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3. Job Setup

Goal

Set up and submit the combined gas-phase workflow jobs in scratch.

Working Directory

In scratch, create a working directory for this tutorial and then create one subfolder for each molecule.

Suggested layout:

scratch/
  GasPhaseTutorial/
    NO/
    H2/
    H2O/
    CO2/
    HNO2/
    NO2/
    CO/
    HNO3/

Per-Molecule Files

For each molecule:

  1. Copy in or create the needed files.
  2. Rename or copy the molecule structure file to molecule.traj.
  3. Update dft_run.py.
  4. Update job.slurm.
  5. Confirm molecule-specific names, paths, and job settings.
  6. Submit one job that runs geometry optimization first and then the vibrational / thermochemistry step in the same directory.

Files Needed In Each Molecule Folder

  • molecule.traj
  • dft_run.py
  • job.slurm

Modify dft_run.py

  • dft_run.py handles the full workflow in one directory.
  • Make sure the input structure file is correctly edited in dft_run.py instead of molecule.traj.
  • Update the thermochemistry settings near the top for each molecule:
  • You have to change geometry, symmetrynumber, and spin
GEOMETRY = "nonlinear"
SYMMETRY_NUMBER = 1
SPIN = 0
  • Luckily their pretty simple to figure out, and because they are post-processing functions it doesn't affect your calculation results
  • Cramer's Computational Chemistry Book Table 10.1 has the symmetry number (or search it up based on the molecular point group)
  • spin is the number of unpaired electrons in your molecule

Modify job.slurm

  • Make sure the virtual environment path is correct:
# Activate your virtualenv
source /home/your_path/virtenv/bin/activate
  • The combined workflow needs enough walltime for both geometry optimization and the frequency / thermochemistry stage. If more time is needed change it here:
#SBATCH --time=5:00:00

Submission

Submit each job with:

sbatch job.slurm

Check queue status with:

sq

Expected Output Files

After a successful run, check for:

  • dft.energy
  • relaxed.traj
  • CONTCAR
  • OUTCAR
  • final.energy

final.energy should contain:

  • DFT Energy
  • ZPE
  • Entropy
  • Enthalpy
  • Thermal correction H-TS
  • Gibbs Free Energy

Notes

  • N/A so far

Next Section

4. Final Results