Structure Optimisation

autoenrich can produce input files for both gaussian and ORCA to run DFT geometry optimisation calculations.

  1. Run the setup_opt autoenrich command from within your molecule folder
    > autoenrich molecule_name setup_opt
    

    This will create input files to run the geometry optimisation calculations using the software you specified in the preferences file. The input files will be put into a new folder called optimisation. Submission scripts will also be produced to run/submit the calculations. As a default, scripts are produced for each 50 input files, but this limit can be changed in the preferences file. Your autoenrich folder should look like this: ```

    • my_autoenrich_folder/
    • molecule_name/
      • molecule.xyz
    • molecule.pkl
    • molecule_nameBACKUP.pkl
    • ENRICH.json
    • confsearch_molecule_name_.sh
    • conf_search/
      • do_confsearch.py
    • OPT_molecule_name_0.sh
    • optimisation/
      • 0_OPT.in
      • 1_OPT.in . . .
      • OPT_IN_ARRAY.txt ```
  2. Run/Submit the calculations using the submission scripts provided
    > bash OPT_molecule_name_0.sh # To run locally
    > qsub OPT_molecule_name_0.sh # To run on a PBS system
    > sbatch OPT_molecule_name_0.sh # To run on a SLURM system
    
  3. Once the calculations have finished, run the following command
    > autoenrich molecule_name process_opt
    

    This will go through the log files, check which have finished successfully and save the conformers to the .pkl file for the molecule.

The next step is to run NMR Calculations.

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