Add option for density pedestal setting by chris-ashe · Pull Request #4181 · ukaea/PROCESS

chris-ashe · 2026-04-13T13:43:28Z

This pull request introduces significant improvements to how plasma density pedestal and separatrix values are set, validated, and documented throughout the codebase and user documentation. The changes standardize the handling of Greenwald limit fractions, clarify user input options, and enhance plotting and metadata consistency. The most important changes are grouped below:

Plasma Density Profile Calculation and Validation:

Introduced a new switch variable i_nd_plasma_pedestal_separatrix to control whether pedestal and separatrix densities are set by user input or as fractions of the Greenwald limit, with corresponding updates to documentation and input handling.
Refactored validation logic in check_process to use the new pedestal/separatrix mode, ensuring correct relationships between densities and their Greenwald fractions depending on the selected method.
Updated input variable ranges and iteration variable definitions for f_nd_plasma_pedestal_greenwald and f_nd_plasma_separatrix_greenwald to reflect physically meaningful limits.

Greenwald Limit Fraction Handling and Metadata:

Added f_nd_plasma_greenwald as a new physics variable representing the Greenwald fraction of the line-averaged electron density, with initialization, metadata, and I/O updates.
Updated the density limit model to compute and assign f_nd_plasma_greenwald for use in plots and further calculations.

Plotting and Output Improvements:

Standardized plot labels and text boxes to use the new Greenwald fraction variable names and added more detailed density and temperature profile information (including line-averaged values).
Added new output variables such as temp_plasma_electron_line_avg_kev to enhance result reporting.
Documentation Updates:
Updated and clarified documentation in plasma_density_profile.md and plasma_profiles.md to reflect the new switch-based approach for setting pedestal and separatrix densities, and removed outdated instructions about negative Greenwald fractions.

Codebase Consistency:

Updated all relevant files and function signatures to consistently use the new variables and logic for plasma density profile handling.

These changes together improve the clarity, robustness, and usability of the plasma density profile modeling in the codebase.

Checklist

I confirm that I have completed the following checks:

My changes follow the PROCESS style guide
I have justified any large differences in the regression tests caused by this pull request in the comments.
I have added new tests where appropriate for the changes I have made.
If I have had to change any existing unit or integration tests, I have justified this change in the pull request comments.
If I have made documentation changes, I have checked they render correctly.
I have added documentation for my change, if appropriate.

codecov-commenter · 2026-04-13T13:52:02Z

Codecov Report

❌ Patch coverage is 51.85185% with 26 lines in your changes missing coverage. Please review.
✅ Project coverage is 50.15%. Comparing base (6a55d75) to head (737b19f).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
process/models/physics/physics.py	0.00%	13 Missing ⚠️
process/models/physics/profiles.py	60.00%	8 Missing ⚠️
process/core/io/plot/summary.py	0.00%	2 Missing ⚠️
process/core/init.py	80.00%	1 Missing ⚠️
process/models/physics/density_limit.py	0.00%	1 Missing ⚠️
process/models/physics/plasma_profiles.py	50.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4181      +/-   ##
==========================================
+ Coverage   50.14%   50.15%   +0.01%     
==========================================
  Files         151      151              
  Lines       29355    29378      +23     
==========================================
+ Hits        14719    14735      +16     
- Misses      14636    14643       +7

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chris-ashe · 2026-04-13T14:29:31Z

Have taken the liberty to add the line averaged density and temp values here. @j-a-foster Can you please check the sanity of the line averaged calcs and also the output changes?

Copilot

Pull request overview

This PR adds a switchable mechanism for setting pedestal/separatrix electron densities (user-input vs Greenwald-fraction) and extends profile reporting by computing and outputting line-averaged electron temperature.

Changes:

Introduced i_nd_plasma_pedestal_separatrix / DensityProfilePedestalType and centralized pedestal/separatrix density assignment via Greenwald fractions.
Added temp_plasma_electron_line_avg_kev computation and surfaced it in outputs and summary plots.
Updated input validation/ranges and refreshed related documentation.

Reviewed changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
`process/models/physics/profiles.py`	Adds `DensityProfilePedestalType` and `NeProfile.set_pedestal_and_separatrix_values()` to centralize pedestal/separatrix density setting.
`process/models/physics/plasma_profiles.py`	Computes/stores line-averaged electron temperature for both parabolic and pedestal parameterisations.
`process/models/physics/physics.py`	Routes pedestal/separatrix density setup through the new `NeProfile` method; outputs line-averaged Te; updates output gating to use the new switch.
`process/data_structure/physics_variables.py`	Adds `i_nd_plasma_pedestal_separatrix` and `temp_plasma_electron_line_avg_kev` to the data structure + initialization defaults.
`process/core/solver/iteration_variables.py`	Adjusts iteration-variable bounds for Greenwald-fraction inputs.
`process/core/io/plot/summary.py`	Displays line-averaged density and temperature in profile summary plots.
`process/core/input.py`	Updates input ranges for Greenwald-fraction variables and attempts to add the new switch (currently with a naming bug).
`process/core/init.py`	Updates density validation logic to use the new switch when interpreting manual pedestal/separatrix densities.
`documentation/source/physics-models/profiles/plasma_profiles.md`	Removes outdated guidance for toggling Greenwald-fraction behavior via negative inputs.
`documentation/source/physics-models/profiles/plasma_density_profile.md`	Documents the new switch and the Greenwald-fraction method (contains an iteration-variable index typo).

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… variables

…stency

…lations

…t validation

…ptions and calculations for Greenwald fractions

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

…ofile.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

… and update tests

…rity

…ations and documentation

Copilot

Pull request overview

Copilot reviewed 14 out of 14 changed files in this pull request and generated 5 comments.

+        if (
+            DensityProfilePedestalType(physics_variables.i_nd_plasma_pedestal_separatrix)
+            == DensityProfilePedestalType.USER_INPUT
+        ):
+            physics_variables.f_nd_plasma_pedestal_greenwald = (
+                physics_variables.nd_plasma_pedestal_electron
+                / (
+                    PlasmaDensityLimit.calculate_greenwald_density_limit(
+                        c_plasma=physics_variables.plasma_current,
+                        rminor=physics_variables.rminor,
+                    )
+                )
+            )
+
+            physics_variables.f_nd_plasma_separatrix_greenwald = (
+                physics_variables.nd_plasma_separatrix_electron
+                / (
+                    PlasmaDensityLimit.calculate_greenwald_density_limit(
+                        c_plasma=physics_variables.plasma_current,
+                        rminor=physics_variables.rminor,
+                    )
+                )
+            )
+        elif (
+            DensityProfilePedestalType(physics_variables.i_nd_plasma_pedestal_separatrix)
+            == DensityProfilePedestalType.GREENWALD_FRACTION
+        ):
+            physics_variables.nd_plasma_pedestal_electron = (
+                physics_variables.f_nd_plasma_pedestal_greenwald
+                * PlasmaDensityLimit.calculate_greenwald_density_limit(
+                    c_plasma=physics_variables.plasma_current,
+                    rminor=physics_variables.rminor,
+                )
+            )
+            physics_variables.nd_plasma_separatrix_electron = (
+                physics_variables.f_nd_plasma_separatrix_greenwald
+                * PlasmaDensityLimit.calculate_greenwald_density_limit(
+                    c_plasma=physics_variables.plasma_current,
+                    rminor=physics_variables.rminor,
+                )


    expected_nd_electron_line: float = 0.0

+    expected_temp_plasma_electron_line_avg_kev: float = 0.0
+
    expected_ti: float = 0.0


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timothy-nunn · 2026-05-21T13:26:11Z

-            po.ovarre(
-                self.outfile,
-                "Pedestal Greenwald fraction",
-                "(fgwped_out)",
-                fgwped_out,
-            )
-            po.ovarre(
-                self.outfile,
-                "Electron density at separatrix (nₑ,ₛₑₚ) (/m³)",
-                "(nd_plasma_separatrix_electron)",
-                physics_variables.nd_plasma_separatrix_electron,
-            )
-            po.ovarre(
-                self.outfile,
-                "Separatrix Greenwald fraction",
-                "(fgwsep_out)",
-                fgwsep_out,
-            )


These variable renames are not obviously listed in the PR body

Have added. They were actually never variables before and calculated in the output 🤢

timothy-nunn · 2026-05-21T14:06:40Z

        if (
-            data_structure.physics_variables.f_nd_plasma_pedestal_greenwald < 0
-            or not (
-                data_structure.numerics.ixc[: data_structure.numerics.nvar] == 145


Why have we stopped checking if itv 145 is active?

As checking if the f_nd_plasma_pedestal_greenwald is an iteration is detached from setting the values. The user may want to input direct values than dont iterate. In essence the new switch means the user ever inputs or has iterating either the true pedestal density value or its Greenwald fraction value

timothy-nunn · 2026-05-21T14:12:21Z

+                data_structure.physics_variables.i_nd_plasma_pedestal_separatrix
+            )
+            == DensityProfilePedestalType.USER_INPUT
+            and data_structure.physics_variables.nd_plasma_pedestal_electron
+            < data_structure.physics_variables.nd_plasma_separatrix_electron
        ):
            # Issue #589 Pedestal density is set manually using nd_plasma_pedestal_electron but it is less than nd_plasma_separatrix_electron.
-            if (
-                data_structure.physics_variables.nd_plasma_pedestal_electron
-                < data_structure.physics_variables.nd_plasma_separatrix_electron
-            ):
-                raise ProcessValidationError(
-                    "Density pedestal is lower than separatrix density",
-                    nd_plasma_pedestal_electron=data_structure.physics_variables.nd_plasma_pedestal_electron,
-                    nd_plasma_separatrix_electron=data_structure.physics_variables.nd_plasma_separatrix_electron,
-                )
+            raise ProcessValidationError(
+                "Density pedestal is lower than separatrix density",
+                nd_plasma_pedestal_electron=data_structure.physics_variables.nd_plasma_pedestal_electron,
+                nd_plasma_separatrix_electron=data_structure.physics_variables.nd_plasma_separatrix_electron,
+            )
+
+        if (
+            DensityProfilePedestalType(
+                data_structure.physics_variables.i_nd_plasma_pedestal_separatrix
+            )
+            == DensityProfilePedestalType.GREENWALD_FRACTION
+            and data_structure.physics_variables.f_nd_plasma_pedestal_greenwald
+            < data_structure.physics_variables.f_nd_plasma_separatrix_greenwald
+        ):
+            # Issue #589 Pedestal density is set manually using nd_plasma_pedestal_electron but it is less than nd_plasma_separatrix_electron.
+            raise ProcessValidationError(
+                "Density pedestal is lower than separatrix density",
+                f_nd_plasma_pedestal_greenwald=data_structure.physics_variables.f_nd_plasma_pedestal_greenwald,
+                f_nd_plasma_separatrix_greenwald=data_structure.physics_variables.f_nd_plasma_separatrix_greenwald,
+            )


Can these two if checks and errors be merged into one since they are raising an error about the same thing ('Density pedestal is lower than separatrix density')

timothy-nunn · 2026-05-21T14:12:38Z

+            and data_structure.physics_variables.f_nd_plasma_pedestal_greenwald
+            < data_structure.physics_variables.f_nd_plasma_separatrix_greenwald
+        ):
+            # Issue #589 Pedestal density is set manually using nd_plasma_pedestal_electron but it is less than nd_plasma_separatrix_electron.


If they cannot be combined, this comment makes no sense here

chris-ashe added Profiles Relating to the plasma profiles Refactor labels Apr 13, 2026

chris-ashe requested a review from j-a-foster April 13, 2026 14:28

chris-ashe marked this pull request as ready for review April 13, 2026 14:28

chris-ashe requested a review from a team as a code owner April 13, 2026 14:28

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Comment thread process/core/input.py Outdated

Comment thread documentation/source/physics-models/profiles/plasma_density_profile.md Outdated

Comment thread process/models/physics/plasma_profiles.py

Comment thread process/models/physics/profiles.py

timothy-nunn self-assigned this Apr 14, 2026

timothy-nunn requested changes Apr 14, 2026

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Comment thread process/models/physics/profiles.py Outdated

Comment thread documentation/source/physics-models/profiles/plasma_density_profile.md Outdated

chris-ashe added 8 commits May 21, 2026 10:28

Add option for density pedestal setting in physics variables

c4c3e53

Update density profile text box to include average density from mfile

2836a48

Add line averaged electron temperature variable to physics variables

fda3c51

Add line-averaged electron temperature calculation and update physics…

0cb8f06

… variables

Add density pedestal setting options and refactor related calculations

c3c0140

Refactor line averaged electron temperature variable naming for consi…

8115249

…stency

Add density pedestal electron input variable and update related calcu…

7d0a621

…lations

Add density pedestal and separatrix setting options with updated inpu…

db349f1

…t validation

chris-ashe force-pushed the add_option_for_density_pedestal_setting branch from 5c1d9f5 to db349f1 Compare May 21, 2026 09:32

chris-ashe and others added 6 commits May 21, 2026 13:35

Enhance density pedestal and separatrix settings with detailed descri…

797487d

…ptions and calculations for Greenwald fractions

Update process/core/input.py

6da2aa1

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Update documentation/source/physics-models/profiles/plasma_density_pr…

ae3402d

…ofile.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Add expected_temp_plasma_electron_line_avg_kev to PlasmaProfilesParam…

cc8c236

… and update tests

Refactor Greenwald density variables and update documentation for cla…

b8c0ae6

…rity

Rename 'dnla_gw' to 'f_nd_plasma_greenwald' and update related calcul…

5390516

…ations and documentation

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timothy-nunn added the Variable rename label May 21, 2026

timothy-nunn requested changes May 21, 2026

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