GEOS–Chem v9–02 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.

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:

1. the standard mechanism (now including bromine chemistry, methyl peroxy nitrate chemistry, isoprene chemistry)
2. the SOA mechanism (with optional semivolatile POA)
3. the dicarbonyls mechanism (NOTE: this simulation is in need of updating)

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

NOTES: 

1. You may omit the secondary organic aerosol tracers (MTPA, LIMO, MTPO, TSOG0–3, TSOA0–3, ISOG1–3, ISOA1–3, ASOG1–3, ASOA1–3, ASOAN, BENZ, TOLU, XYLE) by setting the following switch in the aerosol menu section of the input.geos file. 

    Online 2dy ORG AEROSOLS : F

2. The semivolatile POA and IVOC tracers (POG1–2, POA1–2, OPOG1–2, OPOA1–2, NAP) are optional in the secondary organic aerosol simulation. You may omit these tracers by setting the following switch in the aerosol menu section of the input.geos file. 

     => Semivolatile POA?   : F

3. You may omit the dicarbonyl chemistry tracers (tracers 94 to 107). In this case, you need to set the following switch in the aerosol menu section of the input.geos file:

    Online dicarb. chem.    : F

4. 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).
5. The molecular weight of 31.4 g/mole for the sea salt tracers (SALA and SALC) is consistent with actual average composition of sea salt, and international guidelines from the IAPWS. You may use the molecular weight of any individual constituent of interest.

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

NOTE: You may omit the secondary organic aerosol tracers (MTPA, LIMO, MTPO, TSOG0–3, TSOA0–3, ISOG1–3, ISOA1–3, ASOG1–3, ASOA1–3, ASOAN, BENZ, TOLU, XYLE) 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 20 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 6.1.10: Checklist for Total CO2 and Tagged CO2 simulations
2. GEOS–Chem Wiki: CO2 simulation

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 6.1.9: Checklist for a CH4 offline simulation
2. GEOS–Chem Wiki: CH4 simulation

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

A1.6 POPs simulations

Carey Friedman and Noelle Selin developed the POPs simulation, now available in GEOS–Chem v9-02. Three separate polycyclic aromatic hydrocarbons (PAHs) are modeled: phenanthrene (PHE), pyrene (PYR), and benzo[a]pyrene (BaP).

For more information, please see:

1. Chapter 6.1.8: Checklist for POPs simulation
2. GEOS–Chem Wiki: POPs simulation

NOTE: The molecular weight of PHE is listed in the table above. Use 202.25 g/mole for PYR or 252.31 g/mole for BaP.

A1.7 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

A1.8 Tagged O3 simulations

At present, you can perform two types of tagged O3 simulations:

1. SIMPLE SIMULATION: with total O3 and stratospheric O3 tracers. (This is the default setting.)
2. EXTENDED SIMULATION: with total O3 and stratopsheric O3 tracers, plus several other regional O3 tracers.

NOTES:

1. Stratospheric O3 is always tracer #2. This is for compatibility with the Linoz stratospheric ozone chemistry scheme.
2. We will be streamlining the tagged O3 simulation in GEOS-Chem v10–01.

For more information, please see:

1. Chapter 6.1.3: Checklist for Tagged Ox simulation
2. GEOS–Chem Wiki: Tagged Ox simulation

A1.9 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

A1.10 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

A1.11 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.

A1.12 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.

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