View source for Smoke and coupling with WRF-Chem

{{users guide}}


[[File:Sfire smoke.png|thumb|WRF-SFIRE smoke tracer in action.  See [[File:Smoke small.avi|animation]].]]

Fire emissions can be modeled a passive smoke tracer advected by the wind field,
or as chemical species tracers, which also undergo chemical reactions by WRF-Chem. WRF-Chem is included in the WRF repository. Tracer variables are 3d fields of concentrations on the atmospheric grid. The variables are present in the wrfout files when activated. 

==Passive smoke tracers==

The selection of the tracers in WRF is controlled by namelist variable '''tracer_opt''' in the '''&dynamics'''] section .  The coupling supports the option '''tracer_opt = 1''', which creates a single tracer called '''smoke''',
and the option '''tracer_opt = 2''', which creates passive tracers called '''tr17_1''' to '''tr17_8'''. 

Emissions are computer proportionally to the fuel burned according to the emission factors in file  '''namelist.fire_emissions''' and added to the lowest layer of the active tracer variables. 

There are small differences between the propagation of the different tracers, and also between the propagation when the code is build with or without WRF-Chem.

==Coupling with WRF-Chem==
Compiling the code with support for WRF-Chem is similar to the [[How to compile WRF-Fire|standard procedure]].
You must set an environment variable '''WRF_CHEM''' and configure with the argument '''chem''' as follows.
<pre>
export WRF_CHEM=1
./configure chem
./compile em_fire
</pre>

The selection of the tracers in WRF-Chem is controlled by namelist variable '''chem_opt''' in '''&chem''' section of '''namelist.input'''. If '''chem_opt=0''', no chemical tracers are created.  The coupling supports subsets of RADM2 ('''chem_opt=2'''), MOZART ('''chem_opt=112''' or '''119'''), and GOCART ('''chem_opt=300''') variables. 

It is also possible to use '''tracer_opt = 1''' or '''tracer_opt = 2''' with a code compiled with WRF-Chem. The resulting passive tracers may then be advected by code in WRF-Chem instead of WRF itself.

==Running an idealized example==
An idealized example based on the hill case has been created in [https://github.com/jbeezley/wrf-fire/tree/master/wrfv2_fire/test/em_fire/chem '''test/em_fire/chem''']
Note that '''sfc_full_init =.true.''' is required in the '''&fire''' section of '''namelist.input''' to initialize USGS landuse, which is required by  WRF-Chem.
The tracer selected by '''tracer_opt=1''' will appear as an atmospheric variable in the output file with the name '''smoke'''. The chemical species in the atmosphere, selected by '''chem_opt''', will appear under their respective names, such as '''n2o5'''.

==Configuration==

To use the passive tracers in the code built with WRF-Chem, specify '''tracer_opt=2''' and '''chem_opt=0''' in '''namelist.input'''. The tracers work slightly differently in code built with and without WRF-Chem, as described in file '''chem/module_input_tracer.F'''. A sample emission factors table for this usage is available as '''test/em_fire/chem/namelist.fire_emissions.tracers'''. It can be used in ideal as well as real runs. Different rows in the table can be used to track separate species, e.g., pm10 and pm25, with different emission factors. 

In each time step, the coupling code adds the fire emissions created in the time step to the first layer of atmosphere cells. The chemistry state arrays are have unit of concentrations ('''ppmv'''), so the amounts of the inserted species are scaled by the dry air mass in the first layer. The amount of the chemical species created is determined from the amount of fuel burned directly by an emissions table, while the smoke tracer uses the fire ground heat flux '''GRNHFX''' as a proxy. The emissions table contains the amounts of emissions fuel burned in '''g/kg''' or '''mol/kg'''.  The emissions tables are specified in file '''namelist.fire_emissions'''. This file contains a line for each species like
<pre>
 no2=3.2,3.2,3.2,1.4,1.4,1.4,1.4,2.7,2.7,2.7,3,3,3,
</pre>
with emissions (g/kg fuel or mol/kg fuel) for each of the fuel categories used (by default, the 13 Anderson's categories).

There are two additional variables in '''namelist.fire_emissions''':
<pre>
compatible_chem_opt=112,119
</pre>
is a list of '''chem_opt''' values intended to be used with the table. However, presently, the code does not check if the file lists other chemistry species supported by the coupling code, not just those for the given  '''chem_opt'''.  If it does, the results can be upredictable.
The variable
<pre>
printsums=1
</pre>
will enable printing of the totals of each emissions species at the end of every time step.

Several prototype emissions tables are provided in '''test/em_fire/chem'''. You need to copy or link one of the emissions tables to '''namelist.fire_emissions''' in your run directory, such as
<pre>
ln -s namelist.fire_emissions.RADM2 namelist.fire_emissions
</pre>
and set matching '''chem_opt''' in '''namelist.input''', here '''chem_opt=2'''. See the next section for the available emissions tables. Users can also add their own.

==Chemical species==

The chemical model selected by the '''chem_opt''' flag produces concentrations on 3D grids in every '''wrfout''' file produced, for a set of variables defined in the '''Chem scalars''' part of the file  [https://github.com/openwfm/WRF-SFIRE/blob/262829290d98e419b6839893ecb1a5d36ed4b969/Registry/registry.chem#L1567 '''Registry/registry.chem''']. The first section of the list contains the chemical species common to all models, later sections list species added for specific models. For more detailed information about the species including dusts and aerosols in specific WRF-Chem models, see the [https://ruc.noaa.gov/wrf/wrf-chem/model_info.htm WRF-Chem model documention] and the links to the individual models at the emissions tables below.

The quantities of the chemical species are in '''ppmv''', i.e., 1e6*mol/mol of dry air.

The frequency of writing the outputs into the wrfout files is specified by the user in the '''history_interval''' flags in the WRF '''namelist.input''' file. It can be as often as once every minute, but usually much less. 

SFIRE adds the fire emissions to a subset of the chemical species as specified in the emissions table. It is up to the chemical model to produce other species from them. Note that the parts of the registry.chem file using the word "emissions" are for other emission schemes and not relevant here. SFIRE adds fire emissions directly to the lowest layer of the 3D Chem fiels during the fire simulation.

There are currently three emissions tables available:
* [https://github.com/openwfm/WRF-SFIRE/blob/master/test/em_fire/chem/namelist.fire_emissions.RADM2 namelist.fire_emissions.RADM2] for the [http://ruc.noaa.gov/wrf/WG11/radm2.htm RADM2] model
* [https://github.com/openwfm/WRF-SFIRE/blob/master/test/em_fire/chem/namelist.fire_emissions.MOZART namelist.fire_emissions.MOZART] for the [http://www.acd.ucar.edu/wrf-chem/mozart.shtml MOZART] model
* [https://github.com/openwfm/WRF-SFIRE/blob/master/test/em_fire/chem/namelist.fire_emissions.GOCART namelist.fire_emissions.GOCART] for the [https://tropo.gsfc.nasa.gov/gocart GOCART] model

==Implementation==

WRF-Chem contains a multitude of arrays representing concentrations of chemical species. The typical
method of injecting data into the simulation involves generating emission input data files from standard
sources.  These sources are read into the code using auxiliary input streams and interpolated into
the species arrays in the [https://github.com/jbeezley/wrf-fire/blob/4c0851085eeb25d9143bd5b07e736fe949700497/wrfv2_fire/chem/module_emissions_anthropogenics.F emissions] module.  For the coupling with SFIRE, turning off file
input in the namelist seems to initialize the emission arrays to zero.  This eliminates the need to generate
useless emission files. 

WRF-Chem stores its state in arrays '''chem''' and   '''tracer'''.  These arrays are four dimensional indexed like '''(x,z,y,s)''', where s is the chemical
species. The domain structure contains scalars such as '''p_smoke''' (into the '''tracer''' array) and '''p_nh4''' (into the '''chem''' array) that give the species index for
each type.  The species selections are specific to different chemistry options ('''chem_opt''') 
from the registry; however, even unused species have their index set to 1. The dynamics section of the namelist has an option for '''tracer_opt'''.  This
controls what tracers are generated for Chem.  

Since fuel is given at the fire grid resolution, the emissions are computed at the fire resolution and then averaged to the atmospheric resolution, where the chemistry operates. However, since the memory demands of a 3D array at fire resolution (two surface dimensions and chemical species) would be excessive, the contributions of the emissions are computed on the fly and added to the respective atmospheric cell immediately. This results in code that straddles the otherwise strict division in SFIRE between fire computations on the fire grid, which are independent of WRF, and the atmospheric computations related to WRF, which otherwise consist of interpolation only and should not contain any other code. So, subroutine [https://github.com/jbeezley/wrf-fire/blob/4c0851085eeb25d9143bd5b07e736fe949700497/wrfv2_fire/phys/module_fr_sfire_atm.F#L276 '''add_fire_emissions_to_chem'''], which  adds chemical species to the '''chem''' array, was derived from the utility [https://github.com/jbeezley/wrf-fire/blob/4c0851085eeb25d9143bd5b07e736fe949700497/wrfv2_fire/phys/module_fr_sfire_util.F#L471 '''sum_2d_cells'''] by adding chemistry-specific code.

The chemistry coupling code is compiled only when WRF-Chem is being compiled. It resides in [https://github.com/jbeezley/wrf-fire/blob4c0851085eeb25d9143bd5b07e736fe949700497/wrfv2_fire/phys/module_fr_sfire_atm.F module_fr_sfire_atm.F], which is allowed by the SFIRE architecture to contain code both at atmosphere and fire resolution. Besides subroutine '''add_fire_emissions_to_chem''', the code consists of subroutine [https://github.com/jbeezley/wrf-fire/blob/4c0851085eeb25d9143bd5b07e736fe949700497/wrfv2_fire/phys/module_fr_sfire_atm.F#L151 '''read_emissions_table'''], which reads file '''namelist.fire_emissions''', subroutine [https://github.com/jbeezley/wrf-fire/blob/4c0851085eeb25d9143bd5b07e736fe949700497/wrfv2_fire/phys/module_fr_sfire_atm.F#L276 '''add_fire_emissions_to_chem'''], which  adds chemical species to the '''chem''' array, the [https://github.com/jbeezley/wrf-fire/blob/4c0851085eeb25d9143bd5b07e736fe949700497/wrfv2_fire/phys/module_fr_sfire_atm.F#L78 emissions tables] as module variables, subroutine [https://github.com/jbeezley/wrf-fire/blob/4c0851085eeb25d9143bd5b07e736fe949700497/wrfv2_fire/phys/module_fr_sfire_atm.F#L1914 '''fire_emission'''], which adds the smoke tracer, and the corresponding call statements in [https://github.com/jbeezley/wrf-fire/blob/4c0851085eeb25d9143bd5b07e736fe949700497/wrfv2_fire/phys/module_fr_sfire_driver.F  '''module_fr_sfire_driver'''].

==References==
* Kochanski A. K., Jenkins M.A., Yedinak K., Mandel J., Beezley J, and Lamb B. (2015) '''Toward an integrated system for fire, smoke and air quality simulations''', International Journal of Wildland Fire - http://dx.doi.org/10.1071/WF14074
* Adam K. Kochanski, Jonathan D. Beezley, Jan Mandel, Craig B. Clements, '''Air pollution forecasting by coupled atmosphere-fire model WRF and SFIRE with WRF-Chem''', 4th Fire Behavior and Fuels Conference, February 18-22, 2013, Raleigh, NC, 	{{arXiv|1304.7703}}, 2013
* Adam K. Kochanski, Jonathan D. Beezley, Jan Mandel, and Minjeong Kim, '''WRF fire simulation coupled with a fuel moisture model and smoke transport by WRF-Chem''', [http://www.mmm.ucar.edu/events/2012_wrfusers/ 2012 WRF Users Workshop], [http://www.openwfm.org/wiki/File:WRF_workshop_2012_poster.pdf Poster 51] [http://www.mmm.ucar.edu/events/2012_wrfusers/abstracts/p51.htm abstract] [https://www.regonline.com/AttendeeDocuments/1077122/43365086/wrf2012.pdf paper] {{arXiv|1208.1059}}
* [http://ruc.noaa.gov/wrf/WG11/Users_guide.pdf WRF-Chem Users' Guide]
* Georg A. Grell, Steven E. Peckham, Rainer Schmitz, Stuart A. McKeen, Gregory Frost, William C. Skamarock, Brian Eder, [http://dx.doi.org/10.1016/j.atmosenv.2005.04.027 Fully coupled “online” chemistry within the WRF model], Atmospheric Environment, Volume 39, Issue 37, December 2005, Pages 6957–6975
* C. Wiedinmyer, S. K. Akagi, R. J. Yokelson, L. K. Emmons, J. A. Al-Saadi, J. J. Orlando, and A. J. Soja. [http://dx.doi.org/10.5194/gmd-4-625-2011 The Fire INventory from NCAR (FINN): a high resolution global model to estimate the emissions from open burning], Geosci. Model Dev., 4, 625-641, 2011
* L. K. Emmons, S. Walters, P. G. Hess, J.-F. Lamarque, G. G. Pfister, D. Fillmore, C. Granier, A. Guenther, D. Kinnison, T. Laepple, J. Orlando, X. Tie, G. Tyndall, C. Wiedinmyer, S. L. Baughcum, and S. Kloster, [http://dx.doi.org/10.5194/gmd-3-43-2010 Description and evaluation of the Model for Ozone and Related chemical Tracers, version 4 (MOZART-4)], Geosci. Model Dev., 3, 43-67, 2010

==External links==
* [http://ruc.noaa.gov/wrf/WG11/ WRF-Chem] home page
* [https://www2.acom.ucar.edu/modeling/finn-fire-inventory-ncar Finn]  emissions model
* [http://www.acd.ucar.edu/wrf-chem/mozart.shtml MOZART] chemistry model