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Starting to bring comments up to date and format comments for document extraction of "prototypes".
Merge from branch pre38: o essential mods for cubed sphere o debugged atmosphere, dynamcis + physics (aim) o new packages (mom_vecinv, mom_fluxform, ...)
Added un-compilable lines to make sure configuration is done properly.
define "ALLOW_TIMEAVE" replaces "INCLUDE_DIAGNOSTICS_INTERFACE_CODE"
remove unused CPP_kees
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!
Rescaling of forcing fields done immediately after reading fields.
Introduced CPP flag ALLOW_GMREDI
Added #undef ALLOW_KPP
Added CPP macro ALLOW_OBCS to include/exclude open boundary code.
Removed spaces in macro definitions to accomodate SGI cpp.
o Added "natural BCs" as alternative to "virtual salt flux" o Re-difined precFloat32 and precFloat64 to be 32 and 64 so that their values can be meaningfuly set in the data file o Modified read_write.F to create an exception if readBinaryPrec is not set o Replaced CPP control of viscous BCs with run-time control o Tidied up input-data precision (ie. ini_depths cnh_dbg...) o ini_forcing.F now initialises *all* forcing arrays to zero o Definitively tested verification experiments 0,1,2 and 4 (3 is atmospheric set-up which is in a state of flux)
These are changes concerning geometry on a sphere and BCs: o The calculation of RA used to be wrong if delX != delY. o The details of the cell geometry is now consistent with the "classic" CM-5 code. o Advection near boundaries is now correct. o Lateral no-slip/free-slip now works. o Vertical no-slip/free-slip now works properly. o del^4 viscosity (with no-slip/free-slip) now works properly.
Changes to allow for atmospheric integration builds of the code
The time-averaging diagnostics has been modified to include averages of "intermediate" quantities that exist only on a tile. We currently only time-average K13, K23 and wVel but these should be usable as a template for other diagnostics. We have now split off these routines into a separate module called diags/. Use of these routines is enabled by the CPP flag ALLOW_DIAGNOSTICS set in model/inc/CPP_OPTIONS.h
Chages to make default setup correct for 4 degreee global comparison
Various corrections: o do_gterm_blocking..() is fixed to work with new time-stepping o CPP_OPTIONS.h now contains #define ALLOW_CD
$Id to $Header changes
Initial revision
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