Tutorials

Command Line Scripts:

• Intro to Command Line Scripts
  • Overview
  • File Input/Output
  • Finding Atoms
  • Structure Modification
  • Running Jobs
  • Analyzing Output
• Example BASH Scripts for Common Tasks
  • Optimization and Frequencies
  • Checking and Rerunning Jobs
  • Potential Energy Scans for Stacked Dimers
• Adding Structures to your AaronTools Library
  • Ligands
  • Substituents
  • Rings

Python Scripting:

• Coding with Geometry Objects
  • Overview
  • File Input/Output
  • Finding Atoms
  • Structure Modification
  • Removing Substituents
  • Creating Fused Rings
• Coding with Theory Objects
  • Building Basic Input Files
  • Finer Control
  • Empirical Dispersion
  • Continuum Solvent Model
  • Integration Grid
  • Additional Keywords
• Coding with FileReader objects
  • Creation
  • Getting More Information
• Example Python Scripts for Common Tasks
  • Optimization and Frequencies
  • SAPT Calculations
  • Splitting Up Multi-structure XYZ Files
  • Analyzing XYZ Trajectories
• Converting Z-Matrices to Cartesian Coordinates
  • ZMAT Format
  • Reading ZMAT file
  • Converting Z-Matrix to Cartesian Coordinates

Jupyter Notebooks:

• Working with AaronTools in Jupyter Notebooks
• AaronTools and Psi4
• AaronTools and Matplotlib