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 #473
• Fix regrid for radiation module by @wjge in #477
• update amrex by @baperry2 in #476
• surfchem - modified the ckinu method in the ceptr ck module by @jAnirudh in #478
• Bump Submodules/amrex from 2ecafcf to 9751217 by @dependabot in #479
• Max substep input for CVODE by @ThomasHowarth in #481
• Add citation by @marchdf in #482
• Fix doi url link by @marchdf in #483
• n_files input for DiagFramePlane diagnostic by @ThomasHowarth in #485
• Bump Submodules/amrex from 9751217 to 728eec4 by @dependabot in #488
• Move turb inflow helpers from PeleLMeX and add documentation by @baperry2 in #489
• modify bounds checkings in the radiation module by @wjge in #490
• Add cray to compilers for make TPL by @baperry2 in #491
• GH action deprecation fix by @marchdf in #493
• Bump python versions in CI and CEPTR by @marchdf in #494
• Update black for ceptr by @marchdf in #495
• Bump Submodules/amrex from 728eec4 to 1735fd5 by @dependabot in #496
• update Factory to allow for chained inheritance by @baperry2 in #498
• Fix clang-tidy warning by @marchdf in #501
• Update the CEPTR usage doc slightly. by @EnnaDelfen in #499
• Fix default viscosity_mu_ref value in Sutherland model by @JhonCordova in #502
• Fix codespell by @marchdf in #505
• Add nvhpc compiler to thirdparty by @jrood-nrel in #503
• Update SUNDIALS to 7.0 by @jrood-nrel in #500
• Bump Submodules/amrex from 1735fd5 to f141191 by @dependabot in #506
• peleparams: common data container for PMF, transport (others in future) by @baperry2 in #507
• Fix sundials link order by @jrood-nrel in #508
• update amrex to get kestrel make update by @baperry2 in #509
• Shallow clone submodules by @marchdf in #510
• Manifold Models: Tables and Network capability, wrappers in EOS, Transport by @baperry2 in #492
• update amrex to get bicgcg fix by @baperry2 in #512
• Simplify Make.package in mechanisms by @baperry2 in #515
• Added functions to get nsteps after reading plot file by @SreejithNREL in #516
• revert sundials to 7.0.0 because of 7.1.1 deprecations by @baperry2 in #517
• Update amrex by @marchdf in #518
• Fix warnings by @marchdf in #519
• Bump Submodules/amrex from c09da99 to de4dc97 by @dependabot in #523
• update clang format action version to avoid distutils issue by @baperry2 in #525
• go back to recommending shallow submodules by @baperry2 in #524
• Soot cleanup by @baperry2 in #526
• Update readme with citation by @marchdf in #527
• Support Manifold EoS in RK64 Reactor by @baperry2 in #513
• Add warning report to docs by @jrood-nrel in #528
• Bump Submodules/amrex from de4dc97 to 8349789 by @dependabot in #529
• Remove null pointer dereference for GammaLaw EOS by @baperry2 in #533
• Some fixes for warnings in 2D by @baperry2 in #534
• Update SUNDIALS to 7.1.1 by @jrood-nrel in #531
• Fix clang-tidy by @marchdf in #535
• pin intel-oneapi version in CI by @baperry2 in #541
• Bump Submodules/amrex from 8349789 to 00e6f75 by @dependabot in #540
• Make EOS functions templates to allow for CellData as an argument by @baperry2 in #536
• Unit conversions by @dmontgomeryNREL in #539
• Tidied up nested namespace in Utilities for clang-tidy by @dmontgomeryNREL in #545
• Update CI to ubuntu-24.04 by @jrood-nrel in #546
• Bump Submodules/amrex from 00e6f75 to f27eb69 by @dependabot in #550
• speciesNames for Manifold EOS by @baperry2 in #542
• update sundials - sycl 2025 fix by @baperry2 in #551
• CEPTR: PLOG reaction support at constant pressure by @terencelehmann in #549
• Docs workflow update by @baperry2 in #554
• Bump Submodules/amrex from f27eb69 to b3f6738 by @dependabot in #555
• add link to pubs page in README by @baperry2 in #556
• update cantera to 3.1 to get fix for occasional issue with qss conversion by @baperry2 in #558
• Manifold EOS: variance support by @baperry2 in #552
• Bump Submodules/amrex from b3f6738 to 69f1ac8 by @dependabot in #559
• Inconsistency of MW/iMW precisions in CEPTR by @EnnaDelfen in #560
• Bump Submodules/amrex from 69f1ac8 to 06b4a5b by @dependabot in #562
• Free pmf dynamic data structures by @baperry2 in #563
• Bump Submodules/amrex from 06b4a5b to 7626a3f by @dependabot in #565
• add 4spec nonreacting mech for co2snow by @baperry2 in #567
• update amrex and sundials to latest releases by @baperry2 in #568

New Contributors

• @lainme made their first contribution in #399
• @dependabot made their first contribution in #453
• @ensonun made their first contribution in #457
• @jAnirudh made their first contribution in #473
• @wjge made their first contribution in #477
• @JhonCordova made their first contribution in #502
• @SreejithNREL made their first contribution in #516
• @dmontgomeryNREL made their first contribution in #539
• @terencelehmann made their first contribution in #549

Full Changelog: v23.03...v25.04