Updating main with fmuni branch by fmuni · Pull Request #163 · NatLabRockies/BioReactorDesign

fmuni · 2026-10-12T19:19:39Z

The branch has a few fixes including:

Correct BioReactingPhase model and associated documentation.
Correct path for video in rotating mesh tutorial
Added fvPatchField for recirculating species

… models

* BubbleColumnLES test works with the new of12 module. Uses populationBalance and mass transfer. * mesh_500mL generates a STR mesh using snappyHexMesh

* The old solver is updated as well as some stuff was missing * The new solver also checks for anisotropy in the variations to discard local maxima/minima from the interface

* Removed critical point check for interface tracking. I have to think it through a bit more. * Updated rotating mesh STR with correct patch creation * Added compression and interface tracking to rotating mesh STR tutorial * Rotating mesh STR has been succesfully tested for air/water in Earth, Moon, and space gravity

This can be used to compute the kLA. First compute mdoti = Su + Sp*Yi (no matter the phase). Then kLA = mdoti / ( Yi,g - Yi,l ) with sign depending on the phase chosen for computing mdoti.

* New geometry and properties * Added switch for disabling energy solution

* This model is an alternative to the reactingPhase model that adds an uptake rate to a specie. The DCW should be provided as a scalarField.

* Added --test option to Allrun scripts that allows to run one step on one core and reports the test success * Added missing Allclean scripts * ci file modified accordingly * Added README.md to bubble_column tutorial

* Update to index.rst to include OpenFOAM-13 * Update to multiphase.rst with newer models in multiphaseEuler

* Molar weights are not required as input anymore. They are now read from the physical properties dictionary. * Updated Michaelis-Menten to account for density and volume fraction variations. * Updated documentation.

Copilot

🟡 Changes recommended

The new boundary condition has startup, parallel-reduction, build-integration, and documentation issues.

5 open findings

What changed in this PR

Updates OF13 bioreaction kinetics and introduces a recirculated-species boundary condition.

Changes:

Uses thermodynamic molecular weights and phase-weighted density.
Adds a mapped recirculated-species patch field.
Adds standalone library build metadata.

File	Description
`BioReactingPhaseModel.H`	Removes stored molecular weights.
`BioReactingPhaseModel.C`	Revises reaction-rate calculations.
`recirculatedSpeciesFvPatchScalarField.H`	Declares and documents the boundary condition.
`recirculatedSpeciesFvPatchScalarField.C`	Implements mapped recirculation behavior.
`recirculatedSpecies/Make/options`	Defines library dependencies.
`recirculatedSpecies/Make/files`	Defines the new library target.

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malihass · 2026-10-13T14:35:23Z

+    const scalar alphaRhoPhiTotp = max( mag( sum(alphaRhoPhip)),1e-16 );
+
+    const scalar Yr = mag( sum(alphaRhoPhip*Yp) ) / alphaRhoPhiTotp; // Mean mass fraction from the mapped patch


Yeah I think Co pilot is right about this. If you parallelize such that the inlet patch is owned by different processors, each processor will use a different Y_r

malihass · 2026-10-13T14:22:33Z

@@ -0,0 +1,3 @@
+recirculatedSpeciesFvPatchScalarField.C
+
+LIB = $(FOAM_USER_LIBBIN)/librecirculatedSpecies


Co pilot seems to think that recirculated species won't be compiled. Can you add a regression test under Regression-Test-OF13: in the ci.yml, that use recirculated species as a BC?

malihass · 2026-10-13T14:37:08Z

+    calculated as:
+
+        \f[
+            Y = Y_{0}*(1-r) *Y_{r}


Yeah please fix this too. It really confused me at first when I read the PR haha

malihass · 2026-10-13T14:39:49Z

It took me a while to understand what was happening, it might be worth adding a schematic of the recirculation you are modeling in the documentations (in \docs, I would put maybe a "Boundary condition" section between "Meshing" and "Uncertainty Quantification"). I would probably explain the recirculation BC from a physical perspective and also explain what does the table does for scheduling when Yr is used.

* boundaryConditios folder with master Make folder * added compilation to Allwmake * fixed issues in recirculatedSpecies

* the bubbleColumn tutorial in OF13 has been updated to include recirculation.

* No mapping anymore * The boundary works as a fixedValue, but requires the target patch to be specified

fmuni added 30 commits December 30, 2024 15:12

Merge branch 'main' into fmuni

ea8ecb6

Merge branch 'main' into fmuni

97205fa

Merge branch 'main' into fmuni

9ac2395

Update to disengagement tutorial

70315f9

Added pressure difference option to disengagement functionObject

978d496

Added proper reading of limiter parameters to coalescence and breakup…

063fb17

… models

Fixed debug code wrongfully added to commit

4605c06

Added case for kestrel

b9d3d13

Added new test case

fc6a09e

Added interface capture method

eb6960a

added moon case

9aed700

added switches for interface algorithms

38457e5

Added openfoam12 solver

04ba619

* BubbleColumnLES test works with the new of12 module. Uses populationBalance and mass transfer. * mesh_500mL generates a STR mesh using snappyHexMesh

update to new mesh test

d1ca42b

Added interfaceTracking scheme to oF12 solver

cb042c7

* The old solver is updated as well as some stuff was missing * The new solver also checks for anisotropy in the variations to discard local maxima/minima from the interface

Added rotating mesh case

5976607

Added missing stl file

fe331fa

Writes Su and Sp for dmdi

aefecc9

This can be used to compute the kLA. First compute mdoti = Su + Sp*Yi (no matter the phase). Then kLA = mdoti / ( Yi,g - Yi,l ) with sign depending on the phase chosen for computing mdoti.

It was better to just compute the dmidtf to avoid issues

22c83be

Added dmidtf to header file

bcc4efc

Update to rotating mesh experimental case

16bf30b

* New geometry and properties * Added switch for disabling energy solution

Added BioReacting phase model

94d6fec

* This model is an alternative to the reactingPhase model that adds an uptake rate to a specie. The DCW should be provided as a scalarField.

update to rotating mesh

0b382a2

upgrade to OF13

9c4b956

Added baffles

58617f0

Update to bioreacting model for multiple reactions

6ec610c

Added post for writing kLA

44d75ff

Added kLA with correlations

8137bbe

Added modifications to BioReactingPhaseModel

e509b0a

fmuni added 15 commits July 29, 2026 23:04

cleaned STR_rotating tutorial

3a82470

cleaned STR_MRF tutorial

d4f9f90

removed unused data and geometry folders

6521f6f

Added test workflow for OF13

6dec3dc

* Added --test option to Allrun scripts that allows to run one step on one core and reports the test success * Added missing Allclean scripts * ci file modified accordingly * Added README.md to bubble_column tutorial

Update to documentation

73e7b4a

* Update to index.rst to include OpenFOAM-13 * Update to multiphase.rst with newer models in multiphaseEuler

removed calibration tutorial

a4e37cf

Fixed typos in doc and workflow

033227b

Fix image path in README for rotating mesh example

f499021

Added new rotating case

9e5122b

Update to rotating STR

69e5db8

Better mesh and easier settings for space STR

df79f1e

Added recircultedSpecies fvPatchField

e999384

Update to BioReactingPhase model

3d5c4cf

* Molar weights are not required as input anymore. They are now read from the physical properties dictionary. * Updated Michaelis-Menten to account for density and volume fraction variations. * Updated documentation.

Merge branch 'main' into fmuni

5c85835

Removed fmuni cases directory from tracking

92548ec

fmuni requested review from malihass and mjrahimi October 12, 2026 19:19

fmuni self-assigned this Oct 12, 2026

fmuni added documentation Improvements or additions to documentation enhancement New feature or request labels Oct 12, 2026

mjrahimi approved these changes Oct 12, 2026

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malihass requested a balanced review from Copilot October 13, 2026 13:29

Copilot started reviewing on behalf of malihass October 13, 2026 13:30

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Copilot AI reviewed Oct 13, 2026

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malihass requested changes Oct 13, 2026

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fmuni added 4 commits October 20, 2026 13:21

Update to recirculated BC

384b485

* boundaryConditios folder with master Make folder * added compilation to Allwmake * fixed issues in recirculatedSpecies

Updated tutorial for recirculatedSpecies BC

32f84e3

* the bubbleColumn tutorial in OF13 has been updated to include recirculation.

Rework to recirculatedSpecies BC

085fe09

* No mapping anymore * The boundary works as a fixedValue, but requires the target patch to be specified

Update to bubble_colum tutorial with new recirculatedSpecies BC

0abfab3

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Updating main with fmuni branch - #163

Updating main with fmuni branch#163
fmuni wants to merge 108 commits into
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malihass commented Oct 13, 2026 •

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		const scalar alphaRhoPhiTotp = max( mag( sum(alphaRhoPhip)),1e-16 );

		const scalar Yr = mag( sum(alphaRhoPhip*Yp) ) / alphaRhoPhiTotp; // Mean mass fraction from the mapped patch

		@@ -0,0 +1,3 @@
		recirculatedSpeciesFvPatchScalarField.C

		LIB = $(FOAM_USER_LIBBIN)/librecirculatedSpecies

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🟡 Changes recommended

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malihass commented Oct 13, 2026 •

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