Changes

updated check budgets balance test to be compatible with branch test for testing python 3 version

updating check budgets script on main branch

last minute addition

The big grid change. Converting gr from being an array of types containing 1D arrays, to a type containing 2D arrays. All cases BFB, cam multicolumn+silhs BFB, and cam multicolumn (no silhs) with backwards compatible settings BFB.

Adds to tuning dashboard an arrow plot of biases.

Also adds other plots that show regional biases versus
sensitivity of those regions to parameter values.

For #910.

Removing the zt2zm interface from clubb_api and making the api calls just redirect to the grid class interface for it.

Pushing column loop into mean advection procedures.

Little loop push

Moving above/below index of grid weights to last dimension.

Missed file meant for commit e7ce96456e691ac84abf467670642a8ec90f4bb9.

Changing a few spots that use gr%weights that should have been included in commit 2f3542cea1a4dea1b242dd61947087b6458548fb

Hardcoding 1 into uses of gr arrays where single column versions of gr is used.

Pushing loop into fill_holes.

Forgot small change.

Making compatible with latest clubb change.

Making linear_interpolated_azt_2D and linear_interpolated_azm_2D subroutines just to avoid a needless data copy.

Making update_xp2_mc 2D and creating interface for 1D calls.

Missed file in previous commit.

Just a line to read me, because commit a19386022f26aa17da805381904bcde4c59cb521 fixed the bit diff tests after a previous commit broke it, RESOLVED:991ebceb8caba2ad56c1125871b7de1de3c04dba.

Fixing units in stats_zt_module.F90

This change will be BIT_CHANGING because it will affect the descriptions of variables in the netcdf files, but will not change answers.

Adding config file for nvhpc on casper.

modified clubb_ifort_configuration file to support nan trapping for uninitialized variables

renamed clubb_ifort_build to clubb_ifort_debug_run and updated jenkinsfile to reflect

forgot to change if statements in jenkinsfile

created debug case for gfortran as well as updating jenkins files to work with it, as well as a forgotten change to the ifort debug test jenkinsfile

Adds to the tuning dashboard a quadratic optimizer.
The quadratic optimizer minimizes a quadratic cost function
that includes the 2nd-order term in the Taylor series
expansion of metrics as a function of parameters.
Also uses the high and low parameter values to
calculate the sensitivity matrix, rather than
the default parameter values.

For #910.

Update README

Changed Needler to Nelder (as in Nelder-Mead method)

Changed intent out to inout to fix grid deallocation error during cleanup.

Added a3_coef_min_minmax entry to namelist init_minmax for ALL the tuner input files to prevent error with gfortran compiler (min > max)

Added some comments. Changing some variable names might be nicer, loss might make more sense than energy, n1 and n2 are meaningless, etc.

Updates info on tuner.

Fixing a bug in mono_flux_limiter.F90. (#1026)

* Fixing a bug in mono_flux_limiter.F90.  This code was outputting "xm" instead of "wpxp" in several places.

This commit is BIT_CHANGING since it will affect the netcdf output for these variables, even though there
is no real change to answers.

* Renaming wpthlp_entermfl to wpthlp_enter_mfl which is more consistent with other variable names.

This is BIT_CHANGING due to changing the name and description in the output netcdf files.

* Renaming a few more instances of wpthlp_entermfl to wpthlp_enter_mfl.

Fixing a bug.

Update README

Removing line to trigger nightly tests.

Adds to tuner dashboard a plot of predicted and actual removal of regional biases.
The plot displays an arrow for each regional bias
that points from the default-run bias
to the bias that remains after tuning.

For #910.

Adding line to trigger nightly tests.

Removing line to trigger nightly tests.

Adding line to trigger nightly tests.

Updates tuner with new simulations from Zhun.

For #910.

I discovered a bug when trying to run with all_stats today.  Apparently,
 at some point in the past, the stat variable Richardson_num had been
entered twice.  I am removing one of those instances so the code runs
agaim.

I changed the w_up_in_cloud code in 2 ways:

1)  The denominator term is now the "cloudy updraft" frac in each
PDF component, rather than just the PDF component cloud_frac.  This
is more consistent with the quantity being integrated.

2)  I also added a w_down_in_cloud for cloudy downdraft velocity.

Since these fields are not output as part of standard stats, this
commit will be bit-for-bit for the normal CLUBB output files.

I added stats output for w_down_in_cloud to all_stats.in.

Since this stat was not added to standard_stats.in, official results
will still be bit-for-bit.

I added w_down_in_cloud to the "Ws" variable group in pyplotgen.

I altered the w_up_in_cloud and w_down_in_cloud code so that a
thresholding is used similar to what is seen in the cloud fraction
and cloud water code.  If the PDF component mean of w more than
the maximum allow number of standard deviations away from 0, the
PDF component is either all-updrafty or all-downdrafty, and the
code avoids expensive computations where large magnitude values
can potentially be fed into ERF or EXP.

Of course, the results are not bit-for-bit with the previous version,
meaning that there are some situations where these thresholds come
into effect.  However, plots of all cases show no visible differences
in w_up_in_cloud and w_down_in_cloud.

Since w_up_in_cloud and w_down_in_cloud are not included in normal
stats output, this commit does not change the bit-for-bitness of
CLUBB code.

I have optimized the new w_up_in_cloud and w_down_in_cloud code by
only doing repeated operations one time and then saving them as a
local variable.

Since the numerical order of operations changes for the argument
to the EXP term, the results will differ at the level of numerical
round-off, making this revision not bit-for-bit with the last revision.
This only affects the w_up_in_cloud and w_down_in_cloud statistical
output variables, which in turn are not output as part of
standard_stats.in.

Update README.md

updating timestep_convergence_test.py to python 3 #693

Refactored fill_holes_vertical to make GPUization simple. This is BIT_CHANGING, but results are bit-for-bit when using -O0 optimization, thus it is not answer changing. The first pass over each grid column will not parallelize well, the k-loop needs to be done in serial. Maximum parallelization has been exposed for the global hole-filling though, at the cost of occasionally doing unneccesary calculations. larson-group/clubb#972.

Removing fill_holes_multiplicative and replacing magic numbers with parameters from constants_clubb. larson-group/clubb#972

Moving vertical_avg and vertical_integral to advance_helper_module. larson-group/clubb#972

Making compatible with latest clubb change.

Raw-copy updating src/Morrison_microphys

rewrote run_bindiff_all.bash into python, and added extra functionality to view output of diff_netcdf_outputs.py script that is run inside of it. #980

Removing elementalness from sat_vapor_press_liq and making interal procedures subroutines rather than functions to prevent unneccesary data copies. Doing the same for thlm2T_in_K since it is often used in conjunction with sat_vapor_press_liq. Bit-for-bit confirmed with O0 using all single column cases with or without l_diag_Lscale_from_tau, and with cam_coarse_res. larson-group/clubb#972

Adding comments.

Adding initial subroutine calc_ice_cloud_frac_component.

Cleaning up new subroutine calc_liquid_cloud_frac_component, and making sat_mixrat_ice a subroutine that works the same way as sat_mixrat_liq. larson-group/clubb#972

Comment update

Removing these paratheses is BIT_CHANGING since it modifies the order of operations, but allows for the multiplication and subraction to be done in parallel for complex pipelines.

Adding line to indicate BIT_CHANGING:055f83d512354e6330233a5eecd5cff0456c0292 to fix nightly tests. The commit which introduced calc_ice_cloud_frac_component was not BFB using -O2 optimization. See pull request https://github.com/larson-group/clubb/pull/1034 for detail.

Adding a kludgy but functional trimming for the (non-CLUBB) variables that are
processed via the '_calc' key.  These variables are not trimmed like the others
since they are processed in a different place, and therefore the plots will
not have the correct min/max height without this fix.  This seems to matter
for budget lines from non-CLUBB models (no CLUBB variables have the '_calc' key).

In tuner, creates box and whiskers version of plot

for optimal parameter values.

Adds near-coastal regions to the tuner.

Includes Nambian_near and VOCAL_near regions.

Making multicolumn version of advance_clubb_core in clubb_driver that accepts a number of columns to run clubb with. All bit-for-bit output on standalone cases, so the first column is correct.

Improvements. Netcdf output is now functional and we can detect errors with multiple columns even when the standard output is identical.

Now the multicolumn netcdf output is correct. Adding comments too. larson-group/clubb#1033

Made the multicolumn inout arrays save from timestep to timestep. This makes the extra columns more independent from the main column and allows differences in the extra columns to propagate more. larson-group/clubb#1033

Adding some fields to tweak for extra columns. This might be sufficient, the netcdf data for the column is similar but visually different, and I tested with up to 64 columns and there wasn't any crashes. larson-group/clubb#1033

Adding script to compare netcdf outputs. This will print the max absolute diff and max percent diff for each field. This is made specifically for the multicolumn netcdf output. The script is not done, but this is the basics of it. larson-group/clubb#1033

Casting 0.0 to correct precision that format_date wants.

Updating script to compare netcdf output. larson-group/clubb#1033

Updating column num input in config flags. larson-group/clubb#1033

Adding small check to allow configurable_multi_column_nl to be optional. If configurable_multi_column_nl is omitted from configurable_model_flags, then we assume we only want 1 column and a warning is printed. larson-group/clubb#1033

Small script update

Adding comments to script.

Adding comments, setting to num_standalone_columns=1 by default, and preventing multicolumn output when l_stats=false. larson-group/clubb#1033

Namelists need to be closed with a '/', and omitting it will break many tests.

Making save variables in the multicol code threadprivate, this fixes the openmp test. Also changing the way we name and save the multicol output, this allows the parallel run to run with multiple columns. I've reflected the changes in comments where relevant. larson-group/clubb#1033

Adds commented-out line that prevents the monotonic flux

limiter from acting on rtm.  The comments are included to remind us of how to do this in case we choose to do so in the future.

Updating monotonic flux limiter code to remove spikes. (#1038)

Also putting a commented out code change in advance_xm_wpxp,
in case shutting of the flux limiter entirely for rtm is preferred.

See https://github.com/NCAR/amwg_dev/discussions/134 for discussion.

This commit will be BIT_CHANGING although the differences are only
obvious in sensitive cases like arm_97.

Creating new flags to control monotonic flux limiter (#1039)

* Creating new flags to control monotonic flux limiter and the IF statement fix for the spikes found in CAM.

* Removing no-longer-necessary logical l_mono_flux_lim.

* Adding requested changes from PR (intent statements and editing error statement).

* Accidentally set flag to false. Changing to true.

I am adding cloudy_updraft_frac and cloudy_downdraft_frac as
outputs to the calculate_w_up_in_cloud code.

These fields are non-interactive for the standard set of cases.
Thus, all cases are bit-for-bit identical.

However, for the w_up_in_cloud and w_down_in_cloud results themselves,
it is possible that results might not be bit-for-bit since
the location of the max(eps, ...) clipping in the denominator
is changed.  However, results should not be appreciable different.

I forgot to add cld_updr_frac and cld_downdr_frac to all_stats.in
in the last commit.