This README.txt file was generated on 23 JAN 2025 by Sam Kelly


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GENERAL INFORMATION
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These Matlab scripts analyze raw data from: 

(1) Elmer and Austin (Apr 15 2022). Lake Superior moored temperature and currents, Spring 2015 to Spring 2021. Data Repository for the University of Minnesota (DRUM). 10.13020/nw8b-mk79

(2) National Data Buoy Center meteorological data (https://www.ndbc.noaa.gov/)

(3) Great lakes bathymetry (https://www.ncei.noaa.gov/products/great-lakes-bathymetry)
 
The output is the data included in the plotting_scripts folder, which includes all variables necessary to make the article's figures. The scripts included here are primarily for reference, and will not work without first downloading all of the raw data and organizing it into the expected folders.


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SCRIPT DESCRIPTION OF a_isopycnal_displacement.m
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This script computes local isopycnal excursion (zeta [Nz x Nt]) from a 5-day running average of the background stratification.

Function dependencies: 
None

Input files:
(1) data/NICE_2017_metadata.mat
(2) data/post_QC_T/*.mat

Output files:
(1) data/processed/post_QC_T/*.mat


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SCRIPT DESCRIPTION OF b_compute_modes.m 
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This script uses a function (MODES.m by Sam Kelly, 21 AUG 2015, smkelly@d.umn.edu) to compute the vertical normal modes [Nz x 1] at each mooring, as well as the time series of modal amplitudes [1 x Nt] of reduced pressure (pn), horizontal velocity (Un), and isopyncal displacement (Zn) at each mooring. Uses post-processed time series of potential density profiles (extrapolated to top & bottom of water column), horizontal velocity profiles stored as a complex number, and isopycnal displacements from a 5-day lowpass.

Function dependencies: 
(1) MODES.m

Input files:
(1) data/NICE_2017_metadata.mat
(2) data/processed/*.mat
(3) data/processed/post_QC_T/*.mat

Output files:
(1) data/modes/*.mat


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SCRIPT DESCRIPTION OF c_energy_filter.m 
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Takes time series of modal amplitudes and filters them using a butterworth filter of order & cutoff specified.  Then computes KE, PE, and fluxes by mode for the total, highpassed, & lowpassed data.

Function dependencies: 
None

Input files:
(1) data/NICE_2017_metadata.mat
(2) data/modes/*.mat

Output files:
(1) data/modes/*.mat
(2) data/modes/lowpassed/*.mat
(3) data/modes/highpassed/*.mat


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SCRIPT DESCRIPTION OF d_wind_stress_power.m
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This script takes interpolated wind data (eg. NDBC buoy data) and rotates the axes to match the axes of the nearest mooring. The wind stress is then calculated using the Large & Pond (1981) method (calls stresslp.m from the air-sea toolbox) and is then highpassed and the power "into" each mode of the system is calculated (negative power indicates deceleration of surface currents, units are [W m^-2]).

Function dependencies: 
(1) stresslp.m (air-sea toolbox)

Input files:
(1) data/NICE_2017_metadata.mat
(2) WM_wind.mat
(3) data/modes/*.mat
(4) data/modes/highpassed/*.mat

Output files:
(1) data/modes/*.mat
(2) data/WM_tau.mat
(3) data/modes/highpassed/*.mat


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FUNCTION DESCRIPTION OF MODES.m
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Obtain vertical modes for arbitrary stratification with a rigid lid

INPUTS:
dz  (1 x 1) [m]   vertical spacing (must be uniform)
N2  (Nz x 1) [1/s^2]   stratification 
Nm  (1 x 1 ) []  number of modes to extract 
flag_0 (1 x 1) [] Set to 1 (default) to include mode-0, set to 0 to exclude mode-0

OUTPUTS:
PHI  (Nz x Nm) []  pressure and velocity structure eigenfunctions 
C    (Nm x 1 ) [m/s]  eigenspeeds 
PHI2 (Nz x Nm) []  vertical velocity structure eigenfunctions 


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TOOLBOX DESCRIPTION of air-sea 
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Surface fluxes are computed using functions from the air-sea toolbox at https://github.com/sea-mat/air-sea

STRESSLP: estimates winds stress from wind speed using bulk formulas