TOMAS aerosol microphysics

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The TOMAS aerosol microphysics package was developed at Carnegie-Mellon University.

Authors and collaborators:

  • Peter Adams (Carnegie-Mellon U.) -- Principal Investigator
  • Win Trivitayanurak (Carnegie-Mellon U.)
  • Dan Westervelt (Carnegie-Mellon U.)
  • Jeffrey Pierce (Dalhousie U.)

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 If it can't find files there, it will then search the GeosCore/. 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, such as:

  • Adding a -DTOMAS C-preprocessor switch to the FFLAGS compiler flag settings in 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)


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