Difference between revisions of "TOMAS aerosol microphysics"

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(Computational Information)
(Outstanding issues)
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== Outstanding issues ==
== Outstanding issues ==
None known at this time.
Currently, GC-TOMAS is only compatible with the reduced vertical grids:
Development for the full vertical grids is somewhat impractical due to the added computational burden of both the higher vertical resolution and of TOMAS itself.

Revision as of 01:42, 11 February 2010


The TwO-Moment Aerosol Sectional (TOMAS) microphysics package was developed for implementation into GEOS-Chem at Carnegie-Mellon University. Using a moving sectional and moment-based approach, TOMAS tracks two independent moments (number and mass) of the aerosol size distribution for 30 size bins. It also contains codes to simulate nucleation, condensation, and coagulation processes. The aerosol species that are considered with 30-bin size resolution are sulfate, sea-salt, BC/OC, EC, and dust.

Authors and collaborators:

Questions regarding TOMAS can be directed at Dan (e-mail linked above).

--Dan W. 11:53, 27 January 2010 (EST)


TOMAS is a simulation type 3 and utilizes 310 tracers. Each aerosol species requires 30 tracers for the 30 bin size resolution. Here is the (abbreviated) default setup in input.geos (see run.Tomas directory):

Tracer #   Description        MW (g/mol)
40         H2SO4              98.0
41-70      Number             1.0 
71-100     Sulfate            96.0
101-130    Sea-salt           58.5
131-160    Hydrophilic EC     12.0
161-190    Hydrophobic EC     12.0
191-210    Hydrophilic OC     12.0
211-240    Hydrophobic OC     12.0
241-271    Mineral dust       100.0
271-310    Aerosol water      18.0

--Dan W. 21:08, 28 January 2010 (EST)

Implementation notes

As of Jan 27, 2010, TOMAS is currently being implemented into GEOS-Chem v8-02-05 (version in testing).

Code structure

The main-level Code directory has now been divided into several subdirectories:

GeosCore/    GEOS-Chem "core" routines
GeosTomas/   Parallel copies of GEOS-Chem routines that reference TOMAS
GeosUtil/    "Utility" modules (e.g. error_mod.f, file_mod.f, time_mod.f, etc.
Headers/     Header files (define.h, CMN_SIZE, CMN_DIAG, etc.)
KPP/         KPP solver directory structure
bin/         Directory where executables are placed
doc/         Directory where documentation is created
help/        Directory for GEOS-Chem Help Screen
lib/         Directory where library files are placed
mod/         Directory where module files are placed
obsolete/    Directory where obsolete versions of code are archived

Because there were a lot of TOMAS-related modifications in several GEOS-Chem "core" routines, the routines that need to "talk" to TOMAS were placed into a separate subdirectory named GeosTomas/. The files in GeosTomas are:

Makefile            -- GEOS-Chem routines that have been
aero_drydep.f          modified to reference the TOMAS aerosol
carbon_mod.f           microphysics package.  These are kept
chemdr.f               in a separate GeosTomas directory so that
chemistry_mod.f        they do not interfere with the routines
cleanup.f              in the GeosCore directory.
diag_mod.f             The GeosTomas directory only needs to
diag_pl_mod.f          contain the files that have been modified
drydep_mod.f           for TOMAS.  The Makefile will look for
dust_mod.f             all other files from the GeosCore directory
emissions_mod.f        using the VPATH option in GNU Make.
initialize.f           NOTE to GEOS-Chem developers: When you
input_mod.f            make changes to any of these routines
isoropia_mod.f         in the GeosCore directory, you must also
logical_mod.f          make the same modifications to the
ndxx_setup.f           corresponding routines in the GeosTomas
planeflight_mod.f      directory.
sulfate_mod.f          Maybe in the near future we can work
tomas_mod.f            towards integrating TOMAS into the GeosCore
tomas_tpcore_mod.f90   directory more cleanly.  However, due to
tpcore_mod.f           the large number of modifications that were
tpcore_window_mod.f    necessary for TOMAS, it was quicker to
tracerid_mod.f         implement the TOMAS code in a separate
wetscav_mod.f          subdirectory.    
xtra_read_mod.f            -- Bob Y. (1/25/10)

Each of these files were merged with the corresponding files in the GeosCore subdirectory. Therefore, in addition to having the GEOS-Chem modifications from v8-02-05, these files also have the relevant TOMAS references.

A few technical considerations dictated the placing of these files into a separate GeosTomas/ directory:

  • The ND60 diagnostic in the standard GEOS-Chem code (in GeosCore/) is now used for the CH4 offline simulation, but in TOMAS it's used for something else.
  • Some parameters needed to be declared differently with for simulations with TOMAS.
  • Because not all GEOS-Chem users will choose to use TOMAS, we did not want to unnecessarily bog down the code in GeosCore/ with references to TOMAS-specific routines.

All of these concerns could be best solved by keeping parallel copies of the affected routines in the GeosTomas directory.

--Bob Y. 10:36, 27 January 2010 (EST)

Building GEOS-Chem with TOMAS

The VPATH feature of GNU Make is used to simplify the compilation. When GEOS-Chem is compiled with the TOMAS option, the GNU Make utility will search for files in the GeosTomas/ directory first. If it cannot find files there, it will then search the GeosCore/ directory. Thus, if we make a change to a "core" GEOS-Chem routine in the GeosCore/ subdirectory (say in dao_mod.f or diag49_mod.f), then those changes will automatically be applied when you build GEOS-Chem with TOMAS. Thus, we only need to keep in GeosTomas/ separate copies of those files that have to "talk" with TOMAS.

Several new targets were added to the Makefile in the top-level Code/ directory:

# Targets for TOMAS aerosol microphysics code (win, bmy, 1/25/10)

.PHONY: tomas libtomas exetomas cleantomas

        @$(MAKE) -C $(GEOSTOM) TOMAS=yes all

        @$(MAKE) -C $(GEOSTOM) TOMAS=yes lib

        @$(MAKE) -C $(GEOSTOM) TOMAS=yes exe

        @$(MAKE) -C $(GEOSTOM) TOMAS=yes clean

You can build GEOS-Chem with the TOMAS option by typing:

make TOMAS=yes ...

This will automatically do the proper things to build the TOMAS code into GEOS-Chem, such as:

  • Adding a -DTOMAS C-preprocessor switch to the FFLAGS compiler flag settings in Makefile_header.mk. This will cause TOMAS-specific areas of code to be turned on.
  • Turning off OpenMP parallelization. For now the GEOS-Chem + TOMAS code needs to be run on a single processor. We continue to work on parallelizing the code.
  • Calling the Makefile in the GeosTomas/ subdirectory to build the executable. The executable file is now named geostomas in order to denote that the TOMAS code is built in.

The GEOS-Chem + TOMAS has been built on the following compilers

  • Intel Fortran compiler v10
  • SunStudio 12

--Bob Y. 10:36, 27 January 2010 (EST)

Computational Information

GC-TOMAS v8-02-05 on a single 2.6 GHz processor:

  • 36 hours of real time per month of simulation
  • 4.3 GB RAM per simulation (with full diagnostic output)
  • 3.8 GB RAM per simulation (with minimal diagnostic output)

"Full diagnostic" refers to recording output for optical depths, J-values, wet and dry deposition, tracer concentrations, and microphysical processes (nucleation rates, condensation, coagulation).

"Minimal diagnostic" refers to recording output for all of the above except wet and dry deposition.

--Dan W. 20:40, 10 February 2010 (EST)

Microphysics Routines

The aerosol microphysics code is largely contained within the file tomas_mod.f. Tomas_mod and its subroutines are modular -- they use all their own internal variables


The aerophys routine is where each individual microphysical process is called within the code. Since H2SO4 is the main condensing species, H2SO4 concentrations are calculated using a pseudo-steady state approach as described in Pierce and Adams, 2009, AS&T. Within this routine, nucleation, condensation, and coagulation are calculated at each time step. Cond_nuc is called for coupled nucleation-condensation. Nucleation schemes can either be binary (Vehkamaki et al 2002) or ternary (Napari et al 2002). There is a switch for this in the variable declarations. For nucleation, a parameterization (Kerminen et al 2004) is used to determine the flux of new particles to the first size bin.

--Dan W. 22:36, 28 January 2010 (EST)


GC-TOMAS v8-02-05 generally compares very well with observations and other models. Below are some results of benchmarking GC-TOMAS with earlier versions of the model as well as observations

ModelVsObs v8-02-05.jpg

Figure 1: CN10 concentrations predicted by GC-TOMAS v8-02-05 against observations. Descriptions of observational data can be found on p 5454 of Pierce et al, Atmos. Chem. Phys., 7, 2007.

CCN v8-02-05.jpg

Figure 2: Surface layer CCN concentrations at 0.2% supersaturation averaged over the month of January 2006.

--Dan W. 20:13, 10 February 2010 (EST)

Previous issues now resolved

Segmentation Fault

You may get an early segfault if your stacksize is not set to either unlimited or a very large number. To avoid this, you either have to change the value of an environmental variable (setenv command in .cshrc) or use the ulimit command. See this page for details.

--Dan W. 20:20, 10 February 2010 (EST)

Outstanding issues

Currently, GC-TOMAS is only compatible with the reduced vertical grids:

  • GEOS3_30L
  • GEOS4_30L
  • GEOS5_47L

Development for the full vertical grids is somewhat impractical due to the added computational burden of both the higher vertical resolution and of TOMAS itself.