Version 3.11.0

What's Changed

• Set the temporary value for diffusion coefficient by @boulderdaze in #846
• Add PhaseSpecies class by @boulderdaze in #850
• Auto-format code changes by @github-actions[bot] in #851
• Add find_package support for googletest dependency by @Copilot in #856
• Remove MICM Profiler by @boulderdaze in #858
• Auto-format code changes by @github-actions[bot] in #859
• Remove surface reaction condition checks by @boulderdaze in #863
• Auto-format code changes by @github-actions[bot] in #865
• adding parameterized user-defined reaction by @K20shores in #864
• Auto-format code changes by @github-actions[bot] in #866
• bumping nvida image version to fix build failure by @K20shores in #867
• reverting #864 by @K20shores in #868
• 857 pass number of grid cells to cuda rosenbrock by @K20shores in #869
• Auto-format code changes by @github-actions[bot] in #870
• Update CUDA kernel of NormalizedError calculation for user-defined vector length by @sjsprecious in #872
• Auto-format code changes by @github-actions[bot] in #873
• Auto-format code changes by @github-actions[bot] in #875
• Update CUDA kernel of AlphaMinusJacobian function for user-defined vector length by @sjsprecious in #876
• Auto-format code changes by @github-actions[bot] in #879
• Replace deprecated macos-13 runner with macos-15-large by @Copilot in #878
• Refactor solver results and stats by @K20shores in #881
• Auto-format code changes by @github-actions[bot] in #882
• using shared group on cirrus by @K20shores in #884
• Update the version to 3.11.0 by @boulderdaze in #885

Full Changelog: v3.10.0...v3.11.0

Version 3.10.0

What's Changed

• add intersphinx linking to MICM by @angelapak in #792
• change to run on windows-latest by @angelapak in #793
• Auto-format code changes by @github-actions[bot] in #790
• Adds taylor series rate constant by @mattldawson in #795
• Auto-format code changes by @github-actions[bot] in #796
• Adds features to support cloud chemistry by @boulderdaze in #798
• Auto-format code changes by @github-actions[bot] in #799
• Replace typedef Yield with struct Yield by @boulderdaze in #805
• Update CUDA Sparse Matrix unit tests by @sjsprecious in #814
• Auto-format code changes by @github-actions[bot] in #815
• Add performance-* clang-tidy checks to .clang-tidy configuration by @Copilot in #803
• Extend Process class to handle phase-transfer processes by @boulderdaze in #809
• Auto-format code changes by @github-actions[bot] in #821
• Tighten tolerances for rate constant calculations by @boulderdaze in #817
• Auto-format code changes by @github-actions[bot] in #822
• Update CUDA dense matrix tests with user-defined vector length by @sjsprecious in #819
• SurfaceRateConstant should throw when used with multiple reactants by @boulderdaze in #823
• Auto-format code changes by @github-actions[bot] in #827
• Replace is_error_condition_enum with is_error_code_enum by @boulderdaze in #820
• Auto-format code changes by @github-actions[bot] in #829
• Add a header to include Yield by @boulderdaze in #828
• Add missing headers and use make_unique by @boulderdaze in #830
• Auto-format code changes by @github-actions[bot] in #832
• Update CUDA LU decomposition with user-defined vector length by @sjsprecious in #833
• Correct the data type for storing gas species in PhaseTransferProcess by @boulderdaze in #835
• Update CUDA linear solver unit tests with user-defined vector length by @sjsprecious in #836
• Auto-format code changes by @github-actions[bot] in #837
• Update CUDA ProcessSet unit tests with user-defined vector length by @sjsprecious in #840
• Auto-format code changes by @github-actions[bot] in #841
• Update the version to 3.10.0 by @boulderdaze in #844

New Contributors

• @angelapak made their first contribution in #792
• @Copilot made their first contribution in #803

Full Changelog: v3.9.0...v3.10.0

Version 3.9.0

What's Changed

• Update CUDA LU decomposition kernel with the CPU optimizations by @sjsprecious in #751
• Auto-format code changes by @github-actions in #752
• Update CUDA linear solver with in-place algorithm by @sjsprecious in #753
• Auto-format code changes by @github-actions in #754
• adding a swap method to save on memory copies by @K20shores in #748
• Catch-all header by @K20shores in #755
• Auto-format code changes by @github-actions in #757
• dealing with static initializaiton issue by @K20shores in #759
• adding wall loss regression test by @K20shores in #756
• Using statements by @K20shores in #758
• Auto-format code changes by @github-actions in #760
• Auto-format code changes by @github-actions in #761
• Cuda builder by @K20shores in #762
• Auto-format code changes by @github-actions in #763
• Allow creation of State with specified number of grid cells by @mattldawson in #764
• Auto-format code changes by @github-actions in #765
• Row and column stride functions for dense matrix classes by @mattldawson in #766
• Auto-format code changes by @github-actions in #767
• Update references to NCAR to NSF NCAR by @montythind in #769
• Add maximum grid cells function by @mattldawson in #771
• 676 setup a run on the ncar cloud for gpu runs by @K20shores in #773
• Add a new print function to print non-zero elements of a sparse matrix by @sjsprecious in #779
• Auto-format code changes by @github-actions in #780
• Address out of memory error on GPU with large number of grid cells by @sjsprecious in #777
• Auto-format code changes by @github-actions in #783
• Add default minimum time-step for Rosenbrock solver by @mattldawson in #784
• Add lambda rate constant by @mattldawson in #786
• Update the version by @boulderdaze in #789

Full Changelog: v3.8.0...v3.9.0

Version 3.8.0

What's Changed

• Add sparse matrix option with Compressed Sparse Column ordering by @mattldawson in #693
• Auto-format code changes by @github-actions in #699
• Filter zeros in solver results by @mattldawson in #700
• Auto-format code changes by @github-actions in #701
• Add in-place LU decomposition option for linear solve by @mattldawson in #698
• Auto-format code changes by @github-actions in #702
• Add in-place LU decomposition with Doolittle algorithm by @mattldawson in #705
• Auto-format code changes by @github-actions in #706
• Remove solver_.parameters_ by @montythind in #668
• Auto-format code changes by @github-actions in #708
• Matrix print by @mattldawson in #711
• Auto-format code changes by @github-actions in #712
• Happy New Year by @boulderdaze in #709
• Improve the CPU performance by increasing the iterator directly by @sjsprecious in #710
• Fix bug in inline BE solver by @mattldawson in #714
• Auto-format code changes by @github-actions in #715
• Auto-format code changes by @github-actions in #716
• Fix substepping issue for Rosenbrock solver with inline LU decomposition by @sjsprecious in #717
• Auto-format code changes by @github-actions in #718
• Remove code of conduct by @mattldawson in #719
• Fix bug in parser by @mattldawson in #723
• Reorder Jacobian calculation by @mattldawson in #707
• Auto-format code changes by @github-actions in #725
• moving diagonal elements to state by @K20shores in #724
• Auto-format code changes by @github-actions in #726
• removed references to json things by @K20shores in #727
• Add a workflow to close stale issue/PR by @sjsprecious in #729
• adding state default constructor test by @K20shores in #734
• Auto-format code changes by @github-actions in #735
• correcting more state constructors, adding tests by @K20shores in #737
• Phase names by @K20shores in #738
• Auto-format code changes by @github-actions in #740
• Add types to solver class by @mattldawson in #736
• removing the config reader by @K20shores in #739
• 733 update micm documentation to only use open atmos types by @K20shores in #741
• Add restrict keyword for local raw pointers in ProcessSet by @sjsprecious in #745
• Auto-format code changes by @github-actions in #746
• 678 test to ensure readme is up to date by @K20shores in #747
• bumping version for release by @K20shores in #749
• bumping version for release (#749) by @K20shores in #750

Full Changelog: v.3.7.0...v3.8.0

Version 3.7.0

What's Changed

• Remove singular check for LU decomposition and add const qualifier to the CUDA kernels by @sjsprecious in #671
• Auto-format code changes by @github-actions in #672
• Copyable state by @K20shores in #673
• 662 more strict tolerance for unitintegration tests by @K20shores in #670
• Auto-format code changes by @github-actions in #674
• Fix readme example by @mattldawson in #677
• Set hstart to timestep by @K20shores in #679
• Auto-format code changes by @github-actions in #680
• Change LU decomposition class to be Doolittle-specific by @sjsprecious in #683
• Auto-format code changes by @github-actions in #684
• Fixes a bug in the logic used to calculate alpha - jacobian by @mattldawson in #691
• Add MOZART LU decomposition scheme by @mattldawson in #690
• Auto-format code changes by @github-actions in #692
• Update version by @boulderdaze in #696

Full Changelog: v3.6.0...v.3.7.0

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