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AtChem2 -- CHANGELOG

post v1.2.3

  • implement named arguments (flags) for the build_atchem2.sh script
  • remove the mcm argument from the executable, and redefine it in the build script to indicate the version of the MCM used
  • make shell scripts more robust, and update to openlibm v0.8.6
  • reformat python scripts using black, and add a python format test to the Testsuite
  • add option to use time in user-defined custom Fortran functions
  • update copyright notes

v1.2.3 (May 2025)

  • new implementation of the Testsuite code coverage using Codecov
  • restructure the ci.yml file and streamline the continuous integration process
  • update the Makefile and move the code to run the Testsuite to a secondary makefile (tests/makefile.tests)
  • support chemical mechanisms in KPP format (as generated by the MCM website)
  • change some default values in environmentVariables.config
  • implement use of stoichiometric coefficients in chemical mechanisms
  • implement user-defined custom Fortran functions
  • add option to run AtChem2 in a Docker container
  • major revision of the AtChem2 manual
  • minor changes (mostly cosmetic) to various scripts, and consolidation of .gitignore files
  • implement new workflows to automatically compile and upload the pdf of the user manual via GitHub Actions

v1.2.2 (May 2023)

  • move implementation of continuous integration from TravisCI to GitHub Actions
  • improve reporting of the Testsuite results by using logfiles
  • begin implementation of the new Testsuite ("behaviour tests" now referred to as "model tests")
  • remove unit testing from Codecov (coverage reporting is broken)
  • disable (provisionally) CVODE support for LAPACK and BLAS
  • upgrade the install scripts to openlibm v0.8.1 and numdiff v5.9.0, and add error handling
  • in the Makefile, add optimisation flag for gfortran and compilation flags for ifort
  • fix bug in the input and output of constant photolysis rates
  • add missing comments and tidy several Fortran source files
  • fix error handling for the RO2 sum in build/mech_converter.py
  • update and tidy the .py and .sh scripts in the tools/ directory
  • update .gitignore files, and remove the extension from the LICENSE file (per convention)
  • move and rename the example chemical mechanism file (mcm/mechanism_test.fac) to model/mechanism.fac
  • move and rename the script to generate the user manual (doc/make_pdf.sh) to tools/make_manual_pdf.sh
  • rename the versioning script version.sh to update_version_number.sh
  • update the *.md files, and add Buy Me a Coffee button to the README.md file
  • several updates to the user manual (including new MCM website at Uni. York) and other minor fixes

v1.2.1 (January 2021)

  • implement a new environment variable: ASA (aerosol surface area)
  • fix a bug in the C-binding for gfortran version 9 and above
  • remove tabs from all configuration files
  • update the configuration file for TravisCI
  • tidy the comments and printout messages of various source files
  • update the user manual

v1.2 (May 2020)

  • implement argument parser and named arguments for the atchem2 executable
  • streamline the build procedure, rename and tidy the build scripts, and move them to the build/ directory
  • implement the pre-compilation of the chemical mechanism into a shared library (mechanism.so)
  • implement a new dilution mechanism, and redefine the DILUTE environment variable accordingly
  • convert the documentation to LaTeX format
  • rewrite the user manual (doc/AtChem2-Manual.pdf), and reorganize the wiki pages
  • include the poster presented at the ACM 2018 conference (doc/AtChem_poster_ACM2018.pdf)
  • change the reference in CITATION.md to the GMD paper
  • fix the header of photolysisConstant.config and remove the initialConditionsSetting.output file
  • fix a bug in mech_converter.py affecting chemical reactions with no reactants
  • ensure that all Python scripts are independent of the Python version
  • rename plotting script plot-atchem2.py to plot-atchem2-numpy.py
  • new Python plotting script plot-atchem2-pandas.py (uses pandas instead of numpy)
  • improve the documentation of the behaviour and unit tests
  • remove the behaviour test full (fails with the new dilution mechanism)
  • new script to set the version of AtChem2 before a release (tools/version.sh)
  • minor improvements to the installation procedure
  • move the example chemical mechanism file (tools/mechanism_test.fac) and add a minimal .fac file (mechanism_skel.fac) to the mcm/ directory
  • tidy and improve comments in various source files and scripts
  • various minor fixes and updates

v1.1.1 (January 2019)

  • create the directory doc/, containing the documentation in markdown format
  • add CONTRIBUTING.md file
  • fix the headers of lossRates.output and productionRates.output
  • change the name of the environment variable ROOFOPEN to ROOF

v1.1 (November 2018)

  • implement a new directory structure
  • add CHANGELOG.md and CITATION.md files
  • simplify the installation procedure and remove makefile.local
  • restructure the handling and calculation of photolysis rates
  • fix the calculations of sun declination and solar zenith angle
  • improve handling of dates and numerical precision
  • rename some configuration and output files
  • check calculation of reaction rates and improve the format of instantaneousRates/* files (now called reactionRates/*)
  • merge outputLossRates.config and outputProductionRates.config into outputRates.config
  • fix the output of lossRates.output and productionRates.output
  • implement code coverage testing with Codecov
  • implement a unit testing framework (new requirements: Ruby, FRUIT)
  • add unit tests for atmosphere, configuration, date and solar functions
  • add exact solution behaviour tests
  • improve running and reporting of the Testsuite
  • rework the mechanism conversion procedure, and the related Python scripts
  • add plotting tools in R, Python, Matlab, gnuplot
  • extend the documentation on the wiki
  • fix several minor bugs

v1.0 (July 2017)

  • create a code repository and organization on github.com
  • adopt the MIT open source license
  • upgrade to CVODE v2.9
  • remove the web interface and all the code related to AtChem-online web service
  • standardize the codebase to Fortran 90/95, and use a consistent modular structure for the source code
  • adopt coding style guidelines and standardize the naming of variables, subroutines, source files
  • improve the formatting of output files, screen output, and error reporting
  • improve code comments and create a wiki for the documentation
  • tidy up and improve the Python and shell scripts
  • create a user-friendly command-line interface to install, compile and run the model
  • verify that the model compiles with both GNU gfortran and Intel ifort compilers
  • verify that the model runs on both Linux/Unix and macOS machines
  • implement continuous integration with TravisCI and develop a range of test scenarios (new dependency: numdiff)
  • improve the model stability and numerical accuracy (new dependency: openlibm)
  • correct the calculations of solar angles, water vapour concentration and peroxy radicals summation (RO2)
  • remove air number density (M) as environment variable (now calculated in module atmosphereFunctions)
  • fix several minor bugs