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in response to Jed Brown's comments
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moved Eurochamp reference to acknowledgements and cited Sundials
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simonom authored Apr 8, 2020
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Expand Up @@ -44,9 +44,9 @@ PyCHAM (CHemistry with Aerosol Microphysics in Python) is an open-access 0-D box

With air quality and climate models increasingly important to guiding sustainable societies, the accuracy of simulations must suffice [@Tong:2019]. However, research shows that the simulated aerosol effects in these models provides a relatively high amount of uncertainty [@Johnson:2018]. The combination of box models like PyCHAM with aerosol chamber measurements to better constrain aerosol processes is therefore necessary to ultimately improve societal sustainability.

Funding for model development has been provided by the EUROCHAMP-2020 research project [@EUROCHAMP:2020]. At the time of writing, PyCHAM is being used to investigate the autoxidation of organic vapours in the atmosphere. The autoxidation process has recently been discovered to play a significant role in the formation of airbourne particulates [@Ehn:2014], however its exact chemical mechanism is yet to be elucidated. Through comparison of chamber measurements with PyCHAM outputs using various mechanism possibilities, a constrained autoxidation chemical scheme is being generated.
At the time of writing, PyCHAM is being used to investigate the autoxidation of organic vapours in the atmosphere. The autoxidation process has recently been discovered to play a significant role in the formation of airbourne particulates [@Ehn:2014], however its exact chemical mechanism is yet to be elucidated. Through comparison of chamber measurements with PyCHAM outputs using various mechanism possibilities, a constrained autoxidation chemical scheme is being generated.

The model employs non-equilibrium equations to simulate the known processes occurring in aerosol chambers. At its core is integration of ordinary differential equations (ODEs) for gas-phase photochemistry and gas partitioning to particles and walls. Here, the CVode function of the Assimulo package [@Andersson:2015] for ODE solvers is called on, using the backward differentiation formula, which studies have shown is most reliable for solution of these equations [@Jacobson:2005]. The general equation for chemical reactions is [@Jacobson:2005]:
The model employs non-equilibrium equations to simulate the known processes occurring in aerosol chambers. At its core is integration of ordinary differential equations (ODEs) for gas-phase photochemistry and gas partitioning to particles and walls. Here, the CVode function of the Assimulo package [@Andersson:2015] for ODE solvers is called on, using the backward differentiation formula of the Sundials solvers [@hindmarsh:2005sundials], which studies have shown is most reliable for solution of these equations [@Jacobson:2005]. The general equation for chemical reactions is [@Jacobson:2005]:

$$\frac{d[i_{g}]}{dt} = \pm i_{s}k_{n}[a_{g}]^{a_{s}}[b_{g}]^{b_{s}},
$$
Expand All @@ -73,6 +73,7 @@ Several variables change between different aerosol chambers and different experi

# Acknowledgements

Funding has been provided by the EUROCHAMP-2020 research project [@EUROCHAMP:2020].
This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 730997 and the National Centre for Atmospheric Science.

# References

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