropriate to my data
   CHARACTER (LEN=6), DIMENSION(n2d) :: &
                          units2d=(/ 'W m-2 ', 'K     ', 'kg m-2', 'Pa    ' /)

   CHARACTER (LEN=4), DIMENSION(n2d) :: &
                      positive2d= (/  'down',  '    ', '    ', '    '  /)

                     ! Corresponding IPCC Table A1a entry (variable name) 
  CHARACTER (LEN=5), DIMENSION(n2d) :: &
                        entry2d = (/ 'hfls ', 'tas  ', 'mrsos', 'ps   ' /)

!  uninitialized variables used in communicating with CMOR:
!  ---------------------------------------------------------

  INTEGER :: error_flag
  INTEGER :: znondim_id, zfactor_id
  INTEGER, DIMENSION(n2d) :: var2d_ids
  INTEGER, DIMENSION(n3d) :: var3d_ids
  REAL, DIMENSION(lon,lat) :: data2d
  REAL, DIMENSION(lon,lat,lev2) :: data3d
  DOUBLE PRECISION, DIMENSION(lat) :: alats
  DOUBLE PRECISION, DIMENSION(lon) :: alons
  DOUBLE PRECISION, DIMENSION(lev2) :: plevs
  DOUBLE PRECISION, DIMENSION(1) :: time
  DOUBLE PRECISION, DIMENSION(2,1):: bnds_time
  DOUBLE PRECISION, DIMENSION(2,lat) :: bnds_lat
  DOUBLE PRECISION, DIMENSION(2,lon) :: bnds_lon
  DOUBLE PRECISION, DIMENSION(lev) :: zlevs
  DOUBLE PRECISION, DIMENSION(lev+1) :: zlev_bnds
  REAL, DIMENSION(lev) :: a_coeff
  REAL, DIMENSION(lev) :: b_coeff
  REAL :: p0
  REAL, DIMENSION(lev+1) :: a_coeff_bnds
  REAL, DIMENSION(lev+1) :: b_coeff_bnds
  INTEGER :: ilon, ilat, ipres, ilev, itim, itim2, ilon2,ilat2
  DOUBLE PRECISION bt

  character(256)::  outpath,mycal
  
  !  Other variables:
  !  ---------------------
  
  INTEGER :: it, m  
  bt=0.
  ! ================================
  !  Execution begins here:
  ! ================================
  
  ! Read coordinate information from model into arrays that will be passed 
  !   to CMOR.
  ! Read latitude, longitude, and pressure coordinate values into 
  !   alats, alons, and plevs, respectively.  Also generate latitude and 
  !   longitude bounds, and store in bnds_lat and bnds_lon, respectively.
  !   Note that all variable names in this code can be freely chosen by
  !   the user.

  !   The user must write the subroutine that fills the coordinate arrays 
  !   and their bounds with actual data.  The following line is simply a
  !   a place-holder for the user's code, which should replace it.
  
  !  *** possible user-written call ***
  
  call read_coords(alats, alons, plevs, bnds_lat, bnds_lon)
  
  ! Specify path where tables can be found and indicate that existing 
  !    netCDF files should not be overwritten.
  
  error_flag = cmor_setup(inpath='Test', netcdf_file_action='replace')
  
  ! Define dataset as output from the GICC model (first member of an
  !   ensemble of simulations) run under IPCC 2xCO2 equilibrium
  !   experiment conditions, and provide information to be included as 
  !   attributes in all CF-netCDF files written as part of this dataset.

  mycal = '360_day'

  error_flag = cmor_dataset_json("Test/common_user_input.json")
  
  
  !  Define all axes that will be needed

  ilat = cmor_axis(  &
       table='Tables/CMIP6_Amon.json',    &
       table_entry='latitude',       &
       units='degrees_north',        &  
       length=lat,                   &
       coord_vals=alats,             & 
       cell_bounds=bnds_lat)        
      
  ilon2 = cmor_axis(  &
       table='Tables/CMIP6_Lmon.json',    &
       table_entry='longitude',      &
       length=lon,                   &
       units='degrees_east',         &
       coord_vals=alons,             &
       cell_bounds=bnds_lon)      
        
  ilat2 = cmor_axis(  &
       table='Tables/CMIP6_Lmon.json',    &
       table_entry='latitude',       &
       units='degrees_north',        &  
       length=lat,                   &
       coord_vals=alats,             & 
       cell_bounds=bnds_lat)        
      
  ilon = cmor_axis(  &
       table='Tables/CMIP6_Amon.json',    &
       table_entry='longitude',      &
       length=lon,                   &
       units='degrees_east',         &
       coord_vals=alons,             &
       cell_bounds=bnds_lon)      
        
  ipres = cmor_axis(  &
       table='Tables/CMIP6_Amon.json',    &
       table_entry='plev19',       &
       units='Pa',                   &
       length=lev2,                   &
       coord_vals=plevs)

  !   note that the time axis is defined next, but the time coordinate 
  !   values and bounds will be passed to cmor through function 
  !   cmor_write (later, below).

  itim = cmor_axis(  &
       table='Tables/CMIP6_Amon.json',    &
       table_entry='time',           &
       units='days since 2030-1-1',  &
       length=ntimes,                &
       interval='20 minutes')
  itim2 = cmor_axis(  &
       table='Tables/CMIP6_Lmon.json',    &
       table_entry='time',           &
       units='days since 2030-1-1',  &
       length=ntimes,                &
       interval='20 minutes')
  
  !  define model eta levels (although these must be provided, they will
  !    actually be replaced by a+b before writing the netCDF file)
  zlevs = (/ 0.1, 0.3, 0.55, 0.7, 0.9 /)
  zlev_bnds=(/ 0.,.2, .42, .62, .8, 1. /)

  ilev = cmor_axis(  &
       table='Tables/CMIP6_Amon.json',    &
       table_entry='standard_hybrid_sigma',       &
       units='1', &
       length=lev,                   &
       coord_vals=zlevs,             &
       cell_bounds=zlev_bnds)

  !   define z-factors needed to transform from model level to pressure
  p0 = 1.e5
  a_coeff = (/ 0.1, 0.2, 0.3, 0.22, 0.1 /)
  b_coeff = (/ 0.0, 0.1, 0.2, 0.5, 0.8 /)

  a_coeff_bnds=(/0.,.15, .25, .25, .16, 0./)
  b_coeff_bnds=(/0.,.05, .15, .35, .65, 1./)

  error_flag = cmor_zfactor(  &
       zaxis_id=ilev,                      &
       zfactor_name='p0',                  &
       units='Pa',                         &
       zfactor_values = p0)

  error_flag = cmor_zfactor(  &
       zaxis_id=ilev,                       & 
       zfactor_name='b',                    &
       axis_ids= (/ ilev /),                &
       zfactor_values = b_coeff,            &
       zfactor_bounds = b_coeff_bnds  )

  error_flag = cmor_zfactor(  &
       zaxis_id=ilev,                       &
       zfactor_name='a',                    &
       axis_ids= (/ ilev /),                &
       zfactor_values = a_coeff,            &
       zfactor_bounds = a_coeff_bnds )

  zfactor_id = cmor_zfactor(  &
       zaxis_id=ilev,                         &
       zfactor_name='ps',                     &
       axis_ids=(/ ilon, ilat, itim /),       &
       units='Pa' )

  !  Define the only field to be written that is a function of model level
  !    (appearing in IPCC table A1c)

  var3d_ids(1) = cmor_variable(    &
       table='Tables/CMIP6_Amon.json',  &
       table_entry=entry3d(1),     &
       units=units3d(1),           &
       axis_ids=(/ ilon, ilat, ilev, itim /),  &
       missing_value=1.0e28, &
       original_name=varin3d(1))
  
  !  Define variables appearing in IPCC table A1c that are a function of pressure
  !         (3-d variables)
  
  DO m=2,n3d
     var3d_ids(m) = cmor_variable(    &
          table='Tables/CMIP6_Amon.json',  &
          table_entry=entry3d(m),     &
          units=units3d(m),           &
          axis_ids=(/ ilon, ilat, ipres, itim /), &
          missing_value=1.0e28,       &
          original_name=varin3d(m))
  ENDDO
  

  !  Define variables appearing in IPCC table A1a (2-d variables)
  
  DO m=1,n2d
     if (m.ne.3) then
     var2d_ids(m) = cmor_variable(    &
          table='Tables/CMIP6_Amon.json',      &
          table_entry=entry2d(m),     & 
          units=units2d(m),           & 
          axis_ids=(/ ilon, ilat, itim /), &
          missing_value=1.0e28,       &
          positive=positive2d(m),     &
          original_name=varin2d(m))   
  else
     var2d_ids(m) = cmor_variable(    &
          table='Tables/CMIP6_Lmon.json',      &
          table_entry=entry2d(m),     & 
          units=units2d(m),           & 
          axis_ids=(/ ilon2, ilat2, itim2 /), &
          missing_value=1.0e28,       &
          positive=positive2d(m),     &
          original_name=varin2d(m)) 
  endif
  ENDDO

  PRINT*, ' '
  PRINT*, 'completed everything up to writing output fields '
  PRINT*, ' '

  !  Loop through history files (each containing several different fields, 
  !       but only a single month of data, averaged over the month).  Then 
  !       extract fields of interest and write these to netCDF files (with 
  !       one field per file, but all months included in the loop).
  
  time_loop: DO it=1, ntimes
     
     ! In the following loops over the 3d and 2d fields, the user-written    
     ! subroutines (read_3d_input_files and read_2d_input_files) retrieve 
     ! the requested IPCC table A1c and table A1a fields and store them in 
     ! data3d and data2d, respectively.  In addition a user-written code 
     ! (read_time) retrieves the time and time-bounds associated with the 
     ! time sample (in units of 'days since 1970-1-1', consistent with the 
     ! axis definitions above).  The bounds are set to the beginning and 
     ! the end of the month retrieved, indicating the averaging period.
     
     ! The user must write a code to obtain the times and time-bounds for
     !   the time slice.  The following line is simply a place-holder for
     !   the user's code, which should replace it.
     
    call read_time(it, time(1), bnds_time)

    call read_3d_input_files(it, varin3d(1), data3d)

    error_flag = cmor_write(                                  &
         var_id        = var3d_ids(1),                        &
         data          = data3d,                              &
         ntimes_passed = 1,                                   &
         time_vals     = time,                                &
         time_bnds     = bnds_time   )

    call read_2d_input_files(it, varin2d(4), data2d)                  

    error_flag = cmor_write(                                  &
         var_id        = zfactor_id,                          &
         data          = data2d,                              &
         ntimes_passed = 1,                                   &
         time_vals     = time,                                &
         time_bnds     = bnds_time,                           &
         store_with    = var3d_ids(1) )

    ! Cycle through the 3-d fields (stored on pressure levels), 
    ! and retrieve the requested variable and append each to the 
    ! appropriate netCDF file.

    DO m=2,n3d
        
        ! The user must write the code that fills the arrays of data
        ! that will be passed to CMOR.  The following line is simply a
        ! a place-holder for the user's code, which should replace it.

        call read_3d_input_files(it, varin3d(m), data3d)
       
        ! append a single time sample of data for a single field to 
        ! the appropriate netCDF file.
        error_flag = cmor_write(                                  &
             var_id        = var3d_ids(m),                        &
             data          = data3d,                              &
             ntimes_passed = 1,                                   &
             time_vals     = time,                                &
             time_bnds     = bnds_time  )
        
        IF (error_flag < 0) THEN
           ! write diagnostic messages to standard output device
           write(*,*) ' Error encountered writing IPCC Table A1c ' &
                // 'field ', entry3d(m), ', which I call ', varin3d(m)
           write(*,*) ' Was processing time sample: ', time
                      
        END IF

     END DO
     
     ! Cycle through the 2-d fields, retrieve the requested variable and 
     ! append each to the appropriate netCDF file.
     
     DO m=1,n2d
        
        ! The user must write the code that fills the arrays of data
        ! that will be passed to CMOR.  The following line is simply a
        ! a place-holder for the user's code, which should replace it.
        
        call read_2d_input_files(it, varin2d(m), data2d)                  

        ! append a single time sample of data for a single field to 
        ! the appropriate netCDF file.

        error_flag = cmor_write(                                  &
             var_id        = var2d_ids(m),                        &
             data          = data2d,                              &
             ntimes_passed = 1,                                   &
             time_vals     = time,                                &
             time_bnds     = bnds_time  )
        
       IF (error_flag < 0) THEN
           ! write diagnostic messages to standard output device
           write(*,*) ' Error encountered writing IPCC Table A1a ' &
                // 'field ', entry2d(m), ', which I call ', varin2d(m)
           write(*,*) ' Was processing time sample: ', time 
                      
        END IF
        
     END DO
     
  END DO time_loop
  
  !   Close all files opened by CMOR.
  
  error_flag = cmor_close()  

  print*, ' '
  print*, '******************************'
  print*, ' '
  print*, 'ipcc_test_code executed to completion '   
  print*, ' '
  print*, '******************************'
  
END PROGRAM ipcc_test_code

Tags: