Basic Usage

Since version 1.0.0 pyssianutils is a command line application that aggregates together multiple scripts for the manipulation of gaussian inputs and gaussian outputs. After installation, we will use pyssianutils with the general syntax:

$ pyssianutils [command] [subcommand] inputs*.log --options

At any point during the construction of the command line input we can add a --help option. For example to display the available main commands:

$ pyssianutils --help

For a specific command (for example inputht) we may check the different required inputs and options by typing:

$ pyssianutils inputht --help

Or if we want to check for any special options mid-construction of the command line input:

$ pyssianutils print potential myfile1.log myfile2.log --help

Commonly used command inputs

Let us assume that in our current directory we have 6 files:

- comp_00.com
- comp_00.log
- comp_00_SP.com
- comp_00_SP.log
- comp_01.com
- comp_01.log

To print the final Potential energies:

$ pyssianutils print potential comp_00*.log

Or the thermochemistry and SP corrected Free energy:

$ pyssianutils print summary comp_00*.log --with-sp

To generate a new SP calculation named comp_00_pbeSP.com from the final geometry if comp_00.log :

$ pyssianutils asinput comp_00.log --as-SP --method pbe -m pbeSP

To generate a slurm script for the newly generated input file:

$ pyssianutils submit slurm example comp_00_pbeSP.com --guess-cores --guess-mem

Change the user defaults to make cores and memory guessing the default behaviour

$ pyssianutils defaults set --section submit.slurm guess_default True

Visualize the convergence criteria and energy of a single optimization:

Important

For any plotting related feature, the matplotlib and/or plotly libraries must be installed

$ pyssianutils plot optview comp_00.log --interactive

Interactive visualization of multiple optimizations:

$ pyssianutils plot optmulti comp_00.log comp_01.log --interactive

Visualize how an angle changes over the optimization

$ pyssianutils plot property geometry comp_00.log 1 2 3 --interactive