Last update: 23 Sep 2021 *** PLEASE READ THIS README BEFORE RUNNING SMOKE. *** WE ARE INTERESTED TO KNOW HOW THESE DATA ARE BEING USED. PLEASE EMAIL eyth.alison@epa.gov with a subject: 2016v2 data usage AND A BRIEF NOTE DESCRIBING HOW YOU ARE USING THE DATA. THANK YOU. This package contains files relevant to the 2016 v2 emissions modeling platform. It includes scripts and executables for processing 2016fj, 2023fj, 2026fj, and 2032fj sectors through SMOKE. Methodology changes compared to v1 platform include, but are not limited to: - This platform uses a new chemical speciation mechanism, CB6R3AE7. - This platform uses mostly 2017-based inventories and therefore uses 2017-compatible FIPS codes, including 46102 for Oglala Lakota County, SD. - The ptnonipm and pt_oilgas sectors are processed such that all emissions from those sectors are output to the inline point source file. There are no longer any 2-D gridded emissions for ptnonipm and pt_oilgas. - The ag sector has been split into two sectors: livestock and fertilizer. Fertilizer emissions are not projected, so there is only a 2016 inventory with no separate future year fertilizer inventories. There are livestock inventories for each year. - Onroad emissions are processed with MOVES3, which introduces two new emissions rates: RPHO (on-network idling) and RPS (starts), in addition to RPD, RPP, RPV, and RPH from older versions of MOVES. - The othpt sector has been split into three sectors: canada_ag, canada_og2D, and othpt. Canada_ag contains Canadian ag emissions, and canada_og2D contains low-level Canadian upstream oil and gas emissions. Both of those sectors create gridded 2-D emissions files, not inline point source emissions files. The othpt sector is the same as before except without the Canadian ag and low-level oil and gas emissions which have been split out. - The ptfire sector has been split into ptfire-rx and ptfire-wild. - A new sector 'solvents', formerly part of nonpt, has been created. - Future year ptegu winter emissions are processed as separate sectors "ptegu_wintershld" (winter shoulder season, covering Mar/Apr/Oct/Nov) and and "ptegu_winter" (Dec/Jan/Feb). This is in addition to ptegu_summer which covers May-September as usual. Base year 2016 ptegu emissions are processed normally, as a single sector (ptegu) with different daily run scripts for summer and winter which contain different temporal profiles. This package includes precompiled SMOKE 4.8.1. As of 20 Sep 2021, The Smkreport executable which is part of SMOKE 4.8.1 is not stable and does not work for all sectors. Therefore, the default Smkreport executable included in this package is from SMOKE 4.7. == 1. Introduction == These packages contain scripts, inventories, and ancillary files related to EPA's 2016 v2 platform for air quality modeling. This package includes inputs and scripts for modeling years 2016, 2023, 2026, and 2032. The basis of this platform is a combination of the 2014 National Emissions Inventory, Version 2 (2014NEIv2), and the 2017 National Emissions Inventory (2017NEI). At a future date, the package will be posted by way of a single zip file which includes all scripts and inputs except for MOVES emission factor table. For now, the package is posted in a more piecemeal fashion. The year-specific emissions files are here: https://gaftp.epa.gov/air/emismod/2016/v2/2016emissions/ https://gaftp.epa.gov/air/emismod/2016/v2/2023emissions/ https://gaftp.epa.gov/air/emismod/2016/v2/2026emissions/ https://gaftp.epa.gov/air/emismod/2016/v2/2032emissions/ The ancillary data for all years are here: https://gaftp.epa.gov/air/emismod/2016/v2/ancillary_data/ CMAQ model-ready emissions generated using these packages with SMOKE v4.8.1 should be identical to those used in EPA's 2016 v2 platform, with some exceptions as noted in this README. There may be additional emissions differences resulting from differences in the Linux operating system, hardware platform, and other system-specific differences. The data files are divided into several directories: - 2016emissions/ contains emission inventories for the year 2016, including national CEMS emissions, nonroad inventories and onroad activity data, and point and nonpoint inventories. There are similar directories for the years 2023, 2026, and 2032. - ancillary_inputs contains general ancillary files (ge_dat), including those related to speciation, spatial allocation (gridding), temporalization, and gridded ocean chlorine emissions files, which are included in the final model-ready emissions. - smoke_2016v2_platform_core.zip contains scripts to run the core SMOKE programs along with precompiled SMOKE executables from SMOKE version 4.8.1. - spatial_surrogates contains 36km and 12km spatial surrogates for the US, Canada, and Mexico, and 4km spatial surrogates for the US and Canada. Section 4 of this README includes information about the modeling sectors used in the platform. Section 5 of this README includes information about the inventories provided. Section 6 of this README includes information about the ancillary (non-inventory) files included. == 2. Requirements for processing emissions for air quality modeling == If you are only reviewing inventories and not developing emissions for air quality modeling, you do not need to install SMOKE or to follow the instructions below. Instead, unzip the files with the data of interest and examine those and the corresponding reports that are provided. If you plan to develop emissions for air quality modeling, SMOKE v4.8.1 is REQUIRED to process this case. SMOKE v4.8.1 includes new features and bug fixes required for the platform, particularly for the onroad and ptegu sectors. The SMOKE core script package includes precompiled executables of SMOKE v4.8.1 programs. These executables reflect SMOKE v4.8.1 as of 17 Sep 2021. Python: We also recommend (if not require) python version 3.0 or later, along with select python libraries. Many of the helper scripts included in this package use python. The python scripts within this package reference '#!/usr/bin/env python'; you may need to change this on your computing platform. All of the scripts have been updated for Python 3.5 to match the configuration on EPA's cluster. You should still be able to use Python 2.7 if you install the "future" modules. In most cases that can be done by running: sudo pip install future == 3. Installation of data files and scripts == This readme covers the installation of the SMOKE inventories, scripts, and ancillary files used for the 2016 v2 platform. Choose an install directory on your system; we will refer to this directory as "INSTALL_DIR". To review/reproduce emissions for all sectors, unzip all the .zip files into INSTALL_DIR. The packages have subdirectories embedded within them, so it is important that all files be unpacked in the same place in order for the scripts know where to find the inputs. If you are only interested in reproducing or examining emissions for specific sectors, you may download and unzip only the data for those sectors from the inventory directories, but for SMOKE processing you should also include the files in the ancillary_inputs and spatial_surrogates directories, and also the contents of the SMOKE core script package. Precompiled SMOKE executables and I/O API utilities are available in the SMOKE zip. If you would like to use an alternate set of SMOKE executables instead of the execs in this package, then in each sector run script in #INSTALL_DIR/[CASE]/scripts/*/, setenv SMOKE_LOCATION [location of your execs]. Similarly, to use an alternate set of I/O API utilities (e.g. m3xtract, m3tshift), setenv IOAPI_LOCATION [location of your execs]. All SMOKE inventories, scripts, and ancillary files used for the platform are provided. The full set of emission factor tables is not always permanently stored on the FTP server due to their large size; if they are not posted, they are furnished upon request. Prior to running SMOKE, you will need to edit the INSTALL_DIR (your install directory) and MET_ROOT (location of MCIP meteorology data) environment variable definitions in the "directory_definitions.csh" script located in each CASE/scripts directory. This script is sourced by each of the individual run scripts for each sector. Regarding the MCIP data, SMOKE only uses the GRIDCRO2D, METCRO2D, and METCRO3D files. If you are computing plume rise within SMOKE using the Laypoint program, SMOKE also needs the METDOT3D file. MCIP meteorology data is not included in the package. This is used for the onroad, onroad_ca_adj, dust (afdust/othafdust/othptdust), and biogenics (beis) sectors. == 4. Case description and instructions for each sector == Scripts are provided to process emissions for a 12km national grid (12US1) using CB6R3AE7 speciation for CMAQ. The CB6R3AE7 mechanism includes new species IVOC, APIN, AACD, and FACD which were not in the previous version of CB6. These new species do not impact CAMx modeling. The emissions from this package will work with base CMAQ but not the Multi-Pollutant version used for the National Air Toxics Assessment (NATA). The scripts can be adapted to run for other grids. First, in the directory_definitions.csh script, edit REGION_ABBREV and REGION_IOAPI_GRIDNAME. You also may need to change other inputs in each individual sector script, such as spatial surrogates (SRGPRO / SRGDESC), transportable fractions (XPORTFRAC), gridded meteorology for onroad (METMOVES), ocean chlorine (for the sector merge), and biogenic land use and seasons (BELD4 and BIOSEASON). A sample directory_definitions script for 12US2 is included in this package. If you are changing the grid to 12US2, you do not need to change the spatial surrogates, since 12US2 is a subset of 12US1. You do need to window the other grid-specific input files, however. Emissions for the platform may be processed for CMAQ and CAMx modeling. In addition to scripts for running SMOKE, this package also includes scripts for converting SMOKE outputs (CMAQ-ready emissions) to the format required by CAMx. Emissions processing is split into "sectors". Each sector has its own run scripts for processing, with one (or more) run scripts per case. See Section 7 of this README for information about the run script zips. All sectors are US-only unless otherwise noted. The sectors are: AFDUST: Particulate emissions from fugitive dust sources. This sector is processed in two steps. The first (Annual_afdust_12US1_*) processes the annual inventory, and the second (Annual_afdust_adj_12US1*) applies adjustments - transportable fraction and meteorologically-based - and outputs the adjusted emissions under the sector name "afdust_adj". The afdust scripts must be run in that order. AIRPORTS: Emissions from airports. Formerly part of the ptnonipm sector, this is a newly separate sector for v1 platform. This is a 'point' sector, and like all 'point' sectors, is processed via two scripts: the 'onetime' script, and the 'daily' script. The 'onetime' script must be run first. All emissions in this sector are low-level only (no inline files). BEIS: Biogenic emissions generated using the BEIS model, version 3.6.1. CANADA_AG: Point source emissions from Canada agricultural sources. These emissions were in the othpt sector in prior platforms. This is a 'point' sector, and like all 'point' sectors, is processed via two scripts: the 'onetime' script, and the 'daily' script. The 'onetime' script must be run first. All emissions in this sector are low-level only (no inline files). CANADA_OG2D: Point source emissions from low-level Canada upstream oil and gas sources. These emissions were in the othpt sector in prior platforms. This is a 'point' sector, and like all 'point' sectors, is processed via two scripts: the 'onetime' script, and the 'daily' script. The 'onetime' script must be run first. All emissions in this sector are low-level only (no inline files). CMV_C1C2: Emissions from C1 and C2 commercial marine sources, including ports and navigable waterways. Includes C1/C2 marine emissions in the entire domain, including US, Canada, Mexico, and all bodies of water which lie outside the boundaries of those countries. In previous platforms, Canadian and Mexican CMV emissions were included in the othar and othpt sectors, but now all CMV domain-wide is in the cmv_c1c2 and cmv_c3 sectors. This is a 'point' sector, and like all 'point' sectors, is processed via two scripts: the 'onetime' script, and the 'daily' script. The 'onetime' script must be run first. Inventories for this sector are grid-specific and designed for the 12US1 grid, or 12km grids which are a subset of 12US1 (e.g. 12US2). Therefore, emissions are output under the sector name "cmv_c1c2_12". Inventories for the 36US3 grid will be provided in the future. These inventories may be used in place of the 12US1 inventories for processing those other grids. Scripts are not provided for these other grids; one must replace the EMISINV and EMISHOUR definitions in the run scripts to point to the inventories corresponding to the grid you want to run. We also recommend changing the sector name if not running 12US1, since the inventories are grid-specific. All emissions in this sector are elevated (no low-level contribution). CMV_C3: Emissions from C3 commercial marine sources, including ports and navigable waterways. Includes C3 marine emissions in the entire domain, including US, Canada, Mexico, and all bodies of water which lie outside the boundaries of those countries. In previous platforms, Canadian and Mexican CMV emissions were included in the othar and othpt sectors, but now all CMV domain-wide is in the cmv_c1c2 and cmv_c3 sector. This is a 'point' sector, and like all 'point' sectors, is processed via two scripts: the 'onetime' script, and the 'daily' script. The 'onetime' script must be run first. Inventories for this sector are grid-specific and designed for the 12US1 grid, or 12km grids which are a subset of 12US1 (e.g. 12US2). Therefore, emissions are output under the sector name "cmv_c3_12". Inventories for the 36US3 grid will be provided in the future. These inventories may be used in place of the 12US1 inventories for processing those other grids. Scripts are not provided for these other grids; one must replace the EMISINV and EMISHOUR definitions in the run scripts to point to the inventories corresponding to the grid you want to run. We also recommend changing the sector name if not running 12US1, since the inventories are grid-specific. All emissions in this sector are elevated (no low-level contribution). FERTILIZER: Agricultural emissions from fertilizer. This was part of the 'ag' sector in prior platforms. This is ammonia only. LIVESTOCK: Agricultural emissions from livestock. This was part of the 'ag' sector in prior platforms. This is mostly ammonia, but includes other pollutants from livestock sources as well. NONPT: Area source emissions not included in other sectors. NONROAD: Off highway mobile source emissions. EPA processed this sector using a new SMOKE feature supporting output of multiple subsector emissions files in a single SMOKE run. Specifcially, SMOKE output diesel and gas (including all non-diesel fuels such as LPG and CNG) as separate inputs, in addition to the total onroad emissions. The files and settings needed to output separate emissions for gas and diesel are not included in this package but may be added in the future. NP_OILGAS: Area source oil and gas emissions. ONROAD: On highway mobile source emissions, excluding California. This sector is processed using SMOKE-MOVES with multiple scripts as described in section 4B. EPA processed this sector using a new SMOKE feature supporting output of multiple subsector emissions files in a single SMOKE run. Specifcially, SMOKE-MOVES output diesel and gas (including all non-diesel fuels such as E-85 and CNG) as separate inputs, in addition to the total onroad emissions. The files and settings needed to output separate emissions for gas and diesel are not included in this package but may be added in the future. ONROAD_CA_ADJ: On highway mobile source emissions, California only. This sector is processed using SMOKE-MOVES with multiple scripts as described in section 4B. EPA processed this sector using a new SMOKE feature supporting output of multiple subsector emissions files in a single SMOKE run. Specifcially, SMOKE-MOVES output diesel and gas (including all non-diesel fuels such as E-85 and CNG) as separate inputs, in addition to the total onroad emissions. The files and settings needed to output separate emissions for gas and diesel are not included in this package but may be added in the future. OTHAFDUST: Particulate emissions from fugitive dust sources in Canada. Just like with afdust, this sector is processed in two steps. The first (Annual_othafdust_12US1_*) processes the annual inventory, and the second (Annual_othafdust_adj_12US1*) applies adjustments - transportable fraction and meteorologically-based - and outputs the adjusted emissions under the sector name "othafdust_adj". The othafdust scripts must be run in that order. Fugitive dust emissions in Mexico are included in the othar sector and do not need the same transportable fraction and meteorological adjustments that the Canada fugitive dust emissions in othafdust do. OTHPTDUST: Point source particulate emissions from fugitive dust sources in Canada. In Canada, dust emissions are in area source format for some sources (othafdust sector) and point source format for other sources (othptdust sector). This is a 'point' sector with additional adjustments, and is processed via THREE scripts: the 'onetime' script, the 'daily' script, and then the adjust script (othptdust_adj), in that order. All emissions in this sector are low-level only (no inline files). OTHAR: Area source emissions from Canada and Mexico, including mobile nonroad. ONROAD_CAN: Mobile onroad source emissions from Canada. ONROAD_MEX: Mobile onroad source emissions from Mexico. The onroad Mexico emissions inventory includes pre-speciated VOC emissions for an older CB6 mechanism, so there is an extra script for this sector to convert those emissions to the newer CB6 mechanism needed for CMAQ. This extra script is called *_part2_combine.csh and uses the combine utility to perform the CB6 mechanism conversion. The combine program is included, pre-compiled, in the SMOKE package along with pre-compiled SMOKE executables and I/O API utilities. To help make the distinction between emissions for the two CB6 mechanisms, older CB6 emissions use the sector name "onroad_mex_cb6orig". The combine post-processing step creates emissions files with the final sector name "onroad_mex". OTHPT: Point source emissions from Canada and Mexico. This is a 'point' sector, and like all 'point' sectors, is processed via two scripts: the 'onetime' script, and the 'daily' script. The 'onetime' script must be run first. All emissions in this sector are elevated (no low-level contribution). PTAGFIRE: Point source agricultural burning emissions. The ptagfire sector uses a daily point source inventory. This is a 'point' sector, and like all 'point' sectors, is processed via two scripts: the 'onetime' script, and the 'daily' script. The 'onetime' script must be run first. All emissions in this sector are elevated (no low-level contribution). PTEGU: Electric generating unit emissions. This sector incorporates CEM (Continuous Emissions Monitoring) hourly emissions for a majority of sources. This is a 'point' sector, and like all 'point' sectors, is processed via a 'onetime' script first, followed by a 'daily' script. For ptegu there are two 'daily' scripts for different months of the year: 'summer' (May through September), and 'winter' (October through April). For sources without hourly CEM emissions, summer and winter use different hourly temporalization, and so they are run with separate inputs. All emissions in this sector are elevated (no low-level contribution). For the years 2023, 2026, and 2032, there are three separate ptegu sectors: PTEGU_SUMMER, PTEGU_WINTER, and PTEGU_WINTERSHLD, each with separate season-specific inventories and other inputs. The summer sector is processed for May 1 through September 30, the winter sector is processed for December 1 through February 29, and the "wintershld" (which means winter shoulder season) sector is processed for October, November, March, and April. For 2016, all seasons use the same inventories, and there are no separate input files for the winter shoulder season, so there is only a single "ptegu" sector in 2016 with two daily scripts (summer and winter). PTNONIPM: Point source emissions from industrial activities. This is a 'point' sector, and like all 'point' sectors, is processed via two scripts: the 'onetime' script, and the 'daily' script. The 'onetime' script must be run first. All emissions in this sector are elevated (no low-level contribution). PTFIRE-RX: Point source emissions from year specific controlled (prescribed) burning. Fires are processed in the 'inline' format for CMAQ, and are all elevated (no low-level contribution). This is a 'point' sector, and like all 'point' sectors, is processed via two scripts: the 'onetime' script, and the 'daily' script. The 'onetime' script must be run first. PTFIRE-WILD: Point source emissions from year specific wild fires. Fires are processed in the 'inline' format for CMAQ, and are all elevated (no low-level contribution). This is a 'point' sector, and like all 'point' sectors, is processed via two scripts: the 'onetime' script, and the 'daily' script. The 'onetime' script must be run first. PTFIRE_OTHNA: Point source emissions from year specific controlled burning and wild fires in the rest of North America ('OTHNA' = OTHer North America), including Canada and Mexico. In addition to Canada and Mexico, fire emissions for Central America and the Caribbean are also included. Emissions from those areas are ultimately not modeled due to being outside of the 12US1 modeling domain, but they are provided for possible use in larger grids. These fires are processed in the 'inline' format for CMAQ, and are all elevated (no low-level contribution). This is a 'point' sector, and like all 'point' sectors, is processed via two scripts: the 'onetime' script, and the 'daily' script. The 'onetime' script must be run first. PT_OILGAS: Point source oil and gas emissions, including emissions from offshore oil rigs in the Gulf of Mexico. This is a 'point' sector, and like all 'point' sectors, is processed via two scripts: the 'onetime' script, and the 'daily' script. The 'onetime' script must be run first. All emissions in this sector are elevated (no low-level contribution). RAIL: Area source railway emissions. RWC: Area source residential wood combustion emissions. SOLVENTS: Area source emissions from solvents. These emissions were part of the nonpt sector in prior platforms. == 4B. Notes regarding onroad == Onroad emissions are processed using SMOKE-MOVES. The processing is split into multiple run scripts. In this platform, SMOKE-MOVES inputs were prepared using MOVES3. As in recent platforms, speciation of VOC emissions is handled within the MOVES model. This platform uses MOVES version MOVES3, which supports speciation for the CB6R3AE7 mechanism. As described in the SMOKE online documentation, SMOKE-MOVES handles onroad emissions separately for six types of processes: - On-network emissions (RatePerDistance, or RPD) - Off-network emissions, fuel vapor venting (RatePerProfile, or RPP) - Off-network emissions, extended idling (RatePerHour, or RPH) - On-network idling (ONI) emissions (RatePerHour-ONI, or RPHO) - Off-network emissions, starts (RatePerStart, or RPS) - All other evaporative off-network emissions (RatePerVehicle, or RPV) For each of the two onroad sectors (onroad, onroad_ca_adj), there are separate run scripts for RPD, RPP, RPH, RPHO, RPS, and RPV, plus a merge script that combines emissions from the six streams into a single emissions file per day. These scripts may take a particularly long time to run, especially RPD. Therefore, consideration should be given to running multiple RPD jobs in parallel, such as one job per quarter. The reason onroad has been split into two sectors - onroad and onroad_ca_adj - is in order to match SMOKE-MOVES annual emission totals with those provided by California. To do this, we split California into a separate sector, and run SMOKE-MOVES with a control factor file (CFPRO) which nudges the emissions so that the annual totals post-SMOKE-MOVES equal those provided by CARB. CARB provided separate onroad emissions inventories for use in the beta platform, and we match their provided emissions at the county/SCC level, except that the CARB inventory does not distinguish between different on-network road types (but does distinguish on-network emissions from off-network). == 4B1. DAYS_PER_RUN == SMOKE-MOVES can be run more efficiently if running more than one day at a time. For example, Movesmrg can create one 7-day emissions file more quickly than it can create seven individual 1-day emissions files. To turn on this feature, use the DAYS_PER_RUN variable, set to the number of days you wish to run in a single Movesmrg instance. The recommended value for DAYS_PER_RUN is 7. The onroad scripts include a setting called "DAYS_PER_RUN", set to 1 as the default. If DAYS_PER_RUN > 1, after Movesmrg is run, the run scripts will use the I/O API utility m3xtract to split up the multi-day emissions file into single day (25-hour) emissions files. Multi-day Movesmrg runs will never cross months. For example, if DAYS_PER_RUN = 7, then the last Movesmrg run of January will start on January 29th and end on January 31st (3 days), and the first Movesmrg run of February will start on February 1st and end on February 7th. Using the multi-day Movesmrg functionality requires multi-day MCIP files. For example, if DAYS_PER_RUN = 7, your METCRO2D files must also be 7 days (169 hours) long. These multi-day MCIP files should be stored in MET_ROOT_${Xday}/, where X = DAYS_PER_RUN (i.e. /7day for DAYS_PER_RUN = 7). For example, if the single day MCIP files are in /foo/foo/mcip_dir/, then 7-day MCIP files should be in /foo/foo/mcip_dir_7day/. The primary drawback to using this multi-day Movesmrg functionality is an increase in the memory usage. == 4B2. NMOG == In sectors other than onroad, an additional species called NMOG - non-methane organic gases; equivalent to TOG minus methane - is included in the speciation profiles and CMAQ-ready emissions. Onroad emissions from SMOKE-MOVES do not include NMOG. NMOG is not needed for CMAQ or CAMx and is optional. For those who want to create NMOG emissions for onroad, an extra script is provided to be run after the onroad merge step. For example: Monthly_onroad_add_NMOG_12US1_2023fj_16j.csh This script uses the combine utility to add the NMOG species to the emissions. Emissions output with this script have the sector names "onroad_w_nmog" and "onroad_ca_adj_w_nmog", respectively. Edit the sector names in the SECTORLIST prior to running the overall sector merge (section 4C) to include NMOG-supplemented onroad emissions in your final merged model-ready emissions. == 4C. Sector merge == After all sectors have been processed, the Sector_merge script merges the low-level emissions from all sectors into a single CMAQ-ready emissions file per day. Merged model-ready emissions will be output to: INSTALL_DIR/$CASE/smoke_out/$CASE/$GRID/$SPC/ Inline emissions and stack_groups files will be output to the same directory, except in subdirectories by sector name (e.g. .../$SPC/ptnonipm/). By default, the sector merge scripts are configured to include biogenics and RWC. Some CMAQ modelers may wish to process biogenic emissions inline within CMAQ and not include biogenic emissions in the gridded emissions files. The newest versions of CMAQ include features which require the RWC sector emissions to be passed into CMAQ separately. So, the filenames of merged emissions now indicate whether beis and RWC are included. By default they are both merged, so the filenames say "withbeis_withrwc". The sectorlist file controls which sectors are included in the sector merge. This file is included in the package along with the run scripts, and is located in the $CASE/scripts directory for each case. Within the sectorlist file, the 'mergesector' column controls which sectors are merged (Y or N). For example, to run the sector merge without biogenics or RWC, set the mergesector column to N for the 'beis' and 'rwc' sectors. Many point sectors have mergesector set to N (e.g. ptegu, othpt) because do not have any 2-D gridded emissions. To merge in alternative biogenic emissions files, edit the sectorlist by changing the 'beis' sector name to the sector name of your choice, and make sure your biogenic emissions files exist in the $CASE/premerged/[sector name] directory with filenames adhering to the file name convention used by other sectors. == 5. Description of inventory packages == Inventories for the 2016fj case are included in the following files, all of which should be unpackaged in INSTALL_DIR. 2016fj_CMV_inventory_16sep2021.zip 2016fj_cem_inventory_15sep2021.zip 2016fj_fires_inventory_15sep2021.zip 2016fj_nonpoint_inventory_15sep2021.zip 2016fj_nonroad_inventory_27may2021.zip 2016fj_onroad_activity_27may2021.zip 2016fj_oth_inventory_15sep2021.zip 2016fj_point_inventory_15sep2021.zip 2016fj_onroad_SMOKE-MOVES_emissions_FF10_27may2021.zip Inventories for the 2023fj, 2026fj, and 2032fj cases are organized in a similar manner, except there are no fire inventories for the future years. Past platforms also included a biogenics package. The files from that package are now in the ancillary_data directory. The "cem" package includes the hourly CEM (Continuous Emissions Monitoring) emissions used by the ptegu sector. This is the same data that is available on EPA's Air Markets Program Data website (ampd.epa.gov), except that we've split the data into months and days as needed for our scripts, and run the data through a "CEM correct" program. The CEMSUM file is in the ancillary_data area. The "CMV" package includes annual and hourly inventories for the cmv_c1c2 and cmv_c3 sectors, 12US1 grid. Separate inventories for the 36US3 grid will be provided in a separate zip at a later date. To process CMV inventories for other grids, one should edit the 12US1 scripts and change the EMISINV and EMISHOUR definitions, along with the other grid changes described in Section 4 of this README. The "fires" package includes the inventories for the ptfire-rx, ptfire-wild, ptfire_othna, and ptagfire sectors. The "nonpoint" package includes inventories for the following sectors: afdust, fertilizer, livestock, nonpt, np_oilgas, rail, rwc, solvents. Agricultural fire emissions also come from NEI Nonpoint, but those inventories are included in the fires zip. The "nonroad" package include the inventories for the nonroad sector. To reduce the file size, pollutants not needed for normal CMAQ modeling were removed, such as metals, PAHs, and dioxins and furans. The "onroad_activity" package includes the activity data for the onroad and onroad_ca_adj sectors. It does not include the emission factor tables also required to run SMOKE-MOVES; those are in separate zips posted in the 2016emissions/moves_eftables/ area. Emission factors are only available for CB6. The emission factor tables are provided on FTP with separate zips for each state, e.g. 2016emissions/moves_eftables/2016fj_16j_eftables_cb6r3ae7_st21.zip All of these EF tables already have a NOx humidity adjustment. The "oth" package includes all inventories for Canada and Mexico, except fires. The "point" package includes the inventories for the following sectors: ptnonipm, ptegu, pt_oilgas, airports. The "onroad_SMOKE_MOVES_emissions_ff10" package includes an FF10-formatted inventory representing emissions totals for the onroad sector as calculated by SMOKE-MOVES. This is provided for those who are interested in an onroad emissions inventory or report. It is not needed for SMOKE modeling. See Section 4 of this README for a description of each modeling sector. == 6. Description of ancillary file packages == The following packages should be unpacked in INSTALL_DIR: ancillary_data/2016fj_beis_ge_dat_16sep2021.zip ancillary_data/2016v2_gridding_ge_dat_16sep2021.zip ancillary_data/2016v2_other_ge_dat_16sep2021.zip ancillary_data/2016v2_speciation_ge_dat_15sep2021.zip ancillary_data/2016v2_temporal_ge_dat_15sep2021.zip ancillary_data/ocean_chlorine.zip spatial_surrogates/CONUS12_surrogates_04mar2021.zip spatial_surrogates/CONUS12_np_oilgas_2016_surrogates_04mar2021.zip spatial_surrogates/CONUS12_2015CAN_2010MEX_surrogates_03dec2018.zip The "beis" package includes gridded land use, BIOSEASON, and biogenic emission factor files for input to BEIS 3.6.1. The latest version of BEIS uses different land use and emission factor inputs compared to prior versions, such as BEIS 3.14. The beta platform includes updated land use, BELD 5, with additional updates, including new updates for this platform. This package also includes a b3grd file for 12US1 and 36US3. This file is output by the Normbeis program, and is included in the package for those people who do not wish to run Normbeis and generate their own b3grd using the provided land use and emission factor files. This b3grd file is not speciation-specific and can be used with any speciation mechanism. The "surrogates" packages contain the spatial surrogates at 12km resolution for the US, and for Canada and Mexico. 12km surrogates for the np_oilgas sector are in a separate zip; these oil and gas surrogates are specific for the year 2016 and also include a set of surrogates specifically for the WRAP region. 36km surrogates for the US, Canada, and Mexico are also provided in separate zips. Surrogates are also provided at 4km resolution for the US and Canada. The US 4km surrogate package includes 2016-specific oil and gas surrogates in the "2016_MYR" subdirectory within the zip file. WRAP oil and gas surrogates are not available at 4km resolution. The "gridding" package includes all SMOKE inputs related to spatial allocation other than the surrogates, including cross-references, surrogate descriptions, and gridded transportable fractions used in afdust_adj, othafdust_adj, and othptdust_adj. The "speciation" package includes speciation profiles, cross-references, VOC-to-TOG conversion factors, and inventory tables. This .zip includes files for the CB6 mechanism for CMAQ v5.2. The "temporal" package includes temporal profiles and cross-references, including daily and hourly temporal profiles developed by the SMOKE program Gentpro for use in the rwc and ag sectors. The "other" ge_dat package includes all other SMOKE ancillary files not included in the above packages, including: - SMOKE-MOVES ancillary files, including the reference county (MCXREF) and fuel month (MFMREF) cross-references, pollutant (MEPROC) and emission factor table (MRCLIST) lists, activity SCC to full SCC cross-references (SCCXREF), hourly speed profiles (SPDPRO), daily temperature data (METMOVES), and Movesmrg adjustment factors (CFPRO) - NHAPEXCLUDE files (concerns VOC HAP integration) - Other miscellaneous SMOKE inputs, such as the ARTOPNT, COSTCY, HOLIDAYS, MACTDESC, NAICSDESC, ORISDESC, PELVCONFIG, PSTK, SCCDESC - Smkreport configuration files (REPCONFIG, all in ge_dat/smkreport/repconfig) This ocean_chlorine.zip package contains gridded ocean chlorine emissions, which are included in the sector merge, for 12US1, 12US2, and 36US1. The run scripts (see section 7) are already set up to use the proper ancillary files and inventories for each sector and case. == 7. Description of script packages == The SMOKE core script package should be unpacked in INSTALL_DIR. This includes scripts and precompiled executables for running SMOKE in general, and for running the 2016 modeling case in particular. The scripts in the 2016fj_16j subdirectory are the scripts you run directly in order to replicate our emissions. Separate script(s) are provided for each sector. See section 4 for information pertinent to each sector. In general, you edit the directory_definitions.csh file, in particular INSTALL_DIR and MET_ROOT, and then run each sector. Sector scripts are organized into subdirectories within CASE/scripts by sector category: biogenics, nonpoint, onroad, point, and merge. For afdust sectors, run afdust/othafdust first, then afdust_adj/othafdust_adj. For point sectors, run "onetime" first, and then "daily". Othptdust has an additional "adj" script which comes after the daily script. For onroad sectors, run RPV/RPD/RPH/RPHO/RPP/RPS first, then the merge script. The onroad NMOG script is optional (see section 4B2). For onroad_mex, run the normal script and also the part2_combine script after that. The scripts, programs, and other inputs in the combine, ioapi, and smoke4.8.1 subdirectories are all "helper" scripts and inputs, and generally never need to be run directly. == 7B. Other miscellaneous programs == The beta platform public package includes additional SMOKE utilities in the package smoke_2016beta_platform_utilities.zip. These utilities have not been updated since beta platform, and so they have not been reposted for this platform. Additional information can be found in the README for beta platform. == 8. Preparing emissions for CAMx == Preparing emissions for the CAMx model instead of the CMAQ model requires converting the emissions to CAMx-ready format after SMOKE is run. Conversion scripts are included in the core SMOKE zip, and output to the INSTALL_DIR/CASE/scripts/camx/ directory. Those scripts use helper scripts and programs which are also included in the core SMOKE zip and output to INSTALL_DIR/camx/. Converting CMAQ-ready emissions to CAMx-ready emissions consists of several steps. First, fire emissions must be processed through SMOKE in 3-D format instead of inline format so that the SMOKE outputs include layered emissions. This will need to be done for four sectors: ptfire-rx, ptfire-wild, ptfire_othna, and ptagfire. Scripts for processing these three sectors as 3-D layered sectors are provided in the CASE/scripts/point/ directory, alongside the regular scripts for processing inline emissions for CMAQ. The 3-D scripts specify '3D' in the filename, and '3D' has also been appended to the sector names to distinguish these runs from the inline runs (ptfire-rx3D, ptfire-wild3D, ptagfire3D, ptfire_othna3D). These scripts will produce gridded and layered 3-D emissions in the 2016fj_16j/premerged directory, and will not produce any inline emissions files for CMAQ. Also, the 3-D fire scripts are configured to process emissions for the 12US2 grid, not 12US1. This is because EPA's 12km CAMx modeling was performed for the 12US2 grid. Second, those 3-D fire emissions must be separately converted to CAMx format. Scripts for this step, one per sector, are provided in the 2016fj_16j/scripts/camx/ directory. Third, run the final CAMx conversion script, also available in the same scripts/camx/ directory. The output files should include two emis2d files per day and one mrgpt file per day. The files that CAMx needs are the emis2d file with "+ss" in the name (includes sea salt), and the mrgpt file. This script is currently configured to use 3-D fire emissions from step 2 for the 12US2 grid, combined with other point sector emissions for the 12US1 grid. Because 2016 fire emissions are reused for all future years, only the 2016fj case has scripts for the fire sectors. If you are only running a future year case without running 2016fj first, you will need to run the fire sectors under 2016fj in addition to the future year sectors. if you are running 2016fj plus one or more future years, you only need to process the fires once, under the 2016fj case. All CAMx-ready files will go to: INSTALL_DIR/$CASE/smoke_out/$CASE/12US2/camx/ The newest version of CAMx includes support for multiple input emissions files. So, it is not necessary to merge all point sector emissions together into a single mrgpt file per day. However, to make modeling easier, we included all point sectors in the mrgpt files. If you wish to include only a subset of the point sector emissions in the mrgpt file, in the camx_convert_*_12US2.csh script, and edit the mrg_sectors array. PTSR files from the individual sectors that are not merged will need to be included in CAMx modeling. Individual PTSR sector emissions will be output to the 12US2/camx/sector/ directory. That directory will include ALL PTSR sector emissions, not just the sectors that are not merged. == 8A. FORTRAN programs used by the CAMx converter == The CAMx converter uses several FORTRAN programs. The core SMOKE zip contains both our compiled FORTRAN executables (which may or may not work on your system), and the original FORTRAN source code and Makefiles, so that you may recompile these helper programs yourself. The source code is in INSTALL_DIR/camx/src/, and our executables are in INSTALL_DIR/camx/bin/ and INSTALL_DIR/camx/bin-fires/ (the fires conversion uses different versions of some executables). If you have to recompile the code, this is where the recompiled executables should ultimately go. Fires use a different version of the cmaq2uam program, and the source code for that version is in INSTALL_DIR/camx/src-21oct2013/. == 8B. Other files used by the CAMx converter == The subdirectories 'dates', 'land', 'oceanic_v4.1.1', and 'Species_Mapping_Tables' in INSTALL_DIR/camx/ include other files used by the converter. The addition of sea salt emissions requires CAMx-formatted meteorological data from WRF. Specifically, this requires a 'met3d' file and a 'met2d' file. The WRF_ROOT parameter in the final CAMx conversion script should point to the location of this data. Like the MCIP meteorology, these files are not included in the package. == 8C. Windowing merged low-level emissions from 12US1 to 12US2 == The SMOKE scripts provided in this package are for the 12US1 domain, but CAMx modeling is typically performed for the 12US2 domain. EPA typically processes emissions as follows: Sector and low-level merged emissions are generated for 12US1, and then the merged emissions are windowed to 12US2 prior to conversion to CAMx format. This way, CMAQ-ready emissions are available for both 12US1 and 12US2, since many groups prefer 12US1 for CMAQ modeling. A script is provided to window the merged 12US1 low-level emissions to 12US2: $INSTALL_DIR/2016fj_16j/scripts/camx/m3wndw_loop_merged.csh == 9. Log analyzer == The platform scripts include a Python-based tool called the log analyzer that runs automatically at the conclusion of each SMOKE job. The purpose of the log analyzer is to scan all log files from the sector, search for errors and warnings, and filter out common or "acceptable" warnings. Log analyzer output goes into this directory: $INSTALL_DIR/$CASE/reports/log_analyzer There are two types of output files: Level 1 and Level 3. Level 3 lists every instance of each error and warning individually, while Level 1 combines repeats of common warnings. It is sufficient to look at only the Level 1 output. The Level 1 output includes a "priority" code, the error/warning message, and the log file in which the message appears. The priority code is a number from 0 to 3. If priority = 2 or 3, the message has been identified as common or acceptable. This is based on a file called known_messages.txt, which is located here: $INSTALL_DIR/smoke4.8.1/scripts/log_analyzer/known_messages.txt If priority = 1, the message is included in known_messages and has been identified as NOT acceptable - however, many priority 1 warnings are in fact SOMETIMES acceptable and sometimes not, which is why they are not given priority 2 or 3. Some common priority 1 warnings are listed below. If priority = 0, the message is not included in known_messages. Priority 0 or priority 1 messages which are acceptable include: - WARNING: [*] is not found in both inventory pollutant and model species lists. These are common onroad messages resulting from the CFPRO file including more species than is always necessary. - WARNING: Could not read [BEGHOUR/ENDHOUR] from file "PDAY" This is a common ptfire warning and is acceptable. - WARNING: resetting surrogates ratio of Co/St/Ct (FIPS): ... This warning is in known_messages but is not always picked up by the log analyzer for reasons unknown. - WARNING: Speciation profile "?? " is not in profiles This warning is common/acceptable for onroad_mex. - WARNING: Total annual toxic emissions greater than annual [*]__VOC emissions for source: This warning is common for sectors with monthly inventories such as nonroad. - WARNING: Applying default time zone 5 to country/state/county code: [*] This warning is acceptable for Alaska FIPS and FIPS 85005. - WARNING: Duplicate entry in AR2PT x-ref file: This warning is acceptable but is not in known_messages to let us know we should correct it in the future. - WARNING: Hour-specific ending date/time WARNING: Could not read "INDXH" from file "PHOUR " netCDF error number -40 Error reading netCDF time step flag for PHOUR These four messages may appear in the Temporal logs for January and February for the CMV sectors. - WARNING: Dropping SCC .* not listed in SCCXREF file This is an acceptable warning for the RPP process in onroad. In other platforms which use MOVES3, this warning is also acceptable for RPV. (Platforms which uses MOVES3 also have an "RPS" process.) == 10. SMOKE reports (Smkreport) == By default, the run scripts run the Smkreport program, output to the $CASE/reports/inv directory. For sectors with annual inventories,reports are annual. For sectors with monthly inventories (e.g. nonroad), reports are monthly. Most reports include all inventory pollutants and model species, although PM10 usually appears as zero due to a SMOKE quirk; to get PM10, sum PM2_5 and PMC in the report. For onroad, these reports reflect activity, not emissions, and include some double counting due to how SMOKE allocates activity to different processes; therefore, you should not use the reports/inv reports for the onroad or onroad_ca_adj sectors. The following types of reports are generated. Note that not all types of reports are generated for all sectors: *state.txt: State totals. *county.txt: County totals. *state_scc.txt: State/SCC totals. *county_scc.txt: County/SCC totals. *state_naics.txt: State/NAICS totals. *cell_${GRID}.txt: Totals by grid cell. *cell_county_${GRID}.txt: Totals by grid cell and county. *state_grid_${GRID}.txt: State totals after gridding. *srgid_${GRID}.txt: Emissions totals at various resolutions after gridding, and also including the spatial surrogate assignment. *pm25prof.txt: Totals of PM2.5 at various resolutions, and also including the PM2.5 speciation profile assignment. *vocprof.txt: Totals of VOC at various resolutions, and also including the VOC speciation profile assignment. For sectors which are integrated and have both NONHAPVOC and VOC, or have multiple modes of VOC, there may be multiple VOC profile reports for NONHAPVOC and (no-integrate) VOC and/or for each mode. For all sectors except those processed with SMOKE-MOVES, Smkmerge generates daily county total reports in the $CASE/reports/smkmerge directory. These are then summed to annual by state and county, output to the $CASE/reports/annual_report directory. Emissions totals in the reports/annual_report directory (post-temporalization) should be within 1-2% of the totals in the reports/inv directory (pre-temporalization). For SMOKE-MOVES sectors, the $CASE/reports/smkmerge directory includes daily (or weekly if DAYS_PER_RUN=7) totals by county/SCC. Scripts to aggregate these totals to monthly or annual by state, county, state/SCC, and county/SCC are provided in the SMOKE utilities zip, movesmrg_report_postproc/ directory. == 11. Spinup == A parameter in the run scripts called SPINUP_DURATION supports the processing of emissions for December of the previous year for model spinup purposes. If SPINUP_DURATION > 0, then: - For sectors where emissions are processed for representative dates only, the entire month of December of the previous year will be processed - For sectors where emissions are processed daily, the last X days of December of the previous year will be processed, where X = SPINUP_DURATION However, in EPA emissions modeling platform applications, SPINUP_DURATION is set to a nonzero value (typically 10) ONLY for biogenics processing and for the final sector merge. For all other sectors, SPINUP_DURATION is set to 0 when running SMOKE. The scripts in this package are configured accordingly as the default. When the final sector merge is run, spinup period emissions for all sectors except biogenics are taken from December of the base year. For representative day sectors, dates are mapped based on day-of-week, and also Christmas holidays; for daily sectors, calendar dates are mapped. For example, the 12/28/2015 merged emissions include sectors from the following dates: - beis: 12/28/2015 (actual spinup emissions) - afdust_adj, fertilizer, livestock, onroad, onroad_ca_adj, othafdust_adj, othptdust_adj, rwc: 12/28/2016 (daily sectors use December 2016 matched up by calendar day) - airports, canada_ag, canada_og2D, nonpt, nonroad, onroad_can, onroad_mex, othar, pt_oilgas, ptnonipm: 12/05/2016 (representative dates based on day-of-week) - np_oilgas, rail, solvents: 12/06/2016 (also representative dates, but these sectors have a single day per month) An illustration of how the dates are mapped in the spinup period is available in the smk_merge_dates files, for example: $INSTALL_DIR/smoke4.8.1/scripts/smk_dates/2016/smk_merge_dates_201512.txt Similarly for point sectors, when CMAQ is run, inline emissions from the base year are used to cover the spinup period as follows: - othpt, ptnonipm, pt_oilgas use representative date / day-of-week based mappings - cmv_c1c2, cmv_c3, ptegu use calendar date-based mappings - ptfire-rx, ptfire-wild, ptagfire, ptfire_othna (all fires) use January 1 emissions for all spinup days Sometimes, base year inline point emissions files are physically copied to December spinup dates to simplify the CMAQ setup, but CMAQ scripts can also be configured to point to base year dates while running spinup.