Non-running notebooks

[IanHawke]

Linked to https://github.com/openjournals/jose-reviews/issues/61 .

Having checked the "General" and "Prereqs" section, the following notebooks didn't run for me currently (Julia v 1.1, Mac):

• [x] https://github.com/albi3ro/M4/blob/master/Prerequisites/Time%20Evolution.ipynb : Needs to import FFTW, and a number of places need dot operators adding (eg, cell 4 needs abs(x) changing to abs.(x), I think).
• [x] https://github.com/albi3ro/M4/blob/master/Prerequisites/Imaginary%20Time%20Evolution.ipynb : Didn't run first time, but did later? May be that FFTW isn't in the current environment file or I just messed up.
• [x] https://github.com/albi3ro/M4/blob/master/Prerequisites/Atomic%20Orbitals.ipynb : Error in cell 9 (a plotting issue I don't understand yet).
• [x] https://github.com/albi3ro/M4/blob/master/Prerequisites/Atomic%20Orbitals%202.ipynb : Needs to import Pkg at the top, Add dots in CarttoSph, and doesn't seem to like e (?: I defined it as exp(1) to make it run). As this relies on GLVis in the end, which doesn't install for me, I'm only trying to get the functions to run.

[albi3ro]

I did find some issues in "Time Evolution" that I fixed. I didn't find any issues with "Imaginary Time Evolution", but I had gone through Time Evolution and had added FFTW (so now FFTW is in packages list). Those two should work now. Let me know if they don't.

Going over "Atomic Orbitals", I realize it does generally have problems that I am now trying to fix. I originally used the package PyPlot.jl to plot with, then switched to Plots.jl. I changed the syntax, but I didn't change what I was doing or how I was using the package. I'm working on that now.

"Atomic Orbitals 2" used a confusing and now deprecated package GLVisualize.jl. I've just fully deleted it now.

[IanHawke]

Those all work, thanks.

Here come the next lot:

• [ ] https://github.com/albi3ro/M4/blob/master/Numerics_Prog/HDF5.ipynb : dump() returns nothing which causes println to break. If all println(dump(...)) lines are replaced with dump(...) it works for me. Note that it may make sense to split the cells so the close(fid) line is in a separate cell: this means the later cells can be run even if an earlier cell breaks. However, I'm not sure this is a good suggestion, as keeping it in the same cell implicitly emphasizes that close should be done ASAP.
• [ ] https://github.com/albi3ro/M4/blob/master/Graduate/Chern-Number.ipynb : linspace is now range, needs using LinearAlgebra to get norm, and I think the Array definition syntax needs fixing in places.

I think this is it, in terms of getting the notebooks running.

[albi3ro]

Just fixed the HDF problem.

Seems dump() no longer is a function, at least one I could find in the documentation .

Try the most recent version of Chern Number. I think I have range and the correct Array everywhere now, and am using abs2.() instead of norm().