Edit species_database.yml to be consistent with FJX_j2j.dat

run/shared/species_database.yml - Removed "Is_Photolysis: true" from ACR, APAN, ALK4N2, ALK4P, APINN, AROMPN, BPINN, BPINON, C96N, CHCl3, HC5A, LIMN, LIMNB, LIMPAN, MEKPN, MPAN, PHAN, PIN, PINPAN, R7N2, R7P, and RNO3, as these species are not in FJX_j2j.dat - Added "Is_Photolysis: true" to APINP, BPINOOH, BPINP, C96O2H, H2O, HNO4, LIMAL, LIMO2H, LIMO3H, PINAL, PINO3H, PINONIC, and SO2, as these species are in FJX_j2j.dat and thus are photolyzed. - Moved PINO3H to be in alphabetical order. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <[email protected]>
geoschem · Sep 10, 2024 · 830090b · 830090b
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Added new species ALK4N1 and ALK4N2 to Ox family in KPP
 - Added Cloud-J input parameters to geoschem_config.yml in new photolysis sub-menu called cloud-j
 - Added computation of water concentration to use in photolysis for application of UV absorption by water in Cloud-J v8
+- Added `Is_Photolyis: true` to APINP, BPINOOH, BPINP, C96O2H, H2O, HNO4, LIMAL, LIMO2H, LIMO3H, PINAL, PINO3H, PINONIC, and SO2 in `species_database.yml`
 
 ### Changed
 - Copy values from `State_Chm%KPP_AbsTol` to `ATOL` and `State_Chm%KPP_RelTol` to `RTOL` for fullchem and Hg simulations
@@ -30,6 +31,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Updated `GFED4_Climatology` entries to point to the climatology file for 2010-2023
 - Read aerosol optical properties files from new data directory specified in geoschem_config.yml rather than directory containing photolysis input files
 - Call `RD_AOD` and `CALC_AOD` from `Init_Aerosol` rather than `Init_Photolysis`
+- Moved PINO3H entry in `species_database.yml` to be in alphabetical order
 
 ### Fixed
 - Simplified SOA representations and fixed related AOD and TotalOA/OC calculations in benchmark.
@@ -39,6 +41,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Changed PPN photolysis reaction rate constant to `PHOTOL(167)`
 - Changed photolysis reactions from Travis et al (2024) rate constnats
   to`PHOTOL(168:177)`
+
+### Removed   
+- Removed `Is_Photolysis: true` from ACR, APAN, ALK4N2, ALK4P, APINN, AROMPN, BPINN, BPINON, C96N, CHCl3, HC5A, LIMN, LIMNB, LIMPAN, MEKPN, MPAN, PHAN, PIN, PINPAN, R7N2, R7P, and RNO3 in `species_database.yml` 
 
 ## [14.4.3] - 2024-08-13
 ### Added

diff --git a/run/shared/species_database.yml b/run/shared/species_database.yml
@@ -28,7 +28,6 @@ ACR:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
-  Is_Photolysis: true
   MW_g: 56.06
 ACTA:
   DD_F0: 1.0
@@ -79,7 +78,6 @@ APAN:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
-  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 133.06
   WD_RetFactor: 2.0e-2
@@ -187,7 +185,6 @@ ALK4N2:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
-  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 119.10
   WD_RetFactor: 2.0e-2
@@ -206,7 +203,6 @@ ALK4P:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
-  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 90.14
   WD_RetFactor: 2.0e-2
@@ -272,6 +268,7 @@ APINP:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
+  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 186.28
   WD_RetFactor: 2.0e-2
@@ -285,7 +282,6 @@ APINN:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
-  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 215.28
   WD_RetFactor: 2.0e-2
@@ -358,7 +354,6 @@ AROMPN:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
-  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 207.1
   WD_RetFactor: 2.0e-2
@@ -573,7 +568,6 @@ BPINN:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
-  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 215.28
   WD_RetFactor: 2.0e-2
@@ -610,7 +604,6 @@ BPINON:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
-  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 215.28
   WD_RetFactor: 2.0e-2  
@@ -624,6 +617,7 @@ BPINOOH:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
+  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 186.28
   WD_RetFactor: 2.0e-2
@@ -637,6 +631,7 @@ BPINP:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
+  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 186.28
   WD_RetFactor: 2.0e-2
@@ -862,7 +857,6 @@ C96N:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
-  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 215.28
   WD_RetFactor: 2.0e-2
@@ -881,6 +875,7 @@ C96O2H:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
+  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 186.28
   WD_RetFactor: 2.0e-2
@@ -1143,7 +1138,6 @@ CHCl3:
   FullName: Chloroform
   Is_Advected: true
   Is_Gas: true
-  Is_Photolysis: true
   MW_g: 119.35
 Cl:
   Formula: Cl
@@ -1687,6 +1681,7 @@ H2O:
   FullName: Water vapor
   Is_Advected: true
   Is_Gas: true
+  Is_Photolysis: true
   MW_g: 18.02
 H2O2:
   Background_VV: 4.0e-15
@@ -1755,7 +1750,6 @@ HC5A:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
-  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 100.13
   WD_RetFactor: 2.0e-2
@@ -2364,6 +2358,7 @@ HO2:
   Formula: HO2
   FullName: Hydroperoxyl radical
   Is_Gas: true
+  Is_Photolysis: true
   MW_g: 33.01
 HOBr:
   DD_F0: 0.0
@@ -3095,6 +3090,7 @@ LIMAL:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
+  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 186.28
   WD_RetFactor: 2.0e-2
@@ -3139,7 +3135,6 @@ LIMN:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
-  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 215.28
   WD_RetFactor: 2.0e-2
@@ -3153,7 +3148,6 @@ LIMNB:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
-  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 215.28
   WD_RetFactor: 2.0e-2
@@ -3185,6 +3179,7 @@ LIMO2H:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
+  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 186.28
   WD_RetFactor: 2.0e-2
@@ -3203,6 +3198,7 @@ LIMO3H:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
+  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 186.28
   WD_RetFactor: 2.0e-2
@@ -3216,7 +3212,6 @@ LIMPAN:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
-  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 215.28
   WD_RetFactor: 2.0e-2
@@ -3459,7 +3454,6 @@ MEKPN:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
-  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 151.07
   WD_RetFactor: 2.0e-2
@@ -3635,7 +3629,6 @@ MPAN:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
-  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 147.10
   WD_RetFactor: 2.0e-2
@@ -4321,7 +4314,6 @@ PHAN:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
-  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 137.0483
   WD_RetFactor: 2.0e-2
@@ -4348,7 +4340,6 @@ PIN:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
-  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 215.28
   WD_RetFactor: 2.0e-2
@@ -4362,6 +4353,7 @@ PINAL:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
+  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 186.28
   WD_RetFactor: 2.0e-2
@@ -4370,6 +4362,20 @@ PINO3:
   FullName: Acylperoxy radical from APIN
   Is_Gas: true
   MW_g: 185.27
+PINO3H:
+  DD_F0: 1.0
+  DD_Hstar: 1.0e+5
+  Formula: C10H18O4
+  FullName: Pinonic peracid
+  Henry_CR: 6039.0
+  Henry_K0: 1.0e+5
+  Is_Advected: true
+  Is_DryDep: true
+  Is_Gas: true
+  Is_Photolysis: true
+  Is_WetDep: true
+  MW_g: 186.28
+  WD_RetFactor: 2.0e-2
 PINONIC:
   DD_F0: 1.0
   DD_Hstar: 3.14e+5
@@ -4380,6 +4386,7 @@ PINONIC:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
+  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 186.28
   WD_RetFactor: 2.0e-2
@@ -4393,7 +4400,6 @@ PINPAN:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
-  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 215.28
   WD_RetFactor: 2.0e-2
@@ -4405,19 +4411,6 @@ PIO2:
   FullName: Peroxy radical from MTPA
   Is_Gas: true
   MW_g: 185.27
-PINO3H:
-  DD_F0: 1.0
-  DD_Hstar: 1.0e+5
-  Formula: C10H18O4
-  FullName: Pinonic peracid
-  Henry_CR: 6039.0
-  Henry_K0: 1.0e+5
-  Is_Advected: true
-  Is_DryDep: true
-  Is_Gas: true
-  Is_WetDep: true
-  MW_g: 186.28
-  WD_RetFactor: 2.0e-2
 PIP:
   Formula: C10H18O3
   FullName: Peroxide from MTPA
@@ -4839,7 +4832,6 @@ R7N2:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
-  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 161.2
   WD_RetFactor: 2.0e-2
@@ -4877,7 +4869,6 @@ R7P:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
-  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 132.20
   WD_RetFactor: 2.0e-2
@@ -5003,7 +4994,6 @@ RNO3:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
-  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 203.15
   WD_RetFactor: 2.0e-2
@@ -5113,6 +5103,7 @@ SO2:
   Is_Advected: true
   Is_DryDep: true
   Is_Gas: true
+  Is_Photolysis: true
   Is_WetDep: true
   MW_g: 64.04
   WD_AerScavEff: 1.0