This README.txt file was generated on 9 MAR 2022 by Sam Kelly

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GENERAL INFORMATION
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These are the configuration files for the MIT general circulation model (MITgcm, v 1.1936 2013/11/05, http://mitgcm.org/). The model is extensively documented online. 

There are two sub-folders within the MITgcm folder that contain all the setup information needed for each type of run:
(1) bump: oscillating flow over a coastal bump
(2) Oregon: K1 barotropic tidal velocities over the Oregon continental slope

The standard folders within each run are:
(1) build: all compile-time options for the MITgcm (read with model is compiled)
(2) input: all run-time options for the MITgcm (read when model is executed)
(3) matlab: all Matlab codes used to create input files (gendata.m) and process the output files (main.m)

Only the Matlab scripts and functions are unique and documented here.

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SCRIPT DESCRIPTION OF gendata.m
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Writes input files that are read when MITgcm is executed

Function dependencies: 
CTW_modes.m
LAT2KM.m
LON2KM.m
satbath.m
TPXO.m

Input files:
strat.mat

Output files:
data.mat

Binary output files (read by MITgcm):
delXvar
delYvar
delZvar
tRefvar
topog.init
T.init
EU.ob
EV.ob
ET.ob
NU.ob
NV.ob
NT.ob
SU.ob
SV.ob
ST.ob
WU.ob
WU.ob
WT.ob

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SCRIPT DESCRIPTION OF main.m
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Post-processes all of the MITgcm ouput files. Combines relevant data into small MAT files that can be easily read and plotted. 

Function dependencies: 
post_process.m

Input:
none 

Output files:
mit_L.mat
mit_W.mat

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SCRIPT DESCRIPTION OF post_process.m
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Post-processes a single MITgcm simulation run. Reads data and projects them onto mode. 

Function dependencies: 
CTW_modes.m

Input:
folder (MITgcm output directory path)

Input files:
data.mat (produced by gendata.m)
MITgcm NetCDF output files

Output files:
data_post.mat

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FUNCTION DESCRIPTION OF CSW_modes.m
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see function header

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FUNCTION DESCRIPTION OF LAT2KM.m
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Input:
None

Output:
The number of kilometers per degree of latitude.

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FUNCTION DESCRIPTION OF LON2KM.m
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Input:
Latitude [deg]

Output:
The number of kilometers per degree of longitude.

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FUNCTION DESCRIPTION OF satbath.m
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Builtin matlab function to read the Smith & Sandwell global bathymetry. This function was modified on lines 98-99 and 120 to read the 1-minute bathymetry file (topo_8.2.img).

See Matlab documentation for inputs and outputs.

File dependency (available at https://topex.ucsd.edu/marine_topo/):
topo_8.2.img

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FUNCTION DESCRIPTION OF TPXO.m
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Reads the NetCDF TPXOO8 atlas and returns the amplitudes of the tidal transports and elevations at each lon and lat. The amplitudes can be used to predict the tides for a given constituent using the formula:

U(x,y,t)=Real[U(x,y)*exp(ii*omega*t)]

where t is seconds from the start of the input day

Input:
lon    [m x 1] or [m x n]  Vector of longitudes [0 360]
lat    [n x 1] or [m x n]  Vector of latitudes [-90 90]
conID  [k x 1]             Constituents to include (e.g., see list below, [1 3] returns M2 and K1)
day	   [1 x 1]             The serial day (use 'datenum') for which the phase is set to zero
vel_flag (0 or 1)          If 0 (default) return transports, if 1 return velocity

Output:
U, V   [m x n x k]  Complex amplitude of transport [m^2/s]
eta    [m x n x k]  Complex amplitude of tidal elevation [m] 
omega  [k x 1]      The tidal frequency in rad/s

File dependencies (available at https://www.tpxo.net/):
uv.k1_tpxo8_atlas_30c.nc
hf.k1_tpxo8_atlas_30c.nc
grid_tpxo8atlas_30.nc