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How to install AtChem2

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R. Sommariva edited this page Oct 19, 2022 · 17 revisions

AtChem2 can be installed on Unix/Linux and macOS systems. Download the latest stable release at: https://github.com/AtChem/AtChem2/releases. Alternatively, download the archive file of the development version (master branch) or use git to clone the repository.

For more information, see the AtChem2 manual in the doc/ directory.

Requirements

  • Fortran compiler: GNU gfortran (default) or Intel ifort.
  • Python, cmake.
  • Ruby (optional, required by FRUIT).

Dependencies

The dependencies are installed in a Dependencies Directory (e.g., $HOME/atchem-lib/) using the scripts in the tools/install/ directory. The install scripts must be run from the Main Directory (e.g., $HOME/AtChem2/).

  • CVODE and openlibm:

    ./tools/install/install_cvode.sh ~/atchem-lib/
./tools/install/install_openlibm.sh ~/atchem-lib/

  • numdiff is only required to run the Test Suite. It may already be present on the system, otherwise it can be installed locally in the Dependencies Directory:

    ./tools/install/install_numdiff.sh ~/atchem-lib/numdiff/

    Then, add export PATH=$PATH:$HOME/atchem-lib/numdiff/bin to ~/.bash_profile (or ~/.profile).

  • FRUIT is only required to run the Test Suite. First, add to ~/.bash_profile (or ~/.profile):

    export GEM_HOME=$HOME/.gem
export PATH=$PATH:$GEM_HOME/bin

    Then, run the installation script:

    ./tools/install/install_fruit.sh ~/atchem-lib/

Installation

  1. After installing the dependencies, copy the example Makefile to the Main Directory:

    cp ./tools/install/Makefile.skel ./Makefile (v1.2)

    OR

    cp ./tools/Makefile ./Makefile (v1.1.1 and earlier)

  2. Edit the Makefile to set the correct paths of CVODE, openlibm and (if installed) FRUIT.

  3. To test the installation, compile and run the example mechanism:

    • for v1.2.2 and later:

      ./build/build_atchem2.sh ./model/mechanism.fac
./atchem2

    • for v1.2:

      ./build/build_atchem2.sh ./mcm/mechanism_test.fac
./atchem2

    • for v1.1.1 and earlier:

      ./tools/build.sh ./tools/mcm_example.fac
./atchem2

If the model compiles and runs without errors, AtChem2 has been successfully installed. In case of errors, please check the page of known issues.

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