Command line options

Atomes can be used from the command line, including using the following options:

  • General options:

    • "-h" or "–help": short help.

    • "-v" or "–version": version information.

  • File options:

    • "-awf filename": open Atomes workspace file.

    • "-apf filename": open Atomes project file.

    • "-xyz filename": open coordinates in XYZ format [1].

    • "-pdb filename": open coordinates in PDB format.

    • "-ent filename": open coordinates in PDB format.

    • "-c3d filename": open coordinates in Chem3D format [2].

    • "-cif filename": open coordinates in CIF format.

    • "-trj filename": open CPMD trajectory [3].

    • "-xdatcar filename": open VASP trajectory [4].

    • "-hist filename": open DL_POLY history trajectory [5].

    • "-ipf filename": open ISAACS project file [6].

  1. If no file option(s) is (are) provided then Atomes will try to open the file(s) based on its (their) extension(s) (ex: a file which name end by ".xyz" will be assumed to follow the XYZ structure).

  2. The structure of "filename" is expected to follow the structure introduced with the option (ex: "-xyz" for a file that contains coordinates in the XYZ format), but "filename" is not required to have the corresponding extention (ex: ".xyz").

  3. Since Atomes has a single workspace only a single workspace file can be opened via the command line.

  • Examples:

  • Open all PDB files in the active directory:

    user@localhost ~]$ atomes *.pdb

  • Open a workspace file, and other coordinates files:

    user@localhost ~]$ atomes -pdb this.f file.awf -cif that.f *.xyz

Atomes will parse the command line, detect that a workspace file "file.awf" is to be opened and will open it first.
Then the other coordinate files will be opened and added to the workspace:

  • As enforced by the "-pdb" option, "this.f" is supposed to follow the PDB format.

  • As enforced by the "-cif" option, "that.f" is supposed to follow the CIF format.

  • All files with the ".xyz" extension in the directory will be opened assuming that they follow the XYZ format.

    1. M. S. Center, Xmol, p. http://www.hpc.unm.edu/ chem/xmol/xmol.html, 1993.
    2. CambridgeSoft, Chem3D, pp. Cambridge Scientific Computing, Cambridge Massachusetts, USA, 2009.
    3. "http://www.cpmd.org." .
    4. "http://cms.mpi.univie.ac.at/vasp." .
    5. "https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx." .
    6. S. Le Roux and V. Petkov, J. Appl. Cryst., vol. 43, pp. 181–185, 2010.