Autofile

A Package of the AutoMech Suite

Andreas V. Copan, Kevin B. Moore III, Sarah N. Elliott, and Stephen J. Klippenstein

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• Autofile
  • Overview
  • Getting Started
  • Documentation

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Overview

Autofile directs the filesystem framework for the AutoMech suite. It uses a dual architecture: the run/save filesystems. Under each, Autofile defines rigid Dataseries trunks, branches, and leaves that each store specific data. The save system is the database for AutoMech, storing molecular properties like electronic energies, hessians, and torsional profiles as well as and transition state information like transitory bonds and reaction types.

Getting Started

Installation

We have conda packages on the anaconda cloud for all of our packages. To install them, set up an environment for AutoMech. You can use the environment we have prepared for the suite auto-mech-env. Then activate your environment and install the autofile package.

>>> conda env create auto-mech/auto-mech-env
>>> conda activate auto-mech-env

>>> conda install autofile -c auto-mech

For users new to conda, we have conda-instructions. Each AutoMech package is also available on GitHub.

Tutorial

The first step is to make sure the installation was successful by importing autofile

>>> import autofile

Then we can move on to using the autofile module:

• Species Tutorial

• Theory Tutorial

• Conformer Tutorial

• Z-Matrix Tutorial

• Scan Tutorial

• Reaction Tutorial

• Transition State Tutorial

Documentation

• autofile.fs
• autofile.model
• autofile.schema
  • autofile.schema.loc_maps
  • autofile.schema.data_series
  • autofile.schema.data_files
  • autofile.schema.info_objects
  • autofile.schema
• autofile.data_types
  • autofile.data_types.name
  • autofile.data_types.swrite
  • autofile.data_types.sread
• autofile.info
• autofile.io_
• autofile.json_