Port tardis_opacities script from tardisanalysis

[MarkMageeAstro]

Description
This PR is to copy over the existing tardis opacity script from the tardisanalysis repository. The tardis opacity script was originally written by @unoebauer.

The opacity script allows for the easy calculation of the following properties:

• pure bound-bound opacity per shell
• pure Thomson opacity per shell
• Planck-mean opacity per shell
• Planck-mean optical depth of each shell
• Planck-mean optical depth, integrated from the ejecta surface

Motivation and context
tardisanalysis will eventually be closed. This is to keep the code current with tardis.

How has this been tested?

• Testing pipeline.
• Other.
  Comparisons with older version of the code.

Examples
The following snippet of code can be used to generate the plot shown below.

import tardis
import tardis_opacity as top

config = tardis.yaml_load("tardis_example.yml")
mdl = tardis.run_tardis(config)

# initialise opacity calculator
opacity_diag = top.opacity_calculator(mdl)
# get total opacity on a standard frequency grid for each cell
chi_tot = opacity_diag.kappa_tot
# midpoints of the frequency grid:
nu_grid = 0.5 * (opacity_diag.nu_bins[1:] + opacity_diag.nu_bins[:-1])

plt.loglog(nu_grid, chi_tot[:, 0], label = "cell #0")
plt.loglog(nu_grid, chi_tot[:, -1], label = "cell #19")

Type of change

• Bug fix.
• New feature.
• Breaking change.
• None of the above.

Checklist

• My change requires a change to the documentation.
  • I have updated the documentation accordingly.
  • (optional) I have built the documentation on my fork following the instructions.
• I have assigned and requested two reviewers for this pull request.

[codecov]

Codecov Report

Merging #1580 (d98a303) into master (d361a22) will decrease coverage by 5.27%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master    #1580      +/-   ##
==========================================
- Coverage   67.20%   61.93%   -5.28%     
==========================================
  Files          73       62      -11     
  Lines        6147     5729     -418     
==========================================
- Hits         4131     3548     -583     
- Misses       2016     2181     +165     

Impacted Files	Coverage Δ
tardis/tardis/util/base.py	75.78% <0.00%> (-1.99%)	⬇️
tardis/tardis/montecarlo/montecarlo_numba/base.py	28.73% <0.00%> (-0.90%)	⬇️
tardis/tardis/simulation/base.py	85.16% <0.00%> (-0.47%)	⬇️
...dis/montecarlo/montecarlo_numba/numba_interface.py	49.62% <0.00%> (-0.38%)	⬇️
tardis/tardis/scripts/cmfgen2tardis.py	0.00% <0.00%> (ø)
tardis/tardis/plasma/properties/atomic.py	61.76% <0.00%> (ø)
...ntecarlo_numba/tests/test_numba_formal_integral.py
.../montecarlo/montecarlo_numba/tests/test_vpacket.py
...rdis/montecarlo/montecarlo_numba/tests/conftest.py
...s/montecarlo/montecarlo_numba/tests/test_packet.py
... and 16 more

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[wkerzendorf]

@unoebauer this is the one I was talking about

[jamesgillanders]

I think this is a great job @MarkMageeAstro - great to get this code updated and moved across to the main TARDIS repo. Happy for this to be merged, once a second reviewer signs off! Keep up the good work!

[jaladh-singhal]

I think it's fine to merge it, we can just add @unoebauer as co-author by adding Co-authored by: [email protected] at the end of squash commit message.

(I found this mail from git history - it's linked to his GitHub account)