Difference between revisions of "TOMAS aerosol microphysics"

From Geos-chem
Jump to: navigation, search
(Typo in wetscav_mod.F for TOMAS30 simulation)
(Unresolved issues)
 
(43 intermediate revisions by 4 users not shown)
Line 7: Line 7:
 
=== 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:danielmw@princeton.edu Dan Westervelt] ''(Princeton University, formerly Carnegie-Mellon U.)''
 
* [mailto:danielmw@princeton.edu Dan Westervelt] ''(Princeton University, formerly Carnegie-Mellon U.)''
* [mailto:jeffrey.pierce@dal.ca Jeffrey Pierce] ''(CSU/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.)''
 
* [mailto:sal.farina@gmail.com Salvatore Farina] ''(Colorado State U.)''
*Stephen D'Andrea (CSU)
 
*Robin Stevens (CSU)
 
 
*Marguerite Marks (CMU)
 
*Marguerite Marks (CMU)
  
Line 30: Line 29:
 
| [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>Sal Farina<br>Stephen D'Andrea
+
|[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
Line 74: Line 73:
 
#The original implementation and validation of TOMAS had been done for version [[GEOS-Chem v8-03-01]], which was released 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 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 ===
Line 181: Line 182:
 
[[Image:GEOS-Chem-TOMAS performance update 20140304.png]]
 
[[Image:GEOS-Chem-TOMAS performance update 20140304.png]]
  
--[[User:Jeff Pierce]] 13:21, 4 March 2014 (MST)
+
 
 +
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 features of TOMAS ==
Line 217: Line 224:
  
 
=== Nesting and grid size ===
 
=== Nesting and grid size ===
TOMAS is implemented on a 2x2.5 North American domain. Developed by Jeffrey Pierce (jeffrey.pierce@dal.ca)
+
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 ===
 
=== AOD, CCN post-processing code ===
Line 223: Line 237:
  
 
--[[User:Dan Westervelt|Dan W.]] 2:00, 9 May 2011 (EST)
 
--[[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 ==
 
== References ==
Line 233: Line 260:
 
#'''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 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 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.
+
#'''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 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 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
--[[User:Bmy|Bob Y.]] 09:53, 2 June 2014 (EDT)
+
#'''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)
  
 
=== Input data used by TOMAS ===
 
=== Input data used by TOMAS ===
Line 244: Line 272:
  
 
--[[User:Bmy|Bob Y.]] 17:03, 24 February 2014 (EST)
 
--[[User:Bmy|Bob Y.]] 17:03, 24 February 2014 (EST)
 
== Previous issues now resolved ==
 
 
=== Fixes for TOMAS simulation in v11-02c  ===
 
 
<span style="color:green">'''''These fixes were included in [[GEOS-Chem v11-02#v11-02c|v11-02c]] and approved on 21 Sep 2017.'''''</span>
 
 
Sal Farina provided several updates to get the TOMAS simulation to work in v11-02c, including:
 
 
1) A patch for TOMAS to run in v11.02c (applies to 7c92951206e62). Prior to this fix, the TOMAS simulation was crashing because of 3D emissions added in v11-02a.
 
 
2) A TOMAS data file that has contained a typo for a long time. Sal added a leading space to each line for the formatted read to work correctly on negative numbers. The corrected file can now be found in <tt>GEOS_NATIVE/TOMAS_201402/YuIMN_AMOLF3D.txt</tt> (the original file is named with <tt>pre_v11-02a</tt> for record keeping).
 
 
3) A tweak to the UT for TOMAS to have longer timesteps than the other simulations (30/60, instead of 10/20) by default.
 
 
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 20:21, 26 June 2017 (UTC)
 
 
=== Minor bug in TOMAS sulfate emissions ===
 
 
<span style="color:green">'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02o|v9-02o]] and approved on 03 Sep 2013.'''''</span>
 
 
'''''[mailto:sal.farina@gmail.com Sal Farina] wrote:'''''
 
:Calling mnfix before and after emission ensures the size distribution is well behaved, and eliminates "Negative SF emis" warnings. An edit to mnfix was also introduced, whereby "tiny" mass added to zero mass, "epsilon" number situations resulted in very high mass per particle results - necessitating excessive error detection, correction, and verbosity.
 
 
--[[User:Melissa Payer|Melissa Sulprizio]] 15:08, 7 August 2013 (EDT)
 
 
=== Segmentation Fault ===
 
You may get an early segfault if your stacksize is not set to either unlimited or a very large number. To avoid this, you either have to change the value of an environmental variable (setenv command in <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.
 
 
--[[User:Dan Westervelt|Dan W.]] 20:20, 10 February 2010 (EST)
 
 
=== Updates for GEOS-Chem v9-02 public release ===
 
 
<span style="color:red">'''''NOTE: As described below, there appears to be [[#Potential parallelization problems|a potential parallelizaiton problem with the TOMAS ND60 diagnostic]].  We are currently looking into this.  This issue, however, does not affect the tracer concentrations computed by TOMAS, but only the output of the ND60 diagnostic itself.  For this reason we decided not to delay the [[GEOS-Chem v9-02]] public release process.  TOMAS benchmarks for v9-02 are currently being evaluated.'''''</span>
 
 
We have found and fixed several minor numerical and coding issues prior to the public release of [[GEOS-Chem v9-02]] (03 Mar 2014).  The TOMAS40 simulation has been validated with the [[GEOS-Chem Unit Tester]].  Below is the [[GEOS-Chem Unit Tester#Interpreting_results_generated_by_the_GEOS-Chem_Unit_Tester|output of a unit test]] that was submitted on 2014/02/21 at 12:47:26 PM:
 
 
###############################################################################
 
### VALIDATION OF GEOS-CHEM OUTPUT FILES
 
### In directory: geos5_4x5_TOMAS40
 
###
 
### File 1    : trac_avg.geos5_4x5_TOMAS40.2005070100.sp
 
### File 2    : trac_avg.geos5_4x5_TOMAS40.2005070100.mp
 
### Sizes    : IDENTICAL (680420788 and 680420788)
 
### Checksums : IDENTICAL (179613338 and 179613338)
 
### Diffs    : IDENTICAL
 
###
 
### File 1    : trac_rst.geos5_4x5_TOMAS40.2005070101.sp
 
### File 2    : trac_rst.geos5_4x5_TOMAS40.2005070101.mp
 
### Sizes    : IDENTICAL (263480068 and 263480068)
 
### Checksums : IDENTICAL (1925551193 and 1925551193)
 
### Diffs    : IDENTICAL
 
###
 
### File 1    : soil_rst.geos5_4x5_TOMAS40.2005070101.sp
 
### File 2    : soil_rst.geos5_4x5_TOMAS40.2005070101.mp
 
### Sizes    : IDENTICAL (54040 and 54040)
 
### Checksums : IDENTICAL (3229970876 and 3229970876)
 
### Diffs    : IDENTICAL
 
###############################################################################
 
 
In the subsections below, we describe in more detail the fixes that we made for [[GEOS-Chem v9-02]]:
 
 
==== Fixes for minor coding errors ====
 
 
#<p>In <tt>GeosCore/main.F</tt>, we now replaced <tt>CALL FLUSH()</tt> with <tt>CALL FLUSH(6)</tt>.  The <tt>FLUSH</tt> routine needs to take an argument.  Unit #6 is the unit stdout (i.e. the screen and/or log file).</p>
 
#<p>In routine <tt>CHEM_SO2</tt> (in module <tt>GeosCore/sulfate_mod.F</tt>), we now avoid referencing the dust tracers DST1, DST2, DST3, and DST4 tracers for TOMAS simulations.  TOMAS uses size-resolved dust tracers, and therefore does not carry DST1-4 tracers. This error seems to have been introduced when the fix for cloud pH was introduced in Sep 2013.</p>
 
#<p>In routine <tt>COND_NUC</tt> (in module <tt>GeosCore/tomas_mod.F</tt>), we added error traps to avoid division-by-zero errors that occurred when the variable <tt>CSCH</tt> is zero.  When <tt>CSCH</tt> is zero, we now set variable <tt>ADDT</tt> to zero.  When <tt>ADDT</tt> is zero, it will get reassigned to a minimum time step, so this fix should work OK.</p>
 
#<p>In <tt>GeosCore/gamap_mod.F</tt>, we now have restored several entries to <tt>tracerinfo.dat</tt> for the ND44 diagnostic that were not getting properly printed out when the TOMAS simuation was being used.</p>
 
#<p>In module <tt>GeosCore/drydep_mod.F</tt>, we Now set <tt>MAXDEP=105</tt> for all simulations, including TOMAS.  Formerly, TOMAS had <tt>MAXDEP=100</tt>.  This is close enough.</p>
 
#<p>In module <tt>GeosCore/diag3.F</tt>, we now avoid an out-of-bounds error in <tt>DEPNAME(N)</tt> during TOMAS simulations.  We save the drydep species name from <tt>DEPNAME(N)</tt> into an new variable <tt>DRYDEP_NAME</tt> for <tt>N = 1..NUMDEP</tt>.  We then set <tt>DRYDEP_NAME = ''</tt> for <tt>N > NUMDEP</tt>.  This error occurs because we extend the # of drydep tracers during TOMAS simulations to account for the size bins.</p>
 
#<p>We have fixed a couple of logical errors that prevented dust emissions from happening.  Minor modifications were made to IF statements in <tt>GeosCore/chemistry_mod.F</tt>, <tt>GeosCore/dust_mod.F</tt>, and <tt>GeosCore/input_mod.F</tt>.</p>
 
#<p>In file <tt>GeosCore/Makefile</tt>, make sure to add <tt>tomas_mod.o</tt> to the list of modules used by <tt>wetscav_mod.F</tt> (aka the "dependency listing").  The corrected code should look like this:</p>
 
 
    wetscav_mod.o              : wetscav_mod.F                                  \
 
                                  dao_mod.o              diag_mod.o            \
 
                                  depo_mercury_mod.o      get_ndep_mod.o        \
 
                                  get_popsinfo_mod.o      tracerid_mod.o        \
 
                                  tracer_mod.o            tomas_mod.o
 
 
--[[User:Bmy|Bob Y.]] 10:20, 19 February 2014 (EST)
 
 
==== Fixes for parallelization errors ====
 
 
#<p>In routine <tt>AEROPHYS</tt> (in module <tt>GeosCore/tomas_mod.F</tt>), we need to add the following variables to the <tt>!$OMP+PRIVATE</tt> statement: <tt>TRACNUM</tt>, <tt>NH3_TO_NH4</tt>, and <tt>SURF_AREA</tt>.  Adding these now causes TOMAS to have identical sp vs. mp results when chemistry and microphysics are turned on.</p>
 
#<p>In routine <tt>DEPVEL</tt> (in <tt>GeosCore/drydep_mod.F</tt>): Instead of holding <tt>A_RADI</tt> and <tt>A_DEN</tt> as <tt>!$OMP+PRIVATE</tt> in TOMAS simulations (in the main DO loop in <tt>DEPVEL</tt>), we now save the particle size and density values to private variables <tt>DIAM</tt> and <tt>DEN</tt>.  We then pass those as arguments to function <tt>DUST_SFCRSII</tt>.</p> 
 
#<p>We have corrected an issue in routine <tt>NFCLDMX</tt> (in module <tt>GeosCore/convection_mod.F</tt>) that potentially impacts the TOMAS wet scavenging, as described below:</p>
 
#*<p>We think there are different results for parallel and serial because of an assumption that's true for normal simulations but fails on TOMAS. The assumption is "tracers are independent through wet scavenging." Since TOMAS scavenging is size dependent, removing material from the distribution before calculating the soluble fraction of another component is "wrong." We now compute the fractions explicitly before the removal step.  To do this, we now call routine <tt>COMPUTE_F</tt> in its own parallel DO loop located immediately before the main parallel do loop in <tt>NFCLDMX</tt>.</p>
 
#*<p>This modification also required the ND37 diagnostic IF block to be put into the same loop as <tt>COMPUTE_F</tt>.  Furthermore, because <tt>COMPUTE_F</tt> returns the value of diagnostic index <tt>ISOL</tt>, and because <tt>ISOL</tt> is also used for the ND38 diagnostic in the main parallel loop below, we must also save the values of <tt>ISOL</tt> in a 1-D vector.  This will allow the values of ISOL to be passed from the first parallel loop to the second.  This ensures that the ND37 and ND38 diagnostics will be computed properly for all GEOS-5 simulations that have soluble tracers.</p>
 
#*<p>This modification has been tested in the [[GEOS-Chem Unit Tester]] by Bob Yantosca (04 Feb 2014) and it has yielded identical results for    <tt>geos5_4x5_fullchem</tt>, <tt>geos5_4x5_Hg</tt>, <tt>geos5_4x5_RnPbBe</tt>, <tt>geos5_4x5_soa</tt> and <tt>geos5_4x5_soa_svpoa</tt> simulations.</p>
 
#<p>We have made some fixes in <tt>GeosCore/wetscav_mod.F</tt> that caused single-processor TOMAS runs to have different output than multi-processor runs.  A few instances of code were computing quantities sequentially and then storing them for later use.  These were technically thread-safe, but were susceptible to error because the order of computation would be different when running with parallelization turned on.  These sections of code have now been rewritten accordingly.</p>
 
 
--[[User:Bmy|Bob Y.]] 14:09, 21 February 2014 (EST)
 
 
==== Removed inefficient subroutine calls ====
 
 
#<p>In <tt>GeosCore/diag3.F</tt>, we now use a 2-D array <tt>(J-L)</tt> for archiving into the ND60 TOMAS diagnostic.  This eliminates an array temporary in the call to routine BPCH2.</p>
 
#<p>In routine <tt>AEROPHYS</tt> (in module <tt>GeosCore/tomas_mod.F</tt>), we now use an array <tt>ERR_IND</tt> to pass the I,J,L,N indices to error checking routine <tt>CHECK_VALUE</tt>.  We previously used an array descriptor <tt>(/I,J,L,0/)</tt> which caused an array temporary to be created.</p>
 
#<p>In routine <tt>EMISSCARBON</tt> (in module <tt>GeosCore/carbon_mod.F</tt>), we removed array temporaries from the calls to subroutine <tt>EMITSGC</tt>. We now sum two arrays into a temporary array, and then pass that to <tt>EMITSGC</tt>.</p>
 
#<p>We rewrote the subroutine calls to NH4BULKTOBIN to avoid the creation of array temporaries.  In most cases this was done by replacing <tt>MK(1:IBINS,SRTSO4)</tt> with <tt>MK(:,SRTSO4)</tt>, etc.  By explicitly stating the sub-slice <tt>MK(1:IBINS,SRTSO4)</tt>, this causes the compiler to create an array temporary.  Using <tt>MK(:,SRTSO4)</tt> instead allows for a more efficient pointer slice to be passed.</p>
 
 
--[[User:Bmy|Bob Y.]] 14:47, 31 January 2014 (EST)
 
 
==== Fixes for convenience ====
 
 
<p>We now read many of the TOMAS data files from the directory <tt>TRIM( DATA_DIR_1x1 ) // 'TOMAS_201402/'</tt>.  This avoids us from having to keep these big files (some of which approach 100 MB in size) in individual users' run directories.</p>
 
 
--[[User:Bmy|Bob Y.]] 16:20, 31 January 2014 (EST)
 
 
<p>Standard GC bulk dust is now unavailable in tomas simulations. Including the option for bulk dust in tomas simulations led to very confusing logical constructs, causing neither to function in a TOMAS simulation. </p>
 
--[[User:Salvatore Farina|Salvatore Farina]] 16:01, 3 March 2014 (EST)
 
 
=== Need to increase MAXCAT parameter in gamap_mod.F ===
 
 
<span style="color:green">'''''This update was validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c]] and approved on 29 May 2014.'''''</span>
 
 
In module <tt>GeosCore/gamap_mod.F</tt>, we had to increase the parameter:
 
 
      INTEGER,          PARAMETER  :: MAXCAT    = 150
 
 
by a little bit to account for the increased # of GAMAP diagnostic categories.  We used:
 
 
      INTEGER,          PARAMETER  :: MAXCAT    = 160
 
 
and this worked just fine.
 
 
--[[User:Bmy|Bob Y.]] 15:25, 11 April 2014 (EDT)
 
 
=== Prevent sea salt from being emitted over ice in TOMAS ===
 
 
<span style="color:green">'''''This update was validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c]] and approved on 29 May 2014.'''''</span>
 
 
'''''[[User:Jeff Pierce|Jeff Pierce]] wrote:'''''
 
 
:The <tt>FOCEAN</tt> (fraction of box that is ocean parameter) in TOMAS seasalt emissions didn't consider ice.  I've modified it to do things more like the bulk emissions.  In <tt>GeosCore/seasalt_mod.F</tt>, at line 1954, there is a line...
 
 
    FOCEAN  = 1d0 - State_Met%FRCLND(I,J)
 
 
:I've updated this to be...
 
 
    IF ( IS_WATER( I, J, State_Met ) ) THEN
 
      FOCEAN  = 1d0 - State_Met%FRCLND(I,J)
 
    ELSE
 
      FOCEAN = 0.d0
 
    ENDIF
 
 
:I couldn't figure out a way for <tt>FOCEAN</tt> to take into account the fraction that is land and fraction that is ice, so I will just use the IS_WATER to filter out boxes that are mostly ice.  The box scheme is actually simpler and emits into the full box (or not) depending on the logical variable returned by function <tt>IS_WATER</tt>.
 
 
--[[User:Bmy|Bob Y.]] 17:04, 30 May 2014 (EDT)
 
 
=== Fix for ND61 diagnostic ===
 
 
<span style="color:green">'''''These updates were validated with the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01e|v10-01e]] and approved on Approved 07 Nov 2014.'''''</span>
 
 
'''''Betty Croft wrote:'''''
 
 
:Jeff and I found that the GEOS-Chem ND61 diagnostic (for TOMAS nucleation rates) was not working properly since AD61 was not initialized in <tt>initialize.F</tt>.
 
 
:Please add the following line to <tt>initialize.F</tt> to correct this problem.
 
 
        IF ( ND61 > 0 ) AD61    = 0e0
 
 
--[[User:Melissa Payer|Melissa Sulprizio]] 10:27, 17 September 2014 (EDT)
 
 
=== Updates to TOMAS Jeagle sea salt extension ===
 
 
<span style="color:green">'''''This update was included in the 1-month benchmark simulation [[GEOS-Chem v11-01 benchmark history#v11-01j|v11-01j]] and approved on 03 Dec 2016'''''</span>
 
 
'''''Jack Kodros wrote:'''''
 
 
:I recently made some updates to the TOMAS Jeagle sea salt HEMCO/Extensions file that allows for 12,30, and 40-bin TOMAS simulations (the previous version would run, just with unrealistic bin widths). If possible I would like the attached file the replace the former in the public release of version 11 (or any future development releases).
 
 
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 13:07, 18 July 2016 (UTC)
 
 
=== Add temporary fix to get TOMAS dry deposition to pass unit tests ===
 
 
<span style="color:green">'''''This fix was included in the [[GEOS-Chem v11-01#v11-01 provisional release|v11-01 provisional release]].'''''</span>
 
 
We have reversed the order of the second parallel DO loop in TOMAS routine <tt>GeosCore/aero_drydep.F</tt>.  This prevents a numerical roundoff error in the [[List_of_diagnostics_for_v11-01#ND44:_Dry_deposition_diagnostics|ND44 dry deposition diagnostic]] that was causing TOMAS unit tests to fail.
 
 
We added the code in <span style="color:green">GREEN</span> at approx. line 410:
 
 
      ! Loop over chemically-active grid boxes
 
<span style="color:green">! %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
! %%% TEMPORARY FIX: REVERSE ORDER OF LOOPS IN ORDER TO PASS UNIT TESTS    %%%
 
! %%%                                                                      %%%
 
! %%% Sal Farina wrote: Change the loop order from LJI to IJL or JIL.      %%%
 
! %%% This will make the MP code add up the diagnostic in the same order  %%%
 
! %%% as SP mode (only the outermost loop gets parallelized). Yes looping  %%%
 
! %%% over LJI should be faster than IJL, but (and correct me if i'm      %%%
 
! %%% wrong) if we are looping over species inside that loop, all benefits %%%
 
! %%% are totally lost anyway. The way Spc / STT is defined, tracerid      %%%
 
! %%% should always be the outermost loop...                              %%%
 
! %$%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span>
 
!$OMP PARALLEL DO
 
!$OMP+PRIVATE( L, J, I, AREA_CM2, RKT, flux, JC, BIN )
 
!$OMP+PRIVATE( ID, X0, X, Y0, Y )
 
!$OMP+DEFAULT( SHARED )
 
!$OMP+SCHEDULE( DYNAMIC )
 
      <span style="color:green">DO I = 1, IIPAR
 
      DO J = 1, JJPAR
 
      DO L = 1, LLCHEM</span>
 
 
This prevents roundoff error due to a [https://en.wikipedia.org/wiki/Loss_of_significance loss of numerical significance] (as pointed out by TOMAS team member '''Sal Farina''').
 
 
This is a temporary fix.  The [[GCST]] will work with the TOMAS team to search for a more permanent solution.
 
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 18:05, 7 December 2016 (UTC)
 
 
=== Typo in wetscav_mod.F for TOMAS30 simulation ===
 
 
<span style="color:green">'''''This fix was included in [[GEOS-Chem v11-02#v11-02c|v11-02c]] and approved on 21 Sep 2017.'''''</span>
 
 
'''''Jack Kodros wrote:'''''
 
 
<blockquote>I found a minor typo in wetscav_mod.F in a TOMAS-only if statement (If defined (TOMAS30)). I believe I introduced this in v10 typing "KIMIN" in one instance instead of "KMIN". This typo only applied to 30-bin versions of TOMAS and not for the more popular 15 and 40 bin versions (and not for standard GEOS-Chem).</blockquote>
 
 
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:04, 18 May 2017 (UTC)
 
 
== Unresolved issues ==
 
 
The following issues are still being worked on:
 
 
=== Reactivating dust tracers in TOMAS simulations ===
 
 
<span style="color:green">'''''These updates were validated with the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01e|v10-01e]] and approved on Approved 07 Nov 2014.'''''</span>
 
 
'''''[[User:Jeffrey Pierce|Jeff Pierce]] and [[User:David Ridley|David Ridley]] wrote:'''''
 
 
:Many of you are aware that recent versions of GEOS-Chem-TOMAS haven't worked with dust emissions on.  The fix for this is actually quite simple (sorry it took me a while to get to this). 
 
 
:(1) In routine <tt>READ_AEROSOLS_MENU</tt> in module file <tt>GeosCore/input_mod.F</tt>, add the following USE statement:
 
 
    #if defined( TOMAS )
 
          USE TRACERID_MOD, ONLY : IDTDUST1
 
    #endif
 
 
:(2) In <tt>READ_AEROSOLS_MENU</tt>, find this code (around line 1925 in G-C v9-02):
 
 
          !---------------------------------
 
          ! Error check DUST AEROSOLS
 
          !---------------------------------
 
 
          I = IDTDST1 + IDTDST2 + IDTDST3 + IDTDST4
 
 
:and change it to:
 
 
          !---------------------------------
 
          ! Error check DUST AEROSOLS
 
          !---------------------------------
 
 
    #if defined( TOMAS )
 
 
          ! For TOMAS only: IF DUST1 is present, the other dust tracers are too
 
          I = IDTDUST1
 
 
    #else
 
 
          ! Non-TOMAS simulations: Need all DST1-DST4 tracers
 
          I = IDTDST1 + IDTDST2 + IDTDST3 + IDTDST4
 
 
    #endif
 
 
:(3) Add the following USE statements at the top of routine <tt>AEROSOL_CONC</tt> (in module <tt>GeosCore/aerosol_mod.F</tt>):
 
 
#if  defined( TOMAS )
 
      USE TRACERID_MOD,      ONLY : IDTDUST1
 
      USE TOMAS_MOD,          ONLY : IBINS
 
#endif
 
 
:(4) Modify the following IF block in routine <tt>AEROSOL_CONC</tt> as described below.  These modifications add the new code for TOMAS simulations, while preserving the original code for non-TOMAS simulations.
 
 
          !===========================================================
 
          ! M I N E R A L  D U S T  A E R O S O L S
 
          . . . etc . . .
 
          !===========================================================
 
#if defined( TOMAS )
 
 
          !-----------------------------------------------------------
 
          ! TOMAS simulations only
 
          !-----------------------------------------------------------
 
          IF ( LDUST ) THEN
 
 
            ! Zero SOILDUST
 
            SOILDUST(I,J,L,:) = 0.d0
 
 
            ! Loop over the # of TOMAS dust bins
 
            DO K = 1, IBINS
 
 
                ! Bin #1
 
                IF ( Input_Opt%DUSTREFF(K) < 0.2D-6 ) THEN
 
                  SOILDUST(I,J,L,1) = SOILDUST(I,J,L,1)
 
      &                              + STT(I,J,L,IDTDUST1+K-1) 
 
      &                              / AIRVOL(I,J,L)
 
 
 
                ! Bin #2
 
                ELSE IF ( Input_Opt%DUSTREFF(K) < 0.325D-6 ) THEN
 
                  SOILDUST(I,J,L,2) = SOILDUST(I,J,L,2)
 
      &                              + STT(I,J,L,IDTDUST1+K-1)
 
      &                              / AIRVOL(I,J,L)
 
 
                ! Bin #3
 
                ELSE IF ( Input_Opt%DUSTREFF(K) < 0.6D-6 ) THEN
 
                  SOILDUST(I,J,L,3) = SOILDUST(I,J,L,3)
 
      &                              + STT(I,J,L,IDTDUST1+K-1)
 
      &                              / AIRVOL(I,J,L)
 
 
                ! Bin #4
 
                ELSE IF ( Input_Opt%DUSTREFF(K) < 1.15D-6 ) THEN
 
                  SOILDUST(I,J,L,4) = SOILDUST(I,J,L,4)
 
      &                              + STT(I,J,L,IDTDUST1+K-1)
 
      &                              / AIRVOL(I,J,L)
 
 
                ! Bin #5
 
                ELSE IF ( Input_Opt%DUSTREFF(K) < 2.0D-6 ) THEN
 
                  SOILDUST(I,J,L,5) = SOILDUST(I,J,L,5)
 
      &                              + STT(I,J,L,IDTDUST1+K-1)
 
      &                              / AIRVOL(I,J,L)
 
 
                ! Bin #6
 
                ELSE IF ( Input_Opt%DUSTREFF(K) < 3.25D-6 ) THEN
 
                  SOILDUST(I,J,L,6) = SOILDUST(I,J,L,6)
 
      &                              + STT(I,J,L,IDTDUST1+K-1)
 
      &                              / AIRVOL(I,J,L)
 
 
                ! Bin #7
 
                ELSE
 
                  SOILDUST(I,J,L,7) = SOILDUST(I,J,L,7)
 
      &                              + STT(I,J,L,IDTDUST1+K-1)
 
      &                              / AIRVOL(I,J,L)
 
 
                ENDIF
 
            ENDDO
 
 
          ENDIF
 
#else
 
 
          !-----------------------------------------------------------
 
          ! Preserve original code for non-TOMAS simulations
 
          !-----------------------------------------------------------
 
          IF ( LDUST ) THEN
 
 
            ! Lump 1st dust tracer for het chem
 
            SOILDUST(I,J,L,1) =
 
      &            0.06d0 * STT(I,J,L,IDTDST1) / AIRVOL(I,J,L)
 
            SOILDUST(I,J,L,2) =
 
      &            0.12d0 * STT(I,J,L,IDTDST1) / AIRVOL(I,J,L)
 
            SOILDUST(I,J,L,3) =
 
      &            0.24d0 * STT(I,J,L,IDTDST1) / AIRVOL(I,J,L)
 
            SOILDUST(I,J,L,4) =
 
      &            0.58d0 * STT(I,J,L,IDTDST1) / AIRVOL(I,J,L)
 
 
            ! Other hetchem bins
 
            SOILDUST(I,J,L,5) = STT(I,J,L,IDTDST2) / AIRVOL(I,J,L)
 
            SOILDUST(I,J,L,6) = STT(I,J,L,IDTDST3) / AIRVOL(I,J,L)
 
            SOILDUST(I,J,L,7) = STT(I,J,L,IDTDST4) / AIRVOL(I,J,L)
 
           
 
          ENDIF
 
 
#endif
 
 
--[[User:Bmy|Bob Y.]] 15:30, 17 June 2014 (EDT)
 
 
==== Reactivating Ginoux dust emissions ====
 
 
:[[#Reactivating dust tracers in TOMAS simulations|After making the updates described above]], modify the EMISSIONS MENU section of <tt>input.geos</tt> as follows
 
 
    Online DUST    AEROSOLS : T
 
    => Use DEAD emissions? : F
 
 
and run GEOS-Chem.  This will turn on the Ginoux dust emissions.
 
 
--[[User:Bmy|Bob Y.]] 15:30, 17 June 2014 (EDT)
 
 
==== Reactivating DEAD dust emissions ====
 
 
Info to be posted here shortly.
 
 
--[[User:Bmy|Bob Y.]] 14:26, 16 June 2014 (EDT)
 
 
=== Offline Dust ===
 
 
<span style="color:green">'''''NOTE: [[#Reactivating dust tracers in TOMAS simulations|The fix described above]] will alleviate this bottleneck.'''''</span>
 
 
Currently, GEOS-Chem with TOMAS uses proscribed offline dust aerosol data in radiative transfer / photolysis calculations. Due to complications, this is turned off entirely for 2x2.5 resolution.
 
 
=== Potential parallelization problems ===
 
 
<span style="color:darkorange">'''''NOTE: This is still an open issue.  It does not affect the simulation results but only the ND60 diagnostic output.'''''</span>
 
 
We have noticed that there may be a parallelization error in the TOMAS [http://acmg.seas.harvard.edu/geos/doc/man/appendix_5.html ND60 diagnostic].  This may be caused by a coding error; in particular, one or more variables that may have been omitted from an <tt>!$OMP+PRIVATE</tt> declaration.
 
 
This is illustrated by the following [[GEOS-Chem_Unit_Tester#Interpreting_results_generated_by_the_GEOS-Chem_Unit_Tester|unit test simulation]] of the [[GEOS-Chem v9-01-02]] provisional release code (submitted at 2:11 PM on 21 Feb 2014):
 
 
###############################################################################
 
### VALIDATION OF GEOS-CHEM OUTPUT FILES
 
### In directory: geos5_4x5_TOMAS40
 
###
 
### File 1    : trac_avg.geos5_4x5_TOMAS40.2005070100.sp
 
### File 2    : trac_avg.geos5_4x5_TOMAS40.2005070100.mp
 
### Sizes    : IDENTICAL (707260156 and 707260156)
 
### Checksums : DIFFERENT (895530022 and 2949483685)
 
### Diffs    : DIFFERENT
 
###
 
### File 1    : trac_rst.geos5_4x5_TOMAS40.2005070101.sp
 
### File 2    : trac_rst.geos5_4x5_TOMAS40.2005070101.mp
 
### Sizes    : IDENTICAL (263480068 and 263480068)
 
### Checksums : IDENTICAL (1925551193 and 1925551193)
 
### Diffs    : IDENTICAL
 
###
 
### File 1    : soil_rst.geos5_4x5_TOMAS40.2005070101.sp
 
### File 2    : soil_rst.geos5_4x5_TOMAS40.2005070101.mp
 
### Sizes    : IDENTICAL (54040 and 54040)
 
### Checksums : IDENTICAL (3229970876 and 3229970876)
 
### Diffs    : IDENTICAL
 
###############################################################################
 
 
In the above test, all TOMAS diagnostics (ND59, ND60, and ND61) were turned on.  The restart files (here named <tt>trac_rst.*</tt>) from the single-processor and multi-processor stages of the unit test are identical, but the <tt>ctm.bpch</tt> files (here named <tt>trac_avg.*</tt>) were different.  When the restart files are identical, that means single-processor and multi-processor stages produced the identical tracer concentrations (and soil NOx quantities). 
 
 
The only differences in the <tt>trac.avg.*</tt> files between the single-processor and multi-processor stages of the unit test were in TOMAS diagnostic quantities.  The affected categories appear to be <tt>TMS-COND</tt>, <tt>TMS-COAG</tt>, <tt>TMS-NUCL</tt>, <tt>AERO-FIX</tt>, which points to the ND60 diagnostic.
 
 
In order to confirm that the ND60 diagnostic exhibits the problem, we ran an additional unit test with ND59 and ND61 turned on, but ND60 turned off.  This unit test, which was submitted at 3:33PM on 21 Feb 2014, yielded identical results.
 
 
###############################################################################
 
### VALIDATION OF GEOS-CHEM OUTPUT FILES
 
### In directory: geos5_4x5_TOMAS40
 
###
 
### File 1    : trac_avg.geos5_4x5_TOMAS40.2005070100.sp
 
### File 2    : trac_avg.geos5_4x5_TOMAS40.2005070100.mp
 
### Sizes    : IDENTICAL (690218236 and 690218236)
 
### Checksums : IDENTICAL (4196844107 and 4196844107)
 
### Diffs    : IDENTICAL
 
###
 
### File 1    : trac_rst.geos5_4x5_TOMAS40.2005070101.sp
 
### File 2    : trac_rst.geos5_4x5_TOMAS40.2005070101.mp
 
### Sizes    : IDENTICAL (263480068 and 263480068)
 
### Checksums : IDENTICAL (1925551193 and 1925551193)
 
### Diffs    : IDENTICAL
 
###
 
### File 1    : soil_rst.geos5_4x5_TOMAS40.2005070101.sp
 
### File 2    : soil_rst.geos5_4x5_TOMAS40.2005070101.mp
 
### Sizes    : IDENTICAL (54040 and 54040)
 
### Checksums : IDENTICAL (3229970876 and 3229970876)
 
### Diffs    : IDENTICAL
 
###############################################################################
 
 
We are still looking into this issue.  Because this issue only affects the ND60 diagnostic output, but not tracer concentrations, we are moving ahead with the TOMAS benchmarks for [[GEOS-Chem v9-02]] (as of 21 Feb 2014).
 
 
--[[User:Bmy|Bob Y.]] 16:17, 21 February 2014 (EST)
 
 
=== Vertical Grids ===
 
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.
 
 
--[[User:Dan Westervelt|Dan W.]] 20:43, 10 February 2010 (EST)
 
 
== Obsolete versions of TOMAS ==
 
 
In this section we preserve information that pertained to older versions of TOMAS (before the [[GEOS-Chem v9-02]] release).
 
 
=== Code structure ===
 
 
<span style="color:red">'''''NOTE: This has been rendered obsolete by the [[#Update April 2013|re-integration of TOMAS into GEOS-Chem]], which was included in [[GEOS-Chem v9-02]].  All of the TOMAS routines have now been ported into the <tt>GeosCore</tt> directory.  We shall leave this post here for reference.'''''</span>
 
 
The main-level <tt>Code</tt> directory has now been divided into several subdirectories:
 
 
GeosCore/    GEOS-Chem "core" routines
 
GeosTomas/  Parallel copies of GEOS-Chem routines that reference TOMAS
 
GeosUtil/    "Utility" modules (e.g. error_mod.f, file_mod.f, time_mod.f, etc.
 
Headers/    Header files (define.h, CMN_SIZE, CMN_DIAG, etc.)
 
KPP/        KPP solver directory structure
 
bin/        Directory where executables are placed
 
doc/        Directory where documentation is created
 
help/        Directory for GEOS-Chem Help Screen
 
lib/        Directory where library files are placed
 
mod/        Directory where module files are placed
 
obsolete/    Directory where obsolete versions of code are archived
 
 
Because there were a lot of TOMAS-related modifications in several GEOS-Chem "core" routines, the routines that need to "talk" to TOMAS were placed into a separate subdirectory named <tt>GeosTomas/</tt>.  The files in <tt>GeosTomas</tt> are:
 
 
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 v8-03-01|v8-03-01]], these files also have the relevant TOMAS references.
 
 
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. 
 
* 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 ===
 
 
<span style="color:red">'''''NOTE: This has been rendered obsolete by the [[#Update April 2013|re-integration of TOMAS into GEOS-Chem]], which was included in [[GEOS-Chem v9-02]].  All of the TOMAS routines have now been ported into the <tt>GeosCore</tt> directory.  We shall leave this post here for reference.'''''</span>
 
 
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
 
* Intel Fortran compiler v11.1 (20101201)
 
* SunStudio 12
 
 
--[[User:Bmy|Bob Y.]] 10:36, 27 January 2010 (EST)
 
 
=== Compile from GeosTomas directory ===
 
 
<span style="color:red">'''''NOTE: This has been rendered obsolete by the [[#Update April 2013|re-integration of TOMAS into GEOS-Chem]], which was included in [[GEOS-Chem v9-02]].  We shall leave this post here for reference.'''''</span>
 
 
'''''[[User:Dan Westervelt|Dan Westervelt]] wrote:'''''
 
 
: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):
 
 
  ***fortcom: Error: chemistry_mod.f, line 478: A kind type parameter must be a compile-time constant.  [DP]
 
          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:Bmy|Bob Yantosca]] wrote:'''''
 
 
: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 Westervelt]] wrote:'''''
 
 
:Thanks, that seems to do the trick.
 
 
--[[User:Bmy|Bob Y.]] 14:37, 14 April 2010 (EDT)
 

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)