gaussianutility 0.1.1

Useful utilities to use Gaussian09/16 software

Gaussian Utility

The Gaussian Utility is a Python package that provides useful utilities for working with Gaussian 09/16 software.

Gaussian is a computer program used by chemists, chemical engineers, biochemists, physicists, and other scientists for performing quantum chemistry calculations.

Purpose and Functionalities

The Gaussian Utility package offers several functionalities to enhance the usage of Gaussian software. Especially, this package can address ONIOM-type Gaussian input/output files, which is not widely available in ASE.

Most of the scripts that work on a Gaussian output file are written based Density Functional Theory calculations. Hence, the compatibility with different types of calculations, e.g., coupled cluster, Hartree-Fock, semi-empirical, and Møller–Plesset perturbation methodes has not been confirmed yet.

These functionalities include:

1. Convert input structure file type:

   • com2vasp: Converts Gaussian input files (.com) to VASP input files (.vasp).
   • com2xyz: Converts Gaussian input files (.com) to XYZ coordinate files (.xyz).
   • vasp2com: Converts VASP input files (.vasp) to Gaussian input files (.com).

2. Extract structure from output file:

   • out2com: Generate Gaussian input files (.com) from Gaussian output files (.out).
   • out2xyz: Generate XYZ coordinate files (.xyz) from Gaussian output files (.out).

3. Spectrum utilities:

   • spectrum: Produces Normal-IR, Raman, or UV-Vis spectra from Gaussian output files (.out).

4. Other utilities:

   • gibbsTemp: Calculates the Gibbs free energies at given temperatures from a Gaussian output file with frequency calculation.
   • printE: Prints the energy from a Gaussian output file.
   • freezeLayer: Freezes a specific ONIOM layer of atoms in a Gaussian input file with ONIOM formulation.
   • sortInput: Sorts the atoms in a Gaussian input file based on their atomic numbers, x, y, or z coordiate, or ONIOM layer.

Installation

Gaussian Utility is a pip installable package:

pip install gaussianutility

Alternatively, it can be installed from GitHub following these steps:

1. Clone the GitHub repository:

   git clone https://github.com/Sungil-Hong/gaussianutility.git
   

2. Navigate to the cloned repository:

   cd gaussianutility
   

3. Install the package using setuptools:

   pip install .
   

Dependencies

The Gaussian Utility package has the following dependencies:

• numpy>=1.17.2
• pandas>=1.1.0
• periodictable>=1.6.1
• ase
• argparse>=1.1
• matplotlib>=3.5.3
• mendeleev>=0.12.0

These dependencies will be automatically installed when you install the package using setuptools.

Usage

The Gaussian Utility package provides command-line utilities that can be accessed by running the corresponding command. Here are some examples of how to use the utilities:

1. Convert a Gaussian input file to a VASP input file:

   com2vasp input.com
   

2. Convert a Gaussian input file to an XYZ coordinate file:

   com2xyz input.com
   

3. Convert a VASP input file to a Gaussian input file:

   vasp2com output.vasp
   

4. Extract optimized geometry to a Gaussian input file from a Gaussian output file:

   out2com output.out
   

5. Extract optimized geometry to an XYZ coordinate file:

   out2xyz output.out
   

6. Produce a spectrum from a Gaussian output file:

   spectrum type file_name1 [ratio1 [file_name2 ratio2 ...]]
   

7. Freeze a specific ONIOM layer of atoms in a Gaussian input file:

   freezeLayer [-i [layer index]] file_name
   

8. Calculate the Gibbs free energy at a given temperature:

   gibbsTemp file_name temp1 [temp2 [step_number]]
   

9. Print the energy of a Gaussian output file:

   printE file_name
   

10. Sort the atoms in a Gaussian input file based on their atomic numbers:

    sortInput [-s [sort index]] [-o [order index]] file_name
    

Authors

The Gaussian Utility package was developed by Sungil Hong. For any inquiries or issues, you can contact Sungil Hong via email at [e-mail].

License

The Gaussian Utility package is distributed under the MIT License. Please refer to the LICENSE file for more information.

Additional Information

For more information about the Gaussian Utility package, you can visit the GitHub repository. The repository contains the source code, documentation, and examples of usage for the package.