KPP 3.2.0 release

This is the release commit for KPP version 3.2.0.
Please see CHANGELOG.md for a list of updates.

Signed-off-by: Bob Yantosca <[email protected]>

Author: yantosca

.ci-pipelines/ci-common-defs.sh

@@ -46,6 +46,18 @@ function get_ci_test_path() {
     return
 }
 
+# Prints a headeer with the compiler versions
+function print_compiler_versions() {
+    echo \
+"###########################################################################"
+    echo "         KPP CONTINUOUS INTEGRATION TESTS, USING THESE COMPILERS:"
+    echo ""
+    gcc --version
+    gfortran --version
+    echo \
+"###########################################################################"
+}
+
 # Run a C-I test
 function run_ci_test() {
 

.ci-pipelines/ci-testing-script.sh

@@ -10,6 +10,9 @@
 # Current directory
 cwd=$(pwd -P)
 
+# Print a header with the compiler versions
+print_compiler_versions
+
 # Run C-I tests with various mechanism + integrator combinations
 for this_test in ${GENERAL_TESTS}; do
     run_ci_test "${this_test}" "${cwd}" ""

.gitignore

@@ -15,6 +15,7 @@
 # from compiler:
 *.mod
 *.o
+*.exe
 
 # results from ci-tests:
 /ci-tests/**/*.m
@@ -67,5 +68,5 @@ docs/build/*
 
 # Other files/dirs to exclude
 *.pdf
-/examples/mcm/__pycache__
+/examples/mcm*/__pycache__
 

CHANGELOG.md

@@ -8,6 +8,36 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [3.2.0] - 2025-02-27
+### Added
+- Added new inline key `F90_RCONST_USE` in `src/gdata.h` and `src/scanner.c`
+- Added documentation about `F90_RCONST_USE` for ReadTheDocs
+- Added `F90_RCONST_USE` inlined code to `Update_RConst`and `Update_Photo` routines
+- Added warning that LSODE is not thread-safe to ReadTheDocs documentation
+
+### Changed
+- Updated `Update_RCONST` to use `Y` instead of `C` to account for updated variable species concentrations
+- Updated C-I tests to print the compiler versions that are used
+- Updated routine `GenerateUpdateRconst` to manually write the `SUBROUTINE` and `END SUBROUTINE` lines (F90 only)
+- Updated routine `GenerateUpdateRconst` to inline code from `#INLINE F90_RCONST_USE` before any other F90 variable declarations or statements
+- Updated `.gitignore` to ignore all executable files
+- Changed `Begin INLINED RCONST - F90 USE STATEMENTS` to `Begin inlined code from F90_RCONST_USE` in `src/gen.c`
+- Changed inlined code comments to be more precise (e.g. `Begin inlined code from F90_RCONST`) in `src/gen.c`
+- Updated Flex library installation example on ReadTheDocs
+- Renamed `int/beuler.f90` to the `int/sdirk.f90`, as this is a newer version of the SDIRK integrator
+- Updated documentation for Backwards Euler to instruct user to select `#INTEGRATOR sdirk` with `ICNTRL(3) = 6`
+- Updated ReadTheDocs dependency`jinja2` to version 3.1.5 (fixes a security issue)
+
+### Fixed
+- Added `char* rootFileName` to functions and function prototypes for `Use_C`, `Use_F`, `Use_F90`, `Use_MATLAB`, and `Generate`
+- Updated `docs/requirements.txt` to use `jinja2==3.1.4` (fixes a security issue)
+- Moved `USE constants_mcm` from `F90_RCONST` to `F90_RCONST_USE` in `examples/mcm/mcm_isoprene.eqn`
+- Fixed MacOS-specific handling for x86_64 or arm64 in `src/Makefile.defs`
+
+### Removed
+- Removed `int/beuler.f90`
+- Removed `int/beuler.def`
+
 ## [3.1.1] - 2024-04-30
 ### Changed
 - Updated Python package versions for ReadTheDocs in `docs/requirements.txt`

docs/requirements.txt

@@ -12,4 +12,4 @@ sphinxcontrib-bibtex==2.6.2
 sphinx-autobuild==2021.3.14
 recommonmark==0.7.1
 docutils==0.20.1
-jinja2==3.1.3
+jinja2==3.1.5

docs/source/citations/09_acknowledgments.rst

@@ -41,4 +41,7 @@ Stuart Lacy wrote an export function for the `Master Chemical Mechanism
 used out-of-the-box for the small model in the :file:`examples/mcm`
 directory.
 
+Simon Rosanka improved the :code:`Update_RCONST` subroutine by providing
+time-dependent concentration values via an optional parameter.
+
 Parts of this user manual are based on :cite:t:`Damian-Iordache_1996`.

docs/source/conf.py

@@ -25,7 +25,7 @@
 # The full version, including alpha/beta/rc tags
 # (version numbers must be synchronized in CHANGELOG.md, src/gdata.h,
 # and docs/source/conf.py)
-release = "3.1.1"
+release = "3.2.0"
 
 
 # -- General configuration ---------------------------------------------------

docs/source/getting_started/00_revision_history.rst

@@ -8,20 +8,38 @@ Only the major new features are listed here. For a detailed description
 of the changes, read `CHANGELOG.md
 <https://github.com/KineticPreProcessor/KPP/blob/main/CHANGELOG.md>`_.
 
+.. _kpp320:
+
+=========
+KPP 3.2.0
+=========
+
+- Added new inline key :literal:`F90_RCONST_USE` so that F90
+  :literal:`USE` statements can be inlined into the
+  :code:`Update_RCONST` and :literal:`UPDATE_PHOTO` routines
+- Updated code in :code:`src/gen.c` to generate the
+  :code:`UPDATE_RCONST` routine with an optional argument :code:`Y`
+- Updated C-I tests to print the compiler versions that are used
+- Updated :literal:`int/sdirk.f90` to a newer version
+- Removed :literal:`int/beuler.f90`; Users can select Backward Euler
+  with :literal:`sdirk` integrator and :literal:`ICNTRL(3)=6`
+- Added MacOS architecture-specific compilation flags to the build sequence
+
 .. _kpp311:
 
 =========
 KPP 3.1.1
 =========
 
-.. _kpp310:
 - Use newer Python packages to build ReadTheDocs documentation (see
   :file:`docs/requirements.txt`)
 - Increased :code:`MAX_NO_OF_LINES` and :code:`MAX_EQN` in order to
   parse the entire MCM mechanism
 - Now only add the extra `Aout` argument to `Fun` and `Fun_Split` for
   target language :literal:`Fortran90`.  This fixes a Matlab build error.
 
+.. _kpp310:
+
 =========
 KPP 3.1.0
 =========

docs/source/getting_started/01_installation.rst

@@ -178,8 +178,9 @@ the :envvar:`KPP_FLEX_LIB_DIR`  environment variable in your
 .. code-block:: bash
 
    export KPP_FLEX_LIB_DIR=/usr/lib
+   export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${KPP_FLEX_LIB_DIR}:"
 
-And then apply the changes with:
+Then apply the changes with:
 
 .. code-block:: console
 

docs/source/reference/known-bugs.rst

@@ -1,6 +1,30 @@
-##########
-Known Bugs
-##########
+#####################
+Known bugs and issues
+#####################
 
-Bugs are discussed at the `KPP repository Github issues page
-<https://github.com/KineticPreProcessor/KPP/issues/>`_.
+Please see our `Issue tracker on GitHub
+<https://github.com/KineticPreProcessor/KPP/issues>`_ for a list of recent
+bugs and fixes.
+
+===================
+Current bug reports
+===================
+
+These `bug reports (on GitHub)
+<https://github.com/KineticPreProcessor/KPP/issues?q=is%3Aissue%20state%3Aopen%20label%3Abug>`_
+are currently unresolved. We hope to fix these in future releases.
+
+LSODE integrator is not thread-safe
+-----------------------------------
+
+We have discovered that the current implementation of the LSODE
+integrator is not thread-safe for `OpenMP parallelization
+<https://www.openmp.org/>`_.  When LSODE is called from within an
+OpenMP parallel loop, the integration will fail because key internal
+variables in LSODE will be overwritten by concurrent threads.
+
+============================
+Bugs that have been resolved
+============================
+
+These `bugs (reported on GitHub) <https://github.com/KineticPreProcessor/KPP/issues?q=is%3Aissue%20state%3Aclosed%20label%3Abug>`_ have been resolved.