Create plasmapy.formulary.shocks and add initial functionality #864

KhalilBryant · 2020-07-03T22:16:25Z

I have added a changelog entry for this pull request.

If adding new functionality, I have added tests and
docstrings.

I have fixed any newly failing tests.

(#PlasmaPy 815)

codecov · 2020-07-03T22:52:41Z

Codecov Report

Merging #864 into master will increase coverage by 0.01%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #864      +/-   ##
==========================================
+ Coverage   96.21%   96.23%   +0.01%     
==========================================
  Files          61       62       +1     
  Lines        5423     5443      +20     
==========================================
+ Hits         5218     5238      +20     
  Misses        205      205

Impacted Files	Coverage Δ
plasmapy/formulary/__init__.py	`100.00% <100.00%> (ø)`
plasmapy/formulary/shocks.py	`100.00% <100.00%> (ø)`

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Add module `shocks` and function `entropy_across_shock_polytropic` to the fomulary

KhalilBryant · 2020-07-04T20:11:27Z

I want to add to the tests that ensure that when ds is negative, an error occurs and tells you that entropy change can't be negative, but I'm not sure how to go about it

StanczakDominik · 2020-07-05T15:15:51Z

pytest.raises!

changelog/864.feature.rst

plasmapy/formulary/shocks.py

plasmapy/formulary/tests/test_shocks.py

plasmapy/formulary/shocks.py

plasmapy/formulary/tests/test_shocks.py

Co-authored-by: Erik Everson <[email protected]>

rocco8773 · 2020-10-15T17:09:43Z

@pheuer Would you mind giving a review of this? The equation is taken straight from Drake, but I want to make sure the documentation is correct.

# Conflicts: # docs/formulary/index.rst # plasmapy/formulary/__init__.py

pheuer

@KhalilBryant Thanks for starting this shocks package! Here's a quick review of this function.

pheuer · 2020-10-15T19:04:49Z

plasmapy/formulary/shocks.py

+ c_v={"can_be_negative": False},
+)
+def entropy_jump_polytropic(
+ c_v: u.J / u.K,


Personally I rarely know the specific heat of the plasmas I'm dealing with, so using this function would always require some extra leg work. I would definitely suggest substituting Eq. 4.26 in Drake (which is equivalent to Eq. 3.3) to eliminate c_v, then replacing this input with a plasmapy.Particle instance that represents the ion species to get the atomic number and charge. You can then present Eq. 4.24 and Eq. 4.26 in the documentation to make clear what's happening.

I would keep c_v as is because people could use different methods to calculate it. Instead, we should add a separate function (in a separate PR) to calculate c_v. In the 2006 version of drake c_v is given in eqn 3.5.

Are there different methods that would be valid under this polytropic gas assumption? I haven't been able to find much information on this outside of Drake. Unless there are obvious, well-known models (like there are for resistivity, for example), I think that at the very least the documentation for this function should provide an appropriate equation or point to at least one function in PlasmaPy that will calculate it.

pheuer · 2020-10-15T19:07:30Z

plasmapy/formulary/shocks.py

+ c_v: u.J / u.K,
+ p_1: u.Pa,
+ p_2: u.Pa,
+ rho_1: u.kg / u.m ** 3,


The choice of mass density vs. number density is definitely field-specific: I think using rho is more common in ICF while in space physics/lab astro I see number density more. I'll just point out that if you do use a Particle input for the species, this could be changed to number density and then converted to mass density within the function.

I think you can just get away with annotating with [u.kg / u.m ** 3, u.m ** -3]. This should allow either number density or mass density to pass through. Then below when you to calculate the ratio you can do something like...

try: pressure_ratio = (p_2 / p_1).to(u.dimensionless_unscaled) density_ratio = (rho_1 / rho_2).to(u.dimensionless_unscaled) except u.UnitConversionError as err: raise u.UnitConversionError( f"Upstream and downstream parameters must have the same units, {err}" )

^Yes, this is the right answer.

I'd like to note...Drake's derivation of this uses mass density for rho. Since I can't think of a scenario where you'd have two different species for upstream/downstream, the mass ratio is equal to the number ratio.

pheuer · 2020-10-15T19:08:15Z

plasmapy/formulary/shocks.py

+ r"""
+ Entropy is not conserved across a shock, since a shock is
+ an irreversible, non-adiabatic process. This equation is based on the specific entropy
+ of a polytropic gas before and after the shock has passed. The shock


It wouldn't hurt to define polytropic here or somewhere (since this documentation is meant to be educational)

This is a good point. You can probably get way with something like...

Entropy is not conserved across a shock, since a shock is an irreversible, non-adiabatic process. This equation is based on the specific entropy of a polytropic gas ( :math:`p \propto \rho^\gamma`) before and after the shock has passed. The shock is an isolated steady, perpendicular shock, flowing through a non magnetized, polytropic gas.

pheuer · 2020-10-15T19:09:19Z

plasmapy/formulary/shocks.py

+ p_2={"can_be_negative": True, "pass_equivalent_units": True},
+ c_v={"can_be_negative": False},
+)
+def entropy_jump_polytropic(


Actually, maybe it's worth going one further: since this function only applies to shocks described by a certain model, maybe the namespace should be more like: formulary.shocks.polytropic.entropy_jump?

pheuer · 2020-10-15T19:11:40Z

plasmapy/formulary/shocks.py

+
+ """
+ pressure_ratio = (p_2 / p_1).to(u.dimensionless_unscaled)
+ density_ratio = (rho_1 / rho_2).to(u.dimensionless_unscaled)


Since this only depends on the pressure and density ratios, you could potentially just take those ratios as arguments and then avoid potential confusion about units or the mass density vs. number density question I raised above.

I still think keeping the individual parameters is better, only because I think it's a more explicit signature. However, I'm open to be convinced otherwise.

I agree with you now: the best solution is to take the individual parameters, make no requirements on their units except that they be identical, then construct the ratios (as you suggested above). That way users can use any pressure or density units they want.

pheuer · 2020-10-15T19:13:15Z

plasmapy/formulary/shocks.py

+ )
+ return u.Quantity(nan, unit=c_v.unit)
+
+ elif ds < 0:


You could check for this earlier by checking that the density and pressure ratios are > or < than 1 as expected. The benefit to doing so would be giving better error messages (you could tell the user which of the two they switched).

pheuer · 2020-10-15T19:16:47Z

plasmapy/formulary/shocks.py

+@validate_quantities(
+ rho_1={"can_be_negative": False, "pass_equivalent_units": True},
+ rho_2={"can_be_negative": False, "pass_equivalent_units": True},
+ p_1={"can_be_negative": True, "pass_equivalent_units": True},


Why can the pressures be negative?

rocco8773 · 2020-10-16T19:05:55Z

plasmapy/formulary/shocks.py

+ Here variables indexed by 1 and 2 are upstream (pre shock)
+ and downstream (post shock) respectively.
+ This function is equivalent to Eq. 4.24 in `Drake`_.


I'd also add here descriptions for s, p, rho, and gamma, must like you would do in a journal article.

KhalilBryant and others added 18 commits May 21, 2020 19:17

Create 815.feature.rst

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Add Reynolds_number to the PlasmaPy Formulary

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Add Reynolds_number to the Formulary (PlasmaPy#815)

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(#PlasmaPy 815)

Add Reynolds_number to the Formulary

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KhalilBryant and others added 7 commits July 3, 2020 19:11

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Add module `shocks` and function `entropy_across_shock_polytropic` to the fomulary

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KhalilBryant added 2 commits July 5, 2020 15:16

update changelog

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KhalilBryant marked this pull request as ready for review July 19, 2020 00:34

rocco8773 requested changes Jul 19, 2020

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KhalilBryant and others added 10 commits July 19, 2020 16:56

Update changelog/864.feature.rst

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Co-authored-by: Erik Everson <[email protected]>

Update plasmapy/formulary/shocks.py

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Co-authored-by: Erik Everson <[email protected]>

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Co-authored-by: Erik Everson <[email protected]>

rocco8773 mentioned this pull request Jul 19, 2020

Controlling Formulary Namespace (avoiding pollution and long names) #868

Open

update formulary/shocks.py

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rocco8773 mentioned this pull request Jul 19, 2020

Fix npsphinx-thumbnail for ./docs/notebooks/langmuir_analysis.ipynb #869

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rocco8773 requested a review from a team July 24, 2020 19:37

rocco8773 changed the title ~~Shocks~~ Create plamspay.formulary.shocks and add initial functinality Oct 15, 2020

Merge branch 'master_from_plasmapy' into pull/864-shocks

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# Conflicts: # docs/formulary/index.rst # plasmapy/formulary/__init__.py

pheuer reviewed Oct 15, 2020

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rocco8773 reviewed Oct 16, 2020

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StanczakDominik removed this from the v0.4.0 milestone Mar 10, 2021

rocco8773 added this to the 0.8.0 milestone Jul 20, 2021

namurphy modified the milestones: 0.8.0, 0.9.0 Jun 28, 2022

namurphy removed this from the 0.9.0 milestone Jul 6, 2022

namurphy changed the title ~~Create plamspay.formulary.shocks and add initial functinality~~ Create plasmapy.formulary.shocks and add initial functionality May 26, 2023

namurphy added the status: dormant PRs that are stalled label May 26, 2023

namurphy added this to the Future milestone Apr 9, 2024

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Create plasmapy.formulary.shocks and add initial functionality #864

Create plasmapy.formulary.shocks and add initial functionality #864

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Create plasmapy.formulary.shocks and add initial functionality #864

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