jarvist/polaronmobility.jl

Feynman's variational path-integral model for the Fröhlich polaron. Calculates temperature dependent polaron mobilities, and other polaron observables.

polaronmobility.jl's Issues

Multiple phonon branches

You have a load of half interpreted versions of this in various lab books. So you should actually implement it.
The basic idea is to put multiple phonon branches in the 'true' Lagrangian, against which the model v and w Lagrangian is varied. This should give more temperature dependent structure in the e.g. mobility curves, as individual phonon modes go into resonance.

• figure out a nice way to go from i.r. activity + frequency to dielectric constant contribution
• units? interface with a VASP script? Intermediate .dat file to keep interface cleanly separate?
• implement this simply as a set of contributions to the Frohlich Hamiltonian, used in the calculation of a single v and w polaron at finite T.
• if this is too expensive, consider some variational approximation where you first project the complex spectra onto a representative set of modes
• stare at the results
• compare and contrast to the Hellwarth1999 averaging techniques
• sort out the Hellwarth1999 A scheme (finite temperature). Half implemented in a Jupyter notebook somewhere?
• see whether you can treat mode lifetime (i.e. from Phonopy3) at the same time, by adding a Gaussian width to the resonance

Sort out / delete PlotPolaron

Sort out PlotPolaron (https://github.com/jarvist/PolaronMobility.jl/blob/51aa09add590bd6b68406bbf16eb872d2e502a69/src/PlotPolaron.jl) - this was a temporary fix to keep the Plots dependency away. Either it should be refactored into a Plots recipe, or perhaps just discarded.

Massive performance regression at #1b7f414

Massive performance regression introduced with 1b7f414 . The tests almost suddenly hang, as they start running so slowly! The old 2017 era tests that run first seem to run fine though.
I couldn't see immediately where the issue was, as the diff on GitHub looked pretty confusing - lots of formatting updates at the same time as something mechanistic?

Example Pluto notebook on Binder for v.2

This little webapp will build a working environment / URL to kick off a Binder run: http://pluto-on-binder.glitch.me/

BUT, currently all the Pluto notebooks won't run as they assume you can find PolaronMobility in '../'.
Now that v2 is registered, I suppose just including PolaronMobility as a dependency within the Pluto notebook should be quite consistent & reproducible.

• Figure out best way to run PolaronMobility on Binder
• Put together an exemplary notebook showing off some useful features of the package
• Cross link from the docs

JOSS Review: README.md

@jarvist Please consider simplify the README.md. Some of the information there is now available at the documentation site https://jarvist.github.io/PolaronMobility.jl/ and looks duplicate. It would be nice that README.md is a succinct summary and defer more elaborate discussions to the documentation site. This might be a good example.

See also: #1, openjournals/joss-reviews#566

JOSS Review: Documentation

I think there are a number of steps that can be taken in the documentation to help users get up and running more easily. This is connected to the JOSS review at openjournals/joss-reviews#566

• First off, the documentation is built as a single, large page, if this could be split into multiple pages, that would help ease navigation
• Installation instructions: these are in the README, but should also be included in the documentation
• Example usage: in addition to the plots shown in the readme, it would be helpful to include examples which show both the code usage and the resulting plot

@yxqd may also have some suggestions here.

Optical absorption / Re χ

Optical absorption: https://github.com/jarvist/PolaronMobility.jl/blob/51aa09add590bd6b68406bbf16eb872d2e502a69/src/OedipusRex.jl

• Finish implementing it
• possibly by sorting out the integral
• reproduce the data in https://doi.org/10.1103/PhysRevB.5.2367
• think of some science to do with this?

Fix MyBinder

Error at build currently:

Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2dockeruxnjeh13'...
HEAD is now at 51aa09a Julia 1.0 style Project.toml via gen_project.jl
Building conda environment for python=3.7Error during build:  0.6.0 is not valid SemVer string

Should be on 1.x ?

Register v.2.0.0

@JuliaRegistrator register

Susceptibility / Im χ

Get this code: https://github.com/jarvist/PolaronMobility.jl/blob/51aa09add590bd6b68406bbf16eb872d2e502a69/src/Susceptibility.jl

• working
• with the oscillatory integral understood
• some kind of substitution by parts (?) / rescaling to fix the numerics
• doing some useful science (i.e. like by like comparison to the Drude model, to show where the disagreement becomes stark)

TagBot trigger issue

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I'll open a PR within a few hours, please be patient!

JOSS review: readme

These are just a few minor suggestions accompanying the review, they don't need to hold up the publication.

• it is common to put all of the badges at the top of the readme (where you have the build and coverage), I would suggest including the badge for the docs there as well.
• do you have an example that runs on JuliaBox? https://www.juliabox.com/. I tried getting the package to build there, but the build failed. This might be a helpful way to get people up and running, but again, it is not required for the JOSS submission

Update documentation for v2

Documentation has been touched for years!
Probably this will also be in concert with a code-clean.

• get Documenter.jl working under CI, so it builds
• Fix bug where the sidebar has blank titles
• Update README on /docs subfolder
• Update docs ^)_(^

Type instability in the Polaron type

This is very messy, and should be refactored. I think it also ends up as type Any which is not great for efficiency.

PolaronMobility.jl/src/types.jl

Lines 11 to 36 in 51aa09a

	# Structure to store data of polaron solution + other parameters, for each temperature
	struct Polaron
	T
	# Mobilities
	Kμ; Hμ; FHIPμ
	# Spring constant and renormalised (phonon-drag) mass
	k; M
	# Osaka free energy components (A,B,C) and total (F). See Hellwarth et al. 1999 PRB Part IV
	A; B; C; F
	# Relaxation time from Kadanoff Boltzmann transport equation
	Tau
	# Raw variational parameters
	v; w
	# Reduced thermodynamic beta
	βred
	# Feynman polaron radius (Schultz), in SI units. Then also the small-alpha asymptotic approx
	rfsi; rfsmallalpha
	# Setup of simulation. These parameters are sent to the function.
	# Alpha = Frohlich alpha
	α
	# Band effective mass
	mb
	# Effective dielectric frequency
	ω
	end
	Polaron()=Polaron([],[],[],[],[],[],[],[],[],[],[],[],[],[],[],[],[],[],[]) # structure initialisation