TOMAS aerosol microphysics

This Guide describes the TOMAS aerosol microphysics option in GEOS-Chem. TOMAS is one of two aerosol microphysics packages being incorporated into GEOS-Chem, the other being Advanced Particle Microphysics (APM).

Overview

TOMAS authors and collaborators (in alphabetical order)

Author or Collaborator

Institution

Peter Adams

Carnegie-Mellon University, USA

Betty Croft

Washington University in St. Louis

Salvatore Farina

Colorado State University, USA (formerly)

Jack Kodros

Colorado State University, USA (formerly)

Marguerite Marks

Carnegie-Mellon University, USA (formerly)

Jeffrey Pierce

Colorado State University, USA

Win Trivitayanurak

Chulalongkorn University, Thailand

Dan Westervelt

Carnegie-Mellon University, USA (formerly)

The TwO-Moment Aerosol Sectional (TOMAS) microphysics package was developed for implementation into GEOS-Chem at Carnegie-Mellon University (Adams and Seinfeld [2002], Trivitayanurak et al. [2008]). Using a moving sectional and moment-based approach, TOMAS tracks two independent moments (number and mass) of the aerosol size distribution for a number of discrete size bins. It also contains codes to simulate nucleation, condensation, and coagulation processes. The aerosol species considered with high size resolution are sulfate, sea-salt, OC, EC, and dust. An advantage of TOMAS is the full size resolution for all chemical species and the conservation of aerosol number, the latter of which allows one to construct aerosol and CCN number budgets that will balance.

Croft et al. [2024] have made TOMAS compatible with GEOS-Chem High Performance (aka GCHP). From the abstract:

Global modeling of aerosol-particle number and size is important for understanding aerosol effects on Earth’s climate and air quality. Fine-resolution global models are desirable for representing nonlinear aerosol-microphysical processes, their nonlinear interactions with dynamics and chemistry, and spatial heterogeneity. However, aerosol-microphysical simulations are computationally demanding, which can limit the achievable global horizontal resolution. Here, we present the first coupling of the TwO-Moment Aerosol Sectional (TOMAS) microphysics scheme with the High-Performance configuration of the GEOS-Chem model of atmospheric composition (GCHP), a coupling termed GCHP-TOMAS. GCHP’s architecture allows massively parallel GCHP-TOMAS simulations including on the cloud, using hundreds of computing cores, faster runtimes, more memory, and finer global horizontal resolution (e.g., 25 km × 25 km, 7.8 × 105 model columns) versus the previous single-node capability of GEOS-Chem-TOMAS (tens of cores, 200 km × 250 km, 1.3 × 104 model columns). GCHP-TOMAS runtimes have near-ideal scalability with computing-core number. Simulated global-mean number concentrations increase (dominated by free-tropospheric over-ocean sub-10-nm-diameter particles) toward finer GCHP-TOMAS horizontal resolution. Increasing the horizontal resolution from 200 km × 200–50 km × 50 km increases the global monthly mean free-tropospheric total particle number by 18.5%, and over-ocean sub-10-nm-diameter particles by 39.8% at 4-km altitude. With a cascade of contributing factors, free-tropospheric particle-precursor concentrations increase (32.6% at 4-km altitude) with resolution, promoting new-particle formation and growth that outweigh coagulation changes. These nonlinear effects have the potential to revise current understanding of processes controlling global aerosol number and aerosol impacts on Earth’s climate and air quality.

TOMAS simulations

Size Resolution

The different TOMAS simulations have the following characteristics:

Simulation

Size Resolution

Currently supported?

TOMAS12
(12 bins)

All 7 chemical species have size resolution ranging from 10 nm to 1 µm, spanned by 10 logarithmically spaced (mass quadrupling) bins and two supermicron bins.

Coarser than TOMAS30, with improved computation time.

No

TOMAS15
(15 bins)

Same as TOMAS12 with 3 additional (mass quadrupling) sub-10 nm bins with a lower limit of ~2 nm.

Analogous to TOMAS40 with improved computation time.

Yes

TOMAS30
(30 bins)

All 7 chemical species have size resolution ranging from 10 nm to 10 µm, spanned by 30 logarithmically spaced (mass doubling) bins.

No

TOMAS40
(40 bins)

Same as TOMAS30 with 10 additional (mass doubling) sub-10 nm bins with a lower limit of ~1 nm.

Yes

In the past, all TOMAS versions were supported in GEOS-Chem. At present, only the TOMAS15 and TOMAS40 simulations are supported. The source code for the TOMAS12 and TOMAS30 simulations is still intact, and these simulations could be restored in the future if there is demand.

Species

TOMAS adds the following species to the standard fullchem simulation:

TOMAS15

TOMAS40

Description

H2SO4

H2SO4

Sulfuric acid

NK01 … NK15

NK01 … NK40

Number

SF01 … SF15

SF01 … SF40

Size-resolved sulfate

SS01 … SS15

SS01 … SS40

Size-resolved sea salt

ECOB01 … ECOB15

ECOB01 … ECOB40

Size-resolved hydrophilic elemental carbon

ECIL01 … ECIL15

ECIL01 … ECIL40

Size-resolved hydrophobic elemental carbon

OCOB01 … OCOB15

OCOB01 … OCOB40

Size-resolved hydrophilic organic carbon

OCIL01 … OCIL15

OCIL01 … OCIL40

Size-resolved hydrophobic organic carbon

DUST01 … DUST15

DUST01 … DUST40

Size-resolved mineral dust

AW01 … AW15

AW01 … AW40

Size-resolved aerosol water

Nucleation

The choice of nucleation theory is selected in the header section of GeosCore/tomas_mod.F90. The available options are:

  1. Binary homogeneous nucleation (Vehkamäki et al. [2002])

  2. Ternary homogeneous nucleation (Napari et al. [2002]) — the ternary nucleation rate is typically scaled by a globally uniform tuning factor of 10 -4 or 10-5

  3. Ion-mediated nucleation (Yu [2010])

  4. Activation nucleation (Kulmala and others [2006])

In TOMAS12 and TOMAS30, nucleated particles follow the Kerminen approximation to grow to the smallest size bin. This has a tendency to overpredict the number of particles in the smallest bins of those models. See Lee et al. [2013] for more details.

Condensation

(Documentation forthcoming)

Coagulation

(Documentation forthcoming)

Biomass Burning Subgrid Coagulation Switch

Ramnarine et al. [2018] created code that allows the emitted size distribution in the model to be a function of properties that include the mean emissions rate per fire in the grid box. From the paper:

This parameterization, based on Sakamoto and others [2016], estimates the amount of near-source, sub-grid scale coagulation happening in a biomass burning plume. It can be turned on or off. When on, the default assumption is that each smoke plume is completely separate from the others (i.e., there is no overlap of the plumes). There is also an option for all smoke plumes in a grid box to overlap completely. When being used, this parameterization changes the median diameter and modal width of biomass burning emissions to account for coagulation.

Validation

Figure 1 in Kodros and Pierce [2017] documents the performance of GEOS-Chem-Classic-TOMAS for predicting aerosol number (N10 = number of particles larger than 10 nm, etc.) against measurements at 20 global sites. Details of observations are in D'Andrea et al. [2013].

See Croft et al. [2024] for validation of GCHP-TOMAS.

Source Code

The aerosol microphysics code is largely contained within the file GeosCore/tomas_mod.F90, which is modular—they use all their own internal variables. For details, see the source code.

All TOMAS-specific sections of code are segregated from the rest of GEOS-Chem with C-preprocessor #if defined (or #ifdef for short) statements such as:

#if defined( TOMAS )

# if defined( TOMAS40 )
  ... Code for 40 bin TOMAS simulation (optional) goes here ...
# elif defined( TOMAS12 )
  ... Code for 12 bin TOMAS simulation (optional) goes here ...
# elif defined( TOMAS15 )
  ... Code for 15 bin TOMAS simulation (optional) goes here ...
# else
  ... Code for 30 bin TOMAS simulation (default) goes here ...
# endif

#endif

Note

Although the TOMAS12 and TOMAS30 simulations are not currently supported, we have preserved the source code. These simulations may be restored if there is demand.

TOMAS is invoked by configuring and compiling GEOS-Chem as follows:

$ cmake -DTOMAS=y -DTOMAS_BINS=15 ... etc ...  # For 15 bins, or
$ cmake -DTOMAS=y -DTOMAS_BINS=40 ... etc ...  # For 40 bins
$ make -j
$ make install

References

  1. TOMAS initial paper (sulfate only): Adams and Seinfeld [2002]

  2. TOMAS implementation in GEOS-Chem: Trivitayanurak et al. [2008]

  3. Nucleation in GEOS-Chem: Westervelt et al. [2013]

  4. TOMAS with sea-salt: Pierce and Adams [2006]

  5. TOMAS with carbonaceous aerosol: Pierce et al. [2007], Trivitayanurak and Adams [2014]

  6. TOMAS with dust:Lee et al. [2009]

  7. TOMAS with SOA: D'Andrea et al. [2013]

  8. TOMAS with offline DRE/AIE: Kodros et al. [2016]

  9. TOMAS compared to the standard GEOS-Chem fullchem simulation: Kodros and Pierce [2017]

  10. TOMAS in GCHP: Croft et al. [2024]

  11. Input data used by TOMAS: Usoskin and Kovaltsov [2006], Yu [2010]