Nexus: Add qdens-radial tool

[mcbennet]

Proposed changes

This PR introduces the tool qdens-radial (name negotiable) into the Nexus collection of binaries. The tool calculates radial densities (or their integrals) around atomic sites given .xsf files containing density/spin-density data (tested for QE- and QMCPACK-generated densities). Key functionalities include:

1. QE and QMCPACK radial densities at user-provided radiii (cumulative or non-cummulative).
2. Plotting of atomic radial densities
3. Mixed-estimator bias extrapolation if VMC and DMC .xsf files are provided.
4. Resampling to obtain error bars on computed quantities if +err files are provided.
5. Quantities can be calculated for a subset of species (list provided by user) and species-specific radii can be used (list provided by user)

A usage is provided that describes how the tool is run:

Usage: qdens-radial [options] xsf_file

Options:
  --version             show program's version number and exit
  -h, --help            Print help information and exit (default=False).
  -v, --verbose         Print detailed information (default=False).
  -R RADII, --radii=RADII
                        List of cutoff radii (default=None).
  -S SPECIES, --species=SPECIES
                        List of species (default=None).
  -s SOURCE, --source=SOURCE
                        Source that generated the .xsf file. Options: "pwscf",
                        "qmcpack" (default=qmcpack).
  -c, --cumulative      Evaluate cumulative radial density at cutoff radii
                        (default=False).
  -V VMC_FILE, --vmc_file=VMC_FILE
                        Location of VMC to be used for extrapolating mixed-
                        estimator bias (default=None).
  --vmc_err_file=VMC_ERR_FILE
                        Location of VMC+err to be used for extrapolating
                        mixed-estimator bias and resampling (default=None).
  --dmc_err_file=DMC_ERR_FILE
                        Location of DMC+err to be used for resampling
                        (default=None).
  -n NSAMPLES, --nsamples=NSAMPLES
                        Number of samples for resampling (default=10).
  -p, --plot            Show plots interactively (default=False).

Documentation should be added if this is merged. I can create an issue and assign myself and resolve it promptly after my workshop presentation.

What type(s) of changes does this code introduce?

• New feature

Does this introduce a breaking change?

• No. nxs-test tests pass (I checked since I modified nexus/lib/observables.py slightly)

What systems has this change been tested on?

Linux workstation

Checklist

Update the following with a yes where the items apply. If you're unsure about any of them, don't hesitate to ask. This is
simply a reminder of what we are going to look for before merging your code.

• Yes. This PR is up to date with current the current state of 'develop'
• N/A. Code added or changed in the PR has been clang-formatted
• No. This PR adds tests to cover any new code, or to catch a bug that is being fixed
• No. Documentation has been added (if appropriate)

[qmc-robot]

Can one of the admins verify this patch?

[mcbennet]

I plan to use this tool for my workshop labs. It would be ideal if it could be merged prior, if there are no issues.

[jtkrogel]

Please address comments below. Would be good to get a test + short manual entry for this, but this can wait until after the workshop session if time is tight.

[jtkrogel]

-s

[jtkrogel]

@mcbennet, just a couple more flag name find/replace and then this can go in.

[mcbennet]

Thank you, @jtkrogel . I have addressed your latest comments

[jtkrogel]

LGTM

[prckent]

Test this please

[prckent]

Start testing in-house