PelePhysics 25.04

What's Changed

• Generate qssa.yaml via list by @malihass in #367
• Various CEPTR bug fixes by @malihass in #366
• Fix a couple of Code QL warnings by @esclapez in #368
• The PMF.H kernel was a Fortran converted routine, make it more C++ by @esclapez in #369
• Get rid of ordering diff of qss species by @malihass in #373
• Calculate some CK routines without using thread private arrays by @jrood-nrel in #370
• Put molecular weights in global array by @jrood-nrel in #375
• Use global_(i)mw throughout Eos and Reactors. by @esclapez in #376
• Move diagnostics over from LMeX. by @esclapez in #377
• Revert "Use global_(i)mw throughout Eos and Reactors." by @jrood-nrel in #378
• Update SUNDIALs and MAGMA by @jrood-nrel in #379
• Species as reactant and product by @malihass in #374
• Fix header declarations of ckinu and ckkfkr by @marchdf in #382
• Compute typical values on device by @jrood-nrel in #372
• Disallow Sutherland transport with SRK and GammaLaw by @baperry2 in #384
• Better global mw by @marchdf in #385
• Remove deprecated SinglePoint code by @baperry2 in #386
• Spring Cleaning: Docs and PMF by @baperry2 in #387
• Quiet warnings in Utility/Diagnostics by @esclapez in #388
• Fix one warning left over. by @esclapez in #389
• Yet another missing warning. by @esclapez in #390
• Update DiagFrameFlane with latest LMeX version. by @esclapez in #392
• Update Python in CI by @jrood-nrel in #394
• Update ceptr python requirement to 3.10 by @marchdf in #395
• Update ReactEval for new LMeX format by @esclapez in #393
• Restore CVODE OMP support by @esclapez in #397
• Precompute SRK quantities using CEPTR by @baperry2 in #398
• Fix sundials lib dir detection by @lainme in #399
• Update Intel OneAPI CI by @jrood-nrel in #400
• Fix input files by @jrood-nrel in #402
• Fix input files by @jrood-nrel in #403
• Clang tidy fixes by @marchdf in #404
• Compute cvode typical values using ParallelFor by @jrood-nrel in #406
• Use the sundials submodule for make TPL by @jrood-nrel in #410
• Fix hardcoded double by @jrood-nrel in #411
• Upgrade CEPTR to cantera 3.0 by @marchdf in #409
• add SRK EosEval test to CI by @baperry2 in #412
• Add intel-llvm option to ThirdParty makefile by @jrood-nrel in #413
• fix rescaling for FORD by @malihass in #414
• Fix fixed width formatting in diag headers by @baperry2 in #417
• Remove CMakeLists by @jrood-nrel in #418
• Fix implicit bool by @jrood-nrel in #419
• Fix warnings in PMF by @jrood-nrel in #420
• Fix narrowing conversions by @jrood-nrel in #421
• Replace use of amrex::max to std::max by @marchdf in #422
• Fix values in max by casting to int by @jrood-nrel in #423
• Bump setup python version by @marchdf in #424
• Fix warnings by @jrood-nrel in #425
• Fix codeql by @marchdf in #426
• Add codespell by @marchdf in #427
• Fix last PeleC codeql by @marchdf in #428
• Enable ccache by @marchdf in #429
• Add ifdef to remove BDF for large mechanisms on the GPU by @jrood-nrel in #430
• Changes due to updated black by @baperry2 in #432
• Update isooctane_lu mechanism to allow it to be generated by @jrood-nrel in #431
• Clip the concentrations on fractional pows by @marchdf in #433
• enable COMP=clang for TPL by @baperry2 in #434
• diagPDF: barriers on atomic add to bins by @baperry2 in #436
• Add multiprocessing for ceptr by @marchdf in #437
• Add a cvode switch on the ordering by @marchdf in #383
• Remove tc thread private array by @marchdf in #435
• Simplify ceptr python code by @marchdf in #438
• Move dcvpdtemp by @marchdf in #439
• Upgrade CEPTR thermo generation by @marchdf in #440
• Add NASA9 polynomials by @marchdf in #441
• Fix ceptr format files by @marchdf in #444
• Filter Utility by @baperry2 in #445
• Add the Util folder from PeleMP by @marchdf in #443
• add interp_type option and get rr function for pltfilemanager by @baperry2 in #447
• Move PeleMP Source files to PelePhysics by @marchdf in #448
• Move PeleMP docs into PelePhysics by @marchdf in #449
• Add amrex and sundials as submodules of PelePhysics by @baperry2 in #451
• Bump Submodules/amrex from edb4c25 to 43d71da by @dependabot in #453
• Move a bunch of directories around by @marchdf in #452
• Fix error of PmfData on GPU (resolved conflicts from file reorg) by @ensonun in #457
• Fix warnings by @marchdf in #458
• Move PeleRad source files to PelePhysics by @jrood-nrel in #459
• Fix warnings in PeleRad by @jrood-nrel in #461
• Remove prob parm passing in spray by @marchdf in #462
• Update github cache cleanup by @jrood-nrel in #464
• Use AMReX assert by @jrood-nrel in #463
• Rename macro by @jrood-nrel in #465
• Updates for PeleLMeX by @jrood-nrel in #466
• Fix warnings by @jrood-nrel in #467
• Bump Submodules/amrex from 43d71da to 75571e2 by @dependabot in #468
• Fix dependency warning from pandas about pyarrow by @marchdf in #470
• README updates/citation by @baperry2 in #471
• Need a return statement in BDF even for big mech. by @esclapez in #472
• Bump Submodules/amrex from 75571e2 to 296ed40 by @dependabot in #474
• Add clang-format dependency for ceptr by @marchdf in #475
• Surface Chemistry - Modified mechanism.H preprocessor directives & mechanism.cpp reaction maps by @jAnirudh in https://github.com/AMReX-Combustion/PelePhys...

PelePhysics 23.03

Setup CMake (#364)

* Add CMakeLists in the various subfolders.

* First pass at setting up cmake compilation and targets.

* Add the right include folder for the selected mechanism.

* A few fixes in CMakeLists.txt.

* Update to have CUDA working. Self build of lib functions.

* Jon's suggestions.

* Fixes related to updated cmake minimum version.

* Remove *_api and a few fixes. Tested as a subdir in LMeX with
MPI, MPI+CUDA and MPI+HIP.