How to install AtChem2 - AtChem/AtChem2 GitHub Wiki

AtChem2 can be installed on Linux/Unix and macOS systems. Download the latest stable version 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

• bash (or bash-compatible) shell, with basic unix utilities: wget, tar/zip, make, etc...
• text editor
• Fortran compiler: GNU gfortran (default) or Intel ifort
• Python
• Ruby (optional, required by FRUIT)

Dependencies

The dependencies are installed in the 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/). Compilation of the dependencies requires gcc and cmake.

• CVODE and openlibm:

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

• numdiff is only required to run the Testsuite. 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) and restart the terminal.

• FRUIT is only required to run the unit tests of the Testsuite. First, add to ~/.bash_profile (or ~/.profile):

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

  Then, restart the terminal and 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 and later)

   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.