These scripts are provided for documentation and reference. They are not executable as they require the full CMAQ 4-D output to sample (many TB of data, not provided). Some intermediate outputs of these scripts are provided as csv files. All jupyter notebooks (.ipynb) are also available in html format.

Contact: Havala Pye (pye.havala@epa.gov)
These files associated with:
Pye, H. O. T., Xu, L., Henderson, B. H., Pagonis, D., Campuzano-Jost, P., Guo, H., Jimenez, J. L., Allen, C., Skipper, T. N., Halliday, H. S., Murphy, B. N., D’Ambro, E. L., Wennberg, P. O., Place, B. K., Wiser, F. C., McNeill, V. F., Apel, E. C., Blake, D. R., Coggon, M. M., Crounse, J. D., Gilman, J. B., Gkatzelis, G. I., Hanisco, T. F., Huey, L. G., Katich, J. M., Lamplugh, A., Lindaas, J., Peischl, J., St Clair, J. M., Warneke, C., Wolfe, G. M., and Womack, C.: Evolution of Reactive Organic Compounds and Their Potential Health Risk in Wildfire Smoke, Environ. Sci. Technol., https://doi.org/10.1021/acs.est.4c06187, 2024.

1. CMAQ Code and Main Log Files (see https://github.com/USEPA/CMAQ for guidance on CMAQ)
   CCTMbase3/CCTM/scripts:              Base CMAQ simulation code, contains:
        2019_12US1_81716.txt:           CMAQ simulation main log file
        bldit*.csh:                     CMAQ build scripts
        run_cctm_cracmm_2019_12US1.csh: CMAQ simulation run script
        BLD_CCTM_v54_intel21.4:         CMAQ fortran code and associated files

   CCTMsens3/CCTM/scripts:              Sensitivity CMAQ simulation (adjusted emissions) code, contains:
        2019_12US1_81694.txt:           CMAQ simulation main log file
        bldit*.csh:                     CMAQ build scripts
        run_cctm_cracmm_2019_12US1.csh: CMAQ simulation run script
        BLD_CCTM_v54_intel21.4:         CMAQ fortran code and associated files

2. analysis/
   2024_firexpairv3_hotp_20240304_base3.ipynb:  Aggregates and pairs FIREX-AQ data with base CMAQ simulation.
   2024_firexpairv3_hotp_20240304_sens3.ipynb:  Aggregates and pairs FIREX-AQ data with sensitivity CMAQ simulation.
   definitions20240617.csv:                     Describes which measurements are paired with which model predictions, input to above 2 scripts.
   2024_firexpair_AMSOC.ipnyb:                  Calculates AMS OC on raw AMS time resolution and aggregates that OC and OA to 1 minute values.
   2024_firex_obscuration_GG24update.ipnyb:     Code to gather data for observed species (toxicity values, etc).
   FigureS1_mainanalysiswAMS.ipynb:             Main analysis script, includes options to use mass, mole (ppb), or toxicity units. 
                                                Processes both base and sensitivity simulation based on variable settings. 
                                                Creates Figure S3 panels.

3. figures/ 
   FigureS_CO_gridded_and_vert_profile.*:       Code to make vertical profile and gridded CO plots in Figure S1-S2 (jupyter notebook).
   TOCart.ipynb:                                Table of Contents Figure jupyter notebook
   Figure1/                     		Figure 1 jupyter notebook 
   Figure2/                                     Figure 2 jupyter notebook 
   Figure3/                                     Figure 3 jupyter notebook 
   Figure4/                                     Figure 4 jupyter notebook 

4. data/ (files output from observation-model data pairing script at 1 minute resolution, pkl version used in FigureS1_mainanalysiswAMS.ipnyb script)
   20240617obsv3v3_firexaq_AMS_byminute.csv:         AMS OA and OC data at 1 minute aggregation, output of 2024_firexpair_AMSOC.ipnyb
   20240304base3v3_firexaq_cmaq_paired_byminute.csv: all other observations paired with base model simulation, output of 2024_firexpairv3_hotp_20240304_base3.ipynb
   20240304sens3v3_firexaq_cmaq_paired_byminute.csv: all other observations paired with sensitivity model simulation, output of 2024_firexpairv3_hotp_20240304_sens3.ipynb
   20240304base3v3_firexaq_cmaq_paired_byminute_noobs.csv: base model simulation along flight tracks, output of 2024_firexpairv3_hotp_20240304_base3.ipynb (excluding observations)
   20240304sens3v3_firexaq_cmaq_paired_byminute_noobs.csv: sensitivity model simulation along flight tracks, output of 2024_firexpairv3_hotp_20240304_sens3.ipynb (excluding observations)


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Internal archive location of CMAQ code
/asm2/MOD3DEV/has/2022firex/20240227base3/CCTMbase3.tar
/asm2/MOD3DEV/has/2022firex/20240227sens3/CCTMsens3.tar