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Basic usage

There are two main ways of running QSym²:

  • via the command-line interface provided by the binary qsym2, or
  • via the exposed Python bindings provided by the Python library qsym2.

Command-line interface

Scope

This method is currently able to perform symmetry analysis of:

  • Slater determinants,
  • Hartree–Fock or Kohn–Sham molecular orbitals, and
  • vibrational coordinates

that have been exported by Q-Chem 6 to a HDF5 file named qarchive.h5 saved in the job's scratch directory,

or

  • Slater determinants, and
  • Hartree–Fock or Kohn–Sham molecular orbitals

that have been stored in binary files, together with other basis-set-related data.

Instructions

The command-line interface supports several subcommands and options:

Bash
qsym2 -h

Text Only
A program for Quantum Symbolic Symmetry

Usage: qsym2 <COMMAND>

Commands:
  template
          Generates a template YAML configuration file and exits
  run
          Runs an analysis calculation and exits
  help
          Print this message or the help of the given subcommand(s)

Options:
  -h, --help
          Print help
  -V, --version
          Print version

The subcommand template, runnable as

Bash
qsym2 template
generates a template configuration YAML file populated with some default control parameters. This file can be modified to adjust the parameters to suit the calculation at hand.

The subcommand run, runnable as

Bash
qsym2 run -c path/to/config -o output_name
takes a configuration YAML file as a parameter, performs the specified symmetry analysis, and displays the results in the specified output file.

Examples of symmetry analysis performed by QSym² for several Q-Chem calculations can be found in the User guide.

Python interface

Scope

This method is currently able to perform symmetry analysis of:

  • Slater determinants,
  • Hartree–Fock or Kohn–Sham molecular orbitals,
  • vibrational coordinates, and
  • one-electron densities

that can be computed directly in Python or read into Python from calculation files of quantum-chemistry packages, such as by the use of cclib. The main driver functions of QSym² are all exposed to Python, which means that they can be used and integrated into existing workflows flexibly.

Instructions

To view the documentation for the Python API, execute the following Python commands inside the qsym2-python conda environment (see Python-library compilation), either interactively or in a Python script:

Python
import qsym2
help(qsym2)

An example Python script that performs symmetry analysis for self-consistent-field calculations from Orca output files (parsed by cclib) can be found at utils/qsym2-orca.py. This script requires the Python packages mendeleev, cclib, and numpy to run.

Another example where the Python bindings of QSym² are used extensively for the analysis of unitary and magnetic symmetry in the presence of external fields can be found in QUEST and its complementary GUI, QuestView.