Cloud chemistry module review

[mattldawson]

Reimplements four cloud chemistry modules with new file and module names so that the code can be reviewed.

closes #1

From issue #1, things to consider in review:

• missing descriptions for units for variables
• missing descriptions of functions and function arguments
• unused variables
• cryptically named variables
• dead code blocks
• potential to break up large code blocks, and introduce reusable/testable functions
• compare MAM and CARMA code for consistency
• identify host-model vs aerosol-model portions of the code
• separate configuration data from algorithms
• magic numbers

[dwfncar]

This loop can be condensed and re-ordered.

[tilmes]

not sure how this would work?

[dwfncar]

Could split subroutine into sox_cldaero_tend to compute tendencies and sox_cldaero_update to apply tendencies.

[dwfncar]

Index gymnastics is confusing here.

[tilmes]

This indexing can be removed, similar to what is done in carma_clouds.F90 Line 72 to 102.

[K20shores]

Reviewing cloud_aqueous_chemistry.F90

[K20shores]

What does cloud_borne logically mean?

[mattldawson]

I agree, this needs to be described clearly in the source code. Recent conversations with people who have worked on CAM for years revealed that there is a lot of confusion about what this actually means.

[K20shores]

Do we have a reference for these or is this just known in the ether of science? Is it applicable forever and always or only for a certain range of environmental conditions?

[dmleung]

I am not sure about this. This module is Mary's expertise and she can confirm and add references.

[K20shores]

well did the bug get corrected? Is the correction const0 or the multiplication of const0

[dmleung]

I have no idea about this. Someone needs to figure this out... Maybe in our regular Tue meetings.

[K20shores]

are we sure it's specific? If so, why is it?

[dmleung]

I remember Simone and Mary talked about this a while ago and nobody knew what happened here. I am not sure if they now have an updated view on this...

[K20shores]

do we have a citation for these values?

[K20shores]

also these values

[K20shores]

Is it this paper? If so, let's add a full bibliographical citation that includes the DOI

[K20shores]

cloud_utilities.F90 reivew

[K20shores]

but WHY is it bounded? Because a reference says we have to? Because numerically only values beteween 0.5 - 50 are valid?

[dmleung]

According to line 115 they applied the bounds at line 118 etc to avoid occasional unphysical values. I have no idea why that is the case though.

[K20shores]

We use a constant from another module here, but in cloud_aqueous_chemistry.F90 we defined several constants within the code. We should probably push those constants into mo_constants if they don't exist

[K20shores]

What is the significance of 3/(4 pi)? WHY

[dmleung]

Given xl (liquid water content) they want to estimate the droplet radius.
V = 4*pi/3 * R^3
So
V * 0.75/pi is related to the radius. See line 113 below.

[K20shores]

Is 4.0e4_r8 arbitrary? Why this value? what makes radxnum_cd and why is 4.0e4_r8 related to that?

[dmleung]

I think theses are just bounds. They didn't want radxnum_cd to be smaller than volx34pi_cd*4.0e4 and bigger than volx34pi_cd*4.0e8. Again, I don't know why. This is a question for Mary.

[K20shores]

If this is from mosaic, do we have a reference for where these values come from and why? Do we know if they are always valid or does mosaic assume something we don't?

[dmleung]

I can think of a reference for knudsen number (I am sure some textbooks will have this equation) but Mary probably knows better

[K20shores]

Suggested change

	! *(gas diffusivity)*(fuchs sutugin correction)
	! *(gas diffusivity)*(fuchs sutugin correction)
	! Fuchs Sutugin correction:
	! Fuchs, N.A., Sutugin, A.G., 1971. HIGH-DISPERSED AEROSOLS, in: Hidy, G.M., Brock, J.R. (Eds.),
	! Topics in Current Aerosol Research, International Reviews in Aerosol Physics and Chemistry. Pergamon, p. 1.
	! https://doi.org/10.1016/B978-0-08-016674-2.50006-6

Is this a correct reference? Took me forever to track down

[dmleung]

Yes this is correct. A lot of papers on sulfur chemistry also used Fuchs' formulation. E.g., see
https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2005jd005870

[dmleung]

The unit of this is also kg/m2/s

[dmleung]

These two have a unit of kg/m2/s too.

[K20shores]

carma_clouds.F90

[K20shores]

Can we just delete this since it's commented out?

[dmleung]

Yes I think so

[K20shores]

In other places (the backward euler solver) small is set to 1e-40. I imagine there are other versions of small throughout CAM. Do we happen to know why this particular value of small is more useful for clouds?

[dmleung]

I think it depends on the order of magnitudes of the variables concerned. in the code here the order of magnitudes of chemical tracers (e.g., SO2, H2O2) are typically anywhere between 1e-14 (0.01 ppt) to 1e-5 or (10 ppm) in volume mixing ratios. People then want to disregard the reactions once the concentrations are low enough.
The small_value can definitely change depending on the situation and variable concerned. E.g., the small_value for relative humidity should be 0.1 instead of 1e-20. For solving differential equations, I think it makes sense that people try to make things as accurate as possible by using smaller small_values even for chemical tracers. But I think there's always wiggle room, e.g., setting 1e-30 in the solver probably doesn't hurt at all.

[K20shores]

Perhaps we can delete commented out code?

Suggested change

!integer, allocatable :: bin_idx(:,:) ! table for local indexing of modal aero number and mmr

[dmleung]

I guess Mary is the best to answer this. Mary needs to review the code changes...

[K20shores]

Suggested change

	!st if (id_nh3>0) then
	!st delnh3 = nh3g(i,k) - xnh3(i,k)
	!st delnh4 = - delnh3
	!st endif

[K20shores]

Suggested change

	!st dmsadt_gasuptk_tomsa = dmsadt_gasuptk
	!st if (ntot_msa_c == 0) then
	!st dmsadt_gasuptk_tomsa = 0.0_r8
	!st dmsadt_gasuptk_toso4 = dmsadt_gasuptk
	!st end if

[K20shores]

Suggested change

!qin(i,k,id_h2so4) = MAX( qin(i,k,id_h2so4), small_value )

[K20shores]

Suggested change

! fwetrem = max( 0.0_r8, (1.0_r8-exp(-min(100._r8,dtime*frso2_c*clwlrat(i,k)))) )

[K20shores]

Suggested change

! fwetrem = max( 0.0_r8, (1.0_r8-exp(-min(100._r8,dtime*frh2o2_c*clwlrat(i,k)))) )

[K20shores]

Suggested change

	!st if (id_nh3>0) then
	!st dqdt_aq = delnh3/dtime*cldfrc(i,k)
	!st dqdt = dqdt_aq
	!st qin(i,k,id_nh3) = qin(i,k,id_nh3) + dqdt * dtime
	!st endif

[boulderdaze]

What does inv_* stand for?

[dmleung]

According to Francis and Simone, inv_* stands for invariant. So, it sounds like in certain compsets people holds these tracers (SO2, NH3, H2O2, etc.) constant. In most cases nowadays I don't think we use invariant tracers, so the code mostly uses id_so2 instead of inv_so2, for instance. But, it's used for some compsets.

Francis is the one to answer this question.

[boulderdaze]

What does masterproc mean? (There is a typo: sox_inti -> sox_init.)
It doesn't appear to provide useful information, and it also duplicates the following logs.

[dmleung]

masterproc comes from utils/spmd_utils.F90 and is a flag called when scientists want to write() something in a log file.
Yes, that's a typo and can be changed to sox_init.

[boulderdaze]

Some variables (line435, line 492 and so on) that are constant should be defined outside the loop.

[dmleung]

I am not sure about this. Line 435 and line 458 are different, so the existing approach is to declare xe as real(r8) and update xe for different reactions. xe is a constant in line 435 but get updated in line 458 as a function of work1 (which is dependent on temperature tfld).

[boulderdaze]

Should we verify if this code is valid?

[dmleung]

I think these lines mean that if you remove lines 821-824, lines 818-820 sometimes will not work. This is probably because xso2 was too small (smaller than 1.e-20_r8), but I'm not sure why that is the case. This is something that Mary should comment on.

BTW, I think line 822 can be
xso2(i,k)=small_value

[boulderdaze]

This function is large and difficult to test. I think it would be beneficial to break it down into smaller functions for each step, or a series of steps to make it more testable.

[dmleung]

Sure, I think since the code is being refactored it is up to the software engineers to design how the code looks like, as long as it looks good to Mary (this is her science after all).

[marybarthbrock]

I am a-okay with breaking the code down into smaller functions.

[boulderdaze]

My understanding of this function is that it sets variables to update cldaero by calling sox_cldaero_update(). There are also variables with intent(out) (eg. xphlwc in line 880) that aren't used for updating cldaero. What is the purpose of those variables, and how are they used?

[dmleung]

I think there are two questions here:

1. sox_cldaero_update() is a function that calculates and outputs the production rates of sulfate (so4) with cloud chemistry through several pathways (e.g., so4 formed due to o3 oxidation, due to h2o2 oxidation, etc). So, looking at sox_cldaero_update() under carmo_aero/carma_cloud.F90, the only intent(out) variables are aqso4, aqh2so4, aqso4_h2o2, ... which are sulfate production rates (kg/m2/s). sox_cldaero_update() is called here in aerosol/cloud_aqueous_chemistry.F90, so setsox() gets these arrays as intent(out) too (see line 215). And, when setsox() is called in the aerosol interface, we will see that they are outputted by setsox() just to be set as history variables, as follows:

     call outfld( 'AQSO4_H2O2', aqso4_h2o2(:ncol), ncol, lchnk)
     call outfld( 'AQSO4_O3',   aqso4_o3(:ncol),   ncol, lchnk)
     call outfld( 'XPH_LWC',    xphlwc(:ncol,:),   ncol, lchnk )
   

2. I think lines 875-878 and lines 880-887 are two different things. xphlwc is a separate intent(out) variable that setsox() wants to output when setsox() is called. It is also a history variable in the aerosol interface, as follow:

     call outfld( 'XPH_LWC',    xphlwc(:ncol,:),   ncol, lchnk )
   

=====

I copied the above code for outfld() from the CESM2.2 version. In the older CESM2.2, modal_aero/aero_model.F90 calls setsox(), setsox() calculates xphlwc and calls sox_cldaero_update() that calculates aqso4 etc, and aero_model.F90 gets them and do outfld(), so scientists get the history fields for plotting and analyses. I'm not sure where setsox() is called in this new CAM tag, and Francis and Simone will know better where the aerosol interface is. You can also grep it in this new CAM code.

But basically in one sentence, the purpose of sox_cldaero_update() in CESM2.2 is to output sulfate formation rates to aero_model.F90 so scientists get the history fields.

[boulderdaze]

If fwetrem is zero, then dqdt_wr should also be zero, which seems to be unnecessary logic. Could you confirm?

[dmleung]

Agreed. I'm not sure why h2o2 and so2 wet removals were decided to set as zero. I think Mary should make a decision on whether fwetrem should be non-zero (i.e., using line 424 instead of line 425).

But yes, if we just keep the code as is, I would say this can be deleted or commented out (preferred).

[marybarthbrock]

I believe fwetrem for h2o2 and so2 is set to zero because wet removal (or wet scavenging) is computed elsewhere in CAM-chem (the Neu & Prather scheme, mo_neu_wetdep.F90). Let's confirm this with Francis and Simone. If it's correct, then I suggest removing these lines of code.

[marybarthbrock]

Hi all, Water dissociates: H2O <--> H+ + OH- And Kw is its dissociation equilibrium constant: Kw = [H+] [OH-] = 1.e-14 M^2 (M = Molar = mol/L) So, xkw is the H2O dissociation constant. Reference: Seinfeld and Pandis textbook Some side notes -- Because of this weak dissociation, it allows the pH to be defined: pH = -log10 [H+] where pH = 7.0 for pure water at 298K. If you look at the list of parameter statements, there is a pattern: [Gas] <--> [Aq] where KH = Henry's Law equilibrium constant. [Aq] <--> [H+] + [Aq-] where K1 = first dissociation equilibrium constant [Aq-] <--> [H+] + [Aq=] where K2 = second dissociation equilibrium constant

…

-- Mary ^--^--^--^--^--^--^--^--^--^--^--^--^--^--^-^--^--^--^-^--^ Mary Barth Senior Scientist phone: 303-497-8186 email: ***@***.*** NSF - National Center for Atmospheric Research P.O. Box 3000 Boulder, CO 80307 Staff web page <https://staff.ucar.edu/users/barthm> SIMA Web Site <http://sima.ucar.edu> MUSICA Web Site <http://www2.acom.ucar.edu/sections/multi-scale-infrastructure-chemistry-modeling-musica> DC3 Web Site <http://www2.acom.ucar.edu/dc3/> ^--^--^--^--^--^--^--^--^--^--^--^--^--^--^-^--^--^--^-^--^

On Fri, Feb 21, 2025 at 2:35 PM Danny M. Leung ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In src/chemistry/aerosol/cloud_aqueous_chemistry.F90 <#5 (comment)>: > + real(r8), parameter :: const0 = 1.e3_r8/6.023e23_r8 + real(r8), parameter :: xa0 = 11._r8 + real(r8), parameter :: xb0 = -.1_r8 + real(r8), parameter :: xa1 = 1.053_r8 + real(r8), parameter :: xb1 = -4.368_r8 + real(r8), parameter :: xa2 = 1.016_r8 + real(r8), parameter :: xb2 = -2.54_r8 + real(r8), parameter :: xa3 = .816e-32_r8 + real(r8), parameter :: xb3 = .259_r8 + + real(r8), parameter :: kh0 = 9.e3_r8 ! HO2(g) -> Ho2(a) + real(r8), parameter :: kh1 = 2.05e-5_r8 ! HO2(a) -> H+ + O2- + real(r8), parameter :: kh2 = 8.6e5_r8 ! HO2(a) + ho2(a) -> h2o2(a) + o2 + real(r8), parameter :: kh3 = 1.e8_r8 ! HO2(a) + o2- -> h2o2(a) + o2 + real(r8), parameter :: Ra = 8314._r8/101325._r8 ! universal constant (atm)/(M-K) + real(r8), parameter :: xkw = 1.e-14_r8 ! water acidity Yes, that looks like [H+] when ph=14 and that looks like a scaling factor to me — Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALB5EDQFEY25NV5FDAYIAMT2Q6L3ZAVCNFSM6AAAAABSRA4PC6VHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMZDMMZUGI4TSNRTGU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[mattldawson]

Would it be better to use the CO2 concentration from the model state? (also, this value seems like it might be low for the current atmosphere, unless I'm misinterpreting this) @dmleung - what do you think?

[dmleung]

Hmm I think so! I think in older model treatments CO2 is always fixed, but there is no reason we need to stick with it now given we have active CO2 chemistry in the chem_mech.in. We can follow the treatment of so2g and h2o2g, which are also from the model state.

[marybarthbrock]

Matt, If the model state provides CO2, then please use it! Yes, 330 ppmv is low. It's more representative of 1970 (or earlier) values. However, I did a calculation once that showed me that the CO2 value didn't have a big influence on the pH estimate. That's because sulfate and nitrate dominate the pH calculation. - Mary ^--^--^--^--^--^--^--^--^--^--^--^--^--^--^-^--^--^--^-^--^ Mary Barth Senior Scientist phone: 303-497-8186 email: ***@***.*** NSF - National Center for Atmospheric Research P.O. Box 3000 Boulder, CO 80307 Staff web page <https://staff.ucar.edu/users/barthm> SIMA Web Site <http://sima.ucar.edu> MUSICA Web Site <http://www2.acom.ucar.edu/sections/multi-scale-infrastructure-chemistry-modeling-musica> DC3 Web Site <http://www2.acom.ucar.edu/dc3/> ^--^--^--^--^--^--^--^--^--^--^--^--^--^--^-^--^--^--^-^--^

…

On Thu, Feb 27, 2025 at 10:55 AM Matt Dawson ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In src/chemistry/aerosol/cloud_aqueous_chemistry.F90 <#5 (comment)>: > + xk = 58._r8 *EXP( 4085._r8*work1(i) ) + xe = 1.7e-5_r8*EXP( -4325._r8*work1(i) ) + + fact1_nh3 = (xk*xe*patm/water_dissociation_constant)*(xnh3(i,k)+xnh4(i,k)) + fact2_nh3 = xk*GAS_CONSTANT_L_ATM_MOL_K*temperature(i,k)*xl + fact3_nh3 = xe/water_dissociation_constant + + !----------------------------------------------------------------- + ! ... h2o effects + !----------------------------------------------------------------- + Eh2o = water_dissociation_constant + + !----------------------------------------------------------------- + ! ... co2 effects + !----------------------------------------------------------------- + co2g = 330.e-6_r8 !330 ppm = 330.e-6 atm Would it be better to use the CO2 concentration from the model state? (also, this value seems like it might be low for the current atmosphere, unless I'm misinterpreting this) @dmleung <https://github.com/dmleung> - what do you think? — Reply to this email directly, view it on GitHub <#5 (review)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALB5EDWTUCGC5ICRZ24SGKL2R5GQZAVCNFSM6AAAAABSRA4PC6VHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMZDMNBYGYZDCMBYGU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[dmleung]

@mattldawson By the end of our Tue meeting we touched upon this a bit -- and I am still a little baffled by the unit for conc_obj%xlwc. It looks like [lwc] has a unit of kg water / kg air, and [cfact] is also constructed to be kg air / L air (I checked cfact's calculation and that unit looks right to me). If so, then it looks like xlwc should have a unit of kg water / L air, which is different from the comment here.
Not sure how important this is, but just trying to make sure things are right. What do you think? Let me know if I was wrong.

[mattldawson]

I struggled with this too. I think they might have just been doing an implicit conversion with the (approximate) density of water (1kg/L). That's all I could come up with.

[dmleung]

That actually makes sense, thanks for that. Maybe we can add a bit onto the comment here?

Suggested change

	conc_obj%xlwc(:ncol,:) = lwc(:ncol,:)*cfact(:ncol,:) ! cloud water L(water)/L(air)
	conc_obj%xlwc(:ncol,:) = lwc(:ncol,:)*cfact(:ncol,:) ! cloud water in L(water)/L(air), assuming water has a density of ~ 1 kg (water) / L (water).

[boulderdaze]

Hi @mattldawson and @dmleung, are those vmr variables for gas species, aerosols or a mix of both? NH3, O3 look gas, but SO4, NH4 seem aerosols. Doesn't aerosol use mass mixing ratio?

[dmleung]

All of these variables come from species_vmr. See the code below, which is later of this module:
call so4%mixing_ratio( species_vmr, fixed_concentrations, air_number_density, xso4 )
And, yes, species_vmr stores both gas-phase and aerosol-phase species in volume mixing ratio (here). Simone said aerosol species could be stored as mass mixing ratio elsewhere but i don't know where. Aerosols are definitely outputted as mmr in the history files, but here they are vmr.