neutral_full_velocity: adding transport coef

[malamast]

We now calculate the transport coefficients ie. neutral viscosity and heat conductivity, based on collisions with the same way we do it in the neutral_mixed component.

• an option to use constant transport coefficients is also present.
• added flux limiters
• added more diagnostics
• some rearrangement of the code for atomic physics. Now we collect all the code for the rhs of Nn together. The same with Pn and momentum.

One can call it in the input file like this:

# Neutrals
[d]
type = neutral_full_velocity
AA = 2
adiabatic_index = 5./3 # Ratio of specific heats
constant_transport_coef = false
density_floor = 1e-8
diagnose = true
toroidal_flow = true # default: true 
momentum_advection = false   # default: false
curved_torus = true # default: true (enabled only if toroidal_flow = true)
flux_limit = 1.0
diffusion_collisions_mode = afn
zero_timederivs = false
output_ddt = true

A few things that remain:

• We do not include viscous heating terms in the pressure equation as we do it in the neutral_mixed component
• The neutral_mixed component does not include BC on fluxes with a neutral_gamma (surface heat transmission coefficient). Should we do the same thing at the neutral_mixed component?

[codecov]

Codecov Report

❌ Patch coverage is 0% with 175 lines in your changes missing coverage. Please review.
✅ Project coverage is 25.92%. Comparing base (e0f1ebf) to head (d3cf60f).
⚠️ Report is 12 commits behind head on master.

Files with missing lines	Patch %	Lines
src/neutral_full_velocity.cxx	0.00%	175 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #454      +/-   ##
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- Coverage   26.41%   25.92%   -0.50%     
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  Files          90       90              
  Lines        8105     8259     +154     
  Branches     1133     1154      +21     
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- Misses       5745     5899     +154     
  Partials      219      219              

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