Implement collision source terms for multi-ion MHD #2213

amrueda · 2024-12-17T18:48:03Z

This PR introduces collision source terms for multi-ion MHD, accompanied by detailed documentation and a physically relevant test case based on the following reference:

Ghosh, D., Chapman, T. D., Berger, R. L., Dimits, A., & Banks, J. W. (2019). A multispecies, multifluid model for laser–induced counterstreaming plasma simulations. Computers & Fluids, 186, 38-57.

The Figure shows the temperature of two ion species for the second frictional slow-down test described in the reference above, as computed with examples/tree_2d_dgsem/elixir_mhdmultiion_collisions.jl and source_terms = source_terms_collision_ion_ion.

github-actions · 2024-12-17T18:48:17Z

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src/equations/ideal_glm_mhd_multiion.jl

codecov · 2024-12-17T19:26:13Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 96.38%. Comparing base (f09a707) to head (1b036f4).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2213      +/-   ##
==========================================
+ Coverage   96.37%   96.38%   +0.01%     
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  Files         486      487       +1     
  Lines       39186    39291     +105     
==========================================
+ Hits        37764    37869     +105     
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examples/tree_2d_dgsem/elixir_mhdmultiion_collisions.jl

DanielDoehring · 2024-12-20T15:27:39Z

src/equations/ideal_glm_mhd_multiion.jl

+        v_mag = sqrt(v1^2 + v2^2 + v3^2)
+        gamma = equations.gammas[k]
+        p[k] = (gamma - 1) *
+               (rho_e - 0.5f0 * rho * v_mag^2 - 0.5f0 * (B1^2 + B2^2 + B3^2))


This is a little inconsistent as there is v_mag but no B_mag.

DanielDoehring · 2024-12-20T15:28:25Z

src/equations/ideal_glm_mhd_multiion.jl

+References:
+- P. Rambo, J. Denavit, Interpenetration and ion separation in colliding plasmas, Physics of Plasmas 1 (1994) 4050–4060.
+- Schunk, R. W., Nagy, A. F. (2000). Ionospheres: Physics, plasma physics, and chemistry. 
+  Cambridge university press.


Could you provide the DOI here?

DanielDoehring · 2024-12-20T15:29:52Z

src/equations/ideal_glm_mhd_multiion.jl

+function source_terms_collision_ion_ion(u, x, t,
+                                        equations::AbstractIdealGlmMhdMultiIonEquations)


Out of curiosity: Could one re-use this for a 2 fluid (ion-electron) Euler-Poisson Plasma approximation?

DanielDoehring · 2024-12-20T15:30:12Z

src/equations/ideal_glm_mhd_multiion.jl

+References:
+- P. Rambo, J. Denavit, Interpenetration and ion separation in colliding plasmas, Physics of Plasmas 1 (1994) 4050–4060.
+- Schunk, R. W., Nagy, A. F. (2000). Ionospheres: Physics, plasma physics, and chemistry. 
+  Cambridge university press.


Same as above

DanielDoehring · 2024-12-20T15:31:33Z

src/equations/ideal_glm_mhd_multiion_2d.jl

+- Schunk, R. W., & Nagy, A. F. (2000). Ionospheres: Physics, plasma physics, and chemistry. 
+  Cambridge university press.


As above: DOI would be nice.

DanielDoehring · 2024-12-20T15:34:45Z

examples/tree_2d_dgsem/elixir_mhdmultiion_collisions.jl

+                                           gas_constants = (1.0, 1.0), # [nondimensional]
+                                           molar_masses = (1.0, 1.0), # [nondimensional]
+                                           ion_ion_collision_constants = [0.0 0.4079382480442680;
+                                                                          0.4079382480442680 0.0], # [nondimensional] (computed with eq (4.142) of Schunk&Nagy (2009))


Suggested change

0.4079382480442680 0.0], # [nondimensional] (computed with eq (4.142) of Schunk&Nagy (2009))

0.4079382480442680 0.0], # [nondimensional] (computed with eq (4.142) of Schunk & Nagy (2009))

DanielDoehring · 2024-12-20T15:35:33Z

examples/tree_2d_dgsem/elixir_mhdmultiion_collisions.jl

+    rho_1, _ = Trixi.get_component(1, u, equations)
+    p = pressure(u, equations)
+
+    return p[1] / rho_1 / equations.gas_constants[1]


This looks a bit strange - maybe add some parantheses?

Suggested change

return p[1] / rho_1 / equations.gas_constants[1]

return p[1] / (rho_1 * equations.gas_constants[1])

DanielDoehring · 2024-12-20T15:35:39Z

examples/tree_2d_dgsem/elixir_mhdmultiion_collisions.jl

+    rho_2, _ = Trixi.get_component(2, u, equations)
+    p = pressure(u, equations)
+
+    return p[2] / rho_2 / equations.gas_constants[2]


Same as above

Suggested change

return p[2] / rho_2 / equations.gas_constants[2]

return p[2] / (rho_2 * equations.gas_constants[2])

DanielDoehring · 2024-12-20T15:36:17Z

examples/tree_2d_dgsem/elixir_mhdmultiion_collisions.jl

+mesh = TreeMesh(coordinates_min, coordinates_max,
+                initial_refinement_level = 1,


Maybe mention again here why such a coarse mesh is used?

DanielDoehring · 2024-12-20T15:37:40Z

src/equations/ideal_glm_mhd_multiion.jl

+Compute the ion-ion collision source terms for the momentum and energy equations of each ion species as
+```math
+\begin{aligned}
+  \vec{s}_{\rho_k \vec{v}_k} =&  \rho_k\sum_{k'}\bar{\nu}_{kk'}(\vec{v}_{k'} - \vec{v}_k),\\


I assume you have k' for consistency with the paper. Alternatively, one could maybe think about using l as in the implementation?

DanielDoehring · 2024-12-21T07:31:56Z

src/equations/ideal_glm_mhd_multiion.jl

+The additional coefficient ``\bar{\nu}^1_{kk'}`` is a non-dimensional drift correction factor proposed by Rambo and 
+Denavit.


Suggested change

The additional coefficient ``\bar{\nu}^1_{kk'}`` is a non-dimensional drift correction factor proposed by Rambo and

Denavit.

The additional coefficient ``\bar{\nu}^1_{kk'}`` is a non-dimensional drift correction factor proposed by Rambo and Denavit.

DanielDoehring · 2024-12-21T07:34:53Z

src/equations/ideal_glm_mhd_multiion_2d.jl

+The ion-ion and ion-electron collision source terms can be computed using the functions 
+[`source_terms_collision_ion_ion`](@ref) and [`source_terms_collision_ion_electron`](@ref), respectively.
+
+For ion-ion collision terms, the optional arguments `gas_constants`, `molar_masses`, and `ion_ion_collision_constants` 


Suggested change

For ion-ion collision terms, the optional arguments `gas_constants`, `molar_masses`, and `ion_ion_collision_constants`

For ion-ion collision terms, the optional keyword arguments `gas_constants`, `molar_masses`, and `ion_ion_collision_constants`

DanielDoehring · 2024-12-21T07:35:06Z

src/equations/ideal_glm_mhd_multiion_2d.jl

+[`source_terms_collision_ion_ion`](@ref) and [`source_terms_collision_ion_electron`](@ref), respectively.
+
+For ion-ion collision terms, the optional arguments `gas_constants`, `molar_masses`, and `ion_ion_collision_constants` 
+must be provided.  For ion-electron collision terms, the optional arguments `gas_constants`, `molar_masses`, 


Suggested change

must be provided. For ion-electron collision terms, the optional arguments `gas_constants`, `molar_masses`,

must be provided. For ion-electron collision terms, the optional keyword arguments `gas_constants`, `molar_masses`,

Add collision source terms for multi-ion MHD

23d74ec

amrueda marked this pull request as draft December 17, 2024 18:48

amrueda commented Dec 17, 2024

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src/equations/ideal_glm_mhd_multiion.jl Outdated Show resolved Hide resolved

amrueda added 7 commits December 18, 2024 12:47

Fixed docstring issue

f021401

Use zero(eltype(u)) instead of 0

9ef9542

Removed unexisting function from export

e611c30

Fixed more docstring issues

5dabad1

Skip computation of collision sources of an ion species with itself

5c772f6

Added missing elixir

6104177

Improved documentation

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amrueda commented Dec 18, 2024

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examples/tree_2d_dgsem/elixir_mhdmultiion_collisions.jl Outdated Show resolved Hide resolved

amrueda added 5 commits December 18, 2024 16:10

Merge branch 'main' into arr/multi_ion_collision_sources

02aca9b

Double precision variables in initial condition

0971c19

Removed extra backtick

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Merge branch 'main' into arr/multi_ion_collision_sources

51f651e

Use CarpenterKennedy2N54 for the collision sources' test

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amrueda marked this pull request as ready for review December 19, 2024 17:49

amrueda added 2 commits December 19, 2024 19:59

Rewrote temperature functions in elixir to increase coverage

f6ad4f7

Merge branch 'main' into arr/multi_ion_collision_sources

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Implement collision source terms for multi-ion MHD #2213

Implement collision source terms for multi-ion MHD #2213

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		function source_terms_collision_ion_ion(u, x, t,
		equations::AbstractIdealGlmMhdMultiIonEquations)

		- Schunk, R. W., & Nagy, A. F. (2000). Ionospheres: Physics, plasma physics, and chemistry.
		Cambridge university press.

	0.4079382480442680 0.0], # [nondimensional] (computed with eq (4.142) of Schunk&Nagy (2009))
	0.4079382480442680 0.0], # [nondimensional] (computed with eq (4.142) of Schunk & Nagy (2009))

	return p[1] / rho_1 / equations.gas_constants[1]
	return p[1] / (rho_1 * equations.gas_constants[1])

	return p[2] / rho_2 / equations.gas_constants[2]
	return p[2] / (rho_2 * equations.gas_constants[2])

		mesh = TreeMesh(coordinates_min, coordinates_max,
		initial_refinement_level = 1,

		The additional coefficient ``\bar{\nu}^1_{kk'}`` is a non-dimensional drift correction factor proposed by Rambo and
		Denavit.

	For ion-ion collision terms, the optional arguments `gas_constants`, `molar_masses`, and `ion_ion_collision_constants`
	For ion-ion collision terms, the optional keyword arguments `gas_constants`, `molar_masses`, and `ion_ion_collision_constants`

	must be provided. For ion-electron collision terms, the optional arguments `gas_constants`, `molar_masses`,
	must be provided. For ion-electron collision terms, the optional keyword arguments `gas_constants`, `molar_masses`,

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