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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
</comment><date>2023-09-05 13:19:07 -0500</date><id>c1f62c5040949404906f8d13ecb9cf7ee88f4ce5</id><msg>Fixed some oversights for the bv_efold commits and increased string length for tuning field names for invrs_tau variables - CLUBB ticket #1069 (#1106)</msg><path><editType>edit</editType><file>src/CLUBB_core/advance_helper_module.F90</file></path><path><editType>edit</editType><file>src/error.F90</file></path><path><editType>edit</editType><file>src/CLUBB_core/advance_clubb_core_module.F90</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>src/CLUBB_core/mixing_length.F90</affectedPath><commitId>346643e9a3d430e30182bc4b244f6251fdf50b9e</commitId><timestamp>1693950812000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>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
</comment><date>2023-09-05 16:53:32 -0500</date><id>346643e9a3d430e30182bc4b244f6251fdf50b9e</id><msg>BIT_CHANGING! brunt_vaisala_freq_sqd_mixed now replaces brunt_vaisala_freq_sqd for later calculations - CLUBB ticket #1102</msg><path><editType>edit</editType><file>src/CLUBB_core/mixing_length.F90</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>postprocessing/pyplotgen/config/VariableGroupBaseBudgetsLumpedBuoy.py</affectedPath><affectedPath>postprocessing/pyplotgen/README.md</affectedPath><affectedPath>postprocessing/pyplotgen/src/CaseGallerySetup.py</affectedPath><affectedPath>postprocessing/pyplotgen/pyplotgen.py</affectedPath><commitId>35388814c501b3b4754806ecdb494cbcadc77d0a</commitId><timestamp>1694154859000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/bmg2</absoluteUrl><fullName>bmg2</fullName></author><authorEmail>bmg2@uwm.edu</authorEmail><comment>Added option to plot "Lumped Buoyance Budgets" (wpxp_bp combined with
wpxp_pr3) to the pyplotgen plotter for CLUBB.
</comment><date>2023-09-08 01:34:19 -0500</date><id>35388814c501b3b4754806ecdb494cbcadc77d0a</id><msg>Added option to plot "Lumped Buoyance Budgets" (wpxp_bp combined with</msg><path><editType>edit</editType><file>postprocessing/pyplotgen/src/CaseGallerySetup.py</file></path><path><editType>add</editType><file>postprocessing/pyplotgen/config/VariableGroupBaseBudgetsLumpedBuoy.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/pyplotgen.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/README.md</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>postprocessing/pyplotgen/src/CaseGallerySetup.py</affectedPath><commitId>db8ea9192a6aa0da6612223ebf569e46f293c92d</commitId><timestamp>1694155550000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/bmg2</absoluteUrl><fullName>bmg2</fullName></author><authorEmail>bmg2@uwm.edu</authorEmail><comment>Added a statement that I had previously omitted. The new combined budget
works great!
</comment><date>2023-09-08 01:45:50 -0500</date><id>db8ea9192a6aa0da6612223ebf569e46f293c92d</id><msg>Added a statement that I had previously omitted. The new combined budget</msg><path><editType>edit</editType><file>postprocessing/pyplotgen/src/CaseGallerySetup.py</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>postprocessing/pyplotgen/src/VariableGroup.py</affectedPath><affectedPath>postprocessing/pyplotgen/src/Panel.py</affectedPath><commitId>616669cf5f2194502e9ecbafb2d267635d439c32</commitId><timestamp>1694492156000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/bmg2</absoluteUrl><fullName>bmg2</fullName></author><authorEmail>bmg2@uwm.edu</authorEmail><comment>Updating pyplotgen to include a "contour" plot of rcm in the background.
This will be made optional with the next commit.
</comment><date>2023-09-11 23:15:56 -0500</date><id>616669cf5f2194502e9ecbafb2d267635d439c32</id><msg>Updating pyplotgen to include a "contour" plot of rcm in the background.</msg><path><editType>edit</editType><file>postprocessing/pyplotgen/src/VariableGroup.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/src/Panel.py</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>postprocessing/pyplotgen/config/VariableGroupWs.py</affectedPath><affectedPath>postprocessing/pyplotgen/src/Panel.py</affectedPath><affectedPath>postprocessing/pyplotgen/README.md</affectedPath><affectedPath>postprocessing/pyplotgen/pyplotgen.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupBase.py</affectedPath><affectedPath>postprocessing/pyplotgen/src/VariableGroup.py</affectedPath><affectedPath>postprocessing/pyplotgen/src/CaseGallerySetup.py</affectedPath><commitId>09e01df1a3bf71ada4cc050fa3f0d52f285b6028</commitId><timestamp>1694548709000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/bmg2</absoluteUrl><fullName>bmg2</fullName></author><authorEmail>bmg2@uwm.edu</authorEmail><comment>I added the --background-rcm optional flag to pyplotgen.
</comment><date>2023-09-12 14:58:29 -0500</date><id>09e01df1a3bf71ada4cc050fa3f0d52f285b6028</id><msg>I added the --background-rcm optional flag to pyplotgen.</msg><path><editType>edit</editType><file>postprocessing/pyplotgen/src/VariableGroup.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/src/Panel.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/README.md</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/pyplotgen.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/src/CaseGallerySetup.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupBase.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupWs.py</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>postprocessing/pyplotgen/config/VariableGroupSubcolumns.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupBaseBudgets.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupLiquidMP.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupCorrelations.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupTaus.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupNormalizedVariations.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupKKMP.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupSamBudgets.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupNondimMoments.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupIceMP.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupSamMultilineProfiles.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupBaseBudgetsLumpedBuoy.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupSamProfiles.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupScalars.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupBaseBudgetsSamStyle.py</affectedPath><commitId>cbbd5fc72fb563eb89430f77b0d790b32aea1a4c</commitId><timestamp>1694570526000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/bmg2</absoluteUrl><fullName>bmg2</fullName></author><authorEmail>bmg2@uwm.edu</authorEmail><comment>Small additions that allow all cases to run with pyplotgen.
</comment><date>2023-09-12 21:02:06 -0500</date><id>cbbd5fc72fb563eb89430f77b0d790b32aea1a4c</id><msg>Small additions that allow all cases to run with pyplotgen.</msg><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupBaseBudgets.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupIceMP.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupNormalizedVariations.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupScalars.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupNondimMoments.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupSamProfiles.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupTaus.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupCorrelations.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupSubcolumns.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupSamBudgets.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupSamMultilineProfiles.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupBaseBudgetsLumpedBuoy.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupKKMP.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupBaseBudgetsSamStyle.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupLiquidMP.py</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>postprocessing/pyplotgen/src/VariableGroup.py</affectedPath><commitId>693a178ea4becdb7f4950d8406c89a4953bdbbcd</commitId><timestamp>1694570977000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/bmg2</absoluteUrl><fullName>bmg2</fullName></author><authorEmail>bmg2@uwm.edu</authorEmail><comment>Needed to remove a print statement.
</comment><date>2023-09-12 21:09:37 -0500</date><id>693a178ea4becdb7f4950d8406c89a4953bdbbcd</id><msg>Needed to remove a print statement.</msg><path><editType>edit</editType><file>postprocessing/pyplotgen/src/VariableGroup.py</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>postprocessing/pyplotgen/config/VariableGroupSubcolumns.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupWs.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupBaseBudgets.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupLiquidMP.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupCorrelations.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupTaus.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupKKMP.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupNormalizedVariations.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupBase.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupSamBudgets.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupNondimMoments.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupIceMP.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupSamMultilineProfiles.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupBaseBudgetsLumpedBuoy.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupSamProfiles.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupScalars.py</affectedPath><affectedPath>postprocessing/pyplotgen/src/VariableGroup.py</affectedPath><affectedPath>postprocessing/pyplotgen/src/CaseGallerySetup.py</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupBaseBudgetsSamStyle.py</affectedPath><commitId>f974d0717da12952984f5f165abf99e4f1586115</commitId><timestamp>1694628419000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/bmg2</absoluteUrl><fullName>bmg2</fullName></author><authorEmail>bmg2@uwm.edu</authorEmail><comment>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.
</comment><date>2023-09-13 13:06:59 -0500</date><id>f974d0717da12952984f5f165abf99e4f1586115</id><msg>In the previous commits for the --background-rcm option of pyplotgen,</msg><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupLiquidMP.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupWs.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupTaus.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupBase.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupBaseBudgets.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupBaseBudgetsLumpedBuoy.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupCorrelations.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/src/VariableGroup.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupSamBudgets.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupKKMP.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupSubcolumns.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupSamMultilineProfiles.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/src/CaseGallerySetup.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupScalars.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupIceMP.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupSamProfiles.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupNormalizedVariations.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupBaseBudgetsSamStyle.py</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupNondimMoments.py</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>postprocessing/pyplotgen/src/Panel.py</affectedPath><commitId>1510c34473a4c7b51f7dd08fb75cff28c701af07</commitId><timestamp>1694633655000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/bmg2</absoluteUrl><fullName>bmg2</fullName></author><authorEmail>bmg2@uwm.edu</authorEmail><comment>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.
</comment><date>2023-09-13 14:34:15 -0500</date><id>1510c34473a4c7b51f7dd08fb75cff28c701af07</id><msg>I am updating the --background-rcm option of pyplotgen to make two</msg><path><editType>edit</editType><file>postprocessing/pyplotgen/src/Panel.py</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>input/tunable_parameters_Lscale/configurable_model_flags.in</affectedPath><affectedPath>src/CLUBB_core/model_flags.F90</affectedPath><commitId>e29d9d7e6d8b2857cd4f85382d189b21c31332b7</commitId><timestamp>1694635856000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>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
</comment><date>2023-09-13 15:10:56 -0500</date><id>e29d9d7e6d8b2857cd4f85382d189b21c31332b7</id><msg>BIT_CHANGING for lscale setup. Updated configurable_model_flags.in and model_flags.F90 - CLUBB ticket #1102 (#1108)</msg><path><editType>edit</editType><file>src/CLUBB_core/model_flags.F90</file></path><path><editType>edit</editType><file>input/tunable_parameters_Lscale/configurable_model_flags.in</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>utilities/sens_matrix/set_up_dashboard_inputs.py</affectedPath><affectedPath>utilities/sens_matrix/sens_matrix_dashboard.py</affectedPath><commitId>fb63ca4ea140c4abedef5567d8c33c331cce9ec1</commitId><timestamp>1694692835000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/vlarson</absoluteUrl><fullName>Vince Larson</fullName></author><authorEmail>vlarson@uwm.edu</authorEmail><comment>QuadTune: Adds chisqd metric and bar chart for a global run.
linSolnBiasesCol has been redefined to mean simulation - obs.

For #910.
</comment><date>2023-09-14 07:00:35 -0500</date><id>fb63ca4ea140c4abedef5567d8c33c331cce9ec1</id><msg>QuadTune: Adds chisqd metric and bar chart for a global run.</msg><path><editType>edit</editType><file>utilities/sens_matrix/set_up_dashboard_inputs.py</file></path><path><editType>edit</editType><file>utilities/sens_matrix/sens_matrix_dashboard.py</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>utilities/sens_matrix/sens_matrix_dashboard.py</affectedPath><commitId>5ed8fb8308e908d83cc8c9c34c61b80b0449a995</commitId><timestamp>1695125054000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/vlarson</absoluteUrl><fullName>Vince Larson</fullName></author><authorEmail>vlarson@uwm.edu</authorEmail><comment>QuadTune: adds commented-out attempt to vary the bar base
but it's not working yet.

For #910.
</comment><date>2023-09-19 07:04:14 -0500</date><id>5ed8fb8308e908d83cc8c9c34c61b80b0449a995</id><msg>QuadTune: adds commented-out attempt to vary the bar base</msg><path><editType>edit</editType><file>utilities/sens_matrix/sens_matrix_dashboard.py</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>src/CLUBB_core/advance_clubb_core_module.F90</affectedPath><affectedPath>postprocessing/pyplotgen/config/VariableGroupTaus.py</affectedPath><affectedPath>input/stats/standard_stats.in</affectedPath><affectedPath>src/CLUBB_core/stats_variables.F90</affectedPath><affectedPath>input/stats/all_stats.in</affectedPath><affectedPath>src/CLUBB_core/stats_zm_module.F90</affectedPath><commitId>1a81400d8f997d9c9b3a128a4cf4a001dd849b3e</commitId><timestamp>1695154187000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>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
</comment><date>2023-09-19 15:09:47 -0500</date><id>1a81400d8f997d9c9b3a128a4cf4a001dd849b3e</id><msg>Likely BIT_CHANGING because of added output fields. Added code outputting C6_term and different Brunt Vaisala frequencies to disk - CLUBB ticket #1102 (#1109)</msg><path><editType>edit</editType><file>input/stats/standard_stats.in</file></path><path><editType>edit</editType><file>input/stats/all_stats.in</file></path><path><editType>edit</editType><file>src/CLUBB_core/stats_variables.F90</file></path><path><editType>edit</editType><file>src/CLUBB_core/advance_clubb_core_module.F90</file></path><path><editType>edit</editType><file>src/CLUBB_core/stats_zm_module.F90</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupTaus.py</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>src/CLUBB_core/advance_clubb_core_module.F90</affectedPath><affectedPath>input/stats/standard_stats.in</affectedPath><affectedPath>src/CLUBB_core/stats_variables.F90</affectedPath><affectedPath>src/CLUBB_core/mixing_length.F90</affectedPath><affectedPath>src/CLUBB_core/stats_zm_module.F90</affectedPath><affectedPath>input/stats/all_stats.in</affectedPath><commitId>6654de29a1f573a0a6562d29393a4e18eeabd2ef</commitId><timestamp>1695421268000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>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
</comment><date>2023-09-22 17:21:08 -0500</date><id>6654de29a1f573a0a6562d29393a4e18eeabd2ef</id><msg>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)</msg><path><editType>edit</editType><file>src/CLUBB_core/stats_zm_module.F90</file></path><path><editType>edit</editType><file>src/CLUBB_core/advance_clubb_core_module.F90</file></path><path><editType>edit</editType><file>src/CLUBB_core/stats_variables.F90</file></path><path><editType>edit</editType><file>input/stats/standard_stats.in</file></path><path><editType>edit</editType><file>input/stats/all_stats.in</file></path><path><editType>edit</editType><file>src/CLUBB_core/mixing_length.F90</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>postprocessing/pyplotgen/config/VariableGroupTaus.py</affectedPath><affectedPath>src/CLUBB_core/advance_helper_module.F90</affectedPath><affectedPath>src/CLUBB_core/stats_variables.F90</affectedPath><affectedPath>input/stats/all_stats.in</affectedPath><affectedPath>src/CLUBB_core/stats_zm_module.F90</affectedPath><commitId>405d449ae8bc9a7dad1b37fe5cb4964e397bd92e</commitId><timestamp>1695428333000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>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.
</comment><date>2023-09-22 19:18:53 -0500</date><id>405d449ae8bc9a7dad1b37fe5cb4964e397bd92e</id><msg>BIT_CHANGING! Removed Richardson_num and all corresponding code - CLUBB ticket #1102 (#1111)</msg><path><editType>edit</editType><file>input/stats/all_stats.in</file></path><path><editType>edit</editType><file>src/CLUBB_core/stats_zm_module.F90</file></path><path><editType>edit</editType><file>src/CLUBB_core/stats_variables.F90</file></path><path><editType>edit</editType><file>src/CLUBB_core/advance_helper_module.F90</file></path><path><editType>edit</editType><file>postprocessing/pyplotgen/config/VariableGroupTaus.py</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>utilities/sens_matrix/set_up_dashboard_inputs.py</affectedPath><affectedPath>utilities/sens_matrix/sens_matrix_dashboard.py</affectedPath><commitId>cb5a053323264071fc1a7862137cfd2a06193b19</commitId><timestamp>1695677623000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/vlarson</absoluteUrl><fullName>Vince Larson</fullName></author><authorEmail>vlarson@uwm.edu</authorEmail><comment>QuadTune: Adds fnc to plot a horizonal bar chart for metrics.

For #910
</comment><date>2023-09-25 16:33:43 -0500</date><id>cb5a053323264071fc1a7862137cfd2a06193b19</id><msg>QuadTune: Adds fnc to plot a horizonal bar chart for metrics.</msg><path><editType>edit</editType><file>utilities/sens_matrix/set_up_dashboard_inputs.py</file></path><path><editType>edit</editType><file>utilities/sens_matrix/sens_matrix_dashboard.py</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>utilities/sens_matrix/sens_matrix_dashboard.py</affectedPath><commitId>a4f7432f4f85c2ec4f9d97d723f9574cc1320623</commitId><timestamp>1695694497000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/vlarson</absoluteUrl><fullName>Vince Larson</fullName></author><authorEmail>vlarson@uwm.edu</authorEmail><comment>QuadTune: Includes full perturbation in params bar chart
</comment><date>2023-09-25 21:14:57 -0500</date><id>a4f7432f4f85c2ec4f9d97d723f9574cc1320623</id><msg>QuadTune: Includes full perturbation in params bar chart</msg><path><editType>edit</editType><file>utilities/sens_matrix/sens_matrix_dashboard.py</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>utilities/sens_matrix/sens_matrix_dashboard.py</affectedPath><commitId>59786b03dd4afb944e5e9284a2b207220122dbb9</commitId><timestamp>1696287802000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/vlarson</absoluteUrl><fullName>Vince Larson</fullName></author><authorEmail>vlarson@uwm.edu</authorEmail><comment>QuadTune: Adds new parameter correlation matrix plot.

For #910.
</comment><date>2023-10-02 18:03:22 -0500</date><id>59786b03dd4afb944e5e9284a2b207220122dbb9</id><msg>QuadTune: Adds new parameter correlation matrix plot.</msg><path><editType>edit</editType><file>utilities/sens_matrix/sens_matrix_dashboard.py</file></path></item><item _class='hudson.plugins.git.GitChangeSet'><affectedPath>run_scripts/RUN_CASES</affectedPath><affectedPath>run_scripts/run_bindiff_all.py</affectedPath><affectedPath>input/stats/standard_stats.in</affectedPath><affectedPath>run_scripts/run_scm.bash</affectedPath><affectedPath>input/stats/all_stats.in</affectedPath><commitId>6de84c3d28a538d620009cbe3d98a634782820be</commitId><timestamp>1696965177000</timestamp><author><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></author><authorEmail>noreply@github.com</authorEmail><comment>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
</comment><date>2023-10-10 14:12:57 -0500</date><id>6de84c3d28a538d620009cbe3d98a634782820be</id><msg>Major overhaul of run_bindiff_all.py</msg><path><editType>edit</editType><file>run_scripts/run_bindiff_all.py</file></path><path><editType>edit</editType><file>run_scripts/RUN_CASES</file></path><path><editType>edit</editType><file>input/stats/all_stats.in</file></path><path><editType>edit</editType><file>input/stats/standard_stats.in</file></path><path><editType>edit</editType><file>run_scripts/run_scm.bash</file></path></item><kind>git</kind></changeSet><culprit><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/bmg2</absoluteUrl><fullName>bmg2</fullName></culprit><culprit><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/vlarson</absoluteUrl><fullName>Vince Larson</fullName></culprit><culprit><absoluteUrl>http://carson.math.uwm.edu/jenkins/user/noreply</absoluteUrl><fullName>noreply</fullName></culprit><inProgress>false</inProgress><nextBuild><number>541</number><url>http://carson.math.uwm.edu/jenkins/view/all/job/clubb_mac_gfortran_test/541/</url></nextBuild><previousBuild><number>539</number><url>http://carson.math.uwm.edu/jenkins/view/all/job/clubb_mac_gfortran_test/539/</url></previousBuild></workflowRun>