Rather than having a job fail and have to look into why, this should include a style linter job and a compilation job.

The lewis wahnstrom model is a simple system used to model the behavior of orthoterphenyl. This is going to be very similar to the types of analysis I am performing, and should be very useful as a comparison.

Getting the energy of each crystal structure and the packing fraction as a way of comparing the validity of using packing fraction as a proxy for free energy.

Additionally it shouldn't hurt to include my updated results from the packing.

While #54 introduced backlinks to the bibliography, the links are not styled particularly clearly. This should format them in a way which is clear and readable. Also making note that it is a link.

There is a lot more that needs to be written in the recommendations for computational reproducibility, taking information from the range of sources which I have cited.

Include how each of the relaxation times were calculated. Including the calculation of the actual value and the estimation of the error associated with that value.

This is the different scaling rules that have been developed. In writing them up, I will have a much better understanding of them, and can include some of the ideas within my own analysis.

Most of the measurements of viscosity use the unit of measurement Poise, which should be discussed in the introduction. In particular information about the viscosity of glasses, particularly since this will probably include the Angell plot.

Currently there is a component on the Crystal detection in the Methods chapter and in the Machine learning chapter. These should all be consolidated into the machine learning chapter which would be a more sensible place to put it.

Additionally the discussion on alternative methods, like the orientational order parameter will be useful in the crystallisation chapter where I will be looking at free energy.

The error calculations 2.2.2 are rather sparse and could do with a lot more explanation of the process.

The style of the dynamics figures still includes the small text, so this needs to be
updated to reflect the new style.

Are the results of the shape packing close enough to those using a LJ potential? Include
a comparison of the results.

This should include the equations for the calculations and how I am averaging the quantities and how I am calculating the mean values.

This also includes the relaxation quantities.

• Diffusion Constant
• Structural relaxation
• Rotational relaxation
• Gamma relaxation
• non-gaussian relaxation

How random numbers were used, in particular in the packing code. This should also include some descriptions of the algorithms and which are suitable pseudo random number generators like my talk https://github.com/malramsay64/random_number_generators.

Collect results from ML Crystals project

https://github.com/malramsay64/MLCrystals/projects/1

There are still a number of sections which just contain dot points. This is intended as a broader tracking issue of all the writing that is required with items ideally being checked off fairly regularly.

Introduction

• Introduction to Glasses (in Introduction chapter)
• Characteristic Temperatures
• Dynamics of Supercooled liquids and glasses (in introduction chapter)
• Dynamics in experimental systems (in introduction chapter)
• Un-structured section at the end

Methods

• Simulations
• Choice of program (in methods)
• Simulation details
• Initialise simulation details
• Equilibration
• Production
• Diffusion constant
• Exponential Relaxation times
• Maximum time relaxation

Results

• Rotational Heterogeneity
• Rotational and Translational Heterogeneity
• Single Particle Diffusion
• Reversible relaxations
• Comparison of relaxation times
• Timescale of motions
• Possible investigations

This should give a broad overview of each of my different projects, including how they relate to other projects and what they achieve.

I currently have a text diagram which should be converted to tikz for inclusion in the thesis.

I have some dot points on this, however this is not yet written up in paragraphs
including figures.

The figure currently looks terrible

I want to use git-lint to lint my commit messages ensuring that there are a standard set of messages. These would include at least:

• chore
• writing
• planning
• editing
• project

Include the figures of each crystal in the methods chapter

Explain how the numbers for these quantities were arrived at, including an estimation of the uncertainty in these values.

Much of the work I have done in the statistics of the dynamics calculations assumes that configurations are independent. This is rather different to the standard statistical methods which use a linear sequence of steps. This is mostly so the statistical methods which I use later can be considered valid.

Explain the choice of hoomd over other simulation programs.

• Support for rigid bodies
• GPU acceleration

There are many errors within molecular dynamics calculations. This should document

• sources of errors, where they come from and why
• Methods of estimating the different types of errors
• Introduction to bootstrapping
• How I am calculating these different errors

Have a structure for the introduction which can be used to start writing

There should be an image with the position of each of the atoms in the molecule, includign the virtual R atom. This will assist in the description of the molecule in the methods section.

This provides the ability to cache a collection of the files. Since it takes so long to download from tectonic, caching the build files is a great idea.

https://github.com/actions/cache

It is really frustrating having to go from text to bibliography and back. To simplify this process there should be links within the bibliography back to the pages where the citations appear to make this process easier.

There is a bug in the install command, using conda env update instead of create.

Furthermore, there is no documentation of the npm packages I am using for editing.

Some of the unicode symbols (namely a subsript m) are missing from whatever font is
being used in the svg file for the Altair figures. I need to check the font being used,
and it might be a good idea to match the font of the thesis.

This should include how I know that we have indeed reached equilibrium. Noting it is a slow process for the low temperature configurations.

By using a filter for pandoc to convert the svg images into pdfs, I am able to choose the output format depending on the document format, which solves many of the issues in #5
The only change should be the inclusion of an additional processing file, since it is currently not installable.

There are many different quaternion distance methods described in @Huyng2009. There should be some description of why this particular method is correct.

Additionally the computational complexity should be discussed.

The initial structures which have been generated are rather important in the overall idea of the crystal melting chapter so it makes sense to have some validation of these methods and algorithms in the form of describing how they work.

This should include how a rotational relation and orientation order parameter are calculated from a quaternion, including an analysis of the performance of quaternions generally.

The purpose of averaging over many angles is that we have an isotropic liquid, so any angle which we pick will be equivalent. This should be made explicit in the text.

Collect and analyse the crystal melting results

https://github.com/malramsay64/Crystal_Melting/projects/5

This should include the conditions for initialising the dynamics simulation including the minimisation and other steps

I should start writing up the work I have done on the fluctuations, which will be addressing the why is this so difficult to melt.

This would require some changes, and templating. Additionally all the images would need to be included as svg rather than pdf. By using pandoc most of the infrastructure is already in place, just going to need some high level structural things and relatively minor changes.

I have been using the code \exp{ei\theta} and similar to denote the exponential, however this has issues in that it doesn't surround the text in any grouping symbol. Instead I should be using \exp(ei\theta) so the parentheses show up.

This should add all writing checks as pre-commit hooks. This means that they shouldn't get through to the CI to fail there.

I need to be able to explain how I have calculated the melting point, including figures
detailing why.

https://github.com/malramsay64/Dynamics/projects/2

There are a range of theories of crystal growth, from the classical to other methods

This is the value from the normalised melting rates, found as the parameter of fit. This value should be tabulated as a result.

It is fine having an understanding of simulation dynamics, however being able to relate my results to those of experimental systems is far more powerful.

Which measurements went into determining the temperature of the spinodal, where they came from and why I have arrived at this number.