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This page 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 [[APM aerosol microphysics|APM]].
 +
 
== Overview ==
 
== Overview ==
  
The TwO-Moment Aerosol Sectional (TOMAS) microphysics package was developed 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.  
+
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 a number of discrete size bins. It also contains codes to simulate nucleation, condensation, and coagulation processes. The aerosol species that are 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.
 +
 
 +
=== Authors and collaborators ===
 +
* [mailto:petera@andrew.cmu.edu Peter Adams]  ''(Carnegie-Mellon U.)''  -- Principal Investigator
 +
* [mailto:win.t@chula.ac.uk Win Trivitayanurak] ''(Chulalongkorn University, Thailand)''
 +
* [mailto:danielmw@princeton.edu Dan Westervelt] ''(Princeton University, formerly Carnegie-Mellon U.)''
 +
* [mailto:jeffrey.pierce@colostate.edu Jeffrey Pierce] ''(CSU/Dalhousie U.)''
 +
* [mailto:jkodros@atmos.colostate.edu Jack Kodros] ''(CSU)''
 +
* [mailto:sal.farina@gmail.com Salvatore Farina] ''(Colorado State U.)''
 +
*Marguerite Marks (CMU)
  
'''Authors and collaborators:'''
 
* Peter Adams  ''(Carnegie-Mellon U.)''  -- Principal Investigator
 
* Win Trivitayanurak ''(Carnegie-Mellon U. -- now at U. Edinburgh)''
 
* [mailto:dwesterv@andrew.cmu.edu Dan Westervelt] ''(Carnegie-Mellon U.)''
 
* Jeffrey Pierce ''(Dalhousie U.)''
 
  
 
--[[User:Dan Westervelt|Dan W.]] 11:53, 27 January 2010 (EST)
 
--[[User:Dan Westervelt|Dan W.]] 11:53, 27 January 2010 (EST)
  
== Tracers ==
+
=== TOMAS User Groups ===
  
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):
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{| border=1 cellspacing=0 cellpadding=5
 +
|- bgcolor="#cccccc"
 +
!User Group
 +
!Personnel
 +
!Projects
 +
|-valign="top"
 +
|[http://www.ce.cmu.edu/%7Eadams/ Carnegie-Mellon University]
 +
|[http://www.ce.cmu.edu/%7Eadams/people.htm#peter Peter Adams]<br>[http://www.ce.cmu.edu/~dwesterv/Site/Home.html Dan Westervelt]
 +
| [http://www.atmos-chem-phys-discuss.net/13/8333/2013/acpd-13-8333-2013.html New particle formation evaluation in GC-TOMAS] <br> Sensitivity of CCN to nucleation rates <br> Development of number tagging and source apportionment model for GC-TOMAS
 +
|-valign="top"
 +
|[http://www.atmos.colostate.edu/faculty/pierce.php Colorado State]
 +
|[http://pierce.atmos.colostate.edu/ Jeffrey Pierce]<br>Sal Farina<br>[http://www.engr.colostate.edu/~jkodros/index.html Jack Kodros]
 +
|Sensitivity of CCN to condensational growth rates <br> TOMAS parallelization <br> Aerosol radiative effects
 +
|-valign="top"
 +
|Add yours here
 +
|
 +
|
 +
|}
  
Tracer #  Description
+
--[[User:Bmy|Bob Y.]] 16:35, 12 May 2014 (EDT)
40        H2SO4
+
41-70      Number
+
71-100    Sulfate
+
101-130    Sea-salt
+
131-160    Hydrophilic EC
+
161-190    Hydrophobic EC
+
191-210    Hydrophilic OC
+
211-240    Hydrophobic OC
+
241-271    Mineral dust
+
271-310    Aerosol water
+
  
--[[User:Dan Westervelt|Dan W.]] 21:08, 28 January 2010 (EST)
+
== TOMAS-specific setup ==
 +
TOMAS has its own run directories (run.Tomas) that can be downloaded from the Harvard FTP. The <tt>input.geos</tt> file will look slightly different from standard GEOS-Chem, and between versions.
 +
 
 +
Pre- v9.02:
 +
To turn on TOMAS, see the "Microphysics menu" in <tt>input.geos</tt> and make sure TOMAS is set to '''T'''.
 +
 
 +
v9.02 and later:
 +
TOMAS is enabled or disabled at compile time - the TOMAS flag in input.geos has been removed.
 +
 
 +
 
 +
TOMAS is a simulation type 3 and utilizes 171-423 tracers. Each aerosol species requires 30 tracers for the 30 bin size resolution, 12 for the 12 bin, etc. Here is the (abbreviated) default setup in input.geos for TOMAS-30 in v9.02 and later (see run.Tomas directory):
 +
 
 +
Tracer #  Description 
 +
  1- 62    Std Geos Chem
 +
      63    H2SO4             
 +
  64- 93    Number           
 +
  94-123    Sulfate           
 +
124-153    Sea-salt         
 +
154-183    Hydrophilic EC   
 +
184-213    Hydrophobic EC   
 +
214-243    Hydrophilic OC   
 +
244-273    Hydrophobic OC   
 +
274-303    Mineral dust     
 +
304-333    Aerosol water
 +
 
 +
TOMAS-40 requires 423 tracers (~360 TOMAS tracers for each of the 40-bin species, and ~62 standard GEOS-Chem tracers)
 +
 
 +
--[[User:Salvatore Farina|Salvatore Farina]] 18:48, 8 July 2013 (EDT)
  
 
== Implementation notes ==
 
== Implementation notes ==
  
As of Jan 27, 2010, TOMAS is currently being implemented into [[GEOS-Chem v8-02-05]] (version in testing).  
+
#The original implementation and validation of TOMAS had been done for version [[GEOS-Chem v8-03-01]], which was released on 24 Feb 2010.
 +
#TOMAS was completely re-integrated into [[GEOS-Chem v9-02]], which was released on 03 Mar 2014.
 +
#TOMAS was re-integrated into [[GEOS-Chem v10-01]] to become compatible with HEMCO.
 +
#Updates to TOMAS to use the SOAP/SOAS tracers were made for [[GEOS-Chem v11-02]] (not yet released).  
  
=== Code structure ===
+
=== Update April 2013 ===
  
The main-level <tt>Code</tt> directory has now been divided into several subdirectories:
+
<span style="color:green">'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02k|v9-02k]] and approved on 07 Jun 2013.'''''</span>
  
GeosCore/    GEOS-Chem "core" routines
+
Sal Farina has been working with the GEOS-Chem Support Team to inline the TOMAS aerosol microphysics code into the <tt>GeosCore</tt> directoryAll TOMAS-specific sections of code are now segregated from the rest of GEOS-Chem with C-preprocessor statements such as:
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 <tt>GeosTomas/</tt>The files in <tt>GeosTomas</tt> are:
+
#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
  
Files:
 
------
 
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.
 
diag3.f
 
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.
 
gamap_mod.f
 
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.
 
seasalt_mod.f
 
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 <tt>GeosCore</tt> subdirectory.  Therefore, in addition to having the GEOS-Chem modifications from [[GEOS-Chem v8-02-05|v8-02-05]], these files also have the relevant TOMAS references.
+
TOMAS is now invoked by compiling GEOS-Chem with one of the following options:
  
A few technical considerations dictated the placing of these files into a separate <tt>GeosTomas/</tt> directory:
+
{| border=1 cellspacing=0 cellpadding=5
 +
|- bgcolor="#cccccc"
 +
!width="250px"|Command
 +
!width="450px"|Result
 +
|-valign="top"
 +
|<tt>make -j4 TOMAS=yes ...</tt>
 +
|Compiles GEOS-Chem for the 30 bin (default) TOMAS simulation
 +
|-valign="top"
 +
|<tt>make -j4 TOMAS12=yes ...</tt>
 +
|Compiles GEOS-Chem for the 12 bin (optional) TOMAS simulation
 +
|-valign="top"
 +
|<tt>make -j4 TOMAS15=yes ...</tt>
 +
|Compiles GEOS-Chem for the 15 bin (optional) TOMAS simulation
 +
|-valign="top"
 +
|<tt>make -j4 TOMAS40=yes ...</tt>
 +
|Compiles GEOS-Chem for the 40 bin (optional) TOMAS simulation
 +
|}
  
* The ND60 diagnostic in the standard GEOS-Chem code (in <tt>GeosCore/</tt>) is now used for the CH4 offline simulation, but in TOMAS it's used for something else.   
+
The <tt>-j4</tt> in the above examples tell the GNU Make utility to compile 4 files at a timeThis reduces the overall compilation time.
* 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 <tt>GeosCore/</tt> with references to TOMAS-specific routines.
+
  
All of these concerns could be best solved by keeping parallel copies of the affected routines in the <tt>GeosTomas</tt> directory.
+
All files in the old <tt>GeosTomas/</tt> directory have now been deleted, as these have been rendered obsolete.
  
--[[User:Bmy|Bob Y.]] 10:36, 27 January 2010 (EST)
+
These updates are included in [[GEOS-Chem v9-02]].  These modifications will not affect the existing GEOS-Chem simulations, as all TOMAS code is not compiled into the executable unless you compile with one of the TOMAS options (described in the above table) at compile time.
  
=== Building GEOS-Chem with TOMAS ===
+
--[[User:Salvatore Farina|Salvatore Farina]] 13:49, 4 June 2013 (EDT)<br>
 +
--[[User:Bmy|Bob Y.]] 16:39, 12 May 2014 (EDT)
  
The <tt>VPATH</tt> feature of [http://www.gnu.org/software/make/manual/make.html 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 <tt>GeosTomas/</tt> directory first.  If it cannot find files there, it will then search the <tt>GeosCore/</tt> directory. Thus, if we make a change to a "core" GEOS-Chem routine in the <tt>GeosCore/</tt> subdirectory (say in <tt>dao_mod.f</tt> or <tt>diag49_mod.f</tt>), then those changes will automatically be applied when you build GEOS-Chem with TOMAS.  Thus, we only need to keep in <tt>GeosTomas/</tt> separate copies of those files that have to "talk" with TOMAS.
+
== Computational Information ==
  
Several new targets were added to the <tt>Makefile</tt> in the top-level <tt>Code/</tt> directory:
+
GC-TOMAS v9-02 (30 sections) on 8 processors:  
  
#=============================================================================
+
*One year simulation = 7-8 days wall clock time
# Targets for TOMAS aerosol microphysics code (win, bmy, 1/25/10)
+
#=============================================================================
+
+
.PHONY: tomas libtomas exetomas cleantomas
+
+
tomas:
+
        @$(MAKE) -C $(GEOSTOM) TOMAS=yes all
+
+
libtomas:
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        @$(MAKE) -C $(GEOSTOM) TOMAS=yes lib
+
+
exetomas:
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        @$(MAKE) -C $(GEOSTOM) TOMAS=yes exe
+
+
cleantomas:
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        @$(MAKE) -C $(GEOSTOM) TOMAS=yes clean
+
  
You can build GEOS-Chem with the TOMAS option by typing:
+
More speedups are available using lower aerosol size resolution
  
make TOMAS=yes ...
+
--[[User:Dan Westervelt|Dan W.]] 11:00, 07 May 2013 (EST)
  
This will automatically do the proper things to build the TOMAS code into GEOS-Chem, such as:
 
  
* Adding a <tt>-DTOMAS</tt> C-preprocessor switch to the <tt>FFLAGS</tt> compiler flag settings in <tt>Makefile_header.mk</tt>.  This will cause TOMAS-specific areas of code to be turned on.
+
GC-TOMAS v9-02 on 16 processors (glooscap)
* 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 <tt>GeosTomas/</tt> subdirectory to build the executable.  The executable file is now named <tt>geostomas</tt> in order to denote that the TOMAS code is built in.
+
  
The GEOS-Chem + TOMAS has been built on the following compilers
+
{| border=1 cellspacing=0 cellpadding=5
 +
|- bgcolor="#cccccc"
 +
!width="150px"|Simulation
 +
!width="200px"|Wall time / simulation year
 +
|-
 +
|TOMAS12 (optional)
 +
|2.8 days
 +
|-
 +
|TOMAS15 (optional)
 +
|3.3 days
 +
|-
 +
|TOMAS30 (default)
 +
|6.1 days
 +
|-
 +
|TOMAS40 (optional)
 +
|7.8 days
  
* Intel Fortran compiler v10
+
|}
* SunStudio 12
+
  
--[[User:Bmy|Bob Y.]] 10:36, 27 January 2010 (EST)
+
--[[User:Salvatore Farina|Salvatore Farina]] 15:51, 3 March 2014 (EST)
  
== Microphysics Routines ==
+
== Microphysics Code==
The aerosol microphysics code is largely contained within the file <tt>tomas_mod.f</tt>. Tomas_mod and its subroutines are modular -- they use all their own internal variables
+
The aerosol microphysics code is largely contained within the file <tt>tomas_mod.f</tt>. Tomas_mod and its subroutines are modular -- they use all their own internal variables. For details, see tomas_mod.f and comments.
  
=== Aerophys ===
+
=== Nucleation ===
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. <tt>Cond_nuc</tt> 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.
+
The choice of nucleation theory is selected in the header section of <tt>tomas_mod.f</tt>. The choices are currently binary homogeneous nucleation as in Vehkamaki, 2001 or ternary homogenous nucleation as in Napari et al., 2002. The ternary nucleation rate is typically scaled by a globally uniform tuning factor of 10^-4 or 10^-5. Binary nucleation (Vehkamaki et al. 2002), ion-mediated nucleation (Yu, 2008) and activation nucleation (Kulmala, 2006) are options as well.
  
--[[User:Dan Westervelt|Dan W.]] 22:36, 28 January 2010 (EST)
+
In TOMAS-12 and TOMAS-30, 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 Y. H. Lee, J. R. Pierce, and P. J. Adams 2013 [http://www.geosci-model-dev-discuss.net/6/893/2013/gmdd-6-893-2013.html here] for more details on the consequences of this.
 +
 
 +
=== Condensation ===
 +
 
 +
=== Coagulation ===
 +
 
 +
--[[User:Dan Westervelt|Dan W.]] 14:08, 9 May 2011 (EST)
  
 
== Validation ==
 
== Validation ==
  
Text to be added
+
The following figure documents the performance of GEOS-Chem-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, S. D., Hakkinen, S. A. K., Westervelt, D. M., Kuang, C., Levin, E. J. T., Kanawade, V. P., Leaitch, W. R., Spracklen, D. V., Riipinen, I., and Pierce, J. R.: ''Understanding global secondary organic aerosol amount and size-resolved condensational behavior'', <u>Atmos. Chem. Phys.</u>, '''13''', 11519-11534, doi:10.5194/acp-13-11519-11534, 2013.
 +
 
 +
[[Image:GEOS-Chem-TOMAS performance update 20140304.png]]
 +
 
 +
 
 +
An updated version of this figure is included as Figure 1 in Kodros and Pierce, (2017). Please note that the figure in this paper uses GEOS-Chem v10-01, which included substantial updates to emission inventories (as part of the HEMCO update). Thus, the differences in the comparisons between GEOS-Chem v8-02, v9-03, and v10-01 shown here are not necessarily due to the TOMAS code alone.
 +
 
 +
*Kodros, J. K. and Pierce, J. R.: Important global and regional differences in aerosol cloud-albedo effect estimates between simulations with and without prognostic aerosol microphysics, J. Geophys. Res. Atmos., doi:10.1002/2016JD025886, 2017
 +
 
 +
--[[User:Jeff Pierce|Jeff Pierce]] 13:21, 4 March 2014 (MST) <br>
 +
--[[User:Jkodros|Jack Kodros]] 11:30, 11 June 2018 (MST)
 +
 
 +
== Other features of TOMAS ==
 +
Other varieties of TOMAS are suited for specific science questions, for example with nucleation studies where explicit aerosol dynamics are needed for nanometer-sized particles.
 +
 
 +
=== Set-up Guide ===
 +
 
 +
This [[TOMAS setup guide]] was written for users on ACE-NET's Glooscap cluster, but may be more generally applicable.
 +
 
 +
--[[User:Salvatore Farina|Salvatore Farina]] 11:55, 26 July 2013 (EDT)
 +
 
 +
=== Size Resolution ===
 +
 
 +
The different TOMAS simulations (12, 15, 30, 40 size bins) have the following characteristics:
 +
 
 +
{| border=1 cellspacing=0 cellpadding=5
 +
|- bgcolor="#cccccc"
 +
!width="100px"|Simulation
 +
!width="700px"|Size resolution
 +
|-valign="top"
 +
|TOMAS12
 +
|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 resolution than TOMAS30 - Improved computation time.
 +
|-valign="top"
 +
|TOMAS15
 +
|Same as TOMAS12 with 3 additional (mass quadrupling) sub-10nm bins with a lower limit ~2nm. Analogous to TOMAS40 with improved computation time.
 +
|-valign="top"
 +
|TOMAS30
 +
|All 7 chemical species have size resolution ranging from 10 nm to 10 µm, spanned by 30 logarithmically spaced (mass doubling) bins.
 +
|-valign="top"
 +
|TOMAS40
 +
|Same as TOMAS30 with 10 additional (mass doubling) sub-10nm bins with a lower limit ~1nm.
 +
|}
 +
 
 +
--[[User:Salvatore Farina|Salvatore Farina]] 12:51, 4 June 2013 (EDT)
 +
 
 +
=== Nesting and grid size ===
 +
As of v10.01, TOMAS has been implemented and tested on the 4x5, 2x2.5, 0.5x0.667 (North America and Asia), and 0.25x0.3125 (Asian) domains. To the best of our knowledge, these grids should continue working in upcoming releases of GEOS-Chem (including the grid-independent GEOS-Chem). 
 +
 
 +
=== Sample code ===
 +
To assist new users, sample processing code (in Python) is available for GEOS-Chem-TOMAS output. Specifically, this code reads in GEOS-Chem-TOMAS output and demonstrates some common calculations (such as calculating size distributions, bin diameters, CCN, etc.). The primary focus of this code is to provide a few examples rather than a complete, efficient package. Further, this code was written based on GEOS-Chem-TOMAS v10.01, which outputs monthly tracers in bpch format. We also provide sample IDL scripts to convert bpch files to netCDF using GAMAP routines. Future versions of GEOS-Chem will output netCDF directly, and so these IDL routines will become obsolete. 
 +
 
 +
Git repository for sample TOMAS code: https://bitbucket.org/teampierce/sample_processing/src/master/
 +
 
 +
--[[User:Jkodros|Jack Kodros]] 1:12, 11 June 2018 (MST)
 +
 
 +
=== AOD, CCN post-processing code ===
 +
Codes available for calculating aerosol optical depth using TOMAS predicted aerosol composition and size and Mie Theory. Also CCN concentrations calculated from TOMAS size-resolved composition and Kohler theory. Developed by Yunha Lee and Jeffrey Pierce, adapted for GEOS-Chem output by Jeffrey Pierce.
 +
 
 +
--[[User:Dan Westervelt|Dan W.]] 2:00, 9 May 2011 (EST)
 +
 
 +
=== Biomass burning subgrid coagulation switch ===
 +
 
 +
<span style="color:green">'''''This update was included in [[GEOS-Chem_12#12.2.1|GEOS-Chem 12.2.1]], which was released on 28 Feb 2019.'''''</span>
 +
 
 +
Emily Ramnarine created code that allows the "emitted" size distribution in the model be a function of a number of properties that include the mean emissions rate per fire in the grid box. In order to do this, Emily needed to (1) make changes to carbon_mod.F, (2) add a line or few to HEMCO_config.rc, and (3) modify the FINN input files to include the number of fires. This only affects TOMAS simulations. Emily wrote:
 +
 
 +
:This parameterization, based on Sakamoto et al (2016), estimates the amount of near-source, sub-grid scale coagulation happening in a biomass burning plume. Can be turned on or off. When on, the default assumption is that each smoke plume is completely seperate 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.
 +
 
 +
'''Reference'''
 +
Ramnarine, E., Kodros, J. K., Hodshire, A. L., Lonsdale, C. R., Alvarado, M. J., and Pierce, J. R., ''Effects of Near-Source Coagulation of Biomass Burning Aerosols on Global Predictions of Aerosol Size Distributions and Implications for Aerosol Radiative Effects'', <u>Atmos. Chem. Phys. Discuss.</u>, https://doi.org/10.5194/acp-2018-1084, in review, 2018.
 +
 
 +
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 15:07, 22 February 2019 (UTC)<br>--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 18:54, 28 February 2019 (UTC)
 +
 
 +
== References ==
 +
 
 +
In this section we provide references relevant to TOMAS aerosl microphysics simulations.
  
== Previous issues now resolved ==
+
=== Studies using TOMAS simulations ===
 +
#'''Nucleation in GEOS-Chem:''' Westervelt, D. M., Pierce, J. R., Riipinen, I., Trivitayanurak, W., Hamed, A., Kulmala, M., Laaksonen, A., Decesari, S., and Adams, P. J.: ''Formation and growth of nucleated particles into cloud condensation nuclei: model-measurement comparison'', <u>Atmos. Chem. Phys. Discuss.</u>, '''13''', 8333-8386, doi:10.5194/acpd-13-8333-2013, 2013. [http://www.atmos-chem-phys-discuss.net/13/8333/2013/acpd-13-8333-2013.html LINK]
 +
#'''TOMAS implementation in GEOS-Chem:''' Trivitayanurak, W., Adams, P. J., Spracklen, D. V. and Carslaw, K. S.: ''Tropospheric aerosol microphysics simulation with assimilated meteorology: model description and intermodel comparison'', <u>Atmos. Chem. Phys.</u>, '''8'''(12), 3149-3168, 2008.
 +
#'''TOMAS initial paper, sulfate only:''' Adams, P. J. and Seinfeld, J. H.: ''redicting global aerosol size distributions in general circulation models'', <u>J. Geophys. Res.-Atmos.</u>, '''107'''(D19), -, doi:Artn 4370 Doi 10.1029/2001jd001010, 2002.
 +
#'''TOMAS with sea-salt:''' Pierce, J.R., and Adams P.J., ''Global evaluation of CCN formation by direct emission of sea salt and growth of ultrafine sea salt'', <u>J. Geophys. Res.-Atmos.</u>, '''111''' (D6), doi:10.1029/2005JD006186, 2006.
 +
#'''TOMAS with carbonaceous aerosol:''' Pierce, J. R., Chen, K. and Adams, P. J.: ''Contribution of primary carbonaceous aerosol to cloud condensation nuclei: processes and uncertainties evaluated with a global aerosol microphysics model'', <u>Atmos. Chem. Phys.</u>, '''7'''(20), 5447-5466, doi:10.5194/acp-7-5447-2007, 2007.; Trivitayanurak, W. and Adams, P. J.: ''Does the POA–SOA split matter for global CCN formation?'', <u>Atmos. Chem. Phys.</u>, '''14''', 995–1010, doi:10.5194/acp-14-995-2014, 2014.
 +
#'''TOMAS with dust:''' Lee, Y.H., K. Chen, and P.J. Adams, 2009: ''Development of a global model of mineral dust aerosol microphysics''. <u>Atmos. Chem. Phys.</u>, '''8''', 2441-2558, doi:10.5194/acp-9-2441-2009.
 +
#'''TOMAS with SOA:''' D'Andrea, S. D., Hakkinen, S. A. K., Westervelt, D. M., Kuang, C., Levin, E. J. T., Kanawade, V. P., Leaitch, W. R., Spracklen, D. V., Riipinen, I., and Pierce, J. R.: ''Understanding global secondary organic aerosol amount and size-resolved condensational behavior'', <u>Atmos. Chem. Phys.</u>, '''13''', 11519-11534, doi:10.5194/acp-13-11519-11534, 2013.
 +
#'''TOMAS with offline DRE/AIE:''' Kodros, J. K., Cucinotta, R., Ridley, D. A., Wiedinmyer, C. and Pierce, J. R.: ''The aerosol radiative effects of uncontrolled combustion of domestic waste'', <u>Atmos. Chem. Phys.</u>, 16(11), 6771-6784, doi:10.5194/acp-16- 6771-2016, 2016
 +
#'''TOMAS compared to GEOS-Chem standard:''' Kodros, J. K. and Pierce, J. R.: ''Important global and regional differences in aerosol cloud-albedo effect estimates between simulations with and without prognostic aerosol microphysics'', <u>J. Geophys. Res. Atmos.</u>, doi:10.1002/2016JD025886, 2017.
 +
--[[User:Bmy|Bob Y.]] 09:53, 2 June 2014 (EDT), [[User:Wint|Win T.]] 17:18, 28 June 2021 (EDT)
  
== Outstanding issues ==
+
=== Input data used by TOMAS ===
 +
#Usoskin, I. G. and Kovaltsov, G. A., ''Cosmic ray induced ionization in the atmosphere: Full modeling and practical applications'', <u>J. Geophys. Res.</u>, '''111''', doi:10.1029/2006JD007150, 2006..
 +
#Yu, Fangqun, et al, ''Ion-mediated nucleation in the atmosphere: Key controlling parameters, implications, and look-up table'', <u>J. Geophys. Res.</u>, '''115''', D03206, doi:10.1029/2009JD012630, 2010.
  
Text to be added
+
--[[User:Bmy|Bob Y.]] 17:03, 24 February 2014 (EST)

Latest revision as of 20:18, 22 September 2022

This page 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 APM.

Overview

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 a number of discrete size bins. It also contains codes to simulate nucleation, condensation, and coagulation processes. The aerosol species that are 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.

Authors and collaborators


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

TOMAS User Groups

User Group Personnel Projects
Carnegie-Mellon University Peter Adams
Dan Westervelt
New particle formation evaluation in GC-TOMAS
Sensitivity of CCN to nucleation rates
Development of number tagging and source apportionment model for GC-TOMAS
Colorado State Jeffrey Pierce
Sal Farina
Jack Kodros
Sensitivity of CCN to condensational growth rates
TOMAS parallelization
Aerosol radiative effects
Add yours here

--Bob Y. 16:35, 12 May 2014 (EDT)

TOMAS-specific setup

TOMAS has its own run directories (run.Tomas) that can be downloaded from the Harvard FTP. The input.geos file will look slightly different from standard GEOS-Chem, and between versions.

Pre- v9.02: To turn on TOMAS, see the "Microphysics menu" in input.geos and make sure TOMAS is set to T.

v9.02 and later: TOMAS is enabled or disabled at compile time - the TOMAS flag in input.geos has been removed.


TOMAS is a simulation type 3 and utilizes 171-423 tracers. Each aerosol species requires 30 tracers for the 30 bin size resolution, 12 for the 12 bin, etc. Here is the (abbreviated) default setup in input.geos for TOMAS-30 in v9.02 and later (see run.Tomas directory):

Tracer #   Description   
  1- 62    Std Geos Chem 
     63    H2SO4              
 64- 93    Number             
 94-123    Sulfate            
124-153    Sea-salt           
154-183    Hydrophilic EC     
184-213    Hydrophobic EC     
214-243    Hydrophilic OC     
244-273    Hydrophobic OC     
274-303    Mineral dust       
304-333    Aerosol water

TOMAS-40 requires 423 tracers (~360 TOMAS tracers for each of the 40-bin species, and ~62 standard GEOS-Chem tracers)

--Salvatore Farina 18:48, 8 July 2013 (EDT)

Implementation notes

  1. The original implementation and validation of TOMAS had been done for version GEOS-Chem v8-03-01, which was released on 24 Feb 2010.
  2. TOMAS was completely re-integrated into GEOS-Chem v9-02, which was released on 03 Mar 2014.
  3. TOMAS was re-integrated into GEOS-Chem v10-01 to become compatible with HEMCO.
  4. Updates to TOMAS to use the SOAP/SOAS tracers were made for GEOS-Chem v11-02 (not yet released).

Update April 2013

This update was tested in the 1-month benchmark simulation v9-02k and approved on 07 Jun 2013.

Sal Farina has been working with the GEOS-Chem Support Team to inline the TOMAS aerosol microphysics code into the GeosCore directory. All TOMAS-specific sections of code are now segregated from the rest of GEOS-Chem with C-preprocessor 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 


TOMAS is now invoked by compiling GEOS-Chem with one of the following options:

Command Result
make -j4 TOMAS=yes ... Compiles GEOS-Chem for the 30 bin (default) TOMAS simulation
make -j4 TOMAS12=yes ... Compiles GEOS-Chem for the 12 bin (optional) TOMAS simulation
make -j4 TOMAS15=yes ... Compiles GEOS-Chem for the 15 bin (optional) TOMAS simulation
make -j4 TOMAS40=yes ... Compiles GEOS-Chem for the 40 bin (optional) TOMAS simulation

The -j4 in the above examples tell the GNU Make utility to compile 4 files at a time. This reduces the overall compilation time.

All files in the old GeosTomas/ directory have now been deleted, as these have been rendered obsolete.

These updates are included in GEOS-Chem v9-02. These modifications will not affect the existing GEOS-Chem simulations, as all TOMAS code is not compiled into the executable unless you compile with one of the TOMAS options (described in the above table) at compile time.

--Salvatore Farina 13:49, 4 June 2013 (EDT)
--Bob Y. 16:39, 12 May 2014 (EDT)

Computational Information

GC-TOMAS v9-02 (30 sections) on 8 processors:

  • One year simulation = 7-8 days wall clock time

More speedups are available using lower aerosol size resolution

--Dan W. 11:00, 07 May 2013 (EST)


GC-TOMAS v9-02 on 16 processors (glooscap)

Simulation Wall time / simulation year
TOMAS12 (optional) 2.8 days
TOMAS15 (optional) 3.3 days
TOMAS30 (default) 6.1 days
TOMAS40 (optional) 7.8 days

--Salvatore Farina 15:51, 3 March 2014 (EST)

Microphysics Code

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. For details, see tomas_mod.f and comments.

Nucleation

The choice of nucleation theory is selected in the header section of tomas_mod.f. The choices are currently binary homogeneous nucleation as in Vehkamaki, 2001 or ternary homogenous nucleation as in Napari et al., 2002. The ternary nucleation rate is typically scaled by a globally uniform tuning factor of 10^-4 or 10^-5. Binary nucleation (Vehkamaki et al. 2002), ion-mediated nucleation (Yu, 2008) and activation nucleation (Kulmala, 2006) are options as well.

In TOMAS-12 and TOMAS-30, 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 Y. H. Lee, J. R. Pierce, and P. J. Adams 2013 here for more details on the consequences of this.

Condensation

Coagulation

--Dan W. 14:08, 9 May 2011 (EST)

Validation

The following figure documents the performance of GEOS-Chem-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, S. D., Hakkinen, S. A. K., Westervelt, D. M., Kuang, C., Levin, E. J. T., Kanawade, V. P., Leaitch, W. R., Spracklen, D. V., Riipinen, I., and Pierce, J. R.: Understanding global secondary organic aerosol amount and size-resolved condensational behavior, Atmos. Chem. Phys., 13, 11519-11534, doi:10.5194/acp-13-11519-11534, 2013.

GEOS-Chem-TOMAS performance update 20140304.png


An updated version of this figure is included as Figure 1 in Kodros and Pierce, (2017). Please note that the figure in this paper uses GEOS-Chem v10-01, which included substantial updates to emission inventories (as part of the HEMCO update). Thus, the differences in the comparisons between GEOS-Chem v8-02, v9-03, and v10-01 shown here are not necessarily due to the TOMAS code alone.

  • Kodros, J. K. and Pierce, J. R.: Important global and regional differences in aerosol cloud-albedo effect estimates between simulations with and without prognostic aerosol microphysics, J. Geophys. Res. Atmos., doi:10.1002/2016JD025886, 2017

--Jeff Pierce 13:21, 4 March 2014 (MST)
--Jack Kodros 11:30, 11 June 2018 (MST)

Other features of TOMAS

Other varieties of TOMAS are suited for specific science questions, for example with nucleation studies where explicit aerosol dynamics are needed for nanometer-sized particles.

Set-up Guide

This TOMAS setup guide was written for users on ACE-NET's Glooscap cluster, but may be more generally applicable.

--Salvatore Farina 11:55, 26 July 2013 (EDT)

Size Resolution

The different TOMAS simulations (12, 15, 30, 40 size bins) have the following characteristics:

Simulation Size resolution
TOMAS12 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 resolution than TOMAS30 - Improved computation time.
TOMAS15 Same as TOMAS12 with 3 additional (mass quadrupling) sub-10nm bins with a lower limit ~2nm. Analogous to TOMAS40 with improved computation time.
TOMAS30 All 7 chemical species have size resolution ranging from 10 nm to 10 µm, spanned by 30 logarithmically spaced (mass doubling) bins.
TOMAS40 Same as TOMAS30 with 10 additional (mass doubling) sub-10nm bins with a lower limit ~1nm.

--Salvatore Farina 12:51, 4 June 2013 (EDT)

Nesting and grid size

As of v10.01, TOMAS has been implemented and tested on the 4x5, 2x2.5, 0.5x0.667 (North America and Asia), and 0.25x0.3125 (Asian) domains. To the best of our knowledge, these grids should continue working in upcoming releases of GEOS-Chem (including the grid-independent GEOS-Chem).

Sample code

To assist new users, sample processing code (in Python) is available for GEOS-Chem-TOMAS output. Specifically, this code reads in GEOS-Chem-TOMAS output and demonstrates some common calculations (such as calculating size distributions, bin diameters, CCN, etc.). The primary focus of this code is to provide a few examples rather than a complete, efficient package. Further, this code was written based on GEOS-Chem-TOMAS v10.01, which outputs monthly tracers in bpch format. We also provide sample IDL scripts to convert bpch files to netCDF using GAMAP routines. Future versions of GEOS-Chem will output netCDF directly, and so these IDL routines will become obsolete.

Git repository for sample TOMAS code: https://bitbucket.org/teampierce/sample_processing/src/master/

--Jack Kodros 1:12, 11 June 2018 (MST)

AOD, CCN post-processing code

Codes available for calculating aerosol optical depth using TOMAS predicted aerosol composition and size and Mie Theory. Also CCN concentrations calculated from TOMAS size-resolved composition and Kohler theory. Developed by Yunha Lee and Jeffrey Pierce, adapted for GEOS-Chem output by Jeffrey Pierce.

--Dan W. 2:00, 9 May 2011 (EST)

Biomass burning subgrid coagulation switch

This update was included in GEOS-Chem 12.2.1, which was released on 28 Feb 2019.

Emily Ramnarine created code that allows the "emitted" size distribution in the model be a function of a number of properties that include the mean emissions rate per fire in the grid box. In order to do this, Emily needed to (1) make changes to carbon_mod.F, (2) add a line or few to HEMCO_config.rc, and (3) modify the FINN input files to include the number of fires. This only affects TOMAS simulations. Emily wrote:

This parameterization, based on Sakamoto et al (2016), estimates the amount of near-source, sub-grid scale coagulation happening in a biomass burning plume. Can be turned on or off. When on, the default assumption is that each smoke plume is completely seperate 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.

Reference Ramnarine, E., Kodros, J. K., Hodshire, A. L., Lonsdale, C. R., Alvarado, M. J., and Pierce, J. R., Effects of Near-Source Coagulation of Biomass Burning Aerosols on Global Predictions of Aerosol Size Distributions and Implications for Aerosol Radiative Effects, Atmos. Chem. Phys. Discuss., https://doi.org/10.5194/acp-2018-1084, in review, 2018.

--Melissa Sulprizio (talk) 15:07, 22 February 2019 (UTC)
--Bob Yantosca (talk) 18:54, 28 February 2019 (UTC)

References

In this section we provide references relevant to TOMAS aerosl microphysics simulations.

Studies using TOMAS simulations

  1. Nucleation in GEOS-Chem: Westervelt, D. M., Pierce, J. R., Riipinen, I., Trivitayanurak, W., Hamed, A., Kulmala, M., Laaksonen, A., Decesari, S., and Adams, P. J.: Formation and growth of nucleated particles into cloud condensation nuclei: model-measurement comparison, Atmos. Chem. Phys. Discuss., 13, 8333-8386, doi:10.5194/acpd-13-8333-2013, 2013. LINK
  2. TOMAS implementation in GEOS-Chem: Trivitayanurak, W., Adams, P. J., Spracklen, D. V. and Carslaw, K. S.: Tropospheric aerosol microphysics simulation with assimilated meteorology: model description and intermodel comparison, Atmos. Chem. Phys., 8(12), 3149-3168, 2008.
  3. TOMAS initial paper, sulfate only: Adams, P. J. and Seinfeld, J. H.: redicting global aerosol size distributions in general circulation models, J. Geophys. Res.-Atmos., 107(D19), -, doi:Artn 4370 Doi 10.1029/2001jd001010, 2002.
  4. TOMAS with sea-salt: Pierce, J.R., and Adams P.J., Global evaluation of CCN formation by direct emission of sea salt and growth of ultrafine sea salt, J. Geophys. Res.-Atmos., 111 (D6), doi:10.1029/2005JD006186, 2006.
  5. TOMAS with carbonaceous aerosol: Pierce, J. R., Chen, K. and Adams, P. J.: Contribution of primary carbonaceous aerosol to cloud condensation nuclei: processes and uncertainties evaluated with a global aerosol microphysics model, Atmos. Chem. Phys., 7(20), 5447-5466, doi:10.5194/acp-7-5447-2007, 2007.; Trivitayanurak, W. and Adams, P. J.: Does the POA–SOA split matter for global CCN formation?, Atmos. Chem. Phys., 14, 995–1010, doi:10.5194/acp-14-995-2014, 2014.
  6. TOMAS with dust: Lee, Y.H., K. Chen, and P.J. Adams, 2009: Development of a global model of mineral dust aerosol microphysics. Atmos. Chem. Phys., 8, 2441-2558, doi:10.5194/acp-9-2441-2009.
  7. TOMAS with SOA: D'Andrea, S. D., Hakkinen, S. A. K., Westervelt, D. M., Kuang, C., Levin, E. J. T., Kanawade, V. P., Leaitch, W. R., Spracklen, D. V., Riipinen, I., and Pierce, J. R.: Understanding global secondary organic aerosol amount and size-resolved condensational behavior, Atmos. Chem. Phys., 13, 11519-11534, doi:10.5194/acp-13-11519-11534, 2013.
  8. TOMAS with offline DRE/AIE: Kodros, J. K., Cucinotta, R., Ridley, D. A., Wiedinmyer, C. and Pierce, J. R.: The aerosol radiative effects of uncontrolled combustion of domestic waste, Atmos. Chem. Phys., 16(11), 6771-6784, doi:10.5194/acp-16- 6771-2016, 2016
  9. TOMAS compared to GEOS-Chem standard: Kodros, J. K. and Pierce, J. R.: Important global and regional differences in aerosol cloud-albedo effect estimates between simulations with and without prognostic aerosol microphysics, J. Geophys. Res. Atmos., doi:10.1002/2016JD025886, 2017.

--Bob Y. 09:53, 2 June 2014 (EDT), Win T. 17:18, 28 June 2021 (EDT)

Input data used by TOMAS

  1. Usoskin, I. G. and Kovaltsov, G. A., Cosmic ray induced ionization in the atmosphere: Full modeling and practical applications, J. Geophys. Res., 111, doi:10.1029/2006JD007150, 2006..
  2. Yu, Fangqun, et al, Ion-mediated nucleation in the atmosphere: Key controlling parameters, implications, and look-up table, J. Geophys. Res., 115, D03206, doi:10.1029/2009JD012630, 2010.

--Bob Y. 17:03, 24 February 2014 (EST)