Update initialization for turbulent mixing layer and add validation results #879

hyeoksu-lee · 2025-06-11T19:32:58Z

User description

Description

This PR includes an update on initialization method for turbulent mixing layer. Also, Matlab scripts for computing turbulence statistics are added to examples/3D_turb_mixing/turbulence_stat as well as validation results.

Type of change

Please delete options that are not relevant.

Bug fix (non-breaking change which fixes an issue)
New feature (non-breaking change which adds functionality)
Something else

Scope

This PR comprises a set of related changes with a common goal

If you cannot check the above box, please split your PR into multiple PRs that each have a common goal.

How Has This Been Tested?

Ran examples/3D_turb_mixing on Carpenter

Streamwise velocity field at final time

Vorticity magnitude at final time

Evolution of Reynolds stress

Evolution of TKE budget

TKE budget averaged over self-similar period

Momentum thickness growth rate (see run_turbulence.m for references in legend)

Checklist

I have added comments for the new code
I added Doxygen docstrings to the new code
I have made corresponding changes to the documentation (docs/)
I have added regression tests to the test suite so that people can verify in the future that the feature is behaving as expected
I have added example cases in examples/ that demonstrate my new feature performing as expected.
They run to completion and demonstrate "interesting physics"
I ran ./mfc.sh format before committing my code
New and existing tests pass locally with my changes, including with GPU capability enabled (both NVIDIA hardware with NVHPC compilers and AMD hardware with CRAY compilers) and disabled
This PR does not introduce any repeated code (it follows the DRY principle)
I cannot think of a way to condense this code and reduce any introduced additional line count

PR Type

Enhancement, Documentation, Tests

Description

• Replace linear stability analysis with synthetic turbulence generation method for mixing layer initialization using Guo et al. (2023) approach
• Add comprehensive MATLAB scripts for turbulence statistics computation including Reynolds stress, TKE budget analysis, and validation against reference data
• Update 3D turbulent mixing layer example with higher Reynolds number (320), increased domain size and grid resolution
• Add new configuration parameters mixlayer_perturb_nk and mixlayer_perturb_k0 for synthetic turbulence control
• Remove deprecated mixlayer_domain parameter and associated complex validation requirements
• Implement pseudo-random number generator with supporting constants and helper functions
• Add documentation for new mixing layer perturbation method and turbulence analysis tools
• Update test cases and parameter dictionaries to support new synthetic turbulence approach

Changes walkthrough 📝

Relevant files

Enhancement

6 files

m_perturbation.fpp `Replace linear stability analysis with synthetic turbulence generation` src/pre_process/m_perturbation.fpp • Removed complex linear stability analysis code for mixing layer instability waves • Replaced `s_superposition_instability_wave` with new `s_perturb_mixlayer` function • Added spectrum-based synthetic turbulence generation method using Guo et al. (2023) approach • Implemented pseudo-random number generator and helper functions for perturbation generation	+146/-527
m_initial_condition.fpp `Update function call for mixing layer perturbation` src/pre_process/m_initial_condition.fpp • Changed function call from `s_superposition_instability_wave` to `s_perturb_mixlayer`	+1/-1
m_constants.fpp `Add constants for pseudo-random number generator` src/common/m_constants.fpp • Added constants for pseudo-random number generator implementation • Defined modulus, multiplier, increment, amplifier, and decimal_trim parameters	+7/-0
case.py `Update 3D turbulent mixing layer example configuration` examples/3D_turb_mixing/case.py • Updated Reynolds number from 50 to 320 • Increased domain size and grid resolution significantly • Added grid stretching in y-direction with new parameters • Modified time stepping and output settings	+21/-20
run_turbulence.m `Add MATLAB script for turbulence statistics analysis` examples/3D_turb_mixing/turbulence_stat/run_turbulence.m • Added comprehensive MATLAB script for turbulence statistics computation • Implements Reynolds stress and TKE budget calculations • Includes plotting functions and comparison with reference data • Provides mixing layer thickness and growth rate analysis	+601/-0
average_tke_over_self_similar.m `Add TKE budget averaging and validation script` examples/3D_turb_mixing/turbulence_stat/average_tke_over_self_similar.m • Added MATLAB script to compute time-averaged TKE budget over self-similar period • Implements interpolation and normalization of TKE transport, production, and dissipation terms • Includes plotting functionality with comparison to reference data from multiple studies • Contains helper functions for derivative computation and TKE budget visualization	+118/-0

Configuration changes

7 files

m_mpi_proxy.fpp `Update MPI broadcasts for new mixing layer parameters` src/pre_process/m_mpi_proxy.fpp • Added MPI broadcast for new parameter `mixlayer_perturb_nk` • Added MPI broadcast for new parameter `mixlayer_perturb_k0` • Removed MPI broadcast for deprecated parameter `mixlayer_domain`	+4/-4
m_global_parameters.fpp `Add new mixing layer perturbation parameters` src/pre_process/m_global_parameters.fpp • Added new parameters `mixlayer_perturb_nk` and `mixlayer_perturb_k0` for synthetic turbulence • Removed deprecated parameter `mixlayer_domain` • Set default values for new parameters (nk=100, k0=0.4446)	+6/-2
m_checker.fpp `Simplify mixing layer perturbation validation` src/pre_process/m_checker.fpp • Simplified validation for `mixlayer_perturb` to only require `p > 0` • Removed complex validation requirements for model equations, fluids, and boundary conditions	+1/-5
m_start_up.fpp `Update namelist for new mixing layer parameters` src/pre_process/m_start_up.fpp • Updated namelist to include new parameters `mixlayer_perturb_nk` and `mixlayer_perturb_k0` • Removed deprecated parameter `mixlayer_domain` from namelist	+2/-2
case_dicts.py `Update parameter dictionary for new mixing layer options` toolchain/mfc/run/case_dicts.py • Added new parameter types for `mixlayer_perturb_nk` and `mixlayer_perturb_k0` • Removed deprecated parameter `mixlayer_domain`	+2/-0
set_user_inputs.m `Add user input configuration for turbulence statistics` examples/3D_turb_mixing/turbulence_stat/set_user_inputs.m • Added MATLAB function to configure simulation parameters for turbulent mixing layer analysis • Defines fluid properties, Reynolds number, grid configuration, and time stepping parameters • Sets up domain dimensions and stretched grid parameters for y-direction • Configures system indices for multi-fluid and multi-dimensional simulations	+57/-0
.typos.toml `Allow TKE acronym in typo checker` .typos.toml • Added `TKE` to the list of accepted words in typo checking configuration	+1/-0

Tests

1 files

cases.py `Update test case for new mixing layer perturbation method` toolchain/mfc/test/cases.py • Replaced complex `alter_instability_wave` function with simplified `alter_mixlayer_perturb` • Updated test case configuration for 3D mixing layer with new parameters • Simplified test case setup removing bubble-related configurations	+33/-53

Miscellaneous

1 files

golden-metadata.txt `Update test metadata for new build environment` tests/D13FDB23/golden-metadata.txt • Updated test metadata with new build configuration and environment • Changed from Delta cluster to M4Pro local machine • Updated compiler versions and CMake configuration	+44/-68

Documentation

3 files

case.md `Update documentation for new mixing layer perturbation method` docs/documentation/case.md • Updated documentation for mixing layer parameters • Removed `mixlayer_domain` parameter description • Added description of new synthetic turbulence generation method • Updated requirements for `mixlayer_perturb` option	+3/-6
README.md `Add README for turbulence statistics analysis tools` examples/3D_turb_mixing/turbulence_stat/README.md • Added README file describing turbulence statistics analysis tools • Provides references to relevant literature • Documents file structure and usage instructions	+23/-0
references.md `Add turbulence-related academic references` docs/documentation/references.md • Added reference to Guo et al. (2023) for turbulence generation methods • Added reference to Michalke (1964) for hyperbolic-tangent velocity profile instability	+4/-0

Additional files

9 files

case.py	+0/-2
reference.mat	[link]
golden-metadata.txt	+0/-174
golden.txt	+0/-16
golden-metadata.txt	+0/-174
golden.txt	+0/-10
golden-metadata.txt	+0/-174
golden.txt	+0/-18
golden.txt	+12/-12

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examples/3D_turb_mixing/turbulence_stat/results/Reynolds_stress/tstep_8064.png

examples/3D_turb_mixing/turbulence_stat/submit_batch_job_carpenter.sh

codecov · 2025-06-11T23:52:30Z

Codecov Report

Attention: Patch coverage is 76.05634% with 17 lines in your changes missing coverage. Please review.

Project coverage is 44.00%. Comparing base (4864d36) to head (c937bd9).
Report is 1 commits behind head on master.

Files with missing lines	Patch %	Lines
src/pre_process/m_perturbation.fpp	75.00%	16 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #879      +/-   ##
==========================================
- Coverage   45.98%   44.00%   -1.98%     
==========================================
  Files          68       68              
  Lines       18629    18433     -196     
  Branches     2239     2228      -11     
==========================================
- Hits         8566     8112     -454     
- Misses       8711     9017     +306     
+ Partials     1352     1304      -48

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src/pre_process/m_start_up.fpp

examples/3D_turb_mixing/turbulence_stat/average_tke_over_self_similar.m

hyeoksu-lee · 2025-06-23T04:01:12Z

@sbryngelson Only frontier test fails. I guess something might be wrong with the pseudo-random number generator, but I am still trying to figure out what causes the failure. If you have any idea on what could be possibly wrong, that would be greatly appreciated!

sbryngelson · 2025-06-23T13:28:55Z

@hyeoksu-lee that is indeed weird. if I recall correctly, the Frontier CPU test passes? If that's correct, then it's very strange the GPU case would fail. I notice the failure is for a very small tolerance error. What does that particular test actually look like? Does it meaningfully change the state variables over the ~50 time steps (or whatever it is)? Perhaps it's just not a great test that is very sensitive to compiler optimizations or floating point roundoff.

sbryngelson · 2025-06-25T02:47:24Z

src/pre_process/m_perturbation.fpp

+        integer :: xint, val
+        real(wp) :: x
+
+        x = (multiplier/real(modulus, wp))*a + (increment/real(modulus, wp))


if you think the error in the Cray/Frontier case is due to the RNG, then you can print the random number it generates as a test and see it in the CI output (I think that should work, I believe we print the simulation output of failed tests in the CI output). also: Carpenter is a cray machine, so you can load cray modules there, compile MFC, and see if it passes tests!

using Carpenter for this is probably the fastest way to debug. you'll have to change the modules from the ones ./mfc.sh load uses to the Cray ones. let me know if you can't figure this out, I have Carpenter access (i think)

hyeoksu-lee · 2025-06-25T11:15:49Z

@sbryngelson Thank you for the suggestions! I will try to verify with Carpenter's cray modules. Not sure if I can find all the required modules though. I'll keep you updated

sbryngelson · 2025-06-25T13:59:04Z

@sbryngelson Thank you for the suggestions! I will try to verify with Carpenter's cray modules. Not sure if I can find all the required modules though. I'll keep you updated

Let me know if that's the case and I'll try to help (put it in Slack).

hyeoksu-lee · 2025-06-27T09:36:55Z

@sbryngelson Using Carpenter Cray, I found that the PRNG was sensitive to machine precision errors due to the multiplication of a very large number followed by trimming. I’ve updated the PRNG to make it more robust against such precision issues. Test suite passed on both Carpenter GNU and Cray as well as my local macbook, so I believe the Frontier tests should now pass.

In the meantime, I will have to update the results of example/3D_turb_mixing as its initial condition has been changed and the statistics may change accordingly. I believe the statistics will remain close to the reference, but I want to make sure. This will take a day or two.

sbryngelson · 2025-06-27T13:00:33Z

@hyeoksu-lee ah, good find, very nice! Looks like it passed just fine. FYI the GT (Phoenix) runners are down or acting very strangely right now but I expect them to show fine results. I will mark this PR as a draft PR and you can mark it 'ready to review' once you check your final statistics.

hyeoksu-lee · 2025-06-28T01:43:06Z

@sbryngelson Statistics looks good. This PR is now ready for review.

qodo-merge-pro · 2025-06-28T01:43:19Z

PR Reviewer Guide 🔍

Here are some key observations to aid the review process:

⏱️ Estimated effort to review: 4 🔵🔵🔵🔵⚪
🧪 PR contains tests
🔒 No security concerns identified
⚡ Recommended focus areas for review Possible Issue The new perturbation method uses MPI broadcasts but only generates random numbers on rank 0. This could lead to synchronization issues or deadlocks if MPI communication fails, and the random number generation logic appears complex with potential for numerical instability. if (proc_rank == 0) then call s_generate_random_perturbation(khat, xi, phi, i, y_cc(r)) end if #ifdef MFC_MPI call MPI_BCAST(khat, 3, mpi_p, 0, MPI_COMM_WORLD, ierr) call MPI_BCAST(xi, 3, mpi_p, 0, MPI_COMM_WORLD, ierr) call MPI_BCAST(phi, 1, mpi_p, 0, MPI_COMM_WORLD, ierr) #endif Code Quality The Cholesky decomposition implementation manually checks for small values and sets them to `sgm_eps`, but `sgm_eps` is not defined in the visible code. This could cause compilation errors or undefined behavior. if (abs(Lmat(1, 1)) < sgm_eps) Lmat(1, 1) = sgm_eps Lmat(2, 1) = Rij(2, 1)/Lmat(1, 1) Lmat(2, 2) = sqrt(Rij(2, 2) - Lmat(2, 1)*2._wp) if (abs(Lmat(2, 2)) < sgm_eps) Lmat(2, 2) = sgm_eps Lmat(3, 1) = Rij(3, 1)/Lmat(1, 1) Lmat(3, 2) = (Rij(3, 2) - Lmat(3, 1)Lmat(2, 1))/Lmat(2, 2) Lmat(3, 3) = sqrt(Rij(3, 3) - Lmat(3, 1)2._wp - Lmat(3, 2)2._wp) Duplicate Code The derivative computation functions `f_compute_derivative_1d` and `f_compute_derivative_3d` contain very similar logic for boundary conditions and central differences. This could be refactored to reduce duplication. function dfunds = f_compute_derivative_1d(fun,s) dfunds = zeros(size(fun)); % initialize discrete derivative vector for j = 1:length(s) % for each index in s % if at bottom boundary, use 1-sided derivative dfunds(1) = (fun(2) - fun(1)) / (s(2) - s(1)); % if at top boundary, use 1-sided derivative dfunds(end) = (fun(end) - fun(end-1)) / (s(end) - s(end-1)); % otherwise, if in the interior of the domain, 2-sided derivative for i = 2:length(s)-1 dfunds(i) = (fun(i+1) - fun(i-1)) / (s(i+1) - s(i-1)); end end end % Compute the wall-normal derivative of a discretized function, fun(y) function dfunds = f_compute_derivative_3d(fun,s,dir) dfunds = zeros(size(fun)); % initialize discrete derivative vector if (dir == 1) % Forward difference at start dfunds(1,:,:) = (fun(2,:,:) - fun(1,:,:)) / (s(2) - s(1)); % Backward difference at end dfunds(end,:,:) = (fun(end,:,:) - fun(end-1,:,:)) / (s(end) - s(end-1)); % Central difference for interior for i = 2:length(s)-1 dfunds(i,:,:) = (fun(i+1,:,:) - fun(i-1,:,:)) / (s(i+1) - s(i-1)); end elseif (dir == 2) dfunds(:,1,:) = (fun(:,2,:) - fun(:,1,:)) / (s(2) - s(1)); dfunds(:,end,:) = (fun(:,end,:) - fun(:,end-1,:)) / (s(end) - s(end-1)); for i = 2:length(s)-1 dfunds(:,i,:) = (fun(:,i+1,:) - fun(:,i-1,:)) / (s(i+1) - s(i-1)); end elseif (dir == 3) dfunds(:,:,1) = (fun(:,:,2) - fun(:,:,1)) / (s(2) - s(1)); dfunds(:,:,end) = (fun(:,:,end) - fun(:,:,end-1)) / (s(end) - s(end-1)); for i = 2:length(s)-1 dfunds(:,:,i) = (fun(:,:,i+1) - fun(:,:,i-1)) / (s(i+1) - s(i-1)); end else disp("Wrong dir input"); end end

Copilot

Pull Request Overview

This PR replaces the previous linear-instability initialization of the turbulent mixing layer with a spectrum-based synthetic turbulence generator (Guo et al. 2023), updates all related configuration and broadcast parameters (mixlayer_perturb_nk, mixlayer_perturb_k0), and adds MATLAB tools (and documentation) for turbulence statistics and validation of the 3D mixing layer example.

Replace s_superposition_instability_wave with s_perturb_mixlayer and remove legacy linear-stability code.
Introduce new parameters mixlayer_perturb_nk and mixlayer_perturb_k0, propagate them through global parameters, MPI proxies, start-up, and namelists.
Add MATLAB scripts (run_turbulence.m, average_tke_over_self_similar.m), example README, and reference documentation.

Reviewed Changes

Copilot reviewed 22 out of 31 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
src/pre_process/m_perturbation.fpp	Remove linear-stability routines; add `s_perturb_mixlayer` subroutine and PRNG constants.
src/pre_process/m_initial_condition.fpp	Update initialization to call `s_perturb_mixlayer` instead.
src/common/m_constants.fpp	Define PRNG constants (`modulus`, `multiplier`, `increment`, etc.).
src/pre_process/m_global_parameters.fpp	Add `mixlayer_perturb_nk` and `mixlayer_perturb_k0` defaults.
src/pre_process/m_mpi_proxy.fpp	Broadcast new mixing-layer parameters; remove deprecated `mixlayer_domain`.
src/pre_process/m_start_up.fpp	Include new perturbation parameters in namelist.
src/pre_process/m_checker.fpp	Simplify validation rules for `mixlayer_perturb`.
toolchain/mfc/run/case_dicts.py	Register new parameter types for `mixlayer_perturb_nk` and `mixlayer_perturb_k0`.
toolchain/mfc/test/cases.py	Replace legacy instability-wave test with `alter_mixlayer_perturb`.
examples/3D_turb_mixing/turbulence_stat/*	Add MATLAB scripts, README, and averaging tools for validation.
examples/3D_turb_mixing/case.py	Update 3D example to higher Re, grid stretching, and mixlayer config.
docs/documentation/case.md	Update docs to describe new synthetic turbulence parameters.
docs/documentation/references.md	Add Guo (2023) and Michalke (1964) references.
.typos.toml	Allow “TKE” in typo checker.

Comments suppressed due to low confidence (3)

examples/2D_mixing_artificial_Ma/case.py:110

Enabling mixlayer_perturb for a 2D case (p == 0) will trigger the PROHIBIT check (p > 0) and cause startup to fail. Please disable or guard this setting in 2D examples.

            "mixlayer_vel_coef": 1.0,

src/pre_process/m_checker.fpp:191

The new PROHIBIT rule only checks p > 0 but does not enforce mixlayer_vel_profile = .true.. To avoid misconfiguration, consider adding validation that the velocity profile flag is enabled when perturbations are requested.

        @:PROHIBIT(mixlayer_perturb .and. p == 0, "mixlayer_perturb requires p > 0")

toolchain/mfc/test/cases.py:634

The new test generator only covers 3D (len(dimInfo[0]) == 3) cases. If 2D support is intended, add a branch to test mixlayer perturbations in 2D.

    def alter_mixlayer_perturb(dimInfo):

toolchain/mfc/test/cases.py

hyeoksu-lee · 2025-06-30T17:55:47Z

@sbryngelson I guess this is now ready for merging

…esults (MFlowCode#879) Co-authored-by: Copilot <[email protected]> Co-authored-by: Hyeoksu Lee <[email protected]> Co-authored-by: Hyeoksu Lee <[email protected]> Co-authored-by: Hyeoksu Lee <[email protected]> Co-authored-by: Hyeoksu Lee <[email protected]> Co-authored-by: Hyeoksu Lee <[email protected]> Co-authored-by: Hyeoksu Lee <[email protected]> Co-authored-by: Hyeoksu Lee <[email protected]> Co-authored-by: Hyeoksu Lee <[email protected]> Co-authored-by: Hyeoksu Lee <[email protected]> Co-authored-by: Spencer Bryngelson <[email protected]> Co-authored-by: Hyeoksu Lee <[email protected]> Co-authored-by: Hyeoksu Lee <[email protected]> Co-authored-by: Hyeoksu Lee <[email protected]>

Hyeoksu Lee and others added 16 commits May 24, 2025 17:33

update mixlayer

657344b

update tests for mixlayer

33b8244

fix minor bug in mixlayer_perturb

c384beb

minor fix

44c019e

update prng

0a727c9

test

be036db

update prng

350b6c2

remove obsolete param

3427b0c

update tests and format

83fa91f

update constant and tests

564ce54

update turbulence stat matlab code (draft)

9e9e588

replace some magic numbers by global param

e0e14a5

Update turb stat

48ae773

update matlab code

aff2320

add matlab batch template file

d4f9faf

modify examples/3D_turb_mixing

98e854c

hyeoksu-lee requested review from a team and sbryngelson as code owners June 11, 2025 19:32

hyeoksu-lee and others added 4 commits June 11, 2025 12:34

Merge branch 'master' into mixlayer

b365477

minor fix

d11d153

add TKE as exception for spelling check

ee633d7

fix minor

7ba7baa

sbryngelson reviewed Jun 11, 2025

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remove images and *sh files

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sbryngelson reviewed Jun 13, 2025

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examples/3D_turb_mixing/turbulence_stat/average_tke_over_self_similar.m Outdated Show resolved Hide resolved

minor fix

8a2b530

Hyeoksu Lee and others added 3 commits June 24, 2025 01:08

update test for mixlayer_perturb

4a1b90d

update test for mixlayer_perturb

b68d4c6

update test

6161dd8

sbryngelson reviewed Jun 25, 2025

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hyeoksu-lee and others added 2 commits June 26, 2025 20:46

Merge branch 'master' into mixlayer

12829bd

enhance consistency of prng

c0cfefe

sbryngelson marked this pull request as draft June 27, 2025 13:00

Hyeoksu Lee and others added 2 commits June 27, 2025 17:54

update statistics

79c32ce

Merge branch 'master' into mixlayer

464c7aa

hyeoksu-lee marked this pull request as ready for review June 28, 2025 01:42

qodo-merge-pro bot added the Review effort 4/5 label Jun 28, 2025

sbryngelson requested review from Copilot and sbryngelson June 28, 2025 11:52

sbryngelson approved these changes Jun 28, 2025

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Merge branch 'master' into mixlayer

c937bd9

sbryngelson merged commit 5b8e2eb into MFlowCode:master Jul 1, 2025
40 of 41 checks passed

hyeoksu-lee deleted the mixlayer branch July 16, 2025 22:11

hyeoksu-lee mentioned this pull request Jul 17, 2025

fix docs #947

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Update initialization for turbulent mixing layer and add validation results #879

Update initialization for turbulent mixing layer and add validation results #879

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