Custom Query (964 matches)

In ROMS/Include/globaldefs.h at lines 765-768 the effect of the following lines...

#if (!defined BIO_FENNEL  && defined DIAGNOSTICS_BIO) || \
    (!defined HYPOXIA_SRM && defined DIAGNOSTICS_BIO)
#  undef DIAGNOSTICS_BIO
#endif

...is to undefine DIAGNOSTICS_BIO unless both BIO_FENNEL and HYPOXIA_SRM are defined.

I suggest...

#if defined DIAGNOSTICS_BIO && !(defined BIO_FENNEL || HYPOXIA_SRM)
#  undef DIAGNOSTICS_BIO
#endif

...or its syllogistic equivalent.

Oops, the defined is missing before HYPOXIA_SRM. We need to have instead:

#if defined DIAGNOSTICS_BIO && \
  !(defined BIO_FENNEL      || defined HYPOXIA_SRM)
#  undef DIAGNOSTICS_BIO
#endif

I think, in lines 626 and 701 of def_diags.F the pre-processor conditions should read as:

#if defined DIAGNOSTICS_BIO && defined BIO_FENNEL

Currently, they only read as:

#ifdef BIO_FENNEL

This can cause "undefined variable" errors for iDbio2 and iDbio3 during compilation when other diagnostics but not DIAGNOSTICS_BIO are enabled in combination with BIO_FENNEL.

Yes, thank you for bringing this problem to my attention. I cleaned the logic in def_diags.F, set_diags.F, and wrt_diags.F. I also added the 2D biological diagnotics for HYPOXIA_SRM. It was not included in the above files.

Also removed apostrophes in fennel.h documentation to suppress the warnings from ifort during compilation. I also cleaned a DIAGNOSTIC_BIO bug in hypoxia_srm.h. We don't need the 3D diagnostics arrays in this simple model.

Fixed OMP directives in initial.F, ad_initial.F, rp_initial.F, and tl_initial.F when the 4D-Var algorithms are activated. This bug is of no consequence since we cannot run any of the adjoint-based algorithms in shared-memory (OpenMP).

There are several new colormap functions that are now located in the new matlab/colormaps sub-directory:

• cm_algae.m: A perceptually-uniform 256 colormap by Kristen Thyng, it can be used for phytoplankton (sequential).

• cm_amp.m: A perceptually-uniform 256 colormap by Kristen Thyng (sequential).

• cm_balance.m: A perceptually-uniform 256 colormap by Kristen Thyng, it can be used for sea surface height (diverging colors).

• cm_curl.m: A perceptually-uniform 256 colormap by Kristen Thyng, it can be used for wind curl (diverging color).

• cm_deep.m: A perceptually-uniform 256 colormap by Kristen Thyng, it can be used for bathymetry (sequential).

• cm_delta.m: A perceptually-uniform 512 colormap by Kristen Thyng, it can be used for freshwater (diverging).

• cm_dense.m: A perceptually-uniform 256 colormap by Kristen Thyng, it can be used for density (sequential).

• cm_gray.m: A perceptually-uniform 256 colormap by Kristen Thyng (sequential).

• cm_haline.m: A perceptually-uniform 256 colormap by Kristen Thyng, it can be used for salinity (sequential).

• cm_ice.m: A perceptually-uniform 256 colormap by Kristen Thyng, it can be used for sea ice (sequential).

• cm_matter.m: A perceptually-uniform 256 colormap by Kristen Thyng (sequential).

• cm_oxy.m: A perceptually-uniform 256 colormap by Kristen Thyng, it can be used for oxygen concentration (sequential).

• cm_phase.m: A perceptually-uniform 256 colormap by Kristen Thyng (constant lightness).

• cm_solar.m: A perceptually-uniform 256 colormap by Kristen Thyng (sequential).

• cm_speed.m: A perceptually-uniform 256 colormap by Kristen Thyng, it can be used for velocity magnitude (sequential).

• cm_tempo.m: A perceptually-uniform 256 colormap by Kristen Thyng (sequential).

• cm_thermal.m: A perceptually-uniform 256 color map by Kristen Thyng, it can be used for temperature (sequential).

• cm_turbid.m: A perceptually-uniform 256 colormap by Kristen Thyng, it can be used for sediment (sequential).

The following functions were added for colormap processing:

• cbarrow.m: Places triangle-shaped endmembers on both ends of the current colorbar by Chad A. Greene.

• cmocean.m: Colormap package for oceanographic applications by Chad A. Greene.

• colorspace.m: Transform a color image between color representations by Pascal Getreuer.

Other miscellaneous functions:

• append_contact.m: Appends nesting contact points data to ROMS regular grid data. the resulting grid arrays are expanded to contain the data in the contact region.

• ad_interpolator.m: Adjoint of intepolator.m, which spatially interpolates ROMS field to horizontal path/trajectory. It can be use to set-up functional in various adjoint-based algorithms, like adjoint sensitivities and observation impacts.

• interpolator.m: Given any 2D or 3D ROMS variable FIELD, linearly interpolate to the requested path (Xpath, Ypath) in spherical or Cartesian coordinates. If input variable is 3D, the horizontally interpolated values are returned at all levels of the s-coordinate.

• nc_dfixed.m: Creates a new NetCDF file with the requested record unlimited dimension changed to a fixed dimension.