Update species database files and test_species_database.F90

The species_database*yml files are now taken from GEOS-Chem as of 28 Apr 2020. Made minor changes to test_species_database.F90, to read these updated *.yml files. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
yantosca · Apr 28, 2020 · 8b218df · 8b218df
1 parent 4652f8d
commit 8b218df
Show file tree

Hide file tree

Showing 5 changed files with 32 additions and 152 deletions.
diff --git a/src/species_database.yml b/src/species_database.yml
@@ -1,3 +1,5 @@
+# GEOS-Chem Species Database (28 Apr 2020)
+# Core species only (neglecting microphysics)
 A3O2:
   Formula: CH3CH2CH2OO
   FullName: Primary peroxy radical from C3H8
@@ -2074,12 +2076,16 @@ KO2:
   MW_g: 101.09
 LBRO2H:
   FullName: Dummy species to track oxidation of BRO2 by HO2
+  Is_Gas: true
 LBRO2N:
   FullName: Dummy species to track oxidation of BRO2 by NO
+  Is_Gas: true
 LCH4:
   FullName: Dummy species to track loss rate of CH4
+  Is_Gas: true
 LCO:
   FullName: Dummy species to track loss rate of CO
+  Is_Gas: true
 LIMO:
   DD_F0: 0.0
   DD_Hstar: 7.0e-2
@@ -2100,14 +2106,19 @@ LIMO2:
   MW_g: 185.27
 LISOPNO3:
   FullName: Dummy species to track oxidation of ISOP by NO3
+  Is_Gas: true
 LISOPOH:
   FullName: Dummy species to track oxidation of ISOP by OH
-LOX:
+  Is_Gas: true
+LOx:
   FullName: Dummy species to track loss rate of Ox
+  Is_Gas: true
 LTRO2H:
   FullName: Dummy species to track oxidation of TRO2 by HO2
+  Is_Gas: true
 LTRO2N:
   FullName: Dummy species to track oxidation of TRO2 by NO
+  Is_Gas: true
 LVOC:
   DD_F0: 1.0
   DD_Hstar: 1.0e+8
@@ -2137,8 +2148,10 @@ LVOCOA:
   WD_RainoutEff: [0.8, 0.0, 0.8]
 LXRO2H:
   FullName: Dummy species to track oxidation of XRO2 by HO2
+  Is_Gas: true
 LXRO2N:
   FullName: Dummy species to track oxidation of XRO2 by NO
+  Is_Gas: true
 MACR:
   DD_F0: 1.0
   DD_Hstar: 6.5
@@ -2958,6 +2971,7 @@ Pb210Strat:
   FullName: Lead-210 isotope in stratosphere
 PCO:
   FullName: Dummy species to track production rate of CO
+  Is_Gas: true 
 pFe:
   DD_F0: 0.0
   DD_Hstar: 0.0
@@ -2973,6 +2987,7 @@ pFe:
   WD_RainoutEff: [1.0, 0.0, 1.0]
 PH2O2:
   FullName: Dummy species to track production rate of H2O2
+  Is_Gas: true
 PIO2:
   Formula: C10H17O3
   FullName: Peroxy radical from MTPA
@@ -3243,8 +3258,9 @@ POPOCPO_PYR:
   WD_AerScavEff: 1.0
   WD_KcScaleFac: [0.5, 0.5, 0.5]
   WD_RainoutEff: [0.0, 0.0, 0.0]
-POX:
+POx:
   FullName: Dummy species to track production rate of Ox
+  Is_Gas: true
 PP:
   DD_F0: 1.0
   DD_Hstar: 2.94e+2
@@ -3319,6 +3335,7 @@ PRPN:
   WD_RetFactor: 2.0e-2
 PSO4:
   FullName: Dummy species to track production of SO4
+  Is_Aerosol: true
 PYAC:
   DD_F0: 1.0
   DD_Hstar: 3.14e+5

diff --git a/src/species_database_apm.yml b/src/species_database_apm.yml
@@ -1,3 +1,5 @@
+# GEOS-Chem Species Database (28 Apr 2020)
+# APM microphysics species only
 APMAMINE1:
   DD_DvzAerSnow: 0.03
   DD_DvzMinVal: [0.2, 0.3]

diff --git a/src/species_database_test.yml b/src/species_database_test.yml
diff --git a/src/species_database_tomas.yml b/src/species_database_tomas.yml
@@ -1,3 +1,5 @@
+# GEOS-Chem Species Database (28 Apr 2020)
+# TOMAS microphysics species only
 AW_PROP: &AWproperties
   DD_DvzAerSnow: 0.03
   DD_F0: 0.0

diff --git a/src/test_species_database.F90 b/src/test_species_database.F90
@@ -3,14 +3,15 @@
 !------------------------------------------------------------------------------
 !BOP
 !
-! !IROUTINE: Test_QFYAML
+! !IROUTINE: Test_Species_Database
 !
-! !DESCRIPTION: Test program for developing QFYAML features.
+! !DESCRIPTION: Test program for reading the GEOS-Chem species database
+!  in YAML format.
 !\\
 !\\
 ! !INTERFACE:
 !
-PROGRAM Test_QFYAML
+PROGRAM Test_Species_Database
 !
 ! !USES:
 !
@@ -92,8 +93,8 @@ PROGRAM Test_QFYAML
   tags = (/ "BackgroundVV     ", "DD_AeroDryDep    ", "DD_DustDryDep    ",   &
             "DD_DvzAerSnow    ", "DD_DvzMinVal     ", "DD_F0            ",   &
             "DD_Hstar         ", "DD_KOA           ", "Density          ",   &
-            "Formula          ", "Fullname         ", "Is_ActiveChem    ",   &
-            "Is_Advected      ", "Is_Aero          ", "Is_DryAlt        ",   &
+            "Formula          ", "FullName         ", "Is_ActiveChem    ",   &
+            "Is_Advected      ", "Is_Aerosol       ", "Is_DryAlt        ",   &
             "Is_DryDep        ", "Is_FixedChem     ", "Is_HygroGrowth   ",   &
             "Is_Kpp           ", "Is_Gas           ", "Is_Hg0           ",   &
             "Is_Hg2           ", "Is_HgP           ", "Is_Photolysis    ",   &
@@ -107,7 +108,7 @@ PROGRAM Test_QFYAML
 
   ! Read the YAML file into a config object
   fileName = "species_database.yml"
-  !PRINT*, "### Reading " // TRIM( fileName )
+  PRINT*, "### Reading " // TRIM( fileName )
   CALL QFYAML_Init( fileName, yml1, yml1_anchored, RC )
   IF ( RC /= QFYAML_Success ) STOP
 
@@ -120,8 +121,6 @@ PROGRAM Test_QFYAML
   ! Merge two YAML objects into a single object
   CALL QFYAML_Merge( yml1, yml2, yml, RC )
 
-  yml = yml1
-
   ! FORMAT statements
 10 FORMAT( a30, " | ", a      )
 20 FORMAT( a30, " | ", L10    )
@@ -131,7 +130,7 @@ PROGRAM Test_QFYAML
 40 FORMAT( a30, " | ", i10    )
 
   ! Loop over the number of species
-  DO S = 1, 2 !SIZE( species )
+  DO S = 1, SIZE( species )
 
      ! Species name
      spc = species(S)
@@ -356,30 +355,6 @@ PROGRAM Test_QFYAML
      print*, "###"
   ENDDO
 
-  !========================================================================
-  ! Add a couple of variables manually
-  ! that the anchors can't handle
-  !========================================================================
-!  key   = "Be7%Fullname"
-!  v_str = "Beryllium-7 isotope"
-!  CALL QFYAML_Update( yml, key, v_str )
-!  WRITE( 6, 10 ) TRIM( key ), TRIM( v_str )
-!
-!  key   = "Be7Strat%Fullname"
-!  v_str = "Beryllium-7 isotope in stratosphere"
-!  CALL QFYAML_Update( yml, key, v_str )
-!  WRITE( 6, 10 ) TRIM( key ), TRIM( v_str )
-!
-!  key   = "Be10%Fullname"
-!  v_str = "Beryllium-10 isotope"
-!  CALL QFYAML_Update( yml, key, v_str )
-!  WRITE( 6, 10 ) TRIM( key ), TRIM( v_str )
-!
-!  key   = "Be10Strat%Fullname"
-!  v_str = "Beryllium-10 isotope in stratosphere"
-!  CALL QFYAML_Update( yml, key, v_str )
-!  WRITE( 6, 10 ) TRIM( key ), TRIM( v_str )
-
   !=========================================================================
   ! Finalize the config objects
   !=========================================================================
@@ -391,4 +366,4 @@ PROGRAM Test_QFYAML
   CALL QFYAML_CleanUp( yml2_anchored )
   CALL QFYAML_CleanUp( yml           )
 
-END PROGRAM test_qfyaml
+END PROGRAM Test_Species_Database