Introducing programming to undergraduate chemists: and the tools we’ve developed to help them
the
pythoninchemistry
project.
PYCON UK
— 2018/09/16
DOI:
10.6084/m9.figshare.7092167
Andrew R. McCluskey
PhD Student/Tutor/Demonstrator @ Uni Bath/Diamond Light Source
arm61@bath.ac.uk
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arm61.github.io/talks/pycon18
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chemists aren't usually taught to program
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chemists do data analysis
Source: Google Scholar searches
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many chemists use python
Source: Google Scholar searches
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pythoninchemistry project
Started by
Ben Morgan
and
Fiona Dickinson
Introducing python to chemistry labs and tutorials
Open-source chemistry teaching
tools
The
pythoninchemistry.org
webpage
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pythoninlabs
Students used to have one Excel data analysis lab
Now
two
python labs in each of first and second year
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pythoninlabs
In the process of open-sourcing all labs
Available will be at
pythoninchemistry.org
Journal of Open Source Education
paper coming soon
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pythonintutorials
Physical chemistry is often
mathematically intensive
Programming requires the educator to be explicit about the mathematical process
Jupyter notebooks
provide an user-friendly environment
Students can access the notebook online via
MyBinder
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example
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informal feedback
Students appear anecdotally engaged during tutorials
Tutorial student attached modified notebooks to help emails
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open source tools
Bath Chemistry uniquely has dedicated computional chemistry labs
Needed a tool to introduce
molecular dynamics
/
Monte Carlo
simulation
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time for some chemistry
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chemistry background
Molecular dynamics
is a technique used to computationally probe the structure of a material
This involves using classical motion equations to simulate atoms at a given temperature
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pylj
Open-source, python library to engage students in atomistic simulation
MIT Licence; source code available on
GitHub
Paper in
Journal of Open-Source Education
, 1(2), 19. DOI: 10.21105/jose.00019
Bath physics PDRA
forked
it to make pysing
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Try pylj out
Molecular dynamics -
pythoninchemistry.org/pylj/md
Monte Carlo -
pythoninchemistry.org/pylj/mc
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pythoninchemistry
webpages
Blogs
on basic python skills
Applications
of python in chemical research and teaching
An
information portal
for all aspects of the project
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acknowledgements
Benjamin J. Morgan
Fiona Dickinson
Ian Thompson
James Grant
Karen J. Edler
Stephen C. Parker
PYCON UK
Tania Allard
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Sadie, my dog