fix bug in drivers/mct/cesm1/CICE_RunMod.F90 and update documentation

cicecore/cicedynB/infrastructure/io/io_pio2/ice_history_write.F90

@@ -813,7 +813,11 @@ subroutine ice_write_hist (ns)
                 a,'-',a,'-',a,' at ',a,':',a)
         status = pio_put_att(File,pio_global,'history',trim(start_time))
 
-        status = pio_put_att(File,pio_global,'io_flavor','io_pio')
+        if (history_format == 'pio_pnetcdf') then
+           status = pio_put_att(File,pio_global,'io_flavor','io_pio pnetcdf')
+        else
+           status = pio_put_att(File,pio_global,'io_flavor','io_pio netcdf')
+        endif
 
       !-----------------------------------------------------------------
       ! end define mode

cicecore/drivers/mct/cesm1/CICE_RunMod.F90

@@ -374,7 +374,7 @@ subroutine coupling_prep (iblk)
           fsens, flat, fswabs, flwout, evap, Tref, Qref, &
           scale_fluxes, frzmlt_init, frzmlt, Uref, wind
       use ice_flux_bgc, only: faero_ocn, fiso_ocn, Qref_iso, fiso_evap, &
-          fzsal_ai, fzsal_g_ai, flux_bio, flux_bio_ai
+          fzsal_ai, fzsal_g_ai, flux_bio, flux_bio_aim, &
           fnit, fsil, famm, fdmsp, fdms, fhum, fdust, falgalN, &
           fdoc, fdic, fdon, ffep, ffed, bgcflux_ice_to_ocn
       use ice_grid, only: tmask

doc/source/cice_index.rst

@@ -22,9 +22,11 @@ either Celsius or Kelvin units).
    "a3Dz", "history field accumulations, 3D vertical", ""
    "a3Db", "history field accumulations, 3D bio grid", ""
    "a3Dc", "history field accumulations, 3D categories", ""
+   "a3Df", "history field accumulations, 3D fsd", ""
    "a4Di", "history field accumulations, 4D categories, vertical ice", ""
    "a4Db", "history field accumulations, 4D categories, vertical bio grid", ""
    "a4Ds", "history field accumulations, 4D categories, vertical snow", ""
+   "a4Df", "history field accumulations, 4D categories, fsd", ""
    "a_min", "minimum area concentration for computing velocity", "0.001"
    "a_rapid_mode", ":math:`{\bullet}` brine channel diameter", ""
    "advection", ":math:`\bullet` type of advection algorithm used (‘remap’ or ‘upwind’)", "remap"
@@ -274,6 +276,7 @@ either Celsius or Kelvin units).
    "histfreq_n", ":math:`\bullet` integer output frequency in histfreq units", ""
    "history_dir", ":math:`\bullet` path to history output files", ""
    "history_file", ":math:`\bullet` history output file prefix", ""
+   "history_format", ":math:`\bullet` history file format", ""
    "hm", "land/boundary mask, thickness (T-cell)", ""
    "hmix", "ocean mixed layer depth", "20. m"
    "hour", "hour of the year", ""

doc/source/user_guide/ug_case_settings.rst

@@ -99,8 +99,9 @@ Table of namelist options
    "","", "path/file", "restart file name", ""
    "","``restart``", "true/false", "initialize using restart file", "``.true.``"
    "","``use_restart_time``", "true/false", "set initial date using restart file", "``.true.``"
-   "","``restart_format``", "nc", "read/write  restart files (use with PIO)", ""
-   "","", "bin", "read/write binary restart files", ""
+   "","``restart_format``", "string", "restart file format", "default"
+   "","", "default", "read/write restart files in default format", ""
+   "","", "pio_pnetcdf", "read/write restart files with pnetcdf in pio", ""
    "","``lcdf64``", "true/false", "if true, use 64-bit  format", ""
    "","``numin``", "integer", "minimum internal IO unit number", "11"
    "","``numax``", "integer", "maximum internal IO unit number", "99"
@@ -140,6 +141,9 @@ Table of namelist options
    "","", "false", "write snapshots of data", ""
    "","``history_dir``", "path/", "path to history output directory", ""
    "","``history_file``", "filename prefix", "output file for history", "‘iceh’"
+   "","``history_format``", "string", "history file format", "default"
+   "","", "default", "read/write restart files in default format", ""
+   "","", "pio_pnetcdf", "read/write restart files with pnetcdf in pio", ""
    "","``write_ic``", "true/false", "write initial condition", ""
    "","``incond_dir``", "path/", "path to initial condition directory", ""
    "","``incond_file``", "filename prefix", "output file for initial condition", "‘iceh’"

doc/source/user_guide/ug_implementation.rst

@@ -701,6 +701,15 @@ Model output
 History files
 *************
 
+CICE provides restart data in binary unformatted or netCDF formats via
+separate implementations of binary, netcdf, and pio source code under the 
+directory **infrastructure/io**.  ``ICE_IOTYPE`` defined in cice.settings
+specifies the IO type and defines which source code directory is compiled.
+At the present time, binary, netcdf, and PIO are exclusive formats
+for history and restart files, and history and restart file must use the same 
+io package.  The namelist variable ``history_format`` further refines the
+format approach or style for some io packages.
+
 Model output data is averaged over the period(s) given by ``histfreq`` and
 ``histfreq_n``, and written to binary or netCDF files prepended by ``history_file``
 in **ice_in**. These settings for history files are set in the 
@@ -711,7 +720,7 @@ depending on the output file format chosen in **cice.settings** (set
 ``ICE_IOTYPE``). The netCDF history files are CF-compliant; header information for
 data contained in the netCDF files is displayed with the command ``ncdump -h
 filename.nc``. Parallel netCDF output is available using the PIO library; the
-attribute ``io_flavor`` distinguishes output files written with PIO from
+output file attribute ``io_flavor`` distinguishes output files written with PIO from
 those written with standard netCDF. With binary files, a separate header
 file is written with equivalent information. Standard fields are output
 according to settings in the **icefields\_nml** section of **ice\_in** 
@@ -890,11 +899,14 @@ The timers use *MPI\_WTIME* for parallel runs and the F90 intrinsic
 Restart files
 *************
 
-CICE provides restart data in binary unformatted or netCDF formats, via
-the ``ICE_IOTYPE`` flag in **cice.settings** and namelist variable
-``restart_format``. Restart and history files must use the same format. As
-with the history output, there is also an option for writing parallel netCDF
-restart files using PIO.
+CICE provides restart data in binary unformatted or netCDF formats via
+separate implementations of binary, netcdf, and pio source code under the 
+directory **infrastructure/io**.  ``ICE_IOTYPE`` defined in cice.settings
+specifies the IO type and defines which source code directory is compiled.
+At the present time, binary, netcdf, and PIO are exclusive formats
+for history and restart files, and history and restart file must use the same 
+io package.  The namelist variable ``restart_format`` further refines the
+format approach or style for some io packages.
 
 The restart files created by CICE contain all of the variables needed
 for a full, exact restart. The filename begins with the character string