Command-line interface

OccuProb includes a basic command-line interface (CLI) to calculate the occupation probability and heat capacity for a set of isomers.

Input file format

At the moment, OccuProb only supports input files in the Extended XYZ format. The Extended XYZ format enhances the standard XYZ files by replacing the comment line with a series of key/value pairs. In the case of OccuProb, the required keys are: Energy, for the potential energy; Multiplicity, for the spin multiplicity; and Frequencies, for the vibrational mode frequencies. For example, for a Pt₅ cluster with three isomers, the respective Extended XYZ file is:

5
Properties=species:S:1:pos:R:3 Energy=-4433.120 Multiplicity=3 Frequencies="0.89 1.53 2.13 3.17 4.29 5.41 5.69 6.08 7.22"
Pt       6.021536241   7.747189364   2.514796921
Pt       7.396161795   5.832164691   3.355579003
Pt       5.773696513   7.056151430   4.817413600
Pt       4.255814915   8.954527174   5.248344983
Pt       4.507518660   9.657859127   2.902251298
5
Properties=species:S:1:pos:R:3 Energy=-4433.012318052181 Multiplicity=5 Frequencies="2.11 2.13 2.87 2.92 4.46 4.52 4.59 5.11 6.55"
Pt       7.130670563   7.316490254   2.574869115
Pt       7.205709764   9.241865499   4.365106937
Pt       5.777733370   7.145289063   4.820088212
Pt       4.881553705   9.498560523   5.571968924
Pt       5.039802176   8.845583983   3.029309097
5
Properties=species:S:1:pos:R:3 Energy=-4432.936040563171 Multiplicity=5 Frequencies="0.87 1.07 1.52 3.01 3.85 4.35 4.96 5.83 6.89"
Pt       6.723845677   6.893128486   2.292499726
Pt       7.293610863   5.327356394   4.136932256
Pt       5.761431903   7.076877369   4.975889864
Pt       4.188319017   8.952644393   5.368553185
Pt       5.151406283   8.677468180   3.099167433

Additional details of the Extended XYZ format can be found here.

Usage example

For the aforementioned example of the Pt₅ clusters, the occupation probability of each isomer and the heat capacity at constant volume can be calculated by running:

occuprob Pt5_isomers.xyz -SQR --max_temp=1000 --plot --size 6 4

The first argument is the name of the input file (Pt5_isomers.xyz). The -SQR flags indicate the contributions to the partition function of each isomer that will be calculated: the electronic partition function including spin (-S); the vibrational partition function in the quantum harmonic oscillator approximation (-Q); and the rotational partition function (-R). These two first arguments are required for every calculation, while the rest are optional. By using --max_temp you can specify the upper limit of the temperature range used in the calculations. The argument --plot must be used if you wish to save the results as image files, otherwise they will only be saved as plain text files. The argument --size defines the size (width and height, in inches) of the output images. In this example, OccuProb produces the following images for the heat capacity and the occupation probabilities of Pt₅:

List of options

Argument	Function
in_file	Extended XYZ file contaning the list of isomers
-e, -E	Add electronic partition function
-s, -S	Add electronic partition function (including spin)
-c, -C	Add vibrational partition function (classical harmonic)
-q, -Q	Add vibrational partition function (quantum harmonic)
-r, -R	Add rotational partition function
–out_file OUT_FILE	Output filename prefix
–plot_format PLOT_FORMAT	Output image files plot_format (default: SVG)
–min_temp MIN_TEMP	Maximum temperature in K (default: 0)
–max_temp MAX_TEMP	Maximum temperature in K (default: 500)
–plot	Plot the results and save them as image files
–size SIZE SIZE	Width and height of the output image in inches (default: 8.0 6.0)