Version 3.6.0

What's Changed

• v3.6.0 by @K20shores in #669

Full Changelog: v3.5.0...v3.6.0

What's Changed

• Add CUDA Rosenbrock tests by @sjsprecious in #579
• Auto-format code changes by @github-actions in #586
• Use Fill to reset the L and U matrices in Rosenbrock solve by @mattldawson in #588
• In-place linear solve by @K20shores in #585
• Auto-format code changes by @github-actions in #589
• 498 mimic camchem substep convergence failure integration acceptance by @K20shores in #582
• Auto-format code changes by @github-actions in #590
• 304 reorganize include folder by @K20shores in #591
• Auto-format code changes by @github-actions in #592
• 577 test all parameter types of the dense matrix cpu rosenbrock on the analytical policy tests by @K20shores in #593
• Auto-format code changes by @github-actions in #597
• Fix GPU memory leak for the CUDA unit tests by @sjsprecious in #600
• Auto-format code changes by @github-actions in #601
• Backware Euler with vectorizable matrix types by @mattldawson in #596
• Auto-format code changes by @github-actions in #605
• 572 check for singularity when the solver parameters flag is turned on by @K20shores in #603
• Auto-format code changes by @github-actions in #606
• Provide a way to access the processes_ data member by @sjsprecious in #607
• Auto-format code changes by @github-actions in #608
• Auto-format code changes by @github-actions in #609
• Add missing CUDA tests and fix broken path by @sjsprecious in #611
• throwing error on mismatched size by @K20shores in #610
• Auto-format code changes by @github-actions in #612
• Correct usage of third body species by @K20shores in #614
• Auto-format code changes by @github-actions in #615
• correcting solver builder constructor by @K20shores in #616
• Relax the criteria to pass the GPU test with nvhpc/24.7 on Derecho by @sjsprecious in #618
• Auto-format code changes by @github-actions in #623
• Update fill function for CUDA matrix by @sjsprecious in #626
• Auto-format code changes by @github-actions in #627
• Remove data transfer in cuda matrix constructor and template some CUDA functions by @sjsprecious in #630
• Auto-format code changes by @github-actions in #633
• Remove redundant variable and optimize the copy assignment for the CUDA matrix by @sjsprecious in #636
• Remove local copy of state in solver functions by @mattldawson in #639
• Auto-format code changes by @github-actions in #640
• Add CUDA stream for asynchronous kernel launch by @sjsprecious in #641
• Auto-format code changes by @github-actions in #645
• Remove the local copy of Jacobian matrix when doing LU decomposition by @sjsprecious in #646
• Auto-format code changes by @github-actions in #647
• Add const to solver functions by @mattldawson in #642
• Replace json to yaml 619 by @montythind in #649
• Auto-format code changes by @github-actions in #650
• Add const qualifiers by @mattldawson in #651
• Move Yerror construction outside of the inner solve loop for rosenbrock by @montythind in #652
• Auto-format code changes by @github-actions in #653
• Move temporary variables to the State class by @sjsprecious in #655
• Auto-format code changes by @github-actions in #656
• Use CUDA Rosenbrock parameters by @sjsprecious in #659
• Added license and copyright by @montythind in #661
• Auto-format code changes by @github-actions in #660
• Misc updates by @sjsprecious in #665
• Set LU matrices to zero when jacobian is a zero element by @K20shores in #666
• Auto-format code changes by @github-actions in #667

New Contributors

• @montythind made their first contribution in #649

Full Changelog: v3.5.0...v3.6.0

v3.5.0

What's Changed

• Override NormalizedError function with CUDA by @sjsprecious in #424
• Auto-format code changes by @github-actions in #435
• 393 create cudasparsematrix class by @mwaxmonsky in #426
• Auto-format code changes by @github-actions in #437
• Optimize data movement for CudaRosenbrocksolver and compute minus Jacobian matrix on GPU by @sjsprecious in #436
• Auto-format code changes by @github-actions in #438
• Update the CUDA implementation of AddforcingTerms with the CudaVectorMatrix class by @sjsprecious in #439
• Auto-format code changes by @github-actions in #441
• Allow custom rate parameters to be directly set by @K20shores in #440
• Auto-format code changes by @github-actions in #444
• Rename CUDA matrix class to be Dense or Sparse by @sjsprecious in #443
• Auto-format code changes by @github-actions in #445
• Update the CUDA implementation of SubtractJacobianTerms with the CUDA matrix class by @sjsprecious in #446
• Auto-format code changes by @github-actions in #447
• add support for non-double properties by @mattldawson in #448
• Initial attempt to format cuda code. by @mwaxmonsky in #449
• Fixing bugs in previous PR. by @mwaxmonsky in #450
• Update template arguments for LuDecomposition by @mattldawson in #454
• Add exceptions for species property lookups by @mattldawson in #455
• Update the CUDA implementation of AlphaMinusJacobian and NormalizedError with the CUDA matrix class by @sjsprecious in #452
• Auto-format code changes by @github-actions in #460
• adding a test to show that integrated reaction rates can be collected by @K20shores in #459
• Auto-format code changes by @github-actions in #462
• 456 read and use relative tolerance absolute tolerance by @K20shores in #457
• Auto-format code changes by @github-actions in #463
• Profiling and Optimization for VectorMatrix by @boulderdaze in #429
• Auto-format code changes by @github-actions in #465
• Update the CUDA implementation of CudaLuDecomposition with the CUDA matrix class by @sjsprecious in #464
• Auto-format code changes by @github-actions in #467
• Vectorized NormalizedError by @K20shores in #461
• Auto-format code changes by @github-actions in #469
• Updates to error handling by @mattldawson in #468
• Auto-format code changes by @github-actions in #470
• make error code functions inline by @mattldawson in #477
• Apply rules to order Include headers by @boulderdaze in #476
• Auto-format code changes by @github-actions in #478
• Fix regex in clang-format by @boulderdaze in #479
• Auto-format code changes by @github-actions in #481
• Check if the device pointer is initialized to nullptr in the move constructor by @sjsprecious in #484
• Update the CUDA implementation of CudaLinearSolver with the CUDA matrix class by @sjsprecious in #474
• Auto-format code changes by @github-actions in #486
• Auto-format code changes by @github-actions in #487
• Explicitly call the function from the base class in a CUDA class by @sjsprecious in #483
• Auto-format code changes by @github-actions in #491
• 400 backward euler solver option by @K20shores in #485
• Auto-format code changes by @github-actions in #497
• Fix the profiler driver by @boulderdaze in #493
• Update the assign function inside both CPU and GPU class by @sjsprecious in #495
• Auto-format code changes by @github-actions in #502
• Re-evaluate clang tidy by @mwaxmonsky in #501
• Auto-format code changes by @github-actions in #503
• Rename functions to consistently use CamelCase by @boulderdaze in #489
• Auto-format code changes by @github-actions in #504
• Fix the broken main by @boulderdaze in #506
• Configure clang-tidy to uniformise the style in naming classes, class data members and variables by @boulderdaze in #511
• Auto-format code changes by @github-actions in #515
• Update the tutorial to reflect the changes in the names and the style by @boulderdaze in #513
• Auto-format code changes by @github-actions in #517
• 518 integrate clang tidy workflow with config file by @mwaxmonsky in #519
• 520 clang tidy cert additions by @mwaxmonsky in #525
• Clang-tidy Readability Checks by @boulderdaze in #526
• Auto-format code changes by @github-actions in #528
• CamelCase for getting version by @boulderdaze in #530
• 514 create a builder class that can make a backward euler solver by @K20shores in #527
• Auto-format code changes by @github-actions in #531
• Add new issues to project board by @mattldawson in #533
• Remove issue action by @mattldawson in #537
• actions run on workflow dispatch or pr by @K20shores in #532
• Disable Intel tests by @mattldawson in #542
• enabling intel by @K20shores in #545
• Add GPU memory check for CUDA code by @sjsprecious in #544
• 546 update cmakeliststxt to support latest cuda project type and architectures by @mwaxmonsky in #547
• Add exiting error code for compute-sanitizer by @sjsprecious in #553
• Add error checks for all the CUDA APIs by @sjsprecious in #554
• Auto-format code changes by @github-actions in #555
• removing irrelevant cmake tests by @K20shores in #556
• Add option for creating a third-body species in the MICM configuration by @boulderdaze in #551
• Auto-format code changes by @github-actions in #558
• Use single line comment style for copyright by @boulderdaze in #561
• Apply solver builder to Rosenbrock by @mattldawson in #560
• Auto-format code changes by @github-actions in #562
• Modify regex in clang format by @boulderdaze in #559
• Auto-format code changes by @github-actions in #565
• Run tests on commits to main by @mattldawson in #566
• Share CUBLAS handle between different CUBLAS matrices by @sjsprecious in #543
• Auto-format code changes by @github-actions in #570
• Removing 2019 msvc github actions by @K20shores in #574
• Inline version by @K20shores in #569
• run all actions even if one strategy fails in a matrix by @K20shores in #571
• using header file instead of including cpp file by @K20shores in #573
• testing backward euler with most of the analytical tests by @K20shores in #576
• Auto-format code changes by @github-actions in #580
• read version in the docs from the cmake files by @K20shores in #581
• renaming chapman mechanism and adding readme by @K20shores in #583
• Update the version to v3.5.0 by @boulderdaze in #584

Full Changelog: v.3.4.0...v3.5.0

Version 3.5.0 release candidate

What's Changed

• Override NormalizedError function with CUDA by @sjsprecious in #424
• Auto-format code changes by @github-actions in #435
• 393 create cudasparsematrix class by @mwaxmonsky in #426
• Auto-format code changes by @github-actions in #437
• Optimize data movement for CudaRosenbrocksolver and compute minus Jacobian matrix on GPU by @sjsprecious in #436
• Auto-format code changes by @github-actions in #438
• Update the CUDA implementation of AddforcingTerms with the CudaVectorMatrix class by @sjsprecious in #439
• Auto-format code changes by @github-actions in #441
• Allow custom rate parameters to be directly set by @K20shores in #440
• Auto-format code changes by @github-actions in #444
• Rename CUDA matrix class to be Dense or Sparse by @sjsprecious in #443
• Auto-format code changes by @github-actions in #445
• Update the CUDA implementation of SubtractJacobianTerms with the CUDA matrix class by @sjsprecious in #446
• Auto-format code changes by @github-actions in #447
• add support for non-double properties by @mattldawson in #448
• Initial attempt to format cuda code. by @mwaxmonsky in #449
• Fixing bugs in previous PR. by @mwaxmonsky in #450
• Update template arguments for LuDecomposition by @mattldawson in #454

Full Changelog: v.3.4.0...v3.5.0-release-candidate

v.3.4.0

What's Changed

• Create constructor/destructor for CudaLuDecomposition class to handle data movement between host and device by @sjsprecious in #399
• Auto-format code changes by @github-actions in #402
• Create constructor/destructor for CudaProcessSet class to handle data movement between host and device by @sjsprecious in #403
• Auto-format code changes by @github-actions in #404
• Create constructor/destructor for CudaLinearSolver class to handle data movement between host and device by @sjsprecious in #405
• Auto-format code changes by @github-actions in #406
• Initial CudaVectorMatrix implementation. by @mwaxmonsky in #408
• reseting matrices by @K20shores in #410
• Auto-format code changes by @github-actions in #411
• Adding missing constructor implementaion. by @mwaxmonsky in #418
• Auto-format code changes by @github-actions in #419
• 416 add assignment overridescopy constructors to cudavectormatrix so new matrix has separate device memory by @mwaxmonsky in #420
• Auto-format code changes by @github-actions in #421
• Add cublasDaxpy routine to perform foreach-like calculation on the GPU by @sjsprecious in #422
• Auto-format code changes by @github-actions in #423
• prefixing all options with micm_ by @K20shores in #413
• Actions by @K20shores in #427
• Citation by @K20shores in #430
• Release v3.4.0 by @boulderdaze in #433

New Contributors

• @sjsprecious made their first contribution in #399
• @mwaxmonsky made their first contribution in #408

Full Changelog: v.3.3.1...v.3.4.0

v3.3.1

What's Changed

• Adding missing inline by @boulderdaze in #397
• v3.3.1 Release by @boulderdaze in #398

Full Changelog: v.3.3.0...v.3.3.1

v3.3.0

What's Changed

• README updates by @mattldawson in #252
• 242 add tutorial for rate constant types except custom ones by @K20shores in #251
• Config parser by @dwfncar in #255
• Auto-format code changes by @github-actions in #262
• adding timing functions by @K20shores in #265
• Auto-format code changes by @github-actions in #266
• 260 add tutorial for multiple grid cells by @K20shores in #263
• 253 add tutorial for custom rate constants by @K20shores in #254
• Develop windows tutorial by @mattldawson in #267
• Auto-format code changes by @github-actions in #274
• Update README.md by @K20shores in #275
• 278 add tutorial for use with openmp by @K20shores in #280
• only create the formatting branch if changes are detected by @K20shores in #282
• 157 steal the tests from the json library to test xcode builds by @K20shores in #283
• 264 add tutorial on timing the solver and investigating solver statistics by @K20shores in #270
• Decompose cuda by @qinatan in #257
• 271 add tutorial on configuring the solver for with different parameters by @K20shores in #277
• adding time to hello world example by @K20shores in #281
• adding code of conduct and contributors guide by @K20shores in #284
• hopefully copying the switcher by @K20shores in #285
• Enable openmp by @K20shores in #286
• JitRosenbrockSolver integration and regression tests by @mattldawson in #287
• removing documentation dependencies from readme by @K20shores in #288
• putting docker files into their own folder by @K20shores in #289
• Switcher again by @K20shores in #291
• 292 add a docker image publish by @K20shores in #294
• Fix set concentrations mapping error by @mattldawson in #297
• Test kpp micm by @dwfncar in #295
• adding micm optional dependency pictures by @K20shores in #311
• Actions by @K20shores in #307
• update README example with time output by @mattldawson in #312
• update README by @mattldawson in #313
• adding icon to readme and favicon to docs by @K20shores in #298
• Update README.md by @K20shores in #316
• Develop 245 terminator by @mattldawson in #314
• 299 install micm and use in a new project by @K20shores in #306
• Validation checks by @K20shores in #318
• Bug fix build by @mattldawson in #319
• Develop 82 singular matrix by @mattldawson in #321
• Auto-format code changes by @github-actions in #323
• 164 prevent non standard keys in json by @K20shores in #317
• Auto-format code changes by @github-actions in #328
• 279 make solve function for ode solvers thread safe by @K20shores in #322
• Auto-format code changes by @github-actions in #334
• 256 config parser by @dwfncar in #325
• Auto-format code changes by @github-actions in #335
• 309 add tutorial for jit solver by @K20shores in #332
• Auto-format code changes by @github-actions in #336
• Allow multiple JIT functions with the same name by @mattldawson in #341
• Auto-format code changes by @github-actions in #342
• Develop jit tutorial edits by @mattldawson in #343
• adding jit process set in openmp example by @K20shores in #344
• update line numbers in JIT tutorial by @mattldawson in #345
• Develop 272 ts1 by @K20shores in #340
• Auto-format code changes by @github-actions in #346
• Check for unused species in solver constructor by @mattldawson in #347
• Auto-format code changes by @github-actions in #348
• Parse scaling factors by @mattldawson in #351
• Auto-format code changes by @github-actions in #353
• Changed rate constant expression to allow for N = 0. by @dwfncar in #354
• Auto-format code changes by @github-actions in #355
• 350 rm kpp to micm by @dwfncar in #357
• Develop 337 non si units by @mattldawson in #359
• Auto-format code changes by @github-actions in #360
• Changed reactions.json units to non-SI. by @dwfncar in #361
• 310 add tutorial for the vectorized matrix solver by @K20shores in #362
• Auto-format code changes by @github-actions in #364
• 153 config parser by @dwfncar in #369
• Auto-format code changes by @github-actions in #370
• Cuda solver by @qinatan in #358
• 182 surface reaction example by @dwfncar in #356
• Auto-format code changes by @github-actions in #371
• Command-line driver for MICM by @boulderdaze in #326
• Auto-format code changes by @github-actions in #372
• Update Boltzmann constant by @mattldawson in #375
• Auto-format code changes by @github-actions in #376
• Update CMakeLists.txt by @mattldawson in #377
• 374 tutorial for each example in the examples folder by @K20shores in #378
• using the new state in the tutorials, correcting line numbers, doxyge… by @K20shores in #379
• Auto-format code changes by @github-actions in #380
• trying a different filter by @K20shores in #382
• Develop 374 examples by @mattldawson in #381
• Cuda alpha by @qinatan in #384
• Auto-format code changes by @github-actions in #385
• Happy new year! by @boulderdaze in #386
• v3.3.0 Release by @boulderdaze in #396

Full Changelog: v3.2.0...v.3.3.0

v3.2.0

What's Changed

• Enable openacc by @K20shores in #91
• creating a separate cuda and openacc target by @K20shores in #92
• Redefinition issue by @K20shores in #102
• Vectorizable Sparse Matrix by @mattldawson in #105
• Remove RosenbrockSolver inheritence from ChapmanODESolver by @mattldawson in #109
• Add sparse matrix policy to RosenbrockSolver class by @mattldawson in #111
• Googletest version by @K20shores in #108
• Linear solver by @mattldawson in #114
• Add build instructions to the readme by @aharonYK in #100
• Finish AlphaMinusJacobian function by @mattldawson in #117
• Merge main flipped by @mattldawson in #115
• Multiplatform build by @K20shores in #120
• General Rosenbrock Solver by @mattldawson in #121
• Map params by @boulderdaze in #104
• add CudaProcessSet class by @mattldawson in #124
• Move hard-coded Chapman solver to tests by @mattldawson in #125
• Update parser by @boulderdaze in #119
• Merge Solver class into RosenbrockSolver by @mattldawson in #132
• CUDA AddForcingTerms function by @qinatan in #118
• using c++ compiler... by @K20shores in #133
• ran the formatter by @K20shores in #134
• Example in README by @mattldawson in #135
• Address compiler warnings by @mattldawson in #139
• Add relative tolerance to regression tests by @mattldawson in #140
• 126 unify error handling by @K20shores in #137
• State reordering by @mattldawson in #143
• trying to run formatting automatically by @K20shores in #146
• Getting started docs by @dwfncar in #152
• Ternary chemical activation rate constant by @mattldawson in #155
• Tunneling reaction rate constant by @mattldawson in #156
• trying to separate parameters by @K20shores in #151
• Branched NO + RO2 reaction by @mattldawson in #160
• updating docs to use new stage selector thing by @K20shores in #159
• trying to create a PR after push to main by @K20shores in #161
• Auto-format code changes by @github-actions in #162
• Emission, loss rate constants by @mattldawson in #166
• making it compile for performance repo by @K20shores in #168
• Surface reaction rate constant by @mattldawson in #169
• Auto-format code changes by @github-actions in #170
• KPP to MICM by @dwfncar in #173
• Add LLVM support for JIT compiling by @mattldawson in #174
• Auto-format code changes by @github-actions in #181
• JITed forcing function by @mattldawson in #179
• 158 add integration tests for simple chemistry systems by @K20shores in #180
• Auto-format code changes by @github-actions in #187
• Add jacobian terms cuda by @qinatan in #188
• Auto-format code changes by @github-actions in #192
• Kpp to micm by @dwfncar in #191
• Debug main by @qinatan in #198
• Auto-format code changes by @github-actions in #199
• Parameter fixes by @K20shores in #197
• Auto-format code changes by @github-actions in #201
• Develop jit jacobian function by @mattldawson in #202
• Param by @qinatan in #205
• Auto-format code changes by @github-actions in #210
• Develop 204 jit lu by @mattldawson in #212
• Auto-format code changes by @github-actions in #213
• Add inline files by @boulderdaze in #206
• Auto-format code changes by @github-actions in #214
• 208 add jited alphaminusjacobian function by @K20shores in #215
• put the solver state out of the rosenbrock class to remove need to sp… by @K20shores in #216
• Auto-format code changes by @github-actions in #220
• Robertson by @K20shores in #221
• fix solver test by @mattldawson in #223
• Develop 207 jit linear solve by @mattldawson in #224
• Auto-format code changes by @github-actions in #225
• fix missing namespace in linear solver test by @mattldawson in #227
• Oregonator by @K20shores in #222
• 228 hires by @K20shores in #229
• Auto-format code changes by @github-actions in #235
• Auto-format code changes by @github-actions in #237
• 230 e5 by @K20shores in #231
• lowering computed rate constant by @K20shores in #233
• 236 set up micm documentation builds and gh pages by @K20shores in #240
• Auto-format code changes by @github-actions in #241
• Develop 193 jit rate constants by @mattldawson in #247
• Auto-format code changes by @github-actions in #248
• Add inline keywords by @boulderdaze in #249
• Release version 3.2.0 by @K20shores in #239

New Contributors

• @aharonYK made their first contribution in #100
• @qinatan made their first contribution in #118
• @dwfncar made their first contribution in #152
• @github-actions made their first contribution in #162

Full Changelog: v3.1.0...v3.2.0

Version 3.1.0

What's Changed

• Music box 2 by @mattldawson in #1
• Develop 2 rate constants by @mattldawson in #3
• add preprocessor functions by @mattldawson in #4
• update for domain refactor by @mattldawson in #5
• Develop 46 camp by @mattldawson in #6
• Develop 3 json format by @mattldawson in #9
• Develop 252 evolving conditions by @mattldawson in #10
• 18 hard coded chapman solver by @K20shores in #56
• Develop rosenbrock solver actually by @K20shores in #57
• public const data members by @boulderdaze in #67
• General Rosenbrock rate constants by @mattldawson in #68
• 59 Setup MICM for MUSICA by @K20shores in #71
• Multi-grid-cell state data by @mattldawson in #72
• Add forcing function to general Rosenbrock solver by @mattldawson in #74
• Cmake fixes by @K20shores in #76
• Sparse matrix class by @mattldawson in #77
• Rosenbrock dforce_dy function by @mattldawson in #78
• relax tolerance in Rosenbrock p_force regression test by @mattldawson in #79
• 80 micm cannot compile with nvhpc230 by @K20shores in #81
• 83 add hpc testing framework by @K20shores in #84
• fixing cmake variable name by @K20shores in #90
• Json parsing by @boulderdaze in #89
• Vectorizable matrix class by @mattldawson in #87
• LU decomposition by @mattldawson in #93
• add template parameter to Rosenbrock Solver test by @mattldawson in #97
• updating version number by @K20shores in #101

New Contributors

• @boulderdaze made their first contribution in #67

Full Changelog: v00.001...v3.1.0

micm2_1_8

Update README.md