Extended XYZ cartesian coordinates format (exyz)

A format used by ORCA-AICCM

The “EXYZ” chemical file format is an extended version of the standard “XYZ” chemical file format with additional keywords and informations about the unit cell and virtual atoms.

  • Line one of the file contains the number of atoms in the file.
  • Line two of the file contains a title, comment, filename and/or the following keywords: %PBC or %VIRTUAL

Any remaining lines are parsed for atom information until a blank line. These lines start with the element symbol, followed by X, Y, and Z coordinates in angstroms separated by whitespace and - if %VIRTUAL is specified - the optional word VIRTUAL to mark virtual atoms. If %PBC is specified a second block will be present containing the 3 vectors for the unit cell in angstrom and the offset as shown in the example below:

   C        0.00000        1.40272        0.00000
   H        0.00000        2.49029        0.00000
   C       -1.21479        0.70136        0.00000
   H       -2.15666        1.24515        0.00000

Vector1    2.445200    0.000000    0.000000
Vector2    0.000000    1.000000    0.000000
Vector3    0.000000    0.000000    1.000000
Offset     0.000000    0.000000    0.000000

On output, the first line written is the number of atoms in the molecule. Line two is the title of the molecule or the filename if no title is defined. Remaining lines define the atoms in the file. The first column is the atomic symbol (right-aligned on the third character), followed by the XYZ coordinates in “15.5” format separated by an addition whitespace, in angstroms. This means that all coordinates are printed with five decimal places.

The next block starts with a blank line to separate the coordinates from the unit cell vectors followed by the vectors of the unit cell marked with the keywords Vector1/2/3. The vectors themselves are written in the same format as the atom coordinates. The last line contains the keyword Offset and the offset of the unit cell. The unit is always angstrom.

Read Options

-s Output single bonds only
-b Disable bonding entirely