Multicomponent diffusion fluxes, thermal conduction, and mixture viscosity #934

DimAdam-01 · 2025-07-11T02:43:51Z

User description

Description

Please include a summary of the changes and the related issue(s) if they exist.

This update implements the diffusive fluxes for chemical species, includes thermal conduction in the energy equation, and computes the mixture’s viscosity.

Please also include relevant motivation and context.

Fixes #(issue) [optional]

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?

Please describe the tests that you ran to verify your changes.
Provide instructions so we can reproduce.
Please also list any relevant details for your test configuration

Test A: This test examines one-dimensional multicomponent diffusion of four distinct species, as detailed in DOI 10.2514/6.2020-1751.

Test B: Test B examines a two-dimensional premixed flame with an imposed perturbation, then tracks the ensuing thermo-diffusive instability growth.

Test Configuration:

What computers and compilers did you use to test this:

My Laptop, Delta (A100) and Delta AI (GH)

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

If your code changes any code source files (anything in `src/simulation`)

To make sure the code is performing as expected on GPU devices, I have:

Checked that the code compiles using NVHPC compilers
Checked that the code compiles using CRAY compilers
Ran the code on either V100, A100, or H100 GPUs and ensured the new feature performed as expected (the GPU results match the CPU results)
Ran the code on MI200+ GPUs and ensure the new features performed as expected (the GPU results match the CPU results)
Enclosed the new feature via nvtx ranges so that they can be identified in profiles
Ran a Nsight Systems profile using ./mfc.sh run XXXX --gpu -t simulation --nsys, and have attached the output file (.nsys-rep) and plain text results to this PR
Ran a Rocprof Systems profile using ./mfc.sh run XXXX --gpu -t simulation --rsys --hip-trace, and have attached the output file and plain text results to this PR.
Ran my code using various numbers of different GPUs (1, 2, and 8, for example) in parallel and made sure that the results scale similarly to what happens if you run without the new code/feature

PR Type

Enhancement

Description

Implement multicomponent diffusion fluxes for chemical species
Add thermal conduction to energy equation
Integrate mixture viscosity computation for chemistry
Add new test case for multicomponent diffusion validation

Diagram Walkthrough

flowchart LR
  A["Chemistry Module"] --> B["Diffusion Flux Computation"]
  A --> C["Viscosity Calculation"]
  B --> D["Species Mass Fluxes"]
  B --> E["Thermal Conduction"]
  D --> F["Energy Equation Update"]
  E --> F
  C --> G["Riemann Solver Integration"]
  F --> H["RHS Updates"]
  G --> H

File Walkthrough

Relevant files

Enhancement

3 files

m_rhs.fpp `Add diffusion flux computation and RHS updates`	+131/-37
m_chemistry.fpp `Implement diffusion flux and viscosity calculations`	+166/-1
m_riemann_solvers.fpp `Integrate viscosity computation in Riemann solvers`	+51/-0

Tests

10 files

1dHardcodedIC.fpp `Add hardcoded initial conditions for diffusion test`	+30/-0
cases.py `Add multicomponent diffusion test case`	+16/-2
golden-metadata.txt `Update test metadata for new environment`	+10/-144
golden-metadata.txt `Update test metadata for new environment`	+10/-144
golden-metadata.txt `Update test metadata for new environment`	+10/-144
golden-metadata.txt `Update test metadata for new environment`	+10/-144
golden-metadata.txt `Update test metadata for new environment`	+10/-144
golden-metadata.txt `Update test metadata for new environment`	+10/-144
golden-metadata.txt `Update test metadata for new environment`	+10/-144
golden-metadata.txt `Add new test metadata file`	+18/-0

Bug fix

1 files

m_variables_conversion.fpp `Fix tolerance variable reference in chemistry`	+1/-2

Configuration changes

4 files

m_start_up.fpp `Add GPU memory updates for chemistry parameters`	+3/-0
m_global_parameters.fpp `Update GPU memory for chemistry parameters`	+2/-0
case.py `Update wave speeds and average state parameters`	+2/-2
input.py `Add OpenACC directive to Pyrometheus code generation`	+1/-1

Dependencies

1 files

pyproject.toml `Update Pyrometheus dependency version`	+2/-2

Additional files

5 files

golden.txt	+24/-24
golden.txt	+56/-0
golden.txt	+24/-24
golden.txt	+24/-24
golden.txt	+24/-24

…to Diffusion

…sion

sbryngelson · 2025-08-10T03:35:55Z

@DimAdam-01 can you fix your merge conflicts

sbryngelson · 2025-08-25T15:22:50Z

status? also please use descriptive commit messages. also, spamming commits causes the CI to run dozens of times and clogs up the self hosted runners.

sbryngelson · 2025-09-24T17:59:00Z

this seems to be looking pretty good. is there anything missing at the moment? @DimAdam-01

DimAdam-01 · 2025-09-24T18:50:58Z

this seems to be looking pretty good. is there anything missing at the moment? @DimAdam-01

No everything is there, just to mention, in order to get the code to run on the Frontier , I had to modify the Pyrometheus code generation script (in toolchain/mfc/run/input.py). I added the directive_offload="acc", which was necessary for the code to compile and pass all tests. @sbryngelson

sbryngelson · 2025-09-24T18:53:40Z

this seems to be looking pretty good. is there anything missing at the moment? @DimAdam-01

No everything is there, just to mention, in order to get the code to run on the Frontier , I had to modify the Pyrometheus code generation script (in toolchain/mfc/run/input.py). I added the directive_offload="acc", which was necessary for the code to compile and pass all tests. @sbryngelson

Got it. That's fine. @prathi-wind can fix that, oacc is default for now anyway. I saw his latest push to his draft PR and the only failing OMP test was chemistry, so somethings there need to be fixed anyway.

qodo-merge-pro · 2025-09-25T00:57:08Z

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 diffusion flux energy correction accumulates within the species loop, subtracting h_kYsrho_Vic repeatedly; this looks like it should be applied once after computing rho_Vic and the raw species fluxes, not accumulated per species. Please verify conservation and that Mass_Diffu_Energy is not over-subtracted. $:GPU_LOOP(parallelism='[seq]') do eqn = chemxb, chemxe Mass_Diffu_Flux(eqn - chemxb + 1) = rho_cellmass_diffusivities_mixavg_Cell(eqn - chemxb + 1) & molecular_weights(eqn - chemxb + 1)/MW_celldXk_dxi(eqn - chemxb + 1) rho_Vic = rho_Vic + Mass_Diffu_Flux(eqn - chemxb + 1) Mass_Diffu_Energy = Mass_Diffu_Energy + h_k(eqn - chemxb + 1)Mass_Diffu_Flux(eqn - chemxb + 1) end do ! Apply corrections for mass conservation $:GPU_LOOP(parallelism='[seq]') do eqn = chemxb, chemxe Mass_Diffu_Energy = Mass_Diffu_Energy - h_k(eqn - chemxb + 1)Ys_cell(eqn - chemxb + 1)rho_Vic Mass_Diffu_Flux(eqn - chemxb + 1) = Mass_Diffu_Flux(eqn - chemxb + 1) - rho_VicYs_cell(eqn - chemxb + 1) end do ! Add thermal conduction contribution Mass_Diffu_Energy = lambda_CelldT_dxi + Mass_Diffu_Energy ! Update flux arrays Duplicate Logic The per-direction RHS updates for viscous/surface_tension vs diffusion duplicate the same divergence pattern three times with only dx/dy/dz and index strides differing; consider factoring into a small helper to reduce maintenance risk and keep diffusion and viscous paths consistent. if (surface_tension .or. viscous) then $:GPU_PARALLEL_LOOP(collapse=3) do l = 0, p do k = 0, n do j = 0, m $:GPU_LOOP(parallelism='[seq]') do i = momxb, E_idx rhs_vf(i)%sf(j, k, l) = & rhs_vf(i)%sf(j, k, l) + 1._wp/dx(j)* & (flux_src_n_in(i)%sf(j - 1, k, l) & - flux_src_n_in(i)%sf(j, k, l)) end do end do end do end do end if if (chem_params%diffusion) then $:GPU_PARALLEL_LOOP(collapse=3) do l = 0, p do k = 0, n do j = 0, m $:GPU_LOOP(parallelism='[seq]') do i = chemxb, chemxe rhs_vf(i)%sf(j, k, l) = & rhs_vf(i)%sf(j, k, l) + 1._wp/dx(j)* & (flux_src_n_in(i)%sf(j - 1, k, l) & - flux_src_n_in(i)%sf(j, k, l)) end do if (.not. viscous) then rhs_vf(E_idx)%sf(j, k, l) = & rhs_vf(E_idx)%sf(j, k, l) + 1._wp/dx(j)* & (flux_src_n_in(E_idx)%sf(j - 1, k, l) & - flux_src_n_in(E_idx)%sf(j, k, l)) end if end do end do end do end if elseif (idir == 2) then ! y-direction if (surface_tension) then $:GPU_PARALLEL_LOOP(collapse=3) do l = 0, p do k = 0, n do j = 0, m rhs_vf(c_idx)%sf(j, k, l) = & rhs_vf(c_idx)%sf(j, k, l) + 1._wp/dy(k)* & q_prim_vf(c_idx)%sf(j, k, l)* & (flux_src_n_in(advxb)%sf(j, k, l) - & flux_src_n_in(advxb)%sf(j, k - 1, l)) end do end do end do end if if (cyl_coord .and. ((bc_y%beg == -2) .or. (bc_y%beg == -14))) then if (viscous) then if (p > 0) then call s_compute_viscous_stress_tensor(q_prim_vf, & dq_prim_dx_vf(mom_idx%beg:mom_idx%end), & dq_prim_dy_vf(mom_idx%beg:mom_idx%end), & dq_prim_dz_vf(mom_idx%beg:mom_idx%end), & tau_Re_vf, & idwbuff(1), idwbuff(2), idwbuff(3)) else call s_compute_viscous_stress_tensor(q_prim_vf, & dq_prim_dx_vf(mom_idx%beg:mom_idx%end), & dq_prim_dy_vf(mom_idx%beg:mom_idx%end), & dq_prim_dy_vf(mom_idx%beg:mom_idx%end), & tau_Re_vf, & idwbuff(1), idwbuff(2), idwbuff(3)) end if $:GPU_PARALLEL_LOOP(collapse=2) do l = 0, p do j = 0, m $:GPU_LOOP(parallelism='[seq]') do i = momxb, E_idx rhs_vf(i)%sf(j, 0, l) = & rhs_vf(i)%sf(j, 0, l) + 1._wp/(y_cc(1) - y_cc(-1))* & (tau_Re_vf(i)%sf(j, -1, l) & - tau_Re_vf(i)%sf(j, 1, l)) end do end do end do end if $:GPU_PARALLEL_LOOP(collapse=3) do l = 0, p do k = 1, n do j = 0, m $:GPU_LOOP(parallelism='[seq]') do i = momxb, E_idx rhs_vf(i)%sf(j, k, l) = & rhs_vf(i)%sf(j, k, l) + 1._wp/dy(k)* & (flux_src_n_in(i)%sf(j, k - 1, l) & - flux_src_n_in(i)%sf(j, k, l)) end do end do end do end do else if (viscous .or. surface_tension) then $:GPU_PARALLEL_LOOP(collapse=3) do l = 0, p do k = 0, n do j = 0, m $:GPU_LOOP(parallelism='[seq]') do i = momxb, E_idx rhs_vf(i)%sf(j, k, l) = & rhs_vf(i)%sf(j, k, l) + 1._wp/dy(k)* & (flux_src_n_in(i)%sf(j, k - 1, l) & - flux_src_n_in(i)%sf(j, k, l)) end do end do end do end do end if if (chem_params%diffusion) then $:GPU_PARALLEL_LOOP(collapse=3) do l = 0, p do k = 0, n do j = 0, m $:GPU_LOOP(parallelism='[seq]') do i = chemxb, chemxe rhs_vf(i)%sf(j, k, l) = & rhs_vf(i)%sf(j, k, l) + 1._wp/dy(k)* & (flux_src_n_in(i)%sf(j, k - 1, l) & - flux_src_n_in(i)%sf(j, k, l)) end do if (.not. viscous) then rhs_vf(E_idx)%sf(j, k, l) = & rhs_vf(E_idx)%sf(j, k, l) + 1._wp/dy(k)* & (flux_src_n_in(E_idx)%sf(j, k - 1, l) & - flux_src_n_in(E_idx)%sf(j, k, l)) end if end do end do end do end if end if ! Applying the geometrical viscous Riemann source fluxes calculated as average ! of values at cell boundaries if (cyl_coord) then if ((bc_y%beg == -2) .or. (bc_y%beg == -14)) then $:GPU_PARALLEL_LOOP(collapse=3) do l = 0, p do k = 1, n do j = 0, m $:GPU_LOOP(parallelism='[seq]') do i = momxb, E_idx rhs_vf(i)%sf(j, k, l) = & rhs_vf(i)%sf(j, k, l) - 5.e-1_wp/y_cc(k)* & (flux_src_n_in(i)%sf(j, k - 1, l) & + flux_src_n_in(i)%sf(j, k, l)) end do end do end do end do if (viscous) then $:GPU_PARALLEL_LOOP(collapse=2) do l = 0, p do j = 0, m $:GPU_LOOP(parallelism='[seq]') do i = momxb, E_idx rhs_vf(i)%sf(j, 0, l) = & rhs_vf(i)%sf(j, 0, l) - 1._wp/y_cc(0)* & tau_Re_vf(i)%sf(j, 0, l) end do end do end do end if else $:GPU_PARALLEL_LOOP(collapse=3) do l = 0, p do k = 0, n do j = 0, m $:GPU_LOOP(parallelism='[seq]') do i = momxb, E_idx rhs_vf(i)%sf(j, k, l) = & rhs_vf(i)%sf(j, k, l) - 5.e-1_wp/y_cc(k)* & (flux_src_n_in(i)%sf(j, k - 1, l) & + flux_src_n_in(i)%sf(j, k, l)) end do end do end do end do end if end if elseif (idir == 3) then ! z-direction if (surface_tension) then $:GPU_PARALLEL_LOOP(collapse=3) do l = 0, p do k = 0, n do j = 0, m rhs_vf(c_idx)%sf(j, k, l) = & rhs_vf(c_idx)%sf(j, k, l) + 1._wp/dz(l)* & q_prim_vf(c_idx)%sf(j, k, l)* & (flux_src_n_in(advxb)%sf(j, k, l) - & flux_src_n_in(advxb)%sf(j, k, l - 1)) end do end do end do end if if (viscous .or. surface_tension) then $:GPU_PARALLEL_LOOP(collapse=3) do l = 0, p do k = 0, n do j = 0, m $:GPU_LOOP(parallelism='[seq]') do i = momxb, E_idx rhs_vf(i)%sf(j, k, l) = & rhs_vf(i)%sf(j, k, l) + 1._wp/dz(l)* & (flux_src_n_in(i)%sf(j, k, l - 1) & - flux_src_n_in(i)%sf(j, k, l)) end do end do end do end do end if if (chem_params%diffusion) then $:GPU_PARALLEL_LOOP(collapse=3) do l = 0, p do k = 0, n do j = 0, m $:GPU_LOOP(parallelism='[seq]') do i = chemxb, chemxe rhs_vf(i)%sf(j, k, l) = & rhs_vf(i)%sf(j, k, l) + 1._wp/dz(l)* & (flux_src_n_in(i)%sf(j, k, l - 1) & - flux_src_n_in(i)%sf(j, k, l)) end do if (.not. viscous) then rhs_vf(E_idx)%sf(j, k, l) = & rhs_vf(E_idx)%sf(j, k, l) + 1._wp/dz(l)* & (flux_src_n_in(E_idx)%sf(j, k, l - 1) & - flux_src_n_in(E_idx)%sf(j, k, l)) end if end do end do end do end if Likely Typo The assignment to q_prim_vf at advxb is performed twice consecutively with the same value, which appears redundant and could mask a missing intended variable initialization. q_prim_vf(advxb)%sf(i, 0, 0) = 1.0_wp q_prim_vf(advxb)%sf(i, 0, 0) = 1.0_wp

src/simulation/m_rhs.fpp

src/common/m_chemistry.fpp

src/pre_process/include/1dHardcodedIC.fpp

src/simulation/m_rhs.fpp

Copilot

Pull Request Overview

This PR implements multicomponent diffusion fluxes, thermal conduction, and mixture viscosity for chemical species in the MFC solver. It adds new chemistry functionality to enable more sophisticated multispecies flow simulations with transport phenomena.

Key changes include:

Implementation of species mass diffusion flux computations using mixture-averaged approaches
Addition of thermal conduction in the energy equation for chemistry cases
Integration of mixture viscosity calculations for chemical species

Reviewed Changes

Copilot reviewed 20 out of 24 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
src/common/m_chemistry.fpp	Implements core diffusion flux computation and viscosity calculation routines
src/simulation/m_rhs.fpp	Adds diffusion flux RHS updates and memory allocation for chemistry diffusion
src/simulation/m_riemann_solvers.fpp	Integrates viscosity computation and adds flux source initialization for chemistry
src/pre_process/include/1dHardcodedIC.fpp	Adds hardcoded initial conditions for multicomponent diffusion test case
toolchain/mfc/test/cases.py	Adds new test case for multicomponent diffusion validation
src/simulation/m_start_up.fpp	Updates GPU memory management for chemistry parameters
src/simulation/m_global_parameters.fpp	Updates GPU memory handling for chemistry parameters
src/common/m_variables_conversion.fpp	Fixes tolerance variable reference
toolchain/pyproject.toml	Updates Pyrometheus dependency version
toolchain/mfc/run/input.py	Adds OpenACC directive to Pyrometheus code generation

Comments suppressed due to low confidence (1)

src/simulation/m_rhs.fpp:1

Code duplication detected. The RHS flux update pattern is repeated for viscous/surface_tension and diffusion cases. Consider extracting this into a helper subroutine to follow DRY principles.

!>

src/common/m_chemistry.fpp

toolchain/mfc/test/cases.py

DimAdam-01 and others added 30 commits June 8, 2025 15:06

Diffusion Fluxes

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Debugging

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dff

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MInor Bugs

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Minor Bugs

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Merge branch 'Diffusion' of https://github.com/DimAdam-01/MFC-Adam in…

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…to Diffusion

Loop stuff

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Delta Issue

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Small Changes

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Small Changes V2

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Spelling

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Merge branch 'MFlowCode:master' into Diffusion

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Merge branch 'master' into Diffusion

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Merge branch 'master' into Diffusion

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Merge branch 'master' into Diffusion

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Refactoring and Deallocation

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Merge branch 'Diffusion' of https://github.com/DimAdam-01/MFC-Adam in…

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…to Diffusion

Small Stuff

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Small Changes

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Merge branch 'master' into Diffusion

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Chem ToolChain

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Merge branch 'Diffusion' of https://github.com/DimAdam-01/MFC-Adam in…

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DimAdam-01 added 2 commits July 16, 2025 12:19

Merge branch 'Diffusion' of github.com:DimAdam-01/MFC-Adam into Diffu…

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…sion

Newton Raphson Tolerance Frontier Test

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Dimitrios Adam added 6 commits August 21, 2025 00:26

Merge remote-tracking branch 'upstream/master' into Diffusion

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Small Stuff

aba114a

Resolve Merge Issues

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Frontier Issue Checking

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Formatting

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DimAdam-01 marked this pull request as draft September 2, 2025 17:32

Dimitrios Adam added 3 commits September 23, 2025 20:54

Pyrometheus Pypi

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Small Changes

34497cd

Small Final Changes

100309e

sbryngelson approved these changes Sep 24, 2025

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DimAdam-01 marked this pull request as ready for review September 25, 2025 00:56

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sbryngelson requested a review from Copilot September 25, 2025 18:03

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Dimitrios Adam added 2 commits September 25, 2025 16:03

Suggestions from AI

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Merge remote-tracking branch 'upstream/master' into Diffusion

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DimAdam-01 force-pushed the Diffusion branch from b01d6fa to ad6229b Compare September 25, 2025 20:14

sbryngelson approved these changes Sep 26, 2025

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sbryngelson merged commit eb152c5 into MFlowCode:master Sep 28, 2025
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Multicomponent diffusion fluxes, thermal conduction, and mixture viscosity #934

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Multicomponent diffusion fluxes, thermal conduction, and mixture viscosity #934

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