IMPORTANT: Corrected nesting refinement algorithms

[arango]

Corrected several problems with the grid refinement algorithms. The DOGBONE test case for refinement is work well now. I am now working on nesting application in the Gulf of Mexico and South China Sea to fine tune the algorithms to complex realistic applications.

• Updated several Matlab script to process the contact points NetCDF between refinement grids. This will be explained in ​src:ticket:615.

• Corrected the logic of how the contact grid NetCDF file is processed to load data into structure BRY_CONTACT.

• Fixed a nasty parallel bug in put_refine2d when imposing coarser grid mass flux at the finer grid physical boundaries.

• Added new routine (get_metrics) in nesting.F to process grid spacing metrics on_u and om_v, which are used to impose mass fluxes at the finer grid physical boundaries in refinement applications.

• Added new CPP option ONE_WAY to carry-out one-way nesting in refinement applications. The default is to have two-way nesting.

Additionally, corrected few routines:

• Fixed a bug in ana_m3dobc.h. Few variables are not passed as arguments, so the access is done from the field structures.

• Added logic in inquire.F for better reporting of error messages when the file name is blank (empty).

• Added implicit none to routines in file check_multifile.F and declared a local integer variable. Many thanks to Mark Hadfield for bringing this to my attention.

• Corrected a bug in npzd_iron_inp.h. Used END IF instead of END SELECT. Many thanks to Paul Mattern for ​reporting this problem.