The following files have currently been added or customized for general topology communications.

TBD 
  o for general _RS _RL support the .template forms of exch_ and exch2_ need modifying/creating.
  o MDS based I/O needs to be modified to use tile base coodinates and not to assume a funcional relationship
    between nsx, snx etc...

w2_e2setup.F                   # Does main setting of topology arrays
                               # File is generated from matlab

W2_EXCH2_TOPOLOGY.h            # Holds topology arrays
                               # File is generated from matlab

exch2_xyz_rl.F                 # Does parallel communication for W2 topology
exch2_xy_rl.F                  # Does parallel communication for W2 topology
exch2_uv_xyz_rl.F              # Does parallel communication for W2 topology
exch2_uv_xy_rl.F               # Does parallel communication for W2 topology
exch2_rl2_cube.F               # Does parallel communication for W2 topology
exch2_rl1_cube.F               # Does parallel communication for W2 topology
exch2_get_send_bounds.F        # Does parallel communication for W2 topology
exch2_get_recv_bounds.F        # Does parallel communication for W2 topology
eeboot.F                       # Modified to call W2 toplogy setup
w2_print_comm_sequence.F       # Prints out comms defined by a topology
W2_EXCH2_PARAMS.h              # Mapping between topology and tiled arrays in MITgcm
W2_OPTIONS.h                   # Debug options
CPP_EEMACROS.h                 # Changed to map exch_ to exch2_
EEPARAMS.h                     # Buffer sized modded for debugging and testing
SIZE.h                         # Modified to match topology
                               # Needs to be consistent with
                               # W2_EXCH2_TOPOLOGY.h and
                               # w2_e2setup.F

CPP_EEOPTIONS.h
w2_eeboot.F                    # Drives setting of topology arrays
ini_curvilinear_grid.F         # Reads multi-domain grid definition including overlap 
                               # point at index maxima (i.e. snx+1, sny+1)

exch_uv_xy_rs.F                # call exch2_
exch_uv_xyz_rs.F               # call exch2_
exch_uv_xyz_rl.F               # call exch2_
exch_uv_xy_rl.F                # call exch2_
exch_xy_rl.F                   # call exch2_
exch2_send_rl1.F               # Does parallel communication for W2 topology
exch2_send_rl2.F               # Does parallel communication for W2 topology
exch2_recv_rl1.F               # Does parallel communication for W2 topology
exch2_recv_rl2.F               # Does parallel communication for W2 topology
mom_vi_calc_relvort3.F         # Vorticity switched off for testing

Directories holding example SIZE.h, w2_e2setup.F and W2_EXCH2_TOPOLOGY.h are
as follows. Examples are all for a cs32 index space with different tile sizes.
Until mdsio is fixed to understand tiling only s6t_32x32/, 
s24t_8x32/ and s12t_16x32/ are allowed for runs that rely on global
datasets for input (bathymetry, forcing, pickups etc..) because the cube
global file mode only looks like the cartesian form when sny is the same as
the cube size. However, it is possible to arbitrary size tile runs when using 
tiled input files.

s12t_16x32/                   # 12 tiles of size 16x32
s24t_16x16/                   # 24 tiles of size 16x16 (I/O not available)
s24t_32x8/                    # 24 tiles of size 32x8  (I/O not available)
s24t_8x32/                    # 24 tiles of size  8x32 
s6t_32x32/                    #  6 tiles of size 32x32
s60t_51x510                   # 60 tiles of size 51x510