README.md

qccodec

Encode qcdata inputs into native quantum chemistry files and decode (parse) program outputs into structured qcdata objects.. Uses data structures from qcdata.

qccodec works in harmony with a suite of other quantum chemistry tools for fast, structured, and interoperable quantum chemistry.

The QC Suite of Programs

The QC Suite works in harmony to provide fast, structured, and interoperable quantum chemistry tools.

• qcconst - Physical constants, conversion factors, and a periodic table with clear source information for every value.
• qcdata - Elegant and intuitive data structures for quantum chemistry, featuring seamless Jupyter Notebook visualizations. Documentation
• qcinf - Cheminformatics algorithms and structure utilities using standardized qcdata data structures.
• qccodec - A package for translating between standardized qcdata data structures and native QC program inputs and outputs.
• qccompute - A package for operating quantum chemistry programs using standardized qcdata data structures. Compatible with TeraChem, psi4, QChem, NWChem, ORCA, Molpro, geomeTRIC and many more.
• BigChem - A distributed application for running quantum chemistry calculations at scale across clusters of computers or the cloud. Bring multi-node scaling to your favorite quantum chemistry program.
• ChemCloud - A web application and associated Python client for exposing a BigChem cluster securely over the internet.

✨ Basic Usage

• Installation:

  python -m pip install qccodec

• Parse QC program outputs into structured data files with a single line of code.

  from pathlib import Path
  from qcdata import CalcType
  from qccodec import decode
  
  stdout = Path("tc.out").read_text()
  data = decode("terachem", CalcType.gradient, stdout=stdout)

• The data object will be a qcdata object, either SinglePointData, OptimizationData, ConformerSearchData or other *Data structure depending on the calctype. Run dir(data) inside a Python interpreter to see the various values you can access. A few prominent values are shown here as an example:

  from pathlib import Path
  from qcdata import CalcType
  from qccodec import decode
  
  stdout = Path("tc.out").read_text()
  data = decode("terachem", CalcType.hessian, stdout=stdout)
  
  data.energy
  data.gradient # If a gradient calc
  data.hessian # If a hessian calc
  data.calcinfo_nmo # Number of molecular orbitals

• Parsed values can be written to disk like this:

  with open("data.json", "w") as f:
      f.write(data.model_dumps_json())

• And read from disk like this:

  from qcdata import SinglePointData
  
  data = SinglePointData.open("data.json")

• You can also run qccodec from the command line like this:

  qccodec -h # Get help message for cli
  
  qccodec terachem hessian tests/data/terachem/water.frequencies.out > data.json # Parse TeraChem stdout to json

• More complex parsing can be accomplished by passing the directory containing the scratch files to decode and optionally the input data used to generate the calculation (usually done from qcop which uses structure data):

  from pathlib import Path
  from qcdata import CalcType, ProgramInput
  from qccodec import decode
  
  stdout = Path("tc.out").read_text()
  directory = Path(".") / "scr.geom"
  input_data = ProgramInput.open("prog_inp.json")
  
  data = decode("terachem", CalcType.hessian, stdout=stdout, directory=directory, input_data=input_data)

💻 Contributing

Please see the contributing guide for details on how to contribute new parsers to this project :)

If there's data you'd like parsed from output files or want to support input files for a new program, please open an issue in this repo explaining the data items you'd like parsed and include an example output file containing the data, like this.