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Add full manifold model capability #415

Merged
merged 33 commits into from
Nov 6, 2024
Merged

Add full manifold model capability #415

merged 33 commits into from
Nov 6, 2024

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baperry2
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Depends on #414

@baperry2 baperry2 force-pushed the manifold-specific-capability branch 3 times, most recently from 831c5a2 to f89faee Compare September 18, 2024 21:59
@baperry2 baperry2 force-pushed the manifold-specific-capability branch from f89faee to d55daa0 Compare September 23, 2024 19:45
@baperry2 baperry2 marked this pull request as ready for review October 24, 2024 20:35
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baperry2 commented Oct 24, 2024 •
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This is now mostly ready, except for documentation and adding to the CI.

There is a FlameSheet example case (input.manifold) that can be run by compiling with USE_MANIFOLD = TRUE. That case requires a pmf data file and a tabulated chemistry file that can be run using the script get_pmfdat_and_chemtable.py in the CMLM repo: https://github.com/NREL/cmlm/blob/development/get_pmfdat_and_ctable.py

The test case uses a 1D table based on cantera premixed flames at the same conditions as the detailed chemistry FlameSheet test.

@baperry2 baperry2 changed the title WIP: Add full manifold model capability Add full manifold model capability Oct 24, 2024
marchdf
marchdf reviewed Oct 30, 2024
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Left some minor comments

drummerdoc
drummerdoc reviewed Nov 1, 2024
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@baperry2 baperry2 merged commit 86c4721 into AMReX-Combustion:development Nov 6, 2024
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baperry2 commented Nov 6, 2024

Going to merge this now. Will add docs and more testing in future PRs.

terencelehmann pushed a commit to ITV-RWTH/PeleLMeX that referenced this pull request Nov 14, 2024
@ThomasHowarth @dmontgomeryNREL
@baperry2 @dependabot @marchdf
Latest updates (#1)
7ce8cdd 
* DivU constraint with arbitrary sources (AMReX-Combustion#428)

* Included additional terms in divu constraint to account for external forces on density.

* Updated Docs to include external source terms in model equations and divergence constraint.

* Formatting

* fix a bug in divu calc

* Update deriviation of divu in Docs

* Restored code to development

* Reverted text in line 168

* Minor fix in Docs

* Comment in divu about extRho

---------

Co-authored-by: Bruce Perry <[email protected]>

* "ODE" quantities and user defined external sources (AMReX-Combustion#427)

* Initial commit.  Needs debugging for source terms.

* Added ode_var to typical values. Still debugging initialization and source.

* Minor edit in set_ode_names function.

* Fixed misalignment in plotting. IC's appear to be correct now for multiple ode vars.  Still working on source terms.

* Fix indexing.

* Updated problem_modify_ext_sources.  Works with local case definition.

* Comment arguments in problem_modify_ext_sources in Source code.

* Added compilation variable USE_MODIFIED_SOURCES to avoid unnecessary loops through levels.

* Tested plotting for Efield and Spray.  Tested all args of ProblemSpecificFunctions.

* Added ode_srcstrength to test case, fixed minor bugs.

* Changed flag for user defined external sources.  Added future flag for including external sources in SDC loop.

* Set peleLM.user_defined_ext_sources to true in input file.

* Added Euler step for advancing the ODE quantities in time.

* Changed name of advanceODEQty() to predictODEQty() for consistency with SDC iterations.

* Updated input.2d for validation

* Added .cpp file for ProblemSpecificFunctions to avoid need for static functions.

* Added convergence test for ODE Qty.

* Updated the test case to include 3 odes with increasing stiffness.

* Renamed case

* Combined all external forces in single function call to clean up PeleLMeX_Advance.cpp

* Update README for case.

* Update README for case.

* Update README.md

* Removed NUM_AUX for now.

* Cleaning up

* Documentation for ode quantities.

* Clang-format

* Remove validation tests from case directory.

* Minor fix for soot and spray

* Spelling and unused variable handling.

* Unused variable handling

* Formatting

* Removed unwanted print statements, renamed some files/vars for consistency.

* Added case to CI

* Add USE_EB to EB_ODEQty/CmakeLists.txt

* Add EB_ODEQty to RegTests/CMakeLists.txt

* CI fix

* More CI

* Add ODEQty.cpp to cmake

* More CI...

* Only define predictODEQty if NUM_ODE > 0

* Updated CMake to handle user defined EB's and ProblemSpecificFunctions

* Now passes in MultiFabs for state_old and state_new. This provides access to state_old.Factory() etc.

* Update PeleLMeX_ProblemSpecificFunctions.cpp

* Removed lev argument in problem_modify_ext_sources

* Update comment

---------

Co-authored-by: Bruce Perry <[email protected]>

* pin intel-oneapi version in CI (AMReX-Combustion#434)

* Bump Submodules/AMReX-Hydro from `3ab9864` to `3788361` (AMReX-Combustion#433)

Bumps [Submodules/AMReX-Hydro](https://github.com/AMReX-Fluids/AMReX-Hydro) from `3ab9864` to `3788361`.
- [Commits](AMReX-Fluids/AMReX-Hydro@3ab9864...3788361)

---
updated-dependencies:
- dependency-name: Submodules/AMReX-Hydro
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Bruce Perry <[email protected]>

* Add full manifold model capability (AMReX-Combustion#415)

* basics of having eos_parm in PeleLMeX

* add eosparm to PeleLMeX_K functions

* more eosparm: now everywhere except Efield & BCs

* eosparm in BC stuff

* re-order functions for template

* remove manifold-specfic changes, will go in later PR

* gnu make changes for manifold

* create manifold version of adjust fluxes function

* Add abort for Closed Chamber + Manifold

* Better setup chackes for Manifold + wbar, closed chamber, mixfrac/prog

* advection of rho corrections for manifold models

* manifold-specific transport, derives, divu

* remove divide by zero

* go to templated EOS functions to use cellData

* fix oops in pelephysics

* fix compile errors for Manifold derives

* fix compile condition for transparm initialization

* fix missing RY2RRinvY conversion

* use PelePhysics that free manfunc shared pointer

* clang-formatting

* fux derives for manifold

* add flamesheet test case for manifold

* remove extraneous changes in file

* Update Source/PeleLMeX_Setup.cpp

Co-authored-by: Marc T. Henry de Frahan <[email protected]>

* address Marc HdF's comments with minor formatting

* remove copied line

* update PP for merged RY2R stuff

---------

Co-authored-by: Marc T. Henry de Frahan <[email protected]>

* Update PelePhysics and add path to new utility  (AMReX-Combustion#435)

* Update PelePhysics and add new utility to Make.PeleLMeX

* Add PelePhysics utilities to CMake

* Test PelePhysics:tidy against clang-tidy.

* Update PelePhysics submodule

* Bump Submodules/AMReX-Hydro from `3ab9864` to `3788361` (AMReX-Combustion#438)

Bumps [Submodules/AMReX-Hydro](https://github.com/AMReX-Fluids/AMReX-Hydro) from `3ab9864` to `3788361`.
- [Commits](AMReX-Fluids/AMReX-Hydro@3ab9864...3788361)

---
updated-dependencies:
- dependency-name: Submodules/AMReX-Hydro
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump Submodules/PelePhysics from `327aadb` to `f54b084` (AMReX-Combustion#439)

Bumps [Submodules/PelePhysics](https://github.com/AMReX-Combustion/PelePhysics) from `327aadb` to `f54b084`.
- [Release notes](https://github.com/AMReX-Combustion/PelePhysics/releases)
- [Commits](AMReX-Combustion/PelePhysics@327aadb...f54b084)

---
updated-dependencies:
- dependency-name: Submodules/PelePhysics
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: Dave Montgomery <[email protected]>
Co-authored-by: Bruce Perry <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Marc T. Henry de Frahan <[email protected]>
@baperry2 baperry2 deleted the manifold-specific-capability branch December 17, 2024 00:48
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@marchdf marchdf marchdf approved these changes

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