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It also contains an example chemical mechanism in FACSIMILE format. There can be several such directories (with different names).\n- `obj/` contains the module/object files generated by the Fortran compiler.\n- `src/` contains the Fortran source files.\n- `tests/` contains the Testsuite scripts, files, and logs.\n- `tools/` contains scripts to install AtChem2 and its dependencies, plotting tools in various programming languages, and other utilities.\n\n\nInstall\n-------\n\nAtChem2 compiles and runs both on Unix/Linux and macOS systems: it implements a continuous integration development workflow and an extensive Testsuite, in order to ensure reliable and reproducible results. A working knowledge of the **unix shell** is required to install and use AtChem2.\n\nAtChem2 requires a **Fortran** compiler (GNU `gfortran` or Intel `ifort`), the **CVODE** (part of [SUNDIALS](https://computing.llnl.gov/projects/sundials)) and **openlibm** libraries, **make**, and **Python**. Compilation of CVODE also requires **cmake** and **gcc**. Optionally, **numdiff**, **FRUIT**, and **Ruby** (v3.0) are required to run the Testsuite.\n\nThe latest stable version of AtChem2 can be downloaded from the [Releases page](https://github.com/AtChem/AtChem2/releases), and is associated with a **doi number** for referencing in publications.\n\nAfter installing the required dependencies using the scripts in the `tools/install/` directory, copy the file `tools/install/Makefile.skel` to the _Main Directory_ and rename it `Makefile`. Set the variables `CVODELIBDIR`, `OPENLIBMDIR` and `FRUITDIR` in the `Makefile` to the full paths of CVODE, openlibm and (if installed) FRUIT.\n\nAlternatively, and _optionally_, AtChem2 can be run as a [Docker](https://www.docker.com/) container. Currently the containerized version is available only for AtChem2 v1.2.2, thanks to the [Uni York group](https://github.com/wacl-york/AtChem2/pkgs/container/atchem2).\n\n\nBuild \u0026 Run\n-----------\n\nTo build the AtChem2 model -- using the example chemical mechanism and default settings -- execute the following command from the _Main Directory_:\n\n```\n./build/build_atchem2.sh ./model/mechanism.fac\n```\n\nThe build script converts the chemical mechanism from the FACSIMILE format (`mechanism_test.fac`) to a Fortran-compatible format, and generates the pre-compiled shared library `mechanism.so` in the `model/configuration/` directory. After the build process is completed, an executable file called `atchem2` is created in the _Main Directory_.\n\nSet the model parameters, the initial conditions, and the required outputs by editing the files in the `model/configuration/` directory. If needed, ensure that the constrained data files are in the relevant subdirectory in `model/constraints/`. To run the model with the default configuration, execute the command:\n\n```./atchem2```\n\nThe executable accepts several command line arguments to customize the location of the configuration, input and output directories, and of the shared library. More information on AtChem2, with detailed instructions on its installation, configuration and use can be found in the manual (`doc/AtChem2-Manual.pdf`) and in the GMD paper (see the file `CITATION.md`).\n\nThe [AtChem2 wiki](https://github.com/AtChem/AtChem2/wiki) contains a summary of the instructions to install, compile, run, and contribute to the development of AtChem2, together with additional information, and a list of [known issues](https://github.com/AtChem/AtChem2/wiki/Known-Issues) with the suggested solutions or workarounds.\n\nPython tools designed to help users run AtChem2 box-models and analyze their output are available at the associated repository: [AtChem-tools](https://github.com/AtChem/AtChem-tools).\n","funding_links":["https://ko-fi.com/I3I1JSFJF'"],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["atmospheric-modelling","atmospheric-chemistry","box-model","cvode","master-chemical-mechanism","mcm"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/348405","html_url":"https://ost.ecosyste.ms/projects/348405"}