DOI: 10.5281/zenodo.5016757
title: DMS multiphase chemistry mechanism and model results

description: Open Access DMS multiphase chemistry mechanism


This repository contains the complete DMS multiphase chemistry mechanism developed and applied in Wollesen de Jonge et al. (2021). The DMS multiphase mechanism is located in the folder named DMS_chemistry. The executable mechanism consist of a number of Fortran f90 files, which were generated with the kinetic pre-processor (KPP) (Damian et al., 2002) using the KPP input file DMSchem.def and DMSchem.kpp file. Both the executable Fortran code and the KPP input files are stored in the subfolder DMS_multiphase_chem. The DMSchem.def file list all reactions and reaction rates in the DMS multiphase chemistry mechanism similar to the supplementary Tables S1 in Wollesen de Jonge et al. (2021).  The executable DMS multiphase chemistry mechanism consist of the following Fortran f90 files:


DMSchem_Main.f90


DMSchem_Function.f90


DMSchem_Initialize.f90


DMSchem_Integrator.f90


DMSchem_Jacobian.f90


DMSchem_JacobianSP.f90


DMSchem_LinearAlgebra.f90


DMSchem_mex_Fun.f90


DMSchem_mex_Jac_SP.f90


DMSchem_Model.f90


DMSchem_Monitor.f90


DMSchem_Parameters.f90


DMSchem_Precision.f90


DMSchem_Rates.f90


DMSchem_Util.f90


DMSchem_Global.f90


These f90-files can be linked and compiled with gfortran using the provided Makefile.  


The subfolder photolysis contain vectors with absorption cross sections (cs), quantum yields (qy) and the spectral actinic flux of the UV-lamps in the AURA chamber.


A simplified model setup is provided to illustrate how the DMS-multiphase chemistry routines can be run. The DMS multiphase chemistry mechanism is called and run from a program named main.f90.


In the main.f90 program the temperature, humidity, pressure and initial concentrations of all gas and aqueous phase species in the DMS multiphase chemistry are declared.


After this the main program call the subroutines getKVALUES and getJVALUES from the Fortran module reaction_rates.f90.



	
getKVALUES calculates a number of complex reaction rates (mainly pressure dependent three-body reactions).
	
getJVALUES calculates all gas phase photolysis rates in the DMS multiphase chemistry mechanism using the absorption cross sections, quantum yields and the spectral actinic flux files stored in the photolysis subfolder



The main.f90 program saves the concentration of all species in a file called conc.dat, the time step vector (time.dat) and all species names in SPC_NAMES.dat.


A short Matlab script called plot_concentrations.m is provided to illustrate how the concentrations of all species listed in SPC_NAMES.dat can be plotted along the saved time vector.


The simplified model (only used for demonstration purpose) can be compiled and executed with GFortran using the provided Makefile by typing the following commands in the command line (terminal):


make


./main.exe


 


Stored model results presented in Wollesen de Jonge et al. (2021)


We have saved all model data from each simulated smog chamber experiment and atmospheric relevant base case and sensitivity run presented in Wollesen de Jonge et al. (2021) in the form of 'OutputTable' files.


The columns in the tables related to the DMS smog chamber experiments are classified as follows:



	
1 time [h] (simulation time starting from -1 h hour and ending at 15 h, time = 0 h is defined as the time when the UV-lights were turned on in the AURA smog chamber).
	
2 PN_1.7nm [#/cm^3] (Total particle number concentration of particles 1.7 nm in diameter).
	
3 PN_2.5nm [#/cm^3] (Total particle number concentration of particles 2.5 nm in diameter)
	
4 PN_10nm [#/cm^3] (Total particle number concentration of particles 10 nm in diameter)
	
5 PM_SO4 [μg/m^3] (Sulfate particle mass)
	
6 PM_CH3SO3 [μg/m^3] (Methane sulfonic acid (MSA) particle mass)
	
7 PM_NH4 [μg/m^3] (Ammonium particle mass)
	
8 DMS [ppbv] (Dimethyl sulfide gas phase concentration)
	
9 O3 [ppbv] (Ozone gas phase concentration)
	
10 PV [μm^3/cm^3] (Total particle volume concentration)
	
11 PM [μg/m^3] (Total particle mass concentration)
	
12 NH3 [ppbv] (Ammonia gas phase concentration)
	
13 MSIA [#/cm^3] (Methane sulphinic acid gas phase concentration)
	
14 SO2 [ppbv] (Sulfur dioxide gas phase concentration)
	
15 DMSO [#/cm^3] (Dimethyl sulfoxide gas phase concentration)
	
16 HPMTF [#/cm^3] (Hydroperoxymethyl thioformate  gas phase concentration)
	
17 H2O2 [ppbv] (Hydrogen peroxide gas phase concentration)
	
18 HO2 [#/cm^3] (Hydroperoxyl radical gas phase concentration)
	
19 OH [#/cm^3] (Hydroxyl radical gas phase concentration)
	
20-219 dN/dlogDp [#/m^3] (Particle number size distributions)



 


The header line, rows 20-219, give the corresponding aerosol particle geometric mean diameters (Dp) in unit m, which were used to represent the modelled particle number size distributions (dN/dlogDp). The gas-phase concentrations given in unit ppb are given at the standard temperature and pressure of 273.15 K and 1E5 Pa.


 


The columns in the tables related to the atmospheric relevant runs are classified as follows:



	
1 time [h] ] (simulation time).
	
2 DMS [#/cm^3]  (Dimethyl sulfide gas phase concentration)
	
3 H2SO4 [#/cm^3] (Sulfuric acid gas phase concentration)
	
4 MSA [#/cm^3] (Methane sulfonic acid gas phase concentration)
	
5 HPMTF [#/cm^3] (Hydroperoxymethyl thioformate  gas phase concentration)
	
6 MSIA [#/cm^3] (Methane sulphinic acid gas phase concentration)
	
7 DMSO [#/cm^3] (Dimethyl sulfoxide gas phase concentration)
	
8 UVflux [] (Relative UV light intensity, i.e. UVflux = 1 maximum sunlight, UVflux = 0 no sunlight)
	
9 sinkCL [#/cm^3/s] (DMS loss rate by reactions with Cl radicals)
	
10 sinkOHabs [#/cm^3/s] (DMS loss rate by reactions with OH via the abstraction pathway)
	
11 sinkBrO [#/cm^3/s] (DMS loss rate by reactions with BrO radicals)
	
12 sinkOHadd [#/cm^3/s] (DMS loss rate by reactions with OH via the addition pathway)
	
13 sinkNO3 [#/cm^3/s] (DMS loss rate by reactions with NO3 radicals)
	
14 sinkO3aq [#/cm^3/s] (DMS loss rate by reactions with O3 in the aqueous phase)
	
15 PM_CH3SO3 [μg/m^3] (Methane sulfonic acid (MSA) particle mass)
	
16 PM_SO4 [μg/m^3] (Sulfate particle mass)
	
17 PM_NH4 [μg/m^3] (Ammonium particle mass)
	
18 PM_NO3 [μg/m^3] (Nitrate particle mass)
	
19-218 dN/dlogDp [#/m^3]. (Particle number size distributions)



 


In this case, the header line, rows 19-218, give the corresponding geometric mean diameters in unit m.


The modelled smog chamber experiments result files were named according to the date when the DMS experiments were performed:


Exp. DMS1 - 20180405


Exp. DMS2 - 20180519


Exp. DMS3 - 20180521


Exp. DMS4 - 20180523


Exp. DMS5 - 20180526


Exp. DMS6 - 20190226


Exp. DMS7 - 20190301


 


Details for each output table are given here: 


OutputTable_AtmMain: Base case atmospheric model run


OutputTable_lowWindAtm: Atmospheric model run with 2 m/s wind speed


OutputTable_PolAtm: Atmospheric model run with higher O3 and NOx concentrations


OutputTable_woAqAtm: Atmospheric model simulation without aqueous phase chemistry reactions


OutputTable_woCloudAtm: Atmospheric model simulation without clouds


 


OutputTable20180405_1: Base case smog chamber simulation experiment DMS1


OutputTable20180519_1: Base case smog chamber simulation experiment DMS2


OutputTable20180521_1: Base case smog chamber simulation experiment DMS3


OutputTable20180523_1: Base case smog chamber simulation experiment DMS4


OutputTable20180526_1: Base case smog chamber simulation experiment DMS5


OutputTable20190226_1: Base case smog chamber simulation experiment DMS6


OutputTable20190301_1: Base case smog chamber simulation experiment DMS7


 


 OutputTable20180519_2: MSIA+OH rate analogues to Yin et al, exp. DMS2


 OutputTable20180519_3: MSIA+OH rate analogues to Lucas & Prinn et al. , exp. DMS2


 OutputTable20180519_4: MSIA+OH rate set to 0, exp. DMS2


 OutputTable20180519_5: No gas partitioning to the liquid water film on the chamber walls, exp. DMS2


 OutputTable20180519_6: MCM gas-phase chem. setup, exp. DMS2


 OutputTable20180519_9: CH3SOO isomerization set to 0, exp. DMS2


 OutputTable20180519_10: HPMTF pathway set to 0, exp. DMS2


 


 OutputTable20190226_2: HPMTF pathway analogues to Veres et al. , exp. DMS6


 OutputTable20190226_3: HPMTF pathway analogues to Yin et al. , exp. DMS6


 OutputTable20190226_4: HPMTF patway set to 0 , exp. DMS6


 OutputTable20190226_5: No gas partitioning to the liquid water film on the chamber walls , exp. DMS6


 OutputTable20190226_6: CH3SOO isomerization set to 0 , exp. DMS6


 OutputTable20190226_7: MSIA+OH rate set to 0 , exp. DMS6


 


 OutputTable20180405_12: O3 wall accommodation coefficient = 1E-8, exp. DMS1


 OutputTable20180519_12: O3 wall accommodation coefficient = 1E-8, exp. DMS2


 OutputTable20180521_12: O3 wall accommodation coefficient = 1E-8, exp. DMS3


 OutputTable20180523_12: O3 wall accommodation coefficient = 1E-8, exp. DMS4


 OutputTable20180526_12: O3 wall accommodation coefficient = 1E-8, exp. DMS5


 OutputTable20190226_12: O3 wall accommodation coefficient = 1E-8, exp. DMS6


 OutputTable20190301_12: O3 wall accommodation coefficient = 1E-8, exp. DMS7


 


 OutputTable20180405_13: O3 wall accommodation coefficient = 1E-6, exp. DMS1


 OutputTable20180519_13: O3 wall accommodation coefficient = 1E-6, exp. DMS2


 OutputTable20180521_13: O3 wall accommodation coefficient = 1E-6, exp. DMS3


 OutputTable20180523_13: O3 wall accommodation coefficient = 1E-6, exp. DMS4


 OutputTable20180526_13: O3 wall accommodation coefficient = 1E-6, exp. DMS5


 OutputTable20190226_13: O3 wall accommodation coefficient = 1E-6, exp. DMS6


 OutputTable20190301_13: O3 wall accommodation coefficient = 1E-6, exp. DMS7


 


 OutputTable20180405_14: SO2 wall accommodation coefficient = 1E-8, exp. DMS1


 OutputTable20180519_14: SO2 wall accommodation coefficient = 1E-8, exp. DMS2


 OutputTable20180521_14: SO2 wall accommodation coefficient = 1E-8, exp. DMS3


 OutputTable20180523_14: SO2 wall accommodation coefficient = 1E-8, exp. DMS4


 OutputTable20180526_14: SO2 wall accommodation coefficient = 1E-8, exp. DMS5


 OutputTable20190226_14: SO2 wall accommodation coefficient = 1E-8, exp. DMS6


 OutputTable20190301_14: SO2 wall accommodation coefficient = 1E-8, exp. DMS7


 


 OutputTable20180405_15: SO2 wall accommodation coefficient = 1E-6, exp. DMS1


 OutputTable20180519_15: SO2 wall accommodation coefficient = 1E-6, exp. DMS2


 OutputTable20180521_15: SO2 wall accommodation coefficient = 1E-6, exp. DMS3


 OutputTable20180523_15: SO2 wall accommodation coefficient = 1E-6, exp. DMS4


 OutputTable20180526_15: SO2 wall accommodation coefficient = 1E-6, exp. DMS5


 OutputTable20190226_15: SO2 wall accommodation coefficient = 1E-6, exp. DMS6


 OutputTable20190301_15: SO2 wall accommodation coefficient = 1E-6, exp. DMS7


 


 OutputTable20180405_16: DMS wall accommodation coefficient = 1E-8, exp. DMS1


 OutputTable20180519_16: DMS wall accommodation coefficient = 1E-8, exp. DMS2


 OutputTable20180521_16: DMS wall accommodation coefficient = 1E-8, exp. DMS3


 OutputTable20180523_16: DMS wall accommodation coefficient = 1E-8, exp. DMS4


 OutputTable20180526_16: DMS wall accommodation coefficient = 1E-8, exp. DMS5


 OutputTable20190226_16: DMS wall accommodation coefficient = 1E-8, exp. DMS6


 OutputTable20190301_16: DMS wall accommodation coefficient = 1E-8, exp. DMS7


 


 OutputTable20180405_17: DMS wall accommodation coefficient = 1E-6, exp. DMS1


 OutputTable20180519_17: DMS wall accommodation coefficient = 1E-6, exp. DMS2


 OutputTable20180521_17: DMS wall accommodation coefficient = 1E-6, exp. DMS3


 OutputTable20180523_17: DMS wall accommodation coefficient = 1E-6, exp. DMS4


 OutputTable20180526_17: DMS wall accommodation coefficient = 1E-6, exp. DMS5


 OutputTable20190226_17: DMS wall accommodation coefficient = 1E-6, exp. DMS6


 OutputTable20190301_17: DMS wall accommodation coefficient = 1E-6, exp. DMS7


 


 OutputTable20180405_18: DMSO, DMSO2, MSIA and HPMTF wall accommodation coefficient = 1E-6, exp. DMS1


 OutputTable20180519_18: DMSO, DMSO2, MSIA and HPMTF wall accommodation coefficient = 1E-6, exp. DMS2


 OutputTable20180521_18: DMSO, DMSO2, MSIA and HPMTF wall accommodation coefficient = 1E-6, exp. DMS3


 OutputTable20180523_18: DMSO, DMSO2, MSIA and HPMTF wall accommodation coefficient = 1E-6, exp. DMS4


 OutputTable20180526_18: DMSO, DMSO2, MSIA and HPMTF wall accommodation coefficient = 1E-6, exp. DMS5


 OutputTable20190226_18: DMSO, DMSO2, MSIA and HPMTF wall accommodation coefficient = 1E-6, exp. DMS6


 OutputTable20190301_18: DMSO, DMSO2, MSIA and HPMTF wall accommodation coefficient = 1E-6, exp. DMS7


 


 OutputTable20180405_19: DMSO, DMSO2, MSIA and HPMTF wall accommodation coefficient = 1E-4, exp. DMS1


 OutputTable20180519_19: DMSO, DMSO2, MSIA and HPMTF wall accommodation coefficient = 1E-4, exp. DMS2


 OutputTable20180521_19: DMSO, DMSO2, MSIA and HPMTF wall accommodation coefficient = 1E-4, exp. DMS3


 OutputTable20180523_19: DMSO, DMSO2, MSIA and HPMTF wall accommodation coefficient = 1E-4, exp. DMS4


 OutputTable20180526_19: DMSO, DMSO2, MSIA and HPMTF wall accommodation coefficient = 1E-4, exp. DMS5


 OutputTable20190226_19: DMSO, DMSO2, MSIA and HPMTF wall accommodation coefficient = 1E-4, exp. DMS6


 OutputTable20190301_19: DMSO, DMSO2, MSIA and HPMTF wall accommodation coefficient = 1E-4, exp. DMS7


 


 OutputTable20180519_20: Liquid water content on walls (LWC wall) = 0.3 mg/m^3, exp. DMS2


 OutputTable20190226_20: Liquid water content on walls (LWC wall) = 1.5 g/m^3, exp. DMS6


 OutputTable20190301_20: Liquid water content on walls (LWC wall) = 15 g/m^3, exp. DMS7


 


 OutputTable20180519_21: Liquid water content on walls (LWC wall) = 30 mg/m^3, exp. DMS2


 OutputTable20190226_21: Liquid water content on walls (LWC wall) = 150 g/m^3, exp. DMS6


 OutputTable20190301_21: Liquid water content on walls (LWC wall) = 1000 g/m^3, exp. DMS7


 


References


Wollesen de Jonge, R., Elm, J., Rosati, B., Christiansen, S., Hyttinen, N., Lüdemann, D., Bilde, M., and Roldin, P.: Secondary aerosol formation from dimethyl sulfide – improved mechanistic understanding based on smog chamber experiments and modelling, Atmos. Chem. Phys. https://doi.org/10.5194/acp-2020-1324 (2021)   


Damian, V., Sandu, A., Damian, M., Potra, F., and Carmichael, G. R.: The kinetic preprocessor KPP-a software environment for solving chemical kinetics, Comput. Chem. Eng., 26, 1567–1579, https://doi.org/10.1016/S0098-1354(02)00128-X, 2002.