Following files were modified to consolidate sediment branch code to Hernan’s latest version.

- master.F – added waves_ocean coupling and call to waves_ocean.h.
- nl_ocean.h – added waves_ocean coupling and calls to initialize coupling for atmospheric and waves models.
- Drivers/Module.mk – change CYGWIN special attribute to accomodate df and ifort.
- mod_arrays.F – added rho point source option Q_PSOURCE.
- mod_averages.F – updated sediment averages.
- mod_forces.F – added wave input parameters.
- globaldefs.h – create short notation definitions for combinations of wave data for HWAVE, LWAVE, DWAVE, PWAVE_TOP, PWAVE_BOT, and for BEDLOAD.
- mod_grid.F – added bed_thick arrays to track changes of bed elevation for morphology.
- mod_ncparam.F – added NetCDF cases for waves and radiation stress I/O.
- mod_ocean.F – added stokes velocities.
- mod_parallel.F – added WAVES_OCEAN parallel nodes variables.
- mod_param.F – added setup parameters for new test cases: INLET_TEST, VISSER, SHOREFACE, TEST_CHAN, TRENCH, SED_TOY, BEVANO. Increase unmber of diagnostic terms to include radiation stresses.
- mod_scalars.F – define diagnostics for radiation stresses. Define variables for model coupling.
- mod_sediment.F – define new variables for bed_layer_thickness, morph_fac, bed biodiffusivity.
- mod_sources.F – add Q_PSOURCE.
- mod_stepping.F – add Q_PSOURCE.
- checkdefs.F – add new applications and CPP definitions.
- def_avg.F – change 365.25 to Julian for time description.
- def_diags.F – change 365.25 to Julian for time description.
- def_floats.F – change 365.25 to Julian for time description.
- def_his.F – change 365.25 to Julian for time description, added nearshore radiation stress terms, allow h to vary for morphology, write out rmask for wet_dry, write out waves data.
- def_info.F – change 365.25 to Julian for time description, prevent writing of static h for morphologic simulations.
- def_ini.F – change 365.25 to Julian for time description.
- def_rst.F – change 365.25 to Julian for time description, read in bathy for morphology.
- get_state.F – including read for time dependent h when using sediment and morphology, include read for TKE and GLS when
- inp_par.F – updated read of model coupling input file, added write out of raditaion stress terms, GLS wave breaking criteria, wet_dry, and h for morphology, update reports for stations file.
- coupling.in – update methodology to input coupling parameters for node allocations, time steps between coupling, and reads for input file names.
- waves_coupler.F – new file added that initializes, runs, and finalizes MCT coupling.
- waves_ocean.h – updated logic to determine colors to spawn new file added.
- metrics.F – Use MAX(h) to calculate Courant number for wet_dry.
- mp_routines.F – Added USE ifport statements for CYGWIN-ifort.mk.
- set_scoord.F – Added option for log profile distribution of vertical levels.
- wrt_his.F – Add write of time dependent bathy for morphology, write out radiation stress terms, stokes velocities, wave fields, and write out wet_dry mask. When using Nearshore_Mellor would like to write out velocities in Eulerian form by subtracting Stokes velocities but this may conflict with Adjoint (needs revisiting !!)
- wrt_info.F – suppress write bathy for time dependent h with morphology.
- wrt_rst.F – Add write of time dependent bathy for morphology, Stokes velocities, and write out wet_dry mask.
- analytical.F – Added initial and forcings for various test cases.
- step2d.F – Added contributions from nearshore_mellor radiation stresses, included wet_dry.
- u2dbc_im.F – Update h to be h+zeta for shallow water (SQRT(g h+zeta)).
- v2dbc_im.F – Update h to be h+zeta for shallow water (SQRT(g h+zeta)).
- zetabc.F – Update h to be h+zeta for shallow water (SQRT(g h+zeta)).
- step_floats.F – Modify float types. Float types are 1 = neutral, 2 = constant distance below moving sea surface.
- step3d_uv.F – Include methodology for wet_dry.
- step3d_t.F – Include poitn Q sources and add vertical velowity omega to bottom face for morphology.
- ssw_bbl.h – update routine to account for nearshore velocities, set formdrag as a cpp definition.
- sg_bbl.h – update routine to account for nearshore velocities.
- mb_bbl.h – update routine to account for nearshore velocities.
- rhs3d.F – update to include radiation stresses and include omega BC for morphology.
- pre_step3d.F – update to include radiation stresses diagnostics and include omega BC for morphology.
- omega.F – include bottom boundary condition for morphology, include Q_PSOURCE.
- main2d.F – include coupler to wave model.
- main3d.F – include coupler to wave model.
- sediment.F – Update bedload routines, reform susp load.

Comment by Mark Hadfield — September 26, 2006 @ 16:49 @ 4:49 pm

Comment by arango — November 11, 2006 @ 19:02 @ 7:02 pm