Add option to create drydep velocity plots from benchmark output #280

yantosca · 2023-12-11T15:13:29Z

Name and Institution (Required)

Name: Bob Yantosca
Institution: Harvard + GCST

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Contributing guidelines

Describe the update

This is the companion PR to #273. We have added the option to plot drydep velocities as part of the standard benchmark outputs.

Updates in this version:

Added script gcpy/benchmark/modules/benchmark_utils.py with a few utility functions.
- This is where we can continue to abstract utility function specific to benchmark plotting codes from gcpy/util.py and gcpy/benchmark_funcs.py.
- Eventually, all of the benchmarking code will be moved from gcpy/gcpy to gcpy/benchmark/*, so as to isolate them from other user functionality.
Added script gcpy/benchmark/modules/benchmark.drydep.py, which contains function make_benchmark_drydep_plots.
Modified the following scripts to call make_benchmark_drydep_plots from benchmark_drydep.py:
- gcpy/benchmark/run_benchmark.py
- gcpy/benchmark/modules/run_1yr_fullchem_benchmark.py
Added the plot_drydep:True YAML tag to:
- gcpy/benchmark/config/1yr_fullchem_benchmark.yml
Added the plot_drydep: False YAML tag to:
- gcpy/benchmark/cloud/template.1hr_benchmark.yml
- gcpy/benchmark/cloud/template.1mo_benchmark.yml
- gcpy/benchmark/config/1yr_ftt_benchmark.yml
- gcpy/benchmark/config/1mo_fullchem_benchmark.yml
Changed operations_budget: False to ops_budget_table: False in gcpy/benchmark/config/1yr_tt_benchmark.yml.
- This is to match the nomenclature used in the fullchem YAML files.

Expected changes

By default, drydep velocity plots are ENABED from in 1-yr fullchem benchmark output.
By default, drydep velocity plots are DISABLED in 1-month and 1-hour fullchem benchmark output.
- Enabling this would require an update in the GEOS-Chem repository to archive the DryDep collection when running 1-month benchmark simulations.

Related Github Issue(s)

Closes [FEATURE REQUEST] Add dry deposition velocities to benchmark output #273, based on a suggestion by @mje1398

gcpy/benchmark/modules/benchmark_drydep.py - Module with routine make_benchmark_drydep_plots gcpy/benchmark/modules/benchmark_utils.py - New module w/ utility routines for benchmark plotting/tabling code. We will eventually pull out other benchmark-specific routines from util.py into this module. gcpy/benchmark/run_benchmark.py - Import and call make_benchmark_drydep_plots from benchmark_drydep.py Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

This commit adds YAML tags that toggle plotting of drydep velocities in the benchmark outputs: gcpy/benchmark/cloud/template.1hr_benchmark.yml - Added "plot_drydep: False" gcpy/benchmark/cloud/template.1mo_benchmark.yml gcpy/benchmark/config/1mo_benchmark.yml gcpy/benchmark/1yr_fullchem_benchmark.yml gcpy/benchmark/1yr_tt_benchmark.yml - Add "plot_drydep: True" Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

gcpy/benchmark/config/1yr_tt_benchmark.yml - Change YAML tag "operations_budget" to "ops_budget_table" to match usage in 1-month and 1-year YAML files CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

In this commit, we have fixed issues in the creation of drydep velocity plots. We have also taken steps to start abstracting commonly-used benchmark code into reusable functions in benchmark_utils.py. This process will be continued in subsequent PRs. gcpy/benchmark/modules/benchmark_drydep.py - Remove unused imports - Add the "collection" keyword argument - Rename "datestr" argument to "subdst" for consistency w/ other routines - Set weightsdir to "." by default - Set default spcdb_dir to gcpy/species_database.yml - Updated Pydoc comments - Removed "plots" argument, as we only have drydep at the surface - Now call make_output_dir from benchmark_utils.py to make the directory where plots will be placed - Now call read_ref_and_dev tfrom benchmark_utils.py to read ref & dev data from disk - Update the call to get_common_varnames from benchmark_utils.py - Abstract the code to create the PDF filename to routine "pdf_filename" in benchmark_utils.py - Remove refmetds and devmetds, they're not needed here - Remove "normalize_by_area" keyword to compare_single_level - Now pass "log_color_scale" to compare_single_level - Abstract code to print significant differences to benchmark_utils.py gcpy/benchmark_utils.py - Updated Pydoc headers - Removed unused imports - Renamed "make_collection_subdir" to "make_output_dir" and simplify code - Update code in read_ref_and_dev - Fix bugs in routine "get_common_varnames", add Pydoc - Add routines "print_sigdiffs" and "write_sigdiff" (needs testing) - Add routine "pdf_filename" to get the name of the PDF output file - Add routine "print_benchmark_info" to print a list of which benchmark plots/tables will be created. This is called from the run_benchmark, run_1yr_fullchem_benchmark, run_1yr_tt_benchmark functions. gcpy/benchmark/modules/run_1yr_fullchem_benchmark.py - Now import and call "make_benchmark_drydep_plots" from "benchmark_drydep.py" - Now call "print_benchmark_info" from "benchmark_utils.py" to display the list of plots/tables being generated gcpy/benchmark/run_benchmark.py gcpy/benchmark/modules/run_1yr_fullchem_benchmark.py - Now call "print_benchmark_info" from "benchmark_utils.py" to display the list of plots/tables being generated CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

gcpy/benchmark/cloud/template.1mo_benchmark.yml gcpy/benchmark/config/1mo_benchmark.yml - Set "plot_drydep: False", as right now we do not archive the DryDep collection from the History diagnostics in 1-month benchmarks. Revisit this if we decide to archive this collection. See issue geoschem/geos-chem#2065 for more info. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

gcpy/benchmark/modules/benchmark_drydep.py - Replace "diff_title" with "sigdiff_type" in call to print_sigdiffs gcpy/benchmark/modules/benchmark_utils.py - Fix calls to util.verify_variable_type so that they use the proper variable names and arguments - Updated Pydoc headers gcpy/benchmark/run_benchmark.py - Add drydep plots for GCHP vs GCC and GCHP vs GCHP - Fix additional "cut-n-paste" errors Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

msulprizio

I think there are some typos in the GCHP vs GCC plots for the drydep option that need to be resolved before merging.

msulprizio · 2024-01-30T19:25:43Z

gcpy/benchmark/modules/run_1yr_fullchem_benchmark.py

@@ -1194,6 +1226,66 @@ def gcc_vs_gcc_ops_budg(mon):
                    n_job=config["options"]["n_cores"]
                )

+        # ==================================================================
+        # GCC vs. GCC drydep plots


This should be "GCHP vs GCC"

Now fixed in commit 26b597e

msulprizio · 2024-01-30T19:26:07Z

gcpy/benchmark/modules/run_1yr_fullchem_benchmark.py

+            print("\n%%% Creating GCHP vs. GCC drydep plots %%%")
+
+            # --------------------------------------------------------------
+            # GCC vs GCC drydep plots: Annual mean


This should be "GCHP vs GCC"

Now fixed in commit 26b597e

msulprizio · 2024-01-30T19:27:13Z

gcpy/benchmark/modules/run_1yr_fullchem_benchmark.py

+
+            # Filepaths
+            ref = get_filepaths(
+                gcc_vs_gcc_refdir,


Should this be gchp_vc_gcc_refdir?

Now fixed in commit 26b597e

msulprizio · 2024-01-30T19:27:50Z

gcpy/benchmark/modules/run_1yr_fullchem_benchmark.py

+            )
+
+            # --------------------------------------------------------------
+            # GCC vs GCC drydep plots: Seasonal


This should be "GCHP vs GCC"

Now fixed in commit 26b597e

msulprizio · 2024-01-30T19:31:09Z

gcpy/benchmark/run_benchmark.py

+            print("\n%%% Creating GCHP vs. GCC drydep plots %%%")
+
+            # Filepaths
+            ref = get_filepath(gcc_vs_gcc_refdir, "DryDep", gcc_ref_date)


Should this be gchp_vs_gcc_refdir?

Now fixed in commit 26b597e

gcpy/benchmark/modules/run_1yr_fullchem_benchmark.py - Fix incorrect comments "GCC vs GCC" -> "GCHP vs GCC" - Use gchp_vs_gcc_refdir and all_months_ref in the call to routine get_filepaths for the GCHP vs GCC ref model gcpy/benchmark/run_benchmark.py - Use gchp_vs_gcc_refdir for in the call to routine get_filepaths for the GCHP vs GCC ref model Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

msulprizio

Looks good to merge now!

gcpy/benchmark/modules/benchmark_drydep.py - Add new routine drydepvel_species - Added varlist argument to make_benchmark_drydep_plots - If varlist is None, then call bmk_util.get_common_varnames to get the common variables in ref & dev to plot gcpy/benchmark/modules/run_1yr_fullchem_benchmark.py gcpy/benchmark/modules/run_benchmark.py - Import new function drydepvel_species() from benchmark_drydep - Pass the output of drydepvel_species() to the varlist argument of make_benchmark_drydep_plots Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

yantosca added 6 commits December 7, 2023 10:49

yantosca added category: Feature Request New feature or request topic: Benchmark Plots and Tables Issues pertaining to generating plots/tables from benchmark output labels Dec 11, 2023

yantosca added this to the 1.5.0 milestone Dec 11, 2023

yantosca requested a review from msulprizio December 11, 2023 15:13

yantosca self-assigned this Dec 11, 2023

yantosca linked an issue Dec 11, 2023 that may be closed by this pull request

[FEATURE REQUEST] Add dry deposition velocities to benchmark output #273

Closed

This was referenced Dec 11, 2023

[FEATURE REQUEST] Add comparison plots for other diagnostic collections #211

Open

[FEATURE REQUEST]: Further DRY out various benchmark plotting scripts #141

Open

msulprizio requested changes Jan 30, 2024

View reviewed changes

yantosca requested a review from msulprizio January 30, 2024 20:08

msulprizio approved these changes Jan 30, 2024

View reviewed changes

yantosca merged commit bbc9e0f into dev Jan 30, 2024
0 of 3 checks passed

yantosca deleted the feature/drydep-velocity-plots branch January 30, 2024 21:18

yantosca mentioned this pull request Feb 2, 2024

[FEATURE REQUEST] Add dry deposition velocities to benchmark output #273

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Add option to create drydep velocity plots from benchmark output #280

Add option to create drydep velocity plots from benchmark output #280

yantosca commented Dec 11, 2023

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Add option to create drydep velocity plots from benchmark output #280

Add option to create drydep velocity plots from benchmark output #280

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yantosca commented Dec 11, 2023

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