Static mix by malihass · Pull Request #161 · NatLabRockies/BioReactorDesign

malihass · 2026-09-10T14:04:34Z

Optimization code + loop reactor data
Loop velocity diagnostics + test
Non dimensional number post proc

… correlations

Copilot

🟡 Changes recommended

Several calculations can produce incorrect physical or statistical results, including a 3600× Sherwood error and invalid bootstrap uncertainty.

Once you've addressed the issues Copilot identified, you can request another Copilot review.

Pull request overview

Adds mixer modeling, loop-flow diagnostics, dimensionless post-processing, and scale-up optimization workflows.

Changes:

Adds transport, Froude, Weber, Sherwood, and steady-state statistics with tests.
Adds scale-up case templates, mixer configurations, and loop-velocity tooling.
Adds surrogate selection, constrained optimization, plotting, and generated datasets.

File summaries

File	Description
`tests/postprocess/test_transport.py`	Tests turbulent diffusivity.
`tests/postprocess/test_stats.py`	Tests steady-state statistics.
`tests/postprocess/test_dimensionless.py`	Tests dimensionless quantities.
`tests/io/test_read_global_vars.py`	Tests surface-tension parsing.
`tests/io/test_read_foam_dict.py`	Tests gravity parsing.
`papers/scaleup/SA_optimization/surrogate_selection.csv`	Stores selected surrogate results.
`papers/scaleup/SA_optimization/README.md`	Documents optimization scripts.
`papers/scaleup/SA_optimization/plot_marginal_gain.py`	Plots constrained optima.
`papers/scaleup/SA_optimization/plot_design_schematic.py`	Draws optimized designs.
`papers/scaleup/SA_optimization/model_selection.py`	Selects and caches surrogates.
`papers/scaleup/SA_optimization/marginal_gain_results.csv`	Stores marginal-gain results.
`papers/scaleup/SA_optimization/make_val_rmse_table.py`	Generates validation tables.
`papers/scaleup/SA_optimization/make_hyperparam_tables.py`	Generates hyperparameter tables.
`papers/scaleup/SA_optimization/load_data.py`	Loads and filters study data.
`papers/scaleup/SA_optimization/get_optimal_constrained.py`	Runs constrained optimization.
`papers/scaleup/SA_optimization/data/transfer.sh`	Transfers study datasets.
`papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/split.csv`	Defines lev6 data split.
`papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi/hyperparams_qoi.json`	Stores lev6 QOI model results.
`papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi/cfd_all_spargers.txt`	Stores lev6 CFD reference.
`papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi/best_bootstrap_solution_nn_qoi.csv`	Stores lev6 QOI optimum.
`papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_sum/hyperparams_qoi_sum.json`	Stores lev6 QOI-sum model results.
`papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_sum/cfd_all_spargers.txt`	Stores lev6 QOI-sum reference.
`papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_sum/best_bootstrap_solution_nn_qoi_sum.csv`	Stores lev6 QOI-sum optimum.
`papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_sum_kla/hyperparams_qoi_sum_kla.json`	Stores lev6 combined-kLa results.
`papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_sum_kla/cfd_all_spargers.txt`	Stores lev6 combined-kLa reference.
`papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_sum_kla/best_bootstrap_solution_rbf_qoi_sum_kla.csv`	Stores lev6 combined-kLa optimum.
`papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_kla/hyperparams_qoi_kla.json`	Stores lev6 kLa model results.
`papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_kla/cfd_all_spargers.txt`	Stores lev6 kLa reference.
`papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev6/qoi_kla/best_bootstrap_solution_nn_qoi_kla.csv`	Stores lev6 kLa optimum.
`papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/split.csv`	Defines lev1 data split.
`papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi/hyperparams_qoi.json`	Stores lev1 QOI model results.
`papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi/best_bootstrap_solution_nn_qoi.csv`	Stores lev1 QOI optimum.
`papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi_sum/hyperparams_qoi_sum.json`	Stores lev1 QOI-sum results.
`papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi_sum/best_bootstrap_solution_nn_qoi_sum.csv`	Stores lev1 QOI-sum optimum.
`papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi_sum_kla/hyperparams_qoi_sum_kla.json`	Stores lev1 combined-kLa results.
`papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi_sum_kla/best_bootstrap_solution_nn_qoi_sum_kla.csv`	Stores lev1 combined-kLa optimum.
`papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi_kla/hyperparams_qoi_kla.json`	Stores lev1 kLa model results.
`papers/scaleup/SA_optimization/data/study/study_0_4vvm_lev1/qoi_kla/best_bootstrap_solution_nn_qoi_kla.csv`	Stores lev1 kLa optimum.
`papers/scaleup/SA_optimization/data/study_pbe/study_0_4vvm_lev6/Y_data.csv`	Adds PBE response data.
`papers/scaleup/SA_optimization/data/study_pbe/study_0_4vvm_lev6/X_data.csv`	Adds PBE design data.
`papers/scaleup/SA_optimization/data/study_op/study_0_1vvm_lev6/Y_data.csv`	Adds operating-point responses.
`papers/scaleup/SA_optimization/data/study_op/study_0_1vvm_lev6/X_data.csv`	Adds operating-point designs.
`papers/scaleup/SA_optimization/data/study_fine/study_0_4vvm_lev6/Y_data.csv`	Adds fine-grid responses.
`papers/scaleup/SA_optimization/data/study_fine/study_0_4vvm_lev6/X_data.csv`	Adds fine-grid designs.
`papers/scaleup/generate_scaleup_runs/template/writeGlobalVars.py`	Writes generated case variables.
`papers/scaleup/generate_scaleup_runs/template/test.foam`	Adds ParaView case marker.
`papers/scaleup/generate_scaleup_runs/template/system/setFieldsDict`	Configures initial phase fields.
`papers/scaleup/generate_scaleup_runs/template/system/mixers.json`	Defines template mixer placement.
`papers/scaleup/generate_scaleup_runs/template/system/mesh.json`	Defines reactor mesh geometry.
`papers/scaleup/generate_scaleup_runs/template/system/inlets_outlets.json`	Defines boundary geometry.
`papers/scaleup/generate_scaleup_runs/template/system/fvSolution`	Configures solver algorithms.
`papers/scaleup/generate_scaleup_runs/template/system/fvSchemes`	Configures discretization schemes.
`papers/scaleup/generate_scaleup_runs/template/system/fvConstraints`	Adds field constraints.
`papers/scaleup/generate_scaleup_runs/template/system/decomposeParDict`	Configures parallel decomposition.
`papers/scaleup/generate_scaleup_runs/template/system/controlDict`	Configures simulation execution.
`papers/scaleup/generate_scaleup_runs/template/script_post`	Adds post-processing job script.
`papers/scaleup/generate_scaleup_runs/template/script`	Adds simulation job script.
`papers/scaleup/generate_scaleup_runs/template/run.sh`	Adds direct solver launcher.
`papers/scaleup/generate_scaleup_runs/template/read_history.py`	Extracts transient histories.
`papers/scaleup/generate_scaleup_runs/template/presteps.sh`	Prepares generated cases.
`papers/scaleup/generate_scaleup_runs/template/constant/thermophysicalProperties.liquid`	Defines liquid thermophysics.
`papers/scaleup/generate_scaleup_runs/template/constant/thermophysicalProperties.gas`	Defines gas thermophysics.
`papers/scaleup/generate_scaleup_runs/template/constant/phaseProperties_constantd`	Defines constant-diameter phases.
`papers/scaleup/generate_scaleup_runs/template/constant/phaseProperties`	Defines population-balance phases.
`papers/scaleup/generate_scaleup_runs/template/constant/momentumTransport.liquid`	Configures liquid turbulence.
`papers/scaleup/generate_scaleup_runs/template/constant/momentumTransport.gas`	Configures gas momentum transport.
`papers/scaleup/generate_scaleup_runs/template/constant/globalVars_temp`	Provides variable template.
`papers/scaleup/generate_scaleup_runs/template/constant/globalVars`	Provides default case variables.
`papers/scaleup/generate_scaleup_runs/template/constant/g`	Defines gravity.
`papers/scaleup/generate_scaleup_runs/template/constant/fvModels`	Defines mixer source model.
`papers/scaleup/generate_scaleup_runs/template/computeQOI.sh`	Runs QOI post-processing.
`papers/scaleup/generate_scaleup_runs/template/Allclean`	Cleans generated cases.
`papers/scaleup/generate_scaleup_runs/template/0.orig/Ydefault.liquid`	Defines default liquid composition.
`papers/scaleup/generate_scaleup_runs/template/0.orig/Ydefault.gas`	Defines default gas composition.
`papers/scaleup/generate_scaleup_runs/template/0.orig/U.liquid`	Defines liquid velocity field.
`papers/scaleup/generate_scaleup_runs/template/0.orig/U.gas`	Defines gas velocity field.
`papers/scaleup/generate_scaleup_runs/template/0.orig/T.liquid`	Defines liquid temperature.
`papers/scaleup/generate_scaleup_runs/template/0.orig/T.gas`	Defines gas temperature.
`papers/scaleup/generate_scaleup_runs/template/0.orig/p_rgh`	Defines hydrostatic pressure.
`papers/scaleup/generate_scaleup_runs/template/0.orig/p`	Defines pressure field.
`papers/scaleup/generate_scaleup_runs/template/0.orig/omega.liquid`	Defines liquid omega field.
`papers/scaleup/generate_scaleup_runs/template/0.orig/omega.gas`	Defines gas omega field.
`papers/scaleup/generate_scaleup_runs/template/0.orig/nut.liquid`	Defines liquid eddy viscosity.
`papers/scaleup/generate_scaleup_runs/template/0.orig/nut.gas`	Defines gas eddy viscosity.
`papers/scaleup/generate_scaleup_runs/template/0.orig/N2.gas`	Defines gas nitrogen fraction.
`papers/scaleup/generate_scaleup_runs/template/0.orig/k.liquid`	Defines liquid turbulence energy.
`papers/scaleup/generate_scaleup_runs/template/0.orig/k.gas`	Defines gas turbulence energy.
`papers/scaleup/generate_scaleup_runs/template/0.orig/H2.liquid`	Defines dissolved hydrogen.
`papers/scaleup/generate_scaleup_runs/template/0.orig/H2.gas`	Defines gas hydrogen.
`papers/scaleup/generate_scaleup_runs/template/0.orig/f.gas`	Defines gas size fraction.
`papers/scaleup/generate_scaleup_runs/template/0.orig/CO2.liquid`	Defines dissolved carbon dioxide.
`papers/scaleup/generate_scaleup_runs/template/0.orig/CO2.gas`	Defines gas carbon dioxide.
`papers/scaleup/generate_scaleup_runs/template/0.orig/alphat.liquid`	Defines liquid thermal diffusivity.
`papers/scaleup/generate_scaleup_runs/template/0.orig/alphat.gas`	Defines gas thermal diffusivity.
`papers/scaleup/generate_scaleup_runs/template/0.orig/alpha.liquid`	Defines liquid volume fraction.
`papers/scaleup/generate_scaleup_runs/template/0.orig/alpha.gas`	Defines gas volume fraction.
`papers/scaleup/generate_scaleup_runs/README.md`	Documents case generation.
`papers/scaleup/generate_scaleup_runs/randsim.py`	Generates multi-scale studies.
`bird/version.py`	Bumps package version.
`bird/utilities/ofio/global_vars.py`	Adds surface-tension reading.
`bird/utilities/ofio/foam_dict_io.py`	Adds gravity reading.
`bird/utilities/ofio/__init__.py`	Exports new readers.
`bird/postprocess/stats.py`	Adds tail-window statistics.
`bird/postprocess/post_quantities/transport.py`	Adds turbulent diffusivity.
`bird/postprocess/post_quantities/species.py`	Reuses density lookup helper.
`bird/postprocess/post_quantities/phase.py`	Adds density, velocity, and area helpers.
`bird/postprocess/post_quantities/dimensionless.py`	Adds dimensionless-number calculations.
`bird/postprocess/post_quantities/__init__.py`	Exports new post-processing APIs.
`applications/compute_loop_velocity.py`	Adds loop-velocity CLI.

Review details

Files reviewed: 129/139 changed files
Comments generated: 5
Review effort level: Balanced

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Copilot

🟡 Changes recommended

Field caching corrupts generated time histories, and the new statistics and multi-species fitted-kL paths mishandle valid inputs.

Once you've addressed the issues Copilot identified, you can request another Copilot review.

Review details

Suppressed comments (3)

Previously missed (2) — in code that hasn't changed since the last review.

bird/postprocess/stats.py:236

Partially missing windows are not handled: a single NaN reaches calc_mean, whose mean and autocorrelation then become NaN even when valid samples remain. Filter NaN samples (and their corresponding times) before the size/constant checks.
bird/postprocess/post_quantities/kla.py:344
The annotation declares a two-item tuple, but every return path produces (kl_spec, cstar_spec, field_dict) and callers unpack three values. Correct the public return type so static checking and generated API documentation match the implementation.

This issue also appears on line 639 of the same file.

bird/postprocess/post_quantities/kla.py:642

This new API accepts multiple species and forwards them to compute_fitted_kla, but that function stores c_history[species_name][itime] after its species loop, so only the final species receives data and all earlier species are fitted against zeros. Move that assignment into the inner loop (and cover a two-species call) before exposing multi-species fitted kL results.

    kla_spec, cstar_spec, field_dict = compute_fitted_kla(
        case_folder,
        species_names,
        n_cells=n_cells,

Files reviewed: 133/143 changed files
Comments generated: 1
Review effort level: Balanced

malihass · 2026-09-11T14:34:22Z

+field_dict = {}
+for itime, time in enumerate(time_float_sorted):
+    time_folder = time_str_sorted[itime]
+    print(f"\tTime : {time_folder}")
+    _, field_dict = read_cell_volumes(case_folder)


No field dict cache is actually not used

malihass added 30 commits July 29, 2026 17:15

Add SwirlMixer class

1deecfe

rename to actuator class, swirl is decided later

b9d3df2

ball-source fvModels writer

13ad8c3

format

8a71204

machinery to call the right mixer

7f8e3e5

new tutorial for the new mixer

b6681fd

add actuator mixer test

69652ee

actuator-disk power helper and mixer-model keys for case generation

19eed37

improve design sweep gen

699bb0a

adjust path

a5f9e89

remove te default qos high option

0963bc1

fix _readOFScal NameError, we have a public functions for that

6f47fe0

update template file with the right qoi

b096c07

add static mixer class

a15f682

add write_static_mixer_ball to the static mixer class

fbdd061

make sure we can mix static and dynamic mixers

37c330e

Add template for mixer placement

77be001

doc updates for static/dynamic mixer distinction

8b3e5b1

sign printing was messed up

704ff34

add regression test for later

7b1d084

sign issue

e5f1deb

source is -=

8d596d7

regen fvModels

4024b10

add per level timestepping option

6525f17

robust template folder resolution

2253842

make sure outlets are read from template json

d14d789

use random sampling or shared pool depending on if we need to compute…

da321fc

… correlations

also pack post proc

2a5ca8f

pack post proc together

0e70925

add uloop validation case

bdf264f

malihass added 14 commits September 1, 2026 16:55

update pixi lock

b8535db

fix lib hdf5 link

cc91f70

fix hdf5 lib

fe1ee1c

fix application paths and deploy to pypi

eb5d46d

remove run all and adjust allclean

1064f7b

add data to reproduce plots

4e8868f

Add mesh-agnostic loop velocity post-processing

824a222

Add compute_loop_velocity CLI wrapper

bf0a38d

Add steady_stat windowed

1d1e9e5

Add interfacial area, turbulent diffusivity, and kL post quantities

02b40f1

Froude, Weber, Sherwood dimensionless-number helpers

6fd4167

Add dimensionless numbers calc

8000938

needed for reproducing the loop res

6c55e3b

Merge branch 'main' into static_mix

a28d9e1

Copilot started work on behalf of malihass September 11, 2026 04:29 View session

Copilot stopped work on behalf of malihass due to an error September 11, 2026 04:29
The session was cancelled by the user.

format

8d56542

malihass requested a balanced review from Copilot September 11, 2026 04:34

Copilot started reviewing on behalf of malihass September 11, 2026 04:34 View session

Copilot AI reviewed Sep 11, 2026

View reviewed changes

malihass added 6 commits September 11, 2026 07:22

fix units for dimensionless sherwood

09fd47e

safe globalvar read

a9cd43e

Robust stats

3fa0857

fix docstrings

b93239a

format

3665021

new v

986bdbc

malihass requested a balanced review from Copilot September 11, 2026 13:56

Copilot started reviewing on behalf of malihass September 11, 2026 13:56 View session

Copilot AI reviewed Sep 11, 2026

View reviewed changes

malihass merged commit 6c3a941 into main Sep 11, 2026
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Static mix - #161

Static mix#161
malihass merged 54 commits into
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malihass commented Sep 10, 2026 •

edited

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malihass commented Sep 10, 2026 •

edited

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