Command-line interface (CLI) scripts

TCutility comes with some helpful CLI scripts for you to use. Please find an overview and examples here. You can also access information by using the tc -h command. This will show you an overview of the available CLI scripts. More detailed descriptions can be accessed using the tc {program name} -h commands.

Overview

CLI scripts are invoked using the parent tc command followed by the sub-program (see below). If you have suggestions for useful scripts please contact the developers or open an issue on our GitHub page.

usage: tc [-h] {read,optimize,concat-irc,cite,geo} ...

TCutility command-line scripts

subprogram

Possible choices: read, optimize, concat-irc, cite, geo

Sub-commands

read

Read results from a calculation.

tc read [-h] [-s] [-p] workdir [keys ...]

Positional Arguments

workdir

The calculation directory to read the results from.

keys

The keys to read from the results.

Named Arguments

-s, --status

Shortcut to only print the status of the calculation.

Default: False

-p, --properties

Shortcut to only print calculated properties for the calculation.

Default: False

optimize

Set up and run a geometry optimization on a given structure.

tc optimize [-h] [-l LEVEL] [-c CHARGE] [-s SPINPOL] [-o OUTPUT] [-k] xyzfile

Positional Arguments

xyzfile

The molecule to optimize, in extended xyz-format. See https://theochem-vu.github.io/TCutility/api/tcutility.html#module-tcutility.molecule for more information.

Named Arguments

-l, --level

Set the level of theory for the optimization. For example, “GFN1-xTB” or “BLYP-D3(BJ)/TZ2P” Can be set in the xyz-file with the ‘level_of_theory’ flag.

-c, --charge

The charge of the system. Can be set in the xyz-file with the ‘charge’ flag.

-s, --spinpol

The spin-polarization of the system. Can be set in the xyz-file with the ‘spinpol’ flag.

-o, --output

The file to write the optimized result to. By default will be written to ‘{xyzfile}_optimized.xyz’.

-k, --keep

Keep the calculation directory after finishing the calculation.

Default: False

concat-irc

Scripts that takes in two or more directories containing an IRC file (“ams.rkf”) and concatenates them through the RMSD values. Produces a .xyz and .amv file in the specified output directory. The output directory is specified with the -o flag. If not specified, the output will be written to the current working directory. In addition, the -r flag can be used to reverse the trajectory.

Note: ALWAYS visualize the .amv file in AMSView to verify the trajectory.

tc concat-irc [-h] [-r] [-o OUTPUT] [-l LOG_LEVEL] [jobs ...]

Positional Arguments

jobs

Job directories containing the ams.rkf of the irc calculation(s)

Named Arguments

-r, --reverse

Reverses the trajectory

Default: False

-o, --output

Directory in which the outputfile will be saved

Default: './'

-l, --log_level

Set the log level. The lower the value, the more is printed. Default is 20 (info).

Default: 20

cite

Generate citations for objects. Currently supports generating citations for functionals, basis-sets, programs, methodologies and DOIs. This program also generates, and if possible, opens a Word document that contains the formatted citations. Multiple objects can be given separated by spaces. If the supplied object is also a file path it will read each line as a separate object.

Example usage:

> tc cite ADF Program ORCA

[10.1002/wcms.81] F. Neese, WIREs Comput. Mol. Sci. 2011, 2, 73-78. [10.1063/5.0004608] F. Neese, F. Wennmohs, U. Becker, C. Riplinger, J. Chem. Phys. 2020, 152. [10.1002/wcms.1606] F. Neese, WIREs Comput. Mol. Sci. 2022, 12.

> tc cite BP86 BLYP OLYP OPBE D3BJ Functional BP86

[10.1103/PhysRevA.38.3098] A. D. Becke, Phys. Rev. A 1988, 38, 3098-3100. [10.1103/PhysRevB.33.8800] J. P. Perdew, W. Yue, Phys. Rev. B 1986, 33, 8800-8802.

Functional BLYP

[10.1103/PhysRevA.38.3098] A. D. Becke, Phys. Rev. A 1988, 38, 3098-3100. [10.1103/PhysRevB.37.785] C. Lee, W. Yang, R. G. Parr, Phys. Rev. B 1988, 37, 785-789.

Functional OLYP

[10.1080/00268970010018431] N. C. Handy, A. J. Cohen, Mol. Phys. 2001, 99, 403-412. [10.1103/PhysRevB.37.785] C. Lee, W. Yang, R. G. Parr, Phys. Rev. B 1988, 37, 785-789.

Functional OPBE

[10.1080/00268970010018431] N. C. Handy, A. J. Cohen, Mol. Phys. 2001, 99, 403-412. [10.1103/PhysRevLett.77.3865] J. P. Perdew, K. Burke, M. Ernzerhof, Phys. Rev. Lett. 1996, 77, 3865-3868.

Methodology D3BJ

[10.1002/jcc.21759] S. Grimme, S. Ehrlich, L. Goerigk, J. Comput. Chem. 2011, 32, 1456-1465.

tc cite [-h] [-w] [-a] [-r] [-o OUTPUT] [-l] [objects ...]

Positional Arguments

objects

the objects to generate citations for. This can be functionals, basis-sets, programs, methodologies or DOIs.

Named Arguments

-w, --wiley

set the citation style to Wiley. This is the default style.

-a, --acs

set the citation style to ACS.

-r, --rsc

set the citation style to RSC.

-o, --output

the output Word file to write the citations to.

Default: 'citations.docx'

-l, --list

list currently available citations.

Default: False

geo

Calculate geometrical parameters for atoms at the provided indices.

For 1 index this program returns the cartesian coordinate for this atom. For 2 indices return bond length between atoms. For 3 indices return bond angle, with the second index being the central atom. For 4 indices return dihedral angle by calculating the angle between normal vectors described by atoms at indices 1-2-3 and indices 2-3-4. If the -p/–pyramidal flag is turned on it calculates 360° - ang1 - ang2 - ang3, where ang1, ang2 and ang3 are the angles described by indices 2-1-3, 3-1-4 and 4-1-2 respectively.

tc geo [-h] [-p] xyzfile atom_indices [atom_indices ...]

Positional Arguments

xyzfile

The molecule to calculate the parameter for.

atom_indices

The indices of the atoms to calculate the parameters for.

Named Arguments

-p, --pyramidal

Instead of calculating dihedral angles, calculate pyramidalisation angle.

Default: False