﻿Model code for "Constraining nucleation, condensation, and chemistry in oxidation flow reactors using size-distribution measurements and aerosol microphysical modelling"

The following code is for the TOMAS-VBS model used in Hodshire et al. (2018) (title given above). The model is written in FORTRAN and is set up to be run with a python wrapper.  A sample python script as well as the necessary data files to run the model for an example case is included as well.

For any questions, please contact Anna Hodshire at hodshire@rams.colostate.edu or Jeffrey Pierce at jeffrey.pierce@colostate.edu.

File inventory:

BB192SM9.COM
BT263box.COM
sizecode.COM (Contains information about number of aerosol bins, VBS bins, species, and associated parameters.)
box.f (Main run file for TOMAS.)
smpsAmbInit_8154.npz (Initial SMPS data for the example case.)
smpsChamber_8154.npz (Final SMPS data for the example run.)
initSIVOC_conds_8154.npz (Initial S/IVOC data.)
makefile
so4cond.f
soacond.f
speciesmap.f
storenm.f
tmcond.f
waternacl.f
waterso4.f
aerodens.f
aerodiag.f
array.f
boxchem.f
boxinit.f
dmdt_int.f
eznh3eqm.f
ezwatereqm.f
gasdiff.f
getCondSink.f
getlen.f
getMassSink.f
hetChem.f
initbounds.f
loginit.f
mnfix.f
multicoag.f
report.f
scalemom.f
readme.txt (Readme information)
smpsAmbInit_p8154_aug12.csv (.csv version of smpsAmbInit_p8154_aug12.npz.)
smpsChamber_p8154_aug12.csv (.csv version of smpsChamber_p8154_aug12.npz)
initSIVOC_conds_p8154.csv (.csv version of initSIVOC_conds_p8154.npz)
runArray_p8154days.py (Example python script for running TOMAS.)

Included is an example python script and extra data files to run the 0.82 days of eq. aging as described in Hodshire et al. (2018). 

The .f and .COM files are Fortran files. The .npz files are example data files to be used with the example runArray_p8154days.py python script. If the python is not used, the .csv files replace the .npz files. The initial variables in the initSIVOC_conds_p8154.csv file are as follows (in order by row):

monoterpene concentration (in ppb);
relative humidity (as a fraction); 
temperature (in K); 
residence time of the oxidation flow reactor (in seconds); 
OH exposure (in molec cm-3 s); 
S/IVOC concentration (in ug/m3)

The smpsAmbInit_p8154_aug12.csv and smpsChamber_p8154_aug12.csv files have the SMPS for the initial ambient and final chamber data points. Each row corresponds to one size bin. 

All data was collected at the BEACHON-RoMBAS and GoAmazon2014/15 field campaigns. For further details on all field campaign data, see Palm et al. (2016, 2018). BEACHON-RoMBAS data is available from http://manitou.acom.ucar.edu/. GoAmazon data is available from https://www.arm.gov/research/campaigns/amf2014goamazon. 

In order to run TOMAS,first type 'makeclean', then 'make box.exe'in the command line. (The 'make box.exe' command will create the executable file, box.exe.) Once box.exe successfully compiles, the runArray_p8154days.py file is intended as a python script to run TOMAS. runArray_p8154days.py has been set up to be submitted through a shell (.sh) script using 16 processors; this can be altered to only run on one processor. 

Date of last alteration before submission: 8/6/18 

Citation of the paper (at the time of review and creation of this file):  

Hodshire, A. L., Palm, B. B., Alexander, M. L., Bian, Q., Campuzano-Jost, P., Cross, E. S., Day, D. A., de Sá, S. S., Guenther, A. B., Hansel, A., Hunter, J. F., Jud, W., Karl, T., Kim, S., Kroll, J. H., Park, J.-H., Peng, Z., Seco, R., Smith, J. N., Jimenez, J. L., and Pierce, J. R.: Constraining nucleation, condensation, and chemistry in oxidation flow reactors using size-distribution measurements and aerosol microphysical modelling, Atmos. Chem. Phys. Discuss., https://doi.org/10.5194/acp-2018-223, in review, 2018.

Further citations: 

Palm, B. B., Campuzano-Jost, P., Ortega, A. M., Day, D. A., Kaser, L., Jud, W., Karl, T., Hansel, A., Hunter, J. F., Cross, E. S., Kroll, J. H., Peng, Z., Brune, W. H. and Jimenez, J. L.: In situ secondary organic aerosol formation from ambient pine forest air using an oxidation flow reactor, Atmos. Chem. Phys., 16(5), 2943-2970, doi:10.5194/acp-16-2943-2016, 2016.

Palm, B. B., De Sá, S. S., Day, D. A., Campuzano-Jost, P., Hu, W., Seco, R., Sjostedt, S. J., Park, J.-H., Guenther, A. B., Kim, S., Brito, J., Wurm, F., Artaxo, P., Thalman, R., Wang, J., Yee, L. D., Wernis, R., Isaacman-Vanwertz, G., Goldstein, A. H., Liu, Y., Springston, S. R., Souza, R., Newburn, M. K., Alexander, M. L., Martin, S. T. and Jimenez, J. L.: Secondary organic aerosol formation from ambient air in an oxidation flow reactor in central Amazonia, Atmos. Chem. Phys, 185194, 467-493, doi:10.5194/acp-18-467-2018, 2018.




