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Add pH diagnostics for mozart_mosaic_4bin_aq chemistry (wrf-model#1342)
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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
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@jordanschnell @vlakshmanan-scala
jordanschnell authored and vlakshmanan-scala committed Apr 4, 2024
1 parent 11c6668 commit a688622
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Showing 8 changed files with 56 additions and 8 deletions.
9 changes: 9 additions & 0 deletions Registry/registry.chem
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,12 @@ 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"
state real ph_aer01 ikj misc 1 - - "ph_aer01" "H+ of aerosol bin 1" "mol/kg"
state real ph_aer02 ikj misc 1 - - "ph_aer02" "H+ of aerosol bin 2" "mol/kg"
state real ph_aer03 ikj misc 1 - - "ph_aer03" "H+ of aerosol bin 3" "mol/kg"
state real ph_aer04 ikj misc 1 - - "ph_aer04" "H+ of aerosol bin 4" "mol/kg"

state real ccn1 ikj misc 1 - r "ccn1" "CCN concentration at S=0.02%" "#/cm3"
state real ccn2 ikj misc 1 - r "ccn2" "CCN concentration at S=0.05%" "#/cm3"
state real ccn3 ikj misc 1 - r "ccn3" "CCN concentration at S=0.1%" "#/cm3"
Expand Down Expand Up @@ -3763,6 +3769,7 @@ rconfig integer biomass_emiss_opt namelist,chem max_domains 0
rconfig integer cam_mam_mode namelist,chem 1 3 irh "cam_mam_mode" "" ""
rconfig integer cam_mam_nspec namelist,chem 1 85 irh "cam_mam_nspec" "" ""
rconfig logical CAM_MP_MAM_cpled namelist,chem 1 .true. irh "CAM_MP_MAM_cpled" "" ""
rconfig integer mozart_ph_diag namelist,chem 1 0 rh "mozart_ph_diag" "" ""

# GHG chemistry namelist options:
rconfig character vprm_opt namelist,chem max_domains "VPRM_param_US" - "the file contains VPRM parameters" "" ""
Expand Down Expand Up @@ -4071,6 +4078,8 @@ package biomassb_t1_mozcart biomass_burn_opt==4 - state:me
# GHG biomass burning
package biomassb_ghg biomass_burn_opt==5 - state::mean_fct_agtf,mean_fct_agef,mean_fct_agsv,mean_fct_aggr,firesize_agtf,firesize_agef,firesize_agsv,firesize_aggr;ebu:ebu_co,ebu_co2,ebu_ch4;ebu_in:ebu_in_co,ebu_in_co2,ebu_in_ch4

# Package for mozart pH diagnostics
package do_mozart_ph_diag mozart_ph_diag==1 - state:ph_cw,ph_aer01,ph_aer02,ph_aer03,ph_aer04

package opt_out opt_pars_out==1 - ext_coef:extcof3,extcof55,extcof106,extcof3_5,extcof8_12;bscat_coef:bscof3,bscof55,bscof106;asym_par:asympar3,asympar55,asympar106

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7 changes: 7 additions & 0 deletions chem/aerosol_driver.F
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ SUBROUTINE aerosols_driver (id,curr_secs,ktau,dtstep,ktauc, &
vdrog3, vdrog3_vbs,brch_ratio,dgnum,dgnumwet,wetdens_ap, &
del_h2so4_gasprod,dvmrdt_sv13d,dvmrcwdt_sv13d, &
is_CAMMGMP_used, &!BSINGH:01/31/2013: Added is_CAMMGMP_used for cam_mam_aerchem_driver
ph_aer01, ph_aer02, ph_aer03, ph_aer04, &
ids,ide, jds,jde, kds,kde, &
ims,ime, jms,jme, kms,kme, &
its,ite, jts,jte, kts,kte )
Expand Down Expand Up @@ -190,6 +191,11 @@ SUBROUTINE aerosols_driver (id,curr_secs,ktau,dtstep,ktauc, &
REAL, dimension (ims:ime,kms:kme-0,jms:jme), &
INTENT(INOUT) :: &
vcsulf_old

! output of aerosol pH from MOSAIC 4-bin
REAL, DIMENSION( ims:ime , kms:kme , jms:jme ) , &
INTENT(OUT ) :: &
ph_aer01, ph_aer02, ph_aer03, ph_aer04
!
!tendencies:dvmrdt_sv13d,dvmrcwdt_sv13d are the tendencies which are passsed on from the CAM-MAM cloud chemistry
! to gasaerexch subroutine
Expand Down Expand Up @@ -288,6 +294,7 @@ SUBROUTINE aerosols_driver (id,curr_secs,ktau,dtstep,ktauc, &
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, &
ids,ide, jds,jde, kds,kde, &
ims,ime, jms,jme, kms,kme, &
its,ite, jts,jte, kts,kte )
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2 changes: 2 additions & 0 deletions chem/chem_driver.F
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Expand Up @@ -1548,6 +1548,7 @@ end SUBROUTINE sum_pm_driver
grid%f_ice_phy,grid%f_rain_phy,grid%cldfrai, grid%cldfral, &
moist, grid%cldfra, grid%cldfra_mp_all, grid%ph_no2, &
chem, gas_aqfrac, numgas_mam,grid%is_CAMMGMP_used, &
grid%ph_cw, &
ids,ide, jds,jde, kds,kde, &
ims,ime, jms,jme, kms,kme, &
its,ite, jts,jte, kts,kte )
Expand All @@ -1572,6 +1573,7 @@ end SUBROUTINE sum_pm_driver
vdrog3,vdrog3_vbs,grid%br_rto,grid%dgnum4d,grid%dgnumwet4d,wetdens_ap, &
del_h2so4_gasprod,grid%dvmrdt_sv13d,grid%dvmrcwdt_sv13d, &
grid%is_CAMMGMP_used, &
grid%ph_aer01, grid%ph_aer02, grid%ph_aer03, grid%ph_aer04, &
ids,ide, jds,jde, kds,kde, &
ims,ime, jms,jme, kms,kme, &
its,ite,jts,jte,kts,kte )
Expand Down
6 changes: 4 additions & 2 deletions chem/cloudchem_driver.F
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@ SUBROUTINE cloudchem_driver( &
moist, cldfra, cldfra_mp_all, ph_no2, &
chem, gas_aqfrac, numgas_aqfrac, &
is_CAMMGMP_used, &!BSINGH:01/31/2013: Added is_CAMMGMP_used for CAM_MAM_cloudchem
ph_cw, &
ids,ide, jds,jde, kds,kde, &
ims,ime, jms,jme, kms,kme, &
its,ite, jts,jte, kts,kte )
Expand Down Expand Up @@ -169,7 +170,8 @@ SUBROUTINE cloudchem_driver( &
REAL, DIMENSION( ims:ime, kms:kme, jms:jme, numgas_aqfrac ), &
INTENT(INOUT ) :: gas_aqfrac


REAL, DIMENSION( ims:ime, kms:kme, jms:jme ), &
INTENT(OUT) :: ph_cw ! ph_cw - pH of cloud water

! LOCAL VAR
integer :: ii,jj,kk
Expand Down Expand Up @@ -200,7 +202,7 @@ SUBROUTINE cloudchem_driver( &
id, ktau, ktauc, dtstepc, config_flags, &
p_phy, t_phy, rho_phy, alt, &
cldfra, ph_no2, &
moist, chem, &
moist, chem, ph_cw, &
gas_aqfrac, numgas_aqfrac, &
ids,ide, jds,jde, kds,kde, &
ims,ime, jms,jme, kms,kme, &
Expand Down
3 changes: 2 additions & 1 deletion chem/module_chem_cup.F
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Original file line number Diff line number Diff line change
Expand Up @@ -3205,6 +3205,7 @@ subroutine chem_cup_aqchem( &
integer :: l
real(r8) :: tmpb
real(r8) :: tmp_chem_up(1:num_chem), tmp_chem_up_old(1:num_chem)
real(r4), dimension( 1:1, kts:kte, 1:1 ) :: tmp_ph_cw

! single precision variable used for calls to other wrf-chem routines
real(r4) :: dt_aqchem_sp
Expand Down Expand Up @@ -3276,7 +3277,7 @@ subroutine chem_cup_aqchem( &
grid_id, ktau, ktau, dt_aqchem_sp, config_flags, &
tmp_p_sp, tmp_t_sp, tmp_rho_sp, tmp_alt_sp, &
tmp_cldfra_sp, tmp_ph_no2_sp, &
tmp_moist_sp, tmp_chem_sp, &
tmp_moist_sp, tmp_chem_sp, tmp_ph_cw, &
tmp_gas_aqfrac_sp, num_chem, &
1,1, 1,1, kts,kte, &
1,1, 1,1, kts,kte, &
Expand Down
15 changes: 13 additions & 2 deletions chem/module_mosaic_cloudchem.F
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ subroutine mosaic_cloudchem_driver( &
id, ktau, ktauc, dtstepc, config_flags, &
p_phy, t_phy, rho_phy, alt, &
cldfra, ph_no2, &
moist, chem, &
moist, chem, ph_cw, &
gas_aqfrac, numgas_aqfrac, &
ids,ide, jds,jde, kds,kde, &
ims,ime, jms,jme, kms,kme, &
Expand Down Expand Up @@ -107,6 +107,9 @@ subroutine mosaic_cloudchem_driver( &
gas_aqfrac
! gas_aqfrac - fraction (0-1) of gas that is dissolved in cloud water

real, intent(out), &
dimension( ims:ime, kms:kme, jms:jme ) :: &
ph_cw

! local variables
integer :: it, jt, kt, kpeg, k_pegshift, l, mpeg
Expand Down Expand Up @@ -146,6 +149,14 @@ subroutine mosaic_cloudchem_driver( &
! following line turns aqueous radical chem off unconditionally
iradical_onoff = 0

! Initialize pH of CW ph_cw to a FillValue value
do jt = jts, jte
do kt = kts, kte
do it = its, ite
ph_cw(it,kt,jt) = -9999.
end do
end do
end do

do 3920 jt = jts, jte
do 3910 it = its, ite
Expand Down Expand Up @@ -204,7 +215,7 @@ subroutine mosaic_cloudchem_driver( &
t_phy, p_phy, rho_phy )

gas_aqfrac(it,kt,jt,:) = gas_aqfrac_box(:)

ph_cw(it,kt,jt) = ph_aq_box

3800 continue

Expand Down
9 changes: 8 additions & 1 deletion chem/module_mosaic_driver.F
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Original file line number Diff line number Diff line change
Expand Up @@ -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, &
ids,ide, jds,jde, kds,kde, &
ims,ime, jms,jme, kms,kme, &
its,ite, jts,jte, kts,kte )
Expand Down Expand Up @@ -235,6 +236,10 @@ subroutine mosaic_aerchem_driver( &
! chem - mixing ratios of trace gase (ppm) and aerosol species
! (ug/kg for mass species, #/kg for number species)

real, intent(out), &
dimension( ims:ime, kms:kme, jms:jme ) :: &
ph_aer01, ph_aer02, ph_aer03, ph_aer04

type(grid_config_rec_type), intent(in) :: config_flags
! config_flags - configuration and control parameters

Expand Down Expand Up @@ -449,7 +454,9 @@ subroutine mosaic_aerchem_driver( &
print 93010, 'calling aerchem - it,jt,maerchem =', it, jt, maerchem
! print 93010, 'calling aerchem - it,jt,maerchem =', it, jt, maerchem
call aerchemistry( it, jt, kclm_calcbgn, kclm_calcend, &
dtchem, idiagaa_dum, vbs_nbin )
dtchem, idiagaa_dum, vbs_nbin, &
ph_aer01(it,kms:kme,jt), ph_aer02(it,kms:kme,jt), &
ph_aer03(it,kms:kme,jt), ph_aer04(it,kms:kme,jt), kms,kme )

! note units for aerosol is now ug/m3

Expand Down
13 changes: 11 additions & 2 deletions chem/module_mosaic_therm.F
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Original file line number Diff line number Diff line change
Expand Up @@ -90,8 +90,9 @@ module module_mosaic_therm
! author: rahul a. zaveri
! update: jan 2005
!-----------------------------------------------------------------------
subroutine aerchemistry( iclm, jclm, kclm_calcbgn, kclm_calcend, &
dtchem_sngl, idiagaa,vbs_nbin )
subroutine aerchemistry( iclm, jclm, kclm_calcbgn, kclm_calcend, &
dtchem_sngl, idiagaa,vbs_nbin, &
ph_aer1, ph_aer2, ph_aer3, ph_aer4,kms,kme )

use module_data_mosaic_asect
use module_data_mosaic_other
Expand All @@ -105,6 +106,9 @@ subroutine aerchemistry( iclm, jclm, kclm_calcbgn, kclm_calcend, &
! subr arguments
integer iclm, jclm, kclm_calcbgn, kclm_calcend, idiagaa,vbs_nbin(1)
real dtchem_sngl
integer kms, kme
real, intent(out), dimension(kms:kme) :: &
ph_aer1, ph_aer2, ph_aer3, ph_aer4 ! pH of the aerosols
! local variables
real(kind=8) :: dtchem
integer k, m
Expand Down Expand Up @@ -154,6 +158,11 @@ subroutine aerchemistry( iclm, jclm, kclm_calcbgn, kclm_calcend, &
call move_sections( 1, iclm, jclm, k, m)
call specialoutaa( iclm, jclm, k, m, 'after_movesect' )

ph_aer1(k) = mc(1,1)
ph_aer2(k) = mc(1,2)
ph_aer3(k) = mc(1,3)
ph_aer4(k) = mc(1,4)

100 continue ! k levels

200 continue ! subareas
Expand Down

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