Difference between revisions of "TOMAS aerosol microphysics"

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=== Authors and collaborators ===
 
=== Authors and collaborators ===
 
* [mailto:petera@andrew.cmu.edu Peter Adams]  ''(Carnegie-Mellon U.)''  -- Principal Investigator
 
* [mailto:petera@andrew.cmu.edu Peter Adams]  ''(Carnegie-Mellon U.)''  -- Principal Investigator
* [mailto:wtrivita@staffmail.ed.ac.uk Win Trivitayanurak] ''(Department of Highways, Thailand)''
+
* [mailto:win.t@chula.ac.uk Win Trivitayanurak] ''(Chulalongkorn University, Thailand)''
* [mailto:dwesterv@andrew.cmu.edu Dan Westervelt] ''(Carnegie-Mellon U.)''
+
* [mailto:danielmw@princeton.edu Dan Westervelt] ''(Princeton University, formerly Carnegie-Mellon U.)''
* [mailto:jeffrey.pierce@dal.ca Jeffrey Pierce] ''(Dalhousie 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)
  
Questions regarding TOMAS can be directed at Dan (e-mail linked above).
 
  
 
--[[User:Dan Westervelt|Dan W.]] 11:53, 27 January 2010 (EST)
 
--[[User:Dan Westervelt|Dan W.]] 11:53, 27 January 2010 (EST)
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| [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
 
| [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"
 
|-valign="top"
|[http://fizz.phys.dal.ca/%7Epierce/ Dalhousie University] <br> [http://www.atmos.colostate.edu/faculty/pierce.php Colorado State]
+
|[http://www.atmos.colostate.edu/faculty/pierce.php Colorado State]
|[http://atm.dal.ca/Faculty/Jeffrey_Pierce.php Jeffrey Pierce]<br>Stephen D'Andrea<br>Sal Farina (TOMAS Software Engineer)
+
|[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> Others...
+
|Sensitivity of CCN to condensational growth rates <br> TOMAS parallelization <br> Aerosol radiative effects
 
|-valign="top"
 
|-valign="top"
 
|Add yours here
 
|Add yours here
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|
 
|
 
|}
 
|}
 +
 +
--[[User:Bmy|Bob Y.]] 16:35, 12 May 2014 (EDT)
  
 
== TOMAS-specific setup ==
 
== TOMAS-specific setup ==
TOMAS has its own run directory (run.Tomas) that can be downloaded from the Harvard FTP. The <tt>input.geos</tt> file will look slightly different. To turn on TOMAS, see the "Microphysics menu" in <tt>input.geos</tt> and make sure TOMAS is set to '''T'''.  
+
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 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):
+
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      
+
  Tracer #  Description  
40        H2SO4               
+
  1- 62    Std Geos Chem
41-70      Number             
+
      63    H2SO4               
71-100    Sulfate             
+
  64- 93    Number             
  101-130   Sea-salt           
+
  94-123    Sulfate             
  131-160   Hydrophilic EC     
+
  124-153   Sea-salt           
  161-190   Hydrophobic EC     
+
  154-183   Hydrophilic EC     
  191-210   Hydrophilic OC     
+
  184-213   Hydrophobic EC     
  211-240   Hydrophobic OC     
+
  214-243   Hydrophilic OC     
  241-271   Mineral dust       
+
  244-273   Hydrophobic OC     
  271-310   Aerosol water    
+
  274-303   Mineral dust       
 +
  304-333   Aerosol water
  
TOMAS-40 requires 400 tracers (~360 TOMAS tracers for each of the 40-bin species, and ~40 standard GEOS-Chem tracers)  
+
TOMAS-40 requires 423 tracers (~360 TOMAS tracers for each of the 40-bin species, and ~62 standard GEOS-Chem tracers)  
  
--[[User:Dan Westervelt|Dan W.]] 21:08, 28 January 2010 (EST)
+
--[[User:Salvatore Farina|Salvatore Farina]] 18:48, 8 July 2013 (EDT)
  
 
== Implementation notes ==
 
== Implementation notes ==
  
TOMAS validation in [[GEOS-Chem v8-03-01]] was completed on 24 Feb 2010.
+
#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).  
  
 
=== Update April 2013 ===
 
=== Update April 2013 ===
 +
 +
<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>
  
 
Sal Farina has been working with the GEOS-Chem Support Team to inline the TOMAS aerosol microphysics code into the <tt>GeosCore</tt> directory.  All TOMAS-specific sections of code are now segregated from the rest of GEOS-Chem with C-preprocessor statements such as:
 
Sal Farina has been working with the GEOS-Chem Support Team to inline the TOMAS aerosol microphysics code into the <tt>GeosCore</tt> 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( TOMAS )
  ... Code for 30 bin TOMAS simulation (default) goes here ...
 
 
   
 
   
  #if defined( TOMAS40 )  
+
  # if defined( TOMAS40 )  
 
   ... Code for 40 bin TOMAS simulation (optional) goes here ...
 
   ... Code for 40 bin TOMAS simulation (optional) goes here ...
  #endif
+
# 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  
 
  #endif  
 +
  
 
TOMAS is now invoked by compiling GEOS-Chem with one of the following options:
 
TOMAS is now invoked by compiling GEOS-Chem with one of the following options:
  
make -j4 TOMAS=yes ...     # Compiles GEOS-Chem for the 30 bin (default) TOMAS simulation
+
{| border=1 cellspacing=0 cellpadding=5
                            # -j4 compiles 4 files at a time; this reduces overall compilation time
+
|- bgcolor="#cccccc"
+
!width="250px"|Command
or
+
!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
 +
|}
  
make -j4 TOMAS40=yes ...    # Compiles GEOS-Chem for the 40 bin (optional) TOMAS simulation
+
The <tt>-j4</tt> in the above examples tell the GNU Make utility to compile 4 files at a time.  This reduces the overall compilation time.
                            # -j4 compiles 4 files at a time; this reduces overall compilation time
+
  
 
All files in the old <tt>GeosTomas/</tt> directory have now been deleted, as these have been rendered obsolete.
 
All files in the old <tt>GeosTomas/</tt> directory have now been deleted, as these have been rendered obsolete.
  
We hope to be able to add these updates into [[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 specify either <tt>TOMAS=yes</tt> or <tt>TOMAS40=yes</tt> at compile time.
+
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.
  
We also update the wiki pages again in the near future to reflect these changes.
+
--[[User:Salvatore Farina|Salvatore Farina]] 13:49, 4 June 2013 (EDT)<br>
 +
--[[User:Bmy|Bob Y.]] 16:39, 12 May 2014 (EDT)
  
--[[User:Bmy|Bob Y.]] 13:59, 23 April 2013 (EDT)
+
== Computational Information ==
  
=== Code structure ===
+
GC-TOMAS v9-02 (30 sections) on 8 processors:
  
'''''NOTE: This will be rendered obsolete by the [[#Update April 2013|re-integration of TOMAS into GEOS-Chem]], which is slated for [[GEOS-Chem v9-02]].'''''
+
*One year simulation = 7-8 days wall clock time
  
The main-level <tt>Code</tt> directory has now been divided into several subdirectories:
+
More speedups are available using lower aerosol size resolution
  
GeosCore/    GEOS-Chem "core" routines
+
--[[User:Dan Westervelt|Dan W.]] 11:00, 07 May 2013 (EST)
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:
 
  
Files:
+
GC-TOMAS v9-02 on 16 processors (glooscap)
------
+
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.
+
{| 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
  
A few technical considerations dictated the placing of these files into a separate <tt>GeosTomas/</tt> directory:
+
|}
  
* 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. 
+
--[[User:Salvatore Farina|Salvatore Farina]] 15:51, 3 March 2014 (EST)
* 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.
+
 
+
--[[User:Bmy|Bob Y.]] 13:35, 25 February 2010 (EST)
+
 
+
=== Building GEOS-Chem with TOMAS ===
+
 
+
'''''NOTE: This will be rendered obsolete by the [[#Update April 2013|re-integration of TOMAS into GEOS-Chem]], which is slated for [[GEOS-Chem v9-02]].'''''
+
 
+
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 target, 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.
+
 
+
Several new targets were added to the <tt>Makefile</tt> in the top-level <tt>Code/</tt> directory:
+
 
+
#=============================================================================
+
# Targets for TOMAS aerosol microphysics code (win, bmy, 1/25/10)
+
#=============================================================================
+
+
.PHONY: tomas libtomas exetomas cleantomas
+
+
tomas:
+
        @$(MAKE) -C $(GEOSTOM) TOMAS=yes all
+
+
libtomas:
+
        @$(MAKE) -C $(GEOSTOM) TOMAS=yes lib
+
+
exetomas:
+
        @$(MAKE) -C $(GEOSTOM) TOMAS=yes exe
+
+
cleantomas:
+
        @$(MAKE) -C $(GEOSTOM) TOMAS=yes clean
+
 
+
You can build GEOS-Chem with the TOMAS option by typing:
+
 
+
make tomas ...
+
 
+
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.
+
* 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
+
 
+
* Intel Fortran compiler v10
+
* SunStudio 12
+
 
+
--[[User:Bmy|Bob Y.]] 10:36, 27 January 2010 (EST)
+
 
+
== 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
+
 
+
 
+
--[[User:Dan Westervelt|Dan W.]] 11:00, 07 May 2013 (EST)
+
  
 
== Microphysics Code==
 
== Microphysics Code==
Line 212: Line 164:
  
 
=== Nucleation ===
 
=== Nucleation ===
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. In TOMAS-40, ion-mediated nucleation (Yu, 2008) and activation nucleation (Kulmala, 2006) are options as well.  
+
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.
 +
 
 +
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 ===
 
=== Condensation ===
  
 
=== Coagulation ===
 
=== Coagulation ===
 
=== Size resolved emissions ===
 
 
=== Size resolved deposition ===
 
 
More to be added here shortly.
 
  
 
--[[User:Dan Westervelt|Dan W.]] 14:08, 9 May 2011 (EST)
 
--[[User:Dan Westervelt|Dan W.]] 14:08, 9 May 2011 (EST)
Line 228: Line 176:
 
== Validation ==
 
== Validation ==
  
GC-TOMAS [[GEOS-Chem v8-03-01|v8-03-01]] generally compares very well with observations and other models.  Please see our [http://acmg.seas.harvard.edu/geos/wiki_docs/TOMAS/TOMAS_benchmark_ForHarvard.pdf GC-TOMAS v8-02-05 validation document] for more information and figures.  
+
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
  
Below are some results of benchmarking GC-TOMAS with earlier versions of the model as well as observations:
+
* 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:CN10_smaller.jpg]]
+
[[Image:GEOS-Chem-TOMAS performance update 20140304.png]]
  
'''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.'''
 
  
----
+
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.
  
--[[User:Dan Westervelt|Dan W.]] 20:13, 10 February 2010 (EST)
+
*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
  
== Previous issues now resolved ==
+
--[[User:Jeff Pierce|Jeff Pierce]] 13:21, 4 March 2014 (MST) <br>
 +
--[[User:Jkodros|Jack Kodros]] 11:30, 11 June 2018 (MST)
  
=== Segmentation Fault ===
+
== Other features of TOMAS ==
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 <tt>.cshrc</tt>) or use the <tt>ulimit</tt> command. See [http://wiki.seas.harvard.edu/geos-chem/index.php/Machine_issues_%26_portability#Resetting_stacksize_for_Linux this page] for details.
+
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.  
  
--[[User:Dan Westervelt|Dan W.]] 20:20, 10 February 2010 (EST)
+
=== Set-up Guide ===
  
== Outstanding issues ==
+
This [[TOMAS setup guide]] was written for users on ACE-NET's Glooscap cluster, but may be more generally applicable.
  
=== Vertical Grids ===
+
--[[User:Salvatore Farina|Salvatore Farina]] 11:55, 26 July 2013 (EDT)
Currently, GC-TOMAS is only compatible with the reduced vertical grids:
+
* [http://acmg.seas.harvard.edu/geos/doc/man/appendix_3.html#A3.3.1 GEOS3_30L]
+
* [http://acmg.seas.harvard.edu/geos/doc/man/appendix_3.html#A3.4.1 GEOS4_30L]
+
* [http://acmg.seas.harvard.edu/geos/doc/man/appendix_3.html#A3.5.1 GEOS5_47L]
+
  
Development for the full vertical grids is ongoing.
+
=== Size Resolution ===
  
--[[User:Dan Westervelt|Dan W.]] 20:43, 10 February 2010 (EST)
+
The different TOMAS simulations (12, 15, 30, 40 size bins) have the following characteristics:
  
=== Compile from GeosTomas directory ===
+
{| 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.
 +
|}
  
'''''NOTE: This will be rendered obsolete by the [[#Update April 2013|re-integration of TOMAS into GEOS-Chem]], which is slated for [[GEOS-Chem v9-02]].'''''
+
--[[User:Salvatore Farina|Salvatore Farina]] 12:51, 4 June 2013 (EDT)
  
'''''[mailto:dwesterv@andrew.cmu.edu Dan Westervelt] wrote:'''''
+
=== 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). 
  
:I think there is something going wrong in my compilation, although errors have come up at both compile time and run time. The worst of the problems is this: I'll make a change to any fortran file in the code (even something meaningless like print*, 'foo') and hundreds of compile errors come out with fishy error messages such as (from ifort v10.1):
+
=== 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.
  
  ***fortcom: Error: chemistry_mod.f, line 478: A kind type parameter must be a compile-time constant.  [DP]
+
Git repository for sample TOMAS code: https://bitbucket.org/teampierce/sample_processing/src/master/
          REAL(kind=dp) :: RCNTRL(20)
+
  
:Any advice? The errors I'm having are not unique to any version of GC, any type of met fields, any compiler, etc.
+
--[[User:Jkodros|Jack Kodros]] 1:12, 11 June 2018 (MST)
  
'''''[mailto:yantosca@seas.harvard.edu Bob Yantosca] wrote:'''''
+
=== 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.
  
:Make sure you are always in the GeosTomas subdirectory when you build the code.  Sometimes there is a problem if you build the code from a higher level directory.  This may have to do with the VPATH in the makefile.
+
--[[User:Dan Westervelt|Dan W.]] 2:00, 9 May 2011 (EST)
  
'''''[mailto:dwesterv@andrew.cmu.edu Dan Westervelt] wrote:'''''
+
=== Biomass burning subgrid coagulation switch ===
  
:Thanks, that seems to do the trick.
+
<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>
  
--[[User:Bmy|Bob Y.]] 14:37, 14 April 2010 (EDT)
+
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:
  
== Other features of TOMAS ==
+
: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.
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.  
+
  
=== Size resolution ===
+
'''Reference'''
'''TOMAS-30''': All 7 chemical species have size resolution ranging from 10 nm to 10 microns, spanned by 30 logarithmically spaced bins. Currently in standard GEOS-Chem code
+
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.
  
'''TOMAS-40''': All chemical species have size resolution from 1 nm to 10 micron, again spanned by 40 logarithmically spaced bins. Incorporated into GEOS-Chem v8.03.01, available by request.
+
--[[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)
 
+
'''TOMAS-36''': Size resolution from 3 nm to 10 micron, 36 logarithmically spaced bins. Incorporated into GEOS-Chem v8.03.01, available by request.
+
 
+
'''TOMAS-15''': Size resolution from 10 nm to 10 micron. Coarser bin spacing than TOMAS-30. Improved computation time. 
+
 
+
'''TOMAS-12''': Same as TOMAS-15, but with lumped supermicron bins. Improved computation time, available by request.
+
 
+
'''TOMAS-18''': Same as TOMAS-36, but with coarser size resolution. Improved computation time, available by request.
+
 
+
=== Nesting and grid size ===
+
TOMAS is implemented on a 2x2.5 North American domain. Developed by Jeffrey Pierce (jeffrey.pierce@dal.ca)
+
 
+
=== 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)
+
  
== Reference ==
+
== References ==
'''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, Atmospheric Chemistry and Physics, 8(12), 3149-3168, 2008.
+
  
'''TOMAS initial paper, sulfate only:'''
+
In this section we provide references relevant to TOMAS aerosl microphysics simulations.
Adams, P. J. and Seinfeld, J. H.: Predicting global aerosol size distributions in general circulation models, J Geophys Res-Atmos, 107(D19), -, doi:Artn 4370 Doi 10.1029/2001jd001010, 2002.
+
  
'''TOMAS with sea-salt:'''
+
=== Studies using TOMAS simulations ===
Pierce, J.R., and Adams P.J., Global evaluation of CCN formation by direct emission of sea salt and growth of ultrafine sea salt, Journal of Geophysical Research-Atmospheres, 111 (D6), doi:10.1029/2005JD006186, 2006.
+
#'''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)
  
'''TOMAS with carbonaceous aerosol:'''
+
=== Input data used by TOMAS ===
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.
+
#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.
  
'''TOMAS with dust:'''
+
--[[User:Bmy|Bob Y.]] 17:03, 24 February 2014 (EST)
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.
+

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)