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 tcmu -h command. This will show you an overview of the available CLI scripts. More detailed descriptions can be accessed using the tcmu {program name} -h commands.

CLI scripts are invoked using the parent tcmu 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.

tcmu

TCMU command line interface.

Usage

tcmu [OPTIONS] COMMAND [ARGS]...

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.

Usage

tcmu cite [OPTIONS] [OBJECTS]...

Options

-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 <output>

The output Word file to write the citations to.

-l, --list_citations

List currently available citations.

Arguments

OBJECTS

Optional argument(s)

concat-irc

Combine separated IRC paths.

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.

Usage

tcmu concat-irc [OPTIONS] [JOBS]...

Options

-r, --reverse

Reverses the trajectory

-o, --output <output>

Directory in which the output file will be saved

-l, --log_level <log_level>

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

Arguments

JOBS

Optional argument(s)

geo

Calculate geometrical parameters for atoms at the provided ATOM_INDICES. PATH should be an .xyz-file or a calculation directory.

For 0 indices we return all coordinates of the molecule in PATH.

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.

If the -s/--soa flag is turned on it calculates ang1 + ang2 + ang3.

Note

Atom counting starts at 1.

Usage

tcmu geo [OPTIONS] PATH [ATOM_INDICES]...

Options

-p, --pyramidal

Instead of calculating a dihedral angle, calculate pyramidalisation angle.

-s, --soa

Instead of calculating a dihedral angle, calculate sum-of-angles.

Arguments

PATH

Required argument

ATOM_INDICES

Optional argument(s)

optimize

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

Usage

tcmu optimize [OPTIONS] XYZFILE

Options

-l, --level <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 <charge>

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

-s, --spinpol <spinpol>

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

-o, --output <output>

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

-k, --keep

Whether to keep the calculation directory after finishing the calculation.

Arguments

XYZFILE

Required argument

read

Read results from a calculation.

Usage

tcmu read [OPTIONS] WORKDIR [KEYS]...

Options

-s, --status

Shortcut to only print the status of the calculation.

-p, --properties

Shortcut to only print calculated properties for the calculation.

Arguments

WORKDIR

Required argument

KEYS

Optional argument(s)

resize

Resize images containing molecules.

This CLI-program resizes images in a directory based on detected circles. It will ensure the selected circles are placed at the same location and are also resized to be the same size. When starting the program it will show you for each image numbered detected atoms. Entering the desired number into the CLI will select it for resizing. If you do not enter a number, the figure will be ignored for further processing. New images will be written to the folder postpended with _fixed.

Usage

tcmu resize [OPTIONS]

Options

-f, --folder <folder>

-p, --padding <padding>

The amount of padding to add to the resized figures. If given an integer we use pixel padding. E.g. -p 50 will add a padding of 50 pixels. Add a %-sign to use relative padding. E.g. -p 10% will add a padding of 10%.

workflow

The tcmu workflow subcommand gives a few tools for reading the statuses of, and clearing of past workflow runs.

Usage

tcmu workflow [OPTIONS] COMMAND [ARGS]...

clear

Clears data related to workflow runs. Use the name argument to specify a specific workflow type or a specific hash when the -h/--hash flag is turned on.

Usage

tcmu workflow clear [OPTIONS] NAME

Options

-h, --hash

Arguments

NAME

Required argument

status

Read the statuses of completed and currently running workflow runs. Use the name argument to specify a specific workflow type or a specific hash when the -h/--hash flag is turned on. If name is not given, prints the statuses of all workflow runs and provides an overview of the number of runs per workflow. If the -x/--exit flag is set print the status once and then exit immediately. Otherwise, it will update every second.

Usage

tcmu workflow status [OPTIONS] [NAME]

Options

-h, --hash

-x, --exit

Arguments

NAME

Optional argument

where

Prints where workflow data is stored.

Usage

tcmu workflow where [OPTIONS]