Hackathon TODO list

[jameskermode]

QUIP Hackathon TODO

This issue is to collect tasks for next week's QUIP Hackathon. Please edit the list below, adding links to other issues where appropriate. We can then add tags to assign tasks to people who would like to work on them.

Code Maintenance

• Add support for Python 3 (see Add support for Python 3 #44) - @jameskermode @tdaff
• Deprecate FortranArray (see e.g. quippy documentation and cleanup #53)
  • Resolve inconsistency between zero-based atom indexing (in ASE-inherited Atoms functions) and the one-based indexing in QUIP Atoms functions
• Update element masses to IUPAC (see Update element masses to IUPAC 2016 #54) @tdaff
• Update quippy command line tools such as convert.py to use ASE file formats (see quippy reader should fallback on ase.io.read() for unknown formats #10) @fcmocanu
• Remove unnecessary ellipses (see IndexError: an index can only have a single ellipsis ('...') #56) @molet
• Review and close old issues that have been resolved (e.g. xyz reader fails when .idx file exists but is unreadable #45) @gabor1

Documentation

• Expose documentation of potentials to sphinx (see quippy documentation and cleanup #53)
• Add PDF documentation output (see Successor to quip-reference-manual.pdf? #52)
• Add documentation for XML file formats (see No documentation for xml parameter file format(s) #50) @max-veit
• Introductory IPython tutorial (with emphasis on getting started with quippy) @max-veit

New features

• Add scaling factors to Sum potential (see Add scaling factors to Sum potential #51) @albapa

[jameskermode]

We agreed to deprecate FortranArray by adding warnings whenever accessed

[albapa]

How will atoms/neighbours be indexed in quippy then? Still one-based? It used to be quite convenient to loop over them with frange(at.n).

[jameskermode]

For ASE-style usage such as at.get_positions(), which we will use for all new examples and documentation, you will continue to get a standard numpy array.

For quippy-style usage such asat.pos the FortranArray would still be there but you would get a warning when accessing it. We can then review in ~1 years time and see how many people are using in this way.

[gabor1]

And we will be able to turn off the warning system if you want to write quippy style

[albapa]

Sounds good. The reason I'm asking because I very often use the neighbour() function which expects the arguments as one-based. I'd use ase if the same functionality existed but last time I looked I couldn't find it.

[albapa]

Is anyone working on the scaling factors for the Sum potential?

[gabor1]

You can continue to write quippy code, and it will be fine

[gabor1]

You can't implement scaling in a generic way, so let's just issue the warning. go ahead @albapa and do it if you like

[jameskermode]

we've just been talking about neighbour lists - ASE builtin is $O(N^2)$ and hence slow. ASE-compatible and fast alternative to QUIP is matscipy.neigbour_list.neighbours.

[albapa]

regarding the scaling factors - would that be energy and r-scale both?

[jameskermode]

See Gabor's comments under issue #51 for the scaling factors - I think the current task is only to add warnings.

[jameskermode]

If there are no objections I'm going to close this issue - I think everything is recorded on separate issues. I'll make a PR for Hackathon branch now; hackathon-f90wrap will stay around for a while longer as we continue to work on it.

[jameskermode]

FortranArray is no more. ase convert should do most of what convert.py used to; open an issue at ASE if there's missing functionality