Releases · NCAR/micm · GitHub

26 Sep 18:27

Version 3.6.0 Latest

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

Contributors

sjsprecious, montythind, and 2 other contributors

Assets 2

26 Jun 20:39

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

Contributors

sjsprecious, mattldawson, and 3 other contributors

Assets 2

10 Apr 21:14

v3.5.0-release-candidate

Version 3.5.0 release candidate Pre-release

Pre-release

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

Contributors

sjsprecious, mattldawson, and 2 other contributors

Assets 2

20 Mar 20:21

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

Contributors

sjsprecious, K20shores, and 2 other contributors

Assets 2

08 Jan 21:06

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

Contributors

boulderdaze

Assets 2

05 Jan 20:16

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

Contributors

dwfncar, mattldawson, and 3 other contributors

Assets 2

25 Sep 20:32

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

Contributors

dwfncar, mattldawson, and 4 other contributors

Assets 2

03 Jul 15:50

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

Contributors

mattldawson, K20shores, and boulderdaze

Assets 2

16 May 18:24

Update README.md

Assets 2