bobhanson/qc_json_schema

A JSON Schema for Quantum Chemistry

QC_JSON_Schema

A JSON Schema for Quantum Chemistry

The purpose of this schema is to provide API like access to pre-existing quantum chemistry packages to enable more complex workflows. The core of this is to avoid parsing ASCII-based output files and place output variables, vectors, matrices in a consistent format that can be easily parsed.

High Level Aspirations

In order to help define the overall scope and direction of the specification several high level goals will be pursued:

• Ability to connect to visualizers and GUI's
• Connect to existing Workflows tools
• Transfer data between QM programs (Orbitals, Densities, etc)
• Provide a rigorous record of computation for large scale QM databases
• Provide a framework for QM API access

A concrete list of requirements for this schema can be found here.

Example

The following is an example Python version. Note that the specification is likely to change heavily, especially with regard to units. However, this is an example of the common input and output structures:

>>> json_molecule = {}
>>> json_molecule["geometry"] = [0, 0, 0, 0, 0, 1]
>>> json_molecule["atoms"] = ["He", "He"]

>>> json_input = {}
>>> json_input["molecule"] = json_molecule
>>> json_input["driver"] = "energy"
>>> json_input["method"] = {"expression": "SCF",
                            "basis":     "sto-3g"}

A discussion of each top level component can be found here. Details can also be found on variable names and the technical specifications.

Partners

The following is a list of programs that have agreed to implement this JSON specification once a stable version has been released. If do not see your code here and would like to be part of the project, get in touch!

Organizations

• The Molecular Sciences Software Institute

Visualizers

• Avogadro
• Molecular Design Toolkit
• VTK

Quantum Chemistry Engines

• MPQC
• NWChem
• Psi4

Translators

• cclib

Governance

This project is currently managed by the following members:

• Marcus D. Hanwell - Kitware
• Bert de Jong - LBNL
• Daniel G. A. Smith - MolSSI
• Aaron Virshup - Autodesk

This management group will serve as a nexus for writing the schema and facilitate communication with the community.

Existing JSON Efforts

The following is a list of efforts that are very similar to the current proposed spec. The idea is to pull from this diverse group and coalesce into a single specification to prevent duplication of effort.

• Autodesk JSON
• BAGEL JSON
• Chemical JSON
• MPQC JSON
• NWChem JSON
• Psi4 JSON
• PyQC Schema
• Molpro Database XML
• Chemical Markup Language - http://www.xml-cml.org