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Redoing AFN neutral limiters #8

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Redoing AFN neutral limiters #8

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Commits on Dec 13, 2023

  1. Save individual collision frequencies to state 

    - This allows other components to pick and choose which ones are used rather than using the total frequency all the time. I am leaving the total frequency in there to be refactored later
    @mikekryjak
    mikekryjak committed Dec 13, 2023
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  2. Add individual collision tracking to hydrogen cx

    @mikekryjak
    mikekryjak committed Dec 13, 2023
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  3. Change individual collision notation for consistency

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    mikekryjak committed Dec 13, 2023
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Commits on Dec 14, 2023

  1. Improve comments and diagnostic metadata clarity

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    mikekryjak committed Dec 14, 2023
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Commits on Dec 15, 2023

  1. Add collision frequency to amjuel reactions

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    mikekryjak committed Dec 15, 2023
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Commits on Mar 2, 2024

  1. neutral_mixed: Add FV::Div_a_Grad_perp_limit operator 

    Apply limiter/upwinding to both X and Y advection
    @bendudson
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Commits on Mar 6, 2024

  1. neutral_mixed: Switch perpendicular limiter to Upwind 

    Seems to work better for neutral perpendicular diffusion than MC.
    @bendudson
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Commits on Mar 27, 2024

  1. neutral_mixed: Modify Div_a_Grad_perp_limit operator 

    Take field (Nn, Pn, NVn) and Dnn separately; only upwind the field,
and use cell face average values for Dnn.

Also add neutral_conduction switch.
    @bendudson
    bendudson committed Mar 27, 2024
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Commits on Mar 28, 2024

  1. neutral_boundary: Fix typos in fast reflection coefficients 

    target settings used in SOL and PFR regions, rather than SOL and PFR
settings.
    @bendudson
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  2. neutral_mixed: Change parallel to Upwind 

    Seems to help with smoothness of profiles
    @bendudson
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Commits on Apr 10, 2024

  1. neutral_mixed: Use Div_a_Grad_perp_upwind_flows 

    Same as anomalous_diffusion, obtain flows in X and Y for output
when diagnose = true.

Note: Only saves perpendicular flux, not parallel flux.
    @bendudson
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Commits on Apr 12, 2024

  1. Add flag to suppress lax flux 

    - For debugging purposes
    @mikekryjak
    mikekryjak committed Apr 12, 2024
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Commits on Apr 13, 2024

  1. neutral_mixed: improvements/diags for flooring 

    - added setting for pressure floor. Added temporary debug flags for using floored Nn and Pn in DnnNn and DnnPn calculation (otherwise they could unbalance and lead to density loss - need more testing). There is a secondary floor which kicks in at zero gradient, this is now linked to the primary floor (but 2 orders of magnitude below).
    @mikekryjak
    mikekryjak committed Apr 13, 2024
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Commits on Apr 18, 2024

  1. Merge branch 'master' into neutral-advection

    @mikekryjak
    mikekryjak committed Apr 18, 2024
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Commits on May 1, 2024

  1. Merge branch 'master' into selective-collisions

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  2. Fix species collisions being added in wrong place

    @mikekryjak
    mikekryjak committed May 1, 2024
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  3. Take out IZ/REC collisions from collision sums 

    - The collision sums contain exactly the same collisions as they did in the past, allowing legacy behaviour. Note this means that collision_frequency != sum(collision_frequencies).
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  4. Implement new collisions into 1D neutral diffusion

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Commits on May 2, 2024

  1. Merge branch 'master' into selective-collisions

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Commits on May 3, 2024

  1. Enable Braginskii collisionality in 1D neutral diffusion

    @mikekryjak
    mikekryjak committed May 3, 2024
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  2. Add underscore between species in collision names 

    - Makes it easier to split them up later
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    mikekryjak committed May 3, 2024
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  3. Prevent IZ, REC as registering collisions with electrons

    @mikekryjak
    mikekryjak committed May 3, 2024
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Commits on May 8, 2024

  1. Add collision selector and Braginskii mode for conduction

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  2. Improve conduction collisionality useability and prints 

    - Collisionality mode is now a string input to allow different combinations. It will throw an exception if the string is not "legacy" or "braginskii". Still not sure if "legacy" should be called something else or not.
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    mikekryjak committed May 8, 2024
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Commits on May 9, 2024

  1. Fix typo in CX collision registering

    @mikekryjak
    mikekryjak committed May 9, 2024
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  2. Minor print fix

    @mikekryjak
    mikekryjak committed May 9, 2024
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  3. Refactor conduction and diffusion collision matching

    @mikekryjak
    mikekryjak committed May 9, 2024
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Commits on May 10, 2024

  1. Implement collision selection in viscosity

    @mikekryjak
    mikekryjak committed May 10, 2024
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  2. Fix a few comments

    @mikekryjak
    mikekryjak committed May 10, 2024
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  3. Ensure conduction only considers CX, IZ for neutrals

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  4. Merge branch 'master' into selective-collisions

    @mikekryjak
    mikekryjak committed May 10, 2024
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  5. Fix viscosity collisionality print

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Commits on May 20, 2024

  1. Switch ions to i-i onlky

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    mikekryjak committed May 20, 2024
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  2. Merge branch 'neutral-advection' into fix-2d-neutral-eqns

    @mikekryjak
    mikekryjak committed May 20, 2024
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  3. Fix neutral_mixed eqns as per Horsten 2017 

    - Kappa and eta factors
- Perpendicular advection and conduction factors
- Add viscous heating
Comes from the E AFN version on my fork
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Commits on May 22, 2024

  1. Hardcode correct use of Nnlim and Pnlim in perp neutral advection

    @mikekryjak
    mikekryjak committed May 22, 2024
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  2. Calculate neutral Pnfloor from Nnfloor like evolve_density

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    mikekryjak committed May 22, 2024
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  3. Merge branch 'neutral-advection' into fix-2d-neutral-eqns

    @mikekryjak
    mikekryjak committed May 22, 2024
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  4. Fix comment and blank lines

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    mikekryjak committed May 22, 2024
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  5. Merge branch 'master' into selective-collisions

    @mikekryjak
    mikekryjak committed May 22, 2024
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Commits on May 23, 2024

  1. Improve 1D neutral cond/visc flag names

    @mikekryjak
    mikekryjak committed May 23, 2024
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  2. Fix typo

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    mikekryjak committed May 23, 2024
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  3. Merge branch 'neutral-advection' into fix-2d-neutral-eqns

    @mikekryjak
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  4. Expose max MFP as option

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    mikekryjak committed May 23, 2024
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Commits on May 25, 2024

  1. Add flag to fix gradient bug

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    mikekryjak committed May 25, 2024
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  2. Fix typo in Dmax

    @mikekryjak
    mikekryjak committed May 25, 2024
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  3. Add temporary diagnostics for Dmax and gradlogP

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    mikekryjak committed May 25, 2024
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Commits on May 26, 2024

  1. Add diagnostics for Dnn

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    mikekryjak committed May 26, 2024
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  2. Enable selective collisions for 2D neutral transport

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  3. Merge branch 'selective-collisions' into afn-neutral-limiters

    @mikekryjak
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  4. Hardcode Grad_perp fix

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Commits on May 27, 2024

  1. Correct vth formulation in perp neutral advection limiter

    @mikekryjak
    mikekryjak committed May 27, 2024
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  2. Change flux limiter form and separate adv/cond/visc limiters 

    - Now follows AFN method from SOLPS-ITER
    @mikekryjak
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  3. Add flags to reproduce legacy limiter form

    @mikekryjak
    mikekryjak committed May 27, 2024
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Commits on May 28, 2024

  1. Fix typo

    @mikekryjak
    mikekryjak committed May 28, 2024
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  2. Fix missing kappa in perp conduction

    @mikekryjak
    mikekryjak committed May 28, 2024
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  3. Fix incorrect factor in eta

    @mikekryjak
    mikekryjak committed May 28, 2024
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  4. Change energy flow diagnostic factor from 3/2 to 5/2 

    - Seems to make energy imbalance less imbalanced, but I haven't gone through the maths yet
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  5. Change conduction to upwind and expose fluxes

    @mikekryjak
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  6. Add comments on flow diags and fix conduction one

    @mikekryjak
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  7. Fix typo

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    mikekryjak committed May 28, 2024
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  8. Merge branch 'neutral-advection' into fix-2d-neutral-eqns

    @mikekryjak
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  9. Fix typos

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  10. Merge branch 'fix-2d-neutral-eqns' into afn-neutral-limiters

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  11. Fix missing conduction flows in term, bring multiplier into bracket t… 

    …o avoid segfault
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Commits on May 29, 2024

  1. Add a lot more temporary diagnostics

    @mikekryjak
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  2. Implement separate conduction limiter using old form - 

    kappa_n is limited upstream and passed down. This seemingly has no impact on performance while limiting conduction fluxes downstream has a huge impact.
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Commits on Jun 9, 2024

  1. Add temporary conductivity diagnostics

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  2. More conduction diagnostics

    @mikekryjak
    mikekryjak committed Jun 9, 2024
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  3. Fix seg fault in neutral_mixed

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Commits on Jun 25, 2024

  1. Add asymptotic limiters

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Commits on Jul 5, 2024

  1. Updated to latest next

    @bendudson
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  2. unit tests: Fix FakeMesh 

    Mesh::getBoundaryPar interface changed in BOUT++
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Commits on Jul 8, 2024

  1. freezing conduction in linear solve

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  2. Add C to CMake to prevent SUNDIALS-related find MPI_C bug

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  3. Merge branch 'upgrade-bout' into afn-neutral-limiters

    @mikekryjak
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  4. Take out exception when nonlinear

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  5. Bugfix: make electron conduction kappa Braginskii consistent

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Commits on Jul 9, 2024

  1. Freeze kappa in linear its as flag

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Commits on Jul 18, 2024

  1. Asymptotic kappa limiter fixes

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  2. Fix form of Dnn asymptotic limiter

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Commits on Jul 19, 2024

  1. Add debug prints and freezing kappa after first RHS

    @mikekryjak
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  2. More clearly separate new flux limiting form

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    mikekryjak committed Jul 19, 2024
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Commits on Jul 23, 2024

  1. Improve debug prints for kappa freezing

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Commits on Jul 26, 2024

  1. Add flag for perp upwind operator

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    mikekryjak committed Jul 26, 2024
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  2. Fix segfault

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    mikekryjak committed Jul 26, 2024
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  3. Change default to perp_upwind = true

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Commits on Aug 1, 2024

  1. Add flag to disable Y/Z neutral conduction

    @mikekryjak
    mikekryjak committed Aug 1, 2024
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  2. Fix conduction_xonly flag being wrong way around

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    mikekryjak committed Aug 1, 2024
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Commits on Aug 8, 2024

  1. Merge remote-tracking branch 'origin/selective-collisions' into afn-n… 

    …eutral-limiters
    @mikekryjak
    mikekryjak committed Aug 8, 2024
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