interpolate seawifs onto NAA grid

1) Download the monthly climatology data:
wget http://oceandata.sci.gsfc.nasa.gov/cgi/getfile/S19972442010273.L3m_MC_CHL_chlor_a_9km.nc http://oceandata.sci.gsfc.nasa.gov/cgi/getfile/S19972742010304.L3m_MC_CHL_chlor_a_9km.nc http://oceandata.sci.gsfc.nasa.gov/cgi/getfile/S19973052010334.L3m_MC_CHL_chlor_a_9km.nc http://oceandata.sci.gsfc.nasa.gov/cgi/getfile/S19973352010365.L3m_MC_CHL_chlor_a_9km.nc http://oceandata.sci.gsfc.nasa.gov/cgi/getfile/S19980012010031.L3m_MC_CHL_chlor_a_9km.nc http://oceandata.sci.gsfc.nasa.gov/cgi/getfile/S19980322010059.L3m_MC_CHL_chlor_a_9km.nc http://oceandata.sci.gsfc.nasa.gov/cgi/getfile/S19980602010090.L3m_MC_CHL_chlor_a_9km.nc http://oceandata.sci.gsfc.nasa.gov/cgi/getfile/S19980912010120.L3m_MC_CHL_chlor_a_9km.nc http://oceandata.sci.gsfc.nasa.gov/cgi/getfile/S19981212010151.L3m_MC_CHL_chlor_a_9km.nc http://oceandata.sci.gsfc.nasa.gov/cgi/getfile/S19981522010181.L3m_MC_CHL_chlor_a_9km.nc http://oceandata.sci.gsfc.nasa.gov/cgi/getfile/S19981822010212.L3m_MC_CHL_chlor_a_9km.nc http://oceandata.sci.gsfc.nasa.gov/cgi/getfile/S19982132010243.L3m_MC_CHL_chlor_a_9km.nc

2) Rename the data so that they will appear in the order of months (i.e. from Jan. to Dec.):
for i in $(ls *_MC_*.nc); do `echo "cp $i tmp${i:5}"`;done

ls tmp*.nc
tmp0012010031.L3m_MC_CHL_chlor_a_9km.nc
tmp0322010059.L3m_MC_CHL_chlor_a_9km.nc
tmp0602010090.L3m_MC_CHL_chlor_a_9km.nc
tmp0912010120.L3m_MC_CHL_chlor_a_9km.nc
tmp1212010151.L3m_MC_CHL_chlor_a_9km.nc
tmp1522010181.L3m_MC_CHL_chlor_a_9km.nc
tmp1822010212.L3m_MC_CHL_chlor_a_9km.nc
tmp2132010243.L3m_MC_CHL_chlor_a_9km.nc
tmp2442010273.L3m_MC_CHL_chlor_a_9km.nc
tmp2742010304.L3m_MC_CHL_chlor_a_9km.nc
tmp3052010334.L3m_MC_CHL_chlor_a_9km.nc
tmp3352010365.L3m_MC_CHL_chlor_a_9km.nc

3) Create a new variable called time to each data:
for i in $(ls tmp*9km.nc); do ncap2 -O -s 'time=array(1.,1.,1.)' $i vartime_$i; done

4) Create an unlimited (RECORD) dimension called "time" to each data:
 for i in $(ls vartime_*.nc); do ncecat -u time $i dimtime_$i; done

5) Concatenate the files:
ncrcat -h dimtime_*.nc seawifs_mon_clim.nc

6) Finally use SOSIE to interpolate onto NAA grid:
~/sosie-2.6.4/bin/sosie.x -f namelist.seawifs2naa

lbc_lnk

lbc_lnk is done for all diagnostic variables in LOBSTER, e.g. trcbio.F90:

            CALL lbc_lnk( zw2d(:,:,jl),'T', 1. )

Q: do I need to do this in MY_TRC?

"tra" seems to represent the tracer concentration in the following time step, therefore I need to update tra instead of trn! The words "update the trend" are confusing to me (it seems the time rate of change is represented by tra. rather it should say update tra with the trend (or flux)).

tra, trn, trb for the next time step will be updated by TRP/trcnxt.F90, as well as the OBC and LBC are computed.

Actually, "tra" does represent the time rate of change in tracer concentration. For example PISCES/p4zflx.F90:

            ! compute the trend
            tra(ji,jj,1,jpdic) = tra(ji,jj,1,jpdic) + ( zfld - zflu ) / fse3t(ji,jj,1)

where zfld - zflu represent the flux [mol/m2/s] which is divided by fse3t (vertical scale factor; thickness of first model layer??) [m]. Thus the division gives [mol/m3/s].

NaN in tracer.stat

I finally found the reason for segmentation fault (I think). It is because at least one of the newly added tracers (icechl, iceno3, and/or icenh4 in this case) has value of NaN, as seen in tracer.stat (which calculates sum of all 3d tracers, see ztrai in trcstp.F90):

         1  0.7883947556E+03
         2               NaN

This happens at the second time step. This means that either or both DMSPd or/and DMS becomes NaN in the second time step...

Actually this was not the cause of segmentation fault, as the run passed the second time step when key_my_trc_iceeco was excluded:

         1  0.7883947556E+03
         2               NaN
         3               NaN
         4               NaN
         5               NaN

Anyway, it is good to know that my 3d tracers are erraneous as well :(

time step for tracers in MY_TRC

PISCES/trcini_pisces.F90

rfact = rdttrc(1)

HH this should equal rdt (time step for dynamics) unless different tracer time step is given.

rfact2 = rfact / float (nrdttrc)

HH this would still be rfact unless nrdttrc (time step for biology) is different from tracers.

xstep = rfact2 / rday

HH rday = 86400 sec/day (defined in OPA_SRC/DOM/phycst.F90), so xstep gives the time step in days.. PISCES uses xstep when the rate constant is given in units of d-1. I will avoid using xstep and instead convert the rate constant to s-1 during the initialization as in FABM.

addting a new variable in netcdf

! Re: create new OBC files that include DMS and DMSPd in the water column.

! To run the DMS model, I need to set an open boundary condition for dms and dmspd. For now, I will just create an OBC that has a minimum value (0.01) for all time/space, such as done for some of the PISCES variables (e.g. ZOO). In the current setup, the same OBC files are used (obc_[east,west]_trc_cmoc_y0000m00_canesm.nc) for interannual runs, so I will create two new files (east and west, although they may be identical) that include both dms and dmspd.

! Copy the source OBC files into the tmp folder.
cp obc_east_trc_cmoc_y0000m00_canesm.nc ~/tmp/
cp obc_west_trc_cmoc_y0000m00_canesm.nc ~/tmp/

! Extract the OBC data for ZOO and ZOO2 (which are all constant values of 0.01) and save to a new file.
ncks -v ZOO,ZOO2 obc_east_trc_cmoc_y0000m00_canesm.nc tmp_east.nc
ncks -v ZOO,ZOO2 obc_west_trc_cmoc_y0000m00_canesm.nc tmp_west.nc

! Rename the variables to dms and dmspd.
ncrename -O -v ZOO,dms tmp_east.nc
ncrename -O -v ZOO,dms tmp_west.nc
ncrename -O -v ZOO2,dmspd tmp_east.nc
ncrename -O -v ZOO2,dmspd tmp_west.nc

! Add the new variables to the existing files.
ncks -A -v dms,dmspd tmp_east.nc obc_east_trc_cmoc_y0000m00_canesm.nc
ncks -A -v dms,dmspd tmp_west.nc obc_west_trc_cmoc_y0000m00_canesm.nc

! Rename the files, so that I don't get confused with the source files.
mv obc_east_trc_cmoc_y0000m00_canesm.nc hh_obc_east_trc_cmoc_y0000m00_canesm.nc
mv obc_west_trc_cmoc_y0000m00_canesm.nc hh_obc_west_trc_cmoc_y0000m00_canesm.nc

! Remove the tmp files.
rm tmp_east.nc tmp_west.nc