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<?xml version="1.0" encoding="UTF-8"?>
<chapter id="ch_introduction">
<title>Introduction</title>
<section>
<title>Synopsis of SMOKE</title>
<para>The environmental community has developed advanced numerical air quality models (AQMs) to understand the interactions among meteorology, emissions (both manmade and biogenic), and pollutant chemistry and dynamics. Emissions data from emissions models and regulatory inventories are one of the most important inputs for these air quality models. Scientists use air quality modeling for a number of purposes: for state and federal implementation plan development, for research on improved modeling methods, and most recently for air quality forecasting. In all of these cases, the trend has been to model larger regions, at a finer grid resolution, with more emissions sources, and for more purposes (e.g., ozone, particulates, toxics). These needs require a computationally efficient, user-friendly, and flexible emissions data processing system.</para>
<para>The MCNC Environmental Modeling Center (EMC) created the Sparse Matrix Operator Kernel Emissions (SMOKE) Modeling System to allow emissions data processing methods to integrate high-performance-computing (HPC) sparse-matrix algorithms. The SMOKE system is a significant addition to the available resources for decision-making about emissions controls for both urban and regional applications. It provides a mechanism for preparing specialized inputs for air quality modeling research, and it makes air quality forecasting possible. The SMOKE system continues to develop and improve at the University of North Carolina at Chapel Hill’s Institute for the Environment (IE).</para>
<para>The SMOKE prototype, available since 1996, was an effective tool for emissions processing in a number of regional air quality modeling applications. In 1998 and 1999, SMOKE was redesigned and improved with the support of the U.S. Environmental Protection Agency (EPA). The primary purposes of the first SMOKE redesign were support of (1) emissions processing with user-selected chemical mechanisms (described in more detail in <xref linkend="sect_concepts_chemical_processing" />) and (2) emissions processing for reactivity assessments (described in <xref linkend="sect_concepts_create_reactivity" />). In 2002, SMOKE was enhanced to support driving the MOBILE6 model used to create on-road mobile emission factors and to support on-road and nonroad mobile toxics inventories, resulting in SMOKE v1.5. In 2003, SMOKE v2.0 was created to include all toxic inventories, including point and nonpoint (stationary sources reported at the county level) sources. SMOKE v2.1, released in 2004, included updated versions of the BEIS3 and MOBILE6.2 models, the ability to use humidity data when processing on-road mobile sources with MOBILE6, and support for polar stereographic output grids. In 2009, SMOKE v2.6 enhanced the processing of fire data, streamlined the processing for CAMx and UAM models, and added a new approach to processing CEM data. Version 2.7, SMOKE was enhanced to support processing the MOVES (MOter Vehicle Emission Simulator) emission rates output through the SMOKE system to model on-roadway and off-network mobile sources. As of version 4.0 SMOKE is enhanced to support hemispheric modeling by enabling the processing of global gridded emission inventories, such as EDGAR, for input to chemistry-tranport models.</para>
<para>SMOKE can process criteria gaseous pollutants such as carbon monoxide (CO), nitrogen oxides (NO<subscript>x</subscript>), volatile organic compounds (VOC), ammonia (NH<subscript>3</subscript>), sulfur dioxide (SO<subscript>2</subscript>); particulate matter (PM) pollutants such as PM 2.5 microns or less (PM<subscript>2.5</subscript>) and PM less than 10 microns (PM<subscript>10</subscript>); as well as a large array of toxic pollutants, such as mercury, cadmium, benzene, and formaldehyde. In fact, SMOKE has no limitation regarding the number or types of pollutants it can process.</para>
<para>The purpose of SMOKE (or any emissions processor) is to convert the resolution of the emission inventory data to the resolution needed by an air quality model. Emission inventories are typically available with an annual-total emissions value for each emissions source, or perhaps with an average-day emissions value. The AQMs, however, typically require emissions data on an hourly basis, for each model grid cell (and perhaps model layer), and for each model species. (Refer to <xref linkend="app_glossary" /> for definitions of these terms.) Consequently, emissions processing involves transforming an emission inventory through temporal allocation, chemical speciation, and spatial allocation, to achieve the input requirements of the AQM.</para>
</section>
<section>
<title>SMOKE Users</title>
<para>Possible SMOKE users are individuals who need to prepare emission input files for one of the following air quality models:</para>
<itemizedlist spacing="compact">
<listitem>Community Multiscale Air Quality (CMAQ) modeling system</listitem>
<listitem>Comprehensive Air Quality Model, with Extensions (CAM<subscript>X</subscript>)</listitem>
<listitem>Urban Airshed Model, version 4 (UAM-IV)</listitem>
<listitem>Urban Airshed Model, Variable grid (UAM-V)</listitem>
</itemizedlist>
<para>We anticipate that the typical SMOKE user will have some combination of the following experience and needs:</para>
<orderedlist spacing="compact">
<listitem>Those knowledgeable about emission inventories.</listitem>
<listitem>Those with UNIX experience (including Linux).</listitem>
<listitem>Those with little or no emissions modeling background.</listitem>
<listitem>Those who are somewhat familiar with grid-based air quality models and their emissions input needs.</listitem>
<listitem>Persons with emission inventories in hand who need to process the data for input to an AQM.</listitem>
<listitem>EPA personnel who want to create emission inputs for research or regulatory efforts with AQMs.</listitem>
<listitem>State environmental personnel who want to create emission inputs to AQMs for regulatory efforts, including State Implementation Plans (SIPs).</listitem>
<listitem>Those wishing to generate an on-road mobile inventory using MOVES and either the Weather Research and Forecasting (WRF) modeling system or the Pennsylvania State University/National Center for Atmospheric Research fifth-generation Mesoscale Model (MM5) gridded, hourly meteorology data.</listitem>
</orderedlist>
<para>SMOKE users who have previous UNIX experience can expect to run SMOKE more easily than users who must learn both UNIX and SMOKE. This is because the standard way to run SMOKE is from UNIX scripts.</para>
</section>
<comment>
<section>
<title>SMOKE Features</title>
<para>SMOKE is primarily an emissions processing system and not an emission inventory preparation system. This means that its main purpose is to provide an efficient tool for converting emission inventory data into the formatted emission input files required by an AQM. However, for mobile and biogenic sources, SMOKE does offer emission inventory preparation functions. For mobile sources, SMOKE computes an emission inventory from mobile-source activity data, using emission factors from the MOVES model. Previous versions of SMOKE (version 2.7 and below) supported the MOBILE6 model. For biogenic sources, SMOKE includes BEIS3 model for computation of hour-specific, meteorology-based biogenic emissions from vegetation and soils.</para>
<para>Below, we summarize the major features of SMOKE v3.0.</para>
<itemizedlist>
<listitem><para>item 1 </para></listitem>
<listitem><para>item 2 </para></listitem>
</itemizedlist>
<para>Below, we summarize the major features of SMOKE v2.7.</para>
<itemizedlist>
<listitem><para>Supports processing county-level MOVES emission rates output to model on-roadway and off-network mobile sources.</para></listitem>
<listitem><para>Meteorological data preprocessor - <command>Met4moves</command> prepares spatially and temporally averaged temperature and relative humidity data for use by both MOVES and SMOKE models.</para></listitem>
<listitem><para>Developed a new SMOKE postprocessor, <command>Movesmrg</command>, a new, mobile-sources-only program that uses MOVES emission rate tables to compute the emissions on the fly, by multiplying the emissions factors by hourly VMT or by annual vehicle populations.</para></listitem>
</itemizedlist>
<para>Below, we summarize the major features of SMOKE v2.6.</para>
<itemizedlist>
<listitem><para><command>Smkinven</command> supports new extended EMS-95 point hourly format to enhance the precision of low emissions values. The original EMS-95 format has 7 columns available for the emissions ivalues instead of the 12 columns.</para>
</listitem>
<listitem><para><command>Smkinven</command> has an option to integrate or non-integrate all criteria VOCs and hazardous air pollutants (HAPs) without additional NHAPEXCLUDE file. NHAPEXCLUDE file is only required when user partially combines CAP VOCs and HAPs inventories together.</para>
</listitem>
<listitem><para><command>Spcmat</command> supports source-level tagging functionality by SCC/PlantID/MACT/SIC and state/county using new GSTAG (Speciation Tagging cross-reference) file.</para>
</listitem>
<listitem><para><command>Smkreport</command> creates a report by the status of integration of sources that combines criteria VOCs and HAPs inventories using "BY INTEGRATE".</para>
</listitem>
<listitem><para><command>Layalloc</command> allows users to vertically redistribute 2-D emissions into multiple modle layers after SMOKE has already created surface layer model-ready inputs.</para>
</listitem>
</itemizedlist>
<para>Below, we summarize the major features of SMOKE v2.5.</para>
<itemizedlist>
<listitem><para>Supports in-line plume rise calculation in CMAQ version 4.7 to reduce the size of "traditional" 3-D model-reday input files generated by off-line plume rise calculation in SMOKE.</para></listitem>
<listitem><para>The latest Biogenic Emission Inventory System (BEIS) model version 3.14 is integrated to the SMOKE v2.5 including the sesquiterpene emission factors in <command>NORMBIE3</command> and the estimation of sesquiterpene emissions in <command>TMPBEIS3</command> including 34 species/compounds based upon BEIS 3.13 integrated with SMOKE v2.4.</para></listitem>
</itemizedlist>
<para>Below, we summarize the major features of SMOKE v2.4.</para>
<itemizedlist>
<listitem><para>The latest Biogenic Emission Inventory System (BEIS) model version 3.13 is integrated to the SMOKE v2.4 for generating gridded, hourly emissions in a format consistent for air quality modeling. BEIS 3.13 revises the parameterizations that account for the effects of leaf temperature and solar radiation on emissions.</para></listitem>
<listitem><para>Compatible with the Federal Aviation Administration (FAA)'s Emission Modeling and Dispersion Modeling System (EDMS) used to estimate emissions from airports. A new utility program <command>EDMS2Inv</command> creates SMOKE-ready inventory from EDMS output.</para></listitem>
<listitem><para>Enhancement on combining aggregated criteria VOC and hazardous air pollutant (HAP) inventories were made throughout the SMOKE.</para></listitem>
<listitem><para>The updated <command>Smkinven</command> can optionally support upto 16 character size for the Chemical Abstracts Services (CAS) code, also known as the pollutant code, to allow for all HAPs which have more than 5 characters for the pollutant name in day-specific (PTDAY) and hour-specific (PTHOUR) emission inventories.</para></listitem>
<listitem><para>Support fully extended ORL format for <command>Smkinven</command> and <command>Grwinven</command>.</para></listitem>
</itemizedlist>
<para>Below, we also summarize the major features from the previous SMOKE v2.3 release.</para>
<itemizedlist>
<listitem><para>Supports the extended ORL format. It accepts source type codes for area, nonroad mobile and onroad mobile sources, as well as ORIS and boiler identification codes for point sources.</para></listitem>
<listitem><para>Supports new CEM format with additional variables including flow rate for the boiler unit, and pollutant status flags ( measured/substituted/not used ).</para></listitem>
<listitem><para>Allows multiple plant descriptions and FIPS codes for an ORIS ID when matching hourly point data to annual data and also supports matching hourly point source data to annual data in either IDA or ORL format.</para></listitem>
<listitem><para>Supports 16 characters for the CAS code, also known as the pollutant code, to allow criteria pollutants to be input using the ORL format.</para></listitem>
<listitem><para>Treats duplicate sources as separate sources with a warning message instead of dropping the emission.</para></listitem>
<listitem><para>Supports only new <envar>INVTABLE</envar> format that has emissions MODE in a new column after the SMOKE NAME. These columns will be used together to create the internal SMOKE name.</para></listitem>
<listitem><para>Improves the <envar>SMKINVEN_FORMULA</envar> option to support multiple formula.</para></listitem>
<listitem><para>Outputs ORL-formatted file as a more condensed format in comma delimited format with quotes around all string fields.</para></listitem>
<listitem><para>Supports an optional special header in GSPRO file that defines the meaning of NONHAPVOC to support of combining criteria and toxic VOC using the NONHAPVOC calculation feature of SMOKE.</para></listitem>
<listitem><para>Supports both new and old <envar>GSCNV</envar> file. New <envar>GSCNV</envar> file includes additonal infomation, such as name of pollutant or emission types converting from and to.</para></listitem>
<listitem><para>Accepts source type codes of 03 and 04 for nonroad and onroad mobile respectively, and accept twelve new cases in the projection packet for plant-specific source matching. Fixed a bug in the plant-specific cross reference assignment.</para></listitem>
<listitem><para>Read in surrogates from either one file or multiple files and now requires the SRGDESC file. As a result of this update, Grdmat requires far less memory to run than it did in previous versions.</para></listitem>
<listitem><para>Perform multiple non-sequential processing dates.</para></listitem>
<listitem><para>Re-normalize the assigned temporal profile based on the duration of fires.</para></listitem>
</itemizedlist>
<para>Below, we also list the major features from the previous release SMOKE v2.2.</para>
<itemizedlist>
<listitem>
<para>Supports Inventory Data Analyzer (IDA) formats, Emissions Modeling System, ‘95 (EMS-95) format, and a SMOKE one-record-per-line (ORL) format. The criteria and PM National Emissions Inventory (NEI) data are most readily converted to the IDA formats or ORL format. The toxics inventory must be converted to the ORL format.</para>
</listitem>
<listitem>
<para>Supports both gridded and county-total land use for biogenic emissions modeling.</para>
</listitem>
<listitem>
<para>Includes the BEIS2 or BEIS3 system (and the user can choose which he or she wants).</para>
</listitem>
<listitem>
<para>Includes a driver for MOBILE6 runs and features to improve run time when using MOBILE6 for large domains and long time periods (can support annual, national runs using MOBILE6).</para>
</listitem>
<listitem>
<para>Multicountry capability, up to 10 countries.</para>
</listitem>
<listitem>
<para>Lower disk space requirements over other emissions processing software for the same level of detail in the emissions.</para>
</listitem>
<listitem>
<para><emphasis>Any</emphasis> pollutant can be processed by the system.</para>
</listitem>
<listitem>
<para><emphasis>Any</emphasis> chemical mechanism can be used to partition pollutants to model species, as long as the appropriate input data are supplied.</para>
</listitem>
<listitem>
<para>Supports Lambert conformal, lat-lon, UTM, and polar stereographic output grid projections with any number of grid cells.</para>
</listitem>
<listitem>
<para>Control strategies can include changes in the reactivity of emitted pollutants. This is useful, for example, when a solvent is changed in an industrial process.</para>
</listitem>
<listitem>
<para>Run-time memory allocation, eliminating any need to recompile the source code for different inventories, grids, or chemical mechanisms.</para>
</listitem>
<listitem>
<para>No third-party software is required to run SMOKE, although some input file preparation, such as gridded land use or spatial allocation surrogates, does require other software.</para>
</listitem>
<listitem>
<para>Supports plume in grid (PinG) processing.</para>
</listitem>
<listitem>
<para>Integrated use of Continuous Emissions Monitoring (CEM) data, an hour-specific dataset of emissions from electric generating facilities. Also supports other day-specific and hour-specific point-source data.</para>
</listitem>
<listitem>
<para>Supports hour-specific point-source stack parameters (exit temperature, exit velocity, and exit flow rate).</para>
</listitem>
<listitem>
<para>Supports externally computed hourly plume rise (used for processing wildfires as point sources with a different plume rise algorithm than is available in SMOKE).</para>
</listitem>
<listitem>
<para>Supports emissions data input formats for the following AQMs and chemical mechanisms:</para>
<itemizedlist>
<listitem>
<para>Community Multiscale Air Quality (CMAQ) model: part of the Models-3 system. SMOKE v2.0 and later supports a research toxics version of CMAQ for non-point (stationary area) sources, nonroad mobile sources, on-road mobile sources, point sources, and biogenic sources.</para>
</listitem>
<listitem>
<para>Comprehensive Air Quality Model, with Extensions (CAM<subscript>X</subscript>)</para>
</listitem>
<listitem>
<para>Urban Airshed Model (UAM), versions IV and V</para>
</listitem>
</itemizedlist>
</listitem>
</itemizedlist>
<comment>
<para>The authors anticipate that the following feature will be available in the near future:</para>
<itemizedlist>
<listitem>
<para>A speciation inputs preprocessor, to permit users to construct their own chemical mechanisms and to support the dynamic Statewide Air Pollution Research Center (SAPRC) chemical mechanism. This work is being funded by the American Chemistry Council.</para>
</listitem>
</itemizedlist>
</comment>
</section>
</comment>
<comment>
<section>
<title>How to Use this Manual</title>
<para>This document is the most complete reference available on SMOKE. It is available both as a set of HTML pages and PDF document (including page numbers) from the <ulink url="http://www.cmascenter.org">CMAS center</ulink>.</para>
<comment>
<para>The document’s overall table of contents shows all chapter topics and subtopics, while each chapter includes its own table of contents (without page numbers) at the head of the chapter. In the online version of the manual, the table of contents and the chapter contents use hyperlinks to facilitate navigation of the document.</para>
</comment>
<para>Given below are typical activities for which users need this manual, and the resources available to meet those needs.</para>
<itemizedlist>
<listitem>
<para><emphasis role="bold">Install SMOKE:</emphasis> Installation instructions are available in <xref linkend="ch_installation" />. To register and download SMOKE, visit the <ulink url="http://www.cmascenter.org/html/models.html">CMAS Model Clearinghouse</ulink>.</para>
</listitem>
<listitem>
<para><emphasis role="bold">Compile SMOKE:</emphasis> <xref linkend="sect_install_compile" /> provides instructions for compiling SMOKE for platforms other than the default ones supported by the CMAS Center.</para>
</listitem>
<listitem>
<para><emphasis role="bold">Run SMOKE test case:</emphasis> <xref linkend="sect_scripts_run_example" /> provides instructions for running the test case provided with SMOKE.</para>
</listitem>
<listitem>
<para><emphasis role="bold">Set up and run SMOKE for new inventory, grid, episode, etc.:</emphasis> <xref linkend="sect_scripts_how_use_smoke" /> includes instructions on how users can set up SMOKE for their own cases. The <ulink url="http://www.cmascenter.org/training.cfm">SMOKE classroom training</ulink> available through the CMAS Center covers these topics in more detail.</para>
</listitem>
<listitem>
<para><emphasis role="bold">Prepare input files:</emphasis> Most SMOKE input files are ASCII files that can be prepared using database programs or other tools. Descriptions of all input file formats are found in <xref linkend="ch_input_files" />. Users may obtain input data files (perhaps not in SMOKE input format) from EPA web sites, such as the Clearinghouse for Inventories and Emission Factors (CHIEF) <ulink url="http://www.epa.gov/ttn/chief/emch/">web site</ulink>.</para>
</listitem>
<listitem>
<para><emphasis role="bold">Decide how to assign settings in run scripts:</emphasis> In <xref linkend="ch_scripts" />, we cover the SMOKE scripts and how to use them. The settings are assigned via environment variables, which are explained in general terms in <xref linkend="sect_concepts_assigns" />. Any settings used to control the scripts (not the programs) are described in <xref linkend="sect_scripts_script_settings" />. The settings that are evaluated by SMOKE programs and directly affect their behavior are further explained in <xref linkend="ch_utilities" />, <xref linkend="ch_programs" />, and <xref linkend="ch_quality_assurance" />.</para>
</listitem>
<listitem>
<para><emphasis role="bold">Check that SMOKE has run properly:</emphasis> <xref linkend="sect_qa_methods" /> includes a list of steps regarding how to verify that SMOKE has run properly. This chapter also includes instructions on running the quality assurance (QA) features of SMOKE and documentation on the reporting control file (<xref linkend="sect_qa_repconfig" />) needed for configuring different types of reports for quality assurance. <comment><xref linkend="ch_errors" /> includes SMOKE errors and warnings associated with each program, with explanations about what one might do to correct problems.</comment></para>
</listitem>
<listitem>
<para><emphasis role="bold">Understand the operations that SMOKE is performing:</emphasis> Any available technical documentation regarding SMOKE operations is provided in <xref linkend="ch_utilities" />, <xref linkend="ch_programs" />, and <xref linkend="ch_quality_assurance" /> for each SMOKE program. We are continually working to enhance this documentation and can take suggestions through the CMAS Center Help Desk (see next bullet).</para>
</listitem>
<listitem>
<para><emphasis role="bold">Submit problem reports or questions about SMOKE:</emphasis> All questions and problems concerning SMOKE and other Models-3 components should be submitted through the <ulink url="http://www.cmascenter.org/html/help.html">CMAS Center Help Desk</ulink>.</para>
</listitem>
</itemizedlist>
<para>This manual does not provide substantial technical documentation on the code itself, though some information is provided in <xref linkend="ch_source" />. The code does have extensive in-line documentation to assist Fortran-savvy users in understanding its workings. We hope that in the future we will be able to enhance the documentation in <xref linkend="ch_source" />, but are unsure of the necessity and have not obtained resources for such documentation to date.</para>
</section>
</comment>
</chapter>