Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Conversation

baperry2
Copy link
Collaborator

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 marked this pull request as ready for review October 24, 2024 20:35
@baperry2
Copy link
Collaborator Author

baperry2 commented Oct 24, 2024 •
edited
Loading

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
View reviewed changes
Source/PeleLMeX_Setup.cpp Outdated Show resolved Hide resolved
marchdf
marchdf reviewed Oct 30, 2024
View reviewed changes
Source/PeleLMeX_Setup.cpp Outdated Show resolved Hide resolved
marchdf
marchdf reviewed Oct 30, 2024
View reviewed changes
Source/PeleLMeX_K.H Outdated Show resolved Hide resolved
marchdf
marchdf approved these changes Oct 30, 2024
View reviewed changes
Copy link
Contributor

@marchdf marchdf left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Left some minor comments

drummerdoc
drummerdoc reviewed Nov 1, 2024
View reviewed changes
Exec/Make.PeleLMeX Outdated Show resolved Hide resolved
@baperry2 baperry2 merged commit 86c4721 into AMReX-Combustion:development Nov 6, 2024
24 checks passed
@baperry2
Copy link
Collaborator Author

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 <bruce.perry@nrel.gov>

* "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 <Bruce.Perry@nrel.gov>

* 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] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Bruce Perry <Bruce.Perry@nrel.gov>

* 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 <marchdf@gmail.com>

* 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 <marchdf@gmail.com>

* 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] <support@github.com>
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] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Dave Montgomery <David.Montgomery@nrel.gov>
Co-authored-by: Bruce Perry <bruce.perry@nrel.gov>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Marc T. Henry de Frahan <marchdf@gmail.com>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@marchdf marchdf marchdf approved these changes

@drummerdoc drummerdoc drummerdoc approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@baperry2 @drummerdoc @marchdf