xyz format

Specification

Note

Reference

Simple format to store cartesian coordinates and element symbols. The first line contains the number of atoms in the geometry. The second line is a comment line and ignored, some program store additional information here. The following lines contain a short character identifier and three reals. The first entry is interpreted as element symbol and defines the atomic species. The atomic coordinates are given in Ångström.

A scalar quantity can be added to each atom with one real as well as a vector quantity by three reals, allowing additional four reals per atomic entry.

The format is identified by the file extension xyz or log.

Examples

Caffeine molecule in xyz format

24

C            1.07317000000000        0.04885000000000       -0.07573000000000
N            2.51365000000000        0.01256000000000       -0.07580000000000
C            3.35199000000000        1.09592000000000       -0.07533000000000
N            4.61898000000000        0.73028000000000       -0.07549000000000
C            4.57907000000000       -0.63144000000000       -0.07531000000000
C            3.30131000000000       -1.10256000000000       -0.07524000000000
C            2.98068000000000       -2.48687000000000       -0.07377000000000
O            1.82530000000000       -2.90038000000000       -0.07577000000000
N            4.11440000000000       -3.30433000000000       -0.06936000000000
C            5.45174000000000       -2.85618000000000       -0.07235000000000
O            6.38934000000000       -3.65965000000000       -0.07232000000000
N            5.66240000000000       -1.47682000000000       -0.07487000000000
C            7.00947000000000       -0.93648000000000       -0.07524000000000
C            3.92063000000000       -4.74093000000000       -0.06158000000000
H            0.73398000000000        1.08786000000000       -0.07503000000000
H            0.71239000000000       -0.45698000000000        0.82335000000000
H            0.71240000000000       -0.45580000000000       -0.97549000000000
H            2.99301000000000        2.11762000000000       -0.07478000000000
H            7.76531000000000       -1.72634000000000       -0.07591000000000
H            7.14864000000000       -0.32182000000000        0.81969000000000
H            7.14802000000000       -0.32076000000000       -0.96953000000000
H            2.86501000000000       -5.02316000000000       -0.05833000000000
H            4.40233000000000       -5.15920000000000        0.82837000000000
H            4.40017000000000       -5.16929000000000       -0.94780000000000

Extensions

The reader supports the following extensions:

  • Atomic numbers are allowed instead of element symbols. They are automatically converted to capitalized element symbols

Missing Features

The following features are currently not supported:

  • Scalar atomic quantities are not preserved and dropped.
  • Vector atomic quantities are not preserved and dropped.

Note

Feel free to contribute support for missing features or bring missing features to our attention by opening an issue.