symmy596 / advanced_practical_chemistry_teaching

University of Bath third year advanced practical chemistry teaching material - 2018

Hi there 👋

My name is Adam Symington, a scientist and programmer. I am the data science lead at Fraym. I am own and build the PythonMaps project, a small data visualisation project aimed at showing off the power of Python programming in geospatial data visulationsation. During my academic career I used ab initio and classical simulation techniques to predict and analyse the properties batteries, fuel cells, catalysts and nuclear fuel. In addition to research, I have taught several undergraduate and postgraduate courses in the Department of Chemistry at the University of Bath, introducing students to Python programming and it's application in the chemical sciences.

Where: Bristol / Belfast / Washington
Work: Fraym
Contact: [email protected]
Website: https://www.pythonmaps.com
Twitter: https://twitter.com/PythonMaps
linkedin: https://www.linkedin.com/in/adam-symington/

advanced_practical_chemistry_teaching's Issues

Rewrite course instructions

check if we can use anaconda 3

Strip away parts of Polypy to leave the code applicable to this lab course

lesson plan

right @symmy596, fill the lesson plan with what you think should happen during it and then we can determine learning objectives and plan better.

Paths

Better explanation of Paths needed

Write the intro to md notebook

This probably need to wait until issue #1 has been completed.

Update README

README.md needs to be updated to provide more information on the repository.

clean up

What are you thoughts on pulling the individual weeks out of the course directory now that there are no other top level directories?

Determine what the intro to md should cover

develop analysis notebooks

Get current project stuff on repo

Write MSD / Arhenius tutorials

Second pass at intro to md

@arm61 to make second pass at the intro to md

include programming methodology stuff

error in md equation

Update the lesson plan

Update the lesson plan for week 1 and comment on weeks 2-4

Week 1 assessment

Steve thinks there should be some form of assessment for week 1. In his experience students can fight back a bit if they are working on something that ultimately will not have any impact on their grade.

My thoughts - Could they write a 1 page method covering MD based purely on the week 1 pylj tutorial?

Bug in MSD

Bug in MSD relating to the final diffusion coefficient

Documentation for defect.py

Defect.py works but will be hard to use without documentation.

The output function needs to be rewritten to only add the potential model parameters that are needed. At the moment it is hard coded to output all atoms

Create METADISE input file for CaF2 and write a guide for tweaking this file.

licensing

does the fact that there are dlpoly exes in this repo have an effect on the use of an MIT license?

Contact Claire re: lectures

Write week 1 manual

Logically I think this is on you Andrew

remove introductions

install conda

Need to add an explanation for the building of a conda env and pip install the requirements

currently the requirements are

pip

pylj

conda

nb_conda

Memory

Large history files fill up the individual memory allowances

Scipy

For some reason when creating the envoiroment for week 1 scipy needs to be installed

conda install -c anaconda scipy

Testing

Weeks 1, 2, 3 and 4 need to be tested.
I will test week 1 and Andrew can test 2,3 and 4.

If time is an issue we can get a student to have a look. By design there is gradually less help as weeks 2, 3 and 4 go by.

I am curious about how feasible running the subprocesses within the notebook is.

quick function for defects

made a quick function for adding defects to config

Write manual for weeks 2,3 and 4

3D LJ

Steve has a tutorial for Lenard Jones particles in 3D using DL_POLY. Can it be factored in or too much effort?
Find and upload