Calculating a Chemical Abundance Table Using FastChem

In this section, we outline the process of running FastChem with tabulated lnK files, as opposed to using fitting functions for lnK. This is achieved by employing the lnk_interpolate_dev branch. The utility prep_FastChem is employed to generate lnK files for molecules. These files are derived from the original fitting functions. In contrast, lnK files for atomic ions are produced from the energy level data utilized in Optab.

Warning: It is important to note that for certain atomic ions at elevated temperatures, the lnK values may be subject to inaccuracies, specifically underestimations. This is because these values are calculated using NIST energy level data, which does not comprehensively cover higher levels.

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1. Build FastChem:

   cd <some_working_dir>
   git clone https://github.com/exoclime/FastChem.git
   cd FastChem/
   git checkout lnk_interpolate_dev
   

   • Comment out the following line 37 in fastchem_src/check.cpp:
     if (this->number_density < min_limit) this->number_density = min_limit;

   mkdir build
   cd build/
   cmake .. && make
   cd ../
   

2. Generate necessary files for FastChem including lnK files in input/:

   cd $OPTAB/work/FastChem-lnk_interpolate_dev/input
   

   • Update the OPTAB_DATABASE_DIR preprocessor macro in prep_FastChem.F90 to the correct path.
   • Update the FASTCHEM_INPUT_DIR preprocessor macro in prep_FastChem.F90 to the correct path.

   make prep_FastChem
   

   • Verify the settings in prep_FastChem.dat, including the label, temperature grid, and pressure grid.

   ./prep_FastChem
   

   Warning: prep_FastChem uses quadruple precision and does not run correctly on arm64 Macs due to ABI constraints. arm64 Mac users must run prep_FastChem on a separate x86_64 platform.

3. Run FastChem: Warning: FastChem built with quadruple precision does not run correctly on arm64 Macs due to ABI constraints. arm64 Mac users must run FastChem on a separate x86_64 platform.

   cd $FASTCHEM
   ./fastchem input/config.input_<label>
   

   • Find the created chemical abundance table at output/<label>.dat. Here, <label> is sample in the default setting.