GEOS–Chem v9–01–03 Online User's Guide

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Appendix 1: GEOS–Chem Tracers, by Simulation

With GEOS–Chem, you can perform several different types of chemistry simulations. For each simulation, we provide a list of advected tracers below.

A1.1 NOx–Ox–hydrocarbon–aerosol simulations

Advected tracers fall into two categories:

  1. Tracers having lifetimes long enough to be transported out of the grid box in which they are created, or
  2. "Family tracers", consisting of two or more molecules (e.g. NOx, Ox).

Many advected tracers are also listed as individual species in the chemical mechanism. Please consult Appendix 6 for a complete list of chemical species in GEOS–Chem.

We specify several hydrocarbon tracers (those listed in BOLD ITALICS) as atoms C instead of molecules tracer. We assign to these a molecular weight of 12 g/mole. The number of moles C per moles tracer is listed below.

You can select from different chemistry mechanism options for the NOx–Ox–hydrocarbon–aerosol simulations. In the following table we give the tracers for each option: the standard mechanism, the SOA mechanism, the dicarbonyls mechanism and the Caltech isoprene mechanism.

For more information, please see:

  1. Chapter 6.1.1, Checklist for NOx–Ox–Hydrocarbon–aerosol chemistry simulation with SMVGEAR or KPP
  2. GEOS–Chem Wiki: The "standard" NOx–Ox–Hydrocarbon–aerosol simulation
  3. GEOS–Chem Wiki: Secondary organic aerosols
  4. GEOS–Chem Wiki: Dicarbonyls simulation
  5. GEOS–Chem Wiki: Caltech isoprene mechanism
# Name Description g/mole mole C/
mole tracer
Standard mechanism
1 NOx NO + NO2+ NO3 + HNO2 46 -
2 Ox O3 + NO2 + 2NO3 48 -
3 PAN Peroxyacetyl Nitrate 121 -
4 CO Carbon Monoxide 28 -
5 ALK4 Lumped >= C4 Alkanes 12 4
6 ISOP Isoprene 12 5
7 HNO3 Nitric Acid 63 -
8 H2O2 Hydrogen Peroxide 34 -
9 ACET Acetone 12 3
10 MEK Methyl Ethyl Ketone 12 4
11 ALD2 Acetaldehyde 12 2
12 RCHO Lumped Aldehyde >= C3 58 -
13 MVK Methyl Vinyl Ketone 70 -
14 MACR Methacrolein 70 -
15 PMN Peroxymethacroyl Nitrate 147 -
16 PPN Lumped Peroxypropionyl Nitrate 135 -
17 R4N2 Lumped Alkyl Nitrate 119 -
18 PRPE Lumped >= C3 Alkenes 12 3
19 C3H8 Propane 12 3
20 CH2O Formaldehyde 30 -
21 C2H6 Ethane 12 2
22 N2O5 Dinitrogen Pentoxide 105 -
23 HNO4 Pernitric Acid 79 -
24 MP Methyl Hydro Peroxide 48 -
25 DMS Dimethyl Sulfide 62 -
26 SO2 Sulfur Dioxide 64 -
27 SO4 Sulfate 96 -
28 SO4s Sulfate on surface of sea-salt aerosol 96 -
29 MSA Methyl Sulfonic Acid 96 -
30 NH3 Ammonia 17 -
31 NH4 Ammonium 18 -
32 NIT Inorganic nitrates 62 -
33 NITs Inorganic nitrates on surface of sea-salt aerosol 62 -
34 BCPI Hydrophilic black carbon aerosol 12 1
35 OCPI Hydrophilic organic carbon aerosol 12 1
36 BCPO Hydrophobic black carbon aerosol 12 1
37 OCPO Hydrophobic organic carbon aerosol 12 1
38 DST1 Dust aerosol, Reff = 0.7 microns 29 -
39 DST2 Dust aerosol, Reff = 1.4 microns 29 -
40 DST3 Dust aerosol, Reff = 2.4 microns 29 -
41 DST4 Dust aerosol, Reff = 4.5 microns 29 -
42 SALA Accumulation mode sea salt aerosol
(Reff = 0.01 – 0.5 microns)		 36 -
43 SALC Coarse mode sea salt aerosol
(Reff = 0.5 – 8 microns)		 36 -
44 Br2 Molecular bromine 160 -
45 Br Bromine radical, or atomic bromine 80 -
46 BrO Bromine monoxide 96 -
47 HOBr Hypobromous acid 97 -
48 HBr Hypobromic acid 81 -
49 BrNO2 Nitryl bromide 126 -
50 BrNO3 Bromine nitrate 142 -
51 CHBr3 Bromoform, or tribromomethane 253 -
52 CH2Br2 Dibromomethane 174 -
53 CH3Br Methyl bromide 95 -
SOA mechanism
1-37 Same tracers as for the standard mechanism
38 ALPH A-pinene, B-pinene, sabinene, carene, terpenoid ketones 136.23 -
39 LIMO Limonene 136.23 -
40 ALCO Myrcene, terpenoid alcohols, ocimene 142 -
41 SOG1 Lump of gas products of first 3 (ALPH + LIMO + TERP) hydrocarbon oxidation 150 -
42 SOG2 Gas product of ALCO oxidation 160 -
43 SOG3 Gas product of SESQ oxidation 220 -
44 SOG4 Gas product of ISOP oxidation 130 -
45 SOG5 Gas product of aromatics oxidation 150 -
46 SOA1 Lump of aerosol products of first 3 (ALPH + LIMO + TERP) hydrocarbon oxidation 150 -
47 SOA2 Aerosol product of ALCO oxidation 160 -
48 SOA3 Aerosol product of SESQ oxidation 220 -
49 SOA4 Aerosol product of ISOP oxidation 130 -
50 SOA5 Aerosol product of aromatics oxidation 150 -
51-56 Insert tracers 38-43 (dusts and sea salts) from standard simulation.
57 BENZ Benzene 12 6
58 TOLU Toluene 12 7
59 XYLE Xylene 12 8
Dicarbonyls mechanism
1-56 Same tracers as SOA simulation
57 GLYX Glyoxal 58 -
58 MGLY Methylglyoxal 72 -
59 BENZ Benzene 12 6
60 TOLU Toluene 12 7
61 XYLE Xylene 12 8
62 MONX Monoterpenes 12 10
63 SOAG SOA product of GLYX 58 -
64 SOAM SOA product of MGLY 72 -
65 C2H4 Ethene 12 2
66 C2H2 Acetylene 12 2
67 MBO 2-methyl-3-bute-2-nol 12 5
68 GLYC Glycoaldehyde 60 -
69 HAC Hydroxyacetone 74 -
70 ACRPAN APAN (CH2CHC(O)OONO2) 133 -
71 ENPAN ENPAN (NO2OCH2C(O)OONO2) 182 -
72 GLPAN Peroxyacylnitrate from GLCO3 137 -
73 GPAN Peroxyacylnitrate from GCO3 135 -
74 MPAN 2-methyl-1-oxo-2-propenyl nitroperoxyde 132 -
75 NIPAN NIPAN (NO2OCH2CCH3CHC(O)OONO2,  C5PAN18) 224 -
Caltech isoprene mechanism
1-43 Same tracers as standard simulation (without bromine species)
44 HCOOH Formic acid 46 -
45 ACTA Acetic acid 60 -
46 ISOPN Isoprene nitrate 147 -
47 MOBA 5C acid from isoprene 114 -
48 PROPNN Propanone nitrate 109 -
49 HAC Hydroxyacetone 74 -
50 GLYC Glycolaldehyde 60 -
51 MMN Nitrate from MACR + MVK 149 -
52 RIP Peroxide from RIO2 118 -
53 IEPOX Isoprene epoxide 118 -
54 PYPAN Pyruvic acid PAN 149 -
55 MAP Peroxyacetic acid 76 -
56 AP   76 -

NOTES: 

  1. You may omit the secondary organic aerosol tracers (ALPH, LIMO, ALCO, SOG1, SOG2, SOG3, SOG4, SOG5, SOA1, SOA2, SOA3, SOA4, SOA5, BENZ, TOLU, XYLE) by setting the following switches in the aerosol menu section of the input.geos file.  
     Online 2dy ORG AEROSOLS : F
  2. You may omit the dicarbonyl chemistry tracers (tracers 57 to 75). In this case, you need to set the following switch in the aerosol menu section of the input.geos file: 
     Online dicarb. chem. : F
  3. Each of these chemistry mechanism requires different versions of globchem.dat, jv_spec.dat, mglob.dat and ratj.d. The proper files are included when you download the various GEOS–Chem run directories (see Chapter 2.3).

A1.2 Offine aersosol simulations

You can run a GEOS–Chem "offline" aerosol simulation without having to call the SMVGEAR II or KPP solver. The tracer list is below.

For more information, please see:

  1. Chapter 6.1.6, Checklist for offline aerosol chemistry simulation
  2. GEOS–Chem Wiki: Offline aerosol chemistry simulation
  3. GEOS–Chem Wiki: Sulfate aerosols
  4. GEOS–Chem Wiki: Carbonaceous aerosols
  5. GEOS–Chem Wiki: Secondary organic aerosols
  6. GEOS–Chem Wiki: Mineral dust aerosols
  7. GEOS–Chem Wiki: Sea salt aerosols
# Name Description g/mole
1 DMS Dimethyl sulfide 62
2 SO2 Sulfur dioxide 64
3 SO4 Sulfate 96
4 SO4s Sulfate on surface of sea salt aerosol 96
5 MSA Methane Sulfionic Acid 96
6 NH3 Ammonia 17
7 NH4 Ammonium 18
8 NIT Inorganic sulfur nitrates 62
9 NITs Inorganic sulfur nitrates on surface of sea-salt aerosol 62
10 BCPI Hydrophilic black carbon aerosol 12
11 OCPI Hydrophilic organic carbon aerosol 12
12 BCPO Hydrophobic black carbon aerosol 12
13 OCPO Hydrophobic organic carbon aerosol 12
14 ALPH A-pinene, B-pinene, sabinene, carene, terpenoid ketones 136.23
15 LIMO Limonene 136.23
16 ALCO Myrcene, terpenoid alcohols, ocimene 142
17 SOG1 Lump of gas products of first 3 (ALPH+LIMO+TERP)
hydrocarbon oxidation		 150
18 SOG2 Gas product of ALCO oxidation 160
19 SOG3 Gas product of SESQ oxidation 220
20 SOG4 Gas product of ISOP oxidation 130
21 SOG5 Gas product of aromatics oxidation 150
22 SOA1 Lump of aerosol products of first 3 (ALPH+LIMO+TERP)
hydrocarbon oxidation		 150
23 SOA2 Aerosol product of ALCO oxidation 160
24 SOA3 Aerosol product of SESQ oxidation 220
25 SOA4 Aerosol product of ISOP oxidation 130
26 SOA5 Aerosol product of aromatics oxidation 150
27 DST1 Dust aerosol, Reff = 0.7 microns 29
28 DST2 Dust aerosol, Reff = 1.4 microns 29
29 DST3 Dust aerosol, Reff = 2.4 microns 29
30 DST4 Dust aerosol, Reff = 4.5 microns 29
31 SALA Accumulation mode sea salt aerosol
(Reff = 0.1 – 2.5 microns)		 36
32 SALC Coarse mode sea salt aerosol
(Reff = 2.5 – 4 microns)		 36

NOTE: You may omit the secondary organic aerosol tracers (ALPH, LIMO, ALCO, SOG1, SOG2, SOG3, SOG4, SOG5, SOA1, SOA2, SOA3, SOA4, SOA5) by setting the following switches in the aerosol menu section of the input.geos file.

Online 2dy ORG AEROSOLS : F

If you omit the secondary organic aerosol tracers then there will be a total of 18 tracers.

A1.3 Total CO2 and Tagged CO2 simulations

Ray Nassar updated the CO2 simulation in GEOS–Chem v8–03–02.

For more information, please see:

  1. Chapter 6.1.9: Checklist for Total CO2 and Tagged CO2 simulations
  2. GEOS–Chem Wiki: CO2 simulation
# Name Description g/mole
1 CO2 Total CO2 44

If you wish, you may add tracers for additional CO2 sources:
2 CO2ff CO2 from fossil fuel emissions 44
3 CO2oc CO2 from ocean emissions 44
4 CO2bal CO2 from balanced biosphere 44
5 CO2bb CO2 from biomass burning emissions 44
6 CO2bf CO2 from biofuel emissions 44
7 CO2nte CO2 from net terrestrial exchange 44
8 CO2se CO2 from ship emissions 44
9 CO2av CO2 from aircraft emissions 44
10 CO2ch CO2 from chemical source 44
11 CO2corr CO2 chemical source surface correction 44

For a full tagged CO2 simulation, you can add the following tracers.
NOTE: These extra tracers are only valid for a 2 x 2.5 simulation.
12 CO2bg CO2 background (including only fossil fuel CO2) 44
13-52 CO2xx CO2 tracers produced in various geographic regions 44
53 CO2se CO2 from shipping 44
54 CO2av CO2 from aviation 44

A1.4 CH4 simulations

Christopher Pickett-Heaps and Kevin Wecht updated the CH4 simulation in GEOS–Chem v8–02–03. Kevin Wecht has further refined the CH4 simulation since then.

For more information, please see:

  1. Chapter 6.1.8: Checklist for a CH4 offline simulation
  2. GEOS–Chem Wiki: CH4 simulation
# Name Description g/mole
1 CH4 Total CH4 16
2 CH4og CH4 produced by oil & gas processing 16
3 CH4cm CH4 produced by coal mining 16
4 CH4ls CH4 produced by livestock 16
5 CH4wa CH4 produced by waste 16
6 CH4bf CH4 produced by biofuel 16
7 CH4ri CH4 produced by rice 16
8 CH4an CH4 produced by other anthropogenic processes 16
9 CH4bb CH4 produced by biomass burning 16
10 CH4we CH4 produced by wetlands 16
11 CH4sa CH4 produced by soil absorption 16
12 CH4nat CH4 produced by other natural sources 16

A1.5 Total Hg and Tagged Hg simulations

You can peform the following GEOS–Chem mercury simulations:

  1. Simulation with the total Hg0, Hg2, and HgP tracers only, with or without the Global Terrestrial Mercury Model option.
  2. Simulation with all tagged Hg0, Hg2, and HgP tracers.

For more information, please see:

  1. Chapter 6.1.7: Checklist for Total Hg and Tagged Hg simulations
  2. GEOS–Chem Wiki: Mercury simulation
  3. GEOS–Chem Wiki: Global Terrestrial Mercury Model
# Name Description g/mole
1 Hg0 Elemental mercury (total tracer) 201
2 Hg2 Divalent mercury (total tracer) 201
3 HgP Particulate mercury (total tracer) 201
4 Hg0_an_na Elemental Mercury (anthro N. Am. tagged tracer) 201
5 Hg0_an_eu Elemental Mercury (anthro Europe tagged tracer) 201
6 Hg0_an_as Elemental Mercury (anthro Asia. tagged tracer) 201
7 Hg0_an_rw Elemental Mercury (anthro rest-of-world tagged tracer) 201
8 Hg0_oc Elemental Mercury (oceanic tagged tracer) 201
9 Hg0_ln Elemental Mercury (land re-emission tagged tracer) 201
10 Hg0_nt Elemental Mercury (natural land source tagged tracer) 201
11 Hg2_an_na Divalent Mercury (anthro N. Am. tagged tracer) 201
12 Hg2_an_eu Divalent Mercury (anthro Europe tagged tracer) 201
13 Hg2_an_as Divalent Mercury (anthro Asia. tagged tracer) 201
14 Hg2_an_rw Divalent Mercury (anthro rest-of-world tagged tracer) 201
15 Hg2_oc Divalent Mercury (oceanic tagged tracer) 201
16 Hg2_ln Divalent Mercury (land re-emission tagged tracer) 201
17 Hg2_nt Divalent Mercury (natural land source tagged tracer) 201
18 HgP_an_na Particulate Mercury (anthro N. Am. tagged tracer) 201
19 HgP_an_eu Particulate Mercury (anthro Europe tagged tracer) 201
20 HgP_an_as Particulate Mercury (anthro Asia. tagged tracer) 201
21 HgP_an_rw Particulate Mercury (anthro rest-of-world tagged tracer) 201
22 HgP_oc Particulate Mercury (oceanic tagged tracer) 201
23 HgP_ln Particulate Mercury (land re-emission tagged tracer) 201
24 HgP_nt Particulate Mercury (natural land source tagged tracer) 201

A1.6 Tagged CO simulations

Several GEOS–Chem users have customized the tagged CO simulation to their own purposes. Listed below is the "standard" Tagged CO configuration.

For more information, please see:

  1. Chapter 6.1.4: Checklist for tagged CO simulation
  2. GEOS–Chem Wiki: Tagged CO simulation
# Name Description g/mole
1 CO Total CO 28
2 COus CO from US fossil fuel emissions 28
3 COeur CO from European fossil fuel emissions 28
4 COasia CO from Asian fossil fuel emissions 28
5 COoth CO from fossil fuel emissions -- rest of world 28
6 CObbAm CO from South American biomass burning 28
7 CObbAf CO from African biomass burning 28
8 CObbAs CO from SE Asian biomass burning 28
9 CObbOc CO from Oceania biomass burning 28
10 CObbEu CO from European biomass burning 28
11 CObbNA CO from North American biomass burning 28
12 COch4 CO chemically produced from methane oxidation 28
13 CObiof CO from biofuel burning (whole world) 28
14 COisop CO chemically produced from isoprene oxidation 28
15 COmono CO chemically produced from monoterpenes oxidation 28
16 COmeoh CO chemically produced from methanol oxidation 28
17 COacet CO chemically produced from acetone oxidation 28

A1.7 Tagged Ox simulations

NOTE: We shall update the tagged Ox simulation in the version following v9–01–03.

For more information, please see:

  1. Chapter 6.1.3: Checklist for Tagged Ox simulation
  2. GEOS–Chem Wiki: Tagged Ox simulation
# Name Description g/mole
1 Ox Total Ox (O3 + NO2 + 2NO3) 46
2 OxUT Ox produced in the upper troposphere (above 350 hPa) 46
3 OxMT Ox produced in the middle troposphere (PBL top – 350 hPa) 46
4 OxROW Ox produced in the rest of the world 46
5 OxPcBL Ox produced in the Pacific Ocean boundary layer 46
6 OxNABL Ox produced in the North American boundary layer 46
7 OxAtBL Ox produced in the Atlantic Ocean boundary layer 46
8 OxEuBL Ox produced in the European boundary layer 46
9 OxAfBL Ox produced in the African boundary layer 46
10 OxAsBl Ox produced in the Asian boundary layer 46
11 OxStrt Ox produced in the stratosphere 46
12 OxInit Ox from the initial condition 46
13 OxUSA Ox produced over the United States (surface – tropopause) 46

A1.8 Rn–Pb–Be simulations

We recommend that you run a RnPbBe simulation whenever you modify the convective updraft scavenging or wet deposition algoritms. For more information about this simulation, please see:

  1. Chapter 6.1.2: Checklist for Radon–Lead–Beryllium simulation
  2. GEOS–Chem Wiki: Rn–Pb–Be simulation
# Name Description g/mole
1 Rn222 Radon-222 isotope 222
2 Pb210 Lead-210 isotope 210
3 Be7 Beryllium-7 isotope 7

A1.9 H2 and HD simulation

The H2/HD simulation has not been used very much recently. If you wish to use this simulation, you will have to invest some time in bringing it back to the state of the science.

  1. Chapter 6.1.5: Checklist for H2–HD simulation
# Name Description g/mole
1 H2 Divalent hydrogen 2
2 HD Deuterium 2.0135

A1.10 CH3I simulations

The CH3I simulation has not been used very much recently. If you wish to use this simulation, you will have to invest some time in bringing it back to the state of the science.

# Name Description g/mole
1 CH3I-oc Methyl iodide from oceans 141.939
2 CH3I-bb Methyl iodide from biomass burning 141.939
3 CH3I-bf Methyl iodide from biofuel burning 141.939
4 CH3I-rc Methyl iodide from rice paddies 141.939
5 CH3I-wl Methyl iodide from wetlands 141.939

A1.11 HCN simulations

The HCN simulation has not been used very much recently. If you wish to use this simulation, you will have to invest some time in bringing it back to the state of the science.

# Name Description g/mole
1 HCN Hydrogen Cyanide 27

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