This directoyr has several useful (and several un-useful) scripts related to running GENE, visualizing GENE output, manipulating input files, calculating relevant parameters, etc. mostly for pedestal applications.  Here is a very brief overview of some of the most useful scripts.  Feel free to improve this documentation if you feel so inclined.

D_chi_ratio.py:
Calculates ratios of fluxes and diffusivities from linear GENE output.  Useful for identifying modes in the context of the 'fingerprint' framework (see Kotsch. et al  NF 2019).

ParIO.py:
Routines for reading GENE parameter files.

calc_Er_neoclassical.py:
Calculates Er from profiles based on the standard neoclassical expression.

calc_dimensionless_parameters.py:
Calculates various dimensionless parameters from profiles.

calc_eta_from_gene_profiles:
Calculates eta and other profile info from profile files.

calc_gene_shear_rate_iterdb.py:
Calculates the GENE shear rate from an iterdb file.

calc_omega_from_field.py:
Calculates the growth rate and frequency from linear GENE output (useful in case GENE doesn't converge).


calc_shat_from_efit.py:
Calculates magnetic shear from an efit file.

efit_tools.py:
Script for reading and manipulating data from an eqdsk / efit file.

extend_buffer.py
Script for extending geometry files artificially beyond the separatrix for subsequent GENE run.

fieldlib.py
Library for reading GENE field files.

finite_differences.py:
Routines for 4th order finite differences.

get_nrg.py
Reads GENE output nrg files.

interp.py
Routines for interpolation.

make_iterdb.py
Routine for writing iterdb files.

modProfs_fixedP.py
Tools for modifying profiles in various ways to test sensitivites while keeping pressure fixed.

momlib.py
Library for reading GENE moment files.

mtmDopplerFreqs.py:
Tool for calculating predicted MTM frequencies (omega*) and the Doppler shift.

my_efit_tools.py
Reading and manipulating eqdsk / efit files.

nrgdata.py
Reading GENE nrg files.

plot_mode_structures.py:
GENE tool for plotting linear mode structures from GENE (can be used for local or global).

read_write_geometry.py:
Scripts for reading / writing GENE geometry files (e.g. tracer_efit.dat)

LN_RIP.py: 
Nonloal nonlinear radial magnetic fluctruation for Sythetic diagnostic for RIP (Faraday-Effect Radial Interferometer-Polarimeter) 

k_f_B_contour:
Reads the csv files from the output of LN_RIP.py to replot or add the desired Doppler shift 

remove_edge_opt:
output the array that is the evenly distributed without the effort of edge opt