[pam-users] We are publicly releasing KinSim, a powerful and easy-to-use free kinetics solver

[pam-users]

Dear all,

The short version: we are publicly releasing KinSim, a powerful and
easy-to-use free kinetics solver within Igor. If you are interested, keep
reading. If not, thanks for your time.

For those who keep reading:

The big picture:

As some of you know, we have been developing an Igor-based easy-to-use free
chemical kinetics simulator, named KinSim. We adopted code developed by Jim
Burkholder and Harald Stark at NOAA ten years ago, and have developed it
extensively since 2014. KinSim is easy to use, you can just type reactions
in an easy format, change initial conditions, press a few buttons, and get
a plot with the simulation results. The code is open source, so that you
can read it and edit it if appropriate. We have used KinSim for teaching in
multiple courses, and also in research (15+ published papers so far). It
similarly fast as FACSIMILE (typically used to solve the MCM), so it is
certainly applicable to complex mechanisms. It also allows to easily
include time-dependent emissions, photolysis, dilution, deposition etc.
Basically every box model that we’ve seen in atmospheric chemistry up to
tens of thousands of reactions can be solved with KinSim.

Teaching applications and paper:

We recently published a paper on the Journal of Chemical Education
describing the application to teaching, and including several simple
examples that can be used immediately (stratospheric ozone, tropospheric
ozone, nighttime chemistry, sulfate formation, SOA formation, and O2 in a
lake). The paper provides an introduction to KinSim and can be found at:

https://pubs.acs.org/doi/10.1021/acs.jchemed.9b00033

If you use KinSim in teaching, please contact Jose. I’d love to share tips,
cases, homeworks etc.

Research applications:

We have used KinSim in multiple papers simulating radical chemistry in OFRs
and SOA formation, for example these:

https://www.atmos-chem-phys.net/19/813/2019/

http://pubs.acs.org/doi/abs/10.1021/acs.est.7b02144

We ask that if you use KinSim on a paper or presentation, that you cite the
J Chem Ed paper above. We may write a paper on the research applications,
after we finish some ongoing developments.

Sharing cases:

Something that’s very very easy to do with KinSim now is to save a case
(mechanism, initial conditions, simulation parameters, as a single ITX
file) and give it to someone else (from the KinSim menu → export case, and
then your colleague goes to the KinSim menu → load case). Then your
colleague can run it immediately. We have created a library of cases, by
trying to capture the cases that have been used in publications (a few are
pending upload). They are downloadable from the link below (with the same
password for downloading KinSim, that you get when you register as a user):

https://docs.google.com/document/d/10OuUMtMGJsh90cQ3p4Y_oiKQdPRHYQnxKQr2_l62Kx0/edit

We encourage people to send us their cases for posting there, especially
(but not limited to) the ones included in published papers. We also
encourage people to include their KinSim case(s) in the Supp Info of their
published papers (most journals want researchers to share their code, and
this is an easy way to do it).

Of interest to some of you will be the chemistry within oxidation flow
reactors (OFR, also known as PAM). Zhe is writing a review paper on the
topic, and we will post the OFR chemical mechanisms that he has used on his
5 papers on the topic on the page above when the paper is submitted.

Downloading the code and registering as a user:

To download the code, we only ask that you register at the form below. We
ask that you register even if you have already been using KinSim. This
allows us to keep track of who has KinSim, which is useful for future
communication (e.g. new versions) and also to report to the US NSF, who
supported some of this development.

http://tinyurl.com/KinSim-Download

Learning how to use KinSim:

There is an online help file (top button on the KinSim panel), or directly
at:

https://docs.google.com/document/d/1PyADb1YBjtJ4-BQjnOuVn5Am1UeMbrzYS4gYROb1NUw/edit?usp=sharing


KinSim Users List and (Limited) Support

We have created an email list <kinsim-users at googlegroups.com> to share
information about KinSim. The goal is to keep it a low-traffic list. You
can sign up at the link below, and you can choose the “digest” email format
to receive fewer emails:

https://groups.google.com/d/forum/kinsim-users

We have also created a support system using FreshDesk. If you have support
questions (can’t get it to run, or results seem wrong, or you think you’ve
found a bug, or you want to suggest future developments) please email
support at kinsim.freshdesk.com>. That way everyone involved in development
will get an email at the same time, and we can organize to try to help
(within our time limitations).

Potential collaboration in the future development of KinSim:

We are working with a couple of collaborators on loaders for MCM, RACM and
similar mechanisms into KinSim. This may be ready to share within a month
or so. We are sure there will be many additional developments of interest,
and we hope that a few of you that are programming inclined could
participate in the further development of KinSim in the future. If you are
interested (now or later on), just write to us.

Thanks,

-Jose & Zhe


-- 
J.L. Jimenez; Prof., Dept. of Chem. & Biochem.; CIRES Fellow
Univ. of Colorado UCB 216; Cristol Bldg. Rm. 436; Boulder, CO 80309-0216
jose.jimenez at colorado.edu / http://cires.colorado.edu/jimenez / Scholar:
http://goo.gl/LF3G49
Grad Prog: https://goo.gl/nUKB9T Cheat Sheet: https://goo.gl/LNAugj Jobs:
https://goo.gl/hF5D30

-- 
J.L. Jimenez; Prof., Dept. of Chem. & Biochem.; CIRES Fellow
Univ. of Colorado UCB 216; Cristol Bldg. Rm. 436; Boulder, CO 80309-0216
jose.jimenez at colorado.edu / http://cires.colorado.edu/jimenez / Scholar:
http://goo.gl/LF3G49
Grad Prog: https://goo.gl/nUKB9T Cheat Sheet: https://goo.gl/LNAugj Jobs:
https://goo.gl/hF5D30
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https://asp.reflexion.net/history-detail?hID=35311613082
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