Add distinction between line-averaged and volume-averaged density

[nelsonand]

A pull request to organize solutions to https://github.com/cfs-energy-internal/internal-cfspopcon/issues/237 and https://github.com/cfs-energy-internal/internal-cfspopcon/issues/238. Most of this development was done by Columbia undergrads @aarooshgr and @ThomasWangAPAM

[nelsonand]

Summary of changes

Two average densities now exist:

• The volume-averaged density (<ne>, average_electron_density)
• The line-averaged density (ne_bar, line_average_electron_density)

Ion and electron densities are now handled separately when needed.

These changes were propagated through the code as specified in #238:

• [x] Add a function that relates ne_bar to <ne>
• [x] Add a definition of ne_bar to physics glossary
• [x] Use ne_bar in confinement calcs, profile calcs and upstream density calcs
• [x] Beta definitions should use the one instance of calc_average_total_pressure to be consistent

Full list follows:

Calc_average_total_pressure

• Uses <ne> This is correct
• [x] Now updated to include ion and electron density contributions separately

Calc_beta_general

• [x] Should use average_total_pressure instead of recomputing the average_total_pressure

Run_calc_beta, calc_beta_toroidal, calc_beta_poloidal

• [x] Same as calc_beta_general, use average_total_pressure instead of recomputing

Two_point_model_fixed_fpow

• Computes upstream electron density using nesep_over_nebar
• [x] This should use ne_bar instead of <ne>

Physics_glossary

• [ ] Define aveage_electron_density with the symbol
• [x] Add definition of line average density ne_bar

use_LOC_tau_e_below_threshold

• energy_confinement_time_LOC
• [x] Should use ne_bar

Figures_of_merit

• Calc_normalized_collisionality
• OK to use <ne>

Power_balance_from_tau, Run_calc_power_balance_from_tau_e

• [x] Energy_confinement_time should usene_bar

Operational_limits

• [x] Calc_greenwald_fraction should use ne_bar

Heat exhaust

• run_calc_heat_exhaust
• PBpRnSq = (P_sol * (magnetic_field_on_axis / q_star) / major_radius) / (average_electron_density**2.0)
• Not sure, left as <ne>

Plasma_profiles

• calc_1D_plasma_profiles
• [x] calc_analytic_profiles should use ne_bar
• calc_prf_profiles uses <ne> accroding to @pabloprf
• Evaluate_density_and_temperature_profile_fits

Peaked_profiles

• Run_calc_peaked_profiles
• Calc_effective_collisionality: ok to <ne>
• Peak_electron_density … use<ne>
• [x] calc_1D_plasma_profiles … use ne_bar

Two_point_model_fixed_tet

• Run_two_point_model_fixed_tet
• Not sure, left as <ne>

Two_point_model_fixed_qpart

• Not sure, left as <ne>

Extrinsic_core_radiator

• Run_calc_extrinsic_core_radiator
• Calc_impurity_charge_state
• mean_charge_curve
• Not sure, left as <ne>

Zeff_and_dilution_from_impurities Run_calc_zeff_and_dilution_from_impurities Calc_impurity_charge_state Summed_impurity_density

• Use <ne>
• [x] More correct to call this summed_impurity_average_density

Average_ion_density

• Use <ne>

[nelsonand]

@hassec @djbattagl Should be ready for a review.

This addresses all of https://github.com/cfs-energy-internal/internal-cfspopcon/issues/238, except for updating the symbol as indicated in that issue (I wasn't sure if we want that or not).

https://github.com/cfs-energy-internal/internal-cfspopcon/issues/238 does have a few things as "not sure" - we didn't change these in the end.

[djbattagl]

@tbody-cfs Do you have any quick guidance on whether to use volume averaged density or line-averaged density in these modules: run_calc_heat_exhaust, Run_two_point_model_fixed_tet, Two_point_model_fixed_qpart, Extrinsic_core_radiator ?

[djbattagl]

@nelsonand The code looks good to me. Could you provide an example where line_averaged_density_frac = 1 and compare to the results from an older version (should be the same).

And then show how the results change with the fraction not equal to one.

[tbody-cfs]

@tbody-cfs Do you have any quick guidance on whether to use volume averaged density or line-averaged density in these modules: run_calc_heat_exhaust, Run_two_point_model_fixed_tet, Two_point_model_fixed_qpart, Extrinsic_core_radiator ?

I'd use volume-averaged for these. It really only depends on your choice of nesep_over_nebar = 0.3.

[hassec]

Oh and since we are changing arguments of functions (thus technically breaking our API) can you change version = "4.0.0" to version = "5.0.0.dev" in pyproject.toml ?

[nelsonand]

@hassec I'm having trouble getting radas to install on this branch (and the main cfspopcon branch) Are the installation instructions up to date after the latest updates?

Specifically, when I do 'poetry run radas -d ./radas_dir'

I get the following error:

``` (base) oaknelson@Oaks-MBP-2 aaroosh-fork % poetry run radas -d ./radas_dir ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** unspecified CX donor element ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** unspecified CX donor element ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** unspecified CX donor element ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** unspecified CX donor mass ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** unspecified CX donor element ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** unspecified CX donor element ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** unspecified CX donor element ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** unspecified CX donor element ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** unspecified CX donor element ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** unspecified CX donor element ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** unspecified CX donor element ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** ****************************** xxdata_11 warning ****************************** no class name given in file ****************************** program continues ****************************** At line 355 of file radas_dir/readers/adf11/xxdata_11/xxdata_11.for (unit = 10, file = 'radas_dir/data_files/nitrogen_line_emission_from_excitation.dat') Fortran runtime error: End of file ```

[hassec]

@nelsonand the way to install/use radas did indeed change but should be updated and working on main. That's a change that came in via the merge of #40.

This branch seems to have quite a few conflicts (probably due to the merge of #40). So the best bet is likely a rebase of this branch, fixing the conflicts, and then trying again. That said there is also #41 which might get merged soon. I think you and @tbody-cfs already chatted about that PR, right? So it might make sense to wait for #41 and only rebase after that merge to avoid having to rebase and resolve conflicts twice.

[nelsonand]

Yeah - good call. I guess we'll wait for https://github.com/cfs-energy/cfspopcon/pull/41 to go in first! Thanks.

[nelsonand]

Hi @ThomasWangAPAM , can you rebase this onto https://github.com/cfs-energy/cfspopcon/pull/41 in prep for the merge?

[ThomasWangAPAM]

Hi @ThomasWangAPAM , can you rebase this onto #41 in prep for the merge?

Rebase done!

[ThomasWangAPAM]

@nelsonand The code looks good to me. Could you provide an example where line_averaged_density_frac = 1 and compare to the results from an older version (should be the same).

And then show how the results change with the fraction not equal to one.

POPCON generated by the current cfspopcon/main branch:

POPCON generated by new codes with line_averaged_density_frac = 1:

POPCON generated by new codes with line_averaged_density_frac = 1.5:

[hassec]

@nelsonand @ThomasWangAPAM what is the status of this PR. Is there a plan to rebase and finalize this?

[tbody-cfs]

@hassec I can do the rebase after #80 goes in, since this was already rebased once