Difference between revisions of "Sandbox"

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== Instructions for adding tracers to GEOS-Chem ==
+
=== Species added ===
  
−
'''''By [mailto:mpayer@seas.harvard.edu Melissa Payer]'''''
+
Species added between versions 14.5.0-alpha.5 and 14.5.0-alpha.9:
  
−
These instructions describe how to add advected tracers to GEOS-Chem.  Advected tracers are carried in the <tt>STT</tt> array (which is declared in <tt>GeosCore/tracer_mod.F</tt>), and are transported by the winds. 
+
{| border=1 cellspacing=0 cellpadding=5
 +
!width='100px' bgcolor='#CCCCCC'|Name
 +
!width='100px' bgcolor='#CCCCCC'|Formula
 +
!width='200px' bgcolor='#CCCCCC'|Fullname
 +
!width='30px' bgcolor='#CCCCCC'|Advected
 +
!width='30px' bgcolor='#CCCCCC'|Dry deposited
 +
!width='30px' bgcolor='#CCCCCC'|Gas
 +
!width='30px' bgcolor='#CCCCCC'|Photolyzed
 +
!width='30px' bgcolor='#CCCCCC'|Wet deposited
  
−
NOTE: Some advected tracers are also chemical species, which comprise GEOS-Chem's NOx-Ox-HC-aerosol chemistry mechanism.
+
|-valign='top'
 +
|ACO3
 +
|C3H3O3
 +
|Peroxyacetyl radical for APAN
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|ACR
 +
|C3H4O
 +
|Acrolein
 +
|X
 +
|X
 +
|X
 +
|X
 +
|
 +
 +
|-valign='top'
 +
|ACRO2
 +
|C3H5O4
 +
|Peroxy radical from ACR
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|ALK7
 +
|C7H16
 +
|Lumped >= C6 Alkanes
 +
|X
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|APAN
 +
|C3H3NO5
 +
|Peroxyacryloyl nitrate
 +
|X
 +
|X
 +
|X
 +
|X
 +
|X
 +
 +
|-valign='top'
 +
|APINN
 +
|C10H17NO4
 +
|1st gen organic nitrate from APIN
 +
|X
 +
|X
 +
|X
 +
|X
 +
|X
 +
 +
|-valign='top'
 +
|APINO2
 +
|C10H17O3
 +
|Peroxy radical from APIN
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|APINP
 +
|C10H18O3
 +
|Hydroperoxide from APIN
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|AROMCHO
 +
|C5H6O4
 +
|ACCOMECHO from MCM
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|AROMCO3
 +
|C5H5O6
 +
|Lumped aromatic peroxyacetyl radical
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|AROMPN
 +
|C5H5NO8
 +
|Lumped PN from aromatics
 +
|X
 +
|X
 +
|X
 +
|X
 +
|X
 +
 +
|-valign='top'
 +
|BPINN
 +
|C10H17NO4
 +
|Saturated 1st gen BPIN organic nitrate
 +
|X
 +
|X
 +
|X
 +
|X
 +
|X
 +
 +
|-valign='top'
 +
|BPINO
 +
|C9H14O
 +
|Ketone from BPIN
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|BPINO2
 +
|C10H17O3
 +
|Peroxy radical from BPIN
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|BPINON
 +
|C9H13NO4
 +
|Saturated 2nd gen BPIN organic nitrate
 +
|X
 +
|X
 +
|X
 +
|X
 +
|X
 +
 +
|-valign='top'
 +
|BPINOO2
 +
|C10H17O3
 +
|2nd-gen peroxy radical from BPIN
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|BPINOOH
 +
|C9H14O3
 +
|2nd-gen peroxide from BPIN
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|BPINP
 +
|C10H18O3
 +
|Peroxide from BPIN
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|BUTN
 +
|C4H7NO4
 +
|C4H6 alkyl nitrate
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|BUTO2
 +
|C4H7O3
 +
|peroxy radical from C4H6
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|C4H6
 +
|C4H6
 +
|1,3-butadiene
 +
|X
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|C96N
 +
|C9H15NO4
 +
|Saturated 2nd gen monoterpene organic nitrate
 +
|X
 +
|X
 +
|X
 +
|X
 +
|X
 +
 +
|-valign='top'
 +
|C96O2
 +
|C10H17O3
 +
|2nd-gen peroxy radical from APIN
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|C96O2H
 +
|C9H16O3
 +
|Peroxide from APIN 2nd gen
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|EBZ
 +
|C8H10
 +
|Ethylbenzene
 +
|X
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|GCO3
 +
|HOCH2CO3
 +
|Peroxyacetyl radical for PHAN
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|HACTA
 +
|HOCH2CO2H
 +
|Hydroxyacetic/glycolic acid
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|LIMAL
 +
|C10H16O2
 +
|Aldehyde from limonene
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|LIMKB
 +
|C10H16O3
 +
|2nd gen ketone from limonene
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|LIMKET
 +
|C10H16O2
 +
|Ketone from limonene
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|LIMKO2
 +
|C10H17O3
 +
|2nd-gen peroxy radical from LIMO
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|LIMN
 +
|C10H17NO4
 +
|Saturated 1st gen limonene organic nitrate
 +
|X
 +
|X
 +
|X
 +
|X
 +
|X
 +
 +
|-valign='top'
 +
|LIMNB
 +
|C10H15NO4
 +
|Saturated 1st gen LIMO organic nitrate
 +
|X
 +
|X
 +
|X
 +
|X
 +
|X
 +
 +
|-valign='top'
 +
|LIMO2H
 +
|C10H18O3
 +
|Acid from LIMO
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|LIMO3
 +
|C10H17O3
 +
|Acylperoxy radical from LIMO
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|LIMO3H
 +
|C10H18O4
 +
|Peracid from LIMO
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|LIMPAN
 +
|C10H17NO4
 +
|PAN from LIMO
 +
|X
 +
|X
 +
|X
 +
|X
 +
|X
 +
 +
|-valign='top'
 +
|MEKCO3
 +
|C3H5O4
 +
|False
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|MEKPN
 +
|C3H5NO6
 +
|MEK peroxyacetyl nitrate
 +
|X
 +
|X
 +
|X
 +
|X
 +
|X
 +
 +
|-valign='top'
 +
|MYRCO
 +
|C10H18O3
 +
|Aldehyde or ketone from myrcene
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|PHAN
 +
|C2H3NO6
 +
|Peroxyhydroxyacetic nitric anhydride
 +
|X
 +
|X
 +
|X
 +
|X
 +
|X
 +
 +
|-valign='top'
 +
|PIN
 +
|C10H17NO4
 +
|Saturated 1st gen monoterpene organic nitrate
 +
|X
 +
|X
 +
|X
 +
|X
 +
|X
 +
 +
|-valign='top'
 +
|PINAL
 +
|C10H16O2
 +
|Pinonaldehyde
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|PINO3
 +
|C10H17O3
 +
|Acylperoxy radical from APIN
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|PINO3H
 +
|C10H18O4
 +
|Pinonic peracid
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|PINONIC
 +
|C10H18O3
 +
|Pinonic acid
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|PINPAN
 +
|C10H17NO4
 +
|PAN from pinonaldehyde
 +
|X
 +
|X
 +
|X
 +
|X
 +
|X
 +
 +
|-valign='top'
 +
|R7N1
 +
|C7H15NO5
 +
|Peroxy radical from R7N2
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|R7N2
 +
|RO2NO
 +
|C7 Lumped alkyl nitrate
 +
|X
 +
|X
 +
|X
 +
|X
 +
|X
 +
 +
|-valign='top'
 +
|R7O2
 +
|C7H15O2
 +
|Peroxy radical from ALK7
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|R7P
 +
|C7H16O2
 +
|Peroxide from R7O2
 +
|X
 +
|X
 +
|X
 +
|X
 +
|X
 +
 +
|-valign='top'
 +
|RNO3
 +
|RO2NO
 +
|Lumped aromatic nitrate
 +
|X
 +
|X
 +
|X
 +
|X
 +
|X
 +
 +
|-valign='top'
 +
|STYR
 +
|C8H8
 +
|Styrene
 +
|X
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|TLFUO2
 +
|C5H7O5
 +
|False
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|TLFUONE
 +
|C5H6O2
 +
|Aromatic furanones
 +
|X
 +
|X
 +
|X
 +
|
 +
|X
 +
 +
|-valign='top'
 +
|TMB
 +
|C8H10
 +
|Trimethylbenzenes
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|-valign='top'
 +
|ZRO2
 +
|C7H9O5
 +
|RO2 for making lumped aromatic nitrate
 +
|
 +
|
 +
|X
 +
|
 +
|
 +
 +
|}
  
−
#<p>Add tracers to input.geos under Tracer Menu</p>
+
   
−
##<p>Increase “Number of tracers” accordingly</p>
+
=== Species removed===
−
##<p>Add tracer number, name, molecular weight, and emitted species to end of tracer list</p>
+
−
#<p>Add tracer(s) to restart file – see separate instructions</p>
+
−
#<p>Modify the following source code routines:</p>
+
−
##<p><tt>Headers/CMN_SIZE_mod.F</tt></p>
+
−
###<p>Increase <tt>NNPAR</tt> by number of tracers being added</p>
+
−
###<p>If the species have anthropogenic emissions, increase NEMPARA accordingly</p>
+
−
###<p>If the species have biogenic emissions, increase NEMPARB accordingly</p>
+
−
###<p>If the species have biomass burning emissions, increase NBIOMAX accordingly</p>
+
−
##<p><tt>GeosCore/tracerid_mod.F</tt></p>
+
−
###<p>Increase <tt>NNNTRID</tt> by the number of tracers being added NOTE: <tt>NNNTRID</tt> must be equal to <tt>NNPAR</tt> in <tt>CMN_SIZE_mod.F</tt></p>
+
−
###<p>Define tracer IDs as needed:</p>
+
−
####<p>IDxxxx – ID for SMVGEAR species</p>
+
−
####<p>IDTxxxx – GEOS-Chem tracer ID</p>
+
−
####<p>IDExxxx – GEOS-Chem emission ID</p>
+
−
####<p>IDBFxxxx – GEOS-Chem biofuel ID</p>
+
−
####<p>IDBxxxx – GEOS-Chem biomass ID</p>
+
−
###<p>In subroutine <tt>TRACERID</tt>,</p>
+
−
####<p>Under “Assign tracer, biomass, biofuel, and anthro emission ID’s,” add case for added tracers to initialize IDTxxxx, IDBFxxxx, IDBxxxx</p>
+
−
####<p>Under “Initialize the IDExxx flags,” add IF statement for added tracer IDs and initialize IDExxxx</p>
+
−
####<p>Under “Fill IDEMS with appropriate tracer ID #’s,” add IF statement for added tracers</p>
+
−
####<p>Under “Print additional information,” add WRITE statements for added tracers</p>
+
−
###<p>In subroutine SETTRACE (NOTE: Only do the following if species is included in SMVGEAR chemical mechanism<p>
+
−
####<p>Add IF statement, to initialize IDxxxx</p>
+
−
####<p>In subroutine INIT_TRACERID,</p>
+
−
####<p>Zero all IDs added (IDxxxx, IDTxxxx, IDExxxx, etc.)</p>
+
−
##<p>Other modules that may need to be updated include:</p>
+
−
###<p>wetscav_mod.F</p>
+
−
###<p>drydep_mod.F</p>
+
−
###<p>emissions_mod.F</p>
+
−
###<p>biomass_mod.F</p>
+
−
###<p>biofuel_mod.F</p> etc.
+
  
 +
Species removed between versions 14.5.0-alpha.5 and 14.5.0-alpha.9:
  
 +
{| border=1 cellspacing=0 cellpadding=5
 +
!width='100px' bgcolor='#CCCCCC'|Name
 +
!width='100px' bgcolor='#CCCCCC'|Formula
 +
!width='200px' bgcolor='#CCCCCC'|Fullname
 +
!width='30px' bgcolor='#CCCCCC'|Advected
 +
!width='30px' bgcolor='#CCCCCC'|Dry deposited
 +
!width='30px' bgcolor='#CCCCCC'|Gas
 +
!width='30px' bgcolor='#CCCCCC'|Photolyzed
 +
!width='30px' bgcolor='#CCCCCC'|Wet deposited
  
−
Instructions for adding species to GEOS-Chem
+
|}
−
 
+
−
Modify run directory files
+
−
 
+
−
1) Add tracers to input.geos under Tracer Menu
+
−
c) Increase “Number of tracers” accordingly
+
−
d) Add tracer number, name, molecular weight, and emitted species to end of tracer list
+
−
 
+
−
2) Add tracer(s) to restart file – see separate instructions
+
−
 
+
−
3) Modify globchem.dat to include additional species, kinetic reactions (including emissions and drydep), or photolysis reactions
+
−
NOTE: If you modify globchem.dat and plan to run GEOS-Chem using the KPP chemical solver, you will need to generate new gckpp*.F90 files. For more information see the following wiki pages:
+
−
http://wiki.seas.harvard.edu/geos-chem/index.php/KPP_solvers_FAQ#What_are_the_cons_of_using_KPP.3F
+
−
http://wiki.seas.harvard.edu/geos-chem/index.php/Interfacing_GEOS-Chem_with_KPP#Generating_KPP_input_files_from_GEOS-Chem_globchem.dat
+
−
 
+
−
4) If necessary, modify:
+
−
a) ratj.d – contains species names and branching ratios for FAST–JX photolysis species
+
−
For more information: http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#5.4.1
+
−
b) jv_spec.dat – contains cross-sections and quantum yields for FAST–JX photolysis species
+
−
For more information: http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#5.4.3
+

Latest revision as of 19:10, 3 October 2024

Species added

Species added between versions 14.5.0-alpha.5 and 14.5.0-alpha.9:

Name Formula Fullname Advected Dry deposited Gas Photolyzed Wet deposited
ACO3 C3H3O3 Peroxyacetyl radical for APAN X
ACR C3H4O Acrolein X X X X
ACRO2 C3H5O4 Peroxy radical from ACR X
ALK7 C7H16 Lumped >= C6 Alkanes X X
APAN C3H3NO5 Peroxyacryloyl nitrate X X X X X
APINN C10H17NO4 1st gen organic nitrate from APIN X X X X X
APINO2 C10H17O3 Peroxy radical from APIN X
APINP C10H18O3 Hydroperoxide from APIN X X X X
AROMCHO C5H6O4 ACCOMECHO from MCM X X X X
AROMCO3 C5H5O6 Lumped aromatic peroxyacetyl radical X
AROMPN C5H5NO8 Lumped PN from aromatics X X X X X
BPINN C10H17NO4 Saturated 1st gen BPIN organic nitrate X X X X X
BPINO C9H14O Ketone from BPIN X X X X
BPINO2 C10H17O3 Peroxy radical from BPIN X
BPINON C9H13NO4 Saturated 2nd gen BPIN organic nitrate X X X X X
BPINOO2 C10H17O3 2nd-gen peroxy radical from BPIN X
BPINOOH C9H14O3 2nd-gen peroxide from BPIN X X X X
BPINP C10H18O3 Peroxide from BPIN X X X X
BUTN C4H7NO4 C4H6 alkyl nitrate X X X X
BUTO2 C4H7O3 peroxy radical from C4H6 X
C4H6 C4H6 1,3-butadiene X X
C96N C9H15NO4 Saturated 2nd gen monoterpene organic nitrate X X X X X
C96O2 C10H17O3 2nd-gen peroxy radical from APIN X
C96O2H C9H16O3 Peroxide from APIN 2nd gen X X X X
EBZ C8H10 Ethylbenzene X X
GCO3 HOCH2CO3 Peroxyacetyl radical for PHAN X
HACTA HOCH2CO2H Hydroxyacetic/glycolic acid X X X X
LIMAL C10H16O2 Aldehyde from limonene X X X X
LIMKB C10H16O3 2nd gen ketone from limonene X X X X
LIMKET C10H16O2 Ketone from limonene X X X X
LIMKO2 C10H17O3 2nd-gen peroxy radical from LIMO X
LIMN C10H17NO4 Saturated 1st gen limonene organic nitrate X X X X X
LIMNB C10H15NO4 Saturated 1st gen LIMO organic nitrate X X X X X
LIMO2H C10H18O3 Acid from LIMO X X X X
LIMO3 C10H17O3 Acylperoxy radical from LIMO X
LIMO3H C10H18O4 Peracid from LIMO X X X X
LIMPAN C10H17NO4 PAN from LIMO X X X X X
MEKCO3 C3H5O4 False X
MEKPN C3H5NO6 MEK peroxyacetyl nitrate X X X X X
MYRCO C10H18O3 Aldehyde or ketone from myrcene X X X X
PHAN C2H3NO6 Peroxyhydroxyacetic nitric anhydride X X X X X
PIN C10H17NO4 Saturated 1st gen monoterpene organic nitrate X X X X X
PINAL C10H16O2 Pinonaldehyde X X X X
PINO3 C10H17O3 Acylperoxy radical from APIN X
PINO3H C10H18O4 Pinonic peracid X X X X
PINONIC C10H18O3 Pinonic acid X X X X
PINPAN C10H17NO4 PAN from pinonaldehyde X X X X X
R7N1 C7H15NO5 Peroxy radical from R7N2 X
R7N2 RO2NO C7 Lumped alkyl nitrate X X X X X
R7O2 C7H15O2 Peroxy radical from ALK7 X
R7P C7H16O2 Peroxide from R7O2 X X X X X
RNO3 RO2NO Lumped aromatic nitrate X X X X X
STYR C8H8 Styrene X X
TLFUO2 C5H7O5 False X
TLFUONE C5H6O2 Aromatic furanones X X X X
TMB C8H10 Trimethylbenzenes X
ZRO2 C7H9O5 RO2 for making lumped aromatic nitrate X


Species removed

Species removed between versions 14.5.0-alpha.5 and 14.5.0-alpha.9:

Name Formula Fullname Advected Dry deposited Gas Photolyzed Wet deposited
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