   0      IFILE       type of input file: [0] NetCDF, [1] OA/FM hex, [2] QG hex
   0      JOB         output type (see below)
12070.0   TSTART      input day assigned for initialization
12086.0   TSTOP       last input day to process (TSTOP=TSTART for persisted bc)
   16.0   TSKIP       time interval (days) for scanning input data (see below)
   0      ITS2PSI     compute PSI from TS: [0] no, [1] yes.
   2      IBRY        boundary condition on PSIBAR : [1] stream, [2] d(vort)/dt
   1      IFLAG(5)    switch for setting barotropic velocities  (see below)
 200.0    DEF_DEPTH   default reference depth (m).  (see below)
   0.0    WBOT_DEPTH  Bottom steering depth (m).  (see below)
   3      IFLAG(6)    ageostrophic motion: [1] none, [2] beta, [3] full Coriolis
   9      NT          number of tracers (minimum 2: temperature and salinity)
   0      IBIOM       biological model type (see below)
   1      ITRC        read file for additional tracers: [0] no, [1] yes
   0      INTOPT      interpolation option: [0] linear, [1] cubic-spline
   0      IFILTER     Shapiro filter input fields: [0] no, [1] yes
   2      NORD        order of the Shapiro filter
   2      NREP        number of Shapiro filter applications
   0      IDBUG       write out fields for quick browsing: [0] no, [1] yes
pi_ini.nc
pi_ini.echo
../Other/oag_ini.nc
../Other/ts_mean.dat
../Other/grids_MassBayPfjl.nc
../Other/transport_p08_MassBay_pfjl.dat
../FM/bio_fields2.dat
/dev/null
/dev/null

  ***  Above FILENAMES:

       1st line:  output; NetCDF fields to be read by the PE model.
       2nd line:  output; diagnostic information for processed fields.
       3rd line:  input; hexadecimal or NetCDF fields to be processed.
       4th line:  input; mean T-S profile.
       5th line:  input; GRIDS NetCDF file.
       6th line:  input; transport around islands and along open segments.
       7th line:  input; additional tracer fields.
       8th line:  input; external velocities and transport boundary
                         conditions.
       9th line:  input; surface of no-motion netCDF file (IFLAG(5) > 7)

  ***  Output type:    JOB = [0] initial and boundary condition fields.
                             [1] assimilation fields.
                             [2] initial and boundary conditions with
                                 barotropic mode specification in
                                 (8th line file) for open domains
                                 (all boundaries).
                             [3] initial and boundary conditions with
                                 horizontally uniform T,S and zero velocity.
                                 Used to obtain pressure gradient and/or
                                 shapiro filter biases after removing mean T,S.
                                 *** Note:  This option supercedes IFILE,
                                            the input file (3rd line file)
                                            is a single profile (same format
                                            as 4th line file).

  ***  IBIOM: Biological Model type

              [0] none.
              [1] McGillicuddy et al. (1995).  Four biological tracers:
                  phytoplankton, zooplankton, nitrate, and ammonium
              [2] Anderson expansion of McGillicuddy model.  Five biological
                  tracers: phytoplankton, zooplankton, nitrate, ammonium,
                  and detritus.
              [3] Fasham et al. (1990). Seven biological tracers:
                  phytoplankton, zooplankton, nitrate, particulate organic
                  nitrogen, dissoled organic nitrogen, and bacteria.

  ***  NOTE:  for OA/FM hexadecimal input, TSTART and TSTOP is the year
              day (for instance, 125.0) or the modified Julian day
              (for instance, 8919) whereas for QG model input
              is the model day (for instance, 1.0).
              The modified Julian day is defined to have an offset
              of 2440000 from the standard number.
 
  ***  TSKIP:  time interval for scanning and processing input data.
               If TSKIP>0, output fields having a time-coordinate, like
               boundary conditions and assimilation fields will be
               processed and written every other TSKIP days.  At input,
               the fields are needed every TSKIP days. However,
               if TSKIP=0, then the input data is scanned and 
               processed at its own (input) time frequency.

  ***  If NT>2, the additional tracer field are provided by the tracer
       file (7th line file).  The time clock on these tracer fields
       MUST be the same as in the primary (temperature, salinity, etc)
       fields.

  ***  In the diagnostic initialization (JOB=3) the internal mode
       (baroclinic) velocities are set to zero and the transport 
       streamfunction is set constant (zero external mode velocity).

  ***  In the option JOB=2, the internal model velocities are computed
       from the streamfunction (scaled dynamic height) and the external
       mode velocities are those provided by the user (8th line file ).
       The PE transport streamfunction is computed from those external
       mode velocities by inverting the Poisson's Equation using the
       boundary conditions provided by the user at the bottom of the
       same input file (8th line file).

  ***  If the GRIDS file (5th line file) contains coastal information,
       this package reads the contents of the transport file (6th line file)
       which prescribes the transport around islands and along open segments.
       See the documentation at the bottom of that file.

  ***  IFLAG(5), DEF_DEPTH and WBOT_DEPTH: transport computation controls:

       IFLAG(5): transport component options:

       -------------------------------------------------------------------
                 |  reference surface | baro velocity    | bdy values
       -------------------------------------------------------------------

           0     |     take as is     | do not reset [1] | QG psi [2]
           1     |     take as is     | do not reset [1] | ubaro estimate [3]

           2     |     take as is     |  reset [4]       | QG psi[2]
           3     |     take as is     |  reset [4]       | ubaro estimate [3]

           4     |  set to DEF_DEPTH  | do not reset [1] | QG psi [2]
           5     |  set to DEF_DEPTH  | do not reset [1] | ubaro estimate [3]

           6     |  set to DEF_DEPTH  |  reset [4]       | QG psi[2]
           7     |  set to DEF_DEPTH  |  reset [4]       | ubaro estimate [3]

           8     |  set from nc-file  | do not reset [1] | QG psi [2]
           9     |  set from nc-file  | do not reset [1] | ubaro estimate [3]

          10     |  set from nc-file  |  reset [4]       | QG psi[2]
          11     |  set from nc-file  |  reset [4]       | ubaro estimate [3]
       -------------------------------------------------------------------

       Notes: [1] set guess for barotropic velocity u_baro as estimated from 
                  psi field (u_QG) and 
                  invert for vorticity of u_baro to obtain transport.
                  
              [2] bdy values obtained by vertical integration of QG psi.
     
              [3] bdy values obtained by integration of u_baro along the bdy.

              [4] u_baro=u_QG - a(WBOT_DEPTH) u_BOT.grad(h)/|grad(h)|

                  if WBOT_DEPTH > 0,
                     a=1 if h<WBOT_DEPTH (bottom steering)
                     a=WBOT_DEPTH/h if h > WBOT_DEPTH.

                  if WBOT_DEPTH = 0., a=1.
