Changes

Fixed some oversights for the bv_efold commits and increased string length for tuning field names for invrs_tau variables - CLUBB ticket #1069 (#1106)

This commit is NOT bit changing
- Removed remaining mentions of brunt_vaisala_freq_sqd_plus
- Added assignment for invrs_tau_wp3_zm in Lscale mode in advance_clubb_core
- Increased length of string variables hoc_v, les_v, and t_variables in src/error.F90 to accomodate tuning for invrs_tau fields

BIT_CHANGING! brunt_vaisala_freq_sqd_mixed now replaces brunt_vaisala_freq_sqd for later calculations - CLUBB ticket #1102

Changes in src/CLUBB_core/mixing_length.F90:
- brunt_vaisala_freq_sqd_mixed is now used to calculate brunt_vaisala_freq_sqd_smth and brunt_vaisala_freq_sqd_clipped instead of brunt_vaisala_freq_sqd
- Removed 0.1 factor for bkgnd term in calculation of invrs_tau_xp2_zm
- Commented out clipping of invrs_tau_xp2_zm to 0.003 and lower out of cloud

Added option to plot "Lumped Buoyance Budgets" (wpxp_bp combined with
wpxp_pr3) to the pyplotgen plotter for CLUBB.

Added a statement that I had previously omitted. The new combined budget
works great!

Updating pyplotgen to include a "contour" plot of rcm in the background.
This will be made optional with the next commit.

I added the --background-rcm optional flag to pyplotgen.

Small additions that allow all cases to run with pyplotgen.

Needed to remove a print statement.

In the previous commits for the --background-rcm option of pyplotgen,
I had previously thought that the code to extract values of rcm from
a file wanted the case name as input, but in actuality it required
the directory name instead of the case name. I am correcting that
error in this commitment.

I am updating the --background-rcm option of pyplotgen to make two
changes:

1) Use a grayscale color map.
2) Set the maximum of the colorbar to be twice the largest value in
the rcm plot so that the colors aren't so dark.

BIT_CHANGING for lscale setup. Updated configurable_model_flags.in and model_flags.F90 - CLUBB ticket #1102 (#1108)

- Added new flags to inut/tunable_parameters_Lscale/configurable_model_flags.in
- Changed default setting for l_use_tke_in_wp3_pr_turb_term in model_flags.F90 from false to true

QuadTune: Adds chisqd metric and bar chart for a global run.
linSolnBiasesCol has been redefined to mean simulation - obs.

For #910.

QuadTune: adds commented-out attempt to vary the bar base
but it's not working yet.

For #910.

Likely BIT_CHANGING because of added output fields. Added code outputting C6_term and different Brunt Vaisala frequencies to disk - CLUBB ticket #1102 (#1109)

- Added C6_term and bv_freq fields to all_stats.F90 and standard_stats.F90
- Added new fields to VariableGroupTaus.py in pyplotgen
- Added calls to stat_update_var to advance_clubb_core_module.F90
- Modified stats_variables.F90 and stats_zm_module.F90 accordingly

Changed sqrt_Ri_zm to Ri_zm in preparation of changing the exponent for calculation of invrs_tau_wpxp_zm in mixing_length.F90 - CLUBB ticket #1102 (#1110)

BIT_CHANGING! Changed sqrt_Ri_zm to Ri_zm in preparation of changing the exponent for calculation of invrs_tau_wpxp_zm in mixing_length.F90 - CLUBB ticket #1102
Changes in input/stats/all_stats.in, src/CLUBB_core/advance_clubb_core_module.F90, src/CLUBB_core/mixing_length.F90, src/CLUBB_core/stats_variables.F90, and src/CLUBB_core/stats_zm_module.F90
Ri_zm was added to input/stats/standard_stats.in

BIT_CHANGING! Removed Richardson_num and all corresponding code - CLUBB ticket #1102 (#1111)

This commit is BIT_CHANGING because:
1. the output field Richardson_num was removed.
2. Since the flag l_use_shear_turb_freq_sqd was removed, the variable shear_sqd is now always written to disk. That means previously, the outputted field shear_sqd was 0 everywhere whereas now it is not anymore. The calculation of shear_sqd within CLUBB did not change!
- Removed mentions in input/stats/all_stats.in and standards_stats.in
- Removed mentions in src/CLUBB_core/stats_variables.F90 and stats_zm_module.F90
- In src/CLUBB_core/advance_helper_module.F90 removed mentions to [i]Richardson_num[_clipped], as well as l_use_shear_turb_freq_sqd, l_Richardson_vert_avg, and turb_freq_sqd sinc those are only used for calculation of Richardson_num.

QuadTune: Adds fnc to plot a horizonal bar chart for metrics.

For #910

QuadTune: Includes full perturbation in params bar chart

QuadTune: Adds new parameter correlation matrix plot.

For #910.

Major overhaul of run_bindiff_all.py

CLUBB ticket #1102 - pull request #1113
- Changed the outputs to be more evocative and differentiating between types of differences: Now we can distinguish between differences in the set of variables or differences in specific variables
- Fixed the issue where a variable that appears in only one of the compared files would either not be detected or cause the script to crash, depending on the order of input.
- Changed file output structure
- Changed case handling depending on existing files:
    - Case is still treated even if it is commented in RUN_CASES
    - Case is still treated even if not all files exist and messages are printed accordingly