property

Generate a quick figure for a single property of a single gaussian output calculation file.

Currently 3 possible "properties" may be drawn:

energy

usage: pyssianutils plot property energy [-h] [--outfile OUTFILE]
                                         [--interactive] [--include-scf]
                                         [--method {oniom,mp2,mp2scs,mp4,ccsdt,default}]
                                         ifile

Positional Arguments

ifile

Gaussian Output File

Named Arguments

--outfile

Output image file

Default: screen.png

--interactive

Instead of writing to a file open a window showing the figure

Default: False

--include-scf

include the energies of each step of the SCF cycles

Default: False

--method

Possible choices: oniom, mp2, mp2scs, mp4, ccsdt, default

When not provided it will attempt (and may fail) to guess the method used for the calculation to correctly read the potential energy of each step. If it fails it defaults to the Energy of the 'SCF Done:'

Default: default

parameter

usage: pyssianutils plot property parameter [-h] [--outfile OUTFILE]
                                            [--interactive]
                                            ifile name

Positional Arguments

ifile

Gaussian Output File

name

Name of the parameter. For the available options please look at the definitions on your file using 'pyssianutils others track'

Named Arguments

--outfile

Output image file

Default: screen.png

--interactive

Instead of writing to a file open a window showing the figure

Default: False

geometry

usage: pyssianutils plot property geometry [-h] [--outfile OUTFILE]
                                           [--interactive]
                                           ifile atoms [atoms ...]

Positional Arguments

ifile

Gaussian Output File

atoms

Atom numerical ids following the convention: first atom = 1

Named Arguments

--outfile

Output image file

Default: screen.png

--interactive

Instead of writing to a file open a window showing the figure

Default: False

Examples

All these tools are thought for quick visualizations of key properties. Specifically the potential energy, or any geometrical parameter (either an internal coordinate or some other distance/angle/dihedral).

For all the following examples we will assume that there is a file named Example.log containing a gaussian optimization.

To draw the potential energy of Example.log:, which might give us some insight into the convergence the optimization job:

$ pyssiantuils plot property energy Example.log --interactive

energy_example_interactive

which shows the "interactive" plot where we can zoom in/out at will. If we instead prefer to generate a png for later inspection we should omit the --interactive flag. This will lead to the generation of an image file with a default name, or if we want to specify the name we can enable the --outfile flag.

$ pyssiantuils plot property energy Example.log --outfile example.png
writing -> example.png

energy_example

For a given internal parameter (we can visualize the defined parameters for a given file using pyssianutils others track, see others)

$ pyssiantuils plot property parameter Example.log R1 --interactive

parameter_example

Or if we are interested in a geometrical parameter and we are not sure if it is part of the internal coordinates, we can instead use plot geometry where we will specify the indices of the involved atoms. Specifying 2 atoms will give us a distance, 3 an angle, and 4 a dihedral angle.

$ pyssiantuils plot property geometry Example.log R1 1 4 --interactive

geometry_example