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0. Setup (10 minutes)

Welcome to the AWSCC 2025 Workshop on Intermolecular Interactions! This setup guide will get you ready for the hands-on exercises.

Quick Start​

The GitHub repository for this workshop is the best starting point.

For this workshop, you'll need:

  • OCC (Open Computational Chemistry) - for interaction energy calculations
  • XTB (eXtended Tight-Binding) - for fast quantum calculations
  • Optional: ORCA for advanced calculations (not strictly required but very valuable)
  • Visualization: up to you - CrystalExplorer, Avogadro, Ovito, ChimeraX etc..

Some of those are installable via the scripts in the GitHub repository, but if you wish to manually install them there are instructions below for occ and xtb binaries.

Test Your Setup​

  1. Download workshop materials:

    git clone https://github.com/peterspackman/awscc2025
    cd awscc2025

  2. Quick test:

    cd 01_pair_energies/CE1P
    occ scf A.xyz

    You should see energy output starting with:

          Open
           \
            Comp
             \
              Chem

    ...

    ===============================  Input  ================================
    Method string                         rhf
    Basis name                          3-21G
    Shell kind                      Cartesian
    Net charge                              0
    Multiplicity                            1
    ...
    starting restricted scf iterations
       #         E (Hartrees)       |dE|/E max|FDS-SDF|     T (s)
       1     -75.570107464680  6.47837e-04  5.31104e-02  9.36e-04
       2     -75.584244262199  1.66824e-04  1.96361e-02  8.12e-04
       3     -75.585159528009  1.08006e-05  7.07734e-03  7.40e-04
       4     -75.585320852140  1.90371e-06  1.23457e-03  6.68e-04
       5     -75.585325637001  5.64638e-08  1.10974e-04  6.67e-04
       6     -75.585325703965  7.90206e-10  6.89991e-06  6.89e-04

    ...

Other Installation Options​

# Download from GitHub releases
# https://github.com/peterspackman/occ/releases
export OCC_DATA_PATH=/path/to/occ/share/folder
occ --help

Important: Set the OCC_DATA_PATH environment variable:

export OCC_DATA_PATH=/path/to/occ/data

OCC install via pip or uv​

pip install occpy
occpy --help

# For uv users
uv tool run occpy --help

XTB Installation​

xtb can be installed via compilation of the source code, pre-built binary releases, conda etc.

# Install with conda
conda install -c conda-forge xtb

# Or with pip
pip install xtb-python


Additional Software​

Some examples also use ORCA for calculations, though I've tried to make them optional where I can:

  • Register and download from ORCA Forum
  • Free for academic use
  • Also pre-installed on GADI (requires registration and NCI orca group membership)

Visualization Tools​

Use your preferred program for viewing molecular and crystal structures:

Download a development release from here

Alternatives​

  • Ovito - Excellent for large systems and trajectories
  • VESTA - Great for crystal structures
  • Avogadro, PyMOL, ChimeraX, whatever works for you

Workshop Structure​

We'll cover three main topics in 1.5 hours:

  1. Pair energies/molecular dimers - Understanding two-molecule interactions
  2. Clusters - Moving to multi-molecule systems
  3. Crystal Growth and solvation - Simulating how crystals form

Troubleshooting​

Common Issues​

  1. command not found - Check your PATH variable path
  2. Memory errors - Use smaller basis sets or reduce system size
  3. Slow calculations - Normal for large systems, we have pre-computed results

Getting Help​

  • Ask a question!
  • Check the OCC Wiki
  • Example outputs are in each exercise folder

Extra: Setting Up Your Own Calculations​

If you want to prepare your own molecules:

Getting a structure:​

  • Download from Cambridge Structural Database
  • Manually edit a geometry file or build in a GUI program like Avogadro/GaussView
  • Extract from a crystal structure (might need to add hydrogens, deal with disorder...) Mercury is good for this.
  • Generate conformers from e.g. SMILES strings (lots of options)

Visualize in CrystalExplorer:**​

  • Open the .cif or .xyz file
  • Use "Intermolecular Interactions" tool
  • Color by interaction energy

Ready? Let's explore the fascinating world of intermolecular interactions!