KPP 3.2.0 release #131
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KPP 3.2.0 release #131
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src/code.h - Add "char* rootFileName" as the argument to Use_C, Use_F, Use_F90, and Use_MATLAB function prototypes src/code_c.c - Add "char* rootFileName" as the argument to Use_C src/code_f77.c - Add "char* rootFileName" as the argument to Use_F src/code_f90.c - Add "char *rootFileName" as the argument to Use_F90 src/code_matlab.c - Add "char *rootFileName" as the argument to Use_MATLAB src/gdata.h - Add "char* rootFileName" as the argument to Generate function prototype src/gen.c - Add "char* rootFileName" as the argument to Generate Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This merge brings PR #103 (Update function prototypes to avoid compiler warnings with GCC 13, by @yantosca) into the KPP development stream. This PR makes the compiler warnings consistent with the actual arguments passed to Use_C, Use_F, Use_F90, Use_MATLAB, and Generate functions. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
Update_RCONST now uses variable concentrations for rate constants that depend on species concentrations. To ensure backwards compatibility, YIN is an optional input. If YIN is not passed to Update_RCONST, concentrations from the global C array are used instead.
src/gen.c - Wrap the code to declare UPDATE_RCONST with YIN in an if block that only executes when useLang==F90 - Place code to declare UPDATE_RCONST without any variables in the else block. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
.ci-pipelinoes/ci-common.defs.sh - Add a function "print_compiler_versions" to print the gcc and gfortran compiler versions that are used to run the tests. .ci-pipelines/ci-testing-script.sh - Call "print_compiler_versions" function before running tests. This will print the compiler versions at the top of stdout output. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This merge brings PR #106 ((Use Y instead of C in Update_RCONST, by @srosanka) into the KPP development stream. This PR adds the "Y" variable as an optional argument to the Update_RCONST function (for F90 only). If not passed, the C concentration vector will be used. This should now update the concentrations at each integration timestep properly (unless ICNTRL(15) = -1 is selected). Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
docs/requirements.txt - Use jinja 3.1.4 as there is a dependabot security warning for the previous version 3.1.3. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
src/gen.c - Modified routine GenerateUpdateRconst so that the INLINED RCONST contents will be placed immedately after the start of the UPDATE_RCONST subroutine, and to place F90 variable declarations etc. immediately after that. This will prevent compile-time errors if a USE statement is included via "INLINED RCONST", as USE statements must come before variable declarationas and other statements. - Updated comments CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
src/gen.c - Removed leftover comment about "int UPDATE_RCONST;" variable - Fixed typo Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
src/gdata.h - Declare F90_RCONST_USE as a variable of type "enum inl_code" src/scanner.c - Added F90_RCONST_USE to InlineKeys[] src/gen.c - In routine GenerateUpdateRconst we now proceed in this order: 1. Manually write the "SUBROUTINE UPDATE_RCONST ( YIN )" line 2. Inline code from the "#INLINE F90_RCONST_USE" section 3. Declare YIN optional argument and Y local variable 4. Copy values of YIN to Y (if necessary) 5. Inline code from the "#INLINE F90_RCONST" section 6. Manually write the "END SUBROUTINE UPDATE_RCONST" line .gitignore - Now ignore executable files in MCM example folders CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
.gitignore - Ignore all *.exe files src/gen.c - Updated commments where inlined code is added to be more descriptive (referencing F90_RCONST_USE and F90_RCONST) docs/source/using_kpp/04_input_for_kpp.rst - Added documentation for F90_RCONST_USE CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This merge brings PR #120 (Add code from #INLINE F90_RCONST_USE at the top of the UPDATE_RCONST subroutine, by @yantosca) into the KPP 3.2.0 development stream. This PR adds a new inline key (F90_RCONST_USE) so that USE statements can be placed at the top of subroutine UPDATE_RCONST before any other Fortran statements (as required by the language standard). Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
CHANGELOG.md - Changed note about F90_RCONST_USE to be more general, as all inlined code comments have been updated to be more consistent in PR #122. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This merge brings PR #122 (Consistent comments for inlined code, by @RolfSander) into the KPP 3.2.0 develpment stream. This PR updates the BeginComment statements in src/gen.c towrite comments stating where the inlined code is from (e.g. "Begin inlined code from F90_RCONST"), etc. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
docs/source/getting_started/01_installation.html - Add a line to add the path to the flex library to LD_LIBRARY_PATH in the Flex installation instructions. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
src/gen.c - In routine GenerateUpdatePhoto, we also now inline USE statements from inline block F90_RCONST_USE into routine Update_Photo. This fixes a bug that was found with the MCM mechanism. examples/mcm/mcm_isoprene.eqn - Moved "USE constants_mcm" from the F90_RCONST to the F90_RCONST_USE inline block. This will place it properly at the top of the routines. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
docs/source/using_kpp/04_input_for_kpp.rst - Now state that code specified in an #INLINE F90_RCONST_USE section will be placed into both Update_RCONST and Update_PHOTO. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
docs/requirements.txt - Updated RTD dependency jinja2 to version 3.1.5 (security fix) docs/source/getting_started/00_revision_history.rst - Added what's new in KPP 3.2.0 section - Fixed tag position for KPP 3.1.0 anchor docs/source/reference/known-bugs.rst - Added links to both open and closed bug reports on GitHub - Added a blurb that LSODE is not thread-safe under known issues docs/source/tech_info/07_numerical_methods.rst - Added warning that LSODE is not thread-safe CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This merge brings PR #125 (Add inlined code in the #INLINE F90_RCONST_USE block to the Update_Photo routine, by @yantosca) into the KPP 3.2.0 development stream. This PR introduces a bugfix. F90 USE statements that were added to the #INLINE F90_RCONST_USE section are now placed at the top of the Update_Photo routine (as they are in Update_Rconst). Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
src/Makefile - Now print the value of SYSTEM_M variable in "make list" target - Trimmed trailing whitespace src/Makefile.defs - Now use the $(strip) function when testing the values of SYSTEM and SYSTEM_M. This will make sure that trailing whitespace is removed. This was affecting the string equality tests. - Add option "-arch x86_64" if compiling on Intel x86_64 chipsets - Add option "-arch arm64" if compiling on Apple Silicon chipsets - Trimmed trailing whitespace CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
int/sdirk.f90 - Original version has been deleted - int/beuler.f90 is now renamed to int/sdirk.f90 int/beuler.f90 int/beuler.def - Removed docs/source/tech_info/07_numerical_methods.rst - Added documentation instructing user to select #INTEGRATOR sdirk with ICNTRL(3) = 6 for Backwards Euler integration CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
int/sdirk.f90 - Indented & lined up code for readability - Added () to subroutines taking no arguments - Test if the method is Backward Euler (BEL) before multiplying the RoundOff variable by 101 when computing Hstart - Trimmed trailing whitespace Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This merge brings PR # (Update int/sdirk.f90 to the same version as was in int/beuler.f90, by @yantosca) into the KPP 3.2.0 development stream. This is the companion PR to #129. In this PR we do the following: - Moved int/beuler.f90 to int/sdirk.f90, since the code in int/beuler.f90 was a newer version of the SDIRK integrator module - Removed int/beuler.def - Updated documentation to instruct users wishing to select the Backwards Euler method to use #INTEGRATOR sdirk and set ICNTRL(3) = 6 - Only use 101*Roundoff in the computation for Hstart if the selected integration method is Backward Euler - Trimmed trailing whitespace, indented code Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
docs/source/getting_started/00_revision_history.rst - Added notes about beuler integrator being removed, and that users can use sdirk with ICNTRL(3)=6 to request Backward Euler Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
docs/source/getting_started/00_revision_history.rst - Added a line to KPP 3.2.0 about MacOS architecture specific build compiler flags Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This merge brings in documentation updates for the KPP 3.2.0 release into the release/3.2.0 branch. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
Updated version numbers in - CHANGELOG.md - docs/source/conf.py (for RTD documentation) - src/gdata.h Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
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Thanks @RolfSander! |
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We have added several new features into the dev branch of KPP. I was thinking now might be a good time to bundle them into the KPP 3.2.0 release, as it would certainly facilitate some work that I am doing.
In particular:
F90_RCONST_USEso that F90USEstatements can be inlined into theUpdate_RCONSTandUPDATE_PHOTOroutinessrc/gen.cto generate theUPDATE_RCONSTroutine with an optional argumentYint/sdirk.f90to a newer versionint/beuler.f90; Users can select Backward Euler withsdirkintegrator andICNTRL(3)=6We can add the implicit12 (PR #101) and rosenbrock_h211b (PR #124) integrators into KPP 3.3.0 once they are ready. Also if time permits I would like to try to replace some of the calls to functions in
blas.f90with F90 array operations in the next version and examine the potential speedup.