Supported atomic coordinates file formats

The current version of Atomes can import atomic coordinates in the following formats:

Table 1.1: Atomic coordinates file formats read by Atomes.
\(-\)XYZ [1] \(^{*}\)
\(-\)Chem3D [2]
\(-\)CPMD trajectory [3] \(^{*}\) \(^{**}\)
\(-\)VASP trajectory [4] \(^{*}\) \(^{***}\)
\(-\)ISAACS Project File [5]
\(-\)PDB/ENT (Protein Data Bank) v3.30
\(-\)CIF (Crystallographic information)
\(-\)DL-POLY History file \(^{*}\)

\(^{*}\) including NPT trajectories.
\(^{**}\) atomic units are assumed in the case of CPMD trajectories.
\(^{**}\) and \(^{***}\) require to enter extra parameters through an interactive dialog box:

  • Total number of atoms

  • Number of chemical species

  • Label and number of each atomic species

the input order, label and number of each atomic species will be the one assumed when reading the coordinates from the trajectory file.
Atomes can also export atomic coordinates in XYZ or Chem3D format.

  1. M. S. Center, Xmol, p. chem/xmol/xmol.html, 1993.
  2. CambridgeSoft, Chem3D, pp. Cambridge Scientific Computing, Cambridge Massachusetts, USA, 2009.
  3. "" .
  4. "" .
  5. S. Le Roux and V. Petkov, J. Appl. Cryst., vol. 43, pp. 181–185, 2010.