Add pH diagnostics for mozart_mosaic_4bin_aq chemistry option #999

stacywalters · 2019-10-23T20:37:49Z

TYPE: new feature

KEYWORDS: pH, cloud water, aerosols, mozart_mosaic_4bin_aq

SOURCE: Mary Barth (ACOM/MMM NCAR)

DESCRIPTION OF CHANGES:

Alter Registry/registry.chem to include diagnostic pH variables ph_cw, ph_aer01, ph_aer02,
ph_aer03, and ph_aer04.
Modify files, listed below, to calculate and set pH diagnostic variables

MOZART is a gas-phase chemistry mechanism (set of reactions) in WRF-Chem

MOSAIC is one of the aerosol models in WRF-Chem that represents the size distribution
of the aerosols with 4 size bins (hence "4bin")

The pH is calculated for each of the 4 aerosol size bins. That is why there are 4 variables: pH_aer1,
aer2, aer3, aer4.

pH is a diagnostic variable and is calculated as part of the aerosol model. However what we added
was the ability to write out the field to the history file. It is by default turned off as an output field,
but can be "turned on" using the iofields.txt file.

There is also cloud water pH (pH_CW) which is calculated as part of the cloud chemistry routine.
Same thing as aerosol pH, by default it is not an output field, but can be included in history files
via iofields.txt.

For pretty pictures and a description of what we learned, feel free to look at the report for the
ACOM lab: https://nar.ucar.edu/2019/acom/predicting-acidity-aerosols-and-cloud-water.

Sample:

LIST OF MODIFIED FILES:
Registry/registry.chem
chem/chem_driver.F
chem/cloudchem_driver.F
chem/module_mosaic_cloudchem.F
chem/aerosol_driver.F
chem/module_mosaic_driver.F
chem/module_mosaic_therm.F
chem/module_chem_cup.F

TESTS CONDUCTED:

Small GNU-only WTF on MMM classroom machines (status=0 means bit-for-bit)

Thu Oct 24 09:23:40 MDT 2019
SUCCESS_RUN_WRF_d01_em_real_32_em_real_03FD vs SUCCESS_RUN_WRF_d01_em_real_33_em_real_03FD status = 0
SUCCESS_RUN_WRF_d01_em_real_32_em_real_03FD vs SUCCESS_RUN_WRF_d01_em_real_34_em_real_03FD status = 0
SUCCESS_RUN_WRF_d01_em_real_32_em_real_10 vs SUCCESS_RUN_WRF_d01_em_real_33_em_real_10 status = 0
SUCCESS_RUN_WRF_d01_em_real_32_em_real_10 vs SUCCESS_RUN_WRF_d01_em_real_34_em_real_10 status = 0
SUCCESS_RUN_WRF_d01_em_real_32_em_real_11 vs SUCCESS_RUN_WRF_d01_em_real_33_em_real_11 status = 0
SUCCESS_RUN_WRF_d01_em_real_32_em_real_11 vs SUCCESS_RUN_WRF_d01_em_real_34_em_real_11 status = 0
SUCCESS_RUN_WRF_d01_em_real_32_em_real_20NE vs SUCCESS_RUN_WRF_d01_em_real_33_em_real_20NE status = 0
SUCCESS_RUN_WRF_d01_em_real_32_em_real_20NE vs SUCCESS_RUN_WRF_d01_em_real_34_em_real_20NE status = 0
SUCCESS_RUN_WRF_d01_em_real_32_em_real_conus vs SUCCESS_RUN_WRF_d01_em_real_33_em_real_conus status = 0
SUCCESS_RUN_WRF_d01_em_real_32_em_real_conus vs SUCCESS_RUN_WRF_d01_em_real_34_em_real_conus status = 0
SUCCESS_RUN_WRF_d01_em_real_32_em_real_tropical vs SUCCESS_RUN_WRF_d01_em_real_33_em_real_tropical status = 0
SUCCESS_RUN_WRF_d01_em_real_32_em_real_tropical vs SUCCESS_RUN_WRF_d01_em_real_34_em_real_tropical status = 0
SUCCESS_RUN_WRF_d01_nmm_real_32_nmm_nest_01 vs SUCCESS_RUN_WRF_d01_nmm_real_34_nmm_nest_01 status = 0
SUCCESS_RUN_WRF_d01_nmm_real_32_nmm_nest_03 vs SUCCESS_RUN_WRF_d01_nmm_real_34_nmm_nest_03 status = 0
SUCCESS_RUN_WRF_d01_nmm_real_32_nmm_nest_04a vs SUCCESS_RUN_WRF_d01_nmm_real_34_nmm_nest_04a status = 0
SUCCESS_RUN_WRF_d01_nmm_real_32_nmm_nest_06 vs SUCCESS_RUN_WRF_d01_nmm_real_34_nmm_nest_06 status = 0
SUCCESS_RUN_WRF_d01_em_real_32_em_chem_1 vs SUCCESS_RUN_WRF_d01_em_real_34_em_chem_1 status = 0
SUCCESS_RUN_WRF_d01_em_real_32_em_chem_2 vs SUCCESS_RUN_WRF_d01_em_real_34_em_chem_2 status = 0
SUCCESS_RUN_WRF_d01_em_real_32_em_chem_5 vs SUCCESS_RUN_WRF_d01_em_real_34_em_chem_5 status = 0

davegill · 2019-10-24T14:47:58Z

@stacywalters
Stacy,
The purpose of the regression test is to make sure that we have not broken anything. We also want a "postive" test. Generate a few plots to show the pH diagnostics, and include that in the commit message.

davegill · 2019-10-24T14:49:51Z

Registry/registry.chem

@@ -20,6 +20,12 @@ state    real    QC_B4MP         ikj    misc        1         -      -        "Q
 state    real    QI_B4MP         ikj    misc        1         -      -        "QI_B4MP"             "CLOUD ICE BEFORE MICROPHYSICS"    "kg kg-1"
 state    real    QS_B4MP         ikj    misc        1         -      -        "QS_B4MP"             "SNOW BEFORE MICROPHYSICS"         "kg kg-1"

+state    real    ph_cw           ikj    misc        1         -      -        "ph_cw"               "pH of cloud water"             "unitless"


Stacy,
If these diagnostics are only to be activated when a specific namelist option is selected, these should all be in a package.

@ravanah @kayeekayee
If this is indeed an optional diagnostic, then the namelist option that activates the pH for Mozart should be used for a package for the ph_cw, ph_aer01 through 04.

davegill · 2019-10-24T14:52:46Z

chem/module_mosaic_driver.F

@@ -135,6 +135,7 @@ subroutine mosaic_aerchem_driver(                         &
 		id, curr_secs, ktau, dtstep, ktauc, dtstepc, config_flags, &
 		t_phy, rho_phy, p_phy,                            &
 		moist, chem, vbs_nbin,                            &
+                ph_aer01, ph_aer02, ph_aer03, ph_aer04,           &


Stacy,
Line these up

davegill · 2019-10-24T15:37:25Z

@stacywalters
Stacy,
For the benefit of the non-Chem people ...
Would you please add a few sentences in the description concerning

why there are 4 new fields
what is "in" aer1, 2, 3, 4
brief explanation of what the mozart, mosaic, 4bin pieces all mean
is there a way to turn this off?

davegill · 2019-10-24T19:52:45Z

@stacywalters
Stacy,
I have incorporated Mary's text in the PR. Thanks!

stacywalters · 2019-10-24T20:01:47Z

Dave, Thanks for handling this. I'm trying to reach Mary regarding your suggestion to wrap the ph diagnostics in a package. It should not be difficult. But I need Mary's take on it. Stacy

…

On Thu, Oct 24, 2019 at 3:52 PM Dave Gill ***@***.***> wrote: @stacywalters <https://github.com/stacywalters> Stacy, I have incorporated Mary's text in the PR. Thanks! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#999?email_source=notifications&email_token=ACA4BEVGCBUKSAMQKTJD6IDQQH4I7A5CNFSM4JEJTWWKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOECGHMXY#issuecomment-546076255>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACA4BEVGVB4CF5QZAC2JVJDQQH4I7ANCNFSM4JEJTWWA> .

ravanah

Is the packaging of the arrays done as suggested by Dave?

jordanschnell · 2020-07-06T20:43:09Z

@stacywalters - Can you package the ph_* diagnostics as suggested by the others?

trigger jenkins

KEYWORDS: pH, cloud water, aerosols, mozart_mosaic_4bin_aq SOURCE: Mary Barth (ACOM/MMM NCAR) and Stacy Walters (formerly NCAR) DESCRIPTION OF CHANGES: Originally submitted as PR wrf-model#999, but was resubmitted due to inconsistencies Alter Registry/registry.chem to include diagnostic pH variables ph_cw, ph_aer01, ph_aer02, ph_aer03, and ph_aer04. Modify files, listed below, to calculate and set pH diagnostic variables MOZART is a gas-phase chemistry mechanism (set of reactions) in WRF-Chem Diagnostics are activated with namelist,chem option mozart_ph_diag=1 MOSAIC is one of the aerosol models in WRF-Chem that represents the size distribution of the aerosols with 4 size bins (hence "4bin") The pH is calculated for each of the 4 aerosol size bins. That is why there are 4 variables: pH_aer1, aer2, aer3, aer4. pH is a diagnostic variable and is calculated as part of the aerosol model. However what we added was the ability to write out the field to the history file. It is by default turned off as an output field, but can be "turned on" using the iofields.txt file. There is also cloud water pH (pH_CW) which is calculated as part of the cloud chemistry routine. Same thing as aerosol pH, by default it is not an output field, but can be included in history files via iofields.txt. For pretty pictures and a description of what we learned, feel free to look at the report for the ACOM lab: https://nar.ucar.edu/2019/acom/predicting-acidity-aerosols-and-cloud-water. LIST OF MODIFIED FILES: Registry/registry.chem chem/chem_driver.F chem/cloudchem_driver.F chem/module_mosaic_cloudchem.F chem/aerosol_driver.F chem/module_mosaic_driver.F chem/module_mosaic_therm.F chem/module_chem_cup.F

KEYWORDS: pH, cloud water, aerosols, mozart_mosaic_4bin_aq SOURCE: Mary Barth (ACOM/MMM NCAR) and Stacy Walters (formerly NCAR) DESCRIPTION OF CHANGES: Originally submitted as PR #999, but was resubmitted due to inconsistencies Alter Registry/registry.chem to include diagnostic pH variables ph_cw, ph_aer01, ph_aer02, ph_aer03, and ph_aer04. Modify files, listed below, to calculate and set pH diagnostic variables MOZART is a gas-phase chemistry mechanism (set of reactions) in WRF-Chem Diagnostics are activated with namelist,chem option mozart_ph_diag=1 MOSAIC is one of the aerosol models in WRF-Chem that represents the size distribution of the aerosols with 4 size bins (hence "4bin") The pH is calculated for each of the 4 aerosol size bins. That is why there are 4 variables: pH_aer1, aer2, aer3, aer4. pH is a diagnostic variable and is calculated as part of the aerosol model. However what we added was the ability to write out the field to the history file. It is by default turned off as an output field, but can be "turned on" using the iofields.txt file. There is also cloud water pH (pH_CW) which is calculated as part of the cloud chemistry routine. Same thing as aerosol pH, by default it is not an output field, but can be included in history files via iofields.txt. For pretty pictures and a description of what we learned, feel free to look at the report for the ACOM lab: https://nar.ucar.edu/2019/acom/predicting-acidity-aerosols-and-cloud-water. LIST OF MODIFIED FILES: Registry/registry.chem chem/chem_driver.F chem/cloudchem_driver.F chem/module_mosaic_cloudchem.F chem/aerosol_driver.F chem/module_mosaic_driver.F chem/module_mosaic_therm.F chem/module_chem_cup.F

KEYWORDS: pH, cloud water, aerosols, mozart_mosaic_4bin_aq SOURCE: Mary Barth (ACOM/MMM NCAR) and Stacy Walters (formerly NCAR) DESCRIPTION OF CHANGES: Originally submitted as PR wrf-model#999, but was resubmitted due to inconsistencies Alter Registry/registry.chem to include diagnostic pH variables ph_cw, ph_aer01, ph_aer02, ph_aer03, and ph_aer04. Modify files, listed below, to calculate and set pH diagnostic variables MOZART is a gas-phase chemistry mechanism (set of reactions) in WRF-Chem Diagnostics are activated with namelist,chem option mozart_ph_diag=1 MOSAIC is one of the aerosol models in WRF-Chem that represents the size distribution of the aerosols with 4 size bins (hence "4bin") The pH is calculated for each of the 4 aerosol size bins. That is why there are 4 variables: pH_aer1, aer2, aer3, aer4. pH is a diagnostic variable and is calculated as part of the aerosol model. However what we added was the ability to write out the field to the history file. It is by default turned off as an output field, but can be "turned on" using the iofields.txt file. There is also cloud water pH (pH_CW) which is calculated as part of the cloud chemistry routine. Same thing as aerosol pH, by default it is not an output field, but can be included in history files via iofields.txt. For pretty pictures and a description of what we learned, feel free to look at the report for the ACOM lab: https://nar.ucar.edu/2019/acom/predicting-acidity-aerosols-and-cloud-water. LIST OF MODIFIED FILES: Registry/registry.chem chem/chem_driver.F chem/cloudchem_driver.F chem/module_mosaic_cloudchem.F chem/aerosol_driver.F chem/module_mosaic_driver.F chem/module_mosaic_therm.F chem/module_chem_cup.F

Stacy

edb8a44

stacywalters requested a review from a team as a code owner October 23, 2019 20:37

stacywalters changed the title ~~Stacy~~ Add pH diagnostics for mozart_mosaic_4bin_aq chemistry option Oct 23, 2019

davegill added WRF Chem Enhancement Develop Branch New Feature and removed Enhancement labels Oct 24, 2019

davegill reviewed Oct 24, 2019

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ravanah approved these changes Feb 21, 2020

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ravanah reviewed Feb 21, 2020

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Update cloudchem_driver.F

9dffb9b

trigger jenkins

jordanschnell mentioned this pull request Dec 23, 2020

Add pH diagnostics for mozart_mosaic_4bin_aq chemistry #1342

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jordanschnell closed this Feb 15, 2021

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Add pH diagnostics for mozart_mosaic_4bin_aq chemistry option #999

Add pH diagnostics for mozart_mosaic_4bin_aq chemistry option #999

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edited by davegill

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Add pH diagnostics for mozart_mosaic_4bin_aq chemistry option #999

Add pH diagnostics for mozart_mosaic_4bin_aq chemistry option #999

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