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Bringing comments up to data and formatting for document extraction.
modified for NonLin-FreeSurf : This affects the truncation error ==> all output.txt need to be updated.
Initialization of Adams-Bashforth time stepping for iter.EQ.0 - uses simple forward step - changes trajectories so *ALL* output is affected
Whitespace!
change units of PhiHyd (ocean) to have unified units for all potential Phi
remove "include CG2D.h"
implement a Crank-Nickelson barotropic time-stepping
Made sure each .F and .h file had the CVS keywords Header and Name at its start. Most had header but very few currently have Name, so lots of changes!
Merged changes from branch "branch-atmos-merge" into MAIN (checkpoint34) - substantial modifications to algorithm sequence (dynamics.F) - packaged OBCS, Shapiro filter, Zonal filter, Atmospheric Physics
Cosmetic.
Added myIter as an argument to timestep() to allow proper timestepping at myIter=0
Changes to allow for atmospheric integration builds of the code
Changes for new exchange routines which do general tile <-> tile connectivity, variable width overlap regions and provide hooks for shared memory and DMA protocols like Arctic, Memory Channel etc..
Consistent isomorphism chages
E-implemented the theta* and salt* time-stepping scheme. We did this so that theta/salt/u/v would all be at the same time-level at the end of dynamics() to make I/O easier.
Added code to bring "salt" up-to-date with "theta". One caveat is that implicit diffusion of salt is done with the diffusivity of theta. We'll sort this out later. In explicit mode, diffKzS is used.
Changes to support topography, hydrography and forcing from files
Various corrections: o do_gterm_blocking..() is fixed to work with new time-stepping o CPP_OPTIONS.h now contains #define ALLOW_CD
Merge of GM Redi and spherical polar and inplicit diffusion and CD. Everything for a global run is now included, however, still some discrepancies with GM Redi.
Implemented implicit vertical diffusion (tracers only). Involved introducing a "total" diffusivity array (local 3D) calculated by calc_diffusivity(). Made some small changes to time-stepping algorithm. Switched on by setting implicitZdiffusion. (note: *Not* fully tested with topography. But when switched off this does produce identical results)
Swapped the time-stepping algorithm around (just a little bit). We now officially use the predictor-corrector terminology. We make the prediction step at the end of the dynamics() section and store the result in the gUNm1, gVNm1, gTNm1 arrays. The "tricky" part is that at the beginning of the dynamics section, where the "correction" is made, theses arrays must be initialised at the beginning of any run. A new routine init_predictor() does this. This is "all" in preparation for implicit diffusion. Let's hope it's enough...
Further memory saving macros for particular grids
Added extra IO features - runtime on/off flags - more reporting of configuration
Moved the "K loop" from timestep() upto dynamics(). dynamics() now contains all K loops (two infact).
Removed development debuggin
Further $Id to $Header conversions
Initial revision
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