DOI: 10.5281/zenodo.16099069
title: Code and data from: The risks to human health of air toxics, PM2.5, and ozone from the 2023 Canadian wildfires

description: Supporting data for calculations of the risks to human health of air toxics, PM2.5, and ozone from the 2023 Canadian wildfires

 

Data archive created by Havala Pye 0000-0002-2014-2140

 

 

For use of the data, users are encouraged to cite both this data archive (https://doi.org/10.5281/zenodo.16099070) for transparency and the following article for methods documentation:

H. O. T. Pye, W. T. Hutzell, N. L. Fann, T. N. Skipper, M. Pye, J. Beidler, C. Allen, B. N. Murphy, E. L. D’Ambro, S. Lin, K. Talgo, L. Reynolds, D. Kang, J. Bash, K. M. Seltzer, S. L. Farrell, K. W. Appel, K. Brehme, R. C. Gilliam, B. H. Henderson, and A. W. H. Chan: The risks to human health of air toxics, PM2.5, and ozone from the 2023 Canadian wildfires, ChemRxiv, https://doi.org/10.26434/chemrxiv-2025-fx8f1, 2025. This content is a preprint and has not been peer-reviewed. Please update to the final journal article when available.

 

Additional model-ready data to run CMAQ (emissions, meteorology, and other input files) from this work are available at:

US EPA, 2025, "CMAQ 2023 12US4 CRACMM2 Inputs and Meteorology", https://doi.org/10.15139/S3/GL41QC, UNC Dataverse, V1.

 

Please see documentation on the CMAQ github repository for standard CMAQ conventions.

 

Contents

 

12US4_files: netcdf and shape files with information for the 12US4 domain including 

    shapefiles: shape files and other domain specification information

    population: population data for the U.S. and Canada on 12US4 grid as a netcdf file 

         (acs_2023_5yr_bg_pop_12US4.nc, can_2021_cenus_subd_pop_12US4.nc)

    masks: mask for Canada used to remove fires for that region in CMAQ

 

analysis/inputs: inputs used in analysis of CMAQ output

     cities.txt: Latitude and longitude of locations for data extraction in Figure 2. Formatted as a 

          writesite (https://github.com/USEPA/CMAQ/tree/main/POST/writesite) file.

     20250512Dose_Response_Library_Oct2024.xlsx: HEM toxicity values file from October 2024 and mapping to CRACMM species; 

          CMAQCONCCOMBINE_UGM3 indicates combine species name (without units), CMAQHAP is the CMAQ-CRACMM 

          species name, CMAQEMIS is the emitted species name (without T_ prepending); CMAQ names should not be cross-walked by line; 

          See Pye et al. (2025) supplemental information Table S7 for more details and a readable version with crosswalk. 

     degradelog.txt: excerpt from CMAQ simulation processor log file documenting active hazardous air pollutant (HAP) degradation reactions.

     TableS12_pye2024_erbymass.xlsx: Table S12 from Pye et al. 2024 (https://doi.org/10.1021/acs.est.4c06187) and

          supplemented with Gkatzelis et al. 2024 (https://doi.org/10.5194/acp-24-929-2024). 

     2023hc_CRACMM2_task4_final_sector_reports_withTSpecies_09apr2025.csv: Emissions totals in tons/yr by sector in CRACMM species names.

     Target_Organ_resp_Oct2024.xlsx: subset of HEM target organ file indicating all species with a respiratory target organ impact.

     Target_Organ_neuro_Oct2024.xlsx: subset of HEM target organ file indicating all species with a neurological target organ impact.

 

analysis/scripts: scripts used to analyze concentrations and determine risk in the work of Pye et al. (2025) in python notebook (ipynb) and html.

     FigS19_NAPS_HAPS_Data_processing.ipynb/html: Creates Figure S17 evaluating CMAQ vs NAPS VOCs.

     Pye2025_allsrc_hapemiss_FigS1.ipnyb/html: Creates Figure S1 comparing HAP emissions across sectors and studies.

     Pye2025_FigS14S16S17_aqs_fire_analysis.ipnyb/html: Creates Figures S14,S16,S17 comparing CMAQ to AQS observations.

     Pye2025_Stackedbar_Fig2S6.ipynb/html: Creates Figures 2 and S6 with risk and photochemical age.

     Pye2025_SpeciesSIfigs_HAPs_HItotal_Fig1S5S20.ipynb/html: Creates Figure 1, S5, S20 including concentrations of HAPs.

     Pye2025_SpeciesSIfigs_PMox_S3S4S21S22.ipynmb/html: Creates PM and oxidant figures (S3, S4, S21, S22).

     Pye2025_TOC.ipynb/html: Creates Table of Contents (TOC) art.

 

CMAQscripts: cleaned-up versions of scripts for 2023_12US4 CMAQ-CRACMM. 

             Correctly turns on lightning NOx; does not double count biogenic HAP emissions.

     CMAQv55: CMAQ DESID control file and run script for CRACMM2 in CMAQv55

     CMAQv6dev: CMAQ ELMO2 Chem control files for CRACMM2/CRACMM3/CRACMM3HAPs and run script for developmental version of CMAQ past v55

 

CMAQcode

     BLD: CMAQv5.5 fortran code with additional updates resulting in CRACMM3HAPs as described by Pye et al. (2025)

     base_config: build script, run scripts, control files, and example log files (text files) for the base simulation in Pye et al. (2025). 

          Known issues: 

          - while the control file indicates acrylonitrile emissions were scaled from CO for Canadian fires, 

            the Canadian fire emissions of acrylonitrile were not implemented due to a bug in CMAQv5.5 DESID.  

          - emissions of HAPs from biogenic sources were accidentally doubled in these scripts 

          - lightning NOx was omitted

     nofire_config: build script, run script, control files, and example log files (text files) for the simulation without Canadian fires.

     post: species definitions files used to prepare ONLYHAPS and PMOXIDANTS netcdf output.

 

CMAQoutput: netcdf gridded CMAQ output for base simulation and simulation without Canadian fires (nocanfire)

     Annual average HAP concentrations (and select other species such as CO): 

          ANNUALAVG_20250502cracmm3hap_base_ONLYHAPS_2023_12US4.nc

          ANNUALAVG_20250502cracmm3hap_nocanfire_ONLYHAPS_2023_12US4.nc

     Annual average OH, O3, NO3, and PM2.5:

          ANNUALAVG_20250502cracmm3haps_base_PMOXIDANTS_2023_12US4.nc

          ANNUALAVG_20250502cracmm3haps_nocanfire_PMOXIDANTS_2023_12US4.nc

     Seasonal (Apr-Sept) average of max daily 8hr avg ozone:

          SEASAVG_APR2SEP_20250502cracmm3haps_base_2023_12US4.nc

          SEASAVG_APR2SEP_20250502cracmm3haps_nocanfire_2023_12US4.nc

     Seasonal (Apr-Sept) average of max daily 1 hour ozone: 

          SEASAVG_1hrmaxo3_APR2SEP_20250502cracmm3haps_base_2023_12US4.nc

          SEASAVG_1hrmaxo3_APR2SEP_20250502cracmm3haps_nocanfire_2023_12US4.nc

 

evaluation: output from CMAQ site compare utility by month

     baseaqs.tar: base simulation results by month

     nocanfireaqs.tar: no Canadian fire simulation results by month

     For each month:

Ozone, PM, and major HAPS: AQS_Daily_2023_12US4_* files

Select additional VOCs: AQS_Daily_VOC_2023_12US4_* files

     Canada_NAPS_VOC: intermediate files used in the evaluation of CMAQ predictions of select VOCs with NAPS observations

 

boundaryconditions: sample scripts for how to download and map GEOSCF to CMAQ-CRACMM for boundary conditions

     python_batchfall.csh: cshell batch script that calls the following file to obtain GEOSCF files in original GEOSCF species (step 1)

     2024fall_12US4_getgeoscfonly.py: gets GEOSCF files for fall (run in 2024)

     *expr: files used by aqmbc to map GEOSCF variables to CRACMM2 (also available in AQMBC on github)

     2024_12US4_geoscfBCONbyhour.ipynb: creates BCON files along 12US4 boundary in CRACMM2 species on original GEOSCF time stamps (step 2)

     2024_12US4_geoscfBCONplots.ipynb: QA check on BCON files (step 3)

     2024_12US4_geoscf_modelready.ipynb: Concatenate and time shift the BCON files so they are CMAQ-ready (step 4) 

     GRIDDESC: CMAQ input and grid description used by aqmbc

 

benefits: BenMAP and AQBAT input files, outputs, and additional documentation. Individual files detailed in the Readme.docx.

 

Public tools, data, and repositories related to this work:

CMAQ: https://doi.org/10.5281/zenodo.1079878 and https://github.com/USEPA/CMAQ

CRACMM: https://github.com/USEPA/CRACMM

AMET: https://github.com/USEPA/AMET

AQS data: https://www.epa.gov/aqs

NAPS data: https://www.canada.ca/en/environment-climate-change/services/air-pollution/monitoring-networks-data/national-air-pollution-program.html

BenMAP: https://www.epa.gov/benmap/benmap-downloads

AQBAT: https://health-infobase.canada.ca/aqbat/

AQMBC: https://barronh.github.io/aqmbc/index.html