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Eliminated a potential problem in extract_obs.F and ad_extract_obs.F when the observation depth is given in meters (negative value) instead of fractional model level (positive value). Observations shallower or deeper than the model associated variable, will be flagged out and ignored. Users should be carefull when preparing the 4DVar observation NetCDF file. If assimilating satellite SST, assign as a depth the model top level (N(ng), positive value) instead of zero or negative depth values. The depth value provided to altimetry SSH data is irrelevant but it is recommended to use a zero value.

Updated obs_read.F and obs_write.F to use new generic NetCDF interface (read and write routines in mod_netcdf.F). Also corrected couple of bugs and cleaned obsolete code and variables.

There a couple of missing arguments in wrt_hessian.F when writing ad_svstr when ADJUST_WSTRESS is activated. Also remove the allocation of SF_time in mod_scalars.F. We already allocate this variable in inp_par.F which is the correct place to do so. We need to allocate this variable after the input parameter nSFF is read.

There is a problem in routines nf_fread2d.F, nf_fread3d.F, and nf_fread4d.F when the scale (Ascl) value used to multiply input fields is different than unity and land points are replaced with the _FillValue. The read field was scaled first and then checked for the fill value. This logic needs to be changed to:

            DO i=1,Npts
              IF (wrk(i).ge.spval) THEN
                wrk(i)=0.0_r8           ! land/sea maked with _FillValue
              ELSE
                wrk(i)=Ascl*wrk(i)
                Amin=MIN(Amin,wrk(i))
                Amax=MAX(Amax,wrk(i))
              END IF
            END DO

That is, the read field is unmodified when the conditional wrk(i).ge.spval is executed. Many thanks to Andy Moore for bringing this to my attention.

I also initialized local arrays in the IO routines to avoid denormalized numbers that are treated differently by various compilers. This facilitates processing and debugging. I also initialized such fields in the mp_gather and mp_scatter routines.