Focused Isoprene Experiment at the California Institute of Technology (FIXCIT) photochemical box modeling

These experimental data and Matlab computer code were used to model the atmospheric isoprene chemistry observed during the Focused Isoprene Experiment at the Caltech environmental chamber, called FIXCIT. The model using five different chemical mechanisms and observations were compared for OH, hydroperoxyl (HO2), and isoprene oxidation products that occur at different stages of the oxidation sequence – isoprene hydroxyhydroperoxide (ISOPOOH), isoprene epoxydiol (IEPOX), hydroxyacetone, formaldehyde, methacrolein, and methyl vinyl ketone. The model code is in the F0AM format (Wolfe, G. M., Marvin, M. R., Roberts, S. J., Travis, K. R., & Liao, J. (2016). The Framework for 0‐D Atmospheric Modeling (F0AM) v3.1., Geoscientific Model Development, 9, 3309–3319. https://doi.org/10.5194/gmd‐9‐3309‐2016), the chemical files for the five model mechanisms, and the FIXCIT input merged file used to initialize the model. The data are in Matlab format.

To run the model, run FIX_multiruns_XXX_YYY.mat. It will call the F0AM model input program FIX_F0AM_20240529_ivard24hl0wvar_Jtest2.m. One or the other of these two programs calls the programs FIX_events_v3_2.m, FFIX_experiment_times_isop_v2.m, FIX_replace_initvals.m, and FIX_CombineInterpData_v4.m.

The first step is to change the directories, both input and output, in these programs to the ones being used on your computer. Second, check that the file names and dates are consistent in the FIX_multiruns_XXX_YYY.m file. Third, check that the model switches, such as ModelOptions, and tgauss and kdil in Met, are set to the desired values. Then start FIX_multiruns_XXX_YYY.m.

To replicate the figures in the manuscript and its supplement, change directories in FIX_daily_plots_v20240529_1stmanuscript_varwall.m and run it. It will call FIX_conc_compare_4dailyplots_v5.m and FIX_more_stats_v9.m. The result will be the daily comparison plots and the heatmaps in the manuscript.